Multiple sequence alignment - TraesCS3A01G391900

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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 TraesCS3A01G391900 chr3A 100.000 2924 0 0 1 2924 639501172 639498249 0 5400
1 TraesCS3A01G391900 chr2A 99.315 2336 15 1 590 2924 84594388 84592053 0 4224
2 TraesCS3A01G391900 chr7B 99.315 2335 13 2 591 2924 312341953 312339621 0 4220
3 TraesCS3A01G391900 chr7B 99.273 2337 13 3 591 2924 244397993 244400328 0 4218
4 TraesCS3A01G391900 chr1B 99.272 2335 16 1 591 2924 641515776 641513442 0 4217
5 TraesCS3A01G391900 chr1B 98.930 2337 22 2 591 2924 359601538 359599202 0 4174
6 TraesCS3A01G391900 chr1B 98.887 2335 18 3 591 2924 400295118 400297445 0 4161
7 TraesCS3A01G391900 chr5A 98.980 2352 14 3 582 2924 506137840 506135490 0 4202
8 TraesCS3A01G391900 chr5A 98.845 2337 20 5 590 2924 593169435 593167104 0 4159
9 TraesCS3A01G391900 chr1A 99.016 2338 20 2 590 2924 583541455 583539118 0 4187
10 TraesCS3A01G391900 chr3D 99.652 574 2 0 17 590 500001847 500001274 0 1050
11 TraesCS3A01G391900 chr3B 97.453 589 15 0 1 589 661342377 661341789 0 1005


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 TraesCS3A01G391900 chr3A 639498249 639501172 2923 True 5400 5400 100.000 1 2924 1 chr3A.!!$R1 2923
1 TraesCS3A01G391900 chr2A 84592053 84594388 2335 True 4224 4224 99.315 590 2924 1 chr2A.!!$R1 2334
2 TraesCS3A01G391900 chr7B 312339621 312341953 2332 True 4220 4220 99.315 591 2924 1 chr7B.!!$R1 2333
3 TraesCS3A01G391900 chr7B 244397993 244400328 2335 False 4218 4218 99.273 591 2924 1 chr7B.!!$F1 2333
4 TraesCS3A01G391900 chr1B 641513442 641515776 2334 True 4217 4217 99.272 591 2924 1 chr1B.!!$R2 2333
5 TraesCS3A01G391900 chr1B 359599202 359601538 2336 True 4174 4174 98.930 591 2924 1 chr1B.!!$R1 2333
6 TraesCS3A01G391900 chr1B 400295118 400297445 2327 False 4161 4161 98.887 591 2924 1 chr1B.!!$F1 2333
7 TraesCS3A01G391900 chr5A 506135490 506137840 2350 True 4202 4202 98.980 582 2924 1 chr5A.!!$R1 2342
8 TraesCS3A01G391900 chr5A 593167104 593169435 2331 True 4159 4159 98.845 590 2924 1 chr5A.!!$R2 2334
9 TraesCS3A01G391900 chr1A 583539118 583541455 2337 True 4187 4187 99.016 590 2924 1 chr1A.!!$R1 2334
10 TraesCS3A01G391900 chr3D 500001274 500001847 573 True 1050 1050 99.652 17 590 1 chr3D.!!$R1 573
11 TraesCS3A01G391900 chr3B 661341789 661342377 588 True 1005 1005 97.453 1 589 1 chr3B.!!$R1 588

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
500 501 1.375098 GAGGCAGGAGCACAGCAATC 61.375 60.0 0.87 0.0 44.61 2.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2466 2734 3.131223 CCAGACCTAGACACATCACGATT 59.869 47.826 0.0 0.0 0.0 3.34 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
187 188 8.299570 CACTGCCATAAGTCTTAATTGTCTTTT 58.700 33.333 0.00 0.00 0.00 2.27
188 189 8.515414 ACTGCCATAAGTCTTAATTGTCTTTTC 58.485 33.333 0.00 0.00 0.00 2.29
189 190 7.826690 TGCCATAAGTCTTAATTGTCTTTTCC 58.173 34.615 0.00 0.00 0.00 3.13
190 191 7.450014 TGCCATAAGTCTTAATTGTCTTTTCCA 59.550 33.333 0.00 0.00 0.00 3.53
191 192 8.303876 GCCATAAGTCTTAATTGTCTTTTCCAA 58.696 33.333 0.00 0.00 0.00 3.53
196 197 9.971922 AAGTCTTAATTGTCTTTTCCAAATCAG 57.028 29.630 0.00 0.00 0.00 2.90
197 198 9.354673 AGTCTTAATTGTCTTTTCCAAATCAGA 57.645 29.630 0.00 0.00 0.00 3.27
198 199 9.965824 GTCTTAATTGTCTTTTCCAAATCAGAA 57.034 29.630 0.00 0.00 0.00 3.02
202 203 8.652810 AATTGTCTTTTCCAAATCAGAAACAG 57.347 30.769 0.00 0.00 33.11 3.16
203 204 6.773976 TGTCTTTTCCAAATCAGAAACAGT 57.226 33.333 0.00 0.00 33.11 3.55
204 205 6.563422 TGTCTTTTCCAAATCAGAAACAGTG 58.437 36.000 0.00 0.00 33.11 3.66
205 206 5.979517 GTCTTTTCCAAATCAGAAACAGTGG 59.020 40.000 0.00 0.00 33.11 4.00
206 207 5.890985 TCTTTTCCAAATCAGAAACAGTGGA 59.109 36.000 0.00 0.00 33.11 4.02
207 208 6.550854 TCTTTTCCAAATCAGAAACAGTGGAT 59.449 34.615 0.00 0.00 35.19 3.41
208 209 7.723616 TCTTTTCCAAATCAGAAACAGTGGATA 59.276 33.333 0.00 0.00 35.19 2.59
209 210 6.817765 TTCCAAATCAGAAACAGTGGATAC 57.182 37.500 0.00 0.00 35.19 2.24
210 211 7.286546 TTTTCCAAATCAGAAACAGTGGATACA 59.713 33.333 0.00 0.00 37.30 2.29
238 239 6.478512 TTTTATGCTCCACTTGTTTTTCCT 57.521 33.333 0.00 0.00 0.00 3.36
239 240 6.478512 TTTATGCTCCACTTGTTTTTCCTT 57.521 33.333 0.00 0.00 0.00 3.36
240 241 4.590850 ATGCTCCACTTGTTTTTCCTTC 57.409 40.909 0.00 0.00 0.00 3.46
241 242 3.360867 TGCTCCACTTGTTTTTCCTTCA 58.639 40.909 0.00 0.00 0.00 3.02
242 243 3.766591 TGCTCCACTTGTTTTTCCTTCAA 59.233 39.130 0.00 0.00 0.00 2.69
243 244 4.405358 TGCTCCACTTGTTTTTCCTTCAAT 59.595 37.500 0.00 0.00 0.00 2.57
244 245 5.104982 TGCTCCACTTGTTTTTCCTTCAATT 60.105 36.000 0.00 0.00 0.00 2.32
245 246 5.463392 GCTCCACTTGTTTTTCCTTCAATTC 59.537 40.000 0.00 0.00 0.00 2.17
246 247 6.683861 GCTCCACTTGTTTTTCCTTCAATTCT 60.684 38.462 0.00 0.00 0.00 2.40
247 248 7.181569 TCCACTTGTTTTTCCTTCAATTCTT 57.818 32.000 0.00 0.00 0.00 2.52
248 249 7.264947 TCCACTTGTTTTTCCTTCAATTCTTC 58.735 34.615 0.00 0.00 0.00 2.87
249 250 7.124147 TCCACTTGTTTTTCCTTCAATTCTTCT 59.876 33.333 0.00 0.00 0.00 2.85
250 251 7.765819 CCACTTGTTTTTCCTTCAATTCTTCTT 59.234 33.333 0.00 0.00 0.00 2.52
251 252 9.154847 CACTTGTTTTTCCTTCAATTCTTCTTT 57.845 29.630 0.00 0.00 0.00 2.52
252 253 9.725019 ACTTGTTTTTCCTTCAATTCTTCTTTT 57.275 25.926 0.00 0.00 0.00 2.27
253 254 9.977762 CTTGTTTTTCCTTCAATTCTTCTTTTG 57.022 29.630 0.00 0.00 0.00 2.44
254 255 9.717942 TTGTTTTTCCTTCAATTCTTCTTTTGA 57.282 25.926 0.00 0.00 0.00 2.69
255 256 9.889128 TGTTTTTCCTTCAATTCTTCTTTTGAT 57.111 25.926 0.00 0.00 32.27 2.57
258 259 9.546428 TTTTCCTTCAATTCTTCTTTTGATTCC 57.454 29.630 0.00 0.00 32.27 3.01
259 260 8.482852 TTCCTTCAATTCTTCTTTTGATTCCT 57.517 30.769 0.00 0.00 32.27 3.36
260 261 7.889469 TCCTTCAATTCTTCTTTTGATTCCTG 58.111 34.615 0.00 0.00 32.27 3.86
261 262 7.039504 TCCTTCAATTCTTCTTTTGATTCCTGG 60.040 37.037 0.00 0.00 32.27 4.45
262 263 7.039504 CCTTCAATTCTTCTTTTGATTCCTGGA 60.040 37.037 0.00 0.00 32.27 3.86
263 264 7.458409 TCAATTCTTCTTTTGATTCCTGGAG 57.542 36.000 0.00 0.00 0.00 3.86
264 265 7.006509 TCAATTCTTCTTTTGATTCCTGGAGT 58.993 34.615 0.00 0.00 0.00 3.85
265 266 7.506938 TCAATTCTTCTTTTGATTCCTGGAGTT 59.493 33.333 0.00 0.00 0.00 3.01
266 267 6.884280 TTCTTCTTTTGATTCCTGGAGTTC 57.116 37.500 0.00 0.00 0.00 3.01
267 268 6.192970 TCTTCTTTTGATTCCTGGAGTTCT 57.807 37.500 0.00 0.00 0.00 3.01
268 269 6.605119 TCTTCTTTTGATTCCTGGAGTTCTT 58.395 36.000 0.00 0.00 0.00 2.52
269 270 6.488006 TCTTCTTTTGATTCCTGGAGTTCTTG 59.512 38.462 0.00 0.00 0.00 3.02
270 271 4.520492 TCTTTTGATTCCTGGAGTTCTTGC 59.480 41.667 0.00 0.00 0.00 4.01
271 272 3.795688 TTGATTCCTGGAGTTCTTGCT 57.204 42.857 0.00 0.00 0.00 3.91
272 273 3.340814 TGATTCCTGGAGTTCTTGCTC 57.659 47.619 0.00 0.00 34.89 4.26
273 274 2.639347 TGATTCCTGGAGTTCTTGCTCA 59.361 45.455 0.00 0.00 37.24 4.26
274 275 3.072915 TGATTCCTGGAGTTCTTGCTCAA 59.927 43.478 0.00 0.00 37.24 3.02
275 276 2.847327 TCCTGGAGTTCTTGCTCAAG 57.153 50.000 3.32 3.32 36.53 3.02
276 277 2.050144 TCCTGGAGTTCTTGCTCAAGT 58.950 47.619 9.20 0.00 39.38 3.16
277 278 2.439507 TCCTGGAGTTCTTGCTCAAGTT 59.560 45.455 9.20 0.00 39.38 2.66
278 279 3.117888 TCCTGGAGTTCTTGCTCAAGTTT 60.118 43.478 9.20 0.00 39.38 2.66
279 280 3.251972 CCTGGAGTTCTTGCTCAAGTTTC 59.748 47.826 9.20 6.06 39.38 2.78
280 281 4.133078 CTGGAGTTCTTGCTCAAGTTTCT 58.867 43.478 9.20 6.60 39.38 2.52
281 282 4.526970 TGGAGTTCTTGCTCAAGTTTCTT 58.473 39.130 9.20 0.00 39.38 2.52
282 283 4.576463 TGGAGTTCTTGCTCAAGTTTCTTC 59.424 41.667 9.20 6.29 39.38 2.87
283 284 4.576463 GGAGTTCTTGCTCAAGTTTCTTCA 59.424 41.667 9.20 0.00 39.38 3.02
284 285 5.491635 AGTTCTTGCTCAAGTTTCTTCAC 57.508 39.130 9.20 0.00 39.38 3.18
285 286 4.943705 AGTTCTTGCTCAAGTTTCTTCACA 59.056 37.500 9.20 0.00 39.38 3.58
286 287 5.415701 AGTTCTTGCTCAAGTTTCTTCACAA 59.584 36.000 9.20 0.00 39.38 3.33
287 288 5.490139 TCTTGCTCAAGTTTCTTCACAAG 57.510 39.130 9.20 0.00 39.38 3.16
288 289 4.943705 TCTTGCTCAAGTTTCTTCACAAGT 59.056 37.500 9.20 0.00 39.38 3.16
289 290 5.415701 TCTTGCTCAAGTTTCTTCACAAGTT 59.584 36.000 9.20 0.00 39.38 2.66
290 291 5.235305 TGCTCAAGTTTCTTCACAAGTTC 57.765 39.130 0.00 0.00 0.00 3.01
291 292 4.699735 TGCTCAAGTTTCTTCACAAGTTCA 59.300 37.500 0.00 0.00 0.00 3.18
292 293 5.030936 GCTCAAGTTTCTTCACAAGTTCAC 58.969 41.667 0.00 0.00 0.00 3.18
293 294 5.560966 TCAAGTTTCTTCACAAGTTCACC 57.439 39.130 0.00 0.00 0.00 4.02
294 295 5.253330 TCAAGTTTCTTCACAAGTTCACCT 58.747 37.500 0.00 0.00 0.00 4.00
295 296 6.411376 TCAAGTTTCTTCACAAGTTCACCTA 58.589 36.000 0.00 0.00 0.00 3.08
296 297 6.882140 TCAAGTTTCTTCACAAGTTCACCTAA 59.118 34.615 0.00 0.00 0.00 2.69
297 298 6.679327 AGTTTCTTCACAAGTTCACCTAAC 57.321 37.500 0.00 0.00 38.46 2.34
327 328 9.295825 AGTACAAATAGAACAATTGTTGATCCA 57.704 29.630 27.85 3.95 38.56 3.41
328 329 9.906660 GTACAAATAGAACAATTGTTGATCCAA 57.093 29.630 27.85 6.26 38.56 3.53
335 336 8.597662 AGAACAATTGTTGATCCAATTTGAAG 57.402 30.769 27.85 1.13 41.79 3.02
336 337 6.790285 ACAATTGTTGATCCAATTTGAAGC 57.210 33.333 4.92 0.00 41.79 3.86
337 338 6.527423 ACAATTGTTGATCCAATTTGAAGCT 58.473 32.000 4.92 0.00 41.79 3.74
338 339 6.425721 ACAATTGTTGATCCAATTTGAAGCTG 59.574 34.615 4.92 0.23 41.79 4.24
339 340 5.787953 TTGTTGATCCAATTTGAAGCTGA 57.212 34.783 0.00 0.00 0.00 4.26
340 341 5.787953 TGTTGATCCAATTTGAAGCTGAA 57.212 34.783 0.00 0.00 0.00 3.02
341 342 6.349243 TGTTGATCCAATTTGAAGCTGAAT 57.651 33.333 0.00 0.00 0.00 2.57
342 343 6.160684 TGTTGATCCAATTTGAAGCTGAATG 58.839 36.000 0.00 0.00 0.00 2.67
343 344 5.988310 TGATCCAATTTGAAGCTGAATGT 57.012 34.783 0.00 0.00 0.00 2.71
344 345 5.716094 TGATCCAATTTGAAGCTGAATGTG 58.284 37.500 0.00 0.00 0.00 3.21
345 346 4.524316 TCCAATTTGAAGCTGAATGTGG 57.476 40.909 0.00 0.73 0.00 4.17
346 347 3.896888 TCCAATTTGAAGCTGAATGTGGT 59.103 39.130 0.00 0.00 0.00 4.16
347 348 5.076182 TCCAATTTGAAGCTGAATGTGGTA 58.924 37.500 0.00 0.00 0.00 3.25
348 349 5.538053 TCCAATTTGAAGCTGAATGTGGTAA 59.462 36.000 0.00 0.00 0.00 2.85
349 350 5.865552 CCAATTTGAAGCTGAATGTGGTAAG 59.134 40.000 0.00 0.00 0.00 2.34
350 351 5.649782 ATTTGAAGCTGAATGTGGTAAGG 57.350 39.130 0.00 0.00 0.00 2.69
351 352 3.788227 TGAAGCTGAATGTGGTAAGGT 57.212 42.857 0.00 0.00 0.00 3.50
352 353 4.901197 TGAAGCTGAATGTGGTAAGGTA 57.099 40.909 0.00 0.00 0.00 3.08
353 354 5.235850 TGAAGCTGAATGTGGTAAGGTAA 57.764 39.130 0.00 0.00 0.00 2.85
354 355 5.001232 TGAAGCTGAATGTGGTAAGGTAAC 58.999 41.667 0.00 0.00 0.00 2.50
355 356 3.951663 AGCTGAATGTGGTAAGGTAACC 58.048 45.455 0.00 0.00 40.19 2.85
403 404 9.906660 TTATACCTTGTGATGTTCATTTTGTTC 57.093 29.630 0.00 0.00 0.00 3.18
404 405 6.219417 ACCTTGTGATGTTCATTTTGTTCA 57.781 33.333 0.00 0.00 0.00 3.18
405 406 6.638610 ACCTTGTGATGTTCATTTTGTTCAA 58.361 32.000 0.00 0.00 0.00 2.69
406 407 6.534793 ACCTTGTGATGTTCATTTTGTTCAAC 59.465 34.615 0.00 0.00 0.00 3.18
407 408 6.757947 CCTTGTGATGTTCATTTTGTTCAACT 59.242 34.615 0.00 0.00 0.00 3.16
408 409 7.043192 CCTTGTGATGTTCATTTTGTTCAACTC 60.043 37.037 0.00 0.00 0.00 3.01
409 410 7.099266 TGTGATGTTCATTTTGTTCAACTCT 57.901 32.000 0.00 0.00 0.00 3.24
410 411 6.974048 TGTGATGTTCATTTTGTTCAACTCTG 59.026 34.615 0.00 0.00 0.00 3.35
411 412 5.978919 TGATGTTCATTTTGTTCAACTCTGC 59.021 36.000 0.00 0.00 0.00 4.26
412 413 5.581126 TGTTCATTTTGTTCAACTCTGCT 57.419 34.783 0.00 0.00 0.00 4.24
413 414 5.964758 TGTTCATTTTGTTCAACTCTGCTT 58.035 33.333 0.00 0.00 0.00 3.91
414 415 6.397272 TGTTCATTTTGTTCAACTCTGCTTT 58.603 32.000 0.00 0.00 0.00 3.51
415 416 6.310956 TGTTCATTTTGTTCAACTCTGCTTTG 59.689 34.615 0.00 0.00 0.00 2.77
416 417 6.206395 TCATTTTGTTCAACTCTGCTTTGA 57.794 33.333 0.00 0.00 0.00 2.69
417 418 6.629128 TCATTTTGTTCAACTCTGCTTTGAA 58.371 32.000 0.00 0.00 39.99 2.69
418 419 7.095910 TCATTTTGTTCAACTCTGCTTTGAAA 58.904 30.769 0.00 0.00 42.98 2.69
419 420 7.765360 TCATTTTGTTCAACTCTGCTTTGAAAT 59.235 29.630 0.00 0.00 42.98 2.17
420 421 9.033481 CATTTTGTTCAACTCTGCTTTGAAATA 57.967 29.630 0.00 0.00 42.98 1.40
421 422 8.994429 TTTTGTTCAACTCTGCTTTGAAATAA 57.006 26.923 0.00 0.00 42.98 1.40
422 423 9.598517 TTTTGTTCAACTCTGCTTTGAAATAAT 57.401 25.926 0.00 0.00 42.98 1.28
423 424 8.578308 TTGTTCAACTCTGCTTTGAAATAATG 57.422 30.769 0.00 0.00 42.98 1.90
424 425 7.939782 TGTTCAACTCTGCTTTGAAATAATGA 58.060 30.769 0.00 0.00 42.98 2.57
425 426 7.862372 TGTTCAACTCTGCTTTGAAATAATGAC 59.138 33.333 0.00 0.00 42.98 3.06
426 427 7.509141 TCAACTCTGCTTTGAAATAATGACA 57.491 32.000 0.00 0.00 29.89 3.58
427 428 7.587629 TCAACTCTGCTTTGAAATAATGACAG 58.412 34.615 0.00 0.00 29.89 3.51
428 429 7.445096 TCAACTCTGCTTTGAAATAATGACAGA 59.555 33.333 0.00 0.00 29.89 3.41
429 430 7.934855 ACTCTGCTTTGAAATAATGACAGAT 57.065 32.000 0.00 0.00 32.89 2.90
430 431 7.983307 ACTCTGCTTTGAAATAATGACAGATC 58.017 34.615 0.00 0.00 32.89 2.75
431 432 7.609146 ACTCTGCTTTGAAATAATGACAGATCA 59.391 33.333 0.00 0.00 39.83 2.92
433 434 9.617523 TCTGCTTTGAAATAATGACAGATCATA 57.382 29.630 0.00 0.00 45.26 2.15
446 447 9.623000 AATGACAGATCATATGATTTGAGTTCA 57.377 29.630 32.08 25.95 45.26 3.18
447 448 9.623000 ATGACAGATCATATGATTTGAGTTCAA 57.377 29.630 32.08 16.16 44.11 2.69
462 463 7.630242 TTGAGTTCAAACTGAGATTTCAACT 57.370 32.000 0.00 0.00 39.88 3.16
463 464 7.251704 TGAGTTCAAACTGAGATTTCAACTC 57.748 36.000 13.16 13.16 39.88 3.01
464 465 6.823182 TGAGTTCAAACTGAGATTTCAACTCA 59.177 34.615 16.42 16.42 39.53 3.41
471 472 4.521130 TGAGATTTCAACTCAGCGTACT 57.479 40.909 0.00 0.00 39.10 2.73
472 473 4.883083 TGAGATTTCAACTCAGCGTACTT 58.117 39.130 0.00 0.00 39.10 2.24
473 474 5.297547 TGAGATTTCAACTCAGCGTACTTT 58.702 37.500 0.00 0.00 39.10 2.66
474 475 5.758296 TGAGATTTCAACTCAGCGTACTTTT 59.242 36.000 0.00 0.00 39.10 2.27
475 476 6.260050 TGAGATTTCAACTCAGCGTACTTTTT 59.740 34.615 0.00 0.00 39.10 1.94
476 477 7.439955 TGAGATTTCAACTCAGCGTACTTTTTA 59.560 33.333 0.00 0.00 39.10 1.52
477 478 8.324163 AGATTTCAACTCAGCGTACTTTTTAT 57.676 30.769 0.00 0.00 0.00 1.40
478 479 8.230486 AGATTTCAACTCAGCGTACTTTTTATG 58.770 33.333 0.00 0.00 0.00 1.90
479 480 5.277601 TCAACTCAGCGTACTTTTTATGC 57.722 39.130 0.00 0.00 0.00 3.14
480 481 4.752604 TCAACTCAGCGTACTTTTTATGCA 59.247 37.500 0.00 0.00 32.18 3.96
481 482 4.928661 ACTCAGCGTACTTTTTATGCAG 57.071 40.909 0.00 0.00 32.18 4.41
482 483 4.566004 ACTCAGCGTACTTTTTATGCAGA 58.434 39.130 0.00 0.00 32.18 4.26
483 484 4.627467 ACTCAGCGTACTTTTTATGCAGAG 59.373 41.667 13.40 13.40 43.92 3.35
484 485 3.932710 TCAGCGTACTTTTTATGCAGAGG 59.067 43.478 0.00 0.00 32.18 3.69
485 486 2.678336 AGCGTACTTTTTATGCAGAGGC 59.322 45.455 0.00 0.00 41.68 4.70
495 496 2.436292 GCAGAGGCAGGAGCACAG 60.436 66.667 0.00 0.00 44.61 3.66
496 497 2.436292 CAGAGGCAGGAGCACAGC 60.436 66.667 0.00 0.00 44.61 4.40
497 498 2.926779 AGAGGCAGGAGCACAGCA 60.927 61.111 0.87 0.00 44.61 4.41
498 499 2.033141 GAGGCAGGAGCACAGCAA 59.967 61.111 0.87 0.00 44.61 3.91
499 500 1.378250 GAGGCAGGAGCACAGCAAT 60.378 57.895 0.87 0.00 44.61 3.56
500 501 1.375098 GAGGCAGGAGCACAGCAATC 61.375 60.000 0.87 0.00 44.61 2.67
501 502 1.378250 GGCAGGAGCACAGCAATCT 60.378 57.895 0.87 0.00 44.61 2.40
502 503 1.654954 GGCAGGAGCACAGCAATCTG 61.655 60.000 0.87 0.00 44.61 2.90
503 504 1.801332 CAGGAGCACAGCAATCTGC 59.199 57.895 0.00 0.00 44.10 4.26
518 519 6.156932 GCAATCTGCAAAACAAGGTAAATC 57.843 37.500 0.00 0.00 44.26 2.17
519 520 5.695816 GCAATCTGCAAAACAAGGTAAATCA 59.304 36.000 0.00 0.00 44.26 2.57
520 521 6.202570 GCAATCTGCAAAACAAGGTAAATCAA 59.797 34.615 0.00 0.00 44.26 2.57
521 522 7.254727 GCAATCTGCAAAACAAGGTAAATCAAA 60.255 33.333 0.00 0.00 44.26 2.69
522 523 8.610896 CAATCTGCAAAACAAGGTAAATCAAAA 58.389 29.630 0.00 0.00 0.00 2.44
523 524 8.907222 ATCTGCAAAACAAGGTAAATCAAAAT 57.093 26.923 0.00 0.00 0.00 1.82
524 525 9.995003 ATCTGCAAAACAAGGTAAATCAAAATA 57.005 25.926 0.00 0.00 0.00 1.40
525 526 9.995003 TCTGCAAAACAAGGTAAATCAAAATAT 57.005 25.926 0.00 0.00 0.00 1.28
527 528 9.995003 TGCAAAACAAGGTAAATCAAAATATCT 57.005 25.926 0.00 0.00 0.00 1.98
550 551 9.890629 ATCTACTTATCAGACAATTGTAAAGCA 57.109 29.630 11.95 1.35 0.00 3.91
551 552 9.890629 TCTACTTATCAGACAATTGTAAAGCAT 57.109 29.630 11.95 2.52 0.00 3.79
554 555 8.462016 ACTTATCAGACAATTGTAAAGCATTCC 58.538 33.333 11.95 0.00 0.00 3.01
555 556 6.839124 ATCAGACAATTGTAAAGCATTCCA 57.161 33.333 11.95 0.00 0.00 3.53
556 557 6.839124 TCAGACAATTGTAAAGCATTCCAT 57.161 33.333 11.95 0.00 0.00 3.41
557 558 7.230849 TCAGACAATTGTAAAGCATTCCATT 57.769 32.000 11.95 0.00 0.00 3.16
558 559 8.347004 TCAGACAATTGTAAAGCATTCCATTA 57.653 30.769 11.95 0.00 0.00 1.90
559 560 8.801299 TCAGACAATTGTAAAGCATTCCATTAA 58.199 29.630 11.95 0.00 0.00 1.40
560 561 9.421806 CAGACAATTGTAAAGCATTCCATTAAA 57.578 29.630 11.95 0.00 0.00 1.52
561 562 9.995003 AGACAATTGTAAAGCATTCCATTAAAA 57.005 25.926 11.95 0.00 0.00 1.52
1251 1265 0.179054 GGGAAGTAGATGAACCGGCC 60.179 60.000 0.00 0.00 0.00 6.13
1372 1386 0.322816 GACTCTTCCCCATGCAGCAA 60.323 55.000 0.00 0.00 0.00 3.91
2466 2734 4.262292 GGCGTAGTGGATTGTGGTATATGA 60.262 45.833 0.00 0.00 0.00 2.15
2534 2802 8.954350 GTACTAGTTGGAGTAAGTGAGACAATA 58.046 37.037 0.00 0.00 33.74 1.90
2717 2985 5.978814 AGTATATCCCCGTTTATGCTGATC 58.021 41.667 0.00 0.00 0.00 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
187 188 5.705441 GTGTATCCACTGTTTCTGATTTGGA 59.295 40.000 0.00 0.00 38.61 3.53
188 189 5.473162 TGTGTATCCACTGTTTCTGATTTGG 59.527 40.000 0.00 0.00 42.34 3.28
189 190 6.558771 TGTGTATCCACTGTTTCTGATTTG 57.441 37.500 0.00 0.00 42.34 2.32
190 191 7.765695 AATGTGTATCCACTGTTTCTGATTT 57.234 32.000 0.00 0.00 42.34 2.17
191 192 7.765695 AAATGTGTATCCACTGTTTCTGATT 57.234 32.000 0.00 0.00 42.34 2.57
192 193 7.765695 AAAATGTGTATCCACTGTTTCTGAT 57.234 32.000 0.00 0.00 42.34 2.90
193 194 7.581213 AAAAATGTGTATCCACTGTTTCTGA 57.419 32.000 0.00 0.00 42.34 3.27
214 215 6.883744 AGGAAAAACAAGTGGAGCATAAAAA 58.116 32.000 0.00 0.00 0.00 1.94
215 216 6.478512 AGGAAAAACAAGTGGAGCATAAAA 57.521 33.333 0.00 0.00 0.00 1.52
216 217 6.097554 TGAAGGAAAAACAAGTGGAGCATAAA 59.902 34.615 0.00 0.00 0.00 1.40
217 218 5.596361 TGAAGGAAAAACAAGTGGAGCATAA 59.404 36.000 0.00 0.00 0.00 1.90
218 219 5.136828 TGAAGGAAAAACAAGTGGAGCATA 58.863 37.500 0.00 0.00 0.00 3.14
219 220 3.960102 TGAAGGAAAAACAAGTGGAGCAT 59.040 39.130 0.00 0.00 0.00 3.79
220 221 3.360867 TGAAGGAAAAACAAGTGGAGCA 58.639 40.909 0.00 0.00 0.00 4.26
221 222 4.385358 TTGAAGGAAAAACAAGTGGAGC 57.615 40.909 0.00 0.00 0.00 4.70
222 223 6.809869 AGAATTGAAGGAAAAACAAGTGGAG 58.190 36.000 0.00 0.00 0.00 3.86
223 224 6.790232 AGAATTGAAGGAAAAACAAGTGGA 57.210 33.333 0.00 0.00 0.00 4.02
224 225 7.267857 AGAAGAATTGAAGGAAAAACAAGTGG 58.732 34.615 0.00 0.00 0.00 4.00
225 226 8.707938 AAGAAGAATTGAAGGAAAAACAAGTG 57.292 30.769 0.00 0.00 0.00 3.16
226 227 9.725019 AAAAGAAGAATTGAAGGAAAAACAAGT 57.275 25.926 0.00 0.00 0.00 3.16
227 228 9.977762 CAAAAGAAGAATTGAAGGAAAAACAAG 57.022 29.630 0.00 0.00 0.00 3.16
228 229 9.717942 TCAAAAGAAGAATTGAAGGAAAAACAA 57.282 25.926 0.00 0.00 32.89 2.83
229 230 9.889128 ATCAAAAGAAGAATTGAAGGAAAAACA 57.111 25.926 0.00 0.00 38.88 2.83
232 233 9.546428 GGAATCAAAAGAAGAATTGAAGGAAAA 57.454 29.630 0.00 0.00 38.88 2.29
233 234 8.927411 AGGAATCAAAAGAAGAATTGAAGGAAA 58.073 29.630 0.00 0.00 38.88 3.13
234 235 8.362639 CAGGAATCAAAAGAAGAATTGAAGGAA 58.637 33.333 0.00 0.00 38.88 3.36
235 236 7.039504 CCAGGAATCAAAAGAAGAATTGAAGGA 60.040 37.037 0.00 0.00 38.88 3.36
236 237 7.039504 TCCAGGAATCAAAAGAAGAATTGAAGG 60.040 37.037 0.00 0.00 38.88 3.46
237 238 7.889469 TCCAGGAATCAAAAGAAGAATTGAAG 58.111 34.615 0.00 0.00 38.88 3.02
238 239 7.506938 ACTCCAGGAATCAAAAGAAGAATTGAA 59.493 33.333 0.00 0.00 38.88 2.69
239 240 7.006509 ACTCCAGGAATCAAAAGAAGAATTGA 58.993 34.615 0.00 0.00 39.66 2.57
240 241 7.224522 ACTCCAGGAATCAAAAGAAGAATTG 57.775 36.000 0.00 0.00 0.00 2.32
241 242 7.727634 AGAACTCCAGGAATCAAAAGAAGAATT 59.272 33.333 5.01 0.00 0.00 2.17
242 243 7.237255 AGAACTCCAGGAATCAAAAGAAGAAT 58.763 34.615 5.01 0.00 0.00 2.40
243 244 6.605119 AGAACTCCAGGAATCAAAAGAAGAA 58.395 36.000 5.01 0.00 0.00 2.52
244 245 6.192970 AGAACTCCAGGAATCAAAAGAAGA 57.807 37.500 5.01 0.00 0.00 2.87
245 246 6.675987 CAAGAACTCCAGGAATCAAAAGAAG 58.324 40.000 5.01 0.00 0.00 2.85
246 247 5.010012 GCAAGAACTCCAGGAATCAAAAGAA 59.990 40.000 5.01 0.00 0.00 2.52
247 248 4.520492 GCAAGAACTCCAGGAATCAAAAGA 59.480 41.667 5.01 0.00 0.00 2.52
248 249 4.522022 AGCAAGAACTCCAGGAATCAAAAG 59.478 41.667 5.01 0.00 0.00 2.27
249 250 4.473444 AGCAAGAACTCCAGGAATCAAAA 58.527 39.130 5.01 0.00 0.00 2.44
250 251 4.074970 GAGCAAGAACTCCAGGAATCAAA 58.925 43.478 5.01 0.00 0.00 2.69
251 252 3.072915 TGAGCAAGAACTCCAGGAATCAA 59.927 43.478 5.01 0.00 35.72 2.57
252 253 2.639347 TGAGCAAGAACTCCAGGAATCA 59.361 45.455 5.01 0.00 35.72 2.57
253 254 3.340814 TGAGCAAGAACTCCAGGAATC 57.659 47.619 0.00 0.00 35.72 2.52
254 255 3.073650 ACTTGAGCAAGAACTCCAGGAAT 59.926 43.478 16.47 0.00 40.79 3.01
255 256 2.439507 ACTTGAGCAAGAACTCCAGGAA 59.560 45.455 16.47 0.00 40.79 3.36
256 257 2.050144 ACTTGAGCAAGAACTCCAGGA 58.950 47.619 16.47 0.00 40.79 3.86
257 258 2.557920 ACTTGAGCAAGAACTCCAGG 57.442 50.000 16.47 0.00 40.79 4.45
258 259 4.133078 AGAAACTTGAGCAAGAACTCCAG 58.867 43.478 16.47 0.00 40.79 3.86
259 260 4.156455 AGAAACTTGAGCAAGAACTCCA 57.844 40.909 16.47 0.00 40.79 3.86
260 261 4.576463 TGAAGAAACTTGAGCAAGAACTCC 59.424 41.667 16.47 2.35 40.79 3.85
261 262 5.065218 TGTGAAGAAACTTGAGCAAGAACTC 59.935 40.000 16.47 9.25 40.79 3.01
262 263 4.943705 TGTGAAGAAACTTGAGCAAGAACT 59.056 37.500 16.47 9.21 40.79 3.01
263 264 5.235305 TGTGAAGAAACTTGAGCAAGAAC 57.765 39.130 16.47 7.38 40.79 3.01
264 265 5.415701 ACTTGTGAAGAAACTTGAGCAAGAA 59.584 36.000 16.47 0.00 40.79 2.52
265 266 4.943705 ACTTGTGAAGAAACTTGAGCAAGA 59.056 37.500 16.47 0.00 40.79 3.02
266 267 5.240713 ACTTGTGAAGAAACTTGAGCAAG 57.759 39.130 8.60 8.60 43.79 4.01
267 268 5.182950 TGAACTTGTGAAGAAACTTGAGCAA 59.817 36.000 0.00 0.00 0.00 3.91
268 269 4.699735 TGAACTTGTGAAGAAACTTGAGCA 59.300 37.500 0.00 0.00 0.00 4.26
269 270 5.030936 GTGAACTTGTGAAGAAACTTGAGC 58.969 41.667 0.00 0.00 0.00 4.26
270 271 5.355350 AGGTGAACTTGTGAAGAAACTTGAG 59.645 40.000 0.00 0.00 0.00 3.02
271 272 5.253330 AGGTGAACTTGTGAAGAAACTTGA 58.747 37.500 0.00 0.00 0.00 3.02
272 273 5.567138 AGGTGAACTTGTGAAGAAACTTG 57.433 39.130 0.00 0.00 0.00 3.16
273 274 6.884836 AGTTAGGTGAACTTGTGAAGAAACTT 59.115 34.615 0.00 0.00 46.79 2.66
274 275 6.415573 AGTTAGGTGAACTTGTGAAGAAACT 58.584 36.000 0.00 0.00 46.79 2.66
275 276 6.679327 AGTTAGGTGAACTTGTGAAGAAAC 57.321 37.500 0.00 0.00 46.79 2.78
276 277 8.795842 TTTAGTTAGGTGAACTTGTGAAGAAA 57.204 30.769 0.00 0.00 46.79 2.52
277 278 8.044908 ACTTTAGTTAGGTGAACTTGTGAAGAA 58.955 33.333 0.00 0.00 46.79 2.52
278 279 7.562135 ACTTTAGTTAGGTGAACTTGTGAAGA 58.438 34.615 0.00 0.00 46.79 2.87
279 280 7.787725 ACTTTAGTTAGGTGAACTTGTGAAG 57.212 36.000 0.00 0.00 46.79 3.02
280 281 8.259411 TGTACTTTAGTTAGGTGAACTTGTGAA 58.741 33.333 0.00 0.00 46.79 3.18
281 282 7.784037 TGTACTTTAGTTAGGTGAACTTGTGA 58.216 34.615 0.00 0.00 46.79 3.58
282 283 8.428186 TTGTACTTTAGTTAGGTGAACTTGTG 57.572 34.615 0.00 0.00 46.79 3.33
283 284 9.623000 ATTTGTACTTTAGTTAGGTGAACTTGT 57.377 29.630 0.00 0.00 46.79 3.16
301 302 9.295825 TGGATCAACAATTGTTCTATTTGTACT 57.704 29.630 20.85 0.00 35.83 2.73
302 303 9.906660 TTGGATCAACAATTGTTCTATTTGTAC 57.093 29.630 20.85 8.13 35.83 2.90
316 317 6.349243 TCAGCTTCAAATTGGATCAACAAT 57.651 33.333 0.00 0.00 42.56 2.71
317 318 5.787953 TCAGCTTCAAATTGGATCAACAA 57.212 34.783 0.00 0.00 34.41 2.83
318 319 5.787953 TTCAGCTTCAAATTGGATCAACA 57.212 34.783 0.00 0.00 0.00 3.33
319 320 6.090358 CACATTCAGCTTCAAATTGGATCAAC 59.910 38.462 0.00 0.00 0.00 3.18
320 321 6.160684 CACATTCAGCTTCAAATTGGATCAA 58.839 36.000 0.00 0.00 0.00 2.57
321 322 5.336929 CCACATTCAGCTTCAAATTGGATCA 60.337 40.000 0.00 0.00 0.00 2.92
322 323 5.107133 CCACATTCAGCTTCAAATTGGATC 58.893 41.667 0.00 0.00 0.00 3.36
323 324 4.529377 ACCACATTCAGCTTCAAATTGGAT 59.471 37.500 10.43 0.00 0.00 3.41
324 325 3.896888 ACCACATTCAGCTTCAAATTGGA 59.103 39.130 10.43 0.00 0.00 3.53
325 326 4.261578 ACCACATTCAGCTTCAAATTGG 57.738 40.909 0.00 0.00 0.00 3.16
326 327 5.865552 CCTTACCACATTCAGCTTCAAATTG 59.134 40.000 0.00 0.00 0.00 2.32
327 328 5.539955 ACCTTACCACATTCAGCTTCAAATT 59.460 36.000 0.00 0.00 0.00 1.82
328 329 5.079643 ACCTTACCACATTCAGCTTCAAAT 58.920 37.500 0.00 0.00 0.00 2.32
329 330 4.469657 ACCTTACCACATTCAGCTTCAAA 58.530 39.130 0.00 0.00 0.00 2.69
330 331 4.098914 ACCTTACCACATTCAGCTTCAA 57.901 40.909 0.00 0.00 0.00 2.69
331 332 3.788227 ACCTTACCACATTCAGCTTCA 57.212 42.857 0.00 0.00 0.00 3.02
332 333 4.395231 GGTTACCTTACCACATTCAGCTTC 59.605 45.833 0.00 0.00 38.12 3.86
333 334 4.202524 TGGTTACCTTACCACATTCAGCTT 60.203 41.667 2.07 0.00 43.14 3.74
334 335 3.329520 TGGTTACCTTACCACATTCAGCT 59.670 43.478 2.07 0.00 43.14 4.24
335 336 3.681593 TGGTTACCTTACCACATTCAGC 58.318 45.455 2.07 0.00 43.14 4.26
377 378 9.906660 GAACAAAATGAACATCACAAGGTATAA 57.093 29.630 0.00 0.00 0.00 0.98
378 379 9.072375 TGAACAAAATGAACATCACAAGGTATA 57.928 29.630 0.00 0.00 0.00 1.47
379 380 7.950512 TGAACAAAATGAACATCACAAGGTAT 58.049 30.769 0.00 0.00 0.00 2.73
380 381 7.340122 TGAACAAAATGAACATCACAAGGTA 57.660 32.000 0.00 0.00 0.00 3.08
381 382 6.219417 TGAACAAAATGAACATCACAAGGT 57.781 33.333 0.00 0.00 0.00 3.50
382 383 6.757947 AGTTGAACAAAATGAACATCACAAGG 59.242 34.615 0.00 0.00 0.00 3.61
383 384 7.703621 AGAGTTGAACAAAATGAACATCACAAG 59.296 33.333 0.00 0.00 0.00 3.16
384 385 7.488792 CAGAGTTGAACAAAATGAACATCACAA 59.511 33.333 0.00 0.00 0.00 3.33
385 386 6.974048 CAGAGTTGAACAAAATGAACATCACA 59.026 34.615 0.00 0.00 0.00 3.58
386 387 6.074676 GCAGAGTTGAACAAAATGAACATCAC 60.075 38.462 0.00 0.00 0.00 3.06
387 388 5.978919 GCAGAGTTGAACAAAATGAACATCA 59.021 36.000 0.00 0.00 0.00 3.07
388 389 6.211515 AGCAGAGTTGAACAAAATGAACATC 58.788 36.000 0.00 0.00 0.00 3.06
389 390 6.152932 AGCAGAGTTGAACAAAATGAACAT 57.847 33.333 0.00 0.00 0.00 2.71
390 391 5.581126 AGCAGAGTTGAACAAAATGAACA 57.419 34.783 0.00 0.00 0.00 3.18
391 392 6.531240 TCAAAGCAGAGTTGAACAAAATGAAC 59.469 34.615 0.00 0.00 32.13 3.18
392 393 6.629128 TCAAAGCAGAGTTGAACAAAATGAA 58.371 32.000 0.00 0.00 32.13 2.57
393 394 6.206395 TCAAAGCAGAGTTGAACAAAATGA 57.794 33.333 0.00 0.00 32.13 2.57
394 395 6.890663 TTCAAAGCAGAGTTGAACAAAATG 57.109 33.333 0.00 0.00 39.46 2.32
395 396 9.598517 TTATTTCAAAGCAGAGTTGAACAAAAT 57.401 25.926 0.00 0.00 42.98 1.82
396 397 8.994429 TTATTTCAAAGCAGAGTTGAACAAAA 57.006 26.923 0.00 0.00 42.98 2.44
397 398 9.033481 CATTATTTCAAAGCAGAGTTGAACAAA 57.967 29.630 0.00 0.00 42.98 2.83
398 399 8.412456 TCATTATTTCAAAGCAGAGTTGAACAA 58.588 29.630 0.00 0.00 42.98 2.83
399 400 7.862372 GTCATTATTTCAAAGCAGAGTTGAACA 59.138 33.333 0.00 0.00 42.98 3.18
400 401 7.862372 TGTCATTATTTCAAAGCAGAGTTGAAC 59.138 33.333 0.00 0.00 42.98 3.18
401 402 7.939782 TGTCATTATTTCAAAGCAGAGTTGAA 58.060 30.769 0.00 0.00 41.91 2.69
402 403 7.445096 TCTGTCATTATTTCAAAGCAGAGTTGA 59.555 33.333 0.00 0.00 33.21 3.18
403 404 7.587629 TCTGTCATTATTTCAAAGCAGAGTTG 58.412 34.615 0.00 0.00 0.00 3.16
404 405 7.750229 TCTGTCATTATTTCAAAGCAGAGTT 57.250 32.000 0.00 0.00 0.00 3.01
405 406 7.609146 TGATCTGTCATTATTTCAAAGCAGAGT 59.391 33.333 0.00 0.00 35.59 3.24
406 407 7.982224 TGATCTGTCATTATTTCAAAGCAGAG 58.018 34.615 0.00 0.00 35.59 3.35
407 408 7.926674 TGATCTGTCATTATTTCAAAGCAGA 57.073 32.000 0.00 0.00 36.39 4.26
420 421 9.623000 TGAACTCAAATCATATGATCTGTCATT 57.377 29.630 18.44 10.71 42.37 2.57
421 422 9.623000 TTGAACTCAAATCATATGATCTGTCAT 57.377 29.630 18.44 5.91 39.48 3.06
422 423 9.452287 TTTGAACTCAAATCATATGATCTGTCA 57.548 29.630 18.44 11.68 40.55 3.58
423 424 9.713740 GTTTGAACTCAAATCATATGATCTGTC 57.286 33.333 18.44 9.40 46.12 3.51
424 425 9.458727 AGTTTGAACTCAAATCATATGATCTGT 57.541 29.630 18.44 11.56 46.12 3.41
425 426 9.717892 CAGTTTGAACTCAAATCATATGATCTG 57.282 33.333 18.44 15.15 46.12 2.90
426 427 9.676861 TCAGTTTGAACTCAAATCATATGATCT 57.323 29.630 18.44 1.63 46.12 2.75
427 428 9.932699 CTCAGTTTGAACTCAAATCATATGATC 57.067 33.333 18.44 6.02 46.12 2.92
428 429 9.676861 TCTCAGTTTGAACTCAAATCATATGAT 57.323 29.630 12.62 12.62 46.12 2.45
429 430 9.676861 ATCTCAGTTTGAACTCAAATCATATGA 57.323 29.630 8.10 8.10 46.12 2.15
433 434 8.853126 TGAAATCTCAGTTTGAACTCAAATCAT 58.147 29.630 8.07 0.00 46.12 2.45
434 435 8.224389 TGAAATCTCAGTTTGAACTCAAATCA 57.776 30.769 8.07 3.20 46.12 2.57
435 436 8.962111 GTTGAAATCTCAGTTTGAACTCAAATC 58.038 33.333 8.07 3.24 46.12 2.17
436 437 8.689972 AGTTGAAATCTCAGTTTGAACTCAAAT 58.310 29.630 8.07 0.00 46.12 2.32
437 438 8.055279 AGTTGAAATCTCAGTTTGAACTCAAA 57.945 30.769 0.69 0.69 40.04 2.69
438 439 7.630242 AGTTGAAATCTCAGTTTGAACTCAA 57.370 32.000 0.00 0.00 40.04 3.02
450 451 4.521130 AGTACGCTGAGTTGAAATCTCA 57.479 40.909 0.00 0.00 39.25 3.27
451 452 5.847670 AAAGTACGCTGAGTTGAAATCTC 57.152 39.130 0.00 0.00 0.00 2.75
452 453 6.619801 AAAAAGTACGCTGAGTTGAAATCT 57.380 33.333 0.00 0.00 0.00 2.40
453 454 7.007456 GCATAAAAAGTACGCTGAGTTGAAATC 59.993 37.037 0.00 0.00 0.00 2.17
454 455 6.801862 GCATAAAAAGTACGCTGAGTTGAAAT 59.198 34.615 0.00 0.00 0.00 2.17
455 456 6.140110 GCATAAAAAGTACGCTGAGTTGAAA 58.860 36.000 0.00 0.00 0.00 2.69
456 457 5.237561 TGCATAAAAAGTACGCTGAGTTGAA 59.762 36.000 0.00 0.00 0.00 2.69
457 458 4.752604 TGCATAAAAAGTACGCTGAGTTGA 59.247 37.500 0.00 0.00 0.00 3.18
458 459 5.029650 TGCATAAAAAGTACGCTGAGTTG 57.970 39.130 0.00 0.00 0.00 3.16
459 460 4.994852 TCTGCATAAAAAGTACGCTGAGTT 59.005 37.500 0.00 0.00 0.00 3.01
460 461 4.566004 TCTGCATAAAAAGTACGCTGAGT 58.434 39.130 0.00 0.00 0.00 3.41
461 462 4.033358 CCTCTGCATAAAAAGTACGCTGAG 59.967 45.833 13.07 13.07 43.92 3.35
462 463 3.932710 CCTCTGCATAAAAAGTACGCTGA 59.067 43.478 0.00 0.00 0.00 4.26
463 464 3.485877 GCCTCTGCATAAAAAGTACGCTG 60.486 47.826 0.00 0.00 37.47 5.18
464 465 2.678336 GCCTCTGCATAAAAAGTACGCT 59.322 45.455 0.00 0.00 37.47 5.07
465 466 2.418628 TGCCTCTGCATAAAAAGTACGC 59.581 45.455 0.00 0.00 44.23 4.42
478 479 2.436292 CTGTGCTCCTGCCTCTGC 60.436 66.667 0.00 0.00 38.71 4.26
479 480 2.436292 GCTGTGCTCCTGCCTCTG 60.436 66.667 0.00 0.00 38.71 3.35
480 481 1.849975 ATTGCTGTGCTCCTGCCTCT 61.850 55.000 4.03 0.00 37.22 3.69
481 482 1.375098 GATTGCTGTGCTCCTGCCTC 61.375 60.000 4.03 0.00 37.22 4.70
482 483 1.378250 GATTGCTGTGCTCCTGCCT 60.378 57.895 4.03 0.00 37.22 4.75
483 484 1.378250 AGATTGCTGTGCTCCTGCC 60.378 57.895 4.03 0.00 37.22 4.85
484 485 1.801332 CAGATTGCTGTGCTCCTGC 59.199 57.895 0.00 0.00 37.37 4.85
485 486 0.958876 TGCAGATTGCTGTGCTCCTG 60.959 55.000 2.48 0.00 45.31 3.86
486 487 0.251033 TTGCAGATTGCTGTGCTCCT 60.251 50.000 2.48 0.00 45.31 3.69
487 488 0.599558 TTTGCAGATTGCTGTGCTCC 59.400 50.000 2.48 0.00 45.31 4.70
488 489 2.056577 GTTTTGCAGATTGCTGTGCTC 58.943 47.619 2.48 0.00 45.31 4.26
489 490 1.409790 TGTTTTGCAGATTGCTGTGCT 59.590 42.857 2.48 0.00 45.31 4.40
490 491 1.855513 TGTTTTGCAGATTGCTGTGC 58.144 45.000 2.48 0.00 45.31 4.57
491 492 2.798283 CCTTGTTTTGCAGATTGCTGTG 59.202 45.455 2.48 0.00 45.31 3.66
492 493 2.431782 ACCTTGTTTTGCAGATTGCTGT 59.568 40.909 2.48 0.00 45.31 4.40
493 494 3.102052 ACCTTGTTTTGCAGATTGCTG 57.898 42.857 2.48 0.00 45.31 4.41
494 495 4.935352 TTACCTTGTTTTGCAGATTGCT 57.065 36.364 2.48 0.00 45.31 3.91
495 496 5.695816 TGATTTACCTTGTTTTGCAGATTGC 59.304 36.000 0.00 0.00 45.29 3.56
496 497 7.712264 TTGATTTACCTTGTTTTGCAGATTG 57.288 32.000 0.00 0.00 0.00 2.67
497 498 8.729805 TTTTGATTTACCTTGTTTTGCAGATT 57.270 26.923 0.00 0.00 0.00 2.40
498 499 8.907222 ATTTTGATTTACCTTGTTTTGCAGAT 57.093 26.923 0.00 0.00 0.00 2.90
499 500 9.995003 ATATTTTGATTTACCTTGTTTTGCAGA 57.005 25.926 0.00 0.00 0.00 4.26
501 502 9.995003 AGATATTTTGATTTACCTTGTTTTGCA 57.005 25.926 0.00 0.00 0.00 4.08
524 525 9.890629 TGCTTTACAATTGTCTGATAAGTAGAT 57.109 29.630 15.85 0.00 0.00 1.98
525 526 9.890629 ATGCTTTACAATTGTCTGATAAGTAGA 57.109 29.630 15.85 0.00 0.00 2.59
528 529 8.462016 GGAATGCTTTACAATTGTCTGATAAGT 58.538 33.333 15.85 0.00 0.00 2.24
529 530 8.461222 TGGAATGCTTTACAATTGTCTGATAAG 58.539 33.333 15.85 12.30 0.00 1.73
530 531 8.347004 TGGAATGCTTTACAATTGTCTGATAA 57.653 30.769 15.85 0.00 0.00 1.75
531 532 7.936496 TGGAATGCTTTACAATTGTCTGATA 57.064 32.000 15.85 0.73 0.00 2.15
532 533 6.839124 TGGAATGCTTTACAATTGTCTGAT 57.161 33.333 15.85 0.00 0.00 2.90
533 534 6.839124 ATGGAATGCTTTACAATTGTCTGA 57.161 33.333 15.85 0.00 0.00 3.27
534 535 8.984891 TTAATGGAATGCTTTACAATTGTCTG 57.015 30.769 15.85 7.63 0.00 3.51
535 536 9.995003 TTTTAATGGAATGCTTTACAATTGTCT 57.005 25.926 15.85 0.00 0.00 3.41
563 564 9.403110 GCATCATAACATTGGTTAGATTGATTC 57.597 33.333 0.00 0.00 42.42 2.52
564 565 9.139734 AGCATCATAACATTGGTTAGATTGATT 57.860 29.630 0.00 0.00 42.42 2.57
565 566 8.573885 CAGCATCATAACATTGGTTAGATTGAT 58.426 33.333 0.00 0.00 42.42 2.57
566 567 7.557358 ACAGCATCATAACATTGGTTAGATTGA 59.443 33.333 0.00 0.00 42.42 2.57
567 568 7.709947 ACAGCATCATAACATTGGTTAGATTG 58.290 34.615 0.00 0.00 42.42 2.67
568 569 7.886629 ACAGCATCATAACATTGGTTAGATT 57.113 32.000 0.00 0.00 42.42 2.40
569 570 7.201848 CCAACAGCATCATAACATTGGTTAGAT 60.202 37.037 0.00 0.00 42.42 1.98
570 571 6.095300 CCAACAGCATCATAACATTGGTTAGA 59.905 38.462 0.00 0.00 42.42 2.10
571 572 6.267817 CCAACAGCATCATAACATTGGTTAG 58.732 40.000 0.00 0.00 42.42 2.34
572 573 5.126869 CCCAACAGCATCATAACATTGGTTA 59.873 40.000 0.00 0.00 43.25 2.85
573 574 4.081531 CCCAACAGCATCATAACATTGGTT 60.082 41.667 0.00 0.00 41.06 3.67
574 575 3.448301 CCCAACAGCATCATAACATTGGT 59.552 43.478 0.00 0.00 34.55 3.67
575 576 3.738899 GCCCAACAGCATCATAACATTGG 60.739 47.826 0.00 0.00 35.84 3.16
576 577 3.131577 AGCCCAACAGCATCATAACATTG 59.868 43.478 0.00 0.00 34.23 2.82
577 578 3.131577 CAGCCCAACAGCATCATAACATT 59.868 43.478 0.00 0.00 34.23 2.71
578 579 2.691526 CAGCCCAACAGCATCATAACAT 59.308 45.455 0.00 0.00 34.23 2.71
579 580 2.093890 CAGCCCAACAGCATCATAACA 58.906 47.619 0.00 0.00 34.23 2.41
580 581 2.094675 ACAGCCCAACAGCATCATAAC 58.905 47.619 0.00 0.00 34.23 1.89
581 582 2.093890 CACAGCCCAACAGCATCATAA 58.906 47.619 0.00 0.00 34.23 1.90
582 583 1.004628 ACACAGCCCAACAGCATCATA 59.995 47.619 0.00 0.00 34.23 2.15
583 584 0.251474 ACACAGCCCAACAGCATCAT 60.251 50.000 0.00 0.00 34.23 2.45
584 585 0.890542 GACACAGCCCAACAGCATCA 60.891 55.000 0.00 0.00 34.23 3.07
585 586 0.607489 AGACACAGCCCAACAGCATC 60.607 55.000 0.00 0.00 34.23 3.91
586 587 0.178981 AAGACACAGCCCAACAGCAT 60.179 50.000 0.00 0.00 34.23 3.79
587 588 0.472044 TAAGACACAGCCCAACAGCA 59.528 50.000 0.00 0.00 34.23 4.41
588 589 1.740025 GATAAGACACAGCCCAACAGC 59.260 52.381 0.00 0.00 0.00 4.40
1251 1265 1.605710 CACTCTTCACTTGCCCTGTTG 59.394 52.381 0.00 0.00 0.00 3.33
1372 1386 4.157246 GTTTCCAGGGTTTTCCATACCTT 58.843 43.478 0.00 0.00 42.91 3.50
1921 2189 3.521937 ACTGGAATAATTCGAACCCCTCA 59.478 43.478 0.00 0.00 0.00 3.86
2466 2734 3.131223 CCAGACCTAGACACATCACGATT 59.869 47.826 0.00 0.00 0.00 3.34


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

AutoCloner maintained by Alex Coulton.