Multiple sequence alignment - TraesCS4B01G094100

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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 TraesCS4B01G094100 chr4B 100.000 3383 0 0 1 3383 96642417 96639035 0.000000 6248.0
1 TraesCS4B01G094100 chr4D 98.097 2732 49 3 654 3383 65939614 65936884 0.000000 4754.0
2 TraesCS4B01G094100 chr4D 93.870 522 14 6 1 522 65940172 65939669 0.000000 771.0
3 TraesCS4B01G094100 chr4D 96.970 33 1 0 530 562 153023150 153023182 0.000472 56.5
4 TraesCS4B01G094100 chr4A 97.461 1812 45 1 656 2467 529626584 529628394 0.000000 3090.0
5 TraesCS4B01G094100 chr4A 95.155 1032 37 6 2353 3383 529628392 529629411 0.000000 1616.0
6 TraesCS4B01G094100 chr4A 92.939 524 29 3 1 522 529626010 529626527 0.000000 756.0
7 TraesCS4B01G094100 chr4A 100.000 33 0 0 530 562 289740365 289740397 0.000010 62.1
8 TraesCS4B01G094100 chr3D 89.796 49 1 3 530 577 548565523 548565568 0.000036 60.2
9 TraesCS4B01G094100 chr5A 94.595 37 2 0 526 562 389234191 389234227 0.000131 58.4
10 TraesCS4B01G094100 chr6D 96.970 33 1 0 530 562 152756509 152756477 0.000472 56.5
11 TraesCS4B01G094100 chr6D 96.970 33 1 0 530 562 198952486 198952518 0.000472 56.5
12 TraesCS4B01G094100 chr6D 96.970 33 1 0 530 562 199117225 199117257 0.000472 56.5
13 TraesCS4B01G094100 chr1A 96.970 33 1 0 530 562 238332892 238332924 0.000472 56.5
14 TraesCS4B01G094100 chr1A 96.970 33 1 0 530 562 378352665 378352633 0.000472 56.5


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 TraesCS4B01G094100 chr4B 96639035 96642417 3382 True 6248.000000 6248 100.0000 1 3383 1 chr4B.!!$R1 3382
1 TraesCS4B01G094100 chr4D 65936884 65940172 3288 True 2762.500000 4754 95.9835 1 3383 2 chr4D.!!$R1 3382
2 TraesCS4B01G094100 chr4A 529626010 529629411 3401 False 1820.666667 3090 95.1850 1 3383 3 chr4A.!!$F2 3382

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
705 720 0.732880 CCTACTTGTCTGTCCGTGCG 60.733 60.0 0.0 0.0 0.00 5.34 F
1608 1623 0.916358 AGTCAGGCAAGGTGGGCTAT 60.916 55.0 0.0 0.0 42.46 2.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1740 1755 1.191535 CTGGAATGTACCCTCCGTCA 58.808 55.0 6.0 0.0 34.14 4.35 R
2544 2671 1.519408 ACACCCGTCAACAATAGCAC 58.481 50.0 0.0 0.0 0.00 4.40 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
268 276 3.054503 GCACAGTGAGCCTGGCTG 61.055 66.667 28.82 15.24 46.06 4.85
269 277 2.359602 CACAGTGAGCCTGGCTGG 60.360 66.667 28.82 14.73 46.06 4.85
270 278 2.851102 ACAGTGAGCCTGGCTGGT 60.851 61.111 28.82 15.41 46.06 4.00
271 279 2.433446 CAGTGAGCCTGGCTGGTT 59.567 61.111 28.82 7.81 39.88 3.67
272 280 1.228367 CAGTGAGCCTGGCTGGTTT 60.228 57.895 28.82 0.08 39.88 3.27
273 281 1.228367 AGTGAGCCTGGCTGGTTTG 60.228 57.895 28.82 0.00 39.88 2.93
274 282 2.598394 TGAGCCTGGCTGGTTTGC 60.598 61.111 28.82 11.09 39.88 3.68
275 283 3.741476 GAGCCTGGCTGGTTTGCG 61.741 66.667 28.82 0.00 39.88 4.85
282 290 3.286751 GCTGGTTTGCGCTCCACA 61.287 61.111 9.73 1.83 0.00 4.17
329 339 4.021192 TCCTCAAGCCACATTTTGATTTCC 60.021 41.667 0.00 0.00 33.25 3.13
344 354 4.715523 TCCTTTTCAGCCGGCCGG 62.716 66.667 40.26 40.26 38.57 6.13
422 432 9.030301 TGTATTCACAGATATTGTTGTATGACG 57.970 33.333 0.00 0.00 38.16 4.35
425 435 8.716646 TTCACAGATATTGTTGTATGACGAAT 57.283 30.769 0.00 0.00 38.16 3.34
434 444 7.433708 TTGTTGTATGACGAATGATGTTTCT 57.566 32.000 0.00 0.00 0.00 2.52
453 463 8.865590 TGTTTCTTTCTTTTTGTAACATAGCC 57.134 30.769 0.00 0.00 0.00 3.93
511 521 6.767423 CCTTCCCAATTTGTTGTGAATCTTTT 59.233 34.615 0.00 0.00 0.00 2.27
516 526 7.493971 CCCAATTTGTTGTGAATCTTTTGTACA 59.506 33.333 0.00 0.00 0.00 2.90
536 546 4.833390 ACAATAGTACTCCCTCTTGTTGC 58.167 43.478 0.00 0.00 30.28 4.17
537 547 4.532521 ACAATAGTACTCCCTCTTGTTGCT 59.467 41.667 0.00 0.00 30.28 3.91
538 548 5.112686 CAATAGTACTCCCTCTTGTTGCTC 58.887 45.833 0.00 0.00 0.00 4.26
539 549 2.609747 AGTACTCCCTCTTGTTGCTCA 58.390 47.619 0.00 0.00 0.00 4.26
540 550 2.972713 AGTACTCCCTCTTGTTGCTCAA 59.027 45.455 0.00 0.00 34.61 3.02
541 551 3.391296 AGTACTCCCTCTTGTTGCTCAAA 59.609 43.478 0.00 0.00 35.48 2.69
542 552 3.515602 ACTCCCTCTTGTTGCTCAAAT 57.484 42.857 0.00 0.00 35.48 2.32
543 553 3.152341 ACTCCCTCTTGTTGCTCAAATG 58.848 45.455 0.00 0.00 35.48 2.32
544 554 2.490903 CTCCCTCTTGTTGCTCAAATGG 59.509 50.000 0.00 0.00 35.48 3.16
545 555 2.108075 TCCCTCTTGTTGCTCAAATGGA 59.892 45.455 11.39 7.94 35.48 3.41
546 556 3.094572 CCCTCTTGTTGCTCAAATGGAT 58.905 45.455 11.39 0.00 35.48 3.41
547 557 3.119245 CCCTCTTGTTGCTCAAATGGATG 60.119 47.826 11.39 0.00 35.48 3.51
548 558 3.508793 CCTCTTGTTGCTCAAATGGATGT 59.491 43.478 0.00 0.00 35.48 3.06
549 559 4.701651 CCTCTTGTTGCTCAAATGGATGTA 59.298 41.667 0.00 0.00 35.48 2.29
550 560 5.359009 CCTCTTGTTGCTCAAATGGATGTAT 59.641 40.000 0.00 0.00 35.48 2.29
551 561 6.441093 TCTTGTTGCTCAAATGGATGTATC 57.559 37.500 0.00 0.00 35.48 2.24
552 562 6.182627 TCTTGTTGCTCAAATGGATGTATCT 58.817 36.000 0.00 0.00 35.48 1.98
553 563 7.337938 TCTTGTTGCTCAAATGGATGTATCTA 58.662 34.615 0.00 0.00 35.48 1.98
554 564 7.496920 TCTTGTTGCTCAAATGGATGTATCTAG 59.503 37.037 0.00 0.00 35.48 2.43
555 565 5.528690 TGTTGCTCAAATGGATGTATCTAGC 59.471 40.000 0.00 0.00 0.00 3.42
556 566 5.294734 TGCTCAAATGGATGTATCTAGCA 57.705 39.130 0.00 0.00 35.26 3.49
557 567 5.872963 TGCTCAAATGGATGTATCTAGCAT 58.127 37.500 0.00 0.00 32.88 3.79
558 568 6.301486 TGCTCAAATGGATGTATCTAGCATT 58.699 36.000 0.00 0.00 32.88 3.56
559 569 7.452562 TGCTCAAATGGATGTATCTAGCATTA 58.547 34.615 0.00 0.00 32.88 1.90
560 570 8.105197 TGCTCAAATGGATGTATCTAGCATTAT 58.895 33.333 0.00 0.00 32.88 1.28
561 571 8.954350 GCTCAAATGGATGTATCTAGCATTATT 58.046 33.333 0.00 0.00 0.00 1.40
567 577 8.310406 TGGATGTATCTAGCATTATTGAAACG 57.690 34.615 0.00 0.00 0.00 3.60
568 578 7.387673 TGGATGTATCTAGCATTATTGAAACGG 59.612 37.037 0.00 0.00 0.00 4.44
569 579 7.602644 GGATGTATCTAGCATTATTGAAACGGA 59.397 37.037 0.00 0.00 0.00 4.69
570 580 7.946655 TGTATCTAGCATTATTGAAACGGAG 57.053 36.000 0.00 0.00 0.00 4.63
571 581 6.929049 TGTATCTAGCATTATTGAAACGGAGG 59.071 38.462 0.00 0.00 0.00 4.30
572 582 4.703897 TCTAGCATTATTGAAACGGAGGG 58.296 43.478 0.00 0.00 0.00 4.30
573 583 3.644966 AGCATTATTGAAACGGAGGGA 57.355 42.857 0.00 0.00 0.00 4.20
574 584 3.545703 AGCATTATTGAAACGGAGGGAG 58.454 45.455 0.00 0.00 0.00 4.30
575 585 3.054361 AGCATTATTGAAACGGAGGGAGT 60.054 43.478 0.00 0.00 0.00 3.85
576 586 4.163458 AGCATTATTGAAACGGAGGGAGTA 59.837 41.667 0.00 0.00 0.00 2.59
595 605 5.536538 GGAGTATTTGAAGGAAATCCCATCC 59.463 44.000 0.00 0.00 35.74 3.51
616 631 6.455360 TCCATGTGCTGAATTAATTCCTTC 57.545 37.500 22.42 13.00 35.97 3.46
631 646 9.732130 ATTAATTCCTTCTCCTATTATGCTCAC 57.268 33.333 0.00 0.00 0.00 3.51
632 647 7.385894 AATTCCTTCTCCTATTATGCTCACT 57.614 36.000 0.00 0.00 0.00 3.41
633 648 5.798125 TCCTTCTCCTATTATGCTCACTG 57.202 43.478 0.00 0.00 0.00 3.66
634 649 5.458595 TCCTTCTCCTATTATGCTCACTGA 58.541 41.667 0.00 0.00 0.00 3.41
635 650 5.303078 TCCTTCTCCTATTATGCTCACTGAC 59.697 44.000 0.00 0.00 0.00 3.51
636 651 5.304101 CCTTCTCCTATTATGCTCACTGACT 59.696 44.000 0.00 0.00 0.00 3.41
637 652 5.781210 TCTCCTATTATGCTCACTGACTG 57.219 43.478 0.00 0.00 0.00 3.51
638 653 5.204292 TCTCCTATTATGCTCACTGACTGT 58.796 41.667 0.00 0.00 0.00 3.55
639 654 5.658634 TCTCCTATTATGCTCACTGACTGTT 59.341 40.000 0.00 0.00 0.00 3.16
640 655 6.155221 TCTCCTATTATGCTCACTGACTGTTT 59.845 38.462 0.00 0.00 0.00 2.83
641 656 6.711277 TCCTATTATGCTCACTGACTGTTTT 58.289 36.000 0.00 0.00 0.00 2.43
642 657 7.168219 TCCTATTATGCTCACTGACTGTTTTT 58.832 34.615 0.00 0.00 0.00 1.94
698 713 4.315803 CGAAATGAACCCTACTTGTCTGT 58.684 43.478 0.00 0.00 0.00 3.41
705 720 0.732880 CCTACTTGTCTGTCCGTGCG 60.733 60.000 0.00 0.00 0.00 5.34
719 734 1.819208 GTGCGGCCTATGACATGCA 60.819 57.895 0.00 0.00 0.00 3.96
755 770 4.325030 CCTCTCTTTCTAGTCTGTCCCTCT 60.325 50.000 0.00 0.00 0.00 3.69
976 991 1.445716 CCGGAAGATAGTCTCGCGGT 61.446 60.000 6.13 0.00 0.00 5.68
992 1007 4.779733 GTGAGGAGGAGGCGGGGA 62.780 72.222 0.00 0.00 0.00 4.81
1413 1428 1.153229 GGATGCCTACCGGGTGTTC 60.153 63.158 10.66 0.00 37.43 3.18
1473 1488 2.303022 CACCTACAACACACTCCTGGAT 59.697 50.000 0.00 0.00 0.00 3.41
1491 1506 2.436824 GGGCTCTTCAGGTTCGGC 60.437 66.667 0.00 0.00 0.00 5.54
1605 1620 2.116125 AAGTCAGGCAAGGTGGGC 59.884 61.111 0.00 0.00 0.00 5.36
1608 1623 0.916358 AGTCAGGCAAGGTGGGCTAT 60.916 55.000 0.00 0.00 42.46 2.97
1657 1672 4.776322 CCGAGCATGCCCCGAACA 62.776 66.667 25.56 0.00 0.00 3.18
1694 1709 2.159653 CGGTCATGAAGTGCTGCTTTAC 60.160 50.000 0.00 0.00 37.59 2.01
1698 1713 4.330074 GTCATGAAGTGCTGCTTTACGTAT 59.670 41.667 0.00 0.00 37.59 3.06
1740 1755 3.181440 TGGAGACCTTCTTGTCATTGCTT 60.181 43.478 0.00 0.00 37.73 3.91
1860 1875 1.933021 TGATACGGAGTGGGTTCAGT 58.067 50.000 0.00 0.00 45.73 3.41
1995 2010 7.581213 TGAGTACACATTCTCAATTTTGGTT 57.419 32.000 0.00 0.00 37.69 3.67
2514 2641 8.231692 TGAATTTCAAACATCCAGTTCTTGTA 57.768 30.769 0.00 0.00 40.26 2.41
2544 2671 3.031736 TGGAGGAAGGAAAGTAGGATCG 58.968 50.000 0.00 0.00 0.00 3.69
2917 3046 4.566759 CGTATCGTTGTCATGGAGTTCAAT 59.433 41.667 0.00 0.00 0.00 2.57
2934 3063 7.115378 GGAGTTCAATTTTTGTGTGAAGCATAG 59.885 37.037 0.00 0.00 32.15 2.23
3086 3215 7.499895 AGTCCATTTGTTCATCATTTTTGCTTT 59.500 29.630 0.00 0.00 0.00 3.51
3366 3495 3.249320 CCATTGACTGCATATGGTCTTCG 59.751 47.826 4.56 0.00 35.23 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
268 276 1.094785 ATACATGTGGAGCGCAAACC 58.905 50.000 11.47 10.90 0.00 3.27
269 277 4.552166 ATTATACATGTGGAGCGCAAAC 57.448 40.909 11.47 5.03 0.00 2.93
270 278 5.574891 AAATTATACATGTGGAGCGCAAA 57.425 34.783 11.47 0.00 0.00 3.68
271 279 5.105957 ACAAAATTATACATGTGGAGCGCAA 60.106 36.000 11.47 0.00 0.00 4.85
272 280 4.397730 ACAAAATTATACATGTGGAGCGCA 59.602 37.500 11.47 0.00 0.00 6.09
273 281 4.920376 ACAAAATTATACATGTGGAGCGC 58.080 39.130 9.11 0.00 0.00 5.92
274 282 7.298122 GGATACAAAATTATACATGTGGAGCG 58.702 38.462 9.11 0.00 0.00 5.03
275 283 7.298122 CGGATACAAAATTATACATGTGGAGC 58.702 38.462 9.11 0.00 0.00 4.70
276 284 7.298122 GCGGATACAAAATTATACATGTGGAG 58.702 38.462 9.11 0.00 0.00 3.86
277 285 6.205853 GGCGGATACAAAATTATACATGTGGA 59.794 38.462 9.11 0.00 0.00 4.02
282 290 8.357402 GGAAAAGGCGGATACAAAATTATACAT 58.643 33.333 0.00 0.00 0.00 2.29
418 428 7.973388 ACAAAAAGAAAGAAACATCATTCGTCA 59.027 29.630 0.00 0.00 34.46 4.35
419 429 8.340230 ACAAAAAGAAAGAAACATCATTCGTC 57.660 30.769 0.00 0.00 34.46 4.20
434 444 6.704050 GCTTTGGGCTATGTTACAAAAAGAAA 59.296 34.615 0.00 0.00 38.06 2.52
453 463 5.885230 TCTCATTCACACTAATGCTTTGG 57.115 39.130 0.00 0.00 36.89 3.28
489 499 6.648192 ACAAAAGATTCACAACAAATTGGGA 58.352 32.000 0.00 0.00 46.84 4.37
516 526 4.777896 TGAGCAACAAGAGGGAGTACTATT 59.222 41.667 0.00 0.00 0.00 1.73
522 532 3.152341 CATTTGAGCAACAAGAGGGAGT 58.848 45.455 0.00 0.00 39.77 3.85
523 533 2.490903 CCATTTGAGCAACAAGAGGGAG 59.509 50.000 0.00 0.00 39.77 4.30
524 534 2.108075 TCCATTTGAGCAACAAGAGGGA 59.892 45.455 12.54 10.30 39.77 4.20
525 535 2.517959 TCCATTTGAGCAACAAGAGGG 58.482 47.619 12.54 8.85 39.77 4.30
526 536 3.508793 ACATCCATTTGAGCAACAAGAGG 59.491 43.478 0.00 0.00 39.77 3.69
527 537 4.778534 ACATCCATTTGAGCAACAAGAG 57.221 40.909 0.00 0.00 39.77 2.85
528 538 6.182627 AGATACATCCATTTGAGCAACAAGA 58.817 36.000 0.00 0.00 39.77 3.02
529 539 6.446781 AGATACATCCATTTGAGCAACAAG 57.553 37.500 0.00 0.00 39.77 3.16
530 540 6.038603 GCTAGATACATCCATTTGAGCAACAA 59.961 38.462 0.00 0.00 36.65 2.83
531 541 5.528690 GCTAGATACATCCATTTGAGCAACA 59.471 40.000 0.00 0.00 0.00 3.33
532 542 5.528690 TGCTAGATACATCCATTTGAGCAAC 59.471 40.000 0.00 0.00 34.66 4.17
533 543 5.683681 TGCTAGATACATCCATTTGAGCAA 58.316 37.500 0.00 0.00 34.66 3.91
534 544 5.294734 TGCTAGATACATCCATTTGAGCA 57.705 39.130 0.00 0.00 35.18 4.26
535 545 6.814506 AATGCTAGATACATCCATTTGAGC 57.185 37.500 0.00 0.00 0.00 4.26
541 551 8.939929 CGTTTCAATAATGCTAGATACATCCAT 58.060 33.333 0.00 0.00 0.00 3.41
542 552 7.387673 CCGTTTCAATAATGCTAGATACATCCA 59.612 37.037 0.00 0.00 0.00 3.41
543 553 7.602644 TCCGTTTCAATAATGCTAGATACATCC 59.397 37.037 0.00 0.00 0.00 3.51
544 554 8.534333 TCCGTTTCAATAATGCTAGATACATC 57.466 34.615 0.00 0.00 0.00 3.06
545 555 7.604164 CCTCCGTTTCAATAATGCTAGATACAT 59.396 37.037 0.00 0.00 0.00 2.29
546 556 6.929049 CCTCCGTTTCAATAATGCTAGATACA 59.071 38.462 0.00 0.00 0.00 2.29
547 557 6.369065 CCCTCCGTTTCAATAATGCTAGATAC 59.631 42.308 0.00 0.00 0.00 2.24
548 558 6.269077 TCCCTCCGTTTCAATAATGCTAGATA 59.731 38.462 0.00 0.00 0.00 1.98
549 559 5.071788 TCCCTCCGTTTCAATAATGCTAGAT 59.928 40.000 0.00 0.00 0.00 1.98
550 560 4.407621 TCCCTCCGTTTCAATAATGCTAGA 59.592 41.667 0.00 0.00 0.00 2.43
551 561 4.703897 TCCCTCCGTTTCAATAATGCTAG 58.296 43.478 0.00 0.00 0.00 3.42
552 562 4.163458 ACTCCCTCCGTTTCAATAATGCTA 59.837 41.667 0.00 0.00 0.00 3.49
553 563 3.054361 ACTCCCTCCGTTTCAATAATGCT 60.054 43.478 0.00 0.00 0.00 3.79
554 564 3.279434 ACTCCCTCCGTTTCAATAATGC 58.721 45.455 0.00 0.00 0.00 3.56
555 565 7.282224 TCAAATACTCCCTCCGTTTCAATAATG 59.718 37.037 0.00 0.00 0.00 1.90
556 566 7.343357 TCAAATACTCCCTCCGTTTCAATAAT 58.657 34.615 0.00 0.00 0.00 1.28
557 567 6.713276 TCAAATACTCCCTCCGTTTCAATAA 58.287 36.000 0.00 0.00 0.00 1.40
558 568 6.302535 TCAAATACTCCCTCCGTTTCAATA 57.697 37.500 0.00 0.00 0.00 1.90
559 569 5.174037 TCAAATACTCCCTCCGTTTCAAT 57.826 39.130 0.00 0.00 0.00 2.57
560 570 4.627284 TCAAATACTCCCTCCGTTTCAA 57.373 40.909 0.00 0.00 0.00 2.69
561 571 4.564821 CCTTCAAATACTCCCTCCGTTTCA 60.565 45.833 0.00 0.00 0.00 2.69
562 572 3.939592 CCTTCAAATACTCCCTCCGTTTC 59.060 47.826 0.00 0.00 0.00 2.78
563 573 3.585732 TCCTTCAAATACTCCCTCCGTTT 59.414 43.478 0.00 0.00 0.00 3.60
564 574 3.178865 TCCTTCAAATACTCCCTCCGTT 58.821 45.455 0.00 0.00 0.00 4.44
565 575 2.829023 TCCTTCAAATACTCCCTCCGT 58.171 47.619 0.00 0.00 0.00 4.69
566 576 3.906720 TTCCTTCAAATACTCCCTCCG 57.093 47.619 0.00 0.00 0.00 4.63
567 577 5.133941 GGATTTCCTTCAAATACTCCCTCC 58.866 45.833 0.00 0.00 34.60 4.30
568 578 5.133941 GGGATTTCCTTCAAATACTCCCTC 58.866 45.833 0.00 0.00 37.66 4.30
569 579 4.544152 TGGGATTTCCTTCAAATACTCCCT 59.456 41.667 5.92 0.00 39.94 4.20
570 580 4.867086 TGGGATTTCCTTCAAATACTCCC 58.133 43.478 0.00 0.00 39.78 4.30
571 581 5.536538 GGATGGGATTTCCTTCAAATACTCC 59.463 44.000 0.00 0.00 40.41 3.85
572 582 6.129179 TGGATGGGATTTCCTTCAAATACTC 58.871 40.000 0.00 0.00 40.41 2.59
573 583 6.091076 TGGATGGGATTTCCTTCAAATACT 57.909 37.500 0.00 0.00 40.41 2.12
574 584 6.324770 ACATGGATGGGATTTCCTTCAAATAC 59.675 38.462 0.00 0.00 40.41 1.89
575 585 6.324512 CACATGGATGGGATTTCCTTCAAATA 59.675 38.462 0.00 0.00 40.41 1.40
576 586 5.129815 CACATGGATGGGATTTCCTTCAAAT 59.870 40.000 0.00 0.00 40.41 2.32
595 605 6.320672 AGGAGAAGGAATTAATTCAGCACATG 59.679 38.462 25.55 0.00 38.53 3.21
616 631 5.528043 ACAGTCAGTGAGCATAATAGGAG 57.472 43.478 0.00 0.00 0.00 3.69
641 656 5.177511 CAGTCAGTGAGCACGAATCTAAAAA 59.822 40.000 0.00 0.00 36.20 1.94
642 657 4.686091 CAGTCAGTGAGCACGAATCTAAAA 59.314 41.667 0.00 0.00 36.20 1.52
643 658 4.237724 CAGTCAGTGAGCACGAATCTAAA 58.762 43.478 0.00 0.00 36.20 1.85
644 659 3.255888 ACAGTCAGTGAGCACGAATCTAA 59.744 43.478 0.00 0.00 36.20 2.10
645 660 2.820197 ACAGTCAGTGAGCACGAATCTA 59.180 45.455 0.00 0.00 36.20 1.98
646 661 1.615883 ACAGTCAGTGAGCACGAATCT 59.384 47.619 0.00 0.00 36.20 2.40
647 662 2.071688 ACAGTCAGTGAGCACGAATC 57.928 50.000 0.00 0.00 36.20 2.52
648 663 2.138320 CAACAGTCAGTGAGCACGAAT 58.862 47.619 0.00 0.00 36.20 3.34
649 664 1.570813 CAACAGTCAGTGAGCACGAA 58.429 50.000 0.00 0.00 36.20 3.85
650 665 0.249447 CCAACAGTCAGTGAGCACGA 60.249 55.000 0.00 0.00 36.20 4.35
651 666 1.224069 CCCAACAGTCAGTGAGCACG 61.224 60.000 0.00 0.00 36.20 5.34
652 667 0.179045 ACCCAACAGTCAGTGAGCAC 60.179 55.000 0.00 0.00 0.00 4.40
653 668 0.106708 GACCCAACAGTCAGTGAGCA 59.893 55.000 0.00 0.00 36.73 4.26
654 669 0.106708 TGACCCAACAGTCAGTGAGC 59.893 55.000 0.00 0.00 41.78 4.26
698 713 2.431454 ATGTCATAGGCCGCACGGA 61.431 57.895 14.43 0.00 37.50 4.69
705 720 1.962144 GCCATGCATGTCATAGGCC 59.038 57.895 24.58 0.00 40.42 5.19
739 754 2.729194 GCAGAGAGGGACAGACTAGAA 58.271 52.381 0.00 0.00 0.00 2.10
895 910 1.939934 CAGAACAACTTGCCGAGTTCA 59.060 47.619 0.00 0.00 45.40 3.18
911 926 2.568612 CTCGCTCGCTGTCCAGAA 59.431 61.111 0.00 0.00 0.00 3.02
932 947 1.880340 GCTCGCTTCGACTCCCATG 60.880 63.158 0.00 0.00 0.00 3.66
976 991 3.984186 CTTCCCCGCCTCCTCCTCA 62.984 68.421 0.00 0.00 0.00 3.86
990 1005 0.394899 CCCAGGTCATTGCTCCTTCC 60.395 60.000 0.00 0.00 30.91 3.46
992 1007 1.000396 GCCCAGGTCATTGCTCCTT 60.000 57.895 0.00 0.00 30.91 3.36
1392 1407 1.762460 CACCCGGTAGGCATCCTCT 60.762 63.158 0.00 0.00 40.58 3.69
1473 1488 3.068881 CCGAACCTGAAGAGCCCA 58.931 61.111 0.00 0.00 0.00 5.36
1506 1521 3.430929 GCAGGTACCTGAACATCCTGTAG 60.431 52.174 40.26 13.72 46.30 2.74
1569 1584 1.855295 TGCACAGCCCATTGATCATT 58.145 45.000 0.00 0.00 0.00 2.57
1605 1620 1.302033 GAGGACCATGCGGGCATAG 60.302 63.158 5.74 1.36 45.55 2.23
1608 1623 4.100084 CTGAGGACCATGCGGGCA 62.100 66.667 0.00 0.00 45.55 5.36
1694 1709 1.942657 CCTGATCAAACCTGCCATACG 59.057 52.381 0.00 0.00 0.00 3.06
1698 1713 1.383799 CCCCTGATCAAACCTGCCA 59.616 57.895 0.00 0.00 0.00 4.92
1740 1755 1.191535 CTGGAATGTACCCTCCGTCA 58.808 55.000 6.00 0.00 34.14 4.35
1860 1875 5.691754 CGTATTATAGCATGCACTGTCAAGA 59.308 40.000 21.98 0.00 0.00 3.02
2514 2641 4.043435 ACTTTCCTTCCTCCAGTTTATGCT 59.957 41.667 0.00 0.00 0.00 3.79
2544 2671 1.519408 ACACCCGTCAACAATAGCAC 58.481 50.000 0.00 0.00 0.00 4.40
2872 3000 6.432107 ACGTATTCACTGCGTTAAACAAAAT 58.568 32.000 0.00 0.00 44.15 1.82
3086 3215 5.277825 CCGCTTCACAAGAATTAAACAACA 58.722 37.500 0.00 0.00 32.31 3.33
3215 3344 4.171878 TCTACAGAGTAGGCAGCATAGT 57.828 45.455 0.00 0.00 0.00 2.12
3328 3457 4.441087 GTCAATGGAAAAGAAGCAAACGAC 59.559 41.667 0.00 0.00 0.00 4.34


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

AutoCloner maintained by Alex Coulton.