Multiple sequence alignment - TraesCS6D01G254300

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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 TraesCS6D01G254300 chr6D 100.000 2531 0 0 1 2531 358975521 358978051 0.000000e+00 4674
1 TraesCS6D01G254300 chr6B 92.697 2369 105 29 1 2337 540589583 540591915 0.000000e+00 3354
2 TraesCS6D01G254300 chr6B 91.517 1556 83 25 804 2337 560198834 560197306 0.000000e+00 2097
3 TraesCS6D01G254300 chr6B 94.492 581 24 5 1 580 560199434 560198861 0.000000e+00 889
4 TraesCS6D01G254300 chr6B 92.708 96 7 0 2411 2506 540591916 540592011 3.400000e-29 139
5 TraesCS6D01G254300 chr6B 92.708 96 7 0 2411 2506 560197305 560197210 3.400000e-29 139
6 TraesCS6D01G254300 chr6A 91.792 2388 87 37 1 2337 500504160 500506489 0.000000e+00 3223
7 TraesCS6D01G254300 chr4B 95.652 69 0 2 2341 2409 23660802 23660867 9.570000e-20 108
8 TraesCS6D01G254300 chr3B 95.652 69 0 2 2341 2409 10717523 10717588 9.570000e-20 108
9 TraesCS6D01G254300 chr7D 91.139 79 4 2 2341 2419 448336980 448337055 1.240000e-18 104
10 TraesCS6D01G254300 chr7A 93.151 73 1 3 2341 2412 136806172 136806103 1.240000e-18 104
11 TraesCS6D01G254300 chr5D 94.286 70 1 2 2341 2410 18193854 18193788 1.240000e-18 104
12 TraesCS6D01G254300 chr5D 92.000 75 2 3 2341 2414 2137451 2137380 4.450000e-18 102
13 TraesCS6D01G254300 chr2D 91.139 79 3 3 2341 2419 386707063 386706989 1.240000e-18 104
14 TraesCS6D01G254300 chrUn 87.640 89 5 5 2341 2428 461112350 461112267 5.760000e-17 99
15 TraesCS6D01G254300 chr3D 89.873 79 4 3 2341 2419 341550627 341550553 5.760000e-17 99


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 TraesCS6D01G254300 chr6D 358975521 358978051 2530 False 4674.000000 4674 100.000000 1 2531 1 chr6D.!!$F1 2530
1 TraesCS6D01G254300 chr6B 540589583 540592011 2428 False 1746.500000 3354 92.702500 1 2506 2 chr6B.!!$F1 2505
2 TraesCS6D01G254300 chr6B 560197210 560199434 2224 True 1041.666667 2097 92.905667 1 2506 3 chr6B.!!$R1 2505
3 TraesCS6D01G254300 chr6A 500504160 500506489 2329 False 3223.000000 3223 91.792000 1 2337 1 chr6A.!!$F1 2336

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
843 878 0.037697 GTTCAATTCAAACCCCGGCC 60.038 55.0 0.0 0.0 0.0 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2353 2446 0.107897 ACTGCGGTGTCAGTGTCAAA 60.108 50.0 0.0 0.0 44.88 2.69 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
24 25 0.618458 TGGCGTAATCTGAAGGGCTT 59.382 50.000 0.00 0.00 0.00 4.35
28 29 2.284417 GCGTAATCTGAAGGGCTTTACG 59.716 50.000 12.24 12.24 44.68 3.18
46 47 1.253999 CGTTACGCCGTTCAGTAGTC 58.746 55.000 0.00 0.00 0.00 2.59
109 110 0.179073 CCATCCGTCGAGCATTCCTT 60.179 55.000 0.00 0.00 0.00 3.36
227 228 1.004918 GTTGTGCCTCCTACACGCT 60.005 57.895 0.00 0.00 41.03 5.07
243 244 1.102154 CGCTGCCAAAATACCATCCA 58.898 50.000 0.00 0.00 0.00 3.41
244 245 1.066002 CGCTGCCAAAATACCATCCAG 59.934 52.381 0.00 0.00 0.00 3.86
245 246 1.410153 GCTGCCAAAATACCATCCAGG 59.590 52.381 0.00 0.00 45.67 4.45
247 248 0.752658 GCCAAAATACCATCCAGGGC 59.247 55.000 0.00 0.00 43.89 5.19
248 249 1.689258 GCCAAAATACCATCCAGGGCT 60.689 52.381 0.00 0.00 43.89 5.19
251 252 0.853530 AAATACCATCCAGGGCTCCC 59.146 55.000 0.00 0.00 43.89 4.30
258 259 2.770868 ATCCAGGGCTCCCACACTGA 62.771 60.000 7.82 0.00 38.92 3.41
279 280 2.299521 AGATGTCTACCACTAGACCGC 58.700 52.381 0.00 0.00 46.03 5.68
336 337 3.220110 CCTACGCCTAAGATGTCACCTA 58.780 50.000 0.00 0.00 0.00 3.08
342 343 3.491104 GCCTAAGATGTCACCTAACGGAG 60.491 52.174 0.00 0.00 0.00 4.63
344 345 3.870633 AAGATGTCACCTAACGGAGTC 57.129 47.619 0.00 0.00 45.00 3.36
495 510 1.451028 GTGATGTCCCTGCCTGCTC 60.451 63.158 0.00 0.00 0.00 4.26
496 511 2.191641 GATGTCCCTGCCTGCTCC 59.808 66.667 0.00 0.00 0.00 4.70
497 512 2.285969 ATGTCCCTGCCTGCTCCT 60.286 61.111 0.00 0.00 0.00 3.69
498 513 2.605854 GATGTCCCTGCCTGCTCCTG 62.606 65.000 0.00 0.00 0.00 3.86
499 514 4.792804 GTCCCTGCCTGCTCCTGC 62.793 72.222 0.00 0.00 40.20 4.85
501 516 4.486503 CCCTGCCTGCTCCTGCTC 62.487 72.222 0.00 0.00 40.48 4.26
502 517 4.834453 CCTGCCTGCTCCTGCTCG 62.834 72.222 0.00 0.00 40.48 5.03
839 874 6.061441 AGGAATTTTGTTCAATTCAAACCCC 58.939 36.000 8.11 0.00 42.68 4.95
841 876 3.460857 TTTGTTCAATTCAAACCCCGG 57.539 42.857 0.00 0.00 31.17 5.73
842 877 0.676736 TGTTCAATTCAAACCCCGGC 59.323 50.000 0.00 0.00 0.00 6.13
843 878 0.037697 GTTCAATTCAAACCCCGGCC 60.038 55.000 0.00 0.00 0.00 6.13
844 879 0.178947 TTCAATTCAAACCCCGGCCT 60.179 50.000 0.00 0.00 0.00 5.19
845 880 0.610785 TCAATTCAAACCCCGGCCTC 60.611 55.000 0.00 0.00 0.00 4.70
846 881 0.611896 CAATTCAAACCCCGGCCTCT 60.612 55.000 0.00 0.00 0.00 3.69
902 963 1.125633 ACACCACTACCCACGAAGTT 58.874 50.000 0.00 0.00 41.61 2.66
908 969 1.337167 ACTACCCACGAAGTTAACGCC 60.337 52.381 0.00 0.00 41.61 5.68
1418 1488 2.286425 CCACCTCCATCCCCAGGT 60.286 66.667 0.00 0.00 44.42 4.00
1489 1559 2.361610 CGGTCAGGCAAGGGCAAT 60.362 61.111 0.00 0.00 43.71 3.56
1512 1582 1.218316 GGGCGGAACATTCGTCTCT 59.782 57.895 0.00 0.00 32.30 3.10
1515 1585 1.991430 CGGAACATTCGTCTCTGCG 59.009 57.895 0.00 0.00 0.00 5.18
1544 1614 3.812053 GGTTCATGATCATCACAGTAGCC 59.188 47.826 4.86 0.00 0.00 3.93
1545 1615 4.444022 GGTTCATGATCATCACAGTAGCCT 60.444 45.833 4.86 0.00 0.00 4.58
1634 1711 3.520187 TGATCCATCGGCGATCATG 57.480 52.632 21.25 10.93 40.88 3.07
1719 1796 8.950210 CAGTCACTTCCAGATTGTATTTTGTAT 58.050 33.333 0.00 0.00 0.00 2.29
1745 1823 1.982612 TCATCGAGCAGTGAAGAACG 58.017 50.000 0.00 0.00 0.00 3.95
1803 1881 2.311688 AATCGTCGATGGGGTCCTGC 62.312 60.000 8.83 0.00 0.00 4.85
1906 1984 2.577449 AACCCTGCAACGAAAAACAG 57.423 45.000 0.00 0.00 0.00 3.16
1948 2026 3.575965 AATTCTGCTTTGCTTTACCCG 57.424 42.857 0.00 0.00 0.00 5.28
1969 2047 4.214119 CCGCAAGAATGGACCACAATATAG 59.786 45.833 0.00 0.00 43.02 1.31
1970 2048 4.214119 CGCAAGAATGGACCACAATATAGG 59.786 45.833 0.00 0.00 43.02 2.57
1973 2051 5.234466 AGAATGGACCACAATATAGGAGC 57.766 43.478 0.00 0.00 0.00 4.70
1981 2059 4.716784 ACCACAATATAGGAGCAGTTCAGA 59.283 41.667 0.00 0.00 0.00 3.27
1982 2060 5.189736 ACCACAATATAGGAGCAGTTCAGAA 59.810 40.000 0.00 0.00 0.00 3.02
1983 2061 6.126652 ACCACAATATAGGAGCAGTTCAGAAT 60.127 38.462 0.00 0.00 0.00 2.40
2111 2200 6.588204 ACCTGAAAACATAAAAAGGAAACCC 58.412 36.000 0.00 0.00 0.00 4.11
2154 2243 6.802608 CATCATAAGGATGCATTCACAAACT 58.197 36.000 7.96 0.00 46.35 2.66
2155 2244 6.441093 TCATAAGGATGCATTCACAAACTC 57.559 37.500 7.96 0.00 32.62 3.01
2156 2245 6.182627 TCATAAGGATGCATTCACAAACTCT 58.817 36.000 7.96 0.00 32.62 3.24
2173 2262 9.661187 CACAAACTCTATGATAGAATGCATTTC 57.339 33.333 14.33 8.01 33.75 2.17
2197 2287 7.771183 TCGATTTGAAAAATATTCTGGGAAGG 58.229 34.615 0.00 0.00 0.00 3.46
2213 2303 2.486013 GGAAGGTAAAACCCTCACACGT 60.486 50.000 0.00 0.00 39.75 4.49
2237 2329 8.507249 CGTTCTTATTCTGGAAAGACAAGATTT 58.493 33.333 0.00 0.00 31.62 2.17
2241 2333 6.765915 ATTCTGGAAAGACAAGATTTAGGC 57.234 37.500 0.00 0.00 0.00 3.93
2256 2348 2.489938 TAGGCTGTGGAAAATTCGCT 57.510 45.000 0.00 0.00 0.00 4.93
2313 2405 2.643995 TATGGCATCAGTCCATGTGG 57.356 50.000 1.65 0.00 43.67 4.17
2349 2442 9.685828 ATTTCTCGAAACTACTCATATAAGAGC 57.314 33.333 4.89 0.00 34.60 4.09
2350 2443 6.889494 TCTCGAAACTACTCATATAAGAGCG 58.111 40.000 4.89 0.39 39.26 5.03
2351 2444 6.482641 TCTCGAAACTACTCATATAAGAGCGT 59.517 38.462 4.89 0.54 39.26 5.07
2352 2445 7.012138 TCTCGAAACTACTCATATAAGAGCGTT 59.988 37.037 4.89 6.24 39.26 4.84
2353 2446 7.478322 TCGAAACTACTCATATAAGAGCGTTT 58.522 34.615 18.20 18.20 41.30 3.60
2354 2447 7.972277 TCGAAACTACTCATATAAGAGCGTTTT 59.028 33.333 18.75 10.53 40.01 2.43
2355 2448 8.592998 CGAAACTACTCATATAAGAGCGTTTTT 58.407 33.333 18.75 9.29 40.01 1.94
2356 2449 9.690434 GAAACTACTCATATAAGAGCGTTTTTG 57.310 33.333 18.75 2.02 40.01 2.44
2357 2450 8.997621 AACTACTCATATAAGAGCGTTTTTGA 57.002 30.769 4.89 0.00 39.26 2.69
2358 2451 8.408743 ACTACTCATATAAGAGCGTTTTTGAC 57.591 34.615 4.89 0.00 39.26 3.18
2359 2452 8.033038 ACTACTCATATAAGAGCGTTTTTGACA 58.967 33.333 4.89 0.00 39.26 3.58
2360 2453 7.061752 ACTCATATAAGAGCGTTTTTGACAC 57.938 36.000 4.89 0.00 39.26 3.67
2361 2454 6.874134 ACTCATATAAGAGCGTTTTTGACACT 59.126 34.615 4.89 0.00 39.26 3.55
2362 2455 7.060600 TCATATAAGAGCGTTTTTGACACTG 57.939 36.000 0.00 0.00 0.00 3.66
2363 2456 6.871492 TCATATAAGAGCGTTTTTGACACTGA 59.129 34.615 0.00 0.00 0.00 3.41
2364 2457 3.675467 AAGAGCGTTTTTGACACTGAC 57.325 42.857 0.00 0.00 0.00 3.51
2365 2458 2.627945 AGAGCGTTTTTGACACTGACA 58.372 42.857 0.00 0.00 0.00 3.58
2366 2459 2.351726 AGAGCGTTTTTGACACTGACAC 59.648 45.455 0.00 0.00 0.00 3.67
2367 2460 1.400494 AGCGTTTTTGACACTGACACC 59.600 47.619 0.00 0.00 0.00 4.16
2368 2461 1.854434 GCGTTTTTGACACTGACACCG 60.854 52.381 0.00 0.00 0.00 4.94
2369 2462 1.822581 GTTTTTGACACTGACACCGC 58.177 50.000 0.00 0.00 0.00 5.68
2370 2463 1.131504 GTTTTTGACACTGACACCGCA 59.868 47.619 0.00 0.00 0.00 5.69
2371 2464 1.013596 TTTTGACACTGACACCGCAG 58.986 50.000 0.00 0.00 41.63 5.18
2382 2475 2.853457 CACCGCAGTGTCAAAAACG 58.147 52.632 0.00 0.00 39.30 3.60
2383 2476 1.063488 ACCGCAGTGTCAAAAACGC 59.937 52.632 0.00 0.00 38.74 4.84
2385 2478 0.657368 CCGCAGTGTCAAAAACGCTC 60.657 55.000 0.00 0.00 45.69 5.03
2386 2479 0.304705 CGCAGTGTCAAAAACGCTCT 59.695 50.000 0.00 0.00 45.69 4.09
2387 2480 1.268032 CGCAGTGTCAAAAACGCTCTT 60.268 47.619 0.00 0.00 45.69 2.85
2388 2481 2.033236 CGCAGTGTCAAAAACGCTCTTA 60.033 45.455 0.00 0.00 45.69 2.10
2389 2482 3.363970 CGCAGTGTCAAAAACGCTCTTAT 60.364 43.478 0.00 0.00 45.69 1.73
2390 2483 4.143200 CGCAGTGTCAAAAACGCTCTTATA 60.143 41.667 0.00 0.00 45.69 0.98
2391 2484 5.445939 CGCAGTGTCAAAAACGCTCTTATAT 60.446 40.000 0.00 0.00 45.69 0.86
2392 2485 6.314784 GCAGTGTCAAAAACGCTCTTATATT 58.685 36.000 0.00 0.00 45.69 1.28
2393 2486 7.461107 GCAGTGTCAAAAACGCTCTTATATTA 58.539 34.615 0.00 0.00 45.69 0.98
2394 2487 8.122952 GCAGTGTCAAAAACGCTCTTATATTAT 58.877 33.333 0.00 0.00 45.69 1.28
2395 2488 9.425893 CAGTGTCAAAAACGCTCTTATATTATG 57.574 33.333 0.00 0.00 45.69 1.90
2396 2489 8.612619 AGTGTCAAAAACGCTCTTATATTATGG 58.387 33.333 0.00 0.00 45.69 2.74
2397 2490 7.855904 GTGTCAAAAACGCTCTTATATTATGGG 59.144 37.037 0.00 0.00 35.42 4.00
2398 2491 7.771361 TGTCAAAAACGCTCTTATATTATGGGA 59.229 33.333 0.00 0.00 0.00 4.37
2399 2492 8.068380 GTCAAAAACGCTCTTATATTATGGGAC 58.932 37.037 0.00 0.00 0.00 4.46
2400 2493 6.780706 AAAACGCTCTTATATTATGGGACG 57.219 37.500 0.00 0.00 0.00 4.79
2401 2494 4.451629 ACGCTCTTATATTATGGGACGG 57.548 45.455 0.00 0.00 0.00 4.79
2402 2495 4.084287 ACGCTCTTATATTATGGGACGGA 58.916 43.478 0.00 0.00 0.00 4.69
2403 2496 4.158025 ACGCTCTTATATTATGGGACGGAG 59.842 45.833 0.00 0.00 0.00 4.63
2404 2497 4.440250 CGCTCTTATATTATGGGACGGAGG 60.440 50.000 0.00 0.00 0.00 4.30
2405 2498 4.141914 GCTCTTATATTATGGGACGGAGGG 60.142 50.000 0.00 0.00 0.00 4.30
2406 2499 5.269991 CTCTTATATTATGGGACGGAGGGA 58.730 45.833 0.00 0.00 0.00 4.20
2407 2500 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
2408 2501 3.562108 ATATTATGGGACGGAGGGAGT 57.438 47.619 0.00 0.00 0.00 3.85
2409 2502 1.424638 ATTATGGGACGGAGGGAGTG 58.575 55.000 0.00 0.00 0.00 3.51
2423 2516 5.935789 CGGAGGGAGTGAAAAACAAGTATAA 59.064 40.000 0.00 0.00 0.00 0.98
2428 2521 8.630037 AGGGAGTGAAAAACAAGTATAACAAAG 58.370 33.333 0.00 0.00 0.00 2.77
2485 2578 3.750130 GCAGAGATGTAATGTATGGCAGG 59.250 47.826 0.00 0.00 28.35 4.85
2490 2583 7.332926 CAGAGATGTAATGTATGGCAGGATTAC 59.667 40.741 14.53 14.53 0.00 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 1.068333 TGGACTACTGAACGGCGTAAC 60.068 52.381 15.20 11.72 0.00 2.50
46 47 8.303659 CCTACATACAGGAACAGAGGAACTGG 62.304 50.000 0.00 0.00 43.30 4.00
109 110 2.729675 CGAGAAGCATGCGTCGCAA 61.730 57.895 29.58 7.96 43.62 4.85
195 196 1.135286 GCACAACAATTCTGCCTAGGC 60.135 52.381 27.71 27.71 42.35 3.93
209 210 1.004918 AGCGTGTAGGAGGCACAAC 60.005 57.895 0.00 0.00 37.96 3.32
227 228 1.964344 GCCCTGGATGGTATTTTGGCA 60.964 52.381 0.00 0.00 37.58 4.92
243 244 0.548682 ATCTTCAGTGTGGGAGCCCT 60.549 55.000 7.16 0.00 36.94 5.19
244 245 0.393537 CATCTTCAGTGTGGGAGCCC 60.394 60.000 0.00 0.00 0.00 5.19
245 246 0.326264 ACATCTTCAGTGTGGGAGCC 59.674 55.000 0.00 0.00 0.00 4.70
247 248 3.118956 GGTAGACATCTTCAGTGTGGGAG 60.119 52.174 0.00 0.00 0.00 4.30
248 249 2.832129 GGTAGACATCTTCAGTGTGGGA 59.168 50.000 0.00 0.00 0.00 4.37
251 252 4.527509 AGTGGTAGACATCTTCAGTGTG 57.472 45.455 0.00 0.00 0.00 3.82
279 280 6.063640 TGTTCCATGATATTTGCTCGAATG 57.936 37.500 0.00 0.00 0.00 2.67
307 308 1.551883 TCTTAGGCGTAGGGTTTGGTC 59.448 52.381 0.00 0.00 0.00 4.02
336 337 4.321304 CCTCGCATATAATCAGACTCCGTT 60.321 45.833 0.00 0.00 0.00 4.44
342 343 2.947852 ACGCCTCGCATATAATCAGAC 58.052 47.619 0.00 0.00 0.00 3.51
344 345 4.732285 AAAACGCCTCGCATATAATCAG 57.268 40.909 0.00 0.00 0.00 2.90
747 779 5.866092 GCCCATCTTTTCACTCATTCTTTTC 59.134 40.000 0.00 0.00 0.00 2.29
751 783 3.012518 CGCCCATCTTTTCACTCATTCT 58.987 45.455 0.00 0.00 0.00 2.40
842 877 3.847602 CAGAGGCCGAGGCAGAGG 61.848 72.222 16.65 0.00 44.11 3.69
843 878 4.527583 GCAGAGGCCGAGGCAGAG 62.528 72.222 16.65 3.81 44.11 3.35
901 962 2.403378 GCTTGCGATGGGGCGTTAA 61.403 57.895 0.00 0.00 35.06 2.01
902 963 2.822255 GCTTGCGATGGGGCGTTA 60.822 61.111 0.00 0.00 35.06 3.18
908 969 1.039233 AGGAAATGGCTTGCGATGGG 61.039 55.000 0.00 0.00 0.00 4.00
1398 1468 3.338250 TGGGGATGGAGGTGGTGC 61.338 66.667 0.00 0.00 0.00 5.01
1406 1476 4.731853 TGCCGACCTGGGGATGGA 62.732 66.667 0.00 0.00 38.63 3.41
1407 1477 3.492353 ATGCCGACCTGGGGATGG 61.492 66.667 0.00 0.00 36.69 3.51
1489 1559 0.325602 ACGAATGTTCCGCCCCTTAA 59.674 50.000 0.00 0.00 0.00 1.85
1512 1582 2.535485 ATCATGAACCGGGCTTCGCA 62.535 55.000 6.32 0.00 37.59 5.10
1515 1585 1.876156 GATGATCATGAACCGGGCTTC 59.124 52.381 14.30 1.37 0.00 3.86
1544 1614 3.503363 TGCATCAAGCTGTGAACCTAAAG 59.497 43.478 0.00 0.00 45.94 1.85
1545 1615 3.485394 TGCATCAAGCTGTGAACCTAAA 58.515 40.909 0.00 0.00 45.94 1.85
1634 1711 1.865340 AGAGTGAAGAACGAAAACGCC 59.135 47.619 0.00 0.00 0.00 5.68
1719 1796 7.043391 CGTTCTTCACTGCTCGATGAATTAATA 60.043 37.037 0.00 0.00 34.43 0.98
1745 1823 3.435671 CGTGGTTACTTTGAGAATGGGAC 59.564 47.826 0.00 0.00 0.00 4.46
1803 1881 2.358737 AAGGCCAACGAAGCTCCG 60.359 61.111 5.01 0.00 0.00 4.63
1906 1984 0.452784 CGCTTGAACTAAACGGCTGC 60.453 55.000 0.00 0.00 0.00 5.25
1948 2026 5.376625 TCCTATATTGTGGTCCATTCTTGC 58.623 41.667 0.00 0.00 0.00 4.01
2154 2243 9.492973 TCAAATCGAAATGCATTCTATCATAGA 57.507 29.630 13.38 2.12 35.79 1.98
2173 2262 7.547227 ACCTTCCCAGAATATTTTTCAAATCG 58.453 34.615 0.00 0.00 0.00 3.34
2197 2287 6.426025 AGAATAAGAACGTGTGAGGGTTTTAC 59.574 38.462 0.00 0.00 0.00 2.01
2237 2329 2.489938 AGCGAATTTTCCACAGCCTA 57.510 45.000 0.00 0.00 0.00 3.93
2241 2333 4.207019 GTGACAAAAGCGAATTTTCCACAG 59.793 41.667 15.55 3.23 39.11 3.66
2337 2430 7.063426 TCAGTGTCAAAAACGCTCTTATATGAG 59.937 37.037 10.56 10.56 45.69 2.90
2338 2431 6.871492 TCAGTGTCAAAAACGCTCTTATATGA 59.129 34.615 0.00 0.00 45.69 2.15
2339 2432 6.955963 GTCAGTGTCAAAAACGCTCTTATATG 59.044 38.462 0.00 0.00 45.69 1.78
2340 2433 6.649141 TGTCAGTGTCAAAAACGCTCTTATAT 59.351 34.615 0.00 0.00 45.69 0.86
2341 2434 5.986741 TGTCAGTGTCAAAAACGCTCTTATA 59.013 36.000 0.00 0.00 45.69 0.98
2342 2435 4.814234 TGTCAGTGTCAAAAACGCTCTTAT 59.186 37.500 0.00 0.00 45.69 1.73
2343 2436 4.033587 GTGTCAGTGTCAAAAACGCTCTTA 59.966 41.667 0.00 0.00 45.69 2.10
2344 2437 3.006940 TGTCAGTGTCAAAAACGCTCTT 58.993 40.909 0.00 0.00 45.69 2.85
2345 2438 2.351726 GTGTCAGTGTCAAAAACGCTCT 59.648 45.455 0.00 0.00 45.69 4.09
2346 2439 2.538939 GGTGTCAGTGTCAAAAACGCTC 60.539 50.000 0.00 0.00 45.69 5.03
2348 2441 1.822581 GGTGTCAGTGTCAAAAACGC 58.177 50.000 0.00 0.00 38.74 4.84
2349 2442 1.854434 GCGGTGTCAGTGTCAAAAACG 60.854 52.381 0.00 0.00 0.00 3.60
2350 2443 1.131504 TGCGGTGTCAGTGTCAAAAAC 59.868 47.619 0.00 0.00 0.00 2.43
2351 2444 1.400142 CTGCGGTGTCAGTGTCAAAAA 59.600 47.619 0.00 0.00 0.00 1.94
2352 2445 1.013596 CTGCGGTGTCAGTGTCAAAA 58.986 50.000 0.00 0.00 0.00 2.44
2353 2446 0.107897 ACTGCGGTGTCAGTGTCAAA 60.108 50.000 0.00 0.00 44.88 2.69
2354 2447 1.520192 ACTGCGGTGTCAGTGTCAA 59.480 52.632 0.00 0.00 44.88 3.18
2355 2448 3.216237 ACTGCGGTGTCAGTGTCA 58.784 55.556 0.00 0.00 44.88 3.58
2365 2458 1.063488 GCGTTTTTGACACTGCGGT 59.937 52.632 0.00 0.00 0.00 5.68
2366 2459 0.657368 GAGCGTTTTTGACACTGCGG 60.657 55.000 0.00 0.00 0.00 5.69
2367 2460 0.304705 AGAGCGTTTTTGACACTGCG 59.695 50.000 0.00 0.00 0.00 5.18
2368 2461 2.475200 AAGAGCGTTTTTGACACTGC 57.525 45.000 0.00 0.00 0.00 4.40
2369 2462 9.425893 CATAATATAAGAGCGTTTTTGACACTG 57.574 33.333 0.00 0.00 0.00 3.66
2370 2463 8.612619 CCATAATATAAGAGCGTTTTTGACACT 58.387 33.333 0.00 0.00 0.00 3.55
2371 2464 7.855904 CCCATAATATAAGAGCGTTTTTGACAC 59.144 37.037 0.00 0.00 0.00 3.67
2372 2465 7.771361 TCCCATAATATAAGAGCGTTTTTGACA 59.229 33.333 0.00 0.00 0.00 3.58
2373 2466 8.068380 GTCCCATAATATAAGAGCGTTTTTGAC 58.932 37.037 0.00 0.00 0.00 3.18
2374 2467 7.042321 CGTCCCATAATATAAGAGCGTTTTTGA 60.042 37.037 0.00 0.00 0.00 2.69
2375 2468 7.069569 CGTCCCATAATATAAGAGCGTTTTTG 58.930 38.462 0.00 0.00 0.00 2.44
2376 2469 6.204108 CCGTCCCATAATATAAGAGCGTTTTT 59.796 38.462 0.00 0.00 0.00 1.94
2377 2470 5.699458 CCGTCCCATAATATAAGAGCGTTTT 59.301 40.000 0.00 0.00 0.00 2.43
2378 2471 5.011329 TCCGTCCCATAATATAAGAGCGTTT 59.989 40.000 0.00 0.00 0.00 3.60
2379 2472 4.525487 TCCGTCCCATAATATAAGAGCGTT 59.475 41.667 0.00 0.00 0.00 4.84
2380 2473 4.084287 TCCGTCCCATAATATAAGAGCGT 58.916 43.478 0.00 0.00 0.00 5.07
2381 2474 4.440250 CCTCCGTCCCATAATATAAGAGCG 60.440 50.000 0.00 0.00 0.00 5.03
2382 2475 4.141914 CCCTCCGTCCCATAATATAAGAGC 60.142 50.000 0.00 0.00 0.00 4.09
2383 2476 5.269991 TCCCTCCGTCCCATAATATAAGAG 58.730 45.833 0.00 0.00 0.00 2.85
2384 2477 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
2385 2478 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
2386 2479 4.775780 CACTCCCTCCGTCCCATAATATAA 59.224 45.833 0.00 0.00 0.00 0.98
2387 2480 4.044952 TCACTCCCTCCGTCCCATAATATA 59.955 45.833 0.00 0.00 0.00 0.86
2388 2481 3.173965 CACTCCCTCCGTCCCATAATAT 58.826 50.000 0.00 0.00 0.00 1.28
2389 2482 2.178325 TCACTCCCTCCGTCCCATAATA 59.822 50.000 0.00 0.00 0.00 0.98
2390 2483 1.062428 TCACTCCCTCCGTCCCATAAT 60.062 52.381 0.00 0.00 0.00 1.28
2391 2484 0.337082 TCACTCCCTCCGTCCCATAA 59.663 55.000 0.00 0.00 0.00 1.90
2392 2485 0.337082 TTCACTCCCTCCGTCCCATA 59.663 55.000 0.00 0.00 0.00 2.74
2393 2486 0.546747 TTTCACTCCCTCCGTCCCAT 60.547 55.000 0.00 0.00 0.00 4.00
2394 2487 0.765135 TTTTCACTCCCTCCGTCCCA 60.765 55.000 0.00 0.00 0.00 4.37
2395 2488 0.399075 TTTTTCACTCCCTCCGTCCC 59.601 55.000 0.00 0.00 0.00 4.46
2396 2489 1.202722 TGTTTTTCACTCCCTCCGTCC 60.203 52.381 0.00 0.00 0.00 4.79
2397 2490 2.249844 TGTTTTTCACTCCCTCCGTC 57.750 50.000 0.00 0.00 0.00 4.79
2398 2491 2.092592 ACTTGTTTTTCACTCCCTCCGT 60.093 45.455 0.00 0.00 0.00 4.69
2399 2492 2.572290 ACTTGTTTTTCACTCCCTCCG 58.428 47.619 0.00 0.00 0.00 4.63
2400 2493 6.713450 TGTTATACTTGTTTTTCACTCCCTCC 59.287 38.462 0.00 0.00 0.00 4.30
2401 2494 7.739498 TGTTATACTTGTTTTTCACTCCCTC 57.261 36.000 0.00 0.00 0.00 4.30
2402 2495 8.528044 TTTGTTATACTTGTTTTTCACTCCCT 57.472 30.769 0.00 0.00 0.00 4.20
2403 2496 8.410912 ACTTTGTTATACTTGTTTTTCACTCCC 58.589 33.333 0.00 0.00 0.00 4.30
2452 2545 7.755591 ACATTACATCTCTGCAACACTTTATG 58.244 34.615 0.00 0.00 0.00 1.90


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

AutoCloner maintained by Alex Coulton.