Multiple sequence alignment - TraesCS3D01G307500

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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 TraesCS3D01G307500 chr3D 100.000 2699 0 0 1 2699 421313397 421316095 0.000000e+00 4985.0
1 TraesCS3D01G307500 chr3D 87.694 837 84 6 990 1816 421291127 421291954 0.000000e+00 957.0
2 TraesCS3D01G307500 chr3D 93.509 570 36 1 113 681 421290220 421290789 0.000000e+00 846.0
3 TraesCS3D01G307500 chr3D 81.703 317 47 9 1210 1524 421704307 421704614 1.240000e-63 254.0
4 TraesCS3D01G307500 chr3D 80.126 317 48 11 1210 1524 422022872 422023175 3.500000e-54 222.0
5 TraesCS3D01G307500 chr3D 97.917 48 1 0 737 784 421290799 421290846 1.720000e-12 84.2
6 TraesCS3D01G307500 chr3A 93.467 1898 83 10 821 2699 529777743 529775868 0.000000e+00 2780.0
7 TraesCS3D01G307500 chr3A 87.292 842 88 10 988 1819 529843474 529842642 0.000000e+00 944.0
8 TraesCS3D01G307500 chr3A 94.599 574 30 1 116 688 529844390 529843817 0.000000e+00 887.0
9 TraesCS3D01G307500 chr3A 94.512 492 18 2 206 688 529779798 529779307 0.000000e+00 750.0
10 TraesCS3D01G307500 chr3A 97.576 165 4 0 48 212 529840431 529840267 1.580000e-72 283.0
11 TraesCS3D01G307500 chr3A 96.296 54 2 0 735 788 529843813 529843760 3.700000e-14 89.8
12 TraesCS3D01G307500 chr3A 100.000 33 0 0 734 766 529779304 529779272 8.070000e-06 62.1
13 TraesCS3D01G307500 chr3B 93.937 1171 47 6 731 1888 548044771 548045930 0.000000e+00 1748.0
14 TraesCS3D01G307500 chr3B 95.716 817 35 0 1883 2699 548046097 548046913 0.000000e+00 1315.0
15 TraesCS3D01G307500 chr3B 83.608 1031 114 24 829 1816 548039147 548040165 0.000000e+00 917.0
16 TraesCS3D01G307500 chr3B 93.220 590 34 5 107 692 548044189 548044776 0.000000e+00 863.0
17 TraesCS3D01G307500 chr3B 93.860 570 34 1 113 681 548038428 548038997 0.000000e+00 857.0
18 TraesCS3D01G307500 chr3B 80.442 317 51 8 1210 1524 549427487 549427794 5.810000e-57 231.0
19 TraesCS3D01G307500 chr4A 90.558 233 22 0 299 531 538833223 538833455 2.610000e-80 309.0
20 TraesCS3D01G307500 chr2A 81.731 312 51 6 1225 1534 15815521 15815214 3.450000e-64 255.0
21 TraesCS3D01G307500 chr4D 93.671 79 5 0 398 476 450198733 450198655 4.720000e-23 119.0


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 TraesCS3D01G307500 chr3D 421313397 421316095 2698 False 4985.000000 4985 100.00000 1 2699 1 chr3D.!!$F1 2698
1 TraesCS3D01G307500 chr3D 421290220 421291954 1734 False 629.066667 957 93.04000 113 1816 3 chr3D.!!$F4 1703
2 TraesCS3D01G307500 chr3A 529775868 529779798 3930 True 1197.366667 2780 95.99300 206 2699 3 chr3A.!!$R1 2493
3 TraesCS3D01G307500 chr3A 529840267 529844390 4123 True 550.950000 944 93.94075 48 1819 4 chr3A.!!$R2 1771
4 TraesCS3D01G307500 chr3B 548044189 548046913 2724 False 1308.666667 1748 94.29100 107 2699 3 chr3B.!!$F3 2592
5 TraesCS3D01G307500 chr3B 548038428 548040165 1737 False 887.000000 917 88.73400 113 1816 2 chr3B.!!$F2 1703

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
95 96 0.115745 TAGAAGTCCACCCCGAACCT 59.884 55.0 0.0 0.0 0.0 3.50 F
99 100 0.178912 AGTCCACCCCGAACCTAACT 60.179 55.0 0.0 0.0 0.0 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1163 2752 1.187974 CATGGGGAAAAGCATGAGCA 58.812 50.0 0.00 0.00 45.49 4.26 R
1941 3878 2.364647 GGCGTTATGCTAACCTAGGTCT 59.635 50.0 16.64 8.31 45.43 3.85 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
17 18 4.546637 CGAACCTGTAAGTCGCGT 57.453 55.556 5.77 0.00 0.00 6.01
18 19 2.059575 CGAACCTGTAAGTCGCGTG 58.940 57.895 5.77 0.00 0.00 5.34
19 20 1.779683 GAACCTGTAAGTCGCGTGC 59.220 57.895 5.77 0.00 0.00 5.34
20 21 0.942410 GAACCTGTAAGTCGCGTGCA 60.942 55.000 5.77 0.00 0.00 4.57
21 22 0.531090 AACCTGTAAGTCGCGTGCAA 60.531 50.000 5.77 0.00 0.00 4.08
22 23 0.944311 ACCTGTAAGTCGCGTGCAAG 60.944 55.000 5.77 0.00 0.00 4.01
23 24 1.130613 CTGTAAGTCGCGTGCAAGC 59.869 57.895 15.13 15.13 0.00 4.01
31 32 3.990141 GCGTGCAAGCGAAAAACA 58.010 50.000 9.33 0.00 0.00 2.83
32 33 2.283254 GCGTGCAAGCGAAAAACAA 58.717 47.368 9.33 0.00 0.00 2.83
33 34 0.642800 GCGTGCAAGCGAAAAACAAA 59.357 45.000 9.33 0.00 0.00 2.83
34 35 1.059835 GCGTGCAAGCGAAAAACAAAA 59.940 42.857 9.33 0.00 0.00 2.44
35 36 2.473049 GCGTGCAAGCGAAAAACAAAAA 60.473 40.909 9.33 0.00 0.00 1.94
59 60 1.472990 AAAAACGCAACTTACGCAGC 58.527 45.000 0.00 0.00 0.00 5.25
60 61 0.378962 AAAACGCAACTTACGCAGCA 59.621 45.000 0.00 0.00 0.00 4.41
61 62 0.591170 AAACGCAACTTACGCAGCAT 59.409 45.000 0.00 0.00 0.00 3.79
62 63 1.434555 AACGCAACTTACGCAGCATA 58.565 45.000 0.00 0.00 0.00 3.14
63 64 0.719465 ACGCAACTTACGCAGCATAC 59.281 50.000 0.00 0.00 0.00 2.39
64 65 0.314259 CGCAACTTACGCAGCATACG 60.314 55.000 0.00 0.00 0.00 3.06
65 66 0.996462 GCAACTTACGCAGCATACGA 59.004 50.000 0.00 0.00 0.00 3.43
66 67 1.392168 GCAACTTACGCAGCATACGAA 59.608 47.619 0.00 0.00 0.00 3.85
67 68 2.534939 GCAACTTACGCAGCATACGAAG 60.535 50.000 0.00 2.94 0.00 3.79
68 69 1.922570 ACTTACGCAGCATACGAAGG 58.077 50.000 0.00 0.00 0.00 3.46
69 70 1.475280 ACTTACGCAGCATACGAAGGA 59.525 47.619 0.00 0.00 0.00 3.36
70 71 2.120232 CTTACGCAGCATACGAAGGAG 58.880 52.381 0.00 0.00 0.00 3.69
71 72 0.248907 TACGCAGCATACGAAGGAGC 60.249 55.000 0.00 0.00 0.00 4.70
72 73 1.519234 CGCAGCATACGAAGGAGCA 60.519 57.895 0.00 0.00 0.00 4.26
73 74 1.485838 CGCAGCATACGAAGGAGCAG 61.486 60.000 0.00 0.00 0.00 4.24
74 75 0.179100 GCAGCATACGAAGGAGCAGA 60.179 55.000 0.00 0.00 0.00 4.26
75 76 1.850377 CAGCATACGAAGGAGCAGAG 58.150 55.000 0.00 0.00 0.00 3.35
76 77 1.135915 CAGCATACGAAGGAGCAGAGT 59.864 52.381 0.00 0.00 0.00 3.24
77 78 2.359214 CAGCATACGAAGGAGCAGAGTA 59.641 50.000 0.00 0.00 0.00 2.59
78 79 2.621055 AGCATACGAAGGAGCAGAGTAG 59.379 50.000 0.00 0.00 0.00 2.57
79 80 2.619177 GCATACGAAGGAGCAGAGTAGA 59.381 50.000 0.00 0.00 0.00 2.59
80 81 3.066900 GCATACGAAGGAGCAGAGTAGAA 59.933 47.826 0.00 0.00 0.00 2.10
81 82 4.791411 GCATACGAAGGAGCAGAGTAGAAG 60.791 50.000 0.00 0.00 0.00 2.85
82 83 2.797786 ACGAAGGAGCAGAGTAGAAGT 58.202 47.619 0.00 0.00 0.00 3.01
83 84 2.750712 ACGAAGGAGCAGAGTAGAAGTC 59.249 50.000 0.00 0.00 0.00 3.01
84 85 2.098443 CGAAGGAGCAGAGTAGAAGTCC 59.902 54.545 0.00 0.00 0.00 3.85
85 86 2.909504 AGGAGCAGAGTAGAAGTCCA 57.090 50.000 0.00 0.00 0.00 4.02
86 87 2.452505 AGGAGCAGAGTAGAAGTCCAC 58.547 52.381 0.00 0.00 0.00 4.02
87 88 1.478916 GGAGCAGAGTAGAAGTCCACC 59.521 57.143 0.00 0.00 0.00 4.61
88 89 1.478916 GAGCAGAGTAGAAGTCCACCC 59.521 57.143 0.00 0.00 0.00 4.61
89 90 0.537653 GCAGAGTAGAAGTCCACCCC 59.462 60.000 0.00 0.00 0.00 4.95
90 91 0.818296 CAGAGTAGAAGTCCACCCCG 59.182 60.000 0.00 0.00 0.00 5.73
91 92 0.702902 AGAGTAGAAGTCCACCCCGA 59.297 55.000 0.00 0.00 0.00 5.14
92 93 1.076677 AGAGTAGAAGTCCACCCCGAA 59.923 52.381 0.00 0.00 0.00 4.30
93 94 1.204231 GAGTAGAAGTCCACCCCGAAC 59.796 57.143 0.00 0.00 0.00 3.95
94 95 0.248565 GTAGAAGTCCACCCCGAACC 59.751 60.000 0.00 0.00 0.00 3.62
95 96 0.115745 TAGAAGTCCACCCCGAACCT 59.884 55.000 0.00 0.00 0.00 3.50
96 97 0.115745 AGAAGTCCACCCCGAACCTA 59.884 55.000 0.00 0.00 0.00 3.08
97 98 0.978907 GAAGTCCACCCCGAACCTAA 59.021 55.000 0.00 0.00 0.00 2.69
98 99 0.689055 AAGTCCACCCCGAACCTAAC 59.311 55.000 0.00 0.00 0.00 2.34
99 100 0.178912 AGTCCACCCCGAACCTAACT 60.179 55.000 0.00 0.00 0.00 2.24
100 101 1.077663 AGTCCACCCCGAACCTAACTA 59.922 52.381 0.00 0.00 0.00 2.24
101 102 1.205655 GTCCACCCCGAACCTAACTAC 59.794 57.143 0.00 0.00 0.00 2.73
102 103 1.077663 TCCACCCCGAACCTAACTACT 59.922 52.381 0.00 0.00 0.00 2.57
103 104 1.904537 CCACCCCGAACCTAACTACTT 59.095 52.381 0.00 0.00 0.00 2.24
104 105 2.354403 CCACCCCGAACCTAACTACTTG 60.354 54.545 0.00 0.00 0.00 3.16
105 106 2.301009 CACCCCGAACCTAACTACTTGT 59.699 50.000 0.00 0.00 0.00 3.16
106 107 3.511146 CACCCCGAACCTAACTACTTGTA 59.489 47.826 0.00 0.00 0.00 2.41
107 108 3.766051 ACCCCGAACCTAACTACTTGTAG 59.234 47.826 6.28 6.28 0.00 2.74
108 109 3.766051 CCCCGAACCTAACTACTTGTAGT 59.234 47.826 7.55 7.55 0.00 2.73
109 110 4.949856 CCCCGAACCTAACTACTTGTAGTA 59.050 45.833 13.04 0.00 0.00 1.82
110 111 5.418840 CCCCGAACCTAACTACTTGTAGTAA 59.581 44.000 13.04 0.00 29.00 2.24
111 112 6.325596 CCCGAACCTAACTACTTGTAGTAAC 58.674 44.000 13.04 2.83 29.00 2.50
112 113 6.151817 CCCGAACCTAACTACTTGTAGTAACT 59.848 42.308 13.04 2.13 29.00 2.24
113 114 7.336931 CCCGAACCTAACTACTTGTAGTAACTA 59.663 40.741 13.04 3.09 29.00 2.24
114 115 8.897752 CCGAACCTAACTACTTGTAGTAACTAT 58.102 37.037 13.04 1.49 29.00 2.12
429 430 4.789075 CGTACTCCACCACCGCGG 62.789 72.222 26.86 26.86 42.50 6.46
481 482 2.594962 CGTTCTTGACGCGCAGGTT 61.595 57.895 5.73 0.00 45.86 3.50
692 702 2.981921 TCCATGATGGATGCTACTCCT 58.018 47.619 10.75 0.00 42.67 3.69
693 703 3.321039 TCCATGATGGATGCTACTCCTT 58.679 45.455 10.75 0.00 42.67 3.36
694 704 3.326006 TCCATGATGGATGCTACTCCTTC 59.674 47.826 10.75 8.51 42.67 3.46
695 705 3.558746 CCATGATGGATGCTACTCCTTCC 60.559 52.174 5.27 0.00 40.96 3.46
696 706 1.688735 TGATGGATGCTACTCCTTCCG 59.311 52.381 11.29 0.00 38.23 4.30
697 707 1.689273 GATGGATGCTACTCCTTCCGT 59.311 52.381 2.89 0.00 34.79 4.69
698 708 1.568504 TGGATGCTACTCCTTCCGTT 58.431 50.000 2.89 0.00 36.20 4.44
699 709 1.480954 TGGATGCTACTCCTTCCGTTC 59.519 52.381 2.89 0.00 36.20 3.95
700 710 1.202545 GGATGCTACTCCTTCCGTTCC 60.203 57.143 0.00 0.00 32.18 3.62
701 711 1.480954 GATGCTACTCCTTCCGTTCCA 59.519 52.381 0.00 0.00 0.00 3.53
702 712 1.344065 TGCTACTCCTTCCGTTCCAA 58.656 50.000 0.00 0.00 0.00 3.53
703 713 1.695242 TGCTACTCCTTCCGTTCCAAA 59.305 47.619 0.00 0.00 0.00 3.28
704 714 2.105134 TGCTACTCCTTCCGTTCCAAAA 59.895 45.455 0.00 0.00 0.00 2.44
705 715 3.244770 TGCTACTCCTTCCGTTCCAAAAT 60.245 43.478 0.00 0.00 0.00 1.82
706 716 4.020039 TGCTACTCCTTCCGTTCCAAAATA 60.020 41.667 0.00 0.00 0.00 1.40
707 717 4.939439 GCTACTCCTTCCGTTCCAAAATAA 59.061 41.667 0.00 0.00 0.00 1.40
708 718 5.589050 GCTACTCCTTCCGTTCCAAAATAAT 59.411 40.000 0.00 0.00 0.00 1.28
709 719 6.764560 GCTACTCCTTCCGTTCCAAAATAATA 59.235 38.462 0.00 0.00 0.00 0.98
710 720 7.041984 GCTACTCCTTCCGTTCCAAAATAATAG 60.042 40.741 0.00 0.00 0.00 1.73
711 721 6.954232 ACTCCTTCCGTTCCAAAATAATAGA 58.046 36.000 0.00 0.00 0.00 1.98
712 722 7.574607 ACTCCTTCCGTTCCAAAATAATAGAT 58.425 34.615 0.00 0.00 0.00 1.98
713 723 7.499232 ACTCCTTCCGTTCCAAAATAATAGATG 59.501 37.037 0.00 0.00 0.00 2.90
714 724 6.770785 TCCTTCCGTTCCAAAATAATAGATGG 59.229 38.462 0.00 0.00 0.00 3.51
715 725 6.385649 TTCCGTTCCAAAATAATAGATGGC 57.614 37.500 0.00 0.00 32.87 4.40
716 726 5.690865 TCCGTTCCAAAATAATAGATGGCT 58.309 37.500 0.00 0.00 32.87 4.75
717 727 5.530915 TCCGTTCCAAAATAATAGATGGCTG 59.469 40.000 0.00 0.00 32.87 4.85
718 728 5.530915 CCGTTCCAAAATAATAGATGGCTGA 59.469 40.000 0.00 0.00 32.87 4.26
719 729 6.039270 CCGTTCCAAAATAATAGATGGCTGAA 59.961 38.462 0.00 0.00 32.87 3.02
720 730 6.912591 CGTTCCAAAATAATAGATGGCTGAAC 59.087 38.462 0.00 0.00 32.87 3.18
721 731 7.201732 CGTTCCAAAATAATAGATGGCTGAACT 60.202 37.037 0.00 0.00 32.87 3.01
722 732 8.470002 GTTCCAAAATAATAGATGGCTGAACTT 58.530 33.333 0.00 0.00 32.87 2.66
723 733 8.225603 TCCAAAATAATAGATGGCTGAACTTC 57.774 34.615 0.00 0.00 32.87 3.01
724 734 7.833682 TCCAAAATAATAGATGGCTGAACTTCA 59.166 33.333 0.00 0.00 32.87 3.02
725 735 8.636213 CCAAAATAATAGATGGCTGAACTTCAT 58.364 33.333 0.00 0.00 0.00 2.57
732 742 6.552445 AGATGGCTGAACTTCATACTAAGT 57.448 37.500 0.00 0.00 41.46 2.24
790 2287 4.439837 GCCGAGGTTTGGAACTACTAGTAG 60.440 50.000 25.30 25.30 39.04 2.57
791 2288 4.946157 CCGAGGTTTGGAACTACTAGTAGA 59.054 45.833 31.93 10.54 36.97 2.59
792 2289 5.593502 CCGAGGTTTGGAACTACTAGTAGAT 59.406 44.000 31.93 22.68 36.97 1.98
793 2290 6.459848 CCGAGGTTTGGAACTACTAGTAGATG 60.460 46.154 31.93 11.04 36.97 2.90
798 2295 7.147707 GGTTTGGAACTACTAGTAGATGGATGT 60.148 40.741 31.93 9.57 36.97 3.06
802 2299 6.709846 GGAACTACTAGTAGATGGATGTACGT 59.290 42.308 31.93 7.01 36.97 3.57
836 2377 4.402056 TCCAGAAAATACGTGAGGATCC 57.598 45.455 2.48 2.48 29.01 3.36
858 2399 0.824759 ATCCCTACACGTGAGGAAGC 59.175 55.000 25.01 0.00 35.99 3.86
867 2408 0.319555 CGTGAGGAAGCTCGGTTCAA 60.320 55.000 10.56 0.00 0.00 2.69
942 2508 2.029728 GCCGATATATTCGTGATGCAGC 59.970 50.000 0.00 0.00 46.65 5.25
965 2535 3.069586 TGTTGGGCTCTCAATCGTATAGG 59.930 47.826 0.00 0.00 0.00 2.57
983 2554 7.069578 TCGTATAGGCTAGAAAAAGATTCAGGT 59.930 37.037 0.00 0.00 0.00 4.00
999 2582 2.632996 TCAGGTCAACCAAGATCGAAGT 59.367 45.455 1.33 0.00 38.89 3.01
1130 2713 1.196354 CAGCGACAAAGAAAGGCTCTG 59.804 52.381 0.00 0.00 33.37 3.35
1137 2726 2.816087 CAAAGAAAGGCTCTGCTTGCTA 59.184 45.455 0.00 0.00 33.37 3.49
1138 2727 3.362870 AAGAAAGGCTCTGCTTGCTAT 57.637 42.857 0.00 0.00 33.37 2.97
1141 2730 2.795231 AAGGCTCTGCTTGCTATTGA 57.205 45.000 0.00 0.00 0.00 2.57
1153 2742 6.494842 TGCTTGCTATTGATATTTTCGGTTC 58.505 36.000 0.00 0.00 0.00 3.62
1666 3258 2.368875 CCATGGTATTCTCTACGGCCTT 59.631 50.000 2.57 0.00 0.00 4.35
1688 3280 2.932614 ACAGTTATGACAGATTCAGCGC 59.067 45.455 0.00 0.00 37.77 5.92
1804 3398 7.827819 ATGATTCAATTTGAAGCTGAATGTG 57.172 32.000 23.42 0.00 42.72 3.21
1870 3627 9.654663 AAAATCATACTACTACTTTGTCCTCAC 57.345 33.333 0.00 0.00 0.00 3.51
1881 3646 6.287589 ACTTTGTCCTCACCACTAGATTAG 57.712 41.667 0.00 0.00 0.00 1.73
1941 3878 3.663995 TCAACAAATCTACCGACCGAA 57.336 42.857 0.00 0.00 0.00 4.30
1983 3920 2.620251 TCTGCAGGGAACAATATCCG 57.380 50.000 15.13 0.00 40.62 4.18
2052 3989 4.393062 TGCTACAAAAGAGCAGATTAGTGC 59.607 41.667 0.00 0.00 44.89 4.40
2077 4014 5.163099 TGAAATACACCTATGCCCAAGCTAT 60.163 40.000 0.00 0.00 40.80 2.97
2146 4083 1.327690 TTATCTCCGCGGCTTCTGGT 61.328 55.000 23.51 6.60 0.00 4.00
2193 4130 9.442047 AAACAAGACGAAAGATATCAGATTTCT 57.558 29.630 5.32 0.00 32.08 2.52
2194 4131 9.442047 AACAAGACGAAAGATATCAGATTTCTT 57.558 29.630 9.65 9.65 32.96 2.52
2342 4354 1.551430 CCAAAATTCATGGGCAGCTGA 59.449 47.619 20.43 0.00 34.15 4.26
2345 4357 1.700955 AATTCATGGGCAGCTGATCC 58.299 50.000 20.43 18.15 0.00 3.36
2360 4972 3.407424 TGATCCACAGACTTGAACCAG 57.593 47.619 0.00 0.00 0.00 4.00
2413 5402 2.224606 CCCAAATAGCACATCAGCGAT 58.775 47.619 0.00 0.00 40.15 4.58
2501 6104 1.870055 TAACGACAGGCCGTCCAGAC 61.870 60.000 18.07 0.00 42.54 3.51
2524 6127 2.584791 GACAACCACTGCGCATTTAAG 58.415 47.619 12.24 0.00 0.00 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.941476 GCACGCGACTTACAGGTTCG 61.941 60.000 15.93 0.00 0.00 3.95
2 3 0.531090 TTGCACGCGACTTACAGGTT 60.531 50.000 15.93 0.00 0.00 3.50
5 6 1.130613 GCTTGCACGCGACTTACAG 59.869 57.895 15.93 1.45 0.00 2.74
14 15 0.642800 TTTGTTTTTCGCTTGCACGC 59.357 45.000 4.85 4.85 0.00 5.34
15 16 3.360775 TTTTTGTTTTTCGCTTGCACG 57.639 38.095 0.00 0.00 0.00 5.34
40 41 1.202200 TGCTGCGTAAGTTGCGTTTTT 60.202 42.857 14.86 0.00 39.73 1.94
41 42 0.378962 TGCTGCGTAAGTTGCGTTTT 59.621 45.000 14.86 0.00 39.73 2.43
42 43 0.591170 ATGCTGCGTAAGTTGCGTTT 59.409 45.000 14.86 0.00 39.73 3.60
43 44 1.127951 GTATGCTGCGTAAGTTGCGTT 59.872 47.619 14.86 0.00 39.73 4.84
44 45 0.719465 GTATGCTGCGTAAGTTGCGT 59.281 50.000 14.86 0.00 39.73 5.24
45 46 0.314259 CGTATGCTGCGTAAGTTGCG 60.314 55.000 9.16 9.16 39.73 4.85
46 47 0.996462 TCGTATGCTGCGTAAGTTGC 59.004 50.000 13.20 0.00 41.68 4.17
47 48 2.029244 CCTTCGTATGCTGCGTAAGTTG 59.971 50.000 13.20 8.16 41.68 3.16
48 49 2.094390 TCCTTCGTATGCTGCGTAAGTT 60.094 45.455 13.20 0.00 41.68 2.66
49 50 1.475280 TCCTTCGTATGCTGCGTAAGT 59.525 47.619 13.20 0.00 41.68 2.24
50 51 2.120232 CTCCTTCGTATGCTGCGTAAG 58.880 52.381 2.62 5.81 43.44 2.34
51 52 1.801395 GCTCCTTCGTATGCTGCGTAA 60.801 52.381 2.62 0.00 0.00 3.18
52 53 0.248907 GCTCCTTCGTATGCTGCGTA 60.249 55.000 0.00 0.00 0.00 4.42
53 54 1.519455 GCTCCTTCGTATGCTGCGT 60.519 57.895 0.00 0.00 0.00 5.24
54 55 1.485838 CTGCTCCTTCGTATGCTGCG 61.486 60.000 0.00 0.00 0.00 5.18
55 56 0.179100 TCTGCTCCTTCGTATGCTGC 60.179 55.000 0.00 0.00 0.00 5.25
56 57 1.135915 ACTCTGCTCCTTCGTATGCTG 59.864 52.381 0.00 0.00 0.00 4.41
57 58 1.479709 ACTCTGCTCCTTCGTATGCT 58.520 50.000 0.00 0.00 0.00 3.79
58 59 2.619177 TCTACTCTGCTCCTTCGTATGC 59.381 50.000 0.00 0.00 0.00 3.14
59 60 4.336993 ACTTCTACTCTGCTCCTTCGTATG 59.663 45.833 0.00 0.00 0.00 2.39
60 61 4.528920 ACTTCTACTCTGCTCCTTCGTAT 58.471 43.478 0.00 0.00 0.00 3.06
61 62 3.940221 GACTTCTACTCTGCTCCTTCGTA 59.060 47.826 0.00 0.00 0.00 3.43
62 63 2.750712 GACTTCTACTCTGCTCCTTCGT 59.249 50.000 0.00 0.00 0.00 3.85
63 64 2.098443 GGACTTCTACTCTGCTCCTTCG 59.902 54.545 0.00 0.00 0.00 3.79
64 65 3.093057 TGGACTTCTACTCTGCTCCTTC 58.907 50.000 0.00 0.00 0.00 3.46
65 66 2.829120 GTGGACTTCTACTCTGCTCCTT 59.171 50.000 0.00 0.00 0.00 3.36
66 67 2.452505 GTGGACTTCTACTCTGCTCCT 58.547 52.381 0.00 0.00 0.00 3.69
67 68 1.478916 GGTGGACTTCTACTCTGCTCC 59.521 57.143 0.00 0.00 0.00 4.70
68 69 1.478916 GGGTGGACTTCTACTCTGCTC 59.521 57.143 0.00 0.00 0.00 4.26
69 70 1.562783 GGGTGGACTTCTACTCTGCT 58.437 55.000 0.00 0.00 0.00 4.24
70 71 0.537653 GGGGTGGACTTCTACTCTGC 59.462 60.000 0.00 0.00 0.00 4.26
71 72 0.818296 CGGGGTGGACTTCTACTCTG 59.182 60.000 0.00 0.00 0.00 3.35
72 73 0.702902 TCGGGGTGGACTTCTACTCT 59.297 55.000 0.00 0.00 0.00 3.24
73 74 1.204231 GTTCGGGGTGGACTTCTACTC 59.796 57.143 0.00 0.00 0.00 2.59
74 75 1.264295 GTTCGGGGTGGACTTCTACT 58.736 55.000 0.00 0.00 0.00 2.57
75 76 0.248565 GGTTCGGGGTGGACTTCTAC 59.751 60.000 0.00 0.00 0.00 2.59
76 77 0.115745 AGGTTCGGGGTGGACTTCTA 59.884 55.000 0.00 0.00 0.00 2.10
77 78 0.115745 TAGGTTCGGGGTGGACTTCT 59.884 55.000 0.00 0.00 0.00 2.85
78 79 0.978907 TTAGGTTCGGGGTGGACTTC 59.021 55.000 0.00 0.00 0.00 3.01
79 80 0.689055 GTTAGGTTCGGGGTGGACTT 59.311 55.000 0.00 0.00 0.00 3.01
80 81 0.178912 AGTTAGGTTCGGGGTGGACT 60.179 55.000 0.00 0.00 0.00 3.85
81 82 1.205655 GTAGTTAGGTTCGGGGTGGAC 59.794 57.143 0.00 0.00 0.00 4.02
82 83 1.077663 AGTAGTTAGGTTCGGGGTGGA 59.922 52.381 0.00 0.00 0.00 4.02
83 84 1.565067 AGTAGTTAGGTTCGGGGTGG 58.435 55.000 0.00 0.00 0.00 4.61
84 85 2.301009 ACAAGTAGTTAGGTTCGGGGTG 59.699 50.000 0.00 0.00 0.00 4.61
85 86 2.613129 ACAAGTAGTTAGGTTCGGGGT 58.387 47.619 0.00 0.00 0.00 4.95
86 87 3.766051 ACTACAAGTAGTTAGGTTCGGGG 59.234 47.826 7.05 0.00 43.35 5.73
87 88 6.151817 AGTTACTACAAGTAGTTAGGTTCGGG 59.848 42.308 17.11 0.00 43.35 5.14
88 89 7.150783 AGTTACTACAAGTAGTTAGGTTCGG 57.849 40.000 17.11 0.00 43.35 4.30
95 96 9.120538 CCGGGTAATAGTTACTACAAGTAGTTA 57.879 37.037 17.11 6.59 43.35 2.24
96 97 7.416777 GCCGGGTAATAGTTACTACAAGTAGTT 60.417 40.741 17.11 3.64 43.35 2.24
98 99 6.264067 AGCCGGGTAATAGTTACTACAAGTAG 59.736 42.308 3.10 5.72 39.04 2.57
99 100 6.129179 AGCCGGGTAATAGTTACTACAAGTA 58.871 40.000 3.10 0.00 36.39 2.24
100 101 4.958581 AGCCGGGTAATAGTTACTACAAGT 59.041 41.667 3.10 0.00 36.39 3.16
101 102 5.508657 GGAGCCGGGTAATAGTTACTACAAG 60.509 48.000 5.91 0.00 36.39 3.16
102 103 4.342092 GGAGCCGGGTAATAGTTACTACAA 59.658 45.833 5.91 0.00 36.39 2.41
103 104 3.891366 GGAGCCGGGTAATAGTTACTACA 59.109 47.826 5.91 0.00 36.39 2.74
104 105 3.891366 TGGAGCCGGGTAATAGTTACTAC 59.109 47.826 5.91 0.00 36.39 2.73
105 106 3.891366 GTGGAGCCGGGTAATAGTTACTA 59.109 47.826 5.91 0.00 36.39 1.82
106 107 2.697229 GTGGAGCCGGGTAATAGTTACT 59.303 50.000 5.91 0.00 36.39 2.24
107 108 2.544486 CGTGGAGCCGGGTAATAGTTAC 60.544 54.545 5.91 0.00 35.39 2.50
108 109 1.682854 CGTGGAGCCGGGTAATAGTTA 59.317 52.381 5.91 0.00 0.00 2.24
109 110 0.462789 CGTGGAGCCGGGTAATAGTT 59.537 55.000 5.91 0.00 0.00 2.24
110 111 0.396139 TCGTGGAGCCGGGTAATAGT 60.396 55.000 5.91 0.00 0.00 2.12
111 112 0.314302 CTCGTGGAGCCGGGTAATAG 59.686 60.000 5.91 0.00 0.00 1.73
112 113 1.111116 CCTCGTGGAGCCGGGTAATA 61.111 60.000 5.91 0.00 34.57 0.98
113 114 2.432300 CCTCGTGGAGCCGGGTAAT 61.432 63.158 5.91 0.00 34.57 1.89
114 115 3.072468 CCTCGTGGAGCCGGGTAA 61.072 66.667 5.91 0.00 34.57 2.85
481 482 4.308458 CGCCCACCTTCCACGTCA 62.308 66.667 0.00 0.00 0.00 4.35
647 656 1.792949 CGTCAAAGTTTCGGACAGAGG 59.207 52.381 6.83 0.00 0.00 3.69
687 697 6.954232 TCTATTATTTTGGAACGGAAGGAGT 58.046 36.000 0.00 0.00 0.00 3.85
690 700 6.515035 GCCATCTATTATTTTGGAACGGAAGG 60.515 42.308 0.00 0.00 0.00 3.46
691 701 6.263168 AGCCATCTATTATTTTGGAACGGAAG 59.737 38.462 0.00 0.00 0.00 3.46
692 702 6.039270 CAGCCATCTATTATTTTGGAACGGAA 59.961 38.462 0.00 0.00 0.00 4.30
693 703 5.530915 CAGCCATCTATTATTTTGGAACGGA 59.469 40.000 0.00 0.00 0.00 4.69
694 704 5.530915 TCAGCCATCTATTATTTTGGAACGG 59.469 40.000 0.00 0.00 0.00 4.44
695 705 6.618287 TCAGCCATCTATTATTTTGGAACG 57.382 37.500 0.00 0.00 0.00 3.95
696 706 8.000780 AGTTCAGCCATCTATTATTTTGGAAC 57.999 34.615 0.00 0.00 0.00 3.62
697 707 8.593945 AAGTTCAGCCATCTATTATTTTGGAA 57.406 30.769 0.00 0.00 0.00 3.53
698 708 7.833682 TGAAGTTCAGCCATCTATTATTTTGGA 59.166 33.333 0.08 0.00 0.00 3.53
699 709 7.999679 TGAAGTTCAGCCATCTATTATTTTGG 58.000 34.615 0.08 0.00 0.00 3.28
706 716 8.709308 ACTTAGTATGAAGTTCAGCCATCTATT 58.291 33.333 11.91 0.00 36.19 1.73
707 717 8.256356 ACTTAGTATGAAGTTCAGCCATCTAT 57.744 34.615 11.91 0.00 36.19 1.98
708 718 7.661536 ACTTAGTATGAAGTTCAGCCATCTA 57.338 36.000 11.91 6.48 36.19 1.98
709 719 6.552445 ACTTAGTATGAAGTTCAGCCATCT 57.448 37.500 11.91 7.33 36.19 2.90
719 729 4.705507 TCAGCTCGGAACTTAGTATGAAGT 59.294 41.667 0.00 0.00 41.50 3.01
720 730 5.038033 GTCAGCTCGGAACTTAGTATGAAG 58.962 45.833 0.00 0.00 0.00 3.02
721 731 4.438336 CGTCAGCTCGGAACTTAGTATGAA 60.438 45.833 0.00 0.00 0.00 2.57
722 732 3.064958 CGTCAGCTCGGAACTTAGTATGA 59.935 47.826 0.00 0.00 0.00 2.15
723 733 3.064958 TCGTCAGCTCGGAACTTAGTATG 59.935 47.826 0.00 0.00 0.00 2.39
724 734 3.276857 TCGTCAGCTCGGAACTTAGTAT 58.723 45.455 0.00 0.00 0.00 2.12
725 735 2.676839 CTCGTCAGCTCGGAACTTAGTA 59.323 50.000 0.00 0.00 0.00 1.82
726 736 1.469308 CTCGTCAGCTCGGAACTTAGT 59.531 52.381 0.00 0.00 0.00 2.24
727 737 1.202200 CCTCGTCAGCTCGGAACTTAG 60.202 57.143 0.00 0.00 0.00 2.18
728 738 0.809385 CCTCGTCAGCTCGGAACTTA 59.191 55.000 0.00 0.00 0.00 2.24
729 739 1.587054 CCTCGTCAGCTCGGAACTT 59.413 57.895 0.00 0.00 0.00 2.66
732 742 3.760035 GGCCTCGTCAGCTCGGAA 61.760 66.667 0.00 0.00 0.00 4.30
798 2295 4.297299 CTGGAAGATAAACGGCTACGTA 57.703 45.455 0.00 0.00 46.77 3.57
802 2299 6.477688 CGTATTTTCTGGAAGATAAACGGCTA 59.522 38.462 0.00 0.00 46.36 3.93
836 2377 0.750546 TCCTCACGTGTAGGGATCGG 60.751 60.000 24.56 11.53 34.66 4.18
858 2399 6.815641 CAGGATATATCTGGATTTGAACCGAG 59.184 42.308 12.42 0.00 0.00 4.63
867 2408 5.482908 GCAACGACAGGATATATCTGGATT 58.517 41.667 12.42 3.50 36.62 3.01
942 2508 2.672961 TACGATTGAGAGCCCAACAG 57.327 50.000 0.00 0.00 0.00 3.16
965 2535 5.473504 TGGTTGACCTGAATCTTTTTCTAGC 59.526 40.000 1.34 0.00 36.82 3.42
983 2554 4.466370 AGTCCATACTTCGATCTTGGTTGA 59.534 41.667 0.00 0.00 29.00 3.18
999 2582 1.112113 GCTCCAGGTCGAAGTCCATA 58.888 55.000 0.00 0.00 38.46 2.74
1130 2713 5.915196 GGAACCGAAAATATCAATAGCAAGC 59.085 40.000 0.00 0.00 0.00 4.01
1137 2726 5.125417 CACCAGTGGAACCGAAAATATCAAT 59.875 40.000 18.40 0.00 37.80 2.57
1138 2727 4.457603 CACCAGTGGAACCGAAAATATCAA 59.542 41.667 18.40 0.00 37.80 2.57
1163 2752 1.187974 CATGGGGAAAAGCATGAGCA 58.812 50.000 0.00 0.00 45.49 4.26
1572 3161 4.555709 TTGTCGCGGGTGTTGCCT 62.556 61.111 6.13 0.00 37.43 4.75
1666 3258 4.112634 GCGCTGAATCTGTCATAACTGTA 58.887 43.478 0.00 0.00 35.07 2.74
1688 3280 5.671493 ACCCAAAGATGGTCTACGATTTAG 58.329 41.667 0.00 0.00 46.01 1.85
1804 3398 6.135290 TGTTGGATAATGAATTACAGCAGC 57.865 37.500 0.00 0.00 0.00 5.25
1881 3646 5.812652 TGGTTCACGTCTTGTATTTGTTTC 58.187 37.500 0.00 0.00 0.00 2.78
1941 3878 2.364647 GGCGTTATGCTAACCTAGGTCT 59.635 50.000 16.64 8.31 45.43 3.85
2052 3989 3.316308 GCTTGGGCATAGGTGTATTTCAG 59.684 47.826 0.00 0.00 38.54 3.02
2077 4014 5.550290 TGAGTTTGCTACTGTCAATGATGA 58.450 37.500 0.00 0.00 37.17 2.92
2146 4083 1.301401 CGTTTCAGGTTCTCGGGCA 60.301 57.895 0.00 0.00 0.00 5.36
2193 4130 4.825085 CAGGCCCAGTTTGAACTACTTTAA 59.175 41.667 0.00 0.00 37.08 1.52
2194 4131 4.141344 ACAGGCCCAGTTTGAACTACTTTA 60.141 41.667 0.00 0.00 37.08 1.85
2210 4147 1.474077 CTGAAACAATGCTACAGGCCC 59.526 52.381 0.00 0.00 40.92 5.80
2342 4354 2.057922 ACCTGGTTCAAGTCTGTGGAT 58.942 47.619 0.00 0.00 0.00 3.41
2345 4357 0.947244 GCACCTGGTTCAAGTCTGTG 59.053 55.000 0.00 0.00 0.00 3.66
2360 4972 2.126850 GGAAAGCTTTCGCGCACC 60.127 61.111 28.17 13.78 42.32 5.01
2387 4999 4.747931 GCTGATGTGCTATTTGGGGACTAT 60.748 45.833 0.00 0.00 0.00 2.12
2413 5402 3.077907 GCACAGAAGGCCAGGGTA 58.922 61.111 5.01 0.00 0.00 3.69
2501 6104 2.116736 AATGCGCAGTGGTTGTCGTG 62.117 55.000 18.32 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.