Multiple sequence alignment - TraesCS5B01G201900

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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 TraesCS5B01G201900 chr5B 100.000 7100 0 0 1 7100 366741035 366748134 0.000000e+00 13112
1 TraesCS5B01G201900 chr5D 95.099 4305 67 38 1 4217 317145210 317149458 0.000000e+00 6649
2 TraesCS5B01G201900 chr5D 94.600 2037 53 20 5103 7100 317150333 317152351 0.000000e+00 3099
3 TraesCS5B01G201900 chr5D 93.278 848 34 9 4235 5074 317149522 317150354 0.000000e+00 1229
4 TraesCS5B01G201900 chr5A 91.125 4135 177 83 51 4050 411685678 411689757 0.000000e+00 5428
5 TraesCS5B01G201900 chr5A 90.689 2105 75 49 5089 7100 411690869 411692945 0.000000e+00 2689
6 TraesCS5B01G201900 chr5A 84.670 985 95 26 4139 5096 411689949 411690904 0.000000e+00 931
7 TraesCS5B01G201900 chr5A 86.878 442 23 13 1 422 411666454 411666880 5.020000e-126 462
8 TraesCS5B01G201900 chr5A 95.946 74 2 1 1 73 411685602 411685675 1.250000e-22 119


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 TraesCS5B01G201900 chr5B 366741035 366748134 7099 False 13112.00 13112 100.000000 1 7100 1 chr5B.!!$F1 7099
1 TraesCS5B01G201900 chr5D 317145210 317152351 7141 False 3659.00 6649 94.325667 1 7100 3 chr5D.!!$F1 7099
2 TraesCS5B01G201900 chr5A 411685602 411692945 7343 False 2291.75 5428 90.607500 1 7100 4 chr5A.!!$F2 7099

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
145 181 0.461135 AAAAAGGGTGCAGTGCAGTG 59.539 50.000 20.42 17.56 40.08 3.66 F
551 641 0.614979 ATCCAGTACCACGGCAGTCT 60.615 55.000 0.00 0.00 0.00 3.24 F
2218 2375 0.031994 GTGTTTGGGGATGTGTGTGC 59.968 55.000 0.00 0.00 0.00 4.57 F
2752 2950 0.798771 CGCTCTTGTCTACACCTCGC 60.799 60.000 0.00 0.00 0.00 5.03 F
3854 4075 0.610232 GGGCTTTGACCAGACATGCT 60.610 55.000 0.00 0.00 0.00 3.79 F
3989 4211 1.238439 CACGCCACTCAATTGTTCCT 58.762 50.000 5.13 0.00 0.00 3.36 F
4428 4799 2.063266 CCAAGTGAACATGCATGCAAC 58.937 47.619 26.68 17.78 0.00 4.17 F
5072 5472 3.964031 ACCTCTCTCTCTCTCTCTCTCTC 59.036 52.174 0.00 0.00 0.00 3.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1446 1584 2.481449 CGGATGGTGGTAGCTGTAGAAC 60.481 54.545 0.00 0.0 0.00 3.01 R
2374 2543 0.036448 TTCTCTCTCGTCGTCCCTGT 59.964 55.000 0.00 0.0 0.00 4.00 R
3409 3626 1.489560 GCCCTGTGTGTACCTTCCCT 61.490 60.000 0.00 0.0 0.00 4.20 R
4492 4863 1.154197 GTTTGTCGTTCTAGTGGCCC 58.846 55.000 0.00 0.0 0.00 5.80 R
5644 6077 0.251297 TTGCTACAACTGGGCATGCT 60.251 50.000 18.92 0.0 35.84 3.79 R
5952 6402 3.286353 ACACACAACACACATGGATCAA 58.714 40.909 0.00 0.0 0.00 2.57 R
6018 6469 1.007271 CAGCTCGTGGTTCGACACT 60.007 57.895 4.84 0.0 44.01 3.55 R
7007 7512 0.034059 GATGAGGCATCAGGTACCCG 59.966 60.000 8.74 0.0 40.28 5.28 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
100 136 4.361971 TGTCCCTCCGGCGAGACT 62.362 66.667 9.30 0.00 38.52 3.24
101 137 3.519930 GTCCCTCCGGCGAGACTC 61.520 72.222 9.30 0.00 38.52 3.36
144 180 2.900547 AAAAAGGGTGCAGTGCAGT 58.099 47.368 20.42 3.03 40.08 4.40
145 181 0.461135 AAAAAGGGTGCAGTGCAGTG 59.539 50.000 20.42 17.56 40.08 3.66
146 182 2.019897 AAAAGGGTGCAGTGCAGTGC 62.020 55.000 34.65 34.65 40.08 4.40
292 337 6.588756 CCAACAAACAAAATCAGATCCATCAG 59.411 38.462 0.00 0.00 0.00 2.90
336 388 4.519540 ACAACCAAAACCTACATGCATC 57.480 40.909 0.00 0.00 0.00 3.91
387 443 6.646653 AGTCTGTGTGTGTGTCAATAATAGTG 59.353 38.462 0.00 0.00 0.00 2.74
388 444 6.645003 GTCTGTGTGTGTGTCAATAATAGTGA 59.355 38.462 0.00 0.00 0.00 3.41
390 446 6.521162 TGTGTGTGTGTCAATAATAGTGAGT 58.479 36.000 0.00 0.00 0.00 3.41
391 447 7.662897 TGTGTGTGTGTCAATAATAGTGAGTA 58.337 34.615 0.00 0.00 0.00 2.59
392 448 7.812669 TGTGTGTGTGTCAATAATAGTGAGTAG 59.187 37.037 0.00 0.00 0.00 2.57
393 449 7.813148 GTGTGTGTGTCAATAATAGTGAGTAGT 59.187 37.037 0.00 0.00 0.00 2.73
394 450 9.016438 TGTGTGTGTCAATAATAGTGAGTAGTA 57.984 33.333 0.00 0.00 0.00 1.82
395 451 9.286946 GTGTGTGTCAATAATAGTGAGTAGTAC 57.713 37.037 0.00 0.00 0.00 2.73
396 452 8.179615 TGTGTGTCAATAATAGTGAGTAGTACG 58.820 37.037 0.00 0.00 0.00 3.67
397 453 7.642978 GTGTGTCAATAATAGTGAGTAGTACGG 59.357 40.741 0.00 0.00 0.00 4.02
398 454 7.337689 TGTGTCAATAATAGTGAGTAGTACGGT 59.662 37.037 0.00 0.00 0.00 4.83
399 455 8.830580 GTGTCAATAATAGTGAGTAGTACGGTA 58.169 37.037 0.00 0.00 0.00 4.02
400 456 9.565090 TGTCAATAATAGTGAGTAGTACGGTAT 57.435 33.333 0.00 0.00 0.00 2.73
431 501 0.874175 TGTGCGTGTGTGTGCTACTC 60.874 55.000 0.00 0.00 0.00 2.59
551 641 0.614979 ATCCAGTACCACGGCAGTCT 60.615 55.000 0.00 0.00 0.00 3.24
745 849 6.916909 TGTTAGGAGGTTGAGAGATAGAGAT 58.083 40.000 0.00 0.00 0.00 2.75
914 1043 1.234529 CTTCCTCCGATCCTCCCCT 59.765 63.158 0.00 0.00 0.00 4.79
1638 1776 3.374402 CTCTCCGACACCCTGCGT 61.374 66.667 0.00 0.00 0.00 5.24
2071 2224 1.213926 CCCTCTAGCTTGCTCCCAAAT 59.786 52.381 0.00 0.00 0.00 2.32
2094 2247 1.372997 GGTCTCGCGTCTTCTTGCA 60.373 57.895 5.77 0.00 0.00 4.08
2218 2375 0.031994 GTGTTTGGGGATGTGTGTGC 59.968 55.000 0.00 0.00 0.00 4.57
2369 2538 2.872245 CCACGAAGAAAGAGAAGCACAA 59.128 45.455 0.00 0.00 0.00 3.33
2370 2539 3.303395 CCACGAAGAAAGAGAAGCACAAC 60.303 47.826 0.00 0.00 0.00 3.32
2371 2540 3.557595 CACGAAGAAAGAGAAGCACAACT 59.442 43.478 0.00 0.00 0.00 3.16
2372 2541 3.557595 ACGAAGAAAGAGAAGCACAACTG 59.442 43.478 0.00 0.00 0.00 3.16
2374 2543 2.923121 AGAAAGAGAAGCACAACTGCA 58.077 42.857 0.00 0.00 46.97 4.41
2375 2544 2.615912 AGAAAGAGAAGCACAACTGCAC 59.384 45.455 0.00 0.00 46.97 4.57
2412 2581 6.176183 AGAGAAGAACAAGAGAGAGAGAGAG 58.824 44.000 0.00 0.00 0.00 3.20
2413 2582 6.013379 AGAGAAGAACAAGAGAGAGAGAGAGA 60.013 42.308 0.00 0.00 0.00 3.10
2419 2588 4.163078 ACAAGAGAGAGAGAGAGAGAGAGG 59.837 50.000 0.00 0.00 0.00 3.69
2420 2589 4.271807 AGAGAGAGAGAGAGAGAGAGGA 57.728 50.000 0.00 0.00 0.00 3.71
2566 2743 1.209019 CTTCCCACCTCATCAGTCCTG 59.791 57.143 0.00 0.00 0.00 3.86
2711 2888 1.000274 GGTAATTCGCATTGCCATCCC 60.000 52.381 9.84 0.00 43.10 3.85
2748 2946 1.281899 GCATCGCTCTTGTCTACACC 58.718 55.000 0.00 0.00 0.00 4.16
2749 2947 1.134965 GCATCGCTCTTGTCTACACCT 60.135 52.381 0.00 0.00 0.00 4.00
2751 2949 0.803117 TCGCTCTTGTCTACACCTCG 59.197 55.000 0.00 0.00 0.00 4.63
2752 2950 0.798771 CGCTCTTGTCTACACCTCGC 60.799 60.000 0.00 0.00 0.00 5.03
3023 3225 3.884774 AGGGAACGCCAGCACCAA 61.885 61.111 0.00 0.00 35.15 3.67
3409 3626 1.029408 GCACACACACACACCTGGAA 61.029 55.000 0.00 0.00 0.00 3.53
3757 3978 1.065782 TCTGAGTGTCTCTCTCTCCCG 60.066 57.143 3.71 0.00 43.13 5.14
3846 4067 3.106609 TGGGTGGGGCTTTGACCA 61.107 61.111 0.00 0.00 27.52 4.02
3854 4075 0.610232 GGGCTTTGACCAGACATGCT 60.610 55.000 0.00 0.00 0.00 3.79
3984 4206 4.212425 TGTTACTAACACGCCACTCAATTG 59.788 41.667 0.00 0.00 36.25 2.32
3989 4211 1.238439 CACGCCACTCAATTGTTCCT 58.762 50.000 5.13 0.00 0.00 3.36
4312 4683 8.359875 TGGTTTAAATTGCAGGAGAATCATAA 57.640 30.769 0.00 0.00 36.25 1.90
4313 4684 8.980596 TGGTTTAAATTGCAGGAGAATCATAAT 58.019 29.630 0.00 0.00 36.25 1.28
4314 4685 9.822185 GGTTTAAATTGCAGGAGAATCATAATT 57.178 29.630 0.00 0.00 36.25 1.40
4388 4759 7.141363 GCATAGGTTTTTCTGTATGCTTATGG 58.859 38.462 6.03 0.00 42.91 2.74
4389 4760 7.013274 GCATAGGTTTTTCTGTATGCTTATGGA 59.987 37.037 6.03 0.00 42.91 3.41
4428 4799 2.063266 CCAAGTGAACATGCATGCAAC 58.937 47.619 26.68 17.78 0.00 4.17
4446 4817 8.954350 GCATGCAACTATTTTCCATAGAGATAT 58.046 33.333 14.21 0.00 0.00 1.63
4492 4863 5.914635 AGTTTGTGATTTTGAATGTGCTACG 59.085 36.000 0.00 0.00 0.00 3.51
4529 4900 6.909895 CGACAAACTTGTGTTATGTCATTTCA 59.090 34.615 0.00 0.00 42.43 2.69
4542 4913 9.508567 GTTATGTCATTTCAATTTTAGGCTCTC 57.491 33.333 0.00 0.00 0.00 3.20
4543 4914 6.515272 TGTCATTTCAATTTTAGGCTCTCC 57.485 37.500 0.00 0.00 0.00 3.71
4746 5137 7.599998 ACAACTTCCAAAATGATATTGTGCTTC 59.400 33.333 0.00 0.00 0.00 3.86
4813 5204 5.526115 TGTAAAGTAGTGGCGTATCTATGC 58.474 41.667 0.00 0.00 37.49 3.14
4895 5287 8.349983 GTTCCTATCAAGACAAAAGCACTTTAA 58.650 33.333 0.00 0.00 31.63 1.52
5051 5451 9.204570 GTGGGTCATATATAGTCATACACAAAC 57.795 37.037 0.00 0.00 0.00 2.93
5053 5453 8.594550 GGGTCATATATAGTCATACACAAACCT 58.405 37.037 0.00 0.00 0.00 3.50
5060 5460 5.652994 AGTCATACACAAACCTCTCTCTC 57.347 43.478 0.00 0.00 0.00 3.20
5061 5461 5.329399 AGTCATACACAAACCTCTCTCTCT 58.671 41.667 0.00 0.00 0.00 3.10
5062 5462 5.417580 AGTCATACACAAACCTCTCTCTCTC 59.582 44.000 0.00 0.00 0.00 3.20
5063 5463 5.417580 GTCATACACAAACCTCTCTCTCTCT 59.582 44.000 0.00 0.00 0.00 3.10
5064 5464 5.650266 TCATACACAAACCTCTCTCTCTCTC 59.350 44.000 0.00 0.00 0.00 3.20
5065 5465 4.112634 ACACAAACCTCTCTCTCTCTCT 57.887 45.455 0.00 0.00 0.00 3.10
5066 5466 4.079253 ACACAAACCTCTCTCTCTCTCTC 58.921 47.826 0.00 0.00 0.00 3.20
5067 5467 4.202567 ACACAAACCTCTCTCTCTCTCTCT 60.203 45.833 0.00 0.00 0.00 3.10
5068 5468 4.396166 CACAAACCTCTCTCTCTCTCTCTC 59.604 50.000 0.00 0.00 0.00 3.20
5069 5469 4.289672 ACAAACCTCTCTCTCTCTCTCTCT 59.710 45.833 0.00 0.00 0.00 3.10
5070 5470 4.762289 AACCTCTCTCTCTCTCTCTCTC 57.238 50.000 0.00 0.00 0.00 3.20
5071 5471 4.000928 ACCTCTCTCTCTCTCTCTCTCT 57.999 50.000 0.00 0.00 0.00 3.10
5072 5472 3.964031 ACCTCTCTCTCTCTCTCTCTCTC 59.036 52.174 0.00 0.00 0.00 3.20
5073 5473 4.222336 CCTCTCTCTCTCTCTCTCTCTCT 58.778 52.174 0.00 0.00 0.00 3.10
5074 5474 4.280677 CCTCTCTCTCTCTCTCTCTCTCTC 59.719 54.167 0.00 0.00 0.00 3.20
5075 5475 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
5076 5476 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
5077 5477 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
5078 5478 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
5079 5479 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
5080 5480 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
5081 5481 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
5082 5482 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
5083 5483 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
5084 5484 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
5085 5485 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
5086 5486 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
5087 5487 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
5321 5727 4.338964 TGTTGTTACTCAAGTACACGGAGA 59.661 41.667 13.33 0.00 36.66 3.71
5479 5910 6.086871 CCGGAACATCTTTTAAGAGCTTTTC 58.913 40.000 0.00 0.00 38.66 2.29
5886 6336 7.634671 TGCATGAGCCCATTATTCTAATATG 57.365 36.000 0.00 0.00 41.13 1.78
6018 6469 1.741401 CAGATCAACCGGCTCGCAA 60.741 57.895 0.00 0.00 0.00 4.85
6246 6705 3.251004 AGAAATCAACGGCAACTTCAGAC 59.749 43.478 0.00 0.00 0.00 3.51
6299 6764 2.438021 AGCATGGTCGGGAAAAGCTATA 59.562 45.455 0.00 0.00 0.00 1.31
6300 6765 3.073062 AGCATGGTCGGGAAAAGCTATAT 59.927 43.478 0.00 0.00 0.00 0.86
6352 6817 5.690997 ATTCGAGGTTTCTTTCTTGGTTC 57.309 39.130 0.00 0.00 0.00 3.62
6367 6833 9.736023 CTTTCTTGGTTCCTATATATGTTTTGC 57.264 33.333 0.00 0.00 0.00 3.68
6368 6834 7.817418 TCTTGGTTCCTATATATGTTTTGCC 57.183 36.000 0.00 0.00 0.00 4.52
6369 6835 6.485313 TCTTGGTTCCTATATATGTTTTGCCG 59.515 38.462 0.00 0.00 0.00 5.69
6445 6915 8.548877 AGTAGTTTTATTATCTTCTCTTGGGCA 58.451 33.333 0.00 0.00 0.00 5.36
6485 6955 1.066573 CCTTCTTGTGTGGCGAGATCT 60.067 52.381 0.00 0.00 37.45 2.75
6636 7113 2.880268 TGAGTTGTGGTGAAGCAATCTG 59.120 45.455 0.00 0.00 0.00 2.90
6797 7289 0.038251 TGGTCGTGTCAGCTGATCAC 60.038 55.000 26.37 26.37 0.00 3.06
6904 7403 5.559991 CGCACCGCATCAGCTTAATTAATTA 60.560 40.000 3.71 3.71 39.10 1.40
6905 7404 6.381801 GCACCGCATCAGCTTAATTAATTAT 58.618 36.000 8.70 0.00 39.10 1.28
6906 7405 7.526608 GCACCGCATCAGCTTAATTAATTATA 58.473 34.615 8.70 0.53 39.10 0.98
6959 7461 5.777802 TCAAAAGCCGATTAAGATTGCAAA 58.222 33.333 1.71 0.00 0.00 3.68
6971 7473 2.692817 TTGCAAAGCAAAGCCAAGC 58.307 47.368 0.00 0.00 45.96 4.01
6975 7477 1.268184 GCAAAGCAAAGCCAAGCAAAC 60.268 47.619 0.00 0.00 0.00 2.93
7096 7614 2.435938 GCGAGAACCGGCCATGAA 60.436 61.111 0.00 0.00 39.04 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 57 4.340617 TCTTGTTCTCCCTTCTCTCTCTC 58.659 47.826 0.00 0.00 0.00 3.20
57 58 4.396357 TCTTGTTCTCCCTTCTCTCTCT 57.604 45.455 0.00 0.00 0.00 3.10
58 59 4.620567 GCTTCTTGTTCTCCCTTCTCTCTC 60.621 50.000 0.00 0.00 0.00 3.20
59 60 3.260632 GCTTCTTGTTCTCCCTTCTCTCT 59.739 47.826 0.00 0.00 0.00 3.10
100 136 0.689080 GGGAGCTCATGACAGGGAGA 60.689 60.000 17.19 0.00 32.87 3.71
101 137 1.694133 GGGGAGCTCATGACAGGGAG 61.694 65.000 17.19 3.20 0.00 4.30
142 178 1.821753 CTGTAGGTAGAGCACTGCACT 59.178 52.381 6.22 6.22 33.51 4.40
143 179 1.134965 CCTGTAGGTAGAGCACTGCAC 60.135 57.143 3.30 0.00 0.00 4.57
144 180 1.186200 CCTGTAGGTAGAGCACTGCA 58.814 55.000 3.30 0.00 0.00 4.41
145 181 0.461961 CCCTGTAGGTAGAGCACTGC 59.538 60.000 0.00 0.00 0.00 4.40
146 182 2.028130 CTCCCTGTAGGTAGAGCACTG 58.972 57.143 0.00 0.00 36.75 3.66
147 183 1.063567 CCTCCCTGTAGGTAGAGCACT 60.064 57.143 0.00 0.00 36.75 4.40
148 184 1.404843 CCTCCCTGTAGGTAGAGCAC 58.595 60.000 0.00 0.00 36.75 4.40
149 185 0.261991 CCCTCCCTGTAGGTAGAGCA 59.738 60.000 0.00 0.00 34.56 4.26
150 186 0.556747 TCCCTCCCTGTAGGTAGAGC 59.443 60.000 0.00 0.00 34.56 4.09
151 187 1.477195 CGTCCCTCCCTGTAGGTAGAG 60.477 61.905 0.00 0.00 34.56 2.43
317 366 5.570320 ACTAGATGCATGTAGGTTTTGGTT 58.430 37.500 28.66 7.92 0.00 3.67
365 417 6.646653 ACTCACTATTATTGACACACACACAG 59.353 38.462 0.00 0.00 0.00 3.66
387 443 9.928236 CAAAGAACTACTAATACCGTACTACTC 57.072 37.037 0.00 0.00 0.00 2.59
388 444 9.454859 ACAAAGAACTACTAATACCGTACTACT 57.545 33.333 0.00 0.00 0.00 2.57
390 446 8.184192 GCACAAAGAACTACTAATACCGTACTA 58.816 37.037 0.00 0.00 0.00 1.82
391 447 7.031975 GCACAAAGAACTACTAATACCGTACT 58.968 38.462 0.00 0.00 0.00 2.73
392 448 6.021153 CGCACAAAGAACTACTAATACCGTAC 60.021 42.308 0.00 0.00 0.00 3.67
393 449 6.029607 CGCACAAAGAACTACTAATACCGTA 58.970 40.000 0.00 0.00 0.00 4.02
394 450 4.860907 CGCACAAAGAACTACTAATACCGT 59.139 41.667 0.00 0.00 0.00 4.83
395 451 4.860907 ACGCACAAAGAACTACTAATACCG 59.139 41.667 0.00 0.00 0.00 4.02
396 452 5.636543 ACACGCACAAAGAACTACTAATACC 59.363 40.000 0.00 0.00 0.00 2.73
397 453 6.145048 ACACACGCACAAAGAACTACTAATAC 59.855 38.462 0.00 0.00 0.00 1.89
398 454 6.144886 CACACACGCACAAAGAACTACTAATA 59.855 38.462 0.00 0.00 0.00 0.98
399 455 5.050363 CACACACGCACAAAGAACTACTAAT 60.050 40.000 0.00 0.00 0.00 1.73
400 456 4.269123 CACACACGCACAAAGAACTACTAA 59.731 41.667 0.00 0.00 0.00 2.24
406 462 1.534028 CACACACACGCACAAAGAAC 58.466 50.000 0.00 0.00 0.00 3.01
431 501 9.840427 CATAAAATACACCACCACTTCTAAAAG 57.160 33.333 0.00 0.00 38.54 2.27
551 641 6.672266 AGTCTGAGAAAATGACACTTAGGA 57.328 37.500 0.00 0.00 33.56 2.94
851 975 2.804856 GGCCGTGTTGTGTTGCTT 59.195 55.556 0.00 0.00 0.00 3.91
914 1043 1.381076 GGATTGGTGGGACGGGAAA 59.619 57.895 0.00 0.00 0.00 3.13
1446 1584 2.481449 CGGATGGTGGTAGCTGTAGAAC 60.481 54.545 0.00 0.00 0.00 3.01
2226 2387 4.691860 ATGATGGCAACTTTTTCTCTCG 57.308 40.909 0.00 0.00 37.61 4.04
2369 2538 2.910479 TCGTCGTCCCTGTGCAGT 60.910 61.111 0.00 0.00 0.00 4.40
2370 2539 2.126307 CTCGTCGTCCCTGTGCAG 60.126 66.667 0.00 0.00 0.00 4.41
2371 2540 2.596338 TCTCGTCGTCCCTGTGCA 60.596 61.111 0.00 0.00 0.00 4.57
2372 2541 2.179517 CTCTCGTCGTCCCTGTGC 59.820 66.667 0.00 0.00 0.00 4.57
2374 2543 0.036448 TTCTCTCTCGTCGTCCCTGT 59.964 55.000 0.00 0.00 0.00 4.00
2375 2544 0.730265 CTTCTCTCTCGTCGTCCCTG 59.270 60.000 0.00 0.00 0.00 4.45
2412 2581 5.652452 AGTAGCTTTCTCTCTTTCCTCTCTC 59.348 44.000 0.00 0.00 0.00 3.20
2413 2582 5.418840 CAGTAGCTTTCTCTCTTTCCTCTCT 59.581 44.000 0.00 0.00 0.00 3.10
2566 2743 1.583709 GATTGCAGCGCGGTTTAGC 60.584 57.895 8.73 10.52 0.00 3.09
2711 2888 2.416747 TGCAATGGAGTTCTTGACGAG 58.583 47.619 0.00 0.00 0.00 4.18
2751 2949 3.543680 TGATTACCAGTAAGCAGAGGC 57.456 47.619 4.46 0.00 36.64 4.70
2752 2950 4.818546 CCATTGATTACCAGTAAGCAGAGG 59.181 45.833 8.35 10.20 41.62 3.69
2901 3100 1.358402 GCACATGTTGTTGTCGCCA 59.642 52.632 0.00 0.00 0.00 5.69
3072 3274 4.221342 GTGTGCACAACATTCACATGTAG 58.779 43.478 23.59 0.00 43.34 2.74
3409 3626 1.489560 GCCCTGTGTGTACCTTCCCT 61.490 60.000 0.00 0.00 0.00 4.20
3846 4067 3.581101 TCCTAGGCAATAGAGCATGTCT 58.419 45.455 2.96 0.00 39.59 3.41
3854 4075 7.865530 TGGTTACATATTCCTAGGCAATAGA 57.134 36.000 2.96 0.00 32.76 1.98
4342 4713 1.233019 CTGTGACAGTCCTTGGCTTG 58.767 55.000 4.01 0.00 35.09 4.01
4388 4759 8.711457 CACTTGGTCACCATGAATTAATTTTTC 58.289 33.333 16.54 0.00 33.58 2.29
4389 4760 8.428063 TCACTTGGTCACCATGAATTAATTTTT 58.572 29.630 16.54 0.00 33.58 1.94
4408 4779 2.063266 GTTGCATGCATGTTCACTTGG 58.937 47.619 26.79 0.00 0.00 3.61
4446 4817 5.301551 ACTTTTGCAGTGATGTACATCCAAA 59.698 36.000 28.64 25.44 37.02 3.28
4456 4827 6.592798 AAATCACAAACTTTTGCAGTGATG 57.407 33.333 14.11 3.52 41.79 3.07
4492 4863 1.154197 GTTTGTCGTTCTAGTGGCCC 58.846 55.000 0.00 0.00 0.00 5.80
4529 4900 5.659971 AGCATTTGATGGAGAGCCTAAAATT 59.340 36.000 0.00 0.00 34.31 1.82
4642 5013 7.722728 ACAGATCAATATGCATCCACTACATTT 59.277 33.333 0.19 0.00 0.00 2.32
4685 5072 3.039252 ACATGGGGAAAAGTTCAACCA 57.961 42.857 0.00 6.23 40.78 3.67
4746 5137 3.516981 ACGTCTGGATCAGTTCTGATG 57.483 47.619 18.31 6.24 32.61 3.07
4787 5178 7.170998 GCATAGATACGCCACTACTTTACATTT 59.829 37.037 0.00 0.00 0.00 2.32
4788 5179 6.645415 GCATAGATACGCCACTACTTTACATT 59.355 38.462 0.00 0.00 0.00 2.71
4789 5180 6.015350 AGCATAGATACGCCACTACTTTACAT 60.015 38.462 0.00 0.00 0.00 2.29
4790 5181 5.301045 AGCATAGATACGCCACTACTTTACA 59.699 40.000 0.00 0.00 0.00 2.41
4791 5182 5.770417 AGCATAGATACGCCACTACTTTAC 58.230 41.667 0.00 0.00 0.00 2.01
4792 5183 6.040054 TCAAGCATAGATACGCCACTACTTTA 59.960 38.462 0.00 0.00 0.00 1.85
4813 5204 9.447040 CAGACTTTGCATGTCAATAATATCAAG 57.553 33.333 18.46 3.87 36.94 3.02
4895 5287 0.973496 AACCCAGCACCAAACCGTTT 60.973 50.000 0.00 0.00 0.00 3.60
5051 5451 4.222336 AGAGAGAGAGAGAGAGAGAGAGG 58.778 52.174 0.00 0.00 0.00 3.69
5053 5453 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
5055 5455 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
5057 5457 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
5059 5459 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
5060 5460 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
5061 5461 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
5062 5462 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
5063 5463 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
5064 5464 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
5065 5465 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
5066 5466 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
5067 5467 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
5068 5468 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
5069 5469 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
5070 5470 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
5071 5471 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
5072 5472 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
5073 5473 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
5074 5474 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
5075 5475 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
5076 5476 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
5077 5477 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
5078 5478 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
5079 5479 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
5080 5480 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
5081 5481 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
5082 5482 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
5083 5483 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
5084 5484 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
5085 5485 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
5086 5486 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
5087 5487 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
5205 5609 6.283694 TGCACATATCTAATGACTGGAGTTC 58.716 40.000 0.00 0.00 0.00 3.01
5242 5646 9.606631 AGAGGACTCTTTATACATTGACAATTC 57.393 33.333 0.00 0.00 36.31 2.17
5302 5708 3.919197 GCTTCTCCGTGTACTTGAGTAAC 59.081 47.826 0.00 0.00 31.52 2.50
5303 5709 3.570975 TGCTTCTCCGTGTACTTGAGTAA 59.429 43.478 0.00 0.00 31.52 2.24
5304 5710 3.151554 TGCTTCTCCGTGTACTTGAGTA 58.848 45.455 0.00 0.00 0.00 2.59
5394 5806 1.030457 CCCATCTTCATCAGCAAGCC 58.970 55.000 0.00 0.00 0.00 4.35
5479 5910 6.989169 ACACATATAGCTTCTTTCTAGGCAAG 59.011 38.462 0.00 0.00 0.00 4.01
5561 5992 6.112734 TGAACAATACTTGCCCAGTGTATAG 58.887 40.000 0.00 0.00 35.97 1.31
5595 6026 2.635714 CACTGCAGATAGGAACATGCA 58.364 47.619 23.35 0.00 45.82 3.96
5644 6077 0.251297 TTGCTACAACTGGGCATGCT 60.251 50.000 18.92 0.00 35.84 3.79
5952 6402 3.286353 ACACACAACACACATGGATCAA 58.714 40.909 0.00 0.00 0.00 2.57
6018 6469 1.007271 CAGCTCGTGGTTCGACACT 60.007 57.895 4.84 0.00 44.01 3.55
6270 6729 2.360350 CGACCATGCTGGGTGCTT 60.360 61.111 4.53 0.00 43.37 3.91
6352 6817 2.418628 CGGCCGGCAAAACATATATAGG 59.581 50.000 30.85 0.00 0.00 2.57
6393 6859 4.628963 AGGAGTAGCTAGCTAGGAGTAC 57.371 50.000 24.78 14.40 0.00 2.73
6445 6915 7.234355 AGAAGGGAACACAACTAATCAAAGAT 58.766 34.615 0.00 0.00 0.00 2.40
6485 6955 1.413445 ACACGCCGGGCAACTATAATA 59.587 47.619 20.71 0.00 0.00 0.98
6636 7113 1.005867 CACCACCAATGCAAGGCAC 60.006 57.895 8.36 0.00 43.04 5.01
6646 7123 1.896183 CCGTCATGCACACCACCAA 60.896 57.895 0.00 0.00 0.00 3.67
6797 7289 0.035439 AGGTAATGTCCGTGGCTTGG 60.035 55.000 0.00 0.00 0.00 3.61
6904 7403 3.560068 GTGCGCTAATGTGGCTAGTTTAT 59.440 43.478 9.73 0.00 0.00 1.40
6905 7404 2.933906 GTGCGCTAATGTGGCTAGTTTA 59.066 45.455 9.73 0.00 0.00 2.01
6906 7405 1.737793 GTGCGCTAATGTGGCTAGTTT 59.262 47.619 9.73 0.00 0.00 2.66
6959 7461 0.540923 TTGGTTTGCTTGGCTTTGCT 59.459 45.000 0.00 0.00 0.00 3.91
6967 7469 2.774007 GACGATCGATTGGTTTGCTTG 58.226 47.619 24.34 0.00 0.00 4.01
6968 7470 1.393539 CGACGATCGATTGGTTTGCTT 59.606 47.619 24.34 0.00 43.74 3.91
6969 7471 0.999406 CGACGATCGATTGGTTTGCT 59.001 50.000 24.34 0.00 43.74 3.91
6970 7472 0.719465 ACGACGATCGATTGGTTTGC 59.281 50.000 24.34 0.60 43.74 3.68
6971 7473 1.007422 CGACGACGATCGATTGGTTTG 60.007 52.381 24.34 4.38 45.13 2.93
6975 7477 2.293627 GGCGACGACGATCGATTGG 61.294 63.158 24.34 9.81 45.13 3.16
7007 7512 0.034059 GATGAGGCATCAGGTACCCG 59.966 60.000 8.74 0.00 40.28 5.28
7010 7515 2.369860 TGATGGATGAGGCATCAGGTAC 59.630 50.000 7.33 0.00 42.13 3.34
7026 7544 1.520494 CAGGGAGCAATCGATGATGG 58.480 55.000 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.