Multiple sequence alignment - TraesCS2B01G299700

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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 TraesCS2B01G299700 chr2B 100.000 3371 0 0 1 3371 420201840 420205210 0.000000e+00 6226
1 TraesCS2B01G299700 chr2D 92.433 2709 89 35 241 2866 353349572 353352247 0.000000e+00 3760
2 TraesCS2B01G299700 chr2D 87.269 432 23 18 2866 3275 353352294 353352715 6.590000e-127 464
3 TraesCS2B01G299700 chr2A 91.599 2464 80 46 1 2392 471815502 471817910 0.000000e+00 3286
4 TraesCS2B01G299700 chr2A 84.254 724 40 31 2615 3275 471818162 471818874 3.670000e-179 638
5 TraesCS2B01G299700 chr2A 84.066 182 6 9 2391 2562 471817981 471818149 1.620000e-33 154
6 TraesCS2B01G299700 chr3B 82.298 322 47 8 1596 1912 711641078 711640762 1.540000e-68 270
7 TraesCS2B01G299700 chr3B 81.250 320 54 6 1596 1912 711884248 711883932 1.550000e-63 254


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 TraesCS2B01G299700 chr2B 420201840 420205210 3370 False 6226.000000 6226 100.000000 1 3371 1 chr2B.!!$F1 3370
1 TraesCS2B01G299700 chr2D 353349572 353352715 3143 False 2112.000000 3760 89.851000 241 3275 2 chr2D.!!$F1 3034
2 TraesCS2B01G299700 chr2A 471815502 471818874 3372 False 1359.333333 3286 86.639667 1 3275 3 chr2A.!!$F1 3274

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
628 665 0.108585 CCGAGGAGAGAGAGGGAGAG 59.891 65.0 0.00 0.0 0.00 3.20 F
1041 1114 0.105778 GCTACTCCTGCCATGAGTCC 59.894 60.0 5.88 0.0 41.97 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1595 1678 0.175760 GCAGTAGAACCGGATCTGCA 59.824 55.0 27.07 6.36 46.95 4.41 R
2709 2901 0.179936 CAGTTCCTCTCCCTGCCATC 59.820 60.0 0.00 0.00 0.00 3.51 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
32 33 4.970860 AGCAATGTGGCATAGAGATAGT 57.029 40.909 0.00 0.00 35.83 2.12
33 34 6.425210 AAGCAATGTGGCATAGAGATAGTA 57.575 37.500 0.00 0.00 35.83 1.82
34 35 6.035368 AGCAATGTGGCATAGAGATAGTAG 57.965 41.667 0.00 0.00 35.83 2.57
46 47 2.537625 GAGATAGTAGCAAGCAAGCACG 59.462 50.000 3.19 0.00 36.85 5.34
59 60 1.883275 CAAGCACGGTGGTTAAATCCA 59.117 47.619 23.43 0.00 35.69 3.41
86 87 6.375377 CACCATTTTCATTTTCAATGCAAGG 58.625 36.000 0.00 0.00 0.00 3.61
218 230 3.181484 GCCAATGCAAGATATGTCAAGCA 60.181 43.478 10.36 10.36 39.56 3.91
312 341 9.941325 CCATCTATAATCCAGCAAGATATATCC 57.059 37.037 9.18 0.00 0.00 2.59
339 368 1.216678 TCATGTCACCAACCAACCCTT 59.783 47.619 0.00 0.00 0.00 3.95
340 369 1.613437 CATGTCACCAACCAACCCTTC 59.387 52.381 0.00 0.00 0.00 3.46
341 370 0.923358 TGTCACCAACCAACCCTTCT 59.077 50.000 0.00 0.00 0.00 2.85
342 371 2.128535 TGTCACCAACCAACCCTTCTA 58.871 47.619 0.00 0.00 0.00 2.10
343 372 2.714250 TGTCACCAACCAACCCTTCTAT 59.286 45.455 0.00 0.00 0.00 1.98
344 373 3.081804 GTCACCAACCAACCCTTCTATG 58.918 50.000 0.00 0.00 0.00 2.23
346 375 3.911260 TCACCAACCAACCCTTCTATGTA 59.089 43.478 0.00 0.00 0.00 2.29
347 376 4.007659 CACCAACCAACCCTTCTATGTAC 58.992 47.826 0.00 0.00 0.00 2.90
349 378 4.291249 ACCAACCAACCCTTCTATGTACAT 59.709 41.667 13.93 13.93 0.00 2.29
365 394 5.047566 TGTACATTACATTCCCCATGAGG 57.952 43.478 0.00 0.00 36.24 3.86
367 396 4.170468 ACATTACATTCCCCATGAGGAC 57.830 45.455 0.00 0.00 38.24 3.85
371 400 1.004230 ATTCCCCATGAGGACGGGA 59.996 57.895 0.00 0.00 46.34 5.14
419 448 4.020617 CTCCCCAGCGCCAAGTGA 62.021 66.667 2.29 0.00 0.00 3.41
529 558 5.335897 GCACACACTAACCACAATCATGAAT 60.336 40.000 0.00 0.00 0.00 2.57
539 570 0.263765 AATCATGAATGGCCAGGGCT 59.736 50.000 13.05 0.00 41.60 5.19
610 647 4.769488 AGGAGGAGAAATCAAGAAAAAGCC 59.231 41.667 0.00 0.00 0.00 4.35
627 664 1.990160 GCCGAGGAGAGAGAGGGAGA 61.990 65.000 0.00 0.00 0.00 3.71
628 665 0.108585 CCGAGGAGAGAGAGGGAGAG 59.891 65.000 0.00 0.00 0.00 3.20
808 857 2.092914 CCCATCCTCCTTCCTTGTGTAC 60.093 54.545 0.00 0.00 0.00 2.90
1014 1087 2.125512 GGCATGAAGACGAGGCGT 60.126 61.111 0.00 0.00 45.10 5.68
1039 1112 0.539051 GTGCTACTCCTGCCATGAGT 59.461 55.000 7.77 7.77 44.85 3.41
1041 1114 0.105778 GCTACTCCTGCCATGAGTCC 59.894 60.000 5.88 0.00 41.97 3.85
1042 1115 0.387202 CTACTCCTGCCATGAGTCCG 59.613 60.000 5.88 0.00 41.97 4.79
1043 1116 1.676678 TACTCCTGCCATGAGTCCGC 61.677 60.000 5.88 0.00 41.97 5.54
1044 1117 3.746949 CTCCTGCCATGAGTCCGCC 62.747 68.421 0.00 0.00 0.00 6.13
1153 1232 1.690219 GGACCTGCCGGATGATCTGT 61.690 60.000 5.05 0.00 0.00 3.41
1294 1376 3.711704 GGGATGGAGATGGAGTTCTTACA 59.288 47.826 0.00 0.00 0.00 2.41
1313 1396 0.251341 AGGAGTTGTTGGGATGTGCC 60.251 55.000 0.00 0.00 0.00 5.01
1314 1397 0.251341 GGAGTTGTTGGGATGTGCCT 60.251 55.000 0.00 0.00 36.66 4.75
1348 1431 1.492133 TTCAGGGAGTTGGGCCAGAG 61.492 60.000 6.23 0.00 0.00 3.35
1358 1441 1.531602 GGGCCAGAGCAAGGTTGTT 60.532 57.895 4.39 0.00 42.56 2.83
1373 1456 1.748493 GTTGTTCTTGCCAAGGTGTCA 59.252 47.619 4.30 0.00 0.00 3.58
1486 1569 2.945668 GCTACCTTCTTGGCATGGTAAG 59.054 50.000 0.00 0.00 40.22 2.34
1491 1574 7.823076 TACCTTCTTGGCATGGTAAGAACCG 62.823 48.000 0.00 0.00 44.10 4.44
1512 1595 0.316841 GGGCCTCGCACAAAATCAAA 59.683 50.000 0.84 0.00 0.00 2.69
1513 1596 1.270041 GGGCCTCGCACAAAATCAAAA 60.270 47.619 0.84 0.00 0.00 2.44
1514 1597 2.612721 GGGCCTCGCACAAAATCAAAAT 60.613 45.455 0.84 0.00 0.00 1.82
1531 1614 1.682740 AATCAACCGTGTTCCCGTTT 58.317 45.000 0.00 0.00 0.00 3.60
1532 1615 1.232119 ATCAACCGTGTTCCCGTTTC 58.768 50.000 0.00 0.00 0.00 2.78
1535 1618 1.402613 CAACCGTGTTCCCGTTTCTTT 59.597 47.619 0.00 0.00 0.00 2.52
1538 1621 1.301423 CGTGTTCCCGTTTCTTTCCA 58.699 50.000 0.00 0.00 0.00 3.53
1572 1655 1.161843 CGTTTCGTAACTGGCCCATT 58.838 50.000 0.00 0.00 31.89 3.16
1573 1656 1.135803 CGTTTCGTAACTGGCCCATTG 60.136 52.381 0.00 0.00 31.89 2.82
1574 1657 0.885196 TTTCGTAACTGGCCCATTGC 59.115 50.000 0.00 0.00 40.16 3.56
1591 1674 4.213906 CCATTGCTTCCATTGTTTTTGGTC 59.786 41.667 0.00 0.00 35.64 4.02
1595 1678 4.892934 TGCTTCCATTGTTTTTGGTCTACT 59.107 37.500 0.00 0.00 35.64 2.57
1597 1680 4.846779 TCCATTGTTTTTGGTCTACTGC 57.153 40.909 0.00 0.00 35.64 4.40
1698 1781 2.885861 CTCTACTCGCTGGCCGTT 59.114 61.111 0.00 0.00 38.35 4.44
1923 2006 3.681835 GTCACCACGTCGGCCTCT 61.682 66.667 0.00 0.00 39.03 3.69
1924 2007 2.915659 TCACCACGTCGGCCTCTT 60.916 61.111 0.00 0.00 39.03 2.85
1992 2078 3.184683 CTGCTCAGCGACTTCGGC 61.185 66.667 0.02 0.00 40.23 5.54
2430 2599 3.638627 CTGGCCAGTTCTTTCCTCTTTTT 59.361 43.478 25.53 0.00 0.00 1.94
2431 2600 3.636764 TGGCCAGTTCTTTCCTCTTTTTC 59.363 43.478 0.00 0.00 0.00 2.29
2432 2601 3.891977 GGCCAGTTCTTTCCTCTTTTTCT 59.108 43.478 0.00 0.00 0.00 2.52
2433 2602 4.342378 GGCCAGTTCTTTCCTCTTTTTCTT 59.658 41.667 0.00 0.00 0.00 2.52
2434 2603 5.508153 GGCCAGTTCTTTCCTCTTTTTCTTC 60.508 44.000 0.00 0.00 0.00 2.87
2435 2604 5.508153 GCCAGTTCTTTCCTCTTTTTCTTCC 60.508 44.000 0.00 0.00 0.00 3.46
2436 2605 5.830457 CCAGTTCTTTCCTCTTTTTCTTCCT 59.170 40.000 0.00 0.00 0.00 3.36
2437 2606 6.322456 CCAGTTCTTTCCTCTTTTTCTTCCTT 59.678 38.462 0.00 0.00 0.00 3.36
2438 2607 7.199078 CAGTTCTTTCCTCTTTTTCTTCCTTG 58.801 38.462 0.00 0.00 0.00 3.61
2439 2608 6.322456 AGTTCTTTCCTCTTTTTCTTCCTTGG 59.678 38.462 0.00 0.00 0.00 3.61
2440 2609 5.766590 TCTTTCCTCTTTTTCTTCCTTGGT 58.233 37.500 0.00 0.00 0.00 3.67
2441 2610 5.828328 TCTTTCCTCTTTTTCTTCCTTGGTC 59.172 40.000 0.00 0.00 0.00 4.02
2701 2893 4.008933 GCCCGTCTGCCACTCTGT 62.009 66.667 0.00 0.00 0.00 3.41
2990 3263 1.081892 CGAGTGGATGCCTGTCAAAG 58.918 55.000 0.00 0.00 0.00 2.77
3091 3374 2.143621 CACATATGTCAACGTGTGCG 57.856 50.000 5.07 0.00 44.93 5.34
3131 3418 0.456312 AAACAGATCGACGCGTCCTC 60.456 55.000 31.84 26.47 0.00 3.71
3132 3419 2.024871 CAGATCGACGCGTCCTCC 59.975 66.667 31.84 20.11 0.00 4.30
3173 3460 4.399395 CCGAGGGAAGCAGCAGCA 62.399 66.667 3.17 0.00 45.49 4.41
3175 3462 2.684843 CGAGGGAAGCAGCAGCAAC 61.685 63.158 3.17 0.00 45.49 4.17
3176 3463 2.670934 AGGGAAGCAGCAGCAACG 60.671 61.111 3.17 0.00 45.49 4.10
3177 3464 2.669569 GGGAAGCAGCAGCAACGA 60.670 61.111 3.17 0.00 45.49 3.85
3179 3466 1.963338 GGAAGCAGCAGCAACGAGT 60.963 57.895 3.17 0.00 45.49 4.18
3181 3468 0.440371 GAAGCAGCAGCAACGAGTAC 59.560 55.000 3.17 0.00 45.49 2.73
3205 3500 1.339097 GTATGGACGGATGGCTACCT 58.661 55.000 0.00 0.00 0.00 3.08
3217 3513 2.627933 TGGCTACCTCCAAACTAGGTT 58.372 47.619 0.00 0.00 45.26 3.50
3225 3521 3.490419 CCTCCAAACTAGGTTACGATCCG 60.490 52.174 0.00 0.00 0.00 4.18
3236 3532 3.059051 GGTTACGATCCGCTACTGTCTAG 60.059 52.174 0.00 0.00 0.00 2.43
3237 3533 2.328819 ACGATCCGCTACTGTCTAGT 57.671 50.000 0.00 0.00 40.99 2.57
3238 3534 3.465742 ACGATCCGCTACTGTCTAGTA 57.534 47.619 0.00 0.00 38.36 1.82
3241 3537 4.820716 ACGATCCGCTACTGTCTAGTAATT 59.179 41.667 0.00 0.00 38.85 1.40
3245 3541 7.859377 CGATCCGCTACTGTCTAGTAATTTTTA 59.141 37.037 0.00 0.00 38.85 1.52
3249 3545 9.916397 CCGCTACTGTCTAGTAATTTTTATTTG 57.084 33.333 0.00 0.00 38.85 2.32
3266 3565 6.844696 TTATTTGCTCGTAGAATCCATCAC 57.155 37.500 0.00 0.00 34.09 3.06
3268 3567 3.717400 TGCTCGTAGAATCCATCACTC 57.283 47.619 0.00 0.00 34.09 3.51
3275 3574 7.406031 TCGTAGAATCCATCACTCTTAGTTT 57.594 36.000 0.00 0.00 0.00 2.66
3276 3575 7.837863 TCGTAGAATCCATCACTCTTAGTTTT 58.162 34.615 0.00 0.00 0.00 2.43
3277 3576 8.963725 TCGTAGAATCCATCACTCTTAGTTTTA 58.036 33.333 0.00 0.00 0.00 1.52
3278 3577 9.239002 CGTAGAATCCATCACTCTTAGTTTTAG 57.761 37.037 0.00 0.00 0.00 1.85
3279 3578 9.535878 GTAGAATCCATCACTCTTAGTTTTAGG 57.464 37.037 0.00 0.00 0.00 2.69
3280 3579 7.051000 AGAATCCATCACTCTTAGTTTTAGGC 58.949 38.462 0.00 0.00 0.00 3.93
3281 3580 5.755409 TCCATCACTCTTAGTTTTAGGCA 57.245 39.130 0.00 0.00 0.00 4.75
3282 3581 6.313519 TCCATCACTCTTAGTTTTAGGCAT 57.686 37.500 0.00 0.00 0.00 4.40
3283 3582 7.432148 TCCATCACTCTTAGTTTTAGGCATA 57.568 36.000 0.00 0.00 0.00 3.14
3284 3583 8.034313 TCCATCACTCTTAGTTTTAGGCATAT 57.966 34.615 0.00 0.00 0.00 1.78
3285 3584 9.154632 TCCATCACTCTTAGTTTTAGGCATATA 57.845 33.333 0.00 0.00 0.00 0.86
3286 3585 9.950496 CCATCACTCTTAGTTTTAGGCATATAT 57.050 33.333 0.00 0.00 0.00 0.86
3331 3630 9.907229 ATATAGAAACTCTAACCCTTCCTTTTG 57.093 33.333 0.00 0.00 31.96 2.44
3332 3631 6.014771 AGAAACTCTAACCCTTCCTTTTGT 57.985 37.500 0.00 0.00 0.00 2.83
3333 3632 5.828328 AGAAACTCTAACCCTTCCTTTTGTG 59.172 40.000 0.00 0.00 0.00 3.33
3334 3633 4.790718 ACTCTAACCCTTCCTTTTGTGT 57.209 40.909 0.00 0.00 0.00 3.72
3335 3634 4.461198 ACTCTAACCCTTCCTTTTGTGTG 58.539 43.478 0.00 0.00 0.00 3.82
3336 3635 4.079958 ACTCTAACCCTTCCTTTTGTGTGT 60.080 41.667 0.00 0.00 0.00 3.72
3337 3636 5.131475 ACTCTAACCCTTCCTTTTGTGTGTA 59.869 40.000 0.00 0.00 0.00 2.90
3338 3637 6.003859 TCTAACCCTTCCTTTTGTGTGTAA 57.996 37.500 0.00 0.00 0.00 2.41
3339 3638 6.424883 TCTAACCCTTCCTTTTGTGTGTAAA 58.575 36.000 0.00 0.00 0.00 2.01
3340 3639 7.064229 TCTAACCCTTCCTTTTGTGTGTAAAT 58.936 34.615 0.00 0.00 0.00 1.40
3341 3640 8.219178 TCTAACCCTTCCTTTTGTGTGTAAATA 58.781 33.333 0.00 0.00 0.00 1.40
3342 3641 7.849322 AACCCTTCCTTTTGTGTGTAAATAT 57.151 32.000 0.00 0.00 0.00 1.28
3343 3642 8.943594 AACCCTTCCTTTTGTGTGTAAATATA 57.056 30.769 0.00 0.00 0.00 0.86
3344 3643 9.541884 AACCCTTCCTTTTGTGTGTAAATATAT 57.458 29.630 0.00 0.00 0.00 0.86
3345 3644 9.541884 ACCCTTCCTTTTGTGTGTAAATATATT 57.458 29.630 0.00 0.00 0.00 1.28
3346 3645 9.801873 CCCTTCCTTTTGTGTGTAAATATATTG 57.198 33.333 0.00 0.00 0.00 1.90
3347 3646 9.801873 CCTTCCTTTTGTGTGTAAATATATTGG 57.198 33.333 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 1.965930 CCACCGTGCTTGCTTGCTA 60.966 57.895 0.00 0.00 0.00 3.49
33 34 3.289834 CCACCGTGCTTGCTTGCT 61.290 61.111 0.00 0.00 0.00 3.91
34 35 1.791103 TAACCACCGTGCTTGCTTGC 61.791 55.000 0.00 0.00 0.00 4.01
59 60 6.239396 TGCATTGAAAATGAAAATGGTGGAT 58.761 32.000 4.18 0.00 32.96 3.41
86 87 1.603739 AGCGGGGTTGCTTCCTTTC 60.604 57.895 0.00 0.00 44.46 2.62
218 230 1.474855 GGCAGGCACAACCACATTTTT 60.475 47.619 0.00 0.00 43.14 1.94
312 341 1.541147 GGTTGGTGACATGACATGGTG 59.459 52.381 19.39 0.00 42.32 4.17
313 342 1.144708 TGGTTGGTGACATGACATGGT 59.855 47.619 19.39 5.41 42.32 3.55
340 369 7.256655 TCCTCATGGGGAATGTAATGTACATAG 60.257 40.741 13.43 0.00 41.00 2.23
341 370 6.560687 TCCTCATGGGGAATGTAATGTACATA 59.439 38.462 13.43 0.00 41.00 2.29
342 371 5.372363 TCCTCATGGGGAATGTAATGTACAT 59.628 40.000 13.43 1.41 42.41 2.29
343 372 4.724293 TCCTCATGGGGAATGTAATGTACA 59.276 41.667 13.43 0.00 38.22 2.90
344 373 5.063880 GTCCTCATGGGGAATGTAATGTAC 58.936 45.833 18.26 0.00 37.10 2.90
346 375 3.433598 CGTCCTCATGGGGAATGTAATGT 60.434 47.826 18.26 0.00 37.10 2.71
347 376 3.141398 CGTCCTCATGGGGAATGTAATG 58.859 50.000 18.26 0.00 37.10 1.90
349 378 1.488812 CCGTCCTCATGGGGAATGTAA 59.511 52.381 18.26 0.00 37.10 2.41
411 440 4.354587 CTTTGTTTCTCACTTCACTTGGC 58.645 43.478 0.00 0.00 0.00 4.52
419 448 2.378038 TGCTGCCTTTGTTTCTCACTT 58.622 42.857 0.00 0.00 0.00 3.16
539 570 2.418963 TAAGGGTGGTGGTGGGGCTA 62.419 60.000 0.00 0.00 0.00 3.93
586 623 5.105957 GGCTTTTTCTTGATTTCTCCTCCTC 60.106 44.000 0.00 0.00 0.00 3.71
610 647 1.070758 CTCTCTCCCTCTCTCTCCTCG 59.929 61.905 0.00 0.00 0.00 4.63
627 664 0.396811 CCACCCGTCCTTTGTTCTCT 59.603 55.000 0.00 0.00 0.00 3.10
628 665 0.605589 CCCACCCGTCCTTTGTTCTC 60.606 60.000 0.00 0.00 0.00 2.87
769 817 1.526917 GATGGGATGCCCTCCGTTG 60.527 63.158 0.00 0.00 46.01 4.10
771 819 3.171388 GGATGGGATGCCCTCCGT 61.171 66.667 11.75 0.00 46.01 4.69
772 820 3.958860 GGGATGGGATGCCCTCCG 61.959 72.222 19.06 0.00 46.01 4.63
967 1022 3.842126 CGATGCGGCGTCTGTGTG 61.842 66.667 19.14 0.46 0.00 3.82
992 1047 1.880340 CTCGTCTTCATGCCGCCTC 60.880 63.158 0.00 0.00 0.00 4.70
1014 1087 4.435436 CAGGAGTAGCACGCGCCA 62.435 66.667 5.73 0.00 39.83 5.69
1071 1144 2.754658 GTCCTCCGCCTCTTCCGA 60.755 66.667 0.00 0.00 0.00 4.55
1126 1205 2.579201 CGGCAGGTCCTCGAACAT 59.421 61.111 0.00 0.00 0.00 2.71
1153 1232 3.244875 ACATCAGCAAGTATGGACACCAA 60.245 43.478 0.00 0.00 36.95 3.67
1263 1345 1.459455 ATCTCCATCCCAGCGACGAG 61.459 60.000 0.00 0.00 0.00 4.18
1294 1376 0.251341 GGCACATCCCAACAACTCCT 60.251 55.000 0.00 0.00 0.00 3.69
1358 1441 1.227823 CGGTGACACCTTGGCAAGA 60.228 57.895 28.18 5.07 36.98 3.02
1491 1574 1.212751 GATTTTGTGCGAGGCCCAC 59.787 57.895 0.00 0.35 0.00 4.61
1512 1595 1.605232 GAAACGGGAACACGGTTGATT 59.395 47.619 4.04 0.00 44.90 2.57
1513 1596 1.202722 AGAAACGGGAACACGGTTGAT 60.203 47.619 4.04 0.00 44.90 2.57
1514 1597 0.178533 AGAAACGGGAACACGGTTGA 59.821 50.000 4.04 0.00 44.90 3.18
1531 1614 0.597568 CGCCAAGCACAATGGAAAGA 59.402 50.000 0.00 0.00 40.56 2.52
1532 1615 0.597568 TCGCCAAGCACAATGGAAAG 59.402 50.000 0.00 0.00 40.56 2.62
1535 1618 1.368345 CGATCGCCAAGCACAATGGA 61.368 55.000 0.26 0.00 40.56 3.41
1538 1621 0.881118 AAACGATCGCCAAGCACAAT 59.119 45.000 16.60 0.00 0.00 2.71
1566 1649 2.477845 AAACAATGGAAGCAATGGGC 57.522 45.000 0.00 0.00 45.30 5.36
1572 1655 4.892934 AGTAGACCAAAAACAATGGAAGCA 59.107 37.500 0.00 0.00 40.56 3.91
1573 1656 5.222631 CAGTAGACCAAAAACAATGGAAGC 58.777 41.667 0.00 0.00 40.56 3.86
1574 1657 5.221224 TGCAGTAGACCAAAAACAATGGAAG 60.221 40.000 0.00 0.00 40.56 3.46
1591 1674 2.952978 AGTAGAACCGGATCTGCAGTAG 59.047 50.000 27.07 3.69 34.84 2.57
1595 1678 0.175760 GCAGTAGAACCGGATCTGCA 59.824 55.000 27.07 6.36 46.95 4.41
1597 1680 1.115467 AGGCAGTAGAACCGGATCTG 58.885 55.000 23.44 15.61 0.00 2.90
1698 1781 0.739462 CGCTGCCGTTGAACTGGATA 60.739 55.000 9.73 0.00 0.00 2.59
2386 2478 6.760770 CCAGAAAAATAAAAGAAACTGGTGCA 59.239 34.615 0.00 0.00 38.83 4.57
2392 2561 7.124573 ACTGGCCAGAAAAATAAAAGAAACT 57.875 32.000 39.19 7.29 0.00 2.66
2430 2599 2.440253 TCCGGAAAAAGACCAAGGAAGA 59.560 45.455 0.00 0.00 0.00 2.87
2431 2600 2.552743 GTCCGGAAAAAGACCAAGGAAG 59.447 50.000 5.23 0.00 0.00 3.46
2432 2601 2.578786 GTCCGGAAAAAGACCAAGGAA 58.421 47.619 5.23 0.00 0.00 3.36
2433 2602 2.265589 GTCCGGAAAAAGACCAAGGA 57.734 50.000 5.23 0.00 0.00 3.36
2439 2608 2.038689 AGAGAAGGGTCCGGAAAAAGAC 59.961 50.000 5.23 0.00 0.00 3.01
2440 2609 2.038557 CAGAGAAGGGTCCGGAAAAAGA 59.961 50.000 5.23 0.00 0.00 2.52
2441 2610 2.224548 ACAGAGAAGGGTCCGGAAAAAG 60.225 50.000 5.23 0.00 0.00 2.27
2603 2790 7.631822 TCACATCTCGACGAAACATTTAAAAA 58.368 30.769 0.00 0.00 0.00 1.94
2604 2791 7.179927 TCACATCTCGACGAAACATTTAAAA 57.820 32.000 0.00 0.00 0.00 1.52
2701 2893 2.768527 CTCTCCCTGCCATCTCTGTAAA 59.231 50.000 0.00 0.00 0.00 2.01
2709 2901 0.179936 CAGTTCCTCTCCCTGCCATC 59.820 60.000 0.00 0.00 0.00 3.51
2773 2997 4.719616 GACGCACGCAGAAACCGC 62.720 66.667 0.00 0.00 0.00 5.68
2796 3020 0.450983 GCCGAAGCAGACTACTACGT 59.549 55.000 0.00 0.00 39.53 3.57
2977 3250 5.504665 CGGATATTTGTCTTTGACAGGCATC 60.505 44.000 0.66 5.22 43.69 3.91
2990 3263 0.308993 GCAGCAGCCGGATATTTGTC 59.691 55.000 5.05 0.00 33.58 3.18
3091 3374 1.226547 CCCGCACACACACAAACAC 60.227 57.895 0.00 0.00 0.00 3.32
3092 3375 1.377333 TCCCGCACACACACAAACA 60.377 52.632 0.00 0.00 0.00 2.83
3093 3376 1.063488 GTCCCGCACACACACAAAC 59.937 57.895 0.00 0.00 0.00 2.93
3094 3377 0.960861 TTGTCCCGCACACACACAAA 60.961 50.000 0.00 0.00 33.41 2.83
3095 3378 0.960861 TTTGTCCCGCACACACACAA 60.961 50.000 0.00 0.00 33.41 3.33
3096 3379 1.377333 TTTGTCCCGCACACACACA 60.377 52.632 0.00 0.00 33.41 3.72
3097 3380 1.063488 GTTTGTCCCGCACACACAC 59.937 57.895 0.00 0.00 35.95 3.82
3131 3418 1.799544 AGTTAAACGCCGGTACAAGG 58.200 50.000 1.90 0.00 0.00 3.61
3132 3419 3.062042 AGAAGTTAAACGCCGGTACAAG 58.938 45.455 1.90 0.00 0.00 3.16
3175 3462 2.159531 TCCGTCCATACAAACGTACTCG 60.160 50.000 0.00 0.00 43.34 4.18
3176 3463 3.492421 TCCGTCCATACAAACGTACTC 57.508 47.619 0.00 0.00 37.19 2.59
3177 3464 3.429822 CCATCCGTCCATACAAACGTACT 60.430 47.826 0.00 0.00 37.19 2.73
3179 3466 2.739287 GCCATCCGTCCATACAAACGTA 60.739 50.000 0.00 0.00 37.19 3.57
3181 3468 0.655733 GCCATCCGTCCATACAAACG 59.344 55.000 0.00 0.00 38.58 3.60
3184 3471 1.414919 GGTAGCCATCCGTCCATACAA 59.585 52.381 0.00 0.00 0.00 2.41
3193 3488 0.541863 AGTTTGGAGGTAGCCATCCG 59.458 55.000 0.00 0.00 38.52 4.18
3205 3500 2.159198 GCGGATCGTAACCTAGTTTGGA 60.159 50.000 0.00 0.00 0.00 3.53
3217 3513 3.465742 ACTAGACAGTAGCGGATCGTA 57.534 47.619 0.00 0.00 31.45 3.43
3236 3532 9.997482 TGGATTCTACGAGCAAATAAAAATTAC 57.003 29.630 0.00 0.00 0.00 1.89
3238 3534 9.736023 GATGGATTCTACGAGCAAATAAAAATT 57.264 29.630 0.00 0.00 0.00 1.82
3241 3537 7.552687 AGTGATGGATTCTACGAGCAAATAAAA 59.447 33.333 0.00 0.00 0.00 1.52
3245 3541 5.028549 AGTGATGGATTCTACGAGCAAAT 57.971 39.130 0.00 0.00 0.00 2.32
3249 3545 4.314740 AAGAGTGATGGATTCTACGAGC 57.685 45.455 0.00 0.00 0.00 5.03
3305 3604 9.907229 CAAAAGGAAGGGTTAGAGTTTCTATAT 57.093 33.333 0.00 0.00 0.00 0.86
3306 3605 8.887393 ACAAAAGGAAGGGTTAGAGTTTCTATA 58.113 33.333 0.00 0.00 0.00 1.31
3307 3606 7.665974 CACAAAAGGAAGGGTTAGAGTTTCTAT 59.334 37.037 0.00 0.00 0.00 1.98
3308 3607 6.996282 CACAAAAGGAAGGGTTAGAGTTTCTA 59.004 38.462 0.00 0.00 0.00 2.10
3309 3608 5.828328 CACAAAAGGAAGGGTTAGAGTTTCT 59.172 40.000 0.00 0.00 0.00 2.52
3310 3609 5.593095 ACACAAAAGGAAGGGTTAGAGTTTC 59.407 40.000 0.00 0.00 0.00 2.78
3311 3610 5.359860 CACACAAAAGGAAGGGTTAGAGTTT 59.640 40.000 0.00 0.00 0.00 2.66
3312 3611 4.887655 CACACAAAAGGAAGGGTTAGAGTT 59.112 41.667 0.00 0.00 0.00 3.01
3313 3612 4.079958 ACACACAAAAGGAAGGGTTAGAGT 60.080 41.667 0.00 0.00 0.00 3.24
3314 3613 4.461198 ACACACAAAAGGAAGGGTTAGAG 58.539 43.478 0.00 0.00 0.00 2.43
3315 3614 4.513406 ACACACAAAAGGAAGGGTTAGA 57.487 40.909 0.00 0.00 0.00 2.10
3316 3615 6.702716 TTTACACACAAAAGGAAGGGTTAG 57.297 37.500 0.00 0.00 0.00 2.34
3317 3616 8.943594 ATATTTACACACAAAAGGAAGGGTTA 57.056 30.769 0.00 0.00 0.00 2.85
3318 3617 7.849322 ATATTTACACACAAAAGGAAGGGTT 57.151 32.000 0.00 0.00 0.00 4.11
3319 3618 9.541884 AATATATTTACACACAAAAGGAAGGGT 57.458 29.630 0.00 0.00 0.00 4.34
3320 3619 9.801873 CAATATATTTACACACAAAAGGAAGGG 57.198 33.333 0.00 0.00 0.00 3.95
3321 3620 9.801873 CCAATATATTTACACACAAAAGGAAGG 57.198 33.333 0.00 0.00 0.00 3.46


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

AutoCloner maintained by Alex Coulton.