Multiple sequence alignment - TraesCS7D01G116600

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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 TraesCS7D01G116600 chr7D 100.000 2411 0 0 1 2411 71811579 71813989 0.000000e+00 4453.0
1 TraesCS7D01G116600 chr7D 88.736 870 68 22 717 1569 72128214 72129070 0.000000e+00 1037.0
2 TraesCS7D01G116600 chr7D 82.307 1283 142 53 696 1949 71864783 71863557 0.000000e+00 1033.0
3 TraesCS7D01G116600 chr7D 77.570 321 35 22 1705 2011 71863323 71863026 2.480000e-35 159.0
4 TraesCS7D01G116600 chr7B 89.410 1643 121 17 1 1633 14789484 14787885 0.000000e+00 2021.0
5 TraesCS7D01G116600 chr7B 88.478 1137 79 19 552 1674 14696625 14697723 0.000000e+00 1327.0
6 TraesCS7D01G116600 chr7B 88.808 965 86 16 696 1652 14866742 14865792 0.000000e+00 1164.0
7 TraesCS7D01G116600 chr7B 88.336 703 64 15 717 1412 14980512 14981203 0.000000e+00 828.0
8 TraesCS7D01G116600 chr7B 90.377 478 46 0 51 528 14694997 14695474 1.570000e-176 628.0
9 TraesCS7D01G116600 chr7B 86.351 359 29 8 2051 2409 14778922 14778584 8.140000e-100 374.0
10 TraesCS7D01G116600 chr7B 84.375 384 39 13 2029 2409 14698155 14698520 8.200000e-95 357.0
11 TraesCS7D01G116600 chr7B 87.460 311 21 4 1704 2006 14697878 14698178 2.300000e-90 342.0
12 TraesCS7D01G116600 chr7B 81.333 225 29 8 2183 2398 14863321 14863101 1.150000e-38 171.0
13 TraesCS7D01G116600 chr7B 84.615 156 14 3 1704 1852 14787849 14787697 1.930000e-31 147.0
14 TraesCS7D01G116600 chrUn 89.548 1550 112 27 106 1629 82565060 82566585 0.000000e+00 1919.0
15 TraesCS7D01G116600 chrUn 89.304 991 75 13 717 1703 84331360 84330397 0.000000e+00 1214.0
16 TraesCS7D01G116600 chrUn 89.551 890 70 14 696 1569 84318095 84317213 0.000000e+00 1107.0
17 TraesCS7D01G116600 chrUn 88.736 870 68 21 717 1569 273471143 273470287 0.000000e+00 1037.0
18 TraesCS7D01G116600 chrUn 85.380 1026 93 32 623 1629 82605419 82604432 0.000000e+00 1011.0
19 TraesCS7D01G116600 chrUn 95.223 314 9 1 1704 2011 84330348 84330035 2.150000e-135 492.0
20 TraesCS7D01G116600 chrUn 93.750 208 10 1 2189 2396 84329872 84329668 2.330000e-80 309.0
21 TraesCS7D01G116600 chrUn 89.151 212 18 1 2203 2409 82567139 82567350 2.380000e-65 259.0
22 TraesCS7D01G116600 chrUn 89.474 209 10 4 1798 2006 82566813 82567009 1.110000e-63 254.0
23 TraesCS7D01G116600 chrUn 85.714 161 8 3 2046 2205 84330030 84329884 3.210000e-34 156.0
24 TraesCS7D01G116600 chrUn 84.043 94 9 1 2183 2270 84314224 84314131 4.270000e-13 86.1
25 TraesCS7D01G116600 chr5D 85.639 571 81 1 1 570 217322834 217323404 1.230000e-167 599.0
26 TraesCS7D01G116600 chr7A 84.801 579 85 3 1 577 645899343 645899920 1.610000e-161 579.0
27 TraesCS7D01G116600 chr7A 80.952 315 32 14 1705 2006 77196421 77196720 8.670000e-55 224.0
28 TraesCS7D01G116600 chr7A 77.395 261 37 16 1704 1950 77196054 77196306 4.180000e-28 135.0
29 TraesCS7D01G116600 chr2D 84.444 585 87 4 1 583 315088056 315088638 7.480000e-160 573.0
30 TraesCS7D01G116600 chr2D 82.105 570 95 6 2 568 361240465 361241030 4.660000e-132 481.0
31 TraesCS7D01G116600 chr6D 84.831 534 79 2 1 533 427976251 427976783 9.810000e-149 536.0
32 TraesCS7D01G116600 chr2B 82.960 581 89 8 2 577 688213201 688213776 1.280000e-142 516.0
33 TraesCS7D01G116600 chr1B 90.135 223 12 2 1789 2011 10931489 10931701 5.070000e-72 281.0
34 TraesCS7D01G116600 chr1B 91.925 161 13 0 2117 2277 10931724 10931884 2.410000e-55 226.0


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 TraesCS7D01G116600 chr7D 71811579 71813989 2410 False 4453.000000 4453 100.00000 1 2411 1 chr7D.!!$F1 2410
1 TraesCS7D01G116600 chr7D 72128214 72129070 856 False 1037.000000 1037 88.73600 717 1569 1 chr7D.!!$F2 852
2 TraesCS7D01G116600 chr7D 71863026 71864783 1757 True 596.000000 1033 79.93850 696 2011 2 chr7D.!!$R1 1315
3 TraesCS7D01G116600 chr7B 14787697 14789484 1787 True 1084.000000 2021 87.01250 1 1852 2 chr7B.!!$R2 1851
4 TraesCS7D01G116600 chr7B 14980512 14981203 691 False 828.000000 828 88.33600 717 1412 1 chr7B.!!$F1 695
5 TraesCS7D01G116600 chr7B 14863101 14866742 3641 True 667.500000 1164 85.07050 696 2398 2 chr7B.!!$R3 1702
6 TraesCS7D01G116600 chr7B 14694997 14698520 3523 False 663.500000 1327 87.67250 51 2409 4 chr7B.!!$F2 2358
7 TraesCS7D01G116600 chrUn 273470287 273471143 856 True 1037.000000 1037 88.73600 717 1569 1 chrUn.!!$R2 852
8 TraesCS7D01G116600 chrUn 82604432 82605419 987 True 1011.000000 1011 85.38000 623 1629 1 chrUn.!!$R1 1006
9 TraesCS7D01G116600 chrUn 82565060 82567350 2290 False 810.666667 1919 89.39100 106 2409 3 chrUn.!!$F1 2303
10 TraesCS7D01G116600 chrUn 84314131 84318095 3964 True 596.550000 1107 86.79700 696 2270 2 chrUn.!!$R3 1574
11 TraesCS7D01G116600 chrUn 84329668 84331360 1692 True 542.750000 1214 90.99775 717 2396 4 chrUn.!!$R4 1679
12 TraesCS7D01G116600 chr5D 217322834 217323404 570 False 599.000000 599 85.63900 1 570 1 chr5D.!!$F1 569
13 TraesCS7D01G116600 chr7A 645899343 645899920 577 False 579.000000 579 84.80100 1 577 1 chr7A.!!$F1 576
14 TraesCS7D01G116600 chr2D 315088056 315088638 582 False 573.000000 573 84.44400 1 583 1 chr2D.!!$F1 582
15 TraesCS7D01G116600 chr2D 361240465 361241030 565 False 481.000000 481 82.10500 2 568 1 chr2D.!!$F2 566
16 TraesCS7D01G116600 chr6D 427976251 427976783 532 False 536.000000 536 84.83100 1 533 1 chr6D.!!$F1 532
17 TraesCS7D01G116600 chr2B 688213201 688213776 575 False 516.000000 516 82.96000 2 577 1 chr2B.!!$F1 575

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
712 1857 0.319813 CATCCACGGCATCGCTCATA 60.32 55.0 0.0 0.0 40.63 2.15 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1666 5509 1.780309 TGGATCACAGGAACCAAACCT 59.22 47.619 0.0 0.0 42.37 3.5 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
29 30 2.132762 CGGCATCTATACAAACCGGAC 58.867 52.381 9.46 0.00 37.04 4.79
101 103 2.752903 CCACCAGGTTCCCTTTTATTCG 59.247 50.000 0.00 0.00 0.00 3.34
171 176 3.001736 GTGGTCGCTCTAAATTCTGATGC 59.998 47.826 0.00 0.00 0.00 3.91
298 303 2.957871 CGAATCGGTGATCTTCGCA 58.042 52.632 0.00 0.00 35.85 5.10
301 306 2.748605 GAATCGGTGATCTTCGCATCT 58.251 47.619 0.00 0.00 0.00 2.90
302 307 2.898729 ATCGGTGATCTTCGCATCTT 57.101 45.000 0.00 0.00 0.00 2.40
340 345 4.574013 GTGCAGAGGGTCAATTCTTCTATG 59.426 45.833 0.00 0.00 0.00 2.23
378 383 2.338620 CTCAGTGGCGTCGGACAA 59.661 61.111 9.10 0.00 28.51 3.18
385 390 1.136169 GTGGCGTCGGACAACAAATAC 60.136 52.381 9.10 0.00 28.51 1.89
466 472 6.844696 TTAGCTCATTATTTAGCCAAGTCG 57.155 37.500 0.00 0.00 39.64 4.18
500 506 6.738114 TCTGATGGTCTTTGTGTTTTTCATC 58.262 36.000 0.00 0.00 0.00 2.92
518 524 2.672961 TCCTACTCTGGTTTGCATCG 57.327 50.000 0.00 0.00 0.00 3.84
548 1653 9.947669 ATACTCTATGTAACTATGTTGTTCGAC 57.052 33.333 0.00 0.00 34.45 4.20
570 1703 6.237313 ACTAATAAAGTGCTGACGTTTTCC 57.763 37.500 0.00 0.00 36.93 3.13
571 1704 5.995897 ACTAATAAAGTGCTGACGTTTTCCT 59.004 36.000 0.00 0.00 36.93 3.36
577 1710 5.169836 AGTGCTGACGTTTTCCTAAAAAG 57.830 39.130 0.00 0.00 35.10 2.27
665 1802 4.793028 GCCAGAAAAGAAAAGGGAAACTCG 60.793 45.833 0.00 0.00 0.00 4.18
671 1808 0.584876 AAAAGGGAAACTCGCGTTCG 59.415 50.000 5.77 0.00 30.76 3.95
711 1856 1.596203 CATCCACGGCATCGCTCAT 60.596 57.895 0.00 0.00 40.63 2.90
712 1857 0.319813 CATCCACGGCATCGCTCATA 60.320 55.000 0.00 0.00 40.63 2.15
713 1858 0.319900 ATCCACGGCATCGCTCATAC 60.320 55.000 0.00 0.00 40.63 2.39
960 2119 1.767759 AATCCCAATCTCCAAAGCCG 58.232 50.000 0.00 0.00 0.00 5.52
1510 2707 4.200838 TGGTGTTGATATGATGTGTCGT 57.799 40.909 0.00 0.00 0.00 4.34
1511 2708 4.180817 TGGTGTTGATATGATGTGTCGTC 58.819 43.478 0.00 0.00 0.00 4.20
1512 2709 4.081697 TGGTGTTGATATGATGTGTCGTCT 60.082 41.667 0.00 0.00 0.00 4.18
1513 2710 4.870426 GGTGTTGATATGATGTGTCGTCTT 59.130 41.667 0.00 0.00 0.00 3.01
1514 2711 6.040247 GGTGTTGATATGATGTGTCGTCTTA 58.960 40.000 0.00 0.00 0.00 2.10
1515 2712 6.701841 GGTGTTGATATGATGTGTCGTCTTAT 59.298 38.462 0.00 0.00 0.00 1.73
1516 2713 7.096023 GGTGTTGATATGATGTGTCGTCTTATC 60.096 40.741 13.28 13.28 37.20 1.75
1517 2714 6.923508 TGTTGATATGATGTGTCGTCTTATCC 59.076 38.462 15.60 7.56 36.52 2.59
1518 2715 6.901081 TGATATGATGTGTCGTCTTATCCT 57.099 37.500 15.60 0.00 36.52 3.24
1519 2716 7.996098 TGATATGATGTGTCGTCTTATCCTA 57.004 36.000 15.60 0.00 36.52 2.94
1520 2717 8.404107 TGATATGATGTGTCGTCTTATCCTAA 57.596 34.615 15.60 3.13 36.52 2.69
1521 2718 9.025041 TGATATGATGTGTCGTCTTATCCTAAT 57.975 33.333 15.60 0.00 36.52 1.73
1522 2719 9.295214 GATATGATGTGTCGTCTTATCCTAATG 57.705 37.037 10.87 0.00 33.85 1.90
1523 2720 6.465439 TGATGTGTCGTCTTATCCTAATGT 57.535 37.500 0.00 0.00 0.00 2.71
1524 2721 7.576861 TGATGTGTCGTCTTATCCTAATGTA 57.423 36.000 0.00 0.00 0.00 2.29
1525 2722 8.178313 TGATGTGTCGTCTTATCCTAATGTAT 57.822 34.615 0.00 0.00 0.00 2.29
1526 2723 8.638873 TGATGTGTCGTCTTATCCTAATGTATT 58.361 33.333 0.00 0.00 0.00 1.89
1527 2724 8.818141 ATGTGTCGTCTTATCCTAATGTATTG 57.182 34.615 0.00 0.00 0.00 1.90
1633 5476 3.411446 TCCGTGATTCTGCAATGTTCTT 58.589 40.909 0.00 0.00 0.00 2.52
1634 5477 3.189080 TCCGTGATTCTGCAATGTTCTTG 59.811 43.478 0.00 0.00 0.00 3.02
1635 5478 3.058016 CCGTGATTCTGCAATGTTCTTGT 60.058 43.478 0.00 0.00 0.00 3.16
1637 5480 4.319694 CGTGATTCTGCAATGTTCTTGTGA 60.320 41.667 0.00 0.00 0.00 3.58
1640 5483 4.979943 TTCTGCAATGTTCTTGTGACAA 57.020 36.364 0.00 0.00 0.00 3.18
1641 5484 4.556942 TCTGCAATGTTCTTGTGACAAG 57.443 40.909 18.84 18.84 0.00 3.16
1643 5486 4.639755 TCTGCAATGTTCTTGTGACAAGAA 59.360 37.500 30.67 30.67 34.20 2.52
1645 5488 3.732721 GCAATGTTCTTGTGACAAGAAGC 59.267 43.478 33.75 28.60 36.99 3.86
1646 5489 4.734402 GCAATGTTCTTGTGACAAGAAGCA 60.734 41.667 33.75 30.47 36.99 3.91
1651 5494 2.615447 TCTTGTGACAAGAAGCAAGCTG 59.385 45.455 24.40 0.00 38.44 4.24
1655 5498 4.388485 TGTGACAAGAAGCAAGCTGATTA 58.612 39.130 0.00 0.00 0.00 1.75
1656 5499 5.005740 TGTGACAAGAAGCAAGCTGATTAT 58.994 37.500 0.00 0.00 0.00 1.28
1659 5502 3.760151 ACAAGAAGCAAGCTGATTATGCA 59.240 39.130 9.84 0.00 42.45 3.96
1660 5503 4.219070 ACAAGAAGCAAGCTGATTATGCAA 59.781 37.500 9.84 0.00 42.45 4.08
1661 5504 4.367386 AGAAGCAAGCTGATTATGCAAC 57.633 40.909 9.84 3.51 42.45 4.17
1662 5505 4.015084 AGAAGCAAGCTGATTATGCAACT 58.985 39.130 9.84 5.53 42.45 3.16
1663 5506 3.777465 AGCAAGCTGATTATGCAACTG 57.223 42.857 9.84 0.00 42.45 3.16
1664 5507 3.349927 AGCAAGCTGATTATGCAACTGA 58.650 40.909 9.84 0.00 42.45 3.41
1665 5508 3.952323 AGCAAGCTGATTATGCAACTGAT 59.048 39.130 9.84 0.00 42.45 2.90
1666 5509 5.128205 AGCAAGCTGATTATGCAACTGATA 58.872 37.500 9.84 0.00 42.45 2.15
1667 5510 5.238868 AGCAAGCTGATTATGCAACTGATAG 59.761 40.000 9.84 0.00 42.45 2.08
1668 5511 5.562307 GCAAGCTGATTATGCAACTGATAGG 60.562 44.000 2.44 0.00 39.81 2.57
1669 5512 5.301835 AGCTGATTATGCAACTGATAGGT 57.698 39.130 0.00 0.00 0.00 3.08
1670 5513 5.688807 AGCTGATTATGCAACTGATAGGTT 58.311 37.500 0.00 0.00 0.00 3.50
1671 5514 6.125029 AGCTGATTATGCAACTGATAGGTTT 58.875 36.000 0.00 0.00 0.00 3.27
1672 5515 6.039047 AGCTGATTATGCAACTGATAGGTTTG 59.961 38.462 0.00 0.00 0.00 2.93
1673 5516 6.698008 TGATTATGCAACTGATAGGTTTGG 57.302 37.500 0.00 0.00 0.00 3.28
1674 5517 6.186957 TGATTATGCAACTGATAGGTTTGGT 58.813 36.000 0.00 0.00 0.00 3.67
1675 5518 6.663093 TGATTATGCAACTGATAGGTTTGGTT 59.337 34.615 0.00 0.00 0.00 3.67
1676 5519 6.509418 TTATGCAACTGATAGGTTTGGTTC 57.491 37.500 0.00 0.00 0.00 3.62
1677 5520 3.153919 TGCAACTGATAGGTTTGGTTCC 58.846 45.455 0.00 0.00 0.00 3.62
1678 5521 3.181434 TGCAACTGATAGGTTTGGTTCCT 60.181 43.478 0.00 0.00 38.91 3.36
1679 5522 3.191371 GCAACTGATAGGTTTGGTTCCTG 59.809 47.826 0.00 0.00 36.60 3.86
1680 5523 4.398319 CAACTGATAGGTTTGGTTCCTGT 58.602 43.478 0.00 0.00 36.60 4.00
1681 5524 4.021102 ACTGATAGGTTTGGTTCCTGTG 57.979 45.455 0.00 0.00 36.60 3.66
1682 5525 3.650942 ACTGATAGGTTTGGTTCCTGTGA 59.349 43.478 0.00 0.00 36.60 3.58
1683 5526 4.289672 ACTGATAGGTTTGGTTCCTGTGAT 59.710 41.667 0.00 0.00 36.60 3.06
1684 5527 4.843728 TGATAGGTTTGGTTCCTGTGATC 58.156 43.478 0.00 0.00 36.60 2.92
1685 5528 2.586648 AGGTTTGGTTCCTGTGATCC 57.413 50.000 0.00 0.00 33.62 3.36
1686 5529 1.780309 AGGTTTGGTTCCTGTGATCCA 59.220 47.619 0.00 0.00 38.35 3.41
1687 5530 2.162681 GGTTTGGTTCCTGTGATCCAG 58.837 52.381 4.67 4.67 40.56 3.86
1688 5531 2.489073 GGTTTGGTTCCTGTGATCCAGT 60.489 50.000 9.47 0.00 40.56 4.00
1689 5532 3.222603 GTTTGGTTCCTGTGATCCAGTT 58.777 45.455 9.47 0.00 40.56 3.16
1690 5533 3.593442 TTGGTTCCTGTGATCCAGTTT 57.407 42.857 9.47 0.00 40.56 2.66
1691 5534 3.140325 TGGTTCCTGTGATCCAGTTTC 57.860 47.619 9.47 1.64 39.74 2.78
1692 5535 2.711009 TGGTTCCTGTGATCCAGTTTCT 59.289 45.455 9.47 0.00 39.74 2.52
1693 5536 3.138283 TGGTTCCTGTGATCCAGTTTCTT 59.862 43.478 9.47 0.00 39.74 2.52
1694 5537 3.503748 GGTTCCTGTGATCCAGTTTCTTG 59.496 47.826 9.47 0.00 39.74 3.02
1695 5538 2.783135 TCCTGTGATCCAGTTTCTTGC 58.217 47.619 9.47 0.00 39.74 4.01
1696 5539 2.106338 TCCTGTGATCCAGTTTCTTGCA 59.894 45.455 9.47 0.00 39.74 4.08
1697 5540 2.227388 CCTGTGATCCAGTTTCTTGCAC 59.773 50.000 9.47 0.00 39.74 4.57
1701 5544 5.316167 TGTGATCCAGTTTCTTGCACTTAT 58.684 37.500 0.00 0.00 0.00 1.73
1814 5719 7.048629 TCACCTAGTTGAAAATTTGCAATGA 57.951 32.000 14.72 10.77 0.00 2.57
1979 6418 7.567458 TGTCTTCATGATGATTCTTGTGGATA 58.433 34.615 13.82 0.00 0.00 2.59
2000 6439 7.147976 GGATAAGAAACTTGCAGTTGACAATT 58.852 34.615 2.88 0.00 38.66 2.32
2001 6440 8.296713 GGATAAGAAACTTGCAGTTGACAATTA 58.703 33.333 2.88 0.93 38.66 1.40
2002 6441 9.118236 GATAAGAAACTTGCAGTTGACAATTAC 57.882 33.333 2.88 0.00 38.66 1.89
2003 6442 6.449635 AGAAACTTGCAGTTGACAATTACA 57.550 33.333 2.88 0.00 38.66 2.41
2004 6443 6.498304 AGAAACTTGCAGTTGACAATTACAG 58.502 36.000 2.88 0.00 38.66 2.74
2005 6444 5.835113 AACTTGCAGTTGACAATTACAGT 57.165 34.783 0.00 0.00 37.00 3.55
2006 6445 5.173774 ACTTGCAGTTGACAATTACAGTG 57.826 39.130 0.00 0.00 0.00 3.66
2007 6446 4.036734 ACTTGCAGTTGACAATTACAGTGG 59.963 41.667 0.00 0.00 0.00 4.00
2008 6447 3.814625 TGCAGTTGACAATTACAGTGGA 58.185 40.909 0.00 0.00 0.00 4.02
2009 6448 4.397420 TGCAGTTGACAATTACAGTGGAT 58.603 39.130 0.00 0.00 0.00 3.41
2010 6449 5.555966 TGCAGTTGACAATTACAGTGGATA 58.444 37.500 0.00 0.00 0.00 2.59
2011 6450 6.179756 TGCAGTTGACAATTACAGTGGATAT 58.820 36.000 0.00 0.00 0.00 1.63
2012 6451 6.093909 TGCAGTTGACAATTACAGTGGATATG 59.906 38.462 0.00 0.00 0.00 1.78
2013 6452 6.094048 GCAGTTGACAATTACAGTGGATATGT 59.906 38.462 0.00 0.00 34.62 2.29
2014 6453 7.362056 GCAGTTGACAATTACAGTGGATATGTT 60.362 37.037 0.00 0.00 32.02 2.71
2015 6454 8.514594 CAGTTGACAATTACAGTGGATATGTTT 58.485 33.333 0.00 0.00 32.02 2.83
2016 6455 8.514594 AGTTGACAATTACAGTGGATATGTTTG 58.485 33.333 0.00 0.00 32.02 2.93
2017 6456 6.851609 TGACAATTACAGTGGATATGTTTGC 58.148 36.000 0.00 0.00 32.02 3.68
2018 6457 6.658816 TGACAATTACAGTGGATATGTTTGCT 59.341 34.615 0.00 0.00 32.02 3.91
2019 6458 7.088589 ACAATTACAGTGGATATGTTTGCTC 57.911 36.000 0.00 0.00 32.02 4.26
2020 6459 6.658816 ACAATTACAGTGGATATGTTTGCTCA 59.341 34.615 0.00 0.00 32.02 4.26
2021 6460 7.176515 ACAATTACAGTGGATATGTTTGCTCAA 59.823 33.333 0.00 0.00 32.02 3.02
2022 6461 7.701539 ATTACAGTGGATATGTTTGCTCAAA 57.298 32.000 0.00 0.00 32.02 2.69
2023 6462 7.517614 TTACAGTGGATATGTTTGCTCAAAA 57.482 32.000 0.00 0.00 32.02 2.44
2024 6463 6.403866 ACAGTGGATATGTTTGCTCAAAAA 57.596 33.333 0.00 0.00 31.33 1.94
2083 6538 6.798315 CTGATCATTTCAGTACCATCCATC 57.202 41.667 0.00 0.00 45.79 3.51
2123 6578 4.552166 ACATGCAGTTGTTGAGTTGTAC 57.448 40.909 0.00 0.00 0.00 2.90
2124 6579 4.199310 ACATGCAGTTGTTGAGTTGTACT 58.801 39.130 0.00 0.00 0.00 2.73
2125 6580 4.035558 ACATGCAGTTGTTGAGTTGTACTG 59.964 41.667 0.00 0.00 39.29 2.74
2126 6581 3.605634 TGCAGTTGTTGAGTTGTACTGT 58.394 40.909 0.00 0.00 38.70 3.55
2210 8056 2.271944 ACAGGACACACTTTAAGGCC 57.728 50.000 0.00 0.00 0.00 5.19
2233 8110 7.148407 GGCCATTATTTTCTGTATCATCCTACG 60.148 40.741 0.00 0.00 0.00 3.51
2236 8113 4.746535 TTTTCTGTATCATCCTACGCCA 57.253 40.909 0.00 0.00 0.00 5.69
2270 8151 2.035704 AGAATGCGCAATTTGGTGTCAA 59.964 40.909 17.11 0.00 0.00 3.18
2387 8277 1.888215 CCACTCATCACTGCAGTTGT 58.112 50.000 18.94 5.69 0.00 3.32
2401 8291 8.575589 TCACTGCAGTTGTTATGATATTGTTTT 58.424 29.630 18.94 0.00 0.00 2.43
2405 8295 8.575589 TGCAGTTGTTATGATATTGTTTTCAGT 58.424 29.630 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 2.551032 TGTATCACGTCTATGCGTAGGG 59.449 50.000 13.02 8.03 43.83 3.53
101 103 3.257393 AGAAGATCGCAACATCAGACAC 58.743 45.455 0.00 0.00 0.00 3.67
171 176 0.600782 GCAGGCAACAACACATTGGG 60.601 55.000 0.00 0.00 40.42 4.12
253 258 1.006832 CCTCCCGTGCAAGATAAACG 58.993 55.000 0.00 0.00 37.07 3.60
298 303 3.643792 GCACCAGGGATAGACAGTAAGAT 59.356 47.826 0.00 0.00 0.00 2.40
301 306 2.766263 CTGCACCAGGGATAGACAGTAA 59.234 50.000 0.00 0.00 0.00 2.24
302 307 2.024369 TCTGCACCAGGGATAGACAGTA 60.024 50.000 0.00 0.00 31.51 2.74
356 361 4.457496 CGACGCCACTGAGCCCAT 62.457 66.667 0.00 0.00 0.00 4.00
369 374 0.094046 GCCGTATTTGTTGTCCGACG 59.906 55.000 0.00 0.00 0.00 5.12
378 383 2.126385 TCGACGCGCCGTATTTGT 60.126 55.556 15.85 0.00 41.37 2.83
466 472 4.744795 AAGACCATCAGAGTCCATACAC 57.255 45.455 0.00 0.00 34.67 2.90
500 506 1.656652 CCGATGCAAACCAGAGTAGG 58.343 55.000 0.00 0.00 0.00 3.18
545 1650 5.511088 AAACGTCAGCACTTTATTAGTCG 57.489 39.130 0.00 0.00 33.85 4.18
548 1653 6.481954 AGGAAAACGTCAGCACTTTATTAG 57.518 37.500 0.00 0.00 0.00 1.73
616 1753 0.322816 AATGTACTGCTGCTGGTGGG 60.323 55.000 11.29 0.00 0.00 4.61
618 1755 0.723414 CGAATGTACTGCTGCTGGTG 59.277 55.000 11.29 0.00 0.00 4.17
621 1758 3.677601 CATTTCGAATGTACTGCTGCTG 58.322 45.455 0.00 4.89 0.00 4.41
671 1808 2.010582 TTCCGTTTTGGCACACTGGC 62.011 55.000 0.00 0.00 44.03 4.85
711 1856 1.807226 CGATCCGTGTGCTCTGGTA 59.193 57.895 0.00 0.00 0.00 3.25
712 1857 2.573869 CGATCCGTGTGCTCTGGT 59.426 61.111 0.00 0.00 0.00 4.00
713 1858 2.887568 GCGATCCGTGTGCTCTGG 60.888 66.667 0.00 0.00 0.00 3.86
751 1897 4.796495 GGAGGGCGGCGATTTGGT 62.796 66.667 12.98 0.00 0.00 3.67
1510 2707 9.276590 CAAGCATCACAATACATTAGGATAAGA 57.723 33.333 0.00 0.00 0.00 2.10
1511 2708 9.276590 TCAAGCATCACAATACATTAGGATAAG 57.723 33.333 0.00 0.00 0.00 1.73
1512 2709 9.625747 TTCAAGCATCACAATACATTAGGATAA 57.374 29.630 0.00 0.00 0.00 1.75
1513 2710 9.797642 ATTCAAGCATCACAATACATTAGGATA 57.202 29.630 0.00 0.00 0.00 2.59
1514 2711 8.573885 CATTCAAGCATCACAATACATTAGGAT 58.426 33.333 0.00 0.00 0.00 3.24
1515 2712 7.774625 TCATTCAAGCATCACAATACATTAGGA 59.225 33.333 0.00 0.00 0.00 2.94
1516 2713 7.933396 TCATTCAAGCATCACAATACATTAGG 58.067 34.615 0.00 0.00 0.00 2.69
1517 2714 9.791820 TTTCATTCAAGCATCACAATACATTAG 57.208 29.630 0.00 0.00 0.00 1.73
1519 2716 9.661563 AATTTCATTCAAGCATCACAATACATT 57.338 25.926 0.00 0.00 0.00 2.71
1520 2717 9.093970 CAATTTCATTCAAGCATCACAATACAT 57.906 29.630 0.00 0.00 0.00 2.29
1521 2718 7.063662 GCAATTTCATTCAAGCATCACAATACA 59.936 33.333 0.00 0.00 0.00 2.29
1522 2719 7.063662 TGCAATTTCATTCAAGCATCACAATAC 59.936 33.333 0.00 0.00 0.00 1.89
1523 2720 7.097834 TGCAATTTCATTCAAGCATCACAATA 58.902 30.769 0.00 0.00 0.00 1.90
1524 2721 5.935206 TGCAATTTCATTCAAGCATCACAAT 59.065 32.000 0.00 0.00 0.00 2.71
1525 2722 5.298347 TGCAATTTCATTCAAGCATCACAA 58.702 33.333 0.00 0.00 0.00 3.33
1526 2723 4.884247 TGCAATTTCATTCAAGCATCACA 58.116 34.783 0.00 0.00 0.00 3.58
1527 2724 5.849357 TTGCAATTTCATTCAAGCATCAC 57.151 34.783 0.00 0.00 0.00 3.06
1633 5476 2.330440 TCAGCTTGCTTCTTGTCACA 57.670 45.000 0.00 0.00 0.00 3.58
1634 5477 3.911661 AATCAGCTTGCTTCTTGTCAC 57.088 42.857 0.00 0.00 0.00 3.67
1635 5478 4.142534 GCATAATCAGCTTGCTTCTTGTCA 60.143 41.667 0.00 0.00 33.61 3.58
1637 5480 3.760151 TGCATAATCAGCTTGCTTCTTGT 59.240 39.130 8.68 0.00 37.28 3.16
1640 5483 4.015084 AGTTGCATAATCAGCTTGCTTCT 58.985 39.130 8.68 4.49 37.28 2.85
1641 5484 4.103357 CAGTTGCATAATCAGCTTGCTTC 58.897 43.478 8.68 2.51 37.28 3.86
1643 5486 3.349927 TCAGTTGCATAATCAGCTTGCT 58.650 40.909 8.68 0.00 37.28 3.91
1645 5488 5.530171 ACCTATCAGTTGCATAATCAGCTTG 59.470 40.000 0.00 0.00 0.00 4.01
1646 5489 5.688807 ACCTATCAGTTGCATAATCAGCTT 58.311 37.500 0.00 0.00 0.00 3.74
1651 5494 6.699575 ACCAAACCTATCAGTTGCATAATC 57.300 37.500 0.00 0.00 0.00 1.75
1655 5498 3.763897 GGAACCAAACCTATCAGTTGCAT 59.236 43.478 0.00 0.00 0.00 3.96
1656 5499 3.153919 GGAACCAAACCTATCAGTTGCA 58.846 45.455 0.00 0.00 0.00 4.08
1659 5502 4.104102 TCACAGGAACCAAACCTATCAGTT 59.896 41.667 0.00 0.00 35.84 3.16
1660 5503 3.650942 TCACAGGAACCAAACCTATCAGT 59.349 43.478 0.00 0.00 35.84 3.41
1661 5504 4.286297 TCACAGGAACCAAACCTATCAG 57.714 45.455 0.00 0.00 35.84 2.90
1662 5505 4.324254 GGATCACAGGAACCAAACCTATCA 60.324 45.833 0.00 0.00 36.08 2.15
1663 5506 4.200092 GGATCACAGGAACCAAACCTATC 58.800 47.826 0.00 0.00 36.08 2.08
1664 5507 3.591527 TGGATCACAGGAACCAAACCTAT 59.408 43.478 0.00 0.00 42.37 2.57
1665 5508 2.983192 TGGATCACAGGAACCAAACCTA 59.017 45.455 0.00 0.00 42.37 3.08
1666 5509 1.780309 TGGATCACAGGAACCAAACCT 59.220 47.619 0.00 0.00 42.37 3.50
1667 5510 2.162681 CTGGATCACAGGAACCAAACC 58.837 52.381 0.00 0.00 44.35 3.27
1678 5521 3.213206 AGTGCAAGAAACTGGATCACA 57.787 42.857 0.00 0.00 0.00 3.58
1679 5522 5.163713 GGATAAGTGCAAGAAACTGGATCAC 60.164 44.000 0.00 0.00 0.00 3.06
1680 5523 4.943705 GGATAAGTGCAAGAAACTGGATCA 59.056 41.667 0.00 0.00 0.00 2.92
1681 5524 5.065731 CAGGATAAGTGCAAGAAACTGGATC 59.934 44.000 0.00 0.00 0.00 3.36
1682 5525 4.946157 CAGGATAAGTGCAAGAAACTGGAT 59.054 41.667 0.00 0.00 0.00 3.41
1683 5526 4.202461 ACAGGATAAGTGCAAGAAACTGGA 60.202 41.667 0.00 0.00 0.00 3.86
1684 5527 4.074970 ACAGGATAAGTGCAAGAAACTGG 58.925 43.478 0.00 0.00 0.00 4.00
1685 5528 5.695851 AACAGGATAAGTGCAAGAAACTG 57.304 39.130 0.00 0.00 0.00 3.16
1686 5529 5.010012 CCAAACAGGATAAGTGCAAGAAACT 59.990 40.000 0.00 0.00 41.22 2.66
1687 5530 5.221244 ACCAAACAGGATAAGTGCAAGAAAC 60.221 40.000 0.00 0.00 41.22 2.78
1688 5531 4.892934 ACCAAACAGGATAAGTGCAAGAAA 59.107 37.500 0.00 0.00 41.22 2.52
1689 5532 4.278170 CACCAAACAGGATAAGTGCAAGAA 59.722 41.667 0.00 0.00 41.22 2.52
1690 5533 3.820467 CACCAAACAGGATAAGTGCAAGA 59.180 43.478 0.00 0.00 41.22 3.02
1691 5534 3.569701 ACACCAAACAGGATAAGTGCAAG 59.430 43.478 0.00 0.00 41.22 4.01
1692 5535 3.317711 CACACCAAACAGGATAAGTGCAA 59.682 43.478 0.00 0.00 41.22 4.08
1693 5536 2.884012 CACACCAAACAGGATAAGTGCA 59.116 45.455 0.00 0.00 41.22 4.57
1694 5537 3.146066 TCACACCAAACAGGATAAGTGC 58.854 45.455 0.00 0.00 41.22 4.40
1695 5538 5.707298 AGAATCACACCAAACAGGATAAGTG 59.293 40.000 0.00 0.00 41.22 3.16
1696 5539 5.707298 CAGAATCACACCAAACAGGATAAGT 59.293 40.000 0.00 0.00 41.22 2.24
1697 5540 5.939883 TCAGAATCACACCAAACAGGATAAG 59.060 40.000 0.00 0.00 41.22 1.73
1701 5544 3.855255 TCAGAATCACACCAAACAGGA 57.145 42.857 0.00 0.00 41.22 3.86
1814 5719 8.552296 AGAAATGGAGATAAAGTAGACCACATT 58.448 33.333 0.00 0.00 0.00 2.71
2000 6439 7.517614 TTTTTGAGCAAACATATCCACTGTA 57.482 32.000 0.00 0.00 0.00 2.74
2001 6440 6.403866 TTTTTGAGCAAACATATCCACTGT 57.596 33.333 0.00 0.00 0.00 3.55
2119 6574 9.999009 CTCGTTTCTCTTATAATGTACAGTACA 57.001 33.333 15.90 15.90 43.80 2.90
2124 6579 9.999009 CAGTACTCGTTTCTCTTATAATGTACA 57.001 33.333 0.00 0.00 31.88 2.90
2126 6581 9.999009 CACAGTACTCGTTTCTCTTATAATGTA 57.001 33.333 0.00 0.00 0.00 2.29
2210 8056 7.387673 TGGCGTAGGATGATACAGAAAATAATG 59.612 37.037 0.00 0.00 0.00 1.90
2233 8110 3.365364 GCATTCTGTCAGTTAACAGTGGC 60.365 47.826 8.61 0.14 45.57 5.01
2236 8113 2.480419 GCGCATTCTGTCAGTTAACAGT 59.520 45.455 8.61 0.00 45.57 3.55
2270 8151 4.080526 AGGTTTAATCGAATAGGGTGCTGT 60.081 41.667 0.00 0.00 0.00 4.40
2280 8161 4.323417 TCACAGCACAGGTTTAATCGAAT 58.677 39.130 0.00 0.00 0.00 3.34


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

AutoCloner maintained by Alex Coulton.