Multiple sequence alignment - TraesCS6D01G159900

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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 TraesCS6D01G159900 chr6D 100.000 2216 0 0 1 2216 137527733 137529948 0.000000e+00 4093
1 TraesCS6D01G159900 chr6D 83.036 560 47 26 660 1218 137500988 137501500 4.310000e-127 464
2 TraesCS6D01G159900 chr6B 89.095 1348 75 32 660 1975 237111538 237112845 0.000000e+00 1609
3 TraesCS6D01G159900 chr6B 81.311 915 76 41 660 1519 237108319 237109193 0.000000e+00 654
4 TraesCS6D01G159900 chr6B 94.667 225 12 0 1 225 237111280 237111504 1.260000e-92 350
5 TraesCS6D01G159900 chr6B 93.333 210 12 2 2008 2216 237112848 237113056 2.140000e-80 309
6 TraesCS6D01G159900 chr6A 88.962 915 34 13 670 1565 180370820 180371686 0.000000e+00 1068
7 TraesCS6D01G159900 chr6A 82.641 818 67 39 674 1457 180313706 180314482 0.000000e+00 654
8 TraesCS6D01G159900 chr6A 94.583 240 12 1 1 239 180369910 180370149 9.670000e-99 370
9 TraesCS6D01G159900 chr6A 90.370 270 6 9 1957 2216 180372958 180373217 9.800000e-89 337
10 TraesCS6D01G159900 chr6A 83.721 301 44 5 342 640 116810508 116810805 1.680000e-71 279
11 TraesCS6D01G159900 chr6A 90.821 207 13 5 1762 1965 180372017 180372220 2.800000e-69 272
12 TraesCS6D01G159900 chr6A 89.904 208 16 2 1576 1779 180371793 180371999 1.690000e-66 263
13 TraesCS6D01G159900 chr5D 81.773 406 48 14 250 631 510564261 510563858 1.280000e-82 316
14 TraesCS6D01G159900 chr3A 81.572 407 50 4 248 630 7966895 7967300 1.650000e-81 313
15 TraesCS6D01G159900 chr3A 85.424 295 41 2 342 636 689866516 689866224 2.760000e-79 305
16 TraesCS6D01G159900 chr4A 81.463 410 45 12 248 631 698491005 698491409 7.690000e-80 307
17 TraesCS6D01G159900 chr4A 81.343 402 51 12 250 630 191162642 191162244 2.760000e-79 305
18 TraesCS6D01G159900 chr4B 81.592 402 44 12 250 630 561731455 561731063 2.760000e-79 305
19 TraesCS6D01G159900 chr7B 81.114 413 47 13 248 633 551947407 551947815 3.580000e-78 302
20 TraesCS6D01G159900 chr2A 80.941 404 54 9 248 630 27370185 27369784 4.630000e-77 298
21 TraesCS6D01G159900 chr2A 80.392 408 54 12 248 630 691764735 691764329 1.000000e-73 287


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 TraesCS6D01G159900 chr6D 137527733 137529948 2215 False 4093.0 4093 100.0000 1 2216 1 chr6D.!!$F2 2215
1 TraesCS6D01G159900 chr6D 137500988 137501500 512 False 464.0 464 83.0360 660 1218 1 chr6D.!!$F1 558
2 TraesCS6D01G159900 chr6B 237108319 237113056 4737 False 730.5 1609 89.6015 1 2216 4 chr6B.!!$F1 2215
3 TraesCS6D01G159900 chr6A 180313706 180314482 776 False 654.0 654 82.6410 674 1457 1 chr6A.!!$F2 783
4 TraesCS6D01G159900 chr6A 180369910 180373217 3307 False 462.0 1068 90.9280 1 2216 5 chr6A.!!$F3 2215

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
265 3228 0.182775 AGAACTTGGTGCTTTCGGGT 59.817 50.0 0.0 0.0 0.0 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1637 5032 0.172803 GCACCACCTAGGACGTGTAG 59.827 60.0 24.38 8.05 41.22 2.74 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
129 3092 2.286365 TCCAACCGAGCTTGGATTTT 57.714 45.000 27.65 7.80 44.05 1.82
145 3108 5.363939 TGGATTTTGATTTGGTGTGTTTCC 58.636 37.500 0.00 0.00 0.00 3.13
171 3134 1.021202 TTCGCTTGAACTTGGTGTGG 58.979 50.000 0.00 0.00 0.00 4.17
202 3165 1.686355 TTCACCTGAATTTGGCGTGT 58.314 45.000 0.00 0.00 0.00 4.49
257 3220 5.054477 TCTTACTGTACAAGAACTTGGTGC 58.946 41.667 17.05 8.32 44.45 5.01
258 3221 3.560636 ACTGTACAAGAACTTGGTGCT 57.439 42.857 17.05 1.10 44.45 4.40
259 3222 3.886123 ACTGTACAAGAACTTGGTGCTT 58.114 40.909 17.05 0.78 44.45 3.91
263 3226 1.676006 ACAAGAACTTGGTGCTTTCGG 59.324 47.619 17.05 0.00 44.45 4.30
264 3227 1.001378 CAAGAACTTGGTGCTTTCGGG 60.001 52.381 6.66 0.00 36.95 5.14
265 3228 0.182775 AGAACTTGGTGCTTTCGGGT 59.817 50.000 0.00 0.00 0.00 5.28
266 3229 1.418637 AGAACTTGGTGCTTTCGGGTA 59.581 47.619 0.00 0.00 0.00 3.69
283 3246 3.247006 GGTACCCACGCATCCTATATG 57.753 52.381 0.00 0.00 0.00 1.78
284 3247 2.618053 GTACCCACGCATCCTATATGC 58.382 52.381 0.00 0.00 41.35 3.14
335 3298 7.410120 AGTTCAAGAAACTCCAAATCTTGTT 57.590 32.000 12.79 0.98 45.28 2.83
336 3299 7.840931 AGTTCAAGAAACTCCAAATCTTGTTT 58.159 30.769 12.79 0.00 45.28 2.83
350 3313 8.826546 CAAATCTTGTTTGGAATACTCGTATG 57.173 34.615 0.00 0.00 0.00 2.39
351 3314 8.664798 CAAATCTTGTTTGGAATACTCGTATGA 58.335 33.333 0.00 0.00 0.00 2.15
352 3315 8.786826 AATCTTGTTTGGAATACTCGTATGAA 57.213 30.769 0.00 0.00 0.00 2.57
353 3316 8.786826 ATCTTGTTTGGAATACTCGTATGAAA 57.213 30.769 0.00 0.00 0.00 2.69
354 3317 8.610248 TCTTGTTTGGAATACTCGTATGAAAA 57.390 30.769 0.00 0.00 0.00 2.29
356 3319 7.972832 TGTTTGGAATACTCGTATGAAAAGT 57.027 32.000 0.00 0.00 0.00 2.66
358 3321 8.842280 TGTTTGGAATACTCGTATGAAAAGTTT 58.158 29.630 0.00 0.00 0.00 2.66
359 3322 9.113876 GTTTGGAATACTCGTATGAAAAGTTTG 57.886 33.333 0.00 0.00 0.00 2.93
360 3323 8.610248 TTGGAATACTCGTATGAAAAGTTTGA 57.390 30.769 0.00 0.00 0.00 2.69
361 3324 8.610248 TGGAATACTCGTATGAAAAGTTTGAA 57.390 30.769 0.00 0.00 0.00 2.69
362 3325 8.500773 TGGAATACTCGTATGAAAAGTTTGAAC 58.499 33.333 0.00 0.00 0.00 3.18
363 3326 8.500773 GGAATACTCGTATGAAAAGTTTGAACA 58.499 33.333 0.00 0.00 0.00 3.18
364 3327 9.314501 GAATACTCGTATGAAAAGTTTGAACAC 57.685 33.333 0.00 0.00 0.00 3.32
365 3328 5.734311 ACTCGTATGAAAAGTTTGAACACG 58.266 37.500 0.00 0.00 0.00 4.49
366 3329 5.521010 ACTCGTATGAAAAGTTTGAACACGA 59.479 36.000 12.37 12.37 34.99 4.35
367 3330 6.036300 ACTCGTATGAAAAGTTTGAACACGAA 59.964 34.615 13.37 0.00 35.72 3.85
368 3331 6.773080 TCGTATGAAAAGTTTGAACACGAAA 58.227 32.000 11.19 0.00 33.47 3.46
371 3334 7.374754 CGTATGAAAAGTTTGAACACGAAATGA 59.625 33.333 0.00 0.00 0.00 2.57
372 3335 9.180678 GTATGAAAAGTTTGAACACGAAATGAT 57.819 29.630 0.00 0.00 0.00 2.45
373 3336 8.647143 ATGAAAAGTTTGAACACGAAATGATT 57.353 26.923 0.00 0.00 0.00 2.57
374 3337 8.114359 TGAAAAGTTTGAACACGAAATGATTC 57.886 30.769 0.00 0.00 0.00 2.52
375 3338 7.221838 TGAAAAGTTTGAACACGAAATGATTCC 59.778 33.333 0.00 0.00 31.52 3.01
376 3339 6.391227 AAGTTTGAACACGAAATGATTCCT 57.609 33.333 0.00 0.00 31.52 3.36
377 3340 7.504924 AAGTTTGAACACGAAATGATTCCTA 57.495 32.000 0.00 0.00 31.52 2.94
378 3341 6.899114 AGTTTGAACACGAAATGATTCCTAC 58.101 36.000 0.00 0.00 31.52 3.18
379 3342 6.710744 AGTTTGAACACGAAATGATTCCTACT 59.289 34.615 0.00 0.00 31.52 2.57
381 3344 5.789521 TGAACACGAAATGATTCCTACTGA 58.210 37.500 0.00 0.00 31.52 3.41
383 3346 5.407407 ACACGAAATGATTCCTACTGACT 57.593 39.130 0.00 0.00 31.52 3.41
384 3347 5.794894 ACACGAAATGATTCCTACTGACTT 58.205 37.500 0.00 0.00 31.52 3.01
386 3349 5.063944 CACGAAATGATTCCTACTGACTTGG 59.936 44.000 0.00 0.00 31.52 3.61
387 3350 4.034510 CGAAATGATTCCTACTGACTTGGC 59.965 45.833 0.00 0.00 31.52 4.52
388 3351 4.574674 AATGATTCCTACTGACTTGGCA 57.425 40.909 0.00 0.00 0.00 4.92
389 3352 4.574674 ATGATTCCTACTGACTTGGCAA 57.425 40.909 0.00 0.00 0.00 4.52
390 3353 4.365514 TGATTCCTACTGACTTGGCAAA 57.634 40.909 0.00 0.00 0.00 3.68
391 3354 4.724399 TGATTCCTACTGACTTGGCAAAA 58.276 39.130 0.00 0.00 0.00 2.44
392 3355 5.136828 TGATTCCTACTGACTTGGCAAAAA 58.863 37.500 0.00 0.00 0.00 1.94
421 3384 9.769093 AAAACAAGTTTATGACGACAATATAGC 57.231 29.630 0.00 0.00 31.63 2.97
424 3387 6.749216 AGTTTATGACGACAATATAGCGTG 57.251 37.500 0.00 0.00 38.51 5.34
426 3389 7.420002 AGTTTATGACGACAATATAGCGTGTA 58.580 34.615 0.00 0.00 38.51 2.90
428 3391 9.333497 GTTTATGACGACAATATAGCGTGTATA 57.667 33.333 0.00 0.00 38.51 1.47
431 3394 7.656707 TGACGACAATATAGCGTGTATAGTA 57.343 36.000 0.00 0.00 38.51 1.82
432 3395 8.260270 TGACGACAATATAGCGTGTATAGTAT 57.740 34.615 0.00 0.00 38.51 2.12
434 3397 9.552114 GACGACAATATAGCGTGTATAGTATTT 57.448 33.333 0.00 0.00 38.51 1.40
435 3398 9.338291 ACGACAATATAGCGTGTATAGTATTTG 57.662 33.333 0.00 0.00 36.83 2.32
445 3408 8.671921 AGCGTGTATAGTATTTGTATATAGCGT 58.328 33.333 0.00 0.00 0.00 5.07
446 3409 9.282247 GCGTGTATAGTATTTGTATATAGCGTT 57.718 33.333 0.00 0.00 0.00 4.84
467 3430 2.588027 TTTTGCCAAAACTTCGACCC 57.412 45.000 0.00 0.00 0.00 4.46
469 3432 1.028905 TTGCCAAAACTTCGACCCAG 58.971 50.000 0.00 0.00 0.00 4.45
474 3437 1.200020 CAAAACTTCGACCCAGGATGC 59.800 52.381 0.00 0.00 31.97 3.91
477 3440 0.321653 ACTTCGACCCAGGATGCAAC 60.322 55.000 0.00 0.00 31.97 4.17
481 3444 0.958091 CGACCCAGGATGCAACAAAA 59.042 50.000 0.00 0.00 31.97 2.44
483 3446 1.963515 GACCCAGGATGCAACAAAAGT 59.036 47.619 0.00 0.00 31.97 2.66
485 3448 1.962807 CCCAGGATGCAACAAAAGTCA 59.037 47.619 0.00 0.00 31.97 3.41
486 3449 2.564062 CCCAGGATGCAACAAAAGTCAT 59.436 45.455 0.00 0.00 31.97 3.06
489 3452 4.021719 CCAGGATGCAACAAAAGTCATTCT 60.022 41.667 0.00 0.00 31.97 2.40
490 3453 5.159209 CAGGATGCAACAAAAGTCATTCTC 58.841 41.667 0.00 0.00 0.00 2.87
492 3455 5.048224 AGGATGCAACAAAAGTCATTCTCTG 60.048 40.000 0.00 0.00 0.00 3.35
493 3456 5.048504 GGATGCAACAAAAGTCATTCTCTGA 60.049 40.000 0.00 0.00 0.00 3.27
505 3468 6.712241 GTCATTCTCTGACGAATCTTTTCA 57.288 37.500 0.00 0.00 44.58 2.69
506 3469 7.301068 GTCATTCTCTGACGAATCTTTTCAT 57.699 36.000 0.00 0.00 44.58 2.57
507 3470 8.412608 GTCATTCTCTGACGAATCTTTTCATA 57.587 34.615 0.00 0.00 44.58 2.15
508 3471 8.324567 GTCATTCTCTGACGAATCTTTTCATAC 58.675 37.037 0.00 0.00 44.58 2.39
509 3472 6.871044 TTCTCTGACGAATCTTTTCATACG 57.129 37.500 0.00 0.00 0.00 3.06
510 3473 6.190954 TCTCTGACGAATCTTTTCATACGA 57.809 37.500 0.00 0.00 0.00 3.43
511 3474 6.028368 TCTCTGACGAATCTTTTCATACGAC 58.972 40.000 0.00 0.00 0.00 4.34
512 3475 5.950883 TCTGACGAATCTTTTCATACGACT 58.049 37.500 0.00 0.00 0.00 4.18
513 3476 7.065443 TCTCTGACGAATCTTTTCATACGACTA 59.935 37.037 0.00 0.00 0.00 2.59
516 3479 7.085746 TGACGAATCTTTTCATACGACTACAA 58.914 34.615 0.00 0.00 0.00 2.41
517 3480 7.758076 TGACGAATCTTTTCATACGACTACAAT 59.242 33.333 0.00 0.00 0.00 2.71
518 3481 9.229784 GACGAATCTTTTCATACGACTACAATA 57.770 33.333 0.00 0.00 0.00 1.90
519 3482 9.017669 ACGAATCTTTTCATACGACTACAATAC 57.982 33.333 0.00 0.00 0.00 1.89
527 3490 7.255491 TCATACGACTACAATACTTGATCGT 57.745 36.000 16.36 16.36 43.66 3.73
530 3493 5.706916 ACGACTACAATACTTGATCGTGTT 58.293 37.500 13.48 0.00 41.67 3.32
534 3497 6.228258 ACTACAATACTTGATCGTGTTTGGT 58.772 36.000 0.00 0.00 0.00 3.67
535 3498 7.380536 ACTACAATACTTGATCGTGTTTGGTA 58.619 34.615 0.00 0.00 0.00 3.25
536 3499 6.476243 ACAATACTTGATCGTGTTTGGTAC 57.524 37.500 0.00 0.00 0.00 3.34
537 3500 5.410439 ACAATACTTGATCGTGTTTGGTACC 59.590 40.000 4.43 4.43 0.00 3.34
538 3501 3.478857 ACTTGATCGTGTTTGGTACCA 57.521 42.857 11.60 11.60 0.00 3.25
539 3502 3.811083 ACTTGATCGTGTTTGGTACCAA 58.189 40.909 23.69 23.69 0.00 3.67
540 3503 4.394729 ACTTGATCGTGTTTGGTACCAAT 58.605 39.130 27.57 12.02 35.70 3.16
542 3505 5.300792 ACTTGATCGTGTTTGGTACCAATTT 59.699 36.000 27.57 9.29 35.70 1.82
544 3507 6.150396 TGATCGTGTTTGGTACCAATTTTT 57.850 33.333 27.57 10.98 35.70 1.94
606 3569 8.592529 TTTTAAATTATAGGGTGGGTTGGTAC 57.407 34.615 0.00 0.00 0.00 3.34
616 3579 3.950869 GGTTGGTACCCAGGTTCTC 57.049 57.895 10.07 0.00 38.60 2.87
617 3580 1.359168 GGTTGGTACCCAGGTTCTCT 58.641 55.000 10.07 0.00 38.60 3.10
618 3581 1.278413 GGTTGGTACCCAGGTTCTCTC 59.722 57.143 10.07 0.00 38.60 3.20
621 3584 1.104630 GGTACCCAGGTTCTCTCTCG 58.895 60.000 0.00 0.00 0.00 4.04
623 3586 2.356535 GGTACCCAGGTTCTCTCTCGTA 60.357 54.545 0.00 0.00 0.00 3.43
624 3587 2.830651 ACCCAGGTTCTCTCTCGTAT 57.169 50.000 0.00 0.00 0.00 3.06
626 3589 3.442076 ACCCAGGTTCTCTCTCGTATTT 58.558 45.455 0.00 0.00 0.00 1.40
627 3590 3.838903 ACCCAGGTTCTCTCTCGTATTTT 59.161 43.478 0.00 0.00 0.00 1.82
628 3591 4.081586 ACCCAGGTTCTCTCTCGTATTTTC 60.082 45.833 0.00 0.00 0.00 2.29
630 3593 4.106197 CAGGTTCTCTCTCGTATTTTCCG 58.894 47.826 0.00 0.00 0.00 4.30
631 3594 3.762823 AGGTTCTCTCTCGTATTTTCCGT 59.237 43.478 0.00 0.00 0.00 4.69
633 3596 4.562000 GGTTCTCTCTCGTATTTTCCGTTC 59.438 45.833 0.00 0.00 0.00 3.95
634 3597 5.159209 GTTCTCTCTCGTATTTTCCGTTCA 58.841 41.667 0.00 0.00 0.00 3.18
636 3599 5.579718 TCTCTCTCGTATTTTCCGTTCATC 58.420 41.667 0.00 0.00 0.00 2.92
639 3602 6.395629 TCTCTCGTATTTTCCGTTCATCTTT 58.604 36.000 0.00 0.00 0.00 2.52
644 3620 7.867752 TCGTATTTTCCGTTCATCTTTTCTTT 58.132 30.769 0.00 0.00 0.00 2.52
658 3634 0.383949 TTCTTTTGTTCAGGTGCGCC 59.616 50.000 8.71 8.71 0.00 6.53
892 4121 2.042831 GGCTGCCACTCGAAGCATT 61.043 57.895 15.17 0.00 38.56 3.56
905 4134 3.012518 CGAAGCATTGAATTCCCAGACT 58.987 45.455 2.27 0.00 0.00 3.24
1113 4358 0.028505 GCATCTACTACGTCGGCGAA 59.971 55.000 20.03 0.00 42.00 4.70
1119 4364 3.117175 CTACGTCGGCGAACGGGAT 62.117 63.158 20.03 14.17 46.72 3.85
1191 4436 4.760047 GTCGTGCCCATGACGCCT 62.760 66.667 5.01 0.00 37.56 5.52
1270 4526 1.823899 GATGGTTCCATGGCGGGTC 60.824 63.158 6.96 0.00 34.36 4.46
1347 4603 1.271379 GCTAAAACCTGAGGGTGAGCA 60.271 52.381 16.53 0.00 46.67 4.26
1365 4621 6.952743 GTGAGCACCTGATGAATAATTAGTG 58.047 40.000 0.00 0.00 0.00 2.74
1387 4646 3.408634 AGTGAAGATACGGGGTTGTTTG 58.591 45.455 0.00 0.00 0.00 2.93
1473 4754 9.261180 CAAGACACGGTGAACATATATAAAGAT 57.739 33.333 16.29 0.00 0.00 2.40
1474 4755 9.832445 AAGACACGGTGAACATATATAAAGATT 57.168 29.630 16.29 0.00 0.00 2.40
1608 4989 8.627208 ATTATCAGAATATGTTTCTGGCGATT 57.373 30.769 16.00 4.41 44.43 3.34
1611 4992 5.294306 TCAGAATATGTTTCTGGCGATTGAC 59.706 40.000 16.00 0.00 44.43 3.18
1647 5042 2.632987 AAAAACTGCCTACACGTCCT 57.367 45.000 0.00 0.00 0.00 3.85
1648 5043 3.756933 AAAAACTGCCTACACGTCCTA 57.243 42.857 0.00 0.00 0.00 2.94
1649 5044 3.314541 AAAACTGCCTACACGTCCTAG 57.685 47.619 0.00 0.00 0.00 3.02
1814 5252 3.515104 ACCATGTTTTTCCTTAGGCCATG 59.485 43.478 5.01 0.00 0.00 3.66
1865 5305 2.485657 GCATGGCCTTCCTAGTTCCTAC 60.486 54.545 3.32 0.00 0.00 3.18
1928 5369 5.590663 TGCCAGTTGTATGACACTTTAAACA 59.409 36.000 0.00 0.00 0.00 2.83
1932 5373 8.402472 CCAGTTGTATGACACTTTAAACAAAGA 58.598 33.333 4.23 0.00 34.06 2.52
1978 6165 5.988287 TGTCCAAGTCATGCAATGTATCTA 58.012 37.500 0.00 0.00 46.80 1.98
1995 6182 7.563724 TGTATCTAGGAAAGTTAACTGGGTT 57.436 36.000 9.34 0.00 0.00 4.11
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
202 3165 9.859427 CTATATTCAAAGGAATTTTGCAGAACA 57.141 29.630 0.00 0.00 44.69 3.18
239 3202 4.552767 CGAAAGCACCAAGTTCTTGTACAG 60.553 45.833 10.93 0.00 0.00 2.74
245 3208 1.318576 CCCGAAAGCACCAAGTTCTT 58.681 50.000 0.00 0.00 0.00 2.52
247 3210 1.534163 GTACCCGAAAGCACCAAGTTC 59.466 52.381 0.00 0.00 0.00 3.01
248 3211 1.601166 GTACCCGAAAGCACCAAGTT 58.399 50.000 0.00 0.00 0.00 2.66
249 3212 0.250597 GGTACCCGAAAGCACCAAGT 60.251 55.000 0.00 0.00 0.00 3.16
250 3213 2.551644 GGTACCCGAAAGCACCAAG 58.448 57.895 0.00 0.00 0.00 3.61
251 3214 4.804806 GGTACCCGAAAGCACCAA 57.195 55.556 0.00 0.00 0.00 3.67
263 3226 2.677037 GCATATAGGATGCGTGGGTACC 60.677 54.545 2.17 2.17 41.99 3.34
264 3227 2.618053 GCATATAGGATGCGTGGGTAC 58.382 52.381 0.00 0.00 35.17 3.34
266 3229 3.935993 GCATATAGGATGCGTGGGT 57.064 52.632 0.00 0.00 35.17 4.51
326 3289 8.786826 TCATACGAGTATTCCAAACAAGATTT 57.213 30.769 0.00 0.00 0.00 2.17
327 3290 8.786826 TTCATACGAGTATTCCAAACAAGATT 57.213 30.769 0.00 0.00 0.00 2.40
328 3291 8.786826 TTTCATACGAGTATTCCAAACAAGAT 57.213 30.769 0.00 0.00 0.00 2.40
331 3294 8.385898 ACTTTTCATACGAGTATTCCAAACAA 57.614 30.769 0.00 0.00 0.00 2.83
333 3296 9.113876 CAAACTTTTCATACGAGTATTCCAAAC 57.886 33.333 0.00 0.00 0.00 2.93
335 3298 8.610248 TCAAACTTTTCATACGAGTATTCCAA 57.390 30.769 0.00 0.00 0.00 3.53
336 3299 8.500773 GTTCAAACTTTTCATACGAGTATTCCA 58.499 33.333 0.00 0.00 0.00 3.53
339 3302 8.007716 CGTGTTCAAACTTTTCATACGAGTATT 58.992 33.333 0.00 0.00 0.00 1.89
340 3303 7.383029 TCGTGTTCAAACTTTTCATACGAGTAT 59.617 33.333 0.00 0.00 33.75 2.12
341 3304 6.696583 TCGTGTTCAAACTTTTCATACGAGTA 59.303 34.615 0.00 0.00 33.75 2.59
342 3305 5.521010 TCGTGTTCAAACTTTTCATACGAGT 59.479 36.000 0.00 0.00 33.75 4.18
344 3307 5.970140 TCGTGTTCAAACTTTTCATACGA 57.030 34.783 0.00 0.00 35.94 3.43
345 3308 7.374754 TCATTTCGTGTTCAAACTTTTCATACG 59.625 33.333 0.00 0.00 0.00 3.06
346 3309 8.555166 TCATTTCGTGTTCAAACTTTTCATAC 57.445 30.769 0.00 0.00 0.00 2.39
347 3310 9.743057 AATCATTTCGTGTTCAAACTTTTCATA 57.257 25.926 0.00 0.00 0.00 2.15
348 3311 8.647143 AATCATTTCGTGTTCAAACTTTTCAT 57.353 26.923 0.00 0.00 0.00 2.57
349 3312 7.221838 GGAATCATTTCGTGTTCAAACTTTTCA 59.778 33.333 0.00 0.00 32.28 2.69
350 3313 7.435192 AGGAATCATTTCGTGTTCAAACTTTTC 59.565 33.333 0.00 0.00 32.28 2.29
351 3314 7.264947 AGGAATCATTTCGTGTTCAAACTTTT 58.735 30.769 0.00 0.00 32.28 2.27
352 3315 6.805713 AGGAATCATTTCGTGTTCAAACTTT 58.194 32.000 0.00 0.00 32.28 2.66
353 3316 6.391227 AGGAATCATTTCGTGTTCAAACTT 57.609 33.333 0.00 0.00 32.28 2.66
354 3317 6.710744 AGTAGGAATCATTTCGTGTTCAAACT 59.289 34.615 0.00 0.00 32.50 2.66
356 3319 6.708502 TCAGTAGGAATCATTTCGTGTTCAAA 59.291 34.615 0.00 0.00 32.50 2.69
358 3321 5.637810 GTCAGTAGGAATCATTTCGTGTTCA 59.362 40.000 0.00 0.00 32.50 3.18
359 3322 5.869888 AGTCAGTAGGAATCATTTCGTGTTC 59.130 40.000 0.00 0.00 32.50 3.18
360 3323 5.794894 AGTCAGTAGGAATCATTTCGTGTT 58.205 37.500 0.00 0.00 32.50 3.32
361 3324 5.407407 AGTCAGTAGGAATCATTTCGTGT 57.593 39.130 0.00 0.00 32.50 4.49
362 3325 5.063944 CCAAGTCAGTAGGAATCATTTCGTG 59.936 44.000 0.00 0.00 32.50 4.35
363 3326 5.178797 CCAAGTCAGTAGGAATCATTTCGT 58.821 41.667 0.00 0.00 34.51 3.85
364 3327 4.034510 GCCAAGTCAGTAGGAATCATTTCG 59.965 45.833 0.00 0.00 32.28 3.46
365 3328 4.943705 TGCCAAGTCAGTAGGAATCATTTC 59.056 41.667 0.00 0.00 0.00 2.17
366 3329 4.922206 TGCCAAGTCAGTAGGAATCATTT 58.078 39.130 0.00 0.00 0.00 2.32
367 3330 4.574674 TGCCAAGTCAGTAGGAATCATT 57.425 40.909 0.00 0.00 0.00 2.57
368 3331 4.574674 TTGCCAAGTCAGTAGGAATCAT 57.425 40.909 0.00 0.00 0.00 2.45
395 3358 9.769093 GCTATATTGTCGTCATAAACTTGTTTT 57.231 29.630 4.00 0.00 0.00 2.43
396 3359 8.114290 CGCTATATTGTCGTCATAAACTTGTTT 58.886 33.333 4.14 4.14 0.00 2.83
397 3360 7.277098 ACGCTATATTGTCGTCATAAACTTGTT 59.723 33.333 2.14 0.00 0.00 2.83
398 3361 6.755141 ACGCTATATTGTCGTCATAAACTTGT 59.245 34.615 2.14 0.00 0.00 3.16
399 3362 7.057402 CACGCTATATTGTCGTCATAAACTTG 58.943 38.462 4.35 0.00 33.84 3.16
401 3364 6.270815 ACACGCTATATTGTCGTCATAAACT 58.729 36.000 4.35 0.00 33.84 2.66
402 3365 6.506464 ACACGCTATATTGTCGTCATAAAC 57.494 37.500 4.35 0.00 33.84 2.01
403 3366 9.550811 CTATACACGCTATATTGTCGTCATAAA 57.449 33.333 4.35 0.00 33.84 1.40
406 3369 7.142306 ACTATACACGCTATATTGTCGTCAT 57.858 36.000 4.35 4.50 33.84 3.06
408 3371 9.552114 AAATACTATACACGCTATATTGTCGTC 57.448 33.333 4.35 0.00 33.84 4.20
409 3372 9.338291 CAAATACTATACACGCTATATTGTCGT 57.662 33.333 2.14 2.14 36.84 4.34
410 3373 9.338291 ACAAATACTATACACGCTATATTGTCG 57.662 33.333 0.00 0.00 0.00 4.35
420 3383 8.832487 ACGCTATATACAAATACTATACACGC 57.168 34.615 0.00 0.00 0.00 5.34
447 3410 2.233922 TGGGTCGAAGTTTTGGCAAAAA 59.766 40.909 25.60 8.38 32.82 1.94
448 3411 1.825474 TGGGTCGAAGTTTTGGCAAAA 59.175 42.857 20.81 20.81 0.00 2.44
449 3412 1.407258 CTGGGTCGAAGTTTTGGCAAA 59.593 47.619 8.93 8.93 0.00 3.68
450 3413 1.028905 CTGGGTCGAAGTTTTGGCAA 58.971 50.000 0.00 0.00 0.00 4.52
451 3414 0.821711 CCTGGGTCGAAGTTTTGGCA 60.822 55.000 0.00 0.00 0.00 4.92
454 3417 1.200020 GCATCCTGGGTCGAAGTTTTG 59.800 52.381 0.00 0.00 0.00 2.44
455 3418 1.202879 TGCATCCTGGGTCGAAGTTTT 60.203 47.619 0.00 0.00 0.00 2.43
456 3419 0.400213 TGCATCCTGGGTCGAAGTTT 59.600 50.000 0.00 0.00 0.00 2.66
457 3420 0.400213 TTGCATCCTGGGTCGAAGTT 59.600 50.000 0.00 0.00 0.00 2.66
458 3421 0.321653 GTTGCATCCTGGGTCGAAGT 60.322 55.000 0.00 0.00 0.00 3.01
459 3422 0.321564 TGTTGCATCCTGGGTCGAAG 60.322 55.000 0.00 0.00 0.00 3.79
460 3423 0.109532 TTGTTGCATCCTGGGTCGAA 59.890 50.000 0.00 0.00 0.00 3.71
461 3424 0.109532 TTTGTTGCATCCTGGGTCGA 59.890 50.000 0.00 0.00 0.00 4.20
462 3425 0.958091 TTTTGTTGCATCCTGGGTCG 59.042 50.000 0.00 0.00 0.00 4.79
463 3426 1.963515 ACTTTTGTTGCATCCTGGGTC 59.036 47.619 0.00 0.00 0.00 4.46
464 3427 1.963515 GACTTTTGTTGCATCCTGGGT 59.036 47.619 0.00 0.00 0.00 4.51
466 3429 3.947910 ATGACTTTTGTTGCATCCTGG 57.052 42.857 0.00 0.00 0.00 4.45
467 3430 5.048224 AGAGAATGACTTTTGTTGCATCCTG 60.048 40.000 0.00 0.00 0.00 3.86
469 3432 5.048504 TCAGAGAATGACTTTTGTTGCATCC 60.049 40.000 0.00 0.00 31.12 3.51
483 3446 7.220875 CGTATGAAAAGATTCGTCAGAGAATGA 59.779 37.037 0.00 0.00 40.58 2.57
485 3448 7.221067 GTCGTATGAAAAGATTCGTCAGAGAAT 59.779 37.037 0.00 0.00 42.92 2.40
486 3449 6.527023 GTCGTATGAAAAGATTCGTCAGAGAA 59.473 38.462 0.00 0.00 38.46 2.87
489 3452 5.950883 AGTCGTATGAAAAGATTCGTCAGA 58.049 37.500 0.00 0.00 38.46 3.27
490 3453 6.745907 TGTAGTCGTATGAAAAGATTCGTCAG 59.254 38.462 0.00 0.00 38.46 3.51
492 3455 7.502177 TTGTAGTCGTATGAAAAGATTCGTC 57.498 36.000 0.00 0.00 38.46 4.20
493 3456 9.017669 GTATTGTAGTCGTATGAAAAGATTCGT 57.982 33.333 0.00 0.00 38.46 3.85
494 3457 9.234384 AGTATTGTAGTCGTATGAAAAGATTCG 57.766 33.333 0.00 0.00 38.46 3.34
513 3476 8.384685 TTGGTACCAAACACGATCAAGTATTGT 61.385 37.037 25.19 0.00 39.07 2.71
516 3479 5.155278 TGGTACCAAACACGATCAAGTAT 57.845 39.130 13.60 0.00 0.00 2.12
517 3480 4.603989 TGGTACCAAACACGATCAAGTA 57.396 40.909 13.60 0.00 0.00 2.24
518 3481 3.478857 TGGTACCAAACACGATCAAGT 57.521 42.857 13.60 0.00 0.00 3.16
519 3482 5.371115 AATTGGTACCAAACACGATCAAG 57.629 39.130 30.31 0.00 39.55 3.02
521 3484 5.776173 AAAATTGGTACCAAACACGATCA 57.224 34.783 30.31 5.45 39.55 2.92
580 3543 9.033711 GTACCAACCCACCCTATAATTTAAAAA 57.966 33.333 0.00 0.00 0.00 1.94
581 3544 7.618907 GGTACCAACCCACCCTATAATTTAAAA 59.381 37.037 7.15 0.00 40.21 1.52
583 3546 6.671605 GGTACCAACCCACCCTATAATTTAA 58.328 40.000 7.15 0.00 40.21 1.52
584 3547 6.264771 GGTACCAACCCACCCTATAATTTA 57.735 41.667 7.15 0.00 40.21 1.40
585 3548 5.133383 GGTACCAACCCACCCTATAATTT 57.867 43.478 7.15 0.00 40.21 1.82
586 3549 4.801521 GGTACCAACCCACCCTATAATT 57.198 45.455 7.15 0.00 40.21 1.40
605 3568 2.830651 ATACGAGAGAGAACCTGGGT 57.169 50.000 0.00 0.00 0.00 4.51
606 3569 4.434520 GAAAATACGAGAGAGAACCTGGG 58.565 47.826 0.00 0.00 0.00 4.45
608 3571 4.106197 CGGAAAATACGAGAGAGAACCTG 58.894 47.826 0.00 0.00 0.00 4.00
609 3572 3.762823 ACGGAAAATACGAGAGAGAACCT 59.237 43.478 0.00 0.00 34.93 3.50
610 3573 4.107363 ACGGAAAATACGAGAGAGAACC 57.893 45.455 0.00 0.00 34.93 3.62
612 3575 5.381174 TGAACGGAAAATACGAGAGAGAA 57.619 39.130 0.00 0.00 34.93 2.87
613 3576 5.357314 AGATGAACGGAAAATACGAGAGAGA 59.643 40.000 0.00 0.00 34.93 3.10
614 3577 5.583495 AGATGAACGGAAAATACGAGAGAG 58.417 41.667 0.00 0.00 34.93 3.20
616 3579 6.648725 AAAGATGAACGGAAAATACGAGAG 57.351 37.500 0.00 0.00 34.93 3.20
617 3580 6.872020 AGAAAAGATGAACGGAAAATACGAGA 59.128 34.615 0.00 0.00 34.93 4.04
618 3581 7.061752 AGAAAAGATGAACGGAAAATACGAG 57.938 36.000 0.00 0.00 34.93 4.18
621 3584 9.244799 ACAAAAGAAAAGATGAACGGAAAATAC 57.755 29.630 0.00 0.00 0.00 1.89
623 3586 8.716646 AACAAAAGAAAAGATGAACGGAAAAT 57.283 26.923 0.00 0.00 0.00 1.82
624 3587 7.815068 TGAACAAAAGAAAAGATGAACGGAAAA 59.185 29.630 0.00 0.00 0.00 2.29
626 3589 6.857956 TGAACAAAAGAAAAGATGAACGGAA 58.142 32.000 0.00 0.00 0.00 4.30
627 3590 6.443934 TGAACAAAAGAAAAGATGAACGGA 57.556 33.333 0.00 0.00 0.00 4.69
628 3591 5.687285 CCTGAACAAAAGAAAAGATGAACGG 59.313 40.000 0.00 0.00 0.00 4.44
630 3593 6.019559 GCACCTGAACAAAAGAAAAGATGAAC 60.020 38.462 0.00 0.00 0.00 3.18
631 3594 6.042143 GCACCTGAACAAAAGAAAAGATGAA 58.958 36.000 0.00 0.00 0.00 2.57
633 3596 4.442073 CGCACCTGAACAAAAGAAAAGATG 59.558 41.667 0.00 0.00 0.00 2.90
634 3597 4.610945 CGCACCTGAACAAAAGAAAAGAT 58.389 39.130 0.00 0.00 0.00 2.40
636 3599 2.535574 GCGCACCTGAACAAAAGAAAAG 59.464 45.455 0.30 0.00 0.00 2.27
639 3602 0.383949 GGCGCACCTGAACAAAAGAA 59.616 50.000 10.83 0.00 0.00 2.52
644 3620 3.276091 CACGGCGCACCTGAACAA 61.276 61.111 10.83 0.00 0.00 2.83
658 3634 2.097538 CACATTAACGCCCGCACG 59.902 61.111 0.00 0.00 39.50 5.34
791 4016 4.462417 CGAGCGAGCGACCGAGTT 62.462 66.667 1.05 0.00 0.00 3.01
892 4121 5.091552 ACTTGGTACTAGTCTGGGAATTCA 58.908 41.667 7.93 0.00 0.00 2.57
905 4134 4.294702 TGGGGGAGTTAGTACTTGGTACTA 59.705 45.833 0.00 11.94 45.99 1.82
1113 4358 0.320421 CCTTGTTGTCGACATCCCGT 60.320 55.000 20.80 0.00 38.26 5.28
1119 4364 2.280524 CCGGCCTTGTTGTCGACA 60.281 61.111 15.76 15.76 36.19 4.35
1241 4490 1.074405 TGGAACCATCTTGCTCTTGCT 59.926 47.619 0.00 0.00 40.48 3.91
1242 4491 1.538047 TGGAACCATCTTGCTCTTGC 58.462 50.000 0.00 0.00 40.20 4.01
1243 4492 2.426024 CCATGGAACCATCTTGCTCTTG 59.574 50.000 5.56 0.00 33.90 3.02
1270 4526 1.161843 AAGAACGCCACCAATAACCG 58.838 50.000 0.00 0.00 0.00 4.44
1347 4603 8.762645 TCTTCACTCACTAATTATTCATCAGGT 58.237 33.333 0.00 0.00 0.00 4.00
1363 4619 2.028385 ACAACCCCGTATCTTCACTCAC 60.028 50.000 0.00 0.00 0.00 3.51
1365 4621 3.329929 AACAACCCCGTATCTTCACTC 57.670 47.619 0.00 0.00 0.00 3.51
1473 4754 5.221641 CGAATCCCAGTACCAAGGATGATAA 60.222 44.000 9.11 0.00 39.53 1.75
1474 4755 4.283467 CGAATCCCAGTACCAAGGATGATA 59.717 45.833 9.11 0.00 39.53 2.15
1477 4758 2.434336 TCGAATCCCAGTACCAAGGATG 59.566 50.000 9.11 0.37 39.53 3.51
1608 4989 0.678950 TCAGTGACAATGAGCCGTCA 59.321 50.000 0.51 0.00 39.77 4.35
1611 4992 3.624326 TTTTTCAGTGACAATGAGCCG 57.376 42.857 5.65 0.00 0.00 5.52
1636 5031 0.815734 CACCACCTAGGACGTGTAGG 59.184 60.000 17.98 16.01 42.62 3.18
1637 5032 0.172803 GCACCACCTAGGACGTGTAG 59.827 60.000 24.38 8.05 41.22 2.74
1638 5033 0.540133 TGCACCACCTAGGACGTGTA 60.540 55.000 24.38 20.31 41.22 2.90
1639 5034 1.835267 TGCACCACCTAGGACGTGT 60.835 57.895 24.38 11.35 41.22 4.49
1640 5035 1.374252 GTGCACCACCTAGGACGTG 60.374 63.158 17.98 20.26 41.22 4.49
1641 5036 1.533273 AGTGCACCACCTAGGACGT 60.533 57.895 17.98 7.78 41.22 4.34
1642 5037 1.079819 CAGTGCACCACCTAGGACG 60.080 63.158 17.98 7.06 41.22 4.79
1643 5038 1.376037 GCAGTGCACCACCTAGGAC 60.376 63.158 17.98 1.20 41.22 3.85
1644 5039 1.127567 AAGCAGTGCACCACCTAGGA 61.128 55.000 17.98 0.00 41.22 2.94
1645 5040 0.250901 AAAGCAGTGCACCACCTAGG 60.251 55.000 19.20 7.41 45.67 3.02
1646 5041 1.267806 CAAAAGCAGTGCACCACCTAG 59.732 52.381 19.20 0.00 34.49 3.02
1647 5042 1.317613 CAAAAGCAGTGCACCACCTA 58.682 50.000 19.20 0.00 34.49 3.08
1648 5043 2.019897 GCAAAAGCAGTGCACCACCT 62.020 55.000 19.20 4.33 41.80 4.00
1649 5044 1.592400 GCAAAAGCAGTGCACCACC 60.592 57.895 19.20 1.68 41.80 4.61
1814 5252 7.254727 GCTGACATATGAACTGAATCTTCTTCC 60.255 40.741 10.38 0.00 0.00 3.46
1865 5305 7.240674 TGTTTGTCGATTGATTAAGATTTCCG 58.759 34.615 0.00 0.00 0.00 4.30
1900 5341 4.617253 AGTGTCATACAACTGGCAGTTA 57.383 40.909 30.72 18.16 36.03 2.24
1903 5344 5.940192 TTAAAGTGTCATACAACTGGCAG 57.060 39.130 14.16 14.16 29.89 4.85
1928 5369 5.757099 TTCTTCCCTTTCCGTATCTCTTT 57.243 39.130 0.00 0.00 0.00 2.52
1932 5373 3.585732 TGGTTTCTTCCCTTTCCGTATCT 59.414 43.478 0.00 0.00 0.00 1.98
1935 5376 3.073356 ACATGGTTTCTTCCCTTTCCGTA 59.927 43.478 0.00 0.00 0.00 4.02
1978 6165 5.104067 ACTGAGAAACCCAGTTAACTTTCCT 60.104 40.000 5.07 0.00 41.68 3.36
1995 6182 0.474854 TAACCAGGGGCCACTGAGAA 60.475 55.000 37.27 17.52 40.97 2.87
2139 6336 3.924686 GCAAAATTCAGGTGCTCAAGATG 59.075 43.478 0.00 0.00 35.36 2.90
2188 6385 5.542779 AGAAGAAGTGAAAGACGCACTAAT 58.457 37.500 0.00 0.00 45.27 1.73


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

AutoCloner maintained by Alex Coulton.