Multiple sequence alignment - TraesCS2D01G293100

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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 TraesCS2D01G293100 chr2D 100.000 2525 0 0 1 2525 375374968 375372444 0.000000e+00 4663
1 TraesCS2D01G293100 chr2D 81.022 548 92 9 1 544 524047000 524046461 2.320000e-115 425
2 TraesCS2D01G293100 chr2A 92.621 1301 51 19 635 1923 507717526 507716259 0.000000e+00 1829
3 TraesCS2D01G293100 chr2A 93.460 474 29 2 1901 2373 507714709 507714237 0.000000e+00 702
4 TraesCS2D01G293100 chr2A 91.139 158 13 1 2368 2525 507705703 507705547 1.970000e-51 213
5 TraesCS2D01G293100 chr2B 92.003 1238 64 13 643 1873 445695404 445694195 0.000000e+00 1705
6 TraesCS2D01G293100 chr2B 94.504 655 35 1 1872 2525 445694133 445693479 0.000000e+00 1009
7 TraesCS2D01G293100 chr2B 81.056 549 93 9 1 544 704289017 704289559 6.450000e-116 427
8 TraesCS2D01G293100 chr2B 77.654 179 39 1 2228 2406 131151746 131151569 9.550000e-20 108
9 TraesCS2D01G293100 chr3D 83.060 549 84 8 1 544 475021861 475021317 8.120000e-135 490
10 TraesCS2D01G293100 chr3D 82.456 513 84 4 19 528 48051363 48050854 6.410000e-121 444
11 TraesCS2D01G293100 chr3D 81.111 540 83 11 14 544 32626863 32626334 5.030000e-112 414
12 TraesCS2D01G293100 chr6B 82.515 509 80 7 1 504 681258065 681258569 2.980000e-119 438
13 TraesCS2D01G293100 chr4D 81.341 552 86 14 1 544 82862912 82862370 1.390000e-117 433
14 TraesCS2D01G293100 chr7D 81.203 532 94 3 1 529 568187050 568187578 8.350000e-115 424
15 TraesCS2D01G293100 chr7A 81.238 533 84 14 1 523 485156680 485157206 1.400000e-112 416


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 TraesCS2D01G293100 chr2D 375372444 375374968 2524 True 4663.0 4663 100.0000 1 2525 1 chr2D.!!$R1 2524
1 TraesCS2D01G293100 chr2D 524046461 524047000 539 True 425.0 425 81.0220 1 544 1 chr2D.!!$R2 543
2 TraesCS2D01G293100 chr2A 507714237 507717526 3289 True 1265.5 1829 93.0405 635 2373 2 chr2A.!!$R2 1738
3 TraesCS2D01G293100 chr2B 445693479 445695404 1925 True 1357.0 1705 93.2535 643 2525 2 chr2B.!!$R2 1882
4 TraesCS2D01G293100 chr2B 704289017 704289559 542 False 427.0 427 81.0560 1 544 1 chr2B.!!$F1 543
5 TraesCS2D01G293100 chr3D 475021317 475021861 544 True 490.0 490 83.0600 1 544 1 chr3D.!!$R3 543
6 TraesCS2D01G293100 chr3D 48050854 48051363 509 True 444.0 444 82.4560 19 528 1 chr3D.!!$R2 509
7 TraesCS2D01G293100 chr3D 32626334 32626863 529 True 414.0 414 81.1110 14 544 1 chr3D.!!$R1 530
8 TraesCS2D01G293100 chr6B 681258065 681258569 504 False 438.0 438 82.5150 1 504 1 chr6B.!!$F1 503
9 TraesCS2D01G293100 chr4D 82862370 82862912 542 True 433.0 433 81.3410 1 544 1 chr4D.!!$R1 543
10 TraesCS2D01G293100 chr7D 568187050 568187578 528 False 424.0 424 81.2030 1 529 1 chr7D.!!$F1 528
11 TraesCS2D01G293100 chr7A 485156680 485157206 526 False 416.0 416 81.2380 1 523 1 chr7A.!!$F1 522

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
557 571 0.03213 GGACTCTGCGCGGATTGATA 59.968 55.0 21.31 0.0 0.0 2.15 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1659 1688 0.179156 GATTGTTCCAGCCATGCGTG 60.179 55.0 0.0 0.0 0.0 5.34 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
66 68 2.051518 CCCAGCCGGCTTTTATGCA 61.052 57.895 30.60 0.00 34.04 3.96
145 148 3.797353 GGAGATGGGGAGCGGCAA 61.797 66.667 1.45 0.00 0.00 4.52
156 163 4.389576 GCGGCAAAGTGGTGCGAG 62.390 66.667 0.00 0.00 45.91 5.03
200 207 3.485463 TTAAATAGAGTGCGGATGGGG 57.515 47.619 0.00 0.00 0.00 4.96
235 243 2.798009 CGTTTAATGCCAGCCCGG 59.202 61.111 0.00 0.00 38.11 5.73
245 253 4.351938 CAGCCCGGTCGTGAACGA 62.352 66.667 9.21 0.50 45.97 3.85
288 297 1.747745 GGCTTCCACGCGGGTTTAT 60.748 57.895 12.47 0.00 38.11 1.40
308 317 2.332654 GGAGGCGTTTCAATGCGGT 61.333 57.895 0.00 0.00 41.81 5.68
329 338 2.649034 GAGGCGTGTTCAGTCGGA 59.351 61.111 0.00 0.00 0.00 4.55
399 408 2.981909 TGAGAGGTCGCGTCCGTT 60.982 61.111 16.59 8.93 35.54 4.44
411 420 1.444553 GTCCGTTCTGAGCCGTCTG 60.445 63.158 0.00 0.00 0.00 3.51
422 431 1.672356 GCCGTCTGCAATGTGGAGT 60.672 57.895 0.00 0.00 37.12 3.85
430 439 2.672996 AATGTGGAGTGGCACGCC 60.673 61.111 30.48 30.48 41.54 5.68
475 487 4.681978 GCACCGGGCGAGAACACT 62.682 66.667 6.32 0.00 0.00 3.55
506 520 0.399376 GAAGGGGTTTGGGTGGGTTT 60.399 55.000 0.00 0.00 0.00 3.27
529 543 1.544825 CGGTCAGAAGAGGGCTTGGA 61.545 60.000 0.00 0.00 33.61 3.53
531 545 1.073923 GGTCAGAAGAGGGCTTGGAAA 59.926 52.381 0.00 0.00 33.61 3.13
532 546 2.291217 GGTCAGAAGAGGGCTTGGAAAT 60.291 50.000 0.00 0.00 33.61 2.17
544 558 2.290577 GCTTGGAAATGGTCTGGACTCT 60.291 50.000 0.67 0.00 0.00 3.24
545 559 3.341823 CTTGGAAATGGTCTGGACTCTG 58.658 50.000 0.67 0.00 0.00 3.35
546 560 1.003580 TGGAAATGGTCTGGACTCTGC 59.996 52.381 0.67 0.00 0.00 4.26
547 561 1.363744 GAAATGGTCTGGACTCTGCG 58.636 55.000 0.67 0.00 0.00 5.18
548 562 0.674895 AAATGGTCTGGACTCTGCGC 60.675 55.000 0.00 0.00 0.00 6.09
549 563 2.842394 AATGGTCTGGACTCTGCGCG 62.842 60.000 0.00 0.00 0.00 6.86
550 564 4.803426 GGTCTGGACTCTGCGCGG 62.803 72.222 10.86 10.86 0.00 6.46
551 565 3.749064 GTCTGGACTCTGCGCGGA 61.749 66.667 19.73 19.73 0.00 5.54
552 566 2.755876 TCTGGACTCTGCGCGGAT 60.756 61.111 21.31 10.15 0.00 4.18
553 567 2.185350 CTGGACTCTGCGCGGATT 59.815 61.111 21.31 15.13 0.00 3.01
554 568 2.125552 TGGACTCTGCGCGGATTG 60.126 61.111 21.31 11.88 0.00 2.67
555 569 2.184322 GGACTCTGCGCGGATTGA 59.816 61.111 21.31 0.00 0.00 2.57
556 570 1.227380 GGACTCTGCGCGGATTGAT 60.227 57.895 21.31 5.73 0.00 2.57
557 571 0.032130 GGACTCTGCGCGGATTGATA 59.968 55.000 21.31 0.00 0.00 2.15
558 572 1.132588 GACTCTGCGCGGATTGATAC 58.867 55.000 21.31 0.00 0.00 2.24
559 573 0.459899 ACTCTGCGCGGATTGATACA 59.540 50.000 21.31 0.00 0.00 2.29
560 574 1.069204 ACTCTGCGCGGATTGATACAT 59.931 47.619 21.31 0.00 0.00 2.29
561 575 2.296190 ACTCTGCGCGGATTGATACATA 59.704 45.455 21.31 0.00 0.00 2.29
562 576 3.243737 ACTCTGCGCGGATTGATACATAA 60.244 43.478 21.31 0.00 0.00 1.90
563 577 3.057019 TCTGCGCGGATTGATACATAAC 58.943 45.455 16.69 0.00 0.00 1.89
564 578 2.139917 TGCGCGGATTGATACATAACC 58.860 47.619 8.83 0.00 0.00 2.85
565 579 1.126113 GCGCGGATTGATACATAACCG 59.874 52.381 8.83 0.00 42.63 4.44
566 580 2.400399 CGCGGATTGATACATAACCGT 58.600 47.619 0.00 0.00 41.92 4.83
567 581 2.154963 CGCGGATTGATACATAACCGTG 59.845 50.000 0.00 0.00 42.92 4.94
568 582 3.128349 GCGGATTGATACATAACCGTGT 58.872 45.455 0.00 0.00 41.92 4.49
569 583 3.558418 GCGGATTGATACATAACCGTGTT 59.442 43.478 0.00 0.00 41.92 3.32
570 584 4.034742 GCGGATTGATACATAACCGTGTTT 59.965 41.667 0.00 0.00 41.92 2.83
571 585 5.498159 CGGATTGATACATAACCGTGTTTG 58.502 41.667 0.00 0.00 36.38 2.93
572 586 5.292345 CGGATTGATACATAACCGTGTTTGA 59.708 40.000 0.00 0.00 36.38 2.69
573 587 6.018262 CGGATTGATACATAACCGTGTTTGAT 60.018 38.462 0.00 0.00 36.38 2.57
574 588 7.132213 GGATTGATACATAACCGTGTTTGATG 58.868 38.462 0.00 0.00 33.62 3.07
575 589 7.011950 GGATTGATACATAACCGTGTTTGATGA 59.988 37.037 6.56 0.00 33.62 2.92
576 590 6.656314 TGATACATAACCGTGTTTGATGAC 57.344 37.500 6.56 0.00 33.62 3.06
577 591 6.403049 TGATACATAACCGTGTTTGATGACT 58.597 36.000 6.56 0.00 33.62 3.41
578 592 6.876789 TGATACATAACCGTGTTTGATGACTT 59.123 34.615 6.56 0.00 33.62 3.01
579 593 7.389330 TGATACATAACCGTGTTTGATGACTTT 59.611 33.333 6.56 0.00 33.62 2.66
580 594 6.385649 ACATAACCGTGTTTGATGACTTTT 57.614 33.333 6.56 0.00 0.00 2.27
581 595 7.499321 ACATAACCGTGTTTGATGACTTTTA 57.501 32.000 6.56 0.00 0.00 1.52
582 596 8.106247 ACATAACCGTGTTTGATGACTTTTAT 57.894 30.769 6.56 0.00 0.00 1.40
583 597 8.020819 ACATAACCGTGTTTGATGACTTTTATG 58.979 33.333 0.00 0.00 32.13 1.90
584 598 6.627395 AACCGTGTTTGATGACTTTTATGA 57.373 33.333 0.00 0.00 0.00 2.15
585 599 6.817765 ACCGTGTTTGATGACTTTTATGAT 57.182 33.333 0.00 0.00 0.00 2.45
586 600 6.842163 ACCGTGTTTGATGACTTTTATGATC 58.158 36.000 0.00 0.00 0.00 2.92
587 601 6.128007 ACCGTGTTTGATGACTTTTATGATCC 60.128 38.462 0.00 0.00 0.00 3.36
588 602 5.959527 CGTGTTTGATGACTTTTATGATCCG 59.040 40.000 0.00 0.00 0.00 4.18
589 603 6.183360 CGTGTTTGATGACTTTTATGATCCGA 60.183 38.462 0.00 0.00 0.00 4.55
590 604 7.526608 GTGTTTGATGACTTTTATGATCCGAA 58.473 34.615 0.00 0.00 0.00 4.30
591 605 7.481798 GTGTTTGATGACTTTTATGATCCGAAC 59.518 37.037 0.00 0.00 0.00 3.95
592 606 7.390440 TGTTTGATGACTTTTATGATCCGAACT 59.610 33.333 0.00 0.00 0.00 3.01
593 607 8.879759 GTTTGATGACTTTTATGATCCGAACTA 58.120 33.333 0.00 0.00 0.00 2.24
594 608 9.443323 TTTGATGACTTTTATGATCCGAACTAA 57.557 29.630 0.00 0.00 0.00 2.24
595 609 9.613428 TTGATGACTTTTATGATCCGAACTAAT 57.387 29.630 0.00 0.00 0.00 1.73
596 610 9.045223 TGATGACTTTTATGATCCGAACTAATG 57.955 33.333 0.00 0.00 0.00 1.90
597 611 7.246674 TGACTTTTATGATCCGAACTAATGC 57.753 36.000 0.00 0.00 0.00 3.56
598 612 6.019075 TGACTTTTATGATCCGAACTAATGCG 60.019 38.462 0.00 0.00 0.00 4.73
603 617 4.438346 CCGAACTAATGCGGGAGG 57.562 61.111 0.00 0.00 43.67 4.30
604 618 1.520666 CCGAACTAATGCGGGAGGT 59.479 57.895 0.00 0.00 43.67 3.85
605 619 0.107848 CCGAACTAATGCGGGAGGTT 60.108 55.000 0.00 0.00 43.67 3.50
606 620 1.677820 CCGAACTAATGCGGGAGGTTT 60.678 52.381 0.00 0.00 43.67 3.27
607 621 1.396996 CGAACTAATGCGGGAGGTTTG 59.603 52.381 0.00 0.00 0.00 2.93
608 622 2.706890 GAACTAATGCGGGAGGTTTGA 58.293 47.619 0.00 0.00 0.00 2.69
609 623 2.871096 ACTAATGCGGGAGGTTTGAA 57.129 45.000 0.00 0.00 0.00 2.69
610 624 2.711542 ACTAATGCGGGAGGTTTGAAG 58.288 47.619 0.00 0.00 0.00 3.02
611 625 2.017049 CTAATGCGGGAGGTTTGAAGG 58.983 52.381 0.00 0.00 0.00 3.46
612 626 0.112412 AATGCGGGAGGTTTGAAGGT 59.888 50.000 0.00 0.00 0.00 3.50
613 627 0.322546 ATGCGGGAGGTTTGAAGGTC 60.323 55.000 0.00 0.00 0.00 3.85
614 628 1.674651 GCGGGAGGTTTGAAGGTCC 60.675 63.158 0.00 0.00 0.00 4.46
615 629 1.375523 CGGGAGGTTTGAAGGTCCG 60.376 63.158 0.00 0.00 0.00 4.79
616 630 1.759236 GGGAGGTTTGAAGGTCCGT 59.241 57.895 0.00 0.00 0.00 4.69
617 631 0.605589 GGGAGGTTTGAAGGTCCGTG 60.606 60.000 0.00 0.00 0.00 4.94
618 632 0.108019 GGAGGTTTGAAGGTCCGTGT 59.892 55.000 0.00 0.00 0.00 4.49
619 633 1.476291 GGAGGTTTGAAGGTCCGTGTT 60.476 52.381 0.00 0.00 0.00 3.32
620 634 1.602377 GAGGTTTGAAGGTCCGTGTTG 59.398 52.381 0.00 0.00 0.00 3.33
621 635 0.666374 GGTTTGAAGGTCCGTGTTGG 59.334 55.000 0.00 0.00 40.09 3.77
622 636 1.385528 GTTTGAAGGTCCGTGTTGGT 58.614 50.000 0.00 0.00 39.52 3.67
623 637 1.064952 GTTTGAAGGTCCGTGTTGGTG 59.935 52.381 0.00 0.00 39.52 4.17
624 638 0.542333 TTGAAGGTCCGTGTTGGTGA 59.458 50.000 0.00 0.00 39.52 4.02
625 639 0.762418 TGAAGGTCCGTGTTGGTGAT 59.238 50.000 0.00 0.00 39.52 3.06
626 640 1.156736 GAAGGTCCGTGTTGGTGATG 58.843 55.000 0.00 0.00 39.52 3.07
627 641 0.762418 AAGGTCCGTGTTGGTGATGA 59.238 50.000 0.00 0.00 39.52 2.92
628 642 0.984230 AGGTCCGTGTTGGTGATGAT 59.016 50.000 0.00 0.00 39.52 2.45
629 643 1.066143 AGGTCCGTGTTGGTGATGATC 60.066 52.381 0.00 0.00 39.52 2.92
630 644 0.999406 GTCCGTGTTGGTGATGATCG 59.001 55.000 0.00 0.00 39.52 3.69
631 645 0.606096 TCCGTGTTGGTGATGATCGT 59.394 50.000 0.00 0.00 39.52 3.73
632 646 1.001520 TCCGTGTTGGTGATGATCGTT 59.998 47.619 0.00 0.00 39.52 3.85
633 647 1.804151 CCGTGTTGGTGATGATCGTTT 59.196 47.619 0.00 0.00 0.00 3.60
670 688 5.359194 AGTTCGGATCACATTATCCAACT 57.641 39.130 11.56 11.56 44.98 3.16
699 719 3.244181 AACGACTGTTTCTGCGGATAGC 61.244 50.000 0.00 0.00 40.24 2.97
1041 1066 2.766651 CCGCCCTACTTAGCCCCA 60.767 66.667 0.00 0.00 0.00 4.96
1449 1474 0.182775 ACGGGAGGTTCAAGCTGTTT 59.817 50.000 0.00 0.00 0.00 2.83
1546 1574 2.412037 AAGCAAGCGCACTTTGAGGC 62.412 55.000 11.47 0.53 42.27 4.70
1554 1582 2.125106 ACTTTGAGGCGCCGATCC 60.125 61.111 23.20 12.39 0.00 3.36
1593 1621 0.109458 TAGTGCGTCGGTGACATCAC 60.109 55.000 3.27 3.27 45.72 3.06
1601 1629 2.161012 GTCGGTGACATCACTCGAGTTA 59.839 50.000 17.26 9.00 44.09 2.24
1644 1673 1.936547 GGTCGTGATCATCTTGCCTTC 59.063 52.381 0.00 0.00 0.00 3.46
1647 1676 1.303309 GTGATCATCTTGCCTTCCCG 58.697 55.000 0.00 0.00 0.00 5.14
1648 1677 0.911769 TGATCATCTTGCCTTCCCGT 59.088 50.000 0.00 0.00 0.00 5.28
1649 1678 2.115427 TGATCATCTTGCCTTCCCGTA 58.885 47.619 0.00 0.00 0.00 4.02
1650 1679 2.705658 TGATCATCTTGCCTTCCCGTAT 59.294 45.455 0.00 0.00 0.00 3.06
1651 1680 3.901222 TGATCATCTTGCCTTCCCGTATA 59.099 43.478 0.00 0.00 0.00 1.47
1652 1681 4.346709 TGATCATCTTGCCTTCCCGTATAA 59.653 41.667 0.00 0.00 0.00 0.98
1653 1682 4.974645 TCATCTTGCCTTCCCGTATAAT 57.025 40.909 0.00 0.00 0.00 1.28
1654 1683 4.894784 TCATCTTGCCTTCCCGTATAATC 58.105 43.478 0.00 0.00 0.00 1.75
1655 1684 3.764237 TCTTGCCTTCCCGTATAATCC 57.236 47.619 0.00 0.00 0.00 3.01
1656 1685 3.042682 TCTTGCCTTCCCGTATAATCCA 58.957 45.455 0.00 0.00 0.00 3.41
1657 1686 3.650942 TCTTGCCTTCCCGTATAATCCAT 59.349 43.478 0.00 0.00 0.00 3.41
1658 1687 3.695830 TGCCTTCCCGTATAATCCATC 57.304 47.619 0.00 0.00 0.00 3.51
1659 1688 2.304761 TGCCTTCCCGTATAATCCATCC 59.695 50.000 0.00 0.00 0.00 3.51
1660 1689 2.304761 GCCTTCCCGTATAATCCATCCA 59.695 50.000 0.00 0.00 0.00 3.41
1661 1690 3.868754 GCCTTCCCGTATAATCCATCCAC 60.869 52.174 0.00 0.00 0.00 4.02
1662 1691 3.585862 CTTCCCGTATAATCCATCCACG 58.414 50.000 0.00 0.00 0.00 4.94
1663 1692 1.274167 TCCCGTATAATCCATCCACGC 59.726 52.381 0.00 0.00 0.00 5.34
1664 1693 1.001520 CCCGTATAATCCATCCACGCA 59.998 52.381 0.00 0.00 0.00 5.24
1665 1694 2.354704 CCCGTATAATCCATCCACGCAT 60.355 50.000 0.00 0.00 0.00 4.73
1666 1695 2.672874 CCGTATAATCCATCCACGCATG 59.327 50.000 0.00 0.00 0.00 4.06
1681 1710 1.063006 CATGGCTGGAACAATCGCG 59.937 57.895 0.00 0.00 38.70 5.87
1692 1724 0.027979 ACAATCGCGGCAAATCATCG 59.972 50.000 6.13 0.00 0.00 3.84
1709 1741 2.661866 GCTCACGCGGTCAAGTGT 60.662 61.111 12.47 0.00 39.25 3.55
1710 1742 2.658707 GCTCACGCGGTCAAGTGTC 61.659 63.158 12.47 0.00 39.25 3.67
1711 1743 2.354188 TCACGCGGTCAAGTGTCG 60.354 61.111 12.47 0.00 39.25 4.35
1712 1744 4.059459 CACGCGGTCAAGTGTCGC 62.059 66.667 12.47 10.19 45.15 5.19
1713 1745 4.280494 ACGCGGTCAAGTGTCGCT 62.280 61.111 12.47 0.00 46.23 4.93
1714 1746 3.036084 CGCGGTCAAGTGTCGCTT 61.036 61.111 0.00 0.00 46.23 4.68
1730 1762 5.348724 GTGTCGCTTGATCTAATCTGTTTCA 59.651 40.000 0.00 0.00 0.00 2.69
1733 1765 6.904011 GTCGCTTGATCTAATCTGTTTCATTG 59.096 38.462 0.00 0.00 0.00 2.82
1745 1777 6.005583 TCTGTTTCATTGCATGAGAAGTTC 57.994 37.500 0.00 0.00 40.94 3.01
1747 1779 6.039605 TCTGTTTCATTGCATGAGAAGTTCAA 59.960 34.615 5.50 0.00 40.94 2.69
1748 1780 6.751157 TGTTTCATTGCATGAGAAGTTCAAT 58.249 32.000 5.50 0.00 40.94 2.57
1779 1811 7.432869 AGATACTGCATAGAGACAGTTCAATC 58.567 38.462 0.45 0.00 44.59 2.67
1783 1815 5.414360 TGCATAGAGACAGTTCAATCACTC 58.586 41.667 0.00 0.00 0.00 3.51
1804 1836 4.169508 TCAAACACAACAAACACCAATCG 58.830 39.130 0.00 0.00 0.00 3.34
1918 3587 6.867662 ATTTCAACTCTTACAGTCAAGGTG 57.132 37.500 0.00 0.00 32.30 4.00
2034 3703 5.347342 TGGGCATATTTTTCGCAAATACAG 58.653 37.500 2.72 1.50 0.00 2.74
2171 3841 2.755103 CAGCCCAAAGGATTTAGTCACC 59.245 50.000 0.00 0.00 35.03 4.02
2180 3850 7.360361 CAAAGGATTTAGTCACCAAGTTACAC 58.640 38.462 0.00 0.00 35.03 2.90
2207 3877 2.108514 CAATCGATGCTGCGGGTGT 61.109 57.895 0.00 0.00 0.00 4.16
2217 3887 2.032681 GCGGGTGTCTGCCTTTCT 59.967 61.111 0.00 0.00 39.31 2.52
2257 3928 0.873054 CGATTGAGCTGATCATGGCC 59.127 55.000 0.00 0.00 37.89 5.36
2278 3949 1.795768 TGACAGATGGTTGAGCGTTC 58.204 50.000 0.00 0.00 0.00 3.95
2343 4014 3.033909 TGAGGATGACAATCGAGTCCAT 58.966 45.455 2.68 0.24 37.73 3.41
2382 4053 1.538666 GGGGTAGCTTCCATGCCAT 59.461 57.895 11.91 0.00 0.00 4.40
2393 4064 0.179020 CCATGCCATACGACCACCAT 60.179 55.000 0.00 0.00 0.00 3.55
2404 4075 1.087501 GACCACCATTCGAAGAAGGC 58.912 55.000 3.35 0.00 45.90 4.35
2408 4079 2.009774 CACCATTCGAAGAAGGCGATT 58.990 47.619 3.35 0.00 45.90 3.34
2439 4110 3.445096 GGGCATAACTGATGGGCATTATC 59.555 47.826 0.00 0.00 35.91 1.75
2447 4118 5.802465 ACTGATGGGCATTATCTATGTGAG 58.198 41.667 0.00 0.00 36.57 3.51
2458 4129 7.578571 GCATTATCTATGTGAGGAGGACCTAAG 60.579 44.444 0.00 0.00 40.49 2.18
2468 4139 4.027437 AGGAGGACCTAAGCTACTTTGAG 58.973 47.826 0.00 0.00 45.83 3.02
2511 4182 4.214758 GCGTAGGTGTATCCAAAGTGTTTT 59.785 41.667 0.00 0.00 39.02 2.43
2514 4185 7.515643 CGTAGGTGTATCCAAAGTGTTTTTAG 58.484 38.462 0.00 0.00 39.02 1.85
2522 4193 4.953579 TCCAAAGTGTTTTTAGAAGTGGCT 59.046 37.500 0.00 0.00 0.00 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.408050 GATATGAGCGAGGCAATTCGT 58.592 47.619 6.41 0.00 42.38 3.85
9 10 0.036952 CCGGATATGAGCGAGGCAAT 60.037 55.000 0.00 0.00 0.00 3.56
78 80 0.818445 GGCATCCGACGAGTAGGAGA 60.818 60.000 10.62 0.00 37.78 3.71
79 81 1.101635 TGGCATCCGACGAGTAGGAG 61.102 60.000 10.62 4.87 37.78 3.69
108 110 6.000219 TCTCCTTCTTTCACCATTTTCTCTG 59.000 40.000 0.00 0.00 0.00 3.35
145 148 1.598130 GGCAAGACTCGCACCACTT 60.598 57.895 0.00 0.00 0.00 3.16
200 207 2.256461 CAACGCCAGGCAAGCTTC 59.744 61.111 13.30 0.00 0.00 3.86
245 253 1.119574 ACCTACTCCAGCCACACGTT 61.120 55.000 0.00 0.00 0.00 3.99
288 297 1.578926 CGCATTGAAACGCCTCCAA 59.421 52.632 0.00 0.00 0.00 3.53
308 317 1.666011 GACTGAACACGCCTCCTCA 59.334 57.895 0.00 0.00 0.00 3.86
399 408 0.671472 CACATTGCAGACGGCTCAGA 60.671 55.000 0.00 0.00 45.15 3.27
411 420 2.562912 CGTGCCACTCCACATTGC 59.437 61.111 0.00 0.00 35.47 3.56
430 439 1.935873 CCACATTCATGTCGCTGTAGG 59.064 52.381 0.00 0.00 39.39 3.18
475 487 3.075005 CCCTTCTTCCTCGCCCGA 61.075 66.667 0.00 0.00 0.00 5.14
478 490 0.960861 CAAACCCCTTCTTCCTCGCC 60.961 60.000 0.00 0.00 0.00 5.54
506 520 2.283529 GCCCTCTTCTGACCGTCCA 61.284 63.158 0.00 0.00 0.00 4.02
529 543 0.674895 GCGCAGAGTCCAGACCATTT 60.675 55.000 0.30 0.00 0.00 2.32
531 545 2.581354 GCGCAGAGTCCAGACCAT 59.419 61.111 0.30 0.00 0.00 3.55
532 546 4.056125 CGCGCAGAGTCCAGACCA 62.056 66.667 8.75 0.00 0.00 4.02
544 558 2.139917 GGTTATGTATCAATCCGCGCA 58.860 47.619 8.75 0.00 0.00 6.09
545 559 1.126113 CGGTTATGTATCAATCCGCGC 59.874 52.381 0.00 0.00 0.00 6.86
546 560 2.154963 CACGGTTATGTATCAATCCGCG 59.845 50.000 0.00 0.00 41.33 6.46
547 561 3.128349 ACACGGTTATGTATCAATCCGC 58.872 45.455 0.00 0.00 41.33 5.54
548 562 5.292345 TCAAACACGGTTATGTATCAATCCG 59.708 40.000 0.00 0.00 42.94 4.18
549 563 6.671614 TCAAACACGGTTATGTATCAATCC 57.328 37.500 0.00 0.00 30.75 3.01
550 564 7.850982 GTCATCAAACACGGTTATGTATCAATC 59.149 37.037 0.00 0.00 30.75 2.67
551 565 7.552687 AGTCATCAAACACGGTTATGTATCAAT 59.447 33.333 0.00 0.00 30.75 2.57
552 566 6.876789 AGTCATCAAACACGGTTATGTATCAA 59.123 34.615 0.00 0.00 30.75 2.57
553 567 6.403049 AGTCATCAAACACGGTTATGTATCA 58.597 36.000 0.00 0.00 30.75 2.15
554 568 6.903883 AGTCATCAAACACGGTTATGTATC 57.096 37.500 0.00 0.00 30.75 2.24
555 569 7.681939 AAAGTCATCAAACACGGTTATGTAT 57.318 32.000 0.00 0.00 30.75 2.29
556 570 7.499321 AAAAGTCATCAAACACGGTTATGTA 57.501 32.000 0.00 0.00 30.75 2.29
557 571 6.385649 AAAAGTCATCAAACACGGTTATGT 57.614 33.333 0.00 0.00 0.00 2.29
558 572 8.233868 TCATAAAAGTCATCAAACACGGTTATG 58.766 33.333 0.00 0.00 31.76 1.90
559 573 8.330466 TCATAAAAGTCATCAAACACGGTTAT 57.670 30.769 0.00 0.00 0.00 1.89
560 574 7.731882 TCATAAAAGTCATCAAACACGGTTA 57.268 32.000 0.00 0.00 0.00 2.85
561 575 6.627395 TCATAAAAGTCATCAAACACGGTT 57.373 33.333 0.00 0.00 0.00 4.44
562 576 6.128007 GGATCATAAAAGTCATCAAACACGGT 60.128 38.462 0.00 0.00 0.00 4.83
563 577 6.258160 GGATCATAAAAGTCATCAAACACGG 58.742 40.000 0.00 0.00 0.00 4.94
564 578 5.959527 CGGATCATAAAAGTCATCAAACACG 59.040 40.000 0.00 0.00 0.00 4.49
565 579 7.072177 TCGGATCATAAAAGTCATCAAACAC 57.928 36.000 0.00 0.00 0.00 3.32
566 580 7.390440 AGTTCGGATCATAAAAGTCATCAAACA 59.610 33.333 0.00 0.00 0.00 2.83
567 581 7.752695 AGTTCGGATCATAAAAGTCATCAAAC 58.247 34.615 0.00 0.00 0.00 2.93
568 582 7.921786 AGTTCGGATCATAAAAGTCATCAAA 57.078 32.000 0.00 0.00 0.00 2.69
569 583 9.613428 ATTAGTTCGGATCATAAAAGTCATCAA 57.387 29.630 0.00 0.00 0.00 2.57
570 584 9.045223 CATTAGTTCGGATCATAAAAGTCATCA 57.955 33.333 0.00 0.00 0.00 3.07
571 585 8.012241 GCATTAGTTCGGATCATAAAAGTCATC 58.988 37.037 0.00 0.00 0.00 2.92
572 586 7.307396 CGCATTAGTTCGGATCATAAAAGTCAT 60.307 37.037 0.00 0.00 0.00 3.06
573 587 6.019075 CGCATTAGTTCGGATCATAAAAGTCA 60.019 38.462 0.00 0.00 0.00 3.41
574 588 6.355638 CGCATTAGTTCGGATCATAAAAGTC 58.644 40.000 0.00 0.00 0.00 3.01
575 589 6.287107 CGCATTAGTTCGGATCATAAAAGT 57.713 37.500 0.00 0.00 0.00 2.66
586 600 0.107848 AACCTCCCGCATTAGTTCGG 60.108 55.000 0.00 0.00 44.89 4.30
587 601 1.396996 CAAACCTCCCGCATTAGTTCG 59.603 52.381 0.00 0.00 0.00 3.95
588 602 2.706890 TCAAACCTCCCGCATTAGTTC 58.293 47.619 0.00 0.00 0.00 3.01
589 603 2.871096 TCAAACCTCCCGCATTAGTT 57.129 45.000 0.00 0.00 0.00 2.24
590 604 2.618045 CCTTCAAACCTCCCGCATTAGT 60.618 50.000 0.00 0.00 0.00 2.24
591 605 2.017049 CCTTCAAACCTCCCGCATTAG 58.983 52.381 0.00 0.00 0.00 1.73
592 606 1.353022 ACCTTCAAACCTCCCGCATTA 59.647 47.619 0.00 0.00 0.00 1.90
593 607 0.112412 ACCTTCAAACCTCCCGCATT 59.888 50.000 0.00 0.00 0.00 3.56
594 608 0.322546 GACCTTCAAACCTCCCGCAT 60.323 55.000 0.00 0.00 0.00 4.73
595 609 1.072505 GACCTTCAAACCTCCCGCA 59.927 57.895 0.00 0.00 0.00 5.69
596 610 1.674651 GGACCTTCAAACCTCCCGC 60.675 63.158 0.00 0.00 0.00 6.13
597 611 1.375523 CGGACCTTCAAACCTCCCG 60.376 63.158 0.00 0.00 0.00 5.14
598 612 0.605589 CACGGACCTTCAAACCTCCC 60.606 60.000 0.00 0.00 0.00 4.30
599 613 0.108019 ACACGGACCTTCAAACCTCC 59.892 55.000 0.00 0.00 0.00 4.30
600 614 1.602377 CAACACGGACCTTCAAACCTC 59.398 52.381 0.00 0.00 0.00 3.85
601 615 1.675552 CAACACGGACCTTCAAACCT 58.324 50.000 0.00 0.00 0.00 3.50
602 616 0.666374 CCAACACGGACCTTCAAACC 59.334 55.000 0.00 0.00 36.56 3.27
603 617 1.064952 CACCAACACGGACCTTCAAAC 59.935 52.381 0.00 0.00 38.63 2.93
604 618 1.065345 TCACCAACACGGACCTTCAAA 60.065 47.619 0.00 0.00 38.63 2.69
605 619 0.542333 TCACCAACACGGACCTTCAA 59.458 50.000 0.00 0.00 38.63 2.69
606 620 0.762418 ATCACCAACACGGACCTTCA 59.238 50.000 0.00 0.00 38.63 3.02
607 621 1.156736 CATCACCAACACGGACCTTC 58.843 55.000 0.00 0.00 38.63 3.46
608 622 0.762418 TCATCACCAACACGGACCTT 59.238 50.000 0.00 0.00 38.63 3.50
609 623 0.984230 ATCATCACCAACACGGACCT 59.016 50.000 0.00 0.00 38.63 3.85
610 624 1.369625 GATCATCACCAACACGGACC 58.630 55.000 0.00 0.00 38.63 4.46
611 625 0.999406 CGATCATCACCAACACGGAC 59.001 55.000 0.00 0.00 38.63 4.79
612 626 0.606096 ACGATCATCACCAACACGGA 59.394 50.000 0.00 0.00 38.63 4.69
613 627 1.438651 AACGATCATCACCAACACGG 58.561 50.000 0.00 0.00 42.50 4.94
614 628 3.678072 ACTAAACGATCATCACCAACACG 59.322 43.478 0.00 0.00 0.00 4.49
615 629 5.390567 GGAACTAAACGATCATCACCAACAC 60.391 44.000 0.00 0.00 0.00 3.32
616 630 4.693566 GGAACTAAACGATCATCACCAACA 59.306 41.667 0.00 0.00 0.00 3.33
617 631 4.201685 CGGAACTAAACGATCATCACCAAC 60.202 45.833 0.00 0.00 0.00 3.77
618 632 3.930229 CGGAACTAAACGATCATCACCAA 59.070 43.478 0.00 0.00 0.00 3.67
619 633 3.193903 TCGGAACTAAACGATCATCACCA 59.806 43.478 0.00 0.00 33.69 4.17
620 634 3.777478 TCGGAACTAAACGATCATCACC 58.223 45.455 0.00 0.00 33.69 4.02
621 635 4.863131 AGTTCGGAACTAAACGATCATCAC 59.137 41.667 21.24 0.00 40.69 3.06
622 636 5.068234 AGTTCGGAACTAAACGATCATCA 57.932 39.130 21.24 0.00 40.69 3.07
623 637 6.264088 AGTAGTTCGGAACTAAACGATCATC 58.736 40.000 27.21 14.25 44.95 2.92
624 638 6.205101 AGTAGTTCGGAACTAAACGATCAT 57.795 37.500 27.21 4.83 44.95 2.45
625 639 5.633830 AGTAGTTCGGAACTAAACGATCA 57.366 39.130 27.21 6.87 44.95 2.92
626 640 6.780127 ACTAGTAGTTCGGAACTAAACGATC 58.220 40.000 27.21 16.03 44.95 3.69
627 641 6.749923 ACTAGTAGTTCGGAACTAAACGAT 57.250 37.500 27.21 15.36 44.95 3.73
628 642 6.560253 AACTAGTAGTTCGGAACTAAACGA 57.440 37.500 27.21 16.21 44.95 3.85
629 643 6.845272 GAACTAGTAGTTCGGAACTAAACG 57.155 41.667 27.21 20.05 44.22 3.60
659 673 7.113404 CAGTCGTTTGTTGAAAGTTGGATAATG 59.887 37.037 0.00 0.00 0.00 1.90
670 688 4.162812 GCAGAAACAGTCGTTTGTTGAAA 58.837 39.130 7.79 0.00 45.40 2.69
721 741 1.338136 CGGTAGGGGCCACTTGAGAT 61.338 60.000 16.00 0.00 0.00 2.75
747 767 0.792640 GCGATATGGCACGGATCAAG 59.207 55.000 4.65 0.00 0.00 3.02
909 931 2.176546 GTACGTACGTGCGGCAGA 59.823 61.111 30.25 5.88 35.98 4.26
1068 1093 0.590195 GTGATCTCAATGATGGCGCC 59.410 55.000 22.73 22.73 35.14 6.53
1449 1474 1.305802 ACCGGTCTCAGGGTGCATA 60.306 57.895 0.00 0.00 34.58 3.14
1518 1546 0.321671 TGCGCTTGCTTTCCTAGTCT 59.678 50.000 9.73 0.00 40.12 3.24
1546 1574 0.250038 ATCAATCTGGTGGATCGGCG 60.250 55.000 0.00 0.00 32.76 6.46
1593 1621 3.003897 CGGAAGGAGAGGAATAACTCGAG 59.996 52.174 11.84 11.84 42.31 4.04
1601 1629 2.830321 ACGTTAACGGAAGGAGAGGAAT 59.170 45.455 29.81 3.10 44.95 3.01
1633 1661 4.003648 GGATTATACGGGAAGGCAAGATG 58.996 47.826 0.00 0.00 0.00 2.90
1644 1673 1.001520 TGCGTGGATGGATTATACGGG 59.998 52.381 0.00 0.00 35.49 5.28
1659 1688 0.179156 GATTGTTCCAGCCATGCGTG 60.179 55.000 0.00 0.00 0.00 5.34
1660 1689 1.647545 CGATTGTTCCAGCCATGCGT 61.648 55.000 0.00 0.00 0.00 5.24
1661 1690 1.063006 CGATTGTTCCAGCCATGCG 59.937 57.895 0.00 0.00 0.00 4.73
1662 1691 1.226773 GCGATTGTTCCAGCCATGC 60.227 57.895 0.00 0.00 0.00 4.06
1663 1692 1.063006 CGCGATTGTTCCAGCCATG 59.937 57.895 0.00 0.00 0.00 3.66
1664 1693 2.114670 CCGCGATTGTTCCAGCCAT 61.115 57.895 8.23 0.00 0.00 4.40
1665 1694 2.745884 CCGCGATTGTTCCAGCCA 60.746 61.111 8.23 0.00 0.00 4.75
1666 1695 4.179579 GCCGCGATTGTTCCAGCC 62.180 66.667 8.23 0.00 0.00 4.85
1667 1696 2.470801 TTTGCCGCGATTGTTCCAGC 62.471 55.000 8.23 0.00 0.00 4.85
1681 1710 4.983090 CGTGAGCGATGATTTGCC 57.017 55.556 0.00 0.00 41.33 4.52
1706 1738 5.348724 TGAAACAGATTAGATCAAGCGACAC 59.651 40.000 0.00 0.00 0.00 3.67
1707 1739 5.478407 TGAAACAGATTAGATCAAGCGACA 58.522 37.500 0.00 0.00 0.00 4.35
1708 1740 6.595772 ATGAAACAGATTAGATCAAGCGAC 57.404 37.500 0.00 0.00 0.00 5.19
1709 1741 6.457392 GCAATGAAACAGATTAGATCAAGCGA 60.457 38.462 0.00 0.00 0.00 4.93
1710 1742 5.680229 GCAATGAAACAGATTAGATCAAGCG 59.320 40.000 0.00 0.00 0.00 4.68
1711 1743 6.558009 TGCAATGAAACAGATTAGATCAAGC 58.442 36.000 0.00 0.00 0.00 4.01
1730 1762 7.609146 TCTCAGTTATTGAACTTCTCATGCAAT 59.391 33.333 0.00 0.00 43.70 3.56
1733 1765 6.974932 TCTCAGTTATTGAACTTCTCATGC 57.025 37.500 0.00 0.00 43.70 4.06
1745 1777 8.355913 TGTCTCTATGCAGTATCTCAGTTATTG 58.644 37.037 0.00 0.00 0.00 1.90
1747 1779 7.723616 ACTGTCTCTATGCAGTATCTCAGTTAT 59.276 37.037 0.00 0.00 43.30 1.89
1748 1780 7.057264 ACTGTCTCTATGCAGTATCTCAGTTA 58.943 38.462 0.00 0.00 43.30 2.24
1779 1811 3.906998 TGGTGTTTGTTGTGTTTGAGTG 58.093 40.909 0.00 0.00 0.00 3.51
1783 1815 3.241932 GCGATTGGTGTTTGTTGTGTTTG 60.242 43.478 0.00 0.00 0.00 2.93
1918 3587 4.095036 GGAGTAGCTTCCATTTACAAGTGC 59.905 45.833 0.00 0.00 37.20 4.40
2171 3841 4.591202 GATTGCATCATCCGTGTAACTTG 58.409 43.478 0.00 0.00 31.75 3.16
2207 3877 4.379174 GCGTTGGAGAAAGGCAGA 57.621 55.556 0.00 0.00 46.59 4.26
2217 3887 1.686325 GGAGGAGGCATAGCGTTGGA 61.686 60.000 0.00 0.00 0.00 3.53
2257 3928 1.730501 ACGCTCAACCATCTGTCATG 58.269 50.000 0.00 0.00 0.00 3.07
2278 3949 5.324697 CATCATAATGCATGCATCTTCGAG 58.675 41.667 32.25 18.38 35.31 4.04
2382 4053 2.094390 CCTTCTTCGAATGGTGGTCGTA 60.094 50.000 0.00 0.00 39.52 3.43
2393 4064 0.796312 GCACAATCGCCTTCTTCGAA 59.204 50.000 0.00 0.00 39.54 3.71
2439 4110 3.571590 AGCTTAGGTCCTCCTCACATAG 58.428 50.000 0.00 0.00 43.94 2.23
2447 4118 3.431068 GCTCAAAGTAGCTTAGGTCCTCC 60.431 52.174 0.00 0.00 39.50 4.30
2458 4129 5.880054 TCCACAAATAAGCTCAAAGTAGC 57.120 39.130 0.00 0.00 43.11 3.58
2468 4139 2.595386 CGCCTTGTTCCACAAATAAGC 58.405 47.619 0.00 0.00 37.69 3.09


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

AutoCloner maintained by Alex Coulton.