Multiple sequence alignment - TraesCS2D01G255600

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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 TraesCS2D01G255600 chr2D 100.000 5968 0 0 1 5968 308485805 308479838 0.000000e+00 11021
1 TraesCS2D01G255600 chr2B 96.777 3258 72 18 2011 5262 359613779 359617009 0.000000e+00 5404
2 TraesCS2D01G255600 chr2B 94.525 1936 66 15 1 1921 359611869 359613779 0.000000e+00 2952
3 TraesCS2D01G255600 chr2B 90.756 714 48 13 5262 5968 359618862 359619564 0.000000e+00 937
4 TraesCS2D01G255600 chr2A 93.525 2811 106 30 3181 5968 389441084 389438327 0.000000e+00 4113
5 TraesCS2D01G255600 chr2A 94.525 1717 42 9 1 1687 389444301 389442607 0.000000e+00 2603
6 TraesCS2D01G255600 chr2A 91.950 1441 51 11 1754 3188 389442565 389441184 0.000000e+00 1958
7 TraesCS2D01G255600 chr2A 87.764 237 17 3 2983 3207 466393264 466393028 3.550000e-67 267
8 TraesCS2D01G255600 chr4D 90.222 225 19 3 3258 3481 123581342 123581120 2.100000e-74 291
9 TraesCS2D01G255600 chr5A 87.209 258 24 4 3258 3509 300051329 300051075 9.790000e-73 285
10 TraesCS2D01G255600 chr7B 89.130 230 19 2 3258 3481 743069070 743068841 1.270000e-71 281
11 TraesCS2D01G255600 chr7B 87.243 243 19 3 2977 3207 743110318 743110560 3.550000e-67 267
12 TraesCS2D01G255600 chr7A 89.130 230 19 2 3258 3481 120923078 120923307 1.270000e-71 281
13 TraesCS2D01G255600 chr7A 88.559 236 15 3 2984 3207 120825736 120825971 5.890000e-70 276
14 TraesCS2D01G255600 chr6B 89.130 230 19 3 3258 3481 388218747 388218518 1.270000e-71 281
15 TraesCS2D01G255600 chr5B 89.130 230 19 2 3258 3481 713043449 713043678 1.270000e-71 281
16 TraesCS2D01G255600 chr5B 87.654 243 18 3 2977 3207 713043089 713043331 7.620000e-69 272
17 TraesCS2D01G255600 chr4A 89.130 230 19 2 3258 3481 67552145 67552374 1.270000e-71 281
18 TraesCS2D01G255600 chr7D 88.136 236 16 3 2984 3207 307061784 307062019 2.740000e-68 270
19 TraesCS2D01G255600 chr1B 88.412 233 15 3 2987 3207 339007228 339006996 2.740000e-68 270
20 TraesCS2D01G255600 chr1A 88.136 236 16 3 2984 3207 334073810 334074045 2.740000e-68 270


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 TraesCS2D01G255600 chr2D 308479838 308485805 5967 True 11021.000000 11021 100.000000 1 5968 1 chr2D.!!$R1 5967
1 TraesCS2D01G255600 chr2B 359611869 359619564 7695 False 3097.666667 5404 94.019333 1 5968 3 chr2B.!!$F1 5967
2 TraesCS2D01G255600 chr2A 389438327 389444301 5974 True 2891.333333 4113 93.333333 1 5968 3 chr2A.!!$R2 5967
3 TraesCS2D01G255600 chr5B 713043089 713043678 589 False 276.500000 281 88.392000 2977 3481 2 chr5B.!!$F1 504

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
373 374 1.605058 GCAGAGGCTCGGTTAGGTCA 61.605 60.000 15.97 0.0 36.96 4.02 F
1635 1667 0.806868 CCGAGCACATGAACTGCAAT 59.193 50.000 9.21 0.0 37.08 3.56 F
1985 2034 1.051008 TCTTGCTGGACTTGAGCTGA 58.949 50.000 0.00 0.0 37.35 4.26 F
2514 2563 1.197036 TGAGTTAGAGACACGAGTGCG 59.803 52.381 2.76 0.0 44.79 5.34 F
4151 4394 3.889227 GCAGTCGGCAATGTGCTA 58.111 55.556 0.00 0.0 44.28 3.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1665 1697 2.111756 GCTTTTGCTCACACAAGAACG 58.888 47.619 0.00 0.0 43.35 3.95 R
2625 2674 2.035193 TGGAGCAAAACTTAATGCGCAA 59.965 40.909 17.11 0.0 46.98 4.85 R
3404 3640 2.069273 CTTCTACAAACAGGAGCCACG 58.931 52.381 0.00 0.0 0.00 4.94 R
4470 4717 1.327690 GGTAGATGCCCAGTGACCGA 61.328 60.000 0.00 0.0 0.00 4.69 R
5629 7734 0.616891 GTGTCCGGACATTTAGGGGT 59.383 55.000 38.11 0.0 43.97 4.95 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
287 288 2.119009 CGGAGCTCATGGCAGTCTA 58.881 57.895 17.19 0.00 44.79 2.59
303 304 3.999663 CAGTCTACTTTTCTTCAGGGCAG 59.000 47.826 0.00 0.00 0.00 4.85
364 365 2.236382 GCTTGATCGCAGAGGCTCG 61.236 63.158 9.22 5.44 43.63 5.03
373 374 1.605058 GCAGAGGCTCGGTTAGGTCA 61.605 60.000 15.97 0.00 36.96 4.02
494 495 7.984617 AGAGAAAAGAGAAGATTTTATCCGGAG 59.015 37.037 11.34 0.00 38.17 4.63
505 506 7.394816 AGATTTTATCCGGAGTTTCTTTCAGA 58.605 34.615 11.34 0.00 0.00 3.27
587 588 4.318332 CTCAAGGTCAGAAGTGTGCATAA 58.682 43.478 0.00 0.00 0.00 1.90
879 882 2.631267 CAGTTTGCCTTGCCTTGTTTT 58.369 42.857 0.00 0.00 0.00 2.43
899 902 6.655003 TGTTTTTCTCTCTCTCTCTCTCTCTC 59.345 42.308 0.00 0.00 0.00 3.20
900 903 6.627087 TTTTCTCTCTCTCTCTCTCTCTCT 57.373 41.667 0.00 0.00 0.00 3.10
901 904 5.860941 TTCTCTCTCTCTCTCTCTCTCTC 57.139 47.826 0.00 0.00 0.00 3.20
904 907 5.362143 TCTCTCTCTCTCTCTCTCTCTCAAG 59.638 48.000 0.00 0.00 0.00 3.02
920 923 3.813166 TCTCAAGAAAAGCAGTTAACCCG 59.187 43.478 0.88 0.00 0.00 5.28
930 933 2.857104 GCAGTTAACCCGCAAACAGTTC 60.857 50.000 11.66 0.00 0.00 3.01
933 936 3.444388 AGTTAACCCGCAAACAGTTCAAA 59.556 39.130 0.88 0.00 0.00 2.69
934 937 4.082136 AGTTAACCCGCAAACAGTTCAAAA 60.082 37.500 0.88 0.00 0.00 2.44
935 938 3.320673 AACCCGCAAACAGTTCAAAAA 57.679 38.095 0.00 0.00 0.00 1.94
1041 1044 1.145598 CTCTCACATCCGCCTGCAT 59.854 57.895 0.00 0.00 0.00 3.96
1140 1143 3.785122 GAACCCCGCCACAACCACT 62.785 63.158 0.00 0.00 0.00 4.00
1190 1193 1.383248 CATCCCCTTCCCTCCTCGT 60.383 63.158 0.00 0.00 0.00 4.18
1617 1649 9.490379 TCTTCTGTTTATTTCTTCTCAAGTACC 57.510 33.333 0.00 0.00 0.00 3.34
1619 1651 7.663827 TCTGTTTATTTCTTCTCAAGTACCGA 58.336 34.615 0.00 0.00 0.00 4.69
1635 1667 0.806868 CCGAGCACATGAACTGCAAT 59.193 50.000 9.21 0.00 37.08 3.56
1665 1697 7.162708 GCAATTACGAGACTCGAATGAAATTTC 59.837 37.037 30.56 11.41 43.74 2.17
1669 1701 5.164080 ACGAGACTCGAATGAAATTTCGTTC 60.164 40.000 30.73 30.73 46.50 3.95
1684 1716 3.673746 TCGTTCTTGTGTGAGCAAAAG 57.326 42.857 0.00 0.00 40.47 2.27
1687 1719 3.111098 GTTCTTGTGTGAGCAAAAGCTG 58.889 45.455 0.00 0.00 39.28 4.24
1709 1749 4.756642 TGCAGGAGTTGTCATTTAACAGAG 59.243 41.667 0.00 0.00 0.00 3.35
1744 1790 9.566432 AAATCATATTCTAAGTTGGTCCATCTC 57.434 33.333 2.83 0.00 0.00 2.75
1820 1866 8.259411 TGCATATTTTGTTAGGCTTGAAATGAT 58.741 29.630 0.00 0.00 30.51 2.45
1830 1876 2.620585 GCTTGAAATGATAGTGCCCTCC 59.379 50.000 0.00 0.00 0.00 4.30
1912 1958 8.594687 GTTCCATTGTGATTATTTTCCAATTCG 58.405 33.333 0.00 0.00 0.00 3.34
1936 1982 3.406764 CTGTTTAACCTCAGCAAGCTCT 58.593 45.455 0.00 0.00 0.00 4.09
1937 1983 3.817647 CTGTTTAACCTCAGCAAGCTCTT 59.182 43.478 0.00 0.00 0.00 2.85
1975 2024 8.862325 TTTTCAGTTCTATTTATCTTGCTGGA 57.138 30.769 0.00 0.00 0.00 3.86
1976 2025 7.849804 TTCAGTTCTATTTATCTTGCTGGAC 57.150 36.000 0.00 0.00 0.00 4.02
1977 2026 7.187824 TCAGTTCTATTTATCTTGCTGGACT 57.812 36.000 0.00 0.00 0.00 3.85
1978 2027 7.624549 TCAGTTCTATTTATCTTGCTGGACTT 58.375 34.615 0.00 0.00 0.00 3.01
1979 2028 7.550551 TCAGTTCTATTTATCTTGCTGGACTTG 59.449 37.037 0.00 0.00 0.00 3.16
1980 2029 7.550551 CAGTTCTATTTATCTTGCTGGACTTGA 59.449 37.037 0.00 0.00 0.00 3.02
1981 2030 7.768120 AGTTCTATTTATCTTGCTGGACTTGAG 59.232 37.037 0.00 0.00 0.00 3.02
1982 2031 6.051717 TCTATTTATCTTGCTGGACTTGAGC 58.948 40.000 0.00 0.00 36.95 4.26
1983 2032 3.988976 TTATCTTGCTGGACTTGAGCT 57.011 42.857 0.00 0.00 37.35 4.09
1984 2033 2.110901 ATCTTGCTGGACTTGAGCTG 57.889 50.000 0.00 0.00 37.35 4.24
1985 2034 1.051008 TCTTGCTGGACTTGAGCTGA 58.949 50.000 0.00 0.00 37.35 4.26
1986 2035 1.627329 TCTTGCTGGACTTGAGCTGAT 59.373 47.619 0.00 0.00 37.35 2.90
1987 2036 2.039480 TCTTGCTGGACTTGAGCTGATT 59.961 45.455 0.00 0.00 37.35 2.57
1988 2037 1.817357 TGCTGGACTTGAGCTGATTG 58.183 50.000 0.00 0.00 37.35 2.67
1989 2038 1.348696 TGCTGGACTTGAGCTGATTGA 59.651 47.619 0.00 0.00 37.35 2.57
1990 2039 2.026542 TGCTGGACTTGAGCTGATTGAT 60.027 45.455 0.00 0.00 37.35 2.57
1991 2040 3.015327 GCTGGACTTGAGCTGATTGATT 58.985 45.455 0.00 0.00 33.37 2.57
1992 2041 3.442977 GCTGGACTTGAGCTGATTGATTT 59.557 43.478 0.00 0.00 33.37 2.17
2036 2085 8.969121 TGTCTAAACTGCATTTATTTGATGTG 57.031 30.769 0.00 0.00 32.23 3.21
2060 2109 8.310406 TGTTTTCACACTGTTCTATGACTATG 57.690 34.615 0.00 0.00 0.00 2.23
2104 2153 7.889589 TGAACTGACATGATAAGTAACTGTG 57.110 36.000 0.00 0.00 0.00 3.66
2105 2154 6.368791 TGAACTGACATGATAAGTAACTGTGC 59.631 38.462 0.00 0.00 0.00 4.57
2108 2157 6.710295 ACTGACATGATAAGTAACTGTGCAAA 59.290 34.615 0.00 0.00 0.00 3.68
2109 2158 7.095060 ACTGACATGATAAGTAACTGTGCAAAG 60.095 37.037 1.09 1.09 0.00 2.77
2110 2159 6.710295 TGACATGATAAGTAACTGTGCAAAGT 59.290 34.615 2.82 2.82 0.00 2.66
2111 2160 7.095229 TGACATGATAAGTAACTGTGCAAAGTC 60.095 37.037 10.72 0.00 0.00 3.01
2112 2161 6.149474 ACATGATAAGTAACTGTGCAAAGTCC 59.851 38.462 10.72 4.22 0.00 3.85
2114 2163 6.999950 TGATAAGTAACTGTGCAAAGTCCTA 58.000 36.000 10.72 0.00 0.00 2.94
2116 2165 8.100791 TGATAAGTAACTGTGCAAAGTCCTAAT 58.899 33.333 10.72 0.00 0.00 1.73
2117 2166 6.803154 AAGTAACTGTGCAAAGTCCTAATC 57.197 37.500 10.72 0.00 0.00 1.75
2118 2167 5.865085 AGTAACTGTGCAAAGTCCTAATCA 58.135 37.500 10.72 0.00 0.00 2.57
2119 2168 6.476378 AGTAACTGTGCAAAGTCCTAATCAT 58.524 36.000 10.72 0.00 0.00 2.45
2120 2169 5.633830 AACTGTGCAAAGTCCTAATCATG 57.366 39.130 10.72 0.00 0.00 3.07
2121 2170 4.012374 ACTGTGCAAAGTCCTAATCATGG 58.988 43.478 2.82 0.00 0.00 3.66
2122 2171 2.754552 TGTGCAAAGTCCTAATCATGGC 59.245 45.455 0.00 0.00 0.00 4.40
2123 2172 2.754552 GTGCAAAGTCCTAATCATGGCA 59.245 45.455 0.00 0.00 0.00 4.92
2124 2173 3.382546 GTGCAAAGTCCTAATCATGGCAT 59.617 43.478 0.00 0.00 0.00 4.40
2125 2174 4.025360 TGCAAAGTCCTAATCATGGCATT 58.975 39.130 0.00 0.00 0.00 3.56
2126 2175 4.142116 TGCAAAGTCCTAATCATGGCATTG 60.142 41.667 0.00 0.00 0.00 2.82
2127 2176 4.142093 GCAAAGTCCTAATCATGGCATTGT 60.142 41.667 0.00 0.00 0.00 2.71
2128 2177 5.625197 GCAAAGTCCTAATCATGGCATTGTT 60.625 40.000 0.00 0.00 0.00 2.83
2129 2178 5.841957 AAGTCCTAATCATGGCATTGTTC 57.158 39.130 0.00 0.00 0.00 3.18
2130 2179 5.121380 AGTCCTAATCATGGCATTGTTCT 57.879 39.130 0.00 0.00 0.00 3.01
2131 2180 6.252599 AGTCCTAATCATGGCATTGTTCTA 57.747 37.500 0.00 0.00 0.00 2.10
2334 2383 8.734386 GTTGAGATCAATTTATGTGAAAGGAGT 58.266 33.333 0.00 0.00 38.24 3.85
2434 2483 2.637382 TCTGGAATGCTGTGGTGTTAGA 59.363 45.455 0.00 0.00 0.00 2.10
2514 2563 1.197036 TGAGTTAGAGACACGAGTGCG 59.803 52.381 2.76 0.00 44.79 5.34
2551 2600 9.075678 GATATGGGAATGAATGAGAATGACTTT 57.924 33.333 0.00 0.00 0.00 2.66
2584 2633 9.927081 ATGGTCTATGATTATCCAAAAGTTCTT 57.073 29.630 0.00 0.00 0.00 2.52
2625 2674 8.598041 AGAAGAGATGAACAGTAAGGTGTTTAT 58.402 33.333 0.00 0.00 40.83 1.40
2666 2715 6.534475 TCCATGCTATTTTTCTTTCTGCAT 57.466 33.333 0.00 0.00 39.79 3.96
2852 2901 5.452356 CCCTTTTTGGATAGGCATCAATGAC 60.452 44.000 0.00 0.00 38.35 3.06
2985 3034 8.327941 TGGATTAATGAAAGTCTTGTCTTGAG 57.672 34.615 0.00 0.00 0.00 3.02
3126 3187 7.447238 ACCAATAGTCACCAAATTTATATCGGG 59.553 37.037 0.00 0.00 0.00 5.14
4045 4288 7.542025 ACAAATTGGATTTCTAGTTCTGATGC 58.458 34.615 0.00 0.00 0.00 3.91
4091 4334 7.118971 CCCTTCTCATTTCTATCCGATCAATTC 59.881 40.741 0.00 0.00 0.00 2.17
4151 4394 3.889227 GCAGTCGGCAATGTGCTA 58.111 55.556 0.00 0.00 44.28 3.49
4470 4717 2.143925 GAAGCCAGCGTCAAGTACTTT 58.856 47.619 5.07 0.00 0.00 2.66
4650 4897 3.646162 TGTACCGCATCCATATCCTCTTT 59.354 43.478 0.00 0.00 0.00 2.52
4871 5118 0.100682 CGAGATTCGAAGCCGGAGAA 59.899 55.000 10.29 4.97 43.74 2.87
5018 5268 3.272439 TGTCCTTGACTTGTACGTACG 57.728 47.619 20.18 15.01 33.15 3.67
5255 5505 4.378149 CGGCATGAAAGCAGCTCATATAAG 60.378 45.833 0.00 0.00 32.20 1.73
5286 7390 1.702957 CACCAAGGTACCCAGAAAGGA 59.297 52.381 8.74 0.00 41.22 3.36
5361 7466 6.870971 TTACACAGGATACACAGGAAAAAC 57.129 37.500 0.00 0.00 41.41 2.43
5573 7678 5.781306 TCTCCCAGTACCTGTAAAACACATA 59.219 40.000 0.00 0.00 36.29 2.29
5581 7686 9.344772 AGTACCTGTAAAACACATAACAAATGA 57.655 29.630 0.00 0.00 36.29 2.57
5594 7699 7.061441 CACATAACAAATGACATCAAGTTGCTC 59.939 37.037 0.00 0.00 31.79 4.26
5610 7715 5.809001 AGTTGCTCAATTTAGGACATCTCA 58.191 37.500 0.00 0.00 0.00 3.27
5629 7734 1.136695 CAAACCCTATACGCCGTACCA 59.863 52.381 0.00 0.00 0.00 3.25
5653 7758 2.355716 CCTAAATGTCCGGACACCACAT 60.356 50.000 38.46 20.57 45.05 3.21
5666 7771 2.272678 CACCACATACGCGTCCAAATA 58.727 47.619 18.63 0.00 0.00 1.40
5728 7842 0.034767 ATCCGTCACGTAGGACTCCA 60.035 55.000 8.49 0.00 39.66 3.86
5732 7846 1.201647 CGTCACGTAGGACTCCAACAT 59.798 52.381 4.72 0.00 35.63 2.71
5740 7854 1.550130 GGACTCCAACATCCCCGACA 61.550 60.000 0.00 0.00 0.00 4.35
5757 7871 2.375146 GACACACCCAAAACCTCACTT 58.625 47.619 0.00 0.00 0.00 3.16
5765 7879 2.301346 CAAAACCTCACTTGGAGCTGT 58.699 47.619 0.00 0.00 42.62 4.40
5816 7930 1.656092 TATCCGCTCCCTCCCTGAGT 61.656 60.000 0.00 0.00 32.31 3.41
5820 7934 2.284921 CTCCCTCCCTGAGTGGCA 60.285 66.667 0.00 0.00 0.00 4.92
5832 7946 0.602905 GAGTGGCAGCTACCAACGTT 60.603 55.000 7.42 0.00 42.70 3.99
5843 7957 1.296056 ACCAACGTTGCCGCTGTATC 61.296 55.000 22.93 0.00 37.70 2.24
5844 7958 1.295357 CCAACGTTGCCGCTGTATCA 61.295 55.000 22.93 0.00 37.70 2.15
5845 7959 0.179225 CAACGTTGCCGCTGTATCAC 60.179 55.000 16.51 0.00 37.70 3.06
5846 7960 1.296056 AACGTTGCCGCTGTATCACC 61.296 55.000 0.00 0.00 37.70 4.02
5847 7961 2.461110 CGTTGCCGCTGTATCACCC 61.461 63.158 0.00 0.00 0.00 4.61
5848 7962 2.112815 GTTGCCGCTGTATCACCCC 61.113 63.158 0.00 0.00 0.00 4.95
5849 7963 3.338275 TTGCCGCTGTATCACCCCC 62.338 63.158 0.00 0.00 0.00 5.40
5850 7964 4.910585 GCCGCTGTATCACCCCCG 62.911 72.222 0.00 0.00 0.00 5.73
5851 7965 4.910585 CCGCTGTATCACCCCCGC 62.911 72.222 0.00 0.00 0.00 6.13
5852 7966 3.849951 CGCTGTATCACCCCCGCT 61.850 66.667 0.00 0.00 0.00 5.52
5853 7967 2.203070 GCTGTATCACCCCCGCTG 60.203 66.667 0.00 0.00 0.00 5.18
5854 7968 2.203070 CTGTATCACCCCCGCTGC 60.203 66.667 0.00 0.00 0.00 5.25
5855 7969 3.757248 CTGTATCACCCCCGCTGCC 62.757 68.421 0.00 0.00 0.00 4.85
5856 7970 4.564110 GTATCACCCCCGCTGCCC 62.564 72.222 0.00 0.00 0.00 5.36
5880 7994 2.969238 CGCGCCTATCTGCCTTGG 60.969 66.667 0.00 0.00 0.00 3.61
5932 8053 2.838225 CCCAGGTATCGTCCGCCT 60.838 66.667 0.00 0.00 0.00 5.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
287 288 1.141053 ACGACTGCCCTGAAGAAAAGT 59.859 47.619 0.00 0.00 0.00 2.66
303 304 1.063764 CCTCGTAGCTCTGGTAACGAC 59.936 57.143 3.12 0.00 42.51 4.34
364 365 4.202430 CCCCCACTAATATGTGACCTAACC 60.202 50.000 0.00 0.00 40.12 2.85
373 374 3.669949 AGCTTCTCCCCCACTAATATGT 58.330 45.455 0.00 0.00 0.00 2.29
505 506 2.354805 GGTAAGGAAGAATCACCAGCGT 60.355 50.000 0.00 0.00 0.00 5.07
587 588 2.711547 ACCCACAACTTAGCCTCTCTTT 59.288 45.455 0.00 0.00 0.00 2.52
758 760 1.337823 ACCTTCGACCCAGAACAATCG 60.338 52.381 0.00 0.00 35.91 3.34
821 824 8.731605 TGCTAAACGGTCACATTTGAATTTATA 58.268 29.630 0.00 0.00 31.90 0.98
822 825 7.598278 TGCTAAACGGTCACATTTGAATTTAT 58.402 30.769 0.00 0.00 31.90 1.40
865 868 2.625314 AGAGAGAAAAACAAGGCAAGGC 59.375 45.455 0.00 0.00 0.00 4.35
879 882 5.272402 TGAGAGAGAGAGAGAGAGAGAGAA 58.728 45.833 0.00 0.00 0.00 2.87
899 902 4.147219 CGGGTTAACTGCTTTTCTTGAG 57.853 45.455 5.42 0.00 0.00 3.02
953 956 5.104259 AGGTTTAGCTCTATCCTGTTTGG 57.896 43.478 0.00 0.00 37.10 3.28
1140 1143 1.352622 GGATGGGATAGTGGGTGGCA 61.353 60.000 0.00 0.00 0.00 4.92
1567 1599 6.806668 ATTGAACAAGAAAAAGGAAAGGGA 57.193 33.333 0.00 0.00 0.00 4.20
1617 1649 3.745332 TTATTGCAGTTCATGTGCTCG 57.255 42.857 8.11 0.00 41.78 5.03
1635 1667 6.270064 TCATTCGAGTCTCGTAATTGCATTA 58.730 36.000 21.15 0.00 41.35 1.90
1665 1697 2.111756 GCTTTTGCTCACACAAGAACG 58.888 47.619 0.00 0.00 43.35 3.95
1684 1716 3.253188 TGTTAAATGACAACTCCTGCAGC 59.747 43.478 8.66 0.00 0.00 5.25
1687 1719 4.154918 CCTCTGTTAAATGACAACTCCTGC 59.845 45.833 0.00 0.00 0.00 4.85
1688 1720 4.697352 CCCTCTGTTAAATGACAACTCCTG 59.303 45.833 0.00 0.00 0.00 3.86
1737 1783 3.431905 GCTTCTTGCTCAGATGAGATGGA 60.432 47.826 13.98 4.83 44.74 3.41
1820 1866 2.667470 GTCACTGATAGGAGGGCACTA 58.333 52.381 0.00 0.00 0.00 2.74
1830 1876 2.427095 TGTCATGGTCGGTCACTGATAG 59.573 50.000 0.00 0.00 0.00 2.08
1962 2011 4.005650 CAGCTCAAGTCCAGCAAGATAAA 58.994 43.478 0.00 0.00 39.56 1.40
1971 2020 5.640189 AAAATCAATCAGCTCAAGTCCAG 57.360 39.130 0.00 0.00 0.00 3.86
2036 2085 7.237173 GCATAGTCATAGAACAGTGTGAAAAC 58.763 38.462 0.00 0.00 0.00 2.43
2104 2153 4.142093 ACAATGCCATGATTAGGACTTTGC 60.142 41.667 0.00 0.00 0.00 3.68
2105 2154 5.587388 ACAATGCCATGATTAGGACTTTG 57.413 39.130 0.00 0.00 0.00 2.77
2108 2157 5.121380 AGAACAATGCCATGATTAGGACT 57.879 39.130 0.00 0.00 0.00 3.85
2109 2158 5.049129 GCTAGAACAATGCCATGATTAGGAC 60.049 44.000 0.00 0.00 0.00 3.85
2110 2159 5.065914 GCTAGAACAATGCCATGATTAGGA 58.934 41.667 0.00 0.00 0.00 2.94
2111 2160 4.823442 TGCTAGAACAATGCCATGATTAGG 59.177 41.667 0.00 0.00 0.00 2.69
2112 2161 6.381481 TTGCTAGAACAATGCCATGATTAG 57.619 37.500 0.00 0.00 0.00 1.73
2114 2163 5.186409 AGTTTGCTAGAACAATGCCATGATT 59.814 36.000 0.00 0.00 31.94 2.57
2116 2165 4.081406 AGTTTGCTAGAACAATGCCATGA 58.919 39.130 0.00 0.00 31.94 3.07
2117 2166 4.157289 AGAGTTTGCTAGAACAATGCCATG 59.843 41.667 0.00 0.00 31.94 3.66
2118 2167 4.157289 CAGAGTTTGCTAGAACAATGCCAT 59.843 41.667 0.00 0.00 31.94 4.40
2119 2168 3.503363 CAGAGTTTGCTAGAACAATGCCA 59.497 43.478 0.00 0.00 31.94 4.92
2120 2169 3.753272 TCAGAGTTTGCTAGAACAATGCC 59.247 43.478 0.00 0.00 31.94 4.40
2121 2170 5.049129 ACTTCAGAGTTTGCTAGAACAATGC 60.049 40.000 0.00 0.00 29.87 3.56
2122 2171 6.551385 ACTTCAGAGTTTGCTAGAACAATG 57.449 37.500 0.00 0.00 29.87 2.82
2123 2172 7.386299 CACTACTTCAGAGTTTGCTAGAACAAT 59.614 37.037 0.00 0.00 37.33 2.71
2124 2173 6.701841 CACTACTTCAGAGTTTGCTAGAACAA 59.298 38.462 0.00 0.00 37.33 2.83
2125 2174 6.183360 ACACTACTTCAGAGTTTGCTAGAACA 60.183 38.462 0.00 0.00 37.33 3.18
2126 2175 6.217294 ACACTACTTCAGAGTTTGCTAGAAC 58.783 40.000 0.00 0.00 37.33 3.01
2127 2176 6.406692 ACACTACTTCAGAGTTTGCTAGAA 57.593 37.500 0.00 0.00 37.33 2.10
2128 2177 7.704578 ATACACTACTTCAGAGTTTGCTAGA 57.295 36.000 0.00 0.00 37.33 2.43
2129 2178 8.764524 AAATACACTACTTCAGAGTTTGCTAG 57.235 34.615 0.00 0.00 37.33 3.42
2130 2179 8.364894 TGAAATACACTACTTCAGAGTTTGCTA 58.635 33.333 0.00 0.00 37.33 3.49
2131 2180 7.217200 TGAAATACACTACTTCAGAGTTTGCT 58.783 34.615 0.00 0.00 37.33 3.91
2204 2253 2.171659 TGTGCTTGAACCACCTGAAGTA 59.828 45.455 0.00 0.00 32.30 2.24
2230 2279 2.813754 CGCGATTTGGGGATATGTCAAT 59.186 45.455 0.00 0.00 0.00 2.57
2334 2383 2.287909 GCAAGCACACGTCCCAAAAATA 60.288 45.455 0.00 0.00 0.00 1.40
2434 2483 1.971357 ACGTGACCAATCCAGTCTCTT 59.029 47.619 0.00 0.00 35.21 2.85
2551 2600 5.784906 TGGATAATCATAGACCATAGTGCCA 59.215 40.000 0.00 0.00 0.00 4.92
2584 2633 3.650942 TCTCTTCTAGGCTGAAAAACCCA 59.349 43.478 0.00 0.00 0.00 4.51
2625 2674 2.035193 TGGAGCAAAACTTAATGCGCAA 59.965 40.909 17.11 0.00 46.98 4.85
2666 2715 2.978156 ATTCTTCCAAGTGGGCAAGA 57.022 45.000 0.00 0.00 36.21 3.02
2852 2901 4.374702 GCGGTCAACACTGCGCAG 62.375 66.667 34.89 34.89 45.07 5.18
2985 3034 4.965200 ATAGGGGAGACAACTTAGCATC 57.035 45.455 0.00 0.00 0.00 3.91
3126 3187 2.724454 TCACTGCCTACTCCTCAGTAC 58.276 52.381 0.00 0.00 38.85 2.73
3159 3220 5.305386 TCCTTGACAACTTGAAGAGAGATCA 59.695 40.000 0.00 0.00 0.00 2.92
3165 3226 9.442047 AATATACTTCCTTGACAACTTGAAGAG 57.558 33.333 17.73 0.00 36.72 2.85
3404 3640 2.069273 CTTCTACAAACAGGAGCCACG 58.931 52.381 0.00 0.00 0.00 4.94
4045 4288 2.287788 GGTCAACTGTCAACAAGCCATG 60.288 50.000 0.00 0.00 0.00 3.66
4091 4334 4.401519 TCCTGTAGAAATCGTACCTGGAAG 59.598 45.833 0.00 0.00 0.00 3.46
4264 4507 8.251383 ACTAACTGCACTTATGATGTACCTAT 57.749 34.615 0.00 0.00 0.00 2.57
4470 4717 1.327690 GGTAGATGCCCAGTGACCGA 61.328 60.000 0.00 0.00 0.00 4.69
4650 4897 7.686371 GCCTGTATCATCTCATCTTCTTCTCAA 60.686 40.741 0.00 0.00 0.00 3.02
4871 5118 1.686355 CTGATGTCTCCGGAGTAGCT 58.314 55.000 30.17 14.00 0.00 3.32
5018 5268 5.517770 GTGGAACAGGAATATGTACACGTAC 59.482 44.000 0.00 0.22 41.80 3.67
5071 5321 5.184892 AGTCACAAAGGATCAAATAGGCT 57.815 39.130 0.00 0.00 0.00 4.58
5072 5322 4.336713 GGAGTCACAAAGGATCAAATAGGC 59.663 45.833 0.00 0.00 0.00 3.93
5286 7390 5.189934 AGAAAATACTAGTGCCTAGCCTGTT 59.810 40.000 5.39 0.23 37.57 3.16
5361 7466 1.135575 GCAGCTGAATTTCGTCCTTGG 60.136 52.381 20.43 0.00 0.00 3.61
5573 7678 5.518848 TGAGCAACTTGATGTCATTTGTT 57.481 34.783 0.00 2.15 0.00 2.83
5581 7686 5.769662 TGTCCTAAATTGAGCAACTTGATGT 59.230 36.000 0.00 0.00 0.00 3.06
5594 7699 9.057089 GTATAGGGTTTGAGATGTCCTAAATTG 57.943 37.037 0.00 0.00 34.26 2.32
5610 7715 1.136891 GTGGTACGGCGTATAGGGTTT 59.863 52.381 23.84 0.00 0.00 3.27
5629 7734 0.616891 GTGTCCGGACATTTAGGGGT 59.383 55.000 38.11 0.00 43.97 4.95
5653 7758 1.184431 TCTGGGTATTTGGACGCGTA 58.816 50.000 13.97 0.00 35.12 4.42
5666 7771 2.575455 TTTGGTGCCGGTTTCTGGGT 62.575 55.000 1.90 0.00 0.00 4.51
5705 7819 2.483491 GAGTCCTACGTGACGGATATCC 59.517 54.545 12.14 12.14 40.26 2.59
5728 7842 1.710996 TTGGGTGTGTCGGGGATGTT 61.711 55.000 0.00 0.00 0.00 2.71
5732 7846 1.152922 GTTTTGGGTGTGTCGGGGA 60.153 57.895 0.00 0.00 0.00 4.81
5740 7854 1.286553 TCCAAGTGAGGTTTTGGGTGT 59.713 47.619 3.66 0.00 43.22 4.16
5757 7871 4.134563 GGAGTAAGAAAAACACAGCTCCA 58.865 43.478 0.00 0.00 40.51 3.86
5765 7879 3.181426 GGGAAGGGGGAGTAAGAAAAACA 60.181 47.826 0.00 0.00 0.00 2.83
5816 7930 2.258013 GCAACGTTGGTAGCTGCCA 61.258 57.895 28.33 20.78 36.62 4.92
5832 7946 3.792736 GGGGGTGATACAGCGGCA 61.793 66.667 1.45 0.00 32.08 5.69
5855 7969 4.910585 GATAGGCGCGTGGGTGGG 62.911 72.222 13.84 0.00 0.00 4.61
5856 7970 3.849951 AGATAGGCGCGTGGGTGG 61.850 66.667 13.84 0.00 0.00 4.61
5880 7994 4.980805 TGGAACGGTGCCGCACTC 62.981 66.667 22.41 12.41 44.19 3.51


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

AutoCloner maintained by Alex Coulton.