Multiple sequence alignment - TraesCS7D01G411000

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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 TraesCS7D01G411000 chr7D 100.000 2372 0 0 1 2372 529947353 529949724 0.000000e+00 4381
1 TraesCS7D01G411000 chr7B 89.981 1607 91 30 423 1991 568092341 568093915 0.000000e+00 2012
2 TraesCS7D01G411000 chr7B 93.451 397 22 2 1978 2372 568093930 568094324 9.450000e-164 586
3 TraesCS7D01G411000 chr7A 87.194 1593 129 36 427 1981 609410111 609411666 0.000000e+00 1742


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 TraesCS7D01G411000 chr7D 529947353 529949724 2371 False 4381 4381 100.000 1 2372 1 chr7D.!!$F1 2371
1 TraesCS7D01G411000 chr7B 568092341 568094324 1983 False 1299 2012 91.716 423 2372 2 chr7B.!!$F1 1949
2 TraesCS7D01G411000 chr7A 609410111 609411666 1555 False 1742 1742 87.194 427 1981 1 chr7A.!!$F1 1554

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
887 909 0.032117 TCCCTGTCATCTCCGGACAT 60.032 55.0 0.0 0.0 43.72 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2145 2250 3.069016 ACCGTCGAAATATGAGGCATACA 59.931 43.478 0.0 0.0 0.0 2.29 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
30 31 8.479313 ACGCTAACATCACCATATTATATGTG 57.521 34.615 10.83 9.11 31.44 3.21
31 32 8.094548 ACGCTAACATCACCATATTATATGTGT 58.905 33.333 10.83 6.05 31.44 3.72
32 33 8.595533 CGCTAACATCACCATATTATATGTGTC 58.404 37.037 10.83 0.00 31.44 3.67
33 34 9.435688 GCTAACATCACCATATTATATGTGTCA 57.564 33.333 10.83 0.00 31.44 3.58
60 61 9.667989 TGAAATGACTATCATAAAATTCATGCG 57.332 29.630 0.00 0.00 35.76 4.73
61 62 9.882996 GAAATGACTATCATAAAATTCATGCGA 57.117 29.630 0.00 0.00 35.76 5.10
62 63 9.669353 AAATGACTATCATAAAATTCATGCGAC 57.331 29.630 0.00 0.00 35.76 5.19
63 64 7.784633 TGACTATCATAAAATTCATGCGACA 57.215 32.000 0.00 0.00 0.00 4.35
64 65 8.382030 TGACTATCATAAAATTCATGCGACAT 57.618 30.769 0.00 0.00 0.00 3.06
65 66 8.839343 TGACTATCATAAAATTCATGCGACATT 58.161 29.630 0.00 0.00 0.00 2.71
66 67 9.110617 GACTATCATAAAATTCATGCGACATTG 57.889 33.333 0.00 0.00 0.00 2.82
67 68 8.623903 ACTATCATAAAATTCATGCGACATTGT 58.376 29.630 0.00 0.00 0.00 2.71
70 71 9.800433 ATCATAAAATTCATGCGACATTGTAAA 57.200 25.926 0.00 0.00 0.00 2.01
71 72 9.288124 TCATAAAATTCATGCGACATTGTAAAG 57.712 29.630 0.00 0.00 0.00 1.85
72 73 6.949578 AAAATTCATGCGACATTGTAAAGG 57.050 33.333 0.00 0.00 0.00 3.11
73 74 4.637483 ATTCATGCGACATTGTAAAGGG 57.363 40.909 0.00 0.00 0.00 3.95
74 75 3.342377 TCATGCGACATTGTAAAGGGA 57.658 42.857 0.00 0.00 0.00 4.20
75 76 3.680490 TCATGCGACATTGTAAAGGGAA 58.320 40.909 0.00 0.00 0.00 3.97
76 77 4.075682 TCATGCGACATTGTAAAGGGAAA 58.924 39.130 0.00 0.00 0.00 3.13
77 78 3.907894 TGCGACATTGTAAAGGGAAAC 57.092 42.857 0.00 0.00 0.00 2.78
78 79 3.215151 TGCGACATTGTAAAGGGAAACA 58.785 40.909 0.00 0.00 0.00 2.83
79 80 3.003897 TGCGACATTGTAAAGGGAAACAC 59.996 43.478 0.00 0.00 0.00 3.32
80 81 3.805823 CGACATTGTAAAGGGAAACACG 58.194 45.455 0.00 0.00 0.00 4.49
81 82 3.561503 GACATTGTAAAGGGAAACACGC 58.438 45.455 0.00 0.00 0.00 5.34
82 83 2.952978 ACATTGTAAAGGGAAACACGCA 59.047 40.909 0.00 0.00 0.00 5.24
83 84 3.004315 ACATTGTAAAGGGAAACACGCAG 59.996 43.478 0.00 0.00 0.00 5.18
84 85 1.600023 TGTAAAGGGAAACACGCAGG 58.400 50.000 0.00 0.00 0.00 4.85
85 86 1.141254 TGTAAAGGGAAACACGCAGGA 59.859 47.619 0.00 0.00 0.00 3.86
86 87 1.534163 GTAAAGGGAAACACGCAGGAC 59.466 52.381 0.00 0.00 0.00 3.85
87 88 0.106918 AAAGGGAAACACGCAGGACA 60.107 50.000 0.00 0.00 0.00 4.02
88 89 0.818040 AAGGGAAACACGCAGGACAC 60.818 55.000 0.00 0.00 0.00 3.67
89 90 2.604174 GGGAAACACGCAGGACACG 61.604 63.158 0.00 0.00 0.00 4.49
90 91 1.885850 GGAAACACGCAGGACACGT 60.886 57.895 0.00 0.00 46.42 4.49
91 92 0.598158 GGAAACACGCAGGACACGTA 60.598 55.000 0.00 0.00 42.96 3.57
92 93 0.505655 GAAACACGCAGGACACGTAC 59.494 55.000 0.00 0.00 42.96 3.67
93 94 0.877213 AAACACGCAGGACACGTACC 60.877 55.000 3.17 3.17 42.96 3.34
94 95 1.741327 AACACGCAGGACACGTACCT 61.741 55.000 7.53 7.53 42.96 3.08
98 99 2.809601 CAGGACACGTACCTGCGC 60.810 66.667 22.03 0.00 46.30 6.09
99 100 3.299977 AGGACACGTACCTGCGCA 61.300 61.111 10.98 10.98 36.30 6.09
100 101 2.809601 GGACACGTACCTGCGCAG 60.810 66.667 30.52 30.52 34.88 5.18
115 116 4.559063 CAGCTATGCCGGCAGCCT 62.559 66.667 35.36 25.38 42.71 4.58
116 117 4.559063 AGCTATGCCGGCAGCCTG 62.559 66.667 35.36 23.10 42.71 4.85
117 118 4.552365 GCTATGCCGGCAGCCTGA 62.552 66.667 35.36 15.64 42.71 3.86
118 119 2.429058 CTATGCCGGCAGCCTGAT 59.571 61.111 35.36 19.42 42.71 2.90
119 120 1.228063 CTATGCCGGCAGCCTGATT 60.228 57.895 35.36 18.61 42.71 2.57
120 121 1.512996 CTATGCCGGCAGCCTGATTG 61.513 60.000 35.36 13.85 42.71 2.67
121 122 2.269520 TATGCCGGCAGCCTGATTGT 62.270 55.000 35.36 17.01 42.71 2.71
122 123 3.512516 GCCGGCAGCCTGATTGTC 61.513 66.667 24.80 0.00 34.35 3.18
123 124 2.270205 CCGGCAGCCTGATTGTCT 59.730 61.111 10.54 0.00 0.00 3.41
124 125 1.817099 CCGGCAGCCTGATTGTCTC 60.817 63.158 10.54 0.00 0.00 3.36
125 126 2.169789 CGGCAGCCTGATTGTCTCG 61.170 63.158 10.54 0.00 0.00 4.04
126 127 1.078848 GGCAGCCTGATTGTCTCGT 60.079 57.895 3.29 0.00 0.00 4.18
127 128 1.364626 GGCAGCCTGATTGTCTCGTG 61.365 60.000 3.29 0.00 0.00 4.35
128 129 0.390340 GCAGCCTGATTGTCTCGTGA 60.390 55.000 0.00 0.00 0.00 4.35
129 130 1.741732 GCAGCCTGATTGTCTCGTGAT 60.742 52.381 0.00 0.00 0.00 3.06
130 131 2.200067 CAGCCTGATTGTCTCGTGATC 58.800 52.381 0.00 0.00 0.00 2.92
131 132 1.137872 AGCCTGATTGTCTCGTGATCC 59.862 52.381 0.00 0.00 0.00 3.36
132 133 1.845266 CCTGATTGTCTCGTGATCCG 58.155 55.000 0.00 0.00 38.13 4.18
133 134 1.135139 CCTGATTGTCTCGTGATCCGT 59.865 52.381 3.97 0.00 37.94 4.69
134 135 2.357952 CCTGATTGTCTCGTGATCCGTA 59.642 50.000 3.97 0.00 37.94 4.02
135 136 3.181490 CCTGATTGTCTCGTGATCCGTAA 60.181 47.826 3.97 0.00 37.94 3.18
136 137 4.421058 CTGATTGTCTCGTGATCCGTAAA 58.579 43.478 3.97 0.00 37.94 2.01
137 138 4.421058 TGATTGTCTCGTGATCCGTAAAG 58.579 43.478 3.97 0.00 37.94 1.85
138 139 3.928727 TTGTCTCGTGATCCGTAAAGT 57.071 42.857 3.97 0.00 37.94 2.66
139 140 3.482722 TGTCTCGTGATCCGTAAAGTC 57.517 47.619 3.97 0.00 37.94 3.01
140 141 2.815503 TGTCTCGTGATCCGTAAAGTCA 59.184 45.455 3.97 0.00 37.94 3.41
141 142 3.442625 TGTCTCGTGATCCGTAAAGTCAT 59.557 43.478 3.97 0.00 37.94 3.06
142 143 4.082408 TGTCTCGTGATCCGTAAAGTCATT 60.082 41.667 3.97 0.00 37.94 2.57
143 144 4.265556 GTCTCGTGATCCGTAAAGTCATTG 59.734 45.833 3.97 0.00 37.94 2.82
144 145 3.517602 TCGTGATCCGTAAAGTCATTGG 58.482 45.455 3.97 0.00 37.94 3.16
145 146 3.193903 TCGTGATCCGTAAAGTCATTGGA 59.806 43.478 3.97 0.00 37.94 3.53
146 147 4.119862 CGTGATCCGTAAAGTCATTGGAT 58.880 43.478 0.00 0.00 41.99 3.41
147 148 5.068067 TCGTGATCCGTAAAGTCATTGGATA 59.932 40.000 3.97 0.00 39.47 2.59
148 149 5.175126 CGTGATCCGTAAAGTCATTGGATAC 59.825 44.000 0.00 0.00 39.47 2.24
149 150 5.465724 GTGATCCGTAAAGTCATTGGATACC 59.534 44.000 0.00 0.00 39.47 2.73
150 151 5.129650 TGATCCGTAAAGTCATTGGATACCA 59.870 40.000 0.00 0.00 39.47 3.25
151 152 4.761975 TCCGTAAAGTCATTGGATACCAC 58.238 43.478 0.00 0.00 30.78 4.16
152 153 4.223255 TCCGTAAAGTCATTGGATACCACA 59.777 41.667 0.00 0.00 30.78 4.17
153 154 5.104693 TCCGTAAAGTCATTGGATACCACAT 60.105 40.000 0.00 0.00 30.78 3.21
154 155 5.007626 CCGTAAAGTCATTGGATACCACATG 59.992 44.000 0.00 0.00 30.78 3.21
155 156 5.815222 CGTAAAGTCATTGGATACCACATGA 59.185 40.000 0.00 0.00 32.76 3.07
156 157 6.018751 CGTAAAGTCATTGGATACCACATGAG 60.019 42.308 0.00 0.00 34.41 2.90
157 158 4.428294 AGTCATTGGATACCACATGAGG 57.572 45.455 7.74 7.74 34.41 3.86
158 159 3.137176 AGTCATTGGATACCACATGAGGG 59.863 47.826 14.11 10.10 34.41 4.30
159 160 2.158623 TCATTGGATACCACATGAGGGC 60.159 50.000 14.11 2.61 32.08 5.19
160 161 1.294041 TTGGATACCACATGAGGGCA 58.706 50.000 14.11 1.22 30.78 5.36
161 162 0.546122 TGGATACCACATGAGGGCAC 59.454 55.000 14.11 4.02 0.00 5.01
162 163 0.546122 GGATACCACATGAGGGCACA 59.454 55.000 14.11 0.00 0.00 4.57
163 164 1.064758 GGATACCACATGAGGGCACAA 60.065 52.381 14.11 0.00 0.00 3.33
164 165 2.423373 GGATACCACATGAGGGCACAAT 60.423 50.000 14.11 0.00 0.00 2.71
165 166 3.181445 GGATACCACATGAGGGCACAATA 60.181 47.826 14.11 0.00 0.00 1.90
166 167 2.897271 ACCACATGAGGGCACAATAA 57.103 45.000 14.11 0.00 0.00 1.40
167 168 2.726821 ACCACATGAGGGCACAATAAG 58.273 47.619 14.11 0.00 0.00 1.73
168 169 2.041620 ACCACATGAGGGCACAATAAGT 59.958 45.455 14.11 0.00 0.00 2.24
169 170 3.091545 CCACATGAGGGCACAATAAGTT 58.908 45.455 0.00 0.00 0.00 2.66
170 171 3.511146 CCACATGAGGGCACAATAAGTTT 59.489 43.478 0.00 0.00 0.00 2.66
171 172 4.021192 CCACATGAGGGCACAATAAGTTTT 60.021 41.667 0.00 0.00 0.00 2.43
172 173 5.184864 CCACATGAGGGCACAATAAGTTTTA 59.815 40.000 0.00 0.00 0.00 1.52
173 174 6.295011 CCACATGAGGGCACAATAAGTTTTAA 60.295 38.462 0.00 0.00 0.00 1.52
174 175 6.808212 CACATGAGGGCACAATAAGTTTTAAG 59.192 38.462 0.00 0.00 0.00 1.85
175 176 6.493458 ACATGAGGGCACAATAAGTTTTAAGT 59.507 34.615 0.00 0.00 0.00 2.24
176 177 6.969993 TGAGGGCACAATAAGTTTTAAGTT 57.030 33.333 0.00 0.00 0.00 2.66
177 178 7.354751 TGAGGGCACAATAAGTTTTAAGTTT 57.645 32.000 0.00 0.00 0.00 2.66
178 179 7.787028 TGAGGGCACAATAAGTTTTAAGTTTT 58.213 30.769 0.00 0.00 0.00 2.43
179 180 8.915036 TGAGGGCACAATAAGTTTTAAGTTTTA 58.085 29.630 0.00 0.00 0.00 1.52
180 181 9.406828 GAGGGCACAATAAGTTTTAAGTTTTAG 57.593 33.333 0.00 0.00 0.00 1.85
181 182 7.870954 AGGGCACAATAAGTTTTAAGTTTTAGC 59.129 33.333 0.00 0.00 0.00 3.09
182 183 7.870954 GGGCACAATAAGTTTTAAGTTTTAGCT 59.129 33.333 0.00 0.00 0.00 3.32
183 184 8.912658 GGCACAATAAGTTTTAAGTTTTAGCTC 58.087 33.333 0.00 0.00 0.00 4.09
184 185 9.678941 GCACAATAAGTTTTAAGTTTTAGCTCT 57.321 29.630 0.00 0.00 0.00 4.09
199 200 9.227777 AGTTTTAGCTCTTATAATTTTGTCGGT 57.772 29.630 0.00 0.00 0.00 4.69
200 201 9.486857 GTTTTAGCTCTTATAATTTTGTCGGTC 57.513 33.333 0.00 0.00 0.00 4.79
201 202 5.968387 AGCTCTTATAATTTTGTCGGTCG 57.032 39.130 0.00 0.00 0.00 4.79
202 203 4.270325 AGCTCTTATAATTTTGTCGGTCGC 59.730 41.667 0.00 0.00 0.00 5.19
203 204 4.552184 GCTCTTATAATTTTGTCGGTCGCC 60.552 45.833 0.00 0.00 0.00 5.54
204 205 4.761975 TCTTATAATTTTGTCGGTCGCCT 58.238 39.130 0.00 0.00 0.00 5.52
205 206 4.569162 TCTTATAATTTTGTCGGTCGCCTG 59.431 41.667 0.00 0.00 0.00 4.85
206 207 2.172851 TAATTTTGTCGGTCGCCTGT 57.827 45.000 0.00 0.00 0.00 4.00
207 208 2.172851 AATTTTGTCGGTCGCCTGTA 57.827 45.000 0.00 0.00 0.00 2.74
208 209 1.435577 ATTTTGTCGGTCGCCTGTAC 58.564 50.000 0.00 0.00 0.00 2.90
209 210 0.600782 TTTTGTCGGTCGCCTGTACC 60.601 55.000 0.00 0.00 0.00 3.34
210 211 1.746322 TTTGTCGGTCGCCTGTACCA 61.746 55.000 0.00 0.00 36.78 3.25
211 212 1.746322 TTGTCGGTCGCCTGTACCAA 61.746 55.000 0.00 0.00 36.78 3.67
212 213 1.005867 GTCGGTCGCCTGTACCAAA 60.006 57.895 0.00 0.00 36.78 3.28
213 214 0.390735 GTCGGTCGCCTGTACCAAAT 60.391 55.000 0.00 0.00 36.78 2.32
214 215 0.322322 TCGGTCGCCTGTACCAAATT 59.678 50.000 0.00 0.00 36.78 1.82
215 216 1.161843 CGGTCGCCTGTACCAAATTT 58.838 50.000 0.00 0.00 36.78 1.82
216 217 1.129811 CGGTCGCCTGTACCAAATTTC 59.870 52.381 0.00 0.00 36.78 2.17
217 218 2.156098 GGTCGCCTGTACCAAATTTCA 58.844 47.619 0.00 0.00 36.96 2.69
218 219 2.161609 GGTCGCCTGTACCAAATTTCAG 59.838 50.000 0.00 0.00 36.96 3.02
219 220 1.810151 TCGCCTGTACCAAATTTCAGC 59.190 47.619 0.00 0.00 0.00 4.26
220 221 1.812571 CGCCTGTACCAAATTTCAGCT 59.187 47.619 0.00 0.00 0.00 4.24
221 222 2.414559 CGCCTGTACCAAATTTCAGCTG 60.415 50.000 7.63 7.63 0.00 4.24
222 223 2.558359 GCCTGTACCAAATTTCAGCTGT 59.442 45.455 14.67 0.00 0.00 4.40
223 224 3.005791 GCCTGTACCAAATTTCAGCTGTT 59.994 43.478 14.67 0.00 0.00 3.16
224 225 4.549458 CCTGTACCAAATTTCAGCTGTTG 58.451 43.478 14.67 10.58 0.00 3.33
225 226 4.278170 CCTGTACCAAATTTCAGCTGTTGA 59.722 41.667 14.67 1.04 0.00 3.18
226 227 5.221224 CCTGTACCAAATTTCAGCTGTTGAA 60.221 40.000 14.67 2.62 43.92 2.69
238 239 6.509418 TCAGCTGTTGAAACTTAACAAAGT 57.491 33.333 14.67 0.00 37.56 2.66
239 240 6.919721 TCAGCTGTTGAAACTTAACAAAGTT 58.080 32.000 14.67 0.00 44.25 2.66
240 241 6.806249 TCAGCTGTTGAAACTTAACAAAGTTG 59.194 34.615 14.67 0.00 41.76 3.16
241 242 5.576774 AGCTGTTGAAACTTAACAAAGTTGC 59.423 36.000 4.40 3.46 41.76 4.17
242 243 5.347364 GCTGTTGAAACTTAACAAAGTTGCA 59.653 36.000 7.45 7.45 44.39 4.08
247 248 6.826612 TGAAACTTAACAAAGTTGCAAAAGC 58.173 32.000 0.00 0.00 43.43 3.51
248 249 5.794687 AACTTAACAAAGTTGCAAAAGCC 57.205 34.783 0.00 0.00 41.12 4.35
249 250 4.188462 ACTTAACAAAGTTGCAAAAGCCC 58.812 39.130 0.00 0.00 0.00 5.19
250 251 2.777832 AACAAAGTTGCAAAAGCCCA 57.222 40.000 0.00 0.00 0.00 5.36
251 252 3.280197 AACAAAGTTGCAAAAGCCCAT 57.720 38.095 0.00 0.00 0.00 4.00
252 253 2.837498 ACAAAGTTGCAAAAGCCCATC 58.163 42.857 0.00 0.00 0.00 3.51
253 254 2.170187 ACAAAGTTGCAAAAGCCCATCA 59.830 40.909 0.00 0.00 0.00 3.07
254 255 3.204526 CAAAGTTGCAAAAGCCCATCAA 58.795 40.909 0.00 0.00 0.00 2.57
255 256 3.557228 AAGTTGCAAAAGCCCATCAAA 57.443 38.095 0.00 0.00 0.00 2.69
256 257 3.557228 AGTTGCAAAAGCCCATCAAAA 57.443 38.095 0.00 0.00 0.00 2.44
257 258 3.205338 AGTTGCAAAAGCCCATCAAAAC 58.795 40.909 0.00 0.00 0.00 2.43
258 259 2.941720 GTTGCAAAAGCCCATCAAAACA 59.058 40.909 0.00 0.00 0.00 2.83
259 260 3.488778 TGCAAAAGCCCATCAAAACAT 57.511 38.095 0.00 0.00 0.00 2.71
260 261 4.613925 TGCAAAAGCCCATCAAAACATA 57.386 36.364 0.00 0.00 0.00 2.29
261 262 5.163281 TGCAAAAGCCCATCAAAACATAT 57.837 34.783 0.00 0.00 0.00 1.78
262 263 5.558818 TGCAAAAGCCCATCAAAACATATT 58.441 33.333 0.00 0.00 0.00 1.28
263 264 6.705302 TGCAAAAGCCCATCAAAACATATTA 58.295 32.000 0.00 0.00 0.00 0.98
264 265 7.164122 TGCAAAAGCCCATCAAAACATATTAA 58.836 30.769 0.00 0.00 0.00 1.40
265 266 7.663081 TGCAAAAGCCCATCAAAACATATTAAA 59.337 29.630 0.00 0.00 0.00 1.52
266 267 8.510505 GCAAAAGCCCATCAAAACATATTAAAA 58.489 29.630 0.00 0.00 0.00 1.52
302 303 5.376854 AAAATCCCTCATCACAAGAAACG 57.623 39.130 0.00 0.00 0.00 3.60
303 304 1.808411 TCCCTCATCACAAGAAACGC 58.192 50.000 0.00 0.00 0.00 4.84
304 305 1.071542 TCCCTCATCACAAGAAACGCA 59.928 47.619 0.00 0.00 0.00 5.24
305 306 1.879380 CCCTCATCACAAGAAACGCAA 59.121 47.619 0.00 0.00 0.00 4.85
306 307 2.293122 CCCTCATCACAAGAAACGCAAA 59.707 45.455 0.00 0.00 0.00 3.68
307 308 3.057315 CCCTCATCACAAGAAACGCAAAT 60.057 43.478 0.00 0.00 0.00 2.32
308 309 4.155826 CCCTCATCACAAGAAACGCAAATA 59.844 41.667 0.00 0.00 0.00 1.40
309 310 5.163622 CCCTCATCACAAGAAACGCAAATAT 60.164 40.000 0.00 0.00 0.00 1.28
310 311 5.740569 CCTCATCACAAGAAACGCAAATATG 59.259 40.000 0.00 0.00 0.00 1.78
371 372 9.045223 ACTACAAAAGATTGAAAATCAAAAGGC 57.955 29.630 3.03 0.00 40.12 4.35
372 373 7.862512 ACAAAAGATTGAAAATCAAAAGGCA 57.137 28.000 3.03 0.00 40.12 4.75
373 374 8.278729 ACAAAAGATTGAAAATCAAAAGGCAA 57.721 26.923 3.03 0.00 40.12 4.52
374 375 8.738106 ACAAAAGATTGAAAATCAAAAGGCAAA 58.262 25.926 3.03 0.00 40.12 3.68
375 376 9.570488 CAAAAGATTGAAAATCAAAAGGCAAAA 57.430 25.926 3.03 0.00 40.12 2.44
377 378 9.955208 AAAGATTGAAAATCAAAAGGCAAAATC 57.045 25.926 3.03 0.00 40.12 2.17
378 379 8.680039 AGATTGAAAATCAAAAGGCAAAATCA 57.320 26.923 3.03 0.00 40.12 2.57
379 380 9.122779 AGATTGAAAATCAAAAGGCAAAATCAA 57.877 25.926 3.03 0.00 40.12 2.57
380 381 9.733219 GATTGAAAATCAAAAGGCAAAATCAAA 57.267 25.926 0.00 0.00 40.12 2.69
383 384 9.517609 TGAAAATCAAAAGGCAAAATCAAAATG 57.482 25.926 0.00 0.00 0.00 2.32
384 385 8.874744 AAAATCAAAAGGCAAAATCAAAATGG 57.125 26.923 0.00 0.00 0.00 3.16
385 386 6.578163 ATCAAAAGGCAAAATCAAAATGGG 57.422 33.333 0.00 0.00 0.00 4.00
386 387 5.444176 TCAAAAGGCAAAATCAAAATGGGT 58.556 33.333 0.00 0.00 0.00 4.51
387 388 5.530543 TCAAAAGGCAAAATCAAAATGGGTC 59.469 36.000 0.00 0.00 0.00 4.46
388 389 3.317603 AGGCAAAATCAAAATGGGTCG 57.682 42.857 0.00 0.00 0.00 4.79
389 390 1.731709 GGCAAAATCAAAATGGGTCGC 59.268 47.619 0.00 0.00 0.00 5.19
390 391 1.389784 GCAAAATCAAAATGGGTCGCG 59.610 47.619 0.00 0.00 0.00 5.87
391 392 2.671596 CAAAATCAAAATGGGTCGCGT 58.328 42.857 5.77 0.00 0.00 6.01
392 393 2.346099 AAATCAAAATGGGTCGCGTG 57.654 45.000 5.77 0.00 0.00 5.34
393 394 0.109319 AATCAAAATGGGTCGCGTGC 60.109 50.000 5.77 0.00 0.00 5.34
394 395 1.933115 ATCAAAATGGGTCGCGTGCC 61.933 55.000 5.77 10.09 0.00 5.01
395 396 3.370231 AAAATGGGTCGCGTGCCC 61.370 61.111 26.54 26.54 46.26 5.36
414 415 4.687215 GCTCCTGCGTGCCACAGA 62.687 66.667 0.00 0.00 37.32 3.41
415 416 2.267006 CTCCTGCGTGCCACAGAT 59.733 61.111 0.00 0.00 37.32 2.90
416 417 1.812922 CTCCTGCGTGCCACAGATC 60.813 63.158 0.00 0.00 37.32 2.75
417 418 2.046988 CCTGCGTGCCACAGATCA 60.047 61.111 0.00 0.00 37.32 2.92
418 419 1.450848 CCTGCGTGCCACAGATCAT 60.451 57.895 0.00 0.00 37.32 2.45
419 420 1.028330 CCTGCGTGCCACAGATCATT 61.028 55.000 0.00 0.00 37.32 2.57
420 421 0.098200 CTGCGTGCCACAGATCATTG 59.902 55.000 0.00 0.00 37.32 2.82
421 422 0.606130 TGCGTGCCACAGATCATTGT 60.606 50.000 0.00 0.00 0.00 2.71
422 423 1.338579 TGCGTGCCACAGATCATTGTA 60.339 47.619 0.00 0.00 0.00 2.41
423 424 1.737236 GCGTGCCACAGATCATTGTAA 59.263 47.619 0.00 0.00 0.00 2.41
424 425 2.161410 GCGTGCCACAGATCATTGTAAA 59.839 45.455 0.00 0.00 0.00 2.01
425 426 3.181497 GCGTGCCACAGATCATTGTAAAT 60.181 43.478 0.00 0.00 0.00 1.40
454 457 2.109126 GGGATGTTGCTGCCTCGTC 61.109 63.158 0.00 1.13 0.00 4.20
456 459 1.446099 GATGTTGCTGCCTCGTCGA 60.446 57.895 0.00 0.00 0.00 4.20
458 461 2.049063 GTTGCTGCCTCGTCGACT 60.049 61.111 14.70 0.00 0.00 4.18
578 584 4.892934 AGCATGTTCTTAGAGGAGTAGAGG 59.107 45.833 0.00 0.00 0.00 3.69
635 649 4.202212 CGATACATTATGTCTGACCCCACA 60.202 45.833 0.00 0.00 0.00 4.17
636 650 3.350219 ACATTATGTCTGACCCCACAC 57.650 47.619 5.17 0.00 0.00 3.82
637 651 2.642311 ACATTATGTCTGACCCCACACA 59.358 45.455 5.17 0.00 0.00 3.72
825 847 2.281484 CACCAACCCACGACCAGG 60.281 66.667 0.00 0.00 0.00 4.45
862 884 0.583438 CCGCATGCCTTAACTGATCG 59.417 55.000 13.15 0.00 0.00 3.69
877 899 0.962489 GATCGACCGATCCCTGTCAT 59.038 55.000 18.61 0.00 43.71 3.06
883 905 1.662608 CGATCCCTGTCATCTCCGG 59.337 63.158 0.00 0.00 0.00 5.14
887 909 0.032117 TCCCTGTCATCTCCGGACAT 60.032 55.000 0.00 0.00 43.72 3.06
892 914 1.756561 TCATCTCCGGACATCGCCA 60.757 57.895 0.00 0.00 37.59 5.69
925 950 0.967380 TTCCGTACCGTCCTCCTTCC 60.967 60.000 0.00 0.00 0.00 3.46
961 986 2.483745 CCGAAGCTACGACGAGCA 59.516 61.111 17.47 0.00 45.43 4.26
962 987 1.868251 CCGAAGCTACGACGAGCAC 60.868 63.158 17.47 11.53 45.43 4.40
963 988 1.868251 CGAAGCTACGACGAGCACC 60.868 63.158 17.47 9.81 45.43 5.01
964 989 1.868251 GAAGCTACGACGAGCACCG 60.868 63.158 17.47 0.00 45.43 4.94
965 990 3.966026 AAGCTACGACGAGCACCGC 62.966 63.158 17.47 4.93 45.43 5.68
966 991 4.771356 GCTACGACGAGCACCGCA 62.771 66.667 0.00 0.00 42.36 5.69
986 1015 4.687215 GTGAGTCCTGCTGCCGCA 62.687 66.667 1.88 1.88 45.60 5.69
1320 1352 0.033991 AGGACTTCGAGGAGCTGCTA 60.034 55.000 8.12 0.00 0.00 3.49
1478 1515 1.474017 GCGCGTACGTAGAATGATGT 58.526 50.000 17.90 0.00 42.83 3.06
1513 1555 8.328864 ACTTTTAAAATTAGCTAGATCGCTTCG 58.671 33.333 0.09 0.00 41.30 3.79
1612 1656 1.463056 TCGTCATCGTTGGTTTCATGC 59.537 47.619 0.00 0.00 38.33 4.06
1642 1686 8.511604 TTTGAAGTTCATATCATCTCCCTTTC 57.488 34.615 6.36 0.00 0.00 2.62
1657 1701 4.394729 TCCCTTTCGTTTTTACTGCTGAT 58.605 39.130 0.00 0.00 0.00 2.90
1661 1705 5.402270 CCTTTCGTTTTTACTGCTGATTTGG 59.598 40.000 0.00 0.00 0.00 3.28
1664 1708 3.906008 CGTTTTTACTGCTGATTTGGACG 59.094 43.478 0.00 0.00 0.00 4.79
1665 1709 4.319190 CGTTTTTACTGCTGATTTGGACGA 60.319 41.667 0.00 0.00 0.00 4.20
1667 1711 5.356882 TTTTACTGCTGATTTGGACGAAG 57.643 39.130 0.00 0.00 0.00 3.79
1714 1766 7.096722 CGGAAGTCGCAAAGTAGTAACATATAC 60.097 40.741 0.00 0.00 0.00 1.47
1736 1800 5.377478 ACTACTCTGGAAGTTTTCTTTGGG 58.623 41.667 0.00 0.00 40.61 4.12
1758 1822 4.488879 GATGACAGGAAAAACAAGCATCC 58.511 43.478 0.00 0.00 0.00 3.51
1759 1823 3.565307 TGACAGGAAAAACAAGCATCCT 58.435 40.909 0.00 0.00 43.00 3.24
1760 1824 4.724399 TGACAGGAAAAACAAGCATCCTA 58.276 39.130 0.00 0.00 40.29 2.94
1761 1825 4.761739 TGACAGGAAAAACAAGCATCCTAG 59.238 41.667 0.00 0.00 40.29 3.02
1899 1970 6.253942 GTCACTCGAATTCTAAGCCTAACTTC 59.746 42.308 3.52 0.00 39.97 3.01
1991 2066 9.622004 TCTTTCTAACACGAATAGAAACTACTG 57.378 33.333 13.85 7.80 41.85 2.74
1992 2067 9.622004 CTTTCTAACACGAATAGAAACTACTGA 57.378 33.333 13.85 0.00 41.85 3.41
1993 2068 9.970395 TTTCTAACACGAATAGAAACTACTGAA 57.030 29.630 13.85 0.00 41.85 3.02
1994 2069 8.961294 TCTAACACGAATAGAAACTACTGAAC 57.039 34.615 0.00 0.00 0.00 3.18
1995 2070 6.686130 AACACGAATAGAAACTACTGAACG 57.314 37.500 0.00 0.00 0.00 3.95
2019 2122 6.753279 CGCATGATGATTCCTTGTACAAAATT 59.247 34.615 10.03 0.00 0.00 1.82
2025 2128 3.907894 TCCTTGTACAAAATTCGCACC 57.092 42.857 10.03 0.00 0.00 5.01
2032 2135 2.134346 ACAAAATTCGCACCATGCAAC 58.866 42.857 0.00 0.00 45.36 4.17
2058 2161 0.463654 TGGTCGCTGCACTTTCAGTT 60.464 50.000 0.00 0.00 36.49 3.16
2091 2194 4.233005 ACGATTCGATCTGCTACATCATG 58.767 43.478 13.95 0.00 0.00 3.07
2098 2201 5.297527 TCGATCTGCTACATCATGCAAAATT 59.702 36.000 0.00 0.00 38.81 1.82
2100 2203 5.900865 TCTGCTACATCATGCAAAATTCA 57.099 34.783 0.00 0.00 38.81 2.57
2114 2217 7.332213 TGCAAAATTCATCCGAGAAATATCA 57.668 32.000 0.00 0.00 0.00 2.15
2123 2228 7.704271 TCATCCGAGAAATATCATCCGTATAC 58.296 38.462 0.00 0.00 0.00 1.47
2145 2250 4.943705 ACCACTGCTCAATACGAATTCATT 59.056 37.500 6.22 0.00 0.00 2.57
2146 2251 5.163723 ACCACTGCTCAATACGAATTCATTG 60.164 40.000 6.22 8.94 34.17 2.82
2155 2260 6.765512 TCAATACGAATTCATTGTATGCCTCA 59.234 34.615 14.72 0.00 34.45 3.86
2219 2324 6.773976 TTTGAGGAGCCTTTGTATATTTGG 57.226 37.500 0.00 0.00 0.00 3.28
2245 2350 6.990349 ACGAAGGGAATACTAACACAATATGG 59.010 38.462 0.00 0.00 0.00 2.74
2345 2450 8.547967 TCTAAAGGTTCACTATAAGTGCAAAG 57.452 34.615 2.12 0.00 45.54 2.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 8.935844 CACATATAATATGGTGATGTTAGCGTT 58.064 33.333 0.00 0.00 33.16 4.84
6 7 8.479313 ACACATATAATATGGTGATGTTAGCG 57.521 34.615 11.91 0.00 35.33 4.26
7 8 9.435688 TGACACATATAATATGGTGATGTTAGC 57.564 33.333 11.91 0.00 35.33 3.09
34 35 9.667989 CGCATGAATTTTATGATAGTCATTTCA 57.332 29.630 5.41 3.14 38.26 2.69
35 36 9.882996 TCGCATGAATTTTATGATAGTCATTTC 57.117 29.630 5.41 0.00 38.26 2.17
36 37 9.669353 GTCGCATGAATTTTATGATAGTCATTT 57.331 29.630 5.41 0.00 38.26 2.32
37 38 8.839343 TGTCGCATGAATTTTATGATAGTCATT 58.161 29.630 5.41 0.00 38.26 2.57
38 39 8.382030 TGTCGCATGAATTTTATGATAGTCAT 57.618 30.769 5.41 0.00 40.72 3.06
39 40 7.784633 TGTCGCATGAATTTTATGATAGTCA 57.215 32.000 5.41 0.00 0.00 3.41
40 41 9.110617 CAATGTCGCATGAATTTTATGATAGTC 57.889 33.333 5.41 0.00 0.00 2.59
41 42 8.623903 ACAATGTCGCATGAATTTTATGATAGT 58.376 29.630 5.41 0.00 0.00 2.12
44 45 9.800433 TTTACAATGTCGCATGAATTTTATGAT 57.200 25.926 5.41 0.00 0.00 2.45
45 46 9.288124 CTTTACAATGTCGCATGAATTTTATGA 57.712 29.630 5.41 0.00 0.00 2.15
46 47 8.533965 CCTTTACAATGTCGCATGAATTTTATG 58.466 33.333 0.00 0.00 0.00 1.90
47 48 7.706179 CCCTTTACAATGTCGCATGAATTTTAT 59.294 33.333 0.00 0.00 0.00 1.40
48 49 7.032580 CCCTTTACAATGTCGCATGAATTTTA 58.967 34.615 0.00 0.00 0.00 1.52
49 50 5.868801 CCCTTTACAATGTCGCATGAATTTT 59.131 36.000 0.00 0.00 0.00 1.82
50 51 5.184864 TCCCTTTACAATGTCGCATGAATTT 59.815 36.000 0.00 0.00 0.00 1.82
51 52 4.704540 TCCCTTTACAATGTCGCATGAATT 59.295 37.500 0.00 0.00 0.00 2.17
52 53 4.269183 TCCCTTTACAATGTCGCATGAAT 58.731 39.130 0.00 0.00 0.00 2.57
53 54 3.680490 TCCCTTTACAATGTCGCATGAA 58.320 40.909 0.00 0.00 0.00 2.57
54 55 3.342377 TCCCTTTACAATGTCGCATGA 57.658 42.857 0.00 0.00 0.00 3.07
55 56 4.165779 GTTTCCCTTTACAATGTCGCATG 58.834 43.478 0.00 0.00 0.00 4.06
56 57 3.823873 TGTTTCCCTTTACAATGTCGCAT 59.176 39.130 0.00 0.00 0.00 4.73
57 58 3.003897 GTGTTTCCCTTTACAATGTCGCA 59.996 43.478 0.00 0.00 0.00 5.10
58 59 3.561503 GTGTTTCCCTTTACAATGTCGC 58.438 45.455 0.00 0.00 0.00 5.19
59 60 3.805823 CGTGTTTCCCTTTACAATGTCG 58.194 45.455 0.00 0.00 0.00 4.35
60 61 3.003897 TGCGTGTTTCCCTTTACAATGTC 59.996 43.478 0.00 0.00 0.00 3.06
61 62 2.952978 TGCGTGTTTCCCTTTACAATGT 59.047 40.909 0.00 0.00 0.00 2.71
62 63 3.564511 CTGCGTGTTTCCCTTTACAATG 58.435 45.455 0.00 0.00 0.00 2.82
63 64 2.556622 CCTGCGTGTTTCCCTTTACAAT 59.443 45.455 0.00 0.00 0.00 2.71
64 65 1.950909 CCTGCGTGTTTCCCTTTACAA 59.049 47.619 0.00 0.00 0.00 2.41
65 66 1.141254 TCCTGCGTGTTTCCCTTTACA 59.859 47.619 0.00 0.00 0.00 2.41
66 67 1.534163 GTCCTGCGTGTTTCCCTTTAC 59.466 52.381 0.00 0.00 0.00 2.01
67 68 1.141254 TGTCCTGCGTGTTTCCCTTTA 59.859 47.619 0.00 0.00 0.00 1.85
68 69 0.106918 TGTCCTGCGTGTTTCCCTTT 60.107 50.000 0.00 0.00 0.00 3.11
69 70 0.818040 GTGTCCTGCGTGTTTCCCTT 60.818 55.000 0.00 0.00 0.00 3.95
70 71 1.227853 GTGTCCTGCGTGTTTCCCT 60.228 57.895 0.00 0.00 0.00 4.20
71 72 2.604174 CGTGTCCTGCGTGTTTCCC 61.604 63.158 0.00 0.00 0.00 3.97
72 73 0.598158 TACGTGTCCTGCGTGTTTCC 60.598 55.000 0.00 0.00 42.87 3.13
73 74 0.505655 GTACGTGTCCTGCGTGTTTC 59.494 55.000 0.00 0.00 42.87 2.78
74 75 0.877213 GGTACGTGTCCTGCGTGTTT 60.877 55.000 0.00 0.00 42.87 2.83
75 76 1.300388 GGTACGTGTCCTGCGTGTT 60.300 57.895 0.00 0.00 42.87 3.32
76 77 2.198287 AGGTACGTGTCCTGCGTGT 61.198 57.895 12.25 0.00 42.87 4.49
77 78 1.733041 CAGGTACGTGTCCTGCGTG 60.733 63.158 22.18 6.48 44.46 5.34
78 79 2.649034 CAGGTACGTGTCCTGCGT 59.351 61.111 22.18 0.00 44.46 5.24
82 83 3.282745 CTGCGCAGGTACGTGTCCT 62.283 63.158 29.88 2.93 35.45 3.85
83 84 2.809601 CTGCGCAGGTACGTGTCC 60.810 66.667 29.88 8.60 34.88 4.02
84 85 2.537792 TAGCTGCGCAGGTACGTGTC 62.538 60.000 37.83 20.08 40.09 3.67
85 86 1.945354 ATAGCTGCGCAGGTACGTGT 61.945 55.000 41.95 27.91 43.22 4.49
86 87 1.226974 ATAGCTGCGCAGGTACGTG 60.227 57.895 41.95 18.02 43.22 4.49
87 88 1.226974 CATAGCTGCGCAGGTACGT 60.227 57.895 41.95 28.90 43.22 3.57
88 89 2.589492 GCATAGCTGCGCAGGTACG 61.589 63.158 41.95 36.83 43.22 3.67
89 90 3.324035 GCATAGCTGCGCAGGTAC 58.676 61.111 41.95 29.66 43.22 3.34
98 99 4.559063 AGGCTGCCGGCATAGCTG 62.559 66.667 32.02 21.63 44.01 4.24
99 100 4.559063 CAGGCTGCCGGCATAGCT 62.559 66.667 32.02 19.32 44.01 3.32
100 101 3.839353 ATCAGGCTGCCGGCATAGC 62.839 63.158 32.87 29.85 44.01 2.97
101 102 1.228063 AATCAGGCTGCCGGCATAG 60.228 57.895 32.87 21.18 44.01 2.23
102 103 1.526686 CAATCAGGCTGCCGGCATA 60.527 57.895 32.87 13.72 44.01 3.14
103 104 2.831742 CAATCAGGCTGCCGGCAT 60.832 61.111 32.87 13.54 44.01 4.40
104 105 4.349503 ACAATCAGGCTGCCGGCA 62.350 61.111 30.59 30.59 44.01 5.69
105 106 3.512516 GACAATCAGGCTGCCGGC 61.513 66.667 22.73 22.73 40.90 6.13
106 107 1.817099 GAGACAATCAGGCTGCCGG 60.817 63.158 13.96 13.43 33.72 6.13
107 108 2.169789 CGAGACAATCAGGCTGCCG 61.170 63.158 13.96 8.60 33.72 5.69
108 109 1.078848 ACGAGACAATCAGGCTGCC 60.079 57.895 11.65 11.65 33.72 4.85
109 110 0.390340 TCACGAGACAATCAGGCTGC 60.390 55.000 10.34 0.00 33.72 5.25
110 111 2.200067 GATCACGAGACAATCAGGCTG 58.800 52.381 8.58 8.58 33.72 4.85
111 112 1.137872 GGATCACGAGACAATCAGGCT 59.862 52.381 0.00 0.00 39.48 4.58
112 113 1.576356 GGATCACGAGACAATCAGGC 58.424 55.000 0.00 0.00 0.00 4.85
125 126 5.465724 GGTATCCAATGACTTTACGGATCAC 59.534 44.000 0.00 0.00 37.62 3.06
126 127 5.129650 TGGTATCCAATGACTTTACGGATCA 59.870 40.000 0.00 0.00 37.62 2.92
127 128 5.465724 GTGGTATCCAATGACTTTACGGATC 59.534 44.000 0.00 0.00 37.62 3.36
128 129 5.104693 TGTGGTATCCAATGACTTTACGGAT 60.105 40.000 0.00 0.00 39.73 4.18
129 130 4.223255 TGTGGTATCCAATGACTTTACGGA 59.777 41.667 0.00 0.00 34.18 4.69
130 131 4.509616 TGTGGTATCCAATGACTTTACGG 58.490 43.478 0.00 0.00 34.18 4.02
131 132 5.815222 TCATGTGGTATCCAATGACTTTACG 59.185 40.000 0.00 0.00 34.18 3.18
132 133 6.260936 CCTCATGTGGTATCCAATGACTTTAC 59.739 42.308 5.61 0.00 34.18 2.01
133 134 6.356556 CCTCATGTGGTATCCAATGACTTTA 58.643 40.000 5.61 0.00 34.18 1.85
134 135 5.195940 CCTCATGTGGTATCCAATGACTTT 58.804 41.667 5.61 0.00 34.18 2.66
135 136 4.385643 CCCTCATGTGGTATCCAATGACTT 60.386 45.833 12.65 0.00 34.18 3.01
136 137 3.137176 CCCTCATGTGGTATCCAATGACT 59.863 47.826 12.65 0.00 34.18 3.41
137 138 3.480470 CCCTCATGTGGTATCCAATGAC 58.520 50.000 12.65 0.00 34.18 3.06
138 139 2.158623 GCCCTCATGTGGTATCCAATGA 60.159 50.000 12.65 10.61 34.18 2.57
139 140 2.233271 GCCCTCATGTGGTATCCAATG 58.767 52.381 12.65 0.00 34.18 2.82
140 141 1.852309 TGCCCTCATGTGGTATCCAAT 59.148 47.619 12.65 0.00 34.18 3.16
141 142 1.064758 GTGCCCTCATGTGGTATCCAA 60.065 52.381 12.65 0.00 34.18 3.53
142 143 0.546122 GTGCCCTCATGTGGTATCCA 59.454 55.000 12.65 2.12 0.00 3.41
143 144 0.546122 TGTGCCCTCATGTGGTATCC 59.454 55.000 12.65 0.00 0.00 2.59
144 145 2.418368 TTGTGCCCTCATGTGGTATC 57.582 50.000 12.65 2.69 0.00 2.24
145 146 4.079787 ACTTATTGTGCCCTCATGTGGTAT 60.080 41.667 12.65 1.70 0.00 2.73
146 147 3.265737 ACTTATTGTGCCCTCATGTGGTA 59.734 43.478 12.65 2.16 0.00 3.25
147 148 2.041620 ACTTATTGTGCCCTCATGTGGT 59.958 45.455 12.65 0.00 0.00 4.16
148 149 2.726821 ACTTATTGTGCCCTCATGTGG 58.273 47.619 6.84 6.84 0.00 4.17
149 150 4.789012 AAACTTATTGTGCCCTCATGTG 57.211 40.909 0.00 0.00 0.00 3.21
150 151 6.493458 ACTTAAAACTTATTGTGCCCTCATGT 59.507 34.615 0.00 0.00 0.00 3.21
151 152 6.924111 ACTTAAAACTTATTGTGCCCTCATG 58.076 36.000 0.00 0.00 0.00 3.07
152 153 7.539034 AACTTAAAACTTATTGTGCCCTCAT 57.461 32.000 0.00 0.00 0.00 2.90
153 154 6.969993 AACTTAAAACTTATTGTGCCCTCA 57.030 33.333 0.00 0.00 0.00 3.86
154 155 9.406828 CTAAAACTTAAAACTTATTGTGCCCTC 57.593 33.333 0.00 0.00 0.00 4.30
155 156 7.870954 GCTAAAACTTAAAACTTATTGTGCCCT 59.129 33.333 0.00 0.00 0.00 5.19
156 157 7.870954 AGCTAAAACTTAAAACTTATTGTGCCC 59.129 33.333 0.00 0.00 0.00 5.36
157 158 8.812147 AGCTAAAACTTAAAACTTATTGTGCC 57.188 30.769 0.00 0.00 0.00 5.01
158 159 9.678941 AGAGCTAAAACTTAAAACTTATTGTGC 57.321 29.630 0.00 0.00 0.00 4.57
173 174 9.227777 ACCGACAAAATTATAAGAGCTAAAACT 57.772 29.630 0.00 0.00 0.00 2.66
174 175 9.486857 GACCGACAAAATTATAAGAGCTAAAAC 57.513 33.333 0.00 0.00 0.00 2.43
175 176 8.385111 CGACCGACAAAATTATAAGAGCTAAAA 58.615 33.333 0.00 0.00 0.00 1.52
176 177 7.464977 GCGACCGACAAAATTATAAGAGCTAAA 60.465 37.037 0.00 0.00 0.00 1.85
177 178 6.019318 GCGACCGACAAAATTATAAGAGCTAA 60.019 38.462 0.00 0.00 0.00 3.09
178 179 5.461078 GCGACCGACAAAATTATAAGAGCTA 59.539 40.000 0.00 0.00 0.00 3.32
179 180 4.270325 GCGACCGACAAAATTATAAGAGCT 59.730 41.667 0.00 0.00 0.00 4.09
180 181 4.515432 GCGACCGACAAAATTATAAGAGC 58.485 43.478 0.00 0.00 0.00 4.09
181 182 4.809426 AGGCGACCGACAAAATTATAAGAG 59.191 41.667 0.00 0.00 0.00 2.85
182 183 4.569162 CAGGCGACCGACAAAATTATAAGA 59.431 41.667 0.00 0.00 0.00 2.10
183 184 4.331717 ACAGGCGACCGACAAAATTATAAG 59.668 41.667 0.00 0.00 0.00 1.73
184 185 4.255301 ACAGGCGACCGACAAAATTATAA 58.745 39.130 0.00 0.00 0.00 0.98
185 186 3.864243 ACAGGCGACCGACAAAATTATA 58.136 40.909 0.00 0.00 0.00 0.98
186 187 2.706890 ACAGGCGACCGACAAAATTAT 58.293 42.857 0.00 0.00 0.00 1.28
187 188 2.172851 ACAGGCGACCGACAAAATTA 57.827 45.000 0.00 0.00 0.00 1.40
188 189 1.802365 GTACAGGCGACCGACAAAATT 59.198 47.619 0.00 0.00 0.00 1.82
189 190 1.435577 GTACAGGCGACCGACAAAAT 58.564 50.000 0.00 0.00 0.00 1.82
190 191 0.600782 GGTACAGGCGACCGACAAAA 60.601 55.000 0.00 0.00 0.00 2.44
191 192 1.005867 GGTACAGGCGACCGACAAA 60.006 57.895 0.00 0.00 0.00 2.83
192 193 1.746322 TTGGTACAGGCGACCGACAA 61.746 55.000 0.00 0.00 42.39 3.18
193 194 1.746322 TTTGGTACAGGCGACCGACA 61.746 55.000 0.00 0.00 42.39 4.35
194 195 0.390735 ATTTGGTACAGGCGACCGAC 60.391 55.000 0.00 0.00 42.39 4.79
195 196 0.322322 AATTTGGTACAGGCGACCGA 59.678 50.000 0.00 0.00 42.39 4.69
196 197 1.129811 GAAATTTGGTACAGGCGACCG 59.870 52.381 0.00 0.00 42.39 4.79
197 198 2.156098 TGAAATTTGGTACAGGCGACC 58.844 47.619 0.00 0.00 42.39 4.79
198 199 2.414161 GCTGAAATTTGGTACAGGCGAC 60.414 50.000 0.00 0.00 42.39 5.19
199 200 1.810151 GCTGAAATTTGGTACAGGCGA 59.190 47.619 0.00 0.00 42.39 5.54
200 201 1.812571 AGCTGAAATTTGGTACAGGCG 59.187 47.619 0.00 0.00 42.39 5.52
201 202 2.558359 ACAGCTGAAATTTGGTACAGGC 59.442 45.455 23.35 0.00 42.39 4.85
202 203 4.278170 TCAACAGCTGAAATTTGGTACAGG 59.722 41.667 23.35 0.00 42.39 4.00
203 204 5.437289 TCAACAGCTGAAATTTGGTACAG 57.563 39.130 23.35 0.00 42.39 2.74
204 205 5.843673 TTCAACAGCTGAAATTTGGTACA 57.156 34.783 23.35 0.00 41.21 2.90
213 214 7.375053 ACTTTGTTAAGTTTCAACAGCTGAAA 58.625 30.769 23.35 8.21 41.85 2.69
214 215 6.919721 ACTTTGTTAAGTTTCAACAGCTGAA 58.080 32.000 23.35 0.84 41.85 3.02
215 216 6.509418 ACTTTGTTAAGTTTCAACAGCTGA 57.491 33.333 23.35 0.00 41.85 4.26
240 241 7.608308 TTAATATGTTTTGATGGGCTTTTGC 57.392 32.000 0.00 0.00 46.64 3.68
276 277 8.028938 CGTTTCTTGTGATGAGGGATTTTAAAT 58.971 33.333 0.00 0.00 0.00 1.40
277 278 7.367285 CGTTTCTTGTGATGAGGGATTTTAAA 58.633 34.615 0.00 0.00 0.00 1.52
278 279 6.569610 GCGTTTCTTGTGATGAGGGATTTTAA 60.570 38.462 0.00 0.00 0.00 1.52
279 280 5.106317 GCGTTTCTTGTGATGAGGGATTTTA 60.106 40.000 0.00 0.00 0.00 1.52
280 281 4.321230 GCGTTTCTTGTGATGAGGGATTTT 60.321 41.667 0.00 0.00 0.00 1.82
281 282 3.191371 GCGTTTCTTGTGATGAGGGATTT 59.809 43.478 0.00 0.00 0.00 2.17
282 283 2.749621 GCGTTTCTTGTGATGAGGGATT 59.250 45.455 0.00 0.00 0.00 3.01
283 284 2.290260 TGCGTTTCTTGTGATGAGGGAT 60.290 45.455 0.00 0.00 0.00 3.85
284 285 1.071542 TGCGTTTCTTGTGATGAGGGA 59.928 47.619 0.00 0.00 0.00 4.20
285 286 1.522668 TGCGTTTCTTGTGATGAGGG 58.477 50.000 0.00 0.00 0.00 4.30
286 287 3.624326 TTTGCGTTTCTTGTGATGAGG 57.376 42.857 0.00 0.00 0.00 3.86
287 288 5.228635 GCATATTTGCGTTTCTTGTGATGAG 59.771 40.000 0.00 0.00 39.49 2.90
288 289 5.094812 GCATATTTGCGTTTCTTGTGATGA 58.905 37.500 0.00 0.00 39.49 2.92
289 290 5.365766 GCATATTTGCGTTTCTTGTGATG 57.634 39.130 0.00 0.00 39.49 3.07
345 346 9.045223 GCCTTTTGATTTTCAATCTTTTGTAGT 57.955 29.630 0.00 0.00 36.11 2.73
346 347 9.044150 TGCCTTTTGATTTTCAATCTTTTGTAG 57.956 29.630 0.00 0.00 36.11 2.74
347 348 8.954950 TGCCTTTTGATTTTCAATCTTTTGTA 57.045 26.923 0.00 0.00 36.11 2.41
348 349 7.862512 TGCCTTTTGATTTTCAATCTTTTGT 57.137 28.000 0.00 0.00 36.11 2.83
349 350 9.570488 TTTTGCCTTTTGATTTTCAATCTTTTG 57.430 25.926 0.00 0.00 36.11 2.44
351 352 9.955208 GATTTTGCCTTTTGATTTTCAATCTTT 57.045 25.926 0.00 0.00 36.11 2.52
352 353 9.122779 TGATTTTGCCTTTTGATTTTCAATCTT 57.877 25.926 0.00 0.00 36.11 2.40
353 354 8.680039 TGATTTTGCCTTTTGATTTTCAATCT 57.320 26.923 0.00 0.00 36.11 2.40
354 355 9.733219 TTTGATTTTGCCTTTTGATTTTCAATC 57.267 25.926 0.00 0.00 36.11 2.67
357 358 9.517609 CATTTTGATTTTGCCTTTTGATTTTCA 57.482 25.926 0.00 0.00 0.00 2.69
358 359 8.970293 CCATTTTGATTTTGCCTTTTGATTTTC 58.030 29.630 0.00 0.00 0.00 2.29
359 360 7.927092 CCCATTTTGATTTTGCCTTTTGATTTT 59.073 29.630 0.00 0.00 0.00 1.82
360 361 7.069702 ACCCATTTTGATTTTGCCTTTTGATTT 59.930 29.630 0.00 0.00 0.00 2.17
361 362 6.550481 ACCCATTTTGATTTTGCCTTTTGATT 59.450 30.769 0.00 0.00 0.00 2.57
362 363 6.069994 ACCCATTTTGATTTTGCCTTTTGAT 58.930 32.000 0.00 0.00 0.00 2.57
363 364 5.444176 ACCCATTTTGATTTTGCCTTTTGA 58.556 33.333 0.00 0.00 0.00 2.69
364 365 5.560567 CGACCCATTTTGATTTTGCCTTTTG 60.561 40.000 0.00 0.00 0.00 2.44
365 366 4.514816 CGACCCATTTTGATTTTGCCTTTT 59.485 37.500 0.00 0.00 0.00 2.27
366 367 4.064388 CGACCCATTTTGATTTTGCCTTT 58.936 39.130 0.00 0.00 0.00 3.11
367 368 3.663025 CGACCCATTTTGATTTTGCCTT 58.337 40.909 0.00 0.00 0.00 4.35
368 369 2.612721 GCGACCCATTTTGATTTTGCCT 60.613 45.455 0.00 0.00 0.00 4.75
369 370 1.731709 GCGACCCATTTTGATTTTGCC 59.268 47.619 0.00 0.00 0.00 4.52
370 371 1.389784 CGCGACCCATTTTGATTTTGC 59.610 47.619 0.00 0.00 0.00 3.68
371 372 2.408032 CACGCGACCCATTTTGATTTTG 59.592 45.455 15.93 0.00 0.00 2.44
372 373 2.671596 CACGCGACCCATTTTGATTTT 58.328 42.857 15.93 0.00 0.00 1.82
373 374 1.668628 GCACGCGACCCATTTTGATTT 60.669 47.619 15.93 0.00 0.00 2.17
374 375 0.109319 GCACGCGACCCATTTTGATT 60.109 50.000 15.93 0.00 0.00 2.57
375 376 1.506262 GCACGCGACCCATTTTGAT 59.494 52.632 15.93 0.00 0.00 2.57
376 377 2.622011 GGCACGCGACCCATTTTGA 61.622 57.895 15.93 0.00 0.00 2.69
377 378 2.126502 GGCACGCGACCCATTTTG 60.127 61.111 15.93 0.00 0.00 2.44
403 404 1.368641 TACAATGATCTGTGGCACGC 58.631 50.000 13.77 2.99 40.62 5.34
404 405 4.621068 ATTTACAATGATCTGTGGCACG 57.379 40.909 13.77 8.10 0.00 5.34
405 406 6.683974 ACTATTTACAATGATCTGTGGCAC 57.316 37.500 11.55 11.55 0.00 5.01
406 407 7.564793 ACTACTATTTACAATGATCTGTGGCA 58.435 34.615 0.00 0.00 0.00 4.92
407 408 8.338259 CAACTACTATTTACAATGATCTGTGGC 58.662 37.037 0.00 0.00 0.00 5.01
408 409 9.383519 ACAACTACTATTTACAATGATCTGTGG 57.616 33.333 0.00 0.00 0.00 4.17
416 417 9.832445 ACATCCCTACAACTACTATTTACAATG 57.168 33.333 0.00 0.00 0.00 2.82
418 419 9.661563 CAACATCCCTACAACTACTATTTACAA 57.338 33.333 0.00 0.00 0.00 2.41
419 420 7.767198 GCAACATCCCTACAACTACTATTTACA 59.233 37.037 0.00 0.00 0.00 2.41
420 421 7.985752 AGCAACATCCCTACAACTACTATTTAC 59.014 37.037 0.00 0.00 0.00 2.01
421 422 7.985184 CAGCAACATCCCTACAACTACTATTTA 59.015 37.037 0.00 0.00 0.00 1.40
422 423 6.823689 CAGCAACATCCCTACAACTACTATTT 59.176 38.462 0.00 0.00 0.00 1.40
423 424 6.349300 CAGCAACATCCCTACAACTACTATT 58.651 40.000 0.00 0.00 0.00 1.73
424 425 5.685075 GCAGCAACATCCCTACAACTACTAT 60.685 44.000 0.00 0.00 0.00 2.12
425 426 4.382685 GCAGCAACATCCCTACAACTACTA 60.383 45.833 0.00 0.00 0.00 1.82
454 457 2.894565 CTACTCCGCCGGCTAGTCG 61.895 68.421 28.29 20.70 0.00 4.18
456 459 0.467659 ATTCTACTCCGCCGGCTAGT 60.468 55.000 27.74 27.74 0.00 2.57
458 461 1.461091 CCATTCTACTCCGCCGGCTA 61.461 60.000 26.68 11.82 0.00 3.93
545 551 5.332743 TCTAAGAACATGCTCCCCATTTTT 58.667 37.500 0.00 0.00 29.71 1.94
635 649 4.273969 CGTTGGTTTTATACTGGTGTGTGT 59.726 41.667 0.00 0.00 0.00 3.72
636 650 4.778904 CGTTGGTTTTATACTGGTGTGTG 58.221 43.478 0.00 0.00 0.00 3.82
637 651 3.251487 GCGTTGGTTTTATACTGGTGTGT 59.749 43.478 0.00 0.00 0.00 3.72
841 863 0.466189 ATCAGTTAAGGCATGCGGGG 60.466 55.000 12.44 0.00 0.00 5.73
862 884 0.676736 GGAGATGACAGGGATCGGTC 59.323 60.000 0.00 0.00 38.34 4.79
871 893 0.596083 GCGATGTCCGGAGATGACAG 60.596 60.000 20.44 8.52 45.20 3.51
873 895 1.300233 GGCGATGTCCGGAGATGAC 60.300 63.158 20.44 9.85 39.04 3.06
877 899 3.838271 GCTGGCGATGTCCGGAGA 61.838 66.667 3.06 2.85 39.04 3.71
912 934 2.116772 TCGTGGAAGGAGGACGGT 59.883 61.111 0.00 0.00 33.88 4.83
937 962 2.818274 CGTAGCTTCGGGTTGGCC 60.818 66.667 4.63 0.00 0.00 5.36
939 964 1.804326 CGTCGTAGCTTCGGGTTGG 60.804 63.158 13.03 0.00 0.00 3.77
941 966 1.505353 CTCGTCGTAGCTTCGGGTT 59.495 57.895 13.03 0.00 0.00 4.11
945 970 1.868251 GGTGCTCGTCGTAGCTTCG 60.868 63.158 6.38 6.38 43.19 3.79
961 986 3.991051 CAGGACTCACGGTGCGGT 61.991 66.667 2.51 4.81 41.32 5.68
963 988 4.363990 AGCAGGACTCACGGTGCG 62.364 66.667 2.51 0.00 41.32 5.34
964 989 2.740055 CAGCAGGACTCACGGTGC 60.740 66.667 2.51 0.00 36.48 5.01
965 990 2.740055 GCAGCAGGACTCACGGTG 60.740 66.667 0.56 0.56 0.00 4.94
966 991 4.008933 GGCAGCAGGACTCACGGT 62.009 66.667 0.00 0.00 0.00 4.83
1008 1037 2.420043 GCGCGGAAGTAGCCCATA 59.580 61.111 8.83 0.00 0.00 2.74
1513 1555 4.024387 TCTGTACAATCAAGAACCAAACGC 60.024 41.667 0.00 0.00 0.00 4.84
1612 1656 8.566260 GGGAGATGATATGAACTTCAAATCTTG 58.434 37.037 0.00 0.00 0.00 3.02
1642 1686 3.906008 CGTCCAAATCAGCAGTAAAAACG 59.094 43.478 0.00 0.00 0.00 3.60
1657 1701 1.600164 CGTACCGTGTCTTCGTCCAAA 60.600 52.381 0.00 0.00 0.00 3.28
1661 1705 0.453449 GACCGTACCGTGTCTTCGTC 60.453 60.000 0.00 0.00 0.00 4.20
1664 1708 1.974487 GAAGACCGTACCGTGTCTTC 58.026 55.000 21.83 21.83 45.85 2.87
1665 1709 1.268899 CTGAAGACCGTACCGTGTCTT 59.731 52.381 15.90 15.90 43.85 3.01
1667 1711 0.595095 ACTGAAGACCGTACCGTGTC 59.405 55.000 0.00 0.00 0.00 3.67
1714 1766 5.621193 TCCCAAAGAAAACTTCCAGAGTAG 58.379 41.667 0.00 0.00 37.72 2.57
1736 1800 4.219288 AGGATGCTTGTTTTTCCTGTCATC 59.781 41.667 0.00 0.00 37.22 2.92
1758 1822 6.256757 CCAAAGAAATTTCGTCCTCTAGCTAG 59.743 42.308 15.01 15.01 0.00 3.42
1759 1823 6.070995 TCCAAAGAAATTTCGTCCTCTAGCTA 60.071 38.462 12.42 0.00 0.00 3.32
1760 1824 4.938226 CCAAAGAAATTTCGTCCTCTAGCT 59.062 41.667 12.42 0.00 0.00 3.32
1761 1825 4.935808 TCCAAAGAAATTTCGTCCTCTAGC 59.064 41.667 12.42 0.00 0.00 3.42
1899 1970 7.993821 ATGTTATCAGTCAGAATTACTGTCG 57.006 36.000 6.72 0.00 45.86 4.35
1991 2066 4.332543 TGTACAAGGAATCATCATGCGTTC 59.667 41.667 0.00 0.00 0.00 3.95
1992 2067 4.260985 TGTACAAGGAATCATCATGCGTT 58.739 39.130 0.00 0.00 0.00 4.84
1993 2068 3.872696 TGTACAAGGAATCATCATGCGT 58.127 40.909 0.00 0.00 0.00 5.24
1994 2069 4.880886 TTGTACAAGGAATCATCATGCG 57.119 40.909 3.59 0.00 0.00 4.73
1995 2070 7.043854 CGAATTTTGTACAAGGAATCATCATGC 60.044 37.037 8.56 0.00 0.00 4.06
2058 2161 3.394800 CGAATCGTCGGTGAGTTGA 57.605 52.632 0.00 0.00 43.81 3.18
2091 2194 7.540055 GGATGATATTTCTCGGATGAATTTTGC 59.460 37.037 0.00 0.00 0.00 3.68
2098 2201 6.775594 ATACGGATGATATTTCTCGGATGA 57.224 37.500 0.00 0.00 0.00 2.92
2100 2203 6.605995 TGGTATACGGATGATATTTCTCGGAT 59.394 38.462 0.00 0.00 0.00 4.18
2114 2217 4.321008 CGTATTGAGCAGTGGTATACGGAT 60.321 45.833 21.66 0.00 39.95 4.18
2123 2228 5.163723 ACAATGAATTCGTATTGAGCAGTGG 60.164 40.000 19.84 0.00 37.63 4.00
2145 2250 3.069016 ACCGTCGAAATATGAGGCATACA 59.931 43.478 0.00 0.00 0.00 2.29
2146 2251 3.650139 ACCGTCGAAATATGAGGCATAC 58.350 45.455 0.00 0.00 0.00 2.39
2155 2260 6.918892 TCATGAATTTGACCGTCGAAATAT 57.081 33.333 5.28 0.00 0.00 1.28
2219 2324 7.170998 CCATATTGTGTTAGTATTCCCTTCGTC 59.829 40.741 0.00 0.00 0.00 4.20
2245 2350 8.325421 TCATAAGTATCTTGTAGATCGGAGAC 57.675 38.462 0.00 0.00 42.51 3.36


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

AutoCloner maintained by Alex Coulton.