Multiple sequence alignment - TraesCS3A01G170400

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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 TraesCS3A01G170400 chr3A 100.000 3823 0 0 1 3823 178250922 178254744 0.000000e+00 7060
1 TraesCS3A01G170400 chr3A 92.195 205 15 1 491 695 203841067 203841270 4.830000e-74 289
2 TraesCS3A01G170400 chr3A 92.537 201 14 1 491 691 146592849 146593048 1.740000e-73 287
3 TraesCS3A01G170400 chr3D 93.500 1600 69 13 683 2264 152486645 152485063 0.000000e+00 2346
4 TraesCS3A01G170400 chr3D 94.617 1319 61 7 2263 3574 152485021 152483706 0.000000e+00 2034
5 TraesCS3A01G170400 chr3D 92.975 484 24 6 1 475 152487239 152486757 0.000000e+00 697
6 TraesCS3A01G170400 chr3D 84.163 221 11 3 3606 3823 152483625 152483426 3.900000e-45 193
7 TraesCS3A01G170400 chr3B 92.780 1565 71 14 706 2264 222816031 222814503 0.000000e+00 2226
8 TraesCS3A01G170400 chr3B 87.996 908 75 18 2263 3156 222814464 222813577 0.000000e+00 1042
9 TraesCS3A01G170400 chr3B 92.843 489 23 10 1 480 222816520 222816035 0.000000e+00 699
10 TraesCS3A01G170400 chr3B 92.118 203 15 1 491 693 797016076 797015875 6.250000e-73 285
11 TraesCS3A01G170400 chr3B 79.487 429 37 22 3419 3822 222805398 222804996 1.360000e-64 257
12 TraesCS3A01G170400 chrUn 92.574 202 14 1 491 692 55786445 55786245 4.830000e-74 289
13 TraesCS3A01G170400 chrUn 92.574 202 14 1 491 692 302515312 302515512 4.830000e-74 289
14 TraesCS3A01G170400 chr6B 92.574 202 13 2 491 692 630891812 630892011 4.830000e-74 289
15 TraesCS3A01G170400 chr4A 92.574 202 14 1 491 692 715713641 715713841 4.830000e-74 289
16 TraesCS3A01G170400 chr2B 92.574 202 14 1 491 692 64336646 64336446 4.830000e-74 289
17 TraesCS3A01G170400 chr2B 91.707 205 16 1 488 692 12965795 12965998 2.250000e-72 283


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 TraesCS3A01G170400 chr3A 178250922 178254744 3822 False 7060.000000 7060 100.000000 1 3823 1 chr3A.!!$F2 3822
1 TraesCS3A01G170400 chr3D 152483426 152487239 3813 True 1317.500000 2346 91.313750 1 3823 4 chr3D.!!$R1 3822
2 TraesCS3A01G170400 chr3B 222813577 222816520 2943 True 1322.333333 2226 91.206333 1 3156 3 chr3B.!!$R3 3155

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
542 564 0.036671 CCTCCTCCGTTTTTAGGCGT 60.037 55.0 0.00 0.0 32.55 5.68 F
655 677 0.179468 GAGCCCGGGTGTAATGCTTA 59.821 55.0 24.63 0.0 31.23 3.09 F
1251 1287 0.191064 TGAACCCACCTCTGACCTCT 59.809 55.0 0.00 0.0 0.00 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1405 1441 0.804989 GCACCAGAATACAGCACCAC 59.195 55.000 0.00 0.0 0.00 4.16 R
2091 2129 1.133199 ACCCAAGATGGCCAACTTCAA 60.133 47.619 24.23 0.0 35.79 2.69 R
2827 2939 0.177141 TACTGCGGGAACAGCCATAC 59.823 55.000 0.00 0.0 41.60 2.39 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
53 54 4.016444 TGAATGAAGGGCCTGTTACAATC 58.984 43.478 6.92 8.88 0.00 2.67
218 229 8.279970 TGTTGTTCATATGGGTGAAGAATAAG 57.720 34.615 2.13 0.00 41.48 1.73
352 365 8.456471 GGTGTAAAGATGTAAGATTACCAAACC 58.544 37.037 0.48 0.00 32.72 3.27
403 418 8.839343 TCATGTATGTTAATGGAATTAGTGCTG 58.161 33.333 0.00 0.00 40.40 4.41
407 422 9.503427 GTATGTTAATGGAATTAGTGCTGTTTC 57.497 33.333 0.00 0.00 40.40 2.78
411 426 4.046286 TGGAATTAGTGCTGTTTCCCAT 57.954 40.909 10.45 0.00 37.43 4.00
424 439 6.014755 TGCTGTTTCCCATGTAAATTTCATGA 60.015 34.615 21.91 0.00 43.47 3.07
454 469 9.112725 TGAGATAAATTTGGTGATGATACTGTG 57.887 33.333 0.00 0.00 0.00 3.66
480 502 9.221775 GTCTTTTACATGTTGTCAAAACACTAG 57.778 33.333 2.30 0.00 34.35 2.57
488 510 9.515020 CATGTTGTCAAAACACTAGTAAACAAT 57.485 29.630 0.00 0.00 34.35 2.71
491 513 9.991388 GTTGTCAAAACACTAGTAAACAATACA 57.009 29.630 0.00 0.00 34.35 2.29
493 515 9.991388 TGTCAAAACACTAGTAAACAATACAAC 57.009 29.630 0.00 0.00 0.00 3.32
494 516 9.991388 GTCAAAACACTAGTAAACAATACAACA 57.009 29.630 0.00 0.00 0.00 3.33
497 519 9.959749 AAAACACTAGTAAACAATACAACATGG 57.040 29.630 0.00 0.00 0.00 3.66
498 520 7.681939 ACACTAGTAAACAATACAACATGGG 57.318 36.000 0.00 0.00 0.00 4.00
500 522 7.174253 ACACTAGTAAACAATACAACATGGGTG 59.826 37.037 0.00 0.00 0.00 4.61
501 523 5.975693 AGTAAACAATACAACATGGGTGG 57.024 39.130 0.00 0.00 0.00 4.61
502 524 3.676291 AAACAATACAACATGGGTGGC 57.324 42.857 0.00 0.00 0.00 5.01
503 525 2.300956 ACAATACAACATGGGTGGCA 57.699 45.000 0.00 0.00 0.00 4.92
504 526 2.170166 ACAATACAACATGGGTGGCAG 58.830 47.619 0.00 0.00 0.00 4.85
506 528 0.039472 ATACAACATGGGTGGCAGCA 59.961 50.000 19.48 5.16 0.00 4.41
507 529 0.039472 TACAACATGGGTGGCAGCAT 59.961 50.000 19.48 7.36 0.00 3.79
508 530 1.216977 CAACATGGGTGGCAGCATG 59.783 57.895 19.48 19.83 40.87 4.06
509 531 1.077086 AACATGGGTGGCAGCATGA 59.923 52.632 25.12 9.60 39.69 3.07
512 534 0.467474 CATGGGTGGCAGCATGATCT 60.467 55.000 19.48 0.00 39.69 2.75
513 535 1.142936 ATGGGTGGCAGCATGATCTA 58.857 50.000 19.48 0.00 39.69 1.98
514 536 0.918258 TGGGTGGCAGCATGATCTAA 59.082 50.000 19.48 0.00 39.69 2.10
515 537 1.134007 TGGGTGGCAGCATGATCTAAG 60.134 52.381 19.48 0.00 39.69 2.18
516 538 1.602311 GGTGGCAGCATGATCTAAGG 58.398 55.000 12.58 0.00 39.69 2.69
519 541 3.484407 GTGGCAGCATGATCTAAGGATT 58.516 45.455 0.00 0.00 39.69 3.01
520 542 3.252701 GTGGCAGCATGATCTAAGGATTG 59.747 47.826 0.00 0.00 39.69 2.67
521 543 2.818432 GGCAGCATGATCTAAGGATTGG 59.182 50.000 0.00 0.00 39.69 3.16
522 544 3.484407 GCAGCATGATCTAAGGATTGGT 58.516 45.455 0.00 0.00 39.69 3.67
523 545 3.501445 GCAGCATGATCTAAGGATTGGTC 59.499 47.826 0.00 0.00 39.69 4.02
524 546 4.070716 CAGCATGATCTAAGGATTGGTCC 58.929 47.826 0.00 0.00 41.72 4.46
533 555 2.297937 GGATTGGTCCTCCTCCGTT 58.702 57.895 0.00 0.00 41.60 4.44
534 556 0.618981 GGATTGGTCCTCCTCCGTTT 59.381 55.000 0.00 0.00 41.60 3.60
535 557 1.004394 GGATTGGTCCTCCTCCGTTTT 59.996 52.381 0.00 0.00 41.60 2.43
536 558 2.554564 GGATTGGTCCTCCTCCGTTTTT 60.555 50.000 0.00 0.00 41.60 1.94
537 559 3.307904 GGATTGGTCCTCCTCCGTTTTTA 60.308 47.826 0.00 0.00 41.60 1.52
538 560 3.412237 TTGGTCCTCCTCCGTTTTTAG 57.588 47.619 0.00 0.00 34.23 1.85
539 561 1.626825 TGGTCCTCCTCCGTTTTTAGG 59.373 52.381 0.00 0.00 34.23 2.69
540 562 1.678123 GGTCCTCCTCCGTTTTTAGGC 60.678 57.143 0.00 0.00 32.55 3.93
541 563 0.248289 TCCTCCTCCGTTTTTAGGCG 59.752 55.000 0.00 0.00 32.55 5.52
542 564 0.036671 CCTCCTCCGTTTTTAGGCGT 60.037 55.000 0.00 0.00 32.55 5.68
543 565 1.609841 CCTCCTCCGTTTTTAGGCGTT 60.610 52.381 0.00 0.00 32.55 4.84
544 566 2.354003 CCTCCTCCGTTTTTAGGCGTTA 60.354 50.000 0.00 0.00 32.55 3.18
545 567 3.528532 CTCCTCCGTTTTTAGGCGTTAT 58.471 45.455 0.00 0.00 32.55 1.89
546 568 4.441913 CCTCCTCCGTTTTTAGGCGTTATA 60.442 45.833 0.00 0.00 32.55 0.98
548 570 5.051816 TCCTCCGTTTTTAGGCGTTATATG 58.948 41.667 0.00 0.00 32.55 1.78
549 571 4.212636 CCTCCGTTTTTAGGCGTTATATGG 59.787 45.833 0.00 0.00 0.00 2.74
551 573 4.810491 TCCGTTTTTAGGCGTTATATGGAC 59.190 41.667 0.00 0.00 0.00 4.02
553 575 5.050567 CCGTTTTTAGGCGTTATATGGACTC 60.051 44.000 0.00 0.00 0.00 3.36
555 577 6.919662 CGTTTTTAGGCGTTATATGGACTCTA 59.080 38.462 0.00 0.00 0.00 2.43
556 578 7.096312 CGTTTTTAGGCGTTATATGGACTCTAC 60.096 40.741 0.00 0.00 0.00 2.59
557 579 6.964807 TTTAGGCGTTATATGGACTCTACA 57.035 37.500 0.00 0.00 0.00 2.74
558 580 7.534723 TTTAGGCGTTATATGGACTCTACAT 57.465 36.000 0.00 0.00 0.00 2.29
559 581 5.392767 AGGCGTTATATGGACTCTACATG 57.607 43.478 0.00 0.00 0.00 3.21
561 583 5.304614 AGGCGTTATATGGACTCTACATGTT 59.695 40.000 2.30 0.00 0.00 2.71
562 584 5.989777 GGCGTTATATGGACTCTACATGTTT 59.010 40.000 2.30 0.00 0.00 2.83
563 585 6.482308 GGCGTTATATGGACTCTACATGTTTT 59.518 38.462 2.30 0.00 0.00 2.43
565 587 7.011109 GCGTTATATGGACTCTACATGTTTTGT 59.989 37.037 2.30 0.00 42.62 2.83
566 588 8.879759 CGTTATATGGACTCTACATGTTTTGTT 58.120 33.333 2.30 0.00 39.87 2.83
574 596 9.916397 GGACTCTACATGTTTTGTTATAATTCG 57.084 33.333 2.30 0.00 39.87 3.34
575 597 9.422196 GACTCTACATGTTTTGTTATAATTCGC 57.578 33.333 2.30 0.00 39.87 4.70
576 598 8.395633 ACTCTACATGTTTTGTTATAATTCGCC 58.604 33.333 2.30 0.00 39.87 5.54
577 599 8.500753 TCTACATGTTTTGTTATAATTCGCCT 57.499 30.769 2.30 0.00 39.87 5.52
579 601 9.567848 CTACATGTTTTGTTATAATTCGCCTTT 57.432 29.630 2.30 0.00 39.87 3.11
597 619 9.922305 TTCGCCTTTTTATTTTTATTTTGTGTG 57.078 25.926 0.00 0.00 0.00 3.82
598 620 9.314321 TCGCCTTTTTATTTTTATTTTGTGTGA 57.686 25.926 0.00 0.00 0.00 3.58
599 621 9.579610 CGCCTTTTTATTTTTATTTTGTGTGAG 57.420 29.630 0.00 0.00 0.00 3.51
605 627 9.974980 TTTATTTTTATTTTGTGTGAGAGGGTC 57.025 29.630 0.00 0.00 0.00 4.46
606 628 6.399639 TTTTTATTTTGTGTGAGAGGGTCC 57.600 37.500 0.00 0.00 0.00 4.46
607 629 4.993705 TTATTTTGTGTGAGAGGGTCCT 57.006 40.909 0.00 0.00 0.00 3.85
608 630 6.442541 TTTATTTTGTGTGAGAGGGTCCTA 57.557 37.500 0.00 0.00 0.00 2.94
609 631 6.636454 TTATTTTGTGTGAGAGGGTCCTAT 57.364 37.500 0.00 0.00 0.00 2.57
610 632 4.993705 TTTTGTGTGAGAGGGTCCTATT 57.006 40.909 0.00 0.00 0.00 1.73
611 633 4.993705 TTTGTGTGAGAGGGTCCTATTT 57.006 40.909 0.00 0.00 0.00 1.40
612 634 3.981071 TGTGTGAGAGGGTCCTATTTG 57.019 47.619 0.00 0.00 0.00 2.32
613 635 2.571653 TGTGTGAGAGGGTCCTATTTGG 59.428 50.000 0.00 0.00 37.10 3.28
614 636 1.559682 TGTGAGAGGGTCCTATTTGGC 59.440 52.381 0.00 0.00 35.26 4.52
615 637 1.840635 GTGAGAGGGTCCTATTTGGCT 59.159 52.381 0.00 0.00 35.26 4.75
616 638 1.839994 TGAGAGGGTCCTATTTGGCTG 59.160 52.381 0.00 0.00 35.26 4.85
617 639 1.840635 GAGAGGGTCCTATTTGGCTGT 59.159 52.381 0.00 0.00 35.26 4.40
618 640 1.561542 AGAGGGTCCTATTTGGCTGTG 59.438 52.381 0.00 0.00 35.26 3.66
619 641 1.282157 GAGGGTCCTATTTGGCTGTGT 59.718 52.381 0.00 0.00 35.26 3.72
620 642 1.004745 AGGGTCCTATTTGGCTGTGTG 59.995 52.381 0.00 0.00 35.26 3.82
621 643 0.811281 GGTCCTATTTGGCTGTGTGC 59.189 55.000 0.00 0.00 41.94 4.57
622 644 1.533625 GTCCTATTTGGCTGTGTGCA 58.466 50.000 0.00 0.00 45.15 4.57
623 645 2.094675 GTCCTATTTGGCTGTGTGCAT 58.905 47.619 0.00 0.00 45.15 3.96
624 646 2.098117 GTCCTATTTGGCTGTGTGCATC 59.902 50.000 0.00 0.00 45.15 3.91
625 647 2.025981 TCCTATTTGGCTGTGTGCATCT 60.026 45.455 0.00 0.00 45.15 2.90
626 648 2.756760 CCTATTTGGCTGTGTGCATCTT 59.243 45.455 0.00 0.00 45.15 2.40
627 649 3.947196 CCTATTTGGCTGTGTGCATCTTA 59.053 43.478 0.00 0.00 45.15 2.10
628 650 4.036027 CCTATTTGGCTGTGTGCATCTTAG 59.964 45.833 0.00 0.00 45.15 2.18
629 651 2.566833 TTGGCTGTGTGCATCTTAGT 57.433 45.000 0.00 0.00 45.15 2.24
630 652 2.566833 TGGCTGTGTGCATCTTAGTT 57.433 45.000 0.00 0.00 45.15 2.24
631 653 3.694043 TGGCTGTGTGCATCTTAGTTA 57.306 42.857 0.00 0.00 45.15 2.24
632 654 4.220693 TGGCTGTGTGCATCTTAGTTAT 57.779 40.909 0.00 0.00 45.15 1.89
633 655 3.940852 TGGCTGTGTGCATCTTAGTTATG 59.059 43.478 0.00 0.00 45.15 1.90
642 664 2.890808 TCTTAGTTATGCAGAGCCCG 57.109 50.000 0.00 0.00 0.00 6.13
643 665 1.412710 TCTTAGTTATGCAGAGCCCGG 59.587 52.381 0.00 0.00 0.00 5.73
644 666 0.468226 TTAGTTATGCAGAGCCCGGG 59.532 55.000 19.09 19.09 0.00 5.73
645 667 0.689745 TAGTTATGCAGAGCCCGGGT 60.690 55.000 24.63 9.10 0.00 5.28
646 668 1.819632 GTTATGCAGAGCCCGGGTG 60.820 63.158 24.63 14.30 0.00 4.61
647 669 2.297895 TTATGCAGAGCCCGGGTGT 61.298 57.895 24.63 10.28 0.00 4.16
648 670 0.978667 TTATGCAGAGCCCGGGTGTA 60.979 55.000 24.63 12.98 0.00 2.90
649 671 0.978667 TATGCAGAGCCCGGGTGTAA 60.979 55.000 24.63 5.97 0.00 2.41
650 672 1.635817 ATGCAGAGCCCGGGTGTAAT 61.636 55.000 24.63 8.10 0.00 1.89
651 673 1.819632 GCAGAGCCCGGGTGTAATG 60.820 63.158 24.63 14.93 0.00 1.90
652 674 1.819632 CAGAGCCCGGGTGTAATGC 60.820 63.158 24.63 5.25 0.00 3.56
653 675 1.995626 AGAGCCCGGGTGTAATGCT 60.996 57.895 24.63 11.03 34.40 3.79
654 676 1.077716 GAGCCCGGGTGTAATGCTT 60.078 57.895 24.63 0.00 31.23 3.91
655 677 0.179468 GAGCCCGGGTGTAATGCTTA 59.821 55.000 24.63 0.00 31.23 3.09
656 678 0.621609 AGCCCGGGTGTAATGCTTAA 59.378 50.000 24.63 0.00 0.00 1.85
657 679 1.004979 AGCCCGGGTGTAATGCTTAAA 59.995 47.619 24.63 0.00 0.00 1.52
658 680 2.028876 GCCCGGGTGTAATGCTTAAAT 58.971 47.619 24.63 0.00 0.00 1.40
659 681 2.034179 GCCCGGGTGTAATGCTTAAATC 59.966 50.000 24.63 0.00 0.00 2.17
660 682 3.551846 CCCGGGTGTAATGCTTAAATCT 58.448 45.455 14.18 0.00 0.00 2.40
661 683 3.951680 CCCGGGTGTAATGCTTAAATCTT 59.048 43.478 14.18 0.00 0.00 2.40
662 684 4.401202 CCCGGGTGTAATGCTTAAATCTTT 59.599 41.667 14.18 0.00 0.00 2.52
663 685 5.105513 CCCGGGTGTAATGCTTAAATCTTTT 60.106 40.000 14.18 0.00 0.00 2.27
664 686 6.095720 CCCGGGTGTAATGCTTAAATCTTTTA 59.904 38.462 14.18 0.00 0.00 1.52
665 687 7.363094 CCCGGGTGTAATGCTTAAATCTTTTAA 60.363 37.037 14.18 0.00 0.00 1.52
666 688 7.700656 CCGGGTGTAATGCTTAAATCTTTTAAG 59.299 37.037 13.04 13.04 35.63 1.85
667 689 8.241367 CGGGTGTAATGCTTAAATCTTTTAAGT 58.759 33.333 16.78 4.86 35.14 2.24
681 703 8.507524 AATCTTTTAAGTAATAAAGCGCCTCT 57.492 30.769 2.29 0.00 35.03 3.69
682 704 7.916914 TCTTTTAAGTAATAAAGCGCCTCTT 57.083 32.000 2.29 0.00 35.03 2.85
683 705 8.331730 TCTTTTAAGTAATAAAGCGCCTCTTT 57.668 30.769 2.29 0.06 46.17 2.52
684 706 8.789762 TCTTTTAAGTAATAAAGCGCCTCTTTT 58.210 29.630 2.29 0.00 42.06 2.27
685 707 9.406828 CTTTTAAGTAATAAAGCGCCTCTTTTT 57.593 29.630 2.29 0.00 42.06 1.94
686 708 8.736751 TTTAAGTAATAAAGCGCCTCTTTTTG 57.263 30.769 2.29 0.00 42.06 2.44
689 711 6.977213 AGTAATAAAGCGCCTCTTTTTGAAA 58.023 32.000 2.29 0.00 42.06 2.69
809 843 2.069776 CAAAGCCCAGTCCTCCTGA 58.930 57.895 0.00 0.00 44.49 3.86
998 1034 1.990060 CGGAGGCCAGAAGGAAGGA 60.990 63.158 5.01 0.00 36.89 3.36
1195 1231 2.181021 GTCCTCGTCGGCGTTCAT 59.819 61.111 10.18 0.00 39.49 2.57
1225 1261 2.516460 AGCTCCGACGCCGAGTAT 60.516 61.111 0.00 0.00 38.22 2.12
1251 1287 0.191064 TGAACCCACCTCTGACCTCT 59.809 55.000 0.00 0.00 0.00 3.69
1252 1288 0.899019 GAACCCACCTCTGACCTCTC 59.101 60.000 0.00 0.00 0.00 3.20
1332 1368 6.543465 TCTGGGTGAATGATGTGTAATTGATC 59.457 38.462 0.00 0.00 0.00 2.92
1362 1398 6.817765 TTTGGTGGATTGAGTGATTAAGAC 57.182 37.500 0.00 0.00 0.00 3.01
1392 1428 7.329438 TCGTTAGCGTATCAATAAATAGTGC 57.671 36.000 0.00 0.00 39.49 4.40
1516 1552 3.804786 TGACTCACTTGTCACCGTTAA 57.195 42.857 0.00 0.00 41.43 2.01
1584 1620 4.679373 ATATCTCACTGTGATGGTGTCC 57.321 45.455 11.45 0.00 36.25 4.02
1586 1622 0.603065 CTCACTGTGATGGTGTCCGA 59.397 55.000 11.45 0.00 36.25 4.55
1589 1625 2.038426 TCACTGTGATGGTGTCCGATTT 59.962 45.455 6.36 0.00 36.25 2.17
1633 1669 2.738964 GCTGTCGGAAGGTCCTGAATAC 60.739 54.545 0.00 0.00 33.30 1.89
1709 1745 7.234371 AGCCTCAGAGTCATCTATAAGCAATTA 59.766 37.037 0.00 0.00 33.22 1.40
1713 1749 8.370182 TCAGAGTCATCTATAAGCAATTATGCA 58.630 33.333 3.41 0.00 44.21 3.96
1786 1822 3.503363 CACTTTCTTCAGGTTATGCAGCA 59.497 43.478 0.00 0.00 0.00 4.41
1826 1862 4.718940 AGGTAATACAATGCAACTTGCC 57.281 40.909 11.29 0.00 44.23 4.52
1827 1863 4.085733 AGGTAATACAATGCAACTTGCCA 58.914 39.130 11.29 0.26 44.23 4.92
1838 1874 2.680339 GCAACTTGCCATCTCTACTTCC 59.320 50.000 1.95 0.00 37.42 3.46
1840 1876 2.457598 ACTTGCCATCTCTACTTCCGA 58.542 47.619 0.00 0.00 0.00 4.55
1841 1877 3.034635 ACTTGCCATCTCTACTTCCGAT 58.965 45.455 0.00 0.00 0.00 4.18
1846 1882 3.068873 GCCATCTCTACTTCCGATTCTGT 59.931 47.826 0.00 0.00 0.00 3.41
1866 1902 5.996513 TCTGTAATGGCGTAACCTTTAACAA 59.003 36.000 0.00 0.00 39.17 2.83
1916 1954 9.647918 TCTAAGATGTTATCCTATTCAGTGAGT 57.352 33.333 0.00 0.00 0.00 3.41
2109 2147 5.105228 ACATTATTGAAGTTGGCCATCTTGG 60.105 40.000 29.51 13.74 41.55 3.61
2158 2196 8.697846 TCTTTACATAAGTTCACCTGTATTCG 57.302 34.615 0.00 0.00 0.00 3.34
2172 2210 6.594159 CACCTGTATTCGTATTGAGGTTTTCT 59.406 38.462 0.00 0.00 31.25 2.52
2251 2289 7.472543 ACTGTCCGATTGTTTCATTATAAAGC 58.527 34.615 0.00 0.00 0.00 3.51
2293 2374 4.760530 TCAGATTTGTACTCCCCTGATG 57.239 45.455 0.00 0.00 0.00 3.07
2320 2401 5.988287 TGCCATGAGTATGTCAGTTTATGA 58.012 37.500 0.00 0.00 39.07 2.15
2409 2521 3.914426 TTTGAAGGATCCCTGCTAGAC 57.086 47.619 8.55 0.00 32.13 2.59
2414 2526 1.112113 GGATCCCTGCTAGACGTCAA 58.888 55.000 19.50 0.00 0.00 3.18
2532 2644 6.940739 ACAGATGCTATAACTGACTTGTCTT 58.059 36.000 0.00 0.00 35.85 3.01
2633 2745 0.394192 TTGACTCACCCTCACTGCAG 59.606 55.000 13.48 13.48 0.00 4.41
2827 2939 3.043586 CCGATGAGACTCGTTAAATCCG 58.956 50.000 0.00 0.00 36.93 4.18
2850 2962 1.523938 GCTGTTCCCGCAGTATCCC 60.524 63.158 0.00 0.00 38.65 3.85
2889 3001 5.303971 ACATCTGAGTTATATGGCTTCAGC 58.696 41.667 0.00 0.00 41.14 4.26
2907 3019 6.566753 GCTTCAGCGTAGAATTTTCAGTTTCT 60.567 38.462 0.00 0.00 36.26 2.52
2941 3054 8.903820 GTTGTAGCACAAGGAATCCTAATATTT 58.096 33.333 0.46 0.00 39.00 1.40
3079 3200 1.271001 TGACCCTTGTCATGCACTCTG 60.271 52.381 0.00 0.00 46.40 3.35
3108 3229 1.227853 AACCGGTCTGAGCGCTTTT 60.228 52.632 22.59 12.32 37.85 2.27
3159 3280 8.530311 TGGCAACATAGAATTTGTGTAATCATT 58.470 29.630 0.00 0.00 46.17 2.57
3178 3299 1.542492 TAGTCTTCCCTCGGTCACAC 58.458 55.000 0.00 0.00 0.00 3.82
3181 3302 1.891150 GTCTTCCCTCGGTCACACTTA 59.109 52.381 0.00 0.00 0.00 2.24
3183 3304 0.606604 TTCCCTCGGTCACACTTAGC 59.393 55.000 0.00 0.00 0.00 3.09
3197 3318 7.394872 GTCACACTTAGCGAGAAATCTTTATG 58.605 38.462 0.00 0.00 0.00 1.90
3202 3323 8.324567 CACTTAGCGAGAAATCTTTATGAGTTC 58.675 37.037 0.95 0.95 46.53 3.01
3213 3334 0.253160 TATGAGTTCCACCAGGGCCT 60.253 55.000 0.00 0.00 36.21 5.19
3221 3342 1.296715 CACCAGGGCCTGTACTCAC 59.703 63.158 30.68 0.00 0.00 3.51
3232 3353 4.106197 GCCTGTACTCACGAGTTTAGATG 58.894 47.826 4.79 0.00 42.54 2.90
3239 3360 8.613482 TGTACTCACGAGTTTAGATGATCTTAG 58.387 37.037 4.79 0.00 42.54 2.18
3264 3385 7.383572 AGTGATTTCATCGAGTAGCAATACATC 59.616 37.037 0.00 0.00 0.00 3.06
3267 3388 7.841915 TTTCATCGAGTAGCAATACATCAAA 57.158 32.000 0.00 0.00 0.00 2.69
3272 3393 5.063438 TCGAGTAGCAATACATCAAAGCAAC 59.937 40.000 0.00 0.00 0.00 4.17
3275 3396 2.489329 AGCAATACATCAAAGCAACGCT 59.511 40.909 0.00 0.00 42.56 5.07
3303 3425 2.581246 TCTGTCCCTCCAAGCTACTCTA 59.419 50.000 0.00 0.00 0.00 2.43
3304 3426 3.011369 TCTGTCCCTCCAAGCTACTCTAA 59.989 47.826 0.00 0.00 0.00 2.10
3306 3428 3.245658 TGTCCCTCCAAGCTACTCTAACT 60.246 47.826 0.00 0.00 0.00 2.24
3322 3444 9.321562 CTACTCTAACTGTTCCTGTGTTTTTAA 57.678 33.333 0.00 0.00 0.00 1.52
3347 3472 4.576463 CCCTATATTTGTGACTTGTGAGGC 59.424 45.833 0.00 0.00 0.00 4.70
3382 3507 2.827322 TCATGTGCTTTTCCTGAATGGG 59.173 45.455 0.00 0.00 36.20 4.00
3447 3572 3.248266 CCAGCTGCTTAAATCAACAAGC 58.752 45.455 8.66 0.00 45.90 4.01
3477 3602 9.525409 GCTTGAAATAATCTCTAAAATGCATGT 57.475 29.630 0.00 0.00 0.00 3.21
3576 3701 3.534524 GCTCAAGCAGAAGAGAAACAC 57.465 47.619 0.00 0.00 41.59 3.32
3577 3702 2.874701 GCTCAAGCAGAAGAGAAACACA 59.125 45.455 0.00 0.00 41.59 3.72
3578 3703 3.303659 GCTCAAGCAGAAGAGAAACACAC 60.304 47.826 0.00 0.00 41.59 3.82
3579 3704 3.872696 TCAAGCAGAAGAGAAACACACA 58.127 40.909 0.00 0.00 0.00 3.72
3580 3705 3.623060 TCAAGCAGAAGAGAAACACACAC 59.377 43.478 0.00 0.00 0.00 3.82
3581 3706 3.266510 AGCAGAAGAGAAACACACACA 57.733 42.857 0.00 0.00 0.00 3.72
3582 3707 2.939103 AGCAGAAGAGAAACACACACAC 59.061 45.455 0.00 0.00 0.00 3.82
3583 3708 2.677836 GCAGAAGAGAAACACACACACA 59.322 45.455 0.00 0.00 0.00 3.72
3638 3825 4.770010 TCCAAAACCAATACTTAGGGCTTG 59.230 41.667 0.00 0.00 0.00 4.01
3671 3858 9.177608 CTTAGGACATGAATTTCATAGGAAACA 57.822 33.333 11.44 0.15 45.22 2.83
3683 3870 9.918630 ATTTCATAGGAAACAGTTGAATTTCTG 57.081 29.630 4.42 5.21 45.22 3.02
3684 3871 8.463930 TTCATAGGAAACAGTTGAATTTCTGT 57.536 30.769 0.00 6.21 45.21 3.41
3685 3872 9.567776 TTCATAGGAAACAGTTGAATTTCTGTA 57.432 29.630 10.64 0.00 42.95 2.74
3686 3873 9.219603 TCATAGGAAACAGTTGAATTTCTGTAG 57.780 33.333 10.64 0.00 42.95 2.74
3687 3874 9.003658 CATAGGAAACAGTTGAATTTCTGTAGT 57.996 33.333 10.64 4.69 42.95 2.73
3688 3875 7.497925 AGGAAACAGTTGAATTTCTGTAGTC 57.502 36.000 10.64 10.69 42.95 2.59
3689 3876 7.054124 AGGAAACAGTTGAATTTCTGTAGTCA 58.946 34.615 10.64 0.00 42.95 3.41
3690 3877 7.227512 AGGAAACAGTTGAATTTCTGTAGTCAG 59.772 37.037 10.64 0.00 42.95 3.51
3691 3878 5.931441 ACAGTTGAATTTCTGTAGTCAGC 57.069 39.130 9.16 0.00 42.13 4.26
3692 3879 4.757149 ACAGTTGAATTTCTGTAGTCAGCC 59.243 41.667 9.16 0.00 42.13 4.85
3693 3880 4.999950 CAGTTGAATTTCTGTAGTCAGCCT 59.000 41.667 0.00 0.00 41.10 4.58
3694 3881 6.166279 CAGTTGAATTTCTGTAGTCAGCCTA 58.834 40.000 0.00 0.00 41.10 3.93
3695 3882 6.312426 CAGTTGAATTTCTGTAGTCAGCCTAG 59.688 42.308 0.00 0.00 41.10 3.02
3696 3883 5.344743 TGAATTTCTGTAGTCAGCCTAGG 57.655 43.478 3.67 3.67 41.10 3.02
3697 3884 4.162320 TGAATTTCTGTAGTCAGCCTAGGG 59.838 45.833 11.72 0.00 41.10 3.53
3698 3885 2.921834 TTCTGTAGTCAGCCTAGGGT 57.078 50.000 7.93 7.93 41.10 4.34
3699 3886 2.921834 TCTGTAGTCAGCCTAGGGTT 57.078 50.000 11.77 0.00 41.10 4.11
3700 3887 3.185880 TCTGTAGTCAGCCTAGGGTTT 57.814 47.619 11.77 2.61 41.10 3.27
3701 3888 2.832129 TCTGTAGTCAGCCTAGGGTTTG 59.168 50.000 11.77 0.66 41.10 2.93
3702 3889 1.906574 TGTAGTCAGCCTAGGGTTTGG 59.093 52.381 11.77 0.00 0.00 3.28
3703 3890 1.209747 GTAGTCAGCCTAGGGTTTGGG 59.790 57.143 11.77 0.00 0.00 4.12
3718 3905 1.673767 TTGGGGCCTTCATCTTCTCT 58.326 50.000 0.84 0.00 0.00 3.10
3721 3908 1.134250 GGGGCCTTCATCTTCTCTCAC 60.134 57.143 0.84 0.00 0.00 3.51
3722 3909 1.836802 GGGCCTTCATCTTCTCTCACT 59.163 52.381 0.84 0.00 0.00 3.41
3764 3951 1.375140 CTGAGCGTCACACCTGCAT 60.375 57.895 0.00 0.00 0.00 3.96
3767 3954 1.270571 TGAGCGTCACACCTGCATTTA 60.271 47.619 0.00 0.00 0.00 1.40
3776 3964 3.485378 CACACCTGCATTTACAAAACACG 59.515 43.478 0.00 0.00 0.00 4.49
3781 3969 1.377505 GCATTTACAAAACACGACGCG 59.622 47.619 3.53 3.53 0.00 6.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 54 0.319900 CATCCATCGGCTTACCCTCG 60.320 60.000 0.00 0.00 0.00 4.63
81 82 0.527565 ACATTGCCATCTTCCGTTGC 59.472 50.000 0.00 0.00 0.00 4.17
151 155 5.138276 ACCAATTGCTGATCTTGCATCTAT 58.862 37.500 13.14 3.81 40.34 1.98
218 229 6.884836 ACATTCTACAACCACCTCTAAATTCC 59.115 38.462 0.00 0.00 0.00 3.01
352 365 8.734218 AGTCTGGGTATATATACGTACAGATG 57.266 38.462 27.71 13.92 39.26 2.90
403 418 7.329226 CACTGTCATGAAATTTACATGGGAAAC 59.671 37.037 20.67 15.16 43.38 2.78
407 422 6.375174 TCTCACTGTCATGAAATTTACATGGG 59.625 38.462 20.67 15.84 43.38 4.00
424 439 9.113838 GTATCATCACCAAATTTATCTCACTGT 57.886 33.333 0.00 0.00 0.00 3.55
454 469 9.221775 CTAGTGTTTTGACAACATGTAAAAGAC 57.778 33.333 17.63 17.63 32.65 3.01
480 502 4.021894 TGCCACCCATGTTGTATTGTTTAC 60.022 41.667 0.00 0.00 0.00 2.01
482 504 2.968574 TGCCACCCATGTTGTATTGTTT 59.031 40.909 0.00 0.00 0.00 2.83
483 505 2.562298 CTGCCACCCATGTTGTATTGTT 59.438 45.455 0.00 0.00 0.00 2.83
484 506 2.170166 CTGCCACCCATGTTGTATTGT 58.830 47.619 0.00 0.00 0.00 2.71
488 510 0.039472 ATGCTGCCACCCATGTTGTA 59.961 50.000 0.00 0.00 0.00 2.41
489 511 1.228956 ATGCTGCCACCCATGTTGT 60.229 52.632 0.00 0.00 0.00 3.32
491 513 0.324923 ATCATGCTGCCACCCATGTT 60.325 50.000 0.00 0.00 39.74 2.71
492 514 0.754217 GATCATGCTGCCACCCATGT 60.754 55.000 0.00 0.00 39.74 3.21
493 515 0.467474 AGATCATGCTGCCACCCATG 60.467 55.000 0.00 0.00 40.05 3.66
494 516 1.142936 TAGATCATGCTGCCACCCAT 58.857 50.000 0.00 0.00 0.00 4.00
495 517 0.918258 TTAGATCATGCTGCCACCCA 59.082 50.000 0.00 0.00 0.00 4.51
496 518 1.602311 CTTAGATCATGCTGCCACCC 58.398 55.000 0.00 0.00 0.00 4.61
497 519 1.141657 TCCTTAGATCATGCTGCCACC 59.858 52.381 0.00 0.00 0.00 4.61
498 520 2.627515 TCCTTAGATCATGCTGCCAC 57.372 50.000 0.00 0.00 0.00 5.01
500 522 2.818432 CCAATCCTTAGATCATGCTGCC 59.182 50.000 0.00 0.00 0.00 4.85
501 523 3.484407 ACCAATCCTTAGATCATGCTGC 58.516 45.455 0.00 0.00 0.00 5.25
502 524 4.070716 GGACCAATCCTTAGATCATGCTG 58.929 47.826 0.00 0.00 42.45 4.41
503 525 4.363991 GGACCAATCCTTAGATCATGCT 57.636 45.455 0.00 0.00 42.45 3.79
515 537 0.618981 AAACGGAGGAGGACCAATCC 59.381 55.000 0.00 0.00 46.69 3.01
516 538 2.491675 AAAACGGAGGAGGACCAATC 57.508 50.000 0.00 0.00 38.94 2.67
519 541 1.626825 CCTAAAAACGGAGGAGGACCA 59.373 52.381 0.00 0.00 38.94 4.02
520 542 1.678123 GCCTAAAAACGGAGGAGGACC 60.678 57.143 0.00 0.00 34.46 4.46
521 543 1.735386 GCCTAAAAACGGAGGAGGAC 58.265 55.000 0.00 0.00 34.46 3.85
522 544 0.248289 CGCCTAAAAACGGAGGAGGA 59.752 55.000 0.00 0.00 34.46 3.71
523 545 0.036671 ACGCCTAAAAACGGAGGAGG 60.037 55.000 0.00 0.00 36.99 4.30
524 546 1.804601 AACGCCTAAAAACGGAGGAG 58.195 50.000 0.00 0.00 38.50 3.69
525 547 3.615224 ATAACGCCTAAAAACGGAGGA 57.385 42.857 0.00 0.00 34.46 3.71
527 549 5.050567 GTCCATATAACGCCTAAAAACGGAG 60.051 44.000 0.00 0.00 0.00 4.63
529 551 4.812626 AGTCCATATAACGCCTAAAAACGG 59.187 41.667 0.00 0.00 0.00 4.44
530 552 5.751990 AGAGTCCATATAACGCCTAAAAACG 59.248 40.000 0.00 0.00 0.00 3.60
531 553 7.707893 TGTAGAGTCCATATAACGCCTAAAAAC 59.292 37.037 0.00 0.00 0.00 2.43
533 555 7.350744 TGTAGAGTCCATATAACGCCTAAAA 57.649 36.000 0.00 0.00 0.00 1.52
534 556 6.964807 TGTAGAGTCCATATAACGCCTAAA 57.035 37.500 0.00 0.00 0.00 1.85
535 557 6.492429 ACATGTAGAGTCCATATAACGCCTAA 59.508 38.462 0.00 0.00 0.00 2.69
536 558 6.008331 ACATGTAGAGTCCATATAACGCCTA 58.992 40.000 0.00 0.00 0.00 3.93
537 559 4.833380 ACATGTAGAGTCCATATAACGCCT 59.167 41.667 0.00 0.00 0.00 5.52
538 560 5.135508 ACATGTAGAGTCCATATAACGCC 57.864 43.478 0.00 0.00 0.00 5.68
539 561 7.011109 ACAAAACATGTAGAGTCCATATAACGC 59.989 37.037 0.00 0.00 41.63 4.84
540 562 8.420374 ACAAAACATGTAGAGTCCATATAACG 57.580 34.615 0.00 0.00 41.63 3.18
548 570 9.916397 CGAATTATAACAAAACATGTAGAGTCC 57.084 33.333 0.00 0.00 42.99 3.85
549 571 9.422196 GCGAATTATAACAAAACATGTAGAGTC 57.578 33.333 0.00 0.00 42.99 3.36
551 573 8.612619 AGGCGAATTATAACAAAACATGTAGAG 58.387 33.333 0.00 0.00 42.99 2.43
553 575 9.567848 AAAGGCGAATTATAACAAAACATGTAG 57.432 29.630 0.00 0.00 42.99 2.74
555 577 8.825667 AAAAGGCGAATTATAACAAAACATGT 57.174 26.923 0.00 0.00 46.82 3.21
571 593 9.922305 CACACAAAATAAAAATAAAAAGGCGAA 57.078 25.926 0.00 0.00 0.00 4.70
572 594 9.314321 TCACACAAAATAAAAATAAAAAGGCGA 57.686 25.926 0.00 0.00 0.00 5.54
573 595 9.579610 CTCACACAAAATAAAAATAAAAAGGCG 57.420 29.630 0.00 0.00 0.00 5.52
579 601 9.974980 GACCCTCTCACACAAAATAAAAATAAA 57.025 29.630 0.00 0.00 0.00 1.40
582 604 6.782494 AGGACCCTCTCACACAAAATAAAAAT 59.218 34.615 0.00 0.00 0.00 1.82
584 606 5.701224 AGGACCCTCTCACACAAAATAAAA 58.299 37.500 0.00 0.00 0.00 1.52
585 607 5.319043 AGGACCCTCTCACACAAAATAAA 57.681 39.130 0.00 0.00 0.00 1.40
586 608 4.993705 AGGACCCTCTCACACAAAATAA 57.006 40.909 0.00 0.00 0.00 1.40
587 609 6.636454 AATAGGACCCTCTCACACAAAATA 57.364 37.500 0.00 0.00 0.00 1.40
588 610 5.520748 AATAGGACCCTCTCACACAAAAT 57.479 39.130 0.00 0.00 0.00 1.82
589 611 4.993705 AATAGGACCCTCTCACACAAAA 57.006 40.909 0.00 0.00 0.00 2.44
590 612 4.506625 CCAAATAGGACCCTCTCACACAAA 60.507 45.833 0.00 0.00 41.22 2.83
591 613 3.009033 CCAAATAGGACCCTCTCACACAA 59.991 47.826 0.00 0.00 41.22 3.33
592 614 2.571653 CCAAATAGGACCCTCTCACACA 59.428 50.000 0.00 0.00 41.22 3.72
593 615 2.681097 GCCAAATAGGACCCTCTCACAC 60.681 54.545 0.00 0.00 41.22 3.82
594 616 1.559682 GCCAAATAGGACCCTCTCACA 59.440 52.381 0.00 0.00 41.22 3.58
595 617 1.840635 AGCCAAATAGGACCCTCTCAC 59.159 52.381 0.00 0.00 41.22 3.51
596 618 1.839994 CAGCCAAATAGGACCCTCTCA 59.160 52.381 0.00 0.00 41.22 3.27
597 619 1.840635 ACAGCCAAATAGGACCCTCTC 59.159 52.381 0.00 0.00 41.22 3.20
598 620 1.561542 CACAGCCAAATAGGACCCTCT 59.438 52.381 0.00 0.00 41.22 3.69
599 621 1.282157 ACACAGCCAAATAGGACCCTC 59.718 52.381 0.00 0.00 41.22 4.30
600 622 1.004745 CACACAGCCAAATAGGACCCT 59.995 52.381 0.00 0.00 41.22 4.34
601 623 1.463674 CACACAGCCAAATAGGACCC 58.536 55.000 0.00 0.00 41.22 4.46
602 624 0.811281 GCACACAGCCAAATAGGACC 59.189 55.000 0.00 0.00 41.22 4.46
603 625 1.533625 TGCACACAGCCAAATAGGAC 58.466 50.000 0.00 0.00 44.83 3.85
604 626 2.025981 AGATGCACACAGCCAAATAGGA 60.026 45.455 0.00 0.00 44.83 2.94
605 627 2.372264 AGATGCACACAGCCAAATAGG 58.628 47.619 0.00 0.00 44.83 2.57
606 628 4.637534 ACTAAGATGCACACAGCCAAATAG 59.362 41.667 0.00 0.00 44.83 1.73
607 629 4.588899 ACTAAGATGCACACAGCCAAATA 58.411 39.130 0.00 0.00 44.83 1.40
608 630 3.424703 ACTAAGATGCACACAGCCAAAT 58.575 40.909 0.00 0.00 44.83 2.32
609 631 2.862541 ACTAAGATGCACACAGCCAAA 58.137 42.857 0.00 0.00 44.83 3.28
610 632 2.566833 ACTAAGATGCACACAGCCAA 57.433 45.000 0.00 0.00 44.83 4.52
611 633 2.566833 AACTAAGATGCACACAGCCA 57.433 45.000 0.00 0.00 44.83 4.75
612 634 4.542662 CATAACTAAGATGCACACAGCC 57.457 45.455 0.00 0.00 44.83 4.85
621 643 3.062763 CGGGCTCTGCATAACTAAGATG 58.937 50.000 0.00 0.00 0.00 2.90
622 644 2.037772 CCGGGCTCTGCATAACTAAGAT 59.962 50.000 0.00 0.00 0.00 2.40
623 645 1.412710 CCGGGCTCTGCATAACTAAGA 59.587 52.381 0.00 0.00 0.00 2.10
624 646 1.541233 CCCGGGCTCTGCATAACTAAG 60.541 57.143 8.08 0.00 0.00 2.18
625 647 0.468226 CCCGGGCTCTGCATAACTAA 59.532 55.000 8.08 0.00 0.00 2.24
626 648 0.689745 ACCCGGGCTCTGCATAACTA 60.690 55.000 24.08 0.00 0.00 2.24
627 649 1.995626 ACCCGGGCTCTGCATAACT 60.996 57.895 24.08 0.00 0.00 2.24
628 650 1.819632 CACCCGGGCTCTGCATAAC 60.820 63.158 24.08 0.00 0.00 1.89
629 651 0.978667 TACACCCGGGCTCTGCATAA 60.979 55.000 24.08 0.00 0.00 1.90
630 652 0.978667 TTACACCCGGGCTCTGCATA 60.979 55.000 24.08 0.00 0.00 3.14
631 653 1.635817 ATTACACCCGGGCTCTGCAT 61.636 55.000 24.08 4.68 0.00 3.96
632 654 2.297895 ATTACACCCGGGCTCTGCA 61.298 57.895 24.08 0.00 0.00 4.41
633 655 1.819632 CATTACACCCGGGCTCTGC 60.820 63.158 24.08 0.00 0.00 4.26
634 656 1.819632 GCATTACACCCGGGCTCTG 60.820 63.158 24.08 15.03 0.00 3.35
635 657 1.562672 AAGCATTACACCCGGGCTCT 61.563 55.000 24.08 5.21 32.84 4.09
636 658 0.179468 TAAGCATTACACCCGGGCTC 59.821 55.000 24.08 1.41 32.84 4.70
637 659 0.621609 TTAAGCATTACACCCGGGCT 59.378 50.000 24.08 8.77 36.13 5.19
638 660 1.465794 TTTAAGCATTACACCCGGGC 58.534 50.000 24.08 4.01 0.00 6.13
639 661 3.551846 AGATTTAAGCATTACACCCGGG 58.448 45.455 22.25 22.25 0.00 5.73
640 662 5.576447 AAAGATTTAAGCATTACACCCGG 57.424 39.130 0.00 0.00 0.00 5.73
641 663 8.241367 ACTTAAAAGATTTAAGCATTACACCCG 58.759 33.333 17.94 0.00 35.88 5.28
655 677 8.957466 AGAGGCGCTTTATTACTTAAAAGATTT 58.043 29.630 7.64 0.00 35.19 2.17
656 678 8.507524 AGAGGCGCTTTATTACTTAAAAGATT 57.492 30.769 7.64 0.00 35.19 2.40
657 679 8.507524 AAGAGGCGCTTTATTACTTAAAAGAT 57.492 30.769 7.64 0.00 35.19 2.40
658 680 7.916914 AAGAGGCGCTTTATTACTTAAAAGA 57.083 32.000 7.64 0.00 35.19 2.52
659 681 8.965986 AAAAGAGGCGCTTTATTACTTAAAAG 57.034 30.769 16.59 0.00 45.85 2.27
660 682 9.187455 CAAAAAGAGGCGCTTTATTACTTAAAA 57.813 29.630 16.59 0.00 45.85 1.52
661 683 8.569641 TCAAAAAGAGGCGCTTTATTACTTAAA 58.430 29.630 16.59 0.00 45.85 1.52
662 684 8.101654 TCAAAAAGAGGCGCTTTATTACTTAA 57.898 30.769 16.59 0.00 45.85 1.85
663 685 7.675962 TCAAAAAGAGGCGCTTTATTACTTA 57.324 32.000 16.59 0.00 45.85 2.24
664 686 6.569179 TCAAAAAGAGGCGCTTTATTACTT 57.431 33.333 16.59 4.36 45.85 2.24
665 687 6.569179 TTCAAAAAGAGGCGCTTTATTACT 57.431 33.333 16.59 0.00 45.85 2.24
666 688 7.631915 TTTTCAAAAAGAGGCGCTTTATTAC 57.368 32.000 16.59 0.00 45.85 1.89
667 689 7.923878 ACTTTTTCAAAAAGAGGCGCTTTATTA 59.076 29.630 26.15 2.57 45.85 0.98
668 690 6.761242 ACTTTTTCAAAAAGAGGCGCTTTATT 59.239 30.769 26.15 10.17 45.85 1.40
669 691 6.280643 ACTTTTTCAAAAAGAGGCGCTTTAT 58.719 32.000 26.15 4.85 45.85 1.40
670 692 5.656480 ACTTTTTCAAAAAGAGGCGCTTTA 58.344 33.333 26.15 0.00 45.85 1.85
672 694 4.123497 ACTTTTTCAAAAAGAGGCGCTT 57.877 36.364 26.15 0.00 38.88 4.68
673 695 3.801114 ACTTTTTCAAAAAGAGGCGCT 57.199 38.095 26.15 2.79 0.00 5.92
674 696 5.289917 TGTTTACTTTTTCAAAAAGAGGCGC 59.710 36.000 26.15 13.26 0.00 6.53
675 697 6.879188 TGTTTACTTTTTCAAAAAGAGGCG 57.121 33.333 26.15 3.69 0.00 5.52
713 735 8.678199 GCCACTTATTAGAGCTTGACTTAAAAT 58.322 33.333 0.00 0.00 0.00 1.82
809 843 1.053424 TCTAACAGGCCGGACTTTGT 58.947 50.000 7.41 0.00 0.00 2.83
815 849 0.912487 ATTGGGTCTAACAGGCCGGA 60.912 55.000 10.86 0.00 42.14 5.14
886 920 2.507992 CGGAGTGAGCAGCGGAAG 60.508 66.667 0.00 0.00 0.00 3.46
887 921 4.742201 GCGGAGTGAGCAGCGGAA 62.742 66.667 0.00 0.00 34.19 4.30
998 1034 4.101448 GCACCACGGCCCTCATCT 62.101 66.667 0.00 0.00 0.00 2.90
1054 1090 1.361668 CGGATGTGGCGAACTGAAGG 61.362 60.000 0.00 0.00 0.00 3.46
1222 1258 6.929606 GTCAGAGGTGGGTTCATTACATATAC 59.070 42.308 0.00 0.00 0.00 1.47
1225 1261 4.163458 GGTCAGAGGTGGGTTCATTACATA 59.837 45.833 0.00 0.00 0.00 2.29
1251 1287 0.178958 GCCGAGGATTAGGAGGGAGA 60.179 60.000 0.00 0.00 0.00 3.71
1252 1288 0.470080 TGCCGAGGATTAGGAGGGAG 60.470 60.000 0.00 0.00 0.00 4.30
1362 1398 4.948864 ATTGATACGCTAACGATTGTCG 57.051 40.909 0.00 0.00 46.93 4.35
1392 1428 3.439476 ACAGCACCACGTCTAGTTACTAG 59.561 47.826 12.85 12.85 35.57 2.57
1405 1441 0.804989 GCACCAGAATACAGCACCAC 59.195 55.000 0.00 0.00 0.00 4.16
1570 1606 2.859165 AAATCGGACACCATCACAGT 57.141 45.000 0.00 0.00 0.00 3.55
1584 1620 7.169308 ACGGAAATAGAGTGTTAGCATAAATCG 59.831 37.037 0.00 0.00 0.00 3.34
1586 1622 9.477484 CTACGGAAATAGAGTGTTAGCATAAAT 57.523 33.333 0.00 0.00 0.00 1.40
1589 1625 6.264744 AGCTACGGAAATAGAGTGTTAGCATA 59.735 38.462 0.00 0.00 0.00 3.14
1633 1669 5.517054 GTCTTCTCATTAGTAAACAGCCTCG 59.483 44.000 0.00 0.00 0.00 4.63
1713 1749 4.135306 CAACATGCTGAATGCTCTCCTAT 58.865 43.478 0.00 0.00 40.22 2.57
1786 1822 5.632034 ACCTAACAGGACTTCAAAGTTCT 57.368 39.130 0.00 0.00 45.79 3.01
1826 1862 6.865726 CCATTACAGAATCGGAAGTAGAGATG 59.134 42.308 0.00 0.00 0.00 2.90
1827 1863 6.517529 GCCATTACAGAATCGGAAGTAGAGAT 60.518 42.308 0.00 0.00 0.00 2.75
1838 1874 3.454375 AGGTTACGCCATTACAGAATCG 58.546 45.455 0.00 0.00 40.61 3.34
1840 1876 6.655848 TGTTAAAGGTTACGCCATTACAGAAT 59.344 34.615 0.00 0.00 40.61 2.40
1841 1877 5.996513 TGTTAAAGGTTACGCCATTACAGAA 59.003 36.000 0.00 0.00 40.61 3.02
1846 1882 7.450124 TCAATTGTTAAAGGTTACGCCATTA 57.550 32.000 5.13 0.00 40.61 1.90
1896 1934 9.911788 AAATTGACTCACTGAATAGGATAACAT 57.088 29.630 0.00 0.00 0.00 2.71
2090 2128 2.181975 CCCAAGATGGCCAACTTCAAT 58.818 47.619 24.23 1.95 35.79 2.57
2091 2129 1.133199 ACCCAAGATGGCCAACTTCAA 60.133 47.619 24.23 0.00 35.79 2.69
2109 2147 6.551385 AGATCGATTTGATAATGAAGCACC 57.449 37.500 0.00 0.00 37.47 5.01
2172 2210 4.802583 GCATCCATACATCGGTTACCATGA 60.803 45.833 16.59 1.79 0.00 3.07
2251 2289 6.753279 TCTGAACAAGCAGAATTGAGTTTTTG 59.247 34.615 0.00 0.00 41.65 2.44
2409 2521 1.464608 AGGTTCAATGCGACATTGACG 59.535 47.619 24.95 4.15 37.71 4.35
2414 2526 4.156455 AGGAATAGGTTCAATGCGACAT 57.844 40.909 0.00 0.00 36.01 3.06
2532 2644 8.065473 ACATGCATTCTGGAAAATGTAATGTA 57.935 30.769 0.00 0.00 40.40 2.29
2541 2653 5.239351 CCAATTGACATGCATTCTGGAAAA 58.761 37.500 7.12 0.00 0.00 2.29
2633 2745 1.298014 CCTTGACTGACCAGAGCCC 59.702 63.158 3.76 0.00 0.00 5.19
2827 2939 0.177141 TACTGCGGGAACAGCCATAC 59.823 55.000 0.00 0.00 41.60 2.39
2850 2962 2.034558 AGATGTTCACCAAAACCAAGCG 59.965 45.455 0.00 0.00 0.00 4.68
2889 3001 8.958043 CCTCAAAAAGAAACTGAAAATTCTACG 58.042 33.333 0.00 0.00 34.90 3.51
2907 3019 4.274147 TCCTTGTGCTACAACCTCAAAAA 58.726 39.130 0.00 0.00 33.96 1.94
2977 3090 2.555325 CAAATATCAGCATGCGGATGGT 59.445 45.455 34.46 23.16 41.09 3.55
3079 3200 2.076863 CAGACCGGTTGGATCAAACTC 58.923 52.381 9.42 3.04 39.21 3.01
3108 3229 6.014242 ACAAACTGGAGATGACTCACAATAGA 60.014 38.462 0.00 0.00 44.22 1.98
3159 3280 1.075050 AGTGTGACCGAGGGAAGACTA 59.925 52.381 0.00 0.00 0.00 2.59
3163 3284 1.404315 GCTAAGTGTGACCGAGGGAAG 60.404 57.143 0.00 0.00 0.00 3.46
3166 3287 1.153823 CGCTAAGTGTGACCGAGGG 60.154 63.158 0.00 0.00 0.00 4.30
3167 3288 0.179161 CTCGCTAAGTGTGACCGAGG 60.179 60.000 0.00 0.00 41.04 4.63
3178 3299 7.492669 TGGAACTCATAAAGATTTCTCGCTAAG 59.507 37.037 0.00 0.00 36.47 2.18
3181 3302 5.582665 GTGGAACTCATAAAGATTTCTCGCT 59.417 40.000 0.00 0.00 36.47 4.93
3183 3304 5.874810 TGGTGGAACTCATAAAGATTTCTCG 59.125 40.000 0.00 0.00 36.47 4.04
3197 3318 1.198759 TACAGGCCCTGGTGGAACTC 61.199 60.000 16.70 0.00 35.51 3.01
3202 3323 1.918293 TGAGTACAGGCCCTGGTGG 60.918 63.158 16.70 0.00 35.51 4.61
3213 3334 7.392494 AAGATCATCTAAACTCGTGAGTACA 57.608 36.000 2.42 0.00 41.58 2.90
3221 3342 9.521503 TGAAATCACTAAGATCATCTAAACTCG 57.478 33.333 0.00 0.00 35.39 4.18
3232 3353 7.142021 TGCTACTCGATGAAATCACTAAGATC 58.858 38.462 0.00 0.00 45.97 2.75
3239 3360 6.828502 TGTATTGCTACTCGATGAAATCAC 57.171 37.500 0.00 0.00 45.97 3.06
3267 3388 0.394565 ACAGAAGGAGAAGCGTTGCT 59.605 50.000 0.00 0.00 42.56 3.91
3272 3393 0.174617 GAGGGACAGAAGGAGAAGCG 59.825 60.000 0.00 0.00 0.00 4.68
3275 3396 2.260822 CTTGGAGGGACAGAAGGAGAA 58.739 52.381 0.00 0.00 0.00 2.87
3282 3403 1.359474 AGAGTAGCTTGGAGGGACAGA 59.641 52.381 0.00 0.00 0.00 3.41
3303 3425 5.897250 AGGGATTAAAAACACAGGAACAGTT 59.103 36.000 0.00 0.00 0.00 3.16
3304 3426 5.454966 AGGGATTAAAAACACAGGAACAGT 58.545 37.500 0.00 0.00 0.00 3.55
3306 3428 9.762381 AATATAGGGATTAAAAACACAGGAACA 57.238 29.630 0.00 0.00 0.00 3.18
3322 3444 6.595682 CCTCACAAGTCACAAATATAGGGAT 58.404 40.000 0.00 0.00 0.00 3.85
3347 3472 3.119459 AGCACATGAACTGGAGTAGTACG 60.119 47.826 0.00 0.00 39.18 3.67
3382 3507 6.595716 AGAACCTCAGTTGCATTCAGTATTAC 59.404 38.462 0.00 0.00 35.94 1.89
3470 3595 4.368565 AGCCAGAAGATGATACATGCAT 57.631 40.909 0.00 0.00 0.00 3.96
3626 3813 5.659971 CCTAAGTAGGAACAAGCCCTAAGTA 59.340 44.000 0.00 0.00 46.63 2.24
3638 3825 8.738645 ATGAAATTCATGTCCTAAGTAGGAAC 57.261 34.615 7.79 4.72 41.50 3.62
3665 3852 7.259290 TGACTACAGAAATTCAACTGTTTCC 57.741 36.000 14.72 7.72 43.52 3.13
3671 3858 5.234466 AGGCTGACTACAGAAATTCAACT 57.766 39.130 0.00 0.00 46.03 3.16
3683 3870 1.209747 CCCAAACCCTAGGCTGACTAC 59.790 57.143 2.05 0.00 0.00 2.73
3684 3871 1.580059 CCCAAACCCTAGGCTGACTA 58.420 55.000 2.05 0.00 0.00 2.59
3685 3872 1.208165 CCCCAAACCCTAGGCTGACT 61.208 60.000 2.05 0.00 0.00 3.41
3686 3873 1.303282 CCCCAAACCCTAGGCTGAC 59.697 63.158 2.05 0.00 0.00 3.51
3687 3874 2.612493 GCCCCAAACCCTAGGCTGA 61.612 63.158 2.05 0.00 42.34 4.26
3688 3875 2.043953 GCCCCAAACCCTAGGCTG 60.044 66.667 2.05 0.00 42.34 4.85
3689 3876 3.347590 GGCCCCAAACCCTAGGCT 61.348 66.667 2.05 0.00 45.07 4.58
3690 3877 2.856039 GAAGGCCCCAAACCCTAGGC 62.856 65.000 2.05 0.00 44.99 3.93
3691 3878 1.306633 GAAGGCCCCAAACCCTAGG 59.693 63.158 0.06 0.06 0.00 3.02
3692 3879 0.631212 ATGAAGGCCCCAAACCCTAG 59.369 55.000 0.00 0.00 0.00 3.02
3693 3880 0.629058 GATGAAGGCCCCAAACCCTA 59.371 55.000 0.00 0.00 0.00 3.53
3694 3881 1.149133 AGATGAAGGCCCCAAACCCT 61.149 55.000 0.00 0.00 0.00 4.34
3695 3882 0.252239 AAGATGAAGGCCCCAAACCC 60.252 55.000 0.00 0.00 0.00 4.11
3696 3883 1.186200 GAAGATGAAGGCCCCAAACC 58.814 55.000 0.00 0.00 0.00 3.27
3697 3884 2.095461 GAGAAGATGAAGGCCCCAAAC 58.905 52.381 0.00 0.00 0.00 2.93
3698 3885 1.995542 AGAGAAGATGAAGGCCCCAAA 59.004 47.619 0.00 0.00 0.00 3.28
3699 3886 1.561542 GAGAGAAGATGAAGGCCCCAA 59.438 52.381 0.00 0.00 0.00 4.12
3700 3887 1.207791 GAGAGAAGATGAAGGCCCCA 58.792 55.000 0.00 0.00 0.00 4.96
3701 3888 1.134250 GTGAGAGAAGATGAAGGCCCC 60.134 57.143 0.00 0.00 0.00 5.80
3702 3889 1.836802 AGTGAGAGAAGATGAAGGCCC 59.163 52.381 0.00 0.00 0.00 5.80
3703 3890 2.903798 CAGTGAGAGAAGATGAAGGCC 58.096 52.381 0.00 0.00 0.00 5.19
3764 3951 3.111838 TCTACGCGTCGTGTTTTGTAAA 58.888 40.909 18.63 0.00 41.39 2.01
3767 3954 1.519758 CTTCTACGCGTCGTGTTTTGT 59.480 47.619 18.63 0.00 41.39 2.83
3776 3964 0.179108 ATGGGCTTCTTCTACGCGTC 60.179 55.000 18.63 0.00 0.00 5.19
3781 3969 7.125811 TGGTGGATATATATGGGCTTCTTCTAC 59.874 40.741 0.00 0.00 0.00 2.59


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

AutoCloner maintained by Alex Coulton.