Multiple sequence alignment - TraesCS5A01G474500

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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 TraesCS5A01G474500 chr5A 100.000 2980 0 0 1 2980 650429926 650432905 0.000000e+00 5504.0
1 TraesCS5A01G474500 chr5A 80.565 283 34 14 260 524 650149174 650149453 6.520000e-47 198.0
2 TraesCS5A01G474500 chr5D 90.944 1049 75 13 294 1326 522209513 522210557 0.000000e+00 1393.0
3 TraesCS5A01G474500 chr5D 92.268 582 33 8 1648 2226 522210592 522211164 0.000000e+00 815.0
4 TraesCS5A01G474500 chr5D 90.120 415 31 6 2536 2949 522212114 522212519 5.660000e-147 531.0
5 TraesCS5A01G474500 chr5D 83.666 551 51 24 1 531 522111620 522112151 1.610000e-132 483.0
6 TraesCS5A01G474500 chr5D 83.972 287 18 11 2243 2510 522211398 522211675 1.770000e-62 250.0
7 TraesCS5A01G474500 chr5D 97.500 40 1 0 1423 1462 47332295 47332334 5.330000e-08 69.4
8 TraesCS5A01G474500 chr5B 90.529 718 57 6 702 1408 658560990 658561707 0.000000e+00 939.0
9 TraesCS5A01G474500 chr5B 88.198 788 61 18 1460 2231 658561708 658562479 0.000000e+00 911.0
10 TraesCS5A01G474500 chr5B 89.245 437 39 6 2536 2972 658562951 658563379 9.400000e-150 540.0
11 TraesCS5A01G474500 chr5B 84.502 542 41 17 18 524 658380587 658381120 2.060000e-136 496.0
12 TraesCS5A01G474500 chr5B 85.256 312 31 10 2243 2545 658562624 658562929 1.040000e-79 307.0
13 TraesCS5A01G474500 chr5B 94.186 86 5 0 445 530 658145700 658145785 6.700000e-27 132.0
14 TraesCS5A01G474500 chr5B 97.500 40 1 0 1423 1462 50469174 50469213 5.330000e-08 69.4
15 TraesCS5A01G474500 chr5B 95.238 42 2 0 1421 1462 690622041 690622082 1.920000e-07 67.6
16 TraesCS5A01G474500 chr7A 93.103 87 6 0 438 524 618084858 618084944 8.670000e-26 128.0
17 TraesCS5A01G474500 chr7A 97.436 39 1 0 1424 1462 232745407 232745369 1.920000e-07 67.6
18 TraesCS5A01G474500 chr4D 93.182 88 5 1 444 530 312563919 312563832 8.670000e-26 128.0
19 TraesCS5A01G474500 chr4D 97.619 42 1 0 1421 1462 494866704 494866663 4.120000e-09 73.1
20 TraesCS5A01G474500 chr7D 91.489 94 4 4 444 534 535550403 535550311 3.120000e-25 126.0
21 TraesCS5A01G474500 chr1B 87.037 108 11 3 435 542 520682568 520682672 5.220000e-23 119.0
22 TraesCS5A01G474500 chr4A 92.308 52 4 0 2256 2307 590945767 590945818 1.150000e-09 75.0
23 TraesCS5A01G474500 chr3B 93.617 47 3 0 1419 1465 680423341 680423295 1.480000e-08 71.3
24 TraesCS5A01G474500 chr2A 92.000 50 4 0 1419 1468 376082477 376082428 1.480000e-08 71.3
25 TraesCS5A01G474500 chr2A 97.368 38 1 0 1424 1461 1378665 1378702 6.890000e-07 65.8
26 TraesCS5A01G474500 chr2B 97.436 39 1 0 1424 1462 371164312 371164350 1.920000e-07 67.6


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 TraesCS5A01G474500 chr5A 650429926 650432905 2979 False 5504.00 5504 100.000 1 2980 1 chr5A.!!$F2 2979
1 TraesCS5A01G474500 chr5D 522209513 522212519 3006 False 747.25 1393 89.326 294 2949 4 chr5D.!!$F3 2655
2 TraesCS5A01G474500 chr5D 522111620 522112151 531 False 483.00 483 83.666 1 531 1 chr5D.!!$F2 530
3 TraesCS5A01G474500 chr5B 658560990 658563379 2389 False 674.25 939 88.307 702 2972 4 chr5B.!!$F5 2270
4 TraesCS5A01G474500 chr5B 658380587 658381120 533 False 496.00 496 84.502 18 524 1 chr5B.!!$F3 506

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
218 226 0.826672 AGGTCGACTGAACGTTCCCT 60.827 55.000 24.78 18.73 36.72 4.20 F
229 237 0.828022 ACGTTCCCTTGTGTGTCTCA 59.172 50.000 0.00 0.00 0.00 3.27 F
788 852 1.078567 GCCACAAGAGCCCTCTGAG 60.079 63.158 0.00 0.00 40.36 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1224 1294 0.107214 ATTGTGGATACCCAGCGGTG 60.107 55.0 7.86 7.86 44.55 4.94 R
1721 1817 0.317160 TGCAAGTTGACTCGACCGAT 59.683 50.0 7.16 0.00 0.00 4.18 R
2153 2254 0.525761 TCAACAATAAAGCTGCCGGC 59.474 50.0 22.73 22.73 42.19 6.13 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
112 117 8.867112 AATTATTGAAAATCACAGCATGCTAG 57.133 30.769 22.19 16.21 42.53 3.42
218 226 0.826672 AGGTCGACTGAACGTTCCCT 60.827 55.000 24.78 18.73 36.72 4.20
228 236 1.865340 GAACGTTCCCTTGTGTGTCTC 59.135 52.381 17.68 0.00 0.00 3.36
229 237 0.828022 ACGTTCCCTTGTGTGTCTCA 59.172 50.000 0.00 0.00 0.00 3.27
265 273 8.794335 AAGATTCCCTAAAGAACACAGAATAC 57.206 34.615 0.00 0.00 0.00 1.89
266 274 7.918076 AGATTCCCTAAAGAACACAGAATACA 58.082 34.615 0.00 0.00 0.00 2.29
267 275 8.552296 AGATTCCCTAAAGAACACAGAATACAT 58.448 33.333 0.00 0.00 0.00 2.29
268 276 9.832445 GATTCCCTAAAGAACACAGAATACATA 57.168 33.333 0.00 0.00 0.00 2.29
305 346 9.058174 TCCTAAGACATTAGATAGAAGTCTTCG 57.942 37.037 9.13 4.23 43.80 3.79
339 392 7.549134 TGCAAGTAGTCAGGAATGTATTAACAG 59.451 37.037 0.00 0.00 39.49 3.16
390 445 8.870075 AGCAGGAAGAATACTTTAGACAAAAT 57.130 30.769 0.00 0.00 36.39 1.82
442 497 9.665264 GAGTATTAAAATCTAATGAAAAGCGGG 57.335 33.333 0.00 0.00 0.00 6.13
506 565 3.491104 GGTGAGAGCCAAGTATCCTAACG 60.491 52.174 0.00 0.00 0.00 3.18
518 577 5.863965 AGTATCCTAACGACCTAGACTACC 58.136 45.833 0.00 0.00 0.00 3.18
524 583 1.297664 CGACCTAGACTACCACGGAG 58.702 60.000 0.00 0.00 0.00 4.63
534 593 5.386060 AGACTACCACGGAGATATGATTGA 58.614 41.667 0.00 0.00 0.00 2.57
537 596 5.833667 ACTACCACGGAGATATGATTGAGAA 59.166 40.000 0.00 0.00 0.00 2.87
546 605 6.489361 GGAGATATGATTGAGAATGGCAGTTT 59.511 38.462 0.00 0.00 0.00 2.66
548 607 8.388484 AGATATGATTGAGAATGGCAGTTTAC 57.612 34.615 0.00 0.00 0.00 2.01
552 611 7.994425 TGATTGAGAATGGCAGTTTACTTTA 57.006 32.000 0.00 0.00 0.00 1.85
553 612 7.816640 TGATTGAGAATGGCAGTTTACTTTAC 58.183 34.615 0.00 0.00 0.00 2.01
555 614 7.759489 TTGAGAATGGCAGTTTACTTTACAT 57.241 32.000 0.00 0.00 0.00 2.29
557 616 7.816640 TGAGAATGGCAGTTTACTTTACATTC 58.183 34.615 15.82 15.82 41.61 2.67
558 617 6.842163 AGAATGGCAGTTTACTTTACATTCG 58.158 36.000 16.71 0.00 44.30 3.34
634 695 4.092529 CAGCATCTACGGCATTGATATGTC 59.907 45.833 0.00 0.00 34.12 3.06
718 782 3.921021 GCAACCGAATGACCGATCTATAG 59.079 47.826 0.00 0.00 0.00 1.31
726 790 1.968493 GACCGATCTATAGGGTGCCAA 59.032 52.381 4.10 0.00 33.28 4.52
741 805 1.339055 TGCCAACAAATAGAGCTCGCT 60.339 47.619 8.37 0.00 0.00 4.93
772 836 4.503314 GCCAAGAATGCTGCGGCC 62.503 66.667 16.57 0.00 37.49 6.13
788 852 1.078567 GCCACAAGAGCCCTCTGAG 60.079 63.158 0.00 0.00 40.36 3.35
789 853 1.835927 GCCACAAGAGCCCTCTGAGT 61.836 60.000 3.66 0.00 40.36 3.41
842 908 5.524535 AGCTCTAAAGATAGACAGTTCCCT 58.475 41.667 0.00 0.00 34.45 4.20
853 919 3.007635 GACAGTTCCCTTGAATAACCCG 58.992 50.000 0.00 0.00 31.98 5.28
855 921 1.633945 AGTTCCCTTGAATAACCCGCT 59.366 47.619 0.00 0.00 31.98 5.52
859 925 1.173043 CCTTGAATAACCCGCTTGCA 58.827 50.000 0.00 0.00 0.00 4.08
867 933 4.093952 CCCGCTTGCAGTTGCTCG 62.094 66.667 5.62 6.38 42.66 5.03
971 1041 4.226620 TGTACTCCCATTCCTCCTTTTACC 59.773 45.833 0.00 0.00 0.00 2.85
1032 1102 2.983592 GACAAAGGTGCGGGTGGG 60.984 66.667 0.00 0.00 0.00 4.61
1099 1169 1.277273 GTTACCCTGTTCCGGTAAGCT 59.723 52.381 0.00 0.00 44.53 3.74
1206 1276 2.805807 GCCGAACGTTGCGTATCCC 61.806 63.158 5.00 0.00 39.99 3.85
1211 1281 2.169937 AACGTTGCGTATCCCCCGAA 62.170 55.000 0.00 0.00 39.99 4.30
1212 1282 1.227438 CGTTGCGTATCCCCCGAAT 60.227 57.895 0.00 0.00 0.00 3.34
1252 1325 3.835978 TGGGTATCCACAATATCCTACGG 59.164 47.826 0.00 0.00 41.22 4.02
1318 1391 3.072622 GGTTCCTCCTTATGGTATGTCCC 59.927 52.174 0.00 0.00 34.77 4.46
1343 1416 7.167968 CCTTTACACACACTTCATTTGTTCATG 59.832 37.037 0.00 0.00 0.00 3.07
1351 1424 5.230516 CACTTCATTTGTTCATGTGTGTGTG 59.769 40.000 0.00 0.00 31.44 3.82
1353 1426 4.670347 TCATTTGTTCATGTGTGTGTGTG 58.330 39.130 0.00 0.00 0.00 3.82
1355 1428 3.484334 TTGTTCATGTGTGTGTGTGTG 57.516 42.857 0.00 0.00 0.00 3.82
1357 1430 2.816672 TGTTCATGTGTGTGTGTGTGTT 59.183 40.909 0.00 0.00 0.00 3.32
1359 1432 3.755965 TCATGTGTGTGTGTGTGTTTC 57.244 42.857 0.00 0.00 0.00 2.78
1360 1433 3.077359 TCATGTGTGTGTGTGTGTTTCA 58.923 40.909 0.00 0.00 0.00 2.69
1370 1447 6.533367 GTGTGTGTGTGTTTCAAAATGGTATT 59.467 34.615 0.00 0.00 0.00 1.89
1372 1449 8.251026 TGTGTGTGTGTTTCAAAATGGTATTTA 58.749 29.630 0.00 0.00 0.00 1.40
1373 1450 9.255304 GTGTGTGTGTTTCAAAATGGTATTTAT 57.745 29.630 0.00 0.00 0.00 1.40
1428 1505 6.912426 ACTCCCTCTATAACTGATAGTGTCA 58.088 40.000 0.00 0.00 38.99 3.58
1429 1506 7.355101 ACTCCCTCTATAACTGATAGTGTCAA 58.645 38.462 0.00 0.00 38.99 3.18
1430 1507 7.839705 ACTCCCTCTATAACTGATAGTGTCAAA 59.160 37.037 0.00 0.00 38.99 2.69
1431 1508 8.239038 TCCCTCTATAACTGATAGTGTCAAAG 57.761 38.462 0.00 0.00 38.99 2.77
1432 1509 8.059461 TCCCTCTATAACTGATAGTGTCAAAGA 58.941 37.037 0.00 0.00 38.99 2.52
1433 1510 8.696374 CCCTCTATAACTGATAGTGTCAAAGAA 58.304 37.037 0.00 0.00 38.99 2.52
1439 1516 9.950496 ATAACTGATAGTGTCAAAGAATGTCTT 57.050 29.630 0.00 0.00 38.59 3.01
1441 1518 9.950496 AACTGATAGTGTCAAAGAATGTCTTAT 57.050 29.630 0.00 0.00 35.27 1.73
1460 1537 9.710818 TGTCTTATATTAAGTTACAGAGGGAGT 57.289 33.333 0.00 0.00 0.00 3.85
1477 1554 9.862371 CAGAGGGAGTAATACATATGTATTCAC 57.138 37.037 33.87 27.81 45.22 3.18
1604 1684 5.815740 ACTACTTGCAACAAATAGATACGGG 59.184 40.000 0.00 0.00 0.00 5.28
1636 1716 5.957798 AGTATGCATGTTCATGTCCAAAAG 58.042 37.500 10.16 0.00 0.00 2.27
1642 1722 5.982516 GCATGTTCATGTCCAAAAGTGTTAA 59.017 36.000 13.24 0.00 0.00 2.01
1643 1723 6.144402 GCATGTTCATGTCCAAAAGTGTTAAG 59.856 38.462 13.24 0.00 0.00 1.85
1644 1724 6.767524 TGTTCATGTCCAAAAGTGTTAAGT 57.232 33.333 0.00 0.00 0.00 2.24
1645 1725 7.867305 TGTTCATGTCCAAAAGTGTTAAGTA 57.133 32.000 0.00 0.00 0.00 2.24
1646 1726 7.699566 TGTTCATGTCCAAAAGTGTTAAGTAC 58.300 34.615 0.00 0.00 0.00 2.73
1647 1727 7.554835 TGTTCATGTCCAAAAGTGTTAAGTACT 59.445 33.333 0.00 0.00 0.00 2.73
1652 1732 9.924650 ATGTCCAAAAGTGTTAAGTACTAGTAG 57.075 33.333 1.87 0.00 0.00 2.57
1666 1746 6.810911 AGTACTAGTAGAATGCAATCAGGTG 58.189 40.000 1.87 0.00 0.00 4.00
1668 1748 5.423015 ACTAGTAGAATGCAATCAGGTGTG 58.577 41.667 4.25 0.00 0.00 3.82
1673 1763 5.130292 AGAATGCAATCAGGTGTGAAAAG 57.870 39.130 4.25 0.00 35.88 2.27
1685 1775 3.256631 GGTGTGAAAAGATGGCACTTCAT 59.743 43.478 0.00 0.00 33.83 2.57
1686 1776 4.232221 GTGTGAAAAGATGGCACTTCATG 58.768 43.478 0.00 0.00 33.83 3.07
1704 1800 3.395273 TCATGGTTCATATGGAGGCATGA 59.605 43.478 2.13 0.00 0.00 3.07
1705 1801 3.213206 TGGTTCATATGGAGGCATGAC 57.787 47.619 2.13 0.00 31.04 3.06
1706 1802 2.158623 TGGTTCATATGGAGGCATGACC 60.159 50.000 2.13 0.00 39.61 4.02
1707 1803 2.158623 GGTTCATATGGAGGCATGACCA 60.159 50.000 2.13 1.68 43.14 4.02
1708 1804 3.499202 GGTTCATATGGAGGCATGACCAT 60.499 47.826 18.45 18.45 46.73 3.55
1710 1806 2.712627 TCATATGGAGGCATGACCATGT 59.287 45.455 21.44 15.56 45.08 3.21
1711 1807 3.138839 TCATATGGAGGCATGACCATGTT 59.861 43.478 21.44 11.34 45.08 2.71
1712 1808 4.350520 TCATATGGAGGCATGACCATGTTA 59.649 41.667 21.44 9.96 45.08 2.41
1713 1809 3.889859 ATGGAGGCATGACCATGTTAT 57.110 42.857 15.30 0.00 44.01 1.89
1714 1810 2.934887 TGGAGGCATGACCATGTTATG 58.065 47.619 11.17 0.00 43.14 1.90
1715 1811 2.509131 TGGAGGCATGACCATGTTATGA 59.491 45.455 11.17 0.00 43.14 2.15
1716 1812 3.053768 TGGAGGCATGACCATGTTATGAA 60.054 43.478 11.17 0.00 43.14 2.57
1717 1813 3.316308 GGAGGCATGACCATGTTATGAAC 59.684 47.826 11.17 0.00 43.14 3.18
1718 1814 4.202441 GAGGCATGACCATGTTATGAACT 58.798 43.478 11.17 1.07 43.14 3.01
1719 1815 4.202441 AGGCATGACCATGTTATGAACTC 58.798 43.478 11.17 0.00 43.14 3.01
1720 1816 3.002656 GGCATGACCATGTTATGAACTCG 59.997 47.826 11.17 0.00 40.80 4.18
1721 1817 3.871006 GCATGACCATGTTATGAACTCGA 59.129 43.478 11.17 0.00 40.80 4.04
1893 1989 2.425569 GGGATGTACGGCCACGGTA 61.426 63.158 2.24 0.00 46.48 4.02
2012 2108 1.597742 TACGGCTACTCGGATGTACC 58.402 55.000 0.00 0.00 0.00 3.34
2063 2163 1.189752 TTCGCCATCTTGCTCTCTCT 58.810 50.000 0.00 0.00 0.00 3.10
2084 2184 2.768527 TCATCTCACCAATGACTCCTCC 59.231 50.000 0.00 0.00 0.00 4.30
2111 2212 1.271379 CGCTCAGAAGGGGGAAAAAGA 60.271 52.381 0.00 0.00 0.00 2.52
2123 2224 4.089361 GGGGAAAAAGATGTGATCACCTT 58.911 43.478 22.85 16.08 30.71 3.50
2142 2243 5.918576 CACCTTTGTTATCGTTCCTTTTTCC 59.081 40.000 0.00 0.00 0.00 3.13
2153 2254 3.895232 TCCTTTTTCCTCTGAGGATCG 57.105 47.619 26.14 14.22 45.34 3.69
2155 2256 2.284190 CTTTTTCCTCTGAGGATCGCC 58.716 52.381 26.14 0.00 45.34 5.54
2156 2257 0.175760 TTTTCCTCTGAGGATCGCCG 59.824 55.000 26.14 0.00 45.34 6.46
2226 2328 6.071391 ACTCGCAGAAAATATGGGATTTGTTT 60.071 34.615 0.00 0.00 38.71 2.83
2227 2329 7.122055 ACTCGCAGAAAATATGGGATTTGTTTA 59.878 33.333 0.00 0.00 38.71 2.01
2228 2330 7.479980 TCGCAGAAAATATGGGATTTGTTTAG 58.520 34.615 0.00 0.00 35.01 1.85
2230 2332 7.220683 CGCAGAAAATATGGGATTTGTTTAGTG 59.779 37.037 0.00 0.00 32.69 2.74
2275 2594 5.897824 TCCCTCTAGATAAATCCGTTTGAGT 59.102 40.000 0.00 0.00 0.00 3.41
2278 2597 7.265673 CCTCTAGATAAATCCGTTTGAGTGAA 58.734 38.462 0.00 0.00 0.00 3.18
2317 2636 2.094649 GGGAGTACTGTGTTTCTCTCCG 60.095 54.545 0.00 0.00 41.37 4.63
2341 2660 0.494551 TTCTCCTACCCCAACTCCCA 59.505 55.000 0.00 0.00 0.00 4.37
2374 2702 7.723172 AGTTCTTCAATTCTTCCTCTTGTCATT 59.277 33.333 0.00 0.00 0.00 2.57
2375 2703 7.444629 TCTTCAATTCTTCCTCTTGTCATTG 57.555 36.000 0.00 0.00 0.00 2.82
2376 2704 6.432162 TCTTCAATTCTTCCTCTTGTCATTGG 59.568 38.462 0.00 0.00 0.00 3.16
2377 2705 5.879763 TCAATTCTTCCTCTTGTCATTGGA 58.120 37.500 0.00 0.00 0.00 3.53
2378 2706 6.306199 TCAATTCTTCCTCTTGTCATTGGAA 58.694 36.000 0.00 0.00 37.11 3.53
2511 3229 1.203038 ACATGCAGGTTCCATCCAACA 60.203 47.619 0.00 0.00 0.00 3.33
2520 3238 0.908910 TCCATCCAACATAGCACGGT 59.091 50.000 0.00 0.00 0.00 4.83
2521 3239 1.280710 TCCATCCAACATAGCACGGTT 59.719 47.619 0.00 0.00 0.00 4.44
2529 3247 2.014128 ACATAGCACGGTTTGGCATAC 58.986 47.619 0.00 0.00 0.00 2.39
2583 3332 5.557891 CTGATGCTTCTCAGTTAAAAGGG 57.442 43.478 0.88 0.00 38.27 3.95
2588 3337 4.102524 TGCTTCTCAGTTAAAAGGGAGACA 59.897 41.667 0.00 0.00 36.22 3.41
2597 3346 5.248477 AGTTAAAAGGGAGACAGCACAGATA 59.752 40.000 0.00 0.00 0.00 1.98
2598 3347 4.640771 AAAAGGGAGACAGCACAGATAA 57.359 40.909 0.00 0.00 0.00 1.75
2610 3359 6.351711 ACAGCACAGATAATTCAGATGCTAA 58.648 36.000 0.00 0.00 39.83 3.09
2612 3361 6.259387 CAGCACAGATAATTCAGATGCTAACA 59.741 38.462 0.00 0.00 39.83 2.41
2613 3362 6.259608 AGCACAGATAATTCAGATGCTAACAC 59.740 38.462 0.00 0.00 40.03 3.32
2714 3463 3.507924 GCGGTGGCGATGATTGCA 61.508 61.111 7.02 0.00 0.00 4.08
2756 3505 0.813610 TGCAGACAAACCACCGTCAG 60.814 55.000 0.00 0.00 34.48 3.51
2759 3508 2.285083 CAGACAAACCACCGTCAGAAA 58.715 47.619 0.00 0.00 34.48 2.52
2763 3512 3.020984 ACAAACCACCGTCAGAAAACAT 58.979 40.909 0.00 0.00 0.00 2.71
2766 3515 5.125739 ACAAACCACCGTCAGAAAACATAAA 59.874 36.000 0.00 0.00 0.00 1.40
2767 3516 5.432885 AACCACCGTCAGAAAACATAAAG 57.567 39.130 0.00 0.00 0.00 1.85
2776 3525 7.301054 CGTCAGAAAACATAAAGCAAATCTCT 58.699 34.615 0.00 0.00 0.00 3.10
2820 3569 6.713762 AGACACACATTTGATGGAAAAGAA 57.286 33.333 0.00 0.00 33.60 2.52
2821 3570 7.294017 AGACACACATTTGATGGAAAAGAAT 57.706 32.000 0.00 0.00 33.60 2.40
2842 3591 6.874134 AGAATATGATAGGGCACGTACAAATC 59.126 38.462 0.00 0.00 0.00 2.17
2870 3619 3.541996 TCGTCCCACAGTATCGTACTA 57.458 47.619 0.00 0.00 37.23 1.82
2879 3628 7.547019 TCCCACAGTATCGTACTATAGAATACG 59.453 40.741 6.78 11.23 44.34 3.06
2920 3669 0.813184 CGCTGCAAATCACAAGGGAT 59.187 50.000 0.00 0.00 0.00 3.85
2921 3670 1.202222 CGCTGCAAATCACAAGGGATC 60.202 52.381 0.00 0.00 0.00 3.36
2922 3671 1.202222 GCTGCAAATCACAAGGGATCG 60.202 52.381 0.00 0.00 0.00 3.69
2923 3672 1.402968 CTGCAAATCACAAGGGATCGG 59.597 52.381 0.00 0.00 0.00 4.18
2924 3673 1.004161 TGCAAATCACAAGGGATCGGA 59.996 47.619 0.00 0.00 0.00 4.55
2937 3688 1.202806 GGATCGGATGGGCAGAATTGA 60.203 52.381 0.00 0.00 0.00 2.57
2949 3700 6.480763 TGGGCAGAATTGAGAGTATTTAACA 58.519 36.000 0.00 0.00 0.00 2.41
2972 3723 7.937649 ACACAGTAAAAGAAAATTACCCTGAC 58.062 34.615 0.00 0.00 34.50 3.51
2973 3724 7.075741 CACAGTAAAAGAAAATTACCCTGACG 58.924 38.462 0.00 0.00 34.50 4.35
2974 3725 6.206048 ACAGTAAAAGAAAATTACCCTGACGG 59.794 38.462 0.00 0.00 34.50 4.79
2975 3726 4.514781 AAAAGAAAATTACCCTGACGGC 57.485 40.909 0.00 0.00 33.26 5.68
2976 3727 1.734163 AGAAAATTACCCTGACGGCG 58.266 50.000 4.80 4.80 33.26 6.46
2977 3728 0.730840 GAAAATTACCCTGACGGCGG 59.269 55.000 13.24 0.00 33.26 6.13
2978 3729 0.037160 AAAATTACCCTGACGGCGGT 59.963 50.000 13.24 0.00 36.08 5.68
2979 3730 0.675522 AAATTACCCTGACGGCGGTG 60.676 55.000 13.24 0.00 33.36 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 0.250467 CCTGGTCTGGGTGAACTGTG 60.250 60.000 0.00 0.00 32.49 3.66
13 14 3.507143 AAGCTCCCCTGGTCTGGGT 62.507 63.158 11.24 0.00 45.70 4.51
16 17 3.753787 AAAAAGCTCCCCTGGTCTG 57.246 52.632 0.00 0.00 0.00 3.51
89 92 6.267817 GCTAGCATGCTGTGATTTTCAATAA 58.732 36.000 30.42 3.56 0.00 1.40
112 117 4.733972 AAAGAAAAGAAGACTGCTACGC 57.266 40.909 0.00 0.00 0.00 4.42
132 137 7.189079 ACATAACCCTGAACCTTTTGAAAAA 57.811 32.000 0.00 0.00 0.00 1.94
133 138 6.800072 ACATAACCCTGAACCTTTTGAAAA 57.200 33.333 0.00 0.00 0.00 2.29
134 139 6.407525 CCAACATAACCCTGAACCTTTTGAAA 60.408 38.462 0.00 0.00 0.00 2.69
135 140 5.069781 CCAACATAACCCTGAACCTTTTGAA 59.930 40.000 0.00 0.00 0.00 2.69
147 153 7.519347 TCTTTTACTATCCCAACATAACCCT 57.481 36.000 0.00 0.00 0.00 4.34
152 158 9.747898 ACATGTTTCTTTTACTATCCCAACATA 57.252 29.630 0.00 0.00 33.02 2.29
153 159 8.650143 ACATGTTTCTTTTACTATCCCAACAT 57.350 30.769 0.00 0.00 34.66 2.71
186 194 2.037772 AGTCGACCTGAAACAAGCTGAT 59.962 45.455 13.01 0.00 0.00 2.90
218 226 1.412710 GGGACAGTCTGAGACACACAA 59.587 52.381 15.86 0.00 34.60 3.33
228 236 1.134670 GGGAATCTTCGGGACAGTCTG 60.135 57.143 0.00 0.00 0.00 3.51
229 237 1.196012 GGGAATCTTCGGGACAGTCT 58.804 55.000 0.00 0.00 0.00 3.24
281 289 9.872757 GACGAAGACTTCTATCTAATGTCTTAG 57.127 37.037 13.22 9.00 44.70 2.18
284 292 7.867305 TGACGAAGACTTCTATCTAATGTCT 57.133 36.000 13.22 0.00 39.35 3.41
305 346 2.417933 CCTGACTACTTGCAAGCATGAC 59.582 50.000 26.27 15.73 0.00 3.06
366 419 7.486232 GCATTTTGTCTAAAGTATTCTTCCTGC 59.514 37.037 0.00 0.00 32.90 4.85
390 445 3.266772 AGTTCATCCCAGAAAGTATGGCA 59.733 43.478 0.00 0.00 36.43 4.92
448 507 0.036306 AAGTCCTGGCGACGGAATTT 59.964 50.000 0.00 0.00 46.92 1.82
450 509 1.079127 CAAGTCCTGGCGACGGAAT 60.079 57.895 0.00 0.00 46.92 3.01
461 520 1.152096 AGACCCGGGTTCAAGTCCT 60.152 57.895 30.89 15.82 0.00 3.85
506 565 2.706339 TCTCCGTGGTAGTCTAGGTC 57.294 55.000 0.00 0.00 0.00 3.85
518 577 4.391216 GCCATTCTCAATCATATCTCCGTG 59.609 45.833 0.00 0.00 0.00 4.94
524 583 8.388484 AGTAAACTGCCATTCTCAATCATATC 57.612 34.615 0.00 0.00 0.00 1.63
534 593 6.653320 TCGAATGTAAAGTAAACTGCCATTCT 59.347 34.615 17.96 0.00 35.40 2.40
537 596 5.938125 ACTCGAATGTAAAGTAAACTGCCAT 59.062 36.000 0.00 0.00 0.00 4.40
546 605 6.401688 CGCCATTTTCACTCGAATGTAAAGTA 60.402 38.462 5.01 0.00 32.65 2.24
548 607 4.788100 CGCCATTTTCACTCGAATGTAAAG 59.212 41.667 5.01 0.00 32.65 1.85
552 611 1.135689 GCGCCATTTTCACTCGAATGT 60.136 47.619 0.00 0.00 32.65 2.71
553 612 1.135717 TGCGCCATTTTCACTCGAATG 60.136 47.619 4.18 0.00 33.97 2.67
555 614 0.516877 CTGCGCCATTTTCACTCGAA 59.483 50.000 4.18 0.00 0.00 3.71
557 616 1.135315 CCTGCGCCATTTTCACTCG 59.865 57.895 4.18 0.00 0.00 4.18
558 617 0.109597 CACCTGCGCCATTTTCACTC 60.110 55.000 4.18 0.00 0.00 3.51
611 672 3.999001 ACATATCAATGCCGTAGATGCTG 59.001 43.478 0.00 0.00 36.50 4.41
634 695 5.368989 GTGGGATTAGATAGGGTGAAAGTG 58.631 45.833 0.00 0.00 0.00 3.16
668 729 4.627058 TGTGAAAGCTGTGACGATAGAAA 58.373 39.130 0.00 0.00 41.38 2.52
674 735 2.135139 GACATGTGAAAGCTGTGACGA 58.865 47.619 1.15 0.00 0.00 4.20
718 782 1.745653 GAGCTCTATTTGTTGGCACCC 59.254 52.381 6.43 0.00 0.00 4.61
726 790 1.649664 CTGCAGCGAGCTCTATTTGT 58.350 50.000 12.85 0.00 45.94 2.83
772 836 1.071385 ACAACTCAGAGGGCTCTTGTG 59.929 52.381 1.53 0.00 37.98 3.33
783 847 0.464036 AAGGTGCACGACAACTCAGA 59.536 50.000 11.45 0.00 45.97 3.27
788 852 2.032799 TGATTTGAAGGTGCACGACAAC 59.967 45.455 11.45 6.81 35.58 3.32
789 853 2.293170 TGATTTGAAGGTGCACGACAA 58.707 42.857 11.45 13.43 0.00 3.18
828 893 6.056236 GGGTTATTCAAGGGAACTGTCTATC 58.944 44.000 0.00 0.00 42.68 2.08
836 901 2.124277 AGCGGGTTATTCAAGGGAAC 57.876 50.000 0.00 0.00 35.46 3.62
839 905 0.455815 GCAAGCGGGTTATTCAAGGG 59.544 55.000 0.00 0.00 0.00 3.95
842 908 1.904287 ACTGCAAGCGGGTTATTCAA 58.096 45.000 5.79 0.00 37.60 2.69
853 919 2.332514 TTGCGAGCAACTGCAAGC 59.667 55.556 6.39 12.52 45.45 4.01
971 1041 3.118956 CCCTCTAGCTTGTTCACCTACTG 60.119 52.174 0.00 0.00 0.00 2.74
1221 1291 4.910585 GGATACCCAGCGGTGGCG 62.911 72.222 28.23 21.96 44.40 5.69
1224 1294 0.107214 ATTGTGGATACCCAGCGGTG 60.107 55.000 7.86 7.86 44.55 4.94
1318 1391 7.701924 ACATGAACAAATGAAGTGTGTGTAAAG 59.298 33.333 0.00 0.00 0.00 1.85
1343 1416 4.091220 CCATTTTGAAACACACACACACAC 59.909 41.667 0.00 0.00 0.00 3.82
1434 1511 9.710818 ACTCCCTCTGTAACTTAATATAAGACA 57.289 33.333 4.24 0.00 0.00 3.41
1445 1522 9.435570 ACATATGTATTACTCCCTCTGTAACTT 57.564 33.333 6.56 0.00 33.45 2.66
1581 1661 6.046593 TCCCGTATCTATTTGTTGCAAGTAG 58.953 40.000 0.00 0.60 0.00 2.57
1585 1665 4.396790 GGTTCCCGTATCTATTTGTTGCAA 59.603 41.667 0.00 0.00 0.00 4.08
1586 1666 3.942748 GGTTCCCGTATCTATTTGTTGCA 59.057 43.478 0.00 0.00 0.00 4.08
1587 1667 3.001939 CGGTTCCCGTATCTATTTGTTGC 59.998 47.826 0.00 0.00 42.73 4.17
1604 1684 3.435327 TGAACATGCATACTTGACGGTTC 59.565 43.478 12.77 12.77 35.27 3.62
1609 1689 4.395854 TGGACATGAACATGCATACTTGAC 59.604 41.667 13.71 3.72 42.39 3.18
1636 1716 9.582431 TGATTGCATTCTACTAGTACTTAACAC 57.418 33.333 0.00 0.00 0.00 3.32
1642 1722 6.381420 ACACCTGATTGCATTCTACTAGTACT 59.619 38.462 9.81 0.00 0.00 2.73
1643 1723 6.477033 CACACCTGATTGCATTCTACTAGTAC 59.523 42.308 9.81 0.00 0.00 2.73
1644 1724 6.379988 TCACACCTGATTGCATTCTACTAGTA 59.620 38.462 9.81 1.89 0.00 1.82
1645 1725 5.187772 TCACACCTGATTGCATTCTACTAGT 59.812 40.000 9.81 0.00 0.00 2.57
1646 1726 5.664457 TCACACCTGATTGCATTCTACTAG 58.336 41.667 9.81 0.00 0.00 2.57
1647 1727 5.675684 TCACACCTGATTGCATTCTACTA 57.324 39.130 9.81 0.00 0.00 1.82
1652 1732 5.125100 TCTTTTCACACCTGATTGCATTC 57.875 39.130 1.55 1.55 0.00 2.67
1655 1735 3.256383 CCATCTTTTCACACCTGATTGCA 59.744 43.478 0.00 0.00 0.00 4.08
1666 1746 3.256631 ACCATGAAGTGCCATCTTTTCAC 59.743 43.478 0.00 0.00 32.90 3.18
1668 1748 4.022068 TGAACCATGAAGTGCCATCTTTTC 60.022 41.667 0.00 0.00 0.00 2.29
1673 1763 4.022589 CCATATGAACCATGAAGTGCCATC 60.023 45.833 3.65 0.00 0.00 3.51
1685 1775 2.158623 GGTCATGCCTCCATATGAACCA 60.159 50.000 3.65 0.00 35.48 3.67
1686 1776 2.158623 TGGTCATGCCTCCATATGAACC 60.159 50.000 3.65 0.00 39.66 3.62
1704 1800 3.132289 ACCGATCGAGTTCATAACATGGT 59.868 43.478 18.66 0.00 0.00 3.55
1705 1801 3.717707 ACCGATCGAGTTCATAACATGG 58.282 45.455 18.66 0.00 0.00 3.66
1706 1802 4.956034 GACCGATCGAGTTCATAACATG 57.044 45.455 18.66 0.00 0.00 3.21
1720 1816 0.992802 GCAAGTTGACTCGACCGATC 59.007 55.000 7.16 0.00 0.00 3.69
1721 1817 0.317160 TGCAAGTTGACTCGACCGAT 59.683 50.000 7.16 0.00 0.00 4.18
1738 1834 2.224018 TGACCTGAACAAAATGGCTTGC 60.224 45.455 0.00 0.00 0.00 4.01
1831 1927 1.269778 TGTGAGCTCCATATACTGCGC 60.270 52.381 12.15 0.00 0.00 6.09
1837 1933 3.068165 CGACACCTTGTGAGCTCCATATA 59.932 47.826 12.15 0.00 36.96 0.86
1893 1989 0.681564 TTGAACTTGCCGTGGTGGTT 60.682 50.000 0.00 0.00 41.21 3.67
2063 2163 2.768527 GGAGGAGTCATTGGTGAGATGA 59.231 50.000 0.00 0.00 34.36 2.92
2084 2184 2.435586 CCTTCTGAGCGGCACAGG 60.436 66.667 23.87 11.15 36.22 4.00
2111 2212 5.354234 GGAACGATAACAAAGGTGATCACAT 59.646 40.000 26.47 18.11 34.92 3.21
2123 2224 6.292923 TCAGAGGAAAAAGGAACGATAACAA 58.707 36.000 0.00 0.00 0.00 2.83
2142 2243 3.496875 CTGCCGGCGATCCTCAGAG 62.497 68.421 23.90 6.04 34.55 3.35
2153 2254 0.525761 TCAACAATAAAGCTGCCGGC 59.474 50.000 22.73 22.73 42.19 6.13
2155 2256 3.763097 TCATCAACAATAAAGCTGCCG 57.237 42.857 0.00 0.00 0.00 5.69
2156 2257 4.808558 TGTTCATCAACAATAAAGCTGCC 58.191 39.130 0.00 0.00 39.69 4.85
2226 2328 3.009473 AGCTTTGGAGAATTGGAGCACTA 59.991 43.478 0.00 0.00 32.78 2.74
2227 2329 2.165998 GCTTTGGAGAATTGGAGCACT 58.834 47.619 0.00 0.00 0.00 4.40
2228 2330 2.165998 AGCTTTGGAGAATTGGAGCAC 58.834 47.619 0.00 0.00 32.78 4.40
2230 2332 3.615155 AGTAGCTTTGGAGAATTGGAGC 58.385 45.455 0.00 0.00 0.00 4.70
2275 2594 5.605069 TCCCTCCGATCCATATTACTTTTCA 59.395 40.000 0.00 0.00 0.00 2.69
2278 2597 5.155905 ACTCCCTCCGATCCATATTACTTT 58.844 41.667 0.00 0.00 0.00 2.66
2317 2636 1.840635 AGTTGGGGTAGGAGAAGCATC 59.159 52.381 0.00 0.00 0.00 3.91
2341 2660 8.655901 AGAGGAAGAATTGAAGAACTAGAACTT 58.344 33.333 0.00 1.05 0.00 2.66
2374 2702 3.181445 CGTATCTGGGGATTCCAATTCCA 60.181 47.826 4.80 1.71 46.51 3.53
2375 2703 3.072476 TCGTATCTGGGGATTCCAATTCC 59.928 47.826 4.80 0.00 46.51 3.01
2376 2704 4.351874 TCGTATCTGGGGATTCCAATTC 57.648 45.455 4.80 0.00 46.51 2.17
2377 2705 4.788925 TTCGTATCTGGGGATTCCAATT 57.211 40.909 4.80 0.00 46.51 2.32
2378 2706 4.788925 TTTCGTATCTGGGGATTCCAAT 57.211 40.909 4.80 0.00 46.51 3.16
2459 2789 6.978659 TGCGTATTTTGTACAATGAAAACCAA 59.021 30.769 9.56 0.00 0.00 3.67
2511 3229 2.411628 TGTATGCCAAACCGTGCTAT 57.588 45.000 0.00 0.00 0.00 2.97
2520 3238 6.155827 GCATAAAGTTCAGTTGTATGCCAAA 58.844 36.000 4.34 0.00 40.63 3.28
2521 3239 5.708948 GCATAAAGTTCAGTTGTATGCCAA 58.291 37.500 4.34 0.00 40.63 4.52
2529 3247 7.029563 GGATAAACAGGCATAAAGTTCAGTTG 58.970 38.462 0.00 0.00 0.00 3.16
2583 3332 5.050227 GCATCTGAATTATCTGTGCTGTCTC 60.050 44.000 0.00 0.00 33.30 3.36
2588 3337 6.259608 GTGTTAGCATCTGAATTATCTGTGCT 59.740 38.462 0.00 0.00 40.81 4.40
2597 3346 7.309438 GGGAAGAAAAGTGTTAGCATCTGAATT 60.309 37.037 0.00 0.00 0.00 2.17
2598 3347 6.151817 GGGAAGAAAAGTGTTAGCATCTGAAT 59.848 38.462 0.00 0.00 0.00 2.57
2610 3359 1.348036 CGAGGAGGGGAAGAAAAGTGT 59.652 52.381 0.00 0.00 0.00 3.55
2612 3361 1.348036 CACGAGGAGGGGAAGAAAAGT 59.652 52.381 0.00 0.00 0.00 2.66
2613 3362 1.348036 ACACGAGGAGGGGAAGAAAAG 59.652 52.381 0.00 0.00 0.00 2.27
2714 3463 3.409605 AACGCCGGTGACCTGGTTT 62.410 57.895 24.59 0.00 0.00 3.27
2756 3505 9.129209 GGTAACAGAGATTTGCTTTATGTTTTC 57.871 33.333 0.00 0.00 33.20 2.29
2759 3508 7.665559 TCAGGTAACAGAGATTTGCTTTATGTT 59.334 33.333 0.00 0.00 41.41 2.71
2763 3512 5.637810 CGTCAGGTAACAGAGATTTGCTTTA 59.362 40.000 0.00 0.00 41.41 1.85
2766 3515 3.258372 TCGTCAGGTAACAGAGATTTGCT 59.742 43.478 0.00 0.00 41.41 3.91
2767 3516 3.585862 TCGTCAGGTAACAGAGATTTGC 58.414 45.455 0.00 0.00 41.41 3.68
2776 3525 5.587844 GTCTACCTAGATTCGTCAGGTAACA 59.412 44.000 12.81 4.23 42.80 2.41
2820 3569 5.047590 TCGATTTGTACGTGCCCTATCATAT 60.048 40.000 0.00 0.00 0.00 1.78
2821 3570 4.278919 TCGATTTGTACGTGCCCTATCATA 59.721 41.667 0.00 0.00 0.00 2.15
2870 3619 2.048503 GGCGGCGGCGTATTCTAT 60.049 61.111 32.35 0.00 41.24 1.98
2920 3669 1.139654 CTCTCAATTCTGCCCATCCGA 59.860 52.381 0.00 0.00 0.00 4.55
2921 3670 1.134280 ACTCTCAATTCTGCCCATCCG 60.134 52.381 0.00 0.00 0.00 4.18
2922 3671 2.725221 ACTCTCAATTCTGCCCATCC 57.275 50.000 0.00 0.00 0.00 3.51
2923 3672 7.283127 TGTTAAATACTCTCAATTCTGCCCATC 59.717 37.037 0.00 0.00 0.00 3.51
2924 3673 7.067494 GTGTTAAATACTCTCAATTCTGCCCAT 59.933 37.037 0.00 0.00 0.00 4.00
2949 3700 6.206048 CCGTCAGGGTAATTTTCTTTTACTGT 59.794 38.462 0.00 0.00 31.62 3.55
2956 3707 2.081462 CGCCGTCAGGGTAATTTTCTT 58.919 47.619 0.00 0.00 38.44 2.52
2957 3708 1.677820 CCGCCGTCAGGGTAATTTTCT 60.678 52.381 0.00 0.00 38.44 2.52


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

AutoCloner maintained by Alex Coulton.