Lecture 8 Quiz Please Note: No Grace Period

In [25]:

    

from Bio.Blast import NCBIWWW
fasta_string = "GATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGACATACTGTGTTTTTAAATATAGTATTGCC"
result_handle = NCBIWWW.qblast("blastn", "nt", fasta_string)


    

In [15]:

    

print "type(result_handle):", type(result_handle)
print "len(str(result_handle)):", len(str(result_handle))
print "len(str(result_handle)[0]):", len(str(result_handle)[0])
print "str(result_handle):", str(result_handle)


    

    




type(result_handle): <type 'cStringIO.StringI'>
len(str(result_handle)): 40
len(str(result_handle)[0]): 1
str(result_handle): <cStringIO.StringI object at 0xb1efdd58>

In [26]:

    

from Bio.Blast import NCBIXML
blast_record = NCBIXML.read(result_handle)
print "blast_record:", blast_record
print "type(blast_record):", type(blast_record)
print "len(blast_record.alignments):", len(blast_record.alignments)


    

    




blast_record: <Bio.Blast.Record.Blast object at 0xb0e601ac>
type(blast_record): <class 'Bio.Blast.Record.Blast'>
len(blast_record.alignments): 50

In [28]:

    

E_VALUE_THRESH = 0.01
for alignment in blast_record.alignments:
    for hsp in alignment.hsps:
        if hsp.expect < E_VALUE_THRESH:
            print('****Alignment****')
            print('sequence:', alignment.title)
            print('length:', alignment.length)
            print('e value:', hsp.expect)
            print(hsp.query)
            print(hsp.match)
            print(hsp.sbjct)


    

    




****Alignment****
('sequence:', u'gi|824041056|gb|KR819004.1| Zaire ebolavirus isolate Ebola virus/H.sapiens-wt/COD/2014/Lomela-Lokolia-B11, partial genome')
('length:', 18861)
('e value:', 7.03775e-25)
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTC--GACATACTGTGTTTTTAAATATAGTATTGCC
|||||||||||||||||||||||||||||||||||||||||  |||||||||||||||||||||||||||||||
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
****Alignment****
('sequence:', u'gi|824041261|gb|KR867676.1| Zaire ebolavirus isolate Ebola virus/H.sapiens-tc/COD/1995/Kikwit-9510621, complete genome')
('length:', 18956)
('e value:', 7.03775e-25)
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTC--GACATACTGTGTTTTTAAATATAGTATTGCC
|||||||||||||||||||||||||||||||||||||||||  |||||||||||||||||||||||||||||||
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
****Alignment****
('sequence:', u'gi|824041176|gb|KR824526.1| Zaire ebolavirus isolate Zaire ebolavirus H. sapiens-tc/ZAI/1995/Zaire-199510621, partial genome')
('length:', 18920)
('e value:', 7.03775e-25)
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTC--GACATACTGTGTTTTTAAATATAGTATTGCC
|||||||||||||||||||||||||||||||||||||||||  |||||||||||||||||||||||||||||||
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
****Alignment****
('sequence:', u'gi|803773882|gb|KR063672.1| Ebola virus isolate Ebola virus/H.sapiens-tc/COD/1995/Kikwit-807223, complete genome')
('length:', 18956)
('e value:', 7.03775e-25)
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTC--GACATACTGTGTTTTTAAATATAGTATTGCC
|||||||||||||||||||||||||||||||||||||||||  |||||||||||||||||||||||||||||||
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
****Alignment****
('sequence:', u'gi|803773858|gb|KR063671.1| Ebola virus isolate Ebola virus/H.sapiens-tc/COD/1976/Yambuku-Mayinga, complete genome')
('length:', 18957)
('e value:', 7.03775e-25)
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTC--GACATACTGTGTTTTTAAATATAGTATTGCC
|||||||||||||||||||||||||||||||||||||||||  |||||||||||||||||||||||||||||||
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
****Alignment****
('sequence:', u'gi|733962926|gb|KP271020.1| Zaire ebolavirus isolate Ebola virus/H.sapiens-wt/COD/2014/Lomela-Lokolia19, complete genome')
('length:', 18861)
('e value:', 7.03775e-25)
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTC--GACATACTGTGTTTTTAAATATAGTATTGCC
|||||||||||||||||||||||||||||||||||||||||  |||||||||||||||||||||||||||||||
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
****Alignment****
('sequence:', u'gi|733962903|gb|KP271019.1| Zaire ebolavirus isolate Ebola virus/H.sapiens-wt/COD/2014/Lomela-Lokolia17, partial genome')
('length:', 18760)
('e value:', 7.03775e-25)
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTC--GACATACTGTGTTTTTAAATATAGTATTGCC
|||||||||||||||||||||||||||||||||||||||||  |||||||||||||||||||||||||||||||
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
****Alignment****
('sequence:', u'gi|733962878|gb|KP271018.1| Zaire ebolavirus isolate Ebola virus/H.sapiens-wt/COD/2014/Lomela-Lokolia16, complete genome')
('length:', 18941)
('e value:', 7.03775e-25)
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTC--GACATACTGTGTTTTTAAATATAGTATTGCC
|||||||||||||||||||||||||||||||||||||||||  |||||||||||||||||||||||||||||||
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
****Alignment****
('sequence:', u'gi|685509613|gb|KM519951.1| Zaire ebolavirus isolate Ebola virus/H.sap-wt/COD/2014/Boende-Lokolia, partial genome')
('length:', 18953)
('e value:', 7.03775e-25)
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTC--GACATACTGTGTTTTTAAATATAGTATTGCC
|||||||||||||||||||||||||||||||||||||||||  |||||||||||||||||||||||||||||||
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
****Alignment****
('sequence:', u'gi|692112628|gb|KM655246.1| Zaire ebolavirus isolate Ebola virus/H.sapiens-tc/COD/1976/Yambuku-Ecran, complete genome')
('length:', 18797)
('e value:', 7.03775e-25)
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTC--GACATACTGTGTTTTTAAATATAGTATTGCC
|||||||||||||||||||||||||||||||||||||||||  |||||||||||||||||||||||||||||||
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
****Alignment****
('sequence:', u'gi|684208240|gb|KM517570.1| Zaire ebolavirus isolate Ebola virus/H.sapiens-frag/COD/2014/Lomela-Lokolia16 L protein (L) gene, partial cds >gi|684208242|gb|KM517571.1| Zaire ebolavirus isolate Ebola virus/H.sapiens-frag/COD/2014/Lomela-Lokolia17 L protein (L) gene, partial cds')
('length:', 553)
('e value:', 7.03775e-25)
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTC--GACATACTGTGTTTTTAAATATAGTATTGCC
|||||||||||||||||||||||||||||||||||||||||  |||||||||||||||||||||||||||||||
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
****Alignment****
('sequence:', u'gi|593943825|gb|KF990214.1| Synthetic construct clone rgEBOV-luc2, complete sequence')
('length:', 21051)
('e value:', 7.03775e-25)
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTC--GACATACTGTGTTTTTAAATATAGTATTGCC
|||||||||||||||||||||||||||||||||||||||||  |||||||||||||||||||||||||||||||
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
****Alignment****
('sequence:', u'gi|593943424|gb|KF990213.1| Synthetic construct clone rgEBOV-GFP, complete sequence')
('length:', 20118)
('e value:', 7.03775e-25)
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTC--GACATACTGTGTTTTTAAATATAGTATTGCC
|||||||||||||||||||||||||||||||||||||||||  |||||||||||||||||||||||||||||||
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
****Alignment****
('sequence:', u'gi|566573369|gb|KF827427.1| Mutant Zaire ebolavirus, complete sequence')
('length:', 18959)
('e value:', 7.03775e-25)
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTC--GACATACTGTGTTTTTAAATATAGTATTGCC
|||||||||||||||||||||||||||||||||||||||||  |||||||||||||||||||||||||||||||
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
****Alignment****
('sequence:', u'gi|436409439|gb|KC242801.1| Zaire ebolavirus isolate EBOV/H.sapiens-tc/COD/1976/deRoover, complete genome')
('length:', 18959)
('e value:', 7.03775e-25)
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTC--GACATACTGTGTTTTTAAATATAGTATTGCC
|||||||||||||||||||||||||||||||||||||||||  |||||||||||||||||||||||||||||||
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
****Alignment****
('sequence:', u'gi|436409419|gb|KC242799.1| Zaire ebolavirus isolate EBOV/H.sapiens-tc/COD/1995/13709 Kikwit, complete genome')
('length:', 18959)
('e value:', 7.03775e-25)
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTC--GACATACTGTGTTTTTAAATATAGTATTGCC
|||||||||||||||||||||||||||||||||||||||||  |||||||||||||||||||||||||||||||
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
****Alignment****
('sequence:', u'gi|436409369|gb|KC242794.1| Zaire ebolavirus isolate EBOV/H.sapiens-tc/GAB/1996/2Nza, complete genome >gi|436409409|gb|KC242798.1| Zaire ebolavirus isolate EBOV/H.sapiens-tc/GAB/1996/1Ikot, complete genome')
('length:', 18959)
('e value:', 7.03775e-25)
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTC--GACATACTGTGTTTTTAAATATAGTATTGCC
|||||||||||||||||||||||||||||||||||||||||  |||||||||||||||||||||||||||||||
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
****Alignment****
('sequence:', u'gi|436409389|gb|KC242796.1| Zaire ebolavirus isolate EBOV/H.sapiens-tc/COD/1995/13625 Kikwit, complete genome')
('length:', 18959)
('e value:', 7.03775e-25)
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTC--GACATACTGTGTTTTTAAATATAGTATTGCC
|||||||||||||||||||||||||||||||||||||||||  |||||||||||||||||||||||||||||||
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
****Alignment****
('sequence:', u'gi|436409359|gb|KC242793.1| Zaire ebolavirus isolate EBOV/H.sapiens-tc/GAB/1996/1Eko, complete genome >gi|436409379|gb|KC242795.1| Zaire ebolavirus isolate EBOV/H.sapiens-tc/GAB/1996/1Mbie, complete genome >gi|436409399|gb|KC242797.1| Zaire ebolavirus isolate EBOV/H.sapiens-tc/GAB/1996/1Oba, complete genome')
('length:', 18958)
('e value:', 7.03775e-25)
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTC--GACATACTGTGTTTTTAAATATAGTATTGCC
|||||||||||||||||||||||||||||||||||||||||  |||||||||||||||||||||||||||||||
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
****Alignment****
('sequence:', u'gi|436409349|gb|KC242792.1| Zaire ebolavirus isolate EBOV/H.sapiens-tc/GAB/1994/Gabon, complete genome')
('length:', 18959)
('e value:', 7.03775e-25)
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTC--GACATACTGTGTTTTTAAATATAGTATTGCC
|||||||||||||||||||||||||||||||||||||||||  |||||||||||||||||||||||||||||||
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
****Alignment****
('sequence:', u'gi|436409339|gb|KC242791.1| Zaire ebolavirus isolate EBOV/H.sapiens-tc/COD/1977/Bonduni, complete genome')
('length:', 18959)
('e value:', 7.03775e-25)
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTC--GACATACTGTGTTTTTAAATATAGTATTGCC
|||||||||||||||||||||||||||||||||||||||||  |||||||||||||||||||||||||||||||
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
****Alignment****
('sequence:', u'gi|384406804|gb|JQ352763.1| Zaire ebolavirus strain Kikwit, complete genome')
('length:', 18944)
('e value:', 7.03775e-25)
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTC--GACATACTGTGTTTTTAAATATAGTATTGCC
|||||||||||||||||||||||||||||||||||||||||  |||||||||||||||||||||||||||||||
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
****Alignment****
('sequence:', u'gi|297340571|gb|EU224440.2| Zaire ebolavirus strain Mayinga, complete genome')
('length:', 18959)
('e value:', 7.03775e-25)
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTC--GACATACTGTGTTTTTAAATATAGTATTGCC
|||||||||||||||||||||||||||||||||||||||||  |||||||||||||||||||||||||||||||
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
****Alignment****
('sequence:', u'gi|10141003|gb|AF086833.2| Ebola virus - Mayinga, Zaire, 1976, complete genome')
('length:', 18959)
('e value:', 7.03775e-25)
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTC--GACATACTGTGTTTTTAAATATAGTATTGCC
|||||||||||||||||||||||||||||||||||||||||  |||||||||||||||||||||||||||||||
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
****Alignment****
('sequence:', u'gi|33860540|gb|AY354458.1| Zaire ebolavirus strain Zaire 1995, complete genome')
('length:', 18961)
('e value:', 7.03775e-25)
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTC--GACATACTGTGTTTTTAAATATAGTATTGCC
|||||||||||||||||||||||||||||||||||||||||  |||||||||||||||||||||||||||||||
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
****Alignment****
('sequence:', u'gi|23630482|gb|AY142960.1| Zaire Ebola virus strain Mayinga subtype Zaire, complete genome')
('length:', 18959)
('e value:', 7.03775e-25)
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTC--GACATACTGTGTTTTTAAATATAGTATTGCC
|||||||||||||||||||||||||||||||||||||||||  |||||||||||||||||||||||||||||||
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
****Alignment****
('sequence:', u'gi|21702647|gb|AF499101.1| Zaire Ebola virus strain Mayinga, complete genome')
('length:', 18960)
('e value:', 7.03775e-25)
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTC--GACATACTGTGTTTTTAAATATAGTATTGCC
|||||||||||||||||||||||||||||||||||||||||  |||||||||||||||||||||||||||||||
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
****Alignment****
('sequence:', u'gi|11761745|gb|AF272001.1| Zaire Ebola virus strain Mayinga, complete genome')
('length:', 18959)
('e value:', 7.03775e-25)
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTC--GACATACTGTGTTTTTAAATATAGTATTGCC
|||||||||||||||||||||||||||||||||||||||||  |||||||||||||||||||||||||||||||
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
****Alignment****
('sequence:', u'gi|2546940|emb|X67110.1| Zaire Ebola virus L gene encoding L-polymerase, strain Mayinga')
('length:', 7231)
('e value:', 7.03775e-25)
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTC--GACATACTGTGTTTTTAAATATAGTATTGCC
|||||||||||||||||||||||||||||||||||||||||  |||||||||||||||||||||||||||||||
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
****Alignment****
('sequence:', u'gi|436409329|gb|KC242790.1| Zaire ebolavirus isolate EBOV/H.sapiens-tc/COD/2007/5 Luebo, complete genome')
('length:', 18958)
('e value:', 2.99253e-23)
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTC--GACATACTGTGTTTTTAAATATAGTATTGC
|||||||||||||||||||||||||||||||||||||||||  |||||| |||||||||||||||||||||||
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATATTGTGTTTTTAAATATAGTATTGC
****Alignment****
('sequence:', u'gi|436409319|gb|KC242789.1| Zaire ebolavirus isolate EBOV/H.sapiens-tc/COD/2007/4 Luebo, complete genome')
('length:', 18958)
('e value:', 2.99253e-23)
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTC--GACATACTGTGTTTTTAAATATAGTATTGC
|||||||||||||||||||||||||||||||||||||||||  |||||| |||||||||||||||||||||||
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATATTGTGTTTTTAAATATAGTATTGC
****Alignment****
('sequence:', u'gi|436409309|gb|KC242788.1| Zaire ebolavirus isolate EBOV/H.sapiens-tc/COD/2007/43 Luebo, complete genome')
('length:', 18958)
('e value:', 2.99253e-23)
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTC--GACATACTGTGTTTTTAAATATAGTATTGC
|||||||||||||||||||||||||||||||||||||||||  |||||| |||||||||||||||||||||||
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATATTGTGTTTTTAAATATAGTATTGC
****Alignment****
('sequence:', u'gi|436409299|gb|KC242787.1| Zaire ebolavirus isolate EBOV/H.sapiens-tc/COD/2007/23 Luebo, complete genome')
('length:', 18958)
('e value:', 2.99253e-23)
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTC--GACATACTGTGTTTTTAAATATAGTATTGC
|||||||||||||||||||||||||||||||||||||||||  |||||| |||||||||||||||||||||||
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATATTGTGTTTTTAAATATAGTATTGC
****Alignment****
('sequence:', u'gi|436409289|gb|KC242786.1| Zaire ebolavirus isolate EBOV/H.sapiens-tc/COD/2007/1 Luebo, complete genome')
('length:', 18958)
('e value:', 2.99253e-23)
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTC--GACATACTGTGTTTTTAAATATAGTATTGC
|||||||||||||||||||||||||||||||||||||||||  |||||| |||||||||||||||||||||||
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATATTGTGTTTTTAAATATAGTATTGC
****Alignment****
('sequence:', u'gi|436409279|gb|KC242785.1| Zaire ebolavirus isolate EBOV/H.sapiens-tc/COD/2007/0 Luebo, complete genome')
('length:', 18958)
('e value:', 2.99253e-23)
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTC--GACATACTGTGTTTTTAAATATAGTATTGC
|||||||||||||||||||||||||||||||||||||||||  |||||| |||||||||||||||||||||||
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATATTGTGTTTTTAAATATAGTATTGC
****Alignment****
('sequence:', u'gi|436409269|gb|KC242784.1| Zaire ebolavirus isolate EBOV/H.sapiens-tc/COD/2007/9 Luebo, complete genome')
('length:', 18958)
('e value:', 2.99253e-23)
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTC--GACATACTGTGTTTTTAAATATAGTATTGC
|||||||||||||||||||||||||||||||||||||||||  |||||| |||||||||||||||||||||||
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATATTGTGTTTTTAAATATAGTATTGC
****Alignment****
('sequence:', u'gi|355344232|gb|HQ613403.1| Zaire ebolavirus isolate M-M, partial genome')
('length:', 18807)
('e value:', 2.99253e-23)
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTC--GACATACTGTGTTTTTAAATATAGTATTGC
|||||||||||||||||||||||||||||||||||||||||  |||||| |||||||||||||||||||||||
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATATTGTGTTTTTAAATATAGTATTGC
****Alignment****
('sequence:', u'gi|355344222|gb|HQ613402.1| Zaire ebolavirus isolate 034-KS, partial genome')
('length:', 18774)
('e value:', 2.99253e-23)
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTC--GACATACTGTGTTTTTAAATATAGTATTGC
|||||||||||||||||||||||||||||||||||||||||  |||||| |||||||||||||||||||||||
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATATTGTGTTTTTAAATATAGTATTGC
****Alignment****
('sequence:', u'gi|768029139|gb|KF113528.1| Zaire ebolavirus isolate Kelle 1 NP protein (NP), VP35 protein (VP35), VP40 protein (VP40), GP protein (GP), VP30 protein (VP30), VP24 protein (VP24), and L protein (L) genes, complete cds')
('length:', 18901)
('e value:', 1.27245e-21)
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTC--GACATACTGTGTTTTTAAATATAGTATTGC
|||| ||||||||||||||||||||||||||||||||||||  |||||| |||||||||||||||||||||||
ATGCCACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATATTGTGTTTTTAAATATAGTATTGC
****Alignment****
('sequence:', u'gi|436409429|gb|KC242800.1| Zaire ebolavirus isolate EBOV/H.sapiens-tc/GAB/2002/Ilembe, complete genome')
('length:', 18958)
('e value:', 1.27245e-21)
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTC--GACATACTGTGTTTTTAAATATAGTATTGC
|||| ||||||||||||||||||||||||||||||||||||  |||||| |||||||||||||||||||||||
ATGCCACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATATTGTGTTTTTAAATATAGTATTGC
****Alignment****
('sequence:', u'gi|913075140|gb|KT357860.1| Zaire ebolavirus isolate EBOV/DML14077/SLe/WesternUrban/20150630, complete genome')
('length:', 18752)
('e value:', 1.55017e-20)
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTC--GACATACTGTGTTTTTAAATATAGTATTGC
||||||||||||||||||||||||||||||| |||||||||  |||||| ||||||||||||||||| |||||
ATGCTACGGTGCTAAAAGCATTACGCCCTATCGTGATTTTCGAGACATATTGTGTTTTTAAATATAGCATTGC
****Alignment****
('sequence:', u'gi|913075130|gb|KT357859.1| Zaire ebolavirus isolate EBOV/DML14366/SLe/WesternUrban/20150711, complete genome')
('length:', 18874)
('e value:', 1.55017e-20)
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTC--GACATACTGTGTTTTTAAATATAGTATTGC
||||||||||||||||||||||||||||||| |||||||||  |||||| ||||||||||||||||| |||||
ATGCTACGGTGCTAAAAGCATTACGCCCTATCGTGATTTTCGAGACATATTGTGTTTTTAAATATAGCATTGC
****Alignment****
('sequence:', u'gi|913075120|gb|KT357858.1| Zaire ebolavirus isolate EBOV/DML14163/SLe/WesternUrban/20150703, complete genome')
('length:', 18751)
('e value:', 1.55017e-20)
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTC--GACATACTGTGTTTTTAAATATAGTATTGC
||||||||||||||||||||||||||||||| |||||||||  |||||| ||||||||||||||||| |||||
ATGCTACGGTGCTAAAAGCATTACGCCCTATCGTGATTTTCGAGACATATTGTGTTTTTAAATATAGCATTGC
****Alignment****
('sequence:', u'gi|913075100|gb|KT357856.1| Zaire ebolavirus isolate EBOV/DML25344/SLe/Kono/20150306, complete genome')
('length:', 18752)
('e value:', 1.55017e-20)
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTC--GACATACTGTGTTTTTAAATATAGTATTGC
||||||||||||||||||||||||||||||| |||||||||  |||||| ||||||||||||||||| |||||
ATGCTACGGTGCTAAAAGCATTACGCCCTATCGTGATTTTCGAGACATATTGTGTTTTTAAATATAGCATTGC
****Alignment****
('sequence:', u'gi|913075090|gb|KT357855.1| Zaire ebolavirus isolate EBOV/DML25180/SLe/Kono/20150223, complete genome')
('length:', 18875)
('e value:', 1.55017e-20)
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTC--GACATACTGTGTTTTTAAATATAGTATTGC
||||||||||||||||||||||||||||||| |||||||||  |||||| ||||||||||||||||| |||||
ATGCTACGGTGCTAAAAGCATTACGCCCTATCGTGATTTTCGAGACATATTGTGTTTTTAAATATAGCATTGC
****Alignment****
('sequence:', u'gi|913075080|gb|KT357854.1| Zaire ebolavirus isolate EBOV/DML25123/SLe/Kenema/20150218, partial genome')
('length:', 18736)
('e value:', 1.55017e-20)
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTC--GACATACTGTGTTTTTAAATATAGTATTGC
||||||||||||||||||||||||||||||| |||||||||  |||||| ||||||||||||||||| |||||
ATGCTACGGTGCTAAAAGCATTACGCCCTATCGTGATTTTCGAGACATATTGTGTTTTTAAATATAGCATTGC
****Alignment****
('sequence:', u'gi|913075070|gb|KT357853.1| Zaire ebolavirus isolate EBOV/DML25103/SLe/Kono/20150219, complete genome')
('length:', 18887)
('e value:', 1.55017e-20)
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTC--GACATACTGTGTTTTTAAATATAGTATTGC
||||||||||||||||||||||||||||||| |||||||||  |||||| ||||||||||||||||| |||||
ATGCTACGGTGCTAAAAGCATTACGCCCTATCGTGATTTTCGAGACATATTGTGTTTTTAAATATAGCATTGC
****Alignment****
('sequence:', u'gi|913075060|gb|KT357852.1| Zaire ebolavirus isolate EBOV/DML25083/SLe/Kono/20150218, complete genome')
('length:', 18875)
('e value:', 1.55017e-20)
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTC--GACATACTGTGTTTTTAAATATAGTATTGC
||||||||||||||||||||||||||||||| |||||||||  |||||| ||||||||||||||||| |||||
ATGCTACGGTGCTAAAAGCATTACGCCCTATCGTGATTTTCGAGACATATTGTGTTTTTAAATATAGCATTGC
****Alignment****
('sequence:', u'gi|913075050|gb|KT357851.1| Zaire ebolavirus isolate EBOV/DML24854/SLe/Kono/20150206, complete genome')
('length:', 18875)
('e value:', 1.55017e-20)
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTC--GACATACTGTGTTTTTAAATATAGTATTGC
||||||||||||||||||||||||||||||| |||||||||  |||||| ||||||||||||||||| |||||
ATGCTACGGTGCTAAAAGCATTACGCCCTATCGTGATTTTCGAGACATATTGTGTTTTTAAATATAGCATTGC
****Alignment****
('sequence:', u'gi|913075040|gb|KT357850.1| Zaire ebolavirus isolate EBOV/DML24853/SLe/Kono/20150206, complete genome')
('length:', 18875)
('e value:', 1.55017e-20)
ATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTC--GACATACTGTGTTTTTAAATATAGTATTGC
||||||||||||||||||||||||||||||| |||||||||  |||||| ||||||||||||||||| |||||
ATGCTACGGTGCTAAAAGCATTACGCCCTATCGTGATTTTCGAGACATATTGTGTTTTTAAATATAGCATTGC

In [4]:

    

help(NCBIWWW.qblast)


    

    




Help on function qblast in module Bio.Blast.NCBIWWW:

qblast(program, database, sequence, auto_format=None, composition_based_statistics=None, db_genetic_code=None, endpoints=None, entrez_query='(none)', expect=10.0, filter=None, gapcosts=None, genetic_code=None, hitlist_size=50, i_thresh=None, layout=None, lcase_mask=None, matrix_name=None, nucl_penalty=None, nucl_reward=None, other_advanced=None, perc_ident=None, phi_pattern=None, query_file=None, query_believe_defline=None, query_from=None, query_to=None, searchsp_eff=None, service=None, threshold=None, ungapped_alignment=None, word_size=None, alignments=500, alignment_view=None, descriptions=500, entrez_links_new_window=None, expect_low=None, expect_high=None, format_entrez_query=None, format_object=None, format_type='XML', ncbi_gi=None, results_file=None, show_overview=None, megablast=None)
    Do a BLAST search using the QBLAST server at NCBI.
    
    Supports all parameters of the qblast API for Put and Get.
    Some useful parameters:
    program        blastn, blastp, blastx, tblastn, or tblastx (lower case)
    database       Which database to search against (e.g. "nr").
    sequence       The sequence to search.
    ncbi_gi        TRUE/FALSE whether to give 'gi' identifier.
    descriptions   Number of descriptions to show.  Def 500.
    alignments     Number of alignments to show.  Def 500.
    expect         An expect value cutoff.  Def 10.0.
    matrix_name    Specify an alt. matrix (PAM30, PAM70, BLOSUM80, BLOSUM45).
    filter         "none" turns off filtering.  Default no filtering
    format_type    "HTML", "Text", "ASN.1", or "XML".  Def. "XML".
    entrez_query   Entrez query to limit Blast search
    hitlist_size   Number of hits to return. Default 50
    megablast      TRUE/FALSE whether to use MEga BLAST algorithm (blastn only)
    service        plain, psi, phi, rpsblast, megablast (lower case)
    
    This function does no checking of the validity of the parameters
    and passes the values to the server as is.  More help is available at:
    http://www.ncbi.nlm.nih.gov/BLAST/Doc/urlapi.html

In [6]:

    

import Bio.Blast
help(Bio.Blast)


    

    




Help on package Bio.Blast in Bio:

NAME
    Bio.Blast - Code for dealing with BLAST programs and output.

FILE
    /usr/lib/python2.7/dist-packages/Bio/Blast/__init__.py

PACKAGE CONTENTS
    Applications
    NCBIStandalone
    NCBIWWW
    NCBIXML
    ParseBlastTable
    Record

In [29]:

    

from Bio.Blast import NCBIWWW
fasta_string = "TGGGCCTCATATTTATCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTCGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTATTCTGTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTCTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG"
result_handle = NCBIWWW.qblast("blastn", "nt", fasta_string)


    

In [30]:

    

from Bio.Blast import NCBIXML
blast_record = NCBIXML.read(result_handle)
print "blast_record:", blast_record
print "type(blast_record):", type(blast_record)
print "len(blast_record.alignments):", len(blast_record.alignments)


    

    




blast_record: <Bio.Blast.Record.Blast object at 0xb0d8f1cc>
type(blast_record): <class 'Bio.Blast.Record.Blast'>
len(blast_record.alignments): 50

In [31]:

    

E_VALUE_THRESH = 0.01
for alignment in blast_record.alignments:
    for hsp in alignment.hsps:
        if hsp.expect < E_VALUE_THRESH:
            print('****Alignment****')
            print('sequence:', alignment.title)
            print('length:', alignment.length)
            print('e value:', hsp.expect)
            print(hsp.query)
            print(hsp.match)
            print(hsp.sbjct)


    

    




****Alignment****
('sequence:', u'gi|916446276|gb|KT179379.1| Evolvulus nuttallianus voucher Aust 160 cytochrome c oxidase subunit 3 (coxIII) gene, complete cds; mitochondrial')
('length:', 798)
('e value:', 1.82443e-96)
TGGGCCTCATATTTATCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTCGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTATTCTGTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTCTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
TGGGCCTCATATTTATCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTCGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTATTCTGTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTCTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
****Alignment****
('sequence:', u'gi|756762107|gb|KM207679.1| Nicotiana tabacum/Hyoscyamus niger cybrid clone contig2 mitochondrion, complete sequence')
('length:', 248768)
('e value:', 1.82443e-96)
TGGGCCTCATATTTATCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTCGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTATTCTGTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTCTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
TGGGCCTCATATTTATCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTCGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTATTCTGTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTCTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
****Alignment****
('sequence:', u'gi|698585445|ref|XM_009780350.1| PREDICTED: Nicotiana sylvestris cytochrome c oxidase subunit 3 (LOC104227970), mRNA')
('length:', 1334)
('e value:', 1.82443e-96)
TGGGCCTCATATTTATCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTCGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTATTCTGTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTCTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
TGGGCCTCATATTTATCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTCGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTATTCTGTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTCTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
****Alignment****
('sequence:', u'gi|56806513|dbj|BA000042.1| Nicotiana tabacum mitochondrial DNA, complete genome')
('length:', 430597)
('e value:', 1.82443e-96)
TGGGCCTCATATTTATCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTCGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTATTCTGTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTCTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
TGGGCCTCATATTTATCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTCGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTATTCTGTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTCTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
****Alignment****
('sequence:', u'gi|916446290|gb|KT179384.1| Solanum triflorum voucher Aust 161 cytochrome c oxidase subunit 3 (coxIII) gene, complete cds; mitochondrial')
('length:', 798)
('e value:', 7.75767e-95)
TGGGCCTCATATTTATCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTCGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTATTCTGTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTCTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
|||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
TGGGCCTCATATTTCTCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTCGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTATTCTGTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTCTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
****Alignment****
('sequence:', u'gi|916446288|gb|KT179383.1| Solanum rostratum voucher Aust 178 cytochrome c oxidase subunit 3 (coxIII) gene, complete cds; mitochondrial')
('length:', 798)
('e value:', 7.75767e-95)
TGGGCCTCATATTTATCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTCGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTATTCTGTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTCTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
|||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
TGGGCCTCATATTTCTCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTCGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTATTCTGTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTCTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
****Alignment****
('sequence:', u'gi|916446285|gb|KT179382.1| Solanum carolinense voucher Aust 169 cytochrome c oxidase subunit 3 (coxIII) gene, complete cds; mitochondrial')
('length:', 798)
('e value:', 7.75767e-95)
TGGGCCTCATATTTATCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTCGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTATTCTGTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTCTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
|||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
TGGGCCTCATATTTCTCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTCGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTATTCTGTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTCTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
****Alignment****
('sequence:', u'gi|916446274|gb|KT179378.1| Ipomoea leptophylla voucher Steele 1349 cytochrome c oxidase subunit 3 (coxIII) gene, complete cds; mitochondrial')
('length:', 798)
('e value:', 7.75767e-95)
TGGGCCTCATATTTATCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTCGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTATTCTGTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTCTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
TGGGCCTCATATTTATCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGCGAATCCACGTTCGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTATTCTGTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTCTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
****Alignment****
('sequence:', u'gi|916446271|gb|KT179377.1| Convolvulus arvensis voucher Kellar 1382 cytochrome c oxidase subunit 3 (coxIII) gene, complete cds; mitochondrial')
('length:', 798)
('e value:', 7.75767e-95)
TGGGCCTCATATTTATCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTCGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTATTCTGTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTCTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
TGGGCCTCATATTTATCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGCGAATCCACGTTCGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTATTCTGTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTCTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
****Alignment****
('sequence:', u'gi|756142152|gb|KM207685.1| Hyoscyamus niger mitochondrion, complete genome')
('length:', 501401)
('e value:', 7.75767e-95)
TGGGCCTCATATTTATCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTCGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTATTCTGTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTCTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
|||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
TGGGCCTCATATTTCTCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTCGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTATTCTGTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTCTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
****Alignment****
('sequence:', u'gi|667751905|gb|KJ865410.1| Capsicum annuum cultivar Jeju mitochondrion, complete genome')
('length:', 511530)
('e value:', 9.45077e-94)
TGGGCCTCATATTTATCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTCGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTATTCTGTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTCTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
|||||||||||||| |||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
TGGGCCTCATATTTCTCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGCGAATCCACGTTCGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTATTCTGTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTCTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
****Alignment****
('sequence:', u'gi|667751705|gb|KJ865409.1| Capsicum annuum cultivar CMS line FS4401 mitochondrion, complete genome')
('length:', 507452)
('e value:', 9.45077e-94)
TGGGCCTCATATTTATCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTCGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTATTCTGTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTCTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
|||||||||||||| |||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
TGGGCCTCATATTTCTCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGCGAATCCACGTTCGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTATTCTGTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTCTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
****Alignment****
('sequence:', u'gi|663673444|emb|HG975445.1| Solanum pennellii chromosome ch06, complete genome')
('length:', 60730942)
('e value:', 9.45077e-94)
TGGGCCTCATATTTATCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTCGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTATTCTGTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTCTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
|||||||||||||| ||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
TGGGCCTCATATTTCTCCTATATACCATGTTCGTATGGGGGCGCGATGTTCTACGTGAATCCACGTTCGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTATTCTGTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTCTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
****Alignment****
('sequence:', u'gi|110617815|gb|DQ855008.1| Capsicum annuum cytochrome oxidase subunit III (coIII) gene, partial cds; mitochondrial')
('length:', 653)
('e value:', 1.15134e-92)
TGGGCCTCATATTTATCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTCGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTATTCTGTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTCTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
|||||||||||||| ||||||||||||||||||||||| |||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
TGGGCCTCATATTTCTCCTATATACCATGTTCGTATGGYGGCGCGATGTTCTACGCGAATCCACGTTCGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTATTCTGTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTCTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
****Alignment****
('sequence:', u'gi|916446323|gb|KT179395.1| Nepeta cataria voucher Aust 177 cytochrome c oxidase subunit 3 (coxIII) gene, complete cds; mitochondrial')
('length:', 798)
('e value:', 4.01857e-92)
TGGGCCTCATATTTATCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTCGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTATTCTGTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTCTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||
TGGGCCTCATATTTATCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTGGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTATTCTTTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTTTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
****Alignment****
('sequence:', u'gi|916446320|gb|KT179394.1| Salvia nemorosa voucher Aust 180 cytochrome c oxidase subunit 3 (coxIII) gene, complete cds; mitochondrial')
('length:', 798)
('e value:', 4.01857e-92)
TGGGCCTCATATTTATCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTCGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTATTCTGTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTCTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||
TGGGCCTCATATTTATCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTGGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTATTCTTTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTTTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
****Alignment****
('sequence:', u'gi|916446314|gb|KT179392.1| Ellisia nyctelea voucher Steele 1275 cytochrome c oxidase subunit 3 (coxIII) gene, complete cds; mitochondrial')
('length:', 798)
('e value:', 4.01857e-92)
TGGGCCTCATATTTATCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTCGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTATTCTGTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTCTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||| ||||||||||||||||||||||||||||||||||||||
TGGGCCTCATATTTATCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTGGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTATTCTGTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTTTTTTTTGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
****Alignment****
('sequence:', u'gi|534292244|gb|KF177345.1| Salvia miltiorrhiza mitochondrion, complete genome')
('length:', 499236)
('e value:', 4.01857e-92)
TGGGCCTCATATTTATCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTCGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTATTCTGTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTCTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||
TGGGCCTCATATTTATCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTGGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTATTCTTTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTTTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
****Alignment****
('sequence:', u'gi|314998882|gb|HM590433.1| Antirrhinum majus cytochrome oxidase subunit 3 (cox3) and succinate dehydrogenase subunit 4 (sdh4) genes, complete cds; mitochondrial')
('length:', 1193)
('e value:', 4.01857e-92)
TGGGCCTCATATTTATCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTCGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTATTCTGTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTCTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||
TGGGCCTCATATTTATCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTGGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTATTCTTTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTTTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
****Alignment****
('sequence:', u'gi|259156760|gb|GQ856147.1| Citrullus lanatus mitochondrion, complete genome')
('length:', 379236)
('e value:', 4.01857e-92)
TGGGCCTCATATTTATCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTCGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTATTCTGTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTCTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||| ||||||||||||||||||||||||||||||||||||||||||||
TGGGCCTCATATTTATCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTGGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTATTCTGTTTATCGTATCGGAGGTTATGTTCCTTTTTGCTTTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
****Alignment****
('sequence:', u'gi|134140827|gb|EF121503.1| Sambucus canadensis cytochrome oxidase subunit 3 (cox3) gene, partial cds; mitochondrial')
('length:', 658)
('e value:', 4.01857e-92)
TGGGCCTCATATTTATCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTCGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTATTCTGTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTCTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
|||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||
TGGGCCTCATATTTCTCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTGGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTATTCTGTTTATCGTATCGGAGGTTATGTTCCTTTTTGCTCTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
****Alignment****
('sequence:', u'gi|134140799|gb|EF121489.1| Diervilla sessilifolia cytochrome oxidase subunit 3 (cox3) gene, partial cds; mitochondrial >gi|134140849|gb|EF121514.1| Weigela hortensis cytochrome oxidase subunit 3 (cox3) gene, partial cds; mitochondrial')
('length:', 658)
('e value:', 4.01857e-92)
TGGGCCTCATATTTATCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTCGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTATTCTGTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTCTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
|||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||
TGGGCCTCATATTTCTCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTGGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTATTCTGTTTATCGTATCGGAGGTTATGTTCCTTTTTGCTCTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
****Alignment****
('sequence:', u'gi|134140793|gb|EF121486.1| Adoxa moschatellina cytochrome oxidase subunit 3 (cox3) gene, partial cds; mitochondrial >gi|134140831|gb|EF121505.1| Sinadoxa corydalifolia cytochrome oxidase subunit 3 (cox3) gene, partial cds; mitochondrial >gi|134140835|gb|EF121507.1| Tetradoxa omeiensis cytochrome oxidase subunit 3 (cox3) gene, partial cds; mitochondrial')
('length:', 658)
('e value:', 4.01857e-92)
TGGGCCTCATATTTATCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTCGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTATTCTGTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTCTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||
TGGGCCTCATATTTATCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCTACGTTGGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTATTCTGTTTATCGTATCGGAGGTTATGTTCCTTTTTGCTCTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
****Alignment****
('sequence:', u'gi|134140789|gb|EF121484.1| Abelia chinensis cytochrome oxidase subunit 3 (cox3) gene, partial cds; mitochondrial >gi|134140801|gb|EF121490.1| Dipelta floribunda cytochrome oxidase subunit 3 (cox3) gene, partial cds; mitochondrial >gi|134140809|gb|EF121494.1| Kolkwitzia amabilis cytochrome oxidase subunit 3 (cox3) gene, partial cds; mitochondrial >gi|134140813|gb|EF121496.1| Linnaea borealis cytochrome oxidase subunit 3 (cox3) gene, partial cds; mitochondrial')
('length:', 658)
('e value:', 4.01857e-92)
TGGGCCTCATATTTATCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTCGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTATTCTGTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTCTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
|||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||
TGGGCCTCATATTTCTCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTGGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTATTCTGTTTATCGTATCGGAGGTTATGTTCCTTTTTGCTCTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
****Alignment****
('sequence:', u'gi|94317185|gb|DQ317066.1| Sambucus canadensis cytochrome oxidase subunit III (cox3) gene, partial cds; mitochondrial')
('length:', 689)
('e value:', 4.01857e-92)
TGGGCCTCATATTTATCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTCGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTATTCTGTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTCTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
|||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||
TGGGCCTCATATTTCTCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTGGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTATTCTGTTTATCGTATCGGAGGTTATGTTCCTTTTTGCTCTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
****Alignment****
('sequence:', u'gi|916446334|gb|KT179399.1| Verbena hastata voucher Steele 1369 cytochrome c oxidase subunit 3 (coxIII) gene, complete cds; mitochondrial')
('length:', 798)
('e value:', 4.89562e-91)
TGGGCCTCATATTTATCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTCGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTATTCTGTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTCTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
|||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||
TGGGCCTCATATTTATCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTCCGTGAATCCACGTTGGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTATTCTTTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTTTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
****Alignment****
('sequence:', u'gi|916446331|gb|KT179398.1| Verbascum thapsus voucher Steele 1373 cytochrome c oxidase subunit 3 (coxIII) gene, complete cds; mitochondrial')
('length:', 798)
('e value:', 4.89562e-91)
TGGGCCTCATATTTATCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTCGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTATTCTGTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTCTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||| |||| ||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||
TGGGCCTCATATTTATCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTGGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTCTTCTTTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTTTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
****Alignment****
('sequence:', u'gi|430728036|gb|JX944506.1| Gossypium harknessii mitochondrion, complete genome')
('length:', 666081)
('e value:', 4.89562e-91)
TGGGCCTCATATTTATCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTCGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTATTCTGTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTCTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||| ||||| ||||||||||||||||||||||||||||||||||||||
TGGGCCTCATATTTATCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTGGAAGGACATCATACCAAAGTCGTACAATTAGGACTTCGATATGGTTTTATTCTGTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTTTTTTTTGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
****Alignment****
('sequence:', u'gi|430728001|gb|JX944505.1| Gossypium hirsutum mitochondrion, complete genome')
('length:', 668584)
('e value:', 4.89562e-91)
TGGGCCTCATATTTATCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTCGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTATTCTGTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTCTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||| ||||| ||||||||||||||||||||||||||||||||||||||
TGGGCCTCATATTTATCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTGGAAGGACATCATACCAAAGTCGTACAATTAGGACTTCGATATGGTTTTATTCTGTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTTTTTTTTGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
****Alignment****
('sequence:', u'gi|747106965|ref|XM_011103479.1| PREDICTED: Sesamum indicum cytochrome c oxidase subunit 3 (LOC105179843), mRNA')
('length:', 985)
('e value:', 4.89562e-91)
TGGGCCTCATATTTATCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTCGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTATTCTGTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTCTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||| || ||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||
TGGGCCTCATATTTATCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTGGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTATCCTTTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTTTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
****Alignment****
('sequence:', u'gi|340007640|gb|JN098455.1| Mimulus guttatus mitochondrion, complete genome')
('length:', 525671)
('e value:', 4.89562e-91)
TGGGCCTCATATTTATCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTCGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTATTCTGTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTCTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||
TGGGCCTCATATTTATCCTATATACCATGTTTGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTGGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTATTCTTTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTTTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
****Alignment****
('sequence:', u'gi|340549473|gb|JN107812.1| Boea hygrometrica mitochondrion, complete genome')
('length:', 510519)
('e value:', 4.89562e-91)
TGGGCCTCATATTTATCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTCGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTATTCTGTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTCTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
|||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||
TGGGCCTCATATTTATTCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTGGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTATTCTTTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTTTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
****Alignment****
('sequence:', u'gi|310757466|gb|HM535784.1| Hibiscus cannabinus cultivar P3A cytochrome c oxidase subunit III (cox3) gene, complete cds; mitochondrial')
('length:', 798)
('e value:', 4.89562e-91)
TGGGCCTCATATTTATCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTCGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTATTCTGTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTCTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||| ||||| ||||||||||||||||||||||||||||||||||||||
TGGGCCTCATATTTATCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTGGAAGGACATCATACCAAAGTCGTACAATTAGGACTTCGATATGGTTTTATTCTGTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTTTTTTTTGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
****Alignment****
('sequence:', u'gi|134140821|gb|EF121500.1| Patrinia triloba cytochrome oxidase subunit 3 (cox3) gene, partial cds; mitochondrial')
('length:', 658)
('e value:', 4.89562e-91)
TGGGCCTCATATTTATCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTCGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTATTCTGTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTCTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
|||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||
TGGGCCTCATATTTCTCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTGGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTCTTCTGTTTATCGTATCGGAGGTTATGTTCCTTTTTGCTCTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
****Alignment****
('sequence:', u'gi|134140819|gb|EF121499.1| Valeriana jatamansi cytochrome oxidase subunit 3 (cox3) gene, partial cds; mitochondrial')
('length:', 658)
('e value:', 4.89562e-91)
TGGGCCTCATATTTATCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTCGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTATTCTGTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTCTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||| |||| |||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||
TGGGCCTCATATTTATCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTGGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTCTTCTCTTTATCGTATCGGAGGTTATGTTCCTTTTTGCTCTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
****Alignment****
('sequence:', u'gi|134140807|gb|EF121493.1| Heptacodium miconioides cytochrome oxidase subunit 3 (cox3) gene, partial cds; mitochondrial')
('length:', 658)
('e value:', 4.89562e-91)
TGGGCCTCATATTTATCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTCGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTATTCTGTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTCTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
|||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||
TGGGCCTCATATTTCTCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTGGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTCTTCTGTTTATCGTATCGGAGGTTATGTTCCTTTTTGCTCTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
****Alignment****
('sequence:', u'gi|134140791|gb|EF121485.1| Acanthocalyx albus cytochrome oxidase subunit 3 (cox3) gene, partial cds; mitochondrial')
('length:', 658)
('e value:', 4.89562e-91)
TGGGCCTCATATTTATCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTCGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTATTCTGTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTCTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
|||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||
TGGGCCTCATATTTCTCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTGGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTCTTCTGTTTATCGTATCGGAGGTTATGTTCCTTTTTGCTCTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
****Alignment****
('sequence:', u'gi|27527161|emb|AJ313433.1| Olea europaea subsp. europaea mitochondrial ORFB and COIII gene for cytochrome oxidase subunit III')
('length:', 1878)
('e value:', 4.89562e-91)
TGGGCCTCATATTTATCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTCGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTATTCTGTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTCTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
|||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||
TGGGCCTCATATTTCTCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTGGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTATTCTTTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTTTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
****Alignment****
('sequence:', u'gi|14594884|emb|Z70241.2| Olea europaea cox3 gene (RNA editing)')
('length:', 1818)
('e value:', 4.89562e-91)
TGGGCCTCATATTTATCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTCGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTATTCTGTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTCTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
|||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||
TGGGCCTCATATTTCTCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTGGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTATTCTTTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTTTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
****Alignment****
('sequence:', u'gi|310757468|gb|HM535785.1| Hibiscus cannabinus cultivar P3B cytochrome c oxidase subunit III (cox3) pseudogene, partial sequence; mitochondrial')
('length:', 797)
('e value:', 5.96409e-90)
TGGGCCTCATATTTATCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTCGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTATTCTGTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTCTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||| ||||| ||||||||||||||||||||||||||||||||||||||
TGGGCCTCATATTTATCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTGGAAGGACATCATACCAAAGTCGTACAATTAGGACTTCGATATGGTTTTATTCTGTTTATCGTATCGGAGGTTATGTTCTTTTTTGCT-TTTTTTGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
****Alignment****
('sequence:', u'gi|916446337|gb|KT179400.1| Veronica americana voucher Steele 1269 cytochrome c oxidase subunit 3 (coxIII) gene, complete cds; mitochondrial')
('length:', 798)
('e value:', 2.08167e-89)
TGGGCCTCATATTTATCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTCGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTATTCTGTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTCTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||| ||||||||||| |||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||
TGGGCCTCATATTTATCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTGGAAGGACACCATACCAAAGTAGTACAATTAGGACCTCGATATGGTTTTATTCTTTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTTTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
****Alignment****
('sequence:', u'gi|916446329|gb|KT179397.1| Penstemon gracilis voucher Aust 173 cytochrome c oxidase subunit 3 (coxIII) gene, complete cds; mitochondrial')
('length:', 798)
('e value:', 2.08167e-89)
TGGGCCTCATATTTATCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTCGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTATTCTGTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTCTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
|||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||| |||| ||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||
TGGGCCTCATATTTCTCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTGGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTCTTCTTTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTTTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
****Alignment****
('sequence:', u'gi|916446326|gb|KT179396.1| Penstemon angustifolius voucher Steele 1294 cytochrome c oxidase subunit 3 (coxIII) gene, complete cds; mitochondrial')
('length:', 798)
('e value:', 2.08167e-89)
TGGGCCTCATATTTATCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTCGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTATTCTGTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTCTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
|||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||| |||| ||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||
TGGGCCTCATATTTCTCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTGGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTCTTCTTTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTTTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
****Alignment****
('sequence:', u'gi|916446317|gb|KT179393.1| Monarda fistulosa var. mollis voucher Aust 190 cytochrome c oxidase subunit 3 (coxIII) gene, complete cds; mitochondrial')
('length:', 798)
('e value:', 2.08167e-89)
TGGGCCTCATATTTATCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTCGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTATTCTGTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTCTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||| |||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||| |||||||||||| |||||||||||||||||||||||||||||||
TGGGCCTCATATTTATCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTGGAAGGACATCATACCAAAGTAGTACAATTAGGACCTCGATATGGTTTTATTCTTTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTTTTTTTCGGGCTTTTTCTCATTCTTCTTTGGCACCTACGGTAGAG
****Alignment****
('sequence:', u'gi|916446279|gb|KT179380.1| Physalis heterophylla voucher Aust 182 cytochrome c oxidase subunit 3 (coxIII) gene, complete cds; mitochondrial')
('length:', 798)
('e value:', 2.08167e-89)
TGGGCCTCATATTTATCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTCGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTATTCTGTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTCTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
|||||||||| ||| ||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||
TGGGCCTCATCTTTCTCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACTTTCGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTATTCTCTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTCTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCGCCTACGGTAGAG
****Alignment****
('sequence:', u'gi|916446256|gb|KT179372.1| Symphoricarpos occidentalis voucher Steele 1358 cytochrome c oxidase subunit 3 (coxIII) gene, complete cds; mitochondrial')
('length:', 798)
('e value:', 2.08167e-89)
TGGGCCTCATATTTATCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTCGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTATTCTGTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTCTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
|||||||||| ||| |||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||
TGGGCCTCATCTTTCTCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTGGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTCTTCTGTTTATCGTATCGGAGGTTATGTTCCTTTTTGCTCTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
****Alignment****
('sequence:', u'gi|916446250|gb|KT179370.1| Antennaria neglecta voucher Steele 1258 cytochrome c oxidase subunit 3 (coxIII) gene, complete cds; mitochondrial')
('length:', 798)
('e value:', 2.08167e-89)
TGGGCCTCATATTTATCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTCGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTATTCTGTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTCTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||| ||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||
TGGGCCTAATATTTATCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTGGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGGTTTATTCTGTTTATCGTTTCGGAGGTTATGTTCCTTTTTGCTCTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
****Alignment****
('sequence:', u'gi|916446245|gb|KT179368.1| Vernonia baldwinii voucher Aust 195 cytochrome c oxidase subunit 3 (coxIII) gene, complete cds; mitochondrial')
('length:', 798)
('e value:', 2.08167e-89)
TGGGCCTCATATTTATCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTCGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTATTCTGTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTCTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||| ||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||
TGGGCCTAATATTTATCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTGGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGGTTTATTCTGTTTATCGTTTCGGAGGTTATGTTCCTTTTTGCTCTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
****Alignment****
('sequence:', u'gi|916446187|gb|KT179346.1| Cirsium undulatum voucher Steele 1355 cytochrome c oxidase subunit 3 (coxIII) gene, complete cds; mitochondrial')
('length:', 798)
('e value:', 2.08167e-89)
TGGGCCTCATATTTATCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTCGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTATTCTGTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTCTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||| ||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||
TGGGCCTAATATTTATCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTGGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGGTTTATTCTGTTTATCGTTTCGGAGGTTATGTTCCTTTTTGCTCTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
****Alignment****
('sequence:', u'gi|916446184|gb|KT179345.1| Cirsium canescens voucher Steele 1302 cytochrome c oxidase subunit 3 (coxIII) gene, complete cds; mitochondrial')
('length:', 798)
('e value:', 2.08167e-89)
TGGGCCTCATATTTATCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTCGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTATTCTGTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTCTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG
||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||| ||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||
TGGGCCTAATATTTATCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTGGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGGTTTATTCTGTTTATCGTTTCGGAGGTTATGTTCCTTTTTGCTCTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG

In [51]:

    

from Bio.Seq import Seq
from Bio.Alphabet import generic_protein

help(Seq)
my_seq = Seq("MELKI", generic_protein) + "LV"


    

    




Help on class Seq in module Bio.Seq:

class Seq(__builtin__.object)
 |  A read-only sequence object (essentially a string with an alphabet).
 |  
 |  Like normal python strings, our basic sequence object is immutable.
 |  This prevents you from doing my_seq[5] = "A" for example, but does allow
 |  Seq objects to be used as dictionary keys.
 |  
 |  The Seq object provides a number of string like methods (such as count,
 |  find, split and strip), which are alphabet aware where appropriate.
 |  
 |  In addition to the string like sequence, the Seq object has an alphabet
 |  property. This is an instance of an Alphabet class from Bio.Alphabet,
 |  for example generic DNA, or IUPAC DNA. This describes the type of molecule
 |  (e.g. RNA, DNA, protein) and may also indicate the expected symbols
 |  (letters).
 |  
 |  The Seq object also provides some biological methods, such as complement,
 |  reverse_complement, transcribe, back_transcribe and translate (which are
 |  not applicable to sequences with a protein alphabet).
 |  
 |  Methods defined here:
 |  
 |  __add__(self, other)
 |      Add another sequence or string to this sequence.
 |      
 |      If adding a string to a Seq, the alphabet is preserved:
 |      
 |      >>> from Bio.Seq import Seq
 |      >>> from Bio.Alphabet import generic_protein
 |      >>> Seq("MELKI", generic_protein) + "LV"
 |      Seq('MELKILV', ProteinAlphabet())
 |      
 |      When adding two Seq (like) objects, the alphabets are important.
 |      Consider this example:
 |      
 |      >>> from Bio.Seq import Seq
 |      >>> from Bio.Alphabet.IUPAC import unambiguous_dna, ambiguous_dna
 |      >>> unamb_dna_seq = Seq("ACGT", unambiguous_dna)
 |      >>> ambig_dna_seq = Seq("ACRGT", ambiguous_dna)
 |      >>> unamb_dna_seq
 |      Seq('ACGT', IUPACUnambiguousDNA())
 |      >>> ambig_dna_seq
 |      Seq('ACRGT', IUPACAmbiguousDNA())
 |      
 |      If we add the ambiguous and unambiguous IUPAC DNA alphabets, we get
 |      the more general ambiguous IUPAC DNA alphabet:
 |      
 |      >>> unamb_dna_seq + ambig_dna_seq
 |      Seq('ACGTACRGT', IUPACAmbiguousDNA())
 |      
 |      However, if the default generic alphabet is included, the result is
 |      a generic alphabet:
 |      
 |      >>> Seq("") + ambig_dna_seq
 |      Seq('ACRGT', Alphabet())
 |      
 |      You can't add RNA and DNA sequences:
 |      
 |      >>> from Bio.Alphabet import generic_dna, generic_rna
 |      >>> Seq("ACGT", generic_dna) + Seq("ACGU", generic_rna)
 |      Traceback (most recent call last):
 |         ...
 |      TypeError: Incompatible alphabets DNAAlphabet() and RNAAlphabet()
 |      
 |      You can't add nucleotide and protein sequences:
 |      
 |      >>> from Bio.Alphabet import generic_dna, generic_protein
 |      >>> Seq("ACGT", generic_dna) + Seq("MELKI", generic_protein)
 |      Traceback (most recent call last):
 |         ...
 |      TypeError: Incompatible alphabets DNAAlphabet() and ProteinAlphabet()
 |  
 |  __cmp__(self, other)
 |      Compare the sequence to another sequence or a string (README).
 |      
 |      Historically comparing Seq objects has done Python object comparison.
 |      After considerable discussion (keeping in mind constraints of the
 |      Python language, hashes and dictionary support) a future release of
 |      Biopython will change this to use simple string comparison. The plan is
 |      that comparing incompatible alphabets (e.g. DNA to RNA) will trigger a
 |      warning.
 |      
 |      This version of Biopython still does Python object comparison, but with
 |      a warning about this future change. During this transition period,
 |      please just do explicit comparisons:
 |      
 |      >>> seq1 = Seq("ACGT")
 |      >>> seq2 = Seq("ACGT")
 |      >>> id(seq1) == id(seq2)
 |      False
 |      >>> str(seq1) == str(seq2)
 |      True
 |      
 |      Note - This method indirectly supports ==, < , etc.
 |  
 |  __contains__(self, char)
 |      Implements the 'in' keyword, like a python string.
 |      
 |      e.g.
 |      
 |      >>> from Bio.Seq import Seq
 |      >>> from Bio.Alphabet import generic_dna, generic_rna, generic_protein
 |      >>> my_dna = Seq("ATATGAAATTTGAAAA", generic_dna)
 |      >>> "AAA" in my_dna
 |      True
 |      >>> Seq("AAA") in my_dna
 |      True
 |      >>> Seq("AAA", generic_dna) in my_dna
 |      True
 |      
 |      Like other Seq methods, this will raise a type error if another Seq
 |      (or Seq like) object with an incompatible alphabet is used:
 |      
 |      >>> Seq("AAA", generic_rna) in my_dna
 |      Traceback (most recent call last):
 |         ...
 |      TypeError: Incompatable alphabets DNAAlphabet() and RNAAlphabet()
 |      >>> Seq("AAA", generic_protein) in my_dna
 |      Traceback (most recent call last):
 |         ...
 |      TypeError: Incompatable alphabets DNAAlphabet() and ProteinAlphabet()
 |  
 |  __getitem__(self, index)
 |      Returns a subsequence of single letter, use my_seq[index].
 |  
 |  __hash__(self)
 |      Hash for comparison.
 |      
 |      See the __cmp__ documentation - we plan to change this!
 |  
 |  __init__(self, data, alphabet=Alphabet())
 |      Create a Seq object.
 |      
 |      Arguments:
 |       - seq      - Sequence, required (string)
 |       - alphabet - Optional argument, an Alphabet object from Bio.Alphabet
 |      
 |      You will typically use Bio.SeqIO to read in sequences from files as
 |      SeqRecord objects, whose sequence will be exposed as a Seq object via
 |      the seq property.
 |      
 |      However, will often want to create your own Seq objects directly:
 |      
 |      >>> from Bio.Seq import Seq
 |      >>> from Bio.Alphabet import IUPAC
 |      >>> my_seq = Seq("MKQHKAMIVALIVICITAVVAALVTRKDLCEVHIRTGQTEVAVF",
 |      ...              IUPAC.protein)
 |      >>> my_seq
 |      Seq('MKQHKAMIVALIVICITAVVAALVTRKDLCEVHIRTGQTEVAVF', IUPACProtein())
 |      >>> print(my_seq)
 |      MKQHKAMIVALIVICITAVVAALVTRKDLCEVHIRTGQTEVAVF
 |      >>> my_seq.alphabet
 |      IUPACProtein()
 |  
 |  __len__(self)
 |      Returns the length of the sequence, use len(my_seq).
 |  
 |  __radd__(self, other)
 |      Adding a sequence on the left.
 |      
 |      If adding a string to a Seq, the alphabet is preserved:
 |      
 |      >>> from Bio.Seq import Seq
 |      >>> from Bio.Alphabet import generic_protein
 |      >>> "LV" + Seq("MELKI", generic_protein)
 |      Seq('LVMELKI', ProteinAlphabet())
 |      
 |      Adding two Seq (like) objects is handled via the __add__ method.
 |  
 |  __repr__(self)
 |      Returns a (truncated) representation of the sequence for debugging.
 |  
 |  __str__(self)
 |      Returns the full sequence as a python string, use str(my_seq).
 |      
 |      Note that Biopython 1.44 and earlier would give a truncated
 |      version of repr(my_seq) for str(my_seq).  If you are writing code
 |      which need to be backwards compatible with old Biopython, you
 |      should continue to use my_seq.tostring() rather than str(my_seq).
 |  
 |  back_transcribe(self)
 |      Returns the DNA sequence from an RNA sequence. New Seq object.
 |      
 |      >>> from Bio.Seq import Seq
 |      >>> from Bio.Alphabet import IUPAC
 |      >>> messenger_rna = Seq("AUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAG",
 |      ...                     IUPAC.unambiguous_rna)
 |      >>> messenger_rna
 |      Seq('AUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAG', IUPACUnambiguousRNA())
 |      >>> messenger_rna.back_transcribe()
 |      Seq('ATGGCCATTGTAATGGGCCGCTGAAAGGGTGCCCGATAG', IUPACUnambiguousDNA())
 |      
 |      Trying to back-transcribe a protein or DNA sequence raises an
 |      exception:
 |      
 |      >>> my_protein = Seq("MAIVMGR", IUPAC.protein)
 |      >>> my_protein.back_transcribe()
 |      Traceback (most recent call last):
 |         ...
 |      ValueError: Proteins cannot be back transcribed!
 |  
 |  complement(self)
 |      Returns the complement sequence. New Seq object.
 |      
 |      >>> from Bio.Seq import Seq
 |      >>> from Bio.Alphabet import IUPAC
 |      >>> my_dna = Seq("CCCCCGATAG", IUPAC.unambiguous_dna)
 |      >>> my_dna
 |      Seq('CCCCCGATAG', IUPACUnambiguousDNA())
 |      >>> my_dna.complement()
 |      Seq('GGGGGCTATC', IUPACUnambiguousDNA())
 |      
 |      You can of course used mixed case sequences,
 |      
 |      >>> from Bio.Seq import Seq
 |      >>> from Bio.Alphabet import generic_dna
 |      >>> my_dna = Seq("CCCCCgatA-GD", generic_dna)
 |      >>> my_dna
 |      Seq('CCCCCgatA-GD', DNAAlphabet())
 |      >>> my_dna.complement()
 |      Seq('GGGGGctaT-CH', DNAAlphabet())
 |      
 |      Note in the above example, ambiguous character D denotes
 |      G, A or T so its complement is H (for C, T or A).
 |      
 |      Trying to complement a protein sequence raises an exception.
 |      
 |      >>> my_protein = Seq("MAIVMGR", IUPAC.protein)
 |      >>> my_protein.complement()
 |      Traceback (most recent call last):
 |         ...
 |      ValueError: Proteins do not have complements!
 |  
 |  count(self, sub, start=0, end=2147483647)
 |      Non-overlapping count method, like that of a python string.
 |      
 |      This behaves like the python string method of the same name,
 |      which does a non-overlapping count!
 |      
 |      Returns an integer, the number of occurrences of substring
 |      argument sub in the (sub)sequence given by [start:end].
 |      Optional arguments start and end are interpreted as in slice
 |      notation.
 |      
 |      Arguments:
 |       - sub - a string or another Seq object to look for
 |       - start - optional integer, slice start
 |       - end - optional integer, slice end
 |      
 |      e.g.
 |      
 |      >>> from Bio.Seq import Seq
 |      >>> my_seq = Seq("AAAATGA")
 |      >>> print(my_seq.count("A"))
 |      5
 |      >>> print(my_seq.count("ATG"))
 |      1
 |      >>> print(my_seq.count(Seq("AT")))
 |      1
 |      >>> print(my_seq.count("AT", 2, -1))
 |      1
 |      
 |      HOWEVER, please note because python strings and Seq objects (and
 |      MutableSeq objects) do a non-overlapping search, this may not give
 |      the answer you expect:
 |      
 |      >>> "AAAA".count("AA")
 |      2
 |      >>> print(Seq("AAAA").count("AA"))
 |      2
 |      
 |      A non-overlapping search would give the answer as three!
 |  
 |  endswith(self, suffix, start=0, end=2147483647)
 |      Does the Seq end with the given suffix?  Returns True/False.
 |      
 |      This behaves like the python string method of the same name.
 |      
 |      Return True if the sequence ends with the specified suffix
 |      (a string or another Seq object), False otherwise.
 |      With optional start, test sequence beginning at that position.
 |      With optional end, stop comparing sequence at that position.
 |      suffix can also be a tuple of strings to try.  e.g.
 |      
 |      >>> from Bio.Seq import Seq
 |      >>> my_rna = Seq("GUCAUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAGUUG")
 |      >>> my_rna.endswith("UUG")
 |      True
 |      >>> my_rna.endswith("AUG")
 |      False
 |      >>> my_rna.endswith("AUG", 0, 18)
 |      True
 |      >>> my_rna.endswith(("UCC", "UCA", "UUG"))
 |      True
 |  
 |  find(self, sub, start=0, end=2147483647)
 |      Find method, like that of a python string.
 |      
 |      This behaves like the python string method of the same name.
 |      
 |      Returns an integer, the index of the first occurrence of substring
 |      argument sub in the (sub)sequence given by [start:end].
 |      
 |      Arguments:
 |       - sub - a string or another Seq object to look for
 |       - start - optional integer, slice start
 |       - end - optional integer, slice end
 |      
 |      Returns -1 if the subsequence is NOT found.
 |      
 |      e.g. Locating the first typical start codon, AUG, in an RNA sequence:
 |      
 |      >>> from Bio.Seq import Seq
 |      >>> my_rna = Seq("GUCAUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAGUUG")
 |      >>> my_rna.find("AUG")
 |      3
 |  
 |  lower(self)
 |      Returns a lower case copy of the sequence.
 |      
 |      This will adjust the alphabet if required. Note that the IUPAC alphabets
 |      are upper case only, and thus a generic alphabet must be substituted.
 |      
 |      >>> from Bio.Alphabet import Gapped, generic_dna
 |      >>> from Bio.Alphabet import IUPAC
 |      >>> from Bio.Seq import Seq
 |      >>> my_seq = Seq("CGGTACGCTTATGTCACGTAG*AAAAAA", Gapped(IUPAC.unambiguous_dna, "*"))
 |      >>> my_seq
 |      Seq('CGGTACGCTTATGTCACGTAG*AAAAAA', Gapped(IUPACUnambiguousDNA(), '*'))
 |      >>> my_seq.lower()
 |      Seq('cggtacgcttatgtcacgtag*aaaaaa', Gapped(DNAAlphabet(), '*'))
 |      
 |      See also the upper method.
 |  
 |  lstrip(self, chars=None)
 |      Returns a new Seq object with leading (left) end stripped.
 |      
 |      This behaves like the python string method of the same name.
 |      
 |      Optional argument chars defines which characters to remove.  If
 |      omitted or None (default) then as for the python string method,
 |      this defaults to removing any white space.
 |      
 |      e.g. print(my_seq.lstrip("-"))
 |      
 |      See also the strip and rstrip methods.
 |  
 |  reverse_complement(self)
 |      Returns the reverse complement sequence. New Seq object.
 |      
 |      >>> from Bio.Seq import Seq
 |      >>> from Bio.Alphabet import IUPAC
 |      >>> my_dna = Seq("CCCCCGATAGNR", IUPAC.ambiguous_dna)
 |      >>> my_dna
 |      Seq('CCCCCGATAGNR', IUPACAmbiguousDNA())
 |      >>> my_dna.reverse_complement()
 |      Seq('YNCTATCGGGGG', IUPACAmbiguousDNA())
 |      
 |      Note in the above example, since R = G or A, its complement
 |      is Y (which denotes C or T).
 |      
 |      You can of course used mixed case sequences,
 |      
 |      >>> from Bio.Seq import Seq
 |      >>> from Bio.Alphabet import generic_dna
 |      >>> my_dna = Seq("CCCCCgatA-G", generic_dna)
 |      >>> my_dna
 |      Seq('CCCCCgatA-G', DNAAlphabet())
 |      >>> my_dna.reverse_complement()
 |      Seq('C-TatcGGGGG', DNAAlphabet())
 |      
 |      Trying to complement a protein sequence raises an exception:
 |      
 |      >>> my_protein = Seq("MAIVMGR", IUPAC.protein)
 |      >>> my_protein.reverse_complement()
 |      Traceback (most recent call last):
 |         ...
 |      ValueError: Proteins do not have complements!
 |  
 |  rfind(self, sub, start=0, end=2147483647)
 |      Find from right method, like that of a python string.
 |      
 |      This behaves like the python string method of the same name.
 |      
 |      Returns an integer, the index of the last (right most) occurrence of
 |      substring argument sub in the (sub)sequence given by [start:end].
 |      
 |      Arguments:
 |       - sub - a string or another Seq object to look for
 |       - start - optional integer, slice start
 |       - end - optional integer, slice end
 |      
 |      Returns -1 if the subsequence is NOT found.
 |      
 |      e.g. Locating the last typical start codon, AUG, in an RNA sequence:
 |      
 |      >>> from Bio.Seq import Seq
 |      >>> my_rna = Seq("GUCAUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAGUUG")
 |      >>> my_rna.rfind("AUG")
 |      15
 |  
 |  rsplit(self, sep=None, maxsplit=-1)
 |      Right split method, like that of a python string.
 |      
 |      This behaves like the python string method of the same name.
 |      
 |      Return a list of the 'words' in the string (as Seq objects),
 |      using sep as the delimiter string.  If maxsplit is given, at
 |      most maxsplit splits are done COUNTING FROM THE RIGHT.
 |      If maxsplit is omitted, all splits are made.
 |      
 |      Following the python string method, sep will by default be any
 |      white space (tabs, spaces, newlines) but this is unlikely to
 |      apply to biological sequences.
 |      
 |      e.g. print(my_seq.rsplit("*",1))
 |      
 |      See also the split method.
 |  
 |  rstrip(self, chars=None)
 |      Returns a new Seq object with trailing (right) end stripped.
 |      
 |      This behaves like the python string method of the same name.
 |      
 |      Optional argument chars defines which characters to remove.  If
 |      omitted or None (default) then as for the python string method,
 |      this defaults to removing any white space.
 |      
 |      e.g. Removing a nucleotide sequence's polyadenylation (poly-A tail):
 |      
 |      >>> from Bio.Alphabet import IUPAC
 |      >>> from Bio.Seq import Seq
 |      >>> my_seq = Seq("CGGTACGCTTATGTCACGTAGAAAAAA", IUPAC.unambiguous_dna)
 |      >>> my_seq
 |      Seq('CGGTACGCTTATGTCACGTAGAAAAAA', IUPACUnambiguousDNA())
 |      >>> my_seq.rstrip("A")
 |      Seq('CGGTACGCTTATGTCACGTAG', IUPACUnambiguousDNA())
 |      
 |      See also the strip and lstrip methods.
 |  
 |  split(self, sep=None, maxsplit=-1)
 |      Split method, like that of a python string.
 |      
 |      This behaves like the python string method of the same name.
 |      
 |      Return a list of the 'words' in the string (as Seq objects),
 |      using sep as the delimiter string.  If maxsplit is given, at
 |      most maxsplit splits are done.  If maxsplit is omitted, all
 |      splits are made.
 |      
 |      Following the python string method, sep will by default be any
 |      white space (tabs, spaces, newlines) but this is unlikely to
 |      apply to biological sequences.
 |      
 |      e.g.
 |      
 |      >>> from Bio.Seq import Seq
 |      >>> my_rna = Seq("GUCAUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAGUUG")
 |      >>> my_aa = my_rna.translate()
 |      >>> my_aa
 |      Seq('VMAIVMGR*KGAR*L', HasStopCodon(ExtendedIUPACProtein(), '*'))
 |      >>> my_aa.split("*")
 |      [Seq('VMAIVMGR', HasStopCodon(ExtendedIUPACProtein(), '*')), Seq('KGAR', HasStopCodon(ExtendedIUPACProtein(), '*')), Seq('L', HasStopCodon(ExtendedIUPACProtein(), '*'))]
 |      >>> my_aa.split("*", 1)
 |      [Seq('VMAIVMGR', HasStopCodon(ExtendedIUPACProtein(), '*')), Seq('KGAR*L', HasStopCodon(ExtendedIUPACProtein(), '*'))]
 |      
 |      See also the rsplit method:
 |      
 |      >>> my_aa.rsplit("*", 1)
 |      [Seq('VMAIVMGR*KGAR', HasStopCodon(ExtendedIUPACProtein(), '*')), Seq('L', HasStopCodon(ExtendedIUPACProtein(), '*'))]
 |  
 |  startswith(self, prefix, start=0, end=2147483647)
 |      Does the Seq start with the given prefix?  Returns True/False.
 |      
 |      This behaves like the python string method of the same name.
 |      
 |      Return True if the sequence starts with the specified prefix
 |      (a string or another Seq object), False otherwise.
 |      With optional start, test sequence beginning at that position.
 |      With optional end, stop comparing sequence at that position.
 |      prefix can also be a tuple of strings to try.  e.g.
 |      
 |      >>> from Bio.Seq import Seq
 |      >>> my_rna = Seq("GUCAUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAGUUG")
 |      >>> my_rna.startswith("GUC")
 |      True
 |      >>> my_rna.startswith("AUG")
 |      False
 |      >>> my_rna.startswith("AUG", 3)
 |      True
 |      >>> my_rna.startswith(("UCC", "UCA", "UCG"), 1)
 |      True
 |  
 |  strip(self, chars=None)
 |      Returns a new Seq object with leading and trailing ends stripped.
 |      
 |      This behaves like the python string method of the same name.
 |      
 |      Optional argument chars defines which characters to remove.  If
 |      omitted or None (default) then as for the python string method,
 |      this defaults to removing any white space.
 |      
 |      e.g. print(my_seq.strip("-"))
 |      
 |      See also the lstrip and rstrip methods.
 |  
 |  tomutable(self)
 |      Returns the full sequence as a MutableSeq object.
 |      
 |      >>> from Bio.Seq import Seq
 |      >>> from Bio.Alphabet import IUPAC
 |      >>> my_seq = Seq("MKQHKAMIVALIVICITAVVAAL",
 |      ...              IUPAC.protein)
 |      >>> my_seq
 |      Seq('MKQHKAMIVALIVICITAVVAAL', IUPACProtein())
 |      >>> my_seq.tomutable()
 |      MutableSeq('MKQHKAMIVALIVICITAVVAAL', IUPACProtein())
 |      
 |      Note that the alphabet is preserved.
 |  
 |  tostring(self)
 |      Returns the full sequence as a python string (semi-obsolete).
 |      
 |      Although not formally deprecated, you are now encouraged to use
 |      str(my_seq) instead of my_seq.tostring().
 |  
 |  transcribe(self)
 |      Returns the RNA sequence from a DNA sequence. New Seq object.
 |      
 |      >>> from Bio.Seq import Seq
 |      >>> from Bio.Alphabet import IUPAC
 |      >>> coding_dna = Seq("ATGGCCATTGTAATGGGCCGCTGAAAGGGTGCCCGATAG",
 |      ...                  IUPAC.unambiguous_dna)
 |      >>> coding_dna
 |      Seq('ATGGCCATTGTAATGGGCCGCTGAAAGGGTGCCCGATAG', IUPACUnambiguousDNA())
 |      >>> coding_dna.transcribe()
 |      Seq('AUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAG', IUPACUnambiguousRNA())
 |      
 |      Trying to transcribe a protein or RNA sequence raises an exception:
 |      
 |      >>> my_protein = Seq("MAIVMGR", IUPAC.protein)
 |      >>> my_protein.transcribe()
 |      Traceback (most recent call last):
 |         ...
 |      ValueError: Proteins cannot be transcribed!
 |  
 |  translate(self, table='Standard', stop_symbol='*', to_stop=False, cds=False)
 |      Turns a nucleotide sequence into a protein sequence. New Seq object.
 |      
 |      This method will translate DNA or RNA sequences, and those with a
 |      nucleotide or generic alphabet.  Trying to translate a protein
 |      sequence raises an exception.
 |      
 |      Arguments:
 |       - table - Which codon table to use?  This can be either a name
 |                 (string), an NCBI identifier (integer), or a CodonTable
 |                 object (useful for non-standard genetic codes).  This
 |                 defaults to the "Standard" table.
 |       - stop_symbol - Single character string, what to use for terminators.
 |                       This defaults to the asterisk, "*".
 |       - to_stop - Boolean, defaults to False meaning do a full translation
 |                   continuing on past any stop codons (translated as the
 |                   specified stop_symbol).  If True, translation is
 |                   terminated at the first in frame stop codon (and the
 |                   stop_symbol is not appended to the returned protein
 |                   sequence).
 |       - cds - Boolean, indicates this is a complete CDS.  If True,
 |               this checks the sequence starts with a valid alternative start
 |               codon (which will be translated as methionine, M), that the
 |               sequence length is a multiple of three, and that there is a
 |               single in frame stop codon at the end (this will be excluded
 |               from the protein sequence, regardless of the to_stop option).
 |               If these tests fail, an exception is raised.
 |      
 |      e.g. Using the standard table:
 |      
 |      >>> coding_dna = Seq("GTGGCCATTGTAATGGGCCGCTGAAAGGGTGCCCGATAG")
 |      >>> coding_dna.translate()
 |      Seq('VAIVMGR*KGAR*', HasStopCodon(ExtendedIUPACProtein(), '*'))
 |      >>> coding_dna.translate(stop_symbol="@")
 |      Seq('VAIVMGR@KGAR@', HasStopCodon(ExtendedIUPACProtein(), '@'))
 |      >>> coding_dna.translate(to_stop=True)
 |      Seq('VAIVMGR', ExtendedIUPACProtein())
 |      
 |      Now using NCBI table 2, where TGA is not a stop codon:
 |      
 |      >>> coding_dna.translate(table=2)
 |      Seq('VAIVMGRWKGAR*', HasStopCodon(ExtendedIUPACProtein(), '*'))
 |      >>> coding_dna.translate(table=2, to_stop=True)
 |      Seq('VAIVMGRWKGAR', ExtendedIUPACProtein())
 |      
 |      In fact, GTG is an alternative start codon under NCBI table 2, meaning
 |      this sequence could be a complete CDS:
 |      
 |      >>> coding_dna.translate(table=2, cds=True)
 |      Seq('MAIVMGRWKGAR', ExtendedIUPACProtein())
 |      
 |      It isn't a valid CDS under NCBI table 1, due to both the start codon and
 |      also the in frame stop codons:
 |      
 |      >>> coding_dna.translate(table=1, cds=True)
 |      Traceback (most recent call last):
 |          ...
 |      TranslationError: First codon 'GTG' is not a start codon
 |      
 |      If the sequence has no in-frame stop codon, then the to_stop argument
 |      has no effect:
 |      
 |      >>> coding_dna2 = Seq("TTGGCCATTGTAATGGGCCGC")
 |      >>> coding_dna2.translate()
 |      Seq('LAIVMGR', ExtendedIUPACProtein())
 |      >>> coding_dna2.translate(to_stop=True)
 |      Seq('LAIVMGR', ExtendedIUPACProtein())
 |      
 |      NOTE - Ambiguous codons like "TAN" or "NNN" could be an amino acid
 |      or a stop codon.  These are translated as "X".  Any invalid codon
 |      (e.g. "TA?" or "T-A") will throw a TranslationError.
 |      
 |      NOTE - Does NOT support gapped sequences.
 |      
 |      NOTE - This does NOT behave like the python string's translate
 |      method.  For that use str(my_seq).translate(...) instead.
 |  
 |  ungap(self, gap=None)
 |      Return a copy of the sequence without the gap character(s).
 |      
 |      The gap character can be specified in two ways - either as an explicit
 |      argument, or via the sequence's alphabet. For example:
 |      
 |      >>> from Bio.Seq import Seq
 |      >>> from Bio.Alphabet import generic_dna
 |      >>> my_dna = Seq("-ATA--TGAAAT-TTGAAAA", generic_dna)
 |      >>> my_dna
 |      Seq('-ATA--TGAAAT-TTGAAAA', DNAAlphabet())
 |      >>> my_dna.ungap("-")
 |      Seq('ATATGAAATTTGAAAA', DNAAlphabet())
 |      
 |      If the gap character is not given as an argument, it will be taken from
 |      the sequence's alphabet (if defined). Notice that the returned sequence's
 |      alphabet is adjusted since it no longer requires a gapped alphabet:
 |      
 |      >>> from Bio.Seq import Seq
 |      >>> from Bio.Alphabet import IUPAC, Gapped, HasStopCodon
 |      >>> my_pro = Seq("MVVLE=AD*", HasStopCodon(Gapped(IUPAC.protein, "=")))
 |      >>> my_pro
 |      Seq('MVVLE=AD*', HasStopCodon(Gapped(IUPACProtein(), '='), '*'))
 |      >>> my_pro.ungap()
 |      Seq('MVVLEAD*', HasStopCodon(IUPACProtein(), '*'))
 |      
 |      Or, with a simpler gapped DNA example:
 |      
 |      >>> from Bio.Seq import Seq
 |      >>> from Bio.Alphabet import IUPAC, Gapped
 |      >>> my_seq = Seq("CGGGTAG=AAAAAA", Gapped(IUPAC.unambiguous_dna, "="))
 |      >>> my_seq
 |      Seq('CGGGTAG=AAAAAA', Gapped(IUPACUnambiguousDNA(), '='))
 |      >>> my_seq.ungap()
 |      Seq('CGGGTAGAAAAAA', IUPACUnambiguousDNA())
 |      
 |      As long as it is consistent with the alphabet, although it is redundant,
 |      you can still supply the gap character as an argument to this method:
 |      
 |      >>> my_seq
 |      Seq('CGGGTAG=AAAAAA', Gapped(IUPACUnambiguousDNA(), '='))
 |      >>> my_seq.ungap("=")
 |      Seq('CGGGTAGAAAAAA', IUPACUnambiguousDNA())
 |      
 |      However, if the gap character given as the argument disagrees with that
 |      declared in the alphabet, an exception is raised:
 |      
 |      >>> my_seq
 |      Seq('CGGGTAG=AAAAAA', Gapped(IUPACUnambiguousDNA(), '='))
 |      >>> my_seq.ungap("-")
 |      Traceback (most recent call last):
 |         ...
 |      ValueError: Gap '-' does not match '=' from alphabet
 |      
 |      Finally, if a gap character is not supplied, and the alphabet does not
 |      define one, an exception is raised:
 |      
 |      >>> from Bio.Seq import Seq
 |      >>> from Bio.Alphabet import generic_dna
 |      >>> my_dna = Seq("ATA--TGAAAT-TTGAAAA", generic_dna)
 |      >>> my_dna
 |      Seq('ATA--TGAAAT-TTGAAAA', DNAAlphabet())
 |      >>> my_dna.ungap()
 |      Traceback (most recent call last):
 |         ...
 |      ValueError: Gap character not given and not defined in alphabet
 |  
 |  upper(self)
 |      Returns an upper case copy of the sequence.
 |      
 |      >>> from Bio.Alphabet import HasStopCodon, generic_protein
 |      >>> from Bio.Seq import Seq
 |      >>> my_seq = Seq("VHLTPeeK*", HasStopCodon(generic_protein))
 |      >>> my_seq
 |      Seq('VHLTPeeK*', HasStopCodon(ProteinAlphabet(), '*'))
 |      >>> my_seq.lower()
 |      Seq('vhltpeek*', HasStopCodon(ProteinAlphabet(), '*'))
 |      >>> my_seq.upper()
 |      Seq('VHLTPEEK*', HasStopCodon(ProteinAlphabet(), '*'))
 |      
 |      This will adjust the alphabet if required. See also the lower method.
 |  
 |  ----------------------------------------------------------------------
 |  Data descriptors defined here:
 |  
 |  __dict__
 |      dictionary for instance variables (if defined)
 |  
 |  __weakref__
 |      list of weak references to the object (if defined)

In [41]:

    

help(my_seq)


    

    




Help on Seq in module Bio.Seq object:

class Seq(__builtin__.object)
 |  A read-only sequence object (essentially a string with an alphabet).
 |  
 |  Like normal python strings, our basic sequence object is immutable.
 |  This prevents you from doing my_seq[5] = "A" for example, but does allow
 |  Seq objects to be used as dictionary keys.
 |  
 |  The Seq object provides a number of string like methods (such as count,
 |  find, split and strip), which are alphabet aware where appropriate.
 |  
 |  In addition to the string like sequence, the Seq object has an alphabet
 |  property. This is an instance of an Alphabet class from Bio.Alphabet,
 |  for example generic DNA, or IUPAC DNA. This describes the type of molecule
 |  (e.g. RNA, DNA, protein) and may also indicate the expected symbols
 |  (letters).
 |  
 |  The Seq object also provides some biological methods, such as complement,
 |  reverse_complement, transcribe, back_transcribe and translate (which are
 |  not applicable to sequences with a protein alphabet).
 |  
 |  Methods defined here:
 |  
 |  __add__(self, other)
 |      Add another sequence or string to this sequence.
 |      
 |      If adding a string to a Seq, the alphabet is preserved:
 |      
 |      >>> from Bio.Seq import Seq
 |      >>> from Bio.Alphabet import generic_protein
 |      >>> Seq("MELKI", generic_protein) + "LV"
 |      Seq('MELKILV', ProteinAlphabet())
 |      
 |      When adding two Seq (like) objects, the alphabets are important.
 |      Consider this example:
 |      
 |      >>> from Bio.Seq import Seq
 |      >>> from Bio.Alphabet.IUPAC import unambiguous_dna, ambiguous_dna
 |      >>> unamb_dna_seq = Seq("ACGT", unambiguous_dna)
 |      >>> ambig_dna_seq = Seq("ACRGT", ambiguous_dna)
 |      >>> unamb_dna_seq
 |      Seq('ACGT', IUPACUnambiguousDNA())
 |      >>> ambig_dna_seq
 |      Seq('ACRGT', IUPACAmbiguousDNA())
 |      
 |      If we add the ambiguous and unambiguous IUPAC DNA alphabets, we get
 |      the more general ambiguous IUPAC DNA alphabet:
 |      
 |      >>> unamb_dna_seq + ambig_dna_seq
 |      Seq('ACGTACRGT', IUPACAmbiguousDNA())
 |      
 |      However, if the default generic alphabet is included, the result is
 |      a generic alphabet:
 |      
 |      >>> Seq("") + ambig_dna_seq
 |      Seq('ACRGT', Alphabet())
 |      
 |      You can't add RNA and DNA sequences:
 |      
 |      >>> from Bio.Alphabet import generic_dna, generic_rna
 |      >>> Seq("ACGT", generic_dna) + Seq("ACGU", generic_rna)
 |      Traceback (most recent call last):
 |         ...
 |      TypeError: Incompatible alphabets DNAAlphabet() and RNAAlphabet()
 |      
 |      You can't add nucleotide and protein sequences:
 |      
 |      >>> from Bio.Alphabet import generic_dna, generic_protein
 |      >>> Seq("ACGT", generic_dna) + Seq("MELKI", generic_protein)
 |      Traceback (most recent call last):
 |         ...
 |      TypeError: Incompatible alphabets DNAAlphabet() and ProteinAlphabet()
 |  
 |  __cmp__(self, other)
 |      Compare the sequence to another sequence or a string (README).
 |      
 |      Historically comparing Seq objects has done Python object comparison.
 |      After considerable discussion (keeping in mind constraints of the
 |      Python language, hashes and dictionary support) a future release of
 |      Biopython will change this to use simple string comparison. The plan is
 |      that comparing incompatible alphabets (e.g. DNA to RNA) will trigger a
 |      warning.
 |      
 |      This version of Biopython still does Python object comparison, but with
 |      a warning about this future change. During this transition period,
 |      please just do explicit comparisons:
 |      
 |      >>> seq1 = Seq("ACGT")
 |      >>> seq2 = Seq("ACGT")
 |      >>> id(seq1) == id(seq2)
 |      False
 |      >>> str(seq1) == str(seq2)
 |      True
 |      
 |      Note - This method indirectly supports ==, < , etc.
 |  
 |  __contains__(self, char)
 |      Implements the 'in' keyword, like a python string.
 |      
 |      e.g.
 |      
 |      >>> from Bio.Seq import Seq
 |      >>> from Bio.Alphabet import generic_dna, generic_rna, generic_protein
 |      >>> my_dna = Seq("ATATGAAATTTGAAAA", generic_dna)
 |      >>> "AAA" in my_dna
 |      True
 |      >>> Seq("AAA") in my_dna
 |      True
 |      >>> Seq("AAA", generic_dna) in my_dna
 |      True
 |      
 |      Like other Seq methods, this will raise a type error if another Seq
 |      (or Seq like) object with an incompatible alphabet is used:
 |      
 |      >>> Seq("AAA", generic_rna) in my_dna
 |      Traceback (most recent call last):
 |         ...
 |      TypeError: Incompatable alphabets DNAAlphabet() and RNAAlphabet()
 |      >>> Seq("AAA", generic_protein) in my_dna
 |      Traceback (most recent call last):
 |         ...
 |      TypeError: Incompatable alphabets DNAAlphabet() and ProteinAlphabet()
 |  
 |  __getitem__(self, index)
 |      Returns a subsequence of single letter, use my_seq[index].
 |  
 |  __hash__(self)
 |      Hash for comparison.
 |      
 |      See the __cmp__ documentation - we plan to change this!
 |  
 |  __init__(self, data, alphabet=Alphabet())
 |      Create a Seq object.
 |      
 |      Arguments:
 |       - seq      - Sequence, required (string)
 |       - alphabet - Optional argument, an Alphabet object from Bio.Alphabet
 |      
 |      You will typically use Bio.SeqIO to read in sequences from files as
 |      SeqRecord objects, whose sequence will be exposed as a Seq object via
 |      the seq property.
 |      
 |      However, will often want to create your own Seq objects directly:
 |      
 |      >>> from Bio.Seq import Seq
 |      >>> from Bio.Alphabet import IUPAC
 |      >>> my_seq = Seq("MKQHKAMIVALIVICITAVVAALVTRKDLCEVHIRTGQTEVAVF",
 |      ...              IUPAC.protein)
 |      >>> my_seq
 |      Seq('MKQHKAMIVALIVICITAVVAALVTRKDLCEVHIRTGQTEVAVF', IUPACProtein())
 |      >>> print(my_seq)
 |      MKQHKAMIVALIVICITAVVAALVTRKDLCEVHIRTGQTEVAVF
 |      >>> my_seq.alphabet
 |      IUPACProtein()
 |  
 |  __len__(self)
 |      Returns the length of the sequence, use len(my_seq).
 |  
 |  __radd__(self, other)
 |      Adding a sequence on the left.
 |      
 |      If adding a string to a Seq, the alphabet is preserved:
 |      
 |      >>> from Bio.Seq import Seq
 |      >>> from Bio.Alphabet import generic_protein
 |      >>> "LV" + Seq("MELKI", generic_protein)
 |      Seq('LVMELKI', ProteinAlphabet())
 |      
 |      Adding two Seq (like) objects is handled via the __add__ method.
 |  
 |  __repr__(self)
 |      Returns a (truncated) representation of the sequence for debugging.
 |  
 |  __str__(self)
 |      Returns the full sequence as a python string, use str(my_seq).
 |      
 |      Note that Biopython 1.44 and earlier would give a truncated
 |      version of repr(my_seq) for str(my_seq).  If you are writing code
 |      which need to be backwards compatible with old Biopython, you
 |      should continue to use my_seq.tostring() rather than str(my_seq).
 |  
 |  back_transcribe(self)
 |      Returns the DNA sequence from an RNA sequence. New Seq object.
 |      
 |      >>> from Bio.Seq import Seq
 |      >>> from Bio.Alphabet import IUPAC
 |      >>> messenger_rna = Seq("AUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAG",
 |      ...                     IUPAC.unambiguous_rna)
 |      >>> messenger_rna
 |      Seq('AUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAG', IUPACUnambiguousRNA())
 |      >>> messenger_rna.back_transcribe()
 |      Seq('ATGGCCATTGTAATGGGCCGCTGAAAGGGTGCCCGATAG', IUPACUnambiguousDNA())
 |      
 |      Trying to back-transcribe a protein or DNA sequence raises an
 |      exception:
 |      
 |      >>> my_protein = Seq("MAIVMGR", IUPAC.protein)
 |      >>> my_protein.back_transcribe()
 |      Traceback (most recent call last):
 |         ...
 |      ValueError: Proteins cannot be back transcribed!
 |  
 |  complement(self)
 |      Returns the complement sequence. New Seq object.
 |      
 |      >>> from Bio.Seq import Seq
 |      >>> from Bio.Alphabet import IUPAC
 |      >>> my_dna = Seq("CCCCCGATAG", IUPAC.unambiguous_dna)
 |      >>> my_dna
 |      Seq('CCCCCGATAG', IUPACUnambiguousDNA())
 |      >>> my_dna.complement()
 |      Seq('GGGGGCTATC', IUPACUnambiguousDNA())
 |      
 |      You can of course used mixed case sequences,
 |      
 |      >>> from Bio.Seq import Seq
 |      >>> from Bio.Alphabet import generic_dna
 |      >>> my_dna = Seq("CCCCCgatA-GD", generic_dna)
 |      >>> my_dna
 |      Seq('CCCCCgatA-GD', DNAAlphabet())
 |      >>> my_dna.complement()
 |      Seq('GGGGGctaT-CH', DNAAlphabet())
 |      
 |      Note in the above example, ambiguous character D denotes
 |      G, A or T so its complement is H (for C, T or A).
 |      
 |      Trying to complement a protein sequence raises an exception.
 |      
 |      >>> my_protein = Seq("MAIVMGR", IUPAC.protein)
 |      >>> my_protein.complement()
 |      Traceback (most recent call last):
 |         ...
 |      ValueError: Proteins do not have complements!
 |  
 |  count(self, sub, start=0, end=2147483647)
 |      Non-overlapping count method, like that of a python string.
 |      
 |      This behaves like the python string method of the same name,
 |      which does a non-overlapping count!
 |      
 |      Returns an integer, the number of occurrences of substring
 |      argument sub in the (sub)sequence given by [start:end].
 |      Optional arguments start and end are interpreted as in slice
 |      notation.
 |      
 |      Arguments:
 |       - sub - a string or another Seq object to look for
 |       - start - optional integer, slice start
 |       - end - optional integer, slice end
 |      
 |      e.g.
 |      
 |      >>> from Bio.Seq import Seq
 |      >>> my_seq = Seq("AAAATGA")
 |      >>> print(my_seq.count("A"))
 |      5
 |      >>> print(my_seq.count("ATG"))
 |      1
 |      >>> print(my_seq.count(Seq("AT")))
 |      1
 |      >>> print(my_seq.count("AT", 2, -1))
 |      1
 |      
 |      HOWEVER, please note because python strings and Seq objects (and
 |      MutableSeq objects) do a non-overlapping search, this may not give
 |      the answer you expect:
 |      
 |      >>> "AAAA".count("AA")
 |      2
 |      >>> print(Seq("AAAA").count("AA"))
 |      2
 |      
 |      A non-overlapping search would give the answer as three!
 |  
 |  endswith(self, suffix, start=0, end=2147483647)
 |      Does the Seq end with the given suffix?  Returns True/False.
 |      
 |      This behaves like the python string method of the same name.
 |      
 |      Return True if the sequence ends with the specified suffix
 |      (a string or another Seq object), False otherwise.
 |      With optional start, test sequence beginning at that position.
 |      With optional end, stop comparing sequence at that position.
 |      suffix can also be a tuple of strings to try.  e.g.
 |      
 |      >>> from Bio.Seq import Seq
 |      >>> my_rna = Seq("GUCAUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAGUUG")
 |      >>> my_rna.endswith("UUG")
 |      True
 |      >>> my_rna.endswith("AUG")
 |      False
 |      >>> my_rna.endswith("AUG", 0, 18)
 |      True
 |      >>> my_rna.endswith(("UCC", "UCA", "UUG"))
 |      True
 |  
 |  find(self, sub, start=0, end=2147483647)
 |      Find method, like that of a python string.
 |      
 |      This behaves like the python string method of the same name.
 |      
 |      Returns an integer, the index of the first occurrence of substring
 |      argument sub in the (sub)sequence given by [start:end].
 |      
 |      Arguments:
 |       - sub - a string or another Seq object to look for
 |       - start - optional integer, slice start
 |       - end - optional integer, slice end
 |      
 |      Returns -1 if the subsequence is NOT found.
 |      
 |      e.g. Locating the first typical start codon, AUG, in an RNA sequence:
 |      
 |      >>> from Bio.Seq import Seq
 |      >>> my_rna = Seq("GUCAUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAGUUG")
 |      >>> my_rna.find("AUG")
 |      3
 |  
 |  lower(self)
 |      Returns a lower case copy of the sequence.
 |      
 |      This will adjust the alphabet if required. Note that the IUPAC alphabets
 |      are upper case only, and thus a generic alphabet must be substituted.
 |      
 |      >>> from Bio.Alphabet import Gapped, generic_dna
 |      >>> from Bio.Alphabet import IUPAC
 |      >>> from Bio.Seq import Seq
 |      >>> my_seq = Seq("CGGTACGCTTATGTCACGTAG*AAAAAA", Gapped(IUPAC.unambiguous_dna, "*"))
 |      >>> my_seq
 |      Seq('CGGTACGCTTATGTCACGTAG*AAAAAA', Gapped(IUPACUnambiguousDNA(), '*'))
 |      >>> my_seq.lower()
 |      Seq('cggtacgcttatgtcacgtag*aaaaaa', Gapped(DNAAlphabet(), '*'))
 |      
 |      See also the upper method.
 |  
 |  lstrip(self, chars=None)
 |      Returns a new Seq object with leading (left) end stripped.
 |      
 |      This behaves like the python string method of the same name.
 |      
 |      Optional argument chars defines which characters to remove.  If
 |      omitted or None (default) then as for the python string method,
 |      this defaults to removing any white space.
 |      
 |      e.g. print(my_seq.lstrip("-"))
 |      
 |      See also the strip and rstrip methods.
 |  
 |  reverse_complement(self)
 |      Returns the reverse complement sequence. New Seq object.
 |      
 |      >>> from Bio.Seq import Seq
 |      >>> from Bio.Alphabet import IUPAC
 |      >>> my_dna = Seq("CCCCCGATAGNR", IUPAC.ambiguous_dna)
 |      >>> my_dna
 |      Seq('CCCCCGATAGNR', IUPACAmbiguousDNA())
 |      >>> my_dna.reverse_complement()
 |      Seq('YNCTATCGGGGG', IUPACAmbiguousDNA())
 |      
 |      Note in the above example, since R = G or A, its complement
 |      is Y (which denotes C or T).
 |      
 |      You can of course used mixed case sequences,
 |      
 |      >>> from Bio.Seq import Seq
 |      >>> from Bio.Alphabet import generic_dna
 |      >>> my_dna = Seq("CCCCCgatA-G", generic_dna)
 |      >>> my_dna
 |      Seq('CCCCCgatA-G', DNAAlphabet())
 |      >>> my_dna.reverse_complement()
 |      Seq('C-TatcGGGGG', DNAAlphabet())
 |      
 |      Trying to complement a protein sequence raises an exception:
 |      
 |      >>> my_protein = Seq("MAIVMGR", IUPAC.protein)
 |      >>> my_protein.reverse_complement()
 |      Traceback (most recent call last):
 |         ...
 |      ValueError: Proteins do not have complements!
 |  
 |  rfind(self, sub, start=0, end=2147483647)
 |      Find from right method, like that of a python string.
 |      
 |      This behaves like the python string method of the same name.
 |      
 |      Returns an integer, the index of the last (right most) occurrence of
 |      substring argument sub in the (sub)sequence given by [start:end].
 |      
 |      Arguments:
 |       - sub - a string or another Seq object to look for
 |       - start - optional integer, slice start
 |       - end - optional integer, slice end
 |      
 |      Returns -1 if the subsequence is NOT found.
 |      
 |      e.g. Locating the last typical start codon, AUG, in an RNA sequence:
 |      
 |      >>> from Bio.Seq import Seq
 |      >>> my_rna = Seq("GUCAUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAGUUG")
 |      >>> my_rna.rfind("AUG")
 |      15
 |  
 |  rsplit(self, sep=None, maxsplit=-1)
 |      Right split method, like that of a python string.
 |      
 |      This behaves like the python string method of the same name.
 |      
 |      Return a list of the 'words' in the string (as Seq objects),
 |      using sep as the delimiter string.  If maxsplit is given, at
 |      most maxsplit splits are done COUNTING FROM THE RIGHT.
 |      If maxsplit is omitted, all splits are made.
 |      
 |      Following the python string method, sep will by default be any
 |      white space (tabs, spaces, newlines) but this is unlikely to
 |      apply to biological sequences.
 |      
 |      e.g. print(my_seq.rsplit("*",1))
 |      
 |      See also the split method.
 |  
 |  rstrip(self, chars=None)
 |      Returns a new Seq object with trailing (right) end stripped.
 |      
 |      This behaves like the python string method of the same name.
 |      
 |      Optional argument chars defines which characters to remove.  If
 |      omitted or None (default) then as for the python string method,
 |      this defaults to removing any white space.
 |      
 |      e.g. Removing a nucleotide sequence's polyadenylation (poly-A tail):
 |      
 |      >>> from Bio.Alphabet import IUPAC
 |      >>> from Bio.Seq import Seq
 |      >>> my_seq = Seq("CGGTACGCTTATGTCACGTAGAAAAAA", IUPAC.unambiguous_dna)
 |      >>> my_seq
 |      Seq('CGGTACGCTTATGTCACGTAGAAAAAA', IUPACUnambiguousDNA())
 |      >>> my_seq.rstrip("A")
 |      Seq('CGGTACGCTTATGTCACGTAG', IUPACUnambiguousDNA())
 |      
 |      See also the strip and lstrip methods.
 |  
 |  split(self, sep=None, maxsplit=-1)
 |      Split method, like that of a python string.
 |      
 |      This behaves like the python string method of the same name.
 |      
 |      Return a list of the 'words' in the string (as Seq objects),
 |      using sep as the delimiter string.  If maxsplit is given, at
 |      most maxsplit splits are done.  If maxsplit is omitted, all
 |      splits are made.
 |      
 |      Following the python string method, sep will by default be any
 |      white space (tabs, spaces, newlines) but this is unlikely to
 |      apply to biological sequences.
 |      
 |      e.g.
 |      
 |      >>> from Bio.Seq import Seq
 |      >>> my_rna = Seq("GUCAUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAGUUG")
 |      >>> my_aa = my_rna.translate()
 |      >>> my_aa
 |      Seq('VMAIVMGR*KGAR*L', HasStopCodon(ExtendedIUPACProtein(), '*'))
 |      >>> my_aa.split("*")
 |      [Seq('VMAIVMGR', HasStopCodon(ExtendedIUPACProtein(), '*')), Seq('KGAR', HasStopCodon(ExtendedIUPACProtein(), '*')), Seq('L', HasStopCodon(ExtendedIUPACProtein(), '*'))]
 |      >>> my_aa.split("*", 1)
 |      [Seq('VMAIVMGR', HasStopCodon(ExtendedIUPACProtein(), '*')), Seq('KGAR*L', HasStopCodon(ExtendedIUPACProtein(), '*'))]
 |      
 |      See also the rsplit method:
 |      
 |      >>> my_aa.rsplit("*", 1)
 |      [Seq('VMAIVMGR*KGAR', HasStopCodon(ExtendedIUPACProtein(), '*')), Seq('L', HasStopCodon(ExtendedIUPACProtein(), '*'))]
 |  
 |  startswith(self, prefix, start=0, end=2147483647)
 |      Does the Seq start with the given prefix?  Returns True/False.
 |      
 |      This behaves like the python string method of the same name.
 |      
 |      Return True if the sequence starts with the specified prefix
 |      (a string or another Seq object), False otherwise.
 |      With optional start, test sequence beginning at that position.
 |      With optional end, stop comparing sequence at that position.
 |      prefix can also be a tuple of strings to try.  e.g.
 |      
 |      >>> from Bio.Seq import Seq
 |      >>> my_rna = Seq("GUCAUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAGUUG")
 |      >>> my_rna.startswith("GUC")
 |      True
 |      >>> my_rna.startswith("AUG")
 |      False
 |      >>> my_rna.startswith("AUG", 3)
 |      True
 |      >>> my_rna.startswith(("UCC", "UCA", "UCG"), 1)
 |      True
 |  
 |  strip(self, chars=None)
 |      Returns a new Seq object with leading and trailing ends stripped.
 |      
 |      This behaves like the python string method of the same name.
 |      
 |      Optional argument chars defines which characters to remove.  If
 |      omitted or None (default) then as for the python string method,
 |      this defaults to removing any white space.
 |      
 |      e.g. print(my_seq.strip("-"))
 |      
 |      See also the lstrip and rstrip methods.
 |  
 |  tomutable(self)
 |      Returns the full sequence as a MutableSeq object.
 |      
 |      >>> from Bio.Seq import Seq
 |      >>> from Bio.Alphabet import IUPAC
 |      >>> my_seq = Seq("MKQHKAMIVALIVICITAVVAAL",
 |      ...              IUPAC.protein)
 |      >>> my_seq
 |      Seq('MKQHKAMIVALIVICITAVVAAL', IUPACProtein())
 |      >>> my_seq.tomutable()
 |      MutableSeq('MKQHKAMIVALIVICITAVVAAL', IUPACProtein())
 |      
 |      Note that the alphabet is preserved.
 |  
 |  tostring(self)
 |      Returns the full sequence as a python string (semi-obsolete).
 |      
 |      Although not formally deprecated, you are now encouraged to use
 |      str(my_seq) instead of my_seq.tostring().
 |  
 |  transcribe(self)
 |      Returns the RNA sequence from a DNA sequence. New Seq object.
 |      
 |      >>> from Bio.Seq import Seq
 |      >>> from Bio.Alphabet import IUPAC
 |      >>> coding_dna = Seq("ATGGCCATTGTAATGGGCCGCTGAAAGGGTGCCCGATAG",
 |      ...                  IUPAC.unambiguous_dna)
 |      >>> coding_dna
 |      Seq('ATGGCCATTGTAATGGGCCGCTGAAAGGGTGCCCGATAG', IUPACUnambiguousDNA())
 |      >>> coding_dna.transcribe()
 |      Seq('AUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAG', IUPACUnambiguousRNA())
 |      
 |      Trying to transcribe a protein or RNA sequence raises an exception:
 |      
 |      >>> my_protein = Seq("MAIVMGR", IUPAC.protein)
 |      >>> my_protein.transcribe()
 |      Traceback (most recent call last):
 |         ...
 |      ValueError: Proteins cannot be transcribed!
 |  
 |  translate(self, table='Standard', stop_symbol='*', to_stop=False, cds=False)
 |      Turns a nucleotide sequence into a protein sequence. New Seq object.
 |      
 |      This method will translate DNA or RNA sequences, and those with a
 |      nucleotide or generic alphabet.  Trying to translate a protein
 |      sequence raises an exception.
 |      
 |      Arguments:
 |       - table - Which codon table to use?  This can be either a name
 |                 (string), an NCBI identifier (integer), or a CodonTable
 |                 object (useful for non-standard genetic codes).  This
 |                 defaults to the "Standard" table.
 |       - stop_symbol - Single character string, what to use for terminators.
 |                       This defaults to the asterisk, "*".
 |       - to_stop - Boolean, defaults to False meaning do a full translation
 |                   continuing on past any stop codons (translated as the
 |                   specified stop_symbol).  If True, translation is
 |                   terminated at the first in frame stop codon (and the
 |                   stop_symbol is not appended to the returned protein
 |                   sequence).
 |       - cds - Boolean, indicates this is a complete CDS.  If True,
 |               this checks the sequence starts with a valid alternative start
 |               codon (which will be translated as methionine, M), that the
 |               sequence length is a multiple of three, and that there is a
 |               single in frame stop codon at the end (this will be excluded
 |               from the protein sequence, regardless of the to_stop option).
 |               If these tests fail, an exception is raised.
 |      
 |      e.g. Using the standard table:
 |      
 |      >>> coding_dna = Seq("GTGGCCATTGTAATGGGCCGCTGAAAGGGTGCCCGATAG")
 |      >>> coding_dna.translate()
 |      Seq('VAIVMGR*KGAR*', HasStopCodon(ExtendedIUPACProtein(), '*'))
 |      >>> coding_dna.translate(stop_symbol="@")
 |      Seq('VAIVMGR@KGAR@', HasStopCodon(ExtendedIUPACProtein(), '@'))
 |      >>> coding_dna.translate(to_stop=True)
 |      Seq('VAIVMGR', ExtendedIUPACProtein())
 |      
 |      Now using NCBI table 2, where TGA is not a stop codon:
 |      
 |      >>> coding_dna.translate(table=2)
 |      Seq('VAIVMGRWKGAR*', HasStopCodon(ExtendedIUPACProtein(), '*'))
 |      >>> coding_dna.translate(table=2, to_stop=True)
 |      Seq('VAIVMGRWKGAR', ExtendedIUPACProtein())
 |      
 |      In fact, GTG is an alternative start codon under NCBI table 2, meaning
 |      this sequence could be a complete CDS:
 |      
 |      >>> coding_dna.translate(table=2, cds=True)
 |      Seq('MAIVMGRWKGAR', ExtendedIUPACProtein())
 |      
 |      It isn't a valid CDS under NCBI table 1, due to both the start codon and
 |      also the in frame stop codons:
 |      
 |      >>> coding_dna.translate(table=1, cds=True)
 |      Traceback (most recent call last):
 |          ...
 |      TranslationError: First codon 'GTG' is not a start codon
 |      
 |      If the sequence has no in-frame stop codon, then the to_stop argument
 |      has no effect:
 |      
 |      >>> coding_dna2 = Seq("TTGGCCATTGTAATGGGCCGC")
 |      >>> coding_dna2.translate()
 |      Seq('LAIVMGR', ExtendedIUPACProtein())
 |      >>> coding_dna2.translate(to_stop=True)
 |      Seq('LAIVMGR', ExtendedIUPACProtein())
 |      
 |      NOTE - Ambiguous codons like "TAN" or "NNN" could be an amino acid
 |      or a stop codon.  These are translated as "X".  Any invalid codon
 |      (e.g. "TA?" or "T-A") will throw a TranslationError.
 |      
 |      NOTE - Does NOT support gapped sequences.
 |      
 |      NOTE - This does NOT behave like the python string's translate
 |      method.  For that use str(my_seq).translate(...) instead.
 |  
 |  ungap(self, gap=None)
 |      Return a copy of the sequence without the gap character(s).
 |      
 |      The gap character can be specified in two ways - either as an explicit
 |      argument, or via the sequence's alphabet. For example:
 |      
 |      >>> from Bio.Seq import Seq
 |      >>> from Bio.Alphabet import generic_dna
 |      >>> my_dna = Seq("-ATA--TGAAAT-TTGAAAA", generic_dna)
 |      >>> my_dna
 |      Seq('-ATA--TGAAAT-TTGAAAA', DNAAlphabet())
 |      >>> my_dna.ungap("-")
 |      Seq('ATATGAAATTTGAAAA', DNAAlphabet())
 |      
 |      If the gap character is not given as an argument, it will be taken from
 |      the sequence's alphabet (if defined). Notice that the returned sequence's
 |      alphabet is adjusted since it no longer requires a gapped alphabet:
 |      
 |      >>> from Bio.Seq import Seq
 |      >>> from Bio.Alphabet import IUPAC, Gapped, HasStopCodon
 |      >>> my_pro = Seq("MVVLE=AD*", HasStopCodon(Gapped(IUPAC.protein, "=")))
 |      >>> my_pro
 |      Seq('MVVLE=AD*', HasStopCodon(Gapped(IUPACProtein(), '='), '*'))
 |      >>> my_pro.ungap()
 |      Seq('MVVLEAD*', HasStopCodon(IUPACProtein(), '*'))
 |      
 |      Or, with a simpler gapped DNA example:
 |      
 |      >>> from Bio.Seq import Seq
 |      >>> from Bio.Alphabet import IUPAC, Gapped
 |      >>> my_seq = Seq("CGGGTAG=AAAAAA", Gapped(IUPAC.unambiguous_dna, "="))
 |      >>> my_seq
 |      Seq('CGGGTAG=AAAAAA', Gapped(IUPACUnambiguousDNA(), '='))
 |      >>> my_seq.ungap()
 |      Seq('CGGGTAGAAAAAA', IUPACUnambiguousDNA())
 |      
 |      As long as it is consistent with the alphabet, although it is redundant,
 |      you can still supply the gap character as an argument to this method:
 |      
 |      >>> my_seq
 |      Seq('CGGGTAG=AAAAAA', Gapped(IUPACUnambiguousDNA(), '='))
 |      >>> my_seq.ungap("=")
 |      Seq('CGGGTAGAAAAAA', IUPACUnambiguousDNA())
 |      
 |      However, if the gap character given as the argument disagrees with that
 |      declared in the alphabet, an exception is raised:
 |      
 |      >>> my_seq
 |      Seq('CGGGTAG=AAAAAA', Gapped(IUPACUnambiguousDNA(), '='))
 |      >>> my_seq.ungap("-")
 |      Traceback (most recent call last):
 |         ...
 |      ValueError: Gap '-' does not match '=' from alphabet
 |      
 |      Finally, if a gap character is not supplied, and the alphabet does not
 |      define one, an exception is raised:
 |      
 |      >>> from Bio.Seq import Seq
 |      >>> from Bio.Alphabet import generic_dna
 |      >>> my_dna = Seq("ATA--TGAAAT-TTGAAAA", generic_dna)
 |      >>> my_dna
 |      Seq('ATA--TGAAAT-TTGAAAA', DNAAlphabet())
 |      >>> my_dna.ungap()
 |      Traceback (most recent call last):
 |         ...
 |      ValueError: Gap character not given and not defined in alphabet
 |  
 |  upper(self)
 |      Returns an upper case copy of the sequence.
 |      
 |      >>> from Bio.Alphabet import HasStopCodon, generic_protein
 |      >>> from Bio.Seq import Seq
 |      >>> my_seq = Seq("VHLTPeeK*", HasStopCodon(generic_protein))
 |      >>> my_seq
 |      Seq('VHLTPeeK*', HasStopCodon(ProteinAlphabet(), '*'))
 |      >>> my_seq.lower()
 |      Seq('vhltpeek*', HasStopCodon(ProteinAlphabet(), '*'))
 |      >>> my_seq.upper()
 |      Seq('VHLTPEEK*', HasStopCodon(ProteinAlphabet(), '*'))
 |      
 |      This will adjust the alphabet if required. See also the lower method.
 |  
 |  ----------------------------------------------------------------------
 |  Data descriptors defined here:
 |  
 |  __dict__
 |      dictionary for instance variables (if defined)
 |  
 |  __weakref__
 |      list of weak references to the object (if defined)

In [44]:

    

from Bio.Seq import Seq
from Bio.Alphabet import IUPAC
my_dna = Seq("CCCCCGATAG", IUPAC.unambiguous_dna)
my_dna
my_dna.complement()


    

    
Out[44]:





Seq('GGGGGCTATC', IUPACUnambiguousDNA())

In [45]:

    

from Bio.Seq import Seq
from Bio.Alphabet import IUPAC
my_dna = Seq("CCCCCGATAGNR", IUPAC.ambiguous_dna)
my_dna
my_dna.reverse_complement()


    

    
Out[45]:





Seq('YNCTATCGGGGG', IUPACAmbiguousDNA())

In [46]:

    

if isinstance(my_seq, Seq):
    print('reverse complement is %s' % my_seq.reverse_complement())


    

    




---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
<ipython-input-46-f2f9035a49f3> in <module>()
      1 if isinstance(my_seq, Seq):
----> 2     print('reverse complement is %s' % my_seq.reverse_complement())

/usr/lib/python2.7/dist-packages/Bio/Seq.pyc in reverse_complement(self)
    771         """
    772         #Use -1 stride/step to reverse the complement
--> 773         return self.complement()[::-1]
    774 
    775     def transcribe(self):

/usr/lib/python2.7/dist-packages/Bio/Seq.pyc in complement(self)
    721         base = Alphabet._get_base_alphabet(self.alphabet)
    722         if isinstance(base, Alphabet.ProteinAlphabet):
--> 723             raise ValueError("Proteins do not have complements!")
    724         if isinstance(base, Alphabet.DNAAlphabet):
    725             ttable = _dna_complement_table

ValueError: Proteins do not have complements!

In [52]:

    

from Bio.Blast import NCBIWWW
my_seq = Seq("TGGGCCTCATATTTATCCTATATACCATGTTCGTATGGTGGCGCGATGTTCTACGTGAATCCACGTTCGAAGGACATCATACCAAAGTCGTACAATTAGGACCTCGATATGGTTTTATTCTGTTTATCGTATCGGAGGTTATGTTCTTTTTTGCTCTTTTTCGGGCTTCTTCTCATTCTTCTTTGGCACCTACGGTAGAG")
print my_seq.translate()


    

    




WASYLSYIPCSYGGAMFYVNPRSKDIIPKSYN*DLDMVLFCLSYRRLCSFLLFFGLLLILLWHLR*






    




/usr/lib/python2.7/dist-packages/Bio/Seq.py:1976: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future.
  BiopythonWarning)