Multiple sequence alignment - TraesCS6B01G054100

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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 TraesCS6B01G054100 chr6B 100.000 3233 0 0 1 3233 34218438 34221670 0.000000e+00 5971.0
1 TraesCS6B01G054100 chr6B 85.366 82 9 3 2567 2648 24265137 24265059 7.430000e-12 82.4
2 TraesCS6B01G054100 chr6B 82.979 94 12 4 2567 2657 24348303 24348211 7.430000e-12 82.4
3 TraesCS6B01G054100 chr6D 91.674 2162 105 24 568 2679 20253454 20255590 0.000000e+00 2926.0
4 TraesCS6B01G054100 chr6D 92.593 351 20 3 1 350 20253107 20253452 1.730000e-137 499.0
5 TraesCS6B01G054100 chr6D 86.986 438 50 7 2800 3233 20255815 20256249 1.350000e-133 486.0
6 TraesCS6B01G054100 chr6D 89.286 56 2 4 418 470 48464540 48464594 2.080000e-07 67.6
7 TraesCS6B01G054100 chr6A 91.958 2114 97 25 484 2561 20250159 20252235 0.000000e+00 2894.0
8 TraesCS6B01G054100 chr6A 92.233 412 28 1 1 412 20249643 20250050 6.010000e-162 580.0
9 TraesCS6B01G054100 chr6A 79.049 568 88 21 2684 3230 20252232 20252789 8.530000e-96 361.0
10 TraesCS6B01G054100 chr6A 80.952 126 22 2 2561 2685 604533811 604533687 7.380000e-17 99.0
11 TraesCS6B01G054100 chr3A 84.733 131 16 2 2561 2687 661929035 661928905 9.410000e-26 128.0
12 TraesCS6B01G054100 chr1A 80.992 121 18 5 2565 2681 531310619 531310738 1.240000e-14 91.6
13 TraesCS6B01G054100 chr1A 93.750 48 2 1 416 463 12915845 12915891 1.610000e-08 71.3
14 TraesCS6B01G054100 chr2B 85.227 88 11 2 2561 2646 719440737 719440824 4.440000e-14 89.8
15 TraesCS6B01G054100 chr2B 91.304 46 4 0 422 467 743692772 743692727 2.690000e-06 63.9
16 TraesCS6B01G054100 chrUn 86.250 80 10 1 2563 2641 31728125 31728204 5.750000e-13 86.1
17 TraesCS6B01G054100 chr2D 79.259 135 15 9 2550 2672 624013509 624013642 7.430000e-12 82.4
18 TraesCS6B01G054100 chr2D 91.667 48 2 2 418 463 119819488 119819535 7.490000e-07 65.8
19 TraesCS6B01G054100 chr1B 95.556 45 1 1 423 467 605929078 605929035 1.610000e-08 71.3
20 TraesCS6B01G054100 chr1B 89.583 48 4 1 423 469 543504349 543504302 3.480000e-05 60.2
21 TraesCS6B01G054100 chr2A 97.500 40 1 0 424 463 714336320 714336359 5.790000e-08 69.4
22 TraesCS6B01G054100 chr7A 89.286 56 3 3 418 470 645281446 645281501 2.080000e-07 67.6
23 TraesCS6B01G054100 chr4B 97.368 38 1 0 423 460 535093371 535093334 7.490000e-07 65.8


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 TraesCS6B01G054100 chr6B 34218438 34221670 3232 False 5971.000000 5971 100.000000 1 3233 1 chr6B.!!$F1 3232
1 TraesCS6B01G054100 chr6D 20253107 20256249 3142 False 1303.666667 2926 90.417667 1 3233 3 chr6D.!!$F2 3232
2 TraesCS6B01G054100 chr6A 20249643 20252789 3146 False 1278.333333 2894 87.746667 1 3230 3 chr6A.!!$F1 3229

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
375 377 0.038744 AGGTGCAATCAACCCAGGAG 59.961 55.0 0.00 0.0 0.00 3.69 F
575 662 0.319297 AGCACCGGTCTTAACGACAC 60.319 55.0 2.59 0.0 44.68 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1995 2105 0.031585 CGAAGACGTGGTTGGACTCA 59.968 55.000 0.0 0.0 34.56 3.41 R
2559 2699 2.160615 CGACTGAGATCTAGCCATACCG 59.839 54.545 0.0 0.0 0.00 4.02 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
31 32 3.319972 GGGTGTGGTCGCTATCACTTATA 59.680 47.826 3.04 0.00 37.63 0.98
32 33 4.021368 GGGTGTGGTCGCTATCACTTATAT 60.021 45.833 3.04 0.00 37.63 0.86
33 34 5.184479 GGGTGTGGTCGCTATCACTTATATA 59.816 44.000 3.04 0.00 37.63 0.86
34 35 6.127423 GGGTGTGGTCGCTATCACTTATATAT 60.127 42.308 3.04 0.00 37.63 0.86
41 42 6.021390 GTCGCTATCACTTATATATGTGTGCG 60.021 42.308 30.51 30.51 42.96 5.34
160 162 3.224327 TTATGGTGGGGGTGGGGGA 62.224 63.158 0.00 0.00 0.00 4.81
171 173 3.862309 GGGGGTGGGGGAACATATATATT 59.138 47.826 0.00 0.00 0.00 1.28
172 174 4.296583 GGGGGTGGGGGAACATATATATTT 59.703 45.833 0.00 0.00 0.00 1.40
259 261 0.792960 AGGGCAAAAGGGAGGGAAAT 59.207 50.000 0.00 0.00 0.00 2.17
332 334 2.447408 TAGGCTGATAGTCAACGGGA 57.553 50.000 0.00 0.00 0.00 5.14
375 377 0.038744 AGGTGCAATCAACCCAGGAG 59.961 55.000 0.00 0.00 0.00 3.69
388 390 0.469892 CCAGGAGCACCCAAAAACCT 60.470 55.000 0.00 0.00 37.41 3.50
391 393 1.762370 AGGAGCACCCAAAAACCTTTG 59.238 47.619 0.00 0.00 41.45 2.77
408 410 4.126437 CCTTTGGGTTTTGCCTTGTAAAG 58.874 43.478 0.00 0.00 45.69 1.85
431 433 7.362802 AGACAATAGTACTATCAAGTTCCCC 57.637 40.000 15.72 4.33 37.15 4.81
432 434 6.326843 AGACAATAGTACTATCAAGTTCCCCC 59.673 42.308 15.72 4.03 37.15 5.40
433 435 5.968167 ACAATAGTACTATCAAGTTCCCCCA 59.032 40.000 15.72 0.00 37.15 4.96
434 436 6.445786 ACAATAGTACTATCAAGTTCCCCCAA 59.554 38.462 15.72 0.00 37.15 4.12
435 437 4.838904 AGTACTATCAAGTTCCCCCAAC 57.161 45.455 0.00 0.00 37.15 3.77
437 439 5.596763 AGTACTATCAAGTTCCCCCAACTA 58.403 41.667 0.00 0.00 45.32 2.24
438 440 4.838904 ACTATCAAGTTCCCCCAACTAC 57.161 45.455 0.00 0.00 45.32 2.73
439 441 4.172807 ACTATCAAGTTCCCCCAACTACA 58.827 43.478 0.00 0.00 45.32 2.74
440 442 4.600111 ACTATCAAGTTCCCCCAACTACAA 59.400 41.667 0.00 0.00 45.32 2.41
441 443 3.502123 TCAAGTTCCCCCAACTACAAG 57.498 47.619 0.00 0.00 45.32 3.16
442 444 2.781174 TCAAGTTCCCCCAACTACAAGT 59.219 45.455 0.00 0.00 45.32 3.16
443 445 3.975312 TCAAGTTCCCCCAACTACAAGTA 59.025 43.478 0.00 0.00 45.32 2.24
444 446 4.600111 TCAAGTTCCCCCAACTACAAGTAT 59.400 41.667 0.00 0.00 45.32 2.12
445 447 5.073965 TCAAGTTCCCCCAACTACAAGTATT 59.926 40.000 0.00 0.00 45.32 1.89
446 448 5.594199 AGTTCCCCCAACTACAAGTATTT 57.406 39.130 0.00 0.00 44.13 1.40
447 449 5.567430 AGTTCCCCCAACTACAAGTATTTC 58.433 41.667 0.00 0.00 44.13 2.17
448 450 4.210724 TCCCCCAACTACAAGTATTTCG 57.789 45.455 0.00 0.00 0.00 3.46
449 451 3.054948 TCCCCCAACTACAAGTATTTCGG 60.055 47.826 0.00 0.00 0.00 4.30
450 452 3.307904 CCCCCAACTACAAGTATTTCGGT 60.308 47.826 0.00 0.00 0.00 4.69
451 453 4.080975 CCCCCAACTACAAGTATTTCGGTA 60.081 45.833 0.00 0.00 0.00 4.02
452 454 4.872124 CCCCAACTACAAGTATTTCGGTAC 59.128 45.833 0.00 0.00 0.00 3.34
480 482 6.476378 AGGAGTACTAACAAACATCAGCAAT 58.524 36.000 0.00 0.00 0.00 3.56
482 484 7.549488 AGGAGTACTAACAAACATCAGCAATAC 59.451 37.037 0.00 0.00 0.00 1.89
487 574 8.480643 ACTAACAAACATCAGCAATACTACTC 57.519 34.615 0.00 0.00 0.00 2.59
493 580 6.791867 ACATCAGCAATACTACTCCACTTA 57.208 37.500 0.00 0.00 0.00 2.24
495 582 6.381420 ACATCAGCAATACTACTCCACTTAGT 59.619 38.462 0.00 0.00 34.15 2.24
529 616 2.822561 AGGATGATAGCGTCGACATCAT 59.177 45.455 22.77 22.77 41.06 2.45
541 628 5.331905 GCGTCGACATCATGAGAAAGATAAC 60.332 44.000 17.16 0.00 0.00 1.89
545 632 5.332130 CGACATCATGAGAAAGATAACGCAG 60.332 44.000 0.09 0.00 0.00 5.18
561 648 1.770957 GCAGCACAAAGTAAAGCACC 58.229 50.000 0.00 0.00 0.00 5.01
573 660 1.505425 AAAGCACCGGTCTTAACGAC 58.495 50.000 2.59 0.00 42.07 4.34
575 662 0.319297 AGCACCGGTCTTAACGACAC 60.319 55.000 2.59 0.00 44.68 3.67
586 673 3.060230 TCTTAACGACACGCGAATTGATG 59.940 43.478 15.93 0.68 44.57 3.07
591 678 2.219445 CGACACGCGAATTGATGATCAT 59.781 45.455 15.93 8.25 44.57 2.45
592 679 3.538780 GACACGCGAATTGATGATCATG 58.461 45.455 15.93 0.00 0.00 3.07
593 680 2.288729 ACACGCGAATTGATGATCATGG 59.711 45.455 15.93 0.00 0.00 3.66
594 681 2.545106 CACGCGAATTGATGATCATGGA 59.455 45.455 15.93 1.15 0.00 3.41
595 682 3.187842 CACGCGAATTGATGATCATGGAT 59.812 43.478 15.93 3.74 0.00 3.41
722 809 1.000739 CCTCATGTGGCACCCCATT 59.999 57.895 16.26 0.00 44.51 3.16
795 905 1.680651 CCCGGTGGCAATTAAGGCA 60.681 57.895 0.00 0.00 42.25 4.75
850 960 2.552743 GAGACACCAAGCCTAAACCAAC 59.447 50.000 0.00 0.00 0.00 3.77
868 978 3.373748 CCAACAAAAGACCAAAGCCAAAC 59.626 43.478 0.00 0.00 0.00 2.93
879 989 1.360393 AAGCCAAACCCAGGGACAGA 61.360 55.000 14.54 0.00 0.00 3.41
1013 1123 0.960364 CGTTCCATGACCAACCCCTG 60.960 60.000 0.00 0.00 0.00 4.45
1029 1139 1.684049 CTGCTCCCCGTCTTCTCCT 60.684 63.158 0.00 0.00 0.00 3.69
1036 1146 0.324830 CCCGTCTTCTCCTTCCTCCT 60.325 60.000 0.00 0.00 0.00 3.69
1037 1147 1.107945 CCGTCTTCTCCTTCCTCCTC 58.892 60.000 0.00 0.00 0.00 3.71
1328 1438 0.594602 CGCAAGGTCCGGATATACGA 59.405 55.000 7.81 0.00 35.47 3.43
2272 2382 1.642037 CCATTCTGAGCCAGTGTGCG 61.642 60.000 2.68 0.00 36.02 5.34
2273 2383 0.952497 CATTCTGAGCCAGTGTGCGT 60.952 55.000 2.68 0.00 36.02 5.24
2274 2384 0.608130 ATTCTGAGCCAGTGTGCGTA 59.392 50.000 2.68 0.00 36.02 4.42
2275 2385 0.608130 TTCTGAGCCAGTGTGCGTAT 59.392 50.000 2.68 0.00 36.02 3.06
2276 2386 0.108662 TCTGAGCCAGTGTGCGTATG 60.109 55.000 2.68 0.00 36.02 2.39
2277 2387 0.108662 CTGAGCCAGTGTGCGTATGA 60.109 55.000 0.00 0.00 36.02 2.15
2278 2388 0.389817 TGAGCCAGTGTGCGTATGAC 60.390 55.000 0.00 0.00 36.02 3.06
2279 2389 0.108615 GAGCCAGTGTGCGTATGACT 60.109 55.000 0.00 0.00 36.02 3.41
2280 2390 0.390340 AGCCAGTGTGCGTATGACTG 60.390 55.000 8.18 8.18 37.45 3.51
2368 2479 6.860023 CAGACAAGAAACAAATTTGCTAGAGG 59.140 38.462 18.12 6.95 0.00 3.69
2541 2681 8.946085 GTTGAAGTGAATCTCATATTAACCACA 58.054 33.333 0.00 0.00 0.00 4.17
2544 2684 8.954950 AAGTGAATCTCATATTAACCACAGAG 57.045 34.615 0.00 0.00 0.00 3.35
2563 2703 8.141909 CCACAGAGAGTAATTTTGATATCGGTA 58.858 37.037 0.00 0.00 0.00 4.02
2570 2710 9.088512 GAGTAATTTTGATATCGGTATGGCTAG 57.911 37.037 0.00 0.00 0.00 3.42
2571 2711 8.812972 AGTAATTTTGATATCGGTATGGCTAGA 58.187 33.333 0.00 0.00 0.00 2.43
2577 2717 5.825151 TGATATCGGTATGGCTAGATCTCAG 59.175 44.000 0.00 0.00 0.00 3.35
2581 2721 3.413327 GGTATGGCTAGATCTCAGTCGA 58.587 50.000 0.00 0.00 0.00 4.20
2582 2722 3.189702 GGTATGGCTAGATCTCAGTCGAC 59.810 52.174 7.70 7.70 0.00 4.20
2583 2723 2.719531 TGGCTAGATCTCAGTCGACT 57.280 50.000 13.58 13.58 0.00 4.18
2600 2740 6.368791 CAGTCGACTGAGATTTAACCAAATCA 59.631 38.462 36.73 0.00 45.34 2.57
2659 2808 6.849588 AAAACAAAATTTGCACAGATCTCC 57.150 33.333 5.52 0.00 0.00 3.71
2662 2811 4.341806 ACAAAATTTGCACAGATCTCCACA 59.658 37.500 5.52 0.00 0.00 4.17
2667 2816 3.548745 TGCACAGATCTCCACATAAGG 57.451 47.619 0.00 0.00 0.00 2.69
2673 2822 6.511416 CACAGATCTCCACATAAGGTCTTAG 58.489 44.000 0.00 0.00 31.77 2.18
2687 2918 9.088512 CATAAGGTCTTAGGAATATAACATCGC 57.911 37.037 0.00 0.00 0.00 4.58
2741 2973 7.178573 TGCCCGATCCATATTCCATATTTTAA 58.821 34.615 0.00 0.00 0.00 1.52
2862 3128 4.320608 ACAAACATGACCATTTGTGACC 57.679 40.909 10.40 0.00 45.09 4.02
2873 3139 6.378564 TGACCATTTGTGACCTAGAAAAACAA 59.621 34.615 0.00 0.00 0.00 2.83
2882 3148 8.617809 TGTGACCTAGAAAAACAAATACAAGAC 58.382 33.333 0.00 0.00 0.00 3.01
2901 3168 5.021033 AGACTCAAATGGATAGTGCTCAG 57.979 43.478 0.00 0.00 0.00 3.35
2908 3175 7.217200 TCAAATGGATAGTGCTCAGGTTATAC 58.783 38.462 0.00 0.00 0.00 1.47
2975 3243 8.986477 AAGGCATGTTATGTTATGAGTTTTTC 57.014 30.769 0.00 0.00 0.00 2.29
2982 3250 8.175069 TGTTATGTTATGAGTTTTTCGAGATGC 58.825 33.333 0.00 0.00 0.00 3.91
3074 3350 1.755179 ACAAAGAGATTGGATGGGCG 58.245 50.000 0.00 0.00 43.66 6.13
3075 3351 1.027357 CAAAGAGATTGGATGGGCGG 58.973 55.000 0.00 0.00 35.27 6.13
3082 3358 2.431782 AGATTGGATGGGCGGAAAATTG 59.568 45.455 0.00 0.00 0.00 2.32
3085 3361 2.096248 TGGATGGGCGGAAAATTGTAC 58.904 47.619 0.00 0.00 0.00 2.90
3087 3363 2.693074 GGATGGGCGGAAAATTGTACAT 59.307 45.455 0.00 0.00 0.00 2.29
3092 3368 4.767928 TGGGCGGAAAATTGTACATACTTT 59.232 37.500 0.00 0.00 0.00 2.66
3093 3369 5.106078 TGGGCGGAAAATTGTACATACTTTC 60.106 40.000 0.00 6.36 0.00 2.62
3142 3418 1.544093 CGGCACATGCATCCTAGGATT 60.544 52.381 22.29 4.97 44.36 3.01
3143 3419 2.590821 GGCACATGCATCCTAGGATTT 58.409 47.619 22.29 7.15 44.36 2.17
3146 3422 3.252701 GCACATGCATCCTAGGATTTGAG 59.747 47.826 22.29 17.27 41.59 3.02
3194 3474 9.151471 GTGATGCAACTATACAAAAGAGTCTAA 57.849 33.333 0.00 0.00 0.00 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 9.709600 CATTGTAAACAATATAACGCACACATA 57.290 29.630 7.96 0.00 44.10 2.29
33 34 7.700234 CCATTGTAAACAATATAACGCACACAT 59.300 33.333 7.96 0.00 44.10 3.21
34 35 7.024171 CCATTGTAAACAATATAACGCACACA 58.976 34.615 7.96 0.00 44.10 3.72
171 173 6.375945 TGACCGTTGCGTAGAACTATATAA 57.624 37.500 0.00 0.00 0.00 0.98
172 174 6.564709 ATGACCGTTGCGTAGAACTATATA 57.435 37.500 0.00 0.00 0.00 0.86
186 188 4.272504 AGTGTGTCTTTGTTATGACCGTTG 59.727 41.667 0.00 0.00 32.67 4.10
244 246 5.821097 AGACTCTTATTTCCCTCCCTTTTG 58.179 41.667 0.00 0.00 0.00 2.44
281 283 9.838339 CAATGGTTATTGGTAAGAGAGTTAGAT 57.162 33.333 0.00 0.00 39.98 1.98
290 292 7.773224 CCTATCACACAATGGTTATTGGTAAGA 59.227 37.037 5.17 0.00 46.33 2.10
293 295 5.825679 GCCTATCACACAATGGTTATTGGTA 59.174 40.000 5.17 0.00 46.33 3.25
332 334 6.418101 TGCAAGCTAAAATATCTCCTCAAGT 58.582 36.000 0.00 0.00 0.00 3.16
388 390 4.223032 TGTCTTTACAAGGCAAAACCCAAA 59.777 37.500 0.00 0.00 40.79 3.28
408 410 6.099269 TGGGGGAACTTGATAGTACTATTGTC 59.901 42.308 16.46 5.99 33.17 3.18
412 414 6.210522 AGTTGGGGGAACTTGATAGTACTAT 58.789 40.000 15.37 15.37 42.70 2.12
415 417 4.838904 AGTTGGGGGAACTTGATAGTAC 57.161 45.455 0.00 0.00 42.70 2.73
416 418 5.343715 TGTAGTTGGGGGAACTTGATAGTA 58.656 41.667 0.00 0.00 42.70 1.82
418 420 4.837093 TGTAGTTGGGGGAACTTGATAG 57.163 45.455 0.00 0.00 42.70 2.08
419 421 4.600111 ACTTGTAGTTGGGGGAACTTGATA 59.400 41.667 0.00 0.00 42.70 2.15
420 422 3.397955 ACTTGTAGTTGGGGGAACTTGAT 59.602 43.478 0.00 0.00 42.70 2.57
421 423 2.781174 ACTTGTAGTTGGGGGAACTTGA 59.219 45.455 0.00 0.00 42.70 3.02
422 424 3.223674 ACTTGTAGTTGGGGGAACTTG 57.776 47.619 0.00 0.00 42.70 3.16
423 425 5.594199 AATACTTGTAGTTGGGGGAACTT 57.406 39.130 0.00 0.00 42.70 2.66
425 427 4.393990 CGAAATACTTGTAGTTGGGGGAAC 59.606 45.833 0.00 0.00 34.40 3.62
426 428 4.566070 CCGAAATACTTGTAGTTGGGGGAA 60.566 45.833 12.11 0.00 0.00 3.97
427 429 3.054948 CCGAAATACTTGTAGTTGGGGGA 60.055 47.826 12.11 0.00 0.00 4.81
428 430 3.275999 CCGAAATACTTGTAGTTGGGGG 58.724 50.000 12.11 2.55 0.00 5.40
429 431 3.946606 ACCGAAATACTTGTAGTTGGGG 58.053 45.455 20.08 13.17 29.20 4.96
430 432 4.563976 CGTACCGAAATACTTGTAGTTGGG 59.436 45.833 16.40 16.40 0.00 4.12
431 433 4.563976 CCGTACCGAAATACTTGTAGTTGG 59.436 45.833 0.00 3.87 0.00 3.77
432 434 5.401550 TCCGTACCGAAATACTTGTAGTTG 58.598 41.667 0.00 0.00 0.00 3.16
433 435 5.643379 TCCGTACCGAAATACTTGTAGTT 57.357 39.130 0.00 0.00 0.00 2.24
434 436 5.393461 CCTTCCGTACCGAAATACTTGTAGT 60.393 44.000 0.00 0.00 0.00 2.73
435 437 5.039333 CCTTCCGTACCGAAATACTTGTAG 58.961 45.833 0.00 0.00 0.00 2.74
436 438 4.704540 TCCTTCCGTACCGAAATACTTGTA 59.295 41.667 0.00 0.00 0.00 2.41
437 439 3.511146 TCCTTCCGTACCGAAATACTTGT 59.489 43.478 0.00 0.00 0.00 3.16
438 440 4.110482 CTCCTTCCGTACCGAAATACTTG 58.890 47.826 0.00 0.00 0.00 3.16
439 441 3.766051 ACTCCTTCCGTACCGAAATACTT 59.234 43.478 0.00 0.00 0.00 2.24
440 442 3.359950 ACTCCTTCCGTACCGAAATACT 58.640 45.455 0.00 0.00 0.00 2.12
441 443 3.790152 ACTCCTTCCGTACCGAAATAC 57.210 47.619 0.00 0.00 0.00 1.89
442 444 4.526970 AGTACTCCTTCCGTACCGAAATA 58.473 43.478 0.00 0.00 38.34 1.40
443 445 3.359950 AGTACTCCTTCCGTACCGAAAT 58.640 45.455 0.00 0.00 38.34 2.17
444 446 2.795329 AGTACTCCTTCCGTACCGAAA 58.205 47.619 0.00 0.00 38.34 3.46
445 447 2.496899 AGTACTCCTTCCGTACCGAA 57.503 50.000 0.00 0.00 38.34 4.30
446 448 3.270877 GTTAGTACTCCTTCCGTACCGA 58.729 50.000 0.00 0.00 38.34 4.69
447 449 3.009723 TGTTAGTACTCCTTCCGTACCG 58.990 50.000 0.00 0.00 38.34 4.02
448 450 5.164233 GTTTGTTAGTACTCCTTCCGTACC 58.836 45.833 0.00 0.00 38.34 3.34
449 451 5.772521 TGTTTGTTAGTACTCCTTCCGTAC 58.227 41.667 0.00 0.00 37.96 3.67
450 452 6.209192 TGATGTTTGTTAGTACTCCTTCCGTA 59.791 38.462 0.00 0.00 0.00 4.02
451 453 4.942761 TGTTTGTTAGTACTCCTTCCGT 57.057 40.909 0.00 0.00 0.00 4.69
452 454 5.475719 TGATGTTTGTTAGTACTCCTTCCG 58.524 41.667 0.00 0.00 0.00 4.30
453 455 5.351740 GCTGATGTTTGTTAGTACTCCTTCC 59.648 44.000 0.00 0.00 0.00 3.46
454 456 5.932303 TGCTGATGTTTGTTAGTACTCCTTC 59.068 40.000 0.00 0.00 0.00 3.46
455 457 5.865085 TGCTGATGTTTGTTAGTACTCCTT 58.135 37.500 0.00 0.00 0.00 3.36
456 458 5.483685 TGCTGATGTTTGTTAGTACTCCT 57.516 39.130 0.00 0.00 0.00 3.69
457 459 6.743575 ATTGCTGATGTTTGTTAGTACTCC 57.256 37.500 0.00 0.00 0.00 3.85
458 460 8.480643 AGTATTGCTGATGTTTGTTAGTACTC 57.519 34.615 0.00 0.00 0.00 2.59
459 461 9.367444 GTAGTATTGCTGATGTTTGTTAGTACT 57.633 33.333 0.00 0.00 0.00 2.73
460 462 9.367444 AGTAGTATTGCTGATGTTTGTTAGTAC 57.633 33.333 0.00 0.00 0.00 2.73
461 463 9.582431 GAGTAGTATTGCTGATGTTTGTTAGTA 57.418 33.333 0.00 0.00 0.00 1.82
462 464 7.549488 GGAGTAGTATTGCTGATGTTTGTTAGT 59.451 37.037 0.00 0.00 0.00 2.24
463 465 7.549134 TGGAGTAGTATTGCTGATGTTTGTTAG 59.451 37.037 0.00 0.00 0.00 2.34
464 466 7.333423 GTGGAGTAGTATTGCTGATGTTTGTTA 59.667 37.037 0.00 0.00 0.00 2.41
465 467 6.149474 GTGGAGTAGTATTGCTGATGTTTGTT 59.851 38.462 0.00 0.00 0.00 2.83
466 468 5.643777 GTGGAGTAGTATTGCTGATGTTTGT 59.356 40.000 0.00 0.00 0.00 2.83
467 469 5.877012 AGTGGAGTAGTATTGCTGATGTTTG 59.123 40.000 0.00 0.00 0.00 2.93
468 470 6.054860 AGTGGAGTAGTATTGCTGATGTTT 57.945 37.500 0.00 0.00 0.00 2.83
502 589 2.688446 TCGACGCTATCATCCTTCTGTT 59.312 45.455 0.00 0.00 0.00 3.16
512 599 2.878406 TCTCATGATGTCGACGCTATCA 59.122 45.455 16.60 16.60 35.52 2.15
513 600 3.544356 TCTCATGATGTCGACGCTATC 57.456 47.619 11.62 9.12 0.00 2.08
514 601 3.990318 TTCTCATGATGTCGACGCTAT 57.010 42.857 11.62 0.00 0.00 2.97
515 602 3.377172 TCTTTCTCATGATGTCGACGCTA 59.623 43.478 11.62 0.00 0.00 4.26
529 616 3.038788 TGTGCTGCGTTATCTTTCTCA 57.961 42.857 0.00 0.00 0.00 3.27
541 628 1.398595 GTGCTTTACTTTGTGCTGCG 58.601 50.000 0.00 0.00 0.00 5.18
545 632 0.666374 ACCGGTGCTTTACTTTGTGC 59.334 50.000 6.12 0.00 0.00 4.57
573 660 2.545106 TCCATGATCATCAATTCGCGTG 59.455 45.455 4.86 0.00 0.00 5.34
575 662 4.389687 TGTATCCATGATCATCAATTCGCG 59.610 41.667 4.86 0.00 0.00 5.87
586 673 1.523758 GGGCGGTTGTATCCATGATC 58.476 55.000 0.00 0.00 0.00 2.92
591 678 2.897207 CTCGGGCGGTTGTATCCA 59.103 61.111 0.00 0.00 0.00 3.41
592 679 2.588034 GCTCGGGCGGTTGTATCC 60.588 66.667 0.00 0.00 0.00 2.59
614 701 0.902531 AATCCGGTCGATCAGTTGGT 59.097 50.000 0.00 0.00 0.00 3.67
616 703 2.100916 ACCTAATCCGGTCGATCAGTTG 59.899 50.000 0.00 0.00 29.14 3.16
639 726 2.202518 CCGCAAATGCAAGAGCCG 60.203 61.111 6.18 0.00 42.21 5.52
722 809 2.693591 CCTTTGCGAGATAGGTGGTCTA 59.306 50.000 0.00 0.00 0.00 2.59
795 905 2.941025 TTGGGGCCAGGCTTAGCT 60.941 61.111 12.43 0.00 0.00 3.32
797 907 2.043953 GGTTGGGGCCAGGCTTAG 60.044 66.667 12.43 0.00 0.00 2.18
850 960 2.093235 TGGGTTTGGCTTTGGTCTTTTG 60.093 45.455 0.00 0.00 0.00 2.44
868 978 1.969923 GATGAGAGATCTGTCCCTGGG 59.030 57.143 16.68 6.33 0.00 4.45
879 989 5.365895 TGATGATGAACTGGTGATGAGAGAT 59.634 40.000 0.00 0.00 0.00 2.75
1013 1123 1.518302 GAAGGAGAAGACGGGGAGC 59.482 63.158 0.00 0.00 0.00 4.70
1029 1139 0.793617 AGGTGGGAGAAGAGGAGGAA 59.206 55.000 0.00 0.00 0.00 3.36
1036 1146 2.119611 TGCGGAGGTGGGAGAAGA 59.880 61.111 0.00 0.00 0.00 2.87
1037 1147 2.266055 GTGCGGAGGTGGGAGAAG 59.734 66.667 0.00 0.00 0.00 2.85
1115 1225 2.359478 AAATGCCGTGGTCGACCC 60.359 61.111 31.19 20.60 39.71 4.46
1185 1295 2.106683 CCGGAACTCCCATTCGCAC 61.107 63.158 0.00 0.00 34.14 5.34
1556 1666 4.459331 CCGCCATGGACGTTTGCG 62.459 66.667 18.40 9.73 44.47 4.85
1557 1667 4.776647 GCCGCCATGGACGTTTGC 62.777 66.667 18.40 13.27 42.00 3.68
1659 1769 2.943345 GAACTCCACGCACAGCACG 61.943 63.158 0.00 0.00 0.00 5.34
1995 2105 0.031585 CGAAGACGTGGTTGGACTCA 59.968 55.000 0.00 0.00 34.56 3.41
2226 2336 3.187211 GAGTGTGGCTCGCTATAGC 57.813 57.895 15.09 15.09 41.99 2.97
2272 2382 5.126222 TGAATCTCTCTCACACCAGTCATAC 59.874 44.000 0.00 0.00 0.00 2.39
2273 2383 5.264395 TGAATCTCTCTCACACCAGTCATA 58.736 41.667 0.00 0.00 0.00 2.15
2274 2384 4.092279 TGAATCTCTCTCACACCAGTCAT 58.908 43.478 0.00 0.00 0.00 3.06
2275 2385 3.500343 TGAATCTCTCTCACACCAGTCA 58.500 45.455 0.00 0.00 0.00 3.41
2276 2386 4.734398 ATGAATCTCTCTCACACCAGTC 57.266 45.455 0.00 0.00 0.00 3.51
2277 2387 4.776837 AGAATGAATCTCTCTCACACCAGT 59.223 41.667 0.00 0.00 30.46 4.00
2278 2388 5.341872 AGAATGAATCTCTCTCACACCAG 57.658 43.478 0.00 0.00 30.46 4.00
2279 2389 5.485620 CAAGAATGAATCTCTCTCACACCA 58.514 41.667 0.00 0.00 37.42 4.17
2280 2390 4.332268 GCAAGAATGAATCTCTCTCACACC 59.668 45.833 0.00 0.00 37.42 4.16
2358 2469 2.270434 ATCCCCTGTCCTCTAGCAAA 57.730 50.000 0.00 0.00 0.00 3.68
2368 2479 4.657013 GGGAAAGAATCATATCCCCTGTC 58.343 47.826 6.73 0.00 44.84 3.51
2399 2538 5.147330 TGTCAGGAACGAGTCACATAATT 57.853 39.130 0.00 0.00 0.00 1.40
2403 2542 3.685139 ATTGTCAGGAACGAGTCACAT 57.315 42.857 0.00 0.00 0.00 3.21
2407 2546 6.899114 ACATAAAAATTGTCAGGAACGAGTC 58.101 36.000 0.00 0.00 0.00 3.36
2479 2618 6.799926 AAAAACACACTTCACTTTGCAATT 57.200 29.167 0.00 0.00 0.00 2.32
2483 2622 6.972328 TCATCTAAAAACACACTTCACTTTGC 59.028 34.615 0.00 0.00 0.00 3.68
2486 2625 6.828785 AGGTCATCTAAAAACACACTTCACTT 59.171 34.615 0.00 0.00 0.00 3.16
2488 2627 6.260050 TGAGGTCATCTAAAAACACACTTCAC 59.740 38.462 0.00 0.00 0.00 3.18
2541 2681 7.819900 GCCATACCGATATCAAAATTACTCTCT 59.180 37.037 3.12 0.00 0.00 3.10
2544 2684 7.907214 AGCCATACCGATATCAAAATTACTC 57.093 36.000 3.12 0.00 0.00 2.59
2559 2699 2.160615 CGACTGAGATCTAGCCATACCG 59.839 54.545 0.00 0.00 0.00 4.02
2563 2703 2.884012 CAGTCGACTGAGATCTAGCCAT 59.116 50.000 36.73 0.00 46.59 4.40
2588 2728 5.472137 GTCACTAGCCTGTGATTTGGTTAAA 59.528 40.000 11.70 0.00 46.77 1.52
2592 2732 2.371841 TGTCACTAGCCTGTGATTTGGT 59.628 45.455 11.70 0.00 46.77 3.67
2597 2737 5.620738 ATGTTATGTCACTAGCCTGTGAT 57.379 39.130 11.70 1.47 46.77 3.06
2600 2740 9.899661 TTTTTATATGTTATGTCACTAGCCTGT 57.100 29.630 0.00 0.00 0.00 4.00
2636 2779 6.258507 GTGGAGATCTGTGCAAATTTTGTTTT 59.741 34.615 0.00 0.00 0.00 2.43
2639 2782 4.341806 TGTGGAGATCTGTGCAAATTTTGT 59.658 37.500 0.00 0.00 0.00 2.83
2640 2783 4.873817 TGTGGAGATCTGTGCAAATTTTG 58.126 39.130 0.00 4.72 0.00 2.44
2644 2793 4.885907 CCTTATGTGGAGATCTGTGCAAAT 59.114 41.667 0.00 0.00 0.00 2.32
2647 2796 2.840038 ACCTTATGTGGAGATCTGTGCA 59.160 45.455 0.00 0.00 0.00 4.57
2652 2801 6.031964 TCCTAAGACCTTATGTGGAGATCT 57.968 41.667 0.00 0.00 0.00 2.75
2662 2811 7.974501 CGCGATGTTATATTCCTAAGACCTTAT 59.025 37.037 0.00 0.00 0.00 1.73
2667 2816 4.921515 TGCGCGATGTTATATTCCTAAGAC 59.078 41.667 12.10 0.00 0.00 3.01
2673 2822 2.055838 TCGTGCGCGATGTTATATTCC 58.944 47.619 20.10 0.00 42.81 3.01
2687 2918 2.902484 GCACAAAATCTACTTTCGTGCG 59.098 45.455 0.00 0.00 35.58 5.34
2791 3024 9.647918 CAGGATATAGACCCATAGTATGTATGT 57.352 37.037 9.28 3.56 25.63 2.29
2796 3029 6.381133 TGCACAGGATATAGACCCATAGTATG 59.619 42.308 2.90 2.90 0.00 2.39
2806 3039 3.388024 TCCCAAGTGCACAGGATATAGAC 59.612 47.826 24.91 0.00 0.00 2.59
2815 3048 1.000938 GAGCTTTTCCCAAGTGCACAG 60.001 52.381 21.04 11.05 0.00 3.66
2873 3139 7.341805 AGCACTATCCATTTGAGTCTTGTATT 58.658 34.615 0.00 0.00 0.00 1.89
2882 3148 4.148128 ACCTGAGCACTATCCATTTGAG 57.852 45.455 0.00 0.00 0.00 3.02
2894 3160 5.872617 TGTGTATGTTGTATAACCTGAGCAC 59.127 40.000 0.00 3.61 35.92 4.40
2941 3209 6.832520 AACATAACATGCCTTATTGTGACA 57.167 33.333 0.00 0.00 0.00 3.58
3028 3298 5.195001 TCCCTTCATTTTCCAAGTTTTCG 57.805 39.130 0.00 0.00 0.00 3.46
3058 3334 0.918983 TTCCGCCCATCCAATCTCTT 59.081 50.000 0.00 0.00 0.00 2.85
3092 3368 6.518208 TTGGACCTTTCTTTTCGAAAAAGA 57.482 33.333 22.67 18.11 40.87 2.52
3093 3369 6.035650 GGTTTGGACCTTTCTTTTCGAAAAAG 59.964 38.462 22.67 16.91 42.99 2.27
3120 3396 1.447217 CTAGGATGCATGTGCCGGA 59.553 57.895 5.05 0.00 41.18 5.14
3122 3398 0.035881 ATCCTAGGATGCATGTGCCG 59.964 55.000 23.95 0.00 41.18 5.69
3202 3482 7.310671 CCATAGTTGCCCACTGTATATACTCAT 60.311 40.741 13.89 0.00 35.97 2.90
3203 3483 6.014584 CCATAGTTGCCCACTGTATATACTCA 60.015 42.308 13.89 0.00 35.97 3.41


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

AutoCloner maintained by Alex Coulton.