Multiple sequence alignment - TraesCS3D01G185500

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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 TraesCS3D01G185500 chr3D 100.000 5153 0 0 1 5153 170685034 170679882 0 9516
1 TraesCS3D01G185500 chr3B 95.152 3486 126 11 1698 5153 246162926 246159454 0 5461
2 TraesCS3D01G185500 chr3B 94.318 880 34 6 821 1689 246163850 246162976 0 1334
3 TraesCS3D01G185500 chr3B 96.998 633 14 2 1 628 201480198 201480830 0 1059
4 TraesCS3D01G185500 chr3A 93.633 3487 170 17 1705 5153 208248905 208245433 0 5162
5 TraesCS3D01G185500 chr3A 93.634 1021 43 11 689 1689 208249980 208248962 0 1506
6 TraesCS3D01G185500 chrUn 96.998 633 14 2 1 628 298936176 298935544 0 1059
7 TraesCS3D01G185500 chrUn 96.682 633 16 2 1 628 359774363 359774995 0 1048
8 TraesCS3D01G185500 chr5D 96.998 633 14 2 1 628 6245485 6244853 0 1059
9 TraesCS3D01G185500 chr5D 96.840 633 13 4 1 628 503321286 503321916 0 1051
10 TraesCS3D01G185500 chr5D 96.524 633 17 2 1 628 432326271 432325639 0 1042
11 TraesCS3D01G185500 chr2B 96.850 635 12 4 1 628 683736189 683736822 0 1055
12 TraesCS3D01G185500 chr1A 96.840 633 15 2 1 628 554489818 554490450 0 1053
13 TraesCS3D01G185500 chr7B 96.682 633 16 2 1 628 662747281 662746649 0 1048


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 TraesCS3D01G185500 chr3D 170679882 170685034 5152 True 9516.0 9516 100.0000 1 5153 1 chr3D.!!$R1 5152
1 TraesCS3D01G185500 chr3B 246159454 246163850 4396 True 3397.5 5461 94.7350 821 5153 2 chr3B.!!$R1 4332
2 TraesCS3D01G185500 chr3B 201480198 201480830 632 False 1059.0 1059 96.9980 1 628 1 chr3B.!!$F1 627
3 TraesCS3D01G185500 chr3A 208245433 208249980 4547 True 3334.0 5162 93.6335 689 5153 2 chr3A.!!$R1 4464
4 TraesCS3D01G185500 chrUn 298935544 298936176 632 True 1059.0 1059 96.9980 1 628 1 chrUn.!!$R1 627
5 TraesCS3D01G185500 chrUn 359774363 359774995 632 False 1048.0 1048 96.6820 1 628 1 chrUn.!!$F1 627
6 TraesCS3D01G185500 chr5D 6244853 6245485 632 True 1059.0 1059 96.9980 1 628 1 chr5D.!!$R1 627
7 TraesCS3D01G185500 chr5D 503321286 503321916 630 False 1051.0 1051 96.8400 1 628 1 chr5D.!!$F1 627
8 TraesCS3D01G185500 chr5D 432325639 432326271 632 True 1042.0 1042 96.5240 1 628 1 chr5D.!!$R2 627
9 TraesCS3D01G185500 chr2B 683736189 683736822 633 False 1055.0 1055 96.8500 1 628 1 chr2B.!!$F1 627
10 TraesCS3D01G185500 chr1A 554489818 554490450 632 False 1053.0 1053 96.8400 1 628 1 chr1A.!!$F1 627
11 TraesCS3D01G185500 chr7B 662746649 662747281 632 True 1048.0 1048 96.6820 1 628 1 chr7B.!!$R1 627

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
126 132 0.712380 AAGTCCATGGCCAATTCCCT 59.288 50.0 10.96 0.0 0.0 4.20 F
1226 1243 0.400213 TGCATGTTCCTCGGTTTCCT 59.600 50.0 0.00 0.0 0.0 3.36 F
2203 2302 0.106519 CCAGGCCCAGAATACCTTGG 60.107 60.0 0.00 0.0 0.0 3.61 F
3708 3816 0.106868 CCATGATGCCAGGCTCAAGA 60.107 55.0 14.15 0.0 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1780 1858 0.322456 TCCCAGGCGACCAAGAAATG 60.322 55.0 0.00 0.0 0.00 2.32 R
2850 2958 0.179045 ACGAACTGGCTGTTTCTGCT 60.179 50.0 11.21 0.0 39.30 4.24 R
4127 4235 0.251354 GCTCTCCTGGAATGACTGCA 59.749 55.0 0.00 0.0 0.00 4.41 R
5023 5145 0.179062 GACGGCTTCTGCTCATGGAT 60.179 55.0 0.00 0.0 39.59 3.41 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
73 74 3.542969 AAAGACCCTTATGGCCTTGTT 57.457 42.857 3.32 0.00 37.83 2.83
74 75 4.668138 AAAGACCCTTATGGCCTTGTTA 57.332 40.909 3.32 0.00 37.83 2.41
103 109 4.081476 GCCCTTGTGAGCCTTCAAAATATT 60.081 41.667 0.00 0.00 34.49 1.28
122 128 9.752228 AAAATATTTTTAAGTCCATGGCCAATT 57.248 25.926 10.96 2.44 0.00 2.32
126 132 0.712380 AAGTCCATGGCCAATTCCCT 59.288 50.000 10.96 0.00 0.00 4.20
150 156 9.488762 CCTAATTGGTCCTATACATATGACCTA 57.511 37.037 18.65 14.03 43.92 3.08
228 234 1.136500 GACCACCGGTTACTGGATCTC 59.864 57.143 18.24 3.85 35.25 2.75
257 263 3.606846 CGCGAAAAGTCAGAAATTCTGCA 60.607 43.478 17.58 4.79 43.95 4.41
543 550 4.220602 GGCTTTGTGATAATGGAACCAACT 59.779 41.667 0.00 0.00 0.00 3.16
628 635 6.208988 TCACTAGTTATTTCAGATGCTCGT 57.791 37.500 0.00 0.00 0.00 4.18
629 636 7.329588 TCACTAGTTATTTCAGATGCTCGTA 57.670 36.000 0.00 0.00 0.00 3.43
630 637 7.768240 TCACTAGTTATTTCAGATGCTCGTAA 58.232 34.615 0.00 0.00 0.00 3.18
631 638 8.414003 TCACTAGTTATTTCAGATGCTCGTAAT 58.586 33.333 0.00 0.00 0.00 1.89
632 639 9.678941 CACTAGTTATTTCAGATGCTCGTAATA 57.321 33.333 0.00 0.00 0.00 0.98
640 647 9.896645 ATTTCAGATGCTCGTAATATATCCATT 57.103 29.630 0.00 0.00 0.00 3.16
641 648 8.707938 TTCAGATGCTCGTAATATATCCATTG 57.292 34.615 0.00 0.00 0.00 2.82
642 649 7.267857 TCAGATGCTCGTAATATATCCATTGG 58.732 38.462 0.00 0.00 0.00 3.16
643 650 6.018425 CAGATGCTCGTAATATATCCATTGGC 60.018 42.308 0.00 0.00 0.00 4.52
644 651 5.159273 TGCTCGTAATATATCCATTGGCA 57.841 39.130 0.00 0.00 0.00 4.92
645 652 5.555966 TGCTCGTAATATATCCATTGGCAA 58.444 37.500 0.68 0.68 0.00 4.52
646 653 6.000840 TGCTCGTAATATATCCATTGGCAAA 58.999 36.000 3.01 0.00 0.00 3.68
647 654 6.488344 TGCTCGTAATATATCCATTGGCAAAA 59.512 34.615 3.01 0.00 0.00 2.44
648 655 6.801862 GCTCGTAATATATCCATTGGCAAAAC 59.198 38.462 3.01 0.00 0.00 2.43
649 656 6.893759 TCGTAATATATCCATTGGCAAAACG 58.106 36.000 3.01 2.18 0.00 3.60
650 657 6.706716 TCGTAATATATCCATTGGCAAAACGA 59.293 34.615 3.01 0.00 0.00 3.85
651 658 7.389330 TCGTAATATATCCATTGGCAAAACGAT 59.611 33.333 3.01 8.05 0.00 3.73
652 659 7.692291 CGTAATATATCCATTGGCAAAACGATC 59.308 37.037 3.01 0.00 0.00 3.69
653 660 7.765695 AATATATCCATTGGCAAAACGATCT 57.234 32.000 3.01 1.36 0.00 2.75
654 661 5.695851 ATATCCATTGGCAAAACGATCTC 57.304 39.130 3.01 0.00 0.00 2.75
655 662 2.789213 TCCATTGGCAAAACGATCTCA 58.211 42.857 3.01 0.00 0.00 3.27
656 663 3.355378 TCCATTGGCAAAACGATCTCAT 58.645 40.909 3.01 0.00 0.00 2.90
657 664 3.129113 TCCATTGGCAAAACGATCTCATG 59.871 43.478 3.01 0.00 0.00 3.07
658 665 3.129113 CCATTGGCAAAACGATCTCATGA 59.871 43.478 3.01 0.00 0.00 3.07
659 666 4.380761 CCATTGGCAAAACGATCTCATGAA 60.381 41.667 3.01 0.00 0.00 2.57
660 667 5.345702 CATTGGCAAAACGATCTCATGAAT 58.654 37.500 3.01 0.00 0.00 2.57
661 668 6.459985 CCATTGGCAAAACGATCTCATGAATA 60.460 38.462 3.01 0.00 0.00 1.75
662 669 6.507958 TTGGCAAAACGATCTCATGAATAA 57.492 33.333 0.00 0.00 0.00 1.40
663 670 5.879237 TGGCAAAACGATCTCATGAATAAC 58.121 37.500 0.00 0.00 0.00 1.89
664 671 5.163663 TGGCAAAACGATCTCATGAATAACC 60.164 40.000 0.00 0.00 0.00 2.85
665 672 4.963953 GCAAAACGATCTCATGAATAACCG 59.036 41.667 0.00 0.00 0.00 4.44
666 673 5.501715 CAAAACGATCTCATGAATAACCGG 58.498 41.667 0.00 0.00 0.00 5.28
667 674 4.402056 AACGATCTCATGAATAACCGGT 57.598 40.909 0.00 0.00 0.00 5.28
668 675 3.717707 ACGATCTCATGAATAACCGGTG 58.282 45.455 8.52 0.00 0.00 4.94
669 676 3.132289 ACGATCTCATGAATAACCGGTGT 59.868 43.478 8.52 0.36 0.00 4.16
670 677 4.340097 ACGATCTCATGAATAACCGGTGTA 59.660 41.667 8.52 3.08 0.00 2.90
671 678 4.680110 CGATCTCATGAATAACCGGTGTAC 59.320 45.833 8.52 0.57 0.00 2.90
672 679 4.395959 TCTCATGAATAACCGGTGTACC 57.604 45.455 8.52 0.00 0.00 3.34
673 680 3.133362 TCTCATGAATAACCGGTGTACCC 59.867 47.826 8.52 0.00 0.00 3.69
685 692 3.832615 GGTGTACCCGGAACAATATCT 57.167 47.619 0.73 0.00 0.00 1.98
686 693 4.146745 GGTGTACCCGGAACAATATCTT 57.853 45.455 0.73 0.00 0.00 2.40
687 694 4.520179 GGTGTACCCGGAACAATATCTTT 58.480 43.478 0.73 0.00 0.00 2.52
688 695 4.945543 GGTGTACCCGGAACAATATCTTTT 59.054 41.667 0.73 0.00 0.00 2.27
689 696 5.065602 GGTGTACCCGGAACAATATCTTTTC 59.934 44.000 0.73 0.00 0.00 2.29
690 697 5.644636 GTGTACCCGGAACAATATCTTTTCA 59.355 40.000 0.73 0.00 0.00 2.69
691 698 6.317893 GTGTACCCGGAACAATATCTTTTCAT 59.682 38.462 0.73 0.00 0.00 2.57
692 699 6.887545 TGTACCCGGAACAATATCTTTTCATT 59.112 34.615 0.73 0.00 0.00 2.57
693 700 6.451064 ACCCGGAACAATATCTTTTCATTC 57.549 37.500 0.73 0.00 0.00 2.67
694 701 5.949354 ACCCGGAACAATATCTTTTCATTCA 59.051 36.000 0.73 0.00 0.00 2.57
695 702 6.607198 ACCCGGAACAATATCTTTTCATTCAT 59.393 34.615 0.73 0.00 0.00 2.57
696 703 6.919662 CCCGGAACAATATCTTTTCATTCATG 59.080 38.462 0.73 0.00 0.00 3.07
704 711 3.710724 TCTTTTCATTCATGGGGATGCA 58.289 40.909 0.00 0.00 0.00 3.96
736 743 1.461559 ACACTAGTAGAGGACACGCC 58.538 55.000 3.59 0.00 0.00 5.68
773 780 8.251026 CCATTTCTTAATAAAAGAAGTCCCCAC 58.749 37.037 0.97 0.00 37.54 4.61
775 782 8.631480 TTTCTTAATAAAAGAAGTCCCCACTC 57.369 34.615 0.97 0.00 37.54 3.51
777 784 7.621796 TCTTAATAAAAGAAGTCCCCACTCTC 58.378 38.462 0.00 0.00 29.93 3.20
781 788 4.519906 AAAGAAGTCCCCACTCTCAAAA 57.480 40.909 0.00 0.00 29.93 2.44
782 789 3.493767 AGAAGTCCCCACTCTCAAAAC 57.506 47.619 0.00 0.00 29.93 2.43
802 811 8.862085 TCAAAACCCCTAGTACCTTTTATTTTG 58.138 33.333 11.07 11.07 35.60 2.44
823 832 2.420058 CCCCTTCGGCTTCATACTTT 57.580 50.000 0.00 0.00 0.00 2.66
945 955 1.131126 CAACTTCCAGTGGCAATAGCG 59.869 52.381 3.51 0.00 43.41 4.26
1184 1201 1.407575 GGTTAGCTCAAGGAGGGCTTC 60.408 57.143 0.00 0.00 37.50 3.86
1195 1212 1.373570 GAGGGCTTCTGTTTGATCGG 58.626 55.000 0.00 0.00 0.00 4.18
1226 1243 0.400213 TGCATGTTCCTCGGTTTCCT 59.600 50.000 0.00 0.00 0.00 3.36
1246 1263 1.298157 TGTGAAATCAAGGAGGCGCG 61.298 55.000 0.00 0.00 0.00 6.86
1273 1290 7.201741 CCTTCGTCTCATCATGTTTAGAGTCTA 60.202 40.741 0.00 0.00 0.00 2.59
1331 1358 9.638239 GAATTACTGCAAAATGTTTAGAATCCA 57.362 29.630 0.00 0.00 0.00 3.41
1592 1626 2.048222 TGCAGCGAAAGGTCTCCG 60.048 61.111 0.00 0.00 41.81 4.63
1639 1676 3.610040 TTGTACTACCATGCTGTGAGG 57.390 47.619 0.00 0.00 0.00 3.86
1692 1729 8.738199 TCGTCTATTCATTTTTATACTAGCCG 57.262 34.615 0.00 0.00 0.00 5.52
1693 1730 8.355169 TCGTCTATTCATTTTTATACTAGCCGT 58.645 33.333 0.00 0.00 0.00 5.68
1694 1731 8.636843 CGTCTATTCATTTTTATACTAGCCGTC 58.363 37.037 0.00 0.00 0.00 4.79
1695 1732 9.694137 GTCTATTCATTTTTATACTAGCCGTCT 57.306 33.333 0.00 0.00 0.00 4.18
1696 1733 9.692749 TCTATTCATTTTTATACTAGCCGTCTG 57.307 33.333 0.00 0.00 0.00 3.51
1700 1778 0.956633 TTATACTAGCCGTCTGCCCG 59.043 55.000 0.00 0.00 42.71 6.13
1703 1781 2.547640 TACTAGCCGTCTGCCCGTCT 62.548 60.000 0.00 0.00 42.71 4.18
1731 1809 8.703604 TCAAGATACTACTGTCATAGTTTTGC 57.296 34.615 0.00 0.00 40.89 3.68
1737 1815 4.228912 ACTGTCATAGTTTTGCACTTGC 57.771 40.909 0.00 0.00 35.67 4.01
1738 1816 3.228749 CTGTCATAGTTTTGCACTTGCG 58.771 45.455 0.00 0.00 45.83 4.85
1771 1849 4.865776 TGACCCAATCGAACATTTGTTTC 58.134 39.130 0.00 0.00 38.56 2.78
1780 1858 4.084223 TCGAACATTTGTTTCGAAGTAGCC 60.084 41.667 4.78 0.00 38.56 3.93
1781 1859 4.319190 CGAACATTTGTTTCGAAGTAGCCA 60.319 41.667 0.00 0.00 38.56 4.75
1782 1860 5.616866 CGAACATTTGTTTCGAAGTAGCCAT 60.617 40.000 0.00 0.00 38.56 4.40
1783 1861 5.705609 ACATTTGTTTCGAAGTAGCCATT 57.294 34.783 0.00 0.00 0.00 3.16
1784 1862 6.084326 ACATTTGTTTCGAAGTAGCCATTT 57.916 33.333 0.00 0.00 0.00 2.32
1785 1863 6.149633 ACATTTGTTTCGAAGTAGCCATTTC 58.850 36.000 0.00 0.00 0.00 2.17
1786 1864 6.016276 ACATTTGTTTCGAAGTAGCCATTTCT 60.016 34.615 0.00 0.00 0.00 2.52
1835 1926 9.603921 CCATTTTTGTATATCATTTGCCTTCTT 57.396 29.630 0.00 0.00 0.00 2.52
1851 1948 7.111247 TGCCTTCTTTTCTTCTCATTTTTGA 57.889 32.000 0.00 0.00 0.00 2.69
1923 2020 7.775053 ACCATAGCTGGAGTAAATTGAAAAA 57.225 32.000 0.00 0.00 46.37 1.94
1956 2053 1.894466 TCCATTTGGTGCATGAACAGG 59.106 47.619 6.08 0.00 36.34 4.00
1995 2092 4.592778 TGTTGCCTACATATAGATGGCTGA 59.407 41.667 1.85 0.00 43.57 4.26
2021 2118 2.367567 GGACACAACAGAGTTGGTAGGA 59.632 50.000 13.71 0.00 0.00 2.94
2073 2170 6.460399 GGTTATCAGTTAGGAGTGCAGAGTAG 60.460 46.154 0.00 0.00 0.00 2.57
2074 2171 4.035612 TCAGTTAGGAGTGCAGAGTAGT 57.964 45.455 0.00 0.00 0.00 2.73
2075 2172 5.175388 TCAGTTAGGAGTGCAGAGTAGTA 57.825 43.478 0.00 0.00 0.00 1.82
2093 2190 7.659390 AGAGTAGTAAGCTATCCATGCAAAATC 59.341 37.037 0.00 0.00 0.00 2.17
2143 2240 2.644299 TCAAGGGGCTTCTCATCTTCAA 59.356 45.455 0.00 0.00 0.00 2.69
2151 2248 5.392811 GGGCTTCTCATCTTCAATTGTTCAG 60.393 44.000 5.13 0.83 0.00 3.02
2163 2260 1.208706 TTGTTCAGGAGTGGTCACCA 58.791 50.000 0.00 0.00 0.00 4.17
2167 2266 1.536418 CAGGAGTGGTCACCAGGGA 60.536 63.158 0.00 0.00 32.34 4.20
2179 2278 4.336280 GTCACCAGGGAGCTTCTATTTTT 58.664 43.478 0.00 0.00 0.00 1.94
2203 2302 0.106519 CCAGGCCCAGAATACCTTGG 60.107 60.000 0.00 0.00 0.00 3.61
2221 2320 3.085952 TGGATCTTGTTAAAGCAGGGG 57.914 47.619 0.00 0.00 33.06 4.79
2225 2324 1.165270 CTTGTTAAAGCAGGGGACGG 58.835 55.000 0.00 0.00 0.00 4.79
2232 2331 2.009681 AAGCAGGGGACGGAAAATTT 57.990 45.000 0.00 0.00 0.00 1.82
2341 2441 2.285220 GCGCTAAGCTGATCGAATTTCA 59.715 45.455 0.00 0.00 44.04 2.69
2374 2474 1.228124 CAGCCGAACTTGAACCCCA 60.228 57.895 0.00 0.00 0.00 4.96
2389 2489 3.104519 ACCCCATGATGAATTTCTGCA 57.895 42.857 0.00 0.00 0.00 4.41
2717 2825 8.706322 ACCTTATAGGAACAACACAAAGAAAT 57.294 30.769 0.00 0.00 37.67 2.17
2780 2888 6.091986 CCAGAAGAGAAAGAAGATAGTGCAAC 59.908 42.308 0.00 0.00 0.00 4.17
2850 2958 2.027745 TGCACCACAAGCCAAAGAAAAA 60.028 40.909 0.00 0.00 0.00 1.94
2883 2991 1.617357 AGTTCGTCTACCTTGGACCAC 59.383 52.381 0.00 0.00 0.00 4.16
3515 3623 4.742201 TCAGAACGGAGCGCCTGC 62.742 66.667 2.29 0.00 43.24 4.85
3630 3738 2.994699 CCGGGTGGAAGTATGCCA 59.005 61.111 0.00 0.00 46.75 4.92
3657 3765 2.039480 TGCTTCTCCATCAGAAAGCTGT 59.961 45.455 7.38 0.00 40.83 4.40
3663 3771 2.302733 TCCATCAGAAAGCTGTAGCACA 59.697 45.455 6.65 0.00 45.16 4.57
3708 3816 0.106868 CCATGATGCCAGGCTCAAGA 60.107 55.000 14.15 0.00 0.00 3.02
3714 3822 1.377856 GCCAGGCTCAAGACTTCCC 60.378 63.158 3.29 0.00 0.00 3.97
3723 3831 4.974438 AGACTTCCCGCACCCCCA 62.974 66.667 0.00 0.00 0.00 4.96
3921 4029 4.705110 TCCACAGAAAGATGACAAGGAA 57.295 40.909 0.00 0.00 0.00 3.36
4127 4235 2.604174 CCGCAGCGTTTTCTCGGTT 61.604 57.895 15.05 0.00 39.51 4.44
4316 4424 3.058708 TGCAAAGAGCTTTCATGAGAACG 60.059 43.478 0.00 0.00 45.94 3.95
4317 4425 3.187227 GCAAAGAGCTTTCATGAGAACGA 59.813 43.478 0.00 0.00 41.15 3.85
4329 4437 4.039245 TCATGAGAACGAACTTGAGAGGTT 59.961 41.667 0.00 0.00 0.00 3.50
4432 4540 0.872388 CCTATTATTTCGGTGCGGGC 59.128 55.000 0.00 0.00 0.00 6.13
4505 4613 1.702886 ACAGTTTGAGATGTCGAGCG 58.297 50.000 0.00 0.00 0.00 5.03
4551 4673 2.281484 AGTGTTTCACGCCGCCAT 60.281 55.556 0.00 0.00 39.64 4.40
4626 4748 4.739228 CAGCGACAAACAAATCAACAATGA 59.261 37.500 0.00 0.00 40.57 2.57
4633 4755 4.620589 ACAAATCAACAATGAATGCCCA 57.379 36.364 0.00 0.00 39.49 5.36
4781 4903 0.108615 AACTCCTCGATCACCAAGCG 60.109 55.000 0.00 0.00 38.38 4.68
4784 4906 0.320374 TCCTCGATCACCAAGCGTTT 59.680 50.000 0.00 0.00 38.15 3.60
4785 4907 1.546923 TCCTCGATCACCAAGCGTTTA 59.453 47.619 0.00 0.00 38.15 2.01
4842 4964 4.954826 GTCCTACGGATTAGGCTGGTATAT 59.045 45.833 0.00 0.00 46.72 0.86
4871 4993 1.959085 GTCGGGTGACGGTGTTAGA 59.041 57.895 0.00 0.00 44.45 2.10
4894 5016 6.385467 AGAAAACATCCTAGCTAGAAGTCCAT 59.615 38.462 22.70 3.42 0.00 3.41
5023 5145 4.760204 GGTAGAAGCAAAGCCAAAGACTTA 59.240 41.667 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
73 74 1.302949 GCTCACAAGGGCCCACATA 59.697 57.895 27.56 3.89 0.00 2.29
74 75 2.036256 GCTCACAAGGGCCCACAT 59.964 61.111 27.56 6.76 0.00 3.21
94 100 7.911651 TGGCCATGGACTTAAAAATATTTTGA 58.088 30.769 21.02 3.95 0.00 2.69
103 109 3.517500 GGGAATTGGCCATGGACTTAAAA 59.482 43.478 21.02 4.57 0.00 1.52
122 128 8.375493 GTCATATGTATAGGACCAATTAGGGA 57.625 38.462 1.90 0.00 43.89 4.20
150 156 8.089115 GCTATTGCTATTCTTTTCCTAATCGT 57.911 34.615 0.00 0.00 36.03 3.73
543 550 3.241701 GCAGCGTTAATGCTTTTTGCTA 58.758 40.909 19.61 0.00 44.46 3.49
617 624 7.267857 CCAATGGATATATTACGAGCATCTGA 58.732 38.462 0.00 0.00 0.00 3.27
628 635 8.862325 AGATCGTTTTGCCAATGGATATATTA 57.138 30.769 2.05 0.00 0.00 0.98
629 636 7.448161 TGAGATCGTTTTGCCAATGGATATATT 59.552 33.333 2.05 0.00 0.00 1.28
630 637 6.942005 TGAGATCGTTTTGCCAATGGATATAT 59.058 34.615 2.05 0.00 0.00 0.86
631 638 6.295249 TGAGATCGTTTTGCCAATGGATATA 58.705 36.000 2.05 0.00 0.00 0.86
632 639 5.132502 TGAGATCGTTTTGCCAATGGATAT 58.867 37.500 2.05 0.00 0.00 1.63
633 640 4.522114 TGAGATCGTTTTGCCAATGGATA 58.478 39.130 2.05 0.00 0.00 2.59
634 641 3.355378 TGAGATCGTTTTGCCAATGGAT 58.645 40.909 2.05 0.00 0.00 3.41
635 642 2.789213 TGAGATCGTTTTGCCAATGGA 58.211 42.857 2.05 0.00 0.00 3.41
636 643 3.129113 TCATGAGATCGTTTTGCCAATGG 59.871 43.478 0.00 0.00 0.00 3.16
637 644 4.359971 TCATGAGATCGTTTTGCCAATG 57.640 40.909 0.00 0.00 0.00 2.82
638 645 5.587388 ATTCATGAGATCGTTTTGCCAAT 57.413 34.783 0.00 0.00 0.00 3.16
639 646 6.321717 GTTATTCATGAGATCGTTTTGCCAA 58.678 36.000 0.00 0.00 0.00 4.52
640 647 5.163663 GGTTATTCATGAGATCGTTTTGCCA 60.164 40.000 0.00 0.00 0.00 4.92
641 648 5.273944 GGTTATTCATGAGATCGTTTTGCC 58.726 41.667 0.00 0.00 0.00 4.52
642 649 4.963953 CGGTTATTCATGAGATCGTTTTGC 59.036 41.667 0.00 0.00 0.00 3.68
643 650 5.064707 ACCGGTTATTCATGAGATCGTTTTG 59.935 40.000 0.00 0.00 0.00 2.44
644 651 5.064707 CACCGGTTATTCATGAGATCGTTTT 59.935 40.000 2.97 0.00 0.00 2.43
645 652 4.570772 CACCGGTTATTCATGAGATCGTTT 59.429 41.667 2.97 0.00 0.00 3.60
646 653 4.119862 CACCGGTTATTCATGAGATCGTT 58.880 43.478 2.97 0.00 0.00 3.85
647 654 3.132289 ACACCGGTTATTCATGAGATCGT 59.868 43.478 2.97 0.00 0.00 3.73
648 655 3.717707 ACACCGGTTATTCATGAGATCG 58.282 45.455 2.97 0.00 0.00 3.69
649 656 4.989168 GGTACACCGGTTATTCATGAGATC 59.011 45.833 2.97 0.00 0.00 2.75
650 657 4.202326 GGGTACACCGGTTATTCATGAGAT 60.202 45.833 2.97 0.00 36.71 2.75
651 658 3.133362 GGGTACACCGGTTATTCATGAGA 59.867 47.826 2.97 0.00 36.71 3.27
652 659 3.463944 GGGTACACCGGTTATTCATGAG 58.536 50.000 2.97 0.00 36.71 2.90
653 660 3.547054 GGGTACACCGGTTATTCATGA 57.453 47.619 2.97 0.00 36.71 3.07
665 672 3.832615 AGATATTGTTCCGGGTACACC 57.167 47.619 5.94 0.00 0.00 4.16
666 673 5.644636 TGAAAAGATATTGTTCCGGGTACAC 59.355 40.000 5.94 0.00 0.00 2.90
667 674 5.806818 TGAAAAGATATTGTTCCGGGTACA 58.193 37.500 0.00 1.97 0.00 2.90
668 675 6.937436 ATGAAAAGATATTGTTCCGGGTAC 57.063 37.500 0.00 0.37 0.00 3.34
669 676 7.113437 TGAATGAAAAGATATTGTTCCGGGTA 58.887 34.615 0.00 0.00 0.00 3.69
670 677 5.949354 TGAATGAAAAGATATTGTTCCGGGT 59.051 36.000 0.00 0.00 0.00 5.28
671 678 6.449635 TGAATGAAAAGATATTGTTCCGGG 57.550 37.500 0.00 0.00 0.00 5.73
672 679 6.919662 CCATGAATGAAAAGATATTGTTCCGG 59.080 38.462 0.00 0.00 0.00 5.14
673 680 6.919662 CCCATGAATGAAAAGATATTGTTCCG 59.080 38.462 0.00 0.00 0.00 4.30
674 681 7.069826 TCCCCATGAATGAAAAGATATTGTTCC 59.930 37.037 0.00 0.00 0.00 3.62
675 682 8.010733 TCCCCATGAATGAAAAGATATTGTTC 57.989 34.615 0.00 0.00 0.00 3.18
676 683 7.976414 TCCCCATGAATGAAAAGATATTGTT 57.024 32.000 0.00 0.00 0.00 2.83
677 684 7.472381 GCATCCCCATGAATGAAAAGATATTGT 60.472 37.037 0.00 0.00 30.57 2.71
678 685 6.872020 GCATCCCCATGAATGAAAAGATATTG 59.128 38.462 0.00 0.00 30.57 1.90
679 686 6.555738 TGCATCCCCATGAATGAAAAGATATT 59.444 34.615 0.00 0.00 30.57 1.28
680 687 6.079336 TGCATCCCCATGAATGAAAAGATAT 58.921 36.000 0.00 0.00 30.57 1.63
681 688 5.456779 TGCATCCCCATGAATGAAAAGATA 58.543 37.500 0.00 0.00 30.57 1.98
682 689 4.291792 TGCATCCCCATGAATGAAAAGAT 58.708 39.130 0.00 0.00 30.57 2.40
683 690 3.710724 TGCATCCCCATGAATGAAAAGA 58.289 40.909 0.00 0.00 30.57 2.52
684 691 4.141801 ACATGCATCCCCATGAATGAAAAG 60.142 41.667 9.53 0.00 46.10 2.27
685 692 3.775866 ACATGCATCCCCATGAATGAAAA 59.224 39.130 9.53 0.00 46.10 2.29
686 693 3.133183 CACATGCATCCCCATGAATGAAA 59.867 43.478 9.53 0.00 46.10 2.69
687 694 2.696187 CACATGCATCCCCATGAATGAA 59.304 45.455 9.53 0.00 46.10 2.57
688 695 2.312390 CACATGCATCCCCATGAATGA 58.688 47.619 9.53 0.00 46.10 2.57
690 697 1.045407 GCACATGCATCCCCATGAAT 58.955 50.000 8.93 0.00 44.12 2.57
691 698 2.507213 GCACATGCATCCCCATGAA 58.493 52.632 8.93 0.00 44.12 2.57
692 699 4.263452 GCACATGCATCCCCATGA 57.737 55.556 8.93 0.00 44.12 3.07
704 711 7.560262 TCCTCTACTAGTGTAATAGTTGCACAT 59.440 37.037 5.39 2.09 46.85 3.21
712 719 5.049543 GGCGTGTCCTCTACTAGTGTAATAG 60.050 48.000 5.39 0.00 0.00 1.73
718 725 1.402259 CAGGCGTGTCCTCTACTAGTG 59.598 57.143 5.39 0.00 45.52 2.74
722 729 0.972983 ATGCAGGCGTGTCCTCTACT 60.973 55.000 8.40 0.00 45.52 2.57
773 780 5.500546 AAAGGTACTAGGGGTTTTGAGAG 57.499 43.478 0.00 0.00 38.49 3.20
775 782 8.645814 AAATAAAAGGTACTAGGGGTTTTGAG 57.354 34.615 0.00 0.00 38.49 3.02
777 784 8.092068 CCAAAATAAAAGGTACTAGGGGTTTTG 58.908 37.037 0.00 12.61 38.49 2.44
781 788 5.266788 GCCAAAATAAAAGGTACTAGGGGT 58.733 41.667 0.00 0.00 38.49 4.95
782 789 4.647853 GGCCAAAATAAAAGGTACTAGGGG 59.352 45.833 0.00 0.00 38.49 4.79
816 825 7.895429 ACATGGGGAATATGGGATTAAAGTATG 59.105 37.037 0.00 0.00 0.00 2.39
823 832 6.339220 ACTCTACATGGGGAATATGGGATTA 58.661 40.000 0.00 0.00 0.00 1.75
871 881 0.478507 GGAGGGAGAGGAGAGGAGAG 59.521 65.000 0.00 0.00 0.00 3.20
961 972 3.038417 CGGCAAGGATCGATCGCC 61.038 66.667 24.76 24.76 39.45 5.54
1184 1201 6.291955 GCATATTGAAATTGCCGATCAAACAG 60.292 38.462 0.00 0.00 38.34 3.16
1195 1212 5.174398 CGAGGAACATGCATATTGAAATTGC 59.826 40.000 0.00 0.00 36.91 3.56
1226 1243 0.881118 GCGCCTCCTTGATTTCACAA 59.119 50.000 0.00 0.00 0.00 3.33
1246 1263 4.433615 TCTAAACATGATGAGACGAAGGC 58.566 43.478 0.00 0.00 0.00 4.35
1305 1326 9.638239 TGGATTCTAAACATTTTGCAGTAATTC 57.362 29.630 0.00 0.00 0.00 2.17
1313 1334 4.732784 TCGCTGGATTCTAAACATTTTGC 58.267 39.130 0.00 0.00 0.00 3.68
1331 1358 1.134367 TCGTTCTCCAATTCGATCGCT 59.866 47.619 11.09 0.00 0.00 4.93
1453 1487 1.550524 CTGAGATCCAGACGAAACCCA 59.449 52.381 5.53 0.00 45.78 4.51
1592 1626 3.775654 CTCCGGACCCCACAGCTC 61.776 72.222 0.00 0.00 0.00 4.09
1639 1676 3.795688 TCCCCATTAATCAGCATCTCC 57.204 47.619 0.00 0.00 0.00 3.71
1689 1726 4.148825 ATCAGACGGGCAGACGGC 62.149 66.667 0.00 0.00 43.75 5.68
1690 1727 2.105128 GATCAGACGGGCAGACGG 59.895 66.667 0.00 0.00 38.39 4.79
1692 1729 0.532573 TCTTGATCAGACGGGCAGAC 59.467 55.000 0.00 0.00 0.00 3.51
1693 1730 1.489481 ATCTTGATCAGACGGGCAGA 58.511 50.000 0.00 0.00 32.83 4.26
1694 1731 2.363680 AGTATCTTGATCAGACGGGCAG 59.636 50.000 0.00 0.00 32.83 4.85
1695 1732 2.388735 AGTATCTTGATCAGACGGGCA 58.611 47.619 0.00 0.00 32.83 5.36
1696 1733 3.570550 AGTAGTATCTTGATCAGACGGGC 59.429 47.826 0.00 0.00 32.83 6.13
1700 1778 9.062524 ACTATGACAGTAGTATCTTGATCAGAC 57.937 37.037 0.00 0.00 34.98 3.51
1731 1809 2.912967 GTCATCAAGATTTGCGCAAGTG 59.087 45.455 23.67 18.52 41.68 3.16
1737 1815 3.699067 GATTGGGTCATCAAGATTTGCG 58.301 45.455 0.00 0.00 0.00 4.85
1738 1816 3.378112 TCGATTGGGTCATCAAGATTTGC 59.622 43.478 0.00 0.00 0.00 3.68
1780 1858 0.322456 TCCCAGGCGACCAAGAAATG 60.322 55.000 0.00 0.00 0.00 2.32
1781 1859 0.404040 TTCCCAGGCGACCAAGAAAT 59.596 50.000 0.00 0.00 0.00 2.17
1782 1860 0.536460 GTTCCCAGGCGACCAAGAAA 60.536 55.000 0.00 0.00 0.00 2.52
1783 1861 1.072505 GTTCCCAGGCGACCAAGAA 59.927 57.895 0.00 0.00 0.00 2.52
1784 1862 2.747686 GTTCCCAGGCGACCAAGA 59.252 61.111 0.00 0.00 0.00 3.02
1785 1863 2.359975 GGTTCCCAGGCGACCAAG 60.360 66.667 4.89 0.00 33.61 3.61
1786 1864 3.172106 TGGTTCCCAGGCGACCAA 61.172 61.111 9.21 0.00 40.31 3.67
1866 1963 7.785985 TCCATGTCCAATTTCATTCCATCTTAT 59.214 33.333 0.00 0.00 0.00 1.73
1869 1966 5.521696 TCCATGTCCAATTTCATTCCATCT 58.478 37.500 0.00 0.00 0.00 2.90
1870 1967 5.857471 TCCATGTCCAATTTCATTCCATC 57.143 39.130 0.00 0.00 0.00 3.51
1871 1968 6.818281 ATTCCATGTCCAATTTCATTCCAT 57.182 33.333 0.00 0.00 0.00 3.41
1872 1969 6.623979 AATTCCATGTCCAATTTCATTCCA 57.376 33.333 0.00 0.00 0.00 3.53
1881 1978 8.172741 AGCTATGGTAATAATTCCATGTCCAAT 58.827 33.333 6.65 0.00 43.28 3.16
1885 1982 7.383102 CCAGCTATGGTAATAATTCCATGTC 57.617 40.000 6.65 0.00 43.28 3.06
1923 2020 5.221048 GCACCAAATGGAAGCGATAACTAAT 60.221 40.000 6.42 0.00 38.94 1.73
1956 2053 7.945416 TAGGCAACATGTGGTATGCCATCTC 62.945 48.000 31.13 11.91 46.83 2.75
1995 2092 2.158900 CCAACTCTGTTGTGTCCTCACT 60.159 50.000 9.20 0.00 44.14 3.41
2021 2118 2.089980 GAGGAAGCAGCATGACAACAT 58.910 47.619 0.00 0.00 39.69 2.71
2073 2170 5.766222 CTGGATTTTGCATGGATAGCTTAC 58.234 41.667 0.00 0.00 0.00 2.34
2074 2171 4.279169 GCTGGATTTTGCATGGATAGCTTA 59.721 41.667 0.00 0.00 0.00 3.09
2075 2172 3.069158 GCTGGATTTTGCATGGATAGCTT 59.931 43.478 0.00 0.00 0.00 3.74
2093 2190 1.425412 GCATGCTCAAAACAAGCTGG 58.575 50.000 11.37 0.00 40.50 4.85
2143 2240 1.774254 TGGTGACCACTCCTGAACAAT 59.226 47.619 0.00 0.00 0.00 2.71
2151 2248 2.960688 GCTCCCTGGTGACCACTCC 61.961 68.421 0.00 0.00 0.00 3.85
2163 2260 5.887754 TGGTGTTAAAAATAGAAGCTCCCT 58.112 37.500 0.00 0.00 0.00 4.20
2167 2266 4.462834 GGCCTGGTGTTAAAAATAGAAGCT 59.537 41.667 0.00 0.00 0.00 3.74
2179 2278 1.562475 GGTATTCTGGGCCTGGTGTTA 59.438 52.381 10.79 0.00 0.00 2.41
2203 2302 2.678336 CGTCCCCTGCTTTAACAAGATC 59.322 50.000 0.00 0.00 30.57 2.75
2258 2357 7.633361 ACAAACAAAGATGTACTGTACTACG 57.367 36.000 17.98 4.68 39.40 3.51
2341 2441 2.100584 TCGGCTGCTTGAACACAAAATT 59.899 40.909 0.00 0.00 0.00 1.82
2389 2489 6.369065 CACGGTAAGACAGCTTTAAGAAATCT 59.631 38.462 0.00 0.00 35.56 2.40
2400 2500 3.756933 TTTAACCACGGTAAGACAGCT 57.243 42.857 0.00 0.00 0.00 4.24
2455 2555 5.111293 AGAAAACTTGGAAGCATTGTGTTG 58.889 37.500 0.00 0.00 0.00 3.33
2456 2556 5.343307 AGAAAACTTGGAAGCATTGTGTT 57.657 34.783 0.00 0.00 0.00 3.32
2459 2559 5.473039 GCATAGAAAACTTGGAAGCATTGT 58.527 37.500 0.00 0.00 0.00 2.71
2504 2604 4.579869 TGGCTAACAAAAGATCTGAGGTC 58.420 43.478 0.00 0.00 0.00 3.85
2717 2825 2.565391 TCGCTATCACCTTTGTCTTCCA 59.435 45.455 0.00 0.00 0.00 3.53
2780 2888 2.028112 TCTCTTGGTTCATCACCCTTCG 60.028 50.000 0.00 0.00 46.68 3.79
2850 2958 0.179045 ACGAACTGGCTGTTTCTGCT 60.179 50.000 11.21 0.00 39.30 4.24
2883 2991 1.272092 TGGGCCTGGTCATCTTTCTTG 60.272 52.381 4.53 0.00 0.00 3.02
2948 3056 7.076842 TCGTCATTTGATTTCTTCTCATTCC 57.923 36.000 0.00 0.00 0.00 3.01
3515 3623 3.617284 GGACCAACCCCATTACAGTAAG 58.383 50.000 0.00 0.00 0.00 2.34
3633 3741 3.200385 AGCTTTCTGATGGAGAAGCAGAT 59.800 43.478 12.13 0.00 41.86 2.90
3657 3765 2.740826 GGCGCCGAACTTGTGCTA 60.741 61.111 12.58 0.00 39.17 3.49
3663 3771 2.114670 CATCCATGGCGCCGAACTT 61.115 57.895 23.90 3.19 0.00 2.66
3708 3816 2.781431 GAAATGGGGGTGCGGGAAGT 62.781 60.000 0.00 0.00 0.00 3.01
3714 3822 1.247567 GATATGGAAATGGGGGTGCG 58.752 55.000 0.00 0.00 0.00 5.34
3723 3831 4.137543 GCGGAACAAGAGGATATGGAAAT 58.862 43.478 0.00 0.00 0.00 2.17
3921 4029 3.425162 GGAACCCACAGTGATTTCTCT 57.575 47.619 0.62 0.00 0.00 3.10
4127 4235 0.251354 GCTCTCCTGGAATGACTGCA 59.749 55.000 0.00 0.00 0.00 4.41
4316 4424 7.781548 TTTACAGTACAAACCTCTCAAGTTC 57.218 36.000 0.00 0.00 0.00 3.01
4505 4613 8.910351 ATAATTATCTGGAAAGGAGTAACTGC 57.090 34.615 0.00 0.00 0.00 4.40
4626 4748 4.082026 GCTCTGTGAAACTATTTGGGCATT 60.082 41.667 0.00 0.00 38.04 3.56
4633 4755 7.229506 AGCTTTAACTGCTCTGTGAAACTATTT 59.770 33.333 0.00 0.00 35.67 1.40
4842 4964 2.608506 CGTCACCCGACTGTATTTGTGA 60.609 50.000 0.00 0.00 40.23 3.58
4871 4993 6.567602 ATGGACTTCTAGCTAGGATGTTTT 57.432 37.500 20.58 0.00 0.00 2.43
4894 5016 0.450583 CCTGACGCTTCTACGCACTA 59.549 55.000 0.00 0.00 36.19 2.74
5023 5145 0.179062 GACGGCTTCTGCTCATGGAT 60.179 55.000 0.00 0.00 39.59 3.41


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

AutoCloner maintained by Alex Coulton.