Multiple sequence alignment - TraesCS3B01G484100

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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 TraesCS3B01G484100 chr3B 100.000 2291 0 0 1 2291 730716055 730718345 0.000000e+00 4231.0
1 TraesCS3B01G484100 chr3B 99.765 850 2 0 1 850 730705555 730706404 0.000000e+00 1559.0
2 TraesCS3B01G484100 chr3D 89.555 2202 151 20 1 2150 551067632 551069806 0.000000e+00 2719.0
3 TraesCS3B01G484100 chr3D 92.607 514 37 1 75 587 550711454 550710941 0.000000e+00 737.0
4 TraesCS3B01G484100 chr3A 88.317 1652 139 20 350 1952 688197063 688198709 0.000000e+00 1932.0
5 TraesCS3B01G484100 chr3A 88.257 1652 140 20 350 1952 688229813 688231459 0.000000e+00 1927.0
6 TraesCS3B01G484100 chr3A 92.216 334 19 6 1 328 688196643 688196975 1.240000e-127 466.0
7 TraesCS3B01G484100 chr3A 92.216 334 19 6 1 328 688229393 688229725 1.240000e-127 466.0
8 TraesCS3B01G484100 chr3A 91.667 180 6 2 1979 2150 688198708 688198886 8.180000e-60 241.0
9 TraesCS3B01G484100 chr3A 91.667 180 6 2 1979 2150 688231458 688231636 8.180000e-60 241.0
10 TraesCS3B01G484100 chr1B 97.887 142 3 0 2150 2291 104738537 104738396 1.760000e-61 246.0
11 TraesCS3B01G484100 chr7D 95.205 146 7 0 2146 2291 9173590 9173445 4.920000e-57 231.0
12 TraesCS3B01G484100 chr2B 95.070 142 7 0 2150 2291 519127698 519127557 8.240000e-55 224.0
13 TraesCS3B01G484100 chr2B 92.254 142 6 1 2155 2291 796951425 796951566 1.800000e-46 196.0
14 TraesCS3B01G484100 chr5A 94.286 140 6 1 2152 2291 532565924 532566061 1.780000e-51 213.0
15 TraesCS3B01G484100 chr4D 93.571 140 9 0 2152 2291 202758619 202758480 2.310000e-50 209.0
16 TraesCS3B01G484100 chr7B 96.639 119 4 0 2144 2262 128048092 128048210 4.990000e-47 198.0
17 TraesCS3B01G484100 chr7B 94.286 35 2 0 1841 1875 672759260 672759226 1.000000e-03 54.7
18 TraesCS3B01G484100 chr4B 91.549 142 12 0 2150 2291 604295218 604295077 1.800000e-46 196.0
19 TraesCS3B01G484100 chr2D 90.647 139 13 0 2151 2289 22936670 22936532 3.890000e-43 185.0


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 TraesCS3B01G484100 chr3B 730716055 730718345 2290 False 4231.000000 4231 100.000000 1 2291 1 chr3B.!!$F2 2290
1 TraesCS3B01G484100 chr3B 730705555 730706404 849 False 1559.000000 1559 99.765000 1 850 1 chr3B.!!$F1 849
2 TraesCS3B01G484100 chr3D 551067632 551069806 2174 False 2719.000000 2719 89.555000 1 2150 1 chr3D.!!$F1 2149
3 TraesCS3B01G484100 chr3D 550710941 550711454 513 True 737.000000 737 92.607000 75 587 1 chr3D.!!$R1 512
4 TraesCS3B01G484100 chr3A 688196643 688198886 2243 False 879.666667 1932 90.733333 1 2150 3 chr3A.!!$F1 2149
5 TraesCS3B01G484100 chr3A 688229393 688231636 2243 False 878.000000 1927 90.713333 1 2150 3 chr3A.!!$F2 2149

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
253 269 2.672651 CGTGGCATGGAACCAGCA 60.673 61.111 0.0 0.0 38.04 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1305 1430 0.179009 ACAAGAAGAGGCAGCAGCAA 60.179 50.0 2.65 0.0 44.61 3.91 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
253 269 2.672651 CGTGGCATGGAACCAGCA 60.673 61.111 0.00 0.00 38.04 4.41
959 1075 4.821805 GTGGCAGCAAAGCTATTCCTATTA 59.178 41.667 0.00 0.00 36.40 0.98
971 1087 8.507524 AGCTATTCCTATTACCACTTGTTTTC 57.492 34.615 0.00 0.00 0.00 2.29
982 1098 3.450817 CCACTTGTTTTCCCCTTCAAACT 59.549 43.478 0.00 0.00 34.52 2.66
986 1102 4.379339 TGTTTTCCCCTTCAAACTTTCG 57.621 40.909 0.00 0.00 34.52 3.46
1047 1163 0.988832 TCAACGGGGAGCAAGGTAAT 59.011 50.000 0.00 0.00 0.00 1.89
1182 1298 2.271497 GCTGCCATGCTCCTCTGT 59.729 61.111 0.00 0.00 0.00 3.41
1188 1304 3.709633 ATGCTCCTCTGTGCGGCA 61.710 61.111 0.00 0.00 37.32 5.69
1241 1357 4.117372 CGTCAACGAGTTCGGCGC 62.117 66.667 0.00 0.00 44.95 6.53
1257 1373 2.786495 CGCCGACTACCATGCTCCT 61.786 63.158 0.00 0.00 0.00 3.69
1286 1402 2.558821 CGCCAACGAAAATCGCCA 59.441 55.556 0.00 0.00 45.12 5.69
1324 1449 0.179009 TTGCTGCTGCCTCTTCTTGT 60.179 50.000 13.47 0.00 38.71 3.16
1334 1459 2.670414 GCCTCTTCTTGTTCATCGTGAG 59.330 50.000 0.00 0.00 0.00 3.51
1346 1471 2.362397 TCATCGTGAGTTGGATCTAGCC 59.638 50.000 0.00 0.00 0.00 3.93
1456 1581 2.106332 GTGTCCCGTCCGCATAGG 59.894 66.667 0.00 0.00 42.97 2.57
1474 1599 5.410746 GCATAGGTCGATCAATGTGATGAAT 59.589 40.000 0.00 0.00 37.20 2.57
1486 1611 9.713713 ATCAATGTGATGAATCTCTTCTATGAG 57.286 33.333 0.00 0.00 35.43 2.90
1490 1615 8.071177 TGTGATGAATCTCTTCTATGAGTTCA 57.929 34.615 0.00 0.00 37.87 3.18
1510 1635 5.549742 TCAAATTTGATTTCCCTTGTGCT 57.450 34.783 16.91 0.00 31.01 4.40
1512 1637 5.990996 TCAAATTTGATTTCCCTTGTGCTTC 59.009 36.000 16.91 0.00 31.01 3.86
1527 1652 3.753272 TGTGCTTCTTTACTTGATGAGGC 59.247 43.478 0.00 0.00 33.13 4.70
1533 1658 6.515696 GCTTCTTTACTTGATGAGGCTTGTTT 60.516 38.462 0.00 0.00 0.00 2.83
1537 1662 6.959639 TTACTTGATGAGGCTTGTTTTTCT 57.040 33.333 0.00 0.00 0.00 2.52
1538 1663 5.859205 ACTTGATGAGGCTTGTTTTTCTT 57.141 34.783 0.00 0.00 0.00 2.52
1540 1665 6.643388 ACTTGATGAGGCTTGTTTTTCTTTT 58.357 32.000 0.00 0.00 0.00 2.27
1549 1679 7.564793 AGGCTTGTTTTTCTTTTACTTTCCAT 58.435 30.769 0.00 0.00 0.00 3.41
1556 1686 7.443259 TTTTCTTTTACTTTCCATAGTCCGG 57.557 36.000 0.00 0.00 0.00 5.14
1569 1699 9.689501 TTTCCATAGTCCGGAAGTAATTAATTT 57.310 29.630 5.23 0.00 43.29 1.82
1631 1761 4.517285 GTGTAATGTCACCAGATCACCAT 58.483 43.478 0.00 0.00 32.81 3.55
1642 1772 3.321968 CCAGATCACCATATCGAGGAACA 59.678 47.826 0.00 0.00 31.47 3.18
1643 1773 4.020751 CCAGATCACCATATCGAGGAACAT 60.021 45.833 0.00 0.00 31.47 2.71
1659 1789 6.350629 AGGAACATCCTTTTCTTTTGGATG 57.649 37.500 16.73 16.73 46.91 3.51
1669 1803 7.495934 TCCTTTTCTTTTGGATGTATCGATCTC 59.504 37.037 0.00 0.00 0.00 2.75
1672 1806 6.090483 TCTTTTGGATGTATCGATCTCCTC 57.910 41.667 17.58 9.09 0.00 3.71
1699 1833 2.266376 AAGCTACTCGCATCGTCGCA 62.266 55.000 0.00 0.00 42.61 5.10
1714 1848 4.468689 GCACACGTAGGCCCCTCC 62.469 72.222 0.00 0.00 0.00 4.30
1719 1853 0.396695 CACGTAGGCCCCTCCTTCTA 60.397 60.000 0.00 0.00 44.75 2.10
1723 1857 0.264955 TAGGCCCCTCCTTCTACTGG 59.735 60.000 0.00 0.00 44.75 4.00
1756 1890 1.137513 GGACCATATTACGCTCGCAC 58.862 55.000 0.00 0.00 0.00 5.34
1759 1893 1.282248 CCATATTACGCTCGCACGGG 61.282 60.000 2.08 0.00 37.37 5.28
1760 1894 0.318360 CATATTACGCTCGCACGGGA 60.318 55.000 0.00 0.00 37.37 5.14
1773 1907 1.599542 GCACGGGAGCTTGATGATTAC 59.400 52.381 0.00 0.00 0.00 1.89
1777 1911 3.126831 CGGGAGCTTGATGATTACTCAC 58.873 50.000 0.00 0.00 33.22 3.51
1780 1914 4.141846 GGGAGCTTGATGATTACTCACTGA 60.142 45.833 0.00 0.00 33.22 3.41
1781 1915 5.423015 GGAGCTTGATGATTACTCACTGAA 58.577 41.667 0.00 0.00 33.22 3.02
1788 1922 6.567959 TGATGATTACTCACTGAACTAGCAG 58.432 40.000 0.00 0.00 41.63 4.24
1796 1930 4.973168 TCACTGAACTAGCAGGTTGAAAT 58.027 39.130 0.00 0.00 40.20 2.17
1810 1944 0.665835 TGAAATCAACACCACCGTGC 59.334 50.000 0.00 0.00 44.40 5.34
1813 1947 1.503818 AATCAACACCACCGTGCGTC 61.504 55.000 0.00 0.00 44.40 5.19
1815 1949 2.587753 AACACCACCGTGCGTCAG 60.588 61.111 0.00 0.00 44.40 3.51
1837 1971 3.729462 GCGTGAGACTAGTGCTGTAAGAG 60.729 52.174 0.00 0.00 34.07 2.85
1844 1978 6.915349 AGACTAGTGCTGTAAGAGTTTACTG 58.085 40.000 0.00 0.73 39.90 2.74
1852 1986 2.521105 AAGAGTTTACTGCGTCCGTT 57.479 45.000 0.00 0.00 0.00 4.44
1853 1987 2.521105 AGAGTTTACTGCGTCCGTTT 57.479 45.000 0.00 0.00 0.00 3.60
1854 1988 2.401351 AGAGTTTACTGCGTCCGTTTC 58.599 47.619 0.00 0.00 0.00 2.78
1867 2001 6.509656 TGCGTCCGTTTCATAATATAAGAGT 58.490 36.000 0.00 0.00 0.00 3.24
1905 2039 3.841255 TGAGTATGTATGTTGGGTGGACA 59.159 43.478 0.00 0.00 0.00 4.02
1918 2052 1.310904 GTGGACACCGCAACCTTTTA 58.689 50.000 0.00 0.00 33.65 1.52
1931 2065 5.977129 CGCAACCTTTTACTCTTTTGATTGT 59.023 36.000 0.00 0.00 0.00 2.71
1997 2134 2.035442 GCTGAGCTCCGGTCCAAAC 61.035 63.158 12.15 0.00 0.00 2.93
2049 2186 2.086610 AGTTTCCACAAGGCAATGGT 57.913 45.000 2.19 0.00 37.27 3.55
2050 2187 3.237268 AGTTTCCACAAGGCAATGGTA 57.763 42.857 2.19 0.00 37.27 3.25
2060 2197 1.139520 GCAATGGTAAAGGCTGCCG 59.860 57.895 13.96 0.00 30.90 5.69
2061 2198 1.809207 CAATGGTAAAGGCTGCCGG 59.191 57.895 13.96 0.00 30.90 6.13
2174 2319 2.774439 TTTTGAACAAGAGAAGGCGC 57.226 45.000 0.00 0.00 0.00 6.53
2175 2320 1.967319 TTTGAACAAGAGAAGGCGCT 58.033 45.000 7.64 0.00 0.00 5.92
2176 2321 1.967319 TTGAACAAGAGAAGGCGCTT 58.033 45.000 7.64 0.00 34.28 4.68
2177 2322 2.831685 TGAACAAGAGAAGGCGCTTA 57.168 45.000 7.64 0.00 32.63 3.09
2178 2323 3.120321 TGAACAAGAGAAGGCGCTTAA 57.880 42.857 7.64 0.00 32.63 1.85
2179 2324 3.472652 TGAACAAGAGAAGGCGCTTAAA 58.527 40.909 7.64 0.00 32.63 1.52
2180 2325 3.498397 TGAACAAGAGAAGGCGCTTAAAG 59.502 43.478 7.64 0.00 32.63 1.85
2181 2326 1.807142 ACAAGAGAAGGCGCTTAAAGC 59.193 47.619 7.64 0.00 38.02 3.51
2196 2341 4.853743 GCTTAAAGCGCCAATATATTCAGC 59.146 41.667 2.29 1.17 0.00 4.26
2197 2342 5.335191 GCTTAAAGCGCCAATATATTCAGCT 60.335 40.000 2.29 11.94 34.70 4.24
2198 2343 4.756084 AAAGCGCCAATATATTCAGCTC 57.244 40.909 2.29 8.39 32.57 4.09
2199 2344 3.407424 AGCGCCAATATATTCAGCTCA 57.593 42.857 2.29 0.00 0.00 4.26
2200 2345 3.332919 AGCGCCAATATATTCAGCTCAG 58.667 45.455 2.29 2.46 0.00 3.35
2201 2346 3.070018 GCGCCAATATATTCAGCTCAGT 58.930 45.455 12.79 0.00 0.00 3.41
2202 2347 4.021104 AGCGCCAATATATTCAGCTCAGTA 60.021 41.667 2.29 0.00 0.00 2.74
2203 2348 4.328440 GCGCCAATATATTCAGCTCAGTAG 59.672 45.833 12.79 1.40 0.00 2.57
2217 2362 3.704512 CTCAGTAGCAGAGTACAGCATG 58.295 50.000 0.00 0.00 46.00 4.06
2218 2363 3.356290 TCAGTAGCAGAGTACAGCATGA 58.644 45.455 0.00 0.37 39.69 3.07
2219 2364 3.763897 TCAGTAGCAGAGTACAGCATGAA 59.236 43.478 0.00 0.00 39.69 2.57
2220 2365 4.111198 CAGTAGCAGAGTACAGCATGAAG 58.889 47.826 0.00 0.00 39.69 3.02
2221 2366 3.766591 AGTAGCAGAGTACAGCATGAAGT 59.233 43.478 0.00 0.00 39.69 3.01
2222 2367 4.950475 AGTAGCAGAGTACAGCATGAAGTA 59.050 41.667 0.00 0.00 39.69 2.24
2223 2368 4.116747 AGCAGAGTACAGCATGAAGTAC 57.883 45.455 16.09 16.09 39.69 2.73
2224 2369 3.511540 AGCAGAGTACAGCATGAAGTACA 59.488 43.478 22.23 0.00 42.26 2.90
2225 2370 4.021104 AGCAGAGTACAGCATGAAGTACAA 60.021 41.667 22.23 0.00 42.26 2.41
2226 2371 4.690748 GCAGAGTACAGCATGAAGTACAAA 59.309 41.667 22.23 0.00 42.26 2.83
2227 2372 5.163913 GCAGAGTACAGCATGAAGTACAAAG 60.164 44.000 22.23 14.77 42.26 2.77
2228 2373 4.932200 AGAGTACAGCATGAAGTACAAAGC 59.068 41.667 22.23 12.64 42.26 3.51
2229 2374 4.003648 AGTACAGCATGAAGTACAAAGCC 58.996 43.478 22.23 3.27 42.26 4.35
2230 2375 2.162681 ACAGCATGAAGTACAAAGCCC 58.837 47.619 0.00 0.00 39.69 5.19
2231 2376 2.224867 ACAGCATGAAGTACAAAGCCCT 60.225 45.455 0.00 0.00 39.69 5.19
2232 2377 2.163010 CAGCATGAAGTACAAAGCCCTG 59.837 50.000 0.00 0.00 39.69 4.45
2233 2378 2.162681 GCATGAAGTACAAAGCCCTGT 58.837 47.619 0.00 0.00 0.00 4.00
2234 2379 3.009033 AGCATGAAGTACAAAGCCCTGTA 59.991 43.478 0.00 0.00 35.29 2.74
2235 2380 3.756434 GCATGAAGTACAAAGCCCTGTAA 59.244 43.478 0.00 0.00 33.66 2.41
2236 2381 4.217550 GCATGAAGTACAAAGCCCTGTAAA 59.782 41.667 0.00 0.00 33.66 2.01
2237 2382 5.619981 GCATGAAGTACAAAGCCCTGTAAAG 60.620 44.000 0.00 0.00 33.66 1.85
2238 2383 5.298989 TGAAGTACAAAGCCCTGTAAAGA 57.701 39.130 0.00 0.00 33.66 2.52
2239 2384 5.061179 TGAAGTACAAAGCCCTGTAAAGAC 58.939 41.667 0.00 0.00 33.66 3.01
2240 2385 4.699925 AGTACAAAGCCCTGTAAAGACA 57.300 40.909 0.00 0.00 33.66 3.41
2241 2386 4.386711 AGTACAAAGCCCTGTAAAGACAC 58.613 43.478 0.00 0.00 33.66 3.67
2242 2387 2.218603 ACAAAGCCCTGTAAAGACACG 58.781 47.619 0.00 0.00 0.00 4.49
2243 2388 1.535462 CAAAGCCCTGTAAAGACACGG 59.465 52.381 0.00 0.00 35.48 4.94
2244 2389 0.763035 AAGCCCTGTAAAGACACGGT 59.237 50.000 0.00 0.00 35.00 4.83
2245 2390 1.636148 AGCCCTGTAAAGACACGGTA 58.364 50.000 0.00 0.00 35.00 4.02
2246 2391 1.549170 AGCCCTGTAAAGACACGGTAG 59.451 52.381 0.00 0.00 35.00 3.18
2247 2392 1.547372 GCCCTGTAAAGACACGGTAGA 59.453 52.381 0.00 0.00 35.00 2.59
2248 2393 2.167900 GCCCTGTAAAGACACGGTAGAT 59.832 50.000 0.00 0.00 35.00 1.98
2249 2394 3.382546 GCCCTGTAAAGACACGGTAGATA 59.617 47.826 0.00 0.00 35.00 1.98
2250 2395 4.142093 GCCCTGTAAAGACACGGTAGATAA 60.142 45.833 0.00 0.00 35.00 1.75
2251 2396 5.589192 CCCTGTAAAGACACGGTAGATAAG 58.411 45.833 0.00 0.00 29.69 1.73
2252 2397 5.359009 CCCTGTAAAGACACGGTAGATAAGA 59.641 44.000 0.00 0.00 29.69 2.10
2253 2398 6.040616 CCCTGTAAAGACACGGTAGATAAGAT 59.959 42.308 0.00 0.00 29.69 2.40
2254 2399 7.230108 CCCTGTAAAGACACGGTAGATAAGATA 59.770 40.741 0.00 0.00 29.69 1.98
2255 2400 8.291032 CCTGTAAAGACACGGTAGATAAGATAG 58.709 40.741 0.00 0.00 0.00 2.08
2256 2401 8.969260 TGTAAAGACACGGTAGATAAGATAGA 57.031 34.615 0.00 0.00 0.00 1.98
2257 2402 9.399797 TGTAAAGACACGGTAGATAAGATAGAA 57.600 33.333 0.00 0.00 0.00 2.10
2258 2403 9.881529 GTAAAGACACGGTAGATAAGATAGAAG 57.118 37.037 0.00 0.00 0.00 2.85
2259 2404 8.522542 AAAGACACGGTAGATAAGATAGAAGT 57.477 34.615 0.00 0.00 0.00 3.01
2260 2405 8.522542 AAGACACGGTAGATAAGATAGAAGTT 57.477 34.615 0.00 0.00 0.00 2.66
2261 2406 9.624373 AAGACACGGTAGATAAGATAGAAGTTA 57.376 33.333 0.00 0.00 0.00 2.24
2262 2407 9.054922 AGACACGGTAGATAAGATAGAAGTTAC 57.945 37.037 0.00 0.00 0.00 2.50
2263 2408 8.743085 ACACGGTAGATAAGATAGAAGTTACA 57.257 34.615 0.00 0.00 0.00 2.41
2264 2409 9.352191 ACACGGTAGATAAGATAGAAGTTACAT 57.648 33.333 0.00 0.00 0.00 2.29
2265 2410 9.613957 CACGGTAGATAAGATAGAAGTTACATG 57.386 37.037 0.00 0.00 0.00 3.21
2266 2411 9.570468 ACGGTAGATAAGATAGAAGTTACATGA 57.430 33.333 0.00 0.00 0.00 3.07
2267 2412 9.828852 CGGTAGATAAGATAGAAGTTACATGAC 57.171 37.037 0.00 0.00 0.00 3.06
2273 2418 9.890629 ATAAGATAGAAGTTACATGACAAAGCA 57.109 29.630 0.00 0.00 0.00 3.91
2274 2419 8.798859 AAGATAGAAGTTACATGACAAAGCAT 57.201 30.769 0.00 0.00 0.00 3.79
2284 2429 5.823209 CATGACAAAGCATGGTCTTATGA 57.177 39.130 0.00 0.00 41.45 2.15
2285 2430 5.817988 CATGACAAAGCATGGTCTTATGAG 58.182 41.667 0.00 0.00 41.45 2.90
2286 2431 3.691118 TGACAAAGCATGGTCTTATGAGC 59.309 43.478 0.00 1.05 40.79 4.26
2287 2432 3.944015 GACAAAGCATGGTCTTATGAGCT 59.056 43.478 0.00 0.00 40.98 4.09
2288 2433 3.693085 ACAAAGCATGGTCTTATGAGCTG 59.307 43.478 0.00 6.26 40.98 4.24
2289 2434 3.920231 AAGCATGGTCTTATGAGCTGA 57.080 42.857 0.00 0.00 40.98 4.26
2290 2435 3.920231 AGCATGGTCTTATGAGCTGAA 57.080 42.857 8.99 0.00 40.98 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
253 269 8.386012 TGGTAAACCATGATTAAAAATGGGAT 57.614 30.769 18.90 11.90 46.45 3.85
959 1075 2.838637 TGAAGGGGAAAACAAGTGGT 57.161 45.000 0.00 0.00 0.00 4.16
986 1102 1.883084 CCCATGTTAGGCGCGAGAC 60.883 63.158 12.10 2.06 42.06 3.36
1065 1181 3.056458 CACTCCCTGTACCGCACA 58.944 61.111 0.00 0.00 35.30 4.57
1241 1357 1.360551 CGAGGAGCATGGTAGTCGG 59.639 63.158 16.73 3.23 0.00 4.79
1273 1389 2.595386 GCTTCAATGGCGATTTTCGTT 58.405 42.857 0.00 0.00 42.81 3.85
1305 1430 0.179009 ACAAGAAGAGGCAGCAGCAA 60.179 50.000 2.65 0.00 44.61 3.91
1324 1449 3.181475 GGCTAGATCCAACTCACGATGAA 60.181 47.826 0.00 0.00 0.00 2.57
1334 1459 2.693069 CATGATCCGGCTAGATCCAAC 58.307 52.381 0.00 0.00 41.73 3.77
1346 1471 2.203379 TGGGCCATGCATGATCCG 60.203 61.111 28.31 12.10 0.00 4.18
1368 1493 5.893255 AGATGAAATAAAATACTGCCAGCCA 59.107 36.000 0.00 0.00 0.00 4.75
1439 1564 2.106332 CCTATGCGGACGGGACAC 59.894 66.667 0.00 0.00 33.16 3.67
1452 1577 7.002250 AGATTCATCACATTGATCGACCTAT 57.998 36.000 0.00 0.00 34.28 2.57
1456 1581 6.700960 AGAAGAGATTCATCACATTGATCGAC 59.299 38.462 0.00 0.00 34.28 4.20
1463 1588 9.545105 GAACTCATAGAAGAGATTCATCACATT 57.455 33.333 0.00 0.00 38.98 2.71
1486 1611 5.759763 AGCACAAGGGAAATCAAATTTGAAC 59.240 36.000 23.91 16.93 41.13 3.18
1490 1615 6.178607 AGAAGCACAAGGGAAATCAAATTT 57.821 33.333 0.00 0.00 34.64 1.82
1510 1635 6.959639 AAACAAGCCTCATCAAGTAAAGAA 57.040 33.333 0.00 0.00 0.00 2.52
1512 1637 7.428826 AGAAAAACAAGCCTCATCAAGTAAAG 58.571 34.615 0.00 0.00 0.00 1.85
1533 1658 6.771573 TCCGGACTATGGAAAGTAAAAGAAA 58.228 36.000 0.00 0.00 30.98 2.52
1537 1662 6.117975 ACTTCCGGACTATGGAAAGTAAAA 57.882 37.500 1.83 0.00 44.52 1.52
1538 1663 5.750352 ACTTCCGGACTATGGAAAGTAAA 57.250 39.130 1.83 0.00 44.52 2.01
1540 1665 7.427989 AATTACTTCCGGACTATGGAAAGTA 57.572 36.000 1.83 3.65 44.52 2.24
1612 1742 5.538433 TCGATATGGTGATCTGGTGACATTA 59.462 40.000 0.00 0.00 41.51 1.90
1642 1772 7.995488 AGATCGATACATCCAAAAGAAAAGGAT 59.005 33.333 0.00 0.00 42.71 3.24
1643 1773 7.338710 AGATCGATACATCCAAAAGAAAAGGA 58.661 34.615 0.00 0.00 35.59 3.36
1652 1782 6.325028 AGAAAGAGGAGATCGATACATCCAAA 59.675 38.462 20.18 0.00 34.08 3.28
1655 1785 5.105917 GGAGAAAGAGGAGATCGATACATCC 60.106 48.000 13.43 13.43 0.00 3.51
1657 1787 5.389520 TGGAGAAAGAGGAGATCGATACAT 58.610 41.667 0.00 0.00 0.00 2.29
1658 1788 4.793201 TGGAGAAAGAGGAGATCGATACA 58.207 43.478 0.00 0.00 0.00 2.29
1659 1789 5.768317 CTTGGAGAAAGAGGAGATCGATAC 58.232 45.833 0.00 0.00 38.24 2.24
1664 1798 4.649218 AGTAGCTTGGAGAAAGAGGAGATC 59.351 45.833 0.00 0.00 38.24 2.75
1669 1803 2.737039 GCGAGTAGCTTGGAGAAAGAGG 60.737 54.545 0.00 0.00 44.04 3.69
1706 1840 0.914902 AACCAGTAGAAGGAGGGGCC 60.915 60.000 0.00 0.00 0.00 5.80
1709 1843 8.935741 ACTTAATTATAACCAGTAGAAGGAGGG 58.064 37.037 0.00 0.00 0.00 4.30
1751 1885 1.960040 ATCATCAAGCTCCCGTGCGA 61.960 55.000 0.00 0.00 38.13 5.10
1756 1890 3.126831 GTGAGTAATCATCAAGCTCCCG 58.873 50.000 0.00 0.00 0.00 5.14
1759 1893 6.105333 AGTTCAGTGAGTAATCATCAAGCTC 58.895 40.000 0.00 0.00 0.00 4.09
1760 1894 6.047511 AGTTCAGTGAGTAATCATCAAGCT 57.952 37.500 0.00 0.00 0.00 3.74
1773 1907 3.667497 TCAACCTGCTAGTTCAGTGAG 57.333 47.619 0.00 0.00 32.32 3.51
1777 1911 5.947228 TTGATTTCAACCTGCTAGTTCAG 57.053 39.130 0.00 0.00 0.00 3.02
1796 1930 2.586635 GACGCACGGTGGTGTTGA 60.587 61.111 10.60 0.00 46.13 3.18
1805 1939 4.700365 TCTCACGCTGACGCACGG 62.700 66.667 0.00 0.00 45.53 4.94
1806 1940 2.508755 TAGTCTCACGCTGACGCACG 62.509 60.000 0.00 0.00 45.53 5.34
1813 1947 3.027312 CAGCACTAGTCTCACGCTG 57.973 57.895 15.31 15.31 43.55 5.18
1815 1949 2.161808 TCTTACAGCACTAGTCTCACGC 59.838 50.000 0.00 0.00 0.00 5.34
1844 1978 8.684973 ATACTCTTATATTATGAAACGGACGC 57.315 34.615 0.00 0.00 0.00 5.19
1882 2016 4.473196 TGTCCACCCAACATACATACTCAT 59.527 41.667 0.00 0.00 0.00 2.90
1905 2039 3.949113 TCAAAAGAGTAAAAGGTTGCGGT 59.051 39.130 0.00 0.00 0.00 5.68
1931 2065 1.822990 CTACTTGCGGGGTCACTCTTA 59.177 52.381 0.00 0.00 0.00 2.10
1941 2076 3.857052 TGTGATAACTTCTACTTGCGGG 58.143 45.455 0.00 0.00 0.00 6.13
2049 2186 1.124780 TATAGCACCGGCAGCCTTTA 58.875 50.000 15.17 3.05 44.61 1.85
2050 2187 0.463833 GTATAGCACCGGCAGCCTTT 60.464 55.000 15.17 4.19 44.61 3.11
2060 2197 2.872038 GCAGTAGGCATGGTATAGCACC 60.872 54.545 6.80 5.12 45.02 5.01
2061 2198 2.417719 GCAGTAGGCATGGTATAGCAC 58.582 52.381 6.80 0.00 43.97 4.40
2154 2299 2.687935 AGCGCCTTCTCTTGTTCAAAAA 59.312 40.909 2.29 0.00 0.00 1.94
2155 2300 2.297701 AGCGCCTTCTCTTGTTCAAAA 58.702 42.857 2.29 0.00 0.00 2.44
2156 2301 1.967319 AGCGCCTTCTCTTGTTCAAA 58.033 45.000 2.29 0.00 0.00 2.69
2157 2302 1.967319 AAGCGCCTTCTCTTGTTCAA 58.033 45.000 2.29 0.00 0.00 2.69
2158 2303 2.831685 TAAGCGCCTTCTCTTGTTCA 57.168 45.000 2.29 0.00 0.00 3.18
2159 2304 3.668226 GCTTTAAGCGCCTTCTCTTGTTC 60.668 47.826 2.29 0.00 0.00 3.18
2160 2305 2.226674 GCTTTAAGCGCCTTCTCTTGTT 59.773 45.455 2.29 0.00 0.00 2.83
2161 2306 1.807142 GCTTTAAGCGCCTTCTCTTGT 59.193 47.619 2.29 0.00 0.00 3.16
2162 2307 2.534231 GCTTTAAGCGCCTTCTCTTG 57.466 50.000 2.29 0.00 0.00 3.02
2173 2318 4.853743 GCTGAATATATTGGCGCTTTAAGC 59.146 41.667 7.64 6.92 38.02 3.09
2174 2319 6.073058 TGAGCTGAATATATTGGCGCTTTAAG 60.073 38.462 7.64 0.00 0.00 1.85
2175 2320 5.762711 TGAGCTGAATATATTGGCGCTTTAA 59.237 36.000 7.64 0.44 0.00 1.52
2176 2321 5.304778 TGAGCTGAATATATTGGCGCTTTA 58.695 37.500 7.64 0.00 0.00 1.85
2177 2322 4.136796 TGAGCTGAATATATTGGCGCTTT 58.863 39.130 7.64 0.00 0.00 3.51
2178 2323 3.743521 TGAGCTGAATATATTGGCGCTT 58.256 40.909 7.64 0.00 0.00 4.68
2179 2324 3.244353 ACTGAGCTGAATATATTGGCGCT 60.244 43.478 7.64 14.52 0.00 5.92
2180 2325 3.070018 ACTGAGCTGAATATATTGGCGC 58.930 45.455 1.78 0.00 0.00 6.53
2181 2326 4.328440 GCTACTGAGCTGAATATATTGGCG 59.672 45.833 1.78 0.00 45.98 5.69
2182 2327 5.793026 GCTACTGAGCTGAATATATTGGC 57.207 43.478 1.78 7.23 45.98 4.52
2196 2341 3.379688 TCATGCTGTACTCTGCTACTGAG 59.620 47.826 0.00 0.52 38.91 3.35
2197 2342 3.356290 TCATGCTGTACTCTGCTACTGA 58.644 45.455 0.00 0.00 38.91 3.41
2198 2343 3.790152 TCATGCTGTACTCTGCTACTG 57.210 47.619 0.00 0.00 38.91 2.74
2199 2344 3.766591 ACTTCATGCTGTACTCTGCTACT 59.233 43.478 0.00 0.00 38.91 2.57
2200 2345 4.116747 ACTTCATGCTGTACTCTGCTAC 57.883 45.455 0.00 0.00 38.91 3.58
2201 2346 4.705023 TGTACTTCATGCTGTACTCTGCTA 59.295 41.667 20.59 5.24 39.57 3.49
2202 2347 3.511540 TGTACTTCATGCTGTACTCTGCT 59.488 43.478 20.59 0.00 39.57 4.24
2203 2348 3.849911 TGTACTTCATGCTGTACTCTGC 58.150 45.455 20.59 0.00 39.57 4.26
2204 2349 5.163913 GCTTTGTACTTCATGCTGTACTCTG 60.164 44.000 20.59 14.10 39.57 3.35
2205 2350 4.932200 GCTTTGTACTTCATGCTGTACTCT 59.068 41.667 20.59 0.00 39.57 3.24
2206 2351 4.093556 GGCTTTGTACTTCATGCTGTACTC 59.906 45.833 20.59 11.71 39.57 2.59
2207 2352 4.003648 GGCTTTGTACTTCATGCTGTACT 58.996 43.478 20.59 0.00 39.57 2.73
2208 2353 3.127030 GGGCTTTGTACTTCATGCTGTAC 59.873 47.826 16.16 16.16 39.37 2.90
2209 2354 3.009033 AGGGCTTTGTACTTCATGCTGTA 59.991 43.478 0.00 0.00 0.00 2.74
2210 2355 2.162681 GGGCTTTGTACTTCATGCTGT 58.837 47.619 0.00 0.00 0.00 4.40
2211 2356 2.163010 CAGGGCTTTGTACTTCATGCTG 59.837 50.000 0.00 0.00 0.00 4.41
2212 2357 2.224867 ACAGGGCTTTGTACTTCATGCT 60.225 45.455 0.00 0.00 0.00 3.79
2213 2358 2.162681 ACAGGGCTTTGTACTTCATGC 58.837 47.619 0.00 0.00 0.00 4.06
2214 2359 5.705441 TCTTTACAGGGCTTTGTACTTCATG 59.295 40.000 0.00 0.00 33.50 3.07
2215 2360 5.705905 GTCTTTACAGGGCTTTGTACTTCAT 59.294 40.000 0.00 0.00 33.50 2.57
2216 2361 5.061179 GTCTTTACAGGGCTTTGTACTTCA 58.939 41.667 0.00 0.00 33.50 3.02
2217 2362 5.049612 GTGTCTTTACAGGGCTTTGTACTTC 60.050 44.000 0.00 0.00 35.91 3.01
2218 2363 4.820173 GTGTCTTTACAGGGCTTTGTACTT 59.180 41.667 0.00 0.00 35.91 2.24
2219 2364 4.386711 GTGTCTTTACAGGGCTTTGTACT 58.613 43.478 0.00 0.00 35.91 2.73
2220 2365 3.185797 CGTGTCTTTACAGGGCTTTGTAC 59.814 47.826 2.63 0.00 37.75 2.90
2221 2366 3.395639 CGTGTCTTTACAGGGCTTTGTA 58.604 45.455 0.00 0.00 37.75 2.41
2222 2367 2.218603 CGTGTCTTTACAGGGCTTTGT 58.781 47.619 1.24 1.24 37.75 2.83
2223 2368 2.969443 CGTGTCTTTACAGGGCTTTG 57.031 50.000 0.00 0.00 37.75 2.77
2229 2374 6.446781 TCTTATCTACCGTGTCTTTACAGG 57.553 41.667 0.00 0.00 40.42 4.00
2230 2375 9.053840 TCTATCTTATCTACCGTGTCTTTACAG 57.946 37.037 0.00 0.00 35.91 2.74
2231 2376 8.969260 TCTATCTTATCTACCGTGTCTTTACA 57.031 34.615 0.00 0.00 0.00 2.41
2232 2377 9.881529 CTTCTATCTTATCTACCGTGTCTTTAC 57.118 37.037 0.00 0.00 0.00 2.01
2233 2378 9.624373 ACTTCTATCTTATCTACCGTGTCTTTA 57.376 33.333 0.00 0.00 0.00 1.85
2234 2379 8.522542 ACTTCTATCTTATCTACCGTGTCTTT 57.477 34.615 0.00 0.00 0.00 2.52
2235 2380 8.522542 AACTTCTATCTTATCTACCGTGTCTT 57.477 34.615 0.00 0.00 0.00 3.01
2236 2381 9.054922 GTAACTTCTATCTTATCTACCGTGTCT 57.945 37.037 0.00 0.00 0.00 3.41
2237 2382 8.834465 TGTAACTTCTATCTTATCTACCGTGTC 58.166 37.037 0.00 0.00 0.00 3.67
2238 2383 8.743085 TGTAACTTCTATCTTATCTACCGTGT 57.257 34.615 0.00 0.00 0.00 4.49
2239 2384 9.613957 CATGTAACTTCTATCTTATCTACCGTG 57.386 37.037 0.00 0.00 0.00 4.94
2240 2385 9.570468 TCATGTAACTTCTATCTTATCTACCGT 57.430 33.333 0.00 0.00 0.00 4.83
2241 2386 9.828852 GTCATGTAACTTCTATCTTATCTACCG 57.171 37.037 0.00 0.00 0.00 4.02
2247 2392 9.890629 TGCTTTGTCATGTAACTTCTATCTTAT 57.109 29.630 0.00 0.00 0.00 1.73
2248 2393 9.890629 ATGCTTTGTCATGTAACTTCTATCTTA 57.109 29.630 0.00 0.00 0.00 2.10
2249 2394 8.671921 CATGCTTTGTCATGTAACTTCTATCTT 58.328 33.333 0.00 0.00 39.10 2.40
2250 2395 7.281774 CCATGCTTTGTCATGTAACTTCTATCT 59.718 37.037 0.00 0.00 41.60 1.98
2251 2396 7.066284 ACCATGCTTTGTCATGTAACTTCTATC 59.934 37.037 0.00 0.00 41.60 2.08
2252 2397 6.886459 ACCATGCTTTGTCATGTAACTTCTAT 59.114 34.615 0.00 0.00 41.60 1.98
2253 2398 6.237901 ACCATGCTTTGTCATGTAACTTCTA 58.762 36.000 0.00 0.00 41.60 2.10
2254 2399 5.072741 ACCATGCTTTGTCATGTAACTTCT 58.927 37.500 0.00 0.00 41.60 2.85
2255 2400 5.182001 AGACCATGCTTTGTCATGTAACTTC 59.818 40.000 6.59 0.00 41.60 3.01
2256 2401 5.072741 AGACCATGCTTTGTCATGTAACTT 58.927 37.500 6.59 0.00 41.60 2.66
2257 2402 4.655963 AGACCATGCTTTGTCATGTAACT 58.344 39.130 6.59 0.00 41.60 2.24
2258 2403 5.376854 AAGACCATGCTTTGTCATGTAAC 57.623 39.130 6.59 0.00 41.60 2.50
2259 2404 6.883756 TCATAAGACCATGCTTTGTCATGTAA 59.116 34.615 6.59 0.00 41.60 2.41
2260 2405 6.413892 TCATAAGACCATGCTTTGTCATGTA 58.586 36.000 6.59 0.00 41.60 2.29
2261 2406 5.255687 TCATAAGACCATGCTTTGTCATGT 58.744 37.500 6.59 0.00 41.60 3.21
2262 2407 5.732528 GCTCATAAGACCATGCTTTGTCATG 60.733 44.000 6.59 3.22 42.53 3.07
2263 2408 4.337555 GCTCATAAGACCATGCTTTGTCAT 59.662 41.667 6.59 0.00 33.89 3.06
2264 2409 3.691118 GCTCATAAGACCATGCTTTGTCA 59.309 43.478 6.59 0.00 33.89 3.58
2265 2410 3.944015 AGCTCATAAGACCATGCTTTGTC 59.056 43.478 0.00 0.00 0.00 3.18
2266 2411 3.693085 CAGCTCATAAGACCATGCTTTGT 59.307 43.478 0.00 0.00 0.00 2.83
2267 2412 3.943381 TCAGCTCATAAGACCATGCTTTG 59.057 43.478 0.00 0.00 0.00 2.77
2268 2413 4.226427 TCAGCTCATAAGACCATGCTTT 57.774 40.909 0.00 0.00 0.00 3.51
2269 2414 3.920231 TCAGCTCATAAGACCATGCTT 57.080 42.857 0.00 0.00 0.00 3.91
2270 2415 3.920231 TTCAGCTCATAAGACCATGCT 57.080 42.857 0.00 0.00 0.00 3.79


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

AutoCloner maintained by Alex Coulton.