Multiple sequence alignment - TraesCS5B01G498900

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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 TraesCS5B01G498900 chr5B 100.000 2549 0 0 1 2549 665718477 665721025 0.000000e+00 4708.0
1 TraesCS5B01G498900 chr5B 97.440 1992 43 5 560 2549 641128787 641126802 0.000000e+00 3389.0
2 TraesCS5B01G498900 chr6A 97.732 1984 38 5 569 2549 617222871 617220892 0.000000e+00 3408.0
3 TraesCS5B01G498900 chr6A 97.589 1991 41 6 562 2549 533982331 533980345 0.000000e+00 3404.0
4 TraesCS5B01G498900 chr6A 97.581 1984 43 4 568 2549 616131292 616133272 0.000000e+00 3393.0
5 TraesCS5B01G498900 chr2B 97.540 1992 44 4 559 2549 776222951 776224938 0.000000e+00 3402.0
6 TraesCS5B01G498900 chr2B 97.533 1986 45 3 565 2549 781094235 781096217 0.000000e+00 3393.0
7 TraesCS5B01G498900 chr4B 97.583 1986 42 5 566 2549 368430372 368428391 0.000000e+00 3397.0
8 TraesCS5B01G498900 chr6B 97.629 1982 42 4 570 2549 585915586 585917564 0.000000e+00 3395.0
9 TraesCS5B01G498900 chr4A 97.629 1982 41 5 571 2549 36562913 36564891 0.000000e+00 3395.0
10 TraesCS5B01G498900 chr5D 86.716 542 59 8 23 558 528695886 528696420 7.850000e-165 590.0
11 TraesCS5B01G498900 chr7D 85.629 167 23 1 254 419 6392311 6392145 9.370000e-40 174.0
12 TraesCS5B01G498900 chr3D 81.579 190 31 3 231 419 415981524 415981338 1.220000e-33 154.0
13 TraesCS5B01G498900 chr5A 85.859 99 11 2 254 350 597837085 597836988 4.490000e-18 102.0
14 TraesCS5B01G498900 chr3B 81.553 103 14 4 254 353 542588083 542587983 2.100000e-11 80.5


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 TraesCS5B01G498900 chr5B 665718477 665721025 2548 False 4708 4708 100.000 1 2549 1 chr5B.!!$F1 2548
1 TraesCS5B01G498900 chr5B 641126802 641128787 1985 True 3389 3389 97.440 560 2549 1 chr5B.!!$R1 1989
2 TraesCS5B01G498900 chr6A 617220892 617222871 1979 True 3408 3408 97.732 569 2549 1 chr6A.!!$R2 1980
3 TraesCS5B01G498900 chr6A 533980345 533982331 1986 True 3404 3404 97.589 562 2549 1 chr6A.!!$R1 1987
4 TraesCS5B01G498900 chr6A 616131292 616133272 1980 False 3393 3393 97.581 568 2549 1 chr6A.!!$F1 1981
5 TraesCS5B01G498900 chr2B 776222951 776224938 1987 False 3402 3402 97.540 559 2549 1 chr2B.!!$F1 1990
6 TraesCS5B01G498900 chr2B 781094235 781096217 1982 False 3393 3393 97.533 565 2549 1 chr2B.!!$F2 1984
7 TraesCS5B01G498900 chr4B 368428391 368430372 1981 True 3397 3397 97.583 566 2549 1 chr4B.!!$R1 1983
8 TraesCS5B01G498900 chr6B 585915586 585917564 1978 False 3395 3395 97.629 570 2549 1 chr6B.!!$F1 1979
9 TraesCS5B01G498900 chr4A 36562913 36564891 1978 False 3395 3395 97.629 571 2549 1 chr4A.!!$F1 1978
10 TraesCS5B01G498900 chr5D 528695886 528696420 534 False 590 590 86.716 23 558 1 chr5D.!!$F1 535

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
71 72 0.035439 AGGGTTTGTACATGGAGGCG 60.035 55.0 0.00 0.0 0.00 5.52 F
200 201 0.036952 AGTGATGCTTCTGGTCACGG 60.037 55.0 0.88 0.0 45.17 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1387 1389 0.529833 GCTAGCTCTCTGTCAGTGCA 59.470 55.000 7.7 0.0 43.07 4.57 R
2152 2172 3.092511 AGTCCCCAGCCGCATCAT 61.093 61.111 0.0 0.0 0.00 2.45 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
17 18 4.649705 TGAAGGGGACGGCAGGGA 62.650 66.667 0.00 0.00 0.00 4.20
18 19 3.327404 GAAGGGGACGGCAGGGAA 61.327 66.667 0.00 0.00 0.00 3.97
19 20 3.623703 GAAGGGGACGGCAGGGAAC 62.624 68.421 0.00 0.00 0.00 3.62
20 21 4.658786 AGGGGACGGCAGGGAACT 62.659 66.667 0.00 0.00 46.44 3.01
21 22 3.647771 GGGGACGGCAGGGAACTT 61.648 66.667 0.00 0.00 40.21 2.66
27 28 1.966451 CGGCAGGGAACTTGTGTCC 60.966 63.158 0.00 0.00 40.21 4.02
28 29 1.603739 GGCAGGGAACTTGTGTCCC 60.604 63.158 0.92 0.92 43.88 4.46
33 34 2.258726 GGAACTTGTGTCCCGTGGC 61.259 63.158 0.00 0.00 0.00 5.01
71 72 0.035439 AGGGTTTGTACATGGAGGCG 60.035 55.000 0.00 0.00 0.00 5.52
73 74 0.802494 GGTTTGTACATGGAGGCGTG 59.198 55.000 0.00 0.00 0.00 5.34
84 85 1.964223 TGGAGGCGTGATATCTTCCTC 59.036 52.381 20.60 20.60 41.87 3.71
94 95 0.395311 TATCTTCCTCCGGCGACTGT 60.395 55.000 9.30 0.00 0.00 3.55
101 102 2.754658 CCGGCGACTGTACCTCCT 60.755 66.667 9.30 0.00 0.00 3.69
103 104 2.044555 CGGCGACTGTACCTCCTGA 61.045 63.158 0.00 0.00 0.00 3.86
104 105 1.384989 CGGCGACTGTACCTCCTGAT 61.385 60.000 0.00 0.00 0.00 2.90
106 107 0.103208 GCGACTGTACCTCCTGATGG 59.897 60.000 0.00 0.00 0.00 3.51
108 109 0.103208 GACTGTACCTCCTGATGGCG 59.897 60.000 0.00 0.00 0.00 5.69
133 134 0.950555 GCGCTCCAGTGACAACATGA 60.951 55.000 0.00 0.00 0.00 3.07
137 138 2.693069 CTCCAGTGACAACATGAGGAC 58.307 52.381 0.00 0.00 0.00 3.85
140 141 2.354103 CCAGTGACAACATGAGGACGAT 60.354 50.000 0.00 0.00 0.00 3.73
141 142 2.669924 CAGTGACAACATGAGGACGATG 59.330 50.000 0.00 0.00 0.00 3.84
149 150 2.828520 ACATGAGGACGATGAACTCAGT 59.171 45.455 0.00 0.00 43.67 3.41
151 152 3.303881 TGAGGACGATGAACTCAGTTG 57.696 47.619 0.00 0.00 36.41 3.16
155 156 1.002087 GACGATGAACTCAGTTGGGGT 59.998 52.381 0.00 0.00 0.00 4.95
158 159 2.154462 GATGAACTCAGTTGGGGTGTG 58.846 52.381 0.00 0.00 0.00 3.82
173 174 0.457853 GTGTGATCTACGGCGCAAGA 60.458 55.000 10.83 11.27 43.02 3.02
183 184 4.021925 GCGCAAGACCCCCAGAGT 62.022 66.667 0.30 0.00 43.02 3.24
188 189 0.393537 CAAGACCCCCAGAGTGATGC 60.394 60.000 0.00 0.00 0.00 3.91
192 193 0.548682 ACCCCCAGAGTGATGCTTCT 60.549 55.000 0.88 0.00 0.00 2.85
200 201 0.036952 AGTGATGCTTCTGGTCACGG 60.037 55.000 0.88 0.00 45.17 4.94
229 230 4.115199 GCGGCCCCTCTGTTGGAT 62.115 66.667 0.00 0.00 0.00 3.41
277 278 1.145531 TCTTCCGTATGGATCCGGGTA 59.854 52.381 7.39 0.00 45.91 3.69
278 279 1.965643 CTTCCGTATGGATCCGGGTAA 59.034 52.381 7.39 2.48 45.91 2.85
279 280 2.314071 TCCGTATGGATCCGGGTAAT 57.686 50.000 7.39 0.00 44.32 1.89
290 292 0.466189 CCGGGTAATGAGCTTGCCAT 60.466 55.000 0.00 0.00 41.13 4.40
296 298 1.386533 AATGAGCTTGCCATTCCTCG 58.613 50.000 0.00 0.00 28.89 4.63
298 300 0.543277 TGAGCTTGCCATTCCTCGAT 59.457 50.000 0.00 0.00 0.00 3.59
301 303 1.645455 CTTGCCATTCCTCGATGCG 59.355 57.895 0.00 0.00 0.00 4.73
329 331 1.849039 CTGGAGGTGGGGATTCAGATT 59.151 52.381 0.00 0.00 0.00 2.40
357 359 1.144057 CCCTAGCCGGCACTAGTTG 59.856 63.158 31.54 11.60 38.39 3.16
399 401 4.500265 GGCACTGCCTTTTCTCCA 57.500 55.556 13.28 0.00 46.69 3.86
400 402 2.967270 GGCACTGCCTTTTCTCCAT 58.033 52.632 13.28 0.00 46.69 3.41
401 403 0.529378 GGCACTGCCTTTTCTCCATG 59.471 55.000 13.28 0.00 46.69 3.66
402 404 0.529378 GCACTGCCTTTTCTCCATGG 59.471 55.000 4.97 4.97 0.00 3.66
403 405 1.887956 GCACTGCCTTTTCTCCATGGA 60.888 52.381 15.27 15.27 0.00 3.41
404 406 2.089980 CACTGCCTTTTCTCCATGGAG 58.910 52.381 32.60 32.60 43.21 3.86
414 416 2.456577 TCTCCATGGAGATGTTCGTCA 58.543 47.619 35.92 14.47 45.26 4.35
415 417 2.831526 TCTCCATGGAGATGTTCGTCAA 59.168 45.455 35.92 13.74 45.26 3.18
416 418 3.260632 TCTCCATGGAGATGTTCGTCAAA 59.739 43.478 35.92 13.23 45.26 2.69
417 419 4.080919 TCTCCATGGAGATGTTCGTCAAAT 60.081 41.667 35.92 0.00 45.26 2.32
418 420 4.191544 TCCATGGAGATGTTCGTCAAATC 58.808 43.478 11.44 0.00 0.00 2.17
419 421 4.080919 TCCATGGAGATGTTCGTCAAATCT 60.081 41.667 11.44 0.00 33.36 2.40
420 422 4.637534 CCATGGAGATGTTCGTCAAATCTT 59.362 41.667 5.56 0.00 30.83 2.40
421 423 5.124457 CCATGGAGATGTTCGTCAAATCTTT 59.876 40.000 5.56 0.00 30.83 2.52
422 424 6.349611 CCATGGAGATGTTCGTCAAATCTTTT 60.350 38.462 5.56 0.00 30.83 2.27
423 425 6.241207 TGGAGATGTTCGTCAAATCTTTTC 57.759 37.500 0.00 0.00 30.83 2.29
424 426 5.762711 TGGAGATGTTCGTCAAATCTTTTCA 59.237 36.000 0.00 0.00 30.83 2.69
425 427 6.430925 TGGAGATGTTCGTCAAATCTTTTCAT 59.569 34.615 0.00 0.00 30.83 2.57
426 428 7.040478 TGGAGATGTTCGTCAAATCTTTTCATT 60.040 33.333 0.00 0.00 30.83 2.57
427 429 7.809806 GGAGATGTTCGTCAAATCTTTTCATTT 59.190 33.333 0.00 0.00 30.83 2.32
428 430 9.185192 GAGATGTTCGTCAAATCTTTTCATTTT 57.815 29.630 0.00 0.00 30.83 1.82
429 431 9.533253 AGATGTTCGTCAAATCTTTTCATTTTT 57.467 25.926 0.00 0.00 0.00 1.94
430 432 9.783425 GATGTTCGTCAAATCTTTTCATTTTTC 57.217 29.630 0.00 0.00 0.00 2.29
431 433 8.694975 TGTTCGTCAAATCTTTTCATTTTTCA 57.305 26.923 0.00 0.00 0.00 2.69
432 434 9.311916 TGTTCGTCAAATCTTTTCATTTTTCAT 57.688 25.926 0.00 0.00 0.00 2.57
433 435 9.571804 GTTCGTCAAATCTTTTCATTTTTCATG 57.428 29.630 0.00 0.00 0.00 3.07
434 436 8.870160 TCGTCAAATCTTTTCATTTTTCATGT 57.130 26.923 0.00 0.00 0.00 3.21
435 437 9.311916 TCGTCAAATCTTTTCATTTTTCATGTT 57.688 25.926 0.00 0.00 0.00 2.71
436 438 9.919348 CGTCAAATCTTTTCATTTTTCATGTTT 57.081 25.926 0.00 0.00 0.00 2.83
462 464 9.581099 TTTTCTTTGTGTTTGATCTAGTTTTCC 57.419 29.630 0.00 0.00 0.00 3.13
463 465 8.519799 TTCTTTGTGTTTGATCTAGTTTTCCT 57.480 30.769 0.00 0.00 0.00 3.36
464 466 8.154649 TCTTTGTGTTTGATCTAGTTTTCCTC 57.845 34.615 0.00 0.00 0.00 3.71
465 467 6.877611 TTGTGTTTGATCTAGTTTTCCTCC 57.122 37.500 0.00 0.00 0.00 4.30
466 468 6.187727 TGTGTTTGATCTAGTTTTCCTCCT 57.812 37.500 0.00 0.00 0.00 3.69
467 469 6.601332 TGTGTTTGATCTAGTTTTCCTCCTT 58.399 36.000 0.00 0.00 0.00 3.36
468 470 7.741785 TGTGTTTGATCTAGTTTTCCTCCTTA 58.258 34.615 0.00 0.00 0.00 2.69
469 471 8.383175 TGTGTTTGATCTAGTTTTCCTCCTTAT 58.617 33.333 0.00 0.00 0.00 1.73
470 472 9.232473 GTGTTTGATCTAGTTTTCCTCCTTATT 57.768 33.333 0.00 0.00 0.00 1.40
471 473 9.807921 TGTTTGATCTAGTTTTCCTCCTTATTT 57.192 29.630 0.00 0.00 0.00 1.40
478 480 9.297037 TCTAGTTTTCCTCCTTATTTTTCTTGG 57.703 33.333 0.00 0.00 0.00 3.61
479 481 7.914427 AGTTTTCCTCCTTATTTTTCTTGGT 57.086 32.000 0.00 0.00 0.00 3.67
480 482 8.319057 AGTTTTCCTCCTTATTTTTCTTGGTT 57.681 30.769 0.00 0.00 0.00 3.67
481 483 8.768397 AGTTTTCCTCCTTATTTTTCTTGGTTT 58.232 29.630 0.00 0.00 0.00 3.27
508 510 6.877611 TTTTATTGGTCTTCCACTTCTGTC 57.122 37.500 0.00 0.00 44.22 3.51
509 511 5.560722 TTATTGGTCTTCCACTTCTGTCA 57.439 39.130 0.00 0.00 44.22 3.58
510 512 3.475566 TTGGTCTTCCACTTCTGTCAG 57.524 47.619 0.00 0.00 44.22 3.51
511 513 2.398588 TGGTCTTCCACTTCTGTCAGT 58.601 47.619 0.00 0.00 39.03 3.41
512 514 2.771943 TGGTCTTCCACTTCTGTCAGTT 59.228 45.455 0.00 0.00 39.03 3.16
513 515 3.199946 TGGTCTTCCACTTCTGTCAGTTT 59.800 43.478 0.00 0.00 39.03 2.66
514 516 3.810386 GGTCTTCCACTTCTGTCAGTTTC 59.190 47.826 0.00 0.00 0.00 2.78
515 517 3.810386 GTCTTCCACTTCTGTCAGTTTCC 59.190 47.826 0.00 0.00 0.00 3.13
516 518 3.711704 TCTTCCACTTCTGTCAGTTTCCT 59.288 43.478 0.00 0.00 0.00 3.36
517 519 4.164221 TCTTCCACTTCTGTCAGTTTCCTT 59.836 41.667 0.00 0.00 0.00 3.36
518 520 4.503714 TCCACTTCTGTCAGTTTCCTTT 57.496 40.909 0.00 0.00 0.00 3.11
519 521 4.855340 TCCACTTCTGTCAGTTTCCTTTT 58.145 39.130 0.00 0.00 0.00 2.27
520 522 5.996644 TCCACTTCTGTCAGTTTCCTTTTA 58.003 37.500 0.00 0.00 0.00 1.52
521 523 5.820947 TCCACTTCTGTCAGTTTCCTTTTAC 59.179 40.000 0.00 0.00 0.00 2.01
522 524 5.008712 CCACTTCTGTCAGTTTCCTTTTACC 59.991 44.000 0.00 0.00 0.00 2.85
523 525 5.823045 CACTTCTGTCAGTTTCCTTTTACCT 59.177 40.000 0.00 0.00 0.00 3.08
524 526 6.318900 CACTTCTGTCAGTTTCCTTTTACCTT 59.681 38.462 0.00 0.00 0.00 3.50
525 527 6.318900 ACTTCTGTCAGTTTCCTTTTACCTTG 59.681 38.462 0.00 0.00 0.00 3.61
526 528 5.751586 TCTGTCAGTTTCCTTTTACCTTGT 58.248 37.500 0.00 0.00 0.00 3.16
527 529 6.184789 TCTGTCAGTTTCCTTTTACCTTGTT 58.815 36.000 0.00 0.00 0.00 2.83
528 530 6.317893 TCTGTCAGTTTCCTTTTACCTTGTTC 59.682 38.462 0.00 0.00 0.00 3.18
529 531 5.358725 TGTCAGTTTCCTTTTACCTTGTTCC 59.641 40.000 0.00 0.00 0.00 3.62
530 532 5.593095 GTCAGTTTCCTTTTACCTTGTTCCT 59.407 40.000 0.00 0.00 0.00 3.36
531 533 6.096423 GTCAGTTTCCTTTTACCTTGTTCCTT 59.904 38.462 0.00 0.00 0.00 3.36
532 534 6.666113 TCAGTTTCCTTTTACCTTGTTCCTTT 59.334 34.615 0.00 0.00 0.00 3.11
533 535 7.179516 TCAGTTTCCTTTTACCTTGTTCCTTTT 59.820 33.333 0.00 0.00 0.00 2.27
534 536 7.822334 CAGTTTCCTTTTACCTTGTTCCTTTTT 59.178 33.333 0.00 0.00 0.00 1.94
535 537 8.038944 AGTTTCCTTTTACCTTGTTCCTTTTTC 58.961 33.333 0.00 0.00 0.00 2.29
536 538 7.727578 TTCCTTTTACCTTGTTCCTTTTTCT 57.272 32.000 0.00 0.00 0.00 2.52
537 539 7.727578 TCCTTTTACCTTGTTCCTTTTTCTT 57.272 32.000 0.00 0.00 0.00 2.52
538 540 8.141298 TCCTTTTACCTTGTTCCTTTTTCTTT 57.859 30.769 0.00 0.00 0.00 2.52
539 541 8.598916 TCCTTTTACCTTGTTCCTTTTTCTTTT 58.401 29.630 0.00 0.00 0.00 2.27
540 542 8.879759 CCTTTTACCTTGTTCCTTTTTCTTTTC 58.120 33.333 0.00 0.00 0.00 2.29
541 543 8.780846 TTTTACCTTGTTCCTTTTTCTTTTCC 57.219 30.769 0.00 0.00 0.00 3.13
542 544 7.483580 TTACCTTGTTCCTTTTTCTTTTCCA 57.516 32.000 0.00 0.00 0.00 3.53
543 545 6.560003 ACCTTGTTCCTTTTTCTTTTCCAT 57.440 33.333 0.00 0.00 0.00 3.41
544 546 6.957631 ACCTTGTTCCTTTTTCTTTTCCATT 58.042 32.000 0.00 0.00 0.00 3.16
545 547 7.402054 ACCTTGTTCCTTTTTCTTTTCCATTT 58.598 30.769 0.00 0.00 0.00 2.32
546 548 7.888021 ACCTTGTTCCTTTTTCTTTTCCATTTT 59.112 29.630 0.00 0.00 0.00 1.82
547 549 8.739039 CCTTGTTCCTTTTTCTTTTCCATTTTT 58.261 29.630 0.00 0.00 0.00 1.94
610 612 1.276138 CTCAGTGGTGTCCATGTGCTA 59.724 52.381 0.00 0.00 35.28 3.49
734 736 2.987125 CCCTTACAGGTGGGACCG 59.013 66.667 0.00 0.00 46.15 4.79
766 768 6.267471 AGAAACAGCCAATTTTATTCAGACCA 59.733 34.615 0.00 0.00 0.00 4.02
815 817 0.897863 AGAGCCGTTGAGCAGAGAGT 60.898 55.000 0.00 0.00 34.23 3.24
907 909 1.165907 CGGCGAGAGAGAGAGAGCAT 61.166 60.000 0.00 0.00 0.00 3.79
1121 1123 1.420430 AGGGTTTCTCAGACACCGAA 58.580 50.000 3.82 0.00 33.60 4.30
1171 1173 2.771943 AGCGAGAATGGGGTAAGAATCA 59.228 45.455 0.00 0.00 0.00 2.57
1227 1229 3.841643 GAGCAATGGGTTGATCTGTTTG 58.158 45.455 0.00 0.00 45.03 2.93
1363 1365 3.680786 CCACACCACGAGCTCCGA 61.681 66.667 8.47 0.00 41.76 4.55
1490 1492 4.349342 ACCCATTTGCAAATACTTTTGGGA 59.651 37.500 36.19 7.30 42.09 4.37
1725 1729 4.632538 TGATCAATGAAATGCAGCTCTG 57.367 40.909 0.00 0.00 0.00 3.35
1916 1934 4.799564 TGCTGAAACTTTTTGTGGAAGT 57.200 36.364 0.00 0.00 38.92 3.01
2270 2290 3.645212 GGGTAGGGAAGGAAGGTATACAC 59.355 52.174 5.01 0.00 0.00 2.90
2380 2403 5.903010 ACTTAAATTTTGGAGGGTTGGAAGT 59.097 36.000 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.327404 TTCCCTGCCGTCCCCTTC 61.327 66.667 0.00 0.00 0.00 3.46
4 5 3.647771 AAGTTCCCTGCCGTCCCC 61.648 66.667 0.00 0.00 0.00 4.81
5 6 2.359975 CAAGTTCCCTGCCGTCCC 60.360 66.667 0.00 0.00 0.00 4.46
6 7 1.966451 CACAAGTTCCCTGCCGTCC 60.966 63.158 0.00 0.00 0.00 4.79
7 8 1.227853 ACACAAGTTCCCTGCCGTC 60.228 57.895 0.00 0.00 0.00 4.79
9 10 1.966451 GGACACAAGTTCCCTGCCG 60.966 63.158 0.00 0.00 0.00 5.69
10 11 1.603739 GGGACACAAGTTCCCTGCC 60.604 63.158 0.00 0.00 37.45 4.85
12 13 0.884704 CACGGGACACAAGTTCCCTG 60.885 60.000 5.88 2.49 40.68 4.45
13 14 1.450211 CACGGGACACAAGTTCCCT 59.550 57.895 5.88 0.00 40.68 4.20
14 15 1.599797 CCACGGGACACAAGTTCCC 60.600 63.158 0.00 0.00 40.68 3.97
15 16 2.258726 GCCACGGGACACAAGTTCC 61.259 63.158 0.00 0.00 40.34 3.62
16 17 2.258726 GGCCACGGGACACAAGTTC 61.259 63.158 0.00 0.00 0.00 3.01
17 18 2.203294 GGCCACGGGACACAAGTT 60.203 61.111 0.00 0.00 0.00 2.66
18 19 4.619227 CGGCCACGGGACACAAGT 62.619 66.667 2.24 0.00 36.18 3.16
19 20 4.619227 ACGGCCACGGGACACAAG 62.619 66.667 2.24 0.00 46.48 3.16
46 47 2.504175 TCCATGTACAAACCCTCTAGGC 59.496 50.000 0.00 0.00 40.58 3.93
50 51 1.282157 GCCTCCATGTACAAACCCTCT 59.718 52.381 0.00 0.00 0.00 3.69
84 85 2.754658 AGGAGGTACAGTCGCCGG 60.755 66.667 0.00 0.00 0.00 6.13
94 95 3.536917 CCGCGCCATCAGGAGGTA 61.537 66.667 0.00 0.00 36.89 3.08
114 115 0.950555 TCATGTTGTCACTGGAGCGC 60.951 55.000 0.00 0.00 0.00 5.92
115 116 1.073964 CTCATGTTGTCACTGGAGCG 58.926 55.000 0.00 0.00 0.00 5.03
133 134 1.276421 CCCAACTGAGTTCATCGTCCT 59.724 52.381 0.00 0.00 0.00 3.85
137 138 1.270839 ACACCCCAACTGAGTTCATCG 60.271 52.381 0.00 0.00 0.00 3.84
140 141 1.208706 TCACACCCCAACTGAGTTCA 58.791 50.000 0.00 0.00 0.00 3.18
141 142 2.039084 AGATCACACCCCAACTGAGTTC 59.961 50.000 0.00 0.00 0.00 3.01
149 150 1.600107 GCCGTAGATCACACCCCAA 59.400 57.895 0.00 0.00 0.00 4.12
151 152 2.106332 CGCCGTAGATCACACCCC 59.894 66.667 0.00 0.00 0.00 4.95
155 156 0.457853 GTCTTGCGCCGTAGATCACA 60.458 55.000 4.18 0.00 0.00 3.58
158 159 1.591863 GGGTCTTGCGCCGTAGATC 60.592 63.158 4.18 5.42 0.00 2.75
173 174 0.548682 AGAAGCATCACTCTGGGGGT 60.549 55.000 0.00 0.00 0.00 4.95
174 175 0.107312 CAGAAGCATCACTCTGGGGG 60.107 60.000 0.00 0.00 0.00 5.40
183 184 1.375908 GCCGTGACCAGAAGCATCA 60.376 57.895 0.00 0.00 0.00 3.07
222 223 3.584406 CTCCTAGCCCATCATATCCAACA 59.416 47.826 0.00 0.00 0.00 3.33
225 226 2.191400 GCTCCTAGCCCATCATATCCA 58.809 52.381 0.00 0.00 34.48 3.41
249 250 0.172578 CCATACGGAAGAGCACGACA 59.827 55.000 0.00 0.00 0.00 4.35
251 252 2.876581 TCCATACGGAAGAGCACGA 58.123 52.632 0.00 0.00 38.83 4.35
277 278 1.065199 TCGAGGAATGGCAAGCTCATT 60.065 47.619 0.00 7.99 37.52 2.57
278 279 0.543277 TCGAGGAATGGCAAGCTCAT 59.457 50.000 0.00 0.00 0.00 2.90
279 280 0.543277 ATCGAGGAATGGCAAGCTCA 59.457 50.000 0.00 0.00 0.00 4.26
290 292 1.218047 CTCCAACCGCATCGAGGAA 59.782 57.895 0.00 0.00 0.00 3.36
296 298 1.817099 CTCCAGCTCCAACCGCATC 60.817 63.158 0.00 0.00 0.00 3.91
298 300 4.020617 CCTCCAGCTCCAACCGCA 62.021 66.667 0.00 0.00 0.00 5.69
301 303 2.352805 CCACCTCCAGCTCCAACC 59.647 66.667 0.00 0.00 0.00 3.77
395 397 2.967599 TGACGAACATCTCCATGGAG 57.032 50.000 32.60 32.60 43.21 3.86
396 398 3.694043 TTTGACGAACATCTCCATGGA 57.306 42.857 15.27 15.27 33.82 3.41
397 399 4.194640 AGATTTGACGAACATCTCCATGG 58.805 43.478 4.97 4.97 33.82 3.66
398 400 5.808042 AAGATTTGACGAACATCTCCATG 57.192 39.130 0.00 0.00 35.92 3.66
399 401 6.430925 TGAAAAGATTTGACGAACATCTCCAT 59.569 34.615 0.00 0.00 0.00 3.41
400 402 5.762711 TGAAAAGATTTGACGAACATCTCCA 59.237 36.000 0.00 0.00 0.00 3.86
401 403 6.241207 TGAAAAGATTTGACGAACATCTCC 57.759 37.500 0.00 0.00 0.00 3.71
402 404 8.733857 AAATGAAAAGATTTGACGAACATCTC 57.266 30.769 0.00 0.00 0.00 2.75
403 405 9.533253 AAAAATGAAAAGATTTGACGAACATCT 57.467 25.926 0.00 0.00 0.00 2.90
404 406 9.783425 GAAAAATGAAAAGATTTGACGAACATC 57.217 29.630 0.00 0.00 0.00 3.06
405 407 9.311916 TGAAAAATGAAAAGATTTGACGAACAT 57.688 25.926 0.00 0.00 0.00 2.71
406 408 8.694975 TGAAAAATGAAAAGATTTGACGAACA 57.305 26.923 0.00 0.00 0.00 3.18
407 409 9.571804 CATGAAAAATGAAAAGATTTGACGAAC 57.428 29.630 0.00 0.00 0.00 3.95
408 410 9.311916 ACATGAAAAATGAAAAGATTTGACGAA 57.688 25.926 0.00 0.00 0.00 3.85
409 411 8.870160 ACATGAAAAATGAAAAGATTTGACGA 57.130 26.923 0.00 0.00 0.00 4.20
410 412 9.919348 AAACATGAAAAATGAAAAGATTTGACG 57.081 25.926 0.00 0.00 0.00 4.35
436 438 9.581099 GGAAAACTAGATCAAACACAAAGAAAA 57.419 29.630 0.00 0.00 0.00 2.29
437 439 8.966868 AGGAAAACTAGATCAAACACAAAGAAA 58.033 29.630 0.00 0.00 0.00 2.52
438 440 8.519799 AGGAAAACTAGATCAAACACAAAGAA 57.480 30.769 0.00 0.00 0.00 2.52
439 441 7.228706 GGAGGAAAACTAGATCAAACACAAAGA 59.771 37.037 0.00 0.00 0.00 2.52
440 442 7.229506 AGGAGGAAAACTAGATCAAACACAAAG 59.770 37.037 0.00 0.00 0.00 2.77
441 443 7.060421 AGGAGGAAAACTAGATCAAACACAAA 58.940 34.615 0.00 0.00 0.00 2.83
442 444 6.601332 AGGAGGAAAACTAGATCAAACACAA 58.399 36.000 0.00 0.00 0.00 3.33
443 445 6.187727 AGGAGGAAAACTAGATCAAACACA 57.812 37.500 0.00 0.00 0.00 3.72
444 446 8.794335 ATAAGGAGGAAAACTAGATCAAACAC 57.206 34.615 0.00 0.00 0.00 3.32
445 447 9.807921 AAATAAGGAGGAAAACTAGATCAAACA 57.192 29.630 0.00 0.00 0.00 2.83
452 454 9.297037 CCAAGAAAAATAAGGAGGAAAACTAGA 57.703 33.333 0.00 0.00 0.00 2.43
453 455 9.078990 ACCAAGAAAAATAAGGAGGAAAACTAG 57.921 33.333 0.00 0.00 0.00 2.57
454 456 9.429109 AACCAAGAAAAATAAGGAGGAAAACTA 57.571 29.630 0.00 0.00 0.00 2.24
455 457 7.914427 ACCAAGAAAAATAAGGAGGAAAACT 57.086 32.000 0.00 0.00 0.00 2.66
456 458 8.958119 AAACCAAGAAAAATAAGGAGGAAAAC 57.042 30.769 0.00 0.00 0.00 2.43
491 493 2.398588 ACTGACAGAAGTGGAAGACCA 58.601 47.619 10.08 0.00 44.76 4.02
492 494 3.477210 AACTGACAGAAGTGGAAGACC 57.523 47.619 10.08 0.00 0.00 3.85
493 495 3.810386 GGAAACTGACAGAAGTGGAAGAC 59.190 47.826 10.08 0.00 0.00 3.01
494 496 3.711704 AGGAAACTGACAGAAGTGGAAGA 59.288 43.478 10.08 0.00 41.13 2.87
495 497 4.078639 AGGAAACTGACAGAAGTGGAAG 57.921 45.455 10.08 0.00 41.13 3.46
496 498 4.503714 AAGGAAACTGACAGAAGTGGAA 57.496 40.909 10.08 0.00 42.68 3.53
497 499 4.503714 AAAGGAAACTGACAGAAGTGGA 57.496 40.909 10.08 0.00 42.68 4.02
498 500 5.008712 GGTAAAAGGAAACTGACAGAAGTGG 59.991 44.000 10.08 0.00 42.68 4.00
499 501 5.823045 AGGTAAAAGGAAACTGACAGAAGTG 59.177 40.000 10.08 0.00 42.68 3.16
500 502 6.002653 AGGTAAAAGGAAACTGACAGAAGT 57.997 37.500 10.08 0.00 42.68 3.01
501 503 6.318900 ACAAGGTAAAAGGAAACTGACAGAAG 59.681 38.462 10.08 0.00 42.68 2.85
502 504 6.184789 ACAAGGTAAAAGGAAACTGACAGAA 58.815 36.000 10.08 0.00 42.68 3.02
503 505 5.751586 ACAAGGTAAAAGGAAACTGACAGA 58.248 37.500 10.08 0.00 42.68 3.41
504 506 6.451064 AACAAGGTAAAAGGAAACTGACAG 57.549 37.500 0.00 0.00 42.68 3.51
505 507 5.358725 GGAACAAGGTAAAAGGAAACTGACA 59.641 40.000 0.00 0.00 42.68 3.58
506 508 5.593095 AGGAACAAGGTAAAAGGAAACTGAC 59.407 40.000 0.00 0.00 42.68 3.51
507 509 5.762279 AGGAACAAGGTAAAAGGAAACTGA 58.238 37.500 0.00 0.00 42.68 3.41
508 510 6.465439 AAGGAACAAGGTAAAAGGAAACTG 57.535 37.500 0.00 0.00 42.68 3.16
510 512 8.038944 AGAAAAAGGAACAAGGTAAAAGGAAAC 58.961 33.333 0.00 0.00 0.00 2.78
511 513 8.141298 AGAAAAAGGAACAAGGTAAAAGGAAA 57.859 30.769 0.00 0.00 0.00 3.13
512 514 7.727578 AGAAAAAGGAACAAGGTAAAAGGAA 57.272 32.000 0.00 0.00 0.00 3.36
513 515 7.727578 AAGAAAAAGGAACAAGGTAAAAGGA 57.272 32.000 0.00 0.00 0.00 3.36
514 516 8.786826 AAAAGAAAAAGGAACAAGGTAAAAGG 57.213 30.769 0.00 0.00 0.00 3.11
515 517 8.879759 GGAAAAGAAAAAGGAACAAGGTAAAAG 58.120 33.333 0.00 0.00 0.00 2.27
516 518 8.376270 TGGAAAAGAAAAAGGAACAAGGTAAAA 58.624 29.630 0.00 0.00 0.00 1.52
517 519 7.908453 TGGAAAAGAAAAAGGAACAAGGTAAA 58.092 30.769 0.00 0.00 0.00 2.01
518 520 7.483580 TGGAAAAGAAAAAGGAACAAGGTAA 57.516 32.000 0.00 0.00 0.00 2.85
519 521 7.669089 ATGGAAAAGAAAAAGGAACAAGGTA 57.331 32.000 0.00 0.00 0.00 3.08
520 522 6.560003 ATGGAAAAGAAAAAGGAACAAGGT 57.440 33.333 0.00 0.00 0.00 3.50
521 523 7.864108 AAATGGAAAAGAAAAAGGAACAAGG 57.136 32.000 0.00 0.00 0.00 3.61
564 566 9.674068 GGGCAAAAGAATAATTAACCCAAATTA 57.326 29.630 0.00 0.00 36.15 1.40
565 567 8.390143 AGGGCAAAAGAATAATTAACCCAAATT 58.610 29.630 0.00 0.00 37.28 1.82
566 568 7.927788 AGGGCAAAAGAATAATTAACCCAAAT 58.072 30.769 0.00 0.00 37.28 2.32
567 569 7.016661 TGAGGGCAAAAGAATAATTAACCCAAA 59.983 33.333 0.00 0.00 37.28 3.28
581 583 0.550914 ACACCACTGAGGGCAAAAGA 59.449 50.000 0.00 0.00 43.89 2.52
610 612 0.883833 CGCATCTGAGGGCAAAACTT 59.116 50.000 5.18 0.00 0.00 2.66
747 749 5.046448 TGCAATGGTCTGAATAAAATTGGCT 60.046 36.000 0.00 0.00 0.00 4.75
766 768 3.286751 ACAAGCCACGCGTGCAAT 61.287 55.556 33.17 17.72 41.40 3.56
815 817 1.605971 TATAGCACACCCGCCAACGA 61.606 55.000 0.00 0.00 43.93 3.85
893 895 1.108727 CCGCCATGCTCTCTCTCTCT 61.109 60.000 0.00 0.00 0.00 3.10
894 896 1.363443 CCGCCATGCTCTCTCTCTC 59.637 63.158 0.00 0.00 0.00 3.20
969 971 1.517832 CGAAGGGGATCTCAACGCT 59.482 57.895 0.00 0.00 0.00 5.07
1061 1063 1.154016 CGCGGACAGACGAAGACAT 60.154 57.895 0.00 0.00 35.47 3.06
1121 1123 1.893801 AGAACGGACGATTCTGGTTCT 59.106 47.619 0.00 0.00 39.02 3.01
1171 1173 1.338011 CGAAAATGGTGCAATTGCCCT 60.338 47.619 26.94 11.63 41.18 5.19
1227 1229 1.200716 CATGTCACCTGCATGAACACC 59.799 52.381 0.00 0.00 44.60 4.16
1363 1365 3.539604 CTTCGCCATCCATCTCTTCTTT 58.460 45.455 0.00 0.00 0.00 2.52
1387 1389 0.529833 GCTAGCTCTCTGTCAGTGCA 59.470 55.000 7.70 0.00 43.07 4.57
1490 1492 6.260050 CAGTGCGATTACCATACCTACAAATT 59.740 38.462 0.00 0.00 0.00 1.82
1916 1934 8.307483 TGTTTGGCTCCGAAATAATTCAATTAA 58.693 29.630 0.00 0.00 35.15 1.40
2012 2030 4.996122 GGCACATTTTCCATGACATTTTGA 59.004 37.500 0.00 0.00 0.00 2.69
2152 2172 3.092511 AGTCCCCAGCCGCATCAT 61.093 61.111 0.00 0.00 0.00 2.45
2380 2403 6.920758 GTGGTAGTGCAACATACATTTTCAAA 59.079 34.615 0.00 0.00 41.43 2.69


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

AutoCloner maintained by Alex Coulton.