Multiple sequence alignment - TraesCS6B01G174100

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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 TraesCS6B01G174100 chr6B 100.000 4912 0 0 1 4912 188665168 188670079 0.000000e+00 9071
1 TraesCS6B01G174100 chr6A 92.392 4929 227 71 60 4911 124264679 124269536 0.000000e+00 6889
2 TraesCS6B01G174100 chr6A 82.783 697 64 29 28 703 124234946 124235607 5.520000e-159 571
3 TraesCS6B01G174100 chr6D 94.707 4062 152 29 906 4911 103000993 103005047 0.000000e+00 6252
4 TraesCS6B01G174100 chr6D 77.995 409 27 19 34 409 102994276 102994654 1.080000e-46 198
5 TraesCS6B01G174100 chr7D 76.875 320 56 17 2857 3169 606645867 606645559 1.090000e-36 165
6 TraesCS6B01G174100 chr7B 77.019 322 51 16 2857 3169 690869531 690869224 3.930000e-36 163


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 TraesCS6B01G174100 chr6B 188665168 188670079 4911 False 9071 9071 100.000 1 4912 1 chr6B.!!$F1 4911
1 TraesCS6B01G174100 chr6A 124264679 124269536 4857 False 6889 6889 92.392 60 4911 1 chr6A.!!$F2 4851
2 TraesCS6B01G174100 chr6A 124234946 124235607 661 False 571 571 82.783 28 703 1 chr6A.!!$F1 675
3 TraesCS6B01G174100 chr6D 103000993 103005047 4054 False 6252 6252 94.707 906 4911 1 chr6D.!!$F2 4005

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
615 659 0.031716 TCCAGGAGATCACCCCAGAG 60.032 60.0 5.46 0.0 0.00 3.35 F
968 1024 0.681564 GGAGAGAAGACAGAGGCCGA 60.682 60.0 0.00 0.0 0.00 5.54 F
1950 2035 0.101399 GTGTGATGATCGTCCTCGCT 59.899 55.0 12.42 0.0 36.96 4.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1857 1942 0.534203 GCGTTTCCTCCAGTTCCACA 60.534 55.0 0.0 0.0 0.0 4.17 R
2677 2781 1.359848 GTCCTAGATGCAACCACACG 58.640 55.0 0.0 0.0 0.0 4.49 R
3920 4044 0.384669 CGGATTGTACCCCTCTCGTC 59.615 60.0 0.0 0.0 0.0 4.20 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
49 50 9.921637 TTATTCAATCTAAAACCTTGCGATTTT 57.078 25.926 0.00 0.00 32.85 1.82
58 59 0.523335 CTTGCGATTTTAGGCGTGGC 60.523 55.000 0.00 0.00 0.00 5.01
113 117 2.499685 CCTCGTCCCGGATGAACC 59.500 66.667 0.73 0.00 0.00 3.62
204 208 5.263948 CGTTTCTGCAGATCAATCAATCAG 58.736 41.667 19.04 0.44 0.00 2.90
233 237 8.463607 GGATTAAATGAAAATCGGTTCCTGTAA 58.536 33.333 0.00 0.00 34.74 2.41
250 254 2.879646 TGTAAACGGAATCAAAGGCGTT 59.120 40.909 0.00 0.00 0.00 4.84
368 393 1.065491 TGTACCACCACAGCATCCATC 60.065 52.381 0.00 0.00 0.00 3.51
370 395 1.221566 CCACCACAGCATCCATCGA 59.778 57.895 0.00 0.00 0.00 3.59
371 396 0.179037 CCACCACAGCATCCATCGAT 60.179 55.000 0.00 0.00 0.00 3.59
372 397 1.224075 CACCACAGCATCCATCGATC 58.776 55.000 0.00 0.00 0.00 3.69
374 399 0.032540 CCACAGCATCCATCGATCGA 59.967 55.000 21.86 21.86 0.00 3.59
464 490 4.845580 CGCTGGCTTCCGCTCCAT 62.846 66.667 0.00 0.00 36.09 3.41
465 491 3.207669 GCTGGCTTCCGCTCCATG 61.208 66.667 0.00 0.00 36.09 3.66
466 492 3.207669 CTGGCTTCCGCTCCATGC 61.208 66.667 0.00 0.00 36.09 4.06
467 493 4.802051 TGGCTTCCGCTCCATGCC 62.802 66.667 0.00 0.00 43.49 4.40
468 494 4.496336 GGCTTCCGCTCCATGCCT 62.496 66.667 0.00 0.00 40.36 4.75
494 520 3.054287 TCAACAACCCTACAGAAACACCA 60.054 43.478 0.00 0.00 0.00 4.17
502 528 1.599797 CAGAAACACCACCCGTCCC 60.600 63.158 0.00 0.00 0.00 4.46
503 529 2.281970 GAAACACCACCCGTCCCC 60.282 66.667 0.00 0.00 0.00 4.81
504 530 4.259131 AAACACCACCCGTCCCCG 62.259 66.667 0.00 0.00 0.00 5.73
557 601 2.765807 CACCGCATCCCTCTCCCT 60.766 66.667 0.00 0.00 0.00 4.20
558 602 2.444895 ACCGCATCCCTCTCCCTC 60.445 66.667 0.00 0.00 0.00 4.30
559 603 2.123077 CCGCATCCCTCTCCCTCT 60.123 66.667 0.00 0.00 0.00 3.69
560 604 2.206536 CCGCATCCCTCTCCCTCTC 61.207 68.421 0.00 0.00 0.00 3.20
561 605 2.206536 CGCATCCCTCTCCCTCTCC 61.207 68.421 0.00 0.00 0.00 3.71
562 606 1.841103 GCATCCCTCTCCCTCTCCC 60.841 68.421 0.00 0.00 0.00 4.30
563 607 1.945447 CATCCCTCTCCCTCTCCCT 59.055 63.158 0.00 0.00 0.00 4.20
564 608 1.162505 CATCCCTCTCCCTCTCCCTA 58.837 60.000 0.00 0.00 0.00 3.53
565 609 1.077005 CATCCCTCTCCCTCTCCCTAG 59.923 61.905 0.00 0.00 0.00 3.02
566 610 0.048117 TCCCTCTCCCTCTCCCTAGT 59.952 60.000 0.00 0.00 0.00 2.57
567 611 0.481128 CCCTCTCCCTCTCCCTAGTC 59.519 65.000 0.00 0.00 0.00 2.59
568 612 0.481128 CCTCTCCCTCTCCCTAGTCC 59.519 65.000 0.00 0.00 0.00 3.85
569 613 0.481128 CTCTCCCTCTCCCTAGTCCC 59.519 65.000 0.00 0.00 0.00 4.46
577 621 1.941820 TCCCTAGTCCCTCCTGGCT 60.942 63.158 0.00 0.00 0.00 4.75
583 627 2.683933 TCCCTCCTGGCTCCGTTC 60.684 66.667 0.00 0.00 0.00 3.95
589 633 3.787001 CTGGCTCCGTTCCCCTCC 61.787 72.222 0.00 0.00 0.00 4.30
613 657 3.254217 ATCCAGGAGATCACCCCAG 57.746 57.895 5.46 0.00 0.00 4.45
614 658 0.644380 ATCCAGGAGATCACCCCAGA 59.356 55.000 5.46 0.97 0.00 3.86
615 659 0.031716 TCCAGGAGATCACCCCAGAG 60.032 60.000 5.46 0.00 0.00 3.35
616 660 1.053264 CCAGGAGATCACCCCAGAGG 61.053 65.000 5.46 0.00 43.78 3.69
617 661 1.383803 AGGAGATCACCCCAGAGGC 60.384 63.158 5.46 0.00 40.58 4.70
618 662 2.447714 GGAGATCACCCCAGAGGCC 61.448 68.421 0.00 0.00 40.58 5.19
619 663 1.690633 GAGATCACCCCAGAGGCCA 60.691 63.158 5.01 0.00 40.58 5.36
620 664 1.692042 AGATCACCCCAGAGGCCAG 60.692 63.158 5.01 0.00 40.58 4.85
621 665 1.690633 GATCACCCCAGAGGCCAGA 60.691 63.158 5.01 0.00 40.58 3.86
622 666 1.692042 ATCACCCCAGAGGCCAGAG 60.692 63.158 5.01 0.00 40.58 3.35
623 667 2.186873 ATCACCCCAGAGGCCAGAGA 62.187 60.000 5.01 0.00 40.58 3.10
624 668 2.040278 ACCCCAGAGGCCAGAGAG 59.960 66.667 5.01 0.00 40.58 3.20
633 677 1.490490 GAGGCCAGAGAGAGAGAGAGA 59.510 57.143 5.01 0.00 0.00 3.10
647 695 1.000771 AGAGAGCGGCAGTACTGGA 60.001 57.895 23.95 0.00 0.00 3.86
660 708 5.497474 GCAGTACTGGAATAGAAAAGGGAA 58.503 41.667 23.95 0.00 0.00 3.97
665 713 3.086282 TGGAATAGAAAAGGGAAACGGC 58.914 45.455 0.00 0.00 0.00 5.68
666 714 2.096980 GGAATAGAAAAGGGAAACGGCG 59.903 50.000 4.80 4.80 0.00 6.46
672 720 2.132089 AAAGGGAAACGGCGGGATCA 62.132 55.000 13.24 0.00 0.00 2.92
673 721 2.814913 AAGGGAAACGGCGGGATCAC 62.815 60.000 13.24 7.46 0.00 3.06
763 812 2.040606 CGGGGGAGGGAGGAAGAA 59.959 66.667 0.00 0.00 0.00 2.52
853 903 1.067142 GTATCTTGTCAGACCGGCACA 60.067 52.381 0.00 0.00 0.00 4.57
918 974 1.926665 AGCCCAGGAGTAGAGAGAGAA 59.073 52.381 0.00 0.00 0.00 2.87
919 975 2.091885 AGCCCAGGAGTAGAGAGAGAAG 60.092 54.545 0.00 0.00 0.00 2.85
920 976 2.306847 CCCAGGAGTAGAGAGAGAAGC 58.693 57.143 0.00 0.00 0.00 3.86
921 977 2.091885 CCCAGGAGTAGAGAGAGAAGCT 60.092 54.545 0.00 0.00 0.00 3.74
935 991 3.118112 AGAGAAGCTGAGAGAGAGAGAGG 60.118 52.174 0.00 0.00 0.00 3.69
968 1024 0.681564 GGAGAGAAGACAGAGGCCGA 60.682 60.000 0.00 0.00 0.00 5.54
1036 1093 1.989508 TCTCCATTGCCGCTCCTGA 60.990 57.895 0.00 0.00 0.00 3.86
1045 1117 1.984570 CCGCTCCTGACCCTCTTCA 60.985 63.158 0.00 0.00 0.00 3.02
1170 1242 3.519930 GGCGACCTCGTCTCCTCC 61.520 72.222 0.00 0.00 41.36 4.30
1331 1407 1.065199 CCTGATTCTTGCCCTGTGCTA 60.065 52.381 0.00 0.00 42.00 3.49
1334 1410 2.239402 TGATTCTTGCCCTGTGCTATCA 59.761 45.455 0.00 0.00 42.00 2.15
1494 1573 6.097412 GGAAAAGTGCATCTTATCTTGGGATT 59.903 38.462 0.00 0.00 35.02 3.01
1502 1581 7.231317 TGCATCTTATCTTGGGATTATTTGTCC 59.769 37.037 0.00 0.00 33.71 4.02
1583 1662 5.741982 GCGCACAGTTTTCTTCTTTCTTTTA 59.258 36.000 0.30 0.00 0.00 1.52
1616 1701 4.425577 AAAATTACTACAGCTGCTGCAC 57.574 40.909 28.39 0.00 42.74 4.57
1693 1778 7.188834 TGCTAAGATCGTTGCATTAAATTCAG 58.811 34.615 13.02 0.00 0.00 3.02
1718 1803 3.525268 AGTGTTGCTGTTTCTTTTGGG 57.475 42.857 0.00 0.00 0.00 4.12
1767 1852 2.496070 GGGGTGCTCCAATTTTTACTCC 59.504 50.000 7.20 0.00 37.22 3.85
1769 1854 3.193479 GGGTGCTCCAATTTTTACTCCTG 59.807 47.826 7.20 0.00 35.00 3.86
1820 1905 4.792087 CACCCCAAGTGCGTAACT 57.208 55.556 0.00 0.00 40.28 2.24
1857 1942 1.889105 CCGTGTTGCAGTGCTCACT 60.889 57.895 27.49 0.00 43.61 3.41
1950 2035 0.101399 GTGTGATGATCGTCCTCGCT 59.899 55.000 12.42 0.00 36.96 4.93
2032 2117 1.542915 CCCAAAGCACAGGTCTTGATG 59.457 52.381 0.00 0.00 0.00 3.07
2092 2184 4.116747 AGTGAGTTAGCTACTGATGTGC 57.883 45.455 0.00 0.00 37.17 4.57
2140 2232 2.288961 GCATTGGTGCCAATCTTGAG 57.711 50.000 13.07 4.08 45.76 3.02
2228 2323 2.202479 GCGACGGGCAATTTCAGC 60.202 61.111 0.00 0.00 42.87 4.26
2303 2398 2.281484 GGAGGGTTTGTCGCTGCA 60.281 61.111 0.00 0.00 44.37 4.41
2321 2416 1.462238 AGTGAAGAGGCTGGGGTGT 60.462 57.895 0.00 0.00 0.00 4.16
2336 2431 1.597461 GTGTGAGGGGCAGGAGTAC 59.403 63.158 0.00 0.00 0.00 2.73
2355 2450 5.238583 AGTACGAGAAAGAATTTGAGGTGG 58.761 41.667 0.00 0.00 39.27 4.61
2371 2471 3.997021 GAGGTGGTGATTGTGTTCTACAG 59.003 47.826 0.00 0.00 41.10 2.74
2404 2507 4.040339 TCAGATTGTTGTCTGGTCTTGCTA 59.960 41.667 4.28 0.00 44.51 3.49
2576 2679 8.325787 TGGAAACACAACTTCATGGTAGTATAT 58.674 33.333 0.00 0.00 33.40 0.86
2652 2756 4.833390 AGCTGTGAAGTTGGATAGGTAAC 58.167 43.478 0.00 0.00 0.00 2.50
2799 2903 8.463930 TTTCCTTCATTCTTGTGATTAAGTGT 57.536 30.769 0.00 0.00 0.00 3.55
2877 2981 3.654806 CCAGGGGATTGGAGTATCTTCAT 59.345 47.826 0.00 0.00 40.87 2.57
3032 3136 7.693969 ACTCATATCACTGAAAGGAAAAAGG 57.306 36.000 0.00 0.00 39.30 3.11
3048 3154 7.593825 AGGAAAAAGGAACAGTTCATTAATCG 58.406 34.615 13.40 0.00 31.69 3.34
3051 3157 6.496338 AAAGGAACAGTTCATTAATCGTCC 57.504 37.500 13.40 0.00 31.69 4.79
3126 3232 3.509184 GCAAAGGGAATCTGAAGCTTTCT 59.491 43.478 0.00 0.00 0.00 2.52
3132 3238 3.942115 GGAATCTGAAGCTTTCTGGTACC 59.058 47.826 4.43 4.43 0.00 3.34
3230 3336 9.924650 TGATTCTCTTTGTAGACTAAACCTTAC 57.075 33.333 0.00 0.00 0.00 2.34
3247 3353 6.238648 AACCTTACTTAGAAGGGTGATGTTG 58.761 40.000 7.10 0.00 45.22 3.33
3260 3366 7.490657 AGGGTGATGTTGTACTCTAATTACA 57.509 36.000 0.00 0.00 0.00 2.41
3658 3767 3.069872 TCGGAAGCACTTGTACCAAGTAA 59.930 43.478 9.13 0.00 0.00 2.24
3665 3774 4.393990 GCACTTGTACCAAGTAATACCCAC 59.606 45.833 9.13 0.00 0.00 4.61
3684 3794 5.944007 ACCCACCACTGAAATTACTCATAAC 59.056 40.000 0.00 0.00 0.00 1.89
3719 3829 8.677148 ATTTACATCTGTTGTCACAACTAACT 57.323 30.769 21.23 3.43 39.87 2.24
3720 3830 9.772973 ATTTACATCTGTTGTCACAACTAACTA 57.227 29.630 21.23 0.00 39.87 2.24
3721 3831 8.812147 TTACATCTGTTGTCACAACTAACTAG 57.188 34.615 21.23 10.07 39.87 2.57
3722 3832 6.817184 ACATCTGTTGTCACAACTAACTAGT 58.183 36.000 21.23 9.60 33.32 2.57
3723 3833 7.272978 ACATCTGTTGTCACAACTAACTAGTT 58.727 34.615 21.23 13.68 39.73 2.24
3724 3834 7.769044 ACATCTGTTGTCACAACTAACTAGTTT 59.231 33.333 21.23 0.00 38.07 2.66
3725 3835 7.534085 TCTGTTGTCACAACTAACTAGTTTG 57.466 36.000 21.23 14.45 43.57 2.93
3726 3836 7.324935 TCTGTTGTCACAACTAACTAGTTTGA 58.675 34.615 21.23 12.49 43.57 2.69
3727 3837 7.985184 TCTGTTGTCACAACTAACTAGTTTGAT 59.015 33.333 21.23 8.83 43.57 2.57
3728 3838 7.915508 TGTTGTCACAACTAACTAGTTTGATG 58.084 34.615 21.23 20.77 43.57 3.07
3729 3839 7.551262 TGTTGTCACAACTAACTAGTTTGATGT 59.449 33.333 21.23 21.23 43.57 3.06
3735 3859 8.709646 CACAACTAACTAGTTTGATGTACTTCC 58.290 37.037 24.51 0.00 43.57 3.46
3770 3894 2.281345 GCAGTGGCTGTGCTCTGT 60.281 61.111 4.63 0.00 37.96 3.41
3880 4004 2.722201 GGATCAACCCGGAGTCGCT 61.722 63.158 0.73 0.00 34.56 4.93
3885 4009 3.469863 AACCCGGAGTCGCTTTGCA 62.470 57.895 0.73 0.00 34.56 4.08
3920 4044 5.582269 TCAATCTCCGTGCTGAGAAATAAAG 59.418 40.000 5.49 0.00 44.16 1.85
3923 4047 3.250744 TCCGTGCTGAGAAATAAAGACG 58.749 45.455 0.00 0.00 0.00 4.18
3924 4048 3.057104 TCCGTGCTGAGAAATAAAGACGA 60.057 43.478 0.00 0.00 0.00 4.20
3940 4066 0.324091 ACGAGAGGGGTACAATCCGT 60.324 55.000 0.00 0.00 0.00 4.69
3967 4093 0.036732 GATTCAGTGGGCTCACACCA 59.963 55.000 21.13 1.26 45.91 4.17
4010 4136 4.397420 TGTGATGTTGAGTGCAGGTTATT 58.603 39.130 0.00 0.00 0.00 1.40
4068 4194 3.332187 TGATGATGTGTTCCCCAACCTTA 59.668 43.478 0.00 0.00 0.00 2.69
4105 4232 7.387948 ACATACTTGTTGGTTGAGTTGATAGAC 59.612 37.037 0.00 0.00 29.55 2.59
4119 4246 1.587034 GATAGACTTTTCGGGTTCGCG 59.413 52.381 0.00 0.00 36.13 5.87
4322 4452 4.627611 TCTAATGCTTGCTTGATGCTTC 57.372 40.909 0.00 0.00 43.37 3.86
4385 4515 0.745845 ATGAGATCAGTTGCGTGGCC 60.746 55.000 0.00 0.00 0.00 5.36
4430 4560 6.417191 TGTTCACACTCTTGTTTGTACTTC 57.583 37.500 0.00 0.00 31.66 3.01
4443 4583 6.677913 TGTTTGTACTTCGTAGTAACCTACC 58.322 40.000 3.24 0.00 40.46 3.18
4452 4592 8.411683 ACTTCGTAGTAACCTACCATCAAATAG 58.588 37.037 0.00 0.00 40.46 1.73
4569 4711 3.117663 TCTTCTTTGGGTTGGCACTTAGT 60.118 43.478 0.00 0.00 0.00 2.24
4573 4715 1.136828 TGGGTTGGCACTTAGTCACT 58.863 50.000 0.00 0.00 0.00 3.41
4705 4849 7.890655 AGGTTTCCTTAAGCAAGTGAATCTTAT 59.109 33.333 0.00 0.00 36.70 1.73
4777 4921 2.942376 TGTGCGCATTAGGTAGGAAATG 59.058 45.455 15.91 0.00 36.40 2.32
4800 4944 8.700722 ATGAAGATCTTATCATACGATTGCTC 57.299 34.615 8.25 0.00 34.61 4.26
4801 4945 7.890515 TGAAGATCTTATCATACGATTGCTCT 58.109 34.615 8.25 0.00 32.73 4.09
4867 5012 9.265901 GTATGCATGTCTGATTATATATGGGAC 57.734 37.037 10.16 0.00 0.00 4.46
4885 5030 7.205515 ATGGGACAGATTCTCATTTAGAAGT 57.794 36.000 0.00 0.00 43.67 3.01
4911 5056 3.774766 AGGGTCACACATTCATACTAGCA 59.225 43.478 0.00 0.00 0.00 3.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 1.714899 CCCTGCCACGCCTAAAATCG 61.715 60.000 0.00 0.00 0.00 3.34
58 59 4.039092 CCTCACCTGCCACCCCTG 62.039 72.222 0.00 0.00 0.00 4.45
113 117 3.059597 GGATATTGATTCGGCACTCAACG 60.060 47.826 0.00 0.00 34.43 4.10
117 121 3.438087 CCATGGATATTGATTCGGCACTC 59.562 47.826 5.56 0.00 0.00 3.51
204 208 4.301637 ACCGATTTTCATTTAATCCCGC 57.698 40.909 0.00 0.00 0.00 6.13
233 237 1.679153 ACAAACGCCTTTGATTCCGTT 59.321 42.857 14.05 0.00 44.66 4.44
250 254 2.820787 AGTGTTTGTTTGGAACGGACAA 59.179 40.909 0.00 0.00 34.76 3.18
265 269 1.368579 CCCCGTCGGTACAGTGTTT 59.631 57.895 11.06 0.00 0.00 2.83
267 271 3.688159 GCCCCGTCGGTACAGTGT 61.688 66.667 11.06 0.00 0.00 3.55
291 308 2.367202 TGATTCCCTCCTCCGGTGC 61.367 63.158 0.00 0.00 0.00 5.01
368 393 2.833205 GCGAGATGCGTTCGATCG 59.167 61.111 9.36 9.36 43.41 3.69
399 424 1.592669 CTGCTGGCTCCGGATTACG 60.593 63.158 3.57 0.00 43.80 3.18
400 425 1.889573 GCTGCTGGCTCCGGATTAC 60.890 63.158 3.57 0.00 38.06 1.89
460 486 1.616725 GGTTGTTGATGGAGGCATGGA 60.617 52.381 0.00 0.00 0.00 3.41
461 487 0.819582 GGTTGTTGATGGAGGCATGG 59.180 55.000 0.00 0.00 0.00 3.66
462 488 0.819582 GGGTTGTTGATGGAGGCATG 59.180 55.000 0.00 0.00 0.00 4.06
463 489 0.706433 AGGGTTGTTGATGGAGGCAT 59.294 50.000 0.00 0.00 0.00 4.40
464 490 1.004277 GTAGGGTTGTTGATGGAGGCA 59.996 52.381 0.00 0.00 0.00 4.75
465 491 1.004277 TGTAGGGTTGTTGATGGAGGC 59.996 52.381 0.00 0.00 0.00 4.70
466 492 2.571653 TCTGTAGGGTTGTTGATGGAGG 59.428 50.000 0.00 0.00 0.00 4.30
467 493 3.981071 TCTGTAGGGTTGTTGATGGAG 57.019 47.619 0.00 0.00 0.00 3.86
468 494 4.141367 TGTTTCTGTAGGGTTGTTGATGGA 60.141 41.667 0.00 0.00 0.00 3.41
557 601 1.950748 GCCAGGAGGGACTAGGGAGA 61.951 65.000 0.00 0.00 41.55 3.71
558 602 1.458588 GCCAGGAGGGACTAGGGAG 60.459 68.421 0.00 0.00 41.55 4.30
559 603 1.941820 AGCCAGGAGGGACTAGGGA 60.942 63.158 0.00 0.00 41.55 4.20
560 604 1.458588 GAGCCAGGAGGGACTAGGG 60.459 68.421 0.00 0.00 41.55 3.53
561 605 1.458588 GGAGCCAGGAGGGACTAGG 60.459 68.421 0.00 0.00 41.55 3.02
562 606 1.830408 CGGAGCCAGGAGGGACTAG 60.830 68.421 0.00 0.00 41.55 2.57
563 607 2.164332 AACGGAGCCAGGAGGGACTA 62.164 60.000 0.00 0.00 41.55 2.59
565 609 3.003763 AACGGAGCCAGGAGGGAC 61.004 66.667 0.00 0.00 40.01 4.46
566 610 2.683933 GAACGGAGCCAGGAGGGA 60.684 66.667 0.00 0.00 40.01 4.20
567 611 3.787001 GGAACGGAGCCAGGAGGG 61.787 72.222 0.00 0.00 40.85 4.30
568 612 3.787001 GGGAACGGAGCCAGGAGG 61.787 72.222 0.00 0.00 38.23 4.30
569 613 3.787001 GGGGAACGGAGCCAGGAG 61.787 72.222 0.00 0.00 0.00 3.69
583 627 3.554342 CTGGATCAGCGGGAGGGG 61.554 72.222 0.00 0.00 0.00 4.79
608 652 1.761667 CTCTCTCTGGCCTCTGGGG 60.762 68.421 3.32 0.00 38.36 4.96
609 653 0.756442 CTCTCTCTCTGGCCTCTGGG 60.756 65.000 3.32 0.00 0.00 4.45
610 654 0.258484 TCTCTCTCTCTGGCCTCTGG 59.742 60.000 3.32 0.00 0.00 3.86
611 655 1.212688 TCTCTCTCTCTCTGGCCTCTG 59.787 57.143 3.32 0.00 0.00 3.35
612 656 1.492176 CTCTCTCTCTCTCTGGCCTCT 59.508 57.143 3.32 0.00 0.00 3.69
613 657 1.490490 TCTCTCTCTCTCTCTGGCCTC 59.510 57.143 3.32 0.00 0.00 4.70
614 658 1.492176 CTCTCTCTCTCTCTCTGGCCT 59.508 57.143 3.32 0.00 0.00 5.19
615 659 1.972872 CTCTCTCTCTCTCTCTGGCC 58.027 60.000 0.00 0.00 0.00 5.36
616 660 1.312815 GCTCTCTCTCTCTCTCTGGC 58.687 60.000 0.00 0.00 0.00 4.85
617 661 1.586422 CGCTCTCTCTCTCTCTCTGG 58.414 60.000 0.00 0.00 0.00 3.86
618 662 1.586422 CCGCTCTCTCTCTCTCTCTG 58.414 60.000 0.00 0.00 0.00 3.35
619 663 0.179045 GCCGCTCTCTCTCTCTCTCT 60.179 60.000 0.00 0.00 0.00 3.10
620 664 0.463654 TGCCGCTCTCTCTCTCTCTC 60.464 60.000 0.00 0.00 0.00 3.20
621 665 0.464373 CTGCCGCTCTCTCTCTCTCT 60.464 60.000 0.00 0.00 0.00 3.10
622 666 0.748005 ACTGCCGCTCTCTCTCTCTC 60.748 60.000 0.00 0.00 0.00 3.20
623 667 0.544223 TACTGCCGCTCTCTCTCTCT 59.456 55.000 0.00 0.00 0.00 3.10
624 668 0.661020 GTACTGCCGCTCTCTCTCTC 59.339 60.000 0.00 0.00 0.00 3.20
633 677 1.776662 TCTATTCCAGTACTGCCGCT 58.223 50.000 17.86 4.26 0.00 5.52
647 695 2.089201 CCGCCGTTTCCCTTTTCTATT 58.911 47.619 0.00 0.00 0.00 1.73
660 708 3.064987 CTCGAGTGATCCCGCCGTT 62.065 63.158 3.62 0.00 0.00 4.44
665 713 1.721664 TTACCGCTCGAGTGATCCCG 61.722 60.000 27.11 13.73 0.00 5.14
666 714 0.248949 GTTACCGCTCGAGTGATCCC 60.249 60.000 27.11 8.53 0.00 3.85
672 720 2.178521 CGCTGTTACCGCTCGAGT 59.821 61.111 15.13 0.00 0.00 4.18
673 721 1.868251 GTCGCTGTTACCGCTCGAG 60.868 63.158 8.45 8.45 0.00 4.04
756 804 1.349357 GAGTGGCCTTGTCTTCTTCCT 59.651 52.381 3.32 0.00 0.00 3.36
763 812 0.109342 CAGTTGGAGTGGCCTTGTCT 59.891 55.000 3.32 0.00 37.63 3.41
853 903 2.945668 GACAACAAGAACACAAGAGCCT 59.054 45.455 0.00 0.00 0.00 4.58
918 974 0.552848 CCCCTCTCTCTCTCTCAGCT 59.447 60.000 0.00 0.00 0.00 4.24
919 975 1.109323 GCCCCTCTCTCTCTCTCAGC 61.109 65.000 0.00 0.00 0.00 4.26
920 976 0.552848 AGCCCCTCTCTCTCTCTCAG 59.447 60.000 0.00 0.00 0.00 3.35
921 977 0.258484 CAGCCCCTCTCTCTCTCTCA 59.742 60.000 0.00 0.00 0.00 3.27
935 991 0.107752 CTCTCCTTCTTGCTCAGCCC 60.108 60.000 0.00 0.00 0.00 5.19
1036 1093 3.522750 AGCAAGAAGATGATGAAGAGGGT 59.477 43.478 0.00 0.00 0.00 4.34
1045 1117 2.401967 GCGGCAGCAAGAAGATGAT 58.598 52.632 3.18 0.00 44.35 2.45
1163 1235 4.069232 CGCTGCCGTTGGAGGAGA 62.069 66.667 0.00 0.00 0.00 3.71
1331 1407 0.806868 CACAGGCGAGCAAATGTGAT 59.193 50.000 16.86 0.00 44.56 3.06
1334 1410 0.322816 ATCCACAGGCGAGCAAATGT 60.323 50.000 0.00 0.00 0.00 2.71
1502 1581 2.038659 TCCTTTGCTCAAAGTTTGGGG 58.961 47.619 17.14 10.57 44.66 4.96
1583 1662 7.451566 AGCTGTAGTAATTTTTCCAACCATTCT 59.548 33.333 0.00 0.00 0.00 2.40
1616 1701 5.747565 TCGACAAGTTTTATGAGCACAAAG 58.252 37.500 0.00 0.00 0.00 2.77
1693 1778 6.183360 CCCAAAAGAAACAGCAACACTTTAAC 60.183 38.462 0.00 0.00 31.86 2.01
1718 1803 4.452114 CCAAACCTTCTTTTGCCATTAAGC 59.548 41.667 0.00 0.00 35.48 3.09
1767 1852 4.589216 TGCAAAGATCAACCTTTTCCAG 57.411 40.909 0.00 0.00 34.41 3.86
1769 1854 4.209080 CGTTTGCAAAGATCAACCTTTTCC 59.791 41.667 13.26 0.00 34.41 3.13
1815 1900 3.883489 GGCAAATGGAGGATGGTAGTTAC 59.117 47.826 0.00 0.00 0.00 2.50
1820 1905 1.494721 GGAGGCAAATGGAGGATGGTA 59.505 52.381 0.00 0.00 0.00 3.25
1857 1942 0.534203 GCGTTTCCTCCAGTTCCACA 60.534 55.000 0.00 0.00 0.00 4.17
1864 1949 1.966451 GGTGGTGCGTTTCCTCCAG 60.966 63.158 8.20 0.00 38.19 3.86
1865 1950 2.112297 GGTGGTGCGTTTCCTCCA 59.888 61.111 8.20 0.00 38.19 3.86
1900 1985 2.024871 GAGGACGACGGCGATGAG 59.975 66.667 22.49 3.86 41.64 2.90
1920 2005 1.449423 CATCACACCGGCGATGGAA 60.449 57.895 9.30 0.00 36.24 3.53
2032 2117 5.388944 CAATTAACACAGAGCAAGAAGAGC 58.611 41.667 0.00 0.00 0.00 4.09
2140 2232 2.352127 GCCTTGAATGAGTTGAACCTGC 60.352 50.000 0.00 0.00 0.00 4.85
2303 2398 1.462238 ACACCCCAGCCTCTTCACT 60.462 57.895 0.00 0.00 0.00 3.41
2321 2416 1.379977 CTCGTACTCCTGCCCCTCA 60.380 63.158 0.00 0.00 0.00 3.86
2327 2422 4.929808 TCAAATTCTTTCTCGTACTCCTGC 59.070 41.667 0.00 0.00 0.00 4.85
2336 2431 4.065088 TCACCACCTCAAATTCTTTCTCG 58.935 43.478 0.00 0.00 0.00 4.04
2355 2450 7.478520 AACAACTACTGTAGAACACAATCAC 57.521 36.000 21.01 0.00 37.23 3.06
2576 2679 9.720769 GGAACTCGAGATAATTTAATGGGAATA 57.279 33.333 21.68 0.00 0.00 1.75
2578 2681 7.802117 AGGAACTCGAGATAATTTAATGGGAA 58.198 34.615 21.68 0.00 0.00 3.97
2622 2726 7.601886 CCTATCCAACTTCACAGCTCAATATAG 59.398 40.741 0.00 0.00 0.00 1.31
2677 2781 1.359848 GTCCTAGATGCAACCACACG 58.640 55.000 0.00 0.00 0.00 4.49
2825 2929 8.648097 GTGTAGTTTACCGATGCATATTATGAG 58.352 37.037 0.00 0.00 0.00 2.90
2877 2981 2.064434 TTGGTGGATTGCAGTGTTCA 57.936 45.000 0.00 0.00 0.00 3.18
2996 3100 9.987272 TTCAGTGATATGAGTTATGGTCAATAG 57.013 33.333 0.00 0.00 0.00 1.73
3020 3124 9.764363 ATTAATGAACTGTTCCTTTTTCCTTTC 57.236 29.630 17.26 0.00 0.00 2.62
3031 3135 3.930848 ACGGACGATTAATGAACTGTTCC 59.069 43.478 17.26 0.64 0.00 3.62
3032 3136 4.259292 CGACGGACGATTAATGAACTGTTC 60.259 45.833 13.49 13.49 45.77 3.18
3048 3154 0.949105 AAATCTGCACACCGACGGAC 60.949 55.000 23.38 7.44 0.00 4.79
3051 3157 0.439985 CTGAAATCTGCACACCGACG 59.560 55.000 0.00 0.00 0.00 5.12
3126 3232 1.340600 GCAACATAGCCCAAGGTACCA 60.341 52.381 15.94 0.00 0.00 3.25
3196 3302 4.765339 TCTACAAAGAGAATCACAGACCGA 59.235 41.667 0.00 0.00 37.82 4.69
3198 3304 6.031751 AGTCTACAAAGAGAATCACAGACC 57.968 41.667 0.00 0.00 37.82 3.85
3230 3336 6.287589 AGAGTACAACATCACCCTTCTAAG 57.712 41.667 0.00 0.00 0.00 2.18
3234 3340 8.038944 TGTAATTAGAGTACAACATCACCCTTC 58.961 37.037 0.00 0.00 0.00 3.46
3247 3353 6.976925 AGTGCGGTTACATGTAATTAGAGTAC 59.023 38.462 20.72 17.13 0.00 2.73
3260 3366 3.009723 CCTGAATTCAGTGCGGTTACAT 58.990 45.455 29.03 0.00 42.27 2.29
3658 3767 5.772393 TGAGTAATTTCAGTGGTGGGTAT 57.228 39.130 0.00 0.00 0.00 2.73
3665 3774 9.003658 AGAAACAGTTATGAGTAATTTCAGTGG 57.996 33.333 0.00 0.00 0.00 4.00
3716 3826 6.729569 AGGTAGGGAAGTACATCAAACTAGTT 59.270 38.462 1.12 1.12 0.00 2.24
3717 3827 6.262207 AGGTAGGGAAGTACATCAAACTAGT 58.738 40.000 0.00 0.00 0.00 2.57
3718 3828 6.793505 AGGTAGGGAAGTACATCAAACTAG 57.206 41.667 0.00 0.00 0.00 2.57
3719 3829 7.236019 TGAAAGGTAGGGAAGTACATCAAACTA 59.764 37.037 0.00 0.00 0.00 2.24
3720 3830 6.043938 TGAAAGGTAGGGAAGTACATCAAACT 59.956 38.462 0.00 0.00 0.00 2.66
3721 3831 6.235664 TGAAAGGTAGGGAAGTACATCAAAC 58.764 40.000 0.00 0.00 0.00 2.93
3722 3832 6.442541 TGAAAGGTAGGGAAGTACATCAAA 57.557 37.500 0.00 0.00 0.00 2.69
3723 3833 6.049955 CTGAAAGGTAGGGAAGTACATCAA 57.950 41.667 0.00 0.00 0.00 2.57
3724 3834 5.677319 CTGAAAGGTAGGGAAGTACATCA 57.323 43.478 0.00 0.00 0.00 3.07
3770 3894 2.195567 GCTTGGTTCTGGCTGCACA 61.196 57.895 0.50 0.00 0.00 4.57
3880 4004 3.249799 AGATTGATTTCGTGTCGTGCAAA 59.750 39.130 0.00 0.00 0.00 3.68
3885 4009 2.259618 CGGAGATTGATTTCGTGTCGT 58.740 47.619 0.00 0.00 0.00 4.34
3920 4044 0.384669 CGGATTGTACCCCTCTCGTC 59.615 60.000 0.00 0.00 0.00 4.20
3923 4047 2.963782 ACATACGGATTGTACCCCTCTC 59.036 50.000 0.00 0.00 35.44 3.20
3924 4048 2.698797 CACATACGGATTGTACCCCTCT 59.301 50.000 0.00 0.00 35.44 3.69
3940 4066 0.463654 GCCCACTGAATCGCCACATA 60.464 55.000 0.00 0.00 0.00 2.29
3967 4093 6.100279 TCACAGGCTATCTGAACTATTTGGAT 59.900 38.462 0.00 0.00 46.18 3.41
4010 4136 1.032014 GGCAACTGGAGCAAGAAACA 58.968 50.000 0.00 0.00 0.00 2.83
4068 4194 5.248477 ACCAACAAGTATGTGTAGGTCTCAT 59.752 40.000 0.00 0.00 40.46 2.90
4105 4232 0.863144 TTCTTCGCGAACCCGAAAAG 59.137 50.000 19.38 5.56 45.37 2.27
4119 4246 1.694696 AGGTGTGTGGTCCTCTTCTTC 59.305 52.381 0.00 0.00 0.00 2.87
4322 4452 1.385743 CGAGACGGTTTAACAAGCTCG 59.614 52.381 14.44 14.44 37.93 5.03
4328 4458 2.746269 CCAACTCGAGACGGTTTAACA 58.254 47.619 21.68 0.00 0.00 2.41
4385 4515 1.886542 GGGTAACAAAGAACTGCCTGG 59.113 52.381 0.00 0.00 39.74 4.45
4390 4520 5.124776 TGTGAACAAGGGTAACAAAGAACTG 59.875 40.000 0.00 0.00 39.74 3.16
4430 4560 7.169308 CAAGCTATTTGATGGTAGGTTACTACG 59.831 40.741 0.00 0.00 43.39 3.51
4443 4583 6.500910 TGCATTTCTAGCAAGCTATTTGATG 58.499 36.000 1.74 6.43 39.39 3.07
4452 4592 4.367386 ACAGAATGCATTTCTAGCAAGC 57.633 40.909 14.33 0.00 46.27 4.01
4569 4711 5.560722 TGAAGGTTTGTCTAATCCAGTGA 57.439 39.130 0.00 0.00 0.00 3.41
4573 4715 8.698973 TTAACAATGAAGGTTTGTCTAATCCA 57.301 30.769 0.00 0.00 36.32 3.41
4659 4802 6.538945 ACCTCTTTCTAAGATTCTCCAGAC 57.461 41.667 0.00 0.00 36.82 3.51
4705 4849 5.633655 TTCCCACAACTCAACTAACCTTA 57.366 39.130 0.00 0.00 0.00 2.69
4719 4863 1.826054 CCGCCACTGTTTCCCACAA 60.826 57.895 0.00 0.00 33.87 3.33
4777 4921 7.812191 ACAGAGCAATCGTATGATAAGATCTTC 59.188 37.037 12.24 0.00 34.95 2.87
4794 4938 5.279406 GCCTATGAGTCTATGACAGAGCAAT 60.279 44.000 0.00 0.00 34.60 3.56
4800 4944 2.352225 GCGGCCTATGAGTCTATGACAG 60.352 54.545 0.00 0.00 34.60 3.51
4801 4945 1.613925 GCGGCCTATGAGTCTATGACA 59.386 52.381 0.00 0.00 34.60 3.58
4867 5012 6.541641 CCCTCCAACTTCTAAATGAGAATCTG 59.458 42.308 0.00 0.00 43.39 2.90
4885 5030 3.587061 AGTATGAATGTGTGACCCTCCAA 59.413 43.478 0.00 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.