Multiple sequence alignment - TraesCS2B01G008200

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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 TraesCS2B01G008200 chr2B 100.000 2549 0 0 1 2549 4739306 4741854 0.000000e+00 4708.0
1 TraesCS2B01G008200 chr2B 88.718 390 22 7 1 389 553627584 553627952 8.310000e-125 457.0
2 TraesCS2B01G008200 chr2B 87.624 202 12 3 381 570 553627980 553628180 3.300000e-54 222.0
3 TraesCS2B01G008200 chr6B 98.740 1984 21 3 567 2549 660437747 660435767 0.000000e+00 3522.0
4 TraesCS2B01G008200 chr6B 84.733 262 18 8 128 389 705995707 705995468 2.530000e-60 243.0
5 TraesCS2B01G008200 chr7A 98.490 1987 26 4 565 2549 701581935 701583919 0.000000e+00 3500.0
6 TraesCS2B01G008200 chr3A 98.586 1980 26 2 571 2549 722406047 722404069 0.000000e+00 3500.0
7 TraesCS2B01G008200 chr3A 88.718 390 20 8 1 389 660899666 660900032 2.990000e-124 455.0
8 TraesCS2B01G008200 chr3A 87.624 202 12 3 381 570 660900060 660900260 3.300000e-54 222.0
9 TraesCS2B01G008200 chr7B 98.489 1985 26 3 567 2549 1776635 1774653 0.000000e+00 3496.0
10 TraesCS2B01G008200 chr7B 98.535 1980 25 3 571 2549 552850598 552852574 0.000000e+00 3493.0
11 TraesCS2B01G008200 chr7B 98.436 1982 26 4 571 2549 552932143 552930164 0.000000e+00 3483.0
12 TraesCS2B01G008200 chr6A 98.682 1972 21 4 569 2538 617222871 617220903 0.000000e+00 3493.0
13 TraesCS2B01G008200 chr6A 94.118 51 3 0 231 281 12263793 12263743 7.560000e-11 78.7
14 TraesCS2B01G008200 chr3B 98.486 1982 26 3 569 2549 379294091 379296069 0.000000e+00 3491.0
15 TraesCS2B01G008200 chr3B 82.530 498 37 15 1 469 581650279 581650755 2.380000e-105 392.0
16 TraesCS2B01G008200 chr4A 98.292 1991 28 5 564 2549 661625053 661623064 0.000000e+00 3483.0
17 TraesCS2B01G008200 chr7D 88.718 390 22 7 1 389 595926331 595925963 8.310000e-125 457.0
18 TraesCS2B01G008200 chr7D 83.500 200 16 7 387 570 595925929 595925731 1.210000e-38 171.0
19 TraesCS2B01G008200 chr4D 88.205 390 22 11 1 389 87558226 87558592 6.470000e-121 444.0
20 TraesCS2B01G008200 chr4D 88.732 142 3 3 381 510 87558620 87558760 7.300000e-36 161.0
21 TraesCS2B01G008200 chr3D 82.863 496 37 11 1 469 513614591 513614117 3.950000e-108 401.0
22 TraesCS2B01G008200 chr3D 77.846 325 41 18 71 389 468984121 468983822 3.370000e-39 172.0
23 TraesCS2B01G008200 chr2A 85.496 262 16 8 128 389 199655846 199655607 1.170000e-63 254.0


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 TraesCS2B01G008200 chr2B 4739306 4741854 2548 False 4708.0 4708 100.0000 1 2549 1 chr2B.!!$F1 2548
1 TraesCS2B01G008200 chr2B 553627584 553628180 596 False 339.5 457 88.1710 1 570 2 chr2B.!!$F2 569
2 TraesCS2B01G008200 chr6B 660435767 660437747 1980 True 3522.0 3522 98.7400 567 2549 1 chr6B.!!$R1 1982
3 TraesCS2B01G008200 chr7A 701581935 701583919 1984 False 3500.0 3500 98.4900 565 2549 1 chr7A.!!$F1 1984
4 TraesCS2B01G008200 chr3A 722404069 722406047 1978 True 3500.0 3500 98.5860 571 2549 1 chr3A.!!$R1 1978
5 TraesCS2B01G008200 chr3A 660899666 660900260 594 False 338.5 455 88.1710 1 570 2 chr3A.!!$F1 569
6 TraesCS2B01G008200 chr7B 1774653 1776635 1982 True 3496.0 3496 98.4890 567 2549 1 chr7B.!!$R1 1982
7 TraesCS2B01G008200 chr7B 552850598 552852574 1976 False 3493.0 3493 98.5350 571 2549 1 chr7B.!!$F1 1978
8 TraesCS2B01G008200 chr7B 552930164 552932143 1979 True 3483.0 3483 98.4360 571 2549 1 chr7B.!!$R2 1978
9 TraesCS2B01G008200 chr6A 617220903 617222871 1968 True 3493.0 3493 98.6820 569 2538 1 chr6A.!!$R2 1969
10 TraesCS2B01G008200 chr3B 379294091 379296069 1978 False 3491.0 3491 98.4860 569 2549 1 chr3B.!!$F1 1980
11 TraesCS2B01G008200 chr4A 661623064 661625053 1989 True 3483.0 3483 98.2920 564 2549 1 chr4A.!!$R1 1985
12 TraesCS2B01G008200 chr7D 595925731 595926331 600 True 314.0 457 86.1090 1 570 2 chr7D.!!$R1 569
13 TraesCS2B01G008200 chr4D 87558226 87558760 534 False 302.5 444 88.4685 1 510 2 chr4D.!!$F1 509

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
636 676 1.09805 GCCCTCAGATGCGAATTGTT 58.902 50.0 0.0 0.0 0.0 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2014 2148 4.756135 GGCACATTTTCCATGACATTTTGT 59.244 37.5 0.0 0.0 0.0 2.83 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
80 82 5.643777 GTCATTTAGTGTTGAGGTGCATACT 59.356 40.000 0.00 0.00 0.00 2.12
116 118 9.017509 AGCAAATAAGAATTCTGACATTCTTCA 57.982 29.630 20.69 13.15 46.29 3.02
166 168 5.642919 ACAGAAGAGCTCAATGAAAGATGAC 59.357 40.000 17.77 0.00 0.00 3.06
167 169 5.875910 CAGAAGAGCTCAATGAAAGATGACT 59.124 40.000 17.77 0.00 0.00 3.41
168 170 6.372103 CAGAAGAGCTCAATGAAAGATGACTT 59.628 38.462 17.77 0.00 38.05 3.01
169 171 6.594937 AGAAGAGCTCAATGAAAGATGACTTC 59.405 38.462 17.77 5.53 35.05 3.01
170 172 4.869297 AGAGCTCAATGAAAGATGACTTCG 59.131 41.667 17.77 0.00 35.05 3.79
171 173 4.825422 AGCTCAATGAAAGATGACTTCGA 58.175 39.130 0.00 0.00 35.05 3.71
172 174 4.869297 AGCTCAATGAAAGATGACTTCGAG 59.131 41.667 0.00 0.00 35.05 4.04
173 175 4.629200 GCTCAATGAAAGATGACTTCGAGT 59.371 41.667 0.00 0.00 35.05 4.18
229 231 9.401058 AGAAATCTTTTATACATCTGACTTGGG 57.599 33.333 0.00 0.00 0.00 4.12
431 471 6.909550 ATAATTTTTCCTGGTTGCACTACA 57.090 33.333 0.00 0.00 0.00 2.74
444 484 5.126061 GGTTGCACTACATGATTGAATCCTT 59.874 40.000 0.00 0.00 0.00 3.36
445 485 6.318648 GGTTGCACTACATGATTGAATCCTTA 59.681 38.462 0.00 0.00 0.00 2.69
446 486 6.925610 TGCACTACATGATTGAATCCTTAC 57.074 37.500 0.00 0.00 0.00 2.34
447 487 5.822519 TGCACTACATGATTGAATCCTTACC 59.177 40.000 0.00 0.00 0.00 2.85
448 488 5.050091 GCACTACATGATTGAATCCTTACCG 60.050 44.000 0.00 0.00 0.00 4.02
449 489 5.466728 CACTACATGATTGAATCCTTACCGG 59.533 44.000 0.00 0.00 0.00 5.28
450 490 4.503714 ACATGATTGAATCCTTACCGGT 57.496 40.909 13.98 13.98 0.00 5.28
451 491 5.623956 ACATGATTGAATCCTTACCGGTA 57.376 39.130 11.16 11.16 0.00 4.02
452 492 5.611374 ACATGATTGAATCCTTACCGGTAG 58.389 41.667 15.20 9.06 0.00 3.18
453 493 5.130477 ACATGATTGAATCCTTACCGGTAGT 59.870 40.000 15.20 0.90 0.00 2.73
454 494 6.325545 ACATGATTGAATCCTTACCGGTAGTA 59.674 38.462 15.20 4.76 0.00 1.82
455 495 6.401047 TGATTGAATCCTTACCGGTAGTAG 57.599 41.667 15.20 10.34 30.92 2.57
456 496 5.895534 TGATTGAATCCTTACCGGTAGTAGT 59.104 40.000 15.20 3.51 30.92 2.73
457 497 6.381994 TGATTGAATCCTTACCGGTAGTAGTT 59.618 38.462 15.20 9.01 30.92 2.24
458 498 5.587388 TGAATCCTTACCGGTAGTAGTTG 57.413 43.478 15.20 0.00 30.92 3.16
459 499 4.403432 TGAATCCTTACCGGTAGTAGTTGG 59.597 45.833 15.20 11.04 30.92 3.77
460 500 3.456380 TCCTTACCGGTAGTAGTTGGT 57.544 47.619 15.20 0.00 38.51 3.67
461 501 3.778265 TCCTTACCGGTAGTAGTTGGTT 58.222 45.455 15.20 0.00 35.93 3.67
462 502 3.511146 TCCTTACCGGTAGTAGTTGGTTG 59.489 47.826 15.20 0.00 35.93 3.77
463 503 3.259123 CCTTACCGGTAGTAGTTGGTTGT 59.741 47.826 15.20 0.00 35.93 3.32
464 504 4.462483 CCTTACCGGTAGTAGTTGGTTGTA 59.538 45.833 15.20 0.00 35.93 2.41
465 505 3.942130 ACCGGTAGTAGTTGGTTGTAC 57.058 47.619 4.49 0.00 0.00 2.90
466 506 2.562738 ACCGGTAGTAGTTGGTTGTACC 59.437 50.000 4.49 0.00 39.22 3.34
467 507 6.216936 TTACCGGTAGTAGTTGGTTGTACCA 61.217 44.000 15.20 0.00 38.26 3.25
468 508 7.481695 TTACCGGTAGTAGTTGGTTGTACCAT 61.482 42.308 15.20 0.00 39.18 3.55
469 509 8.886717 TTACCGGTAGTAGTTGGTTGTACCATT 61.887 40.741 15.20 0.00 39.18 3.16
483 523 8.818860 TGGTTGTACCATTTTATCAGTAGTAGT 58.181 33.333 0.00 0.00 44.79 2.73
487 527 9.192642 TGTACCATTTTATCAGTAGTAGTAGCA 57.807 33.333 0.00 0.00 0.00 3.49
488 528 9.680315 GTACCATTTTATCAGTAGTAGTAGCAG 57.320 37.037 0.00 0.00 0.00 4.24
489 529 8.534954 ACCATTTTATCAGTAGTAGTAGCAGA 57.465 34.615 0.00 0.00 0.00 4.26
490 530 8.978472 ACCATTTTATCAGTAGTAGTAGCAGAA 58.022 33.333 0.00 0.00 0.00 3.02
491 531 9.250624 CCATTTTATCAGTAGTAGTAGCAGAAC 57.749 37.037 0.00 0.00 0.00 3.01
496 536 9.902684 TTATCAGTAGTAGTAGCAGAACTAAGT 57.097 33.333 0.00 0.00 33.85 2.24
497 537 7.846644 TCAGTAGTAGTAGCAGAACTAAGTC 57.153 40.000 0.00 0.00 33.85 3.01
498 538 7.392418 TCAGTAGTAGTAGCAGAACTAAGTCA 58.608 38.462 0.00 0.00 33.85 3.41
499 539 8.047911 TCAGTAGTAGTAGCAGAACTAAGTCAT 58.952 37.037 0.00 0.00 33.85 3.06
500 540 9.327628 CAGTAGTAGTAGCAGAACTAAGTCATA 57.672 37.037 0.00 0.00 33.85 2.15
501 541 9.550406 AGTAGTAGTAGCAGAACTAAGTCATAG 57.450 37.037 0.00 0.00 33.85 2.23
502 542 9.545105 GTAGTAGTAGCAGAACTAAGTCATAGA 57.455 37.037 0.00 0.00 33.85 1.98
503 543 8.671384 AGTAGTAGCAGAACTAAGTCATAGAG 57.329 38.462 0.00 0.00 33.85 2.43
504 544 6.385649 AGTAGCAGAACTAAGTCATAGAGC 57.614 41.667 0.00 0.00 35.47 4.09
505 545 6.126409 AGTAGCAGAACTAAGTCATAGAGCT 58.874 40.000 0.00 0.00 35.47 4.09
506 546 5.514274 AGCAGAACTAAGTCATAGAGCTC 57.486 43.478 5.27 5.27 35.47 4.09
507 547 5.200483 AGCAGAACTAAGTCATAGAGCTCT 58.800 41.667 22.17 22.17 35.47 4.09
508 548 5.067674 AGCAGAACTAAGTCATAGAGCTCTG 59.932 44.000 26.78 11.66 38.26 3.35
509 549 5.163561 GCAGAACTAAGTCATAGAGCTCTGT 60.164 44.000 26.78 17.59 37.93 3.41
510 550 6.038825 GCAGAACTAAGTCATAGAGCTCTGTA 59.961 42.308 26.78 7.68 37.93 2.74
511 551 7.255451 GCAGAACTAAGTCATAGAGCTCTGTAT 60.255 40.741 26.78 9.97 37.93 2.29
512 552 8.629158 CAGAACTAAGTCATAGAGCTCTGTATT 58.371 37.037 26.78 16.12 34.85 1.89
513 553 9.196139 AGAACTAAGTCATAGAGCTCTGTATTT 57.804 33.333 26.78 15.43 35.47 1.40
514 554 9.810545 GAACTAAGTCATAGAGCTCTGTATTTT 57.189 33.333 26.78 16.10 35.47 1.82
515 555 9.593134 AACTAAGTCATAGAGCTCTGTATTTTG 57.407 33.333 26.78 15.62 35.47 2.44
516 556 8.754080 ACTAAGTCATAGAGCTCTGTATTTTGT 58.246 33.333 26.78 16.17 35.47 2.83
517 557 9.593134 CTAAGTCATAGAGCTCTGTATTTTGTT 57.407 33.333 26.78 11.11 33.04 2.83
519 559 8.934507 AGTCATAGAGCTCTGTATTTTGTTAC 57.065 34.615 26.78 9.15 0.00 2.50
520 560 8.754080 AGTCATAGAGCTCTGTATTTTGTTACT 58.246 33.333 26.78 11.03 0.00 2.24
521 561 8.812329 GTCATAGAGCTCTGTATTTTGTTACTG 58.188 37.037 26.78 3.23 0.00 2.74
522 562 7.981789 TCATAGAGCTCTGTATTTTGTTACTGG 59.018 37.037 26.78 3.03 0.00 4.00
523 563 6.360370 AGAGCTCTGTATTTTGTTACTGGA 57.640 37.500 17.42 0.00 0.00 3.86
524 564 6.402222 AGAGCTCTGTATTTTGTTACTGGAG 58.598 40.000 17.42 0.00 0.00 3.86
525 565 6.211584 AGAGCTCTGTATTTTGTTACTGGAGA 59.788 38.462 17.42 0.00 31.10 3.71
526 566 6.951971 AGCTCTGTATTTTGTTACTGGAGAT 58.048 36.000 0.00 0.00 31.10 2.75
527 567 7.044798 AGCTCTGTATTTTGTTACTGGAGATC 58.955 38.462 0.00 0.00 31.10 2.75
528 568 7.044798 GCTCTGTATTTTGTTACTGGAGATCT 58.955 38.462 0.00 0.00 31.10 2.75
529 569 7.010923 GCTCTGTATTTTGTTACTGGAGATCTG 59.989 40.741 0.00 0.00 31.10 2.90
530 570 7.907389 TCTGTATTTTGTTACTGGAGATCTGT 58.093 34.615 0.00 0.00 0.00 3.41
531 571 8.375506 TCTGTATTTTGTTACTGGAGATCTGTT 58.624 33.333 0.00 0.00 0.00 3.16
532 572 8.918202 TGTATTTTGTTACTGGAGATCTGTTT 57.082 30.769 0.00 0.00 0.00 2.83
536 576 8.918202 TTTTGTTACTGGAGATCTGTTTATGT 57.082 30.769 0.00 0.00 0.00 2.29
537 577 7.905604 TTGTTACTGGAGATCTGTTTATGTG 57.094 36.000 0.00 0.00 0.00 3.21
538 578 6.406370 TGTTACTGGAGATCTGTTTATGTGG 58.594 40.000 0.00 0.00 0.00 4.17
539 579 6.013725 TGTTACTGGAGATCTGTTTATGTGGT 60.014 38.462 0.00 0.00 0.00 4.16
540 580 5.505181 ACTGGAGATCTGTTTATGTGGTT 57.495 39.130 0.00 0.00 0.00 3.67
541 581 5.248640 ACTGGAGATCTGTTTATGTGGTTG 58.751 41.667 0.00 0.00 0.00 3.77
542 582 4.009675 TGGAGATCTGTTTATGTGGTTGC 58.990 43.478 0.00 0.00 0.00 4.17
543 583 4.263462 TGGAGATCTGTTTATGTGGTTGCT 60.263 41.667 0.00 0.00 0.00 3.91
544 584 5.045942 TGGAGATCTGTTTATGTGGTTGCTA 60.046 40.000 0.00 0.00 0.00 3.49
545 585 5.880332 GGAGATCTGTTTATGTGGTTGCTAA 59.120 40.000 0.00 0.00 0.00 3.09
546 586 6.183360 GGAGATCTGTTTATGTGGTTGCTAAC 60.183 42.308 0.00 0.00 0.00 2.34
547 587 6.476378 AGATCTGTTTATGTGGTTGCTAACT 58.524 36.000 0.00 0.00 0.00 2.24
548 588 6.595716 AGATCTGTTTATGTGGTTGCTAACTC 59.404 38.462 0.00 0.00 0.00 3.01
549 589 5.616270 TCTGTTTATGTGGTTGCTAACTCA 58.384 37.500 0.00 0.00 0.00 3.41
550 590 6.237901 TCTGTTTATGTGGTTGCTAACTCAT 58.762 36.000 6.06 6.06 33.43 2.90
551 591 7.390823 TCTGTTTATGTGGTTGCTAACTCATA 58.609 34.615 4.22 4.22 32.13 2.15
552 592 7.880713 TCTGTTTATGTGGTTGCTAACTCATAA 59.119 33.333 14.05 14.05 36.93 1.90
553 593 8.574251 TGTTTATGTGGTTGCTAACTCATAAT 57.426 30.769 17.29 7.26 37.64 1.28
554 594 9.674068 TGTTTATGTGGTTGCTAACTCATAATA 57.326 29.630 17.29 9.86 37.64 0.98
556 596 9.899661 TTTATGTGGTTGCTAACTCATAATAGT 57.100 29.630 17.29 0.00 37.64 2.12
559 599 8.712285 TGTGGTTGCTAACTCATAATAGTAAC 57.288 34.615 5.54 5.54 41.27 2.50
560 600 8.537016 TGTGGTTGCTAACTCATAATAGTAACT 58.463 33.333 11.60 0.00 41.54 2.24
636 676 1.098050 GCCCTCAGATGCGAATTGTT 58.902 50.000 0.00 0.00 0.00 2.83
792 832 2.197324 GTGGCTTGTGGGACCCAA 59.803 61.111 16.98 0.00 34.18 4.12
877 917 3.295273 ACGGCGACAGAGAGCACA 61.295 61.111 16.62 0.00 34.54 4.57
1557 1685 8.303780 TGTATGGAAAGGCATGAATTATGAAA 57.696 30.769 0.00 0.00 39.21 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
209 211 8.335532 TGAAACCCAAGTCAGATGTATAAAAG 57.664 34.615 0.00 0.00 0.00 2.27
210 212 8.877864 ATGAAACCCAAGTCAGATGTATAAAA 57.122 30.769 0.00 0.00 0.00 1.52
212 214 7.888021 ACAATGAAACCCAAGTCAGATGTATAA 59.112 33.333 0.00 0.00 30.38 0.98
213 215 7.402054 ACAATGAAACCCAAGTCAGATGTATA 58.598 34.615 0.00 0.00 30.38 1.47
214 216 6.248433 ACAATGAAACCCAAGTCAGATGTAT 58.752 36.000 0.00 0.00 30.38 2.29
215 217 5.630121 ACAATGAAACCCAAGTCAGATGTA 58.370 37.500 0.00 0.00 30.38 2.29
216 218 4.473444 ACAATGAAACCCAAGTCAGATGT 58.527 39.130 0.00 0.00 0.00 3.06
217 219 4.763793 AGACAATGAAACCCAAGTCAGATG 59.236 41.667 0.00 0.00 36.76 2.90
218 220 4.990526 AGACAATGAAACCCAAGTCAGAT 58.009 39.130 0.00 0.00 36.76 2.90
219 221 4.437682 AGACAATGAAACCCAAGTCAGA 57.562 40.909 0.00 0.00 36.76 3.27
220 222 5.163519 ACAAAGACAATGAAACCCAAGTCAG 60.164 40.000 0.00 0.00 36.76 3.51
221 223 4.709397 ACAAAGACAATGAAACCCAAGTCA 59.291 37.500 0.00 0.00 36.76 3.41
222 224 5.262588 ACAAAGACAATGAAACCCAAGTC 57.737 39.130 0.00 0.00 35.43 3.01
223 225 5.675684 AACAAAGACAATGAAACCCAAGT 57.324 34.783 0.00 0.00 0.00 3.16
224 226 6.256321 CAGAAACAAAGACAATGAAACCCAAG 59.744 38.462 0.00 0.00 0.00 3.61
225 227 6.105333 CAGAAACAAAGACAATGAAACCCAA 58.895 36.000 0.00 0.00 0.00 4.12
226 228 5.659463 CAGAAACAAAGACAATGAAACCCA 58.341 37.500 0.00 0.00 0.00 4.51
227 229 4.507756 GCAGAAACAAAGACAATGAAACCC 59.492 41.667 0.00 0.00 0.00 4.11
228 230 5.108517 TGCAGAAACAAAGACAATGAAACC 58.891 37.500 0.00 0.00 0.00 3.27
229 231 6.698766 AGATGCAGAAACAAAGACAATGAAAC 59.301 34.615 0.00 0.00 0.00 2.78
319 323 7.851822 AAGTTGCTTAATTAATGTTGTGACG 57.148 32.000 0.00 0.00 0.00 4.35
431 471 5.888982 ACTACCGGTAAGGATTCAATCAT 57.111 39.130 16.65 0.00 45.00 2.45
444 484 3.761752 GGTACAACCAACTACTACCGGTA 59.238 47.826 14.95 14.95 38.42 4.02
445 485 2.562738 GGTACAACCAACTACTACCGGT 59.437 50.000 13.98 13.98 38.42 5.28
446 486 3.236632 GGTACAACCAACTACTACCGG 57.763 52.381 0.00 0.00 38.42 5.28
462 502 9.680315 CTGCTACTACTACTGATAAAATGGTAC 57.320 37.037 0.00 0.00 0.00 3.34
463 503 9.636789 TCTGCTACTACTACTGATAAAATGGTA 57.363 33.333 0.00 0.00 0.00 3.25
464 504 8.534954 TCTGCTACTACTACTGATAAAATGGT 57.465 34.615 0.00 0.00 0.00 3.55
465 505 9.250624 GTTCTGCTACTACTACTGATAAAATGG 57.749 37.037 0.00 0.00 0.00 3.16
470 510 9.902684 ACTTAGTTCTGCTACTACTACTGATAA 57.097 33.333 0.00 0.00 30.62 1.75
471 511 9.545105 GACTTAGTTCTGCTACTACTACTGATA 57.455 37.037 0.00 0.00 30.62 2.15
472 512 8.047911 TGACTTAGTTCTGCTACTACTACTGAT 58.952 37.037 0.00 0.00 30.62 2.90
473 513 7.392418 TGACTTAGTTCTGCTACTACTACTGA 58.608 38.462 0.00 0.00 30.62 3.41
474 514 7.612668 TGACTTAGTTCTGCTACTACTACTG 57.387 40.000 0.00 0.00 30.62 2.74
475 515 9.550406 CTATGACTTAGTTCTGCTACTACTACT 57.450 37.037 0.00 0.00 30.62 2.57
476 516 9.545105 TCTATGACTTAGTTCTGCTACTACTAC 57.455 37.037 0.00 0.00 30.62 2.73
477 517 9.767228 CTCTATGACTTAGTTCTGCTACTACTA 57.233 37.037 0.00 0.00 30.62 1.82
478 518 7.227910 GCTCTATGACTTAGTTCTGCTACTACT 59.772 40.741 0.00 0.00 30.62 2.57
479 519 7.227910 AGCTCTATGACTTAGTTCTGCTACTAC 59.772 40.741 0.00 0.00 30.62 2.73
480 520 7.284074 AGCTCTATGACTTAGTTCTGCTACTA 58.716 38.462 0.00 0.00 0.00 1.82
481 521 6.126409 AGCTCTATGACTTAGTTCTGCTACT 58.874 40.000 0.00 0.00 0.00 2.57
482 522 6.262273 AGAGCTCTATGACTTAGTTCTGCTAC 59.738 42.308 16.50 0.00 0.00 3.58
483 523 6.262049 CAGAGCTCTATGACTTAGTTCTGCTA 59.738 42.308 17.75 0.00 31.71 3.49
484 524 5.067674 CAGAGCTCTATGACTTAGTTCTGCT 59.932 44.000 17.75 0.00 31.71 4.24
485 525 5.163561 ACAGAGCTCTATGACTTAGTTCTGC 60.164 44.000 17.75 9.76 36.52 4.26
486 526 6.449635 ACAGAGCTCTATGACTTAGTTCTG 57.550 41.667 17.75 12.12 37.63 3.02
487 527 8.760980 AATACAGAGCTCTATGACTTAGTTCT 57.239 34.615 17.75 0.00 0.00 3.01
488 528 9.810545 AAAATACAGAGCTCTATGACTTAGTTC 57.189 33.333 17.75 0.00 0.00 3.01
489 529 9.593134 CAAAATACAGAGCTCTATGACTTAGTT 57.407 33.333 17.75 4.08 0.00 2.24
490 530 8.754080 ACAAAATACAGAGCTCTATGACTTAGT 58.246 33.333 17.75 10.05 0.00 2.24
491 531 9.593134 AACAAAATACAGAGCTCTATGACTTAG 57.407 33.333 17.75 3.73 0.00 2.18
493 533 9.372369 GTAACAAAATACAGAGCTCTATGACTT 57.628 33.333 17.75 4.86 0.00 3.01
494 534 8.754080 AGTAACAAAATACAGAGCTCTATGACT 58.246 33.333 17.75 5.47 0.00 3.41
495 535 8.812329 CAGTAACAAAATACAGAGCTCTATGAC 58.188 37.037 17.75 3.32 0.00 3.06
496 536 7.981789 CCAGTAACAAAATACAGAGCTCTATGA 59.018 37.037 17.75 4.80 0.00 2.15
497 537 7.981789 TCCAGTAACAAAATACAGAGCTCTATG 59.018 37.037 17.75 8.82 0.00 2.23
498 538 8.079211 TCCAGTAACAAAATACAGAGCTCTAT 57.921 34.615 17.75 8.14 0.00 1.98
499 539 7.396339 TCTCCAGTAACAAAATACAGAGCTCTA 59.604 37.037 17.75 1.39 32.63 2.43
500 540 6.211584 TCTCCAGTAACAAAATACAGAGCTCT 59.788 38.462 11.45 11.45 32.63 4.09
501 541 6.398918 TCTCCAGTAACAAAATACAGAGCTC 58.601 40.000 5.27 5.27 32.63 4.09
502 542 6.360370 TCTCCAGTAACAAAATACAGAGCT 57.640 37.500 0.00 0.00 32.63 4.09
503 543 7.010923 CAGATCTCCAGTAACAAAATACAGAGC 59.989 40.741 0.00 0.00 32.63 4.09
504 544 8.037758 ACAGATCTCCAGTAACAAAATACAGAG 58.962 37.037 0.00 0.00 33.29 3.35
505 545 7.907389 ACAGATCTCCAGTAACAAAATACAGA 58.093 34.615 0.00 0.00 0.00 3.41
506 546 8.553459 AACAGATCTCCAGTAACAAAATACAG 57.447 34.615 0.00 0.00 0.00 2.74
507 547 8.918202 AAACAGATCTCCAGTAACAAAATACA 57.082 30.769 0.00 0.00 0.00 2.29
510 550 9.520515 ACATAAACAGATCTCCAGTAACAAAAT 57.479 29.630 0.00 0.00 0.00 1.82
511 551 8.783093 CACATAAACAGATCTCCAGTAACAAAA 58.217 33.333 0.00 0.00 0.00 2.44
512 552 7.390440 CCACATAAACAGATCTCCAGTAACAAA 59.610 37.037 0.00 0.00 0.00 2.83
513 553 6.878923 CCACATAAACAGATCTCCAGTAACAA 59.121 38.462 0.00 0.00 0.00 2.83
514 554 6.013725 ACCACATAAACAGATCTCCAGTAACA 60.014 38.462 0.00 0.00 0.00 2.41
515 555 6.407202 ACCACATAAACAGATCTCCAGTAAC 58.593 40.000 0.00 0.00 0.00 2.50
516 556 6.620877 ACCACATAAACAGATCTCCAGTAA 57.379 37.500 0.00 0.00 0.00 2.24
517 557 6.406370 CAACCACATAAACAGATCTCCAGTA 58.594 40.000 0.00 0.00 0.00 2.74
518 558 5.248640 CAACCACATAAACAGATCTCCAGT 58.751 41.667 0.00 0.00 0.00 4.00
519 559 4.095483 GCAACCACATAAACAGATCTCCAG 59.905 45.833 0.00 0.00 0.00 3.86
520 560 4.009675 GCAACCACATAAACAGATCTCCA 58.990 43.478 0.00 0.00 0.00 3.86
521 561 4.265073 AGCAACCACATAAACAGATCTCC 58.735 43.478 0.00 0.00 0.00 3.71
522 562 6.595716 AGTTAGCAACCACATAAACAGATCTC 59.404 38.462 0.00 0.00 0.00 2.75
523 563 6.476378 AGTTAGCAACCACATAAACAGATCT 58.524 36.000 0.00 0.00 0.00 2.75
524 564 6.371548 TGAGTTAGCAACCACATAAACAGATC 59.628 38.462 0.00 0.00 0.00 2.75
525 565 6.237901 TGAGTTAGCAACCACATAAACAGAT 58.762 36.000 0.00 0.00 0.00 2.90
526 566 5.616270 TGAGTTAGCAACCACATAAACAGA 58.384 37.500 0.00 0.00 0.00 3.41
527 567 5.940192 TGAGTTAGCAACCACATAAACAG 57.060 39.130 0.00 0.00 0.00 3.16
528 568 7.987750 TTATGAGTTAGCAACCACATAAACA 57.012 32.000 16.55 0.00 37.76 2.83
530 570 9.899661 ACTATTATGAGTTAGCAACCACATAAA 57.100 29.630 19.38 13.54 40.67 1.40
533 573 9.326413 GTTACTATTATGAGTTAGCAACCACAT 57.674 33.333 0.00 1.35 34.78 3.21
534 574 8.537016 AGTTACTATTATGAGTTAGCAACCACA 58.463 33.333 0.00 0.00 0.00 4.17
535 575 8.943909 AGTTACTATTATGAGTTAGCAACCAC 57.056 34.615 0.00 0.00 0.00 4.16
563 603 9.019656 GGCAAAAGGATAATTAACCCAAAATTT 57.980 29.630 8.09 0.12 0.00 1.82
564 604 7.613801 GGGCAAAAGGATAATTAACCCAAAATT 59.386 33.333 8.09 0.00 34.82 1.82
565 605 7.036935 AGGGCAAAAGGATAATTAACCCAAAAT 60.037 33.333 8.09 0.00 37.28 1.82
636 676 1.628846 GGACTAGGGGCAAAACTGAGA 59.371 52.381 0.00 0.00 0.00 3.27
792 832 0.106708 TCTGCTCAACGGCTCTTTGT 59.893 50.000 0.00 0.00 0.00 2.83
1090 1130 1.002087 AGAAACCCTTCGATCAACGCT 59.998 47.619 0.00 0.00 42.26 5.07
1425 1553 5.308825 TCAAGCTTCCTAACCTTCTTCTTG 58.691 41.667 0.00 0.00 0.00 3.02
1979 2113 5.818136 ATCACGGTGTATTTGAATTGGAG 57.182 39.130 8.17 0.00 0.00 3.86
2014 2148 4.756135 GGCACATTTTCCATGACATTTTGT 59.244 37.500 0.00 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.