Multiple sequence alignment - TraesCS4D01G129800

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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 TraesCS4D01G129800 chr4D 100.000 2870 0 0 1 2870 115931434 115934303 0.000000e+00 5301
1 TraesCS4D01G129800 chr4A 95.571 2190 43 19 715 2870 460905032 460902863 0.000000e+00 3458
2 TraesCS4D01G129800 chr4B 95.026 1568 43 15 715 2258 176268126 176266570 0.000000e+00 2431
3 TraesCS4D01G129800 chr4B 97.249 618 13 2 2257 2870 176266409 176265792 0.000000e+00 1044
4 TraesCS4D01G129800 chr3A 93.673 490 29 2 3 491 547186721 547187209 0.000000e+00 732
5 TraesCS4D01G129800 chr5A 92.871 505 27 6 3 506 465287427 465286931 0.000000e+00 725
6 TraesCS4D01G129800 chr5A 88.090 487 49 7 3 483 491957500 491957017 1.150000e-158 569
7 TraesCS4D01G129800 chr7B 91.313 495 35 5 3 491 663841282 663840790 0.000000e+00 669
8 TraesCS4D01G129800 chr7B 90.581 499 41 5 3 495 103460322 103459824 0.000000e+00 656
9 TraesCS4D01G129800 chr6B 91.000 500 34 6 3 492 691140966 691140468 0.000000e+00 664
10 TraesCS4D01G129800 chr5B 90.726 496 40 3 3 492 463946723 463947218 0.000000e+00 656
11 TraesCS4D01G129800 chr7D 89.505 505 40 8 3 497 452260546 452261047 6.750000e-176 627
12 TraesCS4D01G129800 chr3B 88.981 481 41 7 5 480 129714697 129715170 4.120000e-163 584


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 TraesCS4D01G129800 chr4D 115931434 115934303 2869 False 5301.0 5301 100.0000 1 2870 1 chr4D.!!$F1 2869
1 TraesCS4D01G129800 chr4A 460902863 460905032 2169 True 3458.0 3458 95.5710 715 2870 1 chr4A.!!$R1 2155
2 TraesCS4D01G129800 chr4B 176265792 176268126 2334 True 1737.5 2431 96.1375 715 2870 2 chr4B.!!$R1 2155
3 TraesCS4D01G129800 chr7D 452260546 452261047 501 False 627.0 627 89.5050 3 497 1 chr7D.!!$F1 494

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
523 527 0.031178 GGCTGAAGTGTGTGCCAAAG 59.969 55.0 0.0 0.0 44.34 2.77 F
569 573 0.108804 ACGCTGACGGTGGATGTAAG 60.109 55.0 0.0 0.0 46.04 2.34 F
570 574 0.172578 CGCTGACGGTGGATGTAAGA 59.827 55.0 0.0 0.0 34.97 2.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1558 1627 4.380531 TGCAAACAAGACTACAAGAGAGG 58.619 43.478 0.00 0.00 0.00 3.69 R
1569 1638 5.060940 GCCGAAAATAGAATGCAAACAAGAC 59.939 40.000 0.00 0.00 0.00 3.01 R
2307 2556 6.017934 CACACACTGCTGTTGAGTTATAACTT 60.018 38.462 18.96 3.63 39.88 2.66 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
50 51 3.050275 GCCCGTGCTGTCAAGGAC 61.050 66.667 5.84 0.00 43.37 3.85
51 52 2.743718 CCCGTGCTGTCAAGGACT 59.256 61.111 5.84 0.00 43.37 3.85
61 62 3.165875 CTGTCAAGGACTAGACAAGGGA 58.834 50.000 0.00 0.00 43.48 4.20
70 71 4.959839 GGACTAGACAAGGGAAGAATCTCT 59.040 45.833 0.00 0.00 38.32 3.10
145 149 2.449518 TGACCAAGGCCCACTGGA 60.450 61.111 20.23 0.00 0.00 3.86
158 162 2.765807 CTGGACCCAGATCCGGCT 60.766 66.667 10.47 0.00 46.30 5.52
249 253 4.082523 CTGCCGCGGGGAAGAGAA 62.083 66.667 29.38 0.00 42.33 2.87
250 254 4.388499 TGCCGCGGGGAAGAGAAC 62.388 66.667 29.38 7.00 34.06 3.01
256 260 3.387947 GGGGAAGAGAACCGCCGA 61.388 66.667 0.00 0.00 34.88 5.54
257 261 2.660802 GGGAAGAGAACCGCCGAA 59.339 61.111 0.00 0.00 0.00 4.30
258 262 1.448013 GGGAAGAGAACCGCCGAAG 60.448 63.158 0.00 0.00 0.00 3.79
259 263 2.101233 GGAAGAGAACCGCCGAAGC 61.101 63.158 0.00 0.00 0.00 3.86
349 353 4.436998 CACGAGCGGGAGGACCAC 62.437 72.222 0.00 0.00 40.22 4.16
352 356 3.827898 GAGCGGGAGGACCACGAG 61.828 72.222 7.34 0.00 40.22 4.18
353 357 4.680537 AGCGGGAGGACCACGAGT 62.681 66.667 7.34 0.00 40.22 4.18
354 358 4.131088 GCGGGAGGACCACGAGTC 62.131 72.222 7.34 0.00 45.51 3.36
384 388 4.404654 GGCAACGGCAAGGCTTCG 62.405 66.667 0.00 1.07 43.71 3.79
421 425 4.816984 GTCGGCGAGGGAGGAGGA 62.817 72.222 11.20 0.00 0.00 3.71
422 426 4.507916 TCGGCGAGGGAGGAGGAG 62.508 72.222 4.99 0.00 0.00 3.69
424 428 4.144727 GGCGAGGGAGGAGGAGGA 62.145 72.222 0.00 0.00 0.00 3.71
425 429 2.520741 GCGAGGGAGGAGGAGGAG 60.521 72.222 0.00 0.00 0.00 3.69
426 430 2.197324 CGAGGGAGGAGGAGGAGG 59.803 72.222 0.00 0.00 0.00 4.30
427 431 2.387772 CGAGGGAGGAGGAGGAGGA 61.388 68.421 0.00 0.00 0.00 3.71
428 432 1.541672 GAGGGAGGAGGAGGAGGAG 59.458 68.421 0.00 0.00 0.00 3.69
429 433 0.996762 GAGGGAGGAGGAGGAGGAGA 60.997 65.000 0.00 0.00 0.00 3.71
430 434 0.330431 AGGGAGGAGGAGGAGGAGAT 60.330 60.000 0.00 0.00 0.00 2.75
431 435 0.178935 GGGAGGAGGAGGAGGAGATG 60.179 65.000 0.00 0.00 0.00 2.90
432 436 0.560688 GGAGGAGGAGGAGGAGATGT 59.439 60.000 0.00 0.00 0.00 3.06
433 437 1.703411 GAGGAGGAGGAGGAGATGTG 58.297 60.000 0.00 0.00 0.00 3.21
434 438 0.264359 AGGAGGAGGAGGAGATGTGG 59.736 60.000 0.00 0.00 0.00 4.17
435 439 0.263172 GGAGGAGGAGGAGATGTGGA 59.737 60.000 0.00 0.00 0.00 4.02
436 440 1.703411 GAGGAGGAGGAGATGTGGAG 58.297 60.000 0.00 0.00 0.00 3.86
437 441 1.216678 GAGGAGGAGGAGATGTGGAGA 59.783 57.143 0.00 0.00 0.00 3.71
438 442 1.063266 AGGAGGAGGAGATGTGGAGAC 60.063 57.143 0.00 0.00 0.00 3.36
439 443 1.408969 GAGGAGGAGATGTGGAGACC 58.591 60.000 0.00 0.00 0.00 3.85
440 444 0.396417 AGGAGGAGATGTGGAGACCG 60.396 60.000 0.00 0.00 0.00 4.79
441 445 1.395826 GGAGGAGATGTGGAGACCGG 61.396 65.000 0.00 0.00 0.00 5.28
442 446 2.022240 GAGGAGATGTGGAGACCGGC 62.022 65.000 0.00 0.00 0.00 6.13
443 447 2.105128 GAGATGTGGAGACCGGCG 59.895 66.667 0.00 0.00 0.00 6.46
444 448 3.432051 GAGATGTGGAGACCGGCGG 62.432 68.421 27.06 27.06 0.00 6.13
457 461 4.996434 GGCGGCGATGGGATCTGG 62.996 72.222 12.98 0.00 0.00 3.86
458 462 4.996434 GCGGCGATGGGATCTGGG 62.996 72.222 12.98 0.00 0.00 4.45
459 463 3.233980 CGGCGATGGGATCTGGGA 61.234 66.667 0.00 0.00 0.00 4.37
460 464 2.746359 GGCGATGGGATCTGGGAG 59.254 66.667 0.00 0.00 0.00 4.30
461 465 2.031768 GCGATGGGATCTGGGAGC 59.968 66.667 0.00 0.00 0.00 4.70
462 466 2.746359 CGATGGGATCTGGGAGCC 59.254 66.667 0.00 0.00 37.39 4.70
463 467 2.142761 CGATGGGATCTGGGAGCCA 61.143 63.158 4.24 0.00 40.28 4.75
464 468 1.453669 GATGGGATCTGGGAGCCAC 59.546 63.158 4.24 0.00 40.28 5.01
465 469 2.061790 GATGGGATCTGGGAGCCACC 62.062 65.000 4.24 0.00 40.28 4.61
514 518 1.171308 GCATGTGATGGCTGAAGTGT 58.829 50.000 0.00 0.00 0.00 3.55
515 519 1.135489 GCATGTGATGGCTGAAGTGTG 60.135 52.381 0.00 0.00 0.00 3.82
516 520 2.156917 CATGTGATGGCTGAAGTGTGT 58.843 47.619 0.00 0.00 0.00 3.72
517 521 1.596603 TGTGATGGCTGAAGTGTGTG 58.403 50.000 0.00 0.00 0.00 3.82
518 522 0.239347 GTGATGGCTGAAGTGTGTGC 59.761 55.000 0.00 0.00 0.00 4.57
519 523 0.890542 TGATGGCTGAAGTGTGTGCC 60.891 55.000 0.00 0.00 45.10 5.01
521 525 3.840437 GGCTGAAGTGTGTGCCAA 58.160 55.556 0.00 0.00 44.34 4.52
522 526 2.114638 GGCTGAAGTGTGTGCCAAA 58.885 52.632 0.00 0.00 44.34 3.28
523 527 0.031178 GGCTGAAGTGTGTGCCAAAG 59.969 55.000 0.00 0.00 44.34 2.77
524 528 1.024271 GCTGAAGTGTGTGCCAAAGA 58.976 50.000 0.00 0.00 0.00 2.52
525 529 1.002033 GCTGAAGTGTGTGCCAAAGAG 60.002 52.381 0.00 0.00 0.00 2.85
526 530 1.605710 CTGAAGTGTGTGCCAAAGAGG 59.394 52.381 0.00 0.00 41.84 3.69
535 539 4.623814 CCAAAGAGGCTGCATCGA 57.376 55.556 8.79 0.00 0.00 3.59
536 540 2.391469 CCAAAGAGGCTGCATCGAG 58.609 57.895 8.79 2.96 0.00 4.04
537 541 0.392193 CCAAAGAGGCTGCATCGAGT 60.392 55.000 8.79 0.00 0.00 4.18
538 542 1.446907 CAAAGAGGCTGCATCGAGTT 58.553 50.000 8.79 2.16 0.00 3.01
539 543 1.808945 CAAAGAGGCTGCATCGAGTTT 59.191 47.619 8.79 1.58 0.00 2.66
540 544 2.191128 AAGAGGCTGCATCGAGTTTT 57.809 45.000 8.79 0.00 0.00 2.43
541 545 1.446907 AGAGGCTGCATCGAGTTTTG 58.553 50.000 8.79 0.00 0.00 2.44
542 546 0.179179 GAGGCTGCATCGAGTTTTGC 60.179 55.000 0.50 1.74 39.33 3.68
543 547 0.607489 AGGCTGCATCGAGTTTTGCT 60.607 50.000 9.89 0.00 39.60 3.91
544 548 0.179179 GGCTGCATCGAGTTTTGCTC 60.179 55.000 9.89 2.55 39.60 4.26
545 549 0.518636 GCTGCATCGAGTTTTGCTCA 59.481 50.000 9.89 0.00 44.33 4.26
546 550 1.727213 GCTGCATCGAGTTTTGCTCAC 60.727 52.381 9.89 0.00 44.33 3.51
547 551 0.512518 TGCATCGAGTTTTGCTCACG 59.487 50.000 9.89 0.00 44.33 4.35
548 552 0.512952 GCATCGAGTTTTGCTCACGT 59.487 50.000 1.49 0.00 44.33 4.49
549 553 1.462541 GCATCGAGTTTTGCTCACGTC 60.463 52.381 1.49 0.00 44.33 4.34
550 554 1.792367 CATCGAGTTTTGCTCACGTCA 59.208 47.619 0.00 0.00 44.33 4.35
551 555 1.205657 TCGAGTTTTGCTCACGTCAC 58.794 50.000 0.00 0.00 44.33 3.67
552 556 0.111704 CGAGTTTTGCTCACGTCACG 60.112 55.000 0.00 0.00 44.33 4.35
553 557 0.383124 GAGTTTTGCTCACGTCACGC 60.383 55.000 0.00 0.00 43.58 5.34
554 558 0.810031 AGTTTTGCTCACGTCACGCT 60.810 50.000 0.00 0.00 0.00 5.07
555 559 0.654472 GTTTTGCTCACGTCACGCTG 60.654 55.000 0.00 0.00 0.00 5.18
556 560 0.808060 TTTTGCTCACGTCACGCTGA 60.808 50.000 0.00 0.00 0.00 4.26
557 561 1.487452 TTTGCTCACGTCACGCTGAC 61.487 55.000 0.00 7.74 43.65 3.51
564 568 2.261671 GTCACGCTGACGGTGGAT 59.738 61.111 0.00 0.00 46.04 3.41
565 569 2.094659 GTCACGCTGACGGTGGATG 61.095 63.158 0.00 0.00 46.04 3.51
566 570 2.048222 CACGCTGACGGTGGATGT 60.048 61.111 0.00 0.00 46.04 3.06
567 571 1.214325 CACGCTGACGGTGGATGTA 59.786 57.895 0.00 0.00 46.04 2.29
568 572 0.389296 CACGCTGACGGTGGATGTAA 60.389 55.000 0.00 0.00 46.04 2.41
569 573 0.108804 ACGCTGACGGTGGATGTAAG 60.109 55.000 0.00 0.00 46.04 2.34
570 574 0.172578 CGCTGACGGTGGATGTAAGA 59.827 55.000 0.00 0.00 34.97 2.10
571 575 1.799181 CGCTGACGGTGGATGTAAGAG 60.799 57.143 0.00 0.00 34.97 2.85
572 576 1.476891 GCTGACGGTGGATGTAAGAGA 59.523 52.381 0.00 0.00 0.00 3.10
573 577 2.094182 GCTGACGGTGGATGTAAGAGAA 60.094 50.000 0.00 0.00 0.00 2.87
574 578 3.616560 GCTGACGGTGGATGTAAGAGAAA 60.617 47.826 0.00 0.00 0.00 2.52
575 579 4.177026 CTGACGGTGGATGTAAGAGAAAG 58.823 47.826 0.00 0.00 0.00 2.62
576 580 3.830178 TGACGGTGGATGTAAGAGAAAGA 59.170 43.478 0.00 0.00 0.00 2.52
577 581 4.282449 TGACGGTGGATGTAAGAGAAAGAA 59.718 41.667 0.00 0.00 0.00 2.52
578 582 4.822026 ACGGTGGATGTAAGAGAAAGAAG 58.178 43.478 0.00 0.00 0.00 2.85
579 583 4.527038 ACGGTGGATGTAAGAGAAAGAAGA 59.473 41.667 0.00 0.00 0.00 2.87
580 584 4.865365 CGGTGGATGTAAGAGAAAGAAGAC 59.135 45.833 0.00 0.00 0.00 3.01
581 585 5.336849 CGGTGGATGTAAGAGAAAGAAGACT 60.337 44.000 0.00 0.00 0.00 3.24
582 586 6.468543 GGTGGATGTAAGAGAAAGAAGACTT 58.531 40.000 0.00 0.00 38.05 3.01
584 588 7.095017 GGTGGATGTAAGAGAAAGAAGACTTTG 60.095 40.741 0.00 0.00 44.97 2.77
585 589 7.657761 GTGGATGTAAGAGAAAGAAGACTTTGA 59.342 37.037 0.00 0.00 44.97 2.69
586 590 7.657761 TGGATGTAAGAGAAAGAAGACTTTGAC 59.342 37.037 0.00 0.00 44.97 3.18
587 591 7.118535 GGATGTAAGAGAAAGAAGACTTTGACC 59.881 40.741 0.00 0.00 44.97 4.02
588 592 6.884832 TGTAAGAGAAAGAAGACTTTGACCA 58.115 36.000 0.00 0.00 44.97 4.02
589 593 6.761714 TGTAAGAGAAAGAAGACTTTGACCAC 59.238 38.462 0.00 0.00 44.97 4.16
590 594 5.622346 AGAGAAAGAAGACTTTGACCACT 57.378 39.130 0.00 0.00 44.97 4.00
591 595 5.606505 AGAGAAAGAAGACTTTGACCACTC 58.393 41.667 0.00 0.00 44.97 3.51
592 596 4.709250 AGAAAGAAGACTTTGACCACTCC 58.291 43.478 0.00 0.00 44.97 3.85
593 597 3.493767 AAGAAGACTTTGACCACTCCC 57.506 47.619 0.00 0.00 31.71 4.30
594 598 2.408565 AGAAGACTTTGACCACTCCCA 58.591 47.619 0.00 0.00 0.00 4.37
595 599 2.777692 AGAAGACTTTGACCACTCCCAA 59.222 45.455 0.00 0.00 0.00 4.12
596 600 3.202151 AGAAGACTTTGACCACTCCCAAA 59.798 43.478 0.00 0.00 0.00 3.28
602 606 4.935352 TTTGACCACTCCCAAAGATTTG 57.065 40.909 0.00 0.00 37.90 2.32
603 607 3.874383 TGACCACTCCCAAAGATTTGA 57.126 42.857 6.87 0.00 40.55 2.69
604 608 4.387026 TGACCACTCCCAAAGATTTGAT 57.613 40.909 6.87 0.00 40.55 2.57
605 609 4.739793 TGACCACTCCCAAAGATTTGATT 58.260 39.130 6.87 0.00 40.55 2.57
606 610 4.523943 TGACCACTCCCAAAGATTTGATTG 59.476 41.667 6.87 0.00 40.55 2.67
607 611 4.482990 ACCACTCCCAAAGATTTGATTGT 58.517 39.130 6.87 0.29 40.55 2.71
608 612 5.640147 ACCACTCCCAAAGATTTGATTGTA 58.360 37.500 6.87 0.00 40.55 2.41
609 613 5.711976 ACCACTCCCAAAGATTTGATTGTAG 59.288 40.000 6.87 0.45 40.55 2.74
610 614 5.711976 CCACTCCCAAAGATTTGATTGTAGT 59.288 40.000 6.87 0.97 40.55 2.73
611 615 6.209391 CCACTCCCAAAGATTTGATTGTAGTT 59.791 38.462 6.87 0.00 40.55 2.24
612 616 7.255942 CCACTCCCAAAGATTTGATTGTAGTTT 60.256 37.037 6.87 0.00 40.55 2.66
613 617 8.143835 CACTCCCAAAGATTTGATTGTAGTTTT 58.856 33.333 6.87 0.00 40.55 2.43
614 618 9.362151 ACTCCCAAAGATTTGATTGTAGTTTTA 57.638 29.630 6.87 0.00 40.55 1.52
630 634 9.724839 TTGTAGTTTTATCTTTTTGAAAGGACG 57.275 29.630 1.04 0.00 0.00 4.79
631 635 8.895737 TGTAGTTTTATCTTTTTGAAAGGACGT 58.104 29.630 0.00 0.00 0.00 4.34
632 636 9.166126 GTAGTTTTATCTTTTTGAAAGGACGTG 57.834 33.333 0.00 0.00 0.00 4.49
633 637 6.695713 AGTTTTATCTTTTTGAAAGGACGTGC 59.304 34.615 0.00 0.00 0.00 5.34
634 638 3.643159 ATCTTTTTGAAAGGACGTGCC 57.357 42.857 2.38 0.00 0.00 5.01
667 671 5.746990 TTTCCAAAAGAAAAACAGGTGGA 57.253 34.783 0.00 0.00 41.56 4.02
668 672 5.337578 TTCCAAAAGAAAAACAGGTGGAG 57.662 39.130 0.00 0.00 35.24 3.86
669 673 4.605183 TCCAAAAGAAAAACAGGTGGAGA 58.395 39.130 0.00 0.00 0.00 3.71
670 674 5.208121 TCCAAAAGAAAAACAGGTGGAGAT 58.792 37.500 0.00 0.00 0.00 2.75
671 675 5.068987 TCCAAAAGAAAAACAGGTGGAGATG 59.931 40.000 0.00 0.00 0.00 2.90
672 676 5.291971 CAAAAGAAAAACAGGTGGAGATGG 58.708 41.667 0.00 0.00 0.00 3.51
673 677 3.160679 AGAAAAACAGGTGGAGATGGG 57.839 47.619 0.00 0.00 0.00 4.00
674 678 2.447047 AGAAAAACAGGTGGAGATGGGT 59.553 45.455 0.00 0.00 0.00 4.51
675 679 2.586648 AAAACAGGTGGAGATGGGTC 57.413 50.000 0.00 0.00 0.00 4.46
676 680 0.698818 AAACAGGTGGAGATGGGTCC 59.301 55.000 0.00 0.00 37.10 4.46
677 681 1.553690 AACAGGTGGAGATGGGTCCG 61.554 60.000 0.00 0.00 39.81 4.79
678 682 3.083997 AGGTGGAGATGGGTCCGC 61.084 66.667 0.00 0.00 45.11 5.54
679 683 3.083997 GGTGGAGATGGGTCCGCT 61.084 66.667 3.61 0.00 45.16 5.52
680 684 2.670148 GGTGGAGATGGGTCCGCTT 61.670 63.158 3.61 0.00 45.16 4.68
681 685 1.299976 GTGGAGATGGGTCCGCTTT 59.700 57.895 0.00 0.00 42.90 3.51
682 686 0.322546 GTGGAGATGGGTCCGCTTTT 60.323 55.000 0.00 0.00 42.90 2.27
683 687 1.065709 GTGGAGATGGGTCCGCTTTTA 60.066 52.381 0.00 0.00 42.90 1.52
684 688 1.631388 TGGAGATGGGTCCGCTTTTAA 59.369 47.619 0.00 0.00 39.81 1.52
685 689 2.040545 TGGAGATGGGTCCGCTTTTAAA 59.959 45.455 0.00 0.00 39.81 1.52
686 690 3.086282 GGAGATGGGTCCGCTTTTAAAA 58.914 45.455 0.00 0.00 0.00 1.52
687 691 3.699538 GGAGATGGGTCCGCTTTTAAAAT 59.300 43.478 0.09 0.00 0.00 1.82
688 692 4.159693 GGAGATGGGTCCGCTTTTAAAATT 59.840 41.667 0.09 0.00 0.00 1.82
689 693 5.337250 GGAGATGGGTCCGCTTTTAAAATTT 60.337 40.000 0.09 0.00 0.00 1.82
690 694 5.720202 AGATGGGTCCGCTTTTAAAATTTC 58.280 37.500 0.09 0.00 0.00 2.17
691 695 5.480422 AGATGGGTCCGCTTTTAAAATTTCT 59.520 36.000 0.09 0.00 0.00 2.52
692 696 6.661805 AGATGGGTCCGCTTTTAAAATTTCTA 59.338 34.615 0.09 0.00 0.00 2.10
693 697 6.016213 TGGGTCCGCTTTTAAAATTTCTAC 57.984 37.500 0.09 0.00 0.00 2.59
694 698 5.771165 TGGGTCCGCTTTTAAAATTTCTACT 59.229 36.000 0.09 0.00 0.00 2.57
695 699 6.265876 TGGGTCCGCTTTTAAAATTTCTACTT 59.734 34.615 0.09 0.00 0.00 2.24
696 700 7.149973 GGGTCCGCTTTTAAAATTTCTACTTT 58.850 34.615 0.09 0.00 0.00 2.66
697 701 7.327761 GGGTCCGCTTTTAAAATTTCTACTTTC 59.672 37.037 0.09 0.00 0.00 2.62
698 702 7.327761 GGTCCGCTTTTAAAATTTCTACTTTCC 59.672 37.037 0.09 0.00 0.00 3.13
699 703 7.327761 GTCCGCTTTTAAAATTTCTACTTTCCC 59.672 37.037 0.09 0.00 0.00 3.97
700 704 6.588756 CCGCTTTTAAAATTTCTACTTTCCCC 59.411 38.462 0.09 0.00 0.00 4.81
701 705 6.588756 CGCTTTTAAAATTTCTACTTTCCCCC 59.411 38.462 0.09 0.00 0.00 5.40
702 706 7.446769 GCTTTTAAAATTTCTACTTTCCCCCA 58.553 34.615 0.09 0.00 0.00 4.96
703 707 7.934665 GCTTTTAAAATTTCTACTTTCCCCCAA 59.065 33.333 0.09 0.00 0.00 4.12
704 708 9.839817 CTTTTAAAATTTCTACTTTCCCCCAAA 57.160 29.630 0.09 0.00 0.00 3.28
708 712 8.918202 AAAATTTCTACTTTCCCCCAAAAATC 57.082 30.769 0.00 0.00 0.00 2.17
709 713 7.872061 AATTTCTACTTTCCCCCAAAAATCT 57.128 32.000 0.00 0.00 0.00 2.40
710 714 6.911250 TTTCTACTTTCCCCCAAAAATCTC 57.089 37.500 0.00 0.00 0.00 2.75
711 715 4.930696 TCTACTTTCCCCCAAAAATCTCC 58.069 43.478 0.00 0.00 0.00 3.71
712 716 2.525368 ACTTTCCCCCAAAAATCTCCG 58.475 47.619 0.00 0.00 0.00 4.63
713 717 2.109304 ACTTTCCCCCAAAAATCTCCGA 59.891 45.455 0.00 0.00 0.00 4.55
788 805 2.657143 GACTATGTCGGTCCTCTTCCT 58.343 52.381 0.00 0.00 0.00 3.36
814 831 1.605058 TTCCCGCCTTCTCTTCCTCG 61.605 60.000 0.00 0.00 0.00 4.63
931 948 0.173481 CGCTTCTTGATCCACTCCGA 59.827 55.000 0.00 0.00 0.00 4.55
944 961 5.270893 TCCACTCCGATTTCGATTCAATA 57.729 39.130 0.67 0.00 43.02 1.90
958 975 4.997395 CGATTCAATAGACATTACCCCCAG 59.003 45.833 0.00 0.00 0.00 4.45
990 1007 1.553248 CCAGATTCCACCTCGGTAACA 59.447 52.381 0.00 0.00 35.57 2.41
1014 1032 1.358787 ACAGCAATGGGGATCTCCAAA 59.641 47.619 20.77 0.00 40.62 3.28
1210 1277 2.606826 GGTTCCCCCTCTGGTCGT 60.607 66.667 0.00 0.00 0.00 4.34
1215 1282 2.044650 CCCCTCTGGTCGTCCGTA 60.045 66.667 0.00 0.00 36.30 4.02
1467 1534 4.019312 GCCCCGTTACCGTCCCAA 62.019 66.667 0.00 0.00 0.00 4.12
1543 1610 0.250510 TGTCCACTGCGCATTTGGTA 60.251 50.000 28.31 19.46 0.00 3.25
1615 1686 5.385396 CGAACCATCGTAGTTTGGTAATC 57.615 43.478 0.00 0.00 42.34 1.75
1655 1730 6.716628 AGTGACACCACATGAAGATAAAATGT 59.283 34.615 0.00 0.00 45.54 2.71
1658 1733 7.119699 TGACACCACATGAAGATAAAATGTCTC 59.880 37.037 0.00 0.00 35.04 3.36
2052 2128 4.077822 CTGAAGATGCAGGAAAGTCCTTT 58.922 43.478 0.00 0.00 46.91 3.11
2053 2129 4.473444 TGAAGATGCAGGAAAGTCCTTTT 58.527 39.130 0.00 0.00 46.91 2.27
2055 2131 5.010012 TGAAGATGCAGGAAAGTCCTTTTTC 59.990 40.000 0.00 0.00 46.91 2.29
2123 2204 5.825507 ACTCTTTTCACAGCAAAATCAGTC 58.174 37.500 0.00 0.00 0.00 3.51
2129 2210 3.947196 TCACAGCAAAATCAGTCTTGTGT 59.053 39.130 0.00 0.00 0.00 3.72
2426 2678 5.456763 CCCCTTTGTTCCCTCCTAATGATAG 60.457 48.000 0.00 0.00 0.00 2.08
2717 2970 2.544480 TCTGATGACAGTTCTACGCG 57.456 50.000 3.53 3.53 43.81 6.01
2741 2994 5.310409 TCTGACAAGTTCTCCCATTTCTT 57.690 39.130 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 3.847671 GGAAACCCTAGATCTCCTTGG 57.152 52.381 0.00 0.00 37.50 3.61
38 39 2.300152 CCTTGTCTAGTCCTTGACAGCA 59.700 50.000 10.59 0.00 43.74 4.41
50 51 4.692228 GCAGAGATTCTTCCCTTGTCTAG 58.308 47.826 0.00 0.00 0.00 2.43
51 52 3.131223 CGCAGAGATTCTTCCCTTGTCTA 59.869 47.826 0.00 0.00 0.00 2.59
61 62 3.976339 CGGATCCGCAGAGATTCTT 57.024 52.632 23.37 0.00 0.00 2.52
115 116 0.605319 TTGGTCACTGGATTGCCGTC 60.605 55.000 0.00 0.00 36.79 4.79
128 129 2.449518 TCCAGTGGGCCTTGGTCA 60.450 61.111 21.75 6.32 35.89 4.02
145 149 2.607750 ACACAGCCGGATCTGGGT 60.608 61.111 19.87 19.87 45.24 4.51
332 336 4.436998 GTGGTCCTCCCGCTCGTG 62.437 72.222 0.00 0.00 40.81 4.35
335 339 3.827898 CTCGTGGTCCTCCCGCTC 61.828 72.222 0.00 0.00 41.91 5.03
336 340 4.680537 ACTCGTGGTCCTCCCGCT 62.681 66.667 0.00 0.00 41.91 5.52
337 341 4.131088 GACTCGTGGTCCTCCCGC 62.131 72.222 0.00 0.00 38.93 6.13
366 370 4.404654 GAAGCCTTGCCGTTGCCG 62.405 66.667 0.00 0.00 36.33 5.69
367 371 4.404654 CGAAGCCTTGCCGTTGCC 62.405 66.667 0.00 0.00 36.33 4.52
404 408 4.816984 TCCTCCTCCCTCGCCGAC 62.817 72.222 0.00 0.00 0.00 4.79
405 409 4.507916 CTCCTCCTCCCTCGCCGA 62.508 72.222 0.00 0.00 0.00 5.54
407 411 4.144727 TCCTCCTCCTCCCTCGCC 62.145 72.222 0.00 0.00 0.00 5.54
408 412 2.520741 CTCCTCCTCCTCCCTCGC 60.521 72.222 0.00 0.00 0.00 5.03
409 413 2.197324 CCTCCTCCTCCTCCCTCG 59.803 72.222 0.00 0.00 0.00 4.63
410 414 0.996762 TCTCCTCCTCCTCCTCCCTC 60.997 65.000 0.00 0.00 0.00 4.30
411 415 0.330431 ATCTCCTCCTCCTCCTCCCT 60.330 60.000 0.00 0.00 0.00 4.20
412 416 0.178935 CATCTCCTCCTCCTCCTCCC 60.179 65.000 0.00 0.00 0.00 4.30
413 417 0.560688 ACATCTCCTCCTCCTCCTCC 59.439 60.000 0.00 0.00 0.00 4.30
414 418 1.703411 CACATCTCCTCCTCCTCCTC 58.297 60.000 0.00 0.00 0.00 3.71
415 419 0.264359 CCACATCTCCTCCTCCTCCT 59.736 60.000 0.00 0.00 0.00 3.69
416 420 0.263172 TCCACATCTCCTCCTCCTCC 59.737 60.000 0.00 0.00 0.00 4.30
417 421 1.216678 TCTCCACATCTCCTCCTCCTC 59.783 57.143 0.00 0.00 0.00 3.71
418 422 1.063266 GTCTCCACATCTCCTCCTCCT 60.063 57.143 0.00 0.00 0.00 3.69
419 423 1.408969 GTCTCCACATCTCCTCCTCC 58.591 60.000 0.00 0.00 0.00 4.30
420 424 1.408969 GGTCTCCACATCTCCTCCTC 58.591 60.000 0.00 0.00 0.00 3.71
421 425 0.396417 CGGTCTCCACATCTCCTCCT 60.396 60.000 0.00 0.00 0.00 3.69
422 426 1.395826 CCGGTCTCCACATCTCCTCC 61.396 65.000 0.00 0.00 0.00 4.30
423 427 2.022240 GCCGGTCTCCACATCTCCTC 62.022 65.000 1.90 0.00 0.00 3.71
424 428 2.060980 GCCGGTCTCCACATCTCCT 61.061 63.158 1.90 0.00 0.00 3.69
425 429 2.501610 GCCGGTCTCCACATCTCC 59.498 66.667 1.90 0.00 0.00 3.71
426 430 2.105128 CGCCGGTCTCCACATCTC 59.895 66.667 1.90 0.00 0.00 2.75
427 431 3.461773 CCGCCGGTCTCCACATCT 61.462 66.667 1.90 0.00 0.00 2.90
440 444 4.996434 CCAGATCCCATCGCCGCC 62.996 72.222 0.00 0.00 0.00 6.13
441 445 4.996434 CCCAGATCCCATCGCCGC 62.996 72.222 0.00 0.00 0.00 6.53
442 446 3.231889 CTCCCAGATCCCATCGCCG 62.232 68.421 0.00 0.00 0.00 6.46
443 447 2.746359 CTCCCAGATCCCATCGCC 59.254 66.667 0.00 0.00 0.00 5.54
444 448 2.031768 GCTCCCAGATCCCATCGC 59.968 66.667 0.00 0.00 0.00 4.58
445 449 2.142761 TGGCTCCCAGATCCCATCG 61.143 63.158 0.00 0.00 0.00 3.84
446 450 1.453669 GTGGCTCCCAGATCCCATC 59.546 63.158 0.00 0.00 32.34 3.51
447 451 2.081161 GGTGGCTCCCAGATCCCAT 61.081 63.158 0.00 0.00 32.34 4.00
448 452 2.692368 GGTGGCTCCCAGATCCCA 60.692 66.667 0.00 0.00 32.34 4.37
491 495 2.836360 CAGCCATCACATGCCCCC 60.836 66.667 0.00 0.00 0.00 5.40
492 496 1.380246 TTCAGCCATCACATGCCCC 60.380 57.895 0.00 0.00 0.00 5.80
493 497 0.682209 ACTTCAGCCATCACATGCCC 60.682 55.000 0.00 0.00 0.00 5.36
494 498 0.454600 CACTTCAGCCATCACATGCC 59.545 55.000 0.00 0.00 0.00 4.40
495 499 1.135489 CACACTTCAGCCATCACATGC 60.135 52.381 0.00 0.00 0.00 4.06
496 500 2.095415 CACACACTTCAGCCATCACATG 60.095 50.000 0.00 0.00 0.00 3.21
497 501 2.156917 CACACACTTCAGCCATCACAT 58.843 47.619 0.00 0.00 0.00 3.21
498 502 1.596603 CACACACTTCAGCCATCACA 58.403 50.000 0.00 0.00 0.00 3.58
499 503 0.239347 GCACACACTTCAGCCATCAC 59.761 55.000 0.00 0.00 0.00 3.06
500 504 0.890542 GGCACACACTTCAGCCATCA 60.891 55.000 0.00 0.00 46.26 3.07
501 505 1.878775 GGCACACACTTCAGCCATC 59.121 57.895 0.00 0.00 46.26 3.51
502 506 4.085876 GGCACACACTTCAGCCAT 57.914 55.556 0.00 0.00 46.26 4.40
505 509 1.002033 CTCTTTGGCACACACTTCAGC 60.002 52.381 0.00 0.00 39.29 4.26
506 510 1.605710 CCTCTTTGGCACACACTTCAG 59.394 52.381 0.00 0.00 39.29 3.02
507 511 1.679139 CCTCTTTGGCACACACTTCA 58.321 50.000 0.00 0.00 39.29 3.02
518 522 0.392193 ACTCGATGCAGCCTCTTTGG 60.392 55.000 0.00 0.00 39.35 3.28
519 523 1.446907 AACTCGATGCAGCCTCTTTG 58.553 50.000 0.00 0.00 0.00 2.77
520 524 2.191128 AAACTCGATGCAGCCTCTTT 57.809 45.000 0.00 0.00 0.00 2.52
521 525 1.808945 CAAAACTCGATGCAGCCTCTT 59.191 47.619 0.00 0.00 0.00 2.85
522 526 1.446907 CAAAACTCGATGCAGCCTCT 58.553 50.000 0.00 0.00 0.00 3.69
523 527 0.179179 GCAAAACTCGATGCAGCCTC 60.179 55.000 3.89 0.00 42.12 4.70
524 528 0.607489 AGCAAAACTCGATGCAGCCT 60.607 50.000 11.05 0.00 44.95 4.58
525 529 0.179179 GAGCAAAACTCGATGCAGCC 60.179 55.000 11.05 0.00 44.95 4.85
526 530 3.302968 GAGCAAAACTCGATGCAGC 57.697 52.632 11.05 0.00 44.95 5.25
534 538 0.383124 GCGTGACGTGAGCAAAACTC 60.383 55.000 6.91 0.00 46.45 3.01
535 539 0.810031 AGCGTGACGTGAGCAAAACT 60.810 50.000 6.91 0.00 0.00 2.66
536 540 0.654472 CAGCGTGACGTGAGCAAAAC 60.654 55.000 6.91 0.00 0.00 2.43
537 541 0.808060 TCAGCGTGACGTGAGCAAAA 60.808 50.000 6.91 0.00 0.00 2.44
538 542 1.227118 TCAGCGTGACGTGAGCAAA 60.227 52.632 6.91 0.00 0.00 3.68
539 543 1.949133 GTCAGCGTGACGTGAGCAA 60.949 57.895 6.91 0.00 37.67 3.91
540 544 2.354656 GTCAGCGTGACGTGAGCA 60.355 61.111 6.91 0.00 37.67 4.26
547 551 2.094659 CATCCACCGTCAGCGTGAC 61.095 63.158 7.74 7.74 43.65 3.67
548 552 1.245376 TACATCCACCGTCAGCGTGA 61.245 55.000 0.00 0.00 36.15 4.35
549 553 0.389296 TTACATCCACCGTCAGCGTG 60.389 55.000 0.00 0.00 36.15 5.34
550 554 0.108804 CTTACATCCACCGTCAGCGT 60.109 55.000 0.00 0.00 36.15 5.07
551 555 0.172578 TCTTACATCCACCGTCAGCG 59.827 55.000 0.00 0.00 37.95 5.18
552 556 1.476891 TCTCTTACATCCACCGTCAGC 59.523 52.381 0.00 0.00 0.00 4.26
553 557 3.868757 TTCTCTTACATCCACCGTCAG 57.131 47.619 0.00 0.00 0.00 3.51
554 558 3.830178 TCTTTCTCTTACATCCACCGTCA 59.170 43.478 0.00 0.00 0.00 4.35
555 559 4.451629 TCTTTCTCTTACATCCACCGTC 57.548 45.455 0.00 0.00 0.00 4.79
556 560 4.527038 TCTTCTTTCTCTTACATCCACCGT 59.473 41.667 0.00 0.00 0.00 4.83
557 561 4.865365 GTCTTCTTTCTCTTACATCCACCG 59.135 45.833 0.00 0.00 0.00 4.94
558 562 6.043854 AGTCTTCTTTCTCTTACATCCACC 57.956 41.667 0.00 0.00 0.00 4.61
559 563 7.657761 TCAAAGTCTTCTTTCTCTTACATCCAC 59.342 37.037 0.00 0.00 41.31 4.02
560 564 7.657761 GTCAAAGTCTTCTTTCTCTTACATCCA 59.342 37.037 0.00 0.00 41.31 3.41
561 565 7.118535 GGTCAAAGTCTTCTTTCTCTTACATCC 59.881 40.741 0.00 0.00 41.31 3.51
562 566 7.657761 TGGTCAAAGTCTTCTTTCTCTTACATC 59.342 37.037 0.00 0.00 41.31 3.06
563 567 7.442666 GTGGTCAAAGTCTTCTTTCTCTTACAT 59.557 37.037 0.00 0.00 41.31 2.29
564 568 6.761714 GTGGTCAAAGTCTTCTTTCTCTTACA 59.238 38.462 0.00 0.00 41.31 2.41
565 569 6.987404 AGTGGTCAAAGTCTTCTTTCTCTTAC 59.013 38.462 0.00 0.00 41.31 2.34
566 570 7.125792 AGTGGTCAAAGTCTTCTTTCTCTTA 57.874 36.000 0.00 0.00 41.31 2.10
567 571 5.995446 AGTGGTCAAAGTCTTCTTTCTCTT 58.005 37.500 0.00 0.00 41.31 2.85
568 572 5.454045 GGAGTGGTCAAAGTCTTCTTTCTCT 60.454 44.000 0.00 0.00 41.31 3.10
569 573 4.752604 GGAGTGGTCAAAGTCTTCTTTCTC 59.247 45.833 0.00 0.00 41.31 2.87
570 574 4.445019 GGGAGTGGTCAAAGTCTTCTTTCT 60.445 45.833 0.00 0.00 41.31 2.52
571 575 3.815962 GGGAGTGGTCAAAGTCTTCTTTC 59.184 47.826 0.00 0.00 41.31 2.62
572 576 3.202151 TGGGAGTGGTCAAAGTCTTCTTT 59.798 43.478 0.00 0.00 43.66 2.52
573 577 2.777692 TGGGAGTGGTCAAAGTCTTCTT 59.222 45.455 0.00 0.00 35.14 2.52
574 578 2.408565 TGGGAGTGGTCAAAGTCTTCT 58.591 47.619 0.00 0.00 0.00 2.85
575 579 2.930826 TGGGAGTGGTCAAAGTCTTC 57.069 50.000 0.00 0.00 0.00 2.87
576 580 3.202151 TCTTTGGGAGTGGTCAAAGTCTT 59.798 43.478 13.27 0.00 45.78 3.01
577 581 2.777692 TCTTTGGGAGTGGTCAAAGTCT 59.222 45.455 13.27 0.00 45.78 3.24
578 582 3.208747 TCTTTGGGAGTGGTCAAAGTC 57.791 47.619 13.27 0.00 45.78 3.01
579 583 3.884037 ATCTTTGGGAGTGGTCAAAGT 57.116 42.857 13.27 2.11 45.78 2.66
580 584 4.584325 TCAAATCTTTGGGAGTGGTCAAAG 59.416 41.667 8.89 8.89 46.53 2.77
581 585 4.541705 TCAAATCTTTGGGAGTGGTCAAA 58.458 39.130 3.02 0.00 38.66 2.69
582 586 4.177537 TCAAATCTTTGGGAGTGGTCAA 57.822 40.909 3.02 0.00 38.66 3.18
583 587 3.874383 TCAAATCTTTGGGAGTGGTCA 57.126 42.857 3.02 0.00 38.66 4.02
584 588 4.524328 ACAATCAAATCTTTGGGAGTGGTC 59.476 41.667 3.02 0.00 38.66 4.02
585 589 4.482990 ACAATCAAATCTTTGGGAGTGGT 58.517 39.130 3.02 0.00 38.66 4.16
586 590 5.711976 ACTACAATCAAATCTTTGGGAGTGG 59.288 40.000 3.02 4.28 38.66 4.00
587 591 6.824305 ACTACAATCAAATCTTTGGGAGTG 57.176 37.500 3.02 0.00 38.66 3.51
588 592 7.839680 AAACTACAATCAAATCTTTGGGAGT 57.160 32.000 3.02 0.00 38.66 3.85
604 608 9.724839 CGTCCTTTCAAAAAGATAAAACTACAA 57.275 29.630 1.06 0.00 0.00 2.41
605 609 8.895737 ACGTCCTTTCAAAAAGATAAAACTACA 58.104 29.630 1.06 0.00 0.00 2.74
606 610 9.166126 CACGTCCTTTCAAAAAGATAAAACTAC 57.834 33.333 1.06 0.00 0.00 2.73
607 611 7.858879 GCACGTCCTTTCAAAAAGATAAAACTA 59.141 33.333 1.06 0.00 0.00 2.24
608 612 6.695713 GCACGTCCTTTCAAAAAGATAAAACT 59.304 34.615 1.06 0.00 0.00 2.66
609 613 6.074516 GGCACGTCCTTTCAAAAAGATAAAAC 60.075 38.462 1.06 0.00 0.00 2.43
610 614 5.980715 GGCACGTCCTTTCAAAAAGATAAAA 59.019 36.000 1.06 0.00 0.00 1.52
611 615 5.300792 AGGCACGTCCTTTCAAAAAGATAAA 59.699 36.000 1.06 0.00 44.75 1.40
612 616 4.825085 AGGCACGTCCTTTCAAAAAGATAA 59.175 37.500 1.06 0.00 44.75 1.75
613 617 4.394729 AGGCACGTCCTTTCAAAAAGATA 58.605 39.130 1.06 0.00 44.75 1.98
614 618 3.222603 AGGCACGTCCTTTCAAAAAGAT 58.777 40.909 1.06 0.00 44.75 2.40
615 619 2.650322 AGGCACGTCCTTTCAAAAAGA 58.350 42.857 1.06 0.00 44.75 2.52
645 649 5.482175 TCTCCACCTGTTTTTCTTTTGGAAA 59.518 36.000 0.00 0.00 41.58 3.13
646 650 5.020132 TCTCCACCTGTTTTTCTTTTGGAA 58.980 37.500 0.00 0.00 31.37 3.53
647 651 4.605183 TCTCCACCTGTTTTTCTTTTGGA 58.395 39.130 0.00 0.00 0.00 3.53
648 652 5.291971 CATCTCCACCTGTTTTTCTTTTGG 58.708 41.667 0.00 0.00 0.00 3.28
649 653 5.291971 CCATCTCCACCTGTTTTTCTTTTG 58.708 41.667 0.00 0.00 0.00 2.44
650 654 4.344968 CCCATCTCCACCTGTTTTTCTTTT 59.655 41.667 0.00 0.00 0.00 2.27
651 655 3.897505 CCCATCTCCACCTGTTTTTCTTT 59.102 43.478 0.00 0.00 0.00 2.52
652 656 3.117131 ACCCATCTCCACCTGTTTTTCTT 60.117 43.478 0.00 0.00 0.00 2.52
653 657 2.447047 ACCCATCTCCACCTGTTTTTCT 59.553 45.455 0.00 0.00 0.00 2.52
654 658 2.820197 GACCCATCTCCACCTGTTTTTC 59.180 50.000 0.00 0.00 0.00 2.29
655 659 2.490902 GGACCCATCTCCACCTGTTTTT 60.491 50.000 0.00 0.00 0.00 1.94
656 660 1.075536 GGACCCATCTCCACCTGTTTT 59.924 52.381 0.00 0.00 0.00 2.43
657 661 0.698818 GGACCCATCTCCACCTGTTT 59.301 55.000 0.00 0.00 0.00 2.83
658 662 1.553690 CGGACCCATCTCCACCTGTT 61.554 60.000 0.00 0.00 0.00 3.16
659 663 1.990060 CGGACCCATCTCCACCTGT 60.990 63.158 0.00 0.00 0.00 4.00
660 664 2.903357 CGGACCCATCTCCACCTG 59.097 66.667 0.00 0.00 0.00 4.00
661 665 3.083997 GCGGACCCATCTCCACCT 61.084 66.667 0.00 0.00 0.00 4.00
662 666 2.198304 AAAGCGGACCCATCTCCACC 62.198 60.000 0.00 0.00 0.00 4.61
663 667 0.322546 AAAAGCGGACCCATCTCCAC 60.323 55.000 0.00 0.00 0.00 4.02
664 668 1.281419 TAAAAGCGGACCCATCTCCA 58.719 50.000 0.00 0.00 0.00 3.86
665 669 2.413310 TTAAAAGCGGACCCATCTCC 57.587 50.000 0.00 0.00 0.00 3.71
666 670 4.983671 ATTTTAAAAGCGGACCCATCTC 57.016 40.909 6.79 0.00 0.00 2.75
667 671 5.480422 AGAAATTTTAAAAGCGGACCCATCT 59.520 36.000 6.79 0.00 0.00 2.90
668 672 5.720202 AGAAATTTTAAAAGCGGACCCATC 58.280 37.500 6.79 0.00 0.00 3.51
669 673 5.738619 AGAAATTTTAAAAGCGGACCCAT 57.261 34.783 6.79 0.00 0.00 4.00
670 674 5.771165 AGTAGAAATTTTAAAAGCGGACCCA 59.229 36.000 6.79 0.00 0.00 4.51
671 675 6.263516 AGTAGAAATTTTAAAAGCGGACCC 57.736 37.500 6.79 0.00 0.00 4.46
672 676 7.327761 GGAAAGTAGAAATTTTAAAAGCGGACC 59.672 37.037 6.79 0.00 0.00 4.46
673 677 7.327761 GGGAAAGTAGAAATTTTAAAAGCGGAC 59.672 37.037 6.79 1.58 0.00 4.79
674 678 7.372714 GGGAAAGTAGAAATTTTAAAAGCGGA 58.627 34.615 6.79 0.00 0.00 5.54
675 679 6.588756 GGGGAAAGTAGAAATTTTAAAAGCGG 59.411 38.462 6.79 0.00 0.00 5.52
676 680 6.588756 GGGGGAAAGTAGAAATTTTAAAAGCG 59.411 38.462 6.79 0.00 0.00 4.68
677 681 7.446769 TGGGGGAAAGTAGAAATTTTAAAAGC 58.553 34.615 6.79 0.00 0.00 3.51
678 682 9.839817 TTTGGGGGAAAGTAGAAATTTTAAAAG 57.160 29.630 6.79 0.00 0.00 2.27
683 687 8.723365 AGATTTTTGGGGGAAAGTAGAAATTTT 58.277 29.630 0.00 0.00 0.00 1.82
684 688 8.275187 AGATTTTTGGGGGAAAGTAGAAATTT 57.725 30.769 0.00 0.00 0.00 1.82
685 689 7.038302 GGAGATTTTTGGGGGAAAGTAGAAATT 60.038 37.037 0.00 0.00 0.00 1.82
686 690 6.440647 GGAGATTTTTGGGGGAAAGTAGAAAT 59.559 38.462 0.00 0.00 0.00 2.17
687 691 5.778241 GGAGATTTTTGGGGGAAAGTAGAAA 59.222 40.000 0.00 0.00 0.00 2.52
688 692 5.330233 GGAGATTTTTGGGGGAAAGTAGAA 58.670 41.667 0.00 0.00 0.00 2.10
689 693 4.566907 CGGAGATTTTTGGGGGAAAGTAGA 60.567 45.833 0.00 0.00 0.00 2.59
690 694 3.694566 CGGAGATTTTTGGGGGAAAGTAG 59.305 47.826 0.00 0.00 0.00 2.57
691 695 3.331294 TCGGAGATTTTTGGGGGAAAGTA 59.669 43.478 0.00 0.00 0.00 2.24
692 696 2.109304 TCGGAGATTTTTGGGGGAAAGT 59.891 45.455 0.00 0.00 0.00 2.66
693 697 2.802719 TCGGAGATTTTTGGGGGAAAG 58.197 47.619 0.00 0.00 0.00 2.62
694 698 2.894765 GTTCGGAGATTTTTGGGGGAAA 59.105 45.455 0.00 0.00 35.04 3.13
695 699 2.521126 GTTCGGAGATTTTTGGGGGAA 58.479 47.619 0.00 0.00 35.04 3.97
696 700 1.272258 GGTTCGGAGATTTTTGGGGGA 60.272 52.381 0.00 0.00 35.04 4.81
697 701 1.182667 GGTTCGGAGATTTTTGGGGG 58.817 55.000 0.00 0.00 35.04 5.40
698 702 1.182667 GGGTTCGGAGATTTTTGGGG 58.817 55.000 0.00 0.00 35.04 4.96
699 703 0.808755 CGGGTTCGGAGATTTTTGGG 59.191 55.000 0.00 0.00 35.04 4.12
700 704 1.816074 TCGGGTTCGGAGATTTTTGG 58.184 50.000 0.00 0.00 35.04 3.28
701 705 4.434713 AAATCGGGTTCGGAGATTTTTG 57.565 40.909 0.00 0.00 40.44 2.44
704 708 4.076394 TGAAAAATCGGGTTCGGAGATTT 58.924 39.130 0.00 0.00 43.80 2.17
705 709 3.681593 TGAAAAATCGGGTTCGGAGATT 58.318 40.909 0.00 0.00 35.04 2.40
706 710 3.343941 TGAAAAATCGGGTTCGGAGAT 57.656 42.857 0.00 0.00 35.04 2.75
707 711 2.843401 TGAAAAATCGGGTTCGGAGA 57.157 45.000 0.00 0.00 36.95 3.71
708 712 4.434713 AAATGAAAAATCGGGTTCGGAG 57.565 40.909 0.00 0.00 36.95 4.63
709 713 4.857509 AAAATGAAAAATCGGGTTCGGA 57.142 36.364 0.00 0.00 36.95 4.55
710 714 4.747605 ACAAAAATGAAAAATCGGGTTCGG 59.252 37.500 0.00 0.00 36.95 4.30
711 715 5.460419 TCACAAAAATGAAAAATCGGGTTCG 59.540 36.000 0.00 0.00 37.82 3.95
712 716 6.256757 TGTCACAAAAATGAAAAATCGGGTTC 59.743 34.615 0.00 0.00 0.00 3.62
713 717 6.109359 TGTCACAAAAATGAAAAATCGGGTT 58.891 32.000 0.00 0.00 0.00 4.11
788 805 3.771160 GAAGGCGGGAAGAGCGGA 61.771 66.667 0.00 0.00 35.00 5.54
931 948 6.715264 GGGGGTAATGTCTATTGAATCGAAAT 59.285 38.462 0.00 0.00 0.00 2.17
944 961 0.042131 TCCGTCTGGGGGTAATGTCT 59.958 55.000 0.00 0.00 36.01 3.41
958 975 0.935366 GAATCTGGCGTCGATCCGTC 60.935 60.000 0.00 0.00 0.00 4.79
990 1007 2.357569 GGAGATCCCCATTGCTGTCTTT 60.358 50.000 0.00 0.00 0.00 2.52
1215 1282 2.122954 AGGAAGGGGCCGAAGAGT 59.877 61.111 0.00 0.00 0.00 3.24
1558 1627 4.380531 TGCAAACAAGACTACAAGAGAGG 58.619 43.478 0.00 0.00 0.00 3.69
1560 1629 6.291377 AGAATGCAAACAAGACTACAAGAGA 58.709 36.000 0.00 0.00 0.00 3.10
1561 1630 6.551385 AGAATGCAAACAAGACTACAAGAG 57.449 37.500 0.00 0.00 0.00 2.85
1562 1631 8.621532 AATAGAATGCAAACAAGACTACAAGA 57.378 30.769 0.00 0.00 0.00 3.02
1563 1632 9.683069 AAAATAGAATGCAAACAAGACTACAAG 57.317 29.630 0.00 0.00 0.00 3.16
1564 1633 9.677567 GAAAATAGAATGCAAACAAGACTACAA 57.322 29.630 0.00 0.00 0.00 2.41
1565 1634 8.015087 CGAAAATAGAATGCAAACAAGACTACA 58.985 33.333 0.00 0.00 0.00 2.74
1566 1635 7.481798 CCGAAAATAGAATGCAAACAAGACTAC 59.518 37.037 0.00 0.00 0.00 2.73
1567 1636 7.526608 CCGAAAATAGAATGCAAACAAGACTA 58.473 34.615 0.00 0.00 0.00 2.59
1568 1637 6.381801 CCGAAAATAGAATGCAAACAAGACT 58.618 36.000 0.00 0.00 0.00 3.24
1569 1638 5.060940 GCCGAAAATAGAATGCAAACAAGAC 59.939 40.000 0.00 0.00 0.00 3.01
1615 1686 8.779303 TGTGGTGTCACTTATAAATACAACAAG 58.221 33.333 11.66 0.00 39.31 3.16
1655 1730 6.486320 TGTAAATCATGCACAAAACAGAGAGA 59.514 34.615 0.00 0.00 0.00 3.10
1658 1733 6.144402 GGTTGTAAATCATGCACAAAACAGAG 59.856 38.462 0.00 0.00 34.20 3.35
2052 2128 7.853437 CACATACATTGAACAAACACGTAGAAA 59.147 33.333 0.00 0.00 0.00 2.52
2053 2129 7.011576 ACACATACATTGAACAAACACGTAGAA 59.988 33.333 0.00 0.00 0.00 2.10
2055 2131 6.573357 CACACATACATTGAACAAACACGTAG 59.427 38.462 0.00 0.00 0.00 3.51
2129 2210 7.281098 TCCATTGTAAACCAAAGTGTACACTA 58.719 34.615 28.13 8.61 44.68 2.74
2148 2229 8.115490 AGGATAAGTTCAAGTTTCTTCCATTG 57.885 34.615 4.84 0.00 0.00 2.82
2242 2329 7.072202 AGGCTAGTACCTAGATAGTACTCACAA 59.928 40.741 12.01 0.00 45.70 3.33
2307 2556 6.017934 CACACACTGCTGTTGAGTTATAACTT 60.018 38.462 18.96 3.63 39.88 2.66
2622 2875 7.161773 ACACCCAGAGTTCATTATTGAAATG 57.838 36.000 5.15 4.07 43.29 2.32
2717 2970 5.066593 AGAAATGGGAGAACTTGTCAGAAC 58.933 41.667 0.00 0.00 0.00 3.01
2741 2994 2.586425 CTGGGAAACAAAGGAAGCTCA 58.414 47.619 0.00 0.00 0.00 4.26
2806 3059 3.740832 GCATAAGCAAAACAACTGGGAAC 59.259 43.478 0.00 0.00 41.58 3.62


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

AutoCloner maintained by Alex Coulton.