Multiple sequence alignment - TraesCS2D01G166100

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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 TraesCS2D01G166100 chr2D 100.000 4532 0 0 1 4532 110060622 110065153 0.000000e+00 8370.0
1 TraesCS2D01G166100 chr2A 91.449 2257 111 34 120 2332 105633784 105636002 0.000000e+00 3024.0
2 TraesCS2D01G166100 chr2A 88.817 1234 70 30 2724 3933 105636888 105638077 0.000000e+00 1452.0
3 TraesCS2D01G166100 chr2A 93.223 546 26 9 3998 4532 105638188 105638733 0.000000e+00 793.0
4 TraesCS2D01G166100 chr2A 94.486 399 21 1 2329 2727 105636080 105636477 8.330000e-172 614.0
5 TraesCS2D01G166100 chr2A 86.667 60 6 2 18 75 105633411 105633470 1.050000e-06 65.8
6 TraesCS2D01G166100 chr2B 91.058 1890 88 31 1 1836 159484789 159486651 0.000000e+00 2479.0
7 TraesCS2D01G166100 chr2B 86.331 1529 125 49 3043 4529 159488027 159489513 0.000000e+00 1589.0
8 TraesCS2D01G166100 chr2B 89.344 1173 69 17 1829 2993 159486760 159487884 0.000000e+00 1423.0


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 TraesCS2D01G166100 chr2D 110060622 110065153 4531 False 8370.000000 8370 100.0000 1 4532 1 chr2D.!!$F1 4531
1 TraesCS2D01G166100 chr2A 105633411 105638733 5322 False 1189.760000 3024 90.9284 18 4532 5 chr2A.!!$F1 4514
2 TraesCS2D01G166100 chr2B 159484789 159489513 4724 False 1830.333333 2479 88.9110 1 4529 3 chr2B.!!$F1 4528

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
559 875 0.111089 CTCAACTTGTTCTGCGTCGC 60.111 55.000 11.10 11.1 0.0 5.19 F
621 937 1.062525 GGCGCCGCTGTAGATTTTG 59.937 57.895 12.58 0.0 0.0 2.44 F
1640 1987 2.880268 TGCAGGACTCTTGATTGTGTTG 59.120 45.455 0.00 0.0 0.0 3.33 F
3193 4277 0.836606 TGCCCTTTGTGACAGACTGA 59.163 50.000 10.08 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1415 1759 0.242017 GGACAGCAATGCAAGACCAC 59.758 55.000 8.35 0.0 0.0 4.16 R
1789 2136 1.992667 CAGAAATAAGTCGTGCGCTCA 59.007 47.619 9.73 0.0 0.0 4.26 R
3342 4426 0.174845 TGTTTCCTAGGATGACGGCG 59.825 55.000 13.57 4.8 0.0 6.46 R
4039 5207 0.266152 CTGTATCCCTCCCTCCCACT 59.734 60.000 0.00 0.0 0.0 4.00 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
36 37 5.531287 GTCAGAGGGTCAAACAAACATAAGT 59.469 40.000 0.00 0.00 0.00 2.24
75 82 1.383799 CCCACCCAGAGGCATCAAA 59.616 57.895 0.00 0.00 36.11 2.69
76 83 0.967380 CCCACCCAGAGGCATCAAAC 60.967 60.000 0.00 0.00 36.11 2.93
206 499 2.108970 GTATCCTCCCCAGTTCGTCTT 58.891 52.381 0.00 0.00 0.00 3.01
208 501 1.215647 CCTCCCCAGTTCGTCTTCG 59.784 63.158 0.00 0.00 38.55 3.79
252 553 3.019003 AATGGGAGGAGCGTGACCG 62.019 63.158 0.00 0.00 37.07 4.79
299 605 2.188817 GAGGGTTTCTAGAAGGCTCCA 58.811 52.381 5.12 0.00 0.00 3.86
365 676 3.254411 AGCCTAGCAAGCTTTTGAACTTC 59.746 43.478 0.00 0.00 37.24 3.01
454 768 1.003839 TCGCCGTCCAATCAAGCTT 60.004 52.632 0.00 0.00 0.00 3.74
462 776 4.378874 CCGTCCAATCAAGCTTCTTTTCTC 60.379 45.833 0.00 0.00 0.00 2.87
510 826 2.148558 GATCGACAGGGGAGATCGGC 62.149 65.000 0.00 0.00 36.51 5.54
537 853 2.789813 CGCAGGAGATTCGATCGAC 58.210 57.895 19.26 7.54 0.00 4.20
548 864 5.098893 AGATTCGATCGACTTCTCAACTTG 58.901 41.667 19.26 0.00 0.00 3.16
551 867 4.227538 TCGATCGACTTCTCAACTTGTTC 58.772 43.478 15.15 0.00 0.00 3.18
553 869 4.089208 CGATCGACTTCTCAACTTGTTCTG 59.911 45.833 10.26 0.00 0.00 3.02
554 870 3.123804 TCGACTTCTCAACTTGTTCTGC 58.876 45.455 0.00 0.00 0.00 4.26
555 871 2.097202 CGACTTCTCAACTTGTTCTGCG 60.097 50.000 0.00 0.00 0.00 5.18
556 872 2.866762 GACTTCTCAACTTGTTCTGCGT 59.133 45.455 0.00 0.00 0.00 5.24
558 874 1.487482 TCTCAACTTGTTCTGCGTCG 58.513 50.000 0.00 0.00 0.00 5.12
559 875 0.111089 CTCAACTTGTTCTGCGTCGC 60.111 55.000 11.10 11.10 0.00 5.19
561 877 1.227556 AACTTGTTCTGCGTCGCCT 60.228 52.632 15.88 0.00 0.00 5.52
562 878 1.222115 AACTTGTTCTGCGTCGCCTC 61.222 55.000 15.88 3.08 0.00 4.70
564 880 2.771763 CTTGTTCTGCGTCGCCTCCT 62.772 60.000 15.88 0.00 0.00 3.69
565 881 2.507324 GTTCTGCGTCGCCTCCTC 60.507 66.667 15.88 0.00 0.00 3.71
566 882 4.116328 TTCTGCGTCGCCTCCTCG 62.116 66.667 15.88 0.00 0.00 4.63
569 885 3.456431 CTGCGTCGCCTCCTCGTAG 62.456 68.421 15.88 0.00 0.00 3.51
588 904 8.077386 CCTCGTAGTATTTTTCTAGATCCTGAC 58.923 40.741 0.00 0.00 0.00 3.51
621 937 1.062525 GGCGCCGCTGTAGATTTTG 59.937 57.895 12.58 0.00 0.00 2.44
1640 1987 2.880268 TGCAGGACTCTTGATTGTGTTG 59.120 45.455 0.00 0.00 0.00 3.33
1773 2120 6.071108 AGCTATTGTGTCAGACTGTCATACTT 60.071 38.462 10.88 0.00 0.00 2.24
1775 2122 4.160736 TGTGTCAGACTGTCATACTTCG 57.839 45.455 10.88 0.00 0.00 3.79
1778 2125 5.414765 TGTGTCAGACTGTCATACTTCGTAT 59.585 40.000 10.88 0.00 0.00 3.06
1779 2126 5.739630 GTGTCAGACTGTCATACTTCGTATG 59.260 44.000 10.88 7.51 44.93 2.39
1781 2128 4.640647 TCAGACTGTCATACTTCGTATGCT 59.359 41.667 10.88 0.00 43.72 3.79
1789 2136 5.573282 GTCATACTTCGTATGCTCGCAATAT 59.427 40.000 8.71 0.00 43.72 1.28
1813 2163 2.472397 GCGCACGACTTATTTCTGACAC 60.472 50.000 0.30 0.00 0.00 3.67
1848 2313 5.441500 TGAGGATGTACAAAACAGGAAACA 58.558 37.500 0.00 0.00 42.70 2.83
1860 2325 7.661847 ACAAAACAGGAAACAAATTACACCAAA 59.338 29.630 0.00 0.00 0.00 3.28
1901 2366 4.141390 GGGATGGTGTCATCTATGTTTCCT 60.141 45.833 6.37 0.00 46.70 3.36
1902 2367 4.818546 GGATGGTGTCATCTATGTTTCCTG 59.181 45.833 6.37 0.00 46.70 3.86
1903 2368 5.396772 GGATGGTGTCATCTATGTTTCCTGA 60.397 44.000 6.37 0.00 46.70 3.86
1904 2369 5.698741 TGGTGTCATCTATGTTTCCTGAT 57.301 39.130 0.00 0.00 0.00 2.90
1905 2370 5.430886 TGGTGTCATCTATGTTTCCTGATG 58.569 41.667 0.00 0.00 38.03 3.07
1906 2371 5.045651 TGGTGTCATCTATGTTTCCTGATGT 60.046 40.000 0.00 0.00 37.93 3.06
1907 2372 5.882557 GGTGTCATCTATGTTTCCTGATGTT 59.117 40.000 0.00 0.00 37.93 2.71
1908 2373 6.037610 GGTGTCATCTATGTTTCCTGATGTTC 59.962 42.308 0.00 0.00 37.93 3.18
1944 2417 5.519808 TCAGACTATCTGTGGACTATGGTT 58.480 41.667 5.77 0.00 44.58 3.67
1961 2435 8.191534 ACTATGGTTATAGTCCAGTCCATTAC 57.808 38.462 0.00 0.00 44.83 1.89
2077 2557 5.764686 TGCAAATCCTATGAACTCGCAATAT 59.235 36.000 0.00 0.00 0.00 1.28
2078 2558 6.082338 GCAAATCCTATGAACTCGCAATATG 58.918 40.000 0.00 0.00 0.00 1.78
2112 2592 6.761714 ACTTAGTTCTGACAGTAAAGGTTGTG 59.238 38.462 1.59 0.00 0.00 3.33
2135 2615 6.912591 GTGTGAGAATGTACAAAACAGGAAAG 59.087 38.462 0.00 0.00 42.70 2.62
2174 2654 6.290605 CCATCCAATTTTCATTTGGGGATAC 58.709 40.000 2.84 0.00 43.19 2.24
2229 2709 9.469097 AACTTATCAGACTGTATGTAGACTCTT 57.531 33.333 1.59 0.00 0.00 2.85
2424 2985 4.151335 CAGTTACTTGTAGCTTCAGTGCAG 59.849 45.833 0.00 0.00 34.99 4.41
2480 3041 8.563732 GCTAGGAAAGGATAATTTCTGATTGAC 58.436 37.037 0.00 0.00 38.86 3.18
2619 3181 1.275666 TAGCCACTCTTGCTAGCCAA 58.724 50.000 13.29 5.87 40.23 4.52
2690 3252 7.226523 GCCCTTAAATGTTGTTGAAATCAAGTT 59.773 33.333 0.00 0.00 36.39 2.66
2740 3716 8.934023 ACATTGTTTTAGATCCAGTTCCTTTA 57.066 30.769 0.00 0.00 0.00 1.85
2752 3728 7.016153 TCCAGTTCCTTTATCAAGCTTTAGA 57.984 36.000 0.00 0.00 0.00 2.10
2786 3762 2.691011 TGCCTTTACCTTGAACACAACC 59.309 45.455 0.00 0.00 0.00 3.77
2825 3801 4.636206 GGATCTTGTTCCATCGTTAAGCTT 59.364 41.667 3.48 3.48 35.72 3.74
2944 3920 7.489160 TCTAAACACATTCATATACGCAGAGT 58.511 34.615 0.00 0.00 0.00 3.24
2966 3942 8.092687 AGAGTCAATTTTATCTTTTTGCAGCAT 58.907 29.630 0.00 0.00 0.00 3.79
2981 3957 1.447643 GCATGAGGGGTATGCGAGT 59.552 57.895 0.00 0.00 41.16 4.18
2993 3969 4.167268 GGTATGCGAGTAATCGATTCTCC 58.833 47.826 17.94 13.72 34.64 3.71
2995 3971 3.627732 TGCGAGTAATCGATTCTCCTC 57.372 47.619 17.94 16.10 34.64 3.71
2996 3972 3.215151 TGCGAGTAATCGATTCTCCTCT 58.785 45.455 17.94 6.67 34.64 3.69
2997 3973 4.386711 TGCGAGTAATCGATTCTCCTCTA 58.613 43.478 17.94 7.72 34.64 2.43
2998 3974 5.004448 TGCGAGTAATCGATTCTCCTCTAT 58.996 41.667 17.94 0.00 34.64 1.98
2999 3975 5.122554 TGCGAGTAATCGATTCTCCTCTATC 59.877 44.000 17.94 10.20 34.64 2.08
3000 3976 5.353123 GCGAGTAATCGATTCTCCTCTATCT 59.647 44.000 17.94 0.98 34.64 1.98
3001 3977 6.535865 GCGAGTAATCGATTCTCCTCTATCTA 59.464 42.308 17.94 0.00 34.64 1.98
3002 3978 7.064847 GCGAGTAATCGATTCTCCTCTATCTAA 59.935 40.741 17.94 0.00 34.64 2.10
3003 3979 8.600625 CGAGTAATCGATTCTCCTCTATCTAAG 58.399 40.741 15.25 1.47 34.64 2.18
3004 3980 8.276252 AGTAATCGATTCTCCTCTATCTAAGC 57.724 38.462 15.25 0.00 0.00 3.09
3005 3981 7.885922 AGTAATCGATTCTCCTCTATCTAAGCA 59.114 37.037 15.25 0.00 0.00 3.91
3006 3982 5.950758 TCGATTCTCCTCTATCTAAGCAC 57.049 43.478 0.00 0.00 0.00 4.40
3007 3983 4.762765 TCGATTCTCCTCTATCTAAGCACC 59.237 45.833 0.00 0.00 0.00 5.01
3008 3984 4.082463 CGATTCTCCTCTATCTAAGCACCC 60.082 50.000 0.00 0.00 0.00 4.61
3009 3985 3.973472 TCTCCTCTATCTAAGCACCCA 57.027 47.619 0.00 0.00 0.00 4.51
3010 3986 4.265856 TCTCCTCTATCTAAGCACCCAA 57.734 45.455 0.00 0.00 0.00 4.12
3031 4102 6.942005 CCCAATGCTGTATATTGTCTCCATTA 59.058 38.462 0.00 0.00 34.51 1.90
3063 4144 5.428131 ACCTGCTATTCTTCTCTTCATCCTT 59.572 40.000 0.00 0.00 0.00 3.36
3082 4163 6.254281 TCCTTTAGCTGAAATTGTTAGCAC 57.746 37.500 0.00 0.00 39.84 4.40
3121 4202 5.189659 TGTAAACCAACACAACCATAAGC 57.810 39.130 0.00 0.00 0.00 3.09
3163 4247 7.719871 TCTCTTAAGCTAGTTTGGTGACTAT 57.280 36.000 1.54 0.00 32.07 2.12
3166 4250 6.439375 TCTTAAGCTAGTTTGGTGACTATCCA 59.561 38.462 1.54 0.00 32.07 3.41
3182 4266 8.299570 GTGACTATCCAAATATATTGCCCTTTG 58.700 37.037 0.00 0.00 0.00 2.77
3189 4273 6.096705 CCAAATATATTGCCCTTTGTGACAGA 59.903 38.462 0.00 0.00 0.00 3.41
3190 4274 6.699575 AATATATTGCCCTTTGTGACAGAC 57.300 37.500 0.00 0.00 0.00 3.51
3191 4275 2.664402 ATTGCCCTTTGTGACAGACT 57.336 45.000 0.00 0.00 0.00 3.24
3192 4276 1.679139 TTGCCCTTTGTGACAGACTG 58.321 50.000 0.00 0.00 0.00 3.51
3193 4277 0.836606 TGCCCTTTGTGACAGACTGA 59.163 50.000 10.08 0.00 0.00 3.41
3194 4278 1.230324 GCCCTTTGTGACAGACTGAC 58.770 55.000 10.08 3.32 0.00 3.51
3195 4279 1.475034 GCCCTTTGTGACAGACTGACA 60.475 52.381 10.08 6.48 0.00 3.58
3196 4280 2.487934 CCCTTTGTGACAGACTGACAG 58.512 52.381 10.08 0.00 0.00 3.51
3204 4288 4.202121 TGTGACAGACTGACAGTCCTTTAC 60.202 45.833 28.08 21.37 46.18 2.01
3223 4307 8.598916 TCCTTTACCATCAAAATCTACAGTGTA 58.401 33.333 2.36 2.36 0.00 2.90
3242 4326 8.353684 ACAGTGTACTATATGCAGTAACATCTC 58.646 37.037 0.00 0.00 32.92 2.75
3243 4327 7.535599 CAGTGTACTATATGCAGTAACATCTCG 59.464 40.741 0.00 0.00 32.92 4.04
3249 4333 4.668576 ATGCAGTAACATCTCGTTTGTG 57.331 40.909 0.00 0.00 39.14 3.33
3251 4335 3.247411 TGCAGTAACATCTCGTTTGTGTG 59.753 43.478 0.00 0.00 39.14 3.82
3253 4337 3.186409 CAGTAACATCTCGTTTGTGTGGG 59.814 47.826 0.00 0.00 39.14 4.61
3342 4426 0.179000 ACTTCCGATCACCAGATGGC 59.821 55.000 0.00 0.00 39.32 4.40
3410 4494 1.282930 GGTTCGACGACACCTTCAGC 61.283 60.000 16.89 0.61 0.00 4.26
3411 4495 0.596600 GTTCGACGACACCTTCAGCA 60.597 55.000 0.00 0.00 0.00 4.41
3653 4738 8.634475 TTGAGATCAGATGTTATGTTACTTCG 57.366 34.615 0.00 0.00 0.00 3.79
3726 4814 6.326064 ACTCTAGGTGAGACAATCATGCTATT 59.674 38.462 0.00 0.00 45.39 1.73
3728 4816 4.458397 AGGTGAGACAATCATGCTATTGG 58.542 43.478 10.81 0.00 40.92 3.16
3729 4817 3.567164 GGTGAGACAATCATGCTATTGGG 59.433 47.826 10.81 0.00 40.92 4.12
3731 4819 3.202818 TGAGACAATCATGCTATTGGGGT 59.797 43.478 10.81 0.00 40.48 4.95
3733 4821 2.549754 GACAATCATGCTATTGGGGTCG 59.450 50.000 10.81 0.00 40.48 4.79
3734 4822 2.172505 ACAATCATGCTATTGGGGTCGA 59.827 45.455 10.81 0.00 40.48 4.20
3736 4824 1.496060 TCATGCTATTGGGGTCGAGT 58.504 50.000 0.00 0.00 0.00 4.18
3737 4825 2.673258 TCATGCTATTGGGGTCGAGTA 58.327 47.619 0.00 0.00 0.00 2.59
3738 4826 3.239449 TCATGCTATTGGGGTCGAGTAT 58.761 45.455 0.00 0.00 0.00 2.12
3764 4852 1.818959 GCTGACCCATTTGCTTGCCA 61.819 55.000 0.00 0.00 0.00 4.92
3773 4861 4.154556 CCCATTTGCTTGCCATTTGTTAAG 59.845 41.667 0.00 0.00 0.00 1.85
3774 4862 4.756135 CCATTTGCTTGCCATTTGTTAAGT 59.244 37.500 0.00 0.00 0.00 2.24
3775 4863 5.106987 CCATTTGCTTGCCATTTGTTAAGTC 60.107 40.000 0.00 0.00 0.00 3.01
3776 4864 4.662468 TTGCTTGCCATTTGTTAAGTCA 57.338 36.364 0.00 0.00 0.00 3.41
3777 4865 4.662468 TGCTTGCCATTTGTTAAGTCAA 57.338 36.364 0.00 0.00 0.00 3.18
3780 4868 5.293079 TGCTTGCCATTTGTTAAGTCAAAAC 59.707 36.000 0.00 0.00 40.05 2.43
3781 4869 5.523552 GCTTGCCATTTGTTAAGTCAAAACT 59.476 36.000 0.00 0.00 40.05 2.66
3783 4871 6.463995 TGCCATTTGTTAAGTCAAAACTCT 57.536 33.333 0.00 0.00 40.05 3.24
3784 4872 6.872920 TGCCATTTGTTAAGTCAAAACTCTT 58.127 32.000 0.00 0.00 40.05 2.85
3785 4873 7.327214 TGCCATTTGTTAAGTCAAAACTCTTT 58.673 30.769 0.00 0.00 40.05 2.52
3825 4919 2.050350 CCATTGTGCTGCAGGAGGG 61.050 63.158 17.12 8.25 0.00 4.30
3857 4956 6.985188 TGATGGAACTGCTATTTCTGTTAC 57.015 37.500 0.00 0.00 31.69 2.50
3886 5000 1.302285 CTGGGCTCTGACATGGCTT 59.698 57.895 0.00 0.00 0.00 4.35
3892 5006 3.849002 TCTGACATGGCTTCAGAGC 57.151 52.632 9.76 0.00 43.69 4.09
3908 5022 1.078709 GAGCGCTGTCAATGCAACTA 58.921 50.000 18.48 0.00 0.00 2.24
3972 5140 1.456923 CGCAGGATACGCATACACATG 59.543 52.381 0.00 0.00 46.39 3.21
3974 5142 2.872245 GCAGGATACGCATACACATGTT 59.128 45.455 0.00 0.00 46.39 2.71
3989 5157 4.208355 CACATGTTACAGCACGTTACAAC 58.792 43.478 0.00 0.00 40.31 3.32
4012 5180 5.047847 CGAGTACACCAACTTTTCTTCTCA 58.952 41.667 0.00 0.00 0.00 3.27
4013 5181 5.522460 CGAGTACACCAACTTTTCTTCTCAA 59.478 40.000 0.00 0.00 0.00 3.02
4042 5210 7.988904 GTAGAAAGCTACAGGTACATAAGTG 57.011 40.000 0.00 0.00 45.10 3.16
4044 5212 4.755266 AAGCTACAGGTACATAAGTGGG 57.245 45.455 0.00 0.00 0.00 4.61
4063 5235 1.811645 GAGGGAGGGATACAGCTCGC 61.812 65.000 0.00 0.00 37.85 5.03
4157 5335 2.756283 CGCCGAGACCTTCCTCCT 60.756 66.667 0.00 0.00 0.00 3.69
4356 5534 0.532573 ATGAGATGAGGACACGCGTT 59.467 50.000 10.22 0.17 0.00 4.84
4369 5547 2.280592 GCGTTCTTGGACCCGTGT 60.281 61.111 0.00 0.00 0.00 4.49
4393 5575 3.610242 CGGAGAAAGAAGAGAACACGATG 59.390 47.826 0.00 0.00 0.00 3.84
4437 5619 2.669569 TTGAGGCACGCCAGCTTC 60.670 61.111 11.35 0.00 40.63 3.86
4500 5682 4.147449 CCGATGGCGAGCTCCACA 62.147 66.667 8.47 7.84 39.25 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 1.971357 TGTTTGACCCTCTGACTCTCC 59.029 52.381 0.00 0.00 0.00 3.71
13 14 5.530915 CACTTATGTTTGTTTGACCCTCTGA 59.469 40.000 0.00 0.00 0.00 3.27
36 37 0.260230 TTGGGCTGGTTTGACCTTCA 59.740 50.000 0.00 0.00 39.58 3.02
75 82 1.760527 TGGCAGTATGTGTGGCAGT 59.239 52.632 0.00 0.00 44.85 4.40
76 83 4.720127 TGGCAGTATGTGTGGCAG 57.280 55.556 0.00 0.00 44.85 4.85
220 513 4.776322 CATTGGTGCTCGGGCGGA 62.776 66.667 1.14 0.00 42.25 5.54
329 640 5.207110 TGCTAGGCTATGATGAGAAGTTC 57.793 43.478 0.00 0.00 0.00 3.01
454 768 5.067283 CCCAAAAAGAAACCTCGAGAAAAGA 59.933 40.000 15.71 0.00 0.00 2.52
462 776 5.842907 AGAAAATCCCAAAAAGAAACCTCG 58.157 37.500 0.00 0.00 0.00 4.63
510 826 2.249413 AATCTCCTGCGGGCTCTGTG 62.249 60.000 6.73 0.00 0.00 3.66
537 853 2.097202 CGACGCAGAACAAGTTGAGAAG 60.097 50.000 10.54 0.00 0.00 2.85
548 864 2.507324 GAGGAGGCGACGCAGAAC 60.507 66.667 23.09 8.50 0.00 3.01
551 867 3.456431 CTACGAGGAGGCGACGCAG 62.456 68.421 23.09 3.49 34.83 5.18
553 869 1.505477 ATACTACGAGGAGGCGACGC 61.505 60.000 12.43 12.43 34.83 5.19
554 870 0.942962 AATACTACGAGGAGGCGACG 59.057 55.000 0.00 0.00 34.83 5.12
555 871 3.433513 AAAATACTACGAGGAGGCGAC 57.566 47.619 0.00 0.00 34.83 5.19
556 872 3.698040 AGAAAAATACTACGAGGAGGCGA 59.302 43.478 0.00 0.00 34.83 5.54
558 874 6.388435 TCTAGAAAAATACTACGAGGAGGC 57.612 41.667 0.00 0.00 0.00 4.70
559 875 7.449086 AGGATCTAGAAAAATACTACGAGGAGG 59.551 40.741 0.00 0.00 0.00 4.30
561 877 7.997223 TCAGGATCTAGAAAAATACTACGAGGA 59.003 37.037 0.00 0.00 0.00 3.71
562 878 8.077386 GTCAGGATCTAGAAAAATACTACGAGG 58.923 40.741 0.00 0.00 0.00 4.63
564 880 7.014038 GGGTCAGGATCTAGAAAAATACTACGA 59.986 40.741 0.00 0.00 0.00 3.43
565 881 7.146648 GGGTCAGGATCTAGAAAAATACTACG 58.853 42.308 0.00 0.00 0.00 3.51
566 882 7.146648 CGGGTCAGGATCTAGAAAAATACTAC 58.853 42.308 0.00 0.00 0.00 2.73
569 885 4.750598 GCGGGTCAGGATCTAGAAAAATAC 59.249 45.833 0.00 0.00 0.00 1.89
636 959 6.600822 ACAGTAGTACTAGTTTATTGAGCGGA 59.399 38.462 7.55 0.00 0.00 5.54
727 1052 6.912082 TGATGAAATTCAAAATCGCAGAAGA 58.088 32.000 0.00 0.00 43.58 2.87
730 1055 5.967088 CGATGATGAAATTCAAAATCGCAGA 59.033 36.000 21.88 0.00 38.23 4.26
731 1056 5.172591 CCGATGATGAAATTCAAAATCGCAG 59.827 40.000 25.31 15.70 40.94 5.18
916 1252 0.533308 CGACAGTTCCGGGGAAAACA 60.533 55.000 0.00 0.00 35.75 2.83
1359 1703 4.595538 ACCTGACGTTTCGGCGCA 62.596 61.111 10.83 0.00 37.93 6.09
1415 1759 0.242017 GGACAGCAATGCAAGACCAC 59.758 55.000 8.35 0.00 0.00 4.16
1630 1977 3.885976 TTCCCCCTAACAACACAATCA 57.114 42.857 0.00 0.00 0.00 2.57
1712 2059 4.113815 TTGGGATGCAGAGGCCCG 62.114 66.667 0.00 0.00 45.08 6.13
1789 2136 1.992667 CAGAAATAAGTCGTGCGCTCA 59.007 47.619 9.73 0.00 0.00 4.26
1797 2144 5.230942 ACCTTCAGTGTCAGAAATAAGTCG 58.769 41.667 0.00 0.00 0.00 4.18
1813 2163 3.692257 ACATCCTCAGACAACCTTCAG 57.308 47.619 0.00 0.00 0.00 3.02
1848 2313 7.995488 TGAAAAATGGATGGTTTGGTGTAATTT 59.005 29.630 0.00 0.00 0.00 1.82
1860 2325 5.747342 CATCCCAAATGAAAAATGGATGGT 58.253 37.500 8.17 0.00 43.45 3.55
1901 2366 5.017294 TGATATGTGGCGTTAGAACATCA 57.983 39.130 0.00 0.00 36.08 3.07
1902 2367 5.175856 GTCTGATATGTGGCGTTAGAACATC 59.824 44.000 0.00 0.00 36.08 3.06
1903 2368 5.050490 GTCTGATATGTGGCGTTAGAACAT 58.950 41.667 0.00 0.00 38.13 2.71
1904 2369 4.159693 AGTCTGATATGTGGCGTTAGAACA 59.840 41.667 0.00 0.00 0.00 3.18
1905 2370 4.683832 AGTCTGATATGTGGCGTTAGAAC 58.316 43.478 0.00 0.00 0.00 3.01
1906 2371 6.490381 AGATAGTCTGATATGTGGCGTTAGAA 59.510 38.462 0.00 0.00 0.00 2.10
1907 2372 6.004574 AGATAGTCTGATATGTGGCGTTAGA 58.995 40.000 0.00 0.00 0.00 2.10
1908 2373 6.260870 AGATAGTCTGATATGTGGCGTTAG 57.739 41.667 0.00 0.00 0.00 2.34
1950 2424 7.450074 TGCCATATAGTAAAGTAATGGACTGG 58.550 38.462 3.89 0.00 39.60 4.00
1961 2435 9.935682 CACAACATAAACTGCCATATAGTAAAG 57.064 33.333 0.00 0.00 0.00 1.85
2003 2483 5.589452 TGCATTATCGCATATCATGGCATTA 59.411 36.000 0.00 0.00 36.86 1.90
2004 2484 4.399934 TGCATTATCGCATATCATGGCATT 59.600 37.500 0.00 0.00 36.86 3.56
2017 2497 8.864069 ACTTAGTAGATCATATGCATTATCGC 57.136 34.615 3.54 5.44 0.00 4.58
2077 2557 4.039124 TGTCAGAACTAAGTCATGCACTCA 59.961 41.667 0.00 0.00 32.30 3.41
2078 2558 4.560128 TGTCAGAACTAAGTCATGCACTC 58.440 43.478 0.00 0.00 32.30 3.51
2112 2592 7.259290 TCTTTCCTGTTTTGTACATTCTCAC 57.741 36.000 0.00 0.00 35.85 3.51
2135 2615 6.990341 ATTGGATGGCTTGCTTTAAATTTC 57.010 33.333 0.00 0.00 0.00 2.17
2145 2625 4.976987 CAAATGAAAATTGGATGGCTTGC 58.023 39.130 0.00 0.00 0.00 4.01
2174 2654 6.662865 AGGACATAGGAACATAGATGACAG 57.337 41.667 0.00 0.00 0.00 3.51
2229 2709 5.950544 AACTAATGGACTGTACTATGGCA 57.049 39.130 0.00 0.00 0.00 4.92
2308 2788 7.957992 AGGTAGTAACTAGTAGCTCAAATGT 57.042 36.000 0.00 0.00 35.64 2.71
2368 2929 3.003689 GCAGAACTTGAACTAGCTTGCAA 59.996 43.478 0.00 0.00 0.00 4.08
2373 2934 4.202305 ACTGAAGCAGAACTTGAACTAGCT 60.202 41.667 0.82 0.00 39.29 3.32
2424 2985 3.615155 AGAGCTAGGGAACAAGCAATTC 58.385 45.455 0.00 0.00 40.66 2.17
2480 3041 2.898729 AACGAGTCATGCCTATCTGG 57.101 50.000 0.00 0.00 39.35 3.86
2659 3221 9.435688 GATTTCAACAACATTTAAGGGCTAATT 57.564 29.630 0.00 0.00 0.00 1.40
2690 3252 3.150949 CTGCAGTCTGGTGGACCA 58.849 61.111 5.25 0.00 45.54 4.02
2752 3728 8.207545 TCAAGGTAAAGGCATGTAAAATTTGTT 58.792 29.630 0.00 0.00 0.00 2.83
2763 3739 4.298332 GTTGTGTTCAAGGTAAAGGCATG 58.702 43.478 0.00 0.00 33.97 4.06
2786 3762 3.624777 AGATCCAAAACCAGGCACATAG 58.375 45.455 0.00 0.00 0.00 2.23
2825 3801 9.166173 CAGAAACACAATTATCCACTTATCTGA 57.834 33.333 0.00 0.00 32.01 3.27
2902 3878 6.096987 GTGTTTAGATCCTGACACTGGAGATA 59.903 42.308 13.03 0.00 39.33 1.98
2944 3920 7.332430 CCTCATGCTGCAAAAAGATAAAATTGA 59.668 33.333 6.36 0.00 0.00 2.57
2966 3942 1.611977 CGATTACTCGCATACCCCTCA 59.388 52.381 0.00 0.00 38.20 3.86
2981 3957 7.121463 GGTGCTTAGATAGAGGAGAATCGATTA 59.879 40.741 11.38 0.00 34.37 1.75
3004 3980 5.919721 TGGAGACAATATACAGCATTGGGTG 60.920 44.000 0.00 0.00 42.79 4.61
3005 3981 4.165950 TGGAGACAATATACAGCATTGGGT 59.834 41.667 0.00 0.00 37.64 4.51
3006 3982 4.717877 TGGAGACAATATACAGCATTGGG 58.282 43.478 0.00 0.00 37.64 4.12
3022 4093 5.675538 AGCAGGTAATGAGTTAATGGAGAC 58.324 41.667 0.00 0.00 0.00 3.36
3031 4102 7.430760 AGAGAAGAATAGCAGGTAATGAGTT 57.569 36.000 0.00 0.00 0.00 3.01
3041 4112 7.171337 GCTAAAGGATGAAGAGAAGAATAGCAG 59.829 40.741 0.00 0.00 33.07 4.24
3063 4144 5.237561 TGAACGTGCTAACAATTTCAGCTAA 59.762 36.000 0.00 0.00 36.26 3.09
3082 4163 0.957395 ACAGGGAAGCTGCATGAACG 60.957 55.000 1.02 0.00 0.00 3.95
3094 4175 3.025262 GGTTGTGTTGGTTTACAGGGAA 58.975 45.455 0.00 0.00 0.00 3.97
3163 4247 5.954752 TGTCACAAAGGGCAATATATTTGGA 59.045 36.000 0.00 0.00 37.04 3.53
3166 4250 6.891908 AGTCTGTCACAAAGGGCAATATATTT 59.108 34.615 0.00 0.00 0.00 1.40
3175 4259 1.230324 GTCAGTCTGTCACAAAGGGC 58.770 55.000 0.00 0.00 0.00 5.19
3182 4266 3.460857 AAAGGACTGTCAGTCTGTCAC 57.539 47.619 27.82 13.89 44.46 3.67
3189 4273 4.974645 TTGATGGTAAAGGACTGTCAGT 57.025 40.909 4.81 4.81 0.00 3.41
3190 4274 6.656693 AGATTTTGATGGTAAAGGACTGTCAG 59.343 38.462 10.38 0.00 0.00 3.51
3191 4275 6.542821 AGATTTTGATGGTAAAGGACTGTCA 58.457 36.000 10.38 0.00 0.00 3.58
3192 4276 7.606456 TGTAGATTTTGATGGTAAAGGACTGTC 59.394 37.037 0.00 0.00 0.00 3.51
3193 4277 7.458397 TGTAGATTTTGATGGTAAAGGACTGT 58.542 34.615 0.00 0.00 0.00 3.55
3194 4278 7.607991 ACTGTAGATTTTGATGGTAAAGGACTG 59.392 37.037 0.00 0.00 0.00 3.51
3195 4279 7.607991 CACTGTAGATTTTGATGGTAAAGGACT 59.392 37.037 0.00 0.00 0.00 3.85
3196 4280 7.390718 ACACTGTAGATTTTGATGGTAAAGGAC 59.609 37.037 0.00 0.00 0.00 3.85
3223 4307 7.222805 CACAAACGAGATGTTACTGCATATAGT 59.777 37.037 0.00 0.00 40.84 2.12
3242 4326 2.458951 CAACATGAACCCACACAAACG 58.541 47.619 0.00 0.00 0.00 3.60
3243 4327 2.200899 GCAACATGAACCCACACAAAC 58.799 47.619 0.00 0.00 0.00 2.93
3249 4333 1.134946 GCCTATGCAACATGAACCCAC 59.865 52.381 0.00 0.00 37.47 4.61
3251 4335 1.406539 CAGCCTATGCAACATGAACCC 59.593 52.381 0.00 0.00 41.13 4.11
3253 4337 1.202336 GCCAGCCTATGCAACATGAAC 60.202 52.381 0.00 0.00 41.13 3.18
3300 4384 3.569701 TGGAAAATGTCTGCTTGAGTTCC 59.430 43.478 0.00 0.00 0.00 3.62
3342 4426 0.174845 TGTTTCCTAGGATGACGGCG 59.825 55.000 13.57 4.80 0.00 6.46
3410 4494 3.108289 CTGCAGACGTCGCCTGTG 61.108 66.667 23.01 12.33 34.29 3.66
3651 4736 3.244112 GGAAACAGTCTTCTTCCTTCCGA 60.244 47.826 3.35 0.00 36.48 4.55
3653 4738 4.359434 AGGAAACAGTCTTCTTCCTTCC 57.641 45.455 6.45 0.00 45.37 3.46
3714 4802 2.810274 CTCGACCCCAATAGCATGATTG 59.190 50.000 0.00 0.00 36.70 2.67
3726 4814 2.836360 GCCGGATACTCGACCCCA 60.836 66.667 5.05 0.00 0.00 4.96
3728 4816 2.728817 CTGCCGGATACTCGACCC 59.271 66.667 5.05 0.00 0.00 4.46
3729 4817 2.027751 GCTGCCGGATACTCGACC 59.972 66.667 5.05 0.00 0.00 4.79
3731 4819 1.453197 TCAGCTGCCGGATACTCGA 60.453 57.895 9.47 0.00 0.00 4.04
3733 4821 1.068250 GGTCAGCTGCCGGATACTC 59.932 63.158 9.47 0.00 0.00 2.59
3734 4822 2.435693 GGGTCAGCTGCCGGATACT 61.436 63.158 9.47 0.00 0.00 2.12
3736 4824 1.344953 AATGGGTCAGCTGCCGGATA 61.345 55.000 9.47 2.24 0.00 2.59
3737 4825 2.215451 AAATGGGTCAGCTGCCGGAT 62.215 55.000 9.47 6.66 0.00 4.18
3738 4826 2.905996 AAATGGGTCAGCTGCCGGA 61.906 57.895 9.47 4.57 0.00 5.14
3776 4864 3.739209 GCAGCTCCTTGCAAAAGAGTTTT 60.739 43.478 21.19 9.61 45.94 2.43
3777 4865 2.223900 GCAGCTCCTTGCAAAAGAGTTT 60.224 45.455 21.19 11.43 45.94 2.66
3780 4868 3.788775 GCAGCTCCTTGCAAAAGAG 57.211 52.632 17.79 17.79 45.94 2.85
3787 4875 1.425412 CATTTGTTGCAGCTCCTTGC 58.575 50.000 1.17 0.00 44.33 4.01
3857 4956 2.237143 TCAGAGCCCAGGTGTTGATAAG 59.763 50.000 0.00 0.00 0.00 1.73
3886 5000 0.603439 TTGCATTGACAGCGCTCTGA 60.603 50.000 7.13 0.00 42.95 3.27
3989 5157 5.047847 TGAGAAGAAAAGTTGGTGTACTCG 58.952 41.667 0.00 0.00 0.00 4.18
3990 5158 6.920569 TTGAGAAGAAAAGTTGGTGTACTC 57.079 37.500 0.00 0.00 0.00 2.59
3991 5159 6.884836 AGTTTGAGAAGAAAAGTTGGTGTACT 59.115 34.615 0.00 0.00 0.00 2.73
3992 5160 7.085052 AGTTTGAGAAGAAAAGTTGGTGTAC 57.915 36.000 0.00 0.00 0.00 2.90
3993 5161 8.044908 ACTAGTTTGAGAAGAAAAGTTGGTGTA 58.955 33.333 0.00 0.00 0.00 2.90
3994 5162 6.884836 ACTAGTTTGAGAAGAAAAGTTGGTGT 59.115 34.615 0.00 0.00 0.00 4.16
3995 5163 7.321745 ACTAGTTTGAGAAGAAAAGTTGGTG 57.678 36.000 0.00 0.00 0.00 4.17
3996 5164 8.483758 TCTACTAGTTTGAGAAGAAAAGTTGGT 58.516 33.333 0.00 0.00 0.00 3.67
4000 5168 9.047371 GCTTTCTACTAGTTTGAGAAGAAAAGT 57.953 33.333 14.22 0.00 33.82 2.66
4012 5180 7.771927 TGTACCTGTAGCTTTCTACTAGTTT 57.228 36.000 0.00 0.00 44.26 2.66
4013 5181 7.957992 ATGTACCTGTAGCTTTCTACTAGTT 57.042 36.000 0.00 0.00 44.26 2.24
4039 5207 0.266152 CTGTATCCCTCCCTCCCACT 59.734 60.000 0.00 0.00 0.00 4.00
4040 5208 1.411651 GCTGTATCCCTCCCTCCCAC 61.412 65.000 0.00 0.00 0.00 4.61
4041 5209 1.074471 GCTGTATCCCTCCCTCCCA 60.074 63.158 0.00 0.00 0.00 4.37
4042 5210 0.834261 GAGCTGTATCCCTCCCTCCC 60.834 65.000 0.00 0.00 0.00 4.30
4044 5212 1.811645 GCGAGCTGTATCCCTCCCTC 61.812 65.000 0.00 0.00 0.00 4.30
4063 5235 0.581053 ACGCAAGCGCCAAAATTTTG 59.419 45.000 21.65 21.65 44.19 2.44
4142 5317 1.324005 GGTGAGGAGGAAGGTCTCGG 61.324 65.000 0.00 0.00 34.74 4.63
4143 5321 0.323908 AGGTGAGGAGGAAGGTCTCG 60.324 60.000 0.00 0.00 34.74 4.04
4369 5547 3.817084 TCGTGTTCTCTTCTTTCTCCGTA 59.183 43.478 0.00 0.00 0.00 4.02
4393 5575 1.805945 CGCTCGAGCCAAGGTACAC 60.806 63.158 30.66 0.39 37.91 2.90
4500 5682 2.690510 GAGAAGCCCCCTGAGCCT 60.691 66.667 0.00 0.00 0.00 4.58


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

AutoCloner maintained by Alex Coulton.