Multiple sequence alignment - TraesCS5D01G154300

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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 TraesCS5D01G154300 chr5D 100.000 4449 0 0 1 4449 242621768 242626216 0.000000e+00 8216
1 TraesCS5D01G154300 chr5B 92.961 2202 86 15 1 2163 255976367 255974196 0.000000e+00 3144
2 TraesCS5D01G154300 chr5B 94.759 1431 41 8 2165 3580 255974144 255972733 0.000000e+00 2196
3 TraesCS5D01G154300 chr5B 94.718 568 20 6 3577 4136 255972652 255972087 0.000000e+00 874
4 TraesCS5D01G154300 chr5B 97.826 276 6 0 4174 4449 255971965 255971690 1.120000e-130 477
5 TraesCS5D01G154300 chr5A 91.917 2029 97 33 2165 4136 309690564 309688546 0.000000e+00 2776
6 TraesCS5D01G154300 chr5A 90.830 1734 80 28 1 1706 309692712 309691030 0.000000e+00 2248
7 TraesCS5D01G154300 chr5A 97.691 433 8 1 1719 2151 309691063 309690633 0.000000e+00 743
8 TraesCS5D01G154300 chr5A 97.865 281 5 1 4170 4449 309688385 309688105 6.690000e-133 484


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 TraesCS5D01G154300 chr5D 242621768 242626216 4448 False 8216.00 8216 100.00000 1 4449 1 chr5D.!!$F1 4448
1 TraesCS5D01G154300 chr5B 255971690 255976367 4677 True 1672.75 3144 95.06600 1 4449 4 chr5B.!!$R1 4448
2 TraesCS5D01G154300 chr5A 309688105 309692712 4607 True 1562.75 2776 94.57575 1 4449 4 chr5A.!!$R1 4448

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
86 87 0.468029 CACCCAACTGAAAGGCACCT 60.468 55.000 0.00 0.0 39.30 4.00 F
805 852 0.472471 TATCTGGGAAACATCCGGCC 59.528 55.000 0.00 0.0 0.00 6.13 F
1351 1410 1.070758 CTGCAAGGCCAGTATACCGAT 59.929 52.381 5.01 0.0 0.00 4.18 F
2008 2070 0.180406 ACAAGTTGGTCGCTTCTGGT 59.820 50.000 7.96 0.0 0.00 4.00 F
2870 2998 1.153353 CTTTACGACATGGGTTGCGT 58.847 50.000 0.00 0.0 39.91 5.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1351 1410 0.321564 CCACTCCATTGCAGGACGAA 60.322 55.000 0.00 0.0 33.19 3.85 R
1739 1801 1.001815 GACTTTGCGGCTTAGTTTGCA 60.002 47.619 0.00 0.0 35.15 4.08 R
3140 3290 0.110644 CTCGTTGTTTTCAGCTCGGC 60.111 55.000 0.00 0.0 0.00 5.54 R
3170 3320 0.391263 CGTGTTAGGACAGGAAGCCC 60.391 60.000 0.00 0.0 42.71 5.19 R
4094 4357 1.153489 CCTCGAGTCCCACATGCTG 60.153 63.158 12.31 0.0 0.00 4.41 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
86 87 0.468029 CACCCAACTGAAAGGCACCT 60.468 55.000 0.00 0.00 39.30 4.00
160 184 2.923035 CCGGTCCCACTGACACCT 60.923 66.667 0.00 0.00 46.38 4.00
211 235 2.979649 GAAGACCGGGTCCACTCC 59.020 66.667 23.21 5.01 32.18 3.85
226 250 1.694150 CACTCCTCTTTCAGGTGGACA 59.306 52.381 0.00 0.00 43.95 4.02
448 475 3.211045 CCTTTCTTGGTTCGGTTCTTGA 58.789 45.455 0.00 0.00 0.00 3.02
454 481 5.130350 TCTTGGTTCGGTTCTTGATTCTTT 58.870 37.500 0.00 0.00 0.00 2.52
462 489 3.572682 GGTTCTTGATTCTTTCCCCGTTT 59.427 43.478 0.00 0.00 0.00 3.60
503 530 1.709203 GCAAGTATCGTATCGTGCGAG 59.291 52.381 0.00 0.00 41.83 5.03
596 623 6.053005 GCAATGTTTCATTCCATGATCCAAT 58.947 36.000 0.00 0.00 39.39 3.16
597 624 6.540914 GCAATGTTTCATTCCATGATCCAATT 59.459 34.615 0.00 0.00 39.39 2.32
598 625 7.254658 GCAATGTTTCATTCCATGATCCAATTC 60.255 37.037 0.00 0.00 39.39 2.17
599 626 6.224665 TGTTTCATTCCATGATCCAATTCC 57.775 37.500 0.00 0.00 39.39 3.01
600 627 5.720520 TGTTTCATTCCATGATCCAATTCCA 59.279 36.000 0.00 0.00 39.39 3.53
601 628 6.212993 TGTTTCATTCCATGATCCAATTCCAA 59.787 34.615 0.00 0.00 39.39 3.53
641 668 9.236691 TCAATTCAAAATTTCACTTCGAAAGAG 57.763 29.630 0.00 0.00 46.57 2.85
713 742 5.512232 GCTCCATACCCTAATCCTCTTTCAG 60.512 48.000 0.00 0.00 0.00 3.02
791 838 1.136252 CCCGCGCGAAATTGATATCTG 60.136 52.381 34.63 9.31 0.00 2.90
792 839 1.136252 CCGCGCGAAATTGATATCTGG 60.136 52.381 34.63 4.73 0.00 3.86
793 840 1.136252 CGCGCGAAATTGATATCTGGG 60.136 52.381 28.94 0.00 0.00 4.45
794 841 2.143122 GCGCGAAATTGATATCTGGGA 58.857 47.619 12.10 0.00 0.00 4.37
795 842 2.548057 GCGCGAAATTGATATCTGGGAA 59.452 45.455 12.10 0.00 0.00 3.97
796 843 3.003275 GCGCGAAATTGATATCTGGGAAA 59.997 43.478 12.10 0.00 0.00 3.13
797 844 4.527564 CGCGAAATTGATATCTGGGAAAC 58.472 43.478 0.00 0.00 0.00 2.78
798 845 4.035091 CGCGAAATTGATATCTGGGAAACA 59.965 41.667 0.00 0.00 0.00 2.83
799 846 5.277974 CGCGAAATTGATATCTGGGAAACAT 60.278 40.000 0.00 0.00 0.00 2.71
800 847 6.145535 GCGAAATTGATATCTGGGAAACATC 58.854 40.000 3.98 0.00 0.00 3.06
801 848 6.672147 CGAAATTGATATCTGGGAAACATCC 58.328 40.000 3.98 0.00 0.00 3.51
802 849 6.566564 CGAAATTGATATCTGGGAAACATCCG 60.567 42.308 3.98 0.00 0.00 4.18
803 850 3.769739 TGATATCTGGGAAACATCCGG 57.230 47.619 3.98 0.00 0.00 5.14
804 851 2.224523 TGATATCTGGGAAACATCCGGC 60.225 50.000 3.98 0.00 0.00 6.13
805 852 0.472471 TATCTGGGAAACATCCGGCC 59.528 55.000 0.00 0.00 0.00 6.13
806 853 2.608970 ATCTGGGAAACATCCGGCCG 62.609 60.000 21.04 21.04 0.00 6.13
807 854 4.418328 TGGGAAACATCCGGCCGG 62.418 66.667 39.13 39.13 0.00 6.13
808 855 4.419921 GGGAAACATCCGGCCGGT 62.420 66.667 41.57 26.88 36.47 5.28
818 865 2.126110 CGGCCGGTTTGAAATGGC 60.126 61.111 20.10 13.67 46.82 4.40
920 969 3.525537 TCCTTCGATGTTTCAGATGCTC 58.474 45.455 0.00 0.00 0.00 4.26
921 970 2.283617 CCTTCGATGTTTCAGATGCTCG 59.716 50.000 0.00 0.00 0.00 5.03
1128 1185 2.550606 CAGCACCGGCAAGTAAGTTTTA 59.449 45.455 0.00 0.00 44.61 1.52
1241 1299 6.237901 TGTGAGCAACCATTCAGTAATAGTT 58.762 36.000 0.00 0.00 28.49 2.24
1244 1302 7.119846 GTGAGCAACCATTCAGTAATAGTTTCT 59.880 37.037 0.00 0.00 26.92 2.52
1351 1410 1.070758 CTGCAAGGCCAGTATACCGAT 59.929 52.381 5.01 0.00 0.00 4.18
1403 1462 8.218488 AGTTTAGAACTCTTCCACAAAAGGTAT 58.782 33.333 0.00 0.00 37.02 2.73
1422 1481 9.458374 AAAGGTATGTTAAGTTGTGAAATTTCG 57.542 29.630 13.34 0.00 0.00 3.46
1465 1524 9.657419 CATTCAATTTTGCTTCCCTATTTTAGT 57.343 29.630 0.00 0.00 0.00 2.24
1475 1534 4.258543 TCCCTATTTTAGTTCTGGTTGCG 58.741 43.478 0.00 0.00 0.00 4.85
1505 1564 3.971245 ACAGAAGCAAGGACTCCTTAG 57.029 47.619 10.18 6.48 42.67 2.18
1543 1602 5.126061 AGGAAGTGACATGTATCATTTTGGC 59.874 40.000 0.00 0.00 29.49 4.52
1563 1622 2.962786 CGTTCGGTGTTGCGGTGA 60.963 61.111 0.00 0.00 0.00 4.02
1640 1702 2.169978 AGTTATCCCTAGTTTCGTGGCC 59.830 50.000 0.00 0.00 0.00 5.36
1670 1732 6.491745 TCCCACAACAGATTACAAAATAAGCA 59.508 34.615 0.00 0.00 0.00 3.91
1678 1740 2.791383 ACAAAATAAGCACAGCGCAA 57.209 40.000 11.47 0.00 46.13 4.85
1717 1779 4.383118 GCAAACTAAGCCTCTGTCTATGGA 60.383 45.833 0.00 0.00 0.00 3.41
1739 1801 3.338249 AGCGCAACATAGTTCATCAACT 58.662 40.909 11.47 0.00 45.39 3.16
1999 2061 3.664107 TGAGCTGATACACAAGTTGGTC 58.336 45.455 7.96 0.84 0.00 4.02
2008 2070 0.180406 ACAAGTTGGTCGCTTCTGGT 59.820 50.000 7.96 0.00 0.00 4.00
2079 2141 5.694910 CGCAGGTAATTTATGGTGTACCTAG 59.305 44.000 2.32 0.00 43.59 3.02
2199 2317 5.964958 TTCAGAGATTGTTCCATTCAACC 57.035 39.130 0.00 0.00 0.00 3.77
2245 2371 7.757173 AGCATGCATAATAGATAGACAGTTACG 59.243 37.037 21.98 0.00 0.00 3.18
2339 2465 1.380246 GGGATCCAGCATGCACCAA 60.380 57.895 21.98 2.22 31.97 3.67
2396 2522 5.069781 AGAGTATGCCCATTTCTGTAGACTC 59.930 44.000 0.00 0.00 0.00 3.36
2398 2524 3.616956 TGCCCATTTCTGTAGACTCTG 57.383 47.619 0.00 0.00 0.00 3.35
2446 2574 3.006323 TCCTTCTCAGAGCAGTCTCAAAC 59.994 47.826 0.00 0.00 41.81 2.93
2485 2613 5.473796 CAAAAGAAGTTGCAATGCACTTT 57.526 34.783 7.72 11.45 38.71 2.66
2486 2614 5.871539 CAAAAGAAGTTGCAATGCACTTTT 58.128 33.333 21.03 21.03 39.73 2.27
2538 2666 1.679977 GCAGGGATTTGAGGCTGCA 60.680 57.895 0.50 0.00 37.71 4.41
2796 2924 2.380064 ATGTTTCATGTGTGGTGGGT 57.620 45.000 0.00 0.00 0.00 4.51
2870 2998 1.153353 CTTTACGACATGGGTTGCGT 58.847 50.000 0.00 0.00 39.91 5.24
2895 3023 2.060326 TTTCACTCGGTGACACGATC 57.940 50.000 6.27 0.00 42.60 3.69
3140 3290 8.607713 TCCTAGTCTCTCTCCAGGTAATAATAG 58.392 40.741 0.00 0.00 0.00 1.73
3170 3320 1.858091 AACAACGAGTCAGTGAGCAG 58.142 50.000 0.00 0.00 0.00 4.24
3176 3326 0.390998 GAGTCAGTGAGCAGGGCTTC 60.391 60.000 0.00 0.00 39.88 3.86
3177 3327 1.376553 GTCAGTGAGCAGGGCTTCC 60.377 63.158 0.00 0.00 39.88 3.46
3424 3574 1.302033 AGGCTCCAAGACTGCAACG 60.302 57.895 0.00 0.00 27.71 4.10
3428 3578 1.294659 CTCCAAGACTGCAACGGCTC 61.295 60.000 0.00 0.00 41.91 4.70
3571 3738 7.393234 TCAGGTGAAAATTATCAGGAACGATTT 59.607 33.333 0.00 0.00 0.00 2.17
3585 3836 9.268268 TCAGGAACGATTTATATGTACCAATTC 57.732 33.333 0.00 0.00 0.00 2.17
3605 3860 6.662865 ATTCGTATCCTCAGTTCTCATGAT 57.337 37.500 0.00 0.00 0.00 2.45
3628 3883 6.319048 TCTTGAATAATCAGAGCCCTCTTT 57.681 37.500 0.00 0.00 37.98 2.52
3640 3899 4.282195 AGAGCCCTCTTTCGTCATAATAGG 59.718 45.833 0.00 0.00 36.31 2.57
3708 3967 5.305139 ACCGAACTGTGTAATAAATTGCC 57.695 39.130 0.00 0.00 0.00 4.52
3754 4013 7.861176 AAAAATGTGCAATGCAATCATTTTC 57.139 28.000 31.27 13.28 45.47 2.29
4084 4347 6.642733 AGGTCCTTCCTGAAAGATAAATGA 57.357 37.500 0.00 0.00 46.19 2.57
4130 4393 1.503542 GCTCAATGCCAGGTGAACG 59.496 57.895 0.00 0.00 35.15 3.95
4132 4395 0.606401 CTCAATGCCAGGTGAACGGT 60.606 55.000 0.00 0.00 0.00 4.83
4133 4396 0.687920 TCAATGCCAGGTGAACGGTA 59.312 50.000 0.00 0.00 0.00 4.02
4134 4397 1.280710 TCAATGCCAGGTGAACGGTAT 59.719 47.619 0.00 0.00 0.00 2.73
4137 4400 2.279935 TGCCAGGTGAACGGTATTTT 57.720 45.000 0.00 0.00 0.00 1.82
4138 4401 2.156098 TGCCAGGTGAACGGTATTTTC 58.844 47.619 0.00 0.00 0.00 2.29
4139 4402 2.224670 TGCCAGGTGAACGGTATTTTCT 60.225 45.455 0.00 0.00 0.00 2.52
4141 4404 4.004982 GCCAGGTGAACGGTATTTTCTAA 58.995 43.478 0.00 0.00 0.00 2.10
4143 4406 5.243207 CCAGGTGAACGGTATTTTCTAACT 58.757 41.667 0.00 0.00 0.00 2.24
4145 4408 5.350640 CAGGTGAACGGTATTTTCTAACTCC 59.649 44.000 0.00 0.00 0.00 3.85
4146 4409 5.012354 AGGTGAACGGTATTTTCTAACTCCA 59.988 40.000 0.00 0.00 0.00 3.86
4148 4411 5.697633 GTGAACGGTATTTTCTAACTCCACA 59.302 40.000 0.00 0.00 0.00 4.17
4149 4412 6.203338 GTGAACGGTATTTTCTAACTCCACAA 59.797 38.462 0.00 0.00 0.00 3.33
4151 4414 6.980051 ACGGTATTTTCTAACTCCACAATC 57.020 37.500 0.00 0.00 0.00 2.67
4152 4415 6.708285 ACGGTATTTTCTAACTCCACAATCT 58.292 36.000 0.00 0.00 0.00 2.40
4153 4416 6.817140 ACGGTATTTTCTAACTCCACAATCTC 59.183 38.462 0.00 0.00 0.00 2.75
4154 4417 7.042335 CGGTATTTTCTAACTCCACAATCTCT 58.958 38.462 0.00 0.00 0.00 3.10
4155 4418 7.010552 CGGTATTTTCTAACTCCACAATCTCTG 59.989 40.741 0.00 0.00 0.00 3.35
4156 4419 6.749923 ATTTTCTAACTCCACAATCTCTGC 57.250 37.500 0.00 0.00 0.00 4.26
4157 4420 4.890158 TTCTAACTCCACAATCTCTGCA 57.110 40.909 0.00 0.00 0.00 4.41
4161 4424 6.341316 TCTAACTCCACAATCTCTGCAATAC 58.659 40.000 0.00 0.00 0.00 1.89
4162 4425 4.833478 ACTCCACAATCTCTGCAATACT 57.167 40.909 0.00 0.00 0.00 2.12
4166 4429 4.469586 TCCACAATCTCTGCAATACTACCA 59.530 41.667 0.00 0.00 0.00 3.25
4167 4430 5.045942 TCCACAATCTCTGCAATACTACCAA 60.046 40.000 0.00 0.00 0.00 3.67
4168 4431 5.065218 CCACAATCTCTGCAATACTACCAAC 59.935 44.000 0.00 0.00 0.00 3.77
4236 4627 5.288015 CAGTATCAGTTGGTGAGCATAGAG 58.712 45.833 0.00 0.00 39.07 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 65 0.823356 TGCCTTTCAGTTGGGTGAGC 60.823 55.000 0.00 0.00 0.00 4.26
65 66 0.954452 GTGCCTTTCAGTTGGGTGAG 59.046 55.000 0.00 0.00 0.00 3.51
66 67 0.467290 GGTGCCTTTCAGTTGGGTGA 60.467 55.000 0.00 0.00 0.00 4.02
67 68 0.468029 AGGTGCCTTTCAGTTGGGTG 60.468 55.000 0.00 0.00 0.00 4.61
211 235 0.951040 GCCGTGTCCACCTGAAAGAG 60.951 60.000 0.00 0.00 34.07 2.85
448 475 4.470602 AGAAACAGAAACGGGGAAAGAAT 58.529 39.130 0.00 0.00 0.00 2.40
596 623 3.680156 GCATGAAGCCGGTTGGAA 58.320 55.556 1.90 0.00 37.49 3.53
713 742 0.548031 TCATCAGCTGGATTCCCCAC 59.452 55.000 15.13 0.00 40.82 4.61
800 847 2.571231 CCATTTCAAACCGGCCGG 59.429 61.111 42.17 42.17 42.03 6.13
801 848 2.126110 GCCATTTCAAACCGGCCG 60.126 61.111 21.04 21.04 38.67 6.13
802 849 2.126110 CGCCATTTCAAACCGGCC 60.126 61.111 0.00 0.00 41.71 6.13
803 850 1.732683 CACGCCATTTCAAACCGGC 60.733 57.895 0.00 2.72 41.30 6.13
804 851 0.662970 CACACGCCATTTCAAACCGG 60.663 55.000 0.00 0.00 0.00 5.28
805 852 0.309302 TCACACGCCATTTCAAACCG 59.691 50.000 0.00 0.00 0.00 4.44
806 853 2.030363 TCATCACACGCCATTTCAAACC 60.030 45.455 0.00 0.00 0.00 3.27
807 854 3.281341 TCATCACACGCCATTTCAAAC 57.719 42.857 0.00 0.00 0.00 2.93
808 855 4.699735 ACTATCATCACACGCCATTTCAAA 59.300 37.500 0.00 0.00 0.00 2.69
818 865 7.582435 ACAAAAGAGTTACTATCATCACACG 57.418 36.000 0.00 0.00 0.00 4.49
920 969 3.584250 CTTTGTCTGCAGTGCCGCG 62.584 63.158 14.67 0.00 33.35 6.46
921 970 1.785041 TTCTTTGTCTGCAGTGCCGC 61.785 55.000 14.67 3.13 0.00 6.53
1128 1185 3.645884 GCATTTGCTGTTGAATGACAGT 58.354 40.909 6.85 0.00 46.81 3.55
1142 1199 5.888105 ACAAGTATGAGATGAAGCATTTGC 58.112 37.500 0.00 0.00 42.49 3.68
1351 1410 0.321564 CCACTCCATTGCAGGACGAA 60.322 55.000 0.00 0.00 33.19 3.85
1403 1462 7.280428 TCCACTACGAAATTTCACAACTTAACA 59.720 33.333 17.99 0.00 0.00 2.41
1422 1481 6.866010 TTGAATGCATACATCATCCACTAC 57.134 37.500 0.00 0.00 34.62 2.73
1465 1524 0.902984 TAGAGGAGGCGCAACCAGAA 60.903 55.000 20.85 5.76 43.14 3.02
1475 1534 2.626840 CTTGCTTCTGTTAGAGGAGGC 58.373 52.381 0.00 0.00 35.55 4.70
1505 1564 5.037385 GTCACTTCCTTGCTTCTGTTTTTC 58.963 41.667 0.00 0.00 0.00 2.29
1543 1602 4.368808 CCGCAACACCGAACGCAG 62.369 66.667 0.00 0.00 0.00 5.18
1563 1622 9.289782 GCTAGTTGGATAAGTTGGATCATAATT 57.710 33.333 0.00 0.00 0.00 1.40
1620 1682 2.093341 TGGCCACGAAACTAGGGATAAC 60.093 50.000 0.00 0.00 0.00 1.89
1640 1702 8.606040 ATTTTGTAATCTGTTGTGGGAAAATG 57.394 30.769 0.00 0.00 0.00 2.32
1670 1732 2.698803 TGATGAACTATGTTGCGCTGT 58.301 42.857 9.73 0.00 0.00 4.40
1678 1740 4.072131 AGTTTGCGGTTGATGAACTATGT 58.928 39.130 0.00 0.00 32.15 2.29
1717 1779 3.753272 AGTTGATGAACTATGTTGCGCTT 59.247 39.130 9.73 0.00 40.85 4.68
1739 1801 1.001815 GACTTTGCGGCTTAGTTTGCA 60.002 47.619 0.00 0.00 35.15 4.08
1784 1846 2.710377 TCAGCCGAAACTTGCATATGT 58.290 42.857 4.29 0.00 0.00 2.29
1864 1926 5.912955 CCACGAAACCTGAAAAATCAGTTAC 59.087 40.000 5.23 0.00 36.06 2.50
1999 2061 1.542030 ACTACTGACAGACCAGAAGCG 59.458 52.381 10.08 0.00 37.59 4.68
2008 2070 2.698274 TGTGGCTTCAACTACTGACAGA 59.302 45.455 10.08 0.00 32.21 3.41
2079 2141 3.770666 TGTTACGCAGCTTCATCTAGTC 58.229 45.455 0.00 0.00 0.00 2.59
2195 2313 4.038402 AGCACAAGAGAAAAATGGAGGTTG 59.962 41.667 0.00 0.00 0.00 3.77
2199 2317 4.456911 TGCTAGCACAAGAGAAAAATGGAG 59.543 41.667 14.93 0.00 0.00 3.86
2245 2371 2.817844 AGTTTTGCCGTATCTTTGGTCC 59.182 45.455 0.00 0.00 0.00 4.46
2339 2465 1.398692 AACACAGGAAACCGCACATT 58.601 45.000 0.00 0.00 0.00 2.71
2413 2541 3.999663 CTCTGAGAAGGATTTGAAGCGTT 59.000 43.478 0.00 0.00 0.00 4.84
2485 2613 7.333174 TCGCTTCATCACTACAAAATATGTCAA 59.667 33.333 0.00 0.00 42.70 3.18
2486 2614 6.816140 TCGCTTCATCACTACAAAATATGTCA 59.184 34.615 0.00 0.00 42.70 3.58
2698 2826 4.396790 TCGTTTACACTTGCTTTGGACTTT 59.603 37.500 0.00 0.00 0.00 2.66
2870 2998 1.967779 TGTCACCGAGTGAAATCTCCA 59.032 47.619 8.09 0.09 44.49 3.86
2895 3023 4.789075 CCTGGCGTACCGACACCG 62.789 72.222 0.00 0.00 41.22 4.94
3140 3290 0.110644 CTCGTTGTTTTCAGCTCGGC 60.111 55.000 0.00 0.00 0.00 5.54
3170 3320 0.391263 CGTGTTAGGACAGGAAGCCC 60.391 60.000 0.00 0.00 42.71 5.19
3176 3326 2.841215 TGAAAACCGTGTTAGGACAGG 58.159 47.619 0.00 0.00 40.45 4.00
3177 3327 4.062293 TCATGAAAACCGTGTTAGGACAG 58.938 43.478 0.00 0.00 36.20 3.51
3424 3574 2.103042 CGTTAGCCTGCACAGAGCC 61.103 63.158 0.00 0.00 44.83 4.70
3451 3601 1.192428 GGAGTTCCAGTATGACGGGT 58.808 55.000 0.00 0.00 39.69 5.28
3452 3602 1.191535 TGGAGTTCCAGTATGACGGG 58.808 55.000 0.00 0.00 42.01 5.28
3571 3738 8.645814 ACTGAGGATACGAATTGGTACATATA 57.354 34.615 2.11 0.00 46.39 0.86
3585 3836 5.703978 AGATCATGAGAACTGAGGATACG 57.296 43.478 0.09 0.00 46.39 3.06
3605 3860 5.965033 AAGAGGGCTCTGATTATTCAAGA 57.035 39.130 0.00 0.00 40.36 3.02
3628 3883 5.421056 AGGTCACAACTTCCTATTATGACGA 59.579 40.000 0.00 0.00 36.65 4.20
3754 4013 4.533919 TGGCACACTTGAAATTTATGGG 57.466 40.909 0.00 0.00 0.00 4.00
4075 4338 9.516546 ACATGCTGTCATAATCATCATTTATCT 57.483 29.630 0.00 0.00 0.00 1.98
4083 4346 4.214971 GTCCCACATGCTGTCATAATCATC 59.785 45.833 0.00 0.00 0.00 2.92
4084 4347 4.139786 GTCCCACATGCTGTCATAATCAT 58.860 43.478 0.00 0.00 0.00 2.45
4094 4357 1.153489 CCTCGAGTCCCACATGCTG 60.153 63.158 12.31 0.00 0.00 4.41
4124 4387 5.697633 TGTGGAGTTAGAAAATACCGTTCAC 59.302 40.000 0.00 0.00 0.00 3.18
4125 4388 5.856156 TGTGGAGTTAGAAAATACCGTTCA 58.144 37.500 0.00 0.00 0.00 3.18
4126 4389 6.790285 TTGTGGAGTTAGAAAATACCGTTC 57.210 37.500 0.00 0.00 0.00 3.95
4127 4390 7.166167 AGATTGTGGAGTTAGAAAATACCGTT 58.834 34.615 0.00 0.00 0.00 4.44
4128 4391 6.708285 AGATTGTGGAGTTAGAAAATACCGT 58.292 36.000 0.00 0.00 0.00 4.83
4129 4392 7.010552 CAGAGATTGTGGAGTTAGAAAATACCG 59.989 40.741 0.00 0.00 0.00 4.02
4130 4393 7.201652 GCAGAGATTGTGGAGTTAGAAAATACC 60.202 40.741 0.00 0.00 0.00 2.73
4132 4395 7.394016 TGCAGAGATTGTGGAGTTAGAAAATA 58.606 34.615 0.00 0.00 0.00 1.40
4133 4396 6.240894 TGCAGAGATTGTGGAGTTAGAAAAT 58.759 36.000 0.00 0.00 0.00 1.82
4134 4397 5.620206 TGCAGAGATTGTGGAGTTAGAAAA 58.380 37.500 0.00 0.00 0.00 2.29
4137 4400 4.890158 TTGCAGAGATTGTGGAGTTAGA 57.110 40.909 0.00 0.00 0.00 2.10
4138 4401 6.344500 AGTATTGCAGAGATTGTGGAGTTAG 58.656 40.000 0.00 0.00 0.00 2.34
4139 4402 6.299805 AGTATTGCAGAGATTGTGGAGTTA 57.700 37.500 0.00 0.00 0.00 2.24
4141 4404 4.833478 AGTATTGCAGAGATTGTGGAGT 57.167 40.909 0.00 0.00 0.00 3.85
4143 4406 4.469586 TGGTAGTATTGCAGAGATTGTGGA 59.530 41.667 0.00 0.00 0.00 4.02
4145 4408 5.877012 AGTTGGTAGTATTGCAGAGATTGTG 59.123 40.000 0.00 0.00 0.00 3.33
4146 4409 6.054860 AGTTGGTAGTATTGCAGAGATTGT 57.945 37.500 0.00 0.00 0.00 2.71
4148 4411 6.156256 TGGTAGTTGGTAGTATTGCAGAGATT 59.844 38.462 0.00 0.00 0.00 2.40
4149 4412 5.661312 TGGTAGTTGGTAGTATTGCAGAGAT 59.339 40.000 0.00 0.00 0.00 2.75
4151 4414 5.339008 TGGTAGTTGGTAGTATTGCAGAG 57.661 43.478 0.00 0.00 0.00 3.35
4152 4415 5.730550 CTTGGTAGTTGGTAGTATTGCAGA 58.269 41.667 0.00 0.00 0.00 4.26
4153 4416 4.332819 GCTTGGTAGTTGGTAGTATTGCAG 59.667 45.833 0.00 0.00 0.00 4.41
4154 4417 4.258543 GCTTGGTAGTTGGTAGTATTGCA 58.741 43.478 0.00 0.00 0.00 4.08
4155 4418 4.258543 TGCTTGGTAGTTGGTAGTATTGC 58.741 43.478 0.00 0.00 0.00 3.56
4156 4419 8.677148 ATATTGCTTGGTAGTTGGTAGTATTG 57.323 34.615 0.00 0.00 0.00 1.90
4157 4420 9.120538 CAATATTGCTTGGTAGTTGGTAGTATT 57.879 33.333 1.74 0.00 0.00 1.89
4161 4424 7.336931 AGTTCAATATTGCTTGGTAGTTGGTAG 59.663 37.037 10.76 0.00 0.00 3.18
4162 4425 7.172342 AGTTCAATATTGCTTGGTAGTTGGTA 58.828 34.615 10.76 0.00 0.00 3.25
4166 4429 8.630054 TGTTAGTTCAATATTGCTTGGTAGTT 57.370 30.769 10.76 0.00 0.00 2.24
4167 4430 8.807948 ATGTTAGTTCAATATTGCTTGGTAGT 57.192 30.769 10.76 0.00 0.00 2.73
4204 4595 4.510711 CACCAACTGATACTGCATCATCTC 59.489 45.833 8.62 0.00 42.82 2.75
4236 4627 7.041712 GCTTAGTTAAGATTGCTCAGGTAATCC 60.042 40.741 3.15 0.00 42.75 3.01
4297 4688 4.878397 CCTGGTATCCAAACTCAGATGTTC 59.122 45.833 0.00 0.00 30.80 3.18


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

AutoCloner maintained by Alex Coulton.