Multiple sequence alignment - TraesCS5A01G003300

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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 TraesCS5A01G003300 chr5A 100.000 2495 0 0 1 2495 2413730 2416224 0.000000e+00 4608
1 TraesCS5A01G003300 chr5D 91.866 1881 105 21 1 1873 3570207 3572047 0.000000e+00 2582
2 TraesCS5A01G003300 chr5D 79.808 208 29 11 2200 2401 119379594 119379394 3.350000e-29 139
3 TraesCS5A01G003300 chr5B 91.966 1867 111 21 13 1873 5056484 5058317 0.000000e+00 2580
4 TraesCS5A01G003300 chrUn 82.021 584 61 28 1935 2488 96547168 96547737 8.130000e-125 457
5 TraesCS5A01G003300 chr1A 81.955 532 63 22 1939 2464 10976801 10976297 1.070000e-113 420
6 TraesCS5A01G003300 chr4A 84.031 382 46 11 1904 2280 502896865 502897236 1.100000e-93 353
7 TraesCS5A01G003300 chr1B 77.747 364 39 16 1917 2274 605260170 605260497 4.240000e-43 185
8 TraesCS5A01G003300 chr1B 81.053 190 29 7 2208 2395 573005765 573005581 7.190000e-31 145
9 TraesCS5A01G003300 chr1D 80.228 263 21 9 2221 2473 246389018 246389259 4.270000e-38 169
10 TraesCS5A01G003300 chr7D 74.403 461 82 26 617 1062 610764894 610764455 5.520000e-37 165
11 TraesCS5A01G003300 chr7D 81.111 180 28 6 2200 2376 189326962 189327138 3.350000e-29 139
12 TraesCS5A01G003300 chr6A 82.564 195 27 7 2203 2395 461435495 461435306 5.520000e-37 165
13 TraesCS5A01G003300 chr4B 80.000 230 28 16 2201 2421 599348683 599348903 1.200000e-33 154
14 TraesCS5A01G003300 chr2B 81.579 190 30 5 2201 2388 681399835 681399649 4.300000e-33 152
15 TraesCS5A01G003300 chr3A 78.571 238 43 8 2203 2438 715156467 715156236 1.550000e-32 150
16 TraesCS5A01G003300 chr2A 78.017 232 34 16 2170 2394 758701427 758701648 2.010000e-26 130


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 TraesCS5A01G003300 chr5A 2413730 2416224 2494 False 4608 4608 100.000 1 2495 1 chr5A.!!$F1 2494
1 TraesCS5A01G003300 chr5D 3570207 3572047 1840 False 2582 2582 91.866 1 1873 1 chr5D.!!$F1 1872
2 TraesCS5A01G003300 chr5B 5056484 5058317 1833 False 2580 2580 91.966 13 1873 1 chr5B.!!$F1 1860
3 TraesCS5A01G003300 chrUn 96547168 96547737 569 False 457 457 82.021 1935 2488 1 chrUn.!!$F1 553
4 TraesCS5A01G003300 chr1A 10976297 10976801 504 True 420 420 81.955 1939 2464 1 chr1A.!!$R1 525

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
298 302 0.119155 ACCATGGGGAGAAGAGGACA 59.881 55.0 18.09 0.0 38.05 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1904 1915 0.108329 TTAAGGCGCCGAAGAAGAGG 60.108 55.0 23.2 0.0 0.0 3.69 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
77 81 7.542477 ACACGACTTAGTATGAATTCAGTGAAG 59.458 37.037 19.48 17.33 0.00 3.02
121 125 1.854280 TGGGTTGGGTTTAGTCCTTGT 59.146 47.619 0.00 0.00 0.00 3.16
124 128 3.293337 GGTTGGGTTTAGTCCTTGTTGT 58.707 45.455 0.00 0.00 0.00 3.32
130 134 6.130569 TGGGTTTAGTCCTTGTTGTACAATT 58.869 36.000 12.26 0.00 37.48 2.32
172 176 9.729023 CAAATATATTAAAACGAGTTGCATCCA 57.271 29.630 0.00 0.00 0.00 3.41
183 187 4.452455 CGAGTTGCATCCATCCTAATAACC 59.548 45.833 0.00 0.00 0.00 2.85
187 191 2.552155 GCATCCATCCTAATAACCCGCA 60.552 50.000 0.00 0.00 0.00 5.69
188 192 2.922740 TCCATCCTAATAACCCGCAC 57.077 50.000 0.00 0.00 0.00 5.34
189 193 2.120312 TCCATCCTAATAACCCGCACA 58.880 47.619 0.00 0.00 0.00 4.57
190 194 2.506231 TCCATCCTAATAACCCGCACAA 59.494 45.455 0.00 0.00 0.00 3.33
191 195 2.616842 CCATCCTAATAACCCGCACAAC 59.383 50.000 0.00 0.00 0.00 3.32
192 196 3.275143 CATCCTAATAACCCGCACAACA 58.725 45.455 0.00 0.00 0.00 3.33
193 197 3.420300 TCCTAATAACCCGCACAACAA 57.580 42.857 0.00 0.00 0.00 2.83
199 203 5.652994 AATAACCCGCACAACAATACAAT 57.347 34.783 0.00 0.00 0.00 2.71
219 223 5.647225 ACAATTGCAGTTCCACAAAACAATT 59.353 32.000 5.05 0.00 36.87 2.32
225 229 7.522374 TGCAGTTCCACAAAACAATTAAAAAC 58.478 30.769 0.00 0.00 0.00 2.43
268 272 2.350498 GCCACGTAGTTTCGTATGCATT 59.650 45.455 3.54 0.00 41.61 3.56
275 279 5.742453 CGTAGTTTCGTATGCATTACAGAGT 59.258 40.000 3.54 0.00 0.00 3.24
283 287 5.294306 CGTATGCATTACAGAGTGAAACCAT 59.706 40.000 3.54 0.00 37.80 3.55
287 291 3.433306 TTACAGAGTGAAACCATGGGG 57.567 47.619 18.09 0.00 37.80 4.96
298 302 0.119155 ACCATGGGGAGAAGAGGACA 59.881 55.000 18.09 0.00 38.05 4.02
324 328 5.164620 TCTTGGTGAGTCATTGCTTATCA 57.835 39.130 0.00 0.00 0.00 2.15
332 336 7.710907 GGTGAGTCATTGCTTATCATGTACTAA 59.289 37.037 0.00 0.00 0.00 2.24
360 364 6.881065 ACACATAAGACACATGCTCTAACAAT 59.119 34.615 0.00 0.00 0.00 2.71
442 446 7.118422 AGTTAGCGTTCATGAAAGAGTAAAC 57.882 36.000 23.23 17.95 0.00 2.01
603 611 5.220912 CCACACAATGGCTAATACATGACAG 60.221 44.000 0.00 0.00 43.24 3.51
678 686 9.865321 GTTCTACTACCTTGTATAACACAATCA 57.135 33.333 0.00 0.00 45.96 2.57
775 785 7.961326 AAGAAGCCTTGGAATAACATTACAT 57.039 32.000 0.00 0.00 0.00 2.29
1007 1018 7.225145 CCAAAACAACATTGACAACATGAAGAT 59.775 33.333 0.00 0.00 0.00 2.40
1043 1054 3.807209 GCTTTCCTTGCTCTGGTAGTGAA 60.807 47.826 0.00 0.00 0.00 3.18
1109 1120 4.090588 TCCCACCGCGGATGGTTC 62.091 66.667 35.90 0.00 41.38 3.62
1217 1228 2.967362 TGTTATGGATCGGTGTGTGAC 58.033 47.619 0.00 0.00 0.00 3.67
1240 1251 0.321122 GGATATGCCGCTCTCTTGGG 60.321 60.000 0.00 0.00 0.00 4.12
1250 1261 1.625818 GCTCTCTTGGGTCTTTCCTCA 59.374 52.381 0.00 0.00 36.25 3.86
1283 1294 1.971357 GAGAAGTTGTGAGGAGGTCCA 59.029 52.381 0.00 0.00 38.89 4.02
1403 1414 1.214175 TCAACAAGGTCTGGAAGCCAA 59.786 47.619 0.00 0.00 33.36 4.52
1406 1417 2.962859 ACAAGGTCTGGAAGCCAAAAT 58.037 42.857 0.00 0.00 33.36 1.82
1479 1490 1.915489 TGCAACATCCCCATCACTAGT 59.085 47.619 0.00 0.00 0.00 2.57
1506 1517 2.770164 ACTGGTGATGTAGCTTCCAC 57.230 50.000 0.00 0.00 0.00 4.02
1688 1699 3.733443 ACAAAAGGAATGTGTGGAAGC 57.267 42.857 0.00 0.00 0.00 3.86
1692 1703 0.537143 AGGAATGTGTGGAAGCGCAA 60.537 50.000 11.47 0.00 32.29 4.85
1720 1731 4.495844 GCCTCTCATTGCGTTTTGGTATAC 60.496 45.833 0.00 0.00 0.00 1.47
1727 1738 1.666700 GCGTTTTGGTATACATGGCGA 59.333 47.619 5.01 0.00 0.00 5.54
1728 1739 2.096174 GCGTTTTGGTATACATGGCGAA 59.904 45.455 5.01 0.00 0.00 4.70
1782 1793 4.825085 GTGAACAGATTTTAGTCCCAACCA 59.175 41.667 0.00 0.00 0.00 3.67
1801 1812 3.599343 CCATGAAGGTTGTCGAGAATCA 58.401 45.455 8.42 4.02 33.17 2.57
1809 1820 3.813166 GGTTGTCGAGAATCAAAGAACCA 59.187 43.478 0.00 0.00 41.00 3.67
1811 1822 5.048713 GGTTGTCGAGAATCAAAGAACCATT 60.049 40.000 0.00 0.00 41.00 3.16
1816 1827 8.625651 TGTCGAGAATCAAAGAACCATTAAAAA 58.374 29.630 0.00 0.00 33.17 1.94
1819 1830 8.863049 CGAGAATCAAAGAACCATTAAAAATGG 58.137 33.333 15.50 15.50 39.17 3.16
1867 1878 9.201127 CGGTAGAGGTTATTTTATAGGCTTTAC 57.799 37.037 0.00 0.00 0.00 2.01
1873 1884 9.969001 AGGTTATTTTATAGGCTTTACTCACAA 57.031 29.630 0.00 0.00 0.00 3.33
1874 1885 9.999009 GGTTATTTTATAGGCTTTACTCACAAC 57.001 33.333 0.00 0.00 0.00 3.32
1875 1886 9.698617 GTTATTTTATAGGCTTTACTCACAACG 57.301 33.333 0.00 0.00 0.00 4.10
1876 1887 6.730960 TTTTATAGGCTTTACTCACAACGG 57.269 37.500 0.00 0.00 0.00 4.44
1877 1888 3.975168 ATAGGCTTTACTCACAACGGT 57.025 42.857 0.00 0.00 0.00 4.83
1878 1889 2.632987 AGGCTTTACTCACAACGGTT 57.367 45.000 0.00 0.00 0.00 4.44
1879 1890 2.218603 AGGCTTTACTCACAACGGTTG 58.781 47.619 18.81 18.81 0.00 3.77
1880 1891 1.265905 GGCTTTACTCACAACGGTTGG 59.734 52.381 23.51 13.09 34.12 3.77
1881 1892 1.265905 GCTTTACTCACAACGGTTGGG 59.734 52.381 23.51 20.44 34.65 4.12
1882 1893 2.841215 CTTTACTCACAACGGTTGGGA 58.159 47.619 23.30 23.30 41.69 4.37
1885 1896 2.833227 TCACAACGGTTGGGAGGG 59.167 61.111 21.28 7.00 38.38 4.30
1886 1897 2.282180 CACAACGGTTGGGAGGGG 60.282 66.667 23.51 3.73 35.62 4.79
1887 1898 3.576259 ACAACGGTTGGGAGGGGG 61.576 66.667 23.51 0.00 34.12 5.40
1888 1899 3.576259 CAACGGTTGGGAGGGGGT 61.576 66.667 13.03 0.00 0.00 4.95
1889 1900 3.254617 AACGGTTGGGAGGGGGTC 61.255 66.667 0.00 0.00 0.00 4.46
1890 1901 3.805151 AACGGTTGGGAGGGGGTCT 62.805 63.158 0.00 0.00 0.00 3.85
1891 1902 3.400054 CGGTTGGGAGGGGGTCTC 61.400 72.222 0.00 0.00 41.71 3.36
1909 1920 4.890499 TCTCCTATTGAGACCTCCTCTT 57.110 45.455 0.00 0.00 45.29 2.85
1910 1921 4.798882 TCTCCTATTGAGACCTCCTCTTC 58.201 47.826 0.00 0.00 45.29 2.87
1911 1922 4.480537 TCTCCTATTGAGACCTCCTCTTCT 59.519 45.833 0.00 0.00 45.29 2.85
1912 1923 5.043732 TCTCCTATTGAGACCTCCTCTTCTT 60.044 44.000 0.00 0.00 45.29 2.52
1913 1924 5.205056 TCCTATTGAGACCTCCTCTTCTTC 58.795 45.833 0.00 0.00 42.44 2.87
1914 1925 4.037446 CCTATTGAGACCTCCTCTTCTTCG 59.963 50.000 0.00 0.00 42.44 3.79
1915 1926 1.840737 TGAGACCTCCTCTTCTTCGG 58.159 55.000 0.00 0.00 42.44 4.30
1916 1927 0.458260 GAGACCTCCTCTTCTTCGGC 59.542 60.000 0.00 0.00 38.86 5.54
1917 1928 1.139947 GACCTCCTCTTCTTCGGCG 59.860 63.158 0.00 0.00 0.00 6.46
1918 1929 2.202810 CCTCCTCTTCTTCGGCGC 60.203 66.667 0.00 0.00 0.00 6.53
1919 1930 2.202810 CTCCTCTTCTTCGGCGCC 60.203 66.667 19.07 19.07 0.00 6.53
1920 1931 2.680352 TCCTCTTCTTCGGCGCCT 60.680 61.111 26.68 0.00 0.00 5.52
1921 1932 2.232298 CTCCTCTTCTTCGGCGCCTT 62.232 60.000 26.68 0.00 0.00 4.35
1922 1933 0.968901 TCCTCTTCTTCGGCGCCTTA 60.969 55.000 26.68 9.93 0.00 2.69
1923 1934 0.108329 CCTCTTCTTCGGCGCCTTAA 60.108 55.000 26.68 17.45 0.00 1.85
1924 1935 1.281899 CTCTTCTTCGGCGCCTTAAG 58.718 55.000 26.68 25.57 0.00 1.85
1925 1936 0.739813 TCTTCTTCGGCGCCTTAAGC 60.740 55.000 26.68 0.00 38.52 3.09
1934 1945 3.506096 GCCTTAAGCGCCCGTTCC 61.506 66.667 2.29 0.00 0.00 3.62
1935 1946 2.822701 CCTTAAGCGCCCGTTCCC 60.823 66.667 2.29 0.00 0.00 3.97
1936 1947 2.046700 CTTAAGCGCCCGTTCCCA 60.047 61.111 2.29 0.00 0.00 4.37
1998 2009 2.031163 GCACGCTCACACCTTCCT 59.969 61.111 0.00 0.00 0.00 3.36
2010 2021 4.166144 TCACACCTTCCTTTTCTTCCTTCT 59.834 41.667 0.00 0.00 0.00 2.85
2026 2037 2.887783 CCTTCTATCGCTAGCTCCTTCA 59.112 50.000 13.93 0.00 0.00 3.02
2031 2042 0.179100 TCGCTAGCTCCTTCATGCAC 60.179 55.000 13.93 0.00 0.00 4.57
2047 2058 4.497608 TCATGCACGTTTCTTTCGTTTTTC 59.502 37.500 0.00 0.00 39.55 2.29
2048 2059 4.086199 TGCACGTTTCTTTCGTTTTTCT 57.914 36.364 0.00 0.00 39.55 2.52
2061 2073 4.477780 TCGTTTTTCTTTTTGCTGTTCGT 58.522 34.783 0.00 0.00 0.00 3.85
2107 2119 8.646004 TGAAAACCACATGGATCTGAAAATTAA 58.354 29.630 4.53 0.00 38.94 1.40
2108 2120 9.487790 GAAAACCACATGGATCTGAAAATTAAA 57.512 29.630 4.53 0.00 38.94 1.52
2189 2202 9.546428 AAAAGAAAAAGTTCATCGGATTTGAAT 57.454 25.926 0.00 0.00 35.68 2.57
2190 2203 9.546428 AAAGAAAAAGTTCATCGGATTTGAATT 57.454 25.926 0.00 0.00 35.68 2.17
2191 2204 9.546428 AAGAAAAAGTTCATCGGATTTGAATTT 57.454 25.926 0.00 0.00 35.37 1.82
2192 2205 9.546428 AGAAAAAGTTCATCGGATTTGAATTTT 57.454 25.926 8.25 8.25 41.73 1.82
2217 2230 8.545229 TTTTGCTGAATTTGAAAAGAAGTTCA 57.455 26.923 5.50 0.00 35.72 3.18
2218 2231 8.721019 TTTGCTGAATTTGAAAAGAAGTTCAT 57.279 26.923 5.50 0.00 37.36 2.57
2219 2232 7.935338 TGCTGAATTTGAAAAGAAGTTCATC 57.065 32.000 5.50 1.31 37.36 2.92
2220 2233 7.490840 TGCTGAATTTGAAAAGAAGTTCATCA 58.509 30.769 5.50 3.96 37.36 3.07
2221 2234 7.980662 TGCTGAATTTGAAAAGAAGTTCATCAA 59.019 29.630 5.50 9.66 37.36 2.57
2222 2235 8.819974 GCTGAATTTGAAAAGAAGTTCATCAAA 58.180 29.630 22.60 22.60 42.26 2.69
2238 2251 9.305925 AGTTCATCAAAATTGAGAAAAGTTCAC 57.694 29.630 1.98 0.00 41.08 3.18
2400 2476 6.243811 TGCATCAATTTTGCAAAAGGATTC 57.756 33.333 26.69 23.87 46.48 2.52
2401 2477 5.107026 TGCATCAATTTTGCAAAAGGATTCG 60.107 36.000 26.69 20.66 46.48 3.34
2402 2478 5.671825 GCATCAATTTTGCAAAAGGATTCGG 60.672 40.000 26.69 20.20 39.90 4.30
2415 2491 1.336424 GGATTCGGCGCCTTTGAAAAA 60.336 47.619 26.68 7.33 0.00 1.94
2431 2507 7.168972 CCTTTGAAAAAGTTCACGCATTTATGA 59.831 33.333 0.00 0.00 43.52 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 9.125026 AGACATTGATAAGGAAAATACCATGAC 57.875 33.333 0.00 0.00 0.00 3.06
38 42 9.871238 ATACTAAGTCGTGTTTTAGACATTGAT 57.129 29.630 0.00 0.00 41.10 2.57
54 58 8.467402 AACTTCACTGAATTCATACTAAGTCG 57.533 34.615 8.96 0.00 0.00 4.18
84 88 8.164070 ACCCAACCCACAGATTATAGATAAATC 58.836 37.037 0.00 0.00 34.23 2.17
155 159 3.950397 AGGATGGATGCAACTCGTTTTA 58.050 40.909 0.00 0.00 0.00 1.52
156 160 2.795329 AGGATGGATGCAACTCGTTTT 58.205 42.857 0.00 0.00 0.00 2.43
161 165 4.762251 GGGTTATTAGGATGGATGCAACTC 59.238 45.833 0.00 0.00 0.00 3.01
172 176 3.637911 TGTTGTGCGGGTTATTAGGAT 57.362 42.857 0.00 0.00 0.00 3.24
183 187 2.662637 CTGCAATTGTATTGTTGTGCGG 59.337 45.455 7.40 0.00 34.73 5.69
187 191 5.163468 TGTGGAACTGCAATTGTATTGTTGT 60.163 36.000 7.40 0.00 38.04 3.32
188 192 5.288015 TGTGGAACTGCAATTGTATTGTTG 58.712 37.500 7.40 0.00 38.04 3.33
189 193 5.528043 TGTGGAACTGCAATTGTATTGTT 57.472 34.783 7.40 4.14 38.04 2.83
190 194 5.528043 TTGTGGAACTGCAATTGTATTGT 57.472 34.783 7.40 0.00 38.04 2.71
191 195 6.257411 TGTTTTGTGGAACTGCAATTGTATTG 59.743 34.615 7.40 0.00 38.04 1.90
192 196 6.344500 TGTTTTGTGGAACTGCAATTGTATT 58.656 32.000 7.40 0.00 38.04 1.89
193 197 5.911752 TGTTTTGTGGAACTGCAATTGTAT 58.088 33.333 7.40 0.00 38.04 2.29
199 203 7.672983 TTTTAATTGTTTTGTGGAACTGCAA 57.327 28.000 0.00 0.00 38.04 4.08
219 223 7.644551 CGCGCCTAATATTTGTTATGGTTTTTA 59.355 33.333 0.00 0.00 0.00 1.52
225 229 4.669197 GCTCGCGCCTAATATTTGTTATGG 60.669 45.833 0.00 0.00 0.00 2.74
254 258 5.720202 TCACTCTGTAATGCATACGAAACT 58.280 37.500 0.00 0.00 37.32 2.66
268 272 2.571653 CTCCCCATGGTTTCACTCTGTA 59.428 50.000 11.73 0.00 0.00 2.74
275 279 1.635487 CCTCTTCTCCCCATGGTTTCA 59.365 52.381 11.73 0.00 0.00 2.69
283 287 1.909302 GATGTTGTCCTCTTCTCCCCA 59.091 52.381 0.00 0.00 0.00 4.96
287 291 3.999663 CACCAAGATGTTGTCCTCTTCTC 59.000 47.826 1.49 0.00 29.34 2.87
298 302 3.759581 AGCAATGACTCACCAAGATGTT 58.240 40.909 0.00 0.00 0.00 2.71
332 336 8.040727 TGTTAGAGCATGTGTCTTATGTGTTAT 58.959 33.333 5.21 0.00 0.00 1.89
471 475 7.094549 TGTCCTGCTTTTGGTATTGTATTGTAC 60.095 37.037 0.00 0.00 0.00 2.90
472 476 6.943146 TGTCCTGCTTTTGGTATTGTATTGTA 59.057 34.615 0.00 0.00 0.00 2.41
473 477 5.772672 TGTCCTGCTTTTGGTATTGTATTGT 59.227 36.000 0.00 0.00 0.00 2.71
603 611 8.070769 GTCATCTTCCACTAACTTTCTTTGTTC 58.929 37.037 0.00 0.00 0.00 3.18
678 686 3.027412 AGATCGAGACCATGTTGCTAGT 58.973 45.455 0.00 0.00 0.00 2.57
745 755 7.214467 TGTTATTCCAAGGCTTCTTACTTTG 57.786 36.000 0.00 0.00 0.00 2.77
1007 1018 4.067944 AGGAAAGCTAGGAGGAAGAAGA 57.932 45.455 0.00 0.00 0.00 2.87
1088 1099 4.899239 CATCCGCGGTGGGAGCTC 62.899 72.222 27.15 4.71 40.02 4.09
1109 1120 0.182537 TATCGCAACCCATTCCCCAG 59.817 55.000 0.00 0.00 0.00 4.45
1131 1142 0.603569 CAGAACCACTCGCACTAGGT 59.396 55.000 0.00 0.00 35.47 3.08
1188 1199 4.091945 CACCGATCCATAACATAATCGCTG 59.908 45.833 0.00 0.00 39.63 5.18
1217 1228 0.600557 AGAGAGCGGCATATCCTTCG 59.399 55.000 1.45 0.00 0.00 3.79
1240 1251 1.003696 CCCCCAAGTCTGAGGAAAGAC 59.996 57.143 0.00 0.00 45.82 3.01
1250 1261 2.373502 CAACTTCTCTTCCCCCAAGTCT 59.626 50.000 0.00 0.00 33.27 3.24
1283 1294 4.081752 TCAATTGCTGACAACACTGGTTTT 60.082 37.500 0.00 0.00 38.99 2.43
1396 1407 1.666888 CGTCTGCACCATTTTGGCTTC 60.667 52.381 0.00 0.00 42.67 3.86
1403 1414 1.526575 CTTGGCCGTCTGCACCATTT 61.527 55.000 0.00 0.00 43.89 2.32
1406 1417 3.535629 CTCTTGGCCGTCTGCACCA 62.536 63.158 0.00 0.00 43.89 4.17
1479 1490 6.239600 GGAAGCTACATCACCAGTAATATCCA 60.240 42.308 0.00 0.00 0.00 3.41
1506 1517 7.226720 GGTATGTGATAGTTTATTGGTCACCAG 59.773 40.741 0.00 0.00 38.65 4.00
1666 1677 4.546570 GCTTCCACACATTCCTTTTGTAC 58.453 43.478 0.00 0.00 0.00 2.90
1688 1699 1.595489 GCAATGAGAGGCGTATTTGCG 60.595 52.381 0.00 0.00 35.06 4.85
1705 1716 2.159503 CGCCATGTATACCAAAACGCAA 60.160 45.455 0.00 0.00 0.00 4.85
1782 1793 5.551233 TCTTTGATTCTCGACAACCTTCAT 58.449 37.500 0.00 0.00 0.00 2.57
1816 1827 6.532826 AGGCACATTTTTGTGTTATTTCCAT 58.467 32.000 7.83 0.00 41.53 3.41
1819 1830 5.118510 CCGAGGCACATTTTTGTGTTATTTC 59.881 40.000 7.83 0.00 41.53 2.17
1867 1878 1.302511 CCCTCCCAACCGTTGTGAG 60.303 63.158 14.79 14.79 35.31 3.51
1873 1884 4.265507 AGACCCCCTCCCAACCGT 62.266 66.667 0.00 0.00 0.00 4.83
1874 1885 3.400054 GAGACCCCCTCCCAACCG 61.400 72.222 0.00 0.00 35.87 4.44
1889 1900 4.803452 AGAAGAGGAGGTCTCAATAGGAG 58.197 47.826 0.14 0.00 44.81 3.69
1890 1901 4.890499 AGAAGAGGAGGTCTCAATAGGA 57.110 45.455 0.14 0.00 44.81 2.94
1891 1902 4.037446 CGAAGAAGAGGAGGTCTCAATAGG 59.963 50.000 0.14 0.00 44.81 2.57
1892 1903 4.037446 CCGAAGAAGAGGAGGTCTCAATAG 59.963 50.000 0.14 0.00 44.81 1.73
1893 1904 3.954904 CCGAAGAAGAGGAGGTCTCAATA 59.045 47.826 0.14 0.00 44.81 1.90
1894 1905 2.763448 CCGAAGAAGAGGAGGTCTCAAT 59.237 50.000 0.14 0.00 44.81 2.57
1895 1906 2.171840 CCGAAGAAGAGGAGGTCTCAA 58.828 52.381 0.14 0.00 44.81 3.02
1896 1907 1.840737 CCGAAGAAGAGGAGGTCTCA 58.159 55.000 0.14 0.00 44.81 3.27
1897 1908 0.458260 GCCGAAGAAGAGGAGGTCTC 59.542 60.000 0.00 0.00 42.75 3.36
1898 1909 1.316706 CGCCGAAGAAGAGGAGGTCT 61.317 60.000 0.00 0.00 36.94 3.85
1899 1910 1.139947 CGCCGAAGAAGAGGAGGTC 59.860 63.158 0.00 0.00 0.00 3.85
1900 1911 3.007973 GCGCCGAAGAAGAGGAGGT 62.008 63.158 0.00 0.00 0.00 3.85
1901 1912 2.202810 GCGCCGAAGAAGAGGAGG 60.203 66.667 0.00 0.00 0.00 4.30
1902 1913 2.202810 GGCGCCGAAGAAGAGGAG 60.203 66.667 12.58 0.00 0.00 3.69
1903 1914 0.968901 TAAGGCGCCGAAGAAGAGGA 60.969 55.000 23.20 0.00 0.00 3.71
1904 1915 0.108329 TTAAGGCGCCGAAGAAGAGG 60.108 55.000 23.20 0.00 0.00 3.69
1905 1916 1.281899 CTTAAGGCGCCGAAGAAGAG 58.718 55.000 29.82 15.66 0.00 2.85
1906 1917 0.739813 GCTTAAGGCGCCGAAGAAGA 60.740 55.000 34.73 14.53 0.00 2.87
1907 1918 1.716172 GCTTAAGGCGCCGAAGAAG 59.284 57.895 34.73 27.92 0.00 2.85
1908 1919 3.884900 GCTTAAGGCGCCGAAGAA 58.115 55.556 34.73 21.40 0.00 2.52
1917 1928 3.506096 GGAACGGGCGCTTAAGGC 61.506 66.667 7.64 6.03 37.64 4.35
1918 1929 2.822701 GGGAACGGGCGCTTAAGG 60.823 66.667 7.64 0.00 0.00 2.69
1919 1930 0.179067 TATGGGAACGGGCGCTTAAG 60.179 55.000 7.64 0.00 0.00 1.85
1920 1931 0.179067 CTATGGGAACGGGCGCTTAA 60.179 55.000 7.64 0.00 0.00 1.85
1921 1932 1.444250 CTATGGGAACGGGCGCTTA 59.556 57.895 7.64 0.00 0.00 3.09
1922 1933 2.189521 CTATGGGAACGGGCGCTT 59.810 61.111 7.64 0.00 0.00 4.68
1923 1934 4.547367 GCTATGGGAACGGGCGCT 62.547 66.667 7.64 0.00 0.00 5.92
1998 2009 5.452077 GGAGCTAGCGATAGAAGGAAGAAAA 60.452 44.000 12.82 0.00 39.76 2.29
2010 2021 1.963515 TGCATGAAGGAGCTAGCGATA 59.036 47.619 9.55 0.00 0.00 2.92
2026 2037 4.668289 AGAAAAACGAAAGAAACGTGCAT 58.332 34.783 0.00 0.00 43.16 3.96
2031 2042 6.458284 CAGCAAAAAGAAAAACGAAAGAAACG 59.542 34.615 0.00 0.00 0.00 3.60
2047 2058 3.372060 GAAAGGGACGAACAGCAAAAAG 58.628 45.455 0.00 0.00 0.00 2.27
2048 2059 2.223386 CGAAAGGGACGAACAGCAAAAA 60.223 45.455 0.00 0.00 0.00 1.94
2061 2073 4.011023 TCAGTTTTTGTGAACGAAAGGGA 58.989 39.130 0.00 0.00 34.74 4.20
2107 2119 6.959671 TTCGTGAACTGCTTTTCAAATTTT 57.040 29.167 2.58 0.00 37.24 1.82
2108 2120 7.538303 AATTCGTGAACTGCTTTTCAAATTT 57.462 28.000 2.58 0.00 37.24 1.82
2119 2131 5.949233 ACTTTTTCAAATTCGTGAACTGC 57.051 34.783 0.00 0.00 37.24 4.40
2164 2176 9.546428 AATTCAAATCCGATGAACTTTTTCTTT 57.454 25.926 0.00 0.00 39.43 2.52
2165 2177 9.546428 AAATTCAAATCCGATGAACTTTTTCTT 57.454 25.926 0.00 0.00 39.43 2.52
2166 2178 9.546428 AAAATTCAAATCCGATGAACTTTTTCT 57.454 25.926 0.00 0.00 39.43 2.52
2191 2204 8.997323 TGAACTTCTTTTCAAATTCAGCAAAAA 58.003 25.926 0.00 0.00 32.42 1.94
2192 2205 8.545229 TGAACTTCTTTTCAAATTCAGCAAAA 57.455 26.923 0.00 0.00 32.42 2.44
2193 2206 8.721019 ATGAACTTCTTTTCAAATTCAGCAAA 57.279 26.923 0.00 0.00 38.95 3.68
2194 2207 7.980662 TGATGAACTTCTTTTCAAATTCAGCAA 59.019 29.630 0.04 0.00 38.93 3.91
2195 2208 7.490840 TGATGAACTTCTTTTCAAATTCAGCA 58.509 30.769 0.00 0.00 39.40 4.41
2196 2209 7.935338 TGATGAACTTCTTTTCAAATTCAGC 57.065 32.000 0.00 0.00 38.95 4.26
2211 2224 9.874205 TGAACTTTTCTCAATTTTGATGAACTT 57.126 25.926 0.00 0.00 36.46 2.66
2212 2225 9.305925 GTGAACTTTTCTCAATTTTGATGAACT 57.694 29.630 0.00 0.00 36.46 3.01
2213 2226 9.305925 AGTGAACTTTTCTCAATTTTGATGAAC 57.694 29.630 0.00 0.00 36.46 3.18
2214 2227 9.304731 CAGTGAACTTTTCTCAATTTTGATGAA 57.695 29.630 0.00 0.00 36.46 2.57
2215 2228 8.685427 TCAGTGAACTTTTCTCAATTTTGATGA 58.315 29.630 0.00 0.00 36.46 2.92
2216 2229 8.861033 TCAGTGAACTTTTCTCAATTTTGATG 57.139 30.769 0.00 0.00 36.46 3.07
2218 2231 9.874205 AATTCAGTGAACTTTTCTCAATTTTGA 57.126 25.926 7.96 0.00 35.57 2.69
2220 2233 9.874205 TGAATTCAGTGAACTTTTCTCAATTTT 57.126 25.926 7.96 0.00 0.00 1.82
2221 2234 9.874205 TTGAATTCAGTGAACTTTTCTCAATTT 57.126 25.926 7.96 0.00 0.00 1.82
2222 2235 9.874205 TTTGAATTCAGTGAACTTTTCTCAATT 57.126 25.926 7.96 0.00 0.00 2.32
2223 2236 9.874205 TTTTGAATTCAGTGAACTTTTCTCAAT 57.126 25.926 7.96 0.00 0.00 2.57
2224 2237 9.703892 TTTTTGAATTCAGTGAACTTTTCTCAA 57.296 25.926 7.96 7.73 0.00 3.02
2378 2454 5.318349 CGAATCCTTTTGCAAAATTGATGC 58.682 37.500 25.56 23.62 44.08 3.91
2395 2471 0.242555 TTTTCAAAGGCGCCGAATCC 59.757 50.000 23.20 0.00 0.00 3.01
2396 2472 1.985684 CTTTTTCAAAGGCGCCGAATC 59.014 47.619 23.20 0.00 0.00 2.52
2400 2476 1.128513 GAACTTTTTCAAAGGCGCCG 58.871 50.000 23.20 7.22 0.00 6.46
2401 2477 1.858458 GTGAACTTTTTCAAAGGCGCC 59.142 47.619 21.89 21.89 43.52 6.53
2402 2478 1.516864 CGTGAACTTTTTCAAAGGCGC 59.483 47.619 0.00 0.00 43.52 6.53
2415 2491 6.801539 TCTTTTCTCATAAATGCGTGAACT 57.198 33.333 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.