Multiple sequence alignment - TraesCS5B01G514500

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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 TraesCS5B01G514500 chr5B 100.000 2636 0 0 1 2636 679380421 679377786 0.000000e+00 4868.0
1 TraesCS5B01G514500 chr5B 92.565 1076 50 3 1562 2636 533433015 533434061 0.000000e+00 1517.0
2 TraesCS5B01G514500 chr5B 92.204 667 38 6 6 661 549183319 549183982 0.000000e+00 931.0
3 TraesCS5B01G514500 chr5B 87.557 659 78 2 5 661 572974601 572973945 0.000000e+00 760.0
4 TraesCS5B01G514500 chr5B 84.542 524 39 13 1000 1506 679559834 679559336 5.100000e-132 481.0
5 TraesCS5B01G514500 chr5B 81.350 563 51 20 979 1506 679405342 679404799 2.440000e-110 409.0
6 TraesCS5B01G514500 chr5B 100.000 28 0 0 1388 1415 450022773 450022746 5.000000e-03 52.8
7 TraesCS5B01G514500 chr2B 93.233 1064 40 5 1573 2636 798311595 798310564 0.000000e+00 1537.0
8 TraesCS5B01G514500 chr2B 93.146 1065 42 4 1572 2636 774836603 774835570 0.000000e+00 1533.0
9 TraesCS5B01G514500 chr1B 92.951 1064 44 4 1573 2636 2338236 2337204 0.000000e+00 1520.0
10 TraesCS5B01G514500 chr1B 97.632 887 19 1 1750 2636 577967047 577967931 0.000000e+00 1520.0
11 TraesCS5B01G514500 chr5A 92.857 1064 47 2 1573 2636 87886437 87887471 0.000000e+00 1517.0
12 TraesCS5B01G514500 chr5A 92.479 1077 51 3 1560 2636 510026465 510025419 0.000000e+00 1513.0
13 TraesCS5B01G514500 chr5A 88.989 663 69 3 1 661 146837589 146836929 0.000000e+00 817.0
14 TraesCS5B01G514500 chr5A 90.844 557 46 4 73 627 513275825 513275272 0.000000e+00 741.0
15 TraesCS5B01G514500 chr5A 90.411 73 7 0 7 79 513280067 513279995 2.160000e-16 97.1
16 TraesCS5B01G514500 chr3A 92.481 1064 51 2 1573 2636 64776630 64775596 0.000000e+00 1495.0
17 TraesCS5B01G514500 chrUn 92.315 1067 49 13 1570 2636 95217159 95218192 0.000000e+00 1485.0
18 TraesCS5B01G514500 chrUn 90.592 659 58 3 5 661 1468718 1468062 0.000000e+00 870.0
19 TraesCS5B01G514500 chrUn 86.159 578 39 11 942 1499 67363446 67362890 1.050000e-163 586.0
20 TraesCS5B01G514500 chr3D 91.325 1072 50 10 1573 2636 571207512 571206476 0.000000e+00 1424.0
21 TraesCS5B01G514500 chr3D 79.787 658 124 8 2 655 50871405 50872057 1.100000e-128 470.0
22 TraesCS5B01G514500 chr2D 91.403 663 53 3 1 661 380717160 380717820 0.000000e+00 905.0
23 TraesCS5B01G514500 chr2D 91.721 459 33 3 205 661 457655943 457656398 1.330000e-177 632.0
24 TraesCS5B01G514500 chr5D 90.950 663 45 8 1 661 44895438 44894789 0.000000e+00 878.0
25 TraesCS5B01G514500 chr5D 84.937 717 51 12 837 1528 538417416 538416732 0.000000e+00 673.0
26 TraesCS5B01G514500 chr5D 87.431 541 34 4 995 1519 538655484 538656006 2.260000e-165 592.0
27 TraesCS5B01G514500 chr5D 83.245 567 43 15 968 1506 538425265 538424723 8.540000e-130 473.0
28 TraesCS5B01G514500 chr5D 82.734 556 61 16 982 1526 538442260 538441729 1.850000e-126 462.0
29 TraesCS5B01G514500 chr3B 90.468 619 18 5 1573 2163 29354837 29355442 0.000000e+00 778.0
30 TraesCS5B01G514500 chr2A 88.832 582 61 3 82 661 767960859 767960280 0.000000e+00 712.0
31 TraesCS5B01G514500 chr2A 87.266 534 59 5 2 535 960380 960904 3.750000e-168 601.0
32 TraesCS5B01G514500 chr2A 93.750 80 5 0 5 84 767973693 767973614 1.280000e-23 121.0
33 TraesCS5B01G514500 chr4A 93.333 390 23 3 1562 1950 33969423 33969810 8.180000e-160 573.0
34 TraesCS5B01G514500 chr4A 83.491 636 62 18 951 1567 631507158 631507769 1.070000e-153 553.0
35 TraesCS5B01G514500 chr4A 83.774 567 39 13 972 1519 630899256 630898724 3.050000e-134 488.0
36 TraesCS5B01G514500 chr4A 82.862 566 41 25 968 1506 631494212 631494748 8.600000e-125 457.0
37 TraesCS5B01G514500 chr4A 81.301 615 59 17 981 1567 630878110 630877524 5.180000e-122 448.0
38 TraesCS5B01G514500 chr4A 81.849 584 56 16 968 1526 631475945 631476503 1.860000e-121 446.0
39 TraesCS5B01G514500 chr6A 76.762 667 137 16 4 661 73579238 73578581 8.970000e-95 357.0


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 TraesCS5B01G514500 chr5B 679377786 679380421 2635 True 4868 4868 100.000 1 2636 1 chr5B.!!$R3 2635
1 TraesCS5B01G514500 chr5B 533433015 533434061 1046 False 1517 1517 92.565 1562 2636 1 chr5B.!!$F1 1074
2 TraesCS5B01G514500 chr5B 549183319 549183982 663 False 931 931 92.204 6 661 1 chr5B.!!$F2 655
3 TraesCS5B01G514500 chr5B 572973945 572974601 656 True 760 760 87.557 5 661 1 chr5B.!!$R2 656
4 TraesCS5B01G514500 chr5B 679404799 679405342 543 True 409 409 81.350 979 1506 1 chr5B.!!$R4 527
5 TraesCS5B01G514500 chr2B 798310564 798311595 1031 True 1537 1537 93.233 1573 2636 1 chr2B.!!$R2 1063
6 TraesCS5B01G514500 chr2B 774835570 774836603 1033 True 1533 1533 93.146 1572 2636 1 chr2B.!!$R1 1064
7 TraesCS5B01G514500 chr1B 2337204 2338236 1032 True 1520 1520 92.951 1573 2636 1 chr1B.!!$R1 1063
8 TraesCS5B01G514500 chr1B 577967047 577967931 884 False 1520 1520 97.632 1750 2636 1 chr1B.!!$F1 886
9 TraesCS5B01G514500 chr5A 87886437 87887471 1034 False 1517 1517 92.857 1573 2636 1 chr5A.!!$F1 1063
10 TraesCS5B01G514500 chr5A 510025419 510026465 1046 True 1513 1513 92.479 1560 2636 1 chr5A.!!$R2 1076
11 TraesCS5B01G514500 chr5A 146836929 146837589 660 True 817 817 88.989 1 661 1 chr5A.!!$R1 660
12 TraesCS5B01G514500 chr5A 513275272 513275825 553 True 741 741 90.844 73 627 1 chr5A.!!$R3 554
13 TraesCS5B01G514500 chr3A 64775596 64776630 1034 True 1495 1495 92.481 1573 2636 1 chr3A.!!$R1 1063
14 TraesCS5B01G514500 chrUn 95217159 95218192 1033 False 1485 1485 92.315 1570 2636 1 chrUn.!!$F1 1066
15 TraesCS5B01G514500 chrUn 1468062 1468718 656 True 870 870 90.592 5 661 1 chrUn.!!$R1 656
16 TraesCS5B01G514500 chrUn 67362890 67363446 556 True 586 586 86.159 942 1499 1 chrUn.!!$R2 557
17 TraesCS5B01G514500 chr3D 571206476 571207512 1036 True 1424 1424 91.325 1573 2636 1 chr3D.!!$R1 1063
18 TraesCS5B01G514500 chr3D 50871405 50872057 652 False 470 470 79.787 2 655 1 chr3D.!!$F1 653
19 TraesCS5B01G514500 chr2D 380717160 380717820 660 False 905 905 91.403 1 661 1 chr2D.!!$F1 660
20 TraesCS5B01G514500 chr5D 44894789 44895438 649 True 878 878 90.950 1 661 1 chr5D.!!$R1 660
21 TraesCS5B01G514500 chr5D 538416732 538417416 684 True 673 673 84.937 837 1528 1 chr5D.!!$R2 691
22 TraesCS5B01G514500 chr5D 538655484 538656006 522 False 592 592 87.431 995 1519 1 chr5D.!!$F1 524
23 TraesCS5B01G514500 chr5D 538424723 538425265 542 True 473 473 83.245 968 1506 1 chr5D.!!$R3 538
24 TraesCS5B01G514500 chr5D 538441729 538442260 531 True 462 462 82.734 982 1526 1 chr5D.!!$R4 544
25 TraesCS5B01G514500 chr3B 29354837 29355442 605 False 778 778 90.468 1573 2163 1 chr3B.!!$F1 590
26 TraesCS5B01G514500 chr2A 767960280 767960859 579 True 712 712 88.832 82 661 1 chr2A.!!$R1 579
27 TraesCS5B01G514500 chr2A 960380 960904 524 False 601 601 87.266 2 535 1 chr2A.!!$F1 533
28 TraesCS5B01G514500 chr4A 631507158 631507769 611 False 553 553 83.491 951 1567 1 chr4A.!!$F4 616
29 TraesCS5B01G514500 chr4A 630898724 630899256 532 True 488 488 83.774 972 1519 1 chr4A.!!$R2 547
30 TraesCS5B01G514500 chr4A 631494212 631494748 536 False 457 457 82.862 968 1506 1 chr4A.!!$F3 538
31 TraesCS5B01G514500 chr4A 630877524 630878110 586 True 448 448 81.301 981 1567 1 chr4A.!!$R1 586
32 TraesCS5B01G514500 chr4A 631475945 631476503 558 False 446 446 81.849 968 1526 1 chr4A.!!$F2 558
33 TraesCS5B01G514500 chr6A 73578581 73579238 657 True 357 357 76.762 4 661 1 chr6A.!!$R1 657

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
710 731 0.179045 AAATCCAAGGATCCGCGGAG 60.179 55.0 33.87 18.95 33.08 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2295 2397 1.10051 CATGCTTAGTGCTGCACCAT 58.899 50.0 27.74 20.11 42.26 3.55 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
204 205 5.998363 AGGAAACTAAGTCAAGATCAACACC 59.002 40.000 0.00 0.00 40.61 4.16
236 239 2.079158 CCATCGAGACAAACACTGCAT 58.921 47.619 0.00 0.00 0.00 3.96
266 278 1.035932 CCTAGCCCGTTCTTCCTCGA 61.036 60.000 0.00 0.00 0.00 4.04
312 324 3.182887 CCAGCTAGGGGTCATAGATCT 57.817 52.381 0.00 0.00 0.00 2.75
321 333 4.723789 AGGGGTCATAGATCTGTTCATTGT 59.276 41.667 5.18 0.00 0.00 2.71
408 420 2.025226 TGGAATCCGACTGTCTAGAGGT 60.025 50.000 6.21 0.00 0.00 3.85
489 501 6.525578 TGAAGTTAGAGAGCTTTCCGATAA 57.474 37.500 0.00 0.00 0.00 1.75
568 581 0.238289 GTGTGCTAAGCGTGCATGTT 59.762 50.000 7.93 0.00 42.69 2.71
661 682 3.378112 TCCAGCGAATGCCTTCATTTAAG 59.622 43.478 2.57 0.00 42.60 1.85
662 683 3.129287 CCAGCGAATGCCTTCATTTAAGT 59.871 43.478 2.57 0.00 42.60 2.24
663 684 4.100529 CAGCGAATGCCTTCATTTAAGTG 58.899 43.478 2.57 0.00 42.60 3.16
664 685 2.854185 GCGAATGCCTTCATTTAAGTGC 59.146 45.455 2.57 0.00 42.60 4.40
665 686 3.438360 CGAATGCCTTCATTTAAGTGCC 58.562 45.455 2.57 0.00 42.60 5.01
666 687 3.129287 CGAATGCCTTCATTTAAGTGCCT 59.871 43.478 2.57 0.00 42.60 4.75
667 688 4.427312 GAATGCCTTCATTTAAGTGCCTG 58.573 43.478 0.00 0.00 42.60 4.85
668 689 2.875296 TGCCTTCATTTAAGTGCCTGT 58.125 42.857 0.00 0.00 33.12 4.00
669 690 3.230134 TGCCTTCATTTAAGTGCCTGTT 58.770 40.909 0.00 0.00 33.12 3.16
670 691 3.255642 TGCCTTCATTTAAGTGCCTGTTC 59.744 43.478 0.00 0.00 33.12 3.18
671 692 3.367395 GCCTTCATTTAAGTGCCTGTTCC 60.367 47.826 0.00 0.00 32.89 3.62
672 693 3.119849 CCTTCATTTAAGTGCCTGTTCCG 60.120 47.826 0.00 0.00 32.89 4.30
673 694 1.810151 TCATTTAAGTGCCTGTTCCGC 59.190 47.619 0.00 0.00 0.00 5.54
674 695 1.539388 CATTTAAGTGCCTGTTCCGCA 59.461 47.619 0.00 0.00 0.00 5.69
675 696 1.681538 TTTAAGTGCCTGTTCCGCAA 58.318 45.000 0.00 0.00 38.13 4.85
676 697 1.904287 TTAAGTGCCTGTTCCGCAAT 58.096 45.000 0.00 0.00 38.13 3.56
677 698 1.448985 TAAGTGCCTGTTCCGCAATC 58.551 50.000 0.00 0.00 38.13 2.67
678 699 1.244019 AAGTGCCTGTTCCGCAATCC 61.244 55.000 0.00 0.00 38.13 3.01
679 700 1.971167 GTGCCTGTTCCGCAATCCA 60.971 57.895 0.00 0.00 38.13 3.41
680 701 1.228398 TGCCTGTTCCGCAATCCAA 60.228 52.632 0.00 0.00 32.05 3.53
681 702 1.212751 GCCTGTTCCGCAATCCAAC 59.787 57.895 0.00 0.00 0.00 3.77
682 703 1.523154 GCCTGTTCCGCAATCCAACA 61.523 55.000 0.00 0.00 0.00 3.33
683 704 0.958091 CCTGTTCCGCAATCCAACAA 59.042 50.000 0.00 0.00 29.78 2.83
684 705 1.335872 CCTGTTCCGCAATCCAACAAC 60.336 52.381 0.00 0.00 29.78 3.32
685 706 1.608590 CTGTTCCGCAATCCAACAACT 59.391 47.619 0.00 0.00 29.78 3.16
686 707 2.028130 TGTTCCGCAATCCAACAACTT 58.972 42.857 0.00 0.00 0.00 2.66
687 708 2.034053 TGTTCCGCAATCCAACAACTTC 59.966 45.455 0.00 0.00 0.00 3.01
688 709 2.270352 TCCGCAATCCAACAACTTCT 57.730 45.000 0.00 0.00 0.00 2.85
689 710 3.410631 TCCGCAATCCAACAACTTCTA 57.589 42.857 0.00 0.00 0.00 2.10
690 711 3.745799 TCCGCAATCCAACAACTTCTAA 58.254 40.909 0.00 0.00 0.00 2.10
691 712 4.138290 TCCGCAATCCAACAACTTCTAAA 58.862 39.130 0.00 0.00 0.00 1.85
692 713 4.580995 TCCGCAATCCAACAACTTCTAAAA 59.419 37.500 0.00 0.00 0.00 1.52
693 714 5.067936 TCCGCAATCCAACAACTTCTAAAAA 59.932 36.000 0.00 0.00 0.00 1.94
694 715 5.925969 CCGCAATCCAACAACTTCTAAAAAT 59.074 36.000 0.00 0.00 0.00 1.82
695 716 6.089417 CCGCAATCCAACAACTTCTAAAAATC 59.911 38.462 0.00 0.00 0.00 2.17
696 717 6.089417 CGCAATCCAACAACTTCTAAAAATCC 59.911 38.462 0.00 0.00 0.00 3.01
697 718 6.928492 GCAATCCAACAACTTCTAAAAATCCA 59.072 34.615 0.00 0.00 0.00 3.41
698 719 7.440856 GCAATCCAACAACTTCTAAAAATCCAA 59.559 33.333 0.00 0.00 0.00 3.53
699 720 8.981647 CAATCCAACAACTTCTAAAAATCCAAG 58.018 33.333 0.00 0.00 0.00 3.61
700 721 7.049799 TCCAACAACTTCTAAAAATCCAAGG 57.950 36.000 0.00 0.00 0.00 3.61
701 722 6.836527 TCCAACAACTTCTAAAAATCCAAGGA 59.163 34.615 0.00 0.00 0.00 3.36
702 723 7.508977 TCCAACAACTTCTAAAAATCCAAGGAT 59.491 33.333 0.00 0.00 36.23 3.24
703 724 7.814587 CCAACAACTTCTAAAAATCCAAGGATC 59.185 37.037 1.37 0.00 33.08 3.36
704 725 7.468141 ACAACTTCTAAAAATCCAAGGATCC 57.532 36.000 2.48 2.48 33.08 3.36
705 726 6.151144 ACAACTTCTAAAAATCCAAGGATCCG 59.849 38.462 5.98 0.00 33.08 4.18
706 727 4.640647 ACTTCTAAAAATCCAAGGATCCGC 59.359 41.667 5.98 0.00 33.08 5.54
707 728 3.202906 TCTAAAAATCCAAGGATCCGCG 58.797 45.455 5.98 0.00 33.08 6.46
708 729 1.102978 AAAAATCCAAGGATCCGCGG 58.897 50.000 22.12 22.12 33.08 6.46
709 730 0.254747 AAAATCCAAGGATCCGCGGA 59.745 50.000 33.12 33.12 33.08 5.54
710 731 0.179045 AAATCCAAGGATCCGCGGAG 60.179 55.000 33.87 18.95 33.08 4.63
711 732 2.666596 AATCCAAGGATCCGCGGAGC 62.667 60.000 34.47 34.47 42.11 4.70
725 746 0.659957 CGGAGCAAGGAATTAGCTGC 59.340 55.000 0.00 0.00 42.37 5.25
728 749 2.049888 AGCAAGGAATTAGCTGCTCC 57.950 50.000 4.91 0.62 41.18 4.70
729 750 1.028130 GCAAGGAATTAGCTGCTCCC 58.972 55.000 4.91 3.78 0.00 4.30
730 751 1.409381 GCAAGGAATTAGCTGCTCCCT 60.409 52.381 4.91 6.22 0.00 4.20
731 752 2.295885 CAAGGAATTAGCTGCTCCCTG 58.704 52.381 4.91 0.00 0.00 4.45
732 753 1.885049 AGGAATTAGCTGCTCCCTGA 58.115 50.000 4.91 0.00 0.00 3.86
733 754 2.416638 AGGAATTAGCTGCTCCCTGAT 58.583 47.619 4.91 0.00 0.00 2.90
734 755 2.782341 AGGAATTAGCTGCTCCCTGATT 59.218 45.455 4.91 0.22 0.00 2.57
735 756 3.203934 AGGAATTAGCTGCTCCCTGATTT 59.796 43.478 4.91 0.00 0.00 2.17
736 757 3.956848 GGAATTAGCTGCTCCCTGATTTT 59.043 43.478 4.91 0.00 0.00 1.82
737 758 4.037327 GGAATTAGCTGCTCCCTGATTTTC 59.963 45.833 4.91 0.00 0.00 2.29
738 759 3.719268 TTAGCTGCTCCCTGATTTTCA 57.281 42.857 4.91 0.00 0.00 2.69
739 760 2.592102 AGCTGCTCCCTGATTTTCAA 57.408 45.000 0.00 0.00 0.00 2.69
740 761 3.097342 AGCTGCTCCCTGATTTTCAAT 57.903 42.857 0.00 0.00 0.00 2.57
741 762 3.438183 AGCTGCTCCCTGATTTTCAATT 58.562 40.909 0.00 0.00 0.00 2.32
742 763 4.603131 AGCTGCTCCCTGATTTTCAATTA 58.397 39.130 0.00 0.00 0.00 1.40
743 764 5.206587 AGCTGCTCCCTGATTTTCAATTAT 58.793 37.500 0.00 0.00 0.00 1.28
744 765 6.367983 AGCTGCTCCCTGATTTTCAATTATA 58.632 36.000 0.00 0.00 0.00 0.98
745 766 6.489361 AGCTGCTCCCTGATTTTCAATTATAG 59.511 38.462 0.00 0.00 0.00 1.31
746 767 6.639632 TGCTCCCTGATTTTCAATTATAGC 57.360 37.500 0.00 0.00 0.00 2.97
747 768 5.536161 TGCTCCCTGATTTTCAATTATAGCC 59.464 40.000 0.00 0.00 0.00 3.93
748 769 5.047731 GCTCCCTGATTTTCAATTATAGCCC 60.048 44.000 0.00 0.00 0.00 5.19
749 770 5.393866 TCCCTGATTTTCAATTATAGCCCC 58.606 41.667 0.00 0.00 0.00 5.80
750 771 4.218417 CCCTGATTTTCAATTATAGCCCCG 59.782 45.833 0.00 0.00 0.00 5.73
751 772 4.218417 CCTGATTTTCAATTATAGCCCCGG 59.782 45.833 0.00 0.00 0.00 5.73
752 773 3.572255 TGATTTTCAATTATAGCCCCGGC 59.428 43.478 0.00 0.00 42.33 6.13
753 774 1.989706 TTTCAATTATAGCCCCGGCC 58.010 50.000 1.02 0.00 43.17 6.13
754 775 0.250553 TTCAATTATAGCCCCGGCCG 60.251 55.000 21.04 21.04 43.17 6.13
755 776 2.033602 AATTATAGCCCCGGCCGC 59.966 61.111 22.85 6.25 43.17 6.53
756 777 2.526046 AATTATAGCCCCGGCCGCT 61.526 57.895 22.85 14.83 43.17 5.52
757 778 2.465055 AATTATAGCCCCGGCCGCTC 62.465 60.000 22.85 10.71 43.17 5.03
780 801 3.143675 GCAGAATTGCGGAGTCAGA 57.856 52.632 0.00 0.00 41.13 3.27
781 802 1.005340 GCAGAATTGCGGAGTCAGAG 58.995 55.000 0.00 0.00 41.13 3.35
782 803 1.674221 GCAGAATTGCGGAGTCAGAGT 60.674 52.381 0.00 0.00 41.13 3.24
783 804 1.998315 CAGAATTGCGGAGTCAGAGTG 59.002 52.381 0.00 0.00 0.00 3.51
784 805 1.895798 AGAATTGCGGAGTCAGAGTGA 59.104 47.619 0.00 0.00 0.00 3.41
796 817 3.134458 GTCAGAGTGACTCCAAACAAGG 58.866 50.000 9.33 0.00 43.73 3.61
797 818 1.876156 CAGAGTGACTCCAAACAAGGC 59.124 52.381 9.33 0.00 0.00 4.35
798 819 1.202818 AGAGTGACTCCAAACAAGGCC 60.203 52.381 9.33 0.00 0.00 5.19
799 820 0.846693 AGTGACTCCAAACAAGGCCT 59.153 50.000 0.00 0.00 0.00 5.19
800 821 2.038557 GAGTGACTCCAAACAAGGCCTA 59.961 50.000 5.16 0.00 0.00 3.93
801 822 2.441750 AGTGACTCCAAACAAGGCCTAA 59.558 45.455 5.16 0.00 0.00 2.69
802 823 3.117663 AGTGACTCCAAACAAGGCCTAAA 60.118 43.478 5.16 0.00 0.00 1.85
803 824 3.826729 GTGACTCCAAACAAGGCCTAAAT 59.173 43.478 5.16 0.00 0.00 1.40
804 825 5.007682 GTGACTCCAAACAAGGCCTAAATA 58.992 41.667 5.16 0.00 0.00 1.40
805 826 5.475564 GTGACTCCAAACAAGGCCTAAATAA 59.524 40.000 5.16 0.00 0.00 1.40
806 827 6.015772 GTGACTCCAAACAAGGCCTAAATAAA 60.016 38.462 5.16 0.00 0.00 1.40
807 828 6.208599 TGACTCCAAACAAGGCCTAAATAAAG 59.791 38.462 5.16 1.17 0.00 1.85
808 829 5.047306 ACTCCAAACAAGGCCTAAATAAAGC 60.047 40.000 5.16 0.00 0.00 3.51
809 830 5.083821 TCCAAACAAGGCCTAAATAAAGCT 58.916 37.500 5.16 0.00 0.00 3.74
810 831 5.185056 TCCAAACAAGGCCTAAATAAAGCTC 59.815 40.000 5.16 0.00 0.00 4.09
811 832 5.185828 CCAAACAAGGCCTAAATAAAGCTCT 59.814 40.000 5.16 0.00 0.00 4.09
812 833 6.325596 CAAACAAGGCCTAAATAAAGCTCTC 58.674 40.000 5.16 0.00 0.00 3.20
813 834 5.443230 ACAAGGCCTAAATAAAGCTCTCT 57.557 39.130 5.16 0.00 0.00 3.10
814 835 6.561519 ACAAGGCCTAAATAAAGCTCTCTA 57.438 37.500 5.16 0.00 0.00 2.43
815 836 6.958767 ACAAGGCCTAAATAAAGCTCTCTAA 58.041 36.000 5.16 0.00 0.00 2.10
816 837 7.402862 ACAAGGCCTAAATAAAGCTCTCTAAA 58.597 34.615 5.16 0.00 0.00 1.85
817 838 7.554476 ACAAGGCCTAAATAAAGCTCTCTAAAG 59.446 37.037 5.16 0.00 0.00 1.85
818 839 7.201702 AGGCCTAAATAAAGCTCTCTAAAGT 57.798 36.000 1.29 0.00 0.00 2.66
819 840 7.634718 AGGCCTAAATAAAGCTCTCTAAAGTT 58.365 34.615 1.29 0.00 0.00 2.66
820 841 7.771361 AGGCCTAAATAAAGCTCTCTAAAGTTC 59.229 37.037 1.29 0.00 0.00 3.01
821 842 7.012515 GGCCTAAATAAAGCTCTCTAAAGTTCC 59.987 40.741 0.00 0.00 0.00 3.62
822 843 7.012515 GCCTAAATAAAGCTCTCTAAAGTTCCC 59.987 40.741 0.00 0.00 0.00 3.97
823 844 8.268605 CCTAAATAAAGCTCTCTAAAGTTCCCT 58.731 37.037 0.00 0.00 0.00 4.20
824 845 7.929941 AAATAAAGCTCTCTAAAGTTCCCTG 57.070 36.000 0.00 0.00 0.00 4.45
825 846 6.875972 ATAAAGCTCTCTAAAGTTCCCTGA 57.124 37.500 0.00 0.00 0.00 3.86
826 847 5.568620 AAAGCTCTCTAAAGTTCCCTGAA 57.431 39.130 0.00 0.00 0.00 3.02
827 848 5.568620 AAGCTCTCTAAAGTTCCCTGAAA 57.431 39.130 0.00 0.00 0.00 2.69
828 849 5.568620 AGCTCTCTAAAGTTCCCTGAAAA 57.431 39.130 0.00 0.00 0.00 2.29
829 850 5.941788 AGCTCTCTAAAGTTCCCTGAAAAA 58.058 37.500 0.00 0.00 0.00 1.94
887 908 3.580319 GAGGGTGGGTGGTTGGCT 61.580 66.667 0.00 0.00 0.00 4.75
888 909 3.868200 GAGGGTGGGTGGTTGGCTG 62.868 68.421 0.00 0.00 0.00 4.85
889 910 4.218686 GGGTGGGTGGTTGGCTGT 62.219 66.667 0.00 0.00 0.00 4.40
890 911 2.912025 GGTGGGTGGTTGGCTGTG 60.912 66.667 0.00 0.00 0.00 3.66
891 912 2.123897 GTGGGTGGTTGGCTGTGT 60.124 61.111 0.00 0.00 0.00 3.72
892 913 2.123939 TGGGTGGTTGGCTGTGTG 60.124 61.111 0.00 0.00 0.00 3.82
909 930 0.316204 GTGCTGCTGCCTTGAATTGT 59.684 50.000 13.47 0.00 38.71 2.71
910 931 0.315886 TGCTGCTGCCTTGAATTGTG 59.684 50.000 13.47 0.00 38.71 3.33
927 948 2.407090 TGTGAATTGACGAGTCTGCTG 58.593 47.619 4.78 0.00 0.00 4.41
935 956 4.459089 GAGTCTGCTGCCGTCCCC 62.459 72.222 0.00 0.00 0.00 4.81
942 963 4.506255 CTGCCGTCCCCCATTCCC 62.506 72.222 0.00 0.00 0.00 3.97
944 965 4.506255 GCCGTCCCCCATTCCCTG 62.506 72.222 0.00 0.00 0.00 4.45
945 966 4.506255 CCGTCCCCCATTCCCTGC 62.506 72.222 0.00 0.00 0.00 4.85
946 967 3.411517 CGTCCCCCATTCCCTGCT 61.412 66.667 0.00 0.00 0.00 4.24
947 968 2.597903 GTCCCCCATTCCCTGCTC 59.402 66.667 0.00 0.00 0.00 4.26
949 970 3.023116 CCCCCATTCCCTGCTCCA 61.023 66.667 0.00 0.00 0.00 3.86
965 986 2.716017 CCACCTCCCGAGCAGAGTC 61.716 68.421 0.00 0.00 0.00 3.36
969 990 1.450491 CTCCCGAGCAGAGTCGAGA 60.450 63.158 0.00 0.00 42.85 4.04
976 997 1.140804 GCAGAGTCGAGAAGGAGGC 59.859 63.158 0.00 0.00 0.00 4.70
993 1014 0.729690 GGCAAGGAAGCAGAATCGAC 59.270 55.000 0.00 0.00 35.83 4.20
998 1021 1.065854 AGGAAGCAGAATCGACAAGGG 60.066 52.381 0.00 0.00 0.00 3.95
1166 1218 0.405585 CCCCTTCTTCTTCCTTGCCA 59.594 55.000 0.00 0.00 0.00 4.92
1315 1374 2.387952 CCCAACTACCTCAAGGGCT 58.612 57.895 0.29 0.00 40.27 5.19
1522 1596 3.022287 CCGCCGTGATGGTATTGC 58.978 61.111 0.00 0.00 41.21 3.56
1549 1623 5.308014 CATTCTTGGATCGGATTGGATGTA 58.692 41.667 0.00 0.00 0.00 2.29
1550 1624 5.567037 TTCTTGGATCGGATTGGATGTAT 57.433 39.130 0.00 0.00 0.00 2.29
1554 1628 8.374184 TCTTGGATCGGATTGGATGTATATTA 57.626 34.615 0.00 0.00 0.00 0.98
1593 1667 4.557605 GATCGGGTTCGCGCCGTA 62.558 66.667 20.45 9.97 36.13 4.02
1629 1703 4.551410 CGGTCAGAACGTTTAGACAAAACC 60.551 45.833 25.42 13.76 43.90 3.27
1657 1731 7.885922 TGTAATAATTTGTCAGTAAGAGCCCAA 59.114 33.333 0.00 0.00 0.00 4.12
1705 1779 9.979578 AATTGTGTTAGAAGCAAAACATAATGA 57.020 25.926 9.82 0.00 42.75 2.57
1724 1798 9.274206 CATAATGAGACTGAAGATGAACATCAT 57.726 33.333 15.63 5.05 40.34 2.45
1735 1809 9.034544 TGAAGATGAACATCATGTTATAAGACG 57.965 33.333 2.04 0.00 39.98 4.18
2087 2189 3.701205 TTAGAGCTTGCAACATGAGGA 57.299 42.857 0.00 0.00 0.00 3.71
2114 2216 5.472301 AAATGTGGGAATAGGGAATCACT 57.528 39.130 0.00 0.00 0.00 3.41
2211 2313 9.991906 AAGAGTACTGTTGCTGTAAAATTACTA 57.008 29.630 4.15 0.00 34.77 1.82
2295 2397 7.397476 ACTGGAGTAGTTCAAGATACTGAATCA 59.603 37.037 0.00 0.00 37.63 2.57
2390 2500 3.502211 ACAATCTAACAAGGCAGGTTTCG 59.498 43.478 0.00 0.00 0.00 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
113 114 2.079158 CCGGTATATCCAGCAATGCAG 58.921 52.381 8.35 0.00 35.57 4.41
189 190 2.289631 TGCATCGGTGTTGATCTTGACT 60.290 45.455 0.00 0.00 0.00 3.41
227 228 0.892755 CCTCCAATGCATGCAGTGTT 59.107 50.000 37.14 21.00 39.98 3.32
236 239 2.597340 GGCTAGGCCTCCAATGCA 59.403 61.111 9.68 0.00 46.69 3.96
266 278 0.540365 CACCATGCACCCAGGAAAGT 60.540 55.000 0.00 0.00 0.00 2.66
312 324 3.141398 GAGAGCACCTCAACAATGAACA 58.859 45.455 1.79 0.00 41.58 3.18
321 333 0.614697 TCGGATGGAGAGCACCTCAA 60.615 55.000 8.16 0.00 43.76 3.02
408 420 3.165875 CCAGAGTTCCAGAGGTCAACTA 58.834 50.000 0.00 0.00 30.32 2.24
446 458 2.036475 CAGCTAGAATGGGTGCTACGAT 59.964 50.000 0.00 0.00 38.49 3.73
499 511 7.068962 TCGAGTTACATGGGTAATACTGAATGA 59.931 37.037 0.00 0.00 41.28 2.57
513 526 3.050619 GTTAGCGGATCGAGTTACATGG 58.949 50.000 0.00 0.00 0.00 3.66
568 581 1.945819 GCTTTCAGTCCCATTCAGCGA 60.946 52.381 0.00 0.00 0.00 4.93
661 682 1.523154 TTGGATTGCGGAACAGGCAC 61.523 55.000 0.00 0.00 40.71 5.01
662 683 1.228398 TTGGATTGCGGAACAGGCA 60.228 52.632 0.00 0.00 38.93 4.75
663 684 1.212751 GTTGGATTGCGGAACAGGC 59.787 57.895 0.00 0.00 0.00 4.85
664 685 0.958091 TTGTTGGATTGCGGAACAGG 59.042 50.000 0.00 0.00 31.50 4.00
665 686 1.608590 AGTTGTTGGATTGCGGAACAG 59.391 47.619 0.00 0.00 31.50 3.16
666 687 1.686355 AGTTGTTGGATTGCGGAACA 58.314 45.000 0.00 0.00 0.00 3.18
667 688 2.293399 AGAAGTTGTTGGATTGCGGAAC 59.707 45.455 0.00 0.00 0.00 3.62
668 689 2.582052 AGAAGTTGTTGGATTGCGGAA 58.418 42.857 0.00 0.00 0.00 4.30
669 690 2.270352 AGAAGTTGTTGGATTGCGGA 57.730 45.000 0.00 0.00 0.00 5.54
670 691 4.497473 TTTAGAAGTTGTTGGATTGCGG 57.503 40.909 0.00 0.00 0.00 5.69
671 692 6.089417 GGATTTTTAGAAGTTGTTGGATTGCG 59.911 38.462 0.00 0.00 0.00 4.85
672 693 6.928492 TGGATTTTTAGAAGTTGTTGGATTGC 59.072 34.615 0.00 0.00 0.00 3.56
673 694 8.885494 TTGGATTTTTAGAAGTTGTTGGATTG 57.115 30.769 0.00 0.00 0.00 2.67
674 695 8.150296 CCTTGGATTTTTAGAAGTTGTTGGATT 58.850 33.333 0.00 0.00 0.00 3.01
675 696 7.508977 TCCTTGGATTTTTAGAAGTTGTTGGAT 59.491 33.333 0.00 0.00 0.00 3.41
676 697 6.836527 TCCTTGGATTTTTAGAAGTTGTTGGA 59.163 34.615 0.00 0.00 0.00 3.53
677 698 7.049799 TCCTTGGATTTTTAGAAGTTGTTGG 57.950 36.000 0.00 0.00 0.00 3.77
678 699 7.814587 GGATCCTTGGATTTTTAGAAGTTGTTG 59.185 37.037 3.84 0.00 0.00 3.33
679 700 7.309194 CGGATCCTTGGATTTTTAGAAGTTGTT 60.309 37.037 10.75 0.00 0.00 2.83
680 701 6.151144 CGGATCCTTGGATTTTTAGAAGTTGT 59.849 38.462 10.75 0.00 0.00 3.32
681 702 6.555315 CGGATCCTTGGATTTTTAGAAGTTG 58.445 40.000 10.75 0.00 0.00 3.16
682 703 5.125578 GCGGATCCTTGGATTTTTAGAAGTT 59.874 40.000 10.75 0.00 0.00 2.66
683 704 4.640647 GCGGATCCTTGGATTTTTAGAAGT 59.359 41.667 10.75 0.00 0.00 3.01
684 705 4.260784 CGCGGATCCTTGGATTTTTAGAAG 60.261 45.833 10.75 0.00 0.00 2.85
685 706 3.625764 CGCGGATCCTTGGATTTTTAGAA 59.374 43.478 10.75 0.00 0.00 2.10
686 707 3.202906 CGCGGATCCTTGGATTTTTAGA 58.797 45.455 10.75 0.00 0.00 2.10
687 708 2.290641 CCGCGGATCCTTGGATTTTTAG 59.709 50.000 24.07 0.00 0.00 1.85
688 709 2.092861 TCCGCGGATCCTTGGATTTTTA 60.093 45.455 27.28 0.00 0.00 1.52
689 710 1.102978 CCGCGGATCCTTGGATTTTT 58.897 50.000 24.07 0.00 0.00 1.94
690 711 0.254747 TCCGCGGATCCTTGGATTTT 59.745 50.000 27.28 0.00 0.00 1.82
691 712 0.179045 CTCCGCGGATCCTTGGATTT 60.179 55.000 31.19 0.00 0.00 2.17
692 713 1.447643 CTCCGCGGATCCTTGGATT 59.552 57.895 31.19 0.00 0.00 3.01
693 714 3.142393 CTCCGCGGATCCTTGGAT 58.858 61.111 31.19 1.18 0.00 3.41
694 715 3.849951 GCTCCGCGGATCCTTGGA 61.850 66.667 31.19 17.97 0.00 3.53
695 716 3.680620 TTGCTCCGCGGATCCTTGG 62.681 63.158 31.19 17.24 0.00 3.61
696 717 2.125147 TTGCTCCGCGGATCCTTG 60.125 61.111 31.19 18.06 0.00 3.61
697 718 2.187946 CTTGCTCCGCGGATCCTT 59.812 61.111 31.19 0.00 0.00 3.36
698 719 3.854669 CCTTGCTCCGCGGATCCT 61.855 66.667 31.19 0.00 0.00 3.24
699 720 2.666596 ATTCCTTGCTCCGCGGATCC 62.667 60.000 31.19 22.60 0.00 3.36
700 721 0.815615 AATTCCTTGCTCCGCGGATC 60.816 55.000 31.19 26.15 0.00 3.36
701 722 0.468226 TAATTCCTTGCTCCGCGGAT 59.532 50.000 31.19 13.21 0.00 4.18
702 723 0.179084 CTAATTCCTTGCTCCGCGGA 60.179 55.000 29.03 29.03 0.00 5.54
703 724 1.776034 GCTAATTCCTTGCTCCGCGG 61.776 60.000 22.12 22.12 0.00 6.46
704 725 0.811616 AGCTAATTCCTTGCTCCGCG 60.812 55.000 0.00 0.00 30.41 6.46
705 726 0.659957 CAGCTAATTCCTTGCTCCGC 59.340 55.000 0.00 0.00 34.51 5.54
706 727 0.659957 GCAGCTAATTCCTTGCTCCG 59.340 55.000 0.00 0.00 34.51 4.63
707 728 2.049888 AGCAGCTAATTCCTTGCTCC 57.950 50.000 0.00 0.00 42.89 4.70
710 731 1.028130 GGGAGCAGCTAATTCCTTGC 58.972 55.000 0.00 1.03 36.83 4.01
711 732 2.092753 TCAGGGAGCAGCTAATTCCTTG 60.093 50.000 13.21 13.21 38.90 3.61
712 733 2.200081 TCAGGGAGCAGCTAATTCCTT 58.800 47.619 0.00 0.83 0.00 3.36
713 734 1.885049 TCAGGGAGCAGCTAATTCCT 58.115 50.000 0.00 0.00 0.00 3.36
714 735 2.947127 ATCAGGGAGCAGCTAATTCC 57.053 50.000 0.00 0.00 0.00 3.01
715 736 4.641989 TGAAAATCAGGGAGCAGCTAATTC 59.358 41.667 0.00 0.00 0.00 2.17
716 737 4.603131 TGAAAATCAGGGAGCAGCTAATT 58.397 39.130 0.00 0.00 0.00 1.40
717 738 4.240881 TGAAAATCAGGGAGCAGCTAAT 57.759 40.909 0.00 0.00 0.00 1.73
718 739 3.719268 TGAAAATCAGGGAGCAGCTAA 57.281 42.857 0.00 0.00 0.00 3.09
719 740 3.719268 TTGAAAATCAGGGAGCAGCTA 57.281 42.857 0.00 0.00 0.00 3.32
720 741 2.592102 TTGAAAATCAGGGAGCAGCT 57.408 45.000 0.00 0.00 0.00 4.24
721 742 3.881937 AATTGAAAATCAGGGAGCAGC 57.118 42.857 0.00 0.00 0.00 5.25
722 743 6.294397 GGCTATAATTGAAAATCAGGGAGCAG 60.294 42.308 0.00 0.00 0.00 4.24
723 744 5.536161 GGCTATAATTGAAAATCAGGGAGCA 59.464 40.000 0.00 0.00 0.00 4.26
724 745 5.047731 GGGCTATAATTGAAAATCAGGGAGC 60.048 44.000 0.00 0.00 0.00 4.70
725 746 5.478332 GGGGCTATAATTGAAAATCAGGGAG 59.522 44.000 0.00 0.00 0.00 4.30
726 747 5.393866 GGGGCTATAATTGAAAATCAGGGA 58.606 41.667 0.00 0.00 0.00 4.20
727 748 4.218417 CGGGGCTATAATTGAAAATCAGGG 59.782 45.833 0.00 0.00 0.00 4.45
728 749 4.218417 CCGGGGCTATAATTGAAAATCAGG 59.782 45.833 0.00 0.00 0.00 3.86
729 750 4.321230 GCCGGGGCTATAATTGAAAATCAG 60.321 45.833 2.18 0.00 38.26 2.90
730 751 3.572255 GCCGGGGCTATAATTGAAAATCA 59.428 43.478 2.18 0.00 38.26 2.57
731 752 3.056821 GGCCGGGGCTATAATTGAAAATC 60.057 47.826 14.22 0.00 41.60 2.17
732 753 2.897326 GGCCGGGGCTATAATTGAAAAT 59.103 45.455 14.22 0.00 41.60 1.82
733 754 2.312390 GGCCGGGGCTATAATTGAAAA 58.688 47.619 14.22 0.00 41.60 2.29
734 755 1.816183 CGGCCGGGGCTATAATTGAAA 60.816 52.381 20.10 0.00 41.60 2.69
735 756 0.250553 CGGCCGGGGCTATAATTGAA 60.251 55.000 20.10 0.00 41.60 2.69
736 757 1.373435 CGGCCGGGGCTATAATTGA 59.627 57.895 20.10 0.00 41.60 2.57
737 758 2.332654 GCGGCCGGGGCTATAATTG 61.333 63.158 29.38 1.95 41.60 2.32
738 759 2.033602 GCGGCCGGGGCTATAATT 59.966 61.111 29.38 0.00 41.60 1.40
739 760 2.928396 AGCGGCCGGGGCTATAAT 60.928 61.111 29.38 0.00 39.39 1.28
740 761 3.622826 GAGCGGCCGGGGCTATAA 61.623 66.667 29.38 0.00 41.72 0.98
762 783 1.005340 CTCTGACTCCGCAATTCTGC 58.995 55.000 0.00 0.00 45.75 4.26
763 784 1.998315 CACTCTGACTCCGCAATTCTG 59.002 52.381 0.00 0.00 0.00 3.02
764 785 1.895798 TCACTCTGACTCCGCAATTCT 59.104 47.619 0.00 0.00 0.00 2.40
765 786 1.996191 GTCACTCTGACTCCGCAATTC 59.004 52.381 0.00 0.00 43.73 2.17
766 787 2.086054 GTCACTCTGACTCCGCAATT 57.914 50.000 0.00 0.00 43.73 2.32
767 788 3.822607 GTCACTCTGACTCCGCAAT 57.177 52.632 0.00 0.00 43.73 3.56
776 797 2.485479 GCCTTGTTTGGAGTCACTCTGA 60.485 50.000 4.40 0.00 0.00 3.27
777 798 1.876156 GCCTTGTTTGGAGTCACTCTG 59.124 52.381 4.40 0.00 0.00 3.35
778 799 1.202818 GGCCTTGTTTGGAGTCACTCT 60.203 52.381 4.40 0.00 0.00 3.24
779 800 1.202818 AGGCCTTGTTTGGAGTCACTC 60.203 52.381 0.00 0.00 0.00 3.51
780 801 0.846693 AGGCCTTGTTTGGAGTCACT 59.153 50.000 0.00 0.00 0.00 3.41
781 802 2.561478 TAGGCCTTGTTTGGAGTCAC 57.439 50.000 12.58 0.00 0.00 3.67
782 803 3.586470 TTTAGGCCTTGTTTGGAGTCA 57.414 42.857 12.58 0.00 0.00 3.41
783 804 6.584185 TTTATTTAGGCCTTGTTTGGAGTC 57.416 37.500 12.58 0.00 0.00 3.36
784 805 5.047306 GCTTTATTTAGGCCTTGTTTGGAGT 60.047 40.000 12.58 0.00 0.00 3.85
785 806 5.185828 AGCTTTATTTAGGCCTTGTTTGGAG 59.814 40.000 12.58 2.77 0.00 3.86
786 807 5.083821 AGCTTTATTTAGGCCTTGTTTGGA 58.916 37.500 12.58 0.00 0.00 3.53
787 808 5.185828 AGAGCTTTATTTAGGCCTTGTTTGG 59.814 40.000 12.58 0.00 0.00 3.28
788 809 6.151817 AGAGAGCTTTATTTAGGCCTTGTTTG 59.848 38.462 12.58 0.00 0.00 2.93
789 810 6.249192 AGAGAGCTTTATTTAGGCCTTGTTT 58.751 36.000 12.58 0.00 0.00 2.83
790 811 5.821097 AGAGAGCTTTATTTAGGCCTTGTT 58.179 37.500 12.58 0.00 0.00 2.83
791 812 5.443230 AGAGAGCTTTATTTAGGCCTTGT 57.557 39.130 12.58 0.00 0.00 3.16
792 813 7.554476 ACTTTAGAGAGCTTTATTTAGGCCTTG 59.446 37.037 12.58 0.00 0.00 3.61
793 814 7.634718 ACTTTAGAGAGCTTTATTTAGGCCTT 58.365 34.615 12.58 0.00 0.00 4.35
794 815 7.201702 ACTTTAGAGAGCTTTATTTAGGCCT 57.798 36.000 11.78 11.78 0.00 5.19
795 816 7.012515 GGAACTTTAGAGAGCTTTATTTAGGCC 59.987 40.741 0.00 0.00 0.00 5.19
796 817 7.012515 GGGAACTTTAGAGAGCTTTATTTAGGC 59.987 40.741 0.00 0.00 0.00 3.93
797 818 8.268605 AGGGAACTTTAGAGAGCTTTATTTAGG 58.731 37.037 0.00 0.00 37.44 2.69
798 819 9.103861 CAGGGAACTTTAGAGAGCTTTATTTAG 57.896 37.037 0.00 0.00 40.21 1.85
799 820 8.822805 TCAGGGAACTTTAGAGAGCTTTATTTA 58.177 33.333 0.00 0.00 40.21 1.40
800 821 7.690256 TCAGGGAACTTTAGAGAGCTTTATTT 58.310 34.615 0.00 0.00 40.21 1.40
801 822 7.259088 TCAGGGAACTTTAGAGAGCTTTATT 57.741 36.000 0.00 0.00 40.21 1.40
802 823 6.875972 TCAGGGAACTTTAGAGAGCTTTAT 57.124 37.500 0.00 0.00 40.21 1.40
803 824 6.681729 TTCAGGGAACTTTAGAGAGCTTTA 57.318 37.500 0.00 0.00 40.21 1.85
804 825 5.568620 TTCAGGGAACTTTAGAGAGCTTT 57.431 39.130 0.00 0.00 40.21 3.51
805 826 5.568620 TTTCAGGGAACTTTAGAGAGCTT 57.431 39.130 0.00 0.00 40.21 3.74
806 827 5.568620 TTTTCAGGGAACTTTAGAGAGCT 57.431 39.130 0.00 0.00 40.21 4.09
828 849 6.560711 CGATTCCCTCGGTTTCAATATTTTT 58.439 36.000 0.00 0.00 43.82 1.94
829 850 6.131544 CGATTCCCTCGGTTTCAATATTTT 57.868 37.500 0.00 0.00 43.82 1.82
830 851 5.751243 CGATTCCCTCGGTTTCAATATTT 57.249 39.130 0.00 0.00 43.82 1.40
887 908 0.824595 ATTCAAGGCAGCAGCACACA 60.825 50.000 2.65 0.00 44.61 3.72
888 909 0.316204 AATTCAAGGCAGCAGCACAC 59.684 50.000 2.65 0.00 44.61 3.82
889 910 0.315886 CAATTCAAGGCAGCAGCACA 59.684 50.000 2.65 0.00 44.61 4.57
890 911 0.316204 ACAATTCAAGGCAGCAGCAC 59.684 50.000 2.65 0.00 44.61 4.40
891 912 0.315886 CACAATTCAAGGCAGCAGCA 59.684 50.000 2.65 0.00 44.61 4.41
892 913 0.599558 TCACAATTCAAGGCAGCAGC 59.400 50.000 0.00 0.00 41.10 5.25
909 930 1.432514 GCAGCAGACTCGTCAATTCA 58.567 50.000 0.00 0.00 0.00 2.57
910 931 0.723981 GGCAGCAGACTCGTCAATTC 59.276 55.000 0.00 0.00 0.00 2.17
927 948 4.506255 CAGGGAATGGGGGACGGC 62.506 72.222 0.00 0.00 0.00 5.68
935 956 1.225704 GAGGTGGAGCAGGGAATGG 59.774 63.158 0.00 0.00 0.00 3.16
941 962 3.465403 CTCGGGAGGTGGAGCAGG 61.465 72.222 0.00 0.00 0.00 4.85
945 966 2.363018 TCTGCTCGGGAGGTGGAG 60.363 66.667 0.00 0.00 0.00 3.86
946 967 2.363018 CTCTGCTCGGGAGGTGGA 60.363 66.667 0.00 0.00 0.00 4.02
947 968 2.681778 ACTCTGCTCGGGAGGTGG 60.682 66.667 0.00 0.00 35.34 4.61
949 970 2.752238 CGACTCTGCTCGGGAGGT 60.752 66.667 0.00 0.00 35.34 3.85
965 986 0.742635 GCTTCCTTGCCTCCTTCTCG 60.743 60.000 0.00 0.00 0.00 4.04
969 990 0.773644 TTCTGCTTCCTTGCCTCCTT 59.226 50.000 0.00 0.00 0.00 3.36
976 997 2.417933 CCTTGTCGATTCTGCTTCCTTG 59.582 50.000 0.00 0.00 0.00 3.61
993 1014 0.463654 TCGATTCCGCCATTCCCTTG 60.464 55.000 0.00 0.00 35.37 3.61
998 1021 0.577269 CGAGTTCGATTCCGCCATTC 59.423 55.000 0.00 0.00 43.02 2.67
1184 1240 6.070881 CCAGTCATCATATAAGAGGGGAGAAG 60.071 46.154 0.00 0.00 0.00 2.85
1315 1374 4.498520 GTAGCCGCGCTGCTCTGA 62.499 66.667 29.97 10.32 41.68 3.27
1335 1394 0.316772 CGTATGCCTCGTACACTCCG 60.317 60.000 0.00 0.00 0.00 4.63
1404 1478 4.933064 TTTTGTTTGGCGGCGGCG 62.933 61.111 28.70 28.70 41.24 6.46
1405 1479 3.035503 CTTTTGTTTGGCGGCGGC 61.036 61.111 27.76 27.76 38.90 6.53
1406 1480 2.355718 CCTTTTGTTTGGCGGCGG 60.356 61.111 9.78 0.00 0.00 6.13
1407 1481 3.035503 GCCTTTTGTTTGGCGGCG 61.036 61.111 0.51 0.51 39.71 6.46
1411 1485 1.006220 CCTCCGCCTTTTGTTTGGC 60.006 57.895 0.00 0.00 45.25 4.52
1506 1580 1.643292 CTGCAATACCATCACGGCG 59.357 57.895 4.80 4.80 39.03 6.46
1554 1628 9.629878 CGATCTAGTATAAGATATAACCCACCT 57.370 37.037 0.00 0.00 36.33 4.00
1567 1641 3.744987 CGCGAACCCGATCTAGTATAAG 58.255 50.000 0.00 0.00 38.22 1.73
1629 1703 8.345565 GGGCTCTTACTGACAAATTATTACATG 58.654 37.037 0.00 0.00 0.00 3.21
1657 1731 5.420725 TGGTTGTCTACACATGCTATTCT 57.579 39.130 0.00 0.00 30.55 2.40
1724 1798 5.041287 CGAGCTTGATTCCGTCTTATAACA 58.959 41.667 0.00 0.00 0.00 2.41
1762 1836 5.762179 ATGGTCCTGTGTTTTATCTCTGA 57.238 39.130 0.00 0.00 0.00 3.27
1882 1956 4.196193 TGTTGTCTTTGTAGTGGAAGGTG 58.804 43.478 0.00 0.00 0.00 4.00
1972 2074 4.843984 CGTCGTTACAATTGTTTGATGGTC 59.156 41.667 17.78 5.77 36.64 4.02
2087 2189 4.946160 TCCCTATTCCCACATTTTCTGT 57.054 40.909 0.00 0.00 39.20 3.41
2114 2216 9.913310 CCTCTACAGGATGATGACTATCTAATA 57.087 37.037 0.00 0.00 43.65 0.98
2295 2397 1.100510 CATGCTTAGTGCTGCACCAT 58.899 50.000 27.74 20.11 42.26 3.55


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

AutoCloner maintained by Alex Coulton.