Multiple sequence alignment - TraesCS2B01G067500

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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 TraesCS2B01G067500 chr2B 100.000 2435 0 0 1 2435 34102311 34099877 0.000000e+00 4497.0
1 TraesCS2B01G067500 chr2B 91.597 119 10 0 1 119 41824760 41824878 5.390000e-37 165.0
2 TraesCS2B01G067500 chr2B 90.678 118 10 1 1 118 42272976 42272860 3.240000e-34 156.0
3 TraesCS2B01G067500 chr2B 88.281 128 13 2 1 128 109974793 109974918 4.190000e-33 152.0
4 TraesCS2B01G067500 chrUn 88.333 1980 121 27 513 2435 24450022 24448096 0.000000e+00 2276.0
5 TraesCS2B01G067500 chrUn 89.398 415 25 4 115 516 24450682 24450274 2.790000e-139 505.0
6 TraesCS2B01G067500 chr2A 89.246 1246 111 12 466 1701 21690114 21688882 0.000000e+00 1537.0
7 TraesCS2B01G067500 chr2A 90.260 154 11 3 2281 2434 21688273 21688124 5.310000e-47 198.0
8 TraesCS2B01G067500 chr1D 91.379 116 10 0 1 116 436022312 436022197 2.510000e-35 159.0
9 TraesCS2B01G067500 chr7D 91.304 115 10 0 1 115 266554231 266554117 9.010000e-35 158.0
10 TraesCS2B01G067500 chr3D 91.304 115 10 0 1 115 585678190 585678304 9.010000e-35 158.0
11 TraesCS2B01G067500 chr3B 90.678 118 11 0 1 118 98807362 98807245 9.010000e-35 158.0
12 TraesCS2B01G067500 chr3B 89.600 125 10 3 1 123 19985525 19985648 3.240000e-34 156.0
13 TraesCS2B01G067500 chr4D 90.598 117 11 0 3 119 466732281 466732397 3.240000e-34 156.0
14 TraesCS2B01G067500 chr2D 87.302 63 6 2 2036 2097 43416019 43415958 1.210000e-08 71.3
15 TraesCS2B01G067500 chr6A 94.595 37 2 0 2061 2097 595022528 595022564 9.400000e-05 58.4


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 TraesCS2B01G067500 chr2B 34099877 34102311 2434 True 4497.0 4497 100.0000 1 2435 1 chr2B.!!$R1 2434
1 TraesCS2B01G067500 chrUn 24448096 24450682 2586 True 1390.5 2276 88.8655 115 2435 2 chrUn.!!$R1 2320
2 TraesCS2B01G067500 chr2A 21688124 21690114 1990 True 867.5 1537 89.7530 466 2434 2 chr2A.!!$R1 1968

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
384 398 0.103755 CTTCTCAGCGGCTCAGCATA 59.896 55.0 0.0 0.0 40.15 3.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1773 2087 0.03759 TTCTTGCATTGCCCCGTACT 59.962 50.0 6.12 0.0 0.0 2.73 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
25 26 8.585471 TCAGATGCTCTATTTTCAAAAGGAAT 57.415 30.769 0.00 0.00 34.91 3.01
26 27 9.685276 TCAGATGCTCTATTTTCAAAAGGAATA 57.315 29.630 0.00 0.00 34.91 1.75
69 70 9.747898 ATTTATATTAGGGTGATAAAATCGGCA 57.252 29.630 0.00 0.00 30.90 5.69
70 71 9.575868 TTTATATTAGGGTGATAAAATCGGCAA 57.424 29.630 0.00 0.00 0.00 4.52
71 72 5.767816 ATTAGGGTGATAAAATCGGCAAC 57.232 39.130 0.00 0.00 0.00 4.17
72 73 2.375146 AGGGTGATAAAATCGGCAACC 58.625 47.619 0.00 0.00 38.39 3.77
73 74 2.025321 AGGGTGATAAAATCGGCAACCT 60.025 45.455 0.00 0.00 43.35 3.50
74 75 3.201266 AGGGTGATAAAATCGGCAACCTA 59.799 43.478 0.00 0.00 46.13 3.08
75 76 3.564225 GGGTGATAAAATCGGCAACCTAG 59.436 47.826 0.00 0.00 35.26 3.02
76 77 4.448210 GGTGATAAAATCGGCAACCTAGA 58.552 43.478 0.00 0.00 0.00 2.43
77 78 5.063880 GGTGATAAAATCGGCAACCTAGAT 58.936 41.667 0.00 0.00 0.00 1.98
78 79 6.228258 GGTGATAAAATCGGCAACCTAGATA 58.772 40.000 0.00 0.00 0.00 1.98
79 80 6.879458 GGTGATAAAATCGGCAACCTAGATAT 59.121 38.462 0.00 0.00 0.00 1.63
80 81 8.038944 GGTGATAAAATCGGCAACCTAGATATA 58.961 37.037 0.00 0.00 0.00 0.86
81 82 8.870879 GTGATAAAATCGGCAACCTAGATATAC 58.129 37.037 0.00 0.00 0.00 1.47
82 83 7.758076 TGATAAAATCGGCAACCTAGATATACG 59.242 37.037 0.00 0.00 0.00 3.06
83 84 3.505464 ATCGGCAACCTAGATATACGC 57.495 47.619 0.00 0.00 0.00 4.42
84 85 2.232399 TCGGCAACCTAGATATACGCA 58.768 47.619 0.00 0.00 0.00 5.24
85 86 2.823747 TCGGCAACCTAGATATACGCAT 59.176 45.455 0.00 0.00 0.00 4.73
86 87 4.011698 TCGGCAACCTAGATATACGCATA 58.988 43.478 0.00 0.00 0.00 3.14
87 88 4.095932 TCGGCAACCTAGATATACGCATAG 59.904 45.833 0.00 0.00 0.00 2.23
88 89 4.683832 GGCAACCTAGATATACGCATAGG 58.316 47.826 0.00 0.00 40.58 2.57
89 90 4.401519 GGCAACCTAGATATACGCATAGGA 59.598 45.833 4.19 0.00 38.53 2.94
90 91 5.341617 GCAACCTAGATATACGCATAGGAC 58.658 45.833 4.19 0.00 38.53 3.85
91 92 5.125739 GCAACCTAGATATACGCATAGGACT 59.874 44.000 4.19 0.00 38.53 3.85
92 93 6.350277 GCAACCTAGATATACGCATAGGACTT 60.350 42.308 4.19 0.00 38.53 3.01
93 94 6.761099 ACCTAGATATACGCATAGGACTTG 57.239 41.667 4.19 0.00 38.53 3.16
94 95 6.246919 ACCTAGATATACGCATAGGACTTGT 58.753 40.000 4.19 0.00 38.53 3.16
95 96 7.400439 ACCTAGATATACGCATAGGACTTGTA 58.600 38.462 4.19 0.00 38.53 2.41
96 97 7.886970 ACCTAGATATACGCATAGGACTTGTAA 59.113 37.037 4.19 0.00 38.53 2.41
97 98 8.737175 CCTAGATATACGCATAGGACTTGTAAA 58.263 37.037 0.00 0.00 37.57 2.01
98 99 9.557338 CTAGATATACGCATAGGACTTGTAAAC 57.443 37.037 0.00 0.00 0.00 2.01
99 100 8.179509 AGATATACGCATAGGACTTGTAAACT 57.820 34.615 0.00 0.00 0.00 2.66
100 101 8.082852 AGATATACGCATAGGACTTGTAAACTG 58.917 37.037 0.00 0.00 0.00 3.16
101 102 4.530710 ACGCATAGGACTTGTAAACTGA 57.469 40.909 0.00 0.00 0.00 3.41
102 103 4.890088 ACGCATAGGACTTGTAAACTGAA 58.110 39.130 0.00 0.00 0.00 3.02
103 104 5.302360 ACGCATAGGACTTGTAAACTGAAA 58.698 37.500 0.00 0.00 0.00 2.69
104 105 5.178809 ACGCATAGGACTTGTAAACTGAAAC 59.821 40.000 0.00 0.00 0.00 2.78
105 106 5.618561 GCATAGGACTTGTAAACTGAAACG 58.381 41.667 0.00 0.00 0.00 3.60
106 107 5.178809 GCATAGGACTTGTAAACTGAAACGT 59.821 40.000 0.00 0.00 0.00 3.99
107 108 6.366877 GCATAGGACTTGTAAACTGAAACGTA 59.633 38.462 0.00 0.00 0.00 3.57
108 109 7.411588 GCATAGGACTTGTAAACTGAAACGTAG 60.412 40.741 0.00 0.00 0.00 3.51
109 110 5.295152 AGGACTTGTAAACTGAAACGTAGG 58.705 41.667 0.00 0.00 0.00 3.18
110 111 4.450080 GGACTTGTAAACTGAAACGTAGGG 59.550 45.833 0.00 0.00 0.00 3.53
111 112 5.280654 ACTTGTAAACTGAAACGTAGGGA 57.719 39.130 0.00 0.00 0.00 4.20
112 113 5.295152 ACTTGTAAACTGAAACGTAGGGAG 58.705 41.667 0.00 0.00 0.00 4.30
113 114 4.942761 TGTAAACTGAAACGTAGGGAGT 57.057 40.909 0.00 0.00 0.00 3.85
149 150 9.177608 ACAGTAAGATTATTTGCAGAGCATAAA 57.822 29.630 0.00 0.00 38.76 1.40
178 179 8.999220 ATAAAAGCTACTACAGAAAGTACCAC 57.001 34.615 0.00 0.00 0.00 4.16
203 204 8.258007 ACGAAATGATCATCACCTAGAAAGTTA 58.742 33.333 9.06 0.00 0.00 2.24
288 302 3.707611 AGACGTTGGTGGGCTTATATGTA 59.292 43.478 0.00 0.00 0.00 2.29
290 304 3.198200 ACGTTGGTGGGCTTATATGTACA 59.802 43.478 0.00 0.00 0.00 2.90
319 333 2.741486 TAGGCCAACTCCAACGTGGC 62.741 60.000 5.01 5.33 44.31 5.01
382 396 2.263852 CTTCTCAGCGGCTCAGCA 59.736 61.111 0.00 0.00 40.15 4.41
383 397 1.153409 CTTCTCAGCGGCTCAGCAT 60.153 57.895 0.00 0.00 40.15 3.79
384 398 0.103755 CTTCTCAGCGGCTCAGCATA 59.896 55.000 0.00 0.00 40.15 3.14
385 399 0.755079 TTCTCAGCGGCTCAGCATAT 59.245 50.000 0.00 0.00 40.15 1.78
395 409 4.679106 GCGGCTCAGCATATATATGTGTCT 60.679 45.833 21.10 9.40 36.11 3.41
409 423 1.908299 TGTCTTCCTGGCTCGAGCA 60.908 57.895 36.27 21.81 44.36 4.26
449 463 4.903054 TCTATCCACCATCTCATTGCATC 58.097 43.478 0.00 0.00 0.00 3.91
462 476 5.101648 TCATTGCATCTCAGGTTGACATA 57.898 39.130 0.00 0.00 0.00 2.29
480 494 8.408601 GTTGACATAGCCAGTTCAATCAATTAT 58.591 33.333 0.00 0.00 0.00 1.28
538 808 4.642885 CGAAAAATACAGGGCCCATTCTTA 59.357 41.667 27.56 7.45 0.00 2.10
579 849 0.813184 CATGGCTGCCCAAGTAGTTG 59.187 55.000 17.53 3.09 46.14 3.16
580 850 0.698238 ATGGCTGCCCAAGTAGTTGA 59.302 50.000 17.53 0.00 46.14 3.18
581 851 0.250727 TGGCTGCCCAAGTAGTTGAC 60.251 55.000 17.53 4.32 38.46 3.18
582 852 0.250727 GGCTGCCCAAGTAGTTGACA 60.251 55.000 7.66 8.52 35.46 3.58
583 853 1.614317 GGCTGCCCAAGTAGTTGACAT 60.614 52.381 7.66 0.00 35.46 3.06
584 854 1.470098 GCTGCCCAAGTAGTTGACATG 59.530 52.381 12.04 0.00 35.46 3.21
585 855 1.470098 CTGCCCAAGTAGTTGACATGC 59.530 52.381 12.04 8.96 35.46 4.06
586 856 0.811281 GCCCAAGTAGTTGACATGCC 59.189 55.000 12.04 0.00 35.46 4.40
587 857 1.463674 CCCAAGTAGTTGACATGCCC 58.536 55.000 12.04 0.00 35.46 5.36
588 858 1.271871 CCCAAGTAGTTGACATGCCCA 60.272 52.381 12.04 0.00 35.46 5.36
589 859 2.513753 CCAAGTAGTTGACATGCCCAA 58.486 47.619 12.04 0.00 35.46 4.12
590 860 2.228822 CCAAGTAGTTGACATGCCCAAC 59.771 50.000 18.52 18.52 42.97 3.77
591 861 2.884012 CAAGTAGTTGACATGCCCAACA 59.116 45.455 24.45 13.23 44.54 3.33
592 862 2.783135 AGTAGTTGACATGCCCAACAG 58.217 47.619 24.45 0.00 44.54 3.16
593 863 2.106511 AGTAGTTGACATGCCCAACAGT 59.893 45.455 24.45 14.68 44.54 3.55
594 864 2.071778 AGTTGACATGCCCAACAGTT 57.928 45.000 24.45 9.10 44.54 3.16
670 957 2.593725 CCTCATCATGGCTGCCCG 60.594 66.667 17.53 7.60 0.00 6.13
672 959 1.447217 CTCATCATGGCTGCCCGTA 59.553 57.895 17.53 0.83 0.00 4.02
761 1048 9.039870 CCTTTGTGTAAAAATGAATGCACTTAA 57.960 29.630 0.00 0.00 33.90 1.85
810 1098 0.826256 GCCGGGTCCTTTCCAGTTTT 60.826 55.000 2.18 0.00 0.00 2.43
843 1131 0.169672 TACGAGGCAGAGCGTGTAAC 59.830 55.000 0.00 0.00 41.35 2.50
854 1142 4.742167 CAGAGCGTGTAACCATAGAATCAG 59.258 45.833 0.00 0.00 0.00 2.90
866 1154 5.221783 ACCATAGAATCAGCTCATGCACATA 60.222 40.000 0.00 0.00 42.74 2.29
872 1160 2.171027 TCAGCTCATGCACATATGTCCA 59.829 45.455 5.07 2.99 42.74 4.02
930 1218 1.451028 GCAGCTCCTACCAGCCTTG 60.451 63.158 0.00 0.00 40.65 3.61
939 1227 2.348998 CCAGCCTTGGTCTTCGCT 59.651 61.111 0.00 0.00 39.79 4.93
968 1256 0.833287 GTCCTTAGGGCATCAGCAGA 59.167 55.000 0.00 0.00 44.61 4.26
969 1257 1.419387 GTCCTTAGGGCATCAGCAGAT 59.581 52.381 0.00 0.00 44.61 2.90
1012 1300 5.490159 TCAAGTTCTACATGCATGACATCA 58.510 37.500 32.75 9.69 36.64 3.07
1026 1314 4.552365 ATCATCACTGGCGGGCCG 62.552 66.667 24.35 24.35 39.42 6.13
1044 1332 1.005630 GTCGACTCCAGCAACAGCT 60.006 57.895 8.70 0.00 39.75 4.24
1093 1381 4.653888 CCAACGACCCCACCACCC 62.654 72.222 0.00 0.00 0.00 4.61
1101 1389 3.566210 CCCACCACCCACTTCGGT 61.566 66.667 0.00 0.00 36.18 4.69
1311 1599 0.818445 TCGATACCGTCAGGGAGCTC 60.818 60.000 4.71 4.71 43.47 4.09
1456 1748 3.118408 GGTGCATACCATAGGTCTGAACA 60.118 47.826 12.93 0.00 46.71 3.18
1459 1751 6.467677 GTGCATACCATAGGTCTGAACATAT 58.532 40.000 7.58 0.00 37.99 1.78
1462 1754 7.661437 TGCATACCATAGGTCTGAACATATTTC 59.339 37.037 5.83 0.00 37.09 2.17
1473 1765 6.261603 GTCTGAACATATTTCCATGCATCTGA 59.738 38.462 0.00 0.00 0.00 3.27
1491 1783 3.831333 TCTGATGGGTGCTTGCATAAAAA 59.169 39.130 0.00 0.00 0.00 1.94
1530 1829 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1531 1830 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1532 1831 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1533 1832 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1534 1833 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1535 1834 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1536 1835 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1537 1836 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1538 1837 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1539 1838 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1540 1839 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1541 1840 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1542 1841 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1543 1842 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1544 1843 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1545 1844 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1546 1845 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1547 1846 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1555 1854 3.202906 GTGTGTGTGTGTGTTATGGTCT 58.797 45.455 0.00 0.00 0.00 3.85
1591 1890 3.786516 TGTCAGTGCGTCCGATTTATA 57.213 42.857 0.00 0.00 0.00 0.98
1599 1898 5.694910 AGTGCGTCCGATTTATATGTTTAGG 59.305 40.000 0.00 0.00 0.00 2.69
1647 1948 7.431376 CGAGTTCATGATTGATGGAGATTTTTG 59.569 37.037 0.00 0.00 32.26 2.44
1683 1984 4.331717 AGGTACAACAGTCTCGTTTGTTTG 59.668 41.667 0.00 0.00 35.46 2.93
1689 1990 2.351418 CAGTCTCGTTTGTTTGCTGTCA 59.649 45.455 0.00 0.00 0.00 3.58
1710 2011 8.010733 TGTCATTGAAATTTTCCTTCACTCTT 57.989 30.769 6.68 0.00 32.61 2.85
1713 2014 7.927629 TCATTGAAATTTTCCTTCACTCTTTGG 59.072 33.333 6.68 0.00 32.61 3.28
1718 2019 2.415983 TCCTTCACTCTTTGGGAGGA 57.584 50.000 0.00 0.00 45.83 3.71
1730 2031 2.269241 GGAGGAACAAGAGGCCCG 59.731 66.667 0.00 0.00 0.00 6.13
1733 2034 0.179070 GAGGAACAAGAGGCCCGATC 60.179 60.000 0.00 0.00 0.00 3.69
1734 2035 0.618968 AGGAACAAGAGGCCCGATCT 60.619 55.000 0.00 0.00 0.00 2.75
1740 2041 2.224769 ACAAGAGGCCCGATCTTTGAAA 60.225 45.455 0.00 0.00 34.80 2.69
1741 2042 2.819608 CAAGAGGCCCGATCTTTGAAAA 59.180 45.455 0.00 0.00 34.80 2.29
1742 2043 2.437413 AGAGGCCCGATCTTTGAAAAC 58.563 47.619 0.00 0.00 0.00 2.43
1743 2044 2.159382 GAGGCCCGATCTTTGAAAACA 58.841 47.619 0.00 0.00 0.00 2.83
1744 2045 2.755103 GAGGCCCGATCTTTGAAAACAT 59.245 45.455 0.00 0.00 0.00 2.71
1746 2047 2.417243 GGCCCGATCTTTGAAAACATGG 60.417 50.000 0.00 0.00 0.00 3.66
1748 2049 2.825532 CCCGATCTTTGAAAACATGGGT 59.174 45.455 0.00 0.00 0.00 4.51
1773 2087 3.570975 ACAGCCGGAACATCGTGTATATA 59.429 43.478 5.05 0.00 0.00 0.86
1783 2097 3.138884 TCGTGTATATAGTACGGGGCA 57.861 47.619 15.51 0.00 38.29 5.36
1794 2108 1.476488 GTACGGGGCAATGCAAGAATT 59.524 47.619 7.79 0.00 0.00 2.17
1807 2141 2.925563 GCAAGAATTTCGGCCAGATTTG 59.074 45.455 2.24 0.00 0.00 2.32
1842 2176 5.530915 CACCCAATTATGCGAGATAAAAGGA 59.469 40.000 0.00 0.00 0.00 3.36
1843 2177 6.039270 CACCCAATTATGCGAGATAAAAGGAA 59.961 38.462 0.00 0.00 0.00 3.36
1844 2178 6.777580 ACCCAATTATGCGAGATAAAAGGAAT 59.222 34.615 0.00 0.00 0.00 3.01
1855 2189 7.808381 GCGAGATAAAAGGAATAATTAAAGGGC 59.192 37.037 0.00 0.00 0.00 5.19
1894 2228 3.615592 GCATTGCACCATTGATGAACAGT 60.616 43.478 3.15 0.00 0.00 3.55
1899 2256 6.343716 TGCACCATTGATGAACAGTAAAAT 57.656 33.333 0.00 0.00 0.00 1.82
1903 2260 7.274250 GCACCATTGATGAACAGTAAAATTCTC 59.726 37.037 0.00 0.00 0.00 2.87
1907 2264 9.850628 CATTGATGAACAGTAAAATTCTCACAT 57.149 29.630 0.00 0.00 0.00 3.21
1949 2306 7.650834 GCACAAATTTATTAAGGTGCTTGAA 57.349 32.000 17.24 0.00 45.87 2.69
1960 2317 8.986477 ATTAAGGTGCTTGAATTTTGTATGTC 57.014 30.769 0.00 0.00 0.00 3.06
1967 2324 6.092748 GCTTGAATTTTGTATGTCGGAATGT 58.907 36.000 0.00 0.00 0.00 2.71
1978 2335 2.271800 GTCGGAATGTCATCTGTGGAC 58.728 52.381 0.00 0.00 35.83 4.02
2016 2373 5.757886 TCAAATTAGTGCTCGAACTTTTGG 58.242 37.500 11.66 0.40 32.45 3.28
2034 2391 3.467374 TGGGCACTCATTTTGTTTTCC 57.533 42.857 0.00 0.00 0.00 3.13
2055 2412 1.492133 TTTGTCAGGAGCCCCTCAGG 61.492 60.000 0.00 0.00 42.02 3.86
2097 2459 6.749923 TTTTGCAAGCACCTAAAACATTTT 57.250 29.167 0.00 0.00 0.00 1.82
2114 2476 7.804843 AACATTTTTGCATCTTCAAATCCAA 57.195 28.000 0.00 0.00 36.04 3.53
2159 2525 7.253387 GCATTTTGTTCAAATTTTGCTGTTCAC 60.253 33.333 4.19 0.00 32.24 3.18
2184 2550 1.005294 GTGCAATGCAACCAGCTTCG 61.005 55.000 10.44 0.00 45.94 3.79
2241 2608 6.037610 GCAATAAACTGGAGTTCTCCACATAG 59.962 42.308 16.47 10.10 37.25 2.23
2259 2626 5.468072 CACATAGTTATGGCAACCTCATCTC 59.532 44.000 0.00 0.00 38.00 2.75
2278 2645 6.437477 TCATCTCTCTTAAGACCTACTTTGCA 59.563 38.462 0.00 0.00 39.72 4.08
2294 2692 4.745125 ACTTTGCACATTATATCCTCGTCG 59.255 41.667 0.00 0.00 0.00 5.12
2300 2698 4.067896 ACATTATATCCTCGTCGTACCGT 58.932 43.478 0.00 0.00 0.00 4.83
2372 2770 5.700832 GGATATTCTGTTATGCACATCGGAA 59.299 40.000 0.00 0.00 33.76 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.585471 ATTCCTTTTGAAAATAGAGCATCTGA 57.415 30.769 0.00 0.00 40.91 3.27
43 44 9.747898 TGCCGATTTTATCACCCTAATATAAAT 57.252 29.630 0.00 0.00 0.00 1.40
44 45 9.575868 TTGCCGATTTTATCACCCTAATATAAA 57.424 29.630 0.00 0.00 0.00 1.40
45 46 9.005777 GTTGCCGATTTTATCACCCTAATATAA 57.994 33.333 0.00 0.00 0.00 0.98
46 47 7.608761 GGTTGCCGATTTTATCACCCTAATATA 59.391 37.037 0.00 0.00 0.00 0.86
47 48 6.433093 GGTTGCCGATTTTATCACCCTAATAT 59.567 38.462 0.00 0.00 0.00 1.28
48 49 5.766174 GGTTGCCGATTTTATCACCCTAATA 59.234 40.000 0.00 0.00 0.00 0.98
49 50 4.583073 GGTTGCCGATTTTATCACCCTAAT 59.417 41.667 0.00 0.00 0.00 1.73
50 51 3.949113 GGTTGCCGATTTTATCACCCTAA 59.051 43.478 0.00 0.00 0.00 2.69
51 52 3.201266 AGGTTGCCGATTTTATCACCCTA 59.799 43.478 0.00 0.00 0.00 3.53
52 53 2.025321 AGGTTGCCGATTTTATCACCCT 60.025 45.455 0.00 0.00 0.00 4.34
53 54 2.375146 AGGTTGCCGATTTTATCACCC 58.625 47.619 0.00 0.00 0.00 4.61
54 55 4.448210 TCTAGGTTGCCGATTTTATCACC 58.552 43.478 0.00 0.00 0.00 4.02
55 56 7.907214 ATATCTAGGTTGCCGATTTTATCAC 57.093 36.000 0.00 0.00 0.00 3.06
56 57 7.758076 CGTATATCTAGGTTGCCGATTTTATCA 59.242 37.037 0.00 0.00 0.00 2.15
57 58 7.254017 GCGTATATCTAGGTTGCCGATTTTATC 60.254 40.741 0.00 0.00 0.00 1.75
58 59 6.534079 GCGTATATCTAGGTTGCCGATTTTAT 59.466 38.462 0.00 0.00 0.00 1.40
59 60 5.865552 GCGTATATCTAGGTTGCCGATTTTA 59.134 40.000 0.00 0.00 0.00 1.52
60 61 4.689345 GCGTATATCTAGGTTGCCGATTTT 59.311 41.667 0.00 0.00 0.00 1.82
61 62 4.243270 GCGTATATCTAGGTTGCCGATTT 58.757 43.478 0.00 0.00 0.00 2.17
62 63 3.257375 TGCGTATATCTAGGTTGCCGATT 59.743 43.478 0.00 0.00 0.00 3.34
63 64 2.823747 TGCGTATATCTAGGTTGCCGAT 59.176 45.455 0.00 0.00 0.00 4.18
64 65 2.232399 TGCGTATATCTAGGTTGCCGA 58.768 47.619 0.00 0.00 0.00 5.54
65 66 2.717580 TGCGTATATCTAGGTTGCCG 57.282 50.000 0.00 0.00 0.00 5.69
66 67 4.401519 TCCTATGCGTATATCTAGGTTGCC 59.598 45.833 0.00 0.00 33.81 4.52
67 68 5.125739 AGTCCTATGCGTATATCTAGGTTGC 59.874 44.000 0.00 0.00 33.81 4.17
68 69 6.761099 AGTCCTATGCGTATATCTAGGTTG 57.239 41.667 0.00 0.00 33.81 3.77
69 70 6.720288 ACAAGTCCTATGCGTATATCTAGGTT 59.280 38.462 0.00 0.00 33.81 3.50
70 71 6.246919 ACAAGTCCTATGCGTATATCTAGGT 58.753 40.000 0.00 0.00 33.81 3.08
71 72 6.761099 ACAAGTCCTATGCGTATATCTAGG 57.239 41.667 0.00 0.00 33.46 3.02
72 73 9.557338 GTTTACAAGTCCTATGCGTATATCTAG 57.443 37.037 0.00 0.00 0.00 2.43
73 74 9.293404 AGTTTACAAGTCCTATGCGTATATCTA 57.707 33.333 0.00 0.00 0.00 1.98
74 75 8.082852 CAGTTTACAAGTCCTATGCGTATATCT 58.917 37.037 0.00 0.00 0.00 1.98
75 76 8.080417 TCAGTTTACAAGTCCTATGCGTATATC 58.920 37.037 0.00 0.00 0.00 1.63
76 77 7.948357 TCAGTTTACAAGTCCTATGCGTATAT 58.052 34.615 0.00 0.00 0.00 0.86
77 78 7.337480 TCAGTTTACAAGTCCTATGCGTATA 57.663 36.000 0.00 0.00 0.00 1.47
78 79 6.216801 TCAGTTTACAAGTCCTATGCGTAT 57.783 37.500 0.00 0.00 0.00 3.06
79 80 5.648178 TCAGTTTACAAGTCCTATGCGTA 57.352 39.130 0.00 0.00 0.00 4.42
80 81 4.530710 TCAGTTTACAAGTCCTATGCGT 57.469 40.909 0.00 0.00 0.00 5.24
81 82 5.618561 GTTTCAGTTTACAAGTCCTATGCG 58.381 41.667 0.00 0.00 0.00 4.73
82 83 5.178809 ACGTTTCAGTTTACAAGTCCTATGC 59.821 40.000 0.00 0.00 0.00 3.14
83 84 6.780706 ACGTTTCAGTTTACAAGTCCTATG 57.219 37.500 0.00 0.00 0.00 2.23
84 85 7.095270 CCTACGTTTCAGTTTACAAGTCCTAT 58.905 38.462 0.00 0.00 0.00 2.57
85 86 6.449698 CCTACGTTTCAGTTTACAAGTCCTA 58.550 40.000 0.00 0.00 0.00 2.94
86 87 5.295152 CCTACGTTTCAGTTTACAAGTCCT 58.705 41.667 0.00 0.00 0.00 3.85
87 88 4.450080 CCCTACGTTTCAGTTTACAAGTCC 59.550 45.833 0.00 0.00 0.00 3.85
88 89 5.291971 TCCCTACGTTTCAGTTTACAAGTC 58.708 41.667 0.00 0.00 0.00 3.01
89 90 5.163374 ACTCCCTACGTTTCAGTTTACAAGT 60.163 40.000 0.00 0.00 0.00 3.16
90 91 5.295152 ACTCCCTACGTTTCAGTTTACAAG 58.705 41.667 0.00 0.00 0.00 3.16
91 92 5.280654 ACTCCCTACGTTTCAGTTTACAA 57.719 39.130 0.00 0.00 0.00 2.41
92 93 4.942761 ACTCCCTACGTTTCAGTTTACA 57.057 40.909 0.00 0.00 0.00 2.41
168 169 6.456988 GGTGATGATCATTTCGTGGTACTTTC 60.457 42.308 10.14 0.00 0.00 2.62
175 176 4.948847 TCTAGGTGATGATCATTTCGTGG 58.051 43.478 10.14 9.55 0.00 4.94
178 179 7.545362 AACTTTCTAGGTGATGATCATTTCG 57.455 36.000 10.14 0.00 0.00 3.46
221 222 9.677567 GAAGTGAAATTTGAGCAACAGTATTAA 57.322 29.630 0.00 0.00 0.00 1.40
228 229 4.998671 TGGAAGTGAAATTTGAGCAACA 57.001 36.364 0.00 0.00 0.00 3.33
304 318 1.358759 GTTGCCACGTTGGAGTTGG 59.641 57.895 8.04 0.00 40.96 3.77
305 319 1.358759 GGTTGCCACGTTGGAGTTG 59.641 57.895 8.04 0.00 40.96 3.16
306 320 1.826487 GGGTTGCCACGTTGGAGTT 60.826 57.895 8.04 0.00 40.96 3.01
319 333 1.604604 ATCCACGTCTGTTTGGGTTG 58.395 50.000 0.00 0.00 33.25 3.77
350 364 2.371841 TGAGAAGCTAAGGCCAACTTCA 59.628 45.455 21.63 7.06 40.77 3.02
376 390 7.040494 CCAGGAAGACACATATATATGCTGAG 58.960 42.308 20.46 11.58 37.19 3.35
380 394 5.738909 AGCCAGGAAGACACATATATATGC 58.261 41.667 20.46 6.67 37.19 3.14
382 396 5.952347 TCGAGCCAGGAAGACACATATATAT 59.048 40.000 0.00 0.00 0.00 0.86
383 397 5.321927 TCGAGCCAGGAAGACACATATATA 58.678 41.667 0.00 0.00 0.00 0.86
384 398 4.152647 TCGAGCCAGGAAGACACATATAT 58.847 43.478 0.00 0.00 0.00 0.86
385 399 3.562182 TCGAGCCAGGAAGACACATATA 58.438 45.455 0.00 0.00 0.00 0.86
395 409 2.586245 CCATGCTCGAGCCAGGAA 59.414 61.111 33.23 15.93 41.18 3.36
409 423 1.152819 ATGCAGATGAAGCCGCCAT 60.153 52.632 0.00 0.00 0.00 4.40
449 463 3.265791 GAACTGGCTATGTCAACCTGAG 58.734 50.000 0.00 0.00 0.00 3.35
462 476 5.760253 CCGAGTATAATTGATTGAACTGGCT 59.240 40.000 0.00 0.00 0.00 4.75
480 494 3.494332 GAATAGCCCTAGTTCCCGAGTA 58.506 50.000 0.00 0.00 0.00 2.59
579 849 1.609208 AGTCAACTGTTGGGCATGTC 58.391 50.000 19.55 0.00 0.00 3.06
580 850 1.956477 GAAGTCAACTGTTGGGCATGT 59.044 47.619 19.55 1.02 0.00 3.21
581 851 1.955778 TGAAGTCAACTGTTGGGCATG 59.044 47.619 19.55 0.00 0.00 4.06
582 852 1.956477 GTGAAGTCAACTGTTGGGCAT 59.044 47.619 19.55 7.01 0.00 4.40
583 853 1.340502 TGTGAAGTCAACTGTTGGGCA 60.341 47.619 19.55 10.17 0.00 5.36
584 854 1.388547 TGTGAAGTCAACTGTTGGGC 58.611 50.000 19.55 12.90 0.00 5.36
585 855 4.821805 AGTTATGTGAAGTCAACTGTTGGG 59.178 41.667 19.55 0.00 30.28 4.12
586 856 6.377327 AAGTTATGTGAAGTCAACTGTTGG 57.623 37.500 19.55 2.55 31.80 3.77
587 857 7.915508 TGTAAGTTATGTGAAGTCAACTGTTG 58.084 34.615 14.24 14.24 31.80 3.33
588 858 8.677148 ATGTAAGTTATGTGAAGTCAACTGTT 57.323 30.769 0.00 0.00 31.80 3.16
589 859 9.424319 CTATGTAAGTTATGTGAAGTCAACTGT 57.576 33.333 0.00 0.00 31.80 3.55
590 860 9.639601 TCTATGTAAGTTATGTGAAGTCAACTG 57.360 33.333 0.00 0.00 31.80 3.16
593 863 9.098355 GCATCTATGTAAGTTATGTGAAGTCAA 57.902 33.333 0.00 0.00 0.00 3.18
594 864 7.710907 GGCATCTATGTAAGTTATGTGAAGTCA 59.289 37.037 0.00 0.00 0.00 3.41
794 1081 2.677542 AGGAAAACTGGAAAGGACCC 57.322 50.000 0.00 0.00 0.00 4.46
810 1098 5.001833 TGCCTCGTACCCTTTATATAGGA 57.998 43.478 10.56 0.00 37.50 2.94
825 1113 1.080705 GTTACACGCTCTGCCTCGT 60.081 57.895 0.00 0.00 39.79 4.18
843 1131 3.473625 TGTGCATGAGCTGATTCTATGG 58.526 45.455 0.00 0.00 42.74 2.74
854 1142 4.516321 TGTATTGGACATATGTGCATGAGC 59.484 41.667 27.79 18.44 45.59 4.26
872 1160 5.746065 GCCATGGCTTGTACTAGGATGTATT 60.746 44.000 29.98 0.00 38.26 1.89
930 1218 0.179097 CAAGGGCTAGAGCGAAGACC 60.179 60.000 0.00 0.00 43.15 3.85
968 1256 4.835927 GGATCGTCTCCGTTGCAT 57.164 55.556 0.00 0.00 33.29 3.96
1026 1314 3.555428 GCTGTTGCTGGAGTCGAC 58.445 61.111 7.70 7.70 36.03 4.20
1044 1332 2.358582 CACACCTTTGATGACTTGCACA 59.641 45.455 0.00 0.00 0.00 4.57
1456 1748 4.770531 CACCCATCAGATGCATGGAAATAT 59.229 41.667 2.46 0.00 43.32 1.28
1459 1751 2.380941 CACCCATCAGATGCATGGAAA 58.619 47.619 2.46 0.00 43.32 3.13
1462 1754 0.467474 AGCACCCATCAGATGCATGG 60.467 55.000 2.46 0.00 41.97 3.66
1530 1829 3.486708 CCATAACACACACACACACACAC 60.487 47.826 0.00 0.00 0.00 3.82
1531 1830 2.680339 CCATAACACACACACACACACA 59.320 45.455 0.00 0.00 0.00 3.72
1532 1831 2.680841 ACCATAACACACACACACACAC 59.319 45.455 0.00 0.00 0.00 3.82
1533 1832 2.939756 GACCATAACACACACACACACA 59.060 45.455 0.00 0.00 0.00 3.72
1534 1833 3.002246 CAGACCATAACACACACACACAC 59.998 47.826 0.00 0.00 0.00 3.82
1535 1834 3.202097 CAGACCATAACACACACACACA 58.798 45.455 0.00 0.00 0.00 3.72
1536 1835 2.548057 CCAGACCATAACACACACACAC 59.452 50.000 0.00 0.00 0.00 3.82
1537 1836 2.486370 CCCAGACCATAACACACACACA 60.486 50.000 0.00 0.00 0.00 3.72
1538 1837 2.151202 CCCAGACCATAACACACACAC 58.849 52.381 0.00 0.00 0.00 3.82
1539 1838 2.050918 TCCCAGACCATAACACACACA 58.949 47.619 0.00 0.00 0.00 3.72
1540 1839 2.851263 TCCCAGACCATAACACACAC 57.149 50.000 0.00 0.00 0.00 3.82
1541 1840 2.642311 ACATCCCAGACCATAACACACA 59.358 45.455 0.00 0.00 0.00 3.72
1542 1841 3.055094 AGACATCCCAGACCATAACACAC 60.055 47.826 0.00 0.00 0.00 3.82
1543 1842 3.181329 AGACATCCCAGACCATAACACA 58.819 45.455 0.00 0.00 0.00 3.72
1544 1843 3.914426 AGACATCCCAGACCATAACAC 57.086 47.619 0.00 0.00 0.00 3.32
1545 1844 3.843619 TGAAGACATCCCAGACCATAACA 59.156 43.478 0.00 0.00 0.00 2.41
1546 1845 4.446371 CTGAAGACATCCCAGACCATAAC 58.554 47.826 0.00 0.00 0.00 1.89
1547 1846 3.118261 GCTGAAGACATCCCAGACCATAA 60.118 47.826 0.00 0.00 0.00 1.90
1555 1854 1.629861 TGACATGCTGAAGACATCCCA 59.370 47.619 0.00 0.00 0.00 4.37
1591 1890 3.326880 ACTTCGACCTGGAACCTAAACAT 59.673 43.478 0.00 0.00 0.00 2.71
1599 1898 3.120304 GCATTAACACTTCGACCTGGAAC 60.120 47.826 0.00 0.00 0.00 3.62
1683 1984 6.218746 AGTGAAGGAAAATTTCAATGACAGC 58.781 36.000 8.09 0.00 36.41 4.40
1689 1990 7.071071 TCCCAAAGAGTGAAGGAAAATTTCAAT 59.929 33.333 8.09 0.00 36.41 2.57
1710 2011 1.767692 GGCCTCTTGTTCCTCCCAA 59.232 57.895 0.00 0.00 0.00 4.12
1713 2014 1.627297 ATCGGGCCTCTTGTTCCTCC 61.627 60.000 0.84 0.00 0.00 4.30
1718 2019 1.351017 TCAAAGATCGGGCCTCTTGTT 59.649 47.619 8.65 0.00 33.34 2.83
1730 2031 3.989817 GTGCACCCATGTTTTCAAAGATC 59.010 43.478 5.22 0.00 0.00 2.75
1733 2034 3.125316 CTGTGCACCCATGTTTTCAAAG 58.875 45.455 15.69 0.00 0.00 2.77
1734 2035 2.741228 GCTGTGCACCCATGTTTTCAAA 60.741 45.455 15.69 0.00 0.00 2.69
1740 2041 2.985282 CGGCTGTGCACCCATGTT 60.985 61.111 15.69 0.00 0.00 2.71
1742 2043 4.720902 TCCGGCTGTGCACCCATG 62.721 66.667 15.69 3.52 0.00 3.66
1743 2044 3.965258 TTCCGGCTGTGCACCCAT 61.965 61.111 15.69 0.00 0.00 4.00
1744 2045 4.947147 GTTCCGGCTGTGCACCCA 62.947 66.667 15.69 0.00 0.00 4.51
1746 2047 2.672996 ATGTTCCGGCTGTGCACC 60.673 61.111 15.69 0.00 0.00 5.01
1748 2049 2.741985 CGATGTTCCGGCTGTGCA 60.742 61.111 0.00 0.00 0.00 4.57
1773 2087 0.037590 TTCTTGCATTGCCCCGTACT 59.962 50.000 6.12 0.00 0.00 2.73
1783 2097 2.170166 TCTGGCCGAAATTCTTGCATT 58.830 42.857 0.00 0.00 0.00 3.56
1794 2108 2.192664 TGTAAGCAAATCTGGCCGAA 57.807 45.000 0.00 0.00 0.00 4.30
1807 2141 4.629634 GCATAATTGGGTGGTTTTGTAAGC 59.370 41.667 0.00 0.00 0.00 3.09
1819 2153 5.690865 TCCTTTTATCTCGCATAATTGGGT 58.309 37.500 0.00 0.00 37.12 4.51
1843 2177 9.230122 CCATGTTTTCAAAAGCCCTTTAATTAT 57.770 29.630 0.00 0.00 31.63 1.28
1844 2178 7.663493 CCCATGTTTTCAAAAGCCCTTTAATTA 59.337 33.333 0.00 0.00 31.63 1.40
1855 2189 4.555116 GCAATGCACCCATGTTTTCAAAAG 60.555 41.667 0.00 0.00 0.00 2.27
1938 2295 5.460646 CGACATACAAAATTCAAGCACCTT 58.539 37.500 0.00 0.00 0.00 3.50
1949 2306 6.599244 ACAGATGACATTCCGACATACAAAAT 59.401 34.615 0.00 0.00 29.73 1.82
1954 2311 3.804325 CCACAGATGACATTCCGACATAC 59.196 47.826 0.00 0.00 29.73 2.39
1960 2317 1.208052 AGGTCCACAGATGACATTCCG 59.792 52.381 0.00 0.00 34.36 4.30
1967 2324 2.046292 TGTCACAAGGTCCACAGATGA 58.954 47.619 0.00 0.00 0.00 2.92
2007 2364 4.441792 ACAAAATGAGTGCCCAAAAGTTC 58.558 39.130 0.00 0.00 0.00 3.01
2016 2373 5.353956 ACAAAAGGAAAACAAAATGAGTGCC 59.646 36.000 0.00 0.00 0.00 5.01
2034 2391 0.401738 TGAGGGGCTCCTGACAAAAG 59.598 55.000 11.93 0.00 45.05 2.27
2055 2412 5.388786 GCAAAATTTGAAGGCGAAATGAGAC 60.389 40.000 10.26 0.00 0.00 3.36
2097 2459 8.366401 TGAAACTTATTGGATTTGAAGATGCAA 58.634 29.630 0.00 0.00 40.79 4.08
2144 2510 3.136260 ACCCATGGTGAACAGCAAAATTT 59.864 39.130 11.73 0.00 42.53 1.82
2145 2511 2.705127 ACCCATGGTGAACAGCAAAATT 59.295 40.909 11.73 0.00 42.53 1.82
2159 2525 1.078988 GGTTGCATTGCACCCATGG 60.079 57.895 19.28 4.14 40.91 3.66
2210 2576 5.876357 AGAACTCCAGTTTATTGCCTGTTA 58.124 37.500 0.00 0.00 38.56 2.41
2241 2608 4.414337 AGAGAGATGAGGTTGCCATAAC 57.586 45.455 0.00 0.00 0.00 1.89
2259 2626 8.723942 ATAATGTGCAAAGTAGGTCTTAAGAG 57.276 34.615 5.12 0.00 35.02 2.85
2294 2692 7.924412 TGAATCCTAATTCATGAACTACGGTAC 59.076 37.037 11.07 1.34 44.94 3.34
2372 2770 7.338710 TGATAAATTAACCTGACTAGCAAGCT 58.661 34.615 0.00 0.00 0.00 3.74
2408 2806 8.458052 CACTAACCTAGATATCTACATCAGCTG 58.542 40.741 7.63 7.63 0.00 4.24


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

AutoCloner maintained by Alex Coulton.