Multiple sequence alignment - TraesCS5B01G030600

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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 TraesCS5B01G030600 chr5B 100.000 3275 0 0 1 3275 33998364 34001638 0.000000e+00 6048
1 TraesCS5B01G030600 chr5D 92.557 3305 121 53 1 3275 40699202 40702411 0.000000e+00 4625
2 TraesCS5B01G030600 chr5A 91.975 3053 117 55 1 2988 28663497 28666486 0.000000e+00 4163
3 TraesCS5B01G030600 chr5A 94.615 260 11 3 3017 3275 28666487 28666744 1.830000e-107 399
4 TraesCS5B01G030600 chr3A 77.700 574 72 32 2299 2868 708003052 708002531 1.910000e-77 300


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 TraesCS5B01G030600 chr5B 33998364 34001638 3274 False 6048 6048 100.000 1 3275 1 chr5B.!!$F1 3274
1 TraesCS5B01G030600 chr5D 40699202 40702411 3209 False 4625 4625 92.557 1 3275 1 chr5D.!!$F1 3274
2 TraesCS5B01G030600 chr5A 28663497 28666744 3247 False 2281 4163 93.295 1 3275 2 chr5A.!!$F1 3274
3 TraesCS5B01G030600 chr3A 708002531 708003052 521 True 300 300 77.700 2299 2868 1 chr3A.!!$R1 569

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
719 745 0.179026 CTCCATCCATCCAGCCACTG 60.179 60.0 0.0 0.0 0.00 3.66 F
720 746 0.621280 TCCATCCATCCAGCCACTGA 60.621 55.0 0.0 0.0 32.44 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2079 2150 0.247655 CAACATGTACATGGTCGCGC 60.248 55.0 33.32 0.0 42.91 6.86 R
2422 2517 1.279496 TCTGACCATTCTCCACAGGG 58.721 55.0 0.00 0.0 0.00 4.45 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
57 59 8.717821 CAACTAAGAGTCATCGGTTTAAATTGA 58.282 33.333 0.00 0.00 0.00 2.57
96 98 4.039124 CCCTAACCCCATGTGATAAATTGC 59.961 45.833 0.00 0.00 0.00 3.56
104 106 6.350864 CCCCATGTGATAAATTGCACAAGTTA 60.351 38.462 11.51 5.83 46.74 2.24
112 114 9.926158 TGATAAATTGCACAAGTTATGTTGAAT 57.074 25.926 17.79 0.00 40.35 2.57
114 116 9.926158 ATAAATTGCACAAGTTATGTTGAATCA 57.074 25.926 13.51 0.00 41.46 2.57
121 141 6.864685 CACAAGTTATGTTGAATCATGCTTGT 59.135 34.615 16.92 16.92 44.86 3.16
134 154 3.070302 TCATGCTTGTATATGGGCGTACA 59.930 43.478 0.00 0.00 0.00 2.90
151 174 8.755028 TGGGCGTACAATATATATGATACACTT 58.245 33.333 13.30 0.00 0.00 3.16
275 301 5.801350 TTCGAAAGCTCACTCAATAATGG 57.199 39.130 0.00 0.00 0.00 3.16
283 309 4.818546 GCTCACTCAATAATGGCATACTGT 59.181 41.667 0.00 0.00 0.00 3.55
362 388 1.206849 CCACAACAAGGCAGTGGTTTT 59.793 47.619 0.00 0.00 45.95 2.43
363 389 2.428890 CCACAACAAGGCAGTGGTTTTA 59.571 45.455 0.00 0.00 45.95 1.52
364 390 3.443976 CACAACAAGGCAGTGGTTTTAC 58.556 45.455 0.00 0.00 0.00 2.01
393 419 3.356290 AGCACCATGGTTTTGATCCTAC 58.644 45.455 16.84 0.00 0.00 3.18
404 430 7.287061 TGGTTTTGATCCTACCTTGGTATATG 58.713 38.462 0.00 0.00 33.05 1.78
464 490 4.223320 TGCTCTTAACTTTGCTTTTCCG 57.777 40.909 0.00 0.00 0.00 4.30
611 637 6.816134 AATTGCACCCCAAAATATCAAAAC 57.184 33.333 0.00 0.00 36.92 2.43
617 643 6.349197 GCACCCCAAAATATCAAAACCAAATG 60.349 38.462 0.00 0.00 0.00 2.32
618 644 5.709631 ACCCCAAAATATCAAAACCAAATGC 59.290 36.000 0.00 0.00 0.00 3.56
619 645 5.709164 CCCCAAAATATCAAAACCAAATGCA 59.291 36.000 0.00 0.00 0.00 3.96
718 744 0.326904 TCTCCATCCATCCAGCCACT 60.327 55.000 0.00 0.00 0.00 4.00
719 745 0.179026 CTCCATCCATCCAGCCACTG 60.179 60.000 0.00 0.00 0.00 3.66
720 746 0.621280 TCCATCCATCCAGCCACTGA 60.621 55.000 0.00 0.00 32.44 3.41
721 747 0.179026 CCATCCATCCAGCCACTGAG 60.179 60.000 0.00 0.00 32.44 3.35
722 748 0.818445 CATCCATCCAGCCACTGAGC 60.818 60.000 0.00 0.00 32.44 4.26
723 749 1.992519 ATCCATCCAGCCACTGAGCC 61.993 60.000 0.00 0.00 32.44 4.70
724 750 2.672908 CATCCAGCCACTGAGCCA 59.327 61.111 0.00 0.00 32.44 4.75
725 751 1.748122 CATCCAGCCACTGAGCCAC 60.748 63.158 0.00 0.00 32.44 5.01
757 783 9.504708 TGATTATTGGAGAGCTACTACTAGTAC 57.495 37.037 0.00 0.00 0.00 2.73
811 840 1.064758 TGCACTCCCTCTCTCTCTCTC 60.065 57.143 0.00 0.00 0.00 3.20
812 841 1.212935 GCACTCCCTCTCTCTCTCTCT 59.787 57.143 0.00 0.00 0.00 3.10
933 962 7.504403 CATTTACTCTCTCTCTCTCTCTCTCT 58.496 42.308 0.00 0.00 0.00 3.10
934 963 6.716934 TTACTCTCTCTCTCTCTCTCTCTC 57.283 45.833 0.00 0.00 0.00 3.20
935 964 4.877773 ACTCTCTCTCTCTCTCTCTCTCT 58.122 47.826 0.00 0.00 0.00 3.10
936 965 6.019656 ACTCTCTCTCTCTCTCTCTCTCTA 57.980 45.833 0.00 0.00 0.00 2.43
937 966 5.830991 ACTCTCTCTCTCTCTCTCTCTCTAC 59.169 48.000 0.00 0.00 0.00 2.59
938 967 5.141182 TCTCTCTCTCTCTCTCTCTCTACC 58.859 50.000 0.00 0.00 0.00 3.18
939 968 5.103473 TCTCTCTCTCTCTCTCTCTCTACCT 60.103 48.000 0.00 0.00 0.00 3.08
940 969 5.141182 TCTCTCTCTCTCTCTCTCTACCTC 58.859 50.000 0.00 0.00 0.00 3.85
941 970 5.103473 TCTCTCTCTCTCTCTCTCTACCTCT 60.103 48.000 0.00 0.00 0.00 3.69
942 971 5.141182 TCTCTCTCTCTCTCTCTACCTCTC 58.859 50.000 0.00 0.00 0.00 3.20
943 972 5.103473 TCTCTCTCTCTCTCTCTACCTCTCT 60.103 48.000 0.00 0.00 0.00 3.10
944 973 5.141182 TCTCTCTCTCTCTCTACCTCTCTC 58.859 50.000 0.00 0.00 0.00 3.20
945 974 5.103473 TCTCTCTCTCTCTCTACCTCTCTCT 60.103 48.000 0.00 0.00 0.00 3.10
946 975 5.141182 TCTCTCTCTCTCTACCTCTCTCTC 58.859 50.000 0.00 0.00 0.00 3.20
947 976 5.103473 TCTCTCTCTCTCTACCTCTCTCTCT 60.103 48.000 0.00 0.00 0.00 3.10
948 977 6.102762 TCTCTCTCTCTCTACCTCTCTCTCTA 59.897 46.154 0.00 0.00 0.00 2.43
949 978 6.864421 TCTCTCTCTCTACCTCTCTCTCTAT 58.136 44.000 0.00 0.00 0.00 1.98
950 979 7.996788 TCTCTCTCTCTACCTCTCTCTCTATA 58.003 42.308 0.00 0.00 0.00 1.31
951 980 7.889073 TCTCTCTCTCTACCTCTCTCTCTATAC 59.111 44.444 0.00 0.00 0.00 1.47
952 981 6.952358 TCTCTCTCTACCTCTCTCTCTATACC 59.048 46.154 0.00 0.00 0.00 2.73
1019 1079 1.070577 CAGAAACCACGAGCTCAAACG 60.071 52.381 15.40 2.30 0.00 3.60
1315 1375 1.819905 CTCTTCTTCGGCTCCTCCC 59.180 63.158 0.00 0.00 0.00 4.30
1317 1377 3.075005 TTCTTCGGCTCCTCCCCG 61.075 66.667 0.00 0.00 46.88 5.73
1471 1531 3.851845 TTGGTTGTCGCGAGGGACG 62.852 63.158 10.24 0.00 45.66 4.79
1538 1598 1.347320 GTTGTACGAGGCGAAGAAGG 58.653 55.000 0.00 0.00 0.00 3.46
1585 1645 1.079405 ACACCGTCCCATGCTTACG 60.079 57.895 5.92 5.92 36.42 3.18
1626 1686 3.723348 GGCGTGACGGTGAAAGCC 61.723 66.667 7.25 0.27 37.61 4.35
1929 1995 0.682855 AGGTCGAGAAGGAGGAGCTG 60.683 60.000 0.00 0.00 37.17 4.24
1959 2025 3.170791 TCTGATCGATGAAACCTCAGC 57.829 47.619 0.54 0.00 34.23 4.26
1985 2051 1.813513 ACGCAAGAATTCCACAGGAG 58.186 50.000 0.65 0.00 43.62 3.69
2007 2078 2.167281 CCAGATCAGTTCATGACGGTCT 59.833 50.000 9.88 0.00 41.91 3.85
2009 2080 4.355437 CAGATCAGTTCATGACGGTCTAC 58.645 47.826 9.88 2.94 41.91 2.59
2117 2188 0.034380 GTTCTTAGGAGGTTGGGGGC 60.034 60.000 0.00 0.00 0.00 5.80
2296 2391 0.620121 AAGAGAGAGGGAGCAAGGGG 60.620 60.000 0.00 0.00 0.00 4.79
2307 2402 0.480252 AGCAAGGGGGATGGATTAGC 59.520 55.000 0.00 0.00 0.00 3.09
2308 2403 0.185901 GCAAGGGGGATGGATTAGCA 59.814 55.000 0.00 0.00 0.00 3.49
2309 2404 1.411501 GCAAGGGGGATGGATTAGCAA 60.412 52.381 0.00 0.00 0.00 3.91
2312 2407 4.082125 CAAGGGGGATGGATTAGCAATAC 58.918 47.826 0.00 0.00 0.00 1.89
2468 2568 1.546029 GCCCACATCAAGAGAAAACCC 59.454 52.381 0.00 0.00 0.00 4.11
2478 2578 9.326413 ACATCAAGAGAAAACCCTATTTATACG 57.674 33.333 0.00 0.00 0.00 3.06
2613 2713 1.973515 TGTGGTCTGCTCACTTGATCT 59.026 47.619 0.00 0.00 36.21 2.75
2614 2714 2.028658 TGTGGTCTGCTCACTTGATCTC 60.029 50.000 0.00 0.00 36.21 2.75
2615 2715 1.552337 TGGTCTGCTCACTTGATCTCC 59.448 52.381 0.00 0.00 0.00 3.71
2616 2716 1.830477 GGTCTGCTCACTTGATCTCCT 59.170 52.381 0.00 0.00 0.00 3.69
2617 2717 2.235898 GGTCTGCTCACTTGATCTCCTT 59.764 50.000 0.00 0.00 0.00 3.36
2618 2718 3.307339 GGTCTGCTCACTTGATCTCCTTT 60.307 47.826 0.00 0.00 0.00 3.11
2619 2719 3.683822 GTCTGCTCACTTGATCTCCTTTG 59.316 47.826 0.00 0.00 0.00 2.77
2620 2720 3.008330 CTGCTCACTTGATCTCCTTTGG 58.992 50.000 0.00 0.00 0.00 3.28
2621 2721 2.373169 TGCTCACTTGATCTCCTTTGGT 59.627 45.455 0.00 0.00 0.00 3.67
2622 2722 2.746362 GCTCACTTGATCTCCTTTGGTG 59.254 50.000 0.00 0.00 0.00 4.17
2623 2723 3.557898 GCTCACTTGATCTCCTTTGGTGA 60.558 47.826 0.00 0.00 0.00 4.02
2624 2724 4.645535 CTCACTTGATCTCCTTTGGTGAA 58.354 43.478 0.00 0.00 32.96 3.18
2625 2725 5.246981 TCACTTGATCTCCTTTGGTGAAT 57.753 39.130 0.00 0.00 30.81 2.57
2681 2782 4.142513 GCAATCAACTGAGGGATCTTGTTC 60.143 45.833 0.00 0.00 0.00 3.18
2693 2794 3.376546 GGATCTTGTTCTGCAATGGACTC 59.623 47.826 0.00 0.00 36.36 3.36
2757 2858 5.637387 ACACAATCGTTTTTGATTAATGGCC 59.363 36.000 0.00 0.00 36.46 5.36
2843 2947 1.059006 GGATCCAGATGCAGGGGAGT 61.059 60.000 6.95 0.00 33.47 3.85
2938 3044 3.812053 CCTGCCTAATTGCACTATGAGTC 59.188 47.826 0.00 0.00 36.04 3.36
2939 3045 4.445453 CTGCCTAATTGCACTATGAGTCA 58.555 43.478 0.00 0.00 36.04 3.41
2940 3046 4.445453 TGCCTAATTGCACTATGAGTCAG 58.555 43.478 0.00 0.00 36.04 3.51
2941 3047 4.080919 TGCCTAATTGCACTATGAGTCAGT 60.081 41.667 0.00 0.00 36.04 3.41
3046 3154 4.260985 TGTGAACAACAGTCACTTGATGT 58.739 39.130 6.17 0.00 44.70 3.06
3085 3193 2.584835 TTCTTGGGATGAACAGGGTG 57.415 50.000 0.00 0.00 0.00 4.61
3090 3199 3.320610 TGGGATGAACAGGGTGAAAAA 57.679 42.857 0.00 0.00 0.00 1.94
3125 3234 1.203523 TCACTGTGTTTTTGGTGGTGC 59.796 47.619 7.79 0.00 0.00 5.01
3126 3235 0.534873 ACTGTGTTTTTGGTGGTGCC 59.465 50.000 0.00 0.00 37.90 5.01
3207 3316 4.691685 TCTGCAAGCAAATTAAGCAAATGG 59.308 37.500 5.70 0.00 34.45 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 2.908688 AGGGAACAAAAACATGCCAC 57.091 45.000 0.00 0.00 0.00 5.01
57 59 0.403271 AGGGCACATCAGAACTTGCT 59.597 50.000 0.00 0.00 35.24 3.91
96 98 6.864685 ACAAGCATGATTCAACATAACTTGTG 59.135 34.615 18.94 5.48 44.89 3.33
104 106 6.294899 GCCCATATACAAGCATGATTCAACAT 60.295 38.462 0.00 0.00 0.00 2.71
112 114 2.928801 ACGCCCATATACAAGCATGA 57.071 45.000 0.00 0.00 0.00 3.07
114 116 3.762407 TGTACGCCCATATACAAGCAT 57.238 42.857 0.00 0.00 0.00 3.79
151 174 5.598005 ACCACATGATCAACCTCTTTTTGAA 59.402 36.000 0.00 0.00 36.57 2.69
158 181 2.373169 ACACACCACATGATCAACCTCT 59.627 45.455 0.00 0.00 0.00 3.69
160 183 2.957402 ACACACCACATGATCAACCT 57.043 45.000 0.00 0.00 0.00 3.50
275 301 9.243637 TGTTATTTGTTTCTTTTCACAGTATGC 57.756 29.630 0.00 0.00 42.53 3.14
362 388 0.177836 CCATGGTGCTCATCCGTGTA 59.822 55.000 2.57 0.00 39.53 2.90
363 389 1.078214 CCATGGTGCTCATCCGTGT 60.078 57.895 2.57 0.00 39.53 4.49
364 390 0.677731 AACCATGGTGCTCATCCGTG 60.678 55.000 20.60 0.00 40.50 4.94
393 419 5.657302 CCCTACCTAGCTACATATACCAAGG 59.343 48.000 0.00 0.00 0.00 3.61
404 430 1.755380 CCACACACCCTACCTAGCTAC 59.245 57.143 0.00 0.00 0.00 3.58
464 490 1.795162 GCATGTATGGCTGTGCGTTTC 60.795 52.381 0.00 0.00 0.00 2.78
617 643 1.725557 CTGGATGATGGTGCTGCTGC 61.726 60.000 8.89 8.89 40.20 5.25
618 644 1.725557 GCTGGATGATGGTGCTGCTG 61.726 60.000 0.00 0.00 32.93 4.41
619 645 1.453379 GCTGGATGATGGTGCTGCT 60.453 57.895 0.00 0.00 32.93 4.24
718 744 3.695556 CCAATAATCATGTGTGTGGCTCA 59.304 43.478 0.00 0.00 0.00 4.26
719 745 3.947196 TCCAATAATCATGTGTGTGGCTC 59.053 43.478 0.00 0.00 0.00 4.70
720 746 3.949754 CTCCAATAATCATGTGTGTGGCT 59.050 43.478 0.00 0.00 0.00 4.75
721 747 3.947196 TCTCCAATAATCATGTGTGTGGC 59.053 43.478 0.00 0.00 0.00 5.01
722 748 4.036027 GCTCTCCAATAATCATGTGTGTGG 59.964 45.833 0.00 0.00 0.00 4.17
723 749 4.880120 AGCTCTCCAATAATCATGTGTGTG 59.120 41.667 0.00 0.00 0.00 3.82
724 750 5.108187 AGCTCTCCAATAATCATGTGTGT 57.892 39.130 0.00 0.00 0.00 3.72
725 751 6.286758 AGTAGCTCTCCAATAATCATGTGTG 58.713 40.000 0.00 0.00 0.00 3.82
811 840 6.127507 TGAGAATGATTGGTGTGTCTAGAGAG 60.128 42.308 0.00 0.00 0.00 3.20
812 841 5.716703 TGAGAATGATTGGTGTGTCTAGAGA 59.283 40.000 0.00 0.00 0.00 3.10
933 962 6.871035 AGAGAGGTATAGAGAGAGAGGTAGA 58.129 44.000 0.00 0.00 0.00 2.59
934 963 6.954684 AGAGAGAGGTATAGAGAGAGAGGTAG 59.045 46.154 0.00 0.00 0.00 3.18
935 964 6.871035 AGAGAGAGGTATAGAGAGAGAGGTA 58.129 44.000 0.00 0.00 0.00 3.08
936 965 5.727630 AGAGAGAGGTATAGAGAGAGAGGT 58.272 45.833 0.00 0.00 0.00 3.85
937 966 5.187967 GGAGAGAGAGGTATAGAGAGAGAGG 59.812 52.000 0.00 0.00 0.00 3.69
938 967 5.187967 GGGAGAGAGAGGTATAGAGAGAGAG 59.812 52.000 0.00 0.00 0.00 3.20
939 968 5.091552 GGGAGAGAGAGGTATAGAGAGAGA 58.908 50.000 0.00 0.00 0.00 3.10
940 969 4.225267 GGGGAGAGAGAGGTATAGAGAGAG 59.775 54.167 0.00 0.00 0.00 3.20
941 970 4.172807 GGGGAGAGAGAGGTATAGAGAGA 58.827 52.174 0.00 0.00 0.00 3.10
942 971 3.265995 GGGGGAGAGAGAGGTATAGAGAG 59.734 56.522 0.00 0.00 0.00 3.20
943 972 3.115723 AGGGGGAGAGAGAGGTATAGAGA 60.116 52.174 0.00 0.00 0.00 3.10
944 973 3.265489 AGGGGGAGAGAGAGGTATAGAG 58.735 54.545 0.00 0.00 0.00 2.43
945 974 3.387105 AGGGGGAGAGAGAGGTATAGA 57.613 52.381 0.00 0.00 0.00 1.98
946 975 6.911993 TTATAGGGGGAGAGAGAGGTATAG 57.088 45.833 0.00 0.00 0.00 1.31
947 976 7.257825 CCTTTTATAGGGGGAGAGAGAGGTATA 60.258 44.444 0.00 0.00 40.67 1.47
948 977 6.471015 CCTTTTATAGGGGGAGAGAGAGGTAT 60.471 46.154 0.00 0.00 40.67 2.73
949 978 5.162859 CCTTTTATAGGGGGAGAGAGAGGTA 60.163 48.000 0.00 0.00 40.67 3.08
950 979 4.389264 CCTTTTATAGGGGGAGAGAGAGGT 60.389 50.000 0.00 0.00 40.67 3.85
951 980 4.140663 TCCTTTTATAGGGGGAGAGAGAGG 60.141 50.000 0.00 0.00 44.86 3.69
952 981 4.836175 GTCCTTTTATAGGGGGAGAGAGAG 59.164 50.000 0.00 0.00 44.86 3.20
996 1056 0.880278 TGAGCTCGTGGTTTCTGTGC 60.880 55.000 9.64 0.00 0.00 4.57
1019 1079 4.380233 CCTGCTATGCTATGGCTTATTTGC 60.380 45.833 1.68 1.57 37.67 3.68
1112 1172 0.390124 CTGCCTGCTGATCTCTCTCC 59.610 60.000 0.00 0.00 0.00 3.71
1389 1449 0.392461 TGGAGACGCTAACCATTGGC 60.392 55.000 1.54 0.00 0.00 4.52
1390 1450 1.656652 CTGGAGACGCTAACCATTGG 58.343 55.000 0.00 0.00 33.08 3.16
1391 1451 1.009829 GCTGGAGACGCTAACCATTG 58.990 55.000 0.00 0.00 33.08 2.82
1471 1531 2.359169 TGTCGCCATGGAGGAGGAC 61.359 63.158 18.40 13.70 41.22 3.85
1538 1598 3.486263 CCATCTTCGGCCGAACAC 58.514 61.111 35.81 0.00 0.00 3.32
1616 1676 2.032528 TCAGCCTGGCTTTCACCG 59.967 61.111 20.79 6.80 36.40 4.94
1929 1995 1.799403 CATCGATCAGATCAGGCTTGC 59.201 52.381 11.12 0.00 37.52 4.01
1959 2025 2.799978 GTGGAATTCTTGCGTTTTTGGG 59.200 45.455 5.23 0.00 0.00 4.12
1985 2051 1.293924 CCGTCATGAACTGATCTGGC 58.706 55.000 0.00 0.00 35.97 4.85
2007 2078 5.606505 GTTTGGAAGGCAGGAATTTTTGTA 58.393 37.500 0.00 0.00 0.00 2.41
2009 2080 3.494251 CGTTTGGAAGGCAGGAATTTTTG 59.506 43.478 0.00 0.00 0.00 2.44
2079 2150 0.247655 CAACATGTACATGGTCGCGC 60.248 55.000 33.32 0.00 42.91 6.86
2117 2188 7.868415 CCTTACTAAGTTACTAGCCAGCTAATG 59.132 40.741 0.34 0.00 0.00 1.90
2157 2228 1.833630 TGCACCAGAAGATCTACCCAG 59.166 52.381 0.00 0.00 0.00 4.45
2350 2445 8.391106 CAATGGAAGCTAGTGTAAACAAGATAC 58.609 37.037 0.00 0.00 0.00 2.24
2422 2517 1.279496 TCTGACCATTCTCCACAGGG 58.721 55.000 0.00 0.00 0.00 4.45
2454 2549 7.990886 TGCGTATAAATAGGGTTTTCTCTTGAT 59.009 33.333 0.00 0.00 0.00 2.57
2468 2568 6.706270 AGATTTGGGTGTCTGCGTATAAATAG 59.294 38.462 0.00 0.00 0.00 1.73
2613 2713 2.632512 GCCAAAGGAATTCACCAAAGGA 59.367 45.455 7.93 0.00 0.00 3.36
2614 2714 2.368221 TGCCAAAGGAATTCACCAAAGG 59.632 45.455 7.93 2.49 0.00 3.11
2615 2715 3.749665 TGCCAAAGGAATTCACCAAAG 57.250 42.857 7.93 0.00 0.00 2.77
2616 2716 4.494091 TTTGCCAAAGGAATTCACCAAA 57.506 36.364 7.93 4.48 0.00 3.28
2617 2717 4.102210 TGATTTGCCAAAGGAATTCACCAA 59.898 37.500 7.93 0.00 0.00 3.67
2618 2718 3.645212 TGATTTGCCAAAGGAATTCACCA 59.355 39.130 7.93 0.00 0.00 4.17
2619 2719 4.270245 TGATTTGCCAAAGGAATTCACC 57.730 40.909 7.93 0.00 0.00 4.02
2620 2720 5.178067 CAGTTGATTTGCCAAAGGAATTCAC 59.822 40.000 7.93 0.00 0.00 3.18
2621 2721 5.070180 TCAGTTGATTTGCCAAAGGAATTCA 59.930 36.000 7.93 0.00 0.00 2.57
2622 2722 5.540911 TCAGTTGATTTGCCAAAGGAATTC 58.459 37.500 0.00 0.00 0.00 2.17
2623 2723 5.549742 TCAGTTGATTTGCCAAAGGAATT 57.450 34.783 0.00 0.00 0.00 2.17
2624 2724 5.305128 TCTTCAGTTGATTTGCCAAAGGAAT 59.695 36.000 0.00 0.00 0.00 3.01
2625 2725 4.648762 TCTTCAGTTGATTTGCCAAAGGAA 59.351 37.500 0.00 0.00 0.00 3.36
2681 2782 2.233186 TCACAGAGAGAGTCCATTGCAG 59.767 50.000 0.00 0.00 0.00 4.41
2757 2858 3.643792 ACAGATTTAGATTCTCCTCGGGG 59.356 47.826 0.00 0.00 0.00 5.73
2843 2947 2.112380 TTTATGCAGCTGCTGTGCTA 57.888 45.000 36.61 18.16 41.98 3.49
3046 3154 6.430962 AGAAATATCTAAGAGCCTGATGCA 57.569 37.500 0.00 0.00 36.84 3.96
3125 3234 4.067896 ACTCATGCTCACTTAACAGTTGG 58.932 43.478 0.00 0.00 0.00 3.77
3126 3235 5.468072 AGAACTCATGCTCACTTAACAGTTG 59.532 40.000 0.00 0.00 0.00 3.16
3207 3316 8.886719 AGTAAGCGATTGGTTAATTACTTTACC 58.113 33.333 6.17 0.00 39.57 2.85
3227 3336 2.609916 GCAAGCCAGCTAAGTAGTAAGC 59.390 50.000 0.00 0.00 39.08 3.09


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

AutoCloner maintained by Alex Coulton.