Multiple sequence alignment - TraesCS6D01G280000
Loading Multiple Alignment...
BLAST Results
BLAST Results - Input Sequence
Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this
to extract flanking regions for cloning. If the result of the multiple sequence alignment is
not as expected, these results could be used for further investigation.
qseqid
sseqid
percentage.identical
alignment.length
no.mismatch
no.gap.openings
qstart
qend
sstart
send
evalue
bitscore
0
TraesCS6D01G280000
chr6D
100.000
2381
0
0
1
2381
387881803
387884183
0.000000e+00
4397.0
1
TraesCS6D01G280000
chr6D
77.586
464
83
17
45
502
393927880
393927432
6.530000e-66
261.0
2
TraesCS6D01G280000
chr6D
81.089
349
32
20
956
1279
387780688
387781027
5.080000e-62
248.0
3
TraesCS6D01G280000
chr6B
92.367
773
34
10
728
1481
579094028
579094794
0.000000e+00
1077.0
4
TraesCS6D01G280000
chr6B
91.743
436
27
7
1948
2381
579355591
579356019
4.380000e-167
597.0
5
TraesCS6D01G280000
chr6B
85.560
464
27
11
1475
1909
579094899
579095351
1.300000e-122
449.0
6
TraesCS6D01G280000
chr6B
87.719
342
28
7
857
1189
578950441
578950777
1.030000e-103
387.0
7
TraesCS6D01G280000
chr6B
84.802
329
22
17
643
965
579102337
579102643
2.970000e-79
305.0
8
TraesCS6D01G280000
chr6B
91.667
156
13
0
2226
2381
579101694
579101849
1.430000e-52
217.0
9
TraesCS6D01G280000
chr6B
82.828
198
16
8
1678
1860
579353984
579354178
6.810000e-36
161.0
10
TraesCS6D01G280000
chr6A
90.141
710
33
7
643
1319
533253326
533254031
0.000000e+00
889.0
11
TraesCS6D01G280000
chr6A
94.626
428
15
2
1954
2381
533256492
533256911
0.000000e+00
656.0
12
TraesCS6D01G280000
chr6A
77.808
365
74
7
141
501
457451458
457451097
3.980000e-53
219.0
13
TraesCS6D01G280000
chr6A
88.953
172
11
3
1309
1480
533254450
533254613
3.100000e-49
206.0
14
TraesCS6D01G280000
chr6A
90.741
108
6
2
1475
1578
533254718
533254825
8.870000e-30
141.0
15
TraesCS6D01G280000
chr5D
83.600
500
65
11
3
498
372306505
372306991
1.000000e-123
453.0
16
TraesCS6D01G280000
chr5D
82.236
501
70
8
1
498
470050522
470050038
4.740000e-112
414.0
17
TraesCS6D01G280000
chr5D
79.430
491
87
9
15
498
9289509
9289026
3.790000e-88
335.0
18
TraesCS6D01G280000
chr4A
82.164
499
85
4
3
498
567224389
567224886
2.190000e-115
425.0
19
TraesCS6D01G280000
chr4D
81.783
516
79
8
3
505
324201196
324201709
3.660000e-113
418.0
20
TraesCS6D01G280000
chr4D
83.862
347
49
6
3
348
339455706
339456046
8.210000e-85
324.0
21
TraesCS6D01G280000
chr3B
78.728
503
97
8
3
500
508259755
508259258
6.350000e-86
327.0
22
TraesCS6D01G280000
chr5A
80.806
422
74
6
17
434
693653208
693653626
8.210000e-85
324.0
23
TraesCS6D01G280000
chr2D
81.433
307
45
7
21
317
372703213
372703517
8.500000e-60
241.0
24
TraesCS6D01G280000
chr2D
81.818
275
43
6
227
497
96688531
96688260
8.560000e-55
224.0
25
TraesCS6D01G280000
chr7D
82.310
277
45
4
227
500
83388659
83388384
1.100000e-58
237.0
26
TraesCS6D01G280000
chr5B
94.444
36
0
1
1329
1364
327153881
327153848
1.000000e-03
54.7
27
TraesCS6D01G280000
chr5B
94.444
36
1
1
1329
1363
327435060
327435025
1.000000e-03
54.7
BLAST Results - HSPs grouped
These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the
BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are
purely upstream or downstream may be removed if they don't overlap both primers.
query
scaffold
start
end
length
rev.comp
avg.bitscore
max.bitscore
avg.percent.identical
query.start
query.end
num_hsp
groupid
homo_length
0
TraesCS6D01G280000
chr6D
387881803
387884183
2380
False
4397
4397
100.00000
1
2381
1
chr6D.!!$F2
2380
1
TraesCS6D01G280000
chr6B
579094028
579095351
1323
False
763
1077
88.96350
728
1909
2
chr6B.!!$F2
1181
2
TraesCS6D01G280000
chr6B
579353984
579356019
2035
False
379
597
87.28550
1678
2381
2
chr6B.!!$F4
703
3
TraesCS6D01G280000
chr6B
579101694
579102643
949
False
261
305
88.23450
643
2381
2
chr6B.!!$F3
1738
4
TraesCS6D01G280000
chr6A
533253326
533256911
3585
False
473
889
91.11525
643
2381
4
chr6A.!!$F1
1738
5
TraesCS6D01G280000
chr4D
324201196
324201709
513
False
418
418
81.78300
3
505
1
chr4D.!!$F1
502
AutoCloner calculated primer pairs
These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3),
whilst remaining within the specified product range where possible.
Forward
Primers
Reverse
Primers
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
Orientation
579
580
0.033642
CCATTTGTGTGTGCCATGCA
59.966
50.0
0.0
0.0
35.6
3.96
F
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
Orientation
2054
5088
0.102481
CAGAATGCTTGGCCTCATGC
59.898
55.0
3.32
3.62
42.34
4.06
R
All possible primers
Listed here are all possible primers based on the multiple sequence alignment and SNPs generated
previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work
during PCR or sequencing,
these could be used as alternatives.
Forward
Primers
Reverse
Primers
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
93
94
2.117156
CCGCCATTGCCTTCTCCAG
61.117
63.158
0.00
0.00
0.00
3.86
94
95
2.768492
CGCCATTGCCTTCTCCAGC
61.768
63.158
0.00
0.00
0.00
4.85
115
116
2.998097
CACGGGATGACACCCCAT
59.002
61.111
5.48
0.00
46.62
4.00
120
121
1.202651
CGGGATGACACCCCATTAGAC
60.203
57.143
5.48
0.00
46.62
2.59
147
148
1.611491
GGACTGATCGGAGTCAGATCC
59.389
57.143
24.71
11.67
46.77
3.36
156
157
2.583593
GTCAGATCCGCTGTCCGC
60.584
66.667
0.00
0.00
45.14
5.54
163
164
4.529219
CCGCTGTCCGCCATGCTA
62.529
66.667
0.00
0.00
35.03
3.49
170
171
1.753078
TCCGCCATGCTAGAGACGT
60.753
57.895
0.00
0.00
0.00
4.34
172
173
1.299468
CGCCATGCTAGAGACGTCC
60.299
63.158
13.01
3.77
0.00
4.79
182
183
0.458025
AGAGACGTCCGAAAATCGCC
60.458
55.000
13.01
0.00
38.82
5.54
192
193
0.583917
GAAAATCGCCGGAGATGAGC
59.416
55.000
22.09
9.75
0.00
4.26
194
195
0.249657
AAATCGCCGGAGATGAGCTC
60.250
55.000
22.09
6.82
43.17
4.09
214
215
4.101448
GTGGCGGAGGGAGTGCAT
62.101
66.667
0.00
0.00
0.00
3.96
215
216
4.100084
TGGCGGAGGGAGTGCATG
62.100
66.667
0.00
0.00
0.00
4.06
219
220
2.669133
CGGAGGGAGTGCATGGGAA
61.669
63.158
0.00
0.00
0.00
3.97
220
221
1.691219
GGAGGGAGTGCATGGGAAA
59.309
57.895
0.00
0.00
0.00
3.13
226
227
1.457346
GAGTGCATGGGAAAGGAGTG
58.543
55.000
0.00
0.00
0.00
3.51
246
247
2.173782
TGTGAAGTGGCTAGGGTTTTGA
59.826
45.455
0.00
0.00
0.00
2.69
247
248
3.181434
TGTGAAGTGGCTAGGGTTTTGAT
60.181
43.478
0.00
0.00
0.00
2.57
251
252
0.254747
TGGCTAGGGTTTTGATCCGG
59.745
55.000
0.00
0.00
0.00
5.14
255
256
2.017049
CTAGGGTTTTGATCCGGCAAG
58.983
52.381
0.00
0.00
0.00
4.01
256
257
1.215382
GGGTTTTGATCCGGCAAGC
59.785
57.895
0.00
0.00
0.00
4.01
257
258
1.154035
GGTTTTGATCCGGCAAGCG
60.154
57.895
0.00
0.00
0.00
4.68
259
260
1.302913
TTTTGATCCGGCAAGCGGA
60.303
52.632
5.02
5.02
40.06
5.54
261
262
1.375853
TTTGATCCGGCAAGCGGATG
61.376
55.000
18.43
0.00
45.20
3.51
262
263
2.108976
GATCCGGCAAGCGGATGA
59.891
61.111
18.43
2.99
45.20
2.92
347
348
1.613317
CGCCCCATATCCGCCTCATA
61.613
60.000
0.00
0.00
0.00
2.15
348
349
0.839946
GCCCCATATCCGCCTCATAT
59.160
55.000
0.00
0.00
0.00
1.78
349
350
1.212935
GCCCCATATCCGCCTCATATT
59.787
52.381
0.00
0.00
0.00
1.28
350
351
2.357154
GCCCCATATCCGCCTCATATTT
60.357
50.000
0.00
0.00
0.00
1.40
353
354
3.054434
CCCATATCCGCCTCATATTTGGA
60.054
47.826
0.00
0.00
0.00
3.53
354
355
3.941483
CCATATCCGCCTCATATTTGGAC
59.059
47.826
0.00
0.00
0.00
4.02
355
356
4.323792
CCATATCCGCCTCATATTTGGACT
60.324
45.833
0.00
0.00
0.00
3.85
356
357
2.620251
TCCGCCTCATATTTGGACTG
57.380
50.000
0.00
0.00
0.00
3.51
357
358
1.140852
TCCGCCTCATATTTGGACTGG
59.859
52.381
0.00
0.00
0.00
4.00
359
360
2.224621
CCGCCTCATATTTGGACTGGAT
60.225
50.000
0.00
0.00
0.00
3.41
361
362
4.323792
CCGCCTCATATTTGGACTGGATAT
60.324
45.833
0.00
0.00
0.00
1.63
362
363
4.633126
CGCCTCATATTTGGACTGGATATG
59.367
45.833
0.00
0.00
35.87
1.78
363
364
5.569428
CGCCTCATATTTGGACTGGATATGA
60.569
44.000
0.00
0.00
39.29
2.15
366
367
6.378661
TCATATTTGGACTGGATATGAGGG
57.621
41.667
0.00
0.00
37.67
4.30
367
368
6.090870
TCATATTTGGACTGGATATGAGGGA
58.909
40.000
0.00
0.00
37.67
4.20
368
369
6.737131
TCATATTTGGACTGGATATGAGGGAT
59.263
38.462
0.00
0.00
37.67
3.85
371
372
1.280421
GGACTGGATATGAGGGATGCC
59.720
57.143
0.00
0.00
0.00
4.40
372
373
0.979665
ACTGGATATGAGGGATGCCG
59.020
55.000
0.00
0.00
0.00
5.69
373
374
1.269958
CTGGATATGAGGGATGCCGA
58.730
55.000
0.00
0.00
0.00
5.54
374
375
1.836166
CTGGATATGAGGGATGCCGAT
59.164
52.381
0.00
0.00
0.00
4.18
375
376
1.833630
TGGATATGAGGGATGCCGATC
59.166
52.381
0.00
0.00
0.00
3.69
376
377
1.833630
GGATATGAGGGATGCCGATCA
59.166
52.381
0.00
0.00
0.00
2.92
378
379
0.610174
TATGAGGGATGCCGATCAGC
59.390
55.000
0.00
0.00
0.00
4.26
382
383
3.928779
GGATGCCGATCAGCCCGA
61.929
66.667
0.00
0.00
45.34
5.14
383
384
2.356793
GATGCCGATCAGCCCGAG
60.357
66.667
0.00
0.00
0.00
4.63
384
385
4.615815
ATGCCGATCAGCCCGAGC
62.616
66.667
0.00
0.00
40.32
5.03
389
390
3.093278
GATCAGCCCGAGCGTTTG
58.907
61.111
0.00
0.00
46.67
2.93
390
391
1.447838
GATCAGCCCGAGCGTTTGA
60.448
57.895
0.00
0.00
46.67
2.69
391
392
1.424493
GATCAGCCCGAGCGTTTGAG
61.424
60.000
0.00
0.00
46.67
3.02
392
393
2.859273
ATCAGCCCGAGCGTTTGAGG
62.859
60.000
0.00
0.00
46.67
3.86
396
397
4.697756
CCGAGCGTTTGAGGCCCA
62.698
66.667
0.00
0.00
0.00
5.36
397
398
2.436646
CGAGCGTTTGAGGCCCAT
60.437
61.111
0.00
0.00
0.00
4.00
398
399
2.040544
CGAGCGTTTGAGGCCCATT
61.041
57.895
0.00
0.00
0.00
3.16
399
400
1.586154
CGAGCGTTTGAGGCCCATTT
61.586
55.000
0.00
0.00
0.00
2.32
400
401
0.109132
GAGCGTTTGAGGCCCATTTG
60.109
55.000
0.00
0.00
0.00
2.32
402
403
0.109132
GCGTTTGAGGCCCATTTGAG
60.109
55.000
0.00
0.00
0.00
3.02
403
404
0.527565
CGTTTGAGGCCCATTTGAGG
59.472
55.000
0.00
0.00
0.00
3.86
409
410
3.190878
GCCCATTTGAGGCGTCTG
58.809
61.111
8.06
0.00
41.41
3.51
410
411
1.675641
GCCCATTTGAGGCGTCTGT
60.676
57.895
8.06
0.00
41.41
3.41
411
412
1.244019
GCCCATTTGAGGCGTCTGTT
61.244
55.000
8.06
0.00
41.41
3.16
414
415
1.068333
CCATTTGAGGCGTCTGTTTGG
60.068
52.381
8.06
6.01
0.00
3.28
415
416
1.068333
CATTTGAGGCGTCTGTTTGGG
60.068
52.381
8.06
0.00
0.00
4.12
416
417
0.106918
TTTGAGGCGTCTGTTTGGGT
60.107
50.000
8.06
0.00
0.00
4.51
417
418
0.106918
TTGAGGCGTCTGTTTGGGTT
60.107
50.000
8.06
0.00
0.00
4.11
418
419
0.759959
TGAGGCGTCTGTTTGGGTTA
59.240
50.000
8.06
0.00
0.00
2.85
419
420
1.141254
TGAGGCGTCTGTTTGGGTTAA
59.859
47.619
8.06
0.00
0.00
2.01
420
421
2.223745
GAGGCGTCTGTTTGGGTTAAA
58.776
47.619
0.00
0.00
0.00
1.52
421
422
2.619646
GAGGCGTCTGTTTGGGTTAAAA
59.380
45.455
0.00
0.00
0.00
1.52
422
423
3.227614
AGGCGTCTGTTTGGGTTAAAAT
58.772
40.909
0.00
0.00
0.00
1.82
423
424
3.639561
AGGCGTCTGTTTGGGTTAAAATT
59.360
39.130
0.00
0.00
0.00
1.82
424
425
4.100344
AGGCGTCTGTTTGGGTTAAAATTT
59.900
37.500
0.00
0.00
0.00
1.82
425
426
4.446385
GGCGTCTGTTTGGGTTAAAATTTC
59.554
41.667
0.00
0.00
0.00
2.17
428
429
5.172411
CGTCTGTTTGGGTTAAAATTTCACG
59.828
40.000
0.00
0.00
0.00
4.35
429
430
6.267070
GTCTGTTTGGGTTAAAATTTCACGA
58.733
36.000
0.00
0.00
0.00
4.35
430
431
6.197655
GTCTGTTTGGGTTAAAATTTCACGAC
59.802
38.462
0.00
0.00
0.00
4.34
431
432
5.349809
TGTTTGGGTTAAAATTTCACGACC
58.650
37.500
0.00
0.00
0.00
4.79
432
433
5.105473
TGTTTGGGTTAAAATTTCACGACCA
60.105
36.000
11.77
6.19
0.00
4.02
433
434
4.839668
TGGGTTAAAATTTCACGACCAG
57.160
40.909
11.77
0.00
0.00
4.00
434
435
4.208746
TGGGTTAAAATTTCACGACCAGT
58.791
39.130
11.77
0.00
0.00
4.00
435
436
4.276431
TGGGTTAAAATTTCACGACCAGTC
59.724
41.667
11.77
0.00
0.00
3.51
436
437
4.276431
GGGTTAAAATTTCACGACCAGTCA
59.724
41.667
11.77
0.00
0.00
3.41
437
438
5.449304
GGTTAAAATTTCACGACCAGTCAG
58.551
41.667
0.00
0.00
0.00
3.51
438
439
5.008316
GGTTAAAATTTCACGACCAGTCAGT
59.992
40.000
0.00
0.00
0.00
3.41
440
441
7.254863
GGTTAAAATTTCACGACCAGTCAGTAA
60.255
37.037
0.00
0.00
0.00
2.24
441
442
5.668558
AAATTTCACGACCAGTCAGTAAC
57.331
39.130
0.00
0.00
0.00
2.50
442
443
2.806608
TTCACGACCAGTCAGTAACC
57.193
50.000
0.00
0.00
0.00
2.85
443
444
0.594602
TCACGACCAGTCAGTAACCG
59.405
55.000
0.00
0.00
0.00
4.44
444
445
0.594602
CACGACCAGTCAGTAACCGA
59.405
55.000
0.00
0.00
0.00
4.69
445
446
0.879765
ACGACCAGTCAGTAACCGAG
59.120
55.000
0.00
0.00
0.00
4.63
446
447
0.456312
CGACCAGTCAGTAACCGAGC
60.456
60.000
0.00
0.00
0.00
5.03
447
448
0.456312
GACCAGTCAGTAACCGAGCG
60.456
60.000
0.00
0.00
0.00
5.03
448
449
1.153823
CCAGTCAGTAACCGAGCGG
60.154
63.158
7.48
7.48
42.03
5.52
449
450
1.153823
CAGTCAGTAACCGAGCGGG
60.154
63.158
14.07
0.00
43.62
6.13
452
453
2.509336
CAGTAACCGAGCGGGCTG
60.509
66.667
14.07
13.43
40.62
4.85
453
454
4.452733
AGTAACCGAGCGGGCTGC
62.453
66.667
11.19
11.19
46.98
5.25
467
468
3.423154
CTGCCCGGACGTTTGAGC
61.423
66.667
0.73
0.00
0.00
4.26
471
472
4.675029
CCGGACGTTTGAGCGGGT
62.675
66.667
0.00
0.00
35.98
5.28
473
474
2.248835
CGGACGTTTGAGCGGGTTT
61.249
57.895
0.00
0.00
35.98
3.27
476
477
0.234884
GACGTTTGAGCGGGTTTGAG
59.765
55.000
0.00
0.00
35.98
3.02
477
478
1.164041
ACGTTTGAGCGGGTTTGAGG
61.164
55.000
0.00
0.00
35.98
3.86
478
479
1.285950
GTTTGAGCGGGTTTGAGGC
59.714
57.895
0.00
0.00
0.00
4.70
479
480
2.258013
TTTGAGCGGGTTTGAGGCG
61.258
57.895
0.00
0.00
0.00
5.52
480
481
2.668185
TTTGAGCGGGTTTGAGGCGA
62.668
55.000
0.00
0.00
0.00
5.54
481
482
3.119096
GAGCGGGTTTGAGGCGAC
61.119
66.667
0.00
0.00
0.00
5.19
482
483
4.699522
AGCGGGTTTGAGGCGACC
62.700
66.667
0.00
0.00
35.14
4.79
495
496
1.587054
GCGACCGGCTATAGATGCT
59.413
57.895
0.00
0.00
39.11
3.79
496
497
0.456995
GCGACCGGCTATAGATGCTC
60.457
60.000
0.00
0.00
39.11
4.26
497
498
1.169577
CGACCGGCTATAGATGCTCT
58.830
55.000
0.00
0.00
0.00
4.09
498
499
2.357075
CGACCGGCTATAGATGCTCTA
58.643
52.381
0.00
0.00
32.87
2.43
501
502
4.011023
GACCGGCTATAGATGCTCTAAGA
58.989
47.826
0.00
0.00
31.96
2.10
502
503
4.408276
ACCGGCTATAGATGCTCTAAGAA
58.592
43.478
0.00
0.00
31.96
2.52
503
504
4.833380
ACCGGCTATAGATGCTCTAAGAAA
59.167
41.667
0.00
0.00
31.96
2.52
504
505
5.482175
ACCGGCTATAGATGCTCTAAGAAAT
59.518
40.000
0.00
0.00
31.96
2.17
506
507
7.147983
ACCGGCTATAGATGCTCTAAGAAATAG
60.148
40.741
0.00
0.00
31.96
1.73
523
524
6.389906
AGAAATAGAAAATTTTGACTGGGCG
58.610
36.000
8.47
0.00
0.00
6.13
524
525
5.722021
AATAGAAAATTTTGACTGGGCGT
57.278
34.783
8.47
0.00
0.00
5.68
525
526
5.722021
ATAGAAAATTTTGACTGGGCGTT
57.278
34.783
8.47
0.00
0.00
4.84
527
528
3.383185
AGAAAATTTTGACTGGGCGTTGA
59.617
39.130
8.47
0.00
0.00
3.18
529
530
4.335400
AAATTTTGACTGGGCGTTGAAT
57.665
36.364
0.00
0.00
0.00
2.57
530
531
5.461032
AAATTTTGACTGGGCGTTGAATA
57.539
34.783
0.00
0.00
0.00
1.75
531
532
5.461032
AATTTTGACTGGGCGTTGAATAA
57.539
34.783
0.00
0.00
0.00
1.40
533
534
4.497473
TTTGACTGGGCGTTGAATAAAG
57.503
40.909
0.00
0.00
0.00
1.85
534
535
3.134574
TGACTGGGCGTTGAATAAAGT
57.865
42.857
0.00
0.00
0.00
2.66
535
536
2.811431
TGACTGGGCGTTGAATAAAGTG
59.189
45.455
0.00
0.00
0.00
3.16
536
537
1.539827
ACTGGGCGTTGAATAAAGTGC
59.460
47.619
0.00
0.00
0.00
4.40
537
538
0.519519
TGGGCGTTGAATAAAGTGCG
59.480
50.000
0.00
0.00
0.00
5.34
538
539
0.796870
GGGCGTTGAATAAAGTGCGC
60.797
55.000
0.00
0.00
43.46
6.09
539
540
1.125847
GGCGTTGAATAAAGTGCGCG
61.126
55.000
0.00
0.00
44.86
6.86
540
541
1.720330
GCGTTGAATAAAGTGCGCGC
61.720
55.000
27.26
27.26
35.71
6.86
541
542
0.451957
CGTTGAATAAAGTGCGCGCA
60.452
50.000
33.09
33.09
0.00
6.09
556
557
3.167945
GCATGCGACGCAAAGCAC
61.168
61.111
32.36
16.82
46.83
4.40
557
558
2.557805
CATGCGACGCAAAGCACT
59.442
55.556
28.24
6.01
46.83
4.40
558
559
1.794785
CATGCGACGCAAAGCACTG
60.795
57.895
28.24
15.47
46.83
3.66
559
560
1.960763
ATGCGACGCAAAGCACTGA
60.961
52.632
28.24
0.00
46.83
3.41
560
561
2.127609
GCGACGCAAAGCACTGAC
60.128
61.111
16.42
0.00
0.00
3.51
561
562
2.551270
CGACGCAAAGCACTGACC
59.449
61.111
0.00
0.00
0.00
4.02
563
564
1.568612
CGACGCAAAGCACTGACCAT
61.569
55.000
0.00
0.00
0.00
3.55
564
565
0.593128
GACGCAAAGCACTGACCATT
59.407
50.000
0.00
0.00
0.00
3.16
565
566
1.001378
GACGCAAAGCACTGACCATTT
60.001
47.619
0.00
0.00
0.00
2.32
566
567
1.269206
ACGCAAAGCACTGACCATTTG
60.269
47.619
0.00
0.00
36.07
2.32
567
568
1.269206
CGCAAAGCACTGACCATTTGT
60.269
47.619
0.00
0.00
35.55
2.83
568
569
2.129607
GCAAAGCACTGACCATTTGTG
58.870
47.619
0.00
0.00
35.55
3.33
569
570
2.481795
GCAAAGCACTGACCATTTGTGT
60.482
45.455
0.00
0.00
35.55
3.72
570
571
3.117794
CAAAGCACTGACCATTTGTGTG
58.882
45.455
0.00
0.00
34.52
3.82
571
572
2.057137
AGCACTGACCATTTGTGTGT
57.943
45.000
0.00
0.00
34.52
3.72
572
573
1.677576
AGCACTGACCATTTGTGTGTG
59.322
47.619
0.00
0.00
34.52
3.82
573
574
1.865248
GCACTGACCATTTGTGTGTGC
60.865
52.381
0.00
0.00
41.94
4.57
574
575
1.032014
ACTGACCATTTGTGTGTGCC
58.968
50.000
0.00
0.00
0.00
5.01
576
577
1.614903
CTGACCATTTGTGTGTGCCAT
59.385
47.619
0.00
0.00
0.00
4.40
577
578
1.340568
TGACCATTTGTGTGTGCCATG
59.659
47.619
0.00
0.00
0.00
3.66
578
579
0.033781
ACCATTTGTGTGTGCCATGC
59.966
50.000
0.00
0.00
0.00
4.06
579
580
0.033642
CCATTTGTGTGTGCCATGCA
59.966
50.000
0.00
0.00
35.60
3.96
580
581
1.338294
CCATTTGTGTGTGCCATGCAT
60.338
47.619
0.00
0.00
41.91
3.96
581
582
1.729517
CATTTGTGTGTGCCATGCATG
59.270
47.619
20.19
20.19
41.91
4.06
582
583
0.751452
TTTGTGTGTGCCATGCATGT
59.249
45.000
24.58
0.00
41.91
3.21
583
584
1.613836
TTGTGTGTGCCATGCATGTA
58.386
45.000
24.58
11.07
41.91
2.29
585
586
1.959282
TGTGTGTGCCATGCATGTAAA
59.041
42.857
24.58
6.46
41.91
2.01
586
587
2.288091
TGTGTGTGCCATGCATGTAAAC
60.288
45.455
24.58
17.68
41.91
2.01
587
588
2.030007
GTGTGTGCCATGCATGTAAACT
60.030
45.455
24.58
0.00
41.91
2.66
588
589
2.030096
TGTGTGCCATGCATGTAAACTG
60.030
45.455
24.58
9.73
41.91
3.16
589
590
2.228582
GTGTGCCATGCATGTAAACTGA
59.771
45.455
24.58
3.31
41.91
3.41
591
592
3.320256
TGTGCCATGCATGTAAACTGAAA
59.680
39.130
24.58
2.35
41.91
2.69
592
593
3.674753
GTGCCATGCATGTAAACTGAAAC
59.325
43.478
24.58
7.26
41.91
2.78
594
595
4.764308
TGCCATGCATGTAAACTGAAACTA
59.236
37.500
24.58
0.00
31.71
2.24
595
596
5.106197
TGCCATGCATGTAAACTGAAACTAG
60.106
40.000
24.58
5.77
31.71
2.57
596
597
5.123820
GCCATGCATGTAAACTGAAACTAGA
59.876
40.000
24.58
0.00
0.00
2.43
597
598
6.546395
CCATGCATGTAAACTGAAACTAGAC
58.454
40.000
24.58
0.00
0.00
2.59
598
599
6.149308
CCATGCATGTAAACTGAAACTAGACA
59.851
38.462
24.58
0.00
0.00
3.41
599
600
7.308529
CCATGCATGTAAACTGAAACTAGACAA
60.309
37.037
24.58
0.00
0.00
3.18
600
601
7.189693
TGCATGTAAACTGAAACTAGACAAG
57.810
36.000
0.00
0.00
0.00
3.16
601
602
6.989759
TGCATGTAAACTGAAACTAGACAAGA
59.010
34.615
0.00
0.00
0.00
3.02
602
603
7.042051
TGCATGTAAACTGAAACTAGACAAGAC
60.042
37.037
0.00
0.00
0.00
3.01
603
604
7.042051
GCATGTAAACTGAAACTAGACAAGACA
60.042
37.037
0.00
0.00
0.00
3.41
604
605
7.766219
TGTAAACTGAAACTAGACAAGACAC
57.234
36.000
0.00
0.00
0.00
3.67
605
606
7.324935
TGTAAACTGAAACTAGACAAGACACA
58.675
34.615
0.00
0.00
0.00
3.72
606
607
6.910536
AAACTGAAACTAGACAAGACACAG
57.089
37.500
0.00
0.00
0.00
3.66
607
608
4.950050
ACTGAAACTAGACAAGACACAGG
58.050
43.478
0.00
0.00
0.00
4.00
609
610
3.964688
TGAAACTAGACAAGACACAGGGA
59.035
43.478
0.00
0.00
0.00
4.20
610
611
4.202223
TGAAACTAGACAAGACACAGGGAC
60.202
45.833
0.00
0.00
0.00
4.46
611
612
1.887198
ACTAGACAAGACACAGGGACG
59.113
52.381
0.00
0.00
0.00
4.79
615
616
3.637273
AAGACACAGGGACGGGCC
61.637
66.667
0.00
0.00
0.00
5.80
616
617
4.640690
AGACACAGGGACGGGCCT
62.641
66.667
0.84
0.00
36.66
5.19
619
620
1.833787
GACACAGGGACGGGCCTTTA
61.834
60.000
0.84
0.00
36.66
1.85
620
621
1.205460
ACACAGGGACGGGCCTTTAT
61.205
55.000
0.84
0.00
36.66
1.40
621
622
0.034477
CACAGGGACGGGCCTTTATT
60.034
55.000
0.84
0.00
36.66
1.40
623
624
1.076513
ACAGGGACGGGCCTTTATTTT
59.923
47.619
0.84
0.00
36.66
1.82
641
642
1.996798
TTTTGGGGTACGGCAAATCA
58.003
45.000
0.00
0.00
0.00
2.57
762
771
1.331756
ACTACGCCGGAATACGTACTG
59.668
52.381
5.05
1.28
43.35
2.74
816
825
0.826715
TGAGAATCCAGGAGCGAAGG
59.173
55.000
0.00
0.00
0.00
3.46
872
881
7.254852
TCGTGCTATTTTTCAAAGTTCAAACT
58.745
30.769
0.00
0.00
42.04
2.66
913
923
2.191128
AAACGATGAAGCAGCTTCCT
57.809
45.000
28.73
21.01
39.51
3.36
914
924
1.446907
AACGATGAAGCAGCTTCCTG
58.553
50.000
28.73
20.63
39.51
3.86
1029
1050
3.142174
CCTAGCTAATTTAGTGGCAGCC
58.858
50.000
3.66
3.66
32.58
4.85
1046
1067
2.947652
CAGCCAGAAGAGAGAGAGAGAG
59.052
54.545
0.00
0.00
0.00
3.20
1138
1171
1.003839
GGTCATGGTGTTCTCGGCA
60.004
57.895
0.00
0.00
0.00
5.69
1222
1270
1.496060
TCATCCGGCAGGTGTATCTT
58.504
50.000
1.81
0.00
39.05
2.40
1271
1319
4.135153
CCTCGTGCTCGACCTGGG
62.135
72.222
6.80
3.28
41.35
4.45
1272
1320
3.062466
CTCGTGCTCGACCTGGGA
61.062
66.667
6.80
0.00
41.35
4.37
1284
1335
2.553466
CGACCTGGGACCCAAATAACAA
60.553
50.000
15.87
0.00
30.80
2.83
1323
1803
2.781595
GAAACCGGCGAGAGGAAGCA
62.782
60.000
9.30
0.00
34.54
3.91
1327
1807
1.299773
CGGCGAGAGGAAGCAGATC
60.300
63.158
0.00
0.00
34.54
2.75
1347
1827
3.400054
GCAGAGGCCGGGGTACTT
61.400
66.667
2.18
0.00
0.00
2.24
1580
2183
5.621228
CACTCTTTTGTTCTGCGTATGAAAC
59.379
40.000
0.00
0.00
0.00
2.78
1603
2206
9.654663
AAACTATTGCTCTTTTGGTAGTAGTAG
57.345
33.333
0.00
0.00
0.00
2.57
1604
2207
8.363761
ACTATTGCTCTTTTGGTAGTAGTAGT
57.636
34.615
0.00
0.00
30.03
2.73
1695
3368
7.303261
GCAAAAACTATTCCAGGTGTACTTAC
58.697
38.462
0.00
0.00
0.00
2.34
1704
3382
3.620488
CAGGTGTACTTACATGCCCAAT
58.380
45.455
0.00
0.00
38.63
3.16
1705
3383
4.016444
CAGGTGTACTTACATGCCCAATT
58.984
43.478
0.00
0.00
38.63
2.32
1716
3394
7.602265
ACTTACATGCCCAATTGAATACAAAAC
59.398
33.333
7.12
0.00
39.54
2.43
1737
3415
2.350192
CGCTAACGGTATGCAAACATGA
59.650
45.455
0.00
0.00
35.01
3.07
1738
3416
3.181515
CGCTAACGGTATGCAAACATGAA
60.182
43.478
0.00
0.00
35.01
2.57
1742
3420
3.009723
ACGGTATGCAAACATGAAGAGG
58.990
45.455
0.00
0.00
37.04
3.69
1750
3428
2.403252
AACATGAAGAGGGCCGTAAG
57.597
50.000
0.00
0.00
0.00
2.34
1845
3538
4.151689
ACGGTTACATGTCGATTTTGACTG
59.848
41.667
11.87
3.56
39.64
3.51
1863
3556
2.542595
ACTGTTCCAAAATGTCGTCGTC
59.457
45.455
0.00
0.00
0.00
4.20
1865
3558
2.798283
TGTTCCAAAATGTCGTCGTCTC
59.202
45.455
0.00
0.00
0.00
3.36
1868
4684
1.415374
CAAAATGTCGTCGTCTCGGT
58.585
50.000
0.00
0.00
0.00
4.69
1893
4709
0.546122
TCATGGGCATAGTCCACCAC
59.454
55.000
0.00
0.00
41.42
4.16
1897
4713
1.004277
TGGGCATAGTCCACCACTTTC
59.996
52.381
0.00
0.00
36.43
2.62
1986
5018
3.745723
TTGGCCTCTTCCAAGTTCC
57.254
52.632
3.32
0.00
40.92
3.62
1987
5019
0.850100
TTGGCCTCTTCCAAGTTCCA
59.150
50.000
3.32
0.00
40.92
3.53
1988
5020
0.850100
TGGCCTCTTCCAAGTTCCAA
59.150
50.000
3.32
0.00
32.18
3.53
2032
5065
2.904915
GCTTACTGTCGAAAGCAACAC
58.095
47.619
13.37
0.00
45.89
3.32
2097
5131
6.867816
TGGCAGACATGTATTTCAAAAACATC
59.132
34.615
0.00
0.00
31.60
3.06
2149
5183
0.611200
TTCCACACGTACTCCCATGG
59.389
55.000
4.14
4.14
0.00
3.66
2181
5215
8.733458
CCTCATTTTTGTGAAGACATGAGAATA
58.267
33.333
0.00
0.00
37.55
1.75
2346
5381
3.932710
CCTGCACACTAAAATTCTAGCGA
59.067
43.478
0.00
0.00
0.00
4.93
2355
5390
3.521947
AAATTCTAGCGACGCCTACTT
57.478
42.857
17.79
0.00
0.00
2.24
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
1
2
0.243907
CTGTCCGACACGACTCCATT
59.756
55.000
0.00
0.00
33.70
3.16
74
75
3.521796
GGAGAAGGCAATGGCGGC
61.522
66.667
0.00
0.00
42.47
6.53
115
116
2.879026
CGATCAGTCCGGATCTGTCTAA
59.121
50.000
24.21
12.16
41.21
2.10
152
153
1.725557
GACGTCTCTAGCATGGCGGA
61.726
60.000
8.70
0.00
0.00
5.54
156
157
0.738975
TTCGGACGTCTCTAGCATGG
59.261
55.000
16.46
0.00
0.00
3.66
162
163
1.202222
GGCGATTTTCGGACGTCTCTA
60.202
52.381
16.46
0.00
40.84
2.43
163
164
0.458025
GGCGATTTTCGGACGTCTCT
60.458
55.000
16.46
0.00
40.84
3.10
172
173
0.855349
CTCATCTCCGGCGATTTTCG
59.145
55.000
9.30
0.00
43.89
3.46
182
183
2.415010
CACCCGAGCTCATCTCCG
59.585
66.667
15.40
0.00
38.62
4.63
212
213
2.816087
CACTTCACACTCCTTTCCCATG
59.184
50.000
0.00
0.00
0.00
3.66
214
215
1.142870
CCACTTCACACTCCTTTCCCA
59.857
52.381
0.00
0.00
0.00
4.37
215
216
1.897560
CCACTTCACACTCCTTTCCC
58.102
55.000
0.00
0.00
0.00
3.97
219
220
1.625818
CCTAGCCACTTCACACTCCTT
59.374
52.381
0.00
0.00
0.00
3.36
220
221
1.270907
CCTAGCCACTTCACACTCCT
58.729
55.000
0.00
0.00
0.00
3.69
226
227
2.858745
TCAAAACCCTAGCCACTTCAC
58.141
47.619
0.00
0.00
0.00
3.18
256
257
4.091945
CCTCACATATATTTGCGTCATCCG
59.908
45.833
0.00
0.00
40.40
4.18
257
258
4.997395
ACCTCACATATATTTGCGTCATCC
59.003
41.667
0.00
0.00
0.00
3.51
259
260
4.686091
CGACCTCACATATATTTGCGTCAT
59.314
41.667
14.26
0.00
0.00
3.06
260
261
4.048504
CGACCTCACATATATTTGCGTCA
58.951
43.478
14.26
0.00
0.00
4.35
261
262
3.428870
CCGACCTCACATATATTTGCGTC
59.571
47.826
8.03
8.03
0.00
5.19
262
263
3.390135
CCGACCTCACATATATTTGCGT
58.610
45.455
0.00
0.00
0.00
5.24
331
332
3.054434
TCCAAATATGAGGCGGATATGGG
60.054
47.826
0.00
0.00
0.00
4.00
333
334
4.633126
CAGTCCAAATATGAGGCGGATATG
59.367
45.833
0.00
0.00
0.00
1.78
334
335
4.323792
CCAGTCCAAATATGAGGCGGATAT
60.324
45.833
0.00
0.00
0.00
1.63
335
336
3.007940
CCAGTCCAAATATGAGGCGGATA
59.992
47.826
0.00
0.00
0.00
2.59
337
338
1.140852
CCAGTCCAAATATGAGGCGGA
59.859
52.381
0.00
0.00
0.00
5.54
338
339
1.140852
TCCAGTCCAAATATGAGGCGG
59.859
52.381
0.00
0.00
0.00
6.13
339
340
2.620251
TCCAGTCCAAATATGAGGCG
57.380
50.000
0.00
0.00
0.00
5.52
340
341
5.809001
TCATATCCAGTCCAAATATGAGGC
58.191
41.667
0.00
0.00
37.43
4.70
344
345
6.378661
TCCCTCATATCCAGTCCAAATATG
57.621
41.667
0.00
0.00
35.58
1.78
347
348
4.508047
GCATCCCTCATATCCAGTCCAAAT
60.508
45.833
0.00
0.00
0.00
2.32
348
349
3.181440
GCATCCCTCATATCCAGTCCAAA
60.181
47.826
0.00
0.00
0.00
3.28
349
350
2.373169
GCATCCCTCATATCCAGTCCAA
59.627
50.000
0.00
0.00
0.00
3.53
350
351
1.980765
GCATCCCTCATATCCAGTCCA
59.019
52.381
0.00
0.00
0.00
4.02
353
354
0.979665
CGGCATCCCTCATATCCAGT
59.020
55.000
0.00
0.00
0.00
4.00
354
355
1.269958
TCGGCATCCCTCATATCCAG
58.730
55.000
0.00
0.00
0.00
3.86
355
356
1.833630
GATCGGCATCCCTCATATCCA
59.166
52.381
0.00
0.00
0.00
3.41
356
357
1.833630
TGATCGGCATCCCTCATATCC
59.166
52.381
0.00
0.00
0.00
2.59
357
358
2.741228
GCTGATCGGCATCCCTCATATC
60.741
54.545
21.88
0.00
0.00
1.63
359
360
0.610174
GCTGATCGGCATCCCTCATA
59.390
55.000
21.88
0.00
0.00
2.15
361
362
2.811514
GGCTGATCGGCATCCCTCA
61.812
63.158
27.26
0.00
38.25
3.86
362
363
2.031768
GGCTGATCGGCATCCCTC
59.968
66.667
27.26
5.67
38.25
4.30
365
366
3.873026
CTCGGGCTGATCGGCATCC
62.873
68.421
27.26
18.61
40.61
3.51
366
367
2.356793
CTCGGGCTGATCGGCATC
60.357
66.667
27.26
17.15
40.61
3.91
367
368
4.615815
GCTCGGGCTGATCGGCAT
62.616
66.667
27.26
0.00
40.61
4.40
371
372
2.509336
AAACGCTCGGGCTGATCG
60.509
61.111
17.24
17.24
41.79
3.69
372
373
1.424493
CTCAAACGCTCGGGCTGATC
61.424
60.000
5.36
0.00
36.09
2.92
373
374
1.448540
CTCAAACGCTCGGGCTGAT
60.449
57.895
5.36
0.00
36.09
2.90
374
375
2.048222
CTCAAACGCTCGGGCTGA
60.048
61.111
5.36
0.70
36.09
4.26
375
376
3.121030
CCTCAAACGCTCGGGCTG
61.121
66.667
5.36
0.78
36.09
4.85
380
381
1.586154
AAATGGGCCTCAAACGCTCG
61.586
55.000
4.53
0.00
0.00
5.03
381
382
0.109132
CAAATGGGCCTCAAACGCTC
60.109
55.000
4.53
0.00
0.00
5.03
382
383
0.539438
TCAAATGGGCCTCAAACGCT
60.539
50.000
4.53
0.00
0.00
5.07
383
384
0.109132
CTCAAATGGGCCTCAAACGC
60.109
55.000
4.53
0.00
0.00
4.84
384
385
0.527565
CCTCAAATGGGCCTCAAACG
59.472
55.000
4.53
0.00
0.00
3.60
385
386
0.247460
GCCTCAAATGGGCCTCAAAC
59.753
55.000
4.53
0.00
43.49
2.93
387
388
1.678635
CGCCTCAAATGGGCCTCAA
60.679
57.895
4.53
0.00
46.24
3.02
388
389
2.045045
CGCCTCAAATGGGCCTCA
60.045
61.111
4.53
0.00
46.24
3.86
389
390
2.044946
ACGCCTCAAATGGGCCTC
60.045
61.111
4.53
0.00
46.24
4.70
390
391
2.044946
GACGCCTCAAATGGGCCT
60.045
61.111
4.53
0.00
46.24
5.19
391
392
2.044946
AGACGCCTCAAATGGGCC
60.045
61.111
0.00
0.00
46.24
5.80
392
393
1.244019
AACAGACGCCTCAAATGGGC
61.244
55.000
0.00
0.00
45.57
5.36
393
394
1.068333
CAAACAGACGCCTCAAATGGG
60.068
52.381
0.00
0.00
0.00
4.00
395
396
1.068333
CCCAAACAGACGCCTCAAATG
60.068
52.381
0.00
0.00
0.00
2.32
396
397
1.247567
CCCAAACAGACGCCTCAAAT
58.752
50.000
0.00
0.00
0.00
2.32
397
398
0.106918
ACCCAAACAGACGCCTCAAA
60.107
50.000
0.00
0.00
0.00
2.69
398
399
0.106918
AACCCAAACAGACGCCTCAA
60.107
50.000
0.00
0.00
0.00
3.02
399
400
0.759959
TAACCCAAACAGACGCCTCA
59.240
50.000
0.00
0.00
0.00
3.86
400
401
1.886886
TTAACCCAAACAGACGCCTC
58.113
50.000
0.00
0.00
0.00
4.70
402
403
3.653539
ATTTTAACCCAAACAGACGCC
57.346
42.857
0.00
0.00
0.00
5.68
403
404
5.044558
TGAAATTTTAACCCAAACAGACGC
58.955
37.500
0.00
0.00
0.00
5.19
404
405
5.172411
CGTGAAATTTTAACCCAAACAGACG
59.828
40.000
0.00
0.00
0.00
4.18
405
406
6.197655
GTCGTGAAATTTTAACCCAAACAGAC
59.802
38.462
0.00
0.00
0.00
3.51
407
408
5.460748
GGTCGTGAAATTTTAACCCAAACAG
59.539
40.000
0.00
0.00
0.00
3.16
408
409
5.105473
TGGTCGTGAAATTTTAACCCAAACA
60.105
36.000
0.00
0.00
0.00
2.83
409
410
5.349809
TGGTCGTGAAATTTTAACCCAAAC
58.650
37.500
0.00
0.00
0.00
2.93
410
411
5.127356
ACTGGTCGTGAAATTTTAACCCAAA
59.873
36.000
0.00
0.00
0.00
3.28
411
412
4.645588
ACTGGTCGTGAAATTTTAACCCAA
59.354
37.500
0.00
0.00
0.00
4.12
414
415
5.008316
ACTGACTGGTCGTGAAATTTTAACC
59.992
40.000
0.00
0.00
0.00
2.85
415
416
6.056428
ACTGACTGGTCGTGAAATTTTAAC
57.944
37.500
0.00
0.00
0.00
2.01
416
417
7.254863
GGTTACTGACTGGTCGTGAAATTTTAA
60.255
37.037
0.00
0.00
0.00
1.52
417
418
6.203338
GGTTACTGACTGGTCGTGAAATTTTA
59.797
38.462
0.00
0.00
0.00
1.52
418
419
5.008316
GGTTACTGACTGGTCGTGAAATTTT
59.992
40.000
0.00
0.00
0.00
1.82
419
420
4.514066
GGTTACTGACTGGTCGTGAAATTT
59.486
41.667
0.00
0.00
0.00
1.82
420
421
4.062991
GGTTACTGACTGGTCGTGAAATT
58.937
43.478
7.89
0.00
0.00
1.82
421
422
3.660865
GGTTACTGACTGGTCGTGAAAT
58.339
45.455
7.89
0.00
0.00
2.17
422
423
2.544277
CGGTTACTGACTGGTCGTGAAA
60.544
50.000
7.89
0.00
0.00
2.69
423
424
1.001048
CGGTTACTGACTGGTCGTGAA
60.001
52.381
7.89
0.00
0.00
3.18
424
425
0.594602
CGGTTACTGACTGGTCGTGA
59.405
55.000
7.89
0.00
0.00
4.35
425
426
0.594602
TCGGTTACTGACTGGTCGTG
59.405
55.000
0.00
1.90
35.23
4.35
428
429
0.456312
CGCTCGGTTACTGACTGGTC
60.456
60.000
0.00
0.00
35.23
4.02
429
430
1.585006
CGCTCGGTTACTGACTGGT
59.415
57.895
0.00
0.00
35.23
4.00
430
431
1.153823
CCGCTCGGTTACTGACTGG
60.154
63.158
0.00
0.00
35.23
4.00
431
432
1.153823
CCCGCTCGGTTACTGACTG
60.154
63.158
7.59
0.00
35.87
3.51
432
433
3.003113
GCCCGCTCGGTTACTGACT
62.003
63.158
7.59
0.00
0.00
3.41
433
434
2.508663
GCCCGCTCGGTTACTGAC
60.509
66.667
7.59
0.00
0.00
3.51
434
435
2.678934
AGCCCGCTCGGTTACTGA
60.679
61.111
7.59
0.00
0.00
3.41
435
436
2.509336
CAGCCCGCTCGGTTACTG
60.509
66.667
7.59
7.97
0.00
2.74
436
437
4.452733
GCAGCCCGCTCGGTTACT
62.453
66.667
7.59
0.00
37.77
2.24
449
450
3.423154
CTCAAACGTCCGGGCAGC
61.423
66.667
6.96
0.00
0.00
5.25
456
457
1.161563
TCAAACCCGCTCAAACGTCC
61.162
55.000
0.00
0.00
0.00
4.79
459
460
1.574428
CCTCAAACCCGCTCAAACG
59.426
57.895
0.00
0.00
0.00
3.60
460
461
1.285950
GCCTCAAACCCGCTCAAAC
59.714
57.895
0.00
0.00
0.00
2.93
461
462
2.258013
CGCCTCAAACCCGCTCAAA
61.258
57.895
0.00
0.00
0.00
2.69
462
463
2.668212
CGCCTCAAACCCGCTCAA
60.668
61.111
0.00
0.00
0.00
3.02
463
464
3.621805
TCGCCTCAAACCCGCTCA
61.622
61.111
0.00
0.00
0.00
4.26
464
465
3.119096
GTCGCCTCAAACCCGCTC
61.119
66.667
0.00
0.00
0.00
5.03
465
466
4.699522
GGTCGCCTCAAACCCGCT
62.700
66.667
0.00
0.00
0.00
5.52
469
470
2.588856
ATAGCCGGTCGCCTCAAACC
62.589
60.000
1.90
0.00
38.78
3.27
470
471
0.103572
TATAGCCGGTCGCCTCAAAC
59.896
55.000
1.90
0.00
38.78
2.93
471
472
0.387929
CTATAGCCGGTCGCCTCAAA
59.612
55.000
1.90
0.00
38.78
2.69
473
474
0.251209
ATCTATAGCCGGTCGCCTCA
60.251
55.000
1.90
0.00
38.78
3.86
476
477
1.446272
GCATCTATAGCCGGTCGCC
60.446
63.158
1.90
0.00
38.78
5.54
477
478
0.456995
GAGCATCTATAGCCGGTCGC
60.457
60.000
1.90
0.00
37.98
5.19
478
479
3.704381
GAGCATCTATAGCCGGTCG
57.296
57.895
1.90
0.00
0.00
4.79
496
497
9.358872
GCCCAGTCAAAATTTTCTATTTCTTAG
57.641
33.333
0.00
0.00
0.00
2.18
497
498
8.026607
CGCCCAGTCAAAATTTTCTATTTCTTA
58.973
33.333
0.00
0.00
0.00
2.10
498
499
6.868339
CGCCCAGTCAAAATTTTCTATTTCTT
59.132
34.615
0.00
0.00
0.00
2.52
501
502
6.096673
ACGCCCAGTCAAAATTTTCTATTT
57.903
33.333
0.00
0.00
0.00
1.40
502
503
5.722021
ACGCCCAGTCAAAATTTTCTATT
57.278
34.783
0.00
0.00
0.00
1.73
503
504
5.242838
TCAACGCCCAGTCAAAATTTTCTAT
59.757
36.000
0.00
0.00
0.00
1.98
504
505
4.580995
TCAACGCCCAGTCAAAATTTTCTA
59.419
37.500
0.00
0.00
0.00
2.10
506
507
3.712187
TCAACGCCCAGTCAAAATTTTC
58.288
40.909
0.00
0.00
0.00
2.29
510
511
5.010617
ACTTTATTCAACGCCCAGTCAAAAT
59.989
36.000
0.00
0.00
0.00
1.82
512
513
3.886505
ACTTTATTCAACGCCCAGTCAAA
59.113
39.130
0.00
0.00
0.00
2.69
513
514
3.252215
CACTTTATTCAACGCCCAGTCAA
59.748
43.478
0.00
0.00
0.00
3.18
514
515
2.811431
CACTTTATTCAACGCCCAGTCA
59.189
45.455
0.00
0.00
0.00
3.41
515
516
2.414161
GCACTTTATTCAACGCCCAGTC
60.414
50.000
0.00
0.00
0.00
3.51
516
517
1.539827
GCACTTTATTCAACGCCCAGT
59.460
47.619
0.00
0.00
0.00
4.00
518
519
0.519519
CGCACTTTATTCAACGCCCA
59.480
50.000
0.00
0.00
0.00
5.36
519
520
0.796870
GCGCACTTTATTCAACGCCC
60.797
55.000
0.30
0.00
40.43
6.13
520
521
1.125847
CGCGCACTTTATTCAACGCC
61.126
55.000
8.75
0.00
43.15
5.68
523
524
1.578915
CATGCGCGCACTTTATTCAAC
59.421
47.619
39.05
0.00
0.00
3.18
524
525
1.893759
CATGCGCGCACTTTATTCAA
58.106
45.000
39.05
9.89
0.00
2.69
525
526
0.523125
GCATGCGCGCACTTTATTCA
60.523
50.000
39.05
10.81
0.00
2.57
527
528
4.382728
GCATGCGCGCACTTTATT
57.617
50.000
39.05
17.70
0.00
1.40
538
539
4.740062
TGCTTTGCGTCGCATGCG
62.740
61.111
33.61
33.61
39.74
4.73
539
540
3.167945
GTGCTTTGCGTCGCATGC
61.168
61.111
27.68
27.68
38.76
4.06
540
541
1.794785
CAGTGCTTTGCGTCGCATG
60.795
57.895
22.41
17.42
38.76
4.06
541
542
1.960763
TCAGTGCTTTGCGTCGCAT
60.961
52.632
22.41
1.06
38.76
4.73
546
547
1.032014
AAATGGTCAGTGCTTTGCGT
58.968
45.000
0.00
0.00
0.00
5.24
548
549
2.129607
CACAAATGGTCAGTGCTTTGC
58.870
47.619
0.00
0.00
33.03
3.68
551
552
2.099592
CACACACAAATGGTCAGTGCTT
59.900
45.455
0.00
0.00
36.76
3.91
552
553
1.677576
CACACACAAATGGTCAGTGCT
59.322
47.619
0.00
0.00
36.76
4.40
553
554
1.865248
GCACACACAAATGGTCAGTGC
60.865
52.381
0.00
0.00
44.76
4.40
554
555
1.269206
GGCACACACAAATGGTCAGTG
60.269
52.381
0.00
0.00
39.12
3.66
555
556
1.032014
GGCACACACAAATGGTCAGT
58.968
50.000
0.00
0.00
0.00
3.41
556
557
1.031235
TGGCACACACAAATGGTCAG
58.969
50.000
0.00
0.00
0.00
3.51
557
558
3.197664
TGGCACACACAAATGGTCA
57.802
47.368
0.00
0.00
0.00
4.02
569
570
2.512705
TCAGTTTACATGCATGGCACA
58.487
42.857
29.41
9.76
43.04
4.57
570
571
3.574284
TTCAGTTTACATGCATGGCAC
57.426
42.857
29.41
21.00
43.04
5.01
571
572
3.573538
AGTTTCAGTTTACATGCATGGCA
59.426
39.130
29.41
14.80
44.86
4.92
572
573
4.178545
AGTTTCAGTTTACATGCATGGC
57.821
40.909
29.41
16.20
0.00
4.40
573
574
6.149308
TGTCTAGTTTCAGTTTACATGCATGG
59.851
38.462
29.41
11.47
0.00
3.66
574
575
7.132694
TGTCTAGTTTCAGTTTACATGCATG
57.867
36.000
25.09
25.09
0.00
4.06
576
577
6.989759
TCTTGTCTAGTTTCAGTTTACATGCA
59.010
34.615
0.00
0.00
0.00
3.96
577
578
7.042051
TGTCTTGTCTAGTTTCAGTTTACATGC
60.042
37.037
0.00
0.00
0.00
4.06
578
579
8.276325
GTGTCTTGTCTAGTTTCAGTTTACATG
58.724
37.037
0.00
0.00
0.00
3.21
579
580
7.985184
TGTGTCTTGTCTAGTTTCAGTTTACAT
59.015
33.333
0.00
0.00
0.00
2.29
580
581
7.324935
TGTGTCTTGTCTAGTTTCAGTTTACA
58.675
34.615
0.00
0.00
0.00
2.41
581
582
7.042658
CCTGTGTCTTGTCTAGTTTCAGTTTAC
60.043
40.741
0.00
0.00
0.00
2.01
582
583
6.984474
CCTGTGTCTTGTCTAGTTTCAGTTTA
59.016
38.462
0.00
0.00
0.00
2.01
583
584
5.817816
CCTGTGTCTTGTCTAGTTTCAGTTT
59.182
40.000
0.00
0.00
0.00
2.66
585
586
4.202264
CCCTGTGTCTTGTCTAGTTTCAGT
60.202
45.833
0.00
0.00
0.00
3.41
586
587
4.039245
TCCCTGTGTCTTGTCTAGTTTCAG
59.961
45.833
0.00
0.00
0.00
3.02
587
588
3.964688
TCCCTGTGTCTTGTCTAGTTTCA
59.035
43.478
0.00
0.00
0.00
2.69
588
589
4.308265
GTCCCTGTGTCTTGTCTAGTTTC
58.692
47.826
0.00
0.00
0.00
2.78
589
590
3.243771
CGTCCCTGTGTCTTGTCTAGTTT
60.244
47.826
0.00
0.00
0.00
2.66
591
592
1.887198
CGTCCCTGTGTCTTGTCTAGT
59.113
52.381
0.00
0.00
0.00
2.57
592
593
1.202582
CCGTCCCTGTGTCTTGTCTAG
59.797
57.143
0.00
0.00
0.00
2.43
594
595
1.472662
CCCGTCCCTGTGTCTTGTCT
61.473
60.000
0.00
0.00
0.00
3.41
595
596
1.004918
CCCGTCCCTGTGTCTTGTC
60.005
63.158
0.00
0.00
0.00
3.18
596
597
3.148084
CCCGTCCCTGTGTCTTGT
58.852
61.111
0.00
0.00
0.00
3.16
597
598
2.358737
GCCCGTCCCTGTGTCTTG
60.359
66.667
0.00
0.00
0.00
3.02
598
599
3.637273
GGCCCGTCCCTGTGTCTT
61.637
66.667
0.00
0.00
0.00
3.01
599
600
4.640690
AGGCCCGTCCCTGTGTCT
62.641
66.667
0.00
0.00
32.84
3.41
600
601
1.833787
TAAAGGCCCGTCCCTGTGTC
61.834
60.000
0.00
0.00
34.80
3.67
601
602
1.205460
ATAAAGGCCCGTCCCTGTGT
61.205
55.000
0.00
0.00
34.80
3.72
602
603
0.034477
AATAAAGGCCCGTCCCTGTG
60.034
55.000
0.00
0.00
34.80
3.66
603
604
0.702316
AAATAAAGGCCCGTCCCTGT
59.298
50.000
0.00
0.00
34.80
4.00
604
605
1.847328
AAAATAAAGGCCCGTCCCTG
58.153
50.000
0.00
0.00
34.80
4.45
605
606
2.615986
AAAAATAAAGGCCCGTCCCT
57.384
45.000
0.00
0.00
36.58
4.20
621
622
2.317040
TGATTTGCCGTACCCCAAAAA
58.683
42.857
8.96
0.79
34.93
1.94
623
624
1.996798
TTGATTTGCCGTACCCCAAA
58.003
45.000
7.72
7.72
35.64
3.28
625
626
2.223803
AATTGATTTGCCGTACCCCA
57.776
45.000
0.00
0.00
0.00
4.96
627
628
3.428862
CCAGAAATTGATTTGCCGTACCC
60.429
47.826
0.00
0.00
0.00
3.69
628
629
3.192633
ACCAGAAATTGATTTGCCGTACC
59.807
43.478
0.00
0.00
0.00
3.34
629
630
4.412207
GACCAGAAATTGATTTGCCGTAC
58.588
43.478
0.00
0.00
0.00
3.67
630
631
3.442273
GGACCAGAAATTGATTTGCCGTA
59.558
43.478
0.00
0.00
0.00
4.02
631
632
2.231235
GGACCAGAAATTGATTTGCCGT
59.769
45.455
0.00
0.00
0.00
5.68
633
634
3.959535
TGGACCAGAAATTGATTTGCC
57.040
42.857
0.00
0.00
0.00
4.52
634
635
6.806388
AAATTGGACCAGAAATTGATTTGC
57.194
33.333
0.00
0.00
0.00
3.68
637
638
9.506018
CCTTTAAAATTGGACCAGAAATTGATT
57.494
29.630
0.00
0.00
0.00
2.57
639
640
8.028652
ACCTTTAAAATTGGACCAGAAATTGA
57.971
30.769
0.00
0.00
0.00
2.57
641
642
9.693739
AAAACCTTTAAAATTGGACCAGAAATT
57.306
25.926
0.00
0.00
0.00
1.82
887
896
2.223340
GCTGCTTCATCGTTTACATGGG
60.223
50.000
0.00
0.00
0.00
4.00
1029
1050
3.861840
ACGTCTCTCTCTCTCTCTTCTG
58.138
50.000
0.00
0.00
0.00
3.02
1046
1067
3.002144
GTCCGGTTATCTCTGAGTACGTC
59.998
52.174
0.00
0.00
0.00
4.34
1271
1319
1.548719
GGGGCACTTGTTATTTGGGTC
59.451
52.381
0.00
0.00
0.00
4.46
1272
1320
1.149077
AGGGGCACTTGTTATTTGGGT
59.851
47.619
0.00
0.00
0.00
4.51
1284
1335
0.618680
TGCAGACTATCAGGGGCACT
60.619
55.000
0.00
0.00
0.00
4.40
1323
1803
2.815945
CCCGGCCTCTGCATGATCT
61.816
63.158
0.00
0.00
40.13
2.75
1327
1807
3.479203
TACCCCGGCCTCTGCATG
61.479
66.667
0.00
0.00
40.13
4.06
1580
2183
9.953697
CTACTACTACTACCAAAAGAGCAATAG
57.046
37.037
0.00
0.00
0.00
1.73
1617
3290
4.713792
ACCTGAAGACTGGAGAAACATT
57.286
40.909
0.00
0.00
38.29
2.71
1695
3368
4.201705
GCGTTTTGTATTCAATTGGGCATG
60.202
41.667
5.42
0.00
33.32
4.06
1704
3382
6.535811
CATACCGTTAGCGTTTTGTATTCAA
58.464
36.000
0.00
0.00
36.15
2.69
1705
3383
5.446206
GCATACCGTTAGCGTTTTGTATTCA
60.446
40.000
0.00
0.00
36.15
2.57
1716
3394
2.350192
TCATGTTTGCATACCGTTAGCG
59.650
45.455
4.77
0.00
33.30
4.26
1764
3442
0.834612
TCCAAGTCCACCAAGTCGTT
59.165
50.000
0.00
0.00
0.00
3.85
1845
3538
2.160013
CGAGACGACGACATTTTGGAAC
60.160
50.000
0.00
0.00
35.09
3.62
1863
3556
2.107950
TGCCCATGAAAACTACCGAG
57.892
50.000
0.00
0.00
0.00
4.63
1865
3558
3.541632
ACTATGCCCATGAAAACTACCG
58.458
45.455
0.00
0.00
0.00
4.02
1868
4684
4.523083
GTGGACTATGCCCATGAAAACTA
58.477
43.478
0.00
0.00
35.91
2.24
1893
4709
6.454795
TGAAAATCCCTTGAAAATCCGAAAG
58.545
36.000
0.00
0.00
0.00
2.62
1897
4713
5.723295
ACATGAAAATCCCTTGAAAATCCG
58.277
37.500
0.00
0.00
0.00
4.18
1982
5014
4.252878
CAATAGGCATTTTGGGTTGGAAC
58.747
43.478
0.00
0.00
0.00
3.62
1983
5015
3.262915
CCAATAGGCATTTTGGGTTGGAA
59.737
43.478
12.14
0.00
38.98
3.53
1984
5016
2.836981
CCAATAGGCATTTTGGGTTGGA
59.163
45.455
12.14
0.00
38.98
3.53
1985
5017
3.264998
CCAATAGGCATTTTGGGTTGG
57.735
47.619
12.14
0.00
38.98
3.77
2008
5040
2.143122
TGCTTTCGACAGTAAGCCAAG
58.857
47.619
15.11
0.86
46.14
3.61
2010
5042
1.871039
GTTGCTTTCGACAGTAAGCCA
59.129
47.619
15.11
3.58
46.14
4.75
2054
5088
0.102481
CAGAATGCTTGGCCTCATGC
59.898
55.000
3.32
3.62
42.34
4.06
2097
5131
8.438676
AATGATTAGAAAATGTAGGGAAGACG
57.561
34.615
0.00
0.00
0.00
4.18
2149
5183
5.048504
TGTCTTCACAAAAATGAGGCTGATC
60.049
40.000
0.00
0.00
0.00
2.92
2346
5381
5.458041
TCTGTACAGTTTTAAGTAGGCGT
57.542
39.130
21.99
0.00
0.00
5.68
Based at the University of Bristol with support from BBSRC .
AutoCloner maintained by Alex Coulton.