Multiple sequence alignment - TraesCS5D01G372100

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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 TraesCS5D01G372100 chr5D 100.000 2354 0 0 1 2354 446178592 446176239 0.000000e+00 4348
1 TraesCS5D01G372100 chr5D 98.783 2218 25 1 1 2216 503222514 503220297 0.000000e+00 3945
2 TraesCS5D01G372100 chr5D 100.000 145 0 0 2210 2354 446176897 446176753 3.860000e-68 268
3 TraesCS5D01G372100 chr5D 100.000 145 0 0 2210 2354 503275627 503275771 3.860000e-68 268
4 TraesCS5D01G372100 chr5D 100.000 145 0 0 2210 2354 541029868 541029724 3.860000e-68 268
5 TraesCS5D01G372100 chr3B 99.100 2222 13 3 1 2216 101915474 101913254 0.000000e+00 3986
6 TraesCS5D01G372100 chr3B 98.559 2221 26 2 1 2216 201531322 201529103 0.000000e+00 3919
7 TraesCS5D01G372100 chrUn 99.007 2216 22 0 1 2216 216514309 216516524 0.000000e+00 3971
8 TraesCS5D01G372100 chrUn 100.000 145 0 0 2210 2354 389361734 389361590 3.860000e-68 268
9 TraesCS5D01G372100 chrUn 100.000 145 0 0 2210 2354 421834856 421834712 3.860000e-68 268
10 TraesCS5D01G372100 chr3D 98.872 2216 24 1 1 2216 589272662 589274876 0.000000e+00 3952
11 TraesCS5D01G372100 chr1A 98.784 2221 21 2 1 2216 554516546 554514327 0.000000e+00 3947
12 TraesCS5D01G372100 chr1A 100.000 145 0 0 2210 2354 554514847 554514703 3.860000e-68 268
13 TraesCS5D01G372100 chr1D 98.691 2216 28 1 1 2216 254393818 254396032 0.000000e+00 3930
14 TraesCS5D01G372100 chr1D 100.000 145 0 0 2210 2354 51924071 51924215 3.860000e-68 268
15 TraesCS5D01G372100 chr3A 98.646 2216 27 3 1 2216 672905718 672907930 0.000000e+00 3923
16 TraesCS5D01G372100 chr3A 98.466 2216 32 2 1 2216 594895333 594897546 0.000000e+00 3903
17 TraesCS5D01G372100 chr6D 100.000 145 0 0 2210 2354 168257525 168257381 3.860000e-68 268
18 TraesCS5D01G372100 chr6A 100.000 145 0 0 2210 2354 567833235 567833091 3.860000e-68 268


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 TraesCS5D01G372100 chr5D 446176239 446178592 2353 True 2308.0 4348 100.000 1 2354 2 chr5D.!!$R3 2353
1 TraesCS5D01G372100 chr5D 503220297 503222514 2217 True 3945.0 3945 98.783 1 2216 1 chr5D.!!$R1 2215
2 TraesCS5D01G372100 chr3B 101913254 101915474 2220 True 3986.0 3986 99.100 1 2216 1 chr3B.!!$R1 2215
3 TraesCS5D01G372100 chr3B 201529103 201531322 2219 True 3919.0 3919 98.559 1 2216 1 chr3B.!!$R2 2215
4 TraesCS5D01G372100 chrUn 216514309 216516524 2215 False 3971.0 3971 99.007 1 2216 1 chrUn.!!$F1 2215
5 TraesCS5D01G372100 chr3D 589272662 589274876 2214 False 3952.0 3952 98.872 1 2216 1 chr3D.!!$F1 2215
6 TraesCS5D01G372100 chr1A 554514327 554516546 2219 True 2107.5 3947 99.392 1 2354 2 chr1A.!!$R1 2353
7 TraesCS5D01G372100 chr1D 254393818 254396032 2214 False 3930.0 3930 98.691 1 2216 1 chr1D.!!$F2 2215
8 TraesCS5D01G372100 chr3A 672905718 672907930 2212 False 3923.0 3923 98.646 1 2216 1 chr3A.!!$F2 2215
9 TraesCS5D01G372100 chr3A 594895333 594897546 2213 False 3903.0 3903 98.466 1 2216 1 chr3A.!!$F1 2215

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
525 527 4.814234 GTGTCCTACGGATAATGCAAATCA 59.186 41.667 12.84 0.0 32.73 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2278 2295 0.168128 CGGAATGCTCAAACCGGAAC 59.832 55.0 9.46 0.0 41.41 3.62 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
52 53 8.275187 ACTATACCAGGAATATCAATGAACCA 57.725 34.615 0.00 0.00 0.00 3.67
525 527 4.814234 GTGTCCTACGGATAATGCAAATCA 59.186 41.667 12.84 0.00 32.73 2.57
1528 1544 5.131308 TCCAAAAATGGGTACTATCGGATCA 59.869 40.000 0.00 0.00 0.00 2.92
2226 2243 4.917906 ATAGATAGATTGTCCCAAGGGC 57.082 45.455 0.00 0.00 34.68 5.19
2227 2244 1.417890 AGATAGATTGTCCCAAGGGCG 59.582 52.381 0.00 0.00 34.68 6.13
2228 2245 0.179018 ATAGATTGTCCCAAGGGCGC 60.179 55.000 0.00 0.00 34.68 6.53
2229 2246 2.265467 TAGATTGTCCCAAGGGCGCC 62.265 60.000 21.18 21.18 34.68 6.53
2230 2247 3.936772 GATTGTCCCAAGGGCGCCA 62.937 63.158 30.85 2.40 34.68 5.69
2231 2248 3.301222 ATTGTCCCAAGGGCGCCAT 62.301 57.895 30.85 21.35 34.68 4.40
2232 2249 1.932156 ATTGTCCCAAGGGCGCCATA 61.932 55.000 30.85 3.85 34.68 2.74
2233 2250 1.932156 TTGTCCCAAGGGCGCCATAT 61.932 55.000 30.85 10.95 34.68 1.78
2234 2251 1.152756 GTCCCAAGGGCGCCATATT 60.153 57.895 30.85 16.95 34.68 1.28
2235 2252 1.150536 TCCCAAGGGCGCCATATTC 59.849 57.895 30.85 10.59 34.68 1.75
2236 2253 1.151450 CCCAAGGGCGCCATATTCT 59.849 57.895 30.85 13.15 0.00 2.40
2237 2254 0.400213 CCCAAGGGCGCCATATTCTA 59.600 55.000 30.85 0.00 0.00 2.10
2238 2255 1.611673 CCCAAGGGCGCCATATTCTAG 60.612 57.143 30.85 10.35 0.00 2.43
2239 2256 1.611673 CCAAGGGCGCCATATTCTAGG 60.612 57.143 30.85 13.07 0.00 3.02
2240 2257 1.347707 CAAGGGCGCCATATTCTAGGA 59.652 52.381 30.85 0.00 0.00 2.94
2241 2258 1.270907 AGGGCGCCATATTCTAGGAG 58.729 55.000 30.85 0.00 0.00 3.69
2243 2260 3.145228 GCGCCATATTCTAGGAGCC 57.855 57.895 0.00 0.00 43.75 4.70
2244 2261 0.391793 GCGCCATATTCTAGGAGCCC 60.392 60.000 0.00 0.00 43.75 5.19
2245 2262 0.976641 CGCCATATTCTAGGAGCCCA 59.023 55.000 0.00 0.00 0.00 5.36
2246 2263 1.347707 CGCCATATTCTAGGAGCCCAA 59.652 52.381 0.00 0.00 0.00 4.12
2247 2264 2.613977 CGCCATATTCTAGGAGCCCAAG 60.614 54.545 0.00 0.00 0.00 3.61
2248 2265 2.373502 GCCATATTCTAGGAGCCCAAGT 59.626 50.000 0.00 0.00 0.00 3.16
2249 2266 3.181439 GCCATATTCTAGGAGCCCAAGTT 60.181 47.826 0.00 0.00 0.00 2.66
2250 2267 4.041691 GCCATATTCTAGGAGCCCAAGTTA 59.958 45.833 0.00 0.00 0.00 2.24
2251 2268 5.280727 GCCATATTCTAGGAGCCCAAGTTAT 60.281 44.000 0.00 0.00 0.00 1.89
2252 2269 6.176183 CCATATTCTAGGAGCCCAAGTTATG 58.824 44.000 0.00 0.00 0.00 1.90
2253 2270 3.560636 TTCTAGGAGCCCAAGTTATGC 57.439 47.619 0.00 0.00 0.00 3.14
2254 2271 2.764269 TCTAGGAGCCCAAGTTATGCT 58.236 47.619 0.00 0.00 38.24 3.79
2255 2272 3.923648 TCTAGGAGCCCAAGTTATGCTA 58.076 45.455 0.00 0.00 34.99 3.49
2256 2273 4.493618 TCTAGGAGCCCAAGTTATGCTAT 58.506 43.478 0.00 0.00 34.99 2.97
2257 2274 4.907875 TCTAGGAGCCCAAGTTATGCTATT 59.092 41.667 0.00 0.00 34.99 1.73
2258 2275 3.825328 AGGAGCCCAAGTTATGCTATTG 58.175 45.455 0.00 0.00 34.99 1.90
2259 2276 3.459598 AGGAGCCCAAGTTATGCTATTGA 59.540 43.478 0.00 0.00 34.99 2.57
2260 2277 4.079787 AGGAGCCCAAGTTATGCTATTGAA 60.080 41.667 0.00 0.00 34.99 2.69
2261 2278 4.644685 GGAGCCCAAGTTATGCTATTGAAA 59.355 41.667 0.00 0.00 34.99 2.69
2262 2279 5.127031 GGAGCCCAAGTTATGCTATTGAAAA 59.873 40.000 0.00 0.00 34.99 2.29
2263 2280 6.183360 GGAGCCCAAGTTATGCTATTGAAAAT 60.183 38.462 0.00 0.00 34.99 1.82
2264 2281 7.186570 AGCCCAAGTTATGCTATTGAAAATT 57.813 32.000 0.00 0.00 32.56 1.82
2265 2282 7.267857 AGCCCAAGTTATGCTATTGAAAATTC 58.732 34.615 0.00 0.00 32.56 2.17
2266 2283 6.198966 GCCCAAGTTATGCTATTGAAAATTCG 59.801 38.462 0.00 0.00 0.00 3.34
2267 2284 7.257722 CCCAAGTTATGCTATTGAAAATTCGT 58.742 34.615 0.00 0.00 0.00 3.85
2268 2285 7.759433 CCCAAGTTATGCTATTGAAAATTCGTT 59.241 33.333 0.00 0.00 0.00 3.85
2269 2286 8.798153 CCAAGTTATGCTATTGAAAATTCGTTC 58.202 33.333 0.00 0.00 0.00 3.95
2270 2287 8.798153 CAAGTTATGCTATTGAAAATTCGTTCC 58.202 33.333 0.00 0.00 0.00 3.62
2271 2288 8.281212 AGTTATGCTATTGAAAATTCGTTCCT 57.719 30.769 0.00 0.00 0.00 3.36
2272 2289 8.398665 AGTTATGCTATTGAAAATTCGTTCCTC 58.601 33.333 0.00 0.00 0.00 3.71
2273 2290 8.398665 GTTATGCTATTGAAAATTCGTTCCTCT 58.601 33.333 0.00 0.00 0.00 3.69
2274 2291 9.607988 TTATGCTATTGAAAATTCGTTCCTCTA 57.392 29.630 0.00 0.00 0.00 2.43
2275 2292 7.539712 TGCTATTGAAAATTCGTTCCTCTAG 57.460 36.000 0.00 0.00 0.00 2.43
2276 2293 6.037172 TGCTATTGAAAATTCGTTCCTCTAGC 59.963 38.462 0.00 0.00 33.17 3.42
2277 2294 6.037172 GCTATTGAAAATTCGTTCCTCTAGCA 59.963 38.462 0.00 0.00 32.99 3.49
2278 2295 5.862924 TTGAAAATTCGTTCCTCTAGCAG 57.137 39.130 0.00 0.00 0.00 4.24
2279 2296 4.894784 TGAAAATTCGTTCCTCTAGCAGT 58.105 39.130 0.00 0.00 0.00 4.40
2280 2297 5.305585 TGAAAATTCGTTCCTCTAGCAGTT 58.694 37.500 0.00 0.00 0.00 3.16
2281 2298 5.408604 TGAAAATTCGTTCCTCTAGCAGTTC 59.591 40.000 0.00 0.00 0.00 3.01
2282 2299 3.528597 ATTCGTTCCTCTAGCAGTTCC 57.471 47.619 0.00 0.00 0.00 3.62
2283 2300 0.809385 TCGTTCCTCTAGCAGTTCCG 59.191 55.000 0.00 0.00 0.00 4.30
2284 2301 0.179134 CGTTCCTCTAGCAGTTCCGG 60.179 60.000 0.00 0.00 0.00 5.14
2285 2302 0.896226 GTTCCTCTAGCAGTTCCGGT 59.104 55.000 0.00 0.00 0.00 5.28
2286 2303 1.275573 GTTCCTCTAGCAGTTCCGGTT 59.724 52.381 0.00 0.00 0.00 4.44
2287 2304 1.640917 TCCTCTAGCAGTTCCGGTTT 58.359 50.000 0.00 0.00 0.00 3.27
2288 2305 1.275291 TCCTCTAGCAGTTCCGGTTTG 59.725 52.381 0.00 0.00 0.00 2.93
2289 2306 1.275291 CCTCTAGCAGTTCCGGTTTGA 59.725 52.381 0.00 0.00 0.00 2.69
2290 2307 2.611518 CTCTAGCAGTTCCGGTTTGAG 58.388 52.381 0.00 0.00 0.00 3.02
2291 2308 1.079503 CTAGCAGTTCCGGTTTGAGC 58.920 55.000 0.00 0.51 0.00 4.26
2292 2309 0.394938 TAGCAGTTCCGGTTTGAGCA 59.605 50.000 0.00 0.00 0.00 4.26
2293 2310 0.250901 AGCAGTTCCGGTTTGAGCAT 60.251 50.000 0.00 0.00 0.00 3.79
2294 2311 0.598065 GCAGTTCCGGTTTGAGCATT 59.402 50.000 0.00 0.00 0.00 3.56
2295 2312 1.401539 GCAGTTCCGGTTTGAGCATTC 60.402 52.381 0.00 0.00 0.00 2.67
2296 2313 1.200020 CAGTTCCGGTTTGAGCATTCC 59.800 52.381 0.00 0.00 0.00 3.01
2297 2314 0.168128 GTTCCGGTTTGAGCATTCCG 59.832 55.000 0.00 0.00 42.22 4.30
2298 2315 0.250553 TTCCGGTTTGAGCATTCCGT 60.251 50.000 0.00 0.00 41.17 4.69
2299 2316 0.250553 TCCGGTTTGAGCATTCCGTT 60.251 50.000 0.00 0.00 41.17 4.44
2300 2317 0.168128 CCGGTTTGAGCATTCCGTTC 59.832 55.000 0.00 0.00 41.17 3.95
2301 2318 0.168128 CGGTTTGAGCATTCCGTTCC 59.832 55.000 0.00 0.00 38.45 3.62
2302 2319 0.526211 GGTTTGAGCATTCCGTTCCC 59.474 55.000 0.00 0.00 0.00 3.97
2303 2320 1.534729 GTTTGAGCATTCCGTTCCCT 58.465 50.000 0.00 0.00 0.00 4.20
2304 2321 1.886542 GTTTGAGCATTCCGTTCCCTT 59.113 47.619 0.00 0.00 0.00 3.95
2305 2322 2.286365 TTGAGCATTCCGTTCCCTTT 57.714 45.000 0.00 0.00 0.00 3.11
2306 2323 2.286365 TGAGCATTCCGTTCCCTTTT 57.714 45.000 0.00 0.00 0.00 2.27
2307 2324 2.593026 TGAGCATTCCGTTCCCTTTTT 58.407 42.857 0.00 0.00 0.00 1.94
2308 2325 2.556622 TGAGCATTCCGTTCCCTTTTTC 59.443 45.455 0.00 0.00 0.00 2.29
2309 2326 2.556622 GAGCATTCCGTTCCCTTTTTCA 59.443 45.455 0.00 0.00 0.00 2.69
2310 2327 2.962421 AGCATTCCGTTCCCTTTTTCAA 59.038 40.909 0.00 0.00 0.00 2.69
2311 2328 3.386402 AGCATTCCGTTCCCTTTTTCAAA 59.614 39.130 0.00 0.00 0.00 2.69
2312 2329 3.493129 GCATTCCGTTCCCTTTTTCAAAC 59.507 43.478 0.00 0.00 0.00 2.93
2313 2330 4.739436 GCATTCCGTTCCCTTTTTCAAACT 60.739 41.667 0.00 0.00 0.00 2.66
2314 2331 4.642445 TTCCGTTCCCTTTTTCAAACTC 57.358 40.909 0.00 0.00 0.00 3.01
2315 2332 2.953648 TCCGTTCCCTTTTTCAAACTCC 59.046 45.455 0.00 0.00 0.00 3.85
2316 2333 2.691011 CCGTTCCCTTTTTCAAACTCCA 59.309 45.455 0.00 0.00 0.00 3.86
2317 2334 3.490249 CCGTTCCCTTTTTCAAACTCCAC 60.490 47.826 0.00 0.00 0.00 4.02
2318 2335 3.380320 CGTTCCCTTTTTCAAACTCCACT 59.620 43.478 0.00 0.00 0.00 4.00
2319 2336 4.142249 CGTTCCCTTTTTCAAACTCCACTT 60.142 41.667 0.00 0.00 0.00 3.16
2320 2337 5.348986 GTTCCCTTTTTCAAACTCCACTTC 58.651 41.667 0.00 0.00 0.00 3.01
2321 2338 4.867086 TCCCTTTTTCAAACTCCACTTCT 58.133 39.130 0.00 0.00 0.00 2.85
2322 2339 5.269189 TCCCTTTTTCAAACTCCACTTCTT 58.731 37.500 0.00 0.00 0.00 2.52
2323 2340 5.719563 TCCCTTTTTCAAACTCCACTTCTTT 59.280 36.000 0.00 0.00 0.00 2.52
2324 2341 6.212589 TCCCTTTTTCAAACTCCACTTCTTTT 59.787 34.615 0.00 0.00 0.00 2.27
2325 2342 6.535150 CCCTTTTTCAAACTCCACTTCTTTTC 59.465 38.462 0.00 0.00 0.00 2.29
2326 2343 7.096551 CCTTTTTCAAACTCCACTTCTTTTCA 58.903 34.615 0.00 0.00 0.00 2.69
2327 2344 7.765819 CCTTTTTCAAACTCCACTTCTTTTCAT 59.234 33.333 0.00 0.00 0.00 2.57
2328 2345 9.801873 CTTTTTCAAACTCCACTTCTTTTCATA 57.198 29.630 0.00 0.00 0.00 2.15
2332 2349 8.268850 TCAAACTCCACTTCTTTTCATATAGC 57.731 34.615 0.00 0.00 0.00 2.97
2333 2350 7.882791 TCAAACTCCACTTCTTTTCATATAGCA 59.117 33.333 0.00 0.00 0.00 3.49
2334 2351 8.514594 CAAACTCCACTTCTTTTCATATAGCAA 58.485 33.333 0.00 0.00 0.00 3.91
2335 2352 8.814038 AACTCCACTTCTTTTCATATAGCAAT 57.186 30.769 0.00 0.00 0.00 3.56
2336 2353 8.443953 ACTCCACTTCTTTTCATATAGCAATC 57.556 34.615 0.00 0.00 0.00 2.67
2337 2354 7.500559 ACTCCACTTCTTTTCATATAGCAATCC 59.499 37.037 0.00 0.00 0.00 3.01
2338 2355 6.772716 TCCACTTCTTTTCATATAGCAATCCC 59.227 38.462 0.00 0.00 0.00 3.85
2339 2356 6.774656 CCACTTCTTTTCATATAGCAATCCCT 59.225 38.462 0.00 0.00 0.00 4.20
2340 2357 7.255381 CCACTTCTTTTCATATAGCAATCCCTG 60.255 40.741 0.00 0.00 0.00 4.45
2341 2358 7.500227 CACTTCTTTTCATATAGCAATCCCTGA 59.500 37.037 0.00 0.00 0.00 3.86
2342 2359 8.223330 ACTTCTTTTCATATAGCAATCCCTGAT 58.777 33.333 0.00 0.00 0.00 2.90
2343 2360 8.627208 TTCTTTTCATATAGCAATCCCTGATC 57.373 34.615 0.00 0.00 0.00 2.92
2344 2361 7.748677 TCTTTTCATATAGCAATCCCTGATCA 58.251 34.615 0.00 0.00 0.00 2.92
2345 2362 8.219868 TCTTTTCATATAGCAATCCCTGATCAA 58.780 33.333 0.00 0.00 0.00 2.57
2346 2363 8.765488 TTTTCATATAGCAATCCCTGATCAAA 57.235 30.769 0.00 0.00 0.00 2.69
2347 2364 7.991084 TTCATATAGCAATCCCTGATCAAAG 57.009 36.000 0.00 0.00 0.00 2.77
2348 2365 7.320384 TCATATAGCAATCCCTGATCAAAGA 57.680 36.000 0.00 0.00 0.00 2.52
2349 2366 7.392418 TCATATAGCAATCCCTGATCAAAGAG 58.608 38.462 0.00 0.00 0.00 2.85
2350 2367 5.901413 ATAGCAATCCCTGATCAAAGAGA 57.099 39.130 0.00 0.00 0.00 3.10
2351 2368 4.153673 AGCAATCCCTGATCAAAGAGAG 57.846 45.455 0.00 0.00 0.00 3.20
2352 2369 3.779183 AGCAATCCCTGATCAAAGAGAGA 59.221 43.478 0.00 0.00 0.00 3.10
2353 2370 4.226846 AGCAATCCCTGATCAAAGAGAGAA 59.773 41.667 0.00 0.00 0.00 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 3.159472 TCCTGAGCAATTGCAAGAATGT 58.841 40.909 30.89 9.54 45.16 2.71
525 527 5.879223 CCTGAGTCAGACATCAAATAGCTTT 59.121 40.000 22.09 0.00 32.44 3.51
841 843 7.051623 TGGCTTTTACTGTCTACTTTTCTCAA 58.948 34.615 0.00 0.00 0.00 3.02
1043 1047 0.384353 GTCACTTTTTCCTGTCGCGC 60.384 55.000 0.00 0.00 0.00 6.86
1445 1461 7.016072 TCACCAATCCAATACCTTTGACAAATT 59.984 33.333 0.05 0.00 0.00 1.82
1528 1544 7.129425 ACCTCTGTCTATTCTCTAATTCACCT 58.871 38.462 0.00 0.00 0.00 4.00
1869 1886 1.068333 CGTCGGTCCGAACTAAGGAAA 60.068 52.381 17.32 0.00 39.84 3.13
2216 2233 1.152756 AATATGGCGCCCTTGGGAC 60.153 57.895 26.77 0.00 0.00 4.46
2217 2234 1.150536 GAATATGGCGCCCTTGGGA 59.849 57.895 26.77 3.54 0.00 4.37
2218 2235 0.400213 TAGAATATGGCGCCCTTGGG 59.600 55.000 26.77 0.32 0.00 4.12
2219 2236 1.611673 CCTAGAATATGGCGCCCTTGG 60.612 57.143 26.77 18.94 0.00 3.61
2220 2237 1.347707 TCCTAGAATATGGCGCCCTTG 59.652 52.381 26.77 13.75 0.00 3.61
2221 2238 1.625818 CTCCTAGAATATGGCGCCCTT 59.374 52.381 26.77 15.12 0.00 3.95
2222 2239 1.270907 CTCCTAGAATATGGCGCCCT 58.729 55.000 26.77 18.16 0.00 5.19
2223 2240 0.391793 GCTCCTAGAATATGGCGCCC 60.392 60.000 26.77 7.94 0.00 6.13
2224 2241 0.391793 GGCTCCTAGAATATGGCGCC 60.392 60.000 22.73 22.73 45.31 6.53
2225 2242 0.391793 GGGCTCCTAGAATATGGCGC 60.392 60.000 0.00 0.00 33.70 6.53
2226 2243 0.976641 TGGGCTCCTAGAATATGGCG 59.023 55.000 0.00 0.00 0.00 5.69
2227 2244 2.373502 ACTTGGGCTCCTAGAATATGGC 59.626 50.000 9.06 0.00 31.18 4.40
2228 2245 4.713792 AACTTGGGCTCCTAGAATATGG 57.286 45.455 9.06 0.00 31.18 2.74
2229 2246 5.645497 GCATAACTTGGGCTCCTAGAATATG 59.355 44.000 17.13 17.13 35.45 1.78
2230 2247 5.549619 AGCATAACTTGGGCTCCTAGAATAT 59.450 40.000 9.06 5.41 30.74 1.28
2231 2248 4.907875 AGCATAACTTGGGCTCCTAGAATA 59.092 41.667 9.06 3.79 30.74 1.75
2232 2249 3.718956 AGCATAACTTGGGCTCCTAGAAT 59.281 43.478 9.06 1.58 30.74 2.40
2233 2250 3.115390 AGCATAACTTGGGCTCCTAGAA 58.885 45.455 9.06 0.00 30.74 2.10
2234 2251 2.764269 AGCATAACTTGGGCTCCTAGA 58.236 47.619 9.06 0.00 30.74 2.43
2235 2252 4.899352 ATAGCATAACTTGGGCTCCTAG 57.101 45.455 0.00 2.13 39.01 3.02
2236 2253 4.658435 TCAATAGCATAACTTGGGCTCCTA 59.342 41.667 0.00 0.00 39.01 2.94
2237 2254 3.459598 TCAATAGCATAACTTGGGCTCCT 59.540 43.478 0.00 0.00 39.01 3.69
2238 2255 3.820557 TCAATAGCATAACTTGGGCTCC 58.179 45.455 0.00 0.00 39.01 4.70
2239 2256 5.835113 TTTCAATAGCATAACTTGGGCTC 57.165 39.130 0.00 0.00 39.01 4.70
2240 2257 6.796785 ATTTTCAATAGCATAACTTGGGCT 57.203 33.333 0.00 0.00 41.51 5.19
2241 2258 6.198966 CGAATTTTCAATAGCATAACTTGGGC 59.801 38.462 0.00 0.00 0.00 5.36
2242 2259 7.257722 ACGAATTTTCAATAGCATAACTTGGG 58.742 34.615 0.00 0.00 0.00 4.12
2243 2260 8.687824 AACGAATTTTCAATAGCATAACTTGG 57.312 30.769 0.00 0.00 0.00 3.61
2244 2261 8.798153 GGAACGAATTTTCAATAGCATAACTTG 58.202 33.333 0.00 0.00 0.00 3.16
2245 2262 8.739972 AGGAACGAATTTTCAATAGCATAACTT 58.260 29.630 0.00 0.00 0.00 2.66
2246 2263 8.281212 AGGAACGAATTTTCAATAGCATAACT 57.719 30.769 0.00 0.00 0.00 2.24
2247 2264 8.398665 AGAGGAACGAATTTTCAATAGCATAAC 58.601 33.333 0.00 0.00 0.00 1.89
2248 2265 8.506168 AGAGGAACGAATTTTCAATAGCATAA 57.494 30.769 0.00 0.00 0.00 1.90
2249 2266 9.261180 CTAGAGGAACGAATTTTCAATAGCATA 57.739 33.333 0.00 0.00 0.00 3.14
2250 2267 7.254932 GCTAGAGGAACGAATTTTCAATAGCAT 60.255 37.037 0.00 0.00 35.04 3.79
2251 2268 6.037172 GCTAGAGGAACGAATTTTCAATAGCA 59.963 38.462 0.00 0.00 35.04 3.49
2252 2269 6.037172 TGCTAGAGGAACGAATTTTCAATAGC 59.963 38.462 0.00 10.38 35.26 2.97
2253 2270 7.278868 ACTGCTAGAGGAACGAATTTTCAATAG 59.721 37.037 0.00 0.00 0.00 1.73
2254 2271 7.103641 ACTGCTAGAGGAACGAATTTTCAATA 58.896 34.615 0.00 0.00 0.00 1.90
2255 2272 5.940470 ACTGCTAGAGGAACGAATTTTCAAT 59.060 36.000 0.00 0.00 0.00 2.57
2256 2273 5.305585 ACTGCTAGAGGAACGAATTTTCAA 58.694 37.500 0.00 0.00 0.00 2.69
2257 2274 4.894784 ACTGCTAGAGGAACGAATTTTCA 58.105 39.130 0.00 0.00 0.00 2.69
2258 2275 5.163844 GGAACTGCTAGAGGAACGAATTTTC 60.164 44.000 0.00 0.00 0.00 2.29
2259 2276 4.695928 GGAACTGCTAGAGGAACGAATTTT 59.304 41.667 0.00 0.00 0.00 1.82
2260 2277 4.254492 GGAACTGCTAGAGGAACGAATTT 58.746 43.478 0.00 0.00 0.00 1.82
2261 2278 3.676324 CGGAACTGCTAGAGGAACGAATT 60.676 47.826 0.00 0.00 0.00 2.17
2262 2279 2.159226 CGGAACTGCTAGAGGAACGAAT 60.159 50.000 0.00 0.00 0.00 3.34
2263 2280 1.201647 CGGAACTGCTAGAGGAACGAA 59.798 52.381 0.00 0.00 0.00 3.85
2264 2281 0.809385 CGGAACTGCTAGAGGAACGA 59.191 55.000 0.00 0.00 0.00 3.85
2265 2282 0.179134 CCGGAACTGCTAGAGGAACG 60.179 60.000 0.00 0.00 0.00 3.95
2266 2283 0.896226 ACCGGAACTGCTAGAGGAAC 59.104 55.000 9.46 0.00 0.00 3.62
2267 2284 1.640917 AACCGGAACTGCTAGAGGAA 58.359 50.000 9.46 0.00 0.00 3.36
2268 2285 1.275291 CAAACCGGAACTGCTAGAGGA 59.725 52.381 9.46 0.00 0.00 3.71
2269 2286 1.275291 TCAAACCGGAACTGCTAGAGG 59.725 52.381 9.46 0.00 0.00 3.69
2270 2287 2.611518 CTCAAACCGGAACTGCTAGAG 58.388 52.381 9.46 0.00 0.00 2.43
2271 2288 1.337823 GCTCAAACCGGAACTGCTAGA 60.338 52.381 9.46 0.00 0.00 2.43
2272 2289 1.079503 GCTCAAACCGGAACTGCTAG 58.920 55.000 9.46 0.00 0.00 3.42
2273 2290 0.394938 TGCTCAAACCGGAACTGCTA 59.605 50.000 9.46 0.00 0.00 3.49
2274 2291 0.250901 ATGCTCAAACCGGAACTGCT 60.251 50.000 9.46 0.00 0.00 4.24
2275 2292 0.598065 AATGCTCAAACCGGAACTGC 59.402 50.000 9.46 6.35 0.00 4.40
2276 2293 1.200020 GGAATGCTCAAACCGGAACTG 59.800 52.381 9.46 1.53 0.00 3.16
2277 2294 1.534729 GGAATGCTCAAACCGGAACT 58.465 50.000 9.46 0.00 0.00 3.01
2278 2295 0.168128 CGGAATGCTCAAACCGGAAC 59.832 55.000 9.46 0.00 41.41 3.62
2279 2296 2.550487 CGGAATGCTCAAACCGGAA 58.450 52.632 9.46 0.00 41.41 4.30
2280 2297 4.294523 CGGAATGCTCAAACCGGA 57.705 55.556 9.46 0.00 41.41 5.14
2283 2300 0.526211 GGGAACGGAATGCTCAAACC 59.474 55.000 0.00 0.00 0.00 3.27
2284 2301 1.534729 AGGGAACGGAATGCTCAAAC 58.465 50.000 0.00 0.00 0.00 2.93
2285 2302 2.286365 AAGGGAACGGAATGCTCAAA 57.714 45.000 0.00 0.00 0.00 2.69
2286 2303 2.286365 AAAGGGAACGGAATGCTCAA 57.714 45.000 0.00 0.00 0.00 3.02
2287 2304 2.286365 AAAAGGGAACGGAATGCTCA 57.714 45.000 0.00 0.00 0.00 4.26
2288 2305 2.556622 TGAAAAAGGGAACGGAATGCTC 59.443 45.455 0.00 0.00 0.00 4.26
2289 2306 2.593026 TGAAAAAGGGAACGGAATGCT 58.407 42.857 0.00 0.00 0.00 3.79
2290 2307 3.378911 TTGAAAAAGGGAACGGAATGC 57.621 42.857 0.00 0.00 0.00 3.56
2291 2308 4.944048 AGTTTGAAAAAGGGAACGGAATG 58.056 39.130 0.00 0.00 0.00 2.67
2292 2309 4.038763 GGAGTTTGAAAAAGGGAACGGAAT 59.961 41.667 0.00 0.00 0.00 3.01
2293 2310 3.382227 GGAGTTTGAAAAAGGGAACGGAA 59.618 43.478 0.00 0.00 0.00 4.30
2294 2311 2.953648 GGAGTTTGAAAAAGGGAACGGA 59.046 45.455 0.00 0.00 0.00 4.69
2295 2312 2.691011 TGGAGTTTGAAAAAGGGAACGG 59.309 45.455 0.00 0.00 0.00 4.44
2296 2313 3.380320 AGTGGAGTTTGAAAAAGGGAACG 59.620 43.478 0.00 0.00 0.00 3.95
2297 2314 5.127194 AGAAGTGGAGTTTGAAAAAGGGAAC 59.873 40.000 0.00 0.00 0.00 3.62
2298 2315 5.269189 AGAAGTGGAGTTTGAAAAAGGGAA 58.731 37.500 0.00 0.00 0.00 3.97
2299 2316 4.867086 AGAAGTGGAGTTTGAAAAAGGGA 58.133 39.130 0.00 0.00 0.00 4.20
2300 2317 5.598416 AAGAAGTGGAGTTTGAAAAAGGG 57.402 39.130 0.00 0.00 0.00 3.95
2301 2318 7.096551 TGAAAAGAAGTGGAGTTTGAAAAAGG 58.903 34.615 0.00 0.00 0.00 3.11
2302 2319 8.707938 ATGAAAAGAAGTGGAGTTTGAAAAAG 57.292 30.769 0.00 0.00 0.00 2.27
2306 2323 8.730680 GCTATATGAAAAGAAGTGGAGTTTGAA 58.269 33.333 0.00 0.00 0.00 2.69
2307 2324 7.882791 TGCTATATGAAAAGAAGTGGAGTTTGA 59.117 33.333 0.00 0.00 0.00 2.69
2308 2325 8.044060 TGCTATATGAAAAGAAGTGGAGTTTG 57.956 34.615 0.00 0.00 0.00 2.93
2309 2326 8.635765 TTGCTATATGAAAAGAAGTGGAGTTT 57.364 30.769 0.00 0.00 0.00 2.66
2310 2327 8.814038 ATTGCTATATGAAAAGAAGTGGAGTT 57.186 30.769 0.00 0.00 0.00 3.01
2311 2328 7.500559 GGATTGCTATATGAAAAGAAGTGGAGT 59.499 37.037 0.00 0.00 0.00 3.85
2312 2329 7.040823 GGGATTGCTATATGAAAAGAAGTGGAG 60.041 40.741 0.00 0.00 0.00 3.86
2313 2330 6.772716 GGGATTGCTATATGAAAAGAAGTGGA 59.227 38.462 0.00 0.00 0.00 4.02
2314 2331 6.774656 AGGGATTGCTATATGAAAAGAAGTGG 59.225 38.462 0.00 0.00 0.00 4.00
2315 2332 7.500227 TCAGGGATTGCTATATGAAAAGAAGTG 59.500 37.037 0.00 0.00 0.00 3.16
2316 2333 7.577303 TCAGGGATTGCTATATGAAAAGAAGT 58.423 34.615 0.00 0.00 0.00 3.01
2317 2334 8.632906 ATCAGGGATTGCTATATGAAAAGAAG 57.367 34.615 0.00 0.00 0.00 2.85
2318 2335 8.219868 TGATCAGGGATTGCTATATGAAAAGAA 58.780 33.333 0.00 0.00 0.00 2.52
2319 2336 7.748677 TGATCAGGGATTGCTATATGAAAAGA 58.251 34.615 0.00 0.00 0.00 2.52
2320 2337 7.991084 TGATCAGGGATTGCTATATGAAAAG 57.009 36.000 0.00 0.00 0.00 2.27
2321 2338 8.765488 TTTGATCAGGGATTGCTATATGAAAA 57.235 30.769 0.00 0.00 0.00 2.29
2322 2339 8.219868 TCTTTGATCAGGGATTGCTATATGAAA 58.780 33.333 0.00 0.00 0.00 2.69
2323 2340 7.748677 TCTTTGATCAGGGATTGCTATATGAA 58.251 34.615 0.00 0.00 0.00 2.57
2324 2341 7.236225 TCTCTTTGATCAGGGATTGCTATATGA 59.764 37.037 0.00 0.00 0.00 2.15
2325 2342 7.392418 TCTCTTTGATCAGGGATTGCTATATG 58.608 38.462 0.00 0.00 0.00 1.78
2326 2343 7.457218 TCTCTCTTTGATCAGGGATTGCTATAT 59.543 37.037 0.00 0.00 0.00 0.86
2327 2344 6.784473 TCTCTCTTTGATCAGGGATTGCTATA 59.216 38.462 0.00 0.00 0.00 1.31
2328 2345 5.605908 TCTCTCTTTGATCAGGGATTGCTAT 59.394 40.000 0.00 0.00 0.00 2.97
2329 2346 4.964897 TCTCTCTTTGATCAGGGATTGCTA 59.035 41.667 0.00 0.00 0.00 3.49
2330 2347 3.779183 TCTCTCTTTGATCAGGGATTGCT 59.221 43.478 0.00 0.00 0.00 3.91
2331 2348 4.148128 TCTCTCTTTGATCAGGGATTGC 57.852 45.455 0.00 0.00 0.00 3.56


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

AutoCloner maintained by Alex Coulton.