Multiple sequence alignment - TraesCS4B01G074400

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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 TraesCS4B01G074400 chr4B 100.000 3326 0 0 1 3326 69892378 69889053 0.000000e+00 6143.0
1 TraesCS4B01G074400 chr4D 94.252 2140 78 17 702 2808 47660654 47658527 0.000000e+00 3229.0
2 TraesCS4B01G074400 chr4D 93.256 519 27 6 2807 3325 47657424 47656914 0.000000e+00 758.0
3 TraesCS4B01G074400 chr4A 93.847 2129 93 17 702 2805 550082294 550084409 0.000000e+00 3171.0
4 TraesCS4B01G074400 chr4A 90.458 524 35 8 2804 3323 550084570 550085082 0.000000e+00 676.0
5 TraesCS4B01G074400 chr7D 92.803 528 32 1 1 528 507249313 507248792 0.000000e+00 760.0
6 TraesCS4B01G074400 chr6B 91.917 532 40 2 2 530 142228409 142227878 0.000000e+00 741.0
7 TraesCS4B01G074400 chr3D 79.303 488 66 26 2766 3244 538853327 538853788 3.220000e-80 309.0
8 TraesCS4B01G074400 chr7A 74.174 484 91 26 2765 3244 68754711 68755164 1.590000e-38 171.0
9 TraesCS4B01G074400 chr7A 82.857 105 15 3 414 516 557560268 557560165 1.270000e-14 91.6


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 TraesCS4B01G074400 chr4B 69889053 69892378 3325 True 6143.0 6143 100.0000 1 3326 1 chr4B.!!$R1 3325
1 TraesCS4B01G074400 chr4D 47656914 47660654 3740 True 1993.5 3229 93.7540 702 3325 2 chr4D.!!$R1 2623
2 TraesCS4B01G074400 chr4A 550082294 550085082 2788 False 1923.5 3171 92.1525 702 3323 2 chr4A.!!$F1 2621
3 TraesCS4B01G074400 chr7D 507248792 507249313 521 True 760.0 760 92.8030 1 528 1 chr7D.!!$R1 527
4 TraesCS4B01G074400 chr6B 142227878 142228409 531 True 741.0 741 91.9170 2 530 1 chr6B.!!$R1 528

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
596 600 0.03392 AGATCGTGTTGTGCTGCAGA 59.966 50.0 20.43 0.00 0.00 4.26 F
602 606 0.03659 TGTTGTGCTGCAGATAGCCA 59.963 50.0 20.43 1.69 44.83 4.75 F
1920 1925 0.10741 GTGCAATCCCCATCACGGTA 60.107 55.0 0.00 0.00 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2148 2153 0.036765 GTACACAAGCGATGTCCCCA 60.037 55.0 0.00 0.00 41.46 4.96 R
2265 2270 0.106569 TCGCCATTTGCCATCTCCAT 60.107 50.0 0.00 0.00 36.24 3.41 R
3098 4247 0.892755 ACTCATGTGCTGCAAATGGG 59.107 50.0 27.15 27.15 35.77 4.00 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
36 37 7.338710 CAATTTACCTCCCTCAATTCTAGTCA 58.661 38.462 0.00 0.00 0.00 3.41
60 61 0.625849 GGCCTCCTTCTCCAAATCCA 59.374 55.000 0.00 0.00 0.00 3.41
62 63 1.283321 GCCTCCTTCTCCAAATCCAGT 59.717 52.381 0.00 0.00 0.00 4.00
111 112 4.450757 TCAATGTCGTCGTTGTTCAATGAT 59.549 37.500 13.11 0.00 40.34 2.45
114 115 3.804873 TGTCGTCGTTGTTCAATGATTCA 59.195 39.130 10.07 7.62 0.00 2.57
174 175 2.044555 CCTACTCGGACAGTGCGGA 61.045 63.158 15.10 0.69 36.43 5.54
193 194 0.842030 AGGAGAGGGAACATGTGGCA 60.842 55.000 0.00 0.00 0.00 4.92
210 211 2.676822 AGCGCCAGTCTTCTCCGA 60.677 61.111 2.29 0.00 0.00 4.55
316 319 6.295011 GGAACTGAACAGAGAGAAAGAGATGA 60.295 42.308 8.87 0.00 0.00 2.92
359 362 2.362369 ATGGCAGCTGACTAGGCGT 61.362 57.895 22.80 1.78 34.52 5.68
367 370 1.202313 GCTGACTAGGCGTTGACTAGG 60.202 57.143 11.20 0.00 44.98 3.02
418 422 2.243736 TGGTTTGAGGTGAAGAGGGTTT 59.756 45.455 0.00 0.00 0.00 3.27
431 435 1.752498 GAGGGTTTGTTTTTGTCCGGT 59.248 47.619 0.00 0.00 0.00 5.28
450 454 3.119280 CGGTTTTGAAAGTTCAGGGTTGT 60.119 43.478 0.00 0.00 38.61 3.32
491 495 8.644216 TGAAGTTCAAGGTTGTACATTAGACTA 58.356 33.333 2.20 0.00 31.79 2.59
497 501 5.012239 AGGTTGTACATTAGACTACGGTGA 58.988 41.667 0.00 0.00 0.00 4.02
506 510 5.496133 TTAGACTACGGTGATAGTTCAGC 57.504 43.478 0.00 0.00 45.00 4.26
530 534 8.870879 AGCGTTGTAATATAGACTTTTCTCAAC 58.129 33.333 0.00 0.00 32.75 3.18
531 535 8.870879 GCGTTGTAATATAGACTTTTCTCAACT 58.129 33.333 0.00 0.00 32.75 3.16
543 547 9.660180 AGACTTTTCTCAACTATCTTATCAACC 57.340 33.333 0.00 0.00 0.00 3.77
544 548 9.436957 GACTTTTCTCAACTATCTTATCAACCA 57.563 33.333 0.00 0.00 0.00 3.67
545 549 9.965902 ACTTTTCTCAACTATCTTATCAACCAT 57.034 29.630 0.00 0.00 0.00 3.55
548 552 9.739276 TTTCTCAACTATCTTATCAACCATTGT 57.261 29.630 0.00 0.00 0.00 2.71
549 553 8.722480 TCTCAACTATCTTATCAACCATTGTG 57.278 34.615 0.00 0.00 0.00 3.33
550 554 7.280876 TCTCAACTATCTTATCAACCATTGTGC 59.719 37.037 0.00 0.00 0.00 4.57
551 555 6.883756 TCAACTATCTTATCAACCATTGTGCA 59.116 34.615 0.00 0.00 0.00 4.57
552 556 7.557358 TCAACTATCTTATCAACCATTGTGCAT 59.443 33.333 0.00 0.00 0.00 3.96
553 557 7.268199 ACTATCTTATCAACCATTGTGCATG 57.732 36.000 0.00 0.00 0.00 4.06
554 558 7.056006 ACTATCTTATCAACCATTGTGCATGA 58.944 34.615 0.00 0.00 34.31 3.07
555 559 5.565592 TCTTATCAACCATTGTGCATGAC 57.434 39.130 0.00 0.00 34.31 3.06
556 560 5.255687 TCTTATCAACCATTGTGCATGACT 58.744 37.500 0.00 0.00 34.31 3.41
557 561 5.711506 TCTTATCAACCATTGTGCATGACTT 59.288 36.000 0.00 0.00 34.31 3.01
558 562 6.883756 TCTTATCAACCATTGTGCATGACTTA 59.116 34.615 0.00 0.00 34.31 2.24
559 563 5.981088 ATCAACCATTGTGCATGACTTAA 57.019 34.783 0.00 0.00 34.31 1.85
560 564 5.375417 TCAACCATTGTGCATGACTTAAG 57.625 39.130 0.00 0.00 34.31 1.85
561 565 3.855689 ACCATTGTGCATGACTTAAGC 57.144 42.857 1.29 0.00 34.31 3.09
562 566 3.156293 ACCATTGTGCATGACTTAAGCA 58.844 40.909 1.29 2.15 34.31 3.91
563 567 3.192001 ACCATTGTGCATGACTTAAGCAG 59.808 43.478 1.29 0.00 39.21 4.24
564 568 3.428452 CCATTGTGCATGACTTAAGCAGG 60.428 47.826 1.29 4.90 39.21 4.85
565 569 1.167851 TGTGCATGACTTAAGCAGGC 58.832 50.000 21.52 21.52 42.80 4.85
567 571 1.908344 TGCATGACTTAAGCAGGCAA 58.092 45.000 25.78 15.27 46.92 4.52
568 572 2.237643 TGCATGACTTAAGCAGGCAAA 58.762 42.857 25.78 12.01 46.92 3.68
569 573 2.627221 TGCATGACTTAAGCAGGCAAAA 59.373 40.909 25.78 11.49 46.92 2.44
570 574 3.069300 TGCATGACTTAAGCAGGCAAAAA 59.931 39.130 25.78 11.23 46.92 1.94
593 597 2.238353 ACAGATCGTGTTGTGCTGC 58.762 52.632 0.00 0.00 34.94 5.25
594 598 0.532640 ACAGATCGTGTTGTGCTGCA 60.533 50.000 0.00 0.00 34.94 4.41
595 599 0.165295 CAGATCGTGTTGTGCTGCAG 59.835 55.000 10.11 10.11 0.00 4.41
596 600 0.033920 AGATCGTGTTGTGCTGCAGA 59.966 50.000 20.43 0.00 0.00 4.26
597 601 1.081892 GATCGTGTTGTGCTGCAGAT 58.918 50.000 20.43 0.36 0.00 2.90
598 602 2.094026 AGATCGTGTTGTGCTGCAGATA 60.094 45.455 20.43 1.74 0.00 1.98
599 603 1.713597 TCGTGTTGTGCTGCAGATAG 58.286 50.000 20.43 0.00 0.00 2.08
600 604 0.095935 CGTGTTGTGCTGCAGATAGC 59.904 55.000 20.43 2.64 43.95 2.97
601 605 0.449388 GTGTTGTGCTGCAGATAGCC 59.551 55.000 20.43 0.00 44.83 3.93
602 606 0.036590 TGTTGTGCTGCAGATAGCCA 59.963 50.000 20.43 1.69 44.83 4.75
603 607 1.167851 GTTGTGCTGCAGATAGCCAA 58.832 50.000 20.43 8.74 44.83 4.52
604 608 1.541147 GTTGTGCTGCAGATAGCCAAA 59.459 47.619 20.43 0.00 44.83 3.28
605 609 2.133281 TGTGCTGCAGATAGCCAAAT 57.867 45.000 20.43 0.00 44.83 2.32
606 610 3.280197 TGTGCTGCAGATAGCCAAATA 57.720 42.857 20.43 0.00 44.83 1.40
607 611 3.619419 TGTGCTGCAGATAGCCAAATAA 58.381 40.909 20.43 0.00 44.83 1.40
608 612 4.015764 TGTGCTGCAGATAGCCAAATAAA 58.984 39.130 20.43 0.00 44.83 1.40
609 613 4.142403 TGTGCTGCAGATAGCCAAATAAAC 60.142 41.667 20.43 0.00 44.83 2.01
610 614 4.015764 TGCTGCAGATAGCCAAATAAACA 58.984 39.130 20.43 0.00 44.83 2.83
611 615 4.096833 TGCTGCAGATAGCCAAATAAACAG 59.903 41.667 20.43 0.00 44.83 3.16
612 616 4.604976 CTGCAGATAGCCAAATAAACAGC 58.395 43.478 8.42 0.00 44.83 4.40
613 617 4.272489 TGCAGATAGCCAAATAAACAGCT 58.728 39.130 0.00 0.00 44.83 4.24
614 618 4.706476 TGCAGATAGCCAAATAAACAGCTT 59.294 37.500 0.00 0.00 44.83 3.74
615 619 5.885352 TGCAGATAGCCAAATAAACAGCTTA 59.115 36.000 0.00 0.00 44.83 3.09
616 620 6.038603 TGCAGATAGCCAAATAAACAGCTTAG 59.961 38.462 0.00 0.00 44.83 2.18
617 621 6.038714 GCAGATAGCCAAATAAACAGCTTAGT 59.961 38.462 0.00 0.00 37.23 2.24
618 622 7.412853 CAGATAGCCAAATAAACAGCTTAGTG 58.587 38.462 0.00 0.00 0.00 2.74
619 623 7.066284 CAGATAGCCAAATAAACAGCTTAGTGT 59.934 37.037 0.00 0.00 0.00 3.55
620 624 8.265055 AGATAGCCAAATAAACAGCTTAGTGTA 58.735 33.333 0.00 0.00 0.00 2.90
621 625 6.496338 AGCCAAATAAACAGCTTAGTGTAC 57.504 37.500 0.00 0.00 0.00 2.90
622 626 6.001460 AGCCAAATAAACAGCTTAGTGTACA 58.999 36.000 0.00 0.00 0.00 2.90
623 627 6.149474 AGCCAAATAAACAGCTTAGTGTACAG 59.851 38.462 0.00 0.00 0.00 2.74
624 628 6.622896 GCCAAATAAACAGCTTAGTGTACAGG 60.623 42.308 0.00 0.00 0.00 4.00
625 629 6.128007 CCAAATAAACAGCTTAGTGTACAGGG 60.128 42.308 0.00 0.00 0.00 4.45
626 630 5.757099 ATAAACAGCTTAGTGTACAGGGT 57.243 39.130 0.00 0.00 0.00 4.34
627 631 3.402628 AACAGCTTAGTGTACAGGGTG 57.597 47.619 0.00 5.82 0.00 4.61
628 632 2.326428 ACAGCTTAGTGTACAGGGTGT 58.674 47.619 13.43 13.43 34.48 4.16
629 633 2.299297 ACAGCTTAGTGTACAGGGTGTC 59.701 50.000 13.43 0.00 34.23 3.67
630 634 2.563179 CAGCTTAGTGTACAGGGTGTCT 59.437 50.000 0.00 0.00 0.00 3.41
631 635 3.762288 CAGCTTAGTGTACAGGGTGTCTA 59.238 47.826 0.00 0.00 0.00 2.59
632 636 4.402793 CAGCTTAGTGTACAGGGTGTCTAT 59.597 45.833 0.00 0.00 0.00 1.98
633 637 5.593095 CAGCTTAGTGTACAGGGTGTCTATA 59.407 44.000 0.00 0.00 0.00 1.31
634 638 5.828859 AGCTTAGTGTACAGGGTGTCTATAG 59.171 44.000 0.00 0.00 0.00 1.31
635 639 5.593502 GCTTAGTGTACAGGGTGTCTATAGT 59.406 44.000 0.00 0.00 0.00 2.12
636 640 6.238703 GCTTAGTGTACAGGGTGTCTATAGTC 60.239 46.154 0.00 0.00 0.00 2.59
637 641 5.188988 AGTGTACAGGGTGTCTATAGTCA 57.811 43.478 0.00 0.00 0.00 3.41
638 642 5.767670 AGTGTACAGGGTGTCTATAGTCAT 58.232 41.667 0.00 0.00 0.00 3.06
639 643 5.828859 AGTGTACAGGGTGTCTATAGTCATC 59.171 44.000 0.00 2.46 0.00 2.92
640 644 4.820173 TGTACAGGGTGTCTATAGTCATCG 59.180 45.833 2.97 0.00 0.00 3.84
641 645 3.899726 ACAGGGTGTCTATAGTCATCGT 58.100 45.455 2.97 1.62 0.00 3.73
642 646 3.884091 ACAGGGTGTCTATAGTCATCGTC 59.116 47.826 2.97 0.00 0.00 4.20
643 647 4.138290 CAGGGTGTCTATAGTCATCGTCT 58.862 47.826 2.97 0.00 0.00 4.18
644 648 5.163227 ACAGGGTGTCTATAGTCATCGTCTA 60.163 44.000 2.97 0.00 0.00 2.59
645 649 5.941058 CAGGGTGTCTATAGTCATCGTCTAT 59.059 44.000 2.97 0.00 33.45 1.98
646 650 7.104290 CAGGGTGTCTATAGTCATCGTCTATA 58.896 42.308 2.97 0.00 31.64 1.31
647 651 7.606839 CAGGGTGTCTATAGTCATCGTCTATAA 59.393 40.741 2.97 0.00 32.33 0.98
648 652 8.162085 AGGGTGTCTATAGTCATCGTCTATAAA 58.838 37.037 2.97 0.00 32.33 1.40
649 653 8.235905 GGGTGTCTATAGTCATCGTCTATAAAC 58.764 40.741 2.97 0.00 32.33 2.01
650 654 9.001542 GGTGTCTATAGTCATCGTCTATAAACT 57.998 37.037 2.97 0.00 32.33 2.66
651 655 9.814507 GTGTCTATAGTCATCGTCTATAAACTG 57.185 37.037 2.97 0.00 32.33 3.16
652 656 9.774413 TGTCTATAGTCATCGTCTATAAACTGA 57.226 33.333 0.00 0.00 32.33 3.41
654 658 9.438228 TCTATAGTCATCGTCTATAAACTGAGG 57.562 37.037 0.00 0.00 32.33 3.86
655 659 9.221933 CTATAGTCATCGTCTATAAACTGAGGT 57.778 37.037 0.00 0.00 32.33 3.85
656 660 6.137794 AGTCATCGTCTATAAACTGAGGTG 57.862 41.667 0.00 0.00 0.00 4.00
657 661 5.652891 AGTCATCGTCTATAAACTGAGGTGT 59.347 40.000 0.00 0.00 0.00 4.16
658 662 6.153000 AGTCATCGTCTATAAACTGAGGTGTT 59.847 38.462 0.00 0.00 0.00 3.32
659 663 6.253727 GTCATCGTCTATAAACTGAGGTGTTG 59.746 42.308 0.00 0.00 0.00 3.33
660 664 5.068234 TCGTCTATAAACTGAGGTGTTGG 57.932 43.478 0.00 0.00 0.00 3.77
661 665 4.081862 TCGTCTATAAACTGAGGTGTTGGG 60.082 45.833 0.00 0.00 0.00 4.12
662 666 4.081862 CGTCTATAAACTGAGGTGTTGGGA 60.082 45.833 0.00 0.00 0.00 4.37
663 667 5.568023 CGTCTATAAACTGAGGTGTTGGGAA 60.568 44.000 0.00 0.00 0.00 3.97
664 668 5.642491 GTCTATAAACTGAGGTGTTGGGAAC 59.358 44.000 0.00 0.00 0.00 3.62
693 697 8.414778 ACAGATAGTAGGTGTCTAAACTAATGC 58.585 37.037 0.00 0.00 0.00 3.56
694 698 8.414003 CAGATAGTAGGTGTCTAAACTAATGCA 58.586 37.037 0.00 0.00 0.00 3.96
695 699 8.414778 AGATAGTAGGTGTCTAAACTAATGCAC 58.585 37.037 0.00 0.00 0.00 4.57
696 700 6.354794 AGTAGGTGTCTAAACTAATGCACA 57.645 37.500 0.00 0.00 0.00 4.57
697 701 6.947464 AGTAGGTGTCTAAACTAATGCACAT 58.053 36.000 0.00 0.00 0.00 3.21
698 702 6.818644 AGTAGGTGTCTAAACTAATGCACATG 59.181 38.462 0.00 0.00 0.00 3.21
699 703 4.396166 AGGTGTCTAAACTAATGCACATGC 59.604 41.667 0.00 0.00 42.50 4.06
700 704 4.438744 GGTGTCTAAACTAATGCACATGCC 60.439 45.833 0.49 0.00 41.18 4.40
718 722 2.821991 CCCTAACGGGCTATCTTCAG 57.178 55.000 0.00 0.00 45.33 3.02
743 747 1.381327 TGGGACAGGGTCGGATCTC 60.381 63.158 0.00 0.00 32.65 2.75
888 893 2.661866 CAGGCGGCGGCTACATAC 60.662 66.667 35.69 1.34 36.44 2.39
902 907 5.401376 CGGCTACATACACATACACATACAC 59.599 44.000 0.00 0.00 0.00 2.90
903 908 5.694910 GGCTACATACACATACACATACACC 59.305 44.000 0.00 0.00 0.00 4.16
904 909 5.401376 GCTACATACACATACACATACACCG 59.599 44.000 0.00 0.00 0.00 4.94
905 910 4.116961 ACATACACATACACATACACCGC 58.883 43.478 0.00 0.00 0.00 5.68
906 911 2.753055 ACACATACACATACACCGCA 57.247 45.000 0.00 0.00 0.00 5.69
907 912 2.616960 ACACATACACATACACCGCAG 58.383 47.619 0.00 0.00 0.00 5.18
979 984 4.576993 GCAAACCATTCCCTTGCG 57.423 55.556 0.00 0.00 36.44 4.85
991 996 1.604378 CCTTGCGGACCTCCATCTT 59.396 57.895 0.00 0.00 35.14 2.40
1447 1452 5.717119 ACCAAGTAACCAAGTACATCTACG 58.283 41.667 0.00 0.00 0.00 3.51
1920 1925 0.107410 GTGCAATCCCCATCACGGTA 60.107 55.000 0.00 0.00 0.00 4.02
1992 1997 2.811317 GAGCTCGGCGTCAAGGTG 60.811 66.667 6.85 0.00 0.00 4.00
2034 2039 2.671070 CCGGTCACCAAGATGCCT 59.329 61.111 0.00 0.00 0.00 4.75
2148 2153 0.610687 CCCTCGACTTCTTCAAGGCT 59.389 55.000 0.00 0.00 35.11 4.58
2265 2270 4.536090 AGGGTTCCATCTATGTTTGAGTCA 59.464 41.667 0.00 0.00 0.00 3.41
2334 2339 3.243877 CGCTAGGAATTTGATGTGTCGAG 59.756 47.826 0.00 0.00 0.00 4.04
2454 2475 2.638855 GGGGATGAAGAGAGCTGATGAT 59.361 50.000 0.00 0.00 0.00 2.45
2563 2588 9.696917 TGCATGACATGTTTATATACTAGACTG 57.303 33.333 16.62 0.00 0.00 3.51
2578 2603 5.090139 ACTAGACTGGATATGATGAAGGGG 58.910 45.833 0.00 0.00 0.00 4.79
2723 2760 6.540189 GCTGGAGACAATGCTCTAAAAAGATA 59.460 38.462 5.07 0.00 42.06 1.98
2761 2800 2.734606 TGACTTGAGTTCGCATTTACCG 59.265 45.455 0.00 0.00 0.00 4.02
2880 4025 3.699538 GGAGATTTGGGGTCAATGTTACC 59.300 47.826 0.00 0.00 36.19 2.85
2956 4101 9.500864 GTGTGCATTGTTTTAAATTTTTGTCAT 57.499 25.926 0.00 0.00 0.00 3.06
2989 4134 6.180472 GTGCATATATTAGGGTTACCATGCT 58.820 40.000 17.38 3.61 38.68 3.79
3071 4220 3.778075 TGGAAAAACTCCCGATGGATCTA 59.222 43.478 0.00 0.00 44.69 1.98
3098 4247 9.227777 ACCATAGAACTCAGTTAACCATTTAAC 57.772 33.333 0.88 0.00 45.22 2.01
3217 4366 3.153919 GGGACCACTTTCAATAAGTGCA 58.846 45.455 11.21 0.00 44.62 4.57
3226 4375 9.643693 CCACTTTCAATAAGTGCAGATAAATTT 57.356 29.630 11.21 0.00 44.62 1.82
3280 4429 8.518702 TGAAACTTGTGCAAAGCAACATATATA 58.481 29.630 8.09 0.00 41.47 0.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 0.253347 TTGGAGAAGGAGGCCCTCAT 60.253 55.000 13.90 1.36 43.48 2.90
60 61 1.045407 TCACGGCTGTTACCTTCACT 58.955 50.000 0.00 0.00 0.00 3.41
62 63 1.414919 AGTTCACGGCTGTTACCTTCA 59.585 47.619 0.00 0.00 0.00 3.02
111 112 1.138069 TCCAGCTTCACGTTGTCTGAA 59.862 47.619 5.69 0.00 0.00 3.02
114 115 0.034059 CCTCCAGCTTCACGTTGTCT 59.966 55.000 0.00 0.00 0.00 3.41
174 175 0.842030 TGCCACATGTTCCCTCTCCT 60.842 55.000 0.00 0.00 0.00 3.69
193 194 2.055042 ATCGGAGAAGACTGGCGCT 61.055 57.895 7.64 0.00 43.58 5.92
199 200 3.211288 CGGCCATCGGAGAAGACT 58.789 61.111 2.24 0.00 43.58 3.24
316 319 2.102578 GCATGGGCACTAAACCAATCT 58.897 47.619 0.00 0.00 40.73 2.40
367 370 3.181476 ACTGGTTTTCAATGGTTGACTGC 60.181 43.478 0.00 0.00 39.87 4.40
418 422 4.884247 ACTTTCAAAACCGGACAAAAACA 58.116 34.783 9.46 0.00 0.00 2.83
431 435 7.442656 TGTTTTACAACCCTGAACTTTCAAAA 58.557 30.769 0.00 0.00 32.35 2.44
491 495 1.000506 ACAACGCTGAACTATCACCGT 59.999 47.619 0.00 0.00 46.81 4.83
517 521 9.660180 GGTTGATAAGATAGTTGAGAAAAGTCT 57.340 33.333 0.00 0.00 36.55 3.24
523 527 9.166173 CACAATGGTTGATAAGATAGTTGAGAA 57.834 33.333 0.00 0.00 0.00 2.87
530 534 7.228108 AGTCATGCACAATGGTTGATAAGATAG 59.772 37.037 0.00 0.00 36.86 2.08
531 535 7.056006 AGTCATGCACAATGGTTGATAAGATA 58.944 34.615 0.00 0.00 36.86 1.98
532 536 5.889853 AGTCATGCACAATGGTTGATAAGAT 59.110 36.000 0.00 0.00 36.86 2.40
533 537 5.255687 AGTCATGCACAATGGTTGATAAGA 58.744 37.500 0.00 0.00 36.86 2.10
534 538 5.571784 AGTCATGCACAATGGTTGATAAG 57.428 39.130 0.00 0.00 36.86 1.73
535 539 5.981088 AAGTCATGCACAATGGTTGATAA 57.019 34.783 0.00 0.00 36.86 1.75
536 540 6.404623 GCTTAAGTCATGCACAATGGTTGATA 60.405 38.462 4.02 0.00 36.86 2.15
537 541 5.622914 GCTTAAGTCATGCACAATGGTTGAT 60.623 40.000 4.02 0.00 36.86 2.57
538 542 4.321156 GCTTAAGTCATGCACAATGGTTGA 60.321 41.667 4.02 0.00 36.86 3.18
539 543 3.922240 GCTTAAGTCATGCACAATGGTTG 59.078 43.478 4.02 0.00 36.86 3.77
540 544 3.573538 TGCTTAAGTCATGCACAATGGTT 59.426 39.130 4.02 0.00 36.86 3.67
541 545 3.156293 TGCTTAAGTCATGCACAATGGT 58.844 40.909 4.02 0.00 36.86 3.55
542 546 3.428452 CCTGCTTAAGTCATGCACAATGG 60.428 47.826 4.02 0.00 36.86 3.16
543 547 3.766151 CCTGCTTAAGTCATGCACAATG 58.234 45.455 4.02 0.00 37.66 2.82
544 548 2.165030 GCCTGCTTAAGTCATGCACAAT 59.835 45.455 16.31 0.00 33.96 2.71
545 549 1.541147 GCCTGCTTAAGTCATGCACAA 59.459 47.619 16.31 0.00 33.96 3.33
546 550 1.167851 GCCTGCTTAAGTCATGCACA 58.832 50.000 16.31 1.11 33.96 4.57
547 551 1.167851 TGCCTGCTTAAGTCATGCAC 58.832 50.000 18.46 0.00 33.96 4.57
548 552 1.908344 TTGCCTGCTTAAGTCATGCA 58.092 45.000 18.46 18.46 36.05 3.96
549 553 3.302365 TTTTGCCTGCTTAAGTCATGC 57.698 42.857 15.15 15.15 0.00 4.06
571 575 3.694734 CAGCACAACACGATCTGTTTTT 58.305 40.909 7.54 0.00 41.50 1.94
572 576 2.541588 GCAGCACAACACGATCTGTTTT 60.542 45.455 7.54 0.96 41.50 2.43
573 577 1.002468 GCAGCACAACACGATCTGTTT 60.002 47.619 7.54 0.18 41.50 2.83
574 578 0.588252 GCAGCACAACACGATCTGTT 59.412 50.000 0.00 5.14 44.51 3.16
575 579 0.532640 TGCAGCACAACACGATCTGT 60.533 50.000 0.00 0.00 32.89 3.41
576 580 0.165295 CTGCAGCACAACACGATCTG 59.835 55.000 0.00 0.00 0.00 2.90
577 581 0.033920 TCTGCAGCACAACACGATCT 59.966 50.000 9.47 0.00 0.00 2.75
578 582 1.081892 ATCTGCAGCACAACACGATC 58.918 50.000 9.47 0.00 0.00 3.69
579 583 2.274437 CTATCTGCAGCACAACACGAT 58.726 47.619 9.47 0.00 0.00 3.73
580 584 1.713597 CTATCTGCAGCACAACACGA 58.286 50.000 9.47 0.00 0.00 4.35
581 585 0.095935 GCTATCTGCAGCACAACACG 59.904 55.000 9.47 0.00 41.40 4.49
582 586 0.449388 GGCTATCTGCAGCACAACAC 59.551 55.000 9.47 0.00 43.67 3.32
583 587 0.036590 TGGCTATCTGCAGCACAACA 59.963 50.000 9.47 2.35 43.67 3.33
584 588 1.167851 TTGGCTATCTGCAGCACAAC 58.832 50.000 9.47 0.00 43.67 3.32
585 589 1.908344 TTTGGCTATCTGCAGCACAA 58.092 45.000 9.47 6.56 43.67 3.33
586 590 2.133281 ATTTGGCTATCTGCAGCACA 57.867 45.000 9.47 0.03 43.67 4.57
587 591 4.142403 TGTTTATTTGGCTATCTGCAGCAC 60.142 41.667 9.47 0.00 43.67 4.40
588 592 4.015764 TGTTTATTTGGCTATCTGCAGCA 58.984 39.130 9.47 0.00 43.67 4.41
589 593 4.604976 CTGTTTATTTGGCTATCTGCAGC 58.395 43.478 9.47 0.00 45.15 5.25
590 594 4.337555 AGCTGTTTATTTGGCTATCTGCAG 59.662 41.667 7.63 7.63 45.15 4.41
591 595 4.272489 AGCTGTTTATTTGGCTATCTGCA 58.728 39.130 0.00 0.00 45.15 4.41
592 596 4.907879 AGCTGTTTATTTGGCTATCTGC 57.092 40.909 0.00 0.00 41.94 4.26
593 597 7.066284 ACACTAAGCTGTTTATTTGGCTATCTG 59.934 37.037 0.00 0.00 34.40 2.90
594 598 7.112779 ACACTAAGCTGTTTATTTGGCTATCT 58.887 34.615 0.00 0.00 34.40 1.98
595 599 7.321745 ACACTAAGCTGTTTATTTGGCTATC 57.678 36.000 0.00 0.00 34.40 2.08
596 600 7.827236 TGTACACTAAGCTGTTTATTTGGCTAT 59.173 33.333 0.00 0.00 34.40 2.97
597 601 7.162761 TGTACACTAAGCTGTTTATTTGGCTA 58.837 34.615 0.00 0.00 34.40 3.93
598 602 6.001460 TGTACACTAAGCTGTTTATTTGGCT 58.999 36.000 0.00 0.00 36.53 4.75
599 603 6.249035 TGTACACTAAGCTGTTTATTTGGC 57.751 37.500 0.00 0.00 0.00 4.52
600 604 6.128007 CCCTGTACACTAAGCTGTTTATTTGG 60.128 42.308 0.00 0.00 0.00 3.28
601 605 6.430000 ACCCTGTACACTAAGCTGTTTATTTG 59.570 38.462 0.00 0.00 0.00 2.32
602 606 6.430000 CACCCTGTACACTAAGCTGTTTATTT 59.570 38.462 0.00 0.00 0.00 1.40
603 607 5.938125 CACCCTGTACACTAAGCTGTTTATT 59.062 40.000 0.00 0.00 0.00 1.40
604 608 5.012768 ACACCCTGTACACTAAGCTGTTTAT 59.987 40.000 0.00 0.00 0.00 1.40
605 609 4.345837 ACACCCTGTACACTAAGCTGTTTA 59.654 41.667 0.00 0.00 0.00 2.01
606 610 3.135895 ACACCCTGTACACTAAGCTGTTT 59.864 43.478 0.00 0.00 0.00 2.83
607 611 2.704065 ACACCCTGTACACTAAGCTGTT 59.296 45.455 0.00 0.00 0.00 3.16
608 612 2.299297 GACACCCTGTACACTAAGCTGT 59.701 50.000 0.00 0.00 0.00 4.40
609 613 2.563179 AGACACCCTGTACACTAAGCTG 59.437 50.000 0.00 0.00 0.00 4.24
610 614 2.890814 AGACACCCTGTACACTAAGCT 58.109 47.619 0.00 0.00 0.00 3.74
611 615 5.593502 ACTATAGACACCCTGTACACTAAGC 59.406 44.000 6.78 0.00 0.00 3.09
612 616 6.827251 TGACTATAGACACCCTGTACACTAAG 59.173 42.308 6.78 0.00 0.00 2.18
613 617 6.724351 TGACTATAGACACCCTGTACACTAA 58.276 40.000 6.78 0.00 0.00 2.24
614 618 6.317663 TGACTATAGACACCCTGTACACTA 57.682 41.667 6.78 0.00 0.00 2.74
615 619 5.188988 TGACTATAGACACCCTGTACACT 57.811 43.478 6.78 0.00 0.00 3.55
616 620 5.277876 CGATGACTATAGACACCCTGTACAC 60.278 48.000 6.78 0.00 0.00 2.90
617 621 4.820173 CGATGACTATAGACACCCTGTACA 59.180 45.833 6.78 0.00 0.00 2.90
618 622 4.820716 ACGATGACTATAGACACCCTGTAC 59.179 45.833 6.78 0.00 0.00 2.90
619 623 5.045012 ACGATGACTATAGACACCCTGTA 57.955 43.478 6.78 0.00 0.00 2.74
620 624 3.884091 GACGATGACTATAGACACCCTGT 59.116 47.826 6.78 3.77 0.00 4.00
621 625 4.138290 AGACGATGACTATAGACACCCTG 58.862 47.826 6.78 0.65 0.00 4.45
622 626 4.440826 AGACGATGACTATAGACACCCT 57.559 45.455 6.78 0.00 0.00 4.34
623 627 7.918536 TTATAGACGATGACTATAGACACCC 57.081 40.000 6.78 1.96 35.28 4.61
624 628 9.001542 AGTTTATAGACGATGACTATAGACACC 57.998 37.037 6.78 0.00 38.86 4.16
625 629 9.814507 CAGTTTATAGACGATGACTATAGACAC 57.185 37.037 6.78 1.33 38.86 3.67
626 630 9.774413 TCAGTTTATAGACGATGACTATAGACA 57.226 33.333 6.78 7.10 38.86 3.41
628 632 9.438228 CCTCAGTTTATAGACGATGACTATAGA 57.562 37.037 6.78 0.00 35.28 1.98
629 633 9.221933 ACCTCAGTTTATAGACGATGACTATAG 57.778 37.037 0.00 0.00 35.28 1.31
630 634 9.000486 CACCTCAGTTTATAGACGATGACTATA 58.000 37.037 0.00 0.00 33.43 1.31
631 635 7.502895 ACACCTCAGTTTATAGACGATGACTAT 59.497 37.037 0.00 0.00 35.23 2.12
632 636 6.827251 ACACCTCAGTTTATAGACGATGACTA 59.173 38.462 0.00 0.00 0.00 2.59
633 637 5.652891 ACACCTCAGTTTATAGACGATGACT 59.347 40.000 0.00 0.00 0.00 3.41
634 638 5.892568 ACACCTCAGTTTATAGACGATGAC 58.107 41.667 0.00 0.00 0.00 3.06
635 639 6.330278 CAACACCTCAGTTTATAGACGATGA 58.670 40.000 0.00 0.00 0.00 2.92
636 640 5.520288 CCAACACCTCAGTTTATAGACGATG 59.480 44.000 0.00 0.00 0.00 3.84
637 641 5.395324 CCCAACACCTCAGTTTATAGACGAT 60.395 44.000 0.00 0.00 0.00 3.73
638 642 4.081862 CCCAACACCTCAGTTTATAGACGA 60.082 45.833 0.00 0.00 0.00 4.20
639 643 4.081862 TCCCAACACCTCAGTTTATAGACG 60.082 45.833 0.00 0.00 0.00 4.18
640 644 5.416271 TCCCAACACCTCAGTTTATAGAC 57.584 43.478 0.00 0.00 0.00 2.59
641 645 5.280317 GGTTCCCAACACCTCAGTTTATAGA 60.280 44.000 0.00 0.00 0.00 1.98
642 646 4.941873 GGTTCCCAACACCTCAGTTTATAG 59.058 45.833 0.00 0.00 0.00 1.31
643 647 4.600111 AGGTTCCCAACACCTCAGTTTATA 59.400 41.667 0.00 0.00 41.08 0.98
644 648 3.397955 AGGTTCCCAACACCTCAGTTTAT 59.602 43.478 0.00 0.00 41.08 1.40
645 649 2.781174 AGGTTCCCAACACCTCAGTTTA 59.219 45.455 0.00 0.00 41.08 2.01
646 650 1.569072 AGGTTCCCAACACCTCAGTTT 59.431 47.619 0.00 0.00 41.08 2.66
647 651 1.222567 AGGTTCCCAACACCTCAGTT 58.777 50.000 0.00 0.00 41.08 3.16
648 652 1.697982 GTAGGTTCCCAACACCTCAGT 59.302 52.381 0.00 0.00 44.08 3.41
649 653 1.697432 TGTAGGTTCCCAACACCTCAG 59.303 52.381 0.00 0.00 44.08 3.35
650 654 1.697432 CTGTAGGTTCCCAACACCTCA 59.303 52.381 0.00 0.00 44.08 3.86
651 655 1.975680 TCTGTAGGTTCCCAACACCTC 59.024 52.381 0.00 0.00 44.08 3.85
652 656 2.112279 TCTGTAGGTTCCCAACACCT 57.888 50.000 0.00 0.00 46.95 4.00
653 657 3.518303 ACTATCTGTAGGTTCCCAACACC 59.482 47.826 0.00 0.00 31.96 4.16
654 658 4.820894 ACTATCTGTAGGTTCCCAACAC 57.179 45.455 0.00 0.00 31.96 3.32
667 671 8.414778 GCATTAGTTTAGACACCTACTATCTGT 58.585 37.037 0.00 0.00 0.00 3.41
668 672 8.414003 TGCATTAGTTTAGACACCTACTATCTG 58.586 37.037 0.00 0.00 0.00 2.90
669 673 8.414778 GTGCATTAGTTTAGACACCTACTATCT 58.585 37.037 0.00 0.00 0.00 1.98
670 674 8.195436 TGTGCATTAGTTTAGACACCTACTATC 58.805 37.037 0.00 0.00 0.00 2.08
671 675 8.074613 TGTGCATTAGTTTAGACACCTACTAT 57.925 34.615 0.00 0.00 0.00 2.12
672 676 7.470935 TGTGCATTAGTTTAGACACCTACTA 57.529 36.000 0.00 0.00 0.00 1.82
673 677 6.354794 TGTGCATTAGTTTAGACACCTACT 57.645 37.500 0.00 0.00 0.00 2.57
674 678 6.456988 GCATGTGCATTAGTTTAGACACCTAC 60.457 42.308 0.00 0.00 41.59 3.18
675 679 5.584649 GCATGTGCATTAGTTTAGACACCTA 59.415 40.000 0.00 0.00 41.59 3.08
676 680 4.396166 GCATGTGCATTAGTTTAGACACCT 59.604 41.667 0.00 0.00 41.59 4.00
677 681 4.438744 GGCATGTGCATTAGTTTAGACACC 60.439 45.833 7.36 0.00 44.36 4.16
678 682 4.438744 GGGCATGTGCATTAGTTTAGACAC 60.439 45.833 7.36 0.00 44.36 3.67
679 683 3.694072 GGGCATGTGCATTAGTTTAGACA 59.306 43.478 7.36 0.00 44.36 3.41
680 684 3.947834 AGGGCATGTGCATTAGTTTAGAC 59.052 43.478 7.36 0.00 44.36 2.59
681 685 4.235079 AGGGCATGTGCATTAGTTTAGA 57.765 40.909 7.36 0.00 44.36 2.10
682 686 5.504010 CGTTAGGGCATGTGCATTAGTTTAG 60.504 44.000 7.36 0.00 44.36 1.85
683 687 4.334203 CGTTAGGGCATGTGCATTAGTTTA 59.666 41.667 7.36 0.00 44.36 2.01
684 688 3.128589 CGTTAGGGCATGTGCATTAGTTT 59.871 43.478 7.36 0.00 44.36 2.66
685 689 2.682856 CGTTAGGGCATGTGCATTAGTT 59.317 45.455 7.36 0.00 44.36 2.24
686 690 2.288666 CGTTAGGGCATGTGCATTAGT 58.711 47.619 7.36 0.00 44.36 2.24
687 691 1.603802 CCGTTAGGGCATGTGCATTAG 59.396 52.381 7.36 0.00 44.36 1.73
688 692 1.674359 CCGTTAGGGCATGTGCATTA 58.326 50.000 7.36 0.00 44.36 1.90
689 693 2.492418 CCGTTAGGGCATGTGCATT 58.508 52.632 7.36 0.00 44.36 3.56
690 694 4.240881 CCGTTAGGGCATGTGCAT 57.759 55.556 7.36 0.00 44.36 3.96
700 704 3.821421 AACTGAAGATAGCCCGTTAGG 57.179 47.619 0.00 0.00 39.47 2.69
715 719 1.752198 CCTGTCCCACGGAAACTGA 59.248 57.895 0.00 0.00 31.38 3.41
718 722 1.302271 GACCCTGTCCCACGGAAAC 60.302 63.158 0.00 0.00 31.38 2.78
743 747 0.108662 GGTTACGGGTCTAACGGGTG 60.109 60.000 0.00 0.00 35.23 4.61
888 893 1.933181 CCTGCGGTGTATGTGTATGTG 59.067 52.381 0.00 0.00 0.00 3.21
979 984 0.256177 GGTGGGAAAGATGGAGGTCC 59.744 60.000 0.00 0.00 0.00 4.46
991 996 4.090588 GACGGCCATCGGTGGGAA 62.091 66.667 18.38 0.00 46.14 3.97
1088 1093 2.027073 CTGTGCGGCTCGTTGCTAA 61.027 57.895 0.00 0.00 42.39 3.09
1140 1145 3.546714 AACAGCAGTGGGTACGGGC 62.547 63.158 0.00 0.00 33.84 6.13
1663 1668 2.745100 CTCGACCCTCACGTCCGA 60.745 66.667 0.00 0.00 0.00 4.55
1790 1795 0.104855 TATGCTCATGTCCTCGTGCC 59.895 55.000 0.00 0.00 0.00 5.01
1851 1856 2.355244 GCGAGGTCATAGCCGAGC 60.355 66.667 0.00 0.00 0.00 5.03
1938 1943 0.107410 ACTCAAGGTTGCCAACACGA 60.107 50.000 10.18 1.57 0.00 4.35
2034 2039 1.613925 CTCTCGTTGAAGAGGACACCA 59.386 52.381 0.00 0.00 39.33 4.17
2148 2153 0.036765 GTACACAAGCGATGTCCCCA 60.037 55.000 0.00 0.00 41.46 4.96
2265 2270 0.106569 TCGCCATTTGCCATCTCCAT 60.107 50.000 0.00 0.00 36.24 3.41
2334 2339 5.156355 ACATCAAATCAAAGCATCGACAAC 58.844 37.500 0.00 0.00 0.00 3.32
2340 2345 5.898174 TGATGGACATCAAATCAAAGCATC 58.102 37.500 12.27 0.00 44.14 3.91
2352 2357 0.393402 GGCTGCAGTGATGGACATCA 60.393 55.000 16.64 10.75 44.83 3.07
2353 2358 1.434622 CGGCTGCAGTGATGGACATC 61.435 60.000 16.64 5.37 38.29 3.06
2374 2387 4.931601 TCATATCACTATTCATTGAGGCGC 59.068 41.667 0.00 0.00 0.00 6.53
2375 2388 7.425577 TTTCATATCACTATTCATTGAGGCG 57.574 36.000 0.00 0.00 0.00 5.52
2376 2389 9.622004 CAATTTCATATCACTATTCATTGAGGC 57.378 33.333 0.00 0.00 0.00 4.70
2563 2588 5.779241 TTACATCCCCCTTCATCATATCC 57.221 43.478 0.00 0.00 0.00 2.59
2569 2594 4.236527 ACAGTTTACATCCCCCTTCATC 57.763 45.455 0.00 0.00 0.00 2.92
2616 2653 6.895782 ACCAATGAGTCCGAAATCCTAATAA 58.104 36.000 0.00 0.00 0.00 1.40
2743 2782 2.734606 TGACGGTAAATGCGAACTCAAG 59.265 45.455 0.00 0.00 0.00 3.02
2746 2785 5.459110 TTTATGACGGTAAATGCGAACTC 57.541 39.130 0.00 0.00 0.00 3.01
2880 4025 5.011090 TGGACTATCTCCGATGAAGTTTG 57.989 43.478 0.00 0.00 43.03 2.93
2930 4075 8.886816 TGACAAAAATTTAAAACAATGCACAC 57.113 26.923 0.00 0.00 0.00 3.82
3033 4182 9.647797 GAGTTTTTCCACCTTTTTAGAGAAAAA 57.352 29.630 0.00 0.00 41.24 1.94
3071 4220 9.802039 TTAAATGGTTAACTGAGTTCTATGGTT 57.198 29.630 0.00 0.00 0.00 3.67
3098 4247 0.892755 ACTCATGTGCTGCAAATGGG 59.107 50.000 27.15 27.15 35.77 4.00
3264 4413 9.878599 ATCGTAACTTTATATATGTTGCTTTGC 57.121 29.630 10.22 0.00 0.00 3.68


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

AutoCloner maintained by Alex Coulton.