Multiple sequence alignment - TraesCS5A01G119600

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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 TraesCS5A01G119600 chr5A 100.000 4958 0 0 1 4958 250557448 250562405 0.000000e+00 9156.0
1 TraesCS5A01G119600 chr5A 90.909 572 41 6 1 562 596085839 596086409 0.000000e+00 758.0
2 TraesCS5A01G119600 chr5A 87.356 261 33 0 1112 1372 651447074 651447334 2.900000e-77 300.0
3 TraesCS5A01G119600 chr5A 89.498 219 20 3 555 771 56313812 56313595 1.760000e-69 274.0
4 TraesCS5A01G119600 chr5B 96.636 4192 105 16 798 4956 198033053 198028865 0.000000e+00 6927.0
5 TraesCS5A01G119600 chr5D 95.673 4206 102 19 798 4958 192954614 192950444 0.000000e+00 6685.0
6 TraesCS5A01G119600 chr5D 93.750 48 2 1 4838 4884 192950613 192950566 2.480000e-08 71.3
7 TraesCS5A01G119600 chr3A 92.281 570 29 7 1 559 644663000 644663565 0.000000e+00 795.0
8 TraesCS5A01G119600 chr3A 92.240 567 33 10 1 562 15487344 15487904 0.000000e+00 793.0
9 TraesCS5A01G119600 chr3A 90.451 576 38 8 1 562 547328670 547329242 0.000000e+00 743.0
10 TraesCS5A01G119600 chr6A 92.226 566 31 8 6 559 49748464 49749028 0.000000e+00 789.0
11 TraesCS5A01G119600 chr2A 91.243 571 35 9 1 559 713175744 713176311 0.000000e+00 763.0
12 TraesCS5A01G119600 chr2A 91.228 570 35 8 4 559 72606539 72605971 0.000000e+00 761.0
13 TraesCS5A01G119600 chr4A 90.401 573 38 9 1 559 602051791 602052360 0.000000e+00 737.0
14 TraesCS5A01G119600 chr4A 89.320 206 20 2 558 762 627574142 627574346 1.770000e-64 257.0
15 TraesCS5A01G119600 chr7A 90.368 571 39 11 1 559 191749209 191749775 0.000000e+00 736.0
16 TraesCS5A01G119600 chr6B 88.995 209 23 0 551 759 548388635 548388427 4.920000e-65 259.0
17 TraesCS5A01G119600 chr6B 88.889 207 23 0 546 752 671889302 671889508 6.370000e-64 255.0
18 TraesCS5A01G119600 chr7B 89.216 204 22 0 556 759 380078370 380078167 6.370000e-64 255.0
19 TraesCS5A01G119600 chr7B 87.615 218 26 1 551 767 536642322 536642539 8.240000e-63 252.0
20 TraesCS5A01G119600 chr4B 88.889 207 21 2 558 763 315477281 315477076 2.290000e-63 254.0
21 TraesCS5A01G119600 chrUn 80.645 310 48 9 424 724 60297569 60297875 3.860000e-56 230.0
22 TraesCS5A01G119600 chrUn 79.412 340 57 11 424 754 375799715 375800050 1.390000e-55 228.0
23 TraesCS5A01G119600 chr2B 88.235 51 5 1 749 798 238639852 238639802 5.360000e-05 60.2
24 TraesCS5A01G119600 chr7D 94.444 36 2 0 763 798 61269067 61269032 6.930000e-04 56.5


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5A01G119600 chr5A 250557448 250562405 4957 False 9156 9156 100.000 1 4958 1 chr5A.!!$F1 4957
1 TraesCS5A01G119600 chr5A 596085839 596086409 570 False 758 758 90.909 1 562 1 chr5A.!!$F2 561
2 TraesCS5A01G119600 chr5B 198028865 198033053 4188 True 6927 6927 96.636 798 4956 1 chr5B.!!$R1 4158
3 TraesCS5A01G119600 chr5D 192950444 192954614 4170 True 6685 6685 95.673 798 4958 1 chr5D.!!$R1 4160
4 TraesCS5A01G119600 chr3A 644663000 644663565 565 False 795 795 92.281 1 559 1 chr3A.!!$F3 558
5 TraesCS5A01G119600 chr3A 15487344 15487904 560 False 793 793 92.240 1 562 1 chr3A.!!$F1 561
6 TraesCS5A01G119600 chr3A 547328670 547329242 572 False 743 743 90.451 1 562 1 chr3A.!!$F2 561
7 TraesCS5A01G119600 chr6A 49748464 49749028 564 False 789 789 92.226 6 559 1 chr6A.!!$F1 553
8 TraesCS5A01G119600 chr2A 713175744 713176311 567 False 763 763 91.243 1 559 1 chr2A.!!$F1 558
9 TraesCS5A01G119600 chr2A 72605971 72606539 568 True 761 761 91.228 4 559 1 chr2A.!!$R1 555
10 TraesCS5A01G119600 chr4A 602051791 602052360 569 False 737 737 90.401 1 559 1 chr4A.!!$F1 558
11 TraesCS5A01G119600 chr7A 191749209 191749775 566 False 736 736 90.368 1 559 1 chr7A.!!$F1 558

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
562 584 0.033228 CGGCTGGAGATGCTCTTAGG 59.967 60.000 0.00 0.0 0.0 2.69 F
584 606 0.037590 TTGTACAATGGGAGGCGCTT 59.962 50.000 7.64 0.0 0.0 4.68 F
591 613 0.105964 ATGGGAGGCGCTTAGAGAGA 60.106 55.000 7.64 0.0 0.0 3.10 F
791 813 0.173255 CCATTTGATGCAACGGGTCC 59.827 55.000 0.00 0.0 0.0 4.46 F
2260 2294 0.179000 AGCTGGTTGATAAGGCTCGG 59.821 55.000 0.00 0.0 0.0 4.63 F
2972 3046 2.159170 GCTATGATCTATCCACGGAGCC 60.159 54.545 0.00 0.0 0.0 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1712 1746 0.457166 CTGCATTGTGGTGAATGGCG 60.457 55.000 0.00 0.00 34.42 5.69 R
2516 2590 1.398390 GATCTGCAGGTTTGTTAGCCG 59.602 52.381 15.13 0.00 0.00 5.52 R
2530 2604 6.183360 GGAAACTTATACACACTGTGATCTGC 60.183 42.308 16.30 0.00 36.96 4.26 R
2746 2820 5.273674 TGGCAATGTTTTTCAGATGAACA 57.726 34.783 0.00 2.56 37.64 3.18 R
3193 3269 2.038952 TGCAGTCCACAATCTACAGCTT 59.961 45.455 0.00 0.00 0.00 3.74 R
4409 4494 0.260230 TTTCACCTTGGCACCCTTGA 59.740 50.000 0.00 0.00 0.00 3.02 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
50 51 2.811101 CGATGGAGAAGGAGCGCT 59.189 61.111 11.27 11.27 0.00 5.92
137 144 1.506718 GGAGTCGTCGTCATCTGCA 59.493 57.895 0.00 0.00 0.00 4.41
141 148 1.136690 GTCGTCGTCATCTGCAACAA 58.863 50.000 0.00 0.00 0.00 2.83
360 375 7.986085 ACATGTCTAATATATGCCCAAGTTC 57.014 36.000 0.00 0.00 30.12 3.01
363 378 7.136822 TGTCTAATATATGCCCAAGTTCACT 57.863 36.000 0.00 0.00 0.00 3.41
372 387 5.452078 TGCCCAAGTTCACTGAAATTTAG 57.548 39.130 1.70 0.00 27.08 1.85
526 545 1.451387 CCAGGCGGCGATTTTAGGT 60.451 57.895 12.98 0.00 0.00 3.08
562 584 0.033228 CGGCTGGAGATGCTCTTAGG 59.967 60.000 0.00 0.00 0.00 2.69
563 585 0.250252 GGCTGGAGATGCTCTTAGGC 60.250 60.000 0.00 0.00 35.06 3.93
564 586 0.250252 GCTGGAGATGCTCTTAGGCC 60.250 60.000 0.00 0.00 0.00 5.19
565 587 1.422531 CTGGAGATGCTCTTAGGCCT 58.577 55.000 11.78 11.78 0.00 5.19
566 588 1.767681 CTGGAGATGCTCTTAGGCCTT 59.232 52.381 12.58 0.00 0.00 4.35
567 589 1.487976 TGGAGATGCTCTTAGGCCTTG 59.512 52.381 12.58 4.55 0.00 3.61
568 590 1.488393 GGAGATGCTCTTAGGCCTTGT 59.512 52.381 12.58 0.00 0.00 3.16
569 591 2.700897 GGAGATGCTCTTAGGCCTTGTA 59.299 50.000 12.58 0.00 0.00 2.41
570 592 3.493524 GGAGATGCTCTTAGGCCTTGTAC 60.494 52.174 12.58 0.00 0.00 2.90
571 593 3.107601 AGATGCTCTTAGGCCTTGTACA 58.892 45.455 12.58 3.82 0.00 2.90
572 594 3.519510 AGATGCTCTTAGGCCTTGTACAA 59.480 43.478 12.58 8.28 0.00 2.41
573 595 4.164988 AGATGCTCTTAGGCCTTGTACAAT 59.835 41.667 12.58 0.00 0.00 2.71
574 596 3.609853 TGCTCTTAGGCCTTGTACAATG 58.390 45.455 12.58 7.68 0.00 2.82
575 597 2.945668 GCTCTTAGGCCTTGTACAATGG 59.054 50.000 12.58 13.26 0.00 3.16
576 598 3.545703 CTCTTAGGCCTTGTACAATGGG 58.454 50.000 12.58 14.91 0.00 4.00
577 599 3.186283 TCTTAGGCCTTGTACAATGGGA 58.814 45.455 12.58 6.88 0.00 4.37
578 600 3.199946 TCTTAGGCCTTGTACAATGGGAG 59.800 47.826 12.58 6.16 0.00 4.30
579 601 0.625849 AGGCCTTGTACAATGGGAGG 59.374 55.000 16.08 11.34 0.00 4.30
580 602 2.493547 GCCTTGTACAATGGGAGGC 58.506 57.895 17.46 17.46 45.21 4.70
581 603 1.376609 GCCTTGTACAATGGGAGGCG 61.377 60.000 17.46 0.69 42.91 5.52
582 604 1.376609 CCTTGTACAATGGGAGGCGC 61.377 60.000 9.13 0.00 0.00 6.53
583 605 0.392998 CTTGTACAATGGGAGGCGCT 60.393 55.000 9.13 0.00 0.00 5.92
584 606 0.037590 TTGTACAATGGGAGGCGCTT 59.962 50.000 7.64 0.00 0.00 4.68
585 607 0.906066 TGTACAATGGGAGGCGCTTA 59.094 50.000 7.64 0.00 0.00 3.09
586 608 1.134521 TGTACAATGGGAGGCGCTTAG 60.135 52.381 7.64 0.00 0.00 2.18
587 609 1.138266 GTACAATGGGAGGCGCTTAGA 59.862 52.381 7.64 0.00 0.00 2.10
588 610 0.179000 ACAATGGGAGGCGCTTAGAG 59.821 55.000 7.64 0.00 0.00 2.43
589 611 0.465705 CAATGGGAGGCGCTTAGAGA 59.534 55.000 7.64 0.00 0.00 3.10
590 612 0.755686 AATGGGAGGCGCTTAGAGAG 59.244 55.000 7.64 0.00 0.00 3.20
591 613 0.105964 ATGGGAGGCGCTTAGAGAGA 60.106 55.000 7.64 0.00 0.00 3.10
592 614 0.105964 TGGGAGGCGCTTAGAGAGAT 60.106 55.000 7.64 0.00 0.00 2.75
593 615 0.316841 GGGAGGCGCTTAGAGAGATG 59.683 60.000 7.64 0.00 0.00 2.90
594 616 0.319469 GGAGGCGCTTAGAGAGATGC 60.319 60.000 7.64 0.00 0.00 3.91
595 617 0.673437 GAGGCGCTTAGAGAGATGCT 59.327 55.000 7.64 0.00 0.00 3.79
596 618 1.068434 GAGGCGCTTAGAGAGATGCTT 59.932 52.381 7.64 0.00 0.00 3.91
597 619 2.294791 GAGGCGCTTAGAGAGATGCTTA 59.705 50.000 7.64 0.00 0.00 3.09
598 620 2.295909 AGGCGCTTAGAGAGATGCTTAG 59.704 50.000 7.64 0.00 0.00 2.18
599 621 2.294791 GGCGCTTAGAGAGATGCTTAGA 59.705 50.000 7.64 0.00 0.00 2.10
600 622 3.243569 GGCGCTTAGAGAGATGCTTAGAA 60.244 47.826 7.64 0.00 0.00 2.10
601 623 4.363999 GCGCTTAGAGAGATGCTTAGAAA 58.636 43.478 0.00 0.00 0.00 2.52
602 624 4.806247 GCGCTTAGAGAGATGCTTAGAAAA 59.194 41.667 0.00 0.00 0.00 2.29
603 625 5.292101 GCGCTTAGAGAGATGCTTAGAAAAA 59.708 40.000 0.00 0.00 0.00 1.94
604 626 6.018343 GCGCTTAGAGAGATGCTTAGAAAAAT 60.018 38.462 0.00 0.00 0.00 1.82
605 627 7.169982 GCGCTTAGAGAGATGCTTAGAAAAATA 59.830 37.037 0.00 0.00 0.00 1.40
606 628 9.035607 CGCTTAGAGAGATGCTTAGAAAAATAA 57.964 33.333 0.00 0.00 0.00 1.40
610 632 8.202745 AGAGAGATGCTTAGAAAAATAAACCG 57.797 34.615 0.00 0.00 0.00 4.44
611 633 7.281100 AGAGAGATGCTTAGAAAAATAAACCGG 59.719 37.037 0.00 0.00 0.00 5.28
612 634 6.318900 AGAGATGCTTAGAAAAATAAACCGGG 59.681 38.462 6.32 0.00 0.00 5.73
613 635 5.949952 AGATGCTTAGAAAAATAAACCGGGT 59.050 36.000 6.32 0.00 0.00 5.28
614 636 6.436218 AGATGCTTAGAAAAATAAACCGGGTT 59.564 34.615 10.96 10.96 0.00 4.11
615 637 6.408107 TGCTTAGAAAAATAAACCGGGTTT 57.592 33.333 26.79 26.79 39.24 3.27
616 638 6.818233 TGCTTAGAAAAATAAACCGGGTTTT 58.182 32.000 28.50 11.74 37.01 2.43
617 639 7.273712 TGCTTAGAAAAATAAACCGGGTTTTT 58.726 30.769 28.50 18.85 37.01 1.94
618 640 7.438757 TGCTTAGAAAAATAAACCGGGTTTTTC 59.561 33.333 28.50 23.47 45.36 2.29
622 644 7.773864 GAAAAATAAACCGGGTTTTTCTGAA 57.226 32.000 28.50 11.38 43.37 3.02
623 645 8.199176 GAAAAATAAACCGGGTTTTTCTGAAA 57.801 30.769 28.50 10.66 43.37 2.69
624 646 7.542534 AAAATAAACCGGGTTTTTCTGAAAC 57.457 32.000 28.50 0.00 37.01 2.78
625 647 5.855740 ATAAACCGGGTTTTTCTGAAACA 57.144 34.783 28.50 9.23 37.01 2.83
626 648 3.513680 AACCGGGTTTTTCTGAAACAC 57.486 42.857 6.59 10.22 32.04 3.32
627 649 1.752498 ACCGGGTTTTTCTGAAACACC 59.248 47.619 23.80 23.80 30.05 4.16
628 650 1.268845 CCGGGTTTTTCTGAAACACCG 60.269 52.381 24.46 23.28 40.41 4.94
629 651 1.671845 CGGGTTTTTCTGAAACACCGA 59.328 47.619 24.46 0.64 41.79 4.69
630 652 2.292292 CGGGTTTTTCTGAAACACCGAT 59.708 45.455 24.46 0.00 41.79 4.18
631 653 3.638484 GGGTTTTTCTGAAACACCGATG 58.362 45.455 24.46 0.00 31.93 3.84
632 654 3.049912 GGTTTTTCTGAAACACCGATGC 58.950 45.455 19.35 1.04 32.04 3.91
633 655 3.049912 GTTTTTCTGAAACACCGATGCC 58.950 45.455 7.96 0.00 0.00 4.40
634 656 2.270352 TTTCTGAAACACCGATGCCT 57.730 45.000 0.00 0.00 0.00 4.75
635 657 3.410631 TTTCTGAAACACCGATGCCTA 57.589 42.857 0.00 0.00 0.00 3.93
636 658 3.627395 TTCTGAAACACCGATGCCTAT 57.373 42.857 0.00 0.00 0.00 2.57
637 659 3.627395 TCTGAAACACCGATGCCTATT 57.373 42.857 0.00 0.00 0.00 1.73
638 660 3.950397 TCTGAAACACCGATGCCTATTT 58.050 40.909 0.00 0.00 0.00 1.40
639 661 3.938963 TCTGAAACACCGATGCCTATTTC 59.061 43.478 0.00 0.00 0.00 2.17
640 662 3.941483 CTGAAACACCGATGCCTATTTCT 59.059 43.478 0.00 0.00 0.00 2.52
641 663 5.092554 TGAAACACCGATGCCTATTTCTA 57.907 39.130 0.00 0.00 0.00 2.10
642 664 4.873827 TGAAACACCGATGCCTATTTCTAC 59.126 41.667 0.00 0.00 0.00 2.59
643 665 4.481368 AACACCGATGCCTATTTCTACA 57.519 40.909 0.00 0.00 0.00 2.74
644 666 4.060038 ACACCGATGCCTATTTCTACAG 57.940 45.455 0.00 0.00 0.00 2.74
645 667 2.802816 CACCGATGCCTATTTCTACAGC 59.197 50.000 0.00 0.00 0.00 4.40
646 668 2.434336 ACCGATGCCTATTTCTACAGCA 59.566 45.455 0.00 0.00 37.94 4.41
647 669 3.062763 CCGATGCCTATTTCTACAGCAG 58.937 50.000 0.00 0.00 36.80 4.24
648 670 3.243873 CCGATGCCTATTTCTACAGCAGA 60.244 47.826 0.00 0.00 36.80 4.26
649 671 3.986572 CGATGCCTATTTCTACAGCAGAG 59.013 47.826 0.00 0.00 36.80 3.35
650 672 4.261783 CGATGCCTATTTCTACAGCAGAGA 60.262 45.833 0.00 0.00 36.80 3.10
651 673 4.392921 TGCCTATTTCTACAGCAGAGAC 57.607 45.455 0.00 0.00 33.83 3.36
652 674 3.181486 TGCCTATTTCTACAGCAGAGACG 60.181 47.826 0.00 0.00 33.83 4.18
653 675 3.376540 CCTATTTCTACAGCAGAGACGC 58.623 50.000 0.00 0.00 33.83 5.19
654 676 3.067461 CCTATTTCTACAGCAGAGACGCT 59.933 47.826 0.00 0.00 45.21 5.07
655 677 3.601443 ATTTCTACAGCAGAGACGCTT 57.399 42.857 0.00 0.00 41.38 4.68
656 678 4.720649 ATTTCTACAGCAGAGACGCTTA 57.279 40.909 0.00 0.00 41.38 3.09
657 679 3.766676 TTCTACAGCAGAGACGCTTAG 57.233 47.619 0.00 0.00 41.38 2.18
658 680 2.712709 TCTACAGCAGAGACGCTTAGT 58.287 47.619 0.00 0.00 41.38 2.24
659 681 3.082548 TCTACAGCAGAGACGCTTAGTT 58.917 45.455 0.00 0.00 41.38 2.24
660 682 4.259356 TCTACAGCAGAGACGCTTAGTTA 58.741 43.478 0.00 0.00 41.38 2.24
661 683 3.936372 ACAGCAGAGACGCTTAGTTAA 57.064 42.857 0.00 0.00 41.38 2.01
662 684 4.252971 ACAGCAGAGACGCTTAGTTAAA 57.747 40.909 0.00 0.00 41.38 1.52
663 685 3.988517 ACAGCAGAGACGCTTAGTTAAAC 59.011 43.478 0.00 0.00 41.38 2.01
664 686 3.059570 CAGCAGAGACGCTTAGTTAAACG 59.940 47.826 0.00 0.00 41.38 3.60
665 687 2.985139 GCAGAGACGCTTAGTTAAACGT 59.015 45.455 0.46 0.46 42.27 3.99
666 688 3.427863 GCAGAGACGCTTAGTTAAACGTT 59.572 43.478 0.00 0.00 39.16 3.99
667 689 4.084693 GCAGAGACGCTTAGTTAAACGTTT 60.085 41.667 18.90 18.90 39.16 3.60
668 690 5.117592 GCAGAGACGCTTAGTTAAACGTTTA 59.882 40.000 16.59 16.59 39.16 2.01
669 691 6.183360 GCAGAGACGCTTAGTTAAACGTTTAT 60.183 38.462 20.72 10.13 39.16 1.40
670 692 7.381839 CAGAGACGCTTAGTTAAACGTTTATC 58.618 38.462 20.72 18.96 39.16 1.75
671 693 6.529477 AGAGACGCTTAGTTAAACGTTTATCC 59.471 38.462 20.72 14.21 39.16 2.59
672 694 6.393171 AGACGCTTAGTTAAACGTTTATCCT 58.607 36.000 20.72 19.61 39.16 3.24
673 695 6.309737 AGACGCTTAGTTAAACGTTTATCCTG 59.690 38.462 20.72 13.06 39.16 3.86
674 696 5.928264 ACGCTTAGTTAAACGTTTATCCTGT 59.072 36.000 20.72 10.86 34.62 4.00
675 697 7.090173 ACGCTTAGTTAAACGTTTATCCTGTA 58.910 34.615 20.72 11.20 34.62 2.74
676 698 7.062255 ACGCTTAGTTAAACGTTTATCCTGTAC 59.938 37.037 20.72 14.37 34.62 2.90
677 699 7.062138 CGCTTAGTTAAACGTTTATCCTGTACA 59.938 37.037 20.72 1.31 0.00 2.90
678 700 8.711457 GCTTAGTTAAACGTTTATCCTGTACAA 58.289 33.333 20.72 10.01 0.00 2.41
686 708 9.667989 AAACGTTTATCCTGTACAAATAAACAC 57.332 29.630 29.93 18.29 42.16 3.32
687 709 7.809665 ACGTTTATCCTGTACAAATAAACACC 58.190 34.615 29.93 17.31 42.16 4.16
688 710 7.094677 ACGTTTATCCTGTACAAATAAACACCC 60.095 37.037 29.93 17.10 42.16 4.61
689 711 7.094720 CGTTTATCCTGTACAAATAAACACCCA 60.095 37.037 29.93 10.89 42.16 4.51
690 712 8.745590 GTTTATCCTGTACAAATAAACACCCAT 58.254 33.333 28.22 4.43 41.88 4.00
691 713 6.773976 ATCCTGTACAAATAAACACCCATG 57.226 37.500 0.00 0.00 0.00 3.66
692 714 5.636123 TCCTGTACAAATAAACACCCATGT 58.364 37.500 0.00 0.00 42.46 3.21
703 725 3.636282 ACACCCATGTTTAAGAAACGC 57.364 42.857 0.00 0.00 44.28 4.84
704 726 2.952978 ACACCCATGTTTAAGAAACGCA 59.047 40.909 0.00 0.00 44.28 5.24
705 727 3.243267 ACACCCATGTTTAAGAAACGCAC 60.243 43.478 0.00 0.00 44.28 5.34
706 728 2.952978 ACCCATGTTTAAGAAACGCACA 59.047 40.909 0.00 0.00 44.28 4.57
707 729 3.004315 ACCCATGTTTAAGAAACGCACAG 59.996 43.478 0.00 0.00 44.28 3.66
708 730 3.004315 CCCATGTTTAAGAAACGCACAGT 59.996 43.478 0.00 0.00 44.28 3.55
709 731 4.499019 CCCATGTTTAAGAAACGCACAGTT 60.499 41.667 0.00 0.00 46.76 3.16
722 744 5.532025 ACGCACAGTTTATTTCTCTAAGC 57.468 39.130 0.00 0.00 0.00 3.09
723 745 4.994852 ACGCACAGTTTATTTCTCTAAGCA 59.005 37.500 0.00 0.00 0.00 3.91
724 746 5.643777 ACGCACAGTTTATTTCTCTAAGCAT 59.356 36.000 0.00 0.00 0.00 3.79
725 747 6.149474 ACGCACAGTTTATTTCTCTAAGCATT 59.851 34.615 0.00 0.00 0.00 3.56
726 748 7.023575 CGCACAGTTTATTTCTCTAAGCATTT 58.976 34.615 0.00 0.00 0.00 2.32
727 749 7.538678 CGCACAGTTTATTTCTCTAAGCATTTT 59.461 33.333 0.00 0.00 0.00 1.82
728 750 8.854312 GCACAGTTTATTTCTCTAAGCATTTTC 58.146 33.333 0.00 0.00 0.00 2.29
729 751 9.346725 CACAGTTTATTTCTCTAAGCATTTTCC 57.653 33.333 0.00 0.00 0.00 3.13
730 752 8.523658 ACAGTTTATTTCTCTAAGCATTTTCCC 58.476 33.333 0.00 0.00 0.00 3.97
731 753 8.743714 CAGTTTATTTCTCTAAGCATTTTCCCT 58.256 33.333 0.00 0.00 0.00 4.20
732 754 9.975218 AGTTTATTTCTCTAAGCATTTTCCCTA 57.025 29.630 0.00 0.00 0.00 3.53
735 757 6.759497 TTTCTCTAAGCATTTTCCCTAAGC 57.241 37.500 0.00 0.00 0.00 3.09
736 758 5.435686 TCTCTAAGCATTTTCCCTAAGCA 57.564 39.130 0.00 0.00 0.00 3.91
737 759 6.006275 TCTCTAAGCATTTTCCCTAAGCAT 57.994 37.500 0.00 0.00 0.00 3.79
738 760 6.058183 TCTCTAAGCATTTTCCCTAAGCATC 58.942 40.000 0.00 0.00 0.00 3.91
739 761 6.006275 TCTAAGCATTTTCCCTAAGCATCT 57.994 37.500 0.00 0.00 0.00 2.90
740 762 6.058183 TCTAAGCATTTTCCCTAAGCATCTC 58.942 40.000 0.00 0.00 0.00 2.75
741 763 4.516652 AGCATTTTCCCTAAGCATCTCT 57.483 40.909 0.00 0.00 0.00 3.10
742 764 4.459330 AGCATTTTCCCTAAGCATCTCTC 58.541 43.478 0.00 0.00 0.00 3.20
743 765 4.080129 AGCATTTTCCCTAAGCATCTCTCA 60.080 41.667 0.00 0.00 0.00 3.27
744 766 4.826183 GCATTTTCCCTAAGCATCTCTCAT 59.174 41.667 0.00 0.00 0.00 2.90
745 767 5.301298 GCATTTTCCCTAAGCATCTCTCATT 59.699 40.000 0.00 0.00 0.00 2.57
746 768 6.735145 GCATTTTCCCTAAGCATCTCTCATTG 60.735 42.308 0.00 0.00 0.00 2.82
747 769 5.441718 TTTCCCTAAGCATCTCTCATTGT 57.558 39.130 0.00 0.00 0.00 2.71
748 770 6.560003 TTTCCCTAAGCATCTCTCATTGTA 57.440 37.500 0.00 0.00 0.00 2.41
749 771 5.537300 TCCCTAAGCATCTCTCATTGTAC 57.463 43.478 0.00 0.00 0.00 2.90
750 772 4.962362 TCCCTAAGCATCTCTCATTGTACA 59.038 41.667 0.00 0.00 0.00 2.90
751 773 5.425217 TCCCTAAGCATCTCTCATTGTACAA 59.575 40.000 11.41 11.41 0.00 2.41
752 774 5.757320 CCCTAAGCATCTCTCATTGTACAAG 59.243 44.000 14.65 6.58 0.00 3.16
753 775 5.757320 CCTAAGCATCTCTCATTGTACAAGG 59.243 44.000 13.96 13.96 0.00 3.61
754 776 5.426689 AAGCATCTCTCATTGTACAAGGA 57.573 39.130 20.70 20.70 0.00 3.36
755 777 4.764172 AGCATCTCTCATTGTACAAGGAC 58.236 43.478 18.42 8.30 0.00 3.85
756 778 4.469227 AGCATCTCTCATTGTACAAGGACT 59.531 41.667 18.42 10.36 0.00 3.85
757 779 5.046014 AGCATCTCTCATTGTACAAGGACTT 60.046 40.000 18.42 1.91 0.00 3.01
758 780 6.155221 AGCATCTCTCATTGTACAAGGACTTA 59.845 38.462 18.42 7.37 0.00 2.24
759 781 6.478344 GCATCTCTCATTGTACAAGGACTTAG 59.522 42.308 18.42 15.04 0.00 2.18
760 782 7.551585 CATCTCTCATTGTACAAGGACTTAGT 58.448 38.462 18.42 2.38 0.00 2.24
761 783 6.925211 TCTCTCATTGTACAAGGACTTAGTG 58.075 40.000 18.42 8.48 0.00 2.74
762 784 6.493802 TCTCTCATTGTACAAGGACTTAGTGT 59.506 38.462 18.42 0.00 0.00 3.55
763 785 6.455647 TCTCATTGTACAAGGACTTAGTGTG 58.544 40.000 18.42 7.13 0.00 3.82
764 786 4.994852 TCATTGTACAAGGACTTAGTGTGC 59.005 41.667 18.42 0.00 37.27 4.57
765 787 3.396260 TGTACAAGGACTTAGTGTGCC 57.604 47.619 0.00 0.00 37.77 5.01
766 788 2.969950 TGTACAAGGACTTAGTGTGCCT 59.030 45.455 0.00 0.00 37.77 4.75
767 789 4.154176 TGTACAAGGACTTAGTGTGCCTA 58.846 43.478 0.00 0.00 37.77 3.93
768 790 4.775780 TGTACAAGGACTTAGTGTGCCTAT 59.224 41.667 0.00 0.00 37.77 2.57
769 791 4.207891 ACAAGGACTTAGTGTGCCTATG 57.792 45.455 0.00 0.00 37.77 2.23
770 792 2.939103 CAAGGACTTAGTGTGCCTATGC 59.061 50.000 0.00 0.00 37.77 3.14
771 793 1.137086 AGGACTTAGTGTGCCTATGCG 59.863 52.381 0.00 0.00 41.78 4.73
778 800 4.715983 GTGCCTATGCGCCATTTG 57.284 55.556 4.18 0.00 42.25 2.32
779 801 2.105984 GTGCCTATGCGCCATTTGA 58.894 52.632 4.18 0.00 42.25 2.69
780 802 0.670162 GTGCCTATGCGCCATTTGAT 59.330 50.000 4.18 0.00 42.25 2.57
781 803 0.669619 TGCCTATGCGCCATTTGATG 59.330 50.000 4.18 0.00 41.78 3.07
782 804 0.665369 GCCTATGCGCCATTTGATGC 60.665 55.000 4.18 0.00 0.00 3.91
783 805 0.669619 CCTATGCGCCATTTGATGCA 59.330 50.000 4.18 0.00 42.22 3.96
784 806 1.067364 CCTATGCGCCATTTGATGCAA 59.933 47.619 4.18 0.00 41.22 4.08
785 807 2.121786 CTATGCGCCATTTGATGCAAC 58.878 47.619 4.18 0.00 41.22 4.17
786 808 0.802994 ATGCGCCATTTGATGCAACG 60.803 50.000 4.18 0.00 41.22 4.10
787 809 2.160221 GCGCCATTTGATGCAACGG 61.160 57.895 0.00 0.00 0.00 4.44
788 810 1.516821 CGCCATTTGATGCAACGGG 60.517 57.895 0.00 0.00 0.00 5.28
789 811 1.591183 GCCATTTGATGCAACGGGT 59.409 52.632 0.00 0.00 0.00 5.28
790 812 0.458370 GCCATTTGATGCAACGGGTC 60.458 55.000 0.00 0.00 0.00 4.46
791 813 0.173255 CCATTTGATGCAACGGGTCC 59.827 55.000 0.00 0.00 0.00 4.46
792 814 0.887247 CATTTGATGCAACGGGTCCA 59.113 50.000 0.00 0.00 0.00 4.02
793 815 0.887933 ATTTGATGCAACGGGTCCAC 59.112 50.000 0.00 0.00 0.00 4.02
794 816 0.179004 TTTGATGCAACGGGTCCACT 60.179 50.000 0.00 0.00 0.00 4.00
795 817 0.687920 TTGATGCAACGGGTCCACTA 59.312 50.000 0.00 0.00 0.00 2.74
796 818 0.249120 TGATGCAACGGGTCCACTAG 59.751 55.000 0.00 0.00 0.00 2.57
1227 1252 3.340789 GGCGACCCTGTTGTTGTC 58.659 61.111 0.00 0.00 0.00 3.18
1447 1472 1.167781 GGAAACCGTCGCCCAAGAAA 61.168 55.000 0.00 0.00 0.00 2.52
1548 1582 1.449601 CGTGGTTGCCTCGCCTTAT 60.450 57.895 0.00 0.00 33.90 1.73
1595 1629 2.217393 GCGTTGATCTATTCGCAGTCAG 59.783 50.000 15.14 0.00 46.40 3.51
1667 1701 1.980772 CTGCCCCCAAGAAAGCTGG 60.981 63.158 0.00 0.00 0.00 4.85
1673 1707 1.075482 CCAAGAAAGCTGGGCCAGA 59.925 57.895 37.07 0.00 32.44 3.86
1712 1746 1.077068 TTCCATTGGGATCCACGGC 60.077 57.895 15.23 0.00 44.48 5.68
1874 1908 6.045072 TCAGTACTTACCACCCTTATGTTG 57.955 41.667 0.00 0.00 0.00 3.33
1911 1945 7.170658 GTGAGATAGCTGGATAATTGAGTGAAC 59.829 40.741 0.00 0.00 0.00 3.18
1935 1969 2.603075 TGCAGATTAAGGCAAAGGGT 57.397 45.000 0.00 0.00 37.03 4.34
2165 2199 6.633500 TCTGAAGGTTGATGTTTAAACTGG 57.367 37.500 18.72 0.00 0.00 4.00
2260 2294 0.179000 AGCTGGTTGATAAGGCTCGG 59.821 55.000 0.00 0.00 0.00 4.63
2530 2604 4.759516 ATGTTTACGGCTAACAAACCTG 57.240 40.909 3.87 0.00 38.82 4.00
2746 2820 5.554070 TCTCACACACACATTGATTGAGAT 58.446 37.500 0.00 0.00 39.60 2.75
2972 3046 2.159170 GCTATGATCTATCCACGGAGCC 60.159 54.545 0.00 0.00 0.00 4.70
3013 3087 9.561069 CCTTGGTATATGCTTGTATAGAGTTTT 57.439 33.333 0.00 0.00 0.00 2.43
3072 3148 6.664428 ATTTAGTTTGCATGTACAGGGTTT 57.336 33.333 9.91 0.00 0.00 3.27
3139 3215 6.490040 AGAAACCAGAGCTTGCAAACTAATTA 59.510 34.615 1.52 0.00 0.00 1.40
3147 3223 6.466812 AGCTTGCAAACTAATTAGGCATTTT 58.533 32.000 16.73 5.37 34.03 1.82
3193 3269 8.998377 TCGAAACATAAGATTCAGTTCAAATCA 58.002 29.630 0.00 0.00 35.92 2.57
3254 3332 8.980596 ACTGAAGAGATCTGACTGAATTTCTAT 58.019 33.333 0.00 0.00 0.00 1.98
3352 3432 8.313944 TGGTACTTCATGGCTAAAGTATCTTA 57.686 34.615 13.48 0.00 39.03 2.10
3386 3466 6.941857 TGAGCAGTCACATATAAACTTACCA 58.058 36.000 0.00 0.00 0.00 3.25
3423 3506 6.487299 ACCTATGACCATCTCCTTTACTTC 57.513 41.667 0.00 0.00 0.00 3.01
3484 3567 2.823747 TCCAACTGTACGTGTATGCTCT 59.176 45.455 0.00 0.00 0.00 4.09
3602 3685 5.308825 CACCTGGAACTGTAAGATGAACTT 58.691 41.667 0.00 0.00 42.04 2.66
3624 3708 5.930837 TTCCATGTTTCCACTTCTGTTTT 57.069 34.783 0.00 0.00 0.00 2.43
3640 3724 6.312399 TCTGTTTTCATTTAATGCACGACT 57.688 33.333 0.00 0.00 0.00 4.18
3656 3740 3.937079 CACGACTCCCCTTTGGTAATAAC 59.063 47.826 0.00 0.00 34.77 1.89
3900 3984 6.151817 GGGTTATTTATGGATCTGATCTTGCC 59.848 42.308 16.61 2.13 0.00 4.52
4057 4142 7.934665 TGTGAATTAGTTACTTAAGTTGCCAGA 59.065 33.333 14.49 0.00 0.00 3.86
4106 4191 4.156477 CCTTCTCCCCATTGGTTTGTTTA 58.844 43.478 1.20 0.00 34.77 2.01
4107 4192 4.021456 CCTTCTCCCCATTGGTTTGTTTAC 60.021 45.833 1.20 0.00 34.77 2.01
4229 4314 0.254178 GGATCATGTCACTGCCACCT 59.746 55.000 0.00 0.00 0.00 4.00
4353 4438 3.713248 ACCTGAGCATATCAATCTCACCA 59.287 43.478 0.00 0.00 37.52 4.17
4366 4451 5.241506 TCAATCTCACCAAAAAGATGTGACC 59.758 40.000 0.00 0.00 35.34 4.02
4409 4494 0.681564 TGGTCGGGTTGTTGCACTTT 60.682 50.000 0.00 0.00 0.00 2.66
4432 4517 1.047801 GGGTGCCAAGGTGAAATTGT 58.952 50.000 0.00 0.00 0.00 2.71
4448 4533 9.617975 GGTGAAATTGTTTAAGAAGAATCAGAG 57.382 33.333 0.00 0.00 29.36 3.35
4529 4614 1.614317 CCATGAGTTCTCCCAACCACC 60.614 57.143 0.00 0.00 0.00 4.61
4548 4633 2.031870 CCCTCATCACACCATAGTCGA 58.968 52.381 0.00 0.00 0.00 4.20
4819 4906 1.308216 ATAGCCTGGTGGGAAGCCT 60.308 57.895 0.00 0.00 37.23 4.58
4834 4921 1.962822 GCCTTTGCCTGCAAAAGCC 60.963 57.895 21.75 9.13 43.60 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 2.758327 TATGGAGTCCCTGCGCGT 60.758 61.111 8.43 0.00 0.00 6.01
50 51 1.296715 GCTCCTTCGCCTTCTCCAA 59.703 57.895 0.00 0.00 0.00 3.53
137 144 2.000323 CGTCGTCGTCGTCGTTGTT 61.000 57.895 12.51 0.00 41.73 2.83
360 375 6.077838 GGCTAAACACGACTAAATTTCAGTG 58.922 40.000 0.00 4.04 35.89 3.66
363 378 4.989797 TCGGCTAAACACGACTAAATTTCA 59.010 37.500 0.00 0.00 33.69 2.69
372 387 1.123756 CGAAGTTCGGCTAAACACGAC 59.876 52.381 17.61 0.00 39.04 4.34
460 476 2.348888 CGAGTTGGTCCCTAGCCGT 61.349 63.158 0.00 0.00 0.00 5.68
466 482 3.322466 CTGGGCGAGTTGGTCCCT 61.322 66.667 0.00 0.00 40.69 4.20
562 584 2.493547 GCCTCCCATTGTACAAGGC 58.506 57.895 17.46 17.46 45.11 4.35
563 585 1.376609 GCGCCTCCCATTGTACAAGG 61.377 60.000 14.65 13.92 0.00 3.61
564 586 0.392998 AGCGCCTCCCATTGTACAAG 60.393 55.000 14.65 6.30 0.00 3.16
565 587 0.037590 AAGCGCCTCCCATTGTACAA 59.962 50.000 11.41 11.41 0.00 2.41
566 588 0.906066 TAAGCGCCTCCCATTGTACA 59.094 50.000 2.29 0.00 0.00 2.90
567 589 1.138266 TCTAAGCGCCTCCCATTGTAC 59.862 52.381 2.29 0.00 0.00 2.90
568 590 1.412710 CTCTAAGCGCCTCCCATTGTA 59.587 52.381 2.29 0.00 0.00 2.41
569 591 0.179000 CTCTAAGCGCCTCCCATTGT 59.821 55.000 2.29 0.00 0.00 2.71
570 592 0.465705 TCTCTAAGCGCCTCCCATTG 59.534 55.000 2.29 0.00 0.00 2.82
571 593 0.755686 CTCTCTAAGCGCCTCCCATT 59.244 55.000 2.29 0.00 0.00 3.16
572 594 0.105964 TCTCTCTAAGCGCCTCCCAT 60.106 55.000 2.29 0.00 0.00 4.00
573 595 0.105964 ATCTCTCTAAGCGCCTCCCA 60.106 55.000 2.29 0.00 0.00 4.37
574 596 0.316841 CATCTCTCTAAGCGCCTCCC 59.683 60.000 2.29 0.00 0.00 4.30
575 597 0.319469 GCATCTCTCTAAGCGCCTCC 60.319 60.000 2.29 0.00 0.00 4.30
576 598 0.673437 AGCATCTCTCTAAGCGCCTC 59.327 55.000 2.29 0.00 0.00 4.70
577 599 1.118838 AAGCATCTCTCTAAGCGCCT 58.881 50.000 2.29 0.00 0.00 5.52
578 600 2.294791 TCTAAGCATCTCTCTAAGCGCC 59.705 50.000 2.29 0.00 0.00 6.53
579 601 3.634568 TCTAAGCATCTCTCTAAGCGC 57.365 47.619 0.00 0.00 0.00 5.92
580 602 6.893958 TTTTTCTAAGCATCTCTCTAAGCG 57.106 37.500 0.00 0.00 0.00 4.68
584 606 9.314321 CGGTTTATTTTTCTAAGCATCTCTCTA 57.686 33.333 0.00 0.00 0.00 2.43
585 607 7.281100 CCGGTTTATTTTTCTAAGCATCTCTCT 59.719 37.037 0.00 0.00 0.00 3.10
586 608 7.410485 CCGGTTTATTTTTCTAAGCATCTCTC 58.590 38.462 0.00 0.00 0.00 3.20
587 609 6.318900 CCCGGTTTATTTTTCTAAGCATCTCT 59.681 38.462 0.00 0.00 0.00 3.10
588 610 6.095021 ACCCGGTTTATTTTTCTAAGCATCTC 59.905 38.462 0.00 0.00 0.00 2.75
589 611 5.949952 ACCCGGTTTATTTTTCTAAGCATCT 59.050 36.000 0.00 0.00 0.00 2.90
590 612 6.203808 ACCCGGTTTATTTTTCTAAGCATC 57.796 37.500 0.00 0.00 0.00 3.91
591 613 6.599356 AACCCGGTTTATTTTTCTAAGCAT 57.401 33.333 0.00 0.00 0.00 3.79
592 614 6.408107 AAACCCGGTTTATTTTTCTAAGCA 57.592 33.333 14.16 0.00 33.70 3.91
593 615 7.718272 AAAAACCCGGTTTATTTTTCTAAGC 57.282 32.000 16.03 0.00 34.43 3.09
598 620 7.773864 TTCAGAAAAACCCGGTTTATTTTTC 57.226 32.000 22.79 22.79 45.95 2.29
599 621 7.606839 TGTTTCAGAAAAACCCGGTTTATTTTT 59.393 29.630 16.03 6.68 38.03 1.94
600 622 7.064847 GTGTTTCAGAAAAACCCGGTTTATTTT 59.935 33.333 16.03 7.04 34.43 1.82
601 623 6.535865 GTGTTTCAGAAAAACCCGGTTTATTT 59.464 34.615 16.03 7.76 34.43 1.40
602 624 6.044046 GTGTTTCAGAAAAACCCGGTTTATT 58.956 36.000 16.03 11.90 34.43 1.40
603 625 5.452216 GGTGTTTCAGAAAAACCCGGTTTAT 60.452 40.000 21.18 3.02 34.43 1.40
604 626 4.142204 GGTGTTTCAGAAAAACCCGGTTTA 60.142 41.667 21.18 0.00 34.43 2.01
605 627 3.368635 GGTGTTTCAGAAAAACCCGGTTT 60.369 43.478 21.18 9.92 37.34 3.27
606 628 2.166870 GGTGTTTCAGAAAAACCCGGTT 59.833 45.455 21.18 0.00 0.00 4.44
607 629 1.752498 GGTGTTTCAGAAAAACCCGGT 59.248 47.619 21.18 0.00 0.00 5.28
608 630 1.268845 CGGTGTTTCAGAAAAACCCGG 60.269 52.381 24.44 11.47 38.79 5.73
609 631 1.671845 TCGGTGTTTCAGAAAAACCCG 59.328 47.619 24.44 20.53 41.22 5.28
610 632 3.638484 CATCGGTGTTTCAGAAAAACCC 58.362 45.455 24.44 11.67 0.00 4.11
611 633 3.049912 GCATCGGTGTTTCAGAAAAACC 58.950 45.455 21.70 21.70 0.00 3.27
612 634 3.049912 GGCATCGGTGTTTCAGAAAAAC 58.950 45.455 7.61 7.61 0.00 2.43
613 635 2.955660 AGGCATCGGTGTTTCAGAAAAA 59.044 40.909 0.00 0.00 0.00 1.94
614 636 2.582052 AGGCATCGGTGTTTCAGAAAA 58.418 42.857 0.00 0.00 0.00 2.29
615 637 2.270352 AGGCATCGGTGTTTCAGAAA 57.730 45.000 0.00 0.00 0.00 2.52
616 638 3.627395 ATAGGCATCGGTGTTTCAGAA 57.373 42.857 0.00 0.00 0.00 3.02
617 639 3.627395 AATAGGCATCGGTGTTTCAGA 57.373 42.857 0.00 0.00 0.00 3.27
618 640 3.941483 AGAAATAGGCATCGGTGTTTCAG 59.059 43.478 10.88 0.00 0.00 3.02
619 641 3.950397 AGAAATAGGCATCGGTGTTTCA 58.050 40.909 10.88 0.00 0.00 2.69
620 642 4.873827 TGTAGAAATAGGCATCGGTGTTTC 59.126 41.667 0.00 0.00 0.00 2.78
621 643 4.839121 TGTAGAAATAGGCATCGGTGTTT 58.161 39.130 0.00 0.00 0.00 2.83
622 644 4.442706 CTGTAGAAATAGGCATCGGTGTT 58.557 43.478 0.00 0.00 0.00 3.32
623 645 3.741388 GCTGTAGAAATAGGCATCGGTGT 60.741 47.826 0.00 0.00 0.00 4.16
624 646 2.802816 GCTGTAGAAATAGGCATCGGTG 59.197 50.000 0.00 0.00 0.00 4.94
625 647 2.434336 TGCTGTAGAAATAGGCATCGGT 59.566 45.455 0.00 0.00 0.00 4.69
626 648 3.062763 CTGCTGTAGAAATAGGCATCGG 58.937 50.000 0.00 0.00 32.39 4.18
627 649 3.982475 TCTGCTGTAGAAATAGGCATCG 58.018 45.455 0.00 0.00 30.84 3.84
628 650 4.987912 GTCTCTGCTGTAGAAATAGGCATC 59.012 45.833 0.00 0.00 34.32 3.91
629 651 4.500545 CGTCTCTGCTGTAGAAATAGGCAT 60.501 45.833 0.00 0.00 34.32 4.40
630 652 3.181486 CGTCTCTGCTGTAGAAATAGGCA 60.181 47.826 0.00 0.00 34.32 4.75
631 653 3.376540 CGTCTCTGCTGTAGAAATAGGC 58.623 50.000 0.00 0.00 34.32 3.93
632 654 3.067461 AGCGTCTCTGCTGTAGAAATAGG 59.933 47.826 0.00 0.00 45.28 2.57
633 655 4.300189 AGCGTCTCTGCTGTAGAAATAG 57.700 45.455 0.00 0.00 45.28 1.73
634 656 4.720649 AAGCGTCTCTGCTGTAGAAATA 57.279 40.909 0.00 0.00 46.60 1.40
635 657 3.601443 AAGCGTCTCTGCTGTAGAAAT 57.399 42.857 0.00 0.00 46.60 2.17
636 658 3.506455 ACTAAGCGTCTCTGCTGTAGAAA 59.494 43.478 0.00 0.00 46.60 2.52
637 659 3.082548 ACTAAGCGTCTCTGCTGTAGAA 58.917 45.455 0.00 0.00 46.60 2.10
638 660 2.712709 ACTAAGCGTCTCTGCTGTAGA 58.287 47.619 0.00 0.00 46.60 2.59
639 661 3.495670 AACTAAGCGTCTCTGCTGTAG 57.504 47.619 0.00 0.00 46.60 2.74
640 662 5.159209 GTTTAACTAAGCGTCTCTGCTGTA 58.841 41.667 0.00 0.00 46.60 2.74
641 663 3.936372 TTAACTAAGCGTCTCTGCTGT 57.064 42.857 0.00 0.00 46.60 4.40
642 664 3.059570 CGTTTAACTAAGCGTCTCTGCTG 59.940 47.826 0.00 0.00 46.60 4.41
644 666 3.619751 CGTTTAACTAAGCGTCTCTGC 57.380 47.619 0.00 0.00 35.60 4.26
651 673 6.399204 ACAGGATAAACGTTTAACTAAGCG 57.601 37.500 23.49 14.28 43.91 4.68
652 674 8.243289 TGTACAGGATAAACGTTTAACTAAGC 57.757 34.615 23.49 15.76 0.00 3.09
660 682 9.667989 GTGTTTATTTGTACAGGATAAACGTTT 57.332 29.630 28.71 18.90 43.81 3.60
661 683 8.291740 GGTGTTTATTTGTACAGGATAAACGTT 58.708 33.333 28.71 0.00 43.81 3.99
662 684 7.094677 GGGTGTTTATTTGTACAGGATAAACGT 60.095 37.037 28.71 0.00 43.81 3.99
663 685 7.094720 TGGGTGTTTATTTGTACAGGATAAACG 60.095 37.037 28.71 0.00 43.81 3.60
664 686 8.113173 TGGGTGTTTATTTGTACAGGATAAAC 57.887 34.615 28.45 28.45 42.40 2.01
665 687 8.744652 CATGGGTGTTTATTTGTACAGGATAAA 58.255 33.333 16.38 16.38 0.00 1.40
666 688 7.891183 ACATGGGTGTTTATTTGTACAGGATAA 59.109 33.333 0.00 2.92 34.01 1.75
667 689 7.406916 ACATGGGTGTTTATTTGTACAGGATA 58.593 34.615 0.00 0.00 34.01 2.59
668 690 6.252995 ACATGGGTGTTTATTTGTACAGGAT 58.747 36.000 0.00 0.00 34.01 3.24
669 691 5.636123 ACATGGGTGTTTATTTGTACAGGA 58.364 37.500 0.00 0.00 34.01 3.86
670 692 5.975693 ACATGGGTGTTTATTTGTACAGG 57.024 39.130 0.00 0.00 34.01 4.00
683 705 2.952978 TGCGTTTCTTAAACATGGGTGT 59.047 40.909 0.00 0.00 41.44 4.16
684 706 3.243234 TGTGCGTTTCTTAAACATGGGTG 60.243 43.478 0.00 0.00 41.44 4.61
685 707 2.952978 TGTGCGTTTCTTAAACATGGGT 59.047 40.909 0.00 0.00 41.44 4.51
686 708 3.004315 ACTGTGCGTTTCTTAAACATGGG 59.996 43.478 0.00 0.00 41.44 4.00
687 709 4.223320 ACTGTGCGTTTCTTAAACATGG 57.777 40.909 0.00 0.00 41.44 3.66
688 710 7.851822 ATAAACTGTGCGTTTCTTAAACATG 57.148 32.000 3.68 0.00 44.39 3.21
689 711 8.865590 AAATAAACTGTGCGTTTCTTAAACAT 57.134 26.923 3.68 0.00 44.39 2.71
690 712 8.185505 AGAAATAAACTGTGCGTTTCTTAAACA 58.814 29.630 3.68 0.00 44.39 2.83
691 713 8.556517 AGAAATAAACTGTGCGTTTCTTAAAC 57.443 30.769 8.06 0.00 44.39 2.01
692 714 8.617809 AGAGAAATAAACTGTGCGTTTCTTAAA 58.382 29.630 12.66 0.00 44.39 1.52
693 715 8.149973 AGAGAAATAAACTGTGCGTTTCTTAA 57.850 30.769 12.66 0.00 44.39 1.85
694 716 7.724305 AGAGAAATAAACTGTGCGTTTCTTA 57.276 32.000 12.66 0.00 44.39 2.10
695 717 6.619801 AGAGAAATAAACTGTGCGTTTCTT 57.380 33.333 12.66 0.00 44.39 2.52
696 718 7.571428 GCTTAGAGAAATAAACTGTGCGTTTCT 60.571 37.037 11.77 11.77 44.39 2.52
697 719 6.520104 GCTTAGAGAAATAAACTGTGCGTTTC 59.480 38.462 0.00 4.74 44.39 2.78
698 720 6.017440 TGCTTAGAGAAATAAACTGTGCGTTT 60.017 34.615 0.00 0.00 46.94 3.60
699 721 5.468746 TGCTTAGAGAAATAAACTGTGCGTT 59.531 36.000 0.00 0.00 37.47 4.84
700 722 4.994852 TGCTTAGAGAAATAAACTGTGCGT 59.005 37.500 0.00 0.00 0.00 5.24
701 723 5.530519 TGCTTAGAGAAATAAACTGTGCG 57.469 39.130 0.00 0.00 0.00 5.34
702 724 8.748380 AAAATGCTTAGAGAAATAAACTGTGC 57.252 30.769 0.00 0.00 0.00 4.57
703 725 9.346725 GGAAAATGCTTAGAGAAATAAACTGTG 57.653 33.333 0.00 0.00 0.00 3.66
704 726 8.523658 GGGAAAATGCTTAGAGAAATAAACTGT 58.476 33.333 0.00 0.00 0.00 3.55
705 727 8.743714 AGGGAAAATGCTTAGAGAAATAAACTG 58.256 33.333 0.00 0.00 0.00 3.16
706 728 8.885693 AGGGAAAATGCTTAGAGAAATAAACT 57.114 30.769 0.00 0.00 0.00 2.66
709 731 8.903820 GCTTAGGGAAAATGCTTAGAGAAATAA 58.096 33.333 0.00 0.00 0.00 1.40
710 732 8.052748 TGCTTAGGGAAAATGCTTAGAGAAATA 58.947 33.333 0.00 0.00 0.00 1.40
711 733 6.891908 TGCTTAGGGAAAATGCTTAGAGAAAT 59.108 34.615 0.00 0.00 0.00 2.17
712 734 6.245408 TGCTTAGGGAAAATGCTTAGAGAAA 58.755 36.000 0.00 0.00 0.00 2.52
713 735 5.815581 TGCTTAGGGAAAATGCTTAGAGAA 58.184 37.500 0.00 0.00 0.00 2.87
714 736 5.435686 TGCTTAGGGAAAATGCTTAGAGA 57.564 39.130 0.00 0.00 0.00 3.10
715 737 6.060788 AGATGCTTAGGGAAAATGCTTAGAG 58.939 40.000 0.00 0.00 0.00 2.43
716 738 6.006275 AGATGCTTAGGGAAAATGCTTAGA 57.994 37.500 0.00 0.00 0.00 2.10
717 739 6.060788 AGAGATGCTTAGGGAAAATGCTTAG 58.939 40.000 0.00 0.00 0.00 2.18
718 740 6.006275 AGAGATGCTTAGGGAAAATGCTTA 57.994 37.500 0.00 0.00 0.00 3.09
719 741 4.864726 AGAGATGCTTAGGGAAAATGCTT 58.135 39.130 0.00 0.00 0.00 3.91
720 742 4.080129 TGAGAGATGCTTAGGGAAAATGCT 60.080 41.667 0.00 0.00 0.00 3.79
721 743 4.202441 TGAGAGATGCTTAGGGAAAATGC 58.798 43.478 0.00 0.00 0.00 3.56
722 744 6.320672 ACAATGAGAGATGCTTAGGGAAAATG 59.679 38.462 0.00 0.00 0.00 2.32
723 745 6.430007 ACAATGAGAGATGCTTAGGGAAAAT 58.570 36.000 0.00 0.00 0.00 1.82
724 746 5.819991 ACAATGAGAGATGCTTAGGGAAAA 58.180 37.500 0.00 0.00 0.00 2.29
725 747 5.441718 ACAATGAGAGATGCTTAGGGAAA 57.558 39.130 0.00 0.00 0.00 3.13
726 748 5.425217 TGTACAATGAGAGATGCTTAGGGAA 59.575 40.000 0.00 0.00 0.00 3.97
727 749 4.962362 TGTACAATGAGAGATGCTTAGGGA 59.038 41.667 0.00 0.00 0.00 4.20
728 750 5.282055 TGTACAATGAGAGATGCTTAGGG 57.718 43.478 0.00 0.00 0.00 3.53
729 751 5.757320 CCTTGTACAATGAGAGATGCTTAGG 59.243 44.000 9.13 0.00 0.00 2.69
730 752 6.478344 GTCCTTGTACAATGAGAGATGCTTAG 59.522 42.308 13.13 0.00 0.00 2.18
731 753 6.155221 AGTCCTTGTACAATGAGAGATGCTTA 59.845 38.462 13.13 0.00 0.00 3.09
732 754 5.046014 AGTCCTTGTACAATGAGAGATGCTT 60.046 40.000 13.13 0.00 0.00 3.91
733 755 4.469227 AGTCCTTGTACAATGAGAGATGCT 59.531 41.667 13.13 4.22 0.00 3.79
734 756 4.764172 AGTCCTTGTACAATGAGAGATGC 58.236 43.478 13.13 2.17 0.00 3.91
735 757 7.490725 CACTAAGTCCTTGTACAATGAGAGATG 59.509 40.741 13.13 5.97 0.00 2.90
736 758 7.179338 ACACTAAGTCCTTGTACAATGAGAGAT 59.821 37.037 13.13 4.10 0.00 2.75
737 759 6.493802 ACACTAAGTCCTTGTACAATGAGAGA 59.506 38.462 13.13 1.92 0.00 3.10
738 760 6.587990 CACACTAAGTCCTTGTACAATGAGAG 59.412 42.308 13.13 12.56 0.00 3.20
739 761 6.455647 CACACTAAGTCCTTGTACAATGAGA 58.544 40.000 13.13 6.45 0.00 3.27
740 762 5.120830 GCACACTAAGTCCTTGTACAATGAG 59.879 44.000 13.13 2.24 0.00 2.90
741 763 4.994852 GCACACTAAGTCCTTGTACAATGA 59.005 41.667 9.13 9.19 0.00 2.57
742 764 4.154195 GGCACACTAAGTCCTTGTACAATG 59.846 45.833 9.13 6.65 0.00 2.82
743 765 4.041691 AGGCACACTAAGTCCTTGTACAAT 59.958 41.667 9.13 0.00 0.00 2.71
744 766 3.389983 AGGCACACTAAGTCCTTGTACAA 59.610 43.478 8.28 8.28 0.00 2.41
745 767 2.969950 AGGCACACTAAGTCCTTGTACA 59.030 45.455 0.00 0.00 0.00 2.90
746 768 3.679824 AGGCACACTAAGTCCTTGTAC 57.320 47.619 0.00 0.00 0.00 2.90
747 769 4.382685 GCATAGGCACACTAAGTCCTTGTA 60.383 45.833 0.00 0.00 40.72 2.41
748 770 3.619979 GCATAGGCACACTAAGTCCTTGT 60.620 47.826 0.00 0.00 40.72 3.16
749 771 2.939103 GCATAGGCACACTAAGTCCTTG 59.061 50.000 0.00 0.00 40.72 3.61
750 772 2.418746 CGCATAGGCACACTAAGTCCTT 60.419 50.000 0.00 0.00 41.24 3.36
751 773 1.137086 CGCATAGGCACACTAAGTCCT 59.863 52.381 0.00 0.00 41.24 3.85
752 774 1.571919 CGCATAGGCACACTAAGTCC 58.428 55.000 0.00 0.00 41.24 3.85
753 775 0.931005 GCGCATAGGCACACTAAGTC 59.069 55.000 0.30 0.00 41.24 3.01
754 776 0.462047 GGCGCATAGGCACACTAAGT 60.462 55.000 10.83 0.00 45.92 2.24
755 777 2.311294 GGCGCATAGGCACACTAAG 58.689 57.895 10.83 0.00 45.92 2.18
756 778 4.532490 GGCGCATAGGCACACTAA 57.468 55.556 10.83 0.00 45.92 2.24
763 785 0.665369 GCATCAAATGGCGCATAGGC 60.665 55.000 10.83 0.00 46.95 3.93
764 786 0.669619 TGCATCAAATGGCGCATAGG 59.330 50.000 10.83 0.00 0.00 2.57
765 787 2.121786 GTTGCATCAAATGGCGCATAG 58.878 47.619 10.83 0.00 33.71 2.23
766 788 1.533547 CGTTGCATCAAATGGCGCATA 60.534 47.619 10.83 0.00 33.71 3.14
767 789 0.802994 CGTTGCATCAAATGGCGCAT 60.803 50.000 10.83 0.00 33.71 4.73
768 790 1.444042 CGTTGCATCAAATGGCGCA 60.444 52.632 10.83 0.00 0.00 6.09
769 791 2.160221 CCGTTGCATCAAATGGCGC 61.160 57.895 0.00 0.00 29.67 6.53
770 792 1.516821 CCCGTTGCATCAAATGGCG 60.517 57.895 0.00 0.00 35.24 5.69
771 793 0.458370 GACCCGTTGCATCAAATGGC 60.458 55.000 0.00 0.00 35.24 4.40
772 794 0.173255 GGACCCGTTGCATCAAATGG 59.827 55.000 0.00 0.00 36.18 3.16
773 795 0.887247 TGGACCCGTTGCATCAAATG 59.113 50.000 0.00 0.00 0.00 2.32
774 796 0.887933 GTGGACCCGTTGCATCAAAT 59.112 50.000 0.00 0.00 0.00 2.32
775 797 0.179004 AGTGGACCCGTTGCATCAAA 60.179 50.000 0.00 0.00 0.00 2.69
776 798 0.687920 TAGTGGACCCGTTGCATCAA 59.312 50.000 0.00 0.00 0.00 2.57
777 799 0.249120 CTAGTGGACCCGTTGCATCA 59.751 55.000 0.00 0.00 0.00 3.07
778 800 0.249398 ACTAGTGGACCCGTTGCATC 59.751 55.000 0.00 0.00 0.00 3.91
779 801 0.690762 AACTAGTGGACCCGTTGCAT 59.309 50.000 0.00 0.00 0.00 3.96
780 802 0.250124 CAACTAGTGGACCCGTTGCA 60.250 55.000 0.00 0.00 31.62 4.08
781 803 2.540145 CAACTAGTGGACCCGTTGC 58.460 57.895 0.00 0.00 31.62 4.17
790 812 2.107552 TGGGTTTTCCTCCAACTAGTGG 59.892 50.000 0.00 0.14 42.21 4.00
791 813 3.502123 TGGGTTTTCCTCCAACTAGTG 57.498 47.619 0.00 0.00 40.46 2.74
792 814 4.470602 CTTTGGGTTTTCCTCCAACTAGT 58.529 43.478 0.00 0.00 42.10 2.57
793 815 3.255888 GCTTTGGGTTTTCCTCCAACTAG 59.744 47.826 0.00 0.00 42.10 2.57
794 816 3.227614 GCTTTGGGTTTTCCTCCAACTA 58.772 45.455 0.00 0.00 42.10 2.24
795 817 2.039418 GCTTTGGGTTTTCCTCCAACT 58.961 47.619 0.00 0.00 42.10 3.16
796 818 1.760029 TGCTTTGGGTTTTCCTCCAAC 59.240 47.619 0.00 0.00 42.10 3.77
1107 1132 1.764054 CTCCCGGATCTTGGCCTCT 60.764 63.158 0.73 0.00 0.00 3.69
1227 1252 0.249073 CGGCCTTATCAGACTCCACG 60.249 60.000 0.00 0.00 0.00 4.94
1548 1582 1.518056 CCTTTGCGAGCTTCTTGGCA 61.518 55.000 0.00 0.00 34.17 4.92
1712 1746 0.457166 CTGCATTGTGGTGAATGGCG 60.457 55.000 0.00 0.00 34.42 5.69
1817 1851 2.993899 GCGCTTACTTTCTTGTAGAGCA 59.006 45.455 0.00 0.00 31.98 4.26
1935 1969 1.844771 GCAGCGCTGTCATTGTCACA 61.845 55.000 35.80 0.00 0.00 3.58
2165 2199 3.732943 CGATTAACTCGGACAAAAGCAC 58.267 45.455 0.00 0.00 43.82 4.40
2260 2294 4.736896 GGCTGCAGCTGCTTTGCC 62.737 66.667 35.69 35.69 40.81 4.52
2516 2590 1.398390 GATCTGCAGGTTTGTTAGCCG 59.602 52.381 15.13 0.00 0.00 5.52
2530 2604 6.183360 GGAAACTTATACACACTGTGATCTGC 60.183 42.308 16.30 0.00 36.96 4.26
2746 2820 5.273674 TGGCAATGTTTTTCAGATGAACA 57.726 34.783 0.00 2.56 37.64 3.18
2972 3046 3.430453 ACCAAGGAGAGAAGACTCAGAG 58.570 50.000 0.00 0.00 44.79 3.35
3072 3148 5.661056 TTGACATAAACAACACCCAAACA 57.339 34.783 0.00 0.00 0.00 2.83
3107 3183 2.740981 CAAGCTCTGGTTTCTGTAGCAG 59.259 50.000 0.00 0.00 43.29 4.24
3147 3223 4.512198 TCGAAAGCATAAGAACAACCGAAA 59.488 37.500 0.00 0.00 0.00 3.46
3193 3269 2.038952 TGCAGTCCACAATCTACAGCTT 59.961 45.455 0.00 0.00 0.00 3.74
3254 3332 4.260139 TCCAGTGCTTTGTCGTGTATTA 57.740 40.909 0.00 0.00 0.00 0.98
3352 3432 2.694628 TGTGACTGCTCAATTTTTGGCT 59.305 40.909 0.00 0.00 0.00 4.75
3400 3483 5.069251 CGAAGTAAAGGAGATGGTCATAGGT 59.931 44.000 0.00 0.00 0.00 3.08
3423 3506 2.936498 CCCAACATCTAAAGCACTACCG 59.064 50.000 0.00 0.00 0.00 4.02
3484 3567 7.826744 TGAACACTGATGGTTATTAGCATACAA 59.173 33.333 0.00 0.00 42.29 2.41
3602 3685 5.420421 TGAAAACAGAAGTGGAAACATGGAA 59.580 36.000 0.00 0.00 46.14 3.53
3624 3708 2.238646 AGGGGAGTCGTGCATTAAATGA 59.761 45.455 0.00 0.00 0.00 2.57
3640 3724 7.404481 AGATAAAACGTTATTACCAAAGGGGA 58.596 34.615 0.00 0.00 33.45 4.81
3656 3740 4.215399 TGCTCCCTGTTTTGAGATAAAACG 59.785 41.667 9.77 5.80 41.62 3.60
3765 3849 7.420184 GCAAAAGTGCCAAAACTACAATTAT 57.580 32.000 0.00 0.00 45.68 1.28
3900 3984 2.603173 GGACAGAGTTTGCAGAAAAGCG 60.603 50.000 0.00 0.00 37.31 4.68
4057 4142 6.311735 ACAAGGTTACCTGATACCAACAAAT 58.688 36.000 3.99 0.00 36.87 2.32
4086 4171 3.898741 GGTAAACAAACCAATGGGGAGAA 59.101 43.478 3.55 0.00 39.50 2.87
4128 4213 3.713248 TCATGCCTGACACCTATCTGAAT 59.287 43.478 0.00 0.00 0.00 2.57
4332 4417 4.347360 TGGTGAGATTGATATGCTCAGG 57.653 45.455 0.00 0.00 39.15 3.86
4353 4438 1.702957 TCTCCCGGGTCACATCTTTTT 59.297 47.619 22.86 0.00 0.00 1.94
4366 4451 1.136305 TCGCTATTTCTTGTCTCCCGG 59.864 52.381 0.00 0.00 0.00 5.73
4409 4494 0.260230 TTTCACCTTGGCACCCTTGA 59.740 50.000 0.00 0.00 0.00 3.02
4432 4517 8.138928 TCACTCATCCTCTGATTCTTCTTAAA 57.861 34.615 0.00 0.00 32.10 1.52
4448 4533 1.474077 GGTGCCACATTTCACTCATCC 59.526 52.381 0.00 0.00 33.91 3.51
4529 4614 2.544694 GCTCGACTATGGTGTGATGAGG 60.545 54.545 0.00 0.00 0.00 3.86
4548 4633 8.798859 ACAACAAGACAAAATATCAGATAGCT 57.201 30.769 0.00 0.00 0.00 3.32
4834 4921 4.624882 CAGGCTATAGAAATAGAAGCAGCG 59.375 45.833 3.21 0.00 37.84 5.18


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

AutoCloner maintained by Alex Coulton.