In [1]:
%pylab inline
import pandas as pd
import seaborn as sns
Populating the interactive namespace from numpy and matplotlib
In [2]:
def readseqalign(fname,Verbose=True):
"""
Reads the sequence alignment and returns a dataframe
"""
df_seqalign = pd.DataFrame()
seq=[]
title=None
with open(fname,'r') as infile:
for line in infile:
if(Verbose):
print "line",line
if line.startswith('>'):
if(title):
df_seqalign[title] = seq
seq=[]
title = line.strip('\n')[1:]
if(Verbose):
print "title",title
continue
seq = seq + list(line.strip('\n'))
if(Verbose):
print seq
df_seqalign[title] = seq
return df_seqalign
In [3]:
df_seqalign = readseqalign('aln.fas',Verbose=False)
In [4]:
df_seqalign.head()
Out[4]:
2WNW
1OGS
0
-
A
1
-
R
2
-
P
3
-
C
4
-
I
In [5]:
df_seqalign['2WNW'].values
Out[5]:
array(['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',
'-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-',
'-', '-', '-', '-', '-', '-', 'M', 'K', 'G', 'R', 'L', 'I', 'S',
'S', 'D', 'P', 'Y', 'R', 'Q', 'Q', 'F', 'L', 'V', 'E', 'R', '-',
'A', 'V', 'S', 'F', 'S', 'H', 'R', 'Q', 'R', 'D', 'C', 'S', 'E',
'L', 'I', 'S', 'V', 'L', 'P', 'R', 'H', 'A', 'L', 'Q', 'Q', 'I',
'D', 'G', 'F', 'G', 'G', 'S', 'F', 'T', 'E', 'G', 'A', 'G', 'V',
'V', 'F', 'N', 'S', 'M', 'S', 'E', 'K', 'T', 'K', 'A', 'Q', 'F',
'L', 'S', 'L', 'Y', 'F', 'S', 'A', 'Q', 'E', 'H', 'N', 'Y', 'T',
'L', 'A', 'R', 'M', 'P', 'I', 'Q', 'S', 'C', 'D', 'F', 'S', 'L',
'G', 'N', 'Y', 'A', 'Y', 'V', 'D', 'S', 'S', 'A', 'D', 'L', 'Q',
'Q', 'G', 'R', 'L', 'S', 'F', 'S', 'R', 'D', 'E', 'A', '-', 'H',
'L', 'I', 'P', 'L', 'I', 'S', 'G', 'A', 'L', 'R', 'L', 'N', '-',
'P', 'H', 'M', 'K', 'L', 'M', 'A', 'S', 'P', 'W', 'S', 'P', 'P',
'A', 'F', 'M', 'K', 'T', 'N', 'N', 'D', 'M', 'N', 'G', 'G', 'G',
'K', 'L', 'R', 'R', 'E', '-', '-', '-', '-', 'C', 'Y', 'A', 'D',
'W', 'A', 'D', 'I', 'I', 'I', 'N', 'Y', 'L', 'L', 'E', 'Y', 'R',
'R', 'H', 'G', 'I', 'N', 'V', 'Q', 'A', 'L', 'S', 'V', 'Q', 'N',
'E', 'P', 'V', 'A', 'V', 'K', 'T', '-', '-', '-', '-', 'W', 'D',
'S', 'C', 'L', 'Y', 'S', 'V', 'E', 'E', 'E', 'T', 'A', 'F', 'A',
'V', 'Q', 'Y', 'L', 'R', 'P', 'R', 'L', 'A', 'R', 'Q', 'G', 'M',
'D', 'E', 'M', 'E', 'I', 'Y', 'I', 'W', 'D', 'H', 'D', 'K', 'D',
'G', 'L', 'V', 'D', 'W', 'A', 'E', 'L', 'A', 'F', 'A', 'D', 'E',
'A', 'N', 'Y', 'K', 'G', 'I', 'N', 'G', 'L', 'A', 'F', 'H', 'W',
'Y', 'T', 'G', 'D', 'H', 'F', 'S', 'Q', 'I', '-', '-', '-', 'Q',
'Y', 'L', 'A', 'Q', 'C', 'L', 'P', 'D', 'K', 'K', 'L', 'L', 'F',
'S', 'E', 'G', 'C', 'V', 'P', 'M', 'E', 'S', 'D', '-', 'A', 'G',
'S', 'Q', 'I', 'R', 'H', 'W', '-', '-', '-', 'H', 'T', 'Y', 'L',
'H', 'D', 'M', 'I', 'G', 'N', 'F', 'K', 'S', 'G', 'C', 'S', 'G',
'F', 'I', 'D', 'W', 'N', 'L', 'L', 'L', 'N', 'S', 'E', 'G', 'G',
'P', 'N', 'H', 'Q', 'G', 'N', 'L', 'C', 'E', 'A', 'P', 'I', 'Q',
'Y', 'D', 'A', 'Q', 'N', 'D', 'V', 'L', 'R', 'R', 'N', 'H', 'S',
'W', 'Y', 'G', 'I', 'G', 'H', 'F', 'C', 'R', 'Y', 'V', 'R', 'P',
'G', 'A', '-', 'R', 'V', 'M', 'L', 'S', 'S', 'S', 'Y', 'D', 'N',
'L', 'L', 'E', 'E', 'V', 'G', 'F', 'V', 'N', 'P', 'D', 'G', 'E',
'R', 'V', 'L', 'V', 'V', 'Y', 'N', 'R', 'D', 'V', 'Q', 'E', 'R',
'R', 'C', 'R', 'V', 'L', 'D', 'G', 'D', 'K', 'E', 'I', 'A', 'L',
'T', 'L', '-', 'P', 'P', 'S', 'G', 'A', 'S', 'T', 'L', 'L', 'W',
'R', 'Q', 'E'], dtype=object)
In [6]:
df_seqalign['1OGS'].values
Out[6]:
array(['A', 'R', 'P', 'C', 'I', 'P', 'K', 'S', 'F', 'G', 'Y', 'S', 'S',
'V', 'V', 'C', 'V', 'C', 'N', 'A', 'T', 'Y', 'C', 'D', 'S', 'F',
'D', 'P', 'P', 'T', 'F', 'P', 'A', 'L', 'G', 'T', 'F', 'S', 'R',
'Y', 'E', 'S', 'T', 'R', 'S', 'G', 'R', 'R', 'M', 'E', 'L', 'S',
'M', 'G', 'P', 'I', 'Q', 'A', 'N', 'H', 'T', 'G', 'T', 'G', 'L',
'L', 'L', 'T', 'L', 'Q', 'P', 'E', 'Q', 'K', 'F', 'Q', 'K', 'V',
'K', 'G', 'F', 'G', 'G', 'A', 'M', 'T', 'D', 'A', 'A', 'A', 'L',
'N', 'I', 'L', 'A', 'L', 'S', 'P', 'P', 'A', 'Q', 'N', 'L', 'L',
'L', 'K', 'S', 'Y', 'F', 'S', 'E', 'E', 'G', 'I', 'G', 'Y', 'N',
'I', 'I', 'R', 'V', 'P', 'M', 'A', 'S', 'C', 'D', 'F', 'S', 'I',
'R', 'T', 'Y', 'T', 'Y', 'A', 'D', 'T', 'P', 'D', 'D', 'F', 'Q',
'L', 'H', 'N', 'F', 'S', 'L', 'P', 'E', 'E', 'D', 'T', 'K', 'L',
'K', 'I', 'P', 'L', 'I', 'H', 'R', 'A', 'L', 'Q', 'L', 'A', 'Q',
'R', 'P', 'V', 'S', 'L', 'L', 'A', 'S', 'P', 'W', 'T', 'S', 'P',
'T', 'W', 'L', 'K', 'T', 'N', 'G', 'A', 'V', 'N', 'G', 'K', 'G',
'S', 'L', 'K', 'G', 'Q', 'P', 'G', 'D', 'I', 'Y', 'H', 'Q', 'T',
'W', 'A', 'R', 'Y', 'F', 'V', 'K', 'F', 'L', 'D', 'A', 'Y', 'A',
'E', 'H', 'K', 'L', 'Q', 'F', 'W', 'A', 'V', 'T', 'A', 'E', 'N',
'E', 'P', 'S', 'A', 'G', 'L', 'L', 'S', 'G', 'Y', 'P', 'F', 'Q',
'C', 'L', 'G', 'F', 'T', 'P', 'E', 'H', 'Q', 'R', 'D', 'F', 'I',
'A', 'R', 'D', 'L', 'G', 'P', 'T', 'L', 'A', 'N', 'S', 'T', 'H',
'H', 'N', 'V', 'R', 'L', 'L', 'M', 'L', 'D', 'D', 'Q', 'R', 'L',
'L', 'L', 'P', 'H', 'W', 'A', 'K', 'V', 'V', 'L', 'T', 'D', 'P',
'E', 'A', 'A', 'K', 'Y', 'V', 'H', 'G', 'I', 'A', 'V', 'H', 'W',
'Y', 'L', 'D', 'F', 'L', 'A', 'P', 'A', 'K', 'A', 'T', 'L', 'G',
'E', 'T', 'H', 'R', 'L', 'F', 'P', 'N', 'T', 'M', 'L', 'F', 'A',
'S', 'E', 'A', 'C', 'V', 'G', 'S', 'K', 'F', 'W', 'E', 'Q', 'S',
'V', 'R', 'L', 'G', 'S', 'W', 'D', 'R', 'G', 'M', 'Q', 'Y', 'S',
'H', 'S', 'I', 'I', 'T', 'N', 'L', 'L', 'Y', 'H', 'V', 'V', 'G',
'W', 'T', 'D', 'W', 'N', 'L', 'A', 'L', 'N', 'P', 'E', 'G', 'G',
'P', 'N', 'W', 'V', 'R', 'N', 'F', 'V', 'D', 'S', 'P', 'I', 'I',
'V', 'D', 'I', 'T', 'K', 'D', 'T', 'F', 'Y', 'K', 'Q', 'P', 'M',
'F', 'Y', 'H', 'L', 'G', 'H', 'F', 'S', 'K', 'F', 'I', 'P', 'E',
'G', 'S', 'Q', 'R', 'V', 'G', 'L', 'V', 'A', 'S', 'Q', 'K', 'N',
'D', 'L', 'D', 'A', 'V', 'A', 'L', 'M', 'H', 'P', 'D', 'G', 'S',
'A', 'V', 'V', 'V', 'V', 'L', 'N', 'R', 'S', 'S', 'K', 'D', 'V',
'P', 'L', 'T', 'I', 'K', 'D', 'P', 'A', 'V', 'G', 'F', 'L', 'E',
'T', 'I', 'S', 'P', 'G', 'Y', 'S', 'I', 'H', 'T', 'Y', 'L', 'W',
'H', 'R', 'Q'], dtype=object)
In [7]:
import glob
In [8]:
csvfiles = glob.glob('*.csv')
In [9]:
csvfiles
Out[9]:
['1ogs-dfianalysis.csv', '2wnw-dfianalysis.csv']
In [10]:
dfidict = {fname.split('-')[0].upper(): pd.read_csv(fname) for fname in csvfiles}
In [11]:
dfidict['1OGS'].head()
Out[11]:
ResI
chainID
Res
R
dfi
pctdfi
fdfi
pctfdfi
adfi
ravg
A
0
1
A
ALA
A
0.002001
0.591549
0.313269
0.016097
-0.076459
33.973979
NotA
1
2
A
ARG
R
0.001925
0.559356
0.307688
0.014085
-0.094567
32.913771
NotA
2
3
A
PRO
P
0.001796
0.494970
0.321535
0.018109
-0.116700
31.924200
NotA
3
4
A
CYS
C
0.001666
0.416499
0.336214
0.030181
-0.183099
29.326847
NotA
4
5
A
ILE
I
0.001800
0.496982
0.343122
0.036217
-0.124748
30.730385
NotA
In [12]:
dfidict.keys()
Out[12]:
['2WNW', '1OGS']
In [13]:
dfidict['2WNW'].shape
Out[13]:
(445, 13)
In [14]:
dfalign = pd.DataFrame()
In [15]:
dfalign['1OGS_R'] = dfidict['1OGS']['R'].values
dfalign['1OGS_pctdfi'] = dfidict['1OGS']['pctdfi'].values
In [16]:
dfalign.shape
Out[16]:
(497, 2)
In [17]:
dfidict['2WNW']['R'].values.shape
Out[17]:
(445,)
In [18]:
padding = np.array(['-' for i in range(52)])
In [19]:
dfalign['2WNW_R'] = dfidict['2WNW']['R']
In [20]:
dfalign['2WNW_pctdfi'] = dfidict['2WNW']['pctdfi']
In [21]:
dfalign
Out[21]:
1OGS_R
1OGS_pctdfi
2WNW_R
2WNW_pctdfi
0
A
0.591549
M
0.970787
1
R
0.559356
K
0.961798
2
P
0.494970
G
0.910112
3
C
0.416499
R
0.858427
4
I
0.496982
L
0.683146
5
P
0.503018
I
0.530337
6
K
0.555332
S
0.460674
7
S
0.579477
S
0.485393
8
F
0.619718
D
0.685393
9
G
0.696177
P
0.689888
10
Y
0.605634
Y
0.844944
11
S
0.561368
R
0.876404
12
S
0.428571
Q
0.838202
13
V
0.386318
Q
0.768539
14
V
0.283702
F
0.622472
15
C
0.291751
L
0.586517
16
V
0.380282
V
0.732584
17
C
0.390342
E
0.851685
18
N
0.444668
R
0.923596
19
A
0.515091
A
0.959551
20
T
0.627767
V
0.948315
21
Y
0.565392
S
0.966292
22
C
0.434608
F
0.964045
23
D
0.454728
S
0.986517
24
S
0.356137
H
0.991011
25
F
0.271630
R
0.988764
26
D
0.462777
Q
0.995506
27
P
0.575453
R
1.000000
28
P
0.623742
D
0.997753
29
T
0.814889
C
0.993258
...
...
...
...
...
467
V
0.885312
NaN
NaN
468
P
0.925553
NaN
NaN
469
L
0.883300
NaN
NaN
470
T
0.905433
NaN
NaN
471
I
0.826962
NaN
NaN
472
K
0.887324
NaN
NaN
473
D
0.877264
NaN
NaN
474
P
0.945674
NaN
NaN
475
A
0.971831
NaN
NaN
476
V
0.965795
NaN
NaN
477
G
0.967807
NaN
NaN
478
F
0.947686
NaN
NaN
479
L
0.907445
NaN
NaN
480
E
0.935614
NaN
NaN
481
T
0.875252
NaN
NaN
482
I
0.847082
NaN
NaN
483
S
0.657948
NaN
NaN
484
P
0.708249
NaN
NaN
485
G
0.756539
NaN
NaN
486
Y
0.617706
NaN
NaN
487
S
0.301811
NaN
NaN
488
I
0.068410
NaN
NaN
489
H
0.030181
NaN
NaN
490
T
0.020121
NaN
NaN
491
Y
0.191147
NaN
NaN
492
L
0.446680
NaN
NaN
493
W
0.746479
NaN
NaN
494
H
0.881288
NaN
NaN
495
R
0.913481
NaN
NaN
496
Q
0.979879
NaN
NaN
497 rows × 4 columns
In [22]:
dfalign = pd.DataFrame()
for name in ['1OGS','2WNW']:
dfalign[name+'_R']= dfidict[name]['R']
dfalign[name+'_pctdfi'] = dfidict[name]['pctdfi']
In [23]:
dfalign.head()
Out[23]:
1OGS_R
1OGS_pctdfi
2WNW_R
2WNW_pctdfi
0
A
0.591549
M
0.970787
1
R
0.559356
K
0.961798
2
P
0.494970
G
0.910112
3
C
0.416499
R
0.858427
4
I
0.496982
L
0.683146
In [24]:
len(dfalign)
Out[24]:
497
In [25]:
len(df_seqalign)
Out[25]:
497
In [26]:
def ls_mapdfival(name,df_seqalign,dfalign,Verbose=False):
"""
Map dfi values from dfi csvvalues to aligned seqeuences
Input
-----
name
df_seqalign: sequence from sequence alignment (DataFrame)
dfalign: dfi values (DataFrame)
Output
------
Returned Mapped DFI values
"""
ls_seq=df_seqalign[name].values
ls_dfiseq=dfalign[name+'_R'].values
ls_dfival=dfalign[name+'_pctdfi'].values
no_gap_seq=np.array([pos for pos in ls_seq if pos != '-'])
print "len(ls_dfiseq)",len(ls_dfiseq),"len(ls_seq)",len(ls_seq), "no_gap_seq", len(no_gap_seq), len(ls_dfival)
low = min(len(ls_seq),len(ls_dfiseq))
dfimapval = []
marker=0
for i,seqpos in enumerate(ls_seq):
if(Verbose):
print "seqpos",seqpos,"marker",marker,"i",i
while(marker < len(ls_seq)):
if(seqpos == '-'):
if(Verbose):
print "seqpos",seqpos,"insertion"
dfimapval.append('-')
break
if(seqpos == ls_dfiseq[marker]):
if(Verbose):
print "seqpos",seqpos,"dfiseq",ls_dfiseq[marker],marker
dfimapval.append(ls_dfival[marker])
marker +=1
break
else:
marker +=1
return ls_seq,dfimapval
In [27]:
dfx = pd.DataFrame()
for name in dfidict.keys():
print name
testseq,testval = ls_mapdfival(name,df_seqalign,dfalign,Verbose=True)
#print len(testseq),len(testval)
dfx[name+'_R'] = testseq
dfx[name+'_pctdfi'] = testval
2WNW
len(ls_dfiseq) 497 len(ls_seq) 497 no_gap_seq 445 497
seqpos - marker 0 i 0
seqpos - insertion
seqpos - marker 0 i 1
seqpos - insertion
seqpos - marker 0 i 2
seqpos - insertion
seqpos - marker 0 i 3
seqpos - insertion
seqpos - marker 0 i 4
seqpos - insertion
seqpos - marker 0 i 5
seqpos - insertion
seqpos - marker 0 i 6
seqpos - insertion
seqpos - marker 0 i 7
seqpos - insertion
seqpos - marker 0 i 8
seqpos - insertion
seqpos - marker 0 i 9
seqpos - insertion
seqpos - marker 0 i 10
seqpos - insertion
seqpos - marker 0 i 11
seqpos - insertion
seqpos - marker 0 i 12
seqpos - insertion
seqpos - marker 0 i 13
seqpos - insertion
seqpos - marker 0 i 14
seqpos - insertion
seqpos - marker 0 i 15
seqpos - insertion
seqpos - marker 0 i 16
seqpos - insertion
seqpos - marker 0 i 17
seqpos - insertion
seqpos - marker 0 i 18
seqpos - insertion
seqpos - marker 0 i 19
seqpos - insertion
seqpos - marker 0 i 20
seqpos - insertion
seqpos - marker 0 i 21
seqpos - insertion
seqpos - marker 0 i 22
seqpos - insertion
seqpos - marker 0 i 23
seqpos - insertion
seqpos - marker 0 i 24
seqpos - insertion
seqpos - marker 0 i 25
seqpos - insertion
seqpos - marker 0 i 26
seqpos - insertion
seqpos - marker 0 i 27
seqpos - insertion
seqpos - marker 0 i 28
seqpos - insertion
seqpos - marker 0 i 29
seqpos - insertion
seqpos - marker 0 i 30
seqpos - insertion
seqpos - marker 0 i 31
seqpos - insertion
seqpos M marker 0 i 32
seqpos M dfiseq M 0
seqpos K marker 1 i 33
seqpos K dfiseq K 1
seqpos G marker 2 i 34
seqpos G dfiseq G 2
seqpos R marker 3 i 35
seqpos R dfiseq R 3
seqpos L marker 4 i 36
seqpos L dfiseq L 4
seqpos I marker 5 i 37
seqpos I dfiseq I 5
seqpos S marker 6 i 38
seqpos S dfiseq S 6
seqpos S marker 7 i 39
seqpos S dfiseq S 7
seqpos D marker 8 i 40
seqpos D dfiseq D 8
seqpos P marker 9 i 41
seqpos P dfiseq P 9
seqpos Y marker 10 i 42
seqpos Y dfiseq Y 10
seqpos R marker 11 i 43
seqpos R dfiseq R 11
seqpos Q marker 12 i 44
seqpos Q dfiseq Q 12
seqpos Q marker 13 i 45
seqpos Q dfiseq Q 13
seqpos F marker 14 i 46
seqpos F dfiseq F 14
seqpos L marker 15 i 47
seqpos L dfiseq L 15
seqpos V marker 16 i 48
seqpos V dfiseq V 16
seqpos E marker 17 i 49
seqpos E dfiseq E 17
seqpos R marker 18 i 50
seqpos R dfiseq R 18
seqpos - marker 19 i 51
seqpos - insertion
seqpos A marker 19 i 52
seqpos A dfiseq A 19
seqpos V marker 20 i 53
seqpos V dfiseq V 20
seqpos S marker 21 i 54
seqpos S dfiseq S 21
seqpos F marker 22 i 55
seqpos F dfiseq F 22
seqpos S marker 23 i 56
seqpos S dfiseq S 23
seqpos H marker 24 i 57
seqpos H dfiseq H 24
seqpos R marker 25 i 58
seqpos R dfiseq R 25
seqpos Q marker 26 i 59
seqpos Q dfiseq Q 26
seqpos R marker 27 i 60
seqpos R dfiseq R 27
seqpos D marker 28 i 61
seqpos D dfiseq D 28
seqpos C marker 29 i 62
seqpos C dfiseq C 29
seqpos S marker 30 i 63
seqpos S dfiseq S 30
seqpos E marker 31 i 64
seqpos E dfiseq E 31
seqpos L marker 32 i 65
seqpos L dfiseq L 32
seqpos I marker 33 i 66
seqpos I dfiseq I 33
seqpos S marker 34 i 67
seqpos S dfiseq S 34
seqpos V marker 35 i 68
seqpos V dfiseq V 35
seqpos L marker 36 i 69
seqpos L dfiseq L 36
seqpos P marker 37 i 70
seqpos P dfiseq P 37
seqpos R marker 38 i 71
seqpos R dfiseq R 38
seqpos H marker 39 i 72
seqpos H dfiseq H 39
seqpos A marker 40 i 73
seqpos A dfiseq A 40
seqpos L marker 41 i 74
seqpos L dfiseq L 41
seqpos Q marker 42 i 75
seqpos Q dfiseq Q 42
seqpos Q marker 43 i 76
seqpos Q dfiseq Q 43
seqpos I marker 44 i 77
seqpos I dfiseq I 44
seqpos D marker 45 i 78
seqpos D dfiseq D 45
seqpos G marker 46 i 79
seqpos G dfiseq G 46
seqpos F marker 47 i 80
seqpos F dfiseq F 47
seqpos G marker 48 i 81
seqpos G dfiseq G 48
seqpos G marker 49 i 82
seqpos G dfiseq G 49
seqpos S marker 50 i 83
seqpos S dfiseq S 50
seqpos F marker 51 i 84
seqpos F dfiseq F 51
seqpos T marker 52 i 85
seqpos T dfiseq T 52
seqpos E marker 53 i 86
seqpos E dfiseq E 53
seqpos G marker 54 i 87
seqpos G dfiseq G 54
seqpos A marker 55 i 88
seqpos A dfiseq A 55
seqpos G marker 56 i 89
seqpos G dfiseq G 56
seqpos V marker 57 i 90
seqpos V dfiseq V 57
seqpos V marker 58 i 91
seqpos V dfiseq V 58
seqpos F marker 59 i 92
seqpos F dfiseq F 59
seqpos N marker 60 i 93
seqpos N dfiseq N 60
seqpos S marker 61 i 94
seqpos S dfiseq S 61
seqpos M marker 62 i 95
seqpos M dfiseq M 62
seqpos S marker 63 i 96
seqpos S dfiseq S 63
seqpos E marker 64 i 97
seqpos E dfiseq E 64
seqpos K marker 65 i 98
seqpos K dfiseq K 65
seqpos T marker 66 i 99
seqpos T dfiseq T 66
seqpos K marker 67 i 100
seqpos K dfiseq K 67
seqpos A marker 68 i 101
seqpos A dfiseq A 68
seqpos Q marker 69 i 102
seqpos Q dfiseq Q 69
seqpos F marker 70 i 103
seqpos F dfiseq F 70
seqpos L marker 71 i 104
seqpos L dfiseq L 71
seqpos S marker 72 i 105
seqpos S dfiseq S 72
seqpos L marker 73 i 106
seqpos L dfiseq L 73
seqpos Y marker 74 i 107
seqpos Y dfiseq Y 74
seqpos F marker 75 i 108
seqpos F dfiseq F 75
seqpos S marker 76 i 109
seqpos S dfiseq S 76
seqpos A marker 77 i 110
seqpos A dfiseq A 77
seqpos Q marker 78 i 111
seqpos Q dfiseq Q 78
seqpos E marker 79 i 112
seqpos E dfiseq E 79
seqpos H marker 80 i 113
seqpos H dfiseq H 80
seqpos N marker 81 i 114
seqpos N dfiseq N 81
seqpos Y marker 82 i 115
seqpos Y dfiseq Y 82
seqpos T marker 83 i 116
seqpos T dfiseq T 83
seqpos L marker 84 i 117
seqpos L dfiseq L 84
seqpos A marker 85 i 118
seqpos A dfiseq A 85
seqpos R marker 86 i 119
seqpos R dfiseq R 86
seqpos M marker 87 i 120
seqpos M dfiseq M 87
seqpos P marker 88 i 121
seqpos P dfiseq P 88
seqpos I marker 89 i 122
seqpos I dfiseq I 89
seqpos Q marker 90 i 123
seqpos Q dfiseq Q 90
seqpos S marker 91 i 124
seqpos S dfiseq S 91
seqpos C marker 92 i 125
seqpos C dfiseq C 92
seqpos D marker 93 i 126
seqpos D dfiseq D 93
seqpos F marker 94 i 127
seqpos F dfiseq F 94
seqpos S marker 95 i 128
seqpos S dfiseq S 95
seqpos L marker 96 i 129
seqpos L dfiseq L 96
seqpos G marker 97 i 130
seqpos G dfiseq G 97
seqpos N marker 98 i 131
seqpos N dfiseq N 98
seqpos Y marker 99 i 132
seqpos Y dfiseq Y 99
seqpos A marker 100 i 133
seqpos A dfiseq A 100
seqpos Y marker 101 i 134
seqpos Y dfiseq Y 101
seqpos V marker 102 i 135
seqpos V dfiseq V 102
seqpos D marker 103 i 136
seqpos D dfiseq D 103
seqpos S marker 104 i 137
seqpos S dfiseq S 104
seqpos S marker 105 i 138
seqpos S dfiseq S 105
seqpos A marker 106 i 139
seqpos A dfiseq A 106
seqpos D marker 107 i 140
seqpos D dfiseq D 107
seqpos L marker 108 i 141
seqpos L dfiseq L 108
seqpos Q marker 109 i 142
seqpos Q dfiseq Q 109
seqpos Q marker 110 i 143
seqpos Q dfiseq Q 110
seqpos G marker 111 i 144
seqpos G dfiseq G 111
seqpos R marker 112 i 145
seqpos R dfiseq R 112
seqpos L marker 113 i 146
seqpos L dfiseq L 113
seqpos S marker 114 i 147
seqpos S dfiseq S 114
seqpos F marker 115 i 148
seqpos F dfiseq F 115
seqpos S marker 116 i 149
seqpos S dfiseq S 116
seqpos R marker 117 i 150
seqpos R dfiseq R 117
seqpos D marker 118 i 151
seqpos D dfiseq D 118
seqpos E marker 119 i 152
seqpos E dfiseq E 119
seqpos A marker 120 i 153
seqpos A dfiseq A 120
seqpos - marker 121 i 154
seqpos - insertion
seqpos H marker 121 i 155
seqpos H dfiseq H 121
seqpos L marker 122 i 156
seqpos L dfiseq L 122
seqpos I marker 123 i 157
seqpos I dfiseq I 123
seqpos P marker 124 i 158
seqpos P dfiseq P 124
seqpos L marker 125 i 159
seqpos L dfiseq L 125
seqpos I marker 126 i 160
seqpos I dfiseq I 126
seqpos S marker 127 i 161
seqpos S dfiseq S 127
seqpos G marker 128 i 162
seqpos G dfiseq G 128
seqpos A marker 129 i 163
seqpos A dfiseq A 129
seqpos L marker 130 i 164
seqpos L dfiseq L 130
seqpos R marker 131 i 165
seqpos R dfiseq R 131
seqpos L marker 132 i 166
seqpos L dfiseq L 132
seqpos N marker 133 i 167
seqpos N dfiseq N 133
seqpos - marker 134 i 168
seqpos - insertion
seqpos P marker 134 i 169
seqpos P dfiseq P 134
seqpos H marker 135 i 170
seqpos H dfiseq H 135
seqpos M marker 136 i 171
seqpos M dfiseq M 136
seqpos K marker 137 i 172
seqpos K dfiseq K 137
seqpos L marker 138 i 173
seqpos L dfiseq L 138
seqpos M marker 139 i 174
seqpos M dfiseq M 139
seqpos A marker 140 i 175
seqpos A dfiseq A 140
seqpos S marker 141 i 176
seqpos S dfiseq S 141
seqpos P marker 142 i 177
seqpos P dfiseq P 142
seqpos W marker 143 i 178
seqpos W dfiseq W 143
seqpos S marker 144 i 179
seqpos S dfiseq S 144
seqpos P marker 145 i 180
seqpos P dfiseq P 145
seqpos P marker 146 i 181
seqpos P dfiseq P 146
seqpos A marker 147 i 182
seqpos A dfiseq A 147
seqpos F marker 148 i 183
seqpos F dfiseq F 148
seqpos M marker 149 i 184
seqpos M dfiseq M 149
seqpos K marker 150 i 185
seqpos K dfiseq K 150
seqpos T marker 151 i 186
seqpos T dfiseq T 151
seqpos N marker 152 i 187
seqpos N dfiseq N 152
seqpos N marker 153 i 188
seqpos N dfiseq N 153
seqpos D marker 154 i 189
seqpos D dfiseq D 154
seqpos M marker 155 i 190
seqpos M dfiseq M 155
seqpos N marker 156 i 191
seqpos N dfiseq N 156
seqpos G marker 157 i 192
seqpos G dfiseq G 157
seqpos G marker 158 i 193
seqpos G dfiseq G 158
seqpos G marker 159 i 194
seqpos G dfiseq G 159
seqpos K marker 160 i 195
seqpos K dfiseq K 160
seqpos L marker 161 i 196
seqpos L dfiseq L 161
seqpos R marker 162 i 197
seqpos R dfiseq R 162
seqpos R marker 163 i 198
seqpos R dfiseq R 163
seqpos E marker 164 i 199
seqpos E dfiseq E 164
seqpos - marker 165 i 200
seqpos - insertion
seqpos - marker 165 i 201
seqpos - insertion
seqpos - marker 165 i 202
seqpos - insertion
seqpos - marker 165 i 203
seqpos - insertion
seqpos C marker 165 i 204
seqpos C dfiseq C 165
seqpos Y marker 166 i 205
seqpos Y dfiseq Y 166
seqpos A marker 167 i 206
seqpos A dfiseq A 167
seqpos D marker 168 i 207
seqpos D dfiseq D 168
seqpos W marker 169 i 208
seqpos W dfiseq W 169
seqpos A marker 170 i 209
seqpos A dfiseq A 170
seqpos D marker 171 i 210
seqpos D dfiseq D 171
seqpos I marker 172 i 211
seqpos I dfiseq I 172
seqpos I marker 173 i 212
seqpos I dfiseq I 173
seqpos I marker 174 i 213
seqpos I dfiseq I 174
seqpos N marker 175 i 214
seqpos N dfiseq N 175
seqpos Y marker 176 i 215
seqpos Y dfiseq Y 176
seqpos L marker 177 i 216
seqpos L dfiseq L 177
seqpos L marker 178 i 217
seqpos L dfiseq L 178
seqpos E marker 179 i 218
seqpos E dfiseq E 179
seqpos Y marker 180 i 219
seqpos Y dfiseq Y 180
seqpos R marker 181 i 220
seqpos R dfiseq R 181
seqpos R marker 182 i 221
seqpos R dfiseq R 182
seqpos H marker 183 i 222
seqpos H dfiseq H 183
seqpos G marker 184 i 223
seqpos G dfiseq G 184
seqpos I marker 185 i 224
seqpos I dfiseq I 185
seqpos N marker 186 i 225
seqpos N dfiseq N 186
seqpos V marker 187 i 226
seqpos V dfiseq V 187
seqpos Q marker 188 i 227
seqpos Q dfiseq Q 188
seqpos A marker 189 i 228
seqpos A dfiseq A 189
seqpos L marker 190 i 229
seqpos L dfiseq L 190
seqpos S marker 191 i 230
seqpos S dfiseq S 191
seqpos V marker 192 i 231
seqpos V dfiseq V 192
seqpos Q marker 193 i 232
seqpos Q dfiseq Q 193
seqpos N marker 194 i 233
seqpos N dfiseq N 194
seqpos E marker 195 i 234
seqpos E dfiseq E 195
seqpos P marker 196 i 235
seqpos P dfiseq P 196
seqpos V marker 197 i 236
seqpos V dfiseq V 197
seqpos A marker 198 i 237
seqpos A dfiseq A 198
seqpos V marker 199 i 238
seqpos V dfiseq V 199
seqpos K marker 200 i 239
seqpos K dfiseq K 200
seqpos T marker 201 i 240
seqpos T dfiseq T 201
seqpos - marker 202 i 241
seqpos - insertion
seqpos - marker 202 i 242
seqpos - insertion
seqpos - marker 202 i 243
seqpos - insertion
seqpos - marker 202 i 244
seqpos - insertion
seqpos W marker 202 i 245
seqpos W dfiseq W 202
seqpos D marker 203 i 246
seqpos D dfiseq D 203
seqpos S marker 204 i 247
seqpos S dfiseq S 204
seqpos C marker 205 i 248
seqpos C dfiseq C 205
seqpos L marker 206 i 249
seqpos L dfiseq L 206
seqpos Y marker 207 i 250
seqpos Y dfiseq Y 207
seqpos S marker 208 i 251
seqpos S dfiseq S 208
seqpos V marker 209 i 252
seqpos V dfiseq V 209
seqpos E marker 210 i 253
seqpos E dfiseq E 210
seqpos E marker 211 i 254
seqpos E dfiseq E 211
seqpos E marker 212 i 255
seqpos E dfiseq E 212
seqpos T marker 213 i 256
seqpos T dfiseq T 213
seqpos A marker 214 i 257
seqpos A dfiseq A 214
seqpos F marker 215 i 258
seqpos F dfiseq F 215
seqpos A marker 216 i 259
seqpos A dfiseq A 216
seqpos V marker 217 i 260
seqpos V dfiseq V 217
seqpos Q marker 218 i 261
seqpos Q dfiseq Q 218
seqpos Y marker 219 i 262
seqpos Y dfiseq Y 219
seqpos L marker 220 i 263
seqpos L dfiseq L 220
seqpos R marker 221 i 264
seqpos R dfiseq R 221
seqpos P marker 222 i 265
seqpos P dfiseq P 222
seqpos R marker 223 i 266
seqpos R dfiseq R 223
seqpos L marker 224 i 267
seqpos L dfiseq L 224
seqpos A marker 225 i 268
seqpos A dfiseq A 225
seqpos R marker 226 i 269
seqpos R dfiseq R 226
seqpos Q marker 227 i 270
seqpos Q dfiseq Q 227
seqpos G marker 228 i 271
seqpos G dfiseq G 228
seqpos M marker 229 i 272
seqpos M dfiseq M 229
seqpos D marker 230 i 273
seqpos D dfiseq D 230
seqpos E marker 231 i 274
seqpos E dfiseq E 231
seqpos M marker 232 i 275
seqpos M dfiseq M 232
seqpos E marker 233 i 276
seqpos E dfiseq E 233
seqpos I marker 234 i 277
seqpos I dfiseq I 234
seqpos Y marker 235 i 278
seqpos Y dfiseq Y 235
seqpos I marker 236 i 279
seqpos I dfiseq I 236
seqpos W marker 237 i 280
seqpos W dfiseq W 237
seqpos D marker 238 i 281
seqpos D dfiseq D 238
seqpos H marker 239 i 282
seqpos H dfiseq H 239
seqpos D marker 240 i 283
seqpos D dfiseq D 240
seqpos K marker 241 i 284
seqpos K dfiseq K 241
seqpos D marker 242 i 285
seqpos D dfiseq D 242
seqpos G marker 243 i 286
seqpos G dfiseq G 243
seqpos L marker 244 i 287
seqpos L dfiseq L 244
seqpos V marker 245 i 288
seqpos V dfiseq V 245
seqpos D marker 246 i 289
seqpos D dfiseq D 246
seqpos W marker 247 i 290
seqpos W dfiseq W 247
seqpos A marker 248 i 291
seqpos A dfiseq A 248
seqpos E marker 249 i 292
seqpos E dfiseq E 249
seqpos L marker 250 i 293
seqpos L dfiseq L 250
seqpos A marker 251 i 294
seqpos A dfiseq A 251
seqpos F marker 252 i 295
seqpos F dfiseq F 252
seqpos A marker 253 i 296
seqpos A dfiseq A 253
seqpos D marker 254 i 297
seqpos D dfiseq D 254
seqpos E marker 255 i 298
seqpos E dfiseq E 255
seqpos A marker 256 i 299
seqpos A dfiseq A 256
seqpos N marker 257 i 300
seqpos N dfiseq N 257
seqpos Y marker 258 i 301
seqpos Y dfiseq Y 258
seqpos K marker 259 i 302
seqpos K dfiseq K 259
seqpos G marker 260 i 303
seqpos G dfiseq G 260
seqpos I marker 261 i 304
seqpos I dfiseq I 261
seqpos N marker 262 i 305
seqpos N dfiseq N 262
seqpos G marker 263 i 306
seqpos G dfiseq G 263
seqpos L marker 264 i 307
seqpos L dfiseq L 264
seqpos A marker 265 i 308
seqpos A dfiseq A 265
seqpos F marker 266 i 309
seqpos F dfiseq F 266
seqpos H marker 267 i 310
seqpos H dfiseq H 267
seqpos W marker 268 i 311
seqpos W dfiseq W 268
seqpos Y marker 269 i 312
seqpos Y dfiseq Y 269
seqpos T marker 270 i 313
seqpos T dfiseq T 270
seqpos G marker 271 i 314
seqpos G dfiseq G 271
seqpos D marker 272 i 315
seqpos D dfiseq D 272
seqpos H marker 273 i 316
seqpos H dfiseq H 273
seqpos F marker 274 i 317
seqpos F dfiseq F 274
seqpos S marker 275 i 318
seqpos S dfiseq S 275
seqpos Q marker 276 i 319
seqpos Q dfiseq Q 276
seqpos I marker 277 i 320
seqpos I dfiseq I 277
seqpos - marker 278 i 321
seqpos - insertion
seqpos - marker 278 i 322
seqpos - insertion
seqpos - marker 278 i 323
seqpos - insertion
seqpos Q marker 278 i 324
seqpos Q dfiseq Q 278
seqpos Y marker 279 i 325
seqpos Y dfiseq Y 279
seqpos L marker 280 i 326
seqpos L dfiseq L 280
seqpos A marker 281 i 327
seqpos A dfiseq A 281
seqpos Q marker 282 i 328
seqpos Q dfiseq Q 282
seqpos C marker 283 i 329
seqpos C dfiseq C 283
seqpos L marker 284 i 330
seqpos L dfiseq L 284
seqpos P marker 285 i 331
seqpos P dfiseq P 285
seqpos D marker 286 i 332
seqpos D dfiseq D 286
seqpos K marker 287 i 333
seqpos K dfiseq K 287
seqpos K marker 288 i 334
seqpos K dfiseq K 288
seqpos L marker 289 i 335
seqpos L dfiseq L 289
seqpos L marker 290 i 336
seqpos L dfiseq L 290
seqpos F marker 291 i 337
seqpos F dfiseq F 291
seqpos S marker 292 i 338
seqpos S dfiseq S 292
seqpos E marker 293 i 339
seqpos E dfiseq E 293
seqpos G marker 294 i 340
seqpos G dfiseq G 294
seqpos C marker 295 i 341
seqpos C dfiseq C 295
seqpos V marker 296 i 342
seqpos V dfiseq V 296
seqpos P marker 297 i 343
seqpos P dfiseq P 297
seqpos M marker 298 i 344
seqpos M dfiseq M 298
seqpos E marker 299 i 345
seqpos E dfiseq E 299
seqpos S marker 300 i 346
seqpos S dfiseq S 300
seqpos D marker 301 i 347
seqpos D dfiseq D 301
seqpos - marker 302 i 348
seqpos - insertion
seqpos A marker 302 i 349
seqpos A dfiseq A 302
seqpos G marker 303 i 350
seqpos G dfiseq G 303
seqpos S marker 304 i 351
seqpos S dfiseq S 304
seqpos Q marker 305 i 352
seqpos Q dfiseq Q 305
seqpos I marker 306 i 353
seqpos I dfiseq I 306
seqpos R marker 307 i 354
seqpos R dfiseq R 307
seqpos H marker 308 i 355
seqpos H dfiseq H 308
seqpos W marker 309 i 356
seqpos W dfiseq W 309
seqpos - marker 310 i 357
seqpos - insertion
seqpos - marker 310 i 358
seqpos - insertion
seqpos - marker 310 i 359
seqpos - insertion
seqpos H marker 310 i 360
seqpos H dfiseq H 310
seqpos T marker 311 i 361
seqpos T dfiseq T 311
seqpos Y marker 312 i 362
seqpos Y dfiseq Y 312
seqpos L marker 313 i 363
seqpos L dfiseq L 313
seqpos H marker 314 i 364
seqpos H dfiseq H 314
seqpos D marker 315 i 365
seqpos D dfiseq D 315
seqpos M marker 316 i 366
seqpos M dfiseq M 316
seqpos I marker 317 i 367
seqpos I dfiseq I 317
seqpos G marker 318 i 368
seqpos G dfiseq G 318
seqpos N marker 319 i 369
seqpos N dfiseq N 319
seqpos F marker 320 i 370
seqpos F dfiseq F 320
seqpos K marker 321 i 371
seqpos K dfiseq K 321
seqpos S marker 322 i 372
seqpos S dfiseq S 322
seqpos G marker 323 i 373
seqpos G dfiseq G 323
seqpos C marker 324 i 374
seqpos C dfiseq C 324
seqpos S marker 325 i 375
seqpos S dfiseq S 325
seqpos G marker 326 i 376
seqpos G dfiseq G 326
seqpos F marker 327 i 377
seqpos F dfiseq F 327
seqpos I marker 328 i 378
seqpos I dfiseq I 328
seqpos D marker 329 i 379
seqpos D dfiseq D 329
seqpos W marker 330 i 380
seqpos W dfiseq W 330
seqpos N marker 331 i 381
seqpos N dfiseq N 331
seqpos L marker 332 i 382
seqpos L dfiseq L 332
seqpos L marker 333 i 383
seqpos L dfiseq L 333
seqpos L marker 334 i 384
seqpos L dfiseq L 334
seqpos N marker 335 i 385
seqpos N dfiseq N 335
seqpos S marker 336 i 386
seqpos S dfiseq S 336
seqpos E marker 337 i 387
seqpos E dfiseq E 337
seqpos G marker 338 i 388
seqpos G dfiseq G 338
seqpos G marker 339 i 389
seqpos G dfiseq G 339
seqpos P marker 340 i 390
seqpos P dfiseq P 340
seqpos N marker 341 i 391
seqpos N dfiseq N 341
seqpos H marker 342 i 392
seqpos H dfiseq H 342
seqpos Q marker 343 i 393
seqpos Q dfiseq Q 343
seqpos G marker 344 i 394
seqpos G dfiseq G 344
seqpos N marker 345 i 395
seqpos N dfiseq N 345
seqpos L marker 346 i 396
seqpos L dfiseq L 346
seqpos C marker 347 i 397
seqpos C dfiseq C 347
seqpos E marker 348 i 398
seqpos E dfiseq E 348
seqpos A marker 349 i 399
seqpos A dfiseq A 349
seqpos P marker 350 i 400
seqpos P dfiseq P 350
seqpos I marker 351 i 401
seqpos I dfiseq I 351
seqpos Q marker 352 i 402
seqpos Q dfiseq Q 352
seqpos Y marker 353 i 403
seqpos Y dfiseq Y 353
seqpos D marker 354 i 404
seqpos D dfiseq D 354
seqpos A marker 355 i 405
seqpos A dfiseq A 355
seqpos Q marker 356 i 406
seqpos Q dfiseq Q 356
seqpos N marker 357 i 407
seqpos N dfiseq N 357
seqpos D marker 358 i 408
seqpos D dfiseq D 358
seqpos V marker 359 i 409
seqpos V dfiseq V 359
seqpos L marker 360 i 410
seqpos L dfiseq L 360
seqpos R marker 361 i 411
seqpos R dfiseq R 361
seqpos R marker 362 i 412
seqpos R dfiseq R 362
seqpos N marker 363 i 413
seqpos N dfiseq N 363
seqpos H marker 364 i 414
seqpos H dfiseq H 364
seqpos S marker 365 i 415
seqpos S dfiseq S 365
seqpos W marker 366 i 416
seqpos W dfiseq W 366
seqpos Y marker 367 i 417
seqpos Y dfiseq Y 367
seqpos G marker 368 i 418
seqpos G dfiseq G 368
seqpos I marker 369 i 419
seqpos I dfiseq I 369
seqpos G marker 370 i 420
seqpos G dfiseq G 370
seqpos H marker 371 i 421
seqpos H dfiseq H 371
seqpos F marker 372 i 422
seqpos F dfiseq F 372
seqpos C marker 373 i 423
seqpos C dfiseq C 373
seqpos R marker 374 i 424
seqpos R dfiseq R 374
seqpos Y marker 375 i 425
seqpos Y dfiseq Y 375
seqpos V marker 376 i 426
seqpos V dfiseq V 376
seqpos R marker 377 i 427
seqpos R dfiseq R 377
seqpos P marker 378 i 428
seqpos P dfiseq P 378
seqpos G marker 379 i 429
seqpos G dfiseq G 379
seqpos A marker 380 i 430
seqpos A dfiseq A 380
seqpos - marker 381 i 431
seqpos - insertion
seqpos R marker 381 i 432
seqpos R dfiseq R 381
seqpos V marker 382 i 433
seqpos V dfiseq V 382
seqpos M marker 383 i 434
seqpos M dfiseq M 383
seqpos L marker 384 i 435
seqpos L dfiseq L 384
seqpos S marker 385 i 436
seqpos S dfiseq S 385
seqpos S marker 386 i 437
seqpos S dfiseq S 386
seqpos S marker 387 i 438
seqpos S dfiseq S 387
seqpos Y marker 388 i 439
seqpos Y dfiseq Y 388
seqpos D marker 389 i 440
seqpos D dfiseq D 389
seqpos N marker 390 i 441
seqpos N dfiseq N 390
seqpos L marker 391 i 442
seqpos L dfiseq L 391
seqpos L marker 392 i 443
seqpos L dfiseq L 392
seqpos E marker 393 i 444
seqpos E dfiseq E 393
seqpos E marker 394 i 445
seqpos E dfiseq E 394
seqpos V marker 395 i 446
seqpos V dfiseq V 395
seqpos G marker 396 i 447
seqpos G dfiseq G 396
seqpos F marker 397 i 448
seqpos F dfiseq F 397
seqpos V marker 398 i 449
seqpos V dfiseq V 398
seqpos N marker 399 i 450
seqpos N dfiseq N 399
seqpos P marker 400 i 451
seqpos P dfiseq P 400
seqpos D marker 401 i 452
seqpos D dfiseq D 401
seqpos G marker 402 i 453
seqpos G dfiseq G 402
seqpos E marker 403 i 454
seqpos E dfiseq E 403
seqpos R marker 404 i 455
seqpos R dfiseq R 404
seqpos V marker 405 i 456
seqpos V dfiseq V 405
seqpos L marker 406 i 457
seqpos L dfiseq L 406
seqpos V marker 407 i 458
seqpos V dfiseq V 407
seqpos V marker 408 i 459
seqpos V dfiseq V 408
seqpos Y marker 409 i 460
seqpos Y dfiseq Y 409
seqpos N marker 410 i 461
seqpos N dfiseq N 410
seqpos R marker 411 i 462
seqpos R dfiseq R 411
seqpos D marker 412 i 463
seqpos D dfiseq D 412
seqpos V marker 413 i 464
seqpos V dfiseq V 413
seqpos Q marker 414 i 465
seqpos Q dfiseq Q 414
seqpos E marker 415 i 466
seqpos E dfiseq E 415
seqpos R marker 416 i 467
seqpos R dfiseq R 416
seqpos R marker 417 i 468
seqpos R dfiseq R 417
seqpos C marker 418 i 469
seqpos C dfiseq C 418
seqpos R marker 419 i 470
seqpos R dfiseq R 419
seqpos V marker 420 i 471
seqpos V dfiseq V 420
seqpos L marker 421 i 472
seqpos L dfiseq L 421
seqpos D marker 422 i 473
seqpos D dfiseq D 422
seqpos G marker 423 i 474
seqpos G dfiseq G 423
seqpos D marker 424 i 475
seqpos D dfiseq D 424
seqpos K marker 425 i 476
seqpos K dfiseq K 425
seqpos E marker 426 i 477
seqpos E dfiseq E 426
seqpos I marker 427 i 478
seqpos I dfiseq I 427
seqpos A marker 428 i 479
seqpos A dfiseq A 428
seqpos L marker 429 i 480
seqpos L dfiseq L 429
seqpos T marker 430 i 481
seqpos T dfiseq T 430
seqpos L marker 431 i 482
seqpos L dfiseq L 431
seqpos - marker 432 i 483
seqpos - insertion
seqpos P marker 432 i 484
seqpos P dfiseq P 432
seqpos P marker 433 i 485
seqpos P dfiseq P 433
seqpos S marker 434 i 486
seqpos S dfiseq S 434
seqpos G marker 435 i 487
seqpos G dfiseq G 435
seqpos A marker 436 i 488
seqpos A dfiseq A 436
seqpos S marker 437 i 489
seqpos S dfiseq S 437
seqpos T marker 438 i 490
seqpos T dfiseq T 438
seqpos L marker 439 i 491
seqpos L dfiseq L 439
seqpos L marker 440 i 492
seqpos L dfiseq L 440
seqpos W marker 441 i 493
seqpos W dfiseq W 441
seqpos R marker 442 i 494
seqpos R dfiseq R 442
seqpos Q marker 443 i 495
seqpos Q dfiseq Q 443
seqpos E marker 444 i 496
seqpos E dfiseq E 444
1OGS
len(ls_dfiseq) 497 len(ls_seq) 497 no_gap_seq 497 497
seqpos A marker 0 i 0
seqpos A dfiseq A 0
seqpos R marker 1 i 1
seqpos R dfiseq R 1
seqpos P marker 2 i 2
seqpos P dfiseq P 2
seqpos C marker 3 i 3
seqpos C dfiseq C 3
seqpos I marker 4 i 4
seqpos I dfiseq I 4
seqpos P marker 5 i 5
seqpos P dfiseq P 5
seqpos K marker 6 i 6
seqpos K dfiseq K 6
seqpos S marker 7 i 7
seqpos S dfiseq S 7
seqpos F marker 8 i 8
seqpos F dfiseq F 8
seqpos G marker 9 i 9
seqpos G dfiseq G 9
seqpos Y marker 10 i 10
seqpos Y dfiseq Y 10
seqpos S marker 11 i 11
seqpos S dfiseq S 11
seqpos S marker 12 i 12
seqpos S dfiseq S 12
seqpos V marker 13 i 13
seqpos V dfiseq V 13
seqpos V marker 14 i 14
seqpos V dfiseq V 14
seqpos C marker 15 i 15
seqpos C dfiseq C 15
seqpos V marker 16 i 16
seqpos V dfiseq V 16
seqpos C marker 17 i 17
seqpos C dfiseq C 17
seqpos N marker 18 i 18
seqpos N dfiseq N 18
seqpos A marker 19 i 19
seqpos A dfiseq A 19
seqpos T marker 20 i 20
seqpos T dfiseq T 20
seqpos Y marker 21 i 21
seqpos Y dfiseq Y 21
seqpos C marker 22 i 22
seqpos C dfiseq C 22
seqpos D marker 23 i 23
seqpos D dfiseq D 23
seqpos S marker 24 i 24
seqpos S dfiseq S 24
seqpos F marker 25 i 25
seqpos F dfiseq F 25
seqpos D marker 26 i 26
seqpos D dfiseq D 26
seqpos P marker 27 i 27
seqpos P dfiseq P 27
seqpos P marker 28 i 28
seqpos P dfiseq P 28
seqpos T marker 29 i 29
seqpos T dfiseq T 29
seqpos F marker 30 i 30
seqpos F dfiseq F 30
seqpos P marker 31 i 31
seqpos P dfiseq P 31
seqpos A marker 32 i 32
seqpos A dfiseq A 32
seqpos L marker 33 i 33
seqpos L dfiseq L 33
seqpos G marker 34 i 34
seqpos G dfiseq G 34
seqpos T marker 35 i 35
seqpos T dfiseq T 35
seqpos F marker 36 i 36
seqpos F dfiseq F 36
seqpos S marker 37 i 37
seqpos S dfiseq S 37
seqpos R marker 38 i 38
seqpos R dfiseq R 38
seqpos Y marker 39 i 39
seqpos Y dfiseq Y 39
seqpos E marker 40 i 40
seqpos E dfiseq E 40
seqpos S marker 41 i 41
seqpos S dfiseq S 41
seqpos T marker 42 i 42
seqpos T dfiseq T 42
seqpos R marker 43 i 43
seqpos R dfiseq R 43
seqpos S marker 44 i 44
seqpos S dfiseq S 44
seqpos G marker 45 i 45
seqpos G dfiseq G 45
seqpos R marker 46 i 46
seqpos R dfiseq R 46
seqpos R marker 47 i 47
seqpos R dfiseq R 47
seqpos M marker 48 i 48
seqpos M dfiseq M 48
seqpos E marker 49 i 49
seqpos E dfiseq E 49
seqpos L marker 50 i 50
seqpos L dfiseq L 50
seqpos S marker 51 i 51
seqpos S dfiseq S 51
seqpos M marker 52 i 52
seqpos M dfiseq M 52
seqpos G marker 53 i 53
seqpos G dfiseq G 53
seqpos P marker 54 i 54
seqpos P dfiseq P 54
seqpos I marker 55 i 55
seqpos I dfiseq I 55
seqpos Q marker 56 i 56
seqpos Q dfiseq Q 56
seqpos A marker 57 i 57
seqpos A dfiseq A 57
seqpos N marker 58 i 58
seqpos N dfiseq N 58
seqpos H marker 59 i 59
seqpos H dfiseq H 59
seqpos T marker 60 i 60
seqpos T dfiseq T 60
seqpos G marker 61 i 61
seqpos G dfiseq G 61
seqpos T marker 62 i 62
seqpos T dfiseq T 62
seqpos G marker 63 i 63
seqpos G dfiseq G 63
seqpos L marker 64 i 64
seqpos L dfiseq L 64
seqpos L marker 65 i 65
seqpos L dfiseq L 65
seqpos L marker 66 i 66
seqpos L dfiseq L 66
seqpos T marker 67 i 67
seqpos T dfiseq T 67
seqpos L marker 68 i 68
seqpos L dfiseq L 68
seqpos Q marker 69 i 69
seqpos Q dfiseq Q 69
seqpos P marker 70 i 70
seqpos P dfiseq P 70
seqpos E marker 71 i 71
seqpos E dfiseq E 71
seqpos Q marker 72 i 72
seqpos Q dfiseq Q 72
seqpos K marker 73 i 73
seqpos K dfiseq K 73
seqpos F marker 74 i 74
seqpos F dfiseq F 74
seqpos Q marker 75 i 75
seqpos Q dfiseq Q 75
seqpos K marker 76 i 76
seqpos K dfiseq K 76
seqpos V marker 77 i 77
seqpos V dfiseq V 77
seqpos K marker 78 i 78
seqpos K dfiseq K 78
seqpos G marker 79 i 79
seqpos G dfiseq G 79
seqpos F marker 80 i 80
seqpos F dfiseq F 80
seqpos G marker 81 i 81
seqpos G dfiseq G 81
seqpos G marker 82 i 82
seqpos G dfiseq G 82
seqpos A marker 83 i 83
seqpos A dfiseq A 83
seqpos M marker 84 i 84
seqpos M dfiseq M 84
seqpos T marker 85 i 85
seqpos T dfiseq T 85
seqpos D marker 86 i 86
seqpos D dfiseq D 86
seqpos A marker 87 i 87
seqpos A dfiseq A 87
seqpos A marker 88 i 88
seqpos A dfiseq A 88
seqpos A marker 89 i 89
seqpos A dfiseq A 89
seqpos L marker 90 i 90
seqpos L dfiseq L 90
seqpos N marker 91 i 91
seqpos N dfiseq N 91
seqpos I marker 92 i 92
seqpos I dfiseq I 92
seqpos L marker 93 i 93
seqpos L dfiseq L 93
seqpos A marker 94 i 94
seqpos A dfiseq A 94
seqpos L marker 95 i 95
seqpos L dfiseq L 95
seqpos S marker 96 i 96
seqpos S dfiseq S 96
seqpos P marker 97 i 97
seqpos P dfiseq P 97
seqpos P marker 98 i 98
seqpos P dfiseq P 98
seqpos A marker 99 i 99
seqpos A dfiseq A 99
seqpos Q marker 100 i 100
seqpos Q dfiseq Q 100
seqpos N marker 101 i 101
seqpos N dfiseq N 101
seqpos L marker 102 i 102
seqpos L dfiseq L 102
seqpos L marker 103 i 103
seqpos L dfiseq L 103
seqpos L marker 104 i 104
seqpos L dfiseq L 104
seqpos K marker 105 i 105
seqpos K dfiseq K 105
seqpos S marker 106 i 106
seqpos S dfiseq S 106
seqpos Y marker 107 i 107
seqpos Y dfiseq Y 107
seqpos F marker 108 i 108
seqpos F dfiseq F 108
seqpos S marker 109 i 109
seqpos S dfiseq S 109
seqpos E marker 110 i 110
seqpos E dfiseq E 110
seqpos E marker 111 i 111
seqpos E dfiseq E 111
seqpos G marker 112 i 112
seqpos G dfiseq G 112
seqpos I marker 113 i 113
seqpos I dfiseq I 113
seqpos G marker 114 i 114
seqpos G dfiseq G 114
seqpos Y marker 115 i 115
seqpos Y dfiseq Y 115
seqpos N marker 116 i 116
seqpos N dfiseq N 116
seqpos I marker 117 i 117
seqpos I dfiseq I 117
seqpos I marker 118 i 118
seqpos I dfiseq I 118
seqpos R marker 119 i 119
seqpos R dfiseq R 119
seqpos V marker 120 i 120
seqpos V dfiseq V 120
seqpos P marker 121 i 121
seqpos P dfiseq P 121
seqpos M marker 122 i 122
seqpos M dfiseq M 122
seqpos A marker 123 i 123
seqpos A dfiseq A 123
seqpos S marker 124 i 124
seqpos S dfiseq S 124
seqpos C marker 125 i 125
seqpos C dfiseq C 125
seqpos D marker 126 i 126
seqpos D dfiseq D 126
seqpos F marker 127 i 127
seqpos F dfiseq F 127
seqpos S marker 128 i 128
seqpos S dfiseq S 128
seqpos I marker 129 i 129
seqpos I dfiseq I 129
seqpos R marker 130 i 130
seqpos R dfiseq R 130
seqpos T marker 131 i 131
seqpos T dfiseq T 131
seqpos Y marker 132 i 132
seqpos Y dfiseq Y 132
seqpos T marker 133 i 133
seqpos T dfiseq T 133
seqpos Y marker 134 i 134
seqpos Y dfiseq Y 134
seqpos A marker 135 i 135
seqpos A dfiseq A 135
seqpos D marker 136 i 136
seqpos D dfiseq D 136
seqpos T marker 137 i 137
seqpos T dfiseq T 137
seqpos P marker 138 i 138
seqpos P dfiseq P 138
seqpos D marker 139 i 139
seqpos D dfiseq D 139
seqpos D marker 140 i 140
seqpos D dfiseq D 140
seqpos F marker 141 i 141
seqpos F dfiseq F 141
seqpos Q marker 142 i 142
seqpos Q dfiseq Q 142
seqpos L marker 143 i 143
seqpos L dfiseq L 143
seqpos H marker 144 i 144
seqpos H dfiseq H 144
seqpos N marker 145 i 145
seqpos N dfiseq N 145
seqpos F marker 146 i 146
seqpos F dfiseq F 146
seqpos S marker 147 i 147
seqpos S dfiseq S 147
seqpos L marker 148 i 148
seqpos L dfiseq L 148
seqpos P marker 149 i 149
seqpos P dfiseq P 149
seqpos E marker 150 i 150
seqpos E dfiseq E 150
seqpos E marker 151 i 151
seqpos E dfiseq E 151
seqpos D marker 152 i 152
seqpos D dfiseq D 152
seqpos T marker 153 i 153
seqpos T dfiseq T 153
seqpos K marker 154 i 154
seqpos K dfiseq K 154
seqpos L marker 155 i 155
seqpos L dfiseq L 155
seqpos K marker 156 i 156
seqpos K dfiseq K 156
seqpos I marker 157 i 157
seqpos I dfiseq I 157
seqpos P marker 158 i 158
seqpos P dfiseq P 158
seqpos L marker 159 i 159
seqpos L dfiseq L 159
seqpos I marker 160 i 160
seqpos I dfiseq I 160
seqpos H marker 161 i 161
seqpos H dfiseq H 161
seqpos R marker 162 i 162
seqpos R dfiseq R 162
seqpos A marker 163 i 163
seqpos A dfiseq A 163
seqpos L marker 164 i 164
seqpos L dfiseq L 164
seqpos Q marker 165 i 165
seqpos Q dfiseq Q 165
seqpos L marker 166 i 166
seqpos L dfiseq L 166
seqpos A marker 167 i 167
seqpos A dfiseq A 167
seqpos Q marker 168 i 168
seqpos Q dfiseq Q 168
seqpos R marker 169 i 169
seqpos R dfiseq R 169
seqpos P marker 170 i 170
seqpos P dfiseq P 170
seqpos V marker 171 i 171
seqpos V dfiseq V 171
seqpos S marker 172 i 172
seqpos S dfiseq S 172
seqpos L marker 173 i 173
seqpos L dfiseq L 173
seqpos L marker 174 i 174
seqpos L dfiseq L 174
seqpos A marker 175 i 175
seqpos A dfiseq A 175
seqpos S marker 176 i 176
seqpos S dfiseq S 176
seqpos P marker 177 i 177
seqpos P dfiseq P 177
seqpos W marker 178 i 178
seqpos W dfiseq W 178
seqpos T marker 179 i 179
seqpos T dfiseq T 179
seqpos S marker 180 i 180
seqpos S dfiseq S 180
seqpos P marker 181 i 181
seqpos P dfiseq P 181
seqpos T marker 182 i 182
seqpos T dfiseq T 182
seqpos W marker 183 i 183
seqpos W dfiseq W 183
seqpos L marker 184 i 184
seqpos L dfiseq L 184
seqpos K marker 185 i 185
seqpos K dfiseq K 185
seqpos T marker 186 i 186
seqpos T dfiseq T 186
seqpos N marker 187 i 187
seqpos N dfiseq N 187
seqpos G marker 188 i 188
seqpos G dfiseq G 188
seqpos A marker 189 i 189
seqpos A dfiseq A 189
seqpos V marker 190 i 190
seqpos V dfiseq V 190
seqpos N marker 191 i 191
seqpos N dfiseq N 191
seqpos G marker 192 i 192
seqpos G dfiseq G 192
seqpos K marker 193 i 193
seqpos K dfiseq K 193
seqpos G marker 194 i 194
seqpos G dfiseq G 194
seqpos S marker 195 i 195
seqpos S dfiseq S 195
seqpos L marker 196 i 196
seqpos L dfiseq L 196
seqpos K marker 197 i 197
seqpos K dfiseq K 197
seqpos G marker 198 i 198
seqpos G dfiseq G 198
seqpos Q marker 199 i 199
seqpos Q dfiseq Q 199
seqpos P marker 200 i 200
seqpos P dfiseq P 200
seqpos G marker 201 i 201
seqpos G dfiseq G 201
seqpos D marker 202 i 202
seqpos D dfiseq D 202
seqpos I marker 203 i 203
seqpos I dfiseq I 203
seqpos Y marker 204 i 204
seqpos Y dfiseq Y 204
seqpos H marker 205 i 205
seqpos H dfiseq H 205
seqpos Q marker 206 i 206
seqpos Q dfiseq Q 206
seqpos T marker 207 i 207
seqpos T dfiseq T 207
seqpos W marker 208 i 208
seqpos W dfiseq W 208
seqpos A marker 209 i 209
seqpos A dfiseq A 209
seqpos R marker 210 i 210
seqpos R dfiseq R 210
seqpos Y marker 211 i 211
seqpos Y dfiseq Y 211
seqpos F marker 212 i 212
seqpos F dfiseq F 212
seqpos V marker 213 i 213
seqpos V dfiseq V 213
seqpos K marker 214 i 214
seqpos K dfiseq K 214
seqpos F marker 215 i 215
seqpos F dfiseq F 215
seqpos L marker 216 i 216
seqpos L dfiseq L 216
seqpos D marker 217 i 217
seqpos D dfiseq D 217
seqpos A marker 218 i 218
seqpos A dfiseq A 218
seqpos Y marker 219 i 219
seqpos Y dfiseq Y 219
seqpos A marker 220 i 220
seqpos A dfiseq A 220
seqpos E marker 221 i 221
seqpos E dfiseq E 221
seqpos H marker 222 i 222
seqpos H dfiseq H 222
seqpos K marker 223 i 223
seqpos K dfiseq K 223
seqpos L marker 224 i 224
seqpos L dfiseq L 224
seqpos Q marker 225 i 225
seqpos Q dfiseq Q 225
seqpos F marker 226 i 226
seqpos F dfiseq F 226
seqpos W marker 227 i 227
seqpos W dfiseq W 227
seqpos A marker 228 i 228
seqpos A dfiseq A 228
seqpos V marker 229 i 229
seqpos V dfiseq V 229
seqpos T marker 230 i 230
seqpos T dfiseq T 230
seqpos A marker 231 i 231
seqpos A dfiseq A 231
seqpos E marker 232 i 232
seqpos E dfiseq E 232
seqpos N marker 233 i 233
seqpos N dfiseq N 233
seqpos E marker 234 i 234
seqpos E dfiseq E 234
seqpos P marker 235 i 235
seqpos P dfiseq P 235
seqpos S marker 236 i 236
seqpos S dfiseq S 236
seqpos A marker 237 i 237
seqpos A dfiseq A 237
seqpos G marker 238 i 238
seqpos G dfiseq G 238
seqpos L marker 239 i 239
seqpos L dfiseq L 239
seqpos L marker 240 i 240
seqpos L dfiseq L 240
seqpos S marker 241 i 241
seqpos S dfiseq S 241
seqpos G marker 242 i 242
seqpos G dfiseq G 242
seqpos Y marker 243 i 243
seqpos Y dfiseq Y 243
seqpos P marker 244 i 244
seqpos P dfiseq P 244
seqpos F marker 245 i 245
seqpos F dfiseq F 245
seqpos Q marker 246 i 246
seqpos Q dfiseq Q 246
seqpos C marker 247 i 247
seqpos C dfiseq C 247
seqpos L marker 248 i 248
seqpos L dfiseq L 248
seqpos G marker 249 i 249
seqpos G dfiseq G 249
seqpos F marker 250 i 250
seqpos F dfiseq F 250
seqpos T marker 251 i 251
seqpos T dfiseq T 251
seqpos P marker 252 i 252
seqpos P dfiseq P 252
seqpos E marker 253 i 253
seqpos E dfiseq E 253
seqpos H marker 254 i 254
seqpos H dfiseq H 254
seqpos Q marker 255 i 255
seqpos Q dfiseq Q 255
seqpos R marker 256 i 256
seqpos R dfiseq R 256
seqpos D marker 257 i 257
seqpos D dfiseq D 257
seqpos F marker 258 i 258
seqpos F dfiseq F 258
seqpos I marker 259 i 259
seqpos I dfiseq I 259
seqpos A marker 260 i 260
seqpos A dfiseq A 260
seqpos R marker 261 i 261
seqpos R dfiseq R 261
seqpos D marker 262 i 262
seqpos D dfiseq D 262
seqpos L marker 263 i 263
seqpos L dfiseq L 263
seqpos G marker 264 i 264
seqpos G dfiseq G 264
seqpos P marker 265 i 265
seqpos P dfiseq P 265
seqpos T marker 266 i 266
seqpos T dfiseq T 266
seqpos L marker 267 i 267
seqpos L dfiseq L 267
seqpos A marker 268 i 268
seqpos A dfiseq A 268
seqpos N marker 269 i 269
seqpos N dfiseq N 269
seqpos S marker 270 i 270
seqpos S dfiseq S 270
seqpos T marker 271 i 271
seqpos T dfiseq T 271
seqpos H marker 272 i 272
seqpos H dfiseq H 272
seqpos H marker 273 i 273
seqpos H dfiseq H 273
seqpos N marker 274 i 274
seqpos N dfiseq N 274
seqpos V marker 275 i 275
seqpos V dfiseq V 275
seqpos R marker 276 i 276
seqpos R dfiseq R 276
seqpos L marker 277 i 277
seqpos L dfiseq L 277
seqpos L marker 278 i 278
seqpos L dfiseq L 278
seqpos M marker 279 i 279
seqpos M dfiseq M 279
seqpos L marker 280 i 280
seqpos L dfiseq L 280
seqpos D marker 281 i 281
seqpos D dfiseq D 281
seqpos D marker 282 i 282
seqpos D dfiseq D 282
seqpos Q marker 283 i 283
seqpos Q dfiseq Q 283
seqpos R marker 284 i 284
seqpos R dfiseq R 284
seqpos L marker 285 i 285
seqpos L dfiseq L 285
seqpos L marker 286 i 286
seqpos L dfiseq L 286
seqpos L marker 287 i 287
seqpos L dfiseq L 287
seqpos P marker 288 i 288
seqpos P dfiseq P 288
seqpos H marker 289 i 289
seqpos H dfiseq H 289
seqpos W marker 290 i 290
seqpos W dfiseq W 290
seqpos A marker 291 i 291
seqpos A dfiseq A 291
seqpos K marker 292 i 292
seqpos K dfiseq K 292
seqpos V marker 293 i 293
seqpos V dfiseq V 293
seqpos V marker 294 i 294
seqpos V dfiseq V 294
seqpos L marker 295 i 295
seqpos L dfiseq L 295
seqpos T marker 296 i 296
seqpos T dfiseq T 296
seqpos D marker 297 i 297
seqpos D dfiseq D 297
seqpos P marker 298 i 298
seqpos P dfiseq P 298
seqpos E marker 299 i 299
seqpos E dfiseq E 299
seqpos A marker 300 i 300
seqpos A dfiseq A 300
seqpos A marker 301 i 301
seqpos A dfiseq A 301
seqpos K marker 302 i 302
seqpos K dfiseq K 302
seqpos Y marker 303 i 303
seqpos Y dfiseq Y 303
seqpos V marker 304 i 304
seqpos V dfiseq V 304
seqpos H marker 305 i 305
seqpos H dfiseq H 305
seqpos G marker 306 i 306
seqpos G dfiseq G 306
seqpos I marker 307 i 307
seqpos I dfiseq I 307
seqpos A marker 308 i 308
seqpos A dfiseq A 308
seqpos V marker 309 i 309
seqpos V dfiseq V 309
seqpos H marker 310 i 310
seqpos H dfiseq H 310
seqpos W marker 311 i 311
seqpos W dfiseq W 311
seqpos Y marker 312 i 312
seqpos Y dfiseq Y 312
seqpos L marker 313 i 313
seqpos L dfiseq L 313
seqpos D marker 314 i 314
seqpos D dfiseq D 314
seqpos F marker 315 i 315
seqpos F dfiseq F 315
seqpos L marker 316 i 316
seqpos L dfiseq L 316
seqpos A marker 317 i 317
seqpos A dfiseq A 317
seqpos P marker 318 i 318
seqpos P dfiseq P 318
seqpos A marker 319 i 319
seqpos A dfiseq A 319
seqpos K marker 320 i 320
seqpos K dfiseq K 320
seqpos A marker 321 i 321
seqpos A dfiseq A 321
seqpos T marker 322 i 322
seqpos T dfiseq T 322
seqpos L marker 323 i 323
seqpos L dfiseq L 323
seqpos G marker 324 i 324
seqpos G dfiseq G 324
seqpos E marker 325 i 325
seqpos E dfiseq E 325
seqpos T marker 326 i 326
seqpos T dfiseq T 326
seqpos H marker 327 i 327
seqpos H dfiseq H 327
seqpos R marker 328 i 328
seqpos R dfiseq R 328
seqpos L marker 329 i 329
seqpos L dfiseq L 329
seqpos F marker 330 i 330
seqpos F dfiseq F 330
seqpos P marker 331 i 331
seqpos P dfiseq P 331
seqpos N marker 332 i 332
seqpos N dfiseq N 332
seqpos T marker 333 i 333
seqpos T dfiseq T 333
seqpos M marker 334 i 334
seqpos M dfiseq M 334
seqpos L marker 335 i 335
seqpos L dfiseq L 335
seqpos F marker 336 i 336
seqpos F dfiseq F 336
seqpos A marker 337 i 337
seqpos A dfiseq A 337
seqpos S marker 338 i 338
seqpos S dfiseq S 338
seqpos E marker 339 i 339
seqpos E dfiseq E 339
seqpos A marker 340 i 340
seqpos A dfiseq A 340
seqpos C marker 341 i 341
seqpos C dfiseq C 341
seqpos V marker 342 i 342
seqpos V dfiseq V 342
seqpos G marker 343 i 343
seqpos G dfiseq G 343
seqpos S marker 344 i 344
seqpos S dfiseq S 344
seqpos K marker 345 i 345
seqpos K dfiseq K 345
seqpos F marker 346 i 346
seqpos F dfiseq F 346
seqpos W marker 347 i 347
seqpos W dfiseq W 347
seqpos E marker 348 i 348
seqpos E dfiseq E 348
seqpos Q marker 349 i 349
seqpos Q dfiseq Q 349
seqpos S marker 350 i 350
seqpos S dfiseq S 350
seqpos V marker 351 i 351
seqpos V dfiseq V 351
seqpos R marker 352 i 352
seqpos R dfiseq R 352
seqpos L marker 353 i 353
seqpos L dfiseq L 353
seqpos G marker 354 i 354
seqpos G dfiseq G 354
seqpos S marker 355 i 355
seqpos S dfiseq S 355
seqpos W marker 356 i 356
seqpos W dfiseq W 356
seqpos D marker 357 i 357
seqpos D dfiseq D 357
seqpos R marker 358 i 358
seqpos R dfiseq R 358
seqpos G marker 359 i 359
seqpos G dfiseq G 359
seqpos M marker 360 i 360
seqpos M dfiseq M 360
seqpos Q marker 361 i 361
seqpos Q dfiseq Q 361
seqpos Y marker 362 i 362
seqpos Y dfiseq Y 362
seqpos S marker 363 i 363
seqpos S dfiseq S 363
seqpos H marker 364 i 364
seqpos H dfiseq H 364
seqpos S marker 365 i 365
seqpos S dfiseq S 365
seqpos I marker 366 i 366
seqpos I dfiseq I 366
seqpos I marker 367 i 367
seqpos I dfiseq I 367
seqpos T marker 368 i 368
seqpos T dfiseq T 368
seqpos N marker 369 i 369
seqpos N dfiseq N 369
seqpos L marker 370 i 370
seqpos L dfiseq L 370
seqpos L marker 371 i 371
seqpos L dfiseq L 371
seqpos Y marker 372 i 372
seqpos Y dfiseq Y 372
seqpos H marker 373 i 373
seqpos H dfiseq H 373
seqpos V marker 374 i 374
seqpos V dfiseq V 374
seqpos V marker 375 i 375
seqpos V dfiseq V 375
seqpos G marker 376 i 376
seqpos G dfiseq G 376
seqpos W marker 377 i 377
seqpos W dfiseq W 377
seqpos T marker 378 i 378
seqpos T dfiseq T 378
seqpos D marker 379 i 379
seqpos D dfiseq D 379
seqpos W marker 380 i 380
seqpos W dfiseq W 380
seqpos N marker 381 i 381
seqpos N dfiseq N 381
seqpos L marker 382 i 382
seqpos L dfiseq L 382
seqpos A marker 383 i 383
seqpos A dfiseq A 383
seqpos L marker 384 i 384
seqpos L dfiseq L 384
seqpos N marker 385 i 385
seqpos N dfiseq N 385
seqpos P marker 386 i 386
seqpos P dfiseq P 386
seqpos E marker 387 i 387
seqpos E dfiseq E 387
seqpos G marker 388 i 388
seqpos G dfiseq G 388
seqpos G marker 389 i 389
seqpos G dfiseq G 389
seqpos P marker 390 i 390
seqpos P dfiseq P 390
seqpos N marker 391 i 391
seqpos N dfiseq N 391
seqpos W marker 392 i 392
seqpos W dfiseq W 392
seqpos V marker 393 i 393
seqpos V dfiseq V 393
seqpos R marker 394 i 394
seqpos R dfiseq R 394
seqpos N marker 395 i 395
seqpos N dfiseq N 395
seqpos F marker 396 i 396
seqpos F dfiseq F 396
seqpos V marker 397 i 397
seqpos V dfiseq V 397
seqpos D marker 398 i 398
seqpos D dfiseq D 398
seqpos S marker 399 i 399
seqpos S dfiseq S 399
seqpos P marker 400 i 400
seqpos P dfiseq P 400
seqpos I marker 401 i 401
seqpos I dfiseq I 401
seqpos I marker 402 i 402
seqpos I dfiseq I 402
seqpos V marker 403 i 403
seqpos V dfiseq V 403
seqpos D marker 404 i 404
seqpos D dfiseq D 404
seqpos I marker 405 i 405
seqpos I dfiseq I 405
seqpos T marker 406 i 406
seqpos T dfiseq T 406
seqpos K marker 407 i 407
seqpos K dfiseq K 407
seqpos D marker 408 i 408
seqpos D dfiseq D 408
seqpos T marker 409 i 409
seqpos T dfiseq T 409
seqpos F marker 410 i 410
seqpos F dfiseq F 410
seqpos Y marker 411 i 411
seqpos Y dfiseq Y 411
seqpos K marker 412 i 412
seqpos K dfiseq K 412
seqpos Q marker 413 i 413
seqpos Q dfiseq Q 413
seqpos P marker 414 i 414
seqpos P dfiseq P 414
seqpos M marker 415 i 415
seqpos M dfiseq M 415
seqpos F marker 416 i 416
seqpos F dfiseq F 416
seqpos Y marker 417 i 417
seqpos Y dfiseq Y 417
seqpos H marker 418 i 418
seqpos H dfiseq H 418
seqpos L marker 419 i 419
seqpos L dfiseq L 419
seqpos G marker 420 i 420
seqpos G dfiseq G 420
seqpos H marker 421 i 421
seqpos H dfiseq H 421
seqpos F marker 422 i 422
seqpos F dfiseq F 422
seqpos S marker 423 i 423
seqpos S dfiseq S 423
seqpos K marker 424 i 424
seqpos K dfiseq K 424
seqpos F marker 425 i 425
seqpos F dfiseq F 425
seqpos I marker 426 i 426
seqpos I dfiseq I 426
seqpos P marker 427 i 427
seqpos P dfiseq P 427
seqpos E marker 428 i 428
seqpos E dfiseq E 428
seqpos G marker 429 i 429
seqpos G dfiseq G 429
seqpos S marker 430 i 430
seqpos S dfiseq S 430
seqpos Q marker 431 i 431
seqpos Q dfiseq Q 431
seqpos R marker 432 i 432
seqpos R dfiseq R 432
seqpos V marker 433 i 433
seqpos V dfiseq V 433
seqpos G marker 434 i 434
seqpos G dfiseq G 434
seqpos L marker 435 i 435
seqpos L dfiseq L 435
seqpos V marker 436 i 436
seqpos V dfiseq V 436
seqpos A marker 437 i 437
seqpos A dfiseq A 437
seqpos S marker 438 i 438
seqpos S dfiseq S 438
seqpos Q marker 439 i 439
seqpos Q dfiseq Q 439
seqpos K marker 440 i 440
seqpos K dfiseq K 440
seqpos N marker 441 i 441
seqpos N dfiseq N 441
seqpos D marker 442 i 442
seqpos D dfiseq D 442
seqpos L marker 443 i 443
seqpos L dfiseq L 443
seqpos D marker 444 i 444
seqpos D dfiseq D 444
seqpos A marker 445 i 445
seqpos A dfiseq A 445
seqpos V marker 446 i 446
seqpos V dfiseq V 446
seqpos A marker 447 i 447
seqpos A dfiseq A 447
seqpos L marker 448 i 448
seqpos L dfiseq L 448
seqpos M marker 449 i 449
seqpos M dfiseq M 449
seqpos H marker 450 i 450
seqpos H dfiseq H 450
seqpos P marker 451 i 451
seqpos P dfiseq P 451
seqpos D marker 452 i 452
seqpos D dfiseq D 452
seqpos G marker 453 i 453
seqpos G dfiseq G 453
seqpos S marker 454 i 454
seqpos S dfiseq S 454
seqpos A marker 455 i 455
seqpos A dfiseq A 455
seqpos V marker 456 i 456
seqpos V dfiseq V 456
seqpos V marker 457 i 457
seqpos V dfiseq V 457
seqpos V marker 458 i 458
seqpos V dfiseq V 458
seqpos V marker 459 i 459
seqpos V dfiseq V 459
seqpos L marker 460 i 460
seqpos L dfiseq L 460
seqpos N marker 461 i 461
seqpos N dfiseq N 461
seqpos R marker 462 i 462
seqpos R dfiseq R 462
seqpos S marker 463 i 463
seqpos S dfiseq S 463
seqpos S marker 464 i 464
seqpos S dfiseq S 464
seqpos K marker 465 i 465
seqpos K dfiseq K 465
seqpos D marker 466 i 466
seqpos D dfiseq D 466
seqpos V marker 467 i 467
seqpos V dfiseq V 467
seqpos P marker 468 i 468
seqpos P dfiseq P 468
seqpos L marker 469 i 469
seqpos L dfiseq L 469
seqpos T marker 470 i 470
seqpos T dfiseq T 470
seqpos I marker 471 i 471
seqpos I dfiseq I 471
seqpos K marker 472 i 472
seqpos K dfiseq K 472
seqpos D marker 473 i 473
seqpos D dfiseq D 473
seqpos P marker 474 i 474
seqpos P dfiseq P 474
seqpos A marker 475 i 475
seqpos A dfiseq A 475
seqpos V marker 476 i 476
seqpos V dfiseq V 476
seqpos G marker 477 i 477
seqpos G dfiseq G 477
seqpos F marker 478 i 478
seqpos F dfiseq F 478
seqpos L marker 479 i 479
seqpos L dfiseq L 479
seqpos E marker 480 i 480
seqpos E dfiseq E 480
seqpos T marker 481 i 481
seqpos T dfiseq T 481
seqpos I marker 482 i 482
seqpos I dfiseq I 482
seqpos S marker 483 i 483
seqpos S dfiseq S 483
seqpos P marker 484 i 484
seqpos P dfiseq P 484
seqpos G marker 485 i 485
seqpos G dfiseq G 485
seqpos Y marker 486 i 486
seqpos Y dfiseq Y 486
seqpos S marker 487 i 487
seqpos S dfiseq S 487
seqpos I marker 488 i 488
seqpos I dfiseq I 488
seqpos H marker 489 i 489
seqpos H dfiseq H 489
seqpos T marker 490 i 490
seqpos T dfiseq T 490
seqpos Y marker 491 i 491
seqpos Y dfiseq Y 491
seqpos L marker 492 i 492
seqpos L dfiseq L 492
seqpos W marker 493 i 493
seqpos W dfiseq W 493
seqpos H marker 494 i 494
seqpos H dfiseq H 494
seqpos R marker 495 i 495
seqpos R dfiseq R 495
seqpos Q marker 496 i 496
seqpos Q dfiseq Q 496
In [28]:
dfx.columns
Out[28]:
Index([u'2WNW_R', u'2WNW_pctdfi', u'1OGS_R', u'1OGS_pctdfi'], dtype='object')
In [29]:
dfx = dfx[~(dfx['2WNW_R'] == '-')]
In [30]:
dfx = dfx[~(dfx['1OGS_R'] == '-')]
In [31]:
dfx.T
Out[31]:
32
33
34
35
36
37
38
39
40
41
...
487
488
489
490
491
492
493
494
495
496
2WNW_R
M
K
G
R
L
I
S
S
D
P
...
G
A
S
T
L
L
W
R
Q
E
2WNW_pctdfi
0.970787
0.961798
0.910112
0.858427
0.683146
0.530337
0.460674
0.485393
0.685393
0.689888
...
0.552809
0.173034
0.123596
0.0629213
0.249438
0.54382
0.791011
0.865169
0.925843
0.979775
1OGS_R
A
L
G
T
F
S
R
Y
E
S
...
S
I
H
T
Y
L
W
H
R
Q
1OGS_pctdfi
0.977867
0.973843
0.975855
0.939638
0.812877
0.67002
0.420523
0.1167
0.102616
0.158954
...
0.301811
0.0684105
0.0301811
0.0201207
0.191147
0.44668
0.746479
0.881288
0.913481
0.979879
4 rows × 445 columns
In [32]:
dfx.head()
Out[32]:
2WNW_R
2WNW_pctdfi
1OGS_R
1OGS_pctdfi
32
M
0.970787
A
0.977867
33
K
0.961798
L
0.973843
34
G
0.910112
G
0.975855
35
R
0.858427
T
0.939638
36
L
0.683146
F
0.812877
In [33]:
dficols = [col for col in dfx.columns if '_pctdfi' in col]
In [56]:
dfidict['1OGS'][dfidict['1OGS'].ResI.isin([340,342,235])]
Out[56]:
ResI
chainID
Res
R
dfi
pctdfi
fdfi
pctfdfi
adfi
ravg
A
234
235
A
GLU
E
0.001380
0.213280
2.888694
0.993964
0.002012
8.023082
A
339
340
A
GLU
E
0.001306
0.160966
3.485464
0.997988
-0.002012
5.692670
NotA
341
342
A
CYS
C
0.001368
0.201207
5.581713
1.000000
0.004024
6.970116
NotA
In [59]:
dfx.ix[[234,339,341]]
Out[59]:
2WNW_R
2WNW_pctdfi
1OGS_R
1OGS_pctdfi
234
E
0.150562
E
0.213280
339
E
0.103371
E
0.160966
341
C
0.2
C
0.201207
In [60]:
dfidict['1OGS'][dfidict['1OGS'].ResI.isin([255,123,375])]
Out[60]:
ResI
chainID
Res
R
dfi
pctdfi
fdfi
pctfdfi
adfi
ravg
A
122
123
A
MET
M
0.000917
0.014085
0.711388
0.663984
-0.164990
15.879130
NotA
254
255
A
HIS
H
0.001847
0.521127
0.744313
0.692153
0.086519
20.885014
NotA
374
375
A
VAL
V
0.001774
0.482897
0.836093
0.808853
-0.024145
15.865680
A
In [62]:
dfx.ix[[122,254,374]]
Out[62]:
2WNW_R
2WNW_pctdfi
1OGS_R
1OGS_pctdfi
122
I
0.00898876
M
0.014085
254
E
0.393258
H
0.521127
374
C
0.402247
V
0.482897
In [66]:
dfx
Out[66]:
2WNW_R
2WNW_pctdfi
1OGS_R
1OGS_pctdfi
32
M
0.970787
A
0.977867
33
K
0.961798
L
0.973843
34
G
0.910112
G
0.975855
35
R
0.858427
T
0.939638
36
L
0.683146
F
0.812877
37
I
0.530337
S
0.670020
38
S
0.460674
R
0.420523
39
S
0.485393
Y
0.116700
40
D
0.685393
E
0.102616
41
P
0.689888
S
0.158954
42
Y
0.844944
T
0.311871
43
R
0.876404
R
0.454728
44
Q
0.838202
S
0.565392
45
Q
0.768539
G
0.474849
46
F
0.622472
R
0.374245
47
L
0.586517
R
0.235412
48
V
0.732584
M
0.122736
49
E
0.851685
E
0.285714
50
R
0.923596
L
0.478873
52
A
0.959551
M
0.859155
53
V
0.948315
G
0.933602
54
S
0.966292
P
0.969819
55
F
0.964045
I
0.957746
56
S
0.986517
Q
0.987928
57
H
0.991011
A
0.991952
58
R
0.988764
N
0.997988
59
Q
0.995506
H
0.993964
60
R
1
T
1.000000
61
D
0.997753
G
0.989940
62
C
0.993258
T
0.995976
...
...
...
...
...
466
E
0.919101
D
0.873239
467
R
0.901124
V
0.885312
468
R
0.914607
P
0.925553
469
C
0.898876
L
0.883300
470
R
0.91236
T
0.905433
471
V
0.831461
I
0.826962
472
L
0.903371
K
0.887324
473
D
0.896629
D
0.877264
474
G
0.957303
P
0.945674
475
D
0.982022
A
0.971831
476
K
0.968539
V
0.965795
477
E
0.94382
G
0.967807
478
I
0.937079
F
0.947686
479
A
0.939326
L
0.907445
480
L
0.889888
E
0.935614
481
T
0.892135
T
0.875252
482
L
0.750562
I
0.847082
484
P
0.849438
P
0.708249
485
P
0.853933
G
0.756539
486
S
0.694382
Y
0.617706
487
G
0.552809
S
0.301811
488
A
0.173034
I
0.068410
489
S
0.123596
H
0.030181
490
T
0.0629213
T
0.020121
491
L
0.249438
Y
0.191147
492
L
0.54382
L
0.446680
493
W
0.791011
W
0.746479
494
R
0.865169
H
0.881288
495
Q
0.925843
R
0.913481
496
E
0.979775
Q
0.979879
445 rows × 4 columns
In [44]:
sns.set_style('white')
plt.figure(figsize=(28, 12))
sns.set_context("poster", font_scale=1.5, rc={"lines.linewidth": 1.25,"lines.markersize":8})
dfx['2WNW_pctdfi'].plot(marker='o',label='2WNW',color='red')
dfx['1OGS_pctdfi'].plot(marker='o',label='1OGS',color='blue')
plt.legend(bbox_to_anchor=(0., 1.01, 1., .101), loc=7,ncol=4, borderaxespad=0.)
plt.ylabel('%DFI')
plt.xlabel('Residue Index')
Out[44]:
<matplotlib.text.Text at 0xab9a012c>
In [67]:
sns.set_style('white')
plt.figure(figsize=(28, 12))
sns.set_context("poster", font_scale=1.5, rc={"lines.linewidth": 1.25,"lines.markersize":8})
dfx[dficols].var(axis=1).plot(marker='o',linestyle='',color='black')
plt.ylabel('dev %DFI')
plt.xlabel('Residue Index')
Out[67]:
<matplotlib.text.Text at 0xab9eaaac>
In [35]:
def make_fafsta(name,df_dfi):
seq = ''.join(df_dfi.R.values)
print ">%s"%name
print seq
In [36]:
make_fafsta('2WNW',dfidict['2WNW'])
>2WNW
MKGRLISSDPYRQQFLVERAVSFSHRQRDCSELISVLPRHALQQIDGFGGSFTEGAGVVFNSMSEKTKAQFLSLYFSAQEHNYTLARMPIQSCDFSLGNYAYVDSSADLQQGRLSFSRDEAHLIPLISGALRLNPHMKLMASPWSPPAFMKTNNDMNGGGKLRRECYADWADIIINYLLEYRRHGINVQALSVQNEPVAVKTWDSCLYSVEEETAFAVQYLRPRLARQGMDEMEIYIWDHDKDGLVDWAELAFADEANYKGINGLAFHWYTGDHFSQIQYLAQCLPDKKLLFSEGCVPMESDAGSQIRHWHTYLHDMIGNFKSGCSGFIDWNLLLNSEGGPNHQGNLCEAPIQYDAQNDVLRRNHSWYGIGHFCRYVRPGARVMLSSSYDNLLEEVGFVNPDGERVLVVYNRDVQERRCRVLDGDKEIALTLPPSGASTLLWRQE
In [37]:
make_fafsta('1OGS',dfidict['1OGS'])
>1OGS
ARPCIPKSFGYSSVVCVCNATYCDSFDPPTFPALGTFSRYESTRSGRRMELSMGPIQANHTGTGLLLTLQPEQKFQKVKGFGGAMTDAAALNILALSPPAQNLLLKSYFSEEGIGYNIIRVPMASCDFSIRTYTYADTPDDFQLHNFSLPEEDTKLKIPLIHRALQLAQRPVSLLASPWTSPTWLKTNGAVNGKGSLKGQPGDIYHQTWARYFVKFLDAYAEHKLQFWAVTAENEPSAGLLSGYPFQCLGFTPEHQRDFIARDLGPTLANSTHHNVRLLMLDDQRLLLPHWAKVVLTDPEAAKYVHGIAVHWYLDFLAPAKATLGETHRLFPNTMLFASEACVGSKFWEQSVRLGSWDRGMQYSHSIITNLLYHVVGWTDWNLALNPEGGPNWVRNFVDSPIIVDITKDTFYKQPMFYHLGHFSKFIPEGSQRVGLVASQKNDLDAVALMHPDGSAVVVVLNRSSKDVPLTIKDPAVGFLETISPGYSIHTYLWHRQ
In [63]:
!cat aln.fas
>2WNW
--------------------------------MKGRLISSDPYRQQFLVER-AVSFSHRQ
RDCSELISVLPRHALQQIDGFGGSFTEGAGVVFNSMSEKTKAQFLSLYFSAQEHNYTLAR
MPIQSCDFSLGNYAYVDSSADLQQGRLSFSRDEA-HLIPLISGALRLN-PHMKLMASPWS
PPAFMKTNNDMNGGGKLRRE----CYADWADIIINYLLEYRRHGINVQALSVQNEPVAVK
T----WDSCLYSVEEETAFAVQYLRPRLARQGMDEMEIYIWDHDKDGLVDWAELAFADEA
NYKGINGLAFHWYTGDHFSQI---QYLAQCLPDKKLLFSEGCVPMESD-AGSQIRHW---
HTYLHDMIGNFKSGCSGFIDWNLLLNSEGGPNHQGNLCEAPIQYDAQNDVLRRNHSWYGI
GHFCRYVRPGA-RVMLSSSYDNLLEEVGFVNPDGERVLVVYNRDVQERRCRVLDGDKEIA
LTL-PPSGASTLLWRQE
>1OGS
ARPCIPKSFGYSSVVCVCNATYCDSFDPPTFPALGTFSRYESTRSGRRMELSMGPIQANH
TGTGLLLTLQPEQKFQKVKGFGGAMTDAAALNILALSPPAQNLLLKSYFSEEGIGYNIIR
VPMASCDFSIRTYTYADTPDDFQLHNFSLPEEDTKLKIPLIHRALQLAQRPVSLLASPWT
SPTWLKTNGAVNGKGSLKGQPGDIYHQTWARYFVKFLDAYAEHKLQFWAVTAENEPSAGL
LSGYPFQCLGFTPEHQRDFIARDLGPTLANSTHHNVRLLMLDDQRLLLPHWAKVVLTDPE
AAKYVHGIAVHWYLDFLAPAKATLGETHRLFPNTMLFASEACVGSKFWEQSVRLGSWDRG
MQYSHSIITNLLYHVVGWTDWNLALNPEGGPNWVRNFVDSPIIVDITKDTFYKQPMFYHL
GHFSKFIPEGSQRVGLVASQKNDLDAVALMHPDGSAVVVVLNRSSKDVPLTIKDPAVGFL
ETISPGYSIHTYLWHRQ
In [ ]:
Content source: avishek-r-kumar/dfitools
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