Multiple sequence alignment - TraesCS1A01G108700

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


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 TraesCS1A01G108700 chr1A 100.000 2552 0 0 1 2552 107936215 107938766 0.000000e+00 4713
1 TraesCS1A01G108700 chr4A 95.714 1913 37 15 674 2552 575711417 575709516 0.000000e+00 3037
2 TraesCS1A01G108700 chr4A 97.754 1558 34 1 995 2552 521817113 521818669 0.000000e+00 2682
3 TraesCS1A01G108700 chr4A 98.370 368 4 2 293 659 575711761 575711395 0.000000e+00 645
4 TraesCS1A01G108700 chr7A 98.589 1559 22 0 994 2552 11231164 11232722 0.000000e+00 2758
5 TraesCS1A01G108700 chr7A 97.498 1559 39 0 994 2552 5440235 5438677 0.000000e+00 2663
6 TraesCS1A01G108700 chr7A 93.515 293 18 1 1 292 47774174 47773882 3.900000e-118 435
7 TraesCS1A01G108700 chr5A 96.356 1674 23 4 674 2314 475263894 475262226 0.000000e+00 2719
8 TraesCS1A01G108700 chr5A 97.756 1560 35 0 993 2552 282590969 282592528 0.000000e+00 2687
9 TraesCS1A01G108700 chr5A 97.502 1561 39 0 992 2552 547391270 547389710 0.000000e+00 2667
10 TraesCS1A01G108700 chr5A 97.373 1561 38 1 992 2552 505620059 505618502 0.000000e+00 2652
11 TraesCS1A01G108700 chr5A 97.936 533 9 2 293 825 598094398 598094928 0.000000e+00 922
12 TraesCS1A01G108700 chr5A 96.930 228 4 3 433 659 475264097 475263872 1.850000e-101 379
13 TraesCS1A01G108700 chr5B 97.627 1559 33 2 994 2552 184777930 184776376 0.000000e+00 2671
14 TraesCS1A01G108700 chr6A 97.434 1559 40 0 994 2552 101564726 101566284 0.000000e+00 2658
15 TraesCS1A01G108700 chr6A 92.881 295 18 2 1 292 474452110 474451816 2.350000e-115 425
16 TraesCS1A01G108700 chr6A 92.203 295 19 3 1 292 474881950 474881657 5.080000e-112 414
17 TraesCS1A01G108700 chr6D 86.223 2301 233 41 293 2552 305998629 305996372 0.000000e+00 2416
18 TraesCS1A01G108700 chr6D 94.468 235 9 3 293 525 275465309 275465077 2.410000e-95 359
19 TraesCS1A01G108700 chr5D 92.487 386 25 2 420 805 338528312 338527931 1.330000e-152 549
20 TraesCS1A01G108700 chr5D 92.742 248 12 4 293 538 220702582 220702339 1.120000e-93 353
21 TraesCS1A01G108700 chr5D 92.857 238 12 3 290 525 47533717 47533951 8.740000e-90 340
22 TraesCS1A01G108700 chr1D 93.898 295 15 2 1 292 356417646 356417940 2.330000e-120 442
23 TraesCS1A01G108700 chr1D 91.554 296 21 3 1 292 209523061 209523356 3.060000e-109 405
24 TraesCS1A01G108700 chr3A 92.881 295 18 2 1 292 511212112 511211818 2.350000e-115 425
25 TraesCS1A01G108700 chr2B 91.156 294 21 4 3 292 512925114 512925406 6.620000e-106 394
26 TraesCS1A01G108700 chr2A 90.508 295 25 2 1 292 598465671 598465377 1.110000e-103 387
27 TraesCS1A01G108700 chr2A 90.508 295 25 2 1 292 603916424 603916130 1.110000e-103 387
28 TraesCS1A01G108700 chr3D 89.610 308 20 8 292 597 105444499 105444796 5.150000e-102 381
29 TraesCS1A01G108700 chr3D 91.667 252 14 5 290 538 246601760 246601513 2.430000e-90 342
30 TraesCS1A01G108700 chr7D 94.492 236 9 3 292 525 84266927 84266694 6.710000e-96 361


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 TraesCS1A01G108700 chr1A 107936215 107938766 2551 False 4713 4713 100.000 1 2552 1 chr1A.!!$F1 2551
1 TraesCS1A01G108700 chr4A 521817113 521818669 1556 False 2682 2682 97.754 995 2552 1 chr4A.!!$F1 1557
2 TraesCS1A01G108700 chr4A 575709516 575711761 2245 True 1841 3037 97.042 293 2552 2 chr4A.!!$R1 2259
3 TraesCS1A01G108700 chr7A 11231164 11232722 1558 False 2758 2758 98.589 994 2552 1 chr7A.!!$F1 1558
4 TraesCS1A01G108700 chr7A 5438677 5440235 1558 True 2663 2663 97.498 994 2552 1 chr7A.!!$R1 1558
5 TraesCS1A01G108700 chr5A 282590969 282592528 1559 False 2687 2687 97.756 993 2552 1 chr5A.!!$F1 1559
6 TraesCS1A01G108700 chr5A 547389710 547391270 1560 True 2667 2667 97.502 992 2552 1 chr5A.!!$R2 1560
7 TraesCS1A01G108700 chr5A 505618502 505620059 1557 True 2652 2652 97.373 992 2552 1 chr5A.!!$R1 1560
8 TraesCS1A01G108700 chr5A 475262226 475264097 1871 True 1549 2719 96.643 433 2314 2 chr5A.!!$R3 1881
9 TraesCS1A01G108700 chr5A 598094398 598094928 530 False 922 922 97.936 293 825 1 chr5A.!!$F2 532
10 TraesCS1A01G108700 chr5B 184776376 184777930 1554 True 2671 2671 97.627 994 2552 1 chr5B.!!$R1 1558
11 TraesCS1A01G108700 chr6A 101564726 101566284 1558 False 2658 2658 97.434 994 2552 1 chr6A.!!$F1 1558
12 TraesCS1A01G108700 chr6D 305996372 305998629 2257 True 2416 2416 86.223 293 2552 1 chr6D.!!$R2 2259

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.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
654 655 0.250727 CAAGCCGGTTTTCCTCTGGA 60.251 55.0 0.0 0.0 37.95 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1739 1842 2.07154 CAGCACGAATCTCAGAAAGCA 58.928 47.619 0.0 0.0 0.0 3.91 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.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 5.376854 CAAACTGTGCTAGCCACTTATTT 57.623 39.130 13.29 9.34 44.92 1.40
33 34 5.156355 CAAACTGTGCTAGCCACTTATTTG 58.844 41.667 13.29 15.63 44.92 2.32
34 35 4.021102 ACTGTGCTAGCCACTTATTTGT 57.979 40.909 13.29 0.00 44.92 2.83
35 36 4.398319 ACTGTGCTAGCCACTTATTTGTT 58.602 39.130 13.29 0.00 44.92 2.83
36 37 5.556915 ACTGTGCTAGCCACTTATTTGTTA 58.443 37.500 13.29 0.00 44.92 2.41
37 38 6.001460 ACTGTGCTAGCCACTTATTTGTTAA 58.999 36.000 13.29 0.00 44.92 2.01
38 39 6.659242 ACTGTGCTAGCCACTTATTTGTTAAT 59.341 34.615 13.29 0.00 44.92 1.40
39 40 7.827236 ACTGTGCTAGCCACTTATTTGTTAATA 59.173 33.333 13.29 0.00 44.92 0.98
40 41 8.746052 TGTGCTAGCCACTTATTTGTTAATAT 57.254 30.769 13.29 0.00 44.92 1.28
41 42 8.620416 TGTGCTAGCCACTTATTTGTTAATATG 58.380 33.333 13.29 0.00 44.92 1.78
42 43 7.591426 GTGCTAGCCACTTATTTGTTAATATGC 59.409 37.037 13.29 0.00 41.35 3.14
43 44 7.502226 TGCTAGCCACTTATTTGTTAATATGCT 59.498 33.333 13.29 0.00 0.00 3.79
44 45 8.352942 GCTAGCCACTTATTTGTTAATATGCTT 58.647 33.333 2.29 0.00 0.00 3.91
45 46 9.884465 CTAGCCACTTATTTGTTAATATGCTTC 57.116 33.333 0.00 0.00 0.00 3.86
46 47 8.525290 AGCCACTTATTTGTTAATATGCTTCT 57.475 30.769 0.00 0.00 0.00 2.85
47 48 8.624776 AGCCACTTATTTGTTAATATGCTTCTC 58.375 33.333 0.00 0.00 0.00 2.87
48 49 8.405531 GCCACTTATTTGTTAATATGCTTCTCA 58.594 33.333 0.00 0.00 0.00 3.27
66 67 9.897744 TGCTTCTCAAGTTCTAAACATATTTTG 57.102 29.630 0.00 0.00 0.00 2.44
67 68 9.899226 GCTTCTCAAGTTCTAAACATATTTTGT 57.101 29.630 0.00 0.00 41.53 2.83
81 82 9.683069 AAACATATTTTGTCAGATTTCTCACAC 57.317 29.630 0.00 0.00 37.68 3.82
82 83 8.394971 ACATATTTTGTCAGATTTCTCACACA 57.605 30.769 0.00 0.00 30.89 3.72
83 84 9.017509 ACATATTTTGTCAGATTTCTCACACAT 57.982 29.630 0.00 0.00 30.89 3.21
84 85 9.850628 CATATTTTGTCAGATTTCTCACACATT 57.149 29.630 0.00 0.00 0.00 2.71
85 86 9.850628 ATATTTTGTCAGATTTCTCACACATTG 57.149 29.630 0.00 0.00 0.00 2.82
86 87 6.698008 TTTGTCAGATTTCTCACACATTGT 57.302 33.333 0.00 0.00 0.00 2.71
87 88 7.800155 TTTGTCAGATTTCTCACACATTGTA 57.200 32.000 0.00 0.00 0.00 2.41
88 89 6.785488 TGTCAGATTTCTCACACATTGTAC 57.215 37.500 0.00 0.00 0.00 2.90
89 90 6.287525 TGTCAGATTTCTCACACATTGTACA 58.712 36.000 0.00 0.00 0.00 2.90
90 91 6.765512 TGTCAGATTTCTCACACATTGTACAA 59.234 34.615 11.41 11.41 0.00 2.41
91 92 7.041848 TGTCAGATTTCTCACACATTGTACAAG 60.042 37.037 14.65 8.70 0.00 3.16
92 93 6.427853 TCAGATTTCTCACACATTGTACAAGG 59.572 38.462 18.17 18.17 0.00 3.61
93 94 6.427853 CAGATTTCTCACACATTGTACAAGGA 59.572 38.462 25.73 10.88 0.00 3.36
94 95 7.120285 CAGATTTCTCACACATTGTACAAGGAT 59.880 37.037 25.73 11.06 0.00 3.24
95 96 7.667219 AGATTTCTCACACATTGTACAAGGATT 59.333 33.333 25.73 9.56 0.00 3.01
96 97 8.862325 ATTTCTCACACATTGTACAAGGATTA 57.138 30.769 25.73 7.94 0.00 1.75
97 98 8.862325 TTTCTCACACATTGTACAAGGATTAT 57.138 30.769 25.73 1.16 0.00 1.28
98 99 9.952030 TTTCTCACACATTGTACAAGGATTATA 57.048 29.630 25.73 7.00 0.00 0.98
99 100 9.599866 TTCTCACACATTGTACAAGGATTATAG 57.400 33.333 25.73 14.95 0.00 1.31
100 101 8.758829 TCTCACACATTGTACAAGGATTATAGT 58.241 33.333 25.73 11.06 0.00 2.12
101 102 8.716646 TCACACATTGTACAAGGATTATAGTG 57.283 34.615 25.73 19.76 0.00 2.74
102 103 8.536175 TCACACATTGTACAAGGATTATAGTGA 58.464 33.333 25.73 21.23 0.00 3.41
103 104 9.161629 CACACATTGTACAAGGATTATAGTGAA 57.838 33.333 25.73 0.00 0.00 3.18
104 105 9.905713 ACACATTGTACAAGGATTATAGTGAAT 57.094 29.630 25.73 0.00 0.00 2.57
128 129 9.921637 AATAAATTTTAAAAGAGCGGAATCACA 57.078 25.926 6.79 0.00 0.00 3.58
132 133 9.736023 AATTTTAAAAGAGCGGAATCACATATC 57.264 29.630 6.79 0.00 0.00 1.63
133 134 7.857734 TTTAAAAGAGCGGAATCACATATCA 57.142 32.000 0.00 0.00 0.00 2.15
134 135 7.857734 TTAAAAGAGCGGAATCACATATCAA 57.142 32.000 0.00 0.00 0.00 2.57
135 136 6.757897 AAAAGAGCGGAATCACATATCAAA 57.242 33.333 0.00 0.00 0.00 2.69
136 137 6.757897 AAAGAGCGGAATCACATATCAAAA 57.242 33.333 0.00 0.00 0.00 2.44
137 138 6.757897 AAGAGCGGAATCACATATCAAAAA 57.242 33.333 0.00 0.00 0.00 1.94
138 139 6.369059 AGAGCGGAATCACATATCAAAAAG 57.631 37.500 0.00 0.00 0.00 2.27
139 140 5.882557 AGAGCGGAATCACATATCAAAAAGT 59.117 36.000 0.00 0.00 0.00 2.66
140 141 6.037610 AGAGCGGAATCACATATCAAAAAGTC 59.962 38.462 0.00 0.00 0.00 3.01
141 142 5.066505 AGCGGAATCACATATCAAAAAGTCC 59.933 40.000 0.00 0.00 0.00 3.85
142 143 5.163663 GCGGAATCACATATCAAAAAGTCCA 60.164 40.000 0.00 0.00 0.00 4.02
143 144 6.624861 GCGGAATCACATATCAAAAAGTCCAA 60.625 38.462 0.00 0.00 0.00 3.53
144 145 7.483307 CGGAATCACATATCAAAAAGTCCAAT 58.517 34.615 0.00 0.00 0.00 3.16
145 146 7.975616 CGGAATCACATATCAAAAAGTCCAATT 59.024 33.333 0.00 0.00 0.00 2.32
146 147 9.305925 GGAATCACATATCAAAAAGTCCAATTC 57.694 33.333 0.00 0.00 0.00 2.17
147 148 9.859427 GAATCACATATCAAAAAGTCCAATTCA 57.141 29.630 0.00 0.00 0.00 2.57
156 157 8.225603 TCAAAAAGTCCAATTCATATAGAGGC 57.774 34.615 0.00 0.00 0.00 4.70
157 158 7.833682 TCAAAAAGTCCAATTCATATAGAGGCA 59.166 33.333 0.00 0.00 0.00 4.75
158 159 8.469200 CAAAAAGTCCAATTCATATAGAGGCAA 58.531 33.333 0.00 0.00 0.00 4.52
159 160 8.773033 AAAAGTCCAATTCATATAGAGGCAAT 57.227 30.769 0.00 0.00 0.00 3.56
160 161 7.756395 AAGTCCAATTCATATAGAGGCAATG 57.244 36.000 0.00 0.00 0.00 2.82
161 162 7.083062 AGTCCAATTCATATAGAGGCAATGA 57.917 36.000 0.00 0.00 0.00 2.57
162 163 6.939163 AGTCCAATTCATATAGAGGCAATGAC 59.061 38.462 0.00 0.00 29.64 3.06
163 164 6.150140 GTCCAATTCATATAGAGGCAATGACC 59.850 42.308 0.00 0.00 29.64 4.02
164 165 6.044754 TCCAATTCATATAGAGGCAATGACCT 59.955 38.462 0.00 0.00 45.04 3.85
165 166 7.237471 TCCAATTCATATAGAGGCAATGACCTA 59.763 37.037 0.00 0.00 41.32 3.08
166 167 7.335422 CCAATTCATATAGAGGCAATGACCTAC 59.665 40.741 0.00 0.00 41.32 3.18
167 168 7.805083 ATTCATATAGAGGCAATGACCTACT 57.195 36.000 0.00 0.57 41.32 2.57
168 169 6.596309 TCATATAGAGGCAATGACCTACTG 57.404 41.667 0.00 0.00 41.32 2.74
169 170 6.314917 TCATATAGAGGCAATGACCTACTGA 58.685 40.000 0.00 0.00 41.32 3.41
170 171 6.782494 TCATATAGAGGCAATGACCTACTGAA 59.218 38.462 0.00 0.00 41.32 3.02
171 172 7.455953 TCATATAGAGGCAATGACCTACTGAAT 59.544 37.037 0.00 0.00 41.32 2.57
172 173 4.148128 AGAGGCAATGACCTACTGAATG 57.852 45.455 0.00 0.00 41.32 2.67
173 174 3.521126 AGAGGCAATGACCTACTGAATGT 59.479 43.478 0.00 0.00 41.32 2.71
174 175 4.018960 AGAGGCAATGACCTACTGAATGTT 60.019 41.667 0.00 0.00 41.32 2.71
175 176 4.012374 AGGCAATGACCTACTGAATGTTG 58.988 43.478 0.00 0.00 38.67 3.33
176 177 3.129287 GGCAATGACCTACTGAATGTTGG 59.871 47.826 0.00 0.00 45.12 3.77
188 189 8.292448 CCTACTGAATGTTGGTAATAATGATGC 58.708 37.037 0.00 0.00 36.91 3.91
189 190 7.886629 ACTGAATGTTGGTAATAATGATGCT 57.113 32.000 0.00 0.00 0.00 3.79
190 191 8.978874 ACTGAATGTTGGTAATAATGATGCTA 57.021 30.769 0.00 0.00 0.00 3.49
191 192 8.840321 ACTGAATGTTGGTAATAATGATGCTAC 58.160 33.333 0.00 0.00 0.00 3.58
192 193 8.978874 TGAATGTTGGTAATAATGATGCTACT 57.021 30.769 0.00 0.00 0.00 2.57
223 224 8.976986 TTAGAATAAACTCGAACTACAGGAAC 57.023 34.615 0.00 0.00 0.00 3.62
224 225 6.396450 AGAATAAACTCGAACTACAGGAACC 58.604 40.000 0.00 0.00 0.00 3.62
225 226 5.733620 ATAAACTCGAACTACAGGAACCA 57.266 39.130 0.00 0.00 0.00 3.67
226 227 4.618920 AAACTCGAACTACAGGAACCAT 57.381 40.909 0.00 0.00 0.00 3.55
227 228 5.733620 AAACTCGAACTACAGGAACCATA 57.266 39.130 0.00 0.00 0.00 2.74
228 229 5.934402 AACTCGAACTACAGGAACCATAT 57.066 39.130 0.00 0.00 0.00 1.78
229 230 7.414222 AAACTCGAACTACAGGAACCATATA 57.586 36.000 0.00 0.00 0.00 0.86
230 231 6.636562 ACTCGAACTACAGGAACCATATAG 57.363 41.667 0.00 0.00 0.00 1.31
231 232 6.127793 ACTCGAACTACAGGAACCATATAGT 58.872 40.000 0.00 0.00 0.00 2.12
232 233 7.285566 ACTCGAACTACAGGAACCATATAGTA 58.714 38.462 0.00 0.00 0.00 1.82
233 234 7.444792 ACTCGAACTACAGGAACCATATAGTAG 59.555 40.741 0.00 0.00 36.08 2.57
234 235 7.285566 TCGAACTACAGGAACCATATAGTAGT 58.714 38.462 0.00 0.00 42.64 2.73
235 236 7.228108 TCGAACTACAGGAACCATATAGTAGTG 59.772 40.741 0.00 0.00 40.68 2.74
236 237 7.521748 CGAACTACAGGAACCATATAGTAGTGG 60.522 44.444 0.00 3.44 40.68 4.00
413 414 2.977914 CTATGGCCTCATGGGAATACG 58.022 52.381 3.32 0.00 37.23 3.06
647 648 1.082104 CACGAGCAAGCCGGTTTTC 60.082 57.895 0.00 0.00 0.00 2.29
648 649 2.258726 ACGAGCAAGCCGGTTTTCC 61.259 57.895 0.00 0.00 0.00 3.13
649 650 1.966451 CGAGCAAGCCGGTTTTCCT 60.966 57.895 0.00 0.17 37.95 3.36
650 651 1.876664 GAGCAAGCCGGTTTTCCTC 59.123 57.895 0.00 6.76 37.95 3.71
651 652 0.606673 GAGCAAGCCGGTTTTCCTCT 60.607 55.000 16.54 6.45 37.95 3.69
652 653 0.890996 AGCAAGCCGGTTTTCCTCTG 60.891 55.000 0.00 0.00 37.95 3.35
653 654 1.866853 GCAAGCCGGTTTTCCTCTGG 61.867 60.000 0.00 0.00 37.95 3.86
654 655 0.250727 CAAGCCGGTTTTCCTCTGGA 60.251 55.000 0.00 0.00 37.95 3.86
655 656 0.698818 AAGCCGGTTTTCCTCTGGAT 59.301 50.000 1.90 0.00 37.95 3.41
656 657 0.698818 AGCCGGTTTTCCTCTGGATT 59.301 50.000 1.90 0.00 37.95 3.01
657 658 0.811281 GCCGGTTTTCCTCTGGATTG 59.189 55.000 1.90 0.00 37.95 2.67
658 659 1.613255 GCCGGTTTTCCTCTGGATTGA 60.613 52.381 1.90 0.00 37.95 2.57
659 660 2.359900 CCGGTTTTCCTCTGGATTGAG 58.640 52.381 0.00 0.00 37.95 3.02
660 661 2.290323 CCGGTTTTCCTCTGGATTGAGT 60.290 50.000 0.00 0.00 37.95 3.41
661 662 3.412386 CGGTTTTCCTCTGGATTGAGTT 58.588 45.455 0.00 0.00 37.95 3.01
662 663 3.189287 CGGTTTTCCTCTGGATTGAGTTG 59.811 47.826 0.00 0.00 37.95 3.16
663 664 3.507622 GGTTTTCCTCTGGATTGAGTTGG 59.492 47.826 0.00 0.00 36.94 3.77
664 665 2.496899 TTCCTCTGGATTGAGTTGGC 57.503 50.000 0.00 0.00 32.50 4.52
665 666 0.620556 TCCTCTGGATTGAGTTGGCC 59.379 55.000 0.00 0.00 32.50 5.36
666 667 0.394899 CCTCTGGATTGAGTTGGCCC 60.395 60.000 0.00 0.00 32.50 5.80
667 668 0.394899 CTCTGGATTGAGTTGGCCCC 60.395 60.000 0.00 0.00 0.00 5.80
668 669 1.750399 CTGGATTGAGTTGGCCCCG 60.750 63.158 0.00 0.00 0.00 5.73
669 670 3.140814 GGATTGAGTTGGCCCCGC 61.141 66.667 0.00 0.00 0.00 6.13
670 671 2.044946 GATTGAGTTGGCCCCGCT 60.045 61.111 0.00 0.00 0.00 5.52
671 672 2.044946 ATTGAGTTGGCCCCGCTC 60.045 61.111 0.00 5.79 0.00 5.03
672 673 3.976701 ATTGAGTTGGCCCCGCTCG 62.977 63.158 0.00 0.00 32.32 5.03
674 675 4.821589 GAGTTGGCCCCGCTCGAG 62.822 72.222 8.45 8.45 0.00 4.04
912 1015 1.079127 GCTGATACGTGGTGCTGGT 60.079 57.895 0.00 0.00 0.00 4.00
987 1090 1.878953 CCCCTGACTAACACACACAC 58.121 55.000 0.00 0.00 0.00 3.82
988 1091 1.140052 CCCCTGACTAACACACACACA 59.860 52.381 0.00 0.00 0.00 3.72
989 1092 2.210116 CCCTGACTAACACACACACAC 58.790 52.381 0.00 0.00 0.00 3.82
990 1093 2.419436 CCCTGACTAACACACACACACA 60.419 50.000 0.00 0.00 0.00 3.72
1271 1374 2.479275 CTGCTGATCGTGCTTATGATGG 59.521 50.000 11.02 0.00 0.00 3.51
1488 1591 2.972713 TGGTGATGCCTTATACCTCTCC 59.027 50.000 0.00 0.00 38.35 3.71
1739 1842 2.103263 GCCGTATTTCTCTCATGGAGGT 59.897 50.000 10.23 2.46 42.10 3.85
2189 2295 0.477597 TCCCCATGGGTTCTGGACTT 60.478 55.000 29.33 0.00 44.74 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 5.156355 CAAATAAGTGGCTAGCACAGTTTG 58.844 41.667 22.92 19.47 33.77 2.93
11 12 4.827284 ACAAATAAGTGGCTAGCACAGTTT 59.173 37.500 22.92 14.95 33.77 2.66
12 13 4.398319 ACAAATAAGTGGCTAGCACAGTT 58.602 39.130 18.24 20.65 35.75 3.16
13 14 4.021102 ACAAATAAGTGGCTAGCACAGT 57.979 40.909 18.24 11.97 0.00 3.55
14 15 6.494893 TTAACAAATAAGTGGCTAGCACAG 57.505 37.500 18.24 1.54 0.00 3.66
15 16 8.620416 CATATTAACAAATAAGTGGCTAGCACA 58.380 33.333 18.24 9.44 0.00 4.57
16 17 7.591426 GCATATTAACAAATAAGTGGCTAGCAC 59.409 37.037 18.24 12.66 0.00 4.40
17 18 7.502226 AGCATATTAACAAATAAGTGGCTAGCA 59.498 33.333 18.24 0.00 30.02 3.49
18 19 7.875971 AGCATATTAACAAATAAGTGGCTAGC 58.124 34.615 6.04 6.04 30.02 3.42
19 20 9.884465 GAAGCATATTAACAAATAAGTGGCTAG 57.116 33.333 0.00 0.00 30.97 3.42
20 21 9.627123 AGAAGCATATTAACAAATAAGTGGCTA 57.373 29.630 0.00 0.00 30.97 3.93
21 22 8.525290 AGAAGCATATTAACAAATAAGTGGCT 57.475 30.769 0.00 0.00 31.87 4.75
22 23 8.405531 TGAGAAGCATATTAACAAATAAGTGGC 58.594 33.333 0.00 0.00 0.00 5.01
40 41 9.897744 CAAAATATGTTTAGAACTTGAGAAGCA 57.102 29.630 0.00 0.00 0.00 3.91
41 42 9.899226 ACAAAATATGTTTAGAACTTGAGAAGC 57.101 29.630 0.00 0.00 40.06 3.86
55 56 9.683069 GTGTGAGAAATCTGACAAAATATGTTT 57.317 29.630 4.27 0.00 41.51 2.83
56 57 8.849168 TGTGTGAGAAATCTGACAAAATATGTT 58.151 29.630 4.27 0.00 41.51 2.71
57 58 8.394971 TGTGTGAGAAATCTGACAAAATATGT 57.605 30.769 4.27 0.00 41.51 2.29
58 59 9.850628 AATGTGTGAGAAATCTGACAAAATATG 57.149 29.630 4.27 0.00 41.51 1.78
59 60 9.850628 CAATGTGTGAGAAATCTGACAAAATAT 57.149 29.630 4.27 0.00 41.51 1.28
60 61 8.849168 ACAATGTGTGAGAAATCTGACAAAATA 58.151 29.630 4.27 0.00 41.51 1.40
61 62 7.719483 ACAATGTGTGAGAAATCTGACAAAAT 58.281 30.769 4.27 0.00 41.51 1.82
62 63 7.099266 ACAATGTGTGAGAAATCTGACAAAA 57.901 32.000 4.27 0.00 41.51 2.44
63 64 6.698008 ACAATGTGTGAGAAATCTGACAAA 57.302 33.333 4.27 0.00 41.51 2.83
64 65 6.765512 TGTACAATGTGTGAGAAATCTGACAA 59.234 34.615 4.27 0.00 41.51 3.18
65 66 6.287525 TGTACAATGTGTGAGAAATCTGACA 58.712 36.000 0.00 0.00 37.75 3.58
66 67 6.785488 TGTACAATGTGTGAGAAATCTGAC 57.215 37.500 0.00 0.00 0.00 3.51
67 68 6.427853 CCTTGTACAATGTGTGAGAAATCTGA 59.572 38.462 9.13 0.00 0.00 3.27
68 69 6.427853 TCCTTGTACAATGTGTGAGAAATCTG 59.572 38.462 9.13 0.00 0.00 2.90
69 70 6.533730 TCCTTGTACAATGTGTGAGAAATCT 58.466 36.000 9.13 0.00 0.00 2.40
70 71 6.801539 TCCTTGTACAATGTGTGAGAAATC 57.198 37.500 9.13 0.00 0.00 2.17
71 72 7.765695 AATCCTTGTACAATGTGTGAGAAAT 57.234 32.000 9.13 0.00 0.00 2.17
72 73 8.862325 ATAATCCTTGTACAATGTGTGAGAAA 57.138 30.769 9.13 0.00 0.00 2.52
73 74 9.599866 CTATAATCCTTGTACAATGTGTGAGAA 57.400 33.333 9.13 0.00 0.00 2.87
74 75 8.758829 ACTATAATCCTTGTACAATGTGTGAGA 58.241 33.333 9.13 0.00 0.00 3.27
75 76 8.820933 CACTATAATCCTTGTACAATGTGTGAG 58.179 37.037 9.13 4.62 0.00 3.51
76 77 8.536175 TCACTATAATCCTTGTACAATGTGTGA 58.464 33.333 9.13 11.47 0.00 3.58
77 78 8.716646 TCACTATAATCCTTGTACAATGTGTG 57.283 34.615 9.13 9.64 0.00 3.82
78 79 9.905713 ATTCACTATAATCCTTGTACAATGTGT 57.094 29.630 9.13 2.07 0.00 3.72
102 103 9.921637 TGTGATTCCGCTCTTTTAAAATTTATT 57.078 25.926 0.09 0.00 0.00 1.40
106 107 9.736023 GATATGTGATTCCGCTCTTTTAAAATT 57.264 29.630 0.09 0.00 0.00 1.82
107 108 8.902806 TGATATGTGATTCCGCTCTTTTAAAAT 58.097 29.630 0.09 0.00 0.00 1.82
108 109 8.275015 TGATATGTGATTCCGCTCTTTTAAAA 57.725 30.769 0.00 0.00 0.00 1.52
109 110 7.857734 TGATATGTGATTCCGCTCTTTTAAA 57.142 32.000 0.00 0.00 0.00 1.52
110 111 7.857734 TTGATATGTGATTCCGCTCTTTTAA 57.142 32.000 0.00 0.00 0.00 1.52
111 112 7.857734 TTTGATATGTGATTCCGCTCTTTTA 57.142 32.000 0.00 0.00 0.00 1.52
112 113 6.757897 TTTGATATGTGATTCCGCTCTTTT 57.242 33.333 0.00 0.00 0.00 2.27
113 114 6.757897 TTTTGATATGTGATTCCGCTCTTT 57.242 33.333 0.00 0.00 0.00 2.52
114 115 6.375455 ACTTTTTGATATGTGATTCCGCTCTT 59.625 34.615 0.00 0.00 0.00 2.85
115 116 5.882557 ACTTTTTGATATGTGATTCCGCTCT 59.117 36.000 0.00 0.00 0.00 4.09
116 117 6.124088 ACTTTTTGATATGTGATTCCGCTC 57.876 37.500 0.00 0.00 0.00 5.03
117 118 5.066505 GGACTTTTTGATATGTGATTCCGCT 59.933 40.000 0.00 0.00 0.00 5.52
118 119 5.163663 TGGACTTTTTGATATGTGATTCCGC 60.164 40.000 0.00 0.00 0.00 5.54
119 120 6.435430 TGGACTTTTTGATATGTGATTCCG 57.565 37.500 0.00 0.00 0.00 4.30
120 121 9.305925 GAATTGGACTTTTTGATATGTGATTCC 57.694 33.333 0.00 0.00 0.00 3.01
121 122 9.859427 TGAATTGGACTTTTTGATATGTGATTC 57.141 29.630 0.00 0.00 0.00 2.52
130 131 8.854117 GCCTCTATATGAATTGGACTTTTTGAT 58.146 33.333 0.00 0.00 0.00 2.57
131 132 7.833682 TGCCTCTATATGAATTGGACTTTTTGA 59.166 33.333 0.00 0.00 0.00 2.69
132 133 7.999679 TGCCTCTATATGAATTGGACTTTTTG 58.000 34.615 0.00 0.00 0.00 2.44
133 134 8.593945 TTGCCTCTATATGAATTGGACTTTTT 57.406 30.769 0.00 0.00 0.00 1.94
134 135 8.636213 CATTGCCTCTATATGAATTGGACTTTT 58.364 33.333 0.00 0.00 0.00 2.27
135 136 8.000709 TCATTGCCTCTATATGAATTGGACTTT 58.999 33.333 0.00 0.00 0.00 2.66
136 137 7.446625 GTCATTGCCTCTATATGAATTGGACTT 59.553 37.037 0.00 0.00 30.72 3.01
137 138 6.939163 GTCATTGCCTCTATATGAATTGGACT 59.061 38.462 0.00 0.00 30.72 3.85
138 139 6.150140 GGTCATTGCCTCTATATGAATTGGAC 59.850 42.308 0.00 0.00 30.72 4.02
139 140 6.044754 AGGTCATTGCCTCTATATGAATTGGA 59.955 38.462 0.00 0.00 32.39 3.53
140 141 6.243900 AGGTCATTGCCTCTATATGAATTGG 58.756 40.000 0.00 0.00 32.39 3.16
141 142 8.099537 AGTAGGTCATTGCCTCTATATGAATTG 58.900 37.037 3.35 0.00 39.94 2.32
142 143 8.099537 CAGTAGGTCATTGCCTCTATATGAATT 58.900 37.037 3.35 0.00 39.94 2.17
143 144 7.455953 TCAGTAGGTCATTGCCTCTATATGAAT 59.544 37.037 3.35 0.00 39.94 2.57
144 145 6.782494 TCAGTAGGTCATTGCCTCTATATGAA 59.218 38.462 3.35 0.00 39.94 2.57
145 146 6.314917 TCAGTAGGTCATTGCCTCTATATGA 58.685 40.000 3.35 0.00 39.94 2.15
146 147 6.596309 TCAGTAGGTCATTGCCTCTATATG 57.404 41.667 3.35 0.00 39.94 1.78
147 148 7.236432 ACATTCAGTAGGTCATTGCCTCTATAT 59.764 37.037 3.35 0.00 39.94 0.86
148 149 6.554982 ACATTCAGTAGGTCATTGCCTCTATA 59.445 38.462 3.35 0.00 39.94 1.31
149 150 5.367937 ACATTCAGTAGGTCATTGCCTCTAT 59.632 40.000 3.35 0.00 39.94 1.98
150 151 4.716784 ACATTCAGTAGGTCATTGCCTCTA 59.283 41.667 3.35 0.00 39.94 2.43
151 152 3.521126 ACATTCAGTAGGTCATTGCCTCT 59.479 43.478 3.35 0.33 39.94 3.69
152 153 3.878778 ACATTCAGTAGGTCATTGCCTC 58.121 45.455 3.35 0.00 39.94 4.70
153 154 4.012374 CAACATTCAGTAGGTCATTGCCT 58.988 43.478 5.23 5.23 42.43 4.75
154 155 3.129287 CCAACATTCAGTAGGTCATTGCC 59.871 47.826 0.00 0.00 0.00 4.52
155 156 3.758554 ACCAACATTCAGTAGGTCATTGC 59.241 43.478 0.00 0.00 0.00 3.56
156 157 7.630242 ATTACCAACATTCAGTAGGTCATTG 57.370 36.000 0.00 0.00 33.91 2.82
157 158 9.920946 ATTATTACCAACATTCAGTAGGTCATT 57.079 29.630 0.00 0.00 33.91 2.57
158 159 9.342308 CATTATTACCAACATTCAGTAGGTCAT 57.658 33.333 0.00 0.00 33.91 3.06
159 160 8.544622 TCATTATTACCAACATTCAGTAGGTCA 58.455 33.333 0.00 0.00 33.91 4.02
160 161 8.958119 TCATTATTACCAACATTCAGTAGGTC 57.042 34.615 0.00 0.00 33.91 3.85
161 162 9.342308 CATCATTATTACCAACATTCAGTAGGT 57.658 33.333 0.00 0.00 36.40 3.08
162 163 8.292448 GCATCATTATTACCAACATTCAGTAGG 58.708 37.037 0.00 0.00 0.00 3.18
163 164 9.060347 AGCATCATTATTACCAACATTCAGTAG 57.940 33.333 0.00 0.00 0.00 2.57
164 165 8.978874 AGCATCATTATTACCAACATTCAGTA 57.021 30.769 0.00 0.00 0.00 2.74
165 166 7.886629 AGCATCATTATTACCAACATTCAGT 57.113 32.000 0.00 0.00 0.00 3.41
166 167 9.060347 AGTAGCATCATTATTACCAACATTCAG 57.940 33.333 0.00 0.00 0.00 3.02
167 168 8.978874 AGTAGCATCATTATTACCAACATTCA 57.021 30.769 0.00 0.00 0.00 2.57
197 198 9.415544 GTTCCTGTAGTTCGAGTTTATTCTAAA 57.584 33.333 0.00 0.00 0.00 1.85
198 199 8.031277 GGTTCCTGTAGTTCGAGTTTATTCTAA 58.969 37.037 0.00 0.00 0.00 2.10
199 200 7.177216 TGGTTCCTGTAGTTCGAGTTTATTCTA 59.823 37.037 0.00 0.00 0.00 2.10
200 201 6.014840 TGGTTCCTGTAGTTCGAGTTTATTCT 60.015 38.462 0.00 0.00 0.00 2.40
201 202 6.161381 TGGTTCCTGTAGTTCGAGTTTATTC 58.839 40.000 0.00 0.00 0.00 1.75
202 203 6.105397 TGGTTCCTGTAGTTCGAGTTTATT 57.895 37.500 0.00 0.00 0.00 1.40
203 204 5.733620 TGGTTCCTGTAGTTCGAGTTTAT 57.266 39.130 0.00 0.00 0.00 1.40
204 205 5.733620 ATGGTTCCTGTAGTTCGAGTTTA 57.266 39.130 0.00 0.00 0.00 2.01
205 206 4.618920 ATGGTTCCTGTAGTTCGAGTTT 57.381 40.909 0.00 0.00 0.00 2.66
206 207 5.934402 ATATGGTTCCTGTAGTTCGAGTT 57.066 39.130 0.00 0.00 0.00 3.01
207 208 6.127793 ACTATATGGTTCCTGTAGTTCGAGT 58.872 40.000 0.00 0.00 0.00 4.18
208 209 6.636562 ACTATATGGTTCCTGTAGTTCGAG 57.363 41.667 0.00 0.00 0.00 4.04
209 210 7.228108 CACTACTATATGGTTCCTGTAGTTCGA 59.772 40.741 0.00 0.00 38.62 3.71
210 211 7.361127 CACTACTATATGGTTCCTGTAGTTCG 58.639 42.308 0.00 0.00 38.62 3.95
211 212 7.659186 CCACTACTATATGGTTCCTGTAGTTC 58.341 42.308 0.00 0.00 38.62 3.01
212 213 7.598759 CCACTACTATATGGTTCCTGTAGTT 57.401 40.000 0.00 0.00 38.62 2.24
272 273 9.947433 TCTAACACCTTTAATCCGAATAAGAAA 57.053 29.630 0.00 0.00 0.00 2.52
273 274 9.595823 CTCTAACACCTTTAATCCGAATAAGAA 57.404 33.333 0.00 0.00 0.00 2.52
274 275 8.755977 ACTCTAACACCTTTAATCCGAATAAGA 58.244 33.333 0.00 0.00 0.00 2.10
275 276 8.943909 ACTCTAACACCTTTAATCCGAATAAG 57.056 34.615 0.00 0.00 0.00 1.73
413 414 6.699575 ACCATGTTAGGAAATATGCAACTC 57.300 37.500 0.00 0.00 33.98 3.01
505 506 4.479993 GCAGCGGCCACAGAGGAT 62.480 66.667 2.24 0.00 41.22 3.24
526 527 4.439700 CCGGCTACGATAGACAGAGAAAAA 60.440 45.833 0.00 0.00 44.60 1.94
647 648 0.394899 GGGCCAACTCAATCCAGAGG 60.395 60.000 4.39 0.00 39.97 3.69
648 649 0.394899 GGGGCCAACTCAATCCAGAG 60.395 60.000 4.39 0.00 41.44 3.35
649 650 1.691219 GGGGCCAACTCAATCCAGA 59.309 57.895 4.39 0.00 0.00 3.86
650 651 1.750399 CGGGGCCAACTCAATCCAG 60.750 63.158 4.39 0.00 0.00 3.86
651 652 2.354729 CGGGGCCAACTCAATCCA 59.645 61.111 4.39 0.00 0.00 3.41
652 653 3.140814 GCGGGGCCAACTCAATCC 61.141 66.667 4.39 0.00 0.00 3.01
653 654 2.044946 AGCGGGGCCAACTCAATC 60.045 61.111 4.39 0.00 0.00 2.67
654 655 2.044946 GAGCGGGGCCAACTCAAT 60.045 61.111 17.45 0.00 0.00 2.57
655 656 4.697756 CGAGCGGGGCCAACTCAA 62.698 66.667 20.84 0.00 0.00 3.02
657 658 4.821589 CTCGAGCGGGGCCAACTC 62.822 72.222 4.39 10.55 0.00 3.01
668 669 4.882396 GAGGAAGCCGGCTCGAGC 62.882 72.222 32.93 29.38 41.14 5.03
669 670 3.144193 AGAGGAAGCCGGCTCGAG 61.144 66.667 32.93 8.45 0.00 4.04
670 671 3.452786 CAGAGGAAGCCGGCTCGA 61.453 66.667 32.93 0.00 0.00 4.04
671 672 4.521062 CCAGAGGAAGCCGGCTCG 62.521 72.222 32.93 13.76 0.00 5.03
672 673 2.376228 GATCCAGAGGAAGCCGGCTC 62.376 65.000 32.93 22.38 34.34 4.70
673 674 2.366167 ATCCAGAGGAAGCCGGCT 60.366 61.111 27.08 27.08 34.34 5.52
674 675 2.110006 GATCCAGAGGAAGCCGGC 59.890 66.667 21.89 21.89 34.34 6.13
675 676 1.045350 TCAGATCCAGAGGAAGCCGG 61.045 60.000 0.00 0.00 34.34 6.13
676 677 1.000731 GATCAGATCCAGAGGAAGCCG 59.999 57.143 0.00 0.00 34.34 5.52
677 678 2.037511 CAGATCAGATCCAGAGGAAGCC 59.962 54.545 6.80 0.00 34.34 4.35
678 679 2.548493 GCAGATCAGATCCAGAGGAAGC 60.548 54.545 6.80 0.00 34.34 3.86
679 680 2.967201 AGCAGATCAGATCCAGAGGAAG 59.033 50.000 6.80 0.00 34.34 3.46
680 681 2.699321 CAGCAGATCAGATCCAGAGGAA 59.301 50.000 6.80 0.00 34.34 3.36
681 682 2.317973 CAGCAGATCAGATCCAGAGGA 58.682 52.381 6.80 0.00 35.55 3.71
825 896 2.531206 CGGAGAGCAAAGTAGCACTAC 58.469 52.381 0.00 0.00 35.56 2.73
827 898 0.247736 CCGGAGAGCAAAGTAGCACT 59.752 55.000 0.00 0.00 38.16 4.40
912 1015 1.273688 CGGCGTGACGAATCAATACA 58.726 50.000 10.10 0.00 36.31 2.29
1271 1374 2.025321 TCCTCATAAGCCAAAACCCTCC 60.025 50.000 0.00 0.00 0.00 4.30
1739 1842 2.071540 CAGCACGAATCTCAGAAAGCA 58.928 47.619 0.00 0.00 0.00 3.91
2189 2295 7.170965 AGAAGACATATGAAAAGAAGCTCCAA 58.829 34.615 10.38 0.00 0.00 3.53


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.