Multiple sequence alignment - TraesCS3B01G278100
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
TraesCS3B01G278100
chr3B
100.000
3320
0
0
1
3320
448315709
448312390
0.000000e+00
6131.0
1
TraesCS3B01G278100
chr3A
93.253
1749
78
18
684
2404
467404451
467402715
0.000000e+00
2540.0
2
TraesCS3B01G278100
chr3A
92.336
274
13
5
1
266
467405132
467404859
1.870000e-102
383.0
3
TraesCS3B01G278100
chr3A
93.976
166
8
1
2601
2764
467402720
467402555
1.980000e-62
250.0
4
TraesCS3B01G278100
chr3A
82.609
207
36
0
2398
2604
728367660
728367454
2.030000e-42
183.0
5
TraesCS3B01G278100
chr3D
93.891
1555
75
15
858
2404
348913258
348911716
0.000000e+00
2327.0
6
TraesCS3B01G278100
chr3D
91.713
893
55
9
1
882
348915811
348914927
0.000000e+00
1221.0
7
TraesCS3B01G278100
chr3D
85.740
561
66
10
2764
3317
90351059
90351612
6.170000e-162
580.0
8
TraesCS3B01G278100
chr3D
84.602
565
68
17
2766
3317
8688572
8688014
8.100000e-151
544.0
9
TraesCS3B01G278100
chr3D
93.069
101
5
1
2601
2699
348911721
348911621
2.670000e-31
147.0
10
TraesCS3B01G278100
chr6D
85.689
566
67
11
2764
3317
405819404
405819967
4.770000e-163
584.0
11
TraesCS3B01G278100
chr6D
84.480
567
72
13
2764
3317
359522073
359522636
2.250000e-151
545.0
12
TraesCS3B01G278100
chr2D
84.574
564
72
13
2765
3317
456961729
456961170
2.250000e-151
545.0
13
TraesCS3B01G278100
chr2D
84.468
573
65
17
2764
3317
103169389
103169956
8.100000e-151
544.0
14
TraesCS3B01G278100
chr2D
94.286
35
1
1
1464
1498
643878760
643878793
6.000000e-03
52.8
15
TraesCS3B01G278100
chr7A
84.698
562
67
14
2764
3317
9200021
9199471
8.100000e-151
544.0
16
TraesCS3B01G278100
chr7A
84.058
207
32
1
2398
2604
614080968
614081173
7.260000e-47
198.0
17
TraesCS3B01G278100
chr1A
84.683
568
62
21
2764
3317
583608388
583607832
8.100000e-151
544.0
18
TraesCS3B01G278100
chr6A
84.369
563
71
12
2764
3317
71530044
71530598
1.360000e-148
536.0
19
TraesCS3B01G278100
chr6A
91.787
207
16
1
2398
2603
196951372
196951578
1.510000e-73
287.0
20
TraesCS3B01G278100
chr6A
89.604
202
20
1
2403
2604
521465293
521465093
4.250000e-64
255.0
21
TraesCS3B01G278100
chr6A
85.047
214
29
3
2398
2611
117126339
117126549
7.210000e-52
215.0
22
TraesCS3B01G278100
chr4A
91.176
204
17
1
2401
2604
96449861
96449659
3.260000e-70
276.0
23
TraesCS3B01G278100
chr4A
100.000
30
0
0
1595
1624
164687991
164687962
4.630000e-04
56.5
24
TraesCS3B01G278100
chr5A
88.350
206
22
2
2399
2603
397753517
397753313
2.560000e-61
246.0
25
TraesCS3B01G278100
chr5A
85.572
201
28
1
2401
2601
592604799
592604600
3.360000e-50
209.0
26
TraesCS3B01G278100
chr2A
85.784
204
27
2
2401
2604
502954824
502954623
7.210000e-52
215.0
27
TraesCS3B01G278100
chr4D
100.000
30
0
0
1595
1624
309943995
309944024
4.630000e-04
56.5
28
TraesCS3B01G278100
chr2B
94.286
35
1
1
1464
1498
793169492
793169459
6.000000e-03
52.8
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
TraesCS3B01G278100
chr3B
448312390
448315709
3319
True
6131.000000
6131
100.000000
1
3320
1
chr3B.!!$R1
3319
1
TraesCS3B01G278100
chr3A
467402555
467405132
2577
True
1057.666667
2540
93.188333
1
2764
3
chr3A.!!$R2
2763
2
TraesCS3B01G278100
chr3D
348911621
348915811
4190
True
1231.666667
2327
92.891000
1
2699
3
chr3D.!!$R2
2698
3
TraesCS3B01G278100
chr3D
90351059
90351612
553
False
580.000000
580
85.740000
2764
3317
1
chr3D.!!$F1
553
4
TraesCS3B01G278100
chr3D
8688014
8688572
558
True
544.000000
544
84.602000
2766
3317
1
chr3D.!!$R1
551
5
TraesCS3B01G278100
chr6D
405819404
405819967
563
False
584.000000
584
85.689000
2764
3317
1
chr6D.!!$F2
553
6
TraesCS3B01G278100
chr6D
359522073
359522636
563
False
545.000000
545
84.480000
2764
3317
1
chr6D.!!$F1
553
7
TraesCS3B01G278100
chr2D
456961170
456961729
559
True
545.000000
545
84.574000
2765
3317
1
chr2D.!!$R1
552
8
TraesCS3B01G278100
chr2D
103169389
103169956
567
False
544.000000
544
84.468000
2764
3317
1
chr2D.!!$F1
553
9
TraesCS3B01G278100
chr7A
9199471
9200021
550
True
544.000000
544
84.698000
2764
3317
1
chr7A.!!$R1
553
10
TraesCS3B01G278100
chr1A
583607832
583608388
556
True
544.000000
544
84.683000
2764
3317
1
chr1A.!!$R1
553
11
TraesCS3B01G278100
chr6A
71530044
71530598
554
False
536.000000
536
84.369000
2764
3317
1
chr6A.!!$F1
553
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
928
2698
0.597072
TATTTTCCCGCGCCGTTTTT
59.403
45.0
0.0
0.0
0.0
1.94
F
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
Orientation
2403
4194
0.603065
AATCGCCCAAAAGAACTGGC
59.397
50.0
0.0
0.0
40.54
4.85
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
42
43
1.263217
ACACGCATTTGTTCCGACTTC
59.737
47.619
0.00
0.00
0.00
3.01
56
57
1.336517
CGACTTCGGTACCTCTGCAAA
60.337
52.381
10.90
0.00
35.37
3.68
61
62
0.748005
CGGTACCTCTGCAAATGGGG
60.748
60.000
10.90
0.00
0.00
4.96
286
297
1.067776
ACCGATCCTTCACACGAGAAC
60.068
52.381
0.00
0.00
0.00
3.01
303
314
2.124736
CCGGTGGCCGTCATTGAT
60.125
61.111
0.00
0.00
46.80
2.57
336
347
4.494855
GCTGCGGAGTCACTGATTTATTTC
60.495
45.833
5.62
0.00
0.00
2.17
359
370
1.669115
CCTTGCCACTGTCCAGTCG
60.669
63.158
0.00
0.00
40.20
4.18
360
371
1.669115
CTTGCCACTGTCCAGTCGG
60.669
63.158
0.00
4.56
40.20
4.79
361
372
3.825160
TTGCCACTGTCCAGTCGGC
62.825
63.158
22.85
22.85
46.36
5.54
362
373
4.314440
GCCACTGTCCAGTCGGCA
62.314
66.667
23.85
0.00
45.91
5.69
435
447
6.383415
TGCCAAACGGTGAAATATTCTTTAC
58.617
36.000
0.00
0.00
0.00
2.01
446
458
6.371548
TGAAATATTCTTTACGCACTTGAGCT
59.628
34.615
0.00
0.00
0.00
4.09
509
525
1.876156
GCGGACATGAATTCAGGATCC
59.124
52.381
25.68
23.20
0.00
3.36
516
532
4.353191
ACATGAATTCAGGATCCTATGGCT
59.647
41.667
25.68
0.00
0.00
4.75
530
546
4.102996
TCCTATGGCTGCACAAATATCTGA
59.897
41.667
0.50
0.00
0.00
3.27
531
547
5.008331
CCTATGGCTGCACAAATATCTGAT
58.992
41.667
0.50
0.00
0.00
2.90
533
549
6.656270
CCTATGGCTGCACAAATATCTGATTA
59.344
38.462
0.50
0.00
0.00
1.75
580
596
9.965824
GAAGATCTGGTTGAATTTCAAGTAAAA
57.034
29.630
12.02
0.00
37.00
1.52
581
597
9.750125
AAGATCTGGTTGAATTTCAAGTAAAAC
57.250
29.630
12.02
0.51
37.00
2.43
598
614
2.131776
AACTTTTGGTCCGTTCACCA
57.868
45.000
0.00
0.00
45.25
4.17
604
620
2.060050
TGGTCCGTTCACCAAAATGT
57.940
45.000
0.00
0.00
43.88
2.71
610
637
6.088173
GGTCCGTTCACCAAAATGTAAATAC
58.912
40.000
0.00
0.00
36.32
1.89
616
643
7.322699
CGTTCACCAAAATGTAAATACTGTCAC
59.677
37.037
0.00
0.00
0.00
3.67
645
672
5.743636
ATTTGATTACAGTTGTGGCCAAT
57.256
34.783
7.24
0.00
32.11
3.16
725
797
0.599204
TTCTGACGAAACCTCACCGC
60.599
55.000
0.00
0.00
0.00
5.68
748
820
6.562640
CGCAAGTGAAAAACCATGATTCTTTG
60.563
38.462
0.00
4.70
0.00
2.77
768
840
3.831715
GGTGCTACCAAGAATCAACAC
57.168
47.619
1.01
0.00
38.42
3.32
780
852
6.128336
CCAAGAATCAACACTCTGAATCAGAC
60.128
42.308
9.18
0.00
35.39
3.51
811
884
1.529244
AACAGGACAAGCCACAGCC
60.529
57.895
0.00
0.00
41.25
4.85
905
2675
1.694133
CCCAAGGCCCACAAAGCAAA
61.694
55.000
0.00
0.00
0.00
3.68
928
2698
0.597072
TATTTTCCCGCGCCGTTTTT
59.403
45.000
0.00
0.00
0.00
1.94
958
2728
1.076332
CCTTGACGCCTTAACTTCCG
58.924
55.000
0.00
0.00
0.00
4.30
1072
2845
1.233285
CCTGTGCACAGACAAGCTCC
61.233
60.000
41.50
1.67
46.59
4.70
1077
2850
1.595109
CACAGACAAGCTCCGCACA
60.595
57.895
0.00
0.00
0.00
4.57
1116
2889
2.876645
GCGCTTCTGGTCGACGAG
60.877
66.667
20.34
20.34
0.00
4.18
1117
2890
2.202492
CGCTTCTGGTCGACGAGG
60.202
66.667
24.82
12.60
0.00
4.63
1118
2891
2.687805
CGCTTCTGGTCGACGAGGA
61.688
63.158
24.82
17.28
0.00
3.71
1119
2892
1.137825
GCTTCTGGTCGACGAGGAG
59.862
63.158
26.73
26.73
31.27
3.69
1120
2893
1.803943
CTTCTGGTCGACGAGGAGG
59.196
63.158
24.22
11.98
0.00
4.30
1121
2894
0.677098
CTTCTGGTCGACGAGGAGGA
60.677
60.000
24.22
5.65
0.00
3.71
1122
2895
0.677098
TTCTGGTCGACGAGGAGGAG
60.677
60.000
24.82
2.02
0.00
3.69
1125
2898
1.820481
GGTCGACGAGGAGGAGGAG
60.820
68.421
9.92
0.00
0.00
3.69
1133
2906
2.829458
GGAGGAGGAGGACGACGG
60.829
72.222
0.00
0.00
0.00
4.79
1134
2907
2.045143
GAGGAGGAGGACGACGGT
60.045
66.667
0.00
0.00
0.00
4.83
1136
2909
3.450115
GGAGGAGGACGACGGTGG
61.450
72.222
0.00
0.00
0.00
4.61
1445
3218
3.119495
ACGCTGTGCTCTGTTTTCTTTTT
60.119
39.130
0.00
0.00
0.00
1.94
1521
3297
3.760035
GGCGGCAAGTCGGAGAGA
61.760
66.667
3.07
0.00
36.95
3.10
1582
3358
2.740447
GTCGACAAAATTAAGGCGAGGT
59.260
45.455
11.55
0.00
0.00
3.85
1734
3510
1.081041
CGACGACGTGAACATCCCA
60.081
57.895
4.58
0.00
34.56
4.37
1827
3603
1.888736
GCTCTTAGGTCCGTCCGTT
59.111
57.895
0.00
0.00
41.99
4.44
1832
3608
1.271656
CTTAGGTCCGTCCGTTTGTCT
59.728
52.381
0.00
0.00
41.99
3.41
1839
3615
1.508632
CGTCCGTTTGTCTGTCCATT
58.491
50.000
0.00
0.00
0.00
3.16
1884
3675
7.751732
TGTGTTAATTGATTGATTCTTCTCGG
58.248
34.615
0.00
0.00
0.00
4.63
2345
4136
0.179032
TGAGGGCTTTTTGTCAGCGA
60.179
50.000
0.00
0.00
38.24
4.93
2401
4192
7.064134
TCACATACGAATTGTAGCAAGGTTTAG
59.936
37.037
0.00
0.00
36.25
1.85
2402
4193
6.315393
ACATACGAATTGTAGCAAGGTTTAGG
59.685
38.462
0.00
0.00
36.25
2.69
2403
4194
4.007659
ACGAATTGTAGCAAGGTTTAGGG
58.992
43.478
0.00
0.00
0.00
3.53
2404
4195
3.181500
CGAATTGTAGCAAGGTTTAGGGC
60.181
47.826
0.00
0.00
0.00
5.19
2405
4196
2.209690
TTGTAGCAAGGTTTAGGGCC
57.790
50.000
0.00
0.00
0.00
5.80
2406
4197
1.068948
TGTAGCAAGGTTTAGGGCCA
58.931
50.000
6.18
0.00
0.00
5.36
2407
4198
1.004277
TGTAGCAAGGTTTAGGGCCAG
59.996
52.381
6.18
0.00
0.00
4.85
2408
4199
1.004394
GTAGCAAGGTTTAGGGCCAGT
59.996
52.381
6.18
0.00
0.00
4.00
2409
4200
0.482887
AGCAAGGTTTAGGGCCAGTT
59.517
50.000
6.18
0.00
0.00
3.16
2410
4201
0.888619
GCAAGGTTTAGGGCCAGTTC
59.111
55.000
6.18
0.00
0.00
3.01
2411
4202
1.547901
GCAAGGTTTAGGGCCAGTTCT
60.548
52.381
6.18
0.00
0.00
3.01
2412
4203
2.876581
CAAGGTTTAGGGCCAGTTCTT
58.123
47.619
6.18
0.00
0.00
2.52
2413
4204
3.230976
CAAGGTTTAGGGCCAGTTCTTT
58.769
45.455
6.18
0.00
0.00
2.52
2414
4205
3.612795
AGGTTTAGGGCCAGTTCTTTT
57.387
42.857
6.18
0.00
0.00
2.27
2415
4206
3.230976
AGGTTTAGGGCCAGTTCTTTTG
58.769
45.455
6.18
0.00
0.00
2.44
2416
4207
2.299013
GGTTTAGGGCCAGTTCTTTTGG
59.701
50.000
6.18
0.00
38.78
3.28
2417
4208
2.299013
GTTTAGGGCCAGTTCTTTTGGG
59.701
50.000
6.18
0.00
36.19
4.12
2420
4211
3.758172
GCCAGTTCTTTTGGGCGA
58.242
55.556
0.00
0.00
36.58
5.54
2421
4212
2.267045
GCCAGTTCTTTTGGGCGAT
58.733
52.632
0.00
0.00
36.58
4.58
2422
4213
0.603065
GCCAGTTCTTTTGGGCGATT
59.397
50.000
0.00
0.00
36.58
3.34
2423
4214
1.402852
GCCAGTTCTTTTGGGCGATTC
60.403
52.381
0.00
0.00
36.58
2.52
2424
4215
2.162681
CCAGTTCTTTTGGGCGATTCT
58.837
47.619
0.00
0.00
31.87
2.40
2425
4216
2.558359
CCAGTTCTTTTGGGCGATTCTT
59.442
45.455
0.00
0.00
31.87
2.52
2426
4217
3.005791
CCAGTTCTTTTGGGCGATTCTTT
59.994
43.478
0.00
0.00
31.87
2.52
2427
4218
4.501400
CCAGTTCTTTTGGGCGATTCTTTT
60.501
41.667
0.00
0.00
31.87
2.27
2428
4219
5.278758
CCAGTTCTTTTGGGCGATTCTTTTA
60.279
40.000
0.00
0.00
31.87
1.52
2429
4220
5.858581
CAGTTCTTTTGGGCGATTCTTTTAG
59.141
40.000
0.00
0.00
0.00
1.85
2430
4221
5.768164
AGTTCTTTTGGGCGATTCTTTTAGA
59.232
36.000
0.00
0.00
0.00
2.10
2431
4222
6.264518
AGTTCTTTTGGGCGATTCTTTTAGAA
59.735
34.615
0.00
0.00
38.78
2.10
2432
4223
6.834168
TCTTTTGGGCGATTCTTTTAGAAT
57.166
33.333
1.73
1.73
46.84
2.40
2433
4224
7.227049
TCTTTTGGGCGATTCTTTTAGAATT
57.773
32.000
3.64
0.00
44.41
2.17
2434
4225
7.090173
TCTTTTGGGCGATTCTTTTAGAATTG
58.910
34.615
10.87
10.87
44.41
2.32
2439
4230
4.307443
CGATTCTTTTAGAATTGCCCCC
57.693
45.455
3.64
0.00
44.41
5.40
2547
4338
9.442047
GAAAATATATAGAGTGGTGATTCTGGG
57.558
37.037
0.00
0.00
0.00
4.45
2548
4339
8.742125
AAATATATAGAGTGGTGATTCTGGGA
57.258
34.615
0.00
0.00
0.00
4.37
2549
4340
7.969690
ATATATAGAGTGGTGATTCTGGGAG
57.030
40.000
0.00
0.00
0.00
4.30
2550
4341
2.630889
AGAGTGGTGATTCTGGGAGA
57.369
50.000
0.00
0.00
0.00
3.71
2551
4342
2.907892
AGAGTGGTGATTCTGGGAGAA
58.092
47.619
0.00
0.00
38.78
2.87
2552
4343
2.836981
AGAGTGGTGATTCTGGGAGAAG
59.163
50.000
0.00
0.00
37.69
2.85
2553
4344
1.280421
AGTGGTGATTCTGGGAGAAGC
59.720
52.381
0.00
0.00
40.77
3.86
2554
4345
1.280421
GTGGTGATTCTGGGAGAAGCT
59.720
52.381
3.49
0.00
40.96
3.74
2555
4346
1.280133
TGGTGATTCTGGGAGAAGCTG
59.720
52.381
3.49
0.00
40.96
4.24
2556
4347
1.407989
GGTGATTCTGGGAGAAGCTGG
60.408
57.143
3.49
0.00
40.96
4.85
2557
4348
1.556911
GTGATTCTGGGAGAAGCTGGA
59.443
52.381
3.49
0.00
40.96
3.86
2558
4349
1.836166
TGATTCTGGGAGAAGCTGGAG
59.164
52.381
3.49
0.00
40.96
3.86
2559
4350
2.114616
GATTCTGGGAGAAGCTGGAGA
58.885
52.381
0.00
0.00
37.62
3.71
2560
4351
2.030027
TTCTGGGAGAAGCTGGAGAA
57.970
50.000
0.00
0.00
29.50
2.87
2561
4352
1.566211
TCTGGGAGAAGCTGGAGAAG
58.434
55.000
0.00
0.00
0.00
2.85
2562
4353
1.077828
TCTGGGAGAAGCTGGAGAAGA
59.922
52.381
0.00
0.00
0.00
2.87
2563
4354
1.481772
CTGGGAGAAGCTGGAGAAGAG
59.518
57.143
0.00
0.00
0.00
2.85
2564
4355
0.829990
GGGAGAAGCTGGAGAAGAGG
59.170
60.000
0.00
0.00
0.00
3.69
2565
4356
1.621072
GGGAGAAGCTGGAGAAGAGGA
60.621
57.143
0.00
0.00
0.00
3.71
2566
4357
1.480545
GGAGAAGCTGGAGAAGAGGAC
59.519
57.143
0.00
0.00
0.00
3.85
2567
4358
1.134175
GAGAAGCTGGAGAAGAGGACG
59.866
57.143
0.00
0.00
0.00
4.79
2568
4359
1.178276
GAAGCTGGAGAAGAGGACGA
58.822
55.000
0.00
0.00
0.00
4.20
2569
4360
1.754226
GAAGCTGGAGAAGAGGACGAT
59.246
52.381
0.00
0.00
0.00
3.73
2570
4361
1.859302
AGCTGGAGAAGAGGACGATT
58.141
50.000
0.00
0.00
0.00
3.34
2571
4362
1.754226
AGCTGGAGAAGAGGACGATTC
59.246
52.381
0.00
0.00
0.00
2.52
2572
4363
1.754226
GCTGGAGAAGAGGACGATTCT
59.246
52.381
0.00
0.00
38.46
2.40
2573
4364
2.481104
GCTGGAGAAGAGGACGATTCTG
60.481
54.545
0.00
0.00
35.93
3.02
2574
4365
2.100584
CTGGAGAAGAGGACGATTCTGG
59.899
54.545
0.00
0.00
35.93
3.86
2575
4366
1.410882
GGAGAAGAGGACGATTCTGGG
59.589
57.143
0.00
0.00
35.93
4.45
2576
4367
2.379972
GAGAAGAGGACGATTCTGGGA
58.620
52.381
0.00
0.00
35.93
4.37
2577
4368
2.360801
GAGAAGAGGACGATTCTGGGAG
59.639
54.545
0.00
0.00
35.93
4.30
2578
4369
2.024846
AGAAGAGGACGATTCTGGGAGA
60.025
50.000
0.00
0.00
34.52
3.71
2579
4370
2.534042
AGAGGACGATTCTGGGAGAA
57.466
50.000
0.00
0.00
38.78
2.87
2580
4371
3.039252
AGAGGACGATTCTGGGAGAAT
57.961
47.619
0.00
0.00
46.84
2.40
2593
4384
3.748868
GGGAGAATCGCTGAAAAGAAC
57.251
47.619
0.00
0.00
45.72
3.01
2594
4385
3.339141
GGGAGAATCGCTGAAAAGAACT
58.661
45.455
0.00
0.00
45.72
3.01
2595
4386
3.126000
GGGAGAATCGCTGAAAAGAACTG
59.874
47.826
0.00
0.00
45.72
3.16
2596
4387
3.126000
GGAGAATCGCTGAAAAGAACTGG
59.874
47.826
0.00
0.00
34.37
4.00
2597
4388
2.485814
AGAATCGCTGAAAAGAACTGGC
59.514
45.455
0.00
0.00
0.00
4.85
2598
4389
1.168714
ATCGCTGAAAAGAACTGGCC
58.831
50.000
0.00
0.00
0.00
5.36
2599
4390
0.889186
TCGCTGAAAAGAACTGGCCC
60.889
55.000
0.00
0.00
0.00
5.80
2600
4391
0.890996
CGCTGAAAAGAACTGGCCCT
60.891
55.000
0.00
0.00
0.00
5.19
2601
4392
1.332195
GCTGAAAAGAACTGGCCCTT
58.668
50.000
0.00
0.00
0.00
3.95
2602
4393
2.514803
GCTGAAAAGAACTGGCCCTTA
58.485
47.619
0.00
0.00
0.00
2.69
2603
4394
2.489722
GCTGAAAAGAACTGGCCCTTAG
59.510
50.000
0.00
0.00
0.00
2.18
2628
4419
1.068741
GTTCATAGGATTCTCGCCGGT
59.931
52.381
1.90
0.00
0.00
5.28
2678
4471
3.692593
GTCTCACTCTCACCTACTCCTTC
59.307
52.174
0.00
0.00
0.00
3.46
2694
4487
1.299541
CTTCGCCACACACTTCTGTT
58.700
50.000
0.00
0.00
0.00
3.16
2705
4498
2.092646
ACACTTCTGTTAGGGCAACACA
60.093
45.455
0.00
0.00
42.29
3.72
2742
4535
8.948631
TTTAAAGATAGCTCAAGTATGACCTG
57.051
34.615
0.00
0.00
0.00
4.00
2750
4543
2.823747
TCAAGTATGACCTGCTACACGT
59.176
45.455
0.00
0.00
0.00
4.49
2753
4546
0.736636
TATGACCTGCTACACGTCGG
59.263
55.000
0.00
0.00
0.00
4.79
2779
4572
2.669434
TGCGTCAACTAATTAACGAGCC
59.331
45.455
10.75
0.00
37.31
4.70
2780
4573
2.928116
GCGTCAACTAATTAACGAGCCT
59.072
45.455
10.75
0.00
37.31
4.58
2796
4589
1.990060
CCTTCCTTCGGGAGCCTCA
60.990
63.158
0.00
0.00
45.95
3.86
2804
4599
0.690192
TCGGGAGCCTCACAAATCAA
59.310
50.000
0.00
0.00
0.00
2.57
2849
4644
1.161843
TCGTCATGTGTCGTGCTCTA
58.838
50.000
0.00
0.00
0.00
2.43
2938
4742
0.595567
GGGGTTTTCGACGTTTTGGC
60.596
55.000
0.00
0.00
0.00
4.52
2955
4759
1.674651
GCTTTCCACCGGTCTTCCC
60.675
63.158
2.59
0.00
0.00
3.97
2958
4762
1.626825
CTTTCCACCGGTCTTCCCTAA
59.373
52.381
2.59
0.00
0.00
2.69
2964
4768
3.483421
CACCGGTCTTCCCTAACTTTTT
58.517
45.455
2.59
0.00
0.00
1.94
3053
4869
2.634777
CGGTTTTGCTTCCGCGAA
59.365
55.556
8.23
0.00
40.28
4.70
3070
4886
1.451651
CGAAATGCACGGTTTTGCTTC
59.548
47.619
0.00
0.00
43.41
3.86
3083
4900
2.148916
TTGCTTCACGAGAATCACGT
57.851
45.000
0.00
0.00
44.83
4.49
3179
4999
3.460103
GAGAGGTACGGTTGTGTTTTCA
58.540
45.455
0.00
0.00
0.00
2.69
3319
5147
4.323477
CGTGCCTCCCGGAAACCA
62.323
66.667
0.73
0.00
0.00
3.67
Position
MSA Position
Penalty
Sequence
TM
GC
Self any TH
Self end TH
Hairpin
End Stability
42
43
0.748005
CCCCATTTGCAGAGGTACCG
60.748
60.000
6.18
0.00
0.00
4.02
45
46
1.077787
CGCCCCATTTGCAGAGGTA
60.078
57.895
0.00
0.00
0.00
3.08
48
49
2.420568
ATGCGCCCCATTTGCAGAG
61.421
57.895
4.18
0.00
42.65
3.35
61
62
2.050533
TGGTTTCGTTGCATGCGC
60.051
55.556
14.09
0.00
39.24
6.09
313
324
2.010145
TAAATCAGTGACTCCGCAGC
57.990
50.000
0.00
0.00
0.00
5.25
314
325
4.631377
TGAAATAAATCAGTGACTCCGCAG
59.369
41.667
0.00
0.00
0.00
5.18
336
347
0.250858
TGGACAGTGGCAAGGTGATG
60.251
55.000
0.00
0.00
0.00
3.07
359
370
1.961793
TTTACGGTCATATGCCTGCC
58.038
50.000
12.45
5.40
0.00
4.85
360
371
3.304659
CCATTTTACGGTCATATGCCTGC
60.305
47.826
12.45
0.00
0.00
4.85
361
372
3.882888
ACCATTTTACGGTCATATGCCTG
59.117
43.478
12.45
3.13
27.30
4.85
362
373
3.882888
CACCATTTTACGGTCATATGCCT
59.117
43.478
12.45
4.81
33.25
4.75
435
447
1.326852
CTGATGCTTAGCTCAAGTGCG
59.673
52.381
5.60
0.00
36.55
5.34
446
458
2.872245
GTCCGCTATTTGCTGATGCTTA
59.128
45.455
0.00
0.00
37.26
3.09
473
485
6.759356
TCATGTCCGCTATTATTCGAAGAAAA
59.241
34.615
9.57
1.12
45.90
2.29
475
487
5.838529
TCATGTCCGCTATTATTCGAAGAA
58.161
37.500
7.79
7.79
45.90
2.52
509
525
6.570672
AATCAGATATTTGTGCAGCCATAG
57.429
37.500
0.00
0.00
0.00
2.23
554
570
9.965824
TTTTACTTGAAATTCAACCAGATCTTC
57.034
29.630
4.03
0.00
32.21
2.87
560
576
9.971744
CAAAAGTTTTACTTGAAATTCAACCAG
57.028
29.630
4.03
0.00
38.66
4.00
580
596
3.886324
TGGTGAACGGACCAAAAGT
57.114
47.368
1.05
0.00
43.31
2.66
616
643
9.301153
GGCCACAACTGTAATCAAATAAATTAG
57.699
33.333
0.00
0.00
0.00
1.73
725
797
7.181143
CCAAAGAATCATGGTTTTTCACTTG
57.819
36.000
0.00
0.00
31.84
3.16
748
820
3.412386
AGTGTTGATTCTTGGTAGCACC
58.588
45.455
0.00
0.00
39.22
5.01
768
840
6.483307
TGTTTGTACCAAAGTCTGATTCAGAG
59.517
38.462
16.62
7.38
41.46
3.35
780
852
4.974368
TGTCCTGTTGTTTGTACCAAAG
57.026
40.909
0.00
0.00
0.00
2.77
811
884
4.811555
TTGACTGTGTTGAATTTCCGAG
57.188
40.909
0.00
0.00
0.00
4.63
905
2675
0.812549
ACGGCGCGGGAAAATATTTT
59.187
45.000
19.75
13.24
0.00
1.82
928
2698
1.365699
GCGTCAAGGCGAGGAATTTA
58.634
50.000
0.00
0.00
0.00
1.40
958
2728
3.813166
TCGATTTTTGAGTTGGAGGTGTC
59.187
43.478
0.00
0.00
0.00
3.67
1104
2877
1.078356
CTCCTCCTCGTCGACCAGA
60.078
63.158
12.11
2.26
0.00
3.86
1116
2889
2.829458
CCGTCGTCCTCCTCCTCC
60.829
72.222
0.00
0.00
0.00
4.30
1117
2890
2.045143
ACCGTCGTCCTCCTCCTC
60.045
66.667
0.00
0.00
0.00
3.71
1118
2891
2.361357
CACCGTCGTCCTCCTCCT
60.361
66.667
0.00
0.00
0.00
3.69
1119
2892
3.450115
CCACCGTCGTCCTCCTCC
61.450
72.222
0.00
0.00
0.00
4.30
1120
2893
4.131088
GCCACCGTCGTCCTCCTC
62.131
72.222
0.00
0.00
0.00
3.71
1151
2924
2.672307
AGAAGGACGACGAGCCGT
60.672
61.111
0.00
0.21
46.43
5.68
1314
3087
2.561976
CGAAGCAGTCGTGAAAGAAC
57.438
50.000
1.91
0.00
45.09
3.01
1582
3358
2.032528
CGGGCACTGCTTCTCCAA
59.967
61.111
0.00
0.00
0.00
3.53
1749
3525
2.517450
GCTGAGCGTCATGGCGTAC
61.517
63.158
22.33
15.46
38.18
3.67
1827
3603
1.003580
GGAGCTCCAATGGACAGACAA
59.996
52.381
28.43
0.00
35.64
3.18
1832
3608
1.993653
CAGGGAGCTCCAATGGACA
59.006
57.895
33.29
0.00
38.24
4.02
1839
3615
2.897271
TAAATTTGCAGGGAGCTCCA
57.103
45.000
33.29
13.04
45.94
3.86
1882
3673
4.124351
TACAAGCGGGTCGAGCCG
62.124
66.667
43.01
43.01
38.44
5.52
1884
3675
2.202756
CCTACAAGCGGGTCGAGC
60.203
66.667
5.93
5.93
0.00
5.03
2280
4071
3.866582
CTGATCCGGACCTGCCCC
61.867
72.222
6.12
0.00
0.00
5.80
2345
4136
4.135306
TGAGACCGAGTTAGAATCGCTAT
58.865
43.478
0.00
0.00
38.84
2.97
2349
4140
4.822036
ATCTGAGACCGAGTTAGAATCG
57.178
45.455
0.00
0.00
39.86
3.34
2401
4192
2.931068
CGCCCAAAAGAACTGGCCC
61.931
63.158
0.00
0.00
40.87
5.80
2402
4193
1.250840
ATCGCCCAAAAGAACTGGCC
61.251
55.000
0.00
0.00
40.87
5.36
2403
4194
0.603065
AATCGCCCAAAAGAACTGGC
59.397
50.000
0.00
0.00
40.54
4.85
2404
4195
2.162681
AGAATCGCCCAAAAGAACTGG
58.837
47.619
0.00
0.00
0.00
4.00
2405
4196
3.923017
AAGAATCGCCCAAAAGAACTG
57.077
42.857
0.00
0.00
0.00
3.16
2406
4197
4.937201
AAAAGAATCGCCCAAAAGAACT
57.063
36.364
0.00
0.00
0.00
3.01
2407
4198
6.009115
TCTAAAAGAATCGCCCAAAAGAAC
57.991
37.500
0.00
0.00
0.00
3.01
2408
4199
6.642707
TTCTAAAAGAATCGCCCAAAAGAA
57.357
33.333
0.00
0.00
0.00
2.52
2409
4200
6.834168
ATTCTAAAAGAATCGCCCAAAAGA
57.166
33.333
0.00
0.00
40.75
2.52
2410
4201
6.183360
GCAATTCTAAAAGAATCGCCCAAAAG
60.183
38.462
2.79
0.00
43.67
2.27
2411
4202
5.637387
GCAATTCTAAAAGAATCGCCCAAAA
59.363
36.000
2.79
0.00
43.67
2.44
2412
4203
5.167845
GCAATTCTAAAAGAATCGCCCAAA
58.832
37.500
2.79
0.00
43.67
3.28
2413
4204
4.743493
GCAATTCTAAAAGAATCGCCCAA
58.257
39.130
2.79
0.00
43.67
4.12
2414
4205
4.370364
GCAATTCTAAAAGAATCGCCCA
57.630
40.909
2.79
0.00
43.67
5.36
2417
4208
3.490933
GGGGGCAATTCTAAAAGAATCGC
60.491
47.826
4.37
4.37
43.67
4.58
2418
4209
4.307443
GGGGGCAATTCTAAAAGAATCG
57.693
45.455
2.79
0.00
43.67
3.34
2521
4312
9.442047
CCCAGAATCACCACTCTATATATTTTC
57.558
37.037
0.00
0.00
0.00
2.29
2522
4313
9.170890
TCCCAGAATCACCACTCTATATATTTT
57.829
33.333
0.00
0.00
0.00
1.82
2523
4314
8.742125
TCCCAGAATCACCACTCTATATATTT
57.258
34.615
0.00
0.00
0.00
1.40
2524
4315
8.180165
TCTCCCAGAATCACCACTCTATATATT
58.820
37.037
0.00
0.00
0.00
1.28
2525
4316
7.713518
TCTCCCAGAATCACCACTCTATATAT
58.286
38.462
0.00
0.00
0.00
0.86
2526
4317
7.103745
TCTCCCAGAATCACCACTCTATATA
57.896
40.000
0.00
0.00
0.00
0.86
2527
4318
5.970289
TCTCCCAGAATCACCACTCTATAT
58.030
41.667
0.00
0.00
0.00
0.86
2528
4319
5.403558
TCTCCCAGAATCACCACTCTATA
57.596
43.478
0.00
0.00
0.00
1.31
2529
4320
4.271807
TCTCCCAGAATCACCACTCTAT
57.728
45.455
0.00
0.00
0.00
1.98
2530
4321
3.757947
TCTCCCAGAATCACCACTCTA
57.242
47.619
0.00
0.00
0.00
2.43
2531
4322
2.630889
TCTCCCAGAATCACCACTCT
57.369
50.000
0.00
0.00
0.00
3.24
2532
4323
2.679349
GCTTCTCCCAGAATCACCACTC
60.679
54.545
0.00
0.00
33.13
3.51
2533
4324
1.280421
GCTTCTCCCAGAATCACCACT
59.720
52.381
0.00
0.00
33.13
4.00
2534
4325
1.280421
AGCTTCTCCCAGAATCACCAC
59.720
52.381
0.00
0.00
33.13
4.16
2535
4326
1.280133
CAGCTTCTCCCAGAATCACCA
59.720
52.381
0.00
0.00
33.13
4.17
2536
4327
1.407989
CCAGCTTCTCCCAGAATCACC
60.408
57.143
0.00
0.00
33.13
4.02
2537
4328
1.556911
TCCAGCTTCTCCCAGAATCAC
59.443
52.381
0.00
0.00
33.13
3.06
2538
4329
1.836166
CTCCAGCTTCTCCCAGAATCA
59.164
52.381
0.00
0.00
33.13
2.57
2539
4330
2.114616
TCTCCAGCTTCTCCCAGAATC
58.885
52.381
0.00
0.00
33.13
2.52
2540
4331
2.260639
TCTCCAGCTTCTCCCAGAAT
57.739
50.000
0.00
0.00
33.13
2.40
2541
4332
1.905215
CTTCTCCAGCTTCTCCCAGAA
59.095
52.381
0.00
0.00
32.50
3.02
2542
4333
1.077828
TCTTCTCCAGCTTCTCCCAGA
59.922
52.381
0.00
0.00
0.00
3.86
2543
4334
1.481772
CTCTTCTCCAGCTTCTCCCAG
59.518
57.143
0.00
0.00
0.00
4.45
2544
4335
1.566211
CTCTTCTCCAGCTTCTCCCA
58.434
55.000
0.00
0.00
0.00
4.37
2545
4336
0.829990
CCTCTTCTCCAGCTTCTCCC
59.170
60.000
0.00
0.00
0.00
4.30
2546
4337
1.480545
GTCCTCTTCTCCAGCTTCTCC
59.519
57.143
0.00
0.00
0.00
3.71
2547
4338
1.134175
CGTCCTCTTCTCCAGCTTCTC
59.866
57.143
0.00
0.00
0.00
2.87
2548
4339
1.181786
CGTCCTCTTCTCCAGCTTCT
58.818
55.000
0.00
0.00
0.00
2.85
2549
4340
1.178276
TCGTCCTCTTCTCCAGCTTC
58.822
55.000
0.00
0.00
0.00
3.86
2550
4341
1.859302
ATCGTCCTCTTCTCCAGCTT
58.141
50.000
0.00
0.00
0.00
3.74
2551
4342
1.754226
GAATCGTCCTCTTCTCCAGCT
59.246
52.381
0.00
0.00
0.00
4.24
2552
4343
1.754226
AGAATCGTCCTCTTCTCCAGC
59.246
52.381
0.00
0.00
0.00
4.85
2553
4344
2.100584
CCAGAATCGTCCTCTTCTCCAG
59.899
54.545
0.00
0.00
29.34
3.86
2554
4345
2.103373
CCAGAATCGTCCTCTTCTCCA
58.897
52.381
0.00
0.00
29.34
3.86
2555
4346
1.410882
CCCAGAATCGTCCTCTTCTCC
59.589
57.143
0.00
0.00
29.34
3.71
2556
4347
2.360801
CTCCCAGAATCGTCCTCTTCTC
59.639
54.545
0.00
0.00
29.34
2.87
2557
4348
2.024846
TCTCCCAGAATCGTCCTCTTCT
60.025
50.000
0.00
0.00
31.97
2.85
2558
4349
2.379972
TCTCCCAGAATCGTCCTCTTC
58.620
52.381
0.00
0.00
0.00
2.87
2559
4350
2.534042
TCTCCCAGAATCGTCCTCTT
57.466
50.000
0.00
0.00
0.00
2.85
2560
4351
2.534042
TTCTCCCAGAATCGTCCTCT
57.466
50.000
0.00
0.00
0.00
3.69
2568
4359
3.634397
TTTCAGCGATTCTCCCAGAAT
57.366
42.857
0.00
0.00
46.84
2.40
2569
4360
3.007940
TCTTTTCAGCGATTCTCCCAGAA
59.992
43.478
0.00
0.00
38.78
3.02
2570
4361
2.567169
TCTTTTCAGCGATTCTCCCAGA
59.433
45.455
0.00
0.00
0.00
3.86
2571
4362
2.977914
TCTTTTCAGCGATTCTCCCAG
58.022
47.619
0.00
0.00
0.00
4.45
2572
4363
3.074412
GTTCTTTTCAGCGATTCTCCCA
58.926
45.455
0.00
0.00
0.00
4.37
2573
4364
3.126000
CAGTTCTTTTCAGCGATTCTCCC
59.874
47.826
0.00
0.00
0.00
4.30
2574
4365
3.126000
CCAGTTCTTTTCAGCGATTCTCC
59.874
47.826
0.00
0.00
0.00
3.71
2575
4366
3.425492
GCCAGTTCTTTTCAGCGATTCTC
60.425
47.826
0.00
0.00
0.00
2.87
2576
4367
2.485814
GCCAGTTCTTTTCAGCGATTCT
59.514
45.455
0.00
0.00
0.00
2.40
2577
4368
2.414691
GGCCAGTTCTTTTCAGCGATTC
60.415
50.000
0.00
0.00
0.00
2.52
2578
4369
1.541588
GGCCAGTTCTTTTCAGCGATT
59.458
47.619
0.00
0.00
0.00
3.34
2579
4370
1.168714
GGCCAGTTCTTTTCAGCGAT
58.831
50.000
0.00
0.00
0.00
4.58
2580
4371
0.889186
GGGCCAGTTCTTTTCAGCGA
60.889
55.000
4.39
0.00
0.00
4.93
2581
4372
0.890996
AGGGCCAGTTCTTTTCAGCG
60.891
55.000
6.18
0.00
0.00
5.18
2582
4373
1.332195
AAGGGCCAGTTCTTTTCAGC
58.668
50.000
6.18
0.00
0.00
4.26
2583
4374
3.084786
CCTAAGGGCCAGTTCTTTTCAG
58.915
50.000
6.18
0.00
0.00
3.02
2584
4375
2.225017
CCCTAAGGGCCAGTTCTTTTCA
60.225
50.000
6.18
0.00
35.35
2.69
2585
4376
2.447443
CCCTAAGGGCCAGTTCTTTTC
58.553
52.381
6.18
0.00
35.35
2.29
2586
4377
2.604912
CCCTAAGGGCCAGTTCTTTT
57.395
50.000
6.18
0.00
35.35
2.27
2598
4389
4.660771
AGAATCCTATGAACCACCCTAAGG
59.339
45.833
0.00
0.00
40.04
2.69
2599
4390
5.509840
CGAGAATCCTATGAACCACCCTAAG
60.510
48.000
0.00
0.00
0.00
2.18
2600
4391
4.344102
CGAGAATCCTATGAACCACCCTAA
59.656
45.833
0.00
0.00
0.00
2.69
2601
4392
3.895656
CGAGAATCCTATGAACCACCCTA
59.104
47.826
0.00
0.00
0.00
3.53
2602
4393
2.700897
CGAGAATCCTATGAACCACCCT
59.299
50.000
0.00
0.00
0.00
4.34
2603
4394
2.807108
GCGAGAATCCTATGAACCACCC
60.807
54.545
0.00
0.00
0.00
4.61
2678
4471
1.148310
CCTAACAGAAGTGTGTGGCG
58.852
55.000
0.00
0.00
36.84
5.69
2816
4611
0.673333
TGACGAATGATTGGCAGCGT
60.673
50.000
0.00
0.00
41.94
5.07
2821
4616
2.537529
CGACACATGACGAATGATTGGC
60.538
50.000
0.00
0.99
38.72
4.52
2822
4617
2.672874
ACGACACATGACGAATGATTGG
59.327
45.455
10.57
0.00
38.72
3.16
2849
4644
2.474410
AAAATTCGAAGGGAGCGTCT
57.526
45.000
3.35
0.00
0.00
4.18
2922
4726
2.532723
GGAAAGCCAAAACGTCGAAAAC
59.467
45.455
0.00
0.00
0.00
2.43
2938
4742
1.272807
TAGGGAAGACCGGTGGAAAG
58.727
55.000
14.63
0.00
46.96
2.62
3070
4886
0.710567
GCACAGACGTGATTCTCGTG
59.289
55.000
17.49
7.65
46.80
4.35
3238
5066
1.494824
AAACCGTGACTCTTGCGTAC
58.505
50.000
0.00
0.00
0.00
3.67
3240
5068
0.655733
CAAAACCGTGACTCTTGCGT
59.344
50.000
0.00
0.00
0.00
5.24
Based at the University of Bristol with support from BBSRC .
AutoCloner maintained by Alex Coulton.