Multiple sequence alignment - TraesCS6B01G335100

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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 TraesCS6B01G335100 chr6B 100.000 2318 0 0 1 2318 590028016 590025699 0.000000e+00 4281.0
1 TraesCS6B01G335100 chr6B 90.682 1363 108 9 1 1345 708391337 708389976 0.000000e+00 1796.0
2 TraesCS6B01G335100 chr6B 86.050 1362 170 6 1 1344 623439779 623441138 0.000000e+00 1445.0
3 TraesCS6B01G335100 chr6B 85.473 1363 174 11 1 1344 478884245 478882888 0.000000e+00 1399.0
4 TraesCS6B01G335100 chr7D 89.802 1363 112 10 1 1344 205159913 205158559 0.000000e+00 1722.0
5 TraesCS6B01G335100 chr7D 88.808 1367 126 11 1 1345 76799504 76800865 0.000000e+00 1652.0
6 TraesCS6B01G335100 chr7D 89.620 684 68 3 661 1343 599863983 599864664 0.000000e+00 867.0
7 TraesCS6B01G335100 chr1D 89.427 1362 125 7 1 1344 442379591 442378231 0.000000e+00 1700.0
8 TraesCS6B01G335100 chr7B 86.490 1362 166 2 1 1344 621911870 621910509 0.000000e+00 1480.0
9 TraesCS6B01G335100 chr7B 86.207 58 6 2 2262 2317 628694609 628694552 6.920000e-06 62.1
10 TraesCS6B01G335100 chr2B 85.767 1349 172 9 1 1330 115905344 115903997 0.000000e+00 1410.0
11 TraesCS6B01G335100 chr1B 85.114 1357 180 12 1 1339 539123078 539124430 0.000000e+00 1367.0
12 TraesCS6B01G335100 chr1B 85.131 1298 168 12 1 1278 68936807 68938099 0.000000e+00 1304.0
13 TraesCS6B01G335100 chr3D 93.323 659 43 1 1 659 593737088 593736431 0.000000e+00 972.0
14 TraesCS6B01G335100 chr3D 92.145 662 52 0 683 1344 593711667 593711006 0.000000e+00 935.0
15 TraesCS6B01G335100 chr3D 82.254 710 119 7 1545 2252 302225088 302225792 7.080000e-170 606.0
16 TraesCS6B01G335100 chr3D 81.511 741 119 16 1518 2253 597281746 597282473 5.510000e-166 593.0
17 TraesCS6B01G335100 chr4D 82.797 715 108 13 1525 2233 47557067 47557772 1.960000e-175 625.0
18 TraesCS6B01G335100 chr3B 81.658 736 124 10 1522 2253 418750455 418749727 3.300000e-168 601.0
19 TraesCS6B01G335100 chr1A 81.583 733 128 6 1529 2259 484294140 484294867 1.190000e-167 599.0
20 TraesCS6B01G335100 chr5D 81.250 736 123 15 1525 2254 212007795 212007069 4.290000e-162 580.0
21 TraesCS6B01G335100 chr4B 82.344 674 108 10 1588 2254 168030093 168030762 2.000000e-160 575.0
22 TraesCS6B01G335100 chr5B 80.886 722 119 18 1522 2236 408351434 408350725 3.370000e-153 551.0
23 TraesCS6B01G335100 chr2A 80.133 750 132 15 1522 2265 605249807 605249069 5.630000e-151 544.0
24 TraesCS6B01G335100 chr6D 89.150 341 33 3 1343 1683 394214941 394214605 2.750000e-114 422.0


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 TraesCS6B01G335100 chr6B 590025699 590028016 2317 True 4281 4281 100.000 1 2318 1 chr6B.!!$R2 2317
1 TraesCS6B01G335100 chr6B 708389976 708391337 1361 True 1796 1796 90.682 1 1345 1 chr6B.!!$R3 1344
2 TraesCS6B01G335100 chr6B 623439779 623441138 1359 False 1445 1445 86.050 1 1344 1 chr6B.!!$F1 1343
3 TraesCS6B01G335100 chr6B 478882888 478884245 1357 True 1399 1399 85.473 1 1344 1 chr6B.!!$R1 1343
4 TraesCS6B01G335100 chr7D 205158559 205159913 1354 True 1722 1722 89.802 1 1344 1 chr7D.!!$R1 1343
5 TraesCS6B01G335100 chr7D 76799504 76800865 1361 False 1652 1652 88.808 1 1345 1 chr7D.!!$F1 1344
6 TraesCS6B01G335100 chr7D 599863983 599864664 681 False 867 867 89.620 661 1343 1 chr7D.!!$F2 682
7 TraesCS6B01G335100 chr1D 442378231 442379591 1360 True 1700 1700 89.427 1 1344 1 chr1D.!!$R1 1343
8 TraesCS6B01G335100 chr7B 621910509 621911870 1361 True 1480 1480 86.490 1 1344 1 chr7B.!!$R1 1343
9 TraesCS6B01G335100 chr2B 115903997 115905344 1347 True 1410 1410 85.767 1 1330 1 chr2B.!!$R1 1329
10 TraesCS6B01G335100 chr1B 539123078 539124430 1352 False 1367 1367 85.114 1 1339 1 chr1B.!!$F2 1338
11 TraesCS6B01G335100 chr1B 68936807 68938099 1292 False 1304 1304 85.131 1 1278 1 chr1B.!!$F1 1277
12 TraesCS6B01G335100 chr3D 593736431 593737088 657 True 972 972 93.323 1 659 1 chr3D.!!$R2 658
13 TraesCS6B01G335100 chr3D 593711006 593711667 661 True 935 935 92.145 683 1344 1 chr3D.!!$R1 661
14 TraesCS6B01G335100 chr3D 302225088 302225792 704 False 606 606 82.254 1545 2252 1 chr3D.!!$F1 707
15 TraesCS6B01G335100 chr3D 597281746 597282473 727 False 593 593 81.511 1518 2253 1 chr3D.!!$F2 735
16 TraesCS6B01G335100 chr4D 47557067 47557772 705 False 625 625 82.797 1525 2233 1 chr4D.!!$F1 708
17 TraesCS6B01G335100 chr3B 418749727 418750455 728 True 601 601 81.658 1522 2253 1 chr3B.!!$R1 731
18 TraesCS6B01G335100 chr1A 484294140 484294867 727 False 599 599 81.583 1529 2259 1 chr1A.!!$F1 730
19 TraesCS6B01G335100 chr5D 212007069 212007795 726 True 580 580 81.250 1525 2254 1 chr5D.!!$R1 729
20 TraesCS6B01G335100 chr4B 168030093 168030762 669 False 575 575 82.344 1588 2254 1 chr4B.!!$F1 666
21 TraesCS6B01G335100 chr5B 408350725 408351434 709 True 551 551 80.886 1522 2236 1 chr5B.!!$R1 714
22 TraesCS6B01G335100 chr2A 605249069 605249807 738 True 544 544 80.133 1522 2265 1 chr2A.!!$R1 743

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
38 39 0.396695 TCCTTCCGGCCGATTACTCT 60.397 55.0 30.73 0.0 0.0 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1539 1561 0.109132 GAAGGAAATGTGCGGCTTGG 60.109 55.0 0.0 0.0 0.0 3.61 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
38 39 0.396695 TCCTTCCGGCCGATTACTCT 60.397 55.000 30.73 0.00 0.00 3.24
201 202 2.580322 TGATTTCTTGGCCTGGTATCCA 59.420 45.455 3.32 0.00 0.00 3.41
285 286 2.290197 TGTCACTGCTAATGGTGCATCA 60.290 45.455 0.00 0.00 39.86 3.07
337 338 4.394729 GTGGAACTACATTTGGAAGTCCA 58.605 43.478 0.00 0.00 45.94 4.02
372 373 6.995511 AAAATGAAAATCAATGCATGGAGG 57.004 33.333 10.16 0.00 0.00 4.30
373 374 3.530265 TGAAAATCAATGCATGGAGGC 57.470 42.857 10.16 0.00 0.00 4.70
417 418 1.065854 CAGAGTGGTAAGGCCTTCAGG 60.066 57.143 24.49 0.00 38.35 3.86
427 428 2.887360 CCTTCAGGCATTTGGCGG 59.113 61.111 0.00 0.00 46.16 6.13
447 448 3.052082 CGCCCAACCTGTCAGCTG 61.052 66.667 7.63 7.63 0.00 4.24
456 457 2.920384 TGTCAGCTGTGCGGGGTA 60.920 61.111 14.67 0.00 0.00 3.69
546 547 1.002134 CCGTTGGCCACTTCCTGAT 60.002 57.895 3.88 0.00 0.00 2.90
570 571 7.563724 TGATGATCTCCTTATTCATGATGGA 57.436 36.000 0.00 1.83 30.48 3.41
702 721 2.012051 GCCACCGTCGAATTCTTGGAT 61.012 52.381 12.69 0.00 0.00 3.41
710 729 6.479001 ACCGTCGAATTCTTGGATAGTTATTG 59.521 38.462 12.69 0.00 0.00 1.90
915 934 1.138036 CGTCGGTATGGTGCTTCGA 59.862 57.895 0.00 0.00 0.00 3.71
976 995 5.698104 TCATCTTCTATTGCAATGACCCAT 58.302 37.500 22.27 5.78 0.00 4.00
1066 1085 2.298163 GTGGTTCAAACGGACTCCTCTA 59.702 50.000 0.00 0.00 0.00 2.43
1144 1163 5.258841 TCGTCCTGGAGATTAAGTCACTTA 58.741 41.667 0.00 0.00 0.00 2.24
1146 1165 6.380274 TCGTCCTGGAGATTAAGTCACTTATT 59.620 38.462 0.00 0.00 0.00 1.40
1278 1300 2.169769 GGTTCCACCATGTATCGAGGAA 59.830 50.000 0.00 0.00 38.42 3.36
1305 1327 3.633065 GGCCTCTCGACTGTAACTCTATT 59.367 47.826 0.00 0.00 0.00 1.73
1318 1340 9.988815 ACTGTAACTCTATTCCTATGCAATAAG 57.011 33.333 0.00 0.00 0.00 1.73
1321 1343 9.495572 GTAACTCTATTCCTATGCAATAAGCTT 57.504 33.333 3.48 3.48 45.94 3.74
1322 1344 7.976135 ACTCTATTCCTATGCAATAAGCTTG 57.024 36.000 9.86 0.00 45.94 4.01
1339 1361 0.676736 TTGCTTTACCCCCGCAAAAG 59.323 50.000 0.00 0.00 40.33 2.27
1344 1366 3.386486 CTTTACCCCCGCAAAAGAAAAC 58.614 45.455 0.00 0.00 33.05 2.43
1345 1367 2.068834 TACCCCCGCAAAAGAAAACA 57.931 45.000 0.00 0.00 0.00 2.83
1346 1368 1.196012 ACCCCCGCAAAAGAAAACAA 58.804 45.000 0.00 0.00 0.00 2.83
1347 1369 1.765904 ACCCCCGCAAAAGAAAACAAT 59.234 42.857 0.00 0.00 0.00 2.71
1348 1370 2.142319 CCCCCGCAAAAGAAAACAATG 58.858 47.619 0.00 0.00 0.00 2.82
1349 1371 2.484594 CCCCCGCAAAAGAAAACAATGT 60.485 45.455 0.00 0.00 0.00 2.71
1350 1372 3.243907 CCCCCGCAAAAGAAAACAATGTA 60.244 43.478 0.00 0.00 0.00 2.29
1351 1373 4.562552 CCCCCGCAAAAGAAAACAATGTAT 60.563 41.667 0.00 0.00 0.00 2.29
1352 1374 4.994217 CCCCGCAAAAGAAAACAATGTATT 59.006 37.500 0.00 0.00 0.00 1.89
1353 1375 5.468409 CCCCGCAAAAGAAAACAATGTATTT 59.532 36.000 0.00 0.00 0.00 1.40
1354 1376 6.347321 CCCCGCAAAAGAAAACAATGTATTTC 60.347 38.462 10.75 10.75 36.11 2.17
1355 1377 6.201806 CCCGCAAAAGAAAACAATGTATTTCA 59.798 34.615 16.92 0.00 37.87 2.69
1356 1378 7.095271 CCCGCAAAAGAAAACAATGTATTTCAT 60.095 33.333 16.92 7.76 37.87 2.57
1357 1379 7.951565 CCGCAAAAGAAAACAATGTATTTCATC 59.048 33.333 16.92 0.34 37.87 2.92
1358 1380 8.486383 CGCAAAAGAAAACAATGTATTTCATCA 58.514 29.630 16.92 0.00 37.87 3.07
1394 1416 9.905713 ATATACTTGTAGACAACATCCATTTGT 57.094 29.630 0.00 0.00 39.94 2.83
1396 1418 7.435068 ACTTGTAGACAACATCCATTTGTAC 57.565 36.000 0.00 0.00 37.31 2.90
1397 1419 6.995686 ACTTGTAGACAACATCCATTTGTACA 59.004 34.615 0.00 0.00 37.31 2.90
1398 1420 7.665559 ACTTGTAGACAACATCCATTTGTACAT 59.334 33.333 0.00 0.00 37.31 2.29
1399 1421 7.376435 TGTAGACAACATCCATTTGTACATG 57.624 36.000 0.00 0.00 37.31 3.21
1400 1422 6.939730 TGTAGACAACATCCATTTGTACATGT 59.060 34.615 2.69 2.69 37.31 3.21
1401 1423 6.258230 AGACAACATCCATTTGTACATGTG 57.742 37.500 9.11 0.00 37.31 3.21
1402 1424 5.769662 AGACAACATCCATTTGTACATGTGT 59.230 36.000 9.11 0.00 37.31 3.72
1403 1425 5.771469 ACAACATCCATTTGTACATGTGTG 58.229 37.500 9.11 1.85 35.38 3.82
1404 1426 5.301551 ACAACATCCATTTGTACATGTGTGT 59.698 36.000 9.11 2.42 42.39 3.72
1405 1427 6.183360 ACAACATCCATTTGTACATGTGTGTT 60.183 34.615 9.11 3.99 39.77 3.32
1406 1428 6.403866 ACATCCATTTGTACATGTGTGTTT 57.596 33.333 9.11 0.00 39.77 2.83
1407 1429 6.815089 ACATCCATTTGTACATGTGTGTTTT 58.185 32.000 9.11 0.00 39.77 2.43
1408 1430 7.271511 ACATCCATTTGTACATGTGTGTTTTT 58.728 30.769 9.11 0.00 39.77 1.94
1439 1461 5.850557 TTTTTGAAACTTCATGGAGCTCA 57.149 34.783 17.19 1.33 37.00 4.26
1440 1462 5.443185 TTTTGAAACTTCATGGAGCTCAG 57.557 39.130 17.19 6.24 37.00 3.35
1441 1463 3.063510 TGAAACTTCATGGAGCTCAGG 57.936 47.619 17.19 4.03 31.01 3.86
1442 1464 2.639347 TGAAACTTCATGGAGCTCAGGA 59.361 45.455 17.19 6.58 34.02 3.86
1443 1465 3.269178 GAAACTTCATGGAGCTCAGGAG 58.731 50.000 17.19 11.12 37.48 3.69
1444 1466 6.905027 TGAAACTTCATGGAGCTCAGGAGC 62.905 50.000 17.19 13.27 42.59 4.70
1460 1482 7.630242 CTCAGGAGCCAAAAATCTATTTACA 57.370 36.000 0.00 0.00 0.00 2.41
1461 1483 7.391148 TCAGGAGCCAAAAATCTATTTACAC 57.609 36.000 0.00 0.00 0.00 2.90
1462 1484 6.377146 TCAGGAGCCAAAAATCTATTTACACC 59.623 38.462 0.00 0.00 0.00 4.16
1463 1485 5.656859 AGGAGCCAAAAATCTATTTACACCC 59.343 40.000 0.00 0.00 0.00 4.61
1464 1486 5.420739 GGAGCCAAAAATCTATTTACACCCA 59.579 40.000 0.00 0.00 0.00 4.51
1465 1487 6.405842 GGAGCCAAAAATCTATTTACACCCAG 60.406 42.308 0.00 0.00 0.00 4.45
1466 1488 5.105351 AGCCAAAAATCTATTTACACCCAGC 60.105 40.000 0.00 0.00 0.00 4.85
1467 1489 5.339990 CCAAAAATCTATTTACACCCAGCG 58.660 41.667 0.00 0.00 0.00 5.18
1468 1490 4.632538 AAAATCTATTTACACCCAGCGC 57.367 40.909 0.00 0.00 0.00 5.92
1469 1491 3.560636 AATCTATTTACACCCAGCGCT 57.439 42.857 2.64 2.64 0.00 5.92
1470 1492 2.309528 TCTATTTACACCCAGCGCTG 57.690 50.000 30.52 30.52 0.00 5.18
1471 1493 0.657840 CTATTTACACCCAGCGCTGC 59.342 55.000 31.96 0.00 0.00 5.25
1472 1494 0.746563 TATTTACACCCAGCGCTGCC 60.747 55.000 31.96 0.00 0.00 4.85
1473 1495 2.484287 ATTTACACCCAGCGCTGCCT 62.484 55.000 31.96 15.45 0.00 4.75
1474 1496 1.832719 TTTACACCCAGCGCTGCCTA 61.833 55.000 31.96 13.78 0.00 3.93
1475 1497 1.622607 TTACACCCAGCGCTGCCTAT 61.623 55.000 31.96 18.30 0.00 2.57
1476 1498 1.622607 TACACCCAGCGCTGCCTATT 61.623 55.000 31.96 15.80 0.00 1.73
1477 1499 1.750399 CACCCAGCGCTGCCTATTT 60.750 57.895 31.96 8.27 0.00 1.40
1478 1500 1.750399 ACCCAGCGCTGCCTATTTG 60.750 57.895 31.96 15.78 0.00 2.32
1479 1501 2.484062 CCCAGCGCTGCCTATTTGG 61.484 63.158 31.96 20.86 39.35 3.28
1480 1502 1.750399 CCAGCGCTGCCTATTTGGT 60.750 57.895 31.96 0.00 38.35 3.67
1481 1503 1.430632 CAGCGCTGCCTATTTGGTG 59.569 57.895 26.68 0.00 38.35 4.17
1482 1504 1.026182 CAGCGCTGCCTATTTGGTGA 61.026 55.000 26.68 0.00 38.35 4.02
1483 1505 0.745845 AGCGCTGCCTATTTGGTGAG 60.746 55.000 10.39 0.00 38.35 3.51
1484 1506 0.744414 GCGCTGCCTATTTGGTGAGA 60.744 55.000 0.00 0.00 38.35 3.27
1485 1507 1.737838 CGCTGCCTATTTGGTGAGAA 58.262 50.000 0.00 0.00 38.35 2.87
1486 1508 2.083774 CGCTGCCTATTTGGTGAGAAA 58.916 47.619 0.00 0.00 38.35 2.52
1487 1509 2.487762 CGCTGCCTATTTGGTGAGAAAA 59.512 45.455 0.00 0.00 38.35 2.29
1488 1510 3.129287 CGCTGCCTATTTGGTGAGAAAAT 59.871 43.478 0.00 0.00 38.35 1.82
1489 1511 4.427312 GCTGCCTATTTGGTGAGAAAATG 58.573 43.478 0.00 0.00 38.35 2.32
1490 1512 4.082026 GCTGCCTATTTGGTGAGAAAATGT 60.082 41.667 0.00 0.00 38.35 2.71
1491 1513 5.125417 GCTGCCTATTTGGTGAGAAAATGTA 59.875 40.000 0.00 0.00 38.35 2.29
1492 1514 6.350110 GCTGCCTATTTGGTGAGAAAATGTAA 60.350 38.462 0.00 0.00 38.35 2.41
1493 1515 7.156876 TGCCTATTTGGTGAGAAAATGTAAG 57.843 36.000 0.00 0.00 38.35 2.34
1494 1516 6.152661 TGCCTATTTGGTGAGAAAATGTAAGG 59.847 38.462 0.00 0.00 38.35 2.69
1495 1517 6.377146 GCCTATTTGGTGAGAAAATGTAAGGA 59.623 38.462 0.00 0.00 38.35 3.36
1496 1518 7.068716 GCCTATTTGGTGAGAAAATGTAAGGAT 59.931 37.037 0.00 0.00 38.35 3.24
1497 1519 8.971073 CCTATTTGGTGAGAAAATGTAAGGATT 58.029 33.333 0.00 0.00 28.11 3.01
1500 1522 7.831691 TTGGTGAGAAAATGTAAGGATTTCA 57.168 32.000 0.00 0.00 35.91 2.69
1501 1523 8.421249 TTGGTGAGAAAATGTAAGGATTTCAT 57.579 30.769 0.00 0.00 37.72 2.57
1502 1524 8.055279 TGGTGAGAAAATGTAAGGATTTCATC 57.945 34.615 0.00 0.00 34.89 2.92
1515 1537 5.603170 GGATTTCATCCCATGTGACATTT 57.397 39.130 0.00 0.00 43.88 2.32
1516 1538 5.353938 GGATTTCATCCCATGTGACATTTG 58.646 41.667 0.00 0.00 43.88 2.32
1517 1539 5.105228 GGATTTCATCCCATGTGACATTTGT 60.105 40.000 0.00 0.00 43.88 2.83
1518 1540 5.389859 TTTCATCCCATGTGACATTTGTC 57.610 39.130 0.00 3.72 44.97 3.18
1519 1541 4.305539 TCATCCCATGTGACATTTGTCT 57.694 40.909 11.67 0.00 44.99 3.41
1520 1542 4.011698 TCATCCCATGTGACATTTGTCTG 58.988 43.478 11.67 2.52 44.99 3.51
1539 1561 1.440145 GCTTAGGGCATCTCCAACGC 61.440 60.000 0.00 0.00 41.35 4.84
1543 1565 3.190878 GGCATCTCCAACGCCAAG 58.809 61.111 0.00 0.00 45.52 3.61
1565 1587 1.469703 CGCACATTTCCTTCTGCATCA 59.530 47.619 0.00 0.00 0.00 3.07
1639 1661 1.260561 CAACCGTAGCCGCATACATTC 59.739 52.381 0.00 0.00 0.00 2.67
1674 1698 2.882137 ACAAACCGGATGAAATTCGTGT 59.118 40.909 9.46 0.00 46.20 4.49
1702 1727 6.697019 ACAAGCCGAATTTCATATAAACATGC 59.303 34.615 0.00 0.00 0.00 4.06
1718 1743 5.596836 AACATGCCGGATTTCATACAAAT 57.403 34.783 5.05 0.00 0.00 2.32
1798 1825 1.399744 CCTATCCTACAGCGGTGGCA 61.400 60.000 20.20 5.26 43.41 4.92
1814 1841 3.048602 CACCGGACGTCCAAGACT 58.951 61.111 32.80 7.95 35.14 3.24
1818 1845 2.022129 CGGACGTCCAAGACTGTGC 61.022 63.158 32.80 3.24 35.14 4.57
1880 1908 1.393539 CGATAAAGTGAAGGTGCGGTG 59.606 52.381 0.00 0.00 0.00 4.94
1988 2020 3.371063 GAGTCTGCGACCCGTCCA 61.371 66.667 5.29 0.00 32.18 4.02
2028 2060 1.002624 ACGATGGAAATGGTGGCGT 60.003 52.632 0.00 0.00 0.00 5.68
2030 2062 1.714899 CGATGGAAATGGTGGCGTCC 61.715 60.000 0.00 0.00 0.00 4.79
2046 2078 2.202690 CCGCGCTATCGTTGTCCA 60.203 61.111 5.56 0.00 38.14 4.02
2075 2107 0.250038 CCTGATGGTTCATCGGCGAT 60.250 55.000 18.14 18.14 43.62 4.58
2081 2113 0.512952 GGTTCATCGGCGATGCATAC 59.487 55.000 37.71 31.28 39.63 2.39
2095 2127 1.447838 CATACGAGGCGCAACTGGT 60.448 57.895 10.83 8.20 33.82 4.00
2097 2129 2.167398 ATACGAGGCGCAACTGGTGT 62.167 55.000 10.83 0.53 31.65 4.16
2100 2132 1.733526 GAGGCGCAACTGGTGTTTT 59.266 52.632 10.83 0.00 33.52 2.43
2132 2164 3.490759 CGCCTACAACTGCGCCTG 61.491 66.667 4.18 1.73 44.64 4.85
2165 2197 3.423154 CAGGTGAGCGGCGGTTTC 61.423 66.667 14.71 9.45 0.00 2.78
2261 2293 3.753434 CTCGCTCGCCCACTCACT 61.753 66.667 0.00 0.00 0.00 3.41
2265 2297 1.517832 GCTCGCCCACTCACTGTAT 59.482 57.895 0.00 0.00 0.00 2.29
2266 2298 0.108138 GCTCGCCCACTCACTGTATT 60.108 55.000 0.00 0.00 0.00 1.89
2267 2299 1.645034 CTCGCCCACTCACTGTATTG 58.355 55.000 0.00 0.00 0.00 1.90
2268 2300 0.973632 TCGCCCACTCACTGTATTGT 59.026 50.000 0.00 0.00 0.00 2.71
2269 2301 1.346395 TCGCCCACTCACTGTATTGTT 59.654 47.619 0.00 0.00 0.00 2.83
2270 2302 1.464608 CGCCCACTCACTGTATTGTTG 59.535 52.381 0.00 0.00 0.00 3.33
2271 2303 1.812571 GCCCACTCACTGTATTGTTGG 59.187 52.381 0.00 0.00 0.00 3.77
2272 2304 2.436417 CCCACTCACTGTATTGTTGGG 58.564 52.381 0.00 0.00 35.71 4.12
2273 2305 2.436417 CCACTCACTGTATTGTTGGGG 58.564 52.381 0.00 0.00 0.00 4.96
2274 2306 2.039746 CCACTCACTGTATTGTTGGGGA 59.960 50.000 0.00 0.00 0.00 4.81
2275 2307 3.497763 CCACTCACTGTATTGTTGGGGAA 60.498 47.826 0.00 0.00 0.00 3.97
2276 2308 3.502211 CACTCACTGTATTGTTGGGGAAC 59.498 47.826 0.00 0.00 0.00 3.62
2277 2309 3.137544 ACTCACTGTATTGTTGGGGAACA 59.862 43.478 0.00 0.00 0.00 3.18
2278 2310 4.202567 ACTCACTGTATTGTTGGGGAACAT 60.203 41.667 0.00 0.00 32.01 2.71
2279 2311 4.735369 TCACTGTATTGTTGGGGAACATT 58.265 39.130 0.00 0.00 32.01 2.71
2280 2312 4.522405 TCACTGTATTGTTGGGGAACATTG 59.478 41.667 0.00 0.00 32.01 2.82
2281 2313 3.258123 ACTGTATTGTTGGGGAACATTGC 59.742 43.478 0.00 0.00 32.01 3.56
2282 2314 3.234353 TGTATTGTTGGGGAACATTGCA 58.766 40.909 0.00 0.00 32.01 4.08
2283 2315 3.257873 TGTATTGTTGGGGAACATTGCAG 59.742 43.478 0.00 0.00 32.01 4.41
2284 2316 2.079170 TTGTTGGGGAACATTGCAGA 57.921 45.000 0.00 0.00 32.01 4.26
2285 2317 2.079170 TGTTGGGGAACATTGCAGAA 57.921 45.000 0.00 0.00 0.00 3.02
2286 2318 2.392662 TGTTGGGGAACATTGCAGAAA 58.607 42.857 0.00 0.00 0.00 2.52
2287 2319 2.768527 TGTTGGGGAACATTGCAGAAAA 59.231 40.909 0.00 0.00 0.00 2.29
2288 2320 3.390639 TGTTGGGGAACATTGCAGAAAAT 59.609 39.130 0.00 0.00 0.00 1.82
2289 2321 4.590647 TGTTGGGGAACATTGCAGAAAATA 59.409 37.500 0.00 0.00 0.00 1.40
2290 2322 5.070981 TGTTGGGGAACATTGCAGAAAATAA 59.929 36.000 0.00 0.00 0.00 1.40
2291 2323 5.815233 TGGGGAACATTGCAGAAAATAAA 57.185 34.783 0.00 0.00 0.00 1.40
2292 2324 6.179906 TGGGGAACATTGCAGAAAATAAAA 57.820 33.333 0.00 0.00 0.00 1.52
2293 2325 6.595682 TGGGGAACATTGCAGAAAATAAAAA 58.404 32.000 0.00 0.00 0.00 1.94
2314 2346 5.957842 AAAAATTCTACGCATCACCAAGA 57.042 34.783 0.00 0.00 0.00 3.02
2315 2347 6.515272 AAAAATTCTACGCATCACCAAGAT 57.485 33.333 0.00 0.00 37.48 2.40
2316 2348 5.741388 AAATTCTACGCATCACCAAGATC 57.259 39.130 0.00 0.00 33.72 2.75
2317 2349 3.885724 TTCTACGCATCACCAAGATCA 57.114 42.857 0.00 0.00 33.72 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 1.129058 GGAAGGAATAAGGCCGAGGA 58.871 55.000 0.00 0.00 0.00 3.71
38 39 5.935945 TGTTGAAGTGATAGTTTCCCTTCA 58.064 37.500 4.78 4.78 0.00 3.02
149 150 2.675317 CGAGGCGAGGTTCTGATTTTCT 60.675 50.000 0.00 0.00 0.00 2.52
201 202 2.745152 CGTGAACCCACCACTCTTTTCT 60.745 50.000 0.00 0.00 40.12 2.52
372 373 2.094659 CATCGTCCCTGTCACACGC 61.095 63.158 0.00 0.00 33.46 5.34
373 374 1.446099 CCATCGTCCCTGTCACACG 60.446 63.158 0.00 0.00 34.78 4.49
427 428 3.357079 CTGACAGGTTGGGCGCAC 61.357 66.667 10.83 6.04 0.00 5.34
433 434 2.610694 CGCACAGCTGACAGGTTGG 61.611 63.158 23.35 1.17 0.00 3.77
447 448 2.043248 TCCTCCTCTACCCCGCAC 60.043 66.667 0.00 0.00 0.00 5.34
456 457 3.481559 TGAAATGAGTCCTCCTCCTCT 57.518 47.619 0.00 0.00 39.65 3.69
546 547 7.563724 TCCATCATGAATAAGGAGATCATCA 57.436 36.000 0.00 0.00 31.65 3.07
570 571 3.690460 CAGTGAGGTTAGCCATTCCTTT 58.310 45.455 0.00 0.00 37.19 3.11
681 700 1.644786 CCAAGAATTCGACGGTGGCC 61.645 60.000 0.00 0.00 0.00 5.36
702 721 6.978659 CGAGACTTATGGACTTGCAATAACTA 59.021 38.462 0.00 0.00 0.00 2.24
710 729 2.094417 GCAACGAGACTTATGGACTTGC 59.906 50.000 0.00 0.00 0.00 4.01
845 864 2.094757 ATCAACTGACGACGCCACCA 62.095 55.000 0.00 0.00 0.00 4.17
853 872 3.071023 AGGAAAGAACCATCAACTGACGA 59.929 43.478 0.00 0.00 0.00 4.20
854 873 3.187227 CAGGAAAGAACCATCAACTGACG 59.813 47.826 0.00 0.00 0.00 4.35
976 995 1.992233 GCATGCAATTCCGCCTCGAA 61.992 55.000 14.21 0.00 0.00 3.71
1023 1042 1.369625 CCGGTAGGTCAGAATGTTGC 58.630 55.000 0.00 0.00 37.40 4.17
1134 1153 8.834004 ACTCCATAGTACCAATAAGTGACTTA 57.166 34.615 7.60 7.60 32.84 2.24
1228 1250 2.202395 AAACAGCCGTGGCATGCTT 61.202 52.632 18.92 0.00 44.88 3.91
1278 1300 1.557099 TACAGTCGAGAGGCCACAAT 58.443 50.000 5.01 0.00 35.23 2.71
1318 1340 2.272447 TTGCGGGGGTAAAGCAAGC 61.272 57.895 0.00 0.00 44.66 4.01
1321 1343 0.178987 TCTTTTGCGGGGGTAAAGCA 60.179 50.000 0.00 0.00 39.33 3.91
1322 1344 0.963225 TTCTTTTGCGGGGGTAAAGC 59.037 50.000 0.00 0.00 0.00 3.51
1368 1390 9.905713 ACAAATGGATGTTGTCTACAAGTATAT 57.094 29.630 0.00 0.00 40.89 0.86
1370 1392 9.162764 GTACAAATGGATGTTGTCTACAAGTAT 57.837 33.333 0.00 0.00 40.89 2.12
1371 1393 8.151596 TGTACAAATGGATGTTGTCTACAAGTA 58.848 33.333 0.00 0.00 40.89 2.24
1372 1394 6.995686 TGTACAAATGGATGTTGTCTACAAGT 59.004 34.615 0.00 0.00 40.89 3.16
1373 1395 7.433708 TGTACAAATGGATGTTGTCTACAAG 57.566 36.000 0.00 0.00 40.89 3.16
1374 1396 7.446931 ACATGTACAAATGGATGTTGTCTACAA 59.553 33.333 0.00 0.00 39.80 2.41
1375 1397 6.939730 ACATGTACAAATGGATGTTGTCTACA 59.060 34.615 0.00 0.00 39.80 2.74
1376 1398 7.094805 ACACATGTACAAATGGATGTTGTCTAC 60.095 37.037 0.00 0.00 39.80 2.59
1377 1399 6.939730 ACACATGTACAAATGGATGTTGTCTA 59.060 34.615 0.00 0.00 39.80 2.59
1378 1400 5.769662 ACACATGTACAAATGGATGTTGTCT 59.230 36.000 0.00 0.00 39.80 3.41
1379 1401 5.858049 CACACATGTACAAATGGATGTTGTC 59.142 40.000 0.00 0.00 39.80 3.18
1380 1402 5.301551 ACACACATGTACAAATGGATGTTGT 59.698 36.000 0.00 3.84 41.89 3.32
1381 1403 5.771469 ACACACATGTACAAATGGATGTTG 58.229 37.500 0.00 3.27 37.26 3.33
1382 1404 6.403866 AACACACATGTACAAATGGATGTT 57.596 33.333 0.00 7.14 38.45 2.71
1383 1405 6.403866 AAACACACATGTACAAATGGATGT 57.596 33.333 0.00 1.06 38.45 3.06
1384 1406 7.712264 AAAAACACACATGTACAAATGGATG 57.288 32.000 0.00 0.42 38.45 3.51
1417 1439 5.221303 CCTGAGCTCCATGAAGTTTCAAAAA 60.221 40.000 12.15 0.00 41.13 1.94
1418 1440 4.279169 CCTGAGCTCCATGAAGTTTCAAAA 59.721 41.667 12.15 0.00 41.13 2.44
1419 1441 3.822735 CCTGAGCTCCATGAAGTTTCAAA 59.177 43.478 12.15 0.00 41.13 2.69
1420 1442 3.072915 TCCTGAGCTCCATGAAGTTTCAA 59.927 43.478 12.15 0.00 41.13 2.69
1421 1443 2.639347 TCCTGAGCTCCATGAAGTTTCA 59.361 45.455 12.15 0.00 42.14 2.69
1422 1444 3.269178 CTCCTGAGCTCCATGAAGTTTC 58.731 50.000 12.15 0.00 0.00 2.78
1423 1445 3.347077 CTCCTGAGCTCCATGAAGTTT 57.653 47.619 12.15 0.00 0.00 2.66
1436 1458 7.415653 GGTGTAAATAGATTTTTGGCTCCTGAG 60.416 40.741 0.00 0.00 0.00 3.35
1437 1459 6.377146 GGTGTAAATAGATTTTTGGCTCCTGA 59.623 38.462 0.00 0.00 0.00 3.86
1438 1460 6.405842 GGGTGTAAATAGATTTTTGGCTCCTG 60.406 42.308 0.00 0.00 0.00 3.86
1439 1461 5.656859 GGGTGTAAATAGATTTTTGGCTCCT 59.343 40.000 0.00 0.00 0.00 3.69
1440 1462 5.420739 TGGGTGTAAATAGATTTTTGGCTCC 59.579 40.000 0.00 0.00 0.00 4.70
1441 1463 6.524101 TGGGTGTAAATAGATTTTTGGCTC 57.476 37.500 0.00 0.00 0.00 4.70
1442 1464 5.105351 GCTGGGTGTAAATAGATTTTTGGCT 60.105 40.000 0.00 0.00 0.00 4.75
1443 1465 5.109210 GCTGGGTGTAAATAGATTTTTGGC 58.891 41.667 0.00 0.00 0.00 4.52
1444 1466 5.339990 CGCTGGGTGTAAATAGATTTTTGG 58.660 41.667 0.00 0.00 0.00 3.28
1445 1467 4.798387 GCGCTGGGTGTAAATAGATTTTTG 59.202 41.667 0.00 0.00 0.00 2.44
1446 1468 4.705023 AGCGCTGGGTGTAAATAGATTTTT 59.295 37.500 10.39 0.00 0.00 1.94
1447 1469 4.096382 CAGCGCTGGGTGTAAATAGATTTT 59.904 41.667 29.88 0.00 36.90 1.82
1448 1470 3.627577 CAGCGCTGGGTGTAAATAGATTT 59.372 43.478 29.88 0.00 36.90 2.17
1449 1471 3.206150 CAGCGCTGGGTGTAAATAGATT 58.794 45.455 29.88 0.00 36.90 2.40
1450 1472 2.838736 CAGCGCTGGGTGTAAATAGAT 58.161 47.619 29.88 0.00 36.90 1.98
1451 1473 1.742411 GCAGCGCTGGGTGTAAATAGA 60.742 52.381 36.47 0.00 43.51 1.98
1452 1474 0.657840 GCAGCGCTGGGTGTAAATAG 59.342 55.000 36.47 9.09 43.51 1.73
1453 1475 0.746563 GGCAGCGCTGGGTGTAAATA 60.747 55.000 36.47 0.00 43.51 1.40
1454 1476 2.046285 GGCAGCGCTGGGTGTAAAT 61.046 57.895 36.47 0.00 43.51 1.40
1455 1477 1.832719 TAGGCAGCGCTGGGTGTAAA 61.833 55.000 36.47 0.37 43.51 2.01
1456 1478 1.622607 ATAGGCAGCGCTGGGTGTAA 61.623 55.000 36.47 3.94 43.51 2.41
1457 1479 1.622607 AATAGGCAGCGCTGGGTGTA 61.623 55.000 36.47 9.68 43.51 2.90
1458 1480 2.484287 AAATAGGCAGCGCTGGGTGT 62.484 55.000 36.47 7.77 43.51 4.16
1459 1481 1.750399 AAATAGGCAGCGCTGGGTG 60.750 57.895 36.47 14.93 44.42 4.61
1460 1482 1.750399 CAAATAGGCAGCGCTGGGT 60.750 57.895 36.47 0.00 0.00 4.51
1461 1483 2.484062 CCAAATAGGCAGCGCTGGG 61.484 63.158 36.47 23.56 0.00 4.45
1462 1484 1.750399 ACCAAATAGGCAGCGCTGG 60.750 57.895 36.47 21.66 43.14 4.85
1463 1485 1.026182 TCACCAAATAGGCAGCGCTG 61.026 55.000 32.83 32.83 43.14 5.18
1464 1486 0.745845 CTCACCAAATAGGCAGCGCT 60.746 55.000 2.64 2.64 43.14 5.92
1465 1487 0.744414 TCTCACCAAATAGGCAGCGC 60.744 55.000 0.00 0.00 43.14 5.92
1466 1488 1.737838 TTCTCACCAAATAGGCAGCG 58.262 50.000 0.00 0.00 43.14 5.18
1467 1489 4.082026 ACATTTTCTCACCAAATAGGCAGC 60.082 41.667 0.00 0.00 43.14 5.25
1468 1490 5.649782 ACATTTTCTCACCAAATAGGCAG 57.350 39.130 0.00 0.00 43.14 4.85
1469 1491 6.152661 CCTTACATTTTCTCACCAAATAGGCA 59.847 38.462 0.00 0.00 43.14 4.75
1470 1492 6.377146 TCCTTACATTTTCTCACCAAATAGGC 59.623 38.462 0.00 0.00 43.14 3.93
1471 1493 7.938140 TCCTTACATTTTCTCACCAAATAGG 57.062 36.000 0.00 0.00 45.67 2.57
1474 1496 8.869109 TGAAATCCTTACATTTTCTCACCAAAT 58.131 29.630 0.00 0.00 32.02 2.32
1475 1497 8.243961 TGAAATCCTTACATTTTCTCACCAAA 57.756 30.769 0.00 0.00 32.02 3.28
1476 1498 7.831691 TGAAATCCTTACATTTTCTCACCAA 57.168 32.000 0.00 0.00 32.02 3.67
1477 1499 8.055279 GATGAAATCCTTACATTTTCTCACCA 57.945 34.615 0.00 0.00 37.38 4.17
1494 1516 5.969423 ACAAATGTCACATGGGATGAAATC 58.031 37.500 0.00 0.00 44.55 2.17
1495 1517 5.969423 GACAAATGTCACATGGGATGAAAT 58.031 37.500 0.00 0.00 44.18 2.17
1496 1518 5.389859 GACAAATGTCACATGGGATGAAA 57.610 39.130 0.00 0.00 44.18 2.69
1520 1542 1.440145 GCGTTGGAGATGCCCTAAGC 61.440 60.000 0.00 0.00 44.14 3.09
1539 1561 0.109132 GAAGGAAATGTGCGGCTTGG 60.109 55.000 0.00 0.00 0.00 3.61
1543 1565 1.153958 GCAGAAGGAAATGTGCGGC 60.154 57.895 0.00 0.00 29.41 6.53
1549 1571 2.353889 CGGACTGATGCAGAAGGAAATG 59.646 50.000 0.82 0.00 35.18 2.32
1639 1661 7.436673 TCATCCGGTTTGTTGAAAAATAGTTTG 59.563 33.333 0.00 0.00 0.00 2.93
1702 1727 3.363575 CGCCGTATTTGTATGAAATCCGG 60.364 47.826 0.00 0.00 40.60 5.14
1718 1743 5.502706 CGAAATGTAATGAAAATCCGCCGTA 60.503 40.000 0.00 0.00 0.00 4.02
1760 1785 1.204704 GGTTTAAGGCAGGGTCATTGC 59.795 52.381 0.00 0.00 40.80 3.56
1761 1786 2.807676 AGGTTTAAGGCAGGGTCATTG 58.192 47.619 0.00 0.00 0.00 2.82
1770 1797 3.181469 CGCTGTAGGATAGGTTTAAGGCA 60.181 47.826 0.00 0.00 0.00 4.75
1798 1825 1.831286 ACAGTCTTGGACGTCCGGT 60.831 57.895 28.70 16.19 37.67 5.28
1801 1828 1.668151 GGCACAGTCTTGGACGTCC 60.668 63.158 28.17 28.17 37.67 4.79
1814 1841 3.691342 CGGAAGGAGGACGGCACA 61.691 66.667 0.00 0.00 0.00 4.57
1818 1845 0.824182 AGATAGCGGAAGGAGGACGG 60.824 60.000 0.00 0.00 0.00 4.79
1864 1892 0.818040 GGACACCGCACCTTCACTTT 60.818 55.000 0.00 0.00 0.00 2.66
1880 1908 0.747283 TCTACTCTTCCTCGCCGGAC 60.747 60.000 5.05 0.00 42.97 4.79
1956 1988 1.286553 AGACTCCTCCGAGGATGAGTT 59.713 52.381 24.13 14.68 44.81 3.01
2028 2060 2.103538 GGACAACGATAGCGCGGA 59.896 61.111 8.83 0.00 42.48 5.54
2030 2062 1.343821 GTTGGACAACGATAGCGCG 59.656 57.895 0.00 0.00 42.48 6.86
2036 2068 2.359478 GCCCGGTTGGACAACGAT 60.359 61.111 0.00 0.00 42.02 3.73
2075 2107 2.100031 CAGTTGCGCCTCGTATGCA 61.100 57.895 4.18 0.00 36.72 3.96
2081 2113 2.058829 AAAACACCAGTTGCGCCTCG 62.059 55.000 4.18 0.00 38.17 4.63
2100 2132 1.896220 AGGCGATCACAGAGCAAAAA 58.104 45.000 0.00 0.00 0.00 1.94
2103 2135 0.894835 TGTAGGCGATCACAGAGCAA 59.105 50.000 0.00 0.00 0.00 3.91
2105 2137 1.134965 AGTTGTAGGCGATCACAGAGC 60.135 52.381 0.00 0.00 0.00 4.09
2149 2181 3.883744 CTGAAACCGCCGCTCACCT 62.884 63.158 0.00 0.00 0.00 4.00
2162 2194 2.048597 ATGTCGTCCGCGCTGAAA 60.049 55.556 5.56 0.00 38.14 2.69
2212 2244 2.270205 CATGGCCTCGGTGAAGCT 59.730 61.111 3.32 0.00 0.00 3.74
2214 2246 2.825836 GCCATGGCCTCGGTGAAG 60.826 66.667 27.24 0.00 34.56 3.02
2259 2291 3.258123 GCAATGTTCCCCAACAATACAGT 59.742 43.478 0.00 0.00 45.78 3.55
2261 2293 3.234353 TGCAATGTTCCCCAACAATACA 58.766 40.909 0.00 0.00 45.78 2.29
2265 2297 2.079170 TCTGCAATGTTCCCCAACAA 57.921 45.000 0.00 0.00 45.78 2.83
2266 2298 2.079170 TTCTGCAATGTTCCCCAACA 57.921 45.000 0.00 0.00 46.71 3.33
2267 2299 3.467374 TTTTCTGCAATGTTCCCCAAC 57.533 42.857 0.00 0.00 0.00 3.77
2268 2300 5.815233 TTATTTTCTGCAATGTTCCCCAA 57.185 34.783 0.00 0.00 0.00 4.12
2269 2301 5.815233 TTTATTTTCTGCAATGTTCCCCA 57.185 34.783 0.00 0.00 0.00 4.96
2292 2324 5.957842 TCTTGGTGATGCGTAGAATTTTT 57.042 34.783 0.00 0.00 0.00 1.94
2293 2325 5.647658 TGATCTTGGTGATGCGTAGAATTTT 59.352 36.000 0.00 0.00 35.14 1.82
2294 2326 5.185454 TGATCTTGGTGATGCGTAGAATTT 58.815 37.500 0.00 0.00 35.14 1.82
2295 2327 4.769688 TGATCTTGGTGATGCGTAGAATT 58.230 39.130 0.00 0.00 35.14 2.17
2296 2328 4.406648 TGATCTTGGTGATGCGTAGAAT 57.593 40.909 0.00 0.00 35.14 2.40
2297 2329 3.885724 TGATCTTGGTGATGCGTAGAA 57.114 42.857 0.00 0.00 35.14 2.10


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

AutoCloner maintained by Alex Coulton.