Multiple sequence alignment - TraesCS2B01G611500

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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 TraesCS2B01G611500 chr2B 100.000 2535 0 0 1 2535 790668379 790665845 0.000000e+00 4682
1 TraesCS2B01G611500 chr2B 94.687 2447 76 17 110 2535 790657757 790655344 0.000000e+00 3749
2 TraesCS2B01G611500 chr2B 91.439 1355 62 20 110 1443 790647238 790645917 0.000000e+00 1810
3 TraesCS2B01G611500 chr2B 95.749 1082 39 2 1455 2535 135086651 135087726 0.000000e+00 1736
4 TraesCS2B01G611500 chr2B 95.476 1083 38 3 1455 2535 752860906 752859833 0.000000e+00 1718
5 TraesCS2B01G611500 chr2B 91.589 107 9 0 1 107 790641177 790641071 5.650000e-32 148
6 TraesCS2B01G611500 chr1B 95.749 1082 42 2 1455 2535 668106938 668108016 0.000000e+00 1740
7 TraesCS2B01G611500 chr1B 93.623 1082 44 8 1455 2535 22827617 22826560 0.000000e+00 1592
8 TraesCS2B01G611500 chr5B 95.656 1082 41 1 1454 2535 129726639 129725564 0.000000e+00 1733
9 TraesCS2B01G611500 chr6A 95.568 1083 38 3 1454 2535 616209400 616210473 0.000000e+00 1725
10 TraesCS2B01G611500 chr7B 95.564 1082 39 1 1454 2535 150192987 150194059 0.000000e+00 1724
11 TraesCS2B01G611500 chr7B 95.467 1081 40 5 1455 2535 426362178 426361107 0.000000e+00 1716
12 TraesCS2B01G611500 chr2A 89.145 1391 90 27 110 1454 770254851 770256226 0.000000e+00 1676
13 TraesCS2B01G611500 chr2D 91.827 1040 52 10 437 1454 644896580 644897608 0.000000e+00 1419


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 TraesCS2B01G611500 chr2B 790665845 790668379 2534 True 4682 4682 100.000 1 2535 1 chr2B.!!$R5 2534
1 TraesCS2B01G611500 chr2B 790655344 790657757 2413 True 3749 3749 94.687 110 2535 1 chr2B.!!$R4 2425
2 TraesCS2B01G611500 chr2B 790645917 790647238 1321 True 1810 1810 91.439 110 1443 1 chr2B.!!$R3 1333
3 TraesCS2B01G611500 chr2B 135086651 135087726 1075 False 1736 1736 95.749 1455 2535 1 chr2B.!!$F1 1080
4 TraesCS2B01G611500 chr2B 752859833 752860906 1073 True 1718 1718 95.476 1455 2535 1 chr2B.!!$R1 1080
5 TraesCS2B01G611500 chr1B 668106938 668108016 1078 False 1740 1740 95.749 1455 2535 1 chr1B.!!$F1 1080
6 TraesCS2B01G611500 chr1B 22826560 22827617 1057 True 1592 1592 93.623 1455 2535 1 chr1B.!!$R1 1080
7 TraesCS2B01G611500 chr5B 129725564 129726639 1075 True 1733 1733 95.656 1454 2535 1 chr5B.!!$R1 1081
8 TraesCS2B01G611500 chr6A 616209400 616210473 1073 False 1725 1725 95.568 1454 2535 1 chr6A.!!$F1 1081
9 TraesCS2B01G611500 chr7B 150192987 150194059 1072 False 1724 1724 95.564 1454 2535 1 chr7B.!!$F1 1081
10 TraesCS2B01G611500 chr7B 426361107 426362178 1071 True 1716 1716 95.467 1455 2535 1 chr7B.!!$R1 1080
11 TraesCS2B01G611500 chr2A 770254851 770256226 1375 False 1676 1676 89.145 110 1454 1 chr2A.!!$F1 1344
12 TraesCS2B01G611500 chr2D 644896580 644897608 1028 False 1419 1419 91.827 437 1454 1 chr2D.!!$F1 1017

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
158 159 0.030638 AAAGCAGAAAACGTGCGCAT 59.969 45.0 15.91 0.0 46.06 4.73 F
874 917 0.250124 TGTGTTGTCCTGCCTAACGG 60.250 55.0 0.00 0.0 0.00 4.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1032 1095 1.001520 TCGTGGTCATCGAATTGGTGT 59.998 47.619 0.0 0.0 34.36 4.16 R
2314 2383 0.250858 TTCGTCTACTCCGACCACCA 60.251 55.000 0.0 0.0 33.41 4.17 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
19 20 1.418334 ATGATCAAGAGTCCCCGAGG 58.582 55.000 0.00 0.00 0.00 4.63
20 21 0.041238 TGATCAAGAGTCCCCGAGGT 59.959 55.000 0.00 0.00 0.00 3.85
21 22 0.461961 GATCAAGAGTCCCCGAGGTG 59.538 60.000 0.00 0.00 0.00 4.00
22 23 1.617947 ATCAAGAGTCCCCGAGGTGC 61.618 60.000 0.00 0.00 0.00 5.01
23 24 2.120718 AAGAGTCCCCGAGGTGCT 59.879 61.111 0.00 0.00 0.00 4.40
24 25 0.970937 CAAGAGTCCCCGAGGTGCTA 60.971 60.000 0.00 0.00 0.00 3.49
25 26 0.252103 AAGAGTCCCCGAGGTGCTAA 60.252 55.000 0.00 0.00 0.00 3.09
26 27 0.252103 AGAGTCCCCGAGGTGCTAAA 60.252 55.000 0.00 0.00 0.00 1.85
27 28 0.175989 GAGTCCCCGAGGTGCTAAAG 59.824 60.000 0.00 0.00 0.00 1.85
28 29 1.449778 GTCCCCGAGGTGCTAAAGC 60.450 63.158 0.00 0.00 42.50 3.51
29 30 2.511600 CCCCGAGGTGCTAAAGCG 60.512 66.667 0.00 0.00 45.83 4.68
30 31 2.577059 CCCGAGGTGCTAAAGCGA 59.423 61.111 0.00 0.00 45.83 4.93
31 32 1.079405 CCCGAGGTGCTAAAGCGAA 60.079 57.895 0.00 0.00 45.83 4.70
32 33 0.672401 CCCGAGGTGCTAAAGCGAAA 60.672 55.000 0.00 0.00 45.83 3.46
33 34 1.153353 CCGAGGTGCTAAAGCGAAAA 58.847 50.000 0.00 0.00 45.83 2.29
34 35 1.533731 CCGAGGTGCTAAAGCGAAAAA 59.466 47.619 0.00 0.00 45.83 1.94
35 36 2.412847 CCGAGGTGCTAAAGCGAAAAAG 60.413 50.000 0.00 0.00 45.83 2.27
36 37 2.412847 CGAGGTGCTAAAGCGAAAAAGG 60.413 50.000 0.00 0.00 45.83 3.11
37 38 1.886542 AGGTGCTAAAGCGAAAAAGGG 59.113 47.619 0.00 0.00 45.83 3.95
38 39 1.668919 GGTGCTAAAGCGAAAAAGGGC 60.669 52.381 0.00 0.00 45.83 5.19
39 40 1.000717 GTGCTAAAGCGAAAAAGGGCA 60.001 47.619 0.00 0.00 45.83 5.36
40 41 1.000717 TGCTAAAGCGAAAAAGGGCAC 60.001 47.619 0.00 0.00 45.83 5.01
41 42 1.000717 GCTAAAGCGAAAAAGGGCACA 60.001 47.619 0.00 0.00 0.00 4.57
42 43 2.661594 CTAAAGCGAAAAAGGGCACAC 58.338 47.619 0.00 0.00 0.00 3.82
43 44 0.248866 AAAGCGAAAAAGGGCACACG 60.249 50.000 0.00 0.00 0.00 4.49
44 45 2.050442 GCGAAAAAGGGCACACGG 60.050 61.111 0.00 0.00 0.00 4.94
45 46 2.642700 CGAAAAAGGGCACACGGG 59.357 61.111 0.00 0.00 0.00 5.28
46 47 2.338620 GAAAAAGGGCACACGGGC 59.661 61.111 0.00 0.00 42.44 6.13
47 48 2.443016 AAAAAGGGCACACGGGCA 60.443 55.556 0.00 0.00 45.66 5.36
48 49 1.815817 GAAAAAGGGCACACGGGCAT 61.816 55.000 0.00 0.00 45.66 4.40
50 51 2.203625 AAGGGCACACGGGCATTT 60.204 55.556 0.00 0.00 44.20 2.32
51 52 2.573083 AAGGGCACACGGGCATTTG 61.573 57.895 0.00 0.00 44.20 2.32
52 53 4.740431 GGGCACACGGGCATTTGC 62.740 66.667 0.00 0.00 45.66 3.68
62 63 3.199551 GCATTTGCCGCTGATGGA 58.800 55.556 8.11 0.00 34.31 3.41
63 64 1.737816 GCATTTGCCGCTGATGGAT 59.262 52.632 8.11 0.00 34.31 3.41
64 65 0.596600 GCATTTGCCGCTGATGGATG 60.597 55.000 8.11 0.00 34.31 3.51
65 66 1.026584 CATTTGCCGCTGATGGATGA 58.973 50.000 0.00 0.00 0.00 2.92
66 67 1.611977 CATTTGCCGCTGATGGATGAT 59.388 47.619 0.00 0.00 0.00 2.45
67 68 1.766494 TTTGCCGCTGATGGATGATT 58.234 45.000 0.00 0.00 0.00 2.57
68 69 2.636647 TTGCCGCTGATGGATGATTA 57.363 45.000 0.00 0.00 0.00 1.75
69 70 2.865119 TGCCGCTGATGGATGATTAT 57.135 45.000 0.00 0.00 0.00 1.28
70 71 3.144657 TGCCGCTGATGGATGATTATT 57.855 42.857 0.00 0.00 0.00 1.40
71 72 3.489355 TGCCGCTGATGGATGATTATTT 58.511 40.909 0.00 0.00 0.00 1.40
72 73 3.890756 TGCCGCTGATGGATGATTATTTT 59.109 39.130 0.00 0.00 0.00 1.82
73 74 4.341806 TGCCGCTGATGGATGATTATTTTT 59.658 37.500 0.00 0.00 0.00 1.94
74 75 4.919754 GCCGCTGATGGATGATTATTTTTC 59.080 41.667 0.00 0.00 0.00 2.29
75 76 5.464168 CCGCTGATGGATGATTATTTTTCC 58.536 41.667 0.00 0.00 0.00 3.13
76 77 5.464168 CGCTGATGGATGATTATTTTTCCC 58.536 41.667 0.00 0.00 0.00 3.97
77 78 5.242393 CGCTGATGGATGATTATTTTTCCCT 59.758 40.000 0.00 0.00 0.00 4.20
78 79 6.239120 CGCTGATGGATGATTATTTTTCCCTT 60.239 38.462 0.00 0.00 0.00 3.95
79 80 6.927381 GCTGATGGATGATTATTTTTCCCTTG 59.073 38.462 0.00 0.00 0.00 3.61
80 81 7.201938 GCTGATGGATGATTATTTTTCCCTTGA 60.202 37.037 0.00 0.00 0.00 3.02
81 82 8.786710 TGATGGATGATTATTTTTCCCTTGAT 57.213 30.769 0.00 0.00 0.00 2.57
82 83 9.880254 TGATGGATGATTATTTTTCCCTTGATA 57.120 29.630 0.00 0.00 0.00 2.15
84 85 8.477419 TGGATGATTATTTTTCCCTTGATACC 57.523 34.615 0.00 0.00 0.00 2.73
85 86 7.508977 TGGATGATTATTTTTCCCTTGATACCC 59.491 37.037 0.00 0.00 0.00 3.69
86 87 7.730332 GGATGATTATTTTTCCCTTGATACCCT 59.270 37.037 0.00 0.00 0.00 4.34
87 88 9.807921 GATGATTATTTTTCCCTTGATACCCTA 57.192 33.333 0.00 0.00 0.00 3.53
92 93 9.862149 TTATTTTTCCCTTGATACCCTATTCTC 57.138 33.333 0.00 0.00 0.00 2.87
93 94 5.546621 TTTCCCTTGATACCCTATTCTCG 57.453 43.478 0.00 0.00 0.00 4.04
94 95 3.507411 TCCCTTGATACCCTATTCTCGG 58.493 50.000 0.00 0.00 0.00 4.63
95 96 3.141460 TCCCTTGATACCCTATTCTCGGA 59.859 47.826 0.00 0.00 0.00 4.55
96 97 3.258622 CCCTTGATACCCTATTCTCGGAC 59.741 52.174 0.00 0.00 0.00 4.79
97 98 3.895656 CCTTGATACCCTATTCTCGGACA 59.104 47.826 0.00 0.00 0.00 4.02
98 99 4.344102 CCTTGATACCCTATTCTCGGACAA 59.656 45.833 0.00 0.00 0.00 3.18
99 100 5.509840 CCTTGATACCCTATTCTCGGACAAG 60.510 48.000 0.00 0.00 33.19 3.16
100 101 4.543689 TGATACCCTATTCTCGGACAAGT 58.456 43.478 0.00 0.00 0.00 3.16
101 102 4.960469 TGATACCCTATTCTCGGACAAGTT 59.040 41.667 0.00 0.00 0.00 2.66
102 103 5.424252 TGATACCCTATTCTCGGACAAGTTT 59.576 40.000 0.00 0.00 0.00 2.66
103 104 4.203654 ACCCTATTCTCGGACAAGTTTC 57.796 45.455 0.00 0.00 0.00 2.78
104 105 3.581332 ACCCTATTCTCGGACAAGTTTCA 59.419 43.478 0.00 0.00 0.00 2.69
105 106 4.225267 ACCCTATTCTCGGACAAGTTTCAT 59.775 41.667 0.00 0.00 0.00 2.57
106 107 4.811557 CCCTATTCTCGGACAAGTTTCATC 59.188 45.833 0.00 0.00 0.00 2.92
107 108 5.419542 CCTATTCTCGGACAAGTTTCATCA 58.580 41.667 0.00 0.00 0.00 3.07
108 109 5.292101 CCTATTCTCGGACAAGTTTCATCAC 59.708 44.000 0.00 0.00 0.00 3.06
158 159 0.030638 AAAGCAGAAAACGTGCGCAT 59.969 45.000 15.91 0.00 46.06 4.73
174 175 8.401046 ACGTGCGCATACAAATAAAAATAATT 57.599 26.923 15.91 0.00 0.00 1.40
192 193 1.492133 TTCAGAGGAAGCACCCAGGG 61.492 60.000 2.85 2.85 40.05 4.45
359 368 9.882996 TTCGTATTAATATACACAGTAACGAGG 57.117 33.333 0.00 0.00 37.12 4.63
421 430 0.322456 TTGATCTTGAACCTGGGCCG 60.322 55.000 0.00 0.00 0.00 6.13
460 469 3.826729 ACAAGGAGGCTACAAAATTGACC 59.173 43.478 0.00 0.00 0.00 4.02
475 484 1.659022 TGACCTTCCCCGGTTATTGA 58.341 50.000 0.00 0.00 37.42 2.57
488 497 4.644685 CCGGTTATTGAGGTCCAATCAAAT 59.355 41.667 0.00 0.00 43.96 2.32
591 601 5.446473 CGGAACTCTCGAAATTCAAAGGATG 60.446 44.000 0.00 0.00 0.00 3.51
686 697 4.692155 GGCAACAAATCCTGGAAAGAAATG 59.308 41.667 0.00 0.00 0.00 2.32
724 735 1.581934 CGCGCCTCAGGATTGATTAA 58.418 50.000 0.00 0.00 31.68 1.40
725 736 1.528586 CGCGCCTCAGGATTGATTAAG 59.471 52.381 0.00 0.00 31.68 1.85
733 744 4.539726 TCAGGATTGATTAAGGCATGCTT 58.460 39.130 18.92 7.19 0.00 3.91
829 847 3.975168 TGGCAGTTAGGAAACTACTCC 57.025 47.619 0.00 0.00 44.28 3.85
830 848 3.244582 TGGCAGTTAGGAAACTACTCCA 58.755 45.455 0.00 0.00 44.28 3.86
870 913 0.317160 CTCGTGTGTTGTCCTGCCTA 59.683 55.000 0.00 0.00 0.00 3.93
871 914 0.753867 TCGTGTGTTGTCCTGCCTAA 59.246 50.000 0.00 0.00 0.00 2.69
872 915 0.865769 CGTGTGTTGTCCTGCCTAAC 59.134 55.000 0.00 0.00 0.00 2.34
874 917 0.250124 TGTGTTGTCCTGCCTAACGG 60.250 55.000 0.00 0.00 0.00 4.44
876 919 0.981183 TGTTGTCCTGCCTAACGGAT 59.019 50.000 0.00 0.00 0.00 4.18
879 922 3.008157 TGTTGTCCTGCCTAACGGATTAA 59.992 43.478 0.00 0.00 0.00 1.40
880 923 4.196971 GTTGTCCTGCCTAACGGATTAAT 58.803 43.478 0.00 0.00 0.00 1.40
881 924 4.497291 TGTCCTGCCTAACGGATTAATT 57.503 40.909 0.00 0.00 0.00 1.40
882 925 5.617528 TGTCCTGCCTAACGGATTAATTA 57.382 39.130 0.00 0.00 0.00 1.40
883 926 5.607477 TGTCCTGCCTAACGGATTAATTAG 58.393 41.667 0.00 0.00 0.00 1.73
884 927 5.129815 TGTCCTGCCTAACGGATTAATTAGT 59.870 40.000 0.00 0.00 0.00 2.24
885 928 5.465724 GTCCTGCCTAACGGATTAATTAGTG 59.534 44.000 0.00 0.00 0.00 2.74
886 929 4.213482 CCTGCCTAACGGATTAATTAGTGC 59.787 45.833 0.00 0.00 0.00 4.40
887 930 4.771903 TGCCTAACGGATTAATTAGTGCA 58.228 39.130 0.68 0.00 34.78 4.57
888 931 5.373222 TGCCTAACGGATTAATTAGTGCAT 58.627 37.500 0.00 0.00 33.49 3.96
889 932 5.238432 TGCCTAACGGATTAATTAGTGCATG 59.762 40.000 0.00 0.00 33.49 4.06
890 933 5.689819 CCTAACGGATTAATTAGTGCATGC 58.310 41.667 11.82 11.82 0.00 4.06
891 934 4.568152 AACGGATTAATTAGTGCATGCC 57.432 40.909 16.68 6.65 0.00 4.40
937 980 7.643569 ATTTGCCATACATACAGACATGAAA 57.356 32.000 0.00 0.00 0.00 2.69
958 1014 6.203530 TGAAAGGCGAGTGATTGATATTGATC 59.796 38.462 0.00 0.00 0.00 2.92
962 1018 5.348179 GGCGAGTGATTGATATTGATCTGAG 59.652 44.000 0.00 0.00 32.79 3.35
1013 1076 1.202268 CGATCTACTCCAACCACGACC 60.202 57.143 0.00 0.00 0.00 4.79
1014 1077 1.822990 GATCTACTCCAACCACGACCA 59.177 52.381 0.00 0.00 0.00 4.02
1015 1078 1.254026 TCTACTCCAACCACGACCAG 58.746 55.000 0.00 0.00 0.00 4.00
1016 1079 0.966920 CTACTCCAACCACGACCAGT 59.033 55.000 0.00 0.00 0.00 4.00
1017 1080 0.963962 TACTCCAACCACGACCAGTC 59.036 55.000 0.00 0.00 0.00 3.51
1018 1081 1.004918 CTCCAACCACGACCAGTCC 60.005 63.158 0.00 0.00 0.00 3.85
1019 1082 1.754380 CTCCAACCACGACCAGTCCA 61.754 60.000 0.00 0.00 0.00 4.02
1020 1083 1.597027 CCAACCACGACCAGTCCAC 60.597 63.158 0.00 0.00 0.00 4.02
1032 1095 3.552384 GTCCACCACCACCACCGA 61.552 66.667 0.00 0.00 0.00 4.69
1061 1124 2.486636 GATGACCACGACGACCAGCA 62.487 60.000 0.00 0.00 0.00 4.41
1462 1525 0.108992 ACCGATCGCGCTGTTAGAAA 60.109 50.000 10.32 0.00 35.83 2.52
1470 1536 2.671351 CGCGCTGTTAGAAAGGAGAGAA 60.671 50.000 5.56 0.00 0.00 2.87
1836 1904 1.660614 CGATGTCGATGTAGCCGAGAC 60.661 57.143 0.00 0.00 43.02 3.36
1907 1976 2.283676 ATGTCGAGTCGGGGTGGT 60.284 61.111 13.54 0.00 0.00 4.16
1934 2003 4.070552 GGAAGTCGCCGTGGAGCT 62.071 66.667 0.00 0.00 0.00 4.09
1991 2060 0.677842 GGGTGTCGAAGTAGTGGTGT 59.322 55.000 0.00 0.00 0.00 4.16
2228 2297 1.598130 GGACCTGCACGAGCTGTTT 60.598 57.895 6.36 0.00 42.74 2.83
2314 2383 1.077501 CAGGGCCGATGTCACCAAT 60.078 57.895 0.00 0.00 0.00 3.16
2459 2534 2.360475 GGCGGCCAAAGAAGAGCT 60.360 61.111 15.62 0.00 0.00 4.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 0.041238 ACCTCGGGGACTCTTGATCA 59.959 55.000 9.33 0.00 36.25 2.92
2 3 0.461961 CACCTCGGGGACTCTTGATC 59.538 60.000 9.33 0.00 36.25 2.92
3 4 1.617947 GCACCTCGGGGACTCTTGAT 61.618 60.000 9.33 0.00 36.25 2.57
5 6 0.970937 TAGCACCTCGGGGACTCTTG 60.971 60.000 9.33 0.00 36.25 3.02
7 8 0.252103 TTTAGCACCTCGGGGACTCT 60.252 55.000 9.33 3.90 36.25 3.24
8 9 0.175989 CTTTAGCACCTCGGGGACTC 59.824 60.000 9.33 0.00 36.25 3.36
9 10 1.900545 GCTTTAGCACCTCGGGGACT 61.901 60.000 9.33 7.75 41.59 3.85
10 11 1.449778 GCTTTAGCACCTCGGGGAC 60.450 63.158 9.33 0.00 41.59 4.46
11 12 2.987125 GCTTTAGCACCTCGGGGA 59.013 61.111 9.33 0.00 41.59 4.81
12 13 2.511600 CGCTTTAGCACCTCGGGG 60.512 66.667 0.00 0.00 42.21 5.73
13 14 0.672401 TTTCGCTTTAGCACCTCGGG 60.672 55.000 2.29 0.00 42.21 5.14
14 15 1.153353 TTTTCGCTTTAGCACCTCGG 58.847 50.000 2.29 0.00 42.21 4.63
15 16 2.412847 CCTTTTTCGCTTTAGCACCTCG 60.413 50.000 2.29 0.00 42.21 4.63
16 17 2.095212 CCCTTTTTCGCTTTAGCACCTC 60.095 50.000 2.29 0.00 42.21 3.85
17 18 1.886542 CCCTTTTTCGCTTTAGCACCT 59.113 47.619 2.29 0.00 42.21 4.00
18 19 1.668919 GCCCTTTTTCGCTTTAGCACC 60.669 52.381 2.29 0.00 42.21 5.01
19 20 1.000717 TGCCCTTTTTCGCTTTAGCAC 60.001 47.619 2.29 0.00 42.21 4.40
20 21 1.000717 GTGCCCTTTTTCGCTTTAGCA 60.001 47.619 2.29 0.00 42.21 3.49
21 22 1.000717 TGTGCCCTTTTTCGCTTTAGC 60.001 47.619 0.00 0.00 37.78 3.09
22 23 2.661594 GTGTGCCCTTTTTCGCTTTAG 58.338 47.619 0.00 0.00 0.00 1.85
23 24 1.002251 CGTGTGCCCTTTTTCGCTTTA 60.002 47.619 0.00 0.00 0.00 1.85
24 25 0.248866 CGTGTGCCCTTTTTCGCTTT 60.249 50.000 0.00 0.00 0.00 3.51
25 26 1.358759 CGTGTGCCCTTTTTCGCTT 59.641 52.632 0.00 0.00 0.00 4.68
26 27 2.551912 CCGTGTGCCCTTTTTCGCT 61.552 57.895 0.00 0.00 0.00 4.93
27 28 2.050442 CCGTGTGCCCTTTTTCGC 60.050 61.111 0.00 0.00 0.00 4.70
28 29 2.642700 CCCGTGTGCCCTTTTTCG 59.357 61.111 0.00 0.00 0.00 3.46
29 30 1.815817 ATGCCCGTGTGCCCTTTTTC 61.816 55.000 0.00 0.00 0.00 2.29
30 31 1.406860 AATGCCCGTGTGCCCTTTTT 61.407 50.000 0.00 0.00 0.00 1.94
31 32 1.406860 AAATGCCCGTGTGCCCTTTT 61.407 50.000 0.00 0.00 0.00 2.27
32 33 1.836604 AAATGCCCGTGTGCCCTTT 60.837 52.632 0.00 0.00 0.00 3.11
33 34 2.203625 AAATGCCCGTGTGCCCTT 60.204 55.556 0.00 0.00 0.00 3.95
34 35 2.990967 CAAATGCCCGTGTGCCCT 60.991 61.111 0.00 0.00 0.00 5.19
35 36 4.740431 GCAAATGCCCGTGTGCCC 62.740 66.667 0.00 0.00 34.31 5.36
45 46 0.596600 CATCCATCAGCGGCAAATGC 60.597 55.000 1.45 0.00 41.14 3.56
46 47 1.026584 TCATCCATCAGCGGCAAATG 58.973 50.000 1.45 5.20 0.00 2.32
47 48 1.991121 ATCATCCATCAGCGGCAAAT 58.009 45.000 1.45 0.00 0.00 2.32
48 49 1.766494 AATCATCCATCAGCGGCAAA 58.234 45.000 1.45 0.00 0.00 3.68
49 50 2.636647 TAATCATCCATCAGCGGCAA 57.363 45.000 1.45 0.00 0.00 4.52
50 51 2.865119 ATAATCATCCATCAGCGGCA 57.135 45.000 1.45 0.00 0.00 5.69
51 52 4.510038 AAAATAATCATCCATCAGCGGC 57.490 40.909 0.00 0.00 0.00 6.53
52 53 5.464168 GGAAAAATAATCATCCATCAGCGG 58.536 41.667 0.00 0.00 32.08 5.52
53 54 5.242393 AGGGAAAAATAATCATCCATCAGCG 59.758 40.000 0.00 0.00 33.48 5.18
54 55 6.661304 AGGGAAAAATAATCATCCATCAGC 57.339 37.500 0.00 0.00 33.48 4.26
55 56 8.241497 TCAAGGGAAAAATAATCATCCATCAG 57.759 34.615 0.00 0.00 33.48 2.90
56 57 8.786710 ATCAAGGGAAAAATAATCATCCATCA 57.213 30.769 0.00 0.00 33.48 3.07
58 59 9.093458 GGTATCAAGGGAAAAATAATCATCCAT 57.907 33.333 0.00 0.00 33.48 3.41
59 60 7.508977 GGGTATCAAGGGAAAAATAATCATCCA 59.491 37.037 0.00 0.00 33.48 3.41
60 61 7.730332 AGGGTATCAAGGGAAAAATAATCATCC 59.270 37.037 0.00 0.00 0.00 3.51
61 62 8.712228 AGGGTATCAAGGGAAAAATAATCATC 57.288 34.615 0.00 0.00 0.00 2.92
66 67 9.862149 GAGAATAGGGTATCAAGGGAAAAATAA 57.138 33.333 0.00 0.00 0.00 1.40
67 68 8.154856 CGAGAATAGGGTATCAAGGGAAAAATA 58.845 37.037 0.00 0.00 0.00 1.40
68 69 6.998673 CGAGAATAGGGTATCAAGGGAAAAAT 59.001 38.462 0.00 0.00 0.00 1.82
69 70 6.354130 CGAGAATAGGGTATCAAGGGAAAAA 58.646 40.000 0.00 0.00 0.00 1.94
70 71 5.163237 CCGAGAATAGGGTATCAAGGGAAAA 60.163 44.000 0.00 0.00 0.00 2.29
71 72 4.347000 CCGAGAATAGGGTATCAAGGGAAA 59.653 45.833 0.00 0.00 0.00 3.13
72 73 3.901844 CCGAGAATAGGGTATCAAGGGAA 59.098 47.826 0.00 0.00 0.00 3.97
73 74 3.141460 TCCGAGAATAGGGTATCAAGGGA 59.859 47.826 0.00 0.00 0.00 4.20
74 75 3.258622 GTCCGAGAATAGGGTATCAAGGG 59.741 52.174 0.00 0.00 0.00 3.95
75 76 3.895656 TGTCCGAGAATAGGGTATCAAGG 59.104 47.826 0.00 0.00 0.00 3.61
76 77 5.069251 ACTTGTCCGAGAATAGGGTATCAAG 59.931 44.000 0.00 0.00 35.74 3.02
77 78 4.960469 ACTTGTCCGAGAATAGGGTATCAA 59.040 41.667 0.00 0.00 0.00 2.57
78 79 4.543689 ACTTGTCCGAGAATAGGGTATCA 58.456 43.478 0.00 0.00 0.00 2.15
79 80 5.532664 AACTTGTCCGAGAATAGGGTATC 57.467 43.478 0.00 0.00 0.00 2.24
80 81 5.424252 TGAAACTTGTCCGAGAATAGGGTAT 59.576 40.000 0.00 0.00 0.00 2.73
81 82 4.773674 TGAAACTTGTCCGAGAATAGGGTA 59.226 41.667 0.00 0.00 0.00 3.69
82 83 3.581332 TGAAACTTGTCCGAGAATAGGGT 59.419 43.478 0.00 0.00 0.00 4.34
83 84 4.202245 TGAAACTTGTCCGAGAATAGGG 57.798 45.455 0.00 0.00 0.00 3.53
84 85 5.292101 GTGATGAAACTTGTCCGAGAATAGG 59.708 44.000 0.00 0.00 0.00 2.57
85 86 5.869344 TGTGATGAAACTTGTCCGAGAATAG 59.131 40.000 0.00 0.00 0.00 1.73
86 87 5.789521 TGTGATGAAACTTGTCCGAGAATA 58.210 37.500 0.00 0.00 0.00 1.75
87 88 4.641396 TGTGATGAAACTTGTCCGAGAAT 58.359 39.130 0.00 0.00 0.00 2.40
88 89 4.066646 TGTGATGAAACTTGTCCGAGAA 57.933 40.909 0.00 0.00 0.00 2.87
89 90 3.744238 TGTGATGAAACTTGTCCGAGA 57.256 42.857 0.00 0.00 0.00 4.04
90 91 4.273480 ACTTTGTGATGAAACTTGTCCGAG 59.727 41.667 0.00 0.00 0.00 4.63
91 92 4.196193 ACTTTGTGATGAAACTTGTCCGA 58.804 39.130 0.00 0.00 0.00 4.55
92 93 4.552166 ACTTTGTGATGAAACTTGTCCG 57.448 40.909 0.00 0.00 0.00 4.79
93 94 8.696410 TTTTAACTTTGTGATGAAACTTGTCC 57.304 30.769 0.00 0.00 0.00 4.02
94 95 9.952341 GTTTTTAACTTTGTGATGAAACTTGTC 57.048 29.630 0.00 0.00 0.00 3.18
95 96 8.931775 GGTTTTTAACTTTGTGATGAAACTTGT 58.068 29.630 0.00 0.00 0.00 3.16
96 97 8.930760 TGGTTTTTAACTTTGTGATGAAACTTG 58.069 29.630 0.00 0.00 0.00 3.16
97 98 9.150348 CTGGTTTTTAACTTTGTGATGAAACTT 57.850 29.630 0.00 0.00 0.00 2.66
98 99 8.527810 TCTGGTTTTTAACTTTGTGATGAAACT 58.472 29.630 0.00 0.00 0.00 2.66
99 100 8.696410 TCTGGTTTTTAACTTTGTGATGAAAC 57.304 30.769 0.00 0.00 0.00 2.78
100 101 9.712305 TTTCTGGTTTTTAACTTTGTGATGAAA 57.288 25.926 0.00 0.00 0.00 2.69
101 102 9.712305 TTTTCTGGTTTTTAACTTTGTGATGAA 57.288 25.926 0.00 0.00 0.00 2.57
102 103 9.712305 TTTTTCTGGTTTTTAACTTTGTGATGA 57.288 25.926 0.00 0.00 0.00 2.92
174 175 1.920325 CCCTGGGTGCTTCCTCTGA 60.920 63.158 3.97 0.00 36.25 3.27
247 248 3.643763 AGTCTCACAACGATCACTTGTC 58.356 45.455 3.30 0.00 29.02 3.18
279 280 2.747989 GGGAGCAACTAGTTAACAAGCC 59.252 50.000 8.04 6.78 0.00 4.35
335 336 7.272084 GCCCTCGTTACTGTGTATATTAATACG 59.728 40.741 0.00 0.00 40.84 3.06
336 337 7.543520 GGCCCTCGTTACTGTGTATATTAATAC 59.456 40.741 0.00 0.00 38.80 1.89
359 368 1.742831 TCATATTTGACGTTGCAGGCC 59.257 47.619 0.00 0.00 0.00 5.19
403 412 1.299648 CGGCCCAGGTTCAAGATCA 59.700 57.895 0.00 0.00 0.00 2.92
421 430 6.147985 CCTCCTTGTAAAAGCAGACTAGAAAC 59.852 42.308 0.00 0.00 0.00 2.78
460 469 1.134189 GGACCTCAATAACCGGGGAAG 60.134 57.143 6.32 0.00 0.00 3.46
475 484 8.598041 GGTAGACAGATATATTTGATTGGACCT 58.402 37.037 10.08 0.00 0.00 3.85
546 556 9.704098 GTTCCGTCTAAAAAGATCATATGTTTC 57.296 33.333 1.90 1.73 0.00 2.78
558 568 6.707599 ATTTCGAGAGTTCCGTCTAAAAAG 57.292 37.500 0.00 0.00 0.00 2.27
591 601 5.292834 GGATTAGTTTCCAGTTAACCGCTAC 59.707 44.000 0.88 0.00 35.72 3.58
724 735 3.289836 TGCACACATATAAAGCATGCCT 58.710 40.909 15.66 4.37 0.00 4.75
725 736 3.713858 TGCACACATATAAAGCATGCC 57.286 42.857 15.66 0.00 0.00 4.40
829 847 6.690098 CGAGAAGATTATTTGTTTCCATGCTG 59.310 38.462 0.00 0.00 0.00 4.41
830 848 6.375455 ACGAGAAGATTATTTGTTTCCATGCT 59.625 34.615 0.00 0.00 0.00 3.79
870 913 3.951037 TGGCATGCACTAATTAATCCGTT 59.049 39.130 21.36 0.00 0.00 4.44
871 914 3.550820 TGGCATGCACTAATTAATCCGT 58.449 40.909 21.36 0.00 0.00 4.69
872 915 4.771590 ATGGCATGCACTAATTAATCCG 57.228 40.909 21.36 0.00 0.00 4.18
876 919 9.836864 CCTAGATATATGGCATGCACTAATTAA 57.163 33.333 21.36 0.00 0.00 1.40
879 922 6.294473 GCCTAGATATATGGCATGCACTAAT 58.706 40.000 21.36 9.62 45.46 1.73
880 923 5.674525 GCCTAGATATATGGCATGCACTAA 58.325 41.667 21.36 1.71 45.46 2.24
881 924 5.282055 GCCTAGATATATGGCATGCACTA 57.718 43.478 21.36 10.44 45.46 2.74
882 925 4.148128 GCCTAGATATATGGCATGCACT 57.852 45.455 21.36 8.30 45.46 4.40
937 980 5.011431 TCAGATCAATATCAATCACTCGCCT 59.989 40.000 0.00 0.00 34.28 5.52
972 1035 4.022589 TCGAGGTGAACGAGTAGATTGTTT 60.023 41.667 0.00 0.00 35.52 2.83
1013 1076 2.113139 GGTGGTGGTGGTGGACTG 59.887 66.667 0.00 0.00 0.00 3.51
1014 1077 3.556306 CGGTGGTGGTGGTGGACT 61.556 66.667 0.00 0.00 0.00 3.85
1015 1078 3.552384 TCGGTGGTGGTGGTGGAC 61.552 66.667 0.00 0.00 0.00 4.02
1016 1079 3.552384 GTCGGTGGTGGTGGTGGA 61.552 66.667 0.00 0.00 0.00 4.02
1017 1080 3.867783 TGTCGGTGGTGGTGGTGG 61.868 66.667 0.00 0.00 0.00 4.61
1018 1081 2.590575 GTGTCGGTGGTGGTGGTG 60.591 66.667 0.00 0.00 0.00 4.17
1019 1082 3.868985 GGTGTCGGTGGTGGTGGT 61.869 66.667 0.00 0.00 0.00 4.16
1020 1083 2.690653 ATTGGTGTCGGTGGTGGTGG 62.691 60.000 0.00 0.00 0.00 4.61
1032 1095 1.001520 TCGTGGTCATCGAATTGGTGT 59.998 47.619 0.00 0.00 34.36 4.16
1061 1124 2.270205 CATGGCCTGTCTCCGCTT 59.730 61.111 3.32 0.00 0.00 4.68
1462 1525 3.077359 CGCAACAATTCCTTTCTCTCCT 58.923 45.455 0.00 0.00 0.00 3.69
1470 1536 5.221303 CCATCATATTCCGCAACAATTCCTT 60.221 40.000 0.00 0.00 0.00 3.36
1667 1735 1.972223 CTCCAGTCTGACCGTCCGT 60.972 63.158 3.76 0.00 0.00 4.69
1836 1904 1.362717 CGGCTACACCATCCTACGG 59.637 63.158 0.00 0.00 39.03 4.02
1907 1976 2.974489 GCGACTTCCTCGACACCGA 61.974 63.158 0.00 0.00 46.14 4.69
1991 2060 2.811431 CAACAACATCTTCTTACCGGCA 59.189 45.455 0.00 0.00 0.00 5.69
2099 2168 1.872952 TCAACTTCGTCTTCGTCCGTA 59.127 47.619 0.00 0.00 38.33 4.02
2228 2297 1.215382 CGACTTCTCCGACATGGCA 59.785 57.895 0.00 0.00 37.80 4.92
2314 2383 0.250858 TTCGTCTACTCCGACCACCA 60.251 55.000 0.00 0.00 33.41 4.17


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

AutoCloner maintained by Alex Coulton.