Multiple sequence alignment - TraesCS1A01G187400

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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 TraesCS1A01G187400 chr1A 100.000 6233 0 0 1966 8198 338582913 338589145 0.000000e+00 11511
1 TraesCS1A01G187400 chr1A 100.000 1547 0 0 1 1547 338580948 338582494 0.000000e+00 2857
2 TraesCS1A01G187400 chr1A 79.348 920 166 12 2262 3158 544465521 544466439 6.990000e-175 625
3 TraesCS1A01G187400 chr1A 85.989 364 42 5 6896 7251 544474779 544475141 1.670000e-101 381
4 TraesCS1A01G187400 chr1A 79.815 540 88 12 5177 5703 544468246 544468777 2.790000e-99 374
5 TraesCS1A01G187400 chr1A 81.818 440 73 6 4240 4674 544467394 544467831 6.050000e-96 363
6 TraesCS1A01G187400 chr1A 84.615 338 38 10 4720 5045 544467901 544468236 2.850000e-84 324
7 TraesCS1A01G187400 chr1A 88.745 231 24 2 6232 6461 544474252 544474481 1.740000e-71 281
8 TraesCS1A01G187400 chr1A 94.118 68 3 1 1470 1537 338582336 338582402 1.460000e-17 102
9 TraesCS1A01G187400 chr1A 94.118 68 3 1 1389 1455 338582417 338582484 1.460000e-17 102
10 TraesCS1A01G187400 chr1D 97.057 6287 111 27 1966 8198 261742161 261735895 0.000000e+00 10517
11 TraesCS1A01G187400 chr1D 94.636 839 32 3 519 1357 261743303 261742478 0.000000e+00 1288
12 TraesCS1A01G187400 chr1D 79.393 922 161 14 2262 3158 449274910 449275827 2.510000e-174 623
13 TraesCS1A01G187400 chr1D 77.398 761 131 32 5164 5895 449278301 449279049 1.650000e-111 414
14 TraesCS1A01G187400 chr1D 83.014 418 65 5 4253 4666 449276788 449277203 2.790000e-99 374
15 TraesCS1A01G187400 chr1D 85.205 365 45 5 6896 7252 449279855 449280218 4.680000e-97 366
16 TraesCS1A01G187400 chr1D 85.044 341 37 8 4724 5052 449277285 449277623 1.320000e-87 335
17 TraesCS1A01G187400 chr1D 87.925 265 23 5 227 483 261743566 261743303 3.720000e-78 303
18 TraesCS1A01G187400 chr1D 89.333 225 20 2 1 225 261743847 261743627 6.270000e-71 279
19 TraesCS1A01G187400 chr1B 95.074 4385 125 33 3883 8198 350393340 350397702 0.000000e+00 6817
20 TraesCS1A01G187400 chr1B 96.358 1922 62 4 1966 3886 350391346 350393260 0.000000e+00 3155
21 TraesCS1A01G187400 chr1B 91.484 1233 61 21 243 1459 350389579 350390783 0.000000e+00 1655
22 TraesCS1A01G187400 chr1B 80.399 852 144 11 2262 3091 614789035 614789885 1.940000e-175 627
23 TraesCS1A01G187400 chr1B 85.205 365 45 5 6896 7252 614794129 614794492 4.680000e-97 366
24 TraesCS1A01G187400 chr1B 82.878 403 48 15 4724 5111 614791638 614792034 7.880000e-90 342
25 TraesCS1A01G187400 chr1B 81.773 406 70 3 4264 4666 614791152 614791556 3.670000e-88 337
26 TraesCS1A01G187400 chr1B 88.696 230 21 4 1 230 350389274 350389498 8.100000e-70 276
27 TraesCS1A01G187400 chr1B 89.767 215 21 1 6247 6461 614793628 614793841 2.920000e-69 274
28 TraesCS1A01G187400 chr1B 91.071 112 10 0 1427 1538 350391339 350391450 1.430000e-32 152
29 TraesCS1A01G187400 chr1B 94.203 69 4 0 1470 1538 350390713 350390781 1.130000e-18 106
30 TraesCS1A01G187400 chr5A 87.302 189 22 2 8011 8198 683231722 683231909 1.790000e-51 215
31 TraesCS1A01G187400 chr4B 88.268 179 21 0 8020 8198 644826475 644826653 1.790000e-51 215
32 TraesCS1A01G187400 chr4D 86.243 189 24 2 8011 8198 500849972 500850159 3.880000e-48 204
33 TraesCS1A01G187400 chr4D 85.185 189 26 2 8011 8198 500924406 500924593 8.400000e-45 193
34 TraesCS1A01G187400 chr4D 85.185 189 26 2 8011 8198 500960837 500961024 8.400000e-45 193
35 TraesCS1A01G187400 chr4D 84.656 189 26 3 8011 8198 500886882 500887068 1.410000e-42 185
36 TraesCS1A01G187400 chrUn 86.034 179 25 0 8020 8198 317845302 317845124 8.400000e-45 193


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 TraesCS1A01G187400 chr1A 338580948 338589145 8197 False 3643.000000 11511 97.059000 1 8198 4 chr1A.!!$F1 8197
1 TraesCS1A01G187400 chr1A 544465521 544468777 3256 False 421.500000 625 81.399000 2262 5703 4 chr1A.!!$F2 3441
2 TraesCS1A01G187400 chr1A 544474252 544475141 889 False 331.000000 381 87.367000 6232 7251 2 chr1A.!!$F3 1019
3 TraesCS1A01G187400 chr1D 261735895 261743847 7952 True 3096.750000 10517 92.237750 1 8198 4 chr1D.!!$R1 8197
4 TraesCS1A01G187400 chr1D 449274910 449280218 5308 False 422.400000 623 82.010800 2262 7252 5 chr1D.!!$F1 4990
5 TraesCS1A01G187400 chr1B 350389274 350397702 8428 False 2026.833333 6817 92.814333 1 8198 6 chr1B.!!$F1 8197
6 TraesCS1A01G187400 chr1B 614789035 614794492 5457 False 389.200000 627 84.004400 2262 7252 5 chr1B.!!$F2 4990

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
94 95 0.031994 AACGCACCAAAGTTGCATCC 59.968 50.000 0.00 0.0 0.00 3.51 F
512 582 0.034477 CGGGGGAGCACTAACCAATT 60.034 55.000 0.00 0.0 0.00 2.32 F
993 1100 0.941463 GATACACATCCGCAGCGAGG 60.941 60.000 18.75 7.6 0.00 4.63 F
1505 1612 0.246086 GCGATCTCCCATAGCTCCAG 59.754 60.000 0.00 0.0 0.00 3.86 F
2057 2220 0.754217 CTTCCACCATCAGCCCCATG 60.754 60.000 0.00 0.0 0.00 3.66 F
2428 2612 1.291272 GACAAGCGACCCCTACGTT 59.709 57.895 0.00 0.0 0.00 3.99 F
3091 3275 4.071961 TCTTGTATGGGATGATCCAACG 57.928 45.455 14.36 0.0 40.62 4.10 F
4718 5250 2.027745 TGACTCAGGCATTCAACTCTCC 60.028 50.000 0.00 0.0 0.00 3.71 F
5417 6556 2.420022 CAGGTTCGATTAAGCACCCTTG 59.580 50.000 0.00 0.0 38.08 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1486 1593 0.246086 CTGGAGCTATGGGAGATCGC 59.754 60.000 0.00 0.0 41.83 4.58 R
1487 1594 0.246086 GCTGGAGCTATGGGAGATCG 59.754 60.000 0.00 0.0 41.83 3.69 R
2087 2250 1.327690 ACGATGGGATAGTGCGGTGT 61.328 55.000 0.00 0.0 0.00 4.16 R
3144 3331 2.626266 TGTAAAGACCTCGAGACAGCAA 59.374 45.455 15.71 0.0 0.00 3.91 R
3569 3868 1.542492 CAGCAGATCTTGGGCAAAGT 58.458 50.000 0.67 0.0 37.18 2.66 R
4377 4874 0.809385 CTGCAAGCAGATGACAAGGG 59.191 55.000 16.75 0.0 46.30 3.95 R
5078 5683 6.820656 GGTGTCTGTTCATTAGTCAGATCATT 59.179 38.462 0.00 0.0 39.77 2.57 R
5538 6679 3.008485 CAGACCTACTTCTTTCAAGGCCT 59.992 47.826 0.00 0.0 31.98 5.19 R
7322 8678 2.330216 CCCTACTTGCCTGCTACCTAT 58.670 52.381 0.00 0.0 0.00 2.57 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
29 30 3.116079 CAAAGAAATTGCTGTTGCCCT 57.884 42.857 0.00 0.00 38.71 5.19
47 48 4.376340 CCCTTAACTGGCATTCATTGAC 57.624 45.455 0.00 0.00 0.00 3.18
76 77 2.032634 GGATGCAAGACCACGCGAA 61.033 57.895 15.93 0.00 0.00 4.70
77 78 1.132640 GATGCAAGACCACGCGAAC 59.867 57.895 15.93 0.24 0.00 3.95
81 82 3.335534 AAGACCACGCGAACGCAC 61.336 61.111 15.93 0.00 45.53 5.34
91 92 1.063327 CGAACGCACCAAAGTTGCA 59.937 52.632 0.00 0.00 0.00 4.08
94 95 0.031994 AACGCACCAAAGTTGCATCC 59.968 50.000 0.00 0.00 0.00 3.51
100 101 2.884012 CACCAAAGTTGCATCCAGTGTA 59.116 45.455 0.00 0.00 0.00 2.90
101 102 2.884639 ACCAAAGTTGCATCCAGTGTAC 59.115 45.455 0.00 0.00 0.00 2.90
102 103 3.149196 CCAAAGTTGCATCCAGTGTACT 58.851 45.455 0.00 0.00 0.00 2.73
187 188 6.049149 TGAAGATAGAAAGGAAATAGCACCG 58.951 40.000 0.00 0.00 0.00 4.94
194 195 2.046314 AAATAGCACCGCCGCTGT 60.046 55.556 7.03 0.00 43.68 4.40
202 203 1.868498 GCACCGCCGCTGTAATTATTA 59.132 47.619 0.00 0.00 0.00 0.98
204 205 3.424433 GCACCGCCGCTGTAATTATTATC 60.424 47.826 0.00 0.00 0.00 1.75
225 226 8.889849 TTATCGAATGCTAAGCTAAACAAAAC 57.110 30.769 0.00 0.00 0.00 2.43
242 302 7.608308 AACAAAACTGCTAAAAGCAATTTCA 57.392 28.000 8.57 0.00 46.10 2.69
243 303 7.608308 ACAAAACTGCTAAAAGCAATTTCAA 57.392 28.000 8.57 0.00 46.10 2.69
246 306 8.949953 CAAAACTGCTAAAAGCAATTTCAAATG 58.050 29.630 8.57 0.98 46.10 2.32
247 307 7.134163 AAACTGCTAAAAGCAATTTCAAATGC 58.866 30.769 2.74 0.00 46.10 3.56
248 308 7.012610 AAACTGCTAAAAGCAATTTCAAATGCT 59.987 29.630 2.74 0.00 46.10 3.79
286 354 5.819825 AGAGAAAATAAATGAACCGAGGC 57.180 39.130 0.00 0.00 0.00 4.70
288 356 5.123979 AGAGAAAATAAATGAACCGAGGCAC 59.876 40.000 0.00 0.00 0.00 5.01
324 393 0.036010 CTGATCCACGAGCTTTGGGT 60.036 55.000 13.84 7.98 34.56 4.51
326 395 1.087501 GATCCACGAGCTTTGGGTTC 58.912 55.000 13.84 8.67 34.56 3.62
341 410 1.745489 GTTCCGGATGCAGTGGTCC 60.745 63.158 4.15 0.00 0.00 4.46
451 521 2.435059 GGGACGAGCACTTCAGCC 60.435 66.667 0.00 0.00 34.23 4.85
477 547 4.826556 AGAAGAGTTCATCAGCACTAACC 58.173 43.478 0.00 0.00 0.00 2.85
482 552 6.006449 AGAGTTCATCAGCACTAACCAATTT 58.994 36.000 0.00 0.00 0.00 1.82
483 553 6.491403 AGAGTTCATCAGCACTAACCAATTTT 59.509 34.615 0.00 0.00 0.00 1.82
484 554 7.014615 AGAGTTCATCAGCACTAACCAATTTTT 59.985 33.333 0.00 0.00 0.00 1.94
508 578 3.712907 TGCGGGGGAGCACTAACC 61.713 66.667 0.00 0.00 42.92 2.85
509 579 3.712907 GCGGGGGAGCACTAACCA 61.713 66.667 0.00 0.00 37.05 3.67
510 580 3.074281 CGGGGGAGCACTAACCAA 58.926 61.111 0.00 0.00 0.00 3.67
511 581 1.607612 CGGGGGAGCACTAACCAAT 59.392 57.895 0.00 0.00 0.00 3.16
512 582 0.034477 CGGGGGAGCACTAACCAATT 60.034 55.000 0.00 0.00 0.00 2.32
513 583 1.615919 CGGGGGAGCACTAACCAATTT 60.616 52.381 0.00 0.00 0.00 1.82
514 584 2.356330 CGGGGGAGCACTAACCAATTTA 60.356 50.000 0.00 0.00 0.00 1.40
515 585 3.687264 CGGGGGAGCACTAACCAATTTAT 60.687 47.826 0.00 0.00 0.00 1.40
516 586 4.445162 CGGGGGAGCACTAACCAATTTATA 60.445 45.833 0.00 0.00 0.00 0.98
517 587 5.451354 GGGGGAGCACTAACCAATTTATAA 58.549 41.667 0.00 0.00 0.00 0.98
571 670 3.643159 AATCGAAGTCAAAACAAGGCC 57.357 42.857 0.00 0.00 0.00 5.19
577 676 4.215399 CGAAGTCAAAACAAGGCCTAATCA 59.785 41.667 5.16 0.00 0.00 2.57
599 698 1.548081 TCCCGTCACGTTATCTTCCA 58.452 50.000 0.00 0.00 0.00 3.53
603 702 2.186076 CGTCACGTTATCTTCCAGAGC 58.814 52.381 0.00 0.00 0.00 4.09
824 928 2.476619 CGATTTCGATCTCATTTCCCCG 59.523 50.000 0.00 0.00 43.02 5.73
825 929 2.325583 TTTCGATCTCATTTCCCCGG 57.674 50.000 0.00 0.00 0.00 5.73
826 930 1.200519 TTCGATCTCATTTCCCCGGT 58.799 50.000 0.00 0.00 0.00 5.28
993 1100 0.941463 GATACACATCCGCAGCGAGG 60.941 60.000 18.75 7.60 0.00 4.63
1090 1197 3.589881 CGGAGCCCTACCCGTACG 61.590 72.222 8.69 8.69 40.78 3.67
1149 1256 3.834799 CCGTCCCACTACCTCGCC 61.835 72.222 0.00 0.00 0.00 5.54
1484 1591 2.838693 GGCCTCCTACCCGAGTCC 60.839 72.222 0.00 0.00 0.00 3.85
1485 1592 3.217743 GCCTCCTACCCGAGTCCG 61.218 72.222 0.00 0.00 0.00 4.79
1495 1602 3.967335 CGAGTCCGGCGATCTCCC 61.967 72.222 9.30 0.00 0.00 4.30
1496 1603 2.833582 GAGTCCGGCGATCTCCCA 60.834 66.667 9.30 0.00 0.00 4.37
1497 1604 2.123251 AGTCCGGCGATCTCCCAT 60.123 61.111 9.30 0.00 0.00 4.00
1498 1605 0.894184 GAGTCCGGCGATCTCCCATA 60.894 60.000 9.30 0.00 0.00 2.74
1499 1606 0.896019 AGTCCGGCGATCTCCCATAG 60.896 60.000 9.30 0.00 0.00 2.23
1500 1607 2.262915 CCGGCGATCTCCCATAGC 59.737 66.667 9.30 0.00 0.00 2.97
1501 1608 2.279069 CCGGCGATCTCCCATAGCT 61.279 63.158 9.30 0.00 0.00 3.32
1502 1609 1.214062 CGGCGATCTCCCATAGCTC 59.786 63.158 0.00 0.00 0.00 4.09
1503 1610 1.594310 GGCGATCTCCCATAGCTCC 59.406 63.158 0.00 0.00 0.00 4.70
1504 1611 1.188219 GGCGATCTCCCATAGCTCCA 61.188 60.000 0.00 0.00 0.00 3.86
1505 1612 0.246086 GCGATCTCCCATAGCTCCAG 59.754 60.000 0.00 0.00 0.00 3.86
1506 1613 0.246086 CGATCTCCCATAGCTCCAGC 59.754 60.000 0.00 0.00 42.49 4.85
1516 1623 2.360475 GCTCCAGCTTCCACCACC 60.360 66.667 0.00 0.00 38.21 4.61
1517 1624 3.160585 CTCCAGCTTCCACCACCA 58.839 61.111 0.00 0.00 0.00 4.17
1518 1625 1.002868 CTCCAGCTTCCACCACCAG 60.003 63.158 0.00 0.00 0.00 4.00
1519 1626 2.674380 CCAGCTTCCACCACCAGC 60.674 66.667 0.00 0.00 0.00 4.85
1520 1627 2.674380 CAGCTTCCACCACCAGCC 60.674 66.667 0.00 0.00 33.73 4.85
1521 1628 3.971702 AGCTTCCACCACCAGCCC 61.972 66.667 0.00 0.00 33.73 5.19
1523 1630 3.579302 CTTCCACCACCAGCCCCA 61.579 66.667 0.00 0.00 0.00 4.96
1524 1631 2.863484 TTCCACCACCAGCCCCAT 60.863 61.111 0.00 0.00 0.00 4.00
1525 1632 2.843912 CTTCCACCACCAGCCCCATC 62.844 65.000 0.00 0.00 0.00 3.51
1526 1633 4.447342 CCACCACCAGCCCCATCC 62.447 72.222 0.00 0.00 0.00 3.51
1527 1634 4.447342 CACCACCAGCCCCATCCC 62.447 72.222 0.00 0.00 0.00 3.85
1528 1635 4.701437 ACCACCAGCCCCATCCCT 62.701 66.667 0.00 0.00 0.00 4.20
1529 1636 3.813724 CCACCAGCCCCATCCCTC 61.814 72.222 0.00 0.00 0.00 4.30
1530 1637 4.181010 CACCAGCCCCATCCCTCG 62.181 72.222 0.00 0.00 0.00 4.63
2057 2220 0.754217 CTTCCACCATCAGCCCCATG 60.754 60.000 0.00 0.00 0.00 3.66
2087 2250 3.329542 GAATCACCTGCGGCCTCCA 62.330 63.158 0.00 0.00 0.00 3.86
2428 2612 1.291272 GACAAGCGACCCCTACGTT 59.709 57.895 0.00 0.00 0.00 3.99
3091 3275 4.071961 TCTTGTATGGGATGATCCAACG 57.928 45.455 14.36 0.00 40.62 4.10
3569 3868 7.441836 TCAAGCACTCTTCAGTTCAAGTATTA 58.558 34.615 0.00 0.00 0.00 0.98
3757 4071 8.156820 CCATGACTTATGTATCCTTGGATGTTA 58.843 37.037 12.08 0.00 34.87 2.41
3758 4072 8.993121 CATGACTTATGTATCCTTGGATGTTAC 58.007 37.037 12.08 3.65 31.92 2.50
3759 4073 8.319057 TGACTTATGTATCCTTGGATGTTACT 57.681 34.615 12.08 0.00 0.00 2.24
3760 4074 8.421784 TGACTTATGTATCCTTGGATGTTACTC 58.578 37.037 12.08 0.00 0.00 2.59
3761 4075 7.736893 ACTTATGTATCCTTGGATGTTACTCC 58.263 38.462 12.08 0.00 35.74 3.85
4377 4874 4.214119 TGTCACTGCTCTGAAAGTATTTGC 59.786 41.667 0.00 0.00 39.27 3.68
4718 5250 2.027745 TGACTCAGGCATTCAACTCTCC 60.028 50.000 0.00 0.00 0.00 3.71
4835 5377 4.594136 GGTAACTGAAAACCGAAACACAG 58.406 43.478 0.00 0.00 0.00 3.66
5078 5683 8.696374 TCTAGAGTTCTCTGTTTCTTCTTTTGA 58.304 33.333 12.00 0.00 0.00 2.69
5195 6322 7.434307 GTGTCCATCTAATGAAAATGCAGAATG 59.566 37.037 0.00 0.00 40.87 2.67
5211 6338 6.446318 TGCAGAATGTACCAAATTCTTTGAC 58.554 36.000 4.59 0.00 41.39 3.18
5416 6555 2.711542 CAGGTTCGATTAAGCACCCTT 58.288 47.619 0.00 0.00 38.08 3.95
5417 6556 2.420022 CAGGTTCGATTAAGCACCCTTG 59.580 50.000 0.00 0.00 38.08 3.61
5956 7266 4.421058 CGGATGAATCTTACTGTGAACGA 58.579 43.478 0.00 0.00 0.00 3.85
6198 7511 9.956720 AACTTCTCAGTATTTGAATTTTCACTG 57.043 29.630 0.00 0.00 34.81 3.66
6442 7755 3.865164 GGGCAAATAAAATTTCTGCTCCG 59.135 43.478 11.79 0.00 33.49 4.63
6492 7813 3.439476 AGTTCAAGCTGCTGAATCACATC 59.561 43.478 1.35 0.00 37.63 3.06
6595 7916 4.935205 TGATGTTATGCGTTGCTTAGAACT 59.065 37.500 0.00 0.00 0.00 3.01
6624 7945 8.584157 TGCTTCATTACAATTGTTTCACCTTAT 58.416 29.630 17.78 0.00 0.00 1.73
6874 8223 7.675062 CAGCTGGTATTTCTGGATTATACTCT 58.325 38.462 5.57 0.00 0.00 3.24
6960 8309 7.102346 AGCATATTGGAATTATCGAGGAAGAG 58.898 38.462 0.00 0.00 0.00 2.85
7179 8534 1.299648 CTCCTTCACGGCCATCCAA 59.700 57.895 2.24 0.00 0.00 3.53
7191 8546 2.519013 GCCATCCAAGAAAACCTCACT 58.481 47.619 0.00 0.00 0.00 3.41
7322 8678 5.470098 GGAGAGAATTTCGCAAGCCAATATA 59.530 40.000 2.95 0.00 37.18 0.86
7408 8765 5.335976 CCTTTGGCTGTTCCATTCTTAACTC 60.336 44.000 0.00 0.00 46.04 3.01
7422 8779 7.972277 CCATTCTTAACTCATCATGTTCCTTTG 59.028 37.037 0.00 0.00 0.00 2.77
7446 8803 4.141321 ACATGTACTCGGTCCCTGTATAGA 60.141 45.833 0.00 0.00 0.00 1.98
7456 8813 6.603599 TCGGTCCCTGTATAGATAAGATGATG 59.396 42.308 0.00 0.00 0.00 3.07
7457 8814 6.183360 CGGTCCCTGTATAGATAAGATGATGG 60.183 46.154 0.00 0.00 0.00 3.51
7459 8816 6.382570 GTCCCTGTATAGATAAGATGATGGCT 59.617 42.308 0.00 0.00 0.00 4.75
7498 8855 1.165270 GAACCTGGCGTTTGTAGCAT 58.835 50.000 0.00 0.00 33.74 3.79
7501 8858 1.002659 ACCTGGCGTTTGTAGCATGTA 59.997 47.619 0.00 0.00 36.08 2.29
7514 8871 2.944129 AGCATGTAACAACCACCAAGT 58.056 42.857 0.00 0.00 0.00 3.16
7515 8872 4.093472 AGCATGTAACAACCACCAAGTA 57.907 40.909 0.00 0.00 0.00 2.24
7523 8880 7.932335 TGTAACAACCACCAAGTAAAATAGTG 58.068 34.615 0.00 0.00 0.00 2.74
7604 8986 6.428159 CAGTATTCTGGTTTGCTACTCTTGTT 59.572 38.462 0.00 0.00 37.97 2.83
7621 9003 8.877864 ACTCTTGTTATCAATGGAAATTGGTA 57.122 30.769 0.00 0.00 32.82 3.25
7646 9028 0.757188 ATGTGGCAACCGGTTTCCAA 60.757 50.000 35.53 25.57 0.00 3.53
7681 9063 2.552315 AGTATTGTTGCTTGAACCACCG 59.448 45.455 0.00 0.00 33.07 4.94
7750 9132 6.095860 CAGAGAAATGCATGTTAAAGGGATGA 59.904 38.462 0.00 0.00 0.00 2.92
7841 9224 8.706322 ACAAATTAATCTGTCTAAACCAGGTT 57.294 30.769 0.00 0.00 37.11 3.50
7952 9335 6.765403 TGCCCATATACCTGTACAGATTTAC 58.235 40.000 24.68 5.07 0.00 2.01
7953 9336 6.327887 TGCCCATATACCTGTACAGATTTACA 59.672 38.462 24.68 7.46 0.00 2.41
7955 9338 7.172703 GCCCATATACCTGTACAGATTTACAAC 59.827 40.741 24.68 3.08 31.52 3.32
8001 9397 2.631160 TCAGTATAATTGCGGGGGTG 57.369 50.000 0.00 0.00 0.00 4.61
8006 9402 3.888930 AGTATAATTGCGGGGGTGATTTG 59.111 43.478 0.00 0.00 0.00 2.32
8010 9406 0.322456 TTGCGGGGGTGATTTGAGAG 60.322 55.000 0.00 0.00 0.00 3.20
8104 9500 2.693864 ATGACCCTGAGCCCCCTG 60.694 66.667 0.00 0.00 0.00 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 4.154015 CGACAGTCAATGAATGCCAGTTAA 59.846 41.667 10.83 0.00 30.24 2.01
40 41 0.389817 CCTTCCGCGACAGTCAATGA 60.390 55.000 8.23 0.00 0.00 2.57
47 48 1.699656 CTTGCATCCTTCCGCGACAG 61.700 60.000 8.23 1.90 0.00 3.51
76 77 1.106351 TGGATGCAACTTTGGTGCGT 61.106 50.000 1.62 1.62 0.00 5.24
77 78 0.387622 CTGGATGCAACTTTGGTGCG 60.388 55.000 3.09 0.00 0.00 5.34
81 82 3.149196 AGTACACTGGATGCAACTTTGG 58.851 45.455 0.00 0.00 0.00 3.28
82 83 4.997395 AGTAGTACACTGGATGCAACTTTG 59.003 41.667 2.52 0.00 35.62 2.77
113 114 3.111838 CTCTCACCGAGATGACAATTCG 58.888 50.000 5.30 5.30 42.62 3.34
187 188 5.022021 GCATTCGATAATAATTACAGCGGC 58.978 41.667 6.70 0.00 0.00 6.53
202 203 7.023575 CAGTTTTGTTTAGCTTAGCATTCGAT 58.976 34.615 7.07 0.00 0.00 3.59
204 205 5.059710 GCAGTTTTGTTTAGCTTAGCATTCG 59.940 40.000 7.07 0.00 0.00 3.34
281 349 0.317269 CAAAAGTGTGCTGTGCCTCG 60.317 55.000 0.00 0.00 0.00 4.63
284 352 0.592247 CGTCAAAAGTGTGCTGTGCC 60.592 55.000 0.00 0.00 0.00 5.01
285 353 0.098728 ACGTCAAAAGTGTGCTGTGC 59.901 50.000 0.00 0.00 0.00 4.57
286 354 1.665679 AGACGTCAAAAGTGTGCTGTG 59.334 47.619 19.50 0.00 0.00 3.66
288 356 1.933181 TCAGACGTCAAAAGTGTGCTG 59.067 47.619 19.50 2.96 33.54 4.41
324 393 2.668632 GGACCACTGCATCCGGAA 59.331 61.111 9.01 0.00 0.00 4.30
341 410 7.274468 CGGATCAGAATCAATTTCTCCTATACG 59.726 40.741 0.00 0.00 42.98 3.06
451 521 4.567971 AGTGCTGATGAACTCTTCTTCTG 58.432 43.478 0.00 0.00 35.52 3.02
487 557 0.178987 TTAGTGCTCCCCCGCAAAAA 60.179 50.000 0.00 0.00 42.32 1.94
488 558 0.891904 GTTAGTGCTCCCCCGCAAAA 60.892 55.000 0.00 0.00 42.32 2.44
489 559 1.302993 GTTAGTGCTCCCCCGCAAA 60.303 57.895 0.00 0.00 42.32 3.68
490 560 2.349755 GTTAGTGCTCCCCCGCAA 59.650 61.111 0.00 0.00 42.32 4.85
491 561 3.712907 GGTTAGTGCTCCCCCGCA 61.713 66.667 0.00 0.00 37.62 5.69
492 562 2.552231 ATTGGTTAGTGCTCCCCCGC 62.552 60.000 0.00 0.00 0.00 6.13
493 563 0.034477 AATTGGTTAGTGCTCCCCCG 60.034 55.000 0.00 0.00 0.00 5.73
494 564 2.231716 AAATTGGTTAGTGCTCCCCC 57.768 50.000 0.00 0.00 0.00 5.40
495 565 8.700439 TTATTATAAATTGGTTAGTGCTCCCC 57.300 34.615 0.00 0.00 0.00 4.81
514 584 9.146586 TGGCTTTCTGGCAGATTTTATTATTAT 57.853 29.630 19.50 0.00 46.76 1.28
515 585 8.532186 TGGCTTTCTGGCAGATTTTATTATTA 57.468 30.769 19.50 0.00 46.76 0.98
516 586 7.422465 TGGCTTTCTGGCAGATTTTATTATT 57.578 32.000 19.50 0.00 46.76 1.40
530 625 6.308766 CGATTTGATTAGTTTTGGCTTTCTGG 59.691 38.462 0.00 0.00 0.00 3.86
571 670 2.579207 ACGTGACGGGATGTGATTAG 57.421 50.000 10.66 0.00 0.00 1.73
577 676 2.159142 GGAAGATAACGTGACGGGATGT 60.159 50.000 10.66 0.00 0.00 3.06
603 702 3.790437 ATGCTCCGCTGGACCCAG 61.790 66.667 11.59 11.59 46.15 4.45
649 748 4.673298 TGTCCGTGCGGTGCGATT 62.673 61.111 10.60 0.00 36.47 3.34
698 802 0.371645 CAGTTCGCTCGCTTGATTCC 59.628 55.000 0.00 0.00 0.00 3.01
704 808 1.373497 CTGACCAGTTCGCTCGCTT 60.373 57.895 0.00 0.00 0.00 4.68
947 1054 6.012337 AGATTGTTTTCCCCCAAATTGTTT 57.988 33.333 0.00 0.00 0.00 2.83
993 1100 3.917760 CTCCCCTCCATCGCCGAC 61.918 72.222 0.00 0.00 0.00 4.79
999 1106 1.077429 GTGGTTGCTCCCCTCCATC 60.077 63.158 0.00 0.00 34.77 3.51
1090 1197 1.899437 TACTGCTGGTGCTGGTAGGC 61.899 60.000 0.00 0.00 41.57 3.93
1132 1239 3.834799 GGCGAGGTAGTGGGACGG 61.835 72.222 0.00 0.00 0.00 4.79
1139 1246 3.736224 TCGAGGGGGCGAGGTAGT 61.736 66.667 0.00 0.00 35.01 2.73
1149 1256 2.764547 GGGAAGGAGGTCGAGGGG 60.765 72.222 0.00 0.00 0.00 4.79
1466 1573 3.217743 GACTCGGGTAGGAGGCCG 61.218 72.222 0.00 0.00 35.97 6.13
1468 1575 3.217743 CGGACTCGGGTAGGAGGC 61.218 72.222 0.00 0.00 41.58 4.70
1478 1585 3.967335 GGGAGATCGCCGGACTCG 61.967 72.222 5.05 0.00 0.00 4.18
1479 1586 0.894184 TATGGGAGATCGCCGGACTC 60.894 60.000 5.05 7.75 0.00 3.36
1480 1587 0.896019 CTATGGGAGATCGCCGGACT 60.896 60.000 5.05 0.00 0.00 3.85
1481 1588 1.587054 CTATGGGAGATCGCCGGAC 59.413 63.158 5.05 0.00 0.00 4.79
1482 1589 2.276116 GCTATGGGAGATCGCCGGA 61.276 63.158 5.05 0.00 0.00 5.14
1483 1590 2.219325 GAGCTATGGGAGATCGCCGG 62.219 65.000 9.58 0.00 29.18 6.13
1484 1591 1.214062 GAGCTATGGGAGATCGCCG 59.786 63.158 9.58 0.00 29.18 6.46
1485 1592 1.188219 TGGAGCTATGGGAGATCGCC 61.188 60.000 7.00 7.00 41.83 5.54
1486 1593 0.246086 CTGGAGCTATGGGAGATCGC 59.754 60.000 0.00 0.00 41.83 4.58
1487 1594 0.246086 GCTGGAGCTATGGGAGATCG 59.754 60.000 0.00 0.00 41.83 3.69
1499 1606 2.360475 GGTGGTGGAAGCTGGAGC 60.360 66.667 0.00 0.00 42.49 4.70
1500 1607 1.002868 CTGGTGGTGGAAGCTGGAG 60.003 63.158 0.00 0.00 33.76 3.86
1501 1608 3.160585 CTGGTGGTGGAAGCTGGA 58.839 61.111 0.00 0.00 33.76 3.86
1502 1609 2.674380 GCTGGTGGTGGAAGCTGG 60.674 66.667 0.00 0.00 34.05 4.85
1503 1610 2.674380 GGCTGGTGGTGGAAGCTG 60.674 66.667 0.00 0.00 37.12 4.24
1504 1611 3.971702 GGGCTGGTGGTGGAAGCT 61.972 66.667 0.00 0.00 37.12 3.74
1506 1613 2.843912 GATGGGGCTGGTGGTGGAAG 62.844 65.000 0.00 0.00 0.00 3.46
1507 1614 2.863484 ATGGGGCTGGTGGTGGAA 60.863 61.111 0.00 0.00 0.00 3.53
1508 1615 3.338250 GATGGGGCTGGTGGTGGA 61.338 66.667 0.00 0.00 0.00 4.02
1509 1616 4.447342 GGATGGGGCTGGTGGTGG 62.447 72.222 0.00 0.00 0.00 4.61
1510 1617 4.447342 GGGATGGGGCTGGTGGTG 62.447 72.222 0.00 0.00 0.00 4.17
1511 1618 4.701437 AGGGATGGGGCTGGTGGT 62.701 66.667 0.00 0.00 0.00 4.16
1512 1619 3.813724 GAGGGATGGGGCTGGTGG 61.814 72.222 0.00 0.00 0.00 4.61
1513 1620 4.181010 CGAGGGATGGGGCTGGTG 62.181 72.222 0.00 0.00 0.00 4.17
2087 2250 1.327690 ACGATGGGATAGTGCGGTGT 61.328 55.000 0.00 0.00 0.00 4.16
2167 2330 1.895707 CGGTAGTACGGAGGGCGAT 60.896 63.158 1.72 0.00 0.00 4.58
3091 3275 3.528597 AAGCCGAGAATACTCCTTGAC 57.471 47.619 0.00 0.00 39.76 3.18
3144 3331 2.626266 TGTAAAGACCTCGAGACAGCAA 59.374 45.455 15.71 0.00 0.00 3.91
3569 3868 1.542492 CAGCAGATCTTGGGCAAAGT 58.458 50.000 0.67 0.00 37.18 2.66
3692 4005 2.095853 CCATTCACATTCACTACGTGCC 59.904 50.000 0.00 0.00 32.98 5.01
3757 4071 8.546322 ACAACAGCATGATATATCATATGGAGT 58.454 33.333 27.49 23.59 45.23 3.85
3758 4072 8.827677 CACAACAGCATGATATATCATATGGAG 58.172 37.037 27.49 23.20 45.23 3.86
3759 4073 8.323567 ACACAACAGCATGATATATCATATGGA 58.676 33.333 27.49 7.52 45.23 3.41
3760 4074 8.502105 ACACAACAGCATGATATATCATATGG 57.498 34.615 27.49 21.11 45.23 2.74
4377 4874 0.809385 CTGCAAGCAGATGACAAGGG 59.191 55.000 16.75 0.00 46.30 3.95
4737 5269 6.961554 GTCAATAGAGCGAAACACCTATTTTG 59.038 38.462 0.00 0.00 31.59 2.44
4835 5377 9.655769 CACAAACTGTAGAATATAATGTCATGC 57.344 33.333 0.00 0.00 0.00 4.06
5078 5683 6.820656 GGTGTCTGTTCATTAGTCAGATCATT 59.179 38.462 0.00 0.00 39.77 2.57
5211 6338 3.572632 ACCATCATGAGTTGGGATCAG 57.427 47.619 17.66 0.00 38.65 2.90
5416 6555 5.534654 CCACCAGAACAAATTAGGAAGAACA 59.465 40.000 0.00 0.00 0.00 3.18
5417 6556 5.768164 TCCACCAGAACAAATTAGGAAGAAC 59.232 40.000 0.00 0.00 0.00 3.01
5538 6679 3.008485 CAGACCTACTTCTTTCAAGGCCT 59.992 47.826 0.00 0.00 31.98 5.19
5775 6920 6.761099 ACGTGTCATGACTACTCTCTTTAT 57.239 37.500 25.55 0.00 0.00 1.40
5935 7245 4.567159 GGTCGTTCACAGTAAGATTCATCC 59.433 45.833 0.00 0.00 0.00 3.51
6198 7511 8.995220 TCACAACAACTAGTACATCAAATAACC 58.005 33.333 0.00 0.00 0.00 2.85
6442 7755 3.497879 GGCATTACCTGTCCACGC 58.502 61.111 0.00 0.00 34.51 5.34
6492 7813 3.476552 TGTCTTCTGCAGGTACCAAAAG 58.523 45.455 15.94 8.27 0.00 2.27
6595 7916 5.691305 GTGAAACAATTGTAATGAAGCAGCA 59.309 36.000 12.39 0.00 36.32 4.41
6624 7945 3.511477 AGTTGGAGGCAGTCTCTCTAAA 58.489 45.455 1.07 0.00 42.10 1.85
6701 8037 8.726068 CACCAACAGTATTTATGTGTCATTACA 58.274 33.333 0.00 0.00 34.63 2.41
6960 8309 3.636153 AGGCTCTCTGGATGGTTAAAC 57.364 47.619 0.00 0.00 0.00 2.01
7271 8627 7.027874 ACCTATGTTATCAGGAACCAGAAAA 57.972 36.000 0.00 0.00 35.76 2.29
7322 8678 2.330216 CCCTACTTGCCTGCTACCTAT 58.670 52.381 0.00 0.00 0.00 2.57
7367 8723 4.202141 CCAAAGGCAGAAATGACTTGAACA 60.202 41.667 0.00 0.00 37.20 3.18
7368 8724 4.301628 CCAAAGGCAGAAATGACTTGAAC 58.698 43.478 0.00 0.00 37.20 3.18
7398 8755 8.734386 GTCAAAGGAACATGATGAGTTAAGAAT 58.266 33.333 0.00 0.00 0.00 2.40
7399 8756 7.719193 TGTCAAAGGAACATGATGAGTTAAGAA 59.281 33.333 0.00 0.00 0.00 2.52
7408 8765 6.456047 CGAGTACATGTCAAAGGAACATGATG 60.456 42.308 19.80 0.00 42.60 3.07
7422 8779 1.183549 ACAGGGACCGAGTACATGTC 58.816 55.000 0.00 0.00 36.64 3.06
7430 8787 6.181190 TCATCTTATCTATACAGGGACCGAG 58.819 44.000 0.00 0.00 0.00 4.63
7446 8803 3.870538 TCCAGCAAGCCATCATCTTAT 57.129 42.857 0.00 0.00 0.00 1.73
7456 8813 1.153005 CAGAGGGATCCAGCAAGCC 60.153 63.158 15.23 0.00 0.00 4.35
7457 8814 0.254178 TTCAGAGGGATCCAGCAAGC 59.746 55.000 15.23 0.00 0.00 4.01
7459 8816 0.914644 CCTTCAGAGGGATCCAGCAA 59.085 55.000 15.23 0.00 39.55 3.91
7498 8855 7.013464 CCACTATTTTACTTGGTGGTTGTTACA 59.987 37.037 0.00 0.00 41.52 2.41
7501 8858 6.399639 CCACTATTTTACTTGGTGGTTGTT 57.600 37.500 0.00 0.00 41.52 2.83
7604 8986 6.334378 TCCACCTACCAATTTCCATTGATA 57.666 37.500 0.00 0.00 42.35 2.15
7621 9003 2.034066 CGGTTGCCACATCCACCT 59.966 61.111 0.00 0.00 0.00 4.00
7653 9035 5.106712 GGTTCAAGCAACAATACTTCGATCA 60.107 40.000 0.00 0.00 36.61 2.92
7654 9036 5.106712 TGGTTCAAGCAACAATACTTCGATC 60.107 40.000 0.00 0.00 36.61 3.69
7655 9037 4.759693 TGGTTCAAGCAACAATACTTCGAT 59.240 37.500 0.00 0.00 36.61 3.59
7656 9038 4.024387 GTGGTTCAAGCAACAATACTTCGA 60.024 41.667 0.00 0.00 36.61 3.71
7702 9084 7.714377 TCTGCATTGCAAAATAAGAAGGAAAAA 59.286 29.630 13.18 0.00 38.41 1.94
7750 9132 8.865090 TGTTTGTTGATTATTATGAAACCCAGT 58.135 29.630 0.00 0.00 0.00 4.00
7815 9197 8.706322 ACCTGGTTTAGACAGATTAATTTGTT 57.294 30.769 12.47 6.19 38.20 2.83
7816 9198 8.706322 AACCTGGTTTAGACAGATTAATTTGT 57.294 30.769 11.18 11.18 38.20 2.83
7841 9224 7.244558 TCATGGCATAATATTGTATTTGGGGA 58.755 34.615 0.00 0.00 0.00 4.81
7874 9257 8.945195 ATGATATTTCAAGGAGCCATATTTGA 57.055 30.769 0.00 0.00 34.96 2.69
7880 9263 6.379579 AGGAAATGATATTTCAAGGAGCCAT 58.620 36.000 14.18 0.00 34.96 4.40
7888 9271 7.658982 CGAGAGATGGAGGAAATGATATTTCAA 59.341 37.037 14.18 0.68 34.96 2.69
7952 9335 6.176975 TGAACTCAACTAACACAACTGTTG 57.823 37.500 18.44 18.44 40.98 3.33
7953 9336 7.120579 TGAATGAACTCAACTAACACAACTGTT 59.879 33.333 0.00 0.00 43.39 3.16
7955 9338 7.011389 TCTGAATGAACTCAACTAACACAACTG 59.989 37.037 0.00 0.00 0.00 3.16
8001 9397 4.712763 CAGGTAAACGCAACTCTCAAATC 58.287 43.478 0.00 0.00 0.00 2.17
8006 9402 0.796927 GGCAGGTAAACGCAACTCTC 59.203 55.000 0.00 0.00 0.00 3.20
8010 9406 1.495951 CTCGGCAGGTAAACGCAAC 59.504 57.895 0.00 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.