Multiple sequence alignment - TraesCS4A01G168600

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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 TraesCS4A01G168600 chr4A 100.000 2219 0 0 1 2219 421167045 421169263 0.000000e+00 4098
1 TraesCS4A01G168600 chr4A 82.893 2005 297 22 237 2217 602642052 602644034 0.000000e+00 1760
2 TraesCS4A01G168600 chr4A 99.563 229 1 0 1 229 189960905 189960677 3.410000e-113 418
3 TraesCS4A01G168600 chr4A 99.563 229 1 0 1 229 194664848 194664620 3.410000e-113 418
4 TraesCS4A01G168600 chr4A 99.563 229 1 0 1 229 206706745 206706973 3.410000e-113 418
5 TraesCS4A01G168600 chr4A 99.563 229 1 0 1 229 310302094 310302322 3.410000e-113 418
6 TraesCS4A01G168600 chr4A 99.563 229 1 0 1 229 329373861 329373633 3.410000e-113 418
7 TraesCS4A01G168600 chr4A 99.563 229 1 0 1 229 402868591 402868363 3.410000e-113 418
8 TraesCS4A01G168600 chr4A 69.538 1927 517 58 237 2134 688902781 688904666 2.200000e-60 243
9 TraesCS4A01G168600 chr6D 86.783 2005 238 17 230 2217 225480176 225478182 0.000000e+00 2209
10 TraesCS4A01G168600 chr7B 86.194 1905 257 4 229 2133 351903800 351901902 0.000000e+00 2056
11 TraesCS4A01G168600 chr7B 84.192 2018 285 18 229 2217 706805273 706803261 0.000000e+00 1929
12 TraesCS4A01G168600 chr7B 84.846 1300 188 7 692 1987 70969081 70970375 0.000000e+00 1301
13 TraesCS4A01G168600 chr3B 85.639 1908 265 5 229 2133 180541903 180540002 0.000000e+00 1997
14 TraesCS4A01G168600 chr7D 81.505 2006 320 25 229 2217 599472999 599471028 0.000000e+00 1602
15 TraesCS4A01G168600 chrUn 99.563 229 1 0 1 229 258309153 258308925 3.410000e-113 418
16 TraesCS4A01G168600 chrUn 99.563 229 1 0 1 229 258317348 258317120 3.410000e-113 418
17 TraesCS4A01G168600 chrUn 99.563 229 1 0 1 229 311124368 311124140 3.410000e-113 418
18 TraesCS4A01G168600 chr6A 70.976 1926 502 47 237 2134 307955998 307957894 7.380000e-110 407
19 TraesCS4A01G168600 chr6B 70.249 1926 513 56 237 2134 225885114 225887007 5.910000e-86 327
20 TraesCS4A01G168600 chr6B 70.863 1414 383 27 734 2134 464716887 464718284 3.580000e-78 302
21 TraesCS4A01G168600 chr6B 69.943 1923 521 49 239 2134 686845046 686846938 1.670000e-76 296
22 TraesCS4A01G168600 chr6B 69.782 1926 519 54 239 2134 686839998 686841890 7.810000e-70 274
23 TraesCS4A01G168600 chr2A 70.913 1413 379 28 734 2134 560778855 560777463 9.960000e-79 303
24 TraesCS4A01G168600 chr2A 75.107 233 56 2 1901 2132 549948571 549948340 8.380000e-20 108
25 TraesCS4A01G168600 chr2B 73.913 506 126 6 734 1236 401284651 401285153 4.830000e-47 198
26 TraesCS4A01G168600 chr1A 70.437 1052 285 23 237 1275 566230139 566231177 1.740000e-46 196
27 TraesCS4A01G168600 chr3A 87.421 159 5 8 2073 2217 225871660 225871817 3.790000e-38 169
28 TraesCS4A01G168600 chr5A 70.779 616 158 15 1499 2103 23810583 23811187 1.080000e-23 121


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 TraesCS4A01G168600 chr4A 421167045 421169263 2218 False 4098 4098 100.0000 1 2219 1 chr4A.!!$F3 2218
1 TraesCS4A01G168600 chr4A 602642052 602644034 1982 False 1760 1760 82.8930 237 2217 1 chr4A.!!$F4 1980
2 TraesCS4A01G168600 chr4A 688902781 688904666 1885 False 243 243 69.5380 237 2134 1 chr4A.!!$F5 1897
3 TraesCS4A01G168600 chr6D 225478182 225480176 1994 True 2209 2209 86.7830 230 2217 1 chr6D.!!$R1 1987
4 TraesCS4A01G168600 chr7B 351901902 351903800 1898 True 2056 2056 86.1940 229 2133 1 chr7B.!!$R1 1904
5 TraesCS4A01G168600 chr7B 706803261 706805273 2012 True 1929 1929 84.1920 229 2217 1 chr7B.!!$R2 1988
6 TraesCS4A01G168600 chr7B 70969081 70970375 1294 False 1301 1301 84.8460 692 1987 1 chr7B.!!$F1 1295
7 TraesCS4A01G168600 chr3B 180540002 180541903 1901 True 1997 1997 85.6390 229 2133 1 chr3B.!!$R1 1904
8 TraesCS4A01G168600 chr7D 599471028 599472999 1971 True 1602 1602 81.5050 229 2217 1 chr7D.!!$R1 1988
9 TraesCS4A01G168600 chr6A 307955998 307957894 1896 False 407 407 70.9760 237 2134 1 chr6A.!!$F1 1897
10 TraesCS4A01G168600 chr6B 225885114 225887007 1893 False 327 327 70.2490 237 2134 1 chr6B.!!$F1 1897
11 TraesCS4A01G168600 chr6B 464716887 464718284 1397 False 302 302 70.8630 734 2134 1 chr6B.!!$F2 1400
12 TraesCS4A01G168600 chr6B 686839998 686846938 6940 False 285 296 69.8625 239 2134 2 chr6B.!!$F3 1895
13 TraesCS4A01G168600 chr2A 560777463 560778855 1392 True 303 303 70.9130 734 2134 1 chr2A.!!$R2 1400

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
214 215 0.03563 ATCACAGAACAGGCCAGAGC 60.036 55.0 5.01 0.0 38.76 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1977 7057 0.036388 GCCTGTCCGTTTGAGGATGA 60.036 55.0 0.0 0.0 43.04 2.92 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
32 33 8.986929 AAAAATGTTCAATATTTTGGTTGGGA 57.013 26.923 5.68 0.00 37.68 4.37
33 34 7.977789 AAATGTTCAATATTTTGGTTGGGAC 57.022 32.000 0.00 0.00 33.44 4.46
34 35 5.476091 TGTTCAATATTTTGGTTGGGACC 57.524 39.130 0.00 0.00 46.71 4.46
42 43 3.589139 GGTTGGGACCAGAACCCT 58.411 61.111 11.95 0.00 46.82 4.34
43 44 1.851267 GGTTGGGACCAGAACCCTT 59.149 57.895 11.95 0.00 46.82 3.95
44 45 1.069775 GGTTGGGACCAGAACCCTTA 58.930 55.000 11.95 0.00 46.82 2.69
45 46 1.271762 GGTTGGGACCAGAACCCTTAC 60.272 57.143 11.95 0.00 46.82 2.34
46 47 1.069775 TTGGGACCAGAACCCTTACC 58.930 55.000 0.00 0.00 46.82 2.85
47 48 0.104356 TGGGACCAGAACCCTTACCA 60.104 55.000 0.00 0.00 46.82 3.25
48 49 1.069775 GGGACCAGAACCCTTACCAA 58.930 55.000 0.00 0.00 43.65 3.67
49 50 1.426215 GGGACCAGAACCCTTACCAAA 59.574 52.381 0.00 0.00 43.65 3.28
50 51 2.158430 GGGACCAGAACCCTTACCAAAA 60.158 50.000 0.00 0.00 43.65 2.44
51 52 3.568443 GGACCAGAACCCTTACCAAAAA 58.432 45.455 0.00 0.00 0.00 1.94
52 53 4.157246 GGACCAGAACCCTTACCAAAAAT 58.843 43.478 0.00 0.00 0.00 1.82
53 54 4.591498 GGACCAGAACCCTTACCAAAAATT 59.409 41.667 0.00 0.00 0.00 1.82
54 55 5.776208 GGACCAGAACCCTTACCAAAAATTA 59.224 40.000 0.00 0.00 0.00 1.40
55 56 6.439375 GGACCAGAACCCTTACCAAAAATTAT 59.561 38.462 0.00 0.00 0.00 1.28
56 57 7.363530 GGACCAGAACCCTTACCAAAAATTATC 60.364 40.741 0.00 0.00 0.00 1.75
57 58 7.013834 ACCAGAACCCTTACCAAAAATTATCA 58.986 34.615 0.00 0.00 0.00 2.15
58 59 7.511028 ACCAGAACCCTTACCAAAAATTATCAA 59.489 33.333 0.00 0.00 0.00 2.57
59 60 8.371699 CCAGAACCCTTACCAAAAATTATCAAA 58.628 33.333 0.00 0.00 0.00 2.69
60 61 9.203421 CAGAACCCTTACCAAAAATTATCAAAC 57.797 33.333 0.00 0.00 0.00 2.93
61 62 8.929487 AGAACCCTTACCAAAAATTATCAAACA 58.071 29.630 0.00 0.00 0.00 2.83
62 63 9.719355 GAACCCTTACCAAAAATTATCAAACAT 57.281 29.630 0.00 0.00 0.00 2.71
80 81 8.592105 TCAAACATTTAAGAAGAGCATTTTGG 57.408 30.769 0.00 0.00 0.00 3.28
81 82 8.420222 TCAAACATTTAAGAAGAGCATTTTGGA 58.580 29.630 0.00 0.00 0.00 3.53
82 83 8.706035 CAAACATTTAAGAAGAGCATTTTGGAG 58.294 33.333 0.00 0.00 0.00 3.86
83 84 6.393171 ACATTTAAGAAGAGCATTTTGGAGC 58.607 36.000 0.00 0.00 0.00 4.70
84 85 6.015180 ACATTTAAGAAGAGCATTTTGGAGCA 60.015 34.615 0.00 0.00 0.00 4.26
85 86 6.403866 TTTAAGAAGAGCATTTTGGAGCAA 57.596 33.333 0.00 0.00 0.00 3.91
86 87 6.594788 TTAAGAAGAGCATTTTGGAGCAAT 57.405 33.333 0.00 0.00 0.00 3.56
87 88 4.451629 AGAAGAGCATTTTGGAGCAATG 57.548 40.909 0.00 0.00 35.12 2.82
88 89 4.084287 AGAAGAGCATTTTGGAGCAATGA 58.916 39.130 0.00 0.00 34.05 2.57
89 90 4.525487 AGAAGAGCATTTTGGAGCAATGAA 59.475 37.500 0.00 0.00 34.05 2.57
90 91 5.187186 AGAAGAGCATTTTGGAGCAATGAAT 59.813 36.000 0.00 0.00 34.05 2.57
91 92 4.755411 AGAGCATTTTGGAGCAATGAATG 58.245 39.130 0.00 0.00 34.05 2.67
92 93 4.464951 AGAGCATTTTGGAGCAATGAATGA 59.535 37.500 0.00 0.00 34.05 2.57
93 94 4.755411 AGCATTTTGGAGCAATGAATGAG 58.245 39.130 0.00 0.00 34.05 2.90
94 95 4.464951 AGCATTTTGGAGCAATGAATGAGA 59.535 37.500 0.00 0.00 34.05 3.27
95 96 5.128827 AGCATTTTGGAGCAATGAATGAGAT 59.871 36.000 0.00 0.00 34.05 2.75
96 97 5.815740 GCATTTTGGAGCAATGAATGAGATT 59.184 36.000 0.00 0.00 34.05 2.40
97 98 6.315393 GCATTTTGGAGCAATGAATGAGATTT 59.685 34.615 0.00 0.00 34.05 2.17
98 99 7.465513 GCATTTTGGAGCAATGAATGAGATTTC 60.466 37.037 0.00 0.00 34.05 2.17
99 100 6.845758 TTTGGAGCAATGAATGAGATTTCT 57.154 33.333 0.00 0.00 0.00 2.52
100 101 7.943079 TTTGGAGCAATGAATGAGATTTCTA 57.057 32.000 0.00 0.00 0.00 2.10
101 102 7.563888 TTGGAGCAATGAATGAGATTTCTAG 57.436 36.000 0.00 0.00 0.00 2.43
102 103 6.060136 TGGAGCAATGAATGAGATTTCTAGG 58.940 40.000 0.00 0.00 0.00 3.02
103 104 5.472820 GGAGCAATGAATGAGATTTCTAGGG 59.527 44.000 0.00 0.00 0.00 3.53
104 105 6.011122 AGCAATGAATGAGATTTCTAGGGT 57.989 37.500 0.00 0.00 0.00 4.34
105 106 6.430007 AGCAATGAATGAGATTTCTAGGGTT 58.570 36.000 0.00 0.00 0.00 4.11
106 107 6.894103 AGCAATGAATGAGATTTCTAGGGTTT 59.106 34.615 0.00 0.00 0.00 3.27
107 108 7.398332 AGCAATGAATGAGATTTCTAGGGTTTT 59.602 33.333 0.00 0.00 0.00 2.43
108 109 8.037166 GCAATGAATGAGATTTCTAGGGTTTTT 58.963 33.333 0.00 0.00 0.00 1.94
109 110 9.362539 CAATGAATGAGATTTCTAGGGTTTTTG 57.637 33.333 0.00 0.00 0.00 2.44
110 111 6.924111 TGAATGAGATTTCTAGGGTTTTTGC 58.076 36.000 0.00 0.00 0.00 3.68
111 112 5.921962 ATGAGATTTCTAGGGTTTTTGCC 57.078 39.130 0.00 0.00 0.00 4.52
122 123 4.634012 GGGTTTTTGCCCCTCTTTTATT 57.366 40.909 0.00 0.00 42.89 1.40
123 124 4.980573 GGGTTTTTGCCCCTCTTTTATTT 58.019 39.130 0.00 0.00 42.89 1.40
124 125 6.116711 GGGTTTTTGCCCCTCTTTTATTTA 57.883 37.500 0.00 0.00 42.89 1.40
125 126 6.535540 GGGTTTTTGCCCCTCTTTTATTTAA 58.464 36.000 0.00 0.00 42.89 1.52
126 127 6.653320 GGGTTTTTGCCCCTCTTTTATTTAAG 59.347 38.462 0.00 0.00 42.89 1.85
127 128 7.221450 GGTTTTTGCCCCTCTTTTATTTAAGT 58.779 34.615 0.00 0.00 0.00 2.24
128 129 7.717875 GGTTTTTGCCCCTCTTTTATTTAAGTT 59.282 33.333 0.00 0.00 0.00 2.66
129 130 9.116067 GTTTTTGCCCCTCTTTTATTTAAGTTT 57.884 29.630 0.00 0.00 0.00 2.66
130 131 9.688091 TTTTTGCCCCTCTTTTATTTAAGTTTT 57.312 25.926 0.00 0.00 0.00 2.43
131 132 9.688091 TTTTGCCCCTCTTTTATTTAAGTTTTT 57.312 25.926 0.00 0.00 0.00 1.94
132 133 8.669946 TTGCCCCTCTTTTATTTAAGTTTTTG 57.330 30.769 0.00 0.00 0.00 2.44
133 134 8.024145 TGCCCCTCTTTTATTTAAGTTTTTGA 57.976 30.769 0.00 0.00 0.00 2.69
134 135 8.147704 TGCCCCTCTTTTATTTAAGTTTTTGAG 58.852 33.333 0.00 0.00 0.00 3.02
135 136 7.602644 GCCCCTCTTTTATTTAAGTTTTTGAGG 59.397 37.037 0.00 0.00 37.63 3.86
136 137 7.602644 CCCCTCTTTTATTTAAGTTTTTGAGGC 59.397 37.037 0.00 0.00 36.85 4.70
137 138 8.367911 CCCTCTTTTATTTAAGTTTTTGAGGCT 58.632 33.333 0.00 0.00 36.85 4.58
138 139 9.764363 CCTCTTTTATTTAAGTTTTTGAGGCTT 57.236 29.630 0.00 0.00 32.36 4.35
140 141 9.758651 TCTTTTATTTAAGTTTTTGAGGCTTCC 57.241 29.630 0.00 0.00 0.00 3.46
141 142 9.541143 CTTTTATTTAAGTTTTTGAGGCTTCCA 57.459 29.630 0.00 0.00 0.00 3.53
142 143 9.892130 TTTTATTTAAGTTTTTGAGGCTTCCAA 57.108 25.926 0.00 0.00 0.00 3.53
143 144 9.892130 TTTATTTAAGTTTTTGAGGCTTCCAAA 57.108 25.926 0.00 0.00 0.00 3.28
144 145 9.892130 TTATTTAAGTTTTTGAGGCTTCCAAAA 57.108 25.926 9.34 9.34 40.47 2.44
145 146 8.978874 ATTTAAGTTTTTGAGGCTTCCAAAAT 57.021 26.923 13.02 0.00 41.39 1.82
146 147 8.800370 TTTAAGTTTTTGAGGCTTCCAAAATT 57.200 26.923 13.02 9.03 41.39 1.82
147 148 6.925610 AAGTTTTTGAGGCTTCCAAAATTC 57.074 33.333 13.02 10.16 41.39 2.17
148 149 5.368145 AGTTTTTGAGGCTTCCAAAATTCC 58.632 37.500 13.02 6.56 41.39 3.01
149 150 5.130975 AGTTTTTGAGGCTTCCAAAATTCCT 59.869 36.000 13.02 8.18 41.39 3.36
150 151 4.871933 TTTGAGGCTTCCAAAATTCCTC 57.128 40.909 0.00 0.00 42.67 3.71
152 153 3.424703 TGAGGCTTCCAAAATTCCTCAG 58.575 45.455 5.85 0.00 45.83 3.35
153 154 3.181429 TGAGGCTTCCAAAATTCCTCAGT 60.181 43.478 5.85 0.00 45.83 3.41
154 155 3.829026 GAGGCTTCCAAAATTCCTCAGTT 59.171 43.478 0.00 0.00 42.10 3.16
155 156 3.829026 AGGCTTCCAAAATTCCTCAGTTC 59.171 43.478 0.00 0.00 0.00 3.01
156 157 3.573967 GGCTTCCAAAATTCCTCAGTTCA 59.426 43.478 0.00 0.00 0.00 3.18
157 158 4.039124 GGCTTCCAAAATTCCTCAGTTCAA 59.961 41.667 0.00 0.00 0.00 2.69
158 159 5.225642 GCTTCCAAAATTCCTCAGTTCAAG 58.774 41.667 0.00 0.00 0.00 3.02
159 160 5.221322 GCTTCCAAAATTCCTCAGTTCAAGT 60.221 40.000 0.00 0.00 0.00 3.16
160 161 6.683861 GCTTCCAAAATTCCTCAGTTCAAGTT 60.684 38.462 0.00 0.00 0.00 2.66
161 162 6.790232 TCCAAAATTCCTCAGTTCAAGTTT 57.210 33.333 0.00 0.00 0.00 2.66
162 163 6.805713 TCCAAAATTCCTCAGTTCAAGTTTC 58.194 36.000 0.00 0.00 0.00 2.78
163 164 6.379703 TCCAAAATTCCTCAGTTCAAGTTTCA 59.620 34.615 0.00 0.00 0.00 2.69
164 165 6.698766 CCAAAATTCCTCAGTTCAAGTTTCAG 59.301 38.462 0.00 0.00 0.00 3.02
165 166 7.416664 CCAAAATTCCTCAGTTCAAGTTTCAGA 60.417 37.037 0.00 0.00 0.00 3.27
166 167 7.645058 AAATTCCTCAGTTCAAGTTTCAGAA 57.355 32.000 0.00 0.00 0.00 3.02
167 168 7.645058 AATTCCTCAGTTCAAGTTTCAGAAA 57.355 32.000 0.00 0.00 0.00 2.52
168 169 7.830099 ATTCCTCAGTTCAAGTTTCAGAAAT 57.170 32.000 0.00 0.00 0.00 2.17
169 170 8.924511 ATTCCTCAGTTCAAGTTTCAGAAATA 57.075 30.769 0.00 0.00 0.00 1.40
170 171 8.924511 TTCCTCAGTTCAAGTTTCAGAAATAT 57.075 30.769 0.00 0.00 0.00 1.28
172 173 9.658799 TCCTCAGTTCAAGTTTCAGAAATATAG 57.341 33.333 0.00 0.00 0.00 1.31
173 174 9.658799 CCTCAGTTCAAGTTTCAGAAATATAGA 57.341 33.333 0.00 0.00 0.00 1.98
175 176 9.996554 TCAGTTCAAGTTTCAGAAATATAGACA 57.003 29.630 0.00 0.00 0.00 3.41
181 182 9.661187 CAAGTTTCAGAAATATAGACATGATGC 57.339 33.333 0.00 0.00 0.00 3.91
182 183 8.969260 AGTTTCAGAAATATAGACATGATGCA 57.031 30.769 0.00 0.00 0.00 3.96
183 184 9.399797 AGTTTCAGAAATATAGACATGATGCAA 57.600 29.630 0.00 0.00 0.00 4.08
186 187 8.735692 TCAGAAATATAGACATGATGCAAACA 57.264 30.769 0.00 0.00 0.00 2.83
187 188 9.346005 TCAGAAATATAGACATGATGCAAACAT 57.654 29.630 0.00 0.00 39.98 2.71
194 195 3.239587 CATGATGCAAACATGGAAGCA 57.760 42.857 21.68 10.02 42.66 3.91
195 196 3.591023 CATGATGCAAACATGGAAGCAA 58.409 40.909 21.68 0.00 42.66 3.91
196 197 3.965379 TGATGCAAACATGGAAGCAAT 57.035 38.095 11.34 2.53 40.76 3.56
197 198 3.852286 TGATGCAAACATGGAAGCAATC 58.148 40.909 11.34 9.99 40.76 2.67
198 199 3.258622 TGATGCAAACATGGAAGCAATCA 59.741 39.130 11.34 11.80 40.76 2.57
199 200 3.029320 TGCAAACATGGAAGCAATCAC 57.971 42.857 5.85 0.00 33.48 3.06
200 201 2.364647 TGCAAACATGGAAGCAATCACA 59.635 40.909 5.85 0.00 33.48 3.58
201 202 2.991190 GCAAACATGGAAGCAATCACAG 59.009 45.455 0.00 0.00 0.00 3.66
202 203 3.305539 GCAAACATGGAAGCAATCACAGA 60.306 43.478 0.00 0.00 0.00 3.41
203 204 4.796946 GCAAACATGGAAGCAATCACAGAA 60.797 41.667 0.00 0.00 0.00 3.02
204 205 4.510038 AACATGGAAGCAATCACAGAAC 57.490 40.909 0.00 0.00 0.00 3.01
205 206 3.489355 ACATGGAAGCAATCACAGAACA 58.511 40.909 0.00 0.00 0.00 3.18
206 207 3.504906 ACATGGAAGCAATCACAGAACAG 59.495 43.478 0.00 0.00 0.00 3.16
207 208 2.507484 TGGAAGCAATCACAGAACAGG 58.493 47.619 0.00 0.00 0.00 4.00
208 209 1.200948 GGAAGCAATCACAGAACAGGC 59.799 52.381 0.00 0.00 0.00 4.85
209 210 1.200948 GAAGCAATCACAGAACAGGCC 59.799 52.381 0.00 0.00 0.00 5.19
210 211 0.111061 AGCAATCACAGAACAGGCCA 59.889 50.000 5.01 0.00 0.00 5.36
211 212 0.524862 GCAATCACAGAACAGGCCAG 59.475 55.000 5.01 0.00 0.00 4.85
212 213 1.883638 GCAATCACAGAACAGGCCAGA 60.884 52.381 5.01 0.00 0.00 3.86
213 214 2.082231 CAATCACAGAACAGGCCAGAG 58.918 52.381 5.01 0.00 0.00 3.35
214 215 0.035630 ATCACAGAACAGGCCAGAGC 60.036 55.000 5.01 0.00 38.76 4.09
215 216 1.123861 TCACAGAACAGGCCAGAGCT 61.124 55.000 5.01 0.00 39.73 4.09
216 217 0.610174 CACAGAACAGGCCAGAGCTA 59.390 55.000 5.01 0.00 39.73 3.32
217 218 1.002430 CACAGAACAGGCCAGAGCTAA 59.998 52.381 5.01 0.00 39.73 3.09
218 219 1.277557 ACAGAACAGGCCAGAGCTAAG 59.722 52.381 5.01 0.00 39.73 2.18
219 220 0.908198 AGAACAGGCCAGAGCTAAGG 59.092 55.000 5.01 0.00 39.73 2.69
220 221 0.905357 GAACAGGCCAGAGCTAAGGA 59.095 55.000 5.01 0.00 39.73 3.36
221 222 1.488393 GAACAGGCCAGAGCTAAGGAT 59.512 52.381 5.01 0.00 39.73 3.24
222 223 0.835941 ACAGGCCAGAGCTAAGGATG 59.164 55.000 5.01 7.77 39.73 3.51
223 224 0.835941 CAGGCCAGAGCTAAGGATGT 59.164 55.000 5.01 0.00 39.73 3.06
224 225 0.835941 AGGCCAGAGCTAAGGATGTG 59.164 55.000 5.01 0.00 39.73 3.21
225 226 0.833287 GGCCAGAGCTAAGGATGTGA 59.167 55.000 8.06 0.00 39.73 3.58
226 227 1.474143 GGCCAGAGCTAAGGATGTGAC 60.474 57.143 8.06 0.00 39.73 3.67
227 228 1.208052 GCCAGAGCTAAGGATGTGACA 59.792 52.381 8.06 0.00 35.50 3.58
327 328 1.050988 ATCTCTGTGCGGGCTACCAT 61.051 55.000 0.00 0.00 36.13 3.55
402 403 3.798202 AGGACACTTTGAGTTCACAGTC 58.202 45.455 0.00 0.00 34.93 3.51
425 426 4.681978 GTTCGGGCTCGCAGGTGT 62.682 66.667 0.00 0.00 36.13 4.16
456 457 0.550914 TTTTGGGAGCAGTGACCACT 59.449 50.000 0.00 0.00 43.61 4.00
591 601 3.256631 TGAGAAAAGATTGCTGGAAAGCC 59.743 43.478 0.00 0.00 0.00 4.35
649 659 1.983119 ATACCTGGGGCACACCATCG 61.983 60.000 0.00 0.00 42.91 3.84
672 682 2.047274 CAAGGCGTGTCCACCGAT 60.047 61.111 0.00 0.00 37.29 4.18
699 709 1.549203 AAATTGCAGCCGTGAAGGAT 58.451 45.000 0.00 0.00 45.00 3.24
895 908 0.036952 GCAGCTTGTCTCAGCACCTA 60.037 55.000 0.00 0.00 42.84 3.08
924 937 2.128771 TACCAGATTTCAAGCAGCCC 57.871 50.000 0.00 0.00 0.00 5.19
943 956 3.452474 CCCTTCGTCATTGAGACTGATC 58.548 50.000 0.00 0.00 45.32 2.92
960 973 2.369257 ATCCTAGCGACCGTGGCATG 62.369 60.000 8.33 0.00 0.00 4.06
1071 1084 7.427214 AGAAAGAATACCTCGCTATAGTTGTC 58.573 38.462 0.84 0.00 0.00 3.18
1247 6308 2.069273 CAAGAAAGGCATCGAGAACGT 58.931 47.619 0.00 0.00 40.69 3.99
1331 6392 1.227764 CCACATGGCTCGAGGATGG 60.228 63.158 15.58 4.45 0.00 3.51
1333 6394 2.068821 ACATGGCTCGAGGATGGCT 61.069 57.895 15.58 0.00 0.00 4.75
1335 6396 1.147824 ATGGCTCGAGGATGGCTTG 59.852 57.895 15.58 0.00 0.00 4.01
1354 6415 5.157781 GCTTGAACAGTTACAACAACAACA 58.842 37.500 0.00 0.00 0.00 3.33
1355 6416 5.631512 GCTTGAACAGTTACAACAACAACAA 59.368 36.000 0.00 0.00 0.00 2.83
1356 6417 6.399564 GCTTGAACAGTTACAACAACAACAAC 60.400 38.462 0.00 0.00 0.00 3.32
1381 6442 4.101274 CACATGTCTCTCATCTCCTGGAAT 59.899 45.833 0.00 0.00 34.09 3.01
1538 6615 3.249119 GGGGGCACTCTAGATTCCT 57.751 57.895 0.00 0.00 0.00 3.36
1581 6658 0.879839 GCTTGTTTGCGTGGCCAAAT 60.880 50.000 7.24 0.00 37.09 2.32
1812 6890 3.760684 CCTACTTTTTGCCTCTTGCTCAT 59.239 43.478 0.00 0.00 42.00 2.90
1823 6901 3.118112 CCTCTTGCTCATCCTTACATGGT 60.118 47.826 0.00 0.00 0.00 3.55
1835 6913 3.181475 CCTTACATGGTAGCATCAGTCGT 60.181 47.826 3.96 2.32 0.00 4.34
1837 6915 1.550524 ACATGGTAGCATCAGTCGTGT 59.449 47.619 3.96 0.00 0.00 4.49
1867 6947 5.562506 TCTACACCAAGTCTACAAGATCG 57.437 43.478 0.00 0.00 0.00 3.69
1872 6952 2.479730 CCAAGTCTACAAGATCGACGGG 60.480 54.545 0.00 0.00 33.10 5.28
1878 6958 2.125673 AAGATCGACGGGTTGCCG 60.126 61.111 0.00 0.00 39.31 5.69
1880 6960 4.446413 GATCGACGGGTTGCCGGT 62.446 66.667 1.90 0.00 39.77 5.28
1938 7018 5.793817 AGTCACTTTTGGCAAGAACTTTTT 58.206 33.333 0.00 0.00 0.00 1.94
1940 7020 7.035612 AGTCACTTTTGGCAAGAACTTTTTAG 58.964 34.615 0.00 0.00 0.00 1.85
1946 7026 3.117284 TGGCAAGAACTTTTTAGAGGGGT 60.117 43.478 0.00 0.00 0.00 4.95
1952 7032 5.167921 AGAACTTTTTAGAGGGGTAGGGAA 58.832 41.667 0.00 0.00 0.00 3.97
1954 7034 6.277283 AGAACTTTTTAGAGGGGTAGGGAAAT 59.723 38.462 0.00 0.00 0.00 2.17
1971 7051 4.336713 GGGAAATAACTGAGATTGAGCACC 59.663 45.833 0.00 0.00 0.00 5.01
1977 7057 1.741706 CTGAGATTGAGCACCGCAAAT 59.258 47.619 0.00 0.00 0.00 2.32
1993 7073 2.487762 GCAAATCATCCTCAAACGGACA 59.512 45.455 0.00 0.00 35.52 4.02
2028 7108 2.096909 GGTGAATCAGTGTGTCGAAACG 60.097 50.000 0.32 0.00 0.00 3.60
2134 7214 0.461870 TTCGGCCATCGGAATGACAG 60.462 55.000 2.24 0.00 39.77 3.51
2137 7217 1.442526 GGCCATCGGAATGACAGCAG 61.443 60.000 0.00 0.00 34.61 4.24
2138 7218 0.462581 GCCATCGGAATGACAGCAGA 60.463 55.000 0.00 0.00 34.61 4.26
2139 7219 2.013563 GCCATCGGAATGACAGCAGAA 61.014 52.381 0.00 0.00 34.61 3.02
2140 7220 1.938577 CCATCGGAATGACAGCAGAAG 59.061 52.381 0.00 0.00 34.61 2.85
2141 7221 1.938577 CATCGGAATGACAGCAGAAGG 59.061 52.381 0.00 0.00 34.61 3.46
2142 7222 0.976641 TCGGAATGACAGCAGAAGGT 59.023 50.000 0.00 0.00 0.00 3.50
2143 7223 2.176045 TCGGAATGACAGCAGAAGGTA 58.824 47.619 0.00 0.00 0.00 3.08
2145 7225 2.353704 CGGAATGACAGCAGAAGGTACA 60.354 50.000 0.00 0.00 0.00 2.90
2146 7226 3.679917 CGGAATGACAGCAGAAGGTACAT 60.680 47.826 0.00 0.00 0.00 2.29
2147 7227 3.624861 GGAATGACAGCAGAAGGTACATG 59.375 47.826 0.00 0.00 0.00 3.21
2148 7228 2.099141 TGACAGCAGAAGGTACATGC 57.901 50.000 0.00 0.00 40.29 4.06
2189 7282 2.275318 GCAGAAGGTACATGCTCTGTC 58.725 52.381 10.10 1.25 39.39 3.51
2193 7286 1.656587 AGGTACATGCTCTGTCCCAA 58.343 50.000 0.00 0.00 36.33 4.12
2217 7310 4.698780 CACTTCAATCTTGGCTTGATGAGA 59.301 41.667 6.97 1.42 32.94 3.27
2218 7311 4.942483 ACTTCAATCTTGGCTTGATGAGAG 59.058 41.667 6.97 0.00 32.94 3.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 8.845227 GTCCCAACCAAAATATTGAACATTTTT 58.155 29.630 0.00 0.00 38.94 1.94
8 9 7.446931 GGTCCCAACCAAAATATTGAACATTTT 59.553 33.333 0.00 0.00 45.68 1.82
9 10 6.939730 GGTCCCAACCAAAATATTGAACATTT 59.060 34.615 0.00 0.00 45.68 2.32
10 11 6.472016 GGTCCCAACCAAAATATTGAACATT 58.528 36.000 0.00 0.00 45.68 2.71
11 12 6.048732 GGTCCCAACCAAAATATTGAACAT 57.951 37.500 0.00 0.00 45.68 2.71
12 13 5.476091 GGTCCCAACCAAAATATTGAACA 57.524 39.130 0.00 0.00 45.68 3.18
25 26 1.069775 TAAGGGTTCTGGTCCCAACC 58.930 55.000 10.32 10.32 46.82 3.77
26 27 1.271762 GGTAAGGGTTCTGGTCCCAAC 60.272 57.143 3.79 1.66 46.82 3.77
27 28 1.069775 GGTAAGGGTTCTGGTCCCAA 58.930 55.000 3.79 0.00 46.82 4.12
28 29 0.104356 TGGTAAGGGTTCTGGTCCCA 60.104 55.000 3.79 0.00 46.82 4.37
29 30 1.069775 TTGGTAAGGGTTCTGGTCCC 58.930 55.000 0.00 0.00 44.90 4.46
30 31 2.963599 TTTGGTAAGGGTTCTGGTCC 57.036 50.000 0.00 0.00 0.00 4.46
31 32 5.801531 AATTTTTGGTAAGGGTTCTGGTC 57.198 39.130 0.00 0.00 0.00 4.02
32 33 7.013834 TGATAATTTTTGGTAAGGGTTCTGGT 58.986 34.615 0.00 0.00 0.00 4.00
33 34 7.475137 TGATAATTTTTGGTAAGGGTTCTGG 57.525 36.000 0.00 0.00 0.00 3.86
34 35 9.203421 GTTTGATAATTTTTGGTAAGGGTTCTG 57.797 33.333 0.00 0.00 0.00 3.02
35 36 8.929487 TGTTTGATAATTTTTGGTAAGGGTTCT 58.071 29.630 0.00 0.00 0.00 3.01
36 37 9.719355 ATGTTTGATAATTTTTGGTAAGGGTTC 57.281 29.630 0.00 0.00 0.00 3.62
54 55 9.211485 CCAAAATGCTCTTCTTAAATGTTTGAT 57.789 29.630 0.00 0.00 0.00 2.57
55 56 8.420222 TCCAAAATGCTCTTCTTAAATGTTTGA 58.580 29.630 0.00 0.00 0.00 2.69
56 57 8.592105 TCCAAAATGCTCTTCTTAAATGTTTG 57.408 30.769 0.00 0.00 0.00 2.93
57 58 7.386025 GCTCCAAAATGCTCTTCTTAAATGTTT 59.614 33.333 0.00 0.00 0.00 2.83
58 59 6.870439 GCTCCAAAATGCTCTTCTTAAATGTT 59.130 34.615 0.00 0.00 0.00 2.71
59 60 6.015180 TGCTCCAAAATGCTCTTCTTAAATGT 60.015 34.615 0.00 0.00 0.00 2.71
60 61 6.392354 TGCTCCAAAATGCTCTTCTTAAATG 58.608 36.000 0.00 0.00 0.00 2.32
61 62 6.594788 TGCTCCAAAATGCTCTTCTTAAAT 57.405 33.333 0.00 0.00 0.00 1.40
62 63 6.403866 TTGCTCCAAAATGCTCTTCTTAAA 57.596 33.333 0.00 0.00 0.00 1.52
63 64 6.209192 TCATTGCTCCAAAATGCTCTTCTTAA 59.791 34.615 0.00 0.00 35.43 1.85
64 65 5.711506 TCATTGCTCCAAAATGCTCTTCTTA 59.288 36.000 0.00 0.00 35.43 2.10
65 66 4.525487 TCATTGCTCCAAAATGCTCTTCTT 59.475 37.500 0.00 0.00 35.43 2.52
66 67 4.084287 TCATTGCTCCAAAATGCTCTTCT 58.916 39.130 0.00 0.00 35.43 2.85
67 68 4.445452 TCATTGCTCCAAAATGCTCTTC 57.555 40.909 0.00 0.00 35.43 2.87
68 69 4.877378 TTCATTGCTCCAAAATGCTCTT 57.123 36.364 0.00 0.00 35.43 2.85
69 70 4.464951 TCATTCATTGCTCCAAAATGCTCT 59.535 37.500 0.00 0.00 35.43 4.09
70 71 4.751060 TCATTCATTGCTCCAAAATGCTC 58.249 39.130 0.00 0.00 35.43 4.26
71 72 4.464951 TCTCATTCATTGCTCCAAAATGCT 59.535 37.500 0.00 0.00 35.43 3.79
72 73 4.751060 TCTCATTCATTGCTCCAAAATGC 58.249 39.130 0.00 0.00 35.43 3.56
73 74 7.764443 AGAAATCTCATTCATTGCTCCAAAATG 59.236 33.333 0.00 0.00 36.54 2.32
74 75 7.848128 AGAAATCTCATTCATTGCTCCAAAAT 58.152 30.769 0.00 0.00 0.00 1.82
75 76 7.235935 AGAAATCTCATTCATTGCTCCAAAA 57.764 32.000 0.00 0.00 0.00 2.44
76 77 6.845758 AGAAATCTCATTCATTGCTCCAAA 57.154 33.333 0.00 0.00 0.00 3.28
77 78 6.544931 CCTAGAAATCTCATTCATTGCTCCAA 59.455 38.462 0.00 0.00 0.00 3.53
78 79 6.060136 CCTAGAAATCTCATTCATTGCTCCA 58.940 40.000 0.00 0.00 0.00 3.86
79 80 5.472820 CCCTAGAAATCTCATTCATTGCTCC 59.527 44.000 0.00 0.00 0.00 4.70
80 81 6.060788 ACCCTAGAAATCTCATTCATTGCTC 58.939 40.000 0.00 0.00 0.00 4.26
81 82 6.011122 ACCCTAGAAATCTCATTCATTGCT 57.989 37.500 0.00 0.00 0.00 3.91
82 83 6.705863 AACCCTAGAAATCTCATTCATTGC 57.294 37.500 0.00 0.00 0.00 3.56
83 84 9.362539 CAAAAACCCTAGAAATCTCATTCATTG 57.637 33.333 0.00 0.00 0.00 2.82
84 85 8.037166 GCAAAAACCCTAGAAATCTCATTCATT 58.963 33.333 0.00 0.00 0.00 2.57
85 86 7.364144 GGCAAAAACCCTAGAAATCTCATTCAT 60.364 37.037 0.00 0.00 0.00 2.57
86 87 6.071391 GGCAAAAACCCTAGAAATCTCATTCA 60.071 38.462 0.00 0.00 0.00 2.57
87 88 6.333416 GGCAAAAACCCTAGAAATCTCATTC 58.667 40.000 0.00 0.00 0.00 2.67
88 89 6.286240 GGCAAAAACCCTAGAAATCTCATT 57.714 37.500 0.00 0.00 0.00 2.57
89 90 5.921962 GGCAAAAACCCTAGAAATCTCAT 57.078 39.130 0.00 0.00 0.00 2.90
102 103 7.221450 ACTTAAATAAAAGAGGGGCAAAAACC 58.779 34.615 0.00 0.00 0.00 3.27
103 104 8.671384 AACTTAAATAAAAGAGGGGCAAAAAC 57.329 30.769 0.00 0.00 0.00 2.43
104 105 9.688091 AAAACTTAAATAAAAGAGGGGCAAAAA 57.312 25.926 0.00 0.00 0.00 1.94
105 106 9.688091 AAAAACTTAAATAAAAGAGGGGCAAAA 57.312 25.926 0.00 0.00 0.00 2.44
106 107 9.114952 CAAAAACTTAAATAAAAGAGGGGCAAA 57.885 29.630 0.00 0.00 0.00 3.68
107 108 8.487028 TCAAAAACTTAAATAAAAGAGGGGCAA 58.513 29.630 0.00 0.00 0.00 4.52
108 109 8.024145 TCAAAAACTTAAATAAAAGAGGGGCA 57.976 30.769 0.00 0.00 0.00 5.36
109 110 7.602644 CCTCAAAAACTTAAATAAAAGAGGGGC 59.397 37.037 0.00 0.00 36.24 5.80
110 111 7.602644 GCCTCAAAAACTTAAATAAAAGAGGGG 59.397 37.037 0.00 0.00 39.36 4.79
111 112 8.367911 AGCCTCAAAAACTTAAATAAAAGAGGG 58.632 33.333 0.00 0.00 39.36 4.30
112 113 9.764363 AAGCCTCAAAAACTTAAATAAAAGAGG 57.236 29.630 0.00 0.00 41.32 3.69
114 115 9.758651 GGAAGCCTCAAAAACTTAAATAAAAGA 57.241 29.630 0.00 0.00 0.00 2.52
115 116 9.541143 TGGAAGCCTCAAAAACTTAAATAAAAG 57.459 29.630 0.00 0.00 0.00 2.27
116 117 9.892130 TTGGAAGCCTCAAAAACTTAAATAAAA 57.108 25.926 0.00 0.00 0.00 1.52
117 118 9.892130 TTTGGAAGCCTCAAAAACTTAAATAAA 57.108 25.926 0.00 0.00 32.01 1.40
118 119 9.892130 TTTTGGAAGCCTCAAAAACTTAAATAA 57.108 25.926 0.00 0.00 39.99 1.40
120 121 8.978874 ATTTTGGAAGCCTCAAAAACTTAAAT 57.021 26.923 0.00 0.00 44.10 1.40
121 122 8.800370 AATTTTGGAAGCCTCAAAAACTTAAA 57.200 26.923 0.00 0.00 44.10 1.52
122 123 7.497579 GGAATTTTGGAAGCCTCAAAAACTTAA 59.502 33.333 0.00 0.00 44.10 1.85
123 124 6.989759 GGAATTTTGGAAGCCTCAAAAACTTA 59.010 34.615 0.00 0.00 44.10 2.24
124 125 5.822519 GGAATTTTGGAAGCCTCAAAAACTT 59.177 36.000 0.00 0.00 44.10 2.66
125 126 5.130975 AGGAATTTTGGAAGCCTCAAAAACT 59.869 36.000 0.00 0.00 44.10 2.66
126 127 5.368145 AGGAATTTTGGAAGCCTCAAAAAC 58.632 37.500 0.00 4.92 44.10 2.43
127 128 5.610398 GAGGAATTTTGGAAGCCTCAAAAA 58.390 37.500 0.06 0.06 44.10 1.94
128 129 5.213891 GAGGAATTTTGGAAGCCTCAAAA 57.786 39.130 0.00 10.46 44.71 2.44
129 130 4.871933 GAGGAATTTTGGAAGCCTCAAA 57.128 40.909 0.00 0.00 43.55 2.69
132 133 3.425659 ACTGAGGAATTTTGGAAGCCTC 58.574 45.455 0.00 0.00 44.18 4.70
133 134 3.532641 ACTGAGGAATTTTGGAAGCCT 57.467 42.857 0.00 0.00 0.00 4.58
134 135 3.573967 TGAACTGAGGAATTTTGGAAGCC 59.426 43.478 0.00 0.00 0.00 4.35
135 136 4.853924 TGAACTGAGGAATTTTGGAAGC 57.146 40.909 0.00 0.00 0.00 3.86
136 137 6.396829 ACTTGAACTGAGGAATTTTGGAAG 57.603 37.500 0.00 0.00 0.00 3.46
137 138 6.790232 AACTTGAACTGAGGAATTTTGGAA 57.210 33.333 0.00 0.00 0.00 3.53
138 139 6.379703 TGAAACTTGAACTGAGGAATTTTGGA 59.620 34.615 0.00 0.00 0.00 3.53
139 140 6.572519 TGAAACTTGAACTGAGGAATTTTGG 58.427 36.000 0.00 0.00 0.00 3.28
140 141 7.483307 TCTGAAACTTGAACTGAGGAATTTTG 58.517 34.615 0.00 0.00 0.00 2.44
141 142 7.645058 TCTGAAACTTGAACTGAGGAATTTT 57.355 32.000 0.00 0.00 0.00 1.82
142 143 7.645058 TTCTGAAACTTGAACTGAGGAATTT 57.355 32.000 0.00 0.00 0.00 1.82
143 144 7.645058 TTTCTGAAACTTGAACTGAGGAATT 57.355 32.000 0.00 0.00 0.00 2.17
144 145 7.830099 ATTTCTGAAACTTGAACTGAGGAAT 57.170 32.000 4.73 0.00 0.00 3.01
145 146 8.924511 ATATTTCTGAAACTTGAACTGAGGAA 57.075 30.769 4.73 0.00 0.00 3.36
146 147 9.658799 CTATATTTCTGAAACTTGAACTGAGGA 57.341 33.333 4.73 0.00 0.00 3.71
147 148 9.658799 TCTATATTTCTGAAACTTGAACTGAGG 57.341 33.333 4.73 0.00 0.00 3.86
149 150 9.996554 TGTCTATATTTCTGAAACTTGAACTGA 57.003 29.630 4.73 0.00 0.00 3.41
155 156 9.661187 GCATCATGTCTATATTTCTGAAACTTG 57.339 33.333 4.73 1.75 0.00 3.16
156 157 9.399797 TGCATCATGTCTATATTTCTGAAACTT 57.600 29.630 4.73 0.00 0.00 2.66
157 158 8.969260 TGCATCATGTCTATATTTCTGAAACT 57.031 30.769 4.73 0.00 0.00 2.66
160 161 9.176460 TGTTTGCATCATGTCTATATTTCTGAA 57.824 29.630 0.00 0.00 0.00 3.02
161 162 8.735692 TGTTTGCATCATGTCTATATTTCTGA 57.264 30.769 0.00 0.00 0.00 3.27
162 163 9.394477 CATGTTTGCATCATGTCTATATTTCTG 57.606 33.333 18.33 0.00 38.17 3.02
163 164 8.573885 CCATGTTTGCATCATGTCTATATTTCT 58.426 33.333 22.16 0.00 40.43 2.52
164 165 8.570488 TCCATGTTTGCATCATGTCTATATTTC 58.430 33.333 22.16 0.00 40.43 2.17
165 166 8.467963 TCCATGTTTGCATCATGTCTATATTT 57.532 30.769 22.16 0.00 40.43 1.40
166 167 8.467963 TTCCATGTTTGCATCATGTCTATATT 57.532 30.769 22.16 0.00 40.43 1.28
167 168 7.309012 GCTTCCATGTTTGCATCATGTCTATAT 60.309 37.037 22.16 0.00 40.43 0.86
168 169 6.016860 GCTTCCATGTTTGCATCATGTCTATA 60.017 38.462 22.16 8.82 40.43 1.31
169 170 5.221185 GCTTCCATGTTTGCATCATGTCTAT 60.221 40.000 22.16 0.00 40.43 1.98
170 171 4.096833 GCTTCCATGTTTGCATCATGTCTA 59.903 41.667 22.16 10.90 40.43 2.59
171 172 3.119245 GCTTCCATGTTTGCATCATGTCT 60.119 43.478 22.16 0.00 40.43 3.41
172 173 3.184541 GCTTCCATGTTTGCATCATGTC 58.815 45.455 22.16 10.78 40.43 3.06
173 174 2.563620 TGCTTCCATGTTTGCATCATGT 59.436 40.909 22.16 0.00 40.43 3.21
174 175 3.239587 TGCTTCCATGTTTGCATCATG 57.760 42.857 19.16 19.16 41.34 3.07
175 176 3.965379 TTGCTTCCATGTTTGCATCAT 57.035 38.095 4.93 0.00 35.27 2.45
176 177 3.258622 TGATTGCTTCCATGTTTGCATCA 59.741 39.130 4.93 7.74 35.27 3.07
177 178 3.615496 GTGATTGCTTCCATGTTTGCATC 59.385 43.478 4.93 5.91 35.27 3.91
178 179 3.007074 TGTGATTGCTTCCATGTTTGCAT 59.993 39.130 4.93 0.00 35.27 3.96
179 180 2.364647 TGTGATTGCTTCCATGTTTGCA 59.635 40.909 0.00 0.00 0.00 4.08
180 181 2.991190 CTGTGATTGCTTCCATGTTTGC 59.009 45.455 0.00 0.00 0.00 3.68
181 182 4.508461 TCTGTGATTGCTTCCATGTTTG 57.492 40.909 0.00 0.00 0.00 2.93
182 183 4.341806 TGTTCTGTGATTGCTTCCATGTTT 59.658 37.500 0.00 0.00 0.00 2.83
183 184 3.890756 TGTTCTGTGATTGCTTCCATGTT 59.109 39.130 0.00 0.00 0.00 2.71
184 185 3.489355 TGTTCTGTGATTGCTTCCATGT 58.511 40.909 0.00 0.00 0.00 3.21
185 186 3.119602 CCTGTTCTGTGATTGCTTCCATG 60.120 47.826 0.00 0.00 0.00 3.66
186 187 3.087031 CCTGTTCTGTGATTGCTTCCAT 58.913 45.455 0.00 0.00 0.00 3.41
187 188 2.507484 CCTGTTCTGTGATTGCTTCCA 58.493 47.619 0.00 0.00 0.00 3.53
188 189 1.200948 GCCTGTTCTGTGATTGCTTCC 59.799 52.381 0.00 0.00 0.00 3.46
189 190 1.200948 GGCCTGTTCTGTGATTGCTTC 59.799 52.381 0.00 0.00 0.00 3.86
190 191 1.251251 GGCCTGTTCTGTGATTGCTT 58.749 50.000 0.00 0.00 0.00 3.91
191 192 0.111061 TGGCCTGTTCTGTGATTGCT 59.889 50.000 3.32 0.00 0.00 3.91
192 193 0.524862 CTGGCCTGTTCTGTGATTGC 59.475 55.000 3.32 0.00 0.00 3.56
193 194 2.082231 CTCTGGCCTGTTCTGTGATTG 58.918 52.381 3.32 0.00 0.00 2.67
194 195 1.612726 GCTCTGGCCTGTTCTGTGATT 60.613 52.381 3.32 0.00 0.00 2.57
195 196 0.035630 GCTCTGGCCTGTTCTGTGAT 60.036 55.000 3.32 0.00 0.00 3.06
196 197 1.123861 AGCTCTGGCCTGTTCTGTGA 61.124 55.000 3.32 0.00 39.73 3.58
197 198 0.610174 TAGCTCTGGCCTGTTCTGTG 59.390 55.000 3.32 0.00 39.73 3.66
198 199 1.277557 CTTAGCTCTGGCCTGTTCTGT 59.722 52.381 3.32 0.00 39.73 3.41
199 200 1.406614 CCTTAGCTCTGGCCTGTTCTG 60.407 57.143 3.32 0.00 39.73 3.02
200 201 0.908198 CCTTAGCTCTGGCCTGTTCT 59.092 55.000 3.32 7.89 39.73 3.01
201 202 0.905357 TCCTTAGCTCTGGCCTGTTC 59.095 55.000 3.32 0.00 39.73 3.18
202 203 1.211457 CATCCTTAGCTCTGGCCTGTT 59.789 52.381 3.32 0.00 39.73 3.16
203 204 0.835941 CATCCTTAGCTCTGGCCTGT 59.164 55.000 3.32 0.00 39.73 4.00
204 205 0.835941 ACATCCTTAGCTCTGGCCTG 59.164 55.000 3.32 2.92 39.73 4.85
205 206 0.835941 CACATCCTTAGCTCTGGCCT 59.164 55.000 3.32 0.00 39.73 5.19
206 207 0.833287 TCACATCCTTAGCTCTGGCC 59.167 55.000 0.00 0.00 39.73 5.36
207 208 1.208052 TGTCACATCCTTAGCTCTGGC 59.792 52.381 0.00 0.00 39.06 4.85
208 209 3.055530 ACTTGTCACATCCTTAGCTCTGG 60.056 47.826 0.00 0.00 0.00 3.86
209 210 4.199432 ACTTGTCACATCCTTAGCTCTG 57.801 45.455 0.00 0.00 0.00 3.35
210 211 5.020132 ACTACTTGTCACATCCTTAGCTCT 58.980 41.667 0.00 0.00 0.00 4.09
211 212 5.105752 CACTACTTGTCACATCCTTAGCTC 58.894 45.833 0.00 0.00 0.00 4.09
212 213 4.621747 GCACTACTTGTCACATCCTTAGCT 60.622 45.833 0.00 0.00 0.00 3.32
213 214 3.619038 GCACTACTTGTCACATCCTTAGC 59.381 47.826 0.00 0.00 0.00 3.09
214 215 4.184629 GGCACTACTTGTCACATCCTTAG 58.815 47.826 0.00 0.00 0.00 2.18
215 216 3.055385 GGGCACTACTTGTCACATCCTTA 60.055 47.826 0.00 0.00 0.00 2.69
216 217 2.290323 GGGCACTACTTGTCACATCCTT 60.290 50.000 0.00 0.00 0.00 3.36
217 218 1.279271 GGGCACTACTTGTCACATCCT 59.721 52.381 0.00 0.00 0.00 3.24
218 219 1.003118 TGGGCACTACTTGTCACATCC 59.997 52.381 0.00 0.00 0.00 3.51
219 220 2.472695 TGGGCACTACTTGTCACATC 57.527 50.000 0.00 0.00 0.00 3.06
220 221 2.106511 ACTTGGGCACTACTTGTCACAT 59.893 45.455 0.00 0.00 0.00 3.21
221 222 1.488812 ACTTGGGCACTACTTGTCACA 59.511 47.619 0.00 0.00 0.00 3.58
222 223 2.256117 ACTTGGGCACTACTTGTCAC 57.744 50.000 0.00 0.00 0.00 3.67
223 224 2.038033 GGTACTTGGGCACTACTTGTCA 59.962 50.000 0.00 0.00 0.00 3.58
224 225 2.614734 GGGTACTTGGGCACTACTTGTC 60.615 54.545 0.00 0.00 0.00 3.18
225 226 1.350019 GGGTACTTGGGCACTACTTGT 59.650 52.381 0.00 0.00 0.00 3.16
226 227 1.339727 GGGGTACTTGGGCACTACTTG 60.340 57.143 0.00 0.00 0.00 3.16
227 228 0.989602 GGGGTACTTGGGCACTACTT 59.010 55.000 0.00 0.00 0.00 2.24
306 307 1.395826 GGTAGCCCGCACAGAGATCT 61.396 60.000 0.00 0.00 0.00 2.75
313 314 0.034574 ATTTGATGGTAGCCCGCACA 60.035 50.000 0.00 0.00 0.00 4.57
327 328 1.228398 TGGTGCCAGGCGAATTTGA 60.228 52.632 7.03 0.00 0.00 2.69
425 426 0.854218 TCCCAAAAAGGTGGCTGGTA 59.146 50.000 0.00 0.00 37.34 3.25
456 457 2.868839 GCGGTTAACTGGCTTGAGTGTA 60.869 50.000 16.13 0.00 0.00 2.90
489 490 4.256920 CCAGGATGTCGTCAAAGAAAGAT 58.743 43.478 0.00 0.00 0.00 2.40
492 493 3.485463 ACCAGGATGTCGTCAAAGAAA 57.515 42.857 0.00 0.00 0.00 2.52
567 569 4.922103 GCTTTCCAGCAATCTTTTCTCAAG 59.078 41.667 0.00 0.00 46.49 3.02
591 601 3.970610 CGAAGACACACTTGCTCATTTTG 59.029 43.478 0.00 0.00 39.13 2.44
672 682 0.531657 CGGCTGCAATTTTGGATGGA 59.468 50.000 0.50 0.00 0.00 3.41
699 709 0.675083 CATCAGTTGGTGCTTGCCAA 59.325 50.000 4.31 4.31 45.37 4.52
883 895 1.208052 TGCCAAGATAGGTGCTGAGAC 59.792 52.381 0.00 0.00 0.00 3.36
918 931 0.391661 TCTCAATGACGAAGGGCTGC 60.392 55.000 0.00 0.00 0.00 5.25
943 956 2.586079 CATGCCACGGTCGCTAGG 60.586 66.667 0.00 0.00 0.00 3.02
1071 1084 3.940640 CGCCATTGATCCACCGCG 61.941 66.667 0.00 0.00 0.00 6.46
1216 6277 7.272244 TCGATGCCTTTCTTGTATCTTATTCA 58.728 34.615 0.00 0.00 0.00 2.57
1221 6282 5.344743 TCTCGATGCCTTTCTTGTATCTT 57.655 39.130 0.00 0.00 0.00 2.40
1331 6392 5.157781 TGTTGTTGTTGTAACTGTTCAAGC 58.842 37.500 0.00 0.00 0.00 4.01
1333 6394 5.921408 GGTTGTTGTTGTTGTAACTGTTCAA 59.079 36.000 0.00 0.00 0.00 2.69
1335 6396 4.860352 GGGTTGTTGTTGTTGTAACTGTTC 59.140 41.667 0.00 0.00 0.00 3.18
1354 6415 2.503356 GGAGATGAGAGACATGTGGGTT 59.497 50.000 1.15 0.00 39.56 4.11
1355 6416 2.114616 GGAGATGAGAGACATGTGGGT 58.885 52.381 1.15 0.00 39.56 4.51
1356 6417 2.102757 CAGGAGATGAGAGACATGTGGG 59.897 54.545 1.15 0.00 39.56 4.61
1381 6442 5.047590 TCGGATCTTGTTGAAGTGCTAACTA 60.048 40.000 0.00 0.00 34.77 2.24
1448 6511 0.846427 TCCTCCCAGCCAAATCCTGT 60.846 55.000 0.00 0.00 0.00 4.00
1563 6640 2.430546 TATTTGGCCACGCAAACAAG 57.569 45.000 3.88 0.00 0.00 3.16
1581 6658 8.775151 ACATATTGGAGGATATGCATCTTCATA 58.225 33.333 0.19 0.00 41.56 2.15
1660 6737 1.078989 AGGTAGTGGTTGGAGTAGCCT 59.921 52.381 0.00 0.00 37.63 4.58
1701 6778 6.153067 GTCGACGAAATCCATAGAGATCATT 58.847 40.000 0.00 0.00 0.00 2.57
1812 6890 3.068165 CGACTGATGCTACCATGTAAGGA 59.932 47.826 0.00 0.00 0.00 3.36
1823 6901 7.981102 AGATATAGTTACACGACTGATGCTA 57.019 36.000 0.00 0.00 0.00 3.49
1835 6913 9.910267 TGTAGACTTGGTGTAGATATAGTTACA 57.090 33.333 0.00 0.00 0.00 2.41
1872 6952 1.664151 GACACAATAGCTACCGGCAAC 59.336 52.381 0.00 0.00 44.79 4.17
1878 6958 4.399618 TCTCTGTCAGACACAATAGCTACC 59.600 45.833 0.00 0.00 33.31 3.18
1938 7018 5.197189 TCTCAGTTATTTCCCTACCCCTCTA 59.803 44.000 0.00 0.00 0.00 2.43
1940 7020 4.296056 TCTCAGTTATTTCCCTACCCCTC 58.704 47.826 0.00 0.00 0.00 4.30
1946 7026 6.349300 GTGCTCAATCTCAGTTATTTCCCTA 58.651 40.000 0.00 0.00 0.00 3.53
1952 7032 2.939103 GCGGTGCTCAATCTCAGTTATT 59.061 45.455 0.00 0.00 0.00 1.40
1954 7034 1.275010 TGCGGTGCTCAATCTCAGTTA 59.725 47.619 0.00 0.00 0.00 2.24
1971 7051 1.737236 TCCGTTTGAGGATGATTTGCG 59.263 47.619 0.00 0.00 34.92 4.85
1977 7057 0.036388 GCCTGTCCGTTTGAGGATGA 60.036 55.000 0.00 0.00 43.04 2.92
1993 7073 1.415672 TTCACCCTCTCCGTTTGCCT 61.416 55.000 0.00 0.00 0.00 4.75
2134 7214 2.275318 GACAGAGCATGTACCTTCTGC 58.725 52.381 10.91 6.02 44.17 4.26
2137 7217 3.257393 CAGTGACAGAGCATGTACCTTC 58.743 50.000 0.00 0.00 44.17 3.46
2138 7218 2.027745 CCAGTGACAGAGCATGTACCTT 60.028 50.000 0.00 0.00 44.17 3.50
2139 7219 1.552337 CCAGTGACAGAGCATGTACCT 59.448 52.381 0.00 0.00 44.17 3.08
2140 7220 1.406069 CCCAGTGACAGAGCATGTACC 60.406 57.143 0.00 0.00 44.17 3.34
2141 7221 1.406069 CCCCAGTGACAGAGCATGTAC 60.406 57.143 0.00 0.00 44.17 2.90
2142 7222 0.904649 CCCCAGTGACAGAGCATGTA 59.095 55.000 0.00 0.00 44.17 2.29
2145 7225 0.622738 ATCCCCCAGTGACAGAGCAT 60.623 55.000 0.00 0.00 0.00 3.79
2146 7226 1.229625 ATCCCCCAGTGACAGAGCA 60.230 57.895 0.00 0.00 0.00 4.26
2147 7227 1.267574 TGATCCCCCAGTGACAGAGC 61.268 60.000 0.00 0.00 0.00 4.09
2148 7228 0.539051 GTGATCCCCCAGTGACAGAG 59.461 60.000 0.00 0.00 0.00 3.35
2150 7230 0.251354 CTGTGATCCCCCAGTGACAG 59.749 60.000 0.00 0.00 0.00 3.51
2151 7231 1.841302 GCTGTGATCCCCCAGTGACA 61.841 60.000 0.00 0.00 0.00 3.58
2186 7279 3.221771 CCAAGATTGAAGTGTTGGGACA 58.778 45.455 0.00 0.00 38.49 4.02
2189 7282 2.242043 AGCCAAGATTGAAGTGTTGGG 58.758 47.619 4.28 0.00 41.48 4.12
2193 7286 4.401022 TCATCAAGCCAAGATTGAAGTGT 58.599 39.130 0.00 0.00 41.25 3.55


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

AutoCloner maintained by Alex Coulton.