Multiple sequence alignment - TraesCS3B01G451200

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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 TraesCS3B01G451200 chr3B 100.000 5241 0 0 1 5241 691745739 691750979 0.000000e+00 9679
1 TraesCS3B01G451200 chr3B 91.509 318 17 4 4392 4703 691922145 691922458 3.750000e-116 429
2 TraesCS3B01G451200 chr3B 80.513 195 28 4 4103 4297 691775463 691775647 1.970000e-29 141
3 TraesCS3B01G451200 chr3B 91.753 97 8 0 5145 5241 691922843 691922939 9.150000e-28 135
4 TraesCS3B01G451200 chr3D 94.245 4396 178 40 778 5121 524305516 524309888 0.000000e+00 6647
5 TraesCS3B01G451200 chr3D 85.965 798 62 25 1 779 524304720 524305486 0.000000e+00 808
6 TraesCS3B01G451200 chr3D 87.534 369 18 13 4355 4703 524646312 524646672 8.180000e-108 401
7 TraesCS3B01G451200 chr3D 96.875 96 3 0 5146 5241 524309952 524310047 1.510000e-35 161
8 TraesCS3B01G451200 chr3D 88.710 62 6 1 1523 1583 524313740 524313801 2.020000e-09 75
9 TraesCS3B01G451200 chr3A 91.599 2452 132 34 1943 4366 658902711 658905116 0.000000e+00 3319
10 TraesCS3B01G451200 chr3A 95.833 864 35 1 779 1641 658901312 658902175 0.000000e+00 1395
11 TraesCS3B01G451200 chr3A 87.580 781 60 22 17 779 658900520 658901281 0.000000e+00 870
12 TraesCS3B01G451200 chr3A 87.092 612 33 9 4453 5057 658905122 658905694 0.000000e+00 651
13 TraesCS3B01G451200 chr3A 91.916 334 22 5 1627 1958 658902360 658902690 3.700000e-126 462
14 TraesCS3B01G451200 chr3A 89.607 356 27 6 4355 4703 658983047 658983399 1.340000e-120 444
15 TraesCS3B01G451200 chr3A 78.673 422 36 24 4847 5241 658983459 658983853 1.140000e-56 231
16 TraesCS3B01G451200 chr3A 93.836 146 7 2 5087 5231 658905691 658905835 8.840000e-53 219
17 TraesCS3B01G451200 chr3A 95.420 131 6 0 5111 5241 658905790 658905920 5.320000e-50 209


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 TraesCS3B01G451200 chr3B 691745739 691750979 5240 False 9679.000000 9679 100.000000 1 5241 1 chr3B.!!$F1 5240
1 TraesCS3B01G451200 chr3B 691922145 691922939 794 False 282.000000 429 91.631000 4392 5241 2 chr3B.!!$F3 849
2 TraesCS3B01G451200 chr3D 524304720 524313801 9081 False 1922.750000 6647 91.448750 1 5241 4 chr3D.!!$F2 5240
3 TraesCS3B01G451200 chr3A 658900520 658905920 5400 False 1017.857143 3319 91.896571 17 5241 7 chr3A.!!$F1 5224
4 TraesCS3B01G451200 chr3A 658983047 658983853 806 False 337.500000 444 84.140000 4355 5241 2 chr3A.!!$F2 886

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
484 518 0.099613 CTCTAGCGATCTGTGTGCGT 59.900 55.000 0.00 0.0 0.00 5.24 F
487 521 0.099968 TAGCGATCTGTGTGCGTACC 59.900 55.000 0.00 0.0 0.00 3.34 F
493 527 0.606130 TCTGTGTGCGTACCCGACTA 60.606 55.000 0.00 0.0 35.63 2.59 F
502 536 1.304381 TACCCGACTACCCGTGCTT 60.304 57.895 0.00 0.0 0.00 3.91 F
558 593 1.657181 CAACAACCGCCGCTGAAAC 60.657 57.895 0.00 0.0 0.00 2.78 F
759 794 2.235402 TGGGGTGTTCGAATTAGTCTCC 59.765 50.000 0.00 0.0 0.00 3.71 F
1641 1907 3.004315 GTGACCGTATTATTGGCCCATTG 59.996 47.826 0.00 0.0 0.00 2.82 F
3246 3565 0.773644 GGCATATGATCCAGGTGGGT 59.226 55.000 6.97 0.0 38.11 4.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1623 1690 2.238521 AGCAATGGGCCAATAATACGG 58.761 47.619 11.89 0.00 46.50 4.02 R
1820 2095 3.458118 TCCAAGGAAAAGTGAGGACTTCA 59.542 43.478 0.00 0.00 41.87 3.02 R
1876 2151 6.127451 GGTTACCCAAATCAAACTAGGAATGG 60.127 42.308 0.00 0.00 0.00 3.16 R
2376 2692 6.183360 TGTGAAGAAATTGAGCAATTCACTGT 60.183 34.615 19.64 3.88 39.88 3.55 R
2616 2934 3.492313 GCATTAAGCTTTGACGGTCAAG 58.508 45.455 21.47 16.58 37.70 3.02 R
2798 3117 5.643421 ATTATCTGCCTCAGAAGGAACAT 57.357 39.130 0.27 0.00 46.67 2.71 R
3488 3828 1.062525 GCATTGCTTTCTACGCCCG 59.937 57.895 0.16 0.00 0.00 6.13 R
4357 4711 0.109342 CCATGTACAGATCTGGCCCC 59.891 60.000 26.08 11.17 34.19 5.80 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
34 36 1.141053 ACAGCGAAGAAGGGTTTGTCT 59.859 47.619 0.00 0.00 0.00 3.41
88 94 4.796231 CGCCCACCTTCTCCGACG 62.796 72.222 0.00 0.00 0.00 5.12
90 96 3.382832 CCCACCTTCTCCGACGCT 61.383 66.667 0.00 0.00 0.00 5.07
91 97 2.182030 CCACCTTCTCCGACGCTC 59.818 66.667 0.00 0.00 0.00 5.03
92 98 2.202492 CACCTTCTCCGACGCTCG 60.202 66.667 0.00 1.17 40.07 5.03
304 329 4.981415 GGTAAGCACCGTTCGTCT 57.019 55.556 0.00 0.00 34.36 4.18
306 331 1.069378 GGTAAGCACCGTTCGTCTCG 61.069 60.000 0.00 0.00 34.36 4.04
435 469 3.841255 CTCCCCTAGTTCCTTCAGTTTCT 59.159 47.826 0.00 0.00 0.00 2.52
452 486 0.321034 TCTGCTGCGAATTCTGCTGT 60.321 50.000 20.85 0.00 34.23 4.40
463 497 4.827087 CTGCTGTGCCGCTCGGAT 62.827 66.667 13.11 0.00 37.50 4.18
481 515 2.392821 GATGCTCTAGCGATCTGTGTG 58.607 52.381 0.00 0.00 45.83 3.82
482 516 0.179127 TGCTCTAGCGATCTGTGTGC 60.179 55.000 0.00 0.00 45.83 4.57
483 517 1.205485 GCTCTAGCGATCTGTGTGCG 61.205 60.000 0.00 0.00 0.00 5.34
484 518 0.099613 CTCTAGCGATCTGTGTGCGT 59.900 55.000 0.00 0.00 0.00 5.24
485 519 1.330829 CTCTAGCGATCTGTGTGCGTA 59.669 52.381 0.00 0.00 0.00 4.42
486 520 1.063616 TCTAGCGATCTGTGTGCGTAC 59.936 52.381 0.00 0.00 0.00 3.67
487 521 0.099968 TAGCGATCTGTGTGCGTACC 59.900 55.000 0.00 0.00 0.00 3.34
488 522 2.165301 GCGATCTGTGTGCGTACCC 61.165 63.158 0.00 0.00 0.00 3.69
489 523 1.872234 CGATCTGTGTGCGTACCCG 60.872 63.158 0.00 0.00 37.07 5.28
490 524 1.509463 GATCTGTGTGCGTACCCGA 59.491 57.895 0.00 0.00 35.63 5.14
491 525 0.801067 GATCTGTGTGCGTACCCGAC 60.801 60.000 0.00 0.00 35.63 4.79
492 526 1.248785 ATCTGTGTGCGTACCCGACT 61.249 55.000 0.00 0.00 35.63 4.18
493 527 0.606130 TCTGTGTGCGTACCCGACTA 60.606 55.000 0.00 0.00 35.63 2.59
502 536 1.304381 TACCCGACTACCCGTGCTT 60.304 57.895 0.00 0.00 0.00 3.91
558 593 1.657181 CAACAACCGCCGCTGAAAC 60.657 57.895 0.00 0.00 0.00 2.78
630 665 4.053295 GTCGGCACTGTTGTAGTCTTAAA 58.947 43.478 0.00 0.00 37.60 1.52
632 667 5.178809 GTCGGCACTGTTGTAGTCTTAAATT 59.821 40.000 0.00 0.00 37.60 1.82
668 703 2.574006 AGGAAGCAATGCTGACTTGA 57.426 45.000 9.14 0.00 39.62 3.02
729 764 3.087781 ACACCGGTAGTTCTAGAAGTCC 58.912 50.000 16.16 14.98 0.00 3.85
759 794 2.235402 TGGGGTGTTCGAATTAGTCTCC 59.765 50.000 0.00 0.00 0.00 3.71
953 1019 3.758973 TTCAGCGGTGCGGAAACCA 62.759 57.895 10.38 0.00 39.48 3.67
1047 1113 4.687948 CGGAGGTATGTTCAATGCATCTAG 59.312 45.833 0.00 0.00 0.00 2.43
1063 1129 4.691175 CATCTAGTTCATGGACAGGACTG 58.309 47.826 6.96 0.00 0.00 3.51
1083 1149 6.407525 GGACTGATGCCTAGTGACTTCTAATT 60.408 42.308 0.00 0.00 0.00 1.40
1117 1183 5.690409 GTGCTCCTCAATTGAATGCATAATG 59.310 40.000 23.24 5.96 0.00 1.90
1123 1189 8.697292 TCCTCAATTGAATGCATAATGATTTCA 58.303 29.630 9.88 0.00 0.00 2.69
1302 1369 8.318412 TGTTCTCTTATGCCACATACTTTAGAA 58.682 33.333 0.00 0.00 0.00 2.10
1310 1377 7.399245 TGCCACATACTTTAGAAAATAACCC 57.601 36.000 0.00 0.00 0.00 4.11
1501 1568 3.085952 TGCCAGGCTAGCACTTTTTAT 57.914 42.857 18.24 0.00 34.69 1.40
1515 1582 7.962441 AGCACTTTTTATGGGATTTTGTTAGT 58.038 30.769 0.00 0.00 0.00 2.24
1603 1670 6.523201 CCTGTTTTGTTTAGATCGTACATTGC 59.477 38.462 0.00 0.00 0.00 3.56
1623 1690 7.655732 ACATTGCTTTAGTTAATTTTGGGTGAC 59.344 33.333 0.00 0.00 0.00 3.67
1641 1907 3.004315 GTGACCGTATTATTGGCCCATTG 59.996 47.826 0.00 0.00 0.00 2.82
1648 1914 3.608316 TTATTGGCCCATTGCTTGAAC 57.392 42.857 0.00 0.00 40.92 3.18
1670 1936 6.299805 ACTGCTCCTGTATTTCTCATGTTA 57.700 37.500 0.00 0.00 0.00 2.41
1729 1995 5.106078 GGATGTAAAATTGTTTCTGCCCGTA 60.106 40.000 0.00 0.00 0.00 4.02
1736 2002 8.840833 AAAATTGTTTCTGCCCGTATTAAAAT 57.159 26.923 0.00 0.00 0.00 1.82
1741 2007 4.829064 TCTGCCCGTATTAAAATGATGC 57.171 40.909 0.00 0.00 0.00 3.91
1742 2008 4.203226 TCTGCCCGTATTAAAATGATGCA 58.797 39.130 0.00 0.00 0.00 3.96
1743 2009 4.642437 TCTGCCCGTATTAAAATGATGCAA 59.358 37.500 0.00 0.00 0.00 4.08
1744 2010 5.301551 TCTGCCCGTATTAAAATGATGCAAT 59.698 36.000 0.00 0.00 0.00 3.56
1745 2011 5.288015 TGCCCGTATTAAAATGATGCAATG 58.712 37.500 0.00 0.00 0.00 2.82
1746 2012 4.150451 GCCCGTATTAAAATGATGCAATGC 59.850 41.667 0.00 0.00 0.00 3.56
1747 2013 5.288015 CCCGTATTAAAATGATGCAATGCA 58.712 37.500 11.44 11.44 44.86 3.96
1794 2068 9.944663 GTGTGTAAGTTGATGACTAAATTTTCA 57.055 29.630 0.00 0.00 37.72 2.69
1820 2095 7.303182 TCCTCGATTATCACTGGTATTGATT 57.697 36.000 0.00 0.00 35.31 2.57
1833 2108 6.126863 TGGTATTGATTGAAGTCCTCACTT 57.873 37.500 0.00 0.00 46.21 3.16
1835 2110 7.004086 TGGTATTGATTGAAGTCCTCACTTTT 58.996 34.615 0.00 0.00 43.37 2.27
1837 2112 6.581171 ATTGATTGAAGTCCTCACTTTTCC 57.419 37.500 0.00 0.00 43.37 3.13
1839 2114 5.694995 TGATTGAAGTCCTCACTTTTCCTT 58.305 37.500 0.00 0.00 43.37 3.36
1841 2116 3.820557 TGAAGTCCTCACTTTTCCTTGG 58.179 45.455 0.00 0.00 43.37 3.61
1842 2117 3.458118 TGAAGTCCTCACTTTTCCTTGGA 59.542 43.478 0.00 0.00 43.37 3.53
1843 2118 4.104738 TGAAGTCCTCACTTTTCCTTGGAT 59.895 41.667 0.00 0.00 43.37 3.41
1844 2119 5.309543 TGAAGTCCTCACTTTTCCTTGGATA 59.690 40.000 0.00 0.00 43.37 2.59
1876 2151 5.632034 ATGTGGTTCCTCCTAACTATTCC 57.368 43.478 0.00 0.00 37.07 3.01
1888 2163 7.072581 CCTCCTAACTATTCCCATTCCTAGTTT 59.927 40.741 0.00 0.00 36.24 2.66
2153 2465 7.989826 AGTAGCGAATGATGCTTTTAAATCTT 58.010 30.769 0.00 0.00 43.71 2.40
2155 2467 7.515957 AGCGAATGATGCTTTTAAATCTTTG 57.484 32.000 0.00 0.00 40.48 2.77
2162 2474 7.939782 TGATGCTTTTAAATCTTTGACTGACA 58.060 30.769 0.00 0.00 0.00 3.58
2376 2692 6.587206 TTTGGTAAAACTGATGATGCATCA 57.413 33.333 30.47 30.47 46.84 3.07
2798 3117 5.118729 TGTTTCCTTTCTTGTCACCCTAA 57.881 39.130 0.00 0.00 0.00 2.69
3027 3346 6.127140 ACCTATACCAGTTCCTTATGTGACAC 60.127 42.308 0.00 0.00 0.00 3.67
3072 3391 2.856000 AGGCCAGGCTGGTGTTCT 60.856 61.111 32.80 21.46 40.46 3.01
3126 3445 7.109501 AGGGGCCAAATTGTTTATTGTTAATC 58.890 34.615 4.39 0.00 0.00 1.75
3237 3556 2.094894 GCGCTGTGTATGGCATATGATC 59.905 50.000 10.92 0.00 0.00 2.92
3246 3565 0.773644 GGCATATGATCCAGGTGGGT 59.226 55.000 6.97 0.00 38.11 4.51
3256 3575 3.885976 TCCAGGTGGGTTGTCATTTAA 57.114 42.857 0.00 0.00 38.11 1.52
3308 3630 6.307155 GCTGTATGCTTACACTTTTACACTG 58.693 40.000 8.29 0.00 38.95 3.66
3414 3745 7.762615 CCAATTATCAATTTGACATGTTGCTCT 59.237 33.333 0.00 0.00 0.00 4.09
3415 3746 8.804743 CAATTATCAATTTGACATGTTGCTCTC 58.195 33.333 0.00 0.00 0.00 3.20
3471 3811 5.437946 AGGTCTAGGTTAGCTTAAATTGCC 58.562 41.667 0.00 0.00 0.00 4.52
3478 3818 2.603075 AGCTTAAATTGCCAGGGACA 57.397 45.000 0.00 0.00 0.00 4.02
3487 3827 1.600916 GCCAGGGACACTGTGGAAC 60.601 63.158 13.09 3.31 46.06 3.62
3488 3828 1.073199 CCAGGGACACTGTGGAACC 59.927 63.158 13.09 10.69 46.06 3.62
3508 3849 0.525761 GGGCGTAGAAAGCAATGCAA 59.474 50.000 8.35 0.00 36.08 4.08
3518 3859 6.160576 AGAAAGCAATGCAAAGGAAGTTTA 57.839 33.333 8.35 0.00 0.00 2.01
3524 3865 4.853924 ATGCAAAGGAAGTTTAGTGGTG 57.146 40.909 0.00 0.00 0.00 4.17
3544 3885 7.235399 AGTGGTGTTATTCCTTTGATCCAAAAT 59.765 33.333 0.00 0.00 32.75 1.82
3548 3889 8.306761 GTGTTATTCCTTTGATCCAAAATGAGT 58.693 33.333 0.00 0.00 32.75 3.41
3556 3897 7.977853 CCTTTGATCCAAAATGAGTTTCATAGG 59.022 37.037 0.00 0.00 35.76 2.57
3625 3966 3.319972 CCAAAGGGGTATTCTGCATGATG 59.680 47.826 0.00 0.00 0.00 3.07
3635 3976 7.365741 GGTATTCTGCATGATGAACTATTTGG 58.634 38.462 0.00 0.00 0.00 3.28
3656 3997 5.324409 TGGTGACATTTTCATAGAAGGCTT 58.676 37.500 0.00 0.00 36.32 4.35
3657 3998 6.480763 TGGTGACATTTTCATAGAAGGCTTA 58.519 36.000 0.00 0.00 36.32 3.09
3658 3999 6.599244 TGGTGACATTTTCATAGAAGGCTTAG 59.401 38.462 0.00 0.00 36.32 2.18
3659 4000 6.458888 GGTGACATTTTCATAGAAGGCTTAGC 60.459 42.308 0.00 0.00 36.32 3.09
3710 4051 8.116624 CTCTACGGAGTTGTAATTATGTGTTC 57.883 38.462 0.00 0.00 37.78 3.18
3739 4080 2.101640 ACATGCTTTTCCCAACCCTT 57.898 45.000 0.00 0.00 0.00 3.95
3766 4107 7.891183 TGTCTTACTGAGCTGAAACTATTTC 57.109 36.000 0.00 0.00 40.08 2.17
3775 4116 7.865707 TGAGCTGAAACTATTTCACTCTTTTC 58.134 34.615 21.19 0.00 44.21 2.29
3778 4119 8.907885 AGCTGAAACTATTTCACTCTTTTCTTT 58.092 29.630 0.00 0.00 44.21 2.52
3800 4141 2.192664 TTAAACAGCCGGCTCATGAA 57.807 45.000 30.29 15.10 0.00 2.57
3824 4165 5.534207 AAATTGGAGTTGTTGATGCTCAA 57.466 34.783 0.00 0.00 33.32 3.02
4063 4406 2.709125 TTCTGAACTCCACGCCACGG 62.709 60.000 0.00 0.00 0.00 4.94
4069 4412 4.634703 TCCACGCCACGGCACAAT 62.635 61.111 9.11 0.00 42.06 2.71
4070 4413 4.101790 CCACGCCACGGCACAATC 62.102 66.667 9.11 0.00 42.06 2.67
4073 4416 3.133464 CGCCACGGCACAATCCAT 61.133 61.111 9.11 0.00 42.06 3.41
4076 4419 0.814457 GCCACGGCACAATCCATTTA 59.186 50.000 2.36 0.00 41.49 1.40
4077 4420 1.408702 GCCACGGCACAATCCATTTAT 59.591 47.619 2.36 0.00 41.49 1.40
4078 4421 2.799207 GCCACGGCACAATCCATTTATG 60.799 50.000 2.36 0.00 41.49 1.90
4079 4422 2.462889 CACGGCACAATCCATTTATGC 58.537 47.619 0.00 0.00 35.51 3.14
4089 4440 6.974622 CACAATCCATTTATGCCTTACACTTC 59.025 38.462 0.00 0.00 0.00 3.01
4090 4441 6.663093 ACAATCCATTTATGCCTTACACTTCA 59.337 34.615 0.00 0.00 0.00 3.02
4091 4442 7.342799 ACAATCCATTTATGCCTTACACTTCAT 59.657 33.333 0.00 0.00 0.00 2.57
4094 4445 6.663093 TCCATTTATGCCTTACACTTCATGTT 59.337 34.615 0.00 0.00 43.19 2.71
4101 4452 6.941857 TGCCTTACACTTCATGTTATACTCA 58.058 36.000 0.00 0.00 43.19 3.41
4104 4455 7.333423 GCCTTACACTTCATGTTATACTCAACA 59.667 37.037 0.00 0.00 43.19 3.33
4105 4456 8.656849 CCTTACACTTCATGTTATACTCAACAC 58.343 37.037 0.00 0.00 43.19 3.32
4106 4457 9.424319 CTTACACTTCATGTTATACTCAACACT 57.576 33.333 0.00 0.00 43.19 3.55
4108 4459 8.087982 ACACTTCATGTTATACTCAACACTTG 57.912 34.615 0.00 0.00 38.98 3.16
4109 4460 7.017645 CACTTCATGTTATACTCAACACTTGC 58.982 38.462 0.00 0.00 41.02 4.01
4110 4461 6.936900 ACTTCATGTTATACTCAACACTTGCT 59.063 34.615 0.00 0.00 41.02 3.91
4111 4462 7.445402 ACTTCATGTTATACTCAACACTTGCTT 59.555 33.333 0.00 0.00 41.02 3.91
4112 4463 7.132694 TCATGTTATACTCAACACTTGCTTG 57.867 36.000 0.00 0.00 41.02 4.01
4113 4464 6.934083 TCATGTTATACTCAACACTTGCTTGA 59.066 34.615 0.00 0.00 41.02 3.02
4114 4465 6.539649 TGTTATACTCAACACTTGCTTGAC 57.460 37.500 0.00 0.00 33.55 3.18
4115 4466 5.176774 TGTTATACTCAACACTTGCTTGACG 59.823 40.000 0.00 0.00 33.55 4.35
4120 4471 4.389576 CACTTGCTTGACGGCGCC 62.390 66.667 19.07 19.07 34.52 6.53
4497 4851 6.492007 CACTTATGGTGGATGCAGAATATC 57.508 41.667 0.00 0.00 41.90 1.63
4614 4977 3.955551 TGTAGGTAGGATTGTATCACGCA 59.044 43.478 0.00 0.00 0.00 5.24
4627 4990 4.112341 ACGCAGGTAGTCGTCGCC 62.112 66.667 0.00 0.00 33.09 5.54
4943 5323 2.124983 GCTTCTGCATCTGCCGGA 60.125 61.111 5.05 0.00 41.18 5.14
4946 5326 0.809241 CTTCTGCATCTGCCGGAGTC 60.809 60.000 5.05 0.00 41.18 3.36
5044 5427 1.078848 CCCCTGCTTCTTCTGGACG 60.079 63.158 0.00 0.00 0.00 4.79
5049 5432 2.448705 GCTTCTTCTGGACGAGCGC 61.449 63.158 0.00 0.00 0.00 5.92
5184 5693 2.720758 CGTGCTTCGTCTGCTTCGG 61.721 63.158 0.00 0.00 34.52 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
190 206 4.798344 CTGGCAGGGCTCAGCAGG 62.798 72.222 6.61 0.00 0.00 4.85
337 362 4.273318 AGTTTGAACTGGCCTCAATATCC 58.727 43.478 3.32 0.00 37.98 2.59
397 430 1.134907 GGGAGCAGTTACGAATCGGAA 60.135 52.381 7.80 0.50 0.00 4.30
435 469 1.871077 CACAGCAGAATTCGCAGCA 59.129 52.632 19.45 0.00 0.00 4.41
452 486 2.833121 TAGAGCATCCGAGCGGCA 60.833 61.111 1.45 0.00 40.15 5.69
463 497 0.179127 GCACACAGATCGCTAGAGCA 60.179 55.000 1.89 0.00 42.21 4.26
481 515 3.134127 ACGGGTAGTCGGGTACGC 61.134 66.667 0.00 0.00 40.69 4.42
482 516 2.793946 CACGGGTAGTCGGGTACG 59.206 66.667 0.00 0.00 42.74 3.67
483 517 1.598701 AAGCACGGGTAGTCGGGTAC 61.599 60.000 0.00 0.00 35.72 3.34
484 518 0.899717 AAAGCACGGGTAGTCGGGTA 60.900 55.000 0.00 0.00 35.72 3.69
485 519 2.212110 AAAGCACGGGTAGTCGGGT 61.212 57.895 0.00 0.00 35.72 5.28
486 520 1.740296 CAAAGCACGGGTAGTCGGG 60.740 63.158 0.00 0.00 36.50 5.14
487 521 2.388232 GCAAAGCACGGGTAGTCGG 61.388 63.158 0.00 0.00 0.00 4.79
488 522 1.352156 GAGCAAAGCACGGGTAGTCG 61.352 60.000 0.00 0.00 0.00 4.18
489 523 1.019805 GGAGCAAAGCACGGGTAGTC 61.020 60.000 0.00 0.00 0.00 2.59
490 524 1.003718 GGAGCAAAGCACGGGTAGT 60.004 57.895 0.00 0.00 0.00 2.73
491 525 0.741221 GAGGAGCAAAGCACGGGTAG 60.741 60.000 0.00 0.00 0.00 3.18
492 526 1.295423 GAGGAGCAAAGCACGGGTA 59.705 57.895 0.00 0.00 0.00 3.69
493 527 2.032681 GAGGAGCAAAGCACGGGT 59.967 61.111 0.00 0.00 0.00 5.28
502 536 2.184322 GATCCGCGTGAGGAGCAA 59.816 61.111 4.92 0.00 45.42 3.91
630 665 6.478512 TTCCTAAACTTCCACAAGCAAAAT 57.521 33.333 0.00 0.00 32.09 1.82
632 667 4.202111 GCTTCCTAAACTTCCACAAGCAAA 60.202 41.667 0.00 0.00 35.81 3.68
668 703 9.781633 AGTAGTACATCTAATAATCACGACTCT 57.218 33.333 2.52 0.00 0.00 3.24
683 718 7.862512 ACGTAGCTTTCTTAGTAGTACATCT 57.137 36.000 2.52 0.00 0.00 2.90
729 764 1.000060 TCGAACACCCCAACTAAGACG 60.000 52.381 0.00 0.00 0.00 4.18
759 794 7.246311 ACATCTAAGTTTCGCAATGAATGAAG 58.754 34.615 0.00 0.00 36.22 3.02
953 1019 3.375299 GCGATGGAACTTGTTAGCAGAAT 59.625 43.478 0.00 0.00 0.00 2.40
1038 1104 3.713248 TCCTGTCCATGAACTAGATGCAT 59.287 43.478 0.00 0.00 0.00 3.96
1047 1113 2.012673 GCATCAGTCCTGTCCATGAAC 58.987 52.381 0.00 0.00 0.00 3.18
1083 1149 7.523293 TCAATTGAGGAGCACAGAATAAAAA 57.477 32.000 3.38 0.00 0.00 1.94
1105 1171 6.583562 TGGCAATGAAATCATTATGCATTCA 58.416 32.000 17.31 12.38 44.10 2.57
1117 1183 5.462398 GCTGATGAAGATTGGCAATGAAATC 59.538 40.000 19.07 14.37 33.77 2.17
1123 1189 2.100916 GCTGCTGATGAAGATTGGCAAT 59.899 45.455 13.54 13.54 0.00 3.56
1177 1243 3.966154 ACCGATAACTGCTGAGAATACG 58.034 45.455 0.00 0.00 0.00 3.06
1263 1329 6.677431 GCATAAGAGAACAAGAGATGCAAAGG 60.677 42.308 0.00 0.00 38.43 3.11
1302 1369 7.255139 GCGAAATGCAGATAGTAAGGGTTATTT 60.255 37.037 0.00 0.00 45.45 1.40
1603 1670 6.321848 ACGGTCACCCAAAATTAACTAAAG 57.678 37.500 0.00 0.00 0.00 1.85
1623 1690 2.238521 AGCAATGGGCCAATAATACGG 58.761 47.619 11.89 0.00 46.50 4.02
1641 1907 4.006319 AGAAATACAGGAGCAGTTCAAGC 58.994 43.478 0.00 0.00 0.00 4.01
1648 1914 6.820656 ACTTAACATGAGAAATACAGGAGCAG 59.179 38.462 0.00 0.00 0.00 4.24
1670 1936 5.335348 CCCGGAAATTGAAATTCACGTACTT 60.335 40.000 0.73 0.00 0.00 2.24
1687 1953 4.410883 ACATCCTACATGTAATCCCGGAAA 59.589 41.667 13.14 0.00 0.00 3.13
1745 2011 7.707893 ACACTTCCATAAAGAATGCAATAATGC 59.292 33.333 0.00 0.00 44.44 3.56
1746 2012 9.027129 CACACTTCCATAAAGAATGCAATAATG 57.973 33.333 0.00 0.00 38.44 1.90
1747 2013 8.752187 ACACACTTCCATAAAGAATGCAATAAT 58.248 29.630 0.00 0.00 38.44 1.28
1748 2014 8.121305 ACACACTTCCATAAAGAATGCAATAA 57.879 30.769 0.00 0.00 38.44 1.40
1751 2017 7.230510 ACTTACACACTTCCATAAAGAATGCAA 59.769 33.333 0.00 0.00 38.44 4.08
1794 2068 7.303182 TCAATACCAGTGATAATCGAGGATT 57.697 36.000 0.00 0.00 36.20 3.01
1820 2095 3.458118 TCCAAGGAAAAGTGAGGACTTCA 59.542 43.478 0.00 0.00 41.87 3.02
1876 2151 6.127451 GGTTACCCAAATCAAACTAGGAATGG 60.127 42.308 0.00 0.00 0.00 3.16
1888 2163 8.713708 TTCAATAAAAGAGGTTACCCAAATCA 57.286 30.769 0.00 0.00 0.00 2.57
1992 2304 8.237267 GGTTTGAGGTAACATAAATCTGAACAG 58.763 37.037 0.00 0.00 41.41 3.16
2134 2446 9.630098 TCAGTCAAAGATTTAAAAGCATCATTC 57.370 29.630 0.00 0.00 0.00 2.67
2376 2692 6.183360 TGTGAAGAAATTGAGCAATTCACTGT 60.183 34.615 19.64 3.88 39.88 3.55
2616 2934 3.492313 GCATTAAGCTTTGACGGTCAAG 58.508 45.455 21.47 16.58 37.70 3.02
2640 2958 8.380867 GCATACCACCTAGGGTAAATTATAAGT 58.619 37.037 14.81 0.00 46.00 2.24
2798 3117 5.643421 ATTATCTGCCTCAGAAGGAACAT 57.357 39.130 0.27 0.00 46.67 2.71
2987 3306 2.038863 TAGGTGGGTGATGGTCAAGT 57.961 50.000 0.00 0.00 0.00 3.16
2991 3310 2.368875 CTGGTATAGGTGGGTGATGGTC 59.631 54.545 0.00 0.00 0.00 4.02
3027 3346 6.255887 CCTCGGTTACTCTGTATAAAGCAAAG 59.744 42.308 0.00 0.00 0.00 2.77
3072 3391 3.338250 GGTGGCAGATGGGGGTCA 61.338 66.667 0.00 0.00 0.00 4.02
3237 3556 4.772100 AGATTTAAATGACAACCCACCTGG 59.228 41.667 5.17 0.00 41.37 4.45
3269 3588 4.337555 GCATACAGCTCCAAACAAGATGAT 59.662 41.667 0.00 0.00 41.15 2.45
3308 3630 3.944422 TCAAGTCGTTCTGCAGAAAAC 57.056 42.857 29.99 27.15 35.58 2.43
3345 3667 6.294675 CCACACATTTCCTAAGAGCAAAATCA 60.295 38.462 0.00 0.00 0.00 2.57
3387 3709 6.314400 AGCAACATGTCAAATTGATAATTGGC 59.686 34.615 16.09 10.10 0.00 4.52
3388 3710 7.762615 AGAGCAACATGTCAAATTGATAATTGG 59.237 33.333 16.09 3.70 0.00 3.16
3389 3711 8.697846 AGAGCAACATGTCAAATTGATAATTG 57.302 30.769 0.00 12.49 0.00 2.32
3391 3713 8.058667 TGAGAGCAACATGTCAAATTGATAAT 57.941 30.769 0.00 0.00 0.00 1.28
3401 3732 3.007182 TGATCACTGAGAGCAACATGTCA 59.993 43.478 0.00 0.00 40.22 3.58
3402 3733 3.370366 GTGATCACTGAGAGCAACATGTC 59.630 47.826 18.83 0.00 45.52 3.06
3478 3818 2.918802 TACGCCCGGTTCCACAGT 60.919 61.111 0.00 0.00 0.00 3.55
3487 3827 1.721487 CATTGCTTTCTACGCCCGG 59.279 57.895 0.00 0.00 0.00 5.73
3488 3828 1.062525 GCATTGCTTTCTACGCCCG 59.937 57.895 0.16 0.00 0.00 6.13
3508 3849 6.849151 AGGAATAACACCACTAAACTTCCTT 58.151 36.000 0.00 0.00 38.40 3.36
3518 3859 5.255397 TGGATCAAAGGAATAACACCACT 57.745 39.130 0.00 0.00 0.00 4.00
3524 3865 9.710900 AAACTCATTTTGGATCAAAGGAATAAC 57.289 29.630 0.00 0.00 34.72 1.89
3574 3915 7.568199 AAGGGATTTTGTAGGATTACAATCG 57.432 36.000 1.43 0.00 46.22 3.34
3614 3955 5.945191 TCACCAAATAGTTCATCATGCAGAA 59.055 36.000 0.00 0.00 0.00 3.02
3635 3976 6.458888 GGCTAAGCCTTCTATGAAAATGTCAC 60.459 42.308 0.00 0.00 46.69 3.67
3656 3997 5.247337 TGTCGATATAATTGTGGATGGGCTA 59.753 40.000 0.00 0.00 0.00 3.93
3657 3998 4.041567 TGTCGATATAATTGTGGATGGGCT 59.958 41.667 0.00 0.00 0.00 5.19
3658 3999 4.323417 TGTCGATATAATTGTGGATGGGC 58.677 43.478 0.00 0.00 0.00 5.36
3659 4000 8.450964 GTTATTGTCGATATAATTGTGGATGGG 58.549 37.037 6.32 0.00 0.00 4.00
3710 4051 4.280677 TGGGAAAAGCATGTAAAGTGAAGG 59.719 41.667 0.00 0.00 0.00 3.46
3739 4080 5.474578 AGTTTCAGCTCAGTAAGACATGA 57.525 39.130 0.00 0.00 0.00 3.07
3766 4107 7.326063 CCGGCTGTTTAATTAAAGAAAAGAGTG 59.674 37.037 10.92 0.00 0.00 3.51
3775 4116 4.695217 TGAGCCGGCTGTTTAATTAAAG 57.305 40.909 38.41 1.96 0.00 1.85
3778 4119 3.879998 TCATGAGCCGGCTGTTTAATTA 58.120 40.909 38.41 4.79 0.00 1.40
3800 4141 5.916318 TGAGCATCAACAACTCCAATTTTT 58.084 33.333 0.00 0.00 45.97 1.94
3824 4165 3.744940 ACACCCTGATGAACAATCCAT 57.255 42.857 0.00 0.00 34.00 3.41
4069 4412 6.186957 ACATGAAGTGTAAGGCATAAATGGA 58.813 36.000 0.00 0.00 39.91 3.41
4070 4413 6.455360 ACATGAAGTGTAAGGCATAAATGG 57.545 37.500 0.00 0.00 39.91 3.16
4073 4416 9.899661 AGTATAACATGAAGTGTAAGGCATAAA 57.100 29.630 0.00 0.00 41.14 1.40
4076 4419 7.564793 TGAGTATAACATGAAGTGTAAGGCAT 58.435 34.615 0.00 0.00 41.14 4.40
4077 4420 6.941857 TGAGTATAACATGAAGTGTAAGGCA 58.058 36.000 0.00 0.00 41.14 4.75
4078 4421 7.333423 TGTTGAGTATAACATGAAGTGTAAGGC 59.667 37.037 0.00 0.00 41.14 4.35
4079 4422 8.656849 GTGTTGAGTATAACATGAAGTGTAAGG 58.343 37.037 0.00 0.00 42.02 2.69
4089 4440 7.017645 GTCAAGCAAGTGTTGAGTATAACATG 58.982 38.462 0.00 0.00 42.02 3.21
4090 4441 6.128553 CGTCAAGCAAGTGTTGAGTATAACAT 60.129 38.462 0.00 0.00 42.02 2.71
4091 4442 5.176774 CGTCAAGCAAGTGTTGAGTATAACA 59.823 40.000 0.00 0.00 38.17 2.41
4094 4445 4.242475 CCGTCAAGCAAGTGTTGAGTATA 58.758 43.478 0.00 0.00 34.59 1.47
4101 4452 3.022287 CGCCGTCAAGCAAGTGTT 58.978 55.556 0.00 0.00 0.00 3.32
4115 4466 3.682292 CTCTTACCTGTGGGGCGCC 62.682 68.421 21.18 21.18 39.10 6.53
4120 4471 0.903454 ACCGTCCTCTTACCTGTGGG 60.903 60.000 0.00 0.00 38.88 4.61
4357 4711 0.109342 CCATGTACAGATCTGGCCCC 59.891 60.000 26.08 11.17 34.19 5.80
4943 5323 2.101582 GGTATGATGCTCTTGTCCGACT 59.898 50.000 0.00 0.00 0.00 4.18
4946 5326 1.414181 AGGGTATGATGCTCTTGTCCG 59.586 52.381 0.00 0.00 0.00 4.79
5029 5412 1.075425 CGCTCGTCCAGAAGAAGCAG 61.075 60.000 0.00 0.00 0.00 4.24
5184 5693 2.818274 CTTTCCAGTACGGCGGCC 60.818 66.667 13.24 9.54 33.14 6.13


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

AutoCloner maintained by Alex Coulton.