Multiple sequence alignment - TraesCS7B01G296900

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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 TraesCS7B01G296900 chr7B 100.000 4132 0 0 1 4132 533615940 533611809 0.000000e+00 7631.0
1 TraesCS7B01G296900 chr7B 77.830 848 171 16 1334 2177 334322217 334323051 3.690000e-140 508.0
2 TraesCS7B01G296900 chr7D 90.927 3472 173 66 721 4132 505617089 505613700 0.000000e+00 4536.0
3 TraesCS7B01G296900 chr7D 86.213 573 26 13 1 547 505617735 505617190 4.630000e-159 571.0
4 TraesCS7B01G296900 chr7D 77.647 850 169 19 1334 2177 189430232 189431066 7.980000e-137 497.0
5 TraesCS7B01G296900 chr7A 90.809 1643 73 35 819 2432 573128752 573127159 0.000000e+00 2126.0
6 TraesCS7B01G296900 chr7A 92.105 950 53 9 2579 3506 573127111 573126162 0.000000e+00 1319.0
7 TraesCS7B01G296900 chr7A 78.271 856 171 15 1334 2186 194324647 194323804 1.690000e-148 536.0
8 TraesCS7B01G296900 chr7A 81.263 491 34 29 54 508 573129422 573128954 1.100000e-90 344.0
9 TraesCS7B01G296900 chr7A 83.710 221 15 7 3514 3728 573125301 573125096 5.450000e-44 189.0
10 TraesCS7B01G296900 chr7A 84.375 160 10 7 639 788 573128907 573128753 4.310000e-30 143.0
11 TraesCS7B01G296900 chr6A 80.592 845 140 22 1334 2172 504624711 504623885 7.540000e-177 630.0
12 TraesCS7B01G296900 chr6D 80.237 845 143 22 1334 2172 363597028 363596202 7.590000e-172 614.0
13 TraesCS7B01G296900 chr6B 79.647 850 139 30 1334 2172 548384260 548383434 7.700000e-162 580.0
14 TraesCS7B01G296900 chr5A 84.615 78 6 4 1109 1181 563100909 563100985 5.730000e-09 73.1
15 TraesCS7B01G296900 chr5A 84.615 78 6 4 1109 1181 563164788 563164864 5.730000e-09 73.1


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 TraesCS7B01G296900 chr7B 533611809 533615940 4131 True 7631.0 7631 100.0000 1 4132 1 chr7B.!!$R1 4131
1 TraesCS7B01G296900 chr7B 334322217 334323051 834 False 508.0 508 77.8300 1334 2177 1 chr7B.!!$F1 843
2 TraesCS7B01G296900 chr7D 505613700 505617735 4035 True 2553.5 4536 88.5700 1 4132 2 chr7D.!!$R1 4131
3 TraesCS7B01G296900 chr7D 189430232 189431066 834 False 497.0 497 77.6470 1334 2177 1 chr7D.!!$F1 843
4 TraesCS7B01G296900 chr7A 573125096 573129422 4326 True 824.2 2126 86.4524 54 3728 5 chr7A.!!$R2 3674
5 TraesCS7B01G296900 chr7A 194323804 194324647 843 True 536.0 536 78.2710 1334 2186 1 chr7A.!!$R1 852
6 TraesCS7B01G296900 chr6A 504623885 504624711 826 True 630.0 630 80.5920 1334 2172 1 chr6A.!!$R1 838
7 TraesCS7B01G296900 chr6D 363596202 363597028 826 True 614.0 614 80.2370 1334 2172 1 chr6D.!!$R1 838
8 TraesCS7B01G296900 chr6B 548383434 548384260 826 True 580.0 580 79.6470 1334 2172 1 chr6B.!!$R1 838

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
583 629 0.034756 CATCAGTGGTCAACGGGTGA 59.965 55.0 0.0 0.0 37.27 4.02 F
585 631 0.105964 TCAGTGGTCAACGGGTGAAG 59.894 55.0 0.0 0.0 38.23 3.02 F
586 632 0.105964 CAGTGGTCAACGGGTGAAGA 59.894 55.0 0.0 0.0 38.23 2.87 F
2439 2568 0.179067 TCCGTATTCGTGCAATCCCC 60.179 55.0 0.0 0.0 35.01 4.81 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2452 2581 0.179073 ATGTCCGGCTCCAAAGATCG 60.179 55.000 0.0 0.0 0.00 3.69 R
2565 2699 2.237143 CTGCAAGGAGAACATGGTAGGA 59.763 50.000 0.0 0.0 0.00 2.94 R
2658 2796 2.710471 ACCCCCATTGTCTGCAAAAATT 59.290 40.909 0.0 0.0 38.21 1.82 R
3815 4832 0.036448 TTCGGCCCACCAAACGATTA 59.964 50.000 0.0 0.0 35.10 1.75 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
344 377 1.129058 GACCGTTGGATGGATAGGGT 58.871 55.000 0.00 0.00 33.10 4.34
388 422 2.212652 GCACAGTGATTGATATCCGCA 58.787 47.619 4.15 0.00 0.00 5.69
439 478 3.809905 AGAGATTCGTTAATTGGGGCTC 58.190 45.455 0.00 0.00 0.00 4.70
516 562 0.038343 CAACAAAATGTGGCTCCGGG 60.038 55.000 0.00 0.00 0.00 5.73
519 565 1.606313 AAAATGTGGCTCCGGGTGG 60.606 57.895 0.00 0.00 0.00 4.61
532 578 1.308998 CGGGTGGCTTAGCATTAAGG 58.691 55.000 6.53 0.00 37.37 2.69
562 608 6.521151 CTTCAGATGTTAATTTGAAGGGCT 57.479 37.500 9.86 0.00 45.09 5.19
563 609 5.902613 TCAGATGTTAATTTGAAGGGCTG 57.097 39.130 0.00 0.00 0.00 4.85
566 612 4.713321 AGATGTTAATTTGAAGGGCTGCAT 59.287 37.500 0.50 0.00 0.00 3.96
567 613 4.454728 TGTTAATTTGAAGGGCTGCATC 57.545 40.909 0.50 0.00 0.00 3.91
568 614 3.831333 TGTTAATTTGAAGGGCTGCATCA 59.169 39.130 0.50 0.00 0.00 3.07
569 615 4.082081 TGTTAATTTGAAGGGCTGCATCAG 60.082 41.667 0.50 0.00 34.12 2.90
570 616 2.226962 ATTTGAAGGGCTGCATCAGT 57.773 45.000 0.50 0.00 33.43 3.41
571 617 1.250328 TTTGAAGGGCTGCATCAGTG 58.750 50.000 0.50 0.00 33.43 3.66
572 618 0.609957 TTGAAGGGCTGCATCAGTGG 60.610 55.000 0.50 0.00 33.43 4.00
573 619 1.001641 GAAGGGCTGCATCAGTGGT 60.002 57.895 0.50 0.00 33.43 4.16
574 620 1.001641 AAGGGCTGCATCAGTGGTC 60.002 57.895 0.50 0.00 33.43 4.02
575 621 1.782201 AAGGGCTGCATCAGTGGTCA 61.782 55.000 0.50 0.00 33.43 4.02
576 622 1.303561 GGGCTGCATCAGTGGTCAA 60.304 57.895 0.50 0.00 33.43 3.18
577 623 1.589716 GGGCTGCATCAGTGGTCAAC 61.590 60.000 0.50 0.00 33.43 3.18
578 624 1.499056 GCTGCATCAGTGGTCAACG 59.501 57.895 0.00 0.00 33.43 4.10
579 625 1.915614 GCTGCATCAGTGGTCAACGG 61.916 60.000 0.00 0.00 33.43 4.44
580 626 1.300971 CTGCATCAGTGGTCAACGGG 61.301 60.000 0.00 0.00 0.00 5.28
581 627 1.302511 GCATCAGTGGTCAACGGGT 60.303 57.895 0.00 0.00 0.00 5.28
582 628 1.577328 GCATCAGTGGTCAACGGGTG 61.577 60.000 0.00 0.00 38.05 4.61
583 629 0.034756 CATCAGTGGTCAACGGGTGA 59.965 55.000 0.00 0.00 37.27 4.02
584 630 0.762418 ATCAGTGGTCAACGGGTGAA 59.238 50.000 0.00 0.00 38.23 3.18
585 631 0.105964 TCAGTGGTCAACGGGTGAAG 59.894 55.000 0.00 0.00 38.23 3.02
586 632 0.105964 CAGTGGTCAACGGGTGAAGA 59.894 55.000 0.00 0.00 38.23 2.87
587 633 0.834612 AGTGGTCAACGGGTGAAGAA 59.165 50.000 0.00 0.00 38.23 2.52
588 634 1.210967 AGTGGTCAACGGGTGAAGAAA 59.789 47.619 0.00 0.00 38.23 2.52
589 635 1.602377 GTGGTCAACGGGTGAAGAAAG 59.398 52.381 0.00 0.00 38.23 2.62
590 636 1.210967 TGGTCAACGGGTGAAGAAAGT 59.789 47.619 0.00 0.00 38.23 2.66
591 637 1.602377 GGTCAACGGGTGAAGAAAGTG 59.398 52.381 0.00 0.00 38.23 3.16
592 638 1.602377 GTCAACGGGTGAAGAAAGTGG 59.398 52.381 0.00 0.00 38.23 4.00
593 639 1.210967 TCAACGGGTGAAGAAAGTGGT 59.789 47.619 0.00 0.00 31.51 4.16
594 640 2.435069 TCAACGGGTGAAGAAAGTGGTA 59.565 45.455 0.00 0.00 31.51 3.25
595 641 3.118334 TCAACGGGTGAAGAAAGTGGTAA 60.118 43.478 0.00 0.00 31.51 2.85
596 642 2.842457 ACGGGTGAAGAAAGTGGTAAC 58.158 47.619 0.00 0.00 0.00 2.50
597 643 2.436911 ACGGGTGAAGAAAGTGGTAACT 59.563 45.455 0.00 0.00 38.71 2.24
598 644 3.642848 ACGGGTGAAGAAAGTGGTAACTA 59.357 43.478 0.00 0.00 34.77 2.24
599 645 4.285260 ACGGGTGAAGAAAGTGGTAACTAT 59.715 41.667 0.00 0.00 34.77 2.12
600 646 4.630069 CGGGTGAAGAAAGTGGTAACTATG 59.370 45.833 0.00 0.00 34.77 2.23
601 647 4.395231 GGGTGAAGAAAGTGGTAACTATGC 59.605 45.833 0.00 0.00 34.77 3.14
602 648 5.246307 GGTGAAGAAAGTGGTAACTATGCT 58.754 41.667 0.00 0.00 34.77 3.79
603 649 6.403878 GGTGAAGAAAGTGGTAACTATGCTA 58.596 40.000 0.00 0.00 34.77 3.49
604 650 6.313164 GGTGAAGAAAGTGGTAACTATGCTAC 59.687 42.308 0.00 0.00 34.77 3.58
605 651 7.097834 GTGAAGAAAGTGGTAACTATGCTACT 58.902 38.462 0.00 0.00 34.77 2.57
606 652 7.063544 GTGAAGAAAGTGGTAACTATGCTACTG 59.936 40.741 0.00 0.00 33.43 2.74
607 653 6.607004 AGAAAGTGGTAACTATGCTACTGT 57.393 37.500 0.00 0.00 33.43 3.55
608 654 7.713734 AGAAAGTGGTAACTATGCTACTGTA 57.286 36.000 0.00 0.00 33.43 2.74
609 655 7.773149 AGAAAGTGGTAACTATGCTACTGTAG 58.227 38.462 10.48 10.48 33.43 2.74
610 656 6.466885 AAGTGGTAACTATGCTACTGTAGG 57.533 41.667 16.09 2.54 33.43 3.18
611 657 5.763355 AGTGGTAACTATGCTACTGTAGGA 58.237 41.667 16.09 13.91 31.96 2.94
612 658 6.374588 AGTGGTAACTATGCTACTGTAGGAT 58.625 40.000 22.62 22.62 40.19 3.24
613 659 6.839657 AGTGGTAACTATGCTACTGTAGGATT 59.160 38.462 23.88 11.83 37.96 3.01
614 660 7.344871 AGTGGTAACTATGCTACTGTAGGATTT 59.655 37.037 23.88 16.28 37.96 2.17
615 661 8.636213 GTGGTAACTATGCTACTGTAGGATTTA 58.364 37.037 23.88 15.42 37.96 1.40
616 662 8.636213 TGGTAACTATGCTACTGTAGGATTTAC 58.364 37.037 23.88 23.09 37.96 2.01
617 663 8.858094 GGTAACTATGCTACTGTAGGATTTACT 58.142 37.037 25.92 14.94 37.96 2.24
621 667 8.566260 ACTATGCTACTGTAGGATTTACTTACG 58.434 37.037 23.88 7.99 37.96 3.18
622 668 5.585390 TGCTACTGTAGGATTTACTTACGC 58.415 41.667 16.09 0.00 34.42 4.42
623 669 5.125900 TGCTACTGTAGGATTTACTTACGCA 59.874 40.000 16.09 1.72 34.42 5.24
624 670 5.458126 GCTACTGTAGGATTTACTTACGCAC 59.542 44.000 16.09 0.00 34.42 5.34
625 671 5.395682 ACTGTAGGATTTACTTACGCACA 57.604 39.130 0.00 0.00 34.42 4.57
626 672 5.408356 ACTGTAGGATTTACTTACGCACAG 58.592 41.667 0.00 0.00 37.48 3.66
627 673 5.184479 ACTGTAGGATTTACTTACGCACAGA 59.816 40.000 5.02 0.00 35.85 3.41
628 674 5.647589 TGTAGGATTTACTTACGCACAGAG 58.352 41.667 0.00 0.00 34.42 3.35
629 675 5.416639 TGTAGGATTTACTTACGCACAGAGA 59.583 40.000 0.00 0.00 34.42 3.10
630 676 4.745649 AGGATTTACTTACGCACAGAGAC 58.254 43.478 0.00 0.00 0.00 3.36
631 677 4.219944 AGGATTTACTTACGCACAGAGACA 59.780 41.667 0.00 0.00 0.00 3.41
632 678 4.326548 GGATTTACTTACGCACAGAGACAC 59.673 45.833 0.00 0.00 0.00 3.67
633 679 3.994204 TTACTTACGCACAGAGACACA 57.006 42.857 0.00 0.00 0.00 3.72
637 683 0.241213 TACGCACAGAGACACAGAGC 59.759 55.000 0.00 0.00 0.00 4.09
647 693 0.312416 GACACAGAGCGACAGTGACT 59.688 55.000 13.90 0.00 38.95 3.41
671 717 7.707035 ACTGACTCGAGGTTAATATTGATGAAC 59.293 37.037 18.41 0.00 0.00 3.18
672 718 6.984474 TGACTCGAGGTTAATATTGATGAACC 59.016 38.462 18.41 9.09 41.44 3.62
673 719 6.884832 ACTCGAGGTTAATATTGATGAACCA 58.115 36.000 18.41 0.48 43.20 3.67
674 720 6.986817 ACTCGAGGTTAATATTGATGAACCAG 59.013 38.462 18.41 11.41 43.20 4.00
675 721 5.758296 TCGAGGTTAATATTGATGAACCAGC 59.242 40.000 16.58 9.33 43.20 4.85
676 722 5.049405 CGAGGTTAATATTGATGAACCAGCC 60.049 44.000 16.58 7.36 43.20 4.85
677 723 5.140454 AGGTTAATATTGATGAACCAGCCC 58.860 41.667 16.58 0.00 43.20 5.19
678 724 4.892934 GGTTAATATTGATGAACCAGCCCA 59.107 41.667 11.43 0.00 40.91 5.36
679 725 5.010012 GGTTAATATTGATGAACCAGCCCAG 59.990 44.000 11.43 0.00 40.91 4.45
680 726 2.057137 TATTGATGAACCAGCCCAGC 57.943 50.000 0.00 0.00 0.00 4.85
681 727 0.685458 ATTGATGAACCAGCCCAGCC 60.685 55.000 0.00 0.00 0.00 4.85
682 728 2.440980 GATGAACCAGCCCAGCCC 60.441 66.667 0.00 0.00 0.00 5.19
683 729 2.943265 ATGAACCAGCCCAGCCCT 60.943 61.111 0.00 0.00 0.00 5.19
684 730 3.292481 ATGAACCAGCCCAGCCCTG 62.292 63.158 0.00 0.00 0.00 4.45
685 731 3.650950 GAACCAGCCCAGCCCTGA 61.651 66.667 0.00 0.00 32.03 3.86
686 732 3.635268 GAACCAGCCCAGCCCTGAG 62.635 68.421 0.00 0.00 32.03 3.35
693 755 2.759114 CCAGCCCTGAGCCTCAAA 59.241 61.111 0.00 0.00 45.47 2.69
719 797 4.427661 GCTCGACGCTGGCTGAGT 62.428 66.667 0.00 0.00 35.14 3.41
742 820 8.406730 AGTAGCTTGTTTCTTACTACTGTAGT 57.593 34.615 22.72 22.72 41.41 2.73
781 859 5.366477 ACCCAGAAACATTCCAAAAATGAGT 59.634 36.000 4.86 0.00 0.00 3.41
859 939 3.948719 GGGCCGTGTCCTGGACAA 61.949 66.667 29.84 12.46 44.49 3.18
860 940 2.668550 GGCCGTGTCCTGGACAAC 60.669 66.667 29.84 20.99 44.49 3.32
861 941 3.041940 GCCGTGTCCTGGACAACG 61.042 66.667 29.84 29.19 44.49 4.10
862 942 3.041940 CCGTGTCCTGGACAACGC 61.042 66.667 29.84 17.10 44.49 4.84
863 943 2.279851 CGTGTCCTGGACAACGCA 60.280 61.111 29.84 5.42 44.49 5.24
864 944 1.885388 CGTGTCCTGGACAACGCAA 60.885 57.895 29.84 4.56 44.49 4.85
865 945 1.647084 GTGTCCTGGACAACGCAAC 59.353 57.895 29.84 13.51 44.49 4.17
866 946 1.092921 GTGTCCTGGACAACGCAACA 61.093 55.000 29.84 3.70 44.49 3.33
867 947 0.813610 TGTCCTGGACAACGCAACAG 60.814 55.000 26.54 0.00 39.78 3.16
868 948 3.343972 CCTGGACAACGCAACAGG 58.656 61.111 0.00 0.00 43.87 4.00
869 949 2.260869 CCTGGACAACGCAACAGGG 61.261 63.158 0.00 0.00 45.21 4.45
925 1006 4.180946 CCGCGCGTACTCTCTGCT 62.181 66.667 29.95 0.00 0.00 4.24
940 1021 5.304614 ACTCTCTGCTGTACTGTAAAAAGGA 59.695 40.000 1.46 0.00 0.00 3.36
941 1022 6.169557 TCTCTGCTGTACTGTAAAAAGGAA 57.830 37.500 1.46 0.00 0.00 3.36
987 1068 1.437573 CCTCGCGTAATCCTCAGCA 59.562 57.895 5.77 0.00 0.00 4.41
1006 1090 1.611851 CTGCTCCCACACTCCCTCT 60.612 63.158 0.00 0.00 0.00 3.69
1105 1208 4.016706 CTGTTCCGTCCCCCGCTT 62.017 66.667 0.00 0.00 34.38 4.68
1320 1429 2.581354 CCGAAGCAGGGTCAGGAG 59.419 66.667 0.00 0.00 0.00 3.69
1321 1430 2.125350 CGAAGCAGGGTCAGGAGC 60.125 66.667 0.00 0.00 0.00 4.70
2245 2366 1.098712 GGTGACCGTTTCCTGCACAA 61.099 55.000 0.00 0.00 0.00 3.33
2281 2404 8.434392 AGTTTAGTGGACATGTTACTCCTTTTA 58.566 33.333 16.91 0.59 0.00 1.52
2374 2503 5.388654 AGGAACCTTCATGTGTCATTTTCT 58.611 37.500 0.00 0.00 0.00 2.52
2383 2512 9.254133 CTTCATGTGTCATTTTCTATCGACTAT 57.746 33.333 0.00 0.00 0.00 2.12
2439 2568 0.179067 TCCGTATTCGTGCAATCCCC 60.179 55.000 0.00 0.00 35.01 4.81
2440 2569 1.164041 CCGTATTCGTGCAATCCCCC 61.164 60.000 0.00 0.00 35.01 5.40
2452 2581 2.224793 GCAATCCCCCACCCTAATCTAC 60.225 54.545 0.00 0.00 0.00 2.59
2466 2595 2.802787 ATCTACGATCTTTGGAGCCG 57.197 50.000 0.00 0.00 0.00 5.52
2468 2597 0.744874 CTACGATCTTTGGAGCCGGA 59.255 55.000 5.05 0.00 0.00 5.14
2498 2629 9.752274 TTCATTTTTGTCTTGTTTTCATTTTCG 57.248 25.926 0.00 0.00 0.00 3.46
2501 2632 7.659652 TTTTGTCTTGTTTTCATTTTCGGTT 57.340 28.000 0.00 0.00 0.00 4.44
2509 2640 6.205784 TGTTTTCATTTTCGGTTGCTCTAAG 58.794 36.000 0.00 0.00 0.00 2.18
2525 2659 5.983720 TGCTCTAAGAACAGTTCAGTTGTAC 59.016 40.000 15.85 0.39 0.00 2.90
2526 2660 6.183360 TGCTCTAAGAACAGTTCAGTTGTACT 60.183 38.462 15.85 0.00 0.00 2.73
2565 2699 1.754803 CTGGTGATGCAATGGCTGAAT 59.245 47.619 0.00 0.00 41.91 2.57
2658 2796 4.374689 AGACTGACTCCTCTTACTCACA 57.625 45.455 0.00 0.00 0.00 3.58
2855 2993 3.181434 ACCACTACCACAACACCATCAAT 60.181 43.478 0.00 0.00 0.00 2.57
2880 3018 1.153628 GGCGAGTTATGCCGTGAGT 60.154 57.895 0.00 0.00 43.70 3.41
2989 3127 0.038526 GTGCGGGAGTTCGAGAAGAA 60.039 55.000 0.00 0.00 36.31 2.52
2999 3137 4.461198 AGTTCGAGAAGAAAACCATTGGT 58.539 39.130 1.37 1.37 41.10 3.67
3007 3145 5.304101 AGAAGAAAACCATTGGTAATGTGCA 59.696 36.000 9.20 0.00 37.18 4.57
3087 3231 1.243342 CCGTCCATGAAGCTTGGCAA 61.243 55.000 2.10 0.00 34.06 4.52
3120 3270 6.405286 CCTCATGTTGTGAACCTAACAAACAA 60.405 38.462 0.00 0.00 39.89 2.83
3153 3303 1.427435 GCTTGTGAGCTGACAGAGAC 58.573 55.000 6.03 0.00 45.65 3.36
3155 3306 0.319040 TTGTGAGCTGACAGAGACGC 60.319 55.000 6.03 3.85 0.00 5.19
3158 3309 1.210413 GAGCTGACAGAGACGCGAA 59.790 57.895 15.93 0.00 0.00 4.70
3182 3333 1.890041 CGAAACCGCAACCCTGACA 60.890 57.895 0.00 0.00 0.00 3.58
3185 3336 4.643387 ACCGCAACCCTGACAGCC 62.643 66.667 0.00 0.00 0.00 4.85
3242 3393 5.048504 TGTCAATCTGCAAAGGTGAGAATTC 60.049 40.000 0.00 0.00 0.00 2.17
3270 3422 9.237187 GTATAGAGAAGATACACATCTCATCCA 57.763 37.037 4.98 0.00 43.28 3.41
3321 3474 7.430441 TCAGTCATATTCATTGCATTCCATTG 58.570 34.615 0.00 0.00 0.00 2.82
3329 3483 5.991861 TCATTGCATTCCATTGGCTTAAAT 58.008 33.333 0.00 0.00 0.00 1.40
3354 3508 7.103641 TCTCCAAGTTGATAATAGCTTCGTTT 58.896 34.615 3.87 0.00 0.00 3.60
3400 3555 9.641135 TTCTAGATTAGATGGTTGCACCTTGCA 62.641 40.741 0.00 0.00 42.53 4.08
3421 3576 7.144722 TGCAACTTCCTTTGTTGACTATATG 57.855 36.000 10.29 0.00 45.27 1.78
3433 3588 1.261619 GACTATATGTGCCGCAACAGC 59.738 52.381 0.00 0.00 32.52 4.40
3475 3633 8.293867 CCTAATTTTTGTTGGATCGACAAGTTA 58.706 33.333 11.56 11.08 38.72 2.24
3491 3649 6.347725 CGACAAGTTAATGCTTAAAGCTCACT 60.348 38.462 0.00 0.00 42.97 3.41
3512 4514 2.522060 CTGAATAGATCGGCGCCAC 58.478 57.895 28.98 16.94 0.00 5.01
3553 4564 4.015872 TGTAGGGGTGTGAAAAGTGATC 57.984 45.455 0.00 0.00 0.00 2.92
3581 4592 7.828508 ATCAGCATGGCTCTGATTTTTATTA 57.171 32.000 8.11 0.00 45.99 0.98
3582 4593 7.828508 TCAGCATGGCTCTGATTTTTATTAT 57.171 32.000 0.00 0.00 36.40 1.28
3583 4594 8.241497 TCAGCATGGCTCTGATTTTTATTATT 57.759 30.769 0.00 0.00 36.40 1.40
3584 4595 8.698210 TCAGCATGGCTCTGATTTTTATTATTT 58.302 29.630 0.00 0.00 36.40 1.40
3585 4596 9.321562 CAGCATGGCTCTGATTTTTATTATTTT 57.678 29.630 0.00 0.00 36.40 1.82
3586 4597 9.895138 AGCATGGCTCTGATTTTTATTATTTTT 57.105 25.926 0.00 0.00 30.62 1.94
3609 4620 4.891992 TCCTCCAAACTCCTAAAGTCAG 57.108 45.455 0.00 0.00 37.17 3.51
3634 4645 6.468484 CAAGCAATGCCATAAATTTTGTACG 58.532 36.000 0.00 0.00 0.00 3.67
3635 4646 5.719173 AGCAATGCCATAAATTTTGTACGT 58.281 33.333 0.00 0.00 0.00 3.57
3636 4647 6.857956 AGCAATGCCATAAATTTTGTACGTA 58.142 32.000 0.00 0.00 0.00 3.57
3637 4648 6.750039 AGCAATGCCATAAATTTTGTACGTAC 59.250 34.615 18.90 18.90 0.00 3.67
3638 4649 6.750039 GCAATGCCATAAATTTTGTACGTACT 59.250 34.615 25.12 7.63 0.00 2.73
3641 4652 7.542534 TGCCATAAATTTTGTACGTACTAGG 57.457 36.000 25.12 14.28 0.00 3.02
3652 4663 4.637534 TGTACGTACTAGGTAGAAAGGCAG 59.362 45.833 25.12 0.00 0.00 4.85
3688 4705 0.250209 GAGCGTGATGAGATGGGCAT 60.250 55.000 0.00 0.00 0.00 4.40
3719 4736 1.458209 GCATGATTGGGGAAGGGGG 60.458 63.158 0.00 0.00 0.00 5.40
3772 4789 0.107508 TATTGTCTCCAGCTGCTGCC 60.108 55.000 23.86 11.24 40.80 4.85
3813 4830 2.288961 GCATTTGGCCTGATGTTCTG 57.711 50.000 16.77 1.04 36.11 3.02
3814 4831 1.738030 GCATTTGGCCTGATGTTCTGC 60.738 52.381 16.77 6.38 36.11 4.26
3815 4832 1.822990 CATTTGGCCTGATGTTCTGCT 59.177 47.619 3.32 0.00 0.00 4.24
3816 4833 2.877097 TTTGGCCTGATGTTCTGCTA 57.123 45.000 3.32 0.00 0.00 3.49
3817 4834 2.877097 TTGGCCTGATGTTCTGCTAA 57.123 45.000 3.32 0.00 0.00 3.09
3818 4835 3.370840 TTGGCCTGATGTTCTGCTAAT 57.629 42.857 3.32 0.00 0.00 1.73
3819 4836 2.923121 TGGCCTGATGTTCTGCTAATC 58.077 47.619 3.32 0.00 0.00 1.75
3838 4855 1.241315 CGTTTGGTGGGCCGAATTCT 61.241 55.000 3.52 0.00 40.12 2.40
3839 4856 0.526211 GTTTGGTGGGCCGAATTCTC 59.474 55.000 3.52 0.00 40.12 2.87
3846 4863 0.106719 GGGCCGAATTCTCATTCCCA 60.107 55.000 3.52 0.00 36.18 4.37
3852 4869 3.004106 CCGAATTCTCATTCCCAATCTGC 59.996 47.826 3.52 0.00 36.18 4.26
3853 4870 3.303593 CGAATTCTCATTCCCAATCTGCG 60.304 47.826 3.52 0.00 36.18 5.18
3854 4871 1.382522 TTCTCATTCCCAATCTGCGC 58.617 50.000 0.00 0.00 0.00 6.09
3855 4872 0.464373 TCTCATTCCCAATCTGCGCC 60.464 55.000 4.18 0.00 0.00 6.53
3877 4918 5.761003 CCATTTTGCTGTATTATCATCGCA 58.239 37.500 0.00 0.00 0.00 5.10
3895 4936 1.064389 GCATCAGGTTTTAGGAGCCCT 60.064 52.381 0.00 0.00 37.71 5.19
3906 4947 5.373812 TTTAGGAGCCCTTTCCTGATTAG 57.626 43.478 4.86 0.00 46.94 1.73
3919 4960 6.796705 TTCCTGATTAGTTTCCGTTTCTTC 57.203 37.500 0.00 0.00 0.00 2.87
3923 4964 6.183360 CCTGATTAGTTTCCGTTTCTTCCATC 60.183 42.308 0.00 0.00 0.00 3.51
3924 4965 6.472887 TGATTAGTTTCCGTTTCTTCCATCT 58.527 36.000 0.00 0.00 0.00 2.90
3925 4966 7.617225 TGATTAGTTTCCGTTTCTTCCATCTA 58.383 34.615 0.00 0.00 0.00 1.98
3926 4967 8.098286 TGATTAGTTTCCGTTTCTTCCATCTAA 58.902 33.333 0.00 0.00 0.00 2.10
3935 4976 6.030228 CGTTTCTTCCATCTAATTTTCTGCC 58.970 40.000 0.00 0.00 0.00 4.85
3943 4984 3.852286 TCTAATTTTCTGCCGCGTCTTA 58.148 40.909 4.92 0.00 0.00 2.10
3951 4992 1.083806 TGCCGCGTCTTATTGCTCTG 61.084 55.000 4.92 0.00 0.00 3.35
3954 4995 1.324736 CCGCGTCTTATTGCTCTGTTC 59.675 52.381 4.92 0.00 0.00 3.18
4014 5055 9.914131 GGAATCCATTACCTAGAATAAAATTGC 57.086 33.333 0.00 0.00 0.00 3.56
4029 5070 2.875094 ATTGCTGAGCCTTCTTCACT 57.125 45.000 0.23 0.00 0.00 3.41
4071 5112 3.499918 GCTTACTGCAGTTCATGACAACT 59.500 43.478 27.06 0.00 42.31 3.16
4125 5166 6.419710 CCTCAATATGACAATCGCTACGTTAA 59.580 38.462 0.00 0.00 0.00 2.01
4126 5167 7.116376 CCTCAATATGACAATCGCTACGTTAAT 59.884 37.037 0.00 0.00 0.00 1.40
4127 5168 8.360325 TCAATATGACAATCGCTACGTTAATT 57.640 30.769 0.00 0.00 0.00 1.40
4128 5169 8.272866 TCAATATGACAATCGCTACGTTAATTG 58.727 33.333 0.00 1.85 35.68 2.32
4129 5170 4.850859 TGACAATCGCTACGTTAATTGG 57.149 40.909 0.00 0.00 34.23 3.16
4130 5171 3.062909 TGACAATCGCTACGTTAATTGGC 59.937 43.478 0.00 1.98 37.59 4.52
4131 5172 3.004171 ACAATCGCTACGTTAATTGGCA 58.996 40.909 0.00 0.00 34.23 4.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
233 243 4.329545 TCACCTTGTCAGCGGGGC 62.330 66.667 0.00 0.00 0.00 5.80
236 246 1.961277 GGTGTCACCTTGTCAGCGG 60.961 63.158 15.22 0.00 34.73 5.52
464 506 2.032681 ACCTTCTCGTGCTTGCCC 59.967 61.111 0.00 0.00 0.00 5.36
516 562 0.663153 CCGCCTTAATGCTAAGCCAC 59.337 55.000 1.17 0.00 34.29 5.01
519 565 1.230324 CTCCCGCCTTAATGCTAAGC 58.770 55.000 1.17 0.00 34.29 3.09
521 567 0.837272 AGCTCCCGCCTTAATGCTAA 59.163 50.000 1.17 0.00 36.60 3.09
532 578 2.024176 TTAACATCTGAAGCTCCCGC 57.976 50.000 0.00 0.00 0.00 6.13
544 590 4.454728 TGCAGCCCTTCAAATTAACATC 57.545 40.909 0.00 0.00 0.00 3.06
547 593 4.082026 ACTGATGCAGCCCTTCAAATTAAC 60.082 41.667 0.00 0.00 34.37 2.01
549 595 3.444742 CACTGATGCAGCCCTTCAAATTA 59.555 43.478 0.00 0.00 34.37 1.40
554 600 1.001764 CCACTGATGCAGCCCTTCA 60.002 57.895 0.00 0.00 34.37 3.02
562 608 1.302431 CCCGTTGACCACTGATGCA 60.302 57.895 0.00 0.00 0.00 3.96
563 609 1.302511 ACCCGTTGACCACTGATGC 60.303 57.895 0.00 0.00 0.00 3.91
566 612 0.105964 CTTCACCCGTTGACCACTGA 59.894 55.000 0.00 0.00 32.26 3.41
567 613 0.105964 TCTTCACCCGTTGACCACTG 59.894 55.000 0.00 0.00 32.26 3.66
568 614 0.834612 TTCTTCACCCGTTGACCACT 59.165 50.000 0.00 0.00 32.26 4.00
569 615 1.602377 CTTTCTTCACCCGTTGACCAC 59.398 52.381 0.00 0.00 32.26 4.16
570 616 1.210967 ACTTTCTTCACCCGTTGACCA 59.789 47.619 0.00 0.00 32.26 4.02
571 617 1.602377 CACTTTCTTCACCCGTTGACC 59.398 52.381 0.00 0.00 32.26 4.02
572 618 1.602377 CCACTTTCTTCACCCGTTGAC 59.398 52.381 0.00 0.00 32.26 3.18
573 619 1.210967 ACCACTTTCTTCACCCGTTGA 59.789 47.619 0.00 0.00 0.00 3.18
574 620 1.675552 ACCACTTTCTTCACCCGTTG 58.324 50.000 0.00 0.00 0.00 4.10
575 621 3.118149 AGTTACCACTTTCTTCACCCGTT 60.118 43.478 0.00 0.00 0.00 4.44
576 622 2.436911 AGTTACCACTTTCTTCACCCGT 59.563 45.455 0.00 0.00 0.00 5.28
577 623 3.121738 AGTTACCACTTTCTTCACCCG 57.878 47.619 0.00 0.00 0.00 5.28
578 624 4.395231 GCATAGTTACCACTTTCTTCACCC 59.605 45.833 0.00 0.00 34.06 4.61
579 625 5.246307 AGCATAGTTACCACTTTCTTCACC 58.754 41.667 0.00 0.00 34.06 4.02
580 626 7.063544 CAGTAGCATAGTTACCACTTTCTTCAC 59.936 40.741 0.00 0.00 34.06 3.18
581 627 7.097192 CAGTAGCATAGTTACCACTTTCTTCA 58.903 38.462 0.00 0.00 34.06 3.02
582 628 7.097834 ACAGTAGCATAGTTACCACTTTCTTC 58.902 38.462 0.00 0.00 34.06 2.87
583 629 7.005709 ACAGTAGCATAGTTACCACTTTCTT 57.994 36.000 0.00 0.00 34.06 2.52
584 630 6.607004 ACAGTAGCATAGTTACCACTTTCT 57.393 37.500 0.00 0.00 34.06 2.52
585 631 6.979238 CCTACAGTAGCATAGTTACCACTTTC 59.021 42.308 1.50 0.00 34.06 2.62
586 632 6.666546 TCCTACAGTAGCATAGTTACCACTTT 59.333 38.462 1.50 0.00 34.06 2.66
587 633 6.192773 TCCTACAGTAGCATAGTTACCACTT 58.807 40.000 1.50 0.00 34.06 3.16
588 634 5.763355 TCCTACAGTAGCATAGTTACCACT 58.237 41.667 1.50 0.00 36.99 4.00
589 635 6.651975 ATCCTACAGTAGCATAGTTACCAC 57.348 41.667 1.50 0.00 0.00 4.16
590 636 7.670605 AAATCCTACAGTAGCATAGTTACCA 57.329 36.000 1.50 0.00 0.00 3.25
591 637 8.858094 AGTAAATCCTACAGTAGCATAGTTACC 58.142 37.037 15.41 5.75 0.00 2.85
595 641 8.566260 CGTAAGTAAATCCTACAGTAGCATAGT 58.434 37.037 1.50 0.00 0.00 2.12
596 642 7.537991 GCGTAAGTAAATCCTACAGTAGCATAG 59.462 40.741 1.50 0.00 41.68 2.23
597 643 7.013559 TGCGTAAGTAAATCCTACAGTAGCATA 59.986 37.037 1.50 0.00 41.68 3.14
598 644 6.183360 TGCGTAAGTAAATCCTACAGTAGCAT 60.183 38.462 1.50 0.00 41.68 3.79
599 645 5.125900 TGCGTAAGTAAATCCTACAGTAGCA 59.874 40.000 1.50 0.00 41.68 3.49
600 646 5.458126 GTGCGTAAGTAAATCCTACAGTAGC 59.542 44.000 1.50 0.00 41.68 3.58
601 647 6.558009 TGTGCGTAAGTAAATCCTACAGTAG 58.442 40.000 0.00 0.00 41.68 2.57
602 648 6.375174 TCTGTGCGTAAGTAAATCCTACAGTA 59.625 38.462 0.00 0.00 41.68 2.74
603 649 5.184479 TCTGTGCGTAAGTAAATCCTACAGT 59.816 40.000 0.00 0.00 41.68 3.55
604 650 5.647589 TCTGTGCGTAAGTAAATCCTACAG 58.352 41.667 0.00 0.00 41.68 2.74
605 651 5.416639 TCTCTGTGCGTAAGTAAATCCTACA 59.583 40.000 0.00 0.00 41.68 2.74
606 652 5.742926 GTCTCTGTGCGTAAGTAAATCCTAC 59.257 44.000 0.00 0.00 41.68 3.18
607 653 5.416639 TGTCTCTGTGCGTAAGTAAATCCTA 59.583 40.000 0.00 0.00 41.68 2.94
608 654 4.219944 TGTCTCTGTGCGTAAGTAAATCCT 59.780 41.667 0.00 0.00 41.68 3.24
609 655 4.326548 GTGTCTCTGTGCGTAAGTAAATCC 59.673 45.833 0.00 0.00 41.68 3.01
610 656 4.921515 TGTGTCTCTGTGCGTAAGTAAATC 59.078 41.667 0.00 0.00 41.68 2.17
611 657 4.878439 TGTGTCTCTGTGCGTAAGTAAAT 58.122 39.130 0.00 0.00 41.68 1.40
612 658 4.037089 TCTGTGTCTCTGTGCGTAAGTAAA 59.963 41.667 0.00 0.00 41.68 2.01
613 659 3.566742 TCTGTGTCTCTGTGCGTAAGTAA 59.433 43.478 0.00 0.00 41.68 2.24
614 660 3.143728 TCTGTGTCTCTGTGCGTAAGTA 58.856 45.455 0.00 0.00 41.68 2.24
615 661 1.954382 TCTGTGTCTCTGTGCGTAAGT 59.046 47.619 0.00 0.00 41.68 2.24
616 662 2.590073 CTCTGTGTCTCTGTGCGTAAG 58.410 52.381 0.00 0.00 43.44 2.34
617 663 1.335964 GCTCTGTGTCTCTGTGCGTAA 60.336 52.381 0.00 0.00 0.00 3.18
618 664 0.241213 GCTCTGTGTCTCTGTGCGTA 59.759 55.000 0.00 0.00 0.00 4.42
619 665 1.006805 GCTCTGTGTCTCTGTGCGT 60.007 57.895 0.00 0.00 0.00 5.24
620 666 2.085262 CGCTCTGTGTCTCTGTGCG 61.085 63.158 11.80 11.80 45.46 5.34
621 667 1.006314 GTCGCTCTGTGTCTCTGTGC 61.006 60.000 0.00 0.00 0.00 4.57
622 668 0.312102 TGTCGCTCTGTGTCTCTGTG 59.688 55.000 0.00 0.00 0.00 3.66
623 669 0.595588 CTGTCGCTCTGTGTCTCTGT 59.404 55.000 0.00 0.00 0.00 3.41
624 670 0.595588 ACTGTCGCTCTGTGTCTCTG 59.404 55.000 0.00 0.00 0.00 3.35
625 671 0.595588 CACTGTCGCTCTGTGTCTCT 59.404 55.000 8.44 0.00 39.86 3.10
626 672 0.593618 TCACTGTCGCTCTGTGTCTC 59.406 55.000 13.49 0.00 43.39 3.36
627 673 0.312416 GTCACTGTCGCTCTGTGTCT 59.688 55.000 13.49 0.00 43.39 3.41
628 674 0.312416 AGTCACTGTCGCTCTGTGTC 59.688 55.000 13.49 10.01 43.39 3.67
629 675 0.031314 CAGTCACTGTCGCTCTGTGT 59.969 55.000 0.00 0.00 43.39 3.72
630 676 0.312102 TCAGTCACTGTCGCTCTGTG 59.688 55.000 4.28 9.72 43.98 3.66
631 677 0.312416 GTCAGTCACTGTCGCTCTGT 59.688 55.000 4.28 0.00 32.61 3.41
632 678 0.595588 AGTCAGTCACTGTCGCTCTG 59.404 55.000 4.28 0.00 32.26 3.35
633 679 0.878416 GAGTCAGTCACTGTCGCTCT 59.122 55.000 4.28 0.00 34.41 4.09
637 683 0.167033 CCTCGAGTCAGTCACTGTCG 59.833 60.000 12.31 10.78 34.41 4.35
647 693 6.984474 GGTTCATCAATATTAACCTCGAGTCA 59.016 38.462 12.31 0.00 36.71 3.41
679 725 1.228245 TGTGTTTGAGGCTCAGGGC 60.228 57.895 17.91 11.93 40.90 5.19
680 726 0.890996 GGTGTGTTTGAGGCTCAGGG 60.891 60.000 17.91 0.00 0.00 4.45
681 727 1.230635 CGGTGTGTTTGAGGCTCAGG 61.231 60.000 17.91 0.00 0.00 3.86
682 728 1.230635 CCGGTGTGTTTGAGGCTCAG 61.231 60.000 17.91 3.22 0.00 3.35
683 729 1.227823 CCGGTGTGTTTGAGGCTCA 60.228 57.895 14.43 14.43 0.00 4.26
684 730 1.966451 CCCGGTGTGTTTGAGGCTC 60.966 63.158 7.79 7.79 0.00 4.70
685 731 2.113139 CCCGGTGTGTTTGAGGCT 59.887 61.111 0.00 0.00 0.00 4.58
686 732 3.670377 GCCCGGTGTGTTTGAGGC 61.670 66.667 0.00 0.00 0.00 4.70
719 797 8.400184 TGACTACAGTAGTAAGAAACAAGCTA 57.600 34.615 13.51 0.00 39.59 3.32
742 820 1.122632 TGGGTGGCCTCGTTTACTGA 61.123 55.000 3.32 0.00 0.00 3.41
781 859 4.280436 GGGATCTCATCTCGTCTCTCTA 57.720 50.000 0.00 0.00 0.00 2.43
843 921 2.668550 GTTGTCCAGGACACGGCC 60.669 66.667 22.87 6.87 42.60 6.13
855 935 0.035820 TATCCCCCTGTTGCGTTGTC 60.036 55.000 0.00 0.00 0.00 3.18
859 939 2.582436 CGTATCCCCCTGTTGCGT 59.418 61.111 0.00 0.00 0.00 5.24
860 940 2.203015 CCGTATCCCCCTGTTGCG 60.203 66.667 0.00 0.00 0.00 4.85
861 941 1.451387 CACCGTATCCCCCTGTTGC 60.451 63.158 0.00 0.00 0.00 4.17
862 942 0.107848 GTCACCGTATCCCCCTGTTG 60.108 60.000 0.00 0.00 0.00 3.33
863 943 1.610554 CGTCACCGTATCCCCCTGTT 61.611 60.000 0.00 0.00 0.00 3.16
864 944 2.056223 CGTCACCGTATCCCCCTGT 61.056 63.158 0.00 0.00 0.00 4.00
865 945 2.812499 CGTCACCGTATCCCCCTG 59.188 66.667 0.00 0.00 0.00 4.45
866 946 3.152400 GCGTCACCGTATCCCCCT 61.152 66.667 0.00 0.00 36.15 4.79
867 947 4.231439 GGCGTCACCGTATCCCCC 62.231 72.222 0.00 0.00 36.15 5.40
868 948 2.710724 GATGGCGTCACCGTATCCCC 62.711 65.000 0.00 0.00 43.94 4.81
869 949 1.300697 GATGGCGTCACCGTATCCC 60.301 63.158 0.00 0.00 43.94 3.85
940 1021 3.963383 CGTTGGCGGATTAATTAGCTT 57.037 42.857 13.39 0.00 0.00 3.74
987 1068 1.915769 GAGGGAGTGTGGGAGCAGT 60.916 63.158 0.00 0.00 0.00 4.40
1006 1090 0.548031 GGATGGGGAGCAATGAGTGA 59.452 55.000 0.00 0.00 0.00 3.41
1034 1134 2.045045 TCCGCATTCTTGCCCCTG 60.045 61.111 0.00 0.00 46.57 4.45
1035 1135 2.273449 CTCCGCATTCTTGCCCCT 59.727 61.111 0.00 0.00 46.57 4.79
1036 1136 3.521796 GCTCCGCATTCTTGCCCC 61.522 66.667 0.00 0.00 46.57 5.80
1037 1137 3.880846 CGCTCCGCATTCTTGCCC 61.881 66.667 0.00 0.00 46.57 5.36
1038 1138 2.817423 CTCGCTCCGCATTCTTGCC 61.817 63.158 0.00 0.00 46.57 4.52
1039 1139 2.705826 CTCGCTCCGCATTCTTGC 59.294 61.111 0.00 0.00 45.78 4.01
1040 1140 2.705826 GCTCGCTCCGCATTCTTG 59.294 61.111 0.00 0.00 0.00 3.02
1041 1141 2.512515 GGCTCGCTCCGCATTCTT 60.513 61.111 0.00 0.00 0.00 2.52
1096 1199 4.722700 GCAGAGCAAAGCGGGGGA 62.723 66.667 0.00 0.00 0.00 4.81
1104 1207 1.293498 GAGGTCGGAGCAGAGCAAA 59.707 57.895 10.15 0.00 40.77 3.68
1105 1208 1.471829 TTGAGGTCGGAGCAGAGCAA 61.472 55.000 10.15 5.52 40.77 3.91
1205 1308 2.683933 GGCAGAGGGAGAACGGGA 60.684 66.667 0.00 0.00 0.00 5.14
1279 1385 4.785453 GGAGGCGTTGGAGCTGGG 62.785 72.222 0.00 0.00 37.29 4.45
2194 2315 2.267961 GGCCTCGGAATCGTTGGT 59.732 61.111 0.00 0.00 37.69 3.67
2374 2503 5.071250 ACCAAATGGGCACTTATAGTCGATA 59.929 40.000 4.17 0.00 42.05 2.92
2383 2512 7.607250 CAACTTTATAACCAAATGGGCACTTA 58.393 34.615 4.17 0.00 42.05 2.24
2439 2568 4.344102 TCCAAAGATCGTAGATTAGGGTGG 59.656 45.833 0.00 0.00 45.12 4.61
2440 2569 5.531122 TCCAAAGATCGTAGATTAGGGTG 57.469 43.478 0.00 0.00 45.12 4.61
2452 2581 0.179073 ATGTCCGGCTCCAAAGATCG 60.179 55.000 0.00 0.00 0.00 3.69
2466 2595 8.663911 TGAAAACAAGACAAAAATGAAATGTCC 58.336 29.630 1.81 0.00 43.46 4.02
2498 2629 4.381411 ACTGAACTGTTCTTAGAGCAACC 58.619 43.478 20.18 0.00 0.00 3.77
2501 2632 5.023533 ACAACTGAACTGTTCTTAGAGCA 57.976 39.130 20.18 0.00 0.00 4.26
2525 2659 6.147821 CACCAGAAGTACACTTGAATTACCAG 59.852 42.308 0.00 0.00 36.11 4.00
2526 2660 5.995282 CACCAGAAGTACACTTGAATTACCA 59.005 40.000 0.00 0.00 36.11 3.25
2527 2661 6.228258 TCACCAGAAGTACACTTGAATTACC 58.772 40.000 0.00 0.00 36.11 2.85
2565 2699 2.237143 CTGCAAGGAGAACATGGTAGGA 59.763 50.000 0.00 0.00 0.00 2.94
2658 2796 2.710471 ACCCCCATTGTCTGCAAAAATT 59.290 40.909 0.00 0.00 38.21 1.82
2723 2861 0.454600 GGATCGCGTACTTCCTGTCA 59.545 55.000 5.77 0.00 0.00 3.58
2798 2936 0.601558 GCTCCGTCTTGTGAGTGGTA 59.398 55.000 0.00 0.00 0.00 3.25
2855 2993 1.448893 GCATAACTCGCCGGGAACA 60.449 57.895 2.18 0.00 0.00 3.18
2876 3014 2.904866 GGCACCGGCACAAACTCA 60.905 61.111 0.00 0.00 43.71 3.41
2907 3045 0.313043 GTCTTCTCGGACCACGTCAA 59.687 55.000 0.00 0.00 44.69 3.18
2989 3127 4.040217 ACACATGCACATTACCAATGGTTT 59.960 37.500 11.41 0.00 43.21 3.27
2999 3137 4.643784 TGCCATATTCACACATGCACATTA 59.356 37.500 0.00 0.00 0.00 1.90
3007 3145 5.918426 TTTGTCATGCCATATTCACACAT 57.082 34.783 0.00 0.00 0.00 3.21
3120 3270 4.008330 CTCACAAGCTCCAAATCATGAGT 58.992 43.478 0.09 0.00 0.00 3.41
3143 3293 1.982223 CTTTCTTCGCGTCTCTGTCAG 59.018 52.381 5.77 0.00 0.00 3.51
3147 3297 1.698898 CGCTTTCTTCGCGTCTCTG 59.301 57.895 5.77 0.00 45.13 3.35
3178 3329 0.607217 CACAATCTGCCAGGCTGTCA 60.607 55.000 14.15 5.79 0.00 3.58
3182 3333 1.975407 GCACACAATCTGCCAGGCT 60.975 57.895 14.15 0.00 0.00 4.58
3185 3336 1.736126 CAGTAGCACACAATCTGCCAG 59.264 52.381 0.00 0.00 35.01 4.85
3258 3409 7.981102 ATGAGATTTACATGGATGAGATGTG 57.019 36.000 0.00 0.00 35.62 3.21
3270 3422 8.746530 AGAGCAATTCAACAATGAGATTTACAT 58.253 29.630 0.00 0.00 36.78 2.29
3321 3474 8.293157 GCTATTATCAACTTGGAGATTTAAGCC 58.707 37.037 0.00 0.00 0.00 4.35
3329 3483 6.222038 ACGAAGCTATTATCAACTTGGAGA 57.778 37.500 0.00 0.00 0.00 3.71
3354 3508 8.472413 TCTAGAAATGCATCATCATCATCGATA 58.528 33.333 0.00 0.00 0.00 2.92
3400 3555 6.151144 GGCACATATAGTCAACAAAGGAAGTT 59.849 38.462 0.00 0.00 0.00 2.66
3433 3588 9.573133 CAAAAATTAGGGCTAGAACAGTTTATG 57.427 33.333 0.00 0.00 0.00 1.90
3491 3649 0.243907 GGCGCCGATCTATTCAGCTA 59.756 55.000 12.58 0.00 0.00 3.32
3501 4503 1.868997 CCAATATGTGGCGCCGATC 59.131 57.895 23.90 15.28 41.72 3.69
3524 4535 3.880047 TCACACCCCTACAATACGAAG 57.120 47.619 0.00 0.00 0.00 3.79
3530 4541 4.447138 TCACTTTTCACACCCCTACAAT 57.553 40.909 0.00 0.00 0.00 2.71
3534 4545 2.901192 TCGATCACTTTTCACACCCCTA 59.099 45.455 0.00 0.00 0.00 3.53
3553 4564 0.388294 TCAGAGCCATGCTGATCTCG 59.612 55.000 0.00 0.00 39.88 4.04
3584 4595 6.428295 TGACTTTAGGAGTTTGGAGGAAAAA 58.572 36.000 0.00 0.00 39.19 1.94
3585 4596 6.008696 TGACTTTAGGAGTTTGGAGGAAAA 57.991 37.500 0.00 0.00 39.19 2.29
3586 4597 5.621193 CTGACTTTAGGAGTTTGGAGGAAA 58.379 41.667 0.00 0.00 39.19 3.13
3587 4598 4.505039 GCTGACTTTAGGAGTTTGGAGGAA 60.505 45.833 0.00 0.00 39.19 3.36
3588 4599 3.008049 GCTGACTTTAGGAGTTTGGAGGA 59.992 47.826 0.00 0.00 39.19 3.71
3589 4600 3.244561 TGCTGACTTTAGGAGTTTGGAGG 60.245 47.826 0.00 0.00 39.19 4.30
3590 4601 4.008074 TGCTGACTTTAGGAGTTTGGAG 57.992 45.455 0.00 0.00 39.19 3.86
3591 4602 4.389374 CTTGCTGACTTTAGGAGTTTGGA 58.611 43.478 0.00 0.00 39.19 3.53
3632 4643 3.946558 CTCTGCCTTTCTACCTAGTACGT 59.053 47.826 0.00 0.00 0.00 3.57
3633 4644 3.315749 CCTCTGCCTTTCTACCTAGTACG 59.684 52.174 0.00 0.00 0.00 3.67
3634 4645 4.534797 TCCTCTGCCTTTCTACCTAGTAC 58.465 47.826 0.00 0.00 0.00 2.73
3635 4646 4.875578 TCCTCTGCCTTTCTACCTAGTA 57.124 45.455 0.00 0.00 0.00 1.82
3636 4647 3.759815 TCCTCTGCCTTTCTACCTAGT 57.240 47.619 0.00 0.00 0.00 2.57
3637 4648 3.386402 CCTTCCTCTGCCTTTCTACCTAG 59.614 52.174 0.00 0.00 0.00 3.02
3638 4649 3.012502 TCCTTCCTCTGCCTTTCTACCTA 59.987 47.826 0.00 0.00 0.00 3.08
3641 4652 3.369997 CCTTCCTTCCTCTGCCTTTCTAC 60.370 52.174 0.00 0.00 0.00 2.59
3652 4663 1.616628 TCCCCTGCCTTCCTTCCTC 60.617 63.158 0.00 0.00 0.00 3.71
3772 4789 4.387862 GCCAATGCAAAGAGAAAGAATGTG 59.612 41.667 0.00 0.00 37.47 3.21
3801 4818 2.555199 ACGATTAGCAGAACATCAGGC 58.445 47.619 0.00 0.00 0.00 4.85
3802 4819 4.201851 CCAAACGATTAGCAGAACATCAGG 60.202 45.833 0.00 0.00 0.00 3.86
3803 4820 4.393062 ACCAAACGATTAGCAGAACATCAG 59.607 41.667 0.00 0.00 0.00 2.90
3804 4821 4.154015 CACCAAACGATTAGCAGAACATCA 59.846 41.667 0.00 0.00 0.00 3.07
3805 4822 4.437390 CCACCAAACGATTAGCAGAACATC 60.437 45.833 0.00 0.00 0.00 3.06
3806 4823 3.440173 CCACCAAACGATTAGCAGAACAT 59.560 43.478 0.00 0.00 0.00 2.71
3807 4824 2.811431 CCACCAAACGATTAGCAGAACA 59.189 45.455 0.00 0.00 0.00 3.18
3808 4825 2.161609 CCCACCAAACGATTAGCAGAAC 59.838 50.000 0.00 0.00 0.00 3.01
3811 4828 0.451783 GCCCACCAAACGATTAGCAG 59.548 55.000 0.00 0.00 0.00 4.24
3812 4829 0.963355 GGCCCACCAAACGATTAGCA 60.963 55.000 0.00 0.00 35.26 3.49
3813 4830 1.807226 GGCCCACCAAACGATTAGC 59.193 57.895 0.00 0.00 35.26 3.09
3814 4831 0.391927 TCGGCCCACCAAACGATTAG 60.392 55.000 0.00 0.00 34.57 1.73
3815 4832 0.036448 TTCGGCCCACCAAACGATTA 59.964 50.000 0.00 0.00 35.10 1.75
3816 4833 0.610785 ATTCGGCCCACCAAACGATT 60.611 50.000 0.00 0.00 35.10 3.34
3817 4834 0.610785 AATTCGGCCCACCAAACGAT 60.611 50.000 0.00 0.00 35.10 3.73
3818 4835 1.228306 AATTCGGCCCACCAAACGA 60.228 52.632 0.00 0.00 34.57 3.85
3819 4836 1.211709 GAATTCGGCCCACCAAACG 59.788 57.895 0.00 0.00 34.57 3.60
3838 4855 0.106569 ATGGCGCAGATTGGGAATGA 60.107 50.000 10.83 0.00 31.21 2.57
3839 4856 0.748450 AATGGCGCAGATTGGGAATG 59.252 50.000 10.83 0.00 31.21 2.67
3846 4863 0.604578 ACAGCAAAATGGCGCAGATT 59.395 45.000 10.83 3.54 39.27 2.40
3852 4869 4.847757 CGATGATAATACAGCAAAATGGCG 59.152 41.667 0.00 0.00 39.27 5.69
3853 4870 4.618489 GCGATGATAATACAGCAAAATGGC 59.382 41.667 0.00 0.00 0.00 4.40
3854 4871 5.761003 TGCGATGATAATACAGCAAAATGG 58.239 37.500 0.00 0.00 0.00 3.16
3855 4872 7.079475 TGATGCGATGATAATACAGCAAAATG 58.921 34.615 0.00 0.00 38.15 2.32
3877 4918 3.309193 GGAAAGGGCTCCTAAAACCTGAT 60.309 47.826 0.00 0.00 31.13 2.90
3895 4936 6.206048 GGAAGAAACGGAAACTAATCAGGAAA 59.794 38.462 0.00 0.00 0.00 3.13
3906 4947 8.297426 AGAAAATTAGATGGAAGAAACGGAAAC 58.703 33.333 0.00 0.00 0.00 2.78
3919 4960 1.670811 ACGCGGCAGAAAATTAGATGG 59.329 47.619 12.47 0.00 0.00 3.51
3923 4964 4.795970 ATAAGACGCGGCAGAAAATTAG 57.204 40.909 17.71 0.00 0.00 1.73
3924 4965 4.729458 GCAATAAGACGCGGCAGAAAATTA 60.729 41.667 17.71 2.44 0.00 1.40
3925 4966 3.758300 CAATAAGACGCGGCAGAAAATT 58.242 40.909 17.71 0.00 0.00 1.82
3926 4967 2.477863 GCAATAAGACGCGGCAGAAAAT 60.478 45.455 17.71 0.00 0.00 1.82
3935 4976 2.263077 AGAACAGAGCAATAAGACGCG 58.737 47.619 3.53 3.53 0.00 6.01
3943 4984 4.276926 GGTGAACTGAAAGAACAGAGCAAT 59.723 41.667 0.00 0.00 40.63 3.56
3951 4992 3.945285 TCAACTGGGTGAACTGAAAGAAC 59.055 43.478 0.00 0.00 37.43 3.01
3954 4995 3.278574 TGTCAACTGGGTGAACTGAAAG 58.721 45.455 0.00 0.00 42.29 2.62
3991 5032 9.866655 TCAGCAATTTTATTCTAGGTAATGGAT 57.133 29.630 0.00 0.00 0.00 3.41
3995 5036 8.001292 AGGCTCAGCAATTTTATTCTAGGTAAT 58.999 33.333 0.00 0.00 0.00 1.89
3997 5038 6.900194 AGGCTCAGCAATTTTATTCTAGGTA 58.100 36.000 0.00 0.00 0.00 3.08
3998 5039 5.760131 AGGCTCAGCAATTTTATTCTAGGT 58.240 37.500 0.00 0.00 0.00 3.08
3999 5040 6.545298 AGAAGGCTCAGCAATTTTATTCTAGG 59.455 38.462 0.00 0.00 0.00 3.02
4014 5055 6.214191 TCAAGTATAGTGAAGAAGGCTCAG 57.786 41.667 0.00 0.00 0.00 3.35
4029 5070 3.133542 AGCACAGCAGCTCATCAAGTATA 59.866 43.478 0.00 0.00 42.18 1.47
4060 5101 5.011023 TCAGCTTCTCACTAGTTGTCATGAA 59.989 40.000 0.00 0.00 0.00 2.57
4062 5103 4.814147 TCAGCTTCTCACTAGTTGTCATG 58.186 43.478 0.00 0.00 0.00 3.07
4071 5112 2.115343 TCGCTCTCAGCTTCTCACTA 57.885 50.000 0.00 0.00 39.60 2.74
4089 5130 8.743085 ATTGTCATATTGAGGGCACATATATC 57.257 34.615 0.00 0.00 0.00 1.63
4096 5137 2.031682 GCGATTGTCATATTGAGGGCAC 60.032 50.000 0.00 0.00 0.00 5.01
4097 5138 2.158769 AGCGATTGTCATATTGAGGGCA 60.159 45.455 0.00 0.00 0.00 5.36


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

AutoCloner maintained by Alex Coulton.