Multiple sequence alignment - TraesCS1B01G015800

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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 TraesCS1B01G015800 chr1B 100.000 2600 0 0 1 2600 7557607 7555008 0.000000e+00 4802.0
1 TraesCS1B01G015800 chr1B 97.480 1984 38 7 621 2600 17250548 17252523 0.000000e+00 3376.0
2 TraesCS1B01G015800 chr1B 96.371 1984 55 9 621 2600 22278985 22277015 0.000000e+00 3249.0
3 TraesCS1B01G015800 chr1B 93.548 713 42 4 621 1331 22162814 22162104 0.000000e+00 1059.0
4 TraesCS1B01G015800 chr1B 91.384 708 48 7 1352 2052 22162123 22161422 0.000000e+00 957.0
5 TraesCS1B01G015800 chr1B 84.615 572 64 14 2050 2600 6000928 6001496 4.890000e-152 547.0
6 TraesCS1B01G015800 chr1B 94.245 139 8 0 2 140 17250187 17250325 2.030000e-51 213.0
7 TraesCS1B01G015800 chr1B 93.525 139 9 0 2 140 22163175 22163037 9.430000e-50 207.0
8 TraesCS1B01G015800 chr1B 92.806 139 10 0 2 140 22279345 22279207 4.390000e-48 202.0
9 TraesCS1B01G015800 chr1B 81.699 153 26 2 327 478 29909030 29908879 2.720000e-25 126.0
10 TraesCS1B01G015800 chr1B 97.778 45 1 0 430 474 7557113 7557069 7.710000e-11 78.7
11 TraesCS1B01G015800 chr1B 97.778 45 1 0 495 539 7557178 7557134 7.710000e-11 78.7
12 TraesCS1B01G015800 chr1D 86.620 568 46 13 2052 2599 4000694 4000137 3.700000e-168 601.0
13 TraesCS1B01G015800 chr1D 78.947 589 55 35 2050 2600 4989522 4988965 1.150000e-88 337.0
14 TraesCS1B01G015800 chr1D 83.146 178 24 2 2 173 3146407 3146584 9.630000e-35 158.0
15 TraesCS1B01G015800 chr1A 82.584 178 25 2 2 173 4547908 4548085 4.480000e-33 152.0


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 TraesCS1B01G015800 chr1B 7555008 7557607 2599 True 1653.133333 4802 98.518667 1 2600 3 chr1B.!!$R2 2599
1 TraesCS1B01G015800 chr1B 17250187 17252523 2336 False 1794.500000 3376 95.862500 2 2600 2 chr1B.!!$F2 2598
2 TraesCS1B01G015800 chr1B 22277015 22279345 2330 True 1725.500000 3249 94.588500 2 2600 2 chr1B.!!$R4 2598
3 TraesCS1B01G015800 chr1B 22161422 22163175 1753 True 741.000000 1059 92.819000 2 2052 3 chr1B.!!$R3 2050
4 TraesCS1B01G015800 chr1B 6000928 6001496 568 False 547.000000 547 84.615000 2050 2600 1 chr1B.!!$F1 550
5 TraesCS1B01G015800 chr1D 4000137 4000694 557 True 601.000000 601 86.620000 2052 2599 1 chr1D.!!$R1 547
6 TraesCS1B01G015800 chr1D 4988965 4989522 557 True 337.000000 337 78.947000 2050 2600 1 chr1D.!!$R2 550

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
372 412 0.032912 TATCCGGCCACTGGTCTACA 60.033 55.0 2.24 0.0 0.0 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1809 1857 3.073678 TGATTTGTCGCACAACATAGCT 58.926 40.909 0.0 0.0 37.9 3.32 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
34 35 0.239347 GGTGACAAGCATGTGACTGC 59.761 55.000 11.33 0.00 42.51 4.40
42 43 0.450583 GCATGTGACTGCTCATGTGG 59.549 55.000 0.00 0.00 44.06 4.17
107 108 3.005791 AGTGGAAGTTTTGTAATGCCAGC 59.994 43.478 0.00 0.00 0.00 4.85
188 225 8.210946 TCCTCGTGATTATATTGGTTTGAGAAT 58.789 33.333 0.00 0.00 0.00 2.40
189 226 8.499162 CCTCGTGATTATATTGGTTTGAGAATC 58.501 37.037 0.00 0.00 0.00 2.52
214 251 1.067142 TCAGGCTGTGTACGACCATTC 60.067 52.381 15.27 0.00 0.00 2.67
219 256 4.833380 AGGCTGTGTACGACCATTCTATAT 59.167 41.667 0.00 0.00 0.00 0.86
220 257 5.304614 AGGCTGTGTACGACCATTCTATATT 59.695 40.000 0.00 0.00 0.00 1.28
254 291 3.756963 ACACTATACTCGTCTTGCTCACA 59.243 43.478 0.00 0.00 0.00 3.58
255 292 4.099120 CACTATACTCGTCTTGCTCACAC 58.901 47.826 0.00 0.00 0.00 3.82
256 293 2.656560 ATACTCGTCTTGCTCACACC 57.343 50.000 0.00 0.00 0.00 4.16
257 294 1.324383 TACTCGTCTTGCTCACACCA 58.676 50.000 0.00 0.00 0.00 4.17
258 295 0.681733 ACTCGTCTTGCTCACACCAT 59.318 50.000 0.00 0.00 0.00 3.55
259 296 1.070758 ACTCGTCTTGCTCACACCATT 59.929 47.619 0.00 0.00 0.00 3.16
260 297 1.728971 CTCGTCTTGCTCACACCATTC 59.271 52.381 0.00 0.00 0.00 2.67
261 298 1.344438 TCGTCTTGCTCACACCATTCT 59.656 47.619 0.00 0.00 0.00 2.40
262 299 1.728971 CGTCTTGCTCACACCATTCTC 59.271 52.381 0.00 0.00 0.00 2.87
263 300 2.611473 CGTCTTGCTCACACCATTCTCT 60.611 50.000 0.00 0.00 0.00 3.10
264 301 3.406764 GTCTTGCTCACACCATTCTCTT 58.593 45.455 0.00 0.00 0.00 2.85
265 302 3.434984 GTCTTGCTCACACCATTCTCTTC 59.565 47.826 0.00 0.00 0.00 2.87
266 303 3.326006 TCTTGCTCACACCATTCTCTTCT 59.674 43.478 0.00 0.00 0.00 2.85
267 304 3.325293 TGCTCACACCATTCTCTTCTC 57.675 47.619 0.00 0.00 0.00 2.87
268 305 2.027745 TGCTCACACCATTCTCTTCTCC 60.028 50.000 0.00 0.00 0.00 3.71
269 306 2.886081 CTCACACCATTCTCTTCTCCG 58.114 52.381 0.00 0.00 0.00 4.63
270 307 2.232452 CTCACACCATTCTCTTCTCCGT 59.768 50.000 0.00 0.00 0.00 4.69
271 308 2.632996 TCACACCATTCTCTTCTCCGTT 59.367 45.455 0.00 0.00 0.00 4.44
272 309 2.996621 CACACCATTCTCTTCTCCGTTC 59.003 50.000 0.00 0.00 0.00 3.95
273 310 2.900546 ACACCATTCTCTTCTCCGTTCT 59.099 45.455 0.00 0.00 0.00 3.01
274 311 3.056465 ACACCATTCTCTTCTCCGTTCTC 60.056 47.826 0.00 0.00 0.00 2.87
275 312 2.498078 ACCATTCTCTTCTCCGTTCTCC 59.502 50.000 0.00 0.00 0.00 3.71
276 313 2.497675 CCATTCTCTTCTCCGTTCTCCA 59.502 50.000 0.00 0.00 0.00 3.86
277 314 3.516615 CATTCTCTTCTCCGTTCTCCAC 58.483 50.000 0.00 0.00 0.00 4.02
278 315 2.588464 TCTCTTCTCCGTTCTCCACT 57.412 50.000 0.00 0.00 0.00 4.00
279 316 2.877866 TCTCTTCTCCGTTCTCCACTT 58.122 47.619 0.00 0.00 0.00 3.16
286 323 2.820787 CTCCGTTCTCCACTTCACTAGT 59.179 50.000 0.00 0.00 37.68 2.57
295 332 6.177610 TCTCCACTTCACTAGTTTGTGTTTT 58.822 36.000 14.61 0.00 38.90 2.43
297 334 5.355910 TCCACTTCACTAGTTTGTGTTTTCC 59.644 40.000 14.61 0.00 38.90 3.13
308 345 2.427410 GTTTTCCAGTGCTGCGCG 60.427 61.111 0.00 0.00 0.00 6.86
334 374 1.024271 TCTTAGCATTCCAATGGCGC 58.976 50.000 0.00 0.00 36.90 6.53
337 377 2.283143 TAGCATTCCAATGGCGCCCT 62.283 55.000 26.77 12.40 36.90 5.19
338 378 1.827789 GCATTCCAATGGCGCCCTA 60.828 57.895 26.77 6.41 36.90 3.53
339 379 1.799258 GCATTCCAATGGCGCCCTAG 61.799 60.000 26.77 13.27 36.90 3.02
340 380 0.466189 CATTCCAATGGCGCCCTAGT 60.466 55.000 26.77 1.25 32.78 2.57
341 381 0.466189 ATTCCAATGGCGCCCTAGTG 60.466 55.000 26.77 15.99 0.00 2.74
342 382 2.516930 CCAATGGCGCCCTAGTGG 60.517 66.667 26.77 21.52 37.09 4.00
351 391 2.597340 CCCTAGTGGCCACCATGG 59.403 66.667 32.29 27.64 41.55 3.66
360 400 2.281761 CCACCATGGCTATCCGGC 60.282 66.667 13.04 0.00 38.97 6.13
368 408 2.109181 GCTATCCGGCCACTGGTC 59.891 66.667 2.24 0.00 0.00 4.02
369 409 2.435693 GCTATCCGGCCACTGGTCT 61.436 63.158 2.24 0.00 0.00 3.85
370 410 1.113517 GCTATCCGGCCACTGGTCTA 61.114 60.000 2.24 0.00 0.00 2.59
371 411 0.674534 CTATCCGGCCACTGGTCTAC 59.325 60.000 2.24 0.00 0.00 2.59
372 412 0.032912 TATCCGGCCACTGGTCTACA 60.033 55.000 2.24 0.00 0.00 2.74
373 413 0.907704 ATCCGGCCACTGGTCTACAA 60.908 55.000 2.24 0.00 0.00 2.41
374 414 0.907704 TCCGGCCACTGGTCTACAAT 60.908 55.000 2.24 0.00 0.00 2.71
375 415 0.744414 CCGGCCACTGGTCTACAATG 60.744 60.000 2.24 0.00 0.00 2.82
376 416 1.369091 CGGCCACTGGTCTACAATGC 61.369 60.000 2.24 0.00 0.00 3.56
377 417 0.035056 GGCCACTGGTCTACAATGCT 60.035 55.000 0.00 0.00 0.00 3.79
378 418 1.089920 GCCACTGGTCTACAATGCTG 58.910 55.000 0.00 0.00 0.00 4.41
379 419 1.339055 GCCACTGGTCTACAATGCTGA 60.339 52.381 0.00 0.00 0.00 4.26
380 420 2.681976 GCCACTGGTCTACAATGCTGAT 60.682 50.000 0.00 0.00 0.00 2.90
381 421 2.941064 CCACTGGTCTACAATGCTGATG 59.059 50.000 0.00 0.00 0.00 3.07
382 422 3.369787 CCACTGGTCTACAATGCTGATGA 60.370 47.826 0.00 0.00 0.00 2.92
383 423 3.869832 CACTGGTCTACAATGCTGATGAG 59.130 47.826 0.00 0.00 0.00 2.90
384 424 2.871022 CTGGTCTACAATGCTGATGAGC 59.129 50.000 0.00 0.00 46.44 4.26
393 433 2.938354 GCTGATGAGCAAGGTGTGT 58.062 52.632 0.00 0.00 45.46 3.72
394 434 2.099141 GCTGATGAGCAAGGTGTGTA 57.901 50.000 0.00 0.00 45.46 2.90
395 435 2.005451 GCTGATGAGCAAGGTGTGTAG 58.995 52.381 0.00 0.00 45.46 2.74
396 436 2.005451 CTGATGAGCAAGGTGTGTAGC 58.995 52.381 0.00 0.00 0.00 3.58
397 437 1.625315 TGATGAGCAAGGTGTGTAGCT 59.375 47.619 0.00 0.00 40.60 3.32
399 439 3.145228 GAGCAAGGTGTGTAGCTCC 57.855 57.895 0.00 0.00 45.79 4.70
400 440 0.391793 GAGCAAGGTGTGTAGCTCCC 60.392 60.000 0.00 0.00 45.79 4.30
401 441 0.838122 AGCAAGGTGTGTAGCTCCCT 60.838 55.000 0.00 0.00 32.44 4.20
402 442 0.391793 GCAAGGTGTGTAGCTCCCTC 60.392 60.000 0.00 0.00 32.44 4.30
403 443 0.250513 CAAGGTGTGTAGCTCCCTCC 59.749 60.000 0.00 0.00 32.44 4.30
404 444 0.117340 AAGGTGTGTAGCTCCCTCCT 59.883 55.000 0.00 0.00 32.44 3.69
405 445 1.008403 AGGTGTGTAGCTCCCTCCTA 58.992 55.000 0.00 0.00 0.00 2.94
406 446 1.063567 AGGTGTGTAGCTCCCTCCTAG 60.064 57.143 0.00 0.00 0.00 3.02
407 447 1.063867 GGTGTGTAGCTCCCTCCTAGA 60.064 57.143 0.00 0.00 0.00 2.43
408 448 2.025898 GTGTGTAGCTCCCTCCTAGAC 58.974 57.143 0.00 0.00 31.73 2.59
409 449 1.063867 TGTGTAGCTCCCTCCTAGACC 60.064 57.143 0.00 0.00 30.45 3.85
410 450 1.063867 GTGTAGCTCCCTCCTAGACCA 60.064 57.143 0.00 0.00 0.00 4.02
411 451 1.215673 TGTAGCTCCCTCCTAGACCAG 59.784 57.143 0.00 0.00 0.00 4.00
412 452 1.215924 GTAGCTCCCTCCTAGACCAGT 59.784 57.143 0.00 0.00 0.00 4.00
413 453 1.609626 AGCTCCCTCCTAGACCAGTA 58.390 55.000 0.00 0.00 0.00 2.74
414 454 1.215924 AGCTCCCTCCTAGACCAGTAC 59.784 57.143 0.00 0.00 0.00 2.73
415 455 1.063867 GCTCCCTCCTAGACCAGTACA 60.064 57.143 0.00 0.00 0.00 2.90
416 456 2.623502 GCTCCCTCCTAGACCAGTACAA 60.624 54.545 0.00 0.00 0.00 2.41
417 457 3.292460 CTCCCTCCTAGACCAGTACAAG 58.708 54.545 0.00 0.00 0.00 3.16
418 458 2.024273 TCCCTCCTAGACCAGTACAAGG 60.024 54.545 0.00 0.00 0.00 3.61
419 459 2.292323 CCCTCCTAGACCAGTACAAGGT 60.292 54.545 9.51 9.51 43.46 3.50
420 460 3.053095 CCCTCCTAGACCAGTACAAGGTA 60.053 52.174 9.69 0.00 40.09 3.08
421 461 4.571362 CCCTCCTAGACCAGTACAAGGTAA 60.571 50.000 9.69 2.00 40.09 2.85
422 462 5.209659 CCTCCTAGACCAGTACAAGGTAAT 58.790 45.833 9.69 5.31 40.09 1.89
423 463 5.069251 CCTCCTAGACCAGTACAAGGTAATG 59.931 48.000 9.69 0.00 40.09 1.90
424 464 4.960469 TCCTAGACCAGTACAAGGTAATGG 59.040 45.833 18.24 18.24 40.09 3.16
425 465 4.960469 CCTAGACCAGTACAAGGTAATGGA 59.040 45.833 24.53 6.30 40.09 3.41
426 466 5.069251 CCTAGACCAGTACAAGGTAATGGAG 59.931 48.000 24.53 13.81 40.09 3.86
427 467 3.775316 AGACCAGTACAAGGTAATGGAGG 59.225 47.826 24.53 4.02 40.09 4.30
428 468 2.844348 ACCAGTACAAGGTAATGGAGGG 59.156 50.000 24.53 3.71 37.67 4.30
429 469 3.112263 CCAGTACAAGGTAATGGAGGGA 58.888 50.000 15.65 0.00 34.88 4.20
430 470 3.521937 CCAGTACAAGGTAATGGAGGGAA 59.478 47.826 15.65 0.00 34.88 3.97
431 471 4.166144 CCAGTACAAGGTAATGGAGGGAAT 59.834 45.833 15.65 0.00 34.88 3.01
432 472 5.126067 CAGTACAAGGTAATGGAGGGAATG 58.874 45.833 0.00 0.00 0.00 2.67
433 473 3.669939 ACAAGGTAATGGAGGGAATGG 57.330 47.619 0.00 0.00 0.00 3.16
434 474 3.197983 ACAAGGTAATGGAGGGAATGGA 58.802 45.455 0.00 0.00 0.00 3.41
435 475 3.203040 ACAAGGTAATGGAGGGAATGGAG 59.797 47.826 0.00 0.00 0.00 3.86
436 476 3.438131 AGGTAATGGAGGGAATGGAGA 57.562 47.619 0.00 0.00 0.00 3.71
437 477 3.747852 AGGTAATGGAGGGAATGGAGAA 58.252 45.455 0.00 0.00 0.00 2.87
438 478 3.718956 AGGTAATGGAGGGAATGGAGAAG 59.281 47.826 0.00 0.00 0.00 2.85
439 479 2.744352 AATGGAGGGAATGGAGAAGC 57.256 50.000 0.00 0.00 0.00 3.86
440 480 1.600058 ATGGAGGGAATGGAGAAGCA 58.400 50.000 0.00 0.00 0.00 3.91
441 481 0.914644 TGGAGGGAATGGAGAAGCAG 59.085 55.000 0.00 0.00 0.00 4.24
442 482 0.465278 GGAGGGAATGGAGAAGCAGC 60.465 60.000 0.00 0.00 0.00 5.25
443 483 0.254178 GAGGGAATGGAGAAGCAGCA 59.746 55.000 0.00 0.00 0.00 4.41
444 484 0.924823 AGGGAATGGAGAAGCAGCAT 59.075 50.000 0.00 0.00 0.00 3.79
445 485 2.105477 GAGGGAATGGAGAAGCAGCATA 59.895 50.000 0.00 0.00 0.00 3.14
446 486 2.106166 AGGGAATGGAGAAGCAGCATAG 59.894 50.000 0.00 0.00 0.00 2.23
447 487 2.502295 GGAATGGAGAAGCAGCATAGG 58.498 52.381 0.00 0.00 0.00 2.57
448 488 2.105477 GGAATGGAGAAGCAGCATAGGA 59.895 50.000 0.00 0.00 0.00 2.94
449 489 3.244840 GGAATGGAGAAGCAGCATAGGAT 60.245 47.826 0.00 0.00 0.00 3.24
450 490 4.396522 GAATGGAGAAGCAGCATAGGATT 58.603 43.478 0.00 0.00 0.00 3.01
451 491 3.482156 TGGAGAAGCAGCATAGGATTC 57.518 47.619 0.00 0.00 0.00 2.52
452 492 2.105477 TGGAGAAGCAGCATAGGATTCC 59.895 50.000 0.00 0.00 0.00 3.01
453 493 2.551938 GGAGAAGCAGCATAGGATTCCC 60.552 54.545 0.00 0.00 0.00 3.97
454 494 2.105477 GAGAAGCAGCATAGGATTCCCA 59.895 50.000 0.00 0.00 33.88 4.37
455 495 2.511218 AGAAGCAGCATAGGATTCCCAA 59.489 45.455 0.00 0.00 33.88 4.12
456 496 2.653234 AGCAGCATAGGATTCCCAAG 57.347 50.000 0.00 0.00 33.88 3.61
457 497 0.957362 GCAGCATAGGATTCCCAAGC 59.043 55.000 0.00 0.89 33.88 4.01
458 498 1.233019 CAGCATAGGATTCCCAAGCG 58.767 55.000 0.00 0.00 33.07 4.68
459 499 0.536006 AGCATAGGATTCCCAAGCGC 60.536 55.000 0.00 0.00 33.07 5.92
460 500 0.819259 GCATAGGATTCCCAAGCGCA 60.819 55.000 11.47 0.00 33.88 6.09
461 501 1.679139 CATAGGATTCCCAAGCGCAA 58.321 50.000 11.47 0.00 33.88 4.85
462 502 1.605710 CATAGGATTCCCAAGCGCAAG 59.394 52.381 11.47 0.00 35.73 4.01
474 514 2.796651 CGCAAGCTTCCAGCCATC 59.203 61.111 0.00 0.00 43.77 3.51
475 515 2.042259 CGCAAGCTTCCAGCCATCA 61.042 57.895 0.00 0.00 43.77 3.07
476 516 1.381928 CGCAAGCTTCCAGCCATCAT 61.382 55.000 0.00 0.00 43.77 2.45
477 517 0.384669 GCAAGCTTCCAGCCATCATC 59.615 55.000 0.00 0.00 43.77 2.92
478 518 1.758936 CAAGCTTCCAGCCATCATCA 58.241 50.000 0.00 0.00 43.77 3.07
479 519 2.097036 CAAGCTTCCAGCCATCATCAA 58.903 47.619 0.00 0.00 43.77 2.57
480 520 2.494471 CAAGCTTCCAGCCATCATCAAA 59.506 45.455 0.00 0.00 43.77 2.69
481 521 2.811410 AGCTTCCAGCCATCATCAAAA 58.189 42.857 0.00 0.00 43.77 2.44
482 522 3.371965 AGCTTCCAGCCATCATCAAAAT 58.628 40.909 0.00 0.00 43.77 1.82
483 523 3.132289 AGCTTCCAGCCATCATCAAAATG 59.868 43.478 0.00 0.00 43.77 2.32
484 524 3.454375 CTTCCAGCCATCATCAAAATGC 58.546 45.455 0.00 0.00 32.58 3.56
485 525 1.758280 TCCAGCCATCATCAAAATGCC 59.242 47.619 0.00 0.00 32.58 4.40
486 526 1.483004 CCAGCCATCATCAAAATGCCA 59.517 47.619 0.00 0.00 32.58 4.92
487 527 2.104111 CCAGCCATCATCAAAATGCCAT 59.896 45.455 0.00 0.00 32.58 4.40
488 528 3.390135 CAGCCATCATCAAAATGCCATC 58.610 45.455 0.00 0.00 32.58 3.51
489 529 3.035363 AGCCATCATCAAAATGCCATCA 58.965 40.909 0.00 0.00 32.58 3.07
490 530 3.646162 AGCCATCATCAAAATGCCATCAT 59.354 39.130 0.00 0.00 32.58 2.45
491 531 3.994392 GCCATCATCAAAATGCCATCATC 59.006 43.478 0.00 0.00 32.58 2.92
492 532 4.502431 GCCATCATCAAAATGCCATCATCA 60.502 41.667 0.00 0.00 32.58 3.07
493 533 5.606505 CCATCATCAAAATGCCATCATCAA 58.393 37.500 0.00 0.00 32.58 2.57
494 534 6.052360 CCATCATCAAAATGCCATCATCAAA 58.948 36.000 0.00 0.00 32.58 2.69
495 535 6.540551 CCATCATCAAAATGCCATCATCAAAA 59.459 34.615 0.00 0.00 32.58 2.44
496 536 7.228507 CCATCATCAAAATGCCATCATCAAAAT 59.771 33.333 0.00 0.00 32.58 1.82
497 537 7.546778 TCATCAAAATGCCATCATCAAAATG 57.453 32.000 0.00 0.00 32.58 2.32
498 538 6.540551 TCATCAAAATGCCATCATCAAAATGG 59.459 34.615 0.00 0.00 45.45 3.16
499 539 6.051179 TCAAAATGCCATCATCAAAATGGA 57.949 33.333 6.33 0.00 45.51 3.41
500 540 6.110033 TCAAAATGCCATCATCAAAATGGAG 58.890 36.000 6.33 0.00 45.51 3.86
501 541 5.943349 AAATGCCATCATCAAAATGGAGA 57.057 34.783 6.33 0.00 45.51 3.71
502 542 5.943349 AATGCCATCATCAAAATGGAGAA 57.057 34.783 6.33 0.00 45.51 2.87
503 543 4.994907 TGCCATCATCAAAATGGAGAAG 57.005 40.909 6.33 0.00 45.51 2.85
504 544 3.131577 TGCCATCATCAAAATGGAGAAGC 59.868 43.478 6.33 0.00 45.51 3.86
505 545 3.131577 GCCATCATCAAAATGGAGAAGCA 59.868 43.478 6.33 0.00 45.51 3.91
506 546 4.736759 GCCATCATCAAAATGGAGAAGCAG 60.737 45.833 6.33 0.00 45.51 4.24
507 547 4.360563 CATCATCAAAATGGAGAAGCAGC 58.639 43.478 0.00 0.00 33.42 5.25
508 548 3.423749 TCATCAAAATGGAGAAGCAGCA 58.576 40.909 0.00 0.00 33.42 4.41
509 549 4.021229 TCATCAAAATGGAGAAGCAGCAT 58.979 39.130 0.00 0.00 33.42 3.79
510 550 5.195185 TCATCAAAATGGAGAAGCAGCATA 58.805 37.500 0.00 0.00 33.42 3.14
511 551 5.298527 TCATCAAAATGGAGAAGCAGCATAG 59.701 40.000 0.00 0.00 33.42 2.23
512 552 3.949754 TCAAAATGGAGAAGCAGCATAGG 59.050 43.478 0.00 0.00 0.00 2.57
513 553 3.939740 AAATGGAGAAGCAGCATAGGA 57.060 42.857 0.00 0.00 0.00 2.94
514 554 4.450305 AAATGGAGAAGCAGCATAGGAT 57.550 40.909 0.00 0.00 0.00 3.24
515 555 4.450305 AATGGAGAAGCAGCATAGGATT 57.550 40.909 0.00 0.00 0.00 3.01
516 556 3.482156 TGGAGAAGCAGCATAGGATTC 57.518 47.619 0.00 0.00 0.00 2.52
517 557 2.105477 TGGAGAAGCAGCATAGGATTCC 59.895 50.000 0.00 0.00 0.00 3.01
518 558 2.551938 GGAGAAGCAGCATAGGATTCCC 60.552 54.545 0.00 0.00 0.00 3.97
519 559 2.105477 GAGAAGCAGCATAGGATTCCCA 59.895 50.000 0.00 0.00 33.88 4.37
520 560 2.511218 AGAAGCAGCATAGGATTCCCAA 59.489 45.455 0.00 0.00 33.88 4.12
521 561 2.653234 AGCAGCATAGGATTCCCAAG 57.347 50.000 0.00 0.00 33.88 3.61
522 562 0.957362 GCAGCATAGGATTCCCAAGC 59.043 55.000 0.00 0.89 33.88 4.01
523 563 1.233019 CAGCATAGGATTCCCAAGCG 58.767 55.000 0.00 0.00 33.07 4.68
524 564 0.536006 AGCATAGGATTCCCAAGCGC 60.536 55.000 0.00 0.00 33.07 5.92
525 565 0.819259 GCATAGGATTCCCAAGCGCA 60.819 55.000 11.47 0.00 33.88 6.09
526 566 1.679139 CATAGGATTCCCAAGCGCAA 58.321 50.000 11.47 0.00 33.88 4.85
527 567 1.605710 CATAGGATTCCCAAGCGCAAG 59.394 52.381 11.47 0.00 35.73 4.01
539 579 2.488355 CGCAAGCTTCCAGGCATG 59.512 61.111 0.00 0.00 34.55 4.06
540 580 2.338015 CGCAAGCTTCCAGGCATGT 61.338 57.895 0.00 0.00 34.04 3.21
541 581 1.214589 GCAAGCTTCCAGGCATGTG 59.785 57.895 0.00 0.00 34.04 3.21
542 582 1.214589 CAAGCTTCCAGGCATGTGC 59.785 57.895 0.00 0.00 41.14 4.57
543 583 2.338015 AAGCTTCCAGGCATGTGCG 61.338 57.895 0.00 0.00 43.26 5.34
544 584 2.747460 GCTTCCAGGCATGTGCGA 60.747 61.111 0.00 0.00 43.26 5.10
545 585 2.334946 GCTTCCAGGCATGTGCGAA 61.335 57.895 0.00 0.00 43.26 4.70
546 586 1.660560 GCTTCCAGGCATGTGCGAAT 61.661 55.000 0.00 0.00 43.26 3.34
547 587 0.379669 CTTCCAGGCATGTGCGAATC 59.620 55.000 0.00 0.00 43.26 2.52
548 588 0.035152 TTCCAGGCATGTGCGAATCT 60.035 50.000 0.00 0.00 43.26 2.40
549 589 0.035152 TCCAGGCATGTGCGAATCTT 60.035 50.000 0.00 0.00 43.26 2.40
550 590 0.099968 CCAGGCATGTGCGAATCTTG 59.900 55.000 0.00 0.00 43.26 3.02
551 591 1.089112 CAGGCATGTGCGAATCTTGA 58.911 50.000 0.00 0.00 43.26 3.02
552 592 1.674441 CAGGCATGTGCGAATCTTGAT 59.326 47.619 0.00 0.00 43.26 2.57
553 593 1.945394 AGGCATGTGCGAATCTTGATC 59.055 47.619 0.00 0.00 43.26 2.92
554 594 1.333524 GGCATGTGCGAATCTTGATCG 60.334 52.381 0.00 0.00 43.26 3.69
555 595 1.333524 GCATGTGCGAATCTTGATCGG 60.334 52.381 0.00 0.00 40.54 4.18
556 596 2.204237 CATGTGCGAATCTTGATCGGA 58.796 47.619 0.00 0.00 40.54 4.55
557 597 2.602257 TGTGCGAATCTTGATCGGAT 57.398 45.000 0.00 0.00 42.51 4.18
558 598 2.473816 TGTGCGAATCTTGATCGGATC 58.526 47.619 11.07 11.07 42.51 3.36
559 599 2.159114 TGTGCGAATCTTGATCGGATCA 60.159 45.455 16.44 16.44 42.51 2.92
560 600 2.866156 GTGCGAATCTTGATCGGATCAA 59.134 45.455 26.80 26.80 46.30 2.57
561 601 2.866156 TGCGAATCTTGATCGGATCAAC 59.134 45.455 25.39 16.44 43.84 3.18
562 602 2.866156 GCGAATCTTGATCGGATCAACA 59.134 45.455 25.39 18.03 43.84 3.33
563 603 3.309682 GCGAATCTTGATCGGATCAACAA 59.690 43.478 25.39 17.80 43.84 2.83
564 604 4.201812 GCGAATCTTGATCGGATCAACAAA 60.202 41.667 25.39 15.71 43.84 2.83
565 605 5.504665 GCGAATCTTGATCGGATCAACAAAT 60.505 40.000 25.39 16.96 43.84 2.32
566 606 6.489675 CGAATCTTGATCGGATCAACAAATT 58.510 36.000 25.39 22.36 43.84 1.82
567 607 6.968904 CGAATCTTGATCGGATCAACAAATTT 59.031 34.615 25.39 15.29 43.84 1.82
568 608 8.122330 CGAATCTTGATCGGATCAACAAATTTA 58.878 33.333 25.39 6.90 43.84 1.40
569 609 9.787532 GAATCTTGATCGGATCAACAAATTTAA 57.212 29.630 25.39 6.25 43.84 1.52
570 610 9.573133 AATCTTGATCGGATCAACAAATTTAAC 57.427 29.630 25.39 0.00 43.84 2.01
571 611 8.335532 TCTTGATCGGATCAACAAATTTAACT 57.664 30.769 25.39 0.00 43.84 2.24
572 612 9.443323 TCTTGATCGGATCAACAAATTTAACTA 57.557 29.630 25.39 4.94 43.84 2.24
573 613 9.490663 CTTGATCGGATCAACAAATTTAACTAC 57.509 33.333 25.39 0.00 43.84 2.73
574 614 8.786826 TGATCGGATCAACAAATTTAACTACT 57.213 30.769 17.94 0.00 36.11 2.57
575 615 9.878667 TGATCGGATCAACAAATTTAACTACTA 57.121 29.630 17.94 0.00 36.11 1.82
592 632 9.918630 TTAACTACTAATTGTCACTAGTTGGAC 57.081 33.333 6.44 6.44 29.62 4.02
593 633 6.932947 ACTACTAATTGTCACTAGTTGGACC 58.067 40.000 10.05 0.00 33.09 4.46
594 634 5.161943 ACTAATTGTCACTAGTTGGACCC 57.838 43.478 10.05 0.00 33.09 4.46
595 635 4.595781 ACTAATTGTCACTAGTTGGACCCA 59.404 41.667 10.05 0.00 33.09 4.51
596 636 4.447138 AATTGTCACTAGTTGGACCCAA 57.553 40.909 10.05 0.00 33.09 4.12
597 637 4.657814 ATTGTCACTAGTTGGACCCAAT 57.342 40.909 10.05 3.18 38.28 3.16
598 638 3.417069 TGTCACTAGTTGGACCCAATG 57.583 47.619 10.05 0.00 38.28 2.82
599 639 2.084546 GTCACTAGTTGGACCCAATGC 58.915 52.381 4.63 0.00 38.28 3.56
600 640 1.004277 TCACTAGTTGGACCCAATGCC 59.996 52.381 4.63 0.00 38.28 4.40
601 641 0.331616 ACTAGTTGGACCCAATGCCC 59.668 55.000 4.63 0.00 38.28 5.36
602 642 0.625849 CTAGTTGGACCCAATGCCCT 59.374 55.000 4.63 0.36 38.28 5.19
603 643 1.843851 CTAGTTGGACCCAATGCCCTA 59.156 52.381 4.63 1.49 38.28 3.53
604 644 1.308877 AGTTGGACCCAATGCCCTAT 58.691 50.000 4.63 0.00 38.28 2.57
605 645 1.645919 AGTTGGACCCAATGCCCTATT 59.354 47.619 4.63 0.00 38.28 1.73
606 646 1.756538 GTTGGACCCAATGCCCTATTG 59.243 52.381 4.63 0.00 44.67 1.90
607 647 1.006813 TGGACCCAATGCCCTATTGT 58.993 50.000 0.00 0.00 43.78 2.71
608 648 1.360852 TGGACCCAATGCCCTATTGTT 59.639 47.619 0.00 0.00 43.78 2.83
609 649 1.756538 GGACCCAATGCCCTATTGTTG 59.243 52.381 0.00 0.00 43.78 3.33
610 650 1.756538 GACCCAATGCCCTATTGTTGG 59.243 52.381 0.00 0.00 43.78 3.77
611 651 1.078656 ACCCAATGCCCTATTGTTGGT 59.921 47.619 0.00 0.00 43.78 3.67
612 652 2.187100 CCCAATGCCCTATTGTTGGTT 58.813 47.619 0.00 0.00 43.78 3.67
613 653 2.093553 CCCAATGCCCTATTGTTGGTTG 60.094 50.000 0.00 0.00 43.78 3.77
614 654 2.093553 CCAATGCCCTATTGTTGGTTGG 60.094 50.000 0.00 0.00 43.78 3.77
615 655 2.566724 CAATGCCCTATTGTTGGTTGGT 59.433 45.455 0.00 0.00 41.02 3.67
616 656 1.626686 TGCCCTATTGTTGGTTGGTG 58.373 50.000 0.00 0.00 0.00 4.17
617 657 0.894835 GCCCTATTGTTGGTTGGTGG 59.105 55.000 0.00 0.00 0.00 4.61
618 658 1.825641 GCCCTATTGTTGGTTGGTGGT 60.826 52.381 0.00 0.00 0.00 4.16
619 659 1.892474 CCCTATTGTTGGTTGGTGGTG 59.108 52.381 0.00 0.00 0.00 4.17
717 757 3.362831 CGACAGCGACAGTAATTAAACGT 59.637 43.478 0.00 0.00 40.82 3.99
793 833 4.405680 TCCTCTGAACTCAGTGACTTTGAA 59.594 41.667 9.76 0.00 44.12 2.69
845 885 2.425668 CCACATGATGCATTTGCTGAGA 59.574 45.455 0.00 0.00 42.66 3.27
990 1030 3.118075 GCTATTTCTTGCCCTCTCCTCTT 60.118 47.826 0.00 0.00 0.00 2.85
1005 1045 1.271001 CCTCTTCACACACTCATGGCA 60.271 52.381 0.00 0.00 0.00 4.92
1030 1070 1.646912 TATCTTGTCCAACACCCGGA 58.353 50.000 0.73 0.00 0.00 5.14
1088 1128 1.017177 TTGTCCTTGCACCGTATCGC 61.017 55.000 0.00 0.00 0.00 4.58
1089 1129 1.153628 GTCCTTGCACCGTATCGCT 60.154 57.895 0.00 0.00 0.00 4.93
1092 1132 0.928229 CCTTGCACCGTATCGCTAAC 59.072 55.000 0.00 0.00 0.00 2.34
1685 1732 4.724399 TGTTCACATTTCCATGTACCAGT 58.276 39.130 0.00 0.00 42.14 4.00
1686 1733 5.870706 TGTTCACATTTCCATGTACCAGTA 58.129 37.500 0.00 0.00 42.14 2.74
1807 1855 6.391649 TGGTACTTCCCCTTTCCATGTATTAT 59.608 38.462 0.00 0.00 34.77 1.28
1808 1856 7.091720 TGGTACTTCCCCTTTCCATGTATTATT 60.092 37.037 0.00 0.00 34.77 1.40
1809 1857 8.442374 GGTACTTCCCCTTTCCATGTATTATTA 58.558 37.037 0.00 0.00 0.00 0.98
1810 1858 9.503399 GTACTTCCCCTTTCCATGTATTATTAG 57.497 37.037 0.00 0.00 0.00 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.246420 CTTGTCACCAAATACAAGGAAGAG 57.754 41.667 7.21 0.00 45.68 2.85
34 35 1.536766 ACGTTTGATGCACCACATGAG 59.463 47.619 0.00 0.00 39.84 2.90
38 39 2.741517 CAGATACGTTTGATGCACCACA 59.258 45.455 0.00 0.00 0.00 4.17
42 43 5.029650 TGTTTCAGATACGTTTGATGCAC 57.970 39.130 0.00 0.00 0.00 4.57
78 79 5.652994 TTACAAAACTTCCACTTGCAAGT 57.347 34.783 26.36 26.36 40.60 3.16
107 108 1.357258 GCCATCTGAGACAGTGTGCG 61.357 60.000 0.00 0.00 32.61 5.34
188 225 1.583495 CGTACACAGCCTGAGACGGA 61.583 60.000 0.00 0.00 32.49 4.69
189 226 1.154016 CGTACACAGCCTGAGACGG 60.154 63.158 0.00 0.00 32.49 4.79
219 256 6.015688 ACGAGTATAGTGTTTGAGTTCTCCAA 60.016 38.462 0.00 0.00 0.00 3.53
220 257 5.475909 ACGAGTATAGTGTTTGAGTTCTCCA 59.524 40.000 0.00 0.00 0.00 3.86
254 291 2.498078 GGAGAACGGAGAAGAGAATGGT 59.502 50.000 0.00 0.00 0.00 3.55
255 292 2.497675 TGGAGAACGGAGAAGAGAATGG 59.502 50.000 0.00 0.00 0.00 3.16
256 293 3.194542 AGTGGAGAACGGAGAAGAGAATG 59.805 47.826 0.00 0.00 0.00 2.67
257 294 3.436243 AGTGGAGAACGGAGAAGAGAAT 58.564 45.455 0.00 0.00 0.00 2.40
258 295 2.877866 AGTGGAGAACGGAGAAGAGAA 58.122 47.619 0.00 0.00 0.00 2.87
259 296 2.588464 AGTGGAGAACGGAGAAGAGA 57.412 50.000 0.00 0.00 0.00 3.10
260 297 2.558795 TGAAGTGGAGAACGGAGAAGAG 59.441 50.000 0.00 0.00 0.00 2.85
261 298 2.296471 GTGAAGTGGAGAACGGAGAAGA 59.704 50.000 0.00 0.00 0.00 2.87
262 299 2.297597 AGTGAAGTGGAGAACGGAGAAG 59.702 50.000 0.00 0.00 0.00 2.85
263 300 2.317040 AGTGAAGTGGAGAACGGAGAA 58.683 47.619 0.00 0.00 0.00 2.87
264 301 1.996798 AGTGAAGTGGAGAACGGAGA 58.003 50.000 0.00 0.00 0.00 3.71
265 302 2.820787 ACTAGTGAAGTGGAGAACGGAG 59.179 50.000 0.00 0.00 36.93 4.63
266 303 2.872732 ACTAGTGAAGTGGAGAACGGA 58.127 47.619 0.00 0.00 36.93 4.69
267 304 3.662247 AACTAGTGAAGTGGAGAACGG 57.338 47.619 0.00 0.00 38.88 4.44
268 305 4.209288 CACAAACTAGTGAAGTGGAGAACG 59.791 45.833 12.39 0.00 42.05 3.95
269 306 5.116882 ACACAAACTAGTGAAGTGGAGAAC 58.883 41.667 20.16 0.00 42.05 3.01
270 307 5.353394 ACACAAACTAGTGAAGTGGAGAA 57.647 39.130 20.16 0.00 42.05 2.87
271 308 5.353394 AACACAAACTAGTGAAGTGGAGA 57.647 39.130 20.16 0.00 42.05 3.71
272 309 6.436843 AAAACACAAACTAGTGAAGTGGAG 57.563 37.500 20.16 7.80 42.05 3.86
273 310 5.355910 GGAAAACACAAACTAGTGAAGTGGA 59.644 40.000 20.16 0.00 42.05 4.02
274 311 5.124776 TGGAAAACACAAACTAGTGAAGTGG 59.875 40.000 20.16 8.17 42.05 4.00
275 312 6.128007 ACTGGAAAACACAAACTAGTGAAGTG 60.128 38.462 16.57 16.57 42.05 3.16
276 313 5.944007 ACTGGAAAACACAAACTAGTGAAGT 59.056 36.000 0.00 0.00 42.05 3.01
277 314 6.258160 CACTGGAAAACACAAACTAGTGAAG 58.742 40.000 0.00 0.00 41.82 3.02
278 315 5.392595 GCACTGGAAAACACAAACTAGTGAA 60.393 40.000 0.00 0.00 41.82 3.18
279 316 4.095782 GCACTGGAAAACACAAACTAGTGA 59.904 41.667 0.00 0.00 41.82 3.41
286 323 1.468908 CGCAGCACTGGAAAACACAAA 60.469 47.619 0.00 0.00 0.00 2.83
308 345 4.380867 CCATTGGAATGCTAAGAACCACAC 60.381 45.833 0.00 0.00 35.08 3.82
334 374 2.597340 CCATGGTGGCCACTAGGG 59.403 66.667 34.19 34.19 37.40 3.53
343 383 2.281761 GCCGGATAGCCATGGTGG 60.282 66.667 14.67 7.20 41.55 4.61
351 391 1.113517 TAGACCAGTGGCCGGATAGC 61.114 60.000 9.78 0.00 0.00 2.97
352 392 0.674534 GTAGACCAGTGGCCGGATAG 59.325 60.000 9.78 0.00 0.00 2.08
353 393 0.032912 TGTAGACCAGTGGCCGGATA 60.033 55.000 9.78 0.00 0.00 2.59
354 394 0.907704 TTGTAGACCAGTGGCCGGAT 60.908 55.000 9.78 0.00 0.00 4.18
355 395 0.907704 ATTGTAGACCAGTGGCCGGA 60.908 55.000 9.78 0.00 0.00 5.14
356 396 0.744414 CATTGTAGACCAGTGGCCGG 60.744 60.000 9.78 0.00 0.00 6.13
357 397 1.369091 GCATTGTAGACCAGTGGCCG 61.369 60.000 9.78 0.00 31.77 6.13
358 398 0.035056 AGCATTGTAGACCAGTGGCC 60.035 55.000 9.78 0.00 31.77 5.36
359 399 1.089920 CAGCATTGTAGACCAGTGGC 58.910 55.000 9.78 1.85 31.77 5.01
360 400 2.768253 TCAGCATTGTAGACCAGTGG 57.232 50.000 7.91 7.91 31.77 4.00
361 401 3.865446 TCATCAGCATTGTAGACCAGTG 58.135 45.455 0.00 0.00 34.11 3.66
362 402 3.681034 GCTCATCAGCATTGTAGACCAGT 60.681 47.826 0.00 0.00 46.06 4.00
363 403 2.871022 GCTCATCAGCATTGTAGACCAG 59.129 50.000 0.00 0.00 46.06 4.00
364 404 2.910199 GCTCATCAGCATTGTAGACCA 58.090 47.619 0.00 0.00 46.06 4.02
376 416 2.005451 GCTACACACCTTGCTCATCAG 58.995 52.381 0.00 0.00 0.00 2.90
377 417 1.625315 AGCTACACACCTTGCTCATCA 59.375 47.619 0.00 0.00 0.00 3.07
378 418 2.393271 AGCTACACACCTTGCTCATC 57.607 50.000 0.00 0.00 0.00 2.92
382 422 0.838122 AGGGAGCTACACACCTTGCT 60.838 55.000 0.00 0.00 38.59 3.91
383 423 0.391793 GAGGGAGCTACACACCTTGC 60.392 60.000 0.00 0.00 32.42 4.01
384 424 0.250513 GGAGGGAGCTACACACCTTG 59.749 60.000 0.00 0.00 32.42 3.61
385 425 0.117340 AGGAGGGAGCTACACACCTT 59.883 55.000 0.00 0.00 39.94 3.50
386 426 1.008403 TAGGAGGGAGCTACACACCT 58.992 55.000 11.54 11.54 44.74 4.00
387 427 1.063867 TCTAGGAGGGAGCTACACACC 60.064 57.143 0.00 0.00 32.77 4.16
388 428 2.025898 GTCTAGGAGGGAGCTACACAC 58.974 57.143 0.00 0.00 0.00 3.82
389 429 1.063867 GGTCTAGGAGGGAGCTACACA 60.064 57.143 0.00 0.00 0.00 3.72
390 430 1.063867 TGGTCTAGGAGGGAGCTACAC 60.064 57.143 0.00 0.00 33.06 2.90
391 431 1.215673 CTGGTCTAGGAGGGAGCTACA 59.784 57.143 0.00 0.00 33.06 2.74
392 432 1.215924 ACTGGTCTAGGAGGGAGCTAC 59.784 57.143 0.00 0.00 33.06 3.58
393 433 1.609626 ACTGGTCTAGGAGGGAGCTA 58.390 55.000 0.00 0.00 33.06 3.32
394 434 1.215924 GTACTGGTCTAGGAGGGAGCT 59.784 57.143 0.00 0.00 33.06 4.09
395 435 1.063867 TGTACTGGTCTAGGAGGGAGC 60.064 57.143 0.00 0.00 0.00 4.70
396 436 3.292460 CTTGTACTGGTCTAGGAGGGAG 58.708 54.545 0.00 0.00 0.00 4.30
397 437 2.024273 CCTTGTACTGGTCTAGGAGGGA 60.024 54.545 0.00 0.00 31.39 4.20
398 438 2.292323 ACCTTGTACTGGTCTAGGAGGG 60.292 54.545 5.49 0.00 31.03 4.30
399 439 3.103080 ACCTTGTACTGGTCTAGGAGG 57.897 52.381 5.49 0.00 31.03 4.30
400 440 5.069251 CCATTACCTTGTACTGGTCTAGGAG 59.931 48.000 13.06 2.26 38.88 3.69
401 441 4.960469 CCATTACCTTGTACTGGTCTAGGA 59.040 45.833 13.06 0.00 38.88 2.94
402 442 4.960469 TCCATTACCTTGTACTGGTCTAGG 59.040 45.833 13.06 12.67 38.88 3.02
403 443 5.069251 CCTCCATTACCTTGTACTGGTCTAG 59.931 48.000 13.06 6.01 38.88 2.43
404 444 4.960469 CCTCCATTACCTTGTACTGGTCTA 59.040 45.833 13.06 5.48 38.88 2.59
405 445 3.775316 CCTCCATTACCTTGTACTGGTCT 59.225 47.826 13.06 2.34 38.88 3.85
406 446 3.118371 CCCTCCATTACCTTGTACTGGTC 60.118 52.174 13.06 0.00 38.88 4.02
407 447 2.844348 CCCTCCATTACCTTGTACTGGT 59.156 50.000 13.92 13.92 41.28 4.00
408 448 3.112263 TCCCTCCATTACCTTGTACTGG 58.888 50.000 4.70 4.70 0.00 4.00
409 449 4.837093 TTCCCTCCATTACCTTGTACTG 57.163 45.455 0.00 0.00 0.00 2.74
410 450 4.166144 CCATTCCCTCCATTACCTTGTACT 59.834 45.833 0.00 0.00 0.00 2.73
411 451 4.165372 TCCATTCCCTCCATTACCTTGTAC 59.835 45.833 0.00 0.00 0.00 2.90
412 452 4.376223 TCCATTCCCTCCATTACCTTGTA 58.624 43.478 0.00 0.00 0.00 2.41
413 453 3.197983 TCCATTCCCTCCATTACCTTGT 58.802 45.455 0.00 0.00 0.00 3.16
414 454 3.459598 TCTCCATTCCCTCCATTACCTTG 59.540 47.826 0.00 0.00 0.00 3.61
415 455 3.747852 TCTCCATTCCCTCCATTACCTT 58.252 45.455 0.00 0.00 0.00 3.50
416 456 3.438131 TCTCCATTCCCTCCATTACCT 57.562 47.619 0.00 0.00 0.00 3.08
417 457 3.748989 GCTTCTCCATTCCCTCCATTACC 60.749 52.174 0.00 0.00 0.00 2.85
418 458 3.117888 TGCTTCTCCATTCCCTCCATTAC 60.118 47.826 0.00 0.00 0.00 1.89
419 459 3.122480 TGCTTCTCCATTCCCTCCATTA 58.878 45.455 0.00 0.00 0.00 1.90
420 460 1.925255 TGCTTCTCCATTCCCTCCATT 59.075 47.619 0.00 0.00 0.00 3.16
421 461 1.493871 CTGCTTCTCCATTCCCTCCAT 59.506 52.381 0.00 0.00 0.00 3.41
422 462 0.914644 CTGCTTCTCCATTCCCTCCA 59.085 55.000 0.00 0.00 0.00 3.86
423 463 0.465278 GCTGCTTCTCCATTCCCTCC 60.465 60.000 0.00 0.00 0.00 4.30
424 464 0.254178 TGCTGCTTCTCCATTCCCTC 59.746 55.000 0.00 0.00 0.00 4.30
425 465 0.924823 ATGCTGCTTCTCCATTCCCT 59.075 50.000 0.00 0.00 0.00 4.20
426 466 2.502295 CTATGCTGCTTCTCCATTCCC 58.498 52.381 0.00 0.00 0.00 3.97
427 467 2.105477 TCCTATGCTGCTTCTCCATTCC 59.895 50.000 0.00 0.00 0.00 3.01
428 468 3.482156 TCCTATGCTGCTTCTCCATTC 57.518 47.619 0.00 0.00 0.00 2.67
429 469 4.396522 GAATCCTATGCTGCTTCTCCATT 58.603 43.478 0.00 0.00 0.00 3.16
430 470 3.244840 GGAATCCTATGCTGCTTCTCCAT 60.245 47.826 0.00 0.00 0.00 3.41
431 471 2.105477 GGAATCCTATGCTGCTTCTCCA 59.895 50.000 0.00 0.00 0.00 3.86
432 472 2.551938 GGGAATCCTATGCTGCTTCTCC 60.552 54.545 0.00 0.00 0.00 3.71
433 473 2.105477 TGGGAATCCTATGCTGCTTCTC 59.895 50.000 0.00 0.00 0.00 2.87
434 474 2.130193 TGGGAATCCTATGCTGCTTCT 58.870 47.619 0.00 0.00 0.00 2.85
435 475 2.645838 TGGGAATCCTATGCTGCTTC 57.354 50.000 0.00 0.00 0.00 3.86
436 476 2.941480 CTTGGGAATCCTATGCTGCTT 58.059 47.619 0.00 0.00 0.00 3.91
437 477 1.478288 GCTTGGGAATCCTATGCTGCT 60.478 52.381 14.71 0.00 0.00 4.24
438 478 0.957362 GCTTGGGAATCCTATGCTGC 59.043 55.000 14.71 0.00 0.00 5.25
439 479 1.233019 CGCTTGGGAATCCTATGCTG 58.767 55.000 18.48 10.20 0.00 4.41
440 480 0.536006 GCGCTTGGGAATCCTATGCT 60.536 55.000 18.48 0.00 0.00 3.79
441 481 0.819259 TGCGCTTGGGAATCCTATGC 60.819 55.000 9.73 12.48 0.00 3.14
442 482 1.605710 CTTGCGCTTGGGAATCCTATG 59.394 52.381 9.73 0.00 0.00 2.23
443 483 1.972872 CTTGCGCTTGGGAATCCTAT 58.027 50.000 9.73 0.00 0.00 2.57
444 484 0.748005 GCTTGCGCTTGGGAATCCTA 60.748 55.000 9.73 0.00 0.00 2.94
445 485 2.048603 GCTTGCGCTTGGGAATCCT 61.049 57.895 9.73 0.00 0.00 3.24
446 486 2.048603 AGCTTGCGCTTGGGAATCC 61.049 57.895 9.73 0.00 46.47 3.01
447 487 3.595819 AGCTTGCGCTTGGGAATC 58.404 55.556 9.73 0.00 46.47 2.52
463 503 3.454375 GCATTTTGATGATGGCTGGAAG 58.546 45.455 0.00 0.00 0.00 3.46
464 504 2.168936 GGCATTTTGATGATGGCTGGAA 59.831 45.455 3.73 0.00 44.14 3.53
465 505 1.758280 GGCATTTTGATGATGGCTGGA 59.242 47.619 3.73 0.00 44.14 3.86
466 506 1.483004 TGGCATTTTGATGATGGCTGG 59.517 47.619 11.16 0.00 46.68 4.85
467 507 2.971660 TGGCATTTTGATGATGGCTG 57.028 45.000 11.16 0.00 46.68 4.85
468 508 3.035363 TGATGGCATTTTGATGATGGCT 58.965 40.909 0.00 0.00 46.68 4.75
469 509 3.462483 TGATGGCATTTTGATGATGGC 57.538 42.857 0.00 3.98 46.72 4.40
470 510 5.208463 TGATGATGGCATTTTGATGATGG 57.792 39.130 0.00 0.00 34.11 3.51
471 511 7.546778 TTTTGATGATGGCATTTTGATGATG 57.453 32.000 0.00 0.00 34.11 3.07
472 512 7.228507 CCATTTTGATGATGGCATTTTGATGAT 59.771 33.333 0.00 0.00 37.81 2.45
473 513 6.540551 CCATTTTGATGATGGCATTTTGATGA 59.459 34.615 0.00 0.00 37.81 2.92
474 514 6.540551 TCCATTTTGATGATGGCATTTTGATG 59.459 34.615 0.00 0.91 43.04 3.07
475 515 6.654959 TCCATTTTGATGATGGCATTTTGAT 58.345 32.000 0.00 0.00 43.04 2.57
476 516 6.051179 TCCATTTTGATGATGGCATTTTGA 57.949 33.333 0.00 0.00 43.04 2.69
477 517 6.110033 TCTCCATTTTGATGATGGCATTTTG 58.890 36.000 0.00 0.00 43.04 2.44
478 518 6.302535 TCTCCATTTTGATGATGGCATTTT 57.697 33.333 0.00 0.00 43.04 1.82
479 519 5.943349 TCTCCATTTTGATGATGGCATTT 57.057 34.783 0.00 0.00 43.04 2.32
480 520 5.684030 GCTTCTCCATTTTGATGATGGCATT 60.684 40.000 0.00 0.00 43.04 3.56
481 521 4.202223 GCTTCTCCATTTTGATGATGGCAT 60.202 41.667 0.00 0.00 43.04 4.40
482 522 3.131577 GCTTCTCCATTTTGATGATGGCA 59.868 43.478 0.00 0.00 43.04 4.92
483 523 3.131577 TGCTTCTCCATTTTGATGATGGC 59.868 43.478 0.00 0.00 43.04 4.40
484 524 4.736759 GCTGCTTCTCCATTTTGATGATGG 60.737 45.833 0.00 0.00 44.39 3.51
485 525 4.142249 TGCTGCTTCTCCATTTTGATGATG 60.142 41.667 0.00 0.00 0.00 3.07
486 526 4.021229 TGCTGCTTCTCCATTTTGATGAT 58.979 39.130 0.00 0.00 0.00 2.45
487 527 3.423749 TGCTGCTTCTCCATTTTGATGA 58.576 40.909 0.00 0.00 0.00 2.92
488 528 3.861276 TGCTGCTTCTCCATTTTGATG 57.139 42.857 0.00 0.00 0.00 3.07
489 529 4.583489 CCTATGCTGCTTCTCCATTTTGAT 59.417 41.667 0.00 0.00 0.00 2.57
490 530 3.949754 CCTATGCTGCTTCTCCATTTTGA 59.050 43.478 0.00 0.00 0.00 2.69
491 531 3.949754 TCCTATGCTGCTTCTCCATTTTG 59.050 43.478 0.00 0.00 0.00 2.44
492 532 4.240881 TCCTATGCTGCTTCTCCATTTT 57.759 40.909 0.00 0.00 0.00 1.82
493 533 3.939740 TCCTATGCTGCTTCTCCATTT 57.060 42.857 0.00 0.00 0.00 2.32
494 534 4.396522 GAATCCTATGCTGCTTCTCCATT 58.603 43.478 0.00 0.00 0.00 3.16
495 535 3.244840 GGAATCCTATGCTGCTTCTCCAT 60.245 47.826 0.00 0.00 0.00 3.41
496 536 2.105477 GGAATCCTATGCTGCTTCTCCA 59.895 50.000 0.00 0.00 0.00 3.86
497 537 2.551938 GGGAATCCTATGCTGCTTCTCC 60.552 54.545 0.00 0.00 0.00 3.71
498 538 2.105477 TGGGAATCCTATGCTGCTTCTC 59.895 50.000 0.00 0.00 0.00 2.87
499 539 2.130193 TGGGAATCCTATGCTGCTTCT 58.870 47.619 0.00 0.00 0.00 2.85
500 540 2.645838 TGGGAATCCTATGCTGCTTC 57.354 50.000 0.00 0.00 0.00 3.86
501 541 2.941480 CTTGGGAATCCTATGCTGCTT 58.059 47.619 0.00 0.00 0.00 3.91
502 542 1.478288 GCTTGGGAATCCTATGCTGCT 60.478 52.381 14.71 0.00 0.00 4.24
503 543 0.957362 GCTTGGGAATCCTATGCTGC 59.043 55.000 14.71 0.00 0.00 5.25
504 544 1.233019 CGCTTGGGAATCCTATGCTG 58.767 55.000 18.48 10.20 0.00 4.41
505 545 0.536006 GCGCTTGGGAATCCTATGCT 60.536 55.000 18.48 0.00 0.00 3.79
506 546 0.819259 TGCGCTTGGGAATCCTATGC 60.819 55.000 9.73 12.48 0.00 3.14
507 547 1.605710 CTTGCGCTTGGGAATCCTATG 59.394 52.381 9.73 0.00 0.00 2.23
508 548 1.972872 CTTGCGCTTGGGAATCCTAT 58.027 50.000 9.73 0.00 0.00 2.57
509 549 0.748005 GCTTGCGCTTGGGAATCCTA 60.748 55.000 9.73 0.00 0.00 2.94
510 550 2.048603 GCTTGCGCTTGGGAATCCT 61.049 57.895 9.73 0.00 0.00 3.24
511 551 2.048603 AGCTTGCGCTTGGGAATCC 61.049 57.895 9.73 0.00 46.47 3.01
512 552 3.595819 AGCTTGCGCTTGGGAATC 58.404 55.556 9.73 0.00 46.47 2.52
521 561 3.446570 ATGCCTGGAAGCTTGCGC 61.447 61.111 13.65 11.78 0.00 6.09
522 562 2.338015 ACATGCCTGGAAGCTTGCG 61.338 57.895 13.65 8.02 40.56 4.85
523 563 1.214589 CACATGCCTGGAAGCTTGC 59.785 57.895 11.58 11.58 40.56 4.01
524 564 1.214589 GCACATGCCTGGAAGCTTG 59.785 57.895 2.10 0.00 42.10 4.01
525 565 2.338015 CGCACATGCCTGGAAGCTT 61.338 57.895 0.00 0.00 37.91 3.74
526 566 2.749044 CGCACATGCCTGGAAGCT 60.749 61.111 0.00 0.00 37.91 3.74
527 567 1.660560 ATTCGCACATGCCTGGAAGC 61.661 55.000 0.00 0.00 37.91 3.86
528 568 0.379669 GATTCGCACATGCCTGGAAG 59.620 55.000 0.00 0.00 37.91 3.46
529 569 0.035152 AGATTCGCACATGCCTGGAA 60.035 50.000 0.00 0.00 37.91 3.53
530 570 0.035152 AAGATTCGCACATGCCTGGA 60.035 50.000 0.00 0.00 37.91 3.86
531 571 0.099968 CAAGATTCGCACATGCCTGG 59.900 55.000 0.00 0.00 37.91 4.45
532 572 1.089112 TCAAGATTCGCACATGCCTG 58.911 50.000 0.00 0.00 37.91 4.85
533 573 1.945394 GATCAAGATTCGCACATGCCT 59.055 47.619 0.00 0.00 37.91 4.75
534 574 1.333524 CGATCAAGATTCGCACATGCC 60.334 52.381 0.00 0.00 37.91 4.40
535 575 1.333524 CCGATCAAGATTCGCACATGC 60.334 52.381 0.00 0.00 37.78 4.06
536 576 2.204237 TCCGATCAAGATTCGCACATG 58.796 47.619 0.00 0.00 0.00 3.21
537 577 2.602257 TCCGATCAAGATTCGCACAT 57.398 45.000 0.00 0.00 0.00 3.21
538 578 2.159114 TGATCCGATCAAGATTCGCACA 60.159 45.455 8.70 0.00 36.11 4.57
539 579 2.473816 TGATCCGATCAAGATTCGCAC 58.526 47.619 8.70 0.00 36.11 5.34
540 580 2.888834 TGATCCGATCAAGATTCGCA 57.111 45.000 8.70 0.00 36.11 5.10
548 588 9.226606 AGTAGTTAAATTTGTTGATCCGATCAA 57.773 29.630 18.10 18.10 46.30 2.57
549 589 8.786826 AGTAGTTAAATTTGTTGATCCGATCA 57.213 30.769 7.00 7.00 37.55 2.92
566 606 9.918630 GTCCAACTAGTGACAATTAGTAGTTAA 57.081 33.333 8.16 0.00 40.50 2.01
567 607 8.526147 GGTCCAACTAGTGACAATTAGTAGTTA 58.474 37.037 13.61 0.00 40.50 2.24
568 608 7.384477 GGTCCAACTAGTGACAATTAGTAGTT 58.616 38.462 13.61 0.00 42.20 2.24
569 609 6.070938 GGGTCCAACTAGTGACAATTAGTAGT 60.071 42.308 13.61 0.00 36.19 2.73
570 610 6.070995 TGGGTCCAACTAGTGACAATTAGTAG 60.071 42.308 13.61 0.00 33.09 2.57
571 611 5.781306 TGGGTCCAACTAGTGACAATTAGTA 59.219 40.000 13.61 0.00 33.09 1.82
572 612 4.595781 TGGGTCCAACTAGTGACAATTAGT 59.404 41.667 13.61 0.00 33.09 2.24
573 613 5.160607 TGGGTCCAACTAGTGACAATTAG 57.839 43.478 13.61 0.00 33.09 1.73
574 614 5.570205 TTGGGTCCAACTAGTGACAATTA 57.430 39.130 13.61 0.00 33.09 1.40
575 615 4.447138 TTGGGTCCAACTAGTGACAATT 57.553 40.909 13.61 0.00 33.09 2.32
576 616 4.335416 CATTGGGTCCAACTAGTGACAAT 58.665 43.478 13.61 7.90 38.88 2.71
577 617 3.750371 CATTGGGTCCAACTAGTGACAA 58.250 45.455 13.61 6.26 38.88 3.18
578 618 2.552155 GCATTGGGTCCAACTAGTGACA 60.552 50.000 13.61 0.00 38.88 3.58
579 619 2.084546 GCATTGGGTCCAACTAGTGAC 58.915 52.381 4.37 0.00 38.88 3.67
580 620 1.004277 GGCATTGGGTCCAACTAGTGA 59.996 52.381 4.37 0.00 38.88 3.41
581 621 1.463674 GGCATTGGGTCCAACTAGTG 58.536 55.000 4.37 0.99 38.88 2.74
582 622 0.331616 GGGCATTGGGTCCAACTAGT 59.668 55.000 4.37 0.00 42.53 2.57
583 623 0.625849 AGGGCATTGGGTCCAACTAG 59.374 55.000 4.37 0.08 46.80 2.57
584 624 1.974028 TAGGGCATTGGGTCCAACTA 58.026 50.000 4.37 0.00 46.80 2.24
585 625 1.308877 ATAGGGCATTGGGTCCAACT 58.691 50.000 4.37 0.69 46.80 3.16
586 626 1.756538 CAATAGGGCATTGGGTCCAAC 59.243 52.381 4.37 0.00 46.80 3.77
587 627 1.360852 ACAATAGGGCATTGGGTCCAA 59.639 47.619 4.78 4.78 46.80 3.53
588 628 1.006813 ACAATAGGGCATTGGGTCCA 58.993 50.000 3.04 0.00 46.80 4.02
595 635 2.566724 CACCAACCAACAATAGGGCATT 59.433 45.455 0.00 0.00 0.00 3.56
596 636 2.178580 CACCAACCAACAATAGGGCAT 58.821 47.619 0.00 0.00 0.00 4.40
597 637 1.626686 CACCAACCAACAATAGGGCA 58.373 50.000 0.00 0.00 0.00 5.36
598 638 0.894835 CCACCAACCAACAATAGGGC 59.105 55.000 0.00 0.00 0.00 5.19
599 639 1.892474 CACCACCAACCAACAATAGGG 59.108 52.381 0.00 0.00 0.00 3.53
600 640 2.870175 TCACCACCAACCAACAATAGG 58.130 47.619 0.00 0.00 0.00 2.57
601 641 3.826157 ACATCACCACCAACCAACAATAG 59.174 43.478 0.00 0.00 0.00 1.73
602 642 3.571828 CACATCACCACCAACCAACAATA 59.428 43.478 0.00 0.00 0.00 1.90
603 643 2.364970 CACATCACCACCAACCAACAAT 59.635 45.455 0.00 0.00 0.00 2.71
604 644 1.753649 CACATCACCACCAACCAACAA 59.246 47.619 0.00 0.00 0.00 2.83
605 645 1.397672 CACATCACCACCAACCAACA 58.602 50.000 0.00 0.00 0.00 3.33
606 646 0.031994 GCACATCACCACCAACCAAC 59.968 55.000 0.00 0.00 0.00 3.77
607 647 0.106268 AGCACATCACCACCAACCAA 60.106 50.000 0.00 0.00 0.00 3.67
608 648 0.767998 TAGCACATCACCACCAACCA 59.232 50.000 0.00 0.00 0.00 3.67
609 649 1.539827 GTTAGCACATCACCACCAACC 59.460 52.381 0.00 0.00 0.00 3.77
610 650 2.226330 TGTTAGCACATCACCACCAAC 58.774 47.619 0.00 0.00 0.00 3.77
611 651 2.647683 TGTTAGCACATCACCACCAA 57.352 45.000 0.00 0.00 0.00 3.67
612 652 2.819019 CAATGTTAGCACATCACCACCA 59.181 45.455 0.00 0.00 43.34 4.17
613 653 2.819608 ACAATGTTAGCACATCACCACC 59.180 45.455 0.00 0.00 43.34 4.61
614 654 5.621197 TTACAATGTTAGCACATCACCAC 57.379 39.130 0.00 0.00 43.34 4.16
615 655 6.208402 ACATTTACAATGTTAGCACATCACCA 59.792 34.615 0.00 0.00 43.34 4.17
616 656 6.620678 ACATTTACAATGTTAGCACATCACC 58.379 36.000 0.00 0.00 43.34 4.02
617 657 9.619316 TTTACATTTACAATGTTAGCACATCAC 57.381 29.630 7.40 0.00 43.34 3.06
685 725 2.333291 TCGCTGTCGGTGACTAACA 58.667 52.632 0.00 0.00 36.13 2.41
717 757 8.974060 AGAGACTTAATTACTCCAAACAACAA 57.026 30.769 0.00 0.00 0.00 2.83
793 833 6.041069 GGGTACTAGATAAGAGCAACACATCT 59.959 42.308 0.00 0.00 0.00 2.90
845 885 2.898738 CGTCCAGAGGCATCAGCT 59.101 61.111 0.00 0.00 41.70 4.24
869 909 0.962356 GCCTTGGCTATGTGTGTGCT 60.962 55.000 4.11 0.00 0.00 4.40
990 1030 0.604511 CAGCTGCCATGAGTGTGTGA 60.605 55.000 0.00 0.00 0.00 3.58
1005 1045 3.412386 GGTGTTGGACAAGATAACAGCT 58.588 45.455 10.25 0.00 44.75 4.24
1030 1070 6.546034 GTCTTGTTATAACTGGTGGGCATAAT 59.454 38.462 16.33 0.00 0.00 1.28
1088 1128 0.675522 ATTTGTGTCGGCCCCGTTAG 60.676 55.000 6.61 0.00 40.74 2.34
1089 1129 0.674269 GATTTGTGTCGGCCCCGTTA 60.674 55.000 6.61 0.00 40.74 3.18
1092 1132 1.922135 CTTGATTTGTGTCGGCCCCG 61.922 60.000 0.00 0.00 41.35 5.73
1393 1436 7.980662 CCTATGTGCATGTGGAAAATGAAAATA 59.019 33.333 0.00 0.00 31.34 1.40
1685 1732 8.754080 CACCACCATTAAAAAGGGTCATTATTA 58.246 33.333 0.00 0.00 31.03 0.98
1686 1733 7.236640 ACACCACCATTAAAAAGGGTCATTATT 59.763 33.333 0.00 0.00 31.03 1.40
1807 1855 4.693095 TGATTTGTCGCACAACATAGCTAA 59.307 37.500 0.00 0.00 37.90 3.09
1808 1856 4.249661 TGATTTGTCGCACAACATAGCTA 58.750 39.130 0.00 0.00 37.90 3.32
1809 1857 3.073678 TGATTTGTCGCACAACATAGCT 58.926 40.909 0.00 0.00 37.90 3.32
1810 1858 3.469899 TGATTTGTCGCACAACATAGC 57.530 42.857 1.85 0.00 37.90 2.97


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

AutoCloner maintained by Alex Coulton.