Multiple sequence alignment - TraesCS5D01G170300

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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 TraesCS5D01G170300 chr5D 100.000 3752 0 0 1 3752 267073913 267077664 0.000000e+00 6929.0
1 TraesCS5D01G170300 chr5D 98.908 458 3 2 1 458 267985165 267984710 0.000000e+00 817.0
2 TraesCS5D01G170300 chr5B 96.888 3117 82 6 645 3752 301195914 301199024 0.000000e+00 5204.0
3 TraesCS5D01G170300 chr5A 96.524 2704 60 12 481 3178 353607890 353605215 0.000000e+00 4442.0
4 TraesCS5D01G170300 chr5A 95.060 587 20 5 3171 3752 353605112 353604530 0.000000e+00 915.0
5 TraesCS5D01G170300 chr2D 94.526 475 25 1 1 474 592077902 592077428 0.000000e+00 732.0
6 TraesCS5D01G170300 chr2D 93.347 481 22 4 1 474 630546440 630545963 0.000000e+00 702.0
7 TraesCS5D01G170300 chr1B 85.356 478 59 8 3 474 666786913 666786441 5.630000e-133 484.0
8 TraesCS5D01G170300 chr6A 87.404 389 38 5 3 389 612564706 612564327 1.600000e-118 436.0
9 TraesCS5D01G170300 chr6A 82.558 344 48 12 138 473 105635621 105635960 3.670000e-75 292.0
10 TraesCS5D01G170300 chr4D 91.935 248 12 3 232 474 13574919 13574675 1.290000e-89 340.0
11 TraesCS5D01G170300 chr4D 92.647 136 10 0 7 142 13576030 13575895 2.960000e-46 196.0
12 TraesCS5D01G170300 chr3D 85.473 296 32 9 187 474 10659110 10659402 7.880000e-77 298.0
13 TraesCS5D01G170300 chr7D 81.058 359 50 16 136 480 263347321 263346967 1.720000e-68 270.0
14 TraesCS5D01G170300 chr7D 80.747 348 52 14 136 474 263271915 263272256 1.340000e-64 257.0
15 TraesCS5D01G170300 chr7D 88.158 76 8 1 481 555 46961097 46961172 5.160000e-14 89.8
16 TraesCS5D01G170300 chr7A 80.758 343 55 11 138 474 174587438 174587775 1.340000e-64 257.0
17 TraesCS5D01G170300 chr6D 78.920 389 59 17 106 474 89326995 89327380 3.740000e-60 243.0
18 TraesCS5D01G170300 chr3B 84.722 72 11 0 490 561 30678513 30678584 5.200000e-09 73.1
19 TraesCS5D01G170300 chr7B 97.368 38 1 0 438 475 647008553 647008516 8.700000e-07 65.8
20 TraesCS5D01G170300 chr6B 97.297 37 1 0 438 474 17493579 17493543 3.130000e-06 63.9


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 TraesCS5D01G170300 chr5D 267073913 267077664 3751 False 6929.0 6929 100.000 1 3752 1 chr5D.!!$F1 3751
1 TraesCS5D01G170300 chr5B 301195914 301199024 3110 False 5204.0 5204 96.888 645 3752 1 chr5B.!!$F1 3107
2 TraesCS5D01G170300 chr5A 353604530 353607890 3360 True 2678.5 4442 95.792 481 3752 2 chr5A.!!$R1 3271
3 TraesCS5D01G170300 chr4D 13574675 13576030 1355 True 268.0 340 92.291 7 474 2 chr4D.!!$R1 467

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
468 469 0.171231 GTTTTTCATCCTGGCTCCGC 59.829 55.0 0.0 0.0 0.0 5.54 F
947 954 0.393132 CTCTTTCCCTCGCTTTCCCC 60.393 60.0 0.0 0.0 0.0 4.81 F
948 955 0.840722 TCTTTCCCTCGCTTTCCCCT 60.841 55.0 0.0 0.0 0.0 4.79 F
2247 2260 1.048601 TCCTATGTTCATCCCCGCTC 58.951 55.0 0.0 0.0 0.0 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1383 1396 0.466555 AGGAATCGACGGAGAGGAGG 60.467 60.000 0.00 0.00 0.00 4.30 R
2559 2651 0.969894 GCAGTACTGAGACTGGGTGT 59.030 55.000 27.08 0.00 45.85 4.16 R
2703 2854 2.096013 GCTTTTGAATCGGCTACTGGAC 59.904 50.000 0.00 0.00 0.00 4.02 R
3150 3600 1.378514 GAATGGCCATGTGACCGGT 60.379 57.895 21.63 6.92 0.00 5.28 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
55 56 5.052693 TCAACAATCATGGGGAGATTAGG 57.947 43.478 0.00 0.00 34.14 2.69
63 64 7.895144 ATCATGGGGAGATTAGGAGAAATTA 57.105 36.000 0.00 0.00 0.00 1.40
64 65 7.079451 TCATGGGGAGATTAGGAGAAATTAC 57.921 40.000 0.00 0.00 0.00 1.89
65 66 5.906772 TGGGGAGATTAGGAGAAATTACC 57.093 43.478 0.00 0.00 0.00 2.85
85 86 3.687698 ACCTTACATGGGAAAAATCGTCG 59.312 43.478 0.00 0.00 0.00 5.12
88 89 0.861450 CATGGGAAAAATCGTCGCGC 60.861 55.000 0.00 0.00 0.00 6.86
97 98 3.529210 TCGTCGCGCGATGAAACG 61.529 61.111 42.90 35.36 45.68 3.60
103 104 3.089784 CGCGATGAAACGGAAGGG 58.910 61.111 0.00 0.00 0.00 3.95
113 114 2.435410 CGGAAGGGGGTAACGTGC 60.435 66.667 0.00 0.00 37.60 5.34
180 181 7.763172 ATAAAATGTGTTTCTTTTTCGTGCA 57.237 28.000 0.00 0.00 35.79 4.57
181 182 5.701029 AAATGTGTTTCTTTTTCGTGCAG 57.299 34.783 0.00 0.00 0.00 4.41
182 183 2.525055 TGTGTTTCTTTTTCGTGCAGC 58.475 42.857 0.00 0.00 0.00 5.25
183 184 2.163412 TGTGTTTCTTTTTCGTGCAGCT 59.837 40.909 0.00 0.00 0.00 4.24
184 185 2.783832 GTGTTTCTTTTTCGTGCAGCTC 59.216 45.455 0.00 0.00 0.00 4.09
185 186 2.682856 TGTTTCTTTTTCGTGCAGCTCT 59.317 40.909 0.00 0.00 0.00 4.09
186 187 3.874543 TGTTTCTTTTTCGTGCAGCTCTA 59.125 39.130 0.00 0.00 0.00 2.43
187 188 4.334203 TGTTTCTTTTTCGTGCAGCTCTAA 59.666 37.500 0.00 0.00 0.00 2.10
188 189 4.732285 TTCTTTTTCGTGCAGCTCTAAG 57.268 40.909 0.00 0.00 0.00 2.18
189 190 3.067106 TCTTTTTCGTGCAGCTCTAAGG 58.933 45.455 0.00 0.00 0.00 2.69
190 191 1.156736 TTTTCGTGCAGCTCTAAGGC 58.843 50.000 0.00 0.00 0.00 4.35
191 192 0.321671 TTTCGTGCAGCTCTAAGGCT 59.678 50.000 0.00 0.00 44.10 4.58
192 193 1.182667 TTCGTGCAGCTCTAAGGCTA 58.817 50.000 0.00 0.00 41.00 3.93
193 194 0.741326 TCGTGCAGCTCTAAGGCTAG 59.259 55.000 0.00 0.00 41.00 3.42
194 195 0.741326 CGTGCAGCTCTAAGGCTAGA 59.259 55.000 0.00 0.00 41.00 2.43
195 196 1.135139 CGTGCAGCTCTAAGGCTAGAA 59.865 52.381 0.00 0.00 41.00 2.10
196 197 2.417379 CGTGCAGCTCTAAGGCTAGAAA 60.417 50.000 0.00 0.00 41.00 2.52
197 198 3.739519 CGTGCAGCTCTAAGGCTAGAAAT 60.740 47.826 0.00 0.00 41.00 2.17
198 199 3.807071 GTGCAGCTCTAAGGCTAGAAATC 59.193 47.826 0.00 0.00 41.00 2.17
199 200 3.452264 TGCAGCTCTAAGGCTAGAAATCA 59.548 43.478 0.00 0.00 41.00 2.57
200 201 4.057432 GCAGCTCTAAGGCTAGAAATCAG 58.943 47.826 0.00 0.00 41.00 2.90
201 202 4.630111 CAGCTCTAAGGCTAGAAATCAGG 58.370 47.826 0.00 0.00 41.00 3.86
202 203 3.645687 AGCTCTAAGGCTAGAAATCAGGG 59.354 47.826 0.00 0.00 41.16 4.45
203 204 3.643792 GCTCTAAGGCTAGAAATCAGGGA 59.356 47.826 0.00 0.00 33.66 4.20
204 205 4.285775 GCTCTAAGGCTAGAAATCAGGGAT 59.714 45.833 0.00 0.00 33.66 3.85
205 206 5.792741 CTCTAAGGCTAGAAATCAGGGATG 58.207 45.833 0.00 0.00 33.66 3.51
206 207 5.219739 TCTAAGGCTAGAAATCAGGGATGT 58.780 41.667 0.00 0.00 30.89 3.06
207 208 6.382087 TCTAAGGCTAGAAATCAGGGATGTA 58.618 40.000 0.00 0.00 30.89 2.29
208 209 5.559148 AAGGCTAGAAATCAGGGATGTAG 57.441 43.478 0.00 0.00 0.00 2.74
209 210 3.326297 AGGCTAGAAATCAGGGATGTAGC 59.674 47.826 0.00 0.00 31.50 3.58
210 211 3.071602 GGCTAGAAATCAGGGATGTAGCA 59.928 47.826 0.00 0.00 32.75 3.49
211 212 4.444876 GGCTAGAAATCAGGGATGTAGCAA 60.445 45.833 0.00 0.00 32.75 3.91
212 213 4.513318 GCTAGAAATCAGGGATGTAGCAAC 59.487 45.833 0.00 0.00 32.06 4.17
213 214 4.574674 AGAAATCAGGGATGTAGCAACA 57.425 40.909 0.00 0.00 40.69 3.33
214 215 4.922206 AGAAATCAGGGATGTAGCAACAA 58.078 39.130 0.00 0.00 39.58 2.83
215 216 5.324409 AGAAATCAGGGATGTAGCAACAAA 58.676 37.500 0.00 0.00 39.58 2.83
216 217 5.774690 AGAAATCAGGGATGTAGCAACAAAA 59.225 36.000 0.00 0.00 39.58 2.44
217 218 6.267471 AGAAATCAGGGATGTAGCAACAAAAA 59.733 34.615 0.00 0.00 39.58 1.94
218 219 5.649782 ATCAGGGATGTAGCAACAAAAAG 57.350 39.130 0.00 0.00 39.58 2.27
219 220 3.826157 TCAGGGATGTAGCAACAAAAAGG 59.174 43.478 0.00 0.00 39.58 3.11
220 221 3.826157 CAGGGATGTAGCAACAAAAAGGA 59.174 43.478 0.00 0.00 39.58 3.36
221 222 4.280677 CAGGGATGTAGCAACAAAAAGGAA 59.719 41.667 0.00 0.00 39.58 3.36
222 223 5.047092 CAGGGATGTAGCAACAAAAAGGAAT 60.047 40.000 0.00 0.00 39.58 3.01
223 224 5.047092 AGGGATGTAGCAACAAAAAGGAATG 60.047 40.000 0.00 0.00 39.58 2.67
224 225 4.627035 GGATGTAGCAACAAAAAGGAATGC 59.373 41.667 0.00 0.00 39.58 3.56
225 226 3.988819 TGTAGCAACAAAAAGGAATGCC 58.011 40.909 0.00 0.00 37.73 4.40
226 227 2.153366 AGCAACAAAAAGGAATGCCG 57.847 45.000 0.00 0.00 39.96 5.69
227 228 1.412343 AGCAACAAAAAGGAATGCCGT 59.588 42.857 0.00 0.00 39.96 5.68
228 229 2.625790 AGCAACAAAAAGGAATGCCGTA 59.374 40.909 0.00 0.00 39.96 4.02
229 230 3.258123 AGCAACAAAAAGGAATGCCGTAT 59.742 39.130 0.00 0.00 39.96 3.06
230 231 3.993736 GCAACAAAAAGGAATGCCGTATT 59.006 39.130 0.00 0.00 39.96 1.89
231 232 4.091365 GCAACAAAAAGGAATGCCGTATTC 59.909 41.667 0.80 0.80 43.64 1.75
232 233 5.226396 CAACAAAAAGGAATGCCGTATTCA 58.774 37.500 10.84 0.00 45.70 2.57
233 234 5.659440 ACAAAAAGGAATGCCGTATTCAT 57.341 34.783 10.84 1.26 45.70 2.57
234 235 6.767524 ACAAAAAGGAATGCCGTATTCATA 57.232 33.333 10.84 0.00 45.70 2.15
235 236 7.346751 ACAAAAAGGAATGCCGTATTCATAT 57.653 32.000 10.84 0.00 45.70 1.78
236 237 7.781056 ACAAAAAGGAATGCCGTATTCATATT 58.219 30.769 10.84 1.53 45.70 1.28
237 238 8.257306 ACAAAAAGGAATGCCGTATTCATATTT 58.743 29.630 10.84 6.15 45.70 1.40
238 239 8.755018 CAAAAAGGAATGCCGTATTCATATTTC 58.245 33.333 10.84 0.00 45.70 2.17
239 240 7.823745 AAAGGAATGCCGTATTCATATTTCT 57.176 32.000 10.84 0.00 45.70 2.52
240 241 7.440523 AAGGAATGCCGTATTCATATTTCTC 57.559 36.000 10.84 0.00 45.70 2.87
241 242 6.533730 AGGAATGCCGTATTCATATTTCTCA 58.466 36.000 10.84 0.00 45.70 3.27
242 243 6.998074 AGGAATGCCGTATTCATATTTCTCAA 59.002 34.615 10.84 0.00 45.70 3.02
243 244 7.173907 AGGAATGCCGTATTCATATTTCTCAAG 59.826 37.037 10.84 0.00 45.70 3.02
244 245 5.673337 TGCCGTATTCATATTTCTCAAGC 57.327 39.130 0.00 0.00 0.00 4.01
245 246 5.368145 TGCCGTATTCATATTTCTCAAGCT 58.632 37.500 0.00 0.00 0.00 3.74
246 247 6.521162 TGCCGTATTCATATTTCTCAAGCTA 58.479 36.000 0.00 0.00 0.00 3.32
247 248 7.161404 TGCCGTATTCATATTTCTCAAGCTAT 58.839 34.615 0.00 0.00 0.00 2.97
248 249 7.661437 TGCCGTATTCATATTTCTCAAGCTATT 59.339 33.333 0.00 0.00 0.00 1.73
249 250 7.959651 GCCGTATTCATATTTCTCAAGCTATTG 59.040 37.037 0.00 0.00 37.80 1.90
250 251 8.993121 CCGTATTCATATTTCTCAAGCTATTGT 58.007 33.333 0.00 0.00 37.68 2.71
251 252 9.803130 CGTATTCATATTTCTCAAGCTATTGTG 57.197 33.333 0.00 0.00 37.68 3.33
252 253 9.604626 GTATTCATATTTCTCAAGCTATTGTGC 57.395 33.333 0.00 0.00 37.68 4.57
253 254 6.624352 TCATATTTCTCAAGCTATTGTGCC 57.376 37.500 0.00 0.00 37.68 5.01
254 255 6.359804 TCATATTTCTCAAGCTATTGTGCCT 58.640 36.000 0.00 0.00 37.68 4.75
255 256 6.830324 TCATATTTCTCAAGCTATTGTGCCTT 59.170 34.615 0.00 0.00 37.68 4.35
256 257 5.573337 ATTTCTCAAGCTATTGTGCCTTC 57.427 39.130 0.00 0.00 37.68 3.46
257 258 3.701205 TCTCAAGCTATTGTGCCTTCA 57.299 42.857 0.00 0.00 37.68 3.02
258 259 3.603532 TCTCAAGCTATTGTGCCTTCAG 58.396 45.455 0.00 0.00 37.68 3.02
259 260 3.008375 TCTCAAGCTATTGTGCCTTCAGT 59.992 43.478 0.00 0.00 37.68 3.41
260 261 3.076621 TCAAGCTATTGTGCCTTCAGTG 58.923 45.455 0.00 0.00 37.68 3.66
261 262 2.119801 AGCTATTGTGCCTTCAGTGG 57.880 50.000 0.00 0.00 0.00 4.00
262 263 1.352352 AGCTATTGTGCCTTCAGTGGT 59.648 47.619 0.00 0.00 0.00 4.16
263 264 2.162681 GCTATTGTGCCTTCAGTGGTT 58.837 47.619 0.00 0.00 0.00 3.67
264 265 3.009033 AGCTATTGTGCCTTCAGTGGTTA 59.991 43.478 0.00 0.00 0.00 2.85
265 266 3.375299 GCTATTGTGCCTTCAGTGGTTAG 59.625 47.826 0.00 0.00 0.00 2.34
266 267 3.508845 ATTGTGCCTTCAGTGGTTAGT 57.491 42.857 0.00 0.00 0.00 2.24
267 268 3.290948 TTGTGCCTTCAGTGGTTAGTT 57.709 42.857 0.00 0.00 0.00 2.24
268 269 3.290948 TGTGCCTTCAGTGGTTAGTTT 57.709 42.857 0.00 0.00 0.00 2.66
269 270 4.425180 TGTGCCTTCAGTGGTTAGTTTA 57.575 40.909 0.00 0.00 0.00 2.01
270 271 4.131596 TGTGCCTTCAGTGGTTAGTTTAC 58.868 43.478 0.00 0.00 0.00 2.01
271 272 4.141574 TGTGCCTTCAGTGGTTAGTTTACT 60.142 41.667 0.00 0.00 0.00 2.24
272 273 4.820173 GTGCCTTCAGTGGTTAGTTTACTT 59.180 41.667 0.00 0.00 0.00 2.24
273 274 5.298527 GTGCCTTCAGTGGTTAGTTTACTTT 59.701 40.000 0.00 0.00 0.00 2.66
274 275 5.889289 TGCCTTCAGTGGTTAGTTTACTTTT 59.111 36.000 0.00 0.00 0.00 2.27
275 276 6.038936 TGCCTTCAGTGGTTAGTTTACTTTTC 59.961 38.462 0.00 0.00 0.00 2.29
276 277 6.262496 GCCTTCAGTGGTTAGTTTACTTTTCT 59.738 38.462 0.00 0.00 0.00 2.52
277 278 7.201794 GCCTTCAGTGGTTAGTTTACTTTTCTT 60.202 37.037 0.00 0.00 0.00 2.52
278 279 8.683615 CCTTCAGTGGTTAGTTTACTTTTCTTT 58.316 33.333 0.00 0.00 0.00 2.52
279 280 9.503427 CTTCAGTGGTTAGTTTACTTTTCTTTG 57.497 33.333 0.00 0.00 0.00 2.77
280 281 7.992008 TCAGTGGTTAGTTTACTTTTCTTTGG 58.008 34.615 0.00 0.00 0.00 3.28
281 282 6.695713 CAGTGGTTAGTTTACTTTTCTTTGGC 59.304 38.462 0.00 0.00 0.00 4.52
282 283 6.378848 AGTGGTTAGTTTACTTTTCTTTGGCA 59.621 34.615 0.00 0.00 0.00 4.92
283 284 7.036829 GTGGTTAGTTTACTTTTCTTTGGCAA 58.963 34.615 0.00 0.00 0.00 4.52
284 285 7.709182 GTGGTTAGTTTACTTTTCTTTGGCAAT 59.291 33.333 0.00 0.00 0.00 3.56
285 286 7.708752 TGGTTAGTTTACTTTTCTTTGGCAATG 59.291 33.333 0.00 3.33 0.00 2.82
286 287 7.923878 GGTTAGTTTACTTTTCTTTGGCAATGA 59.076 33.333 11.38 11.38 0.00 2.57
287 288 8.752254 GTTAGTTTACTTTTCTTTGGCAATGAC 58.248 33.333 14.62 2.92 0.00 3.06
288 289 7.112452 AGTTTACTTTTCTTTGGCAATGACT 57.888 32.000 14.62 4.99 0.00 3.41
289 290 6.980397 AGTTTACTTTTCTTTGGCAATGACTG 59.020 34.615 14.62 10.30 0.00 3.51
290 291 6.463995 TTACTTTTCTTTGGCAATGACTGT 57.536 33.333 14.62 14.51 0.00 3.55
291 292 4.685924 ACTTTTCTTTGGCAATGACTGTG 58.314 39.130 14.62 8.54 0.00 3.66
292 293 4.160252 ACTTTTCTTTGGCAATGACTGTGT 59.840 37.500 14.62 9.07 0.00 3.72
293 294 3.988379 TTCTTTGGCAATGACTGTGTC 57.012 42.857 14.62 0.00 0.00 3.67
294 295 2.929641 TCTTTGGCAATGACTGTGTCA 58.070 42.857 11.38 2.77 46.90 3.58
308 309 7.363205 TGACTGTGTCATAATTATGTGTGTG 57.637 36.000 21.89 14.00 37.67 3.82
309 310 6.934083 TGACTGTGTCATAATTATGTGTGTGT 59.066 34.615 21.89 16.39 37.67 3.72
310 311 7.443879 TGACTGTGTCATAATTATGTGTGTGTT 59.556 33.333 21.89 5.81 37.67 3.32
311 312 7.584108 ACTGTGTCATAATTATGTGTGTGTTG 58.416 34.615 21.89 10.41 35.26 3.33
312 313 7.443879 ACTGTGTCATAATTATGTGTGTGTTGA 59.556 33.333 21.89 1.01 35.26 3.18
313 314 7.580600 TGTGTCATAATTATGTGTGTGTTGAC 58.419 34.615 21.89 12.52 35.26 3.18
314 315 7.227512 TGTGTCATAATTATGTGTGTGTTGACA 59.772 33.333 21.89 14.60 38.75 3.58
315 316 8.236586 GTGTCATAATTATGTGTGTGTTGACAT 58.763 33.333 21.89 0.00 41.80 3.06
316 317 8.791675 TGTCATAATTATGTGTGTGTTGACATT 58.208 29.630 21.89 0.00 36.85 2.71
346 347 9.905713 ATATAAGGACATATATGCGATTTTGGT 57.094 29.630 12.79 0.00 29.40 3.67
347 348 6.959639 AAGGACATATATGCGATTTTGGTT 57.040 33.333 12.79 0.00 0.00 3.67
348 349 6.560253 AGGACATATATGCGATTTTGGTTC 57.440 37.500 12.79 0.00 0.00 3.62
349 350 6.299141 AGGACATATATGCGATTTTGGTTCT 58.701 36.000 12.79 0.00 0.00 3.01
350 351 6.772716 AGGACATATATGCGATTTTGGTTCTT 59.227 34.615 12.79 0.00 0.00 2.52
351 352 7.936847 AGGACATATATGCGATTTTGGTTCTTA 59.063 33.333 12.79 0.00 0.00 2.10
352 353 8.015658 GGACATATATGCGATTTTGGTTCTTAC 58.984 37.037 12.79 0.00 0.00 2.34
353 354 8.445275 ACATATATGCGATTTTGGTTCTTACA 57.555 30.769 12.79 0.00 0.00 2.41
354 355 9.066892 ACATATATGCGATTTTGGTTCTTACAT 57.933 29.630 12.79 0.00 0.00 2.29
357 358 8.677148 ATATGCGATTTTGGTTCTTACATACT 57.323 30.769 0.00 0.00 0.00 2.12
358 359 9.772973 ATATGCGATTTTGGTTCTTACATACTA 57.227 29.630 0.00 0.00 0.00 1.82
359 360 8.677148 ATGCGATTTTGGTTCTTACATACTAT 57.323 30.769 0.00 0.00 0.00 2.12
360 361 9.772973 ATGCGATTTTGGTTCTTACATACTATA 57.227 29.630 0.00 0.00 0.00 1.31
361 362 9.772973 TGCGATTTTGGTTCTTACATACTATAT 57.227 29.630 0.00 0.00 0.00 0.86
378 379 6.925610 ACTATATGTATGCTTGTGTGGTTG 57.074 37.500 0.00 0.00 0.00 3.77
379 380 5.822519 ACTATATGTATGCTTGTGTGGTTGG 59.177 40.000 0.00 0.00 0.00 3.77
380 381 2.356665 TGTATGCTTGTGTGGTTGGT 57.643 45.000 0.00 0.00 0.00 3.67
381 382 2.660572 TGTATGCTTGTGTGGTTGGTT 58.339 42.857 0.00 0.00 0.00 3.67
382 383 3.027412 TGTATGCTTGTGTGGTTGGTTT 58.973 40.909 0.00 0.00 0.00 3.27
383 384 3.449018 TGTATGCTTGTGTGGTTGGTTTT 59.551 39.130 0.00 0.00 0.00 2.43
384 385 3.625649 ATGCTTGTGTGGTTGGTTTTT 57.374 38.095 0.00 0.00 0.00 1.94
385 386 4.744795 ATGCTTGTGTGGTTGGTTTTTA 57.255 36.364 0.00 0.00 0.00 1.52
386 387 4.537135 TGCTTGTGTGGTTGGTTTTTAA 57.463 36.364 0.00 0.00 0.00 1.52
387 388 4.894784 TGCTTGTGTGGTTGGTTTTTAAA 58.105 34.783 0.00 0.00 0.00 1.52
388 389 5.305585 TGCTTGTGTGGTTGGTTTTTAAAA 58.694 33.333 0.00 0.00 0.00 1.52
389 390 5.940470 TGCTTGTGTGGTTGGTTTTTAAAAT 59.060 32.000 0.55 0.00 0.00 1.82
390 391 6.128172 TGCTTGTGTGGTTGGTTTTTAAAATG 60.128 34.615 0.55 0.00 0.00 2.32
391 392 6.092807 GCTTGTGTGGTTGGTTTTTAAAATGA 59.907 34.615 0.55 0.00 0.00 2.57
392 393 7.201688 GCTTGTGTGGTTGGTTTTTAAAATGAT 60.202 33.333 0.55 0.00 0.00 2.45
393 394 7.778470 TGTGTGGTTGGTTTTTAAAATGATC 57.222 32.000 0.55 0.00 0.00 2.92
394 395 7.560368 TGTGTGGTTGGTTTTTAAAATGATCT 58.440 30.769 0.55 0.00 0.00 2.75
395 396 8.696374 TGTGTGGTTGGTTTTTAAAATGATCTA 58.304 29.630 0.55 0.00 0.00 1.98
396 397 9.191995 GTGTGGTTGGTTTTTAAAATGATCTAG 57.808 33.333 0.55 0.00 0.00 2.43
397 398 7.870445 TGTGGTTGGTTTTTAAAATGATCTAGC 59.130 33.333 0.55 0.00 0.00 3.42
398 399 7.330946 GTGGTTGGTTTTTAAAATGATCTAGCC 59.669 37.037 0.55 4.06 0.00 3.93
399 400 7.015682 TGGTTGGTTTTTAAAATGATCTAGCCA 59.984 33.333 0.55 6.23 0.00 4.75
400 401 8.040727 GGTTGGTTTTTAAAATGATCTAGCCAT 58.959 33.333 0.55 0.00 0.00 4.40
401 402 9.435688 GTTGGTTTTTAAAATGATCTAGCCATT 57.564 29.630 0.55 4.88 35.92 3.16
404 405 9.249457 GGTTTTTAAAATGATCTAGCCATTAGC 57.751 33.333 0.55 2.05 44.25 3.09
422 423 8.454106 GCCATTAGCTTGTATACATATTTCTGG 58.546 37.037 6.36 11.04 38.99 3.86
423 424 9.725019 CCATTAGCTTGTATACATATTTCTGGA 57.275 33.333 6.36 0.00 0.00 3.86
425 426 9.950496 ATTAGCTTGTATACATATTTCTGGAGG 57.050 33.333 6.36 0.00 0.00 4.30
426 427 6.234177 AGCTTGTATACATATTTCTGGAGGC 58.766 40.000 6.36 0.00 0.00 4.70
427 428 5.997746 GCTTGTATACATATTTCTGGAGGCA 59.002 40.000 6.36 0.00 0.00 4.75
428 429 6.656693 GCTTGTATACATATTTCTGGAGGCAT 59.343 38.462 6.36 0.00 0.00 4.40
429 430 7.361542 GCTTGTATACATATTTCTGGAGGCATG 60.362 40.741 6.36 0.00 0.00 4.06
430 431 7.078249 TGTATACATATTTCTGGAGGCATGT 57.922 36.000 0.08 0.00 0.00 3.21
431 432 8.201242 TGTATACATATTTCTGGAGGCATGTA 57.799 34.615 0.08 0.00 34.43 2.29
432 433 8.825774 TGTATACATATTTCTGGAGGCATGTAT 58.174 33.333 0.08 9.29 40.68 2.29
435 436 7.986085 ACATATTTCTGGAGGCATGTATAAC 57.014 36.000 0.00 0.00 0.00 1.89
436 437 7.749666 ACATATTTCTGGAGGCATGTATAACT 58.250 34.615 0.00 0.00 0.00 2.24
437 438 8.220559 ACATATTTCTGGAGGCATGTATAACTT 58.779 33.333 0.00 0.00 0.00 2.66
438 439 9.071276 CATATTTCTGGAGGCATGTATAACTTT 57.929 33.333 0.00 0.00 0.00 2.66
439 440 6.757897 TTTCTGGAGGCATGTATAACTTTG 57.242 37.500 0.00 0.00 0.00 2.77
440 441 4.199310 TCTGGAGGCATGTATAACTTTGC 58.801 43.478 0.00 0.00 0.00 3.68
441 442 3.287222 TGGAGGCATGTATAACTTTGCC 58.713 45.455 13.38 13.38 42.27 4.52
442 443 2.623416 GGAGGCATGTATAACTTTGCCC 59.377 50.000 16.05 10.36 42.89 5.36
443 444 2.623416 GAGGCATGTATAACTTTGCCCC 59.377 50.000 16.05 5.93 42.89 5.80
444 445 1.686587 GGCATGTATAACTTTGCCCCC 59.313 52.381 11.28 0.00 36.52 5.40
445 446 2.666317 GCATGTATAACTTTGCCCCCT 58.334 47.619 0.00 0.00 0.00 4.79
446 447 2.623416 GCATGTATAACTTTGCCCCCTC 59.377 50.000 0.00 0.00 0.00 4.30
447 448 3.688414 GCATGTATAACTTTGCCCCCTCT 60.688 47.826 0.00 0.00 0.00 3.69
448 449 4.536765 CATGTATAACTTTGCCCCCTCTT 58.463 43.478 0.00 0.00 0.00 2.85
449 450 3.963129 TGTATAACTTTGCCCCCTCTTG 58.037 45.455 0.00 0.00 0.00 3.02
450 451 3.332485 TGTATAACTTTGCCCCCTCTTGT 59.668 43.478 0.00 0.00 0.00 3.16
451 452 3.542969 ATAACTTTGCCCCCTCTTGTT 57.457 42.857 0.00 0.00 0.00 2.83
452 453 2.174685 AACTTTGCCCCCTCTTGTTT 57.825 45.000 0.00 0.00 0.00 2.83
453 454 2.174685 ACTTTGCCCCCTCTTGTTTT 57.825 45.000 0.00 0.00 0.00 2.43
454 455 2.477245 ACTTTGCCCCCTCTTGTTTTT 58.523 42.857 0.00 0.00 0.00 1.94
455 456 2.434336 ACTTTGCCCCCTCTTGTTTTTC 59.566 45.455 0.00 0.00 0.00 2.29
456 457 2.166907 TTGCCCCCTCTTGTTTTTCA 57.833 45.000 0.00 0.00 0.00 2.69
457 458 2.397044 TGCCCCCTCTTGTTTTTCAT 57.603 45.000 0.00 0.00 0.00 2.57
458 459 2.247358 TGCCCCCTCTTGTTTTTCATC 58.753 47.619 0.00 0.00 0.00 2.92
459 460 1.550524 GCCCCCTCTTGTTTTTCATCC 59.449 52.381 0.00 0.00 0.00 3.51
460 461 2.823152 GCCCCCTCTTGTTTTTCATCCT 60.823 50.000 0.00 0.00 0.00 3.24
461 462 2.827921 CCCCCTCTTGTTTTTCATCCTG 59.172 50.000 0.00 0.00 0.00 3.86
462 463 2.827921 CCCCTCTTGTTTTTCATCCTGG 59.172 50.000 0.00 0.00 0.00 4.45
463 464 2.232208 CCCTCTTGTTTTTCATCCTGGC 59.768 50.000 0.00 0.00 0.00 4.85
464 465 3.160269 CCTCTTGTTTTTCATCCTGGCT 58.840 45.455 0.00 0.00 0.00 4.75
465 466 3.192212 CCTCTTGTTTTTCATCCTGGCTC 59.808 47.826 0.00 0.00 0.00 4.70
466 467 3.157087 TCTTGTTTTTCATCCTGGCTCC 58.843 45.455 0.00 0.00 0.00 4.70
467 468 1.533625 TGTTTTTCATCCTGGCTCCG 58.466 50.000 0.00 0.00 0.00 4.63
468 469 0.171231 GTTTTTCATCCTGGCTCCGC 59.829 55.000 0.00 0.00 0.00 5.54
478 479 4.162690 GGCTCCGCCCCTGTACAG 62.163 72.222 16.34 16.34 44.06 2.74
479 480 3.075005 GCTCCGCCCCTGTACAGA 61.075 66.667 24.68 2.12 0.00 3.41
496 497 4.297299 ACAGACAAACAAAGTGCAGATG 57.703 40.909 0.00 0.00 0.00 2.90
500 501 3.784338 ACAAACAAAGTGCAGATGTTGG 58.216 40.909 11.23 10.86 37.36 3.77
507 508 6.042143 ACAAAGTGCAGATGTTGGTTTTTAG 58.958 36.000 0.00 0.00 0.00 1.85
544 545 2.989055 AAGCCCAACCGAGACACACG 62.989 60.000 0.00 0.00 0.00 4.49
564 565 3.051327 CGTGCAATGCAGACAAAAATCA 58.949 40.909 8.73 0.00 40.08 2.57
582 583 3.929417 TCAAAGTAACCAAACACGTCG 57.071 42.857 0.00 0.00 0.00 5.12
612 619 1.336755 ACCAAACACCGCATTTCTGAC 59.663 47.619 0.00 0.00 0.00 3.51
630 637 1.257155 GACGAGACAACGAAACACCAC 59.743 52.381 0.00 0.00 37.03 4.16
700 707 1.538382 ATTGGCATTGGGTTGGGCA 60.538 52.632 0.00 0.00 35.11 5.36
946 953 1.027255 GCTCTTTCCCTCGCTTTCCC 61.027 60.000 0.00 0.00 0.00 3.97
947 954 0.393132 CTCTTTCCCTCGCTTTCCCC 60.393 60.000 0.00 0.00 0.00 4.81
948 955 0.840722 TCTTTCCCTCGCTTTCCCCT 60.841 55.000 0.00 0.00 0.00 4.79
977 984 4.741239 TGCTCCACTCCCCCTCCC 62.741 72.222 0.00 0.00 0.00 4.30
1401 1414 2.034607 CCTCCTCTCCGTCGATTCC 58.965 63.158 0.00 0.00 0.00 3.01
1803 1816 4.250305 AGGGAGCGTGCCGTTGTT 62.250 61.111 0.00 0.00 30.73 2.83
2070 2083 1.393603 CTCTCTGCCTGTGGTCGATA 58.606 55.000 0.00 0.00 0.00 2.92
2247 2260 1.048601 TCCTATGTTCATCCCCGCTC 58.951 55.000 0.00 0.00 0.00 5.03
2439 2531 1.251527 CCGTACAGGAGTCAGCTGGT 61.252 60.000 15.13 5.02 45.00 4.00
2703 2854 3.672767 AAGAAGGCTTTGCAAAGGATG 57.327 42.857 34.02 15.30 36.53 3.51
2709 2860 1.615392 GCTTTGCAAAGGATGTCCAGT 59.385 47.619 34.02 0.00 38.89 4.00
2932 3083 1.135257 CGTGAGTCGAAGCTTCAGGAT 60.135 52.381 25.47 8.57 42.86 3.24
3150 3600 1.220749 GCTAGATGTGGGCGGTGAA 59.779 57.895 0.00 0.00 0.00 3.18
3381 3945 2.297597 AGTGAGACGGAAGAGGAAAGTG 59.702 50.000 0.00 0.00 0.00 3.16
3384 3948 3.578716 TGAGACGGAAGAGGAAAGTGATT 59.421 43.478 0.00 0.00 0.00 2.57
3385 3949 4.040461 TGAGACGGAAGAGGAAAGTGATTT 59.960 41.667 0.00 0.00 0.00 2.17
3386 3950 4.974399 AGACGGAAGAGGAAAGTGATTTT 58.026 39.130 0.00 0.00 0.00 1.82
3387 3951 5.377478 AGACGGAAGAGGAAAGTGATTTTT 58.623 37.500 0.00 0.00 0.00 1.94
3532 4098 8.947055 AGTCAAAATTGAACTAAAAGCATGTT 57.053 26.923 0.00 0.00 39.21 2.71
3618 4185 9.142014 AGCTAACATCATGATTACTCTAGTCTT 57.858 33.333 5.16 0.00 0.00 3.01
3736 4303 4.974399 CCCTTCATTGGGTAGAGAATACC 58.026 47.826 0.00 0.00 42.25 2.73
3743 4310 2.104111 TGGGTAGAGAATACCGCCAATG 59.896 50.000 0.00 0.00 38.46 2.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.693969 ATGTAAGTCTCTTCTTTTTGGATGG 57.306 36.000 0.00 0.00 0.00 3.51
46 47 9.495572 CATGTAAGGTAATTTCTCCTAATCTCC 57.504 37.037 0.00 0.00 33.27 3.71
55 56 9.803315 GATTTTTCCCATGTAAGGTAATTTCTC 57.197 33.333 0.00 0.00 0.00 2.87
63 64 3.687698 CGACGATTTTTCCCATGTAAGGT 59.312 43.478 0.00 0.00 0.00 3.50
64 65 3.486875 GCGACGATTTTTCCCATGTAAGG 60.487 47.826 0.00 0.00 0.00 2.69
65 66 3.680789 GCGACGATTTTTCCCATGTAAG 58.319 45.455 0.00 0.00 0.00 2.34
85 86 2.399611 CCTTCCGTTTCATCGCGC 59.600 61.111 0.00 0.00 0.00 6.86
88 89 0.538118 TACCCCCTTCCGTTTCATCG 59.462 55.000 0.00 0.00 0.00 3.84
97 98 0.614812 TAAGCACGTTACCCCCTTCC 59.385 55.000 0.00 0.00 0.00 3.46
103 104 5.874895 AGAAAATCTTAAGCACGTTACCC 57.125 39.130 0.00 0.00 0.00 3.69
154 155 9.302345 TGCACGAAAAAGAAACACATTTTATAA 57.698 25.926 0.00 0.00 31.06 0.98
155 156 8.858003 TGCACGAAAAAGAAACACATTTTATA 57.142 26.923 0.00 0.00 31.06 0.98
156 157 7.516627 GCTGCACGAAAAAGAAACACATTTTAT 60.517 33.333 0.00 0.00 31.06 1.40
157 158 6.237701 GCTGCACGAAAAAGAAACACATTTTA 60.238 34.615 0.00 0.00 31.06 1.52
158 159 5.445806 GCTGCACGAAAAAGAAACACATTTT 60.446 36.000 0.00 0.00 33.11 1.82
160 161 3.551485 GCTGCACGAAAAAGAAACACATT 59.449 39.130 0.00 0.00 0.00 2.71
162 163 2.163412 AGCTGCACGAAAAAGAAACACA 59.837 40.909 1.02 0.00 0.00 3.72
167 168 3.498397 CCTTAGAGCTGCACGAAAAAGAA 59.502 43.478 1.02 0.00 0.00 2.52
168 169 3.067106 CCTTAGAGCTGCACGAAAAAGA 58.933 45.455 1.02 0.00 0.00 2.52
170 171 1.535462 GCCTTAGAGCTGCACGAAAAA 59.465 47.619 1.02 0.00 0.00 1.94
171 172 1.156736 GCCTTAGAGCTGCACGAAAA 58.843 50.000 1.02 0.00 0.00 2.29
174 175 0.741326 CTAGCCTTAGAGCTGCACGA 59.259 55.000 1.02 0.00 44.67 4.35
175 176 0.741326 TCTAGCCTTAGAGCTGCACG 59.259 55.000 1.02 0.00 44.67 5.34
176 177 2.969628 TTCTAGCCTTAGAGCTGCAC 57.030 50.000 1.02 0.00 44.67 4.57
177 178 3.452264 TGATTTCTAGCCTTAGAGCTGCA 59.548 43.478 1.02 0.00 44.67 4.41
178 179 4.057432 CTGATTTCTAGCCTTAGAGCTGC 58.943 47.826 0.00 0.00 44.67 5.25
179 180 4.502950 CCCTGATTTCTAGCCTTAGAGCTG 60.503 50.000 0.00 0.00 44.67 4.24
181 182 3.643792 TCCCTGATTTCTAGCCTTAGAGC 59.356 47.826 0.00 0.00 37.24 4.09
182 183 5.306678 ACATCCCTGATTTCTAGCCTTAGAG 59.693 44.000 0.00 0.00 37.24 2.43
183 184 5.219739 ACATCCCTGATTTCTAGCCTTAGA 58.780 41.667 0.00 0.00 34.11 2.10
184 185 5.559148 ACATCCCTGATTTCTAGCCTTAG 57.441 43.478 0.00 0.00 0.00 2.18
185 186 5.012148 GCTACATCCCTGATTTCTAGCCTTA 59.988 44.000 0.00 0.00 0.00 2.69
186 187 4.202409 GCTACATCCCTGATTTCTAGCCTT 60.202 45.833 0.00 0.00 0.00 4.35
187 188 3.326297 GCTACATCCCTGATTTCTAGCCT 59.674 47.826 0.00 0.00 0.00 4.58
188 189 3.071602 TGCTACATCCCTGATTTCTAGCC 59.928 47.826 0.00 0.00 0.00 3.93
189 190 4.342862 TGCTACATCCCTGATTTCTAGC 57.657 45.455 0.00 0.00 0.00 3.42
190 191 5.674525 TGTTGCTACATCCCTGATTTCTAG 58.325 41.667 0.00 0.00 0.00 2.43
191 192 5.692115 TGTTGCTACATCCCTGATTTCTA 57.308 39.130 0.00 0.00 0.00 2.10
192 193 4.574674 TGTTGCTACATCCCTGATTTCT 57.425 40.909 0.00 0.00 0.00 2.52
193 194 5.643379 TTTGTTGCTACATCCCTGATTTC 57.357 39.130 0.81 0.00 33.44 2.17
194 195 6.418057 TTTTTGTTGCTACATCCCTGATTT 57.582 33.333 0.81 0.00 33.44 2.17
195 196 5.047092 CCTTTTTGTTGCTACATCCCTGATT 60.047 40.000 0.81 0.00 33.44 2.57
196 197 4.463891 CCTTTTTGTTGCTACATCCCTGAT 59.536 41.667 0.81 0.00 33.44 2.90
197 198 3.826157 CCTTTTTGTTGCTACATCCCTGA 59.174 43.478 0.81 0.00 33.44 3.86
198 199 3.826157 TCCTTTTTGTTGCTACATCCCTG 59.174 43.478 0.81 0.00 33.44 4.45
199 200 4.112634 TCCTTTTTGTTGCTACATCCCT 57.887 40.909 0.81 0.00 33.44 4.20
200 201 4.864704 TTCCTTTTTGTTGCTACATCCC 57.135 40.909 0.81 0.00 33.44 3.85
201 202 4.627035 GCATTCCTTTTTGTTGCTACATCC 59.373 41.667 0.81 0.00 33.44 3.51
202 203 4.627035 GGCATTCCTTTTTGTTGCTACATC 59.373 41.667 0.81 0.00 33.44 3.06
203 204 4.568956 GGCATTCCTTTTTGTTGCTACAT 58.431 39.130 0.81 0.00 33.44 2.29
204 205 3.551863 CGGCATTCCTTTTTGTTGCTACA 60.552 43.478 0.00 0.00 33.86 2.74
205 206 2.986479 CGGCATTCCTTTTTGTTGCTAC 59.014 45.455 0.00 0.00 33.86 3.58
206 207 2.625790 ACGGCATTCCTTTTTGTTGCTA 59.374 40.909 0.00 0.00 33.86 3.49
207 208 1.412343 ACGGCATTCCTTTTTGTTGCT 59.588 42.857 0.00 0.00 33.86 3.91
208 209 1.864565 ACGGCATTCCTTTTTGTTGC 58.135 45.000 0.00 0.00 0.00 4.17
209 210 5.226396 TGAATACGGCATTCCTTTTTGTTG 58.774 37.500 8.89 0.00 42.17 3.33
210 211 5.461032 TGAATACGGCATTCCTTTTTGTT 57.539 34.783 8.89 0.00 42.17 2.83
211 212 5.659440 ATGAATACGGCATTCCTTTTTGT 57.341 34.783 8.89 0.00 42.17 2.83
212 213 8.647143 AAATATGAATACGGCATTCCTTTTTG 57.353 30.769 8.89 0.00 42.17 2.44
213 214 8.695456 AGAAATATGAATACGGCATTCCTTTTT 58.305 29.630 8.89 7.21 42.17 1.94
214 215 8.237811 AGAAATATGAATACGGCATTCCTTTT 57.762 30.769 8.89 6.60 42.17 2.27
215 216 7.502226 TGAGAAATATGAATACGGCATTCCTTT 59.498 33.333 8.89 6.73 42.17 3.11
216 217 6.998074 TGAGAAATATGAATACGGCATTCCTT 59.002 34.615 8.89 1.54 42.17 3.36
217 218 6.533730 TGAGAAATATGAATACGGCATTCCT 58.466 36.000 8.89 3.30 42.17 3.36
218 219 6.801539 TGAGAAATATGAATACGGCATTCC 57.198 37.500 8.89 0.00 42.17 3.01
219 220 6.798959 GCTTGAGAAATATGAATACGGCATTC 59.201 38.462 5.35 5.35 43.01 2.67
220 221 6.488006 AGCTTGAGAAATATGAATACGGCATT 59.512 34.615 0.00 0.00 0.00 3.56
221 222 6.000219 AGCTTGAGAAATATGAATACGGCAT 59.000 36.000 0.00 0.00 0.00 4.40
222 223 5.368145 AGCTTGAGAAATATGAATACGGCA 58.632 37.500 0.00 0.00 0.00 5.69
223 224 5.931441 AGCTTGAGAAATATGAATACGGC 57.069 39.130 0.00 0.00 0.00 5.68
224 225 8.993121 ACAATAGCTTGAGAAATATGAATACGG 58.007 33.333 0.00 0.00 36.20 4.02
225 226 9.803130 CACAATAGCTTGAGAAATATGAATACG 57.197 33.333 0.00 0.00 36.20 3.06
226 227 9.604626 GCACAATAGCTTGAGAAATATGAATAC 57.395 33.333 0.00 0.00 36.20 1.89
227 228 8.786898 GGCACAATAGCTTGAGAAATATGAATA 58.213 33.333 0.00 0.00 36.20 1.75
228 229 7.504911 AGGCACAATAGCTTGAGAAATATGAAT 59.495 33.333 0.00 0.00 36.20 2.57
229 230 6.830324 AGGCACAATAGCTTGAGAAATATGAA 59.170 34.615 0.00 0.00 36.20 2.57
230 231 6.359804 AGGCACAATAGCTTGAGAAATATGA 58.640 36.000 0.00 0.00 36.20 2.15
231 232 6.630444 AGGCACAATAGCTTGAGAAATATG 57.370 37.500 0.00 0.00 36.20 1.78
232 233 6.830324 TGAAGGCACAATAGCTTGAGAAATAT 59.170 34.615 0.00 0.00 36.20 1.28
233 234 6.179756 TGAAGGCACAATAGCTTGAGAAATA 58.820 36.000 0.00 0.00 36.20 1.40
234 235 5.012239 TGAAGGCACAATAGCTTGAGAAAT 58.988 37.500 0.00 0.00 36.20 2.17
235 236 4.397420 TGAAGGCACAATAGCTTGAGAAA 58.603 39.130 0.00 0.00 36.20 2.52
236 237 4.005650 CTGAAGGCACAATAGCTTGAGAA 58.994 43.478 0.00 0.00 36.20 2.87
237 238 3.008375 ACTGAAGGCACAATAGCTTGAGA 59.992 43.478 0.00 0.00 36.20 3.27
238 239 3.126514 CACTGAAGGCACAATAGCTTGAG 59.873 47.826 0.00 0.00 36.20 3.02
239 240 3.076621 CACTGAAGGCACAATAGCTTGA 58.923 45.455 0.00 0.00 36.20 3.02
240 241 2.163010 CCACTGAAGGCACAATAGCTTG 59.837 50.000 0.00 0.00 38.39 4.01
241 242 2.224867 ACCACTGAAGGCACAATAGCTT 60.225 45.455 0.00 0.00 34.17 3.74
242 243 1.352352 ACCACTGAAGGCACAATAGCT 59.648 47.619 0.00 0.00 34.17 3.32
243 244 1.826385 ACCACTGAAGGCACAATAGC 58.174 50.000 0.00 0.00 0.00 2.97
244 245 4.579869 ACTAACCACTGAAGGCACAATAG 58.420 43.478 0.00 0.00 0.00 1.73
245 246 4.634012 ACTAACCACTGAAGGCACAATA 57.366 40.909 0.00 0.00 0.00 1.90
246 247 3.508845 ACTAACCACTGAAGGCACAAT 57.491 42.857 0.00 0.00 0.00 2.71
247 248 3.290948 AACTAACCACTGAAGGCACAA 57.709 42.857 0.00 0.00 0.00 3.33
248 249 3.290948 AAACTAACCACTGAAGGCACA 57.709 42.857 0.00 0.00 0.00 4.57
249 250 4.386711 AGTAAACTAACCACTGAAGGCAC 58.613 43.478 0.00 0.00 0.00 5.01
250 251 4.699925 AGTAAACTAACCACTGAAGGCA 57.300 40.909 0.00 0.00 0.00 4.75
251 252 6.262496 AGAAAAGTAAACTAACCACTGAAGGC 59.738 38.462 0.00 0.00 0.00 4.35
252 253 7.803279 AGAAAAGTAAACTAACCACTGAAGG 57.197 36.000 0.00 0.00 0.00 3.46
253 254 9.503427 CAAAGAAAAGTAAACTAACCACTGAAG 57.497 33.333 0.00 0.00 0.00 3.02
254 255 8.463607 CCAAAGAAAAGTAAACTAACCACTGAA 58.536 33.333 0.00 0.00 0.00 3.02
255 256 7.415877 GCCAAAGAAAAGTAAACTAACCACTGA 60.416 37.037 0.00 0.00 0.00 3.41
256 257 6.695713 GCCAAAGAAAAGTAAACTAACCACTG 59.304 38.462 0.00 0.00 0.00 3.66
257 258 6.378848 TGCCAAAGAAAAGTAAACTAACCACT 59.621 34.615 0.00 0.00 0.00 4.00
258 259 6.566141 TGCCAAAGAAAAGTAAACTAACCAC 58.434 36.000 0.00 0.00 0.00 4.16
259 260 6.777213 TGCCAAAGAAAAGTAAACTAACCA 57.223 33.333 0.00 0.00 0.00 3.67
260 261 7.923878 TCATTGCCAAAGAAAAGTAAACTAACC 59.076 33.333 0.00 0.00 0.00 2.85
261 262 8.752254 GTCATTGCCAAAGAAAAGTAAACTAAC 58.248 33.333 0.00 0.00 0.00 2.34
262 263 8.691797 AGTCATTGCCAAAGAAAAGTAAACTAA 58.308 29.630 0.00 0.00 0.00 2.24
263 264 8.134895 CAGTCATTGCCAAAGAAAAGTAAACTA 58.865 33.333 0.00 0.00 0.00 2.24
264 265 6.980397 CAGTCATTGCCAAAGAAAAGTAAACT 59.020 34.615 0.00 0.00 0.00 2.66
265 266 6.756542 ACAGTCATTGCCAAAGAAAAGTAAAC 59.243 34.615 0.00 0.00 0.00 2.01
266 267 6.756074 CACAGTCATTGCCAAAGAAAAGTAAA 59.244 34.615 0.00 0.00 0.00 2.01
267 268 6.127479 ACACAGTCATTGCCAAAGAAAAGTAA 60.127 34.615 0.00 0.00 0.00 2.24
268 269 5.359576 ACACAGTCATTGCCAAAGAAAAGTA 59.640 36.000 0.00 0.00 0.00 2.24
269 270 4.160252 ACACAGTCATTGCCAAAGAAAAGT 59.840 37.500 0.00 0.00 0.00 2.66
270 271 4.685924 ACACAGTCATTGCCAAAGAAAAG 58.314 39.130 0.00 0.00 0.00 2.27
271 272 4.159321 TGACACAGTCATTGCCAAAGAAAA 59.841 37.500 0.00 0.00 37.67 2.29
272 273 3.698539 TGACACAGTCATTGCCAAAGAAA 59.301 39.130 0.00 0.00 37.67 2.52
273 274 3.286353 TGACACAGTCATTGCCAAAGAA 58.714 40.909 0.00 0.00 37.67 2.52
274 275 2.929641 TGACACAGTCATTGCCAAAGA 58.070 42.857 0.00 0.00 37.67 2.52
284 285 6.934083 ACACACACATAATTATGACACAGTCA 59.066 34.615 28.13 1.95 46.90 3.41
285 286 7.364522 ACACACACATAATTATGACACAGTC 57.635 36.000 28.13 0.00 37.15 3.51
286 287 7.443879 TCAACACACACATAATTATGACACAGT 59.556 33.333 28.13 17.77 37.15 3.55
287 288 7.746034 GTCAACACACACATAATTATGACACAG 59.254 37.037 28.13 17.24 37.15 3.66
288 289 7.227512 TGTCAACACACACATAATTATGACACA 59.772 33.333 28.13 14.13 39.54 3.72
289 290 7.580600 TGTCAACACACACATAATTATGACAC 58.419 34.615 28.13 12.30 39.54 3.67
290 291 7.736447 TGTCAACACACACATAATTATGACA 57.264 32.000 28.13 17.44 41.44 3.58
320 321 9.905713 ACCAAAATCGCATATATGTCCTTATAT 57.094 29.630 14.14 0.00 0.00 0.86
321 322 9.733556 AACCAAAATCGCATATATGTCCTTATA 57.266 29.630 14.14 0.00 0.00 0.98
322 323 8.635765 AACCAAAATCGCATATATGTCCTTAT 57.364 30.769 14.14 0.00 0.00 1.73
323 324 7.936847 AGAACCAAAATCGCATATATGTCCTTA 59.063 33.333 14.14 0.00 0.00 2.69
324 325 6.772716 AGAACCAAAATCGCATATATGTCCTT 59.227 34.615 14.14 2.90 0.00 3.36
325 326 6.299141 AGAACCAAAATCGCATATATGTCCT 58.701 36.000 14.14 0.00 0.00 3.85
326 327 6.560253 AGAACCAAAATCGCATATATGTCC 57.440 37.500 14.14 0.00 0.00 4.02
327 328 8.556194 TGTAAGAACCAAAATCGCATATATGTC 58.444 33.333 14.14 5.93 0.00 3.06
328 329 8.445275 TGTAAGAACCAAAATCGCATATATGT 57.555 30.769 14.14 0.00 0.00 2.29
331 332 9.772973 AGTATGTAAGAACCAAAATCGCATATA 57.227 29.630 0.00 0.00 0.00 0.86
332 333 8.677148 AGTATGTAAGAACCAAAATCGCATAT 57.323 30.769 0.00 0.00 0.00 1.78
333 334 9.772973 ATAGTATGTAAGAACCAAAATCGCATA 57.227 29.630 0.00 0.00 0.00 3.14
334 335 8.677148 ATAGTATGTAAGAACCAAAATCGCAT 57.323 30.769 0.00 0.00 0.00 4.73
335 336 9.772973 ATATAGTATGTAAGAACCAAAATCGCA 57.227 29.630 0.00 0.00 0.00 5.10
353 354 7.661437 CCAACCACACAAGCATACATATAGTAT 59.339 37.037 0.00 0.00 44.20 2.12
354 355 6.989759 CCAACCACACAAGCATACATATAGTA 59.010 38.462 0.00 0.00 37.06 1.82
355 356 5.822519 CCAACCACACAAGCATACATATAGT 59.177 40.000 0.00 0.00 0.00 2.12
356 357 5.822519 ACCAACCACACAAGCATACATATAG 59.177 40.000 0.00 0.00 0.00 1.31
357 358 5.750524 ACCAACCACACAAGCATACATATA 58.249 37.500 0.00 0.00 0.00 0.86
358 359 4.599041 ACCAACCACACAAGCATACATAT 58.401 39.130 0.00 0.00 0.00 1.78
359 360 4.027674 ACCAACCACACAAGCATACATA 57.972 40.909 0.00 0.00 0.00 2.29
360 361 2.875296 ACCAACCACACAAGCATACAT 58.125 42.857 0.00 0.00 0.00 2.29
361 362 2.356665 ACCAACCACACAAGCATACA 57.643 45.000 0.00 0.00 0.00 2.29
362 363 3.726291 AAACCAACCACACAAGCATAC 57.274 42.857 0.00 0.00 0.00 2.39
363 364 4.744795 AAAAACCAACCACACAAGCATA 57.255 36.364 0.00 0.00 0.00 3.14
364 365 3.625649 AAAAACCAACCACACAAGCAT 57.374 38.095 0.00 0.00 0.00 3.79
365 366 4.537135 TTAAAAACCAACCACACAAGCA 57.463 36.364 0.00 0.00 0.00 3.91
366 367 5.864628 TTTTAAAAACCAACCACACAAGC 57.135 34.783 0.00 0.00 0.00 4.01
367 368 7.602517 TCATTTTAAAAACCAACCACACAAG 57.397 32.000 4.44 0.00 0.00 3.16
368 369 8.043710 AGATCATTTTAAAAACCAACCACACAA 58.956 29.630 4.44 0.00 0.00 3.33
369 370 7.560368 AGATCATTTTAAAAACCAACCACACA 58.440 30.769 4.44 0.00 0.00 3.72
370 371 9.191995 CTAGATCATTTTAAAAACCAACCACAC 57.808 33.333 4.44 0.00 0.00 3.82
371 372 7.870445 GCTAGATCATTTTAAAAACCAACCACA 59.130 33.333 4.44 0.00 0.00 4.17
372 373 7.330946 GGCTAGATCATTTTAAAAACCAACCAC 59.669 37.037 4.44 0.00 0.00 4.16
373 374 7.015682 TGGCTAGATCATTTTAAAAACCAACCA 59.984 33.333 4.44 3.47 0.00 3.67
374 375 7.382898 TGGCTAGATCATTTTAAAAACCAACC 58.617 34.615 4.44 1.04 0.00 3.77
375 376 9.435688 AATGGCTAGATCATTTTAAAAACCAAC 57.564 29.630 4.44 0.00 31.49 3.77
378 379 9.249457 GCTAATGGCTAGATCATTTTAAAAACC 57.751 33.333 14.20 0.00 36.40 3.27
396 397 8.454106 CCAGAAATATGTATACAAGCTAATGGC 58.546 37.037 10.14 0.00 42.19 4.40
397 398 9.725019 TCCAGAAATATGTATACAAGCTAATGG 57.275 33.333 10.14 13.83 0.00 3.16
399 400 9.950496 CCTCCAGAAATATGTATACAAGCTAAT 57.050 33.333 10.14 0.00 0.00 1.73
400 401 7.878127 GCCTCCAGAAATATGTATACAAGCTAA 59.122 37.037 10.14 0.00 0.00 3.09
401 402 7.016170 TGCCTCCAGAAATATGTATACAAGCTA 59.984 37.037 10.14 0.00 0.00 3.32
402 403 6.183361 TGCCTCCAGAAATATGTATACAAGCT 60.183 38.462 10.14 0.00 0.00 3.74
403 404 5.997746 TGCCTCCAGAAATATGTATACAAGC 59.002 40.000 10.14 0.00 0.00 4.01
404 405 7.663081 ACATGCCTCCAGAAATATGTATACAAG 59.337 37.037 10.14 0.00 0.00 3.16
405 406 7.517320 ACATGCCTCCAGAAATATGTATACAA 58.483 34.615 10.14 0.00 0.00 2.41
406 407 7.078249 ACATGCCTCCAGAAATATGTATACA 57.922 36.000 8.27 8.27 0.00 2.29
409 410 9.672673 GTTATACATGCCTCCAGAAATATGTAT 57.327 33.333 0.00 0.00 41.73 2.29
410 411 8.880244 AGTTATACATGCCTCCAGAAATATGTA 58.120 33.333 0.00 0.00 36.02 2.29
411 412 7.749666 AGTTATACATGCCTCCAGAAATATGT 58.250 34.615 0.00 0.00 33.74 2.29
412 413 8.627208 AAGTTATACATGCCTCCAGAAATATG 57.373 34.615 0.00 0.00 0.00 1.78
413 414 9.071276 CAAAGTTATACATGCCTCCAGAAATAT 57.929 33.333 0.00 0.00 0.00 1.28
414 415 7.013274 GCAAAGTTATACATGCCTCCAGAAATA 59.987 37.037 0.00 0.00 32.73 1.40
415 416 6.183360 GCAAAGTTATACATGCCTCCAGAAAT 60.183 38.462 0.00 0.00 32.73 2.17
416 417 5.125417 GCAAAGTTATACATGCCTCCAGAAA 59.875 40.000 0.00 0.00 32.73 2.52
417 418 4.640201 GCAAAGTTATACATGCCTCCAGAA 59.360 41.667 0.00 0.00 32.73 3.02
418 419 4.199310 GCAAAGTTATACATGCCTCCAGA 58.801 43.478 0.00 0.00 32.73 3.86
419 420 4.558538 GCAAAGTTATACATGCCTCCAG 57.441 45.455 0.00 0.00 32.73 3.86
425 426 2.623416 GAGGGGGCAAAGTTATACATGC 59.377 50.000 0.00 0.00 38.06 4.06
426 427 4.170468 AGAGGGGGCAAAGTTATACATG 57.830 45.455 0.00 0.00 0.00 3.21
427 428 4.017499 ACAAGAGGGGGCAAAGTTATACAT 60.017 41.667 0.00 0.00 0.00 2.29
428 429 3.332485 ACAAGAGGGGGCAAAGTTATACA 59.668 43.478 0.00 0.00 0.00 2.29
429 430 3.964411 ACAAGAGGGGGCAAAGTTATAC 58.036 45.455 0.00 0.00 0.00 1.47
430 431 4.668138 AACAAGAGGGGGCAAAGTTATA 57.332 40.909 0.00 0.00 0.00 0.98
431 432 3.542969 AACAAGAGGGGGCAAAGTTAT 57.457 42.857 0.00 0.00 0.00 1.89
432 433 3.322191 AAACAAGAGGGGGCAAAGTTA 57.678 42.857 0.00 0.00 0.00 2.24
433 434 2.174685 AAACAAGAGGGGGCAAAGTT 57.825 45.000 0.00 0.00 0.00 2.66
434 435 2.174685 AAAACAAGAGGGGGCAAAGT 57.825 45.000 0.00 0.00 0.00 2.66
435 436 2.433970 TGAAAAACAAGAGGGGGCAAAG 59.566 45.455 0.00 0.00 0.00 2.77
436 437 2.472029 TGAAAAACAAGAGGGGGCAAA 58.528 42.857 0.00 0.00 0.00 3.68
437 438 2.166907 TGAAAAACAAGAGGGGGCAA 57.833 45.000 0.00 0.00 0.00 4.52
438 439 2.247358 GATGAAAAACAAGAGGGGGCA 58.753 47.619 0.00 0.00 0.00 5.36
439 440 1.550524 GGATGAAAAACAAGAGGGGGC 59.449 52.381 0.00 0.00 0.00 5.80
440 441 2.827921 CAGGATGAAAAACAAGAGGGGG 59.172 50.000 0.00 0.00 39.69 5.40
441 442 2.827921 CCAGGATGAAAAACAAGAGGGG 59.172 50.000 0.00 0.00 39.69 4.79
442 443 2.232208 GCCAGGATGAAAAACAAGAGGG 59.768 50.000 0.00 0.00 39.69 4.30
443 444 3.160269 AGCCAGGATGAAAAACAAGAGG 58.840 45.455 0.00 0.00 39.69 3.69
444 445 3.192212 GGAGCCAGGATGAAAAACAAGAG 59.808 47.826 0.00 0.00 39.69 2.85
445 446 3.157087 GGAGCCAGGATGAAAAACAAGA 58.843 45.455 0.00 0.00 39.69 3.02
446 447 2.095059 CGGAGCCAGGATGAAAAACAAG 60.095 50.000 0.00 0.00 39.69 3.16
447 448 1.885887 CGGAGCCAGGATGAAAAACAA 59.114 47.619 0.00 0.00 39.69 2.83
448 449 1.533625 CGGAGCCAGGATGAAAAACA 58.466 50.000 0.00 0.00 39.69 2.83
463 464 1.541310 TTGTCTGTACAGGGGCGGAG 61.541 60.000 22.48 0.00 36.83 4.63
464 465 1.122632 TTTGTCTGTACAGGGGCGGA 61.123 55.000 22.48 0.00 36.83 5.54
465 466 0.953960 GTTTGTCTGTACAGGGGCGG 60.954 60.000 22.48 0.00 36.83 6.13
466 467 0.250124 TGTTTGTCTGTACAGGGGCG 60.250 55.000 22.48 0.00 36.83 6.13
467 468 1.975660 TTGTTTGTCTGTACAGGGGC 58.024 50.000 22.48 13.25 36.83 5.80
468 469 3.315191 CACTTTGTTTGTCTGTACAGGGG 59.685 47.826 22.48 0.43 36.83 4.79
469 470 3.243068 GCACTTTGTTTGTCTGTACAGGG 60.243 47.826 22.48 0.00 36.83 4.45
470 471 3.376859 TGCACTTTGTTTGTCTGTACAGG 59.623 43.478 22.48 5.79 36.83 4.00
471 472 4.332543 TCTGCACTTTGTTTGTCTGTACAG 59.667 41.667 17.17 17.17 36.83 2.74
472 473 4.257731 TCTGCACTTTGTTTGTCTGTACA 58.742 39.130 0.00 0.00 0.00 2.90
473 474 4.875544 TCTGCACTTTGTTTGTCTGTAC 57.124 40.909 0.00 0.00 0.00 2.90
474 475 4.881273 ACATCTGCACTTTGTTTGTCTGTA 59.119 37.500 0.00 0.00 0.00 2.74
475 476 3.696051 ACATCTGCACTTTGTTTGTCTGT 59.304 39.130 0.00 0.00 0.00 3.41
476 477 4.297299 ACATCTGCACTTTGTTTGTCTG 57.703 40.909 0.00 0.00 0.00 3.51
477 478 4.440525 CCAACATCTGCACTTTGTTTGTCT 60.441 41.667 2.30 0.00 31.48 3.41
478 479 3.798337 CCAACATCTGCACTTTGTTTGTC 59.202 43.478 2.30 0.00 31.48 3.18
479 480 3.195396 ACCAACATCTGCACTTTGTTTGT 59.805 39.130 2.30 3.10 31.48 2.83
520 521 1.228124 TCTCGGTTGGGCTTGGTTG 60.228 57.895 0.00 0.00 0.00 3.77
530 531 1.425267 TTGCACGTGTGTCTCGGTTG 61.425 55.000 18.38 0.00 0.00 3.77
544 545 5.006941 ACTTTGATTTTTGTCTGCATTGCAC 59.993 36.000 7.38 0.00 33.79 4.57
564 565 4.630940 TCTTTCGACGTGTTTGGTTACTTT 59.369 37.500 0.00 0.00 0.00 2.66
582 583 2.393764 CGGTGTTTGGTTGCATCTTTC 58.606 47.619 0.00 0.00 0.00 2.62
612 619 0.228742 CGTGGTGTTTCGTTGTCTCG 59.771 55.000 0.00 0.00 0.00 4.04
630 637 1.070821 TCTCGTCAGAAATGCAAGCG 58.929 50.000 0.00 0.00 0.00 4.68
946 953 4.101077 AGCAGGAGGGGGAGGAGG 62.101 72.222 0.00 0.00 0.00 4.30
947 954 2.445654 GAGCAGGAGGGGGAGGAG 60.446 72.222 0.00 0.00 0.00 3.69
948 955 4.095400 GGAGCAGGAGGGGGAGGA 62.095 72.222 0.00 0.00 0.00 3.71
1383 1396 0.466555 AGGAATCGACGGAGAGGAGG 60.467 60.000 0.00 0.00 0.00 4.30
1746 1759 2.894879 TCAAGCACGCGCAACAGT 60.895 55.556 5.73 0.00 42.27 3.55
1974 1987 2.311854 CCCACCCTCCTCAGCCAAT 61.312 63.158 0.00 0.00 0.00 3.16
1979 1992 2.352805 GCAACCCACCCTCCTCAG 59.647 66.667 0.00 0.00 0.00 3.35
2070 2083 1.613630 AAGGTCTCCCATGGACGCT 60.614 57.895 15.22 0.44 34.82 5.07
2247 2260 4.576463 AGGTCTGTTAGTTGTGCAAAGAAG 59.424 41.667 0.00 0.00 0.00 2.85
2559 2651 0.969894 GCAGTACTGAGACTGGGTGT 59.030 55.000 27.08 0.00 45.85 4.16
2703 2854 2.096013 GCTTTTGAATCGGCTACTGGAC 59.904 50.000 0.00 0.00 0.00 4.02
2709 2860 5.123344 GGAAAGTAAGCTTTTGAATCGGCTA 59.877 40.000 3.20 0.00 44.25 3.93
2932 3083 7.148018 CGTACCAGACTATAAAACAGGGAACTA 60.148 40.741 0.00 0.00 40.21 2.24
3150 3600 1.378514 GAATGGCCATGTGACCGGT 60.379 57.895 21.63 6.92 0.00 5.28
3251 3815 8.375493 TGTTAATTTCCACTATCTCTACCTGT 57.625 34.615 0.00 0.00 0.00 4.00
3390 3954 7.821846 CCTATACTTTGGCCTATTTTGCAAAAA 59.178 33.333 27.10 15.47 31.55 1.94
3391 3955 7.327214 CCTATACTTTGGCCTATTTTGCAAAA 58.673 34.615 25.76 25.76 31.12 2.44
3392 3956 6.127196 CCCTATACTTTGGCCTATTTTGCAAA 60.127 38.462 8.05 8.05 0.00 3.68
3393 3957 5.362430 CCCTATACTTTGGCCTATTTTGCAA 59.638 40.000 3.32 0.00 0.00 4.08
3405 3971 2.981859 ACGACTGCCCTATACTTTGG 57.018 50.000 0.00 0.00 0.00 3.28
3532 4098 3.349927 CAATTCTGAGGCTCCACAATCA 58.650 45.455 12.86 0.00 0.00 2.57
3666 4233 6.589523 CAGAACATCTAGTCCTCAGTGAAAAG 59.410 42.308 0.00 0.00 0.00 2.27
3726 4293 4.343814 TCATGACATTGGCGGTATTCTCTA 59.656 41.667 0.00 0.00 0.00 2.43


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

AutoCloner maintained by Alex Coulton.