Multiple sequence alignment - TraesCS1A01G262800

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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 TraesCS1A01G262800 chr1A 100.000 4348 0 0 1 4348 458231027 458226680 0.000000e+00 8030
1 TraesCS1A01G262800 chr1D 93.002 3744 169 41 642 4348 356947198 356943511 0.000000e+00 5376
2 TraesCS1A01G262800 chr1B 96.932 1206 29 5 2212 3414 480479521 480478321 0.000000e+00 2015
3 TraesCS1A01G262800 chr1B 89.145 1474 93 29 650 2103 480481311 480479885 0.000000e+00 1773
4 TraesCS1A01G262800 chr1B 89.749 517 28 12 3854 4348 480477588 480477075 4.740000e-179 638
5 TraesCS1A01G262800 chr1B 90.833 480 17 6 3416 3869 480478080 480477602 6.180000e-173 617
6 TraesCS1A01G262800 chr4B 91.573 534 43 2 1 534 449531138 449530607 0.000000e+00 736
7 TraesCS1A01G262800 chr4B 87.879 528 61 3 1 527 385924909 385924384 6.180000e-173 617
8 TraesCS1A01G262800 chr7B 87.476 527 59 4 1 527 375195730 375196249 6.220000e-168 601
9 TraesCS1A01G262800 chr7B 72.523 535 112 30 24 532 113048990 113048465 1.630000e-29 141
10 TraesCS1A01G262800 chr7D 85.389 527 72 4 1 526 250781668 250782190 3.820000e-150 542
11 TraesCS1A01G262800 chr5D 86.283 452 60 2 76 527 410604916 410605365 1.410000e-134 490
12 TraesCS1A01G262800 chr3A 96.063 254 10 0 273 526 170967502 170967755 8.700000e-112 414
13 TraesCS1A01G262800 chr6A 81.793 368 56 9 165 527 90220056 90219695 9.140000e-77 298
14 TraesCS1A01G262800 chr6D 81.232 357 60 5 173 526 104784767 104784415 9.210000e-72 281
15 TraesCS1A01G262800 chr3B 75.510 392 86 9 1 387 417239484 417239870 2.670000e-42 183


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 TraesCS1A01G262800 chr1A 458226680 458231027 4347 True 8030.00 8030 100.00000 1 4348 1 chr1A.!!$R1 4347
1 TraesCS1A01G262800 chr1D 356943511 356947198 3687 True 5376.00 5376 93.00200 642 4348 1 chr1D.!!$R1 3706
2 TraesCS1A01G262800 chr1B 480477075 480481311 4236 True 1260.75 2015 91.66475 650 4348 4 chr1B.!!$R1 3698
3 TraesCS1A01G262800 chr4B 449530607 449531138 531 True 736.00 736 91.57300 1 534 1 chr4B.!!$R2 533
4 TraesCS1A01G262800 chr4B 385924384 385924909 525 True 617.00 617 87.87900 1 527 1 chr4B.!!$R1 526
5 TraesCS1A01G262800 chr7B 375195730 375196249 519 False 601.00 601 87.47600 1 527 1 chr7B.!!$F1 526
6 TraesCS1A01G262800 chr7D 250781668 250782190 522 False 542.00 542 85.38900 1 526 1 chr7D.!!$F1 525

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
621 623 0.039346 GGCTCGCTAGATACGTTCCC 60.039 60.0 0.00 0.00 0.00 3.97 F
1501 1517 0.527385 GCGCTAGAGTCAGCTCCTTG 60.527 60.0 0.00 0.02 42.59 3.61 F
1953 1973 0.975556 TTATGGCCAGCTCCGACTCA 60.976 55.0 13.05 0.00 0.00 3.41 F
2828 3181 0.036306 GTCCACATCGGTCTGGGTTT 59.964 55.0 0.00 0.00 35.57 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2008 2029 0.385751 AGTATGACCGCATGAGACCG 59.614 55.000 0.0 0.0 35.94 4.79 R
2501 2852 1.073722 CCTGGCTGACTTTGGCTGA 59.926 57.895 0.0 0.0 0.00 4.26 R
3161 3517 2.917933 CCAGTGTGACCTTTTGACTCA 58.082 47.619 0.0 0.0 0.00 3.41 R
4253 4924 0.251653 TACAGCAGACCTTCCTCGGT 60.252 55.000 0.0 0.0 40.80 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
51 52 0.543174 AGACCTCCTCGCACCTCTTT 60.543 55.000 0.00 0.00 0.00 2.52
138 139 0.671472 CACATTCGTGCTGGAGCTCA 60.671 55.000 17.19 0.61 42.66 4.26
147 148 0.250467 GCTGGAGCTCAGGAACAACA 60.250 55.000 17.19 0.19 43.54 3.33
194 195 0.332972 GACCAAGCCTCCCCAAGATT 59.667 55.000 0.00 0.00 0.00 2.40
201 202 1.144057 CTCCCCAAGATTCCGTCGG 59.856 63.158 4.39 4.39 0.00 4.79
281 282 3.181451 TGCACATTCAGAGGAAAGACTGT 60.181 43.478 0.00 0.00 36.43 3.55
310 311 1.929836 GAAGTATCACTGAGGCTTGCG 59.070 52.381 0.00 0.00 0.00 4.85
370 371 1.918293 ATGGAGCACCCGTTCAGGA 60.918 57.895 0.00 0.00 45.00 3.86
397 398 3.187700 CCGTGAGAAATAGCGCTAGTTT 58.812 45.455 28.50 22.81 0.00 2.66
398 399 4.142315 ACCGTGAGAAATAGCGCTAGTTTA 60.142 41.667 28.50 16.42 0.00 2.01
399 400 4.441415 CCGTGAGAAATAGCGCTAGTTTAG 59.559 45.833 28.50 17.63 0.00 1.85
400 401 4.441415 CGTGAGAAATAGCGCTAGTTTAGG 59.559 45.833 28.50 18.96 0.00 2.69
404 405 5.593010 AGAAATAGCGCTAGTTTAGGACTG 58.407 41.667 28.50 0.00 39.48 3.51
547 549 8.956533 AAAAACATATGCTTTTAAGGTGTTGT 57.043 26.923 13.78 0.00 0.00 3.32
548 550 8.956533 AAAACATATGCTTTTAAGGTGTTGTT 57.043 26.923 1.58 0.00 0.00 2.83
549 551 7.945033 AACATATGCTTTTAAGGTGTTGTTG 57.055 32.000 1.58 0.00 0.00 3.33
550 552 6.454795 ACATATGCTTTTAAGGTGTTGTTGG 58.545 36.000 1.58 0.00 0.00 3.77
551 553 3.172229 TGCTTTTAAGGTGTTGTTGGC 57.828 42.857 0.00 0.00 0.00 4.52
552 554 2.159028 TGCTTTTAAGGTGTTGTTGGCC 60.159 45.455 0.00 0.00 0.00 5.36
553 555 2.102420 GCTTTTAAGGTGTTGTTGGCCT 59.898 45.455 3.32 0.00 0.00 5.19
554 556 3.798889 GCTTTTAAGGTGTTGTTGGCCTC 60.799 47.826 3.32 0.00 0.00 4.70
555 557 3.306472 TTTAAGGTGTTGTTGGCCTCT 57.694 42.857 3.32 0.00 0.00 3.69
556 558 3.306472 TTAAGGTGTTGTTGGCCTCTT 57.694 42.857 3.32 0.00 0.00 2.85
557 559 1.402787 AAGGTGTTGTTGGCCTCTTG 58.597 50.000 3.32 0.00 0.00 3.02
558 560 0.468029 AGGTGTTGTTGGCCTCTTGG 60.468 55.000 3.32 0.00 0.00 3.61
559 561 0.467290 GGTGTTGTTGGCCTCTTGGA 60.467 55.000 3.32 0.00 34.57 3.53
560 562 1.620822 GTGTTGTTGGCCTCTTGGAT 58.379 50.000 3.32 0.00 34.57 3.41
561 563 1.963515 GTGTTGTTGGCCTCTTGGATT 59.036 47.619 3.32 0.00 34.57 3.01
562 564 2.365293 GTGTTGTTGGCCTCTTGGATTT 59.635 45.455 3.32 0.00 34.57 2.17
563 565 3.037549 TGTTGTTGGCCTCTTGGATTTT 58.962 40.909 3.32 0.00 34.57 1.82
564 566 3.454082 TGTTGTTGGCCTCTTGGATTTTT 59.546 39.130 3.32 0.00 34.57 1.94
584 586 4.675063 TTTTTAGGGAATCTTGGCCTCT 57.325 40.909 3.32 0.00 0.00 3.69
585 587 4.675063 TTTTAGGGAATCTTGGCCTCTT 57.325 40.909 3.32 0.00 0.00 2.85
586 588 3.652057 TTAGGGAATCTTGGCCTCTTG 57.348 47.619 3.32 0.00 0.00 3.02
587 589 0.627986 AGGGAATCTTGGCCTCTTGG 59.372 55.000 3.32 0.00 0.00 3.61
588 590 0.625849 GGGAATCTTGGCCTCTTGGA 59.374 55.000 3.32 0.00 34.57 3.53
589 591 1.216427 GGGAATCTTGGCCTCTTGGAT 59.784 52.381 3.32 0.00 34.57 3.41
590 592 2.305009 GGAATCTTGGCCTCTTGGATG 58.695 52.381 3.32 0.00 34.57 3.51
591 593 2.305009 GAATCTTGGCCTCTTGGATGG 58.695 52.381 3.32 0.00 34.57 3.51
598 600 2.470983 GCCTCTTGGATGGCTATCTC 57.529 55.000 10.15 1.10 45.26 2.75
599 601 1.337635 GCCTCTTGGATGGCTATCTCG 60.338 57.143 10.15 0.00 45.26 4.04
600 602 2.242926 CCTCTTGGATGGCTATCTCGA 58.757 52.381 10.15 3.64 33.68 4.04
601 603 2.830923 CCTCTTGGATGGCTATCTCGAT 59.169 50.000 10.15 0.00 33.68 3.59
602 604 3.368220 CCTCTTGGATGGCTATCTCGATG 60.368 52.174 10.15 0.00 33.68 3.84
603 605 2.564504 TCTTGGATGGCTATCTCGATGG 59.435 50.000 10.15 0.00 33.68 3.51
604 606 0.610174 TGGATGGCTATCTCGATGGC 59.390 55.000 10.15 6.70 43.50 4.40
605 607 0.901124 GGATGGCTATCTCGATGGCT 59.099 55.000 10.15 0.00 43.69 4.75
606 608 1.134848 GGATGGCTATCTCGATGGCTC 60.135 57.143 10.15 5.79 43.69 4.70
607 609 0.529833 ATGGCTATCTCGATGGCTCG 59.470 55.000 13.71 0.77 43.69 5.03
608 610 1.445238 GGCTATCTCGATGGCTCGC 60.445 63.158 13.71 0.00 43.69 5.03
609 611 1.583986 GCTATCTCGATGGCTCGCT 59.416 57.895 7.85 0.00 44.65 4.93
610 612 0.805614 GCTATCTCGATGGCTCGCTA 59.194 55.000 7.85 0.00 44.65 4.26
611 613 1.202132 GCTATCTCGATGGCTCGCTAG 60.202 57.143 7.85 0.00 44.65 3.42
612 614 2.351455 CTATCTCGATGGCTCGCTAGA 58.649 52.381 0.00 2.17 44.65 2.43
613 615 1.832883 ATCTCGATGGCTCGCTAGAT 58.167 50.000 0.00 4.03 44.65 1.98
614 616 2.474410 TCTCGATGGCTCGCTAGATA 57.526 50.000 0.00 0.00 44.65 1.98
615 617 2.077627 TCTCGATGGCTCGCTAGATAC 58.922 52.381 0.00 0.00 44.65 2.24
616 618 0.796927 TCGATGGCTCGCTAGATACG 59.203 55.000 0.00 0.00 44.65 3.06
617 619 0.517755 CGATGGCTCGCTAGATACGT 59.482 55.000 0.00 0.00 38.20 3.57
618 620 1.069159 CGATGGCTCGCTAGATACGTT 60.069 52.381 0.00 0.00 38.20 3.99
619 621 2.586900 GATGGCTCGCTAGATACGTTC 58.413 52.381 0.00 0.00 0.00 3.95
620 622 0.666913 TGGCTCGCTAGATACGTTCC 59.333 55.000 0.00 0.00 0.00 3.62
621 623 0.039346 GGCTCGCTAGATACGTTCCC 60.039 60.000 0.00 0.00 0.00 3.97
622 624 0.666913 GCTCGCTAGATACGTTCCCA 59.333 55.000 0.00 0.00 0.00 4.37
623 625 1.066605 GCTCGCTAGATACGTTCCCAA 59.933 52.381 0.00 0.00 0.00 4.12
624 626 2.480759 GCTCGCTAGATACGTTCCCAAA 60.481 50.000 0.00 0.00 0.00 3.28
625 627 3.114065 CTCGCTAGATACGTTCCCAAAC 58.886 50.000 0.00 0.00 0.00 2.93
626 628 2.756760 TCGCTAGATACGTTCCCAAACT 59.243 45.455 0.00 0.00 32.95 2.66
627 629 3.194116 TCGCTAGATACGTTCCCAAACTT 59.806 43.478 0.00 0.00 32.95 2.66
628 630 3.550678 CGCTAGATACGTTCCCAAACTTC 59.449 47.826 0.00 0.00 32.95 3.01
629 631 4.677250 CGCTAGATACGTTCCCAAACTTCT 60.677 45.833 0.00 0.00 32.95 2.85
630 632 5.176592 GCTAGATACGTTCCCAAACTTCTT 58.823 41.667 0.00 0.00 32.95 2.52
631 633 5.642491 GCTAGATACGTTCCCAAACTTCTTT 59.358 40.000 0.00 0.00 32.95 2.52
632 634 6.148976 GCTAGATACGTTCCCAAACTTCTTTT 59.851 38.462 0.00 0.00 32.95 2.27
633 635 6.555812 AGATACGTTCCCAAACTTCTTTTC 57.444 37.500 0.00 0.00 32.95 2.29
634 636 6.059484 AGATACGTTCCCAAACTTCTTTTCA 58.941 36.000 0.00 0.00 32.95 2.69
635 637 4.632538 ACGTTCCCAAACTTCTTTTCAG 57.367 40.909 0.00 0.00 32.95 3.02
636 638 4.266714 ACGTTCCCAAACTTCTTTTCAGA 58.733 39.130 0.00 0.00 32.95 3.27
637 639 4.703093 ACGTTCCCAAACTTCTTTTCAGAA 59.297 37.500 0.00 0.00 36.62 3.02
693 700 1.201414 CACCCTTTCATTACAACCCGC 59.799 52.381 0.00 0.00 0.00 6.13
697 704 0.885196 TTTCATTACAACCCGCTGGC 59.115 50.000 0.00 0.00 33.59 4.85
702 709 2.741486 TTACAACCCGCTGGCAGACC 62.741 60.000 20.86 0.00 33.59 3.85
831 838 2.367648 ACACCCACCCACCAGACA 60.368 61.111 0.00 0.00 0.00 3.41
856 863 9.965748 CAAATAATAATAAAGCAAAAACACCGG 57.034 29.630 0.00 0.00 0.00 5.28
889 896 3.322466 CACCCAAGCCTCCGACCT 61.322 66.667 0.00 0.00 0.00 3.85
890 897 3.003763 ACCCAAGCCTCCGACCTC 61.004 66.667 0.00 0.00 0.00 3.85
914 921 2.032634 CGATCCACCACCAACACGG 61.033 63.158 0.00 0.00 42.50 4.94
916 923 2.748058 GATCCACCACCAACACGGCT 62.748 60.000 0.00 0.00 39.03 5.52
1130 1140 1.578926 CCCGCTCGATCTGCTCTAG 59.421 63.158 6.12 0.00 0.00 2.43
1166 1176 1.077429 GGGGTGTTGGAGATCTGGC 60.077 63.158 0.00 0.00 0.00 4.85
1263 1274 6.597672 TCGTCAAGTGCAGAATTATTATGGTT 59.402 34.615 1.68 0.00 0.00 3.67
1326 1337 3.916392 CTCGCGATATCCCCGTGGC 62.916 68.421 10.36 0.31 38.01 5.01
1336 1347 1.528309 CCCCGTGGCAGTTTCACTT 60.528 57.895 0.00 0.00 33.31 3.16
1370 1382 8.723311 TGAATAAATTCACCAGTTTAACCGTAG 58.277 33.333 1.23 0.00 41.51 3.51
1439 1451 2.028112 TGGATTGCTGTAGCGTTTCTCT 60.028 45.455 0.00 0.00 45.83 3.10
1489 1505 2.212652 CAAATAGGTGCATGCGCTAGA 58.787 47.619 28.86 15.55 39.64 2.43
1490 1506 2.160822 AATAGGTGCATGCGCTAGAG 57.839 50.000 28.86 0.00 39.64 2.43
1491 1507 1.043816 ATAGGTGCATGCGCTAGAGT 58.956 50.000 28.86 12.28 39.64 3.24
1493 1509 1.153568 GGTGCATGCGCTAGAGTCA 60.154 57.895 28.86 0.00 39.64 3.41
1494 1510 1.150567 GGTGCATGCGCTAGAGTCAG 61.151 60.000 28.86 0.00 39.64 3.51
1495 1511 1.520120 TGCATGCGCTAGAGTCAGC 60.520 57.895 14.09 1.51 39.64 4.26
1496 1512 1.227205 GCATGCGCTAGAGTCAGCT 60.227 57.895 9.73 0.00 39.51 4.24
1497 1513 1.214373 GCATGCGCTAGAGTCAGCTC 61.214 60.000 9.73 5.63 39.51 4.09
1498 1514 0.597118 CATGCGCTAGAGTCAGCTCC 60.597 60.000 9.73 4.89 42.59 4.70
1499 1515 0.754957 ATGCGCTAGAGTCAGCTCCT 60.755 55.000 9.73 0.00 42.59 3.69
1500 1516 0.967887 TGCGCTAGAGTCAGCTCCTT 60.968 55.000 9.73 0.00 42.59 3.36
1501 1517 0.527385 GCGCTAGAGTCAGCTCCTTG 60.527 60.000 0.00 0.02 42.59 3.61
1502 1518 0.527385 CGCTAGAGTCAGCTCCTTGC 60.527 60.000 11.22 0.00 42.59 4.01
1513 1529 1.413382 GCTCCTTGCTATCGATGTCG 58.587 55.000 8.54 0.00 38.95 4.35
1526 1542 2.601314 TCGATGTCGAAACTATTTGCGG 59.399 45.455 2.12 0.00 46.30 5.69
1531 1547 4.529446 TGTCGAAACTATTTGCGGAAAAC 58.471 39.130 6.08 0.00 0.00 2.43
1563 1579 6.590292 CGAAAATTAGAGCTGTTAGTTCCAGA 59.410 38.462 0.00 0.00 31.38 3.86
1571 1587 3.691118 GCTGTTAGTTCCAGATTGATGCA 59.309 43.478 0.00 0.00 31.38 3.96
1574 1590 5.499313 TGTTAGTTCCAGATTGATGCATCA 58.501 37.500 25.42 25.42 34.44 3.07
1584 1600 1.456296 TGATGCATCACACTTGGAGC 58.544 50.000 25.42 0.00 0.00 4.70
1620 1636 2.992242 GCATTTCTCTGCTATTTCCGC 58.008 47.619 0.00 0.00 39.12 5.54
1626 1642 1.416401 CTCTGCTATTTCCGCCCCTTA 59.584 52.381 0.00 0.00 0.00 2.69
1628 1644 2.038557 TCTGCTATTTCCGCCCCTTATC 59.961 50.000 0.00 0.00 0.00 1.75
1665 1681 6.986904 AGAACTAGCAAAATGGCTAACTAC 57.013 37.500 0.00 0.00 45.13 2.73
1673 1689 5.296780 GCAAAATGGCTAACTACTGCATAGA 59.703 40.000 9.32 0.00 34.65 1.98
1678 1694 4.714802 TGGCTAACTACTGCATAGAAAGGA 59.285 41.667 9.32 0.00 34.65 3.36
1708 1724 4.660789 AAGCAAGATTCATATGTTGGGC 57.339 40.909 1.90 1.24 35.99 5.36
1731 1747 4.786068 CACACCACTTTATTATTTGTCGCG 59.214 41.667 0.00 0.00 0.00 5.87
1751 1768 3.120649 GCGTTTTGCTAGGACTGTTACAG 60.121 47.826 11.21 11.21 41.73 2.74
1769 1786 8.547967 TGTTACAGAATTATTGTCTCTGAACC 57.452 34.615 5.37 0.00 39.15 3.62
1777 1794 4.630644 ATTGTCTCTGAACCACATCACT 57.369 40.909 0.00 0.00 0.00 3.41
1778 1795 3.391506 TGTCTCTGAACCACATCACTG 57.608 47.619 0.00 0.00 0.00 3.66
1779 1796 2.037641 TGTCTCTGAACCACATCACTGG 59.962 50.000 0.00 0.00 37.33 4.00
1780 1797 1.002430 TCTCTGAACCACATCACTGGC 59.998 52.381 0.00 0.00 34.20 4.85
1781 1798 1.002888 CTCTGAACCACATCACTGGCT 59.997 52.381 0.00 0.00 34.20 4.75
1782 1799 1.421268 TCTGAACCACATCACTGGCTT 59.579 47.619 0.00 0.00 34.20 4.35
1783 1800 2.158623 TCTGAACCACATCACTGGCTTT 60.159 45.455 0.00 0.00 34.20 3.51
1784 1801 3.072330 TCTGAACCACATCACTGGCTTTA 59.928 43.478 0.00 0.00 34.20 1.85
1785 1802 3.411446 TGAACCACATCACTGGCTTTAG 58.589 45.455 0.00 0.00 34.20 1.85
1786 1803 3.181445 TGAACCACATCACTGGCTTTAGT 60.181 43.478 0.00 0.00 34.20 2.24
1787 1804 4.041075 TGAACCACATCACTGGCTTTAGTA 59.959 41.667 0.00 0.00 34.20 1.82
1788 1805 4.844349 ACCACATCACTGGCTTTAGTAT 57.156 40.909 0.00 0.00 34.20 2.12
1815 1832 9.875675 TGCATTGTTTTTATTGCTTTTACAATC 57.124 25.926 0.00 0.00 40.64 2.67
1829 1846 8.795513 TGCTTTTACAATCATTTCTCTTCATGA 58.204 29.630 0.00 0.00 33.92 3.07
1854 1871 8.710749 ATAAAAGCCAAGCCATTTCATATCTA 57.289 30.769 0.00 0.00 0.00 1.98
1897 1916 3.137176 AGCAGCATAGCCCTTGATAAAGA 59.863 43.478 0.00 0.00 34.23 2.52
1910 1929 9.355916 GCCCTTGATAAAGAGGAAGTTTAATAT 57.644 33.333 0.00 0.00 34.91 1.28
1921 1940 9.838339 AGAGGAAGTTTAATATAGAACCATGTG 57.162 33.333 0.00 0.00 0.00 3.21
1922 1941 9.614792 GAGGAAGTTTAATATAGAACCATGTGT 57.385 33.333 0.00 0.00 0.00 3.72
1932 1951 3.889815 AGAACCATGTGTCATATGGGTG 58.110 45.455 26.86 7.86 45.40 4.61
1947 1967 4.242602 GTGGTTATGGCCAGCTCC 57.757 61.111 13.05 13.50 39.53 4.70
1948 1968 1.819632 GTGGTTATGGCCAGCTCCG 60.820 63.158 13.05 0.00 39.53 4.63
1953 1973 0.975556 TTATGGCCAGCTCCGACTCA 60.976 55.000 13.05 0.00 0.00 3.41
1963 1983 5.504173 GCCAGCTCCGACTCAATTATTTTAC 60.504 44.000 0.00 0.00 0.00 2.01
1968 1988 9.099454 AGCTCCGACTCAATTATTTTACTTTAG 57.901 33.333 0.00 0.00 0.00 1.85
1974 1995 9.556030 GACTCAATTATTTTACTTTAGTGTGCC 57.444 33.333 0.00 0.00 0.00 5.01
1977 1998 8.861086 TCAATTATTTTACTTTAGTGTGCCCAA 58.139 29.630 0.00 0.00 0.00 4.12
1997 2018 4.326009 CCAAATTATGGTAAAGCGTTGTGC 59.674 41.667 0.00 0.00 44.85 4.57
1999 2020 8.935906 CCAAATTATGGTAAAGCGTTGTGCCA 62.936 42.308 0.94 0.94 44.57 4.92
2008 2029 1.059942 GCGTTGTGCCAAAATGTAGC 58.940 50.000 0.00 0.00 37.76 3.58
2022 2043 1.589196 GTAGCGGTCTCATGCGGTC 60.589 63.158 0.00 0.00 35.87 4.79
2025 2046 1.067416 GCGGTCTCATGCGGTCATA 59.933 57.895 0.00 0.00 0.00 2.15
2070 2091 8.648557 AGTAGCTTCAAATTGGAAAGAAAAAC 57.351 30.769 0.00 0.00 0.00 2.43
2071 2092 8.478066 AGTAGCTTCAAATTGGAAAGAAAAACT 58.522 29.630 0.00 0.00 0.00 2.66
2074 2095 9.098355 AGCTTCAAATTGGAAAGAAAAACTAAC 57.902 29.630 0.00 0.00 0.00 2.34
2075 2096 9.098355 GCTTCAAATTGGAAAGAAAAACTAACT 57.902 29.630 0.00 0.00 0.00 2.24
2103 2126 8.462589 TTGCTCTAAATCATAACCATTGCATA 57.537 30.769 0.00 0.00 0.00 3.14
2113 2136 6.435591 TCATAACCATTGCATACTTTTGGTGA 59.564 34.615 0.00 0.00 40.47 4.02
2126 2149 3.712016 TTTGGTGATGCAGCCTAAGTA 57.288 42.857 0.00 0.00 0.00 2.24
2217 2568 2.752903 ACGTTCACTTTGTTCCTTTGCT 59.247 40.909 0.00 0.00 0.00 3.91
2375 2726 7.056006 ACATCTGAACCAACATCATAGCATAA 58.944 34.615 0.00 0.00 0.00 1.90
2638 2989 2.539344 GCAGTTGCAAATGGTTTTGTGC 60.539 45.455 26.42 7.37 43.43 4.57
2828 3181 0.036306 GTCCACATCGGTCTGGGTTT 59.964 55.000 0.00 0.00 35.57 3.27
2880 3233 6.258727 CGCTATGGTTAGATTTTGTGTGATCT 59.741 38.462 0.00 0.00 36.61 2.75
2947 3301 3.090532 GGGCAGGGTTCCTCCGAT 61.091 66.667 0.00 0.00 37.00 4.18
3088 3444 7.936847 CACTTAAGTTATCCATATGCCCAAGTA 59.063 37.037 5.07 0.00 0.00 2.24
3093 3449 3.275617 TCCATATGCCCAAGTACACAC 57.724 47.619 0.00 0.00 0.00 3.82
3161 3517 7.006865 ACTAGCTGATGATGCATCTAAAGAT 57.993 36.000 26.32 19.74 41.06 2.40
3426 4022 6.092670 ACGGCAGCATATATGATTGATGTAAC 59.907 38.462 17.10 0.88 32.05 2.50
3543 4141 3.072330 TGTGCTCACATAAGTTTCCCTGA 59.928 43.478 0.00 0.00 36.21 3.86
3614 4212 7.937649 AGTTATTGGTTGAACAGTTTTAGACC 58.062 34.615 0.00 0.00 0.00 3.85
3615 4213 7.558444 AGTTATTGGTTGAACAGTTTTAGACCA 59.442 33.333 0.00 6.82 34.16 4.02
3856 4506 8.810427 CAGATGCAAATATTACATGTTCAAACC 58.190 33.333 2.30 0.00 0.00 3.27
3944 4598 4.361420 CATGCATGCGACCAATAAAATCA 58.639 39.130 14.93 0.00 0.00 2.57
3964 4618 9.621629 AAAATCAATGAGGATATTTACGGTACA 57.378 29.630 0.00 0.00 0.00 2.90
3968 4622 8.593679 TCAATGAGGATATTTACGGTACATGAT 58.406 33.333 0.00 0.00 0.00 2.45
3969 4623 8.659491 CAATGAGGATATTTACGGTACATGATG 58.341 37.037 0.00 0.00 0.00 3.07
3970 4624 6.163476 TGAGGATATTTACGGTACATGATGC 58.837 40.000 0.00 0.00 0.00 3.91
3971 4625 5.488341 AGGATATTTACGGTACATGATGCC 58.512 41.667 0.00 0.00 0.00 4.40
3972 4626 5.012664 AGGATATTTACGGTACATGATGCCA 59.987 40.000 0.00 0.00 30.96 4.92
3973 4627 5.121768 GGATATTTACGGTACATGATGCCAC 59.878 44.000 0.00 0.00 30.96 5.01
3974 4628 3.336138 TTTACGGTACATGATGCCACA 57.664 42.857 0.00 0.00 30.96 4.17
3975 4629 2.303163 TACGGTACATGATGCCACAC 57.697 50.000 0.00 0.00 30.96 3.82
3977 4631 1.271108 ACGGTACATGATGCCACACAA 60.271 47.619 0.00 0.00 30.96 3.33
3978 4632 2.016318 CGGTACATGATGCCACACAAT 58.984 47.619 0.00 0.00 30.96 2.71
3979 4633 2.423185 CGGTACATGATGCCACACAATT 59.577 45.455 0.00 0.00 30.96 2.32
3982 4653 5.522456 GGTACATGATGCCACACAATTATG 58.478 41.667 0.00 0.00 32.12 1.90
3996 4667 7.363355 CCACACAATTATGTAAAGGCATAACCA 60.363 37.037 0.00 0.00 42.08 3.67
4042 4713 5.063180 ACATGATGCCACACAATTTAGTG 57.937 39.130 0.00 0.00 44.93 2.74
4071 4742 2.744741 TGTGAACTTGTCTTGCGTTTGA 59.255 40.909 0.00 0.00 0.00 2.69
4075 4746 4.335315 TGAACTTGTCTTGCGTTTGAATCT 59.665 37.500 0.00 0.00 0.00 2.40
4078 4749 6.371809 ACTTGTCTTGCGTTTGAATCTAAA 57.628 33.333 0.00 0.00 0.00 1.85
4079 4750 6.199393 ACTTGTCTTGCGTTTGAATCTAAAC 58.801 36.000 0.00 0.00 37.23 2.01
4088 4759 6.072728 TGCGTTTGAATCTAAACAGCTTACAT 60.073 34.615 16.40 0.00 39.84 2.29
4139 4810 2.783609 ATCTGCAGCACAAGACATCT 57.216 45.000 9.47 0.00 0.00 2.90
4205 4876 2.158667 TGCTGGCAGATCATCACATCAT 60.159 45.455 20.86 0.00 0.00 2.45
4253 4924 7.446769 TGTTGTATTTAAACTCAGACAGCCTA 58.553 34.615 0.00 0.00 0.00 3.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 3.334691 TCGGAAACATAACTGGCAGAAG 58.665 45.455 23.66 9.88 0.00 2.85
85 86 2.401766 CGCACCATGAGGCCACTTC 61.402 63.158 5.01 0.00 39.06 3.01
194 195 0.671163 CGATTTTGTTCCCCGACGGA 60.671 55.000 17.49 0.00 39.68 4.69
201 202 1.934849 GCCAACAGCGATTTTGTTCCC 60.935 52.381 0.00 0.00 36.67 3.97
310 311 1.153086 ATTGCTCCATGTCTCGCCC 60.153 57.895 0.00 0.00 0.00 6.13
370 371 2.864343 GCGCTATTTCTCACGGTACATT 59.136 45.455 0.00 0.00 0.00 2.71
397 398 1.945354 GCGTACAGGCAGCAGTCCTA 61.945 60.000 0.00 0.00 31.52 2.94
398 399 2.973899 CGTACAGGCAGCAGTCCT 59.026 61.111 0.00 0.00 0.00 3.85
399 400 2.815647 GCGTACAGGCAGCAGTCC 60.816 66.667 0.00 0.00 0.00 3.85
400 401 2.048222 TGCGTACAGGCAGCAGTC 60.048 61.111 0.00 0.00 38.17 3.51
527 529 5.348451 GCCAACAACACCTTAAAAGCATATG 59.652 40.000 0.00 0.00 0.00 1.78
528 530 5.478407 GCCAACAACACCTTAAAAGCATAT 58.522 37.500 0.00 0.00 0.00 1.78
529 531 4.262249 GGCCAACAACACCTTAAAAGCATA 60.262 41.667 0.00 0.00 0.00 3.14
530 532 3.494223 GGCCAACAACACCTTAAAAGCAT 60.494 43.478 0.00 0.00 0.00 3.79
531 533 2.159028 GGCCAACAACACCTTAAAAGCA 60.159 45.455 0.00 0.00 0.00 3.91
532 534 2.102420 AGGCCAACAACACCTTAAAAGC 59.898 45.455 5.01 0.00 0.00 3.51
533 535 3.636764 AGAGGCCAACAACACCTTAAAAG 59.363 43.478 5.01 0.00 32.67 2.27
534 536 3.637769 AGAGGCCAACAACACCTTAAAA 58.362 40.909 5.01 0.00 32.67 1.52
535 537 3.306472 AGAGGCCAACAACACCTTAAA 57.694 42.857 5.01 0.00 32.67 1.52
536 538 2.955660 CAAGAGGCCAACAACACCTTAA 59.044 45.455 5.01 0.00 32.67 1.85
537 539 2.582052 CAAGAGGCCAACAACACCTTA 58.418 47.619 5.01 0.00 32.67 2.69
538 540 1.402787 CAAGAGGCCAACAACACCTT 58.597 50.000 5.01 0.00 32.67 3.50
539 541 0.468029 CCAAGAGGCCAACAACACCT 60.468 55.000 5.01 0.00 36.19 4.00
540 542 0.467290 TCCAAGAGGCCAACAACACC 60.467 55.000 5.01 0.00 33.74 4.16
541 543 1.620822 ATCCAAGAGGCCAACAACAC 58.379 50.000 5.01 0.00 33.74 3.32
542 544 2.380064 AATCCAAGAGGCCAACAACA 57.620 45.000 5.01 0.00 33.74 3.33
543 545 3.751479 AAAATCCAAGAGGCCAACAAC 57.249 42.857 5.01 0.00 33.74 3.32
563 565 4.675063 AGAGGCCAAGATTCCCTAAAAA 57.325 40.909 5.01 0.00 0.00 1.94
564 566 4.344104 CAAGAGGCCAAGATTCCCTAAAA 58.656 43.478 5.01 0.00 0.00 1.52
565 567 3.309121 CCAAGAGGCCAAGATTCCCTAAA 60.309 47.826 5.01 0.00 0.00 1.85
566 568 2.242196 CCAAGAGGCCAAGATTCCCTAA 59.758 50.000 5.01 0.00 0.00 2.69
567 569 1.846439 CCAAGAGGCCAAGATTCCCTA 59.154 52.381 5.01 0.00 0.00 3.53
568 570 0.627986 CCAAGAGGCCAAGATTCCCT 59.372 55.000 5.01 0.00 0.00 4.20
569 571 0.625849 TCCAAGAGGCCAAGATTCCC 59.374 55.000 5.01 0.00 33.74 3.97
570 572 2.305009 CATCCAAGAGGCCAAGATTCC 58.695 52.381 5.01 0.00 33.74 3.01
571 573 2.305009 CCATCCAAGAGGCCAAGATTC 58.695 52.381 5.01 0.00 33.74 2.52
572 574 1.687368 GCCATCCAAGAGGCCAAGATT 60.687 52.381 5.01 0.00 45.18 2.40
573 575 0.106318 GCCATCCAAGAGGCCAAGAT 60.106 55.000 5.01 0.00 45.18 2.40
574 576 1.304282 GCCATCCAAGAGGCCAAGA 59.696 57.895 5.01 0.00 45.18 3.02
575 577 3.930504 GCCATCCAAGAGGCCAAG 58.069 61.111 5.01 0.00 45.18 3.61
580 582 2.242926 TCGAGATAGCCATCCAAGAGG 58.757 52.381 0.00 0.00 0.00 3.69
581 583 3.368220 CCATCGAGATAGCCATCCAAGAG 60.368 52.174 0.00 0.00 0.00 2.85
582 584 2.564504 CCATCGAGATAGCCATCCAAGA 59.435 50.000 0.00 0.00 0.00 3.02
583 585 2.934364 GCCATCGAGATAGCCATCCAAG 60.934 54.545 0.00 0.00 0.00 3.61
584 586 1.002430 GCCATCGAGATAGCCATCCAA 59.998 52.381 0.00 0.00 0.00 3.53
585 587 0.610174 GCCATCGAGATAGCCATCCA 59.390 55.000 0.00 0.00 0.00 3.41
586 588 0.901124 AGCCATCGAGATAGCCATCC 59.099 55.000 0.11 0.00 0.00 3.51
587 589 2.292103 GAGCCATCGAGATAGCCATC 57.708 55.000 0.11 0.00 0.00 3.51
599 601 2.586900 GAACGTATCTAGCGAGCCATC 58.413 52.381 0.00 0.00 0.00 3.51
600 602 1.269998 GGAACGTATCTAGCGAGCCAT 59.730 52.381 0.00 0.00 0.00 4.40
601 603 0.666913 GGAACGTATCTAGCGAGCCA 59.333 55.000 0.00 0.00 0.00 4.75
602 604 0.039346 GGGAACGTATCTAGCGAGCC 60.039 60.000 0.00 0.00 0.00 4.70
603 605 0.666913 TGGGAACGTATCTAGCGAGC 59.333 55.000 0.00 0.00 0.00 5.03
604 606 3.114065 GTTTGGGAACGTATCTAGCGAG 58.886 50.000 0.00 0.00 0.00 5.03
605 607 2.756760 AGTTTGGGAACGTATCTAGCGA 59.243 45.455 0.00 0.00 40.75 4.93
606 608 3.160777 AGTTTGGGAACGTATCTAGCG 57.839 47.619 0.00 0.00 40.75 4.26
607 609 4.756502 AGAAGTTTGGGAACGTATCTAGC 58.243 43.478 0.00 0.00 40.75 3.42
608 610 7.386848 TGAAAAGAAGTTTGGGAACGTATCTAG 59.613 37.037 0.00 0.00 40.75 2.43
609 611 7.218614 TGAAAAGAAGTTTGGGAACGTATCTA 58.781 34.615 0.00 0.00 40.75 1.98
610 612 6.059484 TGAAAAGAAGTTTGGGAACGTATCT 58.941 36.000 0.00 0.00 40.75 1.98
611 613 6.204108 TCTGAAAAGAAGTTTGGGAACGTATC 59.796 38.462 0.00 0.00 40.75 2.24
612 614 6.059484 TCTGAAAAGAAGTTTGGGAACGTAT 58.941 36.000 0.00 0.00 40.75 3.06
613 615 5.430007 TCTGAAAAGAAGTTTGGGAACGTA 58.570 37.500 0.00 0.00 40.75 3.57
614 616 4.266714 TCTGAAAAGAAGTTTGGGAACGT 58.733 39.130 0.00 0.00 40.75 3.99
615 617 4.893424 TCTGAAAAGAAGTTTGGGAACG 57.107 40.909 0.00 0.00 40.75 3.95
616 618 6.451064 TCTTCTGAAAAGAAGTTTGGGAAC 57.549 37.500 13.60 0.00 44.06 3.62
617 619 7.660030 AATCTTCTGAAAAGAAGTTTGGGAA 57.340 32.000 13.60 0.00 44.06 3.97
618 620 7.660030 AAATCTTCTGAAAAGAAGTTTGGGA 57.340 32.000 13.60 0.00 44.06 4.37
619 621 8.722480 AAAAATCTTCTGAAAAGAAGTTTGGG 57.278 30.769 13.60 0.00 44.06 4.12
620 622 9.591792 AGAAAAATCTTCTGAAAAGAAGTTTGG 57.408 29.630 13.60 0.00 44.06 3.28
633 635 9.752274 CGTATCTTCTCAAAGAAAAATCTTCTG 57.248 33.333 0.00 0.00 44.49 3.02
634 636 9.495572 ACGTATCTTCTCAAAGAAAAATCTTCT 57.504 29.630 0.00 0.00 44.49 2.85
637 639 8.722394 GGAACGTATCTTCTCAAAGAAAAATCT 58.278 33.333 0.00 0.00 44.49 2.40
638 640 7.963465 GGGAACGTATCTTCTCAAAGAAAAATC 59.037 37.037 0.00 0.00 44.49 2.17
639 641 7.447238 TGGGAACGTATCTTCTCAAAGAAAAAT 59.553 33.333 0.00 0.00 44.49 1.82
640 642 6.768861 TGGGAACGTATCTTCTCAAAGAAAAA 59.231 34.615 0.00 0.00 44.49 1.94
653 655 4.999311 GGTGTTTAGTTTGGGAACGTATCT 59.001 41.667 0.00 0.00 40.75 1.98
693 700 4.039092 CCAGTGGGGGTCTGCCAG 62.039 72.222 0.00 0.00 36.17 4.85
762 769 4.374702 GCTCCGTTGCACGCACAG 62.375 66.667 0.00 0.00 40.91 3.66
765 772 4.927782 AAGGCTCCGTTGCACGCA 62.928 61.111 0.00 0.00 40.91 5.24
766 773 4.090057 GAAGGCTCCGTTGCACGC 62.090 66.667 0.00 0.00 40.91 5.34
767 774 3.777925 CGAAGGCTCCGTTGCACG 61.778 66.667 0.00 0.00 42.11 5.34
831 838 9.930693 TCCGGTGTTTTTGCTTTATTATTATTT 57.069 25.926 0.00 0.00 0.00 1.40
876 883 2.232298 GAGGTGAGGTCGGAGGCTTG 62.232 65.000 0.00 0.00 0.00 4.01
886 893 1.686110 GGTGGATCGGAGGTGAGGT 60.686 63.158 0.00 0.00 0.00 3.85
887 894 1.685765 TGGTGGATCGGAGGTGAGG 60.686 63.158 0.00 0.00 0.00 3.86
888 895 1.517832 GTGGTGGATCGGAGGTGAG 59.482 63.158 0.00 0.00 0.00 3.51
889 896 1.987855 GGTGGTGGATCGGAGGTGA 60.988 63.158 0.00 0.00 0.00 4.02
890 897 1.836999 TTGGTGGTGGATCGGAGGTG 61.837 60.000 0.00 0.00 0.00 4.00
914 921 4.135153 TCCGCCAAGAGCTCGAGC 62.135 66.667 30.01 30.01 40.39 5.03
916 923 3.452786 CCTCCGCCAAGAGCTCGA 61.453 66.667 8.37 0.00 40.39 4.04
1180 1190 1.515954 GACTCTTCGCCGATCCCAA 59.484 57.895 0.00 0.00 0.00 4.12
1260 1271 9.651718 CTTCATAATTAAATAGACTCGCAAACC 57.348 33.333 0.00 0.00 0.00 3.27
1376 1388 5.047377 GGCCAAAAGTATTGGACTGAAATCA 60.047 40.000 11.26 0.00 44.25 2.57
1414 1426 1.290203 ACGCTACAGCAATCCAATCG 58.710 50.000 1.61 0.00 42.21 3.34
1477 1493 1.520120 GCTGACTCTAGCGCATGCA 60.520 57.895 19.57 0.00 46.23 3.96
1494 1510 1.001268 TCGACATCGATAGCAAGGAGC 60.001 52.381 0.00 0.00 44.22 4.70
1509 1525 4.529446 GTTTTCCGCAAATAGTTTCGACA 58.471 39.130 0.00 0.00 0.00 4.35
1539 1555 7.907214 TCTGGAACTAACAGCTCTAATTTTC 57.093 36.000 0.00 0.00 35.94 2.29
1563 1579 2.426024 GCTCCAAGTGTGATGCATCAAT 59.574 45.455 30.24 16.57 38.75 2.57
1571 1587 1.649321 TCAGAGGCTCCAAGTGTGAT 58.351 50.000 11.71 0.00 0.00 3.06
1574 1590 4.851639 ATTTATCAGAGGCTCCAAGTGT 57.148 40.909 11.71 0.00 0.00 3.55
1628 1644 2.638556 AGTTCTTGATCGTCACCTCG 57.361 50.000 0.00 0.00 0.00 4.63
1665 1681 4.771590 TTGCAGTTTCCTTTCTATGCAG 57.228 40.909 0.00 0.00 43.74 4.41
1708 1724 4.786068 CGCGACAAATAATAAAGTGGTGTG 59.214 41.667 0.00 0.00 0.00 3.82
1731 1747 6.803154 ATTCTGTAACAGTCCTAGCAAAAC 57.197 37.500 0.00 0.00 32.61 2.43
1751 1768 7.335422 AGTGATGTGGTTCAGAGACAATAATTC 59.665 37.037 0.00 0.00 0.00 2.17
1769 1786 4.395854 TGCAATACTAAAGCCAGTGATGTG 59.604 41.667 0.00 0.00 0.00 3.21
1777 1794 9.717942 AATAAAAACAATGCAATACTAAAGCCA 57.282 25.926 0.00 0.00 0.00 4.75
1778 1795 9.971744 CAATAAAAACAATGCAATACTAAAGCC 57.028 29.630 0.00 0.00 0.00 4.35
1779 1796 9.476761 GCAATAAAAACAATGCAATACTAAAGC 57.523 29.630 0.00 0.00 38.63 3.51
1814 1831 7.943079 TGGCTTTTATCATGAAGAGAAATGA 57.057 32.000 0.00 0.00 37.30 2.57
1815 1832 7.222224 GCTTGGCTTTTATCATGAAGAGAAATG 59.778 37.037 0.00 2.53 37.30 2.32
1817 1834 6.350445 GGCTTGGCTTTTATCATGAAGAGAAA 60.350 38.462 0.00 0.00 35.76 2.52
1818 1835 5.126061 GGCTTGGCTTTTATCATGAAGAGAA 59.874 40.000 0.00 0.00 0.00 2.87
1829 1846 7.607615 AGATATGAAATGGCTTGGCTTTTAT 57.392 32.000 7.75 5.39 0.00 1.40
1866 1884 2.894126 GGGCTATGCTGCTCTAGACTAA 59.106 50.000 13.05 0.00 0.00 2.24
1878 1896 3.976654 TCCTCTTTATCAAGGGCTATGCT 59.023 43.478 0.00 0.00 33.21 3.79
1897 1916 9.614792 GACACATGGTTCTATATTAAACTTCCT 57.385 33.333 0.00 0.00 0.00 3.36
1910 1929 4.141505 CCACCCATATGACACATGGTTCTA 60.142 45.833 11.77 0.00 41.26 2.10
1915 1934 2.734755 ACCACCCATATGACACATGG 57.265 50.000 5.71 5.71 42.30 3.66
1921 1940 2.158534 TGGCCATAACCACCCATATGAC 60.159 50.000 0.00 0.00 33.75 3.06
1922 1941 2.108075 CTGGCCATAACCACCCATATGA 59.892 50.000 5.51 0.00 35.33 2.15
1927 1946 2.210144 GAGCTGGCCATAACCACCCA 62.210 60.000 5.51 0.00 35.33 4.51
1932 1951 1.523938 GTCGGAGCTGGCCATAACC 60.524 63.158 5.51 9.09 0.00 2.85
1947 1967 9.262472 GCACACTAAAGTAAAATAATTGAGTCG 57.738 33.333 0.00 0.00 25.35 4.18
1948 1968 9.556030 GGCACACTAAAGTAAAATAATTGAGTC 57.444 33.333 0.00 0.00 25.35 3.36
1974 1995 4.326009 GCACAACGCTTTACCATAATTTGG 59.674 41.667 5.44 5.44 44.41 3.28
1977 1998 3.508012 TGGCACAACGCTTTACCATAATT 59.492 39.130 0.00 0.00 41.91 1.40
1979 2000 2.505405 TGGCACAACGCTTTACCATAA 58.495 42.857 0.00 0.00 41.91 1.90
1982 2003 4.561452 TGGCACAACGCTTTACCA 57.439 50.000 0.00 0.00 41.91 3.25
1994 2015 1.130561 GAGACCGCTACATTTTGGCAC 59.869 52.381 0.00 0.00 0.00 5.01
1997 2018 2.223340 GCATGAGACCGCTACATTTTGG 60.223 50.000 0.00 0.00 0.00 3.28
1999 2020 1.665679 CGCATGAGACCGCTACATTTT 59.334 47.619 0.00 0.00 0.00 1.82
2004 2025 1.589196 GACCGCATGAGACCGCTAC 60.589 63.158 0.00 0.00 0.00 3.58
2008 2029 0.385751 AGTATGACCGCATGAGACCG 59.614 55.000 0.00 0.00 35.94 4.79
2025 2046 9.203163 AGCTACTATAAAGTAATGGTCAGAAGT 57.797 33.333 0.00 0.00 37.75 3.01
2069 2090 9.384764 GGTTATGATTTAGAGCAAGAAGTTAGT 57.615 33.333 0.00 0.00 0.00 2.24
2070 2091 9.383519 TGGTTATGATTTAGAGCAAGAAGTTAG 57.616 33.333 0.00 0.00 0.00 2.34
2071 2092 9.905713 ATGGTTATGATTTAGAGCAAGAAGTTA 57.094 29.630 0.00 0.00 0.00 2.24
2073 2094 8.680903 CAATGGTTATGATTTAGAGCAAGAAGT 58.319 33.333 0.00 0.00 0.00 3.01
2074 2095 7.646922 GCAATGGTTATGATTTAGAGCAAGAAG 59.353 37.037 0.00 0.00 0.00 2.85
2075 2096 7.122501 TGCAATGGTTATGATTTAGAGCAAGAA 59.877 33.333 0.00 0.00 0.00 2.52
2103 2126 2.584835 TAGGCTGCATCACCAAAAGT 57.415 45.000 0.50 0.00 0.00 2.66
2109 2132 1.762957 TCCTACTTAGGCTGCATCACC 59.237 52.381 0.50 0.00 43.31 4.02
2118 2141 2.356069 GCAAGTTGCATCCTACTTAGGC 59.644 50.000 22.90 0.00 44.26 3.93
2375 2726 5.363101 ACATGATGCTAATTGATCACGACT 58.637 37.500 0.00 0.00 31.47 4.18
2501 2852 1.073722 CCTGGCTGACTTTGGCTGA 59.926 57.895 0.00 0.00 0.00 4.26
2880 3233 2.957402 AATGAGAGGCACAGGAAACA 57.043 45.000 0.00 0.00 0.00 2.83
2963 3318 5.010314 AGCAGCATCATTTTCTCAACAGAAA 59.990 36.000 0.00 0.00 45.30 2.52
3088 3444 7.445121 TCAGTGATCTAAAATCTTGAGTGTGT 58.555 34.615 0.00 0.00 0.00 3.72
3161 3517 2.917933 CCAGTGTGACCTTTTGACTCA 58.082 47.619 0.00 0.00 0.00 3.41
3426 4022 7.204496 AGGAAGTACTACAATATACAGAGCG 57.796 40.000 0.00 0.00 0.00 5.03
3543 4141 8.270744 ACTGAAGTCCAGCATTAAGATTAAGAT 58.729 33.333 0.00 0.00 46.81 2.40
3790 4411 7.191551 GCGTAATATGATAATACGAGGCTACA 58.808 38.462 20.62 0.00 43.71 2.74
3944 4598 7.334421 GCATCATGTACCGTAAATATCCTCATT 59.666 37.037 0.00 0.00 0.00 2.57
3964 4618 6.683610 GCCTTTACATAATTGTGTGGCATCAT 60.684 38.462 22.37 0.00 41.83 2.45
3968 4622 3.829026 TGCCTTTACATAATTGTGTGGCA 59.171 39.130 24.69 24.69 45.53 4.92
3969 4623 4.448537 TGCCTTTACATAATTGTGTGGC 57.551 40.909 21.21 21.21 42.19 5.01
3970 4624 6.978080 GGTTATGCCTTTACATAATTGTGTGG 59.022 38.462 17.19 11.15 42.73 4.17
3971 4625 7.542890 TGGTTATGCCTTTACATAATTGTGTG 58.457 34.615 17.19 2.44 42.73 3.82
3972 4626 7.396055 ACTGGTTATGCCTTTACATAATTGTGT 59.604 33.333 12.73 12.73 42.73 3.72
3973 4627 7.771183 ACTGGTTATGCCTTTACATAATTGTG 58.229 34.615 0.00 0.00 42.73 3.33
3974 4628 7.954666 ACTGGTTATGCCTTTACATAATTGT 57.045 32.000 0.77 0.00 42.73 2.71
3975 4629 9.086336 CAAACTGGTTATGCCTTTACATAATTG 57.914 33.333 0.77 0.00 42.73 2.32
3977 4631 8.588290 TCAAACTGGTTATGCCTTTACATAAT 57.412 30.769 0.77 0.00 42.73 1.28
3978 4632 8.588290 ATCAAACTGGTTATGCCTTTACATAA 57.412 30.769 0.00 0.00 39.57 1.90
3979 4633 8.588290 AATCAAACTGGTTATGCCTTTACATA 57.412 30.769 0.00 0.00 38.35 2.29
3982 4653 8.135529 GGATAATCAAACTGGTTATGCCTTTAC 58.864 37.037 0.00 0.00 36.25 2.01
4042 4713 4.504097 GCAAGACAAGTTCACACATTTTCC 59.496 41.667 0.00 0.00 0.00 3.13
4116 4787 3.631145 TGTCTTGTGCTGCAGATTTTC 57.369 42.857 20.43 0.00 0.00 2.29
4117 4788 3.825014 AGATGTCTTGTGCTGCAGATTTT 59.175 39.130 20.43 0.00 0.00 1.82
4169 4840 2.799562 GCCAGCAAAACCTGTCAAGAAC 60.800 50.000 0.00 0.00 0.00 3.01
4253 4924 0.251653 TACAGCAGACCTTCCTCGGT 60.252 55.000 0.00 0.00 40.80 4.69


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

AutoCloner maintained by Alex Coulton.