Multiple sequence alignment - TraesCS5B01G234000

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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 TraesCS5B01G234000 chr5B 100.000 3439 0 0 1 3439 411816285 411812847 0.000000e+00 6351
1 TraesCS5B01G234000 chr5D 94.001 2934 112 13 464 3370 351000728 350997832 0.000000e+00 4385
2 TraesCS5B01G234000 chr5D 87.147 389 22 8 25 412 351001225 351000864 1.910000e-112 416
3 TraesCS5B01G234000 chr5A 95.882 1360 51 5 2014 3370 451468642 451467285 0.000000e+00 2196
4 TraesCS5B01G234000 chr5A 92.638 1236 50 16 757 1954 451469898 451468666 0.000000e+00 1740
5 TraesCS5B01G234000 chr5A 87.500 192 22 2 546 736 451470155 451469965 1.610000e-53 220


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 TraesCS5B01G234000 chr5B 411812847 411816285 3438 True 6351.000000 6351 100.000000 1 3439 1 chr5B.!!$R1 3438
1 TraesCS5B01G234000 chr5D 350997832 351001225 3393 True 2400.500000 4385 90.574000 25 3370 2 chr5D.!!$R1 3345
2 TraesCS5B01G234000 chr5A 451467285 451470155 2870 True 1385.333333 2196 92.006667 546 3370 3 chr5A.!!$R1 2824

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
418 420 0.106868 CCATTGAGCATCTCCAGCCA 60.107 55.0 0.00 0.0 34.92 4.75 F
1527 1687 0.037447 GGAAGCAGGACCAGCTCTTT 59.963 55.0 12.36 0.0 42.53 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1720 1896 0.621571 TGGGAGGTTGCCAGAGCTAT 60.622 55.0 0.0 0.0 40.8 2.97 R
3417 3598 0.903942 GGAATTGGCAGGCATTGGAA 59.096 50.0 0.0 0.0 0.0 3.53 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
35 36 4.022849 CCAAAAGAAAATGAGCGTCTTCCT 60.023 41.667 0.00 0.00 31.26 3.36
36 37 5.507985 CCAAAAGAAAATGAGCGTCTTCCTT 60.508 40.000 0.00 0.00 31.26 3.36
45 46 2.739379 GAGCGTCTTCCTTTTTCTCTGG 59.261 50.000 0.00 0.00 0.00 3.86
56 57 4.811024 CCTTTTTCTCTGGAAAACCTTTGC 59.189 41.667 3.80 0.00 46.87 3.68
76 77 1.209127 CGCCAAGCCAACTTTACGG 59.791 57.895 0.00 0.00 32.29 4.02
90 91 3.069729 ACTTTACGGCATCTCCATCTACC 59.930 47.826 0.00 0.00 34.01 3.18
98 99 3.318275 GCATCTCCATCTACCACGTCTTA 59.682 47.826 0.00 0.00 0.00 2.10
103 104 4.338012 TCCATCTACCACGTCTTACTCAA 58.662 43.478 0.00 0.00 0.00 3.02
112 113 2.478894 ACGTCTTACTCAATTTGGCACG 59.521 45.455 0.00 0.00 0.00 5.34
178 179 0.618680 TCCCTCCACATCCTGGACTG 60.619 60.000 0.00 1.48 44.99 3.51
180 181 0.618680 CCTCCACATCCTGGACTGGA 60.619 60.000 19.24 19.24 44.99 3.86
181 182 0.829333 CTCCACATCCTGGACTGGAG 59.171 60.000 26.52 26.52 44.99 3.86
182 183 0.117140 TCCACATCCTGGACTGGAGT 59.883 55.000 17.33 2.23 44.99 3.85
183 184 1.361197 TCCACATCCTGGACTGGAGTA 59.639 52.381 17.33 0.85 44.99 2.59
184 185 1.759445 CCACATCCTGGACTGGAGTAG 59.241 57.143 14.60 0.28 43.95 2.57
185 186 2.461695 CACATCCTGGACTGGAGTAGT 58.538 52.381 0.00 0.82 44.02 2.73
186 187 2.167281 CACATCCTGGACTGGAGTAGTG 59.833 54.545 0.00 8.36 40.53 2.74
187 188 1.137872 CATCCTGGACTGGAGTAGTGC 59.862 57.143 0.00 0.00 46.86 4.40
192 193 2.943449 GGACTGGAGTAGTGCACTAC 57.057 55.000 38.49 38.49 46.05 2.73
203 204 2.912986 TGCACTACTTCGCACTTGG 58.087 52.632 0.00 0.00 31.95 3.61
216 217 1.338020 GCACTTGGTTCTCCCTGTTTG 59.662 52.381 0.00 0.00 0.00 2.93
260 261 3.132111 TGTCCAAGGAGAAAACAAAAGGC 59.868 43.478 0.00 0.00 0.00 4.35
262 263 2.700371 CCAAGGAGAAAACAAAAGGCCT 59.300 45.455 0.00 0.00 0.00 5.19
264 265 1.688735 AGGAGAAAACAAAAGGCCTGC 59.311 47.619 5.69 0.00 0.00 4.85
272 273 2.314323 CAAAAGGCCTGCTTTTGTGT 57.686 45.000 17.00 0.00 43.10 3.72
276 277 0.107831 AGGCCTGCTTTTGTGTCGTA 59.892 50.000 3.11 0.00 0.00 3.43
277 278 0.948678 GGCCTGCTTTTGTGTCGTAA 59.051 50.000 0.00 0.00 0.00 3.18
372 374 2.474266 CGCGCACACACACATACC 59.526 61.111 8.75 0.00 0.00 2.73
374 376 0.734597 CGCGCACACACACATACCTA 60.735 55.000 8.75 0.00 0.00 3.08
389 391 5.293324 CACATACCTATAAACACATGCACGT 59.707 40.000 0.00 0.00 0.00 4.49
401 403 2.703536 ACATGCACGTAATCCTATCCCA 59.296 45.455 0.00 0.00 0.00 4.37
412 414 4.840716 ATCCTATCCCATTGAGCATCTC 57.159 45.455 0.00 0.00 34.92 2.75
414 416 2.641321 CCTATCCCATTGAGCATCTCCA 59.359 50.000 0.00 0.00 34.92 3.86
415 417 2.953284 ATCCCATTGAGCATCTCCAG 57.047 50.000 0.00 0.00 34.92 3.86
416 418 0.182061 TCCCATTGAGCATCTCCAGC 59.818 55.000 0.00 0.00 34.92 4.85
417 419 0.822532 CCCATTGAGCATCTCCAGCC 60.823 60.000 0.00 0.00 34.92 4.85
418 420 0.106868 CCATTGAGCATCTCCAGCCA 60.107 55.000 0.00 0.00 34.92 4.75
419 421 1.309950 CATTGAGCATCTCCAGCCAG 58.690 55.000 0.00 0.00 34.92 4.85
420 422 1.134189 CATTGAGCATCTCCAGCCAGA 60.134 52.381 0.00 0.00 34.92 3.86
434 449 3.129287 CCAGCCAGATAATTGTTCACCAC 59.871 47.826 0.00 0.00 0.00 4.16
441 456 6.350110 CCAGATAATTGTTCACCACGGAAATT 60.350 38.462 0.00 0.00 0.00 1.82
443 458 7.062138 CAGATAATTGTTCACCACGGAAATTTG 59.938 37.037 0.00 0.00 0.00 2.32
478 564 3.983044 ATGTAGTCTTTGTCCCAGACC 57.017 47.619 0.00 0.00 41.55 3.85
494 580 3.330267 CAGACCAAGTTGGACTAAGAGC 58.670 50.000 28.80 6.76 40.43 4.09
505 591 6.210784 AGTTGGACTAAGAGCATTACACACTA 59.789 38.462 0.00 0.00 0.00 2.74
519 605 8.009974 GCATTACACACTAATTAATCGGATCAC 58.990 37.037 0.00 0.00 0.00 3.06
542 628 4.330250 CATATGGCCTAGGTTCAGATTGG 58.670 47.826 11.31 0.00 0.00 3.16
552 638 7.338449 GCCTAGGTTCAGATTGGTTTAATTACA 59.662 37.037 11.31 0.00 0.00 2.41
595 681 4.936685 AGGGCTTAAAAGTCAAGATCCT 57.063 40.909 0.00 0.00 30.55 3.24
676 763 1.995376 TTGCCTCCTGGTTTCCTTTC 58.005 50.000 0.00 0.00 35.27 2.62
860 997 3.635373 CCCCATGATCACTGAAAATCCTG 59.365 47.826 0.00 0.00 0.00 3.86
915 1058 1.641192 ACATTTCCCTCCCCTTTCCTC 59.359 52.381 0.00 0.00 0.00 3.71
1146 1295 1.301558 CAGAGAGATCCATGGCGCC 60.302 63.158 22.73 22.73 0.00 6.53
1340 1500 0.458716 GGTAGGCAGAGCGTCTCAAC 60.459 60.000 9.09 1.53 32.06 3.18
1341 1501 0.458716 GTAGGCAGAGCGTCTCAACC 60.459 60.000 9.09 8.98 32.06 3.77
1342 1502 0.898326 TAGGCAGAGCGTCTCAACCA 60.898 55.000 15.31 4.78 32.46 3.67
1343 1503 1.301716 GGCAGAGCGTCTCAACCAA 60.302 57.895 9.09 0.00 32.06 3.67
1392 1552 0.619832 TCCCTCTCCAGCTCTGCAAT 60.620 55.000 0.00 0.00 0.00 3.56
1527 1687 0.037447 GGAAGCAGGACCAGCTCTTT 59.963 55.000 12.36 0.00 42.53 2.52
1657 1822 4.511454 TCTCGTTCTGGTTTCAGTCATTTG 59.489 41.667 0.00 0.00 41.59 2.32
1664 1829 4.531854 TGGTTTCAGTCATTTGTCTTCCA 58.468 39.130 0.00 0.00 0.00 3.53
1665 1830 4.338118 TGGTTTCAGTCATTTGTCTTCCAC 59.662 41.667 0.00 0.00 0.00 4.02
1720 1896 1.134995 CGTGGTCTGAGCAGCTATTGA 60.135 52.381 10.21 0.00 0.00 2.57
1766 1942 2.350895 CCACGATGAACCCAGCCA 59.649 61.111 0.00 0.00 0.00 4.75
1983 2159 1.211212 TGGCCTGATGATCTCCACTTG 59.789 52.381 3.32 0.00 0.00 3.16
1995 2174 3.031013 TCTCCACTTGACAGAACACTGA 58.969 45.455 0.00 0.00 35.80 3.41
2000 2179 4.758674 CCACTTGACAGAACACTGATGAAT 59.241 41.667 0.00 0.00 35.80 2.57
2009 2188 2.996631 ACACTGATGAATCTCTTGGCC 58.003 47.619 0.00 0.00 0.00 5.36
2010 2189 2.306805 ACACTGATGAATCTCTTGGCCA 59.693 45.455 0.00 0.00 0.00 5.36
2011 2190 3.245016 ACACTGATGAATCTCTTGGCCAA 60.245 43.478 19.25 19.25 0.00 4.52
2012 2191 3.952323 CACTGATGAATCTCTTGGCCAAT 59.048 43.478 20.85 2.71 0.00 3.16
2031 2210 5.404366 GCCAATCAATCATGAATGTGTATGC 59.596 40.000 10.52 5.29 39.49 3.14
2059 2238 3.366781 GGCACTGAAGAAGAATTTGGCTC 60.367 47.826 0.00 0.00 0.00 4.70
2142 2321 7.575414 TTACTGCAAGGTGAATAACAGAAAA 57.425 32.000 0.00 0.00 39.30 2.29
2152 2331 5.626955 GTGAATAACAGAAAAGCAAGCAGTC 59.373 40.000 0.00 0.00 0.00 3.51
2190 2370 2.174210 ACTAGTACATCGCTGGTCCCTA 59.826 50.000 0.00 0.00 0.00 3.53
2290 2470 2.592861 GGCTATCTTGGGCAGCGG 60.593 66.667 0.00 0.00 36.12 5.52
2324 2504 1.878953 ACGAGATCAAGTTGGCGTTT 58.121 45.000 2.34 0.00 0.00 3.60
2348 2528 5.548181 AGAGTAACTTCGGAAAGAACCTT 57.452 39.130 0.00 0.00 36.30 3.50
2527 2707 5.930135 TCTTATCTGAACTTGGGATTAGGC 58.070 41.667 0.00 0.00 0.00 3.93
2537 2717 1.837439 TGGGATTAGGCGAGAACATGT 59.163 47.619 0.00 0.00 0.00 3.21
2767 2947 2.969628 AAGACCCTAGCATTCGTCAG 57.030 50.000 0.00 0.00 0.00 3.51
2867 3047 9.128107 GTATCAACAAAATTGATGAAACACGAT 57.872 29.630 9.68 0.00 42.11 3.73
3006 3187 4.036262 TGTCATCCAAACGAGGAAAACAAG 59.964 41.667 0.00 0.00 41.92 3.16
3029 3210 8.885722 CAAGGAAATTGAAAAATGATGGGTATG 58.114 33.333 0.00 0.00 41.83 2.39
3243 3424 7.687941 AACCTTATCTTTCTTGTGTATGGTG 57.312 36.000 0.00 0.00 0.00 4.17
3298 3479 7.915293 ATTGTACATCAAAACGGATACAAGA 57.085 32.000 0.00 0.00 39.62 3.02
3310 3491 5.715070 ACGGATACAAGAGAGTCAAGAAAG 58.285 41.667 0.00 0.00 0.00 2.62
3317 3498 5.882557 ACAAGAGAGTCAAGAAAGCAGAAAA 59.117 36.000 0.00 0.00 0.00 2.29
3325 3506 5.240403 GTCAAGAAAGCAGAAAATGGAGTCT 59.760 40.000 0.00 0.00 0.00 3.24
3328 3509 4.759183 AGAAAGCAGAAAATGGAGTCTGTC 59.241 41.667 2.90 0.00 42.72 3.51
3344 3525 6.187727 AGTCTGTCCCAAGAAATTACAAGA 57.812 37.500 0.00 0.00 0.00 3.02
3346 3527 6.043243 AGTCTGTCCCAAGAAATTACAAGAGA 59.957 38.462 0.00 0.00 0.00 3.10
3351 3532 8.359642 TGTCCCAAGAAATTACAAGAGAAAATG 58.640 33.333 0.00 0.00 0.00 2.32
3374 3555 9.987272 AATGAATATCATGTGAAGAACTATCGA 57.013 29.630 0.00 0.00 37.15 3.59
3375 3556 9.987272 ATGAATATCATGTGAAGAACTATCGAA 57.013 29.630 0.00 0.00 35.43 3.71
3376 3557 9.249457 TGAATATCATGTGAAGAACTATCGAAC 57.751 33.333 0.00 0.00 0.00 3.95
3377 3558 9.469807 GAATATCATGTGAAGAACTATCGAACT 57.530 33.333 0.00 0.00 0.00 3.01
3381 3562 8.689251 TCATGTGAAGAACTATCGAACTAAAG 57.311 34.615 0.00 0.00 0.00 1.85
3382 3563 8.304596 TCATGTGAAGAACTATCGAACTAAAGT 58.695 33.333 0.00 0.00 0.00 2.66
3383 3564 8.926710 CATGTGAAGAACTATCGAACTAAAGTT 58.073 33.333 0.00 0.00 41.64 2.66
3384 3565 8.294341 TGTGAAGAACTATCGAACTAAAGTTG 57.706 34.615 0.00 0.00 38.56 3.16
3385 3566 7.095774 TGTGAAGAACTATCGAACTAAAGTTGC 60.096 37.037 0.00 0.00 38.56 4.17
3386 3567 6.926826 TGAAGAACTATCGAACTAAAGTTGCA 59.073 34.615 0.00 0.00 38.56 4.08
3387 3568 6.952935 AGAACTATCGAACTAAAGTTGCAG 57.047 37.500 0.00 0.00 38.56 4.41
3388 3569 5.348997 AGAACTATCGAACTAAAGTTGCAGC 59.651 40.000 0.00 0.00 38.56 5.25
3389 3570 4.822026 ACTATCGAACTAAAGTTGCAGCT 58.178 39.130 0.00 0.00 38.56 4.24
3390 3571 5.962433 ACTATCGAACTAAAGTTGCAGCTA 58.038 37.500 2.53 0.00 38.56 3.32
3391 3572 6.395629 ACTATCGAACTAAAGTTGCAGCTAA 58.604 36.000 2.53 0.00 38.56 3.09
3392 3573 7.042335 ACTATCGAACTAAAGTTGCAGCTAAT 58.958 34.615 2.53 0.00 38.56 1.73
3393 3574 8.195436 ACTATCGAACTAAAGTTGCAGCTAATA 58.805 33.333 2.53 0.00 38.56 0.98
3394 3575 6.887376 TCGAACTAAAGTTGCAGCTAATAG 57.113 37.500 16.70 16.70 38.56 1.73
3395 3576 6.627243 TCGAACTAAAGTTGCAGCTAATAGA 58.373 36.000 22.05 7.67 38.56 1.98
3396 3577 7.094631 TCGAACTAAAGTTGCAGCTAATAGAA 58.905 34.615 22.05 8.30 38.56 2.10
3397 3578 7.063074 TCGAACTAAAGTTGCAGCTAATAGAAC 59.937 37.037 22.05 15.67 38.56 3.01
3398 3579 7.148639 CGAACTAAAGTTGCAGCTAATAGAACA 60.149 37.037 22.05 0.00 38.56 3.18
3399 3580 7.602517 ACTAAAGTTGCAGCTAATAGAACAG 57.397 36.000 22.05 7.70 0.00 3.16
3400 3581 7.162082 ACTAAAGTTGCAGCTAATAGAACAGT 58.838 34.615 22.05 8.17 0.00 3.55
3401 3582 8.311836 ACTAAAGTTGCAGCTAATAGAACAGTA 58.688 33.333 22.05 0.00 0.00 2.74
3402 3583 7.602517 AAAGTTGCAGCTAATAGAACAGTAG 57.397 36.000 2.53 0.00 0.00 2.57
3403 3584 6.531503 AGTTGCAGCTAATAGAACAGTAGA 57.468 37.500 0.00 0.00 0.00 2.59
3404 3585 6.936279 AGTTGCAGCTAATAGAACAGTAGAA 58.064 36.000 0.00 0.00 0.00 2.10
3405 3586 7.038659 AGTTGCAGCTAATAGAACAGTAGAAG 58.961 38.462 0.00 0.00 0.00 2.85
3406 3587 5.907207 TGCAGCTAATAGAACAGTAGAAGG 58.093 41.667 0.00 0.00 0.00 3.46
3407 3588 5.422331 TGCAGCTAATAGAACAGTAGAAGGT 59.578 40.000 0.00 0.00 0.00 3.50
3408 3589 5.751028 GCAGCTAATAGAACAGTAGAAGGTG 59.249 44.000 0.00 0.00 35.06 4.00
3409 3590 6.276847 CAGCTAATAGAACAGTAGAAGGTGG 58.723 44.000 0.00 0.00 0.00 4.61
3410 3591 6.096987 CAGCTAATAGAACAGTAGAAGGTGGA 59.903 42.308 0.00 0.00 0.00 4.02
3411 3592 6.841755 AGCTAATAGAACAGTAGAAGGTGGAT 59.158 38.462 0.00 0.00 0.00 3.41
3412 3593 7.345914 AGCTAATAGAACAGTAGAAGGTGGATT 59.654 37.037 0.00 0.00 0.00 3.01
3413 3594 8.639761 GCTAATAGAACAGTAGAAGGTGGATTA 58.360 37.037 0.00 0.00 0.00 1.75
3420 3601 9.274206 GAACAGTAGAAGGTGGATTATAATTCC 57.726 37.037 1.11 4.54 0.00 3.01
3421 3602 8.331931 ACAGTAGAAGGTGGATTATAATTCCA 57.668 34.615 10.72 10.72 0.00 3.53
3422 3603 8.778059 ACAGTAGAAGGTGGATTATAATTCCAA 58.222 33.333 14.45 1.32 35.05 3.53
3423 3604 9.799106 CAGTAGAAGGTGGATTATAATTCCAAT 57.201 33.333 14.45 7.28 35.05 3.16
3424 3605 9.799106 AGTAGAAGGTGGATTATAATTCCAATG 57.201 33.333 14.45 0.00 35.05 2.82
3425 3606 7.530426 AGAAGGTGGATTATAATTCCAATGC 57.470 36.000 14.45 8.25 35.05 3.56
3426 3607 6.494835 AGAAGGTGGATTATAATTCCAATGCC 59.505 38.462 14.45 12.40 35.05 4.40
3427 3608 5.969086 AGGTGGATTATAATTCCAATGCCT 58.031 37.500 14.45 13.78 35.05 4.75
3428 3609 5.776716 AGGTGGATTATAATTCCAATGCCTG 59.223 40.000 14.45 0.00 35.05 4.85
3429 3610 5.473039 GTGGATTATAATTCCAATGCCTGC 58.527 41.667 14.45 0.00 35.05 4.85
3430 3611 4.527816 TGGATTATAATTCCAATGCCTGCC 59.472 41.667 11.82 1.07 0.00 4.85
3431 3612 4.527816 GGATTATAATTCCAATGCCTGCCA 59.472 41.667 0.00 0.00 0.00 4.92
3432 3613 5.011943 GGATTATAATTCCAATGCCTGCCAA 59.988 40.000 0.00 0.00 0.00 4.52
3433 3614 6.296030 GGATTATAATTCCAATGCCTGCCAAT 60.296 38.462 0.00 0.00 0.00 3.16
3434 3615 6.497624 TTATAATTCCAATGCCTGCCAATT 57.502 33.333 0.00 0.00 0.00 2.32
3435 3616 2.994186 ATTCCAATGCCTGCCAATTC 57.006 45.000 0.00 0.00 0.00 2.17
3436 3617 0.903942 TTCCAATGCCTGCCAATTCC 59.096 50.000 0.00 0.00 0.00 3.01
3437 3618 0.977108 TCCAATGCCTGCCAATTCCC 60.977 55.000 0.00 0.00 0.00 3.97
3438 3619 1.266160 CCAATGCCTGCCAATTCCCA 61.266 55.000 0.00 0.00 0.00 4.37
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.876275 TCATTTTCTTTTGGTTTCTCATGAAG 57.124 30.769 0.00 0.00 33.28 3.02
1 2 7.439056 GCTCATTTTCTTTTGGTTTCTCATGAA 59.561 33.333 0.00 0.00 0.00 2.57
2 3 6.925165 GCTCATTTTCTTTTGGTTTCTCATGA 59.075 34.615 0.00 0.00 0.00 3.07
3 4 6.129009 CGCTCATTTTCTTTTGGTTTCTCATG 60.129 38.462 0.00 0.00 0.00 3.07
4 5 5.922544 CGCTCATTTTCTTTTGGTTTCTCAT 59.077 36.000 0.00 0.00 0.00 2.90
5 6 5.163561 ACGCTCATTTTCTTTTGGTTTCTCA 60.164 36.000 0.00 0.00 0.00 3.27
6 7 5.281727 ACGCTCATTTTCTTTTGGTTTCTC 58.718 37.500 0.00 0.00 0.00 2.87
7 8 5.067805 AGACGCTCATTTTCTTTTGGTTTCT 59.932 36.000 0.00 0.00 0.00 2.52
8 9 5.281727 AGACGCTCATTTTCTTTTGGTTTC 58.718 37.500 0.00 0.00 0.00 2.78
9 10 5.262588 AGACGCTCATTTTCTTTTGGTTT 57.737 34.783 0.00 0.00 0.00 3.27
10 11 4.918810 AGACGCTCATTTTCTTTTGGTT 57.081 36.364 0.00 0.00 0.00 3.67
11 12 4.261614 GGAAGACGCTCATTTTCTTTTGGT 60.262 41.667 0.00 0.00 29.54 3.67
12 13 4.022849 AGGAAGACGCTCATTTTCTTTTGG 60.023 41.667 0.00 0.00 29.54 3.28
13 14 5.113502 AGGAAGACGCTCATTTTCTTTTG 57.886 39.130 0.00 0.00 29.54 2.44
14 15 5.774498 AAGGAAGACGCTCATTTTCTTTT 57.226 34.783 0.00 0.00 29.54 2.27
15 16 5.774498 AAAGGAAGACGCTCATTTTCTTT 57.226 34.783 0.00 0.00 29.54 2.52
16 17 5.774498 AAAAGGAAGACGCTCATTTTCTT 57.226 34.783 0.86 0.00 35.07 2.52
17 18 5.532779 AGAAAAAGGAAGACGCTCATTTTCT 59.467 36.000 13.67 13.67 38.10 2.52
18 19 5.763088 AGAAAAAGGAAGACGCTCATTTTC 58.237 37.500 5.84 8.92 38.10 2.29
19 20 5.532779 AGAGAAAAAGGAAGACGCTCATTTT 59.467 36.000 0.00 0.86 40.10 1.82
20 21 5.049129 CAGAGAAAAAGGAAGACGCTCATTT 60.049 40.000 0.00 0.00 30.98 2.32
21 22 4.453819 CAGAGAAAAAGGAAGACGCTCATT 59.546 41.667 0.00 0.00 0.00 2.57
22 23 3.999663 CAGAGAAAAAGGAAGACGCTCAT 59.000 43.478 0.00 0.00 0.00 2.90
23 24 3.393800 CAGAGAAAAAGGAAGACGCTCA 58.606 45.455 0.00 0.00 0.00 4.26
45 46 1.548132 CTTGGCGCGCAAAGGTTTTC 61.548 55.000 35.51 15.22 0.00 2.29
56 57 1.442017 GTAAAGTTGGCTTGGCGCG 60.442 57.895 0.00 0.00 40.44 6.86
76 77 1.683917 AGACGTGGTAGATGGAGATGC 59.316 52.381 0.00 0.00 0.00 3.91
90 91 3.664276 CGTGCCAAATTGAGTAAGACGTG 60.664 47.826 0.00 0.00 0.00 4.49
98 99 1.349688 TCCTACCGTGCCAAATTGAGT 59.650 47.619 0.00 0.00 0.00 3.41
103 104 3.366052 AAAGATCCTACCGTGCCAAAT 57.634 42.857 0.00 0.00 0.00 2.32
112 113 4.207891 TGACAGCAGAAAAGATCCTACC 57.792 45.455 0.00 0.00 0.00 3.18
185 186 0.105964 ACCAAGTGCGAAGTAGTGCA 59.894 50.000 0.00 0.00 39.13 4.57
186 187 1.194772 GAACCAAGTGCGAAGTAGTGC 59.805 52.381 0.00 0.00 0.00 4.40
187 188 2.731976 GAGAACCAAGTGCGAAGTAGTG 59.268 50.000 0.00 0.00 0.00 2.74
188 189 2.288886 GGAGAACCAAGTGCGAAGTAGT 60.289 50.000 0.00 0.00 35.97 2.73
189 190 2.338500 GGAGAACCAAGTGCGAAGTAG 58.662 52.381 0.00 0.00 35.97 2.57
190 191 1.001633 GGGAGAACCAAGTGCGAAGTA 59.998 52.381 0.00 0.00 39.85 2.24
191 192 0.250338 GGGAGAACCAAGTGCGAAGT 60.250 55.000 0.00 0.00 39.85 3.01
192 193 0.035458 AGGGAGAACCAAGTGCGAAG 59.965 55.000 0.00 0.00 43.89 3.79
193 194 0.250295 CAGGGAGAACCAAGTGCGAA 60.250 55.000 0.00 0.00 43.89 4.70
194 195 1.371183 CAGGGAGAACCAAGTGCGA 59.629 57.895 0.00 0.00 43.89 5.10
195 196 0.535102 AACAGGGAGAACCAAGTGCG 60.535 55.000 0.00 0.00 43.89 5.34
196 197 1.338020 CAAACAGGGAGAACCAAGTGC 59.662 52.381 0.00 0.00 43.89 4.40
197 198 1.338020 GCAAACAGGGAGAACCAAGTG 59.662 52.381 0.00 0.00 43.89 3.16
198 199 1.215423 AGCAAACAGGGAGAACCAAGT 59.785 47.619 0.00 0.00 43.89 3.16
199 200 1.986882 AGCAAACAGGGAGAACCAAG 58.013 50.000 0.00 0.00 43.89 3.61
200 201 2.452600 AAGCAAACAGGGAGAACCAA 57.547 45.000 0.00 0.00 43.89 3.67
201 202 2.452600 AAAGCAAACAGGGAGAACCA 57.547 45.000 0.00 0.00 43.89 3.67
202 203 2.959030 AGAAAAGCAAACAGGGAGAACC 59.041 45.455 0.00 0.00 40.67 3.62
203 204 4.655762 AAGAAAAGCAAACAGGGAGAAC 57.344 40.909 0.00 0.00 0.00 3.01
216 217 5.979517 ACAGTTGCAGTTCATAAAGAAAAGC 59.020 36.000 0.00 0.00 38.13 3.51
289 290 1.904287 AGCCGGAAGTTTGCATACAA 58.096 45.000 5.05 0.00 0.00 2.41
297 298 5.313712 TCAGAAAGAATAAGCCGGAAGTTT 58.686 37.500 5.05 0.00 0.00 2.66
358 360 5.410132 TGTGTTTATAGGTATGTGTGTGTGC 59.590 40.000 0.00 0.00 0.00 4.57
363 365 6.486248 GTGCATGTGTTTATAGGTATGTGTG 58.514 40.000 0.00 0.00 0.00 3.82
364 366 5.293324 CGTGCATGTGTTTATAGGTATGTGT 59.707 40.000 0.00 0.00 0.00 3.72
367 369 5.984233 ACGTGCATGTGTTTATAGGTATG 57.016 39.130 11.65 0.00 0.00 2.39
372 374 6.844696 AGGATTACGTGCATGTGTTTATAG 57.155 37.500 21.92 0.00 0.00 1.31
374 376 6.426937 GGATAGGATTACGTGCATGTGTTTAT 59.573 38.462 21.92 11.32 0.00 1.40
389 391 5.190528 GGAGATGCTCAATGGGATAGGATTA 59.809 44.000 0.00 0.00 31.08 1.75
401 403 1.210538 TCTGGCTGGAGATGCTCAAT 58.789 50.000 0.00 0.00 31.08 2.57
412 414 3.129287 GTGGTGAACAATTATCTGGCTGG 59.871 47.826 0.00 0.00 0.00 4.85
414 416 3.009723 CGTGGTGAACAATTATCTGGCT 58.990 45.455 0.00 0.00 0.00 4.75
415 417 2.097466 CCGTGGTGAACAATTATCTGGC 59.903 50.000 0.00 0.00 0.00 4.85
416 418 3.605634 TCCGTGGTGAACAATTATCTGG 58.394 45.455 0.00 0.00 0.00 3.86
417 419 5.621197 TTTCCGTGGTGAACAATTATCTG 57.379 39.130 0.00 0.00 0.00 2.90
418 420 6.834168 AATTTCCGTGGTGAACAATTATCT 57.166 33.333 0.00 0.00 0.00 1.98
419 421 6.866248 ACAAATTTCCGTGGTGAACAATTATC 59.134 34.615 0.00 0.00 0.00 1.75
420 422 6.754193 ACAAATTTCCGTGGTGAACAATTAT 58.246 32.000 0.00 0.00 0.00 1.28
434 449 6.978343 TGTAGGATGAAGTACAAATTTCCG 57.022 37.500 0.00 0.00 31.43 4.30
441 456 8.362464 AGACTACATTGTAGGATGAAGTACAA 57.638 34.615 24.01 0.00 41.98 2.41
443 458 9.088512 CAAAGACTACATTGTAGGATGAAGTAC 57.911 37.037 24.01 7.20 0.00 2.73
478 564 5.700832 TGTGTAATGCTCTTAGTCCAACTTG 59.299 40.000 0.00 0.00 0.00 3.16
494 580 8.495949 GGTGATCCGATTAATTAGTGTGTAATG 58.504 37.037 0.00 0.00 0.00 1.90
505 591 4.949856 GGCCATATGGTGATCCGATTAATT 59.050 41.667 22.79 0.00 37.57 1.40
511 597 2.179427 CTAGGCCATATGGTGATCCGA 58.821 52.381 22.79 10.59 37.57 4.55
512 598 1.208052 CCTAGGCCATATGGTGATCCG 59.792 57.143 22.79 7.17 37.57 4.18
519 605 4.330250 CAATCTGAACCTAGGCCATATGG 58.670 47.826 18.07 18.07 38.53 2.74
542 628 7.862873 GCTTCTAGGGAATGCATGTAATTAAAC 59.137 37.037 0.00 0.00 0.00 2.01
552 638 5.455899 CCTTCTTAGCTTCTAGGGAATGCAT 60.456 44.000 0.00 0.00 32.26 3.96
595 681 2.038269 GGGTTTTCGGCGCTCATGA 61.038 57.895 7.64 0.00 0.00 3.07
676 763 6.721571 TTTAGTCAGAAAAGTAAGCGATGG 57.278 37.500 0.00 0.00 0.00 3.51
752 847 4.080413 TGAAGTCATGTCCTATGATGGCAA 60.080 41.667 0.00 0.00 0.00 4.52
803 936 2.356069 GGCCTTTTTAGCTTCGATGGAG 59.644 50.000 0.00 0.00 0.00 3.86
810 943 6.327279 TGACTTTAAGGCCTTTTTAGCTTC 57.673 37.500 26.08 12.62 0.00 3.86
860 997 2.919494 CGGTTTTGAGTGCAGGGGC 61.919 63.158 0.00 0.00 41.68 5.80
915 1058 1.188863 CAGAAAAGGGGGCAATGGAG 58.811 55.000 0.00 0.00 0.00 3.86
1184 1333 3.781770 CTCTCCGATGTGCTCCGGC 62.782 68.421 0.00 0.00 44.96 6.13
1192 1341 1.047596 ATCTGCTGCCTCTCCGATGT 61.048 55.000 0.00 0.00 0.00 3.06
1194 1343 0.758310 TGATCTGCTGCCTCTCCGAT 60.758 55.000 0.00 0.00 0.00 4.18
1340 1500 2.731976 GACTGAAAGCAGAGTACGTTGG 59.268 50.000 0.00 0.00 45.17 3.77
1341 1501 3.643763 AGACTGAAAGCAGAGTACGTTG 58.356 45.455 0.00 0.00 45.17 4.10
1342 1502 3.318275 TGAGACTGAAAGCAGAGTACGTT 59.682 43.478 0.00 0.00 45.17 3.99
1343 1503 2.885266 TGAGACTGAAAGCAGAGTACGT 59.115 45.455 0.00 0.00 45.17 3.57
1392 1552 0.826715 GCATCCACAGGTAGAGCAGA 59.173 55.000 0.00 0.00 0.00 4.26
1657 1822 4.803098 TTGCTAAGTAGAGGTGGAAGAC 57.197 45.455 0.00 0.00 0.00 3.01
1664 1829 4.354662 AGCTACCTTTGCTAAGTAGAGGT 58.645 43.478 15.82 5.75 42.93 3.85
1665 1830 4.402793 TGAGCTACCTTTGCTAAGTAGAGG 59.597 45.833 15.82 2.61 41.30 3.69
1720 1896 0.621571 TGGGAGGTTGCCAGAGCTAT 60.622 55.000 0.00 0.00 40.80 2.97
1846 2022 2.094494 TCTTGCTGAACATCTCGAGGAC 60.094 50.000 13.56 0.82 0.00 3.85
1983 2159 5.350914 CCAAGAGATTCATCAGTGTTCTGTC 59.649 44.000 0.00 0.00 41.91 3.51
1995 2174 5.205821 TGATTGATTGGCCAAGAGATTCAT 58.794 37.500 24.94 11.45 0.00 2.57
2000 2179 4.239428 TCATGATTGATTGGCCAAGAGA 57.761 40.909 24.94 11.90 0.00 3.10
2009 2188 7.359181 GCATGCATACACATTCATGATTGATTG 60.359 37.037 21.32 13.45 37.83 2.67
2010 2189 6.645003 GCATGCATACACATTCATGATTGATT 59.355 34.615 21.32 11.20 37.83 2.57
2011 2190 6.156519 GCATGCATACACATTCATGATTGAT 58.843 36.000 21.32 12.43 37.83 2.57
2012 2191 5.067936 TGCATGCATACACATTCATGATTGA 59.932 36.000 18.46 2.84 37.83 2.57
2031 2210 1.817357 TCTTCTTCAGTGCCTGCATG 58.183 50.000 0.00 0.00 0.00 4.06
2059 2238 5.465051 TCTCAGAGACTCTTCAAAATCACG 58.535 41.667 0.98 0.00 0.00 4.35
2142 2321 1.694150 TCAAGTACAGGACTGCTTGCT 59.306 47.619 12.14 0.00 38.87 3.91
2190 2370 3.823304 GGCCAAGAACAGAAGAATGAGTT 59.177 43.478 0.00 0.00 0.00 3.01
2290 2470 2.062890 CTCGTTTATGCCGACGTCGC 62.063 60.000 31.73 25.31 40.03 5.19
2324 2504 6.661304 AGGTTCTTTCCGAAGTTACTCTTA 57.339 37.500 0.00 0.00 36.40 2.10
2527 2707 7.474398 ACAGATGAATGATAACATGTTCTCG 57.526 36.000 15.85 2.43 36.79 4.04
2609 2789 7.172019 TGCAGCATACATACATTCTATGTTCTG 59.828 37.037 0.00 5.84 41.63 3.02
2704 2884 3.369147 CGGTGTTTGCATTTGTGTTTCAA 59.631 39.130 0.00 0.00 0.00 2.69
2767 2947 3.446799 GACATGAGAGATGTCAGTGAGC 58.553 50.000 0.00 0.00 45.61 4.26
2822 3002 6.646267 TGATACCAAAAGGCGTAACTATTCT 58.354 36.000 0.00 0.00 0.00 2.40
2867 3047 2.839486 AAGTCAATGCACTTCTCCGA 57.161 45.000 0.00 0.00 30.25 4.55
3006 3187 6.260714 GGCATACCCATCATTTTTCAATTTCC 59.739 38.462 0.00 0.00 0.00 3.13
3029 3210 7.013655 AGGTGAAGTACATGAAATTATGATGGC 59.986 37.037 0.00 0.00 0.00 4.40
3275 3456 7.156000 TCTCTTGTATCCGTTTTGATGTACAA 58.844 34.615 0.00 0.00 36.65 2.41
3297 3478 5.471456 TCCATTTTCTGCTTTCTTGACTCTC 59.529 40.000 0.00 0.00 0.00 3.20
3298 3479 5.380043 TCCATTTTCTGCTTTCTTGACTCT 58.620 37.500 0.00 0.00 0.00 3.24
3310 3491 2.087646 GGGACAGACTCCATTTTCTGC 58.912 52.381 0.00 0.00 42.67 4.26
3317 3498 4.664688 AATTTCTTGGGACAGACTCCAT 57.335 40.909 0.00 0.00 41.63 3.41
3325 3506 7.889873 TTTTCTCTTGTAATTTCTTGGGACA 57.110 32.000 0.00 0.00 0.00 4.02
3328 3509 9.933723 ATTCATTTTCTCTTGTAATTTCTTGGG 57.066 29.630 0.00 0.00 0.00 4.12
3351 3532 9.469807 AGTTCGATAGTTCTTCACATGATATTC 57.530 33.333 0.00 0.00 37.40 1.75
3357 3538 8.467402 ACTTTAGTTCGATAGTTCTTCACATG 57.533 34.615 0.00 0.00 37.40 3.21
3358 3539 8.926710 CAACTTTAGTTCGATAGTTCTTCACAT 58.073 33.333 0.00 0.00 35.83 3.21
3362 3543 7.347508 TGCAACTTTAGTTCGATAGTTCTTC 57.652 36.000 0.00 0.00 35.83 2.87
3365 3546 5.348997 AGCTGCAACTTTAGTTCGATAGTTC 59.651 40.000 1.02 0.00 35.83 3.01
3367 3548 4.822026 AGCTGCAACTTTAGTTCGATAGT 58.178 39.130 1.02 0.00 35.83 2.12
3368 3549 6.887376 TTAGCTGCAACTTTAGTTCGATAG 57.113 37.500 1.02 0.00 35.83 2.08
3369 3550 8.410912 TCTATTAGCTGCAACTTTAGTTCGATA 58.589 33.333 1.02 0.00 35.83 2.92
3370 3551 7.265673 TCTATTAGCTGCAACTTTAGTTCGAT 58.734 34.615 1.02 0.00 35.83 3.59
3371 3552 6.627243 TCTATTAGCTGCAACTTTAGTTCGA 58.373 36.000 1.02 0.00 35.83 3.71
3372 3553 6.887376 TCTATTAGCTGCAACTTTAGTTCG 57.113 37.500 1.02 0.00 35.83 3.95
3373 3554 8.029642 TGTTCTATTAGCTGCAACTTTAGTTC 57.970 34.615 1.02 0.00 35.83 3.01
3374 3555 7.661847 ACTGTTCTATTAGCTGCAACTTTAGTT 59.338 33.333 1.02 0.00 39.12 2.24
3375 3556 7.162082 ACTGTTCTATTAGCTGCAACTTTAGT 58.838 34.615 1.02 0.00 0.00 2.24
3376 3557 7.602517 ACTGTTCTATTAGCTGCAACTTTAG 57.397 36.000 1.02 0.00 0.00 1.85
3377 3558 8.528643 TCTACTGTTCTATTAGCTGCAACTTTA 58.471 33.333 1.02 0.00 0.00 1.85
3378 3559 7.386851 TCTACTGTTCTATTAGCTGCAACTTT 58.613 34.615 1.02 0.00 0.00 2.66
3379 3560 6.936279 TCTACTGTTCTATTAGCTGCAACTT 58.064 36.000 1.02 0.00 0.00 2.66
3380 3561 6.531503 TCTACTGTTCTATTAGCTGCAACT 57.468 37.500 1.02 0.00 0.00 3.16
3381 3562 6.256757 CCTTCTACTGTTCTATTAGCTGCAAC 59.743 42.308 1.02 0.00 0.00 4.17
3382 3563 6.070767 ACCTTCTACTGTTCTATTAGCTGCAA 60.071 38.462 1.02 0.00 0.00 4.08
3383 3564 5.422331 ACCTTCTACTGTTCTATTAGCTGCA 59.578 40.000 1.02 0.00 0.00 4.41
3384 3565 5.751028 CACCTTCTACTGTTCTATTAGCTGC 59.249 44.000 0.00 0.00 0.00 5.25
3385 3566 6.096987 TCCACCTTCTACTGTTCTATTAGCTG 59.903 42.308 0.00 0.00 0.00 4.24
3386 3567 6.195700 TCCACCTTCTACTGTTCTATTAGCT 58.804 40.000 0.00 0.00 0.00 3.32
3387 3568 6.466885 TCCACCTTCTACTGTTCTATTAGC 57.533 41.667 0.00 0.00 0.00 3.09
3394 3575 9.274206 GGAATTATAATCCACCTTCTACTGTTC 57.726 37.037 0.00 0.00 36.92 3.18
3395 3576 8.778059 TGGAATTATAATCCACCTTCTACTGTT 58.222 33.333 10.72 0.00 41.98 3.16
3396 3577 8.331931 TGGAATTATAATCCACCTTCTACTGT 57.668 34.615 10.72 0.00 41.98 3.55
3397 3578 9.799106 ATTGGAATTATAATCCACCTTCTACTG 57.201 33.333 13.15 0.00 46.37 2.74
3398 3579 9.799106 CATTGGAATTATAATCCACCTTCTACT 57.201 33.333 13.15 0.00 46.37 2.57
3399 3580 8.515414 GCATTGGAATTATAATCCACCTTCTAC 58.485 37.037 13.15 0.00 46.37 2.59
3400 3581 7.669722 GGCATTGGAATTATAATCCACCTTCTA 59.330 37.037 13.15 0.00 46.37 2.10
3401 3582 6.494835 GGCATTGGAATTATAATCCACCTTCT 59.505 38.462 13.15 0.00 46.37 2.85
3402 3583 6.494835 AGGCATTGGAATTATAATCCACCTTC 59.505 38.462 13.15 2.17 46.37 3.46
3403 3584 6.268387 CAGGCATTGGAATTATAATCCACCTT 59.732 38.462 13.15 3.47 46.37 3.50
3404 3585 5.776716 CAGGCATTGGAATTATAATCCACCT 59.223 40.000 13.15 13.20 46.37 4.00
3405 3586 5.567423 GCAGGCATTGGAATTATAATCCACC 60.567 44.000 13.15 11.81 46.37 4.61
3406 3587 5.473039 GCAGGCATTGGAATTATAATCCAC 58.527 41.667 13.15 5.77 46.37 4.02
3407 3588 4.527816 GGCAGGCATTGGAATTATAATCCA 59.472 41.667 10.72 10.72 45.09 3.41
3408 3589 4.527816 TGGCAGGCATTGGAATTATAATCC 59.472 41.667 0.00 3.14 37.48 3.01
3409 3590 5.726980 TGGCAGGCATTGGAATTATAATC 57.273 39.130 0.00 0.00 0.00 1.75
3410 3591 6.691255 ATTGGCAGGCATTGGAATTATAAT 57.309 33.333 0.00 0.00 0.00 1.28
3411 3592 6.464180 GGAATTGGCAGGCATTGGAATTATAA 60.464 38.462 0.00 0.00 0.00 0.98
3412 3593 5.011943 GGAATTGGCAGGCATTGGAATTATA 59.988 40.000 0.00 0.00 0.00 0.98
3413 3594 4.202388 GGAATTGGCAGGCATTGGAATTAT 60.202 41.667 0.00 0.00 0.00 1.28
3414 3595 3.134442 GGAATTGGCAGGCATTGGAATTA 59.866 43.478 0.00 0.00 0.00 1.40
3415 3596 2.092807 GGAATTGGCAGGCATTGGAATT 60.093 45.455 0.00 0.00 0.00 2.17
3416 3597 1.487558 GGAATTGGCAGGCATTGGAAT 59.512 47.619 0.00 0.00 0.00 3.01
3417 3598 0.903942 GGAATTGGCAGGCATTGGAA 59.096 50.000 0.00 0.00 0.00 3.53
3418 3599 0.977108 GGGAATTGGCAGGCATTGGA 60.977 55.000 0.00 0.00 0.00 3.53
3419 3600 1.266160 TGGGAATTGGCAGGCATTGG 61.266 55.000 0.00 0.00 0.00 3.16
3420 3601 2.288834 TGGGAATTGGCAGGCATTG 58.711 52.632 0.00 0.00 0.00 2.82
3421 3602 4.892461 TGGGAATTGGCAGGCATT 57.108 50.000 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.