Multiple sequence alignment - TraesCS2B01G382500

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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 TraesCS2B01G382500 chr2B 100.000 2548 0 0 1 2548 546409720 546412267 0.000000e+00 4706
1 TraesCS2B01G382500 chr2B 81.687 415 59 13 159 566 751570296 751569892 1.890000e-86 329
2 TraesCS2B01G382500 chr2D 95.459 2004 71 13 560 2548 64508692 64510690 0.000000e+00 3179
3 TraesCS2B01G382500 chr5B 95.291 1996 76 11 566 2548 26059379 26057389 0.000000e+00 3149
4 TraesCS2B01G382500 chr5B 87.148 568 65 7 1 566 693654549 693655110 2.760000e-179 638
5 TraesCS2B01G382500 chr5B 84.790 572 74 11 1 566 45820725 45821289 1.710000e-156 562
6 TraesCS2B01G382500 chr5B 82.849 344 57 2 42 384 584862960 584863302 8.850000e-80 307
7 TraesCS2B01G382500 chr3B 94.647 1999 88 12 563 2548 53523438 53525430 0.000000e+00 3081
8 TraesCS2B01G382500 chr3B 94.183 1994 101 11 564 2548 804661029 804663016 0.000000e+00 3025
9 TraesCS2B01G382500 chr3B 93.950 2000 99 13 566 2548 687040065 687042059 0.000000e+00 3003
10 TraesCS2B01G382500 chr1B 94.392 1997 95 9 566 2548 542264939 542266932 0.000000e+00 3051
11 TraesCS2B01G382500 chrUn 94.253 2001 92 12 567 2548 60558711 60560707 0.000000e+00 3037
12 TraesCS2B01G382500 chr4B 93.624 1992 111 10 566 2548 585994908 585996892 0.000000e+00 2961
13 TraesCS2B01G382500 chr4B 93.618 1990 107 11 567 2541 645967796 645965812 0.000000e+00 2953
14 TraesCS2B01G382500 chr4B 83.591 323 49 4 12 333 437853743 437853424 1.480000e-77 300
15 TraesCS2B01G382500 chr6B 93.609 266 17 0 1 266 181092739 181092474 5.110000e-107 398
16 TraesCS2B01G382500 chr6B 81.183 372 53 14 204 564 676728795 676729160 1.490000e-72 283
17 TraesCS2B01G382500 chr7A 83.954 349 51 5 12 356 376352727 376352380 1.890000e-86 329


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 TraesCS2B01G382500 chr2B 546409720 546412267 2547 False 4706 4706 100.000 1 2548 1 chr2B.!!$F1 2547
1 TraesCS2B01G382500 chr2D 64508692 64510690 1998 False 3179 3179 95.459 560 2548 1 chr2D.!!$F1 1988
2 TraesCS2B01G382500 chr5B 26057389 26059379 1990 True 3149 3149 95.291 566 2548 1 chr5B.!!$R1 1982
3 TraesCS2B01G382500 chr5B 693654549 693655110 561 False 638 638 87.148 1 566 1 chr5B.!!$F3 565
4 TraesCS2B01G382500 chr5B 45820725 45821289 564 False 562 562 84.790 1 566 1 chr5B.!!$F1 565
5 TraesCS2B01G382500 chr3B 53523438 53525430 1992 False 3081 3081 94.647 563 2548 1 chr3B.!!$F1 1985
6 TraesCS2B01G382500 chr3B 804661029 804663016 1987 False 3025 3025 94.183 564 2548 1 chr3B.!!$F3 1984
7 TraesCS2B01G382500 chr3B 687040065 687042059 1994 False 3003 3003 93.950 566 2548 1 chr3B.!!$F2 1982
8 TraesCS2B01G382500 chr1B 542264939 542266932 1993 False 3051 3051 94.392 566 2548 1 chr1B.!!$F1 1982
9 TraesCS2B01G382500 chrUn 60558711 60560707 1996 False 3037 3037 94.253 567 2548 1 chrUn.!!$F1 1981
10 TraesCS2B01G382500 chr4B 585994908 585996892 1984 False 2961 2961 93.624 566 2548 1 chr4B.!!$F1 1982
11 TraesCS2B01G382500 chr4B 645965812 645967796 1984 True 2953 2953 93.618 567 2541 1 chr4B.!!$R2 1974

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
364 365 0.034186 TGGCTGGGCATTAAGAGTGG 60.034 55.0 0.0 0.0 0.0 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2212 2230 1.039068 CCAAAACCACATGGCAGTGA 58.961 50.0 15.61 0.0 42.05 3.41 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
20 21 4.571250 GCCTGGGCTTAAAAACGC 57.429 55.556 4.12 0.00 38.26 4.84
36 37 1.069765 CGCGGCTGATAAGTGGGAT 59.930 57.895 0.00 0.00 0.00 3.85
70 71 5.291858 TCACTACAAGCTGAAAATATGCTCG 59.708 40.000 0.00 0.00 35.85 5.03
86 87 2.168728 TGCTCGTCTCAGCTACTCTCTA 59.831 50.000 0.00 0.00 40.39 2.43
95 96 7.524202 CGTCTCAGCTACTCTCTAGGTTATCTA 60.524 44.444 0.00 0.00 0.00 1.98
112 113 9.890915 AGGTTATCTAGAGAAGTAGGAATGATT 57.109 33.333 0.00 0.00 0.00 2.57
141 142 3.909427 AATAATGCCTCATGGATGGGT 57.091 42.857 0.00 0.00 34.57 4.51
154 155 0.254178 GATGGGTGTGCAGGTGATCT 59.746 55.000 0.00 0.00 0.00 2.75
168 169 3.265221 AGGTGATCTTGAGGAGAATTGCA 59.735 43.478 0.00 0.00 38.06 4.08
225 226 1.915614 CTGCAAAAGAGCGCGTGGAT 61.916 55.000 8.43 0.00 37.31 3.41
232 233 1.373497 GAGCGCGTGGATAGGATGG 60.373 63.158 8.43 0.00 0.00 3.51
243 244 6.181190 CGTGGATAGGATGGTATCTTCTCTA 58.819 44.000 0.00 0.00 31.11 2.43
250 251 5.077159 AGGATGGTATCTTCTCTATGGGAGT 59.923 44.000 0.00 0.00 42.40 3.85
261 262 1.281867 CTATGGGAGTTGTCCAGGCAA 59.718 52.381 0.00 0.00 46.07 4.52
262 263 0.251341 ATGGGAGTTGTCCAGGCAAC 60.251 55.000 15.31 15.31 46.07 4.17
266 267 3.443588 GTTGTCCAGGCAACCACC 58.556 61.111 13.13 0.00 41.93 4.61
267 268 1.152756 GTTGTCCAGGCAACCACCT 60.153 57.895 13.13 0.00 41.93 4.00
268 269 1.150536 TTGTCCAGGCAACCACCTC 59.849 57.895 0.00 0.00 38.26 3.85
269 270 1.352622 TTGTCCAGGCAACCACCTCT 61.353 55.000 0.00 0.00 38.26 3.69
270 271 1.302832 GTCCAGGCAACCACCTCTG 60.303 63.158 0.00 0.00 38.26 3.35
271 272 2.674380 CCAGGCAACCACCTCTGC 60.674 66.667 0.00 0.00 38.26 4.26
272 273 2.433446 CAGGCAACCACCTCTGCT 59.567 61.111 0.00 0.00 38.26 4.24
273 274 1.970114 CAGGCAACCACCTCTGCTG 60.970 63.158 0.00 0.00 38.26 4.41
274 275 3.368571 GGCAACCACCTCTGCTGC 61.369 66.667 0.00 0.00 38.65 5.25
275 276 2.282040 GCAACCACCTCTGCTGCT 60.282 61.111 0.00 0.00 35.62 4.24
276 277 1.900498 GCAACCACCTCTGCTGCTT 60.900 57.895 0.00 0.00 35.62 3.91
277 278 1.458639 GCAACCACCTCTGCTGCTTT 61.459 55.000 0.00 0.00 35.62 3.51
278 279 0.313043 CAACCACCTCTGCTGCTTTG 59.687 55.000 0.00 0.00 0.00 2.77
279 280 0.825010 AACCACCTCTGCTGCTTTGG 60.825 55.000 0.00 2.57 0.00 3.28
280 281 2.633509 CCACCTCTGCTGCTTTGGC 61.634 63.158 0.00 0.00 39.26 4.52
281 282 2.282745 ACCTCTGCTGCTTTGGCC 60.283 61.111 0.00 0.00 37.74 5.36
282 283 2.282674 CCTCTGCTGCTTTGGCCA 60.283 61.111 0.00 0.00 37.74 5.36
283 284 2.341101 CCTCTGCTGCTTTGGCCAG 61.341 63.158 5.11 0.00 37.74 4.85
284 285 1.303074 CTCTGCTGCTTTGGCCAGA 60.303 57.895 5.11 0.00 36.12 3.86
285 286 1.303074 TCTGCTGCTTTGGCCAGAG 60.303 57.895 18.91 18.91 33.85 3.35
286 287 2.987547 TGCTGCTTTGGCCAGAGC 60.988 61.111 35.26 35.26 38.84 4.09
297 298 4.056805 CCAGAGCCAGGCTAAGGA 57.943 61.111 22.24 0.00 39.88 3.36
298 299 2.300996 CCAGAGCCAGGCTAAGGAA 58.699 57.895 22.24 0.00 39.88 3.36
299 300 0.179936 CCAGAGCCAGGCTAAGGAAG 59.820 60.000 22.24 6.56 39.88 3.46
300 301 1.198713 CAGAGCCAGGCTAAGGAAGA 58.801 55.000 16.16 0.00 39.88 2.87
301 302 1.556911 CAGAGCCAGGCTAAGGAAGAA 59.443 52.381 16.16 0.00 39.88 2.52
302 303 2.026822 CAGAGCCAGGCTAAGGAAGAAA 60.027 50.000 16.16 0.00 39.88 2.52
303 304 2.238395 AGAGCCAGGCTAAGGAAGAAAG 59.762 50.000 16.16 0.00 39.88 2.62
304 305 2.237392 GAGCCAGGCTAAGGAAGAAAGA 59.763 50.000 16.16 0.00 39.88 2.52
305 306 2.238395 AGCCAGGCTAAGGAAGAAAGAG 59.762 50.000 14.18 0.00 36.99 2.85
306 307 2.637947 CCAGGCTAAGGAAGAAAGAGC 58.362 52.381 0.00 0.00 0.00 4.09
307 308 2.238395 CCAGGCTAAGGAAGAAAGAGCT 59.762 50.000 0.00 0.00 33.57 4.09
308 309 3.269178 CAGGCTAAGGAAGAAAGAGCTG 58.731 50.000 0.00 0.00 33.57 4.24
309 310 2.909662 AGGCTAAGGAAGAAAGAGCTGT 59.090 45.455 0.00 0.00 33.57 4.40
310 311 3.006247 GGCTAAGGAAGAAAGAGCTGTG 58.994 50.000 0.00 0.00 33.57 3.66
311 312 3.006247 GCTAAGGAAGAAAGAGCTGTGG 58.994 50.000 0.00 0.00 0.00 4.17
312 313 3.307059 GCTAAGGAAGAAAGAGCTGTGGA 60.307 47.826 0.00 0.00 0.00 4.02
313 314 4.625083 GCTAAGGAAGAAAGAGCTGTGGAT 60.625 45.833 0.00 0.00 0.00 3.41
314 315 3.347077 AGGAAGAAAGAGCTGTGGATG 57.653 47.619 0.00 0.00 0.00 3.51
315 316 2.909006 AGGAAGAAAGAGCTGTGGATGA 59.091 45.455 0.00 0.00 0.00 2.92
316 317 3.328931 AGGAAGAAAGAGCTGTGGATGAA 59.671 43.478 0.00 0.00 0.00 2.57
317 318 3.688673 GGAAGAAAGAGCTGTGGATGAAG 59.311 47.826 0.00 0.00 0.00 3.02
318 319 4.322567 GAAGAAAGAGCTGTGGATGAAGT 58.677 43.478 0.00 0.00 0.00 3.01
319 320 5.482908 GAAGAAAGAGCTGTGGATGAAGTA 58.517 41.667 0.00 0.00 0.00 2.24
320 321 4.826556 AGAAAGAGCTGTGGATGAAGTAC 58.173 43.478 0.00 0.00 0.00 2.73
321 322 4.530161 AGAAAGAGCTGTGGATGAAGTACT 59.470 41.667 0.00 0.00 0.00 2.73
322 323 5.717178 AGAAAGAGCTGTGGATGAAGTACTA 59.283 40.000 0.00 0.00 0.00 1.82
323 324 6.382570 AGAAAGAGCTGTGGATGAAGTACTAT 59.617 38.462 0.00 0.00 0.00 2.12
324 325 7.561722 AGAAAGAGCTGTGGATGAAGTACTATA 59.438 37.037 0.00 0.00 0.00 1.31
325 326 7.847711 AAGAGCTGTGGATGAAGTACTATAT 57.152 36.000 0.00 0.00 0.00 0.86
326 327 7.225784 AGAGCTGTGGATGAAGTACTATATG 57.774 40.000 0.00 0.00 0.00 1.78
327 328 7.007116 AGAGCTGTGGATGAAGTACTATATGA 58.993 38.462 0.00 0.00 0.00 2.15
328 329 7.507277 AGAGCTGTGGATGAAGTACTATATGAA 59.493 37.037 0.00 0.00 0.00 2.57
329 330 7.665690 AGCTGTGGATGAAGTACTATATGAAG 58.334 38.462 0.00 0.00 0.00 3.02
330 331 7.507277 AGCTGTGGATGAAGTACTATATGAAGA 59.493 37.037 0.00 0.00 0.00 2.87
331 332 8.144478 GCTGTGGATGAAGTACTATATGAAGAA 58.856 37.037 0.00 0.00 0.00 2.52
332 333 9.689976 CTGTGGATGAAGTACTATATGAAGAAG 57.310 37.037 0.00 0.00 0.00 2.85
333 334 9.421399 TGTGGATGAAGTACTATATGAAGAAGA 57.579 33.333 0.00 0.00 0.00 2.87
339 340 9.809096 TGAAGTACTATATGAAGAAGAAAGCAG 57.191 33.333 0.00 0.00 0.00 4.24
343 344 9.255304 GTACTATATGAAGAAGAAAGCAGAAGG 57.745 37.037 0.00 0.00 0.00 3.46
344 345 6.765512 ACTATATGAAGAAGAAAGCAGAAGGC 59.234 38.462 0.00 0.00 45.30 4.35
354 355 4.355720 CAGAAGGCTGGCTGGGCA 62.356 66.667 3.84 0.00 38.51 5.36
355 356 3.345028 AGAAGGCTGGCTGGGCAT 61.345 61.111 3.84 0.00 0.00 4.40
356 357 2.363406 GAAGGCTGGCTGGGCATT 60.363 61.111 3.84 2.98 36.40 3.56
357 358 1.076777 GAAGGCTGGCTGGGCATTA 60.077 57.895 3.84 0.00 33.82 1.90
358 359 0.684153 GAAGGCTGGCTGGGCATTAA 60.684 55.000 3.84 0.00 33.82 1.40
359 360 0.685458 AAGGCTGGCTGGGCATTAAG 60.685 55.000 3.84 0.00 31.88 1.85
360 361 1.076777 GGCTGGCTGGGCATTAAGA 60.077 57.895 0.00 0.00 0.00 2.10
361 362 1.105759 GGCTGGCTGGGCATTAAGAG 61.106 60.000 0.00 0.00 0.00 2.85
362 363 0.394899 GCTGGCTGGGCATTAAGAGT 60.395 55.000 0.00 0.00 0.00 3.24
363 364 1.386533 CTGGCTGGGCATTAAGAGTG 58.613 55.000 0.00 0.00 0.00 3.51
364 365 0.034186 TGGCTGGGCATTAAGAGTGG 60.034 55.000 0.00 0.00 0.00 4.00
365 366 0.753111 GGCTGGGCATTAAGAGTGGG 60.753 60.000 0.00 0.00 0.00 4.61
366 367 0.255890 GCTGGGCATTAAGAGTGGGA 59.744 55.000 0.00 0.00 0.00 4.37
367 368 1.133668 GCTGGGCATTAAGAGTGGGAT 60.134 52.381 0.00 0.00 0.00 3.85
368 369 2.579873 CTGGGCATTAAGAGTGGGATG 58.420 52.381 0.00 0.00 0.00 3.51
369 370 1.322442 GGGCATTAAGAGTGGGATGC 58.678 55.000 0.00 0.00 43.06 3.91
370 371 1.133668 GGGCATTAAGAGTGGGATGCT 60.134 52.381 7.06 0.00 43.26 3.79
371 372 2.225467 GGCATTAAGAGTGGGATGCTC 58.775 52.381 7.06 0.00 43.26 4.26
372 373 1.869767 GCATTAAGAGTGGGATGCTCG 59.130 52.381 0.00 0.00 41.16 5.03
373 374 2.743183 GCATTAAGAGTGGGATGCTCGT 60.743 50.000 0.00 0.00 41.16 4.18
374 375 3.535561 CATTAAGAGTGGGATGCTCGTT 58.464 45.455 0.00 0.00 37.99 3.85
375 376 2.672961 TAAGAGTGGGATGCTCGTTG 57.327 50.000 0.00 0.00 37.99 4.10
376 377 0.976641 AAGAGTGGGATGCTCGTTGA 59.023 50.000 0.00 0.00 37.99 3.18
377 378 0.976641 AGAGTGGGATGCTCGTTGAA 59.023 50.000 0.00 0.00 37.99 2.69
378 379 1.066573 AGAGTGGGATGCTCGTTGAAG 60.067 52.381 0.00 0.00 37.99 3.02
379 380 0.036010 AGTGGGATGCTCGTTGAAGG 60.036 55.000 0.00 0.00 0.00 3.46
380 381 0.036388 GTGGGATGCTCGTTGAAGGA 60.036 55.000 0.00 0.00 0.00 3.36
381 382 0.911769 TGGGATGCTCGTTGAAGGAT 59.088 50.000 0.00 0.00 0.00 3.24
382 383 2.115427 TGGGATGCTCGTTGAAGGATA 58.885 47.619 0.00 0.00 0.00 2.59
383 384 2.503765 TGGGATGCTCGTTGAAGGATAA 59.496 45.455 0.00 0.00 0.00 1.75
384 385 3.054728 TGGGATGCTCGTTGAAGGATAAA 60.055 43.478 0.00 0.00 0.00 1.40
385 386 3.561725 GGGATGCTCGTTGAAGGATAAAG 59.438 47.826 0.00 0.00 0.00 1.85
386 387 4.192317 GGATGCTCGTTGAAGGATAAAGT 58.808 43.478 0.00 0.00 0.00 2.66
387 388 5.357257 GGATGCTCGTTGAAGGATAAAGTA 58.643 41.667 0.00 0.00 0.00 2.24
388 389 5.463724 GGATGCTCGTTGAAGGATAAAGTAG 59.536 44.000 0.00 0.00 0.00 2.57
389 390 4.755411 TGCTCGTTGAAGGATAAAGTAGG 58.245 43.478 0.00 0.00 0.00 3.18
390 391 4.464951 TGCTCGTTGAAGGATAAAGTAGGA 59.535 41.667 0.00 0.00 0.00 2.94
391 392 5.044558 GCTCGTTGAAGGATAAAGTAGGAG 58.955 45.833 0.00 0.00 0.00 3.69
392 393 5.163540 GCTCGTTGAAGGATAAAGTAGGAGA 60.164 44.000 0.00 0.00 0.00 3.71
393 394 6.627508 GCTCGTTGAAGGATAAAGTAGGAGAA 60.628 42.308 0.00 0.00 0.00 2.87
394 395 7.419711 TCGTTGAAGGATAAAGTAGGAGAAT 57.580 36.000 0.00 0.00 0.00 2.40
395 396 7.490000 TCGTTGAAGGATAAAGTAGGAGAATC 58.510 38.462 0.00 0.00 0.00 2.52
409 410 3.710209 GAGAATCCCCCATGTATCAGG 57.290 52.381 0.00 0.00 0.00 3.86
410 411 1.707427 AGAATCCCCCATGTATCAGGC 59.293 52.381 0.00 0.00 0.00 4.85
411 412 1.707427 GAATCCCCCATGTATCAGGCT 59.293 52.381 0.00 0.00 0.00 4.58
412 413 1.838611 ATCCCCCATGTATCAGGCTT 58.161 50.000 0.00 0.00 0.00 4.35
413 414 1.607225 TCCCCCATGTATCAGGCTTT 58.393 50.000 0.00 0.00 0.00 3.51
414 415 1.494721 TCCCCCATGTATCAGGCTTTC 59.505 52.381 0.00 0.00 0.00 2.62
415 416 1.496429 CCCCCATGTATCAGGCTTTCT 59.504 52.381 0.00 0.00 0.00 2.52
416 417 2.579873 CCCCATGTATCAGGCTTTCTG 58.420 52.381 0.00 0.00 44.68 3.02
417 418 1.952296 CCCATGTATCAGGCTTTCTGC 59.048 52.381 0.00 0.00 43.06 4.26
418 419 2.422519 CCCATGTATCAGGCTTTCTGCT 60.423 50.000 0.00 0.00 43.06 4.24
419 420 2.617308 CCATGTATCAGGCTTTCTGCTG 59.383 50.000 0.00 0.00 43.06 4.41
420 421 1.742761 TGTATCAGGCTTTCTGCTGC 58.257 50.000 0.00 0.00 43.06 5.25
421 422 0.654683 GTATCAGGCTTTCTGCTGCG 59.345 55.000 0.00 0.00 43.06 5.18
422 423 0.250234 TATCAGGCTTTCTGCTGCGT 59.750 50.000 0.00 0.00 43.06 5.24
423 424 0.250234 ATCAGGCTTTCTGCTGCGTA 59.750 50.000 0.00 0.00 43.06 4.42
424 425 0.390340 TCAGGCTTTCTGCTGCGTAG 60.390 55.000 0.00 0.00 43.06 3.51
425 426 0.390340 CAGGCTTTCTGCTGCGTAGA 60.390 55.000 4.08 0.00 42.39 2.59
426 427 0.539051 AGGCTTTCTGCTGCGTAGAT 59.461 50.000 4.08 0.00 42.39 1.98
427 428 0.654683 GGCTTTCTGCTGCGTAGATG 59.345 55.000 4.08 0.00 42.39 2.90
428 429 0.654683 GCTTTCTGCTGCGTAGATGG 59.345 55.000 4.08 0.00 38.95 3.51
429 430 2.009042 GCTTTCTGCTGCGTAGATGGT 61.009 52.381 4.08 0.00 38.95 3.55
430 431 1.662629 CTTTCTGCTGCGTAGATGGTG 59.337 52.381 4.08 0.00 0.00 4.17
431 432 0.740868 TTCTGCTGCGTAGATGGTGC 60.741 55.000 4.08 0.00 0.00 5.01
432 433 1.448365 CTGCTGCGTAGATGGTGCA 60.448 57.895 4.08 0.00 37.07 4.57
433 434 0.812811 CTGCTGCGTAGATGGTGCAT 60.813 55.000 4.08 0.00 38.07 3.96
434 435 0.392863 TGCTGCGTAGATGGTGCATT 60.393 50.000 4.08 0.00 38.07 3.56
435 436 0.734889 GCTGCGTAGATGGTGCATTT 59.265 50.000 4.08 0.00 38.07 2.32
436 437 1.532505 GCTGCGTAGATGGTGCATTTG 60.533 52.381 4.08 0.00 38.07 2.32
437 438 2.009051 CTGCGTAGATGGTGCATTTGA 58.991 47.619 0.00 0.00 38.07 2.69
438 439 2.419673 CTGCGTAGATGGTGCATTTGAA 59.580 45.455 0.00 0.00 38.07 2.69
439 440 3.016031 TGCGTAGATGGTGCATTTGAAT 58.984 40.909 0.00 0.00 32.86 2.57
440 441 3.443329 TGCGTAGATGGTGCATTTGAATT 59.557 39.130 0.00 0.00 32.86 2.17
441 442 4.082300 TGCGTAGATGGTGCATTTGAATTT 60.082 37.500 0.00 0.00 32.86 1.82
442 443 4.266029 GCGTAGATGGTGCATTTGAATTTG 59.734 41.667 0.00 0.00 0.00 2.32
443 444 5.401550 CGTAGATGGTGCATTTGAATTTGT 58.598 37.500 0.00 0.00 0.00 2.83
444 445 5.512788 CGTAGATGGTGCATTTGAATTTGTC 59.487 40.000 0.00 0.00 0.00 3.18
445 446 4.487948 AGATGGTGCATTTGAATTTGTCG 58.512 39.130 0.00 0.00 0.00 4.35
446 447 3.023946 TGGTGCATTTGAATTTGTCGG 57.976 42.857 0.00 0.00 0.00 4.79
447 448 2.363680 TGGTGCATTTGAATTTGTCGGT 59.636 40.909 0.00 0.00 0.00 4.69
448 449 3.570125 TGGTGCATTTGAATTTGTCGGTA 59.430 39.130 0.00 0.00 0.00 4.02
449 450 4.165779 GGTGCATTTGAATTTGTCGGTAG 58.834 43.478 0.00 0.00 0.00 3.18
450 451 4.165779 GTGCATTTGAATTTGTCGGTAGG 58.834 43.478 0.00 0.00 0.00 3.18
451 452 3.179048 GCATTTGAATTTGTCGGTAGGC 58.821 45.455 0.00 0.00 0.00 3.93
452 453 3.366883 GCATTTGAATTTGTCGGTAGGCA 60.367 43.478 0.00 0.00 0.00 4.75
453 454 4.414852 CATTTGAATTTGTCGGTAGGCAG 58.585 43.478 0.00 0.00 31.37 4.85
454 455 2.107950 TGAATTTGTCGGTAGGCAGG 57.892 50.000 0.00 0.00 31.37 4.85
455 456 1.349688 TGAATTTGTCGGTAGGCAGGT 59.650 47.619 0.00 0.00 31.37 4.00
456 457 2.224670 TGAATTTGTCGGTAGGCAGGTT 60.225 45.455 0.00 0.00 31.37 3.50
457 458 2.579410 ATTTGTCGGTAGGCAGGTTT 57.421 45.000 0.00 0.00 31.37 3.27
458 459 3.706600 ATTTGTCGGTAGGCAGGTTTA 57.293 42.857 0.00 0.00 31.37 2.01
459 460 2.754946 TTGTCGGTAGGCAGGTTTAG 57.245 50.000 0.00 0.00 31.37 1.85
460 461 1.927487 TGTCGGTAGGCAGGTTTAGA 58.073 50.000 0.00 0.00 0.00 2.10
461 462 2.463752 TGTCGGTAGGCAGGTTTAGAT 58.536 47.619 0.00 0.00 0.00 1.98
462 463 2.167693 TGTCGGTAGGCAGGTTTAGATG 59.832 50.000 0.00 0.00 0.00 2.90
463 464 1.760613 TCGGTAGGCAGGTTTAGATGG 59.239 52.381 0.00 0.00 0.00 3.51
464 465 1.485066 CGGTAGGCAGGTTTAGATGGT 59.515 52.381 0.00 0.00 0.00 3.55
465 466 2.093128 CGGTAGGCAGGTTTAGATGGTT 60.093 50.000 0.00 0.00 0.00 3.67
466 467 3.621461 CGGTAGGCAGGTTTAGATGGTTT 60.621 47.826 0.00 0.00 0.00 3.27
467 468 4.383335 CGGTAGGCAGGTTTAGATGGTTTA 60.383 45.833 0.00 0.00 0.00 2.01
468 469 5.686650 CGGTAGGCAGGTTTAGATGGTTTAT 60.687 44.000 0.00 0.00 0.00 1.40
469 470 6.463331 CGGTAGGCAGGTTTAGATGGTTTATA 60.463 42.308 0.00 0.00 0.00 0.98
470 471 7.284820 GGTAGGCAGGTTTAGATGGTTTATAA 58.715 38.462 0.00 0.00 0.00 0.98
471 472 7.444487 GGTAGGCAGGTTTAGATGGTTTATAAG 59.556 40.741 0.00 0.00 0.00 1.73
472 473 6.970191 AGGCAGGTTTAGATGGTTTATAAGT 58.030 36.000 0.00 0.00 0.00 2.24
473 474 6.828785 AGGCAGGTTTAGATGGTTTATAAGTG 59.171 38.462 0.00 0.00 0.00 3.16
474 475 6.826741 GGCAGGTTTAGATGGTTTATAAGTGA 59.173 38.462 0.00 0.00 0.00 3.41
475 476 7.338449 GGCAGGTTTAGATGGTTTATAAGTGAA 59.662 37.037 0.00 0.00 0.00 3.18
476 477 8.182227 GCAGGTTTAGATGGTTTATAAGTGAAC 58.818 37.037 0.00 0.00 0.00 3.18
477 478 9.449719 CAGGTTTAGATGGTTTATAAGTGAACT 57.550 33.333 0.00 0.00 0.00 3.01
484 485 7.980099 AGATGGTTTATAAGTGAACTAAGTCCG 59.020 37.037 0.00 0.00 0.00 4.79
485 486 7.230849 TGGTTTATAAGTGAACTAAGTCCGA 57.769 36.000 0.00 0.00 0.00 4.55
486 487 7.669427 TGGTTTATAAGTGAACTAAGTCCGAA 58.331 34.615 0.00 0.00 0.00 4.30
487 488 8.316214 TGGTTTATAAGTGAACTAAGTCCGAAT 58.684 33.333 0.00 0.00 0.00 3.34
488 489 9.159364 GGTTTATAAGTGAACTAAGTCCGAATT 57.841 33.333 0.00 0.00 0.00 2.17
495 496 9.503399 AAGTGAACTAAGTCCGAATTTAGATTT 57.497 29.630 0.00 0.00 31.16 2.17
496 497 9.503399 AGTGAACTAAGTCCGAATTTAGATTTT 57.497 29.630 0.00 0.00 31.16 1.82
501 502 8.947115 ACTAAGTCCGAATTTAGATTTTTCAGG 58.053 33.333 0.00 0.00 31.16 3.86
502 503 6.196079 AGTCCGAATTTAGATTTTTCAGGC 57.804 37.500 0.00 0.00 0.00 4.85
503 504 5.125578 AGTCCGAATTTAGATTTTTCAGGCC 59.874 40.000 0.00 0.00 0.00 5.19
504 505 4.095782 TCCGAATTTAGATTTTTCAGGCCG 59.904 41.667 0.00 0.00 0.00 6.13
505 506 4.351192 CGAATTTAGATTTTTCAGGCCGG 58.649 43.478 0.00 0.00 0.00 6.13
506 507 4.095782 CGAATTTAGATTTTTCAGGCCGGA 59.904 41.667 5.05 0.00 0.00 5.14
507 508 5.582550 GAATTTAGATTTTTCAGGCCGGAG 58.417 41.667 5.05 0.00 0.00 4.63
526 527 2.361230 GGAGCAAAACCCCTCCCG 60.361 66.667 0.00 0.00 41.42 5.14
527 528 3.062466 GAGCAAAACCCCTCCCGC 61.062 66.667 0.00 0.00 0.00 6.13
537 538 4.832608 CCTCCCGCGGGCTGTAAC 62.833 72.222 39.89 0.00 34.68 2.50
541 542 4.728102 CCGCGGGCTGTAACGACA 62.728 66.667 20.10 0.00 0.00 4.35
542 543 3.475774 CGCGGGCTGTAACGACAC 61.476 66.667 0.00 0.00 0.00 3.67
543 544 2.356553 GCGGGCTGTAACGACACA 60.357 61.111 0.00 0.00 0.00 3.72
544 545 1.740296 GCGGGCTGTAACGACACAT 60.740 57.895 0.00 0.00 0.00 3.21
545 546 1.966493 GCGGGCTGTAACGACACATG 61.966 60.000 0.00 0.00 0.00 3.21
546 547 1.358725 CGGGCTGTAACGACACATGG 61.359 60.000 0.00 0.00 0.00 3.66
547 548 0.036765 GGGCTGTAACGACACATGGA 60.037 55.000 0.00 0.00 0.00 3.41
548 549 1.406887 GGGCTGTAACGACACATGGAT 60.407 52.381 0.00 0.00 0.00 3.41
549 550 2.356135 GGCTGTAACGACACATGGATT 58.644 47.619 0.00 0.00 0.00 3.01
550 551 3.527533 GGCTGTAACGACACATGGATTA 58.472 45.455 0.00 0.00 0.00 1.75
551 552 4.127171 GGCTGTAACGACACATGGATTAT 58.873 43.478 0.00 0.00 0.00 1.28
552 553 4.024893 GGCTGTAACGACACATGGATTATG 60.025 45.833 0.00 0.00 42.68 1.90
697 698 2.915659 TGGCGTCTCCGTCAGGTT 60.916 61.111 0.00 0.00 45.14 3.50
916 917 2.280797 GAGCACAACAGCGGTGGA 60.281 61.111 20.20 0.00 40.15 4.02
993 994 2.363795 AGATCCCGTTCGGCTCCA 60.364 61.111 5.66 0.00 0.00 3.86
1014 1015 0.391661 GCTCCATGTCTTCCGCAAGA 60.392 55.000 0.00 0.00 43.02 3.02
1020 1021 1.218316 GTCTTCCGCAAGATCCCGT 59.782 57.895 0.00 0.00 40.88 5.28
1099 1102 2.813908 GTCGGGCGAGCGTTGATT 60.814 61.111 0.00 0.00 0.00 2.57
1208 1212 0.530744 CGTGGTCGGGATCTTTGAGA 59.469 55.000 0.00 0.00 0.00 3.27
1242 1246 0.888736 TTCCGTGTTCATGCAGGTGG 60.889 55.000 0.00 0.00 0.00 4.61
1281 1285 0.392193 CGATGCTCTGGCCAAGACTT 60.392 55.000 7.01 0.00 37.74 3.01
1405 1409 0.808125 CGCACTGACAGAGAGCTAGT 59.192 55.000 10.08 0.00 36.21 2.57
1521 1525 3.620427 TGGTAATCGCACTGGTTGTAT 57.380 42.857 0.00 0.00 0.00 2.29
1627 1632 7.118390 TGTTGGTCAAAGTTGTTTAAATGTTGG 59.882 33.333 0.00 0.00 0.00 3.77
1751 1763 4.280677 TCCAGAGCCAAACAATTAAGGTTG 59.719 41.667 0.00 0.00 35.25 3.77
1758 1770 7.740805 AGCCAAACAATTAAGGTTGGAAATTA 58.259 30.769 15.07 0.00 33.40 1.40
2090 2102 7.083628 TGGGTAGGGAAGGAATGTATACATAA 58.916 38.462 18.56 0.00 35.10 1.90
2314 2335 7.878477 AAATTTGCATGTTAGTTCATGACTG 57.122 32.000 10.28 0.00 45.41 3.51
2350 2378 2.285743 GGGCTTCTCACCCCCTCT 60.286 66.667 0.00 0.00 42.01 3.69
2351 2379 1.925972 GGGCTTCTCACCCCCTCTT 60.926 63.158 0.00 0.00 42.01 2.85
2352 2380 1.501654 GGGCTTCTCACCCCCTCTTT 61.502 60.000 0.00 0.00 42.01 2.52
2541 2580 3.519908 ATGACGAAACATGACACAACG 57.480 42.857 0.00 0.00 0.00 4.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 2.817538 TATCAGCCGCGTTTTTAAGC 57.182 45.000 4.92 0.00 0.00 3.09
10 11 4.088648 CACTTATCAGCCGCGTTTTTAAG 58.911 43.478 4.92 8.25 0.00 1.85
18 19 0.317160 TATCCCACTTATCAGCCGCG 59.683 55.000 0.00 0.00 0.00 6.46
19 20 2.543777 TTATCCCACTTATCAGCCGC 57.456 50.000 0.00 0.00 0.00 6.53
20 21 3.560068 GTGTTTATCCCACTTATCAGCCG 59.440 47.826 0.00 0.00 0.00 5.52
36 37 5.666462 TCAGCTTGTAGTGACTTGTGTTTA 58.334 37.500 0.00 0.00 0.00 2.01
70 71 6.531021 AGATAACCTAGAGAGTAGCTGAGAC 58.469 44.000 0.00 0.00 0.00 3.36
86 87 9.890915 AATCATTCCTACTTCTCTAGATAACCT 57.109 33.333 0.00 0.00 0.00 3.50
95 96 8.697507 AAAACACAAATCATTCCTACTTCTCT 57.302 30.769 0.00 0.00 0.00 3.10
112 113 7.473735 TCCATGAGGCATTATTAAAACACAA 57.526 32.000 0.00 0.00 33.74 3.33
141 142 1.277273 CTCCTCAAGATCACCTGCACA 59.723 52.381 0.00 0.00 0.00 4.57
154 155 2.040813 AGAAGCCTGCAATTCTCCTCAA 59.959 45.455 3.32 0.00 29.80 3.02
168 169 2.519771 TCCATTGATTGCAGAAGCCT 57.480 45.000 0.00 0.00 41.13 4.58
225 226 6.278239 ACTCCCATAGAGAAGATACCATCCTA 59.722 42.308 0.00 0.00 46.50 2.94
232 233 5.598830 TGGACAACTCCCATAGAGAAGATAC 59.401 44.000 0.00 0.00 46.50 2.24
243 244 0.251341 GTTGCCTGGACAACTCCCAT 60.251 55.000 19.82 0.00 45.20 4.00
250 251 1.150536 GAGGTGGTTGCCTGGACAA 59.849 57.895 0.00 0.00 39.34 3.18
261 262 1.228367 CCAAAGCAGCAGAGGTGGT 60.228 57.895 0.00 0.00 43.62 4.16
262 263 2.633509 GCCAAAGCAGCAGAGGTGG 61.634 63.158 0.00 0.00 39.53 4.61
263 264 2.633509 GGCCAAAGCAGCAGAGGTG 61.634 63.158 0.00 0.00 42.56 4.00
264 265 2.282745 GGCCAAAGCAGCAGAGGT 60.283 61.111 0.00 0.00 42.56 3.85
265 266 2.282674 TGGCCAAAGCAGCAGAGG 60.283 61.111 0.61 0.00 42.56 3.69
266 267 1.303074 TCTGGCCAAAGCAGCAGAG 60.303 57.895 7.01 0.00 42.56 3.35
267 268 1.303074 CTCTGGCCAAAGCAGCAGA 60.303 57.895 7.01 0.00 42.56 4.26
268 269 2.991076 GCTCTGGCCAAAGCAGCAG 61.991 63.158 26.44 1.57 42.56 4.24
269 270 2.987547 GCTCTGGCCAAAGCAGCA 60.988 61.111 26.44 0.00 42.56 4.41
279 280 1.915078 TTCCTTAGCCTGGCTCTGGC 61.915 60.000 27.16 13.00 46.61 4.85
280 281 0.179936 CTTCCTTAGCCTGGCTCTGG 59.820 60.000 27.16 25.92 40.44 3.86
281 282 1.198713 TCTTCCTTAGCCTGGCTCTG 58.801 55.000 27.16 18.24 40.44 3.35
282 283 1.958288 TTCTTCCTTAGCCTGGCTCT 58.042 50.000 27.16 4.80 40.44 4.09
283 284 2.237392 TCTTTCTTCCTTAGCCTGGCTC 59.763 50.000 27.16 0.00 40.44 4.70
284 285 2.238395 CTCTTTCTTCCTTAGCCTGGCT 59.762 50.000 26.52 26.52 43.41 4.75
285 286 2.637947 CTCTTTCTTCCTTAGCCTGGC 58.362 52.381 11.65 11.65 0.00 4.85
286 287 2.238395 AGCTCTTTCTTCCTTAGCCTGG 59.762 50.000 0.00 0.00 33.63 4.45
287 288 3.269178 CAGCTCTTTCTTCCTTAGCCTG 58.731 50.000 0.00 0.00 33.63 4.85
288 289 2.909662 ACAGCTCTTTCTTCCTTAGCCT 59.090 45.455 0.00 0.00 33.63 4.58
289 290 3.006247 CACAGCTCTTTCTTCCTTAGCC 58.994 50.000 0.00 0.00 33.63 3.93
290 291 3.006247 CCACAGCTCTTTCTTCCTTAGC 58.994 50.000 0.00 0.00 0.00 3.09
291 292 4.543590 TCCACAGCTCTTTCTTCCTTAG 57.456 45.455 0.00 0.00 0.00 2.18
292 293 4.532126 TCATCCACAGCTCTTTCTTCCTTA 59.468 41.667 0.00 0.00 0.00 2.69
293 294 3.328931 TCATCCACAGCTCTTTCTTCCTT 59.671 43.478 0.00 0.00 0.00 3.36
294 295 2.909006 TCATCCACAGCTCTTTCTTCCT 59.091 45.455 0.00 0.00 0.00 3.36
295 296 3.340814 TCATCCACAGCTCTTTCTTCC 57.659 47.619 0.00 0.00 0.00 3.46
296 297 4.322567 ACTTCATCCACAGCTCTTTCTTC 58.677 43.478 0.00 0.00 0.00 2.87
297 298 4.363991 ACTTCATCCACAGCTCTTTCTT 57.636 40.909 0.00 0.00 0.00 2.52
298 299 4.530161 AGTACTTCATCCACAGCTCTTTCT 59.470 41.667 0.00 0.00 0.00 2.52
299 300 4.826556 AGTACTTCATCCACAGCTCTTTC 58.173 43.478 0.00 0.00 0.00 2.62
300 301 4.899352 AGTACTTCATCCACAGCTCTTT 57.101 40.909 0.00 0.00 0.00 2.52
301 302 7.507277 TCATATAGTACTTCATCCACAGCTCTT 59.493 37.037 0.00 0.00 0.00 2.85
302 303 7.007116 TCATATAGTACTTCATCCACAGCTCT 58.993 38.462 0.00 0.00 0.00 4.09
303 304 7.220741 TCATATAGTACTTCATCCACAGCTC 57.779 40.000 0.00 0.00 0.00 4.09
304 305 7.507277 TCTTCATATAGTACTTCATCCACAGCT 59.493 37.037 0.00 0.00 0.00 4.24
305 306 7.661968 TCTTCATATAGTACTTCATCCACAGC 58.338 38.462 0.00 0.00 0.00 4.40
306 307 9.689976 CTTCTTCATATAGTACTTCATCCACAG 57.310 37.037 0.00 0.00 0.00 3.66
307 308 9.421399 TCTTCTTCATATAGTACTTCATCCACA 57.579 33.333 0.00 0.00 0.00 4.17
313 314 9.809096 CTGCTTTCTTCTTCATATAGTACTTCA 57.191 33.333 0.00 0.00 0.00 3.02
317 318 9.255304 CCTTCTGCTTTCTTCTTCATATAGTAC 57.745 37.037 0.00 0.00 0.00 2.73
318 319 7.928706 GCCTTCTGCTTTCTTCTTCATATAGTA 59.071 37.037 0.00 0.00 36.87 1.82
319 320 6.765512 GCCTTCTGCTTTCTTCTTCATATAGT 59.234 38.462 0.00 0.00 36.87 2.12
320 321 7.188468 GCCTTCTGCTTTCTTCTTCATATAG 57.812 40.000 0.00 0.00 36.87 1.31
337 338 3.657038 ATGCCCAGCCAGCCTTCTG 62.657 63.158 0.00 0.00 40.02 3.02
338 339 1.574526 TAATGCCCAGCCAGCCTTCT 61.575 55.000 0.00 0.00 0.00 2.85
339 340 0.684153 TTAATGCCCAGCCAGCCTTC 60.684 55.000 0.00 0.00 0.00 3.46
340 341 0.685458 CTTAATGCCCAGCCAGCCTT 60.685 55.000 0.00 0.00 0.00 4.35
341 342 1.076485 CTTAATGCCCAGCCAGCCT 60.076 57.895 0.00 0.00 0.00 4.58
342 343 1.076777 TCTTAATGCCCAGCCAGCC 60.077 57.895 0.00 0.00 0.00 4.85
343 344 0.394899 ACTCTTAATGCCCAGCCAGC 60.395 55.000 0.00 0.00 0.00 4.85
344 345 1.386533 CACTCTTAATGCCCAGCCAG 58.613 55.000 0.00 0.00 0.00 4.85
345 346 0.034186 CCACTCTTAATGCCCAGCCA 60.034 55.000 0.00 0.00 0.00 4.75
346 347 0.753111 CCCACTCTTAATGCCCAGCC 60.753 60.000 0.00 0.00 0.00 4.85
347 348 0.255890 TCCCACTCTTAATGCCCAGC 59.744 55.000 0.00 0.00 0.00 4.85
348 349 2.579873 CATCCCACTCTTAATGCCCAG 58.420 52.381 0.00 0.00 0.00 4.45
349 350 1.410083 GCATCCCACTCTTAATGCCCA 60.410 52.381 0.00 0.00 38.82 5.36
350 351 1.133668 AGCATCCCACTCTTAATGCCC 60.134 52.381 2.78 0.00 44.34 5.36
351 352 2.225467 GAGCATCCCACTCTTAATGCC 58.775 52.381 2.78 0.00 44.34 4.40
352 353 1.869767 CGAGCATCCCACTCTTAATGC 59.130 52.381 0.00 0.00 43.75 3.56
353 354 3.185246 ACGAGCATCCCACTCTTAATG 57.815 47.619 0.00 0.00 31.71 1.90
354 355 3.197766 TCAACGAGCATCCCACTCTTAAT 59.802 43.478 0.00 0.00 31.71 1.40
355 356 2.565391 TCAACGAGCATCCCACTCTTAA 59.435 45.455 0.00 0.00 31.71 1.85
356 357 2.176045 TCAACGAGCATCCCACTCTTA 58.824 47.619 0.00 0.00 31.71 2.10
357 358 0.976641 TCAACGAGCATCCCACTCTT 59.023 50.000 0.00 0.00 31.71 2.85
358 359 0.976641 TTCAACGAGCATCCCACTCT 59.023 50.000 0.00 0.00 31.71 3.24
359 360 1.363744 CTTCAACGAGCATCCCACTC 58.636 55.000 0.00 0.00 0.00 3.51
360 361 0.036010 CCTTCAACGAGCATCCCACT 60.036 55.000 0.00 0.00 0.00 4.00
361 362 0.036388 TCCTTCAACGAGCATCCCAC 60.036 55.000 0.00 0.00 0.00 4.61
362 363 0.911769 ATCCTTCAACGAGCATCCCA 59.088 50.000 0.00 0.00 0.00 4.37
363 364 2.910688 TATCCTTCAACGAGCATCCC 57.089 50.000 0.00 0.00 0.00 3.85
364 365 4.192317 ACTTTATCCTTCAACGAGCATCC 58.808 43.478 0.00 0.00 0.00 3.51
365 366 5.463724 CCTACTTTATCCTTCAACGAGCATC 59.536 44.000 0.00 0.00 0.00 3.91
366 367 5.128827 TCCTACTTTATCCTTCAACGAGCAT 59.871 40.000 0.00 0.00 0.00 3.79
367 368 4.464951 TCCTACTTTATCCTTCAACGAGCA 59.535 41.667 0.00 0.00 0.00 4.26
368 369 5.007385 TCCTACTTTATCCTTCAACGAGC 57.993 43.478 0.00 0.00 0.00 5.03
369 370 6.452494 TCTCCTACTTTATCCTTCAACGAG 57.548 41.667 0.00 0.00 0.00 4.18
370 371 6.845758 TTCTCCTACTTTATCCTTCAACGA 57.154 37.500 0.00 0.00 0.00 3.85
371 372 6.702282 GGATTCTCCTACTTTATCCTTCAACG 59.298 42.308 0.00 0.00 33.54 4.10
372 373 6.993308 GGGATTCTCCTACTTTATCCTTCAAC 59.007 42.308 0.00 0.00 36.57 3.18
373 374 6.101296 GGGGATTCTCCTACTTTATCCTTCAA 59.899 42.308 0.00 0.00 36.57 2.69
374 375 5.607171 GGGGATTCTCCTACTTTATCCTTCA 59.393 44.000 0.00 0.00 36.57 3.02
375 376 5.013287 GGGGGATTCTCCTACTTTATCCTTC 59.987 48.000 1.78 0.00 36.57 3.46
376 377 4.914581 GGGGGATTCTCCTACTTTATCCTT 59.085 45.833 1.78 0.00 36.57 3.36
377 378 4.077387 TGGGGGATTCTCCTACTTTATCCT 60.077 45.833 1.78 0.00 36.57 3.24
378 379 4.240323 TGGGGGATTCTCCTACTTTATCC 58.760 47.826 1.78 0.00 36.57 2.59
379 380 5.310857 ACATGGGGGATTCTCCTACTTTATC 59.689 44.000 1.78 0.00 36.57 1.75
380 381 5.235534 ACATGGGGGATTCTCCTACTTTAT 58.764 41.667 1.78 0.00 36.57 1.40
381 382 4.641868 ACATGGGGGATTCTCCTACTTTA 58.358 43.478 1.78 0.00 36.57 1.85
382 383 3.474920 ACATGGGGGATTCTCCTACTTT 58.525 45.455 1.78 0.00 36.57 2.66
383 384 3.151542 ACATGGGGGATTCTCCTACTT 57.848 47.619 1.78 0.00 36.57 2.24
384 385 2.897823 ACATGGGGGATTCTCCTACT 57.102 50.000 1.78 0.00 36.57 2.57
385 386 4.168101 TGATACATGGGGGATTCTCCTAC 58.832 47.826 1.78 0.00 36.57 3.18
386 387 4.429505 CTGATACATGGGGGATTCTCCTA 58.570 47.826 1.78 0.00 36.57 2.94
387 388 3.254960 CTGATACATGGGGGATTCTCCT 58.745 50.000 1.78 0.00 36.57 3.69
388 389 2.307098 CCTGATACATGGGGGATTCTCC 59.693 54.545 0.00 0.00 35.23 3.71
389 390 2.290577 GCCTGATACATGGGGGATTCTC 60.291 54.545 0.00 0.00 0.00 2.87
390 391 1.707427 GCCTGATACATGGGGGATTCT 59.293 52.381 0.00 0.00 0.00 2.40
391 392 1.707427 AGCCTGATACATGGGGGATTC 59.293 52.381 0.00 0.00 0.00 2.52
392 393 1.838611 AGCCTGATACATGGGGGATT 58.161 50.000 0.00 0.00 0.00 3.01
393 394 1.838611 AAGCCTGATACATGGGGGAT 58.161 50.000 0.00 0.00 0.00 3.85
394 395 1.494721 GAAAGCCTGATACATGGGGGA 59.505 52.381 0.00 0.00 0.00 4.81
395 396 1.496429 AGAAAGCCTGATACATGGGGG 59.504 52.381 0.00 0.00 0.00 5.40
396 397 2.579873 CAGAAAGCCTGATACATGGGG 58.420 52.381 0.00 0.00 45.78 4.96
397 398 1.952296 GCAGAAAGCCTGATACATGGG 59.048 52.381 0.00 0.00 45.78 4.00
398 399 2.617308 CAGCAGAAAGCCTGATACATGG 59.383 50.000 0.00 0.00 45.78 3.66
399 400 2.033049 GCAGCAGAAAGCCTGATACATG 59.967 50.000 0.00 0.00 45.78 3.21
400 401 2.295885 GCAGCAGAAAGCCTGATACAT 58.704 47.619 0.00 0.00 45.78 2.29
401 402 1.742761 GCAGCAGAAAGCCTGATACA 58.257 50.000 0.00 0.00 45.78 2.29
402 403 0.654683 CGCAGCAGAAAGCCTGATAC 59.345 55.000 0.00 0.00 45.78 2.24
403 404 0.250234 ACGCAGCAGAAAGCCTGATA 59.750 50.000 0.00 0.00 45.78 2.15
404 405 0.250234 TACGCAGCAGAAAGCCTGAT 59.750 50.000 0.00 0.00 45.78 2.90
405 406 0.390340 CTACGCAGCAGAAAGCCTGA 60.390 55.000 0.00 0.00 45.78 3.86
409 410 0.654683 CCATCTACGCAGCAGAAAGC 59.345 55.000 0.00 0.00 46.19 3.51
410 411 1.662629 CACCATCTACGCAGCAGAAAG 59.337 52.381 0.00 0.00 0.00 2.62
411 412 1.725641 CACCATCTACGCAGCAGAAA 58.274 50.000 0.00 0.00 0.00 2.52
412 413 0.740868 GCACCATCTACGCAGCAGAA 60.741 55.000 0.00 0.00 0.00 3.02
413 414 1.153568 GCACCATCTACGCAGCAGA 60.154 57.895 0.00 0.00 0.00 4.26
414 415 0.812811 ATGCACCATCTACGCAGCAG 60.813 55.000 0.00 0.00 39.39 4.24
415 416 0.392863 AATGCACCATCTACGCAGCA 60.393 50.000 0.00 0.00 39.39 4.41
416 417 0.734889 AAATGCACCATCTACGCAGC 59.265 50.000 0.00 0.00 39.39 5.25
417 418 2.009051 TCAAATGCACCATCTACGCAG 58.991 47.619 0.00 0.00 39.39 5.18
418 419 2.106477 TCAAATGCACCATCTACGCA 57.894 45.000 0.00 0.00 40.50 5.24
419 420 3.698029 ATTCAAATGCACCATCTACGC 57.302 42.857 0.00 0.00 0.00 4.42
420 421 5.401550 ACAAATTCAAATGCACCATCTACG 58.598 37.500 0.00 0.00 0.00 3.51
421 422 5.512788 CGACAAATTCAAATGCACCATCTAC 59.487 40.000 0.00 0.00 0.00 2.59
422 423 5.392919 CCGACAAATTCAAATGCACCATCTA 60.393 40.000 0.00 0.00 0.00 1.98
423 424 4.487948 CGACAAATTCAAATGCACCATCT 58.512 39.130 0.00 0.00 0.00 2.90
424 425 3.613737 CCGACAAATTCAAATGCACCATC 59.386 43.478 0.00 0.00 0.00 3.51
425 426 3.006752 ACCGACAAATTCAAATGCACCAT 59.993 39.130 0.00 0.00 0.00 3.55
426 427 2.363680 ACCGACAAATTCAAATGCACCA 59.636 40.909 0.00 0.00 0.00 4.17
427 428 3.025287 ACCGACAAATTCAAATGCACC 57.975 42.857 0.00 0.00 0.00 5.01
428 429 4.165779 CCTACCGACAAATTCAAATGCAC 58.834 43.478 0.00 0.00 0.00 4.57
429 430 3.366883 GCCTACCGACAAATTCAAATGCA 60.367 43.478 0.00 0.00 0.00 3.96
430 431 3.179048 GCCTACCGACAAATTCAAATGC 58.821 45.455 0.00 0.00 0.00 3.56
431 432 4.414852 CTGCCTACCGACAAATTCAAATG 58.585 43.478 0.00 0.00 0.00 2.32
432 433 3.443681 CCTGCCTACCGACAAATTCAAAT 59.556 43.478 0.00 0.00 0.00 2.32
433 434 2.817258 CCTGCCTACCGACAAATTCAAA 59.183 45.455 0.00 0.00 0.00 2.69
434 435 2.224670 ACCTGCCTACCGACAAATTCAA 60.225 45.455 0.00 0.00 0.00 2.69
435 436 1.349688 ACCTGCCTACCGACAAATTCA 59.650 47.619 0.00 0.00 0.00 2.57
436 437 2.109425 ACCTGCCTACCGACAAATTC 57.891 50.000 0.00 0.00 0.00 2.17
437 438 2.579410 AACCTGCCTACCGACAAATT 57.421 45.000 0.00 0.00 0.00 1.82
438 439 2.579410 AAACCTGCCTACCGACAAAT 57.421 45.000 0.00 0.00 0.00 2.32
439 440 2.633967 TCTAAACCTGCCTACCGACAAA 59.366 45.455 0.00 0.00 0.00 2.83
440 441 2.250031 TCTAAACCTGCCTACCGACAA 58.750 47.619 0.00 0.00 0.00 3.18
441 442 1.927487 TCTAAACCTGCCTACCGACA 58.073 50.000 0.00 0.00 0.00 4.35
442 443 2.483188 CCATCTAAACCTGCCTACCGAC 60.483 54.545 0.00 0.00 0.00 4.79
443 444 1.760613 CCATCTAAACCTGCCTACCGA 59.239 52.381 0.00 0.00 0.00 4.69
444 445 1.485066 ACCATCTAAACCTGCCTACCG 59.515 52.381 0.00 0.00 0.00 4.02
445 446 3.646736 AACCATCTAAACCTGCCTACC 57.353 47.619 0.00 0.00 0.00 3.18
446 447 7.991460 ACTTATAAACCATCTAAACCTGCCTAC 59.009 37.037 0.00 0.00 0.00 3.18
447 448 7.990886 CACTTATAAACCATCTAAACCTGCCTA 59.009 37.037 0.00 0.00 0.00 3.93
448 449 6.828785 CACTTATAAACCATCTAAACCTGCCT 59.171 38.462 0.00 0.00 0.00 4.75
449 450 6.826741 TCACTTATAAACCATCTAAACCTGCC 59.173 38.462 0.00 0.00 0.00 4.85
450 451 7.859325 TCACTTATAAACCATCTAAACCTGC 57.141 36.000 0.00 0.00 0.00 4.85
451 452 9.449719 AGTTCACTTATAAACCATCTAAACCTG 57.550 33.333 0.00 0.00 0.00 4.00
458 459 7.980099 CGGACTTAGTTCACTTATAAACCATCT 59.020 37.037 0.00 0.00 0.00 2.90
459 460 7.977853 TCGGACTTAGTTCACTTATAAACCATC 59.022 37.037 0.00 0.00 0.00 3.51
460 461 7.844009 TCGGACTTAGTTCACTTATAAACCAT 58.156 34.615 0.00 0.00 0.00 3.55
461 462 7.230849 TCGGACTTAGTTCACTTATAAACCA 57.769 36.000 0.00 0.00 0.00 3.67
462 463 8.713737 ATTCGGACTTAGTTCACTTATAAACC 57.286 34.615 0.00 0.00 0.00 3.27
469 470 9.503399 AAATCTAAATTCGGACTTAGTTCACTT 57.497 29.630 0.00 0.00 0.00 3.16
470 471 9.503399 AAAATCTAAATTCGGACTTAGTTCACT 57.497 29.630 0.00 0.00 0.00 3.41
475 476 8.947115 CCTGAAAAATCTAAATTCGGACTTAGT 58.053 33.333 0.00 0.00 32.39 2.24
476 477 7.910683 GCCTGAAAAATCTAAATTCGGACTTAG 59.089 37.037 0.00 0.00 32.39 2.18
477 478 7.148137 GGCCTGAAAAATCTAAATTCGGACTTA 60.148 37.037 0.00 0.00 32.39 2.24
478 479 6.350194 GGCCTGAAAAATCTAAATTCGGACTT 60.350 38.462 0.00 0.00 32.39 3.01
479 480 5.125578 GGCCTGAAAAATCTAAATTCGGACT 59.874 40.000 0.00 0.00 32.39 3.85
480 481 5.340803 GGCCTGAAAAATCTAAATTCGGAC 58.659 41.667 0.00 0.00 32.39 4.79
481 482 4.095782 CGGCCTGAAAAATCTAAATTCGGA 59.904 41.667 0.00 0.00 32.39 4.55
482 483 4.351192 CGGCCTGAAAAATCTAAATTCGG 58.649 43.478 0.00 0.00 0.00 4.30
483 484 4.095782 TCCGGCCTGAAAAATCTAAATTCG 59.904 41.667 0.00 0.00 0.00 3.34
484 485 5.450550 CCTCCGGCCTGAAAAATCTAAATTC 60.451 44.000 0.00 0.00 0.00 2.17
485 486 4.402474 CCTCCGGCCTGAAAAATCTAAATT 59.598 41.667 0.00 0.00 0.00 1.82
486 487 3.954258 CCTCCGGCCTGAAAAATCTAAAT 59.046 43.478 0.00 0.00 0.00 1.40
487 488 3.352648 CCTCCGGCCTGAAAAATCTAAA 58.647 45.455 0.00 0.00 0.00 1.85
488 489 2.356741 CCCTCCGGCCTGAAAAATCTAA 60.357 50.000 0.00 0.00 0.00 2.10
489 490 1.211949 CCCTCCGGCCTGAAAAATCTA 59.788 52.381 0.00 0.00 0.00 1.98
490 491 0.034089 CCCTCCGGCCTGAAAAATCT 60.034 55.000 0.00 0.00 0.00 2.40
491 492 1.037579 CCCCTCCGGCCTGAAAAATC 61.038 60.000 0.00 0.00 0.00 2.17
492 493 1.000359 CCCCTCCGGCCTGAAAAAT 60.000 57.895 0.00 0.00 0.00 1.82
493 494 2.137177 CTCCCCTCCGGCCTGAAAAA 62.137 60.000 0.00 0.00 0.00 1.94
494 495 2.530661 TCCCCTCCGGCCTGAAAA 60.531 61.111 0.00 0.00 0.00 2.29
495 496 3.009115 CTCCCCTCCGGCCTGAAA 61.009 66.667 0.00 0.00 0.00 2.69
500 501 4.360405 TTTTGCTCCCCTCCGGCC 62.360 66.667 0.00 0.00 0.00 6.13
501 502 3.062466 GTTTTGCTCCCCTCCGGC 61.062 66.667 0.00 0.00 0.00 6.13
502 503 2.361230 GGTTTTGCTCCCCTCCGG 60.361 66.667 0.00 0.00 0.00 5.14
503 504 2.361230 GGGTTTTGCTCCCCTCCG 60.361 66.667 0.00 0.00 39.08 4.63
509 510 2.361230 CGGGAGGGGTTTTGCTCC 60.361 66.667 0.00 0.00 38.29 4.70
510 511 3.062466 GCGGGAGGGGTTTTGCTC 61.062 66.667 0.00 0.00 0.00 4.26
524 525 4.728102 TGTCGTTACAGCCCGCGG 62.728 66.667 21.04 21.04 0.00 6.46
525 526 3.475774 GTGTCGTTACAGCCCGCG 61.476 66.667 0.00 0.00 35.91 6.46
526 527 1.740296 ATGTGTCGTTACAGCCCGC 60.740 57.895 1.55 0.00 35.91 6.13
527 528 1.358725 CCATGTGTCGTTACAGCCCG 61.359 60.000 0.00 0.00 35.91 6.13
528 529 0.036765 TCCATGTGTCGTTACAGCCC 60.037 55.000 0.00 0.00 35.91 5.19
529 530 2.024176 ATCCATGTGTCGTTACAGCC 57.976 50.000 0.00 0.00 35.91 4.85
530 531 4.570772 ACATAATCCATGTGTCGTTACAGC 59.429 41.667 0.00 0.00 46.41 4.40
542 543 7.927629 CCCTAAAATGAAACCACATAATCCATG 59.072 37.037 0.00 0.00 40.78 3.66
543 544 7.623278 ACCCTAAAATGAAACCACATAATCCAT 59.377 33.333 0.00 0.00 0.00 3.41
544 545 6.957020 ACCCTAAAATGAAACCACATAATCCA 59.043 34.615 0.00 0.00 0.00 3.41
545 546 7.418337 ACCCTAAAATGAAACCACATAATCC 57.582 36.000 0.00 0.00 0.00 3.01
552 553 9.811995 GGATAATTAACCCTAAAATGAAACCAC 57.188 33.333 0.24 0.00 0.00 4.16
553 554 9.777008 AGGATAATTAACCCTAAAATGAAACCA 57.223 29.630 8.09 0.00 0.00 3.67
559 560 9.325198 GGCAAAAGGATAATTAACCCTAAAATG 57.675 33.333 8.09 7.33 0.00 2.32
560 561 8.491134 GGGCAAAAGGATAATTAACCCTAAAAT 58.509 33.333 8.09 0.00 31.84 1.82
561 562 7.680739 AGGGCAAAAGGATAATTAACCCTAAAA 59.319 33.333 8.09 0.00 43.36 1.52
562 563 7.193338 AGGGCAAAAGGATAATTAACCCTAAA 58.807 34.615 8.09 0.00 43.36 1.85
697 698 2.871096 AGGGCCGAGTCAAAATGTTA 57.129 45.000 0.00 0.00 0.00 2.41
820 821 2.666508 CGCCCGCTAATATATCACACAC 59.333 50.000 0.00 0.00 0.00 3.82
821 822 2.559231 TCGCCCGCTAATATATCACACA 59.441 45.455 0.00 0.00 0.00 3.72
827 828 1.469251 CGCTGTCGCCCGCTAATATAT 60.469 52.381 0.00 0.00 0.00 0.86
908 909 1.078848 CAGCTAGCTTTCCACCGCT 60.079 57.895 16.46 0.00 40.15 5.52
916 917 1.301293 GCCCTCCACAGCTAGCTTT 59.699 57.895 16.46 5.89 0.00 3.51
993 994 0.036732 TTGCGGAAGACATGGAGCTT 59.963 50.000 0.00 0.00 0.00 3.74
1099 1102 0.472471 GGTGTGTGAGAAACCCTCCA 59.528 55.000 0.00 0.00 41.25 3.86
1208 1212 2.742053 CACGGAACAGATCAACCGATTT 59.258 45.455 20.39 2.72 46.94 2.17
1242 1246 2.669391 CGACCCAAAGAAAGAAGCATGC 60.669 50.000 10.51 10.51 0.00 4.06
1281 1285 6.207221 TGCTCTTCTTGCAGTTCATTTATCAA 59.793 34.615 0.00 0.00 35.31 2.57
1405 1409 5.620206 TCTTCAACATCCTAAGCTCAACAA 58.380 37.500 0.00 0.00 0.00 2.83
1448 1452 3.131396 GGGTATTGGTAGTGCTTGATCG 58.869 50.000 0.00 0.00 0.00 3.69
1521 1525 6.166984 TGCCTTTCCATACATTTTCAACAA 57.833 33.333 0.00 0.00 0.00 2.83
1669 1681 6.633325 TCTGAATTCCTCATTTCTTCTCCT 57.367 37.500 2.27 0.00 32.14 3.69
1726 1738 4.898861 ACCTTAATTGTTTGGCTCTGGAAA 59.101 37.500 0.00 0.00 0.00 3.13
2010 2022 1.302511 CGCAGCCCTAAACACCACT 60.303 57.895 0.00 0.00 0.00 4.00
2212 2230 1.039068 CCAAAACCACATGGCAGTGA 58.961 50.000 15.61 0.00 42.05 3.41
2350 2378 6.279513 AGAACTTGTGGTTGTCATTCAAAA 57.720 33.333 0.00 0.00 38.41 2.44
2351 2379 5.448496 CGAGAACTTGTGGTTGTCATTCAAA 60.448 40.000 6.49 0.00 45.11 2.69
2352 2380 4.035091 CGAGAACTTGTGGTTGTCATTCAA 59.965 41.667 6.49 0.00 45.11 2.69


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

AutoCloner maintained by Alex Coulton.