Multiple sequence alignment - TraesCS2D01G499600

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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 TraesCS2D01G499600 chr2D 100.000 4814 0 0 1 4814 594543220 594548033 0.000000e+00 8890
1 TraesCS2D01G499600 chr2D 83.946 299 34 8 4326 4621 301752885 301752598 1.710000e-69 274
2 TraesCS2D01G499600 chr2B 90.959 3252 172 43 825 4021 722086200 722089384 0.000000e+00 4265
3 TraesCS2D01G499600 chr2B 93.894 737 22 10 4078 4814 722089400 722090113 0.000000e+00 1090
4 TraesCS2D01G499600 chr2B 85.822 529 21 20 277 796 722085651 722086134 3.320000e-141 512
5 TraesCS2D01G499600 chr2B 93.496 123 7 1 1 123 722085517 722085638 1.060000e-41 182
6 TraesCS2D01G499600 chr2A 92.912 2074 72 18 2761 4814 729168391 729170409 0.000000e+00 2946
7 TraesCS2D01G499600 chr2A 92.385 1090 55 10 825 1893 729166588 729167670 0.000000e+00 1528
8 TraesCS2D01G499600 chr2A 96.761 741 24 0 1912 2652 729167654 729168394 0.000000e+00 1236
9 TraesCS2D01G499600 chr2A 89.831 826 34 20 1 796 729165717 729166522 0.000000e+00 1014
10 TraesCS2D01G499600 chr3D 85.405 370 48 4 2169 2534 613927472 613927839 3.520000e-101 379
11 TraesCS2D01G499600 chr3D 79.356 528 78 16 2414 2924 614198040 614198553 4.610000e-90 342
12 TraesCS2D01G499600 chr3A 84.419 353 38 11 3149 3486 750495940 750496290 9.990000e-87 331
13 TraesCS2D01G499600 chr3A 81.323 257 24 13 2817 3072 750495677 750495910 2.290000e-43 187
14 TraesCS2D01G499600 chr1D 78.623 276 21 15 973 1244 334607814 334608055 1.080000e-31 148
15 TraesCS2D01G499600 chr7A 90.991 111 6 2 1146 1252 217752829 217752719 3.880000e-31 147
16 TraesCS2D01G499600 chr7A 90.244 82 7 1 2832 2912 43524224 43524143 6.590000e-19 106
17 TraesCS2D01G499600 chr5A 89.655 116 8 2 1140 1251 245501023 245500908 1.400000e-30 145
18 TraesCS2D01G499600 chr5A 88.889 117 9 2 1140 1252 329387509 329387625 1.810000e-29 141
19 TraesCS2D01G499600 chr4A 90.826 109 6 2 1140 1244 140710818 140710710 5.020000e-30 143
20 TraesCS2D01G499600 chr4A 90.244 82 7 1 2832 2912 652197360 652197279 6.590000e-19 106
21 TraesCS2D01G499600 chr7D 88.889 117 9 3 1140 1252 366721312 366721428 1.810000e-29 141
22 TraesCS2D01G499600 chr1A 87.931 116 10 2 1140 1251 75388524 75388639 3.020000e-27 134


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 TraesCS2D01G499600 chr2D 594543220 594548033 4813 False 8890.00 8890 100.00000 1 4814 1 chr2D.!!$F1 4813
1 TraesCS2D01G499600 chr2B 722085517 722090113 4596 False 1512.25 4265 91.04275 1 4814 4 chr2B.!!$F1 4813
2 TraesCS2D01G499600 chr2A 729165717 729170409 4692 False 1681.00 2946 92.97225 1 4814 4 chr2A.!!$F1 4813
3 TraesCS2D01G499600 chr3D 614198040 614198553 513 False 342.00 342 79.35600 2414 2924 1 chr3D.!!$F2 510
4 TraesCS2D01G499600 chr3A 750495677 750496290 613 False 259.00 331 82.87100 2817 3486 2 chr3A.!!$F1 669

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
242 245 0.406750 TCCACCAGAGGACTCGGTTA 59.593 55.0 11.36 3.48 35.45 2.85 F
819 851 0.902531 GTGACTGTAAGGCCTGCCTA 59.097 55.0 5.69 0.00 46.74 3.93 F
1361 1445 0.470341 GAGCTCAGTCCATTACCCCC 59.530 60.0 9.40 0.00 0.00 5.40 F
1857 1956 0.325933 CTGTTCTGCCTCCATGTGGA 59.674 55.0 1.17 1.17 43.08 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1197 1281 0.674895 ACCTGCTTGAATCCTGACGC 60.675 55.000 0.0 0.0 0.00 5.19 R
1635 1728 0.919710 AGGTAAGCCATCCCAGAACC 59.080 55.000 0.0 0.0 37.19 3.62 R
2759 2916 1.349627 CGCAGCAAATCCTACAGCG 59.650 57.895 0.0 0.0 37.68 5.18 R
3818 4061 1.305219 GGCCGTGCTGCTATTTGACA 61.305 55.000 0.0 0.0 0.00 3.58 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
67 68 3.010420 AGCCAGCTCGACCTTATTTTTC 58.990 45.455 0.00 0.00 0.00 2.29
162 165 5.446860 ACCGAGATCCATAAGAGTACTTCA 58.553 41.667 0.00 0.00 37.53 3.02
183 186 5.762045 TCAAAACTAGCAATCAGAAAGTGC 58.238 37.500 0.00 0.00 38.59 4.40
191 194 3.670627 GCAATCAGAAAGTGCTAAACCGG 60.671 47.826 0.00 0.00 35.36 5.28
204 207 2.891191 AAACCGGGGAGAGCAAATTA 57.109 45.000 6.32 0.00 0.00 1.40
205 208 2.124277 AACCGGGGAGAGCAAATTAC 57.876 50.000 6.32 0.00 0.00 1.89
206 209 0.988832 ACCGGGGAGAGCAAATTACA 59.011 50.000 6.32 0.00 0.00 2.41
207 210 1.564348 ACCGGGGAGAGCAAATTACAT 59.436 47.619 6.32 0.00 0.00 2.29
232 235 2.113433 GCTGCAGCATCCACCAGAG 61.113 63.158 33.36 0.00 41.59 3.35
242 245 0.406750 TCCACCAGAGGACTCGGTTA 59.593 55.000 11.36 3.48 35.45 2.85
291 306 6.930731 AGCTGAACCAAAAAGTAAAACAAGA 58.069 32.000 0.00 0.00 0.00 3.02
296 311 8.097662 TGAACCAAAAAGTAAAACAAGAACCAT 58.902 29.630 0.00 0.00 0.00 3.55
416 437 1.898094 AGCTGCGCAACCACATGAA 60.898 52.632 13.05 0.00 0.00 2.57
446 467 2.360350 CAGCCGCACCCACAGAAT 60.360 61.111 0.00 0.00 0.00 2.40
449 470 2.350895 CCGCACCCACAGAATCCA 59.649 61.111 0.00 0.00 0.00 3.41
453 474 1.586154 GCACCCACAGAATCCAACCG 61.586 60.000 0.00 0.00 0.00 4.44
524 545 4.179599 GGGAGGGGAGAGGGGGAG 62.180 77.778 0.00 0.00 0.00 4.30
525 546 4.179599 GGAGGGGAGAGGGGGAGG 62.180 77.778 0.00 0.00 0.00 4.30
526 547 3.036959 GAGGGGAGAGGGGGAGGA 61.037 72.222 0.00 0.00 0.00 3.71
593 615 4.435436 ACGAGCTTCATCGCGGCA 62.435 61.111 6.13 0.00 46.60 5.69
724 756 4.707791 CCGCCTCGGTTTACCTTT 57.292 55.556 0.00 0.00 42.73 3.11
725 757 2.463592 CCGCCTCGGTTTACCTTTC 58.536 57.895 0.00 0.00 42.73 2.62
726 758 1.022982 CCGCCTCGGTTTACCTTTCC 61.023 60.000 0.00 0.00 42.73 3.13
727 759 1.356527 CGCCTCGGTTTACCTTTCCG 61.357 60.000 0.00 0.00 44.76 4.30
728 760 1.022982 GCCTCGGTTTACCTTTCCGG 61.023 60.000 0.00 0.00 43.75 5.14
739 771 1.623542 CCTTTCCGGGGAATCCTCGT 61.624 60.000 21.21 0.00 33.79 4.18
796 828 2.842936 AGGGAAGATACGGCCCGG 60.843 66.667 8.57 0.00 46.68 5.73
797 829 4.620937 GGGAAGATACGGCCCGGC 62.621 72.222 8.57 0.00 31.06 6.13
798 830 4.620937 GGAAGATACGGCCCGGCC 62.621 72.222 19.64 19.64 46.75 6.13
809 841 3.697747 CCCGGCCCGTGACTGTAA 61.698 66.667 0.85 0.00 0.00 2.41
810 842 2.125673 CCGGCCCGTGACTGTAAG 60.126 66.667 0.85 0.00 42.29 2.34
811 843 2.125673 CGGCCCGTGACTGTAAGG 60.126 66.667 0.00 0.00 39.30 2.69
813 845 2.436115 GCCCGTGACTGTAAGGCC 60.436 66.667 0.00 0.00 46.74 5.19
814 846 2.955881 GCCCGTGACTGTAAGGCCT 61.956 63.158 0.00 0.00 46.74 5.19
816 848 1.741770 CCGTGACTGTAAGGCCTGC 60.742 63.158 5.69 2.70 46.74 4.85
819 851 0.902531 GTGACTGTAAGGCCTGCCTA 59.097 55.000 5.69 0.00 46.74 3.93
820 852 0.902531 TGACTGTAAGGCCTGCCTAC 59.097 55.000 5.69 6.01 46.74 3.18
821 853 1.829666 TGACTGTAAGGCCTGCCTACA 60.830 52.381 5.69 11.09 46.74 2.74
822 854 3.993488 TGACTGTAAGGCCTGCCTACAC 61.993 54.545 5.69 12.75 46.74 2.90
828 897 4.735132 GCCTGCCTACACGACGCA 62.735 66.667 0.00 0.00 0.00 5.24
1361 1445 0.470341 GAGCTCAGTCCATTACCCCC 59.530 60.000 9.40 0.00 0.00 5.40
1391 1480 2.963432 TCGTTGTTCTTACCGGATTCC 58.037 47.619 9.46 0.00 0.00 3.01
1581 1674 6.371548 GCAATTAGGACAACATAGACAGTCAA 59.628 38.462 2.66 0.00 32.79 3.18
1615 1708 3.865745 GTGGAATCAGATGTCTTGGTACG 59.134 47.826 0.00 0.00 0.00 3.67
1635 1728 1.000521 TGGCTCTCCCAAATGGCAG 60.001 57.895 0.00 0.00 41.82 4.85
1717 1812 5.104109 TGTCCATCCTTTCCCTAACATAAGG 60.104 44.000 0.00 0.00 38.78 2.69
1742 1837 3.872511 TGCATTTCCTGTTGCTAATGG 57.127 42.857 0.00 0.00 39.60 3.16
1745 1840 4.157656 TGCATTTCCTGTTGCTAATGGTAC 59.842 41.667 0.00 0.00 39.60 3.34
1764 1859 5.886474 TGGTACCTCTATGTTAGTCTGTGAG 59.114 44.000 14.36 0.00 0.00 3.51
1777 1872 2.554893 GTCTGTGAGAGACTCCTCGTTT 59.445 50.000 2.06 0.00 46.85 3.60
1778 1873 2.554462 TCTGTGAGAGACTCCTCGTTTG 59.446 50.000 0.00 0.00 44.08 2.93
1787 1882 3.385111 AGACTCCTCGTTTGTTCTCTGTT 59.615 43.478 0.00 0.00 0.00 3.16
1788 1883 3.458189 ACTCCTCGTTTGTTCTCTGTTG 58.542 45.455 0.00 0.00 0.00 3.33
1795 1890 6.851330 CCTCGTTTGTTCTCTGTTGTAATTTC 59.149 38.462 0.00 0.00 0.00 2.17
1818 1913 9.478768 TTTCTGTACTAATGTTGATCGTTAACA 57.521 29.630 6.39 0.11 41.72 2.41
1857 1956 0.325933 CTGTTCTGCCTCCATGTGGA 59.674 55.000 1.17 1.17 43.08 4.02
1891 1990 9.354673 GATTTATTGTCCATATTTCCTCTCCAA 57.645 33.333 0.00 0.00 0.00 3.53
1892 1991 9.713684 ATTTATTGTCCATATTTCCTCTCCAAA 57.286 29.630 0.00 0.00 0.00 3.28
1893 1992 9.713684 TTTATTGTCCATATTTCCTCTCCAAAT 57.286 29.630 0.00 0.00 0.00 2.32
1894 1993 9.713684 TTATTGTCCATATTTCCTCTCCAAATT 57.286 29.630 0.00 0.00 0.00 1.82
1895 1994 7.408756 TTGTCCATATTTCCTCTCCAAATTG 57.591 36.000 0.00 0.00 0.00 2.32
1896 1995 5.893255 TGTCCATATTTCCTCTCCAAATTGG 59.107 40.000 5.48 5.48 39.43 3.16
1897 1996 4.895297 TCCATATTTCCTCTCCAAATTGGC 59.105 41.667 7.24 0.00 37.47 4.52
1898 1997 4.650588 CCATATTTCCTCTCCAAATTGGCA 59.349 41.667 7.24 0.00 37.47 4.92
1899 1998 5.129155 CCATATTTCCTCTCCAAATTGGCAA 59.871 40.000 7.24 0.68 37.47 4.52
1900 1999 6.352051 CCATATTTCCTCTCCAAATTGGCAAA 60.352 38.462 7.24 1.86 37.47 3.68
1901 2000 5.767277 ATTTCCTCTCCAAATTGGCAAAT 57.233 34.783 7.24 0.00 37.47 2.32
1902 2001 6.872585 ATTTCCTCTCCAAATTGGCAAATA 57.127 33.333 7.24 0.00 37.47 1.40
1903 2002 5.920193 TTCCTCTCCAAATTGGCAAATAG 57.080 39.130 7.24 0.00 37.47 1.73
1904 2003 5.191727 TCCTCTCCAAATTGGCAAATAGA 57.808 39.130 7.24 3.73 37.47 1.98
1905 2004 5.195940 TCCTCTCCAAATTGGCAAATAGAG 58.804 41.667 16.42 16.42 37.47 2.43
1906 2005 4.340381 CCTCTCCAAATTGGCAAATAGAGG 59.660 45.833 23.70 23.70 43.10 3.69
1907 2006 5.191727 TCTCCAAATTGGCAAATAGAGGA 57.808 39.130 7.24 7.02 37.47 3.71
1908 2007 5.195940 TCTCCAAATTGGCAAATAGAGGAG 58.804 41.667 21.44 21.44 38.41 3.69
1909 2008 3.701040 TCCAAATTGGCAAATAGAGGAGC 59.299 43.478 7.24 0.00 37.47 4.70
1910 2009 3.448301 CCAAATTGGCAAATAGAGGAGCA 59.552 43.478 3.01 0.00 0.00 4.26
1911 2010 4.427312 CAAATTGGCAAATAGAGGAGCAC 58.573 43.478 3.01 0.00 0.00 4.40
1912 2011 2.877097 TTGGCAAATAGAGGAGCACA 57.123 45.000 0.00 0.00 0.00 4.57
1913 2012 3.370840 TTGGCAAATAGAGGAGCACAT 57.629 42.857 0.00 0.00 0.00 3.21
1914 2013 4.502105 TTGGCAAATAGAGGAGCACATA 57.498 40.909 0.00 0.00 0.00 2.29
1915 2014 4.712051 TGGCAAATAGAGGAGCACATAT 57.288 40.909 0.00 0.00 0.00 1.78
1916 2015 5.823861 TGGCAAATAGAGGAGCACATATA 57.176 39.130 0.00 0.00 0.00 0.86
1917 2016 6.378661 TGGCAAATAGAGGAGCACATATAT 57.621 37.500 0.00 0.00 0.00 0.86
1918 2017 6.782986 TGGCAAATAGAGGAGCACATATATT 58.217 36.000 0.00 0.00 0.00 1.28
1919 2018 7.917003 TGGCAAATAGAGGAGCACATATATTA 58.083 34.615 0.00 0.00 0.00 0.98
1920 2019 8.551440 TGGCAAATAGAGGAGCACATATATTAT 58.449 33.333 0.00 0.00 0.00 1.28
1921 2020 9.050601 GGCAAATAGAGGAGCACATATATTATC 57.949 37.037 0.00 0.00 0.00 1.75
1922 2021 9.829507 GCAAATAGAGGAGCACATATATTATCT 57.170 33.333 0.00 0.00 0.00 1.98
2094 2228 5.565592 TTTGACATGTTATGCTGCTAAGG 57.434 39.130 0.00 0.00 0.00 2.69
2176 2311 4.199310 TGTACCTGGCATTTCTTCTATGC 58.801 43.478 0.00 0.00 45.92 3.14
2328 2463 2.159639 GCTAGAAGTTGGAAAGAAGCGC 60.160 50.000 0.00 0.00 0.00 5.92
2729 2886 6.151663 ACTTATAAACGGTTGGCAAGTTTT 57.848 33.333 18.79 12.38 38.74 2.43
2747 2904 7.162385 GCAAGTTTTGATTGAATGTTGTTTTCG 59.838 33.333 0.00 0.00 0.00 3.46
2759 2916 5.924475 TGTTGTTTTCGAGGAGATTTCTC 57.076 39.130 0.00 0.00 42.14 2.87
2773 2950 3.873952 AGATTTCTCGCTGTAGGATTTGC 59.126 43.478 0.00 0.00 0.00 3.68
2781 2958 1.394917 CTGTAGGATTTGCTGCGTGTC 59.605 52.381 0.00 0.00 0.00 3.67
2782 2959 1.001974 TGTAGGATTTGCTGCGTGTCT 59.998 47.619 0.00 0.00 0.00 3.41
2783 2960 2.076863 GTAGGATTTGCTGCGTGTCTT 58.923 47.619 0.00 0.00 0.00 3.01
2786 2963 2.679837 AGGATTTGCTGCGTGTCTTATG 59.320 45.455 0.00 0.00 0.00 1.90
2787 2964 2.677836 GGATTTGCTGCGTGTCTTATGA 59.322 45.455 0.00 0.00 0.00 2.15
2797 2974 4.142337 TGCGTGTCTTATGAAATCCGACTA 60.142 41.667 0.00 0.00 29.98 2.59
2828 3005 7.587629 TGTTCTTTGCATCTAATCAGTTTCAG 58.412 34.615 0.00 0.00 0.00 3.02
2940 3117 6.273071 ACATGTAAGTTTTCTTTGGTCAAGC 58.727 36.000 0.00 0.00 40.91 4.01
2941 3118 5.906113 TGTAAGTTTTCTTTGGTCAAGCA 57.094 34.783 0.00 0.00 40.91 3.91
2942 3119 6.274157 TGTAAGTTTTCTTTGGTCAAGCAA 57.726 33.333 0.00 0.00 40.91 3.91
2943 3120 6.329496 TGTAAGTTTTCTTTGGTCAAGCAAG 58.671 36.000 0.00 0.00 40.91 4.01
3001 3199 2.566952 ATTAAACAAGCAGATGCCGC 57.433 45.000 0.14 0.00 43.38 6.53
3078 3286 6.884295 AGGCACTGCAACAAAGTTATAATCTA 59.116 34.615 2.82 0.00 37.18 1.98
3159 3367 8.918961 TCATGTTTCTTGTTGTCGTTTATTTT 57.081 26.923 0.00 0.00 0.00 1.82
3227 3438 4.022849 GTGTTGTCTCATCCTTCCCAAAAG 60.023 45.833 0.00 0.00 0.00 2.27
3487 3712 3.944015 GCATTTCCTGTTACTGAGCTGAT 59.056 43.478 0.00 0.00 0.00 2.90
3647 3890 6.259550 AGGATGCAAGATTACAACACTTTC 57.740 37.500 0.00 0.00 0.00 2.62
3992 4236 6.129179 TGATCTGGAGAAAGGTCTTGTTTTT 58.871 36.000 0.00 0.00 32.80 1.94
4076 4320 3.475566 TGTGCTATACCTTGCATCTCC 57.524 47.619 0.00 0.00 41.45 3.71
4094 4338 6.183360 GCATCTCCATATCTTTGAACTTGCTT 60.183 38.462 0.00 0.00 0.00 3.91
4112 4356 6.857964 ACTTGCTTTCGAGTAAATTTGTCATG 59.142 34.615 0.00 0.00 35.20 3.07
4116 4360 6.567701 GCTTTCGAGTAAATTTGTCATGTGGA 60.568 38.462 0.00 0.00 0.00 4.02
4163 4407 5.126061 CCAAAATGTAGGGAGGAAATCACTG 59.874 44.000 0.00 0.00 43.44 3.66
4179 4423 5.886960 ATCACTGCTAAAAATCCTGACAC 57.113 39.130 0.00 0.00 0.00 3.67
4195 4439 7.114866 TCCTGACACATAAATATGTACGGAA 57.885 36.000 5.78 0.00 44.57 4.30
4197 4441 8.208224 TCCTGACACATAAATATGTACGGAAAT 58.792 33.333 5.78 0.00 44.57 2.17
4255 4499 6.552008 TCTCAGATACCCCAGAAAACAAAAT 58.448 36.000 0.00 0.00 0.00 1.82
4256 4500 7.695055 TCTCAGATACCCCAGAAAACAAAATA 58.305 34.615 0.00 0.00 0.00 1.40
4257 4501 7.610305 TCTCAGATACCCCAGAAAACAAAATAC 59.390 37.037 0.00 0.00 0.00 1.89
4258 4502 6.373216 TCAGATACCCCAGAAAACAAAATACG 59.627 38.462 0.00 0.00 0.00 3.06
4259 4503 5.650703 AGATACCCCAGAAAACAAAATACGG 59.349 40.000 0.00 0.00 0.00 4.02
4260 4504 3.834938 ACCCCAGAAAACAAAATACGGA 58.165 40.909 0.00 0.00 0.00 4.69
4261 4505 3.824443 ACCCCAGAAAACAAAATACGGAG 59.176 43.478 0.00 0.00 0.00 4.63
4302 4546 5.726980 ACATAGCTTGGAGCATTTCAAAA 57.273 34.783 0.00 0.00 45.56 2.44
4454 4698 6.096141 TGGTTTGAGTTTTCTGCTGTTTCATA 59.904 34.615 0.00 0.00 0.00 2.15
4458 4702 5.827797 TGAGTTTTCTGCTGTTTCATAGGTT 59.172 36.000 0.00 0.00 0.00 3.50
4492 4736 3.369261 GCTTCTTCCAATGCTCTCTCTCA 60.369 47.826 0.00 0.00 0.00 3.27
4714 4958 4.763279 TGTCCAGTAACAATCGACTGACTA 59.237 41.667 0.00 0.00 44.88 2.59
4803 5047 1.758280 AGGGCCACAAATGCATGTATG 59.242 47.619 6.18 2.69 30.84 2.39
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
67 68 2.031120 TGGTTTGCCAGGTGAAGAAAG 58.969 47.619 0.00 0.00 40.46 2.62
162 165 7.510549 TTAGCACTTTCTGATTGCTAGTTTT 57.489 32.000 12.89 0.00 46.67 2.43
183 186 2.420058 ATTTGCTCTCCCCGGTTTAG 57.580 50.000 0.00 0.00 0.00 1.85
184 187 2.891191 AATTTGCTCTCCCCGGTTTA 57.109 45.000 0.00 0.00 0.00 2.01
191 194 3.189287 CGCCATATGTAATTTGCTCTCCC 59.811 47.826 1.24 0.00 0.00 4.30
204 207 2.903855 GCTGCAGCCGCCATATGT 60.904 61.111 28.76 0.00 37.32 2.29
205 208 2.196382 GATGCTGCAGCCGCCATATG 62.196 60.000 34.64 0.00 41.18 1.78
206 209 1.970114 GATGCTGCAGCCGCCATAT 60.970 57.895 34.64 20.67 41.18 1.78
207 210 2.592574 GATGCTGCAGCCGCCATA 60.593 61.111 34.64 16.51 41.18 2.74
242 245 4.023980 TGTGCTCTATGCTAGTGGTTAGT 58.976 43.478 0.00 0.00 43.37 2.24
248 251 3.058450 GCTCATGTGCTCTATGCTAGTG 58.942 50.000 12.42 0.00 43.37 2.74
291 306 4.154942 AGTTCTCCTTTTGCATCATGGTT 58.845 39.130 0.00 0.00 0.00 3.67
296 311 3.149196 GGTGAGTTCTCCTTTTGCATCA 58.851 45.455 0.00 0.00 0.00 3.07
409 424 1.923204 GCTGACTAGCTCGTTCATGTG 59.077 52.381 0.00 0.00 46.57 3.21
434 455 1.586154 CGGTTGGATTCTGTGGGTGC 61.586 60.000 0.00 0.00 0.00 5.01
436 457 1.378762 CCGGTTGGATTCTGTGGGT 59.621 57.895 0.00 0.00 37.49 4.51
522 543 1.916206 GCCAAGGTCCCCTCTTCCTC 61.916 65.000 0.00 0.00 30.89 3.71
523 544 1.925972 GCCAAGGTCCCCTCTTCCT 60.926 63.158 0.00 0.00 30.89 3.36
524 545 2.677848 GCCAAGGTCCCCTCTTCC 59.322 66.667 0.00 0.00 30.89 3.46
525 546 2.269241 CGCCAAGGTCCCCTCTTC 59.731 66.667 0.00 0.00 30.89 2.87
526 547 3.330720 CCGCCAAGGTCCCCTCTT 61.331 66.667 0.00 0.00 30.89 2.85
557 579 4.812476 CACCGCAATCTCGCCCGA 62.812 66.667 0.00 0.00 0.00 5.14
720 752 1.146263 CGAGGATTCCCCGGAAAGG 59.854 63.158 0.73 0.00 40.87 3.11
721 753 0.462047 CACGAGGATTCCCCGGAAAG 60.462 60.000 11.54 0.00 40.87 2.62
722 754 0.905809 TCACGAGGATTCCCCGGAAA 60.906 55.000 11.54 0.00 40.87 3.13
723 755 0.689745 ATCACGAGGATTCCCCGGAA 60.690 55.000 11.54 0.00 40.87 4.30
724 756 0.689745 AATCACGAGGATTCCCCGGA 60.690 55.000 11.54 5.99 42.62 5.14
725 757 1.830145 AATCACGAGGATTCCCCGG 59.170 57.895 11.54 0.00 42.62 5.73
796 828 2.436115 GGCCTTACAGTCACGGGC 60.436 66.667 0.00 0.00 41.80 6.13
797 829 1.079127 CAGGCCTTACAGTCACGGG 60.079 63.158 0.00 0.00 0.00 5.28
798 830 1.741770 GCAGGCCTTACAGTCACGG 60.742 63.158 0.00 0.00 0.00 4.94
800 832 0.902531 TAGGCAGGCCTTACAGTCAC 59.097 55.000 19.37 0.00 45.70 3.67
801 833 0.902531 GTAGGCAGGCCTTACAGTCA 59.097 55.000 19.37 0.00 45.70 3.41
802 834 0.902531 TGTAGGCAGGCCTTACAGTC 59.097 55.000 19.37 0.00 45.70 3.51
804 836 0.460284 CGTGTAGGCAGGCCTTACAG 60.460 60.000 19.37 10.38 45.70 2.74
805 837 0.901114 TCGTGTAGGCAGGCCTTACA 60.901 55.000 19.37 16.31 45.70 2.41
807 839 1.895238 GTCGTGTAGGCAGGCCTTA 59.105 57.895 19.37 5.50 45.70 2.69
808 840 2.663196 GTCGTGTAGGCAGGCCTT 59.337 61.111 19.37 2.83 45.70 4.35
811 843 4.735132 TGCGTCGTGTAGGCAGGC 62.735 66.667 0.00 0.00 43.75 4.85
816 848 3.583276 TTGGGCTGCGTCGTGTAGG 62.583 63.158 0.00 0.00 0.00 3.18
819 851 4.539083 TGTTGGGCTGCGTCGTGT 62.539 61.111 0.00 0.00 0.00 4.49
820 852 3.240606 CTTGTTGGGCTGCGTCGTG 62.241 63.158 0.00 0.00 0.00 4.35
821 853 2.972505 CTTGTTGGGCTGCGTCGT 60.973 61.111 0.00 0.00 0.00 4.34
822 854 4.389576 GCTTGTTGGGCTGCGTCG 62.390 66.667 0.00 0.00 0.00 5.12
828 897 1.768684 TTCTCTCGGCTTGTTGGGCT 61.769 55.000 0.00 0.00 0.00 5.19
920 993 3.787001 GGGGGAGAAGGGAGCACG 61.787 72.222 0.00 0.00 0.00 5.34
957 1030 2.619177 CGAGATGACCGGAGTAACAGAT 59.381 50.000 9.46 0.00 0.00 2.90
1093 1177 3.003763 GGAGTGGAGGAAGGCCGT 61.004 66.667 0.00 0.00 39.96 5.68
1158 1242 3.308014 AAGCAGGCCACGAGAGAGC 62.308 63.158 5.01 0.00 0.00 4.09
1197 1281 0.674895 ACCTGCTTGAATCCTGACGC 60.675 55.000 0.00 0.00 0.00 5.19
1253 1337 3.482783 GAGGCGACGCTGCTGAAC 61.483 66.667 20.77 0.32 34.52 3.18
1314 1398 1.831652 AACCTGTCCTTCCAGAGCCG 61.832 60.000 0.00 0.00 34.23 5.52
1361 1445 4.814771 GGTAAGAACAACGAATCCCCATAG 59.185 45.833 0.00 0.00 0.00 2.23
1391 1480 3.072944 CAGCCTGGAAAAGAAGTCAGAG 58.927 50.000 0.00 0.00 0.00 3.35
1581 1674 8.110860 ACATCTGATTCCACTAAATTCGTTTT 57.889 30.769 0.00 0.00 0.00 2.43
1615 1708 2.054453 GCCATTTGGGAGAGCCACC 61.054 63.158 0.00 0.00 40.01 4.61
1635 1728 0.919710 AGGTAAGCCATCCCAGAACC 59.080 55.000 0.00 0.00 37.19 3.62
1717 1812 3.874392 AGCAACAGGAAATGCATAACC 57.126 42.857 0.00 6.81 44.95 2.85
1718 1813 5.750067 CCATTAGCAACAGGAAATGCATAAC 59.250 40.000 0.00 0.00 44.95 1.89
1742 1837 7.049133 TCTCTCACAGACTAACATAGAGGTAC 58.951 42.308 0.00 0.00 31.91 3.34
1764 1859 3.004944 ACAGAGAACAAACGAGGAGTCTC 59.995 47.826 0.00 0.00 36.69 3.36
1787 1882 9.647797 ACGATCAACATTAGTACAGAAATTACA 57.352 29.630 0.00 0.00 0.00 2.41
1795 1890 8.705134 TGTTGTTAACGATCAACATTAGTACAG 58.295 33.333 0.00 0.00 45.50 2.74
1826 1921 8.593945 TGGAGGCAGAACAGAAATTTAAATAT 57.406 30.769 0.01 0.00 0.00 1.28
1891 1990 3.700538 TGTGCTCCTCTATTTGCCAATT 58.299 40.909 0.00 0.00 0.00 2.32
1892 1991 3.370840 TGTGCTCCTCTATTTGCCAAT 57.629 42.857 0.00 0.00 0.00 3.16
1893 1992 2.877097 TGTGCTCCTCTATTTGCCAA 57.123 45.000 0.00 0.00 0.00 4.52
1894 1993 4.712051 ATATGTGCTCCTCTATTTGCCA 57.288 40.909 0.00 0.00 0.00 4.92
1895 1994 8.970859 ATAATATATGTGCTCCTCTATTTGCC 57.029 34.615 0.00 0.00 0.00 4.52
1896 1995 9.829507 AGATAATATATGTGCTCCTCTATTTGC 57.170 33.333 0.00 0.00 0.00 3.68
1901 2000 9.901172 TTCGTAGATAATATATGTGCTCCTCTA 57.099 33.333 0.00 0.00 35.04 2.43
1902 2001 8.809468 TTCGTAGATAATATATGTGCTCCTCT 57.191 34.615 0.00 0.00 35.04 3.69
1903 2002 8.679100 ACTTCGTAGATAATATATGTGCTCCTC 58.321 37.037 0.00 0.00 35.04 3.71
1904 2003 8.462811 CACTTCGTAGATAATATATGTGCTCCT 58.537 37.037 0.00 0.00 35.04 3.69
1905 2004 8.459635 TCACTTCGTAGATAATATATGTGCTCC 58.540 37.037 0.00 0.00 35.04 4.70
1907 2006 9.794685 CATCACTTCGTAGATAATATATGTGCT 57.205 33.333 0.00 0.00 35.04 4.40
1908 2007 8.535592 GCATCACTTCGTAGATAATATATGTGC 58.464 37.037 0.00 0.00 35.04 4.57
1909 2008 9.573133 TGCATCACTTCGTAGATAATATATGTG 57.427 33.333 0.00 0.00 35.04 3.21
1916 2015 9.547753 ACTTAAATGCATCACTTCGTAGATAAT 57.452 29.630 0.00 0.00 35.04 1.28
1917 2016 8.942338 ACTTAAATGCATCACTTCGTAGATAA 57.058 30.769 0.00 0.00 35.04 1.75
1919 2018 8.942338 TTACTTAAATGCATCACTTCGTAGAT 57.058 30.769 0.00 0.00 35.04 1.98
1920 2019 7.491372 CCTTACTTAAATGCATCACTTCGTAGA 59.509 37.037 0.00 0.00 0.00 2.59
1921 2020 7.491372 TCCTTACTTAAATGCATCACTTCGTAG 59.509 37.037 0.00 0.00 0.00 3.51
1922 2021 7.277098 GTCCTTACTTAAATGCATCACTTCGTA 59.723 37.037 0.00 0.00 0.00 3.43
1923 2022 6.092259 GTCCTTACTTAAATGCATCACTTCGT 59.908 38.462 0.00 0.00 0.00 3.85
1924 2023 6.456988 GGTCCTTACTTAAATGCATCACTTCG 60.457 42.308 0.00 0.00 0.00 3.79
1925 2024 6.599638 AGGTCCTTACTTAAATGCATCACTTC 59.400 38.462 0.00 0.00 0.00 3.01
2094 2228 5.067674 TGGCAATATATTGGTGCAGAAACTC 59.932 40.000 23.57 5.45 40.12 3.01
2328 2463 1.480205 CACAACCTTTTTCAGCAGCG 58.520 50.000 0.00 0.00 0.00 5.18
2367 2502 5.490159 ACATTTGAAATTAAGGTGGCATGG 58.510 37.500 0.00 0.00 0.00 3.66
2583 2719 7.454260 AGATTTGTTAGTTGGTTCAGGATTC 57.546 36.000 0.00 0.00 0.00 2.52
2729 2886 5.762711 TCTCCTCGAAAACAACATTCAATCA 59.237 36.000 0.00 0.00 0.00 2.57
2747 2904 2.952978 TCCTACAGCGAGAAATCTCCTC 59.047 50.000 4.90 0.00 39.79 3.71
2759 2916 1.349627 CGCAGCAAATCCTACAGCG 59.650 57.895 0.00 0.00 37.68 5.18
2773 2950 3.000322 GTCGGATTTCATAAGACACGCAG 60.000 47.826 0.00 0.00 32.57 5.18
2781 2958 8.480643 AACAGAAACTAGTCGGATTTCATAAG 57.519 34.615 0.00 0.00 35.26 1.73
2782 2959 8.311836 AGAACAGAAACTAGTCGGATTTCATAA 58.688 33.333 0.00 0.00 35.26 1.90
2783 2960 7.837863 AGAACAGAAACTAGTCGGATTTCATA 58.162 34.615 0.00 0.00 35.26 2.15
2786 2963 7.291567 CAAAGAACAGAAACTAGTCGGATTTC 58.708 38.462 0.00 0.00 33.40 2.17
2787 2964 6.293462 GCAAAGAACAGAAACTAGTCGGATTT 60.293 38.462 0.00 0.00 0.00 2.17
2797 2974 7.446625 ACTGATTAGATGCAAAGAACAGAAACT 59.553 33.333 13.89 0.00 0.00 2.66
2828 3005 5.695851 ACTCTGAAACACACAAATCCATC 57.304 39.130 0.00 0.00 0.00 3.51
2940 3117 5.762825 AGACATTAATGCTGGCATACTTG 57.237 39.130 15.48 8.70 35.31 3.16
2941 3118 5.887598 TCAAGACATTAATGCTGGCATACTT 59.112 36.000 15.48 5.86 35.31 2.24
2942 3119 5.439721 TCAAGACATTAATGCTGGCATACT 58.560 37.500 15.48 0.00 35.31 2.12
2943 3120 5.756195 TCAAGACATTAATGCTGGCATAC 57.244 39.130 15.48 0.00 35.31 2.39
2974 3172 9.081997 CGGCATCTGCTTGTTTAATTTTAATAA 57.918 29.630 1.70 0.00 41.70 1.40
2975 3173 7.221838 GCGGCATCTGCTTGTTTAATTTTAATA 59.778 33.333 1.70 0.00 41.70 0.98
2976 3174 6.035975 GCGGCATCTGCTTGTTTAATTTTAAT 59.964 34.615 1.70 0.00 41.70 1.40
3001 3199 8.099160 GCAGTTGCTGACAATTAATTGTAGGAG 61.099 40.741 29.07 23.94 43.43 3.69
3227 3438 5.393461 CCACAAAAGCACTGGGAAGATATTC 60.393 44.000 0.00 0.00 0.00 1.75
3487 3712 4.398044 AGCAAGAAGTTTCGAAGAAACCAA 59.602 37.500 18.51 0.00 45.90 3.67
3815 4058 2.286418 GCCGTGCTGCTATTTGACATAC 60.286 50.000 0.00 0.00 0.00 2.39
3818 4061 1.305219 GGCCGTGCTGCTATTTGACA 61.305 55.000 0.00 0.00 0.00 3.58
3856 4099 2.763933 CCTGATTCAGATCCACCATCG 58.236 52.381 15.36 0.00 36.50 3.84
3857 4100 2.158711 TGCCTGATTCAGATCCACCATC 60.159 50.000 15.36 0.00 32.44 3.51
3858 4101 1.848388 TGCCTGATTCAGATCCACCAT 59.152 47.619 15.36 0.00 32.44 3.55
3966 4210 5.511386 ACAAGACCTTTCTCCAGATCATT 57.489 39.130 0.00 0.00 0.00 2.57
4016 4260 8.960591 GGGATTGCTTGCACAAACTATATATAT 58.039 33.333 0.00 0.00 32.27 0.86
4017 4261 8.163408 AGGGATTGCTTGCACAAACTATATATA 58.837 33.333 0.00 0.00 32.27 0.86
4018 4262 7.006509 AGGGATTGCTTGCACAAACTATATAT 58.993 34.615 0.00 0.00 32.27 0.86
4076 4320 6.835914 ACTCGAAAGCAAGTTCAAAGATATG 58.164 36.000 0.00 0.00 0.00 1.78
4094 4338 5.411361 CCTCCACATGACAAATTTACTCGAA 59.589 40.000 0.00 0.00 0.00 3.71
4112 4356 2.027745 TGTGATCTTTGCTCTCCTCCAC 60.028 50.000 0.00 0.00 0.00 4.02
4116 4360 3.181451 TGTTGTGTGATCTTTGCTCTCCT 60.181 43.478 0.00 0.00 0.00 3.69
4203 4447 9.918630 CAATGGAAAGACACATCTTATCTTTTT 57.081 29.630 0.41 0.00 44.82 1.94
4204 4448 9.300681 TCAATGGAAAGACACATCTTATCTTTT 57.699 29.630 0.41 0.00 44.82 2.27
4205 4449 8.868522 TCAATGGAAAGACACATCTTATCTTT 57.131 30.769 0.00 0.00 44.82 2.52
4206 4450 9.118300 GATCAATGGAAAGACACATCTTATCTT 57.882 33.333 0.00 0.00 44.82 2.40
4207 4451 8.492782 AGATCAATGGAAAGACACATCTTATCT 58.507 33.333 0.00 0.00 44.82 1.98
4208 4452 8.674263 AGATCAATGGAAAGACACATCTTATC 57.326 34.615 0.00 0.00 44.82 1.75
4209 4453 8.270030 TGAGATCAATGGAAAGACACATCTTAT 58.730 33.333 0.00 0.00 44.82 1.73
4210 4454 7.623630 TGAGATCAATGGAAAGACACATCTTA 58.376 34.615 0.00 0.00 44.82 2.10
4212 4456 6.058553 TGAGATCAATGGAAAGACACATCT 57.941 37.500 0.00 0.00 36.42 2.90
4213 4457 6.111382 TCTGAGATCAATGGAAAGACACATC 58.889 40.000 0.00 0.00 0.00 3.06
4255 4499 5.972935 TGATTGAATCAAAGCTACTCCGTA 58.027 37.500 5.21 0.00 36.11 4.02
4256 4500 4.832248 TGATTGAATCAAAGCTACTCCGT 58.168 39.130 5.21 0.00 36.11 4.69
4257 4501 5.998454 ATGATTGAATCAAAGCTACTCCG 57.002 39.130 12.36 0.00 43.50 4.63
4258 4502 7.792374 TGTATGATTGAATCAAAGCTACTCC 57.208 36.000 12.36 0.00 43.50 3.85
4260 4504 8.997323 GCTATGTATGATTGAATCAAAGCTACT 58.003 33.333 12.36 0.00 43.50 2.57
4261 4505 8.997323 AGCTATGTATGATTGAATCAAAGCTAC 58.003 33.333 20.54 15.31 43.50 3.58
4324 4568 3.593442 ACACCAACAGGGAGAAATCAA 57.407 42.857 0.00 0.00 41.15 2.57
4454 4698 3.595758 GCGGCACAGCAACAACCT 61.596 61.111 0.00 0.00 37.05 3.50
4458 4702 1.785041 GAAGAAGCGGCACAGCAACA 61.785 55.000 1.45 0.00 40.15 3.33
4492 4736 2.434428 CAGCTTCCTGCATCAGAAACT 58.566 47.619 0.00 0.00 45.94 2.66
4732 4976 7.870509 TGTCTATTCAGCATAGCTTTGATTT 57.129 32.000 8.49 0.00 36.40 2.17
4734 4978 8.461249 AATTGTCTATTCAGCATAGCTTTGAT 57.539 30.769 8.49 0.00 36.40 2.57


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

AutoCloner maintained by Alex Coulton.