Multiple sequence alignment - TraesCS7D01G521600

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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 TraesCS7D01G521600 chr7D 100.000 2264 0 0 1 2264 618713947 618716210 0.000000e+00 4181.0
1 TraesCS7D01G521600 chr7D 90.244 287 14 5 1990 2264 24977013 24976729 1.650000e-96 363.0
2 TraesCS7D01G521600 chr7D 85.106 329 37 2 1019 1335 618378348 618378020 2.170000e-85 326.0
3 TraesCS7D01G521600 chr7D 80.556 360 55 8 999 1356 618333530 618333184 1.720000e-66 263.0
4 TraesCS7D01G521600 chr7D 89.333 75 5 1 2187 2261 180762988 180762917 8.610000e-15 91.6
5 TraesCS7D01G521600 chr7A 92.979 1168 58 14 636 1796 712360539 712361689 0.000000e+00 1681.0
6 TraesCS7D01G521600 chr7A 87.701 374 40 4 999 1371 712093275 712092907 4.470000e-117 431.0
7 TraesCS7D01G521600 chr7A 89.825 285 21 3 1987 2264 4980808 4980525 2.140000e-95 359.0
8 TraesCS7D01G521600 chr7A 93.299 194 8 1 1801 1989 712361981 712362174 4.760000e-72 281.0
9 TraesCS7D01G521600 chr7A 81.513 357 39 15 281 632 712360159 712360493 3.710000e-68 268.0
10 TraesCS7D01G521600 chr7B 93.302 642 37 3 636 1276 713216330 713216966 0.000000e+00 942.0
11 TraesCS7D01G521600 chr7B 88.219 365 40 1 990 1351 712837011 712836647 1.240000e-117 433.0
12 TraesCS7D01G521600 chr7B 87.297 370 28 8 281 632 713215922 713216290 2.710000e-109 405.0
13 TraesCS7D01G521600 chr7B 95.536 224 6 2 1574 1796 713216961 713217181 2.770000e-94 355.0
14 TraesCS7D01G521600 chr1D 89.199 287 17 5 1990 2264 399396947 399396663 1.660000e-91 346.0
15 TraesCS7D01G521600 chr3A 95.270 148 1 1 2122 2263 142929291 142929438 1.750000e-56 230.0
16 TraesCS7D01G521600 chr3A 92.481 133 6 2 1992 2124 142928924 142929052 1.070000e-43 187.0
17 TraesCS7D01G521600 chr1B 79.863 293 36 6 1990 2264 564689698 564689411 2.290000e-45 193.0


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 TraesCS7D01G521600 chr7D 618713947 618716210 2263 False 4181.000000 4181 100.000000 1 2264 1 chr7D.!!$F1 2263
1 TraesCS7D01G521600 chr7A 712360159 712362174 2015 False 743.333333 1681 89.263667 281 1989 3 chr7A.!!$F1 1708
2 TraesCS7D01G521600 chr7B 713215922 713217181 1259 False 567.333333 942 92.045000 281 1796 3 chr7B.!!$F1 1515
3 TraesCS7D01G521600 chr3A 142928924 142929438 514 False 208.500000 230 93.875500 1992 2263 2 chr3A.!!$F1 271

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
231 232 0.042731 CTCCTACCCACCCCTCTCAA 59.957 60.0 0.0 0.0 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1904 2259 0.53264 TTTCTCGCAACTGCAGCTCA 60.533 50.0 15.27 0.0 42.21 4.26 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
50 51 6.108687 AGAAAGCTTTCTTGTTTTTCTTGGG 58.891 36.000 31.56 0.00 44.70 4.12
51 52 4.406648 AGCTTTCTTGTTTTTCTTGGGG 57.593 40.909 0.00 0.00 0.00 4.96
52 53 3.774766 AGCTTTCTTGTTTTTCTTGGGGT 59.225 39.130 0.00 0.00 0.00 4.95
53 54 4.225042 AGCTTTCTTGTTTTTCTTGGGGTT 59.775 37.500 0.00 0.00 0.00 4.11
54 55 4.941263 GCTTTCTTGTTTTTCTTGGGGTTT 59.059 37.500 0.00 0.00 0.00 3.27
55 56 5.414454 GCTTTCTTGTTTTTCTTGGGGTTTT 59.586 36.000 0.00 0.00 0.00 2.43
56 57 6.622679 GCTTTCTTGTTTTTCTTGGGGTTTTG 60.623 38.462 0.00 0.00 0.00 2.44
57 58 5.491323 TCTTGTTTTTCTTGGGGTTTTGT 57.509 34.783 0.00 0.00 0.00 2.83
58 59 5.870706 TCTTGTTTTTCTTGGGGTTTTGTT 58.129 33.333 0.00 0.00 0.00 2.83
59 60 6.299922 TCTTGTTTTTCTTGGGGTTTTGTTT 58.700 32.000 0.00 0.00 0.00 2.83
60 61 6.773200 TCTTGTTTTTCTTGGGGTTTTGTTTT 59.227 30.769 0.00 0.00 0.00 2.43
61 62 6.961360 TGTTTTTCTTGGGGTTTTGTTTTT 57.039 29.167 0.00 0.00 0.00 1.94
82 83 3.518634 TTGTTTTTGGAGGTGAAGTGC 57.481 42.857 0.00 0.00 0.00 4.40
83 84 2.733956 TGTTTTTGGAGGTGAAGTGCT 58.266 42.857 0.00 0.00 0.00 4.40
84 85 3.096092 TGTTTTTGGAGGTGAAGTGCTT 58.904 40.909 0.00 0.00 0.00 3.91
85 86 3.130340 TGTTTTTGGAGGTGAAGTGCTTC 59.870 43.478 5.07 5.07 39.91 3.86
86 87 3.297134 TTTTGGAGGTGAAGTGCTTCT 57.703 42.857 12.44 0.00 40.14 2.85
87 88 3.297134 TTTGGAGGTGAAGTGCTTCTT 57.703 42.857 12.44 0.00 40.14 2.52
88 89 3.297134 TTGGAGGTGAAGTGCTTCTTT 57.703 42.857 12.44 0.00 40.14 2.52
89 90 3.297134 TGGAGGTGAAGTGCTTCTTTT 57.703 42.857 12.44 0.00 40.14 2.27
90 91 3.631250 TGGAGGTGAAGTGCTTCTTTTT 58.369 40.909 12.44 0.00 40.14 1.94
91 92 4.787551 TGGAGGTGAAGTGCTTCTTTTTA 58.212 39.130 12.44 0.00 40.14 1.52
92 93 4.821805 TGGAGGTGAAGTGCTTCTTTTTAG 59.178 41.667 12.44 0.00 40.14 1.85
93 94 4.822350 GGAGGTGAAGTGCTTCTTTTTAGT 59.178 41.667 12.44 0.00 40.14 2.24
94 95 5.299531 GGAGGTGAAGTGCTTCTTTTTAGTT 59.700 40.000 12.44 0.00 40.14 2.24
95 96 6.183360 GGAGGTGAAGTGCTTCTTTTTAGTTT 60.183 38.462 12.44 0.00 40.14 2.66
96 97 7.170393 AGGTGAAGTGCTTCTTTTTAGTTTT 57.830 32.000 12.44 0.00 40.14 2.43
97 98 7.611770 AGGTGAAGTGCTTCTTTTTAGTTTTT 58.388 30.769 12.44 0.00 40.14 1.94
123 124 9.689501 TTCCTAGAAAAGTTTCTTTTTAGGTGA 57.310 29.630 22.94 17.08 44.70 4.02
124 125 9.862149 TCCTAGAAAAGTTTCTTTTTAGGTGAT 57.138 29.630 22.94 2.96 44.70 3.06
150 151 4.640771 TTAGGGAGTCCATGGATTATGC 57.359 45.455 19.62 12.24 35.37 3.14
151 152 1.707427 AGGGAGTCCATGGATTATGCC 59.293 52.381 19.62 20.28 35.37 4.40
152 153 1.272147 GGGAGTCCATGGATTATGCCC 60.272 57.143 19.62 16.56 35.37 5.36
153 154 1.611673 GGAGTCCATGGATTATGCCCG 60.612 57.143 19.62 0.00 35.37 6.13
154 155 0.401738 AGTCCATGGATTATGCCCGG 59.598 55.000 19.62 0.00 35.37 5.73
155 156 1.074775 TCCATGGATTATGCCCGGC 59.925 57.895 11.44 1.04 35.37 6.13
156 157 1.978617 CCATGGATTATGCCCGGCC 60.979 63.158 5.56 0.00 35.37 6.13
157 158 1.978617 CATGGATTATGCCCGGCCC 60.979 63.158 7.03 0.26 0.00 5.80
158 159 2.468868 ATGGATTATGCCCGGCCCA 61.469 57.895 7.03 6.89 0.00 5.36
159 160 2.597510 GGATTATGCCCGGCCCAC 60.598 66.667 7.03 0.00 0.00 4.61
160 161 2.515901 GATTATGCCCGGCCCACT 59.484 61.111 7.03 0.00 0.00 4.00
161 162 1.152756 GATTATGCCCGGCCCACTT 60.153 57.895 7.03 0.00 0.00 3.16
162 163 1.152756 ATTATGCCCGGCCCACTTC 60.153 57.895 7.03 0.00 0.00 3.01
163 164 2.958578 ATTATGCCCGGCCCACTTCG 62.959 60.000 7.03 0.00 0.00 3.79
168 169 3.431725 CCGGCCCACTTCGCTTTC 61.432 66.667 0.00 0.00 0.00 2.62
169 170 3.431725 CGGCCCACTTCGCTTTCC 61.432 66.667 0.00 0.00 0.00 3.13
170 171 3.431725 GGCCCACTTCGCTTTCCG 61.432 66.667 0.00 0.00 38.61 4.30
171 172 3.431725 GCCCACTTCGCTTTCCGG 61.432 66.667 0.00 0.00 37.59 5.14
172 173 3.431725 CCCACTTCGCTTTCCGGC 61.432 66.667 0.00 0.00 37.59 6.13
173 174 3.431725 CCACTTCGCTTTCCGGCC 61.432 66.667 0.00 0.00 37.59 6.13
174 175 3.431725 CACTTCGCTTTCCGGCCC 61.432 66.667 0.00 0.00 37.59 5.80
175 176 3.948719 ACTTCGCTTTCCGGCCCA 61.949 61.111 0.00 0.00 37.59 5.36
176 177 3.431725 CTTCGCTTTCCGGCCCAC 61.432 66.667 0.00 0.00 37.59 4.61
177 178 3.901797 CTTCGCTTTCCGGCCCACT 62.902 63.158 0.00 0.00 37.59 4.00
178 179 2.515996 CTTCGCTTTCCGGCCCACTA 62.516 60.000 0.00 0.00 37.59 2.74
179 180 2.791501 TTCGCTTTCCGGCCCACTAC 62.792 60.000 0.00 0.00 37.59 2.73
180 181 2.669240 GCTTTCCGGCCCACTACT 59.331 61.111 0.00 0.00 0.00 2.57
181 182 1.745489 GCTTTCCGGCCCACTACTG 60.745 63.158 0.00 0.00 0.00 2.74
182 183 1.745489 CTTTCCGGCCCACTACTGC 60.745 63.158 0.00 0.00 0.00 4.40
183 184 3.599285 TTTCCGGCCCACTACTGCG 62.599 63.158 0.00 0.00 0.00 5.18
185 186 4.814294 CCGGCCCACTACTGCGTC 62.814 72.222 0.00 0.00 0.00 5.19
186 187 4.814294 CGGCCCACTACTGCGTCC 62.814 72.222 0.00 0.00 0.00 4.79
187 188 4.814294 GGCCCACTACTGCGTCCG 62.814 72.222 0.00 0.00 0.00 4.79
188 189 4.814294 GCCCACTACTGCGTCCGG 62.814 72.222 0.00 0.00 0.00 5.14
189 190 4.814294 CCCACTACTGCGTCCGGC 62.814 72.222 0.00 0.00 43.96 6.13
212 213 4.486503 CCAGGCCAGCTGCTCCTC 62.487 72.222 19.24 3.06 40.92 3.71
213 214 3.400928 CAGGCCAGCTGCTCCTCT 61.401 66.667 19.24 5.08 40.92 3.69
214 215 3.082701 AGGCCAGCTGCTCCTCTC 61.083 66.667 17.10 0.00 40.92 3.20
215 216 4.173924 GGCCAGCTGCTCCTCTCC 62.174 72.222 8.66 0.00 40.92 3.71
216 217 3.082701 GCCAGCTGCTCCTCTCCT 61.083 66.667 8.66 0.00 36.87 3.69
217 218 1.760086 GCCAGCTGCTCCTCTCCTA 60.760 63.158 8.66 0.00 36.87 2.94
218 219 2.026945 GCCAGCTGCTCCTCTCCTAC 62.027 65.000 8.66 0.00 36.87 3.18
219 220 1.398958 CCAGCTGCTCCTCTCCTACC 61.399 65.000 8.66 0.00 0.00 3.18
220 221 1.075600 AGCTGCTCCTCTCCTACCC 60.076 63.158 0.00 0.00 0.00 3.69
221 222 1.381872 GCTGCTCCTCTCCTACCCA 60.382 63.158 0.00 0.00 0.00 4.51
222 223 1.681486 GCTGCTCCTCTCCTACCCAC 61.681 65.000 0.00 0.00 0.00 4.61
223 224 1.001760 TGCTCCTCTCCTACCCACC 59.998 63.158 0.00 0.00 0.00 4.61
224 225 1.762858 GCTCCTCTCCTACCCACCC 60.763 68.421 0.00 0.00 0.00 4.61
225 226 1.075151 CTCCTCTCCTACCCACCCC 60.075 68.421 0.00 0.00 0.00 4.95
226 227 1.549322 TCCTCTCCTACCCACCCCT 60.549 63.158 0.00 0.00 0.00 4.79
227 228 1.075151 CCTCTCCTACCCACCCCTC 60.075 68.421 0.00 0.00 0.00 4.30
228 229 1.595058 CCTCTCCTACCCACCCCTCT 61.595 65.000 0.00 0.00 0.00 3.69
229 230 0.105913 CTCTCCTACCCACCCCTCTC 60.106 65.000 0.00 0.00 0.00 3.20
230 231 0.854039 TCTCCTACCCACCCCTCTCA 60.854 60.000 0.00 0.00 0.00 3.27
231 232 0.042731 CTCCTACCCACCCCTCTCAA 59.957 60.000 0.00 0.00 0.00 3.02
232 233 0.042731 TCCTACCCACCCCTCTCAAG 59.957 60.000 0.00 0.00 0.00 3.02
233 234 0.042731 CCTACCCACCCCTCTCAAGA 59.957 60.000 0.00 0.00 0.00 3.02
234 235 1.490574 CTACCCACCCCTCTCAAGAG 58.509 60.000 0.00 0.00 41.71 2.85
235 236 0.617820 TACCCACCCCTCTCAAGAGC 60.618 60.000 1.28 0.00 40.75 4.09
236 237 2.581354 CCACCCCTCTCAAGAGCG 59.419 66.667 1.28 0.00 40.75 5.03
237 238 2.286523 CCACCCCTCTCAAGAGCGT 61.287 63.158 1.28 0.00 40.75 5.07
238 239 1.079543 CACCCCTCTCAAGAGCGTG 60.080 63.158 1.28 6.35 40.75 5.34
239 240 2.125350 CCCCTCTCAAGAGCGTGC 60.125 66.667 1.28 0.00 40.75 5.34
240 241 2.654079 CCCCTCTCAAGAGCGTGCT 61.654 63.158 1.28 0.00 40.75 4.40
241 242 1.447489 CCCTCTCAAGAGCGTGCTG 60.447 63.158 0.00 0.00 40.75 4.41
242 243 2.099431 CCTCTCAAGAGCGTGCTGC 61.099 63.158 0.00 0.00 46.98 5.25
251 252 2.047274 GCGTGCTGCCCTAACTGA 60.047 61.111 0.00 0.00 37.76 3.41
252 253 2.391389 GCGTGCTGCCCTAACTGAC 61.391 63.158 0.00 0.00 37.76 3.51
253 254 2.094659 CGTGCTGCCCTAACTGACG 61.095 63.158 0.00 0.00 0.00 4.35
254 255 2.047274 TGCTGCCCTAACTGACGC 60.047 61.111 0.00 0.00 0.00 5.19
255 256 2.820037 GCTGCCCTAACTGACGCC 60.820 66.667 0.00 0.00 0.00 5.68
256 257 2.509336 CTGCCCTAACTGACGCCG 60.509 66.667 0.00 0.00 0.00 6.46
257 258 3.296709 CTGCCCTAACTGACGCCGT 62.297 63.158 0.00 0.00 0.00 5.68
258 259 2.508663 GCCCTAACTGACGCCGTC 60.509 66.667 10.96 10.96 0.00 4.79
259 260 2.202570 CCCTAACTGACGCCGTCG 60.203 66.667 13.18 9.89 42.43 5.12
260 261 2.693762 CCCTAACTGACGCCGTCGA 61.694 63.158 13.18 1.05 39.41 4.20
261 262 1.210931 CCTAACTGACGCCGTCGAA 59.789 57.895 13.18 0.00 39.41 3.71
262 263 0.179145 CCTAACTGACGCCGTCGAAT 60.179 55.000 13.18 3.31 39.41 3.34
263 264 1.625616 CTAACTGACGCCGTCGAATT 58.374 50.000 13.18 8.98 39.41 2.17
264 265 1.320555 CTAACTGACGCCGTCGAATTG 59.679 52.381 13.18 2.95 39.41 2.32
265 266 0.599204 AACTGACGCCGTCGAATTGT 60.599 50.000 13.18 3.57 39.41 2.71
266 267 1.007336 ACTGACGCCGTCGAATTGTC 61.007 55.000 13.18 0.00 39.41 3.18
267 268 0.732880 CTGACGCCGTCGAATTGTCT 60.733 55.000 13.18 0.00 39.41 3.41
268 269 0.731514 TGACGCCGTCGAATTGTCTC 60.732 55.000 13.18 0.00 39.41 3.36
269 270 0.731514 GACGCCGTCGAATTGTCTCA 60.732 55.000 0.00 0.00 39.41 3.27
270 271 0.732880 ACGCCGTCGAATTGTCTCAG 60.733 55.000 0.00 0.00 39.41 3.35
271 272 1.413767 CGCCGTCGAATTGTCTCAGG 61.414 60.000 0.00 0.00 38.10 3.86
272 273 1.084370 GCCGTCGAATTGTCTCAGGG 61.084 60.000 0.00 0.00 0.00 4.45
273 274 0.460284 CCGTCGAATTGTCTCAGGGG 60.460 60.000 0.00 0.00 0.00 4.79
274 275 0.460284 CGTCGAATTGTCTCAGGGGG 60.460 60.000 0.00 0.00 0.00 5.40
275 276 0.902531 GTCGAATTGTCTCAGGGGGA 59.097 55.000 0.00 0.00 0.00 4.81
276 277 1.278127 GTCGAATTGTCTCAGGGGGAA 59.722 52.381 0.00 0.00 0.00 3.97
277 278 1.982226 TCGAATTGTCTCAGGGGGAAA 59.018 47.619 0.00 0.00 0.00 3.13
278 279 2.373836 TCGAATTGTCTCAGGGGGAAAA 59.626 45.455 0.00 0.00 0.00 2.29
279 280 3.153919 CGAATTGTCTCAGGGGGAAAAA 58.846 45.455 0.00 0.00 0.00 1.94
297 298 1.828331 AAAAGTGACGCCGTCGAAGC 61.828 55.000 13.18 2.97 39.41 3.86
360 361 4.767255 CGCCTCTCCACAGCCCAC 62.767 72.222 0.00 0.00 0.00 4.61
396 397 1.760029 CAACCTCTCTTCCTAGCTCCC 59.240 57.143 0.00 0.00 0.00 4.30
460 474 2.090831 AGGCAGGTAGGATCTGTCTGAT 60.091 50.000 0.00 0.00 44.45 2.90
482 496 1.677217 GGGGCTCTCATCTGTGTGTTC 60.677 57.143 0.00 0.00 0.00 3.18
483 497 1.677217 GGGCTCTCATCTGTGTGTTCC 60.677 57.143 0.00 0.00 0.00 3.62
540 554 2.054363 CTGTAATCATAGACTGCGGCG 58.946 52.381 0.51 0.51 0.00 6.46
549 568 1.519408 AGACTGCGGCGTATGTTTTT 58.481 45.000 9.37 0.00 0.00 1.94
581 600 4.989797 TGGTTCTGTATGCAAGCATTTTTG 59.010 37.500 13.32 2.38 37.82 2.44
586 605 4.239304 TGTATGCAAGCATTTTTGAGCTG 58.761 39.130 13.32 0.00 41.70 4.24
596 615 5.532406 AGCATTTTTGAGCTGTGTAGAAAGA 59.468 36.000 0.00 0.00 40.13 2.52
625 644 1.882352 GCAGTGTGTTCTGTAAGGGGG 60.882 57.143 0.00 0.00 37.70 5.40
626 645 1.420138 CAGTGTGTTCTGTAAGGGGGT 59.580 52.381 0.00 0.00 0.00 4.95
627 646 2.635915 CAGTGTGTTCTGTAAGGGGGTA 59.364 50.000 0.00 0.00 0.00 3.69
628 647 2.904434 AGTGTGTTCTGTAAGGGGGTAG 59.096 50.000 0.00 0.00 0.00 3.18
629 648 1.626825 TGTGTTCTGTAAGGGGGTAGC 59.373 52.381 0.00 0.00 0.00 3.58
630 649 1.907255 GTGTTCTGTAAGGGGGTAGCT 59.093 52.381 0.00 0.00 0.00 3.32
631 650 1.906574 TGTTCTGTAAGGGGGTAGCTG 59.093 52.381 0.00 0.00 0.00 4.24
632 651 0.909623 TTCTGTAAGGGGGTAGCTGC 59.090 55.000 0.00 0.00 0.00 5.25
633 652 0.252513 TCTGTAAGGGGGTAGCTGCA 60.253 55.000 3.61 0.00 0.00 4.41
634 653 0.618458 CTGTAAGGGGGTAGCTGCAA 59.382 55.000 3.61 0.00 0.00 4.08
655 715 5.629133 GCAACTAATCCCCATCAGTACTTCA 60.629 44.000 0.00 0.00 0.00 3.02
661 721 3.843619 TCCCCATCAGTACTTCATTCACA 59.156 43.478 0.00 0.00 0.00 3.58
664 724 3.618594 CCATCAGTACTTCATTCACACCG 59.381 47.826 0.00 0.00 0.00 4.94
666 726 1.732259 CAGTACTTCATTCACACCGGC 59.268 52.381 0.00 0.00 0.00 6.13
679 739 1.959985 ACACCGGCATTTGTTTCATCA 59.040 42.857 0.00 0.00 0.00 3.07
683 743 3.119388 ACCGGCATTTGTTTCATCATCAG 60.119 43.478 0.00 0.00 0.00 2.90
686 746 4.925054 CGGCATTTGTTTCATCATCAGTTT 59.075 37.500 0.00 0.00 0.00 2.66
689 749 6.400303 GGCATTTGTTTCATCATCAGTTTTCG 60.400 38.462 0.00 0.00 0.00 3.46
697 758 7.905604 TTCATCATCAGTTTTCGTAGATTGT 57.094 32.000 0.00 0.00 35.04 2.71
758 819 8.816894 AGAGTCCATTATTAGTTTCAGAACTCA 58.183 33.333 0.00 0.00 44.75 3.41
886 950 8.623903 TGAATACTCCATGCTAATGAAATTGTC 58.376 33.333 0.00 0.00 36.99 3.18
893 957 6.421405 CATGCTAATGAAATTGTCGAATCGA 58.579 36.000 0.00 0.00 36.99 3.59
895 959 8.696142 CATGCTAATGAAATTGTCGAATCGACG 61.696 40.741 27.36 12.29 46.54 5.12
940 1004 0.463116 AACTGTGGAACCGGTGTCAC 60.463 55.000 25.07 25.07 34.36 3.67
1271 1335 5.489792 AAGAAGCAGAAGTGATTGTCCTA 57.510 39.130 0.00 0.00 30.57 2.94
1293 1357 8.642432 TCCTAAATCTCATCTGATTTATCGTGT 58.358 33.333 9.26 0.00 43.57 4.49
1294 1358 9.265901 CCTAAATCTCATCTGATTTATCGTGTT 57.734 33.333 9.26 0.00 43.57 3.32
1304 1368 8.703604 TCTGATTTATCGTGTTCTTTCTTAGG 57.296 34.615 0.00 0.00 0.00 2.69
1307 1371 2.467566 TCGTGTTCTTTCTTAGGCCC 57.532 50.000 0.00 0.00 0.00 5.80
1356 1420 1.450312 CCCCTTGCTAGCTGTTCCG 60.450 63.158 17.23 0.00 0.00 4.30
1364 1428 1.872237 GCTAGCTGTTCCGTTGACACA 60.872 52.381 7.70 0.00 0.00 3.72
1368 1432 1.668751 GCTGTTCCGTTGACACAGAAA 59.331 47.619 2.72 0.00 40.43 2.52
1369 1433 2.096819 GCTGTTCCGTTGACACAGAAAA 59.903 45.455 2.72 0.00 40.43 2.29
1375 1442 3.506455 TCCGTTGACACAGAAAAACCAAA 59.494 39.130 0.00 0.00 0.00 3.28
1388 1455 9.139174 ACAGAAAAACCAAATTATTCTTATGCG 57.861 29.630 0.00 0.00 0.00 4.73
1389 1456 8.110002 CAGAAAAACCAAATTATTCTTATGCGC 58.890 33.333 0.00 0.00 0.00 6.09
1390 1457 6.902224 AAAACCAAATTATTCTTATGCGCC 57.098 33.333 4.18 0.00 0.00 6.53
1391 1458 4.584327 ACCAAATTATTCTTATGCGCCC 57.416 40.909 4.18 0.00 0.00 6.13
1392 1459 3.320826 ACCAAATTATTCTTATGCGCCCC 59.679 43.478 4.18 0.00 0.00 5.80
1393 1460 3.573967 CCAAATTATTCTTATGCGCCCCT 59.426 43.478 4.18 0.00 0.00 4.79
1394 1461 4.549458 CAAATTATTCTTATGCGCCCCTG 58.451 43.478 4.18 0.00 0.00 4.45
1455 1522 3.313526 AGCGATGCTCAATGTTGTTATCC 59.686 43.478 0.00 0.00 30.62 2.59
1507 1574 5.177696 GCATCTTTCTTTCTGTACAACTCGT 59.822 40.000 0.00 0.00 0.00 4.18
1537 1604 0.242017 ATGTTCTGCTTTTCGCTGGC 59.758 50.000 0.00 0.00 40.11 4.85
1557 1624 3.817084 GGCAATATATGAGCTTCAGCACA 59.183 43.478 1.19 1.19 45.04 4.57
1563 1630 5.972107 ATATGAGCTTCAGCACAAAAGTT 57.028 34.783 2.92 0.00 44.22 2.66
1565 1632 2.032054 TGAGCTTCAGCACAAAAGTTCG 59.968 45.455 0.75 0.00 45.16 3.95
1578 1645 6.197468 GCACAAAAGTTCGTTGCAGTTAAATA 59.803 34.615 0.00 0.00 0.00 1.40
1643 1710 3.698040 AGCACAAGTGAAATGATCATCCC 59.302 43.478 9.06 4.57 40.97 3.85
1705 1772 3.144506 CAAAGGTCAGAGAACATGCTGT 58.855 45.455 0.00 0.00 33.90 4.40
1767 1835 6.293955 GGTCAGAACTATTGTTAGCAGCAAAA 60.294 38.462 0.00 0.00 36.39 2.44
1768 1836 7.138736 GTCAGAACTATTGTTAGCAGCAAAAA 58.861 34.615 0.00 0.00 36.39 1.94
1796 1864 3.138884 TGTGTAGGAAATTGCTGCTGA 57.861 42.857 4.20 0.00 0.00 4.26
1797 1865 3.485394 TGTGTAGGAAATTGCTGCTGAA 58.515 40.909 4.20 0.00 0.00 3.02
1798 1866 3.253188 TGTGTAGGAAATTGCTGCTGAAC 59.747 43.478 4.20 0.00 0.00 3.18
1799 1867 3.253188 GTGTAGGAAATTGCTGCTGAACA 59.747 43.478 4.20 0.00 0.00 3.18
1900 2255 8.250332 GGCACAAGTCCAAAGATCAAATTATTA 58.750 33.333 0.00 0.00 0.00 0.98
1972 2332 6.211587 TGCTCAATGTTTTCCCTTGATATG 57.788 37.500 0.00 0.00 0.00 1.78
1975 2335 6.127647 GCTCAATGTTTTCCCTTGATATGTGA 60.128 38.462 0.00 0.00 0.00 3.58
1989 2349 5.505780 TGATATGTGAAGGGTAAGTTTGGG 58.494 41.667 0.00 0.00 0.00 4.12
1990 2350 5.251932 TGATATGTGAAGGGTAAGTTTGGGA 59.748 40.000 0.00 0.00 0.00 4.37
2078 2438 1.957177 CGGATCAGAGTAGGCTGCTAA 59.043 52.381 4.68 0.00 35.86 3.09
2079 2439 2.560542 CGGATCAGAGTAGGCTGCTAAT 59.439 50.000 4.68 0.00 35.86 1.73
2080 2440 3.006323 CGGATCAGAGTAGGCTGCTAATT 59.994 47.826 4.68 0.00 35.86 1.40
2081 2441 4.218635 CGGATCAGAGTAGGCTGCTAATTA 59.781 45.833 4.68 0.00 35.86 1.40
2082 2442 5.621104 CGGATCAGAGTAGGCTGCTAATTAG 60.621 48.000 4.68 8.20 35.86 1.73
2083 2443 5.478679 GGATCAGAGTAGGCTGCTAATTAGA 59.521 44.000 16.85 0.00 35.86 2.10
2103 2463 7.914427 TTAGAGTATATGGGTGTCAGACATT 57.086 36.000 6.51 0.00 0.00 2.71
2263 2870 2.872245 GTGTGCCATTGCGATAGTGTAT 59.128 45.455 0.00 0.00 41.78 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 5.294306 CCCCAAGAAAAACAAGAAAGCTTTC 59.706 40.000 28.21 28.21 37.45 2.62
28 29 5.185454 CCCCAAGAAAAACAAGAAAGCTTT 58.815 37.500 12.53 12.53 30.14 3.51
29 30 4.225042 ACCCCAAGAAAAACAAGAAAGCTT 59.775 37.500 0.00 0.00 33.74 3.74
30 31 3.774766 ACCCCAAGAAAAACAAGAAAGCT 59.225 39.130 0.00 0.00 0.00 3.74
31 32 4.137116 ACCCCAAGAAAAACAAGAAAGC 57.863 40.909 0.00 0.00 0.00 3.51
32 33 6.429692 ACAAAACCCCAAGAAAAACAAGAAAG 59.570 34.615 0.00 0.00 0.00 2.62
33 34 6.299922 ACAAAACCCCAAGAAAAACAAGAAA 58.700 32.000 0.00 0.00 0.00 2.52
34 35 5.870706 ACAAAACCCCAAGAAAAACAAGAA 58.129 33.333 0.00 0.00 0.00 2.52
35 36 5.491323 ACAAAACCCCAAGAAAAACAAGA 57.509 34.783 0.00 0.00 0.00 3.02
36 37 6.567687 AAACAAAACCCCAAGAAAAACAAG 57.432 33.333 0.00 0.00 0.00 3.16
37 38 6.961360 AAAACAAAACCCCAAGAAAAACAA 57.039 29.167 0.00 0.00 0.00 2.83
38 39 6.961360 AAAAACAAAACCCCAAGAAAAACA 57.039 29.167 0.00 0.00 0.00 2.83
59 60 4.693095 GCACTTCACCTCCAAAAACAAAAA 59.307 37.500 0.00 0.00 0.00 1.94
60 61 4.020662 AGCACTTCACCTCCAAAAACAAAA 60.021 37.500 0.00 0.00 0.00 2.44
61 62 3.513515 AGCACTTCACCTCCAAAAACAAA 59.486 39.130 0.00 0.00 0.00 2.83
62 63 3.096092 AGCACTTCACCTCCAAAAACAA 58.904 40.909 0.00 0.00 0.00 2.83
63 64 2.733956 AGCACTTCACCTCCAAAAACA 58.266 42.857 0.00 0.00 0.00 2.83
64 65 3.381590 AGAAGCACTTCACCTCCAAAAAC 59.618 43.478 12.65 0.00 41.84 2.43
65 66 3.631250 AGAAGCACTTCACCTCCAAAAA 58.369 40.909 12.65 0.00 41.84 1.94
66 67 3.297134 AGAAGCACTTCACCTCCAAAA 57.703 42.857 12.65 0.00 41.84 2.44
67 68 3.297134 AAGAAGCACTTCACCTCCAAA 57.703 42.857 12.65 0.00 41.84 3.28
68 69 3.297134 AAAGAAGCACTTCACCTCCAA 57.703 42.857 12.65 0.00 41.84 3.53
69 70 3.297134 AAAAGAAGCACTTCACCTCCA 57.703 42.857 12.65 0.00 41.84 3.86
70 71 4.822350 ACTAAAAAGAAGCACTTCACCTCC 59.178 41.667 12.65 0.00 41.84 4.30
71 72 6.378710 AACTAAAAAGAAGCACTTCACCTC 57.621 37.500 12.65 0.00 41.84 3.85
72 73 6.775594 AAACTAAAAAGAAGCACTTCACCT 57.224 33.333 12.65 0.00 41.84 4.00
73 74 7.827819 AAAAACTAAAAAGAAGCACTTCACC 57.172 32.000 12.65 0.00 41.84 4.02
97 98 9.689501 TCACCTAAAAAGAAACTTTTCTAGGAA 57.310 29.630 27.15 19.77 46.22 3.36
98 99 9.862149 ATCACCTAAAAAGAAACTTTTCTAGGA 57.138 29.630 27.15 17.80 46.22 2.94
126 127 5.833131 GCATAATCCATGGACTCCCTAAAAA 59.167 40.000 18.99 0.00 34.97 1.94
127 128 5.385198 GCATAATCCATGGACTCCCTAAAA 58.615 41.667 18.99 0.00 34.97 1.52
128 129 4.202567 GGCATAATCCATGGACTCCCTAAA 60.203 45.833 18.99 0.00 34.97 1.85
129 130 3.330701 GGCATAATCCATGGACTCCCTAA 59.669 47.826 18.99 0.00 34.97 2.69
130 131 2.912956 GGCATAATCCATGGACTCCCTA 59.087 50.000 18.99 4.26 34.97 3.53
131 132 1.707427 GGCATAATCCATGGACTCCCT 59.293 52.381 18.99 0.00 34.97 4.20
132 133 1.272147 GGGCATAATCCATGGACTCCC 60.272 57.143 18.99 18.06 34.97 4.30
133 134 1.611673 CGGGCATAATCCATGGACTCC 60.612 57.143 18.99 13.13 34.97 3.85
134 135 1.611673 CCGGGCATAATCCATGGACTC 60.612 57.143 18.99 2.34 34.97 3.36
135 136 0.401738 CCGGGCATAATCCATGGACT 59.598 55.000 18.99 9.32 34.97 3.85
136 137 1.244019 GCCGGGCATAATCCATGGAC 61.244 60.000 18.99 3.29 34.97 4.02
137 138 1.074775 GCCGGGCATAATCCATGGA 59.925 57.895 18.88 18.88 34.97 3.41
138 139 1.978617 GGCCGGGCATAATCCATGG 60.979 63.158 25.33 4.97 34.97 3.66
139 140 1.978617 GGGCCGGGCATAATCCATG 60.979 63.158 30.95 0.00 37.73 3.66
140 141 2.440599 GGGCCGGGCATAATCCAT 59.559 61.111 30.95 0.00 0.00 3.41
141 142 3.099841 TGGGCCGGGCATAATCCA 61.100 61.111 30.95 15.45 0.00 3.41
142 143 2.597510 GTGGGCCGGGCATAATCC 60.598 66.667 30.95 12.79 0.00 3.01
143 144 1.152756 AAGTGGGCCGGGCATAATC 60.153 57.895 30.95 12.51 0.00 1.75
144 145 1.152756 GAAGTGGGCCGGGCATAAT 60.153 57.895 30.95 14.59 0.00 1.28
145 146 2.274104 GAAGTGGGCCGGGCATAA 59.726 61.111 30.95 12.01 0.00 1.90
146 147 4.169696 CGAAGTGGGCCGGGCATA 62.170 66.667 30.95 15.53 0.00 3.14
151 152 3.431725 GAAAGCGAAGTGGGCCGG 61.432 66.667 0.00 0.00 0.00 6.13
152 153 3.431725 GGAAAGCGAAGTGGGCCG 61.432 66.667 0.00 0.00 0.00 6.13
153 154 3.431725 CGGAAAGCGAAGTGGGCC 61.432 66.667 0.00 0.00 0.00 5.80
154 155 3.431725 CCGGAAAGCGAAGTGGGC 61.432 66.667 0.00 0.00 0.00 5.36
155 156 3.431725 GCCGGAAAGCGAAGTGGG 61.432 66.667 5.05 0.00 0.00 4.61
156 157 3.431725 GGCCGGAAAGCGAAGTGG 61.432 66.667 5.05 0.00 0.00 4.00
157 158 3.431725 GGGCCGGAAAGCGAAGTG 61.432 66.667 5.05 0.00 0.00 3.16
158 159 3.948719 TGGGCCGGAAAGCGAAGT 61.949 61.111 5.05 0.00 0.00 3.01
159 160 2.515996 TAGTGGGCCGGAAAGCGAAG 62.516 60.000 5.05 0.00 0.00 3.79
160 161 2.585341 TAGTGGGCCGGAAAGCGAA 61.585 57.895 5.05 0.00 0.00 4.70
161 162 2.998480 TAGTGGGCCGGAAAGCGA 60.998 61.111 5.05 0.00 0.00 4.93
162 163 2.818274 GTAGTGGGCCGGAAAGCG 60.818 66.667 5.05 0.00 0.00 4.68
163 164 1.745489 CAGTAGTGGGCCGGAAAGC 60.745 63.158 5.05 0.00 0.00 3.51
164 165 1.745489 GCAGTAGTGGGCCGGAAAG 60.745 63.158 5.05 0.00 0.00 2.62
165 166 2.349755 GCAGTAGTGGGCCGGAAA 59.650 61.111 5.05 0.00 0.00 3.13
166 167 4.077184 CGCAGTAGTGGGCCGGAA 62.077 66.667 5.05 0.00 0.00 4.30
195 196 4.486503 GAGGAGCAGCTGGCCTGG 62.487 72.222 17.12 1.66 46.50 4.45
196 197 3.388703 GAGAGGAGCAGCTGGCCTG 62.389 68.421 17.12 4.26 46.50 4.85
197 198 3.082701 GAGAGGAGCAGCTGGCCT 61.083 66.667 17.12 0.00 46.50 5.19
198 199 4.173924 GGAGAGGAGCAGCTGGCC 62.174 72.222 17.12 0.00 46.50 5.36
199 200 1.760086 TAGGAGAGGAGCAGCTGGC 60.760 63.158 17.12 7.98 45.30 4.85
200 201 1.398958 GGTAGGAGAGGAGCAGCTGG 61.399 65.000 17.12 0.00 0.00 4.85
201 202 1.398958 GGGTAGGAGAGGAGCAGCTG 61.399 65.000 10.11 10.11 0.00 4.24
202 203 1.075600 GGGTAGGAGAGGAGCAGCT 60.076 63.158 0.00 0.00 0.00 4.24
203 204 1.381872 TGGGTAGGAGAGGAGCAGC 60.382 63.158 0.00 0.00 0.00 5.25
204 205 1.045911 GGTGGGTAGGAGAGGAGCAG 61.046 65.000 0.00 0.00 0.00 4.24
205 206 1.001760 GGTGGGTAGGAGAGGAGCA 59.998 63.158 0.00 0.00 0.00 4.26
206 207 1.762858 GGGTGGGTAGGAGAGGAGC 60.763 68.421 0.00 0.00 0.00 4.70
207 208 1.075151 GGGGTGGGTAGGAGAGGAG 60.075 68.421 0.00 0.00 0.00 3.69
208 209 1.549322 AGGGGTGGGTAGGAGAGGA 60.549 63.158 0.00 0.00 0.00 3.71
209 210 1.075151 GAGGGGTGGGTAGGAGAGG 60.075 68.421 0.00 0.00 0.00 3.69
210 211 0.105913 GAGAGGGGTGGGTAGGAGAG 60.106 65.000 0.00 0.00 0.00 3.20
211 212 0.854039 TGAGAGGGGTGGGTAGGAGA 60.854 60.000 0.00 0.00 0.00 3.71
212 213 0.042731 TTGAGAGGGGTGGGTAGGAG 59.957 60.000 0.00 0.00 0.00 3.69
213 214 0.042731 CTTGAGAGGGGTGGGTAGGA 59.957 60.000 0.00 0.00 0.00 2.94
214 215 0.042731 TCTTGAGAGGGGTGGGTAGG 59.957 60.000 0.00 0.00 0.00 3.18
215 216 1.490574 CTCTTGAGAGGGGTGGGTAG 58.509 60.000 0.00 0.00 38.48 3.18
216 217 0.617820 GCTCTTGAGAGGGGTGGGTA 60.618 60.000 9.87 0.00 42.29 3.69
217 218 1.920835 GCTCTTGAGAGGGGTGGGT 60.921 63.158 9.87 0.00 42.29 4.51
218 219 2.993853 GCTCTTGAGAGGGGTGGG 59.006 66.667 9.87 0.00 42.29 4.61
224 225 2.099431 GCAGCACGCTCTTGAGAGG 61.099 63.158 9.87 3.21 42.29 3.69
225 226 2.099431 GGCAGCACGCTCTTGAGAG 61.099 63.158 3.63 3.63 44.75 3.20
226 227 2.047844 GGCAGCACGCTCTTGAGA 60.048 61.111 1.30 0.00 41.91 3.27
227 228 3.123620 GGGCAGCACGCTCTTGAG 61.124 66.667 0.00 0.00 38.49 3.02
232 233 2.103042 CAGTTAGGGCAGCACGCTC 61.103 63.158 0.00 0.00 43.89 5.03
233 234 2.046892 CAGTTAGGGCAGCACGCT 60.047 61.111 0.00 2.02 45.01 5.07
234 235 2.047274 TCAGTTAGGGCAGCACGC 60.047 61.111 0.00 0.00 41.28 5.34
235 236 2.094659 CGTCAGTTAGGGCAGCACG 61.095 63.158 0.00 0.00 0.00 5.34
236 237 2.391389 GCGTCAGTTAGGGCAGCAC 61.391 63.158 0.00 0.00 0.00 4.40
237 238 2.047274 GCGTCAGTTAGGGCAGCA 60.047 61.111 0.00 0.00 0.00 4.41
238 239 2.820037 GGCGTCAGTTAGGGCAGC 60.820 66.667 0.00 0.00 38.35 5.25
239 240 2.509336 CGGCGTCAGTTAGGGCAG 60.509 66.667 0.00 0.00 38.38 4.85
240 241 3.291101 GACGGCGTCAGTTAGGGCA 62.291 63.158 33.07 0.00 38.38 5.36
241 242 2.508663 GACGGCGTCAGTTAGGGC 60.509 66.667 33.07 4.36 35.33 5.19
242 243 2.202570 CGACGGCGTCAGTTAGGG 60.203 66.667 35.62 16.53 32.09 3.53
243 244 0.179145 ATTCGACGGCGTCAGTTAGG 60.179 55.000 35.62 20.29 38.98 2.69
244 245 1.320555 CAATTCGACGGCGTCAGTTAG 59.679 52.381 35.62 20.98 38.98 2.34
245 246 1.336148 ACAATTCGACGGCGTCAGTTA 60.336 47.619 35.62 19.34 38.98 2.24
246 247 0.599204 ACAATTCGACGGCGTCAGTT 60.599 50.000 35.62 23.90 38.98 3.16
247 248 1.006571 ACAATTCGACGGCGTCAGT 60.007 52.632 35.62 22.60 38.98 3.41
248 249 0.732880 AGACAATTCGACGGCGTCAG 60.733 55.000 35.62 27.40 38.98 3.51
249 250 0.731514 GAGACAATTCGACGGCGTCA 60.732 55.000 35.62 20.62 38.98 4.35
250 251 0.731514 TGAGACAATTCGACGGCGTC 60.732 55.000 29.06 29.06 38.98 5.19
251 252 0.732880 CTGAGACAATTCGACGGCGT 60.733 55.000 14.65 14.65 38.98 5.68
252 253 1.413767 CCTGAGACAATTCGACGGCG 61.414 60.000 2.87 2.87 39.35 6.46
253 254 1.084370 CCCTGAGACAATTCGACGGC 61.084 60.000 0.00 0.00 0.00 5.68
254 255 0.460284 CCCCTGAGACAATTCGACGG 60.460 60.000 0.00 0.00 0.00 4.79
255 256 0.460284 CCCCCTGAGACAATTCGACG 60.460 60.000 0.00 0.00 0.00 5.12
256 257 0.902531 TCCCCCTGAGACAATTCGAC 59.097 55.000 0.00 0.00 0.00 4.20
257 258 1.651737 TTCCCCCTGAGACAATTCGA 58.348 50.000 0.00 0.00 0.00 3.71
258 259 2.489938 TTTCCCCCTGAGACAATTCG 57.510 50.000 0.00 0.00 0.00 3.34
277 278 0.580104 CTTCGACGGCGTCACTTTTT 59.420 50.000 35.62 0.69 38.98 1.94
278 279 1.828331 GCTTCGACGGCGTCACTTTT 61.828 55.000 35.62 1.56 38.98 2.27
279 280 2.308039 GCTTCGACGGCGTCACTTT 61.308 57.895 35.62 2.43 38.98 2.66
359 360 2.415625 GGTTGACTGAGATCTTACGCGT 60.416 50.000 19.17 19.17 0.00 6.01
360 361 2.159366 AGGTTGACTGAGATCTTACGCG 60.159 50.000 3.53 3.53 0.00 6.01
405 406 2.180204 CGCAAGCAACGGATAGGGG 61.180 63.158 0.00 0.00 0.00 4.79
431 445 2.104331 CTACCTGCCTACGGTGCG 59.896 66.667 0.00 0.00 35.98 5.34
442 456 2.632028 CCCATCAGACAGATCCTACCTG 59.368 54.545 0.00 0.00 33.72 4.00
446 460 1.762827 GCCCCCATCAGACAGATCCTA 60.763 57.143 0.00 0.00 33.72 2.94
460 474 1.229625 ACACAGATGAGAGCCCCCA 60.230 57.895 0.00 0.00 0.00 4.96
482 496 6.306199 TCCAGACCAATTTATACATGGATGG 58.694 40.000 0.00 0.00 41.64 3.51
483 497 7.226441 TCTCCAGACCAATTTATACATGGATG 58.774 38.462 0.00 0.00 37.66 3.51
549 568 3.696548 TGCATACAGAACCAAACACACAA 59.303 39.130 0.00 0.00 0.00 3.33
581 600 5.948992 ACCAAATTCTTTCTACACAGCTC 57.051 39.130 0.00 0.00 0.00 4.09
586 605 5.687285 CACTGCAACCAAATTCTTTCTACAC 59.313 40.000 0.00 0.00 0.00 2.90
596 615 3.195396 ACAGAACACACTGCAACCAAATT 59.805 39.130 0.00 0.00 41.06 1.82
625 644 2.710096 TGGGGATTAGTTGCAGCTAC 57.290 50.000 10.10 0.00 0.00 3.58
626 645 2.777114 TGATGGGGATTAGTTGCAGCTA 59.223 45.455 6.14 6.14 0.00 3.32
627 646 1.565759 TGATGGGGATTAGTTGCAGCT 59.434 47.619 8.54 8.54 0.00 4.24
628 647 1.952296 CTGATGGGGATTAGTTGCAGC 59.048 52.381 0.00 0.00 0.00 5.25
629 648 3.287867 ACTGATGGGGATTAGTTGCAG 57.712 47.619 0.00 0.00 0.00 4.41
630 649 3.780294 AGTACTGATGGGGATTAGTTGCA 59.220 43.478 0.00 0.00 0.00 4.08
631 650 4.423625 AGTACTGATGGGGATTAGTTGC 57.576 45.455 0.00 0.00 0.00 4.17
632 651 5.989477 TGAAGTACTGATGGGGATTAGTTG 58.011 41.667 0.00 0.00 0.00 3.16
633 652 6.831664 ATGAAGTACTGATGGGGATTAGTT 57.168 37.500 0.00 0.00 0.00 2.24
634 653 6.386927 TGAATGAAGTACTGATGGGGATTAGT 59.613 38.462 0.00 0.00 0.00 2.24
655 715 2.363680 TGAAACAAATGCCGGTGTGAAT 59.636 40.909 1.90 0.00 0.00 2.57
661 721 2.824936 TGATGATGAAACAAATGCCGGT 59.175 40.909 1.90 0.00 0.00 5.28
664 724 6.400303 CGAAAACTGATGATGAAACAAATGCC 60.400 38.462 0.00 0.00 0.00 4.40
666 726 7.627585 ACGAAAACTGATGATGAAACAAATG 57.372 32.000 0.00 0.00 0.00 2.32
679 739 6.587990 CAGAGACACAATCTACGAAAACTGAT 59.412 38.462 0.00 0.00 38.00 2.90
683 743 5.227908 TCCAGAGACACAATCTACGAAAAC 58.772 41.667 0.00 0.00 38.00 2.43
686 746 4.082190 CCTTCCAGAGACACAATCTACGAA 60.082 45.833 0.00 0.00 38.00 3.85
689 749 3.055819 TGCCTTCCAGAGACACAATCTAC 60.056 47.826 0.00 0.00 38.00 2.59
697 758 2.659016 CGCTGCCTTCCAGAGACA 59.341 61.111 0.00 0.00 43.18 3.41
758 819 7.063426 GCAGTTCTGAAGCTTTTGTTTTTAGTT 59.937 33.333 0.00 0.00 0.00 2.24
766 827 2.620585 GAGGCAGTTCTGAAGCTTTTGT 59.379 45.455 0.00 0.00 0.00 2.83
767 828 2.883386 AGAGGCAGTTCTGAAGCTTTTG 59.117 45.455 0.00 0.00 0.00 2.44
831 895 5.940470 GGGAATGATCTGTAAACTGTTCACT 59.060 40.000 0.00 0.00 0.00 3.41
865 929 5.185454 TCGACAATTTCATTAGCATGGAGT 58.815 37.500 0.00 0.00 0.00 3.85
886 950 4.484502 CGTATTCAGAAAACGTCGATTCG 58.515 43.478 0.00 0.00 32.16 3.34
893 957 1.787012 ACGGCGTATTCAGAAAACGT 58.213 45.000 12.58 0.00 38.81 3.99
895 959 4.151157 AGTTGTACGGCGTATTCAGAAAAC 59.849 41.667 23.84 12.74 0.00 2.43
940 1004 2.170817 GGTAGCAGAGGTAAGGAAAGGG 59.829 54.545 0.00 0.00 0.00 3.95
1271 1335 8.954950 AGAACACGATAAATCAGATGAGATTT 57.045 30.769 7.06 7.06 46.69 2.17
1293 1357 2.290960 GCAAGAGGGGCCTAAGAAAGAA 60.291 50.000 0.84 0.00 0.00 2.52
1294 1358 1.282157 GCAAGAGGGGCCTAAGAAAGA 59.718 52.381 0.84 0.00 0.00 2.52
1304 1368 1.379642 CGGATCTTTGCAAGAGGGGC 61.380 60.000 0.00 0.00 41.61 5.80
1307 1371 2.675348 GTTCTCGGATCTTTGCAAGAGG 59.325 50.000 10.26 1.56 41.61 3.69
1356 1420 9.313118 AGAATAATTTGGTTTTTCTGTGTCAAC 57.687 29.630 0.00 0.00 36.93 3.18
1364 1428 7.277760 GGCGCATAAGAATAATTTGGTTTTTCT 59.722 33.333 10.83 0.00 39.01 2.52
1368 1432 5.356426 GGGCGCATAAGAATAATTTGGTTT 58.644 37.500 10.83 0.00 0.00 3.27
1369 1433 4.202212 GGGGCGCATAAGAATAATTTGGTT 60.202 41.667 10.83 0.00 0.00 3.67
1375 1442 2.162681 GCAGGGGCGCATAAGAATAAT 58.837 47.619 10.83 0.00 0.00 1.28
1394 1461 8.804163 TTGTTTGTTACACAAGCAGCTAGTGC 62.804 42.308 0.00 8.67 46.93 4.40
1412 1479 1.838913 GCACACAGCGATTTGTTTGT 58.161 45.000 0.00 0.00 32.67 2.83
1438 1505 8.720562 CATATTATCGGATAACAACATTGAGCA 58.279 33.333 12.39 0.00 0.00 4.26
1455 1522 5.733226 TTCCTTGCACACACATATTATCG 57.267 39.130 0.00 0.00 0.00 2.92
1507 1574 7.132213 CGAAAAGCAGAACATCTTCTAACAAA 58.868 34.615 0.00 0.00 34.74 2.83
1537 1604 7.478322 ACTTTTGTGCTGAAGCTCATATATTG 58.522 34.615 7.80 0.40 42.97 1.90
1563 1630 9.906660 ATCTGAAAAATTATTTAACTGCAACGA 57.093 25.926 0.00 0.00 0.00 3.85
1578 1645 8.400186 CCTCAAAAGCAAAACATCTGAAAAATT 58.600 29.630 0.00 0.00 0.00 1.82
1583 1650 5.850557 TCCTCAAAAGCAAAACATCTGAA 57.149 34.783 0.00 0.00 0.00 3.02
1643 1710 4.096231 TGTGTGACAAGTCAAACCAGATTG 59.904 41.667 18.22 0.00 45.08 2.67
1767 1835 5.244626 AGCAATTTCCTACACAAGCAGATTT 59.755 36.000 0.00 0.00 0.00 2.17
1768 1836 4.768968 AGCAATTTCCTACACAAGCAGATT 59.231 37.500 0.00 0.00 0.00 2.40
1769 1837 4.157289 CAGCAATTTCCTACACAAGCAGAT 59.843 41.667 0.00 0.00 0.00 2.90
1796 1864 7.991084 TTTTGAACTGAGAGATCATCATGTT 57.009 32.000 0.00 5.68 26.94 2.71
1797 1865 7.610692 ACATTTTGAACTGAGAGATCATCATGT 59.389 33.333 0.00 0.00 31.31 3.21
1798 1866 7.986562 ACATTTTGAACTGAGAGATCATCATG 58.013 34.615 0.00 0.00 30.17 3.07
1799 1867 8.459635 CAACATTTTGAACTGAGAGATCATCAT 58.540 33.333 0.00 0.00 34.24 2.45
1834 2189 1.600916 AAAACTGACAGAGCCCGCC 60.601 57.895 10.08 0.00 0.00 6.13
1900 2255 1.938577 CTCGCAACTGCAGCTCATAAT 59.061 47.619 15.27 0.00 42.21 1.28
1904 2259 0.532640 TTTCTCGCAACTGCAGCTCA 60.533 50.000 15.27 0.00 42.21 4.26
1946 2306 3.258872 TCAAGGGAAAACATTGAGCATGG 59.741 43.478 0.00 0.00 44.16 3.66
1947 2307 4.524316 TCAAGGGAAAACATTGAGCATG 57.476 40.909 0.00 0.00 44.16 4.06
1972 2332 3.782656 TCTCCCAAACTTACCCTTCAC 57.217 47.619 0.00 0.00 0.00 3.18
1975 2335 3.750922 GCACTTCTCCCAAACTTACCCTT 60.751 47.826 0.00 0.00 0.00 3.95
1989 2349 1.287730 CGTCCAGTGCTGCACTTCTC 61.288 60.000 31.20 21.03 42.59 2.87
1990 2350 1.301244 CGTCCAGTGCTGCACTTCT 60.301 57.895 31.20 9.96 42.59 2.85
2043 2403 2.289565 GATCCGAATCACAAAGGACCC 58.710 52.381 0.00 0.00 35.36 4.46
2044 2404 2.939103 CTGATCCGAATCACAAAGGACC 59.061 50.000 0.00 0.00 36.98 4.46
2046 2406 3.515502 ACTCTGATCCGAATCACAAAGGA 59.484 43.478 0.00 0.00 36.98 3.36
2051 2411 2.362397 GCCTACTCTGATCCGAATCACA 59.638 50.000 0.00 0.00 36.98 3.58
2078 2438 8.370940 CAATGTCTGACACCCATATACTCTAAT 58.629 37.037 13.50 0.00 0.00 1.73
2079 2439 7.344612 ACAATGTCTGACACCCATATACTCTAA 59.655 37.037 13.50 0.00 0.00 2.10
2080 2440 6.839134 ACAATGTCTGACACCCATATACTCTA 59.161 38.462 13.50 0.00 0.00 2.43
2081 2441 5.663106 ACAATGTCTGACACCCATATACTCT 59.337 40.000 13.50 0.00 0.00 3.24
2082 2442 5.918608 ACAATGTCTGACACCCATATACTC 58.081 41.667 13.50 0.00 0.00 2.59
2083 2443 5.957771 ACAATGTCTGACACCCATATACT 57.042 39.130 13.50 0.00 0.00 2.12
2139 2740 3.181397 CACTTGCTTTTGTGTCAGGTTG 58.819 45.455 0.00 0.00 0.00 3.77


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

AutoCloner maintained by Alex Coulton.