Multiple sequence alignment - TraesCS5B01G107900

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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 TraesCS5B01G107900 chr5B 100.000 2553 0 0 1 2553 146913682 146916234 0.000000e+00 4715
1 TraesCS5B01G107900 chr5B 91.525 118 7 2 64 179 561938494 561938610 2.630000e-35 159
2 TraesCS5B01G107900 chr5D 95.787 2445 62 12 142 2553 135238650 135241086 0.000000e+00 3906
3 TraesCS5B01G107900 chr5A 91.803 2318 98 44 273 2553 169818289 169816027 0.000000e+00 3144
4 TraesCS5B01G107900 chr1B 97.000 100 3 0 66 165 4065556 4065655 4.370000e-38 169
5 TraesCS5B01G107900 chr7B 96.970 99 3 0 69 167 565053178 565053276 1.570000e-37 167
6 TraesCS5B01G107900 chr2A 95.146 103 5 0 69 171 619208128 619208026 2.030000e-36 163
7 TraesCS5B01G107900 chr4B 94.286 105 6 0 65 169 498378613 498378509 7.310000e-36 161
8 TraesCS5B01G107900 chr3B 92.241 116 6 3 54 167 560117285 560117399 7.310000e-36 161
9 TraesCS5B01G107900 chr7D 92.727 110 8 0 64 173 561963432 561963323 2.630000e-35 159
10 TraesCS5B01G107900 chr2B 93.396 106 6 1 61 165 403101601 403101706 3.400000e-34 156
11 TraesCS5B01G107900 chr1D 92.593 108 8 0 62 169 483907575 483907682 3.400000e-34 156


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 TraesCS5B01G107900 chr5B 146913682 146916234 2552 False 4715 4715 100.000 1 2553 1 chr5B.!!$F1 2552
1 TraesCS5B01G107900 chr5D 135238650 135241086 2436 False 3906 3906 95.787 142 2553 1 chr5D.!!$F1 2411
2 TraesCS5B01G107900 chr5A 169816027 169818289 2262 True 3144 3144 91.803 273 2553 1 chr5A.!!$R1 2280

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
45 46 0.107945 AGAGCAAGGAACGGAGATGC 60.108 55.0 0.0 0.0 37.28 3.91 F
85 86 0.115745 ACTACTCCCTCCGTCCCAAA 59.884 55.0 0.0 0.0 0.00 3.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1330 1367 1.274728 CCAGTTGCTAGTGTCAGCTCT 59.725 52.381 2.31 0.0 42.3 4.09 R
1695 1735 2.024414 ACTTCTTCTTGGTGTTGGTGC 58.976 47.619 0.00 0.0 0.0 5.01 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
21 22 4.715527 TTAGTAGTTTCTCTCGGGAAGC 57.284 45.455 0.00 0.00 0.00 3.86
22 23 2.526432 AGTAGTTTCTCTCGGGAAGCA 58.474 47.619 0.00 0.00 0.00 3.91
23 24 3.100671 AGTAGTTTCTCTCGGGAAGCAT 58.899 45.455 0.00 0.00 0.00 3.79
24 25 4.279145 AGTAGTTTCTCTCGGGAAGCATA 58.721 43.478 0.00 0.00 0.00 3.14
25 26 4.896482 AGTAGTTTCTCTCGGGAAGCATAT 59.104 41.667 0.00 0.00 0.00 1.78
26 27 6.069331 AGTAGTTTCTCTCGGGAAGCATATA 58.931 40.000 0.00 0.00 0.00 0.86
27 28 5.461032 AGTTTCTCTCGGGAAGCATATAG 57.539 43.478 0.00 0.00 0.00 1.31
28 29 5.141182 AGTTTCTCTCGGGAAGCATATAGA 58.859 41.667 0.00 0.00 0.00 1.98
29 30 5.242838 AGTTTCTCTCGGGAAGCATATAGAG 59.757 44.000 0.00 0.00 33.37 2.43
30 31 3.085533 TCTCTCGGGAAGCATATAGAGC 58.914 50.000 0.00 0.00 32.38 4.09
31 32 2.822561 CTCTCGGGAAGCATATAGAGCA 59.177 50.000 0.00 0.00 0.00 4.26
32 33 3.230976 TCTCGGGAAGCATATAGAGCAA 58.769 45.455 3.18 0.00 0.00 3.91
33 34 3.256879 TCTCGGGAAGCATATAGAGCAAG 59.743 47.826 3.18 0.00 0.00 4.01
34 35 2.300152 TCGGGAAGCATATAGAGCAAGG 59.700 50.000 3.18 0.00 0.00 3.61
35 36 2.300152 CGGGAAGCATATAGAGCAAGGA 59.700 50.000 3.18 0.00 0.00 3.36
36 37 3.244215 CGGGAAGCATATAGAGCAAGGAA 60.244 47.826 3.18 0.00 0.00 3.36
37 38 4.068599 GGGAAGCATATAGAGCAAGGAAC 58.931 47.826 3.18 0.00 0.00 3.62
38 39 3.743396 GGAAGCATATAGAGCAAGGAACG 59.257 47.826 3.18 0.00 0.00 3.95
39 40 3.393089 AGCATATAGAGCAAGGAACGG 57.607 47.619 3.18 0.00 0.00 4.44
40 41 2.965831 AGCATATAGAGCAAGGAACGGA 59.034 45.455 3.18 0.00 0.00 4.69
41 42 3.006323 AGCATATAGAGCAAGGAACGGAG 59.994 47.826 3.18 0.00 0.00 4.63
42 43 3.005897 GCATATAGAGCAAGGAACGGAGA 59.994 47.826 0.00 0.00 0.00 3.71
43 44 4.322349 GCATATAGAGCAAGGAACGGAGAT 60.322 45.833 0.00 0.00 0.00 2.75
44 45 3.742433 ATAGAGCAAGGAACGGAGATG 57.258 47.619 0.00 0.00 0.00 2.90
45 46 0.107945 AGAGCAAGGAACGGAGATGC 60.108 55.000 0.00 0.00 37.28 3.91
46 47 0.391661 GAGCAAGGAACGGAGATGCA 60.392 55.000 0.00 0.00 39.42 3.96
47 48 0.392193 AGCAAGGAACGGAGATGCAG 60.392 55.000 0.00 0.00 39.42 4.41
48 49 0.391661 GCAAGGAACGGAGATGCAGA 60.392 55.000 0.00 0.00 37.00 4.26
49 50 1.945819 GCAAGGAACGGAGATGCAGAA 60.946 52.381 0.00 0.00 37.00 3.02
50 51 2.636830 CAAGGAACGGAGATGCAGAAT 58.363 47.619 0.00 0.00 0.00 2.40
51 52 3.012518 CAAGGAACGGAGATGCAGAATT 58.987 45.455 0.00 0.00 0.00 2.17
52 53 4.191544 CAAGGAACGGAGATGCAGAATTA 58.808 43.478 0.00 0.00 0.00 1.40
53 54 4.696479 AGGAACGGAGATGCAGAATTAT 57.304 40.909 0.00 0.00 0.00 1.28
54 55 4.384056 AGGAACGGAGATGCAGAATTATG 58.616 43.478 0.00 0.00 0.00 1.90
55 56 3.058639 GGAACGGAGATGCAGAATTATGC 60.059 47.826 18.03 18.03 46.68 3.14
56 57 2.498167 ACGGAGATGCAGAATTATGCC 58.502 47.619 21.56 7.82 45.91 4.40
57 58 1.462283 CGGAGATGCAGAATTATGCCG 59.538 52.381 21.56 13.44 45.91 5.69
58 59 2.498167 GGAGATGCAGAATTATGCCGT 58.502 47.619 21.56 10.83 45.91 5.68
59 60 3.664107 GGAGATGCAGAATTATGCCGTA 58.336 45.455 21.56 4.31 45.91 4.02
60 61 4.256920 GGAGATGCAGAATTATGCCGTAT 58.743 43.478 21.56 9.18 45.91 3.06
61 62 4.697352 GGAGATGCAGAATTATGCCGTATT 59.303 41.667 21.56 3.77 45.91 1.89
62 63 5.182001 GGAGATGCAGAATTATGCCGTATTT 59.818 40.000 21.56 4.76 45.91 1.40
63 64 6.294176 GGAGATGCAGAATTATGCCGTATTTT 60.294 38.462 21.56 2.79 45.91 1.82
64 65 6.672147 AGATGCAGAATTATGCCGTATTTTC 58.328 36.000 21.56 7.66 45.91 2.29
65 66 6.488006 AGATGCAGAATTATGCCGTATTTTCT 59.512 34.615 21.56 9.50 45.91 2.52
66 67 7.661437 AGATGCAGAATTATGCCGTATTTTCTA 59.339 33.333 21.56 0.00 45.91 2.10
67 68 6.954944 TGCAGAATTATGCCGTATTTTCTAC 58.045 36.000 21.56 0.00 45.91 2.59
68 69 6.765989 TGCAGAATTATGCCGTATTTTCTACT 59.234 34.615 21.56 0.00 45.91 2.57
69 70 7.929245 TGCAGAATTATGCCGTATTTTCTACTA 59.071 33.333 21.56 0.00 45.91 1.82
70 71 8.221766 GCAGAATTATGCCGTATTTTCTACTAC 58.778 37.037 14.15 0.00 40.43 2.73
71 72 9.477484 CAGAATTATGCCGTATTTTCTACTACT 57.523 33.333 0.00 0.00 0.00 2.57
72 73 9.694137 AGAATTATGCCGTATTTTCTACTACTC 57.306 33.333 0.00 0.00 0.00 2.59
73 74 8.828688 AATTATGCCGTATTTTCTACTACTCC 57.171 34.615 0.00 0.00 0.00 3.85
74 75 4.660789 TGCCGTATTTTCTACTACTCCC 57.339 45.455 0.00 0.00 0.00 4.30
75 76 4.284178 TGCCGTATTTTCTACTACTCCCT 58.716 43.478 0.00 0.00 0.00 4.20
76 77 4.340381 TGCCGTATTTTCTACTACTCCCTC 59.660 45.833 0.00 0.00 0.00 4.30
77 78 4.261952 GCCGTATTTTCTACTACTCCCTCC 60.262 50.000 0.00 0.00 0.00 4.30
78 79 4.023365 CCGTATTTTCTACTACTCCCTCCG 60.023 50.000 0.00 0.00 0.00 4.63
79 80 4.578105 CGTATTTTCTACTACTCCCTCCGT 59.422 45.833 0.00 0.00 0.00 4.69
80 81 5.277731 CGTATTTTCTACTACTCCCTCCGTC 60.278 48.000 0.00 0.00 0.00 4.79
81 82 2.725221 TTCTACTACTCCCTCCGTCC 57.275 55.000 0.00 0.00 0.00 4.79
82 83 0.842635 TCTACTACTCCCTCCGTCCC 59.157 60.000 0.00 0.00 0.00 4.46
83 84 0.549950 CTACTACTCCCTCCGTCCCA 59.450 60.000 0.00 0.00 0.00 4.37
84 85 1.002069 TACTACTCCCTCCGTCCCAA 58.998 55.000 0.00 0.00 0.00 4.12
85 86 0.115745 ACTACTCCCTCCGTCCCAAA 59.884 55.000 0.00 0.00 0.00 3.28
86 87 1.272807 CTACTCCCTCCGTCCCAAAA 58.727 55.000 0.00 0.00 0.00 2.44
87 88 1.838077 CTACTCCCTCCGTCCCAAAAT 59.162 52.381 0.00 0.00 0.00 1.82
88 89 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
89 90 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
90 91 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
91 92 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
92 93 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
93 94 2.290705 CCCTCCGTCCCAAAATAAGTGT 60.291 50.000 0.00 0.00 0.00 3.55
94 95 3.007635 CCTCCGTCCCAAAATAAGTGTC 58.992 50.000 0.00 0.00 0.00 3.67
95 96 3.307480 CCTCCGTCCCAAAATAAGTGTCT 60.307 47.826 0.00 0.00 0.00 3.41
96 97 3.933332 CTCCGTCCCAAAATAAGTGTCTC 59.067 47.826 0.00 0.00 0.00 3.36
97 98 3.325425 TCCGTCCCAAAATAAGTGTCTCA 59.675 43.478 0.00 0.00 0.00 3.27
98 99 4.069304 CCGTCCCAAAATAAGTGTCTCAA 58.931 43.478 0.00 0.00 0.00 3.02
99 100 4.083484 CCGTCCCAAAATAAGTGTCTCAAC 60.083 45.833 0.00 0.00 0.00 3.18
100 101 4.755123 CGTCCCAAAATAAGTGTCTCAACT 59.245 41.667 0.00 0.00 0.00 3.16
101 102 5.238650 CGTCCCAAAATAAGTGTCTCAACTT 59.761 40.000 0.00 0.00 42.89 2.66
102 103 6.238648 CGTCCCAAAATAAGTGTCTCAACTTT 60.239 38.462 0.00 0.00 40.77 2.66
103 104 6.918022 GTCCCAAAATAAGTGTCTCAACTTTG 59.082 38.462 0.00 0.00 40.77 2.77
104 105 6.605594 TCCCAAAATAAGTGTCTCAACTTTGT 59.394 34.615 0.00 0.00 40.77 2.83
105 106 7.776030 TCCCAAAATAAGTGTCTCAACTTTGTA 59.224 33.333 0.00 0.00 40.77 2.41
106 107 7.860872 CCCAAAATAAGTGTCTCAACTTTGTAC 59.139 37.037 0.00 0.00 40.77 2.90
107 108 8.621286 CCAAAATAAGTGTCTCAACTTTGTACT 58.379 33.333 0.00 0.00 40.77 2.73
110 111 8.828688 AATAAGTGTCTCAACTTTGTACTACC 57.171 34.615 0.00 0.00 40.77 3.18
111 112 6.481434 AAGTGTCTCAACTTTGTACTACCT 57.519 37.500 0.00 0.00 37.05 3.08
112 113 6.481434 AGTGTCTCAACTTTGTACTACCTT 57.519 37.500 0.00 0.00 0.00 3.50
113 114 6.885922 AGTGTCTCAACTTTGTACTACCTTT 58.114 36.000 0.00 0.00 0.00 3.11
114 115 8.015185 AGTGTCTCAACTTTGTACTACCTTTA 57.985 34.615 0.00 0.00 0.00 1.85
115 116 8.142551 AGTGTCTCAACTTTGTACTACCTTTAG 58.857 37.037 0.00 0.00 0.00 1.85
116 117 7.924947 GTGTCTCAACTTTGTACTACCTTTAGT 59.075 37.037 0.00 0.00 41.69 2.24
117 118 9.135189 TGTCTCAACTTTGTACTACCTTTAGTA 57.865 33.333 0.00 0.00 39.43 1.82
130 131 8.130671 ACTACCTTTAGTACAAATCTGTGCTA 57.869 34.615 0.00 0.00 45.53 3.49
136 137 5.152623 AGTACAAATCTGTGCTAAGCTCA 57.847 39.130 0.00 0.00 45.53 4.26
137 138 5.551233 AGTACAAATCTGTGCTAAGCTCAA 58.449 37.500 0.00 0.00 45.53 3.02
138 139 5.641209 AGTACAAATCTGTGCTAAGCTCAAG 59.359 40.000 0.00 0.00 45.53 3.02
139 140 4.645535 ACAAATCTGTGCTAAGCTCAAGA 58.354 39.130 0.32 0.00 33.30 3.02
140 141 4.453819 ACAAATCTGTGCTAAGCTCAAGAC 59.546 41.667 0.32 0.00 33.30 3.01
141 142 3.969287 ATCTGTGCTAAGCTCAAGACA 57.031 42.857 0.32 2.10 31.71 3.41
142 143 3.032017 TCTGTGCTAAGCTCAAGACAC 57.968 47.619 12.53 12.53 31.71 3.67
143 144 2.630098 TCTGTGCTAAGCTCAAGACACT 59.370 45.455 16.78 0.00 31.71 3.55
144 145 3.070159 TCTGTGCTAAGCTCAAGACACTT 59.930 43.478 16.78 0.00 31.71 3.16
145 146 4.280929 TCTGTGCTAAGCTCAAGACACTTA 59.719 41.667 16.78 0.00 31.71 2.24
146 147 5.047021 TCTGTGCTAAGCTCAAGACACTTAT 60.047 40.000 16.78 0.00 31.71 1.73
147 148 5.551233 TGTGCTAAGCTCAAGACACTTATT 58.449 37.500 16.78 0.00 0.00 1.40
148 149 5.997746 TGTGCTAAGCTCAAGACACTTATTT 59.002 36.000 16.78 0.00 0.00 1.40
149 150 6.486657 TGTGCTAAGCTCAAGACACTTATTTT 59.513 34.615 16.78 0.00 0.00 1.82
150 151 7.659799 TGTGCTAAGCTCAAGACACTTATTTTA 59.340 33.333 16.78 2.30 0.00 1.52
151 152 8.171840 GTGCTAAGCTCAAGACACTTATTTTAG 58.828 37.037 12.32 0.00 0.00 1.85
152 153 7.334421 TGCTAAGCTCAAGACACTTATTTTAGG 59.666 37.037 0.32 0.00 0.00 2.69
173 174 5.323581 AGGACGGAGGGAGTATAATTCTAC 58.676 45.833 0.00 0.00 0.00 2.59
270 274 3.152341 CACTGAAAGGCTGATGGAGTTT 58.848 45.455 0.00 0.00 39.30 2.66
295 299 6.445786 TGGGTACAGATAGGAAAACCTACATT 59.554 38.462 0.00 0.00 0.00 2.71
345 350 6.523840 AGAAGCCAAAATTAGAATTGTGCAA 58.476 32.000 0.00 0.00 33.23 4.08
388 394 8.103305 TGATCAGACCTAAAAATGCTTCTTACT 58.897 33.333 0.00 0.00 0.00 2.24
389 395 7.672983 TCAGACCTAAAAATGCTTCTTACTG 57.327 36.000 0.00 0.00 0.00 2.74
434 440 5.480422 TCTTAGCAGTCCTAATTGTCTGACA 59.520 40.000 6.36 6.36 35.56 3.58
467 479 4.461081 AGCTCCCTTCATATGATCTACGAC 59.539 45.833 6.17 0.00 0.00 4.34
553 585 5.995282 ACATTTCTCGACAGAATAACAACCA 59.005 36.000 0.00 0.00 38.50 3.67
559 592 4.039973 TCGACAGAATAACAACCAGGTCTT 59.960 41.667 0.00 0.00 0.00 3.01
779 812 6.952773 AGAACTTGTACAGAGCTATAGAGG 57.047 41.667 3.21 0.00 0.00 3.69
873 906 1.086696 GACACGCAACCAGCACATAT 58.913 50.000 0.00 0.00 46.13 1.78
893 926 7.324375 CACATATACAAAGCTCCAATTATTGCG 59.676 37.037 0.00 0.00 0.00 4.85
1014 1047 4.249661 GGTGAGAGATGGAGAAGAAACAC 58.750 47.826 0.00 0.00 0.00 3.32
1104 1138 9.238368 AGAAGTAGTGCCATCTTCTATCTATAC 57.762 37.037 5.09 0.00 43.71 1.47
1125 1159 4.658063 ACTGGTGGAAATATTGAACGGAA 58.342 39.130 0.00 0.00 0.00 4.30
1256 1293 5.201713 GGATACTCAACCAGAATCGATGA 57.798 43.478 0.00 0.00 0.00 2.92
1330 1367 2.297698 TCACCGAGGACTTCAACCTA 57.702 50.000 0.00 0.00 37.93 3.08
1465 1502 2.471815 TCCCCGAGTCCAATGTAGAT 57.528 50.000 0.00 0.00 0.00 1.98
1703 1743 5.534207 AATCATTTCAAAGAGCACCAACA 57.466 34.783 0.00 0.00 0.00 3.33
1711 1751 1.972872 AGAGCACCAACACCAAGAAG 58.027 50.000 0.00 0.00 0.00 2.85
2007 2049 1.066454 AGCCAAAACTGTACGCAAACC 59.934 47.619 0.00 0.00 0.00 3.27
2139 2182 2.432300 CGGCCCCGTCATAGTTCCT 61.432 63.158 0.00 0.00 34.35 3.36
2332 2376 2.775911 TCCTCAGTTCAGATTGCTGG 57.224 50.000 0.00 0.00 42.53 4.85
2388 2433 7.691993 ATATCAGGGACTTAACATTACCTGT 57.308 36.000 8.22 0.10 44.39 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.084287 TGCTTCCCGAGAGAAACTACTAA 58.916 43.478 0.00 0.00 0.00 2.24
1 2 3.693807 TGCTTCCCGAGAGAAACTACTA 58.306 45.455 0.00 0.00 0.00 1.82
2 3 2.526432 TGCTTCCCGAGAGAAACTACT 58.474 47.619 0.00 0.00 0.00 2.57
3 4 3.528597 ATGCTTCCCGAGAGAAACTAC 57.471 47.619 0.00 0.00 0.00 2.73
4 5 6.304624 TCTATATGCTTCCCGAGAGAAACTA 58.695 40.000 0.00 0.00 0.00 2.24
5 6 5.141182 TCTATATGCTTCCCGAGAGAAACT 58.859 41.667 0.00 0.00 0.00 2.66
6 7 5.455056 TCTATATGCTTCCCGAGAGAAAC 57.545 43.478 0.00 0.00 0.00 2.78
10 11 2.822561 TGCTCTATATGCTTCCCGAGAG 59.177 50.000 0.00 0.00 34.77 3.20
11 12 2.876581 TGCTCTATATGCTTCCCGAGA 58.123 47.619 0.00 0.00 0.00 4.04
12 13 3.583806 CTTGCTCTATATGCTTCCCGAG 58.416 50.000 0.00 0.00 0.00 4.63
13 14 2.300152 CCTTGCTCTATATGCTTCCCGA 59.700 50.000 0.00 0.00 0.00 5.14
14 15 2.300152 TCCTTGCTCTATATGCTTCCCG 59.700 50.000 0.00 0.00 0.00 5.14
15 16 4.068599 GTTCCTTGCTCTATATGCTTCCC 58.931 47.826 0.00 0.00 0.00 3.97
16 17 3.743396 CGTTCCTTGCTCTATATGCTTCC 59.257 47.826 0.00 0.00 0.00 3.46
17 18 3.743396 CCGTTCCTTGCTCTATATGCTTC 59.257 47.826 0.00 0.00 0.00 3.86
18 19 3.388024 TCCGTTCCTTGCTCTATATGCTT 59.612 43.478 0.00 0.00 0.00 3.91
19 20 2.965831 TCCGTTCCTTGCTCTATATGCT 59.034 45.455 0.00 0.00 0.00 3.79
20 21 3.005897 TCTCCGTTCCTTGCTCTATATGC 59.994 47.826 0.00 0.00 0.00 3.14
21 22 4.855715 TCTCCGTTCCTTGCTCTATATG 57.144 45.455 0.00 0.00 0.00 1.78
22 23 4.322349 GCATCTCCGTTCCTTGCTCTATAT 60.322 45.833 0.00 0.00 0.00 0.86
23 24 3.005897 GCATCTCCGTTCCTTGCTCTATA 59.994 47.826 0.00 0.00 0.00 1.31
24 25 2.224161 GCATCTCCGTTCCTTGCTCTAT 60.224 50.000 0.00 0.00 0.00 1.98
25 26 1.137086 GCATCTCCGTTCCTTGCTCTA 59.863 52.381 0.00 0.00 0.00 2.43
26 27 0.107945 GCATCTCCGTTCCTTGCTCT 60.108 55.000 0.00 0.00 0.00 4.09
27 28 0.391661 TGCATCTCCGTTCCTTGCTC 60.392 55.000 0.00 0.00 34.47 4.26
28 29 0.392193 CTGCATCTCCGTTCCTTGCT 60.392 55.000 0.00 0.00 34.47 3.91
29 30 0.391661 TCTGCATCTCCGTTCCTTGC 60.392 55.000 0.00 0.00 0.00 4.01
30 31 2.099141 TTCTGCATCTCCGTTCCTTG 57.901 50.000 0.00 0.00 0.00 3.61
31 32 3.356529 AATTCTGCATCTCCGTTCCTT 57.643 42.857 0.00 0.00 0.00 3.36
32 33 4.384056 CATAATTCTGCATCTCCGTTCCT 58.616 43.478 0.00 0.00 0.00 3.36
33 34 3.058639 GCATAATTCTGCATCTCCGTTCC 60.059 47.826 10.68 0.00 41.87 3.62
34 35 3.058639 GGCATAATTCTGCATCTCCGTTC 60.059 47.826 16.60 0.00 44.12 3.95
35 36 2.880890 GGCATAATTCTGCATCTCCGTT 59.119 45.455 16.60 0.00 44.12 4.44
36 37 2.498167 GGCATAATTCTGCATCTCCGT 58.502 47.619 16.60 0.00 44.12 4.69
37 38 1.462283 CGGCATAATTCTGCATCTCCG 59.538 52.381 16.60 7.42 44.12 4.63
38 39 2.498167 ACGGCATAATTCTGCATCTCC 58.502 47.619 16.60 0.00 44.12 3.71
39 40 5.869753 AATACGGCATAATTCTGCATCTC 57.130 39.130 16.60 0.00 44.12 2.75
40 41 6.488006 AGAAAATACGGCATAATTCTGCATCT 59.512 34.615 16.60 6.16 44.12 2.90
41 42 6.672147 AGAAAATACGGCATAATTCTGCATC 58.328 36.000 16.60 0.83 44.12 3.91
42 43 6.639632 AGAAAATACGGCATAATTCTGCAT 57.360 33.333 16.60 7.43 44.12 3.96
43 44 6.765989 AGTAGAAAATACGGCATAATTCTGCA 59.234 34.615 16.60 0.00 44.12 4.41
44 45 7.190920 AGTAGAAAATACGGCATAATTCTGC 57.809 36.000 7.26 7.26 41.53 4.26
45 46 9.477484 AGTAGTAGAAAATACGGCATAATTCTG 57.523 33.333 3.26 0.00 30.08 3.02
46 47 9.694137 GAGTAGTAGAAAATACGGCATAATTCT 57.306 33.333 0.00 0.00 31.48 2.40
47 48 8.923683 GGAGTAGTAGAAAATACGGCATAATTC 58.076 37.037 0.00 0.00 0.00 2.17
48 49 7.876582 GGGAGTAGTAGAAAATACGGCATAATT 59.123 37.037 0.00 0.00 0.00 1.40
49 50 7.234988 AGGGAGTAGTAGAAAATACGGCATAAT 59.765 37.037 0.00 0.00 0.00 1.28
50 51 6.552350 AGGGAGTAGTAGAAAATACGGCATAA 59.448 38.462 0.00 0.00 0.00 1.90
51 52 6.073314 AGGGAGTAGTAGAAAATACGGCATA 58.927 40.000 0.00 0.00 0.00 3.14
52 53 4.900054 AGGGAGTAGTAGAAAATACGGCAT 59.100 41.667 0.00 0.00 0.00 4.40
53 54 4.284178 AGGGAGTAGTAGAAAATACGGCA 58.716 43.478 0.00 0.00 0.00 5.69
54 55 4.261952 GGAGGGAGTAGTAGAAAATACGGC 60.262 50.000 0.00 0.00 0.00 5.68
55 56 4.023365 CGGAGGGAGTAGTAGAAAATACGG 60.023 50.000 0.00 0.00 0.00 4.02
56 57 4.578105 ACGGAGGGAGTAGTAGAAAATACG 59.422 45.833 0.00 0.00 0.00 3.06
57 58 5.009510 GGACGGAGGGAGTAGTAGAAAATAC 59.990 48.000 0.00 0.00 0.00 1.89
58 59 5.136105 GGACGGAGGGAGTAGTAGAAAATA 58.864 45.833 0.00 0.00 0.00 1.40
59 60 3.959449 GGACGGAGGGAGTAGTAGAAAAT 59.041 47.826 0.00 0.00 0.00 1.82
60 61 3.359950 GGACGGAGGGAGTAGTAGAAAA 58.640 50.000 0.00 0.00 0.00 2.29
61 62 2.357569 GGGACGGAGGGAGTAGTAGAAA 60.358 54.545 0.00 0.00 0.00 2.52
62 63 1.213926 GGGACGGAGGGAGTAGTAGAA 59.786 57.143 0.00 0.00 0.00 2.10
63 64 0.842635 GGGACGGAGGGAGTAGTAGA 59.157 60.000 0.00 0.00 0.00 2.59
64 65 0.549950 TGGGACGGAGGGAGTAGTAG 59.450 60.000 0.00 0.00 0.00 2.57
65 66 1.002069 TTGGGACGGAGGGAGTAGTA 58.998 55.000 0.00 0.00 0.00 1.82
66 67 0.115745 TTTGGGACGGAGGGAGTAGT 59.884 55.000 0.00 0.00 0.00 2.73
67 68 1.272807 TTTTGGGACGGAGGGAGTAG 58.727 55.000 0.00 0.00 0.00 2.57
68 69 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
69 70 1.961133 TATTTTGGGACGGAGGGAGT 58.039 50.000 0.00 0.00 0.00 3.85
70 71 2.238898 ACTTATTTTGGGACGGAGGGAG 59.761 50.000 0.00 0.00 0.00 4.30
71 72 2.026636 CACTTATTTTGGGACGGAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
72 73 2.290705 ACACTTATTTTGGGACGGAGGG 60.291 50.000 0.00 0.00 0.00 4.30
73 74 3.007635 GACACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
74 75 3.933332 GAGACACTTATTTTGGGACGGAG 59.067 47.826 0.00 0.00 0.00 4.63
75 76 3.325425 TGAGACACTTATTTTGGGACGGA 59.675 43.478 0.00 0.00 0.00 4.69
76 77 3.670625 TGAGACACTTATTTTGGGACGG 58.329 45.455 0.00 0.00 0.00 4.79
77 78 4.755123 AGTTGAGACACTTATTTTGGGACG 59.245 41.667 0.00 0.00 0.00 4.79
78 79 6.635030 AAGTTGAGACACTTATTTTGGGAC 57.365 37.500 0.00 0.00 35.10 4.46
79 80 6.605594 ACAAAGTTGAGACACTTATTTTGGGA 59.394 34.615 0.00 0.00 35.87 4.37
80 81 6.805713 ACAAAGTTGAGACACTTATTTTGGG 58.194 36.000 0.00 0.00 35.87 4.12
81 82 8.621286 AGTACAAAGTTGAGACACTTATTTTGG 58.379 33.333 0.00 0.00 35.87 3.28
84 85 9.269453 GGTAGTACAAAGTTGAGACACTTATTT 57.731 33.333 2.06 0.00 35.87 1.40
85 86 8.648693 AGGTAGTACAAAGTTGAGACACTTATT 58.351 33.333 2.06 0.00 35.87 1.40
86 87 8.191534 AGGTAGTACAAAGTTGAGACACTTAT 57.808 34.615 2.06 0.00 35.87 1.73
87 88 7.592885 AGGTAGTACAAAGTTGAGACACTTA 57.407 36.000 2.06 0.00 35.87 2.24
88 89 6.481434 AGGTAGTACAAAGTTGAGACACTT 57.519 37.500 2.06 0.00 38.74 3.16
89 90 6.481434 AAGGTAGTACAAAGTTGAGACACT 57.519 37.500 2.06 0.00 0.00 3.55
90 91 7.924947 ACTAAAGGTAGTACAAAGTTGAGACAC 59.075 37.037 2.06 0.00 38.87 3.67
91 92 8.015185 ACTAAAGGTAGTACAAAGTTGAGACA 57.985 34.615 2.06 0.00 38.87 3.41
104 105 8.130671 AGCACAGATTTGTACTAAAGGTAGTA 57.869 34.615 0.00 0.00 41.06 1.82
105 106 7.005709 AGCACAGATTTGTACTAAAGGTAGT 57.994 36.000 0.00 0.00 43.27 2.73
106 107 8.997621 TTAGCACAGATTTGTACTAAAGGTAG 57.002 34.615 6.60 0.00 39.21 3.18
107 108 7.548075 GCTTAGCACAGATTTGTACTAAAGGTA 59.452 37.037 9.63 0.00 40.75 3.08
108 109 6.371825 GCTTAGCACAGATTTGTACTAAAGGT 59.628 38.462 9.63 0.00 40.75 3.50
109 110 6.595716 AGCTTAGCACAGATTTGTACTAAAGG 59.404 38.462 7.07 2.34 40.75 3.11
110 111 7.331934 TGAGCTTAGCACAGATTTGTACTAAAG 59.668 37.037 7.07 6.19 40.75 1.85
111 112 7.158697 TGAGCTTAGCACAGATTTGTACTAAA 58.841 34.615 7.07 0.00 40.75 1.85
112 113 6.697395 TGAGCTTAGCACAGATTTGTACTAA 58.303 36.000 7.07 8.39 39.64 2.24
113 114 6.280855 TGAGCTTAGCACAGATTTGTACTA 57.719 37.500 7.07 0.00 35.25 1.82
114 115 5.152623 TGAGCTTAGCACAGATTTGTACT 57.847 39.130 7.07 0.00 35.25 2.73
115 116 5.639506 TCTTGAGCTTAGCACAGATTTGTAC 59.360 40.000 7.07 0.00 35.25 2.90
116 117 5.639506 GTCTTGAGCTTAGCACAGATTTGTA 59.360 40.000 7.07 0.00 35.25 2.41
117 118 4.453819 GTCTTGAGCTTAGCACAGATTTGT 59.546 41.667 7.07 0.00 38.31 2.83
118 119 4.453478 TGTCTTGAGCTTAGCACAGATTTG 59.547 41.667 7.07 0.00 30.09 2.32
119 120 4.453819 GTGTCTTGAGCTTAGCACAGATTT 59.546 41.667 7.07 0.00 30.09 2.17
120 121 3.999663 GTGTCTTGAGCTTAGCACAGATT 59.000 43.478 7.07 0.00 30.09 2.40
121 122 3.260380 AGTGTCTTGAGCTTAGCACAGAT 59.740 43.478 7.07 0.00 30.09 2.90
122 123 2.630098 AGTGTCTTGAGCTTAGCACAGA 59.370 45.455 7.07 1.31 30.09 3.41
123 124 3.037431 AGTGTCTTGAGCTTAGCACAG 57.963 47.619 7.07 0.00 30.09 3.66
124 125 3.475566 AAGTGTCTTGAGCTTAGCACA 57.524 42.857 7.07 3.01 0.00 4.57
125 126 6.487689 AAATAAGTGTCTTGAGCTTAGCAC 57.512 37.500 7.07 0.00 0.00 4.40
126 127 7.334421 CCTAAAATAAGTGTCTTGAGCTTAGCA 59.666 37.037 7.07 0.00 0.00 3.49
127 128 7.549488 TCCTAAAATAAGTGTCTTGAGCTTAGC 59.451 37.037 0.00 0.00 0.00 3.09
128 129 8.874816 GTCCTAAAATAAGTGTCTTGAGCTTAG 58.125 37.037 0.00 0.00 0.00 2.18
129 130 7.544566 CGTCCTAAAATAAGTGTCTTGAGCTTA 59.455 37.037 0.00 0.00 0.00 3.09
130 131 6.369065 CGTCCTAAAATAAGTGTCTTGAGCTT 59.631 38.462 0.00 0.00 0.00 3.74
131 132 5.869888 CGTCCTAAAATAAGTGTCTTGAGCT 59.130 40.000 0.00 0.00 0.00 4.09
132 133 5.063564 CCGTCCTAAAATAAGTGTCTTGAGC 59.936 44.000 0.00 0.00 0.00 4.26
133 134 6.395629 TCCGTCCTAAAATAAGTGTCTTGAG 58.604 40.000 0.00 0.00 0.00 3.02
134 135 6.349243 TCCGTCCTAAAATAAGTGTCTTGA 57.651 37.500 0.00 0.00 0.00 3.02
135 136 5.581085 CCTCCGTCCTAAAATAAGTGTCTTG 59.419 44.000 0.00 0.00 0.00 3.02
136 137 5.338137 CCCTCCGTCCTAAAATAAGTGTCTT 60.338 44.000 0.00 0.00 0.00 3.01
137 138 4.161754 CCCTCCGTCCTAAAATAAGTGTCT 59.838 45.833 0.00 0.00 0.00 3.41
138 139 4.161001 TCCCTCCGTCCTAAAATAAGTGTC 59.839 45.833 0.00 0.00 0.00 3.67
139 140 4.098894 TCCCTCCGTCCTAAAATAAGTGT 58.901 43.478 0.00 0.00 0.00 3.55
140 141 4.161754 ACTCCCTCCGTCCTAAAATAAGTG 59.838 45.833 0.00 0.00 0.00 3.16
141 142 4.359996 ACTCCCTCCGTCCTAAAATAAGT 58.640 43.478 0.00 0.00 0.00 2.24
142 143 6.667558 ATACTCCCTCCGTCCTAAAATAAG 57.332 41.667 0.00 0.00 0.00 1.73
143 144 8.731591 ATTATACTCCCTCCGTCCTAAAATAA 57.268 34.615 0.00 0.00 0.00 1.40
144 145 8.731591 AATTATACTCCCTCCGTCCTAAAATA 57.268 34.615 0.00 0.00 0.00 1.40
145 146 7.513091 AGAATTATACTCCCTCCGTCCTAAAAT 59.487 37.037 0.00 0.00 0.00 1.82
146 147 6.842807 AGAATTATACTCCCTCCGTCCTAAAA 59.157 38.462 0.00 0.00 0.00 1.52
147 148 6.379579 AGAATTATACTCCCTCCGTCCTAAA 58.620 40.000 0.00 0.00 0.00 1.85
148 149 5.961897 AGAATTATACTCCCTCCGTCCTAA 58.038 41.667 0.00 0.00 0.00 2.69
149 150 5.595814 AGAATTATACTCCCTCCGTCCTA 57.404 43.478 0.00 0.00 0.00 2.94
150 151 4.472690 AGAATTATACTCCCTCCGTCCT 57.527 45.455 0.00 0.00 0.00 3.85
151 152 4.462132 GGTAGAATTATACTCCCTCCGTCC 59.538 50.000 9.93 0.00 0.00 4.79
152 153 5.323581 AGGTAGAATTATACTCCCTCCGTC 58.676 45.833 9.93 0.00 0.00 4.79
173 174 5.756833 ACTGTAGTACCGTTTTTCTTTGAGG 59.243 40.000 0.00 0.00 0.00 3.86
345 350 7.011482 GGTCTGATCATTTTAAGTTCGTATGCT 59.989 37.037 0.00 0.00 0.00 3.79
388 394 0.179234 TTGAGTTCGTGGAGGCAACA 59.821 50.000 0.00 0.00 41.41 3.33
389 395 0.868406 CTTGAGTTCGTGGAGGCAAC 59.132 55.000 0.00 0.00 0.00 4.17
434 440 0.461961 GAAGGGAGCTATGCACGTCT 59.538 55.000 0.00 0.00 0.00 4.18
545 576 1.822425 TGGGGAAGACCTGGTTGTTA 58.178 50.000 0.00 0.00 40.03 2.41
553 585 3.052869 GGGAAATAACATGGGGAAGACCT 60.053 47.826 0.00 0.00 40.03 3.85
559 592 4.292571 TGTTACAGGGAAATAACATGGGGA 59.707 41.667 0.00 0.00 36.59 4.81
633 666 4.654091 AATAAATGCTATGGTGGTGTGC 57.346 40.909 0.00 0.00 0.00 4.57
779 812 5.353678 AGCTTCTGAATGATTGTACTTGCTC 59.646 40.000 0.00 0.00 0.00 4.26
828 861 4.931661 TGTCGTGAATTATCTCCTACCC 57.068 45.455 0.00 0.00 0.00 3.69
873 906 4.201773 CGTCGCAATAATTGGAGCTTTGTA 60.202 41.667 0.00 0.00 0.00 2.41
893 926 3.062763 AGCAAGATACTGCATATGCGTC 58.937 45.455 22.21 16.25 45.18 5.19
1014 1047 2.505405 CTCAGGATGGCCATCTTCATG 58.495 52.381 37.94 29.58 37.92 3.07
1104 1138 5.125417 ACATTCCGTTCAATATTTCCACCAG 59.875 40.000 0.00 0.00 0.00 4.00
1125 1159 5.105392 TGAACCTGCTTCAACAAAAGAACAT 60.105 36.000 0.00 0.00 35.84 2.71
1227 1264 5.923733 TTCTGGTTGAGTATCCTCTCTTC 57.076 43.478 0.00 0.00 38.61 2.87
1250 1287 3.440522 GGTCGATCTGTATCCATCATCGA 59.559 47.826 0.00 0.00 38.75 3.59
1256 1293 4.503817 CCATTGTGGTCGATCTGTATCCAT 60.504 45.833 0.00 0.00 31.35 3.41
1280 1317 3.089284 TCTTCTCGCCTGAGTTGATGTA 58.911 45.455 0.00 0.00 43.09 2.29
1330 1367 1.274728 CCAGTTGCTAGTGTCAGCTCT 59.725 52.381 2.31 0.00 42.30 4.09
1465 1502 3.071457 TGCTCTCATGTTGAAACCTCAGA 59.929 43.478 0.00 0.00 31.69 3.27
1695 1735 2.024414 ACTTCTTCTTGGTGTTGGTGC 58.976 47.619 0.00 0.00 0.00 5.01
1703 1743 3.871594 CAGTTCGTTCACTTCTTCTTGGT 59.128 43.478 0.00 0.00 0.00 3.67
1711 1751 4.443394 ACGATTACACAGTTCGTTCACTTC 59.557 41.667 0.00 0.00 42.99 3.01
2007 2049 3.356529 AGTATCCACCAGGCTTTTCTG 57.643 47.619 0.00 0.00 33.74 3.02
2139 2182 4.721776 AGGAAGTCTTCATGGGCATTACTA 59.278 41.667 14.49 0.00 0.00 1.82
2388 2433 9.362151 ACTTTCAAGTTTATCCCTGTTCATTTA 57.638 29.630 0.00 0.00 35.21 1.40


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

AutoCloner maintained by Alex Coulton.