Multiple sequence alignment - TraesCS2A01G476300

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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 TraesCS2A01G476300 chr2A 100.000 5349 0 0 1 5349 716229272 716234620 0.000000e+00 9878
1 TraesCS2A01G476300 chr2B 95.461 4583 173 20 1 4559 695589208 695593779 0.000000e+00 7278
2 TraesCS2A01G476300 chr2B 86.754 838 49 26 4557 5349 695593837 695594657 0.000000e+00 876
3 TraesCS2A01G476300 chr2D 92.684 2064 125 12 2489 4533 578700793 578702849 0.000000e+00 2952
4 TraesCS2A01G476300 chr2D 93.764 1780 92 11 1 1774 578698312 578700078 0.000000e+00 2654
5 TraesCS2A01G476300 chr2D 84.839 620 31 25 4764 5349 578703183 578703773 2.800000e-157 566
6 TraesCS2A01G476300 chr2D 90.332 331 29 2 2161 2491 578700430 578700757 1.060000e-116 431
7 TraesCS2A01G476300 chr2D 93.304 224 10 4 4557 4775 578702942 578703165 5.170000e-85 326
8 TraesCS2A01G476300 chr2D 91.775 231 15 2 1933 2163 578700123 578700349 8.650000e-83 318


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 TraesCS2A01G476300 chr2A 716229272 716234620 5348 False 9878.000000 9878 100.000000 1 5349 1 chr2A.!!$F1 5348
1 TraesCS2A01G476300 chr2B 695589208 695594657 5449 False 4077.000000 7278 91.107500 1 5349 2 chr2B.!!$F1 5348
2 TraesCS2A01G476300 chr2D 578698312 578703773 5461 False 1207.833333 2952 91.116333 1 5349 6 chr2D.!!$F1 5348

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
535 536 0.617820 GGGGTCAGTTAGAGGAGGCA 60.618 60.0 0.00 0.00 0.00 4.75 F
1597 1603 1.034838 AAAGCCACCACGTTTCAGCA 61.035 50.0 0.00 0.00 0.00 4.41 F
2106 2131 0.039472 TACACAAGTGCATGGGCCAT 59.961 50.0 14.78 14.78 40.13 4.40 F
3137 3289 0.108804 TCGCGGAGTTTGACCATCTC 60.109 55.0 6.13 0.00 0.00 2.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1879 1888 1.573932 CAACCGCTCGTCAAATGCA 59.426 52.632 0.00 0.0 0.00 3.96 R
3523 3679 0.034477 ACGAGCACCTTTATTGGGGG 60.034 55.000 0.00 0.0 0.00 5.40 R
4093 4253 0.307146 GGTAGTAGCTCGCGTCGAAT 59.693 55.000 5.77 0.0 34.74 3.34 R
4533 4705 0.035152 TGTTCATCGAGGCTGGCATT 60.035 50.000 3.38 0.0 0.00 3.56 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
28 29 2.753452 CACTGAAGATGCAATGGAGCTT 59.247 45.455 4.65 4.65 34.99 3.74
106 107 2.289010 GCTTGGCCTTTGTGCTAATGTT 60.289 45.455 3.32 0.00 30.97 2.71
329 330 2.373707 GGGGGAGATGCTGTGAGCT 61.374 63.158 0.00 0.00 42.97 4.09
532 533 1.196012 GTGGGGGTCAGTTAGAGGAG 58.804 60.000 0.00 0.00 0.00 3.69
535 536 0.617820 GGGGTCAGTTAGAGGAGGCA 60.618 60.000 0.00 0.00 0.00 4.75
563 564 4.586841 AGCTAGTGGAGAATGTGGATACTC 59.413 45.833 0.00 0.00 37.61 2.59
700 701 3.343617 ACACTATACCGTGCTTGCAAAT 58.656 40.909 0.00 0.00 38.45 2.32
701 702 3.756434 ACACTATACCGTGCTTGCAAATT 59.244 39.130 0.00 0.00 38.45 1.82
709 710 2.222332 CGTGCTTGCAAATTTGTATGCG 60.222 45.455 28.79 18.46 45.47 4.73
769 770 6.127366 GGAAATTAATGGCTGAAACATCTGGA 60.127 38.462 0.00 0.00 0.00 3.86
790 791 2.760387 GCAAGGAAGCTGGTTGCAGC 62.760 60.000 18.35 12.23 44.87 5.25
858 859 5.303589 CAGATAATGGTCATTTGCCCTGATT 59.696 40.000 1.28 0.00 32.50 2.57
884 885 4.987408 CACCAAATGCATCTGGATTACA 57.013 40.909 25.94 0.00 34.94 2.41
935 936 2.158900 CCGATCCAACATGTAGAGCCTT 60.159 50.000 0.00 0.00 0.00 4.35
1114 1116 6.969043 TGGATAATCTGTTGGGTTACATTCT 58.031 36.000 0.00 0.00 0.00 2.40
1167 1169 3.119495 ACTGTAAAAGATTTGCGGATGCC 60.119 43.478 6.73 0.00 41.78 4.40
1211 1213 5.753438 TGTCAGTATTCTCAATTATGTCCGC 59.247 40.000 0.00 0.00 0.00 5.54
1223 1225 6.542005 TCAATTATGTCCGCTGTATTGATTGT 59.458 34.615 0.00 0.00 29.76 2.71
1256 1258 8.585018 ACAGGTTTATGGTCTTAATCCTTTTTG 58.415 33.333 4.47 0.00 31.71 2.44
1264 1267 8.754991 TGGTCTTAATCCTTTTTGTTACTTCA 57.245 30.769 0.00 0.00 0.00 3.02
1368 1374 4.219944 TGACTATATGGCGATACCCTGTTC 59.780 45.833 0.00 0.00 37.83 3.18
1370 1376 3.963428 ATATGGCGATACCCTGTTCTC 57.037 47.619 0.00 0.00 37.83 2.87
1379 1385 2.950990 ACCCTGTTCTCCCACTCTAT 57.049 50.000 0.00 0.00 0.00 1.98
1421 1427 9.693739 TTTGATATGGGTACAAATGTTGAGTAT 57.306 29.630 0.00 0.00 0.00 2.12
1551 1557 1.670087 CGGTGTCGAGTGAAGCAGATT 60.670 52.381 0.00 0.00 39.00 2.40
1597 1603 1.034838 AAAGCCACCACGTTTCAGCA 61.035 50.000 0.00 0.00 0.00 4.41
1600 1606 1.358759 CCACCACGTTTCAGCAACC 59.641 57.895 0.00 0.00 30.65 3.77
1638 1645 2.627945 TGTTATCGAACCCATGTGCTC 58.372 47.619 0.00 0.00 34.38 4.26
1716 1723 7.816031 CACTACTTTTGATCTGAATGGCAAAAT 59.184 33.333 0.00 0.00 38.89 1.82
1717 1724 9.023962 ACTACTTTTGATCTGAATGGCAAAATA 57.976 29.630 0.00 0.00 38.89 1.40
1813 1822 6.014771 AGTATAGTCCTGACTGATACACCA 57.985 41.667 10.02 0.00 42.52 4.17
1815 1824 5.860941 ATAGTCCTGACTGATACACCAAG 57.139 43.478 10.02 0.00 42.52 3.61
1820 1829 2.417933 CTGACTGATACACCAAGCTTGC 59.582 50.000 21.43 6.74 0.00 4.01
1822 1831 2.675348 GACTGATACACCAAGCTTGCTC 59.325 50.000 21.43 11.52 0.00 4.26
2106 2131 0.039472 TACACAAGTGCATGGGCCAT 59.961 50.000 14.78 14.78 40.13 4.40
2236 2344 4.667573 AGATGCCTCATCCGAGACTATTA 58.332 43.478 3.42 0.00 41.36 0.98
2322 2430 5.625656 GCTGAAGTCTTAGCCAATCTACTGT 60.626 44.000 0.00 0.00 33.89 3.55
2585 2736 1.339438 GCAATCCACCAGAGCTGAAGA 60.339 52.381 0.00 0.00 0.00 2.87
2888 3039 3.093278 CGAGGCTTCGGCACAATC 58.907 61.111 10.87 0.00 43.05 2.67
3049 3201 7.603651 TCAAGTAAGAGAAGTGTCATAGTTCC 58.396 38.462 0.00 0.00 39.16 3.62
3056 3208 6.424207 AGAGAAGTGTCATAGTTCCGAAAAAC 59.576 38.462 0.00 0.00 39.16 2.43
3113 3265 3.603158 AAAACCCACACAGTTTTGACC 57.397 42.857 1.12 0.00 43.80 4.02
3122 3274 2.127383 GTTTTGACCGGCTTCGCG 60.127 61.111 0.00 0.00 0.00 5.87
3131 3283 2.861006 GGCTTCGCGGAGTTTGAC 59.139 61.111 17.40 0.00 0.00 3.18
3137 3289 0.108804 TCGCGGAGTTTGACCATCTC 60.109 55.000 6.13 0.00 0.00 2.75
3140 3292 1.734465 GCGGAGTTTGACCATCTCTTG 59.266 52.381 0.00 0.00 0.00 3.02
3179 3334 1.406614 CCTGCTCTCTTGCTAACCCAG 60.407 57.143 0.00 0.00 0.00 4.45
3423 3578 7.543868 ACTCGATGCATGATCTAATAAACTAGC 59.456 37.037 2.46 0.00 0.00 3.42
3523 3679 5.918608 TCCCAACAAATCTCTAGTAGCATC 58.081 41.667 0.00 0.00 0.00 3.91
3545 3701 2.163613 CCCCAATAAAGGTGCTCGTTTC 59.836 50.000 9.49 0.00 34.27 2.78
3653 3809 7.242914 ACTTTGTCGGTTCTTGTAGTTAAAG 57.757 36.000 0.00 0.00 0.00 1.85
3654 3810 6.259387 ACTTTGTCGGTTCTTGTAGTTAAAGG 59.741 38.462 0.00 0.00 0.00 3.11
3655 3811 4.634199 TGTCGGTTCTTGTAGTTAAAGGG 58.366 43.478 0.00 0.00 0.00 3.95
3656 3812 4.101430 TGTCGGTTCTTGTAGTTAAAGGGT 59.899 41.667 0.00 0.00 0.00 4.34
3657 3813 5.059161 GTCGGTTCTTGTAGTTAAAGGGTT 58.941 41.667 0.00 0.00 0.00 4.11
3658 3814 6.183360 TGTCGGTTCTTGTAGTTAAAGGGTTA 60.183 38.462 0.00 0.00 0.00 2.85
3726 3883 9.939802 ACAAGTATAACTCCTTATTCGAAAACT 57.060 29.630 0.00 0.00 0.00 2.66
3734 3891 7.025963 ACTCCTTATTCGAAAACTAGTACGTG 58.974 38.462 0.00 0.00 0.00 4.49
3760 3917 6.484818 ACATTATTTGCTGTTCATTTTGCC 57.515 33.333 0.00 0.00 0.00 4.52
3767 3924 1.445926 GTTCATTTTGCCCGCGCAT 60.446 52.632 8.75 0.00 46.67 4.73
3800 3957 4.922103 GGTAGAAAACCTCTGTAGTTCACG 59.078 45.833 0.00 0.00 45.75 4.35
3815 3975 9.784680 CTGTAGTTCACGATAAACTAGTAATGT 57.215 33.333 0.00 0.00 39.28 2.71
3823 3983 7.477422 CACGATAAACTAGTAATGTGTTGCAAC 59.523 37.037 22.83 22.83 0.00 4.17
3864 4024 2.455674 TATTGCAGTTCACGCTCTGT 57.544 45.000 0.00 0.00 34.57 3.41
3881 4041 4.010349 CTCTGTAGGAAACCATGGAAACC 58.990 47.826 21.47 17.08 0.00 3.27
3907 4067 7.412891 CGACACATTCTAACTTGTTCATGCATA 60.413 37.037 0.00 0.00 0.00 3.14
3982 4142 0.179070 TGTACAACTTCAGCGGCACA 60.179 50.000 1.45 0.00 0.00 4.57
4076 4236 1.608717 GACGCTGGTGGAGATGGACT 61.609 60.000 0.00 0.00 0.00 3.85
4093 4253 1.984570 CTCGGGGAGCTTCAGGACA 60.985 63.158 0.00 0.00 0.00 4.02
4178 4338 1.852157 ATGCTGGACCCCTTCACCA 60.852 57.895 0.00 0.00 0.00 4.17
4240 4400 1.595357 CTACCCCGCCGAGTTCTTT 59.405 57.895 0.00 0.00 0.00 2.52
4373 4533 1.741770 GGCGGTGGTCAGTGATCAC 60.742 63.158 25.59 25.59 42.37 3.06
4436 4603 4.674475 TGATGTGTATTACGCGTGTACAT 58.326 39.130 29.31 24.87 31.71 2.29
4480 4651 6.773080 TCTTCATTTGCATTGTTTGTTTGTG 58.227 32.000 0.00 0.00 0.00 3.33
4527 4699 3.244976 GTTTGCTTGATTGATTCGGTGG 58.755 45.455 0.00 0.00 0.00 4.61
4533 4705 5.417266 TGCTTGATTGATTCGGTGGAATAAA 59.583 36.000 0.00 0.00 42.86 1.40
4534 4706 6.071672 TGCTTGATTGATTCGGTGGAATAAAA 60.072 34.615 0.00 0.00 42.86 1.52
4540 4717 4.097741 TGATTCGGTGGAATAAAATGCCAG 59.902 41.667 0.00 0.00 42.86 4.85
4554 4731 1.078848 GCCAGCCTCGATGAACACT 60.079 57.895 0.00 0.00 0.00 3.55
4610 4851 2.226674 GCAGAAGAGTTTACTTGGTGCC 59.773 50.000 0.00 0.00 33.74 5.01
4611 4852 3.476552 CAGAAGAGTTTACTTGGTGCCA 58.523 45.455 0.00 0.00 0.00 4.92
4670 4916 7.934457 AGCTAATGGATTAAGCATAACAACAG 58.066 34.615 0.00 0.00 0.00 3.16
4678 4924 7.862873 GGATTAAGCATAACAACAGATTAAGCC 59.137 37.037 0.00 0.00 32.21 4.35
4735 4981 1.867233 TCGTCAACTCTTCAAGCTTGC 59.133 47.619 21.99 3.30 0.00 4.01
4828 5104 8.616076 CAGTTGAGTTGTGAGTAAAAAGAAGAT 58.384 33.333 0.00 0.00 0.00 2.40
4922 5205 8.436046 TTTTTGTTTGAGCTGAGCAATATTTT 57.564 26.923 7.39 0.00 0.00 1.82
4923 5206 8.436046 TTTTGTTTGAGCTGAGCAATATTTTT 57.564 26.923 7.39 0.00 0.00 1.94
4965 5272 1.532868 CACCTTTCTTTGCTCGTCCAG 59.467 52.381 0.00 0.00 0.00 3.86
4966 5273 1.141053 ACCTTTCTTTGCTCGTCCAGT 59.859 47.619 0.00 0.00 0.00 4.00
4967 5274 1.532868 CCTTTCTTTGCTCGTCCAGTG 59.467 52.381 0.00 0.00 0.00 3.66
4968 5275 2.483876 CTTTCTTTGCTCGTCCAGTGA 58.516 47.619 0.00 0.00 0.00 3.41
4969 5276 2.839486 TTCTTTGCTCGTCCAGTGAT 57.161 45.000 0.00 0.00 0.00 3.06
4970 5277 3.953712 TTCTTTGCTCGTCCAGTGATA 57.046 42.857 0.00 0.00 0.00 2.15
4971 5278 4.471904 TTCTTTGCTCGTCCAGTGATAT 57.528 40.909 0.00 0.00 0.00 1.63
4972 5279 4.046938 TCTTTGCTCGTCCAGTGATATC 57.953 45.455 0.00 0.00 0.00 1.63
4973 5280 3.447229 TCTTTGCTCGTCCAGTGATATCA 59.553 43.478 0.00 0.00 0.00 2.15
4974 5281 2.871182 TGCTCGTCCAGTGATATCAC 57.129 50.000 25.47 25.47 46.77 3.06
4997 5304 2.294074 CAAGTTCCCAACCGAAAGACA 58.706 47.619 0.00 0.00 0.00 3.41
4998 5305 2.256117 AGTTCCCAACCGAAAGACAG 57.744 50.000 0.00 0.00 0.00 3.51
4999 5306 1.489230 AGTTCCCAACCGAAAGACAGT 59.511 47.619 0.00 0.00 0.00 3.55
5003 5310 1.602377 CCCAACCGAAAGACAGTGAAC 59.398 52.381 0.00 0.00 0.00 3.18
5093 5407 1.196354 CGCTTTCTGTTCCTTGCTCTG 59.804 52.381 0.00 0.00 0.00 3.35
5114 5428 3.181459 TGTCTTCAAAGAATCACCACGGA 60.181 43.478 0.00 0.00 36.68 4.69
5180 5506 1.674322 GCCAATGCACACGTAGGGT 60.674 57.895 0.00 0.00 37.47 4.34
5321 5653 1.880340 CAAGATCGTCTGCTCGGCC 60.880 63.158 0.00 0.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 2.366533 AGCTCCATTGCATCTTCAGTG 58.633 47.619 0.00 0.00 34.99 3.66
28 29 5.123227 CCCCTACGATAAATCTTGCAGAAA 58.877 41.667 0.00 0.00 0.00 2.52
106 107 4.202451 TGTGTCCCAAATCTGAGACATGAA 60.202 41.667 0.00 0.00 41.01 2.57
532 533 0.833287 TCTCCACTAGCTTCCATGCC 59.167 55.000 0.00 0.00 0.00 4.40
535 536 3.118112 CCACATTCTCCACTAGCTTCCAT 60.118 47.826 0.00 0.00 0.00 3.41
563 564 4.355543 CCAATATTGACGAGTTGGGTTG 57.644 45.455 17.23 0.00 37.92 3.77
628 629 0.603707 TCTTGGCTGCAGTTTCTCCG 60.604 55.000 16.64 0.00 0.00 4.63
700 701 7.721842 TCCCATAAATTAGATTCCGCATACAAA 59.278 33.333 0.00 0.00 0.00 2.83
701 702 7.227873 TCCCATAAATTAGATTCCGCATACAA 58.772 34.615 0.00 0.00 0.00 2.41
709 710 6.488715 AGCATCCTCCCATAAATTAGATTCC 58.511 40.000 0.00 0.00 0.00 3.01
769 770 1.905354 GCAACCAGCTTCCTTGCCT 60.905 57.895 8.09 0.00 41.15 4.75
817 818 9.021807 CCATTATCTGAATATCTTGGAAAGCAT 57.978 33.333 0.00 0.00 45.70 3.79
884 885 1.507140 TGTGGACAAAGGTCTGAGGT 58.493 50.000 0.00 0.00 43.77 3.85
935 936 7.039923 AGTCGGTTAGAGTTTACAAAGATCTGA 60.040 37.037 0.00 0.00 0.00 3.27
1077 1078 8.918658 CAACAGATTATCCAAATGAACAAACTG 58.081 33.333 0.00 0.00 0.00 3.16
1223 1225 5.818678 AAGACCATAAACCTGTGACTGTA 57.181 39.130 0.00 0.00 0.00 2.74
1256 1258 9.646427 ATCAGATAGAGACAACTTTGAAGTAAC 57.354 33.333 0.00 0.00 38.57 2.50
1368 1374 5.248020 AGAAATGGATAGCATAGAGTGGGAG 59.752 44.000 0.00 0.00 0.00 4.30
1370 1376 5.248020 AGAGAAATGGATAGCATAGAGTGGG 59.752 44.000 0.00 0.00 0.00 4.61
1379 1385 7.449395 CCCATATCAAAAGAGAAATGGATAGCA 59.551 37.037 0.00 0.00 36.76 3.49
1551 1557 9.165035 TGGTTTCTCGAGACTTAAAAGTTTAAA 57.835 29.630 16.36 0.00 39.88 1.52
1638 1645 8.742554 ACTCAACAAACAAAACTTAAGTCAAG 57.257 30.769 8.95 4.22 40.38 3.02
1820 1829 1.752753 GTCATGATCGAGCTGACGAG 58.247 55.000 14.38 0.00 45.22 4.18
1879 1888 1.573932 CAACCGCTCGTCAAATGCA 59.426 52.632 0.00 0.00 0.00 3.96
1941 1965 8.206126 TCTGGTAATAATTATCCTCAGATGCA 57.794 34.615 14.96 0.00 33.67 3.96
3034 3185 5.371629 CGTTTTTCGGAACTATGACACTTC 58.628 41.667 0.00 0.00 35.71 3.01
3049 3201 1.433837 CCTATCCCCGCCGTTTTTCG 61.434 60.000 0.00 0.00 39.52 3.46
3056 3208 2.488087 GAATCGTCCTATCCCCGCCG 62.488 65.000 0.00 0.00 0.00 6.46
3122 3274 3.744660 ACACAAGAGATGGTCAAACTCC 58.255 45.455 0.00 0.00 0.00 3.85
3131 3283 6.406370 TGTCCAGTAAATACACAAGAGATGG 58.594 40.000 0.00 0.00 0.00 3.51
3137 3289 6.698380 AGGTACTGTCCAGTAAATACACAAG 58.302 40.000 8.65 0.00 44.62 3.16
3179 3334 6.088616 GTCTGTTGCATAGTGAAAATGAAAGC 59.911 38.462 0.00 0.00 0.00 3.51
3401 3556 6.091305 TGCGCTAGTTTATTAGATCATGCATC 59.909 38.462 9.73 0.00 0.00 3.91
3423 3578 4.328440 CACAAAACTAGGAGAGAAGATGCG 59.672 45.833 0.00 0.00 0.00 4.73
3523 3679 0.034477 ACGAGCACCTTTATTGGGGG 60.034 55.000 0.00 0.00 0.00 5.40
3545 3701 2.417651 CCCATTGCTTAGTTGTGCATGG 60.418 50.000 0.00 0.00 39.07 3.66
3653 3809 2.892374 GGTTTTGCATCATGCTAACCC 58.108 47.619 25.24 17.08 44.88 4.11
3655 3811 4.808558 TCTTGGTTTTGCATCATGCTAAC 58.191 39.130 11.84 14.25 45.31 2.34
3656 3812 4.523943 ACTCTTGGTTTTGCATCATGCTAA 59.476 37.500 11.84 6.82 45.31 3.09
3657 3813 4.081406 ACTCTTGGTTTTGCATCATGCTA 58.919 39.130 11.84 0.00 45.31 3.49
3658 3814 2.895404 ACTCTTGGTTTTGCATCATGCT 59.105 40.909 11.84 0.00 45.31 3.79
3726 3883 6.334989 ACAGCAAATAATGTAGCACGTACTA 58.665 36.000 0.00 0.00 32.19 1.82
3734 3891 7.175410 GCAAAATGAACAGCAAATAATGTAGC 58.825 34.615 0.00 0.00 0.00 3.58
3760 3917 1.669115 CCCCATCTCTTATGCGCGG 60.669 63.158 8.83 0.00 0.00 6.46
3800 3957 9.893305 AAAGTTGCAACACATTACTAGTTTATC 57.107 29.630 30.11 0.00 0.00 1.75
3815 3975 8.129161 CAACAATCAGAAATAAAGTTGCAACA 57.871 30.769 30.11 11.44 0.00 3.33
3857 4017 1.207089 TCCATGGTTTCCTACAGAGCG 59.793 52.381 12.58 0.00 0.00 5.03
3864 4024 2.372504 TGTCGGTTTCCATGGTTTCCTA 59.627 45.455 12.58 2.10 0.00 2.94
3881 4041 5.082059 GCATGAACAAGTTAGAATGTGTCG 58.918 41.667 0.00 0.00 0.00 4.35
4054 4214 1.517257 CATCTCCACCAGCGTCGTC 60.517 63.158 0.00 0.00 0.00 4.20
4058 4218 1.608717 GAGTCCATCTCCACCAGCGT 61.609 60.000 0.00 0.00 37.22 5.07
4076 4236 0.909610 AATGTCCTGAAGCTCCCCGA 60.910 55.000 0.00 0.00 0.00 5.14
4093 4253 0.307146 GGTAGTAGCTCGCGTCGAAT 59.693 55.000 5.77 0.00 34.74 3.34
4133 4293 2.687805 CGTCCGAGGTGAAGAGCGA 61.688 63.158 0.00 0.00 0.00 4.93
4231 4391 0.435008 CGAAGTCCGCAAAGAACTCG 59.565 55.000 0.00 0.00 0.00 4.18
4354 4514 2.213513 TGATCACTGACCACCGCCA 61.214 57.895 0.00 0.00 0.00 5.69
4365 4525 1.546589 TTTACGGGCCGGTGATCACT 61.547 55.000 31.78 8.94 0.00 3.41
4373 4533 1.868469 TTCGATAATTTACGGGCCGG 58.132 50.000 31.78 12.53 0.00 6.13
4436 4603 5.518848 AGAAAGACAATGATGCACACAAA 57.481 34.783 0.00 0.00 0.00 2.83
4523 4695 2.101415 GAGGCTGGCATTTTATTCCACC 59.899 50.000 3.38 0.00 0.00 4.61
4527 4699 3.565482 TCATCGAGGCTGGCATTTTATTC 59.435 43.478 3.38 0.00 0.00 1.75
4533 4705 0.035152 TGTTCATCGAGGCTGGCATT 60.035 50.000 3.38 0.00 0.00 3.56
4534 4706 0.745845 GTGTTCATCGAGGCTGGCAT 60.746 55.000 3.38 0.00 0.00 4.40
4540 4717 2.480416 CCTGTAGAGTGTTCATCGAGGC 60.480 54.545 0.00 0.00 0.00 4.70
4554 4731 2.303022 CCAGCCTCAAGTTTCCTGTAGA 59.697 50.000 0.00 0.00 0.00 2.59
4610 4851 5.817816 GGCCTACGGAAATAGAATATCCATG 59.182 44.000 0.00 0.00 32.58 3.66
4611 4852 5.395324 CGGCCTACGGAAATAGAATATCCAT 60.395 44.000 0.00 0.00 39.42 3.41
4670 4916 1.952296 CCATGTGGAGCTGGCTTAATC 59.048 52.381 0.00 0.00 37.39 1.75
4673 4919 2.695561 TCCATGTGGAGCTGGCTTA 58.304 52.632 0.00 0.00 39.78 3.09
4735 4981 3.555168 GGAAGTGTACAAGGAGTGTGAGG 60.555 52.174 0.00 0.00 41.89 3.86
4842 5119 7.675161 TCATAAACCTGGTCTCATGAGATTA 57.325 36.000 27.51 19.66 39.97 1.75
4843 5120 6.566079 TCATAAACCTGGTCTCATGAGATT 57.434 37.500 27.51 18.24 39.97 2.40
4844 5121 6.760440 ATCATAAACCTGGTCTCATGAGAT 57.240 37.500 27.51 12.74 39.97 2.75
4846 5123 8.915057 AATTATCATAAACCTGGTCTCATGAG 57.085 34.615 17.07 17.07 0.00 2.90
4847 5124 9.342308 GAAATTATCATAAACCTGGTCTCATGA 57.658 33.333 15.87 15.87 0.00 3.07
4849 5126 9.347240 CTGAAATTATCATAAACCTGGTCTCAT 57.653 33.333 0.00 0.00 37.44 2.90
4850 5127 8.548025 TCTGAAATTATCATAAACCTGGTCTCA 58.452 33.333 0.00 0.00 37.44 3.27
4853 5130 8.506168 TGTCTGAAATTATCATAAACCTGGTC 57.494 34.615 0.00 0.00 37.44 4.02
4854 5131 8.739972 GTTGTCTGAAATTATCATAAACCTGGT 58.260 33.333 0.00 0.00 37.44 4.00
4855 5132 8.960591 AGTTGTCTGAAATTATCATAAACCTGG 58.039 33.333 0.00 0.00 37.44 4.45
4921 5204 9.853555 GTGGTGTATACAAATGATGATCAAAAA 57.146 29.630 7.25 0.00 0.00 1.94
4922 5205 8.465999 GGTGGTGTATACAAATGATGATCAAAA 58.534 33.333 7.25 0.00 0.00 2.44
4923 5206 7.833682 AGGTGGTGTATACAAATGATGATCAAA 59.166 33.333 7.25 0.00 0.00 2.69
4924 5207 7.345691 AGGTGGTGTATACAAATGATGATCAA 58.654 34.615 7.25 0.00 0.00 2.57
4925 5208 6.899089 AGGTGGTGTATACAAATGATGATCA 58.101 36.000 7.25 0.00 0.00 2.92
4926 5209 7.807977 AAGGTGGTGTATACAAATGATGATC 57.192 36.000 7.25 0.00 0.00 2.92
4927 5210 8.055181 AGAAAGGTGGTGTATACAAATGATGAT 58.945 33.333 7.25 0.00 0.00 2.45
4928 5211 7.402054 AGAAAGGTGGTGTATACAAATGATGA 58.598 34.615 7.25 0.00 0.00 2.92
4929 5212 7.630242 AGAAAGGTGGTGTATACAAATGATG 57.370 36.000 7.25 0.00 0.00 3.07
4930 5213 8.522830 CAAAGAAAGGTGGTGTATACAAATGAT 58.477 33.333 7.25 0.00 0.00 2.45
4931 5214 7.523052 GCAAAGAAAGGTGGTGTATACAAATGA 60.523 37.037 7.25 0.00 0.00 2.57
4932 5215 6.586082 GCAAAGAAAGGTGGTGTATACAAATG 59.414 38.462 7.25 0.00 0.00 2.32
4933 5216 6.493458 AGCAAAGAAAGGTGGTGTATACAAAT 59.507 34.615 7.25 0.00 0.00 2.32
4965 5272 2.241176 TGGGAACTTGGGGTGATATCAC 59.759 50.000 24.95 24.95 45.72 3.06
4966 5273 2.567862 TGGGAACTTGGGGTGATATCA 58.432 47.619 0.00 0.00 0.00 2.15
4967 5274 3.288092 GTTGGGAACTTGGGGTGATATC 58.712 50.000 0.00 0.00 0.00 1.63
4968 5275 2.024369 GGTTGGGAACTTGGGGTGATAT 60.024 50.000 0.00 0.00 0.00 1.63
4969 5276 1.356398 GGTTGGGAACTTGGGGTGATA 59.644 52.381 0.00 0.00 0.00 2.15
4970 5277 0.114364 GGTTGGGAACTTGGGGTGAT 59.886 55.000 0.00 0.00 0.00 3.06
4971 5278 1.539665 GGTTGGGAACTTGGGGTGA 59.460 57.895 0.00 0.00 0.00 4.02
4972 5279 1.901464 CGGTTGGGAACTTGGGGTG 60.901 63.158 0.00 0.00 0.00 4.61
4973 5280 1.647334 TTCGGTTGGGAACTTGGGGT 61.647 55.000 0.00 0.00 0.00 4.95
4974 5281 0.468400 TTTCGGTTGGGAACTTGGGG 60.468 55.000 0.00 0.00 0.00 4.96
4975 5282 0.958822 CTTTCGGTTGGGAACTTGGG 59.041 55.000 0.00 0.00 0.00 4.12
4976 5283 1.607148 GTCTTTCGGTTGGGAACTTGG 59.393 52.381 0.00 0.00 0.00 3.61
4977 5284 2.290641 CTGTCTTTCGGTTGGGAACTTG 59.709 50.000 0.00 0.00 0.00 3.16
4978 5285 2.092592 ACTGTCTTTCGGTTGGGAACTT 60.093 45.455 0.00 0.00 30.45 2.66
5093 5407 3.186613 GTCCGTGGTGATTCTTTGAAGAC 59.813 47.826 0.00 0.00 34.13 3.01
5114 5428 4.067192 GTTGTTTCGGGTGTTATACTGGT 58.933 43.478 0.00 0.00 0.00 4.00
5180 5506 1.185618 CCTTGTCCGGTCTCTGGTCA 61.186 60.000 0.00 0.00 0.00 4.02
5321 5653 1.904032 GAGGAGCAGGGTGAGGAAG 59.096 63.158 0.00 0.00 0.00 3.46


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

AutoCloner maintained by Alex Coulton.