Multiple sequence alignment - TraesCS1A01G151900

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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 TraesCS1A01G151900 chr1A 100.000 2339 0 0 1 2339 260841565 260843903 0.000000e+00 4320
1 TraesCS1A01G151900 chr1A 95.011 1363 67 1 1 1362 277626961 277625599 0.000000e+00 2139
2 TraesCS1A01G151900 chr4A 97.434 1364 33 2 1 1362 438390309 438391672 0.000000e+00 2324
3 TraesCS1A01G151900 chr4A 87.588 854 67 14 1487 2332 217675832 217675010 0.000000e+00 953
4 TraesCS1A01G151900 chr5A 97.295 1331 35 1 36 1365 634633840 634632510 0.000000e+00 2257
5 TraesCS1A01G151900 chr5A 95.231 1363 63 2 1 1362 343044029 343042668 0.000000e+00 2156
6 TraesCS1A01G151900 chr4D 96.329 1362 49 1 1 1362 126638011 126639371 0.000000e+00 2237
7 TraesCS1A01G151900 chr4D 95.888 1362 54 2 1 1362 463910328 463911687 0.000000e+00 2204
8 TraesCS1A01G151900 chr3B 95.891 1363 55 1 1 1362 541062982 541061620 0.000000e+00 2206
9 TraesCS1A01G151900 chr5D 95.311 1365 60 2 1 1362 63606620 63607983 0.000000e+00 2163
10 TraesCS1A01G151900 chr7B 94.926 1360 68 1 1 1359 33420465 33421824 0.000000e+00 2128
11 TraesCS1A01G151900 chr6A 80.539 334 62 3 1360 1691 466281160 466281492 1.070000e-63 254


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 TraesCS1A01G151900 chr1A 260841565 260843903 2338 False 4320 4320 100.000 1 2339 1 chr1A.!!$F1 2338
1 TraesCS1A01G151900 chr1A 277625599 277626961 1362 True 2139 2139 95.011 1 1362 1 chr1A.!!$R1 1361
2 TraesCS1A01G151900 chr4A 438390309 438391672 1363 False 2324 2324 97.434 1 1362 1 chr4A.!!$F1 1361
3 TraesCS1A01G151900 chr4A 217675010 217675832 822 True 953 953 87.588 1487 2332 1 chr4A.!!$R1 845
4 TraesCS1A01G151900 chr5A 634632510 634633840 1330 True 2257 2257 97.295 36 1365 1 chr5A.!!$R2 1329
5 TraesCS1A01G151900 chr5A 343042668 343044029 1361 True 2156 2156 95.231 1 1362 1 chr5A.!!$R1 1361
6 TraesCS1A01G151900 chr4D 126638011 126639371 1360 False 2237 2237 96.329 1 1362 1 chr4D.!!$F1 1361
7 TraesCS1A01G151900 chr4D 463910328 463911687 1359 False 2204 2204 95.888 1 1362 1 chr4D.!!$F2 1361
8 TraesCS1A01G151900 chr3B 541061620 541062982 1362 True 2206 2206 95.891 1 1362 1 chr3B.!!$R1 1361
9 TraesCS1A01G151900 chr5D 63606620 63607983 1363 False 2163 2163 95.311 1 1362 1 chr5D.!!$F1 1361
10 TraesCS1A01G151900 chr7B 33420465 33421824 1359 False 2128 2128 94.926 1 1359 1 chr7B.!!$F1 1358

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
426 428 1.342473 GCGTACGTTACATGGCACG 59.658 57.895 17.9 15.22 42.29 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1419 1425 0.034896 GAAGCTCTGAAACCCACGGA 59.965 55.0 0.0 0.0 0.0 4.69 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
116 118 4.582869 TCAAGAGTGGTTGATCTGATTGG 58.417 43.478 0.00 0.00 31.31 3.16
331 333 9.444600 GTAAACTAAAACACTCTAATGGGATGA 57.555 33.333 0.00 0.00 0.00 2.92
426 428 1.342473 GCGTACGTTACATGGCACG 59.658 57.895 17.90 15.22 42.29 5.34
751 753 5.852282 ATTAGTGCACAAGGAAACAACTT 57.148 34.783 21.04 0.00 0.00 2.66
1004 1007 2.537560 GCGCGGATGTTCTGATGGG 61.538 63.158 8.83 0.00 0.00 4.00
1049 1052 1.346722 ACTAACACTAGCGCAAAGGGT 59.653 47.619 11.47 11.49 29.76 4.34
1219 1225 9.905713 AACATTGTAATAGAGAGGCAAATAGAA 57.094 29.630 0.00 0.00 0.00 2.10
1377 1383 3.418684 AAAAAGGTGGATAGCTCGTGT 57.581 42.857 0.00 0.00 32.44 4.49
1378 1384 3.418684 AAAAGGTGGATAGCTCGTGTT 57.581 42.857 0.00 0.00 32.44 3.32
1379 1385 2.674796 AAGGTGGATAGCTCGTGTTC 57.325 50.000 0.00 0.00 32.44 3.18
1380 1386 0.824759 AGGTGGATAGCTCGTGTTCC 59.175 55.000 0.00 0.00 0.00 3.62
1381 1387 0.179081 GGTGGATAGCTCGTGTTCCC 60.179 60.000 0.00 0.00 0.00 3.97
1382 1388 0.535335 GTGGATAGCTCGTGTTCCCA 59.465 55.000 0.00 0.00 0.00 4.37
1383 1389 0.535335 TGGATAGCTCGTGTTCCCAC 59.465 55.000 0.00 0.00 38.27 4.61
1384 1390 0.535335 GGATAGCTCGTGTTCCCACA 59.465 55.000 0.00 0.00 41.93 4.17
1385 1391 1.471676 GGATAGCTCGTGTTCCCACAG 60.472 57.143 0.00 0.00 41.93 3.66
1386 1392 0.537188 ATAGCTCGTGTTCCCACAGG 59.463 55.000 0.00 0.00 41.93 4.00
1387 1393 0.830444 TAGCTCGTGTTCCCACAGGT 60.830 55.000 0.00 0.00 41.93 4.00
1388 1394 1.961277 GCTCGTGTTCCCACAGGTG 60.961 63.158 0.00 0.00 41.93 4.00
1399 1405 2.799126 CCACAGGTGGCCTTATAACA 57.201 50.000 3.32 0.00 44.73 2.41
1400 1406 2.365582 CCACAGGTGGCCTTATAACAC 58.634 52.381 3.32 0.00 44.73 3.32
1407 1413 4.450082 GTGGCCTTATAACACCAAAAGG 57.550 45.455 3.32 0.00 41.23 3.11
1408 1414 3.830178 GTGGCCTTATAACACCAAAAGGT 59.170 43.478 3.32 0.00 40.55 3.50
1409 1415 5.011586 GTGGCCTTATAACACCAAAAGGTA 58.988 41.667 3.32 0.00 40.55 3.08
1410 1416 5.477637 GTGGCCTTATAACACCAAAAGGTAA 59.522 40.000 3.32 0.00 40.55 2.85
1411 1417 6.015265 GTGGCCTTATAACACCAAAAGGTAAA 60.015 38.462 3.32 0.00 40.55 2.01
1412 1418 6.726764 TGGCCTTATAACACCAAAAGGTAAAT 59.273 34.615 3.32 0.00 40.55 1.40
1413 1419 7.039270 GGCCTTATAACACCAAAAGGTAAATG 58.961 38.462 0.00 0.00 40.55 2.32
1414 1420 7.310175 GGCCTTATAACACCAAAAGGTAAATGT 60.310 37.037 0.00 0.00 40.55 2.71
1415 1421 7.758076 GCCTTATAACACCAAAAGGTAAATGTC 59.242 37.037 0.00 0.00 40.55 3.06
1416 1422 7.966204 CCTTATAACACCAAAAGGTAAATGTCG 59.034 37.037 0.00 0.00 34.92 4.35
1417 1423 8.618702 TTATAACACCAAAAGGTAAATGTCGA 57.381 30.769 0.00 0.00 0.00 4.20
1418 1424 7.696992 ATAACACCAAAAGGTAAATGTCGAT 57.303 32.000 0.00 0.00 0.00 3.59
1419 1425 6.399639 AACACCAAAAGGTAAATGTCGATT 57.600 33.333 0.00 0.00 0.00 3.34
1420 1426 6.009115 ACACCAAAAGGTAAATGTCGATTC 57.991 37.500 0.00 0.00 0.00 2.52
1421 1427 5.048294 ACACCAAAAGGTAAATGTCGATTCC 60.048 40.000 0.00 0.00 0.00 3.01
1422 1428 4.155280 ACCAAAAGGTAAATGTCGATTCCG 59.845 41.667 0.00 0.00 37.07 4.30
1423 1429 4.155280 CCAAAAGGTAAATGTCGATTCCGT 59.845 41.667 0.00 0.00 37.05 4.69
1424 1430 4.939509 AAAGGTAAATGTCGATTCCGTG 57.060 40.909 0.00 0.00 37.05 4.94
1425 1431 2.901249 AGGTAAATGTCGATTCCGTGG 58.099 47.619 0.00 0.00 37.05 4.94
1426 1432 1.937899 GGTAAATGTCGATTCCGTGGG 59.062 52.381 0.00 0.00 37.05 4.61
1427 1433 2.624636 GTAAATGTCGATTCCGTGGGT 58.375 47.619 0.00 0.00 37.05 4.51
1428 1434 2.194201 AAATGTCGATTCCGTGGGTT 57.806 45.000 0.00 0.00 37.05 4.11
1429 1435 2.194201 AATGTCGATTCCGTGGGTTT 57.806 45.000 0.00 0.00 37.05 3.27
1430 1436 1.734163 ATGTCGATTCCGTGGGTTTC 58.266 50.000 0.00 0.00 37.05 2.78
1431 1437 0.393448 TGTCGATTCCGTGGGTTTCA 59.607 50.000 0.00 0.00 37.05 2.69
1432 1438 1.076332 GTCGATTCCGTGGGTTTCAG 58.924 55.000 0.00 0.00 37.05 3.02
1433 1439 0.970640 TCGATTCCGTGGGTTTCAGA 59.029 50.000 0.00 0.00 37.05 3.27
1434 1440 1.067142 TCGATTCCGTGGGTTTCAGAG 60.067 52.381 0.00 0.00 37.05 3.35
1435 1441 1.087501 GATTCCGTGGGTTTCAGAGC 58.912 55.000 0.00 0.00 0.00 4.09
1436 1442 0.693049 ATTCCGTGGGTTTCAGAGCT 59.307 50.000 0.00 0.00 0.00 4.09
1437 1443 0.472471 TTCCGTGGGTTTCAGAGCTT 59.528 50.000 0.00 0.00 0.00 3.74
1438 1444 0.034896 TCCGTGGGTTTCAGAGCTTC 59.965 55.000 0.00 0.00 0.00 3.86
1439 1445 0.035458 CCGTGGGTTTCAGAGCTTCT 59.965 55.000 0.00 0.00 0.00 2.85
1440 1446 1.151668 CGTGGGTTTCAGAGCTTCTG 58.848 55.000 6.79 6.79 45.59 3.02
1441 1447 1.528129 GTGGGTTTCAGAGCTTCTGG 58.472 55.000 11.63 0.00 44.39 3.86
1442 1448 1.072331 GTGGGTTTCAGAGCTTCTGGA 59.928 52.381 11.63 2.51 44.39 3.86
1443 1449 1.072331 TGGGTTTCAGAGCTTCTGGAC 59.928 52.381 11.63 10.54 44.39 4.02
1444 1450 1.611936 GGGTTTCAGAGCTTCTGGACC 60.612 57.143 19.28 19.28 44.39 4.46
1445 1451 1.072331 GGTTTCAGAGCTTCTGGACCA 59.928 52.381 20.83 0.00 44.39 4.02
1446 1452 2.290577 GGTTTCAGAGCTTCTGGACCAT 60.291 50.000 20.83 0.00 44.39 3.55
1447 1453 3.055094 GGTTTCAGAGCTTCTGGACCATA 60.055 47.826 20.83 0.00 44.39 2.74
1448 1454 4.565652 GGTTTCAGAGCTTCTGGACCATAA 60.566 45.833 20.83 0.00 44.39 1.90
1449 1455 5.189180 GTTTCAGAGCTTCTGGACCATAAT 58.811 41.667 11.63 0.00 44.39 1.28
1450 1456 4.412796 TCAGAGCTTCTGGACCATAATG 57.587 45.455 11.63 0.00 44.39 1.90
1451 1457 3.135348 TCAGAGCTTCTGGACCATAATGG 59.865 47.826 11.63 0.00 44.39 3.16
1452 1458 2.158696 AGAGCTTCTGGACCATAATGGC 60.159 50.000 0.00 0.00 42.67 4.40
1453 1459 1.565759 AGCTTCTGGACCATAATGGCA 59.434 47.619 0.00 0.00 42.67 4.92
1454 1460 2.025037 AGCTTCTGGACCATAATGGCAA 60.025 45.455 0.00 0.00 42.67 4.52
1455 1461 2.961062 GCTTCTGGACCATAATGGCAAT 59.039 45.455 0.00 0.00 42.67 3.56
1456 1462 3.243636 GCTTCTGGACCATAATGGCAATG 60.244 47.826 0.00 0.00 42.67 2.82
1457 1463 3.668141 TCTGGACCATAATGGCAATGT 57.332 42.857 0.00 0.00 42.67 2.71
1458 1464 3.289836 TCTGGACCATAATGGCAATGTG 58.710 45.455 0.00 0.00 42.67 3.21
1459 1465 2.363038 CTGGACCATAATGGCAATGTGG 59.637 50.000 15.89 15.89 42.67 4.17
1460 1466 1.688197 GGACCATAATGGCAATGTGGG 59.312 52.381 20.61 8.38 42.67 4.61
1461 1467 2.665165 GACCATAATGGCAATGTGGGA 58.335 47.619 20.61 0.00 42.67 4.37
1462 1468 3.233507 GACCATAATGGCAATGTGGGAT 58.766 45.455 20.61 2.48 42.67 3.85
1463 1469 2.967201 ACCATAATGGCAATGTGGGATG 59.033 45.455 20.61 0.00 42.67 3.51
1464 1470 3.232662 CCATAATGGCAATGTGGGATGA 58.767 45.455 10.27 0.00 0.00 2.92
1465 1471 3.835978 CCATAATGGCAATGTGGGATGAT 59.164 43.478 10.27 0.00 0.00 2.45
1466 1472 4.322424 CCATAATGGCAATGTGGGATGATG 60.322 45.833 10.27 0.00 0.00 3.07
1467 1473 2.464796 ATGGCAATGTGGGATGATGT 57.535 45.000 0.00 0.00 0.00 3.06
1468 1474 2.234896 TGGCAATGTGGGATGATGTT 57.765 45.000 0.00 0.00 0.00 2.71
1469 1475 3.378861 TGGCAATGTGGGATGATGTTA 57.621 42.857 0.00 0.00 0.00 2.41
1470 1476 3.706183 TGGCAATGTGGGATGATGTTAA 58.294 40.909 0.00 0.00 0.00 2.01
1471 1477 4.092279 TGGCAATGTGGGATGATGTTAAA 58.908 39.130 0.00 0.00 0.00 1.52
1472 1478 4.081752 TGGCAATGTGGGATGATGTTAAAC 60.082 41.667 0.00 0.00 0.00 2.01
1473 1479 4.160252 GGCAATGTGGGATGATGTTAAACT 59.840 41.667 0.00 0.00 0.00 2.66
1474 1480 5.104374 GCAATGTGGGATGATGTTAAACTG 58.896 41.667 0.00 0.00 0.00 3.16
1475 1481 4.989279 ATGTGGGATGATGTTAAACTGC 57.011 40.909 0.00 0.00 0.00 4.40
1476 1482 3.760738 TGTGGGATGATGTTAAACTGCA 58.239 40.909 0.00 0.00 0.00 4.41
1477 1483 4.148079 TGTGGGATGATGTTAAACTGCAA 58.852 39.130 0.00 0.00 0.00 4.08
1478 1484 4.022416 TGTGGGATGATGTTAAACTGCAAC 60.022 41.667 0.00 0.00 0.00 4.17
1479 1485 4.022416 GTGGGATGATGTTAAACTGCAACA 60.022 41.667 0.00 0.00 40.01 3.33
1480 1486 4.218200 TGGGATGATGTTAAACTGCAACAG 59.782 41.667 0.00 0.00 39.15 3.16
1499 1505 3.848975 ACAGTTCTCTCTCCCAATGGATT 59.151 43.478 0.00 0.00 40.80 3.01
1504 1510 5.045012 TCTCTCTCCCAATGGATTTCATG 57.955 43.478 0.00 0.00 40.80 3.07
1506 1512 3.117398 TCTCTCCCAATGGATTTCATGGG 60.117 47.826 0.00 3.24 44.91 4.00
1544 1550 5.677621 AGCCATCTCCAAGATTTGGCTCTA 61.678 45.833 15.22 0.00 45.60 2.43
1566 1572 4.041762 CCTTGGGTGGGCGCCTAA 62.042 66.667 28.56 12.85 0.00 2.69
1633 1639 7.480855 GCTTATAATGAACTTCATGATGCATCG 59.519 37.037 21.34 8.64 37.15 3.84
1647 1653 3.541996 TGCATCGATTAGCTCTTCCAA 57.458 42.857 8.93 0.00 0.00 3.53
1654 1660 5.357257 TCGATTAGCTCTTCCAATACCAAC 58.643 41.667 0.00 0.00 0.00 3.77
1660 1666 5.324409 AGCTCTTCCAATACCAACATTCAA 58.676 37.500 0.00 0.00 0.00 2.69
1696 1702 3.039011 TGGAAAGCTATCTGGTCTACCC 58.961 50.000 0.00 0.00 34.29 3.69
1697 1703 3.039011 GGAAAGCTATCTGGTCTACCCA 58.961 50.000 0.00 0.00 42.51 4.51
1736 1742 2.677914 AGGTCCTTTCTTTTGGTTGGG 58.322 47.619 0.00 0.00 0.00 4.12
1754 1760 3.362706 TGGGGACTAGCTACTAACACTG 58.637 50.000 0.00 0.00 0.00 3.66
1755 1761 3.010920 TGGGGACTAGCTACTAACACTGA 59.989 47.826 0.00 0.00 0.00 3.41
1756 1762 3.380954 GGGGACTAGCTACTAACACTGAC 59.619 52.174 0.00 0.00 0.00 3.51
1760 1768 3.688673 ACTAGCTACTAACACTGACGACC 59.311 47.826 0.00 0.00 0.00 4.79
1776 1784 2.233922 ACGACCTGGAGTAACAAGATGG 59.766 50.000 0.00 0.00 0.00 3.51
1788 1796 8.624776 GGAGTAACAAGATGGAAAGAAATATGG 58.375 37.037 0.00 0.00 0.00 2.74
1789 1797 8.000780 AGTAACAAGATGGAAAGAAATATGGC 57.999 34.615 0.00 0.00 0.00 4.40
1790 1798 7.836183 AGTAACAAGATGGAAAGAAATATGGCT 59.164 33.333 0.00 0.00 0.00 4.75
1791 1799 9.120538 GTAACAAGATGGAAAGAAATATGGCTA 57.879 33.333 0.00 0.00 0.00 3.93
1799 1807 5.334414 GGAAAGAAATATGGCTATGAGTGCG 60.334 44.000 0.00 0.00 0.00 5.34
1820 1828 4.792704 GCGACATGTCTGATTTGTGGTTTT 60.793 41.667 22.95 0.00 0.00 2.43
1829 1837 3.577848 TGATTTGTGGTTTTGGAGATGGG 59.422 43.478 0.00 0.00 0.00 4.00
1867 1876 1.483827 TCTGCTCCTGTCCAATGCTAG 59.516 52.381 0.00 0.00 0.00 3.42
1869 1878 0.833287 GCTCCTGTCCAATGCTAGGA 59.167 55.000 0.00 0.00 37.72 2.94
1876 1885 4.082571 CCTGTCCAATGCTAGGAAACTTTG 60.083 45.833 0.00 0.00 43.67 2.77
1908 1918 3.181483 GCTATTGGATTGGTCTTTGCCAG 60.181 47.826 0.00 0.00 40.01 4.85
1910 1920 1.243342 TGGATTGGTCTTTGCCAGCG 61.243 55.000 0.00 0.00 40.01 5.18
1923 1933 2.087646 TGCCAGCGTTAACATGCATTA 58.912 42.857 6.39 0.00 37.39 1.90
1925 1935 2.097466 GCCAGCGTTAACATGCATTAGT 59.903 45.455 6.39 0.00 37.39 2.24
1926 1936 3.683989 CCAGCGTTAACATGCATTAGTG 58.316 45.455 6.39 0.00 37.39 2.74
1935 1945 3.813596 GCATTAGTGCGACTGGGG 58.186 61.111 0.00 0.00 42.28 4.96
1936 1946 1.220749 GCATTAGTGCGACTGGGGA 59.779 57.895 0.00 0.00 42.28 4.81
1937 1947 0.179045 GCATTAGTGCGACTGGGGAT 60.179 55.000 0.00 0.00 42.28 3.85
1938 1948 1.586422 CATTAGTGCGACTGGGGATG 58.414 55.000 0.00 0.00 0.00 3.51
1939 1949 1.138859 CATTAGTGCGACTGGGGATGA 59.861 52.381 0.00 0.00 0.00 2.92
1940 1950 1.496060 TTAGTGCGACTGGGGATGAT 58.504 50.000 0.00 0.00 0.00 2.45
1941 1951 1.496060 TAGTGCGACTGGGGATGATT 58.504 50.000 0.00 0.00 0.00 2.57
1942 1952 0.107508 AGTGCGACTGGGGATGATTG 60.108 55.000 0.00 0.00 0.00 2.67
1943 1953 0.107703 GTGCGACTGGGGATGATTGA 60.108 55.000 0.00 0.00 0.00 2.57
1962 1972 3.831323 TGATTCTCAGGGTTCTTTTGCA 58.169 40.909 0.00 0.00 0.00 4.08
1964 1974 4.834496 TGATTCTCAGGGTTCTTTTGCAAT 59.166 37.500 0.00 0.00 0.00 3.56
1967 1977 3.822735 TCTCAGGGTTCTTTTGCAATCTG 59.177 43.478 0.00 0.71 0.00 2.90
1970 1980 3.321682 CAGGGTTCTTTTGCAATCTGGAA 59.678 43.478 0.00 0.00 0.00 3.53
1987 1997 1.804151 GGAAGAAGTAATGCGTGCACA 59.196 47.619 18.64 0.00 0.00 4.57
2022 2032 4.338400 TGTTCTAGAGGATGTGGTATGTCG 59.662 45.833 0.00 0.00 0.00 4.35
2027 2037 3.711704 AGAGGATGTGGTATGTCGGAAAT 59.288 43.478 0.00 0.00 0.00 2.17
2046 2056 6.183360 CGGAAATGAGATTGTGCATTCAAAAG 60.183 38.462 0.00 0.00 33.87 2.27
2047 2057 6.869913 GGAAATGAGATTGTGCATTCAAAAGA 59.130 34.615 0.00 0.00 33.87 2.52
2048 2058 7.063074 GGAAATGAGATTGTGCATTCAAAAGAG 59.937 37.037 0.00 0.00 33.87 2.85
2049 2059 4.801891 TGAGATTGTGCATTCAAAAGAGC 58.198 39.130 0.00 0.00 0.00 4.09
2050 2060 4.521639 TGAGATTGTGCATTCAAAAGAGCT 59.478 37.500 0.00 0.00 0.00 4.09
2051 2061 5.056894 AGATTGTGCATTCAAAAGAGCTC 57.943 39.130 5.27 5.27 0.00 4.09
2053 2063 1.536766 TGTGCATTCAAAAGAGCTCCG 59.463 47.619 10.93 0.00 0.00 4.63
2058 2069 3.525537 CATTCAAAAGAGCTCCGCTAGA 58.474 45.455 10.93 0.00 39.88 2.43
2062 2073 2.863137 CAAAAGAGCTCCGCTAGATGAC 59.137 50.000 10.93 0.00 39.88 3.06
2074 2085 3.428870 CGCTAGATGACGTGTCAAAAAGT 59.571 43.478 6.80 0.00 43.58 2.66
2114 2128 6.294564 CCGTACACTATACTCCATTAGCACAT 60.295 42.308 0.00 0.00 0.00 3.21
2128 2142 7.038729 TCCATTAGCACATACCCAAATTTTGAA 60.039 33.333 10.72 0.00 0.00 2.69
2130 2144 5.543507 AGCACATACCCAAATTTTGAACA 57.456 34.783 10.72 0.00 0.00 3.18
2131 2145 6.112927 AGCACATACCCAAATTTTGAACAT 57.887 33.333 10.72 0.00 0.00 2.71
2154 2168 0.752658 AAAGGAAAAGCAGCCACCAC 59.247 50.000 0.00 0.00 0.00 4.16
2155 2169 0.106015 AAGGAAAAGCAGCCACCACT 60.106 50.000 0.00 0.00 0.00 4.00
2166 2180 0.459489 GCCACCACTTTGTGCTTTCA 59.541 50.000 0.00 0.00 34.85 2.69
2197 2211 8.863049 GTTGATTCAATACACAATAAAAGGCTG 58.137 33.333 1.78 0.00 0.00 4.85
2218 2232 2.781923 CAACCTGATGTGATGTGGTCA 58.218 47.619 0.00 0.00 0.00 4.02
2223 2237 1.282738 TGATGTGATGTGGTCATGCCT 59.717 47.619 7.54 0.00 39.48 4.75
2225 2239 1.536940 TGTGATGTGGTCATGCCTTG 58.463 50.000 7.54 0.00 39.48 3.61
2277 2291 4.037923 TGGTTCTTTCCTCAACAATGAAGC 59.962 41.667 0.00 0.00 36.59 3.86
2278 2292 4.037923 GGTTCTTTCCTCAACAATGAAGCA 59.962 41.667 0.00 0.00 36.31 3.91
2279 2293 5.218139 GTTCTTTCCTCAACAATGAAGCAG 58.782 41.667 0.00 0.00 34.49 4.24
2300 2314 0.252479 AGCAGGCATGGTTCTCAGAG 59.748 55.000 0.00 0.00 31.66 3.35
2308 2322 3.794717 CATGGTTCTCAGAGACCATGAG 58.205 50.000 33.08 20.15 45.83 2.90
2310 2324 2.225369 TGGTTCTCAGAGACCATGAGGA 60.225 50.000 14.46 0.00 43.60 3.71
2312 2326 3.096092 GTTCTCAGAGACCATGAGGAGT 58.904 50.000 0.00 0.00 43.60 3.85
2321 2335 7.014711 TCAGAGACCATGAGGAGTCAATTATAC 59.985 40.741 0.00 0.00 35.88 1.47
2328 2342 7.418368 CCATGAGGAGTCAATTATACTCAGTGT 60.418 40.741 17.39 0.00 44.25 3.55
2332 2346 5.292101 GGAGTCAATTATACTCAGTGTGTGC 59.708 44.000 17.39 0.00 44.25 4.57
2333 2347 5.793817 AGTCAATTATACTCAGTGTGTGCA 58.206 37.500 8.09 0.00 0.00 4.57
2334 2348 6.230472 AGTCAATTATACTCAGTGTGTGCAA 58.770 36.000 8.09 2.62 0.00 4.08
2335 2349 6.369890 AGTCAATTATACTCAGTGTGTGCAAG 59.630 38.462 8.09 0.00 0.00 4.01
2336 2350 5.122239 TCAATTATACTCAGTGTGTGCAAGC 59.878 40.000 8.09 0.00 0.00 4.01
2337 2351 2.549064 ATACTCAGTGTGTGCAAGCA 57.451 45.000 8.09 0.00 0.00 3.91
2338 2352 2.323968 TACTCAGTGTGTGCAAGCAA 57.676 45.000 8.09 0.00 0.00 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 4.472108 ACAATTTGGGATCCATGCATCTTT 59.528 37.500 15.23 0.00 31.53 2.52
144 146 5.428253 GGCCACATAGTTTGTCTAATCAGA 58.572 41.667 0.00 0.00 36.00 3.27
751 753 6.938596 CCCATTGATATCTGAGTTGCATTCTA 59.061 38.462 3.98 0.00 0.00 2.10
1004 1007 6.015434 TCCAAATTTGAGGGCTAAAACTTCTC 60.015 38.462 19.86 0.00 0.00 2.87
1049 1052 0.465460 GATTAGGCGATTGCACCCCA 60.465 55.000 7.38 0.00 45.35 4.96
1243 1249 8.031277 CCAATCCAAAGTTGAAGAAAATCTAGG 58.969 37.037 0.00 0.00 0.00 3.02
1362 1368 0.179081 GGGAACACGAGCTATCCACC 60.179 60.000 0.00 0.00 33.48 4.61
1381 1387 2.365582 GGTGTTATAAGGCCACCTGTG 58.634 52.381 5.01 0.00 44.21 3.66
1382 1388 2.801077 GGTGTTATAAGGCCACCTGT 57.199 50.000 5.01 0.00 44.21 4.00
1386 1392 4.450082 CCTTTTGGTGTTATAAGGCCAC 57.550 45.455 5.01 0.00 31.59 5.01
1396 1402 9.586045 CGGAATCGACATTTACCTTTTGGTGTT 62.586 40.741 0.00 0.00 46.06 3.32
1397 1403 8.217892 CGGAATCGACATTTACCTTTTGGTGT 62.218 42.308 0.00 0.00 46.06 4.16
1398 1404 5.898380 CGGAATCGACATTTACCTTTTGGTG 60.898 44.000 0.00 0.00 46.06 4.17
1400 1406 4.155280 ACGGAATCGACATTTACCTTTTGG 59.845 41.667 0.00 0.00 42.09 3.28
1401 1407 5.086058 CACGGAATCGACATTTACCTTTTG 58.914 41.667 0.00 0.00 40.11 2.44
1402 1408 4.155280 CCACGGAATCGACATTTACCTTTT 59.845 41.667 0.00 0.00 40.11 2.27
1403 1409 3.687698 CCACGGAATCGACATTTACCTTT 59.312 43.478 0.00 0.00 40.11 3.11
1404 1410 3.267483 CCACGGAATCGACATTTACCTT 58.733 45.455 0.00 0.00 40.11 3.50
1405 1411 2.419574 CCCACGGAATCGACATTTACCT 60.420 50.000 0.00 0.00 40.11 3.08
1406 1412 1.937899 CCCACGGAATCGACATTTACC 59.062 52.381 0.00 0.00 40.11 2.85
1407 1413 2.624636 ACCCACGGAATCGACATTTAC 58.375 47.619 0.00 0.00 40.11 2.01
1408 1414 3.337694 AACCCACGGAATCGACATTTA 57.662 42.857 0.00 0.00 40.11 1.40
1409 1415 2.194201 AACCCACGGAATCGACATTT 57.806 45.000 0.00 0.00 40.11 2.32
1410 1416 2.081462 GAAACCCACGGAATCGACATT 58.919 47.619 0.00 0.00 40.11 2.71
1411 1417 1.002659 TGAAACCCACGGAATCGACAT 59.997 47.619 0.00 0.00 40.11 3.06
1412 1418 0.393448 TGAAACCCACGGAATCGACA 59.607 50.000 0.00 0.00 40.11 4.35
1413 1419 1.076332 CTGAAACCCACGGAATCGAC 58.924 55.000 0.00 0.00 40.11 4.20
1414 1420 0.970640 TCTGAAACCCACGGAATCGA 59.029 50.000 0.00 0.00 40.11 3.59
1415 1421 1.359848 CTCTGAAACCCACGGAATCG 58.640 55.000 0.00 0.00 43.02 3.34
1416 1422 1.087501 GCTCTGAAACCCACGGAATC 58.912 55.000 0.00 0.00 0.00 2.52
1417 1423 0.693049 AGCTCTGAAACCCACGGAAT 59.307 50.000 0.00 0.00 0.00 3.01
1418 1424 0.472471 AAGCTCTGAAACCCACGGAA 59.528 50.000 0.00 0.00 0.00 4.30
1419 1425 0.034896 GAAGCTCTGAAACCCACGGA 59.965 55.000 0.00 0.00 0.00 4.69
1420 1426 0.035458 AGAAGCTCTGAAACCCACGG 59.965 55.000 0.00 0.00 0.00 4.94
1421 1427 3.614399 AGAAGCTCTGAAACCCACG 57.386 52.632 0.00 0.00 0.00 4.94
1426 1432 7.845042 CCATTATGGTCCAGAAGCTCTGAAAC 61.845 46.154 5.01 10.48 38.60 2.78
1427 1433 5.862846 CCATTATGGTCCAGAAGCTCTGAAA 60.863 44.000 5.01 1.22 38.60 2.69
1428 1434 4.384537 CCATTATGGTCCAGAAGCTCTGAA 60.385 45.833 5.01 1.66 38.60 3.02
1429 1435 3.135348 CCATTATGGTCCAGAAGCTCTGA 59.865 47.826 5.01 0.00 38.60 3.27
1430 1436 3.474600 CCATTATGGTCCAGAAGCTCTG 58.525 50.000 5.01 0.00 37.20 3.35
1431 1437 2.158696 GCCATTATGGTCCAGAAGCTCT 60.159 50.000 13.28 0.00 40.46 4.09
1432 1438 2.225467 GCCATTATGGTCCAGAAGCTC 58.775 52.381 13.28 0.00 40.46 4.09
1433 1439 1.565759 TGCCATTATGGTCCAGAAGCT 59.434 47.619 13.28 0.00 40.46 3.74
1434 1440 2.057137 TGCCATTATGGTCCAGAAGC 57.943 50.000 13.28 4.46 40.46 3.86
1435 1441 3.956199 ACATTGCCATTATGGTCCAGAAG 59.044 43.478 13.28 0.00 40.46 2.85
1436 1442 3.700539 CACATTGCCATTATGGTCCAGAA 59.299 43.478 13.28 0.42 40.46 3.02
1437 1443 3.289836 CACATTGCCATTATGGTCCAGA 58.710 45.455 13.28 0.00 40.46 3.86
1438 1444 2.363038 CCACATTGCCATTATGGTCCAG 59.637 50.000 13.28 4.02 40.46 3.86
1439 1445 2.386779 CCACATTGCCATTATGGTCCA 58.613 47.619 13.28 0.00 40.46 4.02
1440 1446 1.688197 CCCACATTGCCATTATGGTCC 59.312 52.381 13.28 0.00 40.46 4.46
1441 1447 2.665165 TCCCACATTGCCATTATGGTC 58.335 47.619 13.28 5.96 40.46 4.02
1442 1448 2.844654 TCCCACATTGCCATTATGGT 57.155 45.000 13.28 0.00 40.46 3.55
1443 1449 3.232662 TCATCCCACATTGCCATTATGG 58.767 45.455 6.92 6.92 41.55 2.74
1444 1450 4.282449 ACATCATCCCACATTGCCATTATG 59.718 41.667 0.00 0.00 0.00 1.90
1445 1451 4.485875 ACATCATCCCACATTGCCATTAT 58.514 39.130 0.00 0.00 0.00 1.28
1446 1452 3.913509 ACATCATCCCACATTGCCATTA 58.086 40.909 0.00 0.00 0.00 1.90
1447 1453 2.754465 ACATCATCCCACATTGCCATT 58.246 42.857 0.00 0.00 0.00 3.16
1448 1454 2.464796 ACATCATCCCACATTGCCAT 57.535 45.000 0.00 0.00 0.00 4.40
1449 1455 2.234896 AACATCATCCCACATTGCCA 57.765 45.000 0.00 0.00 0.00 4.92
1450 1456 4.160252 AGTTTAACATCATCCCACATTGCC 59.840 41.667 0.00 0.00 0.00 4.52
1451 1457 5.104374 CAGTTTAACATCATCCCACATTGC 58.896 41.667 0.00 0.00 0.00 3.56
1452 1458 5.104374 GCAGTTTAACATCATCCCACATTG 58.896 41.667 0.00 0.00 0.00 2.82
1453 1459 4.771577 TGCAGTTTAACATCATCCCACATT 59.228 37.500 0.00 0.00 0.00 2.71
1454 1460 4.343231 TGCAGTTTAACATCATCCCACAT 58.657 39.130 0.00 0.00 0.00 3.21
1455 1461 3.760738 TGCAGTTTAACATCATCCCACA 58.239 40.909 0.00 0.00 0.00 4.17
1456 1462 4.022416 TGTTGCAGTTTAACATCATCCCAC 60.022 41.667 0.00 0.00 33.43 4.61
1457 1463 4.148079 TGTTGCAGTTTAACATCATCCCA 58.852 39.130 0.00 0.00 33.43 4.37
1458 1464 4.218417 ACTGTTGCAGTTTAACATCATCCC 59.782 41.667 0.00 0.00 42.59 3.85
1459 1465 5.376854 ACTGTTGCAGTTTAACATCATCC 57.623 39.130 0.00 0.00 42.59 3.51
1472 1478 1.345741 TGGGAGAGAGAACTGTTGCAG 59.654 52.381 0.00 0.00 37.52 4.41
1473 1479 1.423584 TGGGAGAGAGAACTGTTGCA 58.576 50.000 0.00 0.00 0.00 4.08
1474 1480 2.550830 TTGGGAGAGAGAACTGTTGC 57.449 50.000 0.00 0.00 0.00 4.17
1475 1481 3.008375 TCCATTGGGAGAGAGAACTGTTG 59.992 47.826 2.09 0.00 38.64 3.33
1476 1482 3.251484 TCCATTGGGAGAGAGAACTGTT 58.749 45.455 2.09 0.00 38.64 3.16
1477 1483 2.907892 TCCATTGGGAGAGAGAACTGT 58.092 47.619 2.09 0.00 38.64 3.55
1483 1489 9.774401 ATTCCCATGAAATCCATTGGGAGAGAG 62.774 44.444 9.33 0.00 45.12 3.20
1484 1490 8.078279 ATTCCCATGAAATCCATTGGGAGAGA 62.078 42.308 9.33 0.00 45.12 3.10
1485 1491 5.930679 ATTCCCATGAAATCCATTGGGAGAG 60.931 44.000 9.33 0.00 45.12 3.20
1544 1550 2.115266 CGCCCACCCAAGGAAGTT 59.885 61.111 0.00 0.00 0.00 2.66
1614 1620 6.348295 GCTAATCGATGCATCATGAAGTTCAT 60.348 38.462 25.70 12.75 37.65 2.57
1633 1639 7.283127 TGAATGTTGGTATTGGAAGAGCTAATC 59.717 37.037 0.00 0.00 0.00 1.75
1647 1653 1.684869 CGCCCCCTTGAATGTTGGTAT 60.685 52.381 0.00 0.00 0.00 2.73
1654 1660 2.440247 GTCCCGCCCCCTTGAATG 60.440 66.667 0.00 0.00 0.00 2.67
1660 1666 2.854032 CCATATGTCCCGCCCCCT 60.854 66.667 1.24 0.00 0.00 4.79
1708 1714 2.398754 AAGAAAGGACCTTTTGGGGG 57.601 50.000 20.47 0.00 46.08 5.40
1713 1719 4.080582 CCCAACCAAAAGAAAGGACCTTTT 60.081 41.667 20.47 8.16 42.58 2.27
1714 1720 3.454447 CCCAACCAAAAGAAAGGACCTTT 59.546 43.478 19.66 19.66 36.29 3.11
1736 1742 3.937706 TCGTCAGTGTTAGTAGCTAGTCC 59.062 47.826 3.81 0.00 0.00 3.85
1754 1760 3.512680 CATCTTGTTACTCCAGGTCGTC 58.487 50.000 0.00 0.00 0.00 4.20
1755 1761 2.233922 CCATCTTGTTACTCCAGGTCGT 59.766 50.000 0.00 0.00 0.00 4.34
1756 1762 2.496070 TCCATCTTGTTACTCCAGGTCG 59.504 50.000 0.00 0.00 0.00 4.79
1760 1768 7.693969 ATTTCTTTCCATCTTGTTACTCCAG 57.306 36.000 0.00 0.00 0.00 3.86
1776 1784 5.466728 TCGCACTCATAGCCATATTTCTTTC 59.533 40.000 0.00 0.00 0.00 2.62
1788 1796 1.857217 CAGACATGTCGCACTCATAGC 59.143 52.381 19.85 0.00 34.09 2.97
1789 1797 3.427161 TCAGACATGTCGCACTCATAG 57.573 47.619 19.85 3.67 34.09 2.23
1790 1798 4.391405 AATCAGACATGTCGCACTCATA 57.609 40.909 19.85 1.71 34.09 2.15
1791 1799 2.975732 ATCAGACATGTCGCACTCAT 57.024 45.000 19.85 4.62 34.09 2.90
1799 1807 4.984161 CCAAAACCACAAATCAGACATGTC 59.016 41.667 18.47 18.47 0.00 3.06
1820 1828 0.991920 GAAAGTGTCCCCCATCTCCA 59.008 55.000 0.00 0.00 0.00 3.86
1850 1858 0.833287 TCCTAGCATTGGACAGGAGC 59.167 55.000 0.00 0.00 32.20 4.70
1867 1876 3.667360 AGCAATGCATTCCAAAGTTTCC 58.333 40.909 9.53 0.00 0.00 3.13
1869 1878 5.644636 CCAATAGCAATGCATTCCAAAGTTT 59.355 36.000 9.53 0.00 0.00 2.66
1876 1885 4.202284 ACCAATCCAATAGCAATGCATTCC 60.202 41.667 9.53 0.00 0.00 3.01
1923 1933 0.107508 CAATCATCCCCAGTCGCACT 60.108 55.000 0.00 0.00 0.00 4.40
1925 1935 0.839277 ATCAATCATCCCCAGTCGCA 59.161 50.000 0.00 0.00 0.00 5.10
1926 1936 1.876156 GAATCAATCATCCCCAGTCGC 59.124 52.381 0.00 0.00 0.00 5.19
1927 1937 3.181462 TGAGAATCAATCATCCCCAGTCG 60.181 47.826 0.00 0.00 45.97 4.18
1928 1938 4.428294 TGAGAATCAATCATCCCCAGTC 57.572 45.455 0.00 0.00 45.97 3.51
1942 1952 4.853924 TTGCAAAAGAACCCTGAGAATC 57.146 40.909 0.00 0.00 0.00 2.52
1943 1953 5.047519 CAGATTGCAAAAGAACCCTGAGAAT 60.048 40.000 1.71 0.00 0.00 2.40
1962 1972 3.375299 GCACGCATTACTTCTTCCAGATT 59.625 43.478 0.00 0.00 0.00 2.40
1964 1974 2.289382 TGCACGCATTACTTCTTCCAGA 60.289 45.455 0.00 0.00 0.00 3.86
1967 1977 1.804151 TGTGCACGCATTACTTCTTCC 59.196 47.619 13.13 0.00 0.00 3.46
1970 1980 2.224079 CACTTGTGCACGCATTACTTCT 59.776 45.455 13.13 0.00 0.00 2.85
1979 1989 1.205064 CAGTAGCACTTGTGCACGC 59.795 57.895 24.82 9.42 37.25 5.34
1987 1997 3.194542 CCTCTAGAACAGCAGTAGCACTT 59.805 47.826 0.00 0.00 45.49 3.16
1998 2008 5.506483 CGACATACCACATCCTCTAGAACAG 60.506 48.000 0.00 0.00 0.00 3.16
2022 2032 6.869913 TCTTTTGAATGCACAATCTCATTTCC 59.130 34.615 0.00 0.00 33.49 3.13
2027 2037 4.521639 AGCTCTTTTGAATGCACAATCTCA 59.478 37.500 0.00 0.00 0.00 3.27
2048 2058 3.201936 TGACACGTCATCTAGCGGAGC 62.202 57.143 0.00 0.00 45.27 4.70
2049 2059 0.733150 TGACACGTCATCTAGCGGAG 59.267 55.000 0.00 0.00 34.14 4.63
2050 2060 1.170442 TTGACACGTCATCTAGCGGA 58.830 50.000 0.00 0.00 39.64 5.54
2051 2061 1.990799 TTTGACACGTCATCTAGCGG 58.009 50.000 0.00 0.00 39.64 5.52
2053 2063 4.992381 ACTTTTTGACACGTCATCTAGC 57.008 40.909 0.00 0.00 39.64 3.42
2091 2102 8.027771 GGTATGTGCTAATGGAGTATAGTGTAC 58.972 40.741 0.00 0.00 0.00 2.90
2114 2128 8.705594 TCCTTTAACATGTTCAAAATTTGGGTA 58.294 29.630 15.85 0.00 0.00 3.69
2128 2142 3.640967 TGGCTGCTTTTCCTTTAACATGT 59.359 39.130 0.00 0.00 0.00 3.21
2130 2144 3.006859 GGTGGCTGCTTTTCCTTTAACAT 59.993 43.478 0.00 0.00 0.00 2.71
2131 2145 2.364002 GGTGGCTGCTTTTCCTTTAACA 59.636 45.455 0.00 0.00 0.00 2.41
2145 2159 0.461135 AAAGCACAAAGTGGTGGCTG 59.539 50.000 2.33 0.00 43.73 4.85
2197 2211 1.470098 GACCACATCACATCAGGTTGC 59.530 52.381 0.00 0.00 31.57 4.17
2223 2237 6.085555 TCAATTTATTTTGGCCGTACACAA 57.914 33.333 0.00 0.00 0.00 3.33
2225 2239 6.588373 ACATTCAATTTATTTTGGCCGTACAC 59.412 34.615 0.00 0.00 0.00 2.90
2277 2291 0.747283 GAGAACCATGCCTGCTCCTG 60.747 60.000 0.00 0.00 0.00 3.86
2278 2292 1.203441 TGAGAACCATGCCTGCTCCT 61.203 55.000 0.00 0.00 0.00 3.69
2279 2293 0.747283 CTGAGAACCATGCCTGCTCC 60.747 60.000 0.00 0.00 0.00 4.70
2300 2314 7.055667 TGAGTATAATTGACTCCTCATGGTC 57.944 40.000 15.80 0.00 42.29 4.02
2308 2322 5.292101 GCACACACTGAGTATAATTGACTCC 59.708 44.000 15.80 3.71 42.29 3.85
2310 2324 5.793817 TGCACACACTGAGTATAATTGACT 58.206 37.500 0.00 0.00 0.00 3.41
2312 2326 5.122239 GCTTGCACACACTGAGTATAATTGA 59.878 40.000 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.