Multiple sequence alignment - TraesCS6B01G101700

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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 TraesCS6B01G101700 chr6B 100.000 2405 0 0 1 2405 79856391 79853987 0.000000e+00 4442
1 TraesCS6B01G101700 chr6A 88.352 1614 94 29 816 2405 46702830 46704373 0.000000e+00 1853
2 TraesCS6B01G101700 chr6A 92.893 788 43 8 1 780 616767244 616766462 0.000000e+00 1133
3 TraesCS6B01G101700 chr6A 91.648 455 30 4 213 661 68650800 68650348 7.300000e-175 623
4 TraesCS6B01G101700 chr6A 92.975 242 10 2 4 238 616769082 616768841 1.770000e-91 346
5 TraesCS6B01G101700 chr6A 93.939 198 12 0 1 198 68654332 68654135 1.400000e-77 300
6 TraesCS6B01G101700 chr3D 94.677 789 31 4 1 780 87431025 87431811 0.000000e+00 1214
7 TraesCS6B01G101700 chr3D 93.266 787 40 8 1 780 140056038 140055258 0.000000e+00 1147
8 TraesCS6B01G101700 chr3D 92.653 245 11 2 1 238 87429117 87429361 1.770000e-91 346
9 TraesCS6B01G101700 chr3D 92.245 245 12 2 1 238 140057951 140057707 8.230000e-90 340
10 TraesCS6B01G101700 chr7D 94.409 787 29 6 1 780 310873345 310874123 0.000000e+00 1195
11 TraesCS6B01G101700 chr7D 93.607 610 30 4 1 603 107667467 107666860 0.000000e+00 902
12 TraesCS6B01G101700 chr7D 92.245 245 12 2 1 238 310867894 310868138 8.230000e-90 340
13 TraesCS6B01G101700 chr7D 91.743 109 4 5 669 774 630185501 630185607 1.930000e-31 147
14 TraesCS6B01G101700 chr5B 93.893 786 27 3 1 779 435213675 435214446 0.000000e+00 1166
15 TraesCS6B01G101700 chr7A 93.622 784 29 6 3 779 657582540 657583309 0.000000e+00 1151
16 TraesCS6B01G101700 chr4A 92.893 802 34 3 1 779 712699747 712698946 0.000000e+00 1144
17 TraesCS6B01G101700 chr4A 93.496 246 8 3 1 238 712701656 712701411 2.270000e-95 359
18 TraesCS6B01G101700 chr1D 92.469 810 28 9 1 780 76949703 76950509 0.000000e+00 1127
19 TraesCS6B01G101700 chr1D 93.469 245 9 2 1 238 76947805 76948049 8.180000e-95 357
20 TraesCS6B01G101700 chr2B 86.421 788 79 22 897 1670 154139920 154140693 0.000000e+00 837
21 TraesCS6B01G101700 chr2A 84.766 768 73 26 898 1660 101845352 101846080 0.000000e+00 730
22 TraesCS6B01G101700 chr2D 84.143 782 77 25 898 1670 102801165 102801908 0.000000e+00 713


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 TraesCS6B01G101700 chr6B 79853987 79856391 2404 True 4442.0 4442 100.0000 1 2405 1 chr6B.!!$R1 2404
1 TraesCS6B01G101700 chr6A 46702830 46704373 1543 False 1853.0 1853 88.3520 816 2405 1 chr6A.!!$F1 1589
2 TraesCS6B01G101700 chr6A 616766462 616769082 2620 True 739.5 1133 92.9340 1 780 2 chr6A.!!$R2 779
3 TraesCS6B01G101700 chr6A 68650348 68654332 3984 True 461.5 623 92.7935 1 661 2 chr6A.!!$R1 660
4 TraesCS6B01G101700 chr3D 87429117 87431811 2694 False 780.0 1214 93.6650 1 780 2 chr3D.!!$F1 779
5 TraesCS6B01G101700 chr3D 140055258 140057951 2693 True 743.5 1147 92.7555 1 780 2 chr3D.!!$R1 779
6 TraesCS6B01G101700 chr7D 310873345 310874123 778 False 1195.0 1195 94.4090 1 780 1 chr7D.!!$F2 779
7 TraesCS6B01G101700 chr7D 107666860 107667467 607 True 902.0 902 93.6070 1 603 1 chr7D.!!$R1 602
8 TraesCS6B01G101700 chr5B 435213675 435214446 771 False 1166.0 1166 93.8930 1 779 1 chr5B.!!$F1 778
9 TraesCS6B01G101700 chr7A 657582540 657583309 769 False 1151.0 1151 93.6220 3 779 1 chr7A.!!$F1 776
10 TraesCS6B01G101700 chr4A 712698946 712701656 2710 True 751.5 1144 93.1945 1 779 2 chr4A.!!$R1 778
11 TraesCS6B01G101700 chr1D 76947805 76950509 2704 False 742.0 1127 92.9690 1 780 2 chr1D.!!$F1 779
12 TraesCS6B01G101700 chr2B 154139920 154140693 773 False 837.0 837 86.4210 897 1670 1 chr2B.!!$F1 773
13 TraesCS6B01G101700 chr2A 101845352 101846080 728 False 730.0 730 84.7660 898 1660 1 chr2A.!!$F1 762
14 TraesCS6B01G101700 chr2D 102801165 102801908 743 False 713.0 713 84.1430 898 1670 1 chr2D.!!$F1 772

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
853 10896 0.669625 CCGACCCGTCTTTCAGAACC 60.67 60.0 0.0 0.0 0.0 3.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2020 12101 0.034337 GCCGCCACCCGATCTAAATA 59.966 55.0 0.0 0.0 40.02 1.4 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
105 2020 8.237811 AGAAAAATTGTGAACCTGAGTTGTAT 57.762 30.769 0.00 0.00 35.94 2.29
126 2041 0.787787 TTGTCTGCAACGATGTACGC 59.212 50.000 0.00 0.00 46.94 4.42
130 2045 3.202923 TGCAACGATGTACGCAGAA 57.797 47.368 0.00 0.00 46.94 3.02
153 2068 4.202243 ACGGTTACTGCTACACTTACCAAA 60.202 41.667 0.00 0.00 0.00 3.28
187 5921 6.889301 TGAGAAGCACATTGAGAGATTTTT 57.111 33.333 0.00 0.00 0.00 1.94
242 10223 3.694566 GCTGAAAGGGACCGTAAATTCAT 59.305 43.478 1.34 0.00 0.00 2.57
252 10233 6.019762 GGACCGTAAATTCATCGAGTTTTTC 58.980 40.000 0.00 0.00 0.00 2.29
280 10263 7.967890 ACATAATGATGTCAAAGCGATGATA 57.032 32.000 0.00 0.00 43.01 2.15
281 10264 8.557592 ACATAATGATGTCAAAGCGATGATAT 57.442 30.769 4.21 4.21 43.01 1.63
522 10505 4.729227 AAAACCTTGTTCGTGGACATTT 57.271 36.364 0.00 0.00 0.00 2.32
541 10524 7.414222 ACATTTGAGATGCCTTGTTATCAAT 57.586 32.000 0.00 0.00 32.82 2.57
545 10528 5.614308 TGAGATGCCTTGTTATCAATCGAT 58.386 37.500 0.00 0.00 35.50 3.59
780 10823 1.747355 GCACGGGCACTCTACTAGTAA 59.253 52.381 3.77 0.00 40.72 2.24
781 10824 2.223525 GCACGGGCACTCTACTAGTAAG 60.224 54.545 3.77 7.19 40.72 2.34
782 10825 3.276857 CACGGGCACTCTACTAGTAAGA 58.723 50.000 14.93 9.31 35.76 2.10
783 10826 3.884091 CACGGGCACTCTACTAGTAAGAT 59.116 47.826 14.93 0.00 35.76 2.40
784 10827 4.338682 CACGGGCACTCTACTAGTAAGATT 59.661 45.833 14.93 3.87 35.76 2.40
785 10828 4.954826 ACGGGCACTCTACTAGTAAGATTT 59.045 41.667 14.93 1.04 35.76 2.17
786 10829 6.039047 CACGGGCACTCTACTAGTAAGATTTA 59.961 42.308 14.93 0.00 35.76 1.40
787 10830 6.604795 ACGGGCACTCTACTAGTAAGATTTAA 59.395 38.462 14.93 0.00 35.76 1.52
788 10831 7.140048 CGGGCACTCTACTAGTAAGATTTAAG 58.860 42.308 14.93 0.23 35.76 1.85
789 10832 7.201803 CGGGCACTCTACTAGTAAGATTTAAGT 60.202 40.741 14.93 4.55 35.76 2.24
790 10833 8.476447 GGGCACTCTACTAGTAAGATTTAAGTT 58.524 37.037 14.93 0.00 35.76 2.66
791 10834 9.872721 GGCACTCTACTAGTAAGATTTAAGTTT 57.127 33.333 14.93 0.00 35.76 2.66
811 10854 8.958119 AAGTTTAGACAAATCTAATATGCGGA 57.042 30.769 0.00 0.00 44.99 5.54
812 10855 8.594881 AGTTTAGACAAATCTAATATGCGGAG 57.405 34.615 0.00 0.00 44.99 4.63
813 10856 7.657761 AGTTTAGACAAATCTAATATGCGGAGG 59.342 37.037 0.00 0.00 44.99 4.30
814 10857 4.899502 AGACAAATCTAATATGCGGAGGG 58.100 43.478 0.00 0.00 31.46 4.30
835 10878 4.758674 GGGAGTAAGAAGTGTAAACAACCC 59.241 45.833 0.00 0.00 0.00 4.11
853 10896 0.669625 CCGACCCGTCTTTCAGAACC 60.670 60.000 0.00 0.00 0.00 3.62
893 10936 4.320456 ACAGCGCCCCACTGTGAG 62.320 66.667 9.86 0.00 46.38 3.51
894 10937 4.007644 CAGCGCCCCACTGTGAGA 62.008 66.667 9.86 0.00 0.00 3.27
928 10991 2.507854 CCACACCGGACACACCTCT 61.508 63.158 9.46 0.00 36.56 3.69
929 10992 1.006102 CACACCGGACACACCTCTC 60.006 63.158 9.46 0.00 36.31 3.20
930 10993 1.456892 ACACCGGACACACCTCTCA 60.457 57.895 9.46 0.00 36.31 3.27
931 10994 1.290324 CACCGGACACACCTCTCAG 59.710 63.158 9.46 0.00 36.31 3.35
932 10995 2.262915 CCGGACACACCTCTCAGC 59.737 66.667 0.00 0.00 36.31 4.26
992 11058 2.607750 AAGGAAGAGAGCCCCGCA 60.608 61.111 0.00 0.00 0.00 5.69
1079 11146 1.860078 CCTTCACCAAAGTCGTCGC 59.140 57.895 0.00 0.00 32.69 5.19
1188 11255 2.045926 CCAACCTTCTCCCCGCAG 60.046 66.667 0.00 0.00 0.00 5.18
1202 11270 1.379977 CGCAGGACTACCCTCTCCA 60.380 63.158 0.00 0.00 45.60 3.86
1215 11283 1.228894 TCTCCACTTCGCTCCCAGT 60.229 57.895 0.00 0.00 0.00 4.00
1222 11290 2.849120 CTTCGCTCCCAGTGGCTCAG 62.849 65.000 2.61 0.00 0.00 3.35
1227 11295 0.690411 CTCCCAGTGGCTCAGATCCT 60.690 60.000 2.61 0.00 0.00 3.24
1376 11445 1.823169 TTCTTCCCCAACGAGTCCGG 61.823 60.000 0.00 0.00 40.78 5.14
1381 11450 3.307906 CCAACGAGTCCGGGGTCA 61.308 66.667 0.00 0.00 40.78 4.02
1463 11540 3.368539 CGCTACCGCAAAAGTGTTACATA 59.631 43.478 0.00 0.00 35.30 2.29
1469 11546 6.740110 ACCGCAAAAGTGTTACATATTTTCA 58.260 32.000 7.84 0.00 0.00 2.69
1518 11598 1.457267 ACTTGGTGTGGGCAATGCA 60.457 52.632 7.79 0.00 0.00 3.96
1519 11599 1.047596 ACTTGGTGTGGGCAATGCAA 61.048 50.000 7.79 0.00 0.00 4.08
1561 11641 2.151202 TGTACCTTGCTGCAAACTAGC 58.849 47.619 16.74 6.60 41.49 3.42
1566 11646 0.955428 TTGCTGCAAACTAGCGAGGG 60.955 55.000 13.51 0.00 44.01 4.30
1670 11751 7.117667 GGGAAATGTTGTGTTAACATGGATTTC 59.882 37.037 22.07 22.07 40.43 2.17
1676 11757 6.811253 TGTGTTAACATGGATTTCAGTACC 57.189 37.500 12.26 0.00 0.00 3.34
1696 11777 7.279536 CAGTACCAGTTAACTCTCTATACACGA 59.720 40.741 4.77 0.00 0.00 4.35
1697 11778 7.992033 AGTACCAGTTAACTCTCTATACACGAT 59.008 37.037 4.77 0.00 0.00 3.73
1699 11780 8.064336 ACCAGTTAACTCTCTATACACGATTT 57.936 34.615 4.77 0.00 0.00 2.17
1741 11822 7.068962 TGGGAGGTTGCGATATTCGATATATAA 59.931 37.037 0.32 0.00 43.74 0.98
1750 11831 8.571328 GCGATATTCGATATATAATGCTTCTCG 58.429 37.037 0.32 0.00 43.74 4.04
1770 11851 2.473816 GCATTGTCTTCGATCGATCCA 58.526 47.619 20.18 12.72 0.00 3.41
1780 11861 1.066152 CGATCGATCCAGTCAGCTGAA 59.934 52.381 20.19 2.47 45.28 3.02
1788 11869 4.572985 TCCAGTCAGCTGAATTTTTGTG 57.427 40.909 20.19 3.81 45.28 3.33
1789 11870 3.953612 TCCAGTCAGCTGAATTTTTGTGT 59.046 39.130 20.19 0.00 45.28 3.72
1796 11877 4.869297 CAGCTGAATTTTTGTGTGTTTGGA 59.131 37.500 8.42 0.00 0.00 3.53
1797 11878 5.524646 CAGCTGAATTTTTGTGTGTTTGGAT 59.475 36.000 8.42 0.00 0.00 3.41
1814 11895 2.888414 TGGATTTCCTTCGGTTTGTTCC 59.112 45.455 0.00 0.00 36.82 3.62
1833 11914 0.875059 CGCCTGGTCTGGTTTTCTTC 59.125 55.000 0.00 0.00 0.00 2.87
1834 11915 1.813862 CGCCTGGTCTGGTTTTCTTCA 60.814 52.381 0.00 0.00 0.00 3.02
1835 11916 1.609072 GCCTGGTCTGGTTTTCTTCAC 59.391 52.381 0.00 0.00 0.00 3.18
1838 11919 1.133606 TGGTCTGGTTTTCTTCACCCC 60.134 52.381 0.00 0.00 32.71 4.95
1839 11920 1.235724 GTCTGGTTTTCTTCACCCCG 58.764 55.000 0.00 0.00 32.71 5.73
1841 11922 0.109723 CTGGTTTTCTTCACCCCGGA 59.890 55.000 0.73 0.00 32.71 5.14
1842 11923 0.774908 TGGTTTTCTTCACCCCGGAT 59.225 50.000 0.73 0.00 32.71 4.18
1843 11924 1.173913 GGTTTTCTTCACCCCGGATG 58.826 55.000 0.73 0.00 0.00 3.51
1844 11925 0.526211 GTTTTCTTCACCCCGGATGC 59.474 55.000 0.73 0.00 0.00 3.91
1845 11926 0.111446 TTTTCTTCACCCCGGATGCA 59.889 50.000 0.73 0.00 0.00 3.96
1846 11927 0.608035 TTTCTTCACCCCGGATGCAC 60.608 55.000 0.73 0.00 0.00 4.57
1847 11928 1.773856 TTCTTCACCCCGGATGCACA 61.774 55.000 0.73 0.00 0.00 4.57
1848 11929 1.077501 CTTCACCCCGGATGCACAT 60.078 57.895 0.73 0.00 0.00 3.21
1880 11961 2.429767 GGTACAGGGGAGGCGGTAC 61.430 68.421 0.00 0.00 36.30 3.34
1908 11989 2.171237 TGAGGGGATTACATCTGCACTG 59.829 50.000 0.00 0.00 0.00 3.66
1930 12011 1.289160 TCCCACTATTTCCTGCTGCT 58.711 50.000 0.00 0.00 0.00 4.24
1931 12012 1.210478 TCCCACTATTTCCTGCTGCTC 59.790 52.381 0.00 0.00 0.00 4.26
1932 12013 1.673168 CCACTATTTCCTGCTGCTCC 58.327 55.000 0.00 0.00 0.00 4.70
1933 12014 1.065199 CCACTATTTCCTGCTGCTCCA 60.065 52.381 0.00 0.00 0.00 3.86
1934 12015 2.286872 CACTATTTCCTGCTGCTCCAG 58.713 52.381 0.00 0.00 34.12 3.86
1994 12075 3.195698 GGTGCTGCCCGTCGATTC 61.196 66.667 0.00 0.00 0.00 2.52
1999 12080 1.138036 CTGCCCGTCGATTCACGTA 59.862 57.895 0.00 0.00 43.13 3.57
2017 12098 1.406180 GTAGTCGGCTTCTCTTCCTCC 59.594 57.143 0.00 0.00 0.00 4.30
2020 12101 1.687493 CGGCTTCTCTTCCTCCCCT 60.687 63.158 0.00 0.00 0.00 4.79
2021 12102 0.397254 CGGCTTCTCTTCCTCCCCTA 60.397 60.000 0.00 0.00 0.00 3.53
2037 12118 1.337823 CCCTATTTAGATCGGGTGGCG 60.338 57.143 0.00 0.00 34.34 5.69
2058 12139 2.885644 CCGTCGTTGGCATCGAGG 60.886 66.667 25.50 25.50 41.00 4.63
2078 12159 0.320683 TGGGTGTTGAGCGAGTGATG 60.321 55.000 0.00 0.00 0.00 3.07
2088 12169 0.390340 GCGAGTGATGGCTCTCAACA 60.390 55.000 0.00 0.00 35.01 3.33
2168 12249 2.943033 CACCTCGCGAATTATTTTCCCT 59.057 45.455 11.33 0.00 0.00 4.20
2169 12250 3.002348 CACCTCGCGAATTATTTTCCCTC 59.998 47.826 11.33 0.00 0.00 4.30
2170 12251 3.118371 ACCTCGCGAATTATTTTCCCTCT 60.118 43.478 11.33 0.00 0.00 3.69
2171 12252 3.495001 CCTCGCGAATTATTTTCCCTCTC 59.505 47.826 11.33 0.00 0.00 3.20
2172 12253 4.372656 CTCGCGAATTATTTTCCCTCTCT 58.627 43.478 11.33 0.00 0.00 3.10
2174 12255 5.909477 TCGCGAATTATTTTCCCTCTCTTA 58.091 37.500 6.20 0.00 0.00 2.10
2196 12278 0.829990 AAAGGTGTGCAAGGGGTTTG 59.170 50.000 0.00 0.00 39.88 2.93
2246 12329 6.628919 ACATTAATATGGTTAAAGCCCGTC 57.371 37.500 0.00 0.00 36.01 4.79
2261 12346 1.315497 CCGTCGATGTAATACGAGCG 58.685 55.000 3.52 0.00 38.89 5.03
2267 12352 5.380651 GTCGATGTAATACGAGCGAACTAT 58.619 41.667 0.00 0.00 39.16 2.12
2268 12353 5.850128 GTCGATGTAATACGAGCGAACTATT 59.150 40.000 0.00 0.00 39.16 1.73
2269 12354 7.011773 GTCGATGTAATACGAGCGAACTATTA 58.988 38.462 0.00 0.00 39.16 0.98
2270 12355 7.531871 GTCGATGTAATACGAGCGAACTATTAA 59.468 37.037 0.00 0.00 39.16 1.40
2271 12356 7.531871 TCGATGTAATACGAGCGAACTATTAAC 59.468 37.037 0.00 0.00 34.49 2.01
2272 12357 7.533222 CGATGTAATACGAGCGAACTATTAACT 59.467 37.037 0.00 0.00 0.00 2.24
2273 12358 9.178427 GATGTAATACGAGCGAACTATTAACTT 57.822 33.333 0.00 0.00 0.00 2.66
2274 12359 8.915871 TGTAATACGAGCGAACTATTAACTTT 57.084 30.769 0.00 0.00 0.00 2.66
2275 12360 8.800972 TGTAATACGAGCGAACTATTAACTTTG 58.199 33.333 0.00 0.00 0.00 2.77
2276 12361 7.823149 AATACGAGCGAACTATTAACTTTGT 57.177 32.000 0.00 0.00 0.00 2.83
2277 12362 5.758570 ACGAGCGAACTATTAACTTTGTC 57.241 39.130 0.00 0.00 0.00 3.18
2278 12363 5.224888 ACGAGCGAACTATTAACTTTGTCA 58.775 37.500 0.00 0.00 0.00 3.58
2279 12364 5.867716 ACGAGCGAACTATTAACTTTGTCAT 59.132 36.000 0.00 0.00 0.00 3.06
2280 12365 6.034683 ACGAGCGAACTATTAACTTTGTCATC 59.965 38.462 0.00 0.00 0.00 2.92
2281 12366 6.508088 CGAGCGAACTATTAACTTTGTCATCC 60.508 42.308 0.00 0.00 0.00 3.51
2282 12367 6.170506 AGCGAACTATTAACTTTGTCATCCA 58.829 36.000 0.00 0.00 0.00 3.41
2283 12368 6.092259 AGCGAACTATTAACTTTGTCATCCAC 59.908 38.462 0.00 0.00 0.00 4.02
2284 12369 6.128391 GCGAACTATTAACTTTGTCATCCACA 60.128 38.462 0.00 0.00 0.00 4.17
2285 12370 7.414098 GCGAACTATTAACTTTGTCATCCACAT 60.414 37.037 0.00 0.00 33.90 3.21
2286 12371 8.450964 CGAACTATTAACTTTGTCATCCACATT 58.549 33.333 0.00 0.00 33.90 2.71
2289 12374 9.520515 ACTATTAACTTTGTCATCCACATTTCT 57.479 29.630 0.00 0.00 33.90 2.52
2338 12423 0.618458 TCAGAAGACCCCCATTTCGG 59.382 55.000 0.00 0.00 0.00 4.30
2377 12462 3.349927 TGGCTGAATCTCACCAATTCTG 58.650 45.455 0.00 0.00 34.80 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
105 2020 2.349060 GCGTACATCGTTGCAGACAAAA 60.349 45.455 0.00 0.00 42.13 2.44
126 2041 3.299340 AGTGTAGCAGTAACCGTTCTG 57.701 47.619 0.00 0.00 35.12 3.02
130 2045 2.892852 TGGTAAGTGTAGCAGTAACCGT 59.107 45.455 0.00 0.00 32.81 4.83
153 2068 6.604396 TCAATGTGCTTCTCAATATCATTGGT 59.396 34.615 12.69 0.00 40.17 3.67
187 5921 3.955145 ACGGCATGTGATTTCTGGA 57.045 47.368 0.00 0.00 0.00 3.86
211 10185 0.108585 TCCCTTTCAGCAACTTCGCT 59.891 50.000 0.00 0.00 45.21 4.93
242 10223 7.870826 ACATCATTATGTTGTGAAAAACTCGA 58.129 30.769 7.97 0.00 44.07 4.04
252 10233 5.630061 TCGCTTTGACATCATTATGTTGTG 58.370 37.500 12.91 4.07 46.49 3.33
468 10451 5.050295 CAGACATGATTGATTCGATGACTGG 60.050 44.000 0.00 0.00 35.18 4.00
522 10505 5.022282 TCGATTGATAACAAGGCATCTCA 57.978 39.130 0.00 0.00 39.46 3.27
541 10524 6.522625 TCAAAAGGCATTCCAAATTATCGA 57.477 33.333 0.00 0.00 33.74 3.59
545 10528 8.373981 TCATCTTTCAAAAGGCATTCCAAATTA 58.626 29.630 2.83 0.00 36.67 1.40
677 10720 7.704899 CACCATCGTGTAAGAACATATCACTTA 59.295 37.037 0.00 0.00 38.08 2.24
786 10829 8.958119 TCCGCATATTAGATTTGTCTAAACTT 57.042 30.769 2.39 0.00 36.02 2.66
787 10830 7.657761 CCTCCGCATATTAGATTTGTCTAAACT 59.342 37.037 2.39 0.00 36.02 2.66
788 10831 7.095187 CCCTCCGCATATTAGATTTGTCTAAAC 60.095 40.741 2.39 0.00 36.02 2.01
789 10832 6.934645 CCCTCCGCATATTAGATTTGTCTAAA 59.065 38.462 2.39 0.00 36.02 1.85
790 10833 6.269077 TCCCTCCGCATATTAGATTTGTCTAA 59.731 38.462 0.86 0.86 36.73 2.10
791 10834 5.778241 TCCCTCCGCATATTAGATTTGTCTA 59.222 40.000 0.00 0.00 0.00 2.59
792 10835 4.593206 TCCCTCCGCATATTAGATTTGTCT 59.407 41.667 0.00 0.00 0.00 3.41
793 10836 4.894784 TCCCTCCGCATATTAGATTTGTC 58.105 43.478 0.00 0.00 0.00 3.18
794 10837 4.348168 ACTCCCTCCGCATATTAGATTTGT 59.652 41.667 0.00 0.00 0.00 2.83
795 10838 4.899502 ACTCCCTCCGCATATTAGATTTG 58.100 43.478 0.00 0.00 0.00 2.32
796 10839 6.497259 TCTTACTCCCTCCGCATATTAGATTT 59.503 38.462 0.00 0.00 0.00 2.17
797 10840 6.017192 TCTTACTCCCTCCGCATATTAGATT 58.983 40.000 0.00 0.00 0.00 2.40
798 10841 5.580998 TCTTACTCCCTCCGCATATTAGAT 58.419 41.667 0.00 0.00 0.00 1.98
799 10842 4.994282 TCTTACTCCCTCCGCATATTAGA 58.006 43.478 0.00 0.00 0.00 2.10
800 10843 5.244178 ACTTCTTACTCCCTCCGCATATTAG 59.756 44.000 0.00 0.00 0.00 1.73
801 10844 5.010719 CACTTCTTACTCCCTCCGCATATTA 59.989 44.000 0.00 0.00 0.00 0.98
802 10845 3.967987 ACTTCTTACTCCCTCCGCATATT 59.032 43.478 0.00 0.00 0.00 1.28
803 10846 3.322254 CACTTCTTACTCCCTCCGCATAT 59.678 47.826 0.00 0.00 0.00 1.78
804 10847 2.693591 CACTTCTTACTCCCTCCGCATA 59.306 50.000 0.00 0.00 0.00 3.14
805 10848 1.482593 CACTTCTTACTCCCTCCGCAT 59.517 52.381 0.00 0.00 0.00 4.73
806 10849 0.895530 CACTTCTTACTCCCTCCGCA 59.104 55.000 0.00 0.00 0.00 5.69
807 10850 0.896226 ACACTTCTTACTCCCTCCGC 59.104 55.000 0.00 0.00 0.00 5.54
808 10851 4.021719 TGTTTACACTTCTTACTCCCTCCG 60.022 45.833 0.00 0.00 0.00 4.63
809 10852 5.479124 TGTTTACACTTCTTACTCCCTCC 57.521 43.478 0.00 0.00 0.00 4.30
810 10853 5.699915 GGTTGTTTACACTTCTTACTCCCTC 59.300 44.000 0.00 0.00 0.00 4.30
811 10854 5.455755 GGGTTGTTTACACTTCTTACTCCCT 60.456 44.000 0.00 0.00 0.00 4.20
812 10855 4.758674 GGGTTGTTTACACTTCTTACTCCC 59.241 45.833 0.00 0.00 0.00 4.30
813 10856 4.450080 CGGGTTGTTTACACTTCTTACTCC 59.550 45.833 0.00 0.00 0.00 3.85
814 10857 5.176406 GTCGGGTTGTTTACACTTCTTACTC 59.824 44.000 0.00 0.00 0.00 2.59
883 10926 1.001406 GGTTCTCAGTCTCACAGTGGG 59.999 57.143 0.00 0.00 0.00 4.61
886 10929 0.962489 CGGGTTCTCAGTCTCACAGT 59.038 55.000 0.00 0.00 0.00 3.55
887 10930 1.201181 CTCGGGTTCTCAGTCTCACAG 59.799 57.143 0.00 0.00 0.00 3.66
888 10931 1.202891 TCTCGGGTTCTCAGTCTCACA 60.203 52.381 0.00 0.00 0.00 3.58
889 10932 1.535833 TCTCGGGTTCTCAGTCTCAC 58.464 55.000 0.00 0.00 0.00 3.51
890 10933 1.887198 GTTCTCGGGTTCTCAGTCTCA 59.113 52.381 0.00 0.00 0.00 3.27
891 10934 1.202817 GGTTCTCGGGTTCTCAGTCTC 59.797 57.143 0.00 0.00 0.00 3.36
892 10935 1.258676 GGTTCTCGGGTTCTCAGTCT 58.741 55.000 0.00 0.00 0.00 3.24
893 10936 0.966920 TGGTTCTCGGGTTCTCAGTC 59.033 55.000 0.00 0.00 0.00 3.51
894 10937 0.680061 GTGGTTCTCGGGTTCTCAGT 59.320 55.000 0.00 0.00 0.00 3.41
928 10991 2.819984 GATTTGGTCGCTGGGGCTGA 62.820 60.000 0.00 0.00 36.09 4.26
929 10992 2.361610 ATTTGGTCGCTGGGGCTG 60.362 61.111 0.00 0.00 36.09 4.85
930 10993 2.044946 GATTTGGTCGCTGGGGCT 60.045 61.111 0.00 0.00 36.09 5.19
931 10994 3.140814 GGATTTGGTCGCTGGGGC 61.141 66.667 0.00 0.00 0.00 5.80
932 10995 2.824041 CGGATTTGGTCGCTGGGG 60.824 66.667 0.00 0.00 0.00 4.96
963 11029 4.404098 TTCCTTCCTTCCGGCGGC 62.404 66.667 23.83 0.00 0.00 6.53
964 11030 2.125106 CTTCCTTCCTTCCGGCGG 60.125 66.667 22.51 22.51 0.00 6.13
1079 11146 1.009389 GTCGAGCGTGGAGAAGTTGG 61.009 60.000 0.00 0.00 0.00 3.77
1188 11255 1.104630 CGAAGTGGAGAGGGTAGTCC 58.895 60.000 0.00 0.00 0.00 3.85
1194 11261 2.726351 GGGAGCGAAGTGGAGAGGG 61.726 68.421 0.00 0.00 0.00 4.30
1202 11270 2.925170 AGCCACTGGGAGCGAAGT 60.925 61.111 0.00 0.00 35.59 3.01
1215 11283 0.753479 GAGGACGAGGATCTGAGCCA 60.753 60.000 15.24 0.00 0.00 4.75
1222 11290 3.967335 CGCCCGAGGACGAGGATC 61.967 72.222 0.00 0.00 42.66 3.36
1306 11375 0.035820 GCGTACATGAACCCTCCCAA 60.036 55.000 0.00 0.00 0.00 4.12
1376 11445 1.074872 GTACTTGTAGCGCGTGACCC 61.075 60.000 8.43 0.00 0.00 4.46
1381 11450 0.038526 AGCTTGTACTTGTAGCGCGT 60.039 50.000 8.43 0.00 39.82 6.01
1409 11478 0.540830 ATGGCGCCTCCTCCTACTAG 60.541 60.000 29.70 0.00 35.26 2.57
1410 11479 0.105658 AATGGCGCCTCCTCCTACTA 60.106 55.000 29.70 2.45 35.26 1.82
1411 11480 0.983378 AAATGGCGCCTCCTCCTACT 60.983 55.000 29.70 0.00 35.26 2.57
1412 11481 0.533085 GAAATGGCGCCTCCTCCTAC 60.533 60.000 29.70 7.11 35.26 3.18
1413 11482 0.691078 AGAAATGGCGCCTCCTCCTA 60.691 55.000 29.70 5.17 35.26 2.94
1414 11483 1.977293 GAGAAATGGCGCCTCCTCCT 61.977 60.000 29.70 17.48 35.26 3.69
1415 11484 1.524849 GAGAAATGGCGCCTCCTCC 60.525 63.158 29.70 12.84 35.26 4.30
1416 11485 1.524849 GGAGAAATGGCGCCTCCTC 60.525 63.158 29.70 24.42 42.36 3.71
1518 11598 7.734942 ACAACAATTATTCAACCAAGACCATT 58.265 30.769 0.00 0.00 0.00 3.16
1519 11599 7.301868 ACAACAATTATTCAACCAAGACCAT 57.698 32.000 0.00 0.00 0.00 3.55
1561 11641 5.954296 AAAATCATAGCATGAATCCCTCG 57.046 39.130 0.00 0.00 43.50 4.63
1566 11646 8.304202 AGACGAGTAAAATCATAGCATGAATC 57.696 34.615 0.00 0.00 43.50 2.52
1670 11751 7.279536 TCGTGTATAGAGAGTTAACTGGTACTG 59.720 40.741 14.14 6.08 0.00 2.74
1706 11787 1.386533 GCAACCTCCCAGATCACATG 58.613 55.000 0.00 0.00 0.00 3.21
1707 11788 0.107508 CGCAACCTCCCAGATCACAT 60.108 55.000 0.00 0.00 0.00 3.21
1708 11789 1.191489 TCGCAACCTCCCAGATCACA 61.191 55.000 0.00 0.00 0.00 3.58
1709 11790 0.179000 ATCGCAACCTCCCAGATCAC 59.821 55.000 0.00 0.00 0.00 3.06
1710 11791 1.788229 TATCGCAACCTCCCAGATCA 58.212 50.000 0.00 0.00 0.00 2.92
1721 11802 9.784824 GAAGCATTATATATCGAATATCGCAAC 57.215 33.333 0.00 0.00 40.21 4.17
1750 11831 2.473816 TGGATCGATCGAAGACAATGC 58.526 47.619 23.50 10.29 42.51 3.56
1770 11851 4.989279 ACACACAAAAATTCAGCTGACT 57.011 36.364 18.03 8.67 0.00 3.41
1780 11861 6.257630 CGAAGGAAATCCAAACACACAAAAAT 59.742 34.615 1.67 0.00 38.89 1.82
1814 11895 0.875059 GAAGAAAACCAGACCAGGCG 59.125 55.000 0.00 0.00 0.00 5.52
1816 11897 2.230660 GGTGAAGAAAACCAGACCAGG 58.769 52.381 0.00 0.00 37.65 4.45
1833 11914 3.067480 GCAATGTGCATCCGGGGTG 62.067 63.158 1.94 1.94 44.26 4.61
1834 11915 2.755469 GCAATGTGCATCCGGGGT 60.755 61.111 0.00 0.00 44.26 4.95
1835 11916 3.891400 CGCAATGTGCATCCGGGG 61.891 66.667 0.00 0.00 45.36 5.73
1843 11924 2.177531 CCTCACTGCGCAATGTGC 59.822 61.111 19.38 12.40 40.69 4.57
1844 11925 2.177531 GCCTCACTGCGCAATGTG 59.822 61.111 19.38 19.97 35.68 3.21
1852 11933 2.125512 CCTGTACCGCCTCACTGC 60.126 66.667 0.00 0.00 0.00 4.40
1863 11944 2.429767 GGTACCGCCTCCCCTGTAC 61.430 68.421 0.00 0.00 34.28 2.90
1880 11961 0.689745 TGTAATCCCCTCACCCTCGG 60.690 60.000 0.00 0.00 0.00 4.63
1908 11989 2.019984 CAGCAGGAAATAGTGGGAAGC 58.980 52.381 0.00 0.00 0.00 3.86
1930 12011 1.001633 GAAGTAGCACGAAACCCTGGA 59.998 52.381 0.00 0.00 0.00 3.86
1931 12012 1.439679 GAAGTAGCACGAAACCCTGG 58.560 55.000 0.00 0.00 0.00 4.45
1932 12013 1.439679 GGAAGTAGCACGAAACCCTG 58.560 55.000 0.00 0.00 0.00 4.45
1933 12014 0.323957 GGGAAGTAGCACGAAACCCT 59.676 55.000 0.00 0.00 33.79 4.34
1934 12015 0.675837 GGGGAAGTAGCACGAAACCC 60.676 60.000 0.00 0.00 35.60 4.11
1935 12016 1.017701 CGGGGAAGTAGCACGAAACC 61.018 60.000 0.00 0.00 0.00 3.27
1936 12017 1.017701 CCGGGGAAGTAGCACGAAAC 61.018 60.000 0.00 0.00 0.00 2.78
1994 12075 1.467713 GGAAGAGAAGCCGACTACGTG 60.468 57.143 0.00 0.00 37.88 4.49
1999 12080 0.973496 GGGAGGAAGAGAAGCCGACT 60.973 60.000 0.00 0.00 0.00 4.18
2020 12101 0.034337 GCCGCCACCCGATCTAAATA 59.966 55.000 0.00 0.00 40.02 1.40
2021 12102 1.227853 GCCGCCACCCGATCTAAAT 60.228 57.895 0.00 0.00 40.02 1.40
2043 12124 2.100631 CCACCTCGATGCCAACGAC 61.101 63.158 0.00 0.00 35.88 4.34
2047 12128 2.063015 AACACCCACCTCGATGCCAA 62.063 55.000 0.00 0.00 0.00 4.52
2058 12139 0.320771 ATCACTCGCTCAACACCCAC 60.321 55.000 0.00 0.00 0.00 4.61
2088 12169 4.217159 GGCGAATACGGGAGGCGT 62.217 66.667 0.00 0.00 40.15 5.68
2103 12184 4.133796 GGGCTTGTTGGCATCGGC 62.134 66.667 0.00 0.00 43.83 5.54
2234 12317 4.085415 CGTATTACATCGACGGGCTTTAAC 60.085 45.833 0.00 0.00 33.01 2.01
2243 12326 2.289890 TCGCTCGTATTACATCGACG 57.710 50.000 0.00 0.00 37.93 5.12
2246 12329 7.533222 AGTTAATAGTTCGCTCGTATTACATCG 59.467 37.037 0.00 0.00 0.00 3.84
2269 12354 8.912988 TCTAAAAGAAATGTGGATGACAAAGTT 58.087 29.630 0.00 0.00 38.36 2.66
2270 12355 8.463930 TCTAAAAGAAATGTGGATGACAAAGT 57.536 30.769 0.00 0.00 38.36 2.66
2271 12356 8.786898 TCTCTAAAAGAAATGTGGATGACAAAG 58.213 33.333 0.00 0.00 38.36 2.77
2272 12357 8.690203 TCTCTAAAAGAAATGTGGATGACAAA 57.310 30.769 0.00 0.00 38.36 2.83
2273 12358 7.939039 ACTCTCTAAAAGAAATGTGGATGACAA 59.061 33.333 0.00 0.00 33.63 3.18
2274 12359 7.453393 ACTCTCTAAAAGAAATGTGGATGACA 58.547 34.615 0.00 0.00 34.18 3.58
2275 12360 7.913674 ACTCTCTAAAAGAAATGTGGATGAC 57.086 36.000 0.00 0.00 32.23 3.06
2276 12361 8.156820 TCAACTCTCTAAAAGAAATGTGGATGA 58.843 33.333 0.00 0.00 32.23 2.92
2277 12362 8.233190 GTCAACTCTCTAAAAGAAATGTGGATG 58.767 37.037 0.00 0.00 32.23 3.51
2278 12363 7.939039 TGTCAACTCTCTAAAAGAAATGTGGAT 59.061 33.333 0.00 0.00 32.23 3.41
2279 12364 7.279615 TGTCAACTCTCTAAAAGAAATGTGGA 58.720 34.615 0.00 0.00 32.23 4.02
2280 12365 7.496529 TGTCAACTCTCTAAAAGAAATGTGG 57.503 36.000 0.00 0.00 32.23 4.17
2281 12366 8.997323 AGATGTCAACTCTCTAAAAGAAATGTG 58.003 33.333 0.00 0.00 32.23 3.21
2282 12367 8.997323 CAGATGTCAACTCTCTAAAAGAAATGT 58.003 33.333 0.00 0.00 32.23 2.71
2283 12368 9.212641 TCAGATGTCAACTCTCTAAAAGAAATG 57.787 33.333 0.00 0.00 32.23 2.32
2284 12369 9.434420 CTCAGATGTCAACTCTCTAAAAGAAAT 57.566 33.333 0.00 0.00 32.23 2.17
2285 12370 8.424918 ACTCAGATGTCAACTCTCTAAAAGAAA 58.575 33.333 0.00 0.00 32.23 2.52
2286 12371 7.957002 ACTCAGATGTCAACTCTCTAAAAGAA 58.043 34.615 0.00 0.00 32.23 2.52
2287 12372 7.531857 ACTCAGATGTCAACTCTCTAAAAGA 57.468 36.000 0.00 0.00 0.00 2.52
2288 12373 9.134734 GTAACTCAGATGTCAACTCTCTAAAAG 57.865 37.037 0.00 0.00 0.00 2.27
2289 12374 8.638873 TGTAACTCAGATGTCAACTCTCTAAAA 58.361 33.333 0.00 0.00 0.00 1.52
2290 12375 8.178313 TGTAACTCAGATGTCAACTCTCTAAA 57.822 34.615 0.00 0.00 0.00 1.85
2338 12423 5.057149 CAGCCATAATAAGGTGTACCAGTC 58.943 45.833 3.56 0.00 38.89 3.51
2377 12462 0.396974 TTATGCTCCCCAATGTGGCC 60.397 55.000 0.00 0.00 35.79 5.36


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

AutoCloner maintained by Alex Coulton.