In [1]:

    

%run ../../shared_setup.ipynb


    

    




docker image cggh/biipy:v1.6.0






    

In [2]:

    

fasta


    

    
Out[2]:





<pyfasta.fasta.Fasta at 0x7f8ba809beb8>

In [3]:

    

sorted(fasta.keys())


    

    
Out[3]:





['Pf3D7_01_v3',
 'Pf3D7_02_v3',
 'Pf3D7_03_v3',
 'Pf3D7_04_v3',
 'Pf3D7_05_v3',
 'Pf3D7_06_v3',
 'Pf3D7_07_v3',
 'Pf3D7_08_v3',
 'Pf3D7_09_v3',
 'Pf3D7_10_v3',
 'Pf3D7_11_v3',
 'Pf3D7_12_v3',
 'Pf3D7_13_v3',
 'Pf3D7_14_v3']

In [4]:

    

fasta['Pf3D7_01_v3']


    

    
Out[4]:





NpyFastaRecord(0..640851)

In [5]:

    

class TandemRepeatTable(etl.Table):
    
    def __init__(self, chrom, unit_length):
        self.chrom = chrom
        self.unit_length = unit_length
        
    def __iter__(self):
        chrom = self.chrom
        unit_length = self.unit_length

        # header row
        yield ('chrom', 'start', 'stop', 'repeat_unit', 'n_units', 'unit_length', 'last_unit_length', 'tract_length')
        
        log('generating tandem repeats for chromosome', chrom, 'unit length', unit_length)

        # obtain sequence
        seq = fasta[chrom]
        
        # begin iteration
        i = 0
        while i < len(seq):
            
            # current repeat unit
            ru = seq[i:i+unit_length]
            
            # decide if repeat unit is not primitive
            primitive = True
            for n in range(1, unit_length):
                if unit_length % n == 0:
                    subs = set([ru[k:k+n] for k in range(0, unit_length, n)])
                    if len(subs) == 1:
                        primitive = False
                        break

            if not primitive:
                i += 1
                continue
                
            # number of repeat units found
            nu = 1
            
            # next potential unit to compare
            next_unit = seq[i+(nu*unit_length):i+((nu+1)*unit_length)]
            
            # discover whole units
            while next_unit == ru:
                nu += 1
                next_unit = seq[i+(nu*unit_length):i+((nu+1)*unit_length)]

            # discovered a repeat
            if nu > 1:

                # compute length of last (partial) unit
                for j, (a, b) in enumerate(zip(ru, next_unit)):
                    if a != b:
                        last_unit_length = j
                        break
                
                # compute tract length
                tract_length = (nu * unit_length) + last_unit_length
            
                yield (chrom, i+1, i+1+tract_length, ru, nu, unit_length, last_unit_length, tract_length)
                i += ((nu - 1) * unit_length) + 1
            
            else:
                i += 1


    

In [6]:

    

tbl1 = TandemRepeatTable('Pf3D7_01_v3', 1)
tbl1.display(10)


    

    




2016-03-13 23:29:04.590688 :: generating tandem repeats for chromosome Pf3D7_01_v3 unit length 1






    








0|chrom
1|start
2|stop
3|repeat_unit
4|n_units
5|unit_length
6|last_unit_length
7|tract_length




Pf3D7_01_v3
3
5
a
2
1
0
2


Pf3D7_01_v3
5
8
c
3
1
0
3


Pf3D7_01_v3
9
13
a
4
1
0
4


Pf3D7_01_v3
13
15
c
2
1
0
2


Pf3D7_01_v3
16
19
a
3
1
0
3


Pf3D7_01_v3
19
22
c
3
1
0
3


Pf3D7_01_v3
23
26
a
3
1
0
3


Pf3D7_01_v3
26
29
c
3
1
0
3


Pf3D7_01_v3
30
33
a
3
1
0
3


Pf3D7_01_v3
33
36
c
3
1
0
3



...

In [7]:

    

tbl2 = TandemRepeatTable('Pf3D7_01_v3', 2)
tbl2.display(10)


    

    




2016-03-13 23:29:05.547180 :: generating tandem repeats for chromosome Pf3D7_01_v3 unit length 2






    








0|chrom
1|start
2|stop
3|repeat_unit
4|n_units
5|unit_length
6|last_unit_length
7|tract_length




Pf3D7_01_v3
401
405
ct
2
2
0
4


Pf3D7_01_v3
429
433
ct
2
2
0
4


Pf3D7_01_v3
443
447
ct
2
2
0
4


Pf3D7_01_v3
485
489
ct
2
2
0
4


Pf3D7_01_v3
499
503
ct
2
2
0
4


Pf3D7_01_v3
527
531
ct
2
2
0
4


Pf3D7_01_v3
569
573
ct
2
2
0
4


Pf3D7_01_v3
583
587
ct
2
2
0
4


Pf3D7_01_v3
597
601
ct
2
2
0
4


Pf3D7_01_v3
611
615
ct
2
2
0
4



...

In [8]:

    

tbl2.gt('start', 94980).display(10)


    

    




2016-03-13 23:29:06.536204 :: generating tandem repeats for chromosome Pf3D7_01_v3 unit length 2






    








0|chrom
1|start
2|stop
3|repeat_unit
4|n_units
5|unit_length
6|last_unit_length
7|tract_length




Pf3D7_01_v3
94981
94988
at
3
2
1
7


Pf3D7_01_v3
94991
94995
ca
2
2
0
4


Pf3D7_01_v3
94994
95022
at
14
2
0
28


Pf3D7_01_v3
95027
95032
ta
2
2
1
5


Pf3D7_01_v3
95034
95038
ct
2
2
0
4


Pf3D7_01_v3
95071
95075
ta
2
2
0
4


Pf3D7_01_v3
95075
95080
at
2
2
1
5


Pf3D7_01_v3
95089
95093
ca
2
2
0
4


Pf3D7_01_v3
95096
95103
ac
3
2
1
7


Pf3D7_01_v3
95157
95161
ca
2
2
0
4



...

In [9]:

    

tbl3 = TandemRepeatTable('Pf3D7_01_v3', 3)
tbl3.display(10)


    

    




2016-03-13 23:29:07.745614 :: generating tandem repeats for chromosome Pf3D7_01_v3 unit length 3






    








0|chrom
1|start
2|stop
3|repeat_unit
4|n_units
5|unit_length
6|last_unit_length
7|tract_length




Pf3D7_01_v3
367
378
ttc
3
3
2
11


Pf3D7_01_v3
379
386
tct
2
3
1
7


Pf3D7_01_v3
449
456
tct
2
3
1
7


Pf3D7_01_v3
505
512
tct
2
3
1
7


Pf3D7_01_v3
547
554
tct
2
3
1
7


Pf3D7_01_v3
617
624
tct
2
3
1
7


Pf3D7_01_v3
673
680
tct
2
3
1
7


Pf3D7_01_v3
759
770
ttc
3
3
2
11


Pf3D7_01_v3
771
778
tct
2
3
1
7


Pf3D7_01_v3
785
792
tct
2
3
1
7



...

In [10]:

    

tbl4 = TandemRepeatTable('Pf3D7_01_v3', 4)
tbl4.display(10)


    

    




2016-03-13 23:29:07.936114 :: generating tandem repeats for chromosome Pf3D7_01_v3 unit length 4






    








0|chrom
1|start
2|stop
3|repeat_unit
4|n_units
5|unit_length
6|last_unit_length
7|tract_length




Pf3D7_01_v3
403
415
ctta
3
4
0
12


Pf3D7_01_v3
417
431
ctta
3
4
2
14


Pf3D7_01_v3
431
445
ctta
3
4
2
14


Pf3D7_01_v3
473
487
ctta
3
4
2
14


Pf3D7_01_v3
487
501
ctta
3
4
2
14


Pf3D7_01_v3
529
543
ctta
3
4
2
14


Pf3D7_01_v3
571
585
ctta
3
4
2
14


Pf3D7_01_v3
585
599
ctta
3
4
2
14


Pf3D7_01_v3
599
613
ctta
3
4
2
14


Pf3D7_01_v3
641
655
ctta
3
4
2
14



...

In [11]:

    

tbl_regions_1b


    

    
Out[11]:







0|region_chrom
1|region_start
2|region_stop
3|region_type
4|region_size




Pf3D7_01_v3
1
27336
SubtelomericRepeat
27336


Pf3D7_01_v3
27337
92900
SubtelomericHypervariable
65564


Pf3D7_01_v3
92901
457931
Core
365031


Pf3D7_01_v3
457932
460311
Centromere
2380


Pf3D7_01_v3
460312
575900
Core
115589



...

In [12]:

    

#!rm -v /data/plasmodium/pfalciparum/pf-crosses/data/genome/sanger/version3/September_2012/*.tr.pickle


    

    




rm: cannot remove '/data/plasmodium/pfalciparum/pf-crosses/data/genome/sanger/version3/September_2012/*.tr.pickle': No such file or directory

In [13]:

    

def tabulate_tr(chrom):
    fn = '/data/plasmodium/pfalciparum/pf-crosses/data/genome/sanger/version3/September_2012/%s.tr.pickle' % chrom
    if not os.path.exists(fn):
        tbl_tr = (
            etl
            .cat(*[TandemRepeatTable(chrom, ul) for ul in range(1, 25, 1)])
            .intervalleftjoin(tbl_regions_1b, lkey='chrom', lstart='start', lstop='stop', include_stop=True,
                              rkey='region_chrom', rstart='region_start', rstop='region_stop')
            .cutout('region_chrom', 'region_start', 'region_stop', 'region_size')
        )
        tbl_tr.topickle(fn)
    tbl_tr = etl.frompickle(fn)
    return tbl_tr


    

In [14]:

    

tbl = tabulate_tr('Pf3D7_01_v3')
tbl


    

    




2016-03-13 23:29:20.904568 :: generating tandem repeats for chromosome Pf3D7_01_v3 unit length 1
2016-03-13 23:29:30.378943 :: generating tandem repeats for chromosome Pf3D7_01_v3 unit length 2
2016-03-13 23:29:38.481936 :: generating tandem repeats for chromosome Pf3D7_01_v3 unit length 3
2016-03-13 23:29:47.537447 :: generating tandem repeats for chromosome Pf3D7_01_v3 unit length 4
2016-03-13 23:29:58.293079 :: generating tandem repeats for chromosome Pf3D7_01_v3 unit length 5
2016-03-13 23:30:08.769620 :: generating tandem repeats for chromosome Pf3D7_01_v3 unit length 6
2016-03-13 23:30:20.928325 :: generating tandem repeats for chromosome Pf3D7_01_v3 unit length 7
2016-03-13 23:30:31.144460 :: generating tandem repeats for chromosome Pf3D7_01_v3 unit length 8
2016-03-13 23:30:43.662936 :: generating tandem repeats for chromosome Pf3D7_01_v3 unit length 9
2016-03-13 23:30:55.600663 :: generating tandem repeats for chromosome Pf3D7_01_v3 unit length 10
2016-03-13 23:31:08.803971 :: generating tandem repeats for chromosome Pf3D7_01_v3 unit length 11
2016-03-13 23:31:19.659678 :: generating tandem repeats for chromosome Pf3D7_01_v3 unit length 12
2016-03-13 23:31:35.577723 :: generating tandem repeats for chromosome Pf3D7_01_v3 unit length 13
2016-03-13 23:31:46.747555 :: generating tandem repeats for chromosome Pf3D7_01_v3 unit length 14
2016-03-13 23:32:00.961624 :: generating tandem repeats for chromosome Pf3D7_01_v3 unit length 15
2016-03-13 23:32:15.121040 :: generating tandem repeats for chromosome Pf3D7_01_v3 unit length 16
2016-03-13 23:32:30.850135 :: generating tandem repeats for chromosome Pf3D7_01_v3 unit length 17
2016-03-13 23:32:42.512199 :: generating tandem repeats for chromosome Pf3D7_01_v3 unit length 18
2016-03-13 23:33:00.296897 :: generating tandem repeats for chromosome Pf3D7_01_v3 unit length 19
2016-03-13 23:33:12.233903 :: generating tandem repeats for chromosome Pf3D7_01_v3 unit length 20
2016-03-13 23:33:30.117061 :: generating tandem repeats for chromosome Pf3D7_01_v3 unit length 21
2016-03-13 23:33:45.459415 :: generating tandem repeats for chromosome Pf3D7_01_v3 unit length 22
2016-03-13 23:34:01.537839 :: generating tandem repeats for chromosome Pf3D7_01_v3 unit length 23
2016-03-13 23:34:13.856803 :: generating tandem repeats for chromosome Pf3D7_01_v3 unit length 24






    
Out[14]:







0|chrom
1|start
2|stop
3|repeat_unit
4|n_units
5|unit_length
6|last_unit_length
7|tract_length
8|region_type




Pf3D7_01_v3
3
5
a
2
1
0
2
SubtelomericRepeat


Pf3D7_01_v3
5
8
c
3
1
0
3
SubtelomericRepeat


Pf3D7_01_v3
9
13
a
4
1
0
4
SubtelomericRepeat


Pf3D7_01_v3
13
15
c
2
1
0
2
SubtelomericRepeat


Pf3D7_01_v3
16
19
a
3
1
0
3
SubtelomericRepeat



...

In [15]:

    

tbl.sort(key=('chrom', 'start')).display(10)


    

    








0|chrom
1|start
2|stop
3|repeat_unit
4|n_units
5|unit_length
6|last_unit_length
7|tract_length
8|region_type




Pf3D7_01_v3
3
5
a
2
1
0
2
SubtelomericRepeat


Pf3D7_01_v3
5
8
c
3
1
0
3
SubtelomericRepeat


Pf3D7_01_v3
9
13
a
4
1
0
4
SubtelomericRepeat


Pf3D7_01_v3
13
15
c
2
1
0
2
SubtelomericRepeat


Pf3D7_01_v3
13
37
cctaaac
3
7
3
24
SubtelomericRepeat


Pf3D7_01_v3
16
19
a
3
1
0
3
SubtelomericRepeat


Pf3D7_01_v3
19
22
c
3
1
0
3
SubtelomericRepeat


Pf3D7_01_v3
23
26
a
3
1
0
3
SubtelomericRepeat


Pf3D7_01_v3
24
65
aaccctaaaccctg
2
14
13
41
SubtelomericRepeat


Pf3D7_01_v3
26
29
c
3
1
0
3
SubtelomericRepeat



...

In [16]:

    

CHROMOSOMES


    

    
Out[16]:





[b'Pf3D7_01_v3',
 b'Pf3D7_02_v3',
 b'Pf3D7_03_v3',
 b'Pf3D7_04_v3',
 b'Pf3D7_05_v3',
 b'Pf3D7_06_v3',
 b'Pf3D7_07_v3',
 b'Pf3D7_08_v3',
 b'Pf3D7_09_v3',
 b'Pf3D7_10_v3',
 b'Pf3D7_11_v3',
 b'Pf3D7_12_v3',
 b'Pf3D7_13_v3',
 b'Pf3D7_14_v3']

In [17]:

    

tbl_tr_wg = etl.cat(*[tabulate_tr(str(chrom, 'ascii')) for chrom in CHROMOSOMES])


    

    




2016-03-13 23:34:38.935962 :: generating tandem repeats for chromosome Pf3D7_02_v3 unit length 1
2016-03-13 23:34:52.743808 :: generating tandem repeats for chromosome Pf3D7_02_v3 unit length 2
2016-03-13 23:35:04.465945 :: generating tandem repeats for chromosome Pf3D7_02_v3 unit length 3
2016-03-13 23:35:17.622739 :: generating tandem repeats for chromosome Pf3D7_02_v3 unit length 4
2016-03-13 23:35:32.424784 :: generating tandem repeats for chromosome Pf3D7_02_v3 unit length 5
2016-03-13 23:35:46.880182 :: generating tandem repeats for chromosome Pf3D7_02_v3 unit length 6
2016-03-13 23:36:04.431485 :: generating tandem repeats for chromosome Pf3D7_02_v3 unit length 7
2016-03-13 23:36:19.590832 :: generating tandem repeats for chromosome Pf3D7_02_v3 unit length 8
2016-03-13 23:36:38.275168 :: generating tandem repeats for chromosome Pf3D7_02_v3 unit length 9
2016-03-13 23:36:55.889858 :: generating tandem repeats for chromosome Pf3D7_02_v3 unit length 10
2016-03-13 23:37:15.354497 :: generating tandem repeats for chromosome Pf3D7_02_v3 unit length 11
2016-03-13 23:37:31.467190 :: generating tandem repeats for chromosome Pf3D7_02_v3 unit length 12
2016-03-13 23:37:55.292714 :: generating tandem repeats for chromosome Pf3D7_02_v3 unit length 13
2016-03-13 23:38:11.946639 :: generating tandem repeats for chromosome Pf3D7_02_v3 unit length 14
2016-03-13 23:38:32.840844 :: generating tandem repeats for chromosome Pf3D7_02_v3 unit length 15
2016-03-13 23:38:53.707835 :: generating tandem repeats for chromosome Pf3D7_02_v3 unit length 16
2016-03-13 23:39:18.781354 :: generating tandem repeats for chromosome Pf3D7_02_v3 unit length 17
2016-03-13 23:39:35.902435 :: generating tandem repeats for chromosome Pf3D7_02_v3 unit length 18
2016-03-13 23:40:01.909358 :: generating tandem repeats for chromosome Pf3D7_02_v3 unit length 19
2016-03-13 23:40:19.653735 :: generating tandem repeats for chromosome Pf3D7_02_v3 unit length 20
2016-03-13 23:40:45.931200 :: generating tandem repeats for chromosome Pf3D7_02_v3 unit length 21
2016-03-13 23:41:09.174829 :: generating tandem repeats for chromosome Pf3D7_02_v3 unit length 22
2016-03-13 23:41:32.580220 :: generating tandem repeats for chromosome Pf3D7_02_v3 unit length 23
2016-03-13 23:41:51.155350 :: generating tandem repeats for chromosome Pf3D7_02_v3 unit length 24
2016-03-13 23:42:24.003126 :: generating tandem repeats for chromosome Pf3D7_03_v3 unit length 1
2016-03-13 23:42:39.759928 :: generating tandem repeats for chromosome Pf3D7_03_v3 unit length 2
2016-03-13 23:42:53.017714 :: generating tandem repeats for chromosome Pf3D7_03_v3 unit length 3
2016-03-13 23:43:07.866114 :: generating tandem repeats for chromosome Pf3D7_03_v3 unit length 4
2016-03-13 23:43:24.598561 :: generating tandem repeats for chromosome Pf3D7_03_v3 unit length 5
2016-03-13 23:43:40.917462 :: generating tandem repeats for chromosome Pf3D7_03_v3 unit length 6
2016-03-13 23:44:00.731620 :: generating tandem repeats for chromosome Pf3D7_03_v3 unit length 7
2016-03-13 23:44:18.128028 :: generating tandem repeats for chromosome Pf3D7_03_v3 unit length 8
2016-03-13 23:44:38.947639 :: generating tandem repeats for chromosome Pf3D7_03_v3 unit length 9
2016-03-13 23:44:59.074622 :: generating tandem repeats for chromosome Pf3D7_03_v3 unit length 10
2016-03-13 23:45:27.336417 :: generating tandem repeats for chromosome Pf3D7_03_v3 unit length 11
2016-03-13 23:45:46.670722 :: generating tandem repeats for chromosome Pf3D7_03_v3 unit length 12
2016-03-13 23:46:19.047962 :: generating tandem repeats for chromosome Pf3D7_03_v3 unit length 13
2016-03-13 23:46:41.961871 :: generating tandem repeats for chromosome Pf3D7_03_v3 unit length 14
2016-03-13 23:47:20.520245 :: generating tandem repeats for chromosome Pf3D7_03_v3 unit length 15
2016-03-13 23:47:54.153098 :: generating tandem repeats for chromosome Pf3D7_03_v3 unit length 16
2016-03-13 23:48:28.015317 :: generating tandem repeats for chromosome Pf3D7_03_v3 unit length 17
2016-03-13 23:48:56.071145 :: generating tandem repeats for chromosome Pf3D7_03_v3 unit length 18
2016-03-13 23:49:36.591582 :: generating tandem repeats for chromosome Pf3D7_03_v3 unit length 19
2016-03-13 23:50:02.358071 :: generating tandem repeats for chromosome Pf3D7_03_v3 unit length 20
2016-03-13 23:50:42.693921 :: generating tandem repeats for chromosome Pf3D7_03_v3 unit length 21
2016-03-13 23:51:19.404952 :: generating tandem repeats for chromosome Pf3D7_03_v3 unit length 22
2016-03-13 23:51:48.384160 :: generating tandem repeats for chromosome Pf3D7_03_v3 unit length 23
2016-03-13 23:52:08.953542 :: generating tandem repeats for chromosome Pf3D7_03_v3 unit length 24
2016-03-13 23:52:45.812590 :: generating tandem repeats for chromosome Pf3D7_04_v3 unit length 1
2016-03-13 23:53:05.847015 :: generating tandem repeats for chromosome Pf3D7_04_v3 unit length 2
2016-03-13 23:53:21.021500 :: generating tandem repeats for chromosome Pf3D7_04_v3 unit length 3
2016-03-13 23:53:37.667434 :: generating tandem repeats for chromosome Pf3D7_04_v3 unit length 4
2016-03-13 23:53:56.578189 :: generating tandem repeats for chromosome Pf3D7_04_v3 unit length 5
2016-03-13 23:54:14.799464 :: generating tandem repeats for chromosome Pf3D7_04_v3 unit length 6
2016-03-13 23:54:36.767241 :: generating tandem repeats for chromosome Pf3D7_04_v3 unit length 7
2016-03-13 23:54:55.987907 :: generating tandem repeats for chromosome Pf3D7_04_v3 unit length 8
2016-03-13 23:55:19.203805 :: generating tandem repeats for chromosome Pf3D7_04_v3 unit length 9
2016-03-13 23:55:41.454305 :: generating tandem repeats for chromosome Pf3D7_04_v3 unit length 10
2016-03-13 23:56:05.897605 :: generating tandem repeats for chromosome Pf3D7_04_v3 unit length 11
2016-03-13 23:56:26.175348 :: generating tandem repeats for chromosome Pf3D7_04_v3 unit length 12
2016-03-13 23:56:55.591688 :: generating tandem repeats for chromosome Pf3D7_04_v3 unit length 13
2016-03-13 23:57:16.300375 :: generating tandem repeats for chromosome Pf3D7_04_v3 unit length 14
2016-03-13 23:57:42.504677 :: generating tandem repeats for chromosome Pf3D7_04_v3 unit length 15
2016-03-13 23:58:08.834892 :: generating tandem repeats for chromosome Pf3D7_04_v3 unit length 16
2016-03-13 23:58:37.872299 :: generating tandem repeats for chromosome Pf3D7_04_v3 unit length 17
2016-03-13 23:58:59.632644 :: generating tandem repeats for chromosome Pf3D7_04_v3 unit length 18
2016-03-13 23:59:32.286771 :: generating tandem repeats for chromosome Pf3D7_04_v3 unit length 19
2016-03-13 23:59:54.500463 :: generating tandem repeats for chromosome Pf3D7_04_v3 unit length 20
2016-03-14 00:00:27.477008 :: generating tandem repeats for chromosome Pf3D7_04_v3 unit length 21
2016-03-14 00:00:55.967618 :: generating tandem repeats for chromosome Pf3D7_04_v3 unit length 22
2016-03-14 00:01:26.752152 :: generating tandem repeats for chromosome Pf3D7_04_v3 unit length 23
2016-03-14 00:01:51.308487 :: generating tandem repeats for chromosome Pf3D7_04_v3 unit length 24
2016-03-14 00:02:32.611727 :: generating tandem repeats for chromosome Pf3D7_05_v3 unit length 1
2016-03-14 00:02:53.104511 :: generating tandem repeats for chromosome Pf3D7_05_v3 unit length 2
2016-03-14 00:03:10.373722 :: generating tandem repeats for chromosome Pf3D7_05_v3 unit length 3
2016-03-14 00:03:29.775859 :: generating tandem repeats for chromosome Pf3D7_05_v3 unit length 4
2016-03-14 00:03:51.376477 :: generating tandem repeats for chromosome Pf3D7_05_v3 unit length 5
2016-03-14 00:04:13.072807 :: generating tandem repeats for chromosome Pf3D7_05_v3 unit length 6
2016-03-14 00:04:38.964356 :: generating tandem repeats for chromosome Pf3D7_05_v3 unit length 7
2016-03-14 00:05:00.488707 :: generating tandem repeats for chromosome Pf3D7_05_v3 unit length 8
2016-03-14 00:05:26.956336 :: generating tandem repeats for chromosome Pf3D7_05_v3 unit length 9
2016-03-14 00:05:53.060361 :: generating tandem repeats for chromosome Pf3D7_05_v3 unit length 10
2016-03-14 00:06:21.528421 :: generating tandem repeats for chromosome Pf3D7_05_v3 unit length 11
2016-03-14 00:06:44.543539 :: generating tandem repeats for chromosome Pf3D7_05_v3 unit length 12
2016-03-14 00:07:18.931612 :: generating tandem repeats for chromosome Pf3D7_05_v3 unit length 13
2016-03-14 00:07:42.909658 :: generating tandem repeats for chromosome Pf3D7_05_v3 unit length 14
2016-03-14 00:08:13.318321 :: generating tandem repeats for chromosome Pf3D7_05_v3 unit length 15
2016-03-14 00:08:43.050903 :: generating tandem repeats for chromosome Pf3D7_05_v3 unit length 16
2016-03-14 00:09:16.081692 :: generating tandem repeats for chromosome Pf3D7_05_v3 unit length 17
2016-03-14 00:09:40.586692 :: generating tandem repeats for chromosome Pf3D7_05_v3 unit length 18
2016-03-14 00:10:17.462571 :: generating tandem repeats for chromosome Pf3D7_05_v3 unit length 19
2016-03-14 00:10:42.605128 :: generating tandem repeats for chromosome Pf3D7_05_v3 unit length 20
2016-03-14 00:11:21.232219 :: generating tandem repeats for chromosome Pf3D7_05_v3 unit length 21
2016-03-14 00:11:54.403406 :: generating tandem repeats for chromosome Pf3D7_05_v3 unit length 22
2016-03-14 00:12:28.752843 :: generating tandem repeats for chromosome Pf3D7_05_v3 unit length 23
2016-03-14 00:12:54.403055 :: generating tandem repeats for chromosome Pf3D7_05_v3 unit length 24
2016-03-14 00:13:39.597699 :: generating tandem repeats for chromosome Pf3D7_06_v3 unit length 1
2016-03-14 00:14:00.488516 :: generating tandem repeats for chromosome Pf3D7_06_v3 unit length 2
2016-03-14 00:14:18.063377 :: generating tandem repeats for chromosome Pf3D7_06_v3 unit length 3
2016-03-14 00:14:37.833216 :: generating tandem repeats for chromosome Pf3D7_06_v3 unit length 4
2016-03-14 00:15:00.064692 :: generating tandem repeats for chromosome Pf3D7_06_v3 unit length 5
2016-03-14 00:15:21.744097 :: generating tandem repeats for chromosome Pf3D7_06_v3 unit length 6
2016-03-14 00:15:47.965307 :: generating tandem repeats for chromosome Pf3D7_06_v3 unit length 7
2016-03-14 00:16:11.092876 :: generating tandem repeats for chromosome Pf3D7_06_v3 unit length 8
2016-03-14 00:16:40.099718 :: generating tandem repeats for chromosome Pf3D7_06_v3 unit length 9
2016-03-14 00:17:06.620091 :: generating tandem repeats for chromosome Pf3D7_06_v3 unit length 10
2016-03-14 00:17:35.869424 :: generating tandem repeats for chromosome Pf3D7_06_v3 unit length 11
2016-03-14 00:18:00.109912 :: generating tandem repeats for chromosome Pf3D7_06_v3 unit length 12
2016-03-14 00:18:35.212834 :: generating tandem repeats for chromosome Pf3D7_06_v3 unit length 13
2016-03-14 00:18:59.729096 :: generating tandem repeats for chromosome Pf3D7_06_v3 unit length 14
2016-03-14 00:19:30.716549 :: generating tandem repeats for chromosome Pf3D7_06_v3 unit length 15
2016-03-14 00:20:01.799106 :: generating tandem repeats for chromosome Pf3D7_06_v3 unit length 16
2016-03-14 00:20:36.950094 :: generating tandem repeats for chromosome Pf3D7_06_v3 unit length 17
2016-03-14 00:21:03.795267 :: generating tandem repeats for chromosome Pf3D7_06_v3 unit length 18
2016-03-14 00:21:45.022285 :: generating tandem repeats for chromosome Pf3D7_06_v3 unit length 19
2016-03-14 00:22:11.840261 :: generating tandem repeats for chromosome Pf3D7_06_v3 unit length 20
2016-03-14 00:22:52.292867 :: generating tandem repeats for chromosome Pf3D7_06_v3 unit length 21
2016-03-14 00:23:26.797123 :: generating tandem repeats for chromosome Pf3D7_06_v3 unit length 22
2016-03-14 00:24:02.191978 :: generating tandem repeats for chromosome Pf3D7_06_v3 unit length 23
2016-03-14 00:24:29.644683 :: generating tandem repeats for chromosome Pf3D7_06_v3 unit length 24
2016-03-14 00:25:17.558507 :: generating tandem repeats for chromosome Pf3D7_07_v3 unit length 1
2016-03-14 00:25:38.741171 :: generating tandem repeats for chromosome Pf3D7_07_v3 unit length 2
2016-03-14 00:25:56.907092 :: generating tandem repeats for chromosome Pf3D7_07_v3 unit length 3
2016-03-14 00:26:17.600045 :: generating tandem repeats for chromosome Pf3D7_07_v3 unit length 4
2016-03-14 00:26:41.741368 :: generating tandem repeats for chromosome Pf3D7_07_v3 unit length 5
2016-03-14 00:27:05.042146 :: generating tandem repeats for chromosome Pf3D7_07_v3 unit length 6
2016-03-14 00:27:32.748157 :: generating tandem repeats for chromosome Pf3D7_07_v3 unit length 7
2016-03-14 00:27:56.219209 :: generating tandem repeats for chromosome Pf3D7_07_v3 unit length 8
2016-03-14 00:28:25.124856 :: generating tandem repeats for chromosome Pf3D7_07_v3 unit length 9
2016-03-14 00:28:52.526636 :: generating tandem repeats for chromosome Pf3D7_07_v3 unit length 10
2016-03-14 00:29:22.669514 :: generating tandem repeats for chromosome Pf3D7_07_v3 unit length 11
2016-03-14 00:29:47.683757 :: generating tandem repeats for chromosome Pf3D7_07_v3 unit length 12
2016-03-14 00:30:23.534198 :: generating tandem repeats for chromosome Pf3D7_07_v3 unit length 13
2016-03-14 00:30:48.844860 :: generating tandem repeats for chromosome Pf3D7_07_v3 unit length 14
2016-03-14 00:31:21.358458 :: generating tandem repeats for chromosome Pf3D7_07_v3 unit length 15
2016-03-14 00:31:53.847452 :: generating tandem repeats for chromosome Pf3D7_07_v3 unit length 16
2016-03-14 00:32:29.485264 :: generating tandem repeats for chromosome Pf3D7_07_v3 unit length 17
2016-03-14 00:32:56.506147 :: generating tandem repeats for chromosome Pf3D7_07_v3 unit length 18
2016-03-14 00:33:37.245925 :: generating tandem repeats for chromosome Pf3D7_07_v3 unit length 19
2016-03-14 00:34:04.615552 :: generating tandem repeats for chromosome Pf3D7_07_v3 unit length 20
2016-03-14 00:34:45.222088 :: generating tandem repeats for chromosome Pf3D7_07_v3 unit length 21
2016-03-14 00:35:20.384682 :: generating tandem repeats for chromosome Pf3D7_07_v3 unit length 22
2016-03-14 00:35:56.179420 :: generating tandem repeats for chromosome Pf3D7_07_v3 unit length 23
2016-03-14 00:36:24.551400 :: generating tandem repeats for chromosome Pf3D7_07_v3 unit length 24
2016-03-14 00:37:14.080601 :: generating tandem repeats for chromosome Pf3D7_08_v3 unit length 1
2016-03-14 00:37:36.301826 :: generating tandem repeats for chromosome Pf3D7_08_v3 unit length 2
2016-03-14 00:37:55.096515 :: generating tandem repeats for chromosome Pf3D7_08_v3 unit length 3
2016-03-14 00:38:15.910737 :: generating tandem repeats for chromosome Pf3D7_08_v3 unit length 4
2016-03-14 00:38:39.475872 :: generating tandem repeats for chromosome Pf3D7_08_v3 unit length 5
2016-03-14 00:39:02.479366 :: generating tandem repeats for chromosome Pf3D7_08_v3 unit length 6
2016-03-14 00:39:29.704929 :: generating tandem repeats for chromosome Pf3D7_08_v3 unit length 7
2016-03-14 00:39:53.288790 :: generating tandem repeats for chromosome Pf3D7_08_v3 unit length 8
2016-03-14 00:40:22.748520 :: generating tandem repeats for chromosome Pf3D7_08_v3 unit length 9
2016-03-14 00:40:51.294541 :: generating tandem repeats for chromosome Pf3D7_08_v3 unit length 10
2016-03-14 00:41:23.938241 :: generating tandem repeats for chromosome Pf3D7_08_v3 unit length 11
2016-03-14 00:41:49.534055 :: generating tandem repeats for chromosome Pf3D7_08_v3 unit length 12
2016-03-14 00:42:26.154114 :: generating tandem repeats for chromosome Pf3D7_08_v3 unit length 13
2016-03-14 00:42:51.891361 :: generating tandem repeats for chromosome Pf3D7_08_v3 unit length 14
2016-03-14 00:43:24.523934 :: generating tandem repeats for chromosome Pf3D7_08_v3 unit length 15
2016-03-14 00:43:57.216627 :: generating tandem repeats for chromosome Pf3D7_08_v3 unit length 16
2016-03-14 00:44:33.004929 :: generating tandem repeats for chromosome Pf3D7_08_v3 unit length 17
2016-03-14 00:45:00.389606 :: generating tandem repeats for chromosome Pf3D7_08_v3 unit length 18
2016-03-14 00:45:40.793966 :: generating tandem repeats for chromosome Pf3D7_08_v3 unit length 19
2016-03-14 00:46:08.015554 :: generating tandem repeats for chromosome Pf3D7_08_v3 unit length 20
2016-03-14 00:46:48.949100 :: generating tandem repeats for chromosome Pf3D7_08_v3 unit length 21
2016-03-14 00:47:24.582691 :: generating tandem repeats for chromosome Pf3D7_08_v3 unit length 22
2016-03-14 00:48:01.138501 :: generating tandem repeats for chromosome Pf3D7_08_v3 unit length 23
2016-03-14 00:48:30.544672 :: generating tandem repeats for chromosome Pf3D7_08_v3 unit length 24
2016-03-14 00:49:23.304465 :: generating tandem repeats for chromosome Pf3D7_09_v3 unit length 1
2016-03-14 00:49:46.354449 :: generating tandem repeats for chromosome Pf3D7_09_v3 unit length 2
2016-03-14 00:50:05.779939 :: generating tandem repeats for chromosome Pf3D7_09_v3 unit length 3
2016-03-14 00:50:27.137311 :: generating tandem repeats for chromosome Pf3D7_09_v3 unit length 4
2016-03-14 00:50:51.271363 :: generating tandem repeats for chromosome Pf3D7_09_v3 unit length 5
2016-03-14 00:51:15.018669 :: generating tandem repeats for chromosome Pf3D7_09_v3 unit length 6
2016-03-14 00:51:44.628034 :: generating tandem repeats for chromosome Pf3D7_09_v3 unit length 7
2016-03-14 00:52:09.217348 :: generating tandem repeats for chromosome Pf3D7_09_v3 unit length 8
2016-03-14 00:52:39.034037 :: generating tandem repeats for chromosome Pf3D7_09_v3 unit length 9
2016-03-14 00:53:08.653096 :: generating tandem repeats for chromosome Pf3D7_09_v3 unit length 10
2016-03-14 00:53:40.076325 :: generating tandem repeats for chromosome Pf3D7_09_v3 unit length 11
2016-03-14 00:54:06.059381 :: generating tandem repeats for chromosome Pf3D7_09_v3 unit length 12
2016-03-14 00:54:45.623639 :: generating tandem repeats for chromosome Pf3D7_09_v3 unit length 13
2016-03-14 00:55:13.368935 :: generating tandem repeats for chromosome Pf3D7_09_v3 unit length 14
2016-03-14 00:55:48.528263 :: generating tandem repeats for chromosome Pf3D7_09_v3 unit length 15
2016-03-14 00:56:22.964153 :: generating tandem repeats for chromosome Pf3D7_09_v3 unit length 16
2016-03-14 00:57:00.356114 :: generating tandem repeats for chromosome Pf3D7_09_v3 unit length 17
2016-03-14 00:57:28.439552 :: generating tandem repeats for chromosome Pf3D7_09_v3 unit length 18
2016-03-14 00:58:11.836737 :: generating tandem repeats for chromosome Pf3D7_09_v3 unit length 19
2016-03-14 00:58:41.195366 :: generating tandem repeats for chromosome Pf3D7_09_v3 unit length 20
2016-03-14 00:59:26.949683 :: generating tandem repeats for chromosome Pf3D7_09_v3 unit length 21
2016-03-14 01:00:03.928405 :: generating tandem repeats for chromosome Pf3D7_09_v3 unit length 22
2016-03-14 01:00:41.722630 :: generating tandem repeats for chromosome Pf3D7_09_v3 unit length 23
2016-03-14 01:01:12.428915 :: generating tandem repeats for chromosome Pf3D7_09_v3 unit length 24
2016-03-14 01:02:05.587373 :: generating tandem repeats for chromosome Pf3D7_10_v3 unit length 1
2016-03-14 01:02:30.314360 :: generating tandem repeats for chromosome Pf3D7_10_v3 unit length 2
2016-03-14 01:02:51.281851 :: generating tandem repeats for chromosome Pf3D7_10_v3 unit length 3
2016-03-14 01:03:14.688377 :: generating tandem repeats for chromosome Pf3D7_10_v3 unit length 4
2016-03-14 01:03:41.547843 :: generating tandem repeats for chromosome Pf3D7_10_v3 unit length 5
2016-03-14 01:04:08.338332 :: generating tandem repeats for chromosome Pf3D7_10_v3 unit length 6
2016-03-14 01:04:39.409222 :: generating tandem repeats for chromosome Pf3D7_10_v3 unit length 7
2016-03-14 01:05:06.237249 :: generating tandem repeats for chromosome Pf3D7_10_v3 unit length 8
2016-03-14 01:05:39.016615 :: generating tandem repeats for chromosome Pf3D7_10_v3 unit length 9
2016-03-14 01:06:10.255047 :: generating tandem repeats for chromosome Pf3D7_10_v3 unit length 10
2016-03-14 01:06:44.686684 :: generating tandem repeats for chromosome Pf3D7_10_v3 unit length 11
2016-03-14 01:07:13.147160 :: generating tandem repeats for chromosome Pf3D7_10_v3 unit length 12
2016-03-14 01:07:54.484386 :: generating tandem repeats for chromosome Pf3D7_10_v3 unit length 13
2016-03-14 01:08:23.568167 :: generating tandem repeats for chromosome Pf3D7_10_v3 unit length 14
2016-03-14 01:09:00.415515 :: generating tandem repeats for chromosome Pf3D7_10_v3 unit length 15
2016-03-14 01:09:37.535211 :: generating tandem repeats for chromosome Pf3D7_10_v3 unit length 16
2016-03-14 01:10:18.878986 :: generating tandem repeats for chromosome Pf3D7_10_v3 unit length 17
2016-03-14 01:10:49.328535 :: generating tandem repeats for chromosome Pf3D7_10_v3 unit length 18
2016-03-14 01:11:35.692593 :: generating tandem repeats for chromosome Pf3D7_10_v3 unit length 19
2016-03-14 01:12:06.548517 :: generating tandem repeats for chromosome Pf3D7_10_v3 unit length 20
2016-03-14 01:12:53.321025 :: generating tandem repeats for chromosome Pf3D7_10_v3 unit length 21
2016-03-14 01:13:33.416096 :: generating tandem repeats for chromosome Pf3D7_10_v3 unit length 22
2016-03-14 01:14:15.140500 :: generating tandem repeats for chromosome Pf3D7_10_v3 unit length 23
2016-03-14 01:14:47.316259 :: generating tandem repeats for chromosome Pf3D7_10_v3 unit length 24
2016-03-14 01:15:44.565186 :: generating tandem repeats for chromosome Pf3D7_11_v3 unit length 1
2016-03-14 01:16:14.301194 :: generating tandem repeats for chromosome Pf3D7_11_v3 unit length 2
2016-03-14 01:16:39.548705 :: generating tandem repeats for chromosome Pf3D7_11_v3 unit length 3
2016-03-14 01:17:07.645929 :: generating tandem repeats for chromosome Pf3D7_11_v3 unit length 4
2016-03-14 01:17:39.318756 :: generating tandem repeats for chromosome Pf3D7_11_v3 unit length 5
2016-03-14 01:18:10.469476 :: generating tandem repeats for chromosome Pf3D7_11_v3 unit length 6
2016-03-14 01:18:48.036627 :: generating tandem repeats for chromosome Pf3D7_11_v3 unit length 7
2016-03-14 01:19:20.460874 :: generating tandem repeats for chromosome Pf3D7_11_v3 unit length 8
2016-03-14 01:19:59.949111 :: generating tandem repeats for chromosome Pf3D7_11_v3 unit length 9
2016-03-14 01:20:37.734372 :: generating tandem repeats for chromosome Pf3D7_11_v3 unit length 10
2016-03-14 01:21:19.382366 :: generating tandem repeats for chromosome Pf3D7_11_v3 unit length 11
2016-03-14 01:21:53.850226 :: generating tandem repeats for chromosome Pf3D7_11_v3 unit length 12
2016-03-14 01:22:43.767551 :: generating tandem repeats for chromosome Pf3D7_11_v3 unit length 13
2016-03-14 01:23:19.058765 :: generating tandem repeats for chromosome Pf3D7_11_v3 unit length 14
2016-03-14 01:24:03.474980 :: generating tandem repeats for chromosome Pf3D7_11_v3 unit length 15
2016-03-14 01:24:47.986793 :: generating tandem repeats for chromosome Pf3D7_11_v3 unit length 16
2016-03-14 01:25:37.301803 :: generating tandem repeats for chromosome Pf3D7_11_v3 unit length 17
2016-03-14 01:26:14.106059 :: generating tandem repeats for chromosome Pf3D7_11_v3 unit length 18
2016-03-14 01:27:09.877968 :: generating tandem repeats for chromosome Pf3D7_11_v3 unit length 19
2016-03-14 01:27:47.285324 :: generating tandem repeats for chromosome Pf3D7_11_v3 unit length 20
2016-03-14 01:28:43.701256 :: generating tandem repeats for chromosome Pf3D7_11_v3 unit length 21
2016-03-14 01:29:32.236380 :: generating tandem repeats for chromosome Pf3D7_11_v3 unit length 22
2016-03-14 01:30:22.219497 :: generating tandem repeats for chromosome Pf3D7_11_v3 unit length 23
2016-03-14 01:31:01.148006 :: generating tandem repeats for chromosome Pf3D7_11_v3 unit length 24
2016-03-14 01:32:10.366936 :: generating tandem repeats for chromosome Pf3D7_12_v3 unit length 1
2016-03-14 01:32:43.991108 :: generating tandem repeats for chromosome Pf3D7_12_v3 unit length 2
2016-03-14 01:33:12.190292 :: generating tandem repeats for chromosome Pf3D7_12_v3 unit length 3
2016-03-14 01:33:43.755113 :: generating tandem repeats for chromosome Pf3D7_12_v3 unit length 4
2016-03-14 01:34:19.112235 :: generating tandem repeats for chromosome Pf3D7_12_v3 unit length 5
2016-03-14 01:34:53.652469 :: generating tandem repeats for chromosome Pf3D7_12_v3 unit length 6
2016-03-14 01:35:35.524171 :: generating tandem repeats for chromosome Pf3D7_12_v3 unit length 7
2016-03-14 01:36:11.662360 :: generating tandem repeats for chromosome Pf3D7_12_v3 unit length 8
2016-03-14 01:36:55.753449 :: generating tandem repeats for chromosome Pf3D7_12_v3 unit length 9
2016-03-14 01:37:37.733796 :: generating tandem repeats for chromosome Pf3D7_12_v3 unit length 10
2016-03-14 01:38:24.013947 :: generating tandem repeats for chromosome Pf3D7_12_v3 unit length 11
2016-03-14 01:39:02.444007 :: generating tandem repeats for chromosome Pf3D7_12_v3 unit length 12
2016-03-14 01:39:58.449175 :: generating tandem repeats for chromosome Pf3D7_12_v3 unit length 13
2016-03-14 01:40:37.964884 :: generating tandem repeats for chromosome Pf3D7_12_v3 unit length 14
2016-03-14 01:41:27.655371 :: generating tandem repeats for chromosome Pf3D7_12_v3 unit length 15
2016-03-14 01:42:17.352439 :: generating tandem repeats for chromosome Pf3D7_12_v3 unit length 16
2016-03-14 01:43:12.780894 :: generating tandem repeats for chromosome Pf3D7_12_v3 unit length 17
2016-03-14 01:43:53.725039 :: generating tandem repeats for chromosome Pf3D7_12_v3 unit length 18
2016-03-14 01:44:56.307157 :: generating tandem repeats for chromosome Pf3D7_12_v3 unit length 19
2016-03-14 01:45:37.970995 :: generating tandem repeats for chromosome Pf3D7_12_v3 unit length 20
2016-03-14 01:46:41.002795 :: generating tandem repeats for chromosome Pf3D7_12_v3 unit length 21
2016-03-14 01:47:34.916932 :: generating tandem repeats for chromosome Pf3D7_12_v3 unit length 22
2016-03-14 01:48:31.089977 :: generating tandem repeats for chromosome Pf3D7_12_v3 unit length 23
2016-03-14 01:49:14.444859 :: generating tandem repeats for chromosome Pf3D7_12_v3 unit length 24
2016-03-14 01:50:31.289134 :: generating tandem repeats for chromosome Pf3D7_13_v3 unit length 1
2016-03-14 01:51:14.472353 :: generating tandem repeats for chromosome Pf3D7_13_v3 unit length 2
2016-03-14 01:51:50.647136 :: generating tandem repeats for chromosome Pf3D7_13_v3 unit length 3
2016-03-14 01:52:31.249784 :: generating tandem repeats for chromosome Pf3D7_13_v3 unit length 4
2016-03-14 01:53:17.027914 :: generating tandem repeats for chromosome Pf3D7_13_v3 unit length 5
2016-03-14 01:54:01.567709 :: generating tandem repeats for chromosome Pf3D7_13_v3 unit length 6
2016-03-14 01:54:55.928484 :: generating tandem repeats for chromosome Pf3D7_13_v3 unit length 7
2016-03-14 01:55:42.705750 :: generating tandem repeats for chromosome Pf3D7_13_v3 unit length 8
2016-03-14 01:56:39.710650 :: generating tandem repeats for chromosome Pf3D7_13_v3 unit length 9
2016-03-14 01:57:34.196523 :: generating tandem repeats for chromosome Pf3D7_13_v3 unit length 10
2016-03-14 01:58:34.167716 :: generating tandem repeats for chromosome Pf3D7_13_v3 unit length 11
2016-03-14 01:59:24.118286 :: generating tandem repeats for chromosome Pf3D7_13_v3 unit length 12
2016-03-14 02:00:36.063201 :: generating tandem repeats for chromosome Pf3D7_13_v3 unit length 13
2016-03-14 02:01:26.642337 :: generating tandem repeats for chromosome Pf3D7_13_v3 unit length 14
2016-03-14 02:02:30.751525 :: generating tandem repeats for chromosome Pf3D7_13_v3 unit length 15
2016-03-14 02:03:35.422241 :: generating tandem repeats for chromosome Pf3D7_13_v3 unit length 16
2016-03-14 02:04:46.431722 :: generating tandem repeats for chromosome Pf3D7_13_v3 unit length 17
2016-03-14 02:05:39.690329 :: generating tandem repeats for chromosome Pf3D7_13_v3 unit length 18
2016-03-14 02:07:00.006581 :: generating tandem repeats for chromosome Pf3D7_13_v3 unit length 19
2016-03-14 02:07:54.271211 :: generating tandem repeats for chromosome Pf3D7_13_v3 unit length 20
2016-03-14 02:09:15.184356 :: generating tandem repeats for chromosome Pf3D7_13_v3 unit length 21
2016-03-14 02:10:25.204177 :: generating tandem repeats for chromosome Pf3D7_13_v3 unit length 22
2016-03-14 02:11:37.029370 :: generating tandem repeats for chromosome Pf3D7_13_v3 unit length 23
2016-03-14 02:12:33.109315 :: generating tandem repeats for chromosome Pf3D7_13_v3 unit length 24
2016-03-14 02:14:12.597565 :: generating tandem repeats for chromosome Pf3D7_14_v3 unit length 1
2016-03-14 02:15:01.274752 :: generating tandem repeats for chromosome Pf3D7_14_v3 unit length 2
2016-03-14 02:15:42.129207 :: generating tandem repeats for chromosome Pf3D7_14_v3 unit length 3
2016-03-14 02:16:27.667238 :: generating tandem repeats for chromosome Pf3D7_14_v3 unit length 4
2016-03-14 02:17:19.269320 :: generating tandem repeats for chromosome Pf3D7_14_v3 unit length 5
2016-03-14 02:18:09.470851 :: generating tandem repeats for chromosome Pf3D7_14_v3 unit length 6
2016-03-14 02:19:10.215342 :: generating tandem repeats for chromosome Pf3D7_14_v3 unit length 7
2016-03-14 02:20:02.665586 :: generating tandem repeats for chromosome Pf3D7_14_v3 unit length 8
2016-03-14 02:21:06.802186 :: generating tandem repeats for chromosome Pf3D7_14_v3 unit length 9
2016-03-14 02:22:08.013042 :: generating tandem repeats for chromosome Pf3D7_14_v3 unit length 10
2016-03-14 02:23:15.586360 :: generating tandem repeats for chromosome Pf3D7_14_v3 unit length 11
2016-03-14 02:24:11.402903 :: generating tandem repeats for chromosome Pf3D7_14_v3 unit length 12
2016-03-14 02:25:32.368951 :: generating tandem repeats for chromosome Pf3D7_14_v3 unit length 13
2016-03-14 02:26:29.445047 :: generating tandem repeats for chromosome Pf3D7_14_v3 unit length 14
2016-03-14 02:27:41.762392 :: generating tandem repeats for chromosome Pf3D7_14_v3 unit length 15
2016-03-14 02:28:54.047087 :: generating tandem repeats for chromosome Pf3D7_14_v3 unit length 16
2016-03-14 02:30:13.960393 :: generating tandem repeats for chromosome Pf3D7_14_v3 unit length 17
2016-03-14 02:31:13.566659 :: generating tandem repeats for chromosome Pf3D7_14_v3 unit length 18
2016-03-14 02:32:43.570940 :: generating tandem repeats for chromosome Pf3D7_14_v3 unit length 19
2016-03-14 02:33:44.286174 :: generating tandem repeats for chromosome Pf3D7_14_v3 unit length 20
2016-03-14 02:35:15.369418 :: generating tandem repeats for chromosome Pf3D7_14_v3 unit length 21
2016-03-14 02:36:33.884608 :: generating tandem repeats for chromosome Pf3D7_14_v3 unit length 22
2016-03-14 02:37:54.565647 :: generating tandem repeats for chromosome Pf3D7_14_v3 unit length 23
2016-03-14 02:38:57.500514 :: generating tandem repeats for chromosome Pf3D7_14_v3 unit length 24

In [18]:

    

tbl_tr_wg


    

    
Out[18]:







0|chrom
1|start
2|stop
3|repeat_unit
4|n_units
5|unit_length
6|last_unit_length
7|tract_length
8|region_type




Pf3D7_01_v3
3
5
a
2
1
0
2
SubtelomericRepeat


Pf3D7_01_v3
5
8
c
3
1
0
3
SubtelomericRepeat


Pf3D7_01_v3
9
13
a
4
1
0
4
SubtelomericRepeat


Pf3D7_01_v3
13
15
c
2
1
0
2
SubtelomericRepeat


Pf3D7_01_v3
16
19
a
3
1
0
3
SubtelomericRepeat



...

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