Multiple sequence alignment - TraesCS6D01G320600

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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 TraesCS6D01G320600 chr6D 100.000 4862 0 0 1 4862 428640253 428645114 0.000000e+00 8979.0
1 TraesCS6D01G320600 chr6B 90.662 4937 295 80 2 4862 645350059 645354905 0.000000e+00 6410.0
2 TraesCS6D01G320600 chr6A 95.415 2312 84 11 637 2933 573405325 573407629 0.000000e+00 3663.0
3 TraesCS6D01G320600 chr6A 95.251 1916 53 17 2953 4862 573407726 573409609 0.000000e+00 3000.0
4 TraesCS6D01G320600 chr6A 86.771 446 52 6 1 442 573403441 573403883 1.570000e-134 490.0
5 TraesCS6D01G320600 chr5B 85.882 85 10 2 1346 1429 65034131 65034048 6.700000e-14 89.8


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 TraesCS6D01G320600 chr6D 428640253 428645114 4861 False 8979.000000 8979 100.000 1 4862 1 chr6D.!!$F1 4861
1 TraesCS6D01G320600 chr6B 645350059 645354905 4846 False 6410.000000 6410 90.662 2 4862 1 chr6B.!!$F1 4860
2 TraesCS6D01G320600 chr6A 573403441 573409609 6168 False 2384.333333 3663 92.479 1 4862 3 chr6A.!!$F1 4861

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
655 1936 0.031585 CCGCCGTCCGATCTAAATCA 59.968 55.0 0.00 0.0 40.02 2.57 F
686 1967 0.463654 TTATGCCACGACTCCCATGC 60.464 55.0 0.00 0.0 0.00 4.06 F
1622 2913 0.530744 TGTGATGTGTCGCTAGGACC 59.469 55.0 8.36 0.0 45.46 4.46 F
2005 3308 1.228657 GCGCAAAGGACCTCGTTTCT 61.229 55.0 0.30 0.0 32.36 2.52 F
2007 3310 1.594331 GCAAAGGACCTCGTTTCTGT 58.406 50.0 0.00 0.0 32.36 3.41 F
3167 4548 2.288825 TGTGACAGTCCGATCTTTGGTC 60.289 50.0 0.00 0.0 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1481 2769 1.336240 GCCACAATTCAACAGCACTCC 60.336 52.381 0.00 0.00 0.00 3.85 R
1852 3155 1.410517 CATGGTACCATGCTCGAGTCT 59.589 52.381 35.69 6.72 45.71 3.24 R
3315 4696 2.466846 CTGCACACAGGCAAGAAAAAG 58.533 47.619 0.00 0.00 44.40 2.27 R
3391 4772 3.845781 ATCCCAGATGCGTACATTCTT 57.154 42.857 0.00 0.00 36.35 2.52 R
3735 5116 4.924019 CCGATAACACGGCCTTCA 57.076 55.556 0.00 0.00 46.20 3.02 R
4160 5546 0.028770 CACGCGCAAAGTTTCTTCCA 59.971 50.000 5.73 0.00 0.00 3.53 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 1.526887 CACTGGTCGATGTGTCAACAC 59.473 52.381 6.33 6.33 46.59 3.32
41 42 2.423185 TGTCAACACTGAAGCCTTTGTG 59.577 45.455 9.12 9.12 31.88 3.33
51 52 1.435515 GCCTTTGTGTTGGCGTTGA 59.564 52.632 0.00 0.00 39.71 3.18
67 68 4.206404 GGCGTTGAAAGCAAGTTTCTAAAC 59.794 41.667 5.34 0.00 44.45 2.01
68 69 4.086277 GCGTTGAAAGCAAGTTTCTAAACG 60.086 41.667 14.11 14.11 46.81 3.60
117 118 3.006859 CAGACTTGTGTGGACTATGACCA 59.993 47.826 0.00 0.00 34.84 4.02
141 142 7.362142 CCAAAGATAAAGGTAGCTTGGTTCTTC 60.362 40.741 19.13 8.20 36.11 2.87
162 163 9.905713 TTCTTCTTTGTATTATGCCTGTATTCT 57.094 29.630 0.00 0.00 0.00 2.40
254 256 2.214376 TGGCGAAATGATCCACCTTT 57.786 45.000 0.00 0.00 0.00 3.11
268 270 8.504811 TGATCCACCTTTATATATCCAAGACA 57.495 34.615 6.26 0.00 0.00 3.41
272 274 8.778059 TCCACCTTTATATATCCAAGACACTTT 58.222 33.333 6.26 0.00 0.00 2.66
320 323 4.527427 AGGGGTTGTAGAGAAGTTAGACAC 59.473 45.833 0.00 0.00 0.00 3.67
335 338 0.713883 GACACGTGACATGTTAGGCG 59.286 55.000 25.01 9.73 0.00 5.52
341 344 2.930040 CGTGACATGTTAGGCGATCTTT 59.070 45.455 0.00 0.00 0.00 2.52
342 345 4.109766 CGTGACATGTTAGGCGATCTTTA 58.890 43.478 0.00 0.00 0.00 1.85
343 346 4.207224 CGTGACATGTTAGGCGATCTTTAG 59.793 45.833 0.00 0.00 0.00 1.85
344 347 4.508124 GTGACATGTTAGGCGATCTTTAGG 59.492 45.833 0.00 0.00 0.00 2.69
345 348 4.161565 TGACATGTTAGGCGATCTTTAGGT 59.838 41.667 0.00 0.00 0.00 3.08
348 351 6.827727 ACATGTTAGGCGATCTTTAGGTAAT 58.172 36.000 0.00 0.00 0.00 1.89
349 352 7.280356 ACATGTTAGGCGATCTTTAGGTAATT 58.720 34.615 0.00 0.00 0.00 1.40
392 396 8.750416 CATAAGTTACGATGAAGTCTCAAGATG 58.250 37.037 0.00 0.00 34.49 2.90
410 419 9.123902 CTCAAGATGTTGTATATTCCAATTCCA 57.876 33.333 2.11 0.00 34.98 3.53
413 422 7.586349 AGATGTTGTATATTCCAATTCCACCT 58.414 34.615 0.00 0.00 0.00 4.00
442 738 0.877071 CCTATTCGGATGGCATGTGC 59.123 55.000 3.81 0.00 35.88 4.57
443 739 1.596603 CTATTCGGATGGCATGTGCA 58.403 50.000 3.81 0.00 44.36 4.57
444 740 2.156917 CTATTCGGATGGCATGTGCAT 58.843 47.619 3.81 0.00 44.36 3.96
453 749 1.474879 TGGCATGTGCATGATGTCTTG 59.525 47.619 15.53 0.00 44.36 3.02
458 767 4.242475 CATGTGCATGATGTCTTGCTTTT 58.758 39.130 18.01 4.26 44.41 2.27
462 771 6.554419 TGTGCATGATGTCTTGCTTTTATAC 58.446 36.000 18.01 9.74 44.41 1.47
476 787 7.341445 TGCTTTTATACATTATCACCCCAAC 57.659 36.000 0.00 0.00 0.00 3.77
490 801 2.014128 CCCCAACGAGCGAACAAATAT 58.986 47.619 0.00 0.00 0.00 1.28
491 802 3.199677 CCCCAACGAGCGAACAAATATA 58.800 45.455 0.00 0.00 0.00 0.86
492 803 3.813166 CCCCAACGAGCGAACAAATATAT 59.187 43.478 0.00 0.00 0.00 0.86
513 824 5.565723 ATTTGTCGGTATATCGTAAACGC 57.434 39.130 5.11 0.00 39.60 4.84
556 867 7.597288 ACATAACAATCCCCTAAATTAAGCC 57.403 36.000 0.00 0.00 0.00 4.35
560 871 5.776358 ACAATCCCCTAAATTAAGCCATCA 58.224 37.500 0.00 0.00 0.00 3.07
571 1852 1.293062 AAGCCATCACCACTCTCCAT 58.707 50.000 0.00 0.00 0.00 3.41
575 1856 2.827921 GCCATCACCACTCTCCATTTTT 59.172 45.455 0.00 0.00 0.00 1.94
605 1886 2.432206 ATAAACCAAACAAGCCGTGC 57.568 45.000 0.00 0.00 0.00 5.34
606 1887 1.103803 TAAACCAAACAAGCCGTGCA 58.896 45.000 0.00 0.00 0.00 4.57
609 1890 1.323412 ACCAAACAAGCCGTGCATTA 58.677 45.000 0.00 0.00 0.00 1.90
611 1892 2.298729 ACCAAACAAGCCGTGCATTAAT 59.701 40.909 0.00 0.00 0.00 1.40
612 1893 3.508012 ACCAAACAAGCCGTGCATTAATA 59.492 39.130 0.00 0.00 0.00 0.98
613 1894 4.104776 CCAAACAAGCCGTGCATTAATAG 58.895 43.478 0.00 0.00 0.00 1.73
616 1897 2.297701 CAAGCCGTGCATTAATAGGGT 58.702 47.619 0.00 0.00 0.00 4.34
617 1898 1.967319 AGCCGTGCATTAATAGGGTG 58.033 50.000 0.00 0.00 0.00 4.61
618 1899 1.211949 AGCCGTGCATTAATAGGGTGT 59.788 47.619 0.00 0.00 0.00 4.16
619 1900 1.602377 GCCGTGCATTAATAGGGTGTC 59.398 52.381 0.00 0.00 0.00 3.67
620 1901 2.912771 CCGTGCATTAATAGGGTGTCA 58.087 47.619 0.00 0.00 0.00 3.58
621 1902 3.275143 CCGTGCATTAATAGGGTGTCAA 58.725 45.455 0.00 0.00 0.00 3.18
622 1903 3.064820 CCGTGCATTAATAGGGTGTCAAC 59.935 47.826 0.00 0.00 0.00 3.18
623 1904 3.064820 CGTGCATTAATAGGGTGTCAACC 59.935 47.826 0.00 0.00 46.81 3.77
655 1936 0.031585 CCGCCGTCCGATCTAAATCA 59.968 55.000 0.00 0.00 40.02 2.57
656 1937 1.409412 CGCCGTCCGATCTAAATCAG 58.591 55.000 0.00 0.00 40.02 2.90
667 1948 8.200792 GTCCGATCTAAATCAGATGGCTTATAT 58.799 37.037 0.00 0.00 44.41 0.86
683 1964 4.562757 GCTTATATTATGCCACGACTCCCA 60.563 45.833 0.00 0.00 0.00 4.37
684 1965 5.734720 CTTATATTATGCCACGACTCCCAT 58.265 41.667 0.00 0.00 0.00 4.00
685 1966 2.260844 ATTATGCCACGACTCCCATG 57.739 50.000 0.00 0.00 0.00 3.66
686 1967 0.463654 TTATGCCACGACTCCCATGC 60.464 55.000 0.00 0.00 0.00 4.06
808 2095 4.079958 GCTTCTTCCCTCCTATAAACCCAA 60.080 45.833 0.00 0.00 0.00 4.12
812 2099 3.036091 TCCCTCCTATAAACCCAACTCG 58.964 50.000 0.00 0.00 0.00 4.18
851 2138 2.362375 GAATTCCCCAAGCCCGCA 60.362 61.111 0.00 0.00 0.00 5.69
945 2232 3.537874 GCCGTGCCCTAGATCGGT 61.538 66.667 13.21 0.00 44.07 4.69
1444 2732 1.883084 CTCGGCATTACGGTGAGCC 60.883 63.158 9.42 9.42 43.61 4.70
1445 2733 2.186903 CGGCATTACGGTGAGCCT 59.813 61.111 15.14 0.00 44.85 4.58
1555 2845 8.802267 TGAATTAAATCCCTTTGACTAGTTTGG 58.198 33.333 0.00 0.00 0.00 3.28
1556 2846 6.584185 TTAAATCCCTTTGACTAGTTTGGC 57.416 37.500 0.00 0.00 0.00 4.52
1588 2878 9.797556 GGATAAACAGACCAATGGTAAAAATAC 57.202 33.333 4.23 0.00 35.25 1.89
1622 2913 0.530744 TGTGATGTGTCGCTAGGACC 59.469 55.000 8.36 0.00 45.46 4.46
1651 2950 7.884877 AGATTGAAGTGATACCAATGTTCAGAA 59.115 33.333 0.00 0.00 31.40 3.02
1655 2954 8.514594 TGAAGTGATACCAATGTTCAGAATTTC 58.485 33.333 0.00 0.00 0.00 2.17
1795 3098 8.715191 TGAAAGCAAACATTTAGAATGTGTTT 57.285 26.923 7.03 5.60 44.35 2.83
1820 3123 2.752903 GTTGGGTGGAATGTGGTATGAC 59.247 50.000 0.00 0.00 0.00 3.06
1851 3154 5.714333 TGTCACTCTTAGCTCTCTGAATCTT 59.286 40.000 0.00 0.00 0.00 2.40
1852 3155 6.887002 TGTCACTCTTAGCTCTCTGAATCTTA 59.113 38.462 0.00 0.00 0.00 2.10
1858 3161 6.481976 TCTTAGCTCTCTGAATCTTAGACTCG 59.518 42.308 0.00 0.00 0.00 4.18
1868 3171 4.839668 ATCTTAGACTCGAGCATGGTAC 57.160 45.455 13.61 0.00 0.00 3.34
1920 3223 5.552870 TCTAGCTGGGGTTCTGATATTTC 57.447 43.478 0.00 0.00 0.00 2.17
1924 3227 4.476479 AGCTGGGGTTCTGATATTTCTCTT 59.524 41.667 0.00 0.00 0.00 2.85
2005 3308 1.228657 GCGCAAAGGACCTCGTTTCT 61.229 55.000 0.30 0.00 32.36 2.52
2007 3310 1.594331 GCAAAGGACCTCGTTTCTGT 58.406 50.000 0.00 0.00 32.36 3.41
2092 3395 8.186178 AGTAAGCTGTCAATATTAACTTGTCG 57.814 34.615 0.00 0.00 0.00 4.35
2138 3441 5.587388 ATCATGGATTTGTTGGTTAGCTG 57.413 39.130 0.00 0.00 0.00 4.24
2244 3547 6.625362 TGTTTGAATAACACAAAGCAACTGA 58.375 32.000 0.00 0.00 37.80 3.41
2266 3569 6.795590 TGATTGACCTGTTTAATCCCCTAAA 58.204 36.000 0.00 0.00 31.47 1.85
2299 3602 6.267817 ACTTGATTTCGGTATGCATGATTTG 58.732 36.000 10.16 0.00 0.00 2.32
3033 4414 5.481824 TGTACAGATTCTTGTGAGGATGTCT 59.518 40.000 0.00 0.00 32.56 3.41
3044 4425 7.604164 TCTTGTGAGGATGTCTTAATTGAGAAC 59.396 37.037 0.82 0.00 0.00 3.01
3068 4449 5.359756 TGCTACATATCTGTTGGTGATGAC 58.640 41.667 0.00 0.00 36.79 3.06
3167 4548 2.288825 TGTGACAGTCCGATCTTTGGTC 60.289 50.000 0.00 0.00 0.00 4.02
3179 4560 8.746530 GTCCGATCTTTGGTCAGGTATATATTA 58.253 37.037 0.00 0.00 0.00 0.98
3315 4696 6.757478 GGAGTATAAAGGTGAAGCTTACACTC 59.243 42.308 20.81 15.47 38.20 3.51
3391 4772 2.550606 GGAGTTGCAAATGTTACGGTGA 59.449 45.455 3.09 0.00 0.00 4.02
3735 5116 7.636150 GCATATATTCCAATGCTCCTACATT 57.364 36.000 1.63 0.00 44.08 2.71
3759 5140 3.340727 CCGTGTTATCGGGTCAGTC 57.659 57.895 0.00 0.00 45.88 3.51
3855 5236 6.588756 TGAACAGTACGGAAGTTGATTATGAC 59.411 38.462 0.00 0.00 46.40 3.06
4115 5501 5.338463 GGCCTTAACTTCTGGTCTCTATTGT 60.338 44.000 0.00 0.00 0.00 2.71
4162 5548 9.798994 ATAAATTCTACGTACTTAAGTCACTGG 57.201 33.333 12.39 1.71 0.00 4.00
4163 5549 7.458409 AATTCTACGTACTTAAGTCACTGGA 57.542 36.000 12.39 4.10 0.00 3.86
4165 5551 6.492007 TCTACGTACTTAAGTCACTGGAAG 57.508 41.667 12.39 0.00 42.29 3.46
4168 5554 6.152932 ACGTACTTAAGTCACTGGAAGAAA 57.847 37.500 12.39 0.00 37.43 2.52
4176 5567 1.333619 TCACTGGAAGAAACTTTGCGC 59.666 47.619 0.00 0.00 37.43 6.09
4259 5650 5.607939 TTTTCAACTCTCTCACACCTGTA 57.392 39.130 0.00 0.00 0.00 2.74
4261 5652 3.157881 TCAACTCTCTCACACCTGTAGG 58.842 50.000 0.00 0.00 42.17 3.18
4339 5731 5.999205 AGTGCCATGGTCATTTCATAAAA 57.001 34.783 14.67 0.00 0.00 1.52
4350 5742 6.863126 GGTCATTTCATAAAATTATCTGCCGG 59.137 38.462 0.00 0.00 32.69 6.13
4399 5793 2.165030 GCAACATGACAGGAAATCAGGG 59.835 50.000 0.00 0.00 32.20 4.45
4400 5794 2.756760 CAACATGACAGGAAATCAGGGG 59.243 50.000 0.00 0.00 32.20 4.79
4476 5870 0.974010 ACCGGGGAAGTAATCTCGCA 60.974 55.000 6.32 0.00 0.00 5.10
4512 5907 4.261489 GGTGATTCACTCATTCCATCATGC 60.261 45.833 16.02 0.00 35.97 4.06
4535 5945 0.539986 TCTAACCATTCCGTCAGCCC 59.460 55.000 0.00 0.00 0.00 5.19
4565 5976 0.804364 TGATCTCCACAAATGCACGC 59.196 50.000 0.00 0.00 0.00 5.34
4566 5977 0.247814 GATCTCCACAAATGCACGCG 60.248 55.000 3.53 3.53 0.00 6.01
4603 6014 4.323868 GGAAGAGAAAAGAGCACCCATAGT 60.324 45.833 0.00 0.00 0.00 2.12
4704 6115 4.455124 CTTTTCTTCTTTGCCGTAGAACG 58.545 43.478 0.00 0.00 42.11 3.95
4787 6199 5.699001 TGACGTTACAAACATGTGCTCTTAT 59.301 36.000 0.00 0.00 0.00 1.73
4788 6200 6.869388 TGACGTTACAAACATGTGCTCTTATA 59.131 34.615 0.00 0.00 0.00 0.98
4789 6201 7.547722 TGACGTTACAAACATGTGCTCTTATAT 59.452 33.333 0.00 0.00 0.00 0.86
4790 6202 8.936070 ACGTTACAAACATGTGCTCTTATATA 57.064 30.769 0.00 0.00 0.00 0.86
4791 6203 9.542462 ACGTTACAAACATGTGCTCTTATATAT 57.458 29.630 0.00 0.00 0.00 0.86
4829 6241 8.882736 TGTTGTCACTATTGTCATGATGATAAC 58.117 33.333 19.36 19.36 38.15 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 1.148310 GTTGACACATCGACCAGTGG 58.852 55.000 7.91 7.91 39.99 4.00
41 42 1.921243 AACTTGCTTTCAACGCCAAC 58.079 45.000 0.00 0.00 0.00 3.77
51 52 9.575783 TTAAACATTCGTTTAGAAACTTGCTTT 57.424 25.926 3.80 5.28 45.78 3.51
67 68 5.296813 CCTCCAAGAGGTTTAAACATTCG 57.703 43.478 19.57 5.64 44.25 3.34
117 118 7.462590 AGAAGAACCAAGCTACCTTTATCTTT 58.537 34.615 0.00 0.00 30.73 2.52
281 283 5.722441 ACAACCCCTCTTCCAAACTTTTAAA 59.278 36.000 0.00 0.00 0.00 1.52
282 284 5.274015 ACAACCCCTCTTCCAAACTTTTAA 58.726 37.500 0.00 0.00 0.00 1.52
320 323 2.209838 AGATCGCCTAACATGTCACG 57.790 50.000 0.00 0.86 0.00 4.35
363 367 7.392494 TGAGACTTCATCGTAACTTATGTCT 57.608 36.000 0.00 0.00 35.35 3.41
392 396 7.778382 AGGTTAGGTGGAATTGGAATATACAAC 59.222 37.037 0.00 0.00 0.00 3.32
410 419 2.305009 CGAATAGGACGGAGGTTAGGT 58.695 52.381 0.00 0.00 0.00 3.08
431 440 1.954382 AGACATCATGCACATGCCATC 59.046 47.619 5.73 3.38 41.18 3.51
453 749 6.261381 TCGTTGGGGTGATAATGTATAAAAGC 59.739 38.462 0.00 0.00 0.00 3.51
458 767 4.559906 CGCTCGTTGGGGTGATAATGTATA 60.560 45.833 0.00 0.00 0.00 1.47
462 771 0.937304 CGCTCGTTGGGGTGATAATG 59.063 55.000 0.00 0.00 0.00 1.90
490 801 6.205071 TGCGTTTACGATATACCGACAAATA 58.795 36.000 6.44 0.00 43.02 1.40
491 802 5.042593 TGCGTTTACGATATACCGACAAAT 58.957 37.500 6.44 0.00 43.02 2.32
492 803 4.419280 TGCGTTTACGATATACCGACAAA 58.581 39.130 6.44 0.00 43.02 2.83
495 806 6.142161 TGTTTATGCGTTTACGATATACCGAC 59.858 38.462 6.44 4.33 43.02 4.79
497 808 6.360414 TCTGTTTATGCGTTTACGATATACCG 59.640 38.462 6.44 0.00 43.02 4.02
502 813 7.758613 TTCATCTGTTTATGCGTTTACGATA 57.241 32.000 6.44 0.00 43.02 2.92
503 814 6.656314 TTCATCTGTTTATGCGTTTACGAT 57.344 33.333 6.44 0.16 43.02 3.73
504 815 6.656314 ATTCATCTGTTTATGCGTTTACGA 57.344 33.333 6.44 0.00 43.02 3.43
533 844 7.595819 TGGCTTAATTTAGGGGATTGTTATG 57.404 36.000 0.00 0.00 0.00 1.90
539 850 5.147767 GGTGATGGCTTAATTTAGGGGATT 58.852 41.667 0.00 0.00 0.00 3.01
554 865 2.134789 AAATGGAGAGTGGTGATGGC 57.865 50.000 0.00 0.00 0.00 4.40
575 1856 9.327628 GGCTTGTTTGGTTTATTAAAAGGTAAA 57.672 29.630 0.00 0.00 0.00 2.01
576 1857 7.652507 CGGCTTGTTTGGTTTATTAAAAGGTAA 59.347 33.333 0.00 0.00 0.00 2.85
577 1858 7.146648 CGGCTTGTTTGGTTTATTAAAAGGTA 58.853 34.615 0.00 0.00 0.00 3.08
578 1859 5.986741 CGGCTTGTTTGGTTTATTAAAAGGT 59.013 36.000 0.00 0.00 0.00 3.50
579 1860 5.986741 ACGGCTTGTTTGGTTTATTAAAAGG 59.013 36.000 0.00 0.00 0.00 3.11
580 1861 6.563196 GCACGGCTTGTTTGGTTTATTAAAAG 60.563 38.462 0.00 0.00 0.00 2.27
581 1862 5.234543 GCACGGCTTGTTTGGTTTATTAAAA 59.765 36.000 0.00 0.00 0.00 1.52
582 1863 4.745620 GCACGGCTTGTTTGGTTTATTAAA 59.254 37.500 0.00 0.00 0.00 1.52
583 1864 4.202121 TGCACGGCTTGTTTGGTTTATTAA 60.202 37.500 0.00 0.00 0.00 1.40
584 1865 3.318275 TGCACGGCTTGTTTGGTTTATTA 59.682 39.130 0.00 0.00 0.00 0.98
585 1866 2.101582 TGCACGGCTTGTTTGGTTTATT 59.898 40.909 0.00 0.00 0.00 1.40
586 1867 1.683917 TGCACGGCTTGTTTGGTTTAT 59.316 42.857 0.00 0.00 0.00 1.40
587 1868 1.103803 TGCACGGCTTGTTTGGTTTA 58.896 45.000 0.00 0.00 0.00 2.01
588 1869 0.463620 ATGCACGGCTTGTTTGGTTT 59.536 45.000 0.00 0.00 0.00 3.27
605 1886 6.693315 ATTTCGGTTGACACCCTATTAATG 57.307 37.500 0.00 0.00 40.52 1.90
606 1887 8.810990 TTTATTTCGGTTGACACCCTATTAAT 57.189 30.769 0.00 0.00 40.52 1.40
609 1890 6.320418 GGATTTATTTCGGTTGACACCCTATT 59.680 38.462 0.00 0.00 40.52 1.73
611 1892 5.045432 AGGATTTATTTCGGTTGACACCCTA 60.045 40.000 0.00 0.00 40.52 3.53
612 1893 4.014406 GGATTTATTTCGGTTGACACCCT 58.986 43.478 0.00 0.00 40.52 4.34
613 1894 4.014406 AGGATTTATTTCGGTTGACACCC 58.986 43.478 0.00 0.00 40.52 4.61
616 1897 3.936453 CGGAGGATTTATTTCGGTTGACA 59.064 43.478 0.00 0.00 0.00 3.58
617 1898 3.242641 GCGGAGGATTTATTTCGGTTGAC 60.243 47.826 0.00 0.00 0.00 3.18
618 1899 2.940410 GCGGAGGATTTATTTCGGTTGA 59.060 45.455 0.00 0.00 0.00 3.18
619 1900 2.032924 GGCGGAGGATTTATTTCGGTTG 59.967 50.000 0.00 0.00 0.00 3.77
620 1901 2.294979 GGCGGAGGATTTATTTCGGTT 58.705 47.619 0.00 0.00 0.00 4.44
621 1902 1.808891 CGGCGGAGGATTTATTTCGGT 60.809 52.381 0.00 0.00 0.00 4.69
622 1903 0.865769 CGGCGGAGGATTTATTTCGG 59.134 55.000 0.00 0.00 0.00 4.30
623 1904 1.525619 GACGGCGGAGGATTTATTTCG 59.474 52.381 13.24 0.00 0.00 3.46
624 1905 1.871676 GGACGGCGGAGGATTTATTTC 59.128 52.381 13.24 0.00 0.00 2.17
625 1906 1.808891 CGGACGGCGGAGGATTTATTT 60.809 52.381 13.24 0.00 0.00 1.40
626 1907 0.249741 CGGACGGCGGAGGATTTATT 60.250 55.000 13.24 0.00 0.00 1.40
627 1908 1.111116 TCGGACGGCGGAGGATTTAT 61.111 55.000 13.24 0.00 0.00 1.40
628 1909 1.111116 ATCGGACGGCGGAGGATTTA 61.111 55.000 13.24 0.00 0.00 1.40
629 1910 2.365095 GATCGGACGGCGGAGGATTT 62.365 60.000 13.24 0.00 0.00 2.17
630 1911 2.838225 ATCGGACGGCGGAGGATT 60.838 61.111 13.24 0.00 0.00 3.01
631 1912 2.407440 TAGATCGGACGGCGGAGGAT 62.407 60.000 13.24 10.25 0.00 3.24
632 1913 2.613660 TTAGATCGGACGGCGGAGGA 62.614 60.000 13.24 5.05 0.00 3.71
633 1914 1.731433 TTTAGATCGGACGGCGGAGG 61.731 60.000 13.24 0.00 0.00 4.30
634 1915 0.314302 ATTTAGATCGGACGGCGGAG 59.686 55.000 13.24 1.46 0.00 4.63
635 1916 0.313043 GATTTAGATCGGACGGCGGA 59.687 55.000 13.24 0.00 0.00 5.54
667 1948 0.463654 GCATGGGAGTCGTGGCATAA 60.464 55.000 0.00 0.00 33.10 1.90
670 1951 2.803155 GAAGCATGGGAGTCGTGGCA 62.803 60.000 0.00 0.00 33.10 4.92
678 1959 0.460987 GACGGTGAGAAGCATGGGAG 60.461 60.000 0.00 0.00 0.00 4.30
683 1964 2.354203 GGAAGAAGACGGTGAGAAGCAT 60.354 50.000 0.00 0.00 0.00 3.79
684 1965 1.000955 GGAAGAAGACGGTGAGAAGCA 59.999 52.381 0.00 0.00 0.00 3.91
685 1966 1.673329 GGGAAGAAGACGGTGAGAAGC 60.673 57.143 0.00 0.00 0.00 3.86
686 1967 1.066787 GGGGAAGAAGACGGTGAGAAG 60.067 57.143 0.00 0.00 0.00 2.85
812 2099 2.676471 ATTGGAGCGGTTGGTGCC 60.676 61.111 0.00 0.00 32.31 5.01
945 2232 2.784095 TCCTTCTTCTCCCCTCGATCTA 59.216 50.000 0.00 0.00 0.00 1.98
952 2239 1.306226 CGGGTCCTTCTTCTCCCCT 60.306 63.158 0.00 0.00 36.84 4.79
1444 2732 5.390613 CATTGCTCCGGTTGTAAGTAAAAG 58.609 41.667 0.00 0.00 0.00 2.27
1445 2733 4.216687 CCATTGCTCCGGTTGTAAGTAAAA 59.783 41.667 0.00 0.00 0.00 1.52
1480 2768 1.955778 CCACAATTCAACAGCACTCCA 59.044 47.619 0.00 0.00 0.00 3.86
1481 2769 1.336240 GCCACAATTCAACAGCACTCC 60.336 52.381 0.00 0.00 0.00 3.85
1482 2770 1.664016 CGCCACAATTCAACAGCACTC 60.664 52.381 0.00 0.00 0.00 3.51
1489 2777 1.539388 TGATCCACGCCACAATTCAAC 59.461 47.619 0.00 0.00 0.00 3.18
1553 2843 3.010027 TGGTCTGTTTATCCATCAAGCCA 59.990 43.478 0.00 0.00 0.00 4.75
1555 2845 5.450965 CCATTGGTCTGTTTATCCATCAAGC 60.451 44.000 0.00 0.00 0.00 4.01
1556 2846 5.653769 ACCATTGGTCTGTTTATCCATCAAG 59.346 40.000 1.37 0.00 0.00 3.02
1588 2878 4.741185 CACATCACACAACAACAATCCTTG 59.259 41.667 0.00 0.00 0.00 3.61
1622 2913 6.668541 ACATTGGTATCACTTCAATCTTCG 57.331 37.500 0.00 0.00 0.00 3.79
1795 3098 2.344592 ACCACATTCCACCCAACTCTA 58.655 47.619 0.00 0.00 0.00 2.43
1820 3123 5.048083 AGAGAGCTAAGAGTGACAGTTCAAG 60.048 44.000 0.00 0.00 31.90 3.02
1851 3154 2.430248 TGGTACCATGCTCGAGTCTA 57.570 50.000 11.60 1.27 0.00 2.59
1852 3155 1.410517 CATGGTACCATGCTCGAGTCT 59.589 52.381 35.69 6.72 45.71 3.24
1868 3171 6.204301 CCTGCTAATCTGAAATCTGTACATGG 59.796 42.308 0.00 0.00 0.00 3.66
1873 3176 6.299805 ACACCTGCTAATCTGAAATCTGTA 57.700 37.500 0.00 0.00 0.00 2.74
1920 3223 2.163509 TCCTTCTCGTCCTGTCAAGAG 58.836 52.381 0.00 0.00 0.00 2.85
1924 3227 1.550524 CCAATCCTTCTCGTCCTGTCA 59.449 52.381 0.00 0.00 0.00 3.58
2005 3308 9.166173 CAAATTCTGTCCATGAATTAGACTACA 57.834 33.333 0.00 0.00 41.54 2.74
2007 3310 9.958180 TTCAAATTCTGTCCATGAATTAGACTA 57.042 29.630 0.00 0.00 41.54 2.59
2083 3386 5.386958 AGATTACACAGCTCGACAAGTTA 57.613 39.130 0.00 0.00 0.00 2.24
2092 3395 3.933332 GGGTGTTGTAGATTACACAGCTC 59.067 47.826 0.00 0.00 44.94 4.09
2138 3441 2.745821 TCTCTCATGCATGTTGCTTCAC 59.254 45.455 25.43 0.00 45.31 3.18
2244 3547 6.663523 CAGTTTAGGGGATTAAACAGGTCAAT 59.336 38.462 10.26 0.00 42.97 2.57
2266 3569 6.037172 GCATACCGAAATCAAGTACATTCAGT 59.963 38.462 0.00 0.00 0.00 3.41
2299 3602 5.064325 ACTTTTAACGAATAAGCGGGACATC 59.936 40.000 0.00 0.00 35.12 3.06
2376 3679 7.553044 AGTGAACTTGCCTATTCAGTATTTACC 59.447 37.037 0.71 0.00 36.85 2.85
2871 4175 2.778299 TGCTTGAAGTAACGCCTGAAT 58.222 42.857 0.00 0.00 0.00 2.57
2940 4244 7.180051 AGTCCCAGATGATACAAGAATCTATCC 59.820 40.741 0.00 0.00 0.00 2.59
2944 4248 5.901853 TCAGTCCCAGATGATACAAGAATCT 59.098 40.000 0.00 0.00 0.00 2.40
3033 4414 9.890629 AACAGATATGTAGCAGTTCTCAATTAA 57.109 29.630 0.00 0.00 0.00 1.40
3044 4425 5.464722 GTCATCACCAACAGATATGTAGCAG 59.535 44.000 0.00 0.00 0.00 4.24
3261 4642 6.985117 TCTATGCAAAAGAATGTGAAAGCTT 58.015 32.000 0.00 0.00 0.00 3.74
3262 4643 6.579666 TCTATGCAAAAGAATGTGAAAGCT 57.420 33.333 0.00 0.00 0.00 3.74
3315 4696 2.466846 CTGCACACAGGCAAGAAAAAG 58.533 47.619 0.00 0.00 44.40 2.27
3391 4772 3.845781 ATCCCAGATGCGTACATTCTT 57.154 42.857 0.00 0.00 36.35 2.52
3735 5116 4.924019 CCGATAACACGGCCTTCA 57.076 55.556 0.00 0.00 46.20 3.02
3759 5140 8.359642 TCTAAATTCTCACATGGTTTTGGAAAG 58.640 33.333 0.00 0.00 0.00 2.62
4141 5527 6.712095 TCTTCCAGTGACTTAAGTACGTAGAA 59.288 38.462 8.42 8.57 0.00 2.10
4147 5533 8.336080 CAAAGTTTCTTCCAGTGACTTAAGTAC 58.664 37.037 8.42 7.50 30.91 2.73
4149 5535 6.183360 GCAAAGTTTCTTCCAGTGACTTAAGT 60.183 38.462 8.13 8.13 30.91 2.24
4150 5536 6.202226 GCAAAGTTTCTTCCAGTGACTTAAG 58.798 40.000 0.00 0.00 30.91 1.85
4151 5537 5.220777 CGCAAAGTTTCTTCCAGTGACTTAA 60.221 40.000 0.00 0.00 30.91 1.85
4152 5538 4.272504 CGCAAAGTTTCTTCCAGTGACTTA 59.727 41.667 0.00 0.00 30.91 2.24
4153 5539 3.065371 CGCAAAGTTTCTTCCAGTGACTT 59.935 43.478 0.00 0.00 32.33 3.01
4154 5540 2.614057 CGCAAAGTTTCTTCCAGTGACT 59.386 45.455 0.00 0.00 0.00 3.41
4155 5541 2.854805 GCGCAAAGTTTCTTCCAGTGAC 60.855 50.000 0.30 0.00 0.00 3.67
4156 5542 1.333619 GCGCAAAGTTTCTTCCAGTGA 59.666 47.619 0.30 0.00 0.00 3.41
4159 5545 0.307760 ACGCGCAAAGTTTCTTCCAG 59.692 50.000 5.73 0.00 0.00 3.86
4160 5546 0.028770 CACGCGCAAAGTTTCTTCCA 59.971 50.000 5.73 0.00 0.00 3.53
4161 5547 0.028902 ACACGCGCAAAGTTTCTTCC 59.971 50.000 5.73 0.00 0.00 3.46
4162 5548 1.267832 TGACACGCGCAAAGTTTCTTC 60.268 47.619 5.73 0.00 0.00 2.87
4163 5549 0.730265 TGACACGCGCAAAGTTTCTT 59.270 45.000 5.73 0.00 0.00 2.52
4165 5551 1.447938 CATTGACACGCGCAAAGTTTC 59.552 47.619 5.73 0.19 0.00 2.78
4168 5554 0.316937 CACATTGACACGCGCAAAGT 60.317 50.000 5.73 2.68 0.00 2.66
4176 5567 0.597568 ATTGGCACCACATTGACACG 59.402 50.000 0.00 0.00 32.78 4.49
4259 5650 6.869206 TTATACCTTCTGCAACTTACTCCT 57.131 37.500 0.00 0.00 0.00 3.69
4339 5731 4.406456 TCCAAAATATGCCGGCAGATAAT 58.594 39.130 34.93 24.00 0.00 1.28
4350 5742 4.320494 CGGCTTCCACTATCCAAAATATGC 60.320 45.833 0.00 0.00 0.00 3.14
4399 5793 1.332065 GCTTTCGCTTTATCTGCCTCC 59.668 52.381 0.00 0.00 0.00 4.30
4400 5794 1.332065 GGCTTTCGCTTTATCTGCCTC 59.668 52.381 0.00 0.00 36.32 4.70
4476 5870 0.548682 AATCACCTGGCTGGGAGAGT 60.549 55.000 15.36 8.59 41.11 3.24
4512 5907 1.927174 CTGACGGAATGGTTAGAAGCG 59.073 52.381 0.00 0.00 0.00 4.68
4535 5945 5.710513 TTGTGGAGATCAGAACAAATTGG 57.289 39.130 0.00 0.00 29.96 3.16
4565 5976 4.046462 TCTCTTCCGTGAAACAGTAAACG 58.954 43.478 0.00 0.00 35.74 3.60
4566 5977 5.978934 TTCTCTTCCGTGAAACAGTAAAC 57.021 39.130 0.00 0.00 35.74 2.01
4603 6014 1.702957 ACAGAAACCCCGGATTTCTCA 59.297 47.619 23.37 0.00 43.06 3.27
4679 6090 1.692411 ACGGCAAAGAAGAAAAGCCT 58.308 45.000 0.00 0.00 43.07 4.58
4704 6115 1.627834 CCATGGAGGAGGCTCTTATCC 59.372 57.143 15.23 18.30 41.22 2.59
4829 6241 3.059597 CACAAGTAAACAAGAGGACGCAG 60.060 47.826 0.00 0.00 0.00 5.18


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

AutoCloner maintained by Alex Coulton.