Multiple sequence alignment - TraesCS3A01G432100

Loading Multiple Alignment...

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 TraesCS3A01G432100 chr3A 100.000 5216 0 0 1 5216 673443715 673438500 0.000000e+00 9633.0
1 TraesCS3A01G432100 chr3A 97.826 46 1 0 327 372 172679529 172679484 4.330000e-11 80.5
2 TraesCS3A01G432100 chr3B 93.539 2724 128 23 1 2693 712568482 712565776 0.000000e+00 4012.0
3 TraesCS3A01G432100 chr3B 96.759 2067 57 5 2678 4741 712565699 712563640 0.000000e+00 3437.0
4 TraesCS3A01G432100 chr3B 85.598 368 20 11 4845 5209 712563641 712563304 6.420000e-94 355.0
5 TraesCS3A01G432100 chr3D 91.407 2793 179 33 1700 4453 537911669 537908899 0.000000e+00 3771.0
6 TraesCS3A01G432100 chr3D 91.130 1691 84 29 1 1670 537913309 537911664 0.000000e+00 2231.0
7 TraesCS3A01G432100 chr3D 85.753 730 57 16 4492 5209 537908516 537907822 0.000000e+00 728.0
8 TraesCS3A01G432100 chr3D 95.918 49 2 0 324 372 574859873 574859921 4.330000e-11 80.5
9 TraesCS3A01G432100 chr4A 97.872 47 1 0 326 372 171066712 171066666 1.200000e-11 82.4
10 TraesCS3A01G432100 chr2A 96.000 50 2 0 325 374 437965406 437965455 1.200000e-11 82.4
11 TraesCS3A01G432100 chr2A 97.872 47 1 0 326 372 602770115 602770069 1.200000e-11 82.4
12 TraesCS3A01G432100 chr7B 97.826 46 1 0 327 372 510387630 510387585 4.330000e-11 80.5
13 TraesCS3A01G432100 chr7B 97.826 46 1 0 327 372 510433766 510433721 4.330000e-11 80.5
14 TraesCS3A01G432100 chr5D 97.826 46 1 0 327 372 278271122 278271077 4.330000e-11 80.5
15 TraesCS3A01G432100 chr5D 97.826 46 1 0 327 372 486112345 486112390 4.330000e-11 80.5


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 TraesCS3A01G432100 chr3A 673438500 673443715 5215 True 9633.000000 9633 100.000000 1 5216 1 chr3A.!!$R2 5215
1 TraesCS3A01G432100 chr3B 712563304 712568482 5178 True 2601.333333 4012 91.965333 1 5209 3 chr3B.!!$R1 5208
2 TraesCS3A01G432100 chr3D 537907822 537913309 5487 True 2243.333333 3771 89.430000 1 5209 3 chr3D.!!$R1 5208

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
335 346 1.066358 CCGTTCCAAACTACTCCCTCC 60.066 57.143 0.0 0.0 0.00 4.30 F
1131 1151 0.405198 TGCACTTCATCCCACCACAT 59.595 50.000 0.0 0.0 0.00 3.21 F
1483 1504 0.179234 TCCGTGGCTGTGTTCTTTCA 59.821 50.000 0.0 0.0 0.00 2.69 F
2763 2902 0.327259 ACAGGCATCAGCACACAGAT 59.673 50.000 0.0 0.0 44.61 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1371 1392 0.179137 TCTCACTTATCCTGTGCGCG 60.179 55.000 0.0 0.0 35.58 6.86 R
2365 2408 0.251787 CCAAAAGGGAAGGGGGTGAG 60.252 60.000 0.0 0.0 40.01 3.51 R
3281 3420 0.179073 AGCAACAGTGAACAGACGCT 60.179 50.000 0.0 0.0 0.00 5.07 R
4560 5078 2.035066 AGGCAGCAAAGTTGTGTTCATC 59.965 45.455 0.0 0.0 0.00 2.92 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
91 92 5.993748 TCCTCATTATCGTGTGCCATATA 57.006 39.130 0.00 0.00 0.00 0.86
146 150 3.243569 CGTTTTTGTAATGTGGGCCTTCA 60.244 43.478 4.53 4.62 0.00 3.02
200 211 2.102578 GTGATTCAACTCCATTGGGGG 58.897 52.381 7.66 1.42 42.10 5.40
233 244 2.945668 GGAATCACGGGGAAAGAATCAG 59.054 50.000 0.00 0.00 0.00 2.90
328 339 6.362210 TGTACTTTTTCCGTTCCAAACTAC 57.638 37.500 0.00 0.00 0.00 2.73
329 340 6.114767 TGTACTTTTTCCGTTCCAAACTACT 58.885 36.000 0.00 0.00 0.00 2.57
330 341 5.746307 ACTTTTTCCGTTCCAAACTACTC 57.254 39.130 0.00 0.00 0.00 2.59
331 342 4.577693 ACTTTTTCCGTTCCAAACTACTCC 59.422 41.667 0.00 0.00 0.00 3.85
333 344 2.019807 TCCGTTCCAAACTACTCCCT 57.980 50.000 0.00 0.00 0.00 4.20
334 345 1.897802 TCCGTTCCAAACTACTCCCTC 59.102 52.381 0.00 0.00 0.00 4.30
335 346 1.066358 CCGTTCCAAACTACTCCCTCC 60.066 57.143 0.00 0.00 0.00 4.30
336 347 1.621814 CGTTCCAAACTACTCCCTCCA 59.378 52.381 0.00 0.00 0.00 3.86
339 350 4.262617 GTTCCAAACTACTCCCTCCATTC 58.737 47.826 0.00 0.00 0.00 2.67
340 351 2.844348 TCCAAACTACTCCCTCCATTCC 59.156 50.000 0.00 0.00 0.00 3.01
341 352 2.576191 CCAAACTACTCCCTCCATTCCA 59.424 50.000 0.00 0.00 0.00 3.53
342 353 3.010138 CCAAACTACTCCCTCCATTCCAA 59.990 47.826 0.00 0.00 0.00 3.53
343 354 4.508405 CCAAACTACTCCCTCCATTCCAAA 60.508 45.833 0.00 0.00 0.00 3.28
346 357 6.652205 AACTACTCCCTCCATTCCAAATTA 57.348 37.500 0.00 0.00 0.00 1.40
353 364 4.096382 CCCTCCATTCCAAATTACTTGTCG 59.904 45.833 0.00 0.00 32.65 4.35
354 365 4.700213 CCTCCATTCCAAATTACTTGTCGT 59.300 41.667 0.00 0.00 32.65 4.34
355 366 5.391950 CCTCCATTCCAAATTACTTGTCGTG 60.392 44.000 0.00 0.00 32.65 4.35
360 371 5.838531 TCCAAATTACTTGTCGTGGTTTT 57.161 34.783 0.00 0.00 32.65 2.43
361 372 6.939132 TCCAAATTACTTGTCGTGGTTTTA 57.061 33.333 0.00 0.00 32.65 1.52
362 373 7.330900 TCCAAATTACTTGTCGTGGTTTTAA 57.669 32.000 0.00 0.00 32.65 1.52
363 374 7.942990 TCCAAATTACTTGTCGTGGTTTTAAT 58.057 30.769 0.00 0.00 32.65 1.40
364 375 8.414778 TCCAAATTACTTGTCGTGGTTTTAATT 58.585 29.630 0.00 0.00 32.65 1.40
365 376 8.696175 CCAAATTACTTGTCGTGGTTTTAATTC 58.304 33.333 0.00 0.00 32.65 2.17
366 377 9.239002 CAAATTACTTGTCGTGGTTTTAATTCA 57.761 29.630 0.00 0.00 0.00 2.57
367 378 9.804758 AAATTACTTGTCGTGGTTTTAATTCAA 57.195 25.926 0.00 0.00 0.00 2.69
368 379 9.804758 AATTACTTGTCGTGGTTTTAATTCAAA 57.195 25.926 0.00 0.00 0.00 2.69
369 380 9.974980 ATTACTTGTCGTGGTTTTAATTCAAAT 57.025 25.926 0.00 0.00 0.00 2.32
370 381 9.804758 TTACTTGTCGTGGTTTTAATTCAAATT 57.195 25.926 0.00 0.00 0.00 1.82
528 539 6.047511 AGATAGAGAAGTTTGACTGCACAT 57.952 37.500 0.00 0.00 0.00 3.21
577 596 5.424121 AGCTTGTAGCAACTAAAAGTGTG 57.576 39.130 6.45 0.00 45.56 3.82
705 724 7.202130 CCTCTCCTTATTGTCCCATTCAGATTA 60.202 40.741 0.00 0.00 0.00 1.75
771 790 9.962783 CCTTCATAGAATCATTCCTTCAAAATC 57.037 33.333 0.00 0.00 0.00 2.17
793 812 5.545588 TCAGAATATGCTGTCCAGATAAGC 58.454 41.667 10.66 0.00 37.20 3.09
828 847 7.448748 TTGGAGTTATTCTTTGTTTCCTAGC 57.551 36.000 0.00 0.00 0.00 3.42
830 849 5.064834 GGAGTTATTCTTTGTTTCCTAGCGG 59.935 44.000 0.00 0.00 0.00 5.52
1008 1028 6.208402 TGCACTAAAGGAAATAAATGACAGCA 59.792 34.615 0.00 0.00 0.00 4.41
1010 1030 6.749118 CACTAAAGGAAATAAATGACAGCAGC 59.251 38.462 0.00 0.00 0.00 5.25
1079 1099 1.929860 CTGGCAGTGGGGGATGATGT 61.930 60.000 6.28 0.00 0.00 3.06
1082 1102 1.680338 GCAGTGGGGGATGATGTTAC 58.320 55.000 0.00 0.00 0.00 2.50
1090 1110 1.933853 GGGATGATGTTACGCAGTGTC 59.066 52.381 0.00 0.00 45.73 3.67
1131 1151 0.405198 TGCACTTCATCCCACCACAT 59.595 50.000 0.00 0.00 0.00 3.21
1371 1392 6.541086 CAAGTTGACAGAAGATCATGTTAGC 58.459 40.000 0.00 0.00 0.00 3.09
1433 1454 2.806608 AAGGAGTGCTTGCAAATGTG 57.193 45.000 0.00 0.00 0.00 3.21
1482 1503 0.586802 GTCCGTGGCTGTGTTCTTTC 59.413 55.000 0.00 0.00 0.00 2.62
1483 1504 0.179234 TCCGTGGCTGTGTTCTTTCA 59.821 50.000 0.00 0.00 0.00 2.69
1529 1550 0.950116 GAGCAGGGCACTGATATTGC 59.050 55.000 23.23 3.21 44.73 3.56
1539 1560 3.727723 GCACTGATATTGCGCATTTCTTC 59.272 43.478 12.75 5.14 0.00 2.87
1582 1603 8.797350 ACTCATAATTGACAAAGATGATGTGA 57.203 30.769 13.06 1.94 0.00 3.58
1586 1607 4.604843 TTGACAAAGATGATGTGATCGC 57.395 40.909 0.00 0.00 0.00 4.58
1601 1622 4.785453 CGCTGGACTTGGGGAGGC 62.785 72.222 0.00 0.00 0.00 4.70
1641 1662 3.863142 ACTACACTCGTTATGGGTGTC 57.137 47.619 13.89 0.00 42.24 3.67
1682 1703 4.270008 ACTTACATATGTTTCCTGGGTGC 58.730 43.478 14.77 0.00 0.00 5.01
1683 1704 4.018415 ACTTACATATGTTTCCTGGGTGCT 60.018 41.667 14.77 0.00 0.00 4.40
1844 1867 7.333921 GCAATATTCTGTATCTTCATGAGGGAG 59.666 40.741 4.83 0.00 0.00 4.30
2015 2039 7.816031 TCAAAGGAACGATACGACTAAAGAAAT 59.184 33.333 0.00 0.00 0.00 2.17
2027 2051 8.754230 ACGACTAAAGAAATAGAAACTGTACC 57.246 34.615 0.00 0.00 0.00 3.34
2349 2392 6.595326 CAGTTGAACTGTTAGGCATCTATGAA 59.405 38.462 16.84 0.00 41.19 2.57
2365 2408 8.155923 GCATCTATGAAAATCGACAAAACAAAC 58.844 33.333 0.00 0.00 0.00 2.93
2371 2414 3.982576 ATCGACAAAACAAACTCACCC 57.017 42.857 0.00 0.00 0.00 4.61
2427 2470 2.489938 TTCCCTTGCCGGCATATATC 57.510 50.000 33.25 0.00 0.00 1.63
2484 2527 8.298854 CAGTTCCAGTAATCAATCACAAAATGA 58.701 33.333 0.00 0.00 43.13 2.57
2584 2631 3.053619 AGCATATCCCCTTTTCTCGGTTT 60.054 43.478 0.00 0.00 0.00 3.27
2702 2841 5.982356 ACATGACAATCTTGCTAGCTTCTA 58.018 37.500 17.23 0.00 0.00 2.10
2717 2856 6.927936 GCTAGCTTCTATGATCTGTTCATCAA 59.072 38.462 7.70 0.26 44.13 2.57
2730 2869 9.875675 GATCTGTTCATCAACATTTATCTTAGC 57.124 33.333 0.00 0.00 41.82 3.09
2763 2902 0.327259 ACAGGCATCAGCACACAGAT 59.673 50.000 0.00 0.00 44.61 2.90
2892 3031 2.169144 TGACACGGAGCATCTTGATGAT 59.831 45.455 14.09 7.92 35.40 2.45
2899 3038 4.354893 GAGCATCTTGATGATCCTTCCT 57.645 45.455 15.53 1.96 32.05 3.36
3234 3373 0.443869 AGAATCATCGTGCACGCAAC 59.556 50.000 33.63 19.33 39.60 4.17
3364 3503 4.872691 AGCTATTCTGTGTACTGAACATGC 59.127 41.667 6.50 10.21 41.10 4.06
3801 3952 5.679734 TTCAAGAAGTCAAGCAATCAGAC 57.320 39.130 0.00 0.00 0.00 3.51
3935 4086 0.671472 GCAAAAAGCATGCCTCCCAC 60.671 55.000 15.66 0.00 44.79 4.61
4056 4207 3.690460 CCAGATTTGCTTGAAGGTACCT 58.310 45.455 9.21 9.21 0.00 3.08
4063 4214 3.244582 TGCTTGAAGGTACCTAGTCCAA 58.755 45.455 16.67 15.13 0.00 3.53
4173 4324 4.599047 ACAAAATGCGAGGGAATTTGAA 57.401 36.364 4.95 0.00 31.52 2.69
4316 4468 0.975040 TTGCTGCCCCTTGTGTTTGT 60.975 50.000 0.00 0.00 0.00 2.83
4475 4648 5.046591 CCGTCTCCCCTATATATTTGCTTCA 60.047 44.000 0.00 0.00 0.00 3.02
4476 4649 5.869888 CGTCTCCCCTATATATTTGCTTCAC 59.130 44.000 0.00 0.00 0.00 3.18
4478 4651 6.651225 GTCTCCCCTATATATTTGCTTCACAC 59.349 42.308 0.00 0.00 0.00 3.82
4479 4652 6.558775 TCTCCCCTATATATTTGCTTCACACT 59.441 38.462 0.00 0.00 0.00 3.55
4480 4653 7.072454 TCTCCCCTATATATTTGCTTCACACTT 59.928 37.037 0.00 0.00 0.00 3.16
4481 4654 7.224297 TCCCCTATATATTTGCTTCACACTTC 58.776 38.462 0.00 0.00 0.00 3.01
4496 5013 3.379372 CACACTTCCATCCAATCATCCAC 59.621 47.826 0.00 0.00 0.00 4.02
4514 5031 2.802816 CCACTAGTAAATGCATCGAGGC 59.197 50.000 16.46 16.46 0.00 4.70
4601 5119 3.276857 CTCATGTGCTATGTTGGCTCTT 58.723 45.455 0.00 0.00 0.00 2.85
4633 5159 5.435686 TCTTGCTTGGAGCTATTTCCTAA 57.564 39.130 1.29 0.00 42.97 2.69
4643 5169 6.158695 TGGAGCTATTTCCTAAAGACATCCTT 59.841 38.462 0.00 0.00 38.12 3.36
4646 5172 7.057264 AGCTATTTCCTAAAGACATCCTTTCC 58.943 38.462 0.00 0.00 43.61 3.13
4660 5186 8.772250 AGACATCCTTTCCTGTTATCTTTATGA 58.228 33.333 0.00 0.00 0.00 2.15
4684 5210 8.672329 TGAAATATATGTCATTCCCTCCTGAAT 58.328 33.333 1.09 0.00 35.36 2.57
4745 5271 2.024414 CAAGGCCAGCTACCAATAACC 58.976 52.381 5.01 0.00 0.00 2.85
4752 5281 3.527533 CAGCTACCAATAACCGCTACAA 58.472 45.455 0.00 0.00 0.00 2.41
4773 5302 4.799564 ACAATTTGTTTGCGGACCATAT 57.200 36.364 0.00 0.00 39.03 1.78
4778 5307 5.461032 TTTGTTTGCGGACCATATTTCTT 57.539 34.783 0.00 0.00 0.00 2.52
4783 5312 3.278574 TGCGGACCATATTTCTTTCAGG 58.721 45.455 0.00 0.00 0.00 3.86
4793 5322 7.038799 ACCATATTTCTTTCAGGTGAATTTGCT 60.039 33.333 0.00 0.00 33.54 3.91
4796 5325 2.297033 TCTTTCAGGTGAATTTGCTGCC 59.703 45.455 0.00 0.00 33.54 4.85
4814 5343 4.387598 CTGCCATATTCTTCTGGAAGGAG 58.612 47.826 10.01 0.00 42.67 3.69
4819 5348 1.553690 TTCTTCTGGAAGGAGCGGGG 61.554 60.000 10.01 0.00 40.36 5.73
4862 5391 6.513317 CAACAAAACACAAAGAAACGTTCTC 58.487 36.000 0.00 1.69 39.61 2.87
4863 5392 4.849383 ACAAAACACAAAGAAACGTTCTCG 59.151 37.500 0.00 0.00 39.61 4.04
4942 5471 5.515797 TTCTTCGAGAAGACAAAGACAGA 57.484 39.130 14.41 0.00 46.13 3.41
4967 5496 4.397032 AGGTACTAGCTTCCTGGCAACAT 61.397 47.826 0.00 0.00 43.47 2.71
4994 5523 2.032302 ACATTGTTTTTACAGCACGCGA 59.968 40.909 15.93 0.00 0.00 5.87
5004 5533 2.679450 ACAGCACGCGACATAGTTTTA 58.321 42.857 15.93 0.00 0.00 1.52
5012 5541 4.746115 ACGCGACATAGTTTTAACAGTCAA 59.254 37.500 15.93 0.00 31.90 3.18
5013 5542 5.070862 CGCGACATAGTTTTAACAGTCAAC 58.929 41.667 0.00 0.00 31.90 3.18
5014 5543 5.379827 GCGACATAGTTTTAACAGTCAACC 58.620 41.667 10.96 0.00 31.90 3.77
5017 5546 5.613329 ACATAGTTTTAACAGTCAACCCGA 58.387 37.500 0.00 0.00 0.00 5.14
5043 5572 7.229907 ACATAGTTTTTACAGTCAACCCGATTT 59.770 33.333 0.00 0.00 0.00 2.17
5046 5575 6.976349 AGTTTTTACAGTCAACCCGATTTTTC 59.024 34.615 0.00 0.00 0.00 2.29
5084 5613 8.813282 GTTCTCTTCTATCAGCTTTTACTAAGC 58.187 37.037 1.38 1.38 43.31 3.09
5146 5676 1.950216 TGCAACAAGACACGCCAATTA 59.050 42.857 0.00 0.00 0.00 1.40
5164 5694 6.761242 GCCAATTAACCAACCAATAATCTTCC 59.239 38.462 0.00 0.00 0.00 3.46
5169 5699 9.807921 ATTAACCAACCAATAATCTTCCGATAT 57.192 29.630 0.00 0.00 0.00 1.63
5171 5701 8.617290 AACCAACCAATAATCTTCCGATATAC 57.383 34.615 0.00 0.00 0.00 1.47
5172 5702 7.974504 ACCAACCAATAATCTTCCGATATACT 58.025 34.615 0.00 0.00 0.00 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 7.490962 TGTAGTATGCCAGCAATTTATGTAC 57.509 36.000 0.00 0.00 0.00 2.90
91 92 5.763876 AGTAAAGAATGGCAACTCCTACT 57.236 39.130 0.00 3.11 35.26 2.57
146 150 7.552050 TCCTGAAATGGACAAATATTTTGGT 57.448 32.000 0.00 0.00 0.00 3.67
200 211 3.467803 CCGTGATTCCCCTATTTCACTC 58.532 50.000 0.00 0.00 37.04 3.51
233 244 4.345547 TCCCACAAAACAAAAAGATACCCC 59.654 41.667 0.00 0.00 0.00 4.95
310 321 3.884693 GGGAGTAGTTTGGAACGGAAAAA 59.115 43.478 0.00 0.00 36.23 1.94
316 327 1.621814 TGGAGGGAGTAGTTTGGAACG 59.378 52.381 0.00 0.00 36.23 3.95
328 339 5.264395 ACAAGTAATTTGGAATGGAGGGAG 58.736 41.667 0.00 0.00 41.25 4.30
329 340 5.261216 GACAAGTAATTTGGAATGGAGGGA 58.739 41.667 0.00 0.00 41.25 4.20
330 341 4.096382 CGACAAGTAATTTGGAATGGAGGG 59.904 45.833 0.00 0.00 41.25 4.30
331 342 4.700213 ACGACAAGTAATTTGGAATGGAGG 59.300 41.667 0.00 0.00 41.25 4.30
333 344 4.457603 CCACGACAAGTAATTTGGAATGGA 59.542 41.667 0.00 0.00 41.25 3.41
334 345 4.217550 ACCACGACAAGTAATTTGGAATGG 59.782 41.667 0.00 3.07 41.25 3.16
335 346 5.371115 ACCACGACAAGTAATTTGGAATG 57.629 39.130 0.00 0.00 41.25 2.67
336 347 6.399639 AAACCACGACAAGTAATTTGGAAT 57.600 33.333 0.00 0.00 41.25 3.01
339 350 8.582433 AATTAAAACCACGACAAGTAATTTGG 57.418 30.769 0.00 0.00 41.25 3.28
340 351 9.239002 TGAATTAAAACCACGACAAGTAATTTG 57.761 29.630 0.00 0.00 42.68 2.32
341 352 9.804758 TTGAATTAAAACCACGACAAGTAATTT 57.195 25.926 0.00 0.00 0.00 1.82
342 353 9.804758 TTTGAATTAAAACCACGACAAGTAATT 57.195 25.926 0.00 0.00 0.00 1.40
343 354 9.974980 ATTTGAATTAAAACCACGACAAGTAAT 57.025 25.926 0.00 0.00 0.00 1.89
346 357 8.710835 AAATTTGAATTAAAACCACGACAAGT 57.289 26.923 0.00 0.00 0.00 3.16
396 407 0.682852 CCCGACTCCTTTACACACCA 59.317 55.000 0.00 0.00 0.00 4.17
559 570 5.179533 TCACACACACTTTTAGTTGCTACA 58.820 37.500 0.13 0.00 0.00 2.74
577 596 1.389106 GACAGAACGGCGTATTCACAC 59.611 52.381 15.20 0.00 0.00 3.82
771 790 4.694509 GGCTTATCTGGACAGCATATTCTG 59.305 45.833 0.38 0.38 39.86 3.02
793 812 4.772100 AGAATAACTCCAAACCACAATGGG 59.228 41.667 0.00 0.00 43.37 4.00
828 847 4.182339 GGAGTTAAGTTTCTCTTAGGCCG 58.818 47.826 0.00 0.00 39.42 6.13
830 849 6.645306 AGATGGAGTTAAGTTTCTCTTAGGC 58.355 40.000 7.40 0.00 39.42 3.93
875 894 0.394216 ATGCGCAATGCCCTCTGTTA 60.394 50.000 17.11 0.00 45.60 2.41
882 901 2.103538 CACAGATGCGCAATGCCC 59.896 61.111 17.11 1.19 45.60 5.36
1001 1021 2.248086 ATCCATGAGCGCTGCTGTCA 62.248 55.000 18.48 6.72 39.88 3.58
1006 1026 2.252346 CCAGATCCATGAGCGCTGC 61.252 63.158 18.48 7.36 0.00 5.25
1008 1028 2.110627 GCCAGATCCATGAGCGCT 59.889 61.111 11.27 11.27 0.00 5.92
1010 1030 0.463295 AGTTGCCAGATCCATGAGCG 60.463 55.000 0.00 0.00 0.00 5.03
1079 1099 0.599558 AGTAAGCCGACACTGCGTAA 59.400 50.000 0.00 0.00 0.00 3.18
1082 1102 0.798771 GAGAGTAAGCCGACACTGCG 60.799 60.000 0.00 0.00 0.00 5.18
1131 1151 6.653320 GGATGTGGACAAGAACTAACAACATA 59.347 38.462 0.00 0.00 0.00 2.29
1192 1212 4.937201 TCAGACAAACTAGAAGCAGACA 57.063 40.909 0.00 0.00 0.00 3.41
1250 1270 2.275134 TTTCTCCAAGCAGCATGACA 57.725 45.000 0.00 0.00 39.69 3.58
1320 1341 1.340017 GCCACTGAAGCTCCCAATACA 60.340 52.381 0.00 0.00 0.00 2.29
1371 1392 0.179137 TCTCACTTATCCTGTGCGCG 60.179 55.000 0.00 0.00 35.58 6.86
1433 1454 5.689383 TTCAGTTTCAGCATTCACCTTAC 57.311 39.130 0.00 0.00 0.00 2.34
1513 1534 1.096967 TGCGCAATATCAGTGCCCTG 61.097 55.000 8.16 0.00 41.59 4.45
1529 1550 2.352960 GCTTGGACCTAGAAGAAATGCG 59.647 50.000 7.17 0.00 0.00 4.73
1539 1560 4.211125 TGAGTATCTCTGCTTGGACCTAG 58.789 47.826 0.00 0.00 34.92 3.02
1582 1603 2.370445 CCTCCCCAAGTCCAGCGAT 61.370 63.158 0.00 0.00 0.00 4.58
1586 1607 2.190488 GACTGCCTCCCCAAGTCCAG 62.190 65.000 0.00 0.00 0.00 3.86
1623 1644 4.603989 TTTGACACCCATAACGAGTGTA 57.396 40.909 0.00 0.00 44.45 2.90
1844 1867 0.320421 TACCTGCTGGCAACGAGAAC 60.320 55.000 9.95 0.00 42.51 3.01
2349 2392 4.440940 GGGGTGAGTTTGTTTTGTCGATTT 60.441 41.667 0.00 0.00 0.00 2.17
2365 2408 0.251787 CCAAAAGGGAAGGGGGTGAG 60.252 60.000 0.00 0.00 40.01 3.51
2371 2414 1.427753 AGTGGTACCAAAAGGGAAGGG 59.572 52.381 18.31 0.00 41.15 3.95
2451 2494 6.595326 TGATTGATTACTGGAACTGCACTTAG 59.405 38.462 0.00 0.00 0.00 2.18
2496 2539 7.944729 ATGCTTGTGTCTCCTTTTATGTATT 57.055 32.000 0.00 0.00 0.00 1.89
2497 2540 7.611467 TGAATGCTTGTGTCTCCTTTTATGTAT 59.389 33.333 0.00 0.00 0.00 2.29
2499 2542 5.769662 TGAATGCTTGTGTCTCCTTTTATGT 59.230 36.000 0.00 0.00 0.00 2.29
2500 2543 6.258230 TGAATGCTTGTGTCTCCTTTTATG 57.742 37.500 0.00 0.00 0.00 1.90
2515 2560 6.105397 ACAATGGACTTCAAATGAATGCTT 57.895 33.333 0.00 0.00 33.01 3.91
2584 2631 7.016153 AGTACAGTCAATCATGTTCCCTTAA 57.984 36.000 0.00 0.00 0.00 1.85
2615 2662 3.695830 AAATCGTTTACTCTGGCAGGA 57.304 42.857 15.73 1.98 0.00 3.86
2717 2856 9.614792 AAATAAACGAGAGGCTAAGATAAATGT 57.385 29.630 0.00 0.00 0.00 2.71
2723 2862 7.210873 CCTGTAAATAAACGAGAGGCTAAGAT 58.789 38.462 0.00 0.00 0.00 2.40
2729 2868 3.267483 TGCCTGTAAATAAACGAGAGGC 58.733 45.455 0.00 0.00 44.02 4.70
2730 2869 5.116180 TGATGCCTGTAAATAAACGAGAGG 58.884 41.667 0.00 0.00 0.00 3.69
2763 2902 3.711863 AGAAGGCATGCCAATTTTCCTA 58.288 40.909 37.18 0.00 38.92 2.94
2892 3031 6.012508 AGGTTGAATTCATCACTAAGGAAGGA 60.013 38.462 9.40 0.00 37.92 3.36
2944 3083 9.167311 GTCAAATGACTTGAGACCAATTATAGT 57.833 33.333 6.30 0.00 44.83 2.12
3229 3368 3.063316 TCATCATGTGTAAATCCGTTGCG 59.937 43.478 0.00 0.00 0.00 4.85
3234 3373 5.353956 TGAAAGGTCATCATGTGTAAATCCG 59.646 40.000 0.00 0.00 0.00 4.18
3281 3420 0.179073 AGCAACAGTGAACAGACGCT 60.179 50.000 0.00 0.00 0.00 5.07
3492 3643 6.425721 GCACTACTTTTGGTGAGTTGTATGTA 59.574 38.462 0.00 0.00 32.67 2.29
3599 3750 8.363390 TGTCAGTGTAATCATGAGATAGAATCC 58.637 37.037 0.09 0.00 33.08 3.01
3669 3820 4.830046 TCTAGATCAGTAATGAGCCCAGAC 59.170 45.833 4.58 0.00 0.00 3.51
3984 4135 3.515602 AAACTCTGCAAGGGAGTCATT 57.484 42.857 7.48 0.00 35.24 2.57
3985 4136 3.152341 CAAAACTCTGCAAGGGAGTCAT 58.848 45.455 7.48 0.00 35.24 3.06
4475 4648 3.267812 AGTGGATGATTGGATGGAAGTGT 59.732 43.478 0.00 0.00 0.00 3.55
4476 4649 3.894759 AGTGGATGATTGGATGGAAGTG 58.105 45.455 0.00 0.00 0.00 3.16
4478 4651 5.301835 ACTAGTGGATGATTGGATGGAAG 57.698 43.478 0.00 0.00 0.00 3.46
4479 4652 6.823286 TTACTAGTGGATGATTGGATGGAA 57.177 37.500 5.39 0.00 0.00 3.53
4480 4653 6.823286 TTTACTAGTGGATGATTGGATGGA 57.177 37.500 5.39 0.00 0.00 3.41
4481 4654 6.072286 GCATTTACTAGTGGATGATTGGATGG 60.072 42.308 18.91 0.00 0.00 3.51
4514 5031 8.425577 AAGTAAAGACGAATGAAGATACCATG 57.574 34.615 0.00 0.00 0.00 3.66
4560 5078 2.035066 AGGCAGCAAAGTTGTGTTCATC 59.965 45.455 0.00 0.00 0.00 2.92
4601 5119 3.815401 GCTCCAAGCAAGAAAGTACAAGA 59.185 43.478 0.00 0.00 41.89 3.02
4633 5159 9.401058 CATAAAGATAACAGGAAAGGATGTCTT 57.599 33.333 0.00 0.00 37.28 3.01
4684 5210 4.052608 TCGTTTTCGCTGTCACATTCTTA 58.947 39.130 0.00 0.00 43.73 2.10
4752 5281 4.799564 ATATGGTCCGCAAACAAATTGT 57.200 36.364 0.00 0.00 41.32 2.71
4765 5294 7.410120 AATTCACCTGAAAGAAATATGGTCC 57.590 36.000 0.00 0.00 37.61 4.46
4773 5302 4.370917 GCAGCAAATTCACCTGAAAGAAA 58.629 39.130 4.66 0.00 37.61 2.52
4778 5307 1.702182 TGGCAGCAAATTCACCTGAA 58.298 45.000 0.00 0.00 38.56 3.02
4783 5312 5.747197 CAGAAGAATATGGCAGCAAATTCAC 59.253 40.000 13.22 8.44 32.04 3.18
4793 5322 3.434167 GCTCCTTCCAGAAGAATATGGCA 60.434 47.826 9.00 0.00 40.79 4.92
4796 5325 3.397482 CCGCTCCTTCCAGAAGAATATG 58.603 50.000 9.00 0.00 40.79 1.78
4819 5348 2.740055 CTGGAGCGGCACACACTC 60.740 66.667 1.45 0.00 0.00 3.51
4830 5359 0.459489 TGTGTTTTGTTGCCTGGAGC 59.541 50.000 0.00 0.00 44.14 4.70
4832 5361 2.828520 TCTTTGTGTTTTGTTGCCTGGA 59.171 40.909 0.00 0.00 0.00 3.86
4862 5391 0.249398 CCCCCACTCAGAAAGTACCG 59.751 60.000 0.00 0.00 36.07 4.02
4863 5392 0.035343 GCCCCCACTCAGAAAGTACC 60.035 60.000 0.00 0.00 36.07 3.34
4942 5471 1.555533 GCCAGGAAGCTAGTACCTTGT 59.444 52.381 0.00 0.00 31.06 3.16
4967 5496 5.739630 CGTGCTGTAAAAACAATGTGTTACA 59.260 36.000 16.88 16.88 40.14 2.41
4973 5502 2.032302 TCGCGTGCTGTAAAAACAATGT 59.968 40.909 5.77 0.00 0.00 2.71
4994 5523 5.467735 GTCGGGTTGACTGTTAAAACTATGT 59.532 40.000 0.00 0.00 44.58 2.29
5012 5541 5.217978 TGACTGTAAAAACTATGTCGGGT 57.782 39.130 0.00 0.00 0.00 5.28
5013 5542 5.106830 GGTTGACTGTAAAAACTATGTCGGG 60.107 44.000 0.00 0.00 0.00 5.14
5014 5543 5.106830 GGGTTGACTGTAAAAACTATGTCGG 60.107 44.000 0.00 0.00 0.00 4.79
5017 5546 5.613329 TCGGGTTGACTGTAAAAACTATGT 58.387 37.500 0.00 0.00 0.00 2.29
5023 5552 6.097129 AGGAAAAATCGGGTTGACTGTAAAAA 59.903 34.615 0.00 0.00 0.00 1.94
5043 5572 5.950549 AGAAGAGAACGACATACCTAGGAAA 59.049 40.000 17.98 3.03 0.00 3.13
5046 5575 6.711194 TGATAGAAGAGAACGACATACCTAGG 59.289 42.308 7.41 7.41 0.00 3.02
5103 5632 6.201806 GCAAACGAATTCTAGCATCTCATAGT 59.798 38.462 3.52 0.00 0.00 2.12
5170 5700 9.138596 GGAAGAGAGGACACTAGATTTATAAGT 57.861 37.037 0.00 0.00 0.00 2.24
5171 5701 9.362151 AGGAAGAGAGGACACTAGATTTATAAG 57.638 37.037 0.00 0.00 0.00 1.73
5172 5702 9.716556 AAGGAAGAGAGGACACTAGATTTATAA 57.283 33.333 0.00 0.00 0.00 0.98


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

AutoCloner maintained by Alex Coulton.