Multiple sequence alignment - TraesCS5A01G387200

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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 TraesCS5A01G387200 chr5A 100.000 2898 0 0 1 2898 584519569 584516672 0.000000e+00 5352.0
1 TraesCS5A01G387200 chr5D 91.037 2209 112 37 10 2145 464092839 464090644 0.000000e+00 2904.0
2 TraesCS5A01G387200 chr5D 91.707 627 26 6 2288 2898 464090625 464090009 0.000000e+00 846.0
3 TraesCS5A01G387200 chr5B 90.259 2125 106 41 7 2060 571188560 571186466 0.000000e+00 2684.0
4 TraesCS5A01G387200 chr5B 92.495 493 20 3 2421 2897 571186259 571185768 0.000000e+00 689.0
5 TraesCS5A01G387200 chr5B 87.059 85 4 6 2288 2372 571186339 571186262 3.980000e-14 89.8
6 TraesCS5A01G387200 chr7D 92.157 51 4 0 1665 1715 535563394 535563344 4.010000e-09 73.1
7 TraesCS5A01G387200 chr7A 92.157 51 4 0 1665 1715 618117453 618117503 4.010000e-09 73.1
8 TraesCS5A01G387200 chr7B 95.455 44 2 0 1665 1708 577301701 577301658 1.440000e-08 71.3
9 TraesCS5A01G387200 chr2A 89.286 56 6 0 1665 1720 406997432 406997487 1.440000e-08 71.3
10 TraesCS5A01G387200 chr2A 89.286 56 6 0 1665 1720 407125929 407125984 1.440000e-08 71.3


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 TraesCS5A01G387200 chr5A 584516672 584519569 2897 True 5352.000000 5352 100.000000 1 2898 1 chr5A.!!$R1 2897
1 TraesCS5A01G387200 chr5D 464090009 464092839 2830 True 1875.000000 2904 91.372000 10 2898 2 chr5D.!!$R1 2888
2 TraesCS5A01G387200 chr5B 571185768 571188560 2792 True 1154.266667 2684 89.937667 7 2897 3 chr5B.!!$R1 2890

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
811 851 0.036306 ACTAAAACCGGGCCTGACAG 59.964 55.0 15.09 4.77 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1930 2078 0.169672 CAGCATCGACAGGGCAAAAG 59.83 55.0 0.0 0.0 0.0 2.27 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
39 40 6.350445 CGAATTCCCTTCCAAAGATGACAAAT 60.350 38.462 0.00 0.00 0.00 2.32
41 42 6.745794 TTCCCTTCCAAAGATGACAAATTT 57.254 33.333 0.00 0.00 0.00 1.82
42 43 6.745794 TCCCTTCCAAAGATGACAAATTTT 57.254 33.333 0.00 0.00 0.00 1.82
43 44 7.135591 TCCCTTCCAAAGATGACAAATTTTT 57.864 32.000 0.00 0.00 0.00 1.94
103 104 1.364171 CGAGGATCATGTCGGGGAC 59.636 63.158 0.00 0.00 33.17 4.46
260 270 4.241999 GGTGGCGCGTGATGATGC 62.242 66.667 8.43 0.00 0.00 3.91
356 366 3.959991 GAAGCACACGGGCTCCTCC 62.960 68.421 0.00 0.00 45.07 4.30
506 516 1.070758 GTCACCTCCAAGAACTGCAGA 59.929 52.381 23.35 0.00 0.00 4.26
515 525 4.943705 TCCAAGAACTGCAGACCAATAATC 59.056 41.667 23.35 5.23 0.00 1.75
536 548 6.892658 ATCGCTCAGAGAATTCTACAGTAT 57.107 37.500 8.25 1.12 30.73 2.12
539 551 6.318900 TCGCTCAGAGAATTCTACAGTATTCA 59.681 38.462 8.25 0.00 35.23 2.57
764 804 4.819769 TCACGTGGGTAGGTTGTTTATAC 58.180 43.478 17.00 0.00 0.00 1.47
807 847 0.676782 CCAGACTAAAACCGGGCCTG 60.677 60.000 6.32 3.88 0.00 4.85
811 851 0.036306 ACTAAAACCGGGCCTGACAG 59.964 55.000 15.09 4.77 0.00 3.51
848 888 2.079088 TTTGGATCCCACCTGCTGCA 62.079 55.000 9.90 0.88 30.78 4.41
859 902 3.899981 CTGCTGCAAGGGCCGTACA 62.900 63.158 3.02 0.00 40.13 2.90
920 968 4.307908 GCAGCGGCGTTCGTTTGT 62.308 61.111 9.37 0.00 41.72 2.83
922 970 3.343421 AGCGGCGTTCGTTTGTCC 61.343 61.111 9.37 0.00 41.72 4.02
965 1014 1.106944 TGTCGTGTCAGAGTGAGCCA 61.107 55.000 0.00 0.00 0.00 4.75
1089 1175 2.696125 ACATTCATCCCGGCCCCT 60.696 61.111 0.00 0.00 0.00 4.79
1203 1334 3.373439 ACGTCGTCTTCTACTCCATGTAC 59.627 47.826 0.00 0.00 0.00 2.90
1206 1337 2.033049 CGTCTTCTACTCCATGTACGGG 59.967 54.545 0.00 0.00 0.00 5.28
1207 1338 2.029623 TCTTCTACTCCATGTACGGGC 58.970 52.381 0.00 0.00 0.00 6.13
1209 1340 1.399714 TCTACTCCATGTACGGGCAG 58.600 55.000 0.00 0.00 0.00 4.85
1747 1895 1.762957 GAGGGGATGTTCGAGATGGAA 59.237 52.381 0.00 0.00 0.00 3.53
1904 2052 0.881600 CGCCGATGCCTGATTCATCA 60.882 55.000 4.22 0.00 40.11 3.07
1905 2053 1.531423 GCCGATGCCTGATTCATCAT 58.469 50.000 4.22 2.38 40.11 2.45
1909 2057 4.572909 CCGATGCCTGATTCATCATCTAA 58.427 43.478 18.67 0.00 40.11 2.10
1910 2058 5.183969 CCGATGCCTGATTCATCATCTAAT 58.816 41.667 18.67 0.00 40.11 1.73
1914 2062 7.435784 CGATGCCTGATTCATCATCTAATAGAG 59.564 40.741 18.67 5.93 40.11 2.43
1915 2063 7.787623 TGCCTGATTCATCATCTAATAGAGA 57.212 36.000 0.00 0.00 39.01 3.10
1916 2064 8.376803 TGCCTGATTCATCATCTAATAGAGAT 57.623 34.615 0.00 0.00 46.52 2.75
1918 2066 9.316730 GCCTGATTCATCATCTAATAGAGATTC 57.683 37.037 0.00 0.00 42.70 2.52
1938 2086 6.603599 AGATTCTACTTACAATCCTTTTGCCC 59.396 38.462 0.00 0.00 30.41 5.36
1944 2092 1.202879 ACAATCCTTTTGCCCTGTCGA 60.203 47.619 0.00 0.00 0.00 4.20
1953 2101 4.827087 CCCTGTCGATGCTGCGCT 62.827 66.667 9.73 0.00 0.00 5.92
1987 2139 5.286082 CGTTTTGTAGATAAACAGCATTGCC 59.714 40.000 4.70 0.00 35.69 4.52
2015 2167 3.809905 CCTAGCCCCAGAATTCAGTTAC 58.190 50.000 8.44 0.00 0.00 2.50
2054 2206 3.670055 GCATGGAGTGTGTTGAATTTTCG 59.330 43.478 0.00 0.00 0.00 3.46
2059 2213 5.818336 TGGAGTGTGTTGAATTTTCGTTAGA 59.182 36.000 0.00 0.00 0.00 2.10
2060 2214 6.134061 GGAGTGTGTTGAATTTTCGTTAGAC 58.866 40.000 0.00 0.00 0.00 2.59
2062 2216 7.259290 AGTGTGTTGAATTTTCGTTAGACAT 57.741 32.000 0.00 0.00 0.00 3.06
2063 2217 7.352739 AGTGTGTTGAATTTTCGTTAGACATC 58.647 34.615 0.00 0.00 0.00 3.06
2064 2218 6.577427 GTGTGTTGAATTTTCGTTAGACATCC 59.423 38.462 0.00 0.00 0.00 3.51
2065 2219 6.084277 GTGTTGAATTTTCGTTAGACATCCC 58.916 40.000 0.00 0.00 0.00 3.85
2066 2220 6.001460 TGTTGAATTTTCGTTAGACATCCCT 58.999 36.000 0.00 0.00 0.00 4.20
2114 2288 9.892130 AGTTCAAATTACCCAAAACACAATAAA 57.108 25.926 0.00 0.00 0.00 1.40
2161 2336 4.934356 AGCAAATCAATCTGTTTAGGGGA 58.066 39.130 0.00 0.00 0.00 4.81
2162 2337 4.706962 AGCAAATCAATCTGTTTAGGGGAC 59.293 41.667 0.00 0.00 0.00 4.46
2163 2338 4.438744 GCAAATCAATCTGTTTAGGGGACG 60.439 45.833 0.00 0.00 0.00 4.79
2170 2345 3.175594 TCTGTTTAGGGGACGTGGTTAT 58.824 45.455 0.00 0.00 0.00 1.89
2171 2346 3.583966 TCTGTTTAGGGGACGTGGTTATT 59.416 43.478 0.00 0.00 0.00 1.40
2172 2347 3.677190 TGTTTAGGGGACGTGGTTATTG 58.323 45.455 0.00 0.00 0.00 1.90
2173 2348 2.406596 TTAGGGGACGTGGTTATTGC 57.593 50.000 0.00 0.00 0.00 3.56
2174 2349 1.277579 TAGGGGACGTGGTTATTGCA 58.722 50.000 0.00 0.00 0.00 4.08
2175 2350 0.322187 AGGGGACGTGGTTATTGCAC 60.322 55.000 0.00 0.00 0.00 4.57
2176 2351 0.606944 GGGGACGTGGTTATTGCACA 60.607 55.000 0.00 0.00 0.00 4.57
2177 2352 1.459450 GGGACGTGGTTATTGCACAT 58.541 50.000 0.00 0.00 0.00 3.21
2178 2353 1.400494 GGGACGTGGTTATTGCACATC 59.600 52.381 0.00 0.00 0.00 3.06
2179 2354 1.062002 GGACGTGGTTATTGCACATCG 59.938 52.381 0.00 0.00 0.00 3.84
2180 2355 1.996898 GACGTGGTTATTGCACATCGA 59.003 47.619 0.00 0.00 0.00 3.59
2181 2356 2.413796 GACGTGGTTATTGCACATCGAA 59.586 45.455 0.00 0.00 0.00 3.71
2182 2357 2.415168 ACGTGGTTATTGCACATCGAAG 59.585 45.455 0.00 0.00 0.00 3.79
2183 2358 2.415168 CGTGGTTATTGCACATCGAAGT 59.585 45.455 0.00 0.00 0.00 3.01
2184 2359 3.724716 CGTGGTTATTGCACATCGAAGTG 60.725 47.826 16.15 16.15 42.37 3.16
2185 2360 3.435327 GTGGTTATTGCACATCGAAGTGA 59.565 43.478 23.91 4.81 42.05 3.41
2186 2361 3.435327 TGGTTATTGCACATCGAAGTGAC 59.565 43.478 23.91 14.92 42.05 3.67
2187 2362 3.684788 GGTTATTGCACATCGAAGTGACT 59.315 43.478 23.91 9.66 42.05 3.41
2188 2363 4.201724 GGTTATTGCACATCGAAGTGACTC 60.202 45.833 23.91 7.39 42.05 3.36
2189 2364 2.524569 TTGCACATCGAAGTGACTCA 57.475 45.000 23.91 9.90 42.05 3.41
2190 2365 2.524569 TGCACATCGAAGTGACTCAA 57.475 45.000 23.91 1.28 42.05 3.02
2191 2366 3.044235 TGCACATCGAAGTGACTCAAT 57.956 42.857 23.91 0.00 42.05 2.57
2192 2367 2.995939 TGCACATCGAAGTGACTCAATC 59.004 45.455 23.91 5.29 42.05 2.67
2193 2368 2.995939 GCACATCGAAGTGACTCAATCA 59.004 45.455 23.91 0.00 42.05 2.57
2194 2369 3.433274 GCACATCGAAGTGACTCAATCAA 59.567 43.478 23.91 0.00 42.05 2.57
2195 2370 4.435253 GCACATCGAAGTGACTCAATCAAG 60.435 45.833 23.91 0.00 42.05 3.02
2196 2371 3.681897 ACATCGAAGTGACTCAATCAAGC 59.318 43.478 0.00 0.00 39.72 4.01
2197 2372 3.385193 TCGAAGTGACTCAATCAAGCA 57.615 42.857 0.00 0.00 39.72 3.91
2198 2373 3.930336 TCGAAGTGACTCAATCAAGCAT 58.070 40.909 0.00 0.00 39.72 3.79
2199 2374 5.072040 TCGAAGTGACTCAATCAAGCATA 57.928 39.130 0.00 0.00 39.72 3.14
2200 2375 5.478407 TCGAAGTGACTCAATCAAGCATAA 58.522 37.500 0.00 0.00 39.72 1.90
2201 2376 5.931724 TCGAAGTGACTCAATCAAGCATAAA 59.068 36.000 0.00 0.00 39.72 1.40
2202 2377 6.426633 TCGAAGTGACTCAATCAAGCATAAAA 59.573 34.615 0.00 0.00 39.72 1.52
2203 2378 7.041440 TCGAAGTGACTCAATCAAGCATAAAAA 60.041 33.333 0.00 0.00 39.72 1.94
2234 2409 2.691409 AATACCCACACAGATCACCG 57.309 50.000 0.00 0.00 0.00 4.94
2235 2410 1.568504 ATACCCACACAGATCACCGT 58.431 50.000 0.00 0.00 0.00 4.83
2236 2411 0.606096 TACCCACACAGATCACCGTG 59.394 55.000 8.03 8.03 39.10 4.94
2238 2413 0.606096 CCCACACAGATCACCGTGTA 59.394 55.000 13.26 0.00 44.34 2.90
2239 2414 1.001520 CCCACACAGATCACCGTGTAA 59.998 52.381 13.26 0.00 44.34 2.41
2240 2415 2.337583 CCACACAGATCACCGTGTAAG 58.662 52.381 13.26 6.59 44.34 2.34
2241 2416 2.029380 CCACACAGATCACCGTGTAAGA 60.029 50.000 13.26 0.00 44.34 2.10
2242 2417 2.987149 CACACAGATCACCGTGTAAGAC 59.013 50.000 13.26 0.00 44.34 3.01
2243 2418 2.626266 ACACAGATCACCGTGTAAGACA 59.374 45.455 12.32 0.00 44.32 3.41
2244 2419 3.258372 ACACAGATCACCGTGTAAGACAT 59.742 43.478 12.32 0.00 44.32 3.06
2245 2420 4.461431 ACACAGATCACCGTGTAAGACATA 59.539 41.667 12.32 0.00 44.32 2.29
2246 2421 5.037385 CACAGATCACCGTGTAAGACATAG 58.963 45.833 0.00 0.00 0.00 2.23
2247 2422 4.098044 ACAGATCACCGTGTAAGACATAGG 59.902 45.833 0.00 3.48 35.70 2.57
2248 2423 4.338400 CAGATCACCGTGTAAGACATAGGA 59.662 45.833 9.95 0.00 34.38 2.94
2249 2424 4.338682 AGATCACCGTGTAAGACATAGGAC 59.661 45.833 9.95 0.00 34.38 3.85
2250 2425 3.693807 TCACCGTGTAAGACATAGGACT 58.306 45.455 9.95 0.00 34.38 3.85
2251 2426 3.693085 TCACCGTGTAAGACATAGGACTC 59.307 47.826 9.95 0.00 34.38 3.36
2252 2427 2.681848 ACCGTGTAAGACATAGGACTCG 59.318 50.000 9.95 0.00 34.38 4.18
2253 2428 2.033049 CCGTGTAAGACATAGGACTCGG 59.967 54.545 0.00 0.00 41.01 4.63
2254 2429 2.941064 CGTGTAAGACATAGGACTCGGA 59.059 50.000 0.00 0.00 0.00 4.55
2255 2430 3.564644 CGTGTAAGACATAGGACTCGGAT 59.435 47.826 0.00 0.00 0.00 4.18
2256 2431 4.554919 CGTGTAAGACATAGGACTCGGATG 60.555 50.000 0.00 0.00 0.00 3.51
2257 2432 4.338682 GTGTAAGACATAGGACTCGGATGT 59.661 45.833 0.00 0.00 36.52 3.06
2258 2433 4.338400 TGTAAGACATAGGACTCGGATGTG 59.662 45.833 0.00 0.00 33.99 3.21
2259 2434 2.311463 AGACATAGGACTCGGATGTGG 58.689 52.381 0.00 0.00 33.99 4.17
2260 2435 2.091830 AGACATAGGACTCGGATGTGGA 60.092 50.000 0.00 0.00 33.99 4.02
2261 2436 2.693591 GACATAGGACTCGGATGTGGAA 59.306 50.000 0.00 0.00 33.99 3.53
2262 2437 3.309296 ACATAGGACTCGGATGTGGAAT 58.691 45.455 0.00 0.00 32.62 3.01
2263 2438 4.480115 ACATAGGACTCGGATGTGGAATA 58.520 43.478 0.00 0.00 32.62 1.75
2264 2439 4.281182 ACATAGGACTCGGATGTGGAATAC 59.719 45.833 0.00 0.00 32.62 1.89
2265 2440 3.033659 AGGACTCGGATGTGGAATACT 57.966 47.619 0.00 0.00 0.00 2.12
2266 2441 3.375699 AGGACTCGGATGTGGAATACTT 58.624 45.455 0.00 0.00 0.00 2.24
2267 2442 4.543689 AGGACTCGGATGTGGAATACTTA 58.456 43.478 0.00 0.00 0.00 2.24
2268 2443 4.341520 AGGACTCGGATGTGGAATACTTAC 59.658 45.833 0.00 0.00 0.00 2.34
2269 2444 4.501058 GGACTCGGATGTGGAATACTTACC 60.501 50.000 0.00 0.00 0.00 2.85
2270 2445 3.067742 ACTCGGATGTGGAATACTTACCG 59.932 47.826 0.00 0.00 39.36 4.02
2271 2446 2.132762 CGGATGTGGAATACTTACCGC 58.867 52.381 0.00 0.00 35.05 5.68
2272 2447 2.132762 GGATGTGGAATACTTACCGCG 58.867 52.381 0.00 0.00 39.24 6.46
2273 2448 1.525619 GATGTGGAATACTTACCGCGC 59.474 52.381 0.00 0.00 39.24 6.86
2274 2449 0.246910 TGTGGAATACTTACCGCGCA 59.753 50.000 8.75 0.00 39.24 6.09
2275 2450 1.134640 TGTGGAATACTTACCGCGCAT 60.135 47.619 8.75 0.00 39.24 4.73
2276 2451 1.260561 GTGGAATACTTACCGCGCATG 59.739 52.381 8.75 0.00 0.00 4.06
2277 2452 1.134640 TGGAATACTTACCGCGCATGT 60.135 47.619 8.75 6.49 0.00 3.21
2278 2453 1.260561 GGAATACTTACCGCGCATGTG 59.739 52.381 8.75 0.66 0.00 3.21
2279 2454 0.655733 AATACTTACCGCGCATGTGC 59.344 50.000 21.37 21.37 37.78 4.57
2280 2455 0.179084 ATACTTACCGCGCATGTGCT 60.179 50.000 27.32 13.48 39.32 4.40
2281 2456 0.390603 TACTTACCGCGCATGTGCTT 60.391 50.000 27.32 16.94 39.32 3.91
2282 2457 1.226101 CTTACCGCGCATGTGCTTG 60.226 57.895 27.32 20.15 39.32 4.01
2283 2458 2.582202 CTTACCGCGCATGTGCTTGG 62.582 60.000 27.32 23.29 39.32 3.61
2286 2461 4.703799 CGCGCATGTGCTTGGCAA 62.704 61.111 27.32 0.00 41.47 4.52
2287 2462 2.356075 GCGCATGTGCTTGGCAAA 60.356 55.556 23.77 0.00 41.47 3.68
2288 2463 1.955157 GCGCATGTGCTTGGCAAAA 60.955 52.632 23.77 0.00 41.47 2.44
2289 2464 1.854664 CGCATGTGCTTGGCAAAAC 59.145 52.632 0.00 3.53 41.47 2.43
2290 2465 0.598158 CGCATGTGCTTGGCAAAACT 60.598 50.000 0.00 0.00 41.47 2.66
2331 2506 2.922503 TGCCGGAAGACAGCCTCA 60.923 61.111 5.05 0.00 0.00 3.86
2332 2507 2.435059 GCCGGAAGACAGCCTCAC 60.435 66.667 5.05 0.00 0.00 3.51
2333 2508 3.059982 CCGGAAGACAGCCTCACA 58.940 61.111 0.00 0.00 0.00 3.58
2334 2509 1.371183 CCGGAAGACAGCCTCACAA 59.629 57.895 0.00 0.00 0.00 3.33
2335 2510 0.671781 CCGGAAGACAGCCTCACAAG 60.672 60.000 0.00 0.00 0.00 3.16
2336 2511 0.034059 CGGAAGACAGCCTCACAAGT 59.966 55.000 0.00 0.00 0.00 3.16
2337 2512 1.802069 GGAAGACAGCCTCACAAGTC 58.198 55.000 0.00 0.00 0.00 3.01
2411 2586 2.437716 AAATGATCCGCCGCCGTT 60.438 55.556 0.00 0.00 0.00 4.44
2421 2596 1.375013 GCCGCCGTTCACTCCTAAA 60.375 57.895 0.00 0.00 0.00 1.85
2470 2645 9.832445 TTCTGATAGTACAAAAGAATATGTCCC 57.168 33.333 0.00 0.00 0.00 4.46
2537 2712 3.034721 TCGACCAACCTCATACAACAC 57.965 47.619 0.00 0.00 0.00 3.32
2570 2745 3.074412 ACTACTCTTTTTCGCATGGGTG 58.926 45.455 9.86 0.00 0.00 4.61
2623 2814 3.629398 CACTCATGGAGCAATCTTAACCC 59.371 47.826 0.00 0.00 32.04 4.11
2632 2824 3.254903 AGCAATCTTAACCCAAAACCGAC 59.745 43.478 0.00 0.00 0.00 4.79
2633 2825 3.254903 GCAATCTTAACCCAAAACCGACT 59.745 43.478 0.00 0.00 0.00 4.18
2715 2907 1.153086 CCTGCTTGGGGATCCTTCG 60.153 63.158 12.58 0.00 0.00 3.79
2786 2978 3.380320 CAGCCATTGCATCTCTTTCATCA 59.620 43.478 0.00 0.00 41.13 3.07
2795 2987 6.651086 TGCATCTCTTTCATCATCTTTCTCT 58.349 36.000 0.00 0.00 0.00 3.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.437049 GGGAATTCGTGTTCCTTCAGAAG 59.563 47.826 16.98 2.78 45.62 2.85
1 2 3.072476 AGGGAATTCGTGTTCCTTCAGAA 59.928 43.478 16.98 0.00 45.62 3.02
2 3 2.637872 AGGGAATTCGTGTTCCTTCAGA 59.362 45.455 16.98 0.00 45.62 3.27
3 4 3.059352 AGGGAATTCGTGTTCCTTCAG 57.941 47.619 16.98 0.00 45.62 3.02
4 5 3.408634 GAAGGGAATTCGTGTTCCTTCA 58.591 45.455 24.32 0.00 45.62 3.02
5 6 2.747989 GGAAGGGAATTCGTGTTCCTTC 59.252 50.000 22.53 22.53 45.62 3.46
41 42 5.084818 TGTAGCAGGATCTTCGATCAAAA 57.915 39.130 6.23 0.00 0.00 2.44
42 43 4.736126 TGTAGCAGGATCTTCGATCAAA 57.264 40.909 6.23 0.00 0.00 2.69
43 44 4.502087 CCATGTAGCAGGATCTTCGATCAA 60.502 45.833 6.23 0.00 0.00 2.57
44 45 3.006217 CCATGTAGCAGGATCTTCGATCA 59.994 47.826 6.23 0.00 0.00 2.92
52 53 2.036992 CCTCAGTCCATGTAGCAGGATC 59.963 54.545 0.00 0.00 36.11 3.36
103 104 1.749638 ACCTACCTGCTCGAGACCG 60.750 63.158 18.75 3.94 37.07 4.79
173 174 4.814294 GGCGCCTCCGTGTACCTG 62.814 72.222 22.15 0.00 36.67 4.00
506 516 5.923204 AGAATTCTCTGAGCGATTATTGGT 58.077 37.500 0.88 0.00 0.00 3.67
515 525 6.499172 TGAATACTGTAGAATTCTCTGAGCG 58.501 40.000 12.24 0.00 34.00 5.03
536 548 7.994911 ACAAGCATCCAATTATATCTGTCTGAA 59.005 33.333 0.00 0.00 0.00 3.02
539 551 6.206243 GCACAAGCATCCAATTATATCTGTCT 59.794 38.462 0.00 0.00 41.58 3.41
613 633 3.268965 GAGCTGACGAGACGGTGCA 62.269 63.158 0.00 0.00 0.00 4.57
616 636 4.104417 GCGAGCTGACGAGACGGT 62.104 66.667 0.00 0.00 35.09 4.83
699 719 0.035881 CTTTCCTCTGCTCCTGCACA 59.964 55.000 0.00 0.00 45.31 4.57
783 823 0.037734 CCGGTTTTAGTCTGGGCCTT 59.962 55.000 4.53 0.00 0.00 4.35
784 824 1.683441 CCGGTTTTAGTCTGGGCCT 59.317 57.895 4.53 0.00 0.00 5.19
807 847 0.393537 CAAGCCCAGTGGATCCTGTC 60.394 60.000 11.95 3.74 0.00 3.51
811 851 0.685458 AATGCAAGCCCAGTGGATCC 60.685 55.000 11.95 4.20 0.00 3.36
910 958 1.700029 CGATCGGGACAAACGAACG 59.300 57.895 7.38 3.39 46.64 3.95
1074 1133 4.209866 GCAGGGGCCGGGATGAAT 62.210 66.667 2.18 0.00 0.00 2.57
1176 1307 5.268118 TGGAGTAGAAGACGACGTAGATA 57.732 43.478 0.00 0.00 0.00 1.98
1848 1996 2.824041 CCAGCGTGGCCATGTACC 60.824 66.667 25.67 9.78 0.00 3.34
1910 2058 9.601217 GCAAAAGGATTGTAAGTAGAATCTCTA 57.399 33.333 7.81 0.00 36.52 2.43
1914 2062 6.603599 AGGGCAAAAGGATTGTAAGTAGAATC 59.396 38.462 0.65 0.65 35.81 2.52
1915 2063 6.378280 CAGGGCAAAAGGATTGTAAGTAGAAT 59.622 38.462 0.00 0.00 0.00 2.40
1916 2064 5.710099 CAGGGCAAAAGGATTGTAAGTAGAA 59.290 40.000 0.00 0.00 0.00 2.10
1918 2066 5.010282 ACAGGGCAAAAGGATTGTAAGTAG 58.990 41.667 0.00 0.00 0.00 2.57
1919 2067 4.993028 ACAGGGCAAAAGGATTGTAAGTA 58.007 39.130 0.00 0.00 0.00 2.24
1920 2068 3.826729 GACAGGGCAAAAGGATTGTAAGT 59.173 43.478 0.00 0.00 0.00 2.24
1921 2069 3.119849 CGACAGGGCAAAAGGATTGTAAG 60.120 47.826 0.00 0.00 0.00 2.34
1922 2070 2.817258 CGACAGGGCAAAAGGATTGTAA 59.183 45.455 0.00 0.00 0.00 2.41
1923 2071 2.039216 TCGACAGGGCAAAAGGATTGTA 59.961 45.455 0.00 0.00 0.00 2.41
1925 2073 1.533625 TCGACAGGGCAAAAGGATTG 58.466 50.000 0.00 0.00 0.00 2.67
1926 2074 2.094675 CATCGACAGGGCAAAAGGATT 58.905 47.619 0.00 0.00 0.00 3.01
1927 2075 1.755179 CATCGACAGGGCAAAAGGAT 58.245 50.000 0.00 0.00 0.00 3.24
1928 2076 0.960364 GCATCGACAGGGCAAAAGGA 60.960 55.000 0.00 0.00 0.00 3.36
1929 2077 0.962356 AGCATCGACAGGGCAAAAGG 60.962 55.000 0.00 0.00 0.00 3.11
1930 2078 0.169672 CAGCATCGACAGGGCAAAAG 59.830 55.000 0.00 0.00 0.00 2.27
1931 2079 1.865788 GCAGCATCGACAGGGCAAAA 61.866 55.000 0.00 0.00 0.00 2.44
1952 2100 1.468520 CTACAAAACGATGGTGCCCAG 59.531 52.381 0.00 0.00 36.75 4.45
1953 2101 1.072489 TCTACAAAACGATGGTGCCCA 59.928 47.619 0.00 0.00 38.19 5.36
1959 2107 6.176975 TGCTGTTTATCTACAAAACGATGG 57.823 37.500 0.00 0.00 39.23 3.51
1961 2109 6.747280 GCAATGCTGTTTATCTACAAAACGAT 59.253 34.615 0.00 0.00 39.23 3.73
1972 2120 4.746611 GGCTAAATGGCAATGCTGTTTATC 59.253 41.667 4.82 6.68 41.37 1.75
1987 2139 3.515602 ATTCTGGGGCTAGGCTAAATG 57.484 47.619 16.80 3.02 0.00 2.32
2049 2201 2.617021 GCCCAGGGATGTCTAACGAAAA 60.617 50.000 10.89 0.00 0.00 2.29
2054 2206 1.068741 CTACGCCCAGGGATGTCTAAC 59.931 57.143 10.89 0.00 0.00 2.34
2059 2213 3.480133 GGCTACGCCCAGGGATGT 61.480 66.667 10.89 9.57 44.06 3.06
2090 2264 9.667107 TGTTTATTGTGTTTTGGGTAATTTGAA 57.333 25.926 0.00 0.00 0.00 2.69
2136 2311 6.951198 TCCCCTAAACAGATTGATTTGCTTAA 59.049 34.615 0.00 0.00 0.00 1.85
2137 2312 6.377146 GTCCCCTAAACAGATTGATTTGCTTA 59.623 38.462 0.00 0.00 0.00 3.09
2139 2314 4.706962 GTCCCCTAAACAGATTGATTTGCT 59.293 41.667 0.00 0.00 0.00 3.91
2140 2315 4.438744 CGTCCCCTAAACAGATTGATTTGC 60.439 45.833 0.00 0.00 0.00 3.68
2141 2316 4.700213 ACGTCCCCTAAACAGATTGATTTG 59.300 41.667 0.00 0.00 0.00 2.32
2146 2321 2.290071 ACCACGTCCCCTAAACAGATTG 60.290 50.000 0.00 0.00 0.00 2.67
2147 2322 1.982958 ACCACGTCCCCTAAACAGATT 59.017 47.619 0.00 0.00 0.00 2.40
2149 2324 1.426751 AACCACGTCCCCTAAACAGA 58.573 50.000 0.00 0.00 0.00 3.41
2151 2326 3.677190 CAATAACCACGTCCCCTAAACA 58.323 45.455 0.00 0.00 0.00 2.83
2152 2327 2.421073 GCAATAACCACGTCCCCTAAAC 59.579 50.000 0.00 0.00 0.00 2.01
2153 2328 2.040012 TGCAATAACCACGTCCCCTAAA 59.960 45.455 0.00 0.00 0.00 1.85
2154 2329 1.629353 TGCAATAACCACGTCCCCTAA 59.371 47.619 0.00 0.00 0.00 2.69
2156 2331 0.322187 GTGCAATAACCACGTCCCCT 60.322 55.000 0.00 0.00 0.00 4.79
2158 2333 1.400494 GATGTGCAATAACCACGTCCC 59.600 52.381 0.00 0.00 41.25 4.46
2159 2334 1.062002 CGATGTGCAATAACCACGTCC 59.938 52.381 7.83 0.00 43.12 4.79
2161 2336 2.087501 TCGATGTGCAATAACCACGT 57.912 45.000 0.00 0.00 36.01 4.49
2162 2337 2.415168 ACTTCGATGTGCAATAACCACG 59.585 45.455 2.72 0.00 36.01 4.94
2163 2338 3.435327 TCACTTCGATGTGCAATAACCAC 59.565 43.478 22.86 0.00 37.81 4.16
2170 2345 2.524569 TGAGTCACTTCGATGTGCAA 57.475 45.000 22.86 7.51 37.81 4.08
2171 2346 2.524569 TTGAGTCACTTCGATGTGCA 57.475 45.000 22.86 14.19 37.81 4.57
2172 2347 2.995939 TGATTGAGTCACTTCGATGTGC 59.004 45.455 22.86 17.93 37.81 4.57
2173 2348 4.435253 GCTTGATTGAGTCACTTCGATGTG 60.435 45.833 21.95 21.95 36.32 3.21
2174 2349 3.681897 GCTTGATTGAGTCACTTCGATGT 59.318 43.478 0.00 0.00 36.32 3.06
2175 2350 3.681417 TGCTTGATTGAGTCACTTCGATG 59.319 43.478 0.00 0.00 36.32 3.84
2176 2351 3.930336 TGCTTGATTGAGTCACTTCGAT 58.070 40.909 0.00 0.00 36.32 3.59
2177 2352 3.385193 TGCTTGATTGAGTCACTTCGA 57.615 42.857 0.00 0.00 36.32 3.71
2178 2353 5.784750 TTATGCTTGATTGAGTCACTTCG 57.215 39.130 0.00 0.00 36.32 3.79
2212 2387 3.756434 CGGTGATCTGTGTGGGTATTTTT 59.244 43.478 0.00 0.00 0.00 1.94
2213 2388 3.244770 ACGGTGATCTGTGTGGGTATTTT 60.245 43.478 0.00 0.00 0.00 1.82
2214 2389 2.304761 ACGGTGATCTGTGTGGGTATTT 59.695 45.455 0.00 0.00 0.00 1.40
2215 2390 1.906574 ACGGTGATCTGTGTGGGTATT 59.093 47.619 0.00 0.00 0.00 1.89
2216 2391 1.207089 CACGGTGATCTGTGTGGGTAT 59.793 52.381 0.74 0.00 43.64 2.73
2217 2392 0.606096 CACGGTGATCTGTGTGGGTA 59.394 55.000 0.74 0.00 43.64 3.69
2218 2393 1.371183 CACGGTGATCTGTGTGGGT 59.629 57.895 0.74 0.00 43.64 4.51
2219 2394 4.284123 CACGGTGATCTGTGTGGG 57.716 61.111 0.74 0.00 43.64 4.61
2224 2399 4.098044 CCTATGTCTTACACGGTGATCTGT 59.902 45.833 16.29 0.00 0.00 3.41
2225 2400 4.338400 TCCTATGTCTTACACGGTGATCTG 59.662 45.833 16.29 2.31 0.00 2.90
2226 2401 4.338682 GTCCTATGTCTTACACGGTGATCT 59.661 45.833 16.29 0.00 0.00 2.75
2227 2402 4.338682 AGTCCTATGTCTTACACGGTGATC 59.661 45.833 16.29 1.11 0.00 2.92
2228 2403 4.279145 AGTCCTATGTCTTACACGGTGAT 58.721 43.478 16.29 1.80 0.00 3.06
2229 2404 3.693085 GAGTCCTATGTCTTACACGGTGA 59.307 47.826 16.29 0.00 0.00 4.02
2230 2405 3.487042 CGAGTCCTATGTCTTACACGGTG 60.487 52.174 6.58 6.58 0.00 4.94
2231 2406 2.681848 CGAGTCCTATGTCTTACACGGT 59.318 50.000 0.00 0.00 0.00 4.83
2232 2407 2.033049 CCGAGTCCTATGTCTTACACGG 59.967 54.545 0.00 0.00 39.15 4.94
2233 2408 2.941064 TCCGAGTCCTATGTCTTACACG 59.059 50.000 0.00 0.00 0.00 4.49
2234 2409 4.338682 ACATCCGAGTCCTATGTCTTACAC 59.661 45.833 0.25 0.00 0.00 2.90
2235 2410 4.338400 CACATCCGAGTCCTATGTCTTACA 59.662 45.833 2.73 0.00 31.60 2.41
2236 2411 4.261656 CCACATCCGAGTCCTATGTCTTAC 60.262 50.000 2.73 0.00 31.60 2.34
2237 2412 3.889538 CCACATCCGAGTCCTATGTCTTA 59.110 47.826 2.73 0.00 31.60 2.10
2238 2413 2.695666 CCACATCCGAGTCCTATGTCTT 59.304 50.000 2.73 0.00 31.60 3.01
2239 2414 2.091830 TCCACATCCGAGTCCTATGTCT 60.092 50.000 2.73 0.00 31.60 3.41
2240 2415 2.307768 TCCACATCCGAGTCCTATGTC 58.692 52.381 2.73 0.00 31.60 3.06
2241 2416 2.454336 TCCACATCCGAGTCCTATGT 57.546 50.000 0.25 0.25 34.22 2.29
2242 2417 4.524714 AGTATTCCACATCCGAGTCCTATG 59.475 45.833 0.00 0.00 0.00 2.23
2243 2418 4.742012 AGTATTCCACATCCGAGTCCTAT 58.258 43.478 0.00 0.00 0.00 2.57
2244 2419 4.180377 AGTATTCCACATCCGAGTCCTA 57.820 45.455 0.00 0.00 0.00 2.94
2245 2420 3.033659 AGTATTCCACATCCGAGTCCT 57.966 47.619 0.00 0.00 0.00 3.85
2246 2421 3.821421 AAGTATTCCACATCCGAGTCC 57.179 47.619 0.00 0.00 0.00 3.85
2247 2422 4.618965 GGTAAGTATTCCACATCCGAGTC 58.381 47.826 0.00 0.00 0.00 3.36
2248 2423 3.067742 CGGTAAGTATTCCACATCCGAGT 59.932 47.826 0.00 0.00 38.36 4.18
2249 2424 3.639538 CGGTAAGTATTCCACATCCGAG 58.360 50.000 0.00 0.00 38.36 4.63
2250 2425 2.223876 GCGGTAAGTATTCCACATCCGA 60.224 50.000 0.00 0.00 38.36 4.55
2251 2426 2.132762 GCGGTAAGTATTCCACATCCG 58.867 52.381 0.00 0.00 38.77 4.18
2252 2427 2.132762 CGCGGTAAGTATTCCACATCC 58.867 52.381 0.00 0.00 0.00 3.51
2253 2428 1.525619 GCGCGGTAAGTATTCCACATC 59.474 52.381 8.83 0.00 0.00 3.06
2254 2429 1.134640 TGCGCGGTAAGTATTCCACAT 60.135 47.619 8.83 0.00 0.00 3.21
2255 2430 0.246910 TGCGCGGTAAGTATTCCACA 59.753 50.000 8.83 0.00 0.00 4.17
2256 2431 1.260561 CATGCGCGGTAAGTATTCCAC 59.739 52.381 8.83 0.00 0.00 4.02
2257 2432 1.134640 ACATGCGCGGTAAGTATTCCA 60.135 47.619 8.83 0.00 0.00 3.53
2258 2433 1.260561 CACATGCGCGGTAAGTATTCC 59.739 52.381 8.83 0.00 0.00 3.01
2259 2434 1.332904 GCACATGCGCGGTAAGTATTC 60.333 52.381 8.83 0.00 0.00 1.75
2260 2435 0.655733 GCACATGCGCGGTAAGTATT 59.344 50.000 8.83 0.00 0.00 1.89
2261 2436 2.307363 GCACATGCGCGGTAAGTAT 58.693 52.632 8.83 0.00 0.00 2.12
2262 2437 3.788817 GCACATGCGCGGTAAGTA 58.211 55.556 8.83 0.00 0.00 2.24
2272 2447 0.863144 CAGTTTTGCCAAGCACATGC 59.137 50.000 0.00 0.00 38.71 4.06
2273 2448 2.129607 GTCAGTTTTGCCAAGCACATG 58.870 47.619 0.00 0.00 38.71 3.21
2274 2449 1.755959 TGTCAGTTTTGCCAAGCACAT 59.244 42.857 0.00 0.00 38.71 3.21
2275 2450 1.134753 CTGTCAGTTTTGCCAAGCACA 59.865 47.619 0.00 0.00 38.71 4.57
2276 2451 1.134946 ACTGTCAGTTTTGCCAAGCAC 59.865 47.619 0.00 0.00 38.71 4.40
2277 2452 1.473258 ACTGTCAGTTTTGCCAAGCA 58.527 45.000 0.00 0.00 36.47 3.91
2278 2453 3.708563 TTACTGTCAGTTTTGCCAAGC 57.291 42.857 11.54 0.00 0.00 4.01
2279 2454 6.099341 ACTTTTTACTGTCAGTTTTGCCAAG 58.901 36.000 11.54 7.86 0.00 3.61
2280 2455 6.031751 ACTTTTTACTGTCAGTTTTGCCAA 57.968 33.333 11.54 0.00 0.00 4.52
2281 2456 5.652994 ACTTTTTACTGTCAGTTTTGCCA 57.347 34.783 11.54 0.00 0.00 4.92
2282 2457 7.649057 AGATACTTTTTACTGTCAGTTTTGCC 58.351 34.615 11.54 0.00 0.00 4.52
2283 2458 8.342634 TGAGATACTTTTTACTGTCAGTTTTGC 58.657 33.333 11.54 0.00 0.00 3.68
2284 2459 9.869844 CTGAGATACTTTTTACTGTCAGTTTTG 57.130 33.333 11.54 0.78 0.00 2.44
2285 2460 9.057089 CCTGAGATACTTTTTACTGTCAGTTTT 57.943 33.333 11.54 0.00 0.00 2.43
2286 2461 7.173390 GCCTGAGATACTTTTTACTGTCAGTTT 59.827 37.037 11.54 0.00 0.00 2.66
2287 2462 6.651225 GCCTGAGATACTTTTTACTGTCAGTT 59.349 38.462 11.54 0.00 0.00 3.16
2288 2463 6.166982 GCCTGAGATACTTTTTACTGTCAGT 58.833 40.000 10.99 10.99 0.00 3.41
2289 2464 5.582665 GGCCTGAGATACTTTTTACTGTCAG 59.417 44.000 0.00 0.00 0.00 3.51
2290 2465 5.248477 AGGCCTGAGATACTTTTTACTGTCA 59.752 40.000 3.11 0.00 0.00 3.58
2331 2506 1.095228 CGCTGTGGGTTGTGACTTGT 61.095 55.000 0.00 0.00 0.00 3.16
2332 2507 1.648720 CGCTGTGGGTTGTGACTTG 59.351 57.895 0.00 0.00 0.00 3.16
2333 2508 2.186826 GCGCTGTGGGTTGTGACTT 61.187 57.895 0.00 0.00 0.00 3.01
2334 2509 2.591715 GCGCTGTGGGTTGTGACT 60.592 61.111 0.00 0.00 0.00 3.41
2335 2510 3.660111 GGCGCTGTGGGTTGTGAC 61.660 66.667 7.64 0.00 0.00 3.67
2336 2511 2.902423 AAAGGCGCTGTGGGTTGTGA 62.902 55.000 7.64 0.00 0.00 3.58
2337 2512 2.406452 GAAAGGCGCTGTGGGTTGTG 62.406 60.000 7.64 0.00 0.00 3.33
2470 2645 1.244019 CGGCCCCTGACCTTTTTCAG 61.244 60.000 0.00 0.00 42.46 3.02
2537 2712 4.744795 AAAGAGTAGTAGGCCAGACATG 57.255 45.455 5.01 0.00 0.00 3.21
2570 2745 6.357367 AGGTTTGTGATGTGTTAGGATATCC 58.643 40.000 14.41 14.41 0.00 2.59
2623 2814 2.729882 CGGTCTACAAGAGTCGGTTTTG 59.270 50.000 0.00 0.00 0.00 2.44
2632 2824 2.271800 GTGCCATTCGGTCTACAAGAG 58.728 52.381 0.00 0.00 33.28 2.85
2633 2825 1.066430 GGTGCCATTCGGTCTACAAGA 60.066 52.381 0.00 0.00 33.28 3.02
2696 2888 1.915078 CGAAGGATCCCCAAGCAGGT 61.915 60.000 8.55 0.00 34.66 4.00
2698 2890 1.821332 GCGAAGGATCCCCAAGCAG 60.821 63.158 8.55 0.00 33.88 4.24
2715 2907 1.396301 CGCTTCTTCATCCAAGACAGC 59.604 52.381 0.00 0.00 41.13 4.40
2786 2978 6.016443 CAGAGAACAAAGGCAAAGAGAAAGAT 60.016 38.462 0.00 0.00 0.00 2.40
2795 2987 1.956477 GCTCCAGAGAACAAAGGCAAA 59.044 47.619 0.00 0.00 0.00 3.68


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

AutoCloner maintained by Alex Coulton.