Multiple sequence alignment - TraesCS6D01G189300

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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 TraesCS6D01G189300 chr6D 100.000 6235 0 0 1 6235 262266463 262272697 0.000000e+00 11514
1 TraesCS6D01G189300 chr6B 96.695 3631 69 19 1744 5367 348707351 348703765 0.000000e+00 5993
2 TraesCS6D01G189300 chr6B 96.453 1748 49 6 1 1746 348709248 348707512 0.000000e+00 2872
3 TraesCS6D01G189300 chr6B 91.737 835 28 15 5423 6235 348696757 348695942 0.000000e+00 1122
4 TraesCS6D01G189300 chr6A 96.601 3236 61 20 610 3815 323002278 322999062 0.000000e+00 5321
5 TraesCS6D01G189300 chr6A 93.404 2441 83 18 3814 6235 322998713 322996332 0.000000e+00 3544
6 TraesCS6D01G189300 chr3B 95.291 446 20 1 2092 2537 666249102 666248658 0.000000e+00 706
7 TraesCS6D01G189300 chr2A 79.377 514 96 10 2477 2985 562604305 562603797 2.760000e-93 353
8 TraesCS6D01G189300 chr2D 79.142 513 97 10 2477 2984 425742025 425742532 4.630000e-91 346
9 TraesCS6D01G189300 chr2B 78.906 512 100 8 2477 2984 501007661 501008168 2.150000e-89 340


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 TraesCS6D01G189300 chr6D 262266463 262272697 6234 False 11514.0 11514 100.0000 1 6235 1 chr6D.!!$F1 6234
1 TraesCS6D01G189300 chr6B 348703765 348709248 5483 True 4432.5 5993 96.5740 1 5367 2 chr6B.!!$R2 5366
2 TraesCS6D01G189300 chr6B 348695942 348696757 815 True 1122.0 1122 91.7370 5423 6235 1 chr6B.!!$R1 812
3 TraesCS6D01G189300 chr6A 322996332 323002278 5946 True 4432.5 5321 95.0025 610 6235 2 chr6A.!!$R1 5625
4 TraesCS6D01G189300 chr2A 562603797 562604305 508 True 353.0 353 79.3770 2477 2985 1 chr2A.!!$R1 508
5 TraesCS6D01G189300 chr2D 425742025 425742532 507 False 346.0 346 79.1420 2477 2984 1 chr2D.!!$F1 507
6 TraesCS6D01G189300 chr2B 501007661 501008168 507 False 340.0 340 78.9060 2477 2984 1 chr2B.!!$F1 507

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
126 127 0.236711 CCGAAGTGAACAAGCTGCAG 59.763 55.000 10.11 10.11 0.00 4.41 F
502 503 0.671251 GAGGGCCATCGACTAGTCTG 59.329 60.000 20.34 12.51 0.00 3.51 F
836 853 2.771943 TGTCCCTCTCTCTCTCTCTCTC 59.228 54.545 0.00 0.00 0.00 3.20 F
2311 2507 2.732597 GCGAGCAATCTTGTCTCGTACT 60.733 50.000 24.02 2.65 46.44 2.73 F
2629 2825 1.601412 GCAGGAAGACAAAGCTTGTGC 60.601 52.381 0.00 0.00 45.52 4.57 F
3564 3760 1.009829 CTCAAGCGGGTGTCATAAGC 58.990 55.000 0.00 0.00 0.00 3.09 F
4785 5343 0.260230 TTGTGCACAAAGGGGGAGAA 59.740 50.000 29.36 2.82 32.11 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1263 1289 0.464452 CTCGCCCCGTCTTAATCCTT 59.536 55.000 0.00 0.0 0.00 3.36 R
2097 2293 1.084935 CGTGGACACACCGTTGACAA 61.085 55.000 3.12 0.0 44.86 3.18 R
2629 2825 2.162408 GGCCTTCATCAAGAAAACGGAG 59.838 50.000 0.00 0.0 35.40 4.63 R
3564 3760 1.131126 CCAGCAACAGCCTTAATGTCG 59.869 52.381 0.00 0.0 0.00 4.35 R
4545 5103 1.985116 GTCTGCGAGGGAGGAAGGT 60.985 63.158 0.00 0.0 0.00 3.50 R
4922 5480 0.114168 TCTTCATTGGGTTGGGTGGG 59.886 55.000 0.00 0.0 0.00 4.61 R
6043 6628 0.321387 CAAGCAAGCAGGCAGAGAGA 60.321 55.000 2.37 0.0 35.83 3.10 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
54 55 4.558226 AGATGCATCCTACACAAACTGA 57.442 40.909 23.06 0.00 0.00 3.41
79 80 5.375417 TCATTCACATGTTTGTCACCATC 57.625 39.130 0.00 0.00 32.34 3.51
101 102 0.321564 TGACAACCTGAGGATTGCCG 60.322 55.000 4.99 0.00 39.96 5.69
112 113 1.425428 GATTGCCGAACAGCCGAAG 59.575 57.895 0.00 0.00 0.00 3.79
114 115 1.577328 ATTGCCGAACAGCCGAAGTG 61.577 55.000 0.00 0.00 0.00 3.16
126 127 0.236711 CCGAAGTGAACAAGCTGCAG 59.763 55.000 10.11 10.11 0.00 4.41
162 163 4.620589 TTTTTGTGTGGGAATGCATCAT 57.379 36.364 0.00 0.00 0.00 2.45
171 172 3.118920 TGGGAATGCATCATTTCTTGCTG 60.119 43.478 0.00 0.00 39.60 4.41
256 257 2.642311 TGAGGAAACTACCATGGAAGCA 59.358 45.455 21.47 0.00 44.43 3.91
320 321 4.564782 TTCTTGATCTGCACAGAAGGAT 57.435 40.909 4.14 0.00 41.36 3.24
324 325 2.169978 TGATCTGCACAGAAGGATGGAG 59.830 50.000 4.14 0.00 41.36 3.86
344 345 2.316119 GCAGGAAGCAACGTTTACAG 57.684 50.000 0.00 0.00 44.79 2.74
357 358 3.244457 ACGTTTACAGGAGGAAGAAAGGG 60.244 47.826 0.00 0.00 0.00 3.95
376 377 2.032620 GGAACGCCTGGAGAGAGAATA 58.967 52.381 3.87 0.00 0.00 1.75
377 378 2.035321 GGAACGCCTGGAGAGAGAATAG 59.965 54.545 3.87 0.00 0.00 1.73
383 384 3.499563 GCCTGGAGAGAGAATAGGAGCTA 60.500 52.174 0.00 0.00 0.00 3.32
410 411 3.838271 GGCGTGAGATGCGGGAGA 61.838 66.667 0.00 0.00 0.00 3.71
413 414 1.880340 CGTGAGATGCGGGAGAAGC 60.880 63.158 0.00 0.00 0.00 3.86
418 419 1.038130 AGATGCGGGAGAAGCTACGT 61.038 55.000 0.00 0.00 27.51 3.57
456 457 5.796350 TTAGCGAACTGAAAAGGCTAATC 57.204 39.130 0.09 0.00 40.23 1.75
460 461 4.870991 GCGAACTGAAAAGGCTAATCTAGT 59.129 41.667 0.00 0.00 0.00 2.57
461 462 5.220491 GCGAACTGAAAAGGCTAATCTAGTG 60.220 44.000 0.00 0.00 0.00 2.74
471 472 2.307768 CTAATCTAGTGCGGGTCCTCA 58.692 52.381 0.00 0.00 0.00 3.86
502 503 0.671251 GAGGGCCATCGACTAGTCTG 59.329 60.000 20.34 12.51 0.00 3.51
506 507 3.093057 GGGCCATCGACTAGTCTGATAT 58.907 50.000 20.34 6.25 0.00 1.63
559 560 5.358160 AGTGCTGCCCTTTATGAAAAGATAC 59.642 40.000 0.00 0.00 44.14 2.24
592 593 7.237055 AGTGGTAGTAGGAGTAGGTTTTTGATT 59.763 37.037 0.00 0.00 0.00 2.57
833 850 4.044065 TCTTTTGTCCCTCTCTCTCTCTCT 59.956 45.833 0.00 0.00 0.00 3.10
834 851 3.644966 TTGTCCCTCTCTCTCTCTCTC 57.355 52.381 0.00 0.00 0.00 3.20
835 852 2.845659 TGTCCCTCTCTCTCTCTCTCT 58.154 52.381 0.00 0.00 0.00 3.10
836 853 2.771943 TGTCCCTCTCTCTCTCTCTCTC 59.228 54.545 0.00 0.00 0.00 3.20
1247 1273 3.981416 CGATTTCTGATTCGGCTTCGATA 59.019 43.478 0.00 0.00 42.93 2.92
1263 1289 6.351881 GGCTTCGATATATGGGTTGGATCTTA 60.352 42.308 0.00 0.00 0.00 2.10
2097 2293 3.330998 CCAAAGGGAAAGAAGACCTACCT 59.669 47.826 0.00 0.00 35.59 3.08
2311 2507 2.732597 GCGAGCAATCTTGTCTCGTACT 60.733 50.000 24.02 2.65 46.44 2.73
2629 2825 1.601412 GCAGGAAGACAAAGCTTGTGC 60.601 52.381 0.00 0.00 45.52 4.57
2688 2884 8.650490 TCTACAAATCAGACATATGGCTCAATA 58.350 33.333 8.55 0.00 0.00 1.90
2902 3098 7.009999 GCTATGATCCGTTAGCAGAATATCTTG 59.990 40.741 12.18 0.00 40.42 3.02
2964 3160 3.711704 TGACTGATTTCCCTATCACTCCC 59.288 47.826 0.00 0.00 31.51 4.30
3222 3418 1.678598 TTGTTGCTGCAGGCTGCTTT 61.679 50.000 36.50 0.00 45.31 3.51
3291 3487 9.672673 TCCTTTCTTTATCCATTCTTAACTCTG 57.327 33.333 0.00 0.00 0.00 3.35
3292 3488 8.401709 CCTTTCTTTATCCATTCTTAACTCTGC 58.598 37.037 0.00 0.00 0.00 4.26
3293 3489 8.862325 TTTCTTTATCCATTCTTAACTCTGCA 57.138 30.769 0.00 0.00 0.00 4.41
3294 3490 8.862325 TTCTTTATCCATTCTTAACTCTGCAA 57.138 30.769 0.00 0.00 0.00 4.08
3295 3491 8.268850 TCTTTATCCATTCTTAACTCTGCAAC 57.731 34.615 0.00 0.00 0.00 4.17
3296 3492 8.103305 TCTTTATCCATTCTTAACTCTGCAACT 58.897 33.333 0.00 0.00 0.00 3.16
3297 3493 7.849804 TTATCCATTCTTAACTCTGCAACTC 57.150 36.000 0.00 0.00 0.00 3.01
3427 3623 4.944317 ACCTAGCTTATCAAAAGGCAGTTC 59.056 41.667 0.00 0.00 0.00 3.01
3428 3624 4.943705 CCTAGCTTATCAAAAGGCAGTTCA 59.056 41.667 0.00 0.00 0.00 3.18
3429 3625 5.415701 CCTAGCTTATCAAAAGGCAGTTCAA 59.584 40.000 0.00 0.00 0.00 2.69
3432 3628 5.048434 AGCTTATCAAAAGGCAGTTCAAGAC 60.048 40.000 0.00 0.00 0.00 3.01
3456 3652 3.688185 GTGCAGATGTCATTGACTGTGAT 59.312 43.478 17.26 2.94 33.15 3.06
3564 3760 1.009829 CTCAAGCGGGTGTCATAAGC 58.990 55.000 0.00 0.00 0.00 3.09
3754 3950 1.130678 GGGAGGCTGGGAATAGGGAG 61.131 65.000 0.00 0.00 0.00 4.30
3757 3953 1.073706 GGCTGGGAATAGGGAGGGA 60.074 63.158 0.00 0.00 0.00 4.20
4064 4621 3.670523 CCGTGTTCACAGCTATGATATCG 59.329 47.826 0.00 1.01 0.00 2.92
4647 5205 6.404734 GCAATTTCCTGATAAACCAGACGAAT 60.405 38.462 0.00 0.00 36.29 3.34
4701 5259 5.508825 CCTTCCAGTCTATGTGTATCTGCTC 60.509 48.000 0.00 0.00 0.00 4.26
4703 5261 5.143369 TCCAGTCTATGTGTATCTGCTCAT 58.857 41.667 0.00 0.00 0.00 2.90
4728 5286 4.879598 ACGAGTTCTTTTCTCAACCGTAT 58.120 39.130 0.00 0.00 31.78 3.06
4785 5343 0.260230 TTGTGCACAAAGGGGGAGAA 59.740 50.000 29.36 2.82 32.11 2.87
4896 5454 5.305128 ACATTTTTCATCCAGTTCACCATGT 59.695 36.000 0.00 0.00 0.00 3.21
4898 5456 6.573664 TTTTTCATCCAGTTCACCATGTAG 57.426 37.500 0.00 0.00 0.00 2.74
4899 5457 5.497464 TTTCATCCAGTTCACCATGTAGA 57.503 39.130 0.00 0.00 0.00 2.59
4901 5459 5.089970 TCATCCAGTTCACCATGTAGAAG 57.910 43.478 0.00 0.00 0.00 2.85
4902 5460 4.532126 TCATCCAGTTCACCATGTAGAAGT 59.468 41.667 0.00 0.00 0.00 3.01
4903 5461 5.719563 TCATCCAGTTCACCATGTAGAAGTA 59.280 40.000 4.86 0.00 0.00 2.24
4906 5464 6.250711 TCCAGTTCACCATGTAGAAGTAGTA 58.749 40.000 4.86 0.00 0.00 1.82
4907 5465 6.377429 TCCAGTTCACCATGTAGAAGTAGTAG 59.623 42.308 4.86 0.00 0.00 2.57
4909 5467 7.338703 CCAGTTCACCATGTAGAAGTAGTAGTA 59.661 40.741 4.86 0.00 0.00 1.82
4911 5469 9.122779 AGTTCACCATGTAGAAGTAGTAGTATC 57.877 37.037 3.61 0.00 0.00 2.24
4915 5473 8.851145 CACCATGTAGAAGTAGTAGTATCATGT 58.149 37.037 0.00 0.00 0.00 3.21
4923 5481 9.122779 AGAAGTAGTAGTATCATGTAGTGAACC 57.877 37.037 0.00 0.00 40.97 3.62
4924 5482 7.820578 AGTAGTAGTATCATGTAGTGAACCC 57.179 40.000 0.00 0.00 40.97 4.11
4925 5483 7.351952 AGTAGTAGTATCATGTAGTGAACCCA 58.648 38.462 0.00 0.00 40.97 4.51
4926 5484 6.466885 AGTAGTATCATGTAGTGAACCCAC 57.533 41.667 0.00 0.00 40.97 4.61
4927 5485 4.755266 AGTATCATGTAGTGAACCCACC 57.245 45.455 0.00 0.00 44.22 4.61
4928 5486 3.454812 AGTATCATGTAGTGAACCCACCC 59.545 47.826 0.00 0.00 44.22 4.61
4929 5487 1.735926 TCATGTAGTGAACCCACCCA 58.264 50.000 0.00 0.00 44.22 4.51
4930 5488 2.058705 TCATGTAGTGAACCCACCCAA 58.941 47.619 0.00 0.00 44.22 4.12
4931 5489 2.159382 CATGTAGTGAACCCACCCAAC 58.841 52.381 0.00 0.00 44.22 3.77
4932 5490 0.475044 TGTAGTGAACCCACCCAACC 59.525 55.000 0.00 0.00 44.22 3.77
4933 5491 0.251033 GTAGTGAACCCACCCAACCC 60.251 60.000 0.00 0.00 44.22 4.11
4934 5492 0.698198 TAGTGAACCCACCCAACCCA 60.698 55.000 0.00 0.00 44.22 4.51
4935 5493 1.075896 GTGAACCCACCCAACCCAA 60.076 57.895 0.00 0.00 37.33 4.12
4936 5494 0.471022 GTGAACCCACCCAACCCAAT 60.471 55.000 0.00 0.00 37.33 3.16
4937 5495 0.470833 TGAACCCACCCAACCCAATG 60.471 55.000 0.00 0.00 0.00 2.82
4938 5496 0.178947 GAACCCACCCAACCCAATGA 60.179 55.000 0.00 0.00 0.00 2.57
4939 5497 0.266152 AACCCACCCAACCCAATGAA 59.734 50.000 0.00 0.00 0.00 2.57
5275 5834 0.988832 TTGGCCACCCGTTCTATTCT 59.011 50.000 3.88 0.00 0.00 2.40
5276 5835 1.868713 TGGCCACCCGTTCTATTCTA 58.131 50.000 0.00 0.00 0.00 2.10
5277 5836 2.404559 TGGCCACCCGTTCTATTCTAT 58.595 47.619 0.00 0.00 0.00 1.98
5414 5977 9.887406 AGTTAAAACAACATTCTGGTAAATACG 57.113 29.630 0.00 0.00 0.00 3.06
5415 5978 9.667989 GTTAAAACAACATTCTGGTAAATACGT 57.332 29.630 0.00 0.00 0.00 3.57
5418 5981 8.611654 AAACAACATTCTGGTAAATACGTACT 57.388 30.769 0.00 0.00 0.00 2.73
5419 5982 7.823149 ACAACATTCTGGTAAATACGTACTC 57.177 36.000 0.00 0.00 0.00 2.59
5420 5983 6.815142 ACAACATTCTGGTAAATACGTACTCC 59.185 38.462 0.00 0.00 0.00 3.85
5421 5984 6.786967 ACATTCTGGTAAATACGTACTCCT 57.213 37.500 0.00 0.00 0.00 3.69
5451 6014 5.794894 TGATGGTTAAAGAGGAGAAGTGAC 58.205 41.667 0.00 0.00 0.00 3.67
5487 6050 1.139095 GTCTAGAGTTGCGGTCCCG 59.861 63.158 0.24 0.24 43.09 5.14
5559 6122 1.482621 CGATTGACATCTGACGGCGG 61.483 60.000 13.24 0.00 0.00 6.13
5576 6139 0.882042 CGGGATGCTCTTATTGCGCT 60.882 55.000 9.73 0.00 0.00 5.92
5577 6140 0.871057 GGGATGCTCTTATTGCGCTC 59.129 55.000 9.73 0.00 0.00 5.03
5655 6218 3.130340 TGATCCAATCTCGAATGTCGTCA 59.870 43.478 0.00 0.00 41.35 4.35
5782 6345 0.243095 GTCTTCGGCCTACTCGTTGT 59.757 55.000 0.00 0.00 0.00 3.32
5889 6465 1.352156 CTTCCGTCCTTTTCGGCTCG 61.352 60.000 0.00 0.00 46.49 5.03
6084 6669 8.118607 GCTTGGAATTTTCTTTTTCTTTGTCAG 58.881 33.333 0.00 0.00 0.00 3.51
6107 6692 4.378874 GGAAGAAACGGAAGCAGAATTCTG 60.379 45.833 27.82 27.82 46.40 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 55 4.583907 TGGTGACAAACATGTGAATGATGT 59.416 37.500 0.00 0.00 37.44 3.06
79 80 1.197721 GCAATCCTCAGGTTGTCAACG 59.802 52.381 9.57 0.00 0.00 4.10
101 102 1.334149 GCTTGTTCACTTCGGCTGTTC 60.334 52.381 0.00 0.00 0.00 3.18
112 113 0.383231 AAGTGCTGCAGCTTGTTCAC 59.617 50.000 36.61 25.35 42.66 3.18
114 115 0.950116 AGAAGTGCTGCAGCTTGTTC 59.050 50.000 36.61 30.99 42.66 3.18
159 160 2.183478 TCGGAAGCAGCAAGAAATGA 57.817 45.000 0.00 0.00 0.00 2.57
162 163 1.967319 AGTTCGGAAGCAGCAAGAAA 58.033 45.000 0.00 0.00 0.00 2.52
171 172 0.741221 CCTGGCAGTAGTTCGGAAGC 60.741 60.000 14.43 0.00 0.00 3.86
256 257 5.530915 TGAGATTGATTTGACGTTGTTTCCT 59.469 36.000 0.00 0.00 0.00 3.36
312 313 0.914644 TTCCTGCCTCCATCCTTCTG 59.085 55.000 0.00 0.00 0.00 3.02
320 321 2.032528 CGTTGCTTCCTGCCTCCA 59.967 61.111 0.00 0.00 42.00 3.86
324 325 0.948678 TGTAAACGTTGCTTCCTGCC 59.051 50.000 0.00 0.00 42.00 4.85
339 340 3.007614 CGTTCCCTTTCTTCCTCCTGTAA 59.992 47.826 0.00 0.00 0.00 2.41
343 344 0.325272 GCGTTCCCTTTCTTCCTCCT 59.675 55.000 0.00 0.00 0.00 3.69
344 345 0.677098 GGCGTTCCCTTTCTTCCTCC 60.677 60.000 0.00 0.00 0.00 4.30
357 358 2.035321 CCTATTCTCTCTCCAGGCGTTC 59.965 54.545 0.00 0.00 0.00 3.95
376 377 1.723288 GCCCTCCACTATTAGCTCCT 58.277 55.000 0.00 0.00 0.00 3.69
377 378 0.318762 CGCCCTCCACTATTAGCTCC 59.681 60.000 0.00 0.00 0.00 4.70
383 384 1.414181 CATCTCACGCCCTCCACTATT 59.586 52.381 0.00 0.00 0.00 1.73
410 411 2.430465 TGAGTCCTTCGTACGTAGCTT 58.570 47.619 16.05 3.16 0.00 3.74
413 414 6.020837 GCTAAAATTGAGTCCTTCGTACGTAG 60.021 42.308 16.05 15.10 0.00 3.51
418 419 5.063180 TCGCTAAAATTGAGTCCTTCGTA 57.937 39.130 0.00 0.00 0.00 3.43
456 457 1.379977 TCCTGAGGACCCGCACTAG 60.380 63.158 0.00 0.00 0.00 2.57
460 461 2.871795 TATGCTCCTGAGGACCCGCA 62.872 60.000 15.10 15.10 35.46 5.69
461 462 1.476007 ATATGCTCCTGAGGACCCGC 61.476 60.000 0.00 0.00 0.00 6.13
471 472 1.915769 GGCCCTCGGATATGCTCCT 60.916 63.158 0.00 0.00 42.47 3.69
482 483 0.820074 AGACTAGTCGATGGCCCTCG 60.820 60.000 22.85 22.85 39.99 4.63
486 487 3.759086 TCATATCAGACTAGTCGATGGCC 59.241 47.826 26.50 0.00 34.09 5.36
519 520 2.421775 AGCACTAGACATCAGACGTCTG 59.578 50.000 34.76 34.76 43.50 3.51
559 560 6.545298 ACCTACTCCTACTACCACTTTTATCG 59.455 42.308 0.00 0.00 0.00 2.92
604 605 6.670695 ATTAACTGGTGATCAAAAAGCCTT 57.329 33.333 0.00 0.00 0.00 4.35
606 607 7.029563 CACTATTAACTGGTGATCAAAAAGCC 58.970 38.462 0.00 0.00 38.56 4.35
608 609 8.110860 ACCACTATTAACTGGTGATCAAAAAG 57.889 34.615 0.00 0.00 39.44 2.27
833 850 1.559149 GCCGCGTTTTAACACCGAGA 61.559 55.000 4.92 0.00 0.00 4.04
834 851 1.154543 GCCGCGTTTTAACACCGAG 60.155 57.895 4.92 0.00 0.00 4.63
835 852 2.606030 GGCCGCGTTTTAACACCGA 61.606 57.895 4.92 0.00 0.00 4.69
836 853 2.127156 GGCCGCGTTTTAACACCG 60.127 61.111 4.92 0.00 0.00 4.94
897 914 3.766591 AGAGAAGGAGAAGAATCGAAGCA 59.233 43.478 0.00 0.00 0.00 3.91
970 987 4.711949 CCGGCAGCAGCTCCAAGT 62.712 66.667 0.00 0.00 41.70 3.16
1247 1273 9.182642 TCTTAATCCTTAAGATCCAACCCATAT 57.817 33.333 3.36 0.00 44.85 1.78
1263 1289 0.464452 CTCGCCCCGTCTTAATCCTT 59.536 55.000 0.00 0.00 0.00 3.36
2097 2293 1.084935 CGTGGACACACCGTTGACAA 61.085 55.000 3.12 0.00 44.86 3.18
2311 2507 5.584649 CGTGAAGCTTCCATCAAACCTATTA 59.415 40.000 23.42 0.00 0.00 0.98
2629 2825 2.162408 GGCCTTCATCAAGAAAACGGAG 59.838 50.000 0.00 0.00 35.40 4.63
2688 2884 9.118300 GTCTTGATGGATGATAGATTTTTCAGT 57.882 33.333 0.00 0.00 0.00 3.41
2902 3098 0.099436 GCACCATTGTCGATGAAGCC 59.901 55.000 1.19 0.00 38.03 4.35
2964 3160 1.067821 GACTCACCGATGGCCTCTAAG 59.932 57.143 3.32 0.00 0.00 2.18
3155 3351 3.972133 TCAGACAAGCCATGATCCAAAT 58.028 40.909 0.00 0.00 0.00 2.32
3222 3418 4.710324 CCTTGGTGTTGTTCAGGTTACTA 58.290 43.478 0.00 0.00 0.00 1.82
3262 3458 8.961634 AGTTAAGAATGGATAAAGAAAGGAAGC 58.038 33.333 0.00 0.00 0.00 3.86
3290 3486 5.865085 ACAGTACTAAATTGAGGAGTTGCA 58.135 37.500 0.00 0.00 0.00 4.08
3291 3487 6.803154 AACAGTACTAAATTGAGGAGTTGC 57.197 37.500 0.00 0.00 0.00 4.17
3320 3516 5.412594 GCAATGTAAATGTGAAGTCTGGAGA 59.587 40.000 0.00 0.00 0.00 3.71
3325 3521 4.460382 CCCTGCAATGTAAATGTGAAGTCT 59.540 41.667 0.00 0.00 0.00 3.24
3427 3623 1.730501 ATGACATCTGCACCGTCTTG 58.269 50.000 6.88 0.00 0.00 3.02
3428 3624 2.079158 CAATGACATCTGCACCGTCTT 58.921 47.619 6.88 0.00 0.00 3.01
3429 3625 1.276138 TCAATGACATCTGCACCGTCT 59.724 47.619 6.88 0.00 0.00 4.18
3432 3628 1.395954 CAGTCAATGACATCTGCACCG 59.604 52.381 16.38 0.00 34.60 4.94
3456 3652 3.698539 TGCCATCTTTTGTCACTTGAACA 59.301 39.130 0.00 0.00 0.00 3.18
3564 3760 1.131126 CCAGCAACAGCCTTAATGTCG 59.869 52.381 0.00 0.00 0.00 4.35
3961 4517 4.578516 TCAATTGTTCACCAGACGTTTGAT 59.421 37.500 7.81 0.00 0.00 2.57
3966 4522 4.488126 CAATCAATTGTTCACCAGACGT 57.512 40.909 5.13 0.00 33.22 4.34
4064 4621 2.101415 GCTAATCTGGCCAAATGGGTTC 59.899 50.000 7.01 0.00 39.65 3.62
4164 4721 8.464404 CACAGTAATCATGATTCCTGACAATTT 58.536 33.333 34.68 16.96 37.04 1.82
4166 4723 6.544931 CCACAGTAATCATGATTCCTGACAAT 59.455 38.462 34.68 17.83 37.04 2.71
4545 5103 1.985116 GTCTGCGAGGGAGGAAGGT 60.985 63.158 0.00 0.00 0.00 3.50
4647 5205 1.251527 GCAGGGACTTGACGAGAGGA 61.252 60.000 0.00 0.00 34.60 3.71
4701 5259 5.444122 GGTTGAGAAAAGAACTCGTTCATG 58.556 41.667 11.90 0.00 41.84 3.07
4703 5261 3.554324 CGGTTGAGAAAAGAACTCGTTCA 59.446 43.478 11.90 0.00 41.84 3.18
4728 5286 1.000163 GTGGCGTCTGAGAAGAAGTCA 60.000 52.381 0.00 0.00 30.14 3.41
4785 5343 2.765807 CCATCCACTCCGCCTCCT 60.766 66.667 0.00 0.00 0.00 3.69
4898 5456 8.351461 GGGTTCACTACATGATACTACTACTTC 58.649 40.741 0.00 0.00 37.11 3.01
4899 5457 7.837689 TGGGTTCACTACATGATACTACTACTT 59.162 37.037 0.00 0.00 37.11 2.24
4901 5459 7.424001 GTGGGTTCACTACATGATACTACTAC 58.576 42.308 0.00 0.00 40.58 2.73
4902 5460 6.548622 GGTGGGTTCACTACATGATACTACTA 59.451 42.308 0.00 0.00 43.17 1.82
4903 5461 5.363005 GGTGGGTTCACTACATGATACTACT 59.637 44.000 0.00 0.00 43.17 2.57
4906 5464 3.454812 GGGTGGGTTCACTACATGATACT 59.545 47.826 0.00 0.00 43.17 2.12
4907 5465 3.199071 TGGGTGGGTTCACTACATGATAC 59.801 47.826 0.00 0.00 43.17 2.24
4909 5467 2.274542 TGGGTGGGTTCACTACATGAT 58.725 47.619 0.00 0.00 43.17 2.45
4911 5469 2.159382 GTTGGGTGGGTTCACTACATG 58.841 52.381 0.00 0.00 43.17 3.21
4915 5473 0.698198 TGGGTTGGGTGGGTTCACTA 60.698 55.000 0.00 0.00 43.17 2.74
4916 5474 1.585651 TTGGGTTGGGTGGGTTCACT 61.586 55.000 0.00 0.00 43.17 3.41
4917 5475 0.471022 ATTGGGTTGGGTGGGTTCAC 60.471 55.000 0.00 0.00 42.91 3.18
4918 5476 0.470833 CATTGGGTTGGGTGGGTTCA 60.471 55.000 0.00 0.00 0.00 3.18
4919 5477 0.178947 TCATTGGGTTGGGTGGGTTC 60.179 55.000 0.00 0.00 0.00 3.62
4920 5478 0.266152 TTCATTGGGTTGGGTGGGTT 59.734 50.000 0.00 0.00 0.00 4.11
4921 5479 0.178935 CTTCATTGGGTTGGGTGGGT 60.179 55.000 0.00 0.00 0.00 4.51
4922 5480 0.114168 TCTTCATTGGGTTGGGTGGG 59.886 55.000 0.00 0.00 0.00 4.61
4923 5481 2.008242 TTCTTCATTGGGTTGGGTGG 57.992 50.000 0.00 0.00 0.00 4.61
4924 5482 3.834231 AGAATTCTTCATTGGGTTGGGTG 59.166 43.478 0.88 0.00 0.00 4.61
4925 5483 4.132122 AGAATTCTTCATTGGGTTGGGT 57.868 40.909 0.88 0.00 0.00 4.51
5039 5597 4.791974 GCAATGCTGCTTTATCCTGTATC 58.208 43.478 0.00 0.00 45.74 2.24
5163 5721 3.507009 GACGGAGACCTCGACGGG 61.507 72.222 0.00 0.00 36.97 5.28
5171 5729 2.544698 CGGGATCGAGACGGAGACC 61.545 68.421 0.00 0.00 39.00 3.85
5259 5818 5.548406 ACATAATAGAATAGAACGGGTGGC 58.452 41.667 0.00 0.00 0.00 5.01
5275 5834 7.652300 AAAATGAATCGCTCGCTACATAATA 57.348 32.000 0.00 0.00 0.00 0.98
5276 5835 6.545504 AAAATGAATCGCTCGCTACATAAT 57.454 33.333 0.00 0.00 0.00 1.28
5277 5836 5.984233 AAAATGAATCGCTCGCTACATAA 57.016 34.783 0.00 0.00 0.00 1.90
5414 5977 9.352191 TCTTTAACCATCATAGAGTAGGAGTAC 57.648 37.037 0.00 0.00 0.00 2.73
5415 5978 9.575868 CTCTTTAACCATCATAGAGTAGGAGTA 57.424 37.037 0.00 0.00 0.00 2.59
5416 5979 7.507616 CCTCTTTAACCATCATAGAGTAGGAGT 59.492 40.741 0.00 0.00 32.39 3.85
5417 5980 7.726291 TCCTCTTTAACCATCATAGAGTAGGAG 59.274 40.741 0.00 0.00 32.39 3.69
5418 5981 7.592736 TCCTCTTTAACCATCATAGAGTAGGA 58.407 38.462 0.00 0.00 32.39 2.94
5419 5982 7.726291 TCTCCTCTTTAACCATCATAGAGTAGG 59.274 40.741 0.00 0.00 32.39 3.18
5420 5983 8.698973 TCTCCTCTTTAACCATCATAGAGTAG 57.301 38.462 0.00 0.00 32.39 2.57
5421 5984 9.137459 CTTCTCCTCTTTAACCATCATAGAGTA 57.863 37.037 0.00 0.00 32.39 2.59
5432 5995 2.994578 GCGTCACTTCTCCTCTTTAACC 59.005 50.000 0.00 0.00 0.00 2.85
5487 6050 3.085952 TCCCACATCAAAATCTGGTCC 57.914 47.619 0.00 0.00 0.00 4.46
5559 6122 1.586422 TGAGCGCAATAAGAGCATCC 58.414 50.000 11.47 0.00 46.42 3.51
5758 6321 1.338337 CGAGTAGGCCGAAGACATCAT 59.662 52.381 0.00 0.00 0.00 2.45
5885 6461 1.005340 CTCTGAACATCTTGCCGAGC 58.995 55.000 0.00 0.00 0.00 5.03
5889 6465 1.372087 CGCCCTCTGAACATCTTGCC 61.372 60.000 0.00 0.00 0.00 4.52
6043 6628 0.321387 CAAGCAAGCAGGCAGAGAGA 60.321 55.000 2.37 0.00 35.83 3.10
6084 6669 3.753797 AGAATTCTGCTTCCGTTTCTTCC 59.246 43.478 7.30 0.00 0.00 3.46
6107 6692 4.424626 TCGCAGACAAGATGAATCACTAC 58.575 43.478 0.00 0.00 0.00 2.73


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

AutoCloner maintained by Alex Coulton.