Multiple sequence alignment - TraesCS5B01G286500

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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 TraesCS5B01G286500 chr5B 100.000 2351 0 0 1 2351 472675123 472677473 0.000000e+00 4342.0
1 TraesCS5B01G286500 chr5D 92.067 1790 65 32 608 2351 391900148 391901906 0.000000e+00 2447.0
2 TraesCS5B01G286500 chr5D 88.514 148 13 2 4 147 391896934 391897081 2.400000e-40 176.0
3 TraesCS5B01G286500 chr5D 92.308 52 3 1 471 522 391897089 391897139 3.240000e-09 73.1
4 TraesCS5B01G286500 chr5A 89.093 1797 85 39 609 2351 495095836 495097575 0.000000e+00 2130.0
5 TraesCS5B01G286500 chr5A 90.584 308 18 3 176 472 510187572 510187879 4.710000e-107 398.0
6 TraesCS5B01G286500 chr5A 89.677 155 16 0 4 158 495093533 495093687 5.120000e-47 198.0
7 TraesCS5B01G286500 chr2A 94.074 270 14 2 176 443 723523037 723523306 2.170000e-110 409.0
8 TraesCS5B01G286500 chr2B 90.820 305 21 6 176 476 211215244 211215545 3.640000e-108 401.0
9 TraesCS5B01G286500 chr2B 90.365 301 19 4 176 473 103194592 103194885 1.020000e-103 387.0
10 TraesCS5B01G286500 chr4B 93.333 270 16 2 176 443 129713024 129713293 4.710000e-107 398.0
11 TraesCS5B01G286500 chr3B 93.333 270 16 2 176 443 659778609 659778878 4.710000e-107 398.0
12 TraesCS5B01G286500 chr7A 92.989 271 16 3 176 443 61804365 61804095 2.190000e-105 392.0
13 TraesCS5B01G286500 chr1B 92.086 278 20 2 168 443 40000451 40000174 7.880000e-105 390.0
14 TraesCS5B01G286500 chr4A 90.000 300 26 3 176 473 643018861 643018564 3.670000e-103 385.0


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 TraesCS5B01G286500 chr5B 472675123 472677473 2350 False 4342.0 4342 100.000 1 2351 1 chr5B.!!$F1 2350
1 TraesCS5B01G286500 chr5D 391896934 391901906 4972 False 898.7 2447 90.963 4 2351 3 chr5D.!!$F1 2347
2 TraesCS5B01G286500 chr5A 495093533 495097575 4042 False 1164.0 2130 89.385 4 2351 2 chr5A.!!$F2 2347

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
411 416 0.028902 GACAACCAAACAGGCGTGAC 59.971 55.0 14.38 0.0 43.14 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1886 5244 0.403271 ATCAAGCAGCAACTCCAGGT 59.597 50.0 0.0 0.0 0.0 4.0 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
110 115 0.108329 TTCTCTCGATTGCCCGGTTC 60.108 55.000 0.00 0.00 0.00 3.62
123 128 1.154225 CGGTTCACCAAATGCGAGC 60.154 57.895 0.00 0.00 35.14 5.03
159 164 3.652274 CAGGTGTGCACAAAAATAAGGG 58.348 45.455 23.59 0.01 0.00 3.95
160 165 3.069443 CAGGTGTGCACAAAAATAAGGGT 59.931 43.478 23.59 0.00 0.00 4.34
161 166 3.069443 AGGTGTGCACAAAAATAAGGGTG 59.931 43.478 23.59 0.00 0.00 4.61
162 167 3.181470 GGTGTGCACAAAAATAAGGGTGT 60.181 43.478 23.59 0.00 33.88 4.16
163 168 3.801594 GTGTGCACAAAAATAAGGGTGTG 59.198 43.478 23.59 0.00 43.38 3.82
164 169 3.449018 TGTGCACAAAAATAAGGGTGTGT 59.551 39.130 19.28 0.00 42.66 3.72
165 170 4.081420 TGTGCACAAAAATAAGGGTGTGTT 60.081 37.500 19.28 0.00 42.66 3.32
166 171 5.127194 TGTGCACAAAAATAAGGGTGTGTTA 59.873 36.000 19.28 0.00 42.66 2.41
167 172 6.183360 TGTGCACAAAAATAAGGGTGTGTTAT 60.183 34.615 19.28 0.00 42.66 1.89
168 173 7.014326 TGTGCACAAAAATAAGGGTGTGTTATA 59.986 33.333 19.28 0.00 42.66 0.98
169 174 7.868415 GTGCACAAAAATAAGGGTGTGTTATAA 59.132 33.333 13.17 0.00 42.66 0.98
170 175 8.085296 TGCACAAAAATAAGGGTGTGTTATAAG 58.915 33.333 4.73 0.00 42.66 1.73
171 176 7.544217 GCACAAAAATAAGGGTGTGTTATAAGG 59.456 37.037 4.73 0.00 42.66 2.69
172 177 8.798402 CACAAAAATAAGGGTGTGTTATAAGGA 58.202 33.333 0.00 0.00 37.25 3.36
173 178 9.541884 ACAAAAATAAGGGTGTGTTATAAGGAT 57.458 29.630 0.00 0.00 0.00 3.24
174 179 9.801873 CAAAAATAAGGGTGTGTTATAAGGATG 57.198 33.333 0.00 0.00 0.00 3.51
175 180 9.541884 AAAAATAAGGGTGTGTTATAAGGATGT 57.458 29.630 0.00 0.00 0.00 3.06
176 181 8.519799 AAATAAGGGTGTGTTATAAGGATGTG 57.480 34.615 0.00 0.00 0.00 3.21
177 182 5.514500 AAGGGTGTGTTATAAGGATGTGT 57.486 39.130 0.00 0.00 0.00 3.72
178 183 5.514500 AGGGTGTGTTATAAGGATGTGTT 57.486 39.130 0.00 0.00 0.00 3.32
179 184 5.887754 AGGGTGTGTTATAAGGATGTGTTT 58.112 37.500 0.00 0.00 0.00 2.83
180 185 5.710099 AGGGTGTGTTATAAGGATGTGTTTG 59.290 40.000 0.00 0.00 0.00 2.93
181 186 5.105917 GGGTGTGTTATAAGGATGTGTTTGG 60.106 44.000 0.00 0.00 0.00 3.28
182 187 5.475564 GGTGTGTTATAAGGATGTGTTTGGT 59.524 40.000 0.00 0.00 0.00 3.67
183 188 6.349033 GGTGTGTTATAAGGATGTGTTTGGTC 60.349 42.308 0.00 0.00 0.00 4.02
184 189 6.430000 GTGTGTTATAAGGATGTGTTTGGTCT 59.570 38.462 0.00 0.00 0.00 3.85
185 190 6.653320 TGTGTTATAAGGATGTGTTTGGTCTC 59.347 38.462 0.00 0.00 0.00 3.36
186 191 6.653320 GTGTTATAAGGATGTGTTTGGTCTCA 59.347 38.462 0.00 0.00 0.00 3.27
187 192 7.174253 GTGTTATAAGGATGTGTTTGGTCTCAA 59.826 37.037 0.00 0.00 0.00 3.02
188 193 7.721842 TGTTATAAGGATGTGTTTGGTCTCAAA 59.278 33.333 0.00 0.00 40.23 2.69
189 194 8.739972 GTTATAAGGATGTGTTTGGTCTCAAAT 58.260 33.333 0.00 0.00 43.73 2.32
190 195 9.967451 TTATAAGGATGTGTTTGGTCTCAAATA 57.033 29.630 0.00 0.00 43.73 1.40
191 196 8.877864 ATAAGGATGTGTTTGGTCTCAAATAA 57.122 30.769 0.00 0.00 43.73 1.40
192 197 6.824305 AGGATGTGTTTGGTCTCAAATAAG 57.176 37.500 0.00 0.00 43.73 1.73
193 198 6.306987 AGGATGTGTTTGGTCTCAAATAAGT 58.693 36.000 0.00 0.00 43.73 2.24
194 199 6.431234 AGGATGTGTTTGGTCTCAAATAAGTC 59.569 38.462 0.00 0.00 43.73 3.01
195 200 6.206634 GGATGTGTTTGGTCTCAAATAAGTCA 59.793 38.462 0.00 0.00 43.73 3.41
196 201 7.094205 GGATGTGTTTGGTCTCAAATAAGTCAT 60.094 37.037 0.00 0.00 43.73 3.06
197 202 7.202016 TGTGTTTGGTCTCAAATAAGTCATC 57.798 36.000 0.00 0.00 43.73 2.92
198 203 6.770303 TGTGTTTGGTCTCAAATAAGTCATCA 59.230 34.615 0.00 0.00 43.73 3.07
199 204 7.284261 TGTGTTTGGTCTCAAATAAGTCATCAA 59.716 33.333 0.00 0.00 43.73 2.57
200 205 7.591426 GTGTTTGGTCTCAAATAAGTCATCAAC 59.409 37.037 0.00 0.00 43.73 3.18
201 206 7.502226 TGTTTGGTCTCAAATAAGTCATCAACT 59.498 33.333 0.00 0.00 43.73 3.16
202 207 8.352942 GTTTGGTCTCAAATAAGTCATCAACTT 58.647 33.333 0.00 0.00 43.73 2.66
216 221 9.490379 AAGTCATCAACTTATAAGTCGAAAAGT 57.510 29.630 18.28 5.95 46.55 2.66
249 254 9.739276 AATGACTTATTTATCAAACAGACCTGA 57.261 29.630 3.76 0.00 0.00 3.86
250 255 9.911788 ATGACTTATTTATCAAACAGACCTGAT 57.088 29.630 3.76 0.00 36.30 2.90
251 256 9.739276 TGACTTATTTATCAAACAGACCTGATT 57.261 29.630 3.76 0.00 34.21 2.57
261 266 8.547967 TCAAACAGACCTGATTTATAAGTCAC 57.452 34.615 6.58 0.00 0.00 3.67
262 267 7.606456 TCAAACAGACCTGATTTATAAGTCACC 59.394 37.037 6.58 0.77 0.00 4.02
263 268 5.990668 ACAGACCTGATTTATAAGTCACCC 58.009 41.667 6.58 0.47 0.00 4.61
264 269 5.104485 ACAGACCTGATTTATAAGTCACCCC 60.104 44.000 6.58 0.17 0.00 4.95
265 270 5.036916 AGACCTGATTTATAAGTCACCCCA 58.963 41.667 6.58 0.00 0.00 4.96
266 271 5.491078 AGACCTGATTTATAAGTCACCCCAA 59.509 40.000 6.58 0.00 0.00 4.12
267 272 5.506708 ACCTGATTTATAAGTCACCCCAAC 58.493 41.667 6.58 0.00 0.00 3.77
268 273 5.253096 ACCTGATTTATAAGTCACCCCAACT 59.747 40.000 6.58 0.00 0.00 3.16
269 274 6.187682 CCTGATTTATAAGTCACCCCAACTT 58.812 40.000 6.58 0.00 40.06 2.66
270 275 7.037153 ACCTGATTTATAAGTCACCCCAACTTA 60.037 37.037 6.58 0.00 41.91 2.24
271 276 7.998964 CCTGATTTATAAGTCACCCCAACTTAT 59.001 37.037 6.58 11.86 46.48 1.73
277 282 5.836024 AAGTCACCCCAACTTATAAGTCA 57.164 39.130 18.28 0.00 38.57 3.41
278 283 6.388619 AAGTCACCCCAACTTATAAGTCAT 57.611 37.500 18.28 1.19 38.57 3.06
279 284 7.504926 AAGTCACCCCAACTTATAAGTCATA 57.495 36.000 18.28 0.00 38.57 2.15
280 285 7.504926 AGTCACCCCAACTTATAAGTCATAA 57.495 36.000 18.28 0.00 38.57 1.90
291 296 7.484035 CTTATAAGTCATAAGTTGCTCCACC 57.516 40.000 4.18 0.00 40.84 4.61
292 297 2.789409 AGTCATAAGTTGCTCCACCC 57.211 50.000 0.00 0.00 0.00 4.61
293 298 1.282157 AGTCATAAGTTGCTCCACCCC 59.718 52.381 0.00 0.00 0.00 4.95
294 299 1.004277 GTCATAAGTTGCTCCACCCCA 59.996 52.381 0.00 0.00 0.00 4.96
295 300 1.707989 TCATAAGTTGCTCCACCCCAA 59.292 47.619 0.00 0.00 0.00 4.12
296 301 1.818674 CATAAGTTGCTCCACCCCAAC 59.181 52.381 0.00 0.00 41.13 3.77
297 302 3.674278 AGTTGCTCCACCCCAACT 58.326 55.556 0.56 0.56 44.86 3.16
298 303 1.930520 AGTTGCTCCACCCCAACTT 59.069 52.632 0.56 0.00 46.86 2.66
299 304 1.145571 AGTTGCTCCACCCCAACTTA 58.854 50.000 0.56 0.00 46.86 2.24
300 305 1.497286 AGTTGCTCCACCCCAACTTAA 59.503 47.619 0.56 0.00 46.86 1.85
301 306 2.091555 AGTTGCTCCACCCCAACTTAAA 60.092 45.455 0.56 0.00 46.86 1.52
302 307 2.696187 GTTGCTCCACCCCAACTTAAAA 59.304 45.455 0.00 0.00 38.55 1.52
303 308 2.312390 TGCTCCACCCCAACTTAAAAC 58.688 47.619 0.00 0.00 0.00 2.43
304 309 2.091555 TGCTCCACCCCAACTTAAAACT 60.092 45.455 0.00 0.00 0.00 2.66
305 310 2.963101 GCTCCACCCCAACTTAAAACTT 59.037 45.455 0.00 0.00 0.00 2.66
306 311 4.146564 GCTCCACCCCAACTTAAAACTTA 58.853 43.478 0.00 0.00 0.00 2.24
307 312 4.770531 GCTCCACCCCAACTTAAAACTTAT 59.229 41.667 0.00 0.00 0.00 1.73
308 313 5.947566 GCTCCACCCCAACTTAAAACTTATA 59.052 40.000 0.00 0.00 0.00 0.98
309 314 6.434965 GCTCCACCCCAACTTAAAACTTATAA 59.565 38.462 0.00 0.00 0.00 0.98
310 315 7.362660 GCTCCACCCCAACTTAAAACTTATAAG 60.363 40.741 11.05 11.05 36.62 1.73
311 316 7.528675 TCCACCCCAACTTAAAACTTATAAGT 58.471 34.615 12.50 12.50 43.57 2.24
312 317 7.666804 TCCACCCCAACTTAAAACTTATAAGTC 59.333 37.037 18.28 0.00 41.49 3.01
313 318 7.449086 CCACCCCAACTTAAAACTTATAAGTCA 59.551 37.037 18.28 4.72 41.49 3.41
314 319 8.294577 CACCCCAACTTAAAACTTATAAGTCAC 58.705 37.037 18.28 0.00 41.49 3.67
315 320 7.449395 ACCCCAACTTAAAACTTATAAGTCACC 59.551 37.037 18.28 0.00 41.49 4.02
316 321 7.094075 CCCCAACTTAAAACTTATAAGTCACCC 60.094 40.741 18.28 0.00 41.49 4.61
317 322 7.094075 CCCAACTTAAAACTTATAAGTCACCCC 60.094 40.741 18.28 0.00 41.49 4.95
318 323 7.094075 CCAACTTAAAACTTATAAGTCACCCCC 60.094 40.741 18.28 0.00 41.49 5.40
319 324 7.339177 ACTTAAAACTTATAAGTCACCCCCT 57.661 36.000 18.28 0.00 38.85 4.79
320 325 7.762610 ACTTAAAACTTATAAGTCACCCCCTT 58.237 34.615 18.28 4.77 38.85 3.95
321 326 8.229605 ACTTAAAACTTATAAGTCACCCCCTTT 58.770 33.333 18.28 14.40 38.85 3.11
322 327 9.085645 CTTAAAACTTATAAGTCACCCCCTTTT 57.914 33.333 18.28 13.78 38.57 2.27
323 328 6.911250 AAACTTATAAGTCACCCCCTTTTG 57.089 37.500 18.28 0.00 38.57 2.44
324 329 4.341487 ACTTATAAGTCACCCCCTTTTGC 58.659 43.478 12.50 0.00 32.86 3.68
325 330 1.834188 ATAAGTCACCCCCTTTTGCG 58.166 50.000 0.00 0.00 0.00 4.85
326 331 0.475044 TAAGTCACCCCCTTTTGCGT 59.525 50.000 0.00 0.00 0.00 5.24
327 332 1.106944 AAGTCACCCCCTTTTGCGTG 61.107 55.000 0.00 0.00 0.00 5.34
328 333 2.203422 TCACCCCCTTTTGCGTGG 60.203 61.111 0.00 0.00 0.00 4.94
329 334 3.302344 CACCCCCTTTTGCGTGGG 61.302 66.667 0.00 0.00 44.03 4.61
330 335 3.828023 ACCCCCTTTTGCGTGGGT 61.828 61.111 0.00 0.00 46.50 4.51
331 336 2.989253 CCCCCTTTTGCGTGGGTC 60.989 66.667 0.00 0.00 41.82 4.46
332 337 2.989253 CCCCTTTTGCGTGGGTCC 60.989 66.667 0.00 0.00 41.82 4.46
333 338 2.989253 CCCTTTTGCGTGGGTCCC 60.989 66.667 0.00 0.00 38.65 4.46
334 339 2.203422 CCTTTTGCGTGGGTCCCA 60.203 61.111 6.47 6.47 0.00 4.37
343 348 2.531428 TGGGTCCCACCATCTGCA 60.531 61.111 6.47 0.00 41.02 4.41
344 349 1.930133 TGGGTCCCACCATCTGCAT 60.930 57.895 6.47 0.00 41.02 3.96
345 350 1.454479 GGGTCCCACCATCTGCATG 60.454 63.158 1.78 0.00 41.02 4.06
346 351 1.609239 GGTCCCACCATCTGCATGA 59.391 57.895 0.00 0.00 38.42 3.07
347 352 0.184451 GGTCCCACCATCTGCATGAT 59.816 55.000 0.00 0.00 38.42 2.45
348 353 1.421268 GGTCCCACCATCTGCATGATA 59.579 52.381 0.00 0.00 38.42 2.15
349 354 2.040813 GGTCCCACCATCTGCATGATAT 59.959 50.000 0.00 0.00 38.42 1.63
350 355 3.499202 GGTCCCACCATCTGCATGATATT 60.499 47.826 0.00 0.00 38.42 1.28
351 356 3.504906 GTCCCACCATCTGCATGATATTG 59.495 47.826 0.00 0.00 33.36 1.90
352 357 3.395273 TCCCACCATCTGCATGATATTGA 59.605 43.478 0.00 0.00 33.36 2.57
353 358 4.043686 TCCCACCATCTGCATGATATTGAT 59.956 41.667 0.00 0.00 33.36 2.57
354 359 4.770531 CCCACCATCTGCATGATATTGATT 59.229 41.667 0.00 0.00 33.36 2.57
355 360 5.336451 CCCACCATCTGCATGATATTGATTG 60.336 44.000 0.00 0.00 33.36 2.67
356 361 5.336451 CCACCATCTGCATGATATTGATTGG 60.336 44.000 0.00 0.00 33.36 3.16
357 362 5.243060 CACCATCTGCATGATATTGATTGGT 59.757 40.000 0.00 0.00 33.36 3.67
358 363 5.243060 ACCATCTGCATGATATTGATTGGTG 59.757 40.000 0.00 0.00 33.36 4.17
359 364 5.243060 CCATCTGCATGATATTGATTGGTGT 59.757 40.000 0.00 0.00 33.36 4.16
360 365 5.761165 TCTGCATGATATTGATTGGTGTG 57.239 39.130 0.00 0.00 0.00 3.82
361 366 4.581409 TCTGCATGATATTGATTGGTGTGG 59.419 41.667 0.00 0.00 0.00 4.17
362 367 4.534797 TGCATGATATTGATTGGTGTGGA 58.465 39.130 0.00 0.00 0.00 4.02
363 368 4.954826 TGCATGATATTGATTGGTGTGGAA 59.045 37.500 0.00 0.00 0.00 3.53
364 369 5.068067 TGCATGATATTGATTGGTGTGGAAG 59.932 40.000 0.00 0.00 0.00 3.46
365 370 5.508489 GCATGATATTGATTGGTGTGGAAGG 60.508 44.000 0.00 0.00 0.00 3.46
366 371 5.191727 TGATATTGATTGGTGTGGAAGGT 57.808 39.130 0.00 0.00 0.00 3.50
367 372 4.949238 TGATATTGATTGGTGTGGAAGGTG 59.051 41.667 0.00 0.00 0.00 4.00
368 373 2.746279 TTGATTGGTGTGGAAGGTGT 57.254 45.000 0.00 0.00 0.00 4.16
369 374 1.979855 TGATTGGTGTGGAAGGTGTG 58.020 50.000 0.00 0.00 0.00 3.82
370 375 1.214175 TGATTGGTGTGGAAGGTGTGT 59.786 47.619 0.00 0.00 0.00 3.72
371 376 1.880027 GATTGGTGTGGAAGGTGTGTC 59.120 52.381 0.00 0.00 0.00 3.67
372 377 0.621082 TTGGTGTGGAAGGTGTGTCA 59.379 50.000 0.00 0.00 0.00 3.58
373 378 0.180171 TGGTGTGGAAGGTGTGTCAG 59.820 55.000 0.00 0.00 0.00 3.51
374 379 0.535102 GGTGTGGAAGGTGTGTCAGG 60.535 60.000 0.00 0.00 0.00 3.86
375 380 0.180406 GTGTGGAAGGTGTGTCAGGT 59.820 55.000 0.00 0.00 0.00 4.00
376 381 0.468226 TGTGGAAGGTGTGTCAGGTC 59.532 55.000 0.00 0.00 0.00 3.85
377 382 0.468226 GTGGAAGGTGTGTCAGGTCA 59.532 55.000 0.00 0.00 0.00 4.02
378 383 0.468226 TGGAAGGTGTGTCAGGTCAC 59.532 55.000 0.00 0.00 38.63 3.67
379 384 0.759346 GGAAGGTGTGTCAGGTCACT 59.241 55.000 0.00 0.00 38.90 3.41
380 385 1.141053 GGAAGGTGTGTCAGGTCACTT 59.859 52.381 0.00 0.00 38.90 3.16
381 386 2.367567 GGAAGGTGTGTCAGGTCACTTA 59.632 50.000 0.00 0.00 38.90 2.24
382 387 3.008049 GGAAGGTGTGTCAGGTCACTTAT 59.992 47.826 0.00 0.00 38.90 1.73
383 388 4.222145 GGAAGGTGTGTCAGGTCACTTATA 59.778 45.833 0.00 0.00 38.90 0.98
384 389 5.279809 GGAAGGTGTGTCAGGTCACTTATAA 60.280 44.000 0.00 0.00 38.90 0.98
385 390 5.407407 AGGTGTGTCAGGTCACTTATAAG 57.593 43.478 11.05 11.05 38.90 1.73
386 391 4.838986 AGGTGTGTCAGGTCACTTATAAGT 59.161 41.667 12.50 12.50 40.60 2.24
387 392 5.047235 AGGTGTGTCAGGTCACTTATAAGTC 60.047 44.000 15.35 5.53 37.08 3.01
388 393 5.279306 GGTGTGTCAGGTCACTTATAAGTCA 60.279 44.000 15.35 0.00 37.08 3.41
389 394 6.220930 GTGTGTCAGGTCACTTATAAGTCAA 58.779 40.000 15.35 4.28 37.08 3.18
390 395 6.366332 GTGTGTCAGGTCACTTATAAGTCAAG 59.634 42.308 15.35 5.22 37.08 3.02
391 396 6.041637 TGTGTCAGGTCACTTATAAGTCAAGT 59.958 38.462 15.35 0.00 37.08 3.16
405 410 3.420839 GTCAAGTGACAACCAAACAGG 57.579 47.619 6.57 0.00 44.18 4.00
406 411 1.748493 TCAAGTGACAACCAAACAGGC 59.252 47.619 0.00 0.00 43.14 4.85
407 412 0.738389 AAGTGACAACCAAACAGGCG 59.262 50.000 0.00 0.00 43.14 5.52
408 413 0.393808 AGTGACAACCAAACAGGCGT 60.394 50.000 0.00 0.00 43.14 5.68
409 414 0.248458 GTGACAACCAAACAGGCGTG 60.248 55.000 4.53 4.53 43.14 5.34
410 415 0.393132 TGACAACCAAACAGGCGTGA 60.393 50.000 14.38 0.00 43.14 4.35
411 416 0.028902 GACAACCAAACAGGCGTGAC 59.971 55.000 14.38 0.00 43.14 3.67
412 417 0.393808 ACAACCAAACAGGCGTGACT 60.394 50.000 14.38 0.00 43.14 3.41
413 418 0.738389 CAACCAAACAGGCGTGACTT 59.262 50.000 14.38 3.10 43.14 3.01
414 419 1.944024 CAACCAAACAGGCGTGACTTA 59.056 47.619 14.38 0.00 43.14 2.24
415 420 2.552315 CAACCAAACAGGCGTGACTTAT 59.448 45.455 14.38 0.00 43.14 1.73
416 421 3.688694 ACCAAACAGGCGTGACTTATA 57.311 42.857 14.38 0.00 43.14 0.98
417 422 4.010667 ACCAAACAGGCGTGACTTATAA 57.989 40.909 14.38 0.00 43.14 0.98
418 423 4.000988 ACCAAACAGGCGTGACTTATAAG 58.999 43.478 14.38 11.05 43.14 1.73
419 424 4.000988 CCAAACAGGCGTGACTTATAAGT 58.999 43.478 18.05 18.05 43.16 2.24
439 444 6.867662 AAGTCACTGGTTTTAAGTCATCTG 57.132 37.500 0.00 0.00 0.00 2.90
440 445 6.174720 AGTCACTGGTTTTAAGTCATCTGA 57.825 37.500 0.00 0.00 0.00 3.27
441 446 5.992217 AGTCACTGGTTTTAAGTCATCTGAC 59.008 40.000 2.01 2.01 45.08 3.51
458 463 9.774742 GTCATCTGACTGGTGATTTATTAAAAC 57.225 33.333 3.07 0.00 41.65 2.43
459 464 8.956426 TCATCTGACTGGTGATTTATTAAAACC 58.044 33.333 3.89 3.89 0.00 3.27
460 465 8.739039 CATCTGACTGGTGATTTATTAAAACCA 58.261 33.333 10.75 10.75 38.57 3.67
461 466 8.698973 TCTGACTGGTGATTTATTAAAACCAA 57.301 30.769 11.85 0.87 40.28 3.67
462 467 9.137459 TCTGACTGGTGATTTATTAAAACCAAA 57.863 29.630 11.85 3.52 40.28 3.28
463 468 9.191995 CTGACTGGTGATTTATTAAAACCAAAC 57.808 33.333 11.85 9.70 40.28 2.93
464 469 8.696374 TGACTGGTGATTTATTAAAACCAAACA 58.304 29.630 11.85 11.37 40.28 2.83
465 470 9.191995 GACTGGTGATTTATTAAAACCAAACAG 57.808 33.333 11.85 14.34 40.28 3.16
466 471 8.147704 ACTGGTGATTTATTAAAACCAAACAGG 58.852 33.333 11.85 5.15 40.28 4.00
467 472 6.931840 TGGTGATTTATTAAAACCAAACAGGC 59.068 34.615 9.34 0.00 43.14 4.85
468 473 6.370442 GGTGATTTATTAAAACCAAACAGGCC 59.630 38.462 0.00 0.00 43.14 5.19
469 474 6.370442 GTGATTTATTAAAACCAAACAGGCCC 59.630 38.462 0.00 0.00 43.14 5.80
509 514 7.750458 CAGCGCAAGAAATGAGTAAAAAGATTA 59.250 33.333 11.47 0.00 43.02 1.75
536 545 3.711059 GACTCCGGACCGAGGGCTA 62.711 68.421 17.49 0.00 33.93 3.93
541 550 2.913060 GGACCGAGGGCTAGCGAT 60.913 66.667 9.00 0.00 0.00 4.58
552 3276 1.545875 GGCTAGCGATAGTGGAGAGGA 60.546 57.143 9.80 0.00 39.35 3.71
554 3278 2.812613 GCTAGCGATAGTGGAGAGGACT 60.813 54.545 9.80 0.00 39.35 3.85
555 3279 1.975660 AGCGATAGTGGAGAGGACTC 58.024 55.000 0.00 0.00 39.51 3.36
556 3280 1.213182 AGCGATAGTGGAGAGGACTCA 59.787 52.381 1.75 0.00 41.02 3.41
557 3281 1.606668 GCGATAGTGGAGAGGACTCAG 59.393 57.143 1.75 0.00 41.02 3.35
558 3282 2.925724 CGATAGTGGAGAGGACTCAGT 58.074 52.381 1.75 0.00 44.22 3.41
560 3284 3.810941 CGATAGTGGAGAGGACTCAGTAC 59.189 52.174 1.75 0.00 44.22 2.73
561 3285 2.517998 AGTGGAGAGGACTCAGTACC 57.482 55.000 1.75 0.98 44.22 3.34
562 3286 1.096416 GTGGAGAGGACTCAGTACCG 58.904 60.000 1.75 0.00 44.22 4.02
563 3287 0.697079 TGGAGAGGACTCAGTACCGT 59.303 55.000 1.75 0.00 44.22 4.83
565 3289 2.508716 TGGAGAGGACTCAGTACCGTAT 59.491 50.000 1.75 0.00 44.22 3.06
566 3290 3.053842 TGGAGAGGACTCAGTACCGTATT 60.054 47.826 1.75 0.00 44.22 1.89
581 3860 1.448985 GTATTCTGAGCAACGGCCAA 58.551 50.000 2.24 0.00 42.56 4.52
582 3861 2.017049 GTATTCTGAGCAACGGCCAAT 58.983 47.619 2.24 0.00 42.56 3.16
583 3862 1.549203 ATTCTGAGCAACGGCCAATT 58.451 45.000 2.24 0.00 42.56 2.32
584 3863 0.597568 TTCTGAGCAACGGCCAATTG 59.402 50.000 11.61 11.61 42.56 2.32
585 3864 0.537143 TCTGAGCAACGGCCAATTGT 60.537 50.000 16.10 5.40 42.56 2.71
586 3865 1.164411 CTGAGCAACGGCCAATTGTA 58.836 50.000 16.10 5.01 42.56 2.41
587 3866 1.131126 CTGAGCAACGGCCAATTGTAG 59.869 52.381 16.10 9.72 42.56 2.74
590 3869 1.003118 AGCAACGGCCAATTGTAGAGA 59.997 47.619 16.10 0.00 42.56 3.10
591 3870 1.398390 GCAACGGCCAATTGTAGAGAG 59.602 52.381 16.10 0.00 0.00 3.20
592 3871 2.009774 CAACGGCCAATTGTAGAGAGG 58.990 52.381 2.24 0.00 0.00 3.69
594 3873 1.207329 ACGGCCAATTGTAGAGAGGAC 59.793 52.381 2.24 0.00 0.00 3.85
595 3874 1.207089 CGGCCAATTGTAGAGAGGACA 59.793 52.381 2.24 0.00 0.00 4.02
596 3875 2.158900 CGGCCAATTGTAGAGAGGACAT 60.159 50.000 2.24 0.00 0.00 3.06
597 3876 3.209410 GGCCAATTGTAGAGAGGACATG 58.791 50.000 4.43 0.00 0.00 3.21
598 3877 2.615912 GCCAATTGTAGAGAGGACATGC 59.384 50.000 4.43 0.00 0.00 4.06
602 3881 4.935352 ATTGTAGAGAGGACATGCTCTC 57.065 45.455 19.58 19.58 44.59 3.20
603 3882 2.660572 TGTAGAGAGGACATGCTCTCC 58.339 52.381 22.47 11.73 45.16 3.71
604 3883 1.606668 GTAGAGAGGACATGCTCTCCG 59.393 57.143 22.47 0.00 45.16 4.63
605 3884 1.067250 GAGAGGACATGCTCTCCGC 59.933 63.158 17.17 7.57 39.96 5.54
606 3885 2.107953 GAGGACATGCTCTCCGCC 59.892 66.667 0.00 0.00 38.05 6.13
650 3929 6.652481 TCGTATAACGGGAACAATTAACCAAA 59.348 34.615 0.00 0.00 42.81 3.28
652 3931 6.904463 ATAACGGGAACAATTAACCAAACT 57.096 33.333 0.00 0.00 0.00 2.66
659 3938 7.522399 CGGGAACAATTAACCAAACTGATAACA 60.522 37.037 0.00 0.00 0.00 2.41
671 3950 9.747898 ACCAAACTGATAACATAAAGAATACCA 57.252 29.630 0.00 0.00 0.00 3.25
727 4016 4.913376 GCACGAGCACTCATTCATTTATT 58.087 39.130 0.00 0.00 41.58 1.40
728 4017 4.966366 GCACGAGCACTCATTCATTTATTC 59.034 41.667 0.00 0.00 41.58 1.75
1152 4498 2.182842 GGTGGCGTCCATGATGCTC 61.183 63.158 8.09 2.86 43.35 4.26
1414 4766 2.301902 CTGCGCTCTGGATTGTTCGC 62.302 60.000 9.73 0.00 42.47 4.70
1418 4770 2.205074 CGCTCTGGATTGTTCGCTATT 58.795 47.619 0.00 0.00 0.00 1.73
1500 4852 2.088674 CTGGGCTCGATCGGGGTTAG 62.089 65.000 18.35 6.76 0.00 2.34
1505 4857 0.737219 CTCGATCGGGGTTAGAACGT 59.263 55.000 16.41 0.00 35.77 3.99
1506 4858 1.133790 CTCGATCGGGGTTAGAACGTT 59.866 52.381 16.41 0.00 35.77 3.99
1507 4859 1.135315 TCGATCGGGGTTAGAACGTTG 60.135 52.381 16.41 0.00 35.77 4.10
1508 4860 1.403249 CGATCGGGGTTAGAACGTTGT 60.403 52.381 5.00 3.64 0.00 3.32
1561 4913 4.931661 AATTTGAAGCATCTATGGCCTG 57.068 40.909 3.32 0.00 0.00 4.85
1583 4936 7.531716 CCTGTGCCGTTTAAATTGTTCTATTA 58.468 34.615 0.00 0.00 0.00 0.98
1626 4980 1.361668 CCTCGTGCGGATCAAACTGG 61.362 60.000 0.00 0.00 0.00 4.00
1734 5089 0.475632 TTCCTCTCTCCCTGGGCAAA 60.476 55.000 8.22 0.00 0.00 3.68
1739 5094 1.710244 TCTCTCCCTGGGCAAATTGAA 59.290 47.619 8.22 0.00 0.00 2.69
1748 5103 5.643348 CCCTGGGCAAATTGAAATTAACTTC 59.357 40.000 0.00 0.00 0.00 3.01
1784 5139 1.356124 CATCCCTACCCCATCTCCTG 58.644 60.000 0.00 0.00 0.00 3.86
1930 5289 6.612456 TGAGTTAAACGAGGGGGAATAGATAA 59.388 38.462 0.00 0.00 0.00 1.75
1951 5310 4.689612 ACTGCCTTAATGACCGTATGAT 57.310 40.909 0.00 0.00 0.00 2.45
1988 5347 7.873505 GGAAAGGAGCAGTAGGTAAACATATAG 59.126 40.741 0.00 0.00 0.00 1.31
2039 5399 2.606308 GGATTTGATTGCCTATGCGCTG 60.606 50.000 9.73 0.00 41.78 5.18
2155 5518 6.639686 TCATAACAAGAATACGTAAGGATCGC 59.360 38.462 0.00 0.00 43.13 4.58
2272 5636 4.380867 GCTGTCACCCTTACATTTCCAATG 60.381 45.833 0.00 0.00 0.00 2.82
2302 5666 8.534778 GCAGACTTTTGAAATAGACAGTTTTTG 58.465 33.333 0.00 0.00 0.00 2.44
2339 5703 4.642885 AGACTGTCTACCTAGTGAGCAATC 59.357 45.833 8.91 0.00 0.00 2.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.503927 TCTACGCCTCTTTCTTTAGGAGTA 58.496 41.667 5.13 5.13 43.12 2.59
1 2 4.342359 TCTACGCCTCTTTCTTTAGGAGT 58.658 43.478 3.32 3.32 46.12 3.85
2 3 4.985538 TCTACGCCTCTTTCTTTAGGAG 57.014 45.455 0.00 0.00 38.51 3.69
20 21 8.246871 CCTACAGCGATCAGAAATGATATTCTA 58.753 37.037 0.00 0.00 37.56 2.10
101 106 2.569354 GCATTTGGTGAACCGGGCA 61.569 57.895 6.32 0.00 39.43 5.36
102 107 2.261361 GCATTTGGTGAACCGGGC 59.739 61.111 6.32 0.00 39.43 6.13
104 109 1.501741 CTCGCATTTGGTGAACCGG 59.498 57.895 0.00 0.00 39.43 5.28
110 115 1.870458 CGCATGCTCGCATTTGGTG 60.870 57.895 17.13 0.00 33.90 4.17
123 128 1.226575 CCTGCAAGCATGTCGCATG 60.227 57.895 13.37 13.37 46.13 4.06
139 144 3.069443 CACCCTTATTTTTGTGCACACCT 59.931 43.478 21.56 6.95 0.00 4.00
151 156 8.113462 ACACATCCTTATAACACACCCTTATTT 58.887 33.333 0.00 0.00 0.00 1.40
153 158 7.208064 ACACATCCTTATAACACACCCTTAT 57.792 36.000 0.00 0.00 0.00 1.73
154 159 6.630203 ACACATCCTTATAACACACCCTTA 57.370 37.500 0.00 0.00 0.00 2.69
155 160 5.514500 ACACATCCTTATAACACACCCTT 57.486 39.130 0.00 0.00 0.00 3.95
156 161 5.514500 AACACATCCTTATAACACACCCT 57.486 39.130 0.00 0.00 0.00 4.34
157 162 5.105917 CCAAACACATCCTTATAACACACCC 60.106 44.000 0.00 0.00 0.00 4.61
158 163 5.475564 ACCAAACACATCCTTATAACACACC 59.524 40.000 0.00 0.00 0.00 4.16
159 164 6.430000 AGACCAAACACATCCTTATAACACAC 59.570 38.462 0.00 0.00 0.00 3.82
160 165 6.539173 AGACCAAACACATCCTTATAACACA 58.461 36.000 0.00 0.00 0.00 3.72
161 166 6.653320 TGAGACCAAACACATCCTTATAACAC 59.347 38.462 0.00 0.00 0.00 3.32
162 167 6.774673 TGAGACCAAACACATCCTTATAACA 58.225 36.000 0.00 0.00 0.00 2.41
163 168 7.681939 TTGAGACCAAACACATCCTTATAAC 57.318 36.000 0.00 0.00 0.00 1.89
164 169 8.877864 ATTTGAGACCAAACACATCCTTATAA 57.122 30.769 0.00 0.00 44.16 0.98
165 170 9.967451 TTATTTGAGACCAAACACATCCTTATA 57.033 29.630 0.00 0.00 44.16 0.98
166 171 8.877864 TTATTTGAGACCAAACACATCCTTAT 57.122 30.769 0.00 0.00 44.16 1.73
167 172 7.942341 ACTTATTTGAGACCAAACACATCCTTA 59.058 33.333 0.00 0.00 44.16 2.69
168 173 6.777580 ACTTATTTGAGACCAAACACATCCTT 59.222 34.615 0.00 0.00 44.16 3.36
169 174 6.306987 ACTTATTTGAGACCAAACACATCCT 58.693 36.000 0.00 0.00 44.16 3.24
170 175 6.206634 TGACTTATTTGAGACCAAACACATCC 59.793 38.462 0.00 0.00 44.16 3.51
171 176 7.202016 TGACTTATTTGAGACCAAACACATC 57.798 36.000 0.00 0.00 44.16 3.06
172 177 7.448161 TGATGACTTATTTGAGACCAAACACAT 59.552 33.333 0.00 0.00 44.16 3.21
173 178 6.770303 TGATGACTTATTTGAGACCAAACACA 59.230 34.615 0.00 0.00 44.16 3.72
174 179 7.202016 TGATGACTTATTTGAGACCAAACAC 57.798 36.000 0.00 0.00 44.16 3.32
175 180 7.502226 AGTTGATGACTTATTTGAGACCAAACA 59.498 33.333 0.00 0.00 39.14 2.83
176 181 7.875971 AGTTGATGACTTATTTGAGACCAAAC 58.124 34.615 0.00 0.00 39.14 2.93
177 182 8.463930 AAGTTGATGACTTATTTGAGACCAAA 57.536 30.769 0.00 0.00 46.61 3.28
190 195 9.490379 ACTTTTCGACTTATAAGTTGATGACTT 57.510 29.630 28.42 14.16 46.07 3.01
223 228 9.739276 TCAGGTCTGTTTGATAAATAAGTCATT 57.261 29.630 0.00 0.00 0.00 2.57
224 229 9.911788 ATCAGGTCTGTTTGATAAATAAGTCAT 57.088 29.630 0.00 0.00 32.50 3.06
225 230 9.739276 AATCAGGTCTGTTTGATAAATAAGTCA 57.261 29.630 0.00 0.00 33.09 3.41
235 240 9.167311 GTGACTTATAAATCAGGTCTGTTTGAT 57.833 33.333 0.00 0.00 35.63 2.57
236 241 7.606456 GGTGACTTATAAATCAGGTCTGTTTGA 59.394 37.037 0.00 0.00 0.00 2.69
237 242 7.148239 GGGTGACTTATAAATCAGGTCTGTTTG 60.148 40.741 0.00 0.00 0.00 2.93
238 243 6.884836 GGGTGACTTATAAATCAGGTCTGTTT 59.115 38.462 0.00 1.97 0.00 2.83
239 244 6.415573 GGGTGACTTATAAATCAGGTCTGTT 58.584 40.000 0.00 0.00 0.00 3.16
240 245 5.104485 GGGGTGACTTATAAATCAGGTCTGT 60.104 44.000 0.00 0.00 0.00 3.41
241 246 5.104527 TGGGGTGACTTATAAATCAGGTCTG 60.105 44.000 0.00 0.00 0.00 3.51
242 247 5.036916 TGGGGTGACTTATAAATCAGGTCT 58.963 41.667 0.00 0.00 0.00 3.85
243 248 5.367945 TGGGGTGACTTATAAATCAGGTC 57.632 43.478 0.00 0.00 0.00 3.85
244 249 5.253096 AGTTGGGGTGACTTATAAATCAGGT 59.747 40.000 0.00 0.00 0.00 4.00
245 250 5.755849 AGTTGGGGTGACTTATAAATCAGG 58.244 41.667 0.00 0.00 0.00 3.86
246 251 8.980481 ATAAGTTGGGGTGACTTATAAATCAG 57.020 34.615 0.00 0.00 44.36 2.90
252 257 8.612486 TGACTTATAAGTTGGGGTGACTTATA 57.388 34.615 18.96 10.90 44.36 0.98
253 258 7.504926 TGACTTATAAGTTGGGGTGACTTAT 57.495 36.000 18.96 12.48 46.52 1.73
254 259 6.938698 TGACTTATAAGTTGGGGTGACTTA 57.061 37.500 18.96 0.00 42.07 2.24
255 260 5.836024 TGACTTATAAGTTGGGGTGACTT 57.164 39.130 18.96 0.00 39.88 3.01
256 261 7.504926 TTATGACTTATAAGTTGGGGTGACT 57.495 36.000 18.96 0.00 39.88 3.41
257 262 7.787725 CTTATGACTTATAAGTTGGGGTGAC 57.212 40.000 18.96 4.87 42.11 3.67
268 273 6.354130 GGGTGGAGCAACTTATGACTTATAA 58.646 40.000 0.00 0.00 0.00 0.98
269 274 5.163237 GGGGTGGAGCAACTTATGACTTATA 60.163 44.000 0.00 0.00 0.00 0.98
270 275 4.385310 GGGGTGGAGCAACTTATGACTTAT 60.385 45.833 0.00 0.00 0.00 1.73
271 276 3.054655 GGGGTGGAGCAACTTATGACTTA 60.055 47.826 0.00 0.00 0.00 2.24
272 277 2.290960 GGGGTGGAGCAACTTATGACTT 60.291 50.000 0.00 0.00 0.00 3.01
273 278 1.282157 GGGGTGGAGCAACTTATGACT 59.718 52.381 0.00 0.00 0.00 3.41
274 279 1.004277 TGGGGTGGAGCAACTTATGAC 59.996 52.381 0.00 0.00 0.00 3.06
275 280 1.367346 TGGGGTGGAGCAACTTATGA 58.633 50.000 0.00 0.00 0.00 2.15
276 281 1.818674 GTTGGGGTGGAGCAACTTATG 59.181 52.381 0.00 0.00 0.00 1.90
277 282 1.710809 AGTTGGGGTGGAGCAACTTAT 59.289 47.619 0.00 0.00 34.63 1.73
278 283 1.145571 AGTTGGGGTGGAGCAACTTA 58.854 50.000 0.00 0.00 34.63 2.24
279 284 0.261696 AAGTTGGGGTGGAGCAACTT 59.738 50.000 0.00 0.00 41.36 2.66
280 285 1.145571 TAAGTTGGGGTGGAGCAACT 58.854 50.000 0.00 0.00 39.27 3.16
281 286 1.989706 TTAAGTTGGGGTGGAGCAAC 58.010 50.000 0.00 0.00 0.00 4.17
282 287 2.696187 GTTTTAAGTTGGGGTGGAGCAA 59.304 45.455 0.00 0.00 0.00 3.91
283 288 2.091555 AGTTTTAAGTTGGGGTGGAGCA 60.092 45.455 0.00 0.00 0.00 4.26
284 289 2.594131 AGTTTTAAGTTGGGGTGGAGC 58.406 47.619 0.00 0.00 0.00 4.70
285 290 7.668469 ACTTATAAGTTTTAAGTTGGGGTGGAG 59.332 37.037 12.50 0.00 36.70 3.86
286 291 7.528675 ACTTATAAGTTTTAAGTTGGGGTGGA 58.471 34.615 12.50 0.00 36.70 4.02
287 292 7.449086 TGACTTATAAGTTTTAAGTTGGGGTGG 59.551 37.037 18.96 0.00 39.40 4.61
288 293 8.294577 GTGACTTATAAGTTTTAAGTTGGGGTG 58.705 37.037 18.96 0.00 39.40 4.61
289 294 7.449395 GGTGACTTATAAGTTTTAAGTTGGGGT 59.551 37.037 18.96 0.00 39.40 4.95
290 295 7.094075 GGGTGACTTATAAGTTTTAAGTTGGGG 60.094 40.741 18.96 0.00 39.40 4.96
291 296 7.094075 GGGGTGACTTATAAGTTTTAAGTTGGG 60.094 40.741 18.96 0.00 39.40 4.12
292 297 7.094075 GGGGGTGACTTATAAGTTTTAAGTTGG 60.094 40.741 18.96 0.00 39.40 3.77
293 298 7.668469 AGGGGGTGACTTATAAGTTTTAAGTTG 59.332 37.037 18.96 0.00 39.40 3.16
294 299 7.762610 AGGGGGTGACTTATAAGTTTTAAGTT 58.237 34.615 18.96 2.13 39.40 2.66
295 300 7.339177 AGGGGGTGACTTATAAGTTTTAAGT 57.661 36.000 18.96 15.86 41.41 2.24
296 301 8.645814 AAAGGGGGTGACTTATAAGTTTTAAG 57.354 34.615 18.96 10.49 39.88 1.85
297 302 8.862085 CAAAAGGGGGTGACTTATAAGTTTTAA 58.138 33.333 18.96 3.77 39.88 1.52
298 303 7.039574 GCAAAAGGGGGTGACTTATAAGTTTTA 60.040 37.037 18.96 6.80 39.88 1.52
299 304 6.239487 GCAAAAGGGGGTGACTTATAAGTTTT 60.239 38.462 18.96 10.67 39.88 2.43
300 305 5.245301 GCAAAAGGGGGTGACTTATAAGTTT 59.755 40.000 18.96 5.24 39.88 2.66
301 306 4.770531 GCAAAAGGGGGTGACTTATAAGTT 59.229 41.667 18.96 3.63 39.88 2.66
302 307 4.341487 GCAAAAGGGGGTGACTTATAAGT 58.659 43.478 18.05 18.05 43.16 2.24
303 308 3.377172 CGCAAAAGGGGGTGACTTATAAG 59.623 47.826 11.05 11.05 0.00 1.73
304 309 3.244981 ACGCAAAAGGGGGTGACTTATAA 60.245 43.478 0.00 0.00 32.17 0.98
305 310 2.306512 ACGCAAAAGGGGGTGACTTATA 59.693 45.455 0.00 0.00 32.17 0.98
306 311 1.074889 ACGCAAAAGGGGGTGACTTAT 59.925 47.619 0.00 0.00 32.17 1.73
307 312 0.475044 ACGCAAAAGGGGGTGACTTA 59.525 50.000 0.00 0.00 32.17 2.24
308 313 1.229076 ACGCAAAAGGGGGTGACTT 59.771 52.632 0.00 0.00 32.17 3.01
309 314 2.923837 ACGCAAAAGGGGGTGACT 59.076 55.556 0.00 0.00 32.17 3.41
317 322 2.203422 TGGGACCCACGCAAAAGG 60.203 61.111 9.95 0.00 38.47 3.11
318 323 3.039134 GTGGGACCCACGCAAAAG 58.961 61.111 27.79 0.00 44.95 2.27
326 331 1.930133 ATGCAGATGGTGGGACCCA 60.930 57.895 9.95 9.95 37.50 4.51
327 332 1.454479 CATGCAGATGGTGGGACCC 60.454 63.158 2.45 2.45 37.50 4.46
328 333 0.184451 ATCATGCAGATGGTGGGACC 59.816 55.000 0.00 0.00 39.22 4.46
329 334 2.936919 TATCATGCAGATGGTGGGAC 57.063 50.000 8.40 0.00 37.57 4.46
330 335 3.395273 TCAATATCATGCAGATGGTGGGA 59.605 43.478 8.40 0.00 37.57 4.37
331 336 3.758425 TCAATATCATGCAGATGGTGGG 58.242 45.455 8.40 0.00 37.57 4.61
332 337 5.336451 CCAATCAATATCATGCAGATGGTGG 60.336 44.000 8.40 0.00 37.57 4.61
333 338 5.243060 ACCAATCAATATCATGCAGATGGTG 59.757 40.000 8.40 6.70 37.57 4.17
334 339 5.243060 CACCAATCAATATCATGCAGATGGT 59.757 40.000 8.40 0.00 37.57 3.55
335 340 5.243060 ACACCAATCAATATCATGCAGATGG 59.757 40.000 8.40 0.00 37.57 3.51
336 341 6.149633 CACACCAATCAATATCATGCAGATG 58.850 40.000 8.40 0.00 37.57 2.90
337 342 5.243060 CCACACCAATCAATATCATGCAGAT 59.757 40.000 0.00 0.00 40.86 2.90
338 343 4.581409 CCACACCAATCAATATCATGCAGA 59.419 41.667 0.00 0.00 0.00 4.26
339 344 4.581409 TCCACACCAATCAATATCATGCAG 59.419 41.667 0.00 0.00 0.00 4.41
340 345 4.534797 TCCACACCAATCAATATCATGCA 58.465 39.130 0.00 0.00 0.00 3.96
341 346 5.508489 CCTTCCACACCAATCAATATCATGC 60.508 44.000 0.00 0.00 0.00 4.06
342 347 5.595542 ACCTTCCACACCAATCAATATCATG 59.404 40.000 0.00 0.00 0.00 3.07
343 348 5.595542 CACCTTCCACACCAATCAATATCAT 59.404 40.000 0.00 0.00 0.00 2.45
344 349 4.949238 CACCTTCCACACCAATCAATATCA 59.051 41.667 0.00 0.00 0.00 2.15
345 350 4.949856 ACACCTTCCACACCAATCAATATC 59.050 41.667 0.00 0.00 0.00 1.63
346 351 4.706476 CACACCTTCCACACCAATCAATAT 59.294 41.667 0.00 0.00 0.00 1.28
347 352 4.078537 CACACCTTCCACACCAATCAATA 58.921 43.478 0.00 0.00 0.00 1.90
348 353 2.892852 CACACCTTCCACACCAATCAAT 59.107 45.455 0.00 0.00 0.00 2.57
349 354 2.305928 CACACCTTCCACACCAATCAA 58.694 47.619 0.00 0.00 0.00 2.57
350 355 1.214175 ACACACCTTCCACACCAATCA 59.786 47.619 0.00 0.00 0.00 2.57
351 356 1.880027 GACACACCTTCCACACCAATC 59.120 52.381 0.00 0.00 0.00 2.67
352 357 1.214175 TGACACACCTTCCACACCAAT 59.786 47.619 0.00 0.00 0.00 3.16
353 358 0.621082 TGACACACCTTCCACACCAA 59.379 50.000 0.00 0.00 0.00 3.67
354 359 0.180171 CTGACACACCTTCCACACCA 59.820 55.000 0.00 0.00 0.00 4.17
355 360 0.535102 CCTGACACACCTTCCACACC 60.535 60.000 0.00 0.00 0.00 4.16
356 361 0.180406 ACCTGACACACCTTCCACAC 59.820 55.000 0.00 0.00 0.00 3.82
357 362 0.468226 GACCTGACACACCTTCCACA 59.532 55.000 0.00 0.00 0.00 4.17
358 363 0.468226 TGACCTGACACACCTTCCAC 59.532 55.000 0.00 0.00 0.00 4.02
359 364 0.468226 GTGACCTGACACACCTTCCA 59.532 55.000 0.00 0.00 40.11 3.53
360 365 0.759346 AGTGACCTGACACACCTTCC 59.241 55.000 0.00 0.00 42.45 3.46
361 366 2.622064 AAGTGACCTGACACACCTTC 57.378 50.000 0.00 0.00 42.45 3.46
362 367 5.307196 ACTTATAAGTGACCTGACACACCTT 59.693 40.000 17.35 0.00 42.45 3.50
363 368 4.838986 ACTTATAAGTGACCTGACACACCT 59.161 41.667 17.35 0.00 42.45 4.00
364 369 5.148651 ACTTATAAGTGACCTGACACACC 57.851 43.478 17.35 0.00 42.45 4.16
365 370 5.779922 TGACTTATAAGTGACCTGACACAC 58.220 41.667 22.68 4.46 42.45 3.82
366 371 6.041637 ACTTGACTTATAAGTGACCTGACACA 59.958 38.462 22.68 8.13 42.45 3.72
367 372 6.456501 ACTTGACTTATAAGTGACCTGACAC 58.543 40.000 22.68 5.64 39.88 3.67
368 373 6.665992 ACTTGACTTATAAGTGACCTGACA 57.334 37.500 22.68 9.51 39.88 3.58
377 382 7.554835 TGTTTGGTTGTCACTTGACTTATAAGT 59.445 33.333 18.05 18.05 44.99 2.24
378 383 7.925993 TGTTTGGTTGTCACTTGACTTATAAG 58.074 34.615 11.05 11.05 44.99 1.73
379 384 7.012894 CCTGTTTGGTTGTCACTTGACTTATAA 59.987 37.037 10.63 0.00 44.99 0.98
380 385 6.485313 CCTGTTTGGTTGTCACTTGACTTATA 59.515 38.462 10.63 0.00 44.99 0.98
381 386 5.299279 CCTGTTTGGTTGTCACTTGACTTAT 59.701 40.000 10.63 0.00 44.99 1.73
382 387 4.638421 CCTGTTTGGTTGTCACTTGACTTA 59.362 41.667 10.63 0.00 44.99 2.24
383 388 3.443681 CCTGTTTGGTTGTCACTTGACTT 59.556 43.478 10.63 0.00 44.99 3.01
384 389 3.016736 CCTGTTTGGTTGTCACTTGACT 58.983 45.455 10.63 0.00 44.99 3.41
385 390 2.479560 GCCTGTTTGGTTGTCACTTGAC 60.480 50.000 2.19 2.19 40.76 3.18
386 391 1.748493 GCCTGTTTGGTTGTCACTTGA 59.252 47.619 0.00 0.00 38.35 3.02
387 392 1.533756 CGCCTGTTTGGTTGTCACTTG 60.534 52.381 0.00 0.00 38.35 3.16
388 393 0.738389 CGCCTGTTTGGTTGTCACTT 59.262 50.000 0.00 0.00 38.35 3.16
389 394 0.393808 ACGCCTGTTTGGTTGTCACT 60.394 50.000 0.00 0.00 38.35 3.41
390 395 0.248458 CACGCCTGTTTGGTTGTCAC 60.248 55.000 0.00 0.00 38.35 3.67
391 396 0.393132 TCACGCCTGTTTGGTTGTCA 60.393 50.000 0.00 0.00 38.35 3.58
392 397 0.028902 GTCACGCCTGTTTGGTTGTC 59.971 55.000 0.00 0.00 38.35 3.18
393 398 0.393808 AGTCACGCCTGTTTGGTTGT 60.394 50.000 0.00 0.00 38.35 3.32
394 399 0.738389 AAGTCACGCCTGTTTGGTTG 59.262 50.000 0.00 0.00 38.35 3.77
395 400 2.335316 TAAGTCACGCCTGTTTGGTT 57.665 45.000 0.00 0.00 38.35 3.67
396 401 2.561478 ATAAGTCACGCCTGTTTGGT 57.439 45.000 0.00 0.00 38.35 3.67
397 402 4.000988 ACTTATAAGTCACGCCTGTTTGG 58.999 43.478 12.50 0.00 32.86 3.28
413 418 9.653287 CAGATGACTTAAAACCAGTGACTTATA 57.347 33.333 0.00 0.00 0.00 0.98
414 419 8.375506 TCAGATGACTTAAAACCAGTGACTTAT 58.624 33.333 0.00 0.00 0.00 1.73
415 420 7.656137 GTCAGATGACTTAAAACCAGTGACTTA 59.344 37.037 5.72 0.00 41.65 2.24
416 421 6.483640 GTCAGATGACTTAAAACCAGTGACTT 59.516 38.462 5.72 0.00 41.65 3.01
417 422 5.992217 GTCAGATGACTTAAAACCAGTGACT 59.008 40.000 5.72 0.00 41.65 3.41
418 423 6.229561 GTCAGATGACTTAAAACCAGTGAC 57.770 41.667 5.72 0.00 41.65 3.67
432 437 9.774742 GTTTTAATAAATCACCAGTCAGATGAC 57.225 33.333 4.77 4.77 45.08 3.06
433 438 8.956426 GGTTTTAATAAATCACCAGTCAGATGA 58.044 33.333 2.60 0.00 0.00 2.92
434 439 8.739039 TGGTTTTAATAAATCACCAGTCAGATG 58.261 33.333 5.45 0.00 29.53 2.90
435 440 8.877864 TGGTTTTAATAAATCACCAGTCAGAT 57.122 30.769 5.45 0.00 29.53 2.90
436 441 8.698973 TTGGTTTTAATAAATCACCAGTCAGA 57.301 30.769 8.70 0.00 34.20 3.27
437 442 9.191995 GTTTGGTTTTAATAAATCACCAGTCAG 57.808 33.333 8.70 0.00 34.20 3.51
438 443 8.696374 TGTTTGGTTTTAATAAATCACCAGTCA 58.304 29.630 8.70 9.15 34.20 3.41
439 444 9.191995 CTGTTTGGTTTTAATAAATCACCAGTC 57.808 33.333 8.70 7.37 34.20 3.51
440 445 8.147704 CCTGTTTGGTTTTAATAAATCACCAGT 58.852 33.333 8.70 0.00 34.20 4.00
441 446 7.117667 GCCTGTTTGGTTTTAATAAATCACCAG 59.882 37.037 8.70 8.05 34.20 4.00
442 447 6.931840 GCCTGTTTGGTTTTAATAAATCACCA 59.068 34.615 5.45 5.45 34.20 4.17
443 448 6.370442 GGCCTGTTTGGTTTTAATAAATCACC 59.630 38.462 0.00 0.79 34.20 4.02
444 449 6.370442 GGGCCTGTTTGGTTTTAATAAATCAC 59.630 38.462 0.84 0.00 34.20 3.06
445 450 6.271159 AGGGCCTGTTTGGTTTTAATAAATCA 59.729 34.615 4.50 0.00 38.35 2.57
446 451 6.707290 AGGGCCTGTTTGGTTTTAATAAATC 58.293 36.000 4.50 0.00 38.35 2.17
447 452 6.696042 AGGGCCTGTTTGGTTTTAATAAAT 57.304 33.333 4.50 0.00 38.35 1.40
448 453 7.613551 TTAGGGCCTGTTTGGTTTTAATAAA 57.386 32.000 18.53 0.00 38.35 1.40
449 454 7.443477 GTTTAGGGCCTGTTTGGTTTTAATAA 58.557 34.615 18.53 0.00 38.35 1.40
450 455 6.014413 GGTTTAGGGCCTGTTTGGTTTTAATA 60.014 38.462 18.53 0.00 38.35 0.98
451 456 5.221762 GGTTTAGGGCCTGTTTGGTTTTAAT 60.222 40.000 18.53 0.00 38.35 1.40
452 457 4.101274 GGTTTAGGGCCTGTTTGGTTTTAA 59.899 41.667 18.53 0.00 38.35 1.52
453 458 3.642377 GGTTTAGGGCCTGTTTGGTTTTA 59.358 43.478 18.53 0.00 38.35 1.52
454 459 2.436542 GGTTTAGGGCCTGTTTGGTTTT 59.563 45.455 18.53 0.00 38.35 2.43
455 460 2.043992 GGTTTAGGGCCTGTTTGGTTT 58.956 47.619 18.53 0.00 38.35 3.27
456 461 1.219469 AGGTTTAGGGCCTGTTTGGTT 59.781 47.619 18.53 0.00 38.35 3.67
457 462 0.857675 AGGTTTAGGGCCTGTTTGGT 59.142 50.000 18.53 0.00 38.35 3.67
458 463 2.891191 TAGGTTTAGGGCCTGTTTGG 57.109 50.000 18.53 0.00 37.54 3.28
459 464 4.028993 TCTTAGGTTTAGGGCCTGTTTG 57.971 45.455 18.53 0.00 37.54 2.93
460 465 4.948062 ATCTTAGGTTTAGGGCCTGTTT 57.052 40.909 18.53 0.00 37.54 2.83
461 466 4.291249 TGAATCTTAGGTTTAGGGCCTGTT 59.709 41.667 18.53 0.00 37.54 3.16
462 467 3.850173 TGAATCTTAGGTTTAGGGCCTGT 59.150 43.478 18.53 0.00 37.54 4.00
463 468 4.455606 CTGAATCTTAGGTTTAGGGCCTG 58.544 47.826 18.53 0.00 37.54 4.85
464 469 3.117851 GCTGAATCTTAGGTTTAGGGCCT 60.118 47.826 12.58 12.58 40.00 5.19
465 470 3.215151 GCTGAATCTTAGGTTTAGGGCC 58.785 50.000 0.00 0.00 0.00 5.80
466 471 2.872858 CGCTGAATCTTAGGTTTAGGGC 59.127 50.000 1.53 0.00 0.00 5.19
467 472 2.872858 GCGCTGAATCTTAGGTTTAGGG 59.127 50.000 9.20 9.20 0.00 3.53
468 473 3.531538 TGCGCTGAATCTTAGGTTTAGG 58.468 45.455 9.73 0.00 0.00 2.69
469 474 4.870426 TCTTGCGCTGAATCTTAGGTTTAG 59.130 41.667 9.73 0.00 0.00 1.85
524 533 1.587933 CTATCGCTAGCCCTCGGTCC 61.588 65.000 9.66 0.00 0.00 4.46
527 536 1.581954 CACTATCGCTAGCCCTCGG 59.418 63.158 9.66 0.00 0.00 4.63
536 545 1.213182 TGAGTCCTCTCCACTATCGCT 59.787 52.381 0.00 0.00 39.75 4.93
540 549 3.433882 CGGTACTGAGTCCTCTCCACTAT 60.434 52.174 0.00 0.00 39.75 2.12
541 550 2.093075 CGGTACTGAGTCCTCTCCACTA 60.093 54.545 0.00 0.00 39.75 2.74
554 3278 3.427098 CGTTGCTCAGAATACGGTACTGA 60.427 47.826 9.17 7.87 38.16 3.41
555 3279 2.852413 CGTTGCTCAGAATACGGTACTG 59.148 50.000 0.00 0.00 0.00 2.74
556 3280 2.159282 CCGTTGCTCAGAATACGGTACT 60.159 50.000 0.00 0.00 46.25 2.73
557 3281 2.190981 CCGTTGCTCAGAATACGGTAC 58.809 52.381 0.00 0.00 46.25 3.34
558 3282 2.572191 CCGTTGCTCAGAATACGGTA 57.428 50.000 0.00 0.00 46.25 4.02
561 3285 0.739462 TGGCCGTTGCTCAGAATACG 60.739 55.000 0.00 0.00 37.74 3.06
562 3286 1.448985 TTGGCCGTTGCTCAGAATAC 58.551 50.000 0.00 0.00 37.74 1.89
563 3287 2.418368 ATTGGCCGTTGCTCAGAATA 57.582 45.000 0.00 0.00 37.74 1.75
565 3289 0.597568 CAATTGGCCGTTGCTCAGAA 59.402 50.000 7.64 0.00 37.74 3.02
566 3290 0.537143 ACAATTGGCCGTTGCTCAGA 60.537 50.000 17.78 0.00 37.74 3.27
571 3850 1.398390 CTCTCTACAATTGGCCGTTGC 59.602 52.381 17.78 0.00 0.00 4.17
603 3882 3.925238 GATAACTGTGCGGCGGCG 61.925 66.667 28.70 28.70 44.10 6.46
604 3883 3.573491 GGATAACTGTGCGGCGGC 61.573 66.667 9.78 9.68 40.52 6.53
605 3884 2.125310 TGGATAACTGTGCGGCGG 60.125 61.111 9.78 0.00 0.00 6.13
606 3885 2.798501 CGTGGATAACTGTGCGGCG 61.799 63.158 0.51 0.51 0.00 6.46
659 3938 9.804977 ATACGGTACTACTCTGGTATTCTTTAT 57.195 33.333 0.00 0.00 0.00 1.40
670 3949 5.125097 ACCAACAGAATACGGTACTACTCTG 59.875 44.000 12.94 12.94 37.04 3.35
671 3950 5.259632 ACCAACAGAATACGGTACTACTCT 58.740 41.667 0.00 0.00 0.00 3.24
672 3951 5.124457 TGACCAACAGAATACGGTACTACTC 59.876 44.000 0.00 0.00 0.00 2.59
725 4014 2.301346 GTGGAGGCCGAATGAATGAAT 58.699 47.619 0.00 0.00 0.00 2.57
727 4016 0.107214 GGTGGAGGCCGAATGAATGA 60.107 55.000 0.00 0.00 0.00 2.57
728 4017 0.394216 TGGTGGAGGCCGAATGAATG 60.394 55.000 0.00 0.00 0.00 2.67
800 4089 0.690077 AATAGAGGTGGGTCGGGGAC 60.690 60.000 0.00 0.00 0.00 4.46
801 4090 0.043637 AAATAGAGGTGGGTCGGGGA 59.956 55.000 0.00 0.00 0.00 4.81
802 4091 0.468648 GAAATAGAGGTGGGTCGGGG 59.531 60.000 0.00 0.00 0.00 5.73
803 4092 1.134491 GTGAAATAGAGGTGGGTCGGG 60.134 57.143 0.00 0.00 0.00 5.14
804 4093 1.134491 GGTGAAATAGAGGTGGGTCGG 60.134 57.143 0.00 0.00 0.00 4.79
805 4094 1.470979 CGGTGAAATAGAGGTGGGTCG 60.471 57.143 0.00 0.00 0.00 4.79
806 4095 1.553704 ACGGTGAAATAGAGGTGGGTC 59.446 52.381 0.00 0.00 0.00 4.46
811 4100 0.175073 GGCGACGGTGAAATAGAGGT 59.825 55.000 0.00 0.00 0.00 3.85
839 4128 1.993369 GCGGATGCGGAAAGGGAAAG 61.993 60.000 9.20 0.00 0.00 2.62
1414 4766 2.794910 ACACGGAATCGAATCGCAATAG 59.205 45.455 0.00 0.00 40.11 1.73
1418 4770 2.281140 TTACACGGAATCGAATCGCA 57.719 45.000 0.00 0.00 40.11 5.10
1430 4782 5.260140 CCAATTACGCTAACATTTACACGG 58.740 41.667 0.00 0.00 0.00 4.94
1500 4852 1.001745 GCGGCCAATTCACAACGTTC 61.002 55.000 2.24 0.00 0.00 3.95
1505 4857 1.861542 CGAAGGCGGCCAATTCACAA 61.862 55.000 23.09 0.00 0.00 3.33
1506 4858 2.331893 CGAAGGCGGCCAATTCACA 61.332 57.895 23.09 0.00 0.00 3.58
1507 4859 2.485122 CGAAGGCGGCCAATTCAC 59.515 61.111 23.09 4.59 0.00 3.18
1508 4860 3.439540 GCGAAGGCGGCCAATTCA 61.440 61.111 23.09 0.00 38.16 2.57
1592 4945 3.492756 GCACGAGGAGCTTCTTCAATATC 59.507 47.826 0.00 0.00 0.00 1.63
1600 4953 2.010582 GATCCGCACGAGGAGCTTCT 62.011 60.000 0.00 0.00 44.55 2.85
1626 4980 3.244770 TGGTGGACCAATCCTACAGTTTC 60.245 47.826 0.00 0.00 46.43 2.78
1748 5103 3.508840 GGCGGGTGCTTCAATCCG 61.509 66.667 0.00 0.00 44.70 4.18
1784 5139 1.075536 TGCTTTCCTTTCCCCTTCTCC 59.924 52.381 0.00 0.00 0.00 3.71
1886 5244 0.403271 ATCAAGCAGCAACTCCAGGT 59.597 50.000 0.00 0.00 0.00 4.00
1930 5289 4.689612 ATCATACGGTCATTAAGGCAGT 57.310 40.909 0.00 0.00 33.84 4.40
1951 5310 4.228210 ACTGCTCCTTTCCCATCTTTGATA 59.772 41.667 0.00 0.00 0.00 2.15
2004 5363 6.587608 GCAATCAAATCCACCTTCACTTTTAG 59.412 38.462 0.00 0.00 0.00 1.85
2174 5538 8.842358 TTTTTCGTTCAATAGACTAGGACATT 57.158 30.769 0.00 0.00 0.00 2.71
2234 5598 6.437162 AGGGTGACAGCAACATGTTAAAATAT 59.563 34.615 11.53 0.00 31.69 1.28
2248 5612 2.107378 TGGAAATGTAAGGGTGACAGCA 59.893 45.455 7.01 0.00 0.00 4.41
2272 5636 6.648725 ACTGTCTATTTCAAAAGTCTGCTCTC 59.351 38.462 0.00 0.00 0.00 3.20
2302 5666 8.697292 AGGTAGACAGTCTCTAATCAAAATACC 58.303 37.037 6.27 4.51 32.96 2.73


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

AutoCloner maintained by Alex Coulton.