Multiple sequence alignment - TraesCS5B01G099100

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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 TraesCS5B01G099100 chr5B 100.000 2369 0 0 1 2369 131716412 131714044 0.000000e+00 4375
1 TraesCS5B01G099100 chr5D 94.556 1837 53 20 569 2369 119254560 119252735 0.000000e+00 2795
2 TraesCS5B01G099100 chr5D 91.129 248 8 4 1 240 119254799 119254558 8.170000e-85 324
3 TraesCS5B01G099100 chr5A 93.869 1843 59 23 569 2368 129276903 129275072 0.000000e+00 2728
4 TraesCS5B01G099100 chr5A 93.750 240 13 2 1 239 129277141 129276903 2.240000e-95 359
5 TraesCS5B01G099100 chr3B 96.188 341 7 3 239 573 166499246 166498906 9.570000e-154 553
6 TraesCS5B01G099100 chr2B 95.942 345 7 4 237 574 586904547 586904891 9.570000e-154 553
7 TraesCS5B01G099100 chr2A 96.188 341 7 3 240 574 423776097 423776437 9.570000e-154 553
8 TraesCS5B01G099100 chr2A 95.640 344 9 3 234 571 740400943 740400600 4.450000e-152 547
9 TraesCS5B01G099100 chr7A 95.918 343 8 3 237 573 317176316 317175974 3.440000e-153 551
10 TraesCS5B01G099100 chr4B 96.176 340 7 3 238 571 128540875 128541214 3.440000e-153 551
11 TraesCS5B01G099100 chr1A 96.176 340 7 3 238 571 341181116 341181455 3.440000e-153 551
12 TraesCS5B01G099100 chr6B 95.894 341 8 3 238 572 546040070 546040410 4.450000e-152 547
13 TraesCS5B01G099100 chr3A 95.894 341 8 3 238 572 146827053 146826713 4.450000e-152 547


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 TraesCS5B01G099100 chr5B 131714044 131716412 2368 True 4375.0 4375 100.0000 1 2369 1 chr5B.!!$R1 2368
1 TraesCS5B01G099100 chr5D 119252735 119254799 2064 True 1559.5 2795 92.8425 1 2369 2 chr5D.!!$R1 2368
2 TraesCS5B01G099100 chr5A 129275072 129277141 2069 True 1543.5 2728 93.8095 1 2368 2 chr5A.!!$R1 2367

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
704 719 0.10212 CTCCTCCTCGTCACATGAGC 59.898 60.0 0.0 0.0 29.93 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1741 1796 0.038166 ATCCACCTGAACGCCACAAT 59.962 50.0 0.0 0.0 0.0 2.71 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
31 32 8.415950 AGATTTTACCATAACACAAACATCCA 57.584 30.769 0.00 0.00 0.00 3.41
76 84 8.837389 GTCTACCCTTAAAATTCGCTCAATAAT 58.163 33.333 0.00 0.00 0.00 1.28
77 85 8.836413 TCTACCCTTAAAATTCGCTCAATAATG 58.164 33.333 0.00 0.00 0.00 1.90
78 86 6.805713 ACCCTTAAAATTCGCTCAATAATGG 58.194 36.000 0.00 0.00 0.00 3.16
79 87 6.605594 ACCCTTAAAATTCGCTCAATAATGGA 59.394 34.615 0.00 0.00 0.00 3.41
80 88 7.141363 CCCTTAAAATTCGCTCAATAATGGAG 58.859 38.462 0.00 0.00 35.47 3.86
118 131 3.181479 GCACCATCATCTCGTGGTAACTA 60.181 47.826 0.00 0.00 46.62 2.24
119 132 4.611943 CACCATCATCTCGTGGTAACTAG 58.388 47.826 0.00 0.00 46.62 2.57
140 153 4.794169 AGTACAAATTTAGCAAGCCAACG 58.206 39.130 0.00 0.00 0.00 4.10
159 172 0.890996 GGACAGTGGCCAAACTCCAG 60.891 60.000 11.25 0.00 33.63 3.86
188 202 2.256461 CTGAAAAGCTGCCACCGC 59.744 61.111 0.00 0.00 0.00 5.68
245 259 6.262056 CCATTATAGTTGGGTTTAGAGGGT 57.738 41.667 0.00 0.00 0.00 4.34
246 260 6.062095 CCATTATAGTTGGGTTTAGAGGGTG 58.938 44.000 0.00 0.00 0.00 4.61
247 261 3.646736 ATAGTTGGGTTTAGAGGGTGC 57.353 47.619 0.00 0.00 0.00 5.01
248 262 1.446016 AGTTGGGTTTAGAGGGTGCT 58.554 50.000 0.00 0.00 0.00 4.40
249 263 1.780919 AGTTGGGTTTAGAGGGTGCTT 59.219 47.619 0.00 0.00 0.00 3.91
250 264 1.886542 GTTGGGTTTAGAGGGTGCTTG 59.113 52.381 0.00 0.00 0.00 4.01
251 265 0.404040 TGGGTTTAGAGGGTGCTTGG 59.596 55.000 0.00 0.00 0.00 3.61
252 266 0.696501 GGGTTTAGAGGGTGCTTGGA 59.303 55.000 0.00 0.00 0.00 3.53
253 267 1.285078 GGGTTTAGAGGGTGCTTGGAT 59.715 52.381 0.00 0.00 0.00 3.41
254 268 2.508300 GGGTTTAGAGGGTGCTTGGATA 59.492 50.000 0.00 0.00 0.00 2.59
255 269 3.542648 GGTTTAGAGGGTGCTTGGATAC 58.457 50.000 0.00 0.00 0.00 2.24
307 321 9.574516 AATCTCTTTTAGAGGCTAAAGTTTCAA 57.425 29.630 7.84 0.00 42.54 2.69
308 322 8.608844 TCTCTTTTAGAGGCTAAAGTTTCAAG 57.391 34.615 7.84 0.00 42.54 3.02
309 323 7.173390 TCTCTTTTAGAGGCTAAAGTTTCAAGC 59.827 37.037 7.84 2.28 42.54 4.01
310 324 6.770785 TCTTTTAGAGGCTAAAGTTTCAAGCA 59.229 34.615 11.51 0.00 38.01 3.91
311 325 5.941948 TTAGAGGCTAAAGTTTCAAGCAC 57.058 39.130 11.51 5.94 38.01 4.40
312 326 3.149981 AGAGGCTAAAGTTTCAAGCACC 58.850 45.455 11.51 3.82 38.01 5.01
313 327 2.229062 GAGGCTAAAGTTTCAAGCACCC 59.771 50.000 11.51 0.00 38.01 4.61
314 328 1.272490 GGCTAAAGTTTCAAGCACCCC 59.728 52.381 11.51 0.00 38.01 4.95
315 329 2.239400 GCTAAAGTTTCAAGCACCCCT 58.761 47.619 5.64 0.00 36.26 4.79
316 330 2.029918 GCTAAAGTTTCAAGCACCCCTG 60.030 50.000 5.64 0.00 36.26 4.45
317 331 2.452600 AAAGTTTCAAGCACCCCTGA 57.547 45.000 0.00 0.00 0.00 3.86
318 332 1.692411 AAGTTTCAAGCACCCCTGAC 58.308 50.000 0.00 0.00 0.00 3.51
319 333 0.846693 AGTTTCAAGCACCCCTGACT 59.153 50.000 0.00 0.00 0.00 3.41
320 334 2.054799 AGTTTCAAGCACCCCTGACTA 58.945 47.619 0.00 0.00 0.00 2.59
321 335 2.441750 AGTTTCAAGCACCCCTGACTAA 59.558 45.455 0.00 0.00 0.00 2.24
322 336 3.117663 AGTTTCAAGCACCCCTGACTAAA 60.118 43.478 0.00 0.00 0.00 1.85
323 337 2.859165 TCAAGCACCCCTGACTAAAG 57.141 50.000 0.00 0.00 0.00 1.85
324 338 2.334977 TCAAGCACCCCTGACTAAAGA 58.665 47.619 0.00 0.00 0.00 2.52
325 339 2.303022 TCAAGCACCCCTGACTAAAGAG 59.697 50.000 0.00 0.00 0.00 2.85
326 340 2.303022 CAAGCACCCCTGACTAAAGAGA 59.697 50.000 0.00 0.00 0.00 3.10
327 341 2.183679 AGCACCCCTGACTAAAGAGAG 58.816 52.381 0.00 0.00 0.00 3.20
328 342 1.208293 GCACCCCTGACTAAAGAGAGG 59.792 57.143 0.00 0.00 0.00 3.69
329 343 1.208293 CACCCCTGACTAAAGAGAGGC 59.792 57.143 0.00 0.00 0.00 4.70
330 344 1.079658 ACCCCTGACTAAAGAGAGGCT 59.920 52.381 0.00 0.00 0.00 4.58
331 345 2.315155 ACCCCTGACTAAAGAGAGGCTA 59.685 50.000 0.00 0.00 0.00 3.93
332 346 2.962421 CCCCTGACTAAAGAGAGGCTAG 59.038 54.545 0.00 0.00 0.00 3.42
333 347 2.962421 CCCTGACTAAAGAGAGGCTAGG 59.038 54.545 0.00 0.00 0.00 3.02
334 348 3.373220 CCCTGACTAAAGAGAGGCTAGGA 60.373 52.174 0.00 0.00 29.08 2.94
335 349 4.479158 CCTGACTAAAGAGAGGCTAGGAT 58.521 47.826 0.00 0.00 29.08 3.24
336 350 4.898861 CCTGACTAAAGAGAGGCTAGGATT 59.101 45.833 0.00 0.00 29.08 3.01
337 351 6.071984 CCTGACTAAAGAGAGGCTAGGATTA 58.928 44.000 0.00 0.00 29.08 1.75
338 352 6.208599 CCTGACTAAAGAGAGGCTAGGATTAG 59.791 46.154 0.00 0.00 29.08 1.73
339 353 6.674573 TGACTAAAGAGAGGCTAGGATTAGT 58.325 40.000 12.35 12.35 35.48 2.24
340 354 6.773685 TGACTAAAGAGAGGCTAGGATTAGTC 59.226 42.308 22.74 22.74 43.81 2.59
341 355 6.918033 ACTAAAGAGAGGCTAGGATTAGTCT 58.082 40.000 8.57 0.00 44.40 3.24
342 356 7.359056 ACTAAAGAGAGGCTAGGATTAGTCTT 58.641 38.462 8.57 0.00 41.84 3.01
343 357 8.504409 ACTAAAGAGAGGCTAGGATTAGTCTTA 58.496 37.037 8.57 0.00 41.84 2.10
344 358 9.357161 CTAAAGAGAGGCTAGGATTAGTCTTAA 57.643 37.037 0.00 0.00 41.84 1.85
345 359 7.833285 AAGAGAGGCTAGGATTAGTCTTAAG 57.167 40.000 0.00 0.00 41.84 1.85
346 360 6.311735 AGAGAGGCTAGGATTAGTCTTAAGG 58.688 44.000 1.85 0.00 41.84 2.69
347 361 4.836175 AGAGGCTAGGATTAGTCTTAAGGC 59.164 45.833 0.00 0.00 41.84 4.35
348 362 4.821940 AGGCTAGGATTAGTCTTAAGGCT 58.178 43.478 15.13 15.13 38.72 4.58
349 363 5.966684 AGGCTAGGATTAGTCTTAAGGCTA 58.033 41.667 12.83 12.83 38.72 3.93
350 364 6.382925 AGGCTAGGATTAGTCTTAAGGCTAA 58.617 40.000 27.11 27.11 38.72 3.09
351 365 6.844917 AGGCTAGGATTAGTCTTAAGGCTAAA 59.155 38.462 28.26 14.26 38.72 1.85
352 366 7.347485 AGGCTAGGATTAGTCTTAAGGCTAAAA 59.653 37.037 28.26 13.29 38.72 1.52
353 367 8.158132 GGCTAGGATTAGTCTTAAGGCTAAAAT 58.842 37.037 28.26 17.13 31.91 1.82
354 368 9.210329 GCTAGGATTAGTCTTAAGGCTAAAATC 57.790 37.037 28.26 22.91 31.91 2.17
373 387 9.025041 CTAAAATCTTTTAGTCATGGGAAACCT 57.975 33.333 12.31 0.00 45.91 3.50
403 417 8.948401 AAATATGTATTAGCTCTCTCTCCTCA 57.052 34.615 0.00 0.00 0.00 3.86
404 418 9.545928 AAATATGTATTAGCTCTCTCTCCTCAT 57.454 33.333 0.00 0.00 0.00 2.90
405 419 9.545928 AATATGTATTAGCTCTCTCTCCTCATT 57.454 33.333 0.00 0.00 0.00 2.57
406 420 7.854166 ATGTATTAGCTCTCTCTCCTCATTT 57.146 36.000 0.00 0.00 0.00 2.32
407 421 8.948401 ATGTATTAGCTCTCTCTCCTCATTTA 57.052 34.615 0.00 0.00 0.00 1.40
408 422 8.768501 TGTATTAGCTCTCTCTCCTCATTTAA 57.231 34.615 0.00 0.00 0.00 1.52
409 423 9.373450 TGTATTAGCTCTCTCTCCTCATTTAAT 57.627 33.333 0.00 0.00 0.00 1.40
412 426 6.173427 AGCTCTCTCTCCTCATTTAATTCC 57.827 41.667 0.00 0.00 0.00 3.01
413 427 5.904750 AGCTCTCTCTCCTCATTTAATTCCT 59.095 40.000 0.00 0.00 0.00 3.36
414 428 6.041979 AGCTCTCTCTCCTCATTTAATTCCTC 59.958 42.308 0.00 0.00 0.00 3.71
415 429 6.041979 GCTCTCTCTCCTCATTTAATTCCTCT 59.958 42.308 0.00 0.00 0.00 3.69
416 430 7.595819 TCTCTCTCCTCATTTAATTCCTCTC 57.404 40.000 0.00 0.00 0.00 3.20
417 431 6.553100 TCTCTCTCCTCATTTAATTCCTCTCC 59.447 42.308 0.00 0.00 0.00 3.71
418 432 6.448202 TCTCTCCTCATTTAATTCCTCTCCT 58.552 40.000 0.00 0.00 0.00 3.69
419 433 6.905776 TCTCTCCTCATTTAATTCCTCTCCTT 59.094 38.462 0.00 0.00 0.00 3.36
420 434 8.068110 TCTCTCCTCATTTAATTCCTCTCCTTA 58.932 37.037 0.00 0.00 0.00 2.69
421 435 8.256356 TCTCCTCATTTAATTCCTCTCCTTAG 57.744 38.462 0.00 0.00 0.00 2.18
422 436 7.846823 TCTCCTCATTTAATTCCTCTCCTTAGT 59.153 37.037 0.00 0.00 0.00 2.24
423 437 8.393959 TCCTCATTTAATTCCTCTCCTTAGTT 57.606 34.615 0.00 0.00 0.00 2.24
424 438 8.487028 TCCTCATTTAATTCCTCTCCTTAGTTC 58.513 37.037 0.00 0.00 0.00 3.01
425 439 8.490311 CCTCATTTAATTCCTCTCCTTAGTTCT 58.510 37.037 0.00 0.00 0.00 3.01
426 440 9.323985 CTCATTTAATTCCTCTCCTTAGTTCTG 57.676 37.037 0.00 0.00 0.00 3.02
427 441 8.267894 TCATTTAATTCCTCTCCTTAGTTCTGG 58.732 37.037 0.00 0.00 0.00 3.86
428 442 7.808279 TTTAATTCCTCTCCTTAGTTCTGGA 57.192 36.000 0.00 0.00 0.00 3.86
429 443 7.996758 TTAATTCCTCTCCTTAGTTCTGGAT 57.003 36.000 0.00 0.00 0.00 3.41
430 444 6.899892 AATTCCTCTCCTTAGTTCTGGATT 57.100 37.500 0.00 0.00 0.00 3.01
431 445 5.683876 TTCCTCTCCTTAGTTCTGGATTG 57.316 43.478 0.00 0.00 0.00 2.67
432 446 4.033709 TCCTCTCCTTAGTTCTGGATTGG 58.966 47.826 0.00 0.00 0.00 3.16
433 447 4.033709 CCTCTCCTTAGTTCTGGATTGGA 58.966 47.826 0.00 0.00 31.05 3.53
434 448 4.100808 CCTCTCCTTAGTTCTGGATTGGAG 59.899 50.000 0.00 0.00 40.47 3.86
435 449 4.033709 TCTCCTTAGTTCTGGATTGGAGG 58.966 47.826 0.00 0.00 39.80 4.30
436 450 3.115390 TCCTTAGTTCTGGATTGGAGGG 58.885 50.000 0.00 0.00 0.00 4.30
437 451 2.846827 CCTTAGTTCTGGATTGGAGGGT 59.153 50.000 0.00 0.00 0.00 4.34
438 452 3.267031 CCTTAGTTCTGGATTGGAGGGTT 59.733 47.826 0.00 0.00 0.00 4.11
439 453 4.263949 CCTTAGTTCTGGATTGGAGGGTTT 60.264 45.833 0.00 0.00 0.00 3.27
440 454 3.160679 AGTTCTGGATTGGAGGGTTTG 57.839 47.619 0.00 0.00 0.00 2.93
441 455 2.171003 GTTCTGGATTGGAGGGTTTGG 58.829 52.381 0.00 0.00 0.00 3.28
442 456 1.753903 TCTGGATTGGAGGGTTTGGA 58.246 50.000 0.00 0.00 0.00 3.53
443 457 1.635487 TCTGGATTGGAGGGTTTGGAG 59.365 52.381 0.00 0.00 0.00 3.86
444 458 0.704076 TGGATTGGAGGGTTTGGAGG 59.296 55.000 0.00 0.00 0.00 4.30
445 459 0.999712 GGATTGGAGGGTTTGGAGGA 59.000 55.000 0.00 0.00 0.00 3.71
446 460 1.570979 GGATTGGAGGGTTTGGAGGAT 59.429 52.381 0.00 0.00 0.00 3.24
447 461 2.783510 GGATTGGAGGGTTTGGAGGATA 59.216 50.000 0.00 0.00 0.00 2.59
448 462 3.204382 GGATTGGAGGGTTTGGAGGATAA 59.796 47.826 0.00 0.00 0.00 1.75
449 463 4.140924 GGATTGGAGGGTTTGGAGGATAAT 60.141 45.833 0.00 0.00 0.00 1.28
450 464 5.074515 GGATTGGAGGGTTTGGAGGATAATA 59.925 44.000 0.00 0.00 0.00 0.98
451 465 6.411554 GGATTGGAGGGTTTGGAGGATAATAA 60.412 42.308 0.00 0.00 0.00 1.40
452 466 6.410222 TTGGAGGGTTTGGAGGATAATAAA 57.590 37.500 0.00 0.00 0.00 1.40
453 467 6.606241 TGGAGGGTTTGGAGGATAATAAAT 57.394 37.500 0.00 0.00 0.00 1.40
454 468 6.372931 TGGAGGGTTTGGAGGATAATAAATG 58.627 40.000 0.00 0.00 0.00 2.32
455 469 5.243954 GGAGGGTTTGGAGGATAATAAATGC 59.756 44.000 0.00 0.00 0.00 3.56
456 470 6.030727 AGGGTTTGGAGGATAATAAATGCT 57.969 37.500 0.00 0.00 0.00 3.79
457 471 6.071320 AGGGTTTGGAGGATAATAAATGCTC 58.929 40.000 0.00 0.00 36.02 4.26
458 472 5.833131 GGGTTTGGAGGATAATAAATGCTCA 59.167 40.000 8.48 0.00 38.10 4.26
459 473 6.323739 GGGTTTGGAGGATAATAAATGCTCAA 59.676 38.462 8.48 0.00 38.10 3.02
460 474 7.015584 GGGTTTGGAGGATAATAAATGCTCAAT 59.984 37.037 8.48 0.00 38.10 2.57
461 475 9.077885 GGTTTGGAGGATAATAAATGCTCAATA 57.922 33.333 8.48 0.00 38.10 1.90
464 478 9.866655 TTGGAGGATAATAAATGCTCAATAACT 57.133 29.630 8.48 0.00 38.10 2.24
497 511 8.056407 AGTTTCTTTAGTATTTGGATCCAAGC 57.944 34.615 25.69 19.18 37.24 4.01
498 512 7.669722 AGTTTCTTTAGTATTTGGATCCAAGCA 59.330 33.333 25.69 14.00 37.24 3.91
499 513 8.470002 GTTTCTTTAGTATTTGGATCCAAGCAT 58.530 33.333 25.69 19.69 37.24 3.79
500 514 7.572523 TCTTTAGTATTTGGATCCAAGCATG 57.427 36.000 25.69 12.43 37.24 4.06
513 527 3.189618 CAAGCATGGATGAGACTAGCA 57.810 47.619 0.00 0.00 0.00 3.49
514 528 3.538591 CAAGCATGGATGAGACTAGCAA 58.461 45.455 0.00 0.00 0.00 3.91
515 529 3.472283 AGCATGGATGAGACTAGCAAG 57.528 47.619 0.00 0.00 0.00 4.01
516 530 2.770802 AGCATGGATGAGACTAGCAAGT 59.229 45.455 0.00 0.00 39.21 3.16
517 531 3.199508 AGCATGGATGAGACTAGCAAGTT 59.800 43.478 0.00 0.00 35.56 2.66
518 532 3.944015 GCATGGATGAGACTAGCAAGTTT 59.056 43.478 0.00 0.00 35.56 2.66
519 533 4.397417 GCATGGATGAGACTAGCAAGTTTT 59.603 41.667 0.00 0.00 35.56 2.43
520 534 5.586243 GCATGGATGAGACTAGCAAGTTTTA 59.414 40.000 0.00 0.00 35.56 1.52
521 535 6.238320 GCATGGATGAGACTAGCAAGTTTTAG 60.238 42.308 0.00 0.00 35.56 1.85
522 536 6.360370 TGGATGAGACTAGCAAGTTTTAGT 57.640 37.500 0.00 0.00 35.56 2.24
523 537 6.398918 TGGATGAGACTAGCAAGTTTTAGTC 58.601 40.000 13.08 13.08 43.83 2.59
524 538 5.813157 GGATGAGACTAGCAAGTTTTAGTCC 59.187 44.000 15.72 10.59 44.32 3.85
525 539 5.148651 TGAGACTAGCAAGTTTTAGTCCC 57.851 43.478 15.72 8.76 44.32 4.46
526 540 4.591498 TGAGACTAGCAAGTTTTAGTCCCA 59.409 41.667 15.72 10.61 44.32 4.37
527 541 4.895961 AGACTAGCAAGTTTTAGTCCCAC 58.104 43.478 15.72 0.00 44.32 4.61
528 542 4.593634 AGACTAGCAAGTTTTAGTCCCACT 59.406 41.667 15.72 1.62 44.32 4.00
529 543 5.778750 AGACTAGCAAGTTTTAGTCCCACTA 59.221 40.000 15.72 0.00 44.32 2.74
530 544 6.440965 AGACTAGCAAGTTTTAGTCCCACTAT 59.559 38.462 15.72 0.85 44.32 2.12
531 545 7.017319 ACTAGCAAGTTTTAGTCCCACTATT 57.983 36.000 0.00 0.00 27.66 1.73
532 546 7.459234 ACTAGCAAGTTTTAGTCCCACTATTT 58.541 34.615 0.00 0.00 27.66 1.40
533 547 7.942894 ACTAGCAAGTTTTAGTCCCACTATTTT 59.057 33.333 0.00 0.00 27.66 1.82
534 548 7.597288 AGCAAGTTTTAGTCCCACTATTTTT 57.403 32.000 0.00 0.00 29.64 1.94
535 549 8.700439 AGCAAGTTTTAGTCCCACTATTTTTA 57.300 30.769 0.00 0.00 29.64 1.52
536 550 8.793592 AGCAAGTTTTAGTCCCACTATTTTTAG 58.206 33.333 0.00 0.00 29.64 1.85
537 551 8.573885 GCAAGTTTTAGTCCCACTATTTTTAGT 58.426 33.333 0.00 0.00 29.64 2.24
539 553 9.856162 AAGTTTTAGTCCCACTATTTTTAGTCA 57.144 29.630 0.00 0.00 29.64 3.41
542 556 8.801882 TTTAGTCCCACTATTTTTAGTCATGG 57.198 34.615 0.00 0.00 29.64 3.66
543 557 5.755849 AGTCCCACTATTTTTAGTCATGGG 58.244 41.667 0.00 0.00 34.08 4.00
544 558 5.491078 AGTCCCACTATTTTTAGTCATGGGA 59.509 40.000 4.97 4.97 37.44 4.37
545 559 5.589050 GTCCCACTATTTTTAGTCATGGGAC 59.411 44.000 20.52 20.52 45.42 4.46
558 572 4.761975 GTCATGGGACTAAAACGTATCCA 58.238 43.478 0.00 0.00 40.99 3.41
559 573 5.180271 GTCATGGGACTAAAACGTATCCAA 58.820 41.667 0.00 0.00 40.99 3.53
560 574 5.293569 GTCATGGGACTAAAACGTATCCAAG 59.706 44.000 0.00 0.00 40.99 3.61
561 575 3.602483 TGGGACTAAAACGTATCCAAGC 58.398 45.455 0.00 0.00 32.45 4.01
562 576 3.008157 TGGGACTAAAACGTATCCAAGCA 59.992 43.478 0.00 0.00 32.45 3.91
563 577 4.196971 GGGACTAAAACGTATCCAAGCAT 58.803 43.478 0.00 0.00 32.45 3.79
564 578 4.035208 GGGACTAAAACGTATCCAAGCATG 59.965 45.833 0.00 0.00 32.45 4.06
565 579 4.495844 GGACTAAAACGTATCCAAGCATGC 60.496 45.833 10.51 10.51 0.00 4.06
566 580 4.261801 ACTAAAACGTATCCAAGCATGCT 58.738 39.130 16.30 16.30 0.00 3.79
567 581 3.764885 AAAACGTATCCAAGCATGCTC 57.235 42.857 22.93 6.18 0.00 4.26
704 719 0.102120 CTCCTCCTCGTCACATGAGC 59.898 60.000 0.00 0.00 29.93 4.26
1445 1497 2.063266 CGTGCTGTTCTTTAAGCGGTA 58.937 47.619 0.00 0.00 42.54 4.02
1539 1591 1.175983 TGGGACATTTGTTGCCGTCC 61.176 55.000 0.00 0.00 45.95 4.79
1560 1612 7.980099 CCGTCCTTGTTGTAAAGTATAAGAGAT 59.020 37.037 0.00 0.00 0.00 2.75
1611 1663 8.715191 TTTGTTATTCTTTGAAGTTTGCATGT 57.285 26.923 0.00 0.00 0.00 3.21
1627 1679 2.928334 CATGTCCCTCTTCCCTTCATG 58.072 52.381 0.00 0.00 0.00 3.07
1665 1717 5.308014 TGATGAACTTGAGCTGCTTTCTTA 58.692 37.500 2.53 0.00 0.00 2.10
1702 1754 8.693542 AGAATGCTTTGCTATTGTTAAATGAC 57.306 30.769 0.00 0.00 0.00 3.06
1708 1760 7.517614 TTTGCTATTGTTAAATGACTGGTGA 57.482 32.000 0.00 0.00 0.00 4.02
1719 1771 1.697432 TGACTGGTGACGGGAGAAAAT 59.303 47.619 0.00 0.00 42.76 1.82
1767 1822 2.025155 GCGTTCAGGTGGATCTAGAGA 58.975 52.381 0.00 0.00 0.00 3.10
1816 1873 6.644592 GTCTAGATGAAGTGCTATCACCAATC 59.355 42.308 0.00 0.00 44.16 2.67
1833 1890 3.819337 CCAATCTGTAGATCTTGGCATGG 59.181 47.826 0.00 0.00 30.31 3.66
1834 1891 4.445305 CCAATCTGTAGATCTTGGCATGGA 60.445 45.833 0.00 0.00 30.31 3.41
1841 1898 1.492176 GATCTTGGCATGGAGGAGGAA 59.508 52.381 0.00 0.00 0.00 3.36
1842 1899 0.620556 TCTTGGCATGGAGGAGGAAC 59.379 55.000 0.00 0.00 0.00 3.62
1844 1901 1.002069 TTGGCATGGAGGAGGAACAT 58.998 50.000 0.00 0.00 0.00 2.71
1845 1902 0.548031 TGGCATGGAGGAGGAACATC 59.452 55.000 0.00 0.00 0.00 3.06
1900 1966 1.215679 TATTTTTGGGCCGGGGAGGA 61.216 55.000 2.18 0.00 45.00 3.71
2098 2168 3.866910 GTGCATCATTTCATTTCGCCAAT 59.133 39.130 0.00 0.00 0.00 3.16
2121 2191 1.414550 CGGGGAGAAGGGAGAAGATTC 59.585 57.143 0.00 0.00 0.00 2.52
2129 2199 7.342581 GGAGAAGGGAGAAGATTCAGTAATTT 58.657 38.462 0.00 0.00 0.00 1.82
2155 2226 1.354506 GGTCATGAGCTGCGCAATC 59.645 57.895 17.59 13.55 0.00 2.67
2260 2338 5.008331 TGTGAAATGACTCGAGGTAGTAGT 58.992 41.667 18.41 0.00 0.00 2.73
2261 2339 6.175471 TGTGAAATGACTCGAGGTAGTAGTA 58.825 40.000 18.41 0.00 0.00 1.82
2262 2340 6.315642 TGTGAAATGACTCGAGGTAGTAGTAG 59.684 42.308 18.41 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 9.301153 GATGGATGTTTGTGTTATGGTAAAATC 57.699 33.333 0.00 0.00 0.00 2.17
31 32 6.127026 GGTAGACAGTGTATTGGAAAGGAGAT 60.127 42.308 0.00 0.00 0.00 2.75
76 84 6.126332 TGGTGCCCTTTTATGATATTACTCCA 60.126 38.462 0.00 0.00 0.00 3.86
77 85 6.303839 TGGTGCCCTTTTATGATATTACTCC 58.696 40.000 0.00 0.00 0.00 3.85
78 86 7.665559 TGATGGTGCCCTTTTATGATATTACTC 59.334 37.037 0.00 0.00 0.00 2.59
79 87 7.526041 TGATGGTGCCCTTTTATGATATTACT 58.474 34.615 0.00 0.00 0.00 2.24
80 88 7.759489 TGATGGTGCCCTTTTATGATATTAC 57.241 36.000 0.00 0.00 0.00 1.89
118 131 4.320935 CCGTTGGCTTGCTAAATTTGTACT 60.321 41.667 0.00 0.00 0.00 2.73
119 132 3.917985 CCGTTGGCTTGCTAAATTTGTAC 59.082 43.478 0.00 0.00 0.00 2.90
140 153 0.890996 CTGGAGTTTGGCCACTGTCC 60.891 60.000 3.88 12.48 0.00 4.02
159 172 1.539157 CTTTTCAGGTGGCCTTCCTC 58.461 55.000 15.40 0.00 32.37 3.71
188 202 0.179045 GAACATGGAGGATCGTGGGG 60.179 60.000 0.00 0.00 34.37 4.96
239 253 1.561542 CCTTGTATCCAAGCACCCTCT 59.438 52.381 0.00 0.00 45.57 3.69
240 254 1.408822 CCCTTGTATCCAAGCACCCTC 60.409 57.143 0.00 0.00 45.57 4.30
241 255 0.625849 CCCTTGTATCCAAGCACCCT 59.374 55.000 0.00 0.00 45.57 4.34
242 256 0.623723 TCCCTTGTATCCAAGCACCC 59.376 55.000 0.00 0.00 45.57 4.61
243 257 1.282157 AGTCCCTTGTATCCAAGCACC 59.718 52.381 0.00 0.00 45.57 5.01
244 258 2.789409 AGTCCCTTGTATCCAAGCAC 57.211 50.000 0.00 0.00 45.57 4.40
245 259 5.450818 AAATAGTCCCTTGTATCCAAGCA 57.549 39.130 0.00 0.00 45.57 3.91
246 260 6.775594 AAAAATAGTCCCTTGTATCCAAGC 57.224 37.500 0.00 0.00 45.57 4.01
247 261 9.462606 AACTAAAAATAGTCCCTTGTATCCAAG 57.537 33.333 0.00 0.00 46.33 3.61
248 262 9.816787 AAACTAAAAATAGTCCCTTGTATCCAA 57.183 29.630 0.00 0.00 0.00 3.53
281 295 9.574516 TTGAAACTTTAGCCTCTAAAAGAGATT 57.425 29.630 5.50 0.00 45.07 2.40
282 296 9.225436 CTTGAAACTTTAGCCTCTAAAAGAGAT 57.775 33.333 5.50 0.00 45.07 2.75
283 297 7.173390 GCTTGAAACTTTAGCCTCTAAAAGAGA 59.827 37.037 5.50 0.00 45.07 3.10
284 298 7.041098 TGCTTGAAACTTTAGCCTCTAAAAGAG 60.041 37.037 2.08 0.00 41.96 2.85
285 299 6.770785 TGCTTGAAACTTTAGCCTCTAAAAGA 59.229 34.615 2.08 0.00 36.43 2.52
286 300 6.858478 GTGCTTGAAACTTTAGCCTCTAAAAG 59.142 38.462 0.00 0.00 38.41 2.27
287 301 6.238925 GGTGCTTGAAACTTTAGCCTCTAAAA 60.239 38.462 0.00 0.00 34.03 1.52
288 302 5.240844 GGTGCTTGAAACTTTAGCCTCTAAA 59.759 40.000 0.00 0.00 34.03 1.85
289 303 4.760204 GGTGCTTGAAACTTTAGCCTCTAA 59.240 41.667 0.00 0.00 34.03 2.10
290 304 4.324267 GGTGCTTGAAACTTTAGCCTCTA 58.676 43.478 0.00 0.00 34.03 2.43
291 305 3.149981 GGTGCTTGAAACTTTAGCCTCT 58.850 45.455 0.00 0.00 34.03 3.69
292 306 2.229062 GGGTGCTTGAAACTTTAGCCTC 59.771 50.000 0.00 0.00 34.03 4.70
293 307 2.239400 GGGTGCTTGAAACTTTAGCCT 58.761 47.619 0.00 0.00 34.03 4.58
294 308 1.272490 GGGGTGCTTGAAACTTTAGCC 59.728 52.381 0.00 0.00 34.03 3.93
295 309 2.029918 CAGGGGTGCTTGAAACTTTAGC 60.030 50.000 0.00 0.00 35.50 3.09
296 310 3.253432 GTCAGGGGTGCTTGAAACTTTAG 59.747 47.826 0.00 0.00 0.00 1.85
297 311 3.117663 AGTCAGGGGTGCTTGAAACTTTA 60.118 43.478 0.00 0.00 0.00 1.85
298 312 2.031870 GTCAGGGGTGCTTGAAACTTT 58.968 47.619 0.00 0.00 0.00 2.66
299 313 1.215423 AGTCAGGGGTGCTTGAAACTT 59.785 47.619 0.00 0.00 0.00 2.66
300 314 0.846693 AGTCAGGGGTGCTTGAAACT 59.153 50.000 0.00 0.00 0.00 2.66
301 315 2.561478 TAGTCAGGGGTGCTTGAAAC 57.439 50.000 0.00 0.00 0.00 2.78
302 316 3.137544 TCTTTAGTCAGGGGTGCTTGAAA 59.862 43.478 0.00 0.00 0.00 2.69
303 317 2.708861 TCTTTAGTCAGGGGTGCTTGAA 59.291 45.455 0.00 0.00 0.00 2.69
304 318 2.303022 CTCTTTAGTCAGGGGTGCTTGA 59.697 50.000 0.00 0.00 0.00 3.02
305 319 2.303022 TCTCTTTAGTCAGGGGTGCTTG 59.697 50.000 0.00 0.00 0.00 4.01
306 320 2.569404 CTCTCTTTAGTCAGGGGTGCTT 59.431 50.000 0.00 0.00 0.00 3.91
307 321 2.183679 CTCTCTTTAGTCAGGGGTGCT 58.816 52.381 0.00 0.00 0.00 4.40
308 322 1.208293 CCTCTCTTTAGTCAGGGGTGC 59.792 57.143 0.00 0.00 0.00 5.01
309 323 1.208293 GCCTCTCTTTAGTCAGGGGTG 59.792 57.143 0.00 0.00 0.00 4.61
310 324 1.079658 AGCCTCTCTTTAGTCAGGGGT 59.920 52.381 0.00 0.00 0.00 4.95
311 325 1.872773 AGCCTCTCTTTAGTCAGGGG 58.127 55.000 0.00 0.00 0.00 4.79
312 326 2.962421 CCTAGCCTCTCTTTAGTCAGGG 59.038 54.545 0.00 0.00 0.00 4.45
313 327 3.904717 TCCTAGCCTCTCTTTAGTCAGG 58.095 50.000 0.00 0.00 0.00 3.86
314 328 6.775629 ACTAATCCTAGCCTCTCTTTAGTCAG 59.224 42.308 0.00 0.00 0.00 3.51
315 329 6.674573 ACTAATCCTAGCCTCTCTTTAGTCA 58.325 40.000 0.00 0.00 0.00 3.41
316 330 7.002276 AGACTAATCCTAGCCTCTCTTTAGTC 58.998 42.308 10.44 10.44 41.85 2.59
317 331 6.918033 AGACTAATCCTAGCCTCTCTTTAGT 58.082 40.000 0.00 0.00 32.67 2.24
318 332 7.833285 AAGACTAATCCTAGCCTCTCTTTAG 57.167 40.000 0.00 0.00 0.00 1.85
319 333 9.357161 CTTAAGACTAATCCTAGCCTCTCTTTA 57.643 37.037 0.00 0.00 0.00 1.85
320 334 7.289084 CCTTAAGACTAATCCTAGCCTCTCTTT 59.711 40.741 3.36 0.00 0.00 2.52
321 335 6.780522 CCTTAAGACTAATCCTAGCCTCTCTT 59.219 42.308 3.36 0.00 0.00 2.85
322 336 6.311735 CCTTAAGACTAATCCTAGCCTCTCT 58.688 44.000 3.36 0.00 0.00 3.10
323 337 5.047590 GCCTTAAGACTAATCCTAGCCTCTC 60.048 48.000 3.36 0.00 0.00 3.20
324 338 4.836175 GCCTTAAGACTAATCCTAGCCTCT 59.164 45.833 3.36 0.00 0.00 3.69
325 339 4.836175 AGCCTTAAGACTAATCCTAGCCTC 59.164 45.833 3.36 0.00 0.00 4.70
326 340 4.821940 AGCCTTAAGACTAATCCTAGCCT 58.178 43.478 3.36 0.00 0.00 4.58
327 341 6.667558 TTAGCCTTAAGACTAATCCTAGCC 57.332 41.667 7.12 0.00 0.00 3.93
328 342 9.210329 GATTTTAGCCTTAAGACTAATCCTAGC 57.790 37.037 11.47 0.00 0.00 3.42
348 362 8.950007 AGGTTTCCCATGACTAAAAGATTTTA 57.050 30.769 0.00 0.00 0.00 1.52
349 363 7.855784 AGGTTTCCCATGACTAAAAGATTTT 57.144 32.000 0.00 0.00 0.00 1.82
350 364 8.170730 AGTAGGTTTCCCATGACTAAAAGATTT 58.829 33.333 0.00 0.00 0.00 2.17
351 365 7.699878 AGTAGGTTTCCCATGACTAAAAGATT 58.300 34.615 0.00 0.00 0.00 2.40
352 366 7.272144 AGTAGGTTTCCCATGACTAAAAGAT 57.728 36.000 0.00 0.00 0.00 2.40
353 367 6.697641 AGTAGGTTTCCCATGACTAAAAGA 57.302 37.500 0.00 0.00 0.00 2.52
354 368 8.857694 TTTAGTAGGTTTCCCATGACTAAAAG 57.142 34.615 8.74 0.00 38.44 2.27
355 369 9.816787 ATTTTAGTAGGTTTCCCATGACTAAAA 57.183 29.630 19.00 19.00 45.07 1.52
359 373 8.557450 ACATATTTTAGTAGGTTTCCCATGACT 58.443 33.333 0.00 0.00 0.00 3.41
360 374 8.747538 ACATATTTTAGTAGGTTTCCCATGAC 57.252 34.615 0.00 0.00 0.00 3.06
377 391 9.373450 TGAGGAGAGAGAGCTAATACATATTTT 57.627 33.333 0.00 0.00 0.00 1.82
378 392 8.948401 TGAGGAGAGAGAGCTAATACATATTT 57.052 34.615 0.00 0.00 0.00 1.40
379 393 9.545928 AATGAGGAGAGAGAGCTAATACATATT 57.454 33.333 0.00 0.00 0.00 1.28
380 394 9.545928 AAATGAGGAGAGAGAGCTAATACATAT 57.454 33.333 0.00 0.00 0.00 1.78
381 395 8.948401 AAATGAGGAGAGAGAGCTAATACATA 57.052 34.615 0.00 0.00 0.00 2.29
382 396 7.854166 AAATGAGGAGAGAGAGCTAATACAT 57.146 36.000 0.00 0.00 0.00 2.29
383 397 8.768501 TTAAATGAGGAGAGAGAGCTAATACA 57.231 34.615 0.00 0.00 0.00 2.29
386 400 8.374743 GGAATTAAATGAGGAGAGAGAGCTAAT 58.625 37.037 0.00 0.00 0.00 1.73
387 401 7.566879 AGGAATTAAATGAGGAGAGAGAGCTAA 59.433 37.037 0.00 0.00 0.00 3.09
388 402 7.072562 AGGAATTAAATGAGGAGAGAGAGCTA 58.927 38.462 0.00 0.00 0.00 3.32
389 403 5.904750 AGGAATTAAATGAGGAGAGAGAGCT 59.095 40.000 0.00 0.00 0.00 4.09
390 404 6.041979 AGAGGAATTAAATGAGGAGAGAGAGC 59.958 42.308 0.00 0.00 0.00 4.09
391 405 7.255942 GGAGAGGAATTAAATGAGGAGAGAGAG 60.256 44.444 0.00 0.00 0.00 3.20
392 406 6.553100 GGAGAGGAATTAAATGAGGAGAGAGA 59.447 42.308 0.00 0.00 0.00 3.10
393 407 6.554605 AGGAGAGGAATTAAATGAGGAGAGAG 59.445 42.308 0.00 0.00 0.00 3.20
394 408 6.448202 AGGAGAGGAATTAAATGAGGAGAGA 58.552 40.000 0.00 0.00 0.00 3.10
395 409 6.745794 AGGAGAGGAATTAAATGAGGAGAG 57.254 41.667 0.00 0.00 0.00 3.20
396 410 7.846823 ACTAAGGAGAGGAATTAAATGAGGAGA 59.153 37.037 0.00 0.00 0.00 3.71
397 411 8.028652 ACTAAGGAGAGGAATTAAATGAGGAG 57.971 38.462 0.00 0.00 0.00 3.69
398 412 7.996758 ACTAAGGAGAGGAATTAAATGAGGA 57.003 36.000 0.00 0.00 0.00 3.71
399 413 8.490311 AGAACTAAGGAGAGGAATTAAATGAGG 58.510 37.037 0.00 0.00 0.00 3.86
400 414 9.323985 CAGAACTAAGGAGAGGAATTAAATGAG 57.676 37.037 0.00 0.00 0.00 2.90
401 415 8.267894 CCAGAACTAAGGAGAGGAATTAAATGA 58.732 37.037 0.00 0.00 0.00 2.57
402 416 8.267894 TCCAGAACTAAGGAGAGGAATTAAATG 58.732 37.037 0.00 0.00 0.00 2.32
403 417 8.393959 TCCAGAACTAAGGAGAGGAATTAAAT 57.606 34.615 0.00 0.00 0.00 1.40
404 418 7.808279 TCCAGAACTAAGGAGAGGAATTAAA 57.192 36.000 0.00 0.00 0.00 1.52
405 419 7.996758 ATCCAGAACTAAGGAGAGGAATTAA 57.003 36.000 0.00 0.00 37.34 1.40
406 420 7.147479 CCAATCCAGAACTAAGGAGAGGAATTA 60.147 40.741 0.00 0.00 37.34 1.40
407 421 6.353429 CCAATCCAGAACTAAGGAGAGGAATT 60.353 42.308 0.00 0.00 37.34 2.17
408 422 5.131809 CCAATCCAGAACTAAGGAGAGGAAT 59.868 44.000 0.00 0.00 37.34 3.01
409 423 4.471386 CCAATCCAGAACTAAGGAGAGGAA 59.529 45.833 0.00 0.00 37.34 3.36
410 424 4.033709 CCAATCCAGAACTAAGGAGAGGA 58.966 47.826 0.00 0.00 37.34 3.71
411 425 4.033709 TCCAATCCAGAACTAAGGAGAGG 58.966 47.826 0.00 0.00 37.34 3.69
412 426 4.100808 CCTCCAATCCAGAACTAAGGAGAG 59.899 50.000 7.12 0.00 42.87 3.20
413 427 4.033709 CCTCCAATCCAGAACTAAGGAGA 58.966 47.826 7.12 0.00 42.87 3.71
414 428 3.135530 CCCTCCAATCCAGAACTAAGGAG 59.864 52.174 0.00 0.00 40.58 3.69
415 429 3.115390 CCCTCCAATCCAGAACTAAGGA 58.885 50.000 0.00 0.00 38.50 3.36
416 430 2.846827 ACCCTCCAATCCAGAACTAAGG 59.153 50.000 0.00 0.00 0.00 2.69
417 431 4.576330 AACCCTCCAATCCAGAACTAAG 57.424 45.455 0.00 0.00 0.00 2.18
418 432 4.508405 CCAAACCCTCCAATCCAGAACTAA 60.508 45.833 0.00 0.00 0.00 2.24
419 433 3.010138 CCAAACCCTCCAATCCAGAACTA 59.990 47.826 0.00 0.00 0.00 2.24
420 434 2.225117 CCAAACCCTCCAATCCAGAACT 60.225 50.000 0.00 0.00 0.00 3.01
421 435 2.171003 CCAAACCCTCCAATCCAGAAC 58.829 52.381 0.00 0.00 0.00 3.01
422 436 2.041620 CTCCAAACCCTCCAATCCAGAA 59.958 50.000 0.00 0.00 0.00 3.02
423 437 1.635487 CTCCAAACCCTCCAATCCAGA 59.365 52.381 0.00 0.00 0.00 3.86
424 438 1.341383 CCTCCAAACCCTCCAATCCAG 60.341 57.143 0.00 0.00 0.00 3.86
425 439 0.704076 CCTCCAAACCCTCCAATCCA 59.296 55.000 0.00 0.00 0.00 3.41
426 440 0.999712 TCCTCCAAACCCTCCAATCC 59.000 55.000 0.00 0.00 0.00 3.01
427 441 4.519906 TTATCCTCCAAACCCTCCAATC 57.480 45.455 0.00 0.00 0.00 2.67
428 442 6.606241 TTATTATCCTCCAAACCCTCCAAT 57.394 37.500 0.00 0.00 0.00 3.16
429 443 6.410222 TTTATTATCCTCCAAACCCTCCAA 57.590 37.500 0.00 0.00 0.00 3.53
430 444 6.372931 CATTTATTATCCTCCAAACCCTCCA 58.627 40.000 0.00 0.00 0.00 3.86
431 445 5.243954 GCATTTATTATCCTCCAAACCCTCC 59.756 44.000 0.00 0.00 0.00 4.30
432 446 6.071320 AGCATTTATTATCCTCCAAACCCTC 58.929 40.000 0.00 0.00 0.00 4.30
433 447 6.030727 AGCATTTATTATCCTCCAAACCCT 57.969 37.500 0.00 0.00 0.00 4.34
434 448 5.833131 TGAGCATTTATTATCCTCCAAACCC 59.167 40.000 0.00 0.00 0.00 4.11
435 449 6.959639 TGAGCATTTATTATCCTCCAAACC 57.040 37.500 0.00 0.00 0.00 3.27
438 452 9.866655 AGTTATTGAGCATTTATTATCCTCCAA 57.133 29.630 0.00 0.00 0.00 3.53
471 485 9.174166 GCTTGGATCCAAATACTAAAGAAACTA 57.826 33.333 26.87 0.00 35.33 2.24
472 486 7.669722 TGCTTGGATCCAAATACTAAAGAAACT 59.330 33.333 26.87 0.00 35.33 2.66
473 487 7.826690 TGCTTGGATCCAAATACTAAAGAAAC 58.173 34.615 26.87 2.44 35.33 2.78
474 488 8.469200 CATGCTTGGATCCAAATACTAAAGAAA 58.531 33.333 26.87 6.40 35.33 2.52
475 489 7.068593 CCATGCTTGGATCCAAATACTAAAGAA 59.931 37.037 26.87 8.73 46.92 2.52
476 490 6.547141 CCATGCTTGGATCCAAATACTAAAGA 59.453 38.462 26.87 1.90 46.92 2.52
477 491 6.742109 CCATGCTTGGATCCAAATACTAAAG 58.258 40.000 26.87 14.21 46.92 1.85
478 492 6.713762 CCATGCTTGGATCCAAATACTAAA 57.286 37.500 26.87 8.81 46.92 1.85
492 506 2.158856 TGCTAGTCTCATCCATGCTTGG 60.159 50.000 12.41 12.41 45.15 3.61
493 507 3.189618 TGCTAGTCTCATCCATGCTTG 57.810 47.619 0.00 0.00 0.00 4.01
494 508 3.199508 ACTTGCTAGTCTCATCCATGCTT 59.800 43.478 0.00 0.00 0.00 3.91
495 509 2.770802 ACTTGCTAGTCTCATCCATGCT 59.229 45.455 0.00 0.00 0.00 3.79
496 510 3.191078 ACTTGCTAGTCTCATCCATGC 57.809 47.619 0.00 0.00 0.00 4.06
497 511 6.820656 ACTAAAACTTGCTAGTCTCATCCATG 59.179 38.462 0.07 0.00 31.99 3.66
498 512 6.951971 ACTAAAACTTGCTAGTCTCATCCAT 58.048 36.000 0.07 0.00 31.99 3.41
499 513 6.360370 ACTAAAACTTGCTAGTCTCATCCA 57.640 37.500 0.07 0.00 31.99 3.41
500 514 5.813157 GGACTAAAACTTGCTAGTCTCATCC 59.187 44.000 0.07 2.53 42.42 3.51
501 515 5.813157 GGGACTAAAACTTGCTAGTCTCATC 59.187 44.000 0.07 0.00 42.76 2.92
502 516 5.248477 TGGGACTAAAACTTGCTAGTCTCAT 59.752 40.000 7.55 0.00 46.12 2.90
503 517 5.148651 GGGACTAAAACTTGCTAGTCTCA 57.851 43.478 0.07 0.00 42.76 3.27
504 518 4.930405 GTGGGACTAAAACTTGCTAGTCTC 59.070 45.833 0.07 1.39 43.29 3.36
505 519 4.593634 AGTGGGACTAAAACTTGCTAGTCT 59.406 41.667 0.07 0.00 42.42 3.24
506 520 4.895961 AGTGGGACTAAAACTTGCTAGTC 58.104 43.478 0.07 0.62 42.17 2.59
507 521 4.976540 AGTGGGACTAAAACTTGCTAGT 57.023 40.909 0.00 0.00 35.68 2.57
508 522 7.923414 AAATAGTGGGACTAAAACTTGCTAG 57.077 36.000 0.00 0.00 33.89 3.42
509 523 8.700439 AAAAATAGTGGGACTAAAACTTGCTA 57.300 30.769 0.00 0.00 33.89 3.49
510 524 7.597288 AAAAATAGTGGGACTAAAACTTGCT 57.403 32.000 0.00 0.00 33.89 3.91
511 525 8.573885 ACTAAAAATAGTGGGACTAAAACTTGC 58.426 33.333 0.00 0.00 33.89 4.01
513 527 9.856162 TGACTAAAAATAGTGGGACTAAAACTT 57.144 29.630 0.00 0.00 33.89 2.66
516 530 9.238368 CCATGACTAAAAATAGTGGGACTAAAA 57.762 33.333 0.00 0.00 33.89 1.52
517 531 7.832187 CCCATGACTAAAAATAGTGGGACTAAA 59.168 37.037 1.30 0.00 34.46 1.85
518 532 7.183112 TCCCATGACTAAAAATAGTGGGACTAA 59.817 37.037 6.15 0.00 35.88 2.24
519 533 6.674861 TCCCATGACTAAAAATAGTGGGACTA 59.325 38.462 6.15 0.00 35.88 2.59
520 534 5.491078 TCCCATGACTAAAAATAGTGGGACT 59.509 40.000 6.15 0.00 35.88 3.85
521 535 5.589050 GTCCCATGACTAAAAATAGTGGGAC 59.411 44.000 20.89 20.89 45.42 4.46
522 536 5.751586 GTCCCATGACTAAAAATAGTGGGA 58.248 41.667 6.15 6.15 37.44 4.37
534 548 5.657745 TGGATACGTTTTAGTCCCATGACTA 59.342 40.000 0.00 0.00 45.97 2.59
536 550 4.761975 TGGATACGTTTTAGTCCCATGAC 58.238 43.478 0.00 0.00 40.25 3.06
537 551 5.423704 TTGGATACGTTTTAGTCCCATGA 57.576 39.130 0.00 0.00 42.51 3.07
538 552 4.035208 GCTTGGATACGTTTTAGTCCCATG 59.965 45.833 0.00 0.00 42.51 3.66
539 553 4.196971 GCTTGGATACGTTTTAGTCCCAT 58.803 43.478 0.00 0.00 42.51 4.00
540 554 3.008157 TGCTTGGATACGTTTTAGTCCCA 59.992 43.478 0.00 0.00 42.51 4.37
541 555 3.602483 TGCTTGGATACGTTTTAGTCCC 58.398 45.455 0.00 0.00 42.51 4.46
542 556 4.495844 GCATGCTTGGATACGTTTTAGTCC 60.496 45.833 11.37 0.00 42.51 3.85
543 557 4.332819 AGCATGCTTGGATACGTTTTAGTC 59.667 41.667 16.30 0.00 42.51 2.59
544 558 4.261801 AGCATGCTTGGATACGTTTTAGT 58.738 39.130 16.30 0.00 42.51 2.24
545 559 4.572389 AGAGCATGCTTGGATACGTTTTAG 59.428 41.667 23.61 0.00 42.51 1.85
546 560 4.513442 AGAGCATGCTTGGATACGTTTTA 58.487 39.130 23.61 0.00 42.51 1.52
547 561 3.347216 AGAGCATGCTTGGATACGTTTT 58.653 40.909 23.61 0.00 42.51 2.43
548 562 2.991250 AGAGCATGCTTGGATACGTTT 58.009 42.857 23.61 0.00 42.51 3.60
549 563 2.698855 AGAGCATGCTTGGATACGTT 57.301 45.000 23.61 0.00 42.51 3.99
550 564 2.698855 AAGAGCATGCTTGGATACGT 57.301 45.000 23.61 2.80 42.51 3.57
551 565 4.751600 TGATTAAGAGCATGCTTGGATACG 59.248 41.667 23.61 0.00 42.51 3.06
552 566 5.180868 CCTGATTAAGAGCATGCTTGGATAC 59.819 44.000 23.61 7.76 0.00 2.24
553 567 5.311265 CCTGATTAAGAGCATGCTTGGATA 58.689 41.667 23.61 9.86 0.00 2.59
554 568 4.142790 CCTGATTAAGAGCATGCTTGGAT 58.857 43.478 23.61 13.45 0.00 3.41
555 569 3.548770 CCTGATTAAGAGCATGCTTGGA 58.451 45.455 23.61 8.99 0.00 3.53
556 570 2.034305 GCCTGATTAAGAGCATGCTTGG 59.966 50.000 23.61 13.93 31.33 3.61
557 571 2.686405 TGCCTGATTAAGAGCATGCTTG 59.314 45.455 23.61 5.01 34.49 4.01
558 572 2.950309 CTGCCTGATTAAGAGCATGCTT 59.050 45.455 23.61 9.66 34.49 3.91
559 573 2.573369 CTGCCTGATTAAGAGCATGCT 58.427 47.619 22.92 22.92 34.49 3.79
560 574 1.001597 GCTGCCTGATTAAGAGCATGC 60.002 52.381 10.51 10.51 34.07 4.06
561 575 2.294979 TGCTGCCTGATTAAGAGCATG 58.705 47.619 0.00 0.00 32.35 4.06
562 576 2.723322 TGCTGCCTGATTAAGAGCAT 57.277 45.000 0.00 0.00 32.35 3.79
563 577 2.362736 CTTGCTGCCTGATTAAGAGCA 58.637 47.619 0.00 0.00 34.76 4.26
564 578 1.065251 GCTTGCTGCCTGATTAAGAGC 59.935 52.381 0.00 0.00 35.15 4.09
565 579 2.355132 CAGCTTGCTGCCTGATTAAGAG 59.645 50.000 9.78 0.00 44.23 2.85
566 580 2.290514 ACAGCTTGCTGCCTGATTAAGA 60.291 45.455 20.92 0.00 44.23 2.10
567 581 2.089980 ACAGCTTGCTGCCTGATTAAG 58.910 47.619 20.92 1.68 44.23 1.85
828 848 3.440522 GTGGGACTGGTGAAATAGAAAGC 59.559 47.826 0.00 0.00 0.00 3.51
1006 1054 2.885861 CACGAGGCTCCTAACGCT 59.114 61.111 9.32 0.00 0.00 5.07
1481 1533 3.064682 GCGGCAACAACCAAAGAAATTTT 59.935 39.130 0.00 0.00 0.00 1.82
1611 1663 2.921221 AGAACATGAAGGGAAGAGGGA 58.079 47.619 0.00 0.00 0.00 4.20
1627 1679 7.604164 TCAAGTTCATCATCTTACTCCAAGAAC 59.396 37.037 0.00 0.00 46.29 3.01
1665 1717 6.120905 AGCAAAGCATTCTCTTGATACAGAT 58.879 36.000 0.00 0.00 0.00 2.90
1702 1754 5.897377 ATTTAATTTTCTCCCGTCACCAG 57.103 39.130 0.00 0.00 0.00 4.00
1708 1760 8.253113 TCGTAGTAGAATTTAATTTTCTCCCGT 58.747 33.333 4.86 0.00 35.19 5.28
1719 1771 9.431887 ACAATGAAAGCTCGTAGTAGAATTTAA 57.568 29.630 0.00 0.00 0.00 1.52
1741 1796 0.038166 ATCCACCTGAACGCCACAAT 59.962 50.000 0.00 0.00 0.00 2.71
1767 1822 3.374058 CGAAAATTGCGGATGGTTCTACT 59.626 43.478 0.00 0.00 0.00 2.57
1816 1873 2.702478 TCCTCCATGCCAAGATCTACAG 59.298 50.000 0.00 0.00 0.00 2.74
1833 1890 5.679601 AGAGCAAAATAGATGTTCCTCCTC 58.320 41.667 0.00 0.00 0.00 3.71
1834 1891 5.707066 AGAGCAAAATAGATGTTCCTCCT 57.293 39.130 0.00 0.00 0.00 3.69
1841 1898 6.127786 GCAAGGAGAAAGAGCAAAATAGATGT 60.128 38.462 0.00 0.00 0.00 3.06
1842 1899 6.127814 TGCAAGGAGAAAGAGCAAAATAGATG 60.128 38.462 0.00 0.00 31.42 2.90
1844 1901 5.182001 GTGCAAGGAGAAAGAGCAAAATAGA 59.818 40.000 0.00 0.00 36.91 1.98
1845 1902 5.048504 TGTGCAAGGAGAAAGAGCAAAATAG 60.049 40.000 0.00 0.00 36.91 1.73
1900 1966 2.158519 CCTCAACCAACCAACCTACCTT 60.159 50.000 0.00 0.00 0.00 3.50
2034 2104 8.475639 ACTAACTGAGTTAATTATCACCATCGT 58.524 33.333 6.51 0.00 33.13 3.73
2098 2168 1.360162 TCTTCTCCCTTCTCCCCGTAA 59.640 52.381 0.00 0.00 0.00 3.18
2107 2177 7.757173 GCAAAAATTACTGAATCTTCTCCCTTC 59.243 37.037 0.00 0.00 0.00 3.46
2121 2191 5.771469 TCATGACCACTGCAAAAATTACTG 58.229 37.500 0.00 0.00 0.00 2.74
2129 2199 1.241165 CAGCTCATGACCACTGCAAA 58.759 50.000 6.65 0.00 0.00 3.68
2155 2226 3.119173 AGCTCAGAGAAGAGAATGGTTCG 60.119 47.826 0.00 0.00 37.87 3.95
2260 2338 5.809001 ACCTTTCACTTCAATGATCAGCTA 58.191 37.500 0.09 0.00 0.00 3.32
2261 2339 4.660168 ACCTTTCACTTCAATGATCAGCT 58.340 39.130 0.09 0.00 0.00 4.24
2262 2340 5.382618 AACCTTTCACTTCAATGATCAGC 57.617 39.130 0.09 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.