Multiple sequence alignment - TraesCS5D01G095600

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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 TraesCS5D01G095600 chr5D 100.000 2931 0 0 1 2931 105102682 105105612 0.000000e+00 5413.0
1 TraesCS5D01G095600 chr5D 97.143 70 2 0 256 325 517710847 517710778 5.130000e-23 119.0
2 TraesCS5D01G095600 chr5B 99.345 1986 12 1 284 2268 115074090 115076075 0.000000e+00 3594.0
3 TraesCS5D01G095600 chr5B 98.879 535 4 2 2398 2931 115076067 115076600 0.000000e+00 953.0
4 TraesCS5D01G095600 chr5B 96.654 269 5 2 1 269 115073837 115074101 7.450000e-121 444.0
5 TraesCS5D01G095600 chr5A 98.563 1948 22 4 327 2268 109278712 109280659 0.000000e+00 3437.0
6 TraesCS5D01G095600 chr5A 97.378 534 11 2 2398 2931 109280651 109281181 0.000000e+00 905.0
7 TraesCS5D01G095600 chr5A 90.530 264 11 4 1 250 109278469 109278732 1.300000e-88 337.0
8 TraesCS5D01G095600 chr5A 95.455 44 2 0 1 44 668224044 668224001 1.460000e-08 71.3
9 TraesCS5D01G095600 chr5A 77.049 122 23 4 1 120 668269468 668269350 6.780000e-07 65.8
10 TraesCS5D01G095600 chr4A 99.130 115 1 0 2289 2403 617221775 617221889 1.060000e-49 207.0
11 TraesCS5D01G095600 chr3D 98.319 119 0 2 2289 2405 384001063 384001181 1.060000e-49 207.0
12 TraesCS5D01G095600 chr3D 99.123 114 0 1 2289 2401 471419819 471419932 1.380000e-48 204.0
13 TraesCS5D01G095600 chr3D 97.222 72 2 0 256 327 274515850 274515921 3.970000e-24 122.0
14 TraesCS5D01G095600 chr7A 98.214 112 2 0 2289 2400 40536354 40536465 2.300000e-46 196.0
15 TraesCS5D01G095600 chr7A 94.737 114 5 1 2289 2401 567451166 567451279 3.000000e-40 176.0
16 TraesCS5D01G095600 chr7A 97.222 72 2 0 256 327 621621271 621621200 3.970000e-24 122.0
17 TraesCS5D01G095600 chr3A 96.491 114 3 1 2289 2401 323392994 323392881 1.390000e-43 187.0
18 TraesCS5D01G095600 chr2A 97.273 110 3 0 2291 2400 307690570 307690461 1.390000e-43 187.0
19 TraesCS5D01G095600 chr2A 97.222 72 2 0 256 327 116451574 116451645 3.970000e-24 122.0
20 TraesCS5D01G095600 chr6A 96.364 110 4 0 2289 2398 523516302 523516411 6.450000e-42 182.0
21 TraesCS5D01G095600 chr7D 92.437 119 7 2 2291 2407 550890859 550890977 5.020000e-38 169.0
22 TraesCS5D01G095600 chr7B 98.630 73 0 1 261 332 440012309 440012381 8.530000e-26 128.0
23 TraesCS5D01G095600 chr6B 97.222 72 2 0 256 327 20231109 20231038 3.970000e-24 122.0
24 TraesCS5D01G095600 chr1D 98.507 67 1 0 261 327 218903710 218903644 5.130000e-23 119.0
25 TraesCS5D01G095600 chr1B 95.833 72 3 0 256 327 679269823 679269894 1.850000e-22 117.0
26 TraesCS5D01G095600 chr1A 97.297 37 1 0 1494 1530 10227983 10227947 2.440000e-06 63.9
27 TraesCS5D01G095600 chr2B 92.500 40 3 0 5 44 787815733 787815694 1.130000e-04 58.4


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 TraesCS5D01G095600 chr5D 105102682 105105612 2930 False 5413.000000 5413 100.000000 1 2931 1 chr5D.!!$F1 2930
1 TraesCS5D01G095600 chr5B 115073837 115076600 2763 False 1663.666667 3594 98.292667 1 2931 3 chr5B.!!$F1 2930
2 TraesCS5D01G095600 chr5A 109278469 109281181 2712 False 1559.666667 3437 95.490333 1 2931 3 chr5A.!!$F1 2930

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
561 579 2.016318 TGCTAGCACCAATGAAATCCG 58.984 47.619 14.93 0.0 0.00 4.18 F
873 894 3.138283 TCCCAAACAGACTGGAGTTCATT 59.862 43.478 7.51 0.0 35.85 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1813 1834 0.033503 TCGGTGATGGTAGCAGAGGA 60.034 55.0 0.00 0.0 0.0 3.71 R
2292 2313 0.322277 CAGAGTGAGGGTGCTGCAAT 60.322 55.0 2.77 0.0 0.0 3.56 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
224 239 7.284261 TGACAGGAATTTTGTTATCAACACTCA 59.716 33.333 0.00 0.00 41.97 3.41
255 270 7.189079 TGAATAATGGTGGGCATATACGATA 57.811 36.000 0.00 0.00 0.00 2.92
256 271 7.045416 TGAATAATGGTGGGCATATACGATAC 58.955 38.462 0.00 0.00 0.00 2.24
257 272 4.901197 AATGGTGGGCATATACGATACA 57.099 40.909 0.00 0.00 0.00 2.29
258 273 4.901197 ATGGTGGGCATATACGATACAA 57.099 40.909 0.00 0.00 0.00 2.41
259 274 4.901197 TGGTGGGCATATACGATACAAT 57.099 40.909 0.00 0.00 0.00 2.71
260 275 6.553953 ATGGTGGGCATATACGATACAATA 57.446 37.500 0.00 0.00 0.00 1.90
261 276 6.361768 TGGTGGGCATATACGATACAATAA 57.638 37.500 0.00 0.00 0.00 1.40
262 277 6.167685 TGGTGGGCATATACGATACAATAAC 58.832 40.000 0.00 0.00 0.00 1.89
263 278 6.167685 GGTGGGCATATACGATACAATAACA 58.832 40.000 0.00 0.00 0.00 2.41
264 279 6.651643 GGTGGGCATATACGATACAATAACAA 59.348 38.462 0.00 0.00 0.00 2.83
265 280 7.360607 GGTGGGCATATACGATACAATAACAAC 60.361 40.741 0.00 0.00 0.00 3.32
266 281 7.171848 GTGGGCATATACGATACAATAACAACA 59.828 37.037 0.00 0.00 0.00 3.33
267 282 7.715686 TGGGCATATACGATACAATAACAACAA 59.284 33.333 0.00 0.00 0.00 2.83
268 283 8.013378 GGGCATATACGATACAATAACAACAAC 58.987 37.037 0.00 0.00 0.00 3.32
269 284 8.552865 GGCATATACGATACAATAACAACAACA 58.447 33.333 0.00 0.00 0.00 3.33
270 285 9.923786 GCATATACGATACAATAACAACAACAA 57.076 29.630 0.00 0.00 0.00 2.83
274 289 7.901874 ACGATACAATAACAACAACAACAAC 57.098 32.000 0.00 0.00 0.00 3.32
275 290 7.473366 ACGATACAATAACAACAACAACAACA 58.527 30.769 0.00 0.00 0.00 3.33
276 291 7.968956 ACGATACAATAACAACAACAACAACAA 59.031 29.630 0.00 0.00 0.00 2.83
277 292 8.256491 CGATACAATAACAACAACAACAACAAC 58.744 33.333 0.00 0.00 0.00 3.32
278 293 8.988064 ATACAATAACAACAACAACAACAACA 57.012 26.923 0.00 0.00 0.00 3.33
279 294 7.715265 ACAATAACAACAACAACAACAACAA 57.285 28.000 0.00 0.00 0.00 2.83
280 295 7.568433 ACAATAACAACAACAACAACAACAAC 58.432 30.769 0.00 0.00 0.00 3.32
281 296 7.224753 ACAATAACAACAACAACAACAACAACA 59.775 29.630 0.00 0.00 0.00 3.33
282 297 7.715265 ATAACAACAACAACAACAACAACAA 57.285 28.000 0.00 0.00 0.00 2.83
303 318 6.988522 ACAACAACAACAAAACCTTTAGTCT 58.011 32.000 0.00 0.00 0.00 3.24
339 354 5.940470 GGGTAGGCTAGAATGAATAATGGTG 59.060 44.000 0.00 0.00 0.00 4.17
561 579 2.016318 TGCTAGCACCAATGAAATCCG 58.984 47.619 14.93 0.00 0.00 4.18
873 894 3.138283 TCCCAAACAGACTGGAGTTCATT 59.862 43.478 7.51 0.00 35.85 2.57
2259 2280 6.826741 TGAGAAGATCATGCTGATTCAATTGA 59.173 34.615 3.38 3.38 37.20 2.57
2260 2281 7.338449 TGAGAAGATCATGCTGATTCAATTGAA 59.662 33.333 22.52 22.52 37.20 2.69
2261 2282 8.063200 AGAAGATCATGCTGATTCAATTGAAA 57.937 30.769 23.91 8.39 37.20 2.69
2262 2283 8.528643 AGAAGATCATGCTGATTCAATTGAAAA 58.471 29.630 23.91 14.40 37.20 2.29
2263 2284 9.314321 GAAGATCATGCTGATTCAATTGAAAAT 57.686 29.630 23.91 9.44 37.20 1.82
2296 2317 8.410030 TGTATTCACAATTGCAGATTAATTGC 57.590 30.769 5.05 12.76 45.06 3.56
2302 2323 2.945447 TGCAGATTAATTGCAGCACC 57.055 45.000 16.37 0.00 45.89 5.01
2303 2324 1.477700 TGCAGATTAATTGCAGCACCC 59.522 47.619 16.37 0.00 45.89 4.61
2304 2325 1.753073 GCAGATTAATTGCAGCACCCT 59.247 47.619 14.05 0.00 41.17 4.34
2305 2326 2.223665 GCAGATTAATTGCAGCACCCTC 60.224 50.000 14.05 0.00 41.17 4.30
2306 2327 3.018856 CAGATTAATTGCAGCACCCTCA 58.981 45.455 0.00 0.00 0.00 3.86
2307 2328 3.019564 AGATTAATTGCAGCACCCTCAC 58.980 45.455 0.00 0.00 0.00 3.51
2308 2329 2.584835 TTAATTGCAGCACCCTCACT 57.415 45.000 0.00 0.00 0.00 3.41
2309 2330 2.113860 TAATTGCAGCACCCTCACTC 57.886 50.000 0.00 0.00 0.00 3.51
2310 2331 0.403271 AATTGCAGCACCCTCACTCT 59.597 50.000 0.00 0.00 0.00 3.24
2311 2332 0.322277 ATTGCAGCACCCTCACTCTG 60.322 55.000 0.00 0.00 0.00 3.35
2312 2333 1.699054 TTGCAGCACCCTCACTCTGT 61.699 55.000 0.00 0.00 0.00 3.41
2313 2334 0.831711 TGCAGCACCCTCACTCTGTA 60.832 55.000 0.00 0.00 0.00 2.74
2314 2335 0.539051 GCAGCACCCTCACTCTGTAT 59.461 55.000 0.00 0.00 0.00 2.29
2315 2336 1.757118 GCAGCACCCTCACTCTGTATA 59.243 52.381 0.00 0.00 0.00 1.47
2316 2337 2.168521 GCAGCACCCTCACTCTGTATAA 59.831 50.000 0.00 0.00 0.00 0.98
2317 2338 3.181461 GCAGCACCCTCACTCTGTATAAT 60.181 47.826 0.00 0.00 0.00 1.28
2318 2339 4.684485 GCAGCACCCTCACTCTGTATAATT 60.684 45.833 0.00 0.00 0.00 1.40
2319 2340 4.813161 CAGCACCCTCACTCTGTATAATTG 59.187 45.833 0.00 0.00 0.00 2.32
2320 2341 3.561725 GCACCCTCACTCTGTATAATTGC 59.438 47.826 0.00 0.00 0.00 3.56
2321 2342 4.130118 CACCCTCACTCTGTATAATTGCC 58.870 47.826 0.00 0.00 0.00 4.52
2322 2343 4.040755 ACCCTCACTCTGTATAATTGCCT 58.959 43.478 0.00 0.00 0.00 4.75
2323 2344 4.101741 ACCCTCACTCTGTATAATTGCCTC 59.898 45.833 0.00 0.00 0.00 4.70
2324 2345 4.503991 CCCTCACTCTGTATAATTGCCTCC 60.504 50.000 0.00 0.00 0.00 4.30
2325 2346 4.346418 CCTCACTCTGTATAATTGCCTCCT 59.654 45.833 0.00 0.00 0.00 3.69
2326 2347 5.540337 CCTCACTCTGTATAATTGCCTCCTA 59.460 44.000 0.00 0.00 0.00 2.94
2327 2348 6.295011 CCTCACTCTGTATAATTGCCTCCTAG 60.295 46.154 0.00 0.00 0.00 3.02
2328 2349 5.540337 TCACTCTGTATAATTGCCTCCTAGG 59.460 44.000 0.82 0.82 38.80 3.02
2329 2350 5.540337 CACTCTGTATAATTGCCTCCTAGGA 59.460 44.000 11.98 11.98 37.67 2.94
2330 2351 5.777732 ACTCTGTATAATTGCCTCCTAGGAG 59.222 44.000 29.27 29.27 37.67 3.69
2344 2365 5.908341 CTCCTAGGAGGATGTAACTGAAAC 58.092 45.833 28.68 0.00 44.81 2.78
2345 2366 4.715297 TCCTAGGAGGATGTAACTGAAACC 59.285 45.833 7.62 0.00 40.06 3.27
2346 2367 4.141688 CCTAGGAGGATGTAACTGAAACCC 60.142 50.000 1.05 0.00 37.67 4.11
2347 2368 2.576648 AGGAGGATGTAACTGAAACCCC 59.423 50.000 0.00 0.00 0.00 4.95
2348 2369 2.576648 GGAGGATGTAACTGAAACCCCT 59.423 50.000 0.00 0.00 0.00 4.79
2349 2370 3.010250 GGAGGATGTAACTGAAACCCCTT 59.990 47.826 0.00 0.00 0.00 3.95
2350 2371 4.262617 GAGGATGTAACTGAAACCCCTTC 58.737 47.826 0.00 0.00 34.31 3.46
2351 2372 3.010250 AGGATGTAACTGAAACCCCTTCC 59.990 47.826 0.00 0.00 32.53 3.46
2352 2373 3.010250 GGATGTAACTGAAACCCCTTCCT 59.990 47.826 0.00 0.00 32.53 3.36
2353 2374 4.508584 GGATGTAACTGAAACCCCTTCCTT 60.509 45.833 0.00 0.00 32.53 3.36
2354 2375 4.529716 TGTAACTGAAACCCCTTCCTTT 57.470 40.909 0.00 0.00 32.53 3.11
2355 2376 4.874199 TGTAACTGAAACCCCTTCCTTTT 58.126 39.130 0.00 0.00 32.53 2.27
2356 2377 4.891168 TGTAACTGAAACCCCTTCCTTTTC 59.109 41.667 0.00 0.00 32.53 2.29
2357 2378 3.680777 ACTGAAACCCCTTCCTTTTCA 57.319 42.857 0.00 0.00 37.00 2.69
2358 2379 3.989056 ACTGAAACCCCTTCCTTTTCAA 58.011 40.909 0.00 0.00 38.45 2.69
2359 2380 4.556697 ACTGAAACCCCTTCCTTTTCAAT 58.443 39.130 0.00 0.00 38.45 2.57
2360 2381 4.344968 ACTGAAACCCCTTCCTTTTCAATG 59.655 41.667 0.00 0.00 38.45 2.82
2361 2382 3.070878 TGAAACCCCTTCCTTTTCAATGC 59.929 43.478 0.00 0.00 36.53 3.56
2362 2383 2.397044 ACCCCTTCCTTTTCAATGCA 57.603 45.000 0.00 0.00 0.00 3.96
2363 2384 2.688477 ACCCCTTCCTTTTCAATGCAA 58.312 42.857 0.00 0.00 0.00 4.08
2364 2385 3.250617 ACCCCTTCCTTTTCAATGCAAT 58.749 40.909 0.00 0.00 0.00 3.56
2365 2386 3.008266 ACCCCTTCCTTTTCAATGCAATG 59.992 43.478 0.00 0.00 0.00 2.82
2366 2387 3.261390 CCCCTTCCTTTTCAATGCAATGA 59.739 43.478 0.00 0.00 0.00 2.57
2367 2388 4.262981 CCCCTTCCTTTTCAATGCAATGAA 60.263 41.667 13.20 13.20 37.53 2.57
2368 2389 5.307204 CCCTTCCTTTTCAATGCAATGAAA 58.693 37.500 22.92 22.92 45.07 2.69
2369 2390 5.179929 CCCTTCCTTTTCAATGCAATGAAAC 59.820 40.000 25.73 0.00 46.06 2.78
2370 2391 5.107375 CCTTCCTTTTCAATGCAATGAAACG 60.107 40.000 25.73 23.18 46.06 3.60
2371 2392 3.740321 TCCTTTTCAATGCAATGAAACGC 59.260 39.130 25.73 0.00 46.06 4.84
2372 2393 3.493877 CCTTTTCAATGCAATGAAACGCA 59.506 39.130 25.73 13.18 46.06 5.24
2373 2394 4.025061 CCTTTTCAATGCAATGAAACGCAA 60.025 37.500 25.73 12.87 46.06 4.85
2374 2395 5.475273 TTTTCAATGCAATGAAACGCAAA 57.525 30.435 25.73 11.15 46.06 3.68
2375 2396 5.670149 TTTCAATGCAATGAAACGCAAAT 57.330 30.435 22.92 0.00 42.68 2.32
2376 2397 4.907188 TCAATGCAATGAAACGCAAATC 57.093 36.364 0.85 0.00 42.37 2.17
2377 2398 4.558178 TCAATGCAATGAAACGCAAATCT 58.442 34.783 0.85 0.00 42.37 2.40
2378 2399 4.989797 TCAATGCAATGAAACGCAAATCTT 59.010 33.333 0.85 0.00 42.37 2.40
2379 2400 5.118971 TCAATGCAATGAAACGCAAATCTTC 59.881 36.000 0.85 0.00 42.37 2.87
2380 2401 4.241590 TGCAATGAAACGCAAATCTTCT 57.758 36.364 0.00 0.00 34.59 2.85
2381 2402 3.982701 TGCAATGAAACGCAAATCTTCTG 59.017 39.130 0.00 0.00 34.59 3.02
2382 2403 3.181537 GCAATGAAACGCAAATCTTCTGC 60.182 43.478 0.00 0.00 36.41 4.26
2391 2412 3.888934 GCAAATCTTCTGCGTTTTCTCA 58.111 40.909 0.00 0.00 0.00 3.27
2392 2413 4.290155 GCAAATCTTCTGCGTTTTCTCAA 58.710 39.130 0.00 0.00 0.00 3.02
2393 2414 4.739716 GCAAATCTTCTGCGTTTTCTCAAA 59.260 37.500 0.00 0.00 0.00 2.69
2394 2415 5.231991 GCAAATCTTCTGCGTTTTCTCAAAA 59.768 36.000 0.00 0.00 0.00 2.44
2395 2416 6.237808 GCAAATCTTCTGCGTTTTCTCAAAAA 60.238 34.615 0.00 0.00 31.13 1.94
2618 2640 3.008049 AGGTCGAACAGCCAAAAGACTAT 59.992 43.478 1.87 0.00 0.00 2.12
2718 2740 8.454106 CAATTTACAGAAACTCCCAAGTCTATG 58.546 37.037 0.00 0.00 33.48 2.23
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
224 239 6.999705 ATGCCCACCATTATTCATTATTGT 57.000 33.333 0.00 0.00 0.00 2.71
251 266 7.900299 TGTTGTTGTTGTTGTTATTGTATCG 57.100 32.000 0.00 0.00 0.00 2.92
255 270 7.224753 TGTTGTTGTTGTTGTTGTTGTTATTGT 59.775 29.630 0.00 0.00 0.00 2.71
256 271 7.567571 TGTTGTTGTTGTTGTTGTTGTTATTG 58.432 30.769 0.00 0.00 0.00 1.90
257 272 7.715265 TGTTGTTGTTGTTGTTGTTGTTATT 57.285 28.000 0.00 0.00 0.00 1.40
258 273 7.224753 TGTTGTTGTTGTTGTTGTTGTTGTTAT 59.775 29.630 0.00 0.00 0.00 1.89
259 274 6.533723 TGTTGTTGTTGTTGTTGTTGTTGTTA 59.466 30.769 0.00 0.00 0.00 2.41
260 275 5.351465 TGTTGTTGTTGTTGTTGTTGTTGTT 59.649 32.000 0.00 0.00 0.00 2.83
261 276 4.870426 TGTTGTTGTTGTTGTTGTTGTTGT 59.130 33.333 0.00 0.00 0.00 3.32
262 277 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
263 278 5.351465 TGTTGTTGTTGTTGTTGTTGTTGTT 59.649 32.000 0.00 0.00 0.00 2.83
264 279 4.870426 TGTTGTTGTTGTTGTTGTTGTTGT 59.130 33.333 0.00 0.00 0.00 3.32
265 280 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
266 281 5.351465 TGTTGTTGTTGTTGTTGTTGTTGTT 59.649 32.000 0.00 0.00 0.00 2.83
267 282 4.870426 TGTTGTTGTTGTTGTTGTTGTTGT 59.130 33.333 0.00 0.00 0.00 3.32
268 283 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
269 284 6.422776 TTTGTTGTTGTTGTTGTTGTTGTT 57.577 29.167 0.00 0.00 0.00 2.83
270 285 6.251549 GTTTTGTTGTTGTTGTTGTTGTTGT 58.748 32.000 0.00 0.00 0.00 3.32
271 286 5.678919 GGTTTTGTTGTTGTTGTTGTTGTTG 59.321 36.000 0.00 0.00 0.00 3.33
272 287 5.586643 AGGTTTTGTTGTTGTTGTTGTTGTT 59.413 32.000 0.00 0.00 0.00 2.83
273 288 5.119694 AGGTTTTGTTGTTGTTGTTGTTGT 58.880 33.333 0.00 0.00 0.00 3.32
274 289 5.665381 AGGTTTTGTTGTTGTTGTTGTTG 57.335 34.783 0.00 0.00 0.00 3.33
275 290 6.685527 AAAGGTTTTGTTGTTGTTGTTGTT 57.314 29.167 0.00 0.00 0.00 2.83
276 291 6.987404 ACTAAAGGTTTTGTTGTTGTTGTTGT 59.013 30.769 0.00 0.00 0.00 3.32
277 292 7.383843 AGACTAAAGGTTTTGTTGTTGTTGTTG 59.616 33.333 0.00 0.00 0.00 3.33
278 293 7.438564 AGACTAAAGGTTTTGTTGTTGTTGTT 58.561 30.769 0.00 0.00 0.00 2.83
279 294 6.988522 AGACTAAAGGTTTTGTTGTTGTTGT 58.011 32.000 0.00 0.00 0.00 3.32
280 295 7.087639 TGAGACTAAAGGTTTTGTTGTTGTTG 58.912 34.615 0.00 0.00 0.00 3.33
281 296 7.222000 TGAGACTAAAGGTTTTGTTGTTGTT 57.778 32.000 0.00 0.00 0.00 2.83
282 297 6.827586 TGAGACTAAAGGTTTTGTTGTTGT 57.172 33.333 0.00 0.00 0.00 3.32
303 318 1.497286 AGCCTACCCCAACTTGTTTGA 59.503 47.619 0.00 0.00 37.39 2.69
561 579 5.240844 AGGTCAGTTTATTTGGTTAGTGTGC 59.759 40.000 0.00 0.00 0.00 4.57
1813 1834 0.033503 TCGGTGATGGTAGCAGAGGA 60.034 55.000 0.00 0.00 0.00 3.71
2029 2050 7.064371 GCACACTTGGAATGCTAGATAGATATG 59.936 40.741 0.00 0.00 36.40 1.78
2270 2291 9.037737 GCAATTAATCTGCAATTGTGAATACAT 57.962 29.630 7.40 0.00 42.67 2.29
2271 2292 8.033626 TGCAATTAATCTGCAATTGTGAATACA 58.966 29.630 17.39 0.00 46.47 2.29
2272 2293 8.410030 TGCAATTAATCTGCAATTGTGAATAC 57.590 30.769 17.39 0.00 46.47 1.89
2284 2305 1.753073 AGGGTGCTGCAATTAATCTGC 59.247 47.619 2.77 12.76 40.35 4.26
2285 2306 3.018856 TGAGGGTGCTGCAATTAATCTG 58.981 45.455 2.77 0.00 0.00 2.90
2286 2307 3.019564 GTGAGGGTGCTGCAATTAATCT 58.980 45.455 2.77 0.00 0.00 2.40
2287 2308 3.019564 AGTGAGGGTGCTGCAATTAATC 58.980 45.455 2.77 0.00 0.00 1.75
2288 2309 3.019564 GAGTGAGGGTGCTGCAATTAAT 58.980 45.455 2.77 0.00 0.00 1.40
2289 2310 2.040278 AGAGTGAGGGTGCTGCAATTAA 59.960 45.455 2.77 0.00 0.00 1.40
2290 2311 1.630369 AGAGTGAGGGTGCTGCAATTA 59.370 47.619 2.77 0.00 0.00 1.40
2291 2312 0.403271 AGAGTGAGGGTGCTGCAATT 59.597 50.000 2.77 0.00 0.00 2.32
2292 2313 0.322277 CAGAGTGAGGGTGCTGCAAT 60.322 55.000 2.77 0.00 0.00 3.56
2293 2314 1.071987 CAGAGTGAGGGTGCTGCAA 59.928 57.895 2.77 0.00 0.00 4.08
2294 2315 0.831711 TACAGAGTGAGGGTGCTGCA 60.832 55.000 0.00 0.00 31.74 4.41
2295 2316 0.539051 ATACAGAGTGAGGGTGCTGC 59.461 55.000 0.00 0.00 31.74 5.25
2296 2317 4.679373 ATTATACAGAGTGAGGGTGCTG 57.321 45.455 0.00 0.00 34.65 4.41
2297 2318 4.684485 GCAATTATACAGAGTGAGGGTGCT 60.684 45.833 0.00 0.00 0.00 4.40
2298 2319 3.561725 GCAATTATACAGAGTGAGGGTGC 59.438 47.826 0.00 0.00 0.00 5.01
2299 2320 4.130118 GGCAATTATACAGAGTGAGGGTG 58.870 47.826 0.00 0.00 0.00 4.61
2300 2321 4.040755 AGGCAATTATACAGAGTGAGGGT 58.959 43.478 0.00 0.00 0.00 4.34
2301 2322 4.503991 GGAGGCAATTATACAGAGTGAGGG 60.504 50.000 0.00 0.00 0.00 4.30
2302 2323 4.346418 AGGAGGCAATTATACAGAGTGAGG 59.654 45.833 0.00 0.00 0.00 3.86
2303 2324 5.543507 AGGAGGCAATTATACAGAGTGAG 57.456 43.478 0.00 0.00 0.00 3.51
2304 2325 5.540337 CCTAGGAGGCAATTATACAGAGTGA 59.460 44.000 1.05 0.00 0.00 3.41
2305 2326 5.540337 TCCTAGGAGGCAATTATACAGAGTG 59.460 44.000 7.62 0.00 34.61 3.51
2306 2327 5.716979 TCCTAGGAGGCAATTATACAGAGT 58.283 41.667 7.62 0.00 34.61 3.24
2307 2328 6.279513 CTCCTAGGAGGCAATTATACAGAG 57.720 45.833 28.68 0.01 38.51 3.35
2323 2344 4.141688 GGGTTTCAGTTACATCCTCCTAGG 60.142 50.000 0.82 0.82 36.46 3.02
2324 2345 4.141688 GGGGTTTCAGTTACATCCTCCTAG 60.142 50.000 0.00 0.00 0.00 3.02
2325 2346 3.778629 GGGGTTTCAGTTACATCCTCCTA 59.221 47.826 0.00 0.00 0.00 2.94
2326 2347 2.576648 GGGGTTTCAGTTACATCCTCCT 59.423 50.000 0.00 0.00 0.00 3.69
2327 2348 2.576648 AGGGGTTTCAGTTACATCCTCC 59.423 50.000 0.00 0.00 0.00 4.30
2328 2349 4.262617 GAAGGGGTTTCAGTTACATCCTC 58.737 47.826 0.00 0.00 35.78 3.71
2329 2350 3.010250 GGAAGGGGTTTCAGTTACATCCT 59.990 47.826 0.00 0.00 37.54 3.24
2330 2351 3.010250 AGGAAGGGGTTTCAGTTACATCC 59.990 47.826 0.00 0.00 37.54 3.51
2331 2352 4.302559 AGGAAGGGGTTTCAGTTACATC 57.697 45.455 0.00 0.00 37.54 3.06
2332 2353 4.741928 AAGGAAGGGGTTTCAGTTACAT 57.258 40.909 0.00 0.00 37.54 2.29
2333 2354 4.529716 AAAGGAAGGGGTTTCAGTTACA 57.470 40.909 0.00 0.00 37.54 2.41
2334 2355 4.891168 TGAAAAGGAAGGGGTTTCAGTTAC 59.109 41.667 0.00 0.00 36.58 2.50
2335 2356 5.132043 TGAAAAGGAAGGGGTTTCAGTTA 57.868 39.130 0.00 0.00 36.58 2.24
2336 2357 3.989056 TGAAAAGGAAGGGGTTTCAGTT 58.011 40.909 0.00 0.00 36.58 3.16
2337 2358 3.680777 TGAAAAGGAAGGGGTTTCAGT 57.319 42.857 0.00 0.00 36.58 3.41
2338 2359 4.800582 GCATTGAAAAGGAAGGGGTTTCAG 60.801 45.833 0.00 0.00 41.06 3.02
2339 2360 3.070878 GCATTGAAAAGGAAGGGGTTTCA 59.929 43.478 0.00 0.00 39.00 2.69
2340 2361 3.070878 TGCATTGAAAAGGAAGGGGTTTC 59.929 43.478 0.00 0.00 34.93 2.78
2341 2362 3.044894 TGCATTGAAAAGGAAGGGGTTT 58.955 40.909 0.00 0.00 0.00 3.27
2342 2363 2.688477 TGCATTGAAAAGGAAGGGGTT 58.312 42.857 0.00 0.00 0.00 4.11
2343 2364 2.397044 TGCATTGAAAAGGAAGGGGT 57.603 45.000 0.00 0.00 0.00 4.95
2344 2365 3.261390 TCATTGCATTGAAAAGGAAGGGG 59.739 43.478 8.80 0.00 0.00 4.79
2345 2366 4.540359 TCATTGCATTGAAAAGGAAGGG 57.460 40.909 8.80 0.00 0.00 3.95
2346 2367 5.107375 CGTTTCATTGCATTGAAAAGGAAGG 60.107 40.000 28.82 14.73 44.71 3.46
2347 2368 5.613142 GCGTTTCATTGCATTGAAAAGGAAG 60.613 40.000 31.90 22.66 44.71 3.46
2348 2369 4.210955 GCGTTTCATTGCATTGAAAAGGAA 59.789 37.500 31.90 15.84 44.71 3.36
2349 2370 3.740321 GCGTTTCATTGCATTGAAAAGGA 59.260 39.130 31.90 16.11 44.71 3.36
2350 2371 3.493877 TGCGTTTCATTGCATTGAAAAGG 59.506 39.130 31.90 26.38 44.71 3.11
2351 2372 4.712191 TGCGTTTCATTGCATTGAAAAG 57.288 36.364 29.50 29.50 44.71 2.27
2352 2373 5.475273 TTTGCGTTTCATTGCATTGAAAA 57.525 30.435 28.82 16.62 44.71 2.29
2353 2374 5.466058 AGATTTGCGTTTCATTGCATTGAAA 59.534 32.000 25.34 25.34 41.92 2.69
2354 2375 4.989797 AGATTTGCGTTTCATTGCATTGAA 59.010 33.333 17.74 17.74 41.42 2.69
2355 2376 4.558178 AGATTTGCGTTTCATTGCATTGA 58.442 34.783 7.19 7.19 41.42 2.57
2356 2377 4.914312 AGATTTGCGTTTCATTGCATTG 57.086 36.364 2.08 2.08 41.42 2.82
2357 2378 5.119588 CAGAAGATTTGCGTTTCATTGCATT 59.880 36.000 0.00 0.00 41.42 3.56
2358 2379 4.624024 CAGAAGATTTGCGTTTCATTGCAT 59.376 37.500 0.00 0.00 41.42 3.96
2359 2380 3.982701 CAGAAGATTTGCGTTTCATTGCA 59.017 39.130 0.00 0.00 39.81 4.08
2360 2381 3.181537 GCAGAAGATTTGCGTTTCATTGC 60.182 43.478 0.00 0.00 0.00 3.56
2361 2382 4.557276 GCAGAAGATTTGCGTTTCATTG 57.443 40.909 0.00 0.00 0.00 2.82
2370 2391 3.888934 TGAGAAAACGCAGAAGATTTGC 58.111 40.909 0.00 0.00 38.18 3.68
2371 2392 6.810888 TTTTGAGAAAACGCAGAAGATTTG 57.189 33.333 0.00 0.00 0.00 2.32
2618 2640 9.202273 GATATTTGTTCTGTAATGTTTTGCCAA 57.798 29.630 0.00 0.00 0.00 4.52
2820 2842 5.879763 TGATTCTGAAATCTTGTCCTCCAA 58.120 37.500 0.00 0.00 41.63 3.53


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

AutoCloner maintained by Alex Coulton.