Multiple sequence alignment - TraesCS2A01G352400

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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 TraesCS2A01G352400 chr2A 100.000 6013 0 0 1 6013 592851144 592857156 0 11105
1 TraesCS2A01G352400 chr2D 97.398 5189 99 22 1 5176 448207300 448212465 0 8802
2 TraesCS2A01G352400 chr2D 88.943 814 49 23 5222 6012 448212468 448213263 0 966
3 TraesCS2A01G352400 chr2B 91.265 6102 340 84 1 6013 528201455 528207452 0 8137
4 TraesCS2A01G352400 chrUn 100.000 416 0 0 4395 4810 477174446 477174031 0 769


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 TraesCS2A01G352400 chr2A 592851144 592857156 6012 False 11105 11105 100.0000 1 6013 1 chr2A.!!$F1 6012
1 TraesCS2A01G352400 chr2D 448207300 448213263 5963 False 4884 8802 93.1705 1 6012 2 chr2D.!!$F1 6011
2 TraesCS2A01G352400 chr2B 528201455 528207452 5997 False 8137 8137 91.2650 1 6013 1 chr2B.!!$F1 6012

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
774 791 0.033504 TGAGTCGAGTTCTTGTGCCC 59.966 55.000 0.00 0.0 0.00 5.36 F
1377 1404 0.465705 GCTCAGATGGTGATCCCGAA 59.534 55.000 0.00 0.0 33.51 4.30 F
2535 2563 1.715931 TGGGTCCCTTCATCAAATGGT 59.284 47.619 10.00 0.0 0.00 3.55 F
3052 3080 1.002544 GCTTGCCTACTGGTCAGTCTT 59.997 52.381 6.91 0.0 42.54 3.01 F
4377 4449 2.035449 CACGGCTCTTATGGTCCGAATA 59.965 50.000 6.52 0.0 44.23 1.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2072 2100 3.181493 GCATCTAGAAATGGCACCAACAG 60.181 47.826 0.00 0.0 0.00 3.16 R
3052 3080 3.327464 TGATCACCATGTGAAGAACTCCA 59.673 43.478 0.46 0.0 45.96 3.86 R
3399 3430 2.298729 ACAAATGTGTGTGCCCATTACC 59.701 45.455 0.00 0.0 36.31 2.85 R
4810 4882 3.948719 GCTGGAACACCCCGGTCA 61.949 66.667 0.00 0.0 35.02 4.02 R
5422 5509 0.242017 GCTGGCAGTTTCATGTGTCC 59.758 55.000 17.16 0.0 0.00 4.02 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
93 94 3.074094 GGGAGGGGAGTAGAAAAACAACT 59.926 47.826 0.00 0.00 0.00 3.16
94 95 4.287845 GGGAGGGGAGTAGAAAAACAACTA 59.712 45.833 0.00 0.00 0.00 2.24
95 96 5.243981 GGAGGGGAGTAGAAAAACAACTAC 58.756 45.833 0.00 0.00 39.15 2.73
147 149 4.750941 AGAATTCCAACCTCCAATCCAAA 58.249 39.130 0.65 0.00 0.00 3.28
168 180 1.751162 CTCGCCCTCTCCTCGTCTT 60.751 63.158 0.00 0.00 0.00 3.01
469 481 1.090052 CGGCTCGAATTGGAGGTTCC 61.090 60.000 17.85 10.23 36.96 3.62
477 489 2.667473 ATTGGAGGTTCCGAGTTACG 57.333 50.000 0.00 0.00 40.17 3.18
495 507 3.684103 ACGCTGAATTTTGTTTCGTCA 57.316 38.095 0.00 0.00 0.00 4.35
566 583 4.503910 GGAACCACAAGTTTGCTTCTTTT 58.496 39.130 0.00 0.00 39.40 2.27
567 584 4.329801 GGAACCACAAGTTTGCTTCTTTTG 59.670 41.667 0.00 0.00 39.40 2.44
568 585 4.799564 ACCACAAGTTTGCTTCTTTTGA 57.200 36.364 0.00 0.00 31.49 2.69
636 653 6.302535 TGAAACGGATAGATTTTACTGGGA 57.697 37.500 0.00 0.00 0.00 4.37
665 682 0.871057 GAGCTTCTGTCTTGTGTGCC 59.129 55.000 0.00 0.00 0.00 5.01
676 693 2.985847 GTGTGCCAGCACCCTTCC 60.986 66.667 19.47 0.00 45.63 3.46
709 726 0.110104 AGGACTTCTGCAGCTGCTTT 59.890 50.000 36.61 17.56 42.66 3.51
722 739 3.339141 AGCTGCTTTAGGCTGTTAACTC 58.661 45.455 7.22 0.00 42.39 3.01
733 750 1.804748 CTGTTAACTCCGGTTGCCTTC 59.195 52.381 7.22 0.00 36.92 3.46
739 756 2.125512 CCGGTTGCCTTCTCCTCG 60.126 66.667 0.00 0.00 0.00 4.63
774 791 0.033504 TGAGTCGAGTTCTTGTGCCC 59.966 55.000 0.00 0.00 0.00 5.36
883 910 2.977914 TGCACTACCAAGATTCTGCTC 58.022 47.619 0.00 0.00 0.00 4.26
897 924 1.143305 CTGCTCTGAAAGGACACACG 58.857 55.000 0.00 0.00 0.00 4.49
900 927 1.336887 GCTCTGAAAGGACACACGCTA 60.337 52.381 0.00 0.00 0.00 4.26
906 933 2.765250 AAGGACACACGCTACTGCCG 62.765 60.000 0.00 0.00 35.36 5.69
907 934 2.049433 GACACACGCTACTGCCGT 60.049 61.111 0.00 0.00 35.36 5.68
1218 1245 0.882042 CATCCTTGGGATCTTCGCCG 60.882 60.000 0.00 0.00 40.98 6.46
1272 1299 2.548067 CGATGCCTATTCCAGTGTACCC 60.548 54.545 0.00 0.00 0.00 3.69
1377 1404 0.465705 GCTCAGATGGTGATCCCGAA 59.534 55.000 0.00 0.00 33.51 4.30
1401 1428 2.838813 AGGAAGTACTAGCTTGGTTCCC 59.161 50.000 16.83 5.59 35.08 3.97
1623 1650 3.245443 TGTTCTCTGCTAAGGAGGAGACT 60.245 47.826 0.00 0.00 44.52 3.24
1800 1827 2.670934 AAGGGCTCTTGCTGTGCG 60.671 61.111 0.00 0.00 39.59 5.34
2072 2100 2.079925 GTGGATGCAAGTCCTCACTTC 58.920 52.381 7.83 0.00 41.24 3.01
2074 2102 2.289882 TGGATGCAAGTCCTCACTTCTG 60.290 50.000 7.83 0.00 41.24 3.02
2144 2172 5.824904 AAATGCTTGTATTCTGGCTACTG 57.175 39.130 0.00 0.00 0.00 2.74
2215 2243 5.381174 TGCACAATCTGGAATTTCTCTTG 57.619 39.130 0.00 0.00 0.00 3.02
2238 2266 6.462500 TGGCACTTACGTTTAATACTTACCA 58.538 36.000 0.00 0.00 0.00 3.25
2338 2366 4.014406 TGAGATTTCTGCTGTGCATCATT 58.986 39.130 0.00 0.00 38.13 2.57
2535 2563 1.715931 TGGGTCCCTTCATCAAATGGT 59.284 47.619 10.00 0.00 0.00 3.55
2586 2614 2.568956 TGTCCTTGATTCTCAGTCAGGG 59.431 50.000 0.00 0.00 42.43 4.45
2673 2701 3.086282 TCATGCATGCACTGAAACTCAT 58.914 40.909 25.37 0.00 0.00 2.90
3052 3080 1.002544 GCTTGCCTACTGGTCAGTCTT 59.997 52.381 6.91 0.00 42.54 3.01
3245 3273 4.650754 AGCATGATTTGAGCTGAAATCC 57.349 40.909 28.50 17.08 40.31 3.01
3274 3302 4.467438 TGAGACTTGTGCTCATCCATCTTA 59.533 41.667 0.00 0.00 37.46 2.10
3365 3396 2.364002 ACGCCTAATTTGTTGGCACTTT 59.636 40.909 0.00 0.00 46.39 2.66
3376 3407 7.532682 TTTGTTGGCACTTTAGAAATTTGAC 57.467 32.000 0.00 0.00 0.00 3.18
3399 3430 7.380333 TGACTAGTTGTGTGTTATGACTTAACG 59.620 37.037 0.00 0.00 42.68 3.18
3426 3457 4.375272 TGGGCACACACATTTGTAATTTG 58.625 39.130 0.00 0.00 33.30 2.32
3431 3462 6.089820 GGCACACACATTTGTAATTTGATCTG 59.910 38.462 0.00 0.00 33.30 2.90
3546 3577 6.732154 CCATTAGCACAATCGATCATCTTTT 58.268 36.000 0.00 0.00 0.00 2.27
4073 4145 7.684529 AGAAGATCCAAACTGTCATTAACTCT 58.315 34.615 0.00 0.00 0.00 3.24
4312 4384 2.751837 GCAGAAAGGGGAAGGCGG 60.752 66.667 0.00 0.00 0.00 6.13
4377 4449 2.035449 CACGGCTCTTATGGTCCGAATA 59.965 50.000 6.52 0.00 44.23 1.75
4393 4465 8.034804 TGGTCCGAATATCACACATCATATTAG 58.965 37.037 0.00 0.00 0.00 1.73
4810 4882 1.133668 AGCCAAGAGGTTCAAGCTGTT 60.134 47.619 0.00 0.00 37.19 3.16
5027 5099 1.000843 TCATGACACGGTGAGGAAGTG 59.999 52.381 16.29 5.00 41.28 3.16
5120 5192 3.323979 AGGGTTTGGTAGTCTGTACTGTG 59.676 47.826 0.00 0.00 36.36 3.66
5171 5243 3.119245 GGCGAACAGGAAGTGTAGTGATA 60.119 47.826 0.00 0.00 39.03 2.15
5183 5255 0.380733 TAGTGATAGTCGTGCAGGCG 59.619 55.000 0.35 0.00 0.00 5.52
5184 5256 2.202743 TGATAGTCGTGCAGGCGC 60.203 61.111 0.00 0.00 39.24 6.53
5215 5287 1.375908 ACAATGTCGTGCCTGCGAT 60.376 52.632 0.00 0.00 43.07 4.58
5258 5332 7.038729 TCCCTGAGAGGATATCATGACAATAAC 60.039 40.741 4.83 0.00 37.67 1.89
5259 5333 7.256439 CCCTGAGAGGATATCATGACAATAACA 60.256 40.741 4.83 0.00 37.67 2.41
5281 5355 2.512515 GTCATGAGGGTCTGCGGC 60.513 66.667 0.00 0.00 0.00 6.53
5298 5372 2.409870 GCGCCTAGCTGCCAATGTT 61.410 57.895 0.00 0.00 44.04 2.71
5299 5373 1.095228 GCGCCTAGCTGCCAATGTTA 61.095 55.000 0.00 0.00 44.04 2.41
5300 5374 1.378531 CGCCTAGCTGCCAATGTTAA 58.621 50.000 0.00 0.00 0.00 2.01
5312 5395 3.006859 GCCAATGTTAAAACTCCTGGCTT 59.993 43.478 18.22 0.00 41.32 4.35
5346 5433 3.976169 CGGAGGAAACAAATGCTTTTGA 58.024 40.909 26.53 0.00 44.11 2.69
5354 5441 3.716601 ACAAATGCTTTTGAACTTCCCG 58.283 40.909 26.53 2.65 44.11 5.14
5409 5496 4.653341 TGAATTTTCCAGTTCCACATTGGT 59.347 37.500 0.00 0.00 39.03 3.67
5410 5497 4.871933 ATTTTCCAGTTCCACATTGGTC 57.128 40.909 0.00 0.00 39.03 4.02
5413 5500 1.142060 TCCAGTTCCACATTGGTCGTT 59.858 47.619 0.00 0.00 39.03 3.85
5414 5501 1.535462 CCAGTTCCACATTGGTCGTTC 59.465 52.381 0.00 0.00 39.03 3.95
5417 5504 0.393448 TTCCACATTGGTCGTTCGGA 59.607 50.000 0.00 0.00 39.03 4.55
5419 5506 1.002659 TCCACATTGGTCGTTCGGAAT 59.997 47.619 0.00 0.00 39.03 3.01
5420 5507 1.396996 CCACATTGGTCGTTCGGAATC 59.603 52.381 0.00 0.00 31.35 2.52
5421 5508 1.060553 CACATTGGTCGTTCGGAATCG 59.939 52.381 0.00 0.20 37.82 3.34
5422 5509 0.650512 CATTGGTCGTTCGGAATCGG 59.349 55.000 11.01 0.00 36.95 4.18
5423 5510 0.461339 ATTGGTCGTTCGGAATCGGG 60.461 55.000 11.01 0.00 36.95 5.14
5424 5511 1.534336 TTGGTCGTTCGGAATCGGGA 61.534 55.000 11.01 0.00 36.95 5.14
5425 5512 1.517913 GGTCGTTCGGAATCGGGAC 60.518 63.158 11.01 8.44 36.95 4.46
5426 5513 1.213537 GTCGTTCGGAATCGGGACA 59.786 57.895 11.01 0.00 36.95 4.02
5427 5514 1.074872 GTCGTTCGGAATCGGGACAC 61.075 60.000 11.01 0.00 36.95 3.67
5428 5515 1.080366 CGTTCGGAATCGGGACACA 60.080 57.895 0.20 0.00 36.95 3.72
5429 5516 0.459585 CGTTCGGAATCGGGACACAT 60.460 55.000 0.20 0.00 36.95 3.21
5430 5517 1.006832 GTTCGGAATCGGGACACATG 58.993 55.000 0.00 0.00 36.95 3.21
5444 5531 1.338973 ACACATGAAACTGCCAGCTTG 59.661 47.619 0.00 0.00 0.00 4.01
5449 5536 2.867624 TGAAACTGCCAGCTTGAATCT 58.132 42.857 0.00 0.00 0.00 2.40
5453 5540 3.920231 ACTGCCAGCTTGAATCTGATA 57.080 42.857 0.00 0.00 33.54 2.15
5460 5547 5.356470 GCCAGCTTGAATCTGATAGTTTTCT 59.644 40.000 0.00 0.00 33.54 2.52
5488 5575 2.358322 TTTGGTGAAACTCCTGGACC 57.642 50.000 0.00 0.00 36.74 4.46
5489 5576 1.518367 TTGGTGAAACTCCTGGACCT 58.482 50.000 0.00 0.00 36.74 3.85
5490 5577 1.056660 TGGTGAAACTCCTGGACCTC 58.943 55.000 0.00 0.00 36.74 3.85
5496 5583 4.755629 GTGAAACTCCTGGACCTCTTTAAC 59.244 45.833 0.00 0.00 0.00 2.01
5501 5588 0.392595 CTGGACCTCTTTAACCGGGC 60.393 60.000 6.32 0.00 0.00 6.13
5519 5606 1.952296 GGCCTGGCTGACAATCTTATG 59.048 52.381 19.68 0.00 0.00 1.90
5520 5607 1.336125 GCCTGGCTGACAATCTTATGC 59.664 52.381 12.43 0.00 0.00 3.14
5523 5610 0.947244 GGCTGACAATCTTATGCCCG 59.053 55.000 0.00 0.00 34.81 6.13
5524 5611 1.668419 GCTGACAATCTTATGCCCGT 58.332 50.000 0.00 0.00 0.00 5.28
5526 5613 2.032178 GCTGACAATCTTATGCCCGTTC 59.968 50.000 0.00 0.00 0.00 3.95
5527 5614 3.270027 CTGACAATCTTATGCCCGTTCA 58.730 45.455 0.00 0.00 0.00 3.18
5529 5616 3.438781 TGACAATCTTATGCCCGTTCAAC 59.561 43.478 0.00 0.00 0.00 3.18
5530 5617 2.752903 ACAATCTTATGCCCGTTCAACC 59.247 45.455 0.00 0.00 0.00 3.77
5531 5618 3.016736 CAATCTTATGCCCGTTCAACCT 58.983 45.455 0.00 0.00 0.00 3.50
5533 5620 3.985019 TCTTATGCCCGTTCAACCTTA 57.015 42.857 0.00 0.00 0.00 2.69
5534 5621 3.602483 TCTTATGCCCGTTCAACCTTAC 58.398 45.455 0.00 0.00 0.00 2.34
5551 5644 8.281531 TCAACCTTACCATGGATAATCTTTCAT 58.718 33.333 21.47 0.00 0.00 2.57
5558 5651 5.884322 CATGGATAATCTTTCATGGAGGGA 58.116 41.667 0.00 0.00 34.89 4.20
5559 5652 5.310409 TGGATAATCTTTCATGGAGGGAC 57.690 43.478 0.00 0.00 0.00 4.46
5561 5654 5.163163 TGGATAATCTTTCATGGAGGGACTG 60.163 44.000 0.00 0.00 41.55 3.51
5562 5655 3.659183 AATCTTTCATGGAGGGACTGG 57.341 47.619 0.00 0.00 41.55 4.00
5563 5656 0.620556 TCTTTCATGGAGGGACTGGC 59.379 55.000 0.00 0.00 41.55 4.85
5564 5657 0.622665 CTTTCATGGAGGGACTGGCT 59.377 55.000 0.00 0.00 41.55 4.75
5565 5658 0.620556 TTTCATGGAGGGACTGGCTC 59.379 55.000 0.00 0.00 41.55 4.70
5566 5659 0.547471 TTCATGGAGGGACTGGCTCA 60.547 55.000 0.00 0.00 41.55 4.26
5568 5661 1.229625 ATGGAGGGACTGGCTCACA 60.230 57.895 0.00 0.00 41.55 3.58
5569 5662 0.842030 ATGGAGGGACTGGCTCACAA 60.842 55.000 0.00 0.00 41.55 3.33
5572 5665 0.908198 GAGGGACTGGCTCACAATCT 59.092 55.000 0.00 0.00 41.55 2.40
5573 5666 1.280421 GAGGGACTGGCTCACAATCTT 59.720 52.381 0.00 0.00 41.55 2.40
5574 5667 2.501723 GAGGGACTGGCTCACAATCTTA 59.498 50.000 0.00 0.00 41.55 2.10
5577 5670 3.135530 GGGACTGGCTCACAATCTTATCT 59.864 47.826 0.00 0.00 0.00 1.98
5578 5671 4.376146 GGACTGGCTCACAATCTTATCTC 58.624 47.826 0.00 0.00 0.00 2.75
5579 5672 4.100808 GGACTGGCTCACAATCTTATCTCT 59.899 45.833 0.00 0.00 0.00 3.10
5580 5673 5.021033 ACTGGCTCACAATCTTATCTCTG 57.979 43.478 0.00 0.00 0.00 3.35
5581 5674 3.801698 TGGCTCACAATCTTATCTCTGC 58.198 45.455 0.00 0.00 0.00 4.26
5582 5675 3.453717 TGGCTCACAATCTTATCTCTGCT 59.546 43.478 0.00 0.00 0.00 4.24
5583 5676 4.057432 GGCTCACAATCTTATCTCTGCTC 58.943 47.826 0.00 0.00 0.00 4.26
5584 5677 4.442612 GGCTCACAATCTTATCTCTGCTCA 60.443 45.833 0.00 0.00 0.00 4.26
5585 5678 4.507388 GCTCACAATCTTATCTCTGCTCAC 59.493 45.833 0.00 0.00 0.00 3.51
5586 5679 5.681954 GCTCACAATCTTATCTCTGCTCACT 60.682 44.000 0.00 0.00 0.00 3.41
5626 5719 5.798125 TTTCCTATGCTGAGATCGAGATT 57.202 39.130 0.00 0.00 0.00 2.40
5627 5720 6.901081 TTTCCTATGCTGAGATCGAGATTA 57.099 37.500 0.00 0.00 0.00 1.75
5701 5794 2.189594 TCTGCAGACACCCAAATCTG 57.810 50.000 13.74 0.00 44.37 2.90
5727 5820 2.125912 GACGAGTCGGCAGCATGT 60.126 61.111 15.05 0.00 39.31 3.21
5787 5881 0.892755 CCAGTTTCCTGCATGCACAT 59.107 50.000 18.46 0.00 37.38 3.21
5792 5886 1.317431 TTCCTGCATGCACATCAGCC 61.317 55.000 18.46 0.00 0.00 4.85
5819 5913 1.901591 ATGCTGTGGAGTTCTGTTGG 58.098 50.000 0.00 0.00 0.00 3.77
5899 5993 1.817099 CATTGAGCGTCTGGGGAGC 60.817 63.158 0.00 0.00 0.00 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
79 80 8.585881 TGAGCTATGAGTAGTTGTTTTTCTACT 58.414 33.333 4.81 4.81 46.12 2.57
80 81 8.758633 TGAGCTATGAGTAGTTGTTTTTCTAC 57.241 34.615 0.00 0.00 37.41 2.59
93 94 2.481969 CGCTGGCTTTGAGCTATGAGTA 60.482 50.000 0.00 0.00 41.99 2.59
94 95 1.741732 CGCTGGCTTTGAGCTATGAGT 60.742 52.381 0.00 0.00 41.99 3.41
95 96 0.935898 CGCTGGCTTTGAGCTATGAG 59.064 55.000 0.00 0.00 41.99 2.90
96 97 0.536724 TCGCTGGCTTTGAGCTATGA 59.463 50.000 0.00 0.00 41.99 2.15
97 98 0.654683 GTCGCTGGCTTTGAGCTATG 59.345 55.000 0.00 0.00 41.99 2.23
98 99 0.462759 GGTCGCTGGCTTTGAGCTAT 60.463 55.000 0.00 0.00 41.99 2.97
168 180 2.921834 ACTACTACTTGCTGGGAGGA 57.078 50.000 0.00 0.00 0.00 3.71
303 315 4.468689 GGCCCCGGACGGAAGAAG 62.469 72.222 13.13 0.00 37.50 2.85
442 454 4.880537 ATTCGAGCCGGCAGAGCG 62.881 66.667 31.54 24.76 34.64 5.03
469 481 4.314708 CGAAACAAAATTCAGCGTAACTCG 59.685 41.667 0.00 0.00 43.12 4.18
477 489 4.024048 TCCTCTGACGAAACAAAATTCAGC 60.024 41.667 0.00 0.00 34.82 4.26
495 507 2.641815 ACTTCACCAAATCAGCTCCTCT 59.358 45.455 0.00 0.00 0.00 3.69
566 583 0.530650 GAGCGCGGAGGAAATCATCA 60.531 55.000 8.83 0.00 0.00 3.07
567 584 0.530650 TGAGCGCGGAGGAAATCATC 60.531 55.000 8.83 0.00 0.00 2.92
568 585 0.531532 CTGAGCGCGGAGGAAATCAT 60.532 55.000 8.83 0.00 0.00 2.45
636 653 3.561143 AGACAGAAGCTCGGTATCTGAT 58.439 45.455 17.24 4.68 42.48 2.90
665 682 4.785453 GGCGGAGGAAGGGTGCTG 62.785 72.222 0.00 0.00 0.00 4.41
676 693 0.035458 AGTCCTGTTTTCTGGCGGAG 59.965 55.000 0.00 0.00 38.56 4.63
709 726 1.338389 GCAACCGGAGTTAACAGCCTA 60.338 52.381 9.46 0.00 33.27 3.93
719 736 1.536662 AGGAGAAGGCAACCGGAGT 60.537 57.895 9.46 0.00 37.17 3.85
722 739 2.125512 CGAGGAGAAGGCAACCGG 60.126 66.667 0.00 0.00 37.17 5.28
760 777 1.399440 CATCATGGGCACAAGAACTCG 59.601 52.381 0.00 0.00 0.00 4.18
774 791 5.211174 TCCTAGATCAGCAGTTCATCATG 57.789 43.478 0.00 0.00 0.00 3.07
883 910 2.061773 CAGTAGCGTGTGTCCTTTCAG 58.938 52.381 0.00 0.00 0.00 3.02
897 924 3.309954 CAGATAAAAAGGACGGCAGTAGC 59.690 47.826 0.00 0.00 41.10 3.58
900 927 3.335579 GACAGATAAAAAGGACGGCAGT 58.664 45.455 0.00 0.00 0.00 4.40
906 933 4.217767 GTGTTGGGGACAGATAAAAAGGAC 59.782 45.833 0.00 0.00 44.54 3.85
907 934 4.141135 TGTGTTGGGGACAGATAAAAAGGA 60.141 41.667 0.00 0.00 44.54 3.36
971 998 1.079503 GCACTCGATTGGTTCCAGAC 58.920 55.000 4.82 0.00 0.00 3.51
1218 1245 1.595382 ACTGACACCAGAAGCACGC 60.595 57.895 0.00 0.00 43.02 5.34
1377 1404 4.262938 GGAACCAAGCTAGTACTTCCTTGT 60.263 45.833 22.88 12.65 34.38 3.16
1480 1507 0.254178 ATCCAGACCTGCGCAAGAAT 59.746 50.000 14.09 0.00 43.02 2.40
1800 1827 3.753272 TCTTTGTGATAAGCTCAAGCACC 59.247 43.478 13.09 0.00 45.16 5.01
2072 2100 3.181493 GCATCTAGAAATGGCACCAACAG 60.181 47.826 0.00 0.00 0.00 3.16
2074 2102 3.427161 GCATCTAGAAATGGCACCAAC 57.573 47.619 0.00 0.00 0.00 3.77
2118 2146 8.243426 CAGTAGCCAGAATACAAGCATTTAAAA 58.757 33.333 0.00 0.00 0.00 1.52
2144 2172 5.048504 CCATGGACAGTGCAATATGAATACC 60.049 44.000 5.56 0.00 0.00 2.73
2238 2266 7.343316 AGTTCACAGCCTACAGAAGAGTAATAT 59.657 37.037 0.00 0.00 0.00 1.28
2338 2366 5.046376 TGAAGAGAACTTGTATCCAGCATCA 60.046 40.000 0.00 0.00 36.39 3.07
2535 2563 4.287326 TGTCCAACATAACCACCATCACTA 59.713 41.667 0.00 0.00 0.00 2.74
2673 2701 4.335416 CAATACCTTGCCCTTTCTCAAGA 58.665 43.478 3.79 0.00 41.50 3.02
3052 3080 3.327464 TGATCACCATGTGAAGAACTCCA 59.673 43.478 0.46 0.00 45.96 3.86
3184 3212 5.779529 AATCAGGACCAATATGATTGCAC 57.220 39.130 6.02 0.00 36.51 4.57
3245 3273 4.153835 GGATGAGCACAAGTCTCAGAAAAG 59.846 45.833 0.00 0.00 43.02 2.27
3274 3302 4.036734 ACGCATGTTCAACAAATGAGAACT 59.963 37.500 17.44 0.00 41.56 3.01
3376 3407 6.643770 ACCGTTAAGTCATAACACACAACTAG 59.356 38.462 0.00 0.00 43.43 2.57
3399 3430 2.298729 ACAAATGTGTGTGCCCATTACC 59.701 45.455 0.00 0.00 36.31 2.85
3426 3457 8.388484 AGAACTATGCCATTATTCAACAGATC 57.612 34.615 4.14 0.00 0.00 2.75
3431 3462 7.355778 GCACTAGAACTATGCCATTATTCAAC 58.644 38.462 0.00 0.00 33.06 3.18
3546 3577 2.311542 ACCATGAGAATGCCCCTTTACA 59.688 45.455 0.00 0.00 0.00 2.41
4377 4449 8.708378 TCCTTCAGAACTAATATGATGTGTGAT 58.292 33.333 0.00 0.00 0.00 3.06
4810 4882 3.948719 GCTGGAACACCCCGGTCA 61.949 66.667 0.00 0.00 35.02 4.02
5183 5255 2.620112 ATTGTGCCTGCACTGTCGC 61.620 57.895 21.62 0.00 46.30 5.19
5184 5256 1.208358 CATTGTGCCTGCACTGTCG 59.792 57.895 21.62 5.67 46.30 4.35
5188 5260 1.227943 ACGACATTGTGCCTGCACT 60.228 52.632 21.62 2.72 46.30 4.40
5199 5271 0.673333 TTCATCGCAGGCACGACATT 60.673 50.000 4.73 0.00 46.28 2.71
5212 5284 2.932614 GACCTCCATGACACTTTCATCG 59.067 50.000 0.00 0.00 43.68 3.84
5215 5287 1.351017 GGGACCTCCATGACACTTTCA 59.649 52.381 0.00 0.00 39.11 2.69
5259 5333 1.676916 CGCAGACCCTCATGACAACAT 60.677 52.381 0.00 0.00 37.19 2.71
5286 5360 3.256631 CAGGAGTTTTAACATTGGCAGCT 59.743 43.478 0.00 0.00 0.00 4.24
5298 5372 4.830046 TGCATAACAAAGCCAGGAGTTTTA 59.170 37.500 0.00 0.00 0.00 1.52
5299 5373 3.640967 TGCATAACAAAGCCAGGAGTTTT 59.359 39.130 0.00 0.00 0.00 2.43
5300 5374 3.230134 TGCATAACAAAGCCAGGAGTTT 58.770 40.909 0.00 0.00 0.00 2.66
5312 5395 0.254462 TCCTCCGGCATGCATAACAA 59.746 50.000 21.36 0.00 0.00 2.83
5335 5418 3.492482 CCACGGGAAGTTCAAAAGCATTT 60.492 43.478 5.01 0.00 42.41 2.32
5340 5423 2.034179 GGAACCACGGGAAGTTCAAAAG 59.966 50.000 5.01 0.00 43.37 2.27
5341 5424 2.025898 GGAACCACGGGAAGTTCAAAA 58.974 47.619 5.01 0.00 43.37 2.44
5343 5426 0.547075 TGGAACCACGGGAAGTTCAA 59.453 50.000 5.01 0.00 43.37 2.69
5346 5433 2.375014 ATTTGGAACCACGGGAAGTT 57.625 45.000 0.00 0.00 0.00 2.66
5354 5441 5.262588 ACAAACAGAGAATTTGGAACCAC 57.737 39.130 2.84 0.00 40.64 4.16
5384 5471 5.453057 CCAATGTGGAACTGGAAAATTCACA 60.453 40.000 0.00 0.00 40.96 3.58
5409 5496 1.213537 GTGTCCCGATTCCGAACGA 59.786 57.895 0.00 0.00 38.22 3.85
5410 5497 0.459585 ATGTGTCCCGATTCCGAACG 60.460 55.000 0.00 0.00 38.22 3.95
5413 5500 0.899019 TTCATGTGTCCCGATTCCGA 59.101 50.000 0.00 0.00 38.22 4.55
5414 5501 1.396996 GTTTCATGTGTCCCGATTCCG 59.603 52.381 0.00 0.00 0.00 4.30
5417 5504 1.812571 GCAGTTTCATGTGTCCCGATT 59.187 47.619 0.00 0.00 0.00 3.34
5419 5506 0.605319 GGCAGTTTCATGTGTCCCGA 60.605 55.000 0.00 0.00 0.00 5.14
5420 5507 0.888736 TGGCAGTTTCATGTGTCCCG 60.889 55.000 0.00 0.00 0.00 5.14
5421 5508 0.883833 CTGGCAGTTTCATGTGTCCC 59.116 55.000 6.28 0.00 0.00 4.46
5422 5509 0.242017 GCTGGCAGTTTCATGTGTCC 59.758 55.000 17.16 0.00 0.00 4.02
5423 5510 1.242076 AGCTGGCAGTTTCATGTGTC 58.758 50.000 17.16 0.00 0.00 3.67
5424 5511 1.338973 CAAGCTGGCAGTTTCATGTGT 59.661 47.619 14.03 0.00 0.00 3.72
5425 5512 1.610038 TCAAGCTGGCAGTTTCATGTG 59.390 47.619 14.03 3.65 0.00 3.21
5426 5513 1.985473 TCAAGCTGGCAGTTTCATGT 58.015 45.000 14.03 0.00 0.00 3.21
5427 5514 3.192844 AGATTCAAGCTGGCAGTTTCATG 59.807 43.478 14.03 4.41 0.00 3.07
5428 5515 3.192844 CAGATTCAAGCTGGCAGTTTCAT 59.807 43.478 14.03 9.07 0.00 2.57
5429 5516 2.555325 CAGATTCAAGCTGGCAGTTTCA 59.445 45.455 14.03 0.00 0.00 2.69
5430 5517 2.816087 TCAGATTCAAGCTGGCAGTTTC 59.184 45.455 14.03 3.13 34.20 2.78
5460 5547 7.726291 TCCAGGAGTTTCACCAAAATTACATAA 59.274 33.333 0.00 0.00 0.00 1.90
5488 5575 1.749258 GCCAGGCCCGGTTAAAGAG 60.749 63.158 6.92 0.00 0.00 2.85
5489 5576 2.228480 AGCCAGGCCCGGTTAAAGA 61.228 57.895 8.22 0.00 0.00 2.52
5490 5577 2.046285 CAGCCAGGCCCGGTTAAAG 61.046 63.158 8.22 0.00 0.00 1.85
5496 5583 4.431131 ATTGTCAGCCAGGCCCGG 62.431 66.667 8.22 0.00 0.00 5.73
5501 5588 1.952296 GGCATAAGATTGTCAGCCAGG 59.048 52.381 0.00 0.00 41.63 4.45
5519 5606 0.808755 CATGGTAAGGTTGAACGGGC 59.191 55.000 0.00 0.00 0.00 6.13
5520 5607 1.003812 TCCATGGTAAGGTTGAACGGG 59.996 52.381 12.58 0.00 0.00 5.28
5523 5610 7.881775 AAGATTATCCATGGTAAGGTTGAAC 57.118 36.000 12.58 0.00 0.00 3.18
5524 5611 8.112822 TGAAAGATTATCCATGGTAAGGTTGAA 58.887 33.333 12.58 0.00 0.00 2.69
5526 5613 7.880160 TGAAAGATTATCCATGGTAAGGTTG 57.120 36.000 12.58 0.00 0.00 3.77
5527 5614 7.506938 CCATGAAAGATTATCCATGGTAAGGTT 59.493 37.037 12.58 5.11 46.62 3.50
5529 5616 7.458409 CCATGAAAGATTATCCATGGTAAGG 57.542 40.000 12.58 1.91 46.62 2.69
5551 5644 0.842030 ATTGTGAGCCAGTCCCTCCA 60.842 55.000 0.00 0.00 0.00 3.86
5558 5651 4.682859 GCAGAGATAAGATTGTGAGCCAGT 60.683 45.833 0.00 0.00 0.00 4.00
5559 5652 3.808726 GCAGAGATAAGATTGTGAGCCAG 59.191 47.826 0.00 0.00 0.00 4.85
5560 5653 3.453717 AGCAGAGATAAGATTGTGAGCCA 59.546 43.478 0.00 0.00 0.00 4.75
5561 5654 4.057432 GAGCAGAGATAAGATTGTGAGCC 58.943 47.826 0.00 0.00 0.00 4.70
5562 5655 4.507388 GTGAGCAGAGATAAGATTGTGAGC 59.493 45.833 0.00 0.00 0.00 4.26
5563 5656 5.904941 AGTGAGCAGAGATAAGATTGTGAG 58.095 41.667 0.00 0.00 0.00 3.51
5564 5657 5.929058 AGTGAGCAGAGATAAGATTGTGA 57.071 39.130 0.00 0.00 0.00 3.58
5565 5658 6.645827 CCATAGTGAGCAGAGATAAGATTGTG 59.354 42.308 0.00 0.00 0.00 3.33
5566 5659 6.552725 TCCATAGTGAGCAGAGATAAGATTGT 59.447 38.462 0.00 0.00 0.00 2.71
5568 5661 7.609097 TTCCATAGTGAGCAGAGATAAGATT 57.391 36.000 0.00 0.00 0.00 2.40
5569 5662 7.795534 ATTCCATAGTGAGCAGAGATAAGAT 57.204 36.000 0.00 0.00 0.00 2.40
5572 5665 7.609097 AGAATTCCATAGTGAGCAGAGATAA 57.391 36.000 0.65 0.00 0.00 1.75
5573 5666 8.891985 ATAGAATTCCATAGTGAGCAGAGATA 57.108 34.615 0.65 0.00 0.00 1.98
5574 5667 7.675195 AGATAGAATTCCATAGTGAGCAGAGAT 59.325 37.037 0.65 0.00 0.00 2.75
5577 5670 6.552725 ACAGATAGAATTCCATAGTGAGCAGA 59.447 38.462 0.65 0.00 0.00 4.26
5578 5671 6.757237 ACAGATAGAATTCCATAGTGAGCAG 58.243 40.000 0.65 0.00 0.00 4.24
5579 5672 6.737720 ACAGATAGAATTCCATAGTGAGCA 57.262 37.500 0.65 0.00 0.00 4.26
5580 5673 8.443953 AAAACAGATAGAATTCCATAGTGAGC 57.556 34.615 0.65 0.00 0.00 4.26
5582 5675 9.396022 GGAAAAACAGATAGAATTCCATAGTGA 57.604 33.333 0.65 0.00 37.02 3.41
5583 5676 9.401058 AGGAAAAACAGATAGAATTCCATAGTG 57.599 33.333 0.65 0.00 38.99 2.74
5626 5719 2.749776 CATCCACATGTAACCGCGATA 58.250 47.619 8.23 0.00 0.00 2.92
5627 5720 1.581934 CATCCACATGTAACCGCGAT 58.418 50.000 8.23 0.00 0.00 4.58
5631 5724 0.930310 CTCGCATCCACATGTAACCG 59.070 55.000 0.00 0.00 31.86 4.44
5633 5726 0.657840 GCCTCGCATCCACATGTAAC 59.342 55.000 0.00 0.00 31.86 2.50
5663 5756 2.771943 AGAAGAGATTTGCCCGGTATCA 59.228 45.455 0.00 0.00 0.00 2.15
5674 5767 2.373169 TGGGTGTCTGCAGAAGAGATTT 59.627 45.455 20.19 0.00 34.84 2.17
5701 5794 3.470567 CGACTCGTCGCTGTTGGC 61.471 66.667 6.52 0.00 46.50 4.52
5727 5820 0.251916 ATCGGGCGAGTCCAAAATGA 59.748 50.000 0.00 0.00 36.21 2.57
5792 5886 4.155733 TCCACAGCATACCCGGCG 62.156 66.667 0.00 0.00 36.08 6.46
5819 5913 4.624452 CAGTACAAACGGTAGCTTTCCTAC 59.376 45.833 0.00 0.00 44.66 3.18


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

AutoCloner maintained by Alex Coulton.