Multiple sequence alignment - TraesCS7B01G026500

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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 TraesCS7B01G026500 chr7B 100.000 4452 0 0 1 4452 25633264 25628813 0.000000e+00 8222.0
1 TraesCS7B01G026500 chr7B 83.145 2836 389 52 959 3753 25655779 25652992 0.000000e+00 2507.0
2 TraesCS7B01G026500 chr7B 85.612 1536 197 13 2053 3583 25887466 25888982 0.000000e+00 1591.0
3 TraesCS7B01G026500 chr7B 88.397 655 76 0 2818 3472 25663476 25662822 0.000000e+00 789.0
4 TraesCS7B01G026500 chr7B 85.135 740 104 6 2053 2788 25664207 25663470 0.000000e+00 752.0
5 TraesCS7B01G026500 chr7B 91.714 531 36 8 1 528 14207973 14208498 0.000000e+00 730.0
6 TraesCS7B01G026500 chr7B 90.395 531 44 7 1 528 14169876 14170402 0.000000e+00 691.0
7 TraesCS7B01G026500 chr7B 90.395 531 42 5 1 528 642534512 642533988 0.000000e+00 689.0
8 TraesCS7B01G026500 chr7B 89.474 532 50 6 1 528 668450820 668450291 0.000000e+00 667.0
9 TraesCS7B01G026500 chr7B 85.034 147 19 3 4302 4447 25890152 25890296 3.590000e-31 147.0
10 TraesCS7B01G026500 chr7B 100.000 44 0 0 650 693 25632573 25632530 1.030000e-11 82.4
11 TraesCS7B01G026500 chr7B 100.000 44 0 0 692 735 25632615 25632572 1.030000e-11 82.4
12 TraesCS7B01G026500 chr7D 95.646 3767 122 19 716 4452 78211392 78207638 0.000000e+00 6010.0
13 TraesCS7B01G026500 chr7D 83.531 2781 374 48 1013 3753 78302582 78299846 0.000000e+00 2521.0
14 TraesCS7B01G026500 chr7D 85.863 1542 197 13 2053 3583 78308160 78306629 0.000000e+00 1620.0
15 TraesCS7B01G026500 chr7A 94.507 3623 161 17 865 4452 81642445 81638826 0.000000e+00 5553.0
16 TraesCS7B01G026500 chr7A 84.065 2780 365 47 1153 3889 81769731 81766987 0.000000e+00 2608.0
17 TraesCS7B01G026500 chr7A 86.838 1436 172 13 2053 3475 81777036 81775605 0.000000e+00 1589.0
18 TraesCS7B01G026500 chr5B 90.772 531 43 6 1 528 645045985 645046512 0.000000e+00 704.0
19 TraesCS7B01G026500 chr6B 90.075 534 47 6 1 531 124562362 124561832 0.000000e+00 688.0
20 TraesCS7B01G026500 chr6B 90.019 531 48 5 1 528 450911564 450912092 0.000000e+00 682.0
21 TraesCS7B01G026500 chr3B 89.454 531 52 4 1 528 564316468 564316997 0.000000e+00 667.0
22 TraesCS7B01G026500 chr3B 89.031 547 49 10 1 539 728998195 728997652 0.000000e+00 667.0
23 TraesCS7B01G026500 chr1D 87.097 62 8 0 716 777 458161708 458161647 2.220000e-08 71.3
24 TraesCS7B01G026500 chr1D 87.097 62 8 0 716 777 458230993 458230932 2.220000e-08 71.3
25 TraesCS7B01G026500 chr1D 93.182 44 3 0 736 779 467027727 467027684 1.030000e-06 65.8
26 TraesCS7B01G026500 chr5A 100.000 36 0 0 538 573 83028374 83028409 2.870000e-07 67.6
27 TraesCS7B01G026500 chr5D 86.885 61 5 2 716 774 520612424 520612365 1.030000e-06 65.8
28 TraesCS7B01G026500 chr1B 97.368 38 1 0 739 776 643557049 643557086 1.030000e-06 65.8
29 TraesCS7B01G026500 chr1B 100.000 29 0 0 748 776 643459589 643459617 2.000000e-03 54.7
30 TraesCS7B01G026500 chr2A 100.000 29 0 0 749 777 590968023 590968051 2.000000e-03 54.7


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 TraesCS7B01G026500 chr7B 25628813 25633264 4451 True 2795.6 8222 100.000 1 4452 3 chr7B.!!$R4 4451
1 TraesCS7B01G026500 chr7B 25652992 25655779 2787 True 2507.0 2507 83.145 959 3753 1 chr7B.!!$R1 2794
2 TraesCS7B01G026500 chr7B 25887466 25890296 2830 False 869.0 1591 85.323 2053 4447 2 chr7B.!!$F3 2394
3 TraesCS7B01G026500 chr7B 25662822 25664207 1385 True 770.5 789 86.766 2053 3472 2 chr7B.!!$R5 1419
4 TraesCS7B01G026500 chr7B 14207973 14208498 525 False 730.0 730 91.714 1 528 1 chr7B.!!$F2 527
5 TraesCS7B01G026500 chr7B 14169876 14170402 526 False 691.0 691 90.395 1 528 1 chr7B.!!$F1 527
6 TraesCS7B01G026500 chr7B 642533988 642534512 524 True 689.0 689 90.395 1 528 1 chr7B.!!$R2 527
7 TraesCS7B01G026500 chr7B 668450291 668450820 529 True 667.0 667 89.474 1 528 1 chr7B.!!$R3 527
8 TraesCS7B01G026500 chr7D 78207638 78211392 3754 True 6010.0 6010 95.646 716 4452 1 chr7D.!!$R1 3736
9 TraesCS7B01G026500 chr7D 78299846 78302582 2736 True 2521.0 2521 83.531 1013 3753 1 chr7D.!!$R2 2740
10 TraesCS7B01G026500 chr7D 78306629 78308160 1531 True 1620.0 1620 85.863 2053 3583 1 chr7D.!!$R3 1530
11 TraesCS7B01G026500 chr7A 81638826 81642445 3619 True 5553.0 5553 94.507 865 4452 1 chr7A.!!$R1 3587
12 TraesCS7B01G026500 chr7A 81766987 81769731 2744 True 2608.0 2608 84.065 1153 3889 1 chr7A.!!$R2 2736
13 TraesCS7B01G026500 chr7A 81775605 81777036 1431 True 1589.0 1589 86.838 2053 3475 1 chr7A.!!$R3 1422
14 TraesCS7B01G026500 chr5B 645045985 645046512 527 False 704.0 704 90.772 1 528 1 chr5B.!!$F1 527
15 TraesCS7B01G026500 chr6B 124561832 124562362 530 True 688.0 688 90.075 1 531 1 chr6B.!!$R1 530
16 TraesCS7B01G026500 chr6B 450911564 450912092 528 False 682.0 682 90.019 1 528 1 chr6B.!!$F1 527
17 TraesCS7B01G026500 chr3B 564316468 564316997 529 False 667.0 667 89.454 1 528 1 chr3B.!!$F1 527
18 TraesCS7B01G026500 chr3B 728997652 728998195 543 True 667.0 667 89.031 1 539 1 chr3B.!!$R1 538

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
573 581 0.038343 ATTGCATGCACGTGAAACCC 60.038 50.0 22.58 0.69 0.00 4.11 F
576 584 0.038343 GCATGCACGTGAAACCCAAT 60.038 50.0 22.23 0.00 0.00 3.16 F
703 711 0.179029 CCCGCCCGATGGTATTTTCT 60.179 55.0 0.00 0.00 0.00 2.52 F
965 984 0.321919 CACATGGCTGTAGCACTGGT 60.322 55.0 6.18 0.00 44.36 4.00 F
2708 2746 0.251354 TGTGATCCAAGGAGAGCAGC 59.749 55.0 0.00 0.00 31.73 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2331 2368 0.036105 CTGCATGTGTGGGCTAGTGA 60.036 55.000 0.0 0.0 0.00 3.41 R
2479 2516 8.748412 TCTCCCATTTATAAACAATCCAACAAG 58.252 33.333 0.0 0.0 0.00 3.16 R
2602 2639 2.744741 GCACCACTTCCTAGCTCTTTTC 59.255 50.000 0.0 0.0 0.00 2.29 R
2956 2997 1.609932 GCTTGACATCACAATGCACG 58.390 50.000 0.0 0.0 36.26 5.34 R
4017 4860 1.584724 GAGGGGGATGAACCAGAGAA 58.415 55.000 0.0 0.0 41.20 2.87 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
86 87 3.435186 GCCCTTCGACTTGCTGCC 61.435 66.667 0.00 0.00 0.00 4.85
112 116 0.625849 GGAGAAGAGCCCCATTTGGA 59.374 55.000 0.00 0.00 37.39 3.53
308 315 4.402528 CGGGTGGTTGGGCGATCA 62.403 66.667 0.00 0.00 0.00 2.92
533 541 3.119849 CCCGTTGGAGTTGCTCTTATTTG 60.120 47.826 0.00 0.00 0.00 2.32
536 544 4.229876 GTTGGAGTTGCTCTTATTTGTGC 58.770 43.478 0.00 0.00 0.00 4.57
537 545 3.485394 TGGAGTTGCTCTTATTTGTGCA 58.515 40.909 0.00 0.00 35.11 4.57
538 546 4.081406 TGGAGTTGCTCTTATTTGTGCAT 58.919 39.130 0.00 0.00 36.53 3.96
539 547 4.156556 TGGAGTTGCTCTTATTTGTGCATC 59.843 41.667 0.00 0.00 36.53 3.91
540 548 4.156556 GGAGTTGCTCTTATTTGTGCATCA 59.843 41.667 0.00 0.00 36.53 3.07
541 549 5.163581 GGAGTTGCTCTTATTTGTGCATCAT 60.164 40.000 0.00 0.00 36.53 2.45
542 550 5.888105 AGTTGCTCTTATTTGTGCATCATC 58.112 37.500 0.00 0.00 36.53 2.92
543 551 5.416639 AGTTGCTCTTATTTGTGCATCATCA 59.583 36.000 0.00 0.00 36.53 3.07
544 552 5.900865 TGCTCTTATTTGTGCATCATCAA 57.099 34.783 0.00 0.00 32.50 2.57
545 553 6.270156 TGCTCTTATTTGTGCATCATCAAA 57.730 33.333 3.05 3.05 37.82 2.69
546 554 6.869695 TGCTCTTATTTGTGCATCATCAAAT 58.130 32.000 14.97 14.97 43.58 2.32
547 555 6.976349 TGCTCTTATTTGTGCATCATCAAATC 59.024 34.615 14.25 3.74 41.40 2.17
548 556 6.420008 GCTCTTATTTGTGCATCATCAAATCC 59.580 38.462 14.25 0.40 41.40 3.01
549 557 7.407393 TCTTATTTGTGCATCATCAAATCCA 57.593 32.000 14.25 4.87 41.40 3.41
550 558 8.014070 TCTTATTTGTGCATCATCAAATCCAT 57.986 30.769 14.25 0.00 41.40 3.41
551 559 9.134055 TCTTATTTGTGCATCATCAAATCCATA 57.866 29.630 14.25 0.00 41.40 2.74
552 560 9.923143 CTTATTTGTGCATCATCAAATCCATAT 57.077 29.630 14.25 0.00 41.40 1.78
557 565 9.699703 TTGTGCATCATCAAATCCATATTATTG 57.300 29.630 0.00 0.00 0.00 1.90
558 566 7.815549 TGTGCATCATCAAATCCATATTATTGC 59.184 33.333 0.00 0.00 0.00 3.56
559 567 7.815549 GTGCATCATCAAATCCATATTATTGCA 59.184 33.333 0.00 0.00 0.00 4.08
560 568 8.536175 TGCATCATCAAATCCATATTATTGCAT 58.464 29.630 0.00 0.00 0.00 3.96
561 569 8.817100 GCATCATCAAATCCATATTATTGCATG 58.183 33.333 0.00 0.00 0.00 4.06
562 570 8.817100 CATCATCAAATCCATATTATTGCATGC 58.183 33.333 11.82 11.82 0.00 4.06
563 571 7.897864 TCATCAAATCCATATTATTGCATGCA 58.102 30.769 18.46 18.46 0.00 3.96
564 572 7.815549 TCATCAAATCCATATTATTGCATGCAC 59.184 33.333 22.58 0.00 0.00 4.57
565 573 6.151004 TCAAATCCATATTATTGCATGCACG 58.849 36.000 22.58 2.87 0.00 5.34
566 574 5.710513 AATCCATATTATTGCATGCACGT 57.289 34.783 22.58 14.89 0.00 4.49
567 575 4.486574 TCCATATTATTGCATGCACGTG 57.513 40.909 22.58 12.28 0.00 4.49
568 576 4.133078 TCCATATTATTGCATGCACGTGA 58.867 39.130 22.58 9.58 0.00 4.35
569 577 4.578105 TCCATATTATTGCATGCACGTGAA 59.422 37.500 22.58 10.11 0.00 3.18
570 578 5.067023 TCCATATTATTGCATGCACGTGAAA 59.933 36.000 22.58 10.59 0.00 2.69
571 579 5.173673 CCATATTATTGCATGCACGTGAAAC 59.826 40.000 22.58 6.33 0.00 2.78
572 580 2.627863 TATTGCATGCACGTGAAACC 57.372 45.000 22.58 4.65 0.00 3.27
573 581 0.038343 ATTGCATGCACGTGAAACCC 60.038 50.000 22.58 0.69 0.00 4.11
574 582 1.387295 TTGCATGCACGTGAAACCCA 61.387 50.000 22.58 7.59 0.00 4.51
575 583 1.361993 GCATGCACGTGAAACCCAA 59.638 52.632 22.23 0.00 0.00 4.12
576 584 0.038343 GCATGCACGTGAAACCCAAT 60.038 50.000 22.23 0.00 0.00 3.16
577 585 1.981254 CATGCACGTGAAACCCAATC 58.019 50.000 22.23 0.00 0.00 2.67
578 586 1.541147 CATGCACGTGAAACCCAATCT 59.459 47.619 22.23 0.00 0.00 2.40
579 587 2.552599 TGCACGTGAAACCCAATCTA 57.447 45.000 22.23 0.00 0.00 1.98
580 588 2.852449 TGCACGTGAAACCCAATCTAA 58.148 42.857 22.23 0.00 0.00 2.10
581 589 3.215151 TGCACGTGAAACCCAATCTAAA 58.785 40.909 22.23 0.00 0.00 1.85
582 590 3.632604 TGCACGTGAAACCCAATCTAAAA 59.367 39.130 22.23 0.00 0.00 1.52
583 591 3.978855 GCACGTGAAACCCAATCTAAAAC 59.021 43.478 22.23 0.00 0.00 2.43
584 592 4.261447 GCACGTGAAACCCAATCTAAAACT 60.261 41.667 22.23 0.00 0.00 2.66
585 593 5.212194 CACGTGAAACCCAATCTAAAACTG 58.788 41.667 10.90 0.00 0.00 3.16
586 594 5.008217 CACGTGAAACCCAATCTAAAACTGA 59.992 40.000 10.90 0.00 0.00 3.41
587 595 5.591067 ACGTGAAACCCAATCTAAAACTGAA 59.409 36.000 0.00 0.00 0.00 3.02
588 596 5.912955 CGTGAAACCCAATCTAAAACTGAAC 59.087 40.000 0.00 0.00 0.00 3.18
589 597 6.213677 GTGAAACCCAATCTAAAACTGAACC 58.786 40.000 0.00 0.00 0.00 3.62
590 598 5.303333 TGAAACCCAATCTAAAACTGAACCC 59.697 40.000 0.00 0.00 0.00 4.11
591 599 4.463050 ACCCAATCTAAAACTGAACCCA 57.537 40.909 0.00 0.00 0.00 4.51
592 600 5.010708 ACCCAATCTAAAACTGAACCCAT 57.989 39.130 0.00 0.00 0.00 4.00
593 601 5.016831 ACCCAATCTAAAACTGAACCCATC 58.983 41.667 0.00 0.00 0.00 3.51
594 602 5.222337 ACCCAATCTAAAACTGAACCCATCT 60.222 40.000 0.00 0.00 0.00 2.90
595 603 5.126061 CCCAATCTAAAACTGAACCCATCTG 59.874 44.000 0.00 0.00 0.00 2.90
596 604 5.126061 CCAATCTAAAACTGAACCCATCTGG 59.874 44.000 0.00 0.00 41.37 3.86
597 605 3.686016 TCTAAAACTGAACCCATCTGGC 58.314 45.455 0.00 0.00 37.83 4.85
598 606 2.683211 AAAACTGAACCCATCTGGCT 57.317 45.000 0.00 0.00 37.83 4.75
599 607 2.206576 AAACTGAACCCATCTGGCTC 57.793 50.000 0.00 0.00 37.83 4.70
600 608 0.329596 AACTGAACCCATCTGGCTCC 59.670 55.000 0.00 0.00 37.83 4.70
601 609 1.153289 CTGAACCCATCTGGCTCCG 60.153 63.158 0.00 0.00 37.83 4.63
602 610 2.514824 GAACCCATCTGGCTCCGC 60.515 66.667 0.00 0.00 37.83 5.54
613 621 4.760047 GCTCCGCCGTGTCCATGT 62.760 66.667 0.00 0.00 0.00 3.21
614 622 2.509336 CTCCGCCGTGTCCATGTC 60.509 66.667 0.00 0.00 0.00 3.06
615 623 2.994995 TCCGCCGTGTCCATGTCT 60.995 61.111 0.00 0.00 0.00 3.41
616 624 2.815211 CCGCCGTGTCCATGTCTG 60.815 66.667 0.00 0.00 0.00 3.51
617 625 2.815211 CGCCGTGTCCATGTCTGG 60.815 66.667 0.00 0.00 44.64 3.86
618 626 3.127533 GCCGTGTCCATGTCTGGC 61.128 66.667 0.00 0.00 42.80 4.85
619 627 2.815211 CCGTGTCCATGTCTGGCG 60.815 66.667 0.00 0.00 42.80 5.69
620 628 2.261361 CGTGTCCATGTCTGGCGA 59.739 61.111 0.00 0.00 42.80 5.54
621 629 1.153568 CGTGTCCATGTCTGGCGAT 60.154 57.895 0.00 0.00 42.80 4.58
622 630 0.740868 CGTGTCCATGTCTGGCGATT 60.741 55.000 0.00 0.00 42.80 3.34
623 631 0.729116 GTGTCCATGTCTGGCGATTG 59.271 55.000 0.00 0.00 42.80 2.67
624 632 0.392863 TGTCCATGTCTGGCGATTGG 60.393 55.000 0.00 0.00 42.80 3.16
625 633 0.392998 GTCCATGTCTGGCGATTGGT 60.393 55.000 0.00 0.00 42.80 3.67
626 634 0.327924 TCCATGTCTGGCGATTGGTT 59.672 50.000 0.00 0.00 42.80 3.67
627 635 0.452987 CCATGTCTGGCGATTGGTTG 59.547 55.000 0.00 0.00 35.23 3.77
628 636 0.179156 CATGTCTGGCGATTGGTTGC 60.179 55.000 0.00 0.00 0.00 4.17
629 637 1.647545 ATGTCTGGCGATTGGTTGCG 61.648 55.000 0.00 0.00 35.44 4.85
657 665 5.920193 CCAAATGTTGGTCTGATGGTATT 57.080 39.130 0.00 0.00 45.93 1.89
658 666 6.284891 CCAAATGTTGGTCTGATGGTATTT 57.715 37.500 0.00 0.00 45.93 1.40
659 667 6.700352 CCAAATGTTGGTCTGATGGTATTTT 58.300 36.000 0.00 0.00 45.93 1.82
660 668 6.813152 CCAAATGTTGGTCTGATGGTATTTTC 59.187 38.462 0.00 0.00 45.93 2.29
661 669 7.309990 CCAAATGTTGGTCTGATGGTATTTTCT 60.310 37.037 0.00 0.00 45.93 2.52
662 670 7.396540 AATGTTGGTCTGATGGTATTTTCTC 57.603 36.000 0.00 0.00 0.00 2.87
663 671 6.126863 TGTTGGTCTGATGGTATTTTCTCT 57.873 37.500 0.00 0.00 0.00 3.10
664 672 6.542821 TGTTGGTCTGATGGTATTTTCTCTT 58.457 36.000 0.00 0.00 0.00 2.85
665 673 6.655003 TGTTGGTCTGATGGTATTTTCTCTTC 59.345 38.462 0.00 0.00 0.00 2.87
666 674 6.627087 TGGTCTGATGGTATTTTCTCTTCT 57.373 37.500 0.00 0.00 0.00 2.85
667 675 6.409704 TGGTCTGATGGTATTTTCTCTTCTG 58.590 40.000 0.00 0.00 0.00 3.02
668 676 6.213397 TGGTCTGATGGTATTTTCTCTTCTGA 59.787 38.462 0.00 0.00 0.00 3.27
669 677 7.106239 GGTCTGATGGTATTTTCTCTTCTGAA 58.894 38.462 0.00 0.00 0.00 3.02
670 678 7.065204 GGTCTGATGGTATTTTCTCTTCTGAAC 59.935 40.741 0.00 0.00 0.00 3.18
671 679 7.065204 GTCTGATGGTATTTTCTCTTCTGAACC 59.935 40.741 0.00 0.00 0.00 3.62
672 680 5.874810 TGATGGTATTTTCTCTTCTGAACCG 59.125 40.000 0.00 0.00 0.00 4.44
673 681 5.223449 TGGTATTTTCTCTTCTGAACCGT 57.777 39.130 0.00 0.00 0.00 4.83
674 682 4.994852 TGGTATTTTCTCTTCTGAACCGTG 59.005 41.667 0.00 0.00 0.00 4.94
675 683 5.221561 TGGTATTTTCTCTTCTGAACCGTGA 60.222 40.000 0.00 0.00 0.00 4.35
676 684 5.120363 GGTATTTTCTCTTCTGAACCGTGAC 59.880 44.000 0.00 0.00 0.00 3.67
677 685 2.814280 TTCTCTTCTGAACCGTGACC 57.186 50.000 0.00 0.00 0.00 4.02
678 686 0.596577 TCTCTTCTGAACCGTGACCG 59.403 55.000 0.00 0.00 0.00 4.79
697 705 3.857038 GAAGCCCGCCCGATGGTA 61.857 66.667 0.00 0.00 0.00 3.25
698 706 3.168528 AAGCCCGCCCGATGGTAT 61.169 61.111 0.00 0.00 0.00 2.73
699 707 2.676163 GAAGCCCGCCCGATGGTATT 62.676 60.000 0.00 0.00 0.00 1.89
700 708 2.203294 GCCCGCCCGATGGTATTT 60.203 61.111 0.00 0.00 0.00 1.40
701 709 1.826487 GCCCGCCCGATGGTATTTT 60.826 57.895 0.00 0.00 0.00 1.82
702 710 1.792118 GCCCGCCCGATGGTATTTTC 61.792 60.000 0.00 0.00 0.00 2.29
703 711 0.179029 CCCGCCCGATGGTATTTTCT 60.179 55.000 0.00 0.00 0.00 2.52
704 712 1.226746 CCGCCCGATGGTATTTTCTC 58.773 55.000 0.00 0.00 0.00 2.87
705 713 1.202651 CCGCCCGATGGTATTTTCTCT 60.203 52.381 0.00 0.00 0.00 3.10
706 714 2.561569 CGCCCGATGGTATTTTCTCTT 58.438 47.619 0.00 0.00 0.00 2.85
707 715 2.544267 CGCCCGATGGTATTTTCTCTTC 59.456 50.000 0.00 0.00 0.00 2.87
708 716 3.741388 CGCCCGATGGTATTTTCTCTTCT 60.741 47.826 0.00 0.00 0.00 2.85
709 717 3.561725 GCCCGATGGTATTTTCTCTTCTG 59.438 47.826 0.00 0.00 0.00 3.02
710 718 4.683400 GCCCGATGGTATTTTCTCTTCTGA 60.683 45.833 0.00 0.00 0.00 3.27
711 719 5.428253 CCCGATGGTATTTTCTCTTCTGAA 58.572 41.667 0.00 0.00 0.00 3.02
712 720 5.294552 CCCGATGGTATTTTCTCTTCTGAAC 59.705 44.000 0.00 0.00 0.00 3.18
713 721 5.294552 CCGATGGTATTTTCTCTTCTGAACC 59.705 44.000 0.00 0.00 0.00 3.62
714 722 5.005779 CGATGGTATTTTCTCTTCTGAACCG 59.994 44.000 0.00 0.00 0.00 4.44
769 777 0.837272 ATGGGGTCCGGTTGTAGATG 59.163 55.000 0.00 0.00 0.00 2.90
786 795 2.975489 AGATGCTCTAACCATTCCGGAT 59.025 45.455 4.15 0.00 38.63 4.18
790 799 2.289506 GCTCTAACCATTCCGGATACCC 60.290 54.545 4.15 0.00 38.63 3.69
834 853 3.769844 TGAAGTCCAGTCCCTCTCATAAC 59.230 47.826 0.00 0.00 0.00 1.89
844 863 4.401837 GTCCCTCTCATAACTCGTAACCTT 59.598 45.833 0.00 0.00 0.00 3.50
965 984 0.321919 CACATGGCTGTAGCACTGGT 60.322 55.000 6.18 0.00 44.36 4.00
1004 1028 2.980541 CCAAGATGGTTGCCATGGT 58.019 52.632 14.67 0.00 45.26 3.55
1083 1110 0.543277 TTGCTCTCGCCAAGGATCAT 59.457 50.000 0.00 0.00 34.43 2.45
1150 1180 1.239296 CGAGGACGACACCACTACCA 61.239 60.000 0.00 0.00 42.66 3.25
1151 1181 0.963962 GAGGACGACACCACTACCAA 59.036 55.000 0.00 0.00 0.00 3.67
1243 1279 1.825474 TCGTCTTCTCCATCTGGTTCC 59.175 52.381 0.00 0.00 36.34 3.62
1430 1466 3.184683 GCTTCTCGACAGCGGCAG 61.185 66.667 1.45 0.00 38.28 4.85
1484 1520 0.750249 TGGACAAGCTTCGACTCACA 59.250 50.000 0.00 0.00 0.00 3.58
1767 1803 6.363357 GTGACAACTTTACATTTGATGCTTCC 59.637 38.462 0.00 0.00 0.00 3.46
1808 1844 3.251484 TGAGGAGGTTGACTCTGGATTT 58.749 45.455 0.00 0.00 45.83 2.17
1871 1907 1.736032 CGATTGGTCGGTCTCTTGGAC 60.736 57.143 0.00 0.00 44.00 4.02
1981 2017 3.325425 TGAAGGTTTCGAGGTGGTTGATA 59.675 43.478 0.00 0.00 0.00 2.15
2002 2038 3.435186 GCGACTGGAGCAAAGGGC 61.435 66.667 0.00 0.00 45.30 5.19
2222 2259 2.125912 CGTCAGGGAGAAGGCACG 60.126 66.667 0.00 0.00 0.00 5.34
2326 2363 2.012673 GCTGTCTTCGCCAGAATTGAT 58.987 47.619 0.00 0.00 35.56 2.57
2331 2368 4.761739 TGTCTTCGCCAGAATTGATTTCTT 59.238 37.500 0.00 0.00 42.15 2.52
2479 2516 5.005394 TCGAAGTAACTTTAATCATCGCTGC 59.995 40.000 0.00 0.00 0.00 5.25
2519 2556 3.025322 TGGGAGAGAAGACCAGAGATC 57.975 52.381 0.00 0.00 0.00 2.75
2558 2595 4.065088 TGATAATATCAAGCCAGTTCCGC 58.935 43.478 0.00 0.00 36.11 5.54
2602 2639 1.664151 GAAGGCAACCGATTACTTCCG 59.336 52.381 0.00 0.00 33.29 4.30
2623 2660 2.481289 AAAGAGCTAGGAAGTGGTGC 57.519 50.000 0.00 0.00 0.00 5.01
2708 2746 0.251354 TGTGATCCAAGGAGAGCAGC 59.749 55.000 0.00 0.00 31.73 5.25
2949 2990 1.625315 TCTCCACCATGAGTGTCTTGG 59.375 52.381 11.73 7.18 45.74 3.61
2956 2997 3.118112 ACCATGAGTGTCTTGGATGGATC 60.118 47.826 14.10 0.00 42.46 3.36
3139 3180 4.151121 TGAATCTTCCAATCACTGGCAAA 58.849 39.130 0.00 0.00 45.98 3.68
3177 3218 3.944055 TGGAGTAGTGCTTCTTGAGTC 57.056 47.619 0.00 0.00 0.00 3.36
3190 3231 2.834549 TCTTGAGTCAGTGAAGGGGATC 59.165 50.000 0.00 0.00 0.00 3.36
3490 4281 6.621316 TTACTACTGCTACATCTAGCTGAC 57.379 41.667 12.65 0.00 45.20 3.51
3549 4344 0.106066 TTGCCCTTATCCCTGCCATG 60.106 55.000 0.00 0.00 0.00 3.66
3629 4444 9.831737 CATTTGTCTATCTGTTTGGAAGTTTAG 57.168 33.333 0.00 0.00 0.00 1.85
3665 4481 6.820656 CACATCTATCTACTTCCAGCAGTTTT 59.179 38.462 0.00 0.00 0.00 2.43
3678 4494 5.593909 TCCAGCAGTTTTGAAGAAGAAATCA 59.406 36.000 0.00 0.00 0.00 2.57
3810 4643 8.310382 CCAACAGATTAATGAACCCAATGTAAA 58.690 33.333 0.00 0.00 0.00 2.01
3894 4737 5.616270 TGTTAAACAATCACCAGTGCTAGA 58.384 37.500 0.00 0.00 0.00 2.43
4017 4860 0.834612 CTGCATTGCCCCCAAATCAT 59.165 50.000 6.12 0.00 34.05 2.45
4024 4867 1.342275 TGCCCCCAAATCATTCTCTGG 60.342 52.381 0.00 0.00 0.00 3.86
4028 4874 3.564133 CCCCCAAATCATTCTCTGGTTCA 60.564 47.826 0.00 0.00 0.00 3.18
4226 5072 4.724697 CTGTGCGCGGCGTTGAAG 62.725 66.667 24.46 12.44 0.00 3.02
4238 5084 3.646715 TTGAAGTGGGCCTCCGGG 61.647 66.667 4.53 0.00 35.24 5.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
127 131 2.089116 AACCAAACCCTAGCCACCCC 62.089 60.000 0.00 0.00 0.00 4.95
291 298 3.910914 TTGATCGCCCAACCACCCG 62.911 63.158 0.00 0.00 0.00 5.28
533 541 7.815549 TGCAATAATATGGATTTGATGATGCAC 59.184 33.333 0.00 0.00 29.89 4.57
536 544 8.817100 GCATGCAATAATATGGATTTGATGATG 58.183 33.333 14.21 0.00 0.00 3.07
537 545 8.536175 TGCATGCAATAATATGGATTTGATGAT 58.464 29.630 20.30 0.00 0.00 2.45
538 546 7.815549 GTGCATGCAATAATATGGATTTGATGA 59.184 33.333 24.58 0.00 0.00 2.92
539 547 7.201401 CGTGCATGCAATAATATGGATTTGATG 60.201 37.037 24.58 0.00 0.00 3.07
540 548 6.809689 CGTGCATGCAATAATATGGATTTGAT 59.190 34.615 24.58 0.00 0.00 2.57
541 549 6.151004 CGTGCATGCAATAATATGGATTTGA 58.849 36.000 24.58 0.00 0.00 2.69
542 550 5.921976 ACGTGCATGCAATAATATGGATTTG 59.078 36.000 24.58 0.50 0.00 2.32
543 551 5.921976 CACGTGCATGCAATAATATGGATTT 59.078 36.000 24.58 0.00 0.00 2.17
544 552 5.241285 TCACGTGCATGCAATAATATGGATT 59.759 36.000 24.58 0.00 0.00 3.01
545 553 4.761227 TCACGTGCATGCAATAATATGGAT 59.239 37.500 24.58 0.00 0.00 3.41
546 554 4.133078 TCACGTGCATGCAATAATATGGA 58.867 39.130 24.58 8.77 0.00 3.41
547 555 4.486574 TCACGTGCATGCAATAATATGG 57.513 40.909 24.58 6.49 0.00 2.74
548 556 5.173673 GGTTTCACGTGCATGCAATAATATG 59.826 40.000 24.58 13.91 0.00 1.78
549 557 5.280945 GGTTTCACGTGCATGCAATAATAT 58.719 37.500 24.58 1.12 0.00 1.28
550 558 4.439426 GGGTTTCACGTGCATGCAATAATA 60.439 41.667 24.58 5.41 0.00 0.98
551 559 3.510719 GGTTTCACGTGCATGCAATAAT 58.489 40.909 24.58 5.10 0.00 1.28
552 560 2.352225 GGGTTTCACGTGCATGCAATAA 60.352 45.455 24.58 11.33 0.00 1.40
553 561 1.201181 GGGTTTCACGTGCATGCAATA 59.799 47.619 24.58 5.12 0.00 1.90
554 562 0.038343 GGGTTTCACGTGCATGCAAT 60.038 50.000 24.58 11.30 0.00 3.56
555 563 1.361993 GGGTTTCACGTGCATGCAA 59.638 52.632 24.58 3.23 0.00 4.08
556 564 1.387295 TTGGGTTTCACGTGCATGCA 61.387 50.000 18.46 18.46 0.00 3.96
557 565 0.038343 ATTGGGTTTCACGTGCATGC 60.038 50.000 11.82 11.82 0.00 4.06
558 566 1.541147 AGATTGGGTTTCACGTGCATG 59.459 47.619 11.67 3.82 0.00 4.06
559 567 1.909700 AGATTGGGTTTCACGTGCAT 58.090 45.000 11.67 0.00 0.00 3.96
560 568 2.552599 TAGATTGGGTTTCACGTGCA 57.447 45.000 11.67 0.00 0.00 4.57
561 569 3.907894 TTTAGATTGGGTTTCACGTGC 57.092 42.857 11.67 0.00 0.00 5.34
562 570 5.008217 TCAGTTTTAGATTGGGTTTCACGTG 59.992 40.000 9.94 9.94 0.00 4.49
563 571 5.127491 TCAGTTTTAGATTGGGTTTCACGT 58.873 37.500 0.00 0.00 0.00 4.49
564 572 5.682943 TCAGTTTTAGATTGGGTTTCACG 57.317 39.130 0.00 0.00 0.00 4.35
565 573 6.213677 GGTTCAGTTTTAGATTGGGTTTCAC 58.786 40.000 0.00 0.00 0.00 3.18
566 574 5.303333 GGGTTCAGTTTTAGATTGGGTTTCA 59.697 40.000 0.00 0.00 0.00 2.69
567 575 5.303333 TGGGTTCAGTTTTAGATTGGGTTTC 59.697 40.000 0.00 0.00 0.00 2.78
568 576 5.212745 TGGGTTCAGTTTTAGATTGGGTTT 58.787 37.500 0.00 0.00 0.00 3.27
569 577 4.810345 TGGGTTCAGTTTTAGATTGGGTT 58.190 39.130 0.00 0.00 0.00 4.11
570 578 4.463050 TGGGTTCAGTTTTAGATTGGGT 57.537 40.909 0.00 0.00 0.00 4.51
571 579 5.126061 CAGATGGGTTCAGTTTTAGATTGGG 59.874 44.000 0.00 0.00 0.00 4.12
572 580 5.126061 CCAGATGGGTTCAGTTTTAGATTGG 59.874 44.000 0.00 0.00 0.00 3.16
573 581 5.393461 GCCAGATGGGTTCAGTTTTAGATTG 60.393 44.000 0.12 0.00 39.65 2.67
574 582 4.706962 GCCAGATGGGTTCAGTTTTAGATT 59.293 41.667 0.12 0.00 39.65 2.40
575 583 4.018050 AGCCAGATGGGTTCAGTTTTAGAT 60.018 41.667 0.00 0.00 44.81 1.98
576 584 3.330701 AGCCAGATGGGTTCAGTTTTAGA 59.669 43.478 0.00 0.00 44.81 2.10
577 585 3.690460 AGCCAGATGGGTTCAGTTTTAG 58.310 45.455 0.00 0.00 44.81 1.85
578 586 3.806949 AGCCAGATGGGTTCAGTTTTA 57.193 42.857 0.00 0.00 44.81 1.52
579 587 2.683211 AGCCAGATGGGTTCAGTTTT 57.317 45.000 0.00 0.00 44.81 2.43
597 605 2.509336 GACATGGACACGGCGGAG 60.509 66.667 13.24 5.87 0.00 4.63
598 606 2.994995 AGACATGGACACGGCGGA 60.995 61.111 13.24 0.00 0.00 5.54
599 607 2.815211 CAGACATGGACACGGCGG 60.815 66.667 13.24 2.35 0.00 6.13
609 617 0.179156 GCAACCAATCGCCAGACATG 60.179 55.000 0.00 0.00 0.00 3.21
610 618 1.647545 CGCAACCAATCGCCAGACAT 61.648 55.000 0.00 0.00 0.00 3.06
611 619 2.324330 CGCAACCAATCGCCAGACA 61.324 57.895 0.00 0.00 0.00 3.41
612 620 2.480555 CGCAACCAATCGCCAGAC 59.519 61.111 0.00 0.00 0.00 3.51
613 621 3.430862 GCGCAACCAATCGCCAGA 61.431 61.111 0.30 0.00 45.01 3.86
636 644 7.605449 AGAAAATACCATCAGACCAACATTTG 58.395 34.615 0.00 0.00 0.00 2.32
637 645 7.671398 AGAGAAAATACCATCAGACCAACATTT 59.329 33.333 0.00 0.00 0.00 2.32
638 646 7.177878 AGAGAAAATACCATCAGACCAACATT 58.822 34.615 0.00 0.00 0.00 2.71
639 647 6.725364 AGAGAAAATACCATCAGACCAACAT 58.275 36.000 0.00 0.00 0.00 2.71
640 648 6.126863 AGAGAAAATACCATCAGACCAACA 57.873 37.500 0.00 0.00 0.00 3.33
641 649 6.881602 AGAAGAGAAAATACCATCAGACCAAC 59.118 38.462 0.00 0.00 0.00 3.77
642 650 6.881065 CAGAAGAGAAAATACCATCAGACCAA 59.119 38.462 0.00 0.00 0.00 3.67
643 651 6.213397 TCAGAAGAGAAAATACCATCAGACCA 59.787 38.462 0.00 0.00 0.00 4.02
644 652 6.644347 TCAGAAGAGAAAATACCATCAGACC 58.356 40.000 0.00 0.00 0.00 3.85
645 653 7.065204 GGTTCAGAAGAGAAAATACCATCAGAC 59.935 40.741 0.00 0.00 0.00 3.51
646 654 7.106239 GGTTCAGAAGAGAAAATACCATCAGA 58.894 38.462 0.00 0.00 0.00 3.27
647 655 6.036517 CGGTTCAGAAGAGAAAATACCATCAG 59.963 42.308 0.00 0.00 0.00 2.90
648 656 5.874810 CGGTTCAGAAGAGAAAATACCATCA 59.125 40.000 0.00 0.00 0.00 3.07
649 657 5.875359 ACGGTTCAGAAGAGAAAATACCATC 59.125 40.000 0.00 0.00 0.00 3.51
650 658 5.643777 CACGGTTCAGAAGAGAAAATACCAT 59.356 40.000 0.00 0.00 0.00 3.55
651 659 4.994852 CACGGTTCAGAAGAGAAAATACCA 59.005 41.667 0.00 0.00 0.00 3.25
652 660 5.120363 GTCACGGTTCAGAAGAGAAAATACC 59.880 44.000 0.00 0.00 0.00 2.73
653 661 5.120363 GGTCACGGTTCAGAAGAGAAAATAC 59.880 44.000 0.00 0.00 0.00 1.89
654 662 5.235516 GGTCACGGTTCAGAAGAGAAAATA 58.764 41.667 0.00 0.00 0.00 1.40
655 663 4.065789 GGTCACGGTTCAGAAGAGAAAAT 58.934 43.478 0.00 0.00 0.00 1.82
656 664 3.463944 GGTCACGGTTCAGAAGAGAAAA 58.536 45.455 0.00 0.00 0.00 2.29
657 665 2.545113 CGGTCACGGTTCAGAAGAGAAA 60.545 50.000 0.00 0.00 36.18 2.52
658 666 1.000607 CGGTCACGGTTCAGAAGAGAA 60.001 52.381 0.00 0.00 36.18 2.87
659 667 0.596577 CGGTCACGGTTCAGAAGAGA 59.403 55.000 0.00 0.00 36.18 3.10
660 668 3.108521 CGGTCACGGTTCAGAAGAG 57.891 57.895 0.00 0.00 36.18 2.85
680 688 2.676163 AATACCATCGGGCGGGCTTC 62.676 60.000 0.26 0.00 37.90 3.86
681 689 2.279037 AAATACCATCGGGCGGGCTT 62.279 55.000 0.26 0.00 37.90 4.35
682 690 2.279037 AAAATACCATCGGGCGGGCT 62.279 55.000 0.26 0.00 37.90 5.19
683 691 1.792118 GAAAATACCATCGGGCGGGC 61.792 60.000 0.00 0.00 37.90 6.13
684 692 0.179029 AGAAAATACCATCGGGCGGG 60.179 55.000 0.00 0.00 37.90 6.13
685 693 1.202651 AGAGAAAATACCATCGGGCGG 60.203 52.381 0.00 0.00 37.90 6.13
686 694 2.240493 AGAGAAAATACCATCGGGCG 57.760 50.000 0.00 0.00 37.90 6.13
687 695 3.561725 CAGAAGAGAAAATACCATCGGGC 59.438 47.826 0.00 0.00 37.90 6.13
688 696 5.023533 TCAGAAGAGAAAATACCATCGGG 57.976 43.478 0.00 0.00 41.29 5.14
689 697 5.294552 GGTTCAGAAGAGAAAATACCATCGG 59.705 44.000 0.00 0.00 0.00 4.18
690 698 5.005779 CGGTTCAGAAGAGAAAATACCATCG 59.994 44.000 0.00 0.00 0.00 3.84
691 699 5.875359 ACGGTTCAGAAGAGAAAATACCATC 59.125 40.000 0.00 0.00 0.00 3.51
692 700 5.643777 CACGGTTCAGAAGAGAAAATACCAT 59.356 40.000 0.00 0.00 0.00 3.55
693 701 4.994852 CACGGTTCAGAAGAGAAAATACCA 59.005 41.667 0.00 0.00 0.00 3.25
694 702 5.120363 GTCACGGTTCAGAAGAGAAAATACC 59.880 44.000 0.00 0.00 0.00 2.73
695 703 5.120363 GGTCACGGTTCAGAAGAGAAAATAC 59.880 44.000 0.00 0.00 0.00 1.89
696 704 5.235516 GGTCACGGTTCAGAAGAGAAAATA 58.764 41.667 0.00 0.00 0.00 1.40
697 705 4.065789 GGTCACGGTTCAGAAGAGAAAAT 58.934 43.478 0.00 0.00 0.00 1.82
698 706 3.463944 GGTCACGGTTCAGAAGAGAAAA 58.536 45.455 0.00 0.00 0.00 2.29
699 707 2.545113 CGGTCACGGTTCAGAAGAGAAA 60.545 50.000 0.00 0.00 36.18 2.52
700 708 1.000607 CGGTCACGGTTCAGAAGAGAA 60.001 52.381 0.00 0.00 36.18 2.87
701 709 0.596577 CGGTCACGGTTCAGAAGAGA 59.403 55.000 0.00 0.00 36.18 3.10
702 710 3.108521 CGGTCACGGTTCAGAAGAG 57.891 57.895 0.00 0.00 36.18 2.85
769 777 2.289506 GGGTATCCGGAATGGTTAGAGC 60.290 54.545 9.01 0.00 39.52 4.09
795 804 0.463204 TCAAACCGTGTAACCGTCCA 59.537 50.000 0.00 0.00 0.00 4.02
834 853 5.299782 ACTCTTCCTGCTATAAGGTTACGAG 59.700 44.000 0.00 0.00 38.58 4.18
844 863 6.543735 TGTAGCATCTACTCTTCCTGCTATA 58.456 40.000 5.92 1.19 44.54 1.31
1083 1110 1.206878 AGCTGGTGCCATGAGTATGA 58.793 50.000 0.00 0.00 40.80 2.15
1139 1169 0.181824 GGTGGTGTTGGTAGTGGTGT 59.818 55.000 0.00 0.00 0.00 4.16
1146 1176 0.402504 GGATGGTGGTGGTGTTGGTA 59.597 55.000 0.00 0.00 0.00 3.25
1150 1180 0.827507 GCAAGGATGGTGGTGGTGTT 60.828 55.000 0.00 0.00 0.00 3.32
1151 1181 1.228552 GCAAGGATGGTGGTGGTGT 60.229 57.895 0.00 0.00 0.00 4.16
1430 1466 2.300152 TCTGGATCCACGATGATAAGGC 59.700 50.000 11.44 0.00 0.00 4.35
1484 1520 2.049063 GCAGAAGCGTGTCGGTCT 60.049 61.111 0.00 0.00 36.27 3.85
1808 1844 1.075374 ACAGCCTTAGGTTGCCATCAA 59.925 47.619 15.05 0.00 37.43 2.57
1981 2017 0.886490 CCTTTGCTCCAGTCGCTTGT 60.886 55.000 0.00 0.00 0.00 3.16
2002 2038 0.039978 TTGTTTACATTGGGCGTGCG 60.040 50.000 0.00 0.00 0.00 5.34
2326 2363 3.411446 CATGTGTGGGCTAGTGAAGAAA 58.589 45.455 0.00 0.00 0.00 2.52
2331 2368 0.036105 CTGCATGTGTGGGCTAGTGA 60.036 55.000 0.00 0.00 0.00 3.41
2479 2516 8.748412 TCTCCCATTTATAAACAATCCAACAAG 58.252 33.333 0.00 0.00 0.00 3.16
2558 2595 9.817809 TTCTGTAACTCCTTGTAGCTAAATATG 57.182 33.333 0.00 0.00 0.00 1.78
2602 2639 2.744741 GCACCACTTCCTAGCTCTTTTC 59.255 50.000 0.00 0.00 0.00 2.29
2623 2660 5.163258 ACTCCCTTATAAACTGCTCCTGATG 60.163 44.000 0.00 0.00 0.00 3.07
2708 2746 4.950050 ACACTTAACTCAGACCTGAACTG 58.050 43.478 1.08 0.00 39.39 3.16
2949 2990 2.615447 ACATCACAATGCACGATCCATC 59.385 45.455 0.00 0.00 36.26 3.51
2956 2997 1.609932 GCTTGACATCACAATGCACG 58.390 50.000 0.00 0.00 36.26 5.34
3145 3186 3.797256 GCACTACTCCATAGCTGTAAACG 59.203 47.826 0.00 0.00 33.73 3.60
3177 3218 1.562672 AACCCGGATCCCCTTCACTG 61.563 60.000 0.73 0.00 0.00 3.66
3810 4643 8.135382 AGTTTGTATAGTGGTGAGTATTCTGT 57.865 34.615 0.00 0.00 0.00 3.41
4017 4860 1.584724 GAGGGGGATGAACCAGAGAA 58.415 55.000 0.00 0.00 41.20 2.87
4024 4867 3.231298 CGGAGGAGGGGGATGAAC 58.769 66.667 0.00 0.00 0.00 3.18
4209 5055 4.724697 CTTCAACGCCGCGCACAG 62.725 66.667 13.88 0.00 0.00 3.66


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

AutoCloner maintained by Alex Coulton.