Multiple sequence alignment - TraesCS6D01G268000

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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 TraesCS6D01G268000 chr6D 100.000 2741 0 0 1 2741 377851622 377848882 0.000000e+00 5062
1 TraesCS6D01G268000 chr6B 96.014 1681 59 6 465 2143 564314693 564313019 0.000000e+00 2726
2 TraesCS6D01G268000 chr6B 92.013 601 45 3 2141 2739 641300853 641301452 0.000000e+00 841
3 TraesCS6D01G268000 chr6A 94.752 1696 60 12 470 2143 519238939 519237251 0.000000e+00 2612
4 TraesCS6D01G268000 chr6A 92.486 173 12 1 2 173 519239140 519238968 2.110000e-61 246
5 TraesCS6D01G268000 chr4B 92.013 601 45 3 2141 2739 649682313 649681714 0.000000e+00 841
6 TraesCS6D01G268000 chr4B 91.987 599 47 1 2142 2739 588581636 588582234 0.000000e+00 839
7 TraesCS6D01G268000 chr4B 91.833 600 47 2 2141 2738 81362336 81362935 0.000000e+00 835
8 TraesCS6D01G268000 chr3B 92.013 601 45 3 2141 2739 256361288 256360689 0.000000e+00 841
9 TraesCS6D01G268000 chr3B 91.833 600 46 3 2142 2739 2342253 2342851 0.000000e+00 833
10 TraesCS6D01G268000 chr2D 91.833 600 48 1 2141 2739 58736938 58736339 0.000000e+00 835
11 TraesCS6D01G268000 chr2D 96.241 266 9 1 200 464 36802955 36803220 4.190000e-118 435
12 TraesCS6D01G268000 chr2D 95.149 268 13 0 199 466 120220546 120220813 9.070000e-115 424
13 TraesCS6D01G268000 chr2D 93.985 266 16 0 199 464 499699478 499699213 1.180000e-108 403
14 TraesCS6D01G268000 chr4D 91.806 598 47 2 2143 2739 28488683 28488087 0.000000e+00 832
15 TraesCS6D01G268000 chr2B 91.514 601 50 1 2140 2739 235578913 235579513 0.000000e+00 826
16 TraesCS6D01G268000 chr3D 93.208 265 18 0 200 464 336590309 336590573 9.200000e-105 390
17 TraesCS6D01G268000 chr2A 92.910 268 19 0 200 467 24549082 24548815 9.200000e-105 390
18 TraesCS6D01G268000 chr2A 93.208 265 18 0 200 464 123414998 123415262 9.200000e-105 390
19 TraesCS6D01G268000 chr3A 92.884 267 19 0 200 466 14076928 14077194 3.310000e-104 388
20 TraesCS6D01G268000 chr7A 92.857 266 19 0 199 464 478282868 478282603 1.190000e-103 387
21 TraesCS6D01G268000 chr5A 92.857 266 19 0 201 466 117126001 117125736 1.190000e-103 387
22 TraesCS6D01G268000 chr7D 86.713 286 32 5 1077 1359 176579094 176578812 2.050000e-81 313
23 TraesCS6D01G268000 chr7B 86.364 286 33 5 1077 1359 143055682 143055400 9.530000e-80 307
24 TraesCS6D01G268000 chr7B 85.614 285 37 4 1077 1359 142866638 142866356 2.060000e-76 296
25 TraesCS6D01G268000 chr7B 84.965 286 37 5 1077 1359 142780575 142780293 4.470000e-73 285


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 TraesCS6D01G268000 chr6D 377848882 377851622 2740 True 5062 5062 100.000 1 2741 1 chr6D.!!$R1 2740
1 TraesCS6D01G268000 chr6B 564313019 564314693 1674 True 2726 2726 96.014 465 2143 1 chr6B.!!$R1 1678
2 TraesCS6D01G268000 chr6B 641300853 641301452 599 False 841 841 92.013 2141 2739 1 chr6B.!!$F1 598
3 TraesCS6D01G268000 chr6A 519237251 519239140 1889 True 1429 2612 93.619 2 2143 2 chr6A.!!$R1 2141
4 TraesCS6D01G268000 chr4B 649681714 649682313 599 True 841 841 92.013 2141 2739 1 chr4B.!!$R1 598
5 TraesCS6D01G268000 chr4B 588581636 588582234 598 False 839 839 91.987 2142 2739 1 chr4B.!!$F2 597
6 TraesCS6D01G268000 chr4B 81362336 81362935 599 False 835 835 91.833 2141 2738 1 chr4B.!!$F1 597
7 TraesCS6D01G268000 chr3B 256360689 256361288 599 True 841 841 92.013 2141 2739 1 chr3B.!!$R1 598
8 TraesCS6D01G268000 chr3B 2342253 2342851 598 False 833 833 91.833 2142 2739 1 chr3B.!!$F1 597
9 TraesCS6D01G268000 chr2D 58736339 58736938 599 True 835 835 91.833 2141 2739 1 chr2D.!!$R1 598
10 TraesCS6D01G268000 chr4D 28488087 28488683 596 True 832 832 91.806 2143 2739 1 chr4D.!!$R1 596
11 TraesCS6D01G268000 chr2B 235578913 235579513 600 False 826 826 91.514 2140 2739 1 chr2B.!!$F1 599

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
943 965 0.542232 AGTCCGTGTTCCCACTAGCT 60.542 55.0 0.0 0.0 39.55 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2385 2416 0.03392 GCAAGGGCTTCACTTTTGGG 59.966 55.0 0.0 0.0 36.96 4.12 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 1.379044 CCTTGGGGCTACCTTGCTG 60.379 63.158 0.00 0.00 41.11 4.41
57 58 7.106239 CCCTATTTTCAGGCGACTCATATAAT 58.894 38.462 0.00 0.00 40.21 1.28
63 64 6.101650 TCAGGCGACTCATATAATTGTCAT 57.898 37.500 0.00 0.00 40.21 3.06
70 71 8.292448 GCGACTCATATAATTGTCATGGATTTT 58.708 33.333 0.00 0.00 0.00 1.82
174 182 3.072211 TCCATGTATCTCCGCGTAGTAG 58.928 50.000 4.92 0.00 0.00 2.57
187 195 4.333633 GCGTAGTAGAAGTTACGTGACT 57.666 45.455 7.24 7.24 43.28 3.41
189 197 5.149977 GCGTAGTAGAAGTTACGTGACTTT 58.850 41.667 24.44 16.66 43.28 2.66
190 198 6.307155 GCGTAGTAGAAGTTACGTGACTTTA 58.693 40.000 24.44 15.82 43.28 1.85
192 200 7.163357 GCGTAGTAGAAGTTACGTGACTTTATC 59.837 40.741 24.44 13.66 43.28 1.75
193 201 8.171196 CGTAGTAGAAGTTACGTGACTTTATCA 58.829 37.037 24.44 9.35 39.84 2.15
194 202 9.831737 GTAGTAGAAGTTACGTGACTTTATCAA 57.168 33.333 24.44 9.96 39.84 2.57
195 203 8.739649 AGTAGAAGTTACGTGACTTTATCAAC 57.260 34.615 24.44 17.19 39.84 3.18
196 204 8.574737 AGTAGAAGTTACGTGACTTTATCAACT 58.425 33.333 24.44 17.70 39.84 3.16
197 205 9.831737 GTAGAAGTTACGTGACTTTATCAACTA 57.168 33.333 24.44 16.82 39.84 2.24
199 207 9.570488 AGAAGTTACGTGACTTTATCAACTATC 57.430 33.333 24.44 9.70 39.84 2.08
200 208 9.570488 GAAGTTACGTGACTTTATCAACTATCT 57.430 33.333 24.44 0.00 39.84 1.98
201 209 9.924650 AAGTTACGTGACTTTATCAACTATCTT 57.075 29.630 19.03 0.00 39.72 2.40
206 214 8.958506 ACGTGACTTTATCAACTATCTTAGACT 58.041 33.333 0.00 0.00 39.72 3.24
217 225 8.687242 TCAACTATCTTAGACTAGTCACAATGG 58.313 37.037 24.44 14.96 0.00 3.16
218 226 7.589958 ACTATCTTAGACTAGTCACAATGGG 57.410 40.000 24.44 11.58 0.00 4.00
219 227 7.126733 ACTATCTTAGACTAGTCACAATGGGT 58.873 38.462 24.44 12.16 0.00 4.51
220 228 8.280084 ACTATCTTAGACTAGTCACAATGGGTA 58.720 37.037 24.44 3.05 0.00 3.69
221 229 7.589958 ATCTTAGACTAGTCACAATGGGTAG 57.410 40.000 24.44 5.67 0.00 3.18
222 230 6.491383 TCTTAGACTAGTCACAATGGGTAGT 58.509 40.000 24.44 2.07 0.00 2.73
223 231 7.636579 TCTTAGACTAGTCACAATGGGTAGTA 58.363 38.462 24.44 1.11 0.00 1.82
224 232 8.111545 TCTTAGACTAGTCACAATGGGTAGTAA 58.888 37.037 24.44 8.71 0.00 2.24
225 233 6.527057 AGACTAGTCACAATGGGTAGTAAC 57.473 41.667 24.44 0.00 0.00 2.50
226 234 6.254522 AGACTAGTCACAATGGGTAGTAACT 58.745 40.000 24.44 0.00 0.00 2.24
227 235 6.724905 AGACTAGTCACAATGGGTAGTAACTT 59.275 38.462 24.44 0.00 0.00 2.66
228 236 7.892241 AGACTAGTCACAATGGGTAGTAACTTA 59.108 37.037 24.44 0.00 0.00 2.24
229 237 8.064336 ACTAGTCACAATGGGTAGTAACTTAG 57.936 38.462 0.00 0.00 0.00 2.18
230 238 7.892241 ACTAGTCACAATGGGTAGTAACTTAGA 59.108 37.037 0.00 0.00 0.00 2.10
231 239 6.932947 AGTCACAATGGGTAGTAACTTAGAC 58.067 40.000 0.00 0.00 0.00 2.59
232 240 6.724905 AGTCACAATGGGTAGTAACTTAGACT 59.275 38.462 0.00 0.00 0.00 3.24
233 241 7.892241 AGTCACAATGGGTAGTAACTTAGACTA 59.108 37.037 0.00 0.00 0.00 2.59
234 242 8.189460 GTCACAATGGGTAGTAACTTAGACTAG 58.811 40.741 0.00 0.00 30.08 2.57
235 243 7.892241 TCACAATGGGTAGTAACTTAGACTAGT 59.108 37.037 0.00 0.00 30.08 2.57
236 244 9.182214 CACAATGGGTAGTAACTTAGACTAGTA 57.818 37.037 0.00 0.00 30.08 1.82
237 245 9.759473 ACAATGGGTAGTAACTTAGACTAGTAA 57.241 33.333 0.00 0.00 30.08 2.24
239 247 9.759473 AATGGGTAGTAACTTAGACTAGTAACA 57.241 33.333 0.00 0.00 30.08 2.41
240 248 9.933240 ATGGGTAGTAACTTAGACTAGTAACAT 57.067 33.333 0.00 0.00 30.08 2.71
241 249 9.182214 TGGGTAGTAACTTAGACTAGTAACATG 57.818 37.037 0.00 0.00 30.08 3.21
242 250 8.134261 GGGTAGTAACTTAGACTAGTAACATGC 58.866 40.741 0.00 0.00 30.08 4.06
243 251 8.680903 GGTAGTAACTTAGACTAGTAACATGCA 58.319 37.037 0.00 0.00 30.08 3.96
259 267 5.887214 ACATGCATATGTTACTACCTCCA 57.113 39.130 0.00 0.00 45.01 3.86
260 268 5.611374 ACATGCATATGTTACTACCTCCAC 58.389 41.667 0.00 0.00 45.01 4.02
261 269 5.130311 ACATGCATATGTTACTACCTCCACA 59.870 40.000 0.00 0.00 45.01 4.17
262 270 5.685520 TGCATATGTTACTACCTCCACAA 57.314 39.130 4.29 0.00 0.00 3.33
263 271 6.247229 TGCATATGTTACTACCTCCACAAT 57.753 37.500 4.29 0.00 0.00 2.71
264 272 6.054941 TGCATATGTTACTACCTCCACAATG 58.945 40.000 4.29 0.00 0.00 2.82
265 273 5.470098 GCATATGTTACTACCTCCACAATGG 59.530 44.000 4.29 0.00 39.43 3.16
266 274 3.992943 TGTTACTACCTCCACAATGGG 57.007 47.619 0.00 0.00 38.32 4.00
267 275 3.253220 TGTTACTACCTCCACAATGGGT 58.747 45.455 0.00 0.00 38.32 4.51
268 276 4.427637 TGTTACTACCTCCACAATGGGTA 58.572 43.478 0.00 0.00 38.32 3.69
273 281 3.994931 ACCTCCACAATGGGTAGTAAC 57.005 47.619 0.00 0.00 38.32 2.50
274 282 3.253220 ACCTCCACAATGGGTAGTAACA 58.747 45.455 0.00 0.00 38.32 2.41
275 283 3.850173 ACCTCCACAATGGGTAGTAACAT 59.150 43.478 0.00 0.00 38.32 2.71
276 284 5.034200 ACCTCCACAATGGGTAGTAACATA 58.966 41.667 0.00 0.00 38.32 2.29
277 285 5.670361 ACCTCCACAATGGGTAGTAACATAT 59.330 40.000 0.00 0.00 38.32 1.78
278 286 5.997746 CCTCCACAATGGGTAGTAACATATG 59.002 44.000 0.00 0.00 38.32 1.78
279 287 6.409234 CCTCCACAATGGGTAGTAACATATGT 60.409 42.308 1.41 1.41 38.32 2.29
280 288 6.353323 TCCACAATGGGTAGTAACATATGTG 58.647 40.000 9.63 8.65 38.32 3.21
281 289 6.069905 TCCACAATGGGTAGTAACATATGTGT 60.070 38.462 9.63 2.63 38.01 3.72
282 290 6.601613 CCACAATGGGTAGTAACATATGTGTT 59.398 38.462 9.63 12.73 41.76 3.32
283 291 7.415095 CCACAATGGGTAGTAACATATGTGTTG 60.415 40.741 17.19 6.43 40.34 3.33
293 301 5.648178 AACATATGTGTTGTGTCATGCAT 57.352 34.783 9.63 0.00 46.43 3.96
294 302 5.239359 ACATATGTGTTGTGTCATGCATC 57.761 39.130 7.78 0.00 34.01 3.91
295 303 4.701171 ACATATGTGTTGTGTCATGCATCA 59.299 37.500 7.78 0.00 34.01 3.07
296 304 3.564235 ATGTGTTGTGTCATGCATCAC 57.436 42.857 10.76 10.76 35.43 3.06
297 305 2.574450 TGTGTTGTGTCATGCATCACT 58.426 42.857 16.78 0.00 35.82 3.41
298 306 2.950975 TGTGTTGTGTCATGCATCACTT 59.049 40.909 16.78 0.00 35.82 3.16
299 307 3.380954 TGTGTTGTGTCATGCATCACTTT 59.619 39.130 16.78 0.00 35.82 2.66
300 308 4.578105 TGTGTTGTGTCATGCATCACTTTA 59.422 37.500 16.78 3.63 35.82 1.85
301 309 5.241285 TGTGTTGTGTCATGCATCACTTTAT 59.759 36.000 16.78 0.00 35.82 1.40
302 310 6.151691 GTGTTGTGTCATGCATCACTTTATT 58.848 36.000 16.78 0.00 35.82 1.40
303 311 6.642131 GTGTTGTGTCATGCATCACTTTATTT 59.358 34.615 16.78 0.00 35.82 1.40
304 312 7.807433 GTGTTGTGTCATGCATCACTTTATTTA 59.193 33.333 16.78 0.00 35.82 1.40
305 313 8.522003 TGTTGTGTCATGCATCACTTTATTTAT 58.478 29.630 16.78 0.00 35.82 1.40
306 314 9.357652 GTTGTGTCATGCATCACTTTATTTATT 57.642 29.630 16.78 0.00 35.82 1.40
309 317 9.158364 GTGTCATGCATCACTTTATTTATTACG 57.842 33.333 1.37 0.00 0.00 3.18
310 318 8.888716 TGTCATGCATCACTTTATTTATTACGT 58.111 29.630 1.37 0.00 0.00 3.57
311 319 9.716507 GTCATGCATCACTTTATTTATTACGTT 57.283 29.630 0.00 0.00 0.00 3.99
312 320 9.715123 TCATGCATCACTTTATTTATTACGTTG 57.285 29.630 0.00 0.00 0.00 4.10
313 321 9.502145 CATGCATCACTTTATTTATTACGTTGT 57.498 29.630 0.00 0.00 0.00 3.32
330 338 6.771188 ACGTTGTAGACTCATCTTTTCTTG 57.229 37.500 0.00 0.00 36.29 3.02
331 339 6.513180 ACGTTGTAGACTCATCTTTTCTTGA 58.487 36.000 0.00 0.00 36.29 3.02
332 340 7.155328 ACGTTGTAGACTCATCTTTTCTTGAT 58.845 34.615 0.00 0.00 36.29 2.57
333 341 8.304596 ACGTTGTAGACTCATCTTTTCTTGATA 58.695 33.333 0.00 0.00 36.29 2.15
334 342 9.307121 CGTTGTAGACTCATCTTTTCTTGATAT 57.693 33.333 0.00 0.00 36.29 1.63
337 345 9.591792 TGTAGACTCATCTTTTCTTGATATGTG 57.408 33.333 0.00 0.00 36.29 3.21
338 346 9.593134 GTAGACTCATCTTTTCTTGATATGTGT 57.407 33.333 0.00 0.00 36.29 3.72
339 347 8.489990 AGACTCATCTTTTCTTGATATGTGTG 57.510 34.615 0.00 0.00 0.00 3.82
340 348 8.316946 AGACTCATCTTTTCTTGATATGTGTGA 58.683 33.333 0.00 0.00 0.00 3.58
341 349 9.107177 GACTCATCTTTTCTTGATATGTGTGAT 57.893 33.333 0.00 0.00 0.00 3.06
342 350 8.890718 ACTCATCTTTTCTTGATATGTGTGATG 58.109 33.333 0.00 0.00 0.00 3.07
343 351 8.797350 TCATCTTTTCTTGATATGTGTGATGT 57.203 30.769 0.00 0.00 32.21 3.06
344 352 9.234827 TCATCTTTTCTTGATATGTGTGATGTT 57.765 29.630 0.00 0.00 32.21 2.71
347 355 9.500785 TCTTTTCTTGATATGTGTGATGTTACA 57.499 29.630 0.00 0.00 0.00 2.41
348 356 9.764870 CTTTTCTTGATATGTGTGATGTTACAG 57.235 33.333 0.00 0.00 0.00 2.74
349 357 8.846943 TTTCTTGATATGTGTGATGTTACAGT 57.153 30.769 0.00 0.00 0.00 3.55
350 358 9.936759 TTTCTTGATATGTGTGATGTTACAGTA 57.063 29.630 0.00 0.00 0.00 2.74
351 359 9.936759 TTCTTGATATGTGTGATGTTACAGTAA 57.063 29.630 0.00 0.00 0.00 2.24
352 360 9.366216 TCTTGATATGTGTGATGTTACAGTAAC 57.634 33.333 15.58 15.58 39.11 2.50
353 361 9.371136 CTTGATATGTGTGATGTTACAGTAACT 57.629 33.333 21.56 9.41 39.38 2.24
356 364 8.873215 ATATGTGTGATGTTACAGTAACTAGC 57.127 34.615 21.56 12.59 39.38 3.42
357 365 6.340962 TGTGTGATGTTACAGTAACTAGCT 57.659 37.500 21.56 6.57 39.38 3.32
358 366 7.457024 TGTGTGATGTTACAGTAACTAGCTA 57.543 36.000 21.56 4.25 39.38 3.32
359 367 8.063200 TGTGTGATGTTACAGTAACTAGCTAT 57.937 34.615 21.56 8.59 39.38 2.97
360 368 7.973944 TGTGTGATGTTACAGTAACTAGCTATG 59.026 37.037 21.56 0.00 39.38 2.23
361 369 7.974501 GTGTGATGTTACAGTAACTAGCTATGT 59.025 37.037 21.56 0.00 39.38 2.29
362 370 8.528643 TGTGATGTTACAGTAACTAGCTATGTT 58.471 33.333 21.56 7.75 39.38 2.71
371 379 7.653713 ACAGTAACTAGCTATGTTATCACATGC 59.346 37.037 14.69 4.91 43.92 4.06
372 380 7.116948 CAGTAACTAGCTATGTTATCACATGCC 59.883 40.741 14.69 0.00 43.92 4.40
373 381 5.815233 ACTAGCTATGTTATCACATGCCT 57.185 39.130 2.68 2.02 43.92 4.75
374 382 5.788450 ACTAGCTATGTTATCACATGCCTC 58.212 41.667 2.68 0.00 43.92 4.70
375 383 4.970860 AGCTATGTTATCACATGCCTCT 57.029 40.909 2.68 0.00 43.92 3.69
376 384 4.892433 AGCTATGTTATCACATGCCTCTC 58.108 43.478 2.68 0.00 43.92 3.20
377 385 4.592351 AGCTATGTTATCACATGCCTCTCT 59.408 41.667 2.68 0.00 43.92 3.10
378 386 5.777223 AGCTATGTTATCACATGCCTCTCTA 59.223 40.000 2.68 0.00 43.92 2.43
379 387 6.440010 AGCTATGTTATCACATGCCTCTCTAT 59.560 38.462 2.68 0.00 43.92 1.98
380 388 6.756074 GCTATGTTATCACATGCCTCTCTATC 59.244 42.308 2.68 0.00 43.92 2.08
381 389 6.931790 ATGTTATCACATGCCTCTCTATCT 57.068 37.500 0.00 0.00 42.46 1.98
382 390 6.737720 TGTTATCACATGCCTCTCTATCTT 57.262 37.500 0.00 0.00 0.00 2.40
383 391 6.753180 TGTTATCACATGCCTCTCTATCTTC 58.247 40.000 0.00 0.00 0.00 2.87
384 392 6.324770 TGTTATCACATGCCTCTCTATCTTCA 59.675 38.462 0.00 0.00 0.00 3.02
385 393 7.015974 TGTTATCACATGCCTCTCTATCTTCAT 59.984 37.037 0.00 0.00 0.00 2.57
386 394 5.883685 TCACATGCCTCTCTATCTTCATT 57.116 39.130 0.00 0.00 0.00 2.57
387 395 6.983906 TCACATGCCTCTCTATCTTCATTA 57.016 37.500 0.00 0.00 0.00 1.90
388 396 7.365497 TCACATGCCTCTCTATCTTCATTAA 57.635 36.000 0.00 0.00 0.00 1.40
389 397 7.971201 TCACATGCCTCTCTATCTTCATTAAT 58.029 34.615 0.00 0.00 0.00 1.40
390 398 8.435187 TCACATGCCTCTCTATCTTCATTAATT 58.565 33.333 0.00 0.00 0.00 1.40
391 399 9.716531 CACATGCCTCTCTATCTTCATTAATTA 57.283 33.333 0.00 0.00 0.00 1.40
392 400 9.717942 ACATGCCTCTCTATCTTCATTAATTAC 57.282 33.333 0.00 0.00 0.00 1.89
393 401 9.716531 CATGCCTCTCTATCTTCATTAATTACA 57.283 33.333 0.00 0.00 0.00 2.41
395 403 9.716531 TGCCTCTCTATCTTCATTAATTACATG 57.283 33.333 0.00 0.00 0.00 3.21
396 404 9.717942 GCCTCTCTATCTTCATTAATTACATGT 57.282 33.333 2.69 2.69 0.00 3.21
415 423 7.886629 ACATGTCACATTATCTATTTTGCCT 57.113 32.000 0.00 0.00 0.00 4.75
416 424 8.978874 ACATGTCACATTATCTATTTTGCCTA 57.021 30.769 0.00 0.00 0.00 3.93
417 425 9.060347 ACATGTCACATTATCTATTTTGCCTAG 57.940 33.333 0.00 0.00 0.00 3.02
418 426 9.276590 CATGTCACATTATCTATTTTGCCTAGA 57.723 33.333 0.00 0.00 0.00 2.43
429 437 8.893219 TCTATTTTGCCTAGATAAGTGTGATG 57.107 34.615 0.00 0.00 0.00 3.07
430 438 8.486210 TCTATTTTGCCTAGATAAGTGTGATGT 58.514 33.333 0.00 0.00 0.00 3.06
431 439 7.944729 ATTTTGCCTAGATAAGTGTGATGTT 57.055 32.000 0.00 0.00 0.00 2.71
433 441 9.632638 ATTTTGCCTAGATAAGTGTGATGTTAT 57.367 29.630 0.00 0.00 0.00 1.89
434 442 8.662781 TTTGCCTAGATAAGTGTGATGTTATC 57.337 34.615 0.00 0.00 36.34 1.75
435 443 7.360113 TGCCTAGATAAGTGTGATGTTATCA 57.640 36.000 0.00 0.00 37.88 2.15
450 458 8.084985 TGATGTTATCACCTATGTTACTTCCA 57.915 34.615 0.00 0.00 33.59 3.53
451 459 8.713971 TGATGTTATCACCTATGTTACTTCCAT 58.286 33.333 0.00 0.00 33.59 3.41
452 460 9.561069 GATGTTATCACCTATGTTACTTCCATT 57.439 33.333 0.00 0.00 0.00 3.16
453 461 8.731275 TGTTATCACCTATGTTACTTCCATTG 57.269 34.615 0.00 0.00 0.00 2.82
454 462 8.325787 TGTTATCACCTATGTTACTTCCATTGT 58.674 33.333 0.00 0.00 0.00 2.71
455 463 8.612619 GTTATCACCTATGTTACTTCCATTGTG 58.387 37.037 0.00 0.00 0.00 3.33
456 464 5.496556 TCACCTATGTTACTTCCATTGTGG 58.503 41.667 0.00 0.00 39.43 4.17
457 465 4.640201 CACCTATGTTACTTCCATTGTGGG 59.360 45.833 0.00 0.00 38.32 4.61
458 466 4.291249 ACCTATGTTACTTCCATTGTGGGT 59.709 41.667 0.00 0.00 38.32 4.51
459 467 5.489637 ACCTATGTTACTTCCATTGTGGGTA 59.510 40.000 0.00 0.00 38.32 3.69
460 468 6.055588 CCTATGTTACTTCCATTGTGGGTAG 58.944 44.000 0.00 0.00 38.32 3.18
461 469 4.986054 TGTTACTTCCATTGTGGGTAGT 57.014 40.909 8.82 8.82 38.32 2.73
462 470 4.901868 TGTTACTTCCATTGTGGGTAGTC 58.098 43.478 7.59 0.00 38.32 2.59
463 471 4.595781 TGTTACTTCCATTGTGGGTAGTCT 59.404 41.667 7.59 0.00 38.32 3.24
467 475 8.480501 GTTACTTCCATTGTGGGTAGTCTTATA 58.519 37.037 7.59 0.00 38.32 0.98
491 499 1.068434 GAGAGCTAGCTGCACCCTAAG 59.932 57.143 24.99 0.00 45.94 2.18
496 504 2.365617 GCTAGCTGCACCCTAAGTATCA 59.634 50.000 7.70 0.00 42.31 2.15
537 546 0.730265 TGCATCCAACGGCGATAAAC 59.270 50.000 16.62 0.00 0.00 2.01
623 632 4.688021 GTGTGTTGGGAAATAGCAAAACA 58.312 39.130 0.00 0.00 0.00 2.83
648 657 1.339727 GGTTGGTCACTCCGGCTTTAT 60.340 52.381 0.00 0.00 39.52 1.40
649 658 2.093341 GGTTGGTCACTCCGGCTTTATA 60.093 50.000 0.00 0.00 39.52 0.98
650 659 3.195661 GTTGGTCACTCCGGCTTTATAG 58.804 50.000 0.00 0.00 39.52 1.31
651 660 2.463752 TGGTCACTCCGGCTTTATAGT 58.536 47.619 0.00 0.00 39.52 2.12
728 742 2.324330 CGCGGCATCACCAGTTCAA 61.324 57.895 0.00 0.00 39.03 2.69
743 757 4.946157 CCAGTTCAAAGATGGAGCAGTAAT 59.054 41.667 0.00 0.00 36.09 1.89
917 939 3.108289 CACACACCAGAGCGAGCG 61.108 66.667 0.00 0.00 0.00 5.03
927 949 2.431601 AGCGAGCGAGCAACAGTC 60.432 61.111 9.01 0.00 40.15 3.51
943 965 0.542232 AGTCCGTGTTCCCACTAGCT 60.542 55.000 0.00 0.00 39.55 3.32
958 980 2.611292 ACTAGCTTAGGTACTACGTGCG 59.389 50.000 0.00 0.00 42.67 5.34
976 998 2.453638 GCGAACAACCCTAGCTCGC 61.454 63.158 0.00 0.00 46.69 5.03
995 1017 0.830648 CCCGATCAGGTTTAGCCAGA 59.169 55.000 0.00 0.00 40.61 3.86
1686 1708 2.129146 CAATGGCCATGGCGGTGAT 61.129 57.895 29.90 15.86 43.06 3.06
1742 1764 1.200948 GACGTTCGGGTACAAGTAGCT 59.799 52.381 9.04 0.00 34.26 3.32
1749 1774 6.205071 GTTCGGGTACAAGTAGCTATCTAAC 58.795 44.000 9.04 0.00 34.26 2.34
1759 1784 1.962100 AGCTATCTAACCCCTGCGTAC 59.038 52.381 0.00 0.00 0.00 3.67
1793 1818 2.202623 AGCGCGTGCAGTAGCTAC 60.203 61.111 24.79 16.43 46.23 3.58
1794 1819 2.506217 GCGCGTGCAGTAGCTACA 60.506 61.111 25.28 2.32 42.74 2.74
1803 1828 2.688446 TGCAGTAGCTACAATCTAGCGT 59.312 45.455 25.28 0.00 44.73 5.07
1858 1887 4.772886 TCTAGCCCCTTTTATCCAGTTC 57.227 45.455 0.00 0.00 0.00 3.01
1908 1937 2.221055 CCAGTTTCACTGTTCGTGTAGC 59.779 50.000 3.30 0.00 44.50 3.58
1978 2007 5.046910 TCTAAATTTAGCTGTGCTGCAAC 57.953 39.130 18.68 0.00 40.10 4.17
2046 2076 1.076332 CGAAGGGATCAAACCGTCAC 58.924 55.000 0.00 0.00 36.46 3.67
2062 2092 3.185594 CCGTCACGCAAATTCAAAGACTA 59.814 43.478 0.00 0.00 0.00 2.59
2118 2149 1.097547 CCTCGCAGCTGGGGTTATTG 61.098 60.000 28.30 12.56 0.00 1.90
2275 2306 2.809861 AATGCCTGTCACCTGCCTCG 62.810 60.000 0.00 0.00 0.00 4.63
2295 2326 2.124983 CACCACCGCAGCAGCTAT 60.125 61.111 0.00 0.00 39.10 2.97
2305 2336 2.094258 CGCAGCAGCTATCGAAGAAAAA 59.906 45.455 9.92 0.00 38.56 1.94
2334 2365 2.526873 ACCACCTCACCCGAGCTT 60.527 61.111 0.00 0.00 38.00 3.74
2370 2401 3.679980 CGCTAATATGCAGCTTTACGGAT 59.320 43.478 7.71 0.00 36.86 4.18
2385 2416 0.462759 CGGATCTTCAAGGTGGCTCC 60.463 60.000 0.00 0.00 0.00 4.70
2430 2461 1.153168 CGAATCAGACCGGGGCAAT 60.153 57.895 6.32 0.00 0.00 3.56
2462 2493 1.410517 GCCATCGAACTCCAGATCTGA 59.589 52.381 24.62 9.26 0.00 3.27
2463 2494 2.159043 GCCATCGAACTCCAGATCTGAA 60.159 50.000 24.62 1.92 0.00 3.02
2481 2512 0.399075 AAACCCCACCACGACTAAGG 59.601 55.000 0.00 0.00 0.00 2.69
2555 2587 0.526211 CCGTCTTCCAGATGTCGTCA 59.474 55.000 0.00 0.00 29.27 4.35
2720 2752 4.482990 ACAGACTGGTTTCCAAATCCATT 58.517 39.130 7.51 0.00 30.80 3.16
2739 2771 2.779429 TCCCAACCATAGGACCGATA 57.221 50.000 0.00 0.00 0.00 2.92
2740 2772 2.605257 TCCCAACCATAGGACCGATAG 58.395 52.381 0.00 0.00 0.00 2.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 4.145052 CCTGAAAATAGGGTTGGGATAGC 58.855 47.826 0.00 0.00 34.06 2.97
87 88 7.791029 AGGTTGGATGTCACTTTGTTAATTTT 58.209 30.769 0.00 0.00 0.00 1.82
88 89 7.287696 AGAGGTTGGATGTCACTTTGTTAATTT 59.712 33.333 0.00 0.00 0.00 1.82
107 108 7.921786 TTGATTAATCAAGGTGTAGAGGTTG 57.078 36.000 23.86 0.00 41.51 3.77
174 182 9.570488 AGATAGTTGATAAAGTCACGTAACTTC 57.430 33.333 4.14 0.00 38.52 3.01
192 200 7.923344 CCCATTGTGACTAGTCTAAGATAGTTG 59.077 40.741 23.01 11.60 32.43 3.16
193 201 7.620094 ACCCATTGTGACTAGTCTAAGATAGTT 59.380 37.037 23.01 1.31 32.43 2.24
194 202 7.126733 ACCCATTGTGACTAGTCTAAGATAGT 58.873 38.462 23.01 10.75 34.96 2.12
195 203 7.589958 ACCCATTGTGACTAGTCTAAGATAG 57.410 40.000 23.01 10.17 0.00 2.08
196 204 8.280084 ACTACCCATTGTGACTAGTCTAAGATA 58.720 37.037 23.01 0.00 0.00 1.98
197 205 7.126733 ACTACCCATTGTGACTAGTCTAAGAT 58.873 38.462 23.01 9.51 0.00 2.40
198 206 6.491383 ACTACCCATTGTGACTAGTCTAAGA 58.509 40.000 23.01 7.69 0.00 2.10
199 207 6.777213 ACTACCCATTGTGACTAGTCTAAG 57.223 41.667 23.01 8.93 0.00 2.18
200 208 7.892241 AGTTACTACCCATTGTGACTAGTCTAA 59.108 37.037 23.01 17.50 32.48 2.10
201 209 7.408543 AGTTACTACCCATTGTGACTAGTCTA 58.591 38.462 23.01 10.02 32.48 2.59
202 210 6.254522 AGTTACTACCCATTGTGACTAGTCT 58.745 40.000 23.01 0.19 32.48 3.24
203 211 6.527057 AGTTACTACCCATTGTGACTAGTC 57.473 41.667 16.32 16.32 32.48 2.59
204 212 6.930068 AAGTTACTACCCATTGTGACTAGT 57.070 37.500 0.00 0.00 32.96 2.57
205 213 8.189460 GTCTAAGTTACTACCCATTGTGACTAG 58.811 40.741 0.00 0.00 32.96 2.57
206 214 7.892241 AGTCTAAGTTACTACCCATTGTGACTA 59.108 37.037 0.00 0.00 32.96 2.59
207 215 6.724905 AGTCTAAGTTACTACCCATTGTGACT 59.275 38.462 0.00 0.00 35.08 3.41
208 216 6.932947 AGTCTAAGTTACTACCCATTGTGAC 58.067 40.000 0.00 0.00 0.00 3.67
209 217 7.892241 ACTAGTCTAAGTTACTACCCATTGTGA 59.108 37.037 0.00 0.00 0.00 3.58
210 218 8.064336 ACTAGTCTAAGTTACTACCCATTGTG 57.936 38.462 0.00 0.00 0.00 3.33
211 219 9.759473 TTACTAGTCTAAGTTACTACCCATTGT 57.241 33.333 0.00 0.00 0.00 2.71
213 221 9.759473 TGTTACTAGTCTAAGTTACTACCCATT 57.241 33.333 0.00 0.00 31.82 3.16
214 222 9.933240 ATGTTACTAGTCTAAGTTACTACCCAT 57.067 33.333 0.00 0.00 31.82 4.00
215 223 9.182214 CATGTTACTAGTCTAAGTTACTACCCA 57.818 37.037 0.00 0.00 31.82 4.51
216 224 8.134261 GCATGTTACTAGTCTAAGTTACTACCC 58.866 40.741 0.00 0.00 31.82 3.69
217 225 8.680903 TGCATGTTACTAGTCTAAGTTACTACC 58.319 37.037 0.00 0.00 31.82 3.18
238 246 5.610398 TGTGGAGGTAGTAACATATGCATG 58.390 41.667 10.16 0.00 38.21 4.06
239 247 5.887214 TGTGGAGGTAGTAACATATGCAT 57.113 39.130 3.79 3.79 0.00 3.96
240 248 5.685520 TTGTGGAGGTAGTAACATATGCA 57.314 39.130 1.58 0.00 0.00 3.96
241 249 5.470098 CCATTGTGGAGGTAGTAACATATGC 59.530 44.000 1.58 0.00 40.96 3.14
242 250 5.997746 CCCATTGTGGAGGTAGTAACATATG 59.002 44.000 0.00 0.00 40.96 1.78
243 251 5.670361 ACCCATTGTGGAGGTAGTAACATAT 59.330 40.000 0.00 0.00 40.96 1.78
244 252 5.034200 ACCCATTGTGGAGGTAGTAACATA 58.966 41.667 0.00 0.00 40.96 2.29
245 253 3.850173 ACCCATTGTGGAGGTAGTAACAT 59.150 43.478 0.00 0.00 40.96 2.71
246 254 3.253220 ACCCATTGTGGAGGTAGTAACA 58.747 45.455 0.00 0.00 40.96 2.41
247 255 3.994931 ACCCATTGTGGAGGTAGTAAC 57.005 47.619 0.00 0.00 40.96 2.50
252 260 4.427637 TGTTACTACCCATTGTGGAGGTA 58.572 43.478 0.00 0.00 40.96 3.08
253 261 3.253220 TGTTACTACCCATTGTGGAGGT 58.747 45.455 0.00 0.00 40.96 3.85
254 262 3.992943 TGTTACTACCCATTGTGGAGG 57.007 47.619 0.00 0.00 40.96 4.30
255 263 6.483307 CACATATGTTACTACCCATTGTGGAG 59.517 42.308 5.37 0.00 40.96 3.86
256 264 6.069905 ACACATATGTTACTACCCATTGTGGA 60.070 38.462 5.37 0.00 35.85 4.02
257 265 6.119536 ACACATATGTTACTACCCATTGTGG 58.880 40.000 5.37 0.00 34.46 4.17
272 280 4.701171 TGATGCATGACACAACACATATGT 59.299 37.500 2.46 1.41 42.46 2.29
273 281 5.032220 GTGATGCATGACACAACACATATG 58.968 41.667 11.72 0.00 37.05 1.78
274 282 4.945543 AGTGATGCATGACACAACACATAT 59.054 37.500 18.76 0.00 39.18 1.78
275 283 4.325972 AGTGATGCATGACACAACACATA 58.674 39.130 18.76 0.00 39.18 2.29
276 284 3.151554 AGTGATGCATGACACAACACAT 58.848 40.909 18.76 0.00 39.18 3.21
277 285 2.574450 AGTGATGCATGACACAACACA 58.426 42.857 18.76 0.00 39.18 3.72
278 286 3.631145 AAGTGATGCATGACACAACAC 57.369 42.857 18.76 11.21 39.18 3.32
279 287 5.963176 ATAAAGTGATGCATGACACAACA 57.037 34.783 18.76 0.00 39.18 3.33
280 288 8.915871 ATAAATAAAGTGATGCATGACACAAC 57.084 30.769 18.76 0.00 39.18 3.32
283 291 9.158364 CGTAATAAATAAAGTGATGCATGACAC 57.842 33.333 18.76 14.04 37.30 3.67
284 292 8.888716 ACGTAATAAATAAAGTGATGCATGACA 58.111 29.630 18.76 1.11 0.00 3.58
285 293 9.716507 AACGTAATAAATAAAGTGATGCATGAC 57.283 29.630 8.39 8.39 0.00 3.06
286 294 9.715123 CAACGTAATAAATAAAGTGATGCATGA 57.285 29.630 2.46 0.00 0.00 3.07
287 295 9.502145 ACAACGTAATAAATAAAGTGATGCATG 57.498 29.630 2.46 0.00 0.00 4.06
304 312 8.926710 CAAGAAAAGATGAGTCTACAACGTAAT 58.073 33.333 0.00 0.00 33.30 1.89
305 313 8.139350 TCAAGAAAAGATGAGTCTACAACGTAA 58.861 33.333 0.00 0.00 33.30 3.18
306 314 7.654568 TCAAGAAAAGATGAGTCTACAACGTA 58.345 34.615 0.00 0.00 33.30 3.57
307 315 6.513180 TCAAGAAAAGATGAGTCTACAACGT 58.487 36.000 0.00 0.00 33.30 3.99
308 316 7.588143 ATCAAGAAAAGATGAGTCTACAACG 57.412 36.000 0.00 0.00 33.30 4.10
311 319 9.591792 CACATATCAAGAAAAGATGAGTCTACA 57.408 33.333 0.00 0.00 33.30 2.74
312 320 9.593134 ACACATATCAAGAAAAGATGAGTCTAC 57.407 33.333 0.00 0.00 33.30 2.59
313 321 9.591792 CACACATATCAAGAAAAGATGAGTCTA 57.408 33.333 0.00 0.00 33.30 2.59
314 322 8.316946 TCACACATATCAAGAAAAGATGAGTCT 58.683 33.333 0.00 0.00 35.82 3.24
315 323 8.484641 TCACACATATCAAGAAAAGATGAGTC 57.515 34.615 0.00 0.00 0.00 3.36
316 324 8.890718 CATCACACATATCAAGAAAAGATGAGT 58.109 33.333 0.00 0.00 32.98 3.41
317 325 8.890718 ACATCACACATATCAAGAAAAGATGAG 58.109 33.333 0.00 0.00 34.73 2.90
318 326 8.797350 ACATCACACATATCAAGAAAAGATGA 57.203 30.769 0.00 0.00 34.73 2.92
321 329 9.500785 TGTAACATCACACATATCAAGAAAAGA 57.499 29.630 0.00 0.00 0.00 2.52
322 330 9.764870 CTGTAACATCACACATATCAAGAAAAG 57.235 33.333 0.00 0.00 0.00 2.27
323 331 9.283768 ACTGTAACATCACACATATCAAGAAAA 57.716 29.630 0.00 0.00 0.00 2.29
324 332 8.846943 ACTGTAACATCACACATATCAAGAAA 57.153 30.769 0.00 0.00 0.00 2.52
325 333 9.936759 TTACTGTAACATCACACATATCAAGAA 57.063 29.630 0.00 0.00 0.00 2.52
326 334 9.366216 GTTACTGTAACATCACACATATCAAGA 57.634 33.333 22.30 0.00 38.52 3.02
327 335 9.371136 AGTTACTGTAACATCACACATATCAAG 57.629 33.333 27.12 0.00 41.07 3.02
330 338 8.969267 GCTAGTTACTGTAACATCACACATATC 58.031 37.037 27.12 5.73 41.07 1.63
331 339 8.696374 AGCTAGTTACTGTAACATCACACATAT 58.304 33.333 27.12 9.43 41.07 1.78
332 340 8.063200 AGCTAGTTACTGTAACATCACACATA 57.937 34.615 27.12 11.12 41.07 2.29
333 341 6.936279 AGCTAGTTACTGTAACATCACACAT 58.064 36.000 27.12 10.64 41.07 3.21
334 342 6.340962 AGCTAGTTACTGTAACATCACACA 57.659 37.500 27.12 7.11 41.07 3.72
335 343 7.974501 ACATAGCTAGTTACTGTAACATCACAC 59.025 37.037 27.12 13.16 41.07 3.82
336 344 8.063200 ACATAGCTAGTTACTGTAACATCACA 57.937 34.615 27.12 12.96 41.07 3.58
337 345 8.928270 AACATAGCTAGTTACTGTAACATCAC 57.072 34.615 27.12 15.70 41.07 3.06
345 353 7.653713 GCATGTGATAACATAGCTAGTTACTGT 59.346 37.037 14.19 4.91 34.59 3.55
346 354 7.116948 GGCATGTGATAACATAGCTAGTTACTG 59.883 40.741 14.19 4.37 34.59 2.74
347 355 7.015682 AGGCATGTGATAACATAGCTAGTTACT 59.984 37.037 14.19 0.00 34.59 2.24
348 356 7.155328 AGGCATGTGATAACATAGCTAGTTAC 58.845 38.462 14.19 8.29 34.59 2.50
349 357 7.233553 AGAGGCATGTGATAACATAGCTAGTTA 59.766 37.037 14.23 14.23 36.06 2.24
350 358 6.042552 AGAGGCATGTGATAACATAGCTAGTT 59.957 38.462 13.85 6.69 0.00 2.24
351 359 5.541868 AGAGGCATGTGATAACATAGCTAGT 59.458 40.000 13.85 0.00 0.00 2.57
352 360 6.035368 AGAGGCATGTGATAACATAGCTAG 57.965 41.667 13.85 0.00 0.00 3.42
353 361 5.777223 AGAGAGGCATGTGATAACATAGCTA 59.223 40.000 13.85 0.00 0.00 3.32
354 362 4.592351 AGAGAGGCATGTGATAACATAGCT 59.408 41.667 13.85 0.00 0.00 3.32
355 363 4.892433 AGAGAGGCATGTGATAACATAGC 58.108 43.478 0.00 2.54 0.00 2.97
356 364 8.065473 AGATAGAGAGGCATGTGATAACATAG 57.935 38.462 0.00 0.00 0.00 2.23
357 365 8.427902 AAGATAGAGAGGCATGTGATAACATA 57.572 34.615 0.00 0.00 0.00 2.29
358 366 6.931790 AGATAGAGAGGCATGTGATAACAT 57.068 37.500 0.00 0.00 0.00 2.71
359 367 6.324770 TGAAGATAGAGAGGCATGTGATAACA 59.675 38.462 0.00 0.00 0.00 2.41
360 368 6.753180 TGAAGATAGAGAGGCATGTGATAAC 58.247 40.000 0.00 0.00 0.00 1.89
361 369 6.983906 TGAAGATAGAGAGGCATGTGATAA 57.016 37.500 0.00 0.00 0.00 1.75
362 370 7.550597 AATGAAGATAGAGAGGCATGTGATA 57.449 36.000 0.00 0.00 0.00 2.15
363 371 6.436738 AATGAAGATAGAGAGGCATGTGAT 57.563 37.500 0.00 0.00 0.00 3.06
364 372 5.883685 AATGAAGATAGAGAGGCATGTGA 57.116 39.130 0.00 0.00 0.00 3.58
365 373 8.618702 AATTAATGAAGATAGAGAGGCATGTG 57.381 34.615 0.00 0.00 0.00 3.21
366 374 9.717942 GTAATTAATGAAGATAGAGAGGCATGT 57.282 33.333 0.00 0.00 0.00 3.21
367 375 9.716531 TGTAATTAATGAAGATAGAGAGGCATG 57.283 33.333 0.00 0.00 0.00 4.06
369 377 9.716531 CATGTAATTAATGAAGATAGAGAGGCA 57.283 33.333 0.00 0.00 0.00 4.75
370 378 9.717942 ACATGTAATTAATGAAGATAGAGAGGC 57.282 33.333 0.00 0.00 0.00 4.70
389 397 9.407380 AGGCAAAATAGATAATGTGACATGTAA 57.593 29.630 0.00 0.00 0.00 2.41
390 398 8.978874 AGGCAAAATAGATAATGTGACATGTA 57.021 30.769 0.00 0.00 0.00 2.29
391 399 7.886629 AGGCAAAATAGATAATGTGACATGT 57.113 32.000 0.00 0.00 0.00 3.21
392 400 9.276590 TCTAGGCAAAATAGATAATGTGACATG 57.723 33.333 0.00 0.00 0.00 3.21
403 411 9.499479 CATCACACTTATCTAGGCAAAATAGAT 57.501 33.333 1.51 1.51 41.66 1.98
404 412 8.486210 ACATCACACTTATCTAGGCAAAATAGA 58.514 33.333 0.00 0.00 33.93 1.98
405 413 8.668510 ACATCACACTTATCTAGGCAAAATAG 57.331 34.615 0.00 0.00 0.00 1.73
407 415 7.944729 AACATCACACTTATCTAGGCAAAAT 57.055 32.000 0.00 0.00 0.00 1.82
408 416 9.109393 GATAACATCACACTTATCTAGGCAAAA 57.891 33.333 0.00 0.00 0.00 2.44
409 417 8.264347 TGATAACATCACACTTATCTAGGCAAA 58.736 33.333 0.00 0.00 33.59 3.68
410 418 7.791029 TGATAACATCACACTTATCTAGGCAA 58.209 34.615 0.00 0.00 33.59 4.52
411 419 7.360113 TGATAACATCACACTTATCTAGGCA 57.640 36.000 0.00 0.00 33.59 4.75
425 433 8.084985 TGGAAGTAACATAGGTGATAACATCA 57.915 34.615 0.00 0.00 36.84 3.07
426 434 9.561069 AATGGAAGTAACATAGGTGATAACATC 57.439 33.333 0.00 0.00 0.00 3.06
427 435 9.342308 CAATGGAAGTAACATAGGTGATAACAT 57.658 33.333 0.00 0.00 0.00 2.71
428 436 8.325787 ACAATGGAAGTAACATAGGTGATAACA 58.674 33.333 0.00 0.00 0.00 2.41
429 437 8.612619 CACAATGGAAGTAACATAGGTGATAAC 58.387 37.037 0.00 0.00 36.58 1.89
430 438 7.773224 CCACAATGGAAGTAACATAGGTGATAA 59.227 37.037 0.00 0.00 40.96 1.75
431 439 7.279615 CCACAATGGAAGTAACATAGGTGATA 58.720 38.462 0.00 0.00 40.96 2.15
432 440 6.122277 CCACAATGGAAGTAACATAGGTGAT 58.878 40.000 0.00 0.00 40.96 3.06
433 441 5.496556 CCACAATGGAAGTAACATAGGTGA 58.503 41.667 0.00 0.00 40.96 4.02
434 442 4.640201 CCCACAATGGAAGTAACATAGGTG 59.360 45.833 0.00 0.00 40.96 4.00
435 443 4.291249 ACCCACAATGGAAGTAACATAGGT 59.709 41.667 0.00 0.00 40.96 3.08
436 444 4.855340 ACCCACAATGGAAGTAACATAGG 58.145 43.478 0.00 0.00 40.96 2.57
437 445 6.650120 ACTACCCACAATGGAAGTAACATAG 58.350 40.000 0.00 0.00 40.96 2.23
438 446 6.442564 AGACTACCCACAATGGAAGTAACATA 59.557 38.462 0.00 0.00 40.96 2.29
439 447 5.250774 AGACTACCCACAATGGAAGTAACAT 59.749 40.000 0.00 0.00 40.96 2.71
440 448 4.595781 AGACTACCCACAATGGAAGTAACA 59.404 41.667 0.00 0.00 40.96 2.41
441 449 5.161943 AGACTACCCACAATGGAAGTAAC 57.838 43.478 0.00 0.00 40.96 2.50
442 450 5.836024 AAGACTACCCACAATGGAAGTAA 57.164 39.130 0.00 0.00 40.96 2.24
443 451 8.612486 TTATAAGACTACCCACAATGGAAGTA 57.388 34.615 0.00 0.00 40.96 2.24
444 452 7.504926 TTATAAGACTACCCACAATGGAAGT 57.495 36.000 0.00 0.00 40.96 3.01
445 453 8.840321 CATTTATAAGACTACCCACAATGGAAG 58.160 37.037 0.00 0.00 40.96 3.46
446 454 8.553153 TCATTTATAAGACTACCCACAATGGAA 58.447 33.333 0.00 0.00 40.96 3.53
447 455 8.096621 TCATTTATAAGACTACCCACAATGGA 57.903 34.615 0.00 0.00 40.96 3.41
448 456 8.210946 TCTCATTTATAAGACTACCCACAATGG 58.789 37.037 0.00 0.00 37.25 3.16
449 457 9.265901 CTCTCATTTATAAGACTACCCACAATG 57.734 37.037 0.00 0.00 0.00 2.82
450 458 7.934120 GCTCTCATTTATAAGACTACCCACAAT 59.066 37.037 0.00 0.00 0.00 2.71
451 459 7.125811 AGCTCTCATTTATAAGACTACCCACAA 59.874 37.037 0.00 0.00 0.00 3.33
452 460 6.611642 AGCTCTCATTTATAAGACTACCCACA 59.388 38.462 0.00 0.00 0.00 4.17
453 461 7.056844 AGCTCTCATTTATAAGACTACCCAC 57.943 40.000 0.00 0.00 0.00 4.61
454 462 7.039644 GCTAGCTCTCATTTATAAGACTACCCA 60.040 40.741 7.70 0.00 0.00 4.51
455 463 7.177744 AGCTAGCTCTCATTTATAAGACTACCC 59.822 40.741 12.68 0.00 0.00 3.69
456 464 8.026607 CAGCTAGCTCTCATTTATAAGACTACC 58.973 40.741 16.15 0.00 0.00 3.18
457 465 7.540745 GCAGCTAGCTCTCATTTATAAGACTAC 59.459 40.741 16.15 0.00 41.15 2.73
458 466 7.231519 TGCAGCTAGCTCTCATTTATAAGACTA 59.768 37.037 16.15 0.00 45.94 2.59
459 467 6.041409 TGCAGCTAGCTCTCATTTATAAGACT 59.959 38.462 16.15 0.00 45.94 3.24
460 468 6.145371 GTGCAGCTAGCTCTCATTTATAAGAC 59.855 42.308 16.15 0.00 45.94 3.01
461 469 6.219473 GTGCAGCTAGCTCTCATTTATAAGA 58.781 40.000 16.15 0.00 45.94 2.10
462 470 5.407995 GGTGCAGCTAGCTCTCATTTATAAG 59.592 44.000 16.15 0.00 45.94 1.73
463 471 5.300752 GGTGCAGCTAGCTCTCATTTATAA 58.699 41.667 16.15 0.00 45.94 0.98
467 475 1.407989 GGGTGCAGCTAGCTCTCATTT 60.408 52.381 16.15 0.00 45.94 2.32
496 504 3.707793 TGCGCTTATTTTCAAACGGTTT 58.292 36.364 9.73 0.00 0.00 3.27
537 546 2.355818 GCTACCTCTGGTAAAACTGGGG 60.356 54.545 0.00 0.00 37.76 4.96
623 632 0.179029 CCGGAGTGACCAACCAAGTT 60.179 55.000 0.00 0.00 38.90 2.66
649 658 8.950210 CCATGGAATCGCTATTATTCAAATACT 58.050 33.333 5.56 0.00 35.46 2.12
650 659 7.698130 GCCATGGAATCGCTATTATTCAAATAC 59.302 37.037 18.40 0.00 35.46 1.89
651 660 7.611467 AGCCATGGAATCGCTATTATTCAAATA 59.389 33.333 18.40 0.00 35.46 1.40
728 742 4.946157 CCTGTGAAATTACTGCTCCATCTT 59.054 41.667 0.00 0.00 0.00 2.40
743 757 2.282180 GGCGGCTTCCCTGTGAAA 60.282 61.111 0.00 0.00 31.06 2.69
812 826 2.520741 GCTAGAGCTCGAGGGGCT 60.521 66.667 23.17 5.87 43.26 5.19
917 939 2.235546 GGAACACGGACTGTTGCTC 58.764 57.895 2.29 0.00 45.40 4.26
943 965 0.801872 TTCGCGCACGTAGTACCTAA 59.198 50.000 8.75 0.00 41.61 2.69
958 980 3.782042 CGAGCTAGGGTTGTTCGC 58.218 61.111 0.00 0.00 32.20 4.70
976 998 0.830648 TCTGGCTAAACCTGATCGGG 59.169 55.000 19.66 19.66 41.17 5.14
995 1017 1.463674 GAAGCCCATGTCCATTTCGT 58.536 50.000 0.00 0.00 0.00 3.85
1155 1177 1.511305 GTCGTCCGAGATCTTGGCA 59.489 57.895 22.79 10.08 34.01 4.92
1742 1764 2.313317 CAGGTACGCAGGGGTTAGATA 58.687 52.381 0.00 0.00 0.00 1.98
1749 1774 2.514592 CATGCAGGTACGCAGGGG 60.515 66.667 0.00 0.00 46.99 4.79
1759 1784 2.046023 TCCTTCGGTGCATGCAGG 60.046 61.111 23.41 18.53 0.00 4.85
1777 1802 1.421410 ATTGTAGCTACTGCACGCGC 61.421 55.000 23.84 0.00 42.74 6.86
1793 1818 1.526041 GCTGCATCAGACGCTAGATTG 59.474 52.381 0.00 0.00 32.44 2.67
1794 1819 1.539929 GGCTGCATCAGACGCTAGATT 60.540 52.381 0.50 0.00 32.44 2.40
1803 1828 1.881973 GTTTCAACAGGCTGCATCAGA 59.118 47.619 15.89 2.59 32.44 3.27
1844 1873 3.859386 GCAAATGCGAACTGGATAAAAGG 59.141 43.478 0.00 0.00 0.00 3.11
1858 1887 3.165318 GCGAACGTGGCAAATGCG 61.165 61.111 6.96 0.00 43.26 4.73
1908 1937 5.447010 GCACTGCACTAAGCTTAGAAAGATG 60.447 44.000 34.65 25.36 45.94 2.90
1945 1974 2.894307 AAATTTAGAAGACGCGCACC 57.106 45.000 5.73 0.00 0.00 5.01
2046 2076 5.095691 ACACACTAGTCTTTGAATTTGCG 57.904 39.130 0.00 0.00 0.00 4.85
2062 2092 6.908825 ACGTCATTAAAATGCATAACACACT 58.091 32.000 0.00 0.00 36.36 3.55
2118 2149 1.507630 TGCGAAGGCATGCATTCAC 59.492 52.632 35.72 29.39 46.21 3.18
2198 2229 8.684386 TCAGTTTTGTCATATTGGTCTTTACA 57.316 30.769 0.00 0.00 0.00 2.41
2305 2336 3.074412 GTGAGGTGGTGATTCGTCATTT 58.926 45.455 0.00 0.00 32.55 2.32
2352 2383 5.368145 TGAAGATCCGTAAAGCTGCATATT 58.632 37.500 1.02 0.00 0.00 1.28
2370 2401 1.065410 TTGGGGAGCCACCTTGAAGA 61.065 55.000 0.00 0.00 38.98 2.87
2385 2416 0.033920 GCAAGGGCTTCACTTTTGGG 59.966 55.000 0.00 0.00 36.96 4.12
2430 2461 3.463585 GATGGCGTGTCCGGGGTA 61.464 66.667 0.00 0.00 37.80 3.69
2462 2493 0.399075 CCTTAGTCGTGGTGGGGTTT 59.601 55.000 0.00 0.00 0.00 3.27
2463 2494 0.765519 ACCTTAGTCGTGGTGGGGTT 60.766 55.000 0.00 0.00 34.90 4.11
2481 2512 0.322546 ATGGTTTCCTCCTTCGGCAC 60.323 55.000 0.00 0.00 0.00 5.01
2576 2608 1.076923 GGAGGTAGTCCAGGAGCGA 60.077 63.158 0.00 0.00 46.10 4.93
2637 2669 2.113243 GACCTGTGTCCTCGGGCTTT 62.113 60.000 0.00 0.00 37.37 3.51
2638 2670 2.526873 ACCTGTGTCCTCGGGCTT 60.527 61.111 0.00 0.00 37.37 4.35
2684 2716 4.018960 ACCAGTCTGTTCAAGCAAGGATAT 60.019 41.667 0.00 0.00 0.00 1.63
2685 2717 3.327757 ACCAGTCTGTTCAAGCAAGGATA 59.672 43.478 0.00 0.00 0.00 2.59
2720 2752 2.605257 CTATCGGTCCTATGGTTGGGA 58.395 52.381 0.00 0.00 0.00 4.37


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

AutoCloner maintained by Alex Coulton.