Multiple sequence alignment - TraesCS5D01G076300

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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 TraesCS5D01G076300 chr5D 100.000 2459 0 0 1 2459 75914144 75911686 0.000000e+00 4542.0
1 TraesCS5D01G076300 chr5D 80.435 368 50 15 6 369 231225180 231225529 6.740000e-66 261.0
2 TraesCS5D01G076300 chr5D 91.304 138 12 0 621 758 163004051 163003914 3.230000e-44 189.0
3 TraesCS5D01G076300 chr5D 86.286 175 15 1 592 757 352942298 352942472 5.400000e-42 182.0
4 TraesCS5D01G076300 chr2A 88.754 987 82 13 779 1749 23958627 23959600 0.000000e+00 1181.0
5 TraesCS5D01G076300 chr2A 86.547 669 64 20 997 1649 23970755 23971413 0.000000e+00 713.0
6 TraesCS5D01G076300 chr2A 87.500 96 12 0 1751 1846 23959664 23959759 7.190000e-21 111.0
7 TraesCS5D01G076300 chr5A 87.666 981 98 8 1499 2459 71240828 71239851 0.000000e+00 1120.0
8 TraesCS5D01G076300 chr5A 84.263 699 99 9 968 1655 327573865 327574563 0.000000e+00 671.0
9 TraesCS5D01G076300 chr5A 85.949 548 60 14 25 564 36951524 36952062 9.870000e-159 569.0
10 TraesCS5D01G076300 chr2D 86.355 1004 84 16 758 1749 22119214 22120176 0.000000e+00 1046.0
11 TraesCS5D01G076300 chr2D 86.634 808 83 20 854 1646 22155168 22155965 0.000000e+00 870.0
12 TraesCS5D01G076300 chr2D 86.576 663 72 11 997 1649 22144341 22144996 0.000000e+00 715.0
13 TraesCS5D01G076300 chr2D 76.769 650 114 32 1021 1649 16910870 16910237 1.820000e-86 329.0
14 TraesCS5D01G076300 chr2D 84.454 238 31 6 2 237 416400054 416399821 1.900000e-56 230.0
15 TraesCS5D01G076300 chr2D 88.119 101 11 1 1751 1850 22120425 22120525 4.300000e-23 119.0
16 TraesCS5D01G076300 chr1B 89.456 607 60 3 1853 2457 95306497 95307101 0.000000e+00 763.0
17 TraesCS5D01G076300 chr1B 91.127 417 35 2 1057 1471 298091105 298090689 4.590000e-157 564.0
18 TraesCS5D01G076300 chr6B 89.421 605 62 1 1853 2457 62638809 62638207 0.000000e+00 761.0
19 TraesCS5D01G076300 chr7D 88.980 608 63 3 1854 2459 107810081 107809476 0.000000e+00 749.0
20 TraesCS5D01G076300 chr7D 89.020 592 63 2 1870 2459 107807587 107806996 0.000000e+00 732.0
21 TraesCS5D01G076300 chr7D 91.983 474 36 2 1057 1528 403146433 403145960 0.000000e+00 664.0
22 TraesCS5D01G076300 chr5B 91.219 558 25 7 758 1309 84623874 84623335 0.000000e+00 737.0
23 TraesCS5D01G076300 chr5B 88.009 442 50 3 1057 1496 580125806 580126246 1.010000e-143 520.0
24 TraesCS5D01G076300 chr5B 80.863 371 56 12 6 369 236255928 236255566 6.700000e-71 278.0
25 TraesCS5D01G076300 chr3B 89.982 569 54 3 1 568 428067391 428066825 0.000000e+00 732.0
26 TraesCS5D01G076300 chr3A 88.506 609 64 5 1853 2459 550728300 550728904 0.000000e+00 732.0
27 TraesCS5D01G076300 chr3A 91.111 135 12 0 618 752 60810849 60810983 1.500000e-42 183.0
28 TraesCS5D01G076300 chr3A 90.580 138 13 0 621 758 352460236 352460099 1.500000e-42 183.0
29 TraesCS5D01G076300 chr4D 88.342 609 67 3 1853 2459 393864741 393865347 0.000000e+00 728.0
30 TraesCS5D01G076300 chr4D 88.013 609 68 3 1853 2459 245467055 245467660 0.000000e+00 715.0
31 TraesCS5D01G076300 chr4D 86.286 175 15 1 592 757 89539771 89539945 5.400000e-42 182.0
32 TraesCS5D01G076300 chr3D 88.013 609 69 3 1853 2459 549247559 549248165 0.000000e+00 717.0
33 TraesCS5D01G076300 chr6D 91.561 474 38 2 1057 1528 29985847 29985374 0.000000e+00 652.0
34 TraesCS5D01G076300 chr1D 81.170 393 57 12 2 381 490325214 490324826 1.430000e-77 300.0
35 TraesCS5D01G076300 chr1D 89.362 141 15 0 618 758 483105323 483105463 6.990000e-41 178.0
36 TraesCS5D01G076300 chr7B 89.362 141 15 0 618 758 510605998 510606138 6.990000e-41 178.0
37 TraesCS5D01G076300 chr1A 89.855 138 14 0 621 758 306130723 306130586 6.990000e-41 178.0
38 TraesCS5D01G076300 chr1A 85.795 176 16 1 592 758 392482720 392482545 6.990000e-41 178.0
39 TraesCS5D01G076300 chr2B 91.379 58 4 1 1794 1850 35139996 35140053 7.290000e-11 78.7


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G076300 chr5D 75911686 75914144 2458 True 4542.0 4542 100.000 1 2459 1 chr5D.!!$R1 2458
1 TraesCS5D01G076300 chr2A 23970755 23971413 658 False 713.0 713 86.547 997 1649 1 chr2A.!!$F1 652
2 TraesCS5D01G076300 chr2A 23958627 23959759 1132 False 646.0 1181 88.127 779 1846 2 chr2A.!!$F2 1067
3 TraesCS5D01G076300 chr5A 71239851 71240828 977 True 1120.0 1120 87.666 1499 2459 1 chr5A.!!$R1 960
4 TraesCS5D01G076300 chr5A 327573865 327574563 698 False 671.0 671 84.263 968 1655 1 chr5A.!!$F2 687
5 TraesCS5D01G076300 chr5A 36951524 36952062 538 False 569.0 569 85.949 25 564 1 chr5A.!!$F1 539
6 TraesCS5D01G076300 chr2D 22155168 22155965 797 False 870.0 870 86.634 854 1646 1 chr2D.!!$F2 792
7 TraesCS5D01G076300 chr2D 22144341 22144996 655 False 715.0 715 86.576 997 1649 1 chr2D.!!$F1 652
8 TraesCS5D01G076300 chr2D 22119214 22120525 1311 False 582.5 1046 87.237 758 1850 2 chr2D.!!$F3 1092
9 TraesCS5D01G076300 chr2D 16910237 16910870 633 True 329.0 329 76.769 1021 1649 1 chr2D.!!$R1 628
10 TraesCS5D01G076300 chr1B 95306497 95307101 604 False 763.0 763 89.456 1853 2457 1 chr1B.!!$F1 604
11 TraesCS5D01G076300 chr6B 62638207 62638809 602 True 761.0 761 89.421 1853 2457 1 chr6B.!!$R1 604
12 TraesCS5D01G076300 chr7D 107806996 107810081 3085 True 740.5 749 89.000 1854 2459 2 chr7D.!!$R2 605
13 TraesCS5D01G076300 chr5B 84623335 84623874 539 True 737.0 737 91.219 758 1309 1 chr5B.!!$R1 551
14 TraesCS5D01G076300 chr3B 428066825 428067391 566 True 732.0 732 89.982 1 568 1 chr3B.!!$R1 567
15 TraesCS5D01G076300 chr3A 550728300 550728904 604 False 732.0 732 88.506 1853 2459 1 chr3A.!!$F2 606
16 TraesCS5D01G076300 chr4D 393864741 393865347 606 False 728.0 728 88.342 1853 2459 1 chr4D.!!$F3 606
17 TraesCS5D01G076300 chr4D 245467055 245467660 605 False 715.0 715 88.013 1853 2459 1 chr4D.!!$F2 606
18 TraesCS5D01G076300 chr3D 549247559 549248165 606 False 717.0 717 88.013 1853 2459 1 chr3D.!!$F1 606

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
569 576 0.025898 GCGCCGGATAGAAACGTTTC 59.974 55.0 29.36 29.36 37.45 2.78 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2014 2332 0.10339 TTCAACTCTTCGCGGTGACA 59.897 50.0 6.13 0.0 0.0 3.58 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
104 105 1.363744 CCCTCATCTCGTTTCACAGC 58.636 55.000 0.00 0.00 0.00 4.40
187 190 3.074673 CCAACAAGGAAGCTTGGAGCG 62.075 57.143 2.10 0.00 43.43 5.03
237 241 1.525077 GTGAGGGGTGTGCAAACGA 60.525 57.895 0.00 0.00 0.00 3.85
292 298 1.348036 GTAGGTCAAGCTCAAGGGTGT 59.652 52.381 0.00 0.00 0.00 4.16
483 490 1.192146 TGGGCCTACAAAGAGCGAGT 61.192 55.000 4.53 0.00 0.00 4.18
512 519 2.048444 GCAGGATTGCTTCTCATCCA 57.952 50.000 1.17 0.00 46.95 3.41
513 520 1.948145 GCAGGATTGCTTCTCATCCAG 59.052 52.381 1.17 0.00 46.95 3.86
514 521 1.948145 CAGGATTGCTTCTCATCCAGC 59.052 52.381 1.17 0.00 35.71 4.85
515 522 0.942962 GGATTGCTTCTCATCCAGCG 59.057 55.000 0.00 0.00 39.04 5.18
516 523 0.307146 GATTGCTTCTCATCCAGCGC 59.693 55.000 0.00 0.00 39.04 5.92
517 524 1.434622 ATTGCTTCTCATCCAGCGCG 61.435 55.000 0.00 0.00 39.04 6.86
518 525 2.510238 GCTTCTCATCCAGCGCGT 60.510 61.111 8.43 0.00 0.00 6.01
519 526 2.520904 GCTTCTCATCCAGCGCGTC 61.521 63.158 8.43 0.00 0.00 5.19
520 527 1.153765 CTTCTCATCCAGCGCGTCA 60.154 57.895 8.43 0.00 0.00 4.35
521 528 1.416813 CTTCTCATCCAGCGCGTCAC 61.417 60.000 8.43 0.00 0.00 3.67
541 548 3.884900 GCATCCGGCGTAACAGTT 58.115 55.556 6.01 0.00 0.00 3.16
542 549 3.053662 GCATCCGGCGTAACAGTTA 57.946 52.632 6.01 0.00 0.00 2.24
543 550 1.361793 GCATCCGGCGTAACAGTTAA 58.638 50.000 6.01 0.00 0.00 2.01
544 551 1.326548 GCATCCGGCGTAACAGTTAAG 59.673 52.381 6.01 2.09 0.00 1.85
545 552 1.326548 CATCCGGCGTAACAGTTAAGC 59.673 52.381 19.65 19.65 39.44 3.09
549 556 1.422662 GCGTAACAGTTAAGCCGGC 59.577 57.895 21.89 21.89 35.07 6.13
550 557 1.705727 CGTAACAGTTAAGCCGGCG 59.294 57.895 23.20 8.17 0.00 6.46
551 558 1.422662 GTAACAGTTAAGCCGGCGC 59.577 57.895 23.20 12.92 0.00 6.53
552 559 2.095847 TAACAGTTAAGCCGGCGCG 61.096 57.895 23.20 0.00 41.18 6.86
564 571 3.637030 GGCGCGCCGGATAGAAAC 61.637 66.667 37.24 7.78 0.00 2.78
565 572 3.984765 GCGCGCCGGATAGAAACG 61.985 66.667 23.24 0.00 0.00 3.60
566 573 2.581409 CGCGCCGGATAGAAACGT 60.581 61.111 5.05 0.00 0.00 3.99
567 574 2.162754 CGCGCCGGATAGAAACGTT 61.163 57.895 5.05 0.00 0.00 3.99
568 575 1.689352 CGCGCCGGATAGAAACGTTT 61.689 55.000 14.57 14.57 0.00 3.60
569 576 0.025898 GCGCCGGATAGAAACGTTTC 59.974 55.000 29.36 29.36 37.45 2.78
570 577 0.648958 CGCCGGATAGAAACGTTTCC 59.351 55.000 31.87 19.75 37.92 3.13
571 578 1.012086 GCCGGATAGAAACGTTTCCC 58.988 55.000 31.87 25.02 37.92 3.97
572 579 1.283736 CCGGATAGAAACGTTTCCCG 58.716 55.000 32.58 32.58 38.44 5.14
573 580 1.135024 CCGGATAGAAACGTTTCCCGA 60.135 52.381 37.07 25.24 39.96 5.14
574 581 2.190981 CGGATAGAAACGTTTCCCGAG 58.809 52.381 34.48 21.53 39.96 4.63
575 582 2.416431 CGGATAGAAACGTTTCCCGAGT 60.416 50.000 34.48 21.86 39.96 4.18
576 583 2.928116 GGATAGAAACGTTTCCCGAGTG 59.072 50.000 31.87 0.00 40.70 3.51
577 584 3.367703 GGATAGAAACGTTTCCCGAGTGA 60.368 47.826 31.87 12.90 40.70 3.41
578 585 2.833631 AGAAACGTTTCCCGAGTGAT 57.166 45.000 31.87 12.52 40.70 3.06
579 586 3.121738 AGAAACGTTTCCCGAGTGATT 57.878 42.857 31.87 11.85 40.70 2.57
580 587 2.806244 AGAAACGTTTCCCGAGTGATTG 59.194 45.455 31.87 0.00 40.70 2.67
581 588 1.519408 AACGTTTCCCGAGTGATTGG 58.481 50.000 0.00 0.00 40.70 3.16
582 589 0.395312 ACGTTTCCCGAGTGATTGGT 59.605 50.000 0.00 0.00 40.70 3.67
583 590 1.202722 ACGTTTCCCGAGTGATTGGTT 60.203 47.619 0.00 0.00 40.70 3.67
584 591 1.463444 CGTTTCCCGAGTGATTGGTTC 59.537 52.381 0.00 0.00 39.56 3.62
585 592 1.463444 GTTTCCCGAGTGATTGGTTCG 59.537 52.381 0.00 0.00 0.00 3.95
587 594 3.486263 CCGAGTGATTGGTTCGGC 58.514 61.111 0.00 0.00 46.10 5.54
588 595 1.079127 CCGAGTGATTGGTTCGGCT 60.079 57.895 0.00 0.00 46.10 5.52
589 596 1.361668 CCGAGTGATTGGTTCGGCTG 61.362 60.000 0.00 0.00 46.10 4.85
590 597 0.670546 CGAGTGATTGGTTCGGCTGT 60.671 55.000 0.00 0.00 0.00 4.40
591 598 0.798776 GAGTGATTGGTTCGGCTGTG 59.201 55.000 0.00 0.00 0.00 3.66
592 599 0.396435 AGTGATTGGTTCGGCTGTGA 59.604 50.000 0.00 0.00 0.00 3.58
593 600 1.003580 AGTGATTGGTTCGGCTGTGAT 59.996 47.619 0.00 0.00 0.00 3.06
594 601 1.812571 GTGATTGGTTCGGCTGTGATT 59.187 47.619 0.00 0.00 0.00 2.57
595 602 2.228822 GTGATTGGTTCGGCTGTGATTT 59.771 45.455 0.00 0.00 0.00 2.17
596 603 2.890311 TGATTGGTTCGGCTGTGATTTT 59.110 40.909 0.00 0.00 0.00 1.82
597 604 2.791383 TTGGTTCGGCTGTGATTTTG 57.209 45.000 0.00 0.00 0.00 2.44
598 605 0.958091 TGGTTCGGCTGTGATTTTGG 59.042 50.000 0.00 0.00 0.00 3.28
599 606 0.388520 GGTTCGGCTGTGATTTTGGC 60.389 55.000 0.00 0.00 0.00 4.52
600 607 0.388520 GTTCGGCTGTGATTTTGGCC 60.389 55.000 0.00 0.00 41.02 5.36
601 608 1.531739 TTCGGCTGTGATTTTGGCCC 61.532 55.000 0.00 0.00 41.35 5.80
602 609 2.573340 GGCTGTGATTTTGGCCCG 59.427 61.111 0.00 0.00 38.77 6.13
603 610 2.275380 GGCTGTGATTTTGGCCCGT 61.275 57.895 0.00 0.00 38.77 5.28
604 611 0.963355 GGCTGTGATTTTGGCCCGTA 60.963 55.000 0.00 0.00 38.77 4.02
605 612 0.451783 GCTGTGATTTTGGCCCGTAG 59.548 55.000 0.00 0.00 0.00 3.51
606 613 0.451783 CTGTGATTTTGGCCCGTAGC 59.548 55.000 0.00 0.00 42.60 3.58
607 614 1.302383 TGTGATTTTGGCCCGTAGCG 61.302 55.000 0.00 0.00 45.17 4.26
621 628 3.018598 CGTAGCGGAATCAGATCATGT 57.981 47.619 0.00 0.00 0.00 3.21
622 629 2.983136 CGTAGCGGAATCAGATCATGTC 59.017 50.000 0.00 0.00 0.00 3.06
623 630 2.540265 AGCGGAATCAGATCATGTCC 57.460 50.000 0.00 0.00 0.00 4.02
624 631 2.045524 AGCGGAATCAGATCATGTCCT 58.954 47.619 0.00 0.00 0.00 3.85
625 632 2.141517 GCGGAATCAGATCATGTCCTG 58.858 52.381 9.71 9.71 0.00 3.86
626 633 2.763933 CGGAATCAGATCATGTCCTGG 58.236 52.381 14.04 0.00 0.00 4.45
627 634 2.549563 CGGAATCAGATCATGTCCTGGG 60.550 54.545 14.04 0.00 0.00 4.45
628 635 2.502295 GAATCAGATCATGTCCTGGGC 58.498 52.381 14.04 0.00 0.00 5.36
629 636 1.817087 ATCAGATCATGTCCTGGGCT 58.183 50.000 14.04 0.00 0.00 5.19
630 637 0.835276 TCAGATCATGTCCTGGGCTG 59.165 55.000 14.04 0.00 0.00 4.85
631 638 0.818445 CAGATCATGTCCTGGGCTGC 60.818 60.000 0.00 0.00 0.00 5.25
632 639 0.987081 AGATCATGTCCTGGGCTGCT 60.987 55.000 0.00 0.00 0.00 4.24
633 640 0.106819 GATCATGTCCTGGGCTGCTT 60.107 55.000 0.00 0.00 0.00 3.91
634 641 0.333993 ATCATGTCCTGGGCTGCTTT 59.666 50.000 0.00 0.00 0.00 3.51
635 642 0.322816 TCATGTCCTGGGCTGCTTTC 60.323 55.000 0.00 0.00 0.00 2.62
636 643 1.377725 ATGTCCTGGGCTGCTTTCG 60.378 57.895 0.00 0.00 0.00 3.46
637 644 3.435186 GTCCTGGGCTGCTTTCGC 61.435 66.667 0.00 0.00 0.00 4.70
638 645 3.640407 TCCTGGGCTGCTTTCGCT 61.640 61.111 0.00 0.00 36.97 4.93
639 646 2.674380 CCTGGGCTGCTTTCGCTT 60.674 61.111 0.00 0.00 36.97 4.68
640 647 2.270986 CCTGGGCTGCTTTCGCTTT 61.271 57.895 0.00 0.00 36.97 3.51
641 648 1.662044 CTGGGCTGCTTTCGCTTTT 59.338 52.632 0.00 0.00 36.97 2.27
642 649 0.665369 CTGGGCTGCTTTCGCTTTTG 60.665 55.000 0.00 0.00 36.97 2.44
643 650 1.373371 GGGCTGCTTTCGCTTTTGG 60.373 57.895 0.00 0.00 36.97 3.28
644 651 1.363807 GGCTGCTTTCGCTTTTGGT 59.636 52.632 0.00 0.00 36.97 3.67
645 652 0.249447 GGCTGCTTTCGCTTTTGGTT 60.249 50.000 0.00 0.00 36.97 3.67
646 653 1.131771 GCTGCTTTCGCTTTTGGTTC 58.868 50.000 0.00 0.00 36.97 3.62
647 654 1.535860 GCTGCTTTCGCTTTTGGTTCA 60.536 47.619 0.00 0.00 36.97 3.18
648 655 2.388121 CTGCTTTCGCTTTTGGTTCAG 58.612 47.619 0.00 0.00 36.97 3.02
649 656 2.020720 TGCTTTCGCTTTTGGTTCAGA 58.979 42.857 0.00 0.00 36.97 3.27
650 657 2.622942 TGCTTTCGCTTTTGGTTCAGAT 59.377 40.909 0.00 0.00 36.97 2.90
651 658 3.068024 TGCTTTCGCTTTTGGTTCAGATT 59.932 39.130 0.00 0.00 36.97 2.40
652 659 4.051237 GCTTTCGCTTTTGGTTCAGATTT 58.949 39.130 0.00 0.00 0.00 2.17
653 660 4.507756 GCTTTCGCTTTTGGTTCAGATTTT 59.492 37.500 0.00 0.00 0.00 1.82
654 661 5.556947 GCTTTCGCTTTTGGTTCAGATTTTG 60.557 40.000 0.00 0.00 0.00 2.44
655 662 4.909696 TCGCTTTTGGTTCAGATTTTGA 57.090 36.364 0.00 0.00 0.00 2.69
656 663 4.606961 TCGCTTTTGGTTCAGATTTTGAC 58.393 39.130 0.00 0.00 34.94 3.18
657 664 4.097135 TCGCTTTTGGTTCAGATTTTGACA 59.903 37.500 0.00 0.00 34.94 3.58
658 665 4.442073 CGCTTTTGGTTCAGATTTTGACAG 59.558 41.667 0.00 0.00 34.94 3.51
659 666 4.209911 GCTTTTGGTTCAGATTTTGACAGC 59.790 41.667 0.00 0.00 34.94 4.40
660 667 3.624326 TTGGTTCAGATTTTGACAGCG 57.376 42.857 0.00 0.00 34.94 5.18
661 668 1.879380 TGGTTCAGATTTTGACAGCGG 59.121 47.619 0.00 0.00 34.94 5.52
662 669 2.151202 GGTTCAGATTTTGACAGCGGA 58.849 47.619 0.00 0.00 34.94 5.54
663 670 2.749621 GGTTCAGATTTTGACAGCGGAT 59.250 45.455 0.00 0.00 34.94 4.18
664 671 3.191371 GGTTCAGATTTTGACAGCGGATT 59.809 43.478 0.00 0.00 34.94 3.01
665 672 4.321230 GGTTCAGATTTTGACAGCGGATTT 60.321 41.667 0.00 0.00 34.94 2.17
666 673 4.685169 TCAGATTTTGACAGCGGATTTC 57.315 40.909 0.00 0.00 0.00 2.17
667 674 4.326826 TCAGATTTTGACAGCGGATTTCT 58.673 39.130 0.00 0.00 0.00 2.52
668 675 4.154737 TCAGATTTTGACAGCGGATTTCTG 59.845 41.667 0.00 0.00 37.56 3.02
669 676 4.154737 CAGATTTTGACAGCGGATTTCTGA 59.845 41.667 0.00 0.00 35.61 3.27
670 677 4.761739 AGATTTTGACAGCGGATTTCTGAA 59.238 37.500 0.00 0.00 35.61 3.02
671 678 4.909696 TTTTGACAGCGGATTTCTGAAA 57.090 36.364 5.15 5.15 35.61 2.69
672 679 5.452078 TTTTGACAGCGGATTTCTGAAAT 57.548 34.783 15.09 15.09 35.61 2.17
673 680 4.685169 TTGACAGCGGATTTCTGAAATC 57.315 40.909 27.18 27.18 45.12 2.17
689 696 6.230849 CTGAAATCAGATGCTGCTAGATTC 57.769 41.667 4.37 0.00 46.59 2.52
690 697 4.748600 TGAAATCAGATGCTGCTAGATTCG 59.251 41.667 0.00 0.00 0.00 3.34
691 698 2.145958 TCAGATGCTGCTAGATTCGC 57.854 50.000 0.00 0.00 0.00 4.70
692 699 1.146637 CAGATGCTGCTAGATTCGCC 58.853 55.000 0.00 0.00 0.00 5.54
693 700 0.034616 AGATGCTGCTAGATTCGCCC 59.965 55.000 0.00 0.00 0.00 6.13
694 701 0.034616 GATGCTGCTAGATTCGCCCT 59.965 55.000 0.00 0.00 0.00 5.19
695 702 0.471617 ATGCTGCTAGATTCGCCCTT 59.528 50.000 0.00 0.00 0.00 3.95
696 703 0.253044 TGCTGCTAGATTCGCCCTTT 59.747 50.000 0.00 0.00 0.00 3.11
697 704 0.659957 GCTGCTAGATTCGCCCTTTG 59.340 55.000 0.00 0.00 0.00 2.77
698 705 1.303309 CTGCTAGATTCGCCCTTTGG 58.697 55.000 0.00 0.00 0.00 3.28
710 717 1.101331 CCCTTTGGCTCAGATTCTGC 58.899 55.000 8.89 0.00 0.00 4.26
711 718 1.340795 CCCTTTGGCTCAGATTCTGCT 60.341 52.381 8.89 0.00 0.00 4.24
712 719 1.743958 CCTTTGGCTCAGATTCTGCTG 59.256 52.381 8.89 5.61 37.24 4.41
713 720 1.132643 CTTTGGCTCAGATTCTGCTGC 59.867 52.381 17.42 17.42 35.86 5.25
714 721 1.022982 TTGGCTCAGATTCTGCTGCG 61.023 55.000 18.37 6.58 35.86 5.18
715 722 2.708255 GCTCAGATTCTGCTGCGC 59.292 61.111 8.89 0.00 39.13 6.09
716 723 3.004283 CTCAGATTCTGCTGCGCG 58.996 61.111 8.89 0.00 35.86 6.86
717 724 2.510012 TCAGATTCTGCTGCGCGG 60.510 61.111 13.18 13.18 35.86 6.46
718 725 4.233635 CAGATTCTGCTGCGCGGC 62.234 66.667 34.00 34.00 34.49 6.53
719 726 4.765449 AGATTCTGCTGCGCGGCA 62.765 61.111 39.10 39.10 40.15 5.69
728 735 3.430862 TGCGCGGCAGTGAAATCC 61.431 61.111 8.83 0.00 33.32 3.01
729 736 3.430862 GCGCGGCAGTGAAATCCA 61.431 61.111 8.83 0.00 0.00 3.41
730 737 2.764314 GCGCGGCAGTGAAATCCAT 61.764 57.895 8.83 0.00 0.00 3.41
731 738 1.063006 CGCGGCAGTGAAATCCATG 59.937 57.895 0.00 0.00 0.00 3.66
732 739 1.434696 GCGGCAGTGAAATCCATGG 59.565 57.895 4.97 4.97 0.00 3.66
733 740 1.031571 GCGGCAGTGAAATCCATGGA 61.032 55.000 18.88 18.88 0.00 3.41
734 741 1.683943 CGGCAGTGAAATCCATGGAT 58.316 50.000 22.15 22.15 36.23 3.41
735 742 2.849942 CGGCAGTGAAATCCATGGATA 58.150 47.619 27.54 9.73 33.97 2.59
736 743 3.213506 CGGCAGTGAAATCCATGGATAA 58.786 45.455 27.54 13.50 33.97 1.75
737 744 3.631686 CGGCAGTGAAATCCATGGATAAA 59.368 43.478 27.54 13.15 33.97 1.40
738 745 4.097741 CGGCAGTGAAATCCATGGATAAAA 59.902 41.667 27.54 12.79 33.97 1.52
739 746 5.394005 CGGCAGTGAAATCCATGGATAAAAA 60.394 40.000 27.54 11.01 33.97 1.94
740 747 5.812127 GGCAGTGAAATCCATGGATAAAAAC 59.188 40.000 27.54 20.83 33.97 2.43
741 748 6.351286 GGCAGTGAAATCCATGGATAAAAACT 60.351 38.462 27.54 22.47 33.97 2.66
742 749 6.532657 GCAGTGAAATCCATGGATAAAAACTG 59.467 38.462 31.65 31.65 36.33 3.16
743 750 7.577426 GCAGTGAAATCCATGGATAAAAACTGA 60.577 37.037 35.55 15.92 35.87 3.41
744 751 8.306038 CAGTGAAATCCATGGATAAAAACTGAA 58.694 33.333 32.01 13.00 35.87 3.02
745 752 8.306761 AGTGAAATCCATGGATAAAAACTGAAC 58.693 33.333 27.54 14.34 33.97 3.18
746 753 7.273381 GTGAAATCCATGGATAAAAACTGAACG 59.727 37.037 27.54 0.00 33.97 3.95
747 754 7.175816 TGAAATCCATGGATAAAAACTGAACGA 59.824 33.333 27.54 0.00 33.97 3.85
748 755 7.461182 AATCCATGGATAAAAACTGAACGAA 57.539 32.000 27.54 0.00 33.97 3.85
749 756 6.885952 TCCATGGATAAAAACTGAACGAAA 57.114 33.333 11.44 0.00 0.00 3.46
750 757 6.674066 TCCATGGATAAAAACTGAACGAAAC 58.326 36.000 11.44 0.00 0.00 2.78
751 758 6.263392 TCCATGGATAAAAACTGAACGAAACA 59.737 34.615 11.44 0.00 0.00 2.83
752 759 6.582295 CCATGGATAAAAACTGAACGAAACAG 59.418 38.462 5.56 0.00 40.68 3.16
753 760 6.067263 TGGATAAAAACTGAACGAAACAGG 57.933 37.500 0.00 0.00 39.38 4.00
754 761 5.009210 TGGATAAAAACTGAACGAAACAGGG 59.991 40.000 0.00 0.00 39.38 4.45
755 762 2.863401 AAAACTGAACGAAACAGGGC 57.137 45.000 0.00 0.00 39.38 5.19
756 763 1.029681 AAACTGAACGAAACAGGGCC 58.970 50.000 0.00 0.00 39.38 5.80
776 783 1.275291 CTGACTCCGTCTTTTGCCCTA 59.725 52.381 0.00 0.00 33.15 3.53
858 869 1.414061 ATCCATCCCGCTCCAAGAGG 61.414 60.000 0.00 0.00 34.70 3.69
861 872 0.253044 CATCCCGCTCCAAGAGGAAA 59.747 55.000 0.00 0.00 45.19 3.13
887 898 1.690283 CGTCACTCTGCTTCCATGCG 61.690 60.000 0.00 0.00 35.36 4.73
913 932 6.635755 ACAAAATCCACCGAAAGAAAGAAAA 58.364 32.000 0.00 0.00 0.00 2.29
938 964 0.555769 AAGAAACCCCACCAAGCTGA 59.444 50.000 0.00 0.00 0.00 4.26
939 965 0.555769 AGAAACCCCACCAAGCTGAA 59.444 50.000 0.00 0.00 0.00 3.02
940 966 0.961753 GAAACCCCACCAAGCTGAAG 59.038 55.000 0.00 0.00 0.00 3.02
941 967 0.469892 AAACCCCACCAAGCTGAAGG 60.470 55.000 0.00 0.00 0.00 3.46
942 968 2.677875 CCCCACCAAGCTGAAGGC 60.678 66.667 0.00 0.00 42.19 4.35
951 977 4.393693 GCTGAAGGCTGAAGTGCT 57.606 55.556 0.00 0.00 38.06 4.40
952 978 1.874562 GCTGAAGGCTGAAGTGCTG 59.125 57.895 0.00 0.00 38.06 4.41
1045 1086 4.785453 CCTCCTGCTGCCGTTCCC 62.785 72.222 0.00 0.00 0.00 3.97
1306 1348 2.203788 TGTCGGAGGAGGCCACTT 60.204 61.111 5.01 0.00 0.00 3.16
1317 1365 3.737172 GCCACTTCGGTGCGCATT 61.737 61.111 15.91 0.00 44.05 3.56
1321 1369 1.005037 ACTTCGGTGCGCATTCTCA 60.005 52.632 15.91 0.00 0.00 3.27
1657 1707 1.358725 CCAACGGTGAGCCATACACG 61.359 60.000 0.00 0.00 38.90 4.49
1659 1709 2.167398 AACGGTGAGCCATACACGCT 62.167 55.000 0.00 0.00 39.95 5.07
1661 1711 1.421410 CGGTGAGCCATACACGCTTC 61.421 60.000 0.00 0.00 36.48 3.86
1662 1712 0.391130 GGTGAGCCATACACGCTTCA 60.391 55.000 0.00 0.00 36.48 3.02
1664 1714 1.328680 GTGAGCCATACACGCTTCATG 59.671 52.381 0.00 0.00 36.48 3.07
1665 1715 1.066215 TGAGCCATACACGCTTCATGT 60.066 47.619 0.00 0.00 36.48 3.21
1666 1716 1.328680 GAGCCATACACGCTTCATGTG 59.671 52.381 0.00 0.00 42.99 3.21
1712 1774 5.941647 GCTTATTTAGGTGTGGTTTGGTCTA 59.058 40.000 0.00 0.00 0.00 2.59
1755 2064 7.436673 GCTTGGTAGATACTTTGATAGTCACTG 59.563 40.741 0.00 0.00 38.33 3.66
1826 2135 7.989170 ACATGCACATATTCAAGATCTACTTCA 59.011 33.333 0.00 0.00 36.61 3.02
1869 2185 2.469516 CGCTTTCGGCCCGCTTTAT 61.470 57.895 0.00 0.00 37.74 1.40
1870 2186 1.155424 CGCTTTCGGCCCGCTTTATA 61.155 55.000 0.00 0.00 37.74 0.98
1943 2261 1.959085 CACACACCCAAGGCATGAC 59.041 57.895 0.00 0.00 0.00 3.06
1945 2263 0.106268 ACACACCCAAGGCATGACAA 60.106 50.000 0.00 0.00 0.00 3.18
1949 2267 2.825532 ACACCCAAGGCATGACAAATAC 59.174 45.455 0.00 0.00 0.00 1.89
1950 2268 2.824936 CACCCAAGGCATGACAAATACA 59.175 45.455 0.00 0.00 0.00 2.29
1954 2272 1.094785 AGGCATGACAAATACACGCC 58.905 50.000 0.00 0.00 45.24 5.68
1957 2275 1.129624 GCATGACAAATACACGCCGAA 59.870 47.619 0.00 0.00 0.00 4.30
1974 2292 3.714487 AACGCAGCAACACCACCCT 62.714 57.895 0.00 0.00 0.00 4.34
2009 2327 3.093835 CCGGGGGCCTCAACCATA 61.094 66.667 4.16 0.00 0.00 2.74
2014 2332 1.342975 GGGGGCCTCAACCATAAACAT 60.343 52.381 4.16 0.00 0.00 2.71
2029 2347 0.033504 AACATGTCACCGCGAAGAGT 59.966 50.000 8.23 0.00 0.00 3.24
2095 2413 1.543358 GGAAGGTTACGAGACCGAAGT 59.457 52.381 0.00 0.00 44.62 3.01
2165 2484 4.687215 GCAGTGAGAGCCGTGGCA 62.687 66.667 14.29 0.00 44.88 4.92
2166 2485 2.433838 CAGTGAGAGCCGTGGCAG 60.434 66.667 14.29 0.00 44.88 4.85
2217 2536 1.774254 TGCCGGTCCATCCAAAGATAT 59.226 47.619 1.90 0.00 35.57 1.63
2222 2541 5.560724 CCGGTCCATCCAAAGATATAACAT 58.439 41.667 0.00 0.00 35.57 2.71
2232 2551 8.877864 TCCAAAGATATAACATGTTTTCACCT 57.122 30.769 17.78 5.50 0.00 4.00
2276 2595 0.548031 CATCACACCCTGGCTACCAT 59.452 55.000 0.00 0.00 30.82 3.55
2302 2621 2.033448 GACGACCATGGCCACCAA 59.967 61.111 8.16 0.00 36.95 3.67
2338 2657 2.672908 CTCTGCCCATGAGCACCA 59.327 61.111 0.00 0.00 38.00 4.17
2355 2674 1.225983 CACAACACCACCACCAGGA 59.774 57.895 0.00 0.00 38.69 3.86
2389 3954 1.227823 CCAAGACCTTGACGCCACA 60.228 57.895 11.06 0.00 42.93 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 4.765856 AGCTACAACCGAAGAGTAGAAAGA 59.234 41.667 0.00 0.00 37.92 2.52
104 105 2.181426 TTGCTTCAACCGAACAAACG 57.819 45.000 0.00 0.00 0.00 3.60
159 162 1.251251 CTTCCTTGTTGGGCTTCTGG 58.749 55.000 0.00 0.00 36.20 3.86
214 218 4.660938 GCACACCCCTCACCACCC 62.661 72.222 0.00 0.00 0.00 4.61
227 231 1.433053 CCAGAACCGTCGTTTGCACA 61.433 55.000 0.00 0.00 30.30 4.57
237 241 2.284699 CCTCCCCTCCAGAACCGT 60.285 66.667 0.00 0.00 0.00 4.83
292 298 0.107643 TCGAACAGCCATGGACACAA 59.892 50.000 18.40 0.00 0.00 3.33
330 336 2.513204 CCTGGCATGCTCCTCGTG 60.513 66.667 18.92 0.38 34.80 4.35
344 351 3.058160 CTTCTGGGCGCCAACCTG 61.058 66.667 30.85 15.03 30.80 4.00
356 363 0.742281 CACATCTCCACGGCCTTCTG 60.742 60.000 0.00 0.00 0.00 3.02
365 372 0.254178 ATCCACCAGCACATCTCCAC 59.746 55.000 0.00 0.00 0.00 4.02
494 501 1.948145 GCTGGATGAGAAGCAATCCTG 59.052 52.381 3.54 4.15 39.31 3.86
500 507 2.510012 CGCGCTGGATGAGAAGCA 60.510 61.111 5.56 0.00 39.47 3.91
505 512 3.250323 CGTGACGCGCTGGATGAG 61.250 66.667 5.73 0.00 0.00 2.90
524 531 1.326548 CTTAACTGTTACGCCGGATGC 59.673 52.381 5.05 0.00 0.00 3.91
525 532 1.326548 GCTTAACTGTTACGCCGGATG 59.673 52.381 15.75 0.00 0.00 3.51
526 533 1.648504 GCTTAACTGTTACGCCGGAT 58.351 50.000 15.75 0.00 0.00 4.18
527 534 0.390209 GGCTTAACTGTTACGCCGGA 60.390 55.000 25.91 0.54 40.17 5.14
528 535 2.084013 GGCTTAACTGTTACGCCGG 58.916 57.895 25.91 0.00 40.17 6.13
530 537 1.974249 GCCGGCTTAACTGTTACGCC 61.974 60.000 28.52 28.52 44.55 5.68
531 538 1.422662 GCCGGCTTAACTGTTACGC 59.577 57.895 22.15 17.71 0.00 4.42
532 539 1.705727 CGCCGGCTTAACTGTTACG 59.294 57.895 26.68 0.00 0.00 3.18
533 540 1.422662 GCGCCGGCTTAACTGTTAC 59.577 57.895 26.68 0.00 35.83 2.50
534 541 2.095847 CGCGCCGGCTTAACTGTTA 61.096 57.895 26.68 0.00 36.88 2.41
535 542 3.419759 CGCGCCGGCTTAACTGTT 61.420 61.111 26.68 0.00 36.88 3.16
547 554 3.637030 GTTTCTATCCGGCGCGCC 61.637 66.667 39.82 39.82 0.00 6.53
548 555 3.984765 CGTTTCTATCCGGCGCGC 61.985 66.667 25.94 25.94 0.00 6.86
549 556 1.689352 AAACGTTTCTATCCGGCGCG 61.689 55.000 7.96 0.00 0.00 6.86
550 557 0.025898 GAAACGTTTCTATCCGGCGC 59.974 55.000 29.27 0.00 34.41 6.53
551 558 0.648958 GGAAACGTTTCTATCCGGCG 59.351 55.000 33.23 0.00 37.35 6.46
552 559 1.012086 GGGAAACGTTTCTATCCGGC 58.988 55.000 33.23 18.48 37.35 6.13
553 560 1.135024 TCGGGAAACGTTTCTATCCGG 60.135 52.381 35.45 26.35 44.69 5.14
554 561 2.190981 CTCGGGAAACGTTTCTATCCG 58.809 52.381 33.19 33.19 44.69 4.18
555 562 2.928116 CACTCGGGAAACGTTTCTATCC 59.072 50.000 33.23 25.85 44.69 2.59
556 563 3.841643 TCACTCGGGAAACGTTTCTATC 58.158 45.455 33.23 23.03 44.69 2.08
557 564 3.947910 TCACTCGGGAAACGTTTCTAT 57.052 42.857 33.23 16.03 44.69 1.98
558 565 3.947910 ATCACTCGGGAAACGTTTCTA 57.052 42.857 33.23 20.76 44.69 2.10
559 566 2.806244 CAATCACTCGGGAAACGTTTCT 59.194 45.455 33.23 15.86 44.69 2.52
560 567 2.095919 CCAATCACTCGGGAAACGTTTC 60.096 50.000 28.83 28.83 44.69 2.78
561 568 1.877443 CCAATCACTCGGGAAACGTTT 59.123 47.619 14.57 14.57 44.69 3.60
562 569 1.202722 ACCAATCACTCGGGAAACGTT 60.203 47.619 0.00 0.00 44.69 3.99
563 570 0.395312 ACCAATCACTCGGGAAACGT 59.605 50.000 0.00 0.00 44.69 3.99
564 571 1.463444 GAACCAATCACTCGGGAAACG 59.537 52.381 0.00 0.00 46.11 3.60
565 572 1.463444 CGAACCAATCACTCGGGAAAC 59.537 52.381 0.00 0.00 0.00 2.78
566 573 1.609580 CCGAACCAATCACTCGGGAAA 60.610 52.381 0.00 0.00 46.66 3.13
567 574 0.036765 CCGAACCAATCACTCGGGAA 60.037 55.000 0.00 0.00 46.66 3.97
568 575 1.594833 CCGAACCAATCACTCGGGA 59.405 57.895 0.00 0.00 46.66 5.14
569 576 4.201951 CCGAACCAATCACTCGGG 57.798 61.111 1.80 0.00 46.66 5.14
571 578 0.670546 ACAGCCGAACCAATCACTCG 60.671 55.000 0.00 0.00 0.00 4.18
572 579 0.798776 CACAGCCGAACCAATCACTC 59.201 55.000 0.00 0.00 0.00 3.51
573 580 0.396435 TCACAGCCGAACCAATCACT 59.604 50.000 0.00 0.00 0.00 3.41
574 581 1.453155 ATCACAGCCGAACCAATCAC 58.547 50.000 0.00 0.00 0.00 3.06
575 582 2.198827 AATCACAGCCGAACCAATCA 57.801 45.000 0.00 0.00 0.00 2.57
576 583 3.244976 CAAAATCACAGCCGAACCAATC 58.755 45.455 0.00 0.00 0.00 2.67
577 584 2.029110 CCAAAATCACAGCCGAACCAAT 60.029 45.455 0.00 0.00 0.00 3.16
578 585 1.339610 CCAAAATCACAGCCGAACCAA 59.660 47.619 0.00 0.00 0.00 3.67
579 586 0.958091 CCAAAATCACAGCCGAACCA 59.042 50.000 0.00 0.00 0.00 3.67
580 587 0.388520 GCCAAAATCACAGCCGAACC 60.389 55.000 0.00 0.00 0.00 3.62
581 588 0.388520 GGCCAAAATCACAGCCGAAC 60.389 55.000 0.00 0.00 35.30 3.95
582 589 1.531739 GGGCCAAAATCACAGCCGAA 61.532 55.000 4.39 0.00 46.75 4.30
583 590 1.976474 GGGCCAAAATCACAGCCGA 60.976 57.895 4.39 0.00 46.75 5.54
584 591 2.573340 GGGCCAAAATCACAGCCG 59.427 61.111 4.39 0.00 46.75 5.52
585 592 0.963355 TACGGGCCAAAATCACAGCC 60.963 55.000 4.39 0.00 44.99 4.85
586 593 0.451783 CTACGGGCCAAAATCACAGC 59.548 55.000 4.39 0.00 0.00 4.40
587 594 0.451783 GCTACGGGCCAAAATCACAG 59.548 55.000 4.39 0.00 34.27 3.66
588 595 1.302383 CGCTACGGGCCAAAATCACA 61.302 55.000 4.39 0.00 37.74 3.58
589 596 1.427819 CGCTACGGGCCAAAATCAC 59.572 57.895 4.39 0.00 37.74 3.06
590 597 1.747367 CCGCTACGGGCCAAAATCA 60.747 57.895 4.39 0.00 44.15 2.57
591 598 3.107447 CCGCTACGGGCCAAAATC 58.893 61.111 4.39 0.00 44.15 2.17
601 608 2.983136 GACATGATCTGATTCCGCTACG 59.017 50.000 0.00 0.00 0.00 3.51
602 609 3.006323 AGGACATGATCTGATTCCGCTAC 59.994 47.826 0.00 0.00 0.00 3.58
603 610 3.006217 CAGGACATGATCTGATTCCGCTA 59.994 47.826 0.00 0.00 33.11 4.26
604 611 2.045524 AGGACATGATCTGATTCCGCT 58.954 47.619 0.00 0.00 0.00 5.52
605 612 2.141517 CAGGACATGATCTGATTCCGC 58.858 52.381 0.00 0.00 33.11 5.54
606 613 2.549563 CCCAGGACATGATCTGATTCCG 60.550 54.545 17.22 4.78 33.11 4.30
607 614 2.813354 GCCCAGGACATGATCTGATTCC 60.813 54.545 17.22 5.17 33.11 3.01
608 615 2.106166 AGCCCAGGACATGATCTGATTC 59.894 50.000 17.22 8.68 33.11 2.52
609 616 2.133520 AGCCCAGGACATGATCTGATT 58.866 47.619 17.22 4.41 33.11 2.57
610 617 1.420514 CAGCCCAGGACATGATCTGAT 59.579 52.381 17.22 0.00 32.92 2.90
611 618 0.835276 CAGCCCAGGACATGATCTGA 59.165 55.000 17.22 0.00 32.92 3.27
612 619 0.818445 GCAGCCCAGGACATGATCTG 60.818 60.000 0.00 6.40 33.73 2.90
613 620 0.987081 AGCAGCCCAGGACATGATCT 60.987 55.000 0.00 0.00 0.00 2.75
614 621 0.106819 AAGCAGCCCAGGACATGATC 60.107 55.000 0.00 0.00 0.00 2.92
615 622 0.333993 AAAGCAGCCCAGGACATGAT 59.666 50.000 0.00 0.00 0.00 2.45
616 623 0.322816 GAAAGCAGCCCAGGACATGA 60.323 55.000 0.00 0.00 0.00 3.07
617 624 1.651240 CGAAAGCAGCCCAGGACATG 61.651 60.000 0.00 0.00 0.00 3.21
618 625 1.377725 CGAAAGCAGCCCAGGACAT 60.378 57.895 0.00 0.00 0.00 3.06
619 626 2.032528 CGAAAGCAGCCCAGGACA 59.967 61.111 0.00 0.00 0.00 4.02
631 638 5.748152 TCAAAATCTGAACCAAAAGCGAAAG 59.252 36.000 0.00 0.00 0.00 2.62
632 639 5.518487 GTCAAAATCTGAACCAAAAGCGAAA 59.482 36.000 0.00 0.00 35.22 3.46
633 640 5.040635 GTCAAAATCTGAACCAAAAGCGAA 58.959 37.500 0.00 0.00 35.22 4.70
634 641 4.097135 TGTCAAAATCTGAACCAAAAGCGA 59.903 37.500 0.00 0.00 35.22 4.93
635 642 4.358851 TGTCAAAATCTGAACCAAAAGCG 58.641 39.130 0.00 0.00 35.22 4.68
636 643 4.209911 GCTGTCAAAATCTGAACCAAAAGC 59.790 41.667 0.00 0.00 35.22 3.51
637 644 4.442073 CGCTGTCAAAATCTGAACCAAAAG 59.558 41.667 0.00 0.00 35.22 2.27
638 645 4.358851 CGCTGTCAAAATCTGAACCAAAA 58.641 39.130 0.00 0.00 35.22 2.44
639 646 3.243367 CCGCTGTCAAAATCTGAACCAAA 60.243 43.478 0.00 0.00 35.22 3.28
640 647 2.293122 CCGCTGTCAAAATCTGAACCAA 59.707 45.455 0.00 0.00 35.22 3.67
641 648 1.879380 CCGCTGTCAAAATCTGAACCA 59.121 47.619 0.00 0.00 35.22 3.67
642 649 2.151202 TCCGCTGTCAAAATCTGAACC 58.849 47.619 0.00 0.00 35.22 3.62
643 650 4.425577 AATCCGCTGTCAAAATCTGAAC 57.574 40.909 0.00 0.00 35.22 3.18
644 651 4.761739 AGAAATCCGCTGTCAAAATCTGAA 59.238 37.500 0.00 0.00 35.22 3.02
645 652 4.154737 CAGAAATCCGCTGTCAAAATCTGA 59.845 41.667 0.00 0.00 35.05 3.27
646 653 4.154737 TCAGAAATCCGCTGTCAAAATCTG 59.845 41.667 0.00 0.00 34.98 2.90
647 654 4.326826 TCAGAAATCCGCTGTCAAAATCT 58.673 39.130 0.00 0.00 34.98 2.40
648 655 4.685169 TCAGAAATCCGCTGTCAAAATC 57.315 40.909 0.00 0.00 34.98 2.17
649 656 5.452078 TTTCAGAAATCCGCTGTCAAAAT 57.548 34.783 0.00 0.00 34.98 1.82
650 657 4.909696 TTTCAGAAATCCGCTGTCAAAA 57.090 36.364 0.00 0.00 34.98 2.44
651 658 4.518590 TGATTTCAGAAATCCGCTGTCAAA 59.481 37.500 26.49 7.75 45.23 2.69
652 659 4.071423 TGATTTCAGAAATCCGCTGTCAA 58.929 39.130 26.49 8.35 45.23 3.18
653 660 3.673902 TGATTTCAGAAATCCGCTGTCA 58.326 40.909 26.49 10.34 45.23 3.58
654 661 4.270178 CTGATTTCAGAAATCCGCTGTC 57.730 45.455 26.49 8.11 46.59 3.51
666 673 5.107414 CGAATCTAGCAGCATCTGATTTCAG 60.107 44.000 0.97 0.97 45.08 3.02
667 674 4.748600 CGAATCTAGCAGCATCTGATTTCA 59.251 41.667 0.00 0.00 32.44 2.69
668 675 4.377226 GCGAATCTAGCAGCATCTGATTTC 60.377 45.833 0.00 0.00 32.44 2.17
669 676 3.497640 GCGAATCTAGCAGCATCTGATTT 59.502 43.478 0.00 0.00 32.44 2.17
670 677 3.065655 GCGAATCTAGCAGCATCTGATT 58.934 45.455 0.00 0.00 32.44 2.57
671 678 2.612471 GGCGAATCTAGCAGCATCTGAT 60.612 50.000 0.00 0.00 32.44 2.90
672 679 1.269988 GGCGAATCTAGCAGCATCTGA 60.270 52.381 0.00 0.00 32.44 3.27
673 680 1.146637 GGCGAATCTAGCAGCATCTG 58.853 55.000 0.00 0.00 36.08 2.90
674 681 0.034616 GGGCGAATCTAGCAGCATCT 59.965 55.000 0.00 0.00 36.08 2.90
675 682 0.034616 AGGGCGAATCTAGCAGCATC 59.965 55.000 0.00 0.00 36.08 3.91
676 683 0.471617 AAGGGCGAATCTAGCAGCAT 59.528 50.000 0.00 0.00 36.08 3.79
677 684 0.253044 AAAGGGCGAATCTAGCAGCA 59.747 50.000 0.00 0.00 36.08 4.41
678 685 0.659957 CAAAGGGCGAATCTAGCAGC 59.340 55.000 0.00 0.00 36.08 5.25
679 686 1.303309 CCAAAGGGCGAATCTAGCAG 58.697 55.000 0.00 0.00 36.08 4.24
680 687 3.476740 CCAAAGGGCGAATCTAGCA 57.523 52.632 0.00 0.00 36.08 3.49
690 697 2.890499 GCAGAATCTGAGCCAAAGGGC 61.890 57.143 15.38 0.00 45.60 5.19
691 698 1.101331 GCAGAATCTGAGCCAAAGGG 58.899 55.000 15.38 0.00 32.44 3.95
692 699 1.743958 CAGCAGAATCTGAGCCAAAGG 59.256 52.381 15.38 0.00 36.19 3.11
693 700 1.132643 GCAGCAGAATCTGAGCCAAAG 59.867 52.381 15.38 0.00 36.19 2.77
694 701 1.171308 GCAGCAGAATCTGAGCCAAA 58.829 50.000 15.38 0.00 36.19 3.28
695 702 1.022982 CGCAGCAGAATCTGAGCCAA 61.023 55.000 15.38 0.00 36.19 4.52
696 703 1.449070 CGCAGCAGAATCTGAGCCA 60.449 57.895 15.38 0.00 36.19 4.75
697 704 3.407657 CGCAGCAGAATCTGAGCC 58.592 61.111 15.38 0.00 36.19 4.70
711 718 3.430862 GGATTTCACTGCCGCGCA 61.431 61.111 8.75 1.04 36.92 6.09
712 719 2.764314 ATGGATTTCACTGCCGCGC 61.764 57.895 0.00 0.00 0.00 6.86
713 720 1.063006 CATGGATTTCACTGCCGCG 59.937 57.895 0.00 0.00 0.00 6.46
714 721 1.031571 TCCATGGATTTCACTGCCGC 61.032 55.000 11.44 0.00 0.00 6.53
715 722 1.683943 ATCCATGGATTTCACTGCCG 58.316 50.000 22.15 0.00 0.00 5.69
716 723 5.596836 TTTTATCCATGGATTTCACTGCC 57.403 39.130 31.70 0.00 36.17 4.85
717 724 6.532657 CAGTTTTTATCCATGGATTTCACTGC 59.467 38.462 31.70 15.64 36.17 4.40
718 725 7.829725 TCAGTTTTTATCCATGGATTTCACTG 58.170 34.615 31.70 30.10 36.17 3.66
719 726 8.306761 GTTCAGTTTTTATCCATGGATTTCACT 58.693 33.333 31.70 22.85 36.17 3.41
720 727 7.273381 CGTTCAGTTTTTATCCATGGATTTCAC 59.727 37.037 31.70 21.22 36.17 3.18
721 728 7.175816 TCGTTCAGTTTTTATCCATGGATTTCA 59.824 33.333 31.70 12.18 36.17 2.69
722 729 7.535139 TCGTTCAGTTTTTATCCATGGATTTC 58.465 34.615 31.70 16.66 36.17 2.17
723 730 7.461182 TCGTTCAGTTTTTATCCATGGATTT 57.539 32.000 31.70 13.00 36.17 2.17
724 731 7.461182 TTCGTTCAGTTTTTATCCATGGATT 57.539 32.000 31.70 15.99 36.17 3.01
725 732 7.040062 TGTTTCGTTCAGTTTTTATCCATGGAT 60.040 33.333 29.66 29.66 38.54 3.41
726 733 6.263392 TGTTTCGTTCAGTTTTTATCCATGGA 59.737 34.615 18.88 18.88 0.00 3.41
727 734 6.442952 TGTTTCGTTCAGTTTTTATCCATGG 58.557 36.000 4.97 4.97 0.00 3.66
728 735 6.582295 CCTGTTTCGTTCAGTTTTTATCCATG 59.418 38.462 0.00 0.00 0.00 3.66
729 736 6.294508 CCCTGTTTCGTTCAGTTTTTATCCAT 60.295 38.462 0.00 0.00 0.00 3.41
730 737 5.009210 CCCTGTTTCGTTCAGTTTTTATCCA 59.991 40.000 0.00 0.00 0.00 3.41
731 738 5.458015 CCCTGTTTCGTTCAGTTTTTATCC 58.542 41.667 0.00 0.00 0.00 2.59
732 739 4.915667 GCCCTGTTTCGTTCAGTTTTTATC 59.084 41.667 0.00 0.00 0.00 1.75
733 740 4.261867 GGCCCTGTTTCGTTCAGTTTTTAT 60.262 41.667 0.00 0.00 0.00 1.40
734 741 3.067040 GGCCCTGTTTCGTTCAGTTTTTA 59.933 43.478 0.00 0.00 0.00 1.52
735 742 2.159156 GGCCCTGTTTCGTTCAGTTTTT 60.159 45.455 0.00 0.00 0.00 1.94
736 743 1.407618 GGCCCTGTTTCGTTCAGTTTT 59.592 47.619 0.00 0.00 0.00 2.43
737 744 1.029681 GGCCCTGTTTCGTTCAGTTT 58.970 50.000 0.00 0.00 0.00 2.66
738 745 0.182775 AGGCCCTGTTTCGTTCAGTT 59.817 50.000 0.00 0.00 0.00 3.16
739 746 0.535102 CAGGCCCTGTTTCGTTCAGT 60.535 55.000 1.39 0.00 0.00 3.41
740 747 0.250295 TCAGGCCCTGTTTCGTTCAG 60.250 55.000 11.27 0.00 32.61 3.02
741 748 0.534203 GTCAGGCCCTGTTTCGTTCA 60.534 55.000 11.27 0.00 32.61 3.18
742 749 0.250338 AGTCAGGCCCTGTTTCGTTC 60.250 55.000 11.27 0.00 32.61 3.95
743 750 0.250338 GAGTCAGGCCCTGTTTCGTT 60.250 55.000 11.27 0.00 32.61 3.85
744 751 1.371558 GAGTCAGGCCCTGTTTCGT 59.628 57.895 11.27 0.00 32.61 3.85
745 752 1.376037 GGAGTCAGGCCCTGTTTCG 60.376 63.158 11.27 0.00 32.61 3.46
746 753 1.376037 CGGAGTCAGGCCCTGTTTC 60.376 63.158 11.27 9.43 32.61 2.78
747 754 2.147387 ACGGAGTCAGGCCCTGTTT 61.147 57.895 11.27 0.00 29.74 2.83
748 755 2.526873 ACGGAGTCAGGCCCTGTT 60.527 61.111 11.27 0.00 29.74 3.16
842 849 0.253044 TTTCCTCTTGGAGCGGGATG 59.747 55.000 0.00 0.00 44.24 3.51
843 850 0.253327 GTTTCCTCTTGGAGCGGGAT 59.747 55.000 0.00 0.00 44.24 3.85
844 851 0.836400 AGTTTCCTCTTGGAGCGGGA 60.836 55.000 0.00 0.00 44.24 5.14
858 869 0.111089 CAGAGTGACGCGCAAGTTTC 60.111 55.000 5.73 0.00 41.68 2.78
861 872 2.978452 AAGCAGAGTGACGCGCAAGT 62.978 55.000 5.73 0.00 41.68 3.16
887 898 6.308371 TCTTTCTTTCGGTGGATTTTGTAC 57.692 37.500 0.00 0.00 0.00 2.90
913 932 0.856982 TGGTGGGGTTTCTTGGATGT 59.143 50.000 0.00 0.00 0.00 3.06
938 964 0.183492 TGGTTCAGCACTTCAGCCTT 59.817 50.000 0.00 0.00 34.23 4.35
939 965 0.403271 ATGGTTCAGCACTTCAGCCT 59.597 50.000 0.00 0.00 34.23 4.58
940 966 0.524862 CATGGTTCAGCACTTCAGCC 59.475 55.000 0.00 0.00 34.23 4.85
941 967 0.524862 CCATGGTTCAGCACTTCAGC 59.475 55.000 2.57 0.00 0.00 4.26
942 968 2.082231 CTCCATGGTTCAGCACTTCAG 58.918 52.381 12.58 0.00 0.00 3.02
943 969 1.699083 TCTCCATGGTTCAGCACTTCA 59.301 47.619 12.58 0.00 0.00 3.02
944 970 2.354259 CTCTCCATGGTTCAGCACTTC 58.646 52.381 12.58 0.00 0.00 3.01
945 971 1.612726 GCTCTCCATGGTTCAGCACTT 60.613 52.381 20.62 0.00 0.00 3.16
946 972 0.035630 GCTCTCCATGGTTCAGCACT 60.036 55.000 20.62 0.00 0.00 4.40
947 973 0.321919 TGCTCTCCATGGTTCAGCAC 60.322 55.000 22.95 7.26 35.17 4.40
948 974 0.321919 GTGCTCTCCATGGTTCAGCA 60.322 55.000 22.95 22.95 37.76 4.41
949 975 1.364626 CGTGCTCTCCATGGTTCAGC 61.365 60.000 19.42 19.42 0.00 4.26
950 976 1.364626 GCGTGCTCTCCATGGTTCAG 61.365 60.000 12.58 7.28 0.00 3.02
951 977 1.375908 GCGTGCTCTCCATGGTTCA 60.376 57.895 12.58 2.87 0.00 3.18
952 978 2.456119 CGCGTGCTCTCCATGGTTC 61.456 63.158 12.58 0.10 0.00 3.62
1306 1348 0.174617 TACATGAGAATGCGCACCGA 59.825 50.000 14.90 0.22 0.00 4.69
1315 1363 2.479730 GGTGCGAGTCGTACATGAGAAT 60.480 50.000 30.34 0.00 43.70 2.40
1317 1365 0.450583 GGTGCGAGTCGTACATGAGA 59.549 55.000 30.34 0.00 43.70 3.27
1321 1369 1.153823 GCAGGTGCGAGTCGTACAT 60.154 57.895 30.34 23.57 43.70 2.29
1415 1463 1.975407 CACACCTCCCCGTAGACGT 60.975 63.158 0.85 0.00 37.74 4.34
1676 1737 4.082949 ACCTAAATAAGCAGAACAAACGGC 60.083 41.667 0.00 0.00 0.00 5.68
1712 1774 8.554011 TCTACCAAGCCTAATAACCAGTTTAAT 58.446 33.333 0.00 0.00 0.00 1.40
1826 2135 9.909644 CGCTATATATTAGTCTTAGTGGTTGTT 57.090 33.333 0.00 0.00 0.00 2.83
1880 2196 4.295141 ACCGGGTTGTTGATGATCTTTA 57.705 40.909 6.32 0.00 0.00 1.85
1943 2261 4.336174 GCGTTCGGCGTGTATTTG 57.664 55.556 6.85 0.00 43.66 2.32
1954 2272 2.052237 GTGGTGTTGCTGCGTTCG 60.052 61.111 0.00 0.00 0.00 3.95
1957 2275 2.332312 TAAGGGTGGTGTTGCTGCGT 62.332 55.000 0.00 0.00 0.00 5.24
1974 2292 2.616960 CGGTTGCTCATGTAGTGCTAA 58.383 47.619 0.00 0.00 37.61 3.09
2007 2325 2.930040 CTCTTCGCGGTGACATGTTTAT 59.070 45.455 6.13 0.00 0.00 1.40
2009 2327 1.148310 CTCTTCGCGGTGACATGTTT 58.852 50.000 6.13 0.00 0.00 2.83
2014 2332 0.103390 TTCAACTCTTCGCGGTGACA 59.897 50.000 6.13 0.00 0.00 3.58
2029 2347 3.504863 GGTTCGTCGTATGTAGCTTCAA 58.495 45.455 0.00 0.00 0.00 2.69
2166 2485 0.955919 CGTCCCCTTCTTGAAGGCAC 60.956 60.000 20.71 17.28 38.63 5.01
2217 2536 2.156098 GGCCGAGGTGAAAACATGTTA 58.844 47.619 12.39 0.00 0.00 2.41
2222 2541 2.570415 TATTGGCCGAGGTGAAAACA 57.430 45.000 0.00 0.00 0.00 2.83
2232 2551 1.525077 GGCGGTGAATATTGGCCGA 60.525 57.895 23.54 0.00 46.33 5.54
2285 2604 2.033448 TTGGTGGCCATGGTCGTC 59.967 61.111 9.72 7.34 31.53 4.20
2289 2608 2.283388 CTGCTTGGTGGCCATGGT 60.283 61.111 9.72 0.00 31.53 3.55
2338 2657 1.226262 GTCCTGGTGGTGGTGTTGT 59.774 57.895 0.00 0.00 34.23 3.32
2365 2684 1.026718 CGTCAAGGTCTTGGATGCCC 61.027 60.000 10.39 0.00 40.78 5.36


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

AutoCloner maintained by Alex Coulton.