Multiple sequence alignment - TraesCS6D01G082500

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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 TraesCS6D01G082500 chr6D 100.000 1458 0 0 1249 2706 47793110 47794567 0.000000e+00 2693
1 TraesCS6D01G082500 chr6D 98.971 1458 15 0 1249 2706 466182476 466183933 0.000000e+00 2610
2 TraesCS6D01G082500 chr6D 100.000 1123 0 0 1 1123 47791862 47792984 0.000000e+00 2074
3 TraesCS6D01G082500 chr6D 95.652 69 2 1 481 549 47792273 47792340 2.850000e-20 110
4 TraesCS6D01G082500 chr6D 95.652 69 2 1 412 479 47792342 47792410 2.850000e-20 110
5 TraesCS6D01G082500 chr3D 99.177 1458 12 0 1249 2706 134599221 134597764 0.000000e+00 2627
6 TraesCS6D01G082500 chr3D 98.973 1460 12 3 1249 2706 535655034 535656492 0.000000e+00 2610
7 TraesCS6D01G082500 chr3D 98.903 1458 16 0 1249 2706 365841930 365840473 0.000000e+00 2604
8 TraesCS6D01G082500 chr3D 98.697 1458 19 0 1249 2706 593933918 593935375 0.000000e+00 2588
9 TraesCS6D01G082500 chr3D 95.192 312 8 4 716 1022 535654340 535654649 1.130000e-133 486
10 TraesCS6D01G082500 chr3D 98.031 254 5 0 870 1123 134599512 134599259 2.470000e-120 442
11 TraesCS6D01G082500 chr3D 97.255 255 6 1 870 1123 593933620 593933874 5.350000e-117 431
12 TraesCS6D01G082500 chr3D 96.850 254 8 0 870 1123 365842221 365841968 2.490000e-115 425
13 TraesCS6D01G082500 chr5D 99.177 1458 11 1 1249 2706 100988771 100990227 0.000000e+00 2625
14 TraesCS6D01G082500 chr5D 98.598 1427 20 0 1280 2706 498267925 498269351 0.000000e+00 2525
15 TraesCS6D01G082500 chr5D 96.850 254 7 1 870 1123 498267623 498267875 8.960000e-115 424
16 TraesCS6D01G082500 chr5D 96.735 245 4 3 870 1114 100987935 100988175 3.240000e-109 405
17 TraesCS6D01G082500 chr2D 98.424 1459 22 1 1249 2706 472192294 472190836 0.000000e+00 2566
18 TraesCS6D01G082500 chr2D 86.765 136 14 4 718 852 610874282 610874150 6.040000e-32 148
19 TraesCS6D01G082500 chr4B 97.188 1458 39 1 1249 2706 592155083 592153628 0.000000e+00 2464
20 TraesCS6D01G082500 chr4B 94.239 243 10 2 881 1123 592031962 592031724 4.260000e-98 368
21 TraesCS6D01G082500 chr7D 93.827 405 10 8 720 1123 162135832 162136222 1.790000e-166 595
22 TraesCS6D01G082500 chr7D 92.736 413 11 6 719 1123 162134380 162134781 1.810000e-161 579
23 TraesCS6D01G082500 chr7D 88.406 138 8 4 713 843 109439229 109439365 2.790000e-35 159
24 TraesCS6D01G082500 chr7D 86.567 134 10 6 719 852 116793402 116793527 1.010000e-29 141
25 TraesCS6D01G082500 chr6B 86.652 457 35 8 1 433 123747965 123747511 1.460000e-132 483
26 TraesCS6D01G082500 chr6A 85.777 457 40 8 1 433 67375016 67374561 6.830000e-126 460
27 TraesCS6D01G082500 chr6A 83.200 250 30 11 479 720 67374584 67374339 4.540000e-53 219
28 TraesCS6D01G082500 chr1D 95.541 157 6 1 720 875 475696854 475696698 1.610000e-62 250
29 TraesCS6D01G082500 chr1D 93.506 154 5 1 719 872 383657518 383657666 9.750000e-55 224
30 TraesCS6D01G082500 chr5B 87.050 139 11 5 718 851 6837492 6837628 1.680000e-32 150


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 TraesCS6D01G082500 chr6D 47791862 47794567 2705 False 1246.75 2693 97.8260 1 2706 4 chr6D.!!$F2 2705
1 TraesCS6D01G082500 chr6D 466182476 466183933 1457 False 2610.00 2610 98.9710 1249 2706 1 chr6D.!!$F1 1457
2 TraesCS6D01G082500 chr3D 535654340 535656492 2152 False 1548.00 2610 97.0825 716 2706 2 chr3D.!!$F1 1990
3 TraesCS6D01G082500 chr3D 134597764 134599512 1748 True 1534.50 2627 98.6040 870 2706 2 chr3D.!!$R1 1836
4 TraesCS6D01G082500 chr3D 365840473 365842221 1748 True 1514.50 2604 97.8765 870 2706 2 chr3D.!!$R2 1836
5 TraesCS6D01G082500 chr3D 593933620 593935375 1755 False 1509.50 2588 97.9760 870 2706 2 chr3D.!!$F2 1836
6 TraesCS6D01G082500 chr5D 100987935 100990227 2292 False 1515.00 2625 97.9560 870 2706 2 chr5D.!!$F1 1836
7 TraesCS6D01G082500 chr5D 498267623 498269351 1728 False 1474.50 2525 97.7240 870 2706 2 chr5D.!!$F2 1836
8 TraesCS6D01G082500 chr2D 472190836 472192294 1458 True 2566.00 2566 98.4240 1249 2706 1 chr2D.!!$R1 1457
9 TraesCS6D01G082500 chr4B 592153628 592155083 1455 True 2464.00 2464 97.1880 1249 2706 1 chr4B.!!$R2 1457
10 TraesCS6D01G082500 chr7D 162134380 162136222 1842 False 587.00 595 93.2815 719 1123 2 chr7D.!!$F3 404
11 TraesCS6D01G082500 chr6A 67374339 67375016 677 True 339.50 460 84.4885 1 720 2 chr6A.!!$R1 719

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
471 496 0.037975 CTGGTTTGGGCTTGTGCATC 60.038 55.0 0.0 0.0 41.91 3.91 F
1029 1327 0.032615 AGATCAAGCTCCGTCTCCCT 60.033 55.0 0.0 0.0 0.00 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1645 3436 2.677542 TGCTCCGGGAGTACTCATAT 57.322 50.000 24.3 0.0 31.39 1.78 R
2367 4159 3.117663 AGGTGGGTTAAGACAAGAAGCAA 60.118 43.478 0.0 0.0 0.00 3.91 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
28 29 1.068434 GCAGTTGCTTGGCACCTTAAA 59.932 47.619 0.00 0.00 38.71 1.52
29 30 2.863704 GCAGTTGCTTGGCACCTTAAAG 60.864 50.000 0.00 0.00 38.71 1.85
42 43 5.416013 GGCACCTTAAAGAACTCTAGCATTT 59.584 40.000 0.00 0.00 0.00 2.32
49 50 8.788325 TTAAAGAACTCTAGCATTTAAGTCCC 57.212 34.615 0.00 0.00 0.00 4.46
58 59 7.633789 TCTAGCATTTAAGTCCCAGAAAGATT 58.366 34.615 0.00 0.00 0.00 2.40
60 61 7.544804 AGCATTTAAGTCCCAGAAAGATTTT 57.455 32.000 0.00 0.00 0.00 1.82
61 62 7.966812 AGCATTTAAGTCCCAGAAAGATTTTT 58.033 30.769 0.00 0.00 0.00 1.94
62 63 8.090831 AGCATTTAAGTCCCAGAAAGATTTTTC 58.909 33.333 0.46 0.46 42.44 2.29
97 98 3.441572 GGTATTTCACATGCTTGCTCACT 59.558 43.478 0.00 0.00 0.00 3.41
104 105 0.403271 ATGCTTGCTCACTCCCACTT 59.597 50.000 0.00 0.00 0.00 3.16
111 112 1.943507 GCTCACTCCCACTTTCTGCTC 60.944 57.143 0.00 0.00 0.00 4.26
140 141 1.133041 TCGATGATGGACCCTGATCCT 60.133 52.381 0.00 0.00 39.75 3.24
171 172 1.800655 CGTCTGCGAAAGAGATCCTGG 60.801 57.143 0.00 0.00 41.33 4.45
173 174 0.179062 CTGCGAAAGAGATCCTGGGG 60.179 60.000 0.00 0.00 0.00 4.96
221 222 1.134371 GCCTCGGCAAAGAAGTAGGAT 60.134 52.381 2.41 0.00 41.49 3.24
222 223 2.555199 CCTCGGCAAAGAAGTAGGATG 58.445 52.381 0.00 0.00 0.00 3.51
230 231 4.521146 CAAAGAAGTAGGATGCCACATCT 58.479 43.478 7.45 0.00 0.00 2.90
235 236 3.044156 AGTAGGATGCCACATCTGTCAT 58.956 45.455 7.45 0.00 0.00 3.06
236 237 3.457380 AGTAGGATGCCACATCTGTCATT 59.543 43.478 7.45 0.00 0.00 2.57
266 267 3.838271 TAGGAGAGCGGGCAAGCG 61.838 66.667 0.00 0.00 43.00 4.68
319 343 5.388654 TCTGAAAGAAGGCTCTCCAAAAAT 58.611 37.500 0.00 0.00 42.31 1.82
329 353 2.432285 CCAAAAATGCGCCACGGG 60.432 61.111 4.18 0.00 0.00 5.28
333 357 1.531739 AAAAATGCGCCACGGGTCAT 61.532 50.000 4.18 0.00 0.00 3.06
336 360 1.933115 AATGCGCCACGGGTCATTTC 61.933 55.000 4.18 0.00 29.15 2.17
337 361 3.810896 GCGCCACGGGTCATTTCC 61.811 66.667 0.00 0.00 0.00 3.13
338 362 3.131478 CGCCACGGGTCATTTCCC 61.131 66.667 0.00 0.00 43.78 3.97
339 363 2.754254 GCCACGGGTCATTTCCCC 60.754 66.667 0.00 0.00 44.32 4.81
368 393 9.632807 CTGATCTATTGTTTCTGTATAGCTACC 57.367 37.037 0.00 0.00 0.00 3.18
372 397 4.913335 TGTTTCTGTATAGCTACCGAGG 57.087 45.455 0.00 0.00 0.00 4.63
373 398 4.529897 TGTTTCTGTATAGCTACCGAGGA 58.470 43.478 0.00 0.00 0.00 3.71
378 403 5.247084 TCTGTATAGCTACCGAGGATTCTC 58.753 45.833 0.00 0.00 36.69 2.87
396 421 2.816087 TCTCAAGCTGTGAAGCCATTTC 59.184 45.455 0.00 0.00 35.22 2.17
402 427 0.890542 TGTGAAGCCATTTCTGCGCT 60.891 50.000 9.73 0.00 36.71 5.92
409 434 0.962356 CCATTTCTGCGCTGGGAACT 60.962 55.000 14.70 5.12 0.00 3.01
410 435 0.883833 CATTTCTGCGCTGGGAACTT 59.116 50.000 14.70 1.76 0.00 2.66
411 436 0.883833 ATTTCTGCGCTGGGAACTTG 59.116 50.000 14.70 0.00 0.00 3.16
412 437 0.179032 TTTCTGCGCTGGGAACTTGA 60.179 50.000 14.70 0.00 0.00 3.02
413 438 0.603707 TTCTGCGCTGGGAACTTGAG 60.604 55.000 14.70 0.00 0.00 3.02
414 439 2.669569 TGCGCTGGGAACTTGAGC 60.670 61.111 9.73 0.00 0.00 4.26
415 440 2.669569 GCGCTGGGAACTTGAGCA 60.670 61.111 0.00 0.00 32.70 4.26
416 441 2.260869 GCGCTGGGAACTTGAGCAA 61.261 57.895 0.00 0.00 32.70 3.91
417 442 1.589716 GCGCTGGGAACTTGAGCAAT 61.590 55.000 0.00 0.00 32.70 3.56
418 443 1.737838 CGCTGGGAACTTGAGCAATA 58.262 50.000 0.00 0.00 32.70 1.90
419 444 2.292267 CGCTGGGAACTTGAGCAATAT 58.708 47.619 0.00 0.00 32.70 1.28
420 445 2.289002 CGCTGGGAACTTGAGCAATATC 59.711 50.000 0.00 0.00 32.70 1.63
421 446 3.549794 GCTGGGAACTTGAGCAATATCT 58.450 45.455 0.00 0.00 32.70 1.98
422 447 3.314635 GCTGGGAACTTGAGCAATATCTG 59.685 47.826 0.00 0.00 32.70 2.90
423 448 4.521146 CTGGGAACTTGAGCAATATCTGT 58.479 43.478 0.00 0.00 0.00 3.41
424 449 5.674525 CTGGGAACTTGAGCAATATCTGTA 58.325 41.667 0.00 0.00 0.00 2.74
425 450 6.061022 TGGGAACTTGAGCAATATCTGTAA 57.939 37.500 0.00 0.00 0.00 2.41
426 451 6.115446 TGGGAACTTGAGCAATATCTGTAAG 58.885 40.000 0.00 0.00 0.00 2.34
427 452 6.116126 GGGAACTTGAGCAATATCTGTAAGT 58.884 40.000 0.00 0.00 33.76 2.24
428 453 6.599638 GGGAACTTGAGCAATATCTGTAAGTT 59.400 38.462 0.00 0.00 37.93 2.66
429 454 7.769044 GGGAACTTGAGCAATATCTGTAAGTTA 59.231 37.037 0.00 0.00 36.67 2.24
430 455 9.331282 GGAACTTGAGCAATATCTGTAAGTTAT 57.669 33.333 0.00 0.00 36.67 1.89
432 457 8.668510 ACTTGAGCAATATCTGTAAGTTATGG 57.331 34.615 0.00 0.00 29.66 2.74
433 458 7.716998 ACTTGAGCAATATCTGTAAGTTATGGG 59.283 37.037 0.00 0.00 29.66 4.00
434 459 5.997746 TGAGCAATATCTGTAAGTTATGGGC 59.002 40.000 0.00 0.00 33.45 5.36
435 460 6.183361 TGAGCAATATCTGTAAGTTATGGGCT 60.183 38.462 0.00 0.00 40.12 5.19
436 461 6.605119 AGCAATATCTGTAAGTTATGGGCTT 58.395 36.000 0.00 0.00 37.04 4.35
437 462 7.745717 AGCAATATCTGTAAGTTATGGGCTTA 58.254 34.615 0.00 0.00 37.04 3.09
438 463 8.386264 AGCAATATCTGTAAGTTATGGGCTTAT 58.614 33.333 0.00 0.00 37.04 1.73
439 464 8.454106 GCAATATCTGTAAGTTATGGGCTTATG 58.546 37.037 0.00 0.00 31.93 1.90
440 465 8.950210 CAATATCTGTAAGTTATGGGCTTATGG 58.050 37.037 0.00 0.00 29.66 2.74
441 466 4.714632 TCTGTAAGTTATGGGCTTATGGC 58.285 43.478 0.00 0.00 36.04 4.40
450 475 3.131478 GCTTATGGCCGCGTTGGT 61.131 61.111 4.92 0.00 41.21 3.67
451 476 2.791256 CTTATGGCCGCGTTGGTG 59.209 61.111 4.92 0.00 41.21 4.17
452 477 3.395470 CTTATGGCCGCGTTGGTGC 62.395 63.158 4.92 0.00 41.21 5.01
453 478 3.910914 TTATGGCCGCGTTGGTGCT 62.911 57.895 4.92 0.00 41.21 4.40
458 483 3.591835 CCGCGTTGGTGCTGGTTT 61.592 61.111 4.92 0.00 0.00 3.27
459 484 2.353376 CGCGTTGGTGCTGGTTTG 60.353 61.111 0.00 0.00 0.00 2.93
460 485 2.027460 GCGTTGGTGCTGGTTTGG 59.973 61.111 0.00 0.00 0.00 3.28
461 486 2.727544 CGTTGGTGCTGGTTTGGG 59.272 61.111 0.00 0.00 0.00 4.12
462 487 2.421314 GTTGGTGCTGGTTTGGGC 59.579 61.111 0.00 0.00 0.00 5.36
463 488 2.133641 GTTGGTGCTGGTTTGGGCT 61.134 57.895 0.00 0.00 0.00 5.19
464 489 1.382420 TTGGTGCTGGTTTGGGCTT 60.382 52.632 0.00 0.00 0.00 4.35
465 490 1.684386 TTGGTGCTGGTTTGGGCTTG 61.684 55.000 0.00 0.00 0.00 4.01
466 491 2.133641 GGTGCTGGTTTGGGCTTGT 61.134 57.895 0.00 0.00 0.00 3.16
467 492 1.067916 GTGCTGGTTTGGGCTTGTG 59.932 57.895 0.00 0.00 0.00 3.33
468 493 2.029518 GCTGGTTTGGGCTTGTGC 59.970 61.111 0.00 0.00 38.76 4.57
469 494 2.795110 GCTGGTTTGGGCTTGTGCA 61.795 57.895 0.00 0.00 41.91 4.57
470 495 2.051941 CTGGTTTGGGCTTGTGCAT 58.948 52.632 0.00 0.00 41.91 3.96
471 496 0.037975 CTGGTTTGGGCTTGTGCATC 60.038 55.000 0.00 0.00 41.91 3.91
472 497 0.469705 TGGTTTGGGCTTGTGCATCT 60.470 50.000 0.00 0.00 41.91 2.90
473 498 0.681175 GGTTTGGGCTTGTGCATCTT 59.319 50.000 0.00 0.00 41.91 2.40
474 499 1.337167 GGTTTGGGCTTGTGCATCTTC 60.337 52.381 0.00 0.00 41.91 2.87
475 500 1.615392 GTTTGGGCTTGTGCATCTTCT 59.385 47.619 0.00 0.00 41.91 2.85
476 501 1.250328 TTGGGCTTGTGCATCTTCTG 58.750 50.000 0.00 0.00 41.91 3.02
477 502 0.111061 TGGGCTTGTGCATCTTCTGT 59.889 50.000 0.00 0.00 41.91 3.41
502 527 6.455647 TCGAGCAATATCTGTAAGTTATGGG 58.544 40.000 0.00 0.00 29.66 4.00
504 529 6.192970 AGCAATATCTGTAAGTTATGGGCT 57.807 37.500 0.00 0.00 36.27 5.19
506 531 7.745717 AGCAATATCTGTAAGTTATGGGCTTA 58.254 34.615 0.00 0.00 37.04 3.09
508 533 8.454106 GCAATATCTGTAAGTTATGGGCTTATG 58.546 37.037 0.00 0.00 31.93 1.90
510 535 4.714632 TCTGTAAGTTATGGGCTTATGGC 58.285 43.478 0.00 0.00 36.04 4.40
519 544 3.525221 GCTTATGGCCGCATTGGT 58.475 55.556 0.00 0.00 41.21 3.67
520 545 1.066257 GCTTATGGCCGCATTGGTG 59.934 57.895 0.00 0.00 41.21 4.17
532 564 2.216331 ATTGGTGGCTGGTTTGGGC 61.216 57.895 0.00 0.00 0.00 5.36
543 575 0.681175 GGTTTGGGCTTGTGCATCTT 59.319 50.000 0.00 0.00 41.91 2.40
544 576 1.337167 GGTTTGGGCTTGTGCATCTTC 60.337 52.381 0.00 0.00 41.91 2.87
545 577 0.968405 TTTGGGCTTGTGCATCTTCC 59.032 50.000 0.00 0.00 41.91 3.46
549 581 0.109597 GGCTTGTGCATCTTCCGTTG 60.110 55.000 0.00 0.00 41.91 4.10
579 611 4.264083 TGGAGAGCCAGGAATTCTTCATTT 60.264 41.667 5.23 0.00 39.92 2.32
593 625 6.403866 TTCTTCATTTGTTTGCTGGTGTAT 57.596 33.333 0.00 0.00 0.00 2.29
599 631 2.937519 TGTTTGCTGGTGTATTGGTGA 58.062 42.857 0.00 0.00 0.00 4.02
600 632 3.495331 TGTTTGCTGGTGTATTGGTGAT 58.505 40.909 0.00 0.00 0.00 3.06
601 633 3.255395 TGTTTGCTGGTGTATTGGTGATG 59.745 43.478 0.00 0.00 0.00 3.07
602 634 1.462616 TGCTGGTGTATTGGTGATGC 58.537 50.000 0.00 0.00 0.00 3.91
608 640 1.745087 GTGTATTGGTGATGCTGTGGG 59.255 52.381 0.00 0.00 0.00 4.61
609 641 0.740737 GTATTGGTGATGCTGTGGGC 59.259 55.000 0.00 0.00 42.22 5.36
633 665 0.675083 TGCTTGACTGCCATTTGGTG 59.325 50.000 0.00 0.00 37.57 4.17
641 673 2.297033 ACTGCCATTTGGTGTTGTGATC 59.703 45.455 0.00 0.00 37.57 2.92
642 674 1.269174 TGCCATTTGGTGTTGTGATCG 59.731 47.619 0.00 0.00 37.57 3.69
643 675 1.402720 GCCATTTGGTGTTGTGATCGG 60.403 52.381 0.00 0.00 37.57 4.18
653 685 0.536233 TTGTGATCGGTTGTGTGGGG 60.536 55.000 0.00 0.00 0.00 4.96
671 703 3.732048 GGGGGAACTAAATGAAGGACA 57.268 47.619 0.00 0.00 0.00 4.02
672 704 4.251103 GGGGGAACTAAATGAAGGACAT 57.749 45.455 0.00 0.00 41.45 3.06
705 737 1.608055 TCAGTTGGACTTGTGGCATG 58.392 50.000 0.00 0.00 0.00 4.06
706 738 0.038892 CAGTTGGACTTGTGGCATGC 60.039 55.000 9.90 9.90 0.00 4.06
709 741 0.895100 TTGGACTTGTGGCATGCTCC 60.895 55.000 18.92 15.60 0.00 4.70
713 745 2.677524 TTGTGGCATGCTCCCAGC 60.678 61.111 18.92 0.00 42.82 4.85
727 759 3.181474 GCTCCCAGCGTAAATCTCTACTT 60.181 47.826 0.00 0.00 0.00 2.24
728 760 4.680975 GCTCCCAGCGTAAATCTCTACTTT 60.681 45.833 0.00 0.00 0.00 2.66
757 789 2.236395 CGAGTTGGTTGAATAGTCCCCT 59.764 50.000 0.00 0.00 0.00 4.79
771 816 0.471211 TCCCCTCACTTTCGTCTGGT 60.471 55.000 0.00 0.00 0.00 4.00
823 869 2.161713 TTTTCCATCCCCACGCCCAT 62.162 55.000 0.00 0.00 0.00 4.00
1029 1327 0.032615 AGATCAAGCTCCGTCTCCCT 60.033 55.000 0.00 0.00 0.00 4.20
2367 4159 0.117140 TCACCACCTCCCTGATGAGT 59.883 55.000 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 5.721960 TCTGGGACTTAAATGCTAGAGTTCT 59.278 40.000 0.00 0.00 0.00 3.01
29 30 5.978814 TCTGGGACTTAAATGCTAGAGTTC 58.021 41.667 0.00 0.00 0.00 3.01
58 59 6.945435 TGAAATACCTGTCATAAGGCAGAAAA 59.055 34.615 0.10 0.00 41.46 2.29
60 61 5.880332 GTGAAATACCTGTCATAAGGCAGAA 59.120 40.000 0.10 0.00 41.46 3.02
61 62 5.045942 TGTGAAATACCTGTCATAAGGCAGA 60.046 40.000 0.10 0.00 41.46 4.26
62 63 5.185454 TGTGAAATACCTGTCATAAGGCAG 58.815 41.667 0.00 0.00 41.46 4.85
63 64 5.172687 TGTGAAATACCTGTCATAAGGCA 57.827 39.130 0.00 0.00 41.46 4.75
64 65 5.506317 GCATGTGAAATACCTGTCATAAGGC 60.506 44.000 0.00 0.00 41.46 4.35
69 70 4.142315 GCAAGCATGTGAAATACCTGTCAT 60.142 41.667 0.00 0.00 0.00 3.06
73 74 3.441222 TGAGCAAGCATGTGAAATACCTG 59.559 43.478 0.00 0.00 0.00 4.00
97 98 2.172505 TGAAAGTGAGCAGAAAGTGGGA 59.827 45.455 0.00 0.00 0.00 4.37
157 158 0.462759 GTGCCCCAGGATCTCTTTCG 60.463 60.000 0.00 0.00 0.00 3.46
171 172 0.039618 TTCTCAAAGATGGGGTGCCC 59.960 55.000 0.00 0.00 45.71 5.36
173 174 0.813821 GCTTCTCAAAGATGGGGTGC 59.186 55.000 0.00 0.00 34.14 5.01
182 183 2.476854 GGCATTACGCAGCTTCTCAAAG 60.477 50.000 0.00 0.00 45.17 2.77
230 231 4.397481 CTACTGCAGGATCTGAATGACA 57.603 45.455 19.93 0.00 32.44 3.58
258 259 4.481112 CCGATGTTGCGCTTGCCC 62.481 66.667 9.73 0.00 38.03 5.36
314 338 1.531739 ATGACCCGTGGCGCATTTTT 61.532 50.000 10.83 0.00 0.00 1.94
319 343 3.053291 GAAATGACCCGTGGCGCA 61.053 61.111 10.83 0.00 0.00 6.09
338 362 4.510167 ACAGAAACAATAGATCAGGGGG 57.490 45.455 0.00 0.00 0.00 5.40
339 363 6.876257 GCTATACAGAAACAATAGATCAGGGG 59.124 42.308 0.00 0.00 0.00 4.79
349 374 5.597182 TCCTCGGTAGCTATACAGAAACAAT 59.403 40.000 0.00 0.00 35.97 2.71
355 380 5.221864 TGAGAATCCTCGGTAGCTATACAGA 60.222 44.000 0.00 0.00 42.33 3.41
368 393 2.662006 TCACAGCTTGAGAATCCTCG 57.338 50.000 0.00 0.00 42.33 4.63
372 397 2.430465 TGGCTTCACAGCTTGAGAATC 58.570 47.619 0.00 0.00 46.44 2.52
373 398 2.574006 TGGCTTCACAGCTTGAGAAT 57.426 45.000 0.00 0.00 46.44 2.40
378 403 2.925306 GCAGAAATGGCTTCACAGCTTG 60.925 50.000 0.00 0.00 46.44 4.01
396 421 2.684843 GCTCAAGTTCCCAGCGCAG 61.685 63.158 11.47 0.00 0.00 5.18
402 427 4.574674 ACAGATATTGCTCAAGTTCCCA 57.425 40.909 0.00 0.00 0.00 4.37
409 434 6.486657 GCCCATAACTTACAGATATTGCTCAA 59.513 38.462 0.00 0.00 0.00 3.02
410 435 5.997746 GCCCATAACTTACAGATATTGCTCA 59.002 40.000 0.00 0.00 0.00 4.26
411 436 6.234177 AGCCCATAACTTACAGATATTGCTC 58.766 40.000 0.00 0.00 0.00 4.26
412 437 6.192970 AGCCCATAACTTACAGATATTGCT 57.807 37.500 0.00 0.00 0.00 3.91
413 438 6.884280 AAGCCCATAACTTACAGATATTGC 57.116 37.500 0.00 0.00 0.00 3.56
414 439 8.950210 CCATAAGCCCATAACTTACAGATATTG 58.050 37.037 0.00 0.00 32.67 1.90
415 440 7.611855 GCCATAAGCCCATAACTTACAGATATT 59.388 37.037 0.00 0.00 32.67 1.28
416 441 7.112779 GCCATAAGCCCATAACTTACAGATAT 58.887 38.462 0.00 0.00 32.67 1.63
417 442 6.472887 GCCATAAGCCCATAACTTACAGATA 58.527 40.000 0.00 0.00 32.67 1.98
418 443 5.316987 GCCATAAGCCCATAACTTACAGAT 58.683 41.667 0.00 0.00 32.67 2.90
419 444 4.714632 GCCATAAGCCCATAACTTACAGA 58.285 43.478 0.00 0.00 32.67 3.41
433 458 3.131478 ACCAACGCGGCCATAAGC 61.131 61.111 12.47 0.00 39.03 3.09
434 459 2.791256 CACCAACGCGGCCATAAG 59.209 61.111 12.47 0.00 39.03 1.73
435 460 3.436055 GCACCAACGCGGCCATAA 61.436 61.111 12.47 0.00 39.03 1.90
436 461 4.402528 AGCACCAACGCGGCCATA 62.403 61.111 12.47 0.00 39.03 2.74
441 466 3.591835 AAACCAGCACCAACGCGG 61.592 61.111 12.47 0.00 42.50 6.46
442 467 2.353376 CAAACCAGCACCAACGCG 60.353 61.111 3.53 3.53 36.85 6.01
443 468 2.027460 CCAAACCAGCACCAACGC 59.973 61.111 0.00 0.00 0.00 4.84
444 469 2.727544 CCCAAACCAGCACCAACG 59.272 61.111 0.00 0.00 0.00 4.10
445 470 1.685355 AAGCCCAAACCAGCACCAAC 61.685 55.000 0.00 0.00 0.00 3.77
446 471 1.382420 AAGCCCAAACCAGCACCAA 60.382 52.632 0.00 0.00 0.00 3.67
447 472 2.132996 CAAGCCCAAACCAGCACCA 61.133 57.895 0.00 0.00 0.00 4.17
448 473 2.133641 ACAAGCCCAAACCAGCACC 61.134 57.895 0.00 0.00 0.00 5.01
449 474 1.067916 CACAAGCCCAAACCAGCAC 59.932 57.895 0.00 0.00 0.00 4.40
450 475 2.795110 GCACAAGCCCAAACCAGCA 61.795 57.895 0.00 0.00 33.58 4.41
451 476 2.029518 GCACAAGCCCAAACCAGC 59.970 61.111 0.00 0.00 33.58 4.85
452 477 0.037975 GATGCACAAGCCCAAACCAG 60.038 55.000 0.00 0.00 41.13 4.00
453 478 0.469705 AGATGCACAAGCCCAAACCA 60.470 50.000 0.00 0.00 41.13 3.67
454 479 0.681175 AAGATGCACAAGCCCAAACC 59.319 50.000 0.00 0.00 41.13 3.27
455 480 1.615392 AGAAGATGCACAAGCCCAAAC 59.385 47.619 0.00 0.00 41.13 2.93
456 481 1.614903 CAGAAGATGCACAAGCCCAAA 59.385 47.619 0.00 0.00 41.13 3.28
457 482 1.250328 CAGAAGATGCACAAGCCCAA 58.750 50.000 0.00 0.00 41.13 4.12
458 483 0.111061 ACAGAAGATGCACAAGCCCA 59.889 50.000 0.00 0.00 41.13 5.36
459 484 1.200948 GAACAGAAGATGCACAAGCCC 59.799 52.381 0.00 0.00 41.13 5.19
460 485 1.135859 CGAACAGAAGATGCACAAGCC 60.136 52.381 0.00 0.00 41.13 4.35
461 486 1.800586 TCGAACAGAAGATGCACAAGC 59.199 47.619 0.00 0.00 42.57 4.01
462 487 2.159734 GCTCGAACAGAAGATGCACAAG 60.160 50.000 0.00 0.00 0.00 3.16
463 488 1.800586 GCTCGAACAGAAGATGCACAA 59.199 47.619 0.00 0.00 0.00 3.33
464 489 1.270252 TGCTCGAACAGAAGATGCACA 60.270 47.619 0.00 0.00 0.00 4.57
465 490 1.432514 TGCTCGAACAGAAGATGCAC 58.567 50.000 0.00 0.00 0.00 4.57
466 491 2.168326 TTGCTCGAACAGAAGATGCA 57.832 45.000 0.00 0.00 0.00 3.96
467 492 4.749099 AGATATTGCTCGAACAGAAGATGC 59.251 41.667 0.00 0.00 0.00 3.91
468 493 5.752472 ACAGATATTGCTCGAACAGAAGATG 59.248 40.000 0.00 0.00 0.00 2.90
469 494 5.911752 ACAGATATTGCTCGAACAGAAGAT 58.088 37.500 0.00 0.00 0.00 2.40
470 495 5.330455 ACAGATATTGCTCGAACAGAAGA 57.670 39.130 0.00 0.00 0.00 2.87
471 496 6.754209 ACTTACAGATATTGCTCGAACAGAAG 59.246 38.462 0.00 0.00 0.00 2.85
472 497 6.631016 ACTTACAGATATTGCTCGAACAGAA 58.369 36.000 0.00 0.00 0.00 3.02
473 498 6.208988 ACTTACAGATATTGCTCGAACAGA 57.791 37.500 0.00 0.00 0.00 3.41
474 499 6.893958 AACTTACAGATATTGCTCGAACAG 57.106 37.500 0.00 0.00 0.00 3.16
475 500 7.438160 CCATAACTTACAGATATTGCTCGAACA 59.562 37.037 0.00 0.00 0.00 3.18
476 501 7.095607 CCCATAACTTACAGATATTGCTCGAAC 60.096 40.741 0.00 0.00 0.00 3.95
477 502 6.929049 CCCATAACTTACAGATATTGCTCGAA 59.071 38.462 0.00 0.00 0.00 3.71
502 527 1.066257 CACCAATGCGGCCATAAGC 59.934 57.895 2.24 0.00 39.03 3.09
504 529 2.422231 GCCACCAATGCGGCCATAA 61.422 57.895 2.24 0.00 42.82 1.90
510 535 2.573083 AAACCAGCCACCAATGCGG 61.573 57.895 0.00 0.00 42.50 5.69
511 536 1.373246 CAAACCAGCCACCAATGCG 60.373 57.895 0.00 0.00 0.00 4.73
512 537 1.004679 CCAAACCAGCCACCAATGC 60.005 57.895 0.00 0.00 0.00 3.56
514 539 2.216331 GCCCAAACCAGCCACCAAT 61.216 57.895 0.00 0.00 0.00 3.16
515 540 2.841988 GCCCAAACCAGCCACCAA 60.842 61.111 0.00 0.00 0.00 3.67
516 541 3.387609 AAGCCCAAACCAGCCACCA 62.388 57.895 0.00 0.00 0.00 4.17
518 543 2.133641 ACAAGCCCAAACCAGCCAC 61.134 57.895 0.00 0.00 0.00 5.01
519 544 2.132996 CACAAGCCCAAACCAGCCA 61.133 57.895 0.00 0.00 0.00 4.75
520 545 2.736531 CACAAGCCCAAACCAGCC 59.263 61.111 0.00 0.00 0.00 4.85
521 546 2.029518 GCACAAGCCCAAACCAGC 59.970 61.111 0.00 0.00 33.58 4.85
522 547 0.037975 GATGCACAAGCCCAAACCAG 60.038 55.000 0.00 0.00 41.13 4.00
526 551 0.968405 GGAAGATGCACAAGCCCAAA 59.032 50.000 0.00 0.00 41.13 3.28
532 564 3.837213 ATTCAACGGAAGATGCACAAG 57.163 42.857 0.00 0.00 36.25 3.16
543 575 1.066143 GCTCTCCAGGAATTCAACGGA 60.066 52.381 7.93 8.47 0.00 4.69
544 576 1.373570 GCTCTCCAGGAATTCAACGG 58.626 55.000 7.93 4.31 0.00 4.44
545 577 1.339055 TGGCTCTCCAGGAATTCAACG 60.339 52.381 7.93 0.00 37.47 4.10
570 602 4.734398 ACACCAGCAAACAAATGAAGAA 57.266 36.364 0.00 0.00 0.00 2.52
579 611 2.937519 TCACCAATACACCAGCAAACA 58.062 42.857 0.00 0.00 0.00 2.83
602 634 1.071987 TCAAGCAGACTGCCCACAG 59.928 57.895 23.74 9.48 46.52 3.66
612 644 1.250328 CCAAATGGCAGTCAAGCAGA 58.750 50.000 0.00 0.00 35.83 4.26
633 665 0.591170 CCCACACAACCGATCACAAC 59.409 55.000 0.00 0.00 0.00 3.32
653 685 6.378280 ACATCAATGTCCTTCATTTAGTTCCC 59.622 38.462 0.00 0.00 43.33 3.97
705 737 2.362717 AGTAGAGATTTACGCTGGGAGC 59.637 50.000 0.00 0.00 38.02 4.70
706 738 4.657436 AAGTAGAGATTTACGCTGGGAG 57.343 45.455 0.00 0.00 0.00 4.30
709 741 7.494625 TCCATTAAAAGTAGAGATTTACGCTGG 59.505 37.037 0.00 0.00 0.00 4.85
713 745 8.624701 TCGTCCATTAAAAGTAGAGATTTACG 57.375 34.615 0.00 0.00 0.00 3.18
714 746 9.583765 ACTCGTCCATTAAAAGTAGAGATTTAC 57.416 33.333 7.36 0.00 0.00 2.01
727 759 6.938030 ACTATTCAACCAACTCGTCCATTAAA 59.062 34.615 0.00 0.00 0.00 1.52
728 760 6.469410 ACTATTCAACCAACTCGTCCATTAA 58.531 36.000 0.00 0.00 0.00 1.40
900 946 1.824329 GGATCGAGAGGAGCGGACA 60.824 63.158 0.00 0.00 0.00 4.02
1645 3436 2.677542 TGCTCCGGGAGTACTCATAT 57.322 50.000 24.30 0.00 31.39 1.78
2367 4159 3.117663 AGGTGGGTTAAGACAAGAAGCAA 60.118 43.478 0.00 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.