Multiple sequence alignment - TraesCS2B01G146200

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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 TraesCS2B01G146200 chr2B 100.000 3383 0 0 1 3383 112200036 112203418 0.000000e+00 6248.0
1 TraesCS2B01G146200 chr2B 87.319 276 24 6 2831 3096 112461506 112461780 4.240000e-79 305.0
2 TraesCS2B01G146200 chr2B 81.586 391 30 25 2740 3115 113162836 113163199 5.520000e-73 285.0
3 TraesCS2B01G146200 chr2B 82.282 333 28 18 2740 3059 112641959 112642273 3.350000e-65 259.0
4 TraesCS2B01G146200 chr2B 82.963 270 31 9 3115 3383 112468632 112468887 2.630000e-56 230.0
5 TraesCS2B01G146200 chr2B 81.569 255 15 19 2740 2982 113028491 113028725 7.460000e-42 182.0
6 TraesCS2B01G146200 chr2B 95.161 62 2 1 591 652 73939718 73939778 2.780000e-16 97.1
7 TraesCS2B01G146200 chr2B 96.875 32 1 0 2416 2447 113028165 113028196 2.000000e-03 54.7
8 TraesCS2B01G146200 chr2B 96.875 32 1 0 2543 2574 113162631 113162662 2.000000e-03 54.7
9 TraesCS2B01G146200 chr2B 100.000 28 0 0 2420 2447 113162496 113162523 6.000000e-03 52.8
10 TraesCS2B01G146200 chr2A 94.891 1781 52 11 854 2627 73282768 73284516 0.000000e+00 2748.0
11 TraesCS2B01G146200 chr2A 87.500 528 44 7 2733 3248 73285233 73285750 1.050000e-164 590.0
12 TraesCS2B01G146200 chr2A 84.536 291 30 11 2831 3115 73376563 73376844 1.200000e-69 274.0
13 TraesCS2B01G146200 chr2A 83.704 270 32 8 3115 3383 73383236 73383494 9.380000e-61 244.0
14 TraesCS2B01G146200 chr2A 84.541 207 18 5 2646 2838 73284575 73284781 3.440000e-45 193.0
15 TraesCS2B01G146200 chr2A 91.241 137 11 1 3244 3379 73298737 73298873 5.760000e-43 185.0
16 TraesCS2B01G146200 chr2A 85.542 83 3 3 2740 2814 73376482 73376563 1.010000e-10 78.7
17 TraesCS2B01G146200 chr2D 96.385 1217 39 2 1412 2627 73861519 73862731 0.000000e+00 1999.0
18 TraesCS2B01G146200 chr2D 93.310 583 38 1 16 597 610670282 610669700 0.000000e+00 859.0
19 TraesCS2B01G146200 chr2D 89.408 557 43 6 2833 3383 73863539 73864085 0.000000e+00 688.0
20 TraesCS2B01G146200 chr2D 96.947 393 11 1 945 1337 73860932 73861323 0.000000e+00 658.0
21 TraesCS2B01G146200 chr2D 82.593 270 35 6 3115 3383 73969217 73969475 9.440000e-56 228.0
22 TraesCS2B01G146200 chr2D 85.057 174 15 3 738 911 73860768 73860930 2.090000e-37 167.0
23 TraesCS2B01G146200 chr3B 93.300 597 40 0 1 597 57868026 57867430 0.000000e+00 881.0
24 TraesCS2B01G146200 chr3B 92.929 594 42 0 4 597 67231279 67230686 0.000000e+00 865.0
25 TraesCS2B01G146200 chr3B 92.797 597 41 2 1 597 353936951 353936357 0.000000e+00 863.0
26 TraesCS2B01G146200 chr3B 95.161 62 2 1 591 652 406552029 406551969 2.780000e-16 97.1
27 TraesCS2B01G146200 chr5B 92.809 598 42 1 1 597 454430593 454431190 0.000000e+00 865.0
28 TraesCS2B01G146200 chr5B 92.462 597 45 0 1 597 658329174 658328578 0.000000e+00 854.0
29 TraesCS2B01G146200 chr5B 95.082 61 2 1 591 651 190906450 190906509 9.990000e-16 95.3
30 TraesCS2B01G146200 chr1B 92.953 596 39 2 3 597 436169073 436168480 0.000000e+00 865.0
31 TraesCS2B01G146200 chr1B 92.617 596 41 2 3 597 436090312 436089719 0.000000e+00 854.0
32 TraesCS2B01G146200 chr1B 98.214 56 1 0 597 652 402686975 402686920 7.730000e-17 99.0
33 TraesCS2B01G146200 chr1B 97.059 34 1 0 617 650 314547919 314547886 1.310000e-04 58.4
34 TraesCS2B01G146200 chr4B 92.462 597 44 1 1 597 448104466 448103871 0.000000e+00 852.0
35 TraesCS2B01G146200 chr4B 93.548 62 3 1 591 652 88318390 88318330 1.290000e-14 91.6
36 TraesCS2B01G146200 chr6B 96.667 60 1 1 591 650 468426621 468426679 7.730000e-17 99.0
37 TraesCS2B01G146200 chr6B 95.161 62 2 1 591 652 303911013 303911073 2.780000e-16 97.1
38 TraesCS2B01G146200 chrUn 89.855 69 6 1 585 652 16683555 16683487 1.670000e-13 87.9


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 TraesCS2B01G146200 chr2B 112200036 112203418 3382 False 6248 6248 100.000000 1 3383 1 chr2B.!!$F2 3382
1 TraesCS2B01G146200 chr2A 73282768 73285750 2982 False 1177 2748 88.977333 854 3248 3 chr2A.!!$F3 2394
2 TraesCS2B01G146200 chr2D 73860768 73864085 3317 False 878 1999 91.949250 738 3383 4 chr2D.!!$F2 2645
3 TraesCS2B01G146200 chr2D 610669700 610670282 582 True 859 859 93.310000 16 597 1 chr2D.!!$R1 581
4 TraesCS2B01G146200 chr3B 57867430 57868026 596 True 881 881 93.300000 1 597 1 chr3B.!!$R1 596
5 TraesCS2B01G146200 chr3B 67230686 67231279 593 True 865 865 92.929000 4 597 1 chr3B.!!$R2 593
6 TraesCS2B01G146200 chr3B 353936357 353936951 594 True 863 863 92.797000 1 597 1 chr3B.!!$R3 596
7 TraesCS2B01G146200 chr5B 454430593 454431190 597 False 865 865 92.809000 1 597 1 chr5B.!!$F2 596
8 TraesCS2B01G146200 chr5B 658328578 658329174 596 True 854 854 92.462000 1 597 1 chr5B.!!$R1 596
9 TraesCS2B01G146200 chr1B 436168480 436169073 593 True 865 865 92.953000 3 597 1 chr1B.!!$R4 594
10 TraesCS2B01G146200 chr1B 436089719 436090312 593 True 854 854 92.617000 3 597 1 chr1B.!!$R3 594
11 TraesCS2B01G146200 chr4B 448103871 448104466 595 True 852 852 92.462000 1 597 1 chr4B.!!$R2 596

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
615 618 0.037303 CAGTGACTCAATGGCAGGGT 59.963 55.0 0.00 0.0 31.98 4.34 F
844 847 0.100682 TAAGAGCCATCTCACGCGTC 59.899 55.0 9.86 0.0 41.81 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1599 1730 1.069204 GCGTAGATGATGAGGAAGGCA 59.931 52.381 0.0 0.0 0.00 4.75 R
2784 2970 0.749454 ATGCCGCTGGGAGATGAAAC 60.749 55.000 0.0 0.0 34.06 2.78 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
65 66 1.687494 GCGAGCACGAAGGATGTCAC 61.687 60.000 8.01 0.00 42.66 3.67
159 160 5.936956 GGAGATTCTGCCTATGTATGGAAAG 59.063 44.000 0.00 0.00 0.00 2.62
161 162 4.502105 TTCTGCCTATGTATGGAAAGCA 57.498 40.909 0.00 0.00 0.00 3.91
178 179 3.849951 ATGTACGCAGAGGGGCCG 61.850 66.667 0.00 0.00 0.00 6.13
388 389 1.149174 CCAATGGGGATCCGTCCTG 59.851 63.158 5.45 0.62 44.44 3.86
395 396 1.123928 GGGATCCGTCCTGAAGATGT 58.876 55.000 5.45 0.00 44.44 3.06
416 417 2.126228 CCTGAGTTTACGCGCCGA 60.126 61.111 5.73 0.00 0.00 5.54
515 518 8.709386 AAGTACTGCAGAGTCATATTACAAAG 57.291 34.615 23.35 0.00 33.21 2.77
539 542 1.070038 CGCCGCGGTTCTAACTAAAA 58.930 50.000 28.70 0.00 0.00 1.52
597 600 0.834687 AGAAACGGGGTGCCTAGTCA 60.835 55.000 0.00 0.00 0.00 3.41
598 601 0.391263 GAAACGGGGTGCCTAGTCAG 60.391 60.000 0.00 0.00 0.00 3.51
599 602 1.125711 AAACGGGGTGCCTAGTCAGT 61.126 55.000 0.00 0.00 0.00 3.41
600 603 1.827399 AACGGGGTGCCTAGTCAGTG 61.827 60.000 0.00 0.00 0.00 3.66
601 604 1.982395 CGGGGTGCCTAGTCAGTGA 60.982 63.158 0.00 0.00 0.00 3.41
602 605 1.597461 GGGGTGCCTAGTCAGTGAC 59.403 63.158 15.78 15.78 0.00 3.67
603 606 0.905337 GGGGTGCCTAGTCAGTGACT 60.905 60.000 27.98 27.98 45.54 3.41
604 607 0.533032 GGGTGCCTAGTCAGTGACTC 59.467 60.000 28.70 15.42 42.40 3.36
605 608 1.257743 GGTGCCTAGTCAGTGACTCA 58.742 55.000 28.70 17.83 42.40 3.41
606 609 1.618837 GGTGCCTAGTCAGTGACTCAA 59.381 52.381 28.70 12.13 42.40 3.02
607 610 2.234908 GGTGCCTAGTCAGTGACTCAAT 59.765 50.000 28.70 8.51 42.40 2.57
608 611 3.257393 GTGCCTAGTCAGTGACTCAATG 58.743 50.000 28.70 15.97 42.40 2.82
609 612 2.234661 TGCCTAGTCAGTGACTCAATGG 59.765 50.000 28.70 23.80 42.40 3.16
610 613 2.898705 CCTAGTCAGTGACTCAATGGC 58.101 52.381 28.70 2.82 42.40 4.40
611 614 2.234661 CCTAGTCAGTGACTCAATGGCA 59.765 50.000 28.70 9.16 42.40 4.92
612 615 2.469274 AGTCAGTGACTCAATGGCAG 57.531 50.000 20.34 0.00 38.71 4.85
613 616 1.002888 AGTCAGTGACTCAATGGCAGG 59.997 52.381 20.34 0.00 38.71 4.85
614 617 0.325933 TCAGTGACTCAATGGCAGGG 59.674 55.000 6.64 0.00 31.98 4.45
615 618 0.037303 CAGTGACTCAATGGCAGGGT 59.963 55.000 0.00 0.00 31.98 4.34
616 619 1.278985 CAGTGACTCAATGGCAGGGTA 59.721 52.381 0.00 0.00 31.98 3.69
617 620 2.092753 CAGTGACTCAATGGCAGGGTAT 60.093 50.000 0.00 0.00 31.98 2.73
618 621 2.092753 AGTGACTCAATGGCAGGGTATG 60.093 50.000 0.00 0.00 31.98 2.39
619 622 2.092968 GTGACTCAATGGCAGGGTATGA 60.093 50.000 0.00 0.00 31.98 2.15
620 623 2.092968 TGACTCAATGGCAGGGTATGAC 60.093 50.000 0.00 0.00 37.50 3.06
624 627 3.739922 TGGCAGGGTATGACAGGG 58.260 61.111 0.00 0.00 44.15 4.45
625 628 1.082019 TGGCAGGGTATGACAGGGA 59.918 57.895 0.00 0.00 44.15 4.20
626 629 0.327480 TGGCAGGGTATGACAGGGAT 60.327 55.000 0.00 0.00 44.15 3.85
627 630 0.846693 GGCAGGGTATGACAGGGATT 59.153 55.000 0.00 0.00 36.67 3.01
628 631 2.054799 GGCAGGGTATGACAGGGATTA 58.945 52.381 0.00 0.00 36.67 1.75
629 632 2.224548 GGCAGGGTATGACAGGGATTAC 60.225 54.545 0.00 0.00 36.67 1.89
630 633 2.438021 GCAGGGTATGACAGGGATTACA 59.562 50.000 0.00 0.00 0.00 2.41
631 634 3.118038 GCAGGGTATGACAGGGATTACAA 60.118 47.826 0.00 0.00 0.00 2.41
632 635 4.627741 GCAGGGTATGACAGGGATTACAAA 60.628 45.833 0.00 0.00 0.00 2.83
633 636 5.126067 CAGGGTATGACAGGGATTACAAAG 58.874 45.833 0.00 0.00 0.00 2.77
634 637 4.788617 AGGGTATGACAGGGATTACAAAGT 59.211 41.667 0.00 0.00 0.00 2.66
635 638 5.104485 AGGGTATGACAGGGATTACAAAGTC 60.104 44.000 0.00 0.00 0.00 3.01
636 639 5.338871 GGGTATGACAGGGATTACAAAGTCA 60.339 44.000 0.00 0.00 39.90 3.41
637 640 5.817816 GGTATGACAGGGATTACAAAGTCAG 59.182 44.000 0.00 0.00 39.10 3.51
638 641 5.762179 ATGACAGGGATTACAAAGTCAGA 57.238 39.130 0.00 0.00 39.10 3.27
639 642 5.152623 TGACAGGGATTACAAAGTCAGAG 57.847 43.478 0.00 0.00 32.76 3.35
640 643 4.020218 TGACAGGGATTACAAAGTCAGAGG 60.020 45.833 0.00 0.00 32.76 3.69
641 644 4.168101 ACAGGGATTACAAAGTCAGAGGA 58.832 43.478 0.00 0.00 0.00 3.71
642 645 4.785376 ACAGGGATTACAAAGTCAGAGGAT 59.215 41.667 0.00 0.00 0.00 3.24
643 646 5.104735 ACAGGGATTACAAAGTCAGAGGATC 60.105 44.000 0.00 0.00 0.00 3.36
644 647 4.410555 AGGGATTACAAAGTCAGAGGATCC 59.589 45.833 2.48 2.48 33.66 3.36
645 648 4.164221 GGGATTACAAAGTCAGAGGATCCA 59.836 45.833 15.82 0.00 34.81 3.41
646 649 5.119694 GGATTACAAAGTCAGAGGATCCAC 58.880 45.833 15.82 8.01 33.66 4.02
647 650 2.751166 ACAAAGTCAGAGGATCCACG 57.249 50.000 15.82 4.66 33.66 4.94
648 651 1.971357 ACAAAGTCAGAGGATCCACGT 59.029 47.619 15.82 0.00 33.66 4.49
649 652 2.028930 ACAAAGTCAGAGGATCCACGTC 60.029 50.000 15.82 2.55 33.66 4.34
650 653 1.187087 AAGTCAGAGGATCCACGTCC 58.813 55.000 15.82 0.79 38.62 4.79
651 654 1.032657 AGTCAGAGGATCCACGTCCG 61.033 60.000 15.82 0.00 43.27 4.79
652 655 1.030488 GTCAGAGGATCCACGTCCGA 61.030 60.000 15.82 0.00 43.27 4.55
653 656 0.106669 TCAGAGGATCCACGTCCGAT 60.107 55.000 15.82 0.00 43.27 4.18
654 657 0.747255 CAGAGGATCCACGTCCGATT 59.253 55.000 15.82 0.00 43.27 3.34
655 658 1.954382 CAGAGGATCCACGTCCGATTA 59.046 52.381 15.82 0.00 43.27 1.75
656 659 2.361119 CAGAGGATCCACGTCCGATTAA 59.639 50.000 15.82 0.00 43.27 1.40
657 660 3.028850 AGAGGATCCACGTCCGATTAAA 58.971 45.455 15.82 0.00 43.27 1.52
658 661 3.449737 AGAGGATCCACGTCCGATTAAAA 59.550 43.478 15.82 0.00 43.27 1.52
659 662 3.528532 AGGATCCACGTCCGATTAAAAC 58.471 45.455 15.82 0.00 43.27 2.43
660 663 2.283351 GGATCCACGTCCGATTAAAACG 59.717 50.000 6.95 0.00 41.93 3.60
661 664 2.721274 TCCACGTCCGATTAAAACGA 57.279 45.000 0.71 0.00 39.59 3.85
662 665 3.235157 TCCACGTCCGATTAAAACGAT 57.765 42.857 0.71 0.00 39.59 3.73
663 666 2.924926 TCCACGTCCGATTAAAACGATG 59.075 45.455 0.71 0.16 39.59 3.84
664 667 2.924926 CCACGTCCGATTAAAACGATGA 59.075 45.455 0.71 0.00 39.59 2.92
665 668 3.000078 CCACGTCCGATTAAAACGATGAG 60.000 47.826 0.71 0.00 39.59 2.90
666 669 3.000078 CACGTCCGATTAAAACGATGAGG 60.000 47.826 0.71 6.50 39.59 3.86
667 670 3.119388 ACGTCCGATTAAAACGATGAGGA 60.119 43.478 0.71 0.00 39.59 3.71
668 671 3.242248 CGTCCGATTAAAACGATGAGGAC 59.758 47.826 6.93 1.55 42.34 3.85
669 672 4.430908 GTCCGATTAAAACGATGAGGACT 58.569 43.478 4.26 0.00 42.44 3.85
670 673 5.585390 GTCCGATTAAAACGATGAGGACTA 58.415 41.667 4.26 0.00 42.44 2.59
671 674 5.686397 GTCCGATTAAAACGATGAGGACTAG 59.314 44.000 4.26 0.00 42.44 2.57
672 675 5.359009 TCCGATTAAAACGATGAGGACTAGT 59.641 40.000 0.00 0.00 0.00 2.57
673 676 6.543465 TCCGATTAAAACGATGAGGACTAGTA 59.457 38.462 0.00 0.00 0.00 1.82
674 677 6.856938 CCGATTAAAACGATGAGGACTAGTAG 59.143 42.308 0.00 0.00 0.00 2.57
675 678 6.360148 CGATTAAAACGATGAGGACTAGTAGC 59.640 42.308 0.00 0.00 0.00 3.58
676 679 3.694535 AAACGATGAGGACTAGTAGCG 57.305 47.619 0.00 0.00 0.00 4.26
677 680 2.616634 ACGATGAGGACTAGTAGCGA 57.383 50.000 7.93 0.00 0.00 4.93
678 681 3.128852 ACGATGAGGACTAGTAGCGAT 57.871 47.619 7.93 0.00 0.00 4.58
679 682 3.478509 ACGATGAGGACTAGTAGCGATT 58.521 45.455 7.93 0.00 0.00 3.34
680 683 3.251245 ACGATGAGGACTAGTAGCGATTG 59.749 47.826 7.93 0.32 0.00 2.67
681 684 3.498777 CGATGAGGACTAGTAGCGATTGA 59.501 47.826 0.00 0.00 0.00 2.57
682 685 4.377943 CGATGAGGACTAGTAGCGATTGAG 60.378 50.000 0.00 0.00 0.00 3.02
683 686 3.887352 TGAGGACTAGTAGCGATTGAGT 58.113 45.455 0.00 0.00 0.00 3.41
684 687 3.878103 TGAGGACTAGTAGCGATTGAGTC 59.122 47.826 0.00 0.00 36.60 3.36
685 688 4.131596 GAGGACTAGTAGCGATTGAGTCT 58.868 47.826 0.00 0.00 37.33 3.24
686 689 4.528920 AGGACTAGTAGCGATTGAGTCTT 58.471 43.478 0.00 0.29 37.33 3.01
687 690 5.682659 AGGACTAGTAGCGATTGAGTCTTA 58.317 41.667 0.00 0.00 37.33 2.10
688 691 6.120905 AGGACTAGTAGCGATTGAGTCTTAA 58.879 40.000 0.00 0.00 37.33 1.85
689 692 6.773685 AGGACTAGTAGCGATTGAGTCTTAAT 59.226 38.462 0.00 0.00 37.33 1.40
690 693 6.858993 GGACTAGTAGCGATTGAGTCTTAATG 59.141 42.308 0.00 0.00 37.33 1.90
691 694 6.740110 ACTAGTAGCGATTGAGTCTTAATGG 58.260 40.000 0.00 0.00 0.00 3.16
692 695 5.599999 AGTAGCGATTGAGTCTTAATGGT 57.400 39.130 0.00 0.00 0.00 3.55
693 696 5.352284 AGTAGCGATTGAGTCTTAATGGTG 58.648 41.667 0.00 0.00 0.00 4.17
694 697 2.939103 AGCGATTGAGTCTTAATGGTGC 59.061 45.455 0.00 0.00 0.00 5.01
695 698 2.032178 GCGATTGAGTCTTAATGGTGCC 59.968 50.000 0.00 0.00 0.00 5.01
696 699 2.285220 CGATTGAGTCTTAATGGTGCCG 59.715 50.000 0.00 0.00 0.00 5.69
697 700 2.107950 TTGAGTCTTAATGGTGCCGG 57.892 50.000 0.00 0.00 0.00 6.13
698 701 1.271856 TGAGTCTTAATGGTGCCGGA 58.728 50.000 5.05 0.00 0.00 5.14
699 702 1.626321 TGAGTCTTAATGGTGCCGGAA 59.374 47.619 5.05 0.00 0.00 4.30
700 703 2.280628 GAGTCTTAATGGTGCCGGAAG 58.719 52.381 5.05 0.00 0.00 3.46
713 716 3.798511 GGAAGGGGGAAGGCGGAG 61.799 72.222 0.00 0.00 0.00 4.63
714 717 3.798511 GAAGGGGGAAGGCGGAGG 61.799 72.222 0.00 0.00 0.00 4.30
760 763 3.482783 GCGTGAAGCCAGTCGAGC 61.483 66.667 0.00 0.00 40.81 5.03
764 767 2.202676 GAAGCCAGTCGAGCGAGG 60.203 66.667 0.00 0.00 34.64 4.63
765 768 3.708220 GAAGCCAGTCGAGCGAGGG 62.708 68.421 6.24 6.24 34.64 4.30
789 792 0.250901 GGCCGCATGATGAAGGGTAT 60.251 55.000 0.00 0.00 0.00 2.73
819 822 3.620488 TGAGAAGTTGTTTCCACTGCTT 58.380 40.909 0.00 0.00 36.40 3.91
826 829 8.691797 AGAAGTTGTTTCCACTGCTTAAAATTA 58.308 29.630 0.00 0.00 36.40 1.40
828 831 8.871686 AGTTGTTTCCACTGCTTAAAATTAAG 57.128 30.769 8.27 8.27 42.30 1.85
829 832 8.691797 AGTTGTTTCCACTGCTTAAAATTAAGA 58.308 29.630 15.33 2.31 42.05 2.10
830 833 8.968242 GTTGTTTCCACTGCTTAAAATTAAGAG 58.032 33.333 15.33 11.71 42.05 2.85
831 834 7.145323 TGTTTCCACTGCTTAAAATTAAGAGC 58.855 34.615 15.33 3.98 42.05 4.09
832 835 5.897377 TCCACTGCTTAAAATTAAGAGCC 57.103 39.130 15.33 0.91 42.05 4.70
833 836 5.321102 TCCACTGCTTAAAATTAAGAGCCA 58.679 37.500 15.33 4.85 42.05 4.75
834 837 5.951747 TCCACTGCTTAAAATTAAGAGCCAT 59.048 36.000 15.33 0.00 42.05 4.40
835 838 6.095440 TCCACTGCTTAAAATTAAGAGCCATC 59.905 38.462 15.33 0.00 42.05 3.51
836 839 6.096001 CCACTGCTTAAAATTAAGAGCCATCT 59.904 38.462 15.33 0.00 42.05 2.90
837 840 7.192232 CACTGCTTAAAATTAAGAGCCATCTC 58.808 38.462 15.33 0.00 42.05 2.75
838 841 6.886459 ACTGCTTAAAATTAAGAGCCATCTCA 59.114 34.615 15.33 2.53 42.05 3.27
839 842 7.088589 TGCTTAAAATTAAGAGCCATCTCAC 57.911 36.000 15.33 0.00 42.05 3.51
844 847 0.100682 TAAGAGCCATCTCACGCGTC 59.899 55.000 9.86 0.00 41.81 5.19
868 871 6.645415 TCTCCTAACACTTTTGAGAATTCGAC 59.355 38.462 0.00 0.00 0.00 4.20
887 890 9.959749 AATTCGACTAGATCTGATTTAACTCTC 57.040 33.333 5.18 0.00 0.00 3.20
929 933 3.008485 AGTTAAGTCCTCTTGAGGCTTGG 59.992 47.826 23.61 2.78 35.36 3.61
936 940 2.355209 CCTCTTGAGGCTTGGGTTAGAC 60.355 54.545 3.51 0.00 0.00 2.59
943 947 1.383523 GCTTGGGTTAGACATGCCTC 58.616 55.000 0.00 0.00 34.15 4.70
967 971 2.418976 CACAGCTCACTCAATCACCATG 59.581 50.000 0.00 0.00 0.00 3.66
1144 1148 4.404640 CATGATTATCTCCAAGCCACCAT 58.595 43.478 0.00 0.00 0.00 3.55
1154 1158 4.759205 GCCACCATTCCGCCCCTT 62.759 66.667 0.00 0.00 0.00 3.95
1599 1730 2.416547 CGTCATCGCCAACTTCATCTTT 59.583 45.455 0.00 0.00 0.00 2.52
1878 2009 0.540830 AGCAGTTCCTCGACCTCACT 60.541 55.000 0.00 0.00 0.00 3.41
1941 2072 2.716217 GTGCAGCTTTCTCCCAACTAT 58.284 47.619 0.00 0.00 0.00 2.12
1970 2101 2.590575 CGTGCACCCAAGGAACGT 60.591 61.111 12.15 0.00 0.00 3.99
1971 2102 2.604174 CGTGCACCCAAGGAACGTC 61.604 63.158 12.15 0.00 0.00 4.34
2055 2186 1.079127 CCGGCAGACGTTCCTCAAT 60.079 57.895 0.00 0.00 42.24 2.57
2082 2213 2.915659 ACGGCGGAGAAGGTGTCA 60.916 61.111 13.24 0.00 0.00 3.58
2191 2322 3.989698 CTCGCGGCGATCAACCTGT 62.990 63.158 26.60 0.00 34.61 4.00
2197 2328 2.325082 GCGATCAACCTGTTGCCGT 61.325 57.895 18.44 4.98 40.24 5.68
2238 2369 1.760268 CGCTGGCGCTGATTCTTCTC 61.760 60.000 7.64 0.00 0.00 2.87
2449 2580 2.401583 TGTAAGACGAAGCCATGCAT 57.598 45.000 0.00 0.00 0.00 3.96
2450 2581 2.009051 TGTAAGACGAAGCCATGCATG 58.991 47.619 20.19 20.19 0.00 4.06
2451 2582 2.009774 GTAAGACGAAGCCATGCATGT 58.990 47.619 24.58 6.98 0.00 3.21
2452 2583 2.401583 AAGACGAAGCCATGCATGTA 57.598 45.000 24.58 0.00 0.00 2.29
2514 2645 4.985409 GGAGATAGTAGAACCGATTTGCAG 59.015 45.833 0.00 0.00 0.00 4.41
2591 2723 6.472887 TCTGATAGTAGGAACCAAGGTTTTG 58.527 40.000 5.87 0.00 38.60 2.44
2627 2759 3.128589 GCCTAATTCTGGTTCGATTTGCA 59.871 43.478 0.00 0.00 0.00 4.08
2628 2760 4.202050 GCCTAATTCTGGTTCGATTTGCAT 60.202 41.667 0.00 0.00 0.00 3.96
2629 2761 5.679638 GCCTAATTCTGGTTCGATTTGCATT 60.680 40.000 0.00 0.00 0.00 3.56
2630 2762 5.973565 CCTAATTCTGGTTCGATTTGCATTC 59.026 40.000 0.00 0.00 0.00 2.67
2631 2763 5.649782 AATTCTGGTTCGATTTGCATTCT 57.350 34.783 0.00 0.00 0.00 2.40
2632 2764 5.649782 ATTCTGGTTCGATTTGCATTCTT 57.350 34.783 0.00 0.00 0.00 2.52
2633 2765 5.452078 TTCTGGTTCGATTTGCATTCTTT 57.548 34.783 0.00 0.00 0.00 2.52
2634 2766 5.452078 TCTGGTTCGATTTGCATTCTTTT 57.548 34.783 0.00 0.00 0.00 2.27
2635 2767 6.567687 TCTGGTTCGATTTGCATTCTTTTA 57.432 33.333 0.00 0.00 0.00 1.52
2637 2769 8.275015 TCTGGTTCGATTTGCATTCTTTTATA 57.725 30.769 0.00 0.00 0.00 0.98
2638 2770 8.735315 TCTGGTTCGATTTGCATTCTTTTATAA 58.265 29.630 0.00 0.00 0.00 0.98
2640 2772 8.300286 TGGTTCGATTTGCATTCTTTTATAACA 58.700 29.630 0.00 0.00 0.00 2.41
2641 2773 9.301153 GGTTCGATTTGCATTCTTTTATAACAT 57.699 29.630 0.00 0.00 0.00 2.71
2643 2775 9.853555 TTCGATTTGCATTCTTTTATAACATGT 57.146 25.926 0.00 0.00 0.00 3.21
2648 2780 8.613613 TTGCATTCTTTTATAACATGTTAGCG 57.386 30.769 22.03 9.43 0.00 4.26
2667 2839 2.661566 CCGAGCTGCACAACACTCG 61.662 63.158 1.02 4.38 43.47 4.18
2733 2911 3.367498 GCCTGATACTGCTAATACCGGAG 60.367 52.174 9.46 0.00 0.00 4.63
2739 2917 0.750850 TGCTAATACCGGAGCCTGAC 59.249 55.000 9.46 0.00 37.94 3.51
2740 2918 0.033642 GCTAATACCGGAGCCTGACC 59.966 60.000 9.46 0.00 32.25 4.02
2742 2920 1.971357 CTAATACCGGAGCCTGACCAT 59.029 52.381 9.46 0.00 0.00 3.55
2758 2937 5.023533 TGACCATTCCAGTACATAAGCTC 57.976 43.478 0.00 0.00 0.00 4.09
2784 2970 3.165058 TGCTGCTCTATAACGTCAAGG 57.835 47.619 0.00 0.00 0.00 3.61
2821 3007 4.502087 CGGCATCAATATCAGAACTGGAGA 60.502 45.833 1.93 0.00 0.00 3.71
2822 3008 5.558818 GGCATCAATATCAGAACTGGAGAT 58.441 41.667 1.93 0.00 0.00 2.75
2826 3601 7.013083 GCATCAATATCAGAACTGGAGATGTTT 59.987 37.037 0.00 0.00 34.43 2.83
2831 3606 5.233083 TCAGAACTGGAGATGTTTGTCAT 57.767 39.130 1.93 0.00 39.77 3.06
2845 3620 9.676861 AGATGTTTGTCATATCTGAATCAGAAA 57.323 29.630 17.59 2.88 39.28 2.52
2855 3630 4.458397 TCTGAATCAGAAATGGAGGCATC 58.542 43.478 10.99 0.00 37.57 3.91
2869 3644 3.055530 GGAGGCATCCGTCATATCTGAAT 60.056 47.826 0.00 0.00 35.37 2.57
2874 3649 4.143242 GCATCCGTCATATCTGAATCAACG 60.143 45.833 0.00 0.00 31.85 4.10
2894 3669 5.366829 ACGTTAAGAAAAATACTGGGTGC 57.633 39.130 0.00 0.00 0.00 5.01
2897 3672 6.084277 CGTTAAGAAAAATACTGGGTGCTTC 58.916 40.000 0.00 0.00 0.00 3.86
2898 3673 6.293735 CGTTAAGAAAAATACTGGGTGCTTCA 60.294 38.462 0.00 0.00 0.00 3.02
2901 3676 3.942130 AAAATACTGGGTGCTTCAAGC 57.058 42.857 1.04 1.04 42.82 4.01
2948 3723 3.255969 AGCAATGCAATCAATTGGGAC 57.744 42.857 8.35 0.00 38.21 4.46
2949 3724 1.928503 GCAATGCAATCAATTGGGACG 59.071 47.619 5.42 0.00 38.21 4.79
2952 3727 2.142356 TGCAATCAATTGGGACGGAT 57.858 45.000 5.42 0.00 38.21 4.18
2956 3731 5.380900 TGCAATCAATTGGGACGGATAATA 58.619 37.500 5.42 0.00 38.21 0.98
2961 3736 5.373222 TCAATTGGGACGGATAATAACCAG 58.627 41.667 5.42 0.00 0.00 4.00
2976 3751 1.538047 ACCAGTACAAGCATGCAAGG 58.462 50.000 21.98 11.05 0.00 3.61
3026 3805 7.772332 AGTAGCTAATACAAACTCAAATCCG 57.228 36.000 0.00 0.00 36.79 4.18
3059 3838 4.599041 ACATTATGGTCCTGCTTTGCTTA 58.401 39.130 0.00 0.00 0.00 3.09
3060 3839 5.203528 ACATTATGGTCCTGCTTTGCTTAT 58.796 37.500 0.00 0.00 0.00 1.73
3061 3840 6.364701 ACATTATGGTCCTGCTTTGCTTATA 58.635 36.000 0.00 0.00 0.00 0.98
3062 3841 6.833416 ACATTATGGTCCTGCTTTGCTTATAA 59.167 34.615 0.00 0.00 0.00 0.98
3066 3846 9.586732 TTATGGTCCTGCTTTGCTTATAATTAT 57.413 29.630 2.97 2.97 0.00 1.28
3129 3909 7.987458 TGAGAAACATATACTTCTTGATGTCCC 59.013 37.037 1.19 0.00 32.01 4.46
3199 3979 9.314321 ACAATTATTACTGACATAGCACACTAC 57.686 33.333 0.00 0.00 0.00 2.73
3200 3980 9.534565 CAATTATTACTGACATAGCACACTACT 57.465 33.333 0.00 0.00 0.00 2.57
3206 3986 6.726230 ACTGACATAGCACACTACTAATACG 58.274 40.000 0.00 0.00 0.00 3.06
3264 4044 6.752815 GTCCTATAGAGTGCAAAGTACAAGTC 59.247 42.308 0.00 0.00 0.00 3.01
3274 4054 5.154222 GCAAAGTACAAGTCTGCAAATACC 58.846 41.667 0.00 0.00 33.19 2.73
3282 4062 2.028112 AGTCTGCAAATACCGAGAGCAA 60.028 45.455 0.00 0.00 34.45 3.91
3294 4074 2.002586 CGAGAGCAAGGTTACCATGTG 58.997 52.381 8.45 2.25 0.00 3.21
3302 4082 3.983044 AGGTTACCATGTGGAAGAGAC 57.017 47.619 3.51 0.00 38.94 3.36
3365 4145 3.931578 ACCTATGTTGCTGAACTGAGAC 58.068 45.455 0.00 0.00 32.79 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
159 160 2.897350 GCCCCTCTGCGTACATGC 60.897 66.667 0.00 0.00 0.00 4.06
161 162 3.849951 CGGCCCCTCTGCGTACAT 61.850 66.667 0.00 0.00 0.00 2.29
388 389 2.100605 AAACTCAGGGCGACATCTTC 57.899 50.000 0.00 0.00 0.00 2.87
416 417 1.695788 ACGTTAACTGGGTAGGCTTGT 59.304 47.619 3.71 0.00 0.00 3.16
539 542 5.126061 GTCCATGACCAAGACAATTGCTATT 59.874 40.000 5.05 0.00 0.00 1.73
597 600 1.656587 TACCCTGCCATTGAGTCACT 58.343 50.000 0.00 0.00 0.00 3.41
598 601 2.092968 TCATACCCTGCCATTGAGTCAC 60.093 50.000 0.00 0.00 0.00 3.67
599 602 2.092968 GTCATACCCTGCCATTGAGTCA 60.093 50.000 0.00 0.00 0.00 3.41
600 603 2.092968 TGTCATACCCTGCCATTGAGTC 60.093 50.000 0.00 0.00 0.00 3.36
601 604 1.915489 TGTCATACCCTGCCATTGAGT 59.085 47.619 0.00 0.00 0.00 3.41
602 605 2.569059 CTGTCATACCCTGCCATTGAG 58.431 52.381 0.00 0.00 0.00 3.02
603 606 1.212688 CCTGTCATACCCTGCCATTGA 59.787 52.381 0.00 0.00 0.00 2.57
604 607 1.683943 CCTGTCATACCCTGCCATTG 58.316 55.000 0.00 0.00 0.00 2.82
605 608 0.552848 CCCTGTCATACCCTGCCATT 59.447 55.000 0.00 0.00 0.00 3.16
606 609 0.327480 TCCCTGTCATACCCTGCCAT 60.327 55.000 0.00 0.00 0.00 4.40
607 610 0.327480 ATCCCTGTCATACCCTGCCA 60.327 55.000 0.00 0.00 0.00 4.92
608 611 0.846693 AATCCCTGTCATACCCTGCC 59.153 55.000 0.00 0.00 0.00 4.85
609 612 2.438021 TGTAATCCCTGTCATACCCTGC 59.562 50.000 0.00 0.00 0.00 4.85
610 613 4.771114 TTGTAATCCCTGTCATACCCTG 57.229 45.455 0.00 0.00 0.00 4.45
611 614 4.788617 ACTTTGTAATCCCTGTCATACCCT 59.211 41.667 0.00 0.00 0.00 4.34
612 615 5.112129 ACTTTGTAATCCCTGTCATACCC 57.888 43.478 0.00 0.00 0.00 3.69
613 616 5.741011 TGACTTTGTAATCCCTGTCATACC 58.259 41.667 0.00 0.00 30.78 2.73
614 617 6.640518 TCTGACTTTGTAATCCCTGTCATAC 58.359 40.000 0.00 0.00 34.57 2.39
615 618 6.127054 CCTCTGACTTTGTAATCCCTGTCATA 60.127 42.308 0.00 0.00 34.57 2.15
616 619 5.338708 CCTCTGACTTTGTAATCCCTGTCAT 60.339 44.000 0.00 0.00 34.57 3.06
617 620 4.020218 CCTCTGACTTTGTAATCCCTGTCA 60.020 45.833 0.00 0.00 34.04 3.58
618 621 4.223032 TCCTCTGACTTTGTAATCCCTGTC 59.777 45.833 0.00 0.00 0.00 3.51
619 622 4.168101 TCCTCTGACTTTGTAATCCCTGT 58.832 43.478 0.00 0.00 0.00 4.00
620 623 4.826274 TCCTCTGACTTTGTAATCCCTG 57.174 45.455 0.00 0.00 0.00 4.45
621 624 4.410555 GGATCCTCTGACTTTGTAATCCCT 59.589 45.833 3.84 0.00 0.00 4.20
622 625 4.164221 TGGATCCTCTGACTTTGTAATCCC 59.836 45.833 14.23 0.00 32.26 3.85
623 626 5.119694 GTGGATCCTCTGACTTTGTAATCC 58.880 45.833 14.23 0.00 33.56 3.01
624 627 4.806247 CGTGGATCCTCTGACTTTGTAATC 59.194 45.833 14.23 0.00 0.00 1.75
625 628 4.223032 ACGTGGATCCTCTGACTTTGTAAT 59.777 41.667 14.23 0.00 0.00 1.89
626 629 3.576982 ACGTGGATCCTCTGACTTTGTAA 59.423 43.478 14.23 0.00 0.00 2.41
627 630 3.162666 ACGTGGATCCTCTGACTTTGTA 58.837 45.455 14.23 0.00 0.00 2.41
628 631 1.971357 ACGTGGATCCTCTGACTTTGT 59.029 47.619 14.23 0.00 0.00 2.83
629 632 2.611518 GACGTGGATCCTCTGACTTTG 58.388 52.381 14.23 0.00 0.00 2.77
630 633 1.550976 GGACGTGGATCCTCTGACTTT 59.449 52.381 14.23 0.00 35.68 2.66
631 634 1.187087 GGACGTGGATCCTCTGACTT 58.813 55.000 14.23 0.00 35.68 3.01
632 635 1.032657 CGGACGTGGATCCTCTGACT 61.033 60.000 14.23 0.00 36.52 3.41
633 636 1.030488 TCGGACGTGGATCCTCTGAC 61.030 60.000 14.23 1.17 36.52 3.51
634 637 0.106669 ATCGGACGTGGATCCTCTGA 60.107 55.000 14.23 13.03 36.52 3.27
635 638 0.747255 AATCGGACGTGGATCCTCTG 59.253 55.000 14.23 7.64 36.52 3.35
636 639 2.359981 TAATCGGACGTGGATCCTCT 57.640 50.000 14.23 0.00 36.52 3.69
637 640 3.447918 TTTAATCGGACGTGGATCCTC 57.552 47.619 14.23 8.71 36.52 3.71
638 641 3.528532 GTTTTAATCGGACGTGGATCCT 58.471 45.455 14.23 0.00 36.52 3.24
639 642 2.283351 CGTTTTAATCGGACGTGGATCC 59.717 50.000 4.20 4.20 35.16 3.36
640 643 3.181397 TCGTTTTAATCGGACGTGGATC 58.819 45.455 0.00 0.00 37.95 3.36
641 644 3.235157 TCGTTTTAATCGGACGTGGAT 57.765 42.857 0.00 0.00 37.95 3.41
642 645 2.721274 TCGTTTTAATCGGACGTGGA 57.279 45.000 0.00 0.00 37.95 4.02
643 646 2.924926 TCATCGTTTTAATCGGACGTGG 59.075 45.455 0.00 0.00 37.95 4.94
644 647 3.000078 CCTCATCGTTTTAATCGGACGTG 60.000 47.826 0.00 0.00 37.95 4.49
645 648 3.119388 TCCTCATCGTTTTAATCGGACGT 60.119 43.478 0.00 0.00 37.95 4.34
646 649 3.242248 GTCCTCATCGTTTTAATCGGACG 59.758 47.826 0.00 0.00 38.09 4.79
647 650 4.430908 AGTCCTCATCGTTTTAATCGGAC 58.569 43.478 0.00 0.00 39.86 4.79
648 651 4.730949 AGTCCTCATCGTTTTAATCGGA 57.269 40.909 0.00 0.00 0.00 4.55
649 652 5.589192 ACTAGTCCTCATCGTTTTAATCGG 58.411 41.667 0.00 0.00 0.00 4.18
650 653 6.360148 GCTACTAGTCCTCATCGTTTTAATCG 59.640 42.308 0.00 0.00 0.00 3.34
651 654 6.360148 CGCTACTAGTCCTCATCGTTTTAATC 59.640 42.308 0.00 0.00 0.00 1.75
652 655 6.039047 TCGCTACTAGTCCTCATCGTTTTAAT 59.961 38.462 0.00 0.00 0.00 1.40
653 656 5.355071 TCGCTACTAGTCCTCATCGTTTTAA 59.645 40.000 0.00 0.00 0.00 1.52
654 657 4.877823 TCGCTACTAGTCCTCATCGTTTTA 59.122 41.667 0.00 0.00 0.00 1.52
655 658 3.693085 TCGCTACTAGTCCTCATCGTTTT 59.307 43.478 0.00 0.00 0.00 2.43
656 659 3.276857 TCGCTACTAGTCCTCATCGTTT 58.723 45.455 0.00 0.00 0.00 3.60
657 660 2.915349 TCGCTACTAGTCCTCATCGTT 58.085 47.619 0.00 0.00 0.00 3.85
658 661 2.616634 TCGCTACTAGTCCTCATCGT 57.383 50.000 0.00 0.00 0.00 3.73
659 662 3.498777 TCAATCGCTACTAGTCCTCATCG 59.501 47.826 0.00 0.00 0.00 3.84
660 663 4.517453 ACTCAATCGCTACTAGTCCTCATC 59.483 45.833 0.00 0.00 0.00 2.92
661 664 4.465886 ACTCAATCGCTACTAGTCCTCAT 58.534 43.478 0.00 0.00 0.00 2.90
662 665 3.878103 GACTCAATCGCTACTAGTCCTCA 59.122 47.826 0.00 0.00 32.27 3.86
663 666 4.131596 AGACTCAATCGCTACTAGTCCTC 58.868 47.826 0.00 0.00 37.82 3.71
664 667 4.159244 AGACTCAATCGCTACTAGTCCT 57.841 45.455 0.00 0.00 37.82 3.85
665 668 4.904253 AAGACTCAATCGCTACTAGTCC 57.096 45.455 0.00 0.00 37.82 3.85
666 669 6.858993 CCATTAAGACTCAATCGCTACTAGTC 59.141 42.308 0.00 0.00 37.44 2.59
667 670 6.321690 ACCATTAAGACTCAATCGCTACTAGT 59.678 38.462 0.00 0.00 0.00 2.57
668 671 6.638873 CACCATTAAGACTCAATCGCTACTAG 59.361 42.308 0.00 0.00 0.00 2.57
669 672 6.504398 CACCATTAAGACTCAATCGCTACTA 58.496 40.000 0.00 0.00 0.00 1.82
670 673 5.352284 CACCATTAAGACTCAATCGCTACT 58.648 41.667 0.00 0.00 0.00 2.57
671 674 4.025647 GCACCATTAAGACTCAATCGCTAC 60.026 45.833 0.00 0.00 0.00 3.58
672 675 4.119862 GCACCATTAAGACTCAATCGCTA 58.880 43.478 0.00 0.00 0.00 4.26
673 676 2.939103 GCACCATTAAGACTCAATCGCT 59.061 45.455 0.00 0.00 0.00 4.93
674 677 2.032178 GGCACCATTAAGACTCAATCGC 59.968 50.000 0.00 0.00 0.00 4.58
675 678 2.285220 CGGCACCATTAAGACTCAATCG 59.715 50.000 0.00 0.00 0.00 3.34
676 679 2.614057 CCGGCACCATTAAGACTCAATC 59.386 50.000 0.00 0.00 0.00 2.67
677 680 2.238646 TCCGGCACCATTAAGACTCAAT 59.761 45.455 0.00 0.00 0.00 2.57
678 681 1.626321 TCCGGCACCATTAAGACTCAA 59.374 47.619 0.00 0.00 0.00 3.02
679 682 1.271856 TCCGGCACCATTAAGACTCA 58.728 50.000 0.00 0.00 0.00 3.41
680 683 2.280628 CTTCCGGCACCATTAAGACTC 58.719 52.381 0.00 0.00 0.00 3.36
681 684 1.065418 CCTTCCGGCACCATTAAGACT 60.065 52.381 0.00 0.00 0.00 3.24
682 685 1.379527 CCTTCCGGCACCATTAAGAC 58.620 55.000 0.00 0.00 0.00 3.01
683 686 0.254747 CCCTTCCGGCACCATTAAGA 59.745 55.000 0.00 0.00 0.00 2.10
684 687 0.751643 CCCCTTCCGGCACCATTAAG 60.752 60.000 0.00 0.00 0.00 1.85
685 688 1.304952 CCCCTTCCGGCACCATTAA 59.695 57.895 0.00 0.00 0.00 1.40
686 689 2.685534 CCCCCTTCCGGCACCATTA 61.686 63.158 0.00 0.00 0.00 1.90
687 690 4.060667 CCCCCTTCCGGCACCATT 62.061 66.667 0.00 0.00 0.00 3.16
690 693 4.426313 CTTCCCCCTTCCGGCACC 62.426 72.222 0.00 0.00 0.00 5.01
691 694 4.426313 CCTTCCCCCTTCCGGCAC 62.426 72.222 0.00 0.00 0.00 5.01
696 699 3.798511 CTCCGCCTTCCCCCTTCC 61.799 72.222 0.00 0.00 0.00 3.46
697 700 3.798511 CCTCCGCCTTCCCCCTTC 61.799 72.222 0.00 0.00 0.00 3.46
710 713 0.392595 CTTTTACCCTCACGGCCTCC 60.393 60.000 0.00 0.00 33.26 4.30
711 714 0.611714 TCTTTTACCCTCACGGCCTC 59.388 55.000 0.00 0.00 33.26 4.70
712 715 1.003233 CTTCTTTTACCCTCACGGCCT 59.997 52.381 0.00 0.00 33.26 5.19
713 716 1.002773 TCTTCTTTTACCCTCACGGCC 59.997 52.381 0.00 0.00 33.26 6.13
714 717 2.467566 TCTTCTTTTACCCTCACGGC 57.532 50.000 0.00 0.00 33.26 5.68
715 718 5.581085 CACTATTCTTCTTTTACCCTCACGG 59.419 44.000 0.00 0.00 37.81 4.94
716 719 6.164176 ACACTATTCTTCTTTTACCCTCACG 58.836 40.000 0.00 0.00 0.00 4.35
717 720 7.159372 TGACACTATTCTTCTTTTACCCTCAC 58.841 38.462 0.00 0.00 0.00 3.51
718 721 7.311092 TGACACTATTCTTCTTTTACCCTCA 57.689 36.000 0.00 0.00 0.00 3.86
719 722 6.314152 GCTGACACTATTCTTCTTTTACCCTC 59.686 42.308 0.00 0.00 0.00 4.30
720 723 6.174049 GCTGACACTATTCTTCTTTTACCCT 58.826 40.000 0.00 0.00 0.00 4.34
721 724 5.063564 CGCTGACACTATTCTTCTTTTACCC 59.936 44.000 0.00 0.00 0.00 3.69
722 725 5.638234 ACGCTGACACTATTCTTCTTTTACC 59.362 40.000 0.00 0.00 0.00 2.85
723 726 6.365247 TCACGCTGACACTATTCTTCTTTTAC 59.635 38.462 0.00 0.00 0.00 2.01
724 727 6.452242 TCACGCTGACACTATTCTTCTTTTA 58.548 36.000 0.00 0.00 0.00 1.52
725 728 5.297547 TCACGCTGACACTATTCTTCTTTT 58.702 37.500 0.00 0.00 0.00 2.27
726 729 4.883083 TCACGCTGACACTATTCTTCTTT 58.117 39.130 0.00 0.00 0.00 2.52
727 730 4.521130 TCACGCTGACACTATTCTTCTT 57.479 40.909 0.00 0.00 0.00 2.52
728 731 4.489810 CTTCACGCTGACACTATTCTTCT 58.510 43.478 0.00 0.00 0.00 2.85
729 732 3.061429 GCTTCACGCTGACACTATTCTTC 59.939 47.826 0.00 0.00 35.14 2.87
730 733 2.996621 GCTTCACGCTGACACTATTCTT 59.003 45.455 0.00 0.00 35.14 2.52
731 734 2.611518 GCTTCACGCTGACACTATTCT 58.388 47.619 0.00 0.00 35.14 2.40
732 735 1.661112 GGCTTCACGCTGACACTATTC 59.339 52.381 0.00 0.00 39.13 1.75
733 736 1.001974 TGGCTTCACGCTGACACTATT 59.998 47.619 0.00 0.00 39.13 1.73
734 737 0.608130 TGGCTTCACGCTGACACTAT 59.392 50.000 0.00 0.00 39.13 2.12
735 738 0.038251 CTGGCTTCACGCTGACACTA 60.038 55.000 0.00 0.00 39.13 2.74
736 739 1.301244 CTGGCTTCACGCTGACACT 60.301 57.895 0.00 0.00 39.13 3.55
751 754 3.522731 CCTCCCTCGCTCGACTGG 61.523 72.222 0.00 0.00 0.00 4.00
765 768 4.916293 TCATCATGCGGCCGCCTC 62.916 66.667 44.42 21.08 41.09 4.70
780 783 4.425772 TCTCAGTGGAAGAATACCCTTCA 58.574 43.478 0.00 0.00 43.19 3.02
789 792 4.881850 GGAAACAACTTCTCAGTGGAAGAA 59.118 41.667 21.20 10.17 43.70 2.52
819 822 4.270084 CGCGTGAGATGGCTCTTAATTTTA 59.730 41.667 0.00 0.00 41.84 1.52
826 829 1.153745 GACGCGTGAGATGGCTCTT 60.154 57.895 20.70 0.00 41.84 2.85
828 831 1.587613 GAGACGCGTGAGATGGCTC 60.588 63.158 20.70 11.70 41.67 4.70
829 832 2.492090 GAGACGCGTGAGATGGCT 59.508 61.111 20.70 4.95 0.00 4.75
830 833 1.725557 TAGGAGACGCGTGAGATGGC 61.726 60.000 20.70 0.00 0.00 4.40
831 834 0.738975 TTAGGAGACGCGTGAGATGG 59.261 55.000 20.70 0.00 0.00 3.51
832 835 1.132453 TGTTAGGAGACGCGTGAGATG 59.868 52.381 20.70 0.00 0.00 2.90
833 836 1.132643 GTGTTAGGAGACGCGTGAGAT 59.867 52.381 20.70 2.07 0.00 2.75
834 837 0.520404 GTGTTAGGAGACGCGTGAGA 59.480 55.000 20.70 0.00 0.00 3.27
835 838 0.522180 AGTGTTAGGAGACGCGTGAG 59.478 55.000 20.70 0.00 35.27 3.51
836 839 0.956633 AAGTGTTAGGAGACGCGTGA 59.043 50.000 20.70 0.00 35.27 4.35
837 840 1.779569 AAAGTGTTAGGAGACGCGTG 58.220 50.000 20.70 0.00 35.27 5.34
838 841 2.132762 CAAAAGTGTTAGGAGACGCGT 58.867 47.619 13.85 13.85 35.27 6.01
839 842 2.400399 TCAAAAGTGTTAGGAGACGCG 58.600 47.619 3.53 3.53 35.27 6.01
844 847 6.647067 AGTCGAATTCTCAAAAGTGTTAGGAG 59.353 38.462 3.52 0.00 0.00 3.69
918 922 2.859165 TGTCTAACCCAAGCCTCAAG 57.141 50.000 0.00 0.00 0.00 3.02
920 924 1.340017 GCATGTCTAACCCAAGCCTCA 60.340 52.381 0.00 0.00 0.00 3.86
929 933 2.744202 CTGTGTTGAGGCATGTCTAACC 59.256 50.000 0.00 0.00 0.00 2.85
936 940 0.520404 GTGAGCTGTGTTGAGGCATG 59.480 55.000 0.00 0.00 0.00 4.06
943 947 2.225019 GGTGATTGAGTGAGCTGTGTTG 59.775 50.000 0.00 0.00 0.00 3.33
967 971 2.743195 CTCAGCGAGCCTGTGTTAC 58.257 57.895 0.00 0.00 42.38 2.50
1032 1036 1.724582 GCTGTGTGGTGTGGGTTGAC 61.725 60.000 0.00 0.00 0.00 3.18
1144 1148 0.538746 GAGTGGAAAAAGGGGCGGAA 60.539 55.000 0.00 0.00 0.00 4.30
1154 1158 1.838073 GAGGGAGGGCGAGTGGAAAA 61.838 60.000 0.00 0.00 0.00 2.29
1209 1213 1.228124 CTTGTTGGCGAGGTGGGAA 60.228 57.895 0.00 0.00 0.00 3.97
1210 1214 2.429930 CTTGTTGGCGAGGTGGGA 59.570 61.111 0.00 0.00 0.00 4.37
1308 1318 4.175489 ACGATGGACGCGAGGACG 62.175 66.667 15.93 14.05 46.94 4.79
1470 1601 2.676121 TCGGGGAAGCCGACGTAA 60.676 61.111 0.00 0.00 34.66 3.18
1578 1709 1.645034 AGATGAAGTTGGCGATGACG 58.355 50.000 0.00 0.00 42.93 4.35
1591 1722 4.305539 TGATGAGGAAGGCAAAGATGAA 57.694 40.909 0.00 0.00 0.00 2.57
1599 1730 1.069204 GCGTAGATGATGAGGAAGGCA 59.931 52.381 0.00 0.00 0.00 4.75
2112 2243 2.752238 CTCGACCTCGCCACCTCT 60.752 66.667 0.00 0.00 39.60 3.69
2391 2522 2.066262 GCAAAATGTTCTCTCGGACGA 58.934 47.619 0.00 0.00 0.00 4.20
2392 2523 1.798223 TGCAAAATGTTCTCTCGGACG 59.202 47.619 0.00 0.00 0.00 4.79
2449 2580 8.962884 ATTTGTGCAAGAGATACATACATACA 57.037 30.769 0.00 0.00 0.00 2.29
2450 2581 9.869844 GAATTTGTGCAAGAGATACATACATAC 57.130 33.333 0.00 0.00 0.00 2.39
2451 2582 9.836864 AGAATTTGTGCAAGAGATACATACATA 57.163 29.630 0.00 0.00 0.00 2.29
2452 2583 8.743085 AGAATTTGTGCAAGAGATACATACAT 57.257 30.769 0.00 0.00 0.00 2.29
2514 2645 2.103094 TGAGGCAGAGTGTATACATGGC 59.897 50.000 18.82 18.82 39.81 4.40
2596 2728 4.725790 ACCAGAATTAGGCAATTTCAGC 57.274 40.909 0.00 0.00 34.44 4.26
2627 2759 6.259167 TCGGCGCTAACATGTTATAAAAGAAT 59.741 34.615 18.35 0.00 0.00 2.40
2628 2760 5.581479 TCGGCGCTAACATGTTATAAAAGAA 59.419 36.000 18.35 0.00 0.00 2.52
2629 2761 5.110598 TCGGCGCTAACATGTTATAAAAGA 58.889 37.500 18.35 12.40 0.00 2.52
2630 2762 5.398176 TCGGCGCTAACATGTTATAAAAG 57.602 39.130 18.35 9.60 0.00 2.27
2631 2763 4.260456 GCTCGGCGCTAACATGTTATAAAA 60.260 41.667 18.35 0.00 35.14 1.52
2632 2764 3.246699 GCTCGGCGCTAACATGTTATAAA 59.753 43.478 18.35 0.00 35.14 1.40
2633 2765 2.798283 GCTCGGCGCTAACATGTTATAA 59.202 45.455 18.35 0.00 35.14 0.98
2634 2766 2.400399 GCTCGGCGCTAACATGTTATA 58.600 47.619 18.35 0.00 35.14 0.98
2635 2767 1.217882 GCTCGGCGCTAACATGTTAT 58.782 50.000 18.35 0.00 35.14 1.89
2637 2769 3.486263 GCTCGGCGCTAACATGTT 58.514 55.556 16.68 16.68 35.14 2.71
2647 2779 4.374702 GTGTTGTGCAGCTCGGCG 62.375 66.667 0.00 0.00 36.28 6.46
2648 2780 2.959357 GAGTGTTGTGCAGCTCGGC 61.959 63.158 0.00 0.00 0.00 5.54
2667 2839 3.605664 AGGCTTGTTTGCGGTGCC 61.606 61.111 0.00 0.00 43.52 5.01
2707 2885 4.508662 GGTATTAGCAGTATCAGGCATCC 58.491 47.826 0.00 0.00 0.00 3.51
2733 2911 2.717639 ATGTACTGGAATGGTCAGGC 57.282 50.000 0.00 0.00 36.62 4.85
2739 2917 4.422073 TGGAGCTTATGTACTGGAATGG 57.578 45.455 0.00 0.00 0.00 3.16
2740 2918 5.431765 ACTTGGAGCTTATGTACTGGAATG 58.568 41.667 0.00 0.00 0.00 2.67
2742 2920 5.245531 CAACTTGGAGCTTATGTACTGGAA 58.754 41.667 0.00 0.00 0.00 3.53
2758 2937 3.262420 ACGTTATAGAGCAGCAACTTGG 58.738 45.455 0.00 0.00 0.00 3.61
2784 2970 0.749454 ATGCCGCTGGGAGATGAAAC 60.749 55.000 0.00 0.00 34.06 2.78
2822 3008 8.680001 CCATTTCTGATTCAGATATGACAAACA 58.320 33.333 31.85 9.90 45.77 2.83
2826 3601 7.222161 CCTCCATTTCTGATTCAGATATGACA 58.778 38.462 31.85 22.15 45.77 3.58
2831 3606 5.635278 TGCCTCCATTTCTGATTCAGATA 57.365 39.130 16.82 12.65 40.39 1.98
2845 3620 2.235650 CAGATATGACGGATGCCTCCAT 59.764 50.000 8.86 0.00 42.19 3.41
2855 3630 6.695713 TCTTAACGTTGATTCAGATATGACGG 59.304 38.462 11.99 0.00 33.74 4.79
2869 3644 6.513720 GCACCCAGTATTTTTCTTAACGTTGA 60.514 38.462 11.99 0.73 0.00 3.18
2874 3649 6.977213 TGAAGCACCCAGTATTTTTCTTAAC 58.023 36.000 0.00 0.00 0.00 2.01
2916 3691 6.267817 TGATTGCATTGCTTAGTATCTTTGC 58.732 36.000 10.49 0.00 0.00 3.68
2930 3705 2.166050 TCCGTCCCAATTGATTGCATTG 59.834 45.455 7.12 0.00 36.48 2.82
2948 3723 5.334105 GCATGCTTGTACTGGTTATTATCCG 60.334 44.000 11.37 0.00 0.00 4.18
2949 3724 5.530915 TGCATGCTTGTACTGGTTATTATCC 59.469 40.000 20.33 0.00 0.00 2.59
2952 3727 5.356751 CCTTGCATGCTTGTACTGGTTATTA 59.643 40.000 20.33 0.00 0.00 0.98
2956 3731 1.888512 CCTTGCATGCTTGTACTGGTT 59.111 47.619 20.33 0.00 0.00 3.67
2961 3736 3.119849 CCTTGTACCTTGCATGCTTGTAC 60.120 47.826 25.04 25.04 33.96 2.90
2976 3751 8.865590 TTCTTTGAAGTTATTTTGCCTTGTAC 57.134 30.769 0.00 0.00 0.00 2.90
3016 3795 5.680619 TGTTCTATTATGCCGGATTTGAGT 58.319 37.500 5.05 0.00 0.00 3.41
3018 3797 8.729756 CATAATGTTCTATTATGCCGGATTTGA 58.270 33.333 5.05 0.00 35.86 2.69
3026 3805 6.127897 GCAGGACCATAATGTTCTATTATGCC 60.128 42.308 12.06 9.65 39.44 4.40
3077 3857 7.815383 TCTTGGGGATATACTCATCATTGTTT 58.185 34.615 0.00 0.00 0.00 2.83
3078 3858 7.392766 TCTTGGGGATATACTCATCATTGTT 57.607 36.000 0.00 0.00 0.00 2.83
3080 3860 7.627311 TCATCTTGGGGATATACTCATCATTG 58.373 38.462 0.00 0.00 32.64 2.82
3086 3866 6.615316 TGTTTCTCATCTTGGGGATATACTCA 59.385 38.462 0.00 0.00 32.64 3.41
3129 3909 4.025480 GCAATTGAAAAGCTGTGGAACTTG 60.025 41.667 10.34 0.00 38.04 3.16
3234 4014 4.081420 ACTTTGCACTCTATAGGACTGTGG 60.081 45.833 0.00 0.00 0.00 4.17
3264 4044 1.667724 CCTTGCTCTCGGTATTTGCAG 59.332 52.381 0.00 0.00 35.02 4.41
3274 4054 2.002586 CACATGGTAACCTTGCTCTCG 58.997 52.381 0.00 0.00 32.73 4.04
3282 4062 2.233922 CGTCTCTTCCACATGGTAACCT 59.766 50.000 0.00 0.00 36.34 3.50
3294 4074 0.966920 TTGTCTCCACCGTCTCTTCC 59.033 55.000 0.00 0.00 0.00 3.46
3302 4082 1.014044 CACCATCGTTGTCTCCACCG 61.014 60.000 0.00 0.00 0.00 4.94


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

AutoCloner maintained by Alex Coulton.