Multiple sequence alignment - TraesCS5B01G247100

Loading Multiple Alignment...

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 TraesCS5B01G247100 chr5B 100.000 2303 0 0 1 2303 429037425 429039727 0.000000e+00 4253.0
1 TraesCS5B01G247100 chr5B 95.367 2137 40 9 224 2303 413608403 413610537 0.000000e+00 3343.0
2 TraesCS5B01G247100 chr5B 93.715 2132 66 28 224 2303 432877690 432879805 0.000000e+00 3133.0
3 TraesCS5B01G247100 chr5B 91.813 171 10 2 56 223 580700611 580700780 3.830000e-58 235.0
4 TraesCS5B01G247100 chr3B 96.310 2114 37 7 229 2303 201559802 201557691 0.000000e+00 3434.0
5 TraesCS5B01G247100 chr3B 86.957 184 10 4 56 226 582472777 582472959 6.490000e-46 195.0
6 TraesCS5B01G247100 chr4D 94.361 2128 64 17 229 2303 245649653 245651777 0.000000e+00 3214.0
7 TraesCS5B01G247100 chr4D 91.813 171 9 3 56 223 416136246 416136078 1.380000e-57 233.0
8 TraesCS5B01G247100 chr4D 85.333 150 7 4 92 227 448393151 448393299 8.580000e-30 141.0
9 TraesCS5B01G247100 chr4A 94.048 2117 83 10 224 2303 310763374 310765484 0.000000e+00 3171.0
10 TraesCS5B01G247100 chr4A 92.613 1259 55 12 1080 2303 219308174 219306919 0.000000e+00 1775.0
11 TraesCS5B01G247100 chr3A 94.441 1529 30 14 229 1704 672877462 672875936 0.000000e+00 2302.0
12 TraesCS5B01G247100 chr2D 96.883 1155 16 2 229 1364 630271258 630272411 0.000000e+00 1916.0
13 TraesCS5B01G247100 chr2D 96.727 1161 16 4 224 1364 33934777 33935935 0.000000e+00 1914.0
14 TraesCS5B01G247100 chr2D 98.004 952 13 3 1358 2303 33935980 33936931 0.000000e+00 1648.0
15 TraesCS5B01G247100 chr2D 97.789 950 14 4 1361 2303 630272457 630273406 0.000000e+00 1631.0
16 TraesCS5B01G247100 chr2D 85.965 171 10 3 56 223 81483293 81483452 1.090000e-38 171.0
17 TraesCS5B01G247100 chrUn 96.727 1161 16 4 224 1364 371049414 371050572 0.000000e+00 1914.0
18 TraesCS5B01G247100 chrUn 92.722 371 4 12 1027 1376 451362693 451362325 4.390000e-142 514.0
19 TraesCS5B01G247100 chr1B 97.666 1071 24 1 224 1294 633727898 633726829 0.000000e+00 1838.0
20 TraesCS5B01G247100 chr5A 97.701 957 15 4 1354 2303 482027244 482026288 0.000000e+00 1639.0
21 TraesCS5B01G247100 chr5A 97.297 74 2 0 1291 1364 482027334 482027261 2.400000e-25 126.0
22 TraesCS5B01G247100 chr7D 94.709 567 10 10 817 1364 231585231 231585796 0.000000e+00 863.0
23 TraesCS5B01G247100 chr7D 85.955 178 17 6 56 227 566240824 566240999 1.410000e-42 183.0
24 TraesCS5B01G247100 chr4B 93.687 396 6 9 988 1364 1 396 1.980000e-160 575.0
25 TraesCS5B01G247100 chr5D 89.941 169 10 3 56 224 139130796 139130635 6.450000e-51 211.0
26 TraesCS5B01G247100 chr5D 87.978 183 8 3 56 225 30720445 30720264 1.080000e-48 204.0
27 TraesCS5B01G247100 chr1A 90.909 44 4 0 181 224 267442512 267442555 2.470000e-05 60.2


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 TraesCS5B01G247100 chr5B 429037425 429039727 2302 False 4253.0 4253 100.0000 1 2303 1 chr5B.!!$F2 2302
1 TraesCS5B01G247100 chr5B 413608403 413610537 2134 False 3343.0 3343 95.3670 224 2303 1 chr5B.!!$F1 2079
2 TraesCS5B01G247100 chr5B 432877690 432879805 2115 False 3133.0 3133 93.7150 224 2303 1 chr5B.!!$F3 2079
3 TraesCS5B01G247100 chr3B 201557691 201559802 2111 True 3434.0 3434 96.3100 229 2303 1 chr3B.!!$R1 2074
4 TraesCS5B01G247100 chr4D 245649653 245651777 2124 False 3214.0 3214 94.3610 229 2303 1 chr4D.!!$F1 2074
5 TraesCS5B01G247100 chr4A 310763374 310765484 2110 False 3171.0 3171 94.0480 224 2303 1 chr4A.!!$F1 2079
6 TraesCS5B01G247100 chr4A 219306919 219308174 1255 True 1775.0 1775 92.6130 1080 2303 1 chr4A.!!$R1 1223
7 TraesCS5B01G247100 chr3A 672875936 672877462 1526 True 2302.0 2302 94.4410 229 1704 1 chr3A.!!$R1 1475
8 TraesCS5B01G247100 chr2D 33934777 33936931 2154 False 1781.0 1914 97.3655 224 2303 2 chr2D.!!$F2 2079
9 TraesCS5B01G247100 chr2D 630271258 630273406 2148 False 1773.5 1916 97.3360 229 2303 2 chr2D.!!$F3 2074
10 TraesCS5B01G247100 chrUn 371049414 371050572 1158 False 1914.0 1914 96.7270 224 1364 1 chrUn.!!$F1 1140
11 TraesCS5B01G247100 chr1B 633726829 633727898 1069 True 1838.0 1838 97.6660 224 1294 1 chr1B.!!$R1 1070
12 TraesCS5B01G247100 chr5A 482026288 482027334 1046 True 882.5 1639 97.4990 1291 2303 2 chr5A.!!$R1 1012
13 TraesCS5B01G247100 chr7D 231585231 231585796 565 False 863.0 863 94.7090 817 1364 1 chr7D.!!$F1 547

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
222 223 0.032815 GCTGAGTTCTAGGCGATCCC 59.967 60.0 0.0 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2013 2127 2.897969 ACAGGCTTCTTCGGTAAAGAGA 59.102 45.455 0.0 0.0 44.69 3.1 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
26 27 9.644993 CGTTTTATGAAATTATATTCACTCGCA 57.355 29.630 0.00 0.00 41.78 5.10
29 30 8.902540 TTATGAAATTATATTCACTCGCAGGT 57.097 30.769 0.00 0.00 41.78 4.00
30 31 6.603237 TGAAATTATATTCACTCGCAGGTG 57.397 37.500 0.23 0.23 34.50 4.00
31 32 5.007626 TGAAATTATATTCACTCGCAGGTGC 59.992 40.000 1.68 0.00 34.50 5.01
41 42 4.403976 GCAGGTGCGCTCTAGTAC 57.596 61.111 9.73 0.00 0.00 2.73
42 43 1.810532 GCAGGTGCGCTCTAGTACT 59.189 57.895 9.73 0.00 0.00 2.73
43 44 0.248702 GCAGGTGCGCTCTAGTACTC 60.249 60.000 9.73 0.00 0.00 2.59
44 45 1.384525 CAGGTGCGCTCTAGTACTCT 58.615 55.000 9.73 0.00 0.00 3.24
45 46 1.332375 CAGGTGCGCTCTAGTACTCTC 59.668 57.143 9.73 0.00 0.00 3.20
46 47 0.664224 GGTGCGCTCTAGTACTCTCC 59.336 60.000 9.73 0.00 0.00 3.71
47 48 1.380524 GTGCGCTCTAGTACTCTCCA 58.619 55.000 9.73 0.00 0.00 3.86
48 49 1.064357 GTGCGCTCTAGTACTCTCCAC 59.936 57.143 9.73 0.00 0.00 4.02
49 50 1.339727 TGCGCTCTAGTACTCTCCACA 60.340 52.381 9.73 0.00 0.00 4.17
50 51 1.064357 GCGCTCTAGTACTCTCCACAC 59.936 57.143 0.00 0.00 0.00 3.82
51 52 2.357075 CGCTCTAGTACTCTCCACACA 58.643 52.381 0.00 0.00 0.00 3.72
52 53 2.946329 CGCTCTAGTACTCTCCACACAT 59.054 50.000 0.00 0.00 0.00 3.21
53 54 4.127907 CGCTCTAGTACTCTCCACACATA 58.872 47.826 0.00 0.00 0.00 2.29
54 55 4.212425 CGCTCTAGTACTCTCCACACATAG 59.788 50.000 0.00 0.00 0.00 2.23
55 56 5.127491 GCTCTAGTACTCTCCACACATAGT 58.873 45.833 0.00 0.00 0.00 2.12
56 57 5.237779 GCTCTAGTACTCTCCACACATAGTC 59.762 48.000 0.00 0.00 0.00 2.59
57 58 6.309389 TCTAGTACTCTCCACACATAGTCA 57.691 41.667 0.00 0.00 0.00 3.41
58 59 6.114089 TCTAGTACTCTCCACACATAGTCAC 58.886 44.000 0.00 0.00 0.00 3.67
59 60 4.663334 AGTACTCTCCACACATAGTCACA 58.337 43.478 0.00 0.00 0.00 3.58
60 61 5.077564 AGTACTCTCCACACATAGTCACAA 58.922 41.667 0.00 0.00 0.00 3.33
61 62 4.258702 ACTCTCCACACATAGTCACAAC 57.741 45.455 0.00 0.00 0.00 3.32
62 63 3.006967 ACTCTCCACACATAGTCACAACC 59.993 47.826 0.00 0.00 0.00 3.77
63 64 2.301870 TCTCCACACATAGTCACAACCC 59.698 50.000 0.00 0.00 0.00 4.11
64 65 2.038426 CTCCACACATAGTCACAACCCA 59.962 50.000 0.00 0.00 0.00 4.51
65 66 2.038426 TCCACACATAGTCACAACCCAG 59.962 50.000 0.00 0.00 0.00 4.45
66 67 1.806542 CACACATAGTCACAACCCAGC 59.193 52.381 0.00 0.00 0.00 4.85
67 68 1.271379 ACACATAGTCACAACCCAGCC 60.271 52.381 0.00 0.00 0.00 4.85
68 69 1.003580 CACATAGTCACAACCCAGCCT 59.996 52.381 0.00 0.00 0.00 4.58
69 70 2.236146 CACATAGTCACAACCCAGCCTA 59.764 50.000 0.00 0.00 0.00 3.93
70 71 2.910319 ACATAGTCACAACCCAGCCTAA 59.090 45.455 0.00 0.00 0.00 2.69
71 72 3.329520 ACATAGTCACAACCCAGCCTAAA 59.670 43.478 0.00 0.00 0.00 1.85
72 73 4.202524 ACATAGTCACAACCCAGCCTAAAA 60.203 41.667 0.00 0.00 0.00 1.52
73 74 3.306472 AGTCACAACCCAGCCTAAAAA 57.694 42.857 0.00 0.00 0.00 1.94
97 98 9.651913 AAAAGAAAGAAAAACAAAGCATAGACA 57.348 25.926 0.00 0.00 0.00 3.41
98 99 8.862550 AAGAAAGAAAAACAAAGCATAGACAG 57.137 30.769 0.00 0.00 0.00 3.51
99 100 6.920210 AGAAAGAAAAACAAAGCATAGACAGC 59.080 34.615 0.00 0.00 0.00 4.40
100 101 5.126396 AGAAAAACAAAGCATAGACAGCC 57.874 39.130 0.00 0.00 0.00 4.85
101 102 3.942130 AAAACAAAGCATAGACAGCCC 57.058 42.857 0.00 0.00 0.00 5.19
102 103 2.584835 AACAAAGCATAGACAGCCCA 57.415 45.000 0.00 0.00 0.00 5.36
103 104 2.119801 ACAAAGCATAGACAGCCCAG 57.880 50.000 0.00 0.00 0.00 4.45
104 105 1.630369 ACAAAGCATAGACAGCCCAGA 59.370 47.619 0.00 0.00 0.00 3.86
105 106 2.040278 ACAAAGCATAGACAGCCCAGAA 59.960 45.455 0.00 0.00 0.00 3.02
106 107 2.681848 CAAAGCATAGACAGCCCAGAAG 59.318 50.000 0.00 0.00 0.00 2.85
107 108 0.835941 AGCATAGACAGCCCAGAAGG 59.164 55.000 0.00 0.00 39.47 3.46
108 109 0.833287 GCATAGACAGCCCAGAAGGA 59.167 55.000 0.00 0.00 38.24 3.36
109 110 1.419387 GCATAGACAGCCCAGAAGGAT 59.581 52.381 0.00 0.00 38.24 3.24
114 115 2.586792 AGCCCAGAAGGATGTCGC 59.413 61.111 0.00 0.00 38.24 5.19
115 116 2.514824 GCCCAGAAGGATGTCGCC 60.515 66.667 0.00 0.00 38.24 5.54
116 117 3.036429 GCCCAGAAGGATGTCGCCT 62.036 63.158 0.00 0.00 40.93 5.52
117 118 1.686325 GCCCAGAAGGATGTCGCCTA 61.686 60.000 0.00 0.00 37.26 3.93
118 119 0.390860 CCCAGAAGGATGTCGCCTAG 59.609 60.000 0.00 0.00 37.26 3.02
119 120 0.249657 CCAGAAGGATGTCGCCTAGC 60.250 60.000 0.00 0.00 37.26 3.42
120 121 0.249657 CAGAAGGATGTCGCCTAGCC 60.250 60.000 0.00 0.00 37.26 3.93
121 122 1.069935 GAAGGATGTCGCCTAGCCC 59.930 63.158 0.00 0.00 37.26 5.19
122 123 1.686325 GAAGGATGTCGCCTAGCCCA 61.686 60.000 0.00 0.00 37.26 5.36
123 124 1.690219 AAGGATGTCGCCTAGCCCAG 61.690 60.000 0.00 0.00 37.26 4.45
124 125 2.134287 GGATGTCGCCTAGCCCAGA 61.134 63.158 0.00 0.00 0.00 3.86
125 126 1.686325 GGATGTCGCCTAGCCCAGAA 61.686 60.000 0.00 0.00 0.00 3.02
126 127 0.178068 GATGTCGCCTAGCCCAGAAA 59.822 55.000 0.00 0.00 0.00 2.52
127 128 0.618458 ATGTCGCCTAGCCCAGAAAA 59.382 50.000 0.00 0.00 0.00 2.29
128 129 0.398696 TGTCGCCTAGCCCAGAAAAA 59.601 50.000 0.00 0.00 0.00 1.94
129 130 0.803117 GTCGCCTAGCCCAGAAAAAC 59.197 55.000 0.00 0.00 0.00 2.43
130 131 0.398696 TCGCCTAGCCCAGAAAAACA 59.601 50.000 0.00 0.00 0.00 2.83
131 132 1.202830 TCGCCTAGCCCAGAAAAACAA 60.203 47.619 0.00 0.00 0.00 2.83
132 133 1.068541 CGCCTAGCCCAGAAAAACAAC 60.069 52.381 0.00 0.00 0.00 3.32
133 134 2.239400 GCCTAGCCCAGAAAAACAACT 58.761 47.619 0.00 0.00 0.00 3.16
134 135 2.229062 GCCTAGCCCAGAAAAACAACTC 59.771 50.000 0.00 0.00 0.00 3.01
135 136 3.486383 CCTAGCCCAGAAAAACAACTCA 58.514 45.455 0.00 0.00 0.00 3.41
136 137 3.253432 CCTAGCCCAGAAAAACAACTCAC 59.747 47.826 0.00 0.00 0.00 3.51
137 138 2.733956 AGCCCAGAAAAACAACTCACA 58.266 42.857 0.00 0.00 0.00 3.58
138 139 2.427095 AGCCCAGAAAAACAACTCACAC 59.573 45.455 0.00 0.00 0.00 3.82
139 140 2.794631 GCCCAGAAAAACAACTCACACG 60.795 50.000 0.00 0.00 0.00 4.49
140 141 2.680841 CCCAGAAAAACAACTCACACGA 59.319 45.455 0.00 0.00 0.00 4.35
141 142 3.486875 CCCAGAAAAACAACTCACACGAC 60.487 47.826 0.00 0.00 0.00 4.34
142 143 3.342269 CAGAAAAACAACTCACACGACG 58.658 45.455 0.00 0.00 0.00 5.12
143 144 2.098870 GAAAAACAACTCACACGACGC 58.901 47.619 0.00 0.00 0.00 5.19
144 145 1.365699 AAAACAACTCACACGACGCT 58.634 45.000 0.00 0.00 0.00 5.07
145 146 0.650512 AAACAACTCACACGACGCTG 59.349 50.000 0.00 0.00 0.00 5.18
146 147 1.151777 AACAACTCACACGACGCTGG 61.152 55.000 0.00 0.00 0.00 4.85
147 148 2.661866 AACTCACACGACGCTGGC 60.662 61.111 0.00 0.00 0.00 4.85
149 150 4.700365 CTCACACGACGCTGGCGA 62.700 66.667 21.77 0.00 42.83 5.54
150 151 4.700365 TCACACGACGCTGGCGAG 62.700 66.667 21.77 15.88 42.83 5.03
171 172 2.048127 GTGGCTGAGGGACACGTC 60.048 66.667 0.00 0.00 44.75 4.34
172 173 2.523168 TGGCTGAGGGACACGTCA 60.523 61.111 0.00 0.00 39.02 4.35
176 177 3.051210 TGAGGGACACGTCAGCTG 58.949 61.111 7.63 7.63 36.65 4.24
177 178 2.262915 GAGGGACACGTCAGCTGG 59.737 66.667 15.13 0.36 0.00 4.85
178 179 3.941657 GAGGGACACGTCAGCTGGC 62.942 68.421 15.13 12.04 0.00 4.85
179 180 4.008933 GGGACACGTCAGCTGGCT 62.009 66.667 17.70 0.00 0.00 4.75
180 181 2.740055 GGACACGTCAGCTGGCTG 60.740 66.667 17.70 15.44 44.86 4.85
187 188 3.890313 TCAGCTGGCTGAGACCAA 58.110 55.556 19.66 0.00 46.80 3.67
188 189 2.144952 TCAGCTGGCTGAGACCAAA 58.855 52.632 19.66 0.00 46.80 3.28
189 190 0.694771 TCAGCTGGCTGAGACCAAAT 59.305 50.000 19.66 0.00 46.80 2.32
190 191 1.074405 TCAGCTGGCTGAGACCAAATT 59.926 47.619 19.66 0.00 46.80 1.82
191 192 2.305635 TCAGCTGGCTGAGACCAAATTA 59.694 45.455 19.66 0.00 46.80 1.40
192 193 2.421424 CAGCTGGCTGAGACCAAATTAC 59.579 50.000 16.59 0.00 46.30 1.89
193 194 1.398390 GCTGGCTGAGACCAAATTACG 59.602 52.381 0.00 0.00 39.86 3.18
194 195 2.699954 CTGGCTGAGACCAAATTACGT 58.300 47.619 0.00 0.00 39.86 3.57
195 196 2.673368 CTGGCTGAGACCAAATTACGTC 59.327 50.000 0.00 0.00 39.86 4.34
196 197 2.301870 TGGCTGAGACCAAATTACGTCT 59.698 45.455 6.98 6.98 42.02 4.18
202 203 4.866508 AGACCAAATTACGTCTCAGTCA 57.133 40.909 0.00 0.00 34.15 3.41
203 204 4.810790 AGACCAAATTACGTCTCAGTCAG 58.189 43.478 0.00 0.00 34.15 3.51
204 205 3.326747 ACCAAATTACGTCTCAGTCAGC 58.673 45.455 0.00 0.00 0.00 4.26
205 206 3.006967 ACCAAATTACGTCTCAGTCAGCT 59.993 43.478 0.00 0.00 0.00 4.24
206 207 3.369147 CCAAATTACGTCTCAGTCAGCTG 59.631 47.826 7.63 7.63 43.87 4.24
216 217 1.821753 TCAGTCAGCTGAGTTCTAGGC 59.178 52.381 21.67 4.93 45.94 3.93
217 218 0.814457 AGTCAGCTGAGTTCTAGGCG 59.186 55.000 18.89 0.00 0.00 5.52
218 219 0.811915 GTCAGCTGAGTTCTAGGCGA 59.188 55.000 18.89 0.00 0.00 5.54
219 220 1.407258 GTCAGCTGAGTTCTAGGCGAT 59.593 52.381 18.89 0.00 0.00 4.58
220 221 1.678627 TCAGCTGAGTTCTAGGCGATC 59.321 52.381 13.74 0.00 0.00 3.69
221 222 1.036707 AGCTGAGTTCTAGGCGATCC 58.963 55.000 0.00 0.00 0.00 3.36
222 223 0.032815 GCTGAGTTCTAGGCGATCCC 59.967 60.000 0.00 0.00 0.00 3.85
227 228 3.134458 GAGTTCTAGGCGATCCCAAATG 58.866 50.000 3.45 0.00 35.39 2.32
636 639 6.055588 CGTGGTATGGAATTCTTTGGACTAT 58.944 40.000 5.23 0.00 0.00 2.12
1024 1027 8.524870 AATGATGTTTGAGCATGTACTTTTTC 57.475 30.769 0.00 0.00 28.65 2.29
1106 1109 7.654116 GGTTAGAGCTCTAATATGTCTTGAACC 59.346 40.741 32.99 24.30 40.20 3.62
1588 1699 3.687212 TCTTCACGCTTTCTCACAAACAA 59.313 39.130 0.00 0.00 0.00 2.83
1912 2025 1.153086 GAATCTGCCTGCCCGACAT 60.153 57.895 0.00 0.00 0.00 3.06
2013 2127 4.810790 ACTTCACTCGAATCGTCTGATTT 58.189 39.130 1.52 0.00 44.79 2.17
2090 2204 9.436957 AGTCAAAACGTATCTTGTCTTTATCAT 57.563 29.630 0.00 0.00 0.00 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.644993 TGCGAGTGAATATAATTTCATAAAACG 57.355 29.630 0.00 0.00 37.88 3.60
5 6 7.095229 GCACCTGCGAGTGAATATAATTTCATA 60.095 37.037 9.91 0.00 40.34 2.15
6 7 6.293626 GCACCTGCGAGTGAATATAATTTCAT 60.294 38.462 9.91 0.00 40.34 2.57
7 8 5.007626 GCACCTGCGAGTGAATATAATTTCA 59.992 40.000 9.91 0.00 40.34 2.69
8 9 5.444122 GCACCTGCGAGTGAATATAATTTC 58.556 41.667 9.91 0.00 40.34 2.17
9 10 5.424121 GCACCTGCGAGTGAATATAATTT 57.576 39.130 9.91 0.00 40.34 1.82
24 25 0.248702 GAGTACTAGAGCGCACCTGC 60.249 60.000 11.47 0.00 37.78 4.85
25 26 1.332375 GAGAGTACTAGAGCGCACCTG 59.668 57.143 11.47 1.12 0.00 4.00
26 27 1.670791 GAGAGTACTAGAGCGCACCT 58.329 55.000 11.47 9.06 0.00 4.00
27 28 0.664224 GGAGAGTACTAGAGCGCACC 59.336 60.000 11.47 0.00 0.00 5.01
28 29 1.064357 GTGGAGAGTACTAGAGCGCAC 59.936 57.143 11.47 2.25 0.00 5.34
29 30 1.339727 TGTGGAGAGTACTAGAGCGCA 60.340 52.381 11.47 0.00 0.00 6.09
30 31 1.064357 GTGTGGAGAGTACTAGAGCGC 59.936 57.143 0.00 0.00 0.00 5.92
31 32 2.357075 TGTGTGGAGAGTACTAGAGCG 58.643 52.381 0.00 0.00 0.00 5.03
32 33 5.127491 ACTATGTGTGGAGAGTACTAGAGC 58.873 45.833 0.00 0.00 0.00 4.09
33 34 6.259167 GTGACTATGTGTGGAGAGTACTAGAG 59.741 46.154 0.00 0.00 0.00 2.43
34 35 6.114089 GTGACTATGTGTGGAGAGTACTAGA 58.886 44.000 0.00 0.00 0.00 2.43
35 36 5.880887 TGTGACTATGTGTGGAGAGTACTAG 59.119 44.000 0.00 0.00 0.00 2.57
36 37 5.812286 TGTGACTATGTGTGGAGAGTACTA 58.188 41.667 0.00 0.00 0.00 1.82
37 38 4.663334 TGTGACTATGTGTGGAGAGTACT 58.337 43.478 0.00 0.00 0.00 2.73
38 39 5.162075 GTTGTGACTATGTGTGGAGAGTAC 58.838 45.833 0.00 0.00 0.00 2.73
39 40 4.219944 GGTTGTGACTATGTGTGGAGAGTA 59.780 45.833 0.00 0.00 0.00 2.59
40 41 3.006967 GGTTGTGACTATGTGTGGAGAGT 59.993 47.826 0.00 0.00 0.00 3.24
41 42 3.589988 GGTTGTGACTATGTGTGGAGAG 58.410 50.000 0.00 0.00 0.00 3.20
42 43 2.301870 GGGTTGTGACTATGTGTGGAGA 59.698 50.000 0.00 0.00 0.00 3.71
43 44 2.038426 TGGGTTGTGACTATGTGTGGAG 59.962 50.000 0.00 0.00 0.00 3.86
44 45 2.038426 CTGGGTTGTGACTATGTGTGGA 59.962 50.000 0.00 0.00 0.00 4.02
45 46 2.426522 CTGGGTTGTGACTATGTGTGG 58.573 52.381 0.00 0.00 0.00 4.17
46 47 1.806542 GCTGGGTTGTGACTATGTGTG 59.193 52.381 0.00 0.00 0.00 3.82
47 48 1.271379 GGCTGGGTTGTGACTATGTGT 60.271 52.381 0.00 0.00 0.00 3.72
48 49 1.003580 AGGCTGGGTTGTGACTATGTG 59.996 52.381 0.00 0.00 0.00 3.21
49 50 1.362224 AGGCTGGGTTGTGACTATGT 58.638 50.000 0.00 0.00 0.00 2.29
50 51 3.627395 TTAGGCTGGGTTGTGACTATG 57.373 47.619 0.00 0.00 0.00 2.23
51 52 4.650972 TTTTAGGCTGGGTTGTGACTAT 57.349 40.909 0.00 0.00 0.00 2.12
52 53 4.440826 TTTTTAGGCTGGGTTGTGACTA 57.559 40.909 0.00 0.00 0.00 2.59
53 54 3.306472 TTTTTAGGCTGGGTTGTGACT 57.694 42.857 0.00 0.00 0.00 3.41
71 72 9.651913 TGTCTATGCTTTGTTTTTCTTTCTTTT 57.348 25.926 0.00 0.00 0.00 2.27
72 73 9.305925 CTGTCTATGCTTTGTTTTTCTTTCTTT 57.694 29.630 0.00 0.00 0.00 2.52
73 74 7.436376 GCTGTCTATGCTTTGTTTTTCTTTCTT 59.564 33.333 0.00 0.00 0.00 2.52
74 75 6.920210 GCTGTCTATGCTTTGTTTTTCTTTCT 59.080 34.615 0.00 0.00 0.00 2.52
75 76 6.144563 GGCTGTCTATGCTTTGTTTTTCTTTC 59.855 38.462 0.00 0.00 0.00 2.62
76 77 5.985530 GGCTGTCTATGCTTTGTTTTTCTTT 59.014 36.000 0.00 0.00 0.00 2.52
77 78 5.509670 GGGCTGTCTATGCTTTGTTTTTCTT 60.510 40.000 0.00 0.00 0.00 2.52
78 79 4.021981 GGGCTGTCTATGCTTTGTTTTTCT 60.022 41.667 0.00 0.00 0.00 2.52
79 80 4.237724 GGGCTGTCTATGCTTTGTTTTTC 58.762 43.478 0.00 0.00 0.00 2.29
80 81 3.640967 TGGGCTGTCTATGCTTTGTTTTT 59.359 39.130 0.00 0.00 0.00 1.94
81 82 3.230134 TGGGCTGTCTATGCTTTGTTTT 58.770 40.909 0.00 0.00 0.00 2.43
82 83 2.821969 CTGGGCTGTCTATGCTTTGTTT 59.178 45.455 0.00 0.00 0.00 2.83
83 84 2.040278 TCTGGGCTGTCTATGCTTTGTT 59.960 45.455 0.00 0.00 0.00 2.83
84 85 1.630369 TCTGGGCTGTCTATGCTTTGT 59.370 47.619 0.00 0.00 0.00 2.83
85 86 2.408271 TCTGGGCTGTCTATGCTTTG 57.592 50.000 0.00 0.00 0.00 2.77
86 87 2.356535 CCTTCTGGGCTGTCTATGCTTT 60.357 50.000 0.00 0.00 0.00 3.51
87 88 1.211457 CCTTCTGGGCTGTCTATGCTT 59.789 52.381 0.00 0.00 0.00 3.91
88 89 0.835941 CCTTCTGGGCTGTCTATGCT 59.164 55.000 0.00 0.00 0.00 3.79
89 90 0.833287 TCCTTCTGGGCTGTCTATGC 59.167 55.000 0.00 0.00 34.39 3.14
90 91 2.437281 ACATCCTTCTGGGCTGTCTATG 59.563 50.000 0.00 0.00 34.39 2.23
91 92 2.703007 GACATCCTTCTGGGCTGTCTAT 59.297 50.000 10.27 0.00 40.27 1.98
92 93 2.111384 GACATCCTTCTGGGCTGTCTA 58.889 52.381 10.27 0.00 40.27 2.59
93 94 0.908198 GACATCCTTCTGGGCTGTCT 59.092 55.000 10.27 0.00 40.27 3.41
94 95 0.460987 CGACATCCTTCTGGGCTGTC 60.461 60.000 8.14 8.14 40.15 3.51
95 96 1.599047 CGACATCCTTCTGGGCTGT 59.401 57.895 0.00 0.00 34.10 4.40
96 97 1.817099 GCGACATCCTTCTGGGCTG 60.817 63.158 0.00 0.00 34.39 4.85
97 98 2.586792 GCGACATCCTTCTGGGCT 59.413 61.111 0.00 0.00 34.39 5.19
98 99 1.686325 TAGGCGACATCCTTCTGGGC 61.686 60.000 0.00 0.00 37.66 5.36
99 100 0.390860 CTAGGCGACATCCTTCTGGG 59.609 60.000 0.00 0.00 37.66 4.45
100 101 0.249657 GCTAGGCGACATCCTTCTGG 60.250 60.000 0.00 0.00 37.66 3.86
101 102 0.249657 GGCTAGGCGACATCCTTCTG 60.250 60.000 0.00 0.00 37.66 3.02
102 103 1.403687 GGGCTAGGCGACATCCTTCT 61.404 60.000 10.58 0.00 37.66 2.85
103 104 1.069935 GGGCTAGGCGACATCCTTC 59.930 63.158 10.58 0.00 37.66 3.46
104 105 1.689233 TGGGCTAGGCGACATCCTT 60.689 57.895 10.58 0.00 37.66 3.36
105 106 2.041922 TGGGCTAGGCGACATCCT 60.042 61.111 10.58 0.00 40.21 3.24
106 107 1.686325 TTCTGGGCTAGGCGACATCC 61.686 60.000 10.58 0.00 0.00 3.51
107 108 0.178068 TTTCTGGGCTAGGCGACATC 59.822 55.000 10.58 0.00 0.00 3.06
108 109 0.618458 TTTTCTGGGCTAGGCGACAT 59.382 50.000 10.58 0.00 0.00 3.06
109 110 0.398696 TTTTTCTGGGCTAGGCGACA 59.601 50.000 10.58 2.58 0.00 4.35
110 111 0.803117 GTTTTTCTGGGCTAGGCGAC 59.197 55.000 10.58 0.00 0.00 5.19
111 112 0.398696 TGTTTTTCTGGGCTAGGCGA 59.601 50.000 10.58 5.39 0.00 5.54
112 113 1.068541 GTTGTTTTTCTGGGCTAGGCG 60.069 52.381 10.58 0.00 0.00 5.52
113 114 2.229062 GAGTTGTTTTTCTGGGCTAGGC 59.771 50.000 8.00 8.00 0.00 3.93
114 115 3.253432 GTGAGTTGTTTTTCTGGGCTAGG 59.747 47.826 0.00 0.00 0.00 3.02
115 116 3.882888 TGTGAGTTGTTTTTCTGGGCTAG 59.117 43.478 0.00 0.00 0.00 3.42
116 117 3.630312 GTGTGAGTTGTTTTTCTGGGCTA 59.370 43.478 0.00 0.00 0.00 3.93
117 118 2.427095 GTGTGAGTTGTTTTTCTGGGCT 59.573 45.455 0.00 0.00 0.00 5.19
118 119 2.794631 CGTGTGAGTTGTTTTTCTGGGC 60.795 50.000 0.00 0.00 0.00 5.36
119 120 2.680841 TCGTGTGAGTTGTTTTTCTGGG 59.319 45.455 0.00 0.00 0.00 4.45
120 121 3.680789 GTCGTGTGAGTTGTTTTTCTGG 58.319 45.455 0.00 0.00 0.00 3.86
121 122 3.342269 CGTCGTGTGAGTTGTTTTTCTG 58.658 45.455 0.00 0.00 0.00 3.02
122 123 2.222953 GCGTCGTGTGAGTTGTTTTTCT 60.223 45.455 0.00 0.00 0.00 2.52
123 124 2.098870 GCGTCGTGTGAGTTGTTTTTC 58.901 47.619 0.00 0.00 0.00 2.29
124 125 1.735571 AGCGTCGTGTGAGTTGTTTTT 59.264 42.857 0.00 0.00 0.00 1.94
125 126 1.062002 CAGCGTCGTGTGAGTTGTTTT 59.938 47.619 0.00 0.00 0.00 2.43
126 127 0.650512 CAGCGTCGTGTGAGTTGTTT 59.349 50.000 0.00 0.00 0.00 2.83
127 128 1.151777 CCAGCGTCGTGTGAGTTGTT 61.152 55.000 0.00 0.00 0.00 2.83
128 129 1.591594 CCAGCGTCGTGTGAGTTGT 60.592 57.895 0.00 0.00 0.00 3.32
129 130 2.943345 GCCAGCGTCGTGTGAGTTG 61.943 63.158 0.00 0.00 0.00 3.16
130 131 2.661866 GCCAGCGTCGTGTGAGTT 60.662 61.111 0.00 0.00 0.00 3.01
132 133 4.700365 TCGCCAGCGTCGTGTGAG 62.700 66.667 12.32 0.00 40.74 3.51
133 134 4.700365 CTCGCCAGCGTCGTGTGA 62.700 66.667 12.32 0.00 40.74 3.58
151 152 4.394712 GTGTCCCTCAGCCACCCG 62.395 72.222 0.00 0.00 0.00 5.28
152 153 4.394712 CGTGTCCCTCAGCCACCC 62.395 72.222 0.00 0.00 0.00 4.61
153 154 3.591254 GACGTGTCCCTCAGCCACC 62.591 68.421 0.00 0.00 0.00 4.61
154 155 2.048127 GACGTGTCCCTCAGCCAC 60.048 66.667 0.00 0.00 0.00 5.01
155 156 2.523168 TGACGTGTCCCTCAGCCA 60.523 61.111 0.00 0.00 0.00 4.75
156 157 2.262915 CTGACGTGTCCCTCAGCC 59.737 66.667 0.00 0.00 0.00 4.85
158 159 1.080230 CAGCTGACGTGTCCCTCAG 60.080 63.158 8.42 0.00 37.55 3.35
159 160 2.574018 CCAGCTGACGTGTCCCTCA 61.574 63.158 17.39 0.00 0.00 3.86
160 161 2.262915 CCAGCTGACGTGTCCCTC 59.737 66.667 17.39 0.00 0.00 4.30
161 162 4.008933 GCCAGCTGACGTGTCCCT 62.009 66.667 17.39 0.00 0.00 4.20
162 163 4.008933 AGCCAGCTGACGTGTCCC 62.009 66.667 17.39 0.00 0.00 4.46
163 164 2.740055 CAGCCAGCTGACGTGTCC 60.740 66.667 17.39 0.00 46.30 4.02
164 165 1.735920 CTCAGCCAGCTGACGTGTC 60.736 63.158 18.14 0.00 46.80 3.67
165 166 2.203082 TCTCAGCCAGCTGACGTGT 61.203 57.895 18.14 0.00 46.80 4.49
166 167 1.735920 GTCTCAGCCAGCTGACGTG 60.736 63.158 18.14 9.37 46.80 4.49
167 168 2.653702 GTCTCAGCCAGCTGACGT 59.346 61.111 18.14 0.00 46.80 4.34
168 169 2.125753 GGTCTCAGCCAGCTGACG 60.126 66.667 18.14 13.83 46.80 4.35
169 170 0.250467 TTTGGTCTCAGCCAGCTGAC 60.250 55.000 18.14 2.52 46.80 3.51
171 172 1.542492 AATTTGGTCTCAGCCAGCTG 58.458 50.000 13.54 13.54 44.86 4.24
172 173 2.716217 GTAATTTGGTCTCAGCCAGCT 58.284 47.619 0.00 0.00 40.01 4.24
173 174 1.398390 CGTAATTTGGTCTCAGCCAGC 59.602 52.381 0.00 0.00 40.01 4.85
174 175 2.673368 GACGTAATTTGGTCTCAGCCAG 59.327 50.000 0.00 0.00 40.01 4.85
175 176 2.301870 AGACGTAATTTGGTCTCAGCCA 59.698 45.455 5.52 0.00 39.18 4.75
176 177 2.973945 AGACGTAATTTGGTCTCAGCC 58.026 47.619 5.52 0.00 39.18 4.85
181 182 4.810790 CTGACTGAGACGTAATTTGGTCT 58.189 43.478 9.96 9.96 45.71 3.85
182 183 3.368236 GCTGACTGAGACGTAATTTGGTC 59.632 47.826 0.00 1.46 0.00 4.02
183 184 3.006967 AGCTGACTGAGACGTAATTTGGT 59.993 43.478 0.00 0.00 0.00 3.67
184 185 3.589988 AGCTGACTGAGACGTAATTTGG 58.410 45.455 0.00 0.00 0.00 3.28
197 198 1.468908 CGCCTAGAACTCAGCTGACTG 60.469 57.143 13.74 6.89 45.95 3.51
198 199 0.814457 CGCCTAGAACTCAGCTGACT 59.186 55.000 13.74 11.48 0.00 3.41
199 200 0.811915 TCGCCTAGAACTCAGCTGAC 59.188 55.000 13.74 3.12 0.00 3.51
200 201 1.678627 GATCGCCTAGAACTCAGCTGA 59.321 52.381 17.19 17.19 0.00 4.26
201 202 1.269517 GGATCGCCTAGAACTCAGCTG 60.270 57.143 7.63 7.63 0.00 4.24
202 203 1.036707 GGATCGCCTAGAACTCAGCT 58.963 55.000 0.00 0.00 0.00 4.24
203 204 0.032815 GGGATCGCCTAGAACTCAGC 59.967 60.000 0.00 0.00 0.00 4.26
204 205 1.403814 TGGGATCGCCTAGAACTCAG 58.596 55.000 7.38 0.00 28.24 3.35
205 206 1.860641 TTGGGATCGCCTAGAACTCA 58.139 50.000 7.38 0.00 29.60 3.41
206 207 2.981859 TTTGGGATCGCCTAGAACTC 57.018 50.000 7.38 0.00 0.00 3.01
207 208 2.505819 ACATTTGGGATCGCCTAGAACT 59.494 45.455 7.38 0.00 0.00 3.01
208 209 2.919228 ACATTTGGGATCGCCTAGAAC 58.081 47.619 7.38 0.00 0.00 3.01
209 210 3.644966 AACATTTGGGATCGCCTAGAA 57.355 42.857 7.38 0.00 0.00 2.10
210 211 3.644966 AAACATTTGGGATCGCCTAGA 57.355 42.857 7.38 0.00 0.00 2.43
211 212 6.231211 AGTATAAACATTTGGGATCGCCTAG 58.769 40.000 7.38 0.00 0.00 3.02
212 213 6.182507 AGTATAAACATTTGGGATCGCCTA 57.817 37.500 7.38 0.00 0.00 3.93
213 214 5.048846 AGTATAAACATTTGGGATCGCCT 57.951 39.130 7.38 0.00 0.00 5.52
214 215 7.448748 AATAGTATAAACATTTGGGATCGCC 57.551 36.000 7.38 0.12 0.00 5.54
701 704 4.957759 ACGGAAGATAAAAATCGGTTGG 57.042 40.909 0.00 0.00 0.00 3.77
1024 1027 8.883731 ACCAATCGAAAATAAATAGACACTCAG 58.116 33.333 0.00 0.00 0.00 3.35
1240 1243 7.316393 TCCTATTACGATGGATGGAAGAAAT 57.684 36.000 0.00 0.00 0.00 2.17
1637 1749 8.638873 TGAGTTATATGTATTGTAGACACCAGG 58.361 37.037 0.00 0.00 0.00 4.45
2013 2127 2.897969 ACAGGCTTCTTCGGTAAAGAGA 59.102 45.455 0.00 0.00 44.69 3.10
2064 2178 8.827177 TGATAAAGACAAGATACGTTTTGACT 57.173 30.769 12.27 9.21 32.23 3.41


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

AutoCloner maintained by Alex Coulton.