Multiple sequence alignment - TraesCS3A01G352500

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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 TraesCS3A01G352500 chr3A 100.000 4631 0 0 1 4631 600343972 600339342 0.000000e+00 8552.0
1 TraesCS3A01G352500 chr3A 89.659 1025 85 13 3262 4268 343940471 343939450 0.000000e+00 1286.0
2 TraesCS3A01G352500 chr3A 90.132 152 12 2 3116 3267 344048347 344048199 1.310000e-45 195.0
3 TraesCS3A01G352500 chr3D 91.701 2410 125 40 1 2369 457558417 457556042 0.000000e+00 3273.0
4 TraesCS3A01G352500 chr3D 92.210 2131 78 40 2404 4494 457556041 457553959 0.000000e+00 2935.0
5 TraesCS3A01G352500 chr3D 100.000 34 0 0 4514 4547 457553901 457553868 3.870000e-06 63.9
6 TraesCS3A01G352500 chr3B 90.327 2450 122 46 2 2384 605271239 605268838 0.000000e+00 3105.0
7 TraesCS3A01G352500 chr3B 93.396 2029 62 30 2517 4499 605268586 605266584 0.000000e+00 2939.0
8 TraesCS3A01G352500 chr1B 93.053 1166 63 6 3116 4268 179860603 179861763 0.000000e+00 1688.0
9 TraesCS3A01G352500 chr1B 92.061 718 42 4 3564 4268 159781221 159781936 0.000000e+00 996.0
10 TraesCS3A01G352500 chr1B 96.029 277 10 1 3116 3392 159780945 159781220 2.540000e-122 449.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3A01G352500 chr3A 600339342 600343972 4630 True 8552.000000 8552 100.0000 1 4631 1 chr3A.!!$R3 4630
1 TraesCS3A01G352500 chr3A 343939450 343940471 1021 True 1286.000000 1286 89.6590 3262 4268 1 chr3A.!!$R1 1006
2 TraesCS3A01G352500 chr3D 457553868 457558417 4549 True 2090.633333 3273 94.6370 1 4547 3 chr3D.!!$R1 4546
3 TraesCS3A01G352500 chr3B 605266584 605271239 4655 True 3022.000000 3105 91.8615 2 4499 2 chr3B.!!$R1 4497
4 TraesCS3A01G352500 chr1B 179860603 179861763 1160 False 1688.000000 1688 93.0530 3116 4268 1 chr1B.!!$F1 1152
5 TraesCS3A01G352500 chr1B 159780945 159781936 991 False 722.500000 996 94.0450 3116 4268 2 chr1B.!!$F2 1152

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
698 739 0.025001 CGTAGCTGATTTCGTTGCCG 59.975 55.000 0.00 0.00 0.0 5.69 F
2157 2240 1.067495 AGGCTGAAGTCGCTAGTTGAC 60.067 52.381 8.66 8.66 36.6 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2427 2532 1.372251 CGTTCGAGTGCTGTGCTCT 60.372 57.895 0.0 0.0 35.00 4.09 R
3636 3874 2.885644 CGCCTGACGTTCATCGGG 60.886 66.667 0.0 0.0 46.61 5.14 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
29 30 0.035343 GGCTACTTCACCACCCCTTC 60.035 60.000 0.00 0.00 0.00 3.46
31 32 1.657804 CTACTTCACCACCCCTTCCT 58.342 55.000 0.00 0.00 0.00 3.36
34 35 1.850755 TTCACCACCCCTTCCTCCC 60.851 63.158 0.00 0.00 0.00 4.30
35 36 3.339093 CACCACCCCTTCCTCCCC 61.339 72.222 0.00 0.00 0.00 4.81
41 42 2.696504 CCCTTCCTCCCCCTTCCC 60.697 72.222 0.00 0.00 0.00 3.97
42 43 2.696504 CCTTCCTCCCCCTTCCCC 60.697 72.222 0.00 0.00 0.00 4.81
43 44 2.696504 CTTCCTCCCCCTTCCCCC 60.697 72.222 0.00 0.00 0.00 5.40
76 77 3.559171 CCATTTCTTCCACTCCTTTCCGA 60.559 47.826 0.00 0.00 0.00 4.55
83 84 4.814294 CTCCTTTCCGACCGCCCG 62.814 72.222 0.00 0.00 0.00 6.13
161 168 3.316573 GACGGGTGGCTTCAGAGGG 62.317 68.421 0.00 0.00 0.00 4.30
164 171 1.613630 GGGTGGCTTCAGAGGGAGA 60.614 63.158 0.00 0.00 0.00 3.71
165 172 1.621672 GGGTGGCTTCAGAGGGAGAG 61.622 65.000 0.00 0.00 0.00 3.20
167 174 0.907230 GTGGCTTCAGAGGGAGAGGT 60.907 60.000 0.00 0.00 0.00 3.85
174 183 3.791586 GAGGGAGAGGTGGGCAGC 61.792 72.222 0.00 0.00 0.00 5.25
267 276 2.688507 TGTGAAAGTCGGATCTCTTGC 58.311 47.619 0.00 0.00 0.00 4.01
324 346 0.667487 TTCCTTGTCGCGCTCTTCTG 60.667 55.000 5.56 0.00 0.00 3.02
362 384 2.096013 GGTGCGGCAGAGTAGATTTTTC 59.904 50.000 1.18 0.00 0.00 2.29
403 426 5.663556 GGGTTTATGTGGGGGATTAAATTCA 59.336 40.000 0.00 0.00 0.00 2.57
427 450 2.878406 CTGTTTCGGTTGGTGTCTGATT 59.122 45.455 0.00 0.00 0.00 2.57
429 452 3.139077 GTTTCGGTTGGTGTCTGATTCT 58.861 45.455 0.00 0.00 0.00 2.40
431 454 2.766313 TCGGTTGGTGTCTGATTCTTG 58.234 47.619 0.00 0.00 0.00 3.02
433 456 2.508526 GGTTGGTGTCTGATTCTTGCT 58.491 47.619 0.00 0.00 0.00 3.91
435 458 1.527034 TGGTGTCTGATTCTTGCTGC 58.473 50.000 0.00 0.00 0.00 5.25
437 460 2.302733 TGGTGTCTGATTCTTGCTGCTA 59.697 45.455 0.00 0.00 0.00 3.49
450 473 4.875536 TCTTGCTGCTATTATTTTCGCTGA 59.124 37.500 0.00 0.00 0.00 4.26
462 485 0.461870 TTCGCTGACCGATTGATGGG 60.462 55.000 0.00 0.00 46.81 4.00
538 561 6.207691 TGCCTTTCTTGCCATATTTTCTAC 57.792 37.500 0.00 0.00 0.00 2.59
562 585 2.203800 TGACGCACGATTATGTCCTC 57.796 50.000 0.00 0.00 0.00 3.71
564 587 0.870307 ACGCACGATTATGTCCTCGC 60.870 55.000 0.00 0.00 38.42 5.03
586 609 6.149640 TCGCTAGCTAATCGTATCAAATCTCT 59.850 38.462 13.93 0.00 0.00 3.10
590 613 5.011533 AGCTAATCGTATCAAATCTCTGCCT 59.988 40.000 0.00 0.00 0.00 4.75
594 617 3.636764 TCGTATCAAATCTCTGCCTGCTA 59.363 43.478 0.00 0.00 0.00 3.49
596 619 4.624882 CGTATCAAATCTCTGCCTGCTATC 59.375 45.833 0.00 0.00 0.00 2.08
598 621 4.069300 TCAAATCTCTGCCTGCTATCTG 57.931 45.455 0.00 0.00 0.00 2.90
599 622 3.139850 CAAATCTCTGCCTGCTATCTGG 58.860 50.000 0.00 0.00 0.00 3.86
600 623 2.395336 ATCTCTGCCTGCTATCTGGA 57.605 50.000 0.00 0.00 33.56 3.86
601 624 1.702182 TCTCTGCCTGCTATCTGGAG 58.298 55.000 0.00 0.00 33.56 3.86
602 625 1.063341 TCTCTGCCTGCTATCTGGAGT 60.063 52.381 0.00 0.00 33.56 3.85
603 626 2.175715 TCTCTGCCTGCTATCTGGAGTA 59.824 50.000 0.00 0.00 33.56 2.59
604 627 2.557924 CTCTGCCTGCTATCTGGAGTAG 59.442 54.545 0.00 0.00 33.56 2.57
605 628 2.091610 TCTGCCTGCTATCTGGAGTAGT 60.092 50.000 0.00 0.00 33.56 2.73
607 630 2.695666 TGCCTGCTATCTGGAGTAGTTC 59.304 50.000 0.00 0.00 33.56 3.01
609 632 4.145807 GCCTGCTATCTGGAGTAGTTCTA 58.854 47.826 0.00 0.00 33.56 2.10
611 634 5.336372 GCCTGCTATCTGGAGTAGTTCTATG 60.336 48.000 0.00 0.00 33.56 2.23
659 700 4.755266 AGAATTGTAGGTCCGCTTACAT 57.245 40.909 0.00 0.00 37.10 2.29
660 701 4.442706 AGAATTGTAGGTCCGCTTACATG 58.557 43.478 0.00 0.00 37.10 3.21
665 706 1.883084 GGTCCGCTTACATGCCTCG 60.883 63.158 0.00 0.00 0.00 4.63
666 707 1.153628 GTCCGCTTACATGCCTCGT 60.154 57.895 0.00 0.00 0.00 4.18
698 739 0.025001 CGTAGCTGATTTCGTTGCCG 59.975 55.000 0.00 0.00 0.00 5.69
719 760 5.622378 CCGATTTTCTGTCAGTAAGCTTTC 58.378 41.667 3.20 0.00 0.00 2.62
732 773 3.971032 AAGCTTTCTTTTCGGTGTCAG 57.029 42.857 0.00 0.00 0.00 3.51
767 808 6.642540 CCTTTCTTTCAGATTTTTACACAGCC 59.357 38.462 0.00 0.00 0.00 4.85
810 851 8.954950 ACAGTATCATAACCTTTTGATCTCTG 57.045 34.615 14.45 14.45 38.68 3.35
867 908 9.201127 CCGATCCACATATGCTATGATTTATAG 57.799 37.037 1.58 0.00 41.46 1.31
868 909 9.971922 CGATCCACATATGCTATGATTTATAGA 57.028 33.333 1.58 0.00 41.10 1.98
872 913 9.881649 CCACATATGCTATGATTTATAGACTGT 57.118 33.333 1.58 0.00 41.10 3.55
954 1003 5.279506 CCCTTCTAGCACTAGTGTTCTGAAA 60.280 44.000 23.44 10.60 34.84 2.69
959 1008 7.272978 TCTAGCACTAGTGTTCTGAAACTTTT 58.727 34.615 23.44 0.00 34.84 2.27
960 1009 6.124088 AGCACTAGTGTTCTGAAACTTTTG 57.876 37.500 23.44 8.50 36.30 2.44
961 1010 5.880332 AGCACTAGTGTTCTGAAACTTTTGA 59.120 36.000 23.44 0.00 36.30 2.69
962 1011 6.543831 AGCACTAGTGTTCTGAAACTTTTGAT 59.456 34.615 23.44 5.19 36.30 2.57
963 1012 6.853362 GCACTAGTGTTCTGAAACTTTTGATC 59.147 38.462 23.44 0.00 36.30 2.92
964 1013 7.254932 GCACTAGTGTTCTGAAACTTTTGATCT 60.255 37.037 23.44 0.00 36.30 2.75
966 1015 9.178758 ACTAGTGTTCTGAAACTTTTGATCTTT 57.821 29.630 0.00 0.00 36.30 2.52
969 1018 8.624776 AGTGTTCTGAAACTTTTGATCTTTAGG 58.375 33.333 0.00 0.00 36.30 2.69
1023 1081 2.035961 GGCAAAGAAAGGGAAGTGGTTC 59.964 50.000 0.00 0.00 0.00 3.62
1282 1344 1.270826 ACAGTGTCAGACATCACTCCG 59.729 52.381 6.51 0.00 42.05 4.63
1315 1377 4.093291 CTGCCGCTGCCTCTTCCT 62.093 66.667 0.00 0.00 36.33 3.36
1321 1383 1.826709 GCTGCCTCTTCCTCCTACC 59.173 63.158 0.00 0.00 0.00 3.18
1340 1402 3.715097 AGCCTCCTCAGCCACAGC 61.715 66.667 0.00 0.00 40.32 4.40
1571 1633 3.400188 CCGCCTTCAGGGGTTACT 58.600 61.111 8.97 0.00 45.67 2.24
1594 1656 3.621268 TGGTAATGAATCTACACTTGCGC 59.379 43.478 0.00 0.00 0.00 6.09
1869 1944 6.855836 TGCTGGTCATTTTCAATCATACTTC 58.144 36.000 0.00 0.00 0.00 3.01
1870 1945 6.660521 TGCTGGTCATTTTCAATCATACTTCT 59.339 34.615 0.00 0.00 0.00 2.85
2003 2081 4.838423 TGTACTTCTTGGGATGAAGAGTCA 59.162 41.667 10.00 4.13 42.37 3.41
2157 2240 1.067495 AGGCTGAAGTCGCTAGTTGAC 60.067 52.381 8.66 8.66 36.60 3.18
2346 2429 5.461526 GTGAGCACCCTTTTTGAAATAGTC 58.538 41.667 0.00 0.00 0.00 2.59
2369 2452 4.922103 CCTTGCAAAGCTCTTCATCTTTTC 59.078 41.667 0.00 0.00 44.44 2.29
2370 2453 5.278858 CCTTGCAAAGCTCTTCATCTTTTCT 60.279 40.000 0.00 0.00 44.44 2.52
2371 2454 5.779529 TGCAAAGCTCTTCATCTTTTCTT 57.220 34.783 0.00 0.00 30.79 2.52
2372 2455 6.152932 TGCAAAGCTCTTCATCTTTTCTTT 57.847 33.333 0.00 0.00 30.79 2.52
2373 2456 6.576185 TGCAAAGCTCTTCATCTTTTCTTTT 58.424 32.000 0.00 0.00 30.79 2.27
2374 2457 6.698766 TGCAAAGCTCTTCATCTTTTCTTTTC 59.301 34.615 0.00 0.00 30.79 2.29
2375 2458 6.145209 GCAAAGCTCTTCATCTTTTCTTTTCC 59.855 38.462 0.00 0.00 30.79 3.13
2378 2461 5.835280 AGCTCTTCATCTTTTCTTTTCCCAA 59.165 36.000 0.00 0.00 0.00 4.12
2380 2463 6.422100 GCTCTTCATCTTTTCTTTTCCCAAAC 59.578 38.462 0.00 0.00 0.00 2.93
2382 2465 8.021898 TCTTCATCTTTTCTTTTCCCAAACAT 57.978 30.769 0.00 0.00 0.00 2.71
2383 2466 9.142014 TCTTCATCTTTTCTTTTCCCAAACATA 57.858 29.630 0.00 0.00 0.00 2.29
2385 2468 9.709495 TTCATCTTTTCTTTTCCCAAACATATG 57.291 29.630 0.00 0.00 0.00 1.78
2386 2469 8.313292 TCATCTTTTCTTTTCCCAAACATATGG 58.687 33.333 7.80 0.00 40.35 2.74
2427 2532 2.605607 CCATGAGACACCCCCTGCA 61.606 63.158 0.00 0.00 0.00 4.41
2437 2542 4.340246 CCCCTGCAGAGCACAGCA 62.340 66.667 17.39 0.73 37.05 4.41
2524 2722 5.452077 GGACAGTTCTCCGCTCTATTTACAT 60.452 44.000 0.00 0.00 0.00 2.29
2531 2729 9.095065 GTTCTCCGCTCTATTTACATAAAAAGA 57.905 33.333 0.00 0.00 0.00 2.52
2827 3055 2.358322 TTGGTTTCCCCTGTGTCTTC 57.642 50.000 0.00 0.00 0.00 2.87
3636 3874 5.278169 GGATGTCAATGTTGCCTGATATGAC 60.278 44.000 0.00 0.00 0.00 3.06
3775 4014 1.418264 TGTCCGGGTTGATTTGAGACA 59.582 47.619 0.00 0.00 0.00 3.41
4013 4253 7.976135 AATTCCTGACTATTGAGATATGCAC 57.024 36.000 0.00 0.00 0.00 4.57
4055 4295 4.397420 TGTTATGCCAACTGAATCACTGT 58.603 39.130 0.65 0.00 0.00 3.55
4164 4417 9.174166 TGTATTTTTCTTCTATCAAAGGCTACC 57.826 33.333 0.00 0.00 0.00 3.18
4217 4491 2.472816 CAACATTGTGGTTGGCAGAAC 58.527 47.619 0.00 0.00 43.39 3.01
4231 4505 0.326264 CAGAACAGAAGGGACCTGGG 59.674 60.000 0.00 0.00 36.03 4.45
4287 4564 5.465390 TGAAGCGTGATTGCTAACCATATAC 59.535 40.000 0.00 0.00 46.60 1.47
4288 4565 5.215252 AGCGTGATTGCTAACCATATACT 57.785 39.130 0.00 0.00 45.14 2.12
4424 4705 4.350368 TGATGCTTGACTTGTACTCCAA 57.650 40.909 0.00 0.00 0.00 3.53
4483 4764 3.876341 ACGTTTCTTCAAAGGTACCACA 58.124 40.909 15.94 0.00 38.54 4.17
4499 4780 5.766174 GGTACCACAACCAACTTCAATAAGA 59.234 40.000 7.15 0.00 39.50 2.10
4500 4781 6.263617 GGTACCACAACCAACTTCAATAAGAA 59.736 38.462 7.15 0.00 39.50 2.52
4561 4880 2.474410 AAAAAGCTCTGGTCCTACCG 57.526 50.000 0.00 0.00 42.58 4.02
4562 4881 0.036294 AAAAGCTCTGGTCCTACCGC 60.036 55.000 0.00 0.00 42.58 5.68
4563 4882 1.900545 AAAGCTCTGGTCCTACCGCC 61.901 60.000 0.00 0.00 42.58 6.13
4564 4883 4.208686 GCTCTGGTCCTACCGCCG 62.209 72.222 0.00 0.00 42.58 6.46
4565 4884 4.208686 CTCTGGTCCTACCGCCGC 62.209 72.222 0.00 0.00 42.58 6.53
4583 4902 2.739784 CCCCCGCATGCACAAAAA 59.260 55.556 19.57 0.00 0.00 1.94
4584 4903 1.296068 CCCCCGCATGCACAAAAAT 59.704 52.632 19.57 0.00 0.00 1.82
4585 4904 0.321475 CCCCCGCATGCACAAAAATT 60.321 50.000 19.57 0.00 0.00 1.82
4586 4905 1.066573 CCCCCGCATGCACAAAAATTA 60.067 47.619 19.57 0.00 0.00 1.40
4587 4906 2.419851 CCCCCGCATGCACAAAAATTAT 60.420 45.455 19.57 0.00 0.00 1.28
4588 4907 2.608546 CCCCGCATGCACAAAAATTATG 59.391 45.455 19.57 0.00 0.00 1.90
4589 4908 3.519579 CCCGCATGCACAAAAATTATGA 58.480 40.909 19.57 0.00 0.00 2.15
4590 4909 3.931468 CCCGCATGCACAAAAATTATGAA 59.069 39.130 19.57 0.00 0.00 2.57
4591 4910 4.391216 CCCGCATGCACAAAAATTATGAAA 59.609 37.500 19.57 0.00 0.00 2.69
4592 4911 5.064962 CCCGCATGCACAAAAATTATGAAAT 59.935 36.000 19.57 0.00 0.00 2.17
4593 4912 6.186785 CCGCATGCACAAAAATTATGAAATC 58.813 36.000 19.57 0.00 0.00 2.17
4594 4913 6.183360 CCGCATGCACAAAAATTATGAAATCA 60.183 34.615 19.57 0.00 0.00 2.57
4595 4914 7.235080 CGCATGCACAAAAATTATGAAATCAA 58.765 30.769 19.57 0.00 0.00 2.57
4596 4915 7.424167 CGCATGCACAAAAATTATGAAATCAAG 59.576 33.333 19.57 0.00 0.00 3.02
4597 4916 8.444715 GCATGCACAAAAATTATGAAATCAAGA 58.555 29.630 14.21 0.00 0.00 3.02
4600 4919 9.322773 TGCACAAAAATTATGAAATCAAGAACA 57.677 25.926 0.00 0.00 0.00 3.18
4612 4931 9.768662 ATGAAATCAAGAACAATTTTGCTAAGT 57.231 25.926 0.00 0.00 0.00 2.24
4613 4932 9.248291 TGAAATCAAGAACAATTTTGCTAAGTC 57.752 29.630 0.00 0.00 0.00 3.01
4614 4933 9.468532 GAAATCAAGAACAATTTTGCTAAGTCT 57.531 29.630 0.00 0.00 0.00 3.24
4615 4934 9.468532 AAATCAAGAACAATTTTGCTAAGTCTC 57.531 29.630 0.00 0.00 0.00 3.36
4616 4935 7.566760 TCAAGAACAATTTTGCTAAGTCTCA 57.433 32.000 0.00 0.00 0.00 3.27
4617 4936 7.642669 TCAAGAACAATTTTGCTAAGTCTCAG 58.357 34.615 0.00 0.00 0.00 3.35
4618 4937 7.283127 TCAAGAACAATTTTGCTAAGTCTCAGT 59.717 33.333 0.00 0.00 0.00 3.41
4619 4938 7.573968 AGAACAATTTTGCTAAGTCTCAGTT 57.426 32.000 0.00 0.00 0.00 3.16
4620 4939 7.420800 AGAACAATTTTGCTAAGTCTCAGTTG 58.579 34.615 0.00 0.00 0.00 3.16
4621 4940 6.942532 ACAATTTTGCTAAGTCTCAGTTGA 57.057 33.333 0.00 0.00 0.00 3.18
4622 4941 6.729187 ACAATTTTGCTAAGTCTCAGTTGAC 58.271 36.000 0.00 0.00 37.23 3.18
4624 4943 5.991328 TTTTGCTAAGTCTCAGTTGACTG 57.009 39.130 4.77 4.77 45.49 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 0.032117 GAAATGGAAAGGGGAGGGGG 60.032 60.000 0.00 0.00 0.00 5.40
42 43 1.010795 AGAAATGGAAAGGGGAGGGG 58.989 55.000 0.00 0.00 0.00 4.79
43 44 2.624293 GGAAGAAATGGAAAGGGGAGGG 60.624 54.545 0.00 0.00 0.00 4.30
161 168 4.106925 CCTGGCTGCCCACCTCTC 62.107 72.222 17.53 0.00 35.79 3.20
291 313 4.214119 CGACAAGGAAGAAGAAGCAATCAA 59.786 41.667 0.00 0.00 0.00 2.57
294 316 2.485814 GCGACAAGGAAGAAGAAGCAAT 59.514 45.455 0.00 0.00 0.00 3.56
324 346 2.226674 GCACCTCAAACTTAACCAGAGC 59.773 50.000 0.00 0.00 0.00 4.09
362 384 4.148825 CTCGCCCAACTCCTCCGG 62.149 72.222 0.00 0.00 0.00 5.14
403 426 1.485066 AGACACCAACCGAAACAGACT 59.515 47.619 0.00 0.00 0.00 3.24
427 450 4.875536 TCAGCGAAAATAATAGCAGCAAGA 59.124 37.500 0.00 0.00 0.00 3.02
429 452 4.201910 GGTCAGCGAAAATAATAGCAGCAA 60.202 41.667 0.00 0.00 0.00 3.91
431 454 3.604772 CGGTCAGCGAAAATAATAGCAGC 60.605 47.826 0.00 0.00 0.00 5.25
433 456 3.787785 TCGGTCAGCGAAAATAATAGCA 58.212 40.909 0.00 0.00 0.00 3.49
435 458 6.525121 TCAATCGGTCAGCGAAAATAATAG 57.475 37.500 1.56 0.00 0.00 1.73
437 460 5.277974 CCATCAATCGGTCAGCGAAAATAAT 60.278 40.000 1.56 0.00 0.00 1.28
450 473 0.695924 TCAACACCCCATCAATCGGT 59.304 50.000 0.00 0.00 0.00 4.69
462 485 1.864176 CGCGTTACCCTTCAACACC 59.136 57.895 0.00 0.00 0.00 4.16
538 561 4.745125 AGGACATAATCGTGCGTCATAAAG 59.255 41.667 0.00 0.00 31.60 1.85
546 569 0.595053 AGCGAGGACATAATCGTGCG 60.595 55.000 0.00 0.00 40.97 5.34
562 585 6.250315 CAGAGATTTGATACGATTAGCTAGCG 59.750 42.308 9.55 14.23 0.00 4.26
564 587 6.529829 GGCAGAGATTTGATACGATTAGCTAG 59.470 42.308 0.00 0.00 0.00 3.42
586 609 2.461300 ACTACTCCAGATAGCAGGCA 57.539 50.000 0.00 0.00 0.00 4.75
590 613 7.661536 AAACATAGAACTACTCCAGATAGCA 57.338 36.000 0.00 0.00 0.00 3.49
594 617 8.152023 AGGAAAAACATAGAACTACTCCAGAT 57.848 34.615 0.00 0.00 0.00 2.90
596 619 9.892130 ATTAGGAAAAACATAGAACTACTCCAG 57.108 33.333 0.00 0.00 0.00 3.86
604 627 9.503427 CCGAATCAATTAGGAAAAACATAGAAC 57.497 33.333 0.00 0.00 34.90 3.01
605 628 9.238368 ACCGAATCAATTAGGAAAAACATAGAA 57.762 29.630 8.63 0.00 36.25 2.10
636 659 5.864418 TGTAAGCGGACCTACAATTCTAT 57.136 39.130 0.00 0.00 0.00 1.98
637 660 5.597806 CATGTAAGCGGACCTACAATTCTA 58.402 41.667 0.00 0.00 0.00 2.10
638 661 4.442706 CATGTAAGCGGACCTACAATTCT 58.557 43.478 0.00 0.00 0.00 2.40
639 662 3.002348 GCATGTAAGCGGACCTACAATTC 59.998 47.826 0.00 0.00 0.00 2.17
640 663 2.943033 GCATGTAAGCGGACCTACAATT 59.057 45.455 0.00 0.00 0.00 2.32
641 664 2.561569 GCATGTAAGCGGACCTACAAT 58.438 47.619 0.00 0.00 0.00 2.71
645 686 0.750850 GAGGCATGTAAGCGGACCTA 59.249 55.000 0.00 0.00 34.64 3.08
698 739 9.175060 GAAAAGAAAGCTTACTGACAGAAAATC 57.825 33.333 10.08 0.00 32.98 2.17
719 760 1.264288 GCAGGTTCTGACACCGAAAAG 59.736 52.381 0.00 0.00 42.33 2.27
732 773 4.137543 TCTGAAAGAAAGGAAGCAGGTTC 58.862 43.478 3.55 3.55 42.31 3.62
767 808 4.489810 ACTGTCGTTCTCTAATGAAGCAG 58.510 43.478 0.00 0.00 32.46 4.24
810 851 7.637709 GAACAGTTGTTCCACCAAAATATTC 57.362 36.000 12.82 0.00 46.42 1.75
867 908 8.244113 CCAGAAAAATCCAAGGTTTATACAGTC 58.756 37.037 0.00 0.00 0.00 3.51
868 909 7.309805 GCCAGAAAAATCCAAGGTTTATACAGT 60.310 37.037 0.00 0.00 0.00 3.55
869 910 7.035612 GCCAGAAAAATCCAAGGTTTATACAG 58.964 38.462 0.00 0.00 0.00 2.74
870 911 6.071051 GGCCAGAAAAATCCAAGGTTTATACA 60.071 38.462 0.00 0.00 0.00 2.29
871 912 6.154534 AGGCCAGAAAAATCCAAGGTTTATAC 59.845 38.462 5.01 0.00 0.00 1.47
872 913 6.260663 AGGCCAGAAAAATCCAAGGTTTATA 58.739 36.000 5.01 0.00 0.00 0.98
873 914 5.093677 AGGCCAGAAAAATCCAAGGTTTAT 58.906 37.500 5.01 0.00 0.00 1.40
926 975 5.307196 AGAACACTAGTGCTAGAAGGGAAAA 59.693 40.000 22.90 0.00 36.97 2.29
938 987 6.119144 TCAAAAGTTTCAGAACACTAGTGC 57.881 37.500 22.90 7.58 38.26 4.40
943 992 8.624776 CCTAAAGATCAAAAGTTTCAGAACACT 58.375 33.333 0.00 0.00 38.26 3.55
954 1003 7.229506 CACCTTCTTCACCTAAAGATCAAAAGT 59.770 37.037 0.00 0.00 35.30 2.66
959 1008 4.041567 TGCACCTTCTTCACCTAAAGATCA 59.958 41.667 0.00 0.00 35.30 2.92
960 1009 4.579869 TGCACCTTCTTCACCTAAAGATC 58.420 43.478 0.00 0.00 35.30 2.75
961 1010 4.287067 TCTGCACCTTCTTCACCTAAAGAT 59.713 41.667 0.00 0.00 35.30 2.40
962 1011 3.646162 TCTGCACCTTCTTCACCTAAAGA 59.354 43.478 0.00 0.00 33.50 2.52
963 1012 4.008074 TCTGCACCTTCTTCACCTAAAG 57.992 45.455 0.00 0.00 0.00 1.85
964 1013 4.431416 TTCTGCACCTTCTTCACCTAAA 57.569 40.909 0.00 0.00 0.00 1.85
966 1015 3.244561 CCTTTCTGCACCTTCTTCACCTA 60.245 47.826 0.00 0.00 0.00 3.08
967 1016 2.487986 CCTTTCTGCACCTTCTTCACCT 60.488 50.000 0.00 0.00 0.00 4.00
968 1017 1.882623 CCTTTCTGCACCTTCTTCACC 59.117 52.381 0.00 0.00 0.00 4.02
969 1018 1.882623 CCCTTTCTGCACCTTCTTCAC 59.117 52.381 0.00 0.00 0.00 3.18
1023 1081 0.678395 ACACTCTCCTGACAGCACTG 59.322 55.000 0.00 0.00 0.00 3.66
1116 1177 3.132289 AGATGAGGGCAGATGCAAAATTG 59.868 43.478 7.19 0.00 44.36 2.32
1252 1314 1.456892 TGACACTGTCGAGGTGGGT 60.457 57.895 18.61 5.33 38.83 4.51
1282 1344 3.917760 AGCGGCGATGGAGCTACC 61.918 66.667 12.98 0.00 39.74 3.18
1309 1371 0.032017 GAGGCTGGGTAGGAGGAAGA 60.032 60.000 0.00 0.00 0.00 2.87
1310 1372 1.051556 GGAGGCTGGGTAGGAGGAAG 61.052 65.000 0.00 0.00 0.00 3.46
1312 1374 1.941820 AGGAGGCTGGGTAGGAGGA 60.942 63.158 0.00 0.00 0.00 3.71
1315 1377 1.311403 CTGAGGAGGCTGGGTAGGA 59.689 63.158 0.00 0.00 0.00 2.94
1321 1383 3.324930 TGTGGCTGAGGAGGCTGG 61.325 66.667 0.00 0.00 45.20 4.85
1340 1402 4.672587 TGACATCTTTTATCTCCTCGGG 57.327 45.455 0.00 0.00 0.00 5.14
1497 1559 1.609208 AACAGGTGTCCTTGATGTGC 58.391 50.000 0.00 0.00 0.00 4.57
1570 1632 5.727791 GCGCAAGTGTAGATTCATTACCAAG 60.728 44.000 0.30 0.00 41.68 3.61
1571 1633 4.094294 GCGCAAGTGTAGATTCATTACCAA 59.906 41.667 0.30 0.00 41.68 3.67
1594 1656 4.229096 ACAACAGCAAGCAATAAACATCG 58.771 39.130 0.00 0.00 0.00 3.84
1747 1821 8.485578 ACCAACCAAATCAGGTATCTTAAAAA 57.514 30.769 0.00 0.00 42.25 1.94
1748 1822 9.238368 CTACCAACCAAATCAGGTATCTTAAAA 57.762 33.333 0.00 0.00 42.25 1.52
1903 1978 5.920903 TCAGCTGTCATATCATCATTCACA 58.079 37.500 14.67 0.00 0.00 3.58
2124 2207 3.007398 ACTTCAGCCTAACAAGTCCTCTG 59.993 47.826 0.00 0.00 0.00 3.35
2341 2424 4.292186 TGAAGAGCTTTGCAAGGACTAT 57.708 40.909 13.48 3.68 0.00 2.12
2346 2429 4.516365 AAAGATGAAGAGCTTTGCAAGG 57.484 40.909 3.80 3.80 36.45 3.61
2385 2468 9.589111 TGGTTGTGTCTCTTTATTTTTAAAACC 57.411 29.630 0.00 0.00 0.00 3.27
2391 2496 8.352942 GTCTCATGGTTGTGTCTCTTTATTTTT 58.647 33.333 0.00 0.00 0.00 1.94
2395 2500 5.934625 GTGTCTCATGGTTGTGTCTCTTTAT 59.065 40.000 0.00 0.00 0.00 1.40
2399 2504 2.037772 GGTGTCTCATGGTTGTGTCTCT 59.962 50.000 0.00 0.00 0.00 3.10
2400 2505 2.417719 GGTGTCTCATGGTTGTGTCTC 58.582 52.381 0.00 0.00 0.00 3.36
2427 2532 1.372251 CGTTCGAGTGCTGTGCTCT 60.372 57.895 0.00 0.00 35.00 4.09
2437 2542 4.657824 CGCCACCCACGTTCGAGT 62.658 66.667 0.00 0.00 0.00 4.18
2546 2744 7.870826 TCAATGTGAGTGGTATGTTTTTACTG 58.129 34.615 0.00 0.00 0.00 2.74
2547 2745 8.458573 TTCAATGTGAGTGGTATGTTTTTACT 57.541 30.769 0.00 0.00 0.00 2.24
2548 2746 8.564574 TCTTCAATGTGAGTGGTATGTTTTTAC 58.435 33.333 0.00 0.00 0.00 2.01
2549 2747 8.684386 TCTTCAATGTGAGTGGTATGTTTTTA 57.316 30.769 0.00 0.00 0.00 1.52
2827 3055 3.393089 AGGAGCACACAACAGAAGTAG 57.607 47.619 0.00 0.00 0.00 2.57
3636 3874 2.885644 CGCCTGACGTTCATCGGG 60.886 66.667 0.00 0.00 46.61 5.14
3775 4014 5.471456 CCTCTGTCTGCAAACAGTTAGAATT 59.529 40.000 19.34 0.00 45.57 2.17
3959 4199 5.393962 GTCTTACATTTCAAGCATGGTGAC 58.606 41.667 0.00 0.00 0.00 3.67
3960 4200 4.154015 CGTCTTACATTTCAAGCATGGTGA 59.846 41.667 0.00 0.00 0.00 4.02
4164 4417 0.099968 CAGCCTGAATGCCAATCGTG 59.900 55.000 0.00 0.00 0.00 4.35
4217 4491 0.326264 CTGAACCCAGGTCCCTTCTG 59.674 60.000 0.00 0.00 36.77 3.02
4287 4564 0.957395 CCACCACAAGCTACAGCCAG 60.957 60.000 0.00 0.00 43.38 4.85
4288 4565 1.073025 CCACCACAAGCTACAGCCA 59.927 57.895 0.00 0.00 43.38 4.75
4424 4705 3.518303 GGGAGTACCACCAGATAAAGTGT 59.482 47.826 8.60 0.00 39.85 3.55
4499 4780 9.303116 CCAAGTCATACCACTAGTATATCTCTT 57.697 37.037 0.00 1.94 39.79 2.85
4500 4781 8.449625 ACCAAGTCATACCACTAGTATATCTCT 58.550 37.037 0.00 0.00 39.79 3.10
4501 4782 8.638629 ACCAAGTCATACCACTAGTATATCTC 57.361 38.462 0.00 0.00 39.79 2.75
4503 4784 7.599245 GCAACCAAGTCATACCACTAGTATATC 59.401 40.741 0.00 0.00 39.79 1.63
4506 4787 5.671493 GCAACCAAGTCATACCACTAGTAT 58.329 41.667 0.00 0.00 42.69 2.12
4507 4788 4.381185 CGCAACCAAGTCATACCACTAGTA 60.381 45.833 0.00 0.00 34.76 1.82
4508 4789 3.616560 CGCAACCAAGTCATACCACTAGT 60.617 47.826 0.00 0.00 0.00 2.57
4509 4790 2.930040 CGCAACCAAGTCATACCACTAG 59.070 50.000 0.00 0.00 0.00 2.57
4510 4791 2.354303 CCGCAACCAAGTCATACCACTA 60.354 50.000 0.00 0.00 0.00 2.74
4511 4792 1.610624 CCGCAACCAAGTCATACCACT 60.611 52.381 0.00 0.00 0.00 4.00
4512 4793 0.802494 CCGCAACCAAGTCATACCAC 59.198 55.000 0.00 0.00 0.00 4.16
4547 4866 4.208686 CGGCGGTAGGACCAGAGC 62.209 72.222 0.00 0.00 38.47 4.09
4548 4867 4.208686 GCGGCGGTAGGACCAGAG 62.209 72.222 9.78 0.00 38.47 3.35
4566 4885 0.321475 AATTTTTGTGCATGCGGGGG 60.321 50.000 14.09 0.00 0.00 5.40
4567 4886 2.376808 TAATTTTTGTGCATGCGGGG 57.623 45.000 14.09 0.00 0.00 5.73
4568 4887 3.519579 TCATAATTTTTGTGCATGCGGG 58.480 40.909 14.09 0.00 0.00 6.13
4569 4888 5.527511 TTTCATAATTTTTGTGCATGCGG 57.472 34.783 14.09 0.00 0.00 5.69
4570 4889 6.763101 TGATTTCATAATTTTTGTGCATGCG 58.237 32.000 14.09 0.00 0.00 4.73
4571 4890 8.444715 TCTTGATTTCATAATTTTTGTGCATGC 58.555 29.630 11.82 11.82 0.00 4.06
4574 4893 9.322773 TGTTCTTGATTTCATAATTTTTGTGCA 57.677 25.926 0.00 0.00 0.00 4.57
4586 4905 9.768662 ACTTAGCAAAATTGTTCTTGATTTCAT 57.231 25.926 0.00 0.00 0.00 2.57
4587 4906 9.248291 GACTTAGCAAAATTGTTCTTGATTTCA 57.752 29.630 0.00 0.00 0.00 2.69
4588 4907 9.468532 AGACTTAGCAAAATTGTTCTTGATTTC 57.531 29.630 0.00 0.00 0.00 2.17
4589 4908 9.468532 GAGACTTAGCAAAATTGTTCTTGATTT 57.531 29.630 0.00 0.00 0.00 2.17
4590 4909 8.632679 TGAGACTTAGCAAAATTGTTCTTGATT 58.367 29.630 0.00 0.00 0.00 2.57
4591 4910 8.169977 TGAGACTTAGCAAAATTGTTCTTGAT 57.830 30.769 0.00 0.00 0.00 2.57
4592 4911 7.283127 ACTGAGACTTAGCAAAATTGTTCTTGA 59.717 33.333 0.00 0.00 0.00 3.02
4593 4912 7.420800 ACTGAGACTTAGCAAAATTGTTCTTG 58.579 34.615 0.00 0.00 0.00 3.02
4594 4913 7.573968 ACTGAGACTTAGCAAAATTGTTCTT 57.426 32.000 0.00 0.00 0.00 2.52
4595 4914 7.283127 TCAACTGAGACTTAGCAAAATTGTTCT 59.717 33.333 0.00 0.00 0.00 3.01
4596 4915 7.377131 GTCAACTGAGACTTAGCAAAATTGTTC 59.623 37.037 0.00 0.00 35.65 3.18
4597 4916 7.067494 AGTCAACTGAGACTTAGCAAAATTGTT 59.933 33.333 0.00 0.00 46.26 2.83
4598 4917 6.543831 AGTCAACTGAGACTTAGCAAAATTGT 59.456 34.615 0.00 0.00 46.26 2.71
4599 4918 6.854892 CAGTCAACTGAGACTTAGCAAAATTG 59.145 38.462 4.05 0.00 46.26 2.32
4600 4919 6.767902 TCAGTCAACTGAGACTTAGCAAAATT 59.232 34.615 8.75 0.00 46.26 1.82
4601 4920 6.291377 TCAGTCAACTGAGACTTAGCAAAAT 58.709 36.000 8.75 0.00 46.26 1.82
4602 4921 5.670485 TCAGTCAACTGAGACTTAGCAAAA 58.330 37.500 8.75 0.00 46.26 2.44
4603 4922 5.276461 TCAGTCAACTGAGACTTAGCAAA 57.724 39.130 8.75 0.00 46.26 3.68
4604 4923 4.937201 TCAGTCAACTGAGACTTAGCAA 57.063 40.909 8.75 0.00 46.26 3.91


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

AutoCloner maintained by Alex Coulton.