Multiple sequence alignment - TraesCS1B01G210900

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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 TraesCS1B01G210900 chr1B 100.000 5054 0 0 1 5054 383804884 383799831 0.000000e+00 9334.0
1 TraesCS1B01G210900 chr1B 92.844 545 39 0 6 550 93966740 93966196 0.000000e+00 791.0
2 TraesCS1B01G210900 chr1D 95.458 2576 78 16 575 3123 282293934 282291371 0.000000e+00 4072.0
3 TraesCS1B01G210900 chr1D 94.784 1572 66 11 3109 4677 282291192 282289634 0.000000e+00 2435.0
4 TraesCS1B01G210900 chr1D 91.652 551 44 2 1 551 58524875 58525423 0.000000e+00 761.0
5 TraesCS1B01G210900 chr1D 95.205 292 7 1 4763 5054 282289447 282289163 5.960000e-124 455.0
6 TraesCS1B01G210900 chr1D 81.385 231 37 6 3466 3694 421069426 421069200 3.110000e-42 183.0
7 TraesCS1B01G210900 chr1D 83.616 177 19 8 3522 3695 337775348 337775179 1.880000e-34 158.0
8 TraesCS1B01G210900 chr1A 96.360 2088 51 9 575 2649 354308203 354306128 0.000000e+00 3411.0
9 TraesCS1B01G210900 chr1A 95.664 1107 42 6 3535 4636 354304564 354303459 0.000000e+00 1773.0
10 TraesCS1B01G210900 chr1A 97.479 833 16 3 2534 3366 354306135 354305308 0.000000e+00 1417.0
11 TraesCS1B01G210900 chr1A 92.336 548 42 0 3 550 21011309 21011856 0.000000e+00 780.0
12 TraesCS1B01G210900 chr1A 99.390 164 1 0 4891 5054 354302831 354302668 1.060000e-76 298.0
13 TraesCS1B01G210900 chr1A 95.192 104 4 1 4765 4867 354303251 354303148 4.050000e-36 163.0
14 TraesCS1B01G210900 chr1A 100.000 32 0 0 3505 3536 354304757 354304726 5.460000e-05 60.2
15 TraesCS1B01G210900 chr5D 93.761 545 34 0 6 550 513888709 513889253 0.000000e+00 819.0
16 TraesCS1B01G210900 chr5D 84.279 229 26 9 3466 3691 240849665 240849444 1.100000e-51 215.0
17 TraesCS1B01G210900 chr7B 92.701 548 40 0 3 550 270177117 270177664 0.000000e+00 791.0
18 TraesCS1B01G210900 chr7B 92.336 548 42 0 3 550 449880544 449881091 0.000000e+00 780.0
19 TraesCS1B01G210900 chr7B 91.927 545 44 0 6 550 16908845 16908301 0.000000e+00 763.0
20 TraesCS1B01G210900 chr6B 92.294 545 42 0 6 550 682322938 682322394 0.000000e+00 774.0
21 TraesCS1B01G210900 chr6B 82.412 199 29 6 3466 3663 20944989 20945182 8.700000e-38 169.0
22 TraesCS1B01G210900 chr4A 91.606 548 46 0 3 550 742304464 742305011 0.000000e+00 758.0
23 TraesCS1B01G210900 chr4B 82.879 257 26 16 3430 3680 82417389 82417633 1.100000e-51 215.0
24 TraesCS1B01G210900 chr5B 84.000 225 29 7 3466 3689 262823006 262823224 5.130000e-50 209.0
25 TraesCS1B01G210900 chrUn 78.788 198 39 3 3468 3665 99118446 99118252 4.110000e-26 130.0


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 TraesCS1B01G210900 chr1B 383799831 383804884 5053 True 9334.000000 9334 100.0000 1 5054 1 chr1B.!!$R2 5053
1 TraesCS1B01G210900 chr1B 93966196 93966740 544 True 791.000000 791 92.8440 6 550 1 chr1B.!!$R1 544
2 TraesCS1B01G210900 chr1D 282289163 282293934 4771 True 2320.666667 4072 95.1490 575 5054 3 chr1D.!!$R3 4479
3 TraesCS1B01G210900 chr1D 58524875 58525423 548 False 761.000000 761 91.6520 1 551 1 chr1D.!!$F1 550
4 TraesCS1B01G210900 chr1A 354302668 354308203 5535 True 1187.033333 3411 97.3475 575 5054 6 chr1A.!!$R1 4479
5 TraesCS1B01G210900 chr1A 21011309 21011856 547 False 780.000000 780 92.3360 3 550 1 chr1A.!!$F1 547
6 TraesCS1B01G210900 chr5D 513888709 513889253 544 False 819.000000 819 93.7610 6 550 1 chr5D.!!$F1 544
7 TraesCS1B01G210900 chr7B 270177117 270177664 547 False 791.000000 791 92.7010 3 550 1 chr7B.!!$F1 547
8 TraesCS1B01G210900 chr7B 449880544 449881091 547 False 780.000000 780 92.3360 3 550 1 chr7B.!!$F2 547
9 TraesCS1B01G210900 chr7B 16908301 16908845 544 True 763.000000 763 91.9270 6 550 1 chr7B.!!$R1 544
10 TraesCS1B01G210900 chr6B 682322394 682322938 544 True 774.000000 774 92.2940 6 550 1 chr6B.!!$R1 544
11 TraesCS1B01G210900 chr4A 742304464 742305011 547 False 758.000000 758 91.6060 3 550 1 chr4A.!!$F1 547

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
654 659 0.111253 GGCTGGCTGGGCAATATAGT 59.889 55.000 0.00 0.0 0.00 2.12 F
690 695 1.068121 CCACCCCTCCTTCTCTTGTT 58.932 55.000 0.00 0.0 0.00 2.83 F
691 696 1.425448 CCACCCCTCCTTCTCTTGTTT 59.575 52.381 0.00 0.0 0.00 2.83 F
1467 1502 1.594331 GCCAATATCCCGACAAGGAC 58.406 55.000 0.00 0.0 45.00 3.85 F
2161 2196 2.223433 GCTTCTGGATGCTGTTACATGC 60.223 50.000 0.00 0.0 38.72 4.06 F
3461 3882 1.002274 CTGGGTGCTACTCCCTCCT 59.998 63.158 6.31 0.0 44.84 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2066 2101 2.507407 TTCAGGGCTGGGAACAATAC 57.493 50.000 0.00 0.0 42.06 1.89 R
2248 2284 3.006537 GCACTCTGTTTCAGTGGGTACTA 59.993 47.826 2.21 0.0 41.49 1.82 R
2451 2493 5.382618 AACCAAAAGAATCATCTGTGCTC 57.617 39.130 0.00 0.0 35.59 4.26 R
3261 3604 2.887152 GCCACAAGTGAACAGAAAGGAT 59.113 45.455 0.94 0.0 0.00 3.24 R
3666 4588 2.125269 CCGTCCGGGCTTACAAGG 60.125 66.667 3.66 0.0 0.00 3.61 R
4488 5411 0.251077 AAGGGTGCAGCTTTCAGAGG 60.251 55.000 16.65 0.0 0.00 3.69 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
55 56 4.019771 AGGGAATTCTTCACCTCTGTTCTC 60.020 45.833 5.23 0.00 31.94 2.87
142 143 6.631016 TGAAGCGTCACAATATTTCTCTAGT 58.369 36.000 0.00 0.00 0.00 2.57
150 151 9.654663 GTCACAATATTTCTCTAGTAGGTTTGT 57.345 33.333 0.00 0.00 0.00 2.83
193 194 1.603802 CTCGCCTTGAAAAGCAACAGA 59.396 47.619 0.00 0.00 44.44 3.41
201 202 5.450965 CCTTGAAAAGCAACAGACTGTCATT 60.451 40.000 8.93 1.45 44.44 2.57
295 296 2.615493 GGATTTCAGGAGGCACGAAAGA 60.615 50.000 0.00 0.00 32.54 2.52
324 325 5.744171 TGCTGCAATCAAGAATAAGTAGGA 58.256 37.500 0.00 0.00 0.00 2.94
371 372 4.642429 TCCTCTAGTTGGTTTGAAAGAGC 58.358 43.478 4.87 0.00 31.23 4.09
454 455 5.215160 GTGTTTATCCACTGTTCTGCAAAG 58.785 41.667 0.00 0.00 32.50 2.77
498 499 7.500559 AGCTCTCAAATATGTTCATTCTAACCC 59.499 37.037 0.00 0.00 0.00 4.11
519 520 5.254737 ACCCATCATAGGCCTTCATCATATT 59.745 40.000 12.58 0.00 0.00 1.28
526 527 8.000709 TCATAGGCCTTCATCATATTCAACTTT 58.999 33.333 12.58 0.00 0.00 2.66
550 551 9.646427 TTTAGTGCACAAAAACTATTTGACTTT 57.354 25.926 21.04 0.00 33.83 2.66
551 552 7.524294 AGTGCACAAAAACTATTTGACTTTG 57.476 32.000 21.04 0.00 33.83 2.77
552 553 7.096551 AGTGCACAAAAACTATTTGACTTTGT 58.903 30.769 21.04 0.00 40.01 2.83
553 554 7.275560 AGTGCACAAAAACTATTTGACTTTGTC 59.724 33.333 21.04 0.00 37.95 3.18
554 555 6.252441 TGCACAAAAACTATTTGACTTTGTCG 59.748 34.615 7.83 0.00 37.95 4.35
555 556 6.252655 GCACAAAAACTATTTGACTTTGTCGT 59.747 34.615 7.83 0.00 37.95 4.34
556 557 7.429920 GCACAAAAACTATTTGACTTTGTCGTA 59.570 33.333 7.83 0.00 37.95 3.43
557 558 9.279904 CACAAAAACTATTTGACTTTGTCGTAA 57.720 29.630 7.83 0.00 37.95 3.18
558 559 9.843334 ACAAAAACTATTTGACTTTGTCGTAAA 57.157 25.926 7.83 0.00 35.82 2.01
562 563 8.502161 AACTATTTGACTTTGTCGTAAAATGC 57.498 30.769 0.00 0.00 34.95 3.56
563 564 7.644490 ACTATTTGACTTTGTCGTAAAATGCA 58.356 30.769 0.00 0.00 34.95 3.96
564 565 8.132362 ACTATTTGACTTTGTCGTAAAATGCAA 58.868 29.630 0.00 0.00 34.95 4.08
565 566 7.763172 ATTTGACTTTGTCGTAAAATGCAAA 57.237 28.000 0.00 0.00 34.95 3.68
566 567 6.561945 TTGACTTTGTCGTAAAATGCAAAC 57.438 33.333 0.00 0.00 34.95 2.93
567 568 5.641709 TGACTTTGTCGTAAAATGCAAACA 58.358 33.333 0.00 0.00 34.95 2.83
568 569 6.269315 TGACTTTGTCGTAAAATGCAAACAT 58.731 32.000 0.00 0.00 34.81 2.71
569 570 6.754209 TGACTTTGTCGTAAAATGCAAACATT 59.246 30.769 0.00 0.00 40.82 2.71
570 571 7.043722 TGACTTTGTCGTAAAATGCAAACATTC 60.044 33.333 0.00 0.00 39.36 2.67
571 572 6.754209 ACTTTGTCGTAAAATGCAAACATTCA 59.246 30.769 0.00 0.00 45.90 2.57
572 573 7.437862 ACTTTGTCGTAAAATGCAAACATTCAT 59.562 29.630 0.00 0.00 45.90 2.57
573 574 8.803201 TTTGTCGTAAAATGCAAACATTCATA 57.197 26.923 0.00 0.00 45.90 2.15
654 659 0.111253 GGCTGGCTGGGCAATATAGT 59.889 55.000 0.00 0.00 0.00 2.12
665 670 2.663602 GGCAATATAGTCTGCGATGACG 59.336 50.000 0.00 0.00 41.47 4.35
690 695 1.068121 CCACCCCTCCTTCTCTTGTT 58.932 55.000 0.00 0.00 0.00 2.83
691 696 1.425448 CCACCCCTCCTTCTCTTGTTT 59.575 52.381 0.00 0.00 0.00 2.83
692 697 2.553247 CCACCCCTCCTTCTCTTGTTTC 60.553 54.545 0.00 0.00 0.00 2.78
938 961 4.003788 CGGTGGTTGTCGCCCTCT 62.004 66.667 0.00 0.00 42.96 3.69
970 993 2.290134 ACCCTAACGGAAAAGGCTTCTC 60.290 50.000 0.00 0.00 34.64 2.87
1167 1193 2.392662 GTACCTACCCCCTTCCACTAC 58.607 57.143 0.00 0.00 0.00 2.73
1306 1341 2.927477 TCGATTTCGAGCGCTATTTTGT 59.073 40.909 11.50 0.00 44.22 2.83
1320 1355 5.334802 CGCTATTTTGTGTCTGATTTGGTCA 60.335 40.000 0.00 0.00 35.05 4.02
1395 1430 6.934645 TCTACAACAACTTCATCTCCGATTTT 59.065 34.615 0.00 0.00 0.00 1.82
1467 1502 1.594331 GCCAATATCCCGACAAGGAC 58.406 55.000 0.00 0.00 45.00 3.85
1828 1863 6.581919 TGCAGTTAACAATTTCATCGATTGTG 59.418 34.615 8.61 0.00 44.55 3.33
1856 1891 7.446625 AGCAGAAGAATGTGTTTTATTCAGTCT 59.553 33.333 0.00 0.00 37.97 3.24
2161 2196 2.223433 GCTTCTGGATGCTGTTACATGC 60.223 50.000 0.00 0.00 38.72 4.06
2248 2284 6.351286 GCAAGTATCAAAGGGATGGATTTTGT 60.351 38.462 0.00 0.00 36.72 2.83
2266 2302 5.617528 TTTGTAGTACCCACTGAAACAGA 57.382 39.130 5.76 0.00 36.14 3.41
2369 2405 4.570772 GCAGTTATAGGCGAGTGATCAAAA 59.429 41.667 0.00 0.00 0.00 2.44
2372 2408 7.042051 GCAGTTATAGGCGAGTGATCAAAATTA 60.042 37.037 0.00 0.00 0.00 1.40
2451 2493 7.984391 TGCACTATATTTACTCATTGGTTGTG 58.016 34.615 0.00 0.00 0.00 3.33
2520 2562 5.715434 TTAGTTGGACAAGTAATTTGGGC 57.285 39.130 7.96 0.00 41.25 5.36
2974 3124 2.548920 CCGGCCATCAGAAGATAGAACC 60.549 54.545 2.24 0.00 31.88 3.62
3059 3209 2.526432 TGAAGAGCCTCTCGGTAACTT 58.474 47.619 0.00 0.00 35.36 2.66
3281 3624 4.214971 CAGATCCTTTCTGTTCACTTGTGG 59.785 45.833 0.64 0.00 45.79 4.17
3288 3631 2.624364 TCTGTTCACTTGTGGCGTACTA 59.376 45.455 0.64 0.00 0.00 1.82
3289 3632 2.729882 CTGTTCACTTGTGGCGTACTAC 59.270 50.000 0.64 0.00 0.00 2.73
3290 3633 2.363038 TGTTCACTTGTGGCGTACTACT 59.637 45.455 0.64 0.00 0.00 2.57
3298 3641 2.892852 TGTGGCGTACTACTGTTTAGGT 59.107 45.455 0.00 0.00 0.00 3.08
3371 3714 6.014070 TGTGAGGTATATACAAATGCCCGTAT 60.014 38.462 14.70 0.00 32.42 3.06
3412 3756 4.016444 ACTGTTTGTGTTGTCTGTCCATT 58.984 39.130 0.00 0.00 0.00 3.16
3416 3760 2.997980 TGTGTTGTCTGTCCATTGTGT 58.002 42.857 0.00 0.00 0.00 3.72
3460 3881 2.736826 GCTGGGTGCTACTCCCTCC 61.737 68.421 6.31 0.00 44.84 4.30
3461 3882 1.002274 CTGGGTGCTACTCCCTCCT 59.998 63.158 6.31 0.00 44.84 3.69
3475 3896 3.265489 TCCCTCCTTCTGGTTTATTGGT 58.735 45.455 0.00 0.00 34.23 3.67
3477 3898 3.267031 CCCTCCTTCTGGTTTATTGGTCT 59.733 47.826 0.00 0.00 34.23 3.85
3483 3905 2.500098 TCTGGTTTATTGGTCTCCCTCG 59.500 50.000 0.00 0.00 0.00 4.63
3666 4588 5.262009 ACTTTAGCCCAAAATAAGAGGGTC 58.738 41.667 0.00 0.00 44.69 4.46
3670 4592 2.760650 GCCCAAAATAAGAGGGTCCTTG 59.239 50.000 0.00 0.00 44.69 3.61
3684 4606 2.660802 CTTGTAAGCCCGGACGGT 59.339 61.111 0.73 0.00 0.00 4.83
3758 4680 3.961408 CCAGTAGTAGTAATGCTGTCCCT 59.039 47.826 13.48 0.00 0.00 4.20
3790 4712 0.171231 GAGCCAAAATCGTGCTTCCC 59.829 55.000 0.00 0.00 34.99 3.97
3793 4715 1.953311 GCCAAAATCGTGCTTCCCCTA 60.953 52.381 0.00 0.00 0.00 3.53
3859 4781 8.684386 TTTGAAACACTCACATATTTCCTGTA 57.316 30.769 0.00 0.00 32.21 2.74
4092 5014 4.158394 TGATTCTGAATAGGCTTTGGTTGC 59.842 41.667 2.28 0.00 0.00 4.17
4093 5015 2.083774 TCTGAATAGGCTTTGGTTGCG 58.916 47.619 0.00 0.00 0.00 4.85
4181 5103 5.103290 TGATAACGAAAACTTGTTGCCTC 57.897 39.130 0.00 0.00 0.00 4.70
4269 5191 1.592223 GCAGAGGGCGTCACTAGTT 59.408 57.895 10.15 0.00 0.00 2.24
4306 5228 7.381408 CGAACTTTATAATCTGTAATCCAGCGA 59.619 37.037 0.00 0.00 41.25 4.93
4317 5239 5.879237 TGTAATCCAGCGATTTGACATTTC 58.121 37.500 0.00 0.00 39.49 2.17
4338 5260 6.992063 TTCTTCTTCTTCCATTGTGCTATC 57.008 37.500 0.00 0.00 0.00 2.08
4448 5371 1.523711 ATACAACGCATGGGCCTCG 60.524 57.895 10.10 8.50 36.38 4.63
4462 5385 3.764434 TGGGCCTCGTTTTTAATTGCATA 59.236 39.130 4.53 0.00 0.00 3.14
4488 5411 6.749923 AGAGCTTCATATTGTTGTTTCTCC 57.250 37.500 0.00 0.00 0.00 3.71
4603 5527 8.787852 TGCAGTATCATACTCTATCTACTTGTG 58.212 37.037 0.00 0.00 36.76 3.33
4619 5543 8.833231 TCTACTTGTGAAACCTCAAGATAAAG 57.167 34.615 11.07 4.40 42.22 1.85
4621 5545 5.827797 ACTTGTGAAACCTCAAGATAAAGCA 59.172 36.000 11.07 0.00 42.22 3.91
4626 5550 6.961554 GTGAAACCTCAAGATAAAGCAATACG 59.038 38.462 0.00 0.00 31.88 3.06
4636 5560 7.295952 AGATAAAGCAATACGACTTTGACAG 57.704 36.000 0.00 0.00 36.78 3.51
4638 5562 7.602644 AGATAAAGCAATACGACTTTGACAGAA 59.397 33.333 0.00 0.00 36.78 3.02
4639 5563 6.560253 AAAGCAATACGACTTTGACAGAAT 57.440 33.333 0.00 0.00 34.88 2.40
4647 5571 6.686130 ACGACTTTGACAGAATTAGTAACG 57.314 37.500 0.00 0.00 0.00 3.18
4651 5575 7.409449 CGACTTTGACAGAATTAGTAACGACAG 60.409 40.741 0.00 0.00 0.00 3.51
4677 5601 7.201513 GCAACAAAGCATTTAGTTTCAACTTGA 60.202 33.333 0.00 0.00 35.03 3.02
4678 5602 8.655092 CAACAAAGCATTTAGTTTCAACTTGAA 58.345 29.630 0.00 0.00 35.03 2.69
4679 5603 8.185003 ACAAAGCATTTAGTTTCAACTTGAAC 57.815 30.769 3.56 0.83 35.03 3.18
4680 5604 8.034804 ACAAAGCATTTAGTTTCAACTTGAACT 58.965 29.630 3.56 7.53 35.03 3.01
4681 5605 8.872845 CAAAGCATTTAGTTTCAACTTGAACTT 58.127 29.630 3.56 0.00 35.03 2.66
4682 5606 7.992180 AGCATTTAGTTTCAACTTGAACTTG 57.008 32.000 3.56 3.09 40.37 3.16
4684 5608 6.978080 GCATTTAGTTTCAACTTGAACTTGGA 59.022 34.615 3.56 0.00 40.37 3.53
4688 5612 9.621629 TTTAGTTTCAACTTGAACTTGGATAGA 57.378 29.630 3.56 0.00 40.37 1.98
4713 5637 6.830114 GTGAAACCATAAGATCTCGTAAGG 57.170 41.667 0.00 0.00 38.47 2.69
4717 5641 3.322254 ACCATAAGATCTCGTAAGGCCTG 59.678 47.826 5.69 0.00 38.47 4.85
4718 5642 3.306364 CCATAAGATCTCGTAAGGCCTGG 60.306 52.174 5.69 0.00 38.47 4.45
4720 5644 1.404843 AGATCTCGTAAGGCCTGGAC 58.595 55.000 5.69 7.06 38.47 4.02
4721 5645 1.063567 AGATCTCGTAAGGCCTGGACT 60.064 52.381 5.69 0.00 38.47 3.85
4723 5647 0.970937 TCTCGTAAGGCCTGGACTGG 60.971 60.000 5.69 3.57 38.47 4.00
4724 5648 0.970937 CTCGTAAGGCCTGGACTGGA 60.971 60.000 5.69 0.00 38.47 3.86
4725 5649 0.325296 TCGTAAGGCCTGGACTGGAT 60.325 55.000 5.69 0.00 38.47 3.41
4726 5650 0.541863 CGTAAGGCCTGGACTGGATT 59.458 55.000 5.69 0.00 0.00 3.01
4727 5651 1.760613 CGTAAGGCCTGGACTGGATTA 59.239 52.381 5.69 0.00 0.00 1.75
4729 5653 3.555168 CGTAAGGCCTGGACTGGATTATC 60.555 52.174 5.69 0.00 0.00 1.75
4730 5654 2.503869 AGGCCTGGACTGGATTATCT 57.496 50.000 3.11 0.00 0.00 1.98
4733 5657 2.439507 GGCCTGGACTGGATTATCTTCA 59.560 50.000 0.00 0.00 0.00 3.02
4734 5658 3.471680 GCCTGGACTGGATTATCTTCAC 58.528 50.000 0.00 0.00 0.00 3.18
4737 5782 4.444022 CCTGGACTGGATTATCTTCACTGG 60.444 50.000 0.00 0.00 0.00 4.00
4742 5787 2.439507 TGGATTATCTTCACTGGAGGCC 59.560 50.000 0.00 0.00 0.00 5.19
4747 5792 1.673665 CTTCACTGGAGGCCTGCAC 60.674 63.158 24.87 7.34 0.00 4.57
4751 5796 2.268280 CTGGAGGCCTGCACTGAG 59.732 66.667 24.87 10.07 0.00 3.35
4755 5800 1.342975 TGGAGGCCTGCACTGAGTATA 60.343 52.381 24.87 0.00 0.00 1.47
4759 5804 1.202580 GGCCTGCACTGAGTATACCTG 60.203 57.143 0.00 0.00 0.00 4.00
4760 5805 1.808133 GCCTGCACTGAGTATACCTGC 60.808 57.143 0.00 2.69 0.00 4.85
4848 5903 5.977635 TCAATGTTACTATGTCCAGACAGG 58.022 41.667 6.63 4.62 45.48 4.00
4889 6244 3.833650 TGTCCAGTACTCGTATTTGGGAA 59.166 43.478 0.00 0.00 0.00 3.97
4890 6245 4.468510 TGTCCAGTACTCGTATTTGGGAAT 59.531 41.667 0.00 0.00 0.00 3.01
4891 6246 5.046159 TGTCCAGTACTCGTATTTGGGAATT 60.046 40.000 0.00 0.00 0.00 2.17
4892 6247 5.293569 GTCCAGTACTCGTATTTGGGAATTG 59.706 44.000 0.00 0.00 0.00 2.32
4893 6248 4.574828 CCAGTACTCGTATTTGGGAATTGG 59.425 45.833 0.00 0.00 0.00 3.16
4894 6249 4.574828 CAGTACTCGTATTTGGGAATTGGG 59.425 45.833 0.00 0.00 0.00 4.12
4895 6250 4.472108 AGTACTCGTATTTGGGAATTGGGA 59.528 41.667 0.00 0.00 0.00 4.37
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
142 143 1.946768 GCAGTTGCAGTGACAAACCTA 59.053 47.619 0.00 0.00 41.59 3.08
150 151 1.123861 AGAGGGAGCAGTTGCAGTGA 61.124 55.000 6.90 0.00 45.16 3.41
193 194 5.047802 CCACCTTCTATTTGCAAATGACAGT 60.048 40.000 30.43 20.28 0.00 3.55
201 202 5.777732 ACCATTAACCACCTTCTATTTGCAA 59.222 36.000 0.00 0.00 0.00 4.08
295 296 0.694771 TCTTGATTGCAGCAGAGGGT 59.305 50.000 0.00 0.00 0.00 4.34
344 345 5.576563 TTCAAACCAACTAGAGGAATCCA 57.423 39.130 0.61 0.00 0.00 3.41
371 372 4.279169 TCTTTTCAATGGTGAGAAGCTTGG 59.721 41.667 2.10 0.00 42.83 3.61
454 455 5.363939 AGAGCTATCATGACTAAACTTGGC 58.636 41.667 0.00 0.00 0.00 4.52
487 488 4.242811 AGGCCTATGATGGGTTAGAATGA 58.757 43.478 1.29 0.00 0.00 2.57
495 496 2.421725 TGATGAAGGCCTATGATGGGT 58.578 47.619 5.16 0.00 0.00 4.51
498 499 7.610692 AGTTGAATATGATGAAGGCCTATGATG 59.389 37.037 5.16 0.00 0.00 3.07
519 520 9.081997 CAAATAGTTTTTGTGCACTAAAGTTGA 57.918 29.630 22.27 12.26 0.00 3.18
526 527 8.247562 ACAAAGTCAAATAGTTTTTGTGCACTA 58.752 29.630 19.41 7.83 39.65 2.74
550 551 7.061673 GCTTATGAATGTTTGCATTTTACGACA 59.938 33.333 0.00 0.00 44.61 4.35
551 552 7.061673 TGCTTATGAATGTTTGCATTTTACGAC 59.938 33.333 0.00 0.00 44.61 4.34
552 553 7.061673 GTGCTTATGAATGTTTGCATTTTACGA 59.938 33.333 0.00 0.00 44.61 3.43
553 554 7.148836 TGTGCTTATGAATGTTTGCATTTTACG 60.149 33.333 0.00 0.00 44.61 3.18
554 555 8.016497 TGTGCTTATGAATGTTTGCATTTTAC 57.984 30.769 0.00 0.00 44.61 2.01
555 556 8.774890 ATGTGCTTATGAATGTTTGCATTTTA 57.225 26.923 0.00 0.00 44.61 1.52
556 557 7.412129 CGATGTGCTTATGAATGTTTGCATTTT 60.412 33.333 0.00 0.00 44.61 1.82
557 558 6.035220 CGATGTGCTTATGAATGTTTGCATTT 59.965 34.615 0.00 0.00 44.61 2.32
558 559 5.517411 CGATGTGCTTATGAATGTTTGCATT 59.483 36.000 0.00 0.00 46.99 3.56
559 560 5.038683 CGATGTGCTTATGAATGTTTGCAT 58.961 37.500 0.00 0.00 36.80 3.96
560 561 4.413969 CGATGTGCTTATGAATGTTTGCA 58.586 39.130 0.00 0.00 0.00 4.08
561 562 3.792956 CCGATGTGCTTATGAATGTTTGC 59.207 43.478 0.00 0.00 0.00 3.68
562 563 4.353737 CCCGATGTGCTTATGAATGTTTG 58.646 43.478 0.00 0.00 0.00 2.93
563 564 3.181487 GCCCGATGTGCTTATGAATGTTT 60.181 43.478 0.00 0.00 0.00 2.83
564 565 2.358898 GCCCGATGTGCTTATGAATGTT 59.641 45.455 0.00 0.00 0.00 2.71
565 566 1.949525 GCCCGATGTGCTTATGAATGT 59.050 47.619 0.00 0.00 0.00 2.71
566 567 1.267806 GGCCCGATGTGCTTATGAATG 59.732 52.381 0.00 0.00 0.00 2.67
567 568 1.609208 GGCCCGATGTGCTTATGAAT 58.391 50.000 0.00 0.00 0.00 2.57
568 569 0.813610 CGGCCCGATGTGCTTATGAA 60.814 55.000 0.00 0.00 0.00 2.57
569 570 1.227527 CGGCCCGATGTGCTTATGA 60.228 57.895 0.00 0.00 0.00 2.15
570 571 2.253758 CCGGCCCGATGTGCTTATG 61.254 63.158 3.71 0.00 0.00 1.90
571 572 2.111043 CCGGCCCGATGTGCTTAT 59.889 61.111 3.71 0.00 0.00 1.73
572 573 4.169696 CCCGGCCCGATGTGCTTA 62.170 66.667 3.71 0.00 0.00 3.09
665 670 3.003763 AAGGAGGGGTGGAGACGC 61.004 66.667 0.00 0.00 41.20 5.19
715 720 1.447314 GGTACGGGTGGAAGAAGCG 60.447 63.158 0.00 0.00 0.00 4.68
894 911 1.911293 GAACAAGAGCAATGCGGCGA 61.911 55.000 12.98 0.00 39.27 5.54
895 912 1.512734 GAACAAGAGCAATGCGGCG 60.513 57.895 0.51 0.51 39.27 6.46
896 913 1.063174 CTAGAACAAGAGCAATGCGGC 59.937 52.381 0.00 0.00 0.00 6.53
897 914 2.350522 ACTAGAACAAGAGCAATGCGG 58.649 47.619 0.00 0.00 0.00 5.69
898 915 3.425359 CCAACTAGAACAAGAGCAATGCG 60.425 47.826 0.00 0.00 0.00 4.73
938 961 1.202769 CGTTAGGGTTTGGGGAGGGA 61.203 60.000 0.00 0.00 0.00 4.20
970 993 2.276309 GAGGGTGGGCCTGAATCTGG 62.276 65.000 4.53 1.42 34.45 3.86
1269 1304 3.548745 ATCGAATTGGAGCATGTGAGA 57.451 42.857 0.00 0.00 0.00 3.27
1306 1341 1.542328 CCGTGGTGACCAAATCAGACA 60.542 52.381 5.57 0.00 38.28 3.41
1320 1355 1.323412 TAAACAGCAATTGCCGTGGT 58.677 45.000 26.45 15.37 43.38 4.16
1395 1430 7.765360 AGTTTGAGCAAATTGATCTTTGTTTCA 59.235 29.630 12.62 9.51 38.19 2.69
1467 1502 4.473520 AGGAAGGTGATGGCGGCG 62.474 66.667 0.51 0.51 0.00 6.46
1828 1863 6.151691 TGAATAAAACACATTCTTCTGCTGC 58.848 36.000 0.00 0.00 34.21 5.25
1880 1915 7.944729 ATACATAGAAATAACATCCATGGCC 57.055 36.000 6.96 0.00 0.00 5.36
2066 2101 2.507407 TTCAGGGCTGGGAACAATAC 57.493 50.000 0.00 0.00 42.06 1.89
2161 2196 5.235186 GGACGATCAAGTATGTGGAAAGATG 59.765 44.000 0.00 0.00 0.00 2.90
2237 2273 5.741011 TCAGTGGGTACTACAAAATCCATC 58.259 41.667 0.00 0.00 44.47 3.51
2248 2284 3.006537 GCACTCTGTTTCAGTGGGTACTA 59.993 47.826 2.21 0.00 41.49 1.82
2315 2351 6.992063 AACTAACATAGTTGCCAATGAGAG 57.008 37.500 2.14 0.00 46.58 3.20
2369 2405 7.885297 TCTGTCAAACTTTTGCATAGCTTAAT 58.115 30.769 0.00 0.00 38.05 1.40
2372 2408 5.772825 TCTGTCAAACTTTTGCATAGCTT 57.227 34.783 0.00 0.00 38.05 3.74
2451 2493 5.382618 AACCAAAAGAATCATCTGTGCTC 57.617 39.130 0.00 0.00 35.59 4.26
2974 3124 5.850557 TGGCAATAACACTTAATGGGATG 57.149 39.130 0.00 0.00 0.00 3.51
3059 3209 3.054728 TGGCGGAAGAATGTAGGAAATGA 60.055 43.478 0.00 0.00 0.00 2.57
3184 3527 4.700213 ACAACCCACTGTCTAAATATGTGC 59.300 41.667 0.00 0.00 0.00 4.57
3261 3604 2.887152 GCCACAAGTGAACAGAAAGGAT 59.113 45.455 0.94 0.00 0.00 3.24
3281 3624 3.227810 AGCACCTAAACAGTAGTACGC 57.772 47.619 0.00 0.00 0.00 4.42
3399 3743 4.836125 AATGACACAATGGACAGACAAC 57.164 40.909 0.00 0.00 0.00 3.32
3412 3756 4.908601 ACAGATGGGAAGTAATGACACA 57.091 40.909 0.00 0.00 0.00 3.72
3416 3760 6.373005 TCTGAAACAGATGGGAAGTAATGA 57.627 37.500 0.00 0.00 35.39 2.57
3475 3896 2.542550 TGACCCAAAATACGAGGGAGA 58.457 47.619 3.32 0.00 45.80 3.71
3477 3898 3.073356 AGTTTGACCCAAAATACGAGGGA 59.927 43.478 3.32 0.00 45.80 4.20
3483 3905 4.062293 GGCCAAAGTTTGACCCAAAATAC 58.938 43.478 17.33 0.00 35.03 1.89
3666 4588 2.125269 CCGTCCGGGCTTACAAGG 60.125 66.667 3.66 0.00 0.00 3.61
3670 4592 2.288788 CTACCACCGTCCGGGCTTAC 62.289 65.000 3.66 0.00 40.62 2.34
3684 4606 6.493802 ACTGAAACAGATCTGAAGTACTACCA 59.506 38.462 29.27 11.25 35.18 3.25
3758 4680 2.673775 TTGGCTCCCAAGAACATTCA 57.326 45.000 0.00 0.00 38.75 2.57
3790 4712 3.118629 TCCACTGCTGCTTCAACTATAGG 60.119 47.826 4.43 0.00 0.00 2.57
3793 4715 2.304180 ACTCCACTGCTGCTTCAACTAT 59.696 45.455 0.00 0.00 0.00 2.12
3859 4781 5.363562 TCTATGAGATGAACCTGCAATGT 57.636 39.130 0.00 0.00 0.00 2.71
4093 5015 4.752879 TACACCGCCGCCTTGCTC 62.753 66.667 0.00 0.00 0.00 4.26
4181 5103 0.178068 CCAGACCAATAGGACACCCG 59.822 60.000 0.00 0.00 38.69 5.28
4306 5228 8.645110 ACAATGGAAGAAGAAGAAATGTCAAAT 58.355 29.630 0.00 0.00 0.00 2.32
4317 5239 5.006165 GTCGATAGCACAATGGAAGAAGAAG 59.994 44.000 0.00 0.00 0.00 2.85
4338 5260 0.948623 TTTCCTGCGTGTCCATGTCG 60.949 55.000 0.00 0.00 0.00 4.35
4439 5362 2.564947 TGCAATTAAAAACGAGGCCCAT 59.435 40.909 0.00 0.00 0.00 4.00
4462 5385 8.084684 GGAGAAACAACAATATGAAGCTCTTTT 58.915 33.333 0.00 0.00 0.00 2.27
4474 5397 5.473504 GCTTTCAGAGGGAGAAACAACAATA 59.526 40.000 0.00 0.00 32.09 1.90
4488 5411 0.251077 AAGGGTGCAGCTTTCAGAGG 60.251 55.000 16.65 0.00 0.00 3.69
4603 5527 7.064728 AGTCGTATTGCTTTATCTTGAGGTTTC 59.935 37.037 0.00 0.00 0.00 2.78
4619 5543 7.061752 ACTAATTCTGTCAAAGTCGTATTGC 57.938 36.000 0.00 0.00 0.00 3.56
4621 5545 8.857216 CGTTACTAATTCTGTCAAAGTCGTATT 58.143 33.333 0.00 0.00 0.00 1.89
4626 5550 7.619571 GCTGTCGTTACTAATTCTGTCAAAGTC 60.620 40.741 0.00 0.00 0.00 3.01
4636 5560 5.564127 GCTTTGTTGCTGTCGTTACTAATTC 59.436 40.000 0.00 0.00 0.00 2.17
4638 5562 4.513692 TGCTTTGTTGCTGTCGTTACTAAT 59.486 37.500 0.00 0.00 0.00 1.73
4639 5563 3.872182 TGCTTTGTTGCTGTCGTTACTAA 59.128 39.130 0.00 0.00 0.00 2.24
4647 5571 5.748152 TGAAACTAAATGCTTTGTTGCTGTC 59.252 36.000 0.00 0.00 0.00 3.51
4651 5575 6.588348 AGTTGAAACTAAATGCTTTGTTGC 57.412 33.333 0.00 0.00 37.52 4.17
4677 5601 4.993705 TGGTTTCACCTCTATCCAAGTT 57.006 40.909 0.00 0.00 39.58 2.66
4678 5602 6.443849 TCTTATGGTTTCACCTCTATCCAAGT 59.556 38.462 0.00 0.00 39.58 3.16
4679 5603 6.889198 TCTTATGGTTTCACCTCTATCCAAG 58.111 40.000 0.00 0.00 39.58 3.61
4680 5604 6.884472 TCTTATGGTTTCACCTCTATCCAA 57.116 37.500 0.00 0.00 39.58 3.53
4681 5605 6.846505 AGATCTTATGGTTTCACCTCTATCCA 59.153 38.462 0.00 0.00 39.58 3.41
4682 5606 7.309770 AGATCTTATGGTTTCACCTCTATCC 57.690 40.000 0.00 0.00 39.58 2.59
4684 5608 6.551601 ACGAGATCTTATGGTTTCACCTCTAT 59.448 38.462 0.00 0.00 39.58 1.98
4688 5612 6.407074 CCTTACGAGATCTTATGGTTTCACCT 60.407 42.308 0.00 0.00 39.58 4.00
4707 5631 0.541863 AATCCAGTCCAGGCCTTACG 59.458 55.000 0.00 1.32 0.00 3.18
4709 5633 3.941629 AGATAATCCAGTCCAGGCCTTA 58.058 45.455 0.00 0.00 0.00 2.69
4710 5634 2.781667 AGATAATCCAGTCCAGGCCTT 58.218 47.619 0.00 0.00 0.00 4.35
4711 5635 2.503869 AGATAATCCAGTCCAGGCCT 57.496 50.000 0.00 0.00 0.00 5.19
4712 5636 2.439507 TGAAGATAATCCAGTCCAGGCC 59.560 50.000 0.00 0.00 0.00 5.19
4713 5637 3.135530 AGTGAAGATAATCCAGTCCAGGC 59.864 47.826 0.00 0.00 0.00 4.85
4717 5641 4.202305 CCTCCAGTGAAGATAATCCAGTCC 60.202 50.000 0.00 0.00 0.00 3.85
4718 5642 4.742138 GCCTCCAGTGAAGATAATCCAGTC 60.742 50.000 0.00 0.00 0.00 3.51
4720 5644 3.495806 GGCCTCCAGTGAAGATAATCCAG 60.496 52.174 0.00 0.00 0.00 3.86
4721 5645 2.439507 GGCCTCCAGTGAAGATAATCCA 59.560 50.000 0.00 0.00 0.00 3.41
4723 5647 3.737850 CAGGCCTCCAGTGAAGATAATC 58.262 50.000 0.00 0.00 0.00 1.75
4724 5648 2.158696 GCAGGCCTCCAGTGAAGATAAT 60.159 50.000 0.00 0.00 0.00 1.28
4725 5649 1.210478 GCAGGCCTCCAGTGAAGATAA 59.790 52.381 0.00 0.00 0.00 1.75
4726 5650 0.833287 GCAGGCCTCCAGTGAAGATA 59.167 55.000 0.00 0.00 0.00 1.98
4727 5651 1.203441 TGCAGGCCTCCAGTGAAGAT 61.203 55.000 0.00 0.00 0.00 2.40
4729 5653 1.673665 GTGCAGGCCTCCAGTGAAG 60.674 63.158 0.00 0.00 0.00 3.02
4730 5654 2.149383 AGTGCAGGCCTCCAGTGAA 61.149 57.895 2.20 0.00 0.00 3.18
4733 5657 2.527624 TCAGTGCAGGCCTCCAGT 60.528 61.111 0.00 0.00 0.00 4.00
4734 5658 1.260538 TACTCAGTGCAGGCCTCCAG 61.261 60.000 0.00 0.00 0.00 3.86
4737 5782 1.069358 GGTATACTCAGTGCAGGCCTC 59.931 57.143 0.00 0.00 0.00 4.70
4742 5787 1.405463 TCGCAGGTATACTCAGTGCAG 59.595 52.381 15.44 10.46 33.59 4.41
4747 5792 2.290916 ACATCGTCGCAGGTATACTCAG 59.709 50.000 2.25 0.00 0.00 3.35
4751 5796 2.124903 CCAACATCGTCGCAGGTATAC 58.875 52.381 0.00 0.00 0.00 1.47
4755 5800 0.821517 TATCCAACATCGTCGCAGGT 59.178 50.000 0.00 0.00 0.00 4.00
4759 5804 1.571919 AGCTTATCCAACATCGTCGC 58.428 50.000 0.00 0.00 0.00 5.19
4760 5805 3.448686 AGAAGCTTATCCAACATCGTCG 58.551 45.455 0.00 0.00 0.00 5.12
4848 5903 8.082242 ACTGGACATAGTAACATTTTCTTTTGC 58.918 33.333 0.00 0.00 0.00 3.68
4889 6244 1.610379 GGCAGGCAAACCTCCCAAT 60.610 57.895 0.00 0.00 46.34 3.16
4890 6245 2.203625 GGCAGGCAAACCTCCCAA 60.204 61.111 0.00 0.00 46.34 4.12
4891 6246 4.659172 CGGCAGGCAAACCTCCCA 62.659 66.667 0.00 0.00 45.54 4.37
4892 6247 4.660938 ACGGCAGGCAAACCTCCC 62.661 66.667 0.00 0.00 46.34 4.30
4893 6248 2.142357 GAAACGGCAGGCAAACCTCC 62.142 60.000 0.00 0.00 46.34 4.30
4894 6249 1.285950 GAAACGGCAGGCAAACCTC 59.714 57.895 0.00 0.00 46.34 3.85


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

AutoCloner maintained by Alex Coulton.