Multiple sequence alignment - TraesCS5B01G102000

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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 TraesCS5B01G102000 chr5B 100.000 4522 0 0 1 4522 136005388 136009909 0.000000e+00 8351.0
1 TraesCS5B01G102000 chr5D 93.554 2994 147 20 1315 4293 122616393 122619355 0.000000e+00 4418.0
2 TraesCS5B01G102000 chr5D 95.079 630 19 6 694 1317 122615742 122616365 0.000000e+00 981.0
3 TraesCS5B01G102000 chr5A 94.697 1980 84 6 2316 4293 135059010 135060970 0.000000e+00 3055.0
4 TraesCS5B01G102000 chr5A 93.688 1014 34 8 1315 2309 135057577 135058579 0.000000e+00 1491.0
5 TraesCS5B01G102000 chr5A 95.231 629 20 4 693 1317 135056927 135057549 0.000000e+00 987.0
6 TraesCS5B01G102000 chr5A 93.989 183 7 3 4340 4522 135061205 135061383 1.600000e-69 274.0
7 TraesCS5B01G102000 chr1D 83.601 561 69 10 16 566 33333694 33333147 5.220000e-139 505.0
8 TraesCS5B01G102000 chr1D 79.115 565 94 14 1 552 431400223 431400776 7.150000e-98 368.0
9 TraesCS5B01G102000 chr2B 82.230 574 84 10 3 566 638289683 638290248 3.160000e-131 479.0
10 TraesCS5B01G102000 chr2B 75.758 462 68 24 6 443 759178204 759178645 4.620000e-45 193.0
11 TraesCS5B01G102000 chr4D 81.901 547 63 21 1 540 374596663 374596146 3.230000e-116 429.0
12 TraesCS5B01G102000 chr2A 81.400 543 69 16 6 540 227490779 227490261 9.050000e-112 414.0
13 TraesCS5B01G102000 chr2A 84.635 384 44 11 16 385 17994853 17995235 7.150000e-98 368.0
14 TraesCS5B01G102000 chr6B 85.422 391 46 6 6 389 454517378 454516992 3.280000e-106 396.0
15 TraesCS5B01G102000 chr1A 82.418 455 65 9 1 443 16911848 16912299 2.550000e-102 383.0
16 TraesCS5B01G102000 chr7D 83.023 430 61 8 16 434 35083110 35083538 3.300000e-101 379.0
17 TraesCS5B01G102000 chr3B 89.362 47 5 0 370 416 474414813 474414767 4.890000e-05 60.2


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 TraesCS5B01G102000 chr5B 136005388 136009909 4521 False 8351.00 8351 100.00000 1 4522 1 chr5B.!!$F1 4521
1 TraesCS5B01G102000 chr5D 122615742 122619355 3613 False 2699.50 4418 94.31650 694 4293 2 chr5D.!!$F1 3599
2 TraesCS5B01G102000 chr5A 135056927 135061383 4456 False 1451.75 3055 94.40125 693 4522 4 chr5A.!!$F1 3829
3 TraesCS5B01G102000 chr1D 33333147 33333694 547 True 505.00 505 83.60100 16 566 1 chr1D.!!$R1 550
4 TraesCS5B01G102000 chr1D 431400223 431400776 553 False 368.00 368 79.11500 1 552 1 chr1D.!!$F1 551
5 TraesCS5B01G102000 chr2B 638289683 638290248 565 False 479.00 479 82.23000 3 566 1 chr2B.!!$F1 563
6 TraesCS5B01G102000 chr4D 374596146 374596663 517 True 429.00 429 81.90100 1 540 1 chr4D.!!$R1 539
7 TraesCS5B01G102000 chr2A 227490261 227490779 518 True 414.00 414 81.40000 6 540 1 chr2A.!!$R1 534

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
596 637 0.030101 TCAAAAAGCGGCGTTTGGAG 59.970 50.0 23.05 13.87 35.79 3.86 F
598 639 0.030235 AAAAAGCGGCGTTTGGAGTC 59.970 50.0 14.37 0.00 0.00 3.36 F
622 663 0.034756 TGGGACAACCACTCATGTCG 59.965 55.0 0.00 0.00 46.80 4.35 F
663 704 0.099436 CAGGCCACGCTATTTCAAGC 59.901 55.0 5.01 0.00 39.21 4.01 F
2610 3131 0.032403 TGTTGTTCGGTAGGGACACG 59.968 55.0 0.00 0.00 0.00 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2222 2319 0.190815 AATGGGCCAAAAGGGTCAGT 59.809 50.000 11.89 0.0 45.89 3.41 R
2434 2955 2.006888 ACTGTTCAAACACACAGACCG 58.993 47.619 6.32 0.0 42.74 4.79 R
2605 3126 1.452399 GCGACAGAGAAGAAACGTGTC 59.548 52.381 0.00 0.0 35.26 3.67 R
2633 3154 0.598065 AACGCATGGAGGCAAACTTC 59.402 50.000 0.00 0.0 0.00 3.01 R
3524 4046 0.321653 GCTGTCCAATGAACCGAGGT 60.322 55.000 0.00 0.0 0.00 3.85 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
34 35 1.594293 CGGCGGCCTCGTCATAAAT 60.594 57.895 18.34 0.00 41.75 1.40
74 78 0.846427 TCCTCCCCACAGCCATCTTT 60.846 55.000 0.00 0.00 0.00 2.52
235 241 1.078214 CGCCCTCAAGAAGATGCCA 60.078 57.895 0.00 0.00 0.00 4.92
352 361 3.255397 AGGGCTGCAGCAAGGACT 61.255 61.111 37.63 23.39 44.36 3.85
410 428 0.970640 TACACCGCCTTCTACAAGCA 59.029 50.000 0.00 0.00 0.00 3.91
417 435 0.608640 CCTTCTACAAGCACCTCGGT 59.391 55.000 0.00 0.00 0.00 4.69
429 448 1.367840 CCTCGGTATGCAGTAGGCC 59.632 63.158 0.00 0.00 43.89 5.19
452 491 1.702491 GGCGGCTGCGTAGTTTTAGG 61.702 60.000 12.29 0.00 44.10 2.69
453 492 1.702491 GCGGCTGCGTAGTTTTAGGG 61.702 60.000 0.00 0.00 0.00 3.53
455 494 0.675522 GGCTGCGTAGTTTTAGGGCA 60.676 55.000 1.53 0.00 0.00 5.36
456 495 1.379527 GCTGCGTAGTTTTAGGGCAT 58.620 50.000 1.53 0.00 32.55 4.40
457 496 2.557317 GCTGCGTAGTTTTAGGGCATA 58.443 47.619 1.53 0.00 32.55 3.14
458 497 2.544267 GCTGCGTAGTTTTAGGGCATAG 59.456 50.000 1.53 0.00 32.55 2.23
459 498 3.793559 CTGCGTAGTTTTAGGGCATAGT 58.206 45.455 0.00 0.00 32.55 2.12
460 499 4.189231 CTGCGTAGTTTTAGGGCATAGTT 58.811 43.478 0.00 0.00 32.55 2.24
461 500 4.581868 TGCGTAGTTTTAGGGCATAGTTT 58.418 39.130 0.00 0.00 0.00 2.66
462 501 5.005094 TGCGTAGTTTTAGGGCATAGTTTT 58.995 37.500 0.00 0.00 0.00 2.43
463 502 5.106475 TGCGTAGTTTTAGGGCATAGTTTTG 60.106 40.000 0.00 0.00 0.00 2.44
464 503 5.675323 GCGTAGTTTTAGGGCATAGTTTTGG 60.675 44.000 0.00 0.00 0.00 3.28
524 565 6.422776 ACATATGTCAATGAAAACCGTCTC 57.577 37.500 1.41 0.00 0.00 3.36
541 582 5.470777 ACCGTCTCAATTTCGTCCAAATTTA 59.529 36.000 0.00 0.00 41.19 1.40
553 594 7.865875 TCGTCCAAATTTATGTCATTTTGTG 57.134 32.000 7.40 1.59 0.00 3.33
554 595 7.429633 TCGTCCAAATTTATGTCATTTTGTGT 58.570 30.769 7.40 0.00 0.00 3.72
555 596 7.380870 TCGTCCAAATTTATGTCATTTTGTGTG 59.619 33.333 7.40 0.00 0.00 3.82
566 607 5.534278 TGTCATTTTGTGTGAAATCTAGCCA 59.466 36.000 0.00 0.00 0.00 4.75
567 608 6.209192 TGTCATTTTGTGTGAAATCTAGCCAT 59.791 34.615 0.00 0.00 0.00 4.40
568 609 6.749118 GTCATTTTGTGTGAAATCTAGCCATC 59.251 38.462 0.00 0.00 0.00 3.51
569 610 6.660521 TCATTTTGTGTGAAATCTAGCCATCT 59.339 34.615 0.00 0.00 0.00 2.90
570 611 6.899393 TTTTGTGTGAAATCTAGCCATCTT 57.101 33.333 0.00 0.00 0.00 2.40
571 612 6.899393 TTTGTGTGAAATCTAGCCATCTTT 57.101 33.333 0.00 0.00 0.00 2.52
572 613 5.885230 TGTGTGAAATCTAGCCATCTTTG 57.115 39.130 0.00 0.00 0.00 2.77
573 614 5.559770 TGTGTGAAATCTAGCCATCTTTGA 58.440 37.500 0.00 0.00 0.00 2.69
574 615 6.182627 TGTGTGAAATCTAGCCATCTTTGAT 58.817 36.000 0.00 0.00 0.00 2.57
575 616 6.660521 TGTGTGAAATCTAGCCATCTTTGATT 59.339 34.615 0.00 0.00 0.00 2.57
576 617 7.177216 TGTGTGAAATCTAGCCATCTTTGATTT 59.823 33.333 0.00 0.00 37.18 2.17
577 618 8.031277 GTGTGAAATCTAGCCATCTTTGATTTT 58.969 33.333 0.00 0.00 35.95 1.82
578 619 8.246180 TGTGAAATCTAGCCATCTTTGATTTTC 58.754 33.333 0.00 0.00 35.95 2.29
579 620 8.246180 GTGAAATCTAGCCATCTTTGATTTTCA 58.754 33.333 0.00 0.00 35.95 2.69
580 621 8.805175 TGAAATCTAGCCATCTTTGATTTTCAA 58.195 29.630 0.00 0.00 35.95 2.69
581 622 9.643693 GAAATCTAGCCATCTTTGATTTTCAAA 57.356 29.630 2.96 2.96 43.37 2.69
584 625 9.649167 ATCTAGCCATCTTTGATTTTCAAAAAG 57.351 29.630 4.43 0.00 44.69 2.27
585 626 6.549912 AGCCATCTTTGATTTTCAAAAAGC 57.450 33.333 4.43 0.00 44.69 3.51
586 627 5.178067 AGCCATCTTTGATTTTCAAAAAGCG 59.822 36.000 4.43 0.00 44.69 4.68
587 628 5.615325 GCCATCTTTGATTTTCAAAAAGCGG 60.615 40.000 4.43 4.38 44.69 5.52
588 629 5.376537 CATCTTTGATTTTCAAAAAGCGGC 58.623 37.500 4.43 0.00 44.69 6.53
589 630 3.489047 TCTTTGATTTTCAAAAAGCGGCG 59.511 39.130 0.51 0.51 44.69 6.46
590 631 2.500509 TGATTTTCAAAAAGCGGCGT 57.499 40.000 9.37 0.00 37.12 5.68
591 632 2.815478 TGATTTTCAAAAAGCGGCGTT 58.185 38.095 9.37 0.00 37.12 4.84
592 633 3.190874 TGATTTTCAAAAAGCGGCGTTT 58.809 36.364 9.37 5.78 37.12 3.60
593 634 3.000724 TGATTTTCAAAAAGCGGCGTTTG 59.999 39.130 14.37 17.49 37.12 2.93
594 635 1.281899 TTTCAAAAAGCGGCGTTTGG 58.718 45.000 23.05 17.32 35.79 3.28
595 636 0.456221 TTCAAAAAGCGGCGTTTGGA 59.544 45.000 23.05 18.97 35.79 3.53
596 637 0.030101 TCAAAAAGCGGCGTTTGGAG 59.970 50.000 23.05 13.87 35.79 3.86
597 638 0.248866 CAAAAAGCGGCGTTTGGAGT 60.249 50.000 14.37 0.00 32.26 3.85
598 639 0.030235 AAAAAGCGGCGTTTGGAGTC 59.970 50.000 14.37 0.00 0.00 3.36
599 640 1.098712 AAAAGCGGCGTTTGGAGTCA 61.099 50.000 10.36 0.00 0.00 3.41
600 641 1.507141 AAAGCGGCGTTTGGAGTCAG 61.507 55.000 10.36 0.00 0.00 3.51
601 642 4.090057 GCGGCGTTTGGAGTCAGC 62.090 66.667 9.37 0.00 0.00 4.26
602 643 2.357517 CGGCGTTTGGAGTCAGCT 60.358 61.111 0.00 0.00 0.00 4.24
603 644 1.961277 CGGCGTTTGGAGTCAGCTT 60.961 57.895 0.00 0.00 0.00 3.74
604 645 1.576421 GGCGTTTGGAGTCAGCTTG 59.424 57.895 0.00 0.00 0.00 4.01
605 646 1.576421 GCGTTTGGAGTCAGCTTGG 59.424 57.895 0.00 0.00 0.00 3.61
606 647 1.856265 GCGTTTGGAGTCAGCTTGGG 61.856 60.000 0.00 0.00 0.00 4.12
607 648 0.250295 CGTTTGGAGTCAGCTTGGGA 60.250 55.000 0.00 0.00 0.00 4.37
608 649 1.239347 GTTTGGAGTCAGCTTGGGAC 58.761 55.000 0.00 0.00 35.50 4.46
609 650 0.843309 TTTGGAGTCAGCTTGGGACA 59.157 50.000 5.57 0.00 37.74 4.02
622 663 0.034756 TGGGACAACCACTCATGTCG 59.965 55.000 0.00 0.00 46.80 4.35
623 664 0.320374 GGGACAACCACTCATGTCGA 59.680 55.000 0.00 0.00 45.39 4.20
624 665 1.066143 GGGACAACCACTCATGTCGAT 60.066 52.381 0.00 0.00 45.39 3.59
625 666 2.615493 GGGACAACCACTCATGTCGATT 60.615 50.000 0.00 0.00 45.39 3.34
626 667 3.074412 GGACAACCACTCATGTCGATTT 58.926 45.455 0.00 0.00 45.39 2.17
627 668 3.502211 GGACAACCACTCATGTCGATTTT 59.498 43.478 0.00 0.00 45.39 1.82
628 669 4.693566 GGACAACCACTCATGTCGATTTTA 59.306 41.667 0.00 0.00 45.39 1.52
629 670 5.354234 GGACAACCACTCATGTCGATTTTAT 59.646 40.000 0.00 0.00 45.39 1.40
630 671 6.128007 GGACAACCACTCATGTCGATTTTATT 60.128 38.462 0.00 0.00 45.39 1.40
631 672 6.611381 ACAACCACTCATGTCGATTTTATTG 58.389 36.000 0.00 0.00 0.00 1.90
632 673 5.235305 ACCACTCATGTCGATTTTATTGC 57.765 39.130 0.00 0.00 0.00 3.56
633 674 4.096382 ACCACTCATGTCGATTTTATTGCC 59.904 41.667 0.00 0.00 0.00 4.52
634 675 4.274069 CACTCATGTCGATTTTATTGCCG 58.726 43.478 0.00 0.00 0.00 5.69
635 676 3.938963 ACTCATGTCGATTTTATTGCCGT 59.061 39.130 0.00 0.00 0.00 5.68
636 677 4.394920 ACTCATGTCGATTTTATTGCCGTT 59.605 37.500 0.00 0.00 0.00 4.44
637 678 5.106317 ACTCATGTCGATTTTATTGCCGTTT 60.106 36.000 0.00 0.00 0.00 3.60
638 679 5.092105 TCATGTCGATTTTATTGCCGTTTG 58.908 37.500 0.00 0.00 0.00 2.93
639 680 4.750952 TGTCGATTTTATTGCCGTTTGA 57.249 36.364 0.00 0.00 0.00 2.69
640 681 5.303747 TGTCGATTTTATTGCCGTTTGAT 57.696 34.783 0.00 0.00 0.00 2.57
641 682 5.328691 TGTCGATTTTATTGCCGTTTGATC 58.671 37.500 0.00 0.00 0.00 2.92
642 683 4.733405 GTCGATTTTATTGCCGTTTGATCC 59.267 41.667 0.00 0.00 0.00 3.36
643 684 4.041723 CGATTTTATTGCCGTTTGATCCC 58.958 43.478 0.00 0.00 0.00 3.85
644 685 3.878160 TTTTATTGCCGTTTGATCCCC 57.122 42.857 0.00 0.00 0.00 4.81
645 686 2.516227 TTATTGCCGTTTGATCCCCA 57.484 45.000 0.00 0.00 0.00 4.96
646 687 2.051334 TATTGCCGTTTGATCCCCAG 57.949 50.000 0.00 0.00 0.00 4.45
647 688 0.684153 ATTGCCGTTTGATCCCCAGG 60.684 55.000 0.00 0.00 0.00 4.45
648 689 3.140814 GCCGTTTGATCCCCAGGC 61.141 66.667 4.08 4.08 37.61 4.85
649 690 2.440247 CCGTTTGATCCCCAGGCC 60.440 66.667 0.00 0.00 0.00 5.19
650 691 2.354729 CGTTTGATCCCCAGGCCA 59.645 61.111 5.01 0.00 0.00 5.36
651 692 2.046285 CGTTTGATCCCCAGGCCAC 61.046 63.158 5.01 0.00 0.00 5.01
652 693 2.046285 GTTTGATCCCCAGGCCACG 61.046 63.158 5.01 0.00 0.00 4.94
653 694 3.936772 TTTGATCCCCAGGCCACGC 62.937 63.158 5.01 0.00 0.00 5.34
655 696 3.161450 GATCCCCAGGCCACGCTA 61.161 66.667 5.01 0.00 0.00 4.26
656 697 2.448542 ATCCCCAGGCCACGCTAT 60.449 61.111 5.01 0.00 0.00 2.97
657 698 2.056906 GATCCCCAGGCCACGCTATT 62.057 60.000 5.01 0.00 0.00 1.73
658 699 1.645402 ATCCCCAGGCCACGCTATTT 61.645 55.000 5.01 0.00 0.00 1.40
659 700 1.823899 CCCCAGGCCACGCTATTTC 60.824 63.158 5.01 0.00 0.00 2.17
660 701 1.077787 CCCAGGCCACGCTATTTCA 60.078 57.895 5.01 0.00 0.00 2.69
661 702 0.679640 CCCAGGCCACGCTATTTCAA 60.680 55.000 5.01 0.00 0.00 2.69
662 703 0.734889 CCAGGCCACGCTATTTCAAG 59.265 55.000 5.01 0.00 0.00 3.02
663 704 0.099436 CAGGCCACGCTATTTCAAGC 59.901 55.000 5.01 0.00 39.21 4.01
664 705 1.032114 AGGCCACGCTATTTCAAGCC 61.032 55.000 5.01 0.00 39.43 4.35
665 706 1.032114 GGCCACGCTATTTCAAGCCT 61.032 55.000 0.00 0.00 39.43 4.58
666 707 0.811281 GCCACGCTATTTCAAGCCTT 59.189 50.000 0.00 0.00 39.43 4.35
667 708 1.468054 GCCACGCTATTTCAAGCCTTG 60.468 52.381 0.00 0.00 39.43 3.61
668 709 1.133025 CCACGCTATTTCAAGCCTTGG 59.867 52.381 4.30 0.00 39.43 3.61
669 710 2.083774 CACGCTATTTCAAGCCTTGGA 58.916 47.619 4.30 0.00 39.43 3.53
670 711 2.096496 CACGCTATTTCAAGCCTTGGAG 59.904 50.000 4.30 0.00 39.43 3.86
671 712 1.672881 CGCTATTTCAAGCCTTGGAGG 59.327 52.381 4.30 0.00 39.43 4.30
680 721 4.778143 CCTTGGAGGCCCGAACGG 62.778 72.222 0.00 6.25 34.29 4.44
689 730 2.202932 CCCGAACGGCCAGAGATG 60.203 66.667 2.24 0.00 0.00 2.90
690 731 2.892425 CCGAACGGCCAGAGATGC 60.892 66.667 2.24 0.00 0.00 3.91
691 732 2.185350 CGAACGGCCAGAGATGCT 59.815 61.111 2.24 0.00 0.00 3.79
692 733 1.880340 CGAACGGCCAGAGATGCTC 60.880 63.158 2.24 0.00 0.00 4.26
731 772 7.967890 TGACATGTCACATGTATATCCATTC 57.032 36.000 23.61 8.31 34.14 2.67
740 781 5.640783 ACATGTATATCCATTCTGCACATCG 59.359 40.000 0.00 0.00 0.00 3.84
742 783 5.852827 TGTATATCCATTCTGCACATCGAA 58.147 37.500 0.00 0.00 0.00 3.71
768 810 7.677745 AGGCTGAGATATCCAACAGATATACTT 59.322 37.037 19.45 2.87 46.27 2.24
769 811 7.978975 GGCTGAGATATCCAACAGATATACTTC 59.021 40.741 19.45 0.77 46.27 3.01
831 873 0.597568 TGCATCAGCGTTCTTTTGGG 59.402 50.000 0.00 0.00 46.23 4.12
849 891 2.092429 TGGGCACTTTATCCTAAGCCTG 60.092 50.000 0.00 0.00 41.71 4.85
1134 1180 5.861251 TCATTTGCATAGTTTTAGTTTGCGG 59.139 36.000 0.00 0.00 36.11 5.69
1257 1303 8.383619 CAATAGTTCACTGAGTAGCATAAACAC 58.616 37.037 0.00 0.00 0.00 3.32
1271 1317 2.492019 AAACACGCTTCCTCTTTTGC 57.508 45.000 0.00 0.00 0.00 3.68
1302 1348 4.692625 GCGATGTTTCTCATATGCCTGTAT 59.307 41.667 0.00 0.00 36.83 2.29
1313 1359 8.264347 TCTCATATGCCTGTATTTTTCACACTA 58.736 33.333 0.00 0.00 0.00 2.74
1363 1440 1.875514 CCCATGCGTTCAGTCCATATG 59.124 52.381 0.00 0.00 0.00 1.78
1437 1514 8.565416 GTTAGAAAGGCAGAAAAGCTTTAACTA 58.435 33.333 13.10 3.76 32.18 2.24
1483 1560 1.416030 ACACTGGTGGGAAAATTTGCC 59.584 47.619 9.45 9.45 42.24 4.52
1561 1638 5.070847 ACTTCAAAGATTCCAAAATGGCTGT 59.929 36.000 0.00 0.00 37.47 4.40
1662 1739 2.906389 TGTAGCCTGGTTCAGAAGATGT 59.094 45.455 0.00 0.00 32.44 3.06
1685 1762 0.393132 GCTCTAGGAAGCCACCCAAC 60.393 60.000 0.00 0.00 36.22 3.77
1752 1829 0.883833 CCAATGTGTTGCTCTCCACC 59.116 55.000 0.00 0.00 33.90 4.61
1757 1834 0.667792 GTGTTGCTCTCCACCTCGAC 60.668 60.000 0.00 0.00 0.00 4.20
1802 1879 4.414337 AATGCCAGCCTTTGTTTTACAA 57.586 36.364 0.00 0.00 36.11 2.41
1821 1898 5.857471 ACAATTGTATATTGCCATGTGCT 57.143 34.783 9.97 0.00 42.00 4.40
1830 1907 0.983467 TGCCATGTGCTTCTGGTCTA 59.017 50.000 7.54 0.00 42.00 2.59
1834 1911 2.026822 CCATGTGCTTCTGGTCTAACCT 60.027 50.000 0.00 0.00 39.58 3.50
1861 1938 3.202818 TGTCCTGCACCATTAGATTCCAT 59.797 43.478 0.00 0.00 0.00 3.41
2025 2121 3.731867 CGGATAATTTGCAGTGCTGGTTC 60.732 47.826 17.60 5.83 0.00 3.62
2049 2146 0.607489 CCAGGAAGCAGGACACTTGG 60.607 60.000 0.00 0.00 0.00 3.61
2050 2147 0.109342 CAGGAAGCAGGACACTTGGT 59.891 55.000 0.00 0.00 0.00 3.67
2051 2148 1.347707 CAGGAAGCAGGACACTTGGTA 59.652 52.381 0.00 0.00 0.00 3.25
2052 2149 2.026822 CAGGAAGCAGGACACTTGGTAT 60.027 50.000 0.00 0.00 0.00 2.73
2053 2150 2.237392 AGGAAGCAGGACACTTGGTATC 59.763 50.000 0.00 0.00 0.00 2.24
2054 2151 2.237392 GGAAGCAGGACACTTGGTATCT 59.763 50.000 0.00 0.00 0.00 1.98
2123 2220 5.450412 CCCAACGATTATTTCACATTCTGGG 60.450 44.000 0.00 0.00 0.00 4.45
2126 2223 6.834168 ACGATTATTTCACATTCTGGGTTT 57.166 33.333 0.00 0.00 0.00 3.27
2132 2229 5.930837 TTTCACATTCTGGGTTTGAAAGT 57.069 34.783 0.00 0.00 32.57 2.66
2222 2319 1.483827 GGATCCAGAGCACTGATCACA 59.516 52.381 13.19 0.00 46.03 3.58
2244 2341 0.321564 GACCCTTTTGGCCCATTTGC 60.322 55.000 0.00 0.00 37.83 3.68
2274 2371 4.821260 TGCAAAATGAGTGAGCAGAAGTTA 59.179 37.500 0.00 0.00 0.00 2.24
2284 2381 2.283298 AGCAGAAGTTACATCATGGCG 58.717 47.619 0.00 0.00 0.00 5.69
2293 2390 1.822613 CATCATGGCGCTCTGGCTT 60.823 57.895 7.64 0.00 45.14 4.35
2329 2850 5.790495 GCTTAAGTTTCATCATGTCGTGTTC 59.210 40.000 4.02 0.00 0.00 3.18
2355 2876 9.354673 CCTTGCTTTATCTATTTTCAAGGGATA 57.645 33.333 9.55 0.00 43.06 2.59
2505 3026 5.478407 GTTGCAGGTGGCTAATGTAATTTT 58.522 37.500 0.00 0.00 45.15 1.82
2529 3050 0.321671 CGGAGCTCAGTTTCCTTCCA 59.678 55.000 17.19 0.00 0.00 3.53
2605 3126 6.376177 GTTTAAGATTTGTTGTTCGGTAGGG 58.624 40.000 0.00 0.00 0.00 3.53
2610 3131 0.032403 TGTTGTTCGGTAGGGACACG 59.968 55.000 0.00 0.00 0.00 4.49
2633 3154 5.228220 CGTTTCTTCTCTGTCGCAATAGTAG 59.772 44.000 0.00 0.00 0.00 2.57
2643 3164 3.933332 GTCGCAATAGTAGAAGTTTGCCT 59.067 43.478 0.00 0.00 40.99 4.75
2744 3265 0.471191 CTGGCTAGCACCATGGATGA 59.529 55.000 21.47 0.00 39.54 2.92
2765 3286 2.356667 GCTAGGCAGCCTGGGTTT 59.643 61.111 25.59 0.00 42.37 3.27
2779 3300 3.604582 CTGGGTTTGATCTGGAACTCTC 58.395 50.000 0.00 0.00 0.00 3.20
2958 3480 5.304686 AGGTGAGAATTGTTTACACTGGA 57.695 39.130 0.00 0.00 0.00 3.86
2961 3483 5.305585 GTGAGAATTGTTTACACTGGAGGA 58.694 41.667 0.00 0.00 0.00 3.71
2989 3511 9.902684 ATTCAAACATTAAATATGGGCAAATCA 57.097 25.926 0.00 0.00 0.00 2.57
3006 3528 6.764085 GGCAAATCATTTCATCATTTCATGGA 59.236 34.615 0.00 0.00 0.00 3.41
3135 3657 3.129813 ACCACGCTCGATGTACTGATTTA 59.870 43.478 0.00 0.00 0.00 1.40
3142 3664 6.074994 CGCTCGATGTACTGATTTAAGGTAAC 60.075 42.308 0.00 0.00 0.00 2.50
3172 3694 1.576421 GTTTCTTGAGCAGGCCACG 59.424 57.895 5.01 0.00 0.00 4.94
3271 3793 2.126307 CCTGTCACAGCGGAGTCG 60.126 66.667 0.00 0.00 39.81 4.18
3382 3904 3.000476 CCGTTCATACGTAACACCGATTG 60.000 47.826 0.00 0.00 46.20 2.67
3515 4037 3.386078 AGAAGCTTGTGACAGAGAAGACA 59.614 43.478 2.10 0.00 0.00 3.41
3563 4085 2.884639 GCTTTAGAAGGCAAAGGTGTCA 59.115 45.455 0.00 0.00 34.28 3.58
3570 4092 1.425066 AGGCAAAGGTGTCATCTGGAA 59.575 47.619 0.00 0.00 0.00 3.53
3572 4094 1.541588 GCAAAGGTGTCATCTGGAACC 59.458 52.381 0.00 0.00 0.00 3.62
3670 4192 7.772166 TGTTGTGTGTTCATTACCATTTGTTA 58.228 30.769 0.00 0.00 0.00 2.41
3839 4361 7.978414 TGAAGAATCACTGCATTTTGTGTTTTA 59.022 29.630 4.00 0.00 35.82 1.52
3840 4362 8.891671 AAGAATCACTGCATTTTGTGTTTTAT 57.108 26.923 4.00 0.00 35.82 1.40
3892 4414 8.694394 GCTGTGAATGTATTGTTTCTTTTCTTC 58.306 33.333 0.00 0.00 0.00 2.87
3915 4437 2.717639 ACCACAGCTATGACCCATTC 57.282 50.000 0.00 0.00 0.00 2.67
3984 4510 2.700371 TCCCATATGATCACTCGCTTGT 59.300 45.455 3.65 0.00 0.00 3.16
3995 4521 9.935241 ATGATCACTCGCTTGTTAGATTATTAT 57.065 29.630 0.00 0.00 0.00 1.28
4211 4738 3.732048 TTGGAAGGACAGGATTAACCC 57.268 47.619 0.00 0.00 40.05 4.11
4212 4739 1.920351 TGGAAGGACAGGATTAACCCC 59.080 52.381 0.00 0.00 40.05 4.95
4216 4743 3.451402 AGGACAGGATTAACCCCAAAC 57.549 47.619 0.00 0.00 40.05 2.93
4226 4753 4.599047 TTAACCCCAAACAATCTGCAAG 57.401 40.909 0.00 0.00 0.00 4.01
4326 5032 1.469940 GCATCATATCGCCCGACCTAG 60.470 57.143 0.00 0.00 0.00 3.02
4393 5108 7.362662 ACATTTAATATGCATCCTTAACTGCG 58.637 34.615 20.36 11.01 41.32 5.18
4460 5175 3.014623 GTTCAATAAACCGGGAAGGGAG 58.985 50.000 6.32 0.00 46.96 4.30
4462 5177 2.237893 TCAATAAACCGGGAAGGGAGAC 59.762 50.000 6.32 0.00 46.96 3.36
4463 5178 1.961133 ATAAACCGGGAAGGGAGACA 58.039 50.000 6.32 0.00 46.96 3.41
4464 5179 0.978907 TAAACCGGGAAGGGAGACAC 59.021 55.000 6.32 0.00 46.96 3.67
4465 5180 1.775934 AAACCGGGAAGGGAGACACC 61.776 60.000 6.32 0.00 46.96 4.16
4514 5229 9.145865 GAAAAGAAGTAGACATAGAAGAACCAG 57.854 37.037 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 4.838152 GAAGGATGGCGGCGCTCA 62.838 66.667 32.30 26.38 0.00 4.26
116 120 4.606071 GTGCTCCTGCTTCACGAT 57.394 55.556 0.00 0.00 40.48 3.73
328 337 3.745803 GCTGCAGCCCTGTCTTGC 61.746 66.667 28.76 0.00 34.31 4.01
331 340 2.033757 CTTGCTGCAGCCCTGTCT 59.966 61.111 34.64 0.00 41.18 3.41
410 428 1.400530 GGCCTACTGCATACCGAGGT 61.401 60.000 0.00 0.00 43.89 3.85
417 435 2.847234 CCCCGGGCCTACTGCATA 60.847 66.667 17.73 0.00 43.89 3.14
439 468 3.899052 ACTATGCCCTAAAACTACGCA 57.101 42.857 0.00 0.00 0.00 5.24
444 473 6.740944 AAACCAAAACTATGCCCTAAAACT 57.259 33.333 0.00 0.00 0.00 2.66
447 486 7.368198 AGAAAAACCAAAACTATGCCCTAAA 57.632 32.000 0.00 0.00 0.00 1.85
448 487 6.987403 AGAAAAACCAAAACTATGCCCTAA 57.013 33.333 0.00 0.00 0.00 2.69
452 491 8.657074 AAACTTAGAAAAACCAAAACTATGCC 57.343 30.769 0.00 0.00 0.00 4.40
504 545 7.447374 AATTGAGACGGTTTTCATTGACATA 57.553 32.000 0.00 0.00 0.00 2.29
541 582 6.209192 TGGCTAGATTTCACACAAAATGACAT 59.791 34.615 0.00 0.00 0.00 3.06
553 594 8.246180 TGAAAATCAAAGATGGCTAGATTTCAC 58.754 33.333 0.00 0.00 37.70 3.18
554 595 8.352137 TGAAAATCAAAGATGGCTAGATTTCA 57.648 30.769 0.00 0.00 37.70 2.69
555 596 9.643693 TTTGAAAATCAAAGATGGCTAGATTTC 57.356 29.630 0.00 0.00 41.02 2.17
566 607 4.150451 CGCCGCTTTTTGAAAATCAAAGAT 59.850 37.500 5.75 0.00 45.77 2.40
567 608 3.489047 CGCCGCTTTTTGAAAATCAAAGA 59.511 39.130 5.75 1.57 45.77 2.52
568 609 3.245048 ACGCCGCTTTTTGAAAATCAAAG 59.755 39.130 5.75 0.00 45.77 2.77
569 610 3.190874 ACGCCGCTTTTTGAAAATCAAA 58.809 36.364 1.57 1.57 43.84 2.69
570 611 2.815478 ACGCCGCTTTTTGAAAATCAA 58.185 38.095 0.00 0.00 34.03 2.57
571 612 2.500509 ACGCCGCTTTTTGAAAATCA 57.499 40.000 0.00 0.00 0.00 2.57
572 613 3.531015 CAAACGCCGCTTTTTGAAAATC 58.469 40.909 8.07 0.00 35.13 2.17
573 614 2.286563 CCAAACGCCGCTTTTTGAAAAT 59.713 40.909 13.32 0.00 35.13 1.82
574 615 1.661112 CCAAACGCCGCTTTTTGAAAA 59.339 42.857 13.32 0.00 35.13 2.29
575 616 1.135083 TCCAAACGCCGCTTTTTGAAA 60.135 42.857 13.32 2.38 35.13 2.69
576 617 0.456221 TCCAAACGCCGCTTTTTGAA 59.544 45.000 13.32 0.00 35.13 2.69
577 618 0.030101 CTCCAAACGCCGCTTTTTGA 59.970 50.000 13.32 6.07 35.13 2.69
578 619 0.248866 ACTCCAAACGCCGCTTTTTG 60.249 50.000 7.15 7.15 33.30 2.44
579 620 0.030235 GACTCCAAACGCCGCTTTTT 59.970 50.000 0.00 0.00 0.00 1.94
580 621 1.098712 TGACTCCAAACGCCGCTTTT 61.099 50.000 0.00 0.00 0.00 2.27
581 622 1.507141 CTGACTCCAAACGCCGCTTT 61.507 55.000 0.00 0.00 0.00 3.51
582 623 1.961277 CTGACTCCAAACGCCGCTT 60.961 57.895 0.00 0.00 0.00 4.68
583 624 2.357517 CTGACTCCAAACGCCGCT 60.358 61.111 0.00 0.00 0.00 5.52
584 625 4.090057 GCTGACTCCAAACGCCGC 62.090 66.667 0.00 0.00 0.00 6.53
585 626 1.961277 AAGCTGACTCCAAACGCCG 60.961 57.895 0.00 0.00 0.00 6.46
586 627 1.576421 CAAGCTGACTCCAAACGCC 59.424 57.895 0.00 0.00 0.00 5.68
587 628 1.576421 CCAAGCTGACTCCAAACGC 59.424 57.895 0.00 0.00 0.00 4.84
588 629 0.250295 TCCCAAGCTGACTCCAAACG 60.250 55.000 0.00 0.00 0.00 3.60
589 630 1.239347 GTCCCAAGCTGACTCCAAAC 58.761 55.000 0.00 0.00 0.00 2.93
590 631 0.843309 TGTCCCAAGCTGACTCCAAA 59.157 50.000 4.51 0.00 33.83 3.28
591 632 0.843309 TTGTCCCAAGCTGACTCCAA 59.157 50.000 4.51 0.00 33.83 3.53
592 633 0.108585 GTTGTCCCAAGCTGACTCCA 59.891 55.000 4.51 0.00 33.83 3.86
593 634 0.606673 GGTTGTCCCAAGCTGACTCC 60.607 60.000 4.51 3.84 33.83 3.85
594 635 0.108585 TGGTTGTCCCAAGCTGACTC 59.891 55.000 7.56 0.00 41.50 3.36
595 636 2.230664 TGGTTGTCCCAAGCTGACT 58.769 52.632 7.56 0.00 41.50 3.41
596 637 4.898607 TGGTTGTCCCAAGCTGAC 57.101 55.556 7.56 0.00 41.50 3.51
603 644 0.034756 CGACATGAGTGGTTGTCCCA 59.965 55.000 0.00 0.00 42.51 4.37
604 645 0.320374 TCGACATGAGTGGTTGTCCC 59.680 55.000 0.00 0.00 39.23 4.46
605 646 2.386661 ATCGACATGAGTGGTTGTCC 57.613 50.000 0.00 0.00 39.23 4.02
606 647 4.749245 AAAATCGACATGAGTGGTTGTC 57.251 40.909 0.00 0.00 39.07 3.18
607 648 6.611381 CAATAAAATCGACATGAGTGGTTGT 58.389 36.000 0.00 0.00 0.00 3.32
608 649 5.512788 GCAATAAAATCGACATGAGTGGTTG 59.487 40.000 0.00 0.00 0.00 3.77
609 650 5.393027 GGCAATAAAATCGACATGAGTGGTT 60.393 40.000 0.00 0.00 0.00 3.67
610 651 4.096382 GGCAATAAAATCGACATGAGTGGT 59.904 41.667 0.00 0.00 0.00 4.16
611 652 4.601019 GGCAATAAAATCGACATGAGTGG 58.399 43.478 0.00 0.00 0.00 4.00
612 653 4.201812 ACGGCAATAAAATCGACATGAGTG 60.202 41.667 0.00 0.00 0.00 3.51
613 654 3.938963 ACGGCAATAAAATCGACATGAGT 59.061 39.130 0.00 0.00 0.00 3.41
614 655 4.536364 ACGGCAATAAAATCGACATGAG 57.464 40.909 0.00 0.00 0.00 2.90
615 656 4.955925 AACGGCAATAAAATCGACATGA 57.044 36.364 0.00 0.00 0.00 3.07
616 657 5.092105 TCAAACGGCAATAAAATCGACATG 58.908 37.500 0.00 0.00 0.00 3.21
617 658 5.303747 TCAAACGGCAATAAAATCGACAT 57.696 34.783 0.00 0.00 0.00 3.06
618 659 4.750952 TCAAACGGCAATAAAATCGACA 57.249 36.364 0.00 0.00 0.00 4.35
619 660 4.733405 GGATCAAACGGCAATAAAATCGAC 59.267 41.667 0.00 0.00 0.00 4.20
620 661 4.201970 GGGATCAAACGGCAATAAAATCGA 60.202 41.667 0.00 0.00 0.00 3.59
621 662 4.041723 GGGATCAAACGGCAATAAAATCG 58.958 43.478 0.00 0.00 0.00 3.34
622 663 4.142049 TGGGGATCAAACGGCAATAAAATC 60.142 41.667 0.00 0.00 0.00 2.17
623 664 3.772025 TGGGGATCAAACGGCAATAAAAT 59.228 39.130 0.00 0.00 0.00 1.82
624 665 3.165875 TGGGGATCAAACGGCAATAAAA 58.834 40.909 0.00 0.00 0.00 1.52
625 666 2.757868 CTGGGGATCAAACGGCAATAAA 59.242 45.455 0.00 0.00 0.00 1.40
626 667 2.374184 CTGGGGATCAAACGGCAATAA 58.626 47.619 0.00 0.00 0.00 1.40
627 668 1.409521 CCTGGGGATCAAACGGCAATA 60.410 52.381 0.00 0.00 0.00 1.90
628 669 0.684153 CCTGGGGATCAAACGGCAAT 60.684 55.000 0.00 0.00 0.00 3.56
629 670 1.304052 CCTGGGGATCAAACGGCAA 60.304 57.895 0.00 0.00 0.00 4.52
630 671 2.354729 CCTGGGGATCAAACGGCA 59.645 61.111 0.00 0.00 0.00 5.69
631 672 3.140814 GCCTGGGGATCAAACGGC 61.141 66.667 0.00 0.00 0.00 5.68
632 673 2.440247 GGCCTGGGGATCAAACGG 60.440 66.667 0.00 0.00 0.00 4.44
633 674 2.046285 GTGGCCTGGGGATCAAACG 61.046 63.158 3.32 0.00 0.00 3.60
634 675 2.046285 CGTGGCCTGGGGATCAAAC 61.046 63.158 3.32 0.00 0.00 2.93
635 676 2.354729 CGTGGCCTGGGGATCAAA 59.645 61.111 3.32 0.00 0.00 2.69
636 677 4.424711 GCGTGGCCTGGGGATCAA 62.425 66.667 3.32 0.00 0.00 2.57
637 678 3.993865 TAGCGTGGCCTGGGGATCA 62.994 63.158 3.32 0.00 0.00 2.92
638 679 2.056906 AATAGCGTGGCCTGGGGATC 62.057 60.000 3.32 0.00 0.00 3.36
639 680 1.645402 AAATAGCGTGGCCTGGGGAT 61.645 55.000 3.32 0.00 0.00 3.85
640 681 2.265467 GAAATAGCGTGGCCTGGGGA 62.265 60.000 3.32 0.00 0.00 4.81
641 682 1.823899 GAAATAGCGTGGCCTGGGG 60.824 63.158 3.32 0.00 0.00 4.96
642 683 0.679640 TTGAAATAGCGTGGCCTGGG 60.680 55.000 3.32 0.00 0.00 4.45
643 684 0.734889 CTTGAAATAGCGTGGCCTGG 59.265 55.000 3.32 0.00 0.00 4.45
644 685 0.099436 GCTTGAAATAGCGTGGCCTG 59.901 55.000 3.32 0.00 0.00 4.85
645 686 1.032114 GGCTTGAAATAGCGTGGCCT 61.032 55.000 3.32 0.00 42.15 5.19
646 687 1.032114 AGGCTTGAAATAGCGTGGCC 61.032 55.000 0.00 0.00 42.15 5.36
647 688 0.811281 AAGGCTTGAAATAGCGTGGC 59.189 50.000 0.00 0.00 42.15 5.01
648 689 1.133025 CCAAGGCTTGAAATAGCGTGG 59.867 52.381 28.18 4.37 42.15 4.94
649 690 2.083774 TCCAAGGCTTGAAATAGCGTG 58.916 47.619 28.18 8.30 42.15 5.34
650 691 2.359900 CTCCAAGGCTTGAAATAGCGT 58.640 47.619 28.18 0.00 42.15 5.07
651 692 1.672881 CCTCCAAGGCTTGAAATAGCG 59.327 52.381 28.18 9.75 42.15 4.26
663 704 4.778143 CCGTTCGGGCCTCCAAGG 62.778 72.222 0.84 0.00 38.80 3.61
672 713 2.202932 CATCTCTGGCCGTTCGGG 60.203 66.667 13.16 0.00 39.58 5.14
673 714 2.892425 GCATCTCTGGCCGTTCGG 60.892 66.667 6.90 6.90 0.00 4.30
674 715 1.880340 GAGCATCTCTGGCCGTTCG 60.880 63.158 0.00 0.00 0.00 3.95
675 716 4.116878 GAGCATCTCTGGCCGTTC 57.883 61.111 0.00 0.00 0.00 3.95
686 727 4.096833 TCATGCCACATTTGTAAGAGCATC 59.903 41.667 0.00 0.00 37.37 3.91
687 728 4.018490 TCATGCCACATTTGTAAGAGCAT 58.982 39.130 0.00 0.00 39.92 3.79
688 729 3.191162 GTCATGCCACATTTGTAAGAGCA 59.809 43.478 0.00 0.00 0.00 4.26
689 730 3.191162 TGTCATGCCACATTTGTAAGAGC 59.809 43.478 0.00 0.00 0.00 4.09
690 731 5.106038 ACATGTCATGCCACATTTGTAAGAG 60.106 40.000 12.91 0.00 34.60 2.85
691 732 4.766373 ACATGTCATGCCACATTTGTAAGA 59.234 37.500 12.91 0.00 34.60 2.10
692 733 5.063180 ACATGTCATGCCACATTTGTAAG 57.937 39.130 12.91 0.00 34.60 2.34
731 772 0.108472 TCTCAGCCTTCGATGTGCAG 60.108 55.000 12.12 6.31 0.00 4.41
740 781 4.679373 TCTGTTGGATATCTCAGCCTTC 57.321 45.455 2.05 0.00 32.17 3.46
742 783 7.188381 AGTATATCTGTTGGATATCTCAGCCT 58.812 38.462 2.05 3.93 44.04 4.58
781 823 4.184629 CGAGTCCGAGAGAAAAATGGAAT 58.815 43.478 0.00 0.00 38.22 3.01
794 836 1.532007 GCACTATACTCCGAGTCCGAG 59.468 57.143 3.74 6.92 38.22 4.63
795 837 1.134310 TGCACTATACTCCGAGTCCGA 60.134 52.381 3.74 0.00 38.22 4.55
796 838 1.306148 TGCACTATACTCCGAGTCCG 58.694 55.000 3.74 0.00 0.00 4.79
797 839 2.885266 TGATGCACTATACTCCGAGTCC 59.115 50.000 3.74 0.00 0.00 3.85
798 840 3.610585 GCTGATGCACTATACTCCGAGTC 60.611 52.174 3.74 0.00 39.41 3.36
799 841 2.294791 GCTGATGCACTATACTCCGAGT 59.705 50.000 6.25 6.25 39.41 4.18
831 873 4.143986 AGACAGGCTTAGGATAAAGTGC 57.856 45.455 0.00 0.00 0.00 4.40
1134 1180 3.350833 ACAGCCTTGGAATCTCATGAAC 58.649 45.455 0.00 0.00 0.00 3.18
1257 1303 3.064545 CCAAGATAGCAAAAGAGGAAGCG 59.935 47.826 0.00 0.00 0.00 4.68
1271 1317 6.401903 GCATATGAGAAACATCGCCAAGATAG 60.402 42.308 6.97 0.00 40.07 2.08
1561 1638 3.280920 ACGCCGGTTACGTTAAACA 57.719 47.368 1.90 0.00 41.93 2.83
1662 1739 1.838077 GGGTGGCTTCCTAGAGCTTTA 59.162 52.381 3.67 0.00 42.32 1.85
1685 1762 3.542648 AGATCTGAAGCATGTGATGTGG 58.457 45.455 0.00 0.00 0.00 4.17
1757 1834 2.542766 ATTTGGCTAACGCATCAACG 57.457 45.000 0.00 0.00 38.10 4.10
1787 1864 9.150348 GCAATATACAATTGTAAAACAAAGGCT 57.850 29.630 21.57 4.54 41.96 4.58
1821 1898 2.897969 GACACTCCAGGTTAGACCAGAA 59.102 50.000 0.00 0.00 41.95 3.02
1830 1907 1.451936 GTGCAGGACACTCCAGGTT 59.548 57.895 0.00 0.00 46.41 3.50
1874 1951 6.723298 AGTCATGTTGAACCCAAAAATACA 57.277 33.333 0.00 0.00 33.49 2.29
2025 2121 3.333219 TCCTGCTTCCTGGCTGGG 61.333 66.667 10.79 0.45 46.66 4.45
2049 2146 6.864342 TGAACTACTAGTGCCTTTCAGATAC 58.136 40.000 5.39 0.00 0.00 2.24
2050 2147 7.661536 ATGAACTACTAGTGCCTTTCAGATA 57.338 36.000 5.39 0.00 0.00 1.98
2051 2148 6.552445 ATGAACTACTAGTGCCTTTCAGAT 57.448 37.500 5.39 0.00 0.00 2.90
2052 2149 6.360370 AATGAACTACTAGTGCCTTTCAGA 57.640 37.500 5.39 0.00 0.00 3.27
2053 2150 5.582665 GGAATGAACTACTAGTGCCTTTCAG 59.417 44.000 5.39 0.00 0.00 3.02
2054 2151 5.248477 AGGAATGAACTACTAGTGCCTTTCA 59.752 40.000 5.39 8.88 0.00 2.69
2094 2191 1.748493 TGAAATAATCGTTGGGCTGCC 59.252 47.619 11.05 11.05 0.00 4.85
2123 2220 2.111756 CGTTGAGCAGCACTTTCAAAC 58.888 47.619 0.00 0.00 33.10 2.93
2126 2223 0.937304 GTCGTTGAGCAGCACTTTCA 59.063 50.000 0.00 0.00 0.00 2.69
2132 2229 1.014044 GGAATCGTCGTTGAGCAGCA 61.014 55.000 0.00 0.00 0.00 4.41
2222 2319 0.190815 AATGGGCCAAAAGGGTCAGT 59.809 50.000 11.89 0.00 45.89 3.41
2244 2341 3.492011 GCTCACTCATTTTGCAAAGTTGG 59.508 43.478 12.41 6.99 0.00 3.77
2258 2355 4.871933 TGATGTAACTTCTGCTCACTCA 57.128 40.909 0.00 0.00 0.00 3.41
2274 2371 2.515523 GCCAGAGCGCCATGATGT 60.516 61.111 2.29 0.00 0.00 3.06
2284 2381 2.419324 CTCACAGATTTCAAGCCAGAGC 59.581 50.000 0.00 0.00 40.32 4.09
2293 2390 7.445096 TGATGAAACTTAAGCTCACAGATTTCA 59.555 33.333 12.98 12.98 38.69 2.69
2329 2850 7.645058 TCCCTTGAAAATAGATAAAGCAAGG 57.355 36.000 0.00 0.00 46.39 3.61
2355 2876 7.837202 CAGTTGATCAACCAAATGCATATTT 57.163 32.000 30.34 8.41 42.06 1.40
2434 2955 2.006888 ACTGTTCAAACACACAGACCG 58.993 47.619 6.32 0.00 42.74 4.79
2529 3050 4.500499 ACAAAGCTCATCTTCTGGCTAT 57.500 40.909 0.00 0.00 32.96 2.97
2605 3126 1.452399 GCGACAGAGAAGAAACGTGTC 59.548 52.381 0.00 0.00 35.26 3.67
2610 3131 6.323266 TCTACTATTGCGACAGAGAAGAAAC 58.677 40.000 0.00 0.00 0.00 2.78
2633 3154 0.598065 AACGCATGGAGGCAAACTTC 59.402 50.000 0.00 0.00 0.00 3.01
2643 3164 7.840931 AGATATAGATATTGTGAACGCATGGA 58.159 34.615 0.00 0.00 0.00 3.41
2683 3204 4.406003 ACTTGGCCACCTATAGAAGTACAG 59.594 45.833 3.88 0.00 0.00 2.74
2866 3388 7.814107 GCAAACAATTCTCACCTATTTCAATCA 59.186 33.333 0.00 0.00 0.00 2.57
2958 3480 8.547173 TGCCCATATTTAATGTTTGAATTTCCT 58.453 29.630 0.00 0.00 0.00 3.36
3006 3528 9.252962 CTAGACTGCAATTTGAAAGAACATTTT 57.747 29.630 0.00 0.00 0.00 1.82
3107 3629 2.157834 ACATCGAGCGTGGTTGTAAA 57.842 45.000 0.00 0.00 0.00 2.01
3108 3630 2.229543 AGTACATCGAGCGTGGTTGTAA 59.770 45.455 0.00 0.00 0.00 2.41
3109 3631 1.814394 AGTACATCGAGCGTGGTTGTA 59.186 47.619 0.00 0.00 0.00 2.41
3113 3635 1.103803 ATCAGTACATCGAGCGTGGT 58.896 50.000 0.00 0.00 0.00 4.16
3142 3664 4.144555 GCTCAAGAAACGAAAGAACATCG 58.855 43.478 0.00 0.00 45.47 3.84
3271 3793 5.460091 GTCAGCACCAAGTTCAGAAAATTTC 59.540 40.000 0.00 0.00 0.00 2.17
3382 3904 3.798337 CACAATCTCAACCTGCAAAACAC 59.202 43.478 0.00 0.00 0.00 3.32
3515 4037 1.080025 GAACCGAGGTGCTTACGCT 60.080 57.895 0.00 0.00 36.97 5.07
3523 4045 1.442769 CTGTCCAATGAACCGAGGTG 58.557 55.000 0.00 0.00 0.00 4.00
3524 4046 0.321653 GCTGTCCAATGAACCGAGGT 60.322 55.000 0.00 0.00 0.00 3.85
3563 4085 1.276421 CAGAAGTCCACGGTTCCAGAT 59.724 52.381 0.00 0.00 0.00 2.90
3570 4092 2.806244 CGAAAAATCAGAAGTCCACGGT 59.194 45.455 0.00 0.00 0.00 4.83
3572 4094 2.806244 ACCGAAAAATCAGAAGTCCACG 59.194 45.455 0.00 0.00 0.00 4.94
3670 4192 7.065563 CACAAAATCTCGAGAGGATGAAGAAAT 59.934 37.037 21.52 0.00 0.00 2.17
3839 4361 9.013229 TGTATAACTTCTCAGACATGCAAAAAT 57.987 29.630 0.00 0.00 0.00 1.82
3840 4362 8.389779 TGTATAACTTCTCAGACATGCAAAAA 57.610 30.769 0.00 0.00 0.00 1.94
3892 4414 1.768275 TGGGTCATAGCTGTGGTATGG 59.232 52.381 10.87 0.00 42.22 2.74
3915 4437 4.946478 ATCGGAGACCCTCTTTATGAAG 57.054 45.455 0.00 0.00 42.51 3.02
3959 4484 4.130118 AGCGAGTGATCATATGGGAAAAC 58.870 43.478 0.00 0.00 0.00 2.43
3995 4521 6.735678 TGCAAGCGAGACATTATCTAAAAA 57.264 33.333 0.00 0.00 38.00 1.94
4084 4610 6.084326 TCTTCCCACTAAATGTGCTTTTTC 57.916 37.500 0.00 0.00 44.92 2.29
4097 4623 6.296836 GGGGAAAGTAGATTTTCTTCCCACTA 60.297 42.308 17.61 0.00 37.94 2.74
4100 4626 4.264217 GGGGGAAAGTAGATTTTCTTCCCA 60.264 45.833 17.61 0.00 42.76 4.37
4211 4738 4.524316 TGGAATCTTGCAGATTGTTTGG 57.476 40.909 13.78 0.00 44.41 3.28
4212 4739 6.255020 GCTTATGGAATCTTGCAGATTGTTTG 59.745 38.462 13.78 3.95 44.41 2.93
4216 4743 5.769484 AGCTTATGGAATCTTGCAGATTG 57.231 39.130 13.78 3.14 44.41 2.67
4293 4820 5.791974 GCGATATGATGCATGTTAATGTCAC 59.208 40.000 2.46 0.00 36.08 3.67
4294 4821 5.106594 GGCGATATGATGCATGTTAATGTCA 60.107 40.000 2.46 0.00 36.08 3.58
4303 4895 0.723414 GTCGGGCGATATGATGCATG 59.277 55.000 2.46 0.00 0.00 4.06
4326 5032 0.454957 TAACGAAGTACTGCGCGTCC 60.455 55.000 23.46 0.00 45.00 4.79
4331 5037 1.654105 CCTTGCTAACGAAGTACTGCG 59.346 52.381 21.99 21.99 45.00 5.18
4384 5099 5.607119 AAAGGATTGTACACGCAGTTAAG 57.393 39.130 0.00 0.00 41.61 1.85
4448 5163 2.606826 GGTGTCTCCCTTCCCGGT 60.607 66.667 0.00 0.00 0.00 5.28
4460 5175 1.227853 GAGGTGTGGTGTGGGTGTC 60.228 63.158 0.00 0.00 0.00 3.67
4462 5177 1.525995 GTGAGGTGTGGTGTGGGTG 60.526 63.158 0.00 0.00 0.00 4.61
4463 5178 2.752807 GGTGAGGTGTGGTGTGGGT 61.753 63.158 0.00 0.00 0.00 4.51
4464 5179 2.113139 GGTGAGGTGTGGTGTGGG 59.887 66.667 0.00 0.00 0.00 4.61
4465 5180 1.071471 GAGGTGAGGTGTGGTGTGG 59.929 63.158 0.00 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.