Multiple sequence alignment - TraesCS2D01G229300

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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 TraesCS2D01G229300 chr2D 100.000 4241 0 0 1 4241 199128130 199123890 0.000000e+00 7832.0
1 TraesCS2D01G229300 chr2D 89.091 55 5 1 689 742 354327317 354327263 2.740000e-07 67.6
2 TraesCS2D01G229300 chr2A 95.292 3866 87 31 384 4241 218126408 218122630 0.000000e+00 6043.0
3 TraesCS2D01G229300 chr2A 93.286 283 17 2 101 381 729555244 729554962 2.360000e-112 416.0
4 TraesCS2D01G229300 chr2A 92.157 102 6 2 1 100 218126514 218126413 4.420000e-30 143.0
5 TraesCS2D01G229300 chr2B 96.349 3342 75 12 384 3723 375136329 375133033 0.000000e+00 5452.0
6 TraesCS2D01G229300 chr2B 96.532 519 13 4 3724 4241 375132927 375132413 0.000000e+00 854.0
7 TraesCS2D01G229300 chr3D 93.333 285 17 2 101 383 488120898 488121182 1.820000e-113 420.0
8 TraesCS2D01G229300 chr3D 92.883 281 18 2 101 379 590751755 590752035 1.420000e-109 407.0
9 TraesCS2D01G229300 chr3D 91.156 294 22 3 94 383 575736355 575736648 3.070000e-106 396.0
10 TraesCS2D01G229300 chr3D 95.918 49 2 0 684 732 53484617 53484665 3.520000e-11 80.5
11 TraesCS2D01G229300 chr4D 92.982 285 18 2 101 383 226455041 226455325 8.480000e-112 414.0
12 TraesCS2D01G229300 chr4D 92.361 288 20 2 98 383 226384946 226385233 3.950000e-110 409.0
13 TraesCS2D01G229300 chr4D 92.373 118 8 1 3707 3824 216748916 216749032 2.620000e-37 167.0
14 TraesCS2D01G229300 chr7D 92.281 285 18 3 101 383 73143783 73143501 6.610000e-108 401.0
15 TraesCS2D01G229300 chr4A 91.638 287 23 1 98 383 738609930 738610216 3.070000e-106 396.0
16 TraesCS2D01G229300 chr4A 97.727 44 1 0 687 730 608228006 608228049 4.550000e-10 76.8
17 TraesCS2D01G229300 chr4A 93.333 45 3 0 687 731 528730280 528730324 2.740000e-07 67.6
18 TraesCS2D01G229300 chr1D 91.901 284 21 2 101 383 116930067 116930349 3.070000e-106 396.0
19 TraesCS2D01G229300 chr3B 97.778 45 1 0 686 730 11603476 11603520 1.260000e-10 78.7
20 TraesCS2D01G229300 chr5B 95.556 45 2 0 687 731 228272293 228272249 5.880000e-09 73.1
21 TraesCS2D01G229300 chr5D 95.455 44 2 0 687 730 439821271 439821314 2.120000e-08 71.3
22 TraesCS2D01G229300 chr5A 91.837 49 2 2 686 732 1808465 1808417 2.740000e-07 67.6
23 TraesCS2D01G229300 chr1A 93.333 45 3 0 691 735 540296253 540296297 2.740000e-07 67.6


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 TraesCS2D01G229300 chr2D 199123890 199128130 4240 True 7832 7832 100.0000 1 4241 1 chr2D.!!$R1 4240
1 TraesCS2D01G229300 chr2A 218122630 218126514 3884 True 3093 6043 93.7245 1 4241 2 chr2A.!!$R2 4240
2 TraesCS2D01G229300 chr2B 375132413 375136329 3916 True 3153 5452 96.4405 384 4241 2 chr2B.!!$R1 3857

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
103 106 0.031994 GCCACTTCGCCATGTGTTTT 59.968 50.0 0.00 0.00 32.76 2.43 F
159 162 0.032130 CGCGCATACACTCACCCTAT 59.968 55.0 8.75 0.00 0.00 2.57 F
291 294 0.036732 TCCTTCCACAGAAAGCGCAT 59.963 50.0 11.47 0.00 0.00 4.73 F
293 296 0.095935 CTTCCACAGAAAGCGCATCG 59.904 55.0 11.47 6.82 0.00 3.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1162 1171 1.269448 AGTAAGCGAACCGTCCGTAAA 59.731 47.619 0.00 0.00 0.00 2.01 R
1189 1198 4.415332 GAACGGTCGGAGCGCAGA 62.415 66.667 27.32 2.59 43.79 4.26 R
2834 2843 3.564235 TCATGTTCTTGTCAATGCAGC 57.436 42.857 0.00 0.00 0.00 5.25 R
3356 3365 6.150140 GCTAGTTTAGGATGGCATAAAGGATG 59.850 42.308 0.00 0.00 38.73 3.51 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
22 23 2.223044 GCGTTTCTGCTGCTTATACCAC 60.223 50.000 0.00 0.00 0.00 4.16
40 41 4.710324 ACCACGAAAGAATGTGAGGTTTA 58.290 39.130 0.00 0.00 38.36 2.01
41 42 4.514066 ACCACGAAAGAATGTGAGGTTTAC 59.486 41.667 0.00 0.00 38.36 2.01
42 43 4.755123 CCACGAAAGAATGTGAGGTTTACT 59.245 41.667 0.00 0.00 38.36 2.24
45 46 7.041644 CCACGAAAGAATGTGAGGTTTACTTTA 60.042 37.037 0.00 0.00 38.36 1.85
63 66 2.188994 CTGCCTGCAGCTACTCCC 59.811 66.667 8.66 0.00 44.23 4.30
71 74 0.530870 GCAGCTACTCCCGAATCACC 60.531 60.000 0.00 0.00 0.00 4.02
100 103 3.049674 CGCCACTTCGCCATGTGT 61.050 61.111 0.00 0.00 32.76 3.72
101 104 2.616330 CGCCACTTCGCCATGTGTT 61.616 57.895 0.00 0.00 32.76 3.32
103 106 0.031994 GCCACTTCGCCATGTGTTTT 59.968 50.000 0.00 0.00 32.76 2.43
104 107 1.537990 GCCACTTCGCCATGTGTTTTT 60.538 47.619 0.00 0.00 32.76 1.94
125 128 6.993786 TTTTTGAACATCAGTACAGACACA 57.006 33.333 0.00 0.00 0.00 3.72
126 129 6.993786 TTTTGAACATCAGTACAGACACAA 57.006 33.333 0.00 0.00 0.00 3.33
127 130 6.603237 TTTGAACATCAGTACAGACACAAG 57.397 37.500 0.00 0.00 0.00 3.16
128 131 4.058124 TGAACATCAGTACAGACACAAGC 58.942 43.478 0.00 0.00 0.00 4.01
129 132 2.677199 ACATCAGTACAGACACAAGCG 58.323 47.619 0.00 0.00 0.00 4.68
130 133 1.391485 CATCAGTACAGACACAAGCGC 59.609 52.381 0.00 0.00 0.00 5.92
131 134 0.673985 TCAGTACAGACACAAGCGCT 59.326 50.000 2.64 2.64 0.00 5.92
132 135 1.063806 CAGTACAGACACAAGCGCTC 58.936 55.000 12.06 0.00 0.00 5.03
133 136 0.673985 AGTACAGACACAAGCGCTCA 59.326 50.000 12.06 0.00 0.00 4.26
134 137 1.273606 AGTACAGACACAAGCGCTCAT 59.726 47.619 12.06 0.00 0.00 2.90
135 138 2.492088 AGTACAGACACAAGCGCTCATA 59.508 45.455 12.06 0.00 0.00 2.15
136 139 1.714794 ACAGACACAAGCGCTCATAC 58.285 50.000 12.06 1.58 0.00 2.39
137 140 1.000843 ACAGACACAAGCGCTCATACA 59.999 47.619 12.06 0.00 0.00 2.29
138 141 2.274437 CAGACACAAGCGCTCATACAT 58.726 47.619 12.06 0.00 0.00 2.29
139 142 2.030091 CAGACACAAGCGCTCATACATG 59.970 50.000 12.06 6.69 0.00 3.21
140 143 0.729116 ACACAAGCGCTCATACATGC 59.271 50.000 12.06 0.00 0.00 4.06
146 149 2.941333 GCTCATACATGCGCGCAT 59.059 55.556 39.13 39.13 37.08 4.73
147 150 2.153039 GCTCATACATGCGCGCATA 58.847 52.632 42.66 30.46 34.91 3.14
148 151 0.179240 GCTCATACATGCGCGCATAC 60.179 55.000 42.66 22.53 34.91 2.39
149 152 1.139163 CTCATACATGCGCGCATACA 58.861 50.000 42.66 32.37 34.91 2.29
150 153 0.858583 TCATACATGCGCGCATACAC 59.141 50.000 42.66 9.47 34.91 2.90
151 154 0.861185 CATACATGCGCGCATACACT 59.139 50.000 42.66 26.91 34.91 3.55
152 155 1.136529 CATACATGCGCGCATACACTC 60.137 52.381 42.66 7.80 34.91 3.51
153 156 0.179124 TACATGCGCGCATACACTCA 60.179 50.000 42.66 22.06 34.91 3.41
154 157 1.011904 CATGCGCGCATACACTCAC 60.012 57.895 42.66 6.14 34.91 3.51
155 158 2.173669 ATGCGCGCATACACTCACC 61.174 57.895 42.74 4.73 34.49 4.02
156 159 3.564027 GCGCGCATACACTCACCC 61.564 66.667 29.10 0.00 0.00 4.61
157 160 2.184322 CGCGCATACACTCACCCT 59.816 61.111 8.75 0.00 0.00 4.34
158 161 1.435925 CGCGCATACACTCACCCTA 59.564 57.895 8.75 0.00 0.00 3.53
159 162 0.032130 CGCGCATACACTCACCCTAT 59.968 55.000 8.75 0.00 0.00 2.57
160 163 1.502231 GCGCATACACTCACCCTATG 58.498 55.000 0.30 0.00 0.00 2.23
161 164 1.068588 GCGCATACACTCACCCTATGA 59.931 52.381 0.30 0.00 35.45 2.15
162 165 2.483013 GCGCATACACTCACCCTATGAA 60.483 50.000 0.30 0.00 36.69 2.57
163 166 3.123804 CGCATACACTCACCCTATGAAC 58.876 50.000 0.00 0.00 36.69 3.18
164 167 3.123804 GCATACACTCACCCTATGAACG 58.876 50.000 0.00 0.00 36.69 3.95
165 168 2.953466 TACACTCACCCTATGAACGC 57.047 50.000 0.00 0.00 36.69 4.84
166 169 0.973632 ACACTCACCCTATGAACGCA 59.026 50.000 0.00 0.00 36.69 5.24
167 170 1.337823 ACACTCACCCTATGAACGCAC 60.338 52.381 0.00 0.00 36.69 5.34
168 171 0.973632 ACTCACCCTATGAACGCACA 59.026 50.000 0.00 0.00 36.69 4.57
169 172 1.337823 ACTCACCCTATGAACGCACAC 60.338 52.381 0.00 0.00 36.69 3.82
170 173 0.682292 TCACCCTATGAACGCACACA 59.318 50.000 0.00 0.00 33.02 3.72
171 174 0.796312 CACCCTATGAACGCACACAC 59.204 55.000 0.00 0.00 0.00 3.82
172 175 0.669318 ACCCTATGAACGCACACACG 60.669 55.000 0.00 0.00 39.50 4.49
173 176 1.419922 CCTATGAACGCACACACGC 59.580 57.895 0.00 0.00 36.19 5.34
174 177 1.288419 CCTATGAACGCACACACGCA 61.288 55.000 0.00 0.00 36.19 5.24
175 178 0.179250 CTATGAACGCACACACGCAC 60.179 55.000 0.00 0.00 36.19 5.34
176 179 0.876342 TATGAACGCACACACGCACA 60.876 50.000 0.00 0.00 36.19 4.57
177 180 2.350760 GAACGCACACACGCACAC 60.351 61.111 0.00 0.00 36.19 3.82
178 181 3.783588 GAACGCACACACGCACACC 62.784 63.158 0.00 0.00 36.19 4.16
181 184 2.280524 GCACACACGCACACCCTA 60.281 61.111 0.00 0.00 0.00 3.53
182 185 1.671054 GCACACACGCACACCCTAT 60.671 57.895 0.00 0.00 0.00 2.57
183 186 1.635663 GCACACACGCACACCCTATC 61.636 60.000 0.00 0.00 0.00 2.08
184 187 1.019278 CACACACGCACACCCTATCC 61.019 60.000 0.00 0.00 0.00 2.59
185 188 1.449601 CACACGCACACCCTATCCC 60.450 63.158 0.00 0.00 0.00 3.85
186 189 1.612442 ACACGCACACCCTATCCCT 60.612 57.895 0.00 0.00 0.00 4.20
187 190 0.324923 ACACGCACACCCTATCCCTA 60.325 55.000 0.00 0.00 0.00 3.53
188 191 1.048601 CACGCACACCCTATCCCTAT 58.951 55.000 0.00 0.00 0.00 2.57
189 192 1.048601 ACGCACACCCTATCCCTATG 58.951 55.000 0.00 0.00 0.00 2.23
190 193 1.338107 CGCACACCCTATCCCTATGA 58.662 55.000 0.00 0.00 0.00 2.15
191 194 1.691976 CGCACACCCTATCCCTATGAA 59.308 52.381 0.00 0.00 0.00 2.57
192 195 2.548067 CGCACACCCTATCCCTATGAAC 60.548 54.545 0.00 0.00 0.00 3.18
193 196 2.438021 GCACACCCTATCCCTATGAACA 59.562 50.000 0.00 0.00 0.00 3.18
194 197 3.744530 GCACACCCTATCCCTATGAACAC 60.745 52.174 0.00 0.00 0.00 3.32
195 198 3.454447 CACACCCTATCCCTATGAACACA 59.546 47.826 0.00 0.00 0.00 3.72
196 199 4.103153 CACACCCTATCCCTATGAACACAT 59.897 45.833 0.00 0.00 0.00 3.21
197 200 4.348168 ACACCCTATCCCTATGAACACATC 59.652 45.833 0.00 0.00 0.00 3.06
198 201 3.910627 ACCCTATCCCTATGAACACATCC 59.089 47.826 0.00 0.00 0.00 3.51
199 202 3.055819 CCCTATCCCTATGAACACATCCG 60.056 52.174 0.00 0.00 0.00 4.18
200 203 3.832490 CCTATCCCTATGAACACATCCGA 59.168 47.826 0.00 0.00 0.00 4.55
201 204 4.081972 CCTATCCCTATGAACACATCCGAG 60.082 50.000 0.00 0.00 0.00 4.63
202 205 3.026707 TCCCTATGAACACATCCGAGA 57.973 47.619 0.00 0.00 0.00 4.04
203 206 2.959030 TCCCTATGAACACATCCGAGAG 59.041 50.000 0.00 0.00 0.00 3.20
204 207 2.959030 CCCTATGAACACATCCGAGAGA 59.041 50.000 0.00 0.00 0.00 3.10
205 208 3.243569 CCCTATGAACACATCCGAGAGAC 60.244 52.174 0.00 0.00 0.00 3.36
206 209 3.634448 CCTATGAACACATCCGAGAGACT 59.366 47.826 0.00 0.00 0.00 3.24
207 210 3.516981 ATGAACACATCCGAGAGACTG 57.483 47.619 0.00 0.00 0.00 3.51
208 211 2.514803 TGAACACATCCGAGAGACTGA 58.485 47.619 0.00 0.00 0.00 3.41
209 212 2.489722 TGAACACATCCGAGAGACTGAG 59.510 50.000 0.00 0.00 0.00 3.35
210 213 0.814457 ACACATCCGAGAGACTGAGC 59.186 55.000 0.00 0.00 0.00 4.26
211 214 0.102120 CACATCCGAGAGACTGAGCC 59.898 60.000 0.00 0.00 0.00 4.70
212 215 1.358402 CATCCGAGAGACTGAGCCG 59.642 63.158 0.00 0.00 0.00 5.52
213 216 1.098129 CATCCGAGAGACTGAGCCGA 61.098 60.000 0.00 0.00 0.00 5.54
214 217 1.098712 ATCCGAGAGACTGAGCCGAC 61.099 60.000 0.00 0.00 0.00 4.79
215 218 2.041115 CCGAGAGACTGAGCCGACA 61.041 63.158 0.00 0.00 0.00 4.35
216 219 1.380403 CCGAGAGACTGAGCCGACAT 61.380 60.000 0.00 0.00 0.00 3.06
217 220 0.248417 CGAGAGACTGAGCCGACATG 60.248 60.000 0.00 0.00 0.00 3.21
218 221 0.814457 GAGAGACTGAGCCGACATGT 59.186 55.000 0.00 0.00 0.00 3.21
219 222 1.203523 GAGAGACTGAGCCGACATGTT 59.796 52.381 0.00 0.00 0.00 2.71
220 223 2.423892 GAGAGACTGAGCCGACATGTTA 59.576 50.000 0.00 0.00 0.00 2.41
221 224 3.027412 AGAGACTGAGCCGACATGTTAT 58.973 45.455 0.00 0.00 0.00 1.89
222 225 3.067461 AGAGACTGAGCCGACATGTTATC 59.933 47.826 0.00 0.00 0.00 1.75
223 226 3.027412 AGACTGAGCCGACATGTTATCT 58.973 45.455 0.00 0.00 0.00 1.98
224 227 3.449018 AGACTGAGCCGACATGTTATCTT 59.551 43.478 0.00 0.00 0.00 2.40
225 228 3.525537 ACTGAGCCGACATGTTATCTTG 58.474 45.455 0.00 0.00 0.00 3.02
226 229 3.195610 ACTGAGCCGACATGTTATCTTGA 59.804 43.478 0.00 0.00 0.00 3.02
227 230 4.183865 CTGAGCCGACATGTTATCTTGAA 58.816 43.478 0.00 0.00 0.00 2.69
228 231 4.574892 TGAGCCGACATGTTATCTTGAAA 58.425 39.130 0.00 0.00 0.00 2.69
229 232 5.185454 TGAGCCGACATGTTATCTTGAAAT 58.815 37.500 0.00 0.00 0.00 2.17
230 233 5.647658 TGAGCCGACATGTTATCTTGAAATT 59.352 36.000 0.00 0.00 0.00 1.82
231 234 6.150976 TGAGCCGACATGTTATCTTGAAATTT 59.849 34.615 0.00 0.00 0.00 1.82
232 235 7.335673 TGAGCCGACATGTTATCTTGAAATTTA 59.664 33.333 0.00 0.00 0.00 1.40
233 236 8.050778 AGCCGACATGTTATCTTGAAATTTAA 57.949 30.769 0.00 0.00 0.00 1.52
234 237 8.184192 AGCCGACATGTTATCTTGAAATTTAAG 58.816 33.333 0.00 0.00 0.00 1.85
235 238 8.181573 GCCGACATGTTATCTTGAAATTTAAGA 58.818 33.333 0.00 2.67 38.42 2.10
247 250 9.231297 TCTTGAAATTTAAGAAGTCACCATAGG 57.769 33.333 0.00 0.00 31.62 2.57
248 251 7.391148 TGAAATTTAAGAAGTCACCATAGGC 57.609 36.000 0.00 0.00 0.00 3.93
249 252 6.093495 TGAAATTTAAGAAGTCACCATAGGCG 59.907 38.462 0.00 0.00 0.00 5.52
250 253 2.596904 TAAGAAGTCACCATAGGCGC 57.403 50.000 0.00 0.00 0.00 6.53
251 254 0.107654 AAGAAGTCACCATAGGCGCC 60.108 55.000 21.89 21.89 0.00 6.53
252 255 0.978146 AGAAGTCACCATAGGCGCCT 60.978 55.000 34.85 34.85 0.00 5.52
253 256 0.530870 GAAGTCACCATAGGCGCCTC 60.531 60.000 36.73 17.40 0.00 4.70
254 257 2.279517 GTCACCATAGGCGCCTCG 60.280 66.667 36.73 25.26 0.00 4.63
255 258 2.758327 TCACCATAGGCGCCTCGT 60.758 61.111 36.73 24.45 0.00 4.18
256 259 2.279517 CACCATAGGCGCCTCGTC 60.280 66.667 36.73 1.08 0.00 4.20
257 260 3.900892 ACCATAGGCGCCTCGTCG 61.901 66.667 36.73 21.01 36.23 5.12
258 261 3.900892 CCATAGGCGCCTCGTCGT 61.901 66.667 36.73 11.27 36.23 4.34
259 262 2.353607 CATAGGCGCCTCGTCGTC 60.354 66.667 36.73 0.00 36.23 4.20
260 263 3.950254 ATAGGCGCCTCGTCGTCG 61.950 66.667 36.73 0.00 39.34 5.12
281 284 2.055299 GGGAACGTCTCCTTCCACA 58.945 57.895 13.94 0.00 44.68 4.17
282 285 0.037232 GGGAACGTCTCCTTCCACAG 60.037 60.000 13.94 0.00 44.68 3.66
283 286 0.966920 GGAACGTCTCCTTCCACAGA 59.033 55.000 8.87 0.00 41.61 3.41
284 287 1.343465 GGAACGTCTCCTTCCACAGAA 59.657 52.381 8.87 0.00 41.61 3.02
285 288 2.224209 GGAACGTCTCCTTCCACAGAAA 60.224 50.000 8.87 0.00 41.61 2.52
286 289 2.821991 ACGTCTCCTTCCACAGAAAG 57.178 50.000 0.00 0.00 0.00 2.62
287 290 1.270358 ACGTCTCCTTCCACAGAAAGC 60.270 52.381 0.00 0.00 0.00 3.51
288 291 1.433534 GTCTCCTTCCACAGAAAGCG 58.566 55.000 0.00 0.00 0.00 4.68
289 292 0.320771 TCTCCTTCCACAGAAAGCGC 60.321 55.000 0.00 0.00 0.00 5.92
290 293 0.603707 CTCCTTCCACAGAAAGCGCA 60.604 55.000 11.47 0.00 0.00 6.09
291 294 0.036732 TCCTTCCACAGAAAGCGCAT 59.963 50.000 11.47 0.00 0.00 4.73
292 295 0.449388 CCTTCCACAGAAAGCGCATC 59.551 55.000 11.47 7.77 0.00 3.91
293 296 0.095935 CTTCCACAGAAAGCGCATCG 59.904 55.000 11.47 6.82 0.00 3.84
304 307 4.131376 CGCATCGCCAGAAATCCT 57.869 55.556 0.00 0.00 0.00 3.24
305 308 1.645455 CGCATCGCCAGAAATCCTG 59.355 57.895 0.00 0.00 42.55 3.86
306 309 0.811219 CGCATCGCCAGAAATCCTGA 60.811 55.000 0.00 0.00 45.78 3.86
307 310 1.382522 GCATCGCCAGAAATCCTGAA 58.617 50.000 0.00 0.00 45.78 3.02
308 311 1.745087 GCATCGCCAGAAATCCTGAAA 59.255 47.619 0.00 0.00 45.78 2.69
309 312 2.360165 GCATCGCCAGAAATCCTGAAAT 59.640 45.455 0.00 0.00 45.78 2.17
310 313 3.565482 GCATCGCCAGAAATCCTGAAATA 59.435 43.478 0.00 0.00 45.78 1.40
311 314 4.036734 GCATCGCCAGAAATCCTGAAATAA 59.963 41.667 0.00 0.00 45.78 1.40
312 315 5.450412 GCATCGCCAGAAATCCTGAAATAAA 60.450 40.000 0.00 0.00 45.78 1.40
313 316 6.736794 GCATCGCCAGAAATCCTGAAATAAAT 60.737 38.462 0.00 0.00 45.78 1.40
314 317 6.377327 TCGCCAGAAATCCTGAAATAAATC 57.623 37.500 0.00 0.00 45.78 2.17
315 318 5.299279 TCGCCAGAAATCCTGAAATAAATCC 59.701 40.000 0.00 0.00 45.78 3.01
316 319 5.067674 CGCCAGAAATCCTGAAATAAATCCA 59.932 40.000 0.00 0.00 45.78 3.41
317 320 6.510536 GCCAGAAATCCTGAAATAAATCCAG 58.489 40.000 0.00 0.00 45.78 3.86
318 321 6.462067 GCCAGAAATCCTGAAATAAATCCAGG 60.462 42.308 0.00 0.00 45.78 4.45
328 331 7.815840 TGAAATAAATCCAGGAATAATGCGA 57.184 32.000 0.00 0.00 0.00 5.10
329 332 7.874940 TGAAATAAATCCAGGAATAATGCGAG 58.125 34.615 0.00 0.00 0.00 5.03
330 333 5.886960 ATAAATCCAGGAATAATGCGAGC 57.113 39.130 0.00 0.00 0.00 5.03
331 334 2.936919 ATCCAGGAATAATGCGAGCA 57.063 45.000 0.00 0.00 0.00 4.26
332 335 1.953559 TCCAGGAATAATGCGAGCAC 58.046 50.000 0.00 0.00 0.00 4.40
333 336 0.947244 CCAGGAATAATGCGAGCACC 59.053 55.000 0.00 0.00 0.00 5.01
334 337 1.667236 CAGGAATAATGCGAGCACCA 58.333 50.000 0.00 0.00 0.00 4.17
335 338 1.600957 CAGGAATAATGCGAGCACCAG 59.399 52.381 0.00 0.00 0.00 4.00
336 339 0.947244 GGAATAATGCGAGCACCAGG 59.053 55.000 0.00 0.00 0.00 4.45
337 340 1.475034 GGAATAATGCGAGCACCAGGA 60.475 52.381 0.00 0.00 0.00 3.86
338 341 1.599542 GAATAATGCGAGCACCAGGAC 59.400 52.381 0.00 0.00 0.00 3.85
339 342 0.833287 ATAATGCGAGCACCAGGACT 59.167 50.000 0.00 0.00 0.00 3.85
340 343 0.613260 TAATGCGAGCACCAGGACTT 59.387 50.000 0.00 0.00 0.00 3.01
341 344 0.957395 AATGCGAGCACCAGGACTTG 60.957 55.000 0.00 0.00 0.00 3.16
342 345 1.830587 ATGCGAGCACCAGGACTTGA 61.831 55.000 0.00 0.00 0.00 3.02
343 346 1.301716 GCGAGCACCAGGACTTGAA 60.302 57.895 0.00 0.00 0.00 2.69
344 347 1.569479 GCGAGCACCAGGACTTGAAC 61.569 60.000 0.00 0.00 0.00 3.18
345 348 0.951040 CGAGCACCAGGACTTGAACC 60.951 60.000 0.00 0.00 0.00 3.62
346 349 0.606673 GAGCACCAGGACTTGAACCC 60.607 60.000 0.00 0.00 0.00 4.11
347 350 1.062488 AGCACCAGGACTTGAACCCT 61.062 55.000 0.00 0.00 0.00 4.34
362 365 2.750350 CCTGATGGGCCGGGATAC 59.250 66.667 2.18 0.00 34.45 2.24
378 381 4.353383 GGATACCATTGTCCCTCTAACC 57.647 50.000 0.00 0.00 0.00 2.85
379 382 3.714798 GGATACCATTGTCCCTCTAACCA 59.285 47.826 0.00 0.00 0.00 3.67
380 383 4.351111 GGATACCATTGTCCCTCTAACCAT 59.649 45.833 0.00 0.00 0.00 3.55
381 384 3.933861 ACCATTGTCCCTCTAACCATC 57.066 47.619 0.00 0.00 0.00 3.51
382 385 2.509964 ACCATTGTCCCTCTAACCATCC 59.490 50.000 0.00 0.00 0.00 3.51
386 389 4.301072 TTGTCCCTCTAACCATCCTTTG 57.699 45.455 0.00 0.00 0.00 2.77
440 443 6.614694 AACACCACCTACAGTTACATCATA 57.385 37.500 0.00 0.00 0.00 2.15
455 458 9.486497 AGTTACATCATATGTCATCTGCTAAAG 57.514 33.333 1.90 0.00 43.67 1.85
460 463 9.264719 CATCATATGTCATCTGCTAAAGTTGTA 57.735 33.333 1.90 0.00 0.00 2.41
469 472 8.296713 TCATCTGCTAAAGTTGTATTTTTGGTC 58.703 33.333 0.00 0.00 0.00 4.02
520 523 3.627123 CCTTATGTTGCATCATCCGTTGA 59.373 43.478 13.46 0.00 39.12 3.18
526 529 2.989909 TGCATCATCCGTTGAAGATGT 58.010 42.857 8.89 0.00 44.62 3.06
540 543 7.646130 CCGTTGAAGATGTTCTAACTATCTCTC 59.354 40.741 4.03 8.12 33.38 3.20
578 581 7.667575 AATAGCCTAATGACTCTCTCAAAGA 57.332 36.000 0.00 0.00 30.60 2.52
579 582 7.667575 ATAGCCTAATGACTCTCTCAAAGAA 57.332 36.000 0.00 0.00 32.23 2.52
580 583 6.365970 AGCCTAATGACTCTCTCAAAGAAA 57.634 37.500 0.00 0.00 32.23 2.52
581 584 6.405538 AGCCTAATGACTCTCTCAAAGAAAG 58.594 40.000 0.00 0.00 32.23 2.62
582 585 6.013812 AGCCTAATGACTCTCTCAAAGAAAGT 60.014 38.462 0.00 0.00 32.23 2.66
590 593 6.764379 ACTCTCTCAAAGAAAGTAAGAAGGG 58.236 40.000 0.00 0.00 32.23 3.95
778 787 7.437713 TCATCCATGAAAATGTAGTACTCCT 57.562 36.000 0.00 0.00 33.08 3.69
780 789 8.421784 TCATCCATGAAAATGTAGTACTCCTAC 58.578 37.037 0.00 0.00 39.18 3.18
794 803 5.873732 GTACTCCTACAAGTACCAGTAACG 58.126 45.833 3.37 0.00 43.80 3.18
795 804 4.401925 ACTCCTACAAGTACCAGTAACGT 58.598 43.478 0.00 0.00 0.00 3.99
796 805 4.217118 ACTCCTACAAGTACCAGTAACGTG 59.783 45.833 0.00 0.00 33.31 4.49
865 874 1.376553 GCTTTTGAGGCCTCTCGCT 60.377 57.895 32.28 0.00 42.79 4.93
869 878 1.485124 TTTGAGGCCTCTCGCTCATA 58.515 50.000 32.28 7.74 42.79 2.15
876 885 1.338337 GCCTCTCGCTCATAGCAGTTA 59.662 52.381 0.00 0.00 42.58 2.24
1051 1060 1.826024 CAGCGCTCCTCCTGGTTAT 59.174 57.895 7.13 0.00 34.23 1.89
1122 1131 0.336737 CTACCACCTCCACCTCCTCT 59.663 60.000 0.00 0.00 0.00 3.69
1189 1198 0.529378 CGGTTCGCTTACTACCACCT 59.471 55.000 0.00 0.00 32.12 4.00
1196 1205 0.818296 CTTACTACCACCTCTGCGCT 59.182 55.000 9.73 0.00 0.00 5.92
1221 1230 0.394080 CGTTCCCGGACTACTCTCCT 60.394 60.000 0.73 0.00 0.00 3.69
1326 1335 1.135960 CTCCTCTCCCCTTCATTCCC 58.864 60.000 0.00 0.00 0.00 3.97
1622 1631 1.758906 CCTTCGACCTCCTCCTCCC 60.759 68.421 0.00 0.00 0.00 4.30
2431 2440 1.304713 CTGTGCAAGCAGGGGGATT 60.305 57.895 0.00 0.00 33.11 3.01
3356 3365 1.583054 ACAGACTCACGAAAAGCACC 58.417 50.000 0.00 0.00 0.00 5.01
3388 3397 4.883585 TGCCATCCTAAACTAGCAATTGAG 59.116 41.667 10.34 0.58 0.00 3.02
3389 3398 4.276926 GCCATCCTAAACTAGCAATTGAGG 59.723 45.833 10.34 5.17 0.00 3.86
3390 3399 5.440610 CCATCCTAAACTAGCAATTGAGGT 58.559 41.667 10.34 1.04 0.00 3.85
3391 3400 6.591935 CCATCCTAAACTAGCAATTGAGGTA 58.408 40.000 10.34 0.00 0.00 3.08
3392 3401 7.227156 CCATCCTAAACTAGCAATTGAGGTAT 58.773 38.462 10.34 0.00 0.00 2.73
3393 3402 8.375506 CCATCCTAAACTAGCAATTGAGGTATA 58.624 37.037 10.34 0.00 0.00 1.47
3394 3403 9.950496 CATCCTAAACTAGCAATTGAGGTATAT 57.050 33.333 10.34 0.00 0.00 0.86
3869 3984 9.561069 AATGGATGGATGTTCAGTAGTAATTAC 57.439 33.333 7.57 7.57 0.00 1.89
3907 4022 8.474831 AGTTACTTTGCTTGTCCTTTGTTTTAT 58.525 29.630 0.00 0.00 0.00 1.40
3908 4023 9.738832 GTTACTTTGCTTGTCCTTTGTTTTATA 57.261 29.630 0.00 0.00 0.00 0.98
3909 4024 9.738832 TTACTTTGCTTGTCCTTTGTTTTATAC 57.261 29.630 0.00 0.00 0.00 1.47
3910 4025 8.007405 ACTTTGCTTGTCCTTTGTTTTATACT 57.993 30.769 0.00 0.00 0.00 2.12
3912 4027 8.865590 TTTGCTTGTCCTTTGTTTTATACTTC 57.134 30.769 0.00 0.00 0.00 3.01
3913 4028 7.575414 TGCTTGTCCTTTGTTTTATACTTCA 57.425 32.000 0.00 0.00 0.00 3.02
3914 4029 7.648142 TGCTTGTCCTTTGTTTTATACTTCAG 58.352 34.615 0.00 0.00 0.00 3.02
3915 4030 7.284489 TGCTTGTCCTTTGTTTTATACTTCAGT 59.716 33.333 0.00 0.00 0.00 3.41
3916 4031 8.780249 GCTTGTCCTTTGTTTTATACTTCAGTA 58.220 33.333 0.00 0.00 34.67 2.74
3987 4104 7.435192 ACAACTGTCTTGTTTATTTTAAGCTGC 59.565 33.333 0.00 0.00 0.00 5.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 4.553330 ACCTCACATTCTTTCGTGGTAT 57.447 40.909 0.00 0.00 33.83 2.73
18 19 2.930826 ACCTCACATTCTTTCGTGGT 57.069 45.000 0.00 0.00 33.83 4.16
22 23 8.009974 CAGTAAAGTAAACCTCACATTCTTTCG 58.990 37.037 0.00 0.00 0.00 3.46
40 41 1.625818 AGTAGCTGCAGGCAGTAAAGT 59.374 47.619 21.19 8.27 45.24 2.66
41 42 2.275318 GAGTAGCTGCAGGCAGTAAAG 58.725 52.381 21.19 0.00 45.24 1.85
42 43 1.066143 GGAGTAGCTGCAGGCAGTAAA 60.066 52.381 21.19 5.81 45.24 2.01
45 46 2.664081 GGGAGTAGCTGCAGGCAGT 61.664 63.158 21.19 11.30 45.24 4.40
63 66 3.485877 GCGAAAGGAAAGATGGTGATTCG 60.486 47.826 0.00 0.00 40.78 3.34
71 74 2.159653 CGAAGTGGCGAAAGGAAAGATG 60.160 50.000 0.00 0.00 0.00 2.90
103 106 6.458206 GCTTGTGTCTGTACTGATGTTCAAAA 60.458 38.462 5.69 0.61 0.00 2.44
104 107 5.007626 GCTTGTGTCTGTACTGATGTTCAAA 59.992 40.000 5.69 0.00 0.00 2.69
105 108 4.511454 GCTTGTGTCTGTACTGATGTTCAA 59.489 41.667 5.69 8.15 0.00 2.69
106 109 4.058124 GCTTGTGTCTGTACTGATGTTCA 58.942 43.478 5.69 0.00 0.00 3.18
107 110 3.121944 CGCTTGTGTCTGTACTGATGTTC 59.878 47.826 5.69 0.00 0.00 3.18
108 111 3.059884 CGCTTGTGTCTGTACTGATGTT 58.940 45.455 5.69 0.00 0.00 2.71
109 112 2.677199 CGCTTGTGTCTGTACTGATGT 58.323 47.619 5.69 0.00 0.00 3.06
110 113 1.391485 GCGCTTGTGTCTGTACTGATG 59.609 52.381 0.00 0.00 0.00 3.07
111 114 1.273606 AGCGCTTGTGTCTGTACTGAT 59.726 47.619 2.64 0.00 0.00 2.90
112 115 0.673985 AGCGCTTGTGTCTGTACTGA 59.326 50.000 2.64 0.00 0.00 3.41
113 116 1.063806 GAGCGCTTGTGTCTGTACTG 58.936 55.000 13.26 0.00 0.00 2.74
114 117 0.673985 TGAGCGCTTGTGTCTGTACT 59.326 50.000 13.26 0.00 0.00 2.73
115 118 1.714794 ATGAGCGCTTGTGTCTGTAC 58.285 50.000 13.26 0.00 0.00 2.90
116 119 2.230266 TGTATGAGCGCTTGTGTCTGTA 59.770 45.455 13.26 0.00 0.00 2.74
117 120 1.000843 TGTATGAGCGCTTGTGTCTGT 59.999 47.619 13.26 0.00 0.00 3.41
118 121 1.713597 TGTATGAGCGCTTGTGTCTG 58.286 50.000 13.26 0.00 0.00 3.51
119 122 2.274437 CATGTATGAGCGCTTGTGTCT 58.726 47.619 13.26 0.00 0.00 3.41
120 123 1.267732 GCATGTATGAGCGCTTGTGTC 60.268 52.381 13.26 0.00 0.00 3.67
121 124 0.729116 GCATGTATGAGCGCTTGTGT 59.271 50.000 13.26 0.12 0.00 3.72
122 125 3.521534 GCATGTATGAGCGCTTGTG 57.478 52.632 13.26 5.84 0.00 3.33
130 133 1.136529 GTGTATGCGCGCATGTATGAG 60.137 52.381 46.79 0.00 37.82 2.90
131 134 0.858583 GTGTATGCGCGCATGTATGA 59.141 50.000 46.79 29.87 37.82 2.15
132 135 0.861185 AGTGTATGCGCGCATGTATG 59.139 50.000 46.79 1.07 37.82 2.39
133 136 1.139989 GAGTGTATGCGCGCATGTAT 58.860 50.000 46.79 32.16 37.82 2.29
134 137 0.179124 TGAGTGTATGCGCGCATGTA 60.179 50.000 46.79 34.35 37.82 2.29
135 138 1.447663 TGAGTGTATGCGCGCATGT 60.448 52.632 46.79 31.42 37.82 3.21
136 139 1.011904 GTGAGTGTATGCGCGCATG 60.012 57.895 46.79 4.08 37.27 4.06
137 140 2.173669 GGTGAGTGTATGCGCGCAT 61.174 57.895 43.68 43.68 37.27 4.73
138 141 2.813474 GGTGAGTGTATGCGCGCA 60.813 61.111 38.27 38.27 32.73 6.09
139 142 2.622903 TAGGGTGAGTGTATGCGCGC 62.623 60.000 27.26 27.26 0.00 6.86
140 143 0.032130 ATAGGGTGAGTGTATGCGCG 59.968 55.000 0.00 0.00 0.00 6.86
141 144 1.068588 TCATAGGGTGAGTGTATGCGC 59.931 52.381 0.00 0.00 31.80 6.09
142 145 3.123804 GTTCATAGGGTGAGTGTATGCG 58.876 50.000 0.00 0.00 38.29 4.73
143 146 3.123804 CGTTCATAGGGTGAGTGTATGC 58.876 50.000 0.00 0.00 38.29 3.14
144 147 3.123804 GCGTTCATAGGGTGAGTGTATG 58.876 50.000 0.00 0.00 38.29 2.39
145 148 2.764010 TGCGTTCATAGGGTGAGTGTAT 59.236 45.455 0.00 0.00 38.29 2.29
146 149 2.094390 GTGCGTTCATAGGGTGAGTGTA 60.094 50.000 0.00 0.00 38.29 2.90
147 150 0.973632 TGCGTTCATAGGGTGAGTGT 59.026 50.000 0.00 0.00 38.29 3.55
148 151 1.337728 TGTGCGTTCATAGGGTGAGTG 60.338 52.381 0.00 0.00 38.29 3.51
149 152 0.973632 TGTGCGTTCATAGGGTGAGT 59.026 50.000 0.00 0.00 38.29 3.41
150 153 1.337728 TGTGTGCGTTCATAGGGTGAG 60.338 52.381 0.00 0.00 38.29 3.51
151 154 0.682292 TGTGTGCGTTCATAGGGTGA 59.318 50.000 0.00 0.00 34.25 4.02
152 155 0.796312 GTGTGTGCGTTCATAGGGTG 59.204 55.000 0.00 0.00 0.00 4.61
153 156 0.669318 CGTGTGTGCGTTCATAGGGT 60.669 55.000 0.00 0.00 0.00 4.34
154 157 1.966493 GCGTGTGTGCGTTCATAGGG 61.966 60.000 0.00 0.00 0.00 3.53
155 158 1.288419 TGCGTGTGTGCGTTCATAGG 61.288 55.000 0.00 0.00 37.81 2.57
156 159 0.179250 GTGCGTGTGTGCGTTCATAG 60.179 55.000 0.00 0.00 37.81 2.23
157 160 0.876342 TGTGCGTGTGTGCGTTCATA 60.876 50.000 0.00 0.00 37.81 2.15
158 161 2.176926 TGTGCGTGTGTGCGTTCAT 61.177 52.632 0.00 0.00 37.81 2.57
159 162 2.815647 TGTGCGTGTGTGCGTTCA 60.816 55.556 0.00 0.00 37.81 3.18
160 163 2.350760 GTGTGCGTGTGTGCGTTC 60.351 61.111 0.00 0.00 37.81 3.95
161 164 3.871574 GGTGTGCGTGTGTGCGTT 61.872 61.111 0.00 0.00 37.81 4.84
164 167 1.635663 GATAGGGTGTGCGTGTGTGC 61.636 60.000 0.00 0.00 0.00 4.57
165 168 1.019278 GGATAGGGTGTGCGTGTGTG 61.019 60.000 0.00 0.00 0.00 3.82
166 169 1.295423 GGATAGGGTGTGCGTGTGT 59.705 57.895 0.00 0.00 0.00 3.72
167 170 1.449601 GGGATAGGGTGTGCGTGTG 60.450 63.158 0.00 0.00 0.00 3.82
168 171 0.324923 TAGGGATAGGGTGTGCGTGT 60.325 55.000 0.00 0.00 0.00 4.49
169 172 1.048601 ATAGGGATAGGGTGTGCGTG 58.951 55.000 0.00 0.00 0.00 5.34
170 173 1.048601 CATAGGGATAGGGTGTGCGT 58.951 55.000 0.00 0.00 0.00 5.24
171 174 1.338107 TCATAGGGATAGGGTGTGCG 58.662 55.000 0.00 0.00 0.00 5.34
172 175 2.438021 TGTTCATAGGGATAGGGTGTGC 59.562 50.000 0.00 0.00 0.00 4.57
173 176 3.454447 TGTGTTCATAGGGATAGGGTGTG 59.546 47.826 0.00 0.00 0.00 3.82
174 177 3.731431 TGTGTTCATAGGGATAGGGTGT 58.269 45.455 0.00 0.00 0.00 4.16
175 178 4.263068 GGATGTGTTCATAGGGATAGGGTG 60.263 50.000 0.00 0.00 34.06 4.61
176 179 3.910627 GGATGTGTTCATAGGGATAGGGT 59.089 47.826 0.00 0.00 34.06 4.34
177 180 3.055819 CGGATGTGTTCATAGGGATAGGG 60.056 52.174 0.00 0.00 34.06 3.53
178 181 3.832490 TCGGATGTGTTCATAGGGATAGG 59.168 47.826 0.00 0.00 34.06 2.57
179 182 4.767409 TCTCGGATGTGTTCATAGGGATAG 59.233 45.833 0.00 0.00 34.06 2.08
180 183 4.736473 TCTCGGATGTGTTCATAGGGATA 58.264 43.478 0.00 0.00 34.06 2.59
181 184 3.576118 CTCTCGGATGTGTTCATAGGGAT 59.424 47.826 0.00 0.00 34.06 3.85
182 185 2.959030 CTCTCGGATGTGTTCATAGGGA 59.041 50.000 0.00 0.00 34.06 4.20
183 186 2.959030 TCTCTCGGATGTGTTCATAGGG 59.041 50.000 0.00 0.00 34.06 3.53
184 187 3.634448 AGTCTCTCGGATGTGTTCATAGG 59.366 47.826 0.00 0.00 34.06 2.57
185 188 4.336713 TCAGTCTCTCGGATGTGTTCATAG 59.663 45.833 0.00 0.00 34.06 2.23
186 189 4.270008 TCAGTCTCTCGGATGTGTTCATA 58.730 43.478 0.00 0.00 34.06 2.15
187 190 3.092301 TCAGTCTCTCGGATGTGTTCAT 58.908 45.455 0.00 0.00 36.95 2.57
188 191 2.489722 CTCAGTCTCTCGGATGTGTTCA 59.510 50.000 0.00 0.00 0.00 3.18
189 192 2.733858 GCTCAGTCTCTCGGATGTGTTC 60.734 54.545 0.00 0.00 0.00 3.18
190 193 1.203523 GCTCAGTCTCTCGGATGTGTT 59.796 52.381 0.00 0.00 0.00 3.32
191 194 0.814457 GCTCAGTCTCTCGGATGTGT 59.186 55.000 0.00 0.00 0.00 3.72
192 195 0.102120 GGCTCAGTCTCTCGGATGTG 59.898 60.000 0.00 0.00 0.00 3.21
193 196 1.380403 CGGCTCAGTCTCTCGGATGT 61.380 60.000 0.00 0.00 0.00 3.06
194 197 1.098129 TCGGCTCAGTCTCTCGGATG 61.098 60.000 0.00 0.00 0.00 3.51
195 198 1.098712 GTCGGCTCAGTCTCTCGGAT 61.099 60.000 0.00 0.00 0.00 4.18
196 199 1.745864 GTCGGCTCAGTCTCTCGGA 60.746 63.158 0.00 0.00 0.00 4.55
197 200 1.380403 ATGTCGGCTCAGTCTCTCGG 61.380 60.000 0.00 0.00 0.00 4.63
198 201 0.248417 CATGTCGGCTCAGTCTCTCG 60.248 60.000 0.00 0.00 0.00 4.04
199 202 0.814457 ACATGTCGGCTCAGTCTCTC 59.186 55.000 0.00 0.00 0.00 3.20
200 203 1.261480 AACATGTCGGCTCAGTCTCT 58.739 50.000 0.00 0.00 0.00 3.10
201 204 2.941453 TAACATGTCGGCTCAGTCTC 57.059 50.000 0.00 0.00 0.00 3.36
202 205 3.027412 AGATAACATGTCGGCTCAGTCT 58.973 45.455 0.00 0.00 0.00 3.24
203 206 3.444703 AGATAACATGTCGGCTCAGTC 57.555 47.619 0.00 0.00 0.00 3.51
204 207 3.195610 TCAAGATAACATGTCGGCTCAGT 59.804 43.478 0.00 0.00 0.00 3.41
205 208 3.785486 TCAAGATAACATGTCGGCTCAG 58.215 45.455 0.00 0.00 0.00 3.35
206 209 3.885724 TCAAGATAACATGTCGGCTCA 57.114 42.857 0.00 0.00 0.00 4.26
207 210 5.741388 ATTTCAAGATAACATGTCGGCTC 57.259 39.130 0.00 0.00 0.00 4.70
208 211 6.515272 AAATTTCAAGATAACATGTCGGCT 57.485 33.333 0.00 0.00 0.00 5.52
209 212 8.181573 TCTTAAATTTCAAGATAACATGTCGGC 58.818 33.333 0.00 0.00 0.00 5.54
221 224 9.231297 CCTATGGTGACTTCTTAAATTTCAAGA 57.769 33.333 0.00 0.30 0.00 3.02
222 225 7.970614 GCCTATGGTGACTTCTTAAATTTCAAG 59.029 37.037 0.00 0.00 0.00 3.02
223 226 7.361713 CGCCTATGGTGACTTCTTAAATTTCAA 60.362 37.037 0.00 0.00 34.74 2.69
224 227 6.093495 CGCCTATGGTGACTTCTTAAATTTCA 59.907 38.462 0.00 0.00 34.74 2.69
225 228 6.487103 CGCCTATGGTGACTTCTTAAATTTC 58.513 40.000 0.00 0.00 34.74 2.17
226 229 5.163652 GCGCCTATGGTGACTTCTTAAATTT 60.164 40.000 0.00 0.00 34.74 1.82
227 230 4.335594 GCGCCTATGGTGACTTCTTAAATT 59.664 41.667 0.00 0.00 34.74 1.82
228 231 3.877508 GCGCCTATGGTGACTTCTTAAAT 59.122 43.478 0.00 0.00 34.74 1.40
229 232 3.267483 GCGCCTATGGTGACTTCTTAAA 58.733 45.455 0.00 0.00 34.74 1.52
230 233 2.419574 GGCGCCTATGGTGACTTCTTAA 60.420 50.000 22.15 0.00 38.38 1.85
231 234 1.138266 GGCGCCTATGGTGACTTCTTA 59.862 52.381 22.15 0.00 38.38 2.10
232 235 0.107654 GGCGCCTATGGTGACTTCTT 60.108 55.000 22.15 0.00 38.38 2.52
233 236 1.522569 GGCGCCTATGGTGACTTCT 59.477 57.895 22.15 0.00 38.38 2.85
234 237 4.126524 GGCGCCTATGGTGACTTC 57.873 61.111 22.15 0.00 38.38 3.01
237 240 2.279517 CGAGGCGCCTATGGTGAC 60.280 66.667 32.97 14.51 42.50 3.67
238 241 2.758327 ACGAGGCGCCTATGGTGA 60.758 61.111 32.97 0.00 34.74 4.02
239 242 2.279517 GACGAGGCGCCTATGGTG 60.280 66.667 32.97 18.94 36.10 4.17
240 243 3.900892 CGACGAGGCGCCTATGGT 61.901 66.667 32.97 26.91 0.00 3.55
241 244 3.825833 GACGACGAGGCGCCTATGG 62.826 68.421 32.97 23.64 33.86 2.74
242 245 2.353607 GACGACGAGGCGCCTATG 60.354 66.667 32.97 27.02 33.86 2.23
265 268 2.814280 TTCTGTGGAAGGAGACGTTC 57.186 50.000 0.00 0.00 0.00 3.95
266 269 2.807108 GCTTTCTGTGGAAGGAGACGTT 60.807 50.000 0.00 0.00 31.28 3.99
267 270 1.270358 GCTTTCTGTGGAAGGAGACGT 60.270 52.381 0.00 0.00 31.28 4.34
268 271 1.433534 GCTTTCTGTGGAAGGAGACG 58.566 55.000 0.00 0.00 31.28 4.18
269 272 1.433534 CGCTTTCTGTGGAAGGAGAC 58.566 55.000 0.00 0.00 32.01 3.36
270 273 0.320771 GCGCTTTCTGTGGAAGGAGA 60.321 55.000 0.00 0.00 32.01 3.71
271 274 0.603707 TGCGCTTTCTGTGGAAGGAG 60.604 55.000 9.73 0.00 33.09 3.69
272 275 0.036732 ATGCGCTTTCTGTGGAAGGA 59.963 50.000 9.73 0.00 31.28 3.36
273 276 0.449388 GATGCGCTTTCTGTGGAAGG 59.551 55.000 9.73 0.00 32.61 3.46
274 277 0.095935 CGATGCGCTTTCTGTGGAAG 59.904 55.000 9.73 0.00 32.61 3.46
275 278 2.161831 CGATGCGCTTTCTGTGGAA 58.838 52.632 9.73 0.00 0.00 3.53
276 279 3.874873 CGATGCGCTTTCTGTGGA 58.125 55.556 9.73 0.00 0.00 4.02
287 290 0.811219 TCAGGATTTCTGGCGATGCG 60.811 55.000 0.00 0.00 43.53 4.73
288 291 1.382522 TTCAGGATTTCTGGCGATGC 58.617 50.000 0.00 0.00 43.53 3.91
289 292 5.756195 TTATTTCAGGATTTCTGGCGATG 57.244 39.130 0.00 0.00 43.53 3.84
290 293 6.015940 GGATTTATTTCAGGATTTCTGGCGAT 60.016 38.462 0.00 0.00 43.53 4.58
291 294 5.299279 GGATTTATTTCAGGATTTCTGGCGA 59.701 40.000 0.00 0.00 43.53 5.54
292 295 5.067674 TGGATTTATTTCAGGATTTCTGGCG 59.932 40.000 0.00 0.00 43.53 5.69
293 296 6.469782 TGGATTTATTTCAGGATTTCTGGC 57.530 37.500 0.00 0.00 43.53 4.85
302 305 7.040478 TCGCATTATTCCTGGATTTATTTCAGG 60.040 37.037 0.00 0.00 46.91 3.86
303 306 7.874940 TCGCATTATTCCTGGATTTATTTCAG 58.125 34.615 0.00 0.00 0.00 3.02
304 307 7.522073 GCTCGCATTATTCCTGGATTTATTTCA 60.522 37.037 0.00 0.00 0.00 2.69
305 308 6.803807 GCTCGCATTATTCCTGGATTTATTTC 59.196 38.462 0.00 0.00 0.00 2.17
306 309 6.265196 TGCTCGCATTATTCCTGGATTTATTT 59.735 34.615 0.00 0.00 0.00 1.40
307 310 5.769662 TGCTCGCATTATTCCTGGATTTATT 59.230 36.000 0.00 0.00 0.00 1.40
308 311 5.182001 GTGCTCGCATTATTCCTGGATTTAT 59.818 40.000 0.00 0.00 0.00 1.40
309 312 4.515191 GTGCTCGCATTATTCCTGGATTTA 59.485 41.667 0.00 0.00 0.00 1.40
310 313 3.316308 GTGCTCGCATTATTCCTGGATTT 59.684 43.478 0.00 0.00 0.00 2.17
311 314 2.880890 GTGCTCGCATTATTCCTGGATT 59.119 45.455 0.00 0.00 0.00 3.01
312 315 2.498167 GTGCTCGCATTATTCCTGGAT 58.502 47.619 0.00 0.00 0.00 3.41
313 316 1.475034 GGTGCTCGCATTATTCCTGGA 60.475 52.381 0.00 0.00 0.00 3.86
314 317 0.947244 GGTGCTCGCATTATTCCTGG 59.053 55.000 0.00 0.00 0.00 4.45
315 318 1.600957 CTGGTGCTCGCATTATTCCTG 59.399 52.381 0.00 0.00 0.00 3.86
316 319 1.475751 CCTGGTGCTCGCATTATTCCT 60.476 52.381 0.00 0.00 0.00 3.36
317 320 0.947244 CCTGGTGCTCGCATTATTCC 59.053 55.000 0.00 0.00 0.00 3.01
318 321 1.599542 GTCCTGGTGCTCGCATTATTC 59.400 52.381 0.00 0.00 0.00 1.75
319 322 1.210478 AGTCCTGGTGCTCGCATTATT 59.790 47.619 0.00 0.00 0.00 1.40
320 323 0.833287 AGTCCTGGTGCTCGCATTAT 59.167 50.000 0.00 0.00 0.00 1.28
321 324 0.613260 AAGTCCTGGTGCTCGCATTA 59.387 50.000 0.00 0.00 0.00 1.90
322 325 0.957395 CAAGTCCTGGTGCTCGCATT 60.957 55.000 0.00 0.00 0.00 3.56
323 326 1.376424 CAAGTCCTGGTGCTCGCAT 60.376 57.895 0.00 0.00 0.00 4.73
324 327 2.031012 CAAGTCCTGGTGCTCGCA 59.969 61.111 0.00 0.00 0.00 5.10
325 328 1.301716 TTCAAGTCCTGGTGCTCGC 60.302 57.895 0.00 0.00 0.00 5.03
326 329 0.951040 GGTTCAAGTCCTGGTGCTCG 60.951 60.000 0.00 0.00 0.00 5.03
327 330 0.606673 GGGTTCAAGTCCTGGTGCTC 60.607 60.000 0.00 0.00 0.00 4.26
328 331 1.062488 AGGGTTCAAGTCCTGGTGCT 61.062 55.000 0.00 0.00 31.11 4.40
329 332 0.890996 CAGGGTTCAAGTCCTGGTGC 60.891 60.000 0.00 0.00 44.99 5.01
330 333 3.329300 CAGGGTTCAAGTCCTGGTG 57.671 57.895 0.00 0.00 44.99 4.17
345 348 2.750350 GTATCCCGGCCCATCAGG 59.250 66.667 0.00 0.00 39.47 3.86
346 349 1.492133 ATGGTATCCCGGCCCATCAG 61.492 60.000 0.00 0.00 33.73 2.90
347 350 1.065410 AATGGTATCCCGGCCCATCA 61.065 55.000 11.95 0.00 38.00 3.07
348 351 0.609131 CAATGGTATCCCGGCCCATC 60.609 60.000 11.95 0.00 38.00 3.51
349 352 1.360393 ACAATGGTATCCCGGCCCAT 61.360 55.000 0.00 1.20 40.68 4.00
350 353 1.990160 GACAATGGTATCCCGGCCCA 61.990 60.000 0.00 0.00 0.00 5.36
351 354 1.228154 GACAATGGTATCCCGGCCC 60.228 63.158 0.00 0.00 0.00 5.80
352 355 1.228154 GGACAATGGTATCCCGGCC 60.228 63.158 0.00 0.00 0.00 6.13
353 356 1.228154 GGGACAATGGTATCCCGGC 60.228 63.158 0.00 0.00 45.26 6.13
357 360 3.714798 TGGTTAGAGGGACAATGGTATCC 59.285 47.826 0.00 0.00 0.00 2.59
358 361 5.513267 GGATGGTTAGAGGGACAATGGTATC 60.513 48.000 0.00 0.00 0.00 2.24
359 362 4.351111 GGATGGTTAGAGGGACAATGGTAT 59.649 45.833 0.00 0.00 0.00 2.73
360 363 3.714798 GGATGGTTAGAGGGACAATGGTA 59.285 47.826 0.00 0.00 0.00 3.25
361 364 2.509964 GGATGGTTAGAGGGACAATGGT 59.490 50.000 0.00 0.00 0.00 3.55
362 365 2.780010 AGGATGGTTAGAGGGACAATGG 59.220 50.000 0.00 0.00 0.00 3.16
363 366 4.510167 AAGGATGGTTAGAGGGACAATG 57.490 45.455 0.00 0.00 0.00 2.82
364 367 4.292306 ACAAAGGATGGTTAGAGGGACAAT 59.708 41.667 0.00 0.00 0.00 2.71
365 368 3.655777 ACAAAGGATGGTTAGAGGGACAA 59.344 43.478 0.00 0.00 0.00 3.18
366 369 3.256704 ACAAAGGATGGTTAGAGGGACA 58.743 45.455 0.00 0.00 0.00 4.02
367 370 4.010349 CAACAAAGGATGGTTAGAGGGAC 58.990 47.826 0.00 0.00 0.00 4.46
368 371 3.913799 TCAACAAAGGATGGTTAGAGGGA 59.086 43.478 0.00 0.00 0.00 4.20
369 372 4.301072 TCAACAAAGGATGGTTAGAGGG 57.699 45.455 0.00 0.00 0.00 4.30
370 373 4.096984 GCATCAACAAAGGATGGTTAGAGG 59.903 45.833 0.00 0.00 41.87 3.69
371 374 5.240713 GCATCAACAAAGGATGGTTAGAG 57.759 43.478 0.00 0.00 41.87 2.43
377 380 4.701651 TGTTAGAGCATCAACAAAGGATGG 59.298 41.667 0.00 0.00 41.87 3.51
378 381 5.885230 TGTTAGAGCATCAACAAAGGATG 57.115 39.130 0.00 0.00 43.89 3.51
379 382 5.106555 CGTTGTTAGAGCATCAACAAAGGAT 60.107 40.000 10.21 0.00 42.85 3.24
380 383 4.213270 CGTTGTTAGAGCATCAACAAAGGA 59.787 41.667 10.21 0.00 42.85 3.36
381 384 4.024048 ACGTTGTTAGAGCATCAACAAAGG 60.024 41.667 19.10 13.24 42.85 3.11
382 385 5.095691 ACGTTGTTAGAGCATCAACAAAG 57.904 39.130 15.81 15.81 42.85 2.77
386 389 8.502161 AAAATAAACGTTGTTAGAGCATCAAC 57.498 30.769 0.00 0.00 37.82 3.18
413 416 3.888323 TGTAACTGTAGGTGGTGTTACGA 59.112 43.478 0.00 0.00 44.26 3.43
425 428 8.087136 AGCAGATGACATATGATGTAACTGTAG 58.913 37.037 14.18 0.00 45.03 2.74
440 443 9.630098 CAAAAATACAACTTTAGCAGATGACAT 57.370 29.630 0.00 0.00 0.00 3.06
455 458 8.600449 TGATTCATTTGGACCAAAAATACAAC 57.400 30.769 23.11 11.81 36.90 3.32
502 505 3.346315 TCTTCAACGGATGATGCAACAT 58.654 40.909 9.49 9.49 38.03 2.71
504 507 3.688272 CATCTTCAACGGATGATGCAAC 58.312 45.455 0.00 0.00 44.03 4.17
520 523 8.830915 TTCCAGAGAGATAGTTAGAACATCTT 57.169 34.615 8.03 2.04 31.56 2.40
540 543 9.784531 TCATTAGGCTATTTTCTCTTATTCCAG 57.215 33.333 0.00 0.00 0.00 3.86
578 581 7.974504 TGATCACTAACTTCCCTTCTTACTTT 58.025 34.615 0.00 0.00 0.00 2.66
579 582 7.554959 TGATCACTAACTTCCCTTCTTACTT 57.445 36.000 0.00 0.00 0.00 2.24
580 583 7.621683 AGATGATCACTAACTTCCCTTCTTACT 59.378 37.037 0.00 0.00 0.00 2.24
581 584 7.708752 CAGATGATCACTAACTTCCCTTCTTAC 59.291 40.741 0.00 0.00 0.00 2.34
582 585 7.147655 CCAGATGATCACTAACTTCCCTTCTTA 60.148 40.741 0.00 0.00 0.00 2.10
590 593 7.327214 AGAGAAACCAGATGATCACTAACTTC 58.673 38.462 0.00 0.00 0.00 3.01
702 710 4.556501 CGTGACACATGTGGTAAGCAATTT 60.557 41.667 28.64 4.36 34.19 1.82
752 760 8.497745 AGGAGTACTACATTTTCATGGATGAAT 58.502 33.333 8.10 0.00 45.30 2.57
774 783 4.456911 TCACGTTACTGGTACTTGTAGGAG 59.543 45.833 0.00 0.00 0.00 3.69
775 784 4.397420 TCACGTTACTGGTACTTGTAGGA 58.603 43.478 0.00 0.00 0.00 2.94
776 785 4.771590 TCACGTTACTGGTACTTGTAGG 57.228 45.455 0.00 0.00 0.00 3.18
777 786 7.795734 CGTATATCACGTTACTGGTACTTGTAG 59.204 40.741 0.00 0.00 45.82 2.74
778 787 7.630026 CGTATATCACGTTACTGGTACTTGTA 58.370 38.462 0.00 0.00 45.82 2.41
780 789 6.964677 CGTATATCACGTTACTGGTACTTG 57.035 41.667 0.00 0.00 45.82 3.16
865 874 3.064408 CGAGGTACACGTAACTGCTATGA 59.936 47.826 0.00 0.00 37.71 2.15
869 878 0.109412 GCGAGGTACACGTAACTGCT 60.109 55.000 0.00 0.00 45.83 4.24
914 923 0.745845 CGGATGGGAAAGCACAGGAG 60.746 60.000 0.00 0.00 0.00 3.69
1162 1171 1.269448 AGTAAGCGAACCGTCCGTAAA 59.731 47.619 0.00 0.00 0.00 2.01
1189 1198 4.415332 GAACGGTCGGAGCGCAGA 62.415 66.667 27.32 2.59 43.79 4.26
2834 2843 3.564235 TCATGTTCTTGTCAATGCAGC 57.436 42.857 0.00 0.00 0.00 5.25
3356 3365 6.150140 GCTAGTTTAGGATGGCATAAAGGATG 59.850 42.308 0.00 0.00 38.73 3.51
3396 3405 9.915629 GAAGTGATTATATACCGAAGAAGTGAT 57.084 33.333 0.00 0.00 0.00 3.06
3397 3406 9.132923 AGAAGTGATTATATACCGAAGAAGTGA 57.867 33.333 0.00 0.00 0.00 3.41
3398 3407 9.751542 AAGAAGTGATTATATACCGAAGAAGTG 57.248 33.333 0.00 0.00 0.00 3.16
3399 3408 9.968870 GAAGAAGTGATTATATACCGAAGAAGT 57.031 33.333 0.00 0.00 0.00 3.01
3405 3414 9.021807 CCCTTAGAAGAAGTGATTATATACCGA 57.978 37.037 0.00 0.00 0.00 4.69
3406 3415 8.804204 ACCCTTAGAAGAAGTGATTATATACCG 58.196 37.037 0.00 0.00 0.00 4.02
3497 3507 0.613777 AAGGTGGCCGTAGAAAGGAG 59.386 55.000 0.00 0.00 0.00 3.69
3869 3984 4.035208 AGCAAAGTAACTCTGTTTTGTCGG 59.965 41.667 0.00 0.00 34.04 4.79
3907 4022 5.533903 ACGTGGAACTCTCTTTACTGAAGTA 59.466 40.000 0.00 0.00 33.54 2.24
3908 4023 4.341520 ACGTGGAACTCTCTTTACTGAAGT 59.658 41.667 0.00 0.00 33.54 3.01
3909 4024 4.872664 ACGTGGAACTCTCTTTACTGAAG 58.127 43.478 0.00 0.00 33.21 3.02
3910 4025 4.931661 ACGTGGAACTCTCTTTACTGAA 57.068 40.909 0.00 0.00 31.75 3.02
3912 4027 4.872664 AGAACGTGGAACTCTCTTTACTG 58.127 43.478 0.00 0.00 31.75 2.74
3913 4028 4.583489 TGAGAACGTGGAACTCTCTTTACT 59.417 41.667 13.73 0.00 38.54 2.24
3914 4029 4.868067 TGAGAACGTGGAACTCTCTTTAC 58.132 43.478 13.73 0.00 38.54 2.01
3915 4030 5.524971 TTGAGAACGTGGAACTCTCTTTA 57.475 39.130 13.73 0.00 38.54 1.85
3916 4031 4.402056 TTGAGAACGTGGAACTCTCTTT 57.598 40.909 13.73 0.00 38.54 2.52


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

AutoCloner maintained by Alex Coulton.