Multiple sequence alignment - TraesCS1D01G303200

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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 TraesCS1D01G303200 chr1D 100.000 4833 0 0 1 4833 401136070 401131238 0.000000e+00 8925
1 TraesCS1D01G303200 chr1D 95.556 135 6 0 373 507 296997846 296997712 2.930000e-52 217
2 TraesCS1D01G303200 chr1A 93.792 4059 164 32 832 4833 497243777 497239750 0.000000e+00 6019
3 TraesCS1D01G303200 chr1A 96.324 136 5 0 373 508 549327863 549327998 1.750000e-54 224
4 TraesCS1D01G303200 chr1B 95.963 3418 85 22 708 4098 538868803 538865412 0.000000e+00 5498
5 TraesCS1D01G303200 chr1B 91.173 759 37 10 4089 4833 538865239 538864497 0.000000e+00 1003
6 TraesCS1D01G303200 chr3A 80.468 2391 378 68 1364 3704 587636058 587638409 0.000000e+00 1746
7 TraesCS1D01G303200 chr3A 85.798 683 79 14 4160 4827 594672401 594673080 0.000000e+00 708
8 TraesCS1D01G303200 chr3A 91.620 179 15 0 1099 1277 587635880 587636058 1.040000e-61 248
9 TraesCS1D01G303200 chr2D 85.458 1004 142 4 1364 2365 612365325 612366326 0.000000e+00 1042
10 TraesCS1D01G303200 chr2D 79.345 886 140 33 2940 3788 612366821 612367700 2.510000e-162 582
11 TraesCS1D01G303200 chr2D 94.624 372 13 5 1 368 56076037 56075669 1.950000e-158 569
12 TraesCS1D01G303200 chr2D 88.462 312 32 4 2441 2750 612366320 612366629 1.640000e-99 374
13 TraesCS1D01G303200 chr2D 94.074 135 8 0 373 507 56075622 56075488 6.340000e-49 206
14 TraesCS1D01G303200 chr2D 87.097 186 18 2 1098 1277 612365140 612365325 6.340000e-49 206
15 TraesCS1D01G303200 chr2B 85.458 1004 142 4 1364 2365 747237628 747238629 0.000000e+00 1042
16 TraesCS1D01G303200 chr2B 78.771 1399 216 66 2441 3788 747238623 747239991 0.000000e+00 863
17 TraesCS1D01G303200 chr2B 86.022 186 20 3 1098 1277 747237443 747237628 1.370000e-45 195
18 TraesCS1D01G303200 chr2A 84.692 1006 146 7 1364 2365 744492303 744493304 0.000000e+00 998
19 TraesCS1D01G303200 chr2A 79.205 1308 194 54 2441 3704 744493298 744494571 0.000000e+00 837
20 TraesCS1D01G303200 chr2A 95.276 381 12 5 1 375 27735524 27735904 2.490000e-167 599
21 TraesCS1D01G303200 chr2A 93.404 379 17 5 1 375 527371630 527371256 5.470000e-154 555
22 TraesCS1D01G303200 chr2A 95.522 134 6 0 373 506 527371207 527371074 1.050000e-51 215
23 TraesCS1D01G303200 chr2A 92.361 144 11 0 373 516 27735953 27736096 6.340000e-49 206
24 TraesCS1D01G303200 chr2A 86.559 186 19 3 1098 1277 744492118 744492303 2.950000e-47 200
25 TraesCS1D01G303200 chr3B 84.677 1005 146 6 1364 2364 584811684 584812684 0.000000e+00 996
26 TraesCS1D01G303200 chr3B 78.610 1295 225 43 2443 3704 584812778 584814053 0.000000e+00 809
27 TraesCS1D01G303200 chr3B 91.620 179 15 0 1099 1277 584811506 584811684 1.040000e-61 248
28 TraesCS1D01G303200 chr3D 83.897 1006 152 7 1364 2364 445858479 445859479 0.000000e+00 952
29 TraesCS1D01G303200 chr3D 78.687 1295 219 49 2443 3704 445859573 445860843 0.000000e+00 809
30 TraesCS1D01G303200 chr3D 91.620 179 15 0 1099 1277 445858301 445858479 1.040000e-61 248
31 TraesCS1D01G303200 chr7D 96.042 379 9 4 1 375 397544830 397545206 3.200000e-171 612
32 TraesCS1D01G303200 chr7D 96.216 370 10 2 1 368 536152333 536152700 1.920000e-168 603
33 TraesCS1D01G303200 chr7D 95.105 143 7 0 373 515 397545256 397545398 4.870000e-55 226
34 TraesCS1D01G303200 chr6B 96.216 370 9 3 1 368 3962857 3962491 6.920000e-168 601
35 TraesCS1D01G303200 chr6B 94.195 379 15 5 1 375 87494170 87494545 5.430000e-159 571
36 TraesCS1D01G303200 chr6B 97.101 138 4 0 373 510 3962444 3962307 2.910000e-57 233
37 TraesCS1D01G303200 chr4B 94.195 379 17 4 1 375 37381002 37380625 1.510000e-159 573
38 TraesCS1D01G303200 chr4B 97.222 144 4 0 373 516 37380575 37380432 1.340000e-60 244
39 TraesCS1D01G303200 chr7A 94.324 370 17 2 1 368 616937090 616936723 9.080000e-157 564
40 TraesCS1D01G303200 chr7A 96.324 136 5 0 373 508 616936664 616936529 1.750000e-54 224
41 TraesCS1D01G303200 chr5B 72.671 966 214 34 1419 2356 35146953 35147896 4.760000e-70 276
42 TraesCS1D01G303200 chr5B 78.916 166 23 10 3128 3284 35148496 35148658 8.560000e-18 102
43 TraesCS1D01G303200 chr5D 83.553 152 25 0 4682 4833 217752498 217752649 5.040000e-30 143


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 TraesCS1D01G303200 chr1D 401131238 401136070 4832 True 8925.000000 8925 100.000000 1 4833 1 chr1D.!!$R2 4832
1 TraesCS1D01G303200 chr1A 497239750 497243777 4027 True 6019.000000 6019 93.792000 832 4833 1 chr1A.!!$R1 4001
2 TraesCS1D01G303200 chr1B 538864497 538868803 4306 True 3250.500000 5498 93.568000 708 4833 2 chr1B.!!$R1 4125
3 TraesCS1D01G303200 chr3A 587635880 587638409 2529 False 997.000000 1746 86.044000 1099 3704 2 chr3A.!!$F2 2605
4 TraesCS1D01G303200 chr3A 594672401 594673080 679 False 708.000000 708 85.798000 4160 4827 1 chr3A.!!$F1 667
5 TraesCS1D01G303200 chr2D 612365140 612367700 2560 False 551.000000 1042 85.090500 1098 3788 4 chr2D.!!$F1 2690
6 TraesCS1D01G303200 chr2D 56075488 56076037 549 True 387.500000 569 94.349000 1 507 2 chr2D.!!$R1 506
7 TraesCS1D01G303200 chr2B 747237443 747239991 2548 False 700.000000 1042 83.417000 1098 3788 3 chr2B.!!$F1 2690
8 TraesCS1D01G303200 chr2A 744492118 744494571 2453 False 678.333333 998 83.485333 1098 3704 3 chr2A.!!$F2 2606
9 TraesCS1D01G303200 chr2A 27735524 27736096 572 False 402.500000 599 93.818500 1 516 2 chr2A.!!$F1 515
10 TraesCS1D01G303200 chr2A 527371074 527371630 556 True 385.000000 555 94.463000 1 506 2 chr2A.!!$R1 505
11 TraesCS1D01G303200 chr3B 584811506 584814053 2547 False 684.333333 996 84.969000 1099 3704 3 chr3B.!!$F1 2605
12 TraesCS1D01G303200 chr3D 445858301 445860843 2542 False 669.666667 952 84.734667 1099 3704 3 chr3D.!!$F1 2605
13 TraesCS1D01G303200 chr7D 397544830 397545398 568 False 419.000000 612 95.573500 1 515 2 chr7D.!!$F2 514
14 TraesCS1D01G303200 chr6B 3962307 3962857 550 True 417.000000 601 96.658500 1 510 2 chr6B.!!$R1 509
15 TraesCS1D01G303200 chr4B 37380432 37381002 570 True 408.500000 573 95.708500 1 516 2 chr4B.!!$R1 515
16 TraesCS1D01G303200 chr7A 616936529 616937090 561 True 394.000000 564 95.324000 1 508 2 chr7A.!!$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
585 673 0.107703 TTCCAGCGAGCCTACCAATG 60.108 55.0 0.00 0.00 0.0 2.82 F
1327 1467 0.031585 TCTGCTTGCTTGCTTGCTTG 59.968 50.0 10.35 5.44 0.0 4.01 F
1339 1479 0.031585 CTTGCTTGCTTGCTTGCTCA 59.968 50.0 10.35 0.00 0.0 4.26 F
1341 1481 0.242825 TGCTTGCTTGCTTGCTCATC 59.757 50.0 10.35 0.00 0.0 2.92 F
1342 1482 0.458025 GCTTGCTTGCTTGCTCATCC 60.458 55.0 3.47 0.00 0.0 3.51 F
2875 3176 1.212616 GCCTTCCGTTGAGATCGATG 58.787 55.0 0.54 0.00 0.0 3.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2415 2571 1.071542 ACAACACCGATCCATGTCACA 59.928 47.619 0.00 0.00 0.00 3.58 R
2875 3176 0.091678 CGTCGTTGCATTGCATTTGC 59.908 50.000 12.95 13.65 38.76 3.68 R
2876 3177 1.122859 CACGTCGTTGCATTGCATTTG 59.877 47.619 12.95 5.61 38.76 2.32 R
2912 3213 1.132834 TCGTGGACAATGCATGCATTC 59.867 47.619 36.90 27.97 43.92 2.67 R
2913 3214 1.133598 CTCGTGGACAATGCATGCATT 59.866 47.619 34.78 34.78 46.35 3.56 R
4464 5016 0.674895 GTCGTGATGCTTTGGAGGCT 60.675 55.000 0.00 0.00 0.00 4.58 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 45 7.709269 TCAGGTAATTAAATGCATCTCGTAC 57.291 36.000 0.00 0.00 0.00 3.67
173 178 1.128692 CTGATCAAAACCGAAGCCGTC 59.871 52.381 0.00 0.00 0.00 4.79
368 378 9.565213 CATGAAGAATGGAGTTAAGTGATTTTC 57.435 33.333 0.00 0.00 32.10 2.29
370 380 8.786898 TGAAGAATGGAGTTAAGTGATTTTCAG 58.213 33.333 0.00 0.00 0.00 3.02
371 381 8.697507 AAGAATGGAGTTAAGTGATTTTCAGT 57.302 30.769 0.00 0.00 0.00 3.41
418 506 3.438216 TGAACAATGCTGGATGGAGAA 57.562 42.857 0.00 0.00 0.00 2.87
484 572 0.874390 GCTTCAAACGACATGCTCCA 59.126 50.000 0.00 0.00 0.00 3.86
516 604 7.717568 TCTTCTAATCAAGTACTAGCATGGAC 58.282 38.462 0.00 0.00 0.00 4.02
517 605 6.406692 TCTAATCAAGTACTAGCATGGACC 57.593 41.667 0.00 0.00 0.00 4.46
518 606 6.136857 TCTAATCAAGTACTAGCATGGACCT 58.863 40.000 0.00 0.00 0.00 3.85
519 607 5.700402 AATCAAGTACTAGCATGGACCTT 57.300 39.130 0.00 0.00 0.00 3.50
520 608 6.808321 AATCAAGTACTAGCATGGACCTTA 57.192 37.500 0.00 0.00 0.00 2.69
521 609 6.808321 ATCAAGTACTAGCATGGACCTTAA 57.192 37.500 0.00 0.00 0.00 1.85
522 610 6.614694 TCAAGTACTAGCATGGACCTTAAA 57.385 37.500 0.00 0.00 0.00 1.52
523 611 6.640518 TCAAGTACTAGCATGGACCTTAAAG 58.359 40.000 0.00 0.00 0.00 1.85
524 612 6.212791 TCAAGTACTAGCATGGACCTTAAAGT 59.787 38.462 0.00 0.00 0.00 2.66
525 613 7.398047 TCAAGTACTAGCATGGACCTTAAAGTA 59.602 37.037 0.00 0.00 0.00 2.24
526 614 7.349412 AGTACTAGCATGGACCTTAAAGTAG 57.651 40.000 0.00 0.00 0.00 2.57
527 615 6.896307 AGTACTAGCATGGACCTTAAAGTAGT 59.104 38.462 0.00 0.00 0.00 2.73
528 616 6.223351 ACTAGCATGGACCTTAAAGTAGTC 57.777 41.667 0.00 0.00 0.00 2.59
535 623 3.771798 GACCTTAAAGTAGTCCAGAGCG 58.228 50.000 0.00 0.00 0.00 5.03
536 624 3.428532 ACCTTAAAGTAGTCCAGAGCGA 58.571 45.455 0.00 0.00 0.00 4.93
537 625 3.444388 ACCTTAAAGTAGTCCAGAGCGAG 59.556 47.826 0.00 0.00 0.00 5.03
538 626 3.181485 CCTTAAAGTAGTCCAGAGCGAGG 60.181 52.174 0.00 0.00 0.00 4.63
539 627 0.533032 AAAGTAGTCCAGAGCGAGGC 59.467 55.000 0.00 0.00 0.00 4.70
540 628 0.323908 AAGTAGTCCAGAGCGAGGCT 60.324 55.000 0.00 0.00 43.88 4.58
551 639 3.181967 CGAGGCTCGCAAGGAACG 61.182 66.667 25.31 0.00 31.14 3.95
552 640 3.491652 GAGGCTCGCAAGGAACGC 61.492 66.667 0.00 0.00 38.47 4.84
553 641 3.941657 GAGGCTCGCAAGGAACGCT 62.942 63.158 0.00 0.00 38.47 5.07
554 642 3.491652 GGCTCGCAAGGAACGCTC 61.492 66.667 0.00 0.00 38.47 5.03
555 643 3.843240 GCTCGCAAGGAACGCTCG 61.843 66.667 0.00 0.00 38.47 5.03
556 644 3.181967 CTCGCAAGGAACGCTCGG 61.182 66.667 0.00 0.00 38.47 4.63
557 645 3.626680 CTCGCAAGGAACGCTCGGA 62.627 63.158 0.00 0.00 38.47 4.55
558 646 2.509336 CGCAAGGAACGCTCGGAT 60.509 61.111 0.00 0.00 0.00 4.18
559 647 2.517450 CGCAAGGAACGCTCGGATC 61.517 63.158 0.00 0.00 0.00 3.36
560 648 1.447838 GCAAGGAACGCTCGGATCA 60.448 57.895 0.00 0.00 0.00 2.92
561 649 1.424493 GCAAGGAACGCTCGGATCAG 61.424 60.000 0.00 0.00 0.00 2.90
562 650 1.153549 AAGGAACGCTCGGATCAGC 60.154 57.895 0.00 0.00 35.90 4.26
563 651 1.608717 AAGGAACGCTCGGATCAGCT 61.609 55.000 3.79 0.00 37.25 4.24
564 652 1.880340 GGAACGCTCGGATCAGCTG 60.880 63.158 7.63 7.63 37.25 4.24
565 653 1.153745 GAACGCTCGGATCAGCTGT 60.154 57.895 14.67 0.42 37.25 4.40
566 654 0.737715 GAACGCTCGGATCAGCTGTT 60.738 55.000 14.67 5.03 38.20 3.16
567 655 0.320771 AACGCTCGGATCAGCTGTTT 60.321 50.000 14.67 2.24 37.25 2.83
568 656 0.737715 ACGCTCGGATCAGCTGTTTC 60.738 55.000 14.67 11.84 37.25 2.78
569 657 1.424493 CGCTCGGATCAGCTGTTTCC 61.424 60.000 21.43 21.43 37.25 3.13
570 658 0.391661 GCTCGGATCAGCTGTTTCCA 60.392 55.000 26.90 17.54 36.38 3.53
571 659 1.649664 CTCGGATCAGCTGTTTCCAG 58.350 55.000 26.90 21.25 41.91 3.86
580 668 2.755929 CTGTTTCCAGCGAGCCTAC 58.244 57.895 0.00 0.00 0.00 3.18
581 669 0.741221 CTGTTTCCAGCGAGCCTACC 60.741 60.000 0.00 0.00 0.00 3.18
582 670 1.295423 GTTTCCAGCGAGCCTACCA 59.705 57.895 0.00 0.00 0.00 3.25
583 671 0.321298 GTTTCCAGCGAGCCTACCAA 60.321 55.000 0.00 0.00 0.00 3.67
584 672 0.618458 TTTCCAGCGAGCCTACCAAT 59.382 50.000 0.00 0.00 0.00 3.16
585 673 0.107703 TTCCAGCGAGCCTACCAATG 60.108 55.000 0.00 0.00 0.00 2.82
586 674 2.182842 CCAGCGAGCCTACCAATGC 61.183 63.158 0.00 0.00 0.00 3.56
587 675 1.450134 CAGCGAGCCTACCAATGCA 60.450 57.895 0.00 0.00 0.00 3.96
588 676 0.816825 CAGCGAGCCTACCAATGCAT 60.817 55.000 0.00 0.00 0.00 3.96
589 677 0.758734 AGCGAGCCTACCAATGCATA 59.241 50.000 0.00 0.00 0.00 3.14
590 678 0.868406 GCGAGCCTACCAATGCATAC 59.132 55.000 0.00 0.00 0.00 2.39
591 679 1.541233 GCGAGCCTACCAATGCATACT 60.541 52.381 0.00 0.00 0.00 2.12
592 680 2.838736 CGAGCCTACCAATGCATACTT 58.161 47.619 0.00 0.00 0.00 2.24
593 681 2.545526 CGAGCCTACCAATGCATACTTG 59.454 50.000 0.00 0.00 0.00 3.16
594 682 3.741075 CGAGCCTACCAATGCATACTTGA 60.741 47.826 0.00 0.00 0.00 3.02
595 683 3.545703 AGCCTACCAATGCATACTTGAC 58.454 45.455 0.00 0.00 0.00 3.18
596 684 2.618709 GCCTACCAATGCATACTTGACC 59.381 50.000 0.00 0.00 0.00 4.02
597 685 3.685550 GCCTACCAATGCATACTTGACCT 60.686 47.826 0.00 0.00 0.00 3.85
598 686 4.130118 CCTACCAATGCATACTTGACCTC 58.870 47.826 0.00 0.00 0.00 3.85
599 687 4.141620 CCTACCAATGCATACTTGACCTCT 60.142 45.833 0.00 0.00 0.00 3.69
600 688 5.070446 CCTACCAATGCATACTTGACCTCTA 59.930 44.000 0.00 0.00 0.00 2.43
601 689 5.636903 ACCAATGCATACTTGACCTCTAT 57.363 39.130 0.00 0.00 0.00 1.98
602 690 5.615289 ACCAATGCATACTTGACCTCTATC 58.385 41.667 0.00 0.00 0.00 2.08
603 691 5.130975 ACCAATGCATACTTGACCTCTATCA 59.869 40.000 0.00 0.00 0.00 2.15
604 692 6.057533 CCAATGCATACTTGACCTCTATCAA 58.942 40.000 0.00 0.00 37.08 2.57
605 693 6.543465 CCAATGCATACTTGACCTCTATCAAA 59.457 38.462 0.00 0.00 38.12 2.69
606 694 7.067372 CCAATGCATACTTGACCTCTATCAAAA 59.933 37.037 0.00 0.00 38.12 2.44
607 695 8.461222 CAATGCATACTTGACCTCTATCAAAAA 58.539 33.333 0.00 0.00 38.12 1.94
608 696 7.377766 TGCATACTTGACCTCTATCAAAAAC 57.622 36.000 0.00 0.00 38.12 2.43
609 697 7.168219 TGCATACTTGACCTCTATCAAAAACT 58.832 34.615 0.00 0.00 38.12 2.66
610 698 7.665559 TGCATACTTGACCTCTATCAAAAACTT 59.334 33.333 0.00 0.00 38.12 2.66
611 699 8.515414 GCATACTTGACCTCTATCAAAAACTTT 58.485 33.333 0.00 0.00 38.12 2.66
612 700 9.831737 CATACTTGACCTCTATCAAAAACTTTG 57.168 33.333 0.00 0.00 38.12 2.77
613 701 7.881775 ACTTGACCTCTATCAAAAACTTTGT 57.118 32.000 0.00 0.00 38.12 2.83
614 702 8.974060 ACTTGACCTCTATCAAAAACTTTGTA 57.026 30.769 0.00 0.00 38.12 2.41
615 703 8.837389 ACTTGACCTCTATCAAAAACTTTGTAC 58.163 33.333 0.00 0.00 38.12 2.90
616 704 8.740123 TTGACCTCTATCAAAAACTTTGTACA 57.260 30.769 0.00 0.00 35.65 2.90
617 705 8.378172 TGACCTCTATCAAAAACTTTGTACAG 57.622 34.615 0.00 0.00 0.00 2.74
618 706 7.041372 TGACCTCTATCAAAAACTTTGTACAGC 60.041 37.037 0.00 0.00 0.00 4.40
619 707 6.073222 ACCTCTATCAAAAACTTTGTACAGCG 60.073 38.462 0.00 0.00 0.00 5.18
620 708 6.147164 CCTCTATCAAAAACTTTGTACAGCGA 59.853 38.462 0.00 0.00 0.00 4.93
621 709 6.884187 TCTATCAAAAACTTTGTACAGCGAC 58.116 36.000 0.00 0.00 0.00 5.19
622 710 4.281525 TCAAAAACTTTGTACAGCGACC 57.718 40.909 0.00 0.00 0.00 4.79
623 711 3.065648 TCAAAAACTTTGTACAGCGACCC 59.934 43.478 0.00 0.00 0.00 4.46
624 712 2.632987 AAACTTTGTACAGCGACCCT 57.367 45.000 0.00 0.00 0.00 4.34
625 713 2.165319 AACTTTGTACAGCGACCCTC 57.835 50.000 0.00 0.00 0.00 4.30
626 714 0.320697 ACTTTGTACAGCGACCCTCC 59.679 55.000 0.00 0.00 0.00 4.30
627 715 0.320374 CTTTGTACAGCGACCCTCCA 59.680 55.000 0.00 0.00 0.00 3.86
628 716 0.759959 TTTGTACAGCGACCCTCCAA 59.240 50.000 0.00 0.00 0.00 3.53
629 717 0.320374 TTGTACAGCGACCCTCCAAG 59.680 55.000 0.00 0.00 0.00 3.61
630 718 1.448013 GTACAGCGACCCTCCAAGC 60.448 63.158 0.00 0.00 0.00 4.01
631 719 1.911269 TACAGCGACCCTCCAAGCA 60.911 57.895 0.00 0.00 0.00 3.91
632 720 1.264749 TACAGCGACCCTCCAAGCAT 61.265 55.000 0.00 0.00 0.00 3.79
633 721 1.264749 ACAGCGACCCTCCAAGCATA 61.265 55.000 0.00 0.00 0.00 3.14
634 722 0.107703 CAGCGACCCTCCAAGCATAA 60.108 55.000 0.00 0.00 0.00 1.90
635 723 0.839946 AGCGACCCTCCAAGCATAAT 59.160 50.000 0.00 0.00 0.00 1.28
636 724 1.202698 AGCGACCCTCCAAGCATAATC 60.203 52.381 0.00 0.00 0.00 1.75
637 725 1.475034 GCGACCCTCCAAGCATAATCA 60.475 52.381 0.00 0.00 0.00 2.57
638 726 2.487934 CGACCCTCCAAGCATAATCAG 58.512 52.381 0.00 0.00 0.00 2.90
639 727 2.158900 CGACCCTCCAAGCATAATCAGT 60.159 50.000 0.00 0.00 0.00 3.41
640 728 3.209410 GACCCTCCAAGCATAATCAGTG 58.791 50.000 0.00 0.00 0.00 3.66
641 729 2.092212 ACCCTCCAAGCATAATCAGTGG 60.092 50.000 0.00 0.00 0.00 4.00
642 730 2.579873 CCTCCAAGCATAATCAGTGGG 58.420 52.381 0.00 0.00 0.00 4.61
643 731 1.952296 CTCCAAGCATAATCAGTGGGC 59.048 52.381 0.00 0.00 0.00 5.36
644 732 1.565759 TCCAAGCATAATCAGTGGGCT 59.434 47.619 0.00 0.00 36.13 5.19
645 733 2.777114 TCCAAGCATAATCAGTGGGCTA 59.223 45.455 0.00 0.00 33.80 3.93
646 734 3.201930 TCCAAGCATAATCAGTGGGCTAA 59.798 43.478 0.00 0.00 33.80 3.09
647 735 4.141181 TCCAAGCATAATCAGTGGGCTAAT 60.141 41.667 0.00 0.00 33.80 1.73
648 736 4.217118 CCAAGCATAATCAGTGGGCTAATC 59.783 45.833 0.00 0.00 33.80 1.75
649 737 4.026356 AGCATAATCAGTGGGCTAATCC 57.974 45.455 0.00 0.00 32.09 3.01
650 738 3.395607 AGCATAATCAGTGGGCTAATCCA 59.604 43.478 0.00 0.00 36.21 3.41
651 739 3.755378 GCATAATCAGTGGGCTAATCCAG 59.245 47.826 0.00 0.00 37.50 3.86
652 740 4.747931 GCATAATCAGTGGGCTAATCCAGT 60.748 45.833 0.00 0.00 40.88 4.00
653 741 3.567478 AATCAGTGGGCTAATCCAGTC 57.433 47.619 0.00 0.00 38.33 3.51
654 742 2.254152 TCAGTGGGCTAATCCAGTCT 57.746 50.000 0.00 0.00 38.33 3.24
655 743 2.111384 TCAGTGGGCTAATCCAGTCTC 58.889 52.381 0.00 0.00 38.33 3.36
656 744 1.139853 CAGTGGGCTAATCCAGTCTCC 59.860 57.143 0.00 0.00 38.33 3.71
657 745 1.008938 AGTGGGCTAATCCAGTCTCCT 59.991 52.381 0.00 0.00 35.69 3.69
658 746 1.840635 GTGGGCTAATCCAGTCTCCTT 59.159 52.381 0.00 0.00 37.50 3.36
659 747 2.239907 GTGGGCTAATCCAGTCTCCTTT 59.760 50.000 0.00 0.00 37.50 3.11
660 748 2.919602 TGGGCTAATCCAGTCTCCTTTT 59.080 45.455 0.00 0.00 36.21 2.27
661 749 3.282885 GGGCTAATCCAGTCTCCTTTTG 58.717 50.000 0.00 0.00 36.21 2.44
662 750 3.308473 GGGCTAATCCAGTCTCCTTTTGT 60.308 47.826 0.00 0.00 36.21 2.83
663 751 4.080526 GGGCTAATCCAGTCTCCTTTTGTA 60.081 45.833 0.00 0.00 36.21 2.41
664 752 5.119694 GGCTAATCCAGTCTCCTTTTGTAG 58.880 45.833 0.00 0.00 34.01 2.74
665 753 5.338463 GGCTAATCCAGTCTCCTTTTGTAGT 60.338 44.000 0.00 0.00 34.01 2.73
666 754 5.813157 GCTAATCCAGTCTCCTTTTGTAGTC 59.187 44.000 0.00 0.00 0.00 2.59
667 755 6.351456 GCTAATCCAGTCTCCTTTTGTAGTCT 60.351 42.308 0.00 0.00 0.00 3.24
668 756 6.441088 AATCCAGTCTCCTTTTGTAGTCTT 57.559 37.500 0.00 0.00 0.00 3.01
669 757 5.215252 TCCAGTCTCCTTTTGTAGTCTTG 57.785 43.478 0.00 0.00 0.00 3.02
670 758 3.748568 CCAGTCTCCTTTTGTAGTCTTGC 59.251 47.826 0.00 0.00 0.00 4.01
671 759 4.380531 CAGTCTCCTTTTGTAGTCTTGCA 58.619 43.478 0.00 0.00 0.00 4.08
672 760 4.999950 CAGTCTCCTTTTGTAGTCTTGCAT 59.000 41.667 0.00 0.00 0.00 3.96
673 761 5.471456 CAGTCTCCTTTTGTAGTCTTGCATT 59.529 40.000 0.00 0.00 0.00 3.56
674 762 6.016777 CAGTCTCCTTTTGTAGTCTTGCATTT 60.017 38.462 0.00 0.00 0.00 2.32
675 763 6.547510 AGTCTCCTTTTGTAGTCTTGCATTTT 59.452 34.615 0.00 0.00 0.00 1.82
676 764 6.858478 GTCTCCTTTTGTAGTCTTGCATTTTC 59.142 38.462 0.00 0.00 0.00 2.29
677 765 5.757886 TCCTTTTGTAGTCTTGCATTTTCG 58.242 37.500 0.00 0.00 0.00 3.46
678 766 5.529430 TCCTTTTGTAGTCTTGCATTTTCGA 59.471 36.000 0.00 0.00 0.00 3.71
679 767 5.853282 CCTTTTGTAGTCTTGCATTTTCGAG 59.147 40.000 0.00 0.00 0.00 4.04
680 768 6.371809 TTTTGTAGTCTTGCATTTTCGAGT 57.628 33.333 0.00 0.00 0.00 4.18
681 769 7.307751 CCTTTTGTAGTCTTGCATTTTCGAGTA 60.308 37.037 0.00 0.00 0.00 2.59
682 770 7.667043 TTTGTAGTCTTGCATTTTCGAGTAT 57.333 32.000 0.00 0.00 0.00 2.12
683 771 6.647212 TGTAGTCTTGCATTTTCGAGTATG 57.353 37.500 0.00 4.88 0.00 2.39
684 772 4.606457 AGTCTTGCATTTTCGAGTATGC 57.394 40.909 20.60 20.60 45.66 3.14
685 773 4.256920 AGTCTTGCATTTTCGAGTATGCT 58.743 39.130 24.87 9.68 45.66 3.79
686 774 4.331168 AGTCTTGCATTTTCGAGTATGCTC 59.669 41.667 24.87 16.15 45.66 4.26
687 775 4.093408 GTCTTGCATTTTCGAGTATGCTCA 59.907 41.667 24.87 15.41 45.66 4.26
688 776 4.093408 TCTTGCATTTTCGAGTATGCTCAC 59.907 41.667 24.87 6.40 45.66 3.51
689 777 2.677836 TGCATTTTCGAGTATGCTCACC 59.322 45.455 24.87 6.13 45.66 4.02
690 778 2.677836 GCATTTTCGAGTATGCTCACCA 59.322 45.455 20.30 0.00 42.91 4.17
691 779 3.242543 GCATTTTCGAGTATGCTCACCAG 60.243 47.826 20.30 0.00 42.91 4.00
692 780 2.672961 TTTCGAGTATGCTCACCAGG 57.327 50.000 11.58 0.00 41.71 4.45
693 781 1.557099 TTCGAGTATGCTCACCAGGT 58.443 50.000 11.58 0.00 41.71 4.00
694 782 2.430248 TCGAGTATGCTCACCAGGTA 57.570 50.000 11.58 0.00 41.71 3.08
695 783 2.730382 TCGAGTATGCTCACCAGGTAA 58.270 47.619 11.58 0.00 41.71 2.85
696 784 3.296854 TCGAGTATGCTCACCAGGTAAT 58.703 45.455 11.58 0.00 41.71 1.89
697 785 3.704566 TCGAGTATGCTCACCAGGTAATT 59.295 43.478 11.58 0.00 41.71 1.40
698 786 4.891168 TCGAGTATGCTCACCAGGTAATTA 59.109 41.667 11.58 0.00 41.71 1.40
699 787 5.361571 TCGAGTATGCTCACCAGGTAATTAA 59.638 40.000 11.58 0.00 41.71 1.40
700 788 5.692204 CGAGTATGCTCACCAGGTAATTAAG 59.308 44.000 11.58 0.00 41.71 1.85
701 789 5.368989 AGTATGCTCACCAGGTAATTAAGC 58.631 41.667 0.00 0.00 0.00 3.09
702 790 3.712016 TGCTCACCAGGTAATTAAGCA 57.288 42.857 0.00 0.12 36.04 3.91
703 791 3.609853 TGCTCACCAGGTAATTAAGCAG 58.390 45.455 0.00 0.00 33.67 4.24
704 792 3.263170 TGCTCACCAGGTAATTAAGCAGA 59.737 43.478 0.00 0.00 33.67 4.26
705 793 3.873952 GCTCACCAGGTAATTAAGCAGAG 59.126 47.826 0.00 0.00 0.00 3.35
706 794 4.624125 GCTCACCAGGTAATTAAGCAGAGT 60.624 45.833 0.00 0.00 0.00 3.24
714 802 6.588756 CAGGTAATTAAGCAGAGTGTAAACGA 59.411 38.462 0.00 0.00 0.00 3.85
715 803 6.589139 AGGTAATTAAGCAGAGTGTAAACGAC 59.411 38.462 0.00 0.00 0.00 4.34
716 804 6.366877 GGTAATTAAGCAGAGTGTAAACGACA 59.633 38.462 0.00 0.00 34.94 4.35
747 835 2.953821 CCGTGCAGAACCGCAAAT 59.046 55.556 0.00 0.00 45.14 2.32
753 841 1.304052 CAGAACCGCAAATCCCCCA 60.304 57.895 0.00 0.00 0.00 4.96
770 858 0.659957 CCAGCCGAAATTAGCAGCTC 59.340 55.000 0.00 0.00 0.00 4.09
771 859 1.661341 CAGCCGAAATTAGCAGCTCT 58.339 50.000 0.00 0.00 0.00 4.09
772 860 1.596727 CAGCCGAAATTAGCAGCTCTC 59.403 52.381 0.00 0.00 0.00 3.20
773 861 1.484240 AGCCGAAATTAGCAGCTCTCT 59.516 47.619 0.00 0.00 0.00 3.10
774 862 2.093235 AGCCGAAATTAGCAGCTCTCTT 60.093 45.455 0.00 0.00 0.00 2.85
775 863 2.031437 GCCGAAATTAGCAGCTCTCTTG 59.969 50.000 0.00 0.00 0.00 3.02
776 864 3.265791 CCGAAATTAGCAGCTCTCTTGT 58.734 45.455 0.00 0.00 0.00 3.16
777 865 3.308323 CCGAAATTAGCAGCTCTCTTGTC 59.692 47.826 0.00 0.00 0.00 3.18
778 866 4.180057 CGAAATTAGCAGCTCTCTTGTCT 58.820 43.478 0.00 0.00 0.00 3.41
779 867 4.629200 CGAAATTAGCAGCTCTCTTGTCTT 59.371 41.667 0.00 0.00 0.00 3.01
780 868 5.121454 CGAAATTAGCAGCTCTCTTGTCTTT 59.879 40.000 0.00 0.00 0.00 2.52
781 869 6.493449 AAATTAGCAGCTCTCTTGTCTTTC 57.507 37.500 0.00 0.00 0.00 2.62
782 870 4.607293 TTAGCAGCTCTCTTGTCTTTCA 57.393 40.909 0.00 0.00 0.00 2.69
783 871 3.482156 AGCAGCTCTCTTGTCTTTCAA 57.518 42.857 0.00 0.00 34.61 2.69
784 872 3.813443 AGCAGCTCTCTTGTCTTTCAAA 58.187 40.909 0.00 0.00 35.48 2.69
785 873 4.202441 AGCAGCTCTCTTGTCTTTCAAAA 58.798 39.130 0.00 0.00 35.48 2.44
786 874 4.641989 AGCAGCTCTCTTGTCTTTCAAAAA 59.358 37.500 0.00 0.00 35.48 1.94
817 905 3.386237 GCTCTCCCACTCACCGCT 61.386 66.667 0.00 0.00 0.00 5.52
885 1014 1.003233 GAACCAGCCACACTCCTCC 60.003 63.158 0.00 0.00 0.00 4.30
886 1015 1.462238 AACCAGCCACACTCCTCCT 60.462 57.895 0.00 0.00 0.00 3.69
887 1016 1.772819 AACCAGCCACACTCCTCCTG 61.773 60.000 0.00 0.00 0.00 3.86
1299 1436 0.663153 GTGCCGTGCCTCCATTAATC 59.337 55.000 0.00 0.00 0.00 1.75
1326 1466 0.748450 TTCTGCTTGCTTGCTTGCTT 59.252 45.000 10.35 0.00 0.00 3.91
1327 1467 0.031585 TCTGCTTGCTTGCTTGCTTG 59.968 50.000 10.35 5.44 0.00 4.01
1328 1468 1.557443 CTGCTTGCTTGCTTGCTTGC 61.557 55.000 10.35 7.41 34.50 4.01
1329 1469 1.300697 GCTTGCTTGCTTGCTTGCT 60.301 52.632 10.35 0.00 0.00 3.91
1330 1470 0.878961 GCTTGCTTGCTTGCTTGCTT 60.879 50.000 10.35 0.00 0.00 3.91
1331 1471 0.859232 CTTGCTTGCTTGCTTGCTTG 59.141 50.000 10.35 0.00 0.00 4.01
1332 1472 1.155424 TTGCTTGCTTGCTTGCTTGC 61.155 50.000 10.35 7.41 34.50 4.01
1333 1473 1.300697 GCTTGCTTGCTTGCTTGCT 60.301 52.632 10.35 0.00 0.00 3.91
1334 1474 0.878961 GCTTGCTTGCTTGCTTGCTT 60.879 50.000 10.35 0.00 0.00 3.91
1335 1475 0.859232 CTTGCTTGCTTGCTTGCTTG 59.141 50.000 10.35 0.00 0.00 4.01
1336 1476 1.155424 TTGCTTGCTTGCTTGCTTGC 61.155 50.000 10.35 7.41 34.50 4.01
1337 1477 1.300697 GCTTGCTTGCTTGCTTGCT 60.301 52.632 10.35 0.00 0.00 3.91
1338 1478 1.282930 GCTTGCTTGCTTGCTTGCTC 61.283 55.000 10.35 0.00 0.00 4.26
1339 1479 0.031585 CTTGCTTGCTTGCTTGCTCA 59.968 50.000 10.35 0.00 0.00 4.26
1340 1480 0.677288 TTGCTTGCTTGCTTGCTCAT 59.323 45.000 10.35 0.00 0.00 2.90
1341 1481 0.242825 TGCTTGCTTGCTTGCTCATC 59.757 50.000 10.35 0.00 0.00 2.92
1342 1482 0.458025 GCTTGCTTGCTTGCTCATCC 60.458 55.000 3.47 0.00 0.00 3.51
1665 1805 2.262915 CTGCTCTTCCTCGGCGTT 59.737 61.111 6.85 0.00 0.00 4.84
2400 2540 2.473816 TCGCACAGATTATACAGCAGC 58.526 47.619 0.00 0.00 0.00 5.25
2710 2977 1.589993 CATCTACGCGCTCCACCTG 60.590 63.158 5.73 0.00 0.00 4.00
2875 3176 1.212616 GCCTTCCGTTGAGATCGATG 58.787 55.000 0.54 0.00 0.00 3.84
2876 3177 1.212616 CCTTCCGTTGAGATCGATGC 58.787 55.000 0.54 0.00 0.00 3.91
2877 3178 1.471501 CCTTCCGTTGAGATCGATGCA 60.472 52.381 0.54 0.00 0.00 3.96
2912 3213 1.127817 GTGTGACGCGACGTGAATG 59.872 57.895 15.93 0.00 41.37 2.67
2913 3214 1.008309 TGTGACGCGACGTGAATGA 60.008 52.632 15.93 0.00 41.37 2.57
3511 3839 2.948720 GGCCAACAGCGAGGAGACT 61.949 63.158 0.00 0.00 45.17 3.24
3777 4117 0.606944 TACGTGACCAATGCCAACCC 60.607 55.000 0.00 0.00 0.00 4.11
3835 4175 2.664851 CGCGGTGGCTTCTGACAA 60.665 61.111 0.00 0.00 36.88 3.18
3956 4296 9.587772 TGTACAATTCTAGCTGATTAACTCTTC 57.412 33.333 0.00 0.00 0.00 2.87
4133 4655 1.734655 TCTGTTCTGCTCCCTTCCTT 58.265 50.000 0.00 0.00 0.00 3.36
4134 4656 1.625818 TCTGTTCTGCTCCCTTCCTTC 59.374 52.381 0.00 0.00 0.00 3.46
4139 4661 3.425162 TCTGCTCCCTTCCTTCTTTTC 57.575 47.619 0.00 0.00 0.00 2.29
4240 4779 0.036388 TGGTCATGCCTTCCGTTCTC 60.036 55.000 7.54 0.00 38.35 2.87
4247 4786 0.309612 GCCTTCCGTTCTCGCAAAAA 59.690 50.000 0.00 0.00 35.54 1.94
4344 4896 6.421202 CCTTAACTACAAAGGCATAGATCGAC 59.579 42.308 0.00 0.00 37.30 4.20
4413 4965 5.064314 TCATCTCAATGATAATTGGGGCA 57.936 39.130 2.61 0.00 36.98 5.36
4415 4967 6.079336 TCATCTCAATGATAATTGGGGCATT 58.921 36.000 2.61 0.00 36.98 3.56
4464 5016 4.696877 CCTTTCATACATGCACAGAGTTCA 59.303 41.667 0.00 0.00 0.00 3.18
4534 5087 6.653526 ATATGATTTTCCCGCAATCATTCA 57.346 33.333 12.76 0.00 45.25 2.57
4727 5288 8.270030 AGGATCATCACATAGATCAAGTTTCAA 58.730 33.333 0.00 0.00 41.84 2.69
4738 5299 4.543590 TCAAGTTTCAAGCCAACCAAAA 57.456 36.364 0.00 0.00 0.00 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
242 251 8.181904 AGATCAGGCAAAATTCTACAGAAAAA 57.818 30.769 0.00 0.00 37.61 1.94
342 352 9.565213 GAAAATCACTTAACTCCATTCTTCATG 57.435 33.333 0.00 0.00 0.00 3.07
418 506 4.141620 CCCTGTCCATAATCACACTAGCTT 60.142 45.833 0.00 0.00 0.00 3.74
484 572 3.914426 ACTTGATTAGAAGATGGCCGT 57.086 42.857 0.00 0.00 0.00 5.68
516 604 3.181485 CCTCGCTCTGGACTACTTTAAGG 60.181 52.174 0.00 0.00 0.00 2.69
517 605 3.735514 GCCTCGCTCTGGACTACTTTAAG 60.736 52.174 0.00 0.00 0.00 1.85
518 606 2.165845 GCCTCGCTCTGGACTACTTTAA 59.834 50.000 0.00 0.00 0.00 1.52
519 607 1.749634 GCCTCGCTCTGGACTACTTTA 59.250 52.381 0.00 0.00 0.00 1.85
520 608 0.533032 GCCTCGCTCTGGACTACTTT 59.467 55.000 0.00 0.00 0.00 2.66
521 609 0.323908 AGCCTCGCTCTGGACTACTT 60.324 55.000 0.00 0.00 30.62 2.24
522 610 1.304952 AGCCTCGCTCTGGACTACT 59.695 57.895 0.00 0.00 30.62 2.57
523 611 3.927501 AGCCTCGCTCTGGACTAC 58.072 61.111 0.00 0.00 30.62 2.73
534 622 3.181967 CGTTCCTTGCGAGCCTCG 61.182 66.667 10.36 10.36 43.89 4.63
535 623 3.491652 GCGTTCCTTGCGAGCCTC 61.492 66.667 0.00 0.00 0.00 4.70
536 624 3.941657 GAGCGTTCCTTGCGAGCCT 62.942 63.158 0.00 0.00 37.44 4.58
537 625 3.491652 GAGCGTTCCTTGCGAGCC 61.492 66.667 0.00 0.00 37.44 4.70
538 626 3.843240 CGAGCGTTCCTTGCGAGC 61.843 66.667 0.00 0.00 37.44 5.03
539 627 2.890847 ATCCGAGCGTTCCTTGCGAG 62.891 60.000 0.00 0.00 37.44 5.03
540 628 2.884087 GATCCGAGCGTTCCTTGCGA 62.884 60.000 0.00 0.00 37.44 5.10
541 629 2.509336 ATCCGAGCGTTCCTTGCG 60.509 61.111 0.00 0.00 37.44 4.85
542 630 1.424493 CTGATCCGAGCGTTCCTTGC 61.424 60.000 0.00 0.00 0.00 4.01
543 631 1.424493 GCTGATCCGAGCGTTCCTTG 61.424 60.000 0.00 0.00 0.00 3.61
544 632 1.153549 GCTGATCCGAGCGTTCCTT 60.154 57.895 0.00 0.00 0.00 3.36
545 633 2.055042 AGCTGATCCGAGCGTTCCT 61.055 57.895 0.00 0.00 44.24 3.36
546 634 1.880340 CAGCTGATCCGAGCGTTCC 60.880 63.158 8.42 0.00 44.24 3.62
547 635 0.737715 AACAGCTGATCCGAGCGTTC 60.738 55.000 23.35 0.00 44.24 3.95
548 636 0.320771 AAACAGCTGATCCGAGCGTT 60.321 50.000 23.35 0.00 44.24 4.84
549 637 0.737715 GAAACAGCTGATCCGAGCGT 60.738 55.000 23.35 0.00 44.24 5.07
550 638 1.424493 GGAAACAGCTGATCCGAGCG 61.424 60.000 23.35 0.00 44.24 5.03
551 639 0.391661 TGGAAACAGCTGATCCGAGC 60.392 55.000 26.79 12.20 39.46 5.03
552 640 3.840831 TGGAAACAGCTGATCCGAG 57.159 52.632 26.79 1.74 35.96 4.63
563 651 1.295423 GGTAGGCTCGCTGGAAACA 59.705 57.895 0.00 0.00 39.59 2.83
564 652 0.321298 TTGGTAGGCTCGCTGGAAAC 60.321 55.000 0.00 0.00 0.00 2.78
565 653 0.618458 ATTGGTAGGCTCGCTGGAAA 59.382 50.000 0.00 0.00 0.00 3.13
566 654 0.107703 CATTGGTAGGCTCGCTGGAA 60.108 55.000 0.00 0.00 0.00 3.53
567 655 1.522092 CATTGGTAGGCTCGCTGGA 59.478 57.895 0.00 0.00 0.00 3.86
568 656 2.182842 GCATTGGTAGGCTCGCTGG 61.183 63.158 0.00 0.00 0.00 4.85
569 657 0.816825 ATGCATTGGTAGGCTCGCTG 60.817 55.000 0.00 0.00 30.95 5.18
570 658 0.758734 TATGCATTGGTAGGCTCGCT 59.241 50.000 3.54 0.00 30.95 4.93
571 659 0.868406 GTATGCATTGGTAGGCTCGC 59.132 55.000 3.54 0.00 30.95 5.03
572 660 2.533266 AGTATGCATTGGTAGGCTCG 57.467 50.000 3.54 0.00 30.95 5.03
573 661 3.561725 GTCAAGTATGCATTGGTAGGCTC 59.438 47.826 3.54 0.00 30.95 4.70
574 662 3.545703 GTCAAGTATGCATTGGTAGGCT 58.454 45.455 3.54 0.00 30.95 4.58
575 663 2.618709 GGTCAAGTATGCATTGGTAGGC 59.381 50.000 3.54 0.00 0.00 3.93
576 664 4.130118 GAGGTCAAGTATGCATTGGTAGG 58.870 47.826 3.54 0.00 0.00 3.18
577 665 5.028549 AGAGGTCAAGTATGCATTGGTAG 57.971 43.478 3.54 0.00 0.00 3.18
578 666 6.326323 TGATAGAGGTCAAGTATGCATTGGTA 59.674 38.462 3.54 0.00 0.00 3.25
579 667 5.130975 TGATAGAGGTCAAGTATGCATTGGT 59.869 40.000 3.54 0.00 0.00 3.67
580 668 5.614308 TGATAGAGGTCAAGTATGCATTGG 58.386 41.667 3.54 0.00 0.00 3.16
581 669 7.558161 TTTGATAGAGGTCAAGTATGCATTG 57.442 36.000 3.54 0.00 39.13 2.82
582 670 8.462016 GTTTTTGATAGAGGTCAAGTATGCATT 58.538 33.333 3.54 0.00 39.13 3.56
583 671 7.831193 AGTTTTTGATAGAGGTCAAGTATGCAT 59.169 33.333 3.79 3.79 39.13 3.96
584 672 7.168219 AGTTTTTGATAGAGGTCAAGTATGCA 58.832 34.615 0.00 0.00 39.13 3.96
585 673 7.617041 AGTTTTTGATAGAGGTCAAGTATGC 57.383 36.000 0.00 0.00 39.13 3.14
586 674 9.831737 CAAAGTTTTTGATAGAGGTCAAGTATG 57.168 33.333 0.00 0.00 39.13 2.39
587 675 9.574516 ACAAAGTTTTTGATAGAGGTCAAGTAT 57.425 29.630 8.41 0.00 39.13 2.12
588 676 8.974060 ACAAAGTTTTTGATAGAGGTCAAGTA 57.026 30.769 8.41 0.00 39.13 2.24
589 677 7.881775 ACAAAGTTTTTGATAGAGGTCAAGT 57.118 32.000 8.41 0.00 39.13 3.16
590 678 8.836413 TGTACAAAGTTTTTGATAGAGGTCAAG 58.164 33.333 8.41 0.00 39.13 3.02
591 679 8.740123 TGTACAAAGTTTTTGATAGAGGTCAA 57.260 30.769 8.41 0.00 36.38 3.18
592 680 7.041372 GCTGTACAAAGTTTTTGATAGAGGTCA 60.041 37.037 8.41 0.00 0.00 4.02
593 681 7.298854 GCTGTACAAAGTTTTTGATAGAGGTC 58.701 38.462 8.41 0.00 0.00 3.85
594 682 6.073222 CGCTGTACAAAGTTTTTGATAGAGGT 60.073 38.462 8.41 0.00 0.00 3.85
595 683 6.147164 TCGCTGTACAAAGTTTTTGATAGAGG 59.853 38.462 8.41 1.47 0.00 3.69
596 684 7.010023 GTCGCTGTACAAAGTTTTTGATAGAG 58.990 38.462 8.41 6.35 0.00 2.43
597 685 6.073440 GGTCGCTGTACAAAGTTTTTGATAGA 60.073 38.462 8.41 0.00 0.00 1.98
598 686 6.077838 GGTCGCTGTACAAAGTTTTTGATAG 58.922 40.000 8.41 4.90 0.00 2.08
599 687 5.049267 GGGTCGCTGTACAAAGTTTTTGATA 60.049 40.000 8.41 0.00 0.00 2.15
600 688 4.261447 GGGTCGCTGTACAAAGTTTTTGAT 60.261 41.667 8.41 0.00 0.00 2.57
601 689 3.065648 GGGTCGCTGTACAAAGTTTTTGA 59.934 43.478 8.41 0.00 0.00 2.69
602 690 3.066203 AGGGTCGCTGTACAAAGTTTTTG 59.934 43.478 0.00 0.28 0.00 2.44
603 691 3.284617 AGGGTCGCTGTACAAAGTTTTT 58.715 40.909 0.00 0.00 0.00 1.94
604 692 2.876550 GAGGGTCGCTGTACAAAGTTTT 59.123 45.455 0.00 0.00 0.00 2.43
605 693 2.490991 GAGGGTCGCTGTACAAAGTTT 58.509 47.619 0.00 0.00 0.00 2.66
606 694 1.270678 GGAGGGTCGCTGTACAAAGTT 60.271 52.381 0.00 0.00 0.00 2.66
607 695 0.320697 GGAGGGTCGCTGTACAAAGT 59.679 55.000 0.00 0.00 0.00 2.66
608 696 0.320374 TGGAGGGTCGCTGTACAAAG 59.680 55.000 0.00 0.00 0.00 2.77
609 697 0.759959 TTGGAGGGTCGCTGTACAAA 59.240 50.000 0.00 0.00 0.00 2.83
610 698 0.320374 CTTGGAGGGTCGCTGTACAA 59.680 55.000 0.00 0.00 0.00 2.41
611 699 1.972198 CTTGGAGGGTCGCTGTACA 59.028 57.895 0.00 0.00 0.00 2.90
612 700 1.448013 GCTTGGAGGGTCGCTGTAC 60.448 63.158 0.00 0.00 0.00 2.90
613 701 1.264749 ATGCTTGGAGGGTCGCTGTA 61.265 55.000 0.00 0.00 0.00 2.74
614 702 1.264749 TATGCTTGGAGGGTCGCTGT 61.265 55.000 0.00 0.00 0.00 4.40
615 703 0.107703 TTATGCTTGGAGGGTCGCTG 60.108 55.000 0.00 0.00 0.00 5.18
616 704 0.839946 ATTATGCTTGGAGGGTCGCT 59.160 50.000 0.00 0.00 0.00 4.93
617 705 1.230324 GATTATGCTTGGAGGGTCGC 58.770 55.000 0.00 0.00 0.00 5.19
618 706 2.158900 ACTGATTATGCTTGGAGGGTCG 60.159 50.000 0.00 0.00 0.00 4.79
619 707 3.209410 CACTGATTATGCTTGGAGGGTC 58.791 50.000 0.00 0.00 0.00 4.46
620 708 2.092212 CCACTGATTATGCTTGGAGGGT 60.092 50.000 0.00 0.00 0.00 4.34
621 709 2.579873 CCACTGATTATGCTTGGAGGG 58.420 52.381 0.00 0.00 0.00 4.30
622 710 2.579873 CCCACTGATTATGCTTGGAGG 58.420 52.381 0.00 0.00 0.00 4.30
623 711 1.952296 GCCCACTGATTATGCTTGGAG 59.048 52.381 0.00 0.00 0.00 3.86
624 712 1.565759 AGCCCACTGATTATGCTTGGA 59.434 47.619 0.00 0.00 0.00 3.53
625 713 2.062971 AGCCCACTGATTATGCTTGG 57.937 50.000 0.00 0.00 0.00 3.61
626 714 4.217118 GGATTAGCCCACTGATTATGCTTG 59.783 45.833 0.00 0.00 33.63 4.01
627 715 4.141181 TGGATTAGCCCACTGATTATGCTT 60.141 41.667 0.00 0.00 34.97 3.91
628 716 3.395607 TGGATTAGCCCACTGATTATGCT 59.604 43.478 0.00 0.00 34.97 3.79
629 717 3.754965 TGGATTAGCCCACTGATTATGC 58.245 45.455 0.00 0.00 34.97 3.14
630 718 4.978099 ACTGGATTAGCCCACTGATTATG 58.022 43.478 0.00 0.00 34.97 1.90
631 719 4.910304 AGACTGGATTAGCCCACTGATTAT 59.090 41.667 0.00 0.00 34.97 1.28
632 720 4.298626 AGACTGGATTAGCCCACTGATTA 58.701 43.478 0.00 0.00 34.97 1.75
633 721 3.118531 AGACTGGATTAGCCCACTGATT 58.881 45.455 0.00 0.00 34.97 2.57
634 722 2.703007 GAGACTGGATTAGCCCACTGAT 59.297 50.000 0.00 0.00 34.97 2.90
635 723 2.111384 GAGACTGGATTAGCCCACTGA 58.889 52.381 0.00 0.00 34.97 3.41
636 724 1.139853 GGAGACTGGATTAGCCCACTG 59.860 57.143 0.00 0.00 34.97 3.66
637 725 1.008938 AGGAGACTGGATTAGCCCACT 59.991 52.381 0.00 0.00 41.13 4.00
638 726 1.501582 AGGAGACTGGATTAGCCCAC 58.498 55.000 0.00 0.00 41.13 4.61
639 727 2.270434 AAGGAGACTGGATTAGCCCA 57.730 50.000 0.00 0.00 42.68 5.36
640 728 3.282885 CAAAAGGAGACTGGATTAGCCC 58.717 50.000 0.00 0.00 42.68 5.19
641 729 3.956744 ACAAAAGGAGACTGGATTAGCC 58.043 45.455 0.00 0.00 42.68 3.93
642 730 5.735766 ACTACAAAAGGAGACTGGATTAGC 58.264 41.667 0.00 0.00 42.68 3.09
643 731 7.176589 AGACTACAAAAGGAGACTGGATTAG 57.823 40.000 0.00 0.00 42.68 1.73
644 732 7.386851 CAAGACTACAAAAGGAGACTGGATTA 58.613 38.462 0.00 0.00 42.68 1.75
645 733 6.234177 CAAGACTACAAAAGGAGACTGGATT 58.766 40.000 0.00 0.00 42.68 3.01
646 734 5.799213 CAAGACTACAAAAGGAGACTGGAT 58.201 41.667 0.00 0.00 42.68 3.41
647 735 4.503296 GCAAGACTACAAAAGGAGACTGGA 60.503 45.833 0.00 0.00 42.68 3.86
648 736 3.748568 GCAAGACTACAAAAGGAGACTGG 59.251 47.826 0.00 0.00 42.68 4.00
649 737 4.380531 TGCAAGACTACAAAAGGAGACTG 58.619 43.478 0.00 0.00 42.68 3.51
651 739 5.948992 AATGCAAGACTACAAAAGGAGAC 57.051 39.130 0.00 0.00 0.00 3.36
652 740 6.293407 CGAAAATGCAAGACTACAAAAGGAGA 60.293 38.462 0.00 0.00 0.00 3.71
653 741 5.853282 CGAAAATGCAAGACTACAAAAGGAG 59.147 40.000 0.00 0.00 0.00 3.69
654 742 5.529430 TCGAAAATGCAAGACTACAAAAGGA 59.471 36.000 0.00 0.00 0.00 3.36
655 743 5.757886 TCGAAAATGCAAGACTACAAAAGG 58.242 37.500 0.00 0.00 0.00 3.11
656 744 6.430451 ACTCGAAAATGCAAGACTACAAAAG 58.570 36.000 0.00 0.00 0.00 2.27
657 745 6.371809 ACTCGAAAATGCAAGACTACAAAA 57.628 33.333 0.00 0.00 0.00 2.44
658 746 7.518161 CATACTCGAAAATGCAAGACTACAAA 58.482 34.615 0.00 0.00 0.00 2.83
659 747 6.402118 GCATACTCGAAAATGCAAGACTACAA 60.402 38.462 20.91 0.00 46.19 2.41
660 748 5.063438 GCATACTCGAAAATGCAAGACTACA 59.937 40.000 20.91 0.00 46.19 2.74
661 749 5.493735 GCATACTCGAAAATGCAAGACTAC 58.506 41.667 20.91 0.00 46.19 2.73
662 750 5.718649 GCATACTCGAAAATGCAAGACTA 57.281 39.130 20.91 0.00 46.19 2.59
663 751 4.606457 GCATACTCGAAAATGCAAGACT 57.394 40.909 20.91 0.00 46.19 3.24
669 757 2.677836 TGGTGAGCATACTCGAAAATGC 59.322 45.455 19.10 19.10 46.69 3.56
670 758 3.310774 CCTGGTGAGCATACTCGAAAATG 59.689 47.826 2.93 2.93 46.69 2.32
671 759 3.055094 ACCTGGTGAGCATACTCGAAAAT 60.055 43.478 0.00 0.00 46.69 1.82
672 760 2.301870 ACCTGGTGAGCATACTCGAAAA 59.698 45.455 0.00 0.00 46.69 2.29
673 761 1.899814 ACCTGGTGAGCATACTCGAAA 59.100 47.619 0.00 0.00 46.69 3.46
674 762 1.557099 ACCTGGTGAGCATACTCGAA 58.443 50.000 0.00 0.00 46.69 3.71
675 763 2.430248 TACCTGGTGAGCATACTCGA 57.570 50.000 10.23 0.00 46.69 4.04
676 764 3.735237 ATTACCTGGTGAGCATACTCG 57.265 47.619 10.23 0.00 46.69 4.18
677 765 5.467063 GCTTAATTACCTGGTGAGCATACTC 59.533 44.000 10.23 0.00 43.76 2.59
678 766 5.104527 TGCTTAATTACCTGGTGAGCATACT 60.105 40.000 10.23 0.00 34.12 2.12
679 767 5.123227 TGCTTAATTACCTGGTGAGCATAC 58.877 41.667 10.23 0.00 34.12 2.39
680 768 5.130311 TCTGCTTAATTACCTGGTGAGCATA 59.870 40.000 10.23 7.16 37.92 3.14
681 769 4.080356 TCTGCTTAATTACCTGGTGAGCAT 60.080 41.667 10.23 0.00 37.92 3.79
682 770 3.263170 TCTGCTTAATTACCTGGTGAGCA 59.737 43.478 10.23 14.61 37.17 4.26
683 771 3.873910 TCTGCTTAATTACCTGGTGAGC 58.126 45.455 10.23 11.03 0.00 4.26
684 772 4.872691 CACTCTGCTTAATTACCTGGTGAG 59.127 45.833 10.23 6.54 0.00 3.51
685 773 4.286032 ACACTCTGCTTAATTACCTGGTGA 59.714 41.667 10.23 0.37 0.00 4.02
686 774 4.579869 ACACTCTGCTTAATTACCTGGTG 58.420 43.478 10.23 0.00 0.00 4.17
687 775 4.910458 ACACTCTGCTTAATTACCTGGT 57.090 40.909 4.05 4.05 0.00 4.00
688 776 6.183360 CGTTTACACTCTGCTTAATTACCTGG 60.183 42.308 0.00 0.00 0.00 4.45
689 777 6.588756 TCGTTTACACTCTGCTTAATTACCTG 59.411 38.462 0.00 0.00 0.00 4.00
690 778 6.589139 GTCGTTTACACTCTGCTTAATTACCT 59.411 38.462 0.00 0.00 0.00 3.08
691 779 6.366877 TGTCGTTTACACTCTGCTTAATTACC 59.633 38.462 0.00 0.00 31.43 2.85
692 780 7.342318 TGTCGTTTACACTCTGCTTAATTAC 57.658 36.000 0.00 0.00 31.43 1.89
693 781 6.588756 CCTGTCGTTTACACTCTGCTTAATTA 59.411 38.462 0.00 0.00 33.45 1.40
694 782 5.408604 CCTGTCGTTTACACTCTGCTTAATT 59.591 40.000 0.00 0.00 33.45 1.40
695 783 4.929808 CCTGTCGTTTACACTCTGCTTAAT 59.070 41.667 0.00 0.00 33.45 1.40
696 784 4.202182 ACCTGTCGTTTACACTCTGCTTAA 60.202 41.667 0.00 0.00 33.45 1.85
697 785 3.319972 ACCTGTCGTTTACACTCTGCTTA 59.680 43.478 0.00 0.00 33.45 3.09
698 786 2.102588 ACCTGTCGTTTACACTCTGCTT 59.897 45.455 0.00 0.00 33.45 3.91
699 787 1.687123 ACCTGTCGTTTACACTCTGCT 59.313 47.619 0.00 0.00 33.45 4.24
700 788 2.059541 GACCTGTCGTTTACACTCTGC 58.940 52.381 0.00 0.00 33.45 4.26
701 789 3.050619 GTGACCTGTCGTTTACACTCTG 58.949 50.000 0.00 0.00 33.45 3.35
702 790 2.691526 TGTGACCTGTCGTTTACACTCT 59.308 45.455 0.00 0.00 33.45 3.24
703 791 3.088194 TGTGACCTGTCGTTTACACTC 57.912 47.619 0.00 0.00 33.45 3.51
704 792 3.530265 TTGTGACCTGTCGTTTACACT 57.470 42.857 0.00 0.00 33.45 3.55
705 793 4.806342 AATTGTGACCTGTCGTTTACAC 57.194 40.909 0.00 0.00 33.45 2.90
706 794 4.445052 CGTAATTGTGACCTGTCGTTTACA 59.555 41.667 0.00 0.00 36.42 2.41
714 802 0.034337 ACGGCGTAATTGTGACCTGT 59.966 50.000 12.58 0.00 0.00 4.00
715 803 0.442310 CACGGCGTAATTGTGACCTG 59.558 55.000 14.22 0.00 35.66 4.00
716 804 1.296056 GCACGGCGTAATTGTGACCT 61.296 55.000 14.22 0.00 35.66 3.85
747 835 1.226262 GCTAATTTCGGCTGGGGGA 59.774 57.895 0.00 0.00 0.00 4.81
789 877 4.013050 GAGTGGGAGAGCTGCTAATTTTT 58.987 43.478 0.15 0.00 0.00 1.94
790 878 3.009473 TGAGTGGGAGAGCTGCTAATTTT 59.991 43.478 0.15 0.00 0.00 1.82
791 879 2.573462 TGAGTGGGAGAGCTGCTAATTT 59.427 45.455 0.15 0.00 0.00 1.82
792 880 2.093235 GTGAGTGGGAGAGCTGCTAATT 60.093 50.000 0.15 0.00 0.00 1.40
793 881 1.484240 GTGAGTGGGAGAGCTGCTAAT 59.516 52.381 0.15 0.00 0.00 1.73
794 882 0.898320 GTGAGTGGGAGAGCTGCTAA 59.102 55.000 0.15 0.00 0.00 3.09
795 883 0.972983 GGTGAGTGGGAGAGCTGCTA 60.973 60.000 0.15 0.00 0.00 3.49
796 884 2.289532 GGTGAGTGGGAGAGCTGCT 61.290 63.158 0.00 0.00 0.00 4.24
797 885 2.267324 GGTGAGTGGGAGAGCTGC 59.733 66.667 0.00 0.00 0.00 5.25
798 886 2.575993 CGGTGAGTGGGAGAGCTG 59.424 66.667 0.00 0.00 0.00 4.24
799 887 3.386237 GCGGTGAGTGGGAGAGCT 61.386 66.667 0.00 0.00 0.00 4.09
800 888 3.386237 AGCGGTGAGTGGGAGAGC 61.386 66.667 0.00 0.00 0.00 4.09
801 889 2.575993 CAGCGGTGAGTGGGAGAG 59.424 66.667 9.50 0.00 0.00 3.20
802 890 3.695606 GCAGCGGTGAGTGGGAGA 61.696 66.667 20.69 0.00 0.00 3.71
817 905 1.138883 GAGAGTATGGACGTGCGCA 59.861 57.895 5.66 5.66 0.00 6.09
822 910 3.942748 GTGAAGAGAGAGAGTATGGACGT 59.057 47.826 0.00 0.00 0.00 4.34
825 913 6.151985 GTCAAAGTGAAGAGAGAGAGTATGGA 59.848 42.308 0.00 0.00 0.00 3.41
885 1014 1.421485 GCTGGATTTCGCGACACAG 59.579 57.895 9.15 15.62 0.00 3.66
886 1015 3.561429 GCTGGATTTCGCGACACA 58.439 55.556 9.15 4.56 0.00 3.72
1326 1466 1.075305 TGGGATGAGCAAGCAAGCA 59.925 52.632 3.19 0.00 36.85 3.91
1327 1467 1.509923 GTGGGATGAGCAAGCAAGC 59.490 57.895 0.00 0.00 0.00 4.01
1328 1468 0.957395 ACGTGGGATGAGCAAGCAAG 60.957 55.000 0.00 0.00 0.00 4.01
1329 1469 0.323302 TACGTGGGATGAGCAAGCAA 59.677 50.000 0.00 0.00 0.00 3.91
1330 1470 0.391130 GTACGTGGGATGAGCAAGCA 60.391 55.000 0.00 0.00 0.00 3.91
1331 1471 1.421410 CGTACGTGGGATGAGCAAGC 61.421 60.000 7.22 0.00 0.00 4.01
1332 1472 0.108804 ACGTACGTGGGATGAGCAAG 60.109 55.000 22.14 0.00 0.00 4.01
1333 1473 1.175654 TACGTACGTGGGATGAGCAA 58.824 50.000 30.25 3.44 0.00 3.91
1334 1474 1.066454 CATACGTACGTGGGATGAGCA 59.934 52.381 30.25 7.71 0.00 4.26
1335 1475 1.066605 ACATACGTACGTGGGATGAGC 59.933 52.381 30.25 0.00 0.00 4.26
1336 1476 2.727777 CACATACGTACGTGGGATGAG 58.272 52.381 30.25 19.32 0.00 2.90
1337 1477 1.202325 GCACATACGTACGTGGGATGA 60.202 52.381 30.25 10.09 33.62 2.92
1338 1478 1.202371 AGCACATACGTACGTGGGATG 60.202 52.381 30.25 25.55 33.62 3.51
1339 1479 1.108776 AGCACATACGTACGTGGGAT 58.891 50.000 30.25 12.29 33.62 3.85
1340 1480 0.171679 CAGCACATACGTACGTGGGA 59.828 55.000 30.25 11.71 33.62 4.37
1341 1481 1.418342 GCAGCACATACGTACGTGGG 61.418 60.000 30.25 22.55 33.62 4.61
1342 1482 0.734597 TGCAGCACATACGTACGTGG 60.735 55.000 30.25 22.89 33.62 4.94
2400 2540 3.722295 ACATTTGGTCGCGTGCGG 61.722 61.111 14.89 0.00 40.25 5.69
2415 2571 1.071542 ACAACACCGATCCATGTCACA 59.928 47.619 0.00 0.00 0.00 3.58
2687 2954 0.245266 TGGAGCGCGTAGATGAACAA 59.755 50.000 8.43 0.00 0.00 2.83
2689 2956 1.146358 GGTGGAGCGCGTAGATGAAC 61.146 60.000 8.43 0.00 0.00 3.18
2761 3028 3.365265 CTGCGGTTCTGGTTGGCC 61.365 66.667 0.00 0.00 0.00 5.36
2875 3176 0.091678 CGTCGTTGCATTGCATTTGC 59.908 50.000 12.95 13.65 38.76 3.68
2876 3177 1.122859 CACGTCGTTGCATTGCATTTG 59.877 47.619 12.95 5.61 38.76 2.32
2877 3178 1.268999 ACACGTCGTTGCATTGCATTT 60.269 42.857 12.95 0.00 38.76 2.32
2902 3203 1.202054 TGCATGCATTCATTCACGTCG 60.202 47.619 18.46 0.00 0.00 5.12
2912 3213 1.132834 TCGTGGACAATGCATGCATTC 59.867 47.619 36.90 27.97 43.92 2.67
2913 3214 1.133598 CTCGTGGACAATGCATGCATT 59.866 47.619 34.78 34.78 46.35 3.56
3456 3784 1.153369 ATGATGGACTCGTTGCCCG 60.153 57.895 0.00 0.00 38.13 6.13
3835 4175 9.504708 CAAGATCCAATTAATCAAGAGCTATCT 57.495 33.333 0.00 0.00 37.39 1.98
3870 4210 0.806492 GCGTGCCTTACTCTACTGGC 60.806 60.000 0.00 0.00 45.10 4.85
3956 4296 5.934625 ACAAGGTCTACATAGCAGAAAACAG 59.065 40.000 0.00 0.00 0.00 3.16
4063 4403 4.502962 CAGGACACCAACACAAACAAAAT 58.497 39.130 0.00 0.00 0.00 1.82
4133 4655 2.631160 TTCTCACCCGCAAGAAAAGA 57.369 45.000 0.00 0.00 43.02 2.52
4134 4656 3.708563 TTTTCTCACCCGCAAGAAAAG 57.291 42.857 6.26 0.00 43.17 2.27
4139 4661 2.293122 TGACAATTTTCTCACCCGCAAG 59.707 45.455 0.00 0.00 0.00 4.01
4225 4763 1.298157 TTGCGAGAACGGAAGGCATG 61.298 55.000 0.00 0.00 44.06 4.06
4452 5004 1.372683 GGAGGCTGAACTCTGTGCA 59.627 57.895 0.00 0.00 37.63 4.57
4464 5016 0.674895 GTCGTGATGCTTTGGAGGCT 60.675 55.000 0.00 0.00 0.00 4.58
4534 5087 1.716503 AGGGGCTGGTATGGTTCTTTT 59.283 47.619 0.00 0.00 0.00 2.27
4568 5121 4.536090 TGAATACAGATGGGTCCTTGTCTT 59.464 41.667 0.00 0.00 0.00 3.01
4727 5288 4.503123 GCTACTTGGAATTTTTGGTTGGCT 60.503 41.667 0.00 0.00 0.00 4.75
4738 5299 8.870075 AGATTTCTTGTTAGCTACTTGGAATT 57.130 30.769 0.00 0.00 0.00 2.17


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

AutoCloner maintained by Alex Coulton.