Multiple sequence alignment - TraesCS3D01G006600

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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 TraesCS3D01G006600 chr3D 100.000 2493 0 0 1 2493 2307673 2310165 0.000000e+00 4604
1 TraesCS3D01G006600 chr3B 91.385 1834 142 12 666 2490 4555674 4557500 0.000000e+00 2497
2 TraesCS3D01G006600 chr3B 86.634 404 50 3 1 401 4555183 4555585 6.330000e-121 444
3 TraesCS3D01G006600 chr3A 82.030 946 137 20 1565 2490 1711741 1710809 0.000000e+00 774
4 TraesCS3D01G006600 chr3A 89.516 620 54 7 924 1538 1712351 1711738 0.000000e+00 774
5 TraesCS3D01G006600 chr3A 87.500 184 20 1 668 851 1712799 1712619 2.510000e-50 209


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 TraesCS3D01G006600 chr3D 2307673 2310165 2492 False 4604.000000 4604 100.000000 1 2493 1 chr3D.!!$F1 2492
1 TraesCS3D01G006600 chr3B 4555183 4557500 2317 False 1470.500000 2497 89.009500 1 2490 2 chr3B.!!$F1 2489
2 TraesCS3D01G006600 chr3A 1710809 1712799 1990 True 585.666667 774 86.348667 668 2490 3 chr3A.!!$R1 1822

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
651 683 0.031178 GAAATAATGCAGGCGCCCAG 59.969 55.0 26.15 18.21 37.32 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1848 2089 0.378257 CGGATGCGAACAAATGAGGG 59.622 55.0 0.0 0.0 0.0 4.3 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
32 33 4.157656 TCACGGATCAAAAATAGCCCAAAG 59.842 41.667 0.00 0.00 0.00 2.77
63 64 2.432444 CCGTTAATGGACTCAAAGCCA 58.568 47.619 8.10 0.00 38.78 4.75
67 68 5.448632 CCGTTAATGGACTCAAAGCCATAAC 60.449 44.000 8.10 0.00 43.85 1.89
87 88 3.943967 GCCAAAAATGGCGCGAAA 58.056 50.000 12.10 0.00 45.79 3.46
109 111 2.862512 CAACACATGCCGTTAATGGAC 58.137 47.619 18.31 9.26 0.00 4.02
118 120 1.135517 CCGTTAATGGACCAAAAGGCG 60.136 52.381 8.10 0.00 0.00 5.52
122 124 1.175983 AATGGACCAAAAGGCGCGAA 61.176 50.000 12.10 0.00 0.00 4.70
152 156 0.391661 ATGCCCTAGACGCAACACAG 60.392 55.000 8.31 0.00 40.22 3.66
153 157 1.004918 GCCCTAGACGCAACACAGT 60.005 57.895 0.00 0.00 0.00 3.55
156 160 0.039437 CCTAGACGCAACACAGTCGT 60.039 55.000 0.00 0.00 41.86 4.34
164 168 2.411031 CGCAACACAGTCGTTAATGGAC 60.411 50.000 0.00 0.00 34.62 4.02
166 170 2.074547 ACACAGTCGTTAATGGACCG 57.925 50.000 6.13 0.25 34.97 4.79
193 197 3.187842 GTGTGAAGGTCAATAAACGGTCC 59.812 47.826 0.00 0.00 0.00 4.46
199 203 1.728425 GTCAATAAACGGTCCGGACAC 59.272 52.381 34.40 22.34 0.00 3.67
205 209 0.882927 AACGGTCCGGACACAACATG 60.883 55.000 34.40 16.67 0.00 3.21
208 212 0.953960 GGTCCGGACACAACATGGAC 60.954 60.000 34.40 10.52 46.58 4.02
212 216 1.593196 CGGACACAACATGGACAGTT 58.407 50.000 0.00 0.00 0.00 3.16
232 236 5.029474 AGTTAATGGGCCAAAATACACCAT 58.971 37.500 11.89 0.00 43.39 3.55
234 238 2.612285 TGGGCCAAAATACACCATGA 57.388 45.000 2.13 0.00 0.00 3.07
236 240 1.136891 GGGCCAAAATACACCATGAGC 59.863 52.381 4.39 0.00 0.00 4.26
241 245 3.129287 CCAAAATACACCATGAGCCAGAC 59.871 47.826 0.00 0.00 0.00 3.51
260 264 0.603707 CATGGCCAAGACACACGACT 60.604 55.000 10.96 0.00 0.00 4.18
262 266 1.961277 GGCCAAGACACACGACTGG 60.961 63.158 0.00 0.00 0.00 4.00
264 268 1.961277 CCAAGACACACGACTGGCC 60.961 63.158 0.00 0.00 0.00 5.36
341 345 4.205792 GTCTTAAACGGATCGGAATACACG 59.794 45.833 7.35 0.00 0.00 4.49
350 354 1.134907 TCGGAATACACGAAAGGCCTC 60.135 52.381 5.23 0.00 37.42 4.70
355 359 4.201920 GGAATACACGAAAGGCCTCAAATC 60.202 45.833 5.23 1.32 0.00 2.17
371 375 1.029947 AATCGCCCGGAAACATCACC 61.030 55.000 0.73 0.00 0.00 4.02
376 380 3.177600 CGGAAACATCACCGGCTG 58.822 61.111 0.00 0.00 44.59 4.85
386 390 1.378514 CACCGGCTGTAATTGGCCT 60.379 57.895 3.32 0.00 45.57 5.19
387 391 1.378514 ACCGGCTGTAATTGGCCTG 60.379 57.895 3.32 11.07 45.57 4.85
394 398 3.243068 GGCTGTAATTGGCCTGAAATACG 60.243 47.826 3.32 0.00 44.48 3.06
401 405 1.557371 TGGCCTGAAATACGTCATGGA 59.443 47.619 3.32 0.00 0.00 3.41
410 442 5.408299 TGAAATACGTCATGGACAGTGAAAG 59.592 40.000 0.00 0.00 32.09 2.62
436 468 6.730960 TCGAAAGCAAGTACGGATAAAAAT 57.269 33.333 0.00 0.00 0.00 1.82
444 476 7.222224 AGCAAGTACGGATAAAAATAGAACGAG 59.778 37.037 0.00 0.00 0.00 4.18
447 479 8.218338 AGTACGGATAAAAATAGAACGAGAGA 57.782 34.615 0.00 0.00 0.00 3.10
449 481 6.860080 ACGGATAAAAATAGAACGAGAGACA 58.140 36.000 0.00 0.00 0.00 3.41
451 483 6.750501 CGGATAAAAATAGAACGAGAGACACA 59.249 38.462 0.00 0.00 0.00 3.72
452 484 7.253684 CGGATAAAAATAGAACGAGAGACACAC 60.254 40.741 0.00 0.00 0.00 3.82
454 486 9.088512 GATAAAAATAGAACGAGAGACACACAT 57.911 33.333 0.00 0.00 0.00 3.21
456 488 5.644977 AATAGAACGAGAGACACACATGA 57.355 39.130 0.00 0.00 0.00 3.07
457 489 3.567576 AGAACGAGAGACACACATGAG 57.432 47.619 0.00 0.00 0.00 2.90
458 490 1.989165 GAACGAGAGACACACATGAGC 59.011 52.381 0.00 0.00 0.00 4.26
459 491 0.244994 ACGAGAGACACACATGAGCC 59.755 55.000 0.00 0.00 0.00 4.70
460 492 0.244721 CGAGAGACACACATGAGCCA 59.755 55.000 0.00 0.00 0.00 4.75
461 493 1.337167 CGAGAGACACACATGAGCCAA 60.337 52.381 0.00 0.00 0.00 4.52
462 494 2.771089 GAGAGACACACATGAGCCAAA 58.229 47.619 0.00 0.00 0.00 3.28
463 495 3.141398 GAGAGACACACATGAGCCAAAA 58.859 45.455 0.00 0.00 0.00 2.44
464 496 3.144506 AGAGACACACATGAGCCAAAAG 58.855 45.455 0.00 0.00 0.00 2.27
465 497 2.880890 GAGACACACATGAGCCAAAAGT 59.119 45.455 0.00 0.00 0.00 2.66
466 498 2.880890 AGACACACATGAGCCAAAAGTC 59.119 45.455 0.00 0.00 0.00 3.01
467 499 2.880890 GACACACATGAGCCAAAAGTCT 59.119 45.455 0.00 0.00 0.00 3.24
468 500 2.880890 ACACACATGAGCCAAAAGTCTC 59.119 45.455 0.00 0.00 0.00 3.36
469 501 2.880268 CACACATGAGCCAAAAGTCTCA 59.120 45.455 0.00 0.00 42.72 3.27
470 502 3.316029 CACACATGAGCCAAAAGTCTCAA 59.684 43.478 0.00 0.00 41.96 3.02
471 503 4.022589 CACACATGAGCCAAAAGTCTCAAT 60.023 41.667 0.00 0.00 41.96 2.57
472 504 4.022589 ACACATGAGCCAAAAGTCTCAATG 60.023 41.667 0.00 0.00 41.96 2.82
473 505 3.508793 ACATGAGCCAAAAGTCTCAATGG 59.491 43.478 0.00 0.00 41.96 3.16
474 506 2.517959 TGAGCCAAAAGTCTCAATGGG 58.482 47.619 0.00 0.00 36.50 4.00
475 507 1.203287 GAGCCAAAAGTCTCAATGGGC 59.797 52.381 0.00 0.00 40.18 5.36
476 508 1.203100 AGCCAAAAGTCTCAATGGGCT 60.203 47.619 0.00 0.00 44.92 5.19
477 509 2.446435 GCCAAAAGTCTCAATGGGCTA 58.554 47.619 0.00 0.00 37.00 3.93
478 510 2.424956 GCCAAAAGTCTCAATGGGCTAG 59.575 50.000 0.00 0.00 37.00 3.42
479 511 3.873801 GCCAAAAGTCTCAATGGGCTAGA 60.874 47.826 0.00 0.00 37.00 2.43
480 512 4.335416 CCAAAAGTCTCAATGGGCTAGAA 58.665 43.478 0.00 0.00 0.00 2.10
481 513 4.156739 CCAAAAGTCTCAATGGGCTAGAAC 59.843 45.833 0.00 0.00 0.00 3.01
482 514 3.636153 AAGTCTCAATGGGCTAGAACC 57.364 47.619 0.00 0.00 0.00 3.62
483 515 2.551270 AGTCTCAATGGGCTAGAACCA 58.449 47.619 8.79 8.79 43.22 3.67
492 524 4.271696 TGGGCTAGAACCATATTCGATG 57.728 45.455 2.73 0.00 31.83 3.84
493 525 3.007940 TGGGCTAGAACCATATTCGATGG 59.992 47.826 1.90 1.90 44.54 3.51
494 526 3.003480 GGCTAGAACCATATTCGATGGC 58.997 50.000 3.39 0.00 42.82 4.40
495 527 3.003480 GCTAGAACCATATTCGATGGCC 58.997 50.000 3.39 0.00 42.82 5.36
496 528 2.568623 AGAACCATATTCGATGGCCC 57.431 50.000 0.00 0.00 42.82 5.80
497 529 1.774254 AGAACCATATTCGATGGCCCA 59.226 47.619 0.00 0.00 42.82 5.36
498 530 1.880027 GAACCATATTCGATGGCCCAC 59.120 52.381 0.00 0.00 42.82 4.61
499 531 0.250295 ACCATATTCGATGGCCCACG 60.250 55.000 11.59 11.59 42.82 4.94
500 532 0.250295 CCATATTCGATGGCCCACGT 60.250 55.000 16.10 3.50 31.75 4.49
501 533 0.867746 CATATTCGATGGCCCACGTG 59.132 55.000 9.08 9.08 0.00 4.49
502 534 0.468226 ATATTCGATGGCCCACGTGT 59.532 50.000 15.65 0.00 0.00 4.49
503 535 0.179094 TATTCGATGGCCCACGTGTC 60.179 55.000 15.65 5.64 0.00 3.67
504 536 3.801850 TATTCGATGGCCCACGTGTCG 62.802 57.143 15.65 16.24 0.00 4.35
505 537 4.735132 CGATGGCCCACGTGTCGT 62.735 66.667 15.65 5.05 42.36 4.34
506 538 2.813908 GATGGCCCACGTGTCGTC 60.814 66.667 15.65 10.48 38.32 4.20
507 539 4.735132 ATGGCCCACGTGTCGTCG 62.735 66.667 15.65 0.00 38.32 5.12
509 541 4.955774 GGCCCACGTGTCGTCGTT 62.956 66.667 15.65 0.00 42.27 3.85
510 542 3.400590 GCCCACGTGTCGTCGTTC 61.401 66.667 15.65 0.00 42.27 3.95
511 543 2.026445 CCCACGTGTCGTCGTTCA 59.974 61.111 15.65 0.00 42.27 3.18
512 544 1.372499 CCCACGTGTCGTCGTTCAT 60.372 57.895 15.65 0.00 42.27 2.57
513 545 0.109643 CCCACGTGTCGTCGTTCATA 60.110 55.000 15.65 0.00 42.27 2.15
514 546 1.256652 CCACGTGTCGTCGTTCATAG 58.743 55.000 15.65 0.00 42.27 2.23
515 547 1.256652 CACGTGTCGTCGTTCATAGG 58.743 55.000 7.58 0.00 42.27 2.57
516 548 0.455633 ACGTGTCGTCGTTCATAGGC 60.456 55.000 0.00 0.00 41.37 3.93
517 549 1.461317 CGTGTCGTCGTTCATAGGCG 61.461 60.000 0.00 0.00 0.00 5.52
518 550 1.515519 TGTCGTCGTTCATAGGCGC 60.516 57.895 0.00 0.00 0.00 6.53
519 551 1.515519 GTCGTCGTTCATAGGCGCA 60.516 57.895 10.83 0.00 0.00 6.09
520 552 0.870307 GTCGTCGTTCATAGGCGCAT 60.870 55.000 10.83 3.98 0.00 4.73
521 553 0.664224 TCGTCGTTCATAGGCGCATA 59.336 50.000 10.83 7.12 0.00 3.14
522 554 1.268625 TCGTCGTTCATAGGCGCATAT 59.731 47.619 9.11 9.11 0.00 1.78
523 555 1.649171 CGTCGTTCATAGGCGCATATC 59.351 52.381 12.35 0.13 0.00 1.63
524 556 2.672714 GTCGTTCATAGGCGCATATCA 58.327 47.619 12.35 0.00 0.00 2.15
525 557 3.254060 GTCGTTCATAGGCGCATATCAT 58.746 45.455 12.35 0.00 0.00 2.45
526 558 3.304559 GTCGTTCATAGGCGCATATCATC 59.695 47.826 12.35 0.00 0.00 2.92
527 559 2.604914 CGTTCATAGGCGCATATCATCC 59.395 50.000 12.35 0.00 0.00 3.51
528 560 2.584492 TCATAGGCGCATATCATCCG 57.416 50.000 12.35 0.55 0.00 4.18
529 561 1.824852 TCATAGGCGCATATCATCCGT 59.175 47.619 12.35 0.00 0.00 4.69
530 562 2.233676 TCATAGGCGCATATCATCCGTT 59.766 45.455 12.35 0.00 0.00 4.44
531 563 2.078849 TAGGCGCATATCATCCGTTG 57.921 50.000 10.83 0.00 0.00 4.10
532 564 0.392706 AGGCGCATATCATCCGTTGA 59.607 50.000 10.83 0.00 39.12 3.18
533 565 0.792640 GGCGCATATCATCCGTTGAG 59.207 55.000 10.83 0.00 37.89 3.02
534 566 1.502231 GCGCATATCATCCGTTGAGT 58.498 50.000 0.30 0.00 37.89 3.41
535 567 1.193203 GCGCATATCATCCGTTGAGTG 59.807 52.381 0.30 0.00 37.89 3.51
536 568 1.794701 CGCATATCATCCGTTGAGTGG 59.205 52.381 0.00 0.00 37.89 4.00
537 569 1.532868 GCATATCATCCGTTGAGTGGC 59.467 52.381 0.00 0.00 37.89 5.01
538 570 1.794701 CATATCATCCGTTGAGTGGCG 59.205 52.381 0.00 0.00 37.89 5.69
539 571 1.107945 TATCATCCGTTGAGTGGCGA 58.892 50.000 0.00 0.00 37.89 5.54
540 572 0.460284 ATCATCCGTTGAGTGGCGAC 60.460 55.000 0.00 0.00 37.89 5.19
541 573 2.100631 CATCCGTTGAGTGGCGACC 61.101 63.158 0.00 0.00 0.00 4.79
542 574 3.310860 ATCCGTTGAGTGGCGACCC 62.311 63.158 0.00 0.00 0.00 4.46
543 575 4.003788 CCGTTGAGTGGCGACCCT 62.004 66.667 0.00 0.00 0.00 4.34
544 576 2.030562 CGTTGAGTGGCGACCCTT 59.969 61.111 0.00 0.00 0.00 3.95
545 577 2.027625 CGTTGAGTGGCGACCCTTC 61.028 63.158 0.00 0.00 0.00 3.46
546 578 1.671379 GTTGAGTGGCGACCCTTCC 60.671 63.158 0.00 0.00 0.00 3.46
547 579 2.144078 TTGAGTGGCGACCCTTCCA 61.144 57.895 0.00 0.00 0.00 3.53
548 580 1.701031 TTGAGTGGCGACCCTTCCAA 61.701 55.000 0.00 0.00 33.57 3.53
549 581 1.671379 GAGTGGCGACCCTTCCAAC 60.671 63.158 0.00 0.00 33.57 3.77
550 582 3.047877 GTGGCGACCCTTCCAACG 61.048 66.667 0.00 0.00 33.57 4.10
551 583 3.235481 TGGCGACCCTTCCAACGA 61.235 61.111 0.00 0.00 0.00 3.85
552 584 2.031465 GGCGACCCTTCCAACGAA 59.969 61.111 0.00 0.00 0.00 3.85
553 585 2.033194 GGCGACCCTTCCAACGAAG 61.033 63.158 0.00 0.00 44.47 3.79
561 593 3.195041 TTCCAACGAAGAGCTGACG 57.805 52.632 0.00 0.00 0.00 4.35
562 594 0.944311 TTCCAACGAAGAGCTGACGC 60.944 55.000 0.00 0.00 0.00 5.19
563 595 2.720758 CCAACGAAGAGCTGACGCG 61.721 63.158 3.53 3.53 42.32 6.01
564 596 2.016704 CAACGAAGAGCTGACGCGT 61.017 57.895 13.85 13.85 42.32 6.01
565 597 2.016704 AACGAAGAGCTGACGCGTG 61.017 57.895 20.70 3.71 42.32 5.34
566 598 3.175240 CGAAGAGCTGACGCGTGG 61.175 66.667 20.70 10.85 42.32 4.94
567 599 2.049063 GAAGAGCTGACGCGTGGT 60.049 61.111 20.70 9.24 42.32 4.16
568 600 1.664965 GAAGAGCTGACGCGTGGTT 60.665 57.895 20.70 7.26 42.32 3.67
569 601 0.388134 GAAGAGCTGACGCGTGGTTA 60.388 55.000 20.70 0.00 42.32 2.85
570 602 0.032952 AAGAGCTGACGCGTGGTTAA 59.967 50.000 20.70 0.00 42.32 2.01
571 603 0.388649 AGAGCTGACGCGTGGTTAAG 60.389 55.000 20.70 7.32 42.32 1.85
572 604 0.666577 GAGCTGACGCGTGGTTAAGT 60.667 55.000 20.70 0.00 42.32 2.24
573 605 0.249741 AGCTGACGCGTGGTTAAGTT 60.250 50.000 20.70 0.89 42.32 2.66
574 606 1.000060 AGCTGACGCGTGGTTAAGTTA 60.000 47.619 20.70 0.00 42.32 2.24
575 607 1.997606 GCTGACGCGTGGTTAAGTTAT 59.002 47.619 20.70 0.00 0.00 1.89
576 608 2.028883 GCTGACGCGTGGTTAAGTTATC 59.971 50.000 20.70 0.00 0.00 1.75
577 609 2.252747 TGACGCGTGGTTAAGTTATCG 58.747 47.619 20.70 0.00 0.00 2.92
578 610 2.095314 TGACGCGTGGTTAAGTTATCGA 60.095 45.455 20.70 0.00 0.00 3.59
579 611 2.916716 GACGCGTGGTTAAGTTATCGAA 59.083 45.455 20.70 0.00 0.00 3.71
580 612 2.663119 ACGCGTGGTTAAGTTATCGAAC 59.337 45.455 12.93 0.00 35.64 3.95
581 613 2.284063 CGCGTGGTTAAGTTATCGAACG 60.284 50.000 0.00 10.91 40.76 3.95
582 614 2.916716 GCGTGGTTAAGTTATCGAACGA 59.083 45.455 16.09 0.00 40.76 3.85
583 615 3.001365 GCGTGGTTAAGTTATCGAACGAG 60.001 47.826 16.09 0.00 40.76 4.18
584 616 4.406069 CGTGGTTAAGTTATCGAACGAGA 58.594 43.478 2.94 0.00 40.76 4.04
585 617 4.853196 CGTGGTTAAGTTATCGAACGAGAA 59.147 41.667 2.94 1.54 40.76 2.87
586 618 5.003214 CGTGGTTAAGTTATCGAACGAGAAG 59.997 44.000 4.57 0.00 40.76 2.85
587 619 4.860907 TGGTTAAGTTATCGAACGAGAAGC 59.139 41.667 4.57 1.50 40.76 3.86
588 620 4.267214 GGTTAAGTTATCGAACGAGAAGCC 59.733 45.833 4.57 0.00 40.76 4.35
589 621 2.190325 AGTTATCGAACGAGAAGCCG 57.810 50.000 4.57 0.00 40.76 5.52
590 622 1.741706 AGTTATCGAACGAGAAGCCGA 59.258 47.619 4.57 0.00 40.76 5.54
591 623 1.844962 GTTATCGAACGAGAAGCCGAC 59.155 52.381 4.57 0.00 33.69 4.79
592 624 1.089112 TATCGAACGAGAAGCCGACA 58.911 50.000 2.94 0.00 33.69 4.35
593 625 0.456312 ATCGAACGAGAAGCCGACAC 60.456 55.000 2.94 0.00 33.69 3.67
594 626 2.426183 CGAACGAGAAGCCGACACG 61.426 63.158 0.00 0.00 0.00 4.49
595 627 1.371389 GAACGAGAAGCCGACACGT 60.371 57.895 0.00 0.00 38.81 4.49
596 628 1.606350 GAACGAGAAGCCGACACGTG 61.606 60.000 15.48 15.48 37.28 4.49
597 629 2.805353 CGAGAAGCCGACACGTGG 60.805 66.667 21.57 2.78 0.00 4.94
598 630 2.649034 GAGAAGCCGACACGTGGA 59.351 61.111 21.57 0.00 0.00 4.02
599 631 1.444553 GAGAAGCCGACACGTGGAG 60.445 63.158 21.57 12.85 0.00 3.86
600 632 2.432628 GAAGCCGACACGTGGAGG 60.433 66.667 21.57 21.99 0.00 4.30
601 633 2.915659 AAGCCGACACGTGGAGGA 60.916 61.111 28.25 0.00 0.00 3.71
602 634 2.227089 GAAGCCGACACGTGGAGGAT 62.227 60.000 28.25 22.12 0.00 3.24
603 635 2.202756 GCCGACACGTGGAGGATC 60.203 66.667 28.25 13.18 0.00 3.36
604 636 2.102357 CCGACACGTGGAGGATCG 59.898 66.667 21.57 18.39 34.37 3.69
605 637 2.697761 CCGACACGTGGAGGATCGT 61.698 63.158 21.57 0.00 40.99 3.73
606 638 1.226323 CGACACGTGGAGGATCGTC 60.226 63.158 21.57 6.88 38.23 4.20
607 639 1.880894 GACACGTGGAGGATCGTCA 59.119 57.895 21.57 1.20 38.23 4.35
608 640 0.456221 GACACGTGGAGGATCGTCAT 59.544 55.000 21.57 0.00 38.23 3.06
609 641 0.895530 ACACGTGGAGGATCGTCATT 59.104 50.000 21.57 0.00 38.23 2.57
610 642 1.275291 ACACGTGGAGGATCGTCATTT 59.725 47.619 21.57 0.00 38.23 2.32
611 643 1.660607 CACGTGGAGGATCGTCATTTG 59.339 52.381 16.71 6.26 38.23 2.32
612 644 1.548719 ACGTGGAGGATCGTCATTTGA 59.451 47.619 16.71 0.00 35.30 2.69
613 645 2.168521 ACGTGGAGGATCGTCATTTGAT 59.831 45.455 16.71 0.00 35.30 2.57
614 646 2.541346 CGTGGAGGATCGTCATTTGATG 59.459 50.000 16.71 0.00 34.37 3.07
615 647 3.535561 GTGGAGGATCGTCATTTGATGT 58.464 45.455 16.71 0.00 34.37 3.06
616 648 4.693283 GTGGAGGATCGTCATTTGATGTA 58.307 43.478 16.71 0.00 34.37 2.29
617 649 4.508124 GTGGAGGATCGTCATTTGATGTAC 59.492 45.833 16.71 0.00 34.37 2.90
618 650 4.058817 GGAGGATCGTCATTTGATGTACC 58.941 47.826 16.71 5.22 34.37 3.34
619 651 4.442893 GGAGGATCGTCATTTGATGTACCA 60.443 45.833 16.71 0.00 34.37 3.25
620 652 5.296151 AGGATCGTCATTTGATGTACCAT 57.704 39.130 14.82 0.00 33.54 3.55
621 653 5.059161 AGGATCGTCATTTGATGTACCATG 58.941 41.667 14.82 0.00 33.54 3.66
622 654 5.056480 GGATCGTCATTTGATGTACCATGA 58.944 41.667 0.00 0.00 33.00 3.07
623 655 5.702670 GGATCGTCATTTGATGTACCATGAT 59.297 40.000 0.00 0.00 33.00 2.45
624 656 6.873605 GGATCGTCATTTGATGTACCATGATA 59.126 38.462 0.00 0.00 33.00 2.15
625 657 7.387673 GGATCGTCATTTGATGTACCATGATAA 59.612 37.037 0.00 0.00 33.00 1.75
626 658 8.675705 ATCGTCATTTGATGTACCATGATAAA 57.324 30.769 0.00 0.00 33.00 1.40
627 659 8.499403 TCGTCATTTGATGTACCATGATAAAA 57.501 30.769 0.00 0.00 33.00 1.52
628 660 8.951243 TCGTCATTTGATGTACCATGATAAAAA 58.049 29.630 0.00 0.00 33.00 1.94
647 679 3.427161 AAAGAGAAATAATGCAGGCGC 57.573 42.857 0.00 0.00 39.24 6.53
648 680 1.312815 AGAGAAATAATGCAGGCGCC 58.687 50.000 21.89 21.89 37.32 6.53
649 681 0.312102 GAGAAATAATGCAGGCGCCC 59.688 55.000 26.15 9.73 37.32 6.13
650 682 0.395586 AGAAATAATGCAGGCGCCCA 60.396 50.000 26.15 16.30 37.32 5.36
651 683 0.031178 GAAATAATGCAGGCGCCCAG 59.969 55.000 26.15 18.21 37.32 4.45
661 693 3.512516 GCGCCCAGCCACTCATTC 61.513 66.667 0.00 0.00 40.81 2.67
662 694 2.046023 CGCCCAGCCACTCATTCA 60.046 61.111 0.00 0.00 0.00 2.57
663 695 1.452651 CGCCCAGCCACTCATTCAT 60.453 57.895 0.00 0.00 0.00 2.57
664 696 1.442526 CGCCCAGCCACTCATTCATC 61.443 60.000 0.00 0.00 0.00 2.92
698 730 1.739035 CGTGAATCCATGCGGTGTACT 60.739 52.381 0.00 0.00 0.00 2.73
791 823 8.777413 TCAGTGCATATTGATTTATTGCTAGTC 58.223 33.333 0.00 0.00 0.00 2.59
855 887 6.862209 TGAAAATATATCCCATTAATGCGGC 58.138 36.000 10.11 0.00 0.00 6.53
873 905 3.306818 CGGCGCTCTATAACTAGAAACC 58.693 50.000 7.64 0.00 33.59 3.27
881 913 7.116948 CGCTCTATAACTAGAAACCATCAATGG 59.883 40.741 7.50 7.50 42.25 3.16
883 915 7.224297 TCTATAACTAGAAACCATCAATGGCC 58.776 38.462 8.97 0.00 40.05 5.36
897 929 5.021033 TCAATGGCCGCATTAATTGAAAT 57.979 34.783 10.60 0.00 36.40 2.17
898 930 5.426504 TCAATGGCCGCATTAATTGAAATT 58.573 33.333 10.60 0.00 36.40 1.82
935 1162 0.733909 GATTGTCCTTGCTTTGGCGC 60.734 55.000 0.00 0.00 42.25 6.53
984 1215 8.034804 CCCAAACAATATTCTAAACAGGAAAGG 58.965 37.037 0.00 0.00 0.00 3.11
993 1224 7.812690 TTCTAAACAGGAAAGGTTAAGTTCC 57.187 36.000 4.89 4.89 43.17 3.62
995 1226 7.348033 TCTAAACAGGAAAGGTTAAGTTCCAA 58.652 34.615 12.69 0.00 44.94 3.53
1078 1309 5.880054 ACTTTCGACCATTCATAAACCTG 57.120 39.130 0.00 0.00 0.00 4.00
1086 1317 6.207691 ACCATTCATAAACCTGCAACATAC 57.792 37.500 0.00 0.00 0.00 2.39
1088 1319 4.955925 TTCATAAACCTGCAACATACGG 57.044 40.909 0.00 0.00 0.00 4.02
1095 1326 2.296692 CTGCAACATACGGCGAGTGC 62.297 60.000 16.62 15.18 41.71 4.40
1133 1364 4.396166 CCAAGGAAGTTAGTATTGCACCTG 59.604 45.833 0.00 0.00 0.00 4.00
1175 1406 6.045072 ACAATTTGCATCATGTCTCCATTT 57.955 33.333 0.00 0.00 0.00 2.32
1252 1484 6.449635 TTCAATGATCCAAGAAATAACCCG 57.550 37.500 0.00 0.00 0.00 5.28
1321 1553 1.305201 GGAAAGACTCAAACACGGCA 58.695 50.000 0.00 0.00 0.00 5.69
1359 1591 4.127171 CACGATAACCCCCAAGTGAATAG 58.873 47.826 0.00 0.00 0.00 1.73
1504 1736 6.037940 CACATGTTGGATAGAACCATTCTCTG 59.962 42.308 0.00 0.00 41.14 3.35
1506 1738 3.845781 TGGATAGAACCATTCTCTGCC 57.154 47.619 0.00 0.00 41.14 4.85
1545 1778 7.275888 TGATCAATAAAGTCTTTGCTGTGTT 57.724 32.000 8.14 0.00 0.00 3.32
1559 1792 2.719798 CTGTGTTTGCACTTTTCTCCG 58.280 47.619 0.00 0.00 45.44 4.63
1574 1807 7.535258 CACTTTTCTCCGTTTCATTTCATACAG 59.465 37.037 0.00 0.00 0.00 2.74
1599 1832 7.122204 AGTTCTTATATAGCCCAAACAACCAAC 59.878 37.037 0.00 0.00 0.00 3.77
1600 1833 6.486056 TCTTATATAGCCCAAACAACCAACA 58.514 36.000 0.00 0.00 0.00 3.33
1673 1910 6.595326 TGTTCTGATCCAATCTTGTACATCAC 59.405 38.462 0.00 0.00 0.00 3.06
1692 1929 5.514274 TCACATCAAAACCAAAGGAAGAC 57.486 39.130 0.00 0.00 0.00 3.01
1800 2041 4.578928 ACCACTCGTTTAGCTTCAACAATT 59.421 37.500 0.00 0.00 0.00 2.32
1834 2075 6.872920 TCATCTTTCTCTAGCTTTCTTCCTC 58.127 40.000 0.00 0.00 0.00 3.71
1848 2089 2.683867 TCTTCCTCCTCGAATCGTTCTC 59.316 50.000 1.52 0.00 0.00 2.87
1853 2094 1.103803 CCTCGAATCGTTCTCCCTCA 58.896 55.000 1.52 0.00 0.00 3.86
1854 2095 1.683917 CCTCGAATCGTTCTCCCTCAT 59.316 52.381 1.52 0.00 0.00 2.90
1855 2096 2.101582 CCTCGAATCGTTCTCCCTCATT 59.898 50.000 1.52 0.00 0.00 2.57
1863 2104 2.151202 GTTCTCCCTCATTTGTTCGCA 58.849 47.619 0.00 0.00 0.00 5.10
1885 2126 3.422204 GGTTGCCTACCATCCCCA 58.578 61.111 0.46 0.00 46.92 4.96
1906 2147 1.191535 CTTCGGGTGGTCTATGGACA 58.808 55.000 11.67 0.00 43.77 4.02
2015 2257 6.130569 ACTTTTGGGAACAGTGGTTATGTTA 58.869 36.000 0.00 0.00 44.54 2.41
2068 2310 2.917713 TGCCCATCACCCTTGTAAAT 57.082 45.000 0.00 0.00 0.00 1.40
2078 2320 7.607991 CCATCACCCTTGTAAATACTGATATCC 59.392 40.741 0.00 0.00 0.00 2.59
2083 2325 6.655003 CCCTTGTAAATACTGATATCCGCAAT 59.345 38.462 0.00 0.00 0.00 3.56
2087 2329 9.772973 TTGTAAATACTGATATCCGCAATAGTT 57.227 29.630 0.00 0.00 0.00 2.24
2088 2330 9.772973 TGTAAATACTGATATCCGCAATAGTTT 57.227 29.630 0.00 0.00 0.00 2.66
2103 2345 5.278957 GCAATAGTTTGGTTGTCATGGAAGT 60.279 40.000 0.00 0.00 33.22 3.01
2165 2407 8.812513 ATTCTTTGGAATCAACATAGTCATCA 57.187 30.769 0.00 0.00 37.61 3.07
2199 2441 2.086869 CCACACGCCAAGAGAATGATT 58.913 47.619 0.00 0.00 0.00 2.57
2216 2458 8.136057 AGAATGATTAGTAACTTGAAGATGCG 57.864 34.615 0.00 0.00 0.00 4.73
2258 2500 3.497482 TCGTATACGAAATTGCGCATG 57.503 42.857 24.97 1.33 46.30 4.06
2266 2508 1.127213 GAAATTGCGCATGCCAAACTG 59.873 47.619 12.75 4.89 41.78 3.16
2338 2591 6.484308 AGGTAAACTTGCATACTAAAACACGT 59.516 34.615 0.00 0.00 0.00 4.49
2345 2598 3.486875 GCATACTAAAACACGTCCATGGC 60.487 47.826 6.96 0.96 0.00 4.40
2347 2600 3.688694 ACTAAAACACGTCCATGGCTA 57.311 42.857 6.96 0.00 0.00 3.93
2438 2691 2.982488 GACCACTCATATCCTCCCCAAT 59.018 50.000 0.00 0.00 0.00 3.16
2444 2697 1.977854 CATATCCTCCCCAATCGTCCA 59.022 52.381 0.00 0.00 0.00 4.02
2467 2720 0.179000 GGACAGCCCGATCATTGTCT 59.821 55.000 12.63 0.00 39.78 3.41
2470 2723 1.153086 AGCCCGATCATTGTCTGGC 60.153 57.895 11.15 11.15 45.56 4.85
2471 2724 1.451927 GCCCGATCATTGTCTGGCA 60.452 57.895 13.02 0.00 44.85 4.92
2472 2725 0.820891 GCCCGATCATTGTCTGGCAT 60.821 55.000 13.02 0.00 44.85 4.40
2490 2743 4.648762 TGGCATAGGAGAGAGAAGAGAAAG 59.351 45.833 0.00 0.00 0.00 2.62
2491 2744 4.039124 GGCATAGGAGAGAGAAGAGAAAGG 59.961 50.000 0.00 0.00 0.00 3.11
2492 2745 4.501400 GCATAGGAGAGAGAAGAGAAAGGC 60.501 50.000 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 3.689649 GCTATTTTTGATCCGTGACACCT 59.310 43.478 0.00 0.00 0.00 4.00
10 11 4.423732 CTTTGGGCTATTTTTGATCCGTG 58.576 43.478 0.00 0.00 0.00 4.94
41 42 1.202031 GCTTTGAGTCCATTAACGGCG 60.202 52.381 4.80 4.80 0.00 6.46
44 45 5.569413 GTTATGGCTTTGAGTCCATTAACG 58.431 41.667 0.00 0.00 42.62 3.18
89 90 2.415357 GGTCCATTAACGGCATGTGTTG 60.415 50.000 13.57 1.11 0.00 3.33
99 100 1.731098 GCGCCTTTTGGTCCATTAACG 60.731 52.381 0.00 0.00 42.99 3.18
109 111 2.181525 CCCATTCGCGCCTTTTGG 59.818 61.111 0.00 3.94 44.18 3.28
118 120 1.368345 GGCATTTTTGGCCCATTCGC 61.368 55.000 0.00 0.00 45.87 4.70
152 156 2.414138 CACCTTTCGGTCCATTAACGAC 59.586 50.000 0.00 0.00 43.24 4.34
153 157 2.037511 ACACCTTTCGGTCCATTAACGA 59.962 45.455 0.00 0.00 43.24 3.85
156 160 3.773418 TCACACCTTTCGGTCCATTAA 57.227 42.857 0.00 0.00 43.24 1.40
164 168 1.961793 TTGACCTTCACACCTTTCGG 58.038 50.000 0.00 0.00 0.00 4.30
166 170 5.449304 CGTTTATTGACCTTCACACCTTTC 58.551 41.667 0.00 0.00 0.00 2.62
174 178 2.613474 CCGGACCGTTTATTGACCTTCA 60.613 50.000 13.94 0.00 0.00 3.02
178 182 1.338011 TGTCCGGACCGTTTATTGACC 60.338 52.381 31.19 2.28 0.00 4.02
180 184 1.343789 TGTGTCCGGACCGTTTATTGA 59.656 47.619 31.19 6.76 0.00 2.57
182 186 2.145536 GTTGTGTCCGGACCGTTTATT 58.854 47.619 31.19 0.00 0.00 1.40
184 188 0.463204 TGTTGTGTCCGGACCGTTTA 59.537 50.000 31.19 10.01 0.00 2.01
193 197 1.593196 AACTGTCCATGTTGTGTCCG 58.407 50.000 0.00 0.00 0.00 4.79
199 203 2.166254 GGCCCATTAACTGTCCATGTTG 59.834 50.000 0.00 0.00 0.00 3.33
205 209 4.464597 TGTATTTTGGCCCATTAACTGTCC 59.535 41.667 0.00 0.00 0.00 4.02
208 212 4.221703 TGGTGTATTTTGGCCCATTAACTG 59.778 41.667 0.00 0.00 0.00 3.16
212 216 4.614475 TCATGGTGTATTTTGGCCCATTA 58.386 39.130 0.00 0.00 33.70 1.90
236 240 0.250858 TGTGTCTTGGCCATGTCTGG 60.251 55.000 17.54 0.01 46.17 3.86
241 245 0.603707 AGTCGTGTGTCTTGGCCATG 60.604 55.000 6.09 9.88 0.00 3.66
264 268 4.155310 GGAATATTTCCGCCCATTTACG 57.845 45.455 0.00 0.00 40.59 3.18
300 304 5.871396 AAGACCCATAGTGTCGTTGATAT 57.129 39.130 0.00 0.00 37.80 1.63
304 308 4.090930 CGTTTAAGACCCATAGTGTCGTTG 59.909 45.833 0.00 0.00 37.80 4.10
309 313 4.441079 CGATCCGTTTAAGACCCATAGTGT 60.441 45.833 0.00 0.00 0.00 3.55
350 354 0.808125 TGATGTTTCCGGGCGATTTG 59.192 50.000 0.00 0.00 0.00 2.32
355 359 3.496131 CGGTGATGTTTCCGGGCG 61.496 66.667 0.00 0.00 42.61 6.13
373 377 3.377172 ACGTATTTCAGGCCAATTACAGC 59.623 43.478 5.01 0.00 0.00 4.40
376 380 5.505654 CCATGACGTATTTCAGGCCAATTAC 60.506 44.000 5.01 1.73 0.00 1.89
386 390 4.529109 TCACTGTCCATGACGTATTTCA 57.471 40.909 0.00 0.00 34.95 2.69
387 391 5.163854 CCTTTCACTGTCCATGACGTATTTC 60.164 44.000 0.00 0.00 34.95 2.17
394 398 2.079925 GAGCCTTTCACTGTCCATGAC 58.920 52.381 0.00 0.00 0.00 3.06
401 405 1.230324 GCTTTCGAGCCTTTCACTGT 58.770 50.000 0.00 0.00 0.00 3.55
410 442 0.389426 TCCGTACTTGCTTTCGAGCC 60.389 55.000 0.00 0.00 0.00 4.70
427 459 7.544566 TGTGTGTCTCTCGTTCTATTTTTATCC 59.455 37.037 0.00 0.00 0.00 2.59
429 461 8.873830 CATGTGTGTCTCTCGTTCTATTTTTAT 58.126 33.333 0.00 0.00 0.00 1.40
431 463 6.929049 TCATGTGTGTCTCTCGTTCTATTTTT 59.071 34.615 0.00 0.00 0.00 1.94
436 468 3.119814 GCTCATGTGTGTCTCTCGTTCTA 60.120 47.826 0.00 0.00 0.00 2.10
444 476 2.880890 ACTTTTGGCTCATGTGTGTCTC 59.119 45.455 0.00 0.00 0.00 3.36
447 479 2.936202 AGACTTTTGGCTCATGTGTGT 58.064 42.857 0.00 0.00 24.84 3.72
456 488 1.203100 AGCCCATTGAGACTTTTGGCT 60.203 47.619 0.00 0.00 43.29 4.75
457 489 1.260544 AGCCCATTGAGACTTTTGGC 58.739 50.000 0.00 0.00 37.68 4.52
458 490 3.955471 TCTAGCCCATTGAGACTTTTGG 58.045 45.455 0.00 0.00 0.00 3.28
459 491 4.156739 GGTTCTAGCCCATTGAGACTTTTG 59.843 45.833 0.00 0.00 0.00 2.44
460 492 4.202567 TGGTTCTAGCCCATTGAGACTTTT 60.203 41.667 0.00 0.00 0.00 2.27
461 493 3.330701 TGGTTCTAGCCCATTGAGACTTT 59.669 43.478 0.00 0.00 0.00 2.66
462 494 2.912956 TGGTTCTAGCCCATTGAGACTT 59.087 45.455 0.00 0.00 0.00 3.01
463 495 2.551270 TGGTTCTAGCCCATTGAGACT 58.449 47.619 0.00 0.00 0.00 3.24
464 496 3.567478 ATGGTTCTAGCCCATTGAGAC 57.433 47.619 7.70 0.00 39.73 3.36
465 497 5.511373 CGAATATGGTTCTAGCCCATTGAGA 60.511 44.000 16.13 2.64 42.63 3.27
466 498 4.692625 CGAATATGGTTCTAGCCCATTGAG 59.307 45.833 16.13 5.65 42.63 3.02
467 499 4.346709 TCGAATATGGTTCTAGCCCATTGA 59.653 41.667 16.13 8.91 42.63 2.57
468 500 4.641396 TCGAATATGGTTCTAGCCCATTG 58.359 43.478 16.13 7.29 42.63 2.82
469 501 4.974645 TCGAATATGGTTCTAGCCCATT 57.025 40.909 16.13 3.72 42.63 3.16
470 502 4.323792 CCATCGAATATGGTTCTAGCCCAT 60.324 45.833 15.48 15.48 44.76 4.00
471 503 3.007940 CCATCGAATATGGTTCTAGCCCA 59.992 47.826 3.75 3.75 34.56 5.36
472 504 3.600388 CCATCGAATATGGTTCTAGCCC 58.400 50.000 0.00 0.00 34.56 5.19
473 505 3.003480 GCCATCGAATATGGTTCTAGCC 58.997 50.000 5.48 0.00 41.17 3.93
474 506 3.003480 GGCCATCGAATATGGTTCTAGC 58.997 50.000 0.00 0.00 41.17 3.42
475 507 3.007940 TGGGCCATCGAATATGGTTCTAG 59.992 47.826 0.00 0.00 41.17 2.43
476 508 2.976185 TGGGCCATCGAATATGGTTCTA 59.024 45.455 0.00 0.00 41.17 2.10
477 509 1.774254 TGGGCCATCGAATATGGTTCT 59.226 47.619 0.00 0.00 41.17 3.01
478 510 1.880027 GTGGGCCATCGAATATGGTTC 59.120 52.381 10.70 0.00 41.17 3.62
479 511 1.813862 CGTGGGCCATCGAATATGGTT 60.814 52.381 10.70 0.00 41.17 3.67
480 512 0.250295 CGTGGGCCATCGAATATGGT 60.250 55.000 10.70 0.00 41.17 3.55
481 513 0.250295 ACGTGGGCCATCGAATATGG 60.250 55.000 27.18 0.00 41.99 2.74
482 514 0.867746 CACGTGGGCCATCGAATATG 59.132 55.000 27.18 15.25 0.00 1.78
483 515 0.468226 ACACGTGGGCCATCGAATAT 59.532 50.000 27.18 8.84 0.00 1.28
484 516 0.179094 GACACGTGGGCCATCGAATA 60.179 55.000 27.18 0.00 0.00 1.75
485 517 1.449601 GACACGTGGGCCATCGAAT 60.450 57.895 27.18 17.34 0.00 3.34
486 518 2.047655 GACACGTGGGCCATCGAA 60.048 61.111 27.18 0.00 0.00 3.71
487 519 4.429212 CGACACGTGGGCCATCGA 62.429 66.667 27.18 0.00 34.77 3.59
488 520 4.735132 ACGACACGTGGGCCATCG 62.735 66.667 22.05 22.05 39.18 3.84
489 521 2.813908 GACGACACGTGGGCCATC 60.814 66.667 21.57 6.77 41.37 3.51
490 522 4.735132 CGACGACACGTGGGCCAT 62.735 66.667 21.57 0.00 41.37 4.40
492 524 4.955774 AACGACGACACGTGGGCC 62.956 66.667 21.57 7.62 45.83 5.80
493 525 3.400590 GAACGACGACACGTGGGC 61.401 66.667 21.57 10.54 45.83 5.36
494 526 0.109643 TATGAACGACGACACGTGGG 60.110 55.000 21.57 13.77 45.83 4.61
495 527 1.256652 CTATGAACGACGACACGTGG 58.743 55.000 21.57 5.28 45.83 4.94
496 528 1.256652 CCTATGAACGACGACACGTG 58.743 55.000 15.48 15.48 45.83 4.49
498 530 1.461317 CGCCTATGAACGACGACACG 61.461 60.000 0.00 0.00 39.31 4.49
499 531 1.740043 GCGCCTATGAACGACGACAC 61.740 60.000 0.00 0.00 0.00 3.67
500 532 1.515519 GCGCCTATGAACGACGACA 60.516 57.895 0.00 1.56 0.00 4.35
501 533 0.870307 ATGCGCCTATGAACGACGAC 60.870 55.000 4.18 0.00 0.00 4.34
502 534 0.664224 TATGCGCCTATGAACGACGA 59.336 50.000 4.18 0.00 0.00 4.20
503 535 1.649171 GATATGCGCCTATGAACGACG 59.351 52.381 10.09 0.00 0.00 5.12
504 536 2.672714 TGATATGCGCCTATGAACGAC 58.327 47.619 10.09 0.00 0.00 4.34
505 537 3.511699 GATGATATGCGCCTATGAACGA 58.488 45.455 10.09 0.00 0.00 3.85
506 538 2.604914 GGATGATATGCGCCTATGAACG 59.395 50.000 10.09 0.00 0.00 3.95
507 539 2.604914 CGGATGATATGCGCCTATGAAC 59.395 50.000 10.09 0.50 37.28 3.18
508 540 2.892374 CGGATGATATGCGCCTATGAA 58.108 47.619 10.09 0.00 37.28 2.57
509 541 2.584492 CGGATGATATGCGCCTATGA 57.416 50.000 10.09 1.82 37.28 2.15
517 549 1.532868 GCCACTCAACGGATGATATGC 59.467 52.381 0.00 0.00 37.44 3.14
518 550 1.794701 CGCCACTCAACGGATGATATG 59.205 52.381 0.00 0.00 37.44 1.78
519 551 1.686587 TCGCCACTCAACGGATGATAT 59.313 47.619 0.00 0.00 37.44 1.63
520 552 1.107945 TCGCCACTCAACGGATGATA 58.892 50.000 0.00 0.00 37.44 2.15
521 553 0.460284 GTCGCCACTCAACGGATGAT 60.460 55.000 0.00 0.00 37.44 2.45
522 554 1.080093 GTCGCCACTCAACGGATGA 60.080 57.895 0.00 0.00 36.38 2.92
523 555 2.100631 GGTCGCCACTCAACGGATG 61.101 63.158 0.00 0.00 0.00 3.51
524 556 2.264794 GGTCGCCACTCAACGGAT 59.735 61.111 0.00 0.00 0.00 4.18
525 557 3.998672 GGGTCGCCACTCAACGGA 61.999 66.667 0.00 0.00 0.00 4.69
526 558 3.530910 AAGGGTCGCCACTCAACGG 62.531 63.158 0.00 0.00 0.00 4.44
527 559 2.027625 GAAGGGTCGCCACTCAACG 61.028 63.158 0.00 0.00 0.00 4.10
528 560 1.671379 GGAAGGGTCGCCACTCAAC 60.671 63.158 0.00 0.00 0.00 3.18
529 561 1.701031 TTGGAAGGGTCGCCACTCAA 61.701 55.000 0.00 0.00 33.01 3.02
530 562 2.144078 TTGGAAGGGTCGCCACTCA 61.144 57.895 0.00 0.00 33.01 3.41
531 563 1.671379 GTTGGAAGGGTCGCCACTC 60.671 63.158 0.00 0.00 33.01 3.51
532 564 2.430367 GTTGGAAGGGTCGCCACT 59.570 61.111 0.00 0.00 33.01 4.00
533 565 2.999739 TTCGTTGGAAGGGTCGCCAC 63.000 60.000 0.00 0.00 33.01 5.01
534 566 2.725203 CTTCGTTGGAAGGGTCGCCA 62.725 60.000 0.00 0.00 44.83 5.69
535 567 2.031465 TTCGTTGGAAGGGTCGCC 59.969 61.111 0.00 0.00 0.00 5.54
536 568 3.562635 CTTCGTTGGAAGGGTCGC 58.437 61.111 0.00 0.00 44.83 5.19
543 575 0.944311 GCGTCAGCTCTTCGTTGGAA 60.944 55.000 0.00 0.00 41.01 3.53
544 576 1.372997 GCGTCAGCTCTTCGTTGGA 60.373 57.895 0.00 0.00 41.01 3.53
545 577 2.720758 CGCGTCAGCTCTTCGTTGG 61.721 63.158 0.00 0.00 42.32 3.77
546 578 2.016704 ACGCGTCAGCTCTTCGTTG 61.017 57.895 5.58 0.00 42.32 4.10
547 579 2.016704 CACGCGTCAGCTCTTCGTT 61.017 57.895 9.86 0.00 42.32 3.85
548 580 2.429236 CACGCGTCAGCTCTTCGT 60.429 61.111 9.86 0.00 42.32 3.85
549 581 3.175240 CCACGCGTCAGCTCTTCG 61.175 66.667 9.86 0.00 42.32 3.79
550 582 0.388134 TAACCACGCGTCAGCTCTTC 60.388 55.000 9.86 0.00 42.32 2.87
551 583 0.032952 TTAACCACGCGTCAGCTCTT 59.967 50.000 9.86 0.00 42.32 2.85
552 584 0.388649 CTTAACCACGCGTCAGCTCT 60.389 55.000 9.86 0.00 42.32 4.09
553 585 0.666577 ACTTAACCACGCGTCAGCTC 60.667 55.000 9.86 0.00 42.32 4.09
554 586 0.249741 AACTTAACCACGCGTCAGCT 60.250 50.000 9.86 0.00 42.32 4.24
555 587 1.421382 TAACTTAACCACGCGTCAGC 58.579 50.000 9.86 0.00 40.74 4.26
556 588 2.278094 CGATAACTTAACCACGCGTCAG 59.722 50.000 9.86 6.50 0.00 3.51
557 589 2.095314 TCGATAACTTAACCACGCGTCA 60.095 45.455 9.86 0.00 0.00 4.35
558 590 2.518949 TCGATAACTTAACCACGCGTC 58.481 47.619 9.86 0.00 0.00 5.19
559 591 2.634982 TCGATAACTTAACCACGCGT 57.365 45.000 5.58 5.58 0.00 6.01
560 592 2.284063 CGTTCGATAACTTAACCACGCG 60.284 50.000 3.53 3.53 33.15 6.01
561 593 2.916716 TCGTTCGATAACTTAACCACGC 59.083 45.455 0.00 0.00 33.15 5.34
562 594 4.406069 TCTCGTTCGATAACTTAACCACG 58.594 43.478 0.00 0.00 33.15 4.94
563 595 5.220172 GCTTCTCGTTCGATAACTTAACCAC 60.220 44.000 0.00 0.00 33.15 4.16
564 596 4.860907 GCTTCTCGTTCGATAACTTAACCA 59.139 41.667 0.00 0.00 33.15 3.67
565 597 4.267214 GGCTTCTCGTTCGATAACTTAACC 59.733 45.833 0.00 0.00 33.15 2.85
566 598 4.027864 CGGCTTCTCGTTCGATAACTTAAC 60.028 45.833 0.00 0.00 33.15 2.01
567 599 4.100529 CGGCTTCTCGTTCGATAACTTAA 58.899 43.478 0.00 0.00 33.15 1.85
568 600 3.374988 TCGGCTTCTCGTTCGATAACTTA 59.625 43.478 0.00 0.00 33.15 2.24
569 601 2.163010 TCGGCTTCTCGTTCGATAACTT 59.837 45.455 0.00 0.00 33.15 2.66
570 602 1.741706 TCGGCTTCTCGTTCGATAACT 59.258 47.619 0.00 0.00 33.15 2.24
571 603 1.844962 GTCGGCTTCTCGTTCGATAAC 59.155 52.381 0.00 0.00 34.13 1.89
572 604 1.469703 TGTCGGCTTCTCGTTCGATAA 59.530 47.619 0.00 0.00 34.13 1.75
573 605 1.089112 TGTCGGCTTCTCGTTCGATA 58.911 50.000 0.00 0.00 34.13 2.92
574 606 0.456312 GTGTCGGCTTCTCGTTCGAT 60.456 55.000 0.00 0.00 34.13 3.59
575 607 1.081641 GTGTCGGCTTCTCGTTCGA 60.082 57.895 0.00 0.00 0.00 3.71
576 608 2.426183 CGTGTCGGCTTCTCGTTCG 61.426 63.158 0.00 0.00 0.00 3.95
577 609 1.371389 ACGTGTCGGCTTCTCGTTC 60.371 57.895 0.00 0.00 32.52 3.95
578 610 1.660575 CACGTGTCGGCTTCTCGTT 60.661 57.895 7.58 0.00 33.82 3.85
579 611 2.050351 CACGTGTCGGCTTCTCGT 60.050 61.111 7.58 0.00 35.87 4.18
580 612 2.805353 CCACGTGTCGGCTTCTCG 60.805 66.667 15.65 0.00 0.00 4.04
581 613 1.444553 CTCCACGTGTCGGCTTCTC 60.445 63.158 15.65 0.00 0.00 2.87
582 614 2.651361 CTCCACGTGTCGGCTTCT 59.349 61.111 15.65 0.00 0.00 2.85
583 615 2.227089 ATCCTCCACGTGTCGGCTTC 62.227 60.000 15.65 0.00 0.00 3.86
584 616 2.227089 GATCCTCCACGTGTCGGCTT 62.227 60.000 15.65 5.25 0.00 4.35
585 617 2.680352 ATCCTCCACGTGTCGGCT 60.680 61.111 15.65 2.82 0.00 5.52
586 618 2.202756 GATCCTCCACGTGTCGGC 60.203 66.667 15.65 0.00 0.00 5.54
587 619 2.102357 CGATCCTCCACGTGTCGG 59.898 66.667 15.65 13.97 0.00 4.79
588 620 1.226323 GACGATCCTCCACGTGTCG 60.226 63.158 19.95 19.95 42.74 4.35
589 621 0.456221 ATGACGATCCTCCACGTGTC 59.544 55.000 15.65 3.82 42.74 3.67
590 622 0.895530 AATGACGATCCTCCACGTGT 59.104 50.000 15.65 0.00 42.74 4.49
591 623 1.660607 CAAATGACGATCCTCCACGTG 59.339 52.381 9.08 9.08 42.74 4.49
592 624 1.548719 TCAAATGACGATCCTCCACGT 59.451 47.619 0.00 0.00 45.32 4.49
593 625 2.293677 TCAAATGACGATCCTCCACG 57.706 50.000 0.00 0.00 0.00 4.94
594 626 3.535561 ACATCAAATGACGATCCTCCAC 58.464 45.455 0.00 0.00 0.00 4.02
595 627 3.912496 ACATCAAATGACGATCCTCCA 57.088 42.857 0.00 0.00 0.00 3.86
596 628 4.058817 GGTACATCAAATGACGATCCTCC 58.941 47.826 0.00 0.00 0.00 4.30
597 629 4.693283 TGGTACATCAAATGACGATCCTC 58.307 43.478 0.00 0.00 0.00 3.71
598 630 4.753516 TGGTACATCAAATGACGATCCT 57.246 40.909 0.00 0.00 0.00 3.24
625 657 4.176271 GCGCCTGCATTATTTCTCTTTTT 58.824 39.130 0.00 0.00 42.15 1.94
626 658 3.429410 GGCGCCTGCATTATTTCTCTTTT 60.429 43.478 22.15 0.00 45.35 2.27
627 659 2.099756 GGCGCCTGCATTATTTCTCTTT 59.900 45.455 22.15 0.00 45.35 2.52
628 660 1.678101 GGCGCCTGCATTATTTCTCTT 59.322 47.619 22.15 0.00 45.35 2.85
629 661 1.312815 GGCGCCTGCATTATTTCTCT 58.687 50.000 22.15 0.00 45.35 3.10
630 662 0.312102 GGGCGCCTGCATTATTTCTC 59.688 55.000 28.56 0.00 45.35 2.87
631 663 0.395586 TGGGCGCCTGCATTATTTCT 60.396 50.000 28.56 0.00 45.35 2.52
632 664 0.031178 CTGGGCGCCTGCATTATTTC 59.969 55.000 28.56 5.64 45.35 2.17
633 665 2.019897 GCTGGGCGCCTGCATTATTT 62.020 55.000 29.91 0.00 45.75 1.40
634 666 2.492773 GCTGGGCGCCTGCATTATT 61.493 57.895 29.91 0.00 45.75 1.40
635 667 2.908940 GCTGGGCGCCTGCATTAT 60.909 61.111 29.91 0.00 45.75 1.28
644 676 3.512516 GAATGAGTGGCTGGGCGC 61.513 66.667 0.00 0.00 38.13 6.53
645 677 1.442526 GATGAATGAGTGGCTGGGCG 61.443 60.000 0.00 0.00 0.00 6.13
646 678 0.394762 TGATGAATGAGTGGCTGGGC 60.395 55.000 0.00 0.00 0.00 5.36
647 679 1.064906 AGTGATGAATGAGTGGCTGGG 60.065 52.381 0.00 0.00 0.00 4.45
648 680 2.414994 AGTGATGAATGAGTGGCTGG 57.585 50.000 0.00 0.00 0.00 4.85
649 681 4.272748 CACATAGTGATGAATGAGTGGCTG 59.727 45.833 0.00 0.00 35.23 4.85
650 682 4.449131 CACATAGTGATGAATGAGTGGCT 58.551 43.478 0.00 0.00 35.23 4.75
651 683 3.562973 CCACATAGTGATGAATGAGTGGC 59.437 47.826 0.00 0.00 38.83 5.01
652 684 5.027293 TCCACATAGTGATGAATGAGTGG 57.973 43.478 0.00 0.00 44.95 4.00
653 685 5.876460 TGTTCCACATAGTGATGAATGAGTG 59.124 40.000 0.00 0.00 35.23 3.51
654 686 5.877012 GTGTTCCACATAGTGATGAATGAGT 59.123 40.000 0.00 0.00 35.23 3.41
655 687 5.006068 CGTGTTCCACATAGTGATGAATGAG 59.994 44.000 0.00 0.00 35.23 2.90
656 688 4.869861 CGTGTTCCACATAGTGATGAATGA 59.130 41.667 0.00 0.00 35.23 2.57
657 689 4.631377 ACGTGTTCCACATAGTGATGAATG 59.369 41.667 0.00 0.00 35.23 2.67
658 690 4.631377 CACGTGTTCCACATAGTGATGAAT 59.369 41.667 7.58 0.00 39.93 2.57
659 691 3.993736 CACGTGTTCCACATAGTGATGAA 59.006 43.478 7.58 0.00 39.93 2.57
660 692 3.257127 TCACGTGTTCCACATAGTGATGA 59.743 43.478 16.51 0.00 40.74 2.92
661 693 3.584834 TCACGTGTTCCACATAGTGATG 58.415 45.455 16.51 0.00 40.74 3.07
662 694 3.953712 TCACGTGTTCCACATAGTGAT 57.046 42.857 16.51 0.00 40.74 3.06
663 695 3.737032 TTCACGTGTTCCACATAGTGA 57.263 42.857 16.51 11.63 42.42 3.41
664 696 3.370978 GGATTCACGTGTTCCACATAGTG 59.629 47.826 25.41 8.35 39.35 2.74
798 830 7.812191 GCGGCCATTGATGATTTGTATATTTAA 59.188 33.333 2.24 0.00 0.00 1.52
805 837 2.373224 TGCGGCCATTGATGATTTGTA 58.627 42.857 2.24 0.00 0.00 2.41
811 843 3.635836 TCAATTAATGCGGCCATTGATGA 59.364 39.130 2.24 0.26 41.58 2.92
821 853 9.874205 AATGGGATATATTTTCAATTAATGCGG 57.126 29.630 0.00 0.00 0.00 5.69
853 885 4.317671 TGGTTTCTAGTTATAGAGCGCC 57.682 45.455 2.29 0.00 39.21 6.53
855 887 7.116948 CCATTGATGGTTTCTAGTTATAGAGCG 59.883 40.741 1.73 0.00 43.05 5.03
873 905 3.979948 TCAATTAATGCGGCCATTGATG 58.020 40.909 2.24 0.00 41.58 3.07
881 913 7.319646 TGGGATATAATTTCAATTAATGCGGC 58.680 34.615 0.00 0.00 34.79 6.53
897 929 6.009589 ACAATCAATGGCGAATGGGATATAA 58.990 36.000 0.00 0.00 0.00 0.98
898 930 5.569355 ACAATCAATGGCGAATGGGATATA 58.431 37.500 0.00 0.00 0.00 0.86
912 944 2.997986 GCCAAAGCAAGGACAATCAATG 59.002 45.455 0.00 0.00 39.53 2.82
935 1162 4.528987 GGAGGGGGCTTTCTAGTTATAGAG 59.471 50.000 0.00 0.00 39.21 2.43
1010 1241 2.625314 AGAAAGGTTGAAGCAAAGGAGC 59.375 45.455 0.00 0.00 0.00 4.70
1078 1309 1.705337 ATGCACTCGCCGTATGTTGC 61.705 55.000 0.00 0.00 37.32 4.17
1086 1317 2.890474 GGTGGTATGCACTCGCCG 60.890 66.667 0.00 0.00 37.32 6.46
1088 1319 3.564027 GCGGTGGTATGCACTCGC 61.564 66.667 0.00 0.00 36.04 5.03
1095 1326 1.656818 CTTGGCAAGGCGGTGGTATG 61.657 60.000 19.55 0.00 0.00 2.39
1133 1364 1.269723 GTAAGAACAAAGCAGGGTGCC 59.730 52.381 0.00 0.00 46.52 5.01
1265 1497 6.295067 GGCCAACTTTGTTCTGTATGGTAAAT 60.295 38.462 0.00 0.00 0.00 1.40
1321 1553 7.389607 GGGTTATCGTGCCTTATACAATTGTAT 59.610 37.037 28.97 28.97 43.15 2.29
1545 1778 4.647424 AATGAAACGGAGAAAAGTGCAA 57.353 36.364 0.00 0.00 0.00 4.08
1574 1807 7.094118 TGTTGGTTGTTTGGGCTATATAAGAAC 60.094 37.037 0.00 0.00 0.00 3.01
1585 1818 3.744238 AAGTATGTTGGTTGTTTGGGC 57.256 42.857 0.00 0.00 0.00 5.36
1599 1832 6.459066 TCAGTCTCCTGTTTGAGAAAGTATG 58.541 40.000 0.00 0.00 42.75 2.39
1600 1833 6.672266 TCAGTCTCCTGTTTGAGAAAGTAT 57.328 37.500 0.00 0.00 42.75 2.12
1642 1875 3.818180 AGATTGGATCAGAACAGGCATC 58.182 45.455 0.00 0.00 0.00 3.91
1643 1876 3.947612 AGATTGGATCAGAACAGGCAT 57.052 42.857 0.00 0.00 0.00 4.40
1644 1877 3.245016 ACAAGATTGGATCAGAACAGGCA 60.245 43.478 0.00 0.00 0.00 4.75
1645 1878 3.350833 ACAAGATTGGATCAGAACAGGC 58.649 45.455 0.00 0.00 0.00 4.85
1646 1879 5.491070 TGTACAAGATTGGATCAGAACAGG 58.509 41.667 0.00 0.00 0.00 4.00
1673 1910 3.857010 GCGGTCTTCCTTTGGTTTTGATG 60.857 47.826 0.00 0.00 0.00 3.07
1692 1929 5.751243 ATAGTTAACCTTTTAGCATGCGG 57.249 39.130 13.01 9.62 0.00 5.69
1781 2022 8.728088 AATAACAATTGTTGAAGCTAAACGAG 57.272 30.769 29.72 0.00 38.90 4.18
1783 2024 8.728088 AGAATAACAATTGTTGAAGCTAAACG 57.272 30.769 29.72 0.00 38.90 3.60
1800 2041 9.950496 AAGCTAGAGAAAGATGAAAGAATAACA 57.050 29.630 0.00 0.00 0.00 2.41
1810 2051 6.127196 GGAGGAAGAAAGCTAGAGAAAGATGA 60.127 42.308 0.00 0.00 0.00 2.92
1834 2075 1.103803 TGAGGGAGAACGATTCGAGG 58.896 55.000 13.95 0.00 34.02 4.63
1848 2089 0.378257 CGGATGCGAACAAATGAGGG 59.622 55.000 0.00 0.00 0.00 4.30
1853 2094 0.525761 CAACCCGGATGCGAACAAAT 59.474 50.000 8.71 0.00 0.00 2.32
1854 2095 1.953017 CAACCCGGATGCGAACAAA 59.047 52.632 8.71 0.00 0.00 2.83
1855 2096 2.622011 GCAACCCGGATGCGAACAA 61.622 57.895 8.71 0.00 33.57 2.83
1885 2126 2.239460 GTCCATAGACCACCCGAAGGT 61.239 57.143 0.00 0.00 41.48 3.50
1989 2231 6.311735 ACATAACCACTGTTCCCAAAAGTAT 58.688 36.000 0.00 0.00 35.87 2.12
2015 2257 6.549736 ACTTGTTTAGCCAGTTCACCTTAATT 59.450 34.615 0.00 0.00 0.00 1.40
2068 2310 6.169557 ACCAAACTATTGCGGATATCAGTA 57.830 37.500 4.83 0.00 35.10 2.74
2078 2320 3.190327 TCCATGACAACCAAACTATTGCG 59.810 43.478 0.00 0.00 35.10 4.85
2083 2325 4.582656 CCAACTTCCATGACAACCAAACTA 59.417 41.667 0.00 0.00 0.00 2.24
2087 2329 2.692557 CACCAACTTCCATGACAACCAA 59.307 45.455 0.00 0.00 0.00 3.67
2088 2330 2.092158 TCACCAACTTCCATGACAACCA 60.092 45.455 0.00 0.00 0.00 3.67
2165 2407 1.694150 CGTGTGGACAGATGGGGATAT 59.306 52.381 0.00 0.00 0.00 1.63
2199 2441 7.862873 CAGATATCACGCATCTTCAAGTTACTA 59.137 37.037 5.32 0.00 30.18 1.82
2395 2648 3.865745 CCGGTTGTAGATGCTCACTTTAG 59.134 47.826 0.00 0.00 0.00 1.85
2467 2720 3.961484 TCTCTTCTCTCTCCTATGCCA 57.039 47.619 0.00 0.00 0.00 4.92
2470 2723 5.200368 GCCTTTCTCTTCTCTCTCCTATG 57.800 47.826 0.00 0.00 0.00 2.23


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

AutoCloner maintained by Alex Coulton.