Multiple sequence alignment - TraesCS4B01G005400

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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 TraesCS4B01G005400 chr4B 100.000 3695 0 0 1 3695 3785601 3789295 0.000000e+00 6824.0
1 TraesCS4B01G005400 chr4B 92.126 508 34 2 102 609 411851319 411851820 0.000000e+00 712.0
2 TraesCS4B01G005400 chr4B 89.548 354 37 0 44 397 3854608 3854255 2.020000e-122 449.0
3 TraesCS4B01G005400 chr3B 93.539 2956 149 18 745 3695 548772277 548775195 0.000000e+00 4362.0
4 TraesCS4B01G005400 chr3B 93.659 2602 147 12 1102 3695 548243263 548245854 0.000000e+00 3875.0
5 TraesCS4B01G005400 chr3B 94.396 2498 124 10 1205 3695 548472452 548474940 0.000000e+00 3823.0
6 TraesCS4B01G005400 chr3B 93.866 2543 121 14 1138 3666 599079069 599076548 0.000000e+00 3799.0
7 TraesCS4B01G005400 chr3B 92.263 685 41 5 3014 3695 454518223 454518898 0.000000e+00 961.0
8 TraesCS4B01G005400 chr5B 92.096 2973 179 24 733 3695 680230627 680227701 0.000000e+00 4137.0
9 TraesCS4B01G005400 chr5B 94.213 2592 135 11 1110 3695 508124190 508121608 0.000000e+00 3941.0
10 TraesCS4B01G005400 chr5B 93.872 2562 129 14 1113 3666 693448032 693445491 0.000000e+00 3836.0
11 TraesCS4B01G005400 chr5B 94.372 2381 115 14 742 3117 452113407 452111041 0.000000e+00 3637.0
12 TraesCS4B01G005400 chr2B 92.147 2967 146 23 742 3695 1180725 1183617 0.000000e+00 4108.0
13 TraesCS4B01G005400 chr2B 93.046 417 26 2 727 1142 788228843 788229257 1.130000e-169 606.0
14 TraesCS4B01G005400 chr2B 87.234 329 42 0 69 397 713694350 713694022 3.480000e-100 375.0
15 TraesCS4B01G005400 chr4A 91.765 2975 164 30 742 3695 616373915 616376829 0.000000e+00 4061.0
16 TraesCS4B01G005400 chr4A 92.635 611 38 4 1 610 602863858 602864462 0.000000e+00 872.0
17 TraesCS4B01G005400 chr4A 94.828 406 20 1 738 1142 603147224 603146819 1.870000e-177 632.0
18 TraesCS4B01G005400 chr4A 89.859 355 34 2 44 397 602260836 602261189 4.350000e-124 455.0
19 TraesCS4B01G005400 chr2D 93.627 2542 125 16 1138 3666 636788583 636786066 0.000000e+00 3762.0
20 TraesCS4B01G005400 chr4D 93.750 592 31 2 1 592 2071707 2072292 0.000000e+00 883.0
21 TraesCS4B01G005400 chr4D 90.294 340 33 0 56 395 3259988 3259649 2.620000e-121 446.0
22 TraesCS4B01G005400 chr4D 91.525 118 10 0 606 723 2072353 2072470 2.950000e-36 163.0
23 TraesCS4B01G005400 chr7B 91.929 508 35 2 102 609 385435290 385434789 0.000000e+00 706.0
24 TraesCS4B01G005400 chr7B 94.279 402 18 2 742 1142 692881452 692881849 8.770000e-171 610.0
25 TraesCS4B01G005400 chrUn 94.763 401 17 1 742 1138 93726510 93726110 4.050000e-174 621.0
26 TraesCS4B01G005400 chr3D 94.264 401 23 0 740 1140 132628048 132627648 6.780000e-172 614.0
27 TraesCS4B01G005400 chr3A 94.279 402 22 1 742 1142 747075302 747074901 6.780000e-172 614.0
28 TraesCS4B01G005400 chr6B 93.269 416 21 4 728 1142 660437755 660437346 1.130000e-169 606.0
29 TraesCS4B01G005400 chr6B 90.909 341 25 2 269 609 187212498 187212164 1.560000e-123 453.0
30 TraesCS4B01G005400 chr2A 92.995 414 24 4 730 1142 738182624 738183033 1.900000e-167 599.0
31 TraesCS4B01G005400 chr2A 90.286 350 28 2 260 609 273357901 273357558 1.560000e-123 453.0
32 TraesCS4B01G005400 chr2A 84.319 389 55 5 9 397 723827801 723827419 3.480000e-100 375.0
33 TraesCS4B01G005400 chr1B 90.492 305 23 2 305 609 331816053 331815755 7.440000e-107 398.0
34 TraesCS4B01G005400 chr5A 96.364 55 2 0 555 609 418903185 418903131 1.410000e-14 91.6


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 TraesCS4B01G005400 chr4B 3785601 3789295 3694 False 6824 6824 100.0000 1 3695 1 chr4B.!!$F1 3694
1 TraesCS4B01G005400 chr4B 411851319 411851820 501 False 712 712 92.1260 102 609 1 chr4B.!!$F2 507
2 TraesCS4B01G005400 chr3B 548772277 548775195 2918 False 4362 4362 93.5390 745 3695 1 chr3B.!!$F4 2950
3 TraesCS4B01G005400 chr3B 548243263 548245854 2591 False 3875 3875 93.6590 1102 3695 1 chr3B.!!$F2 2593
4 TraesCS4B01G005400 chr3B 548472452 548474940 2488 False 3823 3823 94.3960 1205 3695 1 chr3B.!!$F3 2490
5 TraesCS4B01G005400 chr3B 599076548 599079069 2521 True 3799 3799 93.8660 1138 3666 1 chr3B.!!$R1 2528
6 TraesCS4B01G005400 chr3B 454518223 454518898 675 False 961 961 92.2630 3014 3695 1 chr3B.!!$F1 681
7 TraesCS4B01G005400 chr5B 680227701 680230627 2926 True 4137 4137 92.0960 733 3695 1 chr5B.!!$R3 2962
8 TraesCS4B01G005400 chr5B 508121608 508124190 2582 True 3941 3941 94.2130 1110 3695 1 chr5B.!!$R2 2585
9 TraesCS4B01G005400 chr5B 693445491 693448032 2541 True 3836 3836 93.8720 1113 3666 1 chr5B.!!$R4 2553
10 TraesCS4B01G005400 chr5B 452111041 452113407 2366 True 3637 3637 94.3720 742 3117 1 chr5B.!!$R1 2375
11 TraesCS4B01G005400 chr2B 1180725 1183617 2892 False 4108 4108 92.1470 742 3695 1 chr2B.!!$F1 2953
12 TraesCS4B01G005400 chr4A 616373915 616376829 2914 False 4061 4061 91.7650 742 3695 1 chr4A.!!$F3 2953
13 TraesCS4B01G005400 chr4A 602863858 602864462 604 False 872 872 92.6350 1 610 1 chr4A.!!$F2 609
14 TraesCS4B01G005400 chr2D 636786066 636788583 2517 True 3762 3762 93.6270 1138 3666 1 chr2D.!!$R1 2528
15 TraesCS4B01G005400 chr4D 2071707 2072470 763 False 523 883 92.6375 1 723 2 chr4D.!!$F1 722
16 TraesCS4B01G005400 chr7B 385434789 385435290 501 True 706 706 91.9290 102 609 1 chr7B.!!$R1 507

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
379 380 0.040351 AGCACCTGAGGCTCTGAGTA 59.960 55.0 21.42 0.0 36.81 2.59 F
601 602 0.102481 CGATGCTTACGGCCACTACT 59.898 55.0 2.24 0.0 40.92 2.57 F
687 688 0.113580 TTACCCCCTTCAAGTTGCCC 59.886 55.0 0.00 0.0 0.00 5.36 F
1572 1602 0.319555 CACGAGCTCCGGAAGAACAA 60.320 55.0 5.23 0.0 43.93 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2034 2070 0.182775 AAACACGCAAGAGAACCCCT 59.817 50.000 0.00 0.0 43.62 4.79 R
2253 2290 1.003646 ACCTCTACCAGAGCTGAGGA 58.996 55.000 19.46 0.0 46.53 3.71 R
2414 2577 1.579429 CGCAGCCCTAAACACCAAC 59.421 57.895 0.00 0.0 0.00 3.77 R
3552 3794 0.401395 TTCCTCTCCCACCCACAAGT 60.401 55.000 0.00 0.0 0.00 3.16 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
42 43 0.453793 CTCGAGGAAGACTGCGATGT 59.546 55.000 3.91 0.00 31.65 3.06
55 56 2.783284 CTGCGATGTCAACAACAACAAC 59.217 45.455 0.00 0.00 42.37 3.32
58 59 3.796178 GCGATGTCAACAACAACAACAAT 59.204 39.130 0.00 0.00 42.37 2.71
64 65 6.914259 TGTCAACAACAACAACAATAAGTCA 58.086 32.000 0.00 0.00 34.03 3.41
67 68 6.909895 TCAACAACAACAACAATAAGTCATCG 59.090 34.615 0.00 0.00 0.00 3.84
85 86 2.972505 GCTGTGTGGGTGGACGTG 60.973 66.667 0.00 0.00 0.00 4.49
88 89 4.555709 GTGTGGGTGGACGTGCCA 62.556 66.667 4.04 3.44 46.96 4.92
188 189 2.828868 GTGTGGTGTCCCAGAGCA 59.171 61.111 0.00 0.00 42.94 4.26
301 302 2.959372 CGGTACAGGAGCACGACA 59.041 61.111 0.00 0.00 0.00 4.35
377 378 1.218585 CAGCACCTGAGGCTCTGAG 59.781 63.158 21.42 14.30 40.23 3.35
379 380 0.040351 AGCACCTGAGGCTCTGAGTA 59.960 55.000 21.42 0.00 36.81 2.59
396 397 6.640518 TCTGAGTACATCCCATCAAAACTAC 58.359 40.000 0.00 0.00 0.00 2.73
397 398 6.440647 TCTGAGTACATCCCATCAAAACTACT 59.559 38.462 0.00 0.00 0.00 2.57
398 399 6.406370 TGAGTACATCCCATCAAAACTACTG 58.594 40.000 0.00 0.00 0.00 2.74
399 400 6.013725 TGAGTACATCCCATCAAAACTACTGT 60.014 38.462 0.00 0.00 0.00 3.55
400 401 7.179516 TGAGTACATCCCATCAAAACTACTGTA 59.820 37.037 0.00 0.00 0.00 2.74
406 407 4.323485 CCCATCAAAACTACTGTAGCCAGA 60.323 45.833 14.55 8.22 41.50 3.86
498 499 1.001181 TGCAGTTTCAGTACGGGGTAC 59.999 52.381 0.00 0.00 39.10 3.34
499 500 1.001181 GCAGTTTCAGTACGGGGTACA 59.999 52.381 8.46 0.00 41.03 2.90
500 501 2.354403 GCAGTTTCAGTACGGGGTACAT 60.354 50.000 8.46 0.00 41.03 2.29
501 502 3.119029 GCAGTTTCAGTACGGGGTACATA 60.119 47.826 8.46 0.00 41.03 2.29
502 503 4.442472 GCAGTTTCAGTACGGGGTACATAT 60.442 45.833 8.46 0.00 41.03 1.78
503 504 5.047847 CAGTTTCAGTACGGGGTACATATG 58.952 45.833 0.00 0.00 41.03 1.78
504 505 4.713321 AGTTTCAGTACGGGGTACATATGT 59.287 41.667 13.93 13.93 41.03 2.29
505 506 5.893255 AGTTTCAGTACGGGGTACATATGTA 59.107 40.000 11.62 11.62 41.03 2.29
506 507 6.040166 AGTTTCAGTACGGGGTACATATGTAG 59.960 42.308 15.93 7.02 41.03 2.74
507 508 3.822735 TCAGTACGGGGTACATATGTAGC 59.177 47.826 28.92 28.92 45.42 3.58
508 509 3.825014 CAGTACGGGGTACATATGTAGCT 59.175 47.826 32.78 21.42 45.44 3.32
509 510 4.077822 AGTACGGGGTACATATGTAGCTC 58.922 47.826 32.78 30.40 45.44 4.09
510 511 3.240310 ACGGGGTACATATGTAGCTCT 57.760 47.619 31.76 20.69 44.82 4.09
511 512 4.377762 ACGGGGTACATATGTAGCTCTA 57.622 45.455 31.76 6.52 44.82 2.43
512 513 4.077822 ACGGGGTACATATGTAGCTCTAC 58.922 47.826 31.76 20.65 44.82 2.59
513 514 4.202545 ACGGGGTACATATGTAGCTCTACT 60.203 45.833 31.76 17.48 44.82 2.57
514 515 5.013495 ACGGGGTACATATGTAGCTCTACTA 59.987 44.000 31.76 4.49 44.82 1.82
515 516 6.120905 CGGGGTACATATGTAGCTCTACTAT 58.879 44.000 31.76 2.00 44.82 2.12
516 517 6.038382 CGGGGTACATATGTAGCTCTACTATG 59.962 46.154 31.76 17.71 44.82 2.23
517 518 6.321690 GGGGTACATATGTAGCTCTACTATGG 59.678 46.154 32.78 0.00 43.93 2.74
518 519 7.117397 GGGTACATATGTAGCTCTACTATGGA 58.883 42.308 32.78 13.56 45.44 3.41
519 520 7.614583 GGGTACATATGTAGCTCTACTATGGAA 59.385 40.741 32.78 2.88 45.44 3.53
520 521 8.679100 GGTACATATGTAGCTCTACTATGGAAG 58.321 40.741 29.30 0.00 43.49 3.46
521 522 9.451002 GTACATATGTAGCTCTACTATGGAAGA 57.549 37.037 15.93 0.00 37.00 2.87
522 523 8.574251 ACATATGTAGCTCTACTATGGAAGAG 57.426 38.462 6.56 0.00 41.82 2.85
523 524 8.167392 ACATATGTAGCTCTACTATGGAAGAGT 58.833 37.037 6.56 0.00 41.13 3.24
524 525 8.673711 CATATGTAGCTCTACTATGGAAGAGTC 58.326 40.741 8.34 0.00 41.13 3.36
525 526 6.255294 TGTAGCTCTACTATGGAAGAGTCT 57.745 41.667 8.34 0.00 41.13 3.24
526 527 6.292923 TGTAGCTCTACTATGGAAGAGTCTC 58.707 44.000 8.34 0.00 41.13 3.36
527 528 5.381184 AGCTCTACTATGGAAGAGTCTCA 57.619 43.478 1.94 0.00 41.13 3.27
528 529 5.761205 AGCTCTACTATGGAAGAGTCTCAA 58.239 41.667 1.94 0.00 41.13 3.02
529 530 6.191315 AGCTCTACTATGGAAGAGTCTCAAA 58.809 40.000 1.94 0.00 41.13 2.69
530 531 6.665680 AGCTCTACTATGGAAGAGTCTCAAAA 59.334 38.462 1.94 0.00 41.13 2.44
531 532 7.179338 AGCTCTACTATGGAAGAGTCTCAAAAA 59.821 37.037 1.94 0.00 41.13 1.94
562 563 8.538409 AATAAAATGAGTTGATTGAAGCAACC 57.462 30.769 21.07 13.60 45.05 3.77
563 564 5.534207 AAATGAGTTGATTGAAGCAACCA 57.466 34.783 21.07 18.08 45.05 3.67
564 565 5.534207 AATGAGTTGATTGAAGCAACCAA 57.466 34.783 21.07 11.19 45.05 3.67
565 566 5.733620 ATGAGTTGATTGAAGCAACCAAT 57.266 34.783 21.07 12.85 45.05 3.16
566 567 6.839124 ATGAGTTGATTGAAGCAACCAATA 57.161 33.333 21.07 7.17 45.05 1.90
567 568 6.647334 TGAGTTGATTGAAGCAACCAATAA 57.353 33.333 21.07 1.93 45.05 1.40
568 569 7.230849 TGAGTTGATTGAAGCAACCAATAAT 57.769 32.000 21.07 3.07 45.05 1.28
569 570 8.347004 TGAGTTGATTGAAGCAACCAATAATA 57.653 30.769 21.07 0.00 45.05 0.98
570 571 8.801299 TGAGTTGATTGAAGCAACCAATAATAA 58.199 29.630 21.07 0.00 45.05 1.40
571 572 9.638239 GAGTTGATTGAAGCAACCAATAATAAA 57.362 29.630 21.07 0.00 45.05 1.40
572 573 9.995003 AGTTGATTGAAGCAACCAATAATAAAA 57.005 25.926 21.07 0.00 45.05 1.52
582 583 9.816354 AGCAACCAATAATAAAAATATCACCAC 57.184 29.630 0.00 0.00 0.00 4.16
583 584 8.751335 GCAACCAATAATAAAAATATCACCACG 58.249 33.333 0.00 0.00 0.00 4.94
587 588 9.128107 CCAATAATAAAAATATCACCACGATGC 57.872 33.333 0.00 0.00 35.39 3.91
588 589 9.897744 CAATAATAAAAATATCACCACGATGCT 57.102 29.630 0.00 0.00 35.39 3.79
592 593 5.403897 AAAATATCACCACGATGCTTACG 57.596 39.130 0.00 0.00 35.39 3.18
593 594 2.502213 TATCACCACGATGCTTACGG 57.498 50.000 0.00 0.00 35.39 4.02
594 595 0.810031 ATCACCACGATGCTTACGGC 60.810 55.000 0.00 0.00 42.22 5.68
595 596 2.125269 ACCACGATGCTTACGGCC 60.125 61.111 0.00 0.00 40.92 6.13
596 597 2.125310 CCACGATGCTTACGGCCA 60.125 61.111 2.24 0.00 40.92 5.36
597 598 2.461110 CCACGATGCTTACGGCCAC 61.461 63.158 2.24 0.00 40.92 5.01
598 599 1.447838 CACGATGCTTACGGCCACT 60.448 57.895 2.24 0.00 40.92 4.00
599 600 0.179121 CACGATGCTTACGGCCACTA 60.179 55.000 2.24 0.00 40.92 2.74
600 601 0.179119 ACGATGCTTACGGCCACTAC 60.179 55.000 2.24 0.00 40.92 2.73
601 602 0.102481 CGATGCTTACGGCCACTACT 59.898 55.000 2.24 0.00 40.92 2.57
602 603 1.470979 CGATGCTTACGGCCACTACTT 60.471 52.381 2.24 0.00 40.92 2.24
603 604 2.223641 CGATGCTTACGGCCACTACTTA 60.224 50.000 2.24 0.00 40.92 2.24
604 605 2.953466 TGCTTACGGCCACTACTTAG 57.047 50.000 2.24 0.00 40.92 2.18
605 606 2.449464 TGCTTACGGCCACTACTTAGA 58.551 47.619 2.24 0.00 40.92 2.10
606 607 2.165030 TGCTTACGGCCACTACTTAGAC 59.835 50.000 2.24 0.00 40.92 2.59
607 608 2.426381 GCTTACGGCCACTACTTAGACT 59.574 50.000 2.24 0.00 34.27 3.24
608 609 3.629398 GCTTACGGCCACTACTTAGACTA 59.371 47.826 2.24 0.00 34.27 2.59
609 610 4.497173 GCTTACGGCCACTACTTAGACTAC 60.497 50.000 2.24 0.00 34.27 2.73
610 611 3.362870 ACGGCCACTACTTAGACTACT 57.637 47.619 2.24 0.00 0.00 2.57
611 612 3.277715 ACGGCCACTACTTAGACTACTC 58.722 50.000 2.24 0.00 0.00 2.59
612 613 3.054508 ACGGCCACTACTTAGACTACTCT 60.055 47.826 2.24 0.00 0.00 3.24
613 614 3.560896 CGGCCACTACTTAGACTACTCTC 59.439 52.174 2.24 0.00 0.00 3.20
614 615 4.683942 CGGCCACTACTTAGACTACTCTCT 60.684 50.000 2.24 0.00 0.00 3.10
615 616 5.195185 GGCCACTACTTAGACTACTCTCTT 58.805 45.833 0.00 0.00 0.00 2.85
616 617 5.066764 GGCCACTACTTAGACTACTCTCTTG 59.933 48.000 0.00 0.00 0.00 3.02
617 618 5.449451 GCCACTACTTAGACTACTCTCTTGC 60.449 48.000 0.00 0.00 0.00 4.01
618 619 5.648526 CCACTACTTAGACTACTCTCTTGCA 59.351 44.000 0.00 0.00 0.00 4.08
619 620 6.151312 CCACTACTTAGACTACTCTCTTGCAA 59.849 42.308 0.00 0.00 0.00 4.08
620 621 7.309255 CCACTACTTAGACTACTCTCTTGCAAA 60.309 40.741 0.00 0.00 0.00 3.68
621 622 8.082852 CACTACTTAGACTACTCTCTTGCAAAA 58.917 37.037 0.00 0.00 0.00 2.44
622 623 8.808092 ACTACTTAGACTACTCTCTTGCAAAAT 58.192 33.333 0.00 0.00 0.00 1.82
661 662 9.084533 ACAGAAAGATCTACTAGTTGATATCCC 57.915 37.037 18.03 11.03 33.50 3.85
662 663 9.083422 CAGAAAGATCTACTAGTTGATATCCCA 57.917 37.037 18.03 0.00 33.50 4.37
663 664 9.836179 AGAAAGATCTACTAGTTGATATCCCAT 57.164 33.333 18.03 4.97 32.88 4.00
664 665 9.868277 GAAAGATCTACTAGTTGATATCCCATG 57.132 37.037 18.03 0.00 0.00 3.66
665 666 7.416964 AGATCTACTAGTTGATATCCCATGC 57.583 40.000 18.03 5.33 0.00 4.06
666 667 6.382570 AGATCTACTAGTTGATATCCCATGCC 59.617 42.308 18.03 4.72 0.00 4.40
667 668 5.655394 TCTACTAGTTGATATCCCATGCCT 58.345 41.667 0.00 0.00 0.00 4.75
668 669 6.084738 TCTACTAGTTGATATCCCATGCCTT 58.915 40.000 0.00 0.00 0.00 4.35
669 670 5.653255 ACTAGTTGATATCCCATGCCTTT 57.347 39.130 0.00 0.00 0.00 3.11
670 671 6.763715 ACTAGTTGATATCCCATGCCTTTA 57.236 37.500 0.00 0.00 0.00 1.85
671 672 6.534634 ACTAGTTGATATCCCATGCCTTTAC 58.465 40.000 0.00 0.00 0.00 2.01
672 673 4.729868 AGTTGATATCCCATGCCTTTACC 58.270 43.478 0.00 0.00 0.00 2.85
673 674 3.806949 TGATATCCCATGCCTTTACCC 57.193 47.619 0.00 0.00 0.00 3.69
674 675 2.378547 TGATATCCCATGCCTTTACCCC 59.621 50.000 0.00 0.00 0.00 4.95
675 676 1.154430 TATCCCATGCCTTTACCCCC 58.846 55.000 0.00 0.00 0.00 5.40
676 677 0.630478 ATCCCATGCCTTTACCCCCT 60.630 55.000 0.00 0.00 0.00 4.79
677 678 0.853586 TCCCATGCCTTTACCCCCTT 60.854 55.000 0.00 0.00 0.00 3.95
678 679 0.397114 CCCATGCCTTTACCCCCTTC 60.397 60.000 0.00 0.00 0.00 3.46
679 680 0.334676 CCATGCCTTTACCCCCTTCA 59.665 55.000 0.00 0.00 0.00 3.02
680 681 1.272985 CCATGCCTTTACCCCCTTCAA 60.273 52.381 0.00 0.00 0.00 2.69
681 682 2.102578 CATGCCTTTACCCCCTTCAAG 58.897 52.381 0.00 0.00 0.00 3.02
682 683 1.154430 TGCCTTTACCCCCTTCAAGT 58.846 50.000 0.00 0.00 0.00 3.16
683 684 1.501604 TGCCTTTACCCCCTTCAAGTT 59.498 47.619 0.00 0.00 0.00 2.66
684 685 1.893137 GCCTTTACCCCCTTCAAGTTG 59.107 52.381 0.00 0.00 0.00 3.16
685 686 1.893137 CCTTTACCCCCTTCAAGTTGC 59.107 52.381 0.00 0.00 0.00 4.17
686 687 1.893137 CTTTACCCCCTTCAAGTTGCC 59.107 52.381 0.00 0.00 0.00 4.52
687 688 0.113580 TTACCCCCTTCAAGTTGCCC 59.886 55.000 0.00 0.00 0.00 5.36
688 689 1.795951 TACCCCCTTCAAGTTGCCCC 61.796 60.000 0.00 0.00 0.00 5.80
689 690 2.525592 CCCCTTCAAGTTGCCCCA 59.474 61.111 0.00 0.00 0.00 4.96
690 691 1.607467 CCCCTTCAAGTTGCCCCAG 60.607 63.158 0.00 0.00 0.00 4.45
691 692 1.153756 CCCTTCAAGTTGCCCCAGT 59.846 57.895 0.00 0.00 0.00 4.00
692 693 0.404040 CCCTTCAAGTTGCCCCAGTA 59.596 55.000 0.00 0.00 0.00 2.74
693 694 1.534729 CCTTCAAGTTGCCCCAGTAC 58.465 55.000 0.00 0.00 0.00 2.73
694 695 1.202879 CCTTCAAGTTGCCCCAGTACA 60.203 52.381 0.00 0.00 0.00 2.90
695 696 2.582052 CTTCAAGTTGCCCCAGTACAA 58.418 47.619 0.00 0.00 0.00 2.41
696 697 2.969821 TCAAGTTGCCCCAGTACAAT 57.030 45.000 0.00 0.00 0.00 2.71
697 698 2.790433 TCAAGTTGCCCCAGTACAATC 58.210 47.619 0.00 0.00 0.00 2.67
698 699 2.107378 TCAAGTTGCCCCAGTACAATCA 59.893 45.455 0.00 0.00 0.00 2.57
699 700 3.091545 CAAGTTGCCCCAGTACAATCAT 58.908 45.455 0.00 0.00 0.00 2.45
700 701 3.456380 AGTTGCCCCAGTACAATCATT 57.544 42.857 0.00 0.00 0.00 2.57
701 702 3.778265 AGTTGCCCCAGTACAATCATTT 58.222 40.909 0.00 0.00 0.00 2.32
702 703 3.511146 AGTTGCCCCAGTACAATCATTTG 59.489 43.478 0.00 0.00 38.86 2.32
703 704 1.824230 TGCCCCAGTACAATCATTTGC 59.176 47.619 0.00 0.00 36.22 3.68
704 705 2.102578 GCCCCAGTACAATCATTTGCT 58.897 47.619 0.00 0.00 36.22 3.91
705 706 3.287222 GCCCCAGTACAATCATTTGCTA 58.713 45.455 0.00 0.00 36.22 3.49
706 707 3.066760 GCCCCAGTACAATCATTTGCTAC 59.933 47.826 0.00 0.00 36.22 3.58
707 708 4.269183 CCCCAGTACAATCATTTGCTACA 58.731 43.478 0.00 0.00 36.22 2.74
708 709 4.704540 CCCCAGTACAATCATTTGCTACAA 59.295 41.667 0.00 0.00 36.22 2.41
709 710 5.360714 CCCCAGTACAATCATTTGCTACAAT 59.639 40.000 0.00 0.00 36.22 2.71
710 711 6.127366 CCCCAGTACAATCATTTGCTACAATT 60.127 38.462 0.00 0.00 36.22 2.32
711 712 7.068103 CCCCAGTACAATCATTTGCTACAATTA 59.932 37.037 0.00 0.00 36.22 1.40
712 713 7.915397 CCCAGTACAATCATTTGCTACAATTAC 59.085 37.037 0.00 0.00 36.22 1.89
713 714 7.915397 CCAGTACAATCATTTGCTACAATTACC 59.085 37.037 0.00 0.00 36.22 2.85
714 715 8.677300 CAGTACAATCATTTGCTACAATTACCT 58.323 33.333 0.00 0.00 36.22 3.08
715 716 9.243105 AGTACAATCATTTGCTACAATTACCTT 57.757 29.630 0.00 0.00 36.22 3.50
716 717 9.289303 GTACAATCATTTGCTACAATTACCTTG 57.711 33.333 0.00 0.00 37.32 3.61
717 718 6.813152 ACAATCATTTGCTACAATTACCTTGC 59.187 34.615 0.00 0.00 35.90 4.01
718 719 5.973899 TCATTTGCTACAATTACCTTGCA 57.026 34.783 0.00 0.00 38.50 4.08
719 720 5.953183 TCATTTGCTACAATTACCTTGCAG 58.047 37.500 0.00 0.00 38.50 4.41
720 721 4.782019 TTTGCTACAATTACCTTGCAGG 57.218 40.909 1.16 1.16 42.49 4.85
721 722 3.712016 TGCTACAATTACCTTGCAGGA 57.288 42.857 8.91 0.00 37.67 3.86
722 723 3.343617 TGCTACAATTACCTTGCAGGAC 58.656 45.455 8.91 0.00 37.67 3.85
723 724 3.009033 TGCTACAATTACCTTGCAGGACT 59.991 43.478 8.91 0.00 37.67 3.85
724 725 3.375299 GCTACAATTACCTTGCAGGACTG 59.625 47.826 8.91 0.00 37.67 3.51
725 726 3.788227 ACAATTACCTTGCAGGACTGA 57.212 42.857 3.00 0.00 37.67 3.41
726 727 4.098914 ACAATTACCTTGCAGGACTGAA 57.901 40.909 3.00 0.00 37.67 3.02
727 728 4.469657 ACAATTACCTTGCAGGACTGAAA 58.530 39.130 3.00 0.00 37.67 2.69
728 729 4.278419 ACAATTACCTTGCAGGACTGAAAC 59.722 41.667 3.00 0.00 37.67 2.78
729 730 3.569194 TTACCTTGCAGGACTGAAACA 57.431 42.857 3.00 0.00 37.67 2.83
730 731 1.972872 ACCTTGCAGGACTGAAACAG 58.027 50.000 3.00 0.00 37.67 3.16
788 789 3.072330 TGGTGTCCATCTGCTCAGTTTTA 59.928 43.478 0.00 0.00 0.00 1.52
793 794 3.330701 TCCATCTGCTCAGTTTTACCCTT 59.669 43.478 0.00 0.00 0.00 3.95
855 856 0.728466 CGACTCGTTCCGTGAACTCC 60.728 60.000 12.80 2.11 40.05 3.85
864 865 2.963371 GTGAACTCCGCCGTCTCT 59.037 61.111 0.00 0.00 0.00 3.10
873 874 2.336478 CGCCGTCTCTGTCAGGTCT 61.336 63.158 0.00 0.00 0.00 3.85
893 894 0.537371 ACCTTTTGACTCGGCCCTTG 60.537 55.000 0.00 0.00 0.00 3.61
924 925 3.112709 GCGGCAGAGACGACCAAC 61.113 66.667 0.00 0.00 35.20 3.77
1077 1078 1.498865 CGGCGAGAGAGAGAGAGAGC 61.499 65.000 0.00 0.00 0.00 4.09
1083 1113 1.001517 AGAGAGAGAGAGCACGGCA 60.002 57.895 0.00 0.00 0.00 5.69
1099 1129 1.451028 GCAGTGGGAAGCTAGCTGG 60.451 63.158 20.16 0.00 0.00 4.85
1135 1165 1.268283 GGAAGCTAGCTGTGGAGGGT 61.268 60.000 20.16 0.00 0.00 4.34
1154 1184 1.670083 GCGGCGTTGGGAAACTAGT 60.670 57.895 9.37 0.00 0.00 2.57
1338 1368 0.530744 CGAGGAACCAGAATCGTCCA 59.469 55.000 0.00 0.00 0.00 4.02
1368 1398 1.440145 GCAGCGAGAATGGGGTAAGC 61.440 60.000 0.00 0.00 0.00 3.09
1372 1402 1.884235 CGAGAATGGGGTAAGCATCC 58.116 55.000 0.00 0.00 0.00 3.51
1409 1439 3.433306 TTTGTGGTCGGGATCTTTGAT 57.567 42.857 0.00 0.00 0.00 2.57
1488 1518 1.065564 GCTCTGGCCAAGACTCTGATT 60.066 52.381 7.01 0.00 0.00 2.57
1572 1602 0.319555 CACGAGCTCCGGAAGAACAA 60.320 55.000 5.23 0.00 43.93 2.83
1581 1611 1.271926 CCGGAAGAACAAATGGAGGGT 60.272 52.381 0.00 0.00 0.00 4.34
1585 1615 4.089361 GGAAGAACAAATGGAGGGTGAAT 58.911 43.478 0.00 0.00 0.00 2.57
1606 1636 1.068264 CACGCACTGACAGAGAGCTAA 60.068 52.381 10.08 0.00 36.21 3.09
1640 1670 8.231161 GCTTAGAATGTTGAAGAAGAAGGTTAC 58.769 37.037 0.00 0.00 0.00 2.50
1641 1671 9.273016 CTTAGAATGTTGAAGAAGAAGGTTACA 57.727 33.333 0.00 0.00 0.00 2.41
1699 1729 5.698545 TGCAAATACTTTTGGGCATTTGTAC 59.301 36.000 7.49 0.00 42.09 2.90
1912 1946 9.840427 GAGGAATTTCGAAACTTTTGATCAATA 57.160 29.630 13.81 3.48 0.00 1.90
2022 2058 0.544833 ATGGGCCAACTGCATCCAAA 60.545 50.000 11.89 0.00 43.89 3.28
2034 2070 2.318908 GCATCCAAATAGGCCCATTCA 58.681 47.619 0.00 0.00 37.29 2.57
2065 2101 8.373048 TCTCTTGCGTGTTTTTCTATTTTCTA 57.627 30.769 0.00 0.00 0.00 2.10
2227 2264 8.835467 ATTCAAATACACCGTGATTTAAATCG 57.165 30.769 20.45 11.85 38.26 3.34
2233 2270 4.992319 ACACCGTGATTTAAATCGAAGACA 59.008 37.500 20.45 2.79 42.51 3.41
2253 2290 8.735692 AAGACAAAAATGTCATGGAAAATGTT 57.264 26.923 11.17 0.00 41.02 2.71
2549 2713 1.333619 GACCGTGAATGTTTGCACACT 59.666 47.619 4.37 0.00 35.03 3.55
2605 2769 1.227249 TTGGAGGGTTGGAAGGTTGA 58.773 50.000 0.00 0.00 0.00 3.18
2619 2783 8.547894 GTTGGAAGGTTGAAAAATGTATGTTTC 58.452 33.333 1.39 1.39 34.88 2.78
2624 2788 7.791029 AGGTTGAAAAATGTATGTTTCCACTT 58.209 30.769 10.01 2.65 32.66 3.16
2820 3014 6.003950 TGACTTGGTTTAGGGAAGAAATGAG 58.996 40.000 0.00 0.00 0.00 2.90
2830 3024 4.044571 AGGGAAGAAATGAGATGTTTGGGA 59.955 41.667 0.00 0.00 0.00 4.37
2831 3025 4.158579 GGGAAGAAATGAGATGTTTGGGAC 59.841 45.833 0.00 0.00 0.00 4.46
2832 3026 4.142600 GGAAGAAATGAGATGTTTGGGACG 60.143 45.833 0.00 0.00 0.00 4.79
2835 3029 2.403252 ATGAGATGTTTGGGACGGAC 57.597 50.000 0.00 0.00 0.00 4.79
2836 3030 1.052617 TGAGATGTTTGGGACGGACA 58.947 50.000 0.00 0.00 0.00 4.02
3120 3345 0.548682 AGGGAAGGGAGTGCATCTGT 60.549 55.000 0.00 0.00 0.00 3.41
3143 3368 3.037549 CTGGAGTAGGGAAGATGCTCTT 58.962 50.000 0.00 0.00 39.87 2.85
3219 3445 2.284258 ACTTGGCCGAGGAGCTCT 60.284 61.111 24.40 0.00 0.00 4.09
3263 3489 0.818296 GTGACCGTGAGCAGTAGGAT 59.182 55.000 0.00 0.00 0.00 3.24
3271 3497 0.676184 GAGCAGTAGGATGATGCCGA 59.324 55.000 0.00 0.00 40.89 5.54
3352 3578 4.521062 CGGCTCTGAGGAAGGCGG 62.521 72.222 8.89 0.00 45.69 6.13
3393 3619 2.369394 CTCCACCTTGAAATAGCCCAC 58.631 52.381 0.00 0.00 0.00 4.61
3394 3620 1.707989 TCCACCTTGAAATAGCCCACA 59.292 47.619 0.00 0.00 0.00 4.17
3404 3630 0.902984 ATAGCCCACACACACGGAGA 60.903 55.000 0.00 0.00 0.00 3.71
3425 3651 2.729479 CCTCTCCACGAGCATGCCT 61.729 63.158 15.66 1.01 38.49 4.75
3552 3794 3.161067 GGAGAGAATGGATCGGATCTGA 58.839 50.000 16.96 6.72 0.00 3.27
3682 3924 1.154093 CGGACGCGTGTGTGTATCT 60.154 57.895 20.70 0.00 39.39 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 6.909895 CGATGACTTATTGTTGTTGTTGTTGA 59.090 34.615 0.00 0.00 0.00 3.18
55 56 2.352651 CCACACAGCCGATGACTTATTG 59.647 50.000 0.00 0.00 0.00 1.90
58 59 0.249120 CCCACACAGCCGATGACTTA 59.751 55.000 0.00 0.00 0.00 2.24
64 65 2.927856 TCCACCCACACAGCCGAT 60.928 61.111 0.00 0.00 0.00 4.18
67 68 4.250305 ACGTCCACCCACACAGCC 62.250 66.667 0.00 0.00 0.00 4.85
365 366 1.686052 GGGATGTACTCAGAGCCTCAG 59.314 57.143 0.00 0.00 0.00 3.35
377 378 6.258068 GCTACAGTAGTTTTGATGGGATGTAC 59.742 42.308 9.42 0.00 0.00 2.90
379 380 5.186198 GCTACAGTAGTTTTGATGGGATGT 58.814 41.667 9.42 0.00 0.00 3.06
396 397 0.306840 CGCATGCATTCTGGCTACAG 59.693 55.000 19.57 0.00 46.30 2.74
397 398 0.107752 TCGCATGCATTCTGGCTACA 60.108 50.000 19.57 0.00 34.04 2.74
398 399 1.069432 CATCGCATGCATTCTGGCTAC 60.069 52.381 19.57 0.00 34.04 3.58
399 400 1.232119 CATCGCATGCATTCTGGCTA 58.768 50.000 19.57 0.00 34.04 3.93
400 401 2.030551 CATCGCATGCATTCTGGCT 58.969 52.632 19.57 0.00 34.04 4.75
498 499 8.574251 ACTCTTCCATAGTAGAGCTACATATG 57.426 38.462 10.04 0.00 40.27 1.78
499 500 8.611257 AGACTCTTCCATAGTAGAGCTACATAT 58.389 37.037 10.04 3.15 40.27 1.78
500 501 7.980032 AGACTCTTCCATAGTAGAGCTACATA 58.020 38.462 10.04 1.18 40.27 2.29
501 502 6.848069 AGACTCTTCCATAGTAGAGCTACAT 58.152 40.000 10.04 0.01 40.27 2.29
502 503 6.126739 TGAGACTCTTCCATAGTAGAGCTACA 60.127 42.308 10.04 0.00 40.27 2.74
503 504 6.292923 TGAGACTCTTCCATAGTAGAGCTAC 58.707 44.000 3.68 0.00 40.27 3.58
504 505 6.502074 TGAGACTCTTCCATAGTAGAGCTA 57.498 41.667 3.68 0.00 40.27 3.32
505 506 5.381184 TGAGACTCTTCCATAGTAGAGCT 57.619 43.478 3.68 0.00 40.27 4.09
506 507 6.458232 TTTGAGACTCTTCCATAGTAGAGC 57.542 41.667 3.68 0.00 40.27 4.09
536 537 8.992073 GGTTGCTTCAATCAACTCATTTTATTT 58.008 29.630 4.20 0.00 42.40 1.40
537 538 8.149647 TGGTTGCTTCAATCAACTCATTTTATT 58.850 29.630 4.20 0.00 42.40 1.40
538 539 7.669427 TGGTTGCTTCAATCAACTCATTTTAT 58.331 30.769 4.20 0.00 42.40 1.40
539 540 7.048629 TGGTTGCTTCAATCAACTCATTTTA 57.951 32.000 4.20 0.00 42.40 1.52
540 541 5.916318 TGGTTGCTTCAATCAACTCATTTT 58.084 33.333 4.20 0.00 42.40 1.82
541 542 5.534207 TGGTTGCTTCAATCAACTCATTT 57.466 34.783 4.20 0.00 42.40 2.32
542 543 5.534207 TTGGTTGCTTCAATCAACTCATT 57.466 34.783 4.20 0.00 39.19 2.57
543 544 5.733620 ATTGGTTGCTTCAATCAACTCAT 57.266 34.783 7.32 0.00 45.37 2.90
544 545 6.647334 TTATTGGTTGCTTCAATCAACTCA 57.353 33.333 7.32 0.00 45.37 3.41
545 546 9.638239 TTTATTATTGGTTGCTTCAATCAACTC 57.362 29.630 7.32 0.00 45.37 3.01
546 547 9.995003 TTTTATTATTGGTTGCTTCAATCAACT 57.005 25.926 7.32 1.61 45.37 3.16
556 557 9.816354 GTGGTGATATTTTTATTATTGGTTGCT 57.184 29.630 0.00 0.00 0.00 3.91
557 558 8.751335 CGTGGTGATATTTTTATTATTGGTTGC 58.249 33.333 0.00 0.00 0.00 4.17
561 562 9.128107 GCATCGTGGTGATATTTTTATTATTGG 57.872 33.333 0.00 0.00 34.83 3.16
562 563 9.897744 AGCATCGTGGTGATATTTTTATTATTG 57.102 29.630 0.00 0.00 34.83 1.90
566 567 8.067784 CGTAAGCATCGTGGTGATATTTTTATT 58.932 33.333 0.00 0.00 34.83 1.40
567 568 7.307751 CCGTAAGCATCGTGGTGATATTTTTAT 60.308 37.037 0.00 0.00 34.83 1.40
568 569 6.018588 CCGTAAGCATCGTGGTGATATTTTTA 60.019 38.462 0.00 0.00 34.83 1.52
569 570 5.220777 CCGTAAGCATCGTGGTGATATTTTT 60.221 40.000 0.00 0.00 34.83 1.94
570 571 4.272504 CCGTAAGCATCGTGGTGATATTTT 59.727 41.667 0.00 0.00 34.83 1.82
571 572 3.807622 CCGTAAGCATCGTGGTGATATTT 59.192 43.478 0.00 0.00 34.83 1.40
572 573 3.390135 CCGTAAGCATCGTGGTGATATT 58.610 45.455 0.00 0.00 34.83 1.28
573 574 2.866460 GCCGTAAGCATCGTGGTGATAT 60.866 50.000 0.00 0.00 42.97 1.63
574 575 1.537348 GCCGTAAGCATCGTGGTGATA 60.537 52.381 0.00 0.00 42.97 2.15
575 576 0.810031 GCCGTAAGCATCGTGGTGAT 60.810 55.000 0.00 0.00 42.97 3.06
576 577 1.447140 GCCGTAAGCATCGTGGTGA 60.447 57.895 0.00 0.00 42.97 4.02
577 578 2.461110 GGCCGTAAGCATCGTGGTG 61.461 63.158 0.00 0.00 46.50 4.17
578 579 2.125269 GGCCGTAAGCATCGTGGT 60.125 61.111 0.00 0.00 46.50 4.16
579 580 2.125310 TGGCCGTAAGCATCGTGG 60.125 61.111 0.00 0.00 46.50 4.94
580 581 0.179121 TAGTGGCCGTAAGCATCGTG 60.179 55.000 0.00 0.00 46.50 4.35
581 582 0.179119 GTAGTGGCCGTAAGCATCGT 60.179 55.000 0.00 0.00 46.50 3.73
582 583 0.102481 AGTAGTGGCCGTAAGCATCG 59.898 55.000 0.00 0.00 46.50 3.84
583 584 2.311124 AAGTAGTGGCCGTAAGCATC 57.689 50.000 0.00 0.00 46.50 3.91
584 585 3.028850 TCTAAGTAGTGGCCGTAAGCAT 58.971 45.455 0.00 0.00 46.50 3.79
585 586 2.165030 GTCTAAGTAGTGGCCGTAAGCA 59.835 50.000 0.00 0.00 46.50 3.91
586 587 2.426381 AGTCTAAGTAGTGGCCGTAAGC 59.574 50.000 0.00 0.00 42.60 3.09
587 588 4.880696 AGTAGTCTAAGTAGTGGCCGTAAG 59.119 45.833 0.00 0.00 0.00 2.34
588 589 4.848357 AGTAGTCTAAGTAGTGGCCGTAA 58.152 43.478 0.00 0.00 0.00 3.18
589 590 4.163078 AGAGTAGTCTAAGTAGTGGCCGTA 59.837 45.833 0.00 0.00 0.00 4.02
590 591 3.054508 AGAGTAGTCTAAGTAGTGGCCGT 60.055 47.826 0.00 0.00 0.00 5.68
591 592 3.543665 AGAGTAGTCTAAGTAGTGGCCG 58.456 50.000 0.00 0.00 0.00 6.13
592 593 4.784177 AGAGAGTAGTCTAAGTAGTGGCC 58.216 47.826 0.00 0.00 30.97 5.36
593 594 5.449451 GCAAGAGAGTAGTCTAAGTAGTGGC 60.449 48.000 0.00 0.00 30.97 5.01
594 595 5.648526 TGCAAGAGAGTAGTCTAAGTAGTGG 59.351 44.000 0.00 0.00 30.97 4.00
595 596 6.745159 TGCAAGAGAGTAGTCTAAGTAGTG 57.255 41.667 0.00 0.00 30.97 2.74
596 597 7.762588 TTTGCAAGAGAGTAGTCTAAGTAGT 57.237 36.000 0.00 0.00 30.97 2.73
635 636 9.084533 GGGATATCAACTAGTAGATCTTTCTGT 57.915 37.037 0.00 0.00 33.17 3.41
636 637 9.083422 TGGGATATCAACTAGTAGATCTTTCTG 57.917 37.037 0.00 0.00 33.17 3.02
637 638 9.836179 ATGGGATATCAACTAGTAGATCTTTCT 57.164 33.333 0.00 2.88 35.90 2.52
638 639 9.868277 CATGGGATATCAACTAGTAGATCTTTC 57.132 37.037 0.00 0.00 0.00 2.62
639 640 8.317679 GCATGGGATATCAACTAGTAGATCTTT 58.682 37.037 0.00 0.00 0.00 2.52
640 641 7.093112 GGCATGGGATATCAACTAGTAGATCTT 60.093 40.741 0.00 0.00 0.00 2.40
641 642 6.382570 GGCATGGGATATCAACTAGTAGATCT 59.617 42.308 3.59 0.00 0.00 2.75
642 643 6.382570 AGGCATGGGATATCAACTAGTAGATC 59.617 42.308 3.59 0.00 0.00 2.75
643 644 6.267635 AGGCATGGGATATCAACTAGTAGAT 58.732 40.000 3.59 0.00 0.00 1.98
644 645 5.655394 AGGCATGGGATATCAACTAGTAGA 58.345 41.667 3.59 0.00 0.00 2.59
645 646 6.365970 AAGGCATGGGATATCAACTAGTAG 57.634 41.667 4.83 0.00 0.00 2.57
646 647 6.763715 AAAGGCATGGGATATCAACTAGTA 57.236 37.500 4.83 0.00 0.00 1.82
647 648 5.653255 AAAGGCATGGGATATCAACTAGT 57.347 39.130 4.83 0.00 0.00 2.57
648 649 5.940470 GGTAAAGGCATGGGATATCAACTAG 59.060 44.000 4.83 0.00 0.00 2.57
649 650 5.222048 GGGTAAAGGCATGGGATATCAACTA 60.222 44.000 4.83 0.00 0.00 2.24
650 651 4.447762 GGGTAAAGGCATGGGATATCAACT 60.448 45.833 4.83 0.00 0.00 3.16
651 652 3.826729 GGGTAAAGGCATGGGATATCAAC 59.173 47.826 4.83 0.00 0.00 3.18
652 653 3.181423 GGGGTAAAGGCATGGGATATCAA 60.181 47.826 4.83 0.00 0.00 2.57
653 654 2.378547 GGGGTAAAGGCATGGGATATCA 59.621 50.000 4.83 0.00 0.00 2.15
654 655 2.291605 GGGGGTAAAGGCATGGGATATC 60.292 54.545 0.00 0.00 0.00 1.63
655 656 1.716503 GGGGGTAAAGGCATGGGATAT 59.283 52.381 0.00 0.00 0.00 1.63
656 657 1.154430 GGGGGTAAAGGCATGGGATA 58.846 55.000 0.00 0.00 0.00 2.59
657 658 0.630478 AGGGGGTAAAGGCATGGGAT 60.630 55.000 0.00 0.00 0.00 3.85
658 659 0.853586 AAGGGGGTAAAGGCATGGGA 60.854 55.000 0.00 0.00 0.00 4.37
659 660 0.397114 GAAGGGGGTAAAGGCATGGG 60.397 60.000 0.00 0.00 0.00 4.00
660 661 0.334676 TGAAGGGGGTAAAGGCATGG 59.665 55.000 0.00 0.00 0.00 3.66
661 662 2.102578 CTTGAAGGGGGTAAAGGCATG 58.897 52.381 0.00 0.00 0.00 4.06
662 663 1.716503 ACTTGAAGGGGGTAAAGGCAT 59.283 47.619 0.00 0.00 0.00 4.40
663 664 1.154430 ACTTGAAGGGGGTAAAGGCA 58.846 50.000 0.00 0.00 0.00 4.75
664 665 1.893137 CAACTTGAAGGGGGTAAAGGC 59.107 52.381 0.00 0.00 0.00 4.35
665 666 1.893137 GCAACTTGAAGGGGGTAAAGG 59.107 52.381 0.00 0.00 0.00 3.11
666 667 1.893137 GGCAACTTGAAGGGGGTAAAG 59.107 52.381 0.00 0.00 0.00 1.85
667 668 1.481615 GGGCAACTTGAAGGGGGTAAA 60.482 52.381 0.00 0.00 0.00 2.01
668 669 0.113580 GGGCAACTTGAAGGGGGTAA 59.886 55.000 0.00 0.00 0.00 2.85
669 670 1.771646 GGGCAACTTGAAGGGGGTA 59.228 57.895 0.00 0.00 0.00 3.69
670 671 2.526110 GGGCAACTTGAAGGGGGT 59.474 61.111 0.00 0.00 0.00 4.95
671 672 2.283894 GGGGCAACTTGAAGGGGG 60.284 66.667 0.00 0.00 0.00 5.40
672 673 1.607467 CTGGGGCAACTTGAAGGGG 60.607 63.158 0.00 0.00 0.00 4.79
673 674 0.404040 TACTGGGGCAACTTGAAGGG 59.596 55.000 0.00 0.00 0.00 3.95
674 675 1.202879 TGTACTGGGGCAACTTGAAGG 60.203 52.381 0.00 0.00 0.00 3.46
675 676 2.270352 TGTACTGGGGCAACTTGAAG 57.730 50.000 0.00 0.00 0.00 3.02
676 677 2.738587 TTGTACTGGGGCAACTTGAA 57.261 45.000 0.00 0.00 0.00 2.69
677 678 2.107378 TGATTGTACTGGGGCAACTTGA 59.893 45.455 0.00 0.00 0.00 3.02
678 679 2.513753 TGATTGTACTGGGGCAACTTG 58.486 47.619 0.00 0.00 0.00 3.16
679 680 2.969821 TGATTGTACTGGGGCAACTT 57.030 45.000 0.00 0.00 0.00 2.66
680 681 3.456380 AATGATTGTACTGGGGCAACT 57.544 42.857 0.00 0.00 0.00 3.16
681 682 3.848726 CAAATGATTGTACTGGGGCAAC 58.151 45.455 0.00 0.00 0.00 4.17
682 683 2.233431 GCAAATGATTGTACTGGGGCAA 59.767 45.455 0.00 0.00 38.85 4.52
683 684 1.824230 GCAAATGATTGTACTGGGGCA 59.176 47.619 0.00 0.00 38.85 5.36
684 685 2.102578 AGCAAATGATTGTACTGGGGC 58.897 47.619 0.00 0.00 38.85 5.80
685 686 4.269183 TGTAGCAAATGATTGTACTGGGG 58.731 43.478 0.00 0.00 38.85 4.96
686 687 5.895636 TTGTAGCAAATGATTGTACTGGG 57.104 39.130 0.00 0.00 38.85 4.45
687 688 7.915397 GGTAATTGTAGCAAATGATTGTACTGG 59.085 37.037 0.00 0.00 38.85 4.00
688 689 8.677300 AGGTAATTGTAGCAAATGATTGTACTG 58.323 33.333 0.00 0.00 38.85 2.74
689 690 8.807948 AGGTAATTGTAGCAAATGATTGTACT 57.192 30.769 0.00 0.00 38.85 2.73
690 691 9.289303 CAAGGTAATTGTAGCAAATGATTGTAC 57.711 33.333 0.00 0.00 35.18 2.90
691 692 7.973388 GCAAGGTAATTGTAGCAAATGATTGTA 59.027 33.333 0.00 0.00 41.29 2.41
692 693 6.813152 GCAAGGTAATTGTAGCAAATGATTGT 59.187 34.615 0.00 0.00 41.29 2.71
693 694 6.812656 TGCAAGGTAATTGTAGCAAATGATTG 59.187 34.615 0.00 0.00 41.29 2.67
694 695 6.934056 TGCAAGGTAATTGTAGCAAATGATT 58.066 32.000 0.00 0.00 41.29 2.57
695 696 6.528537 TGCAAGGTAATTGTAGCAAATGAT 57.471 33.333 0.00 0.00 41.29 2.45
696 697 5.953183 CTGCAAGGTAATTGTAGCAAATGA 58.047 37.500 0.00 0.00 43.37 2.57
706 707 7.905870 ACTGTTTCAGTCCTGCAAGGTAATTG 61.906 42.308 0.00 0.00 42.99 2.32
707 708 5.923988 ACTGTTTCAGTCCTGCAAGGTAATT 60.924 40.000 0.00 0.00 42.99 1.40
708 709 4.446311 ACTGTTTCAGTCCTGCAAGGTAAT 60.446 41.667 0.00 0.00 42.99 1.89
709 710 3.118038 ACTGTTTCAGTCCTGCAAGGTAA 60.118 43.478 0.00 0.00 42.99 2.85
710 711 2.438021 ACTGTTTCAGTCCTGCAAGGTA 59.562 45.455 0.00 0.00 42.99 3.08
711 712 1.212935 ACTGTTTCAGTCCTGCAAGGT 59.787 47.619 0.00 0.00 42.99 3.50
712 713 1.972872 ACTGTTTCAGTCCTGCAAGG 58.027 50.000 0.00 0.00 41.21 3.61
713 714 4.376340 AAAACTGTTTCAGTCCTGCAAG 57.624 40.909 6.20 0.00 44.62 4.01
714 715 4.799564 AAAAACTGTTTCAGTCCTGCAA 57.200 36.364 6.20 0.00 44.62 4.08
738 739 5.425217 AGGGCAAAAGGATAATTAACCCAAG 59.575 40.000 8.09 0.00 37.28 3.61
740 741 4.954089 AGGGCAAAAGGATAATTAACCCA 58.046 39.130 8.09 0.00 37.28 4.51
788 789 2.017049 GCACAATTCGCATCTAAGGGT 58.983 47.619 0.00 0.00 0.00 4.34
793 794 3.251479 ACTGAGCACAATTCGCATCTA 57.749 42.857 0.00 0.00 0.00 1.98
855 856 1.025113 TAGACCTGACAGAGACGGCG 61.025 60.000 4.80 4.80 0.00 6.46
873 874 1.061546 AAGGGCCGAGTCAAAAGGTA 58.938 50.000 0.00 0.00 0.00 3.08
979 980 4.070552 ACCCGCAACGGCTCTCTC 62.071 66.667 0.00 0.00 46.86 3.20
1077 1078 1.448540 CTAGCTTCCCACTGCCGTG 60.449 63.158 0.56 0.56 40.89 4.94
1083 1113 1.997874 CCCCAGCTAGCTTCCCACT 60.998 63.158 16.46 0.00 0.00 4.00
1135 1165 1.669760 CTAGTTTCCCAACGCCGCA 60.670 57.895 0.00 0.00 38.03 5.69
1142 1172 2.107552 CCCTCCACAACTAGTTTCCCAA 59.892 50.000 5.07 0.00 0.00 4.12
1149 1179 2.663196 GCGCCCTCCACAACTAGT 59.337 61.111 0.00 0.00 0.00 2.57
1197 1227 2.172293 GGAGCTTGAGGAAGACATGGAT 59.828 50.000 0.00 0.00 0.00 3.41
1338 1368 0.526211 TCTCGCTGCACACGTAGAAT 59.474 50.000 0.00 0.00 0.00 2.40
1368 1398 1.678598 ATGGTGCAATTGCCCGGATG 61.679 55.000 26.94 0.00 41.18 3.51
1372 1402 1.197264 CAAAAATGGTGCAATTGCCCG 59.803 47.619 26.94 10.09 41.18 6.13
1422 1452 2.020720 ACCTGCATGAACACGAAACAA 58.979 42.857 0.00 0.00 0.00 2.83
1488 1518 5.247862 TCATGCTCTTCTTGCAGTTCATTA 58.752 37.500 0.00 0.00 44.04 1.90
1572 1602 0.327924 TGCGTGATTCACCCTCCATT 59.672 50.000 11.12 0.00 0.00 3.16
1581 1611 1.613437 TCTCTGTCAGTGCGTGATTCA 59.387 47.619 0.00 0.00 37.56 2.57
1585 1615 1.175347 AGCTCTCTGTCAGTGCGTGA 61.175 55.000 0.00 0.00 44.91 4.35
1606 1636 6.291377 TCTTCAACATTCTAAGCTCAACAGT 58.709 36.000 0.00 0.00 0.00 3.55
1620 1650 7.068716 AGCTTTGTAACCTTCTTCTTCAACATT 59.931 33.333 0.00 0.00 0.00 2.71
1699 1729 2.218953 ACCAGTGCGATTACCATACG 57.781 50.000 0.00 0.00 0.00 3.06
1895 1929 7.685304 GCTGCATTTTATTGATCAAAAGTTTCG 59.315 33.333 13.09 0.30 0.00 3.46
1996 2032 1.075374 TGCAGTTGGCCCATTAGTCTT 59.925 47.619 0.00 0.00 43.89 3.01
2034 2070 0.182775 AAACACGCAAGAGAACCCCT 59.817 50.000 0.00 0.00 43.62 4.79
2227 2264 8.369218 ACATTTTCCATGACATTTTTGTCTTC 57.631 30.769 7.55 0.00 39.41 2.87
2253 2290 1.003646 ACCTCTACCAGAGCTGAGGA 58.996 55.000 19.46 0.00 46.53 3.71
2373 2536 2.036256 GTCCCCAGCTGCACCAAT 59.964 61.111 8.66 0.00 0.00 3.16
2381 2544 3.003763 GGGTTCGAGTCCCCAGCT 61.004 66.667 14.49 0.00 40.88 4.24
2414 2577 1.579429 CGCAGCCCTAAACACCAAC 59.421 57.895 0.00 0.00 0.00 3.77
2415 2578 4.073052 CGCAGCCCTAAACACCAA 57.927 55.556 0.00 0.00 0.00 3.67
2471 2634 6.781014 CACTATGTATACCTTCCTTCCCTACA 59.219 42.308 0.00 0.00 0.00 2.74
2549 2713 3.202906 CAAAGGAAAACCACTCTCACGA 58.797 45.455 0.00 0.00 0.00 4.35
2605 2769 7.118496 TGTGGAAGTGGAAACATACATTTTT 57.882 32.000 0.00 0.00 46.14 1.94
2619 2783 4.605640 AACCAAAATCATGTGGAAGTGG 57.394 40.909 7.06 4.62 38.36 4.00
2624 2788 5.009631 CCACTCTAACCAAAATCATGTGGA 58.990 41.667 7.06 0.00 43.39 4.02
2820 3014 3.934457 AAAATGTCCGTCCCAAACATC 57.066 42.857 0.00 0.00 32.63 3.06
3120 3345 0.833287 GCATCTTCCCTACTCCAGCA 59.167 55.000 0.00 0.00 0.00 4.41
3143 3368 6.569035 CGTCTACAACATCTACACCAACTACA 60.569 42.308 0.00 0.00 0.00 2.74
3352 3578 0.947660 GGTTTCGTCGAACTCACCCC 60.948 60.000 13.99 2.76 0.00 4.95
3393 3619 0.457851 GAGAGGGATCTCCGTGTGTG 59.542 60.000 0.00 0.00 40.83 3.82
3394 3620 0.684805 GGAGAGGGATCTCCGTGTGT 60.685 60.000 8.47 0.00 45.70 3.72
3404 3630 2.037620 GCATGCTCGTGGAGAGGGAT 62.038 60.000 11.37 0.00 46.91 3.85
3425 3651 4.082523 GAGCTGCGCTACCCACCA 62.083 66.667 9.73 0.00 39.88 4.17
3552 3794 0.401395 TTCCTCTCCCACCCACAAGT 60.401 55.000 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.