Multiple sequence alignment - TraesCS7A01G315400

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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 TraesCS7A01G315400 chr7A 100.000 2309 0 0 1 2309 449703327 449705635 0.000000e+00 4265
1 TraesCS7A01G315400 chr7B 94.731 873 39 6 605 1471 399259973 399260844 0.000000e+00 1351
2 TraesCS7A01G315400 chr7B 88.062 645 27 15 1 600 399259032 399259671 0.000000e+00 719
3 TraesCS7A01G315400 chr7B 82.979 141 20 2 2166 2302 330982311 330982451 8.660000e-25 124
4 TraesCS7A01G315400 chr7D 94.805 847 30 9 615 1448 396125255 396126100 0.000000e+00 1308
5 TraesCS7A01G315400 chr7D 80.975 636 82 19 1707 2306 292319975 292320607 3.470000e-128 468
6 TraesCS7A01G315400 chr7D 80.848 637 80 17 1707 2306 32599457 32598826 1.620000e-126 462
7 TraesCS7A01G315400 chr7D 80.794 630 79 17 1714 2306 32585055 32584431 2.700000e-124 455
8 TraesCS7A01G315400 chr7D 92.258 310 17 3 297 600 396124664 396124972 1.270000e-117 433
9 TraesCS7A01G315400 chr7D 84.765 361 8 11 1 314 396124290 396124650 3.700000e-83 318
10 TraesCS7A01G315400 chr7D 94.444 90 5 0 1622 1711 22534366 22534455 3.090000e-29 139
11 TraesCS7A01G315400 chr7D 90.323 93 9 0 1617 1709 121779415 121779323 3.120000e-24 122
12 TraesCS7A01G315400 chr5A 98.540 685 9 1 1622 2306 641400749 641401432 0.000000e+00 1208
13 TraesCS7A01G315400 chr2D 82.047 635 79 15 1703 2306 624168333 624167703 2.050000e-140 508
14 TraesCS7A01G315400 chr2D 91.209 91 8 0 1619 1709 441729706 441729616 8.660000e-25 124
15 TraesCS7A01G315400 chr1D 81.649 643 75 27 1703 2309 452543899 452544534 5.730000e-136 494
16 TraesCS7A01G315400 chr1D 80.818 636 83 19 1707 2306 460577339 460576707 1.620000e-126 462
17 TraesCS7A01G315400 chr1D 92.045 88 7 0 1622 1709 12195318 12195231 8.660000e-25 124
18 TraesCS7A01G315400 chr6D 80.751 639 84 20 1703 2306 226700693 226700059 1.620000e-126 462
19 TraesCS7A01G315400 chr4D 80.503 636 85 19 1707 2306 215031215 215030583 3.500000e-123 451
20 TraesCS7A01G315400 chr4D 82.450 302 42 7 2012 2305 450210802 450211100 1.060000e-63 254
21 TraesCS7A01G315400 chr4D 92.135 89 7 0 1621 1709 124895812 124895724 2.410000e-25 126
22 TraesCS7A01G315400 chr3B 84.729 203 25 3 2109 2305 818869973 818869771 5.030000e-47 198
23 TraesCS7A01G315400 chr3B 88.535 157 18 0 1618 1774 755254849 755255005 8.420000e-45 191
24 TraesCS7A01G315400 chrUn 92.941 85 6 0 1622 1706 95190270 95190354 8.660000e-25 124
25 TraesCS7A01G315400 chr2B 92.941 85 6 0 1622 1706 38236493 38236577 8.660000e-25 124
26 TraesCS7A01G315400 chr2B 84.167 120 15 2 2189 2304 326480597 326480478 1.870000e-21 113


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 TraesCS7A01G315400 chr7A 449703327 449705635 2308 False 4265.000000 4265 100.000000 1 2309 1 chr7A.!!$F1 2308
1 TraesCS7A01G315400 chr7B 399259032 399260844 1812 False 1035.000000 1351 91.396500 1 1471 2 chr7B.!!$F2 1470
2 TraesCS7A01G315400 chr7D 396124290 396126100 1810 False 686.333333 1308 90.609333 1 1448 3 chr7D.!!$F3 1447
3 TraesCS7A01G315400 chr7D 292319975 292320607 632 False 468.000000 468 80.975000 1707 2306 1 chr7D.!!$F2 599
4 TraesCS7A01G315400 chr7D 32598826 32599457 631 True 462.000000 462 80.848000 1707 2306 1 chr7D.!!$R2 599
5 TraesCS7A01G315400 chr7D 32584431 32585055 624 True 455.000000 455 80.794000 1714 2306 1 chr7D.!!$R1 592
6 TraesCS7A01G315400 chr5A 641400749 641401432 683 False 1208.000000 1208 98.540000 1622 2306 1 chr5A.!!$F1 684
7 TraesCS7A01G315400 chr2D 624167703 624168333 630 True 508.000000 508 82.047000 1703 2306 1 chr2D.!!$R2 603
8 TraesCS7A01G315400 chr1D 452543899 452544534 635 False 494.000000 494 81.649000 1703 2309 1 chr1D.!!$F1 606
9 TraesCS7A01G315400 chr1D 460576707 460577339 632 True 462.000000 462 80.818000 1707 2306 1 chr1D.!!$R2 599
10 TraesCS7A01G315400 chr6D 226700059 226700693 634 True 462.000000 462 80.751000 1703 2306 1 chr6D.!!$R1 603
11 TraesCS7A01G315400 chr4D 215030583 215031215 632 True 451.000000 451 80.503000 1707 2306 1 chr4D.!!$R2 599

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
942 1485 0.031314 ACTCGCTCACACTGACACTG 59.969 55.0 0.0 0.0 0.0 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2091 2646 4.515028 TTTATCTACGAGACAGGGAGGA 57.485 45.455 0.0 0.0 0.0 3.71 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 3.495001 CAGTTCCCGAAGTTGAGAAGAAC 59.505 47.826 0.00 0.00 33.91 3.01
27 28 2.433868 TCCCGAAGTTGAGAAGAACG 57.566 50.000 0.00 0.00 0.00 3.95
28 29 1.000506 TCCCGAAGTTGAGAAGAACGG 59.999 52.381 0.00 0.00 38.83 4.44
29 30 1.270147 CCCGAAGTTGAGAAGAACGGT 60.270 52.381 0.00 0.00 37.67 4.83
268 320 1.658596 CTCGATCGCTCTCTCTATCCG 59.341 57.143 11.09 0.00 0.00 4.18
285 337 3.453559 CGCTCACCGGTCCTTAATT 57.546 52.632 2.59 0.00 0.00 1.40
291 343 1.525306 CCGGTCCTTAATTCCCCGC 60.525 63.158 0.00 0.00 37.37 6.13
379 468 0.737219 GTCAAGCACATGAGGATGGC 59.263 55.000 0.00 0.00 33.39 4.40
384 473 1.156645 GCACATGAGGATGGCTCGAC 61.157 60.000 0.00 0.00 33.39 4.20
421 510 0.324552 TCCATCCCTGGGCAATTGTG 60.325 55.000 8.22 0.00 43.34 3.33
434 523 2.512885 CAATTGTGCACGAGCTGAATC 58.487 47.619 13.31 0.00 42.74 2.52
450 539 4.545706 TCCGCGATGGATGCCACC 62.546 66.667 8.23 0.00 43.74 4.61
484 573 4.485163 GTCCATTTGTATTGTCCAGTTGC 58.515 43.478 0.00 0.00 0.00 4.17
523 613 1.732917 CCGTGCAAGTTGGAGCAAA 59.267 52.632 4.75 0.00 43.20 3.68
524 614 0.318107 CCGTGCAAGTTGGAGCAAAG 60.318 55.000 4.75 0.00 43.20 2.77
525 615 0.936297 CGTGCAAGTTGGAGCAAAGC 60.936 55.000 4.75 0.00 43.20 3.51
526 616 0.936297 GTGCAAGTTGGAGCAAAGCG 60.936 55.000 4.75 0.00 43.20 4.68
528 618 0.249031 GCAAGTTGGAGCAAAGCGTT 60.249 50.000 4.75 0.00 0.00 4.84
529 619 1.758783 CAAGTTGGAGCAAAGCGTTC 58.241 50.000 0.00 0.00 0.00 3.95
541 631 1.597742 AAGCGTTCAACTGCTGTGAT 58.402 45.000 7.50 0.00 41.46 3.06
576 668 1.743394 GCCACCGGTTCTTAATCTTGG 59.257 52.381 2.97 0.00 0.00 3.61
600 692 2.029918 CGGGCTATTCATGTCGAGATGA 60.030 50.000 20.37 20.37 0.00 2.92
601 693 3.583806 GGGCTATTCATGTCGAGATGAG 58.416 50.000 22.60 14.01 33.86 2.90
602 694 3.006323 GGGCTATTCATGTCGAGATGAGT 59.994 47.826 22.60 21.99 33.86 3.41
603 695 3.986572 GGCTATTCATGTCGAGATGAGTG 59.013 47.826 24.88 18.60 33.86 3.51
606 1017 3.599730 TTCATGTCGAGATGAGTGCTT 57.400 42.857 22.60 0.00 33.86 3.91
613 1152 3.549471 GTCGAGATGAGTGCTTACATGTG 59.451 47.826 9.11 0.00 0.00 3.21
622 1161 5.696270 TGAGTGCTTACATGTGTAAACTCAG 59.304 40.000 23.48 9.19 44.70 3.35
630 1169 4.692625 ACATGTGTAAACTCAGCAGCTAAG 59.307 41.667 0.00 0.00 0.00 2.18
742 1281 3.772572 TCAAATGGACTCATCCTAACGGA 59.227 43.478 0.00 0.00 46.43 4.69
800 1339 4.817318 TCCTTGGGCAAATTAATTCCAC 57.183 40.909 0.10 0.00 0.00 4.02
801 1340 3.194542 TCCTTGGGCAAATTAATTCCACG 59.805 43.478 0.10 2.97 0.00 4.94
927 1470 3.794028 GCTAGCAACTACTGATGAACTCG 59.206 47.826 10.63 0.00 0.00 4.18
942 1485 0.031314 ACTCGCTCACACTGACACTG 59.969 55.000 0.00 0.00 0.00 3.66
944 1487 2.313172 CGCTCACACTGACACTGGC 61.313 63.158 0.00 0.00 0.00 4.85
949 1492 0.033920 CACACTGACACTGGCTAGCA 59.966 55.000 18.24 1.68 0.00 3.49
1326 1872 0.647925 GATCGCTGCTCGTTTCTTCC 59.352 55.000 0.00 0.00 39.67 3.46
1327 1873 0.247736 ATCGCTGCTCGTTTCTTCCT 59.752 50.000 0.00 0.00 39.67 3.36
1328 1874 0.667487 TCGCTGCTCGTTTCTTCCTG 60.667 55.000 0.00 0.00 39.67 3.86
1373 1921 4.902443 TTTTAGTTCGTGGCATTGACAA 57.098 36.364 0.00 0.00 0.00 3.18
1389 1940 8.137437 GGCATTGACAATATGTACATAGCTTTT 58.863 33.333 19.80 7.54 0.00 2.27
1443 1994 2.159142 GCTCCAAATTCAGGCATTCTGG 60.159 50.000 0.00 0.00 43.53 3.86
1453 2004 0.817229 GGCATTCTGGAGTAGCTGGC 60.817 60.000 0.00 0.00 0.00 4.85
1462 2013 0.654683 GAGTAGCTGGCGAATGCTTG 59.345 55.000 0.00 0.00 42.25 4.01
1471 2022 3.263261 TGGCGAATGCTTGTTAATCGTA 58.737 40.909 0.00 0.00 42.25 3.43
1472 2023 3.874543 TGGCGAATGCTTGTTAATCGTAT 59.125 39.130 0.00 0.00 42.25 3.06
1473 2024 4.334203 TGGCGAATGCTTGTTAATCGTATT 59.666 37.500 0.00 0.00 42.25 1.89
1474 2025 4.904154 GGCGAATGCTTGTTAATCGTATTC 59.096 41.667 0.00 0.00 42.25 1.75
1475 2026 5.277345 GGCGAATGCTTGTTAATCGTATTCT 60.277 40.000 0.00 0.00 42.25 2.40
1476 2027 5.841296 GCGAATGCTTGTTAATCGTATTCTC 59.159 40.000 0.00 0.00 38.39 2.87
1477 2028 6.509517 GCGAATGCTTGTTAATCGTATTCTCA 60.510 38.462 0.00 0.00 38.39 3.27
1478 2029 7.398746 CGAATGCTTGTTAATCGTATTCTCAA 58.601 34.615 0.00 0.00 0.00 3.02
1479 2030 7.580523 CGAATGCTTGTTAATCGTATTCTCAAG 59.419 37.037 0.00 0.00 35.43 3.02
1480 2031 8.492673 AATGCTTGTTAATCGTATTCTCAAGA 57.507 30.769 17.55 10.14 34.62 3.02
1481 2032 7.899178 TGCTTGTTAATCGTATTCTCAAGAA 57.101 32.000 17.55 0.00 38.56 2.52
1482 2033 7.963981 TGCTTGTTAATCGTATTCTCAAGAAG 58.036 34.615 17.55 9.23 37.48 2.85
1483 2034 7.817478 TGCTTGTTAATCGTATTCTCAAGAAGA 59.183 33.333 17.55 0.00 37.48 2.87
1514 2065 6.582677 TTTTTAATCGTGATGGTCCATGTT 57.417 33.333 9.76 0.00 0.00 2.71
1515 2066 6.582677 TTTTAATCGTGATGGTCCATGTTT 57.417 33.333 9.76 0.00 0.00 2.83
1516 2067 6.582677 TTTAATCGTGATGGTCCATGTTTT 57.417 33.333 9.76 0.00 0.00 2.43
1517 2068 4.439305 AATCGTGATGGTCCATGTTTTG 57.561 40.909 9.76 0.00 0.00 2.44
1530 2081 4.818534 CATGTTTTGGATCCTATGGTCG 57.181 45.455 14.23 0.00 0.00 4.79
1531 2082 4.450976 CATGTTTTGGATCCTATGGTCGA 58.549 43.478 14.23 0.00 0.00 4.20
1532 2083 4.771114 TGTTTTGGATCCTATGGTCGAT 57.229 40.909 14.23 0.00 0.00 3.59
1533 2084 4.703897 TGTTTTGGATCCTATGGTCGATC 58.296 43.478 14.23 0.00 35.21 3.69
1534 2085 4.408921 TGTTTTGGATCCTATGGTCGATCT 59.591 41.667 14.23 0.00 36.07 2.75
1535 2086 4.607293 TTTGGATCCTATGGTCGATCTG 57.393 45.455 14.23 0.00 36.07 2.90
1536 2087 3.525800 TGGATCCTATGGTCGATCTGA 57.474 47.619 14.23 0.00 36.07 3.27
1545 2096 3.314339 GTCGATCTGACTCGGTGTG 57.686 57.895 9.51 0.00 44.58 3.82
1546 2097 0.803117 GTCGATCTGACTCGGTGTGA 59.197 55.000 9.51 0.00 44.58 3.58
1547 2098 1.199327 GTCGATCTGACTCGGTGTGAA 59.801 52.381 9.51 0.00 44.58 3.18
1548 2099 2.092323 TCGATCTGACTCGGTGTGAAT 58.908 47.619 8.77 0.00 39.13 2.57
1549 2100 2.097629 TCGATCTGACTCGGTGTGAATC 59.902 50.000 8.77 0.00 39.13 2.52
1550 2101 2.098280 CGATCTGACTCGGTGTGAATCT 59.902 50.000 0.00 0.00 35.03 2.40
1551 2102 3.312697 CGATCTGACTCGGTGTGAATCTA 59.687 47.826 0.00 0.00 35.03 1.98
1552 2103 4.023622 CGATCTGACTCGGTGTGAATCTAT 60.024 45.833 0.00 0.00 35.03 1.98
1553 2104 5.179555 CGATCTGACTCGGTGTGAATCTATA 59.820 44.000 0.00 0.00 35.03 1.31
1554 2105 6.567687 ATCTGACTCGGTGTGAATCTATAG 57.432 41.667 0.00 0.00 0.00 1.31
1555 2106 5.681639 TCTGACTCGGTGTGAATCTATAGA 58.318 41.667 4.57 4.57 0.00 1.98
1556 2107 5.760743 TCTGACTCGGTGTGAATCTATAGAG 59.239 44.000 8.70 0.00 0.00 2.43
1557 2108 4.822350 TGACTCGGTGTGAATCTATAGAGG 59.178 45.833 8.70 0.00 0.00 3.69
1558 2109 5.050126 ACTCGGTGTGAATCTATAGAGGA 57.950 43.478 8.70 0.00 0.00 3.71
1559 2110 5.446860 ACTCGGTGTGAATCTATAGAGGAA 58.553 41.667 8.70 0.00 0.00 3.36
1560 2111 5.299782 ACTCGGTGTGAATCTATAGAGGAAC 59.700 44.000 8.70 6.57 0.00 3.62
1561 2112 4.275196 TCGGTGTGAATCTATAGAGGAACG 59.725 45.833 8.70 4.78 0.00 3.95
1562 2113 4.299978 GGTGTGAATCTATAGAGGAACGC 58.700 47.826 8.70 11.35 0.00 4.84
1563 2114 4.202121 GGTGTGAATCTATAGAGGAACGCA 60.202 45.833 18.88 14.16 0.00 5.24
1564 2115 5.348986 GTGTGAATCTATAGAGGAACGCAA 58.651 41.667 8.70 0.00 0.00 4.85
1565 2116 5.232414 GTGTGAATCTATAGAGGAACGCAAC 59.768 44.000 8.70 0.00 0.00 4.17
1566 2117 4.441415 GTGAATCTATAGAGGAACGCAACG 59.559 45.833 8.70 0.00 0.00 4.10
1567 2118 2.486951 TCTATAGAGGAACGCAACGC 57.513 50.000 0.00 0.00 0.00 4.84
1568 2119 1.746787 TCTATAGAGGAACGCAACGCA 59.253 47.619 0.00 0.00 0.00 5.24
1569 2120 2.361119 TCTATAGAGGAACGCAACGCAT 59.639 45.455 0.00 0.00 0.00 4.73
1570 2121 1.290203 ATAGAGGAACGCAACGCATG 58.710 50.000 0.00 0.00 0.00 4.06
1571 2122 0.739462 TAGAGGAACGCAACGCATGG 60.739 55.000 0.00 0.00 0.00 3.66
1572 2123 2.031919 AGGAACGCAACGCATGGA 59.968 55.556 0.00 0.00 0.00 3.41
1573 2124 1.369091 GAGGAACGCAACGCATGGAT 61.369 55.000 0.00 0.00 0.00 3.41
1574 2125 0.107897 AGGAACGCAACGCATGGATA 60.108 50.000 0.00 0.00 0.00 2.59
1575 2126 0.944386 GGAACGCAACGCATGGATAT 59.056 50.000 0.00 0.00 0.00 1.63
1576 2127 1.069906 GGAACGCAACGCATGGATATC 60.070 52.381 0.00 0.00 0.00 1.63
1577 2128 1.597195 GAACGCAACGCATGGATATCA 59.403 47.619 4.83 0.00 0.00 2.15
1578 2129 1.662517 ACGCAACGCATGGATATCAA 58.337 45.000 4.83 0.00 0.00 2.57
1579 2130 2.013400 ACGCAACGCATGGATATCAAA 58.987 42.857 4.83 0.00 0.00 2.69
1580 2131 2.618241 ACGCAACGCATGGATATCAAAT 59.382 40.909 4.83 0.00 0.00 2.32
1581 2132 2.975193 CGCAACGCATGGATATCAAATG 59.025 45.455 4.83 8.88 0.00 2.32
1582 2133 3.303924 CGCAACGCATGGATATCAAATGA 60.304 43.478 17.45 0.00 0.00 2.57
1583 2134 4.614306 CGCAACGCATGGATATCAAATGAT 60.614 41.667 17.45 1.01 38.51 2.45
1584 2135 5.390779 CGCAACGCATGGATATCAAATGATA 60.391 40.000 17.45 5.64 40.85 2.15
1586 2137 7.031372 GCAACGCATGGATATCAAATGATATT 58.969 34.615 15.18 8.00 45.07 1.28
1587 2138 7.219535 GCAACGCATGGATATCAAATGATATTC 59.780 37.037 15.18 13.98 45.07 1.75
1588 2139 7.008440 ACGCATGGATATCAAATGATATTCG 57.992 36.000 15.18 14.54 45.07 3.34
1589 2140 6.037500 ACGCATGGATATCAAATGATATTCGG 59.962 38.462 15.18 11.20 45.07 4.30
1590 2141 6.512253 CGCATGGATATCAAATGATATTCGGG 60.512 42.308 15.18 10.92 45.07 5.14
1591 2142 6.319658 GCATGGATATCAAATGATATTCGGGT 59.680 38.462 15.18 3.75 45.07 5.28
1592 2143 7.148018 GCATGGATATCAAATGATATTCGGGTT 60.148 37.037 15.18 0.82 45.07 4.11
1593 2144 7.686438 TGGATATCAAATGATATTCGGGTTG 57.314 36.000 15.18 0.00 45.07 3.77
1594 2145 7.457561 TGGATATCAAATGATATTCGGGTTGA 58.542 34.615 15.18 0.00 45.07 3.18
1595 2146 7.941790 TGGATATCAAATGATATTCGGGTTGAA 59.058 33.333 15.18 0.00 45.07 2.69
1596 2147 8.792633 GGATATCAAATGATATTCGGGTTGAAA 58.207 33.333 15.18 0.00 45.07 2.69
1597 2148 9.612620 GATATCAAATGATATTCGGGTTGAAAC 57.387 33.333 15.18 0.00 45.07 2.78
1598 2149 6.825944 TCAAATGATATTCGGGTTGAAACA 57.174 33.333 0.00 0.00 40.71 2.83
1599 2150 7.220741 TCAAATGATATTCGGGTTGAAACAA 57.779 32.000 0.00 0.00 40.71 2.83
1600 2151 7.835822 TCAAATGATATTCGGGTTGAAACAAT 58.164 30.769 0.00 0.00 40.71 2.71
1601 2152 8.961634 TCAAATGATATTCGGGTTGAAACAATA 58.038 29.630 0.00 0.00 40.71 1.90
1602 2153 9.579768 CAAATGATATTCGGGTTGAAACAATAA 57.420 29.630 0.00 0.00 40.71 1.40
1604 2155 9.965824 AATGATATTCGGGTTGAAACAATAATC 57.034 29.630 0.00 0.00 40.71 1.75
1605 2156 7.635423 TGATATTCGGGTTGAAACAATAATCG 58.365 34.615 0.00 0.00 40.71 3.34
1606 2157 5.890424 ATTCGGGTTGAAACAATAATCGT 57.110 34.783 0.00 0.00 40.71 3.73
1607 2158 4.671880 TCGGGTTGAAACAATAATCGTG 57.328 40.909 0.00 0.00 0.00 4.35
1608 2159 3.437395 TCGGGTTGAAACAATAATCGTGG 59.563 43.478 0.00 0.00 0.00 4.94
1609 2160 3.426963 CGGGTTGAAACAATAATCGTGGG 60.427 47.826 0.00 0.00 0.00 4.61
1610 2161 3.119280 GGGTTGAAACAATAATCGTGGGG 60.119 47.826 0.00 0.00 0.00 4.96
1611 2162 3.759618 GGTTGAAACAATAATCGTGGGGA 59.240 43.478 0.00 0.00 0.00 4.81
1612 2163 4.218852 GGTTGAAACAATAATCGTGGGGAA 59.781 41.667 0.00 0.00 0.00 3.97
1613 2164 5.158494 GTTGAAACAATAATCGTGGGGAAC 58.842 41.667 0.00 0.00 0.00 3.62
1614 2165 4.399219 TGAAACAATAATCGTGGGGAACA 58.601 39.130 0.00 0.00 0.00 3.18
1615 2166 4.827835 TGAAACAATAATCGTGGGGAACAA 59.172 37.500 0.00 0.00 0.00 2.83
1616 2167 4.776795 AACAATAATCGTGGGGAACAAC 57.223 40.909 0.00 0.00 0.00 3.32
1617 2168 4.028993 ACAATAATCGTGGGGAACAACT 57.971 40.909 0.00 0.00 0.00 3.16
1618 2169 3.756434 ACAATAATCGTGGGGAACAACTG 59.244 43.478 0.00 0.00 0.00 3.16
1619 2170 3.992943 ATAATCGTGGGGAACAACTGA 57.007 42.857 0.00 0.00 0.00 3.41
1620 2171 2.649531 AATCGTGGGGAACAACTGAA 57.350 45.000 0.00 0.00 0.00 3.02
1876 2429 4.698583 ATCGTACAAGAGTAGTCACACC 57.301 45.455 0.00 0.00 0.00 4.16
2306 2894 2.503765 CAAACTTGGTTTTCTTGGGGGT 59.496 45.455 0.00 0.00 33.10 4.95
2307 2895 1.788229 ACTTGGTTTTCTTGGGGGTG 58.212 50.000 0.00 0.00 0.00 4.61
2308 2896 1.289530 ACTTGGTTTTCTTGGGGGTGA 59.710 47.619 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 2.476997 GCAGACCGTTCTTCTCAACTTC 59.523 50.000 0.00 0.00 0.00 3.01
26 27 0.588252 CACACTTTTCTGGCAGACCG 59.412 55.000 18.55 10.79 39.70 4.79
27 28 0.312102 GCACACTTTTCTGGCAGACC 59.688 55.000 18.55 0.00 0.00 3.85
28 29 0.312102 GGCACACTTTTCTGGCAGAC 59.688 55.000 18.55 2.58 33.24 3.51
29 30 1.165907 CGGCACACTTTTCTGGCAGA 61.166 55.000 14.43 14.43 33.24 4.26
128 133 1.820056 TCGAGAGCAGCTAGACCGG 60.820 63.158 0.00 0.00 0.00 5.28
130 135 0.661020 GAGTCGAGAGCAGCTAGACC 59.339 60.000 16.98 8.66 46.66 3.85
132 137 0.175989 TCGAGTCGAGAGCAGCTAGA 59.824 55.000 12.09 0.00 0.00 2.43
268 320 1.664873 GGAATTAAGGACCGGTGAGC 58.335 55.000 14.63 0.00 0.00 4.26
291 343 0.674534 AGAGCTTACGCCCCGATAAG 59.325 55.000 0.00 0.00 36.60 1.73
421 510 3.918220 CGCGGATTCAGCTCGTGC 61.918 66.667 0.00 0.07 40.05 5.34
523 613 0.870393 CATCACAGCAGTTGAACGCT 59.130 50.000 8.44 8.44 39.66 5.07
524 614 0.727122 GCATCACAGCAGTTGAACGC 60.727 55.000 4.44 4.44 0.00 4.84
525 615 0.110056 GGCATCACAGCAGTTGAACG 60.110 55.000 0.00 0.00 35.83 3.95
526 616 0.953727 TGGCATCACAGCAGTTGAAC 59.046 50.000 0.00 0.00 35.83 3.18
528 618 0.953727 GTTGGCATCACAGCAGTTGA 59.046 50.000 0.00 0.00 35.83 3.18
529 619 0.669619 TGTTGGCATCACAGCAGTTG 59.330 50.000 0.00 0.00 35.83 3.16
541 631 2.899838 GGCTGTCGTGTGTTGGCA 60.900 61.111 0.00 0.00 0.00 4.92
576 668 2.128035 CTCGACATGAATAGCCCGTTC 58.872 52.381 0.00 0.00 0.00 3.95
600 692 4.452455 GCTGAGTTTACACATGTAAGCACT 59.548 41.667 17.47 12.91 41.99 4.40
601 693 4.213270 TGCTGAGTTTACACATGTAAGCAC 59.787 41.667 17.47 12.92 41.99 4.40
602 694 4.384940 TGCTGAGTTTACACATGTAAGCA 58.615 39.130 17.47 13.76 41.99 3.91
603 695 4.670221 GCTGCTGAGTTTACACATGTAAGC 60.670 45.833 9.81 9.81 41.03 3.09
606 1017 4.271696 AGCTGCTGAGTTTACACATGTA 57.728 40.909 0.00 0.00 0.00 2.29
613 1152 3.589988 TGCTCTTAGCTGCTGAGTTTAC 58.410 45.455 19.28 9.25 42.97 2.01
622 1161 4.110482 CAAATTTGGATGCTCTTAGCTGC 58.890 43.478 10.49 0.00 42.97 5.25
652 1191 2.839486 TGAGCACTCAAATCGTTCCT 57.161 45.000 0.00 0.00 36.53 3.36
694 1233 4.045104 GAGATATGCCGCTAATATGGACG 58.955 47.826 0.00 0.00 0.00 4.79
742 1281 0.471591 TCCCCTGGCATGTTGCTTTT 60.472 50.000 0.00 0.00 44.28 2.27
800 1339 3.493503 GTCAGTTGTTAAACCTCCTGACG 59.506 47.826 0.00 0.00 36.94 4.35
801 1340 4.448210 TGTCAGTTGTTAAACCTCCTGAC 58.552 43.478 9.93 9.93 37.85 3.51
927 1470 0.318441 TAGCCAGTGTCAGTGTGAGC 59.682 55.000 6.91 3.47 0.00 4.26
942 1485 2.734079 GCTTCAGTATCGATTGCTAGCC 59.266 50.000 13.29 0.00 0.00 3.93
944 1487 5.973651 TTTGCTTCAGTATCGATTGCTAG 57.026 39.130 1.71 0.00 0.00 3.42
949 1492 9.900710 CTACTAGTATTTGCTTCAGTATCGATT 57.099 33.333 1.71 0.00 0.00 3.34
1185 1731 1.595993 CGAAGCCGAACTCCTCCTCA 61.596 60.000 0.00 0.00 38.22 3.86
1305 1851 1.726791 GAAGAAACGAGCAGCGATCAA 59.273 47.619 5.99 0.00 44.57 2.57
1326 1872 3.526931 TTAACAAGATCTCCTCGCCAG 57.473 47.619 0.00 0.00 0.00 4.85
1327 1873 4.162320 AGAATTAACAAGATCTCCTCGCCA 59.838 41.667 0.00 0.00 0.00 5.69
1328 1874 4.698575 AGAATTAACAAGATCTCCTCGCC 58.301 43.478 0.00 0.00 0.00 5.54
1389 1940 1.666054 AAGTTGCCACGACGGTAAAA 58.334 45.000 0.00 0.00 41.53 1.52
1420 1971 3.132289 CAGAATGCCTGAATTTGGAGCAT 59.868 43.478 3.03 0.00 45.78 3.79
1443 1994 0.654683 CAAGCATTCGCCAGCTACTC 59.345 55.000 0.00 0.00 40.90 2.59
1453 2004 6.933130 TGAGAATACGATTAACAAGCATTCG 58.067 36.000 0.00 0.00 35.99 3.34
1491 2042 6.582677 AACATGGACCATCACGATTAAAAA 57.417 33.333 3.21 0.00 0.00 1.94
1492 2043 6.582677 AAACATGGACCATCACGATTAAAA 57.417 33.333 3.21 0.00 0.00 1.52
1493 2044 6.385843 CAAAACATGGACCATCACGATTAAA 58.614 36.000 3.21 0.00 0.00 1.52
1494 2045 5.948588 CAAAACATGGACCATCACGATTAA 58.051 37.500 3.21 0.00 0.00 1.40
1495 2046 5.559427 CAAAACATGGACCATCACGATTA 57.441 39.130 3.21 0.00 0.00 1.75
1496 2047 4.439305 CAAAACATGGACCATCACGATT 57.561 40.909 3.21 0.00 0.00 3.34
1509 2060 4.450976 TCGACCATAGGATCCAAAACATG 58.549 43.478 15.82 8.64 0.00 3.21
1510 2061 4.771114 TCGACCATAGGATCCAAAACAT 57.229 40.909 15.82 0.00 0.00 2.71
1511 2062 4.408921 AGATCGACCATAGGATCCAAAACA 59.591 41.667 15.82 0.00 39.88 2.83
1512 2063 4.752101 CAGATCGACCATAGGATCCAAAAC 59.248 45.833 15.82 0.00 39.88 2.43
1513 2064 4.653801 TCAGATCGACCATAGGATCCAAAA 59.346 41.667 15.82 0.00 39.88 2.44
1514 2065 4.039245 GTCAGATCGACCATAGGATCCAAA 59.961 45.833 15.82 1.21 39.88 3.28
1515 2066 3.574396 GTCAGATCGACCATAGGATCCAA 59.426 47.826 15.82 0.00 39.88 3.53
1516 2067 3.157881 GTCAGATCGACCATAGGATCCA 58.842 50.000 15.82 0.00 39.88 3.41
1517 2068 3.426615 AGTCAGATCGACCATAGGATCC 58.573 50.000 2.48 2.48 46.69 3.36
1518 2069 3.126171 CGAGTCAGATCGACCATAGGATC 59.874 52.174 12.17 0.00 46.69 3.36
1519 2070 3.078097 CGAGTCAGATCGACCATAGGAT 58.922 50.000 12.17 0.00 46.69 3.24
1520 2071 2.495084 CGAGTCAGATCGACCATAGGA 58.505 52.381 12.17 0.00 46.69 2.94
1521 2072 1.537638 CCGAGTCAGATCGACCATAGG 59.462 57.143 12.17 8.20 46.69 2.57
1522 2073 2.031595 CACCGAGTCAGATCGACCATAG 60.032 54.545 12.17 4.53 46.69 2.23
1523 2074 1.947456 CACCGAGTCAGATCGACCATA 59.053 52.381 12.17 0.00 46.69 2.74
1524 2075 0.741326 CACCGAGTCAGATCGACCAT 59.259 55.000 12.17 0.00 46.69 3.55
1525 2076 0.608308 ACACCGAGTCAGATCGACCA 60.608 55.000 12.17 0.00 46.69 4.02
1526 2077 0.179161 CACACCGAGTCAGATCGACC 60.179 60.000 12.17 5.57 46.69 4.79
1527 2078 0.803117 TCACACCGAGTCAGATCGAC 59.197 55.000 8.94 8.94 45.56 4.20
1528 2079 1.530323 TTCACACCGAGTCAGATCGA 58.470 50.000 0.00 0.00 45.56 3.59
1529 2080 2.098280 AGATTCACACCGAGTCAGATCG 59.902 50.000 0.00 0.00 42.36 3.69
1530 2081 3.791973 AGATTCACACCGAGTCAGATC 57.208 47.619 0.00 0.00 32.88 2.75
1531 2082 6.299922 TCTATAGATTCACACCGAGTCAGAT 58.700 40.000 0.00 0.00 32.88 2.90
1532 2083 5.681639 TCTATAGATTCACACCGAGTCAGA 58.318 41.667 0.00 0.00 32.88 3.27
1533 2084 5.049060 CCTCTATAGATTCACACCGAGTCAG 60.049 48.000 2.11 0.00 32.88 3.51
1534 2085 4.822350 CCTCTATAGATTCACACCGAGTCA 59.178 45.833 2.11 0.00 32.88 3.41
1535 2086 5.064558 TCCTCTATAGATTCACACCGAGTC 58.935 45.833 2.11 0.00 0.00 3.36
1536 2087 5.050126 TCCTCTATAGATTCACACCGAGT 57.950 43.478 2.11 0.00 0.00 4.18
1537 2088 5.561145 CGTTCCTCTATAGATTCACACCGAG 60.561 48.000 2.11 0.00 0.00 4.63
1538 2089 4.275196 CGTTCCTCTATAGATTCACACCGA 59.725 45.833 2.11 0.00 0.00 4.69
1539 2090 4.537965 CGTTCCTCTATAGATTCACACCG 58.462 47.826 2.11 0.00 0.00 4.94
1540 2091 4.202121 TGCGTTCCTCTATAGATTCACACC 60.202 45.833 2.11 0.00 0.00 4.16
1541 2092 4.933330 TGCGTTCCTCTATAGATTCACAC 58.067 43.478 2.11 0.00 0.00 3.82
1542 2093 5.348986 GTTGCGTTCCTCTATAGATTCACA 58.651 41.667 2.11 0.00 0.00 3.58
1543 2094 4.441415 CGTTGCGTTCCTCTATAGATTCAC 59.559 45.833 2.11 0.00 0.00 3.18
1544 2095 4.607955 CGTTGCGTTCCTCTATAGATTCA 58.392 43.478 2.11 0.00 0.00 2.57
1545 2096 3.425858 GCGTTGCGTTCCTCTATAGATTC 59.574 47.826 2.11 0.00 0.00 2.52
1546 2097 3.181479 TGCGTTGCGTTCCTCTATAGATT 60.181 43.478 2.11 0.00 0.00 2.40
1547 2098 2.361119 TGCGTTGCGTTCCTCTATAGAT 59.639 45.455 2.11 0.00 0.00 1.98
1548 2099 1.746787 TGCGTTGCGTTCCTCTATAGA 59.253 47.619 1.69 1.69 0.00 1.98
1549 2100 2.203800 TGCGTTGCGTTCCTCTATAG 57.796 50.000 0.00 0.00 0.00 1.31
1550 2101 2.469826 CATGCGTTGCGTTCCTCTATA 58.530 47.619 0.00 0.00 0.00 1.31
1551 2102 1.290203 CATGCGTTGCGTTCCTCTAT 58.710 50.000 0.00 0.00 0.00 1.98
1552 2103 0.739462 CCATGCGTTGCGTTCCTCTA 60.739 55.000 0.00 0.00 0.00 2.43
1553 2104 2.034879 CCATGCGTTGCGTTCCTCT 61.035 57.895 0.00 0.00 0.00 3.69
1554 2105 1.369091 ATCCATGCGTTGCGTTCCTC 61.369 55.000 0.00 0.00 0.00 3.71
1555 2106 0.107897 TATCCATGCGTTGCGTTCCT 60.108 50.000 0.00 0.00 0.00 3.36
1556 2107 0.944386 ATATCCATGCGTTGCGTTCC 59.056 50.000 0.00 0.00 0.00 3.62
1557 2108 1.597195 TGATATCCATGCGTTGCGTTC 59.403 47.619 0.00 0.00 0.00 3.95
1558 2109 1.662517 TGATATCCATGCGTTGCGTT 58.337 45.000 0.00 0.00 0.00 4.84
1559 2110 1.662517 TTGATATCCATGCGTTGCGT 58.337 45.000 0.00 0.00 0.00 5.24
1560 2111 2.753989 TTTGATATCCATGCGTTGCG 57.246 45.000 0.00 0.00 0.00 4.85
1561 2112 4.227512 TCATTTGATATCCATGCGTTGC 57.772 40.909 0.00 0.00 0.00 4.17
1562 2113 7.427318 CGAATATCATTTGATATCCATGCGTTG 59.573 37.037 12.28 0.00 44.51 4.10
1563 2114 7.414429 CCGAATATCATTTGATATCCATGCGTT 60.414 37.037 12.28 0.00 44.51 4.84
1564 2115 6.037500 CCGAATATCATTTGATATCCATGCGT 59.962 38.462 12.28 0.00 44.51 5.24
1565 2116 6.424683 CCGAATATCATTTGATATCCATGCG 58.575 40.000 12.28 10.83 44.51 4.73
1566 2117 6.319658 ACCCGAATATCATTTGATATCCATGC 59.680 38.462 12.28 2.25 44.51 4.06
1567 2118 7.870509 ACCCGAATATCATTTGATATCCATG 57.129 36.000 12.28 3.15 44.51 3.66
1568 2119 8.108999 TCAACCCGAATATCATTTGATATCCAT 58.891 33.333 12.28 0.00 44.51 3.41
1569 2120 7.457561 TCAACCCGAATATCATTTGATATCCA 58.542 34.615 12.28 0.00 44.51 3.41
1570 2121 7.921786 TCAACCCGAATATCATTTGATATCC 57.078 36.000 12.28 0.86 44.51 2.59
1571 2122 9.612620 GTTTCAACCCGAATATCATTTGATATC 57.387 33.333 12.28 0.00 44.51 1.63
1572 2123 9.130661 TGTTTCAACCCGAATATCATTTGATAT 57.869 29.630 7.16 7.16 46.54 1.63
1573 2124 8.512966 TGTTTCAACCCGAATATCATTTGATA 57.487 30.769 2.90 2.90 40.85 2.15
1574 2125 7.403312 TGTTTCAACCCGAATATCATTTGAT 57.597 32.000 0.00 0.00 38.51 2.57
1575 2126 6.825944 TGTTTCAACCCGAATATCATTTGA 57.174 33.333 0.00 0.00 32.32 2.69
1576 2127 9.579768 TTATTGTTTCAACCCGAATATCATTTG 57.420 29.630 0.00 0.00 32.32 2.32
1578 2129 9.965824 GATTATTGTTTCAACCCGAATATCATT 57.034 29.630 0.00 0.00 32.32 2.57
1579 2130 8.289618 CGATTATTGTTTCAACCCGAATATCAT 58.710 33.333 0.00 0.00 32.32 2.45
1580 2131 7.281324 ACGATTATTGTTTCAACCCGAATATCA 59.719 33.333 0.00 0.00 32.32 2.15
1581 2132 7.586300 CACGATTATTGTTTCAACCCGAATATC 59.414 37.037 0.00 0.00 32.32 1.63
1582 2133 7.414436 CACGATTATTGTTTCAACCCGAATAT 58.586 34.615 0.00 0.00 32.32 1.28
1583 2134 6.183360 CCACGATTATTGTTTCAACCCGAATA 60.183 38.462 0.00 0.00 32.32 1.75
1584 2135 5.392595 CCACGATTATTGTTTCAACCCGAAT 60.393 40.000 0.00 0.00 32.32 3.34
1585 2136 4.083217 CCACGATTATTGTTTCAACCCGAA 60.083 41.667 0.00 0.00 0.00 4.30
1586 2137 3.437395 CCACGATTATTGTTTCAACCCGA 59.563 43.478 0.00 0.00 0.00 5.14
1587 2138 3.426963 CCCACGATTATTGTTTCAACCCG 60.427 47.826 0.00 0.00 0.00 5.28
1588 2139 3.119280 CCCCACGATTATTGTTTCAACCC 60.119 47.826 0.00 0.00 0.00 4.11
1589 2140 3.759618 TCCCCACGATTATTGTTTCAACC 59.240 43.478 0.00 0.00 0.00 3.77
1590 2141 5.158494 GTTCCCCACGATTATTGTTTCAAC 58.842 41.667 0.00 0.00 0.00 3.18
1591 2142 4.827835 TGTTCCCCACGATTATTGTTTCAA 59.172 37.500 0.00 0.00 0.00 2.69
1592 2143 4.399219 TGTTCCCCACGATTATTGTTTCA 58.601 39.130 0.00 0.00 0.00 2.69
1593 2144 5.048294 AGTTGTTCCCCACGATTATTGTTTC 60.048 40.000 0.00 0.00 0.00 2.78
1594 2145 4.830600 AGTTGTTCCCCACGATTATTGTTT 59.169 37.500 0.00 0.00 0.00 2.83
1595 2146 4.217550 CAGTTGTTCCCCACGATTATTGTT 59.782 41.667 0.00 0.00 0.00 2.83
1596 2147 3.756434 CAGTTGTTCCCCACGATTATTGT 59.244 43.478 0.00 0.00 0.00 2.71
1597 2148 4.006989 TCAGTTGTTCCCCACGATTATTG 58.993 43.478 0.00 0.00 0.00 1.90
1598 2149 4.295141 TCAGTTGTTCCCCACGATTATT 57.705 40.909 0.00 0.00 0.00 1.40
1599 2150 3.992943 TCAGTTGTTCCCCACGATTAT 57.007 42.857 0.00 0.00 0.00 1.28
1600 2151 3.773418 TTCAGTTGTTCCCCACGATTA 57.227 42.857 0.00 0.00 0.00 1.75
1601 2152 2.621526 GTTTCAGTTGTTCCCCACGATT 59.378 45.455 0.00 0.00 0.00 3.34
1602 2153 2.158667 AGTTTCAGTTGTTCCCCACGAT 60.159 45.455 0.00 0.00 0.00 3.73
1603 2154 1.210967 AGTTTCAGTTGTTCCCCACGA 59.789 47.619 0.00 0.00 0.00 4.35
1604 2155 1.675552 AGTTTCAGTTGTTCCCCACG 58.324 50.000 0.00 0.00 0.00 4.94
1605 2156 3.816994 ACTAGTTTCAGTTGTTCCCCAC 58.183 45.455 0.00 0.00 0.00 4.61
1606 2157 4.903049 TCTACTAGTTTCAGTTGTTCCCCA 59.097 41.667 0.00 0.00 0.00 4.96
1607 2158 5.479124 TCTACTAGTTTCAGTTGTTCCCC 57.521 43.478 0.00 0.00 0.00 4.81
1608 2159 6.128254 GCATTCTACTAGTTTCAGTTGTTCCC 60.128 42.308 0.00 0.00 0.00 3.97
1609 2160 6.128254 GGCATTCTACTAGTTTCAGTTGTTCC 60.128 42.308 0.00 0.00 0.00 3.62
1610 2161 6.128254 GGGCATTCTACTAGTTTCAGTTGTTC 60.128 42.308 0.00 0.00 0.00 3.18
1611 2162 5.705905 GGGCATTCTACTAGTTTCAGTTGTT 59.294 40.000 0.00 0.00 0.00 2.83
1612 2163 5.246307 GGGCATTCTACTAGTTTCAGTTGT 58.754 41.667 0.00 0.00 0.00 3.32
1613 2164 4.330074 CGGGCATTCTACTAGTTTCAGTTG 59.670 45.833 0.00 0.00 0.00 3.16
1614 2165 4.020485 ACGGGCATTCTACTAGTTTCAGTT 60.020 41.667 0.00 0.00 0.00 3.16
1615 2166 3.514309 ACGGGCATTCTACTAGTTTCAGT 59.486 43.478 0.00 0.00 0.00 3.41
1616 2167 3.865745 CACGGGCATTCTACTAGTTTCAG 59.134 47.826 0.00 0.00 0.00 3.02
1617 2168 3.857052 CACGGGCATTCTACTAGTTTCA 58.143 45.455 0.00 0.00 0.00 2.69
1618 2169 2.608090 GCACGGGCATTCTACTAGTTTC 59.392 50.000 3.77 0.00 40.72 2.78
1619 2170 2.629051 GCACGGGCATTCTACTAGTTT 58.371 47.619 3.77 0.00 40.72 2.66
1620 2171 1.470979 CGCACGGGCATTCTACTAGTT 60.471 52.381 11.77 0.00 41.24 2.24
2091 2646 4.515028 TTTATCTACGAGACAGGGAGGA 57.485 45.455 0.00 0.00 0.00 3.71


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

AutoCloner maintained by Alex Coulton.