Multiple sequence alignment - TraesCS2B01G294200

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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 TraesCS2B01G294200 chr2B 100.000 2198 0 0 1 2198 410942537 410940340 0.000000e+00 4060.0
1 TraesCS2B01G294200 chr2D 90.308 1723 58 26 1 1707 345247787 345246158 0.000000e+00 2156.0
2 TraesCS2B01G294200 chr2D 92.391 460 30 4 1692 2148 345226024 345225567 0.000000e+00 651.0
3 TraesCS2B01G294200 chr2A 90.222 1309 67 29 247 1550 457220827 457219575 0.000000e+00 1652.0
4 TraesCS2B01G294200 chr2A 93.598 328 13 6 1826 2148 457219376 457219052 1.180000e-132 483.0
5 TraesCS2B01G294200 chr2A 93.229 192 13 0 1598 1789 457219562 457219371 1.280000e-72 283.0
6 TraesCS2B01G294200 chr2A 85.398 226 18 8 1 213 457221359 457221136 1.020000e-53 220.0
7 TraesCS2B01G294200 chr2A 92.308 65 4 1 2135 2198 456867699 456867635 8.360000e-15 91.6
8 TraesCS2B01G294200 chr1B 86.458 96 9 1 460 555 655858109 655858018 3.860000e-18 102.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2B01G294200 chr2B 410940340 410942537 2197 True 4060.0 4060 100.00000 1 2198 1 chr2B.!!$R1 2197
1 TraesCS2B01G294200 chr2D 345246158 345247787 1629 True 2156.0 2156 90.30800 1 1707 1 chr2D.!!$R2 1706
2 TraesCS2B01G294200 chr2A 457219052 457221359 2307 True 659.5 1652 90.61175 1 2148 4 chr2A.!!$R2 2147

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
570 859 0.105964 TAGCCTAGCCTGCTAGTGCT 60.106 55.0 28.61 28.61 45.69 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1588 1903 0.109873 CCTCGTTAAGAGTCACGCGT 60.11 55.0 5.58 5.58 45.44 6.01 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
58 59 0.825840 TTCCGGCCCTTTGACCTTTG 60.826 55.000 0.00 0.00 0.00 2.77
64 65 1.328279 CCCTTTGACCTTTGGACACC 58.672 55.000 0.00 0.00 0.00 4.16
66 67 1.675552 CTTTGACCTTTGGACACCGT 58.324 50.000 0.00 0.00 0.00 4.83
213 226 3.263170 TGGCAAGAGCTACCAACAGATAA 59.737 43.478 0.00 0.00 41.70 1.75
239 513 7.883391 TCCTTTCTGACTCGAACTCTATAAT 57.117 36.000 0.00 0.00 0.00 1.28
373 661 1.798223 TGCGTGTCTGTATGCAAGTTC 59.202 47.619 0.00 0.00 39.47 3.01
470 759 8.511321 TGAACAAATAATATTCGTGTTCTTGCT 58.489 29.630 24.56 4.19 45.29 3.91
494 783 3.259064 TGACCCGAACGAATTCAGAATC 58.741 45.455 6.22 0.00 34.14 2.52
570 859 0.105964 TAGCCTAGCCTGCTAGTGCT 60.106 55.000 28.61 28.61 45.69 4.40
571 860 0.105964 AGCCTAGCCTGCTAGTGCTA 60.106 55.000 26.58 11.02 43.98 3.49
576 865 1.025812 AGCCTGCTAGTGCTAGTACG 58.974 55.000 5.25 0.00 40.48 3.67
577 866 0.739561 GCCTGCTAGTGCTAGTACGT 59.260 55.000 5.25 0.00 40.48 3.57
578 867 1.945394 GCCTGCTAGTGCTAGTACGTA 59.055 52.381 5.25 0.00 40.48 3.57
579 868 2.286891 GCCTGCTAGTGCTAGTACGTAC 60.287 54.545 18.10 18.10 40.48 3.67
748 1039 1.588082 TCGTTTACCGAGGGCACTC 59.412 57.895 5.68 5.68 41.60 3.51
760 1051 0.459237 GGGCACTCGACACAGAGATG 60.459 60.000 0.62 0.00 40.57 2.90
832 1123 2.580962 GAGCTTCCTCCAATCCATTCC 58.419 52.381 0.00 0.00 31.68 3.01
874 1165 2.094597 GCCAGACATTGCTGCATACAAA 60.095 45.455 1.84 0.00 34.56 2.83
903 1194 3.627577 AGCAGAACTTCAAGCTCGAAAAA 59.372 39.130 3.60 0.00 30.05 1.94
924 1219 2.124403 CAGGGCACTCCATCCTGC 60.124 66.667 0.00 0.00 41.12 4.85
936 1231 0.247460 CATCCTGCGTCTCTGTTGGA 59.753 55.000 0.00 0.00 0.00 3.53
940 1235 0.994995 CTGCGTCTCTGTTGGATTCG 59.005 55.000 0.00 0.00 0.00 3.34
941 1236 0.389817 TGCGTCTCTGTTGGATTCGG 60.390 55.000 0.00 0.00 0.00 4.30
942 1237 0.389948 GCGTCTCTGTTGGATTCGGT 60.390 55.000 0.00 0.00 0.00 4.69
943 1238 1.630148 CGTCTCTGTTGGATTCGGTC 58.370 55.000 0.00 0.00 0.00 4.79
944 1239 1.202582 CGTCTCTGTTGGATTCGGTCT 59.797 52.381 0.00 0.00 0.00 3.85
945 1240 2.422479 CGTCTCTGTTGGATTCGGTCTA 59.578 50.000 0.00 0.00 0.00 2.59
946 1241 3.731264 CGTCTCTGTTGGATTCGGTCTAC 60.731 52.174 0.00 0.00 0.00 2.59
947 1242 2.422479 TCTCTGTTGGATTCGGTCTACG 59.578 50.000 0.00 0.00 46.11 3.51
977 1272 3.971894 ATCGGGGCGATCTTTCCT 58.028 55.556 0.00 0.00 43.45 3.36
978 1273 1.447643 ATCGGGGCGATCTTTCCTG 59.552 57.895 0.00 0.00 43.45 3.86
979 1274 2.666596 ATCGGGGCGATCTTTCCTGC 62.667 60.000 0.00 0.00 43.45 4.85
980 1275 2.592308 GGGGCGATCTTTCCTGCT 59.408 61.111 0.00 0.00 0.00 4.24
981 1276 1.821332 GGGGCGATCTTTCCTGCTG 60.821 63.158 0.00 0.00 0.00 4.41
982 1277 1.078143 GGGCGATCTTTCCTGCTGT 60.078 57.895 0.00 0.00 0.00 4.40
983 1278 1.092345 GGGCGATCTTTCCTGCTGTC 61.092 60.000 0.00 0.00 0.00 3.51
984 1279 0.107945 GGCGATCTTTCCTGCTGTCT 60.108 55.000 0.00 0.00 0.00 3.41
985 1280 1.137086 GGCGATCTTTCCTGCTGTCTA 59.863 52.381 0.00 0.00 0.00 2.59
986 1281 2.468831 GCGATCTTTCCTGCTGTCTAG 58.531 52.381 0.00 0.00 0.00 2.43
1046 1346 2.647297 GGTGTTGCTGCTCTTGCC 59.353 61.111 0.00 0.00 38.71 4.52
1131 1431 1.079405 GTTGCAGAACGGGATCGGA 60.079 57.895 0.00 0.00 41.39 4.55
1273 1573 3.831911 TCTTTGGTTCATTTGGGATCCAC 59.168 43.478 15.23 3.53 36.61 4.02
1320 1620 1.807142 CCGCTCTTCCTTTGTTTCTCC 59.193 52.381 0.00 0.00 0.00 3.71
1365 1665 2.991190 GTGCAGGATCTTCGTTTTCGTA 59.009 45.455 0.00 0.00 44.46 3.43
1408 1708 5.575957 CGTACGTATGACTATGTCCAGTTT 58.424 41.667 9.25 0.00 0.00 2.66
1419 1719 7.819415 TGACTATGTCCAGTTTCTAACATCTTG 59.181 37.037 0.00 0.00 34.39 3.02
1479 1780 4.202101 CCTGCTCAGTTCGAGAACATATCT 60.202 45.833 17.00 0.00 45.45 1.98
1491 1792 6.377429 TCGAGAACATATCTGGTAGTTTCAGT 59.623 38.462 0.00 0.00 38.96 3.41
1494 1795 9.303537 GAGAACATATCTGGTAGTTTCAGTAAC 57.696 37.037 0.00 0.00 38.96 2.50
1561 1876 5.418692 TTCCTCCCTCCTGTATGATCTAA 57.581 43.478 0.00 0.00 0.00 2.10
1566 1881 5.257262 TCCCTCCTGTATGATCTAATCTCG 58.743 45.833 0.00 0.00 0.00 4.04
1581 1896 3.834489 ATCTCGATTTCTCACAGCCAT 57.166 42.857 0.00 0.00 0.00 4.40
1582 1897 2.897436 TCTCGATTTCTCACAGCCATG 58.103 47.619 0.00 0.00 0.00 3.66
1583 1898 2.234661 TCTCGATTTCTCACAGCCATGT 59.765 45.455 0.00 0.00 41.57 3.21
1584 1899 3.447229 TCTCGATTTCTCACAGCCATGTA 59.553 43.478 0.00 0.00 37.65 2.29
1585 1900 3.785486 TCGATTTCTCACAGCCATGTAG 58.215 45.455 0.00 0.00 37.65 2.74
1586 1901 2.286294 CGATTTCTCACAGCCATGTAGC 59.714 50.000 0.00 0.00 37.65 3.58
1587 1902 2.113860 TTTCTCACAGCCATGTAGCC 57.886 50.000 0.00 0.00 37.65 3.93
1588 1903 0.983467 TTCTCACAGCCATGTAGCCA 59.017 50.000 0.00 0.00 37.65 4.75
1596 1911 2.452813 CCATGTAGCCACGCGTGAC 61.453 63.158 39.10 29.49 0.00 3.67
1743 2062 2.607771 CGTTTGAAGGGGTTTGCATCTG 60.608 50.000 0.00 0.00 0.00 2.90
1748 2067 4.415596 TGAAGGGGTTTGCATCTGTAAAT 58.584 39.130 0.00 0.00 32.58 1.40
1753 2072 4.690280 GGGGTTTGCATCTGTAAATGTTTG 59.310 41.667 0.00 0.00 32.58 2.93
1757 2076 7.173047 GGGTTTGCATCTGTAAATGTTTGAAAT 59.827 33.333 0.00 0.00 32.58 2.17
1763 2082 8.216453 GCATCTGTAAATGTTTGAAATGACAAC 58.784 33.333 0.00 0.00 0.00 3.32
1783 2102 5.640783 ACAACTTTAGTTATACGGAGTTGGC 59.359 40.000 15.73 0.00 44.90 4.52
1784 2103 5.410355 ACTTTAGTTATACGGAGTTGGCA 57.590 39.130 0.00 0.00 37.78 4.92
1785 2104 5.797051 ACTTTAGTTATACGGAGTTGGCAA 58.203 37.500 0.00 0.00 37.78 4.52
1786 2105 6.412214 ACTTTAGTTATACGGAGTTGGCAAT 58.588 36.000 1.92 0.00 37.78 3.56
1787 2106 6.882678 ACTTTAGTTATACGGAGTTGGCAATT 59.117 34.615 1.92 0.00 37.78 2.32
1788 2107 7.392393 ACTTTAGTTATACGGAGTTGGCAATTT 59.608 33.333 1.92 0.00 37.78 1.82
1789 2108 5.813080 AGTTATACGGAGTTGGCAATTTC 57.187 39.130 1.92 4.65 37.78 2.17
1790 2109 5.497474 AGTTATACGGAGTTGGCAATTTCT 58.503 37.500 1.92 0.00 37.78 2.52
1791 2110 5.944007 AGTTATACGGAGTTGGCAATTTCTT 59.056 36.000 1.92 0.00 37.78 2.52
1792 2111 6.433093 AGTTATACGGAGTTGGCAATTTCTTT 59.567 34.615 1.92 0.00 37.78 2.52
1793 2112 7.608761 AGTTATACGGAGTTGGCAATTTCTTTA 59.391 33.333 1.92 1.61 37.78 1.85
1794 2113 4.766404 ACGGAGTTGGCAATTTCTTTAG 57.234 40.909 1.92 1.91 37.78 1.85
1795 2114 4.394729 ACGGAGTTGGCAATTTCTTTAGA 58.605 39.130 1.92 0.00 37.78 2.10
1796 2115 4.825085 ACGGAGTTGGCAATTTCTTTAGAA 59.175 37.500 1.92 0.00 37.78 2.10
1797 2116 5.300792 ACGGAGTTGGCAATTTCTTTAGAAA 59.699 36.000 1.92 7.33 43.41 2.52
1798 2117 5.629435 CGGAGTTGGCAATTTCTTTAGAAAC 59.371 40.000 1.92 0.00 45.55 2.78
1799 2118 6.512297 GGAGTTGGCAATTTCTTTAGAAACA 58.488 36.000 1.92 0.00 45.55 2.83
1800 2119 6.420903 GGAGTTGGCAATTTCTTTAGAAACAC 59.579 38.462 1.92 0.94 45.55 3.32
1801 2120 5.977129 AGTTGGCAATTTCTTTAGAAACACG 59.023 36.000 1.92 1.21 45.55 4.49
1802 2121 5.508200 TGGCAATTTCTTTAGAAACACGT 57.492 34.783 7.05 0.00 45.55 4.49
1803 2122 5.277825 TGGCAATTTCTTTAGAAACACGTG 58.722 37.500 15.48 15.48 45.55 4.49
1804 2123 5.163602 TGGCAATTTCTTTAGAAACACGTGT 60.164 36.000 17.22 17.22 45.55 4.49
1805 2124 5.398416 GGCAATTTCTTTAGAAACACGTGTC 59.602 40.000 23.61 10.71 45.55 3.67
1806 2125 5.968848 GCAATTTCTTTAGAAACACGTGTCA 59.031 36.000 23.61 4.87 45.55 3.58
1807 2126 6.636850 GCAATTTCTTTAGAAACACGTGTCAT 59.363 34.615 23.61 14.35 45.55 3.06
1808 2127 7.167468 GCAATTTCTTTAGAAACACGTGTCATT 59.833 33.333 23.61 13.91 45.55 2.57
1809 2128 9.019764 CAATTTCTTTAGAAACACGTGTCATTT 57.980 29.630 23.61 13.09 45.55 2.32
1810 2129 9.581099 AATTTCTTTAGAAACACGTGTCATTTT 57.419 25.926 23.61 12.68 45.55 1.82
1811 2130 8.609478 TTTCTTTAGAAACACGTGTCATTTTC 57.391 30.769 23.61 20.67 38.94 2.29
1812 2131 7.548196 TCTTTAGAAACACGTGTCATTTTCT 57.452 32.000 27.34 27.34 40.54 2.52
1813 2132 8.651391 TCTTTAGAAACACGTGTCATTTTCTA 57.349 30.769 25.76 25.76 38.80 2.10
1814 2133 8.761497 TCTTTAGAAACACGTGTCATTTTCTAG 58.239 33.333 26.95 22.06 40.12 2.43
1815 2134 8.651391 TTTAGAAACACGTGTCATTTTCTAGA 57.349 30.769 26.95 23.23 40.12 2.43
1816 2135 8.651391 TTAGAAACACGTGTCATTTTCTAGAA 57.349 30.769 26.95 18.89 40.12 2.10
1817 2136 7.548196 AGAAACACGTGTCATTTTCTAGAAA 57.452 32.000 24.70 13.99 36.70 2.52
1818 2137 7.630924 AGAAACACGTGTCATTTTCTAGAAAG 58.369 34.615 24.70 7.91 36.70 2.62
1819 2138 7.494625 AGAAACACGTGTCATTTTCTAGAAAGA 59.505 33.333 24.70 10.04 36.70 2.52
1820 2139 7.548196 AACACGTGTCATTTTCTAGAAAGAA 57.452 32.000 23.61 5.11 40.03 2.52
1821 2140 7.178712 ACACGTGTCATTTTCTAGAAAGAAG 57.821 36.000 17.22 11.43 42.60 2.85
1822 2141 6.984474 ACACGTGTCATTTTCTAGAAAGAAGA 59.016 34.615 17.22 13.28 42.60 2.87
1823 2142 7.494625 ACACGTGTCATTTTCTAGAAAGAAGAA 59.505 33.333 17.22 3.67 42.60 2.52
1824 2143 8.335356 CACGTGTCATTTTCTAGAAAGAAGAAA 58.665 33.333 17.05 9.47 42.60 2.52
1909 2228 3.040147 TGTTCGTTTGACATCTCCCTC 57.960 47.619 0.00 0.00 0.00 4.30
1910 2229 2.289444 TGTTCGTTTGACATCTCCCTCC 60.289 50.000 0.00 0.00 0.00 4.30
1916 2235 0.636647 TGACATCTCCCTCCCAGCTA 59.363 55.000 0.00 0.00 0.00 3.32
1926 2245 2.047655 CCCAGCTAACGTTCGCCA 60.048 61.111 19.91 0.00 0.00 5.69
1988 2311 1.214367 GGTCACCGTGTGTGTGTTAG 58.786 55.000 0.00 0.00 45.61 2.34
2003 2326 6.090898 GTGTGTGTTAGCTACCAACTTCTATG 59.909 42.308 0.00 0.00 0.00 2.23
2074 2398 7.013464 ACGTTTGAACCTAATATGGTGTTGAAA 59.987 33.333 0.00 0.00 40.73 2.69
2104 2428 8.035984 TGTAACATGATAGGAAATGTACGACAA 58.964 33.333 0.00 0.00 35.99 3.18
2150 2474 4.578871 TGCAGTTATAGTGCACAGATTGT 58.421 39.130 21.04 0.00 46.61 2.71
2151 2475 4.392754 TGCAGTTATAGTGCACAGATTGTG 59.607 41.667 21.04 10.45 46.61 3.33
2152 2476 6.597883 TGCAGTTATAGTGCACAGATTGTGG 61.598 44.000 21.04 3.14 46.61 4.17
2153 2477 8.918346 TGCAGTTATAGTGCACAGATTGTGGT 62.918 42.308 21.04 0.00 46.61 4.16
2154 2478 9.624463 TGCAGTTATAGTGCACAGATTGTGGTA 62.624 40.741 21.04 0.00 46.61 3.25
2162 2486 4.220693 CACAGATTGTGGTATTCCTCCA 57.779 45.455 1.31 0.00 44.27 3.86
2163 2487 4.588899 CACAGATTGTGGTATTCCTCCAA 58.411 43.478 1.31 0.00 44.27 3.53
2164 2488 5.195940 CACAGATTGTGGTATTCCTCCAAT 58.804 41.667 1.31 6.57 44.27 3.16
2165 2489 5.066893 CACAGATTGTGGTATTCCTCCAATG 59.933 44.000 10.16 3.81 44.27 2.82
2166 2490 5.044919 ACAGATTGTGGTATTCCTCCAATGA 60.045 40.000 10.16 0.00 36.70 2.57
2167 2491 5.887598 CAGATTGTGGTATTCCTCCAATGAA 59.112 40.000 10.16 0.00 36.70 2.57
2168 2492 6.377996 CAGATTGTGGTATTCCTCCAATGAAA 59.622 38.462 10.16 0.00 36.70 2.69
2169 2493 7.069085 CAGATTGTGGTATTCCTCCAATGAAAT 59.931 37.037 10.16 0.00 36.70 2.17
2170 2494 6.773976 TTGTGGTATTCCTCCAATGAAATC 57.226 37.500 0.00 0.00 36.68 2.17
2171 2495 5.200483 TGTGGTATTCCTCCAATGAAATCC 58.800 41.667 0.00 0.00 36.68 3.01
2172 2496 5.200483 GTGGTATTCCTCCAATGAAATCCA 58.800 41.667 0.00 0.00 36.68 3.41
2173 2497 5.300286 GTGGTATTCCTCCAATGAAATCCAG 59.700 44.000 0.00 0.00 36.68 3.86
2174 2498 5.193527 TGGTATTCCTCCAATGAAATCCAGA 59.806 40.000 0.00 0.00 34.23 3.86
2175 2499 5.767168 GGTATTCCTCCAATGAAATCCAGAG 59.233 44.000 0.00 0.00 0.00 3.35
2176 2500 5.722172 ATTCCTCCAATGAAATCCAGAGA 57.278 39.130 0.00 0.00 0.00 3.10
2177 2501 4.767578 TCCTCCAATGAAATCCAGAGAG 57.232 45.455 0.00 0.00 0.00 3.20
2178 2502 4.107072 TCCTCCAATGAAATCCAGAGAGT 58.893 43.478 0.00 0.00 0.00 3.24
2179 2503 4.537688 TCCTCCAATGAAATCCAGAGAGTT 59.462 41.667 0.00 0.00 31.77 3.01
2180 2504 4.880696 CCTCCAATGAAATCCAGAGAGTTC 59.119 45.833 0.00 0.00 45.23 3.01
2188 2512 6.391227 GAAATCCAGAGAGTTCAAAACCAA 57.609 37.500 0.00 0.00 44.57 3.67
2189 2513 5.774498 AATCCAGAGAGTTCAAAACCAAC 57.226 39.130 0.00 0.00 0.00 3.77
2190 2514 4.229304 TCCAGAGAGTTCAAAACCAACA 57.771 40.909 0.00 0.00 0.00 3.33
2191 2515 4.594970 TCCAGAGAGTTCAAAACCAACAA 58.405 39.130 0.00 0.00 0.00 2.83
2192 2516 4.398044 TCCAGAGAGTTCAAAACCAACAAC 59.602 41.667 0.00 0.00 0.00 3.32
2193 2517 4.342772 CAGAGAGTTCAAAACCAACAACG 58.657 43.478 0.00 0.00 0.00 4.10
2194 2518 3.105937 GAGAGTTCAAAACCAACAACGC 58.894 45.455 0.00 0.00 0.00 4.84
2195 2519 2.752903 AGAGTTCAAAACCAACAACGCT 59.247 40.909 0.00 0.00 0.00 5.07
2196 2520 3.105937 GAGTTCAAAACCAACAACGCTC 58.894 45.455 0.00 0.00 0.00 5.03
2197 2521 1.843753 GTTCAAAACCAACAACGCTCG 59.156 47.619 0.00 0.00 0.00 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 2.481185 TCCAACACGAAAAATACGAGGC 59.519 45.455 0.00 0.00 34.70 4.70
58 59 3.041940 CGGTGCTGAACGGTGTCC 61.042 66.667 0.00 0.00 0.00 4.02
64 65 2.412325 GGTAAATCAACGGTGCTGAACG 60.412 50.000 0.00 0.00 0.00 3.95
66 67 3.134574 AGGTAAATCAACGGTGCTGAA 57.865 42.857 0.00 0.00 0.00 3.02
213 226 6.783708 ATAGAGTTCGAGTCAGAAAGGATT 57.216 37.500 0.00 0.00 0.00 3.01
239 513 0.688487 CCGGTGGACCAAAAGGAGTA 59.312 55.000 0.00 0.00 35.14 2.59
393 681 3.268103 ATGGGTTGGTCCTGGTCGC 62.268 63.158 0.00 0.00 36.25 5.19
470 759 3.468770 TCTGAATTCGTTCGGGTCAAAA 58.531 40.909 0.04 0.00 0.00 2.44
494 783 2.153366 AAAGGAATGCGTGCTTTTGG 57.847 45.000 0.00 0.00 44.79 3.28
574 863 9.765795 AAGTAGAACCGTATAATACTAGTACGT 57.234 33.333 4.31 0.00 39.48 3.57
578 867 8.768955 CGACAAGTAGAACCGTATAATACTAGT 58.231 37.037 0.00 0.00 0.00 2.57
579 868 8.982685 TCGACAAGTAGAACCGTATAATACTAG 58.017 37.037 0.00 0.00 0.00 2.57
690 981 1.734465 GGGAGAATTCGTGCAAGACTG 59.266 52.381 0.40 0.00 0.00 3.51
748 1039 2.887568 GCGGCCATCTCTGTGTCG 60.888 66.667 2.24 0.00 0.00 4.35
775 1066 5.163416 TGTATATATACATGCATGCGGAGCT 60.163 40.000 26.53 8.52 46.19 4.09
780 1071 5.971202 TCGTCTGTATATATACATGCATGCG 59.029 40.000 26.53 15.90 41.92 4.73
832 1123 3.748568 GCTGAGGAACTGAGGTTACTTTG 59.251 47.826 0.00 0.00 45.80 2.77
874 1165 3.445096 AGCTTGAAGTTCTGCTTTTGTGT 59.555 39.130 15.00 0.00 37.59 3.72
903 1194 0.548682 AGGATGGAGTGCCCTGTCTT 60.549 55.000 0.00 0.00 35.38 3.01
924 1219 1.202582 AGACCGAATCCAACAGAGACG 59.797 52.381 0.00 0.00 0.00 4.18
936 1231 3.354467 AGAGAAAGACCGTAGACCGAAT 58.646 45.455 0.00 0.00 39.56 3.34
940 1235 4.674475 GATCAAGAGAAAGACCGTAGACC 58.326 47.826 0.00 0.00 0.00 3.85
941 1236 4.344448 CGATCAAGAGAAAGACCGTAGAC 58.656 47.826 0.00 0.00 0.00 2.59
942 1237 3.377485 CCGATCAAGAGAAAGACCGTAGA 59.623 47.826 0.00 0.00 0.00 2.59
943 1238 3.489398 CCCGATCAAGAGAAAGACCGTAG 60.489 52.174 0.00 0.00 0.00 3.51
944 1239 2.426024 CCCGATCAAGAGAAAGACCGTA 59.574 50.000 0.00 0.00 0.00 4.02
945 1240 1.204941 CCCGATCAAGAGAAAGACCGT 59.795 52.381 0.00 0.00 0.00 4.83
946 1241 1.471676 CCCCGATCAAGAGAAAGACCG 60.472 57.143 0.00 0.00 0.00 4.79
947 1242 1.744114 GCCCCGATCAAGAGAAAGACC 60.744 57.143 0.00 0.00 0.00 3.85
978 1273 3.560563 TGTCGTCGACTAGCTAGACAGC 61.561 54.545 27.45 14.27 39.64 4.40
979 1274 2.269172 TGTCGTCGACTAGCTAGACAG 58.731 52.381 27.45 16.27 34.24 3.51
980 1275 2.375173 TGTCGTCGACTAGCTAGACA 57.625 50.000 27.45 16.30 36.43 3.41
981 1276 3.546417 CCATTGTCGTCGACTAGCTAGAC 60.546 52.174 27.45 19.64 33.15 2.59
982 1277 2.612672 CCATTGTCGTCGACTAGCTAGA 59.387 50.000 27.45 2.04 33.15 2.43
983 1278 2.855187 GCCATTGTCGTCGACTAGCTAG 60.855 54.545 24.75 19.44 33.15 3.42
984 1279 1.065102 GCCATTGTCGTCGACTAGCTA 59.935 52.381 24.75 2.55 33.15 3.32
985 1280 0.179134 GCCATTGTCGTCGACTAGCT 60.179 55.000 24.75 2.16 33.15 3.32
986 1281 1.472276 CGCCATTGTCGTCGACTAGC 61.472 60.000 24.75 19.13 33.15 3.42
987 1282 0.866061 CCGCCATTGTCGTCGACTAG 60.866 60.000 24.75 14.34 33.15 2.57
1046 1346 1.335415 CGCTGGAGATCTGTATCACGG 60.335 57.143 0.00 0.00 34.28 4.94
1104 1404 1.827789 GTTCTGCAACCACTGGCCA 60.828 57.895 4.71 4.71 0.00 5.36
1131 1431 1.676916 CCGAGCATCTGTGTCACCATT 60.677 52.381 0.00 0.00 0.00 3.16
1273 1573 5.063204 TGTACTGTTCATCTTCAAGGTTGG 58.937 41.667 0.00 0.00 0.00 3.77
1320 1620 0.856641 CCACGTACACAGAAACACCG 59.143 55.000 0.00 0.00 0.00 4.94
1365 1665 2.618709 CGCTTTGGTCTCAGAAAAAGGT 59.381 45.455 11.37 0.00 31.67 3.50
1408 1708 5.290493 ACCACAAGTCACAAGATGTTAGA 57.710 39.130 0.00 0.00 0.00 2.10
1419 1719 5.246307 AGGCTTAATTCTACCACAAGTCAC 58.754 41.667 0.00 0.00 0.00 3.67
1454 1754 0.603569 GTTCTCGAACTGAGCAGGGA 59.396 55.000 2.20 0.00 44.86 4.20
1491 1792 3.633525 ACGATGGAGCACCGTAATAGTTA 59.366 43.478 0.00 0.00 39.42 2.24
1494 1795 2.795175 ACGATGGAGCACCGTAATAG 57.205 50.000 0.00 0.00 39.42 1.73
1544 1853 5.257262 TCGAGATTAGATCATACAGGAGGG 58.743 45.833 0.00 0.00 0.00 4.30
1561 1876 3.118482 ACATGGCTGTGAGAAATCGAGAT 60.118 43.478 0.00 0.00 33.22 2.75
1566 1881 2.615912 GGCTACATGGCTGTGAGAAATC 59.384 50.000 0.00 0.00 36.79 2.17
1581 1896 1.802337 AAGAGTCACGCGTGGCTACA 61.802 55.000 42.74 19.97 46.90 2.74
1582 1897 0.169672 TAAGAGTCACGCGTGGCTAC 59.830 55.000 42.74 32.83 46.90 3.58
1583 1898 0.883153 TTAAGAGTCACGCGTGGCTA 59.117 50.000 42.74 27.16 46.90 3.93
1585 1900 1.779683 GTTAAGAGTCACGCGTGGC 59.220 57.895 35.18 35.18 34.93 5.01
1586 1901 0.386352 TCGTTAAGAGTCACGCGTGG 60.386 55.000 36.41 19.49 36.32 4.94
1587 1902 0.975544 CTCGTTAAGAGTCACGCGTG 59.024 55.000 32.76 32.76 41.99 5.34
1588 1903 0.109873 CCTCGTTAAGAGTCACGCGT 60.110 55.000 5.58 5.58 45.44 6.01
1596 1911 4.082463 GCCCTGATATCTCCTCGTTAAGAG 60.082 50.000 3.98 0.00 46.44 2.85
1753 2072 9.148104 ACTCCGTATAACTAAAGTTGTCATTTC 57.852 33.333 5.62 0.00 38.90 2.17
1757 2076 6.869913 CCAACTCCGTATAACTAAAGTTGTCA 59.130 38.462 5.62 0.00 41.09 3.58
1763 2082 6.920569 ATTGCCAACTCCGTATAACTAAAG 57.079 37.500 0.00 0.00 0.00 1.85
1774 2093 5.371115 TTCTAAAGAAATTGCCAACTCCG 57.629 39.130 0.00 0.00 0.00 4.63
1776 2095 6.142320 CGTGTTTCTAAAGAAATTGCCAACTC 59.858 38.462 8.31 0.00 44.69 3.01
1783 2102 8.560576 AATGACACGTGTTTCTAAAGAAATTG 57.439 30.769 24.26 6.61 44.69 2.32
1784 2103 9.581099 AAAATGACACGTGTTTCTAAAGAAATT 57.419 25.926 24.26 7.31 44.69 1.82
1785 2104 9.233232 GAAAATGACACGTGTTTCTAAAGAAAT 57.767 29.630 24.26 0.00 44.69 2.17
1786 2105 8.455682 AGAAAATGACACGTGTTTCTAAAGAAA 58.544 29.630 24.70 1.00 38.28 2.52
1787 2106 7.981142 AGAAAATGACACGTGTTTCTAAAGAA 58.019 30.769 24.70 5.38 38.28 2.52
1788 2107 7.548196 AGAAAATGACACGTGTTTCTAAAGA 57.452 32.000 24.70 4.83 38.28 2.52
1789 2108 8.761497 TCTAGAAAATGACACGTGTTTCTAAAG 58.239 33.333 27.71 22.44 40.33 1.85
1790 2109 8.651391 TCTAGAAAATGACACGTGTTTCTAAA 57.349 30.769 27.71 19.34 40.33 1.85
1791 2110 8.651391 TTCTAGAAAATGACACGTGTTTCTAA 57.349 30.769 27.71 19.30 40.33 2.10
1792 2111 8.651391 TTTCTAGAAAATGACACGTGTTTCTA 57.349 30.769 26.85 26.85 40.08 2.10
1793 2112 7.494625 TCTTTCTAGAAAATGACACGTGTTTCT 59.505 33.333 27.34 27.34 41.79 2.52
1794 2113 7.627340 TCTTTCTAGAAAATGACACGTGTTTC 58.373 34.615 24.26 20.96 0.00 2.78
1795 2114 7.548196 TCTTTCTAGAAAATGACACGTGTTT 57.452 32.000 24.26 13.12 0.00 2.83
1796 2115 7.494625 TCTTCTTTCTAGAAAATGACACGTGTT 59.505 33.333 24.26 6.01 39.80 3.32
1797 2116 6.984474 TCTTCTTTCTAGAAAATGACACGTGT 59.016 34.615 23.64 23.64 39.80 4.49
1798 2117 7.408132 TCTTCTTTCTAGAAAATGACACGTG 57.592 36.000 18.25 15.48 39.80 4.49
1799 2118 8.336080 GTTTCTTCTTTCTAGAAAATGACACGT 58.664 33.333 18.25 0.00 41.72 4.49
1800 2119 8.335356 TGTTTCTTCTTTCTAGAAAATGACACG 58.665 33.333 18.25 5.81 41.72 4.49
1809 2128 8.352942 GCCTCAAATTGTTTCTTCTTTCTAGAA 58.647 33.333 0.00 0.00 38.06 2.10
1810 2129 7.502226 TGCCTCAAATTGTTTCTTCTTTCTAGA 59.498 33.333 0.00 0.00 0.00 2.43
1811 2130 7.651808 TGCCTCAAATTGTTTCTTCTTTCTAG 58.348 34.615 0.00 0.00 0.00 2.43
1812 2131 7.581213 TGCCTCAAATTGTTTCTTCTTTCTA 57.419 32.000 0.00 0.00 0.00 2.10
1813 2132 6.469782 TGCCTCAAATTGTTTCTTCTTTCT 57.530 33.333 0.00 0.00 0.00 2.52
1814 2133 7.538303 TTTGCCTCAAATTGTTTCTTCTTTC 57.462 32.000 0.00 0.00 0.00 2.62
1815 2134 7.920160 TTTTGCCTCAAATTGTTTCTTCTTT 57.080 28.000 0.00 0.00 33.19 2.52
1816 2135 7.920160 TTTTTGCCTCAAATTGTTTCTTCTT 57.080 28.000 0.00 0.00 33.19 2.52
1856 2175 6.023603 TCTTCAACTTTACCTGGTAGGAGAT 58.976 40.000 19.85 9.94 37.67 2.75
1903 2222 0.175989 GAACGTTAGCTGGGAGGGAG 59.824 60.000 0.00 0.00 0.00 4.30
1909 2228 2.047655 TGGCGAACGTTAGCTGGG 60.048 61.111 28.38 4.33 0.00 4.45
1910 2229 0.949105 AACTGGCGAACGTTAGCTGG 60.949 55.000 28.38 22.57 0.00 4.85
1916 2235 3.619929 GGTAATGATAACTGGCGAACGTT 59.380 43.478 0.00 0.00 0.00 3.99
1926 2245 9.860650 TGCAATACAATTAGGGTAATGATAACT 57.139 29.630 0.00 0.00 0.00 2.24
1977 2300 3.830744 AGTTGGTAGCTAACACACACA 57.169 42.857 12.03 0.00 0.00 3.72
1988 2311 1.490910 AGGGGCATAGAAGTTGGTAGC 59.509 52.381 0.00 0.00 0.00 3.58
2003 2326 2.507407 TTATGGTTCTGTTGAGGGGC 57.493 50.000 0.00 0.00 0.00 5.80
2049 2373 6.489127 TCAACACCATATTAGGTTCAAACG 57.511 37.500 0.00 0.00 40.77 3.60
2116 2440 7.121907 TGCACTATAACTGCAAATTGGTAATCA 59.878 33.333 2.85 0.00 41.70 2.57
2145 2469 6.773976 TTTCATTGGAGGAATACCACAATC 57.226 37.500 0.00 0.00 40.97 2.67
2148 2472 5.200483 GGATTTCATTGGAGGAATACCACA 58.800 41.667 0.00 0.00 37.13 4.17
2149 2473 5.200483 TGGATTTCATTGGAGGAATACCAC 58.800 41.667 0.00 0.00 37.13 4.16
2150 2474 5.193527 TCTGGATTTCATTGGAGGAATACCA 59.806 40.000 0.00 0.00 38.94 3.25
2151 2475 5.694995 TCTGGATTTCATTGGAGGAATACC 58.305 41.667 0.00 0.00 0.00 2.73
2152 2476 6.595682 TCTCTGGATTTCATTGGAGGAATAC 58.404 40.000 0.00 0.00 0.00 1.89
2153 2477 6.388100 ACTCTCTGGATTTCATTGGAGGAATA 59.612 38.462 0.00 0.00 0.00 1.75
2154 2478 5.193325 ACTCTCTGGATTTCATTGGAGGAAT 59.807 40.000 0.00 0.00 0.00 3.01
2155 2479 4.537688 ACTCTCTGGATTTCATTGGAGGAA 59.462 41.667 0.00 0.00 0.00 3.36
2156 2480 4.107072 ACTCTCTGGATTTCATTGGAGGA 58.893 43.478 0.00 0.00 0.00 3.71
2157 2481 4.500499 ACTCTCTGGATTTCATTGGAGG 57.500 45.455 0.00 0.00 0.00 4.30
2158 2482 5.494724 TGAACTCTCTGGATTTCATTGGAG 58.505 41.667 0.00 0.00 36.61 3.86
2159 2483 5.503634 TGAACTCTCTGGATTTCATTGGA 57.496 39.130 0.00 0.00 36.61 3.53
2160 2484 6.579666 TTTGAACTCTCTGGATTTCATTGG 57.420 37.500 0.00 0.00 39.62 3.16
2161 2485 6.865205 GGTTTTGAACTCTCTGGATTTCATTG 59.135 38.462 0.00 0.00 39.62 2.82
2162 2486 6.550854 TGGTTTTGAACTCTCTGGATTTCATT 59.449 34.615 0.00 0.00 39.62 2.57
2163 2487 6.070656 TGGTTTTGAACTCTCTGGATTTCAT 58.929 36.000 0.00 0.00 39.62 2.57
2164 2488 5.445069 TGGTTTTGAACTCTCTGGATTTCA 58.555 37.500 0.00 0.00 38.67 2.69
2165 2489 6.183360 TGTTGGTTTTGAACTCTCTGGATTTC 60.183 38.462 0.00 0.00 33.50 2.17
2166 2490 5.656416 TGTTGGTTTTGAACTCTCTGGATTT 59.344 36.000 0.00 0.00 0.00 2.17
2167 2491 5.200483 TGTTGGTTTTGAACTCTCTGGATT 58.800 37.500 0.00 0.00 0.00 3.01
2168 2492 4.792068 TGTTGGTTTTGAACTCTCTGGAT 58.208 39.130 0.00 0.00 0.00 3.41
2169 2493 4.229304 TGTTGGTTTTGAACTCTCTGGA 57.771 40.909 0.00 0.00 0.00 3.86
2170 2494 4.672409 GTTGTTGGTTTTGAACTCTCTGG 58.328 43.478 0.00 0.00 0.00 3.86
2171 2495 4.342772 CGTTGTTGGTTTTGAACTCTCTG 58.657 43.478 0.00 0.00 0.00 3.35
2172 2496 3.181500 GCGTTGTTGGTTTTGAACTCTCT 60.181 43.478 0.00 0.00 0.00 3.10
2173 2497 3.105937 GCGTTGTTGGTTTTGAACTCTC 58.894 45.455 0.00 0.00 0.00 3.20
2174 2498 2.752903 AGCGTTGTTGGTTTTGAACTCT 59.247 40.909 0.00 0.00 0.00 3.24
2175 2499 3.105937 GAGCGTTGTTGGTTTTGAACTC 58.894 45.455 0.00 0.00 0.00 3.01
2176 2500 2.477189 CGAGCGTTGTTGGTTTTGAACT 60.477 45.455 0.00 0.00 0.00 3.01
2177 2501 1.843753 CGAGCGTTGTTGGTTTTGAAC 59.156 47.619 0.00 0.00 0.00 3.18
2178 2502 2.181426 CGAGCGTTGTTGGTTTTGAA 57.819 45.000 0.00 0.00 0.00 2.69
2179 2503 3.907927 CGAGCGTTGTTGGTTTTGA 57.092 47.368 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.