Multiple sequence alignment - TraesCS1D01G055200

Loading Multiple Alignment...

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 TraesCS1D01G055200 chr1D 100.000 7405 0 0 1 7405 36545968 36538564 0.000000e+00 13675
1 TraesCS1D01G055200 chr1A 94.702 7493 249 59 1 7405 35944423 35936991 0.000000e+00 11502
2 TraesCS1D01G055200 chr1A 85.000 100 14 1 6772 6871 7656708 7656610 4.730000e-17 100
3 TraesCS1D01G055200 chr1B 94.840 6763 235 54 1 6676 56323302 56316567 0.000000e+00 10451
4 TraesCS1D01G055200 chr1B 88.781 722 36 14 6717 7405 56316240 56315531 0.000000e+00 843
5 TraesCS1D01G055200 chr2D 94.512 164 5 3 7244 7405 90783105 90783266 4.440000e-62 250
6 TraesCS1D01G055200 chr6D 85.321 109 10 5 6778 6886 458986408 458986510 2.830000e-19 108


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 TraesCS1D01G055200 chr1D 36538564 36545968 7404 True 13675 13675 100.0000 1 7405 1 chr1D.!!$R1 7404
1 TraesCS1D01G055200 chr1A 35936991 35944423 7432 True 11502 11502 94.7020 1 7405 1 chr1A.!!$R2 7404
2 TraesCS1D01G055200 chr1B 56315531 56323302 7771 True 5647 10451 91.8105 1 7405 2 chr1B.!!$R1 7404

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
747 781 1.004918 CGGCTCCCGTTGTCTCTTT 60.005 57.895 0.00 0.0 42.73 2.52 F
1473 1535 1.001406 CCTCTGTCCTGTCACCTGTTC 59.999 57.143 0.00 0.0 0.00 3.18 F
2039 2108 0.186873 AGCCCATTGCCCTTATGGAG 59.813 55.000 3.51 0.0 44.36 3.86 F
2550 2623 0.317160 TGACTCCACCTGTTGTAGCG 59.683 55.000 0.00 0.0 0.00 4.26 F
2640 2713 0.464373 TGCGAGATTCATTGGGAGGC 60.464 55.000 0.00 0.0 0.00 4.70 F
3470 3545 2.232941 CCAGCTCATGGTTTTGCAATCT 59.767 45.455 0.00 0.0 44.91 2.40 F
3996 4072 1.137872 GGCATCTCAACTCGATCACCT 59.862 52.381 0.00 0.0 0.00 4.00 F
4796 4874 1.068474 CGTCACGGTCCATCTCAAAC 58.932 55.000 0.00 0.0 0.00 2.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1577 1645 0.449388 CCTTCTGCTTTGATGACGGC 59.551 55.000 0.00 0.0 0.00 5.68 R
2536 2609 0.602638 TGCTTCGCTACAACAGGTGG 60.603 55.000 0.00 0.0 0.00 4.61 R
3030 3104 0.662619 CTTGCCGCAAACACTTCTGA 59.337 50.000 7.33 0.0 0.00 3.27 R
3975 4051 1.134699 GGTGATCGAGTTGAGATGCCA 60.135 52.381 0.00 0.0 0.00 4.92 R
3996 4072 2.253610 ACCGGTCCATCACAAAGTAGA 58.746 47.619 0.00 0.0 0.00 2.59 R
4748 4826 0.108615 CTCTTAGGTGTCCCTGCACG 60.109 60.000 0.00 0.0 42.67 5.34 R
5710 5825 1.207329 CTCTCCCCGTCCTGGTAAAAG 59.793 57.143 0.00 0.0 35.15 2.27 R
6506 6627 0.032615 AACAGCAAACCCCTCAACCA 60.033 50.000 0.00 0.0 0.00 3.67 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
37 38 3.328535 AAAGAGGGAAAGGAAAGGCAA 57.671 42.857 0.00 0.00 0.00 4.52
38 39 3.328535 AAGAGGGAAAGGAAAGGCAAA 57.671 42.857 0.00 0.00 0.00 3.68
39 40 2.881734 AGAGGGAAAGGAAAGGCAAAG 58.118 47.619 0.00 0.00 0.00 2.77
194 227 1.677966 CATTGCCTCTGCTGCCACT 60.678 57.895 0.00 0.00 38.71 4.00
195 228 1.677966 ATTGCCTCTGCTGCCACTG 60.678 57.895 0.00 0.00 38.71 3.66
199 232 4.340246 CTCTGCTGCCACTGCCCA 62.340 66.667 0.00 0.00 36.33 5.36
275 308 2.028190 CGCTCGGATTGGATCGCT 59.972 61.111 0.00 0.00 0.00 4.93
354 387 3.023119 TGTTTCTGGCTTTGCTTCTTGA 58.977 40.909 0.00 0.00 0.00 3.02
424 457 1.876156 GATCTGATTGCGATGGTTCCC 59.124 52.381 0.00 0.00 0.00 3.97
565 598 7.503566 TGTTTCTCTTTCTGTCTTCCATTTCAT 59.496 33.333 0.00 0.00 0.00 2.57
575 608 5.879777 TGTCTTCCATTTCATCAGCGATTTA 59.120 36.000 0.00 0.00 0.00 1.40
576 609 6.374053 TGTCTTCCATTTCATCAGCGATTTAA 59.626 34.615 0.00 0.00 0.00 1.52
577 610 6.909357 GTCTTCCATTTCATCAGCGATTTAAG 59.091 38.462 0.00 0.00 0.00 1.85
578 611 6.823182 TCTTCCATTTCATCAGCGATTTAAGA 59.177 34.615 0.00 0.00 0.00 2.10
695 729 2.159296 CGGTGAATATCCCATCGCGATA 60.159 50.000 23.22 6.94 31.11 2.92
747 781 1.004918 CGGCTCCCGTTGTCTCTTT 60.005 57.895 0.00 0.00 42.73 2.52
799 845 2.335712 CGGCAGTTTTGGCTCCTCC 61.336 63.158 0.00 0.00 46.99 4.30
916 963 9.787435 TTATGTTTTACAGTTCACCATTCTACT 57.213 29.630 0.00 0.00 0.00 2.57
1244 1306 4.400529 TTTTGTGCTCACTCACTGTCTA 57.599 40.909 1.47 0.00 37.81 2.59
1419 1481 3.513912 ACATCATCTTCCACGGTCACTTA 59.486 43.478 0.00 0.00 0.00 2.24
1473 1535 1.001406 CCTCTGTCCTGTCACCTGTTC 59.999 57.143 0.00 0.00 0.00 3.18
1520 1582 5.518812 TGTTGTTGTTGACTTCATGTATGC 58.481 37.500 0.00 0.00 0.00 3.14
1521 1583 5.067023 TGTTGTTGTTGACTTCATGTATGCA 59.933 36.000 0.00 0.00 0.00 3.96
1522 1584 5.764487 TGTTGTTGACTTCATGTATGCAA 57.236 34.783 0.00 0.00 0.00 4.08
1523 1585 5.518812 TGTTGTTGACTTCATGTATGCAAC 58.481 37.500 13.39 13.39 36.92 4.17
1524 1586 5.299028 TGTTGTTGACTTCATGTATGCAACT 59.701 36.000 17.87 0.00 37.21 3.16
1525 1587 6.484977 TGTTGTTGACTTCATGTATGCAACTA 59.515 34.615 17.87 11.79 37.21 2.24
1566 1634 3.798202 AGTCTAATGATTGGTTCCGAGC 58.202 45.455 0.00 0.00 0.00 5.03
1577 1645 0.955919 GTTCCGAGCAGGTCTTTGGG 60.956 60.000 0.00 0.00 41.99 4.12
1622 1690 3.501828 TGTTTGAACAATCCATCTCACCG 59.498 43.478 0.00 0.00 35.67 4.94
1628 1696 5.596772 TGAACAATCCATCTCACCGATAGTA 59.403 40.000 0.00 0.00 0.00 1.82
1741 1810 4.990426 CAGAAAGGCCAAGGTAAATTGTTG 59.010 41.667 5.01 0.00 0.00 3.33
1751 1820 7.131565 CCAAGGTAAATTGTTGAACATTTTGC 58.868 34.615 21.62 20.16 34.64 3.68
1832 1901 1.689813 TCTAACAACCAGAGTGGCGAA 59.310 47.619 0.00 0.00 42.67 4.70
1844 1913 1.070786 TGGCGAACTCCCAACTGAC 59.929 57.895 0.00 0.00 0.00 3.51
1865 1934 2.030045 GCTGGAGTTATCCCGAGGTCT 61.030 57.143 0.00 0.00 46.04 3.85
1889 1958 5.179368 TGTCAGACAAATTTTCGACATCCTC 59.821 40.000 0.00 0.00 0.00 3.71
2039 2108 0.186873 AGCCCATTGCCCTTATGGAG 59.813 55.000 3.51 0.00 44.36 3.86
2300 2369 5.462068 TGGTTCAGAAAATATATCACGCTCG 59.538 40.000 0.00 0.00 0.00 5.03
2324 2393 4.420168 GTGCTAGAGATGTGAGTGAACTC 58.580 47.826 3.41 3.41 43.15 3.01
2339 2408 6.013379 TGAGTGAACTCCAAATGTCCTATTCT 60.013 38.462 7.96 0.00 42.20 2.40
2536 2609 3.034635 TCTAAGGGCATTCTCCTGACTC 58.965 50.000 0.00 0.00 34.34 3.36
2550 2623 0.317160 TGACTCCACCTGTTGTAGCG 59.683 55.000 0.00 0.00 0.00 4.26
2640 2713 0.464373 TGCGAGATTCATTGGGAGGC 60.464 55.000 0.00 0.00 0.00 4.70
2712 2785 2.474816 GAAGAGACGTTGAGCACACTT 58.525 47.619 0.00 0.00 0.00 3.16
2953 3026 3.818180 TGACCGCCTTAAACAAGGTTTA 58.182 40.909 5.38 0.00 42.00 2.01
3030 3104 6.726764 ACTCACCTAGTCTCCTATCTGTTTTT 59.273 38.462 0.00 0.00 30.33 1.94
3161 3235 8.244113 CCCTTGTTAGATTTGTTCAGATAAACC 58.756 37.037 0.00 0.00 0.00 3.27
3280 3355 5.221481 GGCTAGGGATAAGGTTAGTTGTCTC 60.221 48.000 0.00 0.00 0.00 3.36
3441 3516 7.463961 AACTCGAGAAAACTCAGGTATCTTA 57.536 36.000 21.68 0.00 0.00 2.10
3443 3518 7.893658 ACTCGAGAAAACTCAGGTATCTTAAA 58.106 34.615 21.68 0.00 0.00 1.52
3470 3545 2.232941 CCAGCTCATGGTTTTGCAATCT 59.767 45.455 0.00 0.00 44.91 2.40
3730 3806 9.941664 CATGGTTTGCTCATTTACTTCTTATAG 57.058 33.333 0.00 0.00 0.00 1.31
3738 3814 8.766151 GCTCATTTACTTCTTATAGTTACTGGC 58.234 37.037 0.00 0.00 0.00 4.85
3830 3906 4.503741 TTTCAGTTAGCCAATTGAGTGC 57.496 40.909 7.12 1.65 32.65 4.40
3840 3916 4.637534 AGCCAATTGAGTGCATACTTACTG 59.362 41.667 7.12 0.00 37.25 2.74
3845 3921 7.119116 CCAATTGAGTGCATACTTACTGTGTTA 59.881 37.037 7.12 0.00 37.25 2.41
3975 4051 7.928873 TCTGGTCTATTCTCCAAAATAGGTTT 58.071 34.615 4.35 0.00 38.96 3.27
3996 4072 1.137872 GGCATCTCAACTCGATCACCT 59.862 52.381 0.00 0.00 0.00 4.00
4039 4115 4.747540 TCACTTCAATGGTCATTGTTCG 57.252 40.909 19.31 12.74 46.15 3.95
4210 4286 7.850935 AATGGAAGATGATATGCAATCCTTT 57.149 32.000 0.00 0.00 32.24 3.11
4311 4387 2.611292 GTGGAGTATGACATGCTTGAGC 59.389 50.000 7.52 0.00 42.50 4.26
4462 4538 7.482654 TGAGAAATTGAACTCACAAGTACAG 57.517 36.000 0.00 0.00 38.08 2.74
4532 4608 5.165961 ACTTGTGGTTGCAGTGACTATAT 57.834 39.130 0.00 0.00 0.00 0.86
4748 4826 6.446318 TCTGTTCCAACATTTCTGTTAATGC 58.554 36.000 0.00 0.00 43.76 3.56
4796 4874 1.068474 CGTCACGGTCCATCTCAAAC 58.932 55.000 0.00 0.00 0.00 2.93
5111 5189 7.217200 TGGTAAGTGTTATCCATATCTTCTGC 58.783 38.462 0.00 0.00 0.00 4.26
5113 5191 7.386299 GGTAAGTGTTATCCATATCTTCTGCAG 59.614 40.741 7.63 7.63 0.00 4.41
5180 5288 3.181504 CGTGCTGCTGATGATTGATTGAA 60.182 43.478 0.00 0.00 0.00 2.69
5208 5316 7.878127 AGTTGAACTATTACACAACTGCTACAT 59.122 33.333 0.00 0.00 46.87 2.29
5473 5581 4.034975 GGCTACTTGATGTGATGCTTTCTC 59.965 45.833 0.00 0.00 0.00 2.87
5516 5624 5.063691 TCAGTGCTTAACGTTTTCTCGAAAA 59.936 36.000 5.91 0.93 37.90 2.29
5640 5749 4.473477 AGTCAGGTATTAGCACAGAACC 57.527 45.455 0.00 0.00 0.00 3.62
5703 5818 5.813672 GCAATTGTGAATAGCAATCATGGTT 59.186 36.000 7.40 0.00 38.46 3.67
5710 5825 2.443887 AGCAATCATGGTTTGTGCAC 57.556 45.000 10.75 10.75 32.07 4.57
5872 5988 6.123045 AGTTACTAAAACACAGGGCATAGT 57.877 37.500 0.00 0.00 0.00 2.12
5901 6017 8.822652 ATTTTTCCTCATTTTGATGACAACTC 57.177 30.769 0.00 0.00 35.63 3.01
5919 6036 4.207891 ACTCATGTTATTTCAGGCTCGT 57.792 40.909 0.00 0.00 0.00 4.18
6095 6212 3.826157 GTCATGAAAAGTGATTGGTGGGA 59.174 43.478 0.00 0.00 0.00 4.37
6097 6214 4.523943 TCATGAAAAGTGATTGGTGGGAAG 59.476 41.667 0.00 0.00 0.00 3.46
6100 6217 5.147032 TGAAAAGTGATTGGTGGGAAGATT 58.853 37.500 0.00 0.00 0.00 2.40
6103 6220 2.827921 AGTGATTGGTGGGAAGATTTGC 59.172 45.455 0.00 0.00 0.00 3.68
6116 6233 5.242615 GGGAAGATTTGCTCTTTATCATCCC 59.757 44.000 8.38 8.38 44.42 3.85
6123 6240 3.137533 GCTCTTTATCATCCCTGACAGC 58.862 50.000 0.00 0.00 33.22 4.40
6144 6261 2.229792 GACTGACCAAACCTGCATTGA 58.770 47.619 0.01 0.00 0.00 2.57
6147 6264 3.256631 ACTGACCAAACCTGCATTGAATC 59.743 43.478 0.01 0.00 0.00 2.52
6350 6468 2.185608 GAGGCGCAAGAGGAGTCC 59.814 66.667 10.83 0.00 43.02 3.85
6409 6527 7.119846 CCCCCTTATAGCAAGAAATTAGATTCG 59.880 40.741 0.00 0.00 34.46 3.34
6506 6627 9.550406 CCATCCATTTGATTAATTGCTATTGTT 57.450 29.630 3.49 0.00 0.00 2.83
6540 6661 1.002544 GCTGTTCTTAGGCTGGTCACT 59.997 52.381 0.00 0.00 0.00 3.41
6639 6762 8.798153 GTGAAAGAATAATATTTTTGAGCACCG 58.202 33.333 0.00 0.00 0.00 4.94
6643 6766 8.450578 AGAATAATATTTTTGAGCACCGATGA 57.549 30.769 0.00 0.00 0.00 2.92
6651 6774 1.272781 GAGCACCGATGAAAGACTCG 58.727 55.000 0.00 0.00 34.73 4.18
6691 7107 6.917217 GCTTAATGCACTAGATGACTTTCT 57.083 37.500 0.00 0.00 42.31 2.52
6946 7376 6.348540 GGAGTAGAACATTTGGACATGTGTTC 60.349 42.308 1.15 9.77 46.59 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 1.228988 CCCAGCCTTTGCCTTTCCT 60.229 57.895 0.00 0.00 38.69 3.36
29 30 1.533994 ACCCCAGCCTTTGCCTTTC 60.534 57.895 0.00 0.00 38.69 2.62
34 35 4.299796 TCCCACCCCAGCCTTTGC 62.300 66.667 0.00 0.00 37.95 3.68
35 36 2.283173 GTCCCACCCCAGCCTTTG 60.283 66.667 0.00 0.00 0.00 2.77
37 38 3.260100 CTGTCCCACCCCAGCCTT 61.260 66.667 0.00 0.00 0.00 4.35
38 39 2.194951 TATCTGTCCCACCCCAGCCT 62.195 60.000 0.00 0.00 0.00 4.58
39 40 1.692749 TATCTGTCCCACCCCAGCC 60.693 63.158 0.00 0.00 0.00 4.85
311 344 3.119602 ACAAATCGATCGAGGAAGACGAA 60.120 43.478 23.84 0.00 42.80 3.85
314 347 3.512680 ACACAAATCGATCGAGGAAGAC 58.487 45.455 23.84 0.00 0.00 3.01
316 349 4.627467 AGAAACACAAATCGATCGAGGAAG 59.373 41.667 23.84 14.72 0.00 3.46
354 387 1.818674 GCACCGGAACCAAATCAAGAT 59.181 47.619 9.46 0.00 0.00 2.40
437 470 4.950744 CAAGAACTTGGGCAAGCG 57.049 55.556 6.66 0.00 41.99 4.68
565 598 3.273434 AGCATGCTTCTTAAATCGCTGA 58.727 40.909 16.30 0.00 0.00 4.26
575 608 1.021390 CGAACCGGAGCATGCTTCTT 61.021 55.000 23.61 11.19 0.00 2.52
576 609 1.448540 CGAACCGGAGCATGCTTCT 60.449 57.895 23.61 3.29 0.00 2.85
577 610 3.093278 CGAACCGGAGCATGCTTC 58.907 61.111 23.61 20.08 0.00 3.86
695 729 1.586422 CGGATGCAAATCTCGGATGT 58.414 50.000 0.00 0.00 0.00 3.06
799 845 3.674753 GTCAAACAAATTTGGCCAGATCG 59.325 43.478 21.74 6.66 43.39 3.69
913 960 3.609644 CGCCAAACCGTTTAAATGCAGTA 60.610 43.478 1.60 0.00 0.00 2.74
915 962 1.718711 CGCCAAACCGTTTAAATGCAG 59.281 47.619 1.60 0.00 0.00 4.41
916 963 1.772182 CGCCAAACCGTTTAAATGCA 58.228 45.000 1.60 0.00 0.00 3.96
1128 1187 3.055094 GCACATTGACTCCCTTCTCCTTA 60.055 47.826 0.00 0.00 0.00 2.69
1231 1293 5.056480 CACCAAATTGTAGACAGTGAGTGA 58.944 41.667 0.00 0.00 0.00 3.41
1239 1301 4.218200 CCTGAATGCACCAAATTGTAGACA 59.782 41.667 0.00 0.00 0.00 3.41
1240 1302 4.737054 CCTGAATGCACCAAATTGTAGAC 58.263 43.478 0.00 0.00 0.00 2.59
1244 1306 1.002315 GGCCTGAATGCACCAAATTGT 59.998 47.619 0.00 0.00 0.00 2.71
1274 1336 3.170717 AGTATTCCCCTTTGTCTCGTCA 58.829 45.455 0.00 0.00 0.00 4.35
1343 1405 0.308993 GCTTATTGGCGATGACCTGC 59.691 55.000 0.00 0.00 0.00 4.85
1566 1634 1.002134 ATGACGGCCCAAAGACCTG 60.002 57.895 0.00 0.00 0.00 4.00
1577 1645 0.449388 CCTTCTGCTTTGATGACGGC 59.551 55.000 0.00 0.00 0.00 5.68
1622 1690 4.282195 CCCTCAAGGACCTCATGTACTATC 59.718 50.000 0.00 0.00 37.04 2.08
1628 1696 0.548682 AGCCCTCAAGGACCTCATGT 60.549 55.000 0.00 0.00 38.24 3.21
1741 1810 6.833342 ATTGACTTCAAGTGCAAAATGTTC 57.167 33.333 0.00 0.00 39.47 3.18
1751 1820 9.965824 AGGTACATTTTTAATTGACTTCAAGTG 57.034 29.630 0.00 0.00 39.47 3.16
1808 1877 2.038557 GCCACTCTGGTTGTTAGAGGAA 59.961 50.000 6.92 0.00 44.65 3.36
1813 1882 1.798813 GTTCGCCACTCTGGTTGTTAG 59.201 52.381 0.00 0.00 40.46 2.34
1832 1901 2.743718 CCAGCGTCAGTTGGGAGT 59.256 61.111 0.00 0.00 43.95 3.85
1844 1913 1.364171 CCTCGGGATAACTCCAGCG 59.636 63.158 0.00 0.00 44.08 5.18
1865 1934 5.063204 AGGATGTCGAAAATTTGTCTGACA 58.937 37.500 6.36 6.36 40.24 3.58
2039 2108 3.785122 AACACCACCCTTGCCGTCC 62.785 63.158 0.00 0.00 0.00 4.79
2042 2111 0.529555 CAAAAACACCACCCTTGCCG 60.530 55.000 0.00 0.00 0.00 5.69
2300 2369 2.103373 TCACTCACATCTCTAGCACCC 58.897 52.381 0.00 0.00 0.00 4.61
2339 2408 6.884295 CAGGTACATGGGAAGAAGAAAATACA 59.116 38.462 0.00 0.00 0.00 2.29
2536 2609 0.602638 TGCTTCGCTACAACAGGTGG 60.603 55.000 0.00 0.00 0.00 4.61
2550 2623 2.373224 AGCCCTCTTTAGCAATGCTTC 58.627 47.619 14.85 0.00 40.44 3.86
2817 2890 3.054878 ACACATCGTCAACGTTTCTACC 58.945 45.455 0.00 0.00 40.80 3.18
3030 3104 0.662619 CTTGCCGCAAACACTTCTGA 59.337 50.000 7.33 0.00 0.00 3.27
3232 3306 6.433847 TCTAGATCAACTCCCAGTTTTTCA 57.566 37.500 0.00 0.00 36.03 2.69
3280 3355 2.553602 TGGTTTGCTGTGACATGCTTAG 59.446 45.455 8.13 0.00 0.00 2.18
3730 3806 7.546667 ACAATTGATGATTCATTTGCCAGTAAC 59.453 33.333 13.59 0.00 42.73 2.50
3830 3906 7.329962 TGAATGTCGGTTAACACAGTAAGTATG 59.670 37.037 8.10 0.00 30.55 2.39
3840 3916 6.435428 AGTTTCATTGAATGTCGGTTAACAC 58.565 36.000 8.10 0.00 30.55 3.32
3845 3921 4.037923 AGCAAGTTTCATTGAATGTCGGTT 59.962 37.500 4.93 0.00 31.55 4.44
3975 4051 1.134699 GGTGATCGAGTTGAGATGCCA 60.135 52.381 0.00 0.00 0.00 4.92
3996 4072 2.253610 ACCGGTCCATCACAAAGTAGA 58.746 47.619 0.00 0.00 0.00 2.59
4039 4115 2.579207 TACGCTCTGCCAGTATTCAC 57.421 50.000 0.00 0.00 0.00 3.18
4210 4286 7.707624 AATTGCCTCATCTTTTGAAGATACA 57.292 32.000 3.09 0.00 46.20 2.29
4311 4387 3.088532 TGTGCAGCCTAAAAATGGGTAG 58.911 45.455 0.00 0.00 33.54 3.18
4381 4457 5.530915 TGCTAAATTATCCAGCGCTGTAATT 59.469 36.000 33.75 30.03 38.15 1.40
4445 4521 4.868171 GTGTGACTGTACTTGTGAGTTCAA 59.132 41.667 0.00 0.00 37.33 2.69
4462 4538 4.814147 TCTCAAGATCTGATGTGTGTGAC 58.186 43.478 0.00 0.00 32.14 3.67
4748 4826 0.108615 CTCTTAGGTGTCCCTGCACG 60.109 60.000 0.00 0.00 42.67 5.34
4796 4874 6.863126 GTGAATGGAAGAAACCAACAGTAATG 59.137 38.462 0.00 0.00 43.47 1.90
5149 5257 2.526304 TCAGCAGCACGTAACTTCTT 57.474 45.000 0.00 0.00 0.00 2.52
5150 5258 2.029020 TCATCAGCAGCACGTAACTTCT 60.029 45.455 0.00 0.00 0.00 2.85
5158 5266 2.353579 TCAATCAATCATCAGCAGCACG 59.646 45.455 0.00 0.00 0.00 5.34
5165 5273 8.041829 AGTTCAACTCTTCAATCAATCATCAG 57.958 34.615 0.00 0.00 0.00 2.90
5166 5274 7.991084 AGTTCAACTCTTCAATCAATCATCA 57.009 32.000 0.00 0.00 0.00 3.07
5180 5288 6.525629 AGCAGTTGTGTAATAGTTCAACTCT 58.474 36.000 0.00 5.27 45.36 3.24
5516 5624 1.873591 CCGTCTTAGTTTTGCTGCAGT 59.126 47.619 16.64 0.00 0.00 4.40
5640 5749 9.899226 AAAGAAACTTTAAAATCTTCCAGATCG 57.101 29.630 9.66 0.00 32.89 3.69
5703 5818 1.944024 CGTCCTGGTAAAAGTGCACAA 59.056 47.619 21.04 0.00 0.00 3.33
5710 5825 1.207329 CTCTCCCCGTCCTGGTAAAAG 59.793 57.143 0.00 0.00 35.15 2.27
5872 5988 7.724287 TGTCATCAAAATGAGGAAAAATCACA 58.276 30.769 0.00 0.00 42.53 3.58
5901 6017 4.944962 TCAACGAGCCTGAAATAACATG 57.055 40.909 0.00 0.00 0.00 3.21
5919 6036 1.881925 CGCCTCATGGTCAACCTTCAA 60.882 52.381 0.10 0.00 36.82 2.69
5978 6095 2.372172 ACCCTTCAACTCCGTCATTTCT 59.628 45.455 0.00 0.00 0.00 2.52
6097 6214 5.824624 TGTCAGGGATGATAAAGAGCAAATC 59.175 40.000 0.00 0.00 0.00 2.17
6100 6217 4.774124 CTGTCAGGGATGATAAAGAGCAA 58.226 43.478 0.00 0.00 0.00 3.91
6103 6220 3.068732 TCGCTGTCAGGGATGATAAAGAG 59.931 47.826 15.19 0.00 31.82 2.85
6116 6233 0.861837 GTTTGGTCAGTCGCTGTCAG 59.138 55.000 0.00 0.00 32.61 3.51
6123 6240 1.069022 CAATGCAGGTTTGGTCAGTCG 60.069 52.381 0.00 0.00 0.00 4.18
6144 6261 6.183347 CCTGTCACATTTAAGGAGAAGGATT 58.817 40.000 0.00 0.00 30.92 3.01
6147 6264 4.697352 CACCTGTCACATTTAAGGAGAAGG 59.303 45.833 0.00 0.00 33.78 3.46
6191 6309 1.303282 GATTTCCCGCCTCCTTGGT 59.697 57.895 0.00 0.00 38.35 3.67
6409 6527 3.873952 GCTCCTTTGTACATGATCTGGAC 59.126 47.826 0.00 0.00 39.39 4.02
6506 6627 0.032615 AACAGCAAACCCCTCAACCA 60.033 50.000 0.00 0.00 0.00 3.67
6540 6661 9.107177 GCAGTAGTAAGTACATACTCTTCACTA 57.893 37.037 13.74 0.00 37.34 2.74
6639 6762 3.579709 TCAGCTCAACGAGTCTTTCATC 58.420 45.455 0.00 0.00 31.39 2.92
6643 6766 4.792521 ATACTCAGCTCAACGAGTCTTT 57.207 40.909 7.65 0.00 41.52 2.52
6651 6774 7.074502 GCATTAAGCATAATACTCAGCTCAAC 58.925 38.462 0.00 0.00 44.79 3.18
6677 6800 8.924511 TTTTTCATGGAAGAAAGTCATCTAGT 57.075 30.769 0.00 0.00 38.60 2.57
6737 7153 0.112995 TTGCACCTGGGAGCAGAATT 59.887 50.000 14.31 0.00 42.11 2.17
6971 7401 8.299570 GCTCAGGTGAATAGAAAATCTGAAAAA 58.700 33.333 0.00 0.00 30.76 1.94
6979 7409 6.944862 ACTTTCTGCTCAGGTGAATAGAAAAT 59.055 34.615 14.39 6.71 36.51 1.82
6993 7424 2.634453 TCAGACATGGACTTTCTGCTCA 59.366 45.455 0.00 0.00 37.31 4.26


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

AutoCloner maintained by Alex Coulton.