Multiple sequence alignment - TraesCS2D01G141100

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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 TraesCS2D01G141100 chr2D 100.000 6842 0 0 1 6842 83130777 83137618 0.000 12635.0
1 TraesCS2D01G141100 chr2A 92.881 5366 210 74 1580 6842 83819947 83825243 0.000 7635.0
2 TraesCS2D01G141100 chr2A 88.889 1647 86 37 1 1580 83818166 83819782 0.000 1938.0
3 TraesCS2D01G141100 chr2B 95.449 3428 97 28 3447 6842 135001146 135004546 0.000 5411.0
4 TraesCS2D01G141100 chr2B 93.796 3514 125 29 1 3448 134997556 135001042 0.000 5195.0
5 TraesCS2D01G141100 chr7B 100.000 29 0 0 1551 1579 687682679 687682651 0.003 54.7
6 TraesCS2D01G141100 chr6A 100.000 28 0 0 1553 1580 33013683 33013710 0.012 52.8


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 TraesCS2D01G141100 chr2D 83130777 83137618 6841 False 12635.0 12635 100.0000 1 6842 1 chr2D.!!$F1 6841
1 TraesCS2D01G141100 chr2A 83818166 83825243 7077 False 4786.5 7635 90.8850 1 6842 2 chr2A.!!$F1 6841
2 TraesCS2D01G141100 chr2B 134997556 135004546 6990 False 5303.0 5411 94.6225 1 6842 2 chr2B.!!$F1 6841

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
737 759 0.036388 ATCTGACCACGAACGCCATT 60.036 50.000 0.00 0.0 0.00 3.16 F
1847 2108 0.033601 ACCAGCCACTTCAAACCACA 60.034 50.000 0.00 0.0 0.00 4.17 F
2208 2483 0.683504 GGGCCTCCGAACTACTCTGA 60.684 60.000 0.84 0.0 0.00 3.27 F
2340 2617 1.471684 CTGCAATCCAAGAGTTCTGGC 59.528 52.381 0.00 0.0 0.00 4.85 F
2558 2836 1.492720 GTAAGCGCACATCTAGGCTC 58.507 55.000 11.47 0.0 33.99 4.70 F
3325 3618 2.016318 TCAGAATTAATGGCCAGCACG 58.984 47.619 13.05 0.0 0.00 5.34 F
3474 3871 3.118629 CGGTGCTATATGCTATGGATGGT 60.119 47.826 0.00 0.0 43.37 3.55 F
4163 4564 4.358851 TGTTCTGCATTTTTGTGCTGTAC 58.641 39.130 8.00 8.0 45.27 2.90 F
5376 5788 2.214376 TGGTTGTCTGCCCCTATTTG 57.786 50.000 0.00 0.0 0.00 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2135 2410 0.882927 CTCGGTCCAAAAACGCAGGA 60.883 55.000 0.00 0.0 0.00 3.86 R
3474 3871 0.536724 TTAGCTGCTCTCGCCATGAA 59.463 50.000 4.91 0.0 34.43 2.57 R
4155 4556 2.434359 GGCCTGGTCGTACAGCAC 60.434 66.667 0.00 0.0 37.16 4.40 R
4163 4564 2.917933 TCATCTTTAATGGCCTGGTCG 58.082 47.619 3.32 0.0 0.00 4.79 R
4500 4901 4.357097 AGAACCTTCCCCCTTTGTTATTCT 59.643 41.667 0.00 0.0 0.00 2.40 R
5028 5438 2.145397 TAGGCTCTCCGTCTGATGTT 57.855 50.000 0.00 0.0 37.47 2.71 R
5376 5788 1.134907 CATGCAATCCCTGTGGCTTTC 60.135 52.381 0.00 0.0 0.00 2.62 R
5709 6135 1.534175 GGTCGGTTATGACTCGCTCAG 60.534 57.143 0.00 0.0 38.91 3.35 R
6741 7189 1.222936 GCAGATGGGACTGGGAGTG 59.777 63.158 0.00 0.0 38.22 3.51 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
70 71 9.435570 ACTACATTACTACTGAACCCTGATTAT 57.564 33.333 0.00 0.00 0.00 1.28
81 82 6.726379 TGAACCCTGATTATGAACATTGGTA 58.274 36.000 0.00 0.00 0.00 3.25
119 120 1.395826 CCTCGATTTCCCTCTCGGCT 61.396 60.000 0.00 0.00 35.64 5.52
187 188 1.304547 CCTCCACAGACTCCTCCGT 60.305 63.158 0.00 0.00 0.00 4.69
255 257 4.311816 ACATCTGCAGAAACAAACCAAG 57.688 40.909 22.50 3.42 0.00 3.61
259 261 0.597377 GCAGAAACAAACCAAGCGGG 60.597 55.000 0.00 0.00 44.81 6.13
270 272 0.243636 CCAAGCGGGTTCAAATCACC 59.756 55.000 0.00 0.00 0.00 4.02
271 273 0.958091 CAAGCGGGTTCAAATCACCA 59.042 50.000 0.00 0.00 35.80 4.17
306 308 0.825010 AGCACCAAACAGGCAGGAAG 60.825 55.000 0.00 0.00 43.14 3.46
412 414 1.592223 CTTCCGCTTCTTCTCCGGT 59.408 57.895 0.00 0.00 42.48 5.28
708 730 1.470890 GTTCCCGCGGATCAAAATTCA 59.529 47.619 30.73 0.00 0.00 2.57
737 759 0.036388 ATCTGACCACGAACGCCATT 60.036 50.000 0.00 0.00 0.00 3.16
867 896 2.046892 TCTGCTTCCGCTTCTGGC 60.047 61.111 0.00 0.00 36.97 4.85
1079 1125 2.442272 GAGGAGCAGCGGGAGGTA 60.442 66.667 0.00 0.00 39.46 3.08
1132 1179 0.962356 CTGCTTGGCGATTTCTGGGT 60.962 55.000 0.00 0.00 0.00 4.51
1145 1192 0.895100 TCTGGGTTGCTGATTGGTGC 60.895 55.000 0.00 0.00 0.00 5.01
1154 1201 1.606224 GCTGATTGGTGCTGGTTTTGG 60.606 52.381 0.00 0.00 0.00 3.28
1169 1216 1.067295 TTTGGTGCTGACTCAGGGAT 58.933 50.000 8.17 0.00 31.21 3.85
1199 1246 4.907034 CGATCGGTGGCGAGGACG 62.907 72.222 7.38 0.00 42.93 4.79
1284 1331 2.093288 TGATTGGCTTCAGGAGTAGCAG 60.093 50.000 0.00 0.00 39.64 4.24
1309 1356 2.919229 CTGCAGCGGTGAAATTCATTTC 59.081 45.455 20.69 5.46 44.83 2.17
1352 1399 1.138464 TGCTGCTCTGAGCTAATCTGG 59.862 52.381 28.04 11.55 42.97 3.86
1359 1406 4.469657 CTCTGAGCTAATCTGGTCCTAGT 58.530 47.826 0.00 0.00 33.93 2.57
1378 1425 3.690460 AGTCTCCCATGTTGGTGATTTC 58.310 45.455 0.00 0.00 35.17 2.17
1401 1448 1.655484 TGCAGCTCGTGGTGATATTG 58.345 50.000 19.85 0.00 43.76 1.90
1410 1457 2.032054 CGTGGTGATATTGTGTGCATCC 59.968 50.000 0.00 0.00 0.00 3.51
1411 1458 2.358898 GTGGTGATATTGTGTGCATCCC 59.641 50.000 0.00 0.00 0.00 3.85
1430 1477 2.557452 CCCTTGGTAAAATGGCACTCCT 60.557 50.000 0.00 0.00 0.00 3.69
1440 1487 1.144936 GGCACTCCTTCCGATCCAG 59.855 63.158 0.00 0.00 0.00 3.86
1450 1498 3.821033 CCTTCCGATCCAGAAAAAGTGTT 59.179 43.478 0.00 0.00 0.00 3.32
1461 1509 4.504097 CAGAAAAAGTGTTGTGGCTTTAGC 59.496 41.667 0.00 0.00 34.26 3.09
1479 1542 3.492102 AGCTCTTGAACTAAAGCCACA 57.508 42.857 0.00 0.00 35.32 4.17
1679 1925 8.190784 CCAAATTAGCAAGGGAACTAGTAATTG 58.809 37.037 0.00 0.51 42.68 2.32
1838 2099 2.743718 CCGACTGACCAGCCACTT 59.256 61.111 0.00 0.00 0.00 3.16
1847 2108 0.033601 ACCAGCCACTTCAAACCACA 60.034 50.000 0.00 0.00 0.00 4.17
1851 2112 2.094286 CAGCCACTTCAAACCACAAACA 60.094 45.455 0.00 0.00 0.00 2.83
2052 2326 5.316327 GGAAGCTCCCAATAGTTTTTCTG 57.684 43.478 0.00 0.00 0.00 3.02
2135 2410 3.391382 GGGTCTAGCCGGTGCAGT 61.391 66.667 1.90 0.00 41.13 4.40
2208 2483 0.683504 GGGCCTCCGAACTACTCTGA 60.684 60.000 0.84 0.00 0.00 3.27
2340 2617 1.471684 CTGCAATCCAAGAGTTCTGGC 59.528 52.381 0.00 0.00 0.00 4.85
2365 2642 8.987890 GCTTTATCTTGTTGGCTTTAAATGAAA 58.012 29.630 0.00 0.00 0.00 2.69
2558 2836 1.492720 GTAAGCGCACATCTAGGCTC 58.507 55.000 11.47 0.00 33.99 4.70
2623 2901 7.497249 GCATTTACTTCAGATATGGTCAAGAGT 59.503 37.037 0.00 0.00 0.00 3.24
2624 2902 9.388506 CATTTACTTCAGATATGGTCAAGAGTT 57.611 33.333 0.00 0.00 0.00 3.01
2627 2905 7.962995 ACTTCAGATATGGTCAAGAGTTAGA 57.037 36.000 0.00 0.00 0.00 2.10
2628 2906 8.006298 ACTTCAGATATGGTCAAGAGTTAGAG 57.994 38.462 0.00 0.00 0.00 2.43
2629 2907 7.617723 ACTTCAGATATGGTCAAGAGTTAGAGT 59.382 37.037 0.00 0.00 0.00 3.24
2630 2908 7.340122 TCAGATATGGTCAAGAGTTAGAGTG 57.660 40.000 0.00 0.00 0.00 3.51
2920 3200 8.598916 TGTTGTTTCTGTTATTAGTAGATGGGA 58.401 33.333 0.00 0.00 0.00 4.37
3226 3519 3.850774 TGGAGTCTGGACTACCTTCTCTA 59.149 47.826 10.11 0.00 41.64 2.43
3306 3599 6.109359 AGTGCTATAGGTGAGAAAATGTGTC 58.891 40.000 1.04 0.00 0.00 3.67
3325 3618 2.016318 TCAGAATTAATGGCCAGCACG 58.984 47.619 13.05 0.00 0.00 5.34
3404 3697 8.506437 GTGATGTTAAATCATCTGTTCTTCACA 58.494 33.333 7.38 0.00 43.03 3.58
3474 3871 3.118629 CGGTGCTATATGCTATGGATGGT 60.119 47.826 0.00 0.00 43.37 3.55
4155 4556 7.279758 TCCCTTACTTTTTGTTCTGCATTTTTG 59.720 33.333 0.00 0.00 0.00 2.44
4163 4564 4.358851 TGTTCTGCATTTTTGTGCTGTAC 58.641 39.130 8.00 8.00 45.27 2.90
4538 4939 6.463755 GGGAAGGTTCTTTGGAAAGCAATTTA 60.464 38.462 0.00 0.00 35.99 1.40
4559 4960 4.639135 AGTTCCTTTTCTGTTCAAGTGC 57.361 40.909 0.00 0.00 0.00 4.40
4624 5025 5.886609 TGTCCCTTTTTATCTTGATCACCA 58.113 37.500 0.00 0.00 0.00 4.17
5028 5438 6.476409 TTATTATATGAAGGGGGCAATGGA 57.524 37.500 0.00 0.00 0.00 3.41
5228 5640 7.976734 GTGGATAATCCTGAGCATATGTAGTAC 59.023 40.741 4.29 0.00 37.46 2.73
5376 5788 2.214376 TGGTTGTCTGCCCCTATTTG 57.786 50.000 0.00 0.00 0.00 2.32
5467 5889 4.912586 TGCATTTAACTTGCCTACCACTA 58.087 39.130 7.02 0.00 39.39 2.74
5476 5898 9.555727 TTAACTTGCCTACCACTATAAATGATC 57.444 33.333 0.00 0.00 0.00 2.92
5497 5919 8.565896 TGATCAAGCAAGTTAGTAAACATGAT 57.434 30.769 0.00 0.00 36.61 2.45
5498 5920 9.665719 TGATCAAGCAAGTTAGTAAACATGATA 57.334 29.630 0.00 0.00 36.61 2.15
5569 5991 3.539604 CATGGGTTGTTTTGCCTTTGAA 58.460 40.909 0.00 0.00 0.00 2.69
5579 6001 3.423848 GCCTTTGAAATTCCAGGCG 57.576 52.632 15.01 0.00 42.47 5.52
5709 6135 0.671251 TGTCGCCACCAAAATGTTCC 59.329 50.000 0.00 0.00 0.00 3.62
5860 6286 3.354467 TGATGGCACTACATGATGCAAA 58.646 40.909 18.39 9.68 43.93 3.68
5917 6343 3.604875 TCGAAACCACCTGATACTTCC 57.395 47.619 0.00 0.00 0.00 3.46
5924 6350 2.571653 CCACCTGATACTTCCAGTTCCA 59.428 50.000 0.00 0.00 0.00 3.53
6004 6432 6.096141 TGTGAATTGGAGTTTTGCTTTACTGA 59.904 34.615 0.00 0.00 0.00 3.41
6014 6442 6.745907 AGTTTTGCTTTACTGACGAAAACTTC 59.254 34.615 0.00 0.00 39.44 3.01
6137 6566 1.929836 CTAACAGCGCTCTGATTGACC 59.070 52.381 7.13 0.00 42.95 4.02
6168 6604 6.161855 TGCTAGTATTTACTGGTGGATCAG 57.838 41.667 0.00 0.00 37.16 2.90
6183 6619 6.122277 GGTGGATCAGTTGATTCTATCCAAA 58.878 40.000 4.02 0.00 45.68 3.28
6188 6624 7.012799 GGATCAGTTGATTCTATCCAAAGGAAC 59.987 40.741 0.00 0.00 36.83 3.62
6276 6714 2.401583 TGTTCTTGTGTGCTCACTGT 57.598 45.000 18.85 0.00 44.14 3.55
6312 6750 5.702670 TGTCTAGCCACAGAAGAAGAAAATG 59.297 40.000 0.00 0.00 0.00 2.32
6324 6763 9.734620 CAGAAGAAGAAAATGTGTAAAATGTCA 57.265 29.630 0.00 0.00 0.00 3.58
6333 6772 4.930963 TGTGTAAAATGTCAGGTGCTTTG 58.069 39.130 0.00 0.00 0.00 2.77
6372 6811 5.345702 TGTATGCATAAACTCGGTACTGTC 58.654 41.667 8.28 0.00 0.00 3.51
6399 6838 2.611518 GGTCAAGATTCTCGACACCAG 58.388 52.381 7.06 0.00 0.00 4.00
6474 6914 4.604156 TCTCTCCTGTATCGCATATGGAT 58.396 43.478 4.56 8.17 0.00 3.41
6536 6976 3.760684 CCAGCAGCTCTCCTTAAACATTT 59.239 43.478 0.00 0.00 0.00 2.32
6650 7095 1.527380 GGCAAACAACCTCACGGGA 60.527 57.895 0.00 0.00 38.76 5.14
6741 7189 4.839668 ATAGCCGATCTGTAGAGTGAAC 57.160 45.455 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 8.834004 AATCAGGGTTCAGTAGTAATGTAGTA 57.166 34.615 0.00 0.00 0.00 1.82
44 45 7.735326 AATCAGGGTTCAGTAGTAATGTAGT 57.265 36.000 0.00 0.00 0.00 2.73
45 46 9.698309 CATAATCAGGGTTCAGTAGTAATGTAG 57.302 37.037 0.00 0.00 0.00 2.74
46 47 9.429109 TCATAATCAGGGTTCAGTAGTAATGTA 57.571 33.333 0.00 0.00 0.00 2.29
47 48 8.319057 TCATAATCAGGGTTCAGTAGTAATGT 57.681 34.615 0.00 0.00 0.00 2.71
48 49 9.046296 GTTCATAATCAGGGTTCAGTAGTAATG 57.954 37.037 0.00 0.00 0.00 1.90
49 50 8.768397 TGTTCATAATCAGGGTTCAGTAGTAAT 58.232 33.333 0.00 0.00 0.00 1.89
50 51 8.141298 TGTTCATAATCAGGGTTCAGTAGTAA 57.859 34.615 0.00 0.00 0.00 2.24
70 71 5.664457 TGTTTTGCAATGTACCAATGTTCA 58.336 33.333 0.00 0.00 0.00 3.18
81 82 4.559153 GAGGTAATGCTGTTTTGCAATGT 58.441 39.130 0.00 0.00 46.61 2.71
119 120 4.388499 GTGAGGCGGCGGAAGGAA 62.388 66.667 9.78 0.00 0.00 3.36
255 257 0.388520 GCTTGGTGATTTGAACCCGC 60.389 55.000 0.00 0.00 36.83 6.13
259 261 2.397549 GCTGTGCTTGGTGATTTGAAC 58.602 47.619 0.00 0.00 0.00 3.18
260 262 1.340889 GGCTGTGCTTGGTGATTTGAA 59.659 47.619 0.00 0.00 0.00 2.69
266 268 1.227943 GAGTGGCTGTGCTTGGTGA 60.228 57.895 0.00 0.00 0.00 4.02
270 272 1.954528 CTTGGAGTGGCTGTGCTTG 59.045 57.895 0.00 0.00 0.00 4.01
271 273 1.900498 GCTTGGAGTGGCTGTGCTT 60.900 57.895 0.00 0.00 0.00 3.91
708 730 0.247736 GTGGTCAGATCTCAGCCGTT 59.752 55.000 0.00 0.00 0.00 4.44
867 896 1.027357 GCAAGGCACTGGATACCATG 58.973 55.000 0.00 0.00 40.86 3.66
984 1030 2.588877 ATCTCGCGCGGGGAAATG 60.589 61.111 31.95 11.26 0.00 2.32
1132 1179 1.412079 AAACCAGCACCAATCAGCAA 58.588 45.000 0.00 0.00 0.00 3.91
1145 1192 1.605710 CTGAGTCAGCACCAAAACCAG 59.394 52.381 7.33 0.00 0.00 4.00
1154 1201 1.812922 CGCATCCCTGAGTCAGCAC 60.813 63.158 15.10 0.86 0.00 4.40
1169 1216 4.819761 GATCGCAGCACCTCCGCA 62.820 66.667 0.00 0.00 0.00 5.69
1199 1246 1.325476 CCAAATCCTTCAGGCTGCCC 61.325 60.000 16.57 0.00 34.44 5.36
1284 1331 2.225491 TGAATTTCACCGCTGCAGTAAC 59.775 45.455 16.64 0.00 0.00 2.50
1309 1356 1.272781 CTCGCCGAAAACTAGAGCTG 58.727 55.000 0.00 0.00 0.00 4.24
1352 1399 2.093447 CACCAACATGGGAGACTAGGAC 60.093 54.545 0.00 0.00 43.37 3.85
1359 1406 2.039746 ACGAAATCACCAACATGGGAGA 59.960 45.455 0.00 0.00 43.37 3.71
1378 1425 1.568612 ATCACCACGAGCTGCAAACG 61.569 55.000 1.02 7.36 0.00 3.60
1401 1448 3.368323 CCATTTTACCAAGGGATGCACAC 60.368 47.826 0.00 0.00 0.00 3.82
1410 1457 2.807676 AGGAGTGCCATTTTACCAAGG 58.192 47.619 0.00 0.00 36.29 3.61
1411 1458 3.193479 GGAAGGAGTGCCATTTTACCAAG 59.807 47.826 0.00 0.00 36.29 3.61
1430 1477 4.036262 CACAACACTTTTTCTGGATCGGAA 59.964 41.667 0.00 0.00 0.00 4.30
1440 1487 4.682787 AGCTAAAGCCACAACACTTTTTC 58.317 39.130 0.00 0.00 43.38 2.29
1450 1498 3.492102 AGTTCAAGAGCTAAAGCCACA 57.508 42.857 0.00 0.00 43.38 4.17
1461 1509 5.695851 ATGTTGTGGCTTTAGTTCAAGAG 57.304 39.130 0.00 0.00 0.00 2.85
1679 1925 6.866480 TCATGCAAGGTGAAGGATAAAAATC 58.134 36.000 0.00 0.00 0.00 2.17
1838 2099 2.738000 GCAGTGCATGTTTGTGGTTTGA 60.738 45.455 11.09 0.00 0.00 2.69
2050 2324 2.681848 GAGGTGATCAAGCCATCAACAG 59.318 50.000 0.00 0.00 42.23 3.16
2051 2325 2.306805 AGAGGTGATCAAGCCATCAACA 59.693 45.455 0.00 0.00 42.23 3.33
2052 2326 2.681848 CAGAGGTGATCAAGCCATCAAC 59.318 50.000 0.00 0.00 40.36 3.18
2135 2410 0.882927 CTCGGTCCAAAAACGCAGGA 60.883 55.000 0.00 0.00 0.00 3.86
2208 2483 3.306502 CCAGCTCATTTGCCAAGAACATT 60.307 43.478 0.00 0.00 0.00 2.71
2475 2752 4.543590 ATCACACTAGGCATGCCTATAC 57.456 45.455 39.76 14.56 46.46 1.47
2569 2847 7.040409 GGACTTTGACCATATTAAAGCCATAGG 60.040 40.741 0.00 0.00 35.40 2.57
2623 2901 8.251721 GCTGATAAGAAAGGTCTAACACTCTAA 58.748 37.037 0.00 0.00 32.16 2.10
2624 2902 7.396339 TGCTGATAAGAAAGGTCTAACACTCTA 59.604 37.037 0.00 0.00 32.16 2.43
2625 2903 6.211584 TGCTGATAAGAAAGGTCTAACACTCT 59.788 38.462 0.00 0.00 32.16 3.24
2626 2904 6.398918 TGCTGATAAGAAAGGTCTAACACTC 58.601 40.000 0.00 0.00 32.16 3.51
2627 2905 6.360370 TGCTGATAAGAAAGGTCTAACACT 57.640 37.500 0.00 0.00 32.16 3.55
2628 2906 6.457528 GCATGCTGATAAGAAAGGTCTAACAC 60.458 42.308 11.37 0.00 32.16 3.32
2629 2907 5.586243 GCATGCTGATAAGAAAGGTCTAACA 59.414 40.000 11.37 0.00 32.16 2.41
2630 2908 5.819901 AGCATGCTGATAAGAAAGGTCTAAC 59.180 40.000 21.98 0.00 32.16 2.34
2748 3028 2.935201 GTCCAAGATAGCAGCTGTTCAG 59.065 50.000 16.64 7.14 0.00 3.02
2920 3200 4.100808 AGTGCCACAATTACCAACAACAAT 59.899 37.500 0.00 0.00 0.00 2.71
3200 3493 2.280103 AGGTAGTCCAGACTCCAGAGA 58.720 52.381 3.00 0.00 42.54 3.10
3226 3519 9.905713 TCTTTGCTATAAATCTGGTCTACAAAT 57.094 29.630 0.00 0.00 0.00 2.32
3306 3599 1.066002 CCGTGCTGGCCATTAATTCTG 59.934 52.381 5.51 0.00 0.00 3.02
3461 3858 2.522185 GCCATGAACCATCCATAGCAT 58.478 47.619 0.00 0.00 30.78 3.79
3474 3871 0.536724 TTAGCTGCTCTCGCCATGAA 59.463 50.000 4.91 0.00 34.43 2.57
3604 4002 8.153479 TCGTGTGATTTAAGCTTATGCATATT 57.847 30.769 7.36 1.68 42.74 1.28
3645 4043 7.602644 TCTTTTATGAGCAGTCACTTCGTTTAT 59.397 33.333 0.00 0.00 34.75 1.40
4155 4556 2.434359 GGCCTGGTCGTACAGCAC 60.434 66.667 0.00 0.00 37.16 4.40
4163 4564 2.917933 TCATCTTTAATGGCCTGGTCG 58.082 47.619 3.32 0.00 0.00 4.79
4499 4900 5.554350 AGAACCTTCCCCCTTTGTTATTCTA 59.446 40.000 0.00 0.00 0.00 2.10
4500 4901 4.357097 AGAACCTTCCCCCTTTGTTATTCT 59.643 41.667 0.00 0.00 0.00 2.40
4516 4917 7.124573 ACTAAATTGCTTTCCAAAGAACCTT 57.875 32.000 3.11 0.00 38.28 3.50
4538 4939 7.845042 CTGAGCACTTGAACAGAAAAGGAACT 61.845 42.308 0.00 0.00 34.10 3.01
4559 4960 2.240667 ACAGATGAATGAACCCCCTGAG 59.759 50.000 0.00 0.00 0.00 3.35
4746 5148 7.440523 ACTGACTGAATGAAAATAGTTCCAC 57.559 36.000 0.00 0.00 0.00 4.02
4796 5200 7.121315 GCTTCCAAAGTATCTTGGTATTCAGTT 59.879 37.037 2.48 0.00 45.29 3.16
5028 5438 2.145397 TAGGCTCTCCGTCTGATGTT 57.855 50.000 0.00 0.00 37.47 2.71
5173 5583 8.782144 TGAAAATGTCAAAAGAAAAACAGCTTT 58.218 25.926 0.00 0.00 35.97 3.51
5228 5640 9.515020 AATGAAACAGTAAACAGTACAAATGTG 57.485 29.630 0.00 0.00 0.00 3.21
5376 5788 1.134907 CATGCAATCCCTGTGGCTTTC 60.135 52.381 0.00 0.00 0.00 2.62
5434 5856 4.243007 AGTTAAATGCAAGGTGCTGAAC 57.757 40.909 0.00 1.47 45.31 3.18
5435 5857 4.619973 CAAGTTAAATGCAAGGTGCTGAA 58.380 39.130 0.00 0.00 45.31 3.02
5437 5859 2.733026 GCAAGTTAAATGCAAGGTGCTG 59.267 45.455 9.08 0.00 45.31 4.41
5438 5860 2.289010 GGCAAGTTAAATGCAAGGTGCT 60.289 45.455 14.40 0.00 45.31 4.40
5439 5861 2.068519 GGCAAGTTAAATGCAAGGTGC 58.931 47.619 14.40 2.31 45.60 5.01
5440 5862 3.665745 AGGCAAGTTAAATGCAAGGTG 57.334 42.857 14.40 0.00 45.60 4.00
5569 5991 5.659440 AAATGTAAATGACGCCTGGAATT 57.341 34.783 0.00 0.00 0.00 2.17
5709 6135 1.534175 GGTCGGTTATGACTCGCTCAG 60.534 57.143 0.00 0.00 38.91 3.35
5860 6286 1.668419 GTGTTATCAGGCGCAGGATT 58.332 50.000 16.65 3.79 0.00 3.01
5890 6316 3.762407 TCAGGTGGTTTCGAAAGATGA 57.238 42.857 11.66 8.35 41.60 2.92
5917 6343 2.738521 CCACGGCGACTGGAACTG 60.739 66.667 16.62 0.00 32.37 3.16
6004 6432 3.004734 CCTCCATTGCTTGAAGTTTTCGT 59.995 43.478 0.00 0.00 0.00 3.85
6014 6442 2.928334 ACTATGAGCCTCCATTGCTTG 58.072 47.619 0.00 0.00 39.69 4.01
6137 6566 4.389992 CCAGTAAATACTAGCATCCATGCG 59.610 45.833 5.89 0.00 45.94 4.73
6168 6604 5.649831 AGCAGTTCCTTTGGATAGAATCAAC 59.350 40.000 0.00 0.00 0.00 3.18
6183 6619 4.460263 TGTCAAACAACATAGCAGTTCCT 58.540 39.130 0.00 0.00 0.00 3.36
6188 6624 7.326789 CCTTTACAATGTCAAACAACATAGCAG 59.673 37.037 0.00 0.00 38.92 4.24
6276 6714 4.576873 TGTGGCTAGACAAAATCAAACGAA 59.423 37.500 0.00 0.00 0.00 3.85
6312 6750 4.932146 ACAAAGCACCTGACATTTTACAC 58.068 39.130 0.00 0.00 0.00 2.90
6333 6772 3.916776 GCATACAAGAAAGCAAGCTTGAC 59.083 43.478 30.39 19.88 43.11 3.18
6372 6811 3.304559 GTCGAGAATCTTGACCGTTGATG 59.695 47.826 17.76 0.00 38.56 3.07
6474 6914 6.492087 CAGGGGAAAATCCTTTTACAAGTGTA 59.508 38.462 0.00 0.00 35.10 2.90
6477 6917 5.711698 TCAGGGGAAAATCCTTTTACAAGT 58.288 37.500 0.00 0.00 35.10 3.16
6536 6976 7.397892 TCTAATTCGATTTTAACCATGGCAA 57.602 32.000 13.04 3.06 0.00 4.52
6565 7005 4.193090 TGTAGCCGAACTCTTTTGAACAA 58.807 39.130 0.00 0.00 0.00 2.83
6566 7006 3.799366 TGTAGCCGAACTCTTTTGAACA 58.201 40.909 0.00 0.00 0.00 3.18
6650 7095 5.147767 GGTATGGGCTTTGGATTAGGATTT 58.852 41.667 0.00 0.00 0.00 2.17
6693 7139 2.420568 TACCTCATCCACGTCGCCC 61.421 63.158 0.00 0.00 0.00 6.13
6696 7142 2.121116 GATGTACCTCATCCACGTCG 57.879 55.000 0.00 0.00 45.05 5.12
6741 7189 1.222936 GCAGATGGGACTGGGAGTG 59.777 63.158 0.00 0.00 38.22 3.51


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

AutoCloner maintained by Alex Coulton.