Multiple sequence alignment - TraesCS1B01G224400

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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 TraesCS1B01G224400 chr1B 100.000 2401 0 0 1 2401 402502388 402504788 0.000000e+00 4434.0
1 TraesCS1B01G224400 chr1B 77.901 181 35 5 5 182 642053675 642053497 9.080000e-20 108.0
2 TraesCS1B01G224400 chr1A 89.724 2170 198 12 1 2152 379139280 379137118 0.000000e+00 2748.0
3 TraesCS1B01G224400 chr1A 92.038 942 68 7 465 1402 379616346 379617284 0.000000e+00 1317.0
4 TraesCS1B01G224400 chr1A 86.525 1128 126 8 1261 2379 379145981 379144871 0.000000e+00 1218.0
5 TraesCS1B01G224400 chr1A 90.493 873 57 11 1 851 379146857 379145989 0.000000e+00 1129.0
6 TraesCS1B01G224400 chr1A 83.092 828 115 9 1560 2379 379626980 379627790 0.000000e+00 730.0
7 TraesCS1B01G224400 chr6D 85.507 138 17 2 2193 2329 135251344 135251479 8.950000e-30 141.0
8 TraesCS1B01G224400 chr6D 85.075 134 15 5 2197 2329 365770765 365770636 5.390000e-27 132.0
9 TraesCS1B01G224400 chr6D 85.600 125 16 2 2197 2320 125659537 125659660 1.940000e-26 130.0
10 TraesCS1B01G224400 chr6D 100.000 28 0 0 2374 2401 117345628 117345601 4.000000e-03 52.8
11 TraesCS1B01G224400 chr2D 85.401 137 16 4 2193 2328 276047164 276047031 3.220000e-29 139.0
12 TraesCS1B01G224400 chr2D 85.075 134 15 5 2197 2329 170907126 170907255 5.390000e-27 132.0
13 TraesCS1B01G224400 chr2D 100.000 28 0 0 2374 2401 372580981 372581008 4.000000e-03 52.8
14 TraesCS1B01G224400 chr1D 86.047 129 14 3 2193 2320 256723849 256723974 4.160000e-28 135.0
15 TraesCS1B01G224400 chr4D 84.962 133 16 4 2197 2328 444537430 444537559 5.390000e-27 132.0
16 TraesCS1B01G224400 chr4D 100.000 28 0 0 2374 2401 113772370 113772397 4.000000e-03 52.8
17 TraesCS1B01G224400 chr3D 85.600 125 16 2 2197 2320 115669437 115669560 1.940000e-26 130.0
18 TraesCS1B01G224400 chr3D 100.000 29 0 0 2373 2401 451786681 451786653 1.000000e-03 54.7
19 TraesCS1B01G224400 chr3A 96.970 33 0 1 2369 2401 513852831 513852800 1.000000e-03 54.7
20 TraesCS1B01G224400 chr3B 100.000 28 0 0 2374 2401 352247940 352247913 4.000000e-03 52.8


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 TraesCS1B01G224400 chr1B 402502388 402504788 2400 False 4434.0 4434 100.000 1 2401 1 chr1B.!!$F1 2400
1 TraesCS1B01G224400 chr1A 379137118 379139280 2162 True 2748.0 2748 89.724 1 2152 1 chr1A.!!$R1 2151
2 TraesCS1B01G224400 chr1A 379616346 379617284 938 False 1317.0 1317 92.038 465 1402 1 chr1A.!!$F1 937
3 TraesCS1B01G224400 chr1A 379144871 379146857 1986 True 1173.5 1218 88.509 1 2379 2 chr1A.!!$R2 2378
4 TraesCS1B01G224400 chr1A 379626980 379627790 810 False 730.0 730 83.092 1560 2379 1 chr1A.!!$F2 819

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
997 1032 0.111061 AATCACTTGCTGGCCTCACA 59.889 50.0 3.32 0.0 0.0 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2229 2267 0.038166 ACGGAGTGCCAATCCAATGT 59.962 50.0 12.24 0.0 42.51 2.71 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
69 73 2.101209 AAAGCAAGCGTTCGGTGTCG 62.101 55.000 0.00 0.00 37.82 4.35
78 82 1.542544 GTTCGGTGTCGATTCGGTAG 58.457 55.000 6.18 0.00 45.51 3.18
133 137 6.183360 ACGAATCCTACCTTTAGATCCCTTTC 60.183 42.308 0.00 0.00 0.00 2.62
137 141 6.036631 TCCTACCTTTAGATCCCTTTCCTTT 58.963 40.000 0.00 0.00 0.00 3.11
149 153 3.068165 CCCTTTCCTTTGACACTCCAAAC 59.932 47.826 0.00 0.00 33.07 2.93
154 158 6.877611 TTCCTTTGACACTCCAAACTTATC 57.122 37.500 0.00 0.00 33.07 1.75
160 164 4.254492 GACACTCCAAACTTATCACCTCC 58.746 47.826 0.00 0.00 0.00 4.30
162 166 4.104102 ACACTCCAAACTTATCACCTCCAA 59.896 41.667 0.00 0.00 0.00 3.53
164 168 6.012858 ACACTCCAAACTTATCACCTCCAATA 60.013 38.462 0.00 0.00 0.00 1.90
184 188 9.237187 TCCAATATGAAAAGTGCTACAATAACA 57.763 29.630 0.00 0.00 0.00 2.41
185 189 9.289303 CCAATATGAAAAGTGCTACAATAACAC 57.711 33.333 0.00 0.00 34.48 3.32
188 192 5.381757 TGAAAAGTGCTACAATAACACCCT 58.618 37.500 0.00 0.00 34.83 4.34
189 193 5.240623 TGAAAAGTGCTACAATAACACCCTG 59.759 40.000 0.00 0.00 34.83 4.45
190 194 4.367039 AAGTGCTACAATAACACCCTGT 57.633 40.909 0.00 0.00 34.83 4.00
252 256 6.336566 AGTCAAAACACATTGTGCACAATAA 58.663 32.000 37.40 17.93 44.10 1.40
253 257 6.476380 AGTCAAAACACATTGTGCACAATAAG 59.524 34.615 37.40 32.14 44.10 1.73
266 270 4.620982 GCACAATAAGTTGAGCAAGGTTT 58.379 39.130 5.85 0.00 46.80 3.27
628 662 8.423349 CCCCACATTGATACACAAAATATTGAT 58.577 33.333 0.00 0.00 42.03 2.57
744 778 9.443323 TTGATACGGAAAGATTTTCTATGAACA 57.557 29.630 2.03 0.00 0.00 3.18
784 819 5.863397 ACACAACTAATGCATTTACATGTGC 59.137 36.000 28.32 3.58 41.61 4.57
908 943 6.810911 AGTACTCGAAAGATGCATCAATAGT 58.189 36.000 27.81 21.94 40.84 2.12
926 961 7.149973 TCAATAGTCACCTATATAAACACCGC 58.850 38.462 0.00 0.00 32.57 5.68
936 971 5.968528 ATATAAACACCGCCAAAGTGAAA 57.031 34.783 0.00 0.00 38.63 2.69
948 983 5.461737 CGCCAAAGTGAAATTTGTAACACAT 59.538 36.000 9.60 0.00 38.28 3.21
971 1006 8.623903 ACATCGCATATTAGAACAACAATTGAT 58.376 29.630 13.59 0.00 0.00 2.57
997 1032 0.111061 AATCACTTGCTGGCCTCACA 59.889 50.000 3.32 0.00 0.00 3.58
1040 1075 1.760029 TCTTGGTCCCTTGTTTTTGGC 59.240 47.619 0.00 0.00 0.00 4.52
1099 1134 3.627123 CCATGCGAACAATGAGGTTATGA 59.373 43.478 0.00 0.00 0.00 2.15
1103 1138 6.544038 TGCGAACAATGAGGTTATGATATG 57.456 37.500 0.00 0.00 0.00 1.78
1106 1141 7.170828 TGCGAACAATGAGGTTATGATATGTAC 59.829 37.037 0.00 0.00 0.00 2.90
1107 1142 7.170828 GCGAACAATGAGGTTATGATATGTACA 59.829 37.037 0.00 0.00 0.00 2.90
1124 1159 5.512942 TGTACATTCCTTTCTGAATCCCA 57.487 39.130 0.00 0.00 32.71 4.37
1256 1292 2.525055 ACGTGTGTTGATTTTGTGCAC 58.475 42.857 10.75 10.75 0.00 4.57
1298 1334 2.840651 AGTACCTGCAAGTTGCTATCCT 59.159 45.455 27.17 13.93 45.31 3.24
1320 1356 6.599244 TCCTATGAAGTTTCCTAAATGCACTG 59.401 38.462 0.00 0.00 0.00 3.66
1322 1358 6.899393 ATGAAGTTTCCTAAATGCACTGAA 57.101 33.333 0.00 0.00 0.00 3.02
1413 1449 4.602340 ATCGACTAAACACCACTCAACT 57.398 40.909 0.00 0.00 0.00 3.16
1416 1452 3.057734 GACTAAACACCACTCAACTCCG 58.942 50.000 0.00 0.00 0.00 4.63
1423 1459 0.176680 CCACTCAACTCCGGAGATGG 59.823 60.000 37.69 27.57 36.26 3.51
1439 1475 3.888930 GAGATGGAACTTTTGGGTTGTCA 59.111 43.478 0.00 0.00 0.00 3.58
1441 1477 4.281688 AGATGGAACTTTTGGGTTGTCATG 59.718 41.667 0.00 0.00 0.00 3.07
1447 1483 6.989759 GGAACTTTTGGGTTGTCATGTTTAAT 59.010 34.615 0.00 0.00 0.00 1.40
1483 1519 7.318893 AGAAAGCTTGCTATTTTCTTTCCATC 58.681 34.615 4.67 0.00 41.92 3.51
1492 1528 9.373603 TGCTATTTTCTTTCCATCATTGAAATG 57.626 29.630 0.00 0.00 37.75 2.32
1516 1552 3.028094 AGCCTTGCTCATGAATTGGAT 57.972 42.857 0.00 0.00 30.62 3.41
1518 1554 2.223971 GCCTTGCTCATGAATTGGATGG 60.224 50.000 0.00 0.00 0.00 3.51
1524 1560 5.447757 TGCTCATGAATTGGATGGATAACA 58.552 37.500 0.00 0.00 0.00 2.41
1598 1634 4.404073 TGCACCATTTTGTAAACCTTGTCT 59.596 37.500 0.00 0.00 0.00 3.41
1609 1645 9.974980 TTTGTAAACCTTGTCTAAAATGAATCC 57.025 29.630 0.00 0.00 0.00 3.01
1610 1646 7.812648 TGTAAACCTTGTCTAAAATGAATCCG 58.187 34.615 0.00 0.00 0.00 4.18
1681 1717 9.339850 CCAATTAAATCTCATGAACATCTCTCT 57.660 33.333 0.00 0.00 0.00 3.10
1714 1750 7.256154 CCTTGGCAAGAGTTTTAAAGGGAATTA 60.256 37.037 28.18 0.00 31.12 1.40
1734 1771 8.214364 GGAATTATCAACTCTTCCCTATTCACT 58.786 37.037 0.00 0.00 32.67 3.41
1736 1773 7.733773 TTATCAACTCTTCCCTATTCACTGA 57.266 36.000 0.00 0.00 0.00 3.41
1737 1774 5.667539 TCAACTCTTCCCTATTCACTGAG 57.332 43.478 0.00 0.00 0.00 3.35
1738 1775 4.081420 TCAACTCTTCCCTATTCACTGAGC 60.081 45.833 0.00 0.00 0.00 4.26
1739 1776 3.718723 ACTCTTCCCTATTCACTGAGCT 58.281 45.455 0.00 0.00 0.00 4.09
1740 1777 3.450457 ACTCTTCCCTATTCACTGAGCTG 59.550 47.826 0.00 0.00 0.00 4.24
1761 1798 7.406104 AGCTGGAGATTAACTTCCATAAAAGT 58.594 34.615 9.54 0.00 41.20 2.66
1785 1822 3.628008 TCTCGTGCCTATTGGAGTAGAA 58.372 45.455 0.00 0.00 34.57 2.10
1793 1830 5.012664 TGCCTATTGGAGTAGAACACAAAGA 59.987 40.000 0.00 0.00 34.57 2.52
1829 1866 1.616327 AGGTCATGTGCTGCCCCTA 60.616 57.895 0.00 0.00 0.00 3.53
1839 1877 2.164422 GTGCTGCCCCTATCAACTTTTC 59.836 50.000 0.00 0.00 0.00 2.29
1841 1879 2.621668 GCTGCCCCTATCAACTTTTCCT 60.622 50.000 0.00 0.00 0.00 3.36
1852 1890 2.287977 ACTTTTCCTTGCACCTACCC 57.712 50.000 0.00 0.00 0.00 3.69
1857 1895 2.584608 CTTGCACCTACCCGGGAG 59.415 66.667 32.02 19.84 36.97 4.30
1862 1900 4.326227 ACCTACCCGGGAGTGCCA 62.326 66.667 32.02 3.38 36.97 4.92
1885 1923 7.147915 GCCACTATCAATAAACAAGATTTCCCA 60.148 37.037 0.00 0.00 0.00 4.37
1886 1924 8.190784 CCACTATCAATAAACAAGATTTCCCAC 58.809 37.037 0.00 0.00 0.00 4.61
1887 1925 8.739039 CACTATCAATAAACAAGATTTCCCACA 58.261 33.333 0.00 0.00 0.00 4.17
1890 1928 7.452880 TCAATAAACAAGATTTCCCACAGAG 57.547 36.000 0.00 0.00 0.00 3.35
1899 1937 6.319048 AGATTTCCCACAGAGTAATGATGT 57.681 37.500 0.00 0.00 0.00 3.06
1901 1939 3.801114 TCCCACAGAGTAATGATGTCG 57.199 47.619 0.00 0.00 0.00 4.35
1917 1955 0.997196 GTCGGTTATCCAGCGTGTTC 59.003 55.000 0.00 0.00 46.86 3.18
1931 1969 4.675114 CAGCGTGTTCACAAAAGGTTATTC 59.325 41.667 3.87 0.00 0.00 1.75
1934 1972 4.260866 CGTGTTCACAAAAGGTTATTCGGT 60.261 41.667 3.87 0.00 0.00 4.69
1943 1981 0.814457 GGTTATTCGGTTGGCATGCA 59.186 50.000 21.36 2.54 0.00 3.96
1951 1989 1.187567 GGTTGGCATGCAACCTTCCT 61.188 55.000 29.41 0.00 46.28 3.36
1952 1990 0.244721 GTTGGCATGCAACCTTCCTC 59.755 55.000 21.36 0.00 0.00 3.71
2000 2038 1.213537 CTCCGTTTTGGCTGCCATG 59.786 57.895 24.03 12.48 37.80 3.66
2015 2053 1.205417 GCCATGCCAAACTACTGCATT 59.795 47.619 0.00 0.00 42.79 3.56
2017 2055 2.492881 CCATGCCAAACTACTGCATTGA 59.507 45.455 0.00 0.00 42.79 2.57
2043 2081 0.783206 TCTTTGGCCCAAGGAATCCA 59.217 50.000 16.16 0.00 0.00 3.41
2053 2091 3.626729 CCCAAGGAATCCATTGAGAAGCT 60.627 47.826 0.61 0.00 0.00 3.74
2057 2095 6.183360 CCAAGGAATCCATTGAGAAGCTAAAG 60.183 42.308 0.61 0.00 0.00 1.85
2063 2101 4.532126 TCCATTGAGAAGCTAAAGAGACCA 59.468 41.667 0.00 0.00 0.00 4.02
2066 2104 6.038050 CCATTGAGAAGCTAAAGAGACCAATC 59.962 42.308 0.00 0.00 0.00 2.67
2087 2125 0.679321 GAGCTTTCCTCTGGCAAGGG 60.679 60.000 13.42 7.32 37.60 3.95
2089 2127 0.251341 GCTTTCCTCTGGCAAGGGAA 60.251 55.000 14.33 14.33 37.02 3.97
2091 2129 2.597455 CTTTCCTCTGGCAAGGGAAAA 58.403 47.619 24.10 14.03 44.94 2.29
2104 2142 2.750814 AGGGAAAAACTATGCCCATGG 58.249 47.619 4.14 4.14 43.20 3.66
2106 2144 3.103742 GGGAAAAACTATGCCCATGGAA 58.896 45.455 15.22 0.49 40.39 3.53
2108 2146 3.769300 GGAAAAACTATGCCCATGGAAGT 59.231 43.478 15.22 8.21 0.00 3.01
2109 2147 4.222810 GGAAAAACTATGCCCATGGAAGTT 59.777 41.667 15.22 13.76 31.94 2.66
2114 2152 3.523564 ACTATGCCCATGGAAGTTACTGT 59.476 43.478 15.22 0.00 0.00 3.55
2152 2190 2.309755 AGACATTCCAGATGCCTTCCAA 59.690 45.455 0.00 0.00 0.00 3.53
2153 2191 2.686915 GACATTCCAGATGCCTTCCAAG 59.313 50.000 0.00 0.00 0.00 3.61
2157 2195 2.795329 TCCAGATGCCTTCCAAGTTTC 58.205 47.619 0.00 0.00 0.00 2.78
2166 2204 4.018506 TGCCTTCCAAGTTTCCATGATAGA 60.019 41.667 0.00 0.00 0.00 1.98
2171 2209 3.879295 CCAAGTTTCCATGATAGACGCAT 59.121 43.478 0.00 0.00 0.00 4.73
2172 2210 4.336433 CCAAGTTTCCATGATAGACGCATT 59.664 41.667 0.00 0.00 0.00 3.56
2173 2211 5.527214 CCAAGTTTCCATGATAGACGCATTA 59.473 40.000 0.00 0.00 0.00 1.90
2174 2212 6.205464 CCAAGTTTCCATGATAGACGCATTAT 59.795 38.462 0.00 0.00 0.00 1.28
2175 2213 7.387673 CCAAGTTTCCATGATAGACGCATTATA 59.612 37.037 0.00 0.00 0.00 0.98
2176 2214 8.939929 CAAGTTTCCATGATAGACGCATTATAT 58.060 33.333 0.00 0.00 0.00 0.86
2229 2267 3.566322 TGCATTCATCATCGCATCATTCA 59.434 39.130 0.00 0.00 0.00 2.57
2238 2276 4.581409 TCATCGCATCATTCACATTGGATT 59.419 37.500 0.00 0.00 0.00 3.01
2239 2277 4.295857 TCGCATCATTCACATTGGATTG 57.704 40.909 0.00 0.00 0.00 2.67
2251 2289 0.179004 TTGGATTGGCACTCCGTTGT 60.179 50.000 17.81 0.00 35.41 3.32
2261 2299 3.443976 GCACTCCGTTGTTGTCATTTTT 58.556 40.909 0.00 0.00 0.00 1.94
2291 2331 1.134487 CATGCGTTGGTAGTTGCCG 59.866 57.895 0.00 0.00 0.00 5.69
2304 2344 0.869730 GTTGCCGCTTCTTTCCGTTA 59.130 50.000 0.00 0.00 0.00 3.18
2320 2360 2.733026 CCGTTATCTTCGTTGACCGTTT 59.267 45.455 0.00 0.00 37.94 3.60
2331 2377 0.464735 TGACCGTTTTGGGACCACAG 60.465 55.000 0.00 0.00 44.64 3.66
2341 2387 0.537143 GGGACCACAGTTGCACATGA 60.537 55.000 0.00 0.00 0.00 3.07
2348 2394 1.610038 ACAGTTGCACATGACACATGG 59.390 47.619 14.70 6.35 0.00 3.66
2388 2434 1.760613 TCCAAGTGGGATGATACGTCC 59.239 52.381 0.00 0.00 42.15 4.79
2389 2435 1.484653 CCAAGTGGGATGATACGTCCA 59.515 52.381 11.36 0.00 40.01 4.02
2390 2436 2.104792 CCAAGTGGGATGATACGTCCAT 59.895 50.000 11.36 0.00 40.01 3.41
2391 2437 3.433598 CCAAGTGGGATGATACGTCCATT 60.434 47.826 11.36 0.00 40.01 3.16
2392 2438 4.199310 CAAGTGGGATGATACGTCCATTT 58.801 43.478 11.36 0.00 37.49 2.32
2393 2439 4.503714 AGTGGGATGATACGTCCATTTT 57.496 40.909 11.36 0.00 37.49 1.82
2394 2440 4.199310 AGTGGGATGATACGTCCATTTTG 58.801 43.478 11.36 0.00 37.49 2.44
2395 2441 2.948979 TGGGATGATACGTCCATTTTGC 59.051 45.455 11.36 0.00 37.49 3.68
2396 2442 2.948979 GGGATGATACGTCCATTTTGCA 59.051 45.455 11.36 0.00 37.49 4.08
2397 2443 3.569701 GGGATGATACGTCCATTTTGCAT 59.430 43.478 11.36 0.00 37.49 3.96
2398 2444 4.320494 GGGATGATACGTCCATTTTGCATC 60.320 45.833 11.36 0.00 37.49 3.91
2399 2445 4.275689 GGATGATACGTCCATTTTGCATCA 59.724 41.667 0.00 0.00 35.76 3.07
2400 2446 5.048504 GGATGATACGTCCATTTTGCATCAT 60.049 40.000 0.00 0.00 35.07 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
133 137 5.048713 GGTGATAAGTTTGGAGTGTCAAAGG 60.049 44.000 0.00 0.00 37.31 3.11
137 141 4.262894 GGAGGTGATAAGTTTGGAGTGTCA 60.263 45.833 0.00 0.00 0.00 3.58
149 153 7.284034 AGCACTTTTCATATTGGAGGTGATAAG 59.716 37.037 0.00 0.00 37.13 1.73
154 158 5.647658 TGTAGCACTTTTCATATTGGAGGTG 59.352 40.000 0.00 0.00 0.00 4.00
160 164 9.289303 GGTGTTATTGTAGCACTTTTCATATTG 57.711 33.333 4.40 0.00 39.48 1.90
162 166 7.834181 AGGGTGTTATTGTAGCACTTTTCATAT 59.166 33.333 4.40 0.00 39.48 1.78
164 168 6.010219 AGGGTGTTATTGTAGCACTTTTCAT 58.990 36.000 4.40 0.00 39.48 2.57
184 188 3.977999 TCGATAATCCCCAATTACAGGGT 59.022 43.478 7.14 0.00 45.28 4.34
185 189 4.324267 GTCGATAATCCCCAATTACAGGG 58.676 47.826 0.00 1.65 46.36 4.45
188 192 5.455612 GGAAGGTCGATAATCCCCAATTACA 60.456 44.000 0.00 0.00 32.68 2.41
189 193 5.001874 GGAAGGTCGATAATCCCCAATTAC 58.998 45.833 0.00 0.00 32.68 1.89
190 194 4.661240 TGGAAGGTCGATAATCCCCAATTA 59.339 41.667 9.87 0.00 34.37 1.40
205 209 8.336801 ACTTGAGTTATATTGTTTGGAAGGTC 57.663 34.615 0.00 0.00 0.00 3.85
266 270 2.092103 ACTGACAGTGGTGGCCTAAAAA 60.092 45.455 7.47 0.00 0.00 1.94
292 297 7.626452 GCACTAACTATGGGAAAAATCAGTGTC 60.626 40.741 0.00 0.00 33.82 3.67
297 302 7.450014 TGAAAGCACTAACTATGGGAAAAATCA 59.550 33.333 0.00 0.00 0.00 2.57
725 759 9.696917 ACAACATTGTTCATAGAAAATCTTTCC 57.303 29.630 0.00 0.00 38.47 3.13
885 920 6.697455 TGACTATTGATGCATCTTTCGAGTAC 59.303 38.462 26.32 14.82 0.00 2.73
908 943 4.757019 TTGGCGGTGTTTATATAGGTGA 57.243 40.909 0.00 0.00 0.00 4.02
926 961 6.345723 GCGATGTGTTACAAATTTCACTTTGG 60.346 38.462 8.64 1.49 39.83 3.28
936 971 8.888716 TGTTCTAATATGCGATGTGTTACAAAT 58.111 29.630 0.00 0.00 0.00 2.32
971 1006 5.116084 AGGCCAGCAAGTGATTTCTATTA 57.884 39.130 5.01 0.00 0.00 0.98
972 1007 3.950395 GAGGCCAGCAAGTGATTTCTATT 59.050 43.478 5.01 0.00 0.00 1.73
997 1032 5.549742 TTCATCTTGAAGGTTGCCATTTT 57.450 34.783 0.00 0.00 31.83 1.82
1040 1075 2.503061 CCAGGACCATGAGAGCCG 59.497 66.667 0.00 0.00 0.00 5.52
1099 1134 7.815383 TGGGATTCAGAAAGGAATGTACATAT 58.185 34.615 9.21 0.00 37.61 1.78
1103 1138 6.834168 TTTGGGATTCAGAAAGGAATGTAC 57.166 37.500 0.00 0.00 37.61 2.90
1106 1141 6.596497 CCATTTTTGGGATTCAGAAAGGAATG 59.404 38.462 0.00 0.00 37.61 2.67
1107 1142 6.501453 TCCATTTTTGGGATTCAGAAAGGAAT 59.499 34.615 0.00 0.00 40.10 3.01
1272 1308 1.725164 GCAACTTGCAGGTACTCGTAC 59.275 52.381 8.97 0.00 44.26 3.67
1298 1334 7.994425 TTCAGTGCATTTAGGAAACTTCATA 57.006 32.000 0.00 0.00 43.67 2.15
1320 1356 4.800471 GCAATACTTGTAGCATGCCTTTTC 59.200 41.667 15.66 1.17 0.00 2.29
1322 1358 3.763360 TGCAATACTTGTAGCATGCCTTT 59.237 39.130 15.66 0.00 33.01 3.11
1413 1449 1.004277 CCCAAAAGTTCCATCTCCGGA 59.996 52.381 2.93 2.93 0.00 5.14
1416 1452 3.230976 ACAACCCAAAAGTTCCATCTCC 58.769 45.455 0.00 0.00 0.00 3.71
1423 1459 7.926018 AGATTAAACATGACAACCCAAAAGTTC 59.074 33.333 0.00 0.00 0.00 3.01
1447 1483 9.672673 AAATAGCAAGCTTTCTTTAGTCATAGA 57.327 29.630 3.35 0.00 0.00 1.98
1479 1515 5.779922 CAAGGCTATCCATTTCAATGATGG 58.220 41.667 0.81 0.00 44.39 3.51
1483 1519 4.340097 TGAGCAAGGCTATCCATTTCAATG 59.660 41.667 0.00 0.00 39.88 2.82
1492 1528 3.255149 CCAATTCATGAGCAAGGCTATCC 59.745 47.826 0.00 0.00 39.88 2.59
1549 1585 5.761165 TCATGGTGCATTCATGTATCTTG 57.239 39.130 23.29 6.91 41.79 3.02
1556 1592 2.863740 GCATGTTCATGGTGCATTCATG 59.136 45.455 20.30 20.30 42.28 3.07
1677 1713 0.117140 TTGCCAAGGAGGAGGAGAGA 59.883 55.000 0.00 0.00 41.22 3.10
1681 1717 0.178891 ACTCTTGCCAAGGAGGAGGA 60.179 55.000 4.30 0.00 41.22 3.71
1714 1750 5.396213 GCTCAGTGAATAGGGAAGAGTTGAT 60.396 44.000 0.00 0.00 0.00 2.57
1727 1764 6.798427 AGTTAATCTCCAGCTCAGTGAATA 57.202 37.500 0.00 0.00 0.00 1.75
1728 1765 5.690464 AGTTAATCTCCAGCTCAGTGAAT 57.310 39.130 0.00 0.00 0.00 2.57
1730 1767 4.081420 GGAAGTTAATCTCCAGCTCAGTGA 60.081 45.833 0.00 0.00 0.00 3.41
1731 1768 4.187694 GGAAGTTAATCTCCAGCTCAGTG 58.812 47.826 0.00 0.00 0.00 3.66
1732 1769 3.840666 TGGAAGTTAATCTCCAGCTCAGT 59.159 43.478 4.74 0.00 0.00 3.41
1734 1771 6.560003 TTATGGAAGTTAATCTCCAGCTCA 57.440 37.500 12.49 0.00 35.54 4.26
1736 1773 7.406104 ACTTTTATGGAAGTTAATCTCCAGCT 58.594 34.615 12.49 0.00 36.49 4.24
1737 1774 7.631717 ACTTTTATGGAAGTTAATCTCCAGC 57.368 36.000 12.49 0.00 36.49 4.85
1738 1775 9.892130 AGTACTTTTATGGAAGTTAATCTCCAG 57.108 33.333 12.49 3.69 40.24 3.86
1739 1776 9.886132 GAGTACTTTTATGGAAGTTAATCTCCA 57.114 33.333 10.07 10.07 40.24 3.86
1767 1804 3.187700 GTGTTCTACTCCAATAGGCACG 58.812 50.000 0.00 0.00 33.74 5.34
1785 1822 6.093219 CAGCAATCTGTATAGCTTCTTTGTGT 59.907 38.462 0.00 0.00 34.61 3.72
1793 1830 4.406972 TGACCTCAGCAATCTGTATAGCTT 59.593 41.667 0.00 0.00 41.10 3.74
1829 1866 3.826729 GGTAGGTGCAAGGAAAAGTTGAT 59.173 43.478 0.00 0.00 0.00 2.57
1839 1877 3.006728 TCCCGGGTAGGTGCAAGG 61.007 66.667 22.86 0.00 38.74 3.61
1841 1879 2.203877 ACTCCCGGGTAGGTGCAA 60.204 61.111 22.86 0.00 38.74 4.08
1852 1890 3.469008 TTATTGATAGTGGCACTCCCG 57.531 47.619 25.80 0.00 35.87 5.14
1857 1895 7.702348 GGAAATCTTGTTTATTGATAGTGGCAC 59.298 37.037 10.29 10.29 0.00 5.01
1862 1900 8.877864 TGTGGGAAATCTTGTTTATTGATAGT 57.122 30.769 0.00 0.00 0.00 2.12
1885 1923 5.362717 TGGATAACCGACATCATTACTCTGT 59.637 40.000 0.00 0.00 39.42 3.41
1886 1924 5.842907 TGGATAACCGACATCATTACTCTG 58.157 41.667 0.00 0.00 39.42 3.35
1887 1925 5.509840 GCTGGATAACCGACATCATTACTCT 60.510 44.000 0.00 0.00 39.42 3.24
1890 1928 3.428870 CGCTGGATAACCGACATCATTAC 59.571 47.826 0.00 0.00 39.42 1.89
1899 1937 0.604073 TGAACACGCTGGATAACCGA 59.396 50.000 0.00 0.00 39.42 4.69
1901 1939 1.803334 TGTGAACACGCTGGATAACC 58.197 50.000 0.57 0.00 0.00 2.85
1917 1955 3.243569 TGCCAACCGAATAACCTTTTGTG 60.244 43.478 0.00 0.00 0.00 3.33
1934 1972 0.112995 AGAGGAAGGTTGCATGCCAA 59.887 50.000 16.68 6.85 0.00 4.52
1943 1981 1.662686 CTCCCCAAGAGAGGAAGGTT 58.337 55.000 0.00 0.00 46.50 3.50
1952 1990 8.889220 ATCATGATGATGTACTCTCCCCAAGAG 61.889 44.444 7.59 0.59 45.19 2.85
1963 2001 5.069648 ACGGAGTTGATCATGATGATGTACT 59.930 40.000 14.30 14.44 37.78 2.73
1965 2003 5.535753 ACGGAGTTGATCATGATGATGTA 57.464 39.130 14.30 0.00 37.78 2.29
2000 2038 5.567138 AATAGTCAATGCAGTAGTTTGGC 57.433 39.130 0.00 0.00 0.00 4.52
2015 2053 3.831911 CCTTGGGCCAAAGAAAATAGTCA 59.168 43.478 22.44 0.00 0.00 3.41
2017 2055 4.126520 TCCTTGGGCCAAAGAAAATAGT 57.873 40.909 22.44 0.00 0.00 2.12
2043 2081 6.715280 TGATTGGTCTCTTTAGCTTCTCAAT 58.285 36.000 0.00 0.00 0.00 2.57
2053 2091 5.249393 AGGAAAGCTCTGATTGGTCTCTTTA 59.751 40.000 0.00 0.00 0.00 1.85
2057 2095 3.197549 AGAGGAAAGCTCTGATTGGTCTC 59.802 47.826 0.00 0.00 0.00 3.36
2066 2104 1.451067 CTTGCCAGAGGAAAGCTCTG 58.549 55.000 0.00 0.00 45.65 3.35
2087 2125 5.405935 AACTTCCATGGGCATAGTTTTTC 57.594 39.130 13.02 0.00 0.00 2.29
2089 2127 5.418840 CAGTAACTTCCATGGGCATAGTTTT 59.581 40.000 13.02 6.43 31.94 2.43
2091 2129 4.018415 ACAGTAACTTCCATGGGCATAGTT 60.018 41.667 13.02 17.17 33.89 2.24
2114 2152 5.836821 ATGTCTATCTCGAGCTGTTACAA 57.163 39.130 7.81 0.00 0.00 2.41
2124 2162 3.256879 GGCATCTGGAATGTCTATCTCGA 59.743 47.826 0.00 0.00 0.00 4.04
2130 2168 3.114606 TGGAAGGCATCTGGAATGTCTA 58.885 45.455 0.00 0.00 32.02 2.59
2132 2170 2.425143 TGGAAGGCATCTGGAATGTC 57.575 50.000 0.00 0.00 0.00 3.06
2229 2267 0.038166 ACGGAGTGCCAATCCAATGT 59.962 50.000 12.24 0.00 42.51 2.71
2238 2276 0.179032 ATGACAACAACGGAGTGCCA 60.179 50.000 0.00 0.00 45.00 4.92
2239 2277 0.951558 AATGACAACAACGGAGTGCC 59.048 50.000 0.00 0.00 45.00 5.01
2261 2299 4.184629 ACCAACGCATGCAAGTTTTTAAA 58.815 34.783 19.57 0.00 0.00 1.52
2262 2300 3.786635 ACCAACGCATGCAAGTTTTTAA 58.213 36.364 19.57 0.00 0.00 1.52
2263 2301 3.444703 ACCAACGCATGCAAGTTTTTA 57.555 38.095 19.57 0.00 0.00 1.52
2291 2331 4.387862 TCAACGAAGATAACGGAAAGAAGC 59.612 41.667 0.00 0.00 34.93 3.86
2320 2360 0.106268 ATGTGCAACTGTGGTCCCAA 60.106 50.000 0.00 0.00 38.04 4.12
2331 2377 0.314618 TGCCATGTGTCATGTGCAAC 59.685 50.000 16.87 0.00 37.35 4.17
2341 2387 5.643379 AATTCTTTAACGATGCCATGTGT 57.357 34.783 0.00 0.00 0.00 3.72
2348 2394 9.353999 ACTTGGAAAATAATTCTTTAACGATGC 57.646 29.630 0.00 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.