Multiple sequence alignment - TraesCS1B01G177900

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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 TraesCS1B01G177900 chr1B 100.000 4816 0 0 1 4816 322487605 322482790 0.000000e+00 8894.0
1 TraesCS1B01G177900 chr1A 94.060 4091 129 53 560 4590 290205425 290201389 0.000000e+00 6104.0
2 TraesCS1B01G177900 chr1A 94.359 195 10 1 4623 4816 290201387 290201193 1.010000e-76 298.0
3 TraesCS1B01G177900 chr1A 86.667 165 14 7 1 160 290205577 290205416 4.950000e-40 176.0
4 TraesCS1B01G177900 chr7D 93.916 3386 97 48 596 3910 617975293 617971946 0.000000e+00 5011.0
5 TraesCS1B01G177900 chr7D 92.434 912 62 4 3912 4816 617971896 617970985 0.000000e+00 1295.0
6 TraesCS1B01G177900 chr7D 87.277 393 44 4 168 558 99616329 99616717 1.230000e-120 444.0
7 TraesCS1B01G177900 chr7D 89.157 166 11 4 1 164 617975673 617975513 2.940000e-47 200.0
8 TraesCS1B01G177900 chr7D 100.000 45 0 0 560 604 617975519 617975475 3.090000e-12 84.2
9 TraesCS1B01G177900 chr1D 93.820 3382 103 48 596 3910 223174472 223171130 0.000000e+00 4990.0
10 TraesCS1B01G177900 chr1D 92.325 912 63 4 3912 4816 223171080 223170169 0.000000e+00 1290.0
11 TraesCS1B01G177900 chr1D 89.157 166 14 2 1 164 223174855 223174692 2.270000e-48 204.0
12 TraesCS1B01G177900 chr3A 87.940 398 38 10 166 558 80127405 80127797 1.220000e-125 460.0
13 TraesCS1B01G177900 chr3D 87.437 398 42 6 162 558 590228732 590229122 7.350000e-123 451.0
14 TraesCS1B01G177900 chr2D 87.786 393 36 8 174 563 485642039 485642422 2.640000e-122 449.0
15 TraesCS1B01G177900 chr2D 87.532 393 36 9 174 563 485598841 485599223 4.420000e-120 442.0
16 TraesCS1B01G177900 chr2D 86.902 397 45 5 168 562 18624645 18624254 5.720000e-119 438.0
17 TraesCS1B01G177900 chr7A 87.792 385 44 3 168 551 674406676 674407058 9.510000e-122 448.0
18 TraesCS1B01G177900 chr4A 87.468 391 44 5 169 558 241019515 241019129 3.420000e-121 446.0
19 TraesCS1B01G177900 chr3B 87.597 387 42 5 174 559 650059158 650058777 1.230000e-120 444.0
20 TraesCS1B01G177900 chrUn 92.881 295 7 10 3622 3910 480384347 480384061 2.680000e-112 416.0


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 TraesCS1B01G177900 chr1B 322482790 322487605 4815 True 8894.000000 8894 100.000000 1 4816 1 chr1B.!!$R1 4815
1 TraesCS1B01G177900 chr1A 290201193 290205577 4384 True 2192.666667 6104 91.695333 1 4816 3 chr1A.!!$R1 4815
2 TraesCS1B01G177900 chr7D 617970985 617975673 4688 True 1647.550000 5011 93.876750 1 4816 4 chr7D.!!$R1 4815
3 TraesCS1B01G177900 chr1D 223170169 223174855 4686 True 2161.333333 4990 91.767333 1 4816 3 chr1D.!!$R1 4815

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
444 450 0.103390 TCTCCGAAACTTGACGTGCA 59.897 50.0 0.00 0.00 0.00 4.57 F
445 451 0.232303 CTCCGAAACTTGACGTGCAC 59.768 55.0 6.82 6.82 0.00 4.57 F
671 876 0.247185 CACGGGCATGGCAGAAAAAT 59.753 50.0 25.42 0.00 0.00 1.82 F
1739 1960 1.507562 TCGACAACGTGTGCATGATT 58.492 45.0 0.00 0.00 40.69 2.57 F
2746 2998 0.464373 ATGGACGCATGCGAATTCCT 60.464 50.0 43.72 24.89 42.83 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2411 2632 0.659427 ATAGCATCGTGTGTGCATGC 59.341 50.000 11.82 11.82 44.87 4.06 R
2415 2640 2.221749 CCATGTATAGCATCGTGTGTGC 59.778 50.000 0.00 0.00 42.81 4.57 R
2532 2772 1.142262 TCCTCATGCAGATGATGTGGG 59.858 52.381 5.71 0.00 37.97 4.61 R
3620 3888 1.267574 ATCACCGGAGAGCACACCAT 61.268 55.000 9.46 0.00 0.00 3.55 R
4220 4581 0.544697 AGTTGACCAACCAGACCGTT 59.455 50.000 9.07 0.00 42.06 4.44 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
102 108 5.484715 GAGTGCACCTTATTTACTGGTACA 58.515 41.667 14.63 0.00 32.13 2.90
173 179 0.585357 GCAATATGCACTGGAGAGCG 59.415 55.000 0.00 0.00 44.26 5.03
174 180 1.224075 CAATATGCACTGGAGAGCGG 58.776 55.000 0.00 0.00 34.29 5.52
175 181 0.533755 AATATGCACTGGAGAGCGGC 60.534 55.000 0.00 0.00 34.29 6.53
176 182 2.705934 ATATGCACTGGAGAGCGGCG 62.706 60.000 0.51 0.51 34.29 6.46
179 185 2.357517 CACTGGAGAGCGGCGTTT 60.358 61.111 9.37 0.00 0.00 3.60
180 186 2.357517 ACTGGAGAGCGGCGTTTG 60.358 61.111 9.37 0.00 0.00 2.93
181 187 3.121030 CTGGAGAGCGGCGTTTGG 61.121 66.667 9.37 0.00 0.00 3.28
182 188 4.697756 TGGAGAGCGGCGTTTGGG 62.698 66.667 9.37 0.00 0.00 4.12
189 195 4.418401 CGGCGTTTGGGCACATGG 62.418 66.667 0.00 0.00 42.43 3.66
190 196 4.067913 GGCGTTTGGGCACATGGG 62.068 66.667 0.00 0.00 41.77 4.00
191 197 2.988684 GCGTTTGGGCACATGGGA 60.989 61.111 0.00 0.00 0.00 4.37
192 198 2.993471 GCGTTTGGGCACATGGGAG 61.993 63.158 0.00 0.00 0.00 4.30
193 199 2.973082 GTTTGGGCACATGGGAGC 59.027 61.111 0.00 0.00 0.00 4.70
194 200 2.676121 TTTGGGCACATGGGAGCG 60.676 61.111 0.00 0.00 0.00 5.03
209 215 3.488090 GCGCGCGCTCCTAGTTTT 61.488 61.111 44.38 0.00 38.26 2.43
210 216 3.023591 GCGCGCGCTCCTAGTTTTT 62.024 57.895 44.38 0.00 38.26 1.94
211 217 1.689352 GCGCGCGCTCCTAGTTTTTA 61.689 55.000 44.38 0.00 38.26 1.52
212 218 0.717224 CGCGCGCTCCTAGTTTTTAA 59.283 50.000 30.48 0.00 0.00 1.52
213 219 1.127213 CGCGCGCTCCTAGTTTTTAAA 59.873 47.619 30.48 0.00 0.00 1.52
214 220 2.411806 CGCGCGCTCCTAGTTTTTAAAA 60.412 45.455 30.48 0.00 0.00 1.52
215 221 3.726782 CGCGCGCTCCTAGTTTTTAAAAT 60.727 43.478 30.48 0.00 0.00 1.82
216 222 3.542310 GCGCGCTCCTAGTTTTTAAAATG 59.458 43.478 26.67 0.00 0.00 2.32
217 223 4.719040 CGCGCTCCTAGTTTTTAAAATGT 58.281 39.130 5.56 0.00 0.00 2.71
218 224 4.553429 CGCGCTCCTAGTTTTTAAAATGTG 59.447 41.667 5.56 0.00 0.00 3.21
219 225 5.458015 GCGCTCCTAGTTTTTAAAATGTGT 58.542 37.500 0.00 0.00 0.00 3.72
220 226 5.918576 GCGCTCCTAGTTTTTAAAATGTGTT 59.081 36.000 0.00 0.00 0.00 3.32
221 227 6.419710 GCGCTCCTAGTTTTTAAAATGTGTTT 59.580 34.615 0.00 0.00 0.00 2.83
222 228 7.042992 GCGCTCCTAGTTTTTAAAATGTGTTTT 60.043 33.333 0.00 0.00 40.48 2.43
223 229 9.453325 CGCTCCTAGTTTTTAAAATGTGTTTTA 57.547 29.630 0.55 0.00 38.44 1.52
267 273 9.419737 CAAATAATTCCAAACAAAAACTTGACG 57.580 29.630 0.00 0.00 0.00 4.35
268 274 5.463499 AATTCCAAACAAAAACTTGACGC 57.537 34.783 0.00 0.00 0.00 5.19
269 275 2.520979 TCCAAACAAAAACTTGACGCG 58.479 42.857 3.53 3.53 0.00 6.01
270 276 2.095161 TCCAAACAAAAACTTGACGCGT 60.095 40.909 13.85 13.85 0.00 6.01
271 277 3.126514 TCCAAACAAAAACTTGACGCGTA 59.873 39.130 13.97 0.00 0.00 4.42
272 278 3.238798 CCAAACAAAAACTTGACGCGTAC 59.761 43.478 13.97 6.75 0.00 3.67
273 279 3.743567 AACAAAAACTTGACGCGTACA 57.256 38.095 13.97 9.74 0.00 2.90
274 280 3.955771 ACAAAAACTTGACGCGTACAT 57.044 38.095 13.97 0.00 0.00 2.29
275 281 3.868835 ACAAAAACTTGACGCGTACATC 58.131 40.909 13.97 0.00 0.00 3.06
276 282 3.558418 ACAAAAACTTGACGCGTACATCT 59.442 39.130 13.97 0.00 0.00 2.90
277 283 4.034742 ACAAAAACTTGACGCGTACATCTT 59.965 37.500 13.97 0.00 0.00 2.40
278 284 3.788434 AAACTTGACGCGTACATCTTG 57.212 42.857 13.97 0.77 0.00 3.02
279 285 2.717580 ACTTGACGCGTACATCTTGA 57.282 45.000 13.97 0.00 0.00 3.02
280 286 3.232213 ACTTGACGCGTACATCTTGAT 57.768 42.857 13.97 0.00 0.00 2.57
281 287 4.365899 ACTTGACGCGTACATCTTGATA 57.634 40.909 13.97 0.00 0.00 2.15
282 288 4.933330 ACTTGACGCGTACATCTTGATAT 58.067 39.130 13.97 0.00 0.00 1.63
283 289 5.348986 ACTTGACGCGTACATCTTGATATT 58.651 37.500 13.97 0.00 0.00 1.28
284 290 5.232202 ACTTGACGCGTACATCTTGATATTG 59.768 40.000 13.97 0.00 0.00 1.90
285 291 4.678622 TGACGCGTACATCTTGATATTGT 58.321 39.130 13.97 0.00 0.00 2.71
286 292 5.823353 TGACGCGTACATCTTGATATTGTA 58.177 37.500 13.97 0.00 0.00 2.41
287 293 5.684184 TGACGCGTACATCTTGATATTGTAC 59.316 40.000 13.97 5.05 41.33 2.90
288 294 5.584442 ACGCGTACATCTTGATATTGTACA 58.416 37.500 11.67 0.00 43.67 2.90
289 295 6.213677 ACGCGTACATCTTGATATTGTACAT 58.786 36.000 11.67 0.00 43.67 2.29
290 296 6.143919 ACGCGTACATCTTGATATTGTACATG 59.856 38.462 11.67 0.00 43.67 3.21
291 297 6.299604 GCGTACATCTTGATATTGTACATGC 58.700 40.000 12.74 6.95 43.67 4.06
292 298 6.146184 GCGTACATCTTGATATTGTACATGCT 59.854 38.462 12.74 0.00 43.67 3.79
293 299 7.620188 GCGTACATCTTGATATTGTACATGCTC 60.620 40.741 12.74 0.00 43.67 4.26
294 300 7.382218 CGTACATCTTGATATTGTACATGCTCA 59.618 37.037 12.74 0.00 43.67 4.26
295 301 7.488187 ACATCTTGATATTGTACATGCTCAC 57.512 36.000 0.00 0.00 0.00 3.51
296 302 7.049754 ACATCTTGATATTGTACATGCTCACA 58.950 34.615 0.00 0.00 0.00 3.58
297 303 7.553760 ACATCTTGATATTGTACATGCTCACAA 59.446 33.333 9.69 9.69 38.89 3.33
298 304 7.920160 TCTTGATATTGTACATGCTCACAAA 57.080 32.000 10.93 3.76 38.11 2.83
299 305 7.977904 TCTTGATATTGTACATGCTCACAAAG 58.022 34.615 10.93 5.45 38.11 2.77
300 306 7.607607 TCTTGATATTGTACATGCTCACAAAGT 59.392 33.333 10.93 4.68 38.11 2.66
301 307 7.307493 TGATATTGTACATGCTCACAAAGTC 57.693 36.000 10.93 11.54 38.11 3.01
302 308 4.668576 ATTGTACATGCTCACAAAGTCG 57.331 40.909 10.93 0.00 38.11 4.18
303 309 3.106242 TGTACATGCTCACAAAGTCGT 57.894 42.857 0.00 0.00 0.00 4.34
304 310 3.462982 TGTACATGCTCACAAAGTCGTT 58.537 40.909 0.00 0.00 0.00 3.85
305 311 3.874543 TGTACATGCTCACAAAGTCGTTT 59.125 39.130 0.00 0.00 0.00 3.60
306 312 3.609103 ACATGCTCACAAAGTCGTTTC 57.391 42.857 0.00 0.00 0.00 2.78
307 313 2.032894 ACATGCTCACAAAGTCGTTTCG 60.033 45.455 0.00 0.00 0.00 3.46
308 314 0.303493 TGCTCACAAAGTCGTTTCGC 59.697 50.000 0.00 0.00 0.00 4.70
309 315 0.303493 GCTCACAAAGTCGTTTCGCA 59.697 50.000 0.00 0.00 0.00 5.10
310 316 1.267832 GCTCACAAAGTCGTTTCGCAA 60.268 47.619 0.00 0.00 0.00 4.85
311 317 2.789779 GCTCACAAAGTCGTTTCGCAAA 60.790 45.455 0.00 0.00 0.00 3.68
312 318 3.029074 CTCACAAAGTCGTTTCGCAAAG 58.971 45.455 0.00 0.00 0.00 2.77
313 319 2.673862 TCACAAAGTCGTTTCGCAAAGA 59.326 40.909 0.00 0.00 0.00 2.52
314 320 3.125487 TCACAAAGTCGTTTCGCAAAGAA 59.875 39.130 0.00 0.00 37.01 2.52
315 321 3.237433 CACAAAGTCGTTTCGCAAAGAAC 59.763 43.478 0.00 0.00 38.83 3.01
316 322 2.750301 AAGTCGTTTCGCAAAGAACC 57.250 45.000 0.00 0.00 38.83 3.62
317 323 0.580104 AGTCGTTTCGCAAAGAACCG 59.420 50.000 0.00 0.00 44.58 4.44
319 325 0.578211 TCGTTTCGCAAAGAACCGAC 59.422 50.000 0.00 0.00 46.33 4.79
320 326 0.302288 CGTTTCGCAAAGAACCGACA 59.698 50.000 0.00 0.00 45.83 4.35
321 327 1.267632 CGTTTCGCAAAGAACCGACAA 60.268 47.619 0.00 0.00 45.83 3.18
322 328 2.788030 GTTTCGCAAAGAACCGACAAA 58.212 42.857 0.00 0.00 38.83 2.83
323 329 3.368495 GTTTCGCAAAGAACCGACAAAT 58.632 40.909 0.00 0.00 38.83 2.32
324 330 3.701532 TTCGCAAAGAACCGACAAATT 57.298 38.095 0.00 0.00 33.14 1.82
325 331 4.815040 TTCGCAAAGAACCGACAAATTA 57.185 36.364 0.00 0.00 33.14 1.40
326 332 5.365403 TTCGCAAAGAACCGACAAATTAT 57.635 34.783 0.00 0.00 33.14 1.28
327 333 4.717991 TCGCAAAGAACCGACAAATTATG 58.282 39.130 0.00 0.00 0.00 1.90
328 334 5.278071 TTCGCAAAGAACCGACAAATTATGT 60.278 36.000 0.00 0.00 38.39 2.29
329 335 4.320690 CGCAAAGAACCGACAAATTATGTG 59.679 41.667 0.00 0.00 44.12 3.21
330 336 5.219633 GCAAAGAACCGACAAATTATGTGT 58.780 37.500 0.00 0.00 44.12 3.72
331 337 5.342259 GCAAAGAACCGACAAATTATGTGTC 59.658 40.000 5.48 5.48 44.12 3.67
337 343 3.449322 GACAAATTATGTGTCGCGTGT 57.551 42.857 5.77 0.00 44.12 4.49
338 344 3.152983 GACAAATTATGTGTCGCGTGTG 58.847 45.455 5.77 0.00 44.12 3.82
339 345 2.803386 ACAAATTATGTGTCGCGTGTGA 59.197 40.909 5.77 0.00 41.93 3.58
340 346 3.248841 ACAAATTATGTGTCGCGTGTGAA 59.751 39.130 5.77 0.00 41.93 3.18
341 347 4.215201 CAAATTATGTGTCGCGTGTGAAA 58.785 39.130 5.77 0.00 0.00 2.69
342 348 4.475763 AATTATGTGTCGCGTGTGAAAA 57.524 36.364 5.77 0.00 0.00 2.29
343 349 3.946308 TTATGTGTCGCGTGTGAAAAA 57.054 38.095 5.77 0.00 0.00 1.94
344 350 2.383298 ATGTGTCGCGTGTGAAAAAG 57.617 45.000 5.77 0.00 0.00 2.27
345 351 1.360820 TGTGTCGCGTGTGAAAAAGA 58.639 45.000 5.77 0.00 0.00 2.52
346 352 1.937223 TGTGTCGCGTGTGAAAAAGAT 59.063 42.857 5.77 0.00 0.00 2.40
347 353 3.124560 TGTGTCGCGTGTGAAAAAGATA 58.875 40.909 5.77 0.00 0.00 1.98
348 354 3.556365 TGTGTCGCGTGTGAAAAAGATAA 59.444 39.130 5.77 0.00 0.00 1.75
349 355 4.034163 TGTGTCGCGTGTGAAAAAGATAAA 59.966 37.500 5.77 0.00 0.00 1.40
350 356 4.965158 GTGTCGCGTGTGAAAAAGATAAAA 59.035 37.500 5.77 0.00 0.00 1.52
351 357 5.623673 GTGTCGCGTGTGAAAAAGATAAAAT 59.376 36.000 5.77 0.00 0.00 1.82
352 358 6.141685 GTGTCGCGTGTGAAAAAGATAAAATT 59.858 34.615 5.77 0.00 0.00 1.82
353 359 6.358558 TGTCGCGTGTGAAAAAGATAAAATTC 59.641 34.615 5.77 0.00 0.00 2.17
354 360 5.562248 TCGCGTGTGAAAAAGATAAAATTCG 59.438 36.000 5.77 0.00 0.00 3.34
355 361 5.562248 CGCGTGTGAAAAAGATAAAATTCGA 59.438 36.000 0.00 0.00 0.00 3.71
356 362 6.248420 CGCGTGTGAAAAAGATAAAATTCGAT 59.752 34.615 0.00 0.00 0.00 3.59
357 363 7.375781 GCGTGTGAAAAAGATAAAATTCGATG 58.624 34.615 0.00 0.00 0.00 3.84
358 364 7.060633 GCGTGTGAAAAAGATAAAATTCGATGT 59.939 33.333 0.00 0.00 0.00 3.06
359 365 8.901748 CGTGTGAAAAAGATAAAATTCGATGTT 58.098 29.630 0.00 0.00 0.00 2.71
386 392 8.791327 AAAAATGTTTTTCACAAGACATCCTT 57.209 26.923 0.00 0.00 36.85 3.36
387 393 8.791327 AAAATGTTTTTCACAAGACATCCTTT 57.209 26.923 0.00 0.00 36.85 3.11
388 394 8.791327 AAATGTTTTTCACAAGACATCCTTTT 57.209 26.923 0.00 0.00 36.85 2.27
389 395 7.775397 ATGTTTTTCACAAGACATCCTTTTG 57.225 32.000 0.00 0.00 39.50 2.44
390 396 6.696411 TGTTTTTCACAAGACATCCTTTTGT 58.304 32.000 0.00 0.00 34.87 2.83
391 397 6.811170 TGTTTTTCACAAGACATCCTTTTGTC 59.189 34.615 0.00 0.00 45.15 3.18
440 446 3.249013 GGTTTTCTCCGAAACTTGACG 57.751 47.619 0.00 0.00 39.05 4.35
441 447 2.610833 GGTTTTCTCCGAAACTTGACGT 59.389 45.455 0.00 0.00 39.05 4.34
442 448 3.545426 GGTTTTCTCCGAAACTTGACGTG 60.545 47.826 0.00 0.00 39.05 4.49
443 449 1.214367 TTCTCCGAAACTTGACGTGC 58.786 50.000 0.00 0.00 0.00 5.34
444 450 0.103390 TCTCCGAAACTTGACGTGCA 59.897 50.000 0.00 0.00 0.00 4.57
445 451 0.232303 CTCCGAAACTTGACGTGCAC 59.768 55.000 6.82 6.82 0.00 4.57
446 452 0.460459 TCCGAAACTTGACGTGCACA 60.460 50.000 18.64 0.00 0.00 4.57
447 453 0.315869 CCGAAACTTGACGTGCACAC 60.316 55.000 18.64 10.76 0.00 3.82
448 454 0.371989 CGAAACTTGACGTGCACACA 59.628 50.000 18.64 13.38 0.00 3.72
449 455 1.003972 CGAAACTTGACGTGCACACAT 60.004 47.619 18.64 0.56 0.00 3.21
450 456 2.219903 CGAAACTTGACGTGCACACATA 59.780 45.455 18.64 6.68 0.00 2.29
451 457 3.120683 CGAAACTTGACGTGCACACATAT 60.121 43.478 18.64 4.91 0.00 1.78
452 458 4.090786 CGAAACTTGACGTGCACACATATA 59.909 41.667 18.64 1.12 0.00 0.86
453 459 5.388994 CGAAACTTGACGTGCACACATATAA 60.389 40.000 18.64 2.04 0.00 0.98
454 460 6.494893 AAACTTGACGTGCACACATATAAT 57.505 33.333 18.64 0.00 0.00 1.28
455 461 7.463515 CGAAACTTGACGTGCACACATATAATA 60.464 37.037 18.64 0.00 0.00 0.98
456 462 7.786178 AACTTGACGTGCACACATATAATAT 57.214 32.000 18.64 0.00 0.00 1.28
457 463 7.408132 ACTTGACGTGCACACATATAATATC 57.592 36.000 18.64 0.00 0.00 1.63
458 464 6.983890 ACTTGACGTGCACACATATAATATCA 59.016 34.615 18.64 1.53 0.00 2.15
459 465 7.494298 ACTTGACGTGCACACATATAATATCAA 59.506 33.333 18.64 8.72 0.00 2.57
460 466 7.406799 TGACGTGCACACATATAATATCAAG 57.593 36.000 18.64 0.00 0.00 3.02
461 467 7.206687 TGACGTGCACACATATAATATCAAGA 58.793 34.615 18.64 0.00 0.00 3.02
462 468 7.872483 TGACGTGCACACATATAATATCAAGAT 59.128 33.333 18.64 0.00 0.00 2.40
463 469 8.021955 ACGTGCACACATATAATATCAAGATG 57.978 34.615 18.64 0.00 0.00 2.90
464 470 7.657354 ACGTGCACACATATAATATCAAGATGT 59.343 33.333 18.64 0.00 0.00 3.06
465 471 9.139174 CGTGCACACATATAATATCAAGATGTA 57.861 33.333 18.64 0.00 0.00 2.29
468 474 9.926751 GCACACATATAATATCAAGATGTATGC 57.073 33.333 11.12 11.12 41.89 3.14
526 532 3.849064 TTTTTCCCCGTGTGCAGG 58.151 55.556 0.00 0.00 0.00 4.85
527 533 2.494530 TTTTTCCCCGTGTGCAGGC 61.495 57.895 0.00 0.00 0.00 4.85
550 556 2.125912 CTCTCGGGAGCACCAACG 60.126 66.667 0.00 0.00 40.22 4.10
551 557 3.649277 CTCTCGGGAGCACCAACGG 62.649 68.421 0.00 0.00 40.22 4.44
552 558 3.691342 CTCGGGAGCACCAACGGA 61.691 66.667 1.58 0.00 40.22 4.69
553 559 3.934391 CTCGGGAGCACCAACGGAC 62.934 68.421 1.58 0.00 40.22 4.79
554 560 4.003788 CGGGAGCACCAACGGACT 62.004 66.667 1.58 0.00 40.22 3.85
555 561 2.430367 GGGAGCACCAACGGACTT 59.570 61.111 1.58 0.00 39.85 3.01
556 562 1.228154 GGGAGCACCAACGGACTTT 60.228 57.895 1.58 0.00 39.85 2.66
557 563 1.235281 GGGAGCACCAACGGACTTTC 61.235 60.000 1.58 0.00 39.85 2.62
558 564 1.566018 GGAGCACCAACGGACTTTCG 61.566 60.000 0.00 0.00 35.97 3.46
604 610 4.968626 CAAACTTTGCCAAAACCAGAAAC 58.031 39.130 0.00 0.00 0.00 2.78
606 803 2.093181 ACTTTGCCAAAACCAGAAACCC 60.093 45.455 0.00 0.00 0.00 4.11
627 824 2.161855 TGGCACAAATCTCGAAGCAAT 58.838 42.857 0.00 0.00 31.92 3.56
663 868 1.290203 CGATATATCACGGGCATGGC 58.710 55.000 11.56 11.56 0.00 4.40
671 876 0.247185 CACGGGCATGGCAGAAAAAT 59.753 50.000 25.42 0.00 0.00 1.82
677 882 2.417787 GGCATGGCAGAAAAATCACTCC 60.418 50.000 15.47 0.00 0.00 3.85
679 884 3.696051 GCATGGCAGAAAAATCACTCCTA 59.304 43.478 0.00 0.00 0.00 2.94
681 886 5.163478 GCATGGCAGAAAAATCACTCCTATT 60.163 40.000 0.00 0.00 0.00 1.73
682 887 6.039717 GCATGGCAGAAAAATCACTCCTATTA 59.960 38.462 0.00 0.00 0.00 0.98
683 888 7.255730 GCATGGCAGAAAAATCACTCCTATTAT 60.256 37.037 0.00 0.00 0.00 1.28
685 890 9.866655 ATGGCAGAAAAATCACTCCTATTATAA 57.133 29.630 0.00 0.00 0.00 0.98
686 891 9.342308 TGGCAGAAAAATCACTCCTATTATAAG 57.658 33.333 0.00 0.00 0.00 1.73
687 892 9.561069 GGCAGAAAAATCACTCCTATTATAAGA 57.439 33.333 0.00 0.00 0.00 2.10
742 947 1.984990 CGAAACATGAACGCCAAATGG 59.015 47.619 0.00 0.00 38.53 3.16
1001 1206 3.417069 AATCACACATTCCTCGTTCCA 57.583 42.857 0.00 0.00 0.00 3.53
1032 1243 1.634757 CGCACACACACACACACACT 61.635 55.000 0.00 0.00 0.00 3.55
1089 1310 4.783764 ATCTGCATATCCAATCGTACGA 57.216 40.909 21.93 21.93 0.00 3.43
1092 1313 4.048241 TGCATATCCAATCGTACGAACA 57.952 40.909 23.56 6.66 0.00 3.18
1208 1429 2.048127 GTGCAGACGGTGGAGGTC 60.048 66.667 0.00 0.00 34.62 3.85
1232 1453 2.411547 CGTGGCAGTTTTCATCTTCGTC 60.412 50.000 0.00 0.00 0.00 4.20
1346 1567 2.794981 CGACATGTACGAGTGGATCACC 60.795 54.545 0.00 0.00 34.49 4.02
1739 1960 1.507562 TCGACAACGTGTGCATGATT 58.492 45.000 0.00 0.00 40.69 2.57
2467 2696 1.612950 TCATGTTGCGACCTTGCATTT 59.387 42.857 0.45 0.00 45.78 2.32
2532 2772 1.302832 CCCAAGTGTGTGAGCCCTC 60.303 63.158 0.00 0.00 0.00 4.30
2535 2775 1.770110 AAGTGTGTGAGCCCTCCCA 60.770 57.895 0.00 0.00 0.00 4.37
2584 2825 2.112190 GCCAAGGTAGCTTCTCCTACT 58.888 52.381 3.68 0.00 38.18 2.57
2597 2838 5.107568 GCTTCTCCTACTACAAAACAACGAC 60.108 44.000 0.00 0.00 0.00 4.34
2746 2998 0.464373 ATGGACGCATGCGAATTCCT 60.464 50.000 43.72 24.89 42.83 3.36
2748 3000 1.202639 TGGACGCATGCGAATTCCTAT 60.203 47.619 43.72 21.09 42.83 2.57
2902 3154 5.195001 TGTTTCTGGGTATCTTTTGTTGC 57.805 39.130 0.00 0.00 0.00 4.17
2904 3156 5.127845 TGTTTCTGGGTATCTTTTGTTGCAA 59.872 36.000 0.00 0.00 0.00 4.08
2905 3157 5.452078 TTCTGGGTATCTTTTGTTGCAAG 57.548 39.130 0.00 0.00 0.00 4.01
2906 3158 3.826157 TCTGGGTATCTTTTGTTGCAAGG 59.174 43.478 0.00 0.00 0.00 3.61
2907 3159 2.298729 TGGGTATCTTTTGTTGCAAGGC 59.701 45.455 0.00 0.00 0.00 4.35
2908 3160 2.562738 GGGTATCTTTTGTTGCAAGGCT 59.437 45.455 0.00 0.00 0.00 4.58
2910 3162 3.367395 GGTATCTTTTGTTGCAAGGCTCC 60.367 47.826 0.00 0.00 0.00 4.70
2911 3163 1.774110 TCTTTTGTTGCAAGGCTCCA 58.226 45.000 0.00 0.00 0.00 3.86
3054 3318 9.651718 CTTGTACAAAACTCAAAAGTAGATCAC 57.348 33.333 10.03 0.00 33.48 3.06
3055 3319 8.725405 TGTACAAAACTCAAAAGTAGATCACA 57.275 30.769 0.00 0.00 33.48 3.58
3056 3320 8.826710 TGTACAAAACTCAAAAGTAGATCACAG 58.173 33.333 0.00 0.00 33.48 3.66
3057 3321 6.729187 ACAAAACTCAAAAGTAGATCACAGC 58.271 36.000 0.00 0.00 33.48 4.40
3058 3322 6.318648 ACAAAACTCAAAAGTAGATCACAGCA 59.681 34.615 0.00 0.00 33.48 4.41
3059 3323 7.013655 ACAAAACTCAAAAGTAGATCACAGCAT 59.986 33.333 0.00 0.00 33.48 3.79
3060 3324 6.492007 AACTCAAAAGTAGATCACAGCATG 57.508 37.500 0.00 0.00 37.02 4.06
3061 3325 5.555017 ACTCAAAAGTAGATCACAGCATGT 58.445 37.500 0.00 0.00 42.67 3.21
3488 3756 3.536917 CATCCTCCGCCGCTACCA 61.537 66.667 0.00 0.00 0.00 3.25
3555 3823 0.661552 CGCTCTTCATGAAGCATGGG 59.338 55.000 27.45 21.78 41.66 4.00
3620 3888 0.900182 ACCACATCAGCCTCGTCTGA 60.900 55.000 7.11 7.11 45.97 3.27
3880 4187 0.107116 AGGTGTTGTTGTTACCGGCA 60.107 50.000 0.00 0.00 39.46 5.69
3964 4319 9.585099 TTTTTAAATAAATGCGCTCTCAATCAT 57.415 25.926 9.73 0.00 0.00 2.45
4043 4402 2.431683 GCAGCAACCAGGGACTCA 59.568 61.111 0.00 0.00 34.60 3.41
4044 4403 1.228245 GCAGCAACCAGGGACTCAA 60.228 57.895 0.00 0.00 34.60 3.02
4045 4404 1.518903 GCAGCAACCAGGGACTCAAC 61.519 60.000 0.00 0.00 34.60 3.18
4046 4405 0.179020 CAGCAACCAGGGACTCAACA 60.179 55.000 0.00 0.00 34.60 3.33
4047 4406 0.109342 AGCAACCAGGGACTCAACAG 59.891 55.000 0.00 0.00 34.60 3.16
4048 4407 0.890996 GCAACCAGGGACTCAACAGG 60.891 60.000 0.00 0.00 34.60 4.00
4055 4414 4.078571 ACCAGGGACTCAACAGGATATCTA 60.079 45.833 2.05 0.00 34.60 1.98
4169 4530 5.298276 TGGTAATCCATGGCTTTTTATCGAC 59.702 40.000 6.96 0.00 39.03 4.20
4247 4608 1.064017 TGGTTGGTCAACTTCAAGCCT 60.064 47.619 12.75 0.00 40.94 4.58
4294 4655 4.773674 TCAGCCACAAAATTCTCCATGAAT 59.226 37.500 0.00 0.00 46.49 2.57
4309 4670 4.588106 TCCATGAATTTGTGCCTTTTCTCA 59.412 37.500 0.00 0.00 0.00 3.27
4356 4717 4.092529 GCAGAGTGAACTATGTGTCATGTG 59.907 45.833 6.92 0.00 37.50 3.21
4363 4725 8.043113 AGTGAACTATGTGTCATGTGTGAATAT 58.957 33.333 0.00 0.00 35.80 1.28
4451 4813 8.198109 ACAAGTGATTATACTTAGCACTACCTG 58.802 37.037 0.00 0.00 38.78 4.00
4779 5143 1.909302 ACCTGCAGGCTATGTGTAACT 59.091 47.619 33.06 5.36 39.32 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 43 9.313118 ACGCAATAAGAGAAAAGAAAAACATTT 57.687 25.926 0.00 0.00 0.00 2.32
41 44 8.871686 ACGCAATAAGAGAAAAGAAAAACATT 57.128 26.923 0.00 0.00 0.00 2.71
44 50 8.212372 GGTACGCAATAAGAGAAAAGAAAAAC 57.788 34.615 0.00 0.00 0.00 2.43
102 108 2.603110 GTGTATCACAATGCATCGTCGT 59.397 45.455 0.00 0.00 34.08 4.34
144 150 3.991773 CAGTGCATATTGCTTTGTTTGCT 59.008 39.130 0.00 0.00 45.31 3.91
150 156 3.488721 GCTCTCCAGTGCATATTGCTTTG 60.489 47.826 0.00 0.00 45.31 2.77
157 163 1.070445 GCCGCTCTCCAGTGCATAT 59.930 57.895 0.00 0.00 34.50 1.78
158 164 2.501128 GCCGCTCTCCAGTGCATA 59.499 61.111 0.00 0.00 34.50 3.14
159 165 4.827087 CGCCGCTCTCCAGTGCAT 62.827 66.667 0.00 0.00 34.50 3.96
162 168 2.357517 AAACGCCGCTCTCCAGTG 60.358 61.111 0.00 0.00 0.00 3.66
163 169 2.357517 CAAACGCCGCTCTCCAGT 60.358 61.111 0.00 0.00 0.00 4.00
164 170 3.121030 CCAAACGCCGCTCTCCAG 61.121 66.667 0.00 0.00 0.00 3.86
165 171 4.697756 CCCAAACGCCGCTCTCCA 62.698 66.667 0.00 0.00 0.00 3.86
172 178 4.418401 CCATGTGCCCAAACGCCG 62.418 66.667 0.00 0.00 0.00 6.46
173 179 4.067913 CCCATGTGCCCAAACGCC 62.068 66.667 0.00 0.00 0.00 5.68
174 180 2.988684 TCCCATGTGCCCAAACGC 60.989 61.111 0.00 0.00 0.00 4.84
175 181 2.993471 GCTCCCATGTGCCCAAACG 61.993 63.158 0.00 0.00 0.00 3.60
176 182 2.973082 GCTCCCATGTGCCCAAAC 59.027 61.111 0.00 0.00 0.00 2.93
177 183 2.676121 CGCTCCCATGTGCCCAAA 60.676 61.111 0.00 0.00 0.00 3.28
192 198 1.689352 TAAAAACTAGGAGCGCGCGC 61.689 55.000 45.10 45.10 42.33 6.86
193 199 0.717224 TTAAAAACTAGGAGCGCGCG 59.283 50.000 28.44 28.44 0.00 6.86
194 200 2.886587 TTTAAAAACTAGGAGCGCGC 57.113 45.000 26.66 26.66 0.00 6.86
195 201 4.553429 CACATTTTAAAAACTAGGAGCGCG 59.447 41.667 0.00 0.00 0.00 6.86
196 202 5.458015 ACACATTTTAAAAACTAGGAGCGC 58.542 37.500 4.44 0.00 0.00 5.92
197 203 7.924103 AAACACATTTTAAAAACTAGGAGCG 57.076 32.000 4.44 0.00 0.00 5.03
241 247 9.419737 CGTCAAGTTTTTGTTTGGAATTATTTG 57.580 29.630 0.00 0.00 35.73 2.32
242 248 8.119845 GCGTCAAGTTTTTGTTTGGAATTATTT 58.880 29.630 0.00 0.00 35.73 1.40
243 249 7.515998 CGCGTCAAGTTTTTGTTTGGAATTATT 60.516 33.333 0.00 0.00 35.73 1.40
244 250 6.074569 CGCGTCAAGTTTTTGTTTGGAATTAT 60.075 34.615 0.00 0.00 35.73 1.28
245 251 5.230306 CGCGTCAAGTTTTTGTTTGGAATTA 59.770 36.000 0.00 0.00 35.73 1.40
246 252 4.032331 CGCGTCAAGTTTTTGTTTGGAATT 59.968 37.500 0.00 0.00 35.73 2.17
247 253 3.549873 CGCGTCAAGTTTTTGTTTGGAAT 59.450 39.130 0.00 0.00 35.73 3.01
248 254 2.917971 CGCGTCAAGTTTTTGTTTGGAA 59.082 40.909 0.00 0.00 35.73 3.53
249 255 2.095161 ACGCGTCAAGTTTTTGTTTGGA 60.095 40.909 5.58 0.00 35.73 3.53
250 256 2.255316 ACGCGTCAAGTTTTTGTTTGG 58.745 42.857 5.58 0.00 35.73 3.28
251 257 3.846896 TGTACGCGTCAAGTTTTTGTTTG 59.153 39.130 18.63 0.00 35.73 2.93
252 258 4.080969 TGTACGCGTCAAGTTTTTGTTT 57.919 36.364 18.63 0.00 35.73 2.83
253 259 3.743567 TGTACGCGTCAAGTTTTTGTT 57.256 38.095 18.63 0.00 35.73 2.83
254 260 3.558418 AGATGTACGCGTCAAGTTTTTGT 59.442 39.130 18.63 0.00 35.73 2.83
255 261 4.128554 AGATGTACGCGTCAAGTTTTTG 57.871 40.909 18.63 0.00 35.57 2.44
256 262 4.271533 TCAAGATGTACGCGTCAAGTTTTT 59.728 37.500 18.63 0.00 33.18 1.94
257 263 3.805422 TCAAGATGTACGCGTCAAGTTTT 59.195 39.130 18.63 1.58 33.18 2.43
258 264 3.386486 TCAAGATGTACGCGTCAAGTTT 58.614 40.909 18.63 3.42 33.18 2.66
259 265 3.021269 TCAAGATGTACGCGTCAAGTT 57.979 42.857 18.63 8.79 33.18 2.66
260 266 2.717580 TCAAGATGTACGCGTCAAGT 57.282 45.000 18.63 0.00 33.18 3.16
261 267 5.232202 ACAATATCAAGATGTACGCGTCAAG 59.768 40.000 18.63 6.29 33.18 3.02
262 268 5.106442 ACAATATCAAGATGTACGCGTCAA 58.894 37.500 18.63 5.41 33.18 3.18
263 269 4.678622 ACAATATCAAGATGTACGCGTCA 58.321 39.130 18.63 14.75 33.18 4.35
264 270 6.125079 GTACAATATCAAGATGTACGCGTC 57.875 41.667 18.63 8.55 39.78 5.19
269 275 8.491152 GTGAGCATGTACAATATCAAGATGTAC 58.509 37.037 0.00 8.04 46.01 2.90
270 276 8.203485 TGTGAGCATGTACAATATCAAGATGTA 58.797 33.333 0.00 0.00 0.00 2.29
271 277 7.049754 TGTGAGCATGTACAATATCAAGATGT 58.950 34.615 0.00 0.00 0.00 3.06
272 278 7.486802 TGTGAGCATGTACAATATCAAGATG 57.513 36.000 0.00 0.00 0.00 2.90
273 279 8.510243 TTTGTGAGCATGTACAATATCAAGAT 57.490 30.769 0.00 0.00 36.75 2.40
274 280 7.607607 ACTTTGTGAGCATGTACAATATCAAGA 59.392 33.333 0.00 0.00 36.75 3.02
275 281 7.755591 ACTTTGTGAGCATGTACAATATCAAG 58.244 34.615 0.00 2.06 36.75 3.02
276 282 7.412891 CGACTTTGTGAGCATGTACAATATCAA 60.413 37.037 0.00 0.00 36.75 2.57
277 283 6.035975 CGACTTTGTGAGCATGTACAATATCA 59.964 38.462 0.00 1.18 36.75 2.15
278 284 6.036083 ACGACTTTGTGAGCATGTACAATATC 59.964 38.462 0.00 0.00 36.75 1.63
279 285 5.874810 ACGACTTTGTGAGCATGTACAATAT 59.125 36.000 0.00 5.17 36.75 1.28
280 286 5.234752 ACGACTTTGTGAGCATGTACAATA 58.765 37.500 0.00 4.79 36.75 1.90
281 287 4.065088 ACGACTTTGTGAGCATGTACAAT 58.935 39.130 0.00 0.00 36.75 2.71
282 288 3.462982 ACGACTTTGTGAGCATGTACAA 58.537 40.909 0.00 7.82 35.20 2.41
283 289 3.106242 ACGACTTTGTGAGCATGTACA 57.894 42.857 0.00 0.00 0.00 2.90
284 290 4.455124 GAAACGACTTTGTGAGCATGTAC 58.545 43.478 0.00 0.00 0.00 2.90
285 291 3.183574 CGAAACGACTTTGTGAGCATGTA 59.816 43.478 0.00 0.00 0.00 2.29
286 292 2.032894 CGAAACGACTTTGTGAGCATGT 60.033 45.455 0.00 0.00 0.00 3.21
287 293 2.563976 CGAAACGACTTTGTGAGCATG 58.436 47.619 0.00 0.00 0.00 4.06
288 294 1.069906 GCGAAACGACTTTGTGAGCAT 60.070 47.619 0.00 0.00 0.00 3.79
289 295 0.303493 GCGAAACGACTTTGTGAGCA 59.697 50.000 0.00 0.00 0.00 4.26
290 296 0.303493 TGCGAAACGACTTTGTGAGC 59.697 50.000 0.00 0.00 0.00 4.26
291 297 2.730183 TTGCGAAACGACTTTGTGAG 57.270 45.000 0.00 0.00 0.00 3.51
292 298 2.673862 TCTTTGCGAAACGACTTTGTGA 59.326 40.909 0.00 0.00 0.00 3.58
293 299 3.046285 TCTTTGCGAAACGACTTTGTG 57.954 42.857 0.00 0.00 0.00 3.33
294 300 3.422655 GTTCTTTGCGAAACGACTTTGT 58.577 40.909 0.00 0.00 32.41 2.83
295 301 2.781646 GGTTCTTTGCGAAACGACTTTG 59.218 45.455 0.00 0.00 32.41 2.77
296 302 3.060978 GGTTCTTTGCGAAACGACTTT 57.939 42.857 0.00 0.00 32.41 2.66
297 303 2.750301 GGTTCTTTGCGAAACGACTT 57.250 45.000 0.00 0.00 32.41 3.01
302 308 2.461897 TTGTCGGTTCTTTGCGAAAC 57.538 45.000 0.00 0.00 35.94 2.78
303 309 3.701532 ATTTGTCGGTTCTTTGCGAAA 57.298 38.095 0.00 0.00 32.41 3.46
304 310 3.701532 AATTTGTCGGTTCTTTGCGAA 57.298 38.095 0.00 0.00 0.00 4.70
305 311 4.214545 ACATAATTTGTCGGTTCTTTGCGA 59.785 37.500 0.00 0.00 30.89 5.10
306 312 4.320690 CACATAATTTGTCGGTTCTTTGCG 59.679 41.667 0.00 0.00 36.00 4.85
307 313 5.219633 ACACATAATTTGTCGGTTCTTTGC 58.780 37.500 0.00 0.00 36.00 3.68
308 314 6.911484 GACACATAATTTGTCGGTTCTTTG 57.089 37.500 0.00 0.00 36.00 2.77
317 323 3.120820 TCACACGCGACACATAATTTGTC 60.121 43.478 15.93 0.00 40.10 3.18
318 324 2.803386 TCACACGCGACACATAATTTGT 59.197 40.909 15.93 0.00 39.91 2.83
319 325 3.447752 TCACACGCGACACATAATTTG 57.552 42.857 15.93 0.00 0.00 2.32
320 326 4.475763 TTTCACACGCGACACATAATTT 57.524 36.364 15.93 0.00 0.00 1.82
321 327 4.475763 TTTTCACACGCGACACATAATT 57.524 36.364 15.93 0.00 0.00 1.40
322 328 4.212425 TCTTTTTCACACGCGACACATAAT 59.788 37.500 15.93 0.00 0.00 1.28
323 329 3.556365 TCTTTTTCACACGCGACACATAA 59.444 39.130 15.93 0.00 0.00 1.90
324 330 3.124560 TCTTTTTCACACGCGACACATA 58.875 40.909 15.93 0.00 0.00 2.29
325 331 1.937223 TCTTTTTCACACGCGACACAT 59.063 42.857 15.93 0.00 0.00 3.21
326 332 1.360820 TCTTTTTCACACGCGACACA 58.639 45.000 15.93 0.00 0.00 3.72
327 333 2.663279 ATCTTTTTCACACGCGACAC 57.337 45.000 15.93 0.00 0.00 3.67
328 334 4.797693 TTTATCTTTTTCACACGCGACA 57.202 36.364 15.93 0.00 0.00 4.35
329 335 6.449387 CGAATTTTATCTTTTTCACACGCGAC 60.449 38.462 15.93 0.00 0.00 5.19
330 336 5.562248 CGAATTTTATCTTTTTCACACGCGA 59.438 36.000 15.93 0.00 0.00 5.87
331 337 5.562248 TCGAATTTTATCTTTTTCACACGCG 59.438 36.000 3.53 3.53 0.00 6.01
332 338 6.904954 TCGAATTTTATCTTTTTCACACGC 57.095 33.333 0.00 0.00 0.00 5.34
333 339 8.434870 ACATCGAATTTTATCTTTTTCACACG 57.565 30.769 0.00 0.00 0.00 4.49
361 367 8.791327 AAGGATGTCTTGTGAAAAACATTTTT 57.209 26.923 2.00 2.00 38.99 1.94
362 368 8.791327 AAAGGATGTCTTGTGAAAAACATTTT 57.209 26.923 0.00 0.00 38.99 1.82
363 369 8.667463 CAAAAGGATGTCTTGTGAAAAACATTT 58.333 29.630 0.00 0.00 38.99 2.32
364 370 7.823799 ACAAAAGGATGTCTTGTGAAAAACATT 59.176 29.630 3.25 0.00 38.99 2.71
365 371 7.330262 ACAAAAGGATGTCTTGTGAAAAACAT 58.670 30.769 3.25 0.00 38.99 2.71
366 372 6.696411 ACAAAAGGATGTCTTGTGAAAAACA 58.304 32.000 3.25 0.00 35.55 2.83
367 373 7.221828 GACAAAAGGATGTCTTGTGAAAAAC 57.778 36.000 3.25 0.00 44.98 2.43
420 426 2.610833 ACGTCAAGTTTCGGAGAAAACC 59.389 45.455 0.00 0.00 45.90 3.27
421 427 3.604392 CACGTCAAGTTTCGGAGAAAAC 58.396 45.455 0.00 0.00 45.90 2.43
422 428 2.031191 GCACGTCAAGTTTCGGAGAAAA 59.969 45.455 0.00 0.00 45.90 2.29
423 429 1.595794 GCACGTCAAGTTTCGGAGAAA 59.404 47.619 0.00 0.00 45.90 2.52
424 430 1.214367 GCACGTCAAGTTTCGGAGAA 58.786 50.000 0.00 0.00 45.90 2.87
425 431 0.103390 TGCACGTCAAGTTTCGGAGA 59.897 50.000 0.00 0.00 0.00 3.71
426 432 0.232303 GTGCACGTCAAGTTTCGGAG 59.768 55.000 0.00 0.00 0.00 4.63
427 433 0.460459 TGTGCACGTCAAGTTTCGGA 60.460 50.000 13.13 0.00 0.00 4.55
428 434 0.315869 GTGTGCACGTCAAGTTTCGG 60.316 55.000 13.13 0.00 0.00 4.30
429 435 0.371989 TGTGTGCACGTCAAGTTTCG 59.628 50.000 13.13 0.00 0.00 3.46
430 436 2.755836 ATGTGTGCACGTCAAGTTTC 57.244 45.000 13.13 0.00 0.00 2.78
431 437 5.933187 TTATATGTGTGCACGTCAAGTTT 57.067 34.783 13.13 2.09 0.00 2.66
432 438 7.494298 TGATATTATATGTGTGCACGTCAAGTT 59.506 33.333 13.13 2.43 0.00 2.66
433 439 6.983890 TGATATTATATGTGTGCACGTCAAGT 59.016 34.615 13.13 9.32 0.00 3.16
434 440 7.406799 TGATATTATATGTGTGCACGTCAAG 57.593 36.000 13.13 0.00 0.00 3.02
435 441 7.708752 TCTTGATATTATATGTGTGCACGTCAA 59.291 33.333 13.13 8.17 0.00 3.18
436 442 7.206687 TCTTGATATTATATGTGTGCACGTCA 58.793 34.615 13.13 14.22 0.00 4.35
437 443 7.637709 TCTTGATATTATATGTGTGCACGTC 57.362 36.000 13.13 8.59 0.00 4.34
438 444 7.657354 ACATCTTGATATTATATGTGTGCACGT 59.343 33.333 13.13 3.31 29.93 4.49
439 445 8.021955 ACATCTTGATATTATATGTGTGCACG 57.978 34.615 13.13 0.00 29.93 5.34
509 515 2.494530 GCCTGCACACGGGGAAAAA 61.495 57.895 0.00 0.00 43.31 1.94
510 516 2.909965 GCCTGCACACGGGGAAAA 60.910 61.111 0.00 0.00 43.31 2.29
533 539 2.125912 CGTTGGTGCTCCCGAGAG 60.126 66.667 1.59 0.00 43.57 3.20
534 540 3.691342 CCGTTGGTGCTCCCGAGA 61.691 66.667 1.59 0.00 35.15 4.04
535 541 3.691342 TCCGTTGGTGCTCCCGAG 61.691 66.667 1.59 0.00 35.15 4.63
536 542 3.998672 GTCCGTTGGTGCTCCCGA 61.999 66.667 1.59 0.00 35.15 5.14
537 543 3.530910 AAGTCCGTTGGTGCTCCCG 62.531 63.158 1.59 0.00 35.15 5.14
538 544 1.228154 AAAGTCCGTTGGTGCTCCC 60.228 57.895 1.59 0.00 0.00 4.30
539 545 1.566018 CGAAAGTCCGTTGGTGCTCC 61.566 60.000 0.00 0.00 0.00 4.70
540 546 0.599204 TCGAAAGTCCGTTGGTGCTC 60.599 55.000 0.00 0.00 0.00 4.26
541 547 0.034896 ATCGAAAGTCCGTTGGTGCT 59.965 50.000 0.00 0.00 0.00 4.40
542 548 1.717194 TATCGAAAGTCCGTTGGTGC 58.283 50.000 0.00 0.00 0.00 5.01
543 549 2.030457 GCATATCGAAAGTCCGTTGGTG 59.970 50.000 0.00 0.00 0.00 4.17
544 550 2.277084 GCATATCGAAAGTCCGTTGGT 58.723 47.619 0.00 0.00 0.00 3.67
545 551 2.276201 TGCATATCGAAAGTCCGTTGG 58.724 47.619 0.00 0.00 0.00 3.77
546 552 4.536364 ATTGCATATCGAAAGTCCGTTG 57.464 40.909 0.00 0.00 0.00 4.10
547 553 5.234329 CAGTATTGCATATCGAAAGTCCGTT 59.766 40.000 0.00 0.00 0.00 4.44
548 554 4.745125 CAGTATTGCATATCGAAAGTCCGT 59.255 41.667 0.00 0.00 0.00 4.69
549 555 4.745125 ACAGTATTGCATATCGAAAGTCCG 59.255 41.667 0.00 0.00 0.00 4.79
550 556 5.753438 TCACAGTATTGCATATCGAAAGTCC 59.247 40.000 0.00 0.00 0.00 3.85
551 557 6.828502 TCACAGTATTGCATATCGAAAGTC 57.171 37.500 0.00 0.00 0.00 3.01
552 558 7.926018 TGTATCACAGTATTGCATATCGAAAGT 59.074 33.333 0.00 0.00 0.00 2.66
553 559 8.298030 TGTATCACAGTATTGCATATCGAAAG 57.702 34.615 0.00 0.00 0.00 2.62
554 560 8.655651 TTGTATCACAGTATTGCATATCGAAA 57.344 30.769 0.00 0.00 0.00 3.46
555 561 7.384932 CCTTGTATCACAGTATTGCATATCGAA 59.615 37.037 0.00 0.00 0.00 3.71
556 562 6.868339 CCTTGTATCACAGTATTGCATATCGA 59.132 38.462 0.00 0.00 0.00 3.59
557 563 6.401474 GCCTTGTATCACAGTATTGCATATCG 60.401 42.308 0.00 0.00 0.00 2.92
558 564 6.427853 TGCCTTGTATCACAGTATTGCATATC 59.572 38.462 0.00 0.00 0.00 1.63
604 610 1.089920 CTTCGAGATTTGTGCCAGGG 58.910 55.000 0.00 0.00 0.00 4.45
606 803 1.159285 TGCTTCGAGATTTGTGCCAG 58.841 50.000 0.00 0.00 0.00 4.85
627 824 7.769044 TGATATATCGTACATGGATTCTCTCGA 59.231 37.037 8.19 0.00 0.00 4.04
685 890 9.217278 CTCTTGCAAGCACTTATCATATAATCT 57.783 33.333 21.99 0.00 0.00 2.40
686 891 9.212641 TCTCTTGCAAGCACTTATCATATAATC 57.787 33.333 21.99 0.00 0.00 1.75
687 892 9.736414 ATCTCTTGCAAGCACTTATCATATAAT 57.264 29.630 21.99 0.00 0.00 1.28
690 895 9.565090 TTTATCTCTTGCAAGCACTTATCATAT 57.435 29.630 21.99 3.01 0.00 1.78
691 896 8.962884 TTTATCTCTTGCAAGCACTTATCATA 57.037 30.769 21.99 5.69 0.00 2.15
692 897 7.555554 ACTTTATCTCTTGCAAGCACTTATCAT 59.444 33.333 21.99 6.55 0.00 2.45
742 947 1.348276 TGCGCTACAAATTGCATTGC 58.652 45.000 9.73 0.46 33.52 3.56
1208 1429 1.813513 AGATGAAAACTGCCACGAGG 58.186 50.000 0.00 0.00 38.23 4.63
2406 2627 1.135632 CATCGTGTGTGCATGCATGAA 60.136 47.619 30.64 18.49 34.76 2.57
2408 2629 1.137459 GCATCGTGTGTGCATGCATG 61.137 55.000 25.64 22.70 42.18 4.06
2409 2630 1.138036 GCATCGTGTGTGCATGCAT 59.862 52.632 25.64 2.10 42.18 3.96
2410 2631 0.673022 TAGCATCGTGTGTGCATGCA 60.673 50.000 18.46 18.46 44.57 3.96
2411 2632 0.659427 ATAGCATCGTGTGTGCATGC 59.341 50.000 11.82 11.82 44.87 4.06
2412 2633 2.865551 TGTATAGCATCGTGTGTGCATG 59.134 45.455 0.00 0.00 44.87 4.06
2415 2640 2.221749 CCATGTATAGCATCGTGTGTGC 59.778 50.000 0.00 0.00 42.81 4.57
2467 2696 2.418910 CCACCAAACACCAACGCCA 61.419 57.895 0.00 0.00 0.00 5.69
2532 2772 1.142262 TCCTCATGCAGATGATGTGGG 59.858 52.381 5.71 0.00 37.97 4.61
2535 2775 7.649533 TTTAATTTCCTCATGCAGATGATGT 57.350 32.000 0.00 0.00 37.97 3.06
2584 2825 6.586868 AATTCTACACGTCGTTGTTTTGTA 57.413 33.333 0.00 0.00 0.00 2.41
2746 2998 7.604927 AGTTAGTGAGGTGCAACGAATTAAATA 59.395 33.333 0.00 0.00 38.12 1.40
2748 3000 5.761234 AGTTAGTGAGGTGCAACGAATTAAA 59.239 36.000 0.00 0.00 38.12 1.52
2844 3096 5.711036 CCAACTGACAACCTACTACTCTACT 59.289 44.000 0.00 0.00 0.00 2.57
2902 3154 2.892852 TCAACCTTTTGATGGAGCCTTG 59.107 45.455 0.00 0.00 36.79 3.61
2904 3156 2.158475 TGTCAACCTTTTGATGGAGCCT 60.158 45.455 0.00 0.00 43.72 4.58
2905 3157 2.229784 CTGTCAACCTTTTGATGGAGCC 59.770 50.000 0.00 0.00 43.72 4.70
2906 3158 3.149196 TCTGTCAACCTTTTGATGGAGC 58.851 45.455 0.00 0.00 43.72 4.70
2907 3159 4.453819 GTCTCTGTCAACCTTTTGATGGAG 59.546 45.833 10.60 10.60 43.72 3.86
2908 3160 4.141505 TGTCTCTGTCAACCTTTTGATGGA 60.142 41.667 0.00 0.00 43.72 3.41
2910 3162 4.319046 CGTGTCTCTGTCAACCTTTTGATG 60.319 45.833 0.00 0.00 43.72 3.07
2911 3163 3.809832 CGTGTCTCTGTCAACCTTTTGAT 59.190 43.478 0.00 0.00 43.72 2.57
3021 3275 5.351233 TTGAGTTTTGTACAAGCATACCG 57.649 39.130 8.56 0.00 0.00 4.02
3054 3318 3.937079 TGACTAAAGATGCTGACATGCTG 59.063 43.478 0.00 0.00 36.35 4.41
3055 3319 4.081254 TCTGACTAAAGATGCTGACATGCT 60.081 41.667 0.00 0.00 36.35 3.79
3056 3320 4.186926 TCTGACTAAAGATGCTGACATGC 58.813 43.478 0.00 0.00 36.35 4.06
3057 3321 6.018913 GTGATCTGACTAAAGATGCTGACATG 60.019 42.308 0.00 0.00 37.03 3.21
3058 3322 6.047870 GTGATCTGACTAAAGATGCTGACAT 58.952 40.000 0.00 0.00 37.03 3.06
3059 3323 5.414360 GTGATCTGACTAAAGATGCTGACA 58.586 41.667 0.00 0.00 37.03 3.58
3060 3324 4.808364 GGTGATCTGACTAAAGATGCTGAC 59.192 45.833 0.00 0.00 37.03 3.51
3061 3325 4.713814 AGGTGATCTGACTAAAGATGCTGA 59.286 41.667 0.00 0.00 37.03 4.26
3555 3823 3.426568 GCCAGCGTCACCTTGAGC 61.427 66.667 0.00 0.00 0.00 4.26
3620 3888 1.267574 ATCACCGGAGAGCACACCAT 61.268 55.000 9.46 0.00 0.00 3.55
3952 4307 5.468592 AGCAGTTCTATATGATTGAGAGCG 58.531 41.667 0.00 0.00 0.00 5.03
4020 4379 1.078497 CCCTGGTTGCTGCGTATGA 60.078 57.895 0.00 0.00 0.00 2.15
4025 4384 2.743928 GAGTCCCTGGTTGCTGCG 60.744 66.667 0.00 0.00 0.00 5.18
4029 4388 0.890996 CCTGTTGAGTCCCTGGTTGC 60.891 60.000 0.00 0.00 0.00 4.17
4032 4391 2.642171 TATCCTGTTGAGTCCCTGGT 57.358 50.000 0.00 0.00 0.00 4.00
4043 4402 9.482175 ACAAGACTCTTTACTAGATATCCTGTT 57.518 33.333 0.00 0.00 30.92 3.16
4044 4403 9.127277 GACAAGACTCTTTACTAGATATCCTGT 57.873 37.037 0.00 1.37 30.73 4.00
4045 4404 9.126151 TGACAAGACTCTTTACTAGATATCCTG 57.874 37.037 0.00 0.00 30.92 3.86
4046 4405 9.875708 ATGACAAGACTCTTTACTAGATATCCT 57.124 33.333 0.00 0.00 30.92 3.24
4076 4435 6.595772 AACGCTAGAGCTTTGAATAATGAG 57.404 37.500 0.00 0.00 39.32 2.90
4087 4448 0.690762 TCCCCAAAACGCTAGAGCTT 59.309 50.000 0.00 0.00 39.32 3.74
4169 4530 2.014128 ACCAACTTTCACCAACTCACG 58.986 47.619 0.00 0.00 0.00 4.35
4206 4567 4.431131 CGTTGGCTGGGAGGGCAT 62.431 66.667 0.00 0.00 41.29 4.40
4220 4581 0.544697 AGTTGACCAACCAGACCGTT 59.455 50.000 9.07 0.00 42.06 4.44
4247 4608 3.173151 TCTATGAAGAGTGGAGTGGCAA 58.827 45.455 0.00 0.00 0.00 4.52
4294 4655 2.880890 GAGAGCTGAGAAAAGGCACAAA 59.119 45.455 0.00 0.00 0.00 2.83
4309 4670 1.071434 AGGCTGGGAAAAAGAGAGCT 58.929 50.000 0.00 0.00 0.00 4.09
4356 4717 7.824289 TGCTGTAGCCTTCCATTATATATTCAC 59.176 37.037 0.80 0.00 41.18 3.18
4363 4725 6.115446 GCATATGCTGTAGCCTTCCATTATA 58.885 40.000 20.64 0.00 41.18 0.98
4386 4748 5.933790 TGGTTCTCAATATAAACACAACGC 58.066 37.500 0.00 0.00 0.00 4.84
4390 4752 9.173021 CCTTGTATGGTTCTCAATATAAACACA 57.827 33.333 0.00 0.00 0.00 3.72
4391 4753 9.174166 ACCTTGTATGGTTCTCAATATAAACAC 57.826 33.333 0.00 0.00 36.89 3.32
4400 4762 9.880157 GTTATAAGTACCTTGTATGGTTCTCAA 57.120 33.333 0.00 0.00 41.22 3.02
4443 4805 8.158169 ACATATATTTTGACATGCAGGTAGTG 57.842 34.615 2.88 0.00 0.00 2.74
4621 4984 7.174946 CCAAGGTCAGTCATTTAATGTACAACT 59.825 37.037 0.00 0.00 0.00 3.16
4755 5119 0.463295 CACATAGCCTGCAGGTGAGG 60.463 60.000 32.81 23.66 37.57 3.86
4766 5130 2.985896 TGGCTTCAGTTACACATAGCC 58.014 47.619 0.00 0.00 46.43 3.93
4779 5143 8.107095 AGTTATGTTAAGGTCTAATTGGCTTCA 58.893 33.333 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.