Multiple sequence alignment - TraesCS1D01G415300

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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 TraesCS1D01G415300 chr1D 100.000 2606 0 0 1 2606 474752408 474755013 0.000000e+00 4813
1 TraesCS1D01G415300 chr1D 78.594 313 57 9 1889 2194 3535228 3534919 5.690000e-47 198
2 TraesCS1D01G415300 chr1A 86.708 1941 165 40 716 2606 570264950 570266847 0.000000e+00 2069
3 TraesCS1D01G415300 chr1B 85.825 1933 159 48 750 2596 659988623 659990526 0.000000e+00 1945
4 TraesCS1D01G415300 chr1B 86.325 702 54 21 1083 1752 659997510 659998201 0.000000e+00 726
5 TraesCS1D01G415300 chr1B 91.700 506 23 9 1 489 659988116 659988619 0.000000e+00 684
6 TraesCS1D01G415300 chr3B 76.934 737 129 22 1898 2600 117718528 117719257 5.260000e-102 381
7 TraesCS1D01G415300 chr3D 75.469 746 132 33 1898 2601 519245056 519244320 1.510000e-82 316
8 TraesCS1D01G415300 chr5B 75.965 570 107 21 1898 2444 15257032 15256470 1.540000e-67 267
9 TraesCS1D01G415300 chr5B 71.813 557 134 20 1898 2438 134117198 134116649 1.260000e-28 137
10 TraesCS1D01G415300 chr7D 76.250 560 96 19 1901 2441 39052006 39051465 1.990000e-66 263
11 TraesCS1D01G415300 chr7D 76.454 361 76 8 1889 2242 404380489 404380131 1.230000e-43 187
12 TraesCS1D01G415300 chr2D 74.419 559 112 24 1898 2435 81475433 81475981 7.310000e-51 211
13 TraesCS1D01G415300 chr2D 79.211 279 52 6 1898 2173 43735441 43735716 3.420000e-44 189
14 TraesCS1D01G415300 chr2D 76.454 361 76 7 1889 2242 45839712 45840070 1.230000e-43 187
15 TraesCS1D01G415300 chr2D 72.469 563 124 24 1898 2438 2745326 2744773 4.490000e-33 152
16 TraesCS1D01G415300 chr4A 74.194 558 115 20 1898 2438 729879798 729879253 3.400000e-49 206
17 TraesCS1D01G415300 chr4A 74.251 501 94 23 1898 2374 614236097 614235608 7.410000e-41 178


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 TraesCS1D01G415300 chr1D 474752408 474755013 2605 False 4813.0 4813 100.0000 1 2606 1 chr1D.!!$F1 2605
1 TraesCS1D01G415300 chr1A 570264950 570266847 1897 False 2069.0 2069 86.7080 716 2606 1 chr1A.!!$F1 1890
2 TraesCS1D01G415300 chr1B 659988116 659990526 2410 False 1314.5 1945 88.7625 1 2596 2 chr1B.!!$F2 2595
3 TraesCS1D01G415300 chr1B 659997510 659998201 691 False 726.0 726 86.3250 1083 1752 1 chr1B.!!$F1 669
4 TraesCS1D01G415300 chr3B 117718528 117719257 729 False 381.0 381 76.9340 1898 2600 1 chr3B.!!$F1 702
5 TraesCS1D01G415300 chr3D 519244320 519245056 736 True 316.0 316 75.4690 1898 2601 1 chr3D.!!$R1 703
6 TraesCS1D01G415300 chr5B 15256470 15257032 562 True 267.0 267 75.9650 1898 2444 1 chr5B.!!$R1 546
7 TraesCS1D01G415300 chr7D 39051465 39052006 541 True 263.0 263 76.2500 1901 2441 1 chr7D.!!$R1 540
8 TraesCS1D01G415300 chr2D 81475433 81475981 548 False 211.0 211 74.4190 1898 2435 1 chr2D.!!$F3 537
9 TraesCS1D01G415300 chr4A 729879253 729879798 545 True 206.0 206 74.1940 1898 2438 1 chr4A.!!$R2 540

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
527 545 0.038526 TTTTCCGAGGCGAGACTCAC 60.039 55.0 6.77 0.0 37.34 3.51 F
547 565 0.109723 GCTCACCCCCTGTTGTAACA 59.890 55.0 0.00 0.0 37.37 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1376 1420 0.097150 GACGAAATTCTCCTTGCCGC 59.903 55.0 0.0 0.0 0.0 6.53 R
2060 2174 0.251916 CCACTTTCCTCCGCATACCA 59.748 55.0 0.0 0.0 0.0 3.25 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
28 29 9.676861 TCATTTCTCTCACATATCAGACAATTT 57.323 29.630 0.00 0.00 0.00 1.82
29 30 9.717892 CATTTCTCTCACATATCAGACAATTTG 57.282 33.333 0.00 0.00 0.00 2.32
33 41 7.708322 TCTCTCACATATCAGACAATTTGTAGC 59.292 37.037 1.15 0.00 0.00 3.58
52 60 8.466617 TTGTAGCTAACCTCCAAAATTGTTTA 57.533 30.769 0.00 0.00 0.00 2.01
64 72 0.243636 ATTGTTTAACTGCGGCTGCC 59.756 50.000 16.57 9.11 41.78 4.85
99 107 5.689514 TGGATGTTGTTTTATTTCTGTTGCG 59.310 36.000 0.00 0.00 0.00 4.85
114 122 2.135903 TTGCGGGATTTCAGCCCAGA 62.136 55.000 0.00 0.00 46.36 3.86
173 181 1.827969 CTTTTCCACCCACAACACCAA 59.172 47.619 0.00 0.00 0.00 3.67
175 183 3.314307 TTTCCACCCACAACACCAATA 57.686 42.857 0.00 0.00 0.00 1.90
179 187 2.754552 CCACCCACAACACCAATAGATG 59.245 50.000 0.00 0.00 0.00 2.90
206 214 0.884259 CATGCGTGAAGACCACACCA 60.884 55.000 0.00 0.00 45.98 4.17
208 216 0.179032 TGCGTGAAGACCACACCAAT 60.179 50.000 0.00 0.00 45.98 3.16
243 251 5.131067 ACCTAACTTGGTTCTCAAAAGTCC 58.869 41.667 0.00 0.00 36.89 3.85
252 260 5.045869 TGGTTCTCAAAAGTCCCGATATCTT 60.046 40.000 0.34 0.00 0.00 2.40
307 315 0.178990 AGGCCAACCTCTTCCACAAC 60.179 55.000 5.01 0.00 46.34 3.32
314 322 1.270839 ACCTCTTCCACAACACCATCG 60.271 52.381 0.00 0.00 0.00 3.84
365 382 2.421739 ACACAGACTGGCCGTGTC 59.578 61.111 17.78 17.78 39.64 3.67
367 384 0.826256 ACACAGACTGGCCGTGTCTA 60.826 55.000 24.70 0.00 42.21 2.59
420 437 2.244946 GAGTTGGTTTGGGACTCGC 58.755 57.895 0.00 0.00 31.54 5.03
447 465 2.285083 CCTTTGGTCTCGACAACAACA 58.715 47.619 0.00 0.00 0.00 3.33
489 507 0.983467 CATCCTTTGGGGGTTTTGGG 59.017 55.000 0.00 0.00 35.33 4.12
490 508 0.871024 ATCCTTTGGGGGTTTTGGGA 59.129 50.000 0.00 0.00 35.33 4.37
491 509 0.871024 TCCTTTGGGGGTTTTGGGAT 59.129 50.000 0.00 0.00 35.33 3.85
492 510 1.224381 TCCTTTGGGGGTTTTGGGATT 59.776 47.619 0.00 0.00 35.33 3.01
493 511 1.628340 CCTTTGGGGGTTTTGGGATTC 59.372 52.381 0.00 0.00 0.00 2.52
494 512 1.628340 CTTTGGGGGTTTTGGGATTCC 59.372 52.381 0.00 0.00 0.00 3.01
495 513 0.568192 TTGGGGGTTTTGGGATTCCA 59.432 50.000 4.80 0.00 42.25 3.53
496 514 0.116143 TGGGGGTTTTGGGATTCCAG 59.884 55.000 4.80 0.00 45.04 3.86
497 515 0.411848 GGGGGTTTTGGGATTCCAGA 59.588 55.000 4.80 0.00 45.04 3.86
498 516 1.203250 GGGGGTTTTGGGATTCCAGAA 60.203 52.381 4.80 0.00 45.04 3.02
499 517 2.615391 GGGGTTTTGGGATTCCAGAAA 58.385 47.619 4.80 2.07 45.04 2.52
500 518 2.976185 GGGGTTTTGGGATTCCAGAAAA 59.024 45.455 4.80 6.42 45.04 2.29
501 519 3.244422 GGGGTTTTGGGATTCCAGAAAAC 60.244 47.826 22.45 22.45 45.04 2.43
503 521 4.002906 GTTTTGGGATTCCAGAAAACCC 57.997 45.455 21.11 14.97 45.04 4.11
504 522 3.336509 TTTGGGATTCCAGAAAACCCA 57.663 42.857 18.51 18.51 45.04 4.51
506 524 2.888212 TGGGATTCCAGAAAACCCAAG 58.112 47.619 19.50 0.00 43.02 3.61
507 525 2.448961 TGGGATTCCAGAAAACCCAAGA 59.551 45.455 19.50 4.33 43.02 3.02
508 526 3.077391 TGGGATTCCAGAAAACCCAAGAT 59.923 43.478 19.50 0.00 43.02 2.40
509 527 4.096681 GGGATTCCAGAAAACCCAAGATT 58.903 43.478 16.21 0.00 39.27 2.40
510 528 4.532126 GGGATTCCAGAAAACCCAAGATTT 59.468 41.667 16.21 0.00 39.27 2.17
511 529 5.013079 GGGATTCCAGAAAACCCAAGATTTT 59.987 40.000 16.21 0.00 39.27 1.82
512 530 6.166279 GGATTCCAGAAAACCCAAGATTTTC 58.834 40.000 0.00 2.67 43.43 2.29
513 531 5.545063 TTCCAGAAAACCCAAGATTTTCC 57.455 39.130 6.59 0.00 43.92 3.13
514 532 3.572255 TCCAGAAAACCCAAGATTTTCCG 59.428 43.478 6.59 0.00 43.92 4.30
515 533 3.572255 CCAGAAAACCCAAGATTTTCCGA 59.428 43.478 6.59 0.00 43.92 4.55
516 534 4.321230 CCAGAAAACCCAAGATTTTCCGAG 60.321 45.833 6.59 0.00 43.92 4.63
517 535 3.826729 AGAAAACCCAAGATTTTCCGAGG 59.173 43.478 6.59 0.00 43.92 4.63
518 536 1.545841 AACCCAAGATTTTCCGAGGC 58.454 50.000 0.00 0.00 0.00 4.70
519 537 0.676782 ACCCAAGATTTTCCGAGGCG 60.677 55.000 0.00 0.00 0.00 5.52
520 538 0.392461 CCCAAGATTTTCCGAGGCGA 60.392 55.000 0.00 0.00 0.00 5.54
521 539 1.009829 CCAAGATTTTCCGAGGCGAG 58.990 55.000 0.00 0.00 0.00 5.03
522 540 1.405526 CCAAGATTTTCCGAGGCGAGA 60.406 52.381 0.00 0.00 0.00 4.04
523 541 1.661112 CAAGATTTTCCGAGGCGAGAC 59.339 52.381 0.00 0.00 0.00 3.36
524 542 1.187087 AGATTTTCCGAGGCGAGACT 58.813 50.000 0.00 0.00 0.00 3.24
525 543 1.135333 AGATTTTCCGAGGCGAGACTC 59.865 52.381 0.00 0.00 0.00 3.36
526 544 0.895530 ATTTTCCGAGGCGAGACTCA 59.104 50.000 6.77 0.00 37.34 3.41
527 545 0.038526 TTTTCCGAGGCGAGACTCAC 60.039 55.000 6.77 0.00 37.34 3.51
528 546 2.196382 TTTCCGAGGCGAGACTCACG 62.196 60.000 6.77 2.79 37.34 4.35
535 553 2.179517 CGAGACTCACGCTCACCC 59.820 66.667 2.82 0.00 32.67 4.61
536 554 2.574399 GAGACTCACGCTCACCCC 59.426 66.667 0.00 0.00 32.67 4.95
537 555 2.997897 AGACTCACGCTCACCCCC 60.998 66.667 0.00 0.00 0.00 5.40
538 556 2.997897 GACTCACGCTCACCCCCT 60.998 66.667 0.00 0.00 0.00 4.79
539 557 3.302347 GACTCACGCTCACCCCCTG 62.302 68.421 0.00 0.00 0.00 4.45
540 558 3.314331 CTCACGCTCACCCCCTGT 61.314 66.667 0.00 0.00 0.00 4.00
541 559 2.847234 TCACGCTCACCCCCTGTT 60.847 61.111 0.00 0.00 0.00 3.16
542 560 2.669569 CACGCTCACCCCCTGTTG 60.670 66.667 0.00 0.00 0.00 3.33
543 561 3.168528 ACGCTCACCCCCTGTTGT 61.169 61.111 0.00 0.00 0.00 3.32
544 562 1.839747 ACGCTCACCCCCTGTTGTA 60.840 57.895 0.00 0.00 0.00 2.41
545 563 1.373435 CGCTCACCCCCTGTTGTAA 59.627 57.895 0.00 0.00 0.00 2.41
546 564 0.953960 CGCTCACCCCCTGTTGTAAC 60.954 60.000 0.00 0.00 0.00 2.50
547 565 0.109723 GCTCACCCCCTGTTGTAACA 59.890 55.000 0.00 0.00 37.37 2.41
548 566 1.477923 GCTCACCCCCTGTTGTAACAA 60.478 52.381 0.00 0.00 38.66 2.83
549 567 2.817839 GCTCACCCCCTGTTGTAACAAT 60.818 50.000 0.00 0.00 38.66 2.71
550 568 3.560453 GCTCACCCCCTGTTGTAACAATA 60.560 47.826 0.00 0.00 38.66 1.90
551 569 4.658063 CTCACCCCCTGTTGTAACAATAA 58.342 43.478 0.00 0.00 38.66 1.40
552 570 5.063017 TCACCCCCTGTTGTAACAATAAA 57.937 39.130 0.00 0.00 38.66 1.40
553 571 5.074115 TCACCCCCTGTTGTAACAATAAAG 58.926 41.667 0.00 0.00 38.66 1.85
554 572 5.074115 CACCCCCTGTTGTAACAATAAAGA 58.926 41.667 0.00 0.00 38.66 2.52
555 573 5.536916 CACCCCCTGTTGTAACAATAAAGAA 59.463 40.000 0.00 0.00 38.66 2.52
556 574 5.537295 ACCCCCTGTTGTAACAATAAAGAAC 59.463 40.000 0.00 0.00 38.66 3.01
557 575 5.536916 CCCCCTGTTGTAACAATAAAGAACA 59.463 40.000 0.00 0.00 38.66 3.18
558 576 6.210584 CCCCCTGTTGTAACAATAAAGAACAT 59.789 38.462 0.00 0.00 38.66 2.71
559 577 7.312899 CCCCTGTTGTAACAATAAAGAACATC 58.687 38.462 0.00 0.00 38.66 3.06
560 578 7.021196 CCCTGTTGTAACAATAAAGAACATCG 58.979 38.462 0.00 0.00 38.66 3.84
561 579 7.308348 CCCTGTTGTAACAATAAAGAACATCGT 60.308 37.037 0.00 0.00 38.66 3.73
562 580 8.714179 CCTGTTGTAACAATAAAGAACATCGTA 58.286 33.333 0.00 0.00 38.66 3.43
563 581 9.741168 CTGTTGTAACAATAAAGAACATCGTAG 57.259 33.333 0.00 0.00 38.66 3.51
564 582 8.225107 TGTTGTAACAATAAAGAACATCGTAGC 58.775 33.333 0.00 0.00 35.67 3.58
565 583 6.985013 TGTAACAATAAAGAACATCGTAGCG 58.015 36.000 0.00 0.00 0.00 4.26
566 584 5.464965 AACAATAAAGAACATCGTAGCGG 57.535 39.130 0.00 0.00 0.00 5.52
567 585 4.751060 ACAATAAAGAACATCGTAGCGGA 58.249 39.130 0.00 0.00 0.00 5.54
568 586 5.357257 ACAATAAAGAACATCGTAGCGGAT 58.643 37.500 0.00 0.00 0.00 4.18
569 587 5.815740 ACAATAAAGAACATCGTAGCGGATT 59.184 36.000 0.00 0.00 0.00 3.01
570 588 6.315393 ACAATAAAGAACATCGTAGCGGATTT 59.685 34.615 0.00 0.00 0.00 2.17
571 589 6.920569 ATAAAGAACATCGTAGCGGATTTT 57.079 33.333 0.00 0.00 0.00 1.82
572 590 8.332464 CAATAAAGAACATCGTAGCGGATTTTA 58.668 33.333 0.00 0.00 0.00 1.52
573 591 5.968387 AAGAACATCGTAGCGGATTTTAG 57.032 39.130 0.00 0.00 0.00 1.85
574 592 5.258456 AGAACATCGTAGCGGATTTTAGA 57.742 39.130 0.00 0.00 0.00 2.10
575 593 5.844004 AGAACATCGTAGCGGATTTTAGAT 58.156 37.500 0.00 0.00 0.00 1.98
576 594 6.281405 AGAACATCGTAGCGGATTTTAGATT 58.719 36.000 0.00 0.00 0.00 2.40
577 595 6.761714 AGAACATCGTAGCGGATTTTAGATTT 59.238 34.615 0.00 0.00 0.00 2.17
578 596 6.920569 ACATCGTAGCGGATTTTAGATTTT 57.079 33.333 0.00 0.00 0.00 1.82
579 597 8.428186 AACATCGTAGCGGATTTTAGATTTTA 57.572 30.769 0.00 0.00 0.00 1.52
580 598 7.848491 ACATCGTAGCGGATTTTAGATTTTAC 58.152 34.615 0.00 0.00 0.00 2.01
581 599 7.709613 ACATCGTAGCGGATTTTAGATTTTACT 59.290 33.333 0.00 0.00 0.00 2.24
582 600 7.689953 TCGTAGCGGATTTTAGATTTTACTC 57.310 36.000 0.00 0.00 0.00 2.59
583 601 7.486647 TCGTAGCGGATTTTAGATTTTACTCT 58.513 34.615 0.00 0.00 0.00 3.24
584 602 7.977853 TCGTAGCGGATTTTAGATTTTACTCTT 59.022 33.333 0.00 0.00 0.00 2.85
585 603 8.601476 CGTAGCGGATTTTAGATTTTACTCTTT 58.399 33.333 0.00 0.00 0.00 2.52
588 606 9.110502 AGCGGATTTTAGATTTTACTCTTTAGG 57.889 33.333 0.00 0.00 0.00 2.69
589 607 9.106070 GCGGATTTTAGATTTTACTCTTTAGGA 57.894 33.333 0.00 0.00 0.00 2.94
602 620 8.840200 TTACTCTTTAGGATCATAGGTCTTGT 57.160 34.615 0.00 0.00 0.00 3.16
603 621 7.118496 ACTCTTTAGGATCATAGGTCTTGTG 57.882 40.000 0.00 0.00 0.00 3.33
604 622 6.897966 ACTCTTTAGGATCATAGGTCTTGTGA 59.102 38.462 0.00 0.00 0.00 3.58
605 623 7.400339 ACTCTTTAGGATCATAGGTCTTGTGAA 59.600 37.037 0.00 0.00 0.00 3.18
606 624 7.556844 TCTTTAGGATCATAGGTCTTGTGAAC 58.443 38.462 0.00 0.00 0.00 3.18
607 625 4.762289 AGGATCATAGGTCTTGTGAACC 57.238 45.455 0.68 0.68 35.68 3.62
608 626 4.366267 AGGATCATAGGTCTTGTGAACCT 58.634 43.478 4.98 4.98 39.45 3.50
609 627 5.529289 AGGATCATAGGTCTTGTGAACCTA 58.471 41.667 8.41 4.60 41.56 3.08
610 628 5.600484 AGGATCATAGGTCTTGTGAACCTAG 59.400 44.000 8.41 1.78 41.56 3.02
611 629 4.737855 TCATAGGTCTTGTGAACCTAGC 57.262 45.455 7.95 0.00 39.23 3.42
612 630 3.451178 TCATAGGTCTTGTGAACCTAGCC 59.549 47.826 7.95 0.00 39.23 3.93
613 631 1.729586 AGGTCTTGTGAACCTAGCCA 58.270 50.000 0.00 0.00 31.06 4.75
614 632 2.054799 AGGTCTTGTGAACCTAGCCAA 58.945 47.619 0.00 0.00 31.06 4.52
615 633 2.441750 AGGTCTTGTGAACCTAGCCAAA 59.558 45.455 0.00 0.00 31.06 3.28
616 634 3.117663 AGGTCTTGTGAACCTAGCCAAAA 60.118 43.478 0.00 0.00 31.06 2.44
617 635 3.253432 GGTCTTGTGAACCTAGCCAAAAG 59.747 47.826 0.00 0.00 0.00 2.27
618 636 3.253432 GTCTTGTGAACCTAGCCAAAAGG 59.747 47.826 7.59 0.00 40.20 3.11
619 637 1.616159 TGTGAACCTAGCCAAAAGGC 58.384 50.000 0.00 0.00 37.67 4.35
620 638 0.888619 GTGAACCTAGCCAAAAGGCC 59.111 55.000 2.33 0.00 37.67 5.19
621 639 0.608035 TGAACCTAGCCAAAAGGCCG 60.608 55.000 2.33 0.00 37.67 6.13
622 640 1.934220 GAACCTAGCCAAAAGGCCGC 61.934 60.000 2.33 0.00 37.67 6.53
623 641 3.140814 CCTAGCCAAAAGGCCGCC 61.141 66.667 0.00 0.00 35.12 6.13
624 642 3.508840 CTAGCCAAAAGGCCGCCG 61.509 66.667 3.05 0.00 35.12 6.46
640 658 4.351938 CGCCACGTCTTGACGGGA 62.352 66.667 24.55 0.00 39.14 5.14
641 659 2.432628 GCCACGTCTTGACGGGAG 60.433 66.667 24.55 15.80 39.14 4.30
642 660 2.432628 CCACGTCTTGACGGGAGC 60.433 66.667 24.55 0.00 39.14 4.70
643 661 2.338620 CACGTCTTGACGGGAGCA 59.661 61.111 23.99 0.00 39.14 4.26
644 662 2.022129 CACGTCTTGACGGGAGCAC 61.022 63.158 23.99 0.00 39.14 4.40
645 663 2.338620 CGTCTTGACGGGAGCACA 59.661 61.111 14.53 0.00 0.00 4.57
646 664 1.079819 CGTCTTGACGGGAGCACAT 60.080 57.895 14.53 0.00 0.00 3.21
647 665 1.078759 CGTCTTGACGGGAGCACATC 61.079 60.000 14.53 0.00 0.00 3.06
648 666 0.247736 GTCTTGACGGGAGCACATCT 59.752 55.000 0.00 0.00 0.00 2.90
649 667 0.532573 TCTTGACGGGAGCACATCTC 59.467 55.000 0.00 0.00 41.15 2.75
656 674 4.728058 GAGCACATCTCCTCGAGC 57.272 61.111 6.99 0.00 35.77 5.03
657 675 1.812525 GAGCACATCTCCTCGAGCA 59.187 57.895 6.99 0.00 35.77 4.26
658 676 0.527385 GAGCACATCTCCTCGAGCAC 60.527 60.000 6.99 0.00 35.77 4.40
659 677 1.520342 GCACATCTCCTCGAGCACC 60.520 63.158 6.99 0.00 0.00 5.01
660 678 1.226802 CACATCTCCTCGAGCACCG 60.227 63.158 6.99 0.00 40.25 4.94
661 679 2.415010 CATCTCCTCGAGCACCGG 59.585 66.667 6.99 0.00 39.14 5.28
662 680 3.532155 ATCTCCTCGAGCACCGGC 61.532 66.667 6.99 0.00 39.14 6.13
664 682 4.803426 CTCCTCGAGCACCGGCAC 62.803 72.222 6.99 0.00 44.61 5.01
666 684 4.680237 CCTCGAGCACCGGCACAA 62.680 66.667 6.99 0.00 44.61 3.33
667 685 3.414700 CTCGAGCACCGGCACAAC 61.415 66.667 0.00 0.00 44.61 3.32
668 686 4.980805 TCGAGCACCGGCACAACC 62.981 66.667 0.00 0.00 44.61 3.77
682 700 2.277084 CACAACCGGTGTATTCCTAGC 58.723 52.381 8.52 0.00 42.75 3.42
683 701 1.208776 ACAACCGGTGTATTCCTAGCC 59.791 52.381 8.52 0.00 39.29 3.93
684 702 1.208535 CAACCGGTGTATTCCTAGCCA 59.791 52.381 8.52 0.00 0.00 4.75
685 703 1.575419 ACCGGTGTATTCCTAGCCAA 58.425 50.000 6.12 0.00 0.00 4.52
686 704 1.208776 ACCGGTGTATTCCTAGCCAAC 59.791 52.381 6.12 0.00 0.00 3.77
687 705 1.485066 CCGGTGTATTCCTAGCCAACT 59.515 52.381 0.00 0.00 0.00 3.16
688 706 2.696707 CCGGTGTATTCCTAGCCAACTA 59.303 50.000 0.00 0.00 0.00 2.24
689 707 3.492137 CCGGTGTATTCCTAGCCAACTAC 60.492 52.174 0.00 0.00 0.00 2.73
690 708 3.383825 CGGTGTATTCCTAGCCAACTACT 59.616 47.826 0.00 0.00 0.00 2.57
691 709 4.499357 CGGTGTATTCCTAGCCAACTACTC 60.499 50.000 0.00 0.00 0.00 2.59
692 710 4.202233 GGTGTATTCCTAGCCAACTACTCC 60.202 50.000 0.00 0.00 0.00 3.85
693 711 4.650131 GTGTATTCCTAGCCAACTACTCCT 59.350 45.833 0.00 0.00 0.00 3.69
694 712 5.832060 GTGTATTCCTAGCCAACTACTCCTA 59.168 44.000 0.00 0.00 0.00 2.94
695 713 6.016108 GTGTATTCCTAGCCAACTACTCCTAG 60.016 46.154 0.00 0.00 0.00 3.02
696 714 4.604784 TTCCTAGCCAACTACTCCTAGT 57.395 45.455 0.00 0.00 34.38 2.57
697 715 4.604784 TCCTAGCCAACTACTCCTAGTT 57.395 45.455 0.00 0.00 42.95 2.24
698 716 4.944177 TCCTAGCCAACTACTCCTAGTTT 58.056 43.478 0.00 0.00 40.64 2.66
699 717 4.710375 TCCTAGCCAACTACTCCTAGTTTG 59.290 45.833 0.00 0.00 40.64 2.93
700 718 3.983044 AGCCAACTACTCCTAGTTTGG 57.017 47.619 6.27 6.27 40.64 3.28
701 719 2.027100 AGCCAACTACTCCTAGTTTGGC 60.027 50.000 20.43 20.43 45.71 4.52
702 720 2.027100 GCCAACTACTCCTAGTTTGGCT 60.027 50.000 20.61 0.00 44.16 4.75
703 721 3.863041 CCAACTACTCCTAGTTTGGCTC 58.137 50.000 0.00 0.00 40.64 4.70
704 722 3.515901 CCAACTACTCCTAGTTTGGCTCT 59.484 47.826 0.00 0.00 40.64 4.09
705 723 4.020128 CCAACTACTCCTAGTTTGGCTCTT 60.020 45.833 0.00 0.00 40.64 2.85
706 724 5.513267 CCAACTACTCCTAGTTTGGCTCTTT 60.513 44.000 0.00 0.00 40.64 2.52
707 725 5.153950 ACTACTCCTAGTTTGGCTCTTTG 57.846 43.478 0.00 0.00 27.62 2.77
708 726 4.838986 ACTACTCCTAGTTTGGCTCTTTGA 59.161 41.667 0.00 0.00 27.62 2.69
709 727 4.278975 ACTCCTAGTTTGGCTCTTTGAG 57.721 45.455 0.00 0.00 0.00 3.02
710 728 3.648545 ACTCCTAGTTTGGCTCTTTGAGT 59.351 43.478 0.00 0.00 31.39 3.41
711 729 4.838986 ACTCCTAGTTTGGCTCTTTGAGTA 59.161 41.667 0.00 0.00 31.39 2.59
712 730 5.046950 ACTCCTAGTTTGGCTCTTTGAGTAG 60.047 44.000 0.00 0.00 31.39 2.57
713 731 3.935828 CCTAGTTTGGCTCTTTGAGTAGC 59.064 47.826 0.00 0.00 38.03 3.58
714 732 3.492102 AGTTTGGCTCTTTGAGTAGCA 57.508 42.857 0.00 0.00 40.61 3.49
724 742 5.450137 GCTCTTTGAGTAGCAATGCATTCAT 60.450 40.000 9.53 3.45 38.63 2.57
828 850 2.394563 GCCGAGCAAGAGTGGAAGC 61.395 63.158 0.00 0.00 0.00 3.86
830 852 2.097038 CGAGCAAGAGTGGAAGCCG 61.097 63.158 0.00 0.00 0.00 5.52
933 956 1.361632 CGTAGTAGTTAGGGCGGGC 59.638 63.158 0.00 0.00 0.00 6.13
934 957 1.361632 GTAGTAGTTAGGGCGGGCG 59.638 63.158 0.00 0.00 0.00 6.13
935 958 2.492773 TAGTAGTTAGGGCGGGCGC 61.493 63.158 0.00 0.00 41.06 6.53
964 987 1.009389 CACGCGTGAGAAGAGAACCC 61.009 60.000 34.93 0.00 0.00 4.11
965 988 1.179814 ACGCGTGAGAAGAGAACCCT 61.180 55.000 12.93 0.00 0.00 4.34
980 1003 5.361285 AGAGAACCCTATGTTACAGTAGCAG 59.639 44.000 3.31 0.00 37.29 4.24
1197 1220 2.126618 CTGCTCGTGGACGCGTTA 60.127 61.111 15.53 2.44 39.60 3.18
1389 1433 4.101448 AGCGGCGGCAAGGAGAAT 62.101 61.111 19.21 0.00 43.41 2.40
1423 1467 3.170362 CCAGCCCTTCCAACTCCA 58.830 61.111 0.00 0.00 0.00 3.86
1545 1607 0.599558 CGTTCCTCCCGTACAGACAA 59.400 55.000 0.00 0.00 0.00 3.18
1782 1851 5.733373 GCGGGTGAATTTCATATGTTCCTTC 60.733 44.000 1.78 3.45 0.00 3.46
1809 1878 6.725246 ACTTTATGCAGTACACTTTGTTCAC 58.275 36.000 0.00 0.00 0.00 3.18
1812 1881 5.924475 ATGCAGTACACTTTGTTCACTAC 57.076 39.130 0.00 0.00 0.00 2.73
1820 1889 5.671493 ACACTTTGTTCACTACTGCTACTT 58.329 37.500 0.00 0.00 0.00 2.24
1821 1890 6.812998 ACACTTTGTTCACTACTGCTACTTA 58.187 36.000 0.00 0.00 0.00 2.24
1822 1891 6.700520 ACACTTTGTTCACTACTGCTACTTAC 59.299 38.462 0.00 0.00 0.00 2.34
1823 1892 6.700081 CACTTTGTTCACTACTGCTACTTACA 59.300 38.462 0.00 0.00 0.00 2.41
1824 1893 7.385205 CACTTTGTTCACTACTGCTACTTACAT 59.615 37.037 0.00 0.00 0.00 2.29
1825 1894 7.931948 ACTTTGTTCACTACTGCTACTTACATT 59.068 33.333 0.00 0.00 0.00 2.71
1826 1895 7.884816 TTGTTCACTACTGCTACTTACATTC 57.115 36.000 0.00 0.00 0.00 2.67
1827 1896 7.228314 TGTTCACTACTGCTACTTACATTCT 57.772 36.000 0.00 0.00 0.00 2.40
1833 1902 8.598924 CACTACTGCTACTTACATTCTGAATTG 58.401 37.037 0.00 0.00 0.00 2.32
1862 1944 2.978010 CCACACGGAACACCTGCC 60.978 66.667 0.00 0.00 0.00 4.85
1911 2014 1.388547 AAAAGAACAACGGCAGCTCA 58.611 45.000 0.00 0.00 0.00 4.26
2000 2113 1.001181 ACGCCGTGTACCAAGTAACAT 59.999 47.619 0.00 0.00 0.00 2.71
2007 2120 5.467399 CCGTGTACCAAGTAACATCTTCAAA 59.533 40.000 0.00 0.00 0.00 2.69
2106 2220 1.072331 GGTACATCCGATGCCCTTCAT 59.928 52.381 8.36 0.00 38.32 2.57
2196 2312 0.774908 CCCCAAACCACTACCCAGAA 59.225 55.000 0.00 0.00 0.00 3.02
2200 2316 3.245264 CCCAAACCACTACCCAGAAGATT 60.245 47.826 0.00 0.00 0.00 2.40
2327 2457 2.951475 GAATCGGGGGCGGCAATACA 62.951 60.000 12.47 0.00 0.00 2.29
2338 2468 2.511373 CAATACAGAGGCCGCGCA 60.511 61.111 8.75 0.00 0.00 6.09
2459 2611 2.742372 CCACAAAGCCTCGACCGG 60.742 66.667 0.00 0.00 0.00 5.28
2557 2711 4.421479 CGACAGAAGAGCCGCCGT 62.421 66.667 0.00 0.00 0.00 5.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 6.969993 AAACAATTTTGGAGGTTAGCTACA 57.030 33.333 0.00 0.00 0.00 2.74
29 30 8.573885 AGTTAAACAATTTTGGAGGTTAGCTAC 58.426 33.333 0.00 0.00 0.00 3.58
33 41 6.362283 CGCAGTTAAACAATTTTGGAGGTTAG 59.638 38.462 0.00 0.00 0.00 2.34
99 107 2.092212 TCTTGATCTGGGCTGAAATCCC 60.092 50.000 0.00 0.00 44.17 3.85
114 122 3.189287 GGAAGCGTTGTCATTGTCTTGAT 59.811 43.478 0.00 0.00 0.00 2.57
156 164 2.443632 TCTATTGGTGTTGTGGGTGGAA 59.556 45.455 0.00 0.00 0.00 3.53
173 181 3.575687 TCACGCATGAGGATGTCATCTAT 59.424 43.478 12.54 2.08 44.73 1.98
175 183 1.758862 TCACGCATGAGGATGTCATCT 59.241 47.619 12.54 0.00 44.73 2.90
179 187 1.929836 GTCTTCACGCATGAGGATGTC 59.070 52.381 0.00 0.00 42.39 3.06
206 214 1.802365 GTTAGGTTCGGCGTTGTGATT 59.198 47.619 6.85 0.00 0.00 2.57
208 216 0.390124 AGTTAGGTTCGGCGTTGTGA 59.610 50.000 6.85 0.00 0.00 3.58
252 260 1.406887 GCCCAAATAGAAGCCAGTCGA 60.407 52.381 0.00 0.00 0.00 4.20
307 315 1.655484 TGCTATTGTGAGCGATGGTG 58.345 50.000 0.00 0.00 45.99 4.17
335 343 0.038618 TCTGTGTCGTGTTCCCATCG 60.039 55.000 0.00 0.00 0.00 3.84
350 358 1.251527 CCTAGACACGGCCAGTCTGT 61.252 60.000 28.88 13.63 45.38 3.41
447 465 0.929244 AGAGCTACCCATGGCCAAAT 59.071 50.000 10.96 0.00 31.21 2.32
483 501 3.658725 TGGGTTTTCTGGAATCCCAAAA 58.341 40.909 14.04 0.00 42.98 2.44
489 507 6.166279 GGAAAATCTTGGGTTTTCTGGAATC 58.834 40.000 13.38 0.00 42.40 2.52
490 508 5.279456 CGGAAAATCTTGGGTTTTCTGGAAT 60.279 40.000 13.84 0.00 43.36 3.01
491 509 4.038642 CGGAAAATCTTGGGTTTTCTGGAA 59.961 41.667 13.84 0.00 43.36 3.53
492 510 3.572255 CGGAAAATCTTGGGTTTTCTGGA 59.428 43.478 13.84 0.00 43.36 3.86
493 511 3.572255 TCGGAAAATCTTGGGTTTTCTGG 59.428 43.478 18.69 10.80 45.43 3.86
494 512 4.321230 CCTCGGAAAATCTTGGGTTTTCTG 60.321 45.833 14.94 14.94 46.15 3.02
495 513 3.826729 CCTCGGAAAATCTTGGGTTTTCT 59.173 43.478 13.38 0.00 42.40 2.52
496 514 3.614150 GCCTCGGAAAATCTTGGGTTTTC 60.614 47.826 7.29 7.29 42.17 2.29
497 515 2.299013 GCCTCGGAAAATCTTGGGTTTT 59.701 45.455 0.00 0.00 0.00 2.43
498 516 1.893137 GCCTCGGAAAATCTTGGGTTT 59.107 47.619 0.00 0.00 0.00 3.27
499 517 1.545841 GCCTCGGAAAATCTTGGGTT 58.454 50.000 0.00 0.00 0.00 4.11
500 518 0.676782 CGCCTCGGAAAATCTTGGGT 60.677 55.000 0.00 0.00 0.00 4.51
501 519 0.392461 TCGCCTCGGAAAATCTTGGG 60.392 55.000 0.00 0.00 0.00 4.12
502 520 1.009829 CTCGCCTCGGAAAATCTTGG 58.990 55.000 0.00 0.00 0.00 3.61
503 521 1.661112 GTCTCGCCTCGGAAAATCTTG 59.339 52.381 0.00 0.00 0.00 3.02
504 522 1.550976 AGTCTCGCCTCGGAAAATCTT 59.449 47.619 0.00 0.00 0.00 2.40
505 523 1.135333 GAGTCTCGCCTCGGAAAATCT 59.865 52.381 0.00 0.00 0.00 2.40
506 524 1.135083 TGAGTCTCGCCTCGGAAAATC 60.135 52.381 0.00 0.00 34.04 2.17
507 525 0.895530 TGAGTCTCGCCTCGGAAAAT 59.104 50.000 0.00 0.00 34.04 1.82
508 526 0.038526 GTGAGTCTCGCCTCGGAAAA 60.039 55.000 1.65 0.00 34.04 2.29
509 527 1.585006 GTGAGTCTCGCCTCGGAAA 59.415 57.895 1.65 0.00 34.04 3.13
510 528 2.687805 CGTGAGTCTCGCCTCGGAA 61.688 63.158 7.82 0.00 34.04 4.30
511 529 3.125573 CGTGAGTCTCGCCTCGGA 61.126 66.667 7.82 0.00 34.04 4.55
512 530 4.838486 GCGTGAGTCTCGCCTCGG 62.838 72.222 25.06 0.00 46.61 4.63
518 536 2.179517 GGGTGAGCGTGAGTCTCG 59.820 66.667 10.16 10.16 37.16 4.04
519 537 2.574399 GGGGTGAGCGTGAGTCTC 59.426 66.667 0.00 0.00 35.67 3.36
520 538 2.997897 GGGGGTGAGCGTGAGTCT 60.998 66.667 0.00 0.00 0.00 3.24
521 539 2.997897 AGGGGGTGAGCGTGAGTC 60.998 66.667 0.00 0.00 0.00 3.36
522 540 3.314331 CAGGGGGTGAGCGTGAGT 61.314 66.667 0.00 0.00 0.00 3.41
523 541 2.883828 AACAGGGGGTGAGCGTGAG 61.884 63.158 0.00 0.00 0.00 3.51
524 542 2.847234 AACAGGGGGTGAGCGTGA 60.847 61.111 0.00 0.00 0.00 4.35
525 543 2.107041 TACAACAGGGGGTGAGCGTG 62.107 60.000 0.00 0.00 0.00 5.34
526 544 1.412453 TTACAACAGGGGGTGAGCGT 61.412 55.000 0.00 0.00 0.00 5.07
527 545 0.953960 GTTACAACAGGGGGTGAGCG 60.954 60.000 0.00 0.00 0.00 5.03
528 546 0.109723 TGTTACAACAGGGGGTGAGC 59.890 55.000 0.00 0.00 34.30 4.26
529 547 2.649531 TTGTTACAACAGGGGGTGAG 57.350 50.000 0.00 0.00 40.50 3.51
530 548 4.726035 TTATTGTTACAACAGGGGGTGA 57.274 40.909 0.00 0.00 40.50 4.02
531 549 5.074115 TCTTTATTGTTACAACAGGGGGTG 58.926 41.667 0.00 0.00 40.50 4.61
532 550 5.327737 TCTTTATTGTTACAACAGGGGGT 57.672 39.130 0.00 0.00 40.50 4.95
533 551 5.536916 TGTTCTTTATTGTTACAACAGGGGG 59.463 40.000 0.00 0.00 40.50 5.40
534 552 6.642707 TGTTCTTTATTGTTACAACAGGGG 57.357 37.500 0.00 0.00 40.50 4.79
535 553 7.021196 CGATGTTCTTTATTGTTACAACAGGG 58.979 38.462 0.00 0.00 40.50 4.45
536 554 7.581476 ACGATGTTCTTTATTGTTACAACAGG 58.419 34.615 0.00 0.00 40.50 4.00
537 555 9.741168 CTACGATGTTCTTTATTGTTACAACAG 57.259 33.333 0.00 0.00 40.50 3.16
538 556 8.225107 GCTACGATGTTCTTTATTGTTACAACA 58.775 33.333 0.00 0.00 37.08 3.33
539 557 7.421613 CGCTACGATGTTCTTTATTGTTACAAC 59.578 37.037 0.00 0.00 0.00 3.32
540 558 7.412129 CCGCTACGATGTTCTTTATTGTTACAA 60.412 37.037 0.00 0.00 0.00 2.41
541 559 6.035220 CCGCTACGATGTTCTTTATTGTTACA 59.965 38.462 0.00 0.00 0.00 2.41
542 560 6.254157 TCCGCTACGATGTTCTTTATTGTTAC 59.746 38.462 0.00 0.00 0.00 2.50
543 561 6.331845 TCCGCTACGATGTTCTTTATTGTTA 58.668 36.000 0.00 0.00 0.00 2.41
544 562 5.172934 TCCGCTACGATGTTCTTTATTGTT 58.827 37.500 0.00 0.00 0.00 2.83
545 563 4.751060 TCCGCTACGATGTTCTTTATTGT 58.249 39.130 0.00 0.00 0.00 2.71
546 564 5.907197 ATCCGCTACGATGTTCTTTATTG 57.093 39.130 0.00 0.00 0.00 1.90
547 565 6.920569 AAATCCGCTACGATGTTCTTTATT 57.079 33.333 0.00 0.00 0.00 1.40
548 566 6.920569 AAAATCCGCTACGATGTTCTTTAT 57.079 33.333 0.00 0.00 0.00 1.40
549 567 7.259882 TCTAAAATCCGCTACGATGTTCTTTA 58.740 34.615 0.00 0.00 0.00 1.85
550 568 6.103997 TCTAAAATCCGCTACGATGTTCTTT 58.896 36.000 0.00 0.00 0.00 2.52
551 569 5.657474 TCTAAAATCCGCTACGATGTTCTT 58.343 37.500 0.00 0.00 0.00 2.52
552 570 5.258456 TCTAAAATCCGCTACGATGTTCT 57.742 39.130 0.00 0.00 0.00 3.01
553 571 6.526566 AATCTAAAATCCGCTACGATGTTC 57.473 37.500 0.00 0.00 0.00 3.18
554 572 6.920569 AAATCTAAAATCCGCTACGATGTT 57.079 33.333 0.00 0.00 0.00 2.71
555 573 6.920569 AAAATCTAAAATCCGCTACGATGT 57.079 33.333 0.00 0.00 0.00 3.06
556 574 8.073355 AGTAAAATCTAAAATCCGCTACGATG 57.927 34.615 0.00 0.00 0.00 3.84
557 575 8.142551 AGAGTAAAATCTAAAATCCGCTACGAT 58.857 33.333 0.00 0.00 0.00 3.73
558 576 7.486647 AGAGTAAAATCTAAAATCCGCTACGA 58.513 34.615 0.00 0.00 0.00 3.43
559 577 7.695869 AGAGTAAAATCTAAAATCCGCTACG 57.304 36.000 0.00 0.00 0.00 3.51
562 580 9.110502 CCTAAAGAGTAAAATCTAAAATCCGCT 57.889 33.333 0.00 0.00 0.00 5.52
563 581 9.106070 TCCTAAAGAGTAAAATCTAAAATCCGC 57.894 33.333 0.00 0.00 0.00 5.54
576 594 9.268282 ACAAGACCTATGATCCTAAAGAGTAAA 57.732 33.333 0.00 0.00 0.00 2.01
577 595 8.696374 CACAAGACCTATGATCCTAAAGAGTAA 58.304 37.037 0.00 0.00 0.00 2.24
578 596 8.059461 TCACAAGACCTATGATCCTAAAGAGTA 58.941 37.037 0.00 0.00 0.00 2.59
579 597 6.897966 TCACAAGACCTATGATCCTAAAGAGT 59.102 38.462 0.00 0.00 0.00 3.24
580 598 7.353414 TCACAAGACCTATGATCCTAAAGAG 57.647 40.000 0.00 0.00 0.00 2.85
581 599 7.364762 GGTTCACAAGACCTATGATCCTAAAGA 60.365 40.741 0.00 0.00 31.95 2.52
582 600 6.763610 GGTTCACAAGACCTATGATCCTAAAG 59.236 42.308 0.00 0.00 31.95 1.85
583 601 6.443849 AGGTTCACAAGACCTATGATCCTAAA 59.556 38.462 10.04 0.00 39.64 1.85
584 602 5.964477 AGGTTCACAAGACCTATGATCCTAA 59.036 40.000 10.04 0.00 39.64 2.69
585 603 5.529289 AGGTTCACAAGACCTATGATCCTA 58.471 41.667 10.04 0.00 39.64 2.94
586 604 4.366267 AGGTTCACAAGACCTATGATCCT 58.634 43.478 0.00 0.00 37.61 3.24
587 605 4.762289 AGGTTCACAAGACCTATGATCC 57.238 45.455 0.00 0.00 33.94 3.36
588 606 5.293560 GCTAGGTTCACAAGACCTATGATC 58.706 45.833 3.68 0.00 35.78 2.92
589 607 4.101741 GGCTAGGTTCACAAGACCTATGAT 59.898 45.833 3.68 0.00 35.78 2.45
590 608 3.451178 GGCTAGGTTCACAAGACCTATGA 59.549 47.826 3.68 0.00 35.78 2.15
591 609 3.197766 TGGCTAGGTTCACAAGACCTATG 59.802 47.826 3.68 1.01 35.78 2.23
592 610 3.450904 TGGCTAGGTTCACAAGACCTAT 58.549 45.455 3.68 0.00 35.78 2.57
593 611 2.897350 TGGCTAGGTTCACAAGACCTA 58.103 47.619 3.27 3.27 35.24 3.08
594 612 1.729586 TGGCTAGGTTCACAAGACCT 58.270 50.000 1.04 1.04 37.64 3.85
595 613 2.561478 TTGGCTAGGTTCACAAGACC 57.439 50.000 0.00 0.00 0.00 3.85
596 614 3.253432 CCTTTTGGCTAGGTTCACAAGAC 59.747 47.826 0.00 0.00 0.00 3.01
597 615 3.486383 CCTTTTGGCTAGGTTCACAAGA 58.514 45.455 0.00 0.00 0.00 3.02
598 616 3.923017 CCTTTTGGCTAGGTTCACAAG 57.077 47.619 0.00 0.00 0.00 3.16
629 647 0.247736 AGATGTGCTCCCGTCAAGAC 59.752 55.000 0.00 0.00 0.00 3.01
630 648 0.532573 GAGATGTGCTCCCGTCAAGA 59.467 55.000 0.00 0.00 37.69 3.02
631 649 3.056628 GAGATGTGCTCCCGTCAAG 57.943 57.895 0.00 0.00 37.69 3.02
639 657 0.527385 GTGCTCGAGGAGATGTGCTC 60.527 60.000 15.58 0.78 43.17 4.26
640 658 1.515020 GTGCTCGAGGAGATGTGCT 59.485 57.895 15.58 0.00 0.00 4.40
641 659 1.520342 GGTGCTCGAGGAGATGTGC 60.520 63.158 15.58 0.00 0.00 4.57
642 660 1.226802 CGGTGCTCGAGGAGATGTG 60.227 63.158 15.58 0.00 42.43 3.21
643 661 2.418910 CCGGTGCTCGAGGAGATGT 61.419 63.158 15.58 0.00 42.43 3.06
644 662 2.415010 CCGGTGCTCGAGGAGATG 59.585 66.667 15.58 3.78 42.43 2.90
645 663 3.532155 GCCGGTGCTCGAGGAGAT 61.532 66.667 15.58 0.00 42.43 2.75
647 665 4.803426 GTGCCGGTGCTCGAGGAG 62.803 72.222 15.58 0.37 42.43 3.69
649 667 4.680237 TTGTGCCGGTGCTCGAGG 62.680 66.667 15.58 0.00 42.43 4.63
650 668 3.414700 GTTGTGCCGGTGCTCGAG 61.415 66.667 8.45 8.45 42.43 4.04
651 669 4.980805 GGTTGTGCCGGTGCTCGA 62.981 66.667 1.90 0.00 42.43 4.04
663 681 1.208776 GGCTAGGAATACACCGGTTGT 59.791 52.381 2.97 9.80 42.84 3.32
664 682 1.208535 TGGCTAGGAATACACCGGTTG 59.791 52.381 2.97 2.94 34.73 3.77
665 683 1.575419 TGGCTAGGAATACACCGGTT 58.425 50.000 2.97 0.00 34.73 4.44
666 684 1.208776 GTTGGCTAGGAATACACCGGT 59.791 52.381 0.00 0.00 34.73 5.28
667 685 1.485066 AGTTGGCTAGGAATACACCGG 59.515 52.381 0.00 0.00 34.73 5.28
668 686 2.981859 AGTTGGCTAGGAATACACCG 57.018 50.000 0.00 0.00 34.73 4.94
669 687 4.202233 GGAGTAGTTGGCTAGGAATACACC 60.202 50.000 0.00 0.00 0.00 4.16
670 688 4.650131 AGGAGTAGTTGGCTAGGAATACAC 59.350 45.833 0.00 0.00 0.00 2.90
671 689 4.880164 AGGAGTAGTTGGCTAGGAATACA 58.120 43.478 0.00 0.00 0.00 2.29
672 690 6.069994 ACTAGGAGTAGTTGGCTAGGAATAC 58.930 44.000 0.00 0.00 35.88 1.89
673 691 6.277064 ACTAGGAGTAGTTGGCTAGGAATA 57.723 41.667 0.00 0.00 35.88 1.75
674 692 5.145513 ACTAGGAGTAGTTGGCTAGGAAT 57.854 43.478 0.00 0.00 35.88 3.01
675 693 4.604784 ACTAGGAGTAGTTGGCTAGGAA 57.395 45.455 0.00 0.00 35.88 3.36
676 694 4.604784 AACTAGGAGTAGTTGGCTAGGA 57.395 45.455 0.00 0.00 45.99 2.94
677 695 4.141914 CCAAACTAGGAGTAGTTGGCTAGG 60.142 50.000 0.00 0.00 46.88 3.02
678 696 4.680975 GCCAAACTAGGAGTAGTTGGCTAG 60.681 50.000 20.44 0.00 46.88 3.42
679 697 3.197116 GCCAAACTAGGAGTAGTTGGCTA 59.803 47.826 20.44 0.00 46.88 3.93
680 698 2.027100 GCCAAACTAGGAGTAGTTGGCT 60.027 50.000 20.44 0.00 46.88 4.75
681 699 2.027100 AGCCAAACTAGGAGTAGTTGGC 60.027 50.000 20.26 20.26 46.88 4.52
682 700 3.515901 AGAGCCAAACTAGGAGTAGTTGG 59.484 47.826 5.92 5.92 46.88 3.77
683 701 4.810191 AGAGCCAAACTAGGAGTAGTTG 57.190 45.455 0.00 0.00 46.88 3.16
684 702 8.836955 ACTCAAAGAGCCAAACTAGGAGTAGTT 61.837 40.741 0.00 0.00 40.92 2.24
685 703 4.838986 TCAAAGAGCCAAACTAGGAGTAGT 59.161 41.667 0.00 0.00 41.61 2.73
686 704 5.046950 ACTCAAAGAGCCAAACTAGGAGTAG 60.047 44.000 0.00 0.00 32.89 2.57
687 705 4.838986 ACTCAAAGAGCCAAACTAGGAGTA 59.161 41.667 0.00 0.00 32.89 2.59
688 706 3.648545 ACTCAAAGAGCCAAACTAGGAGT 59.351 43.478 0.00 0.00 32.04 3.85
689 707 4.278975 ACTCAAAGAGCCAAACTAGGAG 57.721 45.455 0.00 0.00 32.04 3.69
690 708 4.322801 GCTACTCAAAGAGCCAAACTAGGA 60.323 45.833 0.00 0.00 32.04 2.94
691 709 3.935828 GCTACTCAAAGAGCCAAACTAGG 59.064 47.826 0.00 0.00 32.04 3.02
692 710 4.569943 TGCTACTCAAAGAGCCAAACTAG 58.430 43.478 0.00 0.00 37.94 2.57
693 711 4.617253 TGCTACTCAAAGAGCCAAACTA 57.383 40.909 0.00 0.00 37.94 2.24
694 712 3.492102 TGCTACTCAAAGAGCCAAACT 57.508 42.857 0.00 0.00 37.94 2.66
695 713 4.479619 CATTGCTACTCAAAGAGCCAAAC 58.520 43.478 0.00 0.00 38.34 2.93
696 714 3.057315 GCATTGCTACTCAAAGAGCCAAA 60.057 43.478 0.16 0.00 38.34 3.28
697 715 2.489329 GCATTGCTACTCAAAGAGCCAA 59.511 45.455 0.16 0.00 38.34 4.52
698 716 2.086869 GCATTGCTACTCAAAGAGCCA 58.913 47.619 0.16 0.00 38.34 4.75
699 717 2.086869 TGCATTGCTACTCAAAGAGCC 58.913 47.619 10.49 0.00 38.34 4.70
700 718 4.142534 TGAATGCATTGCTACTCAAAGAGC 60.143 41.667 18.59 0.00 38.34 4.09
701 719 5.556355 TGAATGCATTGCTACTCAAAGAG 57.444 39.130 18.59 0.00 38.34 2.85
702 720 5.886992 CATGAATGCATTGCTACTCAAAGA 58.113 37.500 18.59 0.00 38.34 2.52
828 850 5.404946 CACATATACTTATACGAACCCCGG 58.595 45.833 0.00 0.00 43.93 5.73
830 852 5.173664 GGCACATATACTTATACGAACCCC 58.826 45.833 0.00 0.00 0.00 4.95
867 889 2.757868 GCTCAGCTTCTCCTCTCAACTA 59.242 50.000 0.00 0.00 0.00 2.24
894 916 1.112113 ACTGCCATGTCCTAGTACGG 58.888 55.000 0.00 0.00 0.00 4.02
944 967 0.039437 GGTTCTCTTCTCACGCGTGA 60.039 55.000 36.96 36.96 38.06 4.35
945 968 1.009389 GGGTTCTCTTCTCACGCGTG 61.009 60.000 32.76 32.76 0.00 5.34
946 969 1.179814 AGGGTTCTCTTCTCACGCGT 61.180 55.000 5.58 5.58 0.00 6.01
964 987 7.012515 ACAGCTACTACTGCTACTGTAACATAG 59.987 40.741 0.00 0.53 41.60 2.23
965 988 6.827251 ACAGCTACTACTGCTACTGTAACATA 59.173 38.462 0.00 0.00 41.60 2.29
980 1003 1.941294 TGCTCTCGCTACAGCTACTAC 59.059 52.381 0.00 0.00 39.32 2.73
1244 1276 3.302555 CACGAACAGTAGCACGTCTTTA 58.697 45.455 0.00 0.00 36.86 1.85
1376 1420 0.097150 GACGAAATTCTCCTTGCCGC 59.903 55.000 0.00 0.00 0.00 6.53
1423 1467 4.729918 CCCCTTGCGCTTGGAGCT 62.730 66.667 18.33 0.00 39.60 4.09
1545 1607 2.035940 AAGAGCCCGACGAGGTCT 59.964 61.111 5.15 5.15 43.67 3.85
1613 1680 0.861837 CAAATGCTCTACGGATCCGC 59.138 55.000 33.62 17.43 44.19 5.54
1752 1820 5.868801 ACATATGAAATTCACCCGCAAAAAG 59.131 36.000 10.38 0.00 0.00 2.27
1753 1821 5.788450 ACATATGAAATTCACCCGCAAAAA 58.212 33.333 10.38 0.00 0.00 1.94
1782 1851 5.985781 ACAAAGTGTACTGCATAAAGTTCG 58.014 37.500 0.00 0.00 0.00 3.95
1809 1878 8.709386 ACAATTCAGAATGTAAGTAGCAGTAG 57.291 34.615 0.00 0.00 37.40 2.57
1812 1881 8.709386 AGTACAATTCAGAATGTAAGTAGCAG 57.291 34.615 0.00 0.00 37.40 4.24
1820 1889 7.602644 GGTTGTGAGAGTACAATTCAGAATGTA 59.397 37.037 0.00 0.00 42.02 2.29
1821 1890 6.428159 GGTTGTGAGAGTACAATTCAGAATGT 59.572 38.462 0.00 0.46 42.02 2.71
1822 1891 6.427853 TGGTTGTGAGAGTACAATTCAGAATG 59.572 38.462 0.00 0.00 42.02 2.67
1823 1892 6.428159 GTGGTTGTGAGAGTACAATTCAGAAT 59.572 38.462 0.00 0.00 42.02 2.40
1824 1893 5.758296 GTGGTTGTGAGAGTACAATTCAGAA 59.242 40.000 0.00 0.00 42.02 3.02
1825 1894 5.163353 TGTGGTTGTGAGAGTACAATTCAGA 60.163 40.000 0.00 0.00 42.02 3.27
1826 1895 5.050091 GTGTGGTTGTGAGAGTACAATTCAG 60.050 44.000 0.00 0.00 42.02 3.02
1827 1896 4.814234 GTGTGGTTGTGAGAGTACAATTCA 59.186 41.667 0.00 0.00 42.02 2.57
1833 1902 1.338973 TCCGTGTGGTTGTGAGAGTAC 59.661 52.381 0.00 0.00 36.30 2.73
1841 1910 0.746563 CAGGTGTTCCGTGTGGTTGT 60.747 55.000 0.00 0.00 39.05 3.32
1862 1944 0.887247 TTGATGTGATGTTTGCCCCG 59.113 50.000 0.00 0.00 0.00 5.73
1911 2014 1.953772 GGGTCATCCGCGTTTTGTT 59.046 52.632 4.92 0.00 33.83 2.83
1960 2064 0.971386 TTCGGGGTACTTGGAGTGTC 59.029 55.000 0.00 0.00 0.00 3.67
2000 2113 4.034626 TCGTTGTCGCATTCTTTTTGAAGA 59.965 37.500 0.00 0.00 36.15 2.87
2007 2120 1.191647 GTCGTCGTTGTCGCATTCTTT 59.808 47.619 0.00 0.00 36.96 2.52
2060 2174 0.251916 CCACTTTCCTCCGCATACCA 59.748 55.000 0.00 0.00 0.00 3.25
2063 2177 1.868713 TACCCACTTTCCTCCGCATA 58.131 50.000 0.00 0.00 0.00 3.14
2106 2220 2.361104 GGTGCCGCCATTCCTTCA 60.361 61.111 0.00 0.00 37.17 3.02
2180 2295 4.827284 ACAAATCTTCTGGGTAGTGGTTTG 59.173 41.667 0.00 0.00 36.56 2.93
2196 2312 5.520748 ACTGGATGGAAGGTTACAAATCT 57.479 39.130 0.00 0.00 0.00 2.40
2200 2316 3.572255 GCAAACTGGATGGAAGGTTACAA 59.428 43.478 0.00 0.00 0.00 2.41
2383 2513 2.874780 CTACCGTGACGACGCTGC 60.875 66.667 6.54 0.00 44.68 5.25
2496 2648 0.895530 GGTGGTGAGTCGGAATCTGA 59.104 55.000 7.01 0.00 0.00 3.27
2532 2686 0.318784 GCTCTTCTGTCGACGGTGTT 60.319 55.000 23.27 0.00 0.00 3.32
2538 2692 2.507324 GGCGGCTCTTCTGTCGAC 60.507 66.667 9.11 9.11 0.00 4.20


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

AutoCloner maintained by Alex Coulton.