Multiple sequence alignment - TraesCS7B01G081400

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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 TraesCS7B01G081400 chr7B 100.000 2846 0 0 1 2846 92016348 92013503 0.000000e+00 5256.0
1 TraesCS7B01G081400 chr7B 92.632 95 7 0 1715 1809 33414640 33414546 1.380000e-28 137.0
2 TraesCS7B01G081400 chr7B 85.185 135 17 3 1715 1849 33528602 33528471 4.950000e-28 135.0
3 TraesCS7B01G081400 chr7D 89.871 2172 122 34 19 2153 130925673 130923563 0.000000e+00 2702.0
4 TraesCS7B01G081400 chr7D 96.809 94 3 0 2153 2246 130765762 130765669 1.060000e-34 158.0
5 TraesCS7B01G081400 chr7D 94.737 95 5 0 1715 1809 83663366 83663272 6.350000e-32 148.0
6 TraesCS7B01G081400 chr7D 86.567 134 15 3 1715 1848 83754980 83754850 8.220000e-31 145.0
7 TraesCS7B01G081400 chr7A 89.707 2050 124 38 27 2025 129705940 129703927 0.000000e+00 2536.0
8 TraesCS7B01G081400 chr7A 91.042 547 37 6 2272 2814 54684720 54684182 0.000000e+00 728.0
9 TraesCS7B01G081400 chr7A 92.157 102 8 0 1708 1809 85347344 85347243 8.220000e-31 145.0
10 TraesCS7B01G081400 chr7A 86.441 118 15 1 1715 1832 85412424 85412308 8.280000e-26 128.0
11 TraesCS7B01G081400 chr2B 97.198 571 16 0 2276 2846 97014431 97013861 0.000000e+00 966.0
12 TraesCS7B01G081400 chr2B 83.951 81 11 2 2566 2644 134375474 134375554 3.040000e-10 76.8
13 TraesCS7B01G081400 chr1D 90.398 427 24 9 2397 2814 470909041 470908623 1.930000e-151 545.0
14 TraesCS7B01G081400 chr1D 87.368 95 12 0 2308 2402 470909161 470909067 3.000000e-20 110.0
15 TraesCS7B01G081400 chr2A 78.632 117 21 4 2566 2680 18657667 18657781 1.090000e-09 75.0
16 TraesCS7B01G081400 chr4A 80.488 82 14 2 2280 2360 501059731 501059651 8.510000e-06 62.1


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 TraesCS7B01G081400 chr7B 92013503 92016348 2845 True 5256.0 5256 100.000 1 2846 1 chr7B.!!$R3 2845
1 TraesCS7B01G081400 chr7D 130923563 130925673 2110 True 2702.0 2702 89.871 19 2153 1 chr7D.!!$R4 2134
2 TraesCS7B01G081400 chr7A 129703927 129705940 2013 True 2536.0 2536 89.707 27 2025 1 chr7A.!!$R4 1998
3 TraesCS7B01G081400 chr7A 54684182 54684720 538 True 728.0 728 91.042 2272 2814 1 chr7A.!!$R1 542
4 TraesCS7B01G081400 chr2B 97013861 97014431 570 True 966.0 966 97.198 2276 2846 1 chr2B.!!$R1 570
5 TraesCS7B01G081400 chr1D 470908623 470909161 538 True 327.5 545 88.883 2308 2814 2 chr1D.!!$R1 506

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
293 295 0.179161 CACTCGTCAGTAGCCTTCCG 60.179 60.0 0.0 0.0 0.0 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2203 2281 0.179034 ATGAGGATTTGGAGCCGAGC 60.179 55.0 0.0 0.0 36.12 5.03 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
65 66 2.202797 CTGCCCGTCGTCATCAGG 60.203 66.667 0.00 0.00 0.00 3.86
67 68 4.148825 GCCCGTCGTCATCAGGCT 62.149 66.667 1.24 0.00 40.57 4.58
137 138 2.613691 CCGCCACTAGATTTGTAACGT 58.386 47.619 0.00 0.00 0.00 3.99
235 236 2.672478 CGAGCTGATGTTTCTCGGTCTT 60.672 50.000 0.00 0.00 44.06 3.01
249 250 1.986378 CGGTCTTTGATCGAGACACAC 59.014 52.381 22.85 10.56 44.15 3.82
250 251 2.338500 GGTCTTTGATCGAGACACACC 58.662 52.381 22.85 9.05 44.15 4.16
256 258 1.671328 TGATCGAGACACACCGAGATC 59.329 52.381 0.00 0.00 38.25 2.75
293 295 0.179161 CACTCGTCAGTAGCCTTCCG 60.179 60.000 0.00 0.00 0.00 4.30
341 343 0.890996 CAGTCCAACTCCAACCTGCC 60.891 60.000 0.00 0.00 0.00 4.85
376 378 0.390472 GTCCAAACCGCTCTCCTCTG 60.390 60.000 0.00 0.00 0.00 3.35
385 387 1.377536 GCTCTCCTCTGCATGGAAAC 58.622 55.000 9.45 0.21 32.61 2.78
396 398 2.746904 TGCATGGAAACGTCGATTTCAT 59.253 40.909 12.29 11.38 39.85 2.57
508 512 0.954449 GTCAGAGAGACACGGACCGA 60.954 60.000 23.38 0.00 46.77 4.69
748 780 3.885521 GGCGCAGGAATGCAGCTC 61.886 66.667 10.83 0.00 35.70 4.09
817 856 2.095263 CGTTGTTTATTGACAGGCCAGG 60.095 50.000 5.01 0.00 0.00 4.45
845 884 2.048127 GCTGTCACGGTCCAGGAC 60.048 66.667 11.70 11.70 0.00 3.85
855 895 1.920835 GTCCAGGACCCAGAGCCTT 60.921 63.158 8.65 0.00 30.41 4.35
859 899 2.022428 TCCAGGACCCAGAGCCTTATAA 60.022 50.000 0.00 0.00 30.41 0.98
860 900 2.370189 CCAGGACCCAGAGCCTTATAAG 59.630 54.545 5.43 5.43 30.41 1.73
905 950 2.033801 GGCACTGCATTATTCATCGCTT 59.966 45.455 2.82 0.00 0.00 4.68
911 959 3.001228 TGCATTATTCATCGCTTCGACAC 59.999 43.478 0.00 0.00 39.18 3.67
912 960 3.246226 GCATTATTCATCGCTTCGACACT 59.754 43.478 0.00 0.00 39.18 3.55
913 961 4.607114 GCATTATTCATCGCTTCGACACTC 60.607 45.833 0.00 0.00 39.18 3.51
914 962 1.550065 ATTCATCGCTTCGACACTCG 58.450 50.000 0.00 0.00 39.18 4.18
994 1042 1.062587 GTCGGAGTTTGATCGCCATTG 59.937 52.381 0.00 0.00 0.00 2.82
1288 1343 3.317149 CGTGCAAGCCCAGTACTATAGTA 59.683 47.826 8.59 8.59 0.00 1.82
1320 1375 2.617274 GCAAGAAGCACGTGGGGTC 61.617 63.158 18.88 0.00 44.79 4.46
1321 1376 2.030562 AAGAAGCACGTGGGGTCG 59.969 61.111 18.88 0.00 0.00 4.79
1322 1377 2.504274 AAGAAGCACGTGGGGTCGA 61.504 57.895 18.88 0.00 34.70 4.20
1378 1433 3.605749 GAAGCTGTAGTGGCGGCCA 62.606 63.158 19.77 19.77 41.44 5.36
1482 1537 0.875059 CAGTCGCCCAAGAAGAAACC 59.125 55.000 0.00 0.00 0.00 3.27
1853 1908 4.951963 GGCACGCTAGCCGCCTAG 62.952 72.222 27.68 9.17 46.12 3.02
1866 1921 3.845259 CCTAGCCGGTGCCGCTAA 61.845 66.667 1.90 0.00 38.69 3.09
1868 1923 2.756691 TAGCCGGTGCCGCTAAGA 60.757 61.111 1.90 0.00 38.69 2.10
1888 1943 0.022106 CGATCGTCTCGTTCGTTTGC 59.978 55.000 7.03 0.00 41.89 3.68
1922 1980 8.677300 GGAGAATATTTCATTTGCTTGTACAGA 58.323 33.333 0.00 0.00 0.00 3.41
1975 2033 3.374745 GACAGCACACAGTTTTGGATTG 58.625 45.455 0.00 0.00 0.00 2.67
1976 2034 2.129607 CAGCACACAGTTTTGGATTGC 58.870 47.619 0.00 0.00 0.00 3.56
1989 2047 5.699097 TTTGGATTGCTTACTGTAACCAC 57.301 39.130 6.39 0.00 0.00 4.16
1998 2060 4.623171 GCTTACTGTAACCACATACTGGCT 60.623 45.833 0.00 0.00 45.32 4.75
2003 2065 3.580895 TGTAACCACATACTGGCTGAGAA 59.419 43.478 0.00 0.00 45.32 2.87
2030 2107 2.222886 CCAAAACATCGCACATCTCTCG 60.223 50.000 0.00 0.00 0.00 4.04
2037 2114 1.520342 GCACATCTCTCGACCTGCC 60.520 63.158 0.00 0.00 0.00 4.85
2060 2137 4.748679 GACGGGTCGACGACGGTG 62.749 72.222 27.20 16.45 40.21 4.94
2062 2139 3.422303 CGGGTCGACGACGGTGTA 61.422 66.667 20.92 0.00 40.21 2.90
2120 2197 2.738147 GGTGACGATGACGGTGAAG 58.262 57.895 0.00 0.00 44.46 3.02
2153 2231 1.588674 TTACCACCAGACTGTTTGCG 58.411 50.000 0.93 0.00 0.00 4.85
2154 2232 0.753867 TACCACCAGACTGTTTGCGA 59.246 50.000 0.93 0.00 0.00 5.10
2155 2233 0.107410 ACCACCAGACTGTTTGCGAA 60.107 50.000 0.93 0.00 0.00 4.70
2156 2234 1.238439 CCACCAGACTGTTTGCGAAT 58.762 50.000 0.93 0.00 0.00 3.34
2157 2235 1.197721 CCACCAGACTGTTTGCGAATC 59.802 52.381 0.93 0.00 0.00 2.52
2158 2236 1.872952 CACCAGACTGTTTGCGAATCA 59.127 47.619 0.93 0.00 0.00 2.57
2159 2237 2.290367 CACCAGACTGTTTGCGAATCAA 59.710 45.455 0.93 0.00 0.00 2.57
2160 2238 3.058016 CACCAGACTGTTTGCGAATCAAT 60.058 43.478 0.93 0.00 34.12 2.57
2161 2239 3.189287 ACCAGACTGTTTGCGAATCAATC 59.811 43.478 0.93 0.00 34.12 2.67
2174 2252 4.889832 GAATCAATCGGAATGCTCAACT 57.110 40.909 0.00 0.00 0.00 3.16
2175 2253 5.240713 GAATCAATCGGAATGCTCAACTT 57.759 39.130 0.00 0.00 0.00 2.66
2176 2254 5.644644 GAATCAATCGGAATGCTCAACTTT 58.355 37.500 0.00 0.00 0.00 2.66
2177 2255 5.649782 ATCAATCGGAATGCTCAACTTTT 57.350 34.783 0.00 0.00 0.00 2.27
2178 2256 4.797471 TCAATCGGAATGCTCAACTTTTG 58.203 39.130 0.00 0.00 0.00 2.44
2179 2257 4.518590 TCAATCGGAATGCTCAACTTTTGA 59.481 37.500 0.00 0.00 38.17 2.69
2194 2272 8.506168 TCAACTTTTGAGCTTCTTTTCTTAGA 57.494 30.769 0.00 0.00 34.08 2.10
2195 2273 8.616076 TCAACTTTTGAGCTTCTTTTCTTAGAG 58.384 33.333 0.00 0.00 34.08 2.43
2196 2274 6.964908 ACTTTTGAGCTTCTTTTCTTAGAGC 58.035 36.000 0.00 0.00 0.00 4.09
2197 2275 6.543831 ACTTTTGAGCTTCTTTTCTTAGAGCA 59.456 34.615 0.00 0.00 0.00 4.26
2198 2276 7.230309 ACTTTTGAGCTTCTTTTCTTAGAGCAT 59.770 33.333 0.00 0.00 0.00 3.79
2199 2277 6.734104 TTGAGCTTCTTTTCTTAGAGCATC 57.266 37.500 0.00 0.00 0.00 3.91
2200 2278 4.867047 TGAGCTTCTTTTCTTAGAGCATCG 59.133 41.667 0.00 0.00 42.67 3.84
2201 2279 3.620821 AGCTTCTTTTCTTAGAGCATCGC 59.379 43.478 0.00 0.00 42.67 4.58
2202 2280 3.372206 GCTTCTTTTCTTAGAGCATCGCA 59.628 43.478 0.00 0.00 42.67 5.10
2203 2281 4.493872 GCTTCTTTTCTTAGAGCATCGCAG 60.494 45.833 0.00 0.00 42.67 5.18
2204 2282 2.932614 TCTTTTCTTAGAGCATCGCAGC 59.067 45.455 0.00 0.00 42.67 5.25
2211 2289 4.887987 AGCATCGCAGCTCGGCTC 62.888 66.667 5.87 0.00 42.18 4.70
2213 2291 4.519437 CATCGCAGCTCGGCTCCA 62.519 66.667 5.87 0.00 36.40 3.86
2214 2292 3.774528 ATCGCAGCTCGGCTCCAA 61.775 61.111 5.87 0.00 36.40 3.53
2215 2293 3.315142 ATCGCAGCTCGGCTCCAAA 62.315 57.895 5.87 0.00 36.40 3.28
2216 2294 2.599645 ATCGCAGCTCGGCTCCAAAT 62.600 55.000 5.87 0.00 36.40 2.32
2217 2295 2.817423 CGCAGCTCGGCTCCAAATC 61.817 63.158 0.00 0.00 36.40 2.17
2218 2296 2.476320 GCAGCTCGGCTCCAAATCC 61.476 63.158 0.00 0.00 36.40 3.01
2219 2297 1.222936 CAGCTCGGCTCCAAATCCT 59.777 57.895 0.00 0.00 36.40 3.24
2220 2298 0.813210 CAGCTCGGCTCCAAATCCTC 60.813 60.000 0.00 0.00 36.40 3.71
2221 2299 1.221840 GCTCGGCTCCAAATCCTCA 59.778 57.895 0.00 0.00 0.00 3.86
2222 2300 0.179034 GCTCGGCTCCAAATCCTCAT 60.179 55.000 0.00 0.00 0.00 2.90
2223 2301 1.748591 GCTCGGCTCCAAATCCTCATT 60.749 52.381 0.00 0.00 0.00 2.57
2224 2302 1.945394 CTCGGCTCCAAATCCTCATTG 59.055 52.381 0.00 0.00 0.00 2.82
2225 2303 0.383231 CGGCTCCAAATCCTCATTGC 59.617 55.000 0.00 0.00 0.00 3.56
2226 2304 1.772836 GGCTCCAAATCCTCATTGCT 58.227 50.000 0.00 0.00 0.00 3.91
2227 2305 1.680207 GGCTCCAAATCCTCATTGCTC 59.320 52.381 0.00 0.00 0.00 4.26
2228 2306 2.652590 GCTCCAAATCCTCATTGCTCT 58.347 47.619 0.00 0.00 0.00 4.09
2229 2307 2.358267 GCTCCAAATCCTCATTGCTCTG 59.642 50.000 0.00 0.00 0.00 3.35
2230 2308 2.950309 CTCCAAATCCTCATTGCTCTGG 59.050 50.000 0.00 0.00 0.00 3.86
2231 2309 2.577563 TCCAAATCCTCATTGCTCTGGA 59.422 45.455 0.00 0.00 0.00 3.86
2232 2310 3.203710 TCCAAATCCTCATTGCTCTGGAT 59.796 43.478 0.00 0.00 40.65 3.41
2233 2311 4.413189 TCCAAATCCTCATTGCTCTGGATA 59.587 41.667 0.00 0.00 38.25 2.59
2234 2312 4.518211 CCAAATCCTCATTGCTCTGGATAC 59.482 45.833 0.00 0.00 38.25 2.24
2236 2314 3.827008 TCCTCATTGCTCTGGATACAC 57.173 47.619 0.00 0.00 46.17 2.90
2237 2315 3.106827 TCCTCATTGCTCTGGATACACA 58.893 45.455 0.00 0.00 46.17 3.72
2238 2316 3.519107 TCCTCATTGCTCTGGATACACAA 59.481 43.478 0.00 0.00 46.17 3.33
2239 2317 3.624861 CCTCATTGCTCTGGATACACAAC 59.375 47.826 0.00 0.00 46.17 3.32
2240 2318 4.256110 CTCATTGCTCTGGATACACAACA 58.744 43.478 0.00 0.00 46.17 3.33
2241 2319 4.650734 TCATTGCTCTGGATACACAACAA 58.349 39.130 0.00 0.00 46.17 2.83
2242 2320 4.455533 TCATTGCTCTGGATACACAACAAC 59.544 41.667 0.00 0.00 46.17 3.32
2243 2321 3.483808 TGCTCTGGATACACAACAACA 57.516 42.857 0.00 0.00 46.17 3.33
2244 2322 3.138304 TGCTCTGGATACACAACAACAC 58.862 45.455 0.00 0.00 46.17 3.32
2245 2323 3.181455 TGCTCTGGATACACAACAACACT 60.181 43.478 0.00 0.00 46.17 3.55
2246 2324 4.039852 TGCTCTGGATACACAACAACACTA 59.960 41.667 0.00 0.00 46.17 2.74
2247 2325 4.389077 GCTCTGGATACACAACAACACTAC 59.611 45.833 0.00 0.00 46.17 2.73
2248 2326 4.890088 TCTGGATACACAACAACACTACC 58.110 43.478 0.00 0.00 46.17 3.18
2249 2327 4.000988 CTGGATACACAACAACACTACCC 58.999 47.826 0.00 0.00 46.17 3.69
2250 2328 3.649023 TGGATACACAACAACACTACCCT 59.351 43.478 0.00 0.00 46.17 4.34
2251 2329 4.839550 TGGATACACAACAACACTACCCTA 59.160 41.667 0.00 0.00 46.17 3.53
2252 2330 5.307456 TGGATACACAACAACACTACCCTAA 59.693 40.000 0.00 0.00 46.17 2.69
2253 2331 6.183361 TGGATACACAACAACACTACCCTAAA 60.183 38.462 0.00 0.00 46.17 1.85
2254 2332 6.148315 GGATACACAACAACACTACCCTAAAC 59.852 42.308 0.00 0.00 0.00 2.01
2255 2333 4.201657 ACACAACAACACTACCCTAAACC 58.798 43.478 0.00 0.00 0.00 3.27
2256 2334 4.080186 ACACAACAACACTACCCTAAACCT 60.080 41.667 0.00 0.00 0.00 3.50
2257 2335 4.885325 CACAACAACACTACCCTAAACCTT 59.115 41.667 0.00 0.00 0.00 3.50
2258 2336 6.056884 CACAACAACACTACCCTAAACCTTA 58.943 40.000 0.00 0.00 0.00 2.69
2259 2337 6.543100 CACAACAACACTACCCTAAACCTTAA 59.457 38.462 0.00 0.00 0.00 1.85
2260 2338 7.229907 CACAACAACACTACCCTAAACCTTAAT 59.770 37.037 0.00 0.00 0.00 1.40
2261 2339 7.781219 ACAACAACACTACCCTAAACCTTAATT 59.219 33.333 0.00 0.00 0.00 1.40
2262 2340 8.635328 CAACAACACTACCCTAAACCTTAATTT 58.365 33.333 0.00 0.00 0.00 1.82
2263 2341 8.173542 ACAACACTACCCTAAACCTTAATTTG 57.826 34.615 0.00 0.00 0.00 2.32
2264 2342 7.781219 ACAACACTACCCTAAACCTTAATTTGT 59.219 33.333 0.00 0.00 0.00 2.83
2265 2343 8.635328 CAACACTACCCTAAACCTTAATTTGTT 58.365 33.333 0.00 0.00 0.00 2.83
2266 2344 8.400184 ACACTACCCTAAACCTTAATTTGTTC 57.600 34.615 0.00 0.00 0.00 3.18
2267 2345 8.000127 ACACTACCCTAAACCTTAATTTGTTCA 59.000 33.333 0.00 0.00 0.00 3.18
2268 2346 8.852135 CACTACCCTAAACCTTAATTTGTTCAA 58.148 33.333 0.00 0.00 0.00 2.69
2269 2347 9.423964 ACTACCCTAAACCTTAATTTGTTCAAA 57.576 29.630 0.44 0.44 0.00 2.69
2270 2348 9.687210 CTACCCTAAACCTTAATTTGTTCAAAC 57.313 33.333 0.00 0.00 0.00 2.93
2360 2438 1.140589 CATCTCGCTCAACGCTCCT 59.859 57.895 0.00 0.00 43.23 3.69
2475 2585 1.080025 GAGAACGACCTGAACCCCG 60.080 63.158 0.00 0.00 0.00 5.73
2710 2830 1.141881 CTCCCGTCAACTCCATCCG 59.858 63.158 0.00 0.00 0.00 4.18
2843 2963 1.705186 ACCATCCCTATTTCCATCCCG 59.295 52.381 0.00 0.00 0.00 5.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
65 66 2.582498 CGCCTACAGGTGCGTAGC 60.582 66.667 0.00 0.00 45.43 3.58
137 138 0.457035 GTCCTGGTTACGCGTATCCA 59.543 55.000 34.92 34.92 34.67 3.41
216 217 3.070018 CAAAGACCGAGAAACATCAGCT 58.930 45.455 0.00 0.00 0.00 4.24
235 236 1.530323 TCTCGGTGTGTCTCGATCAA 58.470 50.000 0.00 0.00 34.77 2.57
246 247 0.247736 GTGCAGGAAGATCTCGGTGT 59.752 55.000 0.00 0.00 0.00 4.16
249 250 0.803768 CGTGTGCAGGAAGATCTCGG 60.804 60.000 0.00 0.00 0.00 4.63
250 251 0.109086 ACGTGTGCAGGAAGATCTCG 60.109 55.000 0.00 0.00 0.00 4.04
256 258 0.813610 TGGTCAACGTGTGCAGGAAG 60.814 55.000 0.00 0.00 0.00 3.46
376 378 2.892373 TGAAATCGACGTTTCCATGC 57.108 45.000 15.45 0.00 37.31 4.06
385 387 2.009774 AGGCAGGAAATGAAATCGACG 58.990 47.619 0.00 0.00 0.00 5.12
817 856 2.126307 TGACAGCTCTTCTCGCGC 60.126 61.111 0.00 0.00 0.00 6.86
825 864 2.279069 CCTGGACCGTGACAGCTCT 61.279 63.158 0.00 0.00 33.43 4.09
845 884 2.364324 TGCGTACTTATAAGGCTCTGGG 59.636 50.000 16.73 0.61 0.00 4.45
855 895 3.021695 AGGTGAGCTGTGCGTACTTATA 58.978 45.455 4.97 0.00 0.00 0.98
859 899 1.179174 TCAGGTGAGCTGTGCGTACT 61.179 55.000 11.78 0.00 0.00 2.73
860 900 0.734253 CTCAGGTGAGCTGTGCGTAC 60.734 60.000 11.78 0.00 35.13 3.67
912 960 2.954611 CTCTGTGTCGGCTGTCGA 59.045 61.111 0.00 0.00 46.77 4.20
913 961 2.807045 GCTCTGTGTCGGCTGTCG 60.807 66.667 0.00 0.00 40.90 4.35
914 962 2.807045 CGCTCTGTGTCGGCTGTC 60.807 66.667 0.00 0.00 0.00 3.51
915 963 3.274455 CTCGCTCTGTGTCGGCTGT 62.274 63.158 0.00 0.00 0.00 4.40
916 964 2.505777 CTCGCTCTGTGTCGGCTG 60.506 66.667 0.00 0.00 0.00 4.85
917 965 2.983930 GACTCGCTCTGTGTCGGCT 61.984 63.158 0.00 0.00 32.03 5.52
936 984 1.860484 GCTTGCTTGCTCTGGGTGAC 61.860 60.000 0.00 0.00 0.00 3.67
1288 1343 3.677424 GCTTCTTGCTCTTGGATCGTAGT 60.677 47.826 0.00 0.00 38.95 2.73
1314 1369 4.242586 TCCACCCTGTCGACCCCA 62.243 66.667 14.12 0.00 0.00 4.96
1316 1371 4.083862 GCTCCACCCTGTCGACCC 62.084 72.222 14.12 0.00 0.00 4.46
1378 1433 4.988598 CGGCGAGGTGGCTGTTGT 62.989 66.667 0.00 0.00 42.02 3.32
1431 1486 1.547675 GGCTCCACCATCCTTTTCACA 60.548 52.381 0.00 0.00 38.86 3.58
1437 1492 2.285368 TCGGGCTCCACCATCCTT 60.285 61.111 0.00 0.00 42.05 3.36
1462 1517 0.875059 GTTTCTTCTTGGGCGACTGG 59.125 55.000 0.00 0.00 0.00 4.00
1714 1769 2.269241 CACCTCCGCCTTCCCTTC 59.731 66.667 0.00 0.00 0.00 3.46
1850 1905 2.279517 CTTAGCGGCACCGGCTAG 60.280 66.667 11.65 0.00 40.87 3.42
1851 1906 2.756691 TCTTAGCGGCACCGGCTA 60.757 61.111 11.65 9.79 40.87 3.93
1852 1907 4.452733 GTCTTAGCGGCACCGGCT 62.453 66.667 11.65 10.76 40.87 5.52
1858 1913 1.063649 GACGATCGTCTTAGCGGCA 59.936 57.895 34.97 0.00 41.57 5.69
1884 1939 6.873997 TGAAATATTCTCCTCTCTACGCAAA 58.126 36.000 0.00 0.00 0.00 3.68
1886 1941 6.656632 ATGAAATATTCTCCTCTCTACGCA 57.343 37.500 0.00 0.00 0.00 5.24
1888 1943 7.655328 AGCAAATGAAATATTCTCCTCTCTACG 59.345 37.037 0.00 0.00 0.00 3.51
1989 2047 2.421424 GGCAGTTTTCTCAGCCAGTATG 59.579 50.000 0.00 0.00 46.26 2.39
1998 2060 3.795150 GCGATGTTTTGGCAGTTTTCTCA 60.795 43.478 0.00 0.00 0.00 3.27
2003 2065 1.135915 TGTGCGATGTTTTGGCAGTTT 59.864 42.857 0.00 0.00 37.36 2.66
2030 2107 2.434359 CCGTCCTTTCGGCAGGTC 60.434 66.667 1.26 0.00 43.96 3.85
2037 2114 2.503375 CGTCGACCCGTCCTTTCG 60.503 66.667 10.58 0.00 0.00 3.46
2050 2127 1.070309 GGTATAGCTACACCGTCGTCG 60.070 57.143 5.21 0.00 0.00 5.12
2120 2197 1.003223 GTGGTAATCAATTACGCCGGC 60.003 52.381 19.07 19.07 42.66 6.13
2153 2231 4.889832 AGTTGAGCATTCCGATTGATTC 57.110 40.909 0.00 0.00 0.00 2.52
2154 2232 5.649782 AAAGTTGAGCATTCCGATTGATT 57.350 34.783 0.00 0.00 0.00 2.57
2155 2233 5.183713 TCAAAAGTTGAGCATTCCGATTGAT 59.816 36.000 0.00 0.00 34.08 2.57
2156 2234 4.518590 TCAAAAGTTGAGCATTCCGATTGA 59.481 37.500 0.00 0.00 34.08 2.57
2157 2235 4.797471 TCAAAAGTTGAGCATTCCGATTG 58.203 39.130 0.00 0.00 34.08 2.67
2169 2247 8.506168 TCTAAGAAAAGAAGCTCAAAAGTTGA 57.494 30.769 0.00 0.00 38.17 3.18
2170 2248 7.378194 GCTCTAAGAAAAGAAGCTCAAAAGTTG 59.622 37.037 0.00 0.00 0.00 3.16
2171 2249 7.067494 TGCTCTAAGAAAAGAAGCTCAAAAGTT 59.933 33.333 0.00 0.00 0.00 2.66
2172 2250 6.543831 TGCTCTAAGAAAAGAAGCTCAAAAGT 59.456 34.615 0.00 0.00 0.00 2.66
2173 2251 6.963796 TGCTCTAAGAAAAGAAGCTCAAAAG 58.036 36.000 0.00 0.00 0.00 2.27
2174 2252 6.942532 TGCTCTAAGAAAAGAAGCTCAAAA 57.057 33.333 0.00 0.00 0.00 2.44
2175 2253 6.128445 CGATGCTCTAAGAAAAGAAGCTCAAA 60.128 38.462 0.00 0.00 0.00 2.69
2176 2254 5.349817 CGATGCTCTAAGAAAAGAAGCTCAA 59.650 40.000 0.00 0.00 0.00 3.02
2177 2255 4.867047 CGATGCTCTAAGAAAAGAAGCTCA 59.133 41.667 0.00 0.00 0.00 4.26
2178 2256 4.260172 GCGATGCTCTAAGAAAAGAAGCTC 60.260 45.833 0.00 0.00 0.00 4.09
2179 2257 3.620821 GCGATGCTCTAAGAAAAGAAGCT 59.379 43.478 0.00 0.00 0.00 3.74
2180 2258 3.372206 TGCGATGCTCTAAGAAAAGAAGC 59.628 43.478 0.00 0.00 0.00 3.86
2181 2259 4.493872 GCTGCGATGCTCTAAGAAAAGAAG 60.494 45.833 0.00 0.00 0.00 2.85
2182 2260 3.372206 GCTGCGATGCTCTAAGAAAAGAA 59.628 43.478 0.00 0.00 0.00 2.52
2183 2261 2.932614 GCTGCGATGCTCTAAGAAAAGA 59.067 45.455 0.00 0.00 0.00 2.52
2184 2262 2.935201 AGCTGCGATGCTCTAAGAAAAG 59.065 45.455 0.00 0.00 39.34 2.27
2185 2263 2.977914 AGCTGCGATGCTCTAAGAAAA 58.022 42.857 0.00 0.00 39.34 2.29
2186 2264 2.680312 AGCTGCGATGCTCTAAGAAA 57.320 45.000 0.00 0.00 39.34 2.52
2201 2279 0.813210 GAGGATTTGGAGCCGAGCTG 60.813 60.000 2.98 0.00 39.88 4.24
2202 2280 1.267574 TGAGGATTTGGAGCCGAGCT 61.268 55.000 0.00 0.00 43.88 4.09
2203 2281 0.179034 ATGAGGATTTGGAGCCGAGC 60.179 55.000 0.00 0.00 36.12 5.03
2204 2282 1.945394 CAATGAGGATTTGGAGCCGAG 59.055 52.381 0.00 0.00 36.12 4.63
2205 2283 2.018644 GCAATGAGGATTTGGAGCCGA 61.019 52.381 0.00 0.00 36.12 5.54
2206 2284 0.383231 GCAATGAGGATTTGGAGCCG 59.617 55.000 0.00 0.00 36.12 5.52
2207 2285 1.680207 GAGCAATGAGGATTTGGAGCC 59.320 52.381 0.00 0.00 0.00 4.70
2208 2286 2.358267 CAGAGCAATGAGGATTTGGAGC 59.642 50.000 0.00 0.00 0.00 4.70
2209 2287 2.950309 CCAGAGCAATGAGGATTTGGAG 59.050 50.000 0.00 0.00 0.00 3.86
2210 2288 2.577563 TCCAGAGCAATGAGGATTTGGA 59.422 45.455 0.00 0.00 0.00 3.53
2211 2289 3.008835 TCCAGAGCAATGAGGATTTGG 57.991 47.619 0.00 0.00 0.00 3.28
2212 2290 5.008415 GTGTATCCAGAGCAATGAGGATTTG 59.992 44.000 0.00 0.00 41.03 2.32
2213 2291 5.128919 GTGTATCCAGAGCAATGAGGATTT 58.871 41.667 0.00 0.00 41.03 2.17
2214 2292 4.164796 TGTGTATCCAGAGCAATGAGGATT 59.835 41.667 0.00 0.00 41.03 3.01
2215 2293 3.713248 TGTGTATCCAGAGCAATGAGGAT 59.287 43.478 0.00 0.00 43.07 3.24
2216 2294 3.106827 TGTGTATCCAGAGCAATGAGGA 58.893 45.455 0.00 0.00 34.12 3.71
2217 2295 3.548745 TGTGTATCCAGAGCAATGAGG 57.451 47.619 0.00 0.00 0.00 3.86
2218 2296 4.256110 TGTTGTGTATCCAGAGCAATGAG 58.744 43.478 0.00 0.00 0.00 2.90
2219 2297 4.284829 TGTTGTGTATCCAGAGCAATGA 57.715 40.909 0.00 0.00 0.00 2.57
2220 2298 4.216042 TGTTGTTGTGTATCCAGAGCAATG 59.784 41.667 0.00 0.00 37.39 2.82
2221 2299 4.216257 GTGTTGTTGTGTATCCAGAGCAAT 59.784 41.667 0.00 0.00 37.39 3.56
2222 2300 3.563808 GTGTTGTTGTGTATCCAGAGCAA 59.436 43.478 0.00 0.00 33.64 3.91
2223 2301 3.138304 GTGTTGTTGTGTATCCAGAGCA 58.862 45.455 0.00 0.00 0.00 4.26
2224 2302 3.403038 AGTGTTGTTGTGTATCCAGAGC 58.597 45.455 0.00 0.00 0.00 4.09
2225 2303 4.929808 GGTAGTGTTGTTGTGTATCCAGAG 59.070 45.833 0.00 0.00 0.00 3.35
2226 2304 4.262721 GGGTAGTGTTGTTGTGTATCCAGA 60.263 45.833 0.00 0.00 0.00 3.86
2227 2305 4.000988 GGGTAGTGTTGTTGTGTATCCAG 58.999 47.826 0.00 0.00 0.00 3.86
2228 2306 3.649023 AGGGTAGTGTTGTTGTGTATCCA 59.351 43.478 0.00 0.00 0.00 3.41
2229 2307 4.281898 AGGGTAGTGTTGTTGTGTATCC 57.718 45.455 0.00 0.00 0.00 2.59
2230 2308 6.148315 GGTTTAGGGTAGTGTTGTTGTGTATC 59.852 42.308 0.00 0.00 0.00 2.24
2231 2309 5.999600 GGTTTAGGGTAGTGTTGTTGTGTAT 59.000 40.000 0.00 0.00 0.00 2.29
2232 2310 5.130809 AGGTTTAGGGTAGTGTTGTTGTGTA 59.869 40.000 0.00 0.00 0.00 2.90
2233 2311 4.080186 AGGTTTAGGGTAGTGTTGTTGTGT 60.080 41.667 0.00 0.00 0.00 3.72
2234 2312 4.457466 AGGTTTAGGGTAGTGTTGTTGTG 58.543 43.478 0.00 0.00 0.00 3.33
2235 2313 4.783560 AGGTTTAGGGTAGTGTTGTTGT 57.216 40.909 0.00 0.00 0.00 3.32
2236 2314 7.754851 ATTAAGGTTTAGGGTAGTGTTGTTG 57.245 36.000 0.00 0.00 0.00 3.33
2237 2315 8.635328 CAAATTAAGGTTTAGGGTAGTGTTGTT 58.365 33.333 0.00 0.00 0.00 2.83
2238 2316 7.781219 ACAAATTAAGGTTTAGGGTAGTGTTGT 59.219 33.333 0.00 0.00 0.00 3.32
2239 2317 8.173542 ACAAATTAAGGTTTAGGGTAGTGTTG 57.826 34.615 0.00 0.00 0.00 3.33
2240 2318 8.771521 AACAAATTAAGGTTTAGGGTAGTGTT 57.228 30.769 0.00 0.00 0.00 3.32
2241 2319 8.000127 TGAACAAATTAAGGTTTAGGGTAGTGT 59.000 33.333 0.00 0.00 0.00 3.55
2242 2320 8.398878 TGAACAAATTAAGGTTTAGGGTAGTG 57.601 34.615 0.00 0.00 0.00 2.74
2243 2321 8.999905 TTGAACAAATTAAGGTTTAGGGTAGT 57.000 30.769 0.00 0.00 0.00 2.73
2244 2322 9.687210 GTTTGAACAAATTAAGGTTTAGGGTAG 57.313 33.333 3.34 0.00 32.36 3.18
2245 2323 9.198475 TGTTTGAACAAATTAAGGTTTAGGGTA 57.802 29.630 3.34 0.00 35.67 3.69
2246 2324 8.080363 TGTTTGAACAAATTAAGGTTTAGGGT 57.920 30.769 3.34 0.00 35.67 4.34
2247 2325 9.554395 AATGTTTGAACAAATTAAGGTTTAGGG 57.446 29.630 0.10 0.00 43.03 3.53
2252 2330 9.225436 ACAACAATGTTTGAACAAATTAAGGTT 57.775 25.926 0.00 3.43 43.03 3.50
2253 2331 8.785329 ACAACAATGTTTGAACAAATTAAGGT 57.215 26.923 0.00 0.00 43.03 3.50
2260 2338 9.046296 ACTGTTTTACAACAATGTTTGAACAAA 57.954 25.926 0.00 0.00 42.53 2.83
2261 2339 8.594881 ACTGTTTTACAACAATGTTTGAACAA 57.405 26.923 0.00 0.00 42.53 2.83
2262 2340 9.692749 TTACTGTTTTACAACAATGTTTGAACA 57.307 25.926 0.00 4.83 42.53 3.18
2268 2346 9.915629 TCTGTTTTACTGTTTTACAACAATGTT 57.084 25.926 0.00 0.00 42.53 2.71
2269 2347 9.567848 CTCTGTTTTACTGTTTTACAACAATGT 57.432 29.630 0.00 0.00 42.53 2.71
2270 2348 8.531530 GCTCTGTTTTACTGTTTTACAACAATG 58.468 33.333 0.00 0.00 42.53 2.82
2360 2438 1.514087 GCCGACGGTAAGATGACCA 59.486 57.895 16.73 0.00 39.72 4.02
2475 2585 2.659731 GCTGCATTAGCGAATGAGAC 57.340 50.000 21.93 6.26 44.59 3.36
2631 2746 2.096218 GGATGAATAAGACGCGGCAATC 60.096 50.000 17.71 7.08 0.00 2.67


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

AutoCloner maintained by Alex Coulton.