Multiple sequence alignment - TraesCS4A01G074000

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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 TraesCS4A01G074000 chr4A 100.000 2669 0 0 1 2669 73176186 73178854 0.000000e+00 4929.0
1 TraesCS4A01G074000 chr4A 98.594 498 7 0 1 498 596856297 596855800 0.000000e+00 881.0
2 TraesCS4A01G074000 chr4A 98.016 504 9 1 1 503 570825398 570824895 0.000000e+00 874.0
3 TraesCS4A01G074000 chr4A 89.474 114 12 0 501 614 574929808 574929695 7.700000e-31 145.0
4 TraesCS4A01G074000 chr4D 91.954 1044 55 12 655 1672 391471740 391472780 0.000000e+00 1435.0
5 TraesCS4A01G074000 chr4B 92.668 982 50 9 760 1720 481492252 481493232 0.000000e+00 1395.0
6 TraesCS4A01G074000 chr4B 91.176 102 6 2 1777 1876 481493249 481493349 4.630000e-28 135.0
7 TraesCS4A01G074000 chr4B 97.143 70 2 0 1863 1932 481493374 481493443 4.670000e-23 119.0
8 TraesCS4A01G074000 chr6D 94.880 664 30 3 2006 2668 58004506 58005166 0.000000e+00 1035.0
9 TraesCS4A01G074000 chr6D 87.402 127 10 5 499 622 19719401 19719524 9.960000e-30 141.0
10 TraesCS4A01G074000 chr5D 93.824 680 39 2 1990 2669 422764622 422765298 0.000000e+00 1020.0
11 TraesCS4A01G074000 chr5D 91.545 686 49 5 1990 2669 521485348 521486030 0.000000e+00 937.0
12 TraesCS4A01G074000 chr5D 89.516 124 12 1 499 622 482344778 482344656 3.560000e-34 156.0
13 TraesCS4A01G074000 chr1D 93.469 689 42 2 1981 2669 25761639 25760954 0.000000e+00 1020.0
14 TraesCS4A01G074000 chr5A 93.235 680 43 2 1990 2669 655090880 655091556 0.000000e+00 998.0
15 TraesCS4A01G074000 chr5A 98.394 498 8 0 1 498 230053797 230053300 0.000000e+00 876.0
16 TraesCS4A01G074000 chr5A 98.397 499 7 1 1 498 230060572 230060074 0.000000e+00 876.0
17 TraesCS4A01G074000 chr5A 98.207 502 8 1 1 502 535251256 535250756 0.000000e+00 876.0
18 TraesCS4A01G074000 chr7D 93.778 659 38 2 2011 2669 544624392 544623737 0.000000e+00 987.0
19 TraesCS4A01G074000 chr7D 92.647 680 47 2 1990 2669 436462986 436462310 0.000000e+00 976.0
20 TraesCS4A01G074000 chr2D 93.124 669 42 3 2001 2669 619396329 619395665 0.000000e+00 977.0
21 TraesCS4A01G074000 chr3D 91.837 686 45 6 1990 2669 113029135 113028455 0.000000e+00 946.0
22 TraesCS4A01G074000 chr7A 98.594 498 7 0 1 498 728875779 728876276 0.000000e+00 881.0
23 TraesCS4A01G074000 chr6A 98.394 498 8 0 1 498 449296982 449297479 0.000000e+00 876.0
24 TraesCS4A01G074000 chr6A 91.346 104 9 0 519 622 499788087 499788190 2.770000e-30 143.0
25 TraesCS4A01G074000 chr1A 98.394 498 8 0 1 498 296888190 296887693 0.000000e+00 876.0
26 TraesCS4A01G074000 chr1A 98.394 498 8 0 1 498 520070058 520069561 0.000000e+00 876.0
27 TraesCS4A01G074000 chr2B 91.870 123 10 0 499 621 546824931 546824809 3.530000e-39 172.0
28 TraesCS4A01G074000 chr7B 83.486 109 14 3 499 605 637568948 637568842 6.080000e-17 99.0
29 TraesCS4A01G074000 chr7B 80.952 126 19 4 499 622 640269380 640269502 7.870000e-16 95.3
30 TraesCS4A01G074000 chr1B 92.308 65 5 0 541 605 18862030 18861966 2.830000e-15 93.5


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 TraesCS4A01G074000 chr4A 73176186 73178854 2668 False 4929.000000 4929 100.000000 1 2669 1 chr4A.!!$F1 2668
1 TraesCS4A01G074000 chr4A 570824895 570825398 503 True 874.000000 874 98.016000 1 503 1 chr4A.!!$R1 502
2 TraesCS4A01G074000 chr4D 391471740 391472780 1040 False 1435.000000 1435 91.954000 655 1672 1 chr4D.!!$F1 1017
3 TraesCS4A01G074000 chr4B 481492252 481493443 1191 False 549.666667 1395 93.662333 760 1932 3 chr4B.!!$F1 1172
4 TraesCS4A01G074000 chr6D 58004506 58005166 660 False 1035.000000 1035 94.880000 2006 2668 1 chr6D.!!$F2 662
5 TraesCS4A01G074000 chr5D 422764622 422765298 676 False 1020.000000 1020 93.824000 1990 2669 1 chr5D.!!$F1 679
6 TraesCS4A01G074000 chr5D 521485348 521486030 682 False 937.000000 937 91.545000 1990 2669 1 chr5D.!!$F2 679
7 TraesCS4A01G074000 chr1D 25760954 25761639 685 True 1020.000000 1020 93.469000 1981 2669 1 chr1D.!!$R1 688
8 TraesCS4A01G074000 chr5A 655090880 655091556 676 False 998.000000 998 93.235000 1990 2669 1 chr5A.!!$F1 679
9 TraesCS4A01G074000 chr5A 535250756 535251256 500 True 876.000000 876 98.207000 1 502 1 chr5A.!!$R3 501
10 TraesCS4A01G074000 chr7D 544623737 544624392 655 True 987.000000 987 93.778000 2011 2669 1 chr7D.!!$R2 658
11 TraesCS4A01G074000 chr7D 436462310 436462986 676 True 976.000000 976 92.647000 1990 2669 1 chr7D.!!$R1 679
12 TraesCS4A01G074000 chr2D 619395665 619396329 664 True 977.000000 977 93.124000 2001 2669 1 chr2D.!!$R1 668
13 TraesCS4A01G074000 chr3D 113028455 113029135 680 True 946.000000 946 91.837000 1990 2669 1 chr3D.!!$R1 679

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
573 575 0.107831 TAGCTTGTTGGCGGACTGTT 59.892 50.0 0.0 0.0 37.29 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1945 2011 0.027979 CGACGCCACATATTGCCAAG 59.972 55.0 0.0 0.0 0.0 3.61 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
46 47 2.014128 CTCGAAATACGCCAACCCAAT 58.986 47.619 0.00 0.00 42.26 3.16
51 52 4.274950 CGAAATACGCCAACCCAATATCTT 59.725 41.667 0.00 0.00 34.51 2.40
292 293 8.241367 GTGATCCCGTTAATCAAATAACAACTT 58.759 33.333 0.00 0.00 35.89 2.66
346 347 6.586463 TCTTTGATTAACGAGCTAGTCAAGTG 59.414 38.462 0.00 0.00 31.56 3.16
422 423 9.290988 TGTTTCTGGTTAATACAATTCTAGCAA 57.709 29.630 0.00 0.00 0.00 3.91
500 502 4.655963 TCTAGGGCATATTTCCTTCATGC 58.344 43.478 0.00 0.00 43.43 4.06
503 505 2.287788 GGGCATATTTCCTTCATGCACG 60.288 50.000 7.94 0.00 45.45 5.34
504 506 2.618241 GGCATATTTCCTTCATGCACGA 59.382 45.455 7.94 0.00 45.45 4.35
505 507 3.254166 GGCATATTTCCTTCATGCACGAT 59.746 43.478 7.94 0.00 45.45 3.73
506 508 4.261741 GGCATATTTCCTTCATGCACGATT 60.262 41.667 7.94 0.00 45.45 3.34
507 509 4.678287 GCATATTTCCTTCATGCACGATTG 59.322 41.667 0.00 0.00 43.59 2.67
508 510 5.506151 GCATATTTCCTTCATGCACGATTGA 60.506 40.000 0.00 0.00 43.59 2.57
509 511 3.829886 TTTCCTTCATGCACGATTGAC 57.170 42.857 0.00 0.00 0.00 3.18
523 525 3.717830 CGATTGACGTTACCGAAAGTTG 58.282 45.455 0.00 0.00 37.88 3.16
524 526 3.422603 CGATTGACGTTACCGAAAGTTGG 60.423 47.826 0.00 0.00 37.88 3.77
525 527 2.886862 TGACGTTACCGAAAGTTGGA 57.113 45.000 0.00 0.00 37.88 3.53
526 528 3.389925 TGACGTTACCGAAAGTTGGAT 57.610 42.857 0.00 0.00 37.88 3.41
527 529 3.731089 TGACGTTACCGAAAGTTGGATT 58.269 40.909 0.00 0.00 37.88 3.01
528 530 3.495377 TGACGTTACCGAAAGTTGGATTG 59.505 43.478 0.00 0.00 37.88 2.67
529 531 2.809696 ACGTTACCGAAAGTTGGATTGG 59.190 45.455 0.00 0.00 37.88 3.16
530 532 2.413634 CGTTACCGAAAGTTGGATTGGC 60.414 50.000 0.00 0.00 35.63 4.52
531 533 2.554893 GTTACCGAAAGTTGGATTGGCA 59.445 45.455 0.00 0.00 0.00 4.92
532 534 1.923356 ACCGAAAGTTGGATTGGCAT 58.077 45.000 0.00 0.00 0.00 4.40
533 535 2.247358 ACCGAAAGTTGGATTGGCATT 58.753 42.857 0.00 0.00 0.00 3.56
534 536 2.029110 ACCGAAAGTTGGATTGGCATTG 60.029 45.455 0.00 0.00 0.00 2.82
535 537 2.029110 CCGAAAGTTGGATTGGCATTGT 60.029 45.455 0.00 0.00 0.00 2.71
536 538 3.554752 CCGAAAGTTGGATTGGCATTGTT 60.555 43.478 0.00 0.00 0.00 2.83
537 539 3.674753 CGAAAGTTGGATTGGCATTGTTC 59.325 43.478 0.00 0.00 0.00 3.18
538 540 4.559300 CGAAAGTTGGATTGGCATTGTTCT 60.559 41.667 0.00 0.00 0.00 3.01
539 541 4.961438 AAGTTGGATTGGCATTGTTCTT 57.039 36.364 0.00 0.00 0.00 2.52
540 542 6.418057 AAAGTTGGATTGGCATTGTTCTTA 57.582 33.333 0.00 0.00 0.00 2.10
541 543 5.649782 AGTTGGATTGGCATTGTTCTTAG 57.350 39.130 0.00 0.00 0.00 2.18
542 544 4.082026 AGTTGGATTGGCATTGTTCTTAGC 60.082 41.667 0.00 0.00 0.00 3.09
543 545 3.700538 TGGATTGGCATTGTTCTTAGCT 58.299 40.909 0.00 0.00 0.00 3.32
544 546 4.088634 TGGATTGGCATTGTTCTTAGCTT 58.911 39.130 0.00 0.00 0.00 3.74
545 547 4.158394 TGGATTGGCATTGTTCTTAGCTTC 59.842 41.667 0.00 0.00 0.00 3.86
546 548 4.440663 GGATTGGCATTGTTCTTAGCTTCC 60.441 45.833 0.00 0.00 0.00 3.46
547 549 3.439857 TGGCATTGTTCTTAGCTTCCT 57.560 42.857 0.00 0.00 0.00 3.36
548 550 3.084039 TGGCATTGTTCTTAGCTTCCTG 58.916 45.455 0.00 0.00 0.00 3.86
549 551 3.244875 TGGCATTGTTCTTAGCTTCCTGA 60.245 43.478 0.00 0.00 0.00 3.86
550 552 3.127721 GGCATTGTTCTTAGCTTCCTGAC 59.872 47.826 0.00 0.00 0.00 3.51
551 553 3.127721 GCATTGTTCTTAGCTTCCTGACC 59.872 47.826 0.00 0.00 0.00 4.02
552 554 4.326826 CATTGTTCTTAGCTTCCTGACCA 58.673 43.478 0.00 0.00 0.00 4.02
553 555 3.685139 TGTTCTTAGCTTCCTGACCAG 57.315 47.619 0.00 0.00 0.00 4.00
554 556 2.972713 TGTTCTTAGCTTCCTGACCAGT 59.027 45.455 0.00 0.00 0.00 4.00
555 557 4.157246 TGTTCTTAGCTTCCTGACCAGTA 58.843 43.478 0.00 0.00 0.00 2.74
556 558 4.220821 TGTTCTTAGCTTCCTGACCAGTAG 59.779 45.833 0.00 0.00 0.00 2.57
557 559 2.761208 TCTTAGCTTCCTGACCAGTAGC 59.239 50.000 0.00 11.20 35.63 3.58
558 560 2.534042 TAGCTTCCTGACCAGTAGCT 57.466 50.000 20.16 20.16 42.90 3.32
559 561 1.650528 AGCTTCCTGACCAGTAGCTT 58.349 50.000 14.29 4.14 39.77 3.74
560 562 1.277557 AGCTTCCTGACCAGTAGCTTG 59.722 52.381 14.29 0.00 39.77 4.01
561 563 1.002544 GCTTCCTGACCAGTAGCTTGT 59.997 52.381 0.00 0.00 33.84 3.16
562 564 2.551071 GCTTCCTGACCAGTAGCTTGTT 60.551 50.000 0.00 0.00 33.84 2.83
563 565 2.839486 TCCTGACCAGTAGCTTGTTG 57.161 50.000 0.00 0.00 0.00 3.33
564 566 1.347707 TCCTGACCAGTAGCTTGTTGG 59.652 52.381 0.00 0.00 37.98 3.77
565 567 1.160137 CTGACCAGTAGCTTGTTGGC 58.840 55.000 9.90 5.13 35.35 4.52
566 568 0.602638 TGACCAGTAGCTTGTTGGCG 60.603 55.000 9.90 0.00 35.35 5.69
567 569 1.298859 GACCAGTAGCTTGTTGGCGG 61.299 60.000 9.90 0.00 35.35 6.13
568 570 1.003839 CCAGTAGCTTGTTGGCGGA 60.004 57.895 0.00 0.00 37.29 5.54
569 571 1.298859 CCAGTAGCTTGTTGGCGGAC 61.299 60.000 0.00 0.00 37.29 4.79
570 572 0.320771 CAGTAGCTTGTTGGCGGACT 60.321 55.000 0.00 0.00 37.29 3.85
571 573 0.320771 AGTAGCTTGTTGGCGGACTG 60.321 55.000 0.00 0.00 34.00 3.51
572 574 0.602905 GTAGCTTGTTGGCGGACTGT 60.603 55.000 0.00 0.00 37.29 3.55
573 575 0.107831 TAGCTTGTTGGCGGACTGTT 59.892 50.000 0.00 0.00 37.29 3.16
574 576 1.166531 AGCTTGTTGGCGGACTGTTC 61.167 55.000 0.00 0.00 37.29 3.18
575 577 1.569493 CTTGTTGGCGGACTGTTCG 59.431 57.895 3.60 3.60 0.00 3.95
576 578 1.841663 CTTGTTGGCGGACTGTTCGG 61.842 60.000 10.96 0.00 0.00 4.30
581 583 3.774702 GCGGACTGTTCGGCGAAC 61.775 66.667 37.98 37.98 42.26 3.95
582 584 3.467119 CGGACTGTTCGGCGAACG 61.467 66.667 37.75 32.99 44.55 3.95
583 585 3.774702 GGACTGTTCGGCGAACGC 61.775 66.667 37.75 29.95 44.55 4.84
584 586 2.733593 GACTGTTCGGCGAACGCT 60.734 61.111 37.75 28.36 44.55 5.07
585 587 2.279918 ACTGTTCGGCGAACGCTT 60.280 55.556 37.75 25.58 44.55 4.68
586 588 1.828331 GACTGTTCGGCGAACGCTTT 61.828 55.000 37.75 25.42 44.55 3.51
587 589 1.278637 CTGTTCGGCGAACGCTTTT 59.721 52.632 37.75 0.00 44.55 2.27
588 590 0.509499 CTGTTCGGCGAACGCTTTTA 59.491 50.000 37.75 23.42 44.55 1.52
589 591 1.127951 CTGTTCGGCGAACGCTTTTAT 59.872 47.619 37.75 0.00 44.55 1.40
590 592 1.532007 TGTTCGGCGAACGCTTTTATT 59.468 42.857 37.75 0.00 44.55 1.40
591 593 2.735663 TGTTCGGCGAACGCTTTTATTA 59.264 40.909 37.75 20.62 44.55 0.98
592 594 3.186001 TGTTCGGCGAACGCTTTTATTAA 59.814 39.130 37.75 19.96 44.55 1.40
593 595 4.150343 GTTCGGCGAACGCTTTTATTAAA 58.850 39.130 33.45 0.00 43.86 1.52
594 596 4.603231 TCGGCGAACGCTTTTATTAAAT 57.397 36.364 18.14 0.00 43.86 1.40
595 597 5.715429 TCGGCGAACGCTTTTATTAAATA 57.285 34.783 18.14 0.00 43.86 1.40
596 598 6.104439 TCGGCGAACGCTTTTATTAAATAA 57.896 33.333 18.14 0.00 43.86 1.40
597 599 6.541086 TCGGCGAACGCTTTTATTAAATAAA 58.459 32.000 18.14 0.00 43.86 1.40
598 600 6.683708 TCGGCGAACGCTTTTATTAAATAAAG 59.316 34.615 18.14 7.82 43.86 1.85
599 601 6.557171 CGGCGAACGCTTTTATTAAATAAAGC 60.557 38.462 19.77 19.77 41.60 3.51
600 602 6.471198 GGCGAACGCTTTTATTAAATAAAGCT 59.529 34.615 23.74 13.49 41.60 3.74
601 603 7.305247 GGCGAACGCTTTTATTAAATAAAGCTC 60.305 37.037 23.74 17.84 41.60 4.09
602 604 7.428472 GCGAACGCTTTTATTAAATAAAGCTCT 59.572 33.333 23.74 15.71 36.23 4.09
603 605 8.934947 CGAACGCTTTTATTAAATAAAGCTCTC 58.065 33.333 23.74 19.63 36.23 3.20
604 606 9.769093 GAACGCTTTTATTAAATAAAGCTCTCA 57.231 29.630 23.74 0.00 36.23 3.27
605 607 9.774742 AACGCTTTTATTAAATAAAGCTCTCAG 57.225 29.630 23.74 15.53 36.23 3.35
606 608 8.947115 ACGCTTTTATTAAATAAAGCTCTCAGT 58.053 29.630 23.74 15.94 36.23 3.41
607 609 9.214953 CGCTTTTATTAAATAAAGCTCTCAGTG 57.785 33.333 23.74 11.11 36.23 3.66
613 615 5.966742 AAATAAAGCTCTCAGTGTTTCCC 57.033 39.130 0.00 0.00 0.00 3.97
614 616 2.278332 AAAGCTCTCAGTGTTTCCCC 57.722 50.000 0.00 0.00 0.00 4.81
615 617 1.140312 AAGCTCTCAGTGTTTCCCCA 58.860 50.000 0.00 0.00 0.00 4.96
616 618 0.398318 AGCTCTCAGTGTTTCCCCAC 59.602 55.000 0.00 0.00 35.53 4.61
617 619 0.108585 GCTCTCAGTGTTTCCCCACA 59.891 55.000 0.00 0.00 37.82 4.17
618 620 1.476833 GCTCTCAGTGTTTCCCCACAA 60.477 52.381 0.00 0.00 37.82 3.33
619 621 2.930950 CTCTCAGTGTTTCCCCACAAA 58.069 47.619 0.00 0.00 37.82 2.83
620 622 3.287222 CTCTCAGTGTTTCCCCACAAAA 58.713 45.455 0.00 0.00 37.82 2.44
621 623 3.699038 CTCTCAGTGTTTCCCCACAAAAA 59.301 43.478 0.00 0.00 37.82 1.94
622 624 4.285863 TCTCAGTGTTTCCCCACAAAAAT 58.714 39.130 0.00 0.00 37.82 1.82
623 625 4.714308 TCTCAGTGTTTCCCCACAAAAATT 59.286 37.500 0.00 0.00 37.82 1.82
624 626 5.188751 TCTCAGTGTTTCCCCACAAAAATTT 59.811 36.000 0.00 0.00 37.82 1.82
625 627 5.810095 TCAGTGTTTCCCCACAAAAATTTT 58.190 33.333 0.00 0.00 37.82 1.82
626 628 6.241645 TCAGTGTTTCCCCACAAAAATTTTT 58.758 32.000 10.41 10.41 37.82 1.94
627 629 7.394816 TCAGTGTTTCCCCACAAAAATTTTTA 58.605 30.769 15.55 0.00 37.82 1.52
628 630 8.049721 TCAGTGTTTCCCCACAAAAATTTTTAT 58.950 29.630 15.55 1.83 37.82 1.40
629 631 9.331282 CAGTGTTTCCCCACAAAAATTTTTATA 57.669 29.630 15.55 0.00 37.82 0.98
630 632 9.907229 AGTGTTTCCCCACAAAAATTTTTATAA 57.093 25.926 15.55 2.60 37.82 0.98
646 648 8.935614 ATTTTTATAAGAGTATAAGGTGGGCC 57.064 34.615 0.00 0.00 34.42 5.80
647 649 5.733620 TTATAAGAGTATAAGGTGGGCCG 57.266 43.478 0.00 0.00 40.50 6.13
648 650 2.170012 AAGAGTATAAGGTGGGCCGA 57.830 50.000 0.00 0.00 40.50 5.54
649 651 1.411041 AGAGTATAAGGTGGGCCGAC 58.589 55.000 9.83 9.83 40.50 4.79
650 652 0.391966 GAGTATAAGGTGGGCCGACC 59.608 60.000 28.45 28.45 40.50 4.79
678 680 4.035091 TGACACAAATCTTGTTTGAGACCG 59.965 41.667 7.44 0.00 43.23 4.79
681 683 3.564225 ACAAATCTTGTTTGAGACCGACC 59.436 43.478 7.44 0.00 42.22 4.79
709 711 2.104622 ACCCACTGGCCTTGAATTTTTG 59.895 45.455 3.32 0.00 33.59 2.44
716 718 1.337728 GCCTTGAATTTTTGGGTCGGG 60.338 52.381 0.00 0.00 0.00 5.14
718 720 2.367241 CCTTGAATTTTTGGGTCGGGTT 59.633 45.455 0.00 0.00 0.00 4.11
721 723 3.834938 TGAATTTTTGGGTCGGGTTAGT 58.165 40.909 0.00 0.00 0.00 2.24
748 750 2.981302 GGCAAACCCAGCCCATTC 59.019 61.111 0.00 0.00 46.50 2.67
754 756 2.203394 CCCAGCCCATTCCCATCG 60.203 66.667 0.00 0.00 0.00 3.84
757 759 1.077501 CAGCCCATTCCCATCGTGT 60.078 57.895 0.00 0.00 0.00 4.49
808 810 4.945246 TCTTCTCGTCTAAAGTTTGCAGT 58.055 39.130 0.00 0.00 0.00 4.40
822 824 7.500720 AAGTTTGCAGTAAGGTTTACGTTAT 57.499 32.000 0.00 0.00 0.00 1.89
877 879 1.070758 GCCAGATCCATCATGTACGGT 59.929 52.381 0.00 0.00 0.00 4.83
910 912 4.832608 CCAACGCCGGCCTACCTC 62.833 72.222 23.46 0.00 0.00 3.85
940 965 2.534349 CACTGGCTAATTACACTACGCG 59.466 50.000 3.53 3.53 0.00 6.01
1077 1103 3.951332 CTCTCGCAGCAACGGAAA 58.049 55.556 0.00 0.00 0.00 3.13
1078 1104 2.234613 CTCTCGCAGCAACGGAAAA 58.765 52.632 0.00 0.00 0.00 2.29
1123 1149 2.772691 GCGGTCACCCTACTCTCCG 61.773 68.421 0.00 0.00 40.72 4.63
1135 1161 1.078356 CTCTCCGTCGTCCTCCTGA 60.078 63.158 0.00 0.00 0.00 3.86
1315 1341 2.742372 CCTTCACCGCCTTCGTGG 60.742 66.667 0.00 0.00 45.89 4.94
1398 1424 2.494918 GCCAGCGACGACACCTAT 59.505 61.111 0.00 0.00 0.00 2.57
1672 1698 5.426833 TCTCTTTCCCTTCAGAATTAGAGGG 59.573 44.000 0.76 0.76 33.98 4.30
1703 1729 6.479972 TCAACCTCGTATTAACATCATCCT 57.520 37.500 0.00 0.00 0.00 3.24
1720 1746 6.954487 TCATCCTGAATTCCTGATGAAATG 57.046 37.500 23.97 8.91 36.33 2.32
1722 1748 6.320418 TCATCCTGAATTCCTGATGAAATGTG 59.680 38.462 23.97 7.89 36.33 3.21
1723 1749 5.573219 TCCTGAATTCCTGATGAAATGTGT 58.427 37.500 2.27 0.00 36.33 3.72
1724 1750 6.012113 TCCTGAATTCCTGATGAAATGTGTT 58.988 36.000 2.27 0.00 36.33 3.32
1727 1753 7.053316 TGAATTCCTGATGAAATGTGTTTGT 57.947 32.000 2.27 0.00 36.33 2.83
1728 1754 6.924612 TGAATTCCTGATGAAATGTGTTTGTG 59.075 34.615 2.27 0.00 36.33 3.33
1729 1755 4.241590 TCCTGATGAAATGTGTTTGTGC 57.758 40.909 0.00 0.00 0.00 4.57
1730 1756 3.890756 TCCTGATGAAATGTGTTTGTGCT 59.109 39.130 0.00 0.00 0.00 4.40
1731 1757 4.341806 TCCTGATGAAATGTGTTTGTGCTT 59.658 37.500 0.00 0.00 0.00 3.91
1732 1758 5.051816 CCTGATGAAATGTGTTTGTGCTTT 58.948 37.500 0.00 0.00 0.00 3.51
1733 1759 5.524646 CCTGATGAAATGTGTTTGTGCTTTT 59.475 36.000 0.00 0.00 0.00 2.27
1734 1760 6.037391 CCTGATGAAATGTGTTTGTGCTTTTT 59.963 34.615 0.00 0.00 0.00 1.94
1788 1814 3.911964 CCGAAGTTAATTTGTTGCCTTCG 59.088 43.478 11.44 11.44 46.41 3.79
1806 1834 1.567649 TCGGGATCTGTAGTGTAGGGT 59.432 52.381 0.00 0.00 0.00 4.34
1840 1868 1.552792 TGCTGTCCATATTGTCGTCCA 59.447 47.619 0.00 0.00 0.00 4.02
1841 1869 1.933853 GCTGTCCATATTGTCGTCCAC 59.066 52.381 0.00 0.00 0.00 4.02
1861 1889 1.131504 CTTCCTCTCCGTCGAGTTCAG 59.868 57.143 0.00 0.00 37.40 3.02
1885 1951 5.163844 GCTTCTTCTCGGGACTTGAATTAAC 60.164 44.000 0.00 0.00 0.00 2.01
1889 1955 4.240096 TCTCGGGACTTGAATTAACGAAC 58.760 43.478 0.00 0.00 0.00 3.95
1944 2010 3.777925 CGGACGTCCTTTGCGCTG 61.778 66.667 30.92 10.14 0.00 5.18
1945 2011 4.090057 GGACGTCCTTTGCGCTGC 62.090 66.667 27.64 0.00 0.00 5.25
1946 2012 3.044305 GACGTCCTTTGCGCTGCT 61.044 61.111 9.73 0.00 0.00 4.24
1947 2013 2.591715 ACGTCCTTTGCGCTGCTT 60.592 55.556 9.73 0.00 0.00 3.91
1948 2014 2.127118 CGTCCTTTGCGCTGCTTG 60.127 61.111 9.73 0.00 0.00 4.01
1949 2015 2.256461 GTCCTTTGCGCTGCTTGG 59.744 61.111 9.73 4.01 0.00 3.61
1950 2016 3.673484 TCCTTTGCGCTGCTTGGC 61.673 61.111 9.73 0.00 0.00 4.52
1951 2017 3.980989 CCTTTGCGCTGCTTGGCA 61.981 61.111 9.73 0.00 37.39 4.92
1952 2018 2.027897 CTTTGCGCTGCTTGGCAA 59.972 55.556 9.73 8.96 46.52 4.52
1954 2020 3.678841 TTGCGCTGCTTGGCAATA 58.321 50.000 9.73 0.00 43.63 1.90
1955 2021 2.191680 TTGCGCTGCTTGGCAATAT 58.808 47.368 9.73 0.00 43.63 1.28
1956 2022 0.179132 TTGCGCTGCTTGGCAATATG 60.179 50.000 9.73 0.00 43.63 1.78
1957 2023 1.314534 TGCGCTGCTTGGCAATATGT 61.315 50.000 9.73 0.00 38.41 2.29
1958 2024 0.868602 GCGCTGCTTGGCAATATGTG 60.869 55.000 0.00 1.67 38.41 3.21
1959 2025 0.248743 CGCTGCTTGGCAATATGTGG 60.249 55.000 0.00 0.00 38.41 4.17
1965 2031 3.808036 GGCAATATGTGGCGTCGT 58.192 55.556 0.00 0.00 43.81 4.34
1966 2032 1.351707 GGCAATATGTGGCGTCGTG 59.648 57.895 0.00 0.00 43.81 4.35
1967 2033 1.297598 GCAATATGTGGCGTCGTGC 60.298 57.895 0.00 0.00 45.38 5.34
1979 2045 3.715854 GTCGTGCATAGACGGTTCT 57.284 52.632 9.08 0.00 39.88 3.01
1988 2054 3.005578 GCATAGACGGTTCTAACCCTAGG 59.994 52.174 0.06 0.06 46.53 3.02
1992 2058 5.865719 TAGACGGTTCTAACCCTAGGGTCA 61.866 50.000 33.95 20.01 46.53 4.02
2056 2125 3.090532 CCCTTTCCCCTCCCTCCG 61.091 72.222 0.00 0.00 0.00 4.63
2149 2226 0.458543 CTCCTCGCGCAAAGAGCTTA 60.459 55.000 8.75 0.00 42.61 3.09
2161 2238 4.410400 AGCTTAGTGTGCCGGGGC 62.410 66.667 2.18 1.86 42.35 5.80
2474 2553 2.051971 CCACAACGACGACGACGA 60.052 61.111 25.15 0.00 42.66 4.20
2475 2554 2.352333 CCACAACGACGACGACGAC 61.352 63.158 25.15 7.02 42.66 4.34
2516 2595 3.056536 TCCTTGGAGTCTTCGTTGAGATG 60.057 47.826 0.00 0.00 0.00 2.90
2518 2597 1.895798 TGGAGTCTTCGTTGAGATGCT 59.104 47.619 0.00 0.00 0.00 3.79
2533 2612 4.101448 GCTGACAGGGATGGCGGT 62.101 66.667 4.26 0.00 0.00 5.68
2597 2676 5.105351 GGTGAAAACCTGCTATTGGCTATTT 60.105 40.000 0.00 0.00 42.39 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 4.168101 ACAGGTGTCTCCAAAGGAAGATA 58.832 43.478 0.00 0.00 39.02 1.98
51 52 3.559171 GCATTACAGGTGTCTCCAAAGGA 60.559 47.826 0.00 0.00 39.02 3.36
292 293 9.444600 GTTATGTTTCCTAACCATAGACAAAGA 57.555 33.333 0.00 0.00 33.15 2.52
346 347 3.067461 CAGAGTGTCACTAGTATGCCTCC 59.933 52.174 5.21 0.00 0.00 4.30
510 512 2.554893 TGCCAATCCAACTTTCGGTAAC 59.445 45.455 0.00 0.00 0.00 2.50
511 513 2.865079 TGCCAATCCAACTTTCGGTAA 58.135 42.857 0.00 0.00 0.00 2.85
512 514 2.570415 TGCCAATCCAACTTTCGGTA 57.430 45.000 0.00 0.00 0.00 4.02
513 515 1.923356 ATGCCAATCCAACTTTCGGT 58.077 45.000 0.00 0.00 0.00 4.69
514 516 2.029110 ACAATGCCAATCCAACTTTCGG 60.029 45.455 0.00 0.00 0.00 4.30
515 517 3.302365 ACAATGCCAATCCAACTTTCG 57.698 42.857 0.00 0.00 0.00 3.46
516 518 4.886579 AGAACAATGCCAATCCAACTTTC 58.113 39.130 0.00 0.00 0.00 2.62
517 519 4.961438 AGAACAATGCCAATCCAACTTT 57.039 36.364 0.00 0.00 0.00 2.66
518 520 4.961438 AAGAACAATGCCAATCCAACTT 57.039 36.364 0.00 0.00 0.00 2.66
519 521 4.082026 GCTAAGAACAATGCCAATCCAACT 60.082 41.667 0.00 0.00 0.00 3.16
520 522 4.082026 AGCTAAGAACAATGCCAATCCAAC 60.082 41.667 0.00 0.00 0.00 3.77
521 523 4.088634 AGCTAAGAACAATGCCAATCCAA 58.911 39.130 0.00 0.00 0.00 3.53
522 524 3.700538 AGCTAAGAACAATGCCAATCCA 58.299 40.909 0.00 0.00 0.00 3.41
523 525 4.440663 GGAAGCTAAGAACAATGCCAATCC 60.441 45.833 0.00 0.00 0.00 3.01
524 526 4.400567 AGGAAGCTAAGAACAATGCCAATC 59.599 41.667 0.00 0.00 0.00 2.67
525 527 4.159135 CAGGAAGCTAAGAACAATGCCAAT 59.841 41.667 0.00 0.00 0.00 3.16
526 528 3.507233 CAGGAAGCTAAGAACAATGCCAA 59.493 43.478 0.00 0.00 0.00 4.52
527 529 3.084039 CAGGAAGCTAAGAACAATGCCA 58.916 45.455 0.00 0.00 0.00 4.92
528 530 3.127721 GTCAGGAAGCTAAGAACAATGCC 59.872 47.826 0.00 0.00 0.00 4.40
529 531 3.127721 GGTCAGGAAGCTAAGAACAATGC 59.872 47.826 0.00 0.00 0.00 3.56
530 532 4.326826 TGGTCAGGAAGCTAAGAACAATG 58.673 43.478 0.00 0.00 0.00 2.82
531 533 4.042187 ACTGGTCAGGAAGCTAAGAACAAT 59.958 41.667 2.87 0.00 0.00 2.71
532 534 3.391296 ACTGGTCAGGAAGCTAAGAACAA 59.609 43.478 2.87 0.00 0.00 2.83
533 535 2.972713 ACTGGTCAGGAAGCTAAGAACA 59.027 45.455 2.87 0.00 0.00 3.18
534 536 3.686916 ACTGGTCAGGAAGCTAAGAAC 57.313 47.619 2.87 0.00 0.00 3.01
535 537 3.195825 GCTACTGGTCAGGAAGCTAAGAA 59.804 47.826 15.64 0.00 38.06 2.52
536 538 2.761208 GCTACTGGTCAGGAAGCTAAGA 59.239 50.000 15.64 0.00 38.06 2.10
537 539 2.763448 AGCTACTGGTCAGGAAGCTAAG 59.237 50.000 20.84 0.00 44.61 2.18
538 540 2.821437 AGCTACTGGTCAGGAAGCTAA 58.179 47.619 20.84 0.00 44.61 3.09
539 541 2.497675 CAAGCTACTGGTCAGGAAGCTA 59.502 50.000 21.83 0.00 45.23 3.32
540 542 1.277557 CAAGCTACTGGTCAGGAAGCT 59.722 52.381 18.25 18.25 46.77 3.74
541 543 1.002544 ACAAGCTACTGGTCAGGAAGC 59.997 52.381 15.32 15.32 40.01 3.86
542 544 3.070018 CAACAAGCTACTGGTCAGGAAG 58.930 50.000 2.87 1.33 0.00 3.46
543 545 2.224523 CCAACAAGCTACTGGTCAGGAA 60.225 50.000 2.87 0.00 0.00 3.36
544 546 1.347707 CCAACAAGCTACTGGTCAGGA 59.652 52.381 2.87 0.00 0.00 3.86
545 547 1.813513 CCAACAAGCTACTGGTCAGG 58.186 55.000 2.87 0.00 0.00 3.86
546 548 1.160137 GCCAACAAGCTACTGGTCAG 58.840 55.000 9.66 0.00 32.46 3.51
547 549 0.602638 CGCCAACAAGCTACTGGTCA 60.603 55.000 9.66 0.00 32.46 4.02
548 550 1.298859 CCGCCAACAAGCTACTGGTC 61.299 60.000 9.66 3.09 32.46 4.02
549 551 1.302511 CCGCCAACAAGCTACTGGT 60.303 57.895 9.66 0.00 32.46 4.00
550 552 1.003839 TCCGCCAACAAGCTACTGG 60.004 57.895 4.62 4.62 0.00 4.00
551 553 0.320771 AGTCCGCCAACAAGCTACTG 60.321 55.000 0.00 0.00 0.00 2.74
552 554 0.320771 CAGTCCGCCAACAAGCTACT 60.321 55.000 0.00 0.00 0.00 2.57
553 555 0.602905 ACAGTCCGCCAACAAGCTAC 60.603 55.000 0.00 0.00 0.00 3.58
554 556 0.107831 AACAGTCCGCCAACAAGCTA 59.892 50.000 0.00 0.00 0.00 3.32
555 557 1.152963 AACAGTCCGCCAACAAGCT 60.153 52.632 0.00 0.00 0.00 3.74
556 558 1.282875 GAACAGTCCGCCAACAAGC 59.717 57.895 0.00 0.00 0.00 4.01
557 559 1.569493 CGAACAGTCCGCCAACAAG 59.431 57.895 0.00 0.00 0.00 3.16
558 560 1.890041 CCGAACAGTCCGCCAACAA 60.890 57.895 0.00 0.00 0.00 2.83
559 561 2.280524 CCGAACAGTCCGCCAACA 60.281 61.111 0.00 0.00 0.00 3.33
560 562 3.723348 GCCGAACAGTCCGCCAAC 61.723 66.667 0.00 0.00 0.00 3.77
564 566 3.774702 GTTCGCCGAACAGTCCGC 61.775 66.667 24.00 0.00 41.62 5.54
565 567 3.467119 CGTTCGCCGAACAGTCCG 61.467 66.667 27.37 11.21 42.05 4.79
566 568 3.774702 GCGTTCGCCGAACAGTCC 61.775 66.667 27.37 10.30 42.05 3.85
567 569 1.828331 AAAGCGTTCGCCGAACAGTC 61.828 55.000 27.37 16.11 42.05 3.51
568 570 1.433837 AAAAGCGTTCGCCGAACAGT 61.434 50.000 27.37 12.43 42.05 3.55
569 571 0.509499 TAAAAGCGTTCGCCGAACAG 59.491 50.000 27.37 20.33 42.05 3.16
570 572 1.149987 ATAAAAGCGTTCGCCGAACA 58.850 45.000 27.37 9.17 42.05 3.18
571 573 2.236741 AATAAAAGCGTTCGCCGAAC 57.763 45.000 19.59 19.59 39.56 3.95
572 574 4.401525 TTTAATAAAAGCGTTCGCCGAA 57.598 36.364 13.54 0.00 39.56 4.30
573 575 4.603231 ATTTAATAAAAGCGTTCGCCGA 57.397 36.364 13.54 0.00 39.56 5.54
574 576 6.557171 GCTTTATTTAATAAAAGCGTTCGCCG 60.557 38.462 13.54 0.00 34.59 6.46
575 577 6.471198 AGCTTTATTTAATAAAAGCGTTCGCC 59.529 34.615 20.56 0.00 35.72 5.54
576 578 7.428472 AGAGCTTTATTTAATAAAAGCGTTCGC 59.572 33.333 20.56 9.24 35.72 4.70
577 579 8.822105 AGAGCTTTATTTAATAAAAGCGTTCG 57.178 30.769 20.56 0.47 35.72 3.95
578 580 9.769093 TGAGAGCTTTATTTAATAAAAGCGTTC 57.231 29.630 20.56 20.36 35.72 3.95
579 581 9.774742 CTGAGAGCTTTATTTAATAAAAGCGTT 57.225 29.630 20.56 15.61 35.72 4.84
580 582 8.947115 ACTGAGAGCTTTATTTAATAAAAGCGT 58.053 29.630 20.56 15.35 35.72 5.07
581 583 9.214953 CACTGAGAGCTTTATTTAATAAAAGCG 57.785 33.333 20.56 13.06 35.72 4.68
587 589 9.174166 GGGAAACACTGAGAGCTTTATTTAATA 57.826 33.333 0.00 0.00 0.00 0.98
588 590 7.122799 GGGGAAACACTGAGAGCTTTATTTAAT 59.877 37.037 0.00 0.00 0.00 1.40
589 591 6.433093 GGGGAAACACTGAGAGCTTTATTTAA 59.567 38.462 0.00 0.00 0.00 1.52
590 592 5.944007 GGGGAAACACTGAGAGCTTTATTTA 59.056 40.000 0.00 0.00 0.00 1.40
591 593 4.767409 GGGGAAACACTGAGAGCTTTATTT 59.233 41.667 0.00 0.00 0.00 1.40
592 594 4.202567 TGGGGAAACACTGAGAGCTTTATT 60.203 41.667 0.00 0.00 31.84 1.40
593 595 3.330701 TGGGGAAACACTGAGAGCTTTAT 59.669 43.478 0.00 0.00 31.84 1.40
594 596 2.708861 TGGGGAAACACTGAGAGCTTTA 59.291 45.455 0.00 0.00 31.84 1.85
595 597 1.494721 TGGGGAAACACTGAGAGCTTT 59.505 47.619 0.00 0.00 31.84 3.51
596 598 1.140312 TGGGGAAACACTGAGAGCTT 58.860 50.000 0.00 0.00 31.84 3.74
597 599 0.398318 GTGGGGAAACACTGAGAGCT 59.602 55.000 0.00 0.00 38.32 4.09
598 600 0.108585 TGTGGGGAAACACTGAGAGC 59.891 55.000 0.00 0.00 41.84 4.09
599 601 2.638480 TTGTGGGGAAACACTGAGAG 57.362 50.000 0.00 0.00 41.84 3.20
600 602 3.374042 TTTTGTGGGGAAACACTGAGA 57.626 42.857 0.00 0.00 41.84 3.27
601 603 4.670896 ATTTTTGTGGGGAAACACTGAG 57.329 40.909 0.00 0.00 41.84 3.35
602 604 5.428184 AAATTTTTGTGGGGAAACACTGA 57.572 34.783 0.00 0.00 41.84 3.41
603 605 6.507958 AAAAATTTTTGTGGGGAAACACTG 57.492 33.333 15.25 0.00 41.84 3.66
604 606 9.907229 TTATAAAAATTTTTGTGGGGAAACACT 57.093 25.926 23.36 0.00 41.84 3.55
620 622 9.363401 GGCCCACCTTATACTCTTATAAAAATT 57.637 33.333 0.00 0.00 31.11 1.82
621 623 7.664318 CGGCCCACCTTATACTCTTATAAAAAT 59.336 37.037 0.00 0.00 31.11 1.82
622 624 6.993902 CGGCCCACCTTATACTCTTATAAAAA 59.006 38.462 0.00 0.00 31.11 1.94
623 625 6.327104 TCGGCCCACCTTATACTCTTATAAAA 59.673 38.462 0.00 0.00 31.11 1.52
624 626 5.840149 TCGGCCCACCTTATACTCTTATAAA 59.160 40.000 0.00 0.00 31.11 1.40
625 627 5.244626 GTCGGCCCACCTTATACTCTTATAA 59.755 44.000 0.00 0.00 0.00 0.98
626 628 4.768968 GTCGGCCCACCTTATACTCTTATA 59.231 45.833 0.00 0.00 0.00 0.98
627 629 3.577415 GTCGGCCCACCTTATACTCTTAT 59.423 47.826 0.00 0.00 0.00 1.73
628 630 2.961062 GTCGGCCCACCTTATACTCTTA 59.039 50.000 0.00 0.00 0.00 2.10
629 631 1.761198 GTCGGCCCACCTTATACTCTT 59.239 52.381 0.00 0.00 0.00 2.85
630 632 1.411041 GTCGGCCCACCTTATACTCT 58.589 55.000 0.00 0.00 0.00 3.24
631 633 0.391966 GGTCGGCCCACCTTATACTC 59.608 60.000 13.04 0.00 33.08 2.59
632 634 2.524611 GGTCGGCCCACCTTATACT 58.475 57.895 13.04 0.00 33.08 2.12
643 645 2.818274 GTGTCAATCGGGTCGGCC 60.818 66.667 0.00 0.00 0.00 6.13
644 646 1.231958 TTTGTGTCAATCGGGTCGGC 61.232 55.000 0.00 0.00 0.00 5.54
645 647 1.396996 GATTTGTGTCAATCGGGTCGG 59.603 52.381 0.00 0.00 0.00 4.79
646 648 2.346803 AGATTTGTGTCAATCGGGTCG 58.653 47.619 0.00 0.00 0.00 4.79
647 649 3.502211 ACAAGATTTGTGTCAATCGGGTC 59.498 43.478 0.00 0.00 43.48 4.46
648 650 3.486383 ACAAGATTTGTGTCAATCGGGT 58.514 40.909 0.00 0.00 43.48 5.28
649 651 4.503741 AACAAGATTTGTGTCAATCGGG 57.496 40.909 0.00 0.00 44.59 5.14
650 652 5.518812 TCAAACAAGATTTGTGTCAATCGG 58.481 37.500 0.00 0.00 44.59 4.18
651 653 6.358030 GTCTCAAACAAGATTTGTGTCAATCG 59.642 38.462 0.00 0.00 44.59 3.34
652 654 6.638468 GGTCTCAAACAAGATTTGTGTCAATC 59.362 38.462 0.00 0.00 44.59 2.67
653 655 6.507023 GGTCTCAAACAAGATTTGTGTCAAT 58.493 36.000 0.00 0.00 44.59 2.57
678 680 1.002134 CCAGTGGGTCATGTGGGTC 60.002 63.158 0.00 0.00 0.00 4.46
681 683 2.361610 GGCCAGTGGGTCATGTGG 60.362 66.667 12.15 0.00 39.19 4.17
734 736 0.325577 GATGGGAATGGGCTGGGTTT 60.326 55.000 0.00 0.00 0.00 3.27
735 737 1.311059 GATGGGAATGGGCTGGGTT 59.689 57.895 0.00 0.00 0.00 4.11
739 741 1.077501 ACACGATGGGAATGGGCTG 60.078 57.895 0.00 0.00 0.00 4.85
748 750 1.742880 CAGGTCAGCACACGATGGG 60.743 63.158 0.00 0.00 0.00 4.00
757 759 0.469705 AAATGTTGGGCAGGTCAGCA 60.470 50.000 0.00 0.00 35.83 4.41
808 810 3.108144 GAGCGCGATAACGTAAACCTTA 58.892 45.455 12.10 0.00 41.98 2.69
822 824 2.738521 GCTGGAAACTGAGCGCGA 60.739 61.111 12.10 0.00 0.00 5.87
855 857 2.224378 CCGTACATGATGGATCTGGCTT 60.224 50.000 0.00 0.00 36.09 4.35
856 858 1.345741 CCGTACATGATGGATCTGGCT 59.654 52.381 0.00 0.00 36.09 4.75
866 868 2.279252 GGCGCGACCGTACATGAT 60.279 61.111 12.10 0.00 36.67 2.45
908 910 2.857575 TAGCCAGTGGTGCATGCGAG 62.858 60.000 14.09 0.00 0.00 5.03
910 912 1.378882 ATTAGCCAGTGGTGCATGCG 61.379 55.000 14.09 0.00 0.00 4.73
911 913 0.819582 AATTAGCCAGTGGTGCATGC 59.180 50.000 11.82 11.82 0.00 4.06
912 914 3.016031 TGTAATTAGCCAGTGGTGCATG 58.984 45.455 11.74 0.00 0.00 4.06
913 915 3.016736 GTGTAATTAGCCAGTGGTGCAT 58.983 45.455 11.74 0.00 0.00 3.96
1039 1065 3.775654 CCGTGGCCTGAGAGGGAC 61.776 72.222 3.32 0.00 35.37 4.46
1074 1100 1.809869 GAGGCCGGCAAGGATTTTC 59.190 57.895 30.85 7.16 45.00 2.29
1076 1102 2.438434 CGAGGCCGGCAAGGATTT 60.438 61.111 30.85 3.57 45.00 2.17
1123 1149 1.314730 GAGGAGATCAGGAGGACGAC 58.685 60.000 0.00 0.00 0.00 4.34
1135 1161 2.446802 GGCGGGAAGGGAGGAGAT 60.447 66.667 0.00 0.00 0.00 2.75
1189 1215 3.490759 GGTCGTGGATGCTGCGTG 61.491 66.667 0.00 0.00 0.00 5.34
1213 1239 4.459089 GCAGTGAGCGGGAGGACC 62.459 72.222 0.00 0.00 0.00 4.46
1485 1511 2.283966 ACGGAGTCCAGGTCCAGG 60.284 66.667 10.49 0.00 29.74 4.45
1703 1729 6.924612 CACAAACACATTTCATCAGGAATTCA 59.075 34.615 7.93 0.00 34.91 2.57
1757 1783 9.401873 GCAACAAATTAACTTCGGTTTTACTAT 57.598 29.630 0.00 0.00 39.17 2.12
1758 1784 7.861872 GGCAACAAATTAACTTCGGTTTTACTA 59.138 33.333 0.00 0.00 39.17 1.82
1759 1785 6.698329 GGCAACAAATTAACTTCGGTTTTACT 59.302 34.615 0.00 0.00 39.17 2.24
1760 1786 6.698329 AGGCAACAAATTAACTTCGGTTTTAC 59.302 34.615 0.00 0.00 38.09 2.01
1761 1787 6.807789 AGGCAACAAATTAACTTCGGTTTTA 58.192 32.000 0.00 0.00 38.09 1.52
1762 1788 5.666462 AGGCAACAAATTAACTTCGGTTTT 58.334 33.333 0.00 0.00 38.09 2.43
1763 1789 5.270893 AGGCAACAAATTAACTTCGGTTT 57.729 34.783 0.00 0.00 38.09 3.27
1764 1790 4.929819 AGGCAACAAATTAACTTCGGTT 57.070 36.364 0.00 0.00 39.78 4.44
1765 1791 4.555906 CGAAGGCAACAAATTAACTTCGGT 60.556 41.667 14.62 0.00 42.99 4.69
1766 1792 3.911964 CGAAGGCAACAAATTAACTTCGG 59.088 43.478 14.62 0.00 42.99 4.30
1767 1793 3.911964 CCGAAGGCAACAAATTAACTTCG 59.088 43.478 15.27 15.27 46.14 3.79
1788 1814 1.413077 GCACCCTACACTACAGATCCC 59.587 57.143 0.00 0.00 0.00 3.85
1840 1868 1.166989 GAACTCGACGGAGAGGAAGT 58.833 55.000 12.83 0.00 43.27 3.01
1841 1869 1.131504 CTGAACTCGACGGAGAGGAAG 59.868 57.143 12.83 4.76 43.27 3.46
1861 1889 2.457366 TTCAAGTCCCGAGAAGAAGC 57.543 50.000 0.00 0.00 0.00 3.86
1885 1951 0.532862 AGCTGTTCACCTGGTGTTCG 60.533 55.000 25.15 13.55 34.79 3.95
1889 1955 0.674895 GCCTAGCTGTTCACCTGGTG 60.675 60.000 20.86 20.86 34.45 4.17
1932 1998 2.256461 CCAAGCAGCGCAAAGGAC 59.744 61.111 11.47 0.00 0.00 3.85
1933 1999 3.673484 GCCAAGCAGCGCAAAGGA 61.673 61.111 11.47 0.00 0.00 3.36
1934 2000 3.502990 TTGCCAAGCAGCGCAAAGG 62.503 57.895 11.47 4.99 41.80 3.11
1935 2001 2.027897 TTGCCAAGCAGCGCAAAG 59.972 55.556 11.47 0.00 41.80 2.77
1938 2004 1.314534 ACATATTGCCAAGCAGCGCA 61.315 50.000 11.47 0.00 40.61 6.09
1939 2005 0.868602 CACATATTGCCAAGCAGCGC 60.869 55.000 0.00 0.00 40.61 5.92
1940 2006 0.248743 CCACATATTGCCAAGCAGCG 60.249 55.000 0.00 0.00 40.61 5.18
1941 2007 0.529119 GCCACATATTGCCAAGCAGC 60.529 55.000 0.00 0.00 40.61 5.25
1942 2008 0.248743 CGCCACATATTGCCAAGCAG 60.249 55.000 0.00 0.00 40.61 4.24
1943 2009 0.964860 ACGCCACATATTGCCAAGCA 60.965 50.000 0.00 0.00 36.47 3.91
1944 2010 0.248621 GACGCCACATATTGCCAAGC 60.249 55.000 0.00 0.00 0.00 4.01
1945 2011 0.027979 CGACGCCACATATTGCCAAG 59.972 55.000 0.00 0.00 0.00 3.61
1946 2012 0.675208 ACGACGCCACATATTGCCAA 60.675 50.000 0.00 0.00 0.00 4.52
1947 2013 1.078778 ACGACGCCACATATTGCCA 60.079 52.632 0.00 0.00 0.00 4.92
1948 2014 1.351707 CACGACGCCACATATTGCC 59.648 57.895 0.00 0.00 0.00 4.52
1949 2015 1.297598 GCACGACGCCACATATTGC 60.298 57.895 0.00 0.00 32.94 3.56
1950 2016 0.657312 ATGCACGACGCCACATATTG 59.343 50.000 0.00 0.00 41.33 1.90
1951 2017 2.135139 CTATGCACGACGCCACATATT 58.865 47.619 0.00 0.00 41.33 1.28
1952 2018 1.339929 TCTATGCACGACGCCACATAT 59.660 47.619 0.00 0.00 41.33 1.78
1953 2019 0.741915 TCTATGCACGACGCCACATA 59.258 50.000 0.00 0.00 41.33 2.29
1954 2020 0.806102 GTCTATGCACGACGCCACAT 60.806 55.000 0.00 0.00 41.33 3.21
1955 2021 1.445410 GTCTATGCACGACGCCACA 60.445 57.895 0.00 0.00 41.33 4.17
1956 2022 2.505498 CGTCTATGCACGACGCCAC 61.505 63.158 22.26 0.00 46.12 5.01
1957 2023 2.202557 CGTCTATGCACGACGCCA 60.203 61.111 22.26 0.00 46.12 5.69
1961 2027 2.838386 TAGAACCGTCTATGCACGAC 57.162 50.000 7.69 7.69 42.69 4.34
1962 2028 2.159338 GGTTAGAACCGTCTATGCACGA 60.159 50.000 0.00 0.00 42.69 4.35
1963 2029 2.190981 GGTTAGAACCGTCTATGCACG 58.809 52.381 0.00 0.00 39.66 5.34
1988 2054 3.775654 CGCCCCAGAGGAGTGACC 61.776 72.222 0.00 0.00 38.24 4.02
1992 2058 2.363147 GAGTCGCCCCAGAGGAGT 60.363 66.667 0.00 0.00 38.24 3.85
2056 2125 2.892425 CTTGTGGCGGCGAGATCC 60.892 66.667 12.98 1.84 0.00 3.36
2140 2217 0.321653 CCCGGCACACTAAGCTCTTT 60.322 55.000 0.00 0.00 0.00 2.52
2141 2218 1.296715 CCCGGCACACTAAGCTCTT 59.703 57.895 0.00 0.00 0.00 2.85
2305 2384 2.583593 GCGCAGGTCGATCCAGAC 60.584 66.667 0.30 0.00 41.67 3.51
2516 2595 4.101448 ACCGCCATCCCTGTCAGC 62.101 66.667 0.00 0.00 0.00 4.26
2518 2597 3.716195 CCACCGCCATCCCTGTCA 61.716 66.667 0.00 0.00 0.00 3.58
2622 2701 2.434359 GGAAGGGAACGACGCAGG 60.434 66.667 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.