Multiple sequence alignment - TraesCS3A01G337100

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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 TraesCS3A01G337100 chr3A 100.000 2986 0 0 422 3407 584011823 584008838 0.000000e+00 5515.0
1 TraesCS3A01G337100 chr3A 100.000 45 0 0 1 45 584012244 584012200 2.180000e-12 84.2
2 TraesCS3A01G337100 chr3B 90.163 2704 168 46 724 3391 580353395 580350754 0.000000e+00 3430.0
3 TraesCS3A01G337100 chr3D 90.541 2590 122 54 733 3278 442809112 442806602 0.000000e+00 3312.0
4 TraesCS3A01G337100 chr7A 94.444 144 5 3 581 723 351612884 351612743 5.720000e-53 219.0
5 TraesCS3A01G337100 chr7A 94.853 136 5 2 574 708 596743040 596742906 9.580000e-51 211.0
6 TraesCS3A01G337100 chr6A 97.638 127 3 0 582 708 594970386 594970512 5.720000e-53 219.0
7 TraesCS3A01G337100 chr6A 96.183 131 5 0 579 709 617047775 617047905 7.400000e-52 215.0
8 TraesCS3A01G337100 chr4B 95.588 136 5 1 582 716 210282884 210282749 2.060000e-52 217.0
9 TraesCS3A01G337100 chr5A 96.875 128 4 0 582 709 688512346 688512219 7.400000e-52 215.0
10 TraesCS3A01G337100 chr2B 94.286 140 6 2 581 720 627325098 627325235 2.660000e-51 213.0
11 TraesCS3A01G337100 chr2B 93.617 141 7 2 582 722 89552373 89552511 3.450000e-50 209.0
12 TraesCS3A01G337100 chr1A 93.056 144 7 3 567 708 42225362 42225220 1.240000e-49 207.0
13 TraesCS3A01G337100 chr6B 84.615 65 9 1 440 504 213838019 213838082 2.840000e-06 63.9


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 TraesCS3A01G337100 chr3A 584008838 584012244 3406 True 2799.6 5515 100.000 1 3407 2 chr3A.!!$R1 3406
1 TraesCS3A01G337100 chr3B 580350754 580353395 2641 True 3430.0 3430 90.163 724 3391 1 chr3B.!!$R1 2667
2 TraesCS3A01G337100 chr3D 442806602 442809112 2510 True 3312.0 3312 90.541 733 3278 1 chr3D.!!$R1 2545

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
527 528 0.034380 TCGTCCCGAATCACCTCTCT 60.034 55.0 0.0 0.0 31.06 3.10 F
898 914 0.234625 GCTGCGACAATCAAACGTCA 59.765 50.0 0.0 0.0 32.24 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2013 2044 0.110238 GCACGTTGTTCATGCATCGT 60.110 50.0 0.00 0.0 43.0 3.73 R
2885 2938 0.892755 AGGCCATGATGCACAACTTG 59.107 50.0 5.01 0.0 0.0 3.16 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
446 447 6.732896 TGTCCCATTCTTCTCTAATACTCC 57.267 41.667 0.00 0.00 0.00 3.85
447 448 6.444704 TGTCCCATTCTTCTCTAATACTCCT 58.555 40.000 0.00 0.00 0.00 3.69
448 449 7.592736 TGTCCCATTCTTCTCTAATACTCCTA 58.407 38.462 0.00 0.00 0.00 2.94
449 450 7.506261 TGTCCCATTCTTCTCTAATACTCCTAC 59.494 40.741 0.00 0.00 0.00 3.18
450 451 7.011382 TCCCATTCTTCTCTAATACTCCTACC 58.989 42.308 0.00 0.00 0.00 3.18
451 452 7.013834 CCCATTCTTCTCTAATACTCCTACCT 58.986 42.308 0.00 0.00 0.00 3.08
452 453 7.177744 CCCATTCTTCTCTAATACTCCTACCTC 59.822 44.444 0.00 0.00 0.00 3.85
453 454 7.094549 CCATTCTTCTCTAATACTCCTACCTCG 60.095 44.444 0.00 0.00 0.00 4.63
454 455 5.867330 TCTTCTCTAATACTCCTACCTCGG 58.133 45.833 0.00 0.00 0.00 4.63
455 456 5.369110 TCTTCTCTAATACTCCTACCTCGGT 59.631 44.000 0.00 0.00 0.00 4.69
456 457 5.643421 TCTCTAATACTCCTACCTCGGTT 57.357 43.478 0.00 0.00 0.00 4.44
457 458 5.619220 TCTCTAATACTCCTACCTCGGTTC 58.381 45.833 0.00 0.00 0.00 3.62
458 459 4.723309 TCTAATACTCCTACCTCGGTTCC 58.277 47.826 0.00 0.00 0.00 3.62
459 460 1.978454 ATACTCCTACCTCGGTTCCG 58.022 55.000 4.74 4.74 0.00 4.30
460 461 0.911769 TACTCCTACCTCGGTTCCGA 59.088 55.000 13.34 13.34 36.95 4.55
461 462 0.038744 ACTCCTACCTCGGTTCCGAA 59.961 55.000 14.79 0.04 38.03 4.30
462 463 1.341778 ACTCCTACCTCGGTTCCGAAT 60.342 52.381 14.79 8.76 38.03 3.34
463 464 1.755380 CTCCTACCTCGGTTCCGAATT 59.245 52.381 14.79 7.32 38.03 2.17
464 465 2.954318 CTCCTACCTCGGTTCCGAATTA 59.046 50.000 14.79 8.02 38.03 1.40
465 466 3.569491 TCCTACCTCGGTTCCGAATTAT 58.431 45.455 14.79 3.96 38.03 1.28
466 467 3.962718 TCCTACCTCGGTTCCGAATTATT 59.037 43.478 14.79 1.26 38.03 1.40
467 468 4.406649 TCCTACCTCGGTTCCGAATTATTT 59.593 41.667 14.79 0.00 38.03 1.40
468 469 5.598005 TCCTACCTCGGTTCCGAATTATTTA 59.402 40.000 14.79 0.77 38.03 1.40
469 470 6.268387 TCCTACCTCGGTTCCGAATTATTTAT 59.732 38.462 14.79 0.00 38.03 1.40
470 471 6.589139 CCTACCTCGGTTCCGAATTATTTATC 59.411 42.308 14.79 0.00 38.03 1.75
471 472 6.170846 ACCTCGGTTCCGAATTATTTATCT 57.829 37.500 14.79 0.00 38.03 1.98
472 473 6.589135 ACCTCGGTTCCGAATTATTTATCTT 58.411 36.000 14.79 0.00 38.03 2.40
473 474 7.729116 ACCTCGGTTCCGAATTATTTATCTTA 58.271 34.615 14.79 0.00 38.03 2.10
474 475 8.206189 ACCTCGGTTCCGAATTATTTATCTTAA 58.794 33.333 14.79 0.00 38.03 1.85
475 476 9.048446 CCTCGGTTCCGAATTATTTATCTTAAA 57.952 33.333 14.79 0.00 38.03 1.52
506 507 9.147732 TCCAGATACAGATGTATTTAGACATGT 57.852 33.333 0.00 0.00 40.99 3.21
507 508 9.770097 CCAGATACAGATGTATTTAGACATGTT 57.230 33.333 0.00 0.00 40.99 2.71
511 512 9.817809 ATACAGATGTATTTAGACATGTTTCGT 57.182 29.630 0.00 0.00 40.18 3.85
512 513 8.186178 ACAGATGTATTTAGACATGTTTCGTC 57.814 34.615 0.00 0.00 40.18 4.20
513 514 7.277981 ACAGATGTATTTAGACATGTTTCGTCC 59.722 37.037 0.00 0.00 40.18 4.79
514 515 6.761714 AGATGTATTTAGACATGTTTCGTCCC 59.238 38.462 0.00 0.00 40.18 4.46
515 516 4.865925 TGTATTTAGACATGTTTCGTCCCG 59.134 41.667 0.00 0.00 33.70 5.14
516 517 3.663995 TTTAGACATGTTTCGTCCCGA 57.336 42.857 0.00 0.00 33.70 5.14
517 518 3.663995 TTAGACATGTTTCGTCCCGAA 57.336 42.857 0.00 0.00 44.28 4.30
518 519 2.762535 AGACATGTTTCGTCCCGAAT 57.237 45.000 0.00 0.00 45.28 3.34
519 520 2.618053 AGACATGTTTCGTCCCGAATC 58.382 47.619 0.00 0.62 45.28 2.52
520 521 2.028476 AGACATGTTTCGTCCCGAATCA 60.028 45.455 0.00 11.20 45.28 2.57
521 522 2.073816 ACATGTTTCGTCCCGAATCAC 58.926 47.619 11.07 3.91 44.43 3.06
522 523 1.396996 CATGTTTCGTCCCGAATCACC 59.603 52.381 11.07 0.00 44.43 4.02
523 524 0.682852 TGTTTCGTCCCGAATCACCT 59.317 50.000 6.14 0.00 45.28 4.00
524 525 1.337447 TGTTTCGTCCCGAATCACCTC 60.337 52.381 6.14 0.00 45.28 3.85
525 526 1.067071 GTTTCGTCCCGAATCACCTCT 60.067 52.381 0.00 0.00 45.28 3.69
526 527 0.815734 TTCGTCCCGAATCACCTCTC 59.184 55.000 0.00 0.00 41.05 3.20
527 528 0.034380 TCGTCCCGAATCACCTCTCT 60.034 55.000 0.00 0.00 31.06 3.10
528 529 0.818296 CGTCCCGAATCACCTCTCTT 59.182 55.000 0.00 0.00 0.00 2.85
529 530 2.022195 CGTCCCGAATCACCTCTCTTA 58.978 52.381 0.00 0.00 0.00 2.10
530 531 2.426024 CGTCCCGAATCACCTCTCTTAA 59.574 50.000 0.00 0.00 0.00 1.85
531 532 3.119245 CGTCCCGAATCACCTCTCTTAAA 60.119 47.826 0.00 0.00 0.00 1.52
532 533 4.441634 CGTCCCGAATCACCTCTCTTAAAT 60.442 45.833 0.00 0.00 0.00 1.40
533 534 5.429130 GTCCCGAATCACCTCTCTTAAATT 58.571 41.667 0.00 0.00 0.00 1.82
534 535 5.880887 GTCCCGAATCACCTCTCTTAAATTT 59.119 40.000 0.00 0.00 0.00 1.82
535 536 7.046033 GTCCCGAATCACCTCTCTTAAATTTA 58.954 38.462 0.00 0.00 0.00 1.40
536 537 7.715686 GTCCCGAATCACCTCTCTTAAATTTAT 59.284 37.037 0.00 0.00 0.00 1.40
537 538 8.930527 TCCCGAATCACCTCTCTTAAATTTATA 58.069 33.333 0.00 0.00 0.00 0.98
538 539 9.726438 CCCGAATCACCTCTCTTAAATTTATAT 57.274 33.333 0.00 0.00 0.00 0.86
562 563 6.282199 AGATACAAATGAACCTAGACACGT 57.718 37.500 0.00 0.00 0.00 4.49
563 564 7.400599 AGATACAAATGAACCTAGACACGTA 57.599 36.000 0.00 0.00 0.00 3.57
564 565 7.481642 AGATACAAATGAACCTAGACACGTAG 58.518 38.462 0.00 0.00 0.00 3.51
565 566 4.817517 ACAAATGAACCTAGACACGTAGG 58.182 43.478 0.36 0.36 44.77 3.18
566 567 4.181578 CAAATGAACCTAGACACGTAGGG 58.818 47.826 7.02 0.00 43.67 3.53
567 568 2.885135 TGAACCTAGACACGTAGGGA 57.115 50.000 7.02 0.00 43.67 4.20
568 569 3.159213 TGAACCTAGACACGTAGGGAA 57.841 47.619 7.02 0.00 43.67 3.97
569 570 3.087031 TGAACCTAGACACGTAGGGAAG 58.913 50.000 7.02 0.00 43.67 3.46
570 571 2.895242 ACCTAGACACGTAGGGAAGT 57.105 50.000 7.02 0.00 43.67 3.01
571 572 4.263462 TGAACCTAGACACGTAGGGAAGTA 60.263 45.833 7.02 0.00 43.67 2.24
572 573 3.615155 ACCTAGACACGTAGGGAAGTAC 58.385 50.000 7.02 0.00 43.67 2.73
584 585 7.840342 CGTAGGGAAGTACGTATATGATACT 57.160 40.000 0.00 0.87 40.75 2.12
585 586 7.904094 CGTAGGGAAGTACGTATATGATACTC 58.096 42.308 0.00 0.00 40.75 2.59
586 587 7.010923 CGTAGGGAAGTACGTATATGATACTCC 59.989 44.444 0.00 6.74 40.75 3.85
587 588 6.186234 AGGGAAGTACGTATATGATACTCCC 58.814 44.000 18.92 18.92 36.98 4.30
588 589 6.011805 AGGGAAGTACGTATATGATACTCCCT 60.012 42.308 20.81 20.81 39.38 4.20
589 590 6.318396 GGGAAGTACGTATATGATACTCCCTC 59.682 46.154 19.07 11.09 35.53 4.30
590 591 6.318396 GGAAGTACGTATATGATACTCCCTCC 59.682 46.154 0.00 4.30 0.00 4.30
591 592 5.426504 AGTACGTATATGATACTCCCTCCG 58.573 45.833 0.00 0.00 0.00 4.63
592 593 4.298103 ACGTATATGATACTCCCTCCGT 57.702 45.455 0.00 0.00 0.00 4.69
593 594 4.660168 ACGTATATGATACTCCCTCCGTT 58.340 43.478 0.00 0.00 0.00 4.44
594 595 4.699257 ACGTATATGATACTCCCTCCGTTC 59.301 45.833 0.00 0.00 0.00 3.95
595 596 4.096081 CGTATATGATACTCCCTCCGTTCC 59.904 50.000 0.00 0.00 0.00 3.62
596 597 1.329256 ATGATACTCCCTCCGTTCCG 58.671 55.000 0.00 0.00 0.00 4.30
597 598 0.256752 TGATACTCCCTCCGTTCCGA 59.743 55.000 0.00 0.00 0.00 4.55
598 599 1.341285 TGATACTCCCTCCGTTCCGAA 60.341 52.381 0.00 0.00 0.00 4.30
599 600 1.962100 GATACTCCCTCCGTTCCGAAT 59.038 52.381 0.00 0.00 0.00 3.34
600 601 1.856629 TACTCCCTCCGTTCCGAATT 58.143 50.000 0.00 0.00 0.00 2.17
601 602 1.856629 ACTCCCTCCGTTCCGAATTA 58.143 50.000 0.00 0.00 0.00 1.40
602 603 1.479730 ACTCCCTCCGTTCCGAATTAC 59.520 52.381 0.00 0.00 0.00 1.89
603 604 1.755380 CTCCCTCCGTTCCGAATTACT 59.245 52.381 0.00 0.00 0.00 2.24
604 605 2.167900 CTCCCTCCGTTCCGAATTACTT 59.832 50.000 0.00 0.00 0.00 2.24
605 606 2.093869 TCCCTCCGTTCCGAATTACTTG 60.094 50.000 0.00 0.00 0.00 3.16
606 607 2.354403 CCCTCCGTTCCGAATTACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
607 608 2.928116 CCTCCGTTCCGAATTACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
608 609 3.368116 CCTCCGTTCCGAATTACTTGTCT 60.368 47.826 0.00 0.00 0.00 3.41
609 610 4.243270 CTCCGTTCCGAATTACTTGTCTT 58.757 43.478 0.00 0.00 0.00 3.01
610 611 3.991773 TCCGTTCCGAATTACTTGTCTTG 59.008 43.478 0.00 0.00 0.00 3.02
611 612 3.124636 CCGTTCCGAATTACTTGTCTTGG 59.875 47.826 0.00 0.00 0.00 3.61
612 613 3.991773 CGTTCCGAATTACTTGTCTTGGA 59.008 43.478 0.00 0.00 0.00 3.53
613 614 4.630069 CGTTCCGAATTACTTGTCTTGGAT 59.370 41.667 0.00 0.00 0.00 3.41
614 615 5.121768 CGTTCCGAATTACTTGTCTTGGATT 59.878 40.000 0.00 0.00 0.00 3.01
615 616 6.348213 CGTTCCGAATTACTTGTCTTGGATTT 60.348 38.462 0.00 0.00 0.00 2.17
616 617 6.494893 TCCGAATTACTTGTCTTGGATTTG 57.505 37.500 0.00 0.00 0.00 2.32
617 618 6.001460 TCCGAATTACTTGTCTTGGATTTGT 58.999 36.000 0.00 0.00 0.00 2.83
618 619 6.148811 TCCGAATTACTTGTCTTGGATTTGTC 59.851 38.462 0.00 0.00 0.00 3.18
619 620 6.149474 CCGAATTACTTGTCTTGGATTTGTCT 59.851 38.462 0.00 0.00 0.00 3.41
620 621 7.333423 CCGAATTACTTGTCTTGGATTTGTCTA 59.667 37.037 0.00 0.00 0.00 2.59
621 622 8.383619 CGAATTACTTGTCTTGGATTTGTCTAG 58.616 37.037 0.00 0.00 0.00 2.43
622 623 9.436957 GAATTACTTGTCTTGGATTTGTCTAGA 57.563 33.333 0.00 0.00 0.00 2.43
623 624 9.965902 AATTACTTGTCTTGGATTTGTCTAGAT 57.034 29.630 0.00 0.00 0.00 1.98
625 626 9.871238 TTACTTGTCTTGGATTTGTCTAGATAC 57.129 33.333 0.00 0.00 0.00 2.24
626 627 7.036220 ACTTGTCTTGGATTTGTCTAGATACG 58.964 38.462 0.00 0.00 0.00 3.06
627 628 5.902681 TGTCTTGGATTTGTCTAGATACGG 58.097 41.667 0.00 0.00 0.00 4.02
628 629 5.655090 TGTCTTGGATTTGTCTAGATACGGA 59.345 40.000 0.00 0.00 0.00 4.69
629 630 6.323996 TGTCTTGGATTTGTCTAGATACGGAT 59.676 38.462 0.00 0.00 0.00 4.18
630 631 6.642950 GTCTTGGATTTGTCTAGATACGGATG 59.357 42.308 0.00 0.00 0.00 3.51
631 632 6.323996 TCTTGGATTTGTCTAGATACGGATGT 59.676 38.462 0.00 0.00 0.00 3.06
632 633 7.504574 TCTTGGATTTGTCTAGATACGGATGTA 59.495 37.037 0.00 0.00 34.45 2.29
633 634 7.776618 TGGATTTGTCTAGATACGGATGTAT 57.223 36.000 0.00 0.00 43.97 2.29
648 649 7.441890 ACGGATGTATCTACACTCATCTTAG 57.558 40.000 0.00 0.00 39.30 2.18
649 650 6.999272 ACGGATGTATCTACACTCATCTTAGT 59.001 38.462 0.00 0.00 39.30 2.24
660 661 6.892658 CACTCATCTTAGTGCTAGATACCT 57.107 41.667 0.00 0.00 40.40 3.08
661 662 6.908825 CACTCATCTTAGTGCTAGATACCTC 58.091 44.000 0.00 0.00 40.40 3.85
662 663 6.007703 ACTCATCTTAGTGCTAGATACCTCC 58.992 44.000 0.00 0.00 0.00 4.30
663 664 5.004448 TCATCTTAGTGCTAGATACCTCCG 58.996 45.833 0.00 0.00 0.00 4.63
664 665 4.434545 TCTTAGTGCTAGATACCTCCGT 57.565 45.455 0.00 0.00 0.00 4.69
665 666 5.557576 TCTTAGTGCTAGATACCTCCGTA 57.442 43.478 0.00 0.00 0.00 4.02
666 667 6.124316 TCTTAGTGCTAGATACCTCCGTAT 57.876 41.667 0.00 0.00 37.92 3.06
678 679 7.690952 GATACCTCCGTATCTAGACAAATCT 57.309 40.000 0.00 0.00 45.11 2.40
679 680 8.789825 GATACCTCCGTATCTAGACAAATCTA 57.210 38.462 0.00 0.00 45.11 1.98
680 681 9.228949 GATACCTCCGTATCTAGACAAATCTAA 57.771 37.037 0.00 0.00 45.11 2.10
681 682 7.513371 ACCTCCGTATCTAGACAAATCTAAG 57.487 40.000 0.00 0.00 36.98 2.18
682 683 7.288560 ACCTCCGTATCTAGACAAATCTAAGA 58.711 38.462 0.00 0.00 36.98 2.10
683 684 7.778853 ACCTCCGTATCTAGACAAATCTAAGAA 59.221 37.037 0.00 0.00 36.98 2.52
684 685 8.630917 CCTCCGTATCTAGACAAATCTAAGAAA 58.369 37.037 0.00 0.00 36.98 2.52
687 688 9.804758 CCGTATCTAGACAAATCTAAGAAAAGT 57.195 33.333 0.00 0.00 36.98 2.66
695 696 9.720769 AGACAAATCTAAGAAAAGTAATTCGGA 57.279 29.630 0.00 0.00 31.78 4.55
712 713 2.551355 GGAACGAAGGGAGTACGTAC 57.449 55.000 18.10 18.10 39.31 3.67
713 714 2.087646 GGAACGAAGGGAGTACGTACT 58.912 52.381 27.71 27.71 39.31 2.73
714 715 3.270877 GGAACGAAGGGAGTACGTACTA 58.729 50.000 27.44 0.00 39.31 1.82
715 716 3.311048 GGAACGAAGGGAGTACGTACTAG 59.689 52.174 27.44 16.00 39.31 2.57
716 717 3.618690 ACGAAGGGAGTACGTACTAGT 57.381 47.619 27.44 16.56 38.47 2.57
717 718 3.265791 ACGAAGGGAGTACGTACTAGTG 58.734 50.000 27.44 15.87 38.47 2.74
718 719 2.031437 CGAAGGGAGTACGTACTAGTGC 59.969 54.545 27.44 14.99 36.50 4.40
719 720 2.795231 AGGGAGTACGTACTAGTGCA 57.205 50.000 27.44 0.00 36.50 4.57
720 721 3.294038 AGGGAGTACGTACTAGTGCAT 57.706 47.619 27.44 7.25 36.50 3.96
721 722 4.428294 AGGGAGTACGTACTAGTGCATA 57.572 45.455 27.44 0.00 36.50 3.14
722 723 4.983053 AGGGAGTACGTACTAGTGCATAT 58.017 43.478 27.44 2.98 36.50 1.78
723 724 5.383476 AGGGAGTACGTACTAGTGCATATT 58.617 41.667 27.44 2.20 36.50 1.28
724 725 6.537355 AGGGAGTACGTACTAGTGCATATTA 58.463 40.000 27.44 0.00 36.50 0.98
725 726 7.173722 AGGGAGTACGTACTAGTGCATATTAT 58.826 38.462 27.44 1.42 36.50 1.28
726 727 7.668886 AGGGAGTACGTACTAGTGCATATTATT 59.331 37.037 27.44 0.96 36.50 1.40
727 728 7.967303 GGGAGTACGTACTAGTGCATATTATTC 59.033 40.741 27.44 10.26 36.50 1.75
728 729 8.728833 GGAGTACGTACTAGTGCATATTATTCT 58.271 37.037 27.44 0.00 36.50 2.40
788 789 6.260936 AGAGTGTGAATCAAACGAAAACTCAT 59.739 34.615 0.00 0.00 35.18 2.90
850 855 2.291741 AGAGGAAGCAAACAAAGCGAAG 59.708 45.455 0.00 0.00 37.01 3.79
851 856 2.290641 GAGGAAGCAAACAAAGCGAAGA 59.709 45.455 0.00 0.00 37.01 2.87
856 872 1.068954 GCAAACAAAGCGAAGAGGAGG 60.069 52.381 0.00 0.00 0.00 4.30
865 881 0.612174 CGAAGAGGAGGTGAGGTCCA 60.612 60.000 0.00 0.00 36.43 4.02
889 905 4.093952 GCTGTGCGCTGCGACAAT 62.094 61.111 28.07 0.00 35.14 2.71
890 906 2.097160 CTGTGCGCTGCGACAATC 59.903 61.111 28.07 12.23 0.00 2.67
891 907 2.664518 TGTGCGCTGCGACAATCA 60.665 55.556 28.07 14.52 0.00 2.57
892 908 2.173951 CTGTGCGCTGCGACAATCAA 62.174 55.000 28.07 8.73 0.00 2.57
893 909 1.082169 GTGCGCTGCGACAATCAAA 60.082 52.632 28.07 0.00 0.00 2.69
894 910 1.082169 TGCGCTGCGACAATCAAAC 60.082 52.632 28.07 4.82 0.00 2.93
895 911 2.139811 GCGCTGCGACAATCAAACG 61.140 57.895 28.07 0.00 0.00 3.60
896 912 1.204062 CGCTGCGACAATCAAACGT 59.796 52.632 18.66 0.00 0.00 3.99
897 913 0.785708 CGCTGCGACAATCAAACGTC 60.786 55.000 18.66 0.00 0.00 4.34
898 914 0.234625 GCTGCGACAATCAAACGTCA 59.765 50.000 0.00 0.00 32.24 4.35
899 915 1.333702 GCTGCGACAATCAAACGTCAA 60.334 47.619 0.00 0.00 32.24 3.18
900 916 2.665519 GCTGCGACAATCAAACGTCAAT 60.666 45.455 0.00 0.00 32.24 2.57
901 917 3.424302 GCTGCGACAATCAAACGTCAATA 60.424 43.478 0.00 0.00 32.24 1.90
906 922 6.304445 TGCGACAATCAAACGTCAATATTTTC 59.696 34.615 0.00 0.00 32.24 2.29
1012 1028 4.885270 CACCCAACCACCGCACCA 62.885 66.667 0.00 0.00 0.00 4.17
1021 1037 4.116585 ACCGCACCACACCACCAA 62.117 61.111 0.00 0.00 0.00 3.67
1032 1048 1.754226 ACACCACCAAATCACACCAAC 59.246 47.619 0.00 0.00 0.00 3.77
1944 1975 2.291043 CCTGCGGTACCAGACCCTT 61.291 63.158 13.54 0.00 46.81 3.95
2007 2038 3.744660 GGTCTTCAAGGTGTCTGTGATT 58.255 45.455 0.00 0.00 0.00 2.57
2010 2041 2.936919 TCAAGGTGTCTGTGATTGCT 57.063 45.000 0.00 0.00 0.00 3.91
2013 2044 3.578282 TCAAGGTGTCTGTGATTGCTCTA 59.422 43.478 0.00 0.00 0.00 2.43
2016 2047 2.094700 GGTGTCTGTGATTGCTCTACGA 60.095 50.000 0.00 0.00 0.00 3.43
2040 2071 0.393132 TGAACAACGTGCTTGGTGGA 60.393 50.000 0.00 0.00 33.66 4.02
2133 2164 2.371510 AGCCAAGGAGAGATTGATAGCC 59.628 50.000 0.00 0.00 0.00 3.93
2378 2409 5.007136 GTGTTATGAGATGGCTTGCTTAGAC 59.993 44.000 0.00 0.00 0.00 2.59
2427 2458 2.290367 CTCGTGTGCTCATTTGGTCAAA 59.710 45.455 0.00 0.00 34.46 2.69
2431 2462 5.030295 CGTGTGCTCATTTGGTCAAATATC 58.970 41.667 8.40 2.91 38.84 1.63
2438 2469 6.040166 GCTCATTTGGTCAAATATCCATCTGT 59.960 38.462 8.40 0.00 38.84 3.41
2486 2536 5.585445 TGTTGATTTGTCTGCTTGCATTTTT 59.415 32.000 0.00 0.00 0.00 1.94
2554 2604 9.506018 TTTGATGACAAGATCTTTATGAGTTGA 57.494 29.630 4.86 0.00 37.32 3.18
2601 2651 2.286872 CAGAGCCAAATCTAGCCACAG 58.713 52.381 0.00 0.00 0.00 3.66
2604 2654 1.176527 GCCAAATCTAGCCACAGCAA 58.823 50.000 0.00 0.00 43.56 3.91
2619 2669 1.674441 CAGCAATGTGCCGAGATGATT 59.326 47.619 0.00 0.00 46.52 2.57
2669 2719 4.826183 AGTGTCGTAACTTTGGACTAGTCT 59.174 41.667 21.88 4.14 0.00 3.24
2732 2782 4.963276 TTGCATTTCTCTTGGTAATCGG 57.037 40.909 0.00 0.00 0.00 4.18
2825 2877 8.253810 AGAATGATTGTCTCGATCTGAAGTTTA 58.746 33.333 0.00 0.00 0.00 2.01
2826 2878 7.763172 ATGATTGTCTCGATCTGAAGTTTAC 57.237 36.000 0.00 0.00 0.00 2.01
2837 2889 7.017645 CGATCTGAAGTTTACACAGGATTTTG 58.982 38.462 0.00 0.00 33.19 2.44
2838 2890 7.307989 CGATCTGAAGTTTACACAGGATTTTGT 60.308 37.037 0.00 0.00 33.19 2.83
2839 2891 8.918202 ATCTGAAGTTTACACAGGATTTTGTA 57.082 30.769 0.00 0.00 33.19 2.41
2852 2905 6.101150 ACAGGATTTTGTAGGGAGTATATGCA 59.899 38.462 0.00 0.00 0.00 3.96
2881 2934 5.877012 CACTGTGTACTGGCTCATAATTTCT 59.123 40.000 0.00 0.00 0.00 2.52
2885 2938 5.294552 GTGTACTGGCTCATAATTTCTCCAC 59.705 44.000 0.00 0.00 0.00 4.02
2908 2963 2.903855 GTGCATCATGGCCTCCCG 60.904 66.667 3.32 0.00 0.00 5.14
2946 3001 5.824097 ACATTCCACGGTTGTAGTTTTAGTT 59.176 36.000 0.00 0.00 0.00 2.24
2952 3007 6.183360 CCACGGTTGTAGTTTTAGTTCTTGTT 60.183 38.462 0.00 0.00 0.00 2.83
2953 3008 6.685403 CACGGTTGTAGTTTTAGTTCTTGTTG 59.315 38.462 0.00 0.00 0.00 3.33
2954 3009 6.372381 ACGGTTGTAGTTTTAGTTCTTGTTGT 59.628 34.615 0.00 0.00 0.00 3.32
2955 3010 6.903479 CGGTTGTAGTTTTAGTTCTTGTTGTC 59.097 38.462 0.00 0.00 0.00 3.18
2956 3011 7.201582 CGGTTGTAGTTTTAGTTCTTGTTGTCT 60.202 37.037 0.00 0.00 0.00 3.41
2957 3012 7.908601 GGTTGTAGTTTTAGTTCTTGTTGTCTG 59.091 37.037 0.00 0.00 0.00 3.51
2958 3013 8.448615 GTTGTAGTTTTAGTTCTTGTTGTCTGT 58.551 33.333 0.00 0.00 0.00 3.41
2960 3015 8.038944 TGTAGTTTTAGTTCTTGTTGTCTGTCT 58.961 33.333 0.00 0.00 0.00 3.41
2977 3032 4.348168 TCTGTCTGGCTTCTAAAAAGGAGT 59.652 41.667 0.00 0.00 0.00 3.85
2979 3034 4.102524 TGTCTGGCTTCTAAAAAGGAGTCA 59.897 41.667 0.00 0.00 0.00 3.41
2982 3037 6.879458 GTCTGGCTTCTAAAAAGGAGTCATTA 59.121 38.462 0.00 0.00 0.00 1.90
2984 3039 7.554118 TCTGGCTTCTAAAAAGGAGTCATTATG 59.446 37.037 0.00 0.00 0.00 1.90
2987 3042 8.523658 GGCTTCTAAAAAGGAGTCATTATGTTT 58.476 33.333 0.00 0.00 0.00 2.83
2993 3048 4.510167 AGGAGTCATTATGTTTGGGGAG 57.490 45.455 0.00 0.00 0.00 4.30
3009 3064 4.785301 TGGGGAGCTAAATCTTGATCTTG 58.215 43.478 0.00 0.00 0.00 3.02
3010 3065 4.474651 TGGGGAGCTAAATCTTGATCTTGA 59.525 41.667 0.00 0.00 0.00 3.02
3011 3066 5.044919 TGGGGAGCTAAATCTTGATCTTGAA 60.045 40.000 0.00 0.00 0.00 2.69
3060 3115 2.421424 GGCTAACCTTTCTGCTGACATG 59.579 50.000 0.00 0.00 0.00 3.21
3070 3125 2.622942 TCTGCTGACATGGTTCCAAAAC 59.377 45.455 0.00 0.00 34.46 2.43
3124 3179 0.307453 TGATGCTGTCGTTGTTGCAC 59.693 50.000 0.00 0.00 38.29 4.57
3126 3181 2.052237 GCTGTCGTTGTTGCACGG 60.052 61.111 0.00 0.00 40.74 4.94
3131 3186 2.425124 CGTTGTTGCACGGAAGCG 60.425 61.111 0.00 0.00 36.47 4.68
3153 3208 1.674817 CGGAAGTATTGGCTGGTCGTT 60.675 52.381 0.00 0.00 0.00 3.85
3165 3220 2.671632 GCTGGTCGTTCCTCTTGTAGAC 60.672 54.545 1.80 0.00 37.07 2.59
3171 3226 2.342179 GTTCCTCTTGTAGACTGCTGC 58.658 52.381 0.00 0.00 0.00 5.25
3176 3231 0.319900 CTTGTAGACTGCTGCGTGGT 60.320 55.000 2.10 0.00 0.00 4.16
3177 3232 0.105964 TTGTAGACTGCTGCGTGGTT 59.894 50.000 2.10 0.00 0.00 3.67
3178 3233 0.319555 TGTAGACTGCTGCGTGGTTC 60.320 55.000 2.10 0.00 0.00 3.62
3179 3234 1.080772 TAGACTGCTGCGTGGTTCG 60.081 57.895 2.10 0.00 43.12 3.95
3180 3235 2.486636 TAGACTGCTGCGTGGTTCGG 62.487 60.000 2.10 0.00 40.26 4.30
3181 3236 4.988598 ACTGCTGCGTGGTTCGGG 62.989 66.667 0.00 0.00 40.26 5.14
3196 3251 3.102097 GGGCTATGCACGAACAGC 58.898 61.111 0.00 0.00 0.00 4.40
3199 3254 2.170738 GCTATGCACGAACAGCCAA 58.829 52.632 0.00 0.00 0.00 4.52
3314 3392 4.264460 AGCTTCTCGACAAGTTTCTCAT 57.736 40.909 2.30 0.00 0.00 2.90
3328 3406 4.137543 GTTTCTCATGAGGGTTTGAGTGT 58.862 43.478 22.42 0.00 40.22 3.55
3339 3417 2.543653 GGTTTGAGTGTGACATGGTTGC 60.544 50.000 0.00 0.00 0.00 4.17
3357 3435 1.004918 CTGGTGGACGGTGAGGTTC 60.005 63.158 0.00 0.00 0.00 3.62
3373 3451 3.266230 TTCCAATTGCTGTGCGCCG 62.266 57.895 4.18 0.00 38.05 6.46
3391 3469 1.101049 CGTGGTTGGTGAAGCAAGGT 61.101 55.000 0.00 0.00 41.15 3.50
3392 3470 1.111277 GTGGTTGGTGAAGCAAGGTT 58.889 50.000 0.00 0.00 41.15 3.50
3393 3471 1.480545 GTGGTTGGTGAAGCAAGGTTT 59.519 47.619 0.00 0.00 41.15 3.27
3394 3472 1.754226 TGGTTGGTGAAGCAAGGTTTC 59.246 47.619 0.00 0.00 36.64 2.78
3395 3473 1.068588 GGTTGGTGAAGCAAGGTTTCC 59.931 52.381 0.00 0.00 0.00 3.13
3396 3474 1.754226 GTTGGTGAAGCAAGGTTTCCA 59.246 47.619 0.00 6.01 0.00 3.53
3397 3475 2.151502 TGGTGAAGCAAGGTTTCCAA 57.848 45.000 7.16 0.00 0.00 3.53
3398 3476 2.676748 TGGTGAAGCAAGGTTTCCAAT 58.323 42.857 7.16 0.00 0.00 3.16
3399 3477 3.037549 TGGTGAAGCAAGGTTTCCAATT 58.962 40.909 7.16 0.00 0.00 2.32
3400 3478 3.181467 TGGTGAAGCAAGGTTTCCAATTG 60.181 43.478 0.00 0.00 0.00 2.32
3404 3482 1.150827 GCAAGGTTTCCAATTGCTGC 58.849 50.000 0.00 0.00 44.57 5.25
3405 3483 1.421382 CAAGGTTTCCAATTGCTGCG 58.579 50.000 0.00 0.00 0.00 5.18
3406 3484 0.319813 AAGGTTTCCAATTGCTGCGC 60.320 50.000 0.00 0.00 0.00 6.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
424 425 6.987403 AGGAGTATTAGAGAAGAATGGGAC 57.013 41.667 0.00 0.00 0.00 4.46
425 426 7.011382 GGTAGGAGTATTAGAGAAGAATGGGA 58.989 42.308 0.00 0.00 0.00 4.37
426 427 7.013834 AGGTAGGAGTATTAGAGAAGAATGGG 58.986 42.308 0.00 0.00 0.00 4.00
427 428 7.094549 CGAGGTAGGAGTATTAGAGAAGAATGG 60.095 44.444 0.00 0.00 0.00 3.16
428 429 7.094549 CCGAGGTAGGAGTATTAGAGAAGAATG 60.095 44.444 0.00 0.00 0.00 2.67
429 430 6.943718 CCGAGGTAGGAGTATTAGAGAAGAAT 59.056 42.308 0.00 0.00 0.00 2.40
430 431 6.126536 ACCGAGGTAGGAGTATTAGAGAAGAA 60.127 42.308 0.00 0.00 34.73 2.52
431 432 5.369110 ACCGAGGTAGGAGTATTAGAGAAGA 59.631 44.000 0.00 0.00 34.73 2.87
432 433 5.623169 ACCGAGGTAGGAGTATTAGAGAAG 58.377 45.833 0.00 0.00 34.73 2.85
433 434 5.643421 ACCGAGGTAGGAGTATTAGAGAA 57.357 43.478 0.00 0.00 34.73 2.87
434 435 5.455899 GGAACCGAGGTAGGAGTATTAGAGA 60.456 48.000 0.00 0.00 34.73 3.10
435 436 4.761227 GGAACCGAGGTAGGAGTATTAGAG 59.239 50.000 0.00 0.00 34.73 2.43
436 437 4.723309 GGAACCGAGGTAGGAGTATTAGA 58.277 47.826 0.00 0.00 34.73 2.10
437 438 3.501445 CGGAACCGAGGTAGGAGTATTAG 59.499 52.174 7.53 0.00 42.83 1.73
438 439 3.136443 TCGGAACCGAGGTAGGAGTATTA 59.864 47.826 12.04 0.00 44.01 0.98
439 440 2.092212 TCGGAACCGAGGTAGGAGTATT 60.092 50.000 12.04 0.00 44.01 1.89
440 441 1.492176 TCGGAACCGAGGTAGGAGTAT 59.508 52.381 12.04 0.00 44.01 2.12
441 442 0.911769 TCGGAACCGAGGTAGGAGTA 59.088 55.000 12.04 0.00 44.01 2.59
442 443 1.687612 TCGGAACCGAGGTAGGAGT 59.312 57.895 12.04 0.00 44.01 3.85
443 444 4.651867 TCGGAACCGAGGTAGGAG 57.348 61.111 12.04 0.00 44.01 3.69
480 481 9.147732 ACATGTCTAAATACATCTGTATCTGGA 57.852 33.333 3.44 0.00 40.10 3.86
481 482 9.770097 AACATGTCTAAATACATCTGTATCTGG 57.230 33.333 0.00 0.00 40.10 3.86
485 486 9.817809 ACGAAACATGTCTAAATACATCTGTAT 57.182 29.630 0.00 0.00 42.60 2.29
486 487 9.297586 GACGAAACATGTCTAAATACATCTGTA 57.702 33.333 0.00 0.00 38.01 2.74
487 488 7.277981 GGACGAAACATGTCTAAATACATCTGT 59.722 37.037 0.00 0.00 38.01 3.41
488 489 7.254455 GGGACGAAACATGTCTAAATACATCTG 60.254 40.741 0.00 0.00 38.01 2.90
489 490 6.761714 GGGACGAAACATGTCTAAATACATCT 59.238 38.462 0.00 0.00 38.01 2.90
490 491 6.945072 GGGACGAAACATGTCTAAATACATC 58.055 40.000 0.00 0.00 38.01 3.06
491 492 6.920569 GGGACGAAACATGTCTAAATACAT 57.079 37.500 0.00 0.00 40.75 2.29
510 511 4.467198 TTTAAGAGAGGTGATTCGGGAC 57.533 45.455 0.00 0.00 0.00 4.46
511 512 5.693769 AATTTAAGAGAGGTGATTCGGGA 57.306 39.130 0.00 0.00 0.00 5.14
512 513 9.726438 ATATAAATTTAAGAGAGGTGATTCGGG 57.274 33.333 1.21 0.00 0.00 5.14
536 537 9.128404 ACGTGTCTAGGTTCATTTGTATCTATA 57.872 33.333 0.00 0.00 0.00 1.31
537 538 8.008513 ACGTGTCTAGGTTCATTTGTATCTAT 57.991 34.615 0.00 0.00 0.00 1.98
538 539 7.400599 ACGTGTCTAGGTTCATTTGTATCTA 57.599 36.000 0.00 0.00 0.00 1.98
539 540 6.282199 ACGTGTCTAGGTTCATTTGTATCT 57.718 37.500 0.00 0.00 0.00 1.98
540 541 6.696148 CCTACGTGTCTAGGTTCATTTGTATC 59.304 42.308 0.00 0.00 0.00 2.24
541 542 6.406624 CCCTACGTGTCTAGGTTCATTTGTAT 60.407 42.308 0.00 0.00 32.52 2.29
542 543 5.105635 CCCTACGTGTCTAGGTTCATTTGTA 60.106 44.000 0.00 0.00 32.52 2.41
543 544 4.322499 CCCTACGTGTCTAGGTTCATTTGT 60.322 45.833 0.00 0.00 32.52 2.83
544 545 4.081862 TCCCTACGTGTCTAGGTTCATTTG 60.082 45.833 0.00 0.00 32.52 2.32
545 546 4.091549 TCCCTACGTGTCTAGGTTCATTT 58.908 43.478 0.00 0.00 32.52 2.32
546 547 3.705051 TCCCTACGTGTCTAGGTTCATT 58.295 45.455 0.00 0.00 32.52 2.57
547 548 3.377253 TCCCTACGTGTCTAGGTTCAT 57.623 47.619 0.00 0.00 32.52 2.57
548 549 2.885135 TCCCTACGTGTCTAGGTTCA 57.115 50.000 0.00 0.00 32.52 3.18
549 550 3.087781 ACTTCCCTACGTGTCTAGGTTC 58.912 50.000 0.00 0.00 32.52 3.62
550 551 3.166560 ACTTCCCTACGTGTCTAGGTT 57.833 47.619 0.00 0.00 32.52 3.50
551 552 2.895242 ACTTCCCTACGTGTCTAGGT 57.105 50.000 0.00 0.00 32.52 3.08
552 553 2.611292 CGTACTTCCCTACGTGTCTAGG 59.389 54.545 0.00 0.00 35.74 3.02
553 554 3.940657 CGTACTTCCCTACGTGTCTAG 57.059 52.381 0.00 0.00 35.74 2.43
559 560 7.547370 GAGTATCATATACGTACTTCCCTACGT 59.453 40.741 0.00 9.16 44.54 3.57
560 561 7.010923 GGAGTATCATATACGTACTTCCCTACG 59.989 44.444 0.00 0.00 40.61 3.51
561 562 7.281999 GGGAGTATCATATACGTACTTCCCTAC 59.718 44.444 0.00 0.00 37.90 3.18
562 563 7.183475 AGGGAGTATCATATACGTACTTCCCTA 59.817 40.741 16.48 0.14 42.65 3.53
563 564 6.011805 AGGGAGTATCATATACGTACTTCCCT 60.012 42.308 13.93 13.93 42.65 4.20
564 565 6.186234 AGGGAGTATCATATACGTACTTCCC 58.814 44.000 6.16 10.96 42.65 3.97
565 566 6.318396 GGAGGGAGTATCATATACGTACTTCC 59.682 46.154 0.00 0.00 42.20 3.46
566 567 6.036953 CGGAGGGAGTATCATATACGTACTTC 59.963 46.154 0.00 0.00 36.25 3.01
567 568 5.879223 CGGAGGGAGTATCATATACGTACTT 59.121 44.000 0.00 0.00 36.25 2.24
568 569 5.046014 ACGGAGGGAGTATCATATACGTACT 60.046 44.000 0.00 0.00 36.25 2.73
569 570 5.181748 ACGGAGGGAGTATCATATACGTAC 58.818 45.833 0.00 0.00 36.25 3.67
570 571 5.426689 ACGGAGGGAGTATCATATACGTA 57.573 43.478 0.00 0.00 36.25 3.57
571 572 4.298103 ACGGAGGGAGTATCATATACGT 57.702 45.455 0.00 0.00 36.25 3.57
572 573 4.096081 GGAACGGAGGGAGTATCATATACG 59.904 50.000 0.00 0.00 36.25 3.06
573 574 5.579564 GGAACGGAGGGAGTATCATATAC 57.420 47.826 0.00 0.00 36.25 1.47
591 592 6.496338 AATCCAAGACAAGTAATTCGGAAC 57.504 37.500 0.00 0.00 0.00 3.62
592 593 6.488683 ACAAATCCAAGACAAGTAATTCGGAA 59.511 34.615 0.00 0.00 0.00 4.30
593 594 6.001460 ACAAATCCAAGACAAGTAATTCGGA 58.999 36.000 0.00 0.00 0.00 4.55
594 595 6.149474 AGACAAATCCAAGACAAGTAATTCGG 59.851 38.462 0.00 0.00 0.00 4.30
595 596 7.133891 AGACAAATCCAAGACAAGTAATTCG 57.866 36.000 0.00 0.00 0.00 3.34
596 597 9.436957 TCTAGACAAATCCAAGACAAGTAATTC 57.563 33.333 0.00 0.00 0.00 2.17
597 598 9.965902 ATCTAGACAAATCCAAGACAAGTAATT 57.034 29.630 0.00 0.00 0.00 1.40
599 600 9.871238 GTATCTAGACAAATCCAAGACAAGTAA 57.129 33.333 0.00 0.00 0.00 2.24
600 601 8.188799 CGTATCTAGACAAATCCAAGACAAGTA 58.811 37.037 0.00 0.00 0.00 2.24
601 602 7.036220 CGTATCTAGACAAATCCAAGACAAGT 58.964 38.462 0.00 0.00 0.00 3.16
602 603 6.477033 CCGTATCTAGACAAATCCAAGACAAG 59.523 42.308 0.00 0.00 0.00 3.16
603 604 6.153851 TCCGTATCTAGACAAATCCAAGACAA 59.846 38.462 0.00 0.00 0.00 3.18
604 605 5.655090 TCCGTATCTAGACAAATCCAAGACA 59.345 40.000 0.00 0.00 0.00 3.41
605 606 6.145338 TCCGTATCTAGACAAATCCAAGAC 57.855 41.667 0.00 0.00 0.00 3.01
606 607 6.323996 ACATCCGTATCTAGACAAATCCAAGA 59.676 38.462 0.00 0.00 0.00 3.02
607 608 6.516718 ACATCCGTATCTAGACAAATCCAAG 58.483 40.000 0.00 0.00 0.00 3.61
608 609 6.479972 ACATCCGTATCTAGACAAATCCAA 57.520 37.500 0.00 0.00 0.00 3.53
609 610 7.776618 ATACATCCGTATCTAGACAAATCCA 57.223 36.000 0.00 0.00 32.66 3.41
622 623 9.168451 CTAAGATGAGTGTAGATACATCCGTAT 57.832 37.037 0.00 0.00 41.16 3.06
623 624 8.155510 ACTAAGATGAGTGTAGATACATCCGTA 58.844 37.037 0.00 0.00 39.61 4.02
624 625 6.999272 ACTAAGATGAGTGTAGATACATCCGT 59.001 38.462 0.00 0.00 39.61 4.69
625 626 7.301789 CACTAAGATGAGTGTAGATACATCCG 58.698 42.308 0.00 0.00 41.67 4.18
638 639 6.007703 GGAGGTATCTAGCACTAAGATGAGT 58.992 44.000 0.00 0.00 0.00 3.41
639 640 5.123186 CGGAGGTATCTAGCACTAAGATGAG 59.877 48.000 0.00 0.00 0.00 2.90
640 641 5.004448 CGGAGGTATCTAGCACTAAGATGA 58.996 45.833 0.00 0.00 0.00 2.92
641 642 4.762765 ACGGAGGTATCTAGCACTAAGATG 59.237 45.833 0.00 0.00 0.00 2.90
642 643 4.988029 ACGGAGGTATCTAGCACTAAGAT 58.012 43.478 0.00 0.00 0.00 2.40
643 644 4.434545 ACGGAGGTATCTAGCACTAAGA 57.565 45.455 0.00 0.00 0.00 2.10
655 656 9.233649 CTTAGATTTGTCTAGATACGGAGGTAT 57.766 37.037 0.00 0.00 42.01 2.73
656 657 8.435187 TCTTAGATTTGTCTAGATACGGAGGTA 58.565 37.037 0.00 0.00 0.00 3.08
657 658 7.288560 TCTTAGATTTGTCTAGATACGGAGGT 58.711 38.462 0.00 0.00 0.00 3.85
658 659 7.747155 TCTTAGATTTGTCTAGATACGGAGG 57.253 40.000 0.00 0.00 0.00 4.30
661 662 9.804758 ACTTTTCTTAGATTTGTCTAGATACGG 57.195 33.333 0.00 0.00 0.00 4.02
669 670 9.720769 TCCGAATTACTTTTCTTAGATTTGTCT 57.279 29.630 0.00 0.00 0.00 3.41
672 673 9.262472 CGTTCCGAATTACTTTTCTTAGATTTG 57.738 33.333 0.00 0.00 0.00 2.32
673 674 9.211485 TCGTTCCGAATTACTTTTCTTAGATTT 57.789 29.630 0.00 0.00 31.06 2.17
674 675 8.767478 TCGTTCCGAATTACTTTTCTTAGATT 57.233 30.769 0.00 0.00 31.06 2.40
675 676 8.767478 TTCGTTCCGAATTACTTTTCTTAGAT 57.233 30.769 0.00 0.00 41.05 1.98
676 677 7.330208 CCTTCGTTCCGAATTACTTTTCTTAGA 59.670 37.037 0.00 0.00 44.85 2.10
677 678 7.412672 CCCTTCGTTCCGAATTACTTTTCTTAG 60.413 40.741 0.00 0.00 44.85 2.18
678 679 6.369615 CCCTTCGTTCCGAATTACTTTTCTTA 59.630 38.462 0.00 0.00 44.85 2.10
679 680 5.180680 CCCTTCGTTCCGAATTACTTTTCTT 59.819 40.000 0.00 0.00 44.85 2.52
680 681 4.694037 CCCTTCGTTCCGAATTACTTTTCT 59.306 41.667 0.00 0.00 44.85 2.52
681 682 4.692155 TCCCTTCGTTCCGAATTACTTTTC 59.308 41.667 0.00 0.00 44.85 2.29
682 683 4.644498 TCCCTTCGTTCCGAATTACTTTT 58.356 39.130 0.00 0.00 44.85 2.27
683 684 4.251268 CTCCCTTCGTTCCGAATTACTTT 58.749 43.478 0.00 0.00 44.85 2.66
684 685 3.260128 ACTCCCTTCGTTCCGAATTACTT 59.740 43.478 0.00 0.00 44.85 2.24
685 686 2.830321 ACTCCCTTCGTTCCGAATTACT 59.170 45.455 0.00 0.00 44.85 2.24
686 687 3.242549 ACTCCCTTCGTTCCGAATTAC 57.757 47.619 0.00 0.00 44.85 1.89
687 688 3.181497 CGTACTCCCTTCGTTCCGAATTA 60.181 47.826 0.00 0.00 44.85 1.40
688 689 2.416431 CGTACTCCCTTCGTTCCGAATT 60.416 50.000 0.00 0.00 44.85 2.17
689 690 1.133790 CGTACTCCCTTCGTTCCGAAT 59.866 52.381 0.00 0.00 44.85 3.34
690 691 0.523072 CGTACTCCCTTCGTTCCGAA 59.477 55.000 0.00 0.00 43.75 4.30
691 692 0.606401 ACGTACTCCCTTCGTTCCGA 60.606 55.000 0.00 0.00 34.07 4.55
692 693 1.086696 TACGTACTCCCTTCGTTCCG 58.913 55.000 0.00 0.00 38.69 4.30
693 694 2.087646 AGTACGTACTCCCTTCGTTCC 58.912 52.381 22.45 0.00 38.69 3.62
694 695 3.935828 ACTAGTACGTACTCCCTTCGTTC 59.064 47.826 30.53 0.00 38.69 3.95
695 696 3.686726 CACTAGTACGTACTCCCTTCGTT 59.313 47.826 30.53 7.49 38.69 3.85
696 697 3.265791 CACTAGTACGTACTCCCTTCGT 58.734 50.000 30.53 15.70 40.78 3.85
697 698 2.031437 GCACTAGTACGTACTCCCTTCG 59.969 54.545 30.53 15.24 37.73 3.79
698 699 3.012518 TGCACTAGTACGTACTCCCTTC 58.987 50.000 30.53 16.99 37.73 3.46
699 700 3.077484 TGCACTAGTACGTACTCCCTT 57.923 47.619 30.53 10.46 37.73 3.95
700 701 2.795231 TGCACTAGTACGTACTCCCT 57.205 50.000 30.53 12.10 37.73 4.20
701 702 5.702349 AATATGCACTAGTACGTACTCCC 57.298 43.478 30.53 17.09 37.73 4.30
702 703 8.728833 AGAATAATATGCACTAGTACGTACTCC 58.271 37.037 30.53 17.40 37.73 3.85
788 789 4.501915 CCTCCAAGCTCTGAAAATTTTGCA 60.502 41.667 8.47 5.64 0.00 4.08
850 855 1.893919 GCTGTGGACCTCACCTCCTC 61.894 65.000 0.00 0.00 45.48 3.71
851 856 1.915769 GCTGTGGACCTCACCTCCT 60.916 63.158 0.00 0.00 45.48 3.69
874 890 1.780025 TTTGATTGTCGCAGCGCACA 61.780 50.000 10.87 12.71 0.00 4.57
875 891 1.082169 TTTGATTGTCGCAGCGCAC 60.082 52.632 10.87 10.08 0.00 5.34
878 894 0.785708 GACGTTTGATTGTCGCAGCG 60.786 55.000 9.06 9.06 0.00 5.18
881 897 4.937696 ATATTGACGTTTGATTGTCGCA 57.062 36.364 0.00 0.00 37.94 5.10
882 898 6.237201 GGAAAATATTGACGTTTGATTGTCGC 60.237 38.462 0.00 0.00 37.94 5.19
883 899 6.250527 GGGAAAATATTGACGTTTGATTGTCG 59.749 38.462 0.00 0.00 37.94 4.35
884 900 6.530181 GGGGAAAATATTGACGTTTGATTGTC 59.470 38.462 0.00 0.00 35.67 3.18
885 901 6.394809 GGGGAAAATATTGACGTTTGATTGT 58.605 36.000 0.00 0.00 0.00 2.71
887 903 5.482175 TGGGGGAAAATATTGACGTTTGATT 59.518 36.000 0.00 0.00 0.00 2.57
888 904 5.020132 TGGGGGAAAATATTGACGTTTGAT 58.980 37.500 0.00 0.00 0.00 2.57
889 905 4.218852 GTGGGGGAAAATATTGACGTTTGA 59.781 41.667 0.00 0.00 0.00 2.69
890 906 4.490743 GTGGGGGAAAATATTGACGTTTG 58.509 43.478 0.00 0.00 0.00 2.93
891 907 3.191791 CGTGGGGGAAAATATTGACGTTT 59.808 43.478 0.00 0.00 0.00 3.60
892 908 2.750712 CGTGGGGGAAAATATTGACGTT 59.249 45.455 0.00 0.00 0.00 3.99
893 909 2.027007 TCGTGGGGGAAAATATTGACGT 60.027 45.455 0.00 0.00 0.00 4.34
894 910 2.612212 CTCGTGGGGGAAAATATTGACG 59.388 50.000 0.00 0.00 0.00 4.35
895 911 2.357952 GCTCGTGGGGGAAAATATTGAC 59.642 50.000 0.00 0.00 0.00 3.18
896 912 2.650322 GCTCGTGGGGGAAAATATTGA 58.350 47.619 0.00 0.00 0.00 2.57
897 913 1.333619 CGCTCGTGGGGGAAAATATTG 59.666 52.381 0.00 0.00 0.00 1.90
898 914 1.675552 CGCTCGTGGGGGAAAATATT 58.324 50.000 0.00 0.00 0.00 1.28
899 915 3.396951 CGCTCGTGGGGGAAAATAT 57.603 52.632 0.00 0.00 0.00 1.28
900 916 4.946038 CGCTCGTGGGGGAAAATA 57.054 55.556 0.00 0.00 0.00 1.40
999 1015 3.591835 GGTGTGGTGCGGTGGTTG 61.592 66.667 0.00 0.00 0.00 3.77
1012 1028 1.754226 GTTGGTGTGATTTGGTGGTGT 59.246 47.619 0.00 0.00 0.00 4.16
1239 1258 3.855853 GCGGAGGAGGAGGAAGCC 61.856 72.222 0.00 0.00 0.00 4.35
1241 1260 4.214327 GCGCGGAGGAGGAGGAAG 62.214 72.222 8.83 0.00 0.00 3.46
1242 1261 4.761058 AGCGCGGAGGAGGAGGAA 62.761 66.667 8.83 0.00 0.00 3.36
1278 1297 3.489513 GGGAACGGGGATGGGGAG 61.490 72.222 0.00 0.00 0.00 4.30
1902 1933 1.225426 GCTGATGCCCATGTGGAGA 59.775 57.895 0.00 0.00 37.39 3.71
1944 1975 4.508405 CCAAGAAGGAACTCAACCCCATTA 60.508 45.833 0.00 0.00 38.49 1.90
1953 1984 3.149196 GACATTGCCAAGAAGGAACTCA 58.851 45.455 0.00 0.00 38.49 3.41
2007 2038 2.671130 TGTTCATGCATCGTAGAGCA 57.329 45.000 0.00 0.00 43.63 4.26
2010 2041 2.666022 CACGTTGTTCATGCATCGTAGA 59.334 45.455 8.32 0.00 41.14 2.59
2013 2044 0.110238 GCACGTTGTTCATGCATCGT 60.110 50.000 0.00 0.00 43.00 3.73
2016 2047 1.336148 CCAAGCACGTTGTTCATGCAT 60.336 47.619 0.00 0.00 41.97 3.96
2040 2071 1.148310 CGAGCAACACGAAGGACATT 58.852 50.000 0.00 0.00 0.00 2.71
2407 2438 1.960417 TTGACCAAATGAGCACACGA 58.040 45.000 0.00 0.00 0.00 4.35
2554 2604 6.183360 GGCCTCATTGCATCAATAAGTTTACT 60.183 38.462 0.00 0.00 32.35 2.24
2601 2651 2.857592 AAATCATCTCGGCACATTGC 57.142 45.000 0.00 0.00 44.08 3.56
2604 2654 7.807977 AATTTAGTAAATCATCTCGGCACAT 57.192 32.000 8.56 0.00 0.00 3.21
2669 2719 7.396339 ACTGAGATAGTACAATGTAACCTGTCA 59.604 37.037 9.30 4.68 38.04 3.58
2732 2782 3.742640 GCCACCAGACTGATACATCCTTC 60.743 52.174 3.32 0.00 0.00 3.46
2825 2877 7.509546 CATATACTCCCTACAAAATCCTGTGT 58.490 38.462 0.00 0.00 0.00 3.72
2826 2878 6.428159 GCATATACTCCCTACAAAATCCTGTG 59.572 42.308 0.00 0.00 0.00 3.66
2837 2889 2.496070 TGCCGATGCATATACTCCCTAC 59.504 50.000 0.00 0.00 44.23 3.18
2838 2890 2.815158 TGCCGATGCATATACTCCCTA 58.185 47.619 0.00 0.00 44.23 3.53
2839 2891 1.644509 TGCCGATGCATATACTCCCT 58.355 50.000 0.00 0.00 44.23 4.20
2852 2905 1.079127 GCCAGTACACAGTGCCGAT 60.079 57.895 0.00 0.00 0.00 4.18
2885 2938 0.892755 AGGCCATGATGCACAACTTG 59.107 50.000 5.01 0.00 0.00 3.16
2908 2963 3.023119 TGGAATGTCAATGTGCATACCC 58.977 45.455 0.00 0.00 0.00 3.69
2946 3001 2.435805 AGAAGCCAGACAGACAACAAGA 59.564 45.455 0.00 0.00 0.00 3.02
2952 3007 4.102524 TCCTTTTTAGAAGCCAGACAGACA 59.897 41.667 0.00 0.00 0.00 3.41
2953 3008 4.642429 TCCTTTTTAGAAGCCAGACAGAC 58.358 43.478 0.00 0.00 0.00 3.51
2954 3009 4.348168 ACTCCTTTTTAGAAGCCAGACAGA 59.652 41.667 0.00 0.00 0.00 3.41
2955 3010 4.646572 ACTCCTTTTTAGAAGCCAGACAG 58.353 43.478 0.00 0.00 0.00 3.51
2956 3011 4.102524 TGACTCCTTTTTAGAAGCCAGACA 59.897 41.667 0.00 0.00 0.00 3.41
2957 3012 4.642429 TGACTCCTTTTTAGAAGCCAGAC 58.358 43.478 0.00 0.00 0.00 3.51
2958 3013 4.974645 TGACTCCTTTTTAGAAGCCAGA 57.025 40.909 0.00 0.00 0.00 3.86
2960 3015 7.175104 ACATAATGACTCCTTTTTAGAAGCCA 58.825 34.615 0.00 0.00 0.00 4.75
2977 3032 6.672593 AGATTTAGCTCCCCAAACATAATGA 58.327 36.000 0.00 0.00 0.00 2.57
2979 3034 7.125391 TCAAGATTTAGCTCCCCAAACATAAT 58.875 34.615 0.00 0.00 0.00 1.28
2982 3037 4.934356 TCAAGATTTAGCTCCCCAAACAT 58.066 39.130 0.00 0.00 0.00 2.71
2984 3039 5.196695 AGATCAAGATTTAGCTCCCCAAAC 58.803 41.667 0.00 0.00 0.00 2.93
2987 3042 4.474651 TCAAGATCAAGATTTAGCTCCCCA 59.525 41.667 0.00 0.00 0.00 4.96
2993 3048 7.066766 AGTCACCATTCAAGATCAAGATTTAGC 59.933 37.037 0.00 0.00 0.00 3.09
3009 3064 7.173218 TGAAATCTGAAACACTAGTCACCATTC 59.827 37.037 0.00 0.00 0.00 2.67
3010 3065 6.998074 TGAAATCTGAAACACTAGTCACCATT 59.002 34.615 0.00 0.00 0.00 3.16
3011 3066 6.533730 TGAAATCTGAAACACTAGTCACCAT 58.466 36.000 0.00 0.00 0.00 3.55
3070 3125 7.972277 AGCAGTGCAAACTATTGATATTTTGAG 59.028 33.333 19.20 5.51 38.94 3.02
3105 3160 0.307453 GTGCAACAACGACAGCATCA 59.693 50.000 0.00 0.00 39.43 3.07
3124 3179 0.921347 CAATACTTCCGACGCTTCCG 59.079 55.000 0.00 0.00 41.14 4.30
3126 3181 0.651031 GCCAATACTTCCGACGCTTC 59.349 55.000 0.00 0.00 0.00 3.86
3131 3186 1.653151 GACCAGCCAATACTTCCGAC 58.347 55.000 0.00 0.00 0.00 4.79
3153 3208 0.528017 CGCAGCAGTCTACAAGAGGA 59.472 55.000 0.00 0.00 0.00 3.71
3171 3226 2.125310 TGCATAGCCCGAACCACG 60.125 61.111 0.00 0.00 42.18 4.94
3176 3231 0.739462 CTGTTCGTGCATAGCCCGAA 60.739 55.000 5.26 5.26 38.18 4.30
3177 3232 1.153647 CTGTTCGTGCATAGCCCGA 60.154 57.895 0.00 0.00 0.00 5.14
3178 3233 2.813179 GCTGTTCGTGCATAGCCCG 61.813 63.158 0.00 0.00 0.00 6.13
3179 3234 3.102097 GCTGTTCGTGCATAGCCC 58.898 61.111 0.00 0.00 0.00 5.19
3181 3236 0.097674 CTTGGCTGTTCGTGCATAGC 59.902 55.000 0.00 0.00 35.49 2.97
3182 3237 0.729116 CCTTGGCTGTTCGTGCATAG 59.271 55.000 0.00 0.00 0.00 2.23
3183 3238 0.676466 CCCTTGGCTGTTCGTGCATA 60.676 55.000 0.00 0.00 0.00 3.14
3196 3251 0.752054 TTGCTGCAACTTTCCCTTGG 59.248 50.000 11.69 0.00 0.00 3.61
3199 3254 1.143684 TCTCTTGCTGCAACTTTCCCT 59.856 47.619 11.69 0.00 0.00 4.20
3314 3392 2.487086 CCATGTCACACTCAAACCCTCA 60.487 50.000 0.00 0.00 0.00 3.86
3328 3406 0.537143 GTCCACCAGCAACCATGTCA 60.537 55.000 0.00 0.00 0.00 3.58
3339 3417 1.004918 GAACCTCACCGTCCACCAG 60.005 63.158 0.00 0.00 0.00 4.00
3373 3451 1.111277 AACCTTGCTTCACCAACCAC 58.889 50.000 0.00 0.00 0.00 4.16


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

AutoCloner maintained by Alex Coulton.