Multiple sequence alignment - TraesCS3D01G372600

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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 TraesCS3D01G372600 chr3D 100.000 3089 0 0 1 3089 485363359 485360271 0.000000e+00 5705.0
1 TraesCS3D01G372600 chr3B 95.521 1496 50 9 897 2386 648108320 648106836 0.000000e+00 2375.0
2 TraesCS3D01G372600 chr3B 95.549 337 9 2 2753 3089 648105791 648105461 4.530000e-148 534.0
3 TraesCS3D01G372600 chr3B 90.805 174 15 1 1 174 648109980 648109808 6.660000e-57 231.0
4 TraesCS3D01G372600 chr3B 96.154 52 2 0 2702 2753 648105798 648105747 5.490000e-13 86.1
5 TraesCS3D01G372600 chr3A 95.173 1471 50 5 892 2343 628308025 628306557 0.000000e+00 2303.0
6 TraesCS3D01G372600 chr3A 95.252 337 10 3 2753 3089 628305087 628304757 2.110000e-146 529.0
7 TraesCS3D01G372600 chr3A 86.538 364 33 7 2395 2753 628305395 628305043 1.340000e-103 387.0


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 TraesCS3D01G372600 chr3D 485360271 485363359 3088 True 5705.000 5705 100.00000 1 3089 1 chr3D.!!$R1 3088
1 TraesCS3D01G372600 chr3B 648105461 648109980 4519 True 806.525 2375 94.50725 1 3089 4 chr3B.!!$R1 3088
2 TraesCS3D01G372600 chr3A 628304757 628308025 3268 True 1073.000 2303 92.32100 892 3089 3 chr3A.!!$R1 2197

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
530 682 0.169009 GTCGTGCTCAATTTCCAGGC 59.831 55.0 0.0 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2393 4002 1.031571 TGCGAGGAAATCATGTGCCC 61.032 55.0 0.0 0.0 0.0 5.36 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
107 108 9.549078 TTTTCAAATGGGAGGTTTATTTGTTAC 57.451 29.630 0.00 0.00 40.72 2.50
108 109 7.841282 TCAAATGGGAGGTTTATTTGTTACA 57.159 32.000 0.00 0.00 40.72 2.41
154 155 2.323939 TTTACATTTGCTGAACGCCG 57.676 45.000 0.00 0.00 38.05 6.46
156 157 1.231296 TACATTTGCTGAACGCCGCA 61.231 50.000 0.00 0.00 38.05 5.69
168 319 2.325509 ACGCCGCACTTTTCAAATAC 57.674 45.000 0.00 0.00 0.00 1.89
174 325 4.466828 CCGCACTTTTCAAATACTGTGAG 58.533 43.478 0.00 0.00 0.00 3.51
184 335 2.386661 ATACTGTGAGGTTGCTTCGG 57.613 50.000 0.00 0.00 0.00 4.30
238 390 1.813192 GGAGGCTGGAGAGAAGTCG 59.187 63.158 0.00 0.00 0.00 4.18
286 438 6.240894 AGGATGTTAGAAATCACACATGTGT 58.759 36.000 25.76 25.76 45.76 3.72
289 441 8.124823 GGATGTTAGAAATCACACATGTGTATG 58.875 37.037 30.11 19.25 45.76 2.39
290 442 7.376435 TGTTAGAAATCACACATGTGTATGG 57.624 36.000 30.11 18.49 45.76 2.74
307 459 7.946207 TGTGTATGGAATTCAGTTTTGCTAAA 58.054 30.769 7.93 0.00 0.00 1.85
310 462 4.545610 TGGAATTCAGTTTTGCTAAAGCG 58.454 39.130 7.93 0.00 45.83 4.68
330 482 4.818534 CGCATCTAAATGTGCCATAAGT 57.181 40.909 0.00 0.00 36.65 2.24
331 483 5.922739 CGCATCTAAATGTGCCATAAGTA 57.077 39.130 0.00 0.00 36.65 2.24
332 484 6.486253 CGCATCTAAATGTGCCATAAGTAT 57.514 37.500 0.00 0.00 36.65 2.12
333 485 7.595311 CGCATCTAAATGTGCCATAAGTATA 57.405 36.000 0.00 0.00 36.65 1.47
334 486 7.456253 CGCATCTAAATGTGCCATAAGTATAC 58.544 38.462 0.00 0.00 36.65 1.47
335 487 7.413000 CGCATCTAAATGTGCCATAAGTATACC 60.413 40.741 0.00 0.00 36.65 2.73
336 488 7.607991 GCATCTAAATGTGCCATAAGTATACCT 59.392 37.037 0.00 0.00 35.35 3.08
337 489 8.939929 CATCTAAATGTGCCATAAGTATACCTG 58.060 37.037 0.00 0.00 0.00 4.00
338 490 8.257602 TCTAAATGTGCCATAAGTATACCTGA 57.742 34.615 0.00 0.00 0.00 3.86
339 491 8.367911 TCTAAATGTGCCATAAGTATACCTGAG 58.632 37.037 0.00 0.00 0.00 3.35
340 492 4.336889 TGTGCCATAAGTATACCTGAGC 57.663 45.455 0.00 0.00 0.00 4.26
341 493 3.709141 TGTGCCATAAGTATACCTGAGCA 59.291 43.478 0.00 0.32 0.00 4.26
342 494 4.347876 TGTGCCATAAGTATACCTGAGCAT 59.652 41.667 0.00 0.00 0.00 3.79
343 495 5.542251 TGTGCCATAAGTATACCTGAGCATA 59.458 40.000 0.00 0.00 0.00 3.14
344 496 6.213397 TGTGCCATAAGTATACCTGAGCATAT 59.787 38.462 0.00 0.00 0.00 1.78
345 497 6.758886 GTGCCATAAGTATACCTGAGCATATC 59.241 42.308 0.00 0.00 0.00 1.63
346 498 6.669591 TGCCATAAGTATACCTGAGCATATCT 59.330 38.462 0.00 0.00 0.00 1.98
347 499 7.147828 TGCCATAAGTATACCTGAGCATATCTC 60.148 40.741 0.00 0.00 42.23 2.75
354 506 2.052779 TGAGCATATCTCAGGCCGG 58.947 57.895 0.00 0.00 46.34 6.13
355 507 1.375268 GAGCATATCTCAGGCCGGC 60.375 63.158 21.18 21.18 41.51 6.13
356 508 2.359230 GCATATCTCAGGCCGGCC 60.359 66.667 39.29 39.29 0.00 6.13
357 509 2.047844 CATATCTCAGGCCGGCCG 60.048 66.667 38.88 31.40 41.95 6.13
358 510 3.314331 ATATCTCAGGCCGGCCGG 61.314 66.667 40.26 40.26 41.95 6.13
398 550 4.674281 AAAAACCGGTGCTAAAAATCCA 57.326 36.364 8.52 0.00 0.00 3.41
399 551 3.934457 AAACCGGTGCTAAAAATCCAG 57.066 42.857 8.52 0.00 0.00 3.86
400 552 1.834188 ACCGGTGCTAAAAATCCAGG 58.166 50.000 6.12 0.00 0.00 4.45
401 553 1.074889 ACCGGTGCTAAAAATCCAGGT 59.925 47.619 6.12 0.00 0.00 4.00
402 554 2.167662 CCGGTGCTAAAAATCCAGGTT 58.832 47.619 0.00 0.00 0.00 3.50
403 555 2.163613 CCGGTGCTAAAAATCCAGGTTC 59.836 50.000 0.00 0.00 0.00 3.62
404 556 2.817258 CGGTGCTAAAAATCCAGGTTCA 59.183 45.455 0.00 0.00 0.00 3.18
405 557 3.254657 CGGTGCTAAAAATCCAGGTTCAA 59.745 43.478 0.00 0.00 0.00 2.69
406 558 4.615912 CGGTGCTAAAAATCCAGGTTCAAG 60.616 45.833 0.00 0.00 0.00 3.02
407 559 4.237724 GTGCTAAAAATCCAGGTTCAAGC 58.762 43.478 0.00 0.00 0.00 4.01
408 560 3.258123 TGCTAAAAATCCAGGTTCAAGCC 59.742 43.478 0.00 0.00 0.00 4.35
409 561 3.368427 GCTAAAAATCCAGGTTCAAGCCC 60.368 47.826 0.00 0.00 0.00 5.19
410 562 1.256812 AAAATCCAGGTTCAAGCCCG 58.743 50.000 0.00 0.00 0.00 6.13
411 563 0.611896 AAATCCAGGTTCAAGCCCGG 60.612 55.000 0.00 0.00 0.00 5.73
412 564 3.645268 ATCCAGGTTCAAGCCCGGC 62.645 63.158 0.00 0.00 0.00 6.13
434 586 2.192175 CCCAACCATCGGGCCTAC 59.808 66.667 0.84 0.00 36.72 3.18
435 587 2.375345 CCCAACCATCGGGCCTACT 61.375 63.158 0.84 0.00 36.72 2.57
436 588 1.052124 CCCAACCATCGGGCCTACTA 61.052 60.000 0.84 0.00 36.72 1.82
437 589 0.834612 CCAACCATCGGGCCTACTAA 59.165 55.000 0.84 0.00 37.90 2.24
438 590 1.210967 CCAACCATCGGGCCTACTAAA 59.789 52.381 0.84 0.00 37.90 1.85
439 591 2.158667 CCAACCATCGGGCCTACTAAAT 60.159 50.000 0.84 0.00 37.90 1.40
440 592 3.139077 CAACCATCGGGCCTACTAAATC 58.861 50.000 0.84 0.00 37.90 2.17
441 593 1.343465 ACCATCGGGCCTACTAAATCG 59.657 52.381 0.84 0.00 37.90 3.34
442 594 1.337823 CCATCGGGCCTACTAAATCGG 60.338 57.143 0.84 0.00 0.00 4.18
443 595 0.974383 ATCGGGCCTACTAAATCGGG 59.026 55.000 0.84 0.00 0.00 5.14
444 596 0.397535 TCGGGCCTACTAAATCGGGT 60.398 55.000 0.84 0.00 0.00 5.28
445 597 1.133513 TCGGGCCTACTAAATCGGGTA 60.134 52.381 0.84 0.00 0.00 3.69
446 598 1.897802 CGGGCCTACTAAATCGGGTAT 59.102 52.381 0.84 0.00 0.00 2.73
447 599 2.353406 CGGGCCTACTAAATCGGGTATG 60.353 54.545 0.84 0.00 0.00 2.39
448 600 2.901839 GGGCCTACTAAATCGGGTATGA 59.098 50.000 0.84 0.00 0.00 2.15
449 601 3.056035 GGGCCTACTAAATCGGGTATGAG 60.056 52.174 0.84 0.00 0.00 2.90
450 602 3.586892 GCCTACTAAATCGGGTATGAGC 58.413 50.000 0.00 0.00 0.00 4.26
451 603 3.616802 GCCTACTAAATCGGGTATGAGCC 60.617 52.174 0.00 0.00 0.00 4.70
452 604 3.056035 CCTACTAAATCGGGTATGAGCCC 60.056 52.174 0.00 0.00 45.21 5.19
460 612 4.603946 GTATGAGCCCGCCCCGAC 62.604 72.222 0.00 0.00 0.00 4.79
461 613 4.853142 TATGAGCCCGCCCCGACT 62.853 66.667 0.00 0.00 0.00 4.18
462 614 3.440162 TATGAGCCCGCCCCGACTA 62.440 63.158 0.00 0.00 0.00 2.59
463 615 2.725127 TATGAGCCCGCCCCGACTAT 62.725 60.000 0.00 0.00 0.00 2.12
464 616 4.301027 GAGCCCGCCCCGACTATG 62.301 72.222 0.00 0.00 0.00 2.23
468 620 2.915659 CCGCCCCGACTATGGCTA 60.916 66.667 0.00 0.00 45.71 3.93
469 621 2.504274 CCGCCCCGACTATGGCTAA 61.504 63.158 0.00 0.00 45.71 3.09
470 622 1.444250 CGCCCCGACTATGGCTAAA 59.556 57.895 0.00 0.00 45.71 1.85
471 623 0.179067 CGCCCCGACTATGGCTAAAA 60.179 55.000 0.00 0.00 45.71 1.52
472 624 1.542547 CGCCCCGACTATGGCTAAAAT 60.543 52.381 0.00 0.00 45.71 1.82
473 625 2.583143 GCCCCGACTATGGCTAAAATT 58.417 47.619 0.00 0.00 44.46 1.82
474 626 2.293399 GCCCCGACTATGGCTAAAATTG 59.707 50.000 0.00 0.00 44.46 2.32
475 627 3.551846 CCCCGACTATGGCTAAAATTGT 58.448 45.455 0.00 0.00 0.00 2.71
476 628 3.315191 CCCCGACTATGGCTAAAATTGTG 59.685 47.826 0.00 0.00 0.00 3.33
477 629 3.945285 CCCGACTATGGCTAAAATTGTGT 59.055 43.478 0.00 0.00 0.00 3.72
478 630 4.398044 CCCGACTATGGCTAAAATTGTGTT 59.602 41.667 0.00 0.00 0.00 3.32
479 631 5.105917 CCCGACTATGGCTAAAATTGTGTTT 60.106 40.000 0.00 0.00 0.00 2.83
480 632 6.386654 CCGACTATGGCTAAAATTGTGTTTT 58.613 36.000 0.00 0.00 0.00 2.43
481 633 6.526674 CCGACTATGGCTAAAATTGTGTTTTC 59.473 38.462 0.00 0.00 0.00 2.29
482 634 7.305474 CGACTATGGCTAAAATTGTGTTTTCT 58.695 34.615 0.00 0.00 0.00 2.52
483 635 7.271223 CGACTATGGCTAAAATTGTGTTTTCTG 59.729 37.037 0.00 0.00 0.00 3.02
484 636 6.868339 ACTATGGCTAAAATTGTGTTTTCTGC 59.132 34.615 0.00 0.00 0.00 4.26
485 637 5.016051 TGGCTAAAATTGTGTTTTCTGCA 57.984 34.783 10.78 0.00 0.00 4.41
486 638 5.049167 TGGCTAAAATTGTGTTTTCTGCAG 58.951 37.500 7.63 7.63 0.00 4.41
487 639 4.448732 GGCTAAAATTGTGTTTTCTGCAGG 59.551 41.667 15.13 0.00 0.00 4.85
488 640 5.288804 GCTAAAATTGTGTTTTCTGCAGGA 58.711 37.500 15.13 0.46 0.00 3.86
489 641 5.175673 GCTAAAATTGTGTTTTCTGCAGGAC 59.824 40.000 15.13 10.99 0.00 3.85
490 642 5.343307 AAAATTGTGTTTTCTGCAGGACT 57.657 34.783 15.13 0.00 0.00 3.85
491 643 3.996150 ATTGTGTTTTCTGCAGGACTG 57.004 42.857 15.13 0.00 0.00 3.51
492 644 2.708216 TGTGTTTTCTGCAGGACTGA 57.292 45.000 15.13 0.00 0.00 3.41
493 645 2.564771 TGTGTTTTCTGCAGGACTGAG 58.435 47.619 15.13 0.00 0.00 3.35
494 646 1.265365 GTGTTTTCTGCAGGACTGAGC 59.735 52.381 15.13 0.00 0.00 4.26
495 647 0.877743 GTTTTCTGCAGGACTGAGCC 59.122 55.000 15.13 0.00 0.00 4.70
496 648 0.767375 TTTTCTGCAGGACTGAGCCT 59.233 50.000 15.13 0.00 39.37 4.58
504 656 3.474570 GACTGAGCCTGGCCCGAT 61.475 66.667 16.57 0.00 0.00 4.18
505 657 3.453070 GACTGAGCCTGGCCCGATC 62.453 68.421 16.57 6.90 0.00 3.69
506 658 3.160047 CTGAGCCTGGCCCGATCT 61.160 66.667 16.57 0.00 0.00 2.75
507 659 3.457625 CTGAGCCTGGCCCGATCTG 62.458 68.421 16.57 6.61 0.00 2.90
508 660 4.925861 GAGCCTGGCCCGATCTGC 62.926 72.222 16.57 0.00 0.00 4.26
516 668 4.873129 CCCGATCTGCCCGTCGTG 62.873 72.222 0.00 0.00 36.17 4.35
518 670 4.498520 CGATCTGCCCGTCGTGCT 62.499 66.667 0.47 0.00 33.42 4.40
519 671 2.583593 GATCTGCCCGTCGTGCTC 60.584 66.667 0.47 0.00 0.00 4.26
520 672 3.356639 GATCTGCCCGTCGTGCTCA 62.357 63.158 0.47 0.00 0.00 4.26
521 673 2.835701 GATCTGCCCGTCGTGCTCAA 62.836 60.000 0.47 0.00 0.00 3.02
522 674 2.244117 ATCTGCCCGTCGTGCTCAAT 62.244 55.000 0.47 0.00 0.00 2.57
523 675 2.031919 TGCCCGTCGTGCTCAATT 59.968 55.556 0.47 0.00 0.00 2.32
524 676 1.577328 CTGCCCGTCGTGCTCAATTT 61.577 55.000 0.47 0.00 0.00 1.82
525 677 1.134694 GCCCGTCGTGCTCAATTTC 59.865 57.895 0.00 0.00 0.00 2.17
526 678 1.794222 CCCGTCGTGCTCAATTTCC 59.206 57.895 0.00 0.00 0.00 3.13
527 679 0.953471 CCCGTCGTGCTCAATTTCCA 60.953 55.000 0.00 0.00 0.00 3.53
528 680 0.443869 CCGTCGTGCTCAATTTCCAG 59.556 55.000 0.00 0.00 0.00 3.86
529 681 0.443869 CGTCGTGCTCAATTTCCAGG 59.556 55.000 0.00 0.00 0.00 4.45
530 682 0.169009 GTCGTGCTCAATTTCCAGGC 59.831 55.000 0.00 0.00 0.00 4.85
531 683 0.960364 TCGTGCTCAATTTCCAGGCC 60.960 55.000 0.00 0.00 0.00 5.19
532 684 1.893062 GTGCTCAATTTCCAGGCCC 59.107 57.895 0.00 0.00 0.00 5.80
533 685 1.678635 TGCTCAATTTCCAGGCCCG 60.679 57.895 0.00 0.00 0.00 6.13
534 686 1.378514 GCTCAATTTCCAGGCCCGA 60.379 57.895 0.00 0.00 0.00 5.14
535 687 1.379642 GCTCAATTTCCAGGCCCGAG 61.380 60.000 0.00 0.00 0.00 4.63
536 688 1.378514 TCAATTTCCAGGCCCGAGC 60.379 57.895 0.00 0.00 38.76 5.03
563 715 4.007644 TGGCACACTCGGGCTCAG 62.008 66.667 0.00 0.00 0.00 3.35
574 726 2.043953 GGCTCAGCCCGGGATTTT 60.044 61.111 29.31 2.39 44.06 1.82
575 727 2.121538 GGCTCAGCCCGGGATTTTC 61.122 63.158 29.31 8.70 44.06 2.29
576 728 2.472909 GCTCAGCCCGGGATTTTCG 61.473 63.158 29.31 5.93 0.00 3.46
577 729 1.819632 CTCAGCCCGGGATTTTCGG 60.820 63.158 29.31 5.45 46.43 4.30
582 734 2.512974 CCGGGATTTTCGGGTCGG 60.513 66.667 0.00 0.00 43.45 4.79
583 735 2.512974 CGGGATTTTCGGGTCGGG 60.513 66.667 0.00 0.00 0.00 5.14
584 736 2.672908 GGGATTTTCGGGTCGGGT 59.327 61.111 0.00 0.00 0.00 5.28
585 737 1.450848 GGGATTTTCGGGTCGGGTC 60.451 63.158 0.00 0.00 0.00 4.46
586 738 1.812507 GGATTTTCGGGTCGGGTCG 60.813 63.158 0.00 0.00 0.00 4.79
587 739 1.812507 GATTTTCGGGTCGGGTCGG 60.813 63.158 0.00 0.00 0.00 4.79
588 740 2.511545 GATTTTCGGGTCGGGTCGGT 62.512 60.000 0.00 0.00 0.00 4.69
589 741 2.511545 ATTTTCGGGTCGGGTCGGTC 62.512 60.000 0.00 0.00 0.00 4.79
660 812 5.853282 GCATTTAAGTCATATGCCGTTGATC 59.147 40.000 0.00 0.00 38.92 2.92
664 816 3.384668 AGTCATATGCCGTTGATCTTCG 58.615 45.455 0.00 0.00 0.00 3.79
683 835 0.804933 GCGGAGATTCGTGTGGGTAC 60.805 60.000 0.00 0.00 0.00 3.34
714 866 8.810652 TTTATTTTTATGTTTGACTGGCTCAC 57.189 30.769 0.00 0.00 0.00 3.51
718 870 6.801539 TTTATGTTTGACTGGCTCACTTAG 57.198 37.500 0.00 0.00 0.00 2.18
721 873 4.569943 TGTTTGACTGGCTCACTTAGATC 58.430 43.478 0.00 0.00 0.00 2.75
724 876 3.435275 TGACTGGCTCACTTAGATCTGT 58.565 45.455 5.18 0.00 0.00 3.41
726 878 4.642437 TGACTGGCTCACTTAGATCTGTAG 59.358 45.833 5.18 5.33 0.00 2.74
734 886 8.130469 GGCTCACTTAGATCTGTAGTAACTTAC 58.870 40.741 5.18 0.00 0.00 2.34
819 1119 8.432110 TGATATTAAGCTAAGATTCGTGCAAA 57.568 30.769 0.00 0.00 0.00 3.68
825 1125 6.494893 AGCTAAGATTCGTGCAAACATTTA 57.505 33.333 0.00 0.00 0.00 1.40
826 1126 7.088589 AGCTAAGATTCGTGCAAACATTTAT 57.911 32.000 0.00 0.00 0.00 1.40
827 1127 7.538575 AGCTAAGATTCGTGCAAACATTTATT 58.461 30.769 0.00 0.00 0.00 1.40
828 1128 8.028938 AGCTAAGATTCGTGCAAACATTTATTT 58.971 29.630 0.00 0.00 0.00 1.40
829 1129 8.647226 GCTAAGATTCGTGCAAACATTTATTTT 58.353 29.630 0.00 0.00 0.00 1.82
864 1164 8.934023 TTCTAGTTTGATTGGGTTGTTTAGAT 57.066 30.769 0.00 0.00 0.00 1.98
865 1165 8.335532 TCTAGTTTGATTGGGTTGTTTAGATG 57.664 34.615 0.00 0.00 0.00 2.90
867 1167 6.748132 AGTTTGATTGGGTTGTTTAGATGTG 58.252 36.000 0.00 0.00 0.00 3.21
868 1168 4.782019 TGATTGGGTTGTTTAGATGTGC 57.218 40.909 0.00 0.00 0.00 4.57
869 1169 3.509575 TGATTGGGTTGTTTAGATGTGCC 59.490 43.478 0.00 0.00 0.00 5.01
870 1170 1.917872 TGGGTTGTTTAGATGTGCCC 58.082 50.000 0.00 0.00 35.37 5.36
871 1171 1.427368 TGGGTTGTTTAGATGTGCCCT 59.573 47.619 0.00 0.00 35.79 5.19
873 1173 2.554344 GGGTTGTTTAGATGTGCCCTGA 60.554 50.000 0.00 0.00 0.00 3.86
874 1174 3.356290 GGTTGTTTAGATGTGCCCTGAT 58.644 45.455 0.00 0.00 0.00 2.90
875 1175 3.763897 GGTTGTTTAGATGTGCCCTGATT 59.236 43.478 0.00 0.00 0.00 2.57
887 1247 1.004745 GCCCTGATTCCCTGAACAGAA 59.995 52.381 3.19 0.00 32.90 3.02
888 1248 2.716217 CCCTGATTCCCTGAACAGAAC 58.284 52.381 3.19 0.00 32.90 3.01
889 1249 2.619074 CCCTGATTCCCTGAACAGAACC 60.619 54.545 3.19 0.00 32.90 3.62
890 1250 2.040278 CCTGATTCCCTGAACAGAACCA 59.960 50.000 3.19 0.00 32.90 3.67
938 2004 1.270305 TGCACTTCTGTCGGGAGAAAG 60.270 52.381 0.00 0.00 45.87 2.62
990 2057 4.452733 CCGGACGGAAGAGGGTGC 62.453 72.222 4.40 0.00 37.50 5.01
1701 2768 2.434359 GGGAAGGACGCCAACTCG 60.434 66.667 0.00 0.00 0.00 4.18
1744 2811 1.982395 CGGTACCTGCTGGAGTCCA 60.982 63.158 17.64 12.40 37.04 4.02
1896 2963 4.974438 TTCCTGGGGTCGGTGGCT 62.974 66.667 0.00 0.00 0.00 4.75
2108 3175 4.293648 TGACTGACCCCACGCACG 62.294 66.667 0.00 0.00 0.00 5.34
2146 3213 1.724582 AATAAACCGAGCCCATGCGC 61.725 55.000 0.00 0.00 44.33 6.09
2213 3297 5.118286 GCTTTGTTCATGGGATTAATTGGG 58.882 41.667 0.00 0.00 0.00 4.12
2228 3319 6.860790 TTAATTGGGGATTTGGGTTTCTAC 57.139 37.500 0.00 0.00 0.00 2.59
2229 3320 4.692523 ATTGGGGATTTGGGTTTCTACT 57.307 40.909 0.00 0.00 0.00 2.57
2230 3321 5.806955 ATTGGGGATTTGGGTTTCTACTA 57.193 39.130 0.00 0.00 0.00 1.82
2231 3322 4.855298 TGGGGATTTGGGTTTCTACTAG 57.145 45.455 0.00 0.00 0.00 2.57
2232 3323 4.440808 TGGGGATTTGGGTTTCTACTAGA 58.559 43.478 0.00 0.00 0.00 2.43
2233 3324 4.473559 TGGGGATTTGGGTTTCTACTAGAG 59.526 45.833 0.00 0.00 0.00 2.43
2234 3325 4.141459 GGGGATTTGGGTTTCTACTAGAGG 60.141 50.000 0.00 0.00 0.00 3.69
2300 3391 3.405831 TGCCTTGTTCAGTTCATCAGAG 58.594 45.455 0.00 0.00 0.00 3.35
2343 3434 6.946340 TCTGCAGTTCATGAGATTTTACCTA 58.054 36.000 14.67 0.00 0.00 3.08
2344 3435 7.044181 TCTGCAGTTCATGAGATTTTACCTAG 58.956 38.462 14.67 0.00 0.00 3.02
2345 3436 6.115446 TGCAGTTCATGAGATTTTACCTAGG 58.885 40.000 7.41 7.41 0.00 3.02
2348 3439 7.769044 GCAGTTCATGAGATTTTACCTAGGTTA 59.231 37.037 22.11 8.46 0.00 2.85
2350 3441 9.838339 AGTTCATGAGATTTTACCTAGGTTATG 57.162 33.333 22.11 11.52 0.00 1.90
2371 3980 2.541547 TAGGGCAGATGCAGTGTGGC 62.542 60.000 7.19 9.95 44.79 5.01
2387 3996 3.138128 GCCCGGCTTATGCGGTTT 61.138 61.111 0.71 0.00 40.82 3.27
2388 3997 2.706834 GCCCGGCTTATGCGGTTTT 61.707 57.895 0.71 0.00 40.82 2.43
2390 3999 1.431845 CCGGCTTATGCGGTTTTCC 59.568 57.895 7.28 0.00 40.82 3.13
2391 4000 1.029947 CCGGCTTATGCGGTTTTCCT 61.030 55.000 7.28 0.00 40.82 3.36
2393 4002 1.597663 CGGCTTATGCGGTTTTCCTAG 59.402 52.381 0.54 0.00 40.82 3.02
2412 4620 1.031571 GGGCACATGATTTCCTCGCA 61.032 55.000 0.00 0.00 0.00 5.10
2421 4629 1.133025 GATTTCCTCGCAACCACATGG 59.867 52.381 0.00 0.00 42.17 3.66
2448 4656 0.988832 TCCGTTTTGGCTCCTGGTAT 59.011 50.000 0.00 0.00 37.80 2.73
2449 4657 2.189676 TCCGTTTTGGCTCCTGGTATA 58.810 47.619 0.00 0.00 37.80 1.47
2462 4670 4.562767 TCCTGGTATAATAAGGCTGGTGA 58.437 43.478 0.00 0.00 0.00 4.02
2517 4725 9.632638 ATCACTAACTACAATAGAAAATGCCAT 57.367 29.630 0.00 0.00 0.00 4.40
2535 4770 3.565482 GCCATACCACAACACAGATATGG 59.435 47.826 4.10 4.10 41.28 2.74
2554 4789 3.857052 TGGCAGAAGTTAGACAATACCG 58.143 45.455 0.00 0.00 0.00 4.02
2582 4843 5.331756 CGCAATAAAAGCAGACACAACAAAG 60.332 40.000 0.00 0.00 0.00 2.77
2602 4865 1.678101 GCTTTCAGTCACAAACAGCCT 59.322 47.619 0.00 0.00 0.00 4.58
2647 4913 4.590850 AATCTTTCAGTCCCAAACAAGC 57.409 40.909 0.00 0.00 0.00 4.01
2653 4919 0.538287 AGTCCCAAACAAGCTGAGGC 60.538 55.000 0.00 0.00 39.06 4.70
2692 4960 4.008074 AGAACGGGCATATCACCATAAG 57.992 45.455 0.00 0.00 0.00 1.73
2741 5128 5.297776 CCAGATGAATTACCTAGTTGCCTTG 59.702 44.000 0.00 0.00 0.00 3.61
2742 5129 5.297776 CAGATGAATTACCTAGTTGCCTTGG 59.702 44.000 0.00 0.00 39.25 3.61
2743 5130 4.919774 TGAATTACCTAGTTGCCTTGGA 57.080 40.909 0.00 0.00 37.09 3.53
2744 5131 5.249780 TGAATTACCTAGTTGCCTTGGAA 57.750 39.130 0.00 0.00 37.09 3.53
2745 5132 5.826643 TGAATTACCTAGTTGCCTTGGAAT 58.173 37.500 0.00 0.00 37.09 3.01
2746 5133 6.964464 TGAATTACCTAGTTGCCTTGGAATA 58.036 36.000 0.00 0.00 37.09 1.75
2747 5134 7.582719 TGAATTACCTAGTTGCCTTGGAATAT 58.417 34.615 0.00 0.00 37.09 1.28
2748 5135 8.058847 TGAATTACCTAGTTGCCTTGGAATATT 58.941 33.333 0.00 0.00 37.09 1.28
2749 5136 8.838649 AATTACCTAGTTGCCTTGGAATATTT 57.161 30.769 0.00 0.00 37.09 1.40
2750 5137 8.838649 ATTACCTAGTTGCCTTGGAATATTTT 57.161 30.769 0.00 0.00 37.09 1.82
2751 5138 8.658840 TTACCTAGTTGCCTTGGAATATTTTT 57.341 30.769 0.00 0.00 37.09 1.94
2752 5139 7.170393 ACCTAGTTGCCTTGGAATATTTTTC 57.830 36.000 0.00 0.00 37.09 2.29
2753 5140 6.723977 ACCTAGTTGCCTTGGAATATTTTTCA 59.276 34.615 0.00 0.00 37.09 2.69
2754 5141 7.234577 ACCTAGTTGCCTTGGAATATTTTTCAA 59.765 33.333 0.00 0.00 37.09 2.69
2755 5142 7.761249 CCTAGTTGCCTTGGAATATTTTTCAAG 59.239 37.037 9.36 9.36 44.84 3.02
2761 5148 6.726258 CTTGGAATATTTTTCAAGGGCAAC 57.274 37.500 8.62 0.00 42.53 4.17
2783 5170 6.506538 ACCAGATGAATTATCTAGTTGCCT 57.493 37.500 0.00 0.00 44.34 4.75
2784 5171 6.904626 ACCAGATGAATTATCTAGTTGCCTT 58.095 36.000 0.00 0.00 44.34 4.35
2785 5172 8.034313 ACCAGATGAATTATCTAGTTGCCTTA 57.966 34.615 0.00 0.00 44.34 2.69
2844 5231 9.053840 CATCATATATCAGCAGTTGAAGAAGTT 57.946 33.333 0.00 0.00 39.77 2.66
3049 5436 0.868602 CTGTATACGTTCCGCCGGTG 60.869 60.000 8.42 8.42 0.00 4.94
3063 5450 1.211709 CGGTGCAACGGGGAAAATC 59.788 57.895 18.51 0.00 38.12 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.892374 TGCATGTCAGTACTCCATTCG 58.108 47.619 0.00 0.00 0.00 3.34
154 155 5.438761 ACCTCACAGTATTTGAAAAGTGC 57.561 39.130 0.00 0.00 0.00 4.40
156 157 5.594317 AGCAACCTCACAGTATTTGAAAAGT 59.406 36.000 0.00 0.00 0.00 2.66
168 319 1.002468 CAAACCGAAGCAACCTCACAG 60.002 52.381 0.00 0.00 0.00 3.66
174 325 2.729491 GCGCAAACCGAAGCAACC 60.729 61.111 0.30 0.00 40.02 3.77
200 351 5.124936 CCTCCGGTGAAAAAGGTATAAAAGG 59.875 44.000 4.76 0.00 0.00 3.11
203 354 4.011698 GCCTCCGGTGAAAAAGGTATAAA 58.988 43.478 4.76 0.00 0.00 1.40
204 355 3.264964 AGCCTCCGGTGAAAAAGGTATAA 59.735 43.478 4.76 0.00 0.00 0.98
206 357 1.633945 AGCCTCCGGTGAAAAAGGTAT 59.366 47.619 4.76 0.00 0.00 2.73
279 431 6.015180 AGCAAAACTGAATTCCATACACATGT 60.015 34.615 2.27 0.00 0.00 3.21
280 432 6.392354 AGCAAAACTGAATTCCATACACATG 58.608 36.000 2.27 0.00 0.00 3.21
283 435 7.062255 GCTTTAGCAAAACTGAATTCCATACAC 59.938 37.037 2.27 0.00 41.59 2.90
286 438 6.321717 CGCTTTAGCAAAACTGAATTCCATA 58.678 36.000 2.27 0.00 42.21 2.74
289 441 3.364920 GCGCTTTAGCAAAACTGAATTCC 59.635 43.478 0.00 0.00 42.21 3.01
290 442 3.980775 TGCGCTTTAGCAAAACTGAATTC 59.019 39.130 9.73 0.00 45.06 2.17
307 459 3.173540 TGGCACATTTAGATGCGCT 57.826 47.368 9.73 0.00 43.02 5.92
337 489 1.375268 GCCGGCCTGAGATATGCTC 60.375 63.158 18.11 0.00 44.21 4.26
338 490 2.746359 GCCGGCCTGAGATATGCT 59.254 61.111 18.11 0.00 0.00 3.79
339 491 2.359230 GGCCGGCCTGAGATATGC 60.359 66.667 38.76 7.31 0.00 3.14
340 492 2.047844 CGGCCGGCCTGAGATATG 60.048 66.667 41.01 20.75 0.00 1.78
341 493 3.314331 CCGGCCGGCCTGAGATAT 61.314 66.667 41.01 0.00 0.00 1.63
377 529 4.502431 CCTGGATTTTTAGCACCGGTTTTT 60.502 41.667 2.97 0.00 0.00 1.94
378 530 3.006430 CCTGGATTTTTAGCACCGGTTTT 59.994 43.478 2.97 0.00 0.00 2.43
379 531 2.560981 CCTGGATTTTTAGCACCGGTTT 59.439 45.455 2.97 0.00 0.00 3.27
380 532 2.167662 CCTGGATTTTTAGCACCGGTT 58.832 47.619 2.97 0.00 0.00 4.44
381 533 1.074889 ACCTGGATTTTTAGCACCGGT 59.925 47.619 0.00 0.00 0.00 5.28
382 534 1.834188 ACCTGGATTTTTAGCACCGG 58.166 50.000 0.00 0.00 0.00 5.28
383 535 2.817258 TGAACCTGGATTTTTAGCACCG 59.183 45.455 0.00 0.00 0.00 4.94
384 536 4.809673 CTTGAACCTGGATTTTTAGCACC 58.190 43.478 0.00 0.00 0.00 5.01
385 537 4.237724 GCTTGAACCTGGATTTTTAGCAC 58.762 43.478 0.00 0.00 0.00 4.40
386 538 3.258123 GGCTTGAACCTGGATTTTTAGCA 59.742 43.478 0.00 0.00 0.00 3.49
387 539 3.368427 GGGCTTGAACCTGGATTTTTAGC 60.368 47.826 0.00 1.39 0.00 3.09
388 540 3.119495 CGGGCTTGAACCTGGATTTTTAG 60.119 47.826 0.00 0.00 31.89 1.85
389 541 2.823154 CGGGCTTGAACCTGGATTTTTA 59.177 45.455 0.00 0.00 31.89 1.52
390 542 1.618343 CGGGCTTGAACCTGGATTTTT 59.382 47.619 0.00 0.00 31.89 1.94
391 543 1.256812 CGGGCTTGAACCTGGATTTT 58.743 50.000 0.00 0.00 31.89 1.82
392 544 2.961424 CGGGCTTGAACCTGGATTT 58.039 52.632 0.00 0.00 31.89 2.17
393 545 4.743018 CGGGCTTGAACCTGGATT 57.257 55.556 0.00 0.00 31.89 3.01
412 564 4.820744 CCCGATGGTTGGGCTGGG 62.821 72.222 0.00 0.00 40.47 4.45
418 570 0.834612 TTAGTAGGCCCGATGGTTGG 59.165 55.000 0.00 0.00 0.00 3.77
419 571 2.702592 TTTAGTAGGCCCGATGGTTG 57.297 50.000 0.00 0.00 0.00 3.77
420 572 2.224209 CGATTTAGTAGGCCCGATGGTT 60.224 50.000 0.00 0.00 0.00 3.67
421 573 1.343465 CGATTTAGTAGGCCCGATGGT 59.657 52.381 0.00 0.00 0.00 3.55
422 574 1.337823 CCGATTTAGTAGGCCCGATGG 60.338 57.143 0.00 0.00 0.00 3.51
423 575 1.337823 CCCGATTTAGTAGGCCCGATG 60.338 57.143 0.00 0.00 0.00 3.84
424 576 0.974383 CCCGATTTAGTAGGCCCGAT 59.026 55.000 0.00 0.00 0.00 4.18
425 577 0.397535 ACCCGATTTAGTAGGCCCGA 60.398 55.000 0.00 0.00 0.00 5.14
426 578 1.331214 TACCCGATTTAGTAGGCCCG 58.669 55.000 0.00 0.00 0.00 6.13
427 579 2.901839 TCATACCCGATTTAGTAGGCCC 59.098 50.000 0.00 0.00 0.00 5.80
428 580 3.616802 GCTCATACCCGATTTAGTAGGCC 60.617 52.174 0.00 0.00 0.00 5.19
429 581 3.586892 GCTCATACCCGATTTAGTAGGC 58.413 50.000 0.00 0.00 0.00 3.93
430 582 3.056035 GGGCTCATACCCGATTTAGTAGG 60.056 52.174 0.00 0.00 40.98 3.18
431 583 4.189639 GGGCTCATACCCGATTTAGTAG 57.810 50.000 0.00 0.00 40.98 2.57
443 595 4.603946 GTCGGGGCGGGCTCATAC 62.604 72.222 1.21 0.00 0.00 2.39
444 596 2.725127 ATAGTCGGGGCGGGCTCATA 62.725 60.000 1.21 0.00 0.00 2.15
445 597 4.853142 TAGTCGGGGCGGGCTCAT 62.853 66.667 1.21 0.00 0.00 2.90
446 598 4.853142 ATAGTCGGGGCGGGCTCA 62.853 66.667 1.21 0.00 0.00 4.26
447 599 4.301027 CATAGTCGGGGCGGGCTC 62.301 72.222 0.26 0.00 0.00 4.70
454 606 3.315191 CACAATTTTAGCCATAGTCGGGG 59.685 47.826 0.00 0.00 0.00 5.73
455 607 3.945285 ACACAATTTTAGCCATAGTCGGG 59.055 43.478 0.00 0.00 0.00 5.14
456 608 5.560966 AACACAATTTTAGCCATAGTCGG 57.439 39.130 0.00 0.00 0.00 4.79
457 609 7.271223 CAGAAAACACAATTTTAGCCATAGTCG 59.729 37.037 0.00 0.00 0.00 4.18
458 610 7.062255 GCAGAAAACACAATTTTAGCCATAGTC 59.938 37.037 0.00 0.00 0.00 2.59
459 611 6.868339 GCAGAAAACACAATTTTAGCCATAGT 59.132 34.615 0.00 0.00 0.00 2.12
460 612 6.867816 TGCAGAAAACACAATTTTAGCCATAG 59.132 34.615 0.00 0.00 0.00 2.23
461 613 6.753180 TGCAGAAAACACAATTTTAGCCATA 58.247 32.000 0.00 0.00 0.00 2.74
462 614 5.609423 TGCAGAAAACACAATTTTAGCCAT 58.391 33.333 0.00 0.00 0.00 4.40
463 615 5.016051 TGCAGAAAACACAATTTTAGCCA 57.984 34.783 0.00 0.00 0.00 4.75
464 616 4.448732 CCTGCAGAAAACACAATTTTAGCC 59.551 41.667 17.39 0.00 0.00 3.93
465 617 5.175673 GTCCTGCAGAAAACACAATTTTAGC 59.824 40.000 17.39 0.00 0.00 3.09
466 618 6.418819 CAGTCCTGCAGAAAACACAATTTTAG 59.581 38.462 17.39 0.00 0.00 1.85
467 619 6.096141 TCAGTCCTGCAGAAAACACAATTTTA 59.904 34.615 17.39 0.00 0.00 1.52
468 620 5.105392 TCAGTCCTGCAGAAAACACAATTTT 60.105 36.000 17.39 0.00 0.00 1.82
469 621 4.402155 TCAGTCCTGCAGAAAACACAATTT 59.598 37.500 17.39 0.00 0.00 1.82
470 622 3.953612 TCAGTCCTGCAGAAAACACAATT 59.046 39.130 17.39 0.00 0.00 2.32
471 623 3.554934 TCAGTCCTGCAGAAAACACAAT 58.445 40.909 17.39 0.00 0.00 2.71
472 624 2.945008 CTCAGTCCTGCAGAAAACACAA 59.055 45.455 17.39 0.00 0.00 3.33
473 625 2.564771 CTCAGTCCTGCAGAAAACACA 58.435 47.619 17.39 0.60 0.00 3.72
474 626 1.265365 GCTCAGTCCTGCAGAAAACAC 59.735 52.381 17.39 3.51 0.00 3.32
475 627 1.597742 GCTCAGTCCTGCAGAAAACA 58.402 50.000 17.39 0.00 0.00 2.83
476 628 0.877743 GGCTCAGTCCTGCAGAAAAC 59.122 55.000 17.39 10.43 0.00 2.43
477 629 0.767375 AGGCTCAGTCCTGCAGAAAA 59.233 50.000 17.39 0.00 34.56 2.29
478 630 0.035881 CAGGCTCAGTCCTGCAGAAA 59.964 55.000 17.39 0.00 46.11 2.52
479 631 1.675801 CAGGCTCAGTCCTGCAGAA 59.324 57.895 17.39 0.00 46.11 3.02
480 632 3.385469 CAGGCTCAGTCCTGCAGA 58.615 61.111 17.39 0.00 46.11 4.26
487 639 3.453070 GATCGGGCCAGGCTCAGTC 62.453 68.421 13.26 4.48 0.00 3.51
488 640 3.474570 GATCGGGCCAGGCTCAGT 61.475 66.667 13.26 0.00 0.00 3.41
489 641 3.160047 AGATCGGGCCAGGCTCAG 61.160 66.667 13.26 4.30 0.00 3.35
490 642 3.473647 CAGATCGGGCCAGGCTCA 61.474 66.667 13.26 0.00 0.00 4.26
491 643 4.925861 GCAGATCGGGCCAGGCTC 62.926 72.222 12.43 6.22 0.00 4.70
499 651 4.873129 CACGACGGGCAGATCGGG 62.873 72.222 0.00 6.16 42.67 5.14
501 653 4.498520 AGCACGACGGGCAGATCG 62.499 66.667 26.14 0.00 43.97 3.69
502 654 2.583593 GAGCACGACGGGCAGATC 60.584 66.667 26.14 9.66 0.00 2.75
503 655 2.244117 ATTGAGCACGACGGGCAGAT 62.244 55.000 26.14 11.79 0.00 2.90
504 656 2.449031 AATTGAGCACGACGGGCAGA 62.449 55.000 26.14 9.77 0.00 4.26
505 657 1.577328 AAATTGAGCACGACGGGCAG 61.577 55.000 26.14 0.00 0.00 4.85
506 658 1.573829 GAAATTGAGCACGACGGGCA 61.574 55.000 26.14 3.46 0.00 5.36
507 659 1.134694 GAAATTGAGCACGACGGGC 59.865 57.895 15.88 15.88 0.00 6.13
508 660 0.953471 TGGAAATTGAGCACGACGGG 60.953 55.000 0.00 0.00 0.00 5.28
509 661 0.443869 CTGGAAATTGAGCACGACGG 59.556 55.000 0.00 0.00 0.00 4.79
510 662 0.443869 CCTGGAAATTGAGCACGACG 59.556 55.000 0.00 0.00 0.00 5.12
511 663 0.169009 GCCTGGAAATTGAGCACGAC 59.831 55.000 0.00 0.00 0.00 4.34
512 664 0.960364 GGCCTGGAAATTGAGCACGA 60.960 55.000 0.00 0.00 0.00 4.35
513 665 1.508088 GGCCTGGAAATTGAGCACG 59.492 57.895 0.00 0.00 0.00 5.34
514 666 1.893062 GGGCCTGGAAATTGAGCAC 59.107 57.895 0.84 0.00 0.00 4.40
515 667 1.678635 CGGGCCTGGAAATTGAGCA 60.679 57.895 2.57 0.00 0.00 4.26
516 668 1.378514 TCGGGCCTGGAAATTGAGC 60.379 57.895 12.87 0.00 0.00 4.26
517 669 1.379642 GCTCGGGCCTGGAAATTGAG 61.380 60.000 12.87 0.12 0.00 3.02
518 670 1.378514 GCTCGGGCCTGGAAATTGA 60.379 57.895 12.87 0.00 0.00 2.57
519 671 3.200522 GCTCGGGCCTGGAAATTG 58.799 61.111 12.87 0.00 0.00 2.32
537 689 4.082523 AGTGTGCCATCGGACCGG 62.083 66.667 15.25 0.00 0.00 5.28
538 690 2.509336 GAGTGTGCCATCGGACCG 60.509 66.667 7.84 7.84 0.00 4.79
539 691 2.509336 CGAGTGTGCCATCGGACC 60.509 66.667 0.00 0.00 35.33 4.46
543 695 4.457496 AGCCCGAGTGTGCCATCG 62.457 66.667 0.00 0.00 38.65 3.84
544 696 2.512515 GAGCCCGAGTGTGCCATC 60.513 66.667 0.00 0.00 0.00 3.51
545 697 3.320879 CTGAGCCCGAGTGTGCCAT 62.321 63.158 0.00 0.00 0.00 4.40
546 698 4.007644 CTGAGCCCGAGTGTGCCA 62.008 66.667 0.00 0.00 0.00 4.92
558 710 2.472909 CGAAAATCCCGGGCTGAGC 61.473 63.158 18.49 3.81 0.00 4.26
559 711 1.819632 CCGAAAATCCCGGGCTGAG 60.820 63.158 18.49 4.48 43.05 3.35
560 712 2.270850 CCGAAAATCCCGGGCTGA 59.729 61.111 18.49 0.00 43.05 4.26
565 717 2.512974 CCGACCCGAAAATCCCGG 60.513 66.667 0.00 0.00 46.10 5.73
566 718 2.512974 CCCGACCCGAAAATCCCG 60.513 66.667 0.00 0.00 0.00 5.14
567 719 1.450848 GACCCGACCCGAAAATCCC 60.451 63.158 0.00 0.00 0.00 3.85
568 720 1.812507 CGACCCGACCCGAAAATCC 60.813 63.158 0.00 0.00 0.00 3.01
569 721 1.812507 CCGACCCGACCCGAAAATC 60.813 63.158 0.00 0.00 0.00 2.17
570 722 2.266689 CCGACCCGACCCGAAAAT 59.733 61.111 0.00 0.00 0.00 1.82
571 723 3.225069 GACCGACCCGACCCGAAAA 62.225 63.158 0.00 0.00 0.00 2.29
572 724 3.683937 GACCGACCCGACCCGAAA 61.684 66.667 0.00 0.00 0.00 3.46
606 758 4.404691 GCTATACCTGGCCATGGC 57.595 61.111 29.47 29.47 41.06 4.40
612 764 6.483640 GCATAATACTTATGGCTATACCTGGC 59.516 42.308 8.51 0.00 42.53 4.85
613 765 7.564793 TGCATAATACTTATGGCTATACCTGG 58.435 38.462 8.51 0.00 42.53 4.45
614 766 9.618890 AATGCATAATACTTATGGCTATACCTG 57.381 33.333 0.00 0.00 42.53 4.00
621 773 9.573166 TGACTTAAATGCATAATACTTATGGCT 57.427 29.630 0.00 0.00 42.53 4.75
647 799 1.139989 CGCGAAGATCAACGGCATAT 58.860 50.000 0.00 0.00 0.00 1.78
652 804 0.249073 ATCTCCGCGAAGATCAACGG 60.249 55.000 8.23 10.47 46.97 4.44
660 812 1.413767 CCACACGAATCTCCGCGAAG 61.414 60.000 8.23 0.00 0.00 3.79
664 816 0.804933 GTACCCACACGAATCTCCGC 60.805 60.000 0.00 0.00 0.00 5.54
706 858 6.320164 AGTTACTACAGATCTAAGTGAGCCAG 59.680 42.308 16.51 0.83 0.00 4.85
798 1098 6.494893 TGTTTGCACGAATCTTAGCTTAAT 57.505 33.333 0.00 0.00 0.00 1.40
802 1102 5.376854 AAATGTTTGCACGAATCTTAGCT 57.623 34.783 0.00 0.00 0.00 3.32
844 1144 5.405269 GCACATCTAAACAACCCAATCAAAC 59.595 40.000 0.00 0.00 0.00 2.93
853 1153 2.790433 TCAGGGCACATCTAAACAACC 58.210 47.619 0.00 0.00 0.00 3.77
864 1164 0.038166 GTTCAGGGAATCAGGGCACA 59.962 55.000 0.00 0.00 0.00 4.57
865 1165 0.038166 TGTTCAGGGAATCAGGGCAC 59.962 55.000 0.00 0.00 0.00 5.01
867 1167 0.620556 TCTGTTCAGGGAATCAGGGC 59.379 55.000 0.00 0.00 0.00 5.19
868 1168 2.619074 GGTTCTGTTCAGGGAATCAGGG 60.619 54.545 0.00 0.00 0.00 4.45
869 1169 2.040278 TGGTTCTGTTCAGGGAATCAGG 59.960 50.000 0.00 0.00 30.36 3.86
870 1170 3.423539 TGGTTCTGTTCAGGGAATCAG 57.576 47.619 0.00 0.00 30.36 2.90
871 1171 3.498481 CCTTGGTTCTGTTCAGGGAATCA 60.498 47.826 0.00 0.00 32.62 2.57
873 1173 2.716424 TCCTTGGTTCTGTTCAGGGAAT 59.284 45.455 0.00 0.00 36.42 3.01
874 1174 2.131854 TCCTTGGTTCTGTTCAGGGAA 58.868 47.619 0.00 0.00 36.42 3.97
875 1175 1.814429 TCCTTGGTTCTGTTCAGGGA 58.186 50.000 0.00 0.00 36.91 4.20
912 1978 0.110056 CCGACAGAAGTGCACATTGC 60.110 55.000 21.04 4.88 45.29 3.56
913 1979 0.518636 CCCGACAGAAGTGCACATTG 59.481 55.000 21.04 15.71 0.00 2.82
938 2004 0.310854 CACCCTGTCCGTTTTCTTGC 59.689 55.000 0.00 0.00 0.00 4.01
990 2057 1.026718 GGGAGGCCATCACACTTTCG 61.027 60.000 5.01 0.00 0.00 3.46
1724 2791 1.215647 GACTCCAGCAGGTACCGTG 59.784 63.158 6.18 6.62 35.89 4.94
1725 2792 1.982938 GGACTCCAGCAGGTACCGT 60.983 63.158 6.18 0.00 35.89 4.83
1832 2899 2.029844 GACTCCCACTTGCACTCGC 61.030 63.158 0.00 0.00 39.24 5.03
1833 2900 1.734477 CGACTCCCACTTGCACTCG 60.734 63.158 0.00 0.00 0.00 4.18
1835 2902 2.140792 ACCGACTCCCACTTGCACT 61.141 57.895 0.00 0.00 0.00 4.40
2146 3213 3.431922 TCCGAATAAGGCGTTCTACAG 57.568 47.619 0.00 0.00 0.00 2.74
2148 3215 3.059800 GCAATCCGAATAAGGCGTTCTAC 60.060 47.826 0.00 0.00 0.00 2.59
2157 3224 1.665679 ACGCACAGCAATCCGAATAAG 59.334 47.619 0.00 0.00 0.00 1.73
2213 3297 4.141459 CCCCTCTAGTAGAAACCCAAATCC 60.141 50.000 0.64 0.00 0.00 3.01
2228 3319 1.153349 GCGGTCTTTGCCCCTCTAG 60.153 63.158 0.00 0.00 0.00 2.43
2229 3320 1.612442 AGCGGTCTTTGCCCCTCTA 60.612 57.895 0.00 0.00 0.00 2.43
2230 3321 2.930562 AGCGGTCTTTGCCCCTCT 60.931 61.111 0.00 0.00 0.00 3.69
2231 3322 2.436824 GAGCGGTCTTTGCCCCTC 60.437 66.667 7.51 0.00 0.00 4.30
2232 3323 2.930562 AGAGCGGTCTTTGCCCCT 60.931 61.111 12.24 0.00 0.00 4.79
2233 3324 2.747855 CAGAGCGGTCTTTGCCCC 60.748 66.667 15.83 0.00 0.00 5.80
2234 3325 2.032681 ACAGAGCGGTCTTTGCCC 59.967 61.111 15.83 0.00 0.00 5.36
2300 3391 2.007608 GATACCGGCACTTTCTGAACC 58.992 52.381 0.00 0.00 0.00 3.62
2350 3441 1.094073 CACACTGCATCTGCCCTAGC 61.094 60.000 0.00 0.00 41.18 3.42
2371 3980 1.431845 GAAAACCGCATAAGCCGGG 59.568 57.895 2.18 0.00 38.29 5.73
2383 3992 2.507407 TCATGTGCCCTAGGAAAACC 57.493 50.000 11.48 0.00 0.00 3.27
2386 3995 3.269381 AGGAAATCATGTGCCCTAGGAAA 59.731 43.478 11.48 0.00 0.00 3.13
2387 3996 2.852449 AGGAAATCATGTGCCCTAGGAA 59.148 45.455 11.48 0.00 0.00 3.36
2388 3997 2.439507 GAGGAAATCATGTGCCCTAGGA 59.560 50.000 11.48 0.00 0.00 2.94
2390 3999 2.487934 CGAGGAAATCATGTGCCCTAG 58.512 52.381 0.00 0.00 0.00 3.02
2391 4000 1.475034 GCGAGGAAATCATGTGCCCTA 60.475 52.381 0.00 0.00 0.00 3.53
2393 4002 1.031571 TGCGAGGAAATCATGTGCCC 61.032 55.000 0.00 0.00 0.00 5.36
2412 4620 1.892474 CGGATTTGGTTCCATGTGGTT 59.108 47.619 0.00 0.00 35.34 3.67
2448 4656 2.627945 CGTTGCTCACCAGCCTTATTA 58.372 47.619 0.00 0.00 46.26 0.98
2449 4657 1.453155 CGTTGCTCACCAGCCTTATT 58.547 50.000 0.00 0.00 46.26 1.40
2462 4670 1.374758 GCTGTGTCCTAGCGTTGCT 60.375 57.895 0.00 0.00 43.41 3.91
2517 4725 3.517500 TCTGCCATATCTGTGTTGTGGTA 59.482 43.478 0.00 0.00 32.56 3.25
2535 4770 3.858247 ACCGGTATTGTCTAACTTCTGC 58.142 45.455 4.49 0.00 0.00 4.26
2554 4789 3.187637 TGTGTCTGCTTTTATTGCGTACC 59.812 43.478 0.00 0.00 0.00 3.34
2582 4843 1.678101 AGGCTGTTTGTGACTGAAAGC 59.322 47.619 0.00 0.00 37.60 3.51
2647 4913 7.604164 TCTTATTGTGAAACTTCTTAGCCTCAG 59.396 37.037 0.00 0.00 38.04 3.35
2653 4919 7.519002 CCCGTTCTTATTGTGAAACTTCTTAG 58.481 38.462 0.00 0.00 38.04 2.18
2654 4920 6.072893 GCCCGTTCTTATTGTGAAACTTCTTA 60.073 38.462 0.00 0.00 38.04 2.10
2655 4921 5.278315 GCCCGTTCTTATTGTGAAACTTCTT 60.278 40.000 0.00 0.00 38.04 2.52
2657 4923 4.023536 TGCCCGTTCTTATTGTGAAACTTC 60.024 41.667 0.00 0.00 38.04 3.01
2692 4960 3.503748 GCCCTTGGATGTACATAATCTGC 59.496 47.826 8.71 4.32 0.00 4.26
2741 5128 5.046663 TCTGGTTGCCCTTGAAAAATATTCC 60.047 40.000 0.00 0.00 0.00 3.01
2742 5129 6.036577 TCTGGTTGCCCTTGAAAAATATTC 57.963 37.500 0.00 0.00 0.00 1.75
2743 5130 6.213195 TCATCTGGTTGCCCTTGAAAAATATT 59.787 34.615 0.00 0.00 0.00 1.28
2744 5131 5.721000 TCATCTGGTTGCCCTTGAAAAATAT 59.279 36.000 0.00 0.00 0.00 1.28
2745 5132 5.083122 TCATCTGGTTGCCCTTGAAAAATA 58.917 37.500 0.00 0.00 0.00 1.40
2746 5133 3.903090 TCATCTGGTTGCCCTTGAAAAAT 59.097 39.130 0.00 0.00 0.00 1.82
2747 5134 3.303938 TCATCTGGTTGCCCTTGAAAAA 58.696 40.909 0.00 0.00 0.00 1.94
2748 5135 2.956132 TCATCTGGTTGCCCTTGAAAA 58.044 42.857 0.00 0.00 0.00 2.29
2749 5136 2.673775 TCATCTGGTTGCCCTTGAAA 57.326 45.000 0.00 0.00 0.00 2.69
2750 5137 2.673775 TTCATCTGGTTGCCCTTGAA 57.326 45.000 0.00 0.00 0.00 2.69
2751 5138 2.905415 ATTCATCTGGTTGCCCTTGA 57.095 45.000 0.00 0.00 0.00 3.02
2752 5139 4.891756 AGATAATTCATCTGGTTGCCCTTG 59.108 41.667 0.00 0.00 42.69 3.61
2753 5140 5.134725 AGATAATTCATCTGGTTGCCCTT 57.865 39.130 0.00 0.00 42.69 3.95
2754 5141 4.803329 AGATAATTCATCTGGTTGCCCT 57.197 40.909 0.00 0.00 42.69 5.19
2777 5164 9.860898 ATGTGAAGAAAAATATTCTAAGGCAAC 57.139 29.630 0.00 0.00 0.00 4.17
2860 5247 2.932855 TTGGACCACGTAATTGACCA 57.067 45.000 0.00 0.00 0.00 4.02
2861 5248 2.095415 GCTTTGGACCACGTAATTGACC 60.095 50.000 0.00 0.00 0.00 4.02
2887 5274 4.202524 TGGTCTACTGTTGTAAAGGGCATT 60.203 41.667 0.00 0.00 0.00 3.56
2924 5311 9.696917 CAGAAGGCTGTAAAATTAGTTGAAAAT 57.303 29.630 0.00 0.00 37.37 1.82
2948 5335 3.001414 CCTTCACATGAGCAAGAGACAG 58.999 50.000 0.00 0.00 0.00 3.51
3049 5436 1.611491 TGTTGAGATTTTCCCCGTTGC 59.389 47.619 0.00 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.