Multiple sequence alignment - TraesCS6A01G321100

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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 TraesCS6A01G321100 chr6A 100.000 2291 0 0 1 2291 555672434 555674724 0.000000e+00 4231
1 TraesCS6A01G321100 chr6B 90.334 1407 69 26 472 1867 617127917 617129267 0.000000e+00 1783
2 TraesCS6A01G321100 chr6B 86.933 375 32 9 1927 2290 617129258 617129626 2.740000e-109 405
3 TraesCS6A01G321100 chr6B 86.316 285 5 12 138 411 617127630 617127891 1.730000e-71 279
4 TraesCS6A01G321100 chr6D 89.531 1385 83 29 472 1842 410174985 410176321 0.000000e+00 1698
5 TraesCS6A01G321100 chr6D 86.102 295 27 5 1930 2210 410176339 410176633 2.860000e-79 305
6 TraesCS6A01G321100 chr6D 79.825 456 43 21 3 411 410174502 410174955 1.040000e-73 287
7 TraesCS6A01G321100 chr6D 82.573 241 23 5 2057 2291 410220204 410220431 6.460000e-46 195


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 TraesCS6A01G321100 chr6A 555672434 555674724 2290 False 4231.000000 4231 100.000000 1 2291 1 chr6A.!!$F1 2290
1 TraesCS6A01G321100 chr6B 617127630 617129626 1996 False 822.333333 1783 87.861000 138 2290 3 chr6B.!!$F1 2152
2 TraesCS6A01G321100 chr6D 410174502 410176633 2131 False 763.333333 1698 85.152667 3 2210 3 chr6D.!!$F2 2207

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
200 216 0.030773 GACAGCTGACGTCACAGTGA 59.969 55.0 23.35 0.0 39.73 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1333 1412 0.038159 GATGGATGGACCGATCGGAC 60.038 60.0 39.55 32.26 42.61 4.79 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
26 27 0.670546 CATCCTCGCCGAACACAACT 60.671 55.000 0.00 0.00 0.00 3.16
32 33 2.930040 CTCGCCGAACACAACTTATCAT 59.070 45.455 0.00 0.00 0.00 2.45
39 40 6.129194 GCCGAACACAACTTATCATGAAAAAC 60.129 38.462 0.00 0.00 0.00 2.43
40 41 6.915300 CCGAACACAACTTATCATGAAAAACA 59.085 34.615 0.00 0.00 0.00 2.83
53 55 6.969366 TCATGAAAAACACTCGATTTGTCAT 58.031 32.000 9.04 9.04 42.31 3.06
57 59 1.453155 ACACTCGATTTGTCATGCCC 58.547 50.000 0.00 0.00 0.00 5.36
60 62 2.086869 ACTCGATTTGTCATGCCCAAG 58.913 47.619 0.00 0.00 0.00 3.61
68 70 2.995283 TGTCATGCCCAAGAATCTGAG 58.005 47.619 0.00 0.00 0.00 3.35
74 76 1.066143 GCCCAAGAATCTGAGGTTCGA 60.066 52.381 0.00 0.00 0.00 3.71
84 86 6.865726 AGAATCTGAGGTTCGATGAATATTCG 59.134 38.462 10.80 0.00 37.94 3.34
85 87 4.871513 TCTGAGGTTCGATGAATATTCGG 58.128 43.478 10.80 3.22 37.22 4.30
88 90 3.728845 AGGTTCGATGAATATTCGGGTG 58.271 45.455 10.80 1.40 37.22 4.61
97 99 4.839121 TGAATATTCGGGTGCTTACAACT 58.161 39.130 10.80 0.00 32.44 3.16
101 103 2.623878 TCGGGTGCTTACAACTGAAA 57.376 45.000 0.00 0.00 46.07 2.69
102 104 2.920524 TCGGGTGCTTACAACTGAAAA 58.079 42.857 0.00 0.00 46.07 2.29
104 106 4.643463 TCGGGTGCTTACAACTGAAAATA 58.357 39.130 0.00 0.00 46.07 1.40
105 107 5.250200 TCGGGTGCTTACAACTGAAAATAT 58.750 37.500 0.00 0.00 46.07 1.28
107 109 6.027749 CGGGTGCTTACAACTGAAAATATTC 58.972 40.000 0.00 0.00 43.07 1.75
108 110 6.348950 CGGGTGCTTACAACTGAAAATATTCA 60.349 38.462 0.00 0.00 43.07 2.57
113 117 7.594758 TGCTTACAACTGAAAATATTCACAAGC 59.405 33.333 0.00 0.00 40.59 4.01
125 129 2.569259 CACAAGCAGTGCACGTTTG 58.431 52.632 24.74 24.74 42.15 2.93
126 130 0.866906 CACAAGCAGTGCACGTTTGG 60.867 55.000 27.46 18.52 42.15 3.28
127 131 1.029408 ACAAGCAGTGCACGTTTGGA 61.029 50.000 27.46 0.00 0.00 3.53
128 132 0.100325 CAAGCAGTGCACGTTTGGAA 59.900 50.000 19.20 0.00 0.00 3.53
129 133 0.814457 AAGCAGTGCACGTTTGGAAA 59.186 45.000 19.20 0.00 0.00 3.13
130 134 0.814457 AGCAGTGCACGTTTGGAAAA 59.186 45.000 19.20 0.00 0.00 2.29
153 169 1.551883 GAATTGCCTTGGATTGCCAGT 59.448 47.619 0.00 0.00 46.91 4.00
179 195 2.432972 GCTGGTTTGGCAATGGCG 60.433 61.111 0.00 0.00 42.47 5.69
200 216 0.030773 GACAGCTGACGTCACAGTGA 59.969 55.000 23.35 0.00 39.73 3.41
305 332 1.664151 GGCTAAGCATTGACCGTACAC 59.336 52.381 0.00 0.00 0.00 2.90
366 413 5.414789 TTGAACGAAGTCCCATCTTATCA 57.585 39.130 0.00 0.00 45.00 2.15
373 420 6.432783 ACGAAGTCCCATCTTATCATCTAGAG 59.567 42.308 0.00 0.00 29.74 2.43
376 428 5.943416 AGTCCCATCTTATCATCTAGAGACG 59.057 44.000 0.00 0.00 0.00 4.18
407 459 3.006859 TGATCAAGTTGGTCACGACTGAT 59.993 43.478 14.95 0.00 40.52 2.90
408 460 3.026630 TCAAGTTGGTCACGACTGATC 57.973 47.619 2.34 0.00 40.52 2.92
410 462 3.130633 CAAGTTGGTCACGACTGATCAA 58.869 45.455 0.00 0.00 43.93 2.57
411 463 3.032017 AGTTGGTCACGACTGATCAAG 57.968 47.619 2.19 0.00 46.21 3.02
413 465 2.731976 GTTGGTCACGACTGATCAAGTC 59.268 50.000 2.19 12.59 46.21 3.01
434 500 1.604593 GGCTGGTGTGTCATTGCCT 60.605 57.895 0.00 0.00 37.58 4.75
435 501 1.589716 GGCTGGTGTGTCATTGCCTC 61.590 60.000 0.00 0.00 37.58 4.70
436 502 0.890542 GCTGGTGTGTCATTGCCTCA 60.891 55.000 0.00 0.00 0.00 3.86
437 503 1.830279 CTGGTGTGTCATTGCCTCAT 58.170 50.000 0.00 0.00 0.00 2.90
438 504 1.471287 CTGGTGTGTCATTGCCTCATG 59.529 52.381 0.00 0.00 0.00 3.07
439 505 1.073603 TGGTGTGTCATTGCCTCATGA 59.926 47.619 0.00 0.00 0.00 3.07
440 506 1.741706 GGTGTGTCATTGCCTCATGAG 59.258 52.381 16.24 16.24 0.00 2.90
441 507 2.430465 GTGTGTCATTGCCTCATGAGT 58.570 47.619 21.11 0.00 0.00 3.41
442 508 2.816087 GTGTGTCATTGCCTCATGAGTT 59.184 45.455 21.11 0.74 0.00 3.01
443 509 3.076621 TGTGTCATTGCCTCATGAGTTC 58.923 45.455 21.11 12.71 0.00 3.01
444 510 3.244665 TGTGTCATTGCCTCATGAGTTCT 60.245 43.478 21.11 0.55 0.00 3.01
445 511 3.755378 GTGTCATTGCCTCATGAGTTCTT 59.245 43.478 21.11 1.09 0.00 2.52
446 512 4.217118 GTGTCATTGCCTCATGAGTTCTTT 59.783 41.667 21.11 0.00 0.00 2.52
447 513 4.828939 TGTCATTGCCTCATGAGTTCTTTT 59.171 37.500 21.11 0.00 0.00 2.27
448 514 5.302568 TGTCATTGCCTCATGAGTTCTTTTT 59.697 36.000 21.11 0.00 0.00 1.94
480 546 2.435418 TTTTTGCGGGTGATTGCCT 58.565 47.368 0.00 0.00 0.00 4.75
502 568 5.413833 CCTCATGAGTTCAACACTATTGCTT 59.586 40.000 21.11 0.00 35.01 3.91
545 611 3.054728 TCCGTTTTGCTATCTGGAATGGA 60.055 43.478 0.00 0.00 0.00 3.41
546 612 3.694072 CCGTTTTGCTATCTGGAATGGAA 59.306 43.478 0.00 0.00 0.00 3.53
547 613 4.339247 CCGTTTTGCTATCTGGAATGGAAT 59.661 41.667 0.00 0.00 0.00 3.01
548 614 5.276270 CGTTTTGCTATCTGGAATGGAATG 58.724 41.667 0.00 0.00 0.00 2.67
549 615 5.594926 GTTTTGCTATCTGGAATGGAATGG 58.405 41.667 0.00 0.00 0.00 3.16
554 620 2.806945 TCTGGAATGGAATGGACCAC 57.193 50.000 0.00 0.00 43.03 4.16
627 706 1.467374 GCGTCCGCAGCAAAAATGTAT 60.467 47.619 6.82 0.00 41.49 2.29
628 707 2.176369 CGTCCGCAGCAAAAATGTATG 58.824 47.619 0.00 0.00 0.00 2.39
629 708 2.414029 CGTCCGCAGCAAAAATGTATGT 60.414 45.455 0.00 0.00 0.00 2.29
630 709 2.916716 GTCCGCAGCAAAAATGTATGTG 59.083 45.455 0.00 0.00 0.00 3.21
631 710 1.655099 CCGCAGCAAAAATGTATGTGC 59.345 47.619 0.00 0.00 37.26 4.57
632 711 2.326664 CGCAGCAAAAATGTATGTGCA 58.673 42.857 0.00 0.00 39.50 4.57
896 975 5.336849 GCCATGGATCTCGGGTATATATAGC 60.337 48.000 18.40 12.61 0.00 2.97
898 977 6.151985 CCATGGATCTCGGGTATATATAGCTC 59.848 46.154 18.77 9.77 0.00 4.09
951 1030 1.131504 GTACGCACTCTCTGTCTGAGG 59.868 57.143 6.87 1.38 42.86 3.86
959 1038 1.620819 TCTCTGTCTGAGGGAGCAAAC 59.379 52.381 6.87 0.00 42.86 2.93
963 1042 1.425066 TGTCTGAGGGAGCAAACCATT 59.575 47.619 0.00 0.00 0.00 3.16
964 1043 1.815003 GTCTGAGGGAGCAAACCATTG 59.185 52.381 0.00 0.00 39.65 2.82
965 1044 1.425066 TCTGAGGGAGCAAACCATTGT 59.575 47.619 0.00 0.00 38.85 2.71
967 1046 2.749621 CTGAGGGAGCAAACCATTGTAC 59.250 50.000 0.00 0.00 38.85 2.90
968 1047 1.737793 GAGGGAGCAAACCATTGTACG 59.262 52.381 0.00 0.00 38.85 3.67
969 1048 0.170339 GGGAGCAAACCATTGTACGC 59.830 55.000 0.00 0.00 38.85 4.42
970 1049 0.878416 GGAGCAAACCATTGTACGCA 59.122 50.000 0.00 0.00 38.85 5.24
971 1050 1.401018 GGAGCAAACCATTGTACGCAC 60.401 52.381 0.00 0.00 38.85 5.34
972 1051 1.265635 GAGCAAACCATTGTACGCACA 59.734 47.619 0.00 0.00 38.85 4.57
973 1052 1.266718 AGCAAACCATTGTACGCACAG 59.733 47.619 0.00 0.00 38.85 3.66
974 1053 1.265635 GCAAACCATTGTACGCACAGA 59.734 47.619 0.00 0.00 38.85 3.41
975 1054 2.665519 GCAAACCATTGTACGCACAGAG 60.666 50.000 0.00 0.00 38.85 3.35
976 1055 2.805671 CAAACCATTGTACGCACAGAGA 59.194 45.455 0.00 0.00 35.67 3.10
977 1056 2.370281 ACCATTGTACGCACAGAGAG 57.630 50.000 0.00 0.00 35.67 3.20
978 1057 1.893137 ACCATTGTACGCACAGAGAGA 59.107 47.619 0.00 0.00 35.67 3.10
979 1058 2.299013 ACCATTGTACGCACAGAGAGAA 59.701 45.455 0.00 0.00 35.67 2.87
980 1059 3.244078 ACCATTGTACGCACAGAGAGAAA 60.244 43.478 0.00 0.00 35.67 2.52
981 1060 3.369147 CCATTGTACGCACAGAGAGAAAG 59.631 47.826 0.00 0.00 35.67 2.62
982 1061 4.237724 CATTGTACGCACAGAGAGAAAGA 58.762 43.478 0.00 0.00 35.67 2.52
983 1062 4.316205 TTGTACGCACAGAGAGAAAGAA 57.684 40.909 0.00 0.00 35.67 2.52
984 1063 4.316205 TGTACGCACAGAGAGAAAGAAA 57.684 40.909 0.00 0.00 0.00 2.52
985 1064 4.299155 TGTACGCACAGAGAGAAAGAAAG 58.701 43.478 0.00 0.00 0.00 2.62
986 1065 2.760374 ACGCACAGAGAGAAAGAAAGG 58.240 47.619 0.00 0.00 0.00 3.11
1293 1372 4.253257 GACCTCGACGCCTAGCCG 62.253 72.222 0.00 0.00 0.00 5.52
1295 1374 2.898840 CCTCGACGCCTAGCCGTA 60.899 66.667 0.00 0.00 42.24 4.02
1296 1375 2.632541 CTCGACGCCTAGCCGTAG 59.367 66.667 0.00 0.00 42.24 3.51
1297 1376 3.524330 CTCGACGCCTAGCCGTAGC 62.524 68.421 0.00 0.00 42.24 3.58
1301 1380 4.286320 CGCCTAGCCGTAGCCTGG 62.286 72.222 0.00 0.00 41.25 4.45
1303 1382 1.831286 GCCTAGCCGTAGCCTGGTA 60.831 63.158 0.00 0.00 41.25 3.25
1304 1383 2.039509 CCTAGCCGTAGCCTGGTAC 58.960 63.158 0.00 0.00 41.25 3.34
1305 1384 0.467659 CCTAGCCGTAGCCTGGTACT 60.468 60.000 5.13 0.00 41.25 2.73
1306 1385 1.202855 CCTAGCCGTAGCCTGGTACTA 60.203 57.143 5.13 0.00 41.25 1.82
1307 1386 2.152830 CTAGCCGTAGCCTGGTACTAG 58.847 57.143 0.00 0.00 41.25 2.57
1308 1387 1.108132 AGCCGTAGCCTGGTACTAGC 61.108 60.000 0.00 7.39 41.25 3.42
1333 1412 2.106166 AGCAGCCTCCCAATAATCTCTG 59.894 50.000 0.00 0.00 0.00 3.35
1349 1428 1.107538 TCTGTCCGATCGGTCCATCC 61.108 60.000 32.15 14.90 36.47 3.51
1350 1429 1.380650 TGTCCGATCGGTCCATCCA 60.381 57.895 32.15 17.04 36.47 3.41
1351 1430 0.759060 TGTCCGATCGGTCCATCCAT 60.759 55.000 32.15 0.00 36.47 3.41
1352 1431 0.038159 GTCCGATCGGTCCATCCATC 60.038 60.000 32.15 9.85 36.47 3.51
1479 1568 0.318441 TGTGTGTGCTACTGGCTCTC 59.682 55.000 0.00 0.00 42.39 3.20
1510 1599 4.920376 TCTTTTTGTTCTTTCCTGCTTCG 58.080 39.130 0.00 0.00 0.00 3.79
1521 1610 1.691976 TCCTGCTTCGGAAGTTCAGAA 59.308 47.619 20.28 16.14 0.00 3.02
1581 1675 2.606725 GCATCTTCAGTGATCAGAACCG 59.393 50.000 0.00 0.00 0.00 4.44
1589 1683 5.977635 TCAGTGATCAGAACCGTATGATTT 58.022 37.500 0.00 0.00 35.82 2.17
1593 1687 5.463724 GTGATCAGAACCGTATGATTTCTCC 59.536 44.000 0.00 0.00 35.82 3.71
1628 1722 4.395854 TGGTCTGTGTGTGAATAATGATGC 59.604 41.667 0.00 0.00 0.00 3.91
1643 1737 1.344438 TGATGCTTGGAGACGTTGTCT 59.656 47.619 0.00 0.00 46.42 3.41
1703 1800 2.762535 TAAGCACCAACAGCTCCTAC 57.237 50.000 0.00 0.00 42.53 3.18
1725 1822 2.432456 TGCACAGCGACGGACATC 60.432 61.111 0.00 0.00 0.00 3.06
1726 1823 3.545481 GCACAGCGACGGACATCG 61.545 66.667 0.00 0.00 45.09 3.84
1763 1860 6.074356 GCACACAACTTGATAACATGGTTTTC 60.074 38.462 0.00 0.00 0.00 2.29
1764 1861 7.202526 CACACAACTTGATAACATGGTTTTCT 58.797 34.615 0.00 0.00 0.00 2.52
1765 1862 7.167968 CACACAACTTGATAACATGGTTTTCTG 59.832 37.037 0.00 0.00 0.00 3.02
1766 1863 7.147915 ACACAACTTGATAACATGGTTTTCTGT 60.148 33.333 0.00 0.00 0.00 3.41
1767 1864 7.706179 CACAACTTGATAACATGGTTTTCTGTT 59.294 33.333 0.00 0.00 38.95 3.16
1831 1932 8.785101 CAACCGAACAAAATATATCAAAACGAG 58.215 33.333 0.00 0.00 0.00 4.18
1852 1954 2.552315 GGAACTGAAAATGGCTGTTCGA 59.448 45.455 0.00 0.00 41.93 3.71
1869 1971 6.677781 TGTTCGAAAAACAGAGAGTTCATT 57.322 33.333 0.00 0.00 40.26 2.57
1870 1972 7.083875 TGTTCGAAAAACAGAGAGTTCATTT 57.916 32.000 0.00 0.00 40.26 2.32
1871 1973 7.535139 TGTTCGAAAAACAGAGAGTTCATTTT 58.465 30.769 0.00 0.00 40.26 1.82
1872 1974 8.026607 TGTTCGAAAAACAGAGAGTTCATTTTT 58.973 29.630 0.00 0.00 40.26 1.94
1899 2001 3.485764 GGGGGCAGAGAGTTCATTC 57.514 57.895 0.00 0.00 0.00 2.67
1900 2002 0.620556 GGGGGCAGAGAGTTCATTCA 59.379 55.000 0.00 0.00 0.00 2.57
1901 2003 1.680249 GGGGGCAGAGAGTTCATTCAC 60.680 57.143 0.00 0.00 0.00 3.18
1902 2004 1.003580 GGGGCAGAGAGTTCATTCACA 59.996 52.381 0.00 0.00 0.00 3.58
1903 2005 2.079925 GGGCAGAGAGTTCATTCACAC 58.920 52.381 0.00 0.00 0.00 3.82
1904 2006 2.550855 GGGCAGAGAGTTCATTCACACA 60.551 50.000 0.00 0.00 0.00 3.72
1905 2007 3.341823 GGCAGAGAGTTCATTCACACAT 58.658 45.455 0.00 0.00 0.00 3.21
1906 2008 4.507710 GGCAGAGAGTTCATTCACACATA 58.492 43.478 0.00 0.00 0.00 2.29
1907 2009 4.331168 GGCAGAGAGTTCATTCACACATAC 59.669 45.833 0.00 0.00 0.00 2.39
1908 2010 4.931601 GCAGAGAGTTCATTCACACATACA 59.068 41.667 0.00 0.00 0.00 2.29
1909 2011 5.163913 GCAGAGAGTTCATTCACACATACAC 60.164 44.000 0.00 0.00 0.00 2.90
1910 2012 5.928264 CAGAGAGTTCATTCACACATACACA 59.072 40.000 0.00 0.00 0.00 3.72
1911 2013 5.928839 AGAGAGTTCATTCACACATACACAC 59.071 40.000 0.00 0.00 0.00 3.82
1912 2014 4.997395 AGAGTTCATTCACACATACACACC 59.003 41.667 0.00 0.00 0.00 4.16
1913 2015 4.713553 AGTTCATTCACACATACACACCA 58.286 39.130 0.00 0.00 0.00 4.17
1914 2016 5.129634 AGTTCATTCACACATACACACCAA 58.870 37.500 0.00 0.00 0.00 3.67
1915 2017 5.592282 AGTTCATTCACACATACACACCAAA 59.408 36.000 0.00 0.00 0.00 3.28
1916 2018 6.096141 AGTTCATTCACACATACACACCAAAA 59.904 34.615 0.00 0.00 0.00 2.44
1917 2019 6.456795 TCATTCACACATACACACCAAAAA 57.543 33.333 0.00 0.00 0.00 1.94
1950 2052 7.013274 CCCAGAGAGTTCAGATAAAACACAAAA 59.987 37.037 0.00 0.00 0.00 2.44
1981 2084 4.297299 AGTCGTTCGAAACTGTCAACTA 57.703 40.909 0.00 0.00 0.00 2.24
1992 2095 6.237942 CGAAACTGTCAACTATAGCTCCATTG 60.238 42.308 0.00 0.00 0.00 2.82
2047 2150 6.153340 ACAAAACCTATGCACTATGCTCAAAT 59.847 34.615 2.02 0.00 45.31 2.32
2052 2155 7.879070 ACCTATGCACTATGCTCAAATATTTG 58.121 34.615 20.13 20.13 45.31 2.32
2138 2255 2.625737 CCTAGCAAGGTCACATGTCTG 58.374 52.381 0.00 0.00 38.19 3.51
2213 2335 3.064271 GTGTAGCCGTGAGAACAACAAAA 59.936 43.478 0.00 0.00 0.00 2.44
2214 2336 3.880490 TGTAGCCGTGAGAACAACAAAAT 59.120 39.130 0.00 0.00 0.00 1.82
2222 2344 7.572353 GCCGTGAGAACAACAAAATATACTTGA 60.572 37.037 4.83 0.00 0.00 3.02
2238 2360 3.861840 ACTTGACACTAACCCGATCATG 58.138 45.455 0.00 0.00 0.00 3.07
2249 2371 2.592861 GATCATGGGCAGTCCGGC 60.593 66.667 0.00 0.00 38.76 6.13
2284 2406 0.755327 ACCAGGCCGTGCTTCTTTTT 60.755 50.000 0.00 0.00 0.00 1.94
2290 2412 1.664302 GCCGTGCTTCTTTTTCAGCTC 60.664 52.381 0.00 0.00 36.92 4.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.845580 CGGCGAGGATGGCAAGCT 62.846 66.667 0.00 0.00 43.90 3.74
1 2 4.838152 TCGGCGAGGATGGCAAGC 62.838 66.667 4.99 0.00 43.90 4.01
6 7 1.375396 TTGTGTTCGGCGAGGATGG 60.375 57.895 10.46 0.00 0.00 3.51
15 16 6.915300 TGTTTTTCATGATAAGTTGTGTTCGG 59.085 34.615 0.00 0.00 0.00 4.30
16 17 7.643764 AGTGTTTTTCATGATAAGTTGTGTTCG 59.356 33.333 0.00 0.00 0.00 3.95
26 27 8.563732 TGACAAATCGAGTGTTTTTCATGATAA 58.436 29.630 0.00 0.00 0.00 1.75
32 33 4.975502 GCATGACAAATCGAGTGTTTTTCA 59.024 37.500 0.00 4.07 0.00 2.69
39 40 1.452110 TGGGCATGACAAATCGAGTG 58.548 50.000 0.00 0.00 0.00 3.51
40 41 2.086869 CTTGGGCATGACAAATCGAGT 58.913 47.619 0.00 0.00 0.00 4.18
53 55 1.339055 CGAACCTCAGATTCTTGGGCA 60.339 52.381 7.23 0.00 0.00 5.36
57 59 7.959689 ATATTCATCGAACCTCAGATTCTTG 57.040 36.000 0.00 0.00 0.00 3.02
60 62 6.090088 CCGAATATTCATCGAACCTCAGATTC 59.910 42.308 15.57 0.00 42.76 2.52
68 70 2.223377 GCACCCGAATATTCATCGAACC 59.777 50.000 15.57 0.00 42.76 3.62
74 76 5.296780 CAGTTGTAAGCACCCGAATATTCAT 59.703 40.000 15.57 0.00 0.00 2.57
84 86 6.806739 GTGAATATTTTCAGTTGTAAGCACCC 59.193 38.462 0.00 0.00 42.41 4.61
85 87 7.367285 TGTGAATATTTTCAGTTGTAAGCACC 58.633 34.615 0.00 0.00 42.41 5.01
88 90 7.594758 TGCTTGTGAATATTTTCAGTTGTAAGC 59.405 33.333 16.02 16.02 42.41 3.09
108 110 1.029408 TCCAAACGTGCACTGCTTGT 61.029 50.000 16.19 1.41 0.00 3.16
128 132 4.074259 GGCAATCCAAGGCAATTCTTTTT 58.926 39.130 0.00 0.00 0.00 1.94
129 133 3.072768 TGGCAATCCAAGGCAATTCTTTT 59.927 39.130 0.00 0.00 39.99 2.27
130 134 2.638855 TGGCAATCCAAGGCAATTCTTT 59.361 40.909 0.00 0.00 39.99 2.52
132 136 1.829222 CTGGCAATCCAAGGCAATTCT 59.171 47.619 0.00 0.00 42.91 2.40
133 137 1.551883 ACTGGCAATCCAAGGCAATTC 59.448 47.619 0.00 0.00 42.91 2.17
134 138 1.276989 CACTGGCAATCCAAGGCAATT 59.723 47.619 0.00 0.00 42.91 2.32
135 139 0.899720 CACTGGCAATCCAAGGCAAT 59.100 50.000 0.00 0.00 42.91 3.56
136 140 1.186917 CCACTGGCAATCCAAGGCAA 61.187 55.000 0.00 0.00 42.91 4.52
137 141 1.607178 CCACTGGCAATCCAAGGCA 60.607 57.895 0.00 0.00 42.91 4.75
138 142 3.291611 CCACTGGCAATCCAAGGC 58.708 61.111 0.00 0.00 42.91 4.35
170 186 2.437359 AGCTGTCTCGCCATTGCC 60.437 61.111 0.00 0.00 0.00 4.52
179 195 0.312416 ACTGTGACGTCAGCTGTCTC 59.688 55.000 20.73 5.76 38.84 3.36
305 332 1.071605 CTTCCTTCCGAGAAGCAACG 58.928 55.000 7.82 0.00 34.77 4.10
366 413 3.826524 TCAGCATTCTCCGTCTCTAGAT 58.173 45.455 0.00 0.00 0.00 1.98
373 420 2.898705 ACTTGATCAGCATTCTCCGTC 58.101 47.619 0.00 0.00 0.00 4.79
376 428 3.350833 ACCAACTTGATCAGCATTCTCC 58.649 45.455 0.00 0.00 0.00 3.71
407 459 1.344953 ACACACCAGCCAGGACTTGA 61.345 55.000 0.00 0.00 41.22 3.02
408 460 0.886490 GACACACCAGCCAGGACTTG 60.886 60.000 0.00 0.00 41.22 3.16
410 462 1.130054 ATGACACACCAGCCAGGACT 61.130 55.000 0.00 0.00 41.22 3.85
411 463 0.250901 AATGACACACCAGCCAGGAC 60.251 55.000 0.00 0.00 41.22 3.85
413 465 1.870055 GCAATGACACACCAGCCAGG 61.870 60.000 0.00 0.00 45.67 4.45
414 466 1.582968 GCAATGACACACCAGCCAG 59.417 57.895 0.00 0.00 0.00 4.85
416 468 1.589716 GAGGCAATGACACACCAGCC 61.590 60.000 0.00 0.00 42.31 4.85
417 469 0.890542 TGAGGCAATGACACACCAGC 60.891 55.000 0.00 0.00 0.00 4.85
462 528 0.316841 GAGGCAATCACCCGCAAAAA 59.683 50.000 0.00 0.00 0.00 1.94
463 529 0.825425 TGAGGCAATCACCCGCAAAA 60.825 50.000 0.00 0.00 31.12 2.44
464 530 0.611618 ATGAGGCAATCACCCGCAAA 60.612 50.000 0.00 0.00 41.91 3.68
465 531 1.001020 ATGAGGCAATCACCCGCAA 60.001 52.632 0.00 0.00 41.91 4.85
466 532 1.750018 CATGAGGCAATCACCCGCA 60.750 57.895 0.00 0.00 41.91 5.69
467 533 1.442526 CTCATGAGGCAATCACCCGC 61.443 60.000 15.38 0.00 41.91 6.13
468 534 0.107508 ACTCATGAGGCAATCACCCG 60.108 55.000 26.08 0.00 41.91 5.28
469 535 2.019984 GAACTCATGAGGCAATCACCC 58.980 52.381 26.08 1.57 41.91 4.61
470 536 2.715046 TGAACTCATGAGGCAATCACC 58.285 47.619 26.08 6.79 41.91 4.02
471 537 3.503363 TGTTGAACTCATGAGGCAATCAC 59.497 43.478 25.97 18.47 41.91 3.06
472 538 3.503363 GTGTTGAACTCATGAGGCAATCA 59.497 43.478 25.97 22.28 43.70 2.57
473 539 3.755378 AGTGTTGAACTCATGAGGCAATC 59.245 43.478 25.97 21.95 31.64 2.67
474 540 3.759581 AGTGTTGAACTCATGAGGCAAT 58.240 40.909 25.97 14.69 31.64 3.56
475 541 3.213206 AGTGTTGAACTCATGAGGCAA 57.787 42.857 26.08 23.73 31.64 4.52
476 542 2.936919 AGTGTTGAACTCATGAGGCA 57.063 45.000 26.08 19.73 31.64 4.75
477 543 4.437930 GCAATAGTGTTGAACTCATGAGGC 60.438 45.833 26.08 17.48 40.56 4.70
478 544 4.940046 AGCAATAGTGTTGAACTCATGAGG 59.060 41.667 26.08 8.94 40.56 3.86
479 545 6.312487 CAAGCAATAGTGTTGAACTCATGAG 58.688 40.000 21.37 21.37 40.56 2.90
480 546 5.181811 CCAAGCAATAGTGTTGAACTCATGA 59.818 40.000 3.47 0.00 40.56 3.07
502 568 4.651503 GGATCAAGAGAGATTAGTCCACCA 59.348 45.833 0.00 0.00 0.00 4.17
545 611 0.249489 GATCGCTAGCGTGGTCCATT 60.249 55.000 34.10 11.66 40.74 3.16
546 612 1.364171 GATCGCTAGCGTGGTCCAT 59.636 57.895 34.10 20.45 40.74 3.41
547 613 2.805546 GATCGCTAGCGTGGTCCA 59.194 61.111 34.10 16.43 40.74 4.02
548 614 2.353607 CGATCGCTAGCGTGGTCC 60.354 66.667 34.10 18.59 40.74 4.46
549 615 2.353607 CCGATCGCTAGCGTGGTC 60.354 66.667 34.10 26.61 40.74 4.02
554 620 4.569023 TGTGCCCGATCGCTAGCG 62.569 66.667 30.91 30.91 41.35 4.26
627 706 0.817229 TGACTTCAACGGCATGCACA 60.817 50.000 21.36 2.29 0.00 4.57
628 707 0.310543 TTGACTTCAACGGCATGCAC 59.689 50.000 21.36 8.08 0.00 4.57
629 708 1.001487 CTTTGACTTCAACGGCATGCA 60.001 47.619 21.36 0.00 35.28 3.96
630 709 1.666888 CCTTTGACTTCAACGGCATGC 60.667 52.381 9.90 9.90 38.23 4.06
631 710 2.336554 CCTTTGACTTCAACGGCATG 57.663 50.000 1.85 0.00 38.23 4.06
694 773 1.968540 GGCAGCCTGGTGACTTCAC 60.969 63.158 3.29 0.34 45.72 3.18
794 873 0.519519 TTTGATGCGTTGTTAGGCGG 59.480 50.000 0.00 0.00 37.97 6.13
925 1004 1.328439 CAGAGAGTGCGTACGTGTTC 58.672 55.000 17.90 11.43 0.00 3.18
951 1030 0.878416 TGCGTACAATGGTTTGCTCC 59.122 50.000 0.00 0.00 36.22 4.70
959 1038 2.654749 TCTCTCTGTGCGTACAATGG 57.345 50.000 7.96 1.07 36.14 3.16
963 1042 4.299155 CTTTCTTTCTCTCTGTGCGTACA 58.701 43.478 6.10 6.10 35.08 2.90
964 1043 3.675698 CCTTTCTTTCTCTCTGTGCGTAC 59.324 47.826 0.00 0.00 0.00 3.67
965 1044 3.572682 TCCTTTCTTTCTCTCTGTGCGTA 59.427 43.478 0.00 0.00 0.00 4.42
967 1046 3.032017 TCCTTTCTTTCTCTCTGTGCG 57.968 47.619 0.00 0.00 0.00 5.34
968 1047 4.636249 TCTTCCTTTCTTTCTCTCTGTGC 58.364 43.478 0.00 0.00 0.00 4.57
969 1048 5.576384 CGATCTTCCTTTCTTTCTCTCTGTG 59.424 44.000 0.00 0.00 0.00 3.66
970 1049 5.478679 TCGATCTTCCTTTCTTTCTCTCTGT 59.521 40.000 0.00 0.00 0.00 3.41
971 1050 5.960113 TCGATCTTCCTTTCTTTCTCTCTG 58.040 41.667 0.00 0.00 0.00 3.35
972 1051 5.127031 CCTCGATCTTCCTTTCTTTCTCTCT 59.873 44.000 0.00 0.00 0.00 3.10
973 1052 5.126384 TCCTCGATCTTCCTTTCTTTCTCTC 59.874 44.000 0.00 0.00 0.00 3.20
974 1053 5.020132 TCCTCGATCTTCCTTTCTTTCTCT 58.980 41.667 0.00 0.00 0.00 3.10
975 1054 5.331876 TCCTCGATCTTCCTTTCTTTCTC 57.668 43.478 0.00 0.00 0.00 2.87
976 1055 4.161377 CCTCCTCGATCTTCCTTTCTTTCT 59.839 45.833 0.00 0.00 0.00 2.52
977 1056 4.160626 TCCTCCTCGATCTTCCTTTCTTTC 59.839 45.833 0.00 0.00 0.00 2.62
978 1057 4.097418 TCCTCCTCGATCTTCCTTTCTTT 58.903 43.478 0.00 0.00 0.00 2.52
979 1058 3.714144 TCCTCCTCGATCTTCCTTTCTT 58.286 45.455 0.00 0.00 0.00 2.52
980 1059 3.390175 TCCTCCTCGATCTTCCTTTCT 57.610 47.619 0.00 0.00 0.00 2.52
981 1060 3.244044 CCATCCTCCTCGATCTTCCTTTC 60.244 52.174 0.00 0.00 0.00 2.62
982 1061 2.703007 CCATCCTCCTCGATCTTCCTTT 59.297 50.000 0.00 0.00 0.00 3.11
983 1062 2.324541 CCATCCTCCTCGATCTTCCTT 58.675 52.381 0.00 0.00 0.00 3.36
984 1063 2.008242 CCATCCTCCTCGATCTTCCT 57.992 55.000 0.00 0.00 0.00 3.36
985 1064 0.320050 GCCATCCTCCTCGATCTTCC 59.680 60.000 0.00 0.00 0.00 3.46
986 1065 0.038709 CGCCATCCTCCTCGATCTTC 60.039 60.000 0.00 0.00 0.00 2.87
1293 1372 1.067821 CTGCTGCTAGTACCAGGCTAC 59.932 57.143 0.00 0.00 0.00 3.58
1294 1373 1.403814 CTGCTGCTAGTACCAGGCTA 58.596 55.000 0.00 0.00 0.00 3.93
1295 1374 1.965754 GCTGCTGCTAGTACCAGGCT 61.966 60.000 8.53 0.00 36.03 4.58
1296 1375 1.522580 GCTGCTGCTAGTACCAGGC 60.523 63.158 8.53 0.00 36.03 4.85
1297 1376 0.179089 CTGCTGCTGCTAGTACCAGG 60.179 60.000 17.00 0.00 40.48 4.45
1301 1380 0.529555 GAGGCTGCTGCTGCTAGTAC 60.530 60.000 26.79 12.74 40.48 2.73
1303 1382 2.583520 GAGGCTGCTGCTGCTAGT 59.416 61.111 26.79 14.43 40.48 2.57
1304 1383 2.203042 GGAGGCTGCTGCTGCTAG 60.203 66.667 26.79 12.70 40.48 3.42
1305 1384 3.790437 GGGAGGCTGCTGCTGCTA 61.790 66.667 26.79 2.62 40.48 3.49
1307 1386 2.898920 TATTGGGAGGCTGCTGCTGC 62.899 60.000 21.42 21.42 39.59 5.25
1308 1387 0.394762 TTATTGGGAGGCTGCTGCTG 60.395 55.000 15.64 0.77 39.59 4.41
1333 1412 0.038159 GATGGATGGACCGATCGGAC 60.038 60.000 39.55 32.26 42.61 4.79
1444 1533 4.562394 CACACACAACACAAAATCCACTTC 59.438 41.667 0.00 0.00 0.00 3.01
1479 1568 5.515270 GGAAAGAACAAAAAGAAACAGGTCG 59.485 40.000 0.00 0.00 0.00 4.79
1521 1610 6.073003 GGTTCAGTCGTTCATTTTTCAGAGAT 60.073 38.462 0.00 0.00 0.00 2.75
1538 1628 1.781555 CACGTGCATCGGTTCAGTC 59.218 57.895 0.82 0.00 44.69 3.51
1539 1629 2.317609 GCACGTGCATCGGTTCAGT 61.318 57.895 34.52 0.00 44.69 3.41
1593 1687 0.389391 ACAGACCACGTCTCCAAGTG 59.611 55.000 0.00 0.00 41.37 3.16
1601 1695 1.865865 ATTCACACACAGACCACGTC 58.134 50.000 0.00 0.00 0.00 4.34
1628 1722 1.784525 GGTCAGACAACGTCTCCAAG 58.215 55.000 2.17 0.00 41.37 3.61
1763 1860 2.742589 GGTCGCTCCCTTAGAAAAACAG 59.257 50.000 0.00 0.00 0.00 3.16
1764 1861 2.370849 AGGTCGCTCCCTTAGAAAAACA 59.629 45.455 0.00 0.00 36.75 2.83
1765 1862 2.742589 CAGGTCGCTCCCTTAGAAAAAC 59.257 50.000 0.00 0.00 36.75 2.43
1766 1863 2.635915 TCAGGTCGCTCCCTTAGAAAAA 59.364 45.455 0.00 0.00 36.75 1.94
1767 1864 2.253610 TCAGGTCGCTCCCTTAGAAAA 58.746 47.619 0.00 0.00 36.75 2.29
1831 1932 2.552315 TCGAACAGCCATTTTCAGTTCC 59.448 45.455 0.00 0.00 36.20 3.62
1842 1944 2.872245 CTCTCTGTTTTTCGAACAGCCA 59.128 45.455 10.29 0.00 45.34 4.75
1881 1983 0.620556 TGAATGAACTCTCTGCCCCC 59.379 55.000 0.00 0.00 0.00 5.40
1882 1984 1.003580 TGTGAATGAACTCTCTGCCCC 59.996 52.381 0.00 0.00 0.00 5.80
1883 1985 2.079925 GTGTGAATGAACTCTCTGCCC 58.920 52.381 0.00 0.00 0.00 5.36
1884 1986 2.771089 TGTGTGAATGAACTCTCTGCC 58.229 47.619 0.00 0.00 0.00 4.85
1885 1987 4.931601 TGTATGTGTGAATGAACTCTCTGC 59.068 41.667 0.00 0.00 0.00 4.26
1886 1988 5.928264 TGTGTATGTGTGAATGAACTCTCTG 59.072 40.000 0.00 0.00 0.00 3.35
1887 1989 5.928839 GTGTGTATGTGTGAATGAACTCTCT 59.071 40.000 0.00 0.00 0.00 3.10
1888 1990 5.120830 GGTGTGTATGTGTGAATGAACTCTC 59.879 44.000 0.00 0.00 0.00 3.20
1889 1991 4.997395 GGTGTGTATGTGTGAATGAACTCT 59.003 41.667 0.00 0.00 0.00 3.24
1890 1992 4.754618 TGGTGTGTATGTGTGAATGAACTC 59.245 41.667 0.00 0.00 0.00 3.01
1891 1993 4.713553 TGGTGTGTATGTGTGAATGAACT 58.286 39.130 0.00 0.00 0.00 3.01
1892 1994 5.431420 TTGGTGTGTATGTGTGAATGAAC 57.569 39.130 0.00 0.00 0.00 3.18
1893 1995 6.456795 TTTTGGTGTGTATGTGTGAATGAA 57.543 33.333 0.00 0.00 0.00 2.57
1894 1996 6.456795 TTTTTGGTGTGTATGTGTGAATGA 57.543 33.333 0.00 0.00 0.00 2.57
1919 2021 7.559897 TGTTTTATCTGAACTCTCTGGGTTTTT 59.440 33.333 0.00 0.00 0.00 1.94
1920 2022 7.013369 GTGTTTTATCTGAACTCTCTGGGTTTT 59.987 37.037 0.00 0.00 0.00 2.43
1921 2023 6.486993 GTGTTTTATCTGAACTCTCTGGGTTT 59.513 38.462 0.00 0.00 0.00 3.27
1922 2024 5.998363 GTGTTTTATCTGAACTCTCTGGGTT 59.002 40.000 0.00 0.00 0.00 4.11
1923 2025 5.071788 TGTGTTTTATCTGAACTCTCTGGGT 59.928 40.000 0.00 0.00 0.00 4.51
1924 2026 5.551233 TGTGTTTTATCTGAACTCTCTGGG 58.449 41.667 0.00 0.00 0.00 4.45
1925 2027 7.496529 TTTGTGTTTTATCTGAACTCTCTGG 57.503 36.000 0.00 0.00 0.00 3.86
1926 2028 9.956720 AATTTTGTGTTTTATCTGAACTCTCTG 57.043 29.630 0.00 0.00 0.00 3.35
1950 2052 6.202188 ACAGTTTCGAACGACTTTGATGTAAT 59.798 34.615 0.00 0.00 36.23 1.89
2013 2116 9.899661 ATAGTGCATAGGTTTTGTATTCTACAA 57.100 29.630 0.00 0.00 46.13 2.41
2052 2155 8.988064 TCACTTATTGTGTATGAGACTCTTTC 57.012 34.615 3.68 0.00 46.27 2.62
2106 2223 2.193248 GCTAGGGGTGGGTCATGC 59.807 66.667 0.00 0.00 0.00 4.06
2109 2226 1.923395 CCTTGCTAGGGGTGGGTCA 60.923 63.158 6.27 0.00 37.94 4.02
2138 2255 9.343103 CAACCATATGATAACATAGTAGACGTC 57.657 37.037 7.70 7.70 41.44 4.34
2213 2335 6.971726 TGATCGGGTTAGTGTCAAGTATAT 57.028 37.500 0.00 0.00 0.00 0.86
2214 2336 6.239204 CCATGATCGGGTTAGTGTCAAGTATA 60.239 42.308 0.00 0.00 0.00 1.47
2262 2384 1.172812 AAGAAGCACGGCCTGGTTTC 61.173 55.000 17.05 13.98 40.80 2.78
2267 2389 0.667993 TGAAAAAGAAGCACGGCCTG 59.332 50.000 0.00 0.00 0.00 4.85
2268 2390 0.954452 CTGAAAAAGAAGCACGGCCT 59.046 50.000 0.00 0.00 0.00 5.19
2271 2393 2.322371 GAGCTGAAAAAGAAGCACGG 57.678 50.000 0.00 0.00 42.06 4.94


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

AutoCloner maintained by Alex Coulton.