Multiple sequence alignment - TraesCS6D01G160100

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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 TraesCS6D01G160100 chr6D 100.000 6300 0 0 1 6300 138358332 138364631 0.000000e+00 11635
1 TraesCS6D01G160100 chr6D 97.183 71 1 1 5371 5441 138363659 138363728 1.110000e-22 119
2 TraesCS6D01G160100 chr6D 97.183 71 1 1 5328 5397 138363702 138363772 1.110000e-22 119
3 TraesCS6D01G160100 chr6B 97.320 5410 113 20 1 5397 237695389 237700779 0.000000e+00 9158
4 TraesCS6D01G160100 chr6B 90.748 962 40 14 5371 6300 237700710 237701654 0.000000e+00 1238
5 TraesCS6D01G160100 chr6B 89.041 219 24 0 2574 2792 514607429 514607211 8.050000e-69 272
6 TraesCS6D01G160100 chr6A 96.729 5411 133 21 1 5397 180919174 180924554 0.000000e+00 8972
7 TraesCS6D01G160100 chr6A 91.399 965 41 14 5371 6300 180924485 180925442 0.000000e+00 1284
8 TraesCS6D01G160100 chr5A 90.741 378 20 3 5371 5735 509964909 509964534 2.040000e-134 490
9 TraesCS6D01G160100 chr5A 96.429 112 4 0 5286 5397 509964951 509964840 1.080000e-42 185
10 TraesCS6D01G160100 chr2A 86.893 412 47 6 2716 3123 339109702 339110110 7.450000e-124 455
11 TraesCS6D01G160100 chr7A 88.802 384 23 3 5371 5735 475840810 475840428 2.680000e-123 453
12 TraesCS6D01G160100 chr7A 96.429 112 4 0 5286 5397 475840852 475840741 1.080000e-42 185
13 TraesCS6D01G160100 chr7D 92.366 131 9 1 2574 2703 175877287 175877417 1.080000e-42 185


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 TraesCS6D01G160100 chr6D 138358332 138364631 6299 False 3957.666667 11635 98.122 1 6300 3 chr6D.!!$F1 6299
1 TraesCS6D01G160100 chr6B 237695389 237701654 6265 False 5198.000000 9158 94.034 1 6300 2 chr6B.!!$F1 6299
2 TraesCS6D01G160100 chr6A 180919174 180925442 6268 False 5128.000000 8972 94.064 1 6300 2 chr6A.!!$F1 6299

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
92 93 0.105778 TGACCGTGTGATTGTCTGCA 59.894 50.000 0.0 0.0 0.00 4.41 F
1340 1354 0.107268 CGTCCATGATGATGCAGGGA 59.893 55.000 0.0 0.0 45.54 4.20 F
1475 1489 0.460284 CCGTCAAGGAGGTCATTCCG 60.460 60.000 0.0 0.0 45.00 4.30 F
2854 2869 1.038280 GGGAACTCGATACGGACCAT 58.962 55.000 0.0 0.0 0.00 3.55 F
3358 3373 3.321039 TGATTCCCATGTCTATGCCTCT 58.679 45.455 0.0 0.0 32.79 3.69 F
4781 4797 0.108186 TCGCAGAGTGCCAATCGAAT 60.108 50.000 0.0 0.0 41.12 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1475 1489 0.304705 GCATGCGTATGTGTACCTGC 59.695 55.000 15.13 0.00 36.65 4.85 R
2797 2812 4.989044 TCACATAGAAATGCTCGTACGAA 58.011 39.130 20.00 5.69 36.50 3.85 R
3379 3394 9.587772 TGAAAGAAAGATCTAATAGTGCTGTAC 57.412 33.333 0.00 0.00 33.77 2.90 R
4430 4446 0.997932 CTCTTCACGCATCTGCAGTC 59.002 55.000 14.67 3.54 42.21 3.51 R
5000 5017 0.599204 AGTACGTTGTGGTTCCAGCG 60.599 55.000 0.00 0.83 43.52 5.18 R
5785 5830 0.112995 AAAAGATGGCCAGGAGCACA 59.887 50.000 13.05 0.00 46.50 4.57 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
20 21 0.173708 GGTGAGGCACTAGTTCTCCG 59.826 60.000 16.20 0.00 41.55 4.63
92 93 0.105778 TGACCGTGTGATTGTCTGCA 59.894 50.000 0.00 0.00 0.00 4.41
95 96 3.000041 GACCGTGTGATTGTCTGCAATA 59.000 45.455 0.00 0.00 44.61 1.90
209 210 5.957798 TGAAATTTCATGGCTTGAGATCAC 58.042 37.500 16.91 5.53 35.27 3.06
213 215 3.986996 TCATGGCTTGAGATCACTGAA 57.013 42.857 0.00 0.00 0.00 3.02
219 221 6.017400 TGGCTTGAGATCACTGAATTTTTC 57.983 37.500 0.00 0.00 0.00 2.29
327 329 4.453751 ACCACGCTAGTTCCAAACTAAAA 58.546 39.130 1.61 0.00 42.99 1.52
336 338 8.135529 GCTAGTTCCAAACTAAAAAGAACATGT 58.864 33.333 0.00 0.00 42.99 3.21
536 539 2.158158 ACCATTAGGAGATCCCATCCGA 60.158 50.000 0.00 0.00 42.02 4.55
597 601 0.804989 GCATCCGACCTGGTTTTCAG 59.195 55.000 0.00 0.00 43.00 3.02
630 640 7.224753 ACGGTATGTCAATCATGTTGTAGATTC 59.775 37.037 0.00 0.00 37.91 2.52
633 643 5.178061 TGTCAATCATGTTGTAGATTCGCT 58.822 37.500 0.00 0.00 32.43 4.93
789 799 9.569167 TTGTGTTTGTATGAAATTTGTACGAAA 57.431 25.926 0.00 0.00 0.00 3.46
972 982 1.475682 CCGTTAGCTAACCGGTCTTCT 59.524 52.381 26.86 7.66 32.69 2.85
1340 1354 0.107268 CGTCCATGATGATGCAGGGA 59.893 55.000 0.00 0.00 45.54 4.20
1475 1489 0.460284 CCGTCAAGGAGGTCATTCCG 60.460 60.000 0.00 0.00 45.00 4.30
1623 1637 1.720301 GAGCAGAAGAGGCAATGCG 59.280 57.895 0.00 0.00 43.41 4.73
1632 1646 6.159293 CAGAAGAGGCAATGCGTATCTATAA 58.841 40.000 13.03 0.00 0.00 0.98
1933 1947 6.447162 CGTGAGCATATCAACTAACCATCTA 58.553 40.000 0.00 0.00 40.43 1.98
2733 2748 6.442112 GCTTTTTGCTTCTGTCTCTTTGTAT 58.558 36.000 0.00 0.00 38.95 2.29
2797 2812 9.280174 TCATTTCTCGTTTTCTGTAGGTATTTT 57.720 29.630 0.00 0.00 0.00 1.82
2854 2869 1.038280 GGGAACTCGATACGGACCAT 58.962 55.000 0.00 0.00 0.00 3.55
2991 3006 6.263842 TCAGATCATTCAAGTTTCTGCACTTT 59.736 34.615 0.00 0.00 34.60 2.66
2995 3010 6.198687 TCATTCAAGTTTCTGCACTTTTACG 58.801 36.000 0.00 0.00 34.60 3.18
3357 3372 3.777106 TGATTCCCATGTCTATGCCTC 57.223 47.619 0.00 0.00 32.79 4.70
3358 3373 3.321039 TGATTCCCATGTCTATGCCTCT 58.679 45.455 0.00 0.00 32.79 3.69
3379 3394 8.447053 GCCTCTTCTTCTATAAACAAGTTTCTG 58.553 37.037 0.81 0.00 34.23 3.02
3708 3723 8.814931 ACAAGGGATTGAAAAATGATTATGTGA 58.185 29.630 0.00 0.00 0.00 3.58
3758 3774 6.376018 TCTTTAACATGGGTATTCGGAAAAGG 59.624 38.462 0.00 0.00 0.00 3.11
3784 3800 8.789767 AAATCTACTCCTGAGATCATAGGAAA 57.210 34.615 16.06 8.69 42.25 3.13
3918 3934 7.950512 TGGTTGTGTGATTTAATTTGAGATGT 58.049 30.769 0.00 0.00 0.00 3.06
4397 4413 3.788797 GCGCTGATATTTTTGGTCTTCCG 60.789 47.826 0.00 0.00 36.30 4.30
4430 4446 7.325660 ACATTATGTGCTTTCTCCTAATGTG 57.674 36.000 0.00 0.00 36.78 3.21
4781 4797 0.108186 TCGCAGAGTGCCAATCGAAT 60.108 50.000 0.00 0.00 41.12 3.34
4994 5011 4.805192 GCCATATGTTCGAATTGTGCATTT 59.195 37.500 0.00 0.00 0.00 2.32
5000 5017 3.476295 TCGAATTGTGCATTTGCTCTC 57.524 42.857 3.94 0.00 42.66 3.20
5262 5285 4.342378 TGTACAACTATCAGCTCTGGATCC 59.658 45.833 4.20 4.20 0.00 3.36
5376 5400 3.503827 ATGCTGAATTGATGTGCAGTG 57.496 42.857 0.00 0.00 37.07 3.66
5384 5408 5.587443 TGAATTGATGTGCAGTGAAGATAGG 59.413 40.000 0.00 0.00 0.00 2.57
5385 5409 2.910199 TGATGTGCAGTGAAGATAGGC 58.090 47.619 0.00 0.00 0.00 3.93
5386 5410 2.216898 GATGTGCAGTGAAGATAGGCC 58.783 52.381 0.00 0.00 0.00 5.19
5387 5411 0.983467 TGTGCAGTGAAGATAGGCCA 59.017 50.000 5.01 0.00 0.00 5.36
5388 5412 1.065926 TGTGCAGTGAAGATAGGCCAG 60.066 52.381 5.01 0.00 0.00 4.85
5389 5413 0.543277 TGCAGTGAAGATAGGCCAGG 59.457 55.000 5.01 0.00 0.00 4.45
5390 5414 0.833287 GCAGTGAAGATAGGCCAGGA 59.167 55.000 5.01 0.00 0.00 3.86
5391 5415 1.202627 GCAGTGAAGATAGGCCAGGAG 60.203 57.143 5.01 0.00 0.00 3.69
5392 5416 1.415659 CAGTGAAGATAGGCCAGGAGG 59.584 57.143 5.01 0.00 38.23 4.30
5412 5436 4.660789 GGCAAACCTATGCTGAATTGAT 57.339 40.909 0.00 0.00 45.68 2.57
5413 5437 4.365723 GGCAAACCTATGCTGAATTGATG 58.634 43.478 0.00 0.00 45.68 3.07
5414 5438 4.142093 GGCAAACCTATGCTGAATTGATGT 60.142 41.667 0.00 0.00 45.68 3.06
5415 5439 4.802039 GCAAACCTATGCTGAATTGATGTG 59.198 41.667 0.00 0.00 43.06 3.21
5416 5440 4.644103 AACCTATGCTGAATTGATGTGC 57.356 40.909 0.00 0.00 0.00 4.57
5417 5441 3.623703 ACCTATGCTGAATTGATGTGCA 58.376 40.909 0.00 0.00 38.05 4.57
5418 5442 3.630769 ACCTATGCTGAATTGATGTGCAG 59.369 43.478 0.00 0.00 37.07 4.41
5419 5443 3.630769 CCTATGCTGAATTGATGTGCAGT 59.369 43.478 0.00 0.00 37.07 4.40
5420 5444 3.503827 ATGCTGAATTGATGTGCAGTG 57.496 42.857 0.00 0.00 37.07 3.66
5421 5445 2.506444 TGCTGAATTGATGTGCAGTGA 58.494 42.857 0.00 0.00 0.00 3.41
5422 5446 2.885894 TGCTGAATTGATGTGCAGTGAA 59.114 40.909 0.00 0.00 0.00 3.18
5423 5447 3.057806 TGCTGAATTGATGTGCAGTGAAG 60.058 43.478 0.00 0.00 0.00 3.02
5424 5448 3.189910 GCTGAATTGATGTGCAGTGAAGA 59.810 43.478 0.00 0.00 0.00 2.87
5425 5449 4.142447 GCTGAATTGATGTGCAGTGAAGAT 60.142 41.667 0.00 0.00 0.00 2.40
5426 5450 5.065602 GCTGAATTGATGTGCAGTGAAGATA 59.934 40.000 0.00 0.00 0.00 1.98
5427 5451 6.673154 TGAATTGATGTGCAGTGAAGATAG 57.327 37.500 0.00 0.00 0.00 2.08
5485 5522 2.754552 GCAGTGGGCAAATCAACAGATA 59.245 45.455 0.00 0.00 43.97 1.98
5536 5579 5.182760 GGGATTATCATGAAAGGCTGCTTAG 59.817 44.000 0.00 0.00 0.00 2.18
5540 5583 4.220693 TCATGAAAGGCTGCTTAGCTAA 57.779 40.909 5.60 5.94 34.73 3.09
5546 5589 1.208293 AGGCTGCTTAGCTAACACCTC 59.792 52.381 5.60 0.00 34.73 3.85
5673 5716 1.133009 AGAGGAGACAAGGACACTGGT 60.133 52.381 0.00 0.00 32.05 4.00
5778 5823 5.063817 CCAGAAAGAAAAACAAAAGGCTGTG 59.936 40.000 0.00 0.00 0.00 3.66
5779 5824 4.631377 AGAAAGAAAAACAAAAGGCTGTGC 59.369 37.500 0.00 0.00 0.00 4.57
5780 5825 3.893326 AGAAAAACAAAAGGCTGTGCT 57.107 38.095 0.00 0.00 0.00 4.40
5781 5826 4.206477 AGAAAAACAAAAGGCTGTGCTT 57.794 36.364 0.00 0.00 0.00 3.91
5782 5827 4.578871 AGAAAAACAAAAGGCTGTGCTTT 58.421 34.783 0.00 0.00 0.00 3.51
5783 5828 4.392754 AGAAAAACAAAAGGCTGTGCTTTG 59.607 37.500 7.63 7.63 36.37 2.77
5784 5829 1.655484 AACAAAAGGCTGTGCTTTGC 58.345 45.000 8.84 0.00 34.15 3.68
5785 5830 0.826062 ACAAAAGGCTGTGCTTTGCT 59.174 45.000 8.84 0.00 34.15 3.91
5786 5831 1.214367 CAAAAGGCTGTGCTTTGCTG 58.786 50.000 0.00 0.00 0.00 4.41
5787 5832 0.826062 AAAAGGCTGTGCTTTGCTGT 59.174 45.000 0.00 0.00 0.00 4.40
5845 5900 5.710984 CAGAAAGAAGCAATCAAGCATTCT 58.289 37.500 0.00 0.00 35.21 2.40
5893 5948 3.957671 ATTGTAAGCAGCGATGTCATG 57.042 42.857 1.22 0.00 0.00 3.07
5940 5995 9.474920 CACCAGCTAAAGAAAATGAACATAAAA 57.525 29.630 0.00 0.00 0.00 1.52
5979 6034 8.690680 TCTTTGTTACGTGCTTTACAAAAATT 57.309 26.923 0.00 0.00 39.26 1.82
6075 6131 8.912988 TGGTGCATCACGAGATCATATATAATA 58.087 33.333 0.00 0.00 34.83 0.98
6076 6132 9.186323 GGTGCATCACGAGATCATATATAATAC 57.814 37.037 0.00 0.00 34.83 1.89
6103 6172 7.556275 AGAGAGAAAACTAACATCAAAACACCA 59.444 33.333 0.00 0.00 0.00 4.17
6155 6225 7.867403 AGGATTAAATATTTATTGCGTGCTTGG 59.133 33.333 8.70 0.00 0.00 3.61
6199 6269 2.278857 ATGGCGCGTCGTGATCTC 60.279 61.111 3.74 0.00 0.00 2.75
6200 6270 3.774959 ATGGCGCGTCGTGATCTCC 62.775 63.158 3.74 1.42 0.00 3.71
6242 6312 4.546570 CATCACGATCTTATCAGCGGTTA 58.453 43.478 0.00 0.00 0.00 2.85
6283 6353 7.501892 TCAAAGGAATTCCAAAGAAAATTTGGG 59.498 33.333 26.22 5.22 46.71 4.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 3.011818 TCTTTGGTAGCAGTCGTCGATA 58.988 45.455 0.00 0.00 0.00 2.92
92 93 1.602237 CACCCGCCCACAGACTATT 59.398 57.895 0.00 0.00 0.00 1.73
128 129 0.107897 TGTCGGCGCCAATGATAAGT 60.108 50.000 28.98 0.00 0.00 2.24
233 235 9.643693 CATGCATTATCTTTTTGTAAGAAAGGT 57.356 29.630 0.00 0.00 35.37 3.50
234 236 9.859427 TCATGCATTATCTTTTTGTAAGAAAGG 57.141 29.630 0.00 0.00 35.37 3.11
249 251 8.824159 ACTCACATACTAGTTCATGCATTATC 57.176 34.615 0.00 0.00 0.00 1.75
327 329 7.165485 TGCTACTTTGGTACATACATGTTCTT 58.835 34.615 2.30 0.00 41.97 2.52
597 601 2.098607 TGATTGACATACCGTCTCGACC 59.901 50.000 0.00 0.00 45.60 4.79
626 636 7.579726 ACATAATGCAGAATTCTTAGCGAATC 58.420 34.615 4.86 0.00 41.42 2.52
630 640 7.975866 AAAACATAATGCAGAATTCTTAGCG 57.024 32.000 4.86 0.00 0.00 4.26
789 799 3.553096 CCAGCTCTAAACAGTTCGACAGT 60.553 47.826 0.00 0.00 0.00 3.55
1214 1225 3.633094 GAGCCAGTGCGCGAAGAGA 62.633 63.158 12.10 0.00 44.33 3.10
1475 1489 0.304705 GCATGCGTATGTGTACCTGC 59.695 55.000 15.13 0.00 36.65 4.85
1623 1637 5.963004 CGAAGAGCTGCTCGATTATAGATAC 59.037 44.000 22.77 0.00 35.36 2.24
1632 1646 3.764810 CGGCGAAGAGCTGCTCGAT 62.765 63.158 22.77 16.23 46.36 3.59
1866 1880 9.241317 CATGATAATTGACAATTTAAGCTGGTC 57.759 33.333 18.15 5.81 32.38 4.02
2754 2769 6.533730 AGAAATGATTGGTGTCTCACAAGTA 58.466 36.000 2.41 0.00 35.86 2.24
2797 2812 4.989044 TCACATAGAAATGCTCGTACGAA 58.011 39.130 20.00 5.69 36.50 3.85
3379 3394 9.587772 TGAAAGAAAGATCTAATAGTGCTGTAC 57.412 33.333 0.00 0.00 33.77 2.90
3708 3723 8.647143 AAAATTTCAATGAACGTCTCACAAAT 57.353 26.923 0.00 0.00 36.69 2.32
3758 3774 8.415950 TTCCTATGATCTCAGGAGTAGATTTC 57.584 38.462 13.46 0.00 41.89 2.17
3784 3800 2.172293 GGATGTTTCTCCTGAGGCAGAT 59.828 50.000 0.00 0.00 32.44 2.90
4397 4413 4.701956 AAGCACATAATGTTAGCACCAC 57.298 40.909 0.00 0.00 0.00 4.16
4430 4446 0.997932 CTCTTCACGCATCTGCAGTC 59.002 55.000 14.67 3.54 42.21 3.51
4781 4797 7.733773 TGGATGGAAGTATCTGTCTTTAGAA 57.266 36.000 0.00 0.00 0.00 2.10
5000 5017 0.599204 AGTACGTTGTGGTTCCAGCG 60.599 55.000 0.00 0.83 43.52 5.18
5262 5285 6.994496 TCCCTGATTGTATATTTGCTCTCAAG 59.006 38.462 0.00 0.00 33.12 3.02
5385 5409 0.257039 AGCATAGGTTTGCCTCCTGG 59.743 55.000 2.35 0.00 45.64 4.45
5386 5410 1.065199 TCAGCATAGGTTTGCCTCCTG 60.065 52.381 2.35 0.00 45.64 3.86
5387 5411 1.289160 TCAGCATAGGTTTGCCTCCT 58.711 50.000 0.00 0.00 45.64 3.69
5388 5412 2.128771 TTCAGCATAGGTTTGCCTCC 57.871 50.000 0.00 0.00 45.64 4.30
5389 5413 3.696051 TCAATTCAGCATAGGTTTGCCTC 59.304 43.478 0.00 0.00 45.64 4.70
5391 5415 4.142093 ACATCAATTCAGCATAGGTTTGCC 60.142 41.667 0.00 0.00 43.83 4.52
5392 5416 4.802039 CACATCAATTCAGCATAGGTTTGC 59.198 41.667 0.00 0.00 43.09 3.68
5393 5417 4.802039 GCACATCAATTCAGCATAGGTTTG 59.198 41.667 0.00 0.00 0.00 2.93
5394 5418 4.463539 TGCACATCAATTCAGCATAGGTTT 59.536 37.500 0.00 0.00 0.00 3.27
5395 5419 4.018490 TGCACATCAATTCAGCATAGGTT 58.982 39.130 0.00 0.00 0.00 3.50
5396 5420 3.623703 TGCACATCAATTCAGCATAGGT 58.376 40.909 0.00 0.00 0.00 3.08
5397 5421 3.630769 ACTGCACATCAATTCAGCATAGG 59.369 43.478 0.00 0.00 34.35 2.57
5398 5422 4.334481 TCACTGCACATCAATTCAGCATAG 59.666 41.667 0.00 0.00 34.35 2.23
5399 5423 4.263435 TCACTGCACATCAATTCAGCATA 58.737 39.130 0.00 0.00 34.35 3.14
5400 5424 3.086282 TCACTGCACATCAATTCAGCAT 58.914 40.909 0.00 0.00 34.35 3.79
5401 5425 2.506444 TCACTGCACATCAATTCAGCA 58.494 42.857 0.00 0.00 0.00 4.41
5402 5426 3.189910 TCTTCACTGCACATCAATTCAGC 59.810 43.478 0.00 0.00 0.00 4.26
5403 5427 5.562506 ATCTTCACTGCACATCAATTCAG 57.437 39.130 0.00 0.00 0.00 3.02
5404 5428 5.587443 CCTATCTTCACTGCACATCAATTCA 59.413 40.000 0.00 0.00 0.00 2.57
5405 5429 5.505324 GCCTATCTTCACTGCACATCAATTC 60.505 44.000 0.00 0.00 0.00 2.17
5406 5430 4.337555 GCCTATCTTCACTGCACATCAATT 59.662 41.667 0.00 0.00 0.00 2.32
5407 5431 3.881688 GCCTATCTTCACTGCACATCAAT 59.118 43.478 0.00 0.00 0.00 2.57
5408 5432 3.273434 GCCTATCTTCACTGCACATCAA 58.727 45.455 0.00 0.00 0.00 2.57
5409 5433 2.420547 GGCCTATCTTCACTGCACATCA 60.421 50.000 0.00 0.00 0.00 3.07
5410 5434 2.216898 GGCCTATCTTCACTGCACATC 58.783 52.381 0.00 0.00 0.00 3.06
5411 5435 1.561076 TGGCCTATCTTCACTGCACAT 59.439 47.619 3.32 0.00 0.00 3.21
5412 5436 0.983467 TGGCCTATCTTCACTGCACA 59.017 50.000 3.32 0.00 0.00 4.57
5413 5437 1.661341 CTGGCCTATCTTCACTGCAC 58.339 55.000 3.32 0.00 0.00 4.57
5414 5438 0.543277 CCTGGCCTATCTTCACTGCA 59.457 55.000 3.32 0.00 0.00 4.41
5415 5439 0.833287 TCCTGGCCTATCTTCACTGC 59.167 55.000 3.32 0.00 0.00 4.40
5416 5440 1.415659 CCTCCTGGCCTATCTTCACTG 59.584 57.143 3.32 0.00 0.00 3.66
5417 5441 1.799933 CCTCCTGGCCTATCTTCACT 58.200 55.000 3.32 0.00 0.00 3.41
5442 5466 4.925646 GCTTTTGCCAAGACCATAGAAAAG 59.074 41.667 0.00 0.00 40.15 2.27
5509 5552 3.825014 CAGCCTTTCATGATAATCCCCTG 59.175 47.826 0.00 0.00 0.00 4.45
5536 5579 3.084786 AGCAAAAGATGGAGGTGTTAGC 58.915 45.455 0.00 0.00 0.00 3.09
5540 5583 6.267471 TCAATTAAAGCAAAAGATGGAGGTGT 59.733 34.615 0.00 0.00 0.00 4.16
5673 5716 2.952293 GCAGCTCAGCCACTCAGGA 61.952 63.158 0.00 0.00 41.22 3.86
5697 5740 5.877012 GCATGATCATACATACCCAAGGTAG 59.123 44.000 8.15 0.00 41.83 3.18
5778 5823 2.960170 CCAGGAGCACAGCAAAGC 59.040 61.111 0.00 0.00 0.00 3.51
5779 5824 2.633509 GGCCAGGAGCACAGCAAAG 61.634 63.158 0.00 0.00 46.50 2.77
5780 5825 2.598394 GGCCAGGAGCACAGCAAA 60.598 61.111 0.00 0.00 46.50 3.68
5781 5826 3.214190 ATGGCCAGGAGCACAGCAA 62.214 57.895 13.05 0.00 46.50 3.91
5782 5827 3.633609 GATGGCCAGGAGCACAGCA 62.634 63.158 13.05 0.00 46.50 4.41
5783 5828 2.827642 GATGGCCAGGAGCACAGC 60.828 66.667 13.05 0.00 46.50 4.40
5784 5829 0.323178 AAAGATGGCCAGGAGCACAG 60.323 55.000 13.05 0.00 46.50 3.66
5785 5830 0.112995 AAAAGATGGCCAGGAGCACA 59.887 50.000 13.05 0.00 46.50 4.57
5786 5831 0.529378 CAAAAGATGGCCAGGAGCAC 59.471 55.000 13.05 0.00 46.50 4.40
5787 5832 0.405198 TCAAAAGATGGCCAGGAGCA 59.595 50.000 13.05 0.00 46.50 4.26
5845 5900 4.712829 TCCACCGTTGTAGGAAAGATGATA 59.287 41.667 0.00 0.00 34.73 2.15
5893 5948 5.458779 GGTGTGTTGCTGTTCAAGATTTTAC 59.541 40.000 0.00 0.00 34.91 2.01
5940 5995 6.879458 ACGTAACAAAGATTTAATCCTCAGCT 59.121 34.615 0.78 0.00 0.00 4.24
5952 6007 8.690680 TTTTTGTAAAGCACGTAACAAAGATT 57.309 26.923 0.00 0.00 41.38 2.40
5957 6012 9.517609 ACATAATTTTTGTAAAGCACGTAACAA 57.482 25.926 0.00 0.00 0.00 2.83
5959 6014 7.942538 GCACATAATTTTTGTAAAGCACGTAAC 59.057 33.333 0.00 0.00 0.00 2.50
5979 6034 8.567948 GCTAAAGAGGCAATTAATTAGCACATA 58.432 33.333 18.16 10.84 42.80 2.29
6075 6131 8.398665 GTGTTTTGATGTTAGTTTTCTCTCTGT 58.601 33.333 0.00 0.00 0.00 3.41
6076 6132 7.857885 GGTGTTTTGATGTTAGTTTTCTCTCTG 59.142 37.037 0.00 0.00 0.00 3.35
6103 6172 8.103305 TCAGTCTTTATGTCCATTTTTCTAGCT 58.897 33.333 0.00 0.00 0.00 3.32
6155 6225 6.867662 AGTCGAATAAAATGATGGACCATC 57.132 37.500 25.21 25.21 40.88 3.51
6186 6256 1.068474 AAAAAGGAGATCACGACGCG 58.932 50.000 3.53 3.53 0.00 6.01
6207 6277 1.001068 TCGTGATGCACCGGTCTTTAA 59.999 47.619 2.59 0.00 0.00 1.52
6208 6278 0.604073 TCGTGATGCACCGGTCTTTA 59.396 50.000 2.59 0.00 0.00 1.85
6211 6281 1.141881 GATCGTGATGCACCGGTCT 59.858 57.895 2.59 0.00 0.00 3.85
6212 6282 0.460284 AAGATCGTGATGCACCGGTC 60.460 55.000 2.59 7.28 0.00 4.79
6213 6283 0.821517 TAAGATCGTGATGCACCGGT 59.178 50.000 0.00 0.00 0.00 5.28
6214 6284 2.061773 GATAAGATCGTGATGCACCGG 58.938 52.381 0.00 0.00 0.00 5.28
6215 6285 2.728318 CTGATAAGATCGTGATGCACCG 59.272 50.000 0.00 0.00 0.00 4.94
6216 6286 2.478134 GCTGATAAGATCGTGATGCACC 59.522 50.000 0.00 0.00 0.00 5.01
6217 6287 2.154580 CGCTGATAAGATCGTGATGCAC 59.845 50.000 0.00 0.00 0.00 4.57
6218 6288 2.397549 CGCTGATAAGATCGTGATGCA 58.602 47.619 0.00 0.00 0.00 3.96
6219 6289 1.723542 CCGCTGATAAGATCGTGATGC 59.276 52.381 0.00 0.00 0.00 3.91
6242 6312 2.470057 TTTGAACCAAAGAGGCCCTT 57.530 45.000 0.00 0.00 43.14 3.95


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

AutoCloner maintained by Alex Coulton.