Multiple sequence alignment - TraesCS6B01G084100

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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 TraesCS6B01G084100 chr6B 100.000 2555 0 0 1 2555 60927365 60929919 0.000000e+00 4719.0
1 TraesCS6B01G084100 chr6B 88.396 586 49 14 797 1375 54663206 54662633 0.000000e+00 688.0
2 TraesCS6B01G084100 chr6B 89.633 463 38 9 1061 1519 59588304 59587848 4.740000e-162 580.0
3 TraesCS6B01G084100 chr6B 87.780 491 46 10 886 1375 55121669 55122146 1.720000e-156 562.0
4 TraesCS6B01G084100 chr6B 84.762 105 14 2 1981 2085 77879207 77879105 1.250000e-18 104.0
5 TraesCS6B01G084100 chr6B 77.922 154 22 5 1863 2015 77922592 77922450 4.530000e-13 86.1
6 TraesCS6B01G084100 chr6B 77.922 154 22 5 1863 2015 78150036 78149894 4.530000e-13 86.1
7 TraesCS6B01G084100 chr6D 89.811 1060 75 13 818 1857 28992905 28991859 0.000000e+00 1328.0
8 TraesCS6B01G084100 chr6D 90.968 465 25 7 1058 1519 29384819 29385269 6.040000e-171 610.0
9 TraesCS6B01G084100 chr6D 91.087 460 24 10 1061 1517 28708075 28707630 7.820000e-170 606.0
10 TraesCS6B01G084100 chr6D 86.967 422 29 9 156 574 28993318 28992920 3.880000e-123 451.0
11 TraesCS6B01G084100 chr6D 85.667 300 13 5 2115 2414 28991640 28991371 3.220000e-74 289.0
12 TraesCS6B01G084100 chr6D 92.126 127 7 2 2429 2555 28991387 28991264 2.610000e-40 176.0
13 TraesCS6B01G084100 chr6D 88.435 147 12 4 3 144 28993574 28993428 3.380000e-39 172.0
14 TraesCS6B01G084100 chr6D 86.420 162 3 10 1938 2098 28991859 28991716 2.630000e-35 159.0
15 TraesCS6B01G084100 chr6D 82.645 121 18 3 2433 2551 28706748 28706629 1.250000e-18 104.0
16 TraesCS6B01G084100 chr6A 85.340 1296 89 36 717 1981 33547772 33548997 0.000000e+00 1247.0
17 TraesCS6B01G084100 chr6A 90.810 457 21 13 1061 1517 33008596 33008161 2.190000e-165 592.0
18 TraesCS6B01G084100 chr6A 90.759 303 24 4 2114 2414 33549762 33550062 3.960000e-108 401.0
19 TraesCS6B01G084100 chr6A 87.719 228 22 4 744 969 33546126 33546349 7.010000e-66 261.0
20 TraesCS6B01G084100 chr6A 93.605 172 11 0 151 322 33545866 33546037 9.070000e-65 257.0
21 TraesCS6B01G084100 chr6A 95.000 140 7 0 3 142 33545618 33545757 1.190000e-53 220.0
22 TraesCS6B01G084100 chr6A 93.694 111 7 0 623 733 33546035 33546145 1.570000e-37 167.0
23 TraesCS6B01G084100 chrUn 87.395 595 49 21 799 1380 103527717 103527136 0.000000e+00 660.0
24 TraesCS6B01G084100 chr5A 86.876 541 56 14 842 1375 556534531 556533999 2.190000e-165 592.0


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 TraesCS6B01G084100 chr6B 60927365 60929919 2554 False 4719.000000 4719 100.000000 1 2555 1 chr6B.!!$F2 2554
1 TraesCS6B01G084100 chr6B 54662633 54663206 573 True 688.000000 688 88.396000 797 1375 1 chr6B.!!$R1 578
2 TraesCS6B01G084100 chr6D 28991264 28993574 2310 True 429.166667 1328 88.237667 3 2555 6 chr6D.!!$R2 2552
3 TraesCS6B01G084100 chr6D 28706629 28708075 1446 True 355.000000 606 86.866000 1061 2551 2 chr6D.!!$R1 1490
4 TraesCS6B01G084100 chr6A 33545618 33550062 4444 False 425.500000 1247 91.019500 3 2414 6 chr6A.!!$F1 2411
5 TraesCS6B01G084100 chrUn 103527136 103527717 581 True 660.000000 660 87.395000 799 1380 1 chrUn.!!$R1 581
6 TraesCS6B01G084100 chr5A 556533999 556534531 532 True 592.000000 592 86.876000 842 1375 1 chr5A.!!$R1 533

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
764 872 0.108585 AATGTCCACACCGAGTTGCT 59.891 50.0 0.0 0.0 0.0 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1935 3895 0.320421 TCCAACGCCAAGAGTAGTGC 60.32 55.0 0.0 0.0 0.0 4.4 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
55 58 5.006153 AGGTAAACAAACAACCTGCTTTC 57.994 39.130 0.00 0.00 42.08 2.62
85 91 4.576463 CCCTTTGATCCCTGAAAATCTACG 59.424 45.833 0.00 0.00 0.00 3.51
144 150 3.673543 TTGTACTCCAAACAAAGGGGT 57.326 42.857 0.00 0.00 43.76 4.95
146 152 2.510382 TGTACTCCAAACAAAGGGGTCA 59.490 45.455 0.00 0.00 39.65 4.02
148 154 4.351407 TGTACTCCAAACAAAGGGGTCATA 59.649 41.667 0.00 0.00 39.65 2.15
151 157 3.758554 CTCCAAACAAAGGGGTCATACTG 59.241 47.826 0.00 0.00 0.00 2.74
152 158 2.231235 CCAAACAAAGGGGTCATACTGC 59.769 50.000 0.00 0.00 0.00 4.40
154 160 0.331616 ACAAAGGGGTCATACTGCCC 59.668 55.000 0.00 0.00 44.09 5.36
219 325 5.427036 TCGTTTATTTTTGCTCGTTCCTT 57.573 34.783 0.00 0.00 0.00 3.36
233 339 2.744202 CGTTCCTTTGCTGTATGCTCTT 59.256 45.455 0.00 0.00 43.37 2.85
437 544 9.833182 TGAAAAGGCAAAGTTTTAAAAATTCAC 57.167 25.926 13.47 8.88 0.00 3.18
496 603 5.684550 AACCTGAGTGGAAACGAATAAAC 57.315 39.130 0.00 0.00 39.71 2.01
497 604 4.710324 ACCTGAGTGGAAACGAATAAACA 58.290 39.130 0.00 0.00 39.71 2.83
498 605 5.127491 ACCTGAGTGGAAACGAATAAACAA 58.873 37.500 0.00 0.00 39.71 2.83
499 606 5.591067 ACCTGAGTGGAAACGAATAAACAAA 59.409 36.000 0.00 0.00 39.71 2.83
500 607 6.095720 ACCTGAGTGGAAACGAATAAACAAAA 59.904 34.615 0.00 0.00 39.71 2.44
501 608 6.975772 CCTGAGTGGAAACGAATAAACAAAAA 59.024 34.615 0.00 0.00 38.35 1.94
532 640 2.362077 GTGCCTCACAAACCTGTTGAAT 59.638 45.455 0.00 0.00 31.64 2.57
543 651 9.150348 CACAAACCTGTTGAATTTTTCTTTACT 57.850 29.630 0.00 0.00 31.64 2.24
652 760 3.045601 TGAGCCTGCTCACTTAAAGAC 57.954 47.619 17.46 0.00 46.80 3.01
667 775 3.775654 GACCTGTCCCGGAGCTGG 61.776 72.222 0.73 11.24 0.00 4.85
691 799 2.608752 GGTCCAATACACGTGAACGAGT 60.609 50.000 25.01 10.45 44.65 4.18
700 808 1.002250 CGTGAACGAGTCCGAAGGTG 61.002 60.000 0.00 0.00 46.72 4.00
701 809 3.591764 CGTGAACGAGTCCGAAGGTGT 62.592 57.143 0.00 0.00 46.72 4.16
733 841 1.273759 AAAGGACCTACCCCGAGTTC 58.726 55.000 0.00 0.00 40.05 3.01
736 844 0.616964 GGACCTACCCCGAGTTCCTT 60.617 60.000 0.00 0.00 0.00 3.36
737 845 0.822811 GACCTACCCCGAGTTCCTTC 59.177 60.000 0.00 0.00 0.00 3.46
738 846 0.412640 ACCTACCCCGAGTTCCTTCT 59.587 55.000 0.00 0.00 0.00 2.85
741 849 3.102204 CCTACCCCGAGTTCCTTCTAAA 58.898 50.000 0.00 0.00 0.00 1.85
742 850 3.516700 CCTACCCCGAGTTCCTTCTAAAA 59.483 47.826 0.00 0.00 0.00 1.52
762 870 3.708563 AAAAATGTCCACACCGAGTTG 57.291 42.857 0.00 0.00 0.00 3.16
763 871 0.951558 AAATGTCCACACCGAGTTGC 59.048 50.000 0.00 0.00 0.00 4.17
764 872 0.108585 AATGTCCACACCGAGTTGCT 59.891 50.000 0.00 0.00 0.00 3.91
765 873 0.108585 ATGTCCACACCGAGTTGCTT 59.891 50.000 0.00 0.00 0.00 3.91
766 874 0.753867 TGTCCACACCGAGTTGCTTA 59.246 50.000 0.00 0.00 0.00 3.09
767 875 1.139256 TGTCCACACCGAGTTGCTTAA 59.861 47.619 0.00 0.00 0.00 1.85
768 876 2.215196 GTCCACACCGAGTTGCTTAAA 58.785 47.619 0.00 0.00 0.00 1.52
769 877 2.614983 GTCCACACCGAGTTGCTTAAAA 59.385 45.455 0.00 0.00 0.00 1.52
770 878 3.065648 GTCCACACCGAGTTGCTTAAAAA 59.934 43.478 0.00 0.00 0.00 1.94
902 2676 0.477204 CAGCCATCCATCACCCATCT 59.523 55.000 0.00 0.00 0.00 2.90
949 2724 2.586792 GTGCCCTTCTCATCGCCT 59.413 61.111 0.00 0.00 0.00 5.52
955 2730 1.065854 CCCTTCTCATCGCCTGAAACT 60.066 52.381 0.00 0.00 32.14 2.66
966 2741 2.550978 GCCTGAAACTTCGCAGCTATA 58.449 47.619 0.00 0.00 0.00 1.31
991 2766 4.473520 CCACGCCCGAGCTCCATT 62.474 66.667 8.47 0.00 36.60 3.16
1003 2778 0.034186 GCTCCATTCACATCACCCCA 60.034 55.000 0.00 0.00 0.00 4.96
1065 2879 2.560542 ACACAGAGAAGCGAAGATGTCT 59.439 45.455 0.00 0.00 0.00 3.41
1089 2903 2.941583 GGCAAGGGAGGGAAGGGT 60.942 66.667 0.00 0.00 0.00 4.34
1176 2990 4.194720 GCCATCCGTCGTCTCGCT 62.195 66.667 0.00 0.00 0.00 4.93
1436 3264 0.731417 CTGCTGTTCTGGTGCTATGC 59.269 55.000 0.00 0.00 0.00 3.14
1452 3280 3.780801 GCTATGCGTTTCGTTTCTGAATG 59.219 43.478 0.00 0.00 0.00 2.67
1454 3282 0.967803 GCGTTTCGTTTCTGAATGCG 59.032 50.000 8.07 8.07 33.06 4.73
1455 3283 1.659211 GCGTTTCGTTTCTGAATGCGT 60.659 47.619 12.30 0.00 32.74 5.24
1456 3284 1.962547 CGTTTCGTTTCTGAATGCGTG 59.037 47.619 12.30 2.15 0.00 5.34
1457 3285 1.708680 GTTTCGTTTCTGAATGCGTGC 59.291 47.619 12.30 0.00 0.00 5.34
1521 3349 2.548707 GGCGATGGATCTGAATGCAGTA 60.549 50.000 0.00 0.00 42.84 2.74
1545 3373 1.145759 CGTCAGAGTGCGTGTGTTGT 61.146 55.000 0.00 0.00 0.00 3.32
1587 3415 1.153289 CCTCTGTGGAAGGCGATGG 60.153 63.158 0.00 0.00 38.35 3.51
1628 3456 8.314021 GGATTGTTGGTTCTTCCTATTTGAATT 58.686 33.333 0.00 0.00 37.07 2.17
1655 3483 1.272212 CCACCAACTTGTTATGCCACC 59.728 52.381 0.00 0.00 0.00 4.61
1661 3491 5.542251 ACCAACTTGTTATGCCACCTAAAAT 59.458 36.000 0.00 0.00 0.00 1.82
1758 3607 3.031013 CCAGTCCCCTTTGTTCTGTTTT 58.969 45.455 0.00 0.00 0.00 2.43
1760 3609 4.647399 CCAGTCCCCTTTGTTCTGTTTTTA 59.353 41.667 0.00 0.00 0.00 1.52
1770 3619 9.796120 CCTTTGTTCTGTTTTTACTGTATTTCA 57.204 29.630 0.00 0.00 0.00 2.69
1780 3629 9.030301 GTTTTTACTGTATTTCATTGTGCAGTT 57.970 29.630 0.00 0.00 38.09 3.16
1786 3635 6.567959 TGTATTTCATTGTGCAGTTTGTTCA 58.432 32.000 0.00 0.00 0.00 3.18
1806 3655 1.912043 ACAAACCTAGCTCCTCTGCAT 59.088 47.619 0.00 0.00 34.99 3.96
1810 3659 1.006337 CTAGCTCCTCTGCATCCGC 60.006 63.158 0.00 0.00 39.24 5.54
1879 3814 2.012673 GGTGCTGCTGTTTAGATCCTG 58.987 52.381 0.00 0.00 0.00 3.86
1880 3815 2.616510 GGTGCTGCTGTTTAGATCCTGT 60.617 50.000 0.00 0.00 0.00 4.00
1881 3816 3.369471 GGTGCTGCTGTTTAGATCCTGTA 60.369 47.826 0.00 0.00 0.00 2.74
1882 3817 4.446371 GTGCTGCTGTTTAGATCCTGTAT 58.554 43.478 0.00 0.00 0.00 2.29
1884 3819 4.080919 TGCTGCTGTTTAGATCCTGTATGT 60.081 41.667 0.00 0.00 0.00 2.29
1899 3859 7.129457 TCCTGTATGTTTTATCTCTGATGCT 57.871 36.000 0.00 0.00 0.00 3.79
1906 3866 6.558009 TGTTTTATCTCTGATGCTTTGATGC 58.442 36.000 0.00 0.00 0.00 3.91
1908 3868 6.762702 TTTATCTCTGATGCTTTGATGCAA 57.237 33.333 0.00 0.00 46.61 4.08
1911 3871 4.014406 TCTCTGATGCTTTGATGCAACAT 58.986 39.130 0.00 0.00 46.61 2.71
1925 3885 4.492791 TGCAACATGATTCTGTTCTGTG 57.507 40.909 0.00 0.00 37.25 3.66
1926 3886 3.240069 GCAACATGATTCTGTTCTGTGC 58.760 45.455 0.00 0.00 37.25 4.57
1935 3895 5.698089 TGATTCTGTTCTGTGCTACTTTCAG 59.302 40.000 0.00 0.00 0.00 3.02
1936 3896 3.393800 TCTGTTCTGTGCTACTTTCAGC 58.606 45.455 0.00 0.00 42.15 4.26
2032 4570 7.064728 AGCGATCCTTCTGTTTTTCTGTAATAC 59.935 37.037 0.00 0.00 0.00 1.89
2100 4640 6.603201 TGTCATCAGTCATACTCATGTACTCA 59.397 38.462 0.00 0.00 33.57 3.41
2101 4641 7.286316 TGTCATCAGTCATACTCATGTACTCAT 59.714 37.037 0.00 0.00 33.57 2.90
2103 4643 8.699130 TCATCAGTCATACTCATGTACTCATTT 58.301 33.333 0.00 0.00 33.57 2.32
2104 4644 9.971922 CATCAGTCATACTCATGTACTCATTTA 57.028 33.333 0.00 0.00 33.57 1.40
2109 4649 9.894783 GTCATACTCATGTACTCATTTATACGT 57.105 33.333 0.00 0.00 33.57 3.57
2141 4744 7.907389 AGTATGTTCTAAAACTCTGGTGATGA 58.093 34.615 0.00 0.00 36.30 2.92
2192 4795 6.528537 TGGTTATAGAATTGCACATTGCTT 57.471 33.333 0.00 0.00 45.31 3.91
2265 4871 9.890629 AATCTTACAATCATCTTGTGCTAGTAA 57.109 29.630 1.02 0.00 34.11 2.24
2274 4880 7.161404 TCATCTTGTGCTAGTAATTTGTCAGT 58.839 34.615 0.00 0.00 0.00 3.41
2279 4885 5.049474 TGTGCTAGTAATTTGTCAGTTGCTG 60.049 40.000 0.00 0.00 0.00 4.41
2287 4893 2.565210 TGTCAGTTGCTGTTTTGCTG 57.435 45.000 0.00 0.00 32.61 4.41
2293 4899 0.468958 TTGCTGTTTTGCTGCCCCTA 60.469 50.000 0.00 0.00 40.74 3.53
2395 5011 6.368791 GGCTAACATTTGAATTTCAACCCTTC 59.631 38.462 11.30 0.00 35.89 3.46
2414 5030 5.470437 CCCTTCCAAGAGTTCTCTTAACAAC 59.530 44.000 13.66 0.00 0.00 3.32
2415 5031 5.470437 CCTTCCAAGAGTTCTCTTAACAACC 59.530 44.000 13.66 0.00 0.00 3.77
2416 5032 4.969484 TCCAAGAGTTCTCTTAACAACCC 58.031 43.478 13.66 0.00 0.00 4.11
2417 5033 4.072839 CCAAGAGTTCTCTTAACAACCCC 58.927 47.826 13.66 0.00 0.00 4.95
2418 5034 3.679824 AGAGTTCTCTTAACAACCCCG 57.320 47.619 0.00 0.00 0.00 5.73
2419 5035 2.074576 GAGTTCTCTTAACAACCCCGC 58.925 52.381 0.00 0.00 0.00 6.13
2420 5036 1.418637 AGTTCTCTTAACAACCCCGCA 59.581 47.619 0.00 0.00 0.00 5.69
2421 5037 2.158726 AGTTCTCTTAACAACCCCGCAA 60.159 45.455 0.00 0.00 0.00 4.85
2422 5038 2.619646 GTTCTCTTAACAACCCCGCAAA 59.380 45.455 0.00 0.00 0.00 3.68
2423 5039 2.933573 TCTCTTAACAACCCCGCAAAA 58.066 42.857 0.00 0.00 0.00 2.44
2424 5040 3.288964 TCTCTTAACAACCCCGCAAAAA 58.711 40.909 0.00 0.00 0.00 1.94
2450 5066 9.579932 AAGAAAGAGTTCTCTTAACAAATGGAT 57.420 29.630 14.29 0.00 43.59 3.41
2466 5082 6.723052 ACAAATGGATCTTTTCACTTCCTCAT 59.277 34.615 0.00 0.00 0.00 2.90
2470 5086 8.884124 ATGGATCTTTTCACTTCCTCATAAAA 57.116 30.769 0.00 0.00 0.00 1.52
2471 5087 8.704849 TGGATCTTTTCACTTCCTCATAAAAA 57.295 30.769 0.00 0.00 0.00 1.94
2472 5088 8.796475 TGGATCTTTTCACTTCCTCATAAAAAG 58.204 33.333 0.00 0.00 35.87 2.27
2473 5089 9.014297 GGATCTTTTCACTTCCTCATAAAAAGA 57.986 33.333 9.67 9.67 43.10 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.655615 TGTAGGAGTTGTTTGGGTTGT 57.344 42.857 0.00 0.00 0.00 3.32
1 2 3.067601 GGTTGTAGGAGTTGTTTGGGTTG 59.932 47.826 0.00 0.00 0.00 3.77
55 58 1.144503 CAGGGATCAAAGGGGGATCAG 59.855 57.143 0.00 0.00 42.31 2.90
85 91 0.890683 CTTGGGAATGAGTTGTGGCC 59.109 55.000 0.00 0.00 0.00 5.36
129 135 3.758554 CAGTATGACCCCTTTGTTTGGAG 59.241 47.826 0.00 0.00 39.69 3.86
130 136 3.761897 CAGTATGACCCCTTTGTTTGGA 58.238 45.455 0.00 0.00 39.69 3.53
144 150 4.504864 GCATGTGTTATAGGGGCAGTATGA 60.505 45.833 0.00 0.00 39.69 2.15
146 152 3.652869 AGCATGTGTTATAGGGGCAGTAT 59.347 43.478 0.00 0.00 0.00 2.12
148 154 1.846439 AGCATGTGTTATAGGGGCAGT 59.154 47.619 0.00 0.00 0.00 4.40
151 157 1.070134 TCGAGCATGTGTTATAGGGGC 59.930 52.381 0.00 0.00 0.00 5.80
152 158 2.548067 GGTCGAGCATGTGTTATAGGGG 60.548 54.545 10.30 0.00 0.00 4.79
154 160 2.034179 TCGGTCGAGCATGTGTTATAGG 59.966 50.000 15.89 0.00 0.00 2.57
219 325 4.746395 TTTCTGTGGAAGAGCATACAGCAA 60.746 41.667 0.00 0.00 40.15 3.91
233 339 9.739276 AAATGTGATATCTACTTTTTCTGTGGA 57.261 29.630 3.98 0.00 0.00 4.02
415 522 9.619316 GTTTGTGAATTTTTAAAACTTTGCCTT 57.381 25.926 0.00 0.00 0.00 4.35
416 523 8.787852 TGTTTGTGAATTTTTAAAACTTTGCCT 58.212 25.926 0.00 0.00 33.07 4.75
417 524 8.956617 TGTTTGTGAATTTTTAAAACTTTGCC 57.043 26.923 0.00 0.00 33.07 4.52
466 573 4.573201 CGTTTCCACTCAGGTTTTGTCTAA 59.427 41.667 0.00 0.00 39.02 2.10
501 608 0.178975 TGTGAGGCACCCGGATTTTT 60.179 50.000 0.73 0.00 32.73 1.94
514 621 6.340522 AGAAAAATTCAACAGGTTTGTGAGG 58.659 36.000 0.00 0.00 37.67 3.86
515 622 7.832503 AAGAAAAATTCAACAGGTTTGTGAG 57.167 32.000 0.00 0.00 37.67 3.51
611 719 9.989869 GGCTCATGTAAAGACTATTTTTAGTTC 57.010 33.333 0.00 0.00 0.00 3.01
612 720 9.740710 AGGCTCATGTAAAGACTATTTTTAGTT 57.259 29.630 0.00 0.00 27.36 2.24
613 721 9.167311 CAGGCTCATGTAAAGACTATTTTTAGT 57.833 33.333 0.00 0.00 28.46 2.24
614 722 8.125448 GCAGGCTCATGTAAAGACTATTTTTAG 58.875 37.037 0.00 0.00 28.46 1.85
615 723 7.829211 AGCAGGCTCATGTAAAGACTATTTTTA 59.171 33.333 0.00 0.00 28.46 1.52
616 724 6.660949 AGCAGGCTCATGTAAAGACTATTTTT 59.339 34.615 0.00 0.00 28.46 1.94
617 725 6.183347 AGCAGGCTCATGTAAAGACTATTTT 58.817 36.000 0.00 0.00 28.46 1.82
667 775 1.463444 GTTCACGTGTATTGGACCAGC 59.537 52.381 16.51 0.00 0.00 4.85
672 780 2.352030 GGACTCGTTCACGTGTATTGGA 60.352 50.000 16.51 6.43 44.60 3.53
691 799 1.758592 CCTTGGGAACACCTTCGGA 59.241 57.895 0.00 0.00 42.67 4.55
700 808 0.471022 TCCTTTTGGGCCTTGGGAAC 60.471 55.000 4.53 0.00 40.87 3.62
701 809 0.471022 GTCCTTTTGGGCCTTGGGAA 60.471 55.000 4.53 0.00 38.54 3.97
742 850 2.223711 GCAACTCGGTGTGGACATTTTT 60.224 45.455 0.00 0.00 0.00 1.94
746 854 0.108585 AAGCAACTCGGTGTGGACAT 59.891 50.000 0.00 0.00 0.00 3.06
747 855 0.753867 TAAGCAACTCGGTGTGGACA 59.246 50.000 0.00 0.00 0.00 4.02
748 856 1.873698 TTAAGCAACTCGGTGTGGAC 58.126 50.000 0.00 0.00 0.00 4.02
749 857 2.623878 TTTAAGCAACTCGGTGTGGA 57.376 45.000 0.00 0.00 0.00 4.02
750 858 3.701532 TTTTTAAGCAACTCGGTGTGG 57.298 42.857 0.00 0.00 0.00 4.17
768 876 5.338056 GGGGTGGACTTGTTTTTCTCTTTTT 60.338 40.000 0.00 0.00 0.00 1.94
769 877 4.161565 GGGGTGGACTTGTTTTTCTCTTTT 59.838 41.667 0.00 0.00 0.00 2.27
770 878 3.704566 GGGGTGGACTTGTTTTTCTCTTT 59.295 43.478 0.00 0.00 0.00 2.52
771 879 3.296854 GGGGTGGACTTGTTTTTCTCTT 58.703 45.455 0.00 0.00 0.00 2.85
772 880 2.748465 CGGGGTGGACTTGTTTTTCTCT 60.748 50.000 0.00 0.00 0.00 3.10
773 881 1.607148 CGGGGTGGACTTGTTTTTCTC 59.393 52.381 0.00 0.00 0.00 2.87
774 882 1.213430 TCGGGGTGGACTTGTTTTTCT 59.787 47.619 0.00 0.00 0.00 2.52
775 883 1.335810 GTCGGGGTGGACTTGTTTTTC 59.664 52.381 0.00 0.00 34.09 2.29
776 884 1.395635 GTCGGGGTGGACTTGTTTTT 58.604 50.000 0.00 0.00 34.09 1.94
777 885 0.466739 GGTCGGGGTGGACTTGTTTT 60.467 55.000 0.00 0.00 37.12 2.43
949 2724 5.065988 GGGATTTTATAGCTGCGAAGTTTCA 59.934 40.000 0.00 0.00 0.00 2.69
955 2730 2.173782 TGGGGGATTTTATAGCTGCGAA 59.826 45.455 0.00 0.00 0.00 4.70
966 2741 3.638592 CTCGGGCGTGGGGGATTTT 62.639 63.158 0.00 0.00 0.00 1.82
991 2766 1.772156 TGGTGGTGGGGTGATGTGA 60.772 57.895 0.00 0.00 0.00 3.58
1230 3044 2.500910 CTCCAGGAAGATCTTGAGCACT 59.499 50.000 14.00 0.25 0.00 4.40
1305 3119 4.430765 ACGACGTCCATGGCGGTC 62.431 66.667 25.35 22.40 35.57 4.79
1391 3212 0.722848 GAGTCAGAGTCGACGGAGAC 59.277 60.000 21.61 21.61 40.98 3.36
1436 3264 1.962547 CACGCATTCAGAAACGAAACG 59.037 47.619 14.11 0.00 35.70 3.60
1457 3285 4.589700 AACAGCAACGCACGCACG 62.590 61.111 0.00 0.00 39.50 5.34
1521 3349 0.102481 ACACGCACTCTGACGAACTT 59.898 50.000 0.00 0.00 0.00 2.66
1545 3373 5.100344 ACTGACTACAGAGACCGATAGAA 57.900 43.478 0.00 0.00 46.03 2.10
1587 3415 5.929992 CCAACAATCCCATTGCATTCATATC 59.070 40.000 0.00 0.00 43.98 1.63
1758 3607 7.711846 ACAAACTGCACAATGAAATACAGTAA 58.288 30.769 0.00 0.00 37.38 2.24
1760 3609 6.147864 ACAAACTGCACAATGAAATACAGT 57.852 33.333 0.00 0.00 39.92 3.55
1780 3629 3.391296 AGAGGAGCTAGGTTTGTGAACAA 59.609 43.478 0.00 0.00 37.51 2.83
1786 3635 1.352083 TGCAGAGGAGCTAGGTTTGT 58.648 50.000 0.00 0.00 34.99 2.83
1806 3655 4.015406 ACCTCGTTGCCATGCGGA 62.015 61.111 0.00 0.00 0.00 5.54
1810 3659 1.378882 CCATCCACCTCGTTGCCATG 61.379 60.000 0.00 0.00 0.00 3.66
1814 3663 2.270874 ATCCCCATCCACCTCGTTGC 62.271 60.000 0.00 0.00 0.00 4.17
1848 3765 0.982704 AGCAGCACCTCTTCAGATGT 59.017 50.000 0.00 0.00 0.00 3.06
1879 3814 9.661187 CATCAAAGCATCAGAGATAAAACATAC 57.339 33.333 0.00 0.00 0.00 2.39
1880 3815 8.347771 GCATCAAAGCATCAGAGATAAAACATA 58.652 33.333 0.00 0.00 0.00 2.29
1881 3816 7.147966 TGCATCAAAGCATCAGAGATAAAACAT 60.148 33.333 0.00 0.00 40.11 2.71
1882 3817 6.151480 TGCATCAAAGCATCAGAGATAAAACA 59.849 34.615 0.00 0.00 40.11 2.83
1884 3819 6.762702 TGCATCAAAGCATCAGAGATAAAA 57.237 33.333 0.00 0.00 40.11 1.52
1899 3859 6.153756 CAGAACAGAATCATGTTGCATCAAA 58.846 36.000 0.75 0.00 43.32 2.69
1906 3866 4.761235 AGCACAGAACAGAATCATGTTG 57.239 40.909 0.00 0.00 43.32 3.33
1907 3867 5.555017 AGTAGCACAGAACAGAATCATGTT 58.445 37.500 0.00 0.00 45.89 2.71
1908 3868 5.157940 AGTAGCACAGAACAGAATCATGT 57.842 39.130 0.00 0.00 33.96 3.21
1911 3871 5.610398 TGAAAGTAGCACAGAACAGAATCA 58.390 37.500 0.00 0.00 0.00 2.57
1925 3885 3.929610 CCAAGAGTAGTGCTGAAAGTAGC 59.070 47.826 0.00 0.00 43.95 3.58
1926 3886 3.929610 GCCAAGAGTAGTGCTGAAAGTAG 59.070 47.826 0.00 0.00 35.30 2.57
1935 3895 0.320421 TCCAACGCCAAGAGTAGTGC 60.320 55.000 0.00 0.00 0.00 4.40
1936 3896 2.163818 TTCCAACGCCAAGAGTAGTG 57.836 50.000 0.00 0.00 0.00 2.74
2032 4570 4.443394 AGAACGTTTCTGCGTAACTAACTG 59.557 41.667 0.46 0.00 45.00 3.16
2037 4576 3.050619 CAGAGAACGTTTCTGCGTAACT 58.949 45.455 20.00 4.32 45.00 2.24
2075 4614 6.603201 TGAGTACATGAGTATGACTGATGACA 59.397 38.462 12.18 5.09 37.73 3.58
2076 4615 7.032377 TGAGTACATGAGTATGACTGATGAC 57.968 40.000 12.18 6.75 37.73 3.06
2077 4616 7.830099 ATGAGTACATGAGTATGACTGATGA 57.170 36.000 12.18 0.00 37.73 2.92
2100 4640 7.938715 AGAACATACTCCGAGAACGTATAAAT 58.061 34.615 1.33 0.00 37.88 1.40
2101 4641 7.325660 AGAACATACTCCGAGAACGTATAAA 57.674 36.000 1.33 0.00 37.88 1.40
2103 4643 8.437360 TTTAGAACATACTCCGAGAACGTATA 57.563 34.615 1.33 0.00 37.88 1.47
2104 4644 6.932356 TTAGAACATACTCCGAGAACGTAT 57.068 37.500 1.33 0.00 37.88 3.06
2105 4645 6.741992 TTTAGAACATACTCCGAGAACGTA 57.258 37.500 1.33 0.00 37.88 3.57
2106 4646 5.633830 TTTAGAACATACTCCGAGAACGT 57.366 39.130 1.33 0.00 37.88 3.99
2107 4647 6.091437 AGTTTTAGAACATACTCCGAGAACG 58.909 40.000 1.33 0.00 38.26 3.95
2108 4648 7.273815 CAGAGTTTTAGAACATACTCCGAGAAC 59.726 40.741 1.33 0.00 38.17 3.01
2109 4649 7.313646 CAGAGTTTTAGAACATACTCCGAGAA 58.686 38.462 1.33 0.00 38.17 2.87
2111 4651 6.037098 CCAGAGTTTTAGAACATACTCCGAG 58.963 44.000 0.00 0.00 38.17 4.63
2112 4652 5.479375 ACCAGAGTTTTAGAACATACTCCGA 59.521 40.000 0.00 0.00 38.17 4.55
2192 4795 4.517453 ACAAGTTCGCCAGCTTTTATGTTA 59.483 37.500 0.00 0.00 0.00 2.41
2208 4811 4.213694 TCTCTCTCACGTCACTACAAGTTC 59.786 45.833 0.00 0.00 0.00 3.01
2265 4871 3.866910 CAGCAAAACAGCAACTGACAAAT 59.133 39.130 0.78 0.00 35.18 2.32
2274 4880 0.468958 TAGGGGCAGCAAAACAGCAA 60.469 50.000 0.00 0.00 36.85 3.91
2319 4925 8.316497 TCATCAGAGAGGAGAAAAATATGTCT 57.684 34.615 0.00 0.00 0.00 3.41
2423 5039 9.408648 TCCATTTGTTAAGAGAACTCTTTCTTT 57.591 29.630 19.79 1.04 46.95 2.52
2424 5040 8.980481 TCCATTTGTTAAGAGAACTCTTTCTT 57.020 30.769 19.79 2.84 46.95 2.52
2425 5041 9.225436 GATCCATTTGTTAAGAGAACTCTTTCT 57.775 33.333 19.79 0.00 46.95 2.52
2426 5042 9.225436 AGATCCATTTGTTAAGAGAACTCTTTC 57.775 33.333 19.79 14.23 46.95 2.62
2427 5043 9.579932 AAGATCCATTTGTTAAGAGAACTCTTT 57.420 29.630 19.79 6.97 46.95 2.52
2429 5045 9.579932 AAAAGATCCATTTGTTAAGAGAACTCT 57.420 29.630 0.00 0.00 42.75 3.24
2430 5046 9.833182 GAAAAGATCCATTTGTTAAGAGAACTC 57.167 33.333 0.00 0.00 0.00 3.01
2431 5047 9.354673 TGAAAAGATCCATTTGTTAAGAGAACT 57.645 29.630 0.00 0.00 0.00 3.01
2432 5048 9.399403 GTGAAAAGATCCATTTGTTAAGAGAAC 57.601 33.333 0.00 0.00 0.00 3.01
2433 5049 9.354673 AGTGAAAAGATCCATTTGTTAAGAGAA 57.645 29.630 0.00 0.00 0.00 2.87
2434 5050 8.924511 AGTGAAAAGATCCATTTGTTAAGAGA 57.075 30.769 0.00 0.00 0.00 3.10
2435 5051 9.617975 GAAGTGAAAAGATCCATTTGTTAAGAG 57.382 33.333 0.00 0.00 0.00 2.85
2436 5052 8.576442 GGAAGTGAAAAGATCCATTTGTTAAGA 58.424 33.333 0.00 0.00 32.08 2.10
2437 5053 8.579863 AGGAAGTGAAAAGATCCATTTGTTAAG 58.420 33.333 0.00 0.00 34.30 1.85
2438 5054 8.477419 AGGAAGTGAAAAGATCCATTTGTTAA 57.523 30.769 0.00 0.00 34.30 2.01
2439 5055 7.723616 TGAGGAAGTGAAAAGATCCATTTGTTA 59.276 33.333 0.00 0.00 34.30 2.41
2440 5056 6.550854 TGAGGAAGTGAAAAGATCCATTTGTT 59.449 34.615 0.00 0.00 34.30 2.83
2441 5057 6.070656 TGAGGAAGTGAAAAGATCCATTTGT 58.929 36.000 0.00 0.00 34.30 2.83
2442 5058 6.579666 TGAGGAAGTGAAAAGATCCATTTG 57.420 37.500 0.00 0.00 34.30 2.32
2443 5059 8.884124 TTATGAGGAAGTGAAAAGATCCATTT 57.116 30.769 0.00 0.00 34.30 2.32
2444 5060 8.884124 TTTATGAGGAAGTGAAAAGATCCATT 57.116 30.769 0.00 0.00 34.30 3.16
2497 5117 7.050377 TCACTTTAATTCAGCCTATCCTTGAG 58.950 38.462 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.