Multiple sequence alignment - TraesCS3B01G311300

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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 TraesCS3B01G311300 chr3B 100.000 4897 0 0 1 4897 499814638 499809742 0.000000e+00 9044
1 TraesCS3B01G311300 chr3B 97.132 523 11 2 4379 4897 707898458 707898980 0.000000e+00 880
2 TraesCS3B01G311300 chr3A 92.974 3743 162 47 488 4178 507130318 507126625 0.000000e+00 5361
3 TraesCS3B01G311300 chr3A 92.060 529 31 7 4379 4897 506392893 506392366 0.000000e+00 734
4 TraesCS3B01G311300 chr3A 96.269 134 3 1 4253 4384 507126623 507126490 8.250000e-53 219
5 TraesCS3B01G311300 chr3D 93.998 2899 103 23 1302 4178 384577555 384574706 0.000000e+00 4324
6 TraesCS3B01G311300 chr3D 90.661 771 34 15 488 1248 384578300 384577558 0.000000e+00 990
7 TraesCS3B01G311300 chr3D 86.215 428 44 5 19 432 399372226 399371800 2.690000e-122 449
8 TraesCS3B01G311300 chr3D 94.845 97 3 1 4245 4339 384574672 384574576 3.050000e-32 150
9 TraesCS3B01G311300 chr4B 99.615 519 2 0 4379 4897 85602314 85602832 0.000000e+00 948
10 TraesCS3B01G311300 chr2B 96.023 528 15 4 4374 4896 605445477 605446003 0.000000e+00 854
11 TraesCS3B01G311300 chr6B 96.176 523 15 3 4379 4897 429619758 429619237 0.000000e+00 850
12 TraesCS3B01G311300 chr6B 86.742 528 30 13 4379 4897 44824839 44824343 7.160000e-153 551
13 TraesCS3B01G311300 chr7A 95.251 379 17 1 1 378 27961689 27962067 2.520000e-167 599
14 TraesCS3B01G311300 chr7A 86.011 529 34 13 4378 4897 120099711 120099214 9.330000e-147 531
15 TraesCS3B01G311300 chr7A 82.910 433 50 11 10 426 24375128 24375552 7.740000e-98 368
16 TraesCS3B01G311300 chr7A 82.910 433 50 11 10 426 24394098 24394522 7.740000e-98 368
17 TraesCS3B01G311300 chr4A 86.553 528 31 13 4379 4897 738879111 738879607 3.330000e-151 545
18 TraesCS3B01G311300 chr4A 85.880 432 43 7 9 424 715078487 715078058 1.250000e-120 444
19 TraesCS3B01G311300 chr4A 85.880 432 43 7 9 424 715081198 715080769 1.250000e-120 444
20 TraesCS3B01G311300 chr4A 86.994 346 33 6 4379 4721 552029290 552029626 3.580000e-101 379
21 TraesCS3B01G311300 chr5B 86.364 528 32 13 4379 4897 321631850 321631354 1.550000e-149 540
22 TraesCS3B01G311300 chr6A 87.778 450 41 5 1 437 197038079 197037631 9.400000e-142 514
23 TraesCS3B01G311300 chr1B 85.122 531 46 17 4379 4880 107924438 107923912 3.380000e-141 512
24 TraesCS3B01G311300 chr7B 87.857 420 33 8 1 407 521129240 521129654 1.230000e-130 477
25 TraesCS3B01G311300 chr7D 87.321 418 38 7 1 407 491796592 491797005 9.600000e-127 464
26 TraesCS3B01G311300 chr6D 85.847 431 47 4 10 426 306319037 306319467 3.480000e-121 446
27 TraesCS3B01G311300 chr2A 85.036 421 46 8 19 426 447371056 447370640 3.530000e-111 412
28 TraesCS3B01G311300 chr2A 78.588 439 63 14 1 425 100672979 100672558 1.350000e-65 261
29 TraesCS3B01G311300 chrUn 78.995 438 63 18 1 424 87057514 87057092 6.250000e-69 272


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 TraesCS3B01G311300 chr3B 499809742 499814638 4896 True 9044.000000 9044 100.0000 1 4897 1 chr3B.!!$R1 4896
1 TraesCS3B01G311300 chr3B 707898458 707898980 522 False 880.000000 880 97.1320 4379 4897 1 chr3B.!!$F1 518
2 TraesCS3B01G311300 chr3A 507126490 507130318 3828 True 2790.000000 5361 94.6215 488 4384 2 chr3A.!!$R2 3896
3 TraesCS3B01G311300 chr3A 506392366 506392893 527 True 734.000000 734 92.0600 4379 4897 1 chr3A.!!$R1 518
4 TraesCS3B01G311300 chr3D 384574576 384578300 3724 True 1821.333333 4324 93.1680 488 4339 3 chr3D.!!$R2 3851
5 TraesCS3B01G311300 chr4B 85602314 85602832 518 False 948.000000 948 99.6150 4379 4897 1 chr4B.!!$F1 518
6 TraesCS3B01G311300 chr2B 605445477 605446003 526 False 854.000000 854 96.0230 4374 4896 1 chr2B.!!$F1 522
7 TraesCS3B01G311300 chr6B 429619237 429619758 521 True 850.000000 850 96.1760 4379 4897 1 chr6B.!!$R2 518
8 TraesCS3B01G311300 chr4A 715078058 715081198 3140 True 444.000000 444 85.8800 9 424 2 chr4A.!!$R1 415
9 TraesCS3B01G311300 chr1B 107923912 107924438 526 True 512.000000 512 85.1220 4379 4880 1 chr1B.!!$R1 501

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
333 350 0.171903 GATGTTGGCTGTGTGCATCC 59.828 55.0 0.00 0.0 45.15 3.51 F
2113 2262 0.098376 CTTCTTTGCGCTCATGGCTC 59.902 55.0 9.73 0.0 39.13 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2160 2309 0.326264 CCTTAGCAGCTCCCTTGTGT 59.674 55.0 0.00 0.00 0.0 3.72 R
3899 4225 0.601558 AACTAGAGCGTGCTCCGAAA 59.398 50.0 17.76 1.53 43.7 3.46 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 2.364970 TGTTCCCTTGTTGAAGGCATTG 59.635 45.455 0.00 0.00 46.89 2.82
52 53 1.332889 TGCTCGGATGTGCTCTGGAT 61.333 55.000 0.00 0.00 35.65 3.41
63 64 2.670414 GTGCTCTGGATTCGTTCTTCAG 59.330 50.000 0.00 0.00 0.00 3.02
65 66 2.898705 CTCTGGATTCGTTCTTCAGGG 58.101 52.381 0.00 0.00 0.00 4.45
72 73 4.320275 GGATTCGTTCTTCAGGGTGAAAAC 60.320 45.833 0.00 0.00 35.73 2.43
83 84 3.691609 CAGGGTGAAAACCTAGATTCTGC 59.308 47.826 0.00 0.00 36.32 4.26
143 156 2.945008 TGAAGGTGTTGCTGTTGAAGAG 59.055 45.455 0.00 0.00 0.00 2.85
144 157 3.206150 GAAGGTGTTGCTGTTGAAGAGA 58.794 45.455 0.00 0.00 0.00 3.10
145 158 2.565841 AGGTGTTGCTGTTGAAGAGAC 58.434 47.619 0.00 0.00 0.00 3.36
146 159 2.171448 AGGTGTTGCTGTTGAAGAGACT 59.829 45.455 0.00 0.00 0.00 3.24
147 160 2.545946 GGTGTTGCTGTTGAAGAGACTC 59.454 50.000 0.00 0.00 0.00 3.36
148 161 2.219674 GTGTTGCTGTTGAAGAGACTCG 59.780 50.000 0.00 0.00 0.00 4.18
150 163 2.866762 GTTGCTGTTGAAGAGACTCGTT 59.133 45.455 0.00 0.00 0.00 3.85
151 164 2.473816 TGCTGTTGAAGAGACTCGTTG 58.526 47.619 0.00 0.00 0.00 4.10
154 167 3.053455 CTGTTGAAGAGACTCGTTGTCC 58.947 50.000 0.00 1.55 46.46 4.02
155 168 2.693591 TGTTGAAGAGACTCGTTGTCCT 59.306 45.455 0.00 3.36 46.46 3.85
164 177 0.937304 CTCGTTGTCCTTGTGGTGTG 59.063 55.000 0.00 0.00 34.23 3.82
208 224 3.127203 TGGTTGTTGTTGTAGTTTGTCGG 59.873 43.478 0.00 0.00 0.00 4.79
211 227 2.604011 TGTTGTTGTAGTTTGTCGGTCG 59.396 45.455 0.00 0.00 0.00 4.79
216 232 2.195096 TGTAGTTTGTCGGTCGTTGTG 58.805 47.619 0.00 0.00 0.00 3.33
251 267 5.293560 AGAGGACTTTTTCTTTCTCACTCG 58.706 41.667 0.00 0.00 0.00 4.18
253 269 3.058846 GGACTTTTTCTTTCTCACTCGGC 60.059 47.826 0.00 0.00 0.00 5.54
254 270 3.541632 ACTTTTTCTTTCTCACTCGGCA 58.458 40.909 0.00 0.00 0.00 5.69
255 271 4.137543 ACTTTTTCTTTCTCACTCGGCAT 58.862 39.130 0.00 0.00 0.00 4.40
256 272 5.305585 ACTTTTTCTTTCTCACTCGGCATA 58.694 37.500 0.00 0.00 0.00 3.14
258 274 5.607119 TTTTCTTTCTCACTCGGCATAAC 57.393 39.130 0.00 0.00 0.00 1.89
262 278 4.690748 TCTTTCTCACTCGGCATAACTTTG 59.309 41.667 0.00 0.00 0.00 2.77
264 280 2.301870 TCTCACTCGGCATAACTTTGGT 59.698 45.455 0.00 0.00 0.00 3.67
265 281 3.074412 CTCACTCGGCATAACTTTGGTT 58.926 45.455 0.00 0.00 39.26 3.67
290 307 0.525761 TGACTTTGCTATTTGCCGGC 59.474 50.000 22.73 22.73 42.00 6.13
295 312 1.917782 TTGCTATTTGCCGGCGTGTC 61.918 55.000 23.90 9.07 42.00 3.67
304 321 1.296056 GCCGGCGTGTCTATTTGTGT 61.296 55.000 12.58 0.00 0.00 3.72
311 328 2.659023 CGTGTCTATTTGTGTGTGTGCG 60.659 50.000 0.00 0.00 0.00 5.34
315 332 3.001838 GTCTATTTGTGTGTGTGCGTTGA 59.998 43.478 0.00 0.00 0.00 3.18
321 338 0.380024 TGTGTGTGCGTTGATGTTGG 59.620 50.000 0.00 0.00 0.00 3.77
329 346 0.661187 CGTTGATGTTGGCTGTGTGC 60.661 55.000 0.00 0.00 41.94 4.57
330 347 0.385029 GTTGATGTTGGCTGTGTGCA 59.615 50.000 0.00 0.00 45.15 4.57
331 348 1.000060 GTTGATGTTGGCTGTGTGCAT 60.000 47.619 0.00 0.00 45.15 3.96
332 349 0.883153 TGATGTTGGCTGTGTGCATC 59.117 50.000 0.00 0.00 45.15 3.91
333 350 0.171903 GATGTTGGCTGTGTGCATCC 59.828 55.000 0.00 0.00 45.15 3.51
334 351 0.251474 ATGTTGGCTGTGTGCATCCT 60.251 50.000 0.00 0.00 45.15 3.24
335 352 0.399833 TGTTGGCTGTGTGCATCCTA 59.600 50.000 0.00 0.00 45.15 2.94
336 353 1.089920 GTTGGCTGTGTGCATCCTAG 58.910 55.000 0.00 0.00 45.15 3.02
337 354 0.692476 TTGGCTGTGTGCATCCTAGT 59.308 50.000 0.00 0.00 45.15 2.57
338 355 0.692476 TGGCTGTGTGCATCCTAGTT 59.308 50.000 0.00 0.00 45.15 2.24
339 356 1.905894 TGGCTGTGTGCATCCTAGTTA 59.094 47.619 0.00 0.00 45.15 2.24
340 357 2.505407 TGGCTGTGTGCATCCTAGTTAT 59.495 45.455 0.00 0.00 45.15 1.89
341 358 2.874701 GGCTGTGTGCATCCTAGTTATG 59.125 50.000 0.00 0.00 45.15 1.90
349 366 3.051081 CATCCTAGTTATGCAGAGGCC 57.949 52.381 0.00 0.00 40.13 5.19
350 367 1.040646 TCCTAGTTATGCAGAGGCCG 58.959 55.000 0.00 0.00 40.13 6.13
351 368 1.040646 CCTAGTTATGCAGAGGCCGA 58.959 55.000 0.00 0.00 40.13 5.54
352 369 1.412710 CCTAGTTATGCAGAGGCCGAA 59.587 52.381 0.00 0.00 40.13 4.30
353 370 2.037772 CCTAGTTATGCAGAGGCCGAAT 59.962 50.000 0.00 0.00 40.13 3.34
354 371 1.959042 AGTTATGCAGAGGCCGAATG 58.041 50.000 0.00 0.00 40.13 2.67
355 372 1.210478 AGTTATGCAGAGGCCGAATGT 59.790 47.619 0.00 0.00 40.13 2.71
356 373 1.331756 GTTATGCAGAGGCCGAATGTG 59.668 52.381 0.00 0.00 40.13 3.21
357 374 0.541392 TATGCAGAGGCCGAATGTGT 59.459 50.000 0.00 0.00 40.13 3.72
358 375 1.028330 ATGCAGAGGCCGAATGTGTG 61.028 55.000 0.00 0.00 40.13 3.82
359 376 3.044059 GCAGAGGCCGAATGTGTGC 62.044 63.158 0.00 0.00 0.00 4.57
360 377 1.376424 CAGAGGCCGAATGTGTGCT 60.376 57.895 0.00 0.00 0.00 4.40
361 378 1.078848 AGAGGCCGAATGTGTGCTC 60.079 57.895 0.00 0.00 0.00 4.26
362 379 1.375908 GAGGCCGAATGTGTGCTCA 60.376 57.895 0.00 0.00 0.00 4.26
363 380 0.745845 GAGGCCGAATGTGTGCTCAT 60.746 55.000 0.00 0.00 0.00 2.90
364 381 0.322816 AGGCCGAATGTGTGCTCATT 60.323 50.000 0.00 0.00 40.20 2.57
365 382 0.179156 GGCCGAATGTGTGCTCATTG 60.179 55.000 4.49 0.00 38.03 2.82
366 383 0.523072 GCCGAATGTGTGCTCATTGT 59.477 50.000 4.49 0.00 38.03 2.71
367 384 1.730121 GCCGAATGTGTGCTCATTGTG 60.730 52.381 4.49 0.00 38.03 3.33
368 385 1.536766 CCGAATGTGTGCTCATTGTGT 59.463 47.619 4.49 0.00 38.03 3.72
369 386 2.030893 CCGAATGTGTGCTCATTGTGTT 60.031 45.455 4.49 0.00 38.03 3.32
370 387 3.550639 CCGAATGTGTGCTCATTGTGTTT 60.551 43.478 4.49 0.00 38.03 2.83
371 388 3.422876 CGAATGTGTGCTCATTGTGTTTG 59.577 43.478 4.49 0.00 38.03 2.93
372 389 4.362279 GAATGTGTGCTCATTGTGTTTGT 58.638 39.130 4.49 0.00 38.03 2.83
373 390 5.512753 AATGTGTGCTCATTGTGTTTGTA 57.487 34.783 0.00 0.00 36.78 2.41
374 391 5.710513 ATGTGTGCTCATTGTGTTTGTAT 57.289 34.783 0.00 0.00 0.00 2.29
375 392 5.512753 TGTGTGCTCATTGTGTTTGTATT 57.487 34.783 0.00 0.00 0.00 1.89
376 393 5.518812 TGTGTGCTCATTGTGTTTGTATTC 58.481 37.500 0.00 0.00 0.00 1.75
377 394 5.067023 TGTGTGCTCATTGTGTTTGTATTCA 59.933 36.000 0.00 0.00 0.00 2.57
378 395 5.399301 GTGTGCTCATTGTGTTTGTATTCAC 59.601 40.000 0.00 0.00 35.43 3.18
379 396 5.299028 TGTGCTCATTGTGTTTGTATTCACT 59.701 36.000 0.00 0.00 35.82 3.41
380 397 6.183360 TGTGCTCATTGTGTTTGTATTCACTT 60.183 34.615 0.00 0.00 35.82 3.16
381 398 6.142798 GTGCTCATTGTGTTTGTATTCACTTG 59.857 38.462 0.00 0.00 35.82 3.16
382 399 6.039159 TGCTCATTGTGTTTGTATTCACTTGA 59.961 34.615 0.00 0.00 35.82 3.02
383 400 7.086376 GCTCATTGTGTTTGTATTCACTTGAT 58.914 34.615 0.00 0.00 35.82 2.57
384 401 7.061441 GCTCATTGTGTTTGTATTCACTTGATG 59.939 37.037 0.00 0.00 35.82 3.07
385 402 6.862608 TCATTGTGTTTGTATTCACTTGATGC 59.137 34.615 0.00 0.00 35.82 3.91
386 403 6.389830 TTGTGTTTGTATTCACTTGATGCT 57.610 33.333 0.00 0.00 35.82 3.79
387 404 6.389830 TGTGTTTGTATTCACTTGATGCTT 57.610 33.333 0.00 0.00 35.82 3.91
388 405 6.437928 TGTGTTTGTATTCACTTGATGCTTC 58.562 36.000 0.00 0.00 35.82 3.86
389 406 6.039159 TGTGTTTGTATTCACTTGATGCTTCA 59.961 34.615 0.00 0.00 35.82 3.02
390 407 7.086376 GTGTTTGTATTCACTTGATGCTTCAT 58.914 34.615 2.75 0.00 0.00 2.57
391 408 7.596248 GTGTTTGTATTCACTTGATGCTTCATT 59.404 33.333 2.75 0.00 0.00 2.57
392 409 8.143193 TGTTTGTATTCACTTGATGCTTCATTT 58.857 29.630 2.75 0.00 0.00 2.32
393 410 8.981647 GTTTGTATTCACTTGATGCTTCATTTT 58.018 29.630 2.75 0.00 0.00 1.82
394 411 8.523523 TTGTATTCACTTGATGCTTCATTTTG 57.476 30.769 2.75 1.89 0.00 2.44
395 412 7.884257 TGTATTCACTTGATGCTTCATTTTGA 58.116 30.769 2.75 4.09 0.00 2.69
396 413 8.024865 TGTATTCACTTGATGCTTCATTTTGAG 58.975 33.333 2.75 0.28 0.00 3.02
397 414 6.395426 TTCACTTGATGCTTCATTTTGAGT 57.605 33.333 2.75 0.90 0.00 3.41
398 415 6.005583 TCACTTGATGCTTCATTTTGAGTC 57.994 37.500 2.75 0.00 0.00 3.36
399 416 5.532032 TCACTTGATGCTTCATTTTGAGTCA 59.468 36.000 2.75 0.00 0.00 3.41
400 417 6.039605 TCACTTGATGCTTCATTTTGAGTCAA 59.960 34.615 0.08 0.08 0.00 3.18
401 418 6.866770 CACTTGATGCTTCATTTTGAGTCAAT 59.133 34.615 6.36 0.00 0.00 2.57
402 419 8.024865 CACTTGATGCTTCATTTTGAGTCAATA 58.975 33.333 6.36 1.98 0.00 1.90
403 420 8.579006 ACTTGATGCTTCATTTTGAGTCAATAA 58.421 29.630 6.36 4.84 0.00 1.40
404 421 9.414295 CTTGATGCTTCATTTTGAGTCAATAAA 57.586 29.630 6.36 0.00 0.00 1.40
405 422 9.761504 TTGATGCTTCATTTTGAGTCAATAAAA 57.238 25.926 6.36 0.00 0.00 1.52
406 423 9.932207 TGATGCTTCATTTTGAGTCAATAAAAT 57.068 25.926 6.36 0.85 37.06 1.82
408 425 8.761575 TGCTTCATTTTGAGTCAATAAAATCC 57.238 30.769 6.36 0.00 35.07 3.01
409 426 8.366401 TGCTTCATTTTGAGTCAATAAAATCCA 58.634 29.630 6.36 0.00 35.07 3.41
410 427 8.650714 GCTTCATTTTGAGTCAATAAAATCCAC 58.349 33.333 6.36 0.00 35.07 4.02
411 428 9.143631 CTTCATTTTGAGTCAATAAAATCCACC 57.856 33.333 6.36 0.00 35.07 4.61
412 429 7.610865 TCATTTTGAGTCAATAAAATCCACCC 58.389 34.615 6.36 0.00 35.07 4.61
413 430 7.454380 TCATTTTGAGTCAATAAAATCCACCCT 59.546 33.333 6.36 0.00 35.07 4.34
414 431 7.610580 TTTTGAGTCAATAAAATCCACCCTT 57.389 32.000 6.36 0.00 0.00 3.95
415 432 7.610580 TTTGAGTCAATAAAATCCACCCTTT 57.389 32.000 6.36 0.00 0.00 3.11
416 433 8.713708 TTTGAGTCAATAAAATCCACCCTTTA 57.286 30.769 6.36 0.00 0.00 1.85
417 434 8.893563 TTGAGTCAATAAAATCCACCCTTTAT 57.106 30.769 0.08 0.00 30.70 1.40
418 435 8.519799 TGAGTCAATAAAATCCACCCTTTATC 57.480 34.615 0.00 0.00 29.50 1.75
419 436 7.282224 TGAGTCAATAAAATCCACCCTTTATCG 59.718 37.037 0.00 0.00 29.50 2.92
420 437 7.343357 AGTCAATAAAATCCACCCTTTATCGA 58.657 34.615 0.00 0.00 29.50 3.59
421 438 7.832187 AGTCAATAAAATCCACCCTTTATCGAA 59.168 33.333 0.00 0.00 29.50 3.71
422 439 8.463607 GTCAATAAAATCCACCCTTTATCGAAA 58.536 33.333 0.00 0.00 29.50 3.46
423 440 9.026121 TCAATAAAATCCACCCTTTATCGAAAA 57.974 29.630 0.00 0.00 29.50 2.29
424 441 9.646427 CAATAAAATCCACCCTTTATCGAAAAA 57.354 29.630 0.00 0.00 29.50 1.94
447 464 8.816640 AAAATTACTGGCACTAAACAAATCAG 57.183 30.769 0.00 0.00 0.00 2.90
448 465 7.524717 AATTACTGGCACTAAACAAATCAGT 57.475 32.000 0.00 0.00 37.66 3.41
449 466 6.952773 TTACTGGCACTAAACAAATCAGTT 57.047 33.333 0.00 0.00 35.84 3.16
450 467 5.852282 ACTGGCACTAAACAAATCAGTTT 57.148 34.783 0.00 0.00 43.58 2.66
451 468 6.952773 ACTGGCACTAAACAAATCAGTTTA 57.047 33.333 0.00 0.00 41.58 2.01
503 520 1.083209 CGACGTCACTCGACACGAA 60.083 57.895 17.16 0.00 42.74 3.85
514 531 0.721155 CGACACGAACCAATGTTGCG 60.721 55.000 0.00 0.00 33.97 4.85
561 579 0.388134 GCTCACGCGTCAACCTTAGA 60.388 55.000 9.86 0.00 0.00 2.10
627 653 4.645809 AGGAAATTCCTCGCTGCC 57.354 55.556 9.08 0.00 45.66 4.85
793 827 4.759096 GCGCACACCATTCCACGC 62.759 66.667 0.30 0.00 39.49 5.34
794 828 3.353029 CGCACACCATTCCACGCA 61.353 61.111 0.00 0.00 0.00 5.24
795 829 2.255252 GCACACCATTCCACGCAC 59.745 61.111 0.00 0.00 0.00 5.34
796 830 2.555782 CACACCATTCCACGCACG 59.444 61.111 0.00 0.00 0.00 5.34
855 889 3.474570 GCATCAGCCCGTCCTCCT 61.475 66.667 0.00 0.00 33.58 3.69
856 890 2.818132 CATCAGCCCGTCCTCCTC 59.182 66.667 0.00 0.00 0.00 3.71
862 896 4.862823 CCCGTCCTCCTCCCTCCC 62.863 77.778 0.00 0.00 0.00 4.30
884 918 1.550374 TCTTCCTCCCCTCCCCTCT 60.550 63.158 0.00 0.00 0.00 3.69
885 919 1.074850 CTTCCTCCCCTCCCCTCTC 60.075 68.421 0.00 0.00 0.00 3.20
886 920 2.613576 CTTCCTCCCCTCCCCTCTCC 62.614 70.000 0.00 0.00 0.00 3.71
887 921 3.039526 CCTCCCCTCCCCTCTCCT 61.040 72.222 0.00 0.00 0.00 3.69
888 922 2.612251 CTCCCCTCCCCTCTCCTC 59.388 72.222 0.00 0.00 0.00 3.71
902 936 1.148027 TCTCCTCCACTCCACTCAACT 59.852 52.381 0.00 0.00 0.00 3.16
904 938 1.051812 CCTCCACTCCACTCAACTGT 58.948 55.000 0.00 0.00 0.00 3.55
910 944 1.202417 ACTCCACTCAACTGTCACACG 60.202 52.381 0.00 0.00 0.00 4.49
911 945 0.529773 TCCACTCAACTGTCACACGC 60.530 55.000 0.00 0.00 0.00 5.34
969 1003 0.815213 AGCAAGTTCTTGTCAGCGCA 60.815 50.000 11.47 0.00 0.00 6.09
972 1006 1.070309 CAAGTTCTTGTCAGCGCAGAC 60.070 52.381 24.38 24.38 38.99 3.51
978 1012 4.724602 GTCAGCGCAGACGAGGCA 62.725 66.667 17.47 0.00 43.93 4.75
1096 1130 1.000955 TCCTTCAGTTCGTCTTCTGGC 59.999 52.381 0.00 0.00 33.13 4.85
1099 1133 1.040646 TCAGTTCGTCTTCTGGCACT 58.959 50.000 0.00 0.00 33.13 4.40
1100 1134 2.235891 TCAGTTCGTCTTCTGGCACTA 58.764 47.619 0.00 0.00 33.13 2.74
1101 1135 2.030185 TCAGTTCGTCTTCTGGCACTAC 60.030 50.000 0.00 0.00 33.13 2.73
1102 1136 2.029828 CAGTTCGTCTTCTGGCACTACT 60.030 50.000 0.00 0.00 0.00 2.57
1103 1137 2.229302 AGTTCGTCTTCTGGCACTACTC 59.771 50.000 0.00 0.00 0.00 2.59
1149 1183 7.814587 CCCTTTTGGAATGTGAAATCTTAGTTC 59.185 37.037 0.00 0.00 44.07 3.01
1191 1225 3.850098 CTTGCTTCCCGCTGGGTGT 62.850 63.158 12.46 0.00 44.74 4.16
1222 1261 1.591158 CAATGCGTATGGTACCGTGAC 59.409 52.381 17.34 8.60 0.00 3.67
1263 1302 4.095946 TCTTTTGGGGGAAATCCAATGAG 58.904 43.478 1.22 0.00 43.01 2.90
1311 1355 6.442541 TCTACCCAACCTTCAGATTGTTTA 57.557 37.500 0.00 0.00 0.00 2.01
1382 1429 4.946784 AAAATAAAGAGAGATTGCGCGT 57.053 36.364 8.43 0.00 0.00 6.01
1449 1598 2.758327 ACCGGCATCTGCTACGGA 60.758 61.111 21.44 0.00 44.81 4.69
1535 1684 0.247934 TACGTGCGCATCTACGACAG 60.248 55.000 22.66 5.44 42.54 3.51
1668 1817 1.280133 CTCAAGAACAGCATCCTCCCA 59.720 52.381 0.00 0.00 0.00 4.37
1887 2036 1.026718 GGGCGTTCAACAGCAGCTAT 61.027 55.000 0.00 0.00 34.54 2.97
1899 2048 2.012237 CAGCTATGCGCACTTCCTG 58.988 57.895 14.90 13.42 42.61 3.86
2100 2249 3.274288 GCAGGTCGATTCCATCTTCTTT 58.726 45.455 0.00 0.00 0.00 2.52
2113 2262 0.098376 CTTCTTTGCGCTCATGGCTC 59.902 55.000 9.73 0.00 39.13 4.70
2175 2324 2.433446 CCACACAAGGGAGCTGCT 59.567 61.111 0.00 0.00 0.00 4.24
2184 2333 0.041833 AGGGAGCTGCTAAGGAGACA 59.958 55.000 0.15 0.00 0.00 3.41
2190 2339 0.980231 CTGCTAAGGAGACAGGGGCT 60.980 60.000 0.00 0.00 0.00 5.19
2199 2348 1.457831 GACAGGGGCTACTCCGGAT 60.458 63.158 3.57 0.00 34.94 4.18
2241 2390 4.761739 ACCAATCTGATTCGTCATGTTGTT 59.238 37.500 0.00 0.00 0.00 2.83
2388 2537 4.599047 AAGCTCCATCTACAGCATAGAC 57.401 45.455 0.16 0.00 38.18 2.59
2421 2570 3.624777 AGGAAATGTGGACATCATGACC 58.375 45.455 0.00 0.00 35.10 4.02
2442 2591 1.067846 GGAGGAAACCGTTCAAATGGC 60.068 52.381 0.77 0.00 38.70 4.40
2494 2643 3.207669 CGGCTCTGCAGAATGGCC 61.208 66.667 27.50 27.50 39.43 5.36
2746 2898 6.369890 AGGAATGCTTGCACTGTATAATATCG 59.630 38.462 0.00 0.00 0.00 2.92
2783 2935 7.071196 ACTGGCTTTGGATGTAGTCTGAATATA 59.929 37.037 0.00 0.00 0.00 0.86
2818 2970 7.010552 GTCAATTGTAAGTCTACATTCGCAGAT 59.989 37.037 5.13 0.00 37.86 2.90
3104 3325 4.810191 ATTACGTTTTCTCTCCTCTGCT 57.190 40.909 0.00 0.00 0.00 4.24
3221 3468 6.753913 AGGATTCACAGGCATAATCTTCTA 57.246 37.500 0.00 0.00 31.66 2.10
3222 3469 7.327064 AGGATTCACAGGCATAATCTTCTAT 57.673 36.000 0.00 0.00 31.66 1.98
3223 3470 7.753630 AGGATTCACAGGCATAATCTTCTATT 58.246 34.615 0.00 0.00 31.66 1.73
3224 3471 7.882271 AGGATTCACAGGCATAATCTTCTATTC 59.118 37.037 0.00 0.00 31.66 1.75
3225 3472 7.882271 GGATTCACAGGCATAATCTTCTATTCT 59.118 37.037 0.00 0.00 31.66 2.40
3226 3473 9.282569 GATTCACAGGCATAATCTTCTATTCTT 57.717 33.333 0.00 0.00 0.00 2.52
3227 3474 8.668510 TTCACAGGCATAATCTTCTATTCTTC 57.331 34.615 0.00 0.00 0.00 2.87
3228 3475 8.027524 TCACAGGCATAATCTTCTATTCTTCT 57.972 34.615 0.00 0.00 0.00 2.85
3271 3518 7.946207 AGAATCGACTTATGCTCTGATAAGAA 58.054 34.615 8.16 0.00 37.91 2.52
3272 3519 8.081633 AGAATCGACTTATGCTCTGATAAGAAG 58.918 37.037 8.16 0.00 37.91 2.85
3574 3824 5.493133 TGTTACTGTCGATGTTGCTTTTT 57.507 34.783 0.00 0.00 0.00 1.94
3596 3846 4.414337 AGTGTCAGCTGGATAATCTTCC 57.586 45.455 15.13 0.00 36.24 3.46
3719 4030 1.224592 CATGCCCACCTACTGGTCC 59.775 63.158 0.00 0.00 46.60 4.46
3882 4208 1.188863 GCTTCCCATTGTGATTGCCT 58.811 50.000 0.00 0.00 0.00 4.75
3884 4210 2.760092 GCTTCCCATTGTGATTGCCTTA 59.240 45.455 0.00 0.00 0.00 2.69
3940 4266 4.088421 CGTTCGGATCGAAGGTGG 57.912 61.111 12.63 0.00 46.54 4.61
3984 4310 6.620877 AGGAACCAGTAATGTTCTGATGTA 57.379 37.500 0.00 0.00 41.42 2.29
4011 4337 0.032017 AGGTGGCAGTAGGGACCTAG 60.032 60.000 0.00 0.00 37.04 3.02
4012 4338 0.325390 GGTGGCAGTAGGGACCTAGT 60.325 60.000 0.00 0.00 32.83 2.57
4013 4339 1.063417 GGTGGCAGTAGGGACCTAGTA 60.063 57.143 5.44 0.00 31.55 1.82
4043 4369 9.657419 TGCAGTATGTTATTATCTATGGATGTG 57.343 33.333 1.10 0.00 39.31 3.21
4098 4424 5.760253 CCACTGAGAACTAGAAATGTGTTGT 59.240 40.000 0.00 0.00 0.00 3.32
4100 4426 5.237344 ACTGAGAACTAGAAATGTGTTGTGC 59.763 40.000 0.00 0.00 0.00 4.57
4102 4428 3.498397 AGAACTAGAAATGTGTTGTGCCG 59.502 43.478 0.00 0.00 0.00 5.69
4103 4429 3.120321 ACTAGAAATGTGTTGTGCCGA 57.880 42.857 0.00 0.00 0.00 5.54
4106 4432 2.229792 AGAAATGTGTTGTGCCGATGT 58.770 42.857 0.00 0.00 0.00 3.06
4107 4433 2.030893 AGAAATGTGTTGTGCCGATGTG 60.031 45.455 0.00 0.00 0.00 3.21
4108 4434 0.597568 AATGTGTTGTGCCGATGTGG 59.402 50.000 0.00 0.00 42.50 4.17
4196 4522 7.412853 TTTTTGGGATTGGTTATTAGTAGGC 57.587 36.000 0.00 0.00 0.00 3.93
4197 4523 4.345859 TGGGATTGGTTATTAGTAGGCG 57.654 45.455 0.00 0.00 0.00 5.52
4199 4525 4.039973 TGGGATTGGTTATTAGTAGGCGAG 59.960 45.833 0.00 0.00 0.00 5.03
4201 4527 5.244626 GGGATTGGTTATTAGTAGGCGAGTA 59.755 44.000 0.00 0.00 0.00 2.59
4203 4529 7.384477 GGATTGGTTATTAGTAGGCGAGTATT 58.616 38.462 0.00 0.00 0.00 1.89
4207 4533 9.754382 TTGGTTATTAGTAGGCGAGTATTTTAG 57.246 33.333 0.00 0.00 0.00 1.85
4208 4534 7.869429 TGGTTATTAGTAGGCGAGTATTTTAGC 59.131 37.037 0.00 0.00 0.00 3.09
4209 4535 7.869429 GGTTATTAGTAGGCGAGTATTTTAGCA 59.131 37.037 0.00 0.00 0.00 3.49
4210 4536 9.252962 GTTATTAGTAGGCGAGTATTTTAGCAA 57.747 33.333 0.00 0.00 0.00 3.91
4211 4537 9.820725 TTATTAGTAGGCGAGTATTTTAGCAAA 57.179 29.630 0.00 0.00 0.00 3.68
4214 4540 3.014623 AGGCGAGTATTTTAGCAAACCC 58.985 45.455 0.00 0.00 0.00 4.11
4215 4541 3.014623 GGCGAGTATTTTAGCAAACCCT 58.985 45.455 0.00 0.00 0.00 4.34
4217 4543 4.412207 GCGAGTATTTTAGCAAACCCTTG 58.588 43.478 0.00 0.00 35.49 3.61
4218 4544 4.674362 GCGAGTATTTTAGCAAACCCTTGG 60.674 45.833 0.00 0.00 32.76 3.61
4219 4545 4.142469 CGAGTATTTTAGCAAACCCTTGGG 60.142 45.833 3.77 3.77 32.76 4.12
4220 4546 5.005628 AGTATTTTAGCAAACCCTTGGGA 57.994 39.130 13.39 0.00 32.76 4.37
4221 4547 5.016831 AGTATTTTAGCAAACCCTTGGGAG 58.983 41.667 13.39 3.19 32.76 4.30
4222 4548 2.302587 TTTAGCAAACCCTTGGGAGG 57.697 50.000 13.39 2.45 43.15 4.30
4223 4549 0.251608 TTAGCAAACCCTTGGGAGGC 60.252 55.000 13.39 11.96 42.09 4.70
4224 4550 1.431195 TAGCAAACCCTTGGGAGGCA 61.431 55.000 13.39 1.97 42.09 4.75
4225 4551 2.278330 GCAAACCCTTGGGAGGCAG 61.278 63.158 13.39 0.00 42.09 4.85
4226 4552 1.607467 CAAACCCTTGGGAGGCAGG 60.607 63.158 13.39 0.00 42.09 4.85
4227 4553 2.091283 AAACCCTTGGGAGGCAGGT 61.091 57.895 13.39 0.00 42.09 4.00
4228 4554 2.371897 AAACCCTTGGGAGGCAGGTG 62.372 60.000 13.39 0.00 42.09 4.00
4229 4555 4.052518 CCCTTGGGAGGCAGGTGG 62.053 72.222 0.00 0.00 42.09 4.61
4231 4557 2.311854 CCTTGGGAGGCAGGTGGAT 61.312 63.158 0.00 0.00 35.94 3.41
4233 4559 0.918983 CTTGGGAGGCAGGTGGATTA 59.081 55.000 0.00 0.00 0.00 1.75
4234 4560 1.496429 CTTGGGAGGCAGGTGGATTAT 59.504 52.381 0.00 0.00 0.00 1.28
4237 4563 1.202818 GGGAGGCAGGTGGATTATCAC 60.203 57.143 0.00 0.00 36.95 3.06
4238 4564 1.490490 GGAGGCAGGTGGATTATCACA 59.510 52.381 0.00 0.00 39.27 3.58
4241 4567 2.158564 AGGCAGGTGGATTATCACATGG 60.159 50.000 10.79 0.00 45.89 3.66
4242 4568 2.233271 GCAGGTGGATTATCACATGGG 58.767 52.381 10.79 0.00 45.89 4.00
4243 4569 2.423373 GCAGGTGGATTATCACATGGGT 60.423 50.000 10.79 0.00 45.89 4.51
4348 4775 2.507058 TCTAGTAACTCCTCCGCCTGTA 59.493 50.000 0.00 0.00 0.00 2.74
4357 4784 2.093658 TCCTCCGCCTGTACATTTTCTC 60.094 50.000 0.00 0.00 0.00 2.87
4500 4964 9.292195 TCTATATGTACAACTAATCGACATGGA 57.708 33.333 0.00 0.00 33.05 3.41
4650 5115 6.072563 GCAATTAGTACCGGGTAAAACTTCAA 60.073 38.462 8.81 0.00 0.00 2.69
4770 5251 5.757099 AGTATACACAACCAAGTTAGGCT 57.243 39.130 5.50 0.00 0.00 4.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.112927 ACAAGGGAACAATGCAAATAACAT 57.887 33.333 0.00 0.00 0.00 2.71
2 3 5.988561 TCAACAAGGGAACAATGCAAATAAC 59.011 36.000 0.00 0.00 0.00 1.89
5 6 4.686191 TCAACAAGGGAACAATGCAAAT 57.314 36.364 0.00 0.00 0.00 2.32
7 8 3.181467 CCTTCAACAAGGGAACAATGCAA 60.181 43.478 0.00 0.00 45.27 4.08
8 9 2.364970 CCTTCAACAAGGGAACAATGCA 59.635 45.455 0.00 0.00 45.27 3.96
9 10 3.030668 CCTTCAACAAGGGAACAATGC 57.969 47.619 0.00 0.00 45.27 3.56
10 11 2.364970 TGCCTTCAACAAGGGAACAATG 59.635 45.455 2.98 0.00 46.64 2.82
11 12 2.676748 TGCCTTCAACAAGGGAACAAT 58.323 42.857 2.98 0.00 46.64 2.71
12 13 2.151502 TGCCTTCAACAAGGGAACAA 57.848 45.000 2.98 0.00 46.64 2.83
13 14 3.913855 TGCCTTCAACAAGGGAACA 57.086 47.368 2.98 0.00 46.64 3.18
34 35 0.179062 AATCCAGAGCACATCCGAGC 60.179 55.000 0.00 0.00 0.00 5.03
52 53 2.946990 GGTTTTCACCCTGAAGAACGAA 59.053 45.455 0.00 0.00 37.70 3.85
63 64 3.017442 GGCAGAATCTAGGTTTTCACCC 58.983 50.000 0.00 0.00 45.63 4.61
65 66 4.579869 TCTGGCAGAATCTAGGTTTTCAC 58.420 43.478 16.28 0.00 0.00 3.18
83 84 1.865865 CCATCGTTACCGGATTCTGG 58.134 55.000 9.46 10.13 33.95 3.86
105 116 2.892852 CTTCAGGAAGGAATGGCACAAA 59.107 45.455 1.01 0.00 36.93 2.83
118 131 2.023673 CAACAGCAACACCTTCAGGAA 58.976 47.619 0.00 0.00 38.94 3.36
128 141 2.159099 ACGAGTCTCTTCAACAGCAACA 60.159 45.455 0.00 0.00 0.00 3.33
130 143 2.866156 CAACGAGTCTCTTCAACAGCAA 59.134 45.455 0.00 0.00 0.00 3.91
133 146 3.053455 GGACAACGAGTCTCTTCAACAG 58.947 50.000 11.36 0.00 46.72 3.16
143 156 1.217882 CACCACAAGGACAACGAGTC 58.782 55.000 0.00 0.00 46.83 3.36
144 157 0.539986 ACACCACAAGGACAACGAGT 59.460 50.000 0.00 0.00 38.69 4.18
145 158 0.937304 CACACCACAAGGACAACGAG 59.063 55.000 0.00 0.00 38.69 4.18
146 159 0.537653 TCACACCACAAGGACAACGA 59.462 50.000 0.00 0.00 38.69 3.85
147 160 1.330521 CTTCACACCACAAGGACAACG 59.669 52.381 0.00 0.00 38.69 4.10
148 161 2.614057 CTCTTCACACCACAAGGACAAC 59.386 50.000 0.00 0.00 38.69 3.32
150 163 2.115427 TCTCTTCACACCACAAGGACA 58.885 47.619 0.00 0.00 38.69 4.02
151 164 2.910688 TCTCTTCACACCACAAGGAC 57.089 50.000 0.00 0.00 38.69 3.85
154 167 3.131709 ACCATCTCTTCACACCACAAG 57.868 47.619 0.00 0.00 0.00 3.16
155 168 3.213506 CAACCATCTCTTCACACCACAA 58.786 45.455 0.00 0.00 0.00 3.33
164 177 0.036388 TCCGCACCAACCATCTCTTC 60.036 55.000 0.00 0.00 0.00 2.87
208 224 3.737266 TCTAAACCGATCAACACAACGAC 59.263 43.478 0.00 0.00 0.00 4.34
211 227 4.151867 GTCCTCTAAACCGATCAACACAAC 59.848 45.833 0.00 0.00 0.00 3.32
216 232 6.427242 AGAAAAAGTCCTCTAAACCGATCAAC 59.573 38.462 0.00 0.00 0.00 3.18
251 267 9.869757 AAAGTCATATAAAACCAAAGTTATGCC 57.130 29.630 0.00 0.00 34.19 4.40
290 307 2.659023 CGCACACACACAAATAGACACG 60.659 50.000 0.00 0.00 0.00 4.49
295 312 3.600717 TCAACGCACACACACAAATAG 57.399 42.857 0.00 0.00 0.00 1.73
304 321 1.100463 AGCCAACATCAACGCACACA 61.100 50.000 0.00 0.00 0.00 3.72
311 328 0.385029 TGCACACAGCCAACATCAAC 59.615 50.000 0.00 0.00 44.83 3.18
329 346 2.611473 CGGCCTCTGCATAACTAGGATG 60.611 54.545 0.00 0.00 40.13 3.51
330 347 1.620819 CGGCCTCTGCATAACTAGGAT 59.379 52.381 0.00 0.00 40.13 3.24
331 348 1.040646 CGGCCTCTGCATAACTAGGA 58.959 55.000 0.00 0.00 40.13 2.94
332 349 1.040646 TCGGCCTCTGCATAACTAGG 58.959 55.000 0.00 0.00 40.13 3.02
333 350 2.890808 TTCGGCCTCTGCATAACTAG 57.109 50.000 0.00 0.00 40.13 2.57
334 351 2.434336 ACATTCGGCCTCTGCATAACTA 59.566 45.455 0.00 0.00 40.13 2.24
335 352 1.210478 ACATTCGGCCTCTGCATAACT 59.790 47.619 0.00 0.00 40.13 2.24
336 353 1.331756 CACATTCGGCCTCTGCATAAC 59.668 52.381 0.00 0.00 40.13 1.89
337 354 1.065491 ACACATTCGGCCTCTGCATAA 60.065 47.619 0.00 0.00 40.13 1.90
338 355 0.541392 ACACATTCGGCCTCTGCATA 59.459 50.000 0.00 0.00 40.13 3.14
339 356 1.028330 CACACATTCGGCCTCTGCAT 61.028 55.000 0.00 0.00 40.13 3.96
340 357 1.672030 CACACATTCGGCCTCTGCA 60.672 57.895 0.00 0.00 40.13 4.41
341 358 3.044059 GCACACATTCGGCCTCTGC 62.044 63.158 0.00 0.00 0.00 4.26
342 359 1.364626 GAGCACACATTCGGCCTCTG 61.365 60.000 0.00 0.00 0.00 3.35
343 360 1.078848 GAGCACACATTCGGCCTCT 60.079 57.895 0.00 0.00 0.00 3.69
344 361 0.745845 ATGAGCACACATTCGGCCTC 60.746 55.000 0.00 0.00 0.00 4.70
345 362 0.322816 AATGAGCACACATTCGGCCT 60.323 50.000 0.00 0.00 35.92 5.19
346 363 0.179156 CAATGAGCACACATTCGGCC 60.179 55.000 0.00 0.00 38.25 6.13
347 364 0.523072 ACAATGAGCACACATTCGGC 59.477 50.000 0.00 0.00 38.25 5.54
348 365 1.536766 ACACAATGAGCACACATTCGG 59.463 47.619 0.00 0.00 38.25 4.30
349 366 2.975410 ACACAATGAGCACACATTCG 57.025 45.000 0.00 0.00 38.25 3.34
350 367 4.362279 ACAAACACAATGAGCACACATTC 58.638 39.130 0.00 0.00 38.25 2.67
351 368 4.389890 ACAAACACAATGAGCACACATT 57.610 36.364 0.00 0.00 40.50 2.71
352 369 5.710513 ATACAAACACAATGAGCACACAT 57.289 34.783 0.00 0.00 0.00 3.21
353 370 5.067023 TGAATACAAACACAATGAGCACACA 59.933 36.000 0.00 0.00 0.00 3.72
354 371 5.399301 GTGAATACAAACACAATGAGCACAC 59.601 40.000 0.00 0.00 37.05 3.82
355 372 5.299028 AGTGAATACAAACACAATGAGCACA 59.701 36.000 0.00 0.00 39.18 4.57
356 373 5.762045 AGTGAATACAAACACAATGAGCAC 58.238 37.500 0.00 0.00 39.18 4.40
357 374 6.039159 TCAAGTGAATACAAACACAATGAGCA 59.961 34.615 0.00 0.00 39.18 4.26
358 375 6.437928 TCAAGTGAATACAAACACAATGAGC 58.562 36.000 0.00 0.00 39.18 4.26
359 376 7.061441 GCATCAAGTGAATACAAACACAATGAG 59.939 37.037 0.00 0.00 37.96 2.90
360 377 6.862608 GCATCAAGTGAATACAAACACAATGA 59.137 34.615 0.00 0.00 38.45 2.57
361 378 6.864685 AGCATCAAGTGAATACAAACACAATG 59.135 34.615 0.00 0.00 39.18 2.82
362 379 6.985117 AGCATCAAGTGAATACAAACACAAT 58.015 32.000 0.00 0.00 39.18 2.71
363 380 6.389830 AGCATCAAGTGAATACAAACACAA 57.610 33.333 0.00 0.00 39.18 3.33
364 381 6.039159 TGAAGCATCAAGTGAATACAAACACA 59.961 34.615 0.00 0.00 39.18 3.72
365 382 6.437928 TGAAGCATCAAGTGAATACAAACAC 58.562 36.000 0.00 0.00 37.30 3.32
366 383 6.631971 TGAAGCATCAAGTGAATACAAACA 57.368 33.333 0.00 0.00 30.99 2.83
367 384 8.524870 AAATGAAGCATCAAGTGAATACAAAC 57.475 30.769 0.00 0.00 39.49 2.93
368 385 8.980610 CAAAATGAAGCATCAAGTGAATACAAA 58.019 29.630 0.00 0.00 39.49 2.83
369 386 8.358895 TCAAAATGAAGCATCAAGTGAATACAA 58.641 29.630 0.00 0.00 39.49 2.41
370 387 7.884257 TCAAAATGAAGCATCAAGTGAATACA 58.116 30.769 0.00 0.00 39.49 2.29
371 388 8.025445 ACTCAAAATGAAGCATCAAGTGAATAC 58.975 33.333 0.00 0.00 39.49 1.89
372 389 8.114331 ACTCAAAATGAAGCATCAAGTGAATA 57.886 30.769 0.00 0.00 39.49 1.75
373 390 6.989659 ACTCAAAATGAAGCATCAAGTGAAT 58.010 32.000 0.00 0.00 39.49 2.57
374 391 6.039605 TGACTCAAAATGAAGCATCAAGTGAA 59.960 34.615 0.00 0.00 39.49 3.18
375 392 5.532032 TGACTCAAAATGAAGCATCAAGTGA 59.468 36.000 0.00 0.00 39.49 3.41
376 393 5.765176 TGACTCAAAATGAAGCATCAAGTG 58.235 37.500 0.00 0.00 39.49 3.16
377 394 6.395426 TTGACTCAAAATGAAGCATCAAGT 57.605 33.333 0.00 0.00 39.49 3.16
378 395 8.975410 TTATTGACTCAAAATGAAGCATCAAG 57.025 30.769 0.00 0.00 39.49 3.02
379 396 9.761504 TTTTATTGACTCAAAATGAAGCATCAA 57.238 25.926 0.00 0.00 39.49 2.57
380 397 9.932207 ATTTTATTGACTCAAAATGAAGCATCA 57.068 25.926 0.00 0.00 40.57 3.07
382 399 9.374838 GGATTTTATTGACTCAAAATGAAGCAT 57.625 29.630 0.00 0.00 35.14 3.79
383 400 8.366401 TGGATTTTATTGACTCAAAATGAAGCA 58.634 29.630 0.00 0.00 35.14 3.91
384 401 8.650714 GTGGATTTTATTGACTCAAAATGAAGC 58.349 33.333 0.00 0.00 35.14 3.86
385 402 9.143631 GGTGGATTTTATTGACTCAAAATGAAG 57.856 33.333 0.00 0.00 35.14 3.02
386 403 8.093927 GGGTGGATTTTATTGACTCAAAATGAA 58.906 33.333 0.00 0.00 35.14 2.57
387 404 7.454380 AGGGTGGATTTTATTGACTCAAAATGA 59.546 33.333 0.00 0.00 35.14 2.57
388 405 7.614494 AGGGTGGATTTTATTGACTCAAAATG 58.386 34.615 0.00 0.00 35.14 2.32
389 406 7.797121 AGGGTGGATTTTATTGACTCAAAAT 57.203 32.000 0.00 0.00 37.12 1.82
390 407 7.610580 AAGGGTGGATTTTATTGACTCAAAA 57.389 32.000 0.00 0.00 0.00 2.44
391 408 7.610580 AAAGGGTGGATTTTATTGACTCAAA 57.389 32.000 0.00 0.00 0.00 2.69
392 409 8.893563 ATAAAGGGTGGATTTTATTGACTCAA 57.106 30.769 0.00 0.00 0.00 3.02
393 410 7.282224 CGATAAAGGGTGGATTTTATTGACTCA 59.718 37.037 0.00 0.00 34.63 3.41
394 411 7.497909 TCGATAAAGGGTGGATTTTATTGACTC 59.502 37.037 3.83 0.00 35.91 3.36
395 412 7.343357 TCGATAAAGGGTGGATTTTATTGACT 58.657 34.615 3.83 0.00 35.91 3.41
396 413 7.562454 TCGATAAAGGGTGGATTTTATTGAC 57.438 36.000 3.83 0.00 35.91 3.18
397 414 8.582657 TTTCGATAAAGGGTGGATTTTATTGA 57.417 30.769 0.00 3.83 37.65 2.57
398 415 9.646427 TTTTTCGATAAAGGGTGGATTTTATTG 57.354 29.630 0.00 0.00 34.27 1.90
421 438 9.260002 CTGATTTGTTTAGTGCCAGTAATTTTT 57.740 29.630 0.00 0.00 0.00 1.94
422 439 8.421002 ACTGATTTGTTTAGTGCCAGTAATTTT 58.579 29.630 0.00 0.00 32.39 1.82
423 440 7.951591 ACTGATTTGTTTAGTGCCAGTAATTT 58.048 30.769 0.00 0.00 32.39 1.82
424 441 7.524717 ACTGATTTGTTTAGTGCCAGTAATT 57.475 32.000 0.00 0.00 32.39 1.40
425 442 7.524717 AACTGATTTGTTTAGTGCCAGTAAT 57.475 32.000 0.00 0.00 33.61 1.89
426 443 6.952773 AACTGATTTGTTTAGTGCCAGTAA 57.047 33.333 0.00 0.00 33.61 2.24
427 444 6.952773 AAACTGATTTGTTTAGTGCCAGTA 57.047 33.333 0.00 0.00 38.25 2.74
428 445 5.852282 AAACTGATTTGTTTAGTGCCAGT 57.148 34.783 0.00 0.00 38.25 4.00
470 487 1.156736 CGTCGAAACAGCCAAGGATT 58.843 50.000 0.00 0.00 0.00 3.01
471 488 0.034896 ACGTCGAAACAGCCAAGGAT 59.965 50.000 0.00 0.00 0.00 3.24
472 489 0.599204 GACGTCGAAACAGCCAAGGA 60.599 55.000 0.00 0.00 0.00 3.36
473 490 0.878523 TGACGTCGAAACAGCCAAGG 60.879 55.000 11.62 0.00 0.00 3.61
474 491 0.232303 GTGACGTCGAAACAGCCAAG 59.768 55.000 11.62 0.00 0.00 3.61
475 492 0.179094 AGTGACGTCGAAACAGCCAA 60.179 50.000 11.62 0.00 0.00 4.52
476 493 0.596600 GAGTGACGTCGAAACAGCCA 60.597 55.000 11.62 0.00 0.00 4.75
477 494 1.606350 CGAGTGACGTCGAAACAGCC 61.606 60.000 11.62 0.00 42.85 4.85
478 495 0.659417 TCGAGTGACGTCGAAACAGC 60.659 55.000 11.62 0.00 45.74 4.40
479 496 3.449789 TCGAGTGACGTCGAAACAG 57.550 52.632 11.62 2.79 45.74 3.16
503 520 1.909700 AATGACCTCGCAACATTGGT 58.090 45.000 0.00 0.00 33.79 3.67
782 816 1.667830 CAGACGTGCGTGGAATGGT 60.668 57.895 0.67 0.00 0.00 3.55
850 884 1.598856 AAGAGAGGGGAGGGAGGAGG 61.599 65.000 0.00 0.00 0.00 4.30
851 885 0.105709 GAAGAGAGGGGAGGGAGGAG 60.106 65.000 0.00 0.00 0.00 3.69
852 886 1.595058 GGAAGAGAGGGGAGGGAGGA 61.595 65.000 0.00 0.00 0.00 3.71
853 887 1.074850 GGAAGAGAGGGGAGGGAGG 60.075 68.421 0.00 0.00 0.00 4.30
854 888 0.105709 GAGGAAGAGAGGGGAGGGAG 60.106 65.000 0.00 0.00 0.00 4.30
855 889 1.595058 GGAGGAAGAGAGGGGAGGGA 61.595 65.000 0.00 0.00 0.00 4.20
856 890 1.074850 GGAGGAAGAGAGGGGAGGG 60.075 68.421 0.00 0.00 0.00 4.30
862 896 1.074850 GGGAGGGGAGGAAGAGAGG 60.075 68.421 0.00 0.00 0.00 3.69
884 918 1.342074 CAGTTGAGTGGAGTGGAGGA 58.658 55.000 0.00 0.00 0.00 3.71
885 919 1.001406 GACAGTTGAGTGGAGTGGAGG 59.999 57.143 0.00 0.00 0.00 4.30
886 920 1.688735 TGACAGTTGAGTGGAGTGGAG 59.311 52.381 0.00 0.00 0.00 3.86
887 921 1.412710 GTGACAGTTGAGTGGAGTGGA 59.587 52.381 0.00 0.00 0.00 4.02
888 922 1.138859 TGTGACAGTTGAGTGGAGTGG 59.861 52.381 0.00 0.00 0.00 4.00
942 976 0.386478 CAAGAACTTGCTCTTGCCGC 60.386 55.000 1.60 0.00 44.24 6.53
956 990 0.664466 CTCGTCTGCGCTGACAAGAA 60.664 55.000 36.11 21.75 36.82 2.52
1149 1183 2.874010 CTAGCACTCGCCGTCCACTG 62.874 65.000 0.00 0.00 39.83 3.66
1222 1261 2.479049 AGAACATATTCGTCGGACACCG 60.479 50.000 9.10 3.66 43.34 4.94
1263 1302 2.443255 AGGTCATGGACATGGGGATTAC 59.557 50.000 11.98 2.40 39.24 1.89
1382 1429 1.565759 CCCCACATCAGGATTCAGGAA 59.434 52.381 0.00 0.00 0.00 3.36
1495 1644 2.512515 GATGGACTGCTGCCGGAC 60.513 66.667 5.05 0.00 0.00 4.79
1719 1868 1.153349 GACGTTGATGGGGCTCTCC 60.153 63.158 0.00 0.00 0.00 3.71
1887 2036 2.669569 GGCTTCAGGAAGTGCGCA 60.670 61.111 5.66 5.66 40.45 6.09
2113 2262 5.987953 TGATCTTGAGTGTCTTGAAGTTCAG 59.012 40.000 5.56 1.19 0.00 3.02
2160 2309 0.326264 CCTTAGCAGCTCCCTTGTGT 59.674 55.000 0.00 0.00 0.00 3.72
2175 2324 1.063114 GGAGTAGCCCCTGTCTCCTTA 60.063 57.143 0.00 0.00 42.02 2.69
2184 2333 1.645710 CATTATCCGGAGTAGCCCCT 58.354 55.000 11.34 0.00 0.00 4.79
2190 2339 3.833732 AGTCTGAGCATTATCCGGAGTA 58.166 45.455 11.34 0.00 0.00 2.59
2199 2348 5.222079 TGGTGTTGTAAGTCTGAGCATTA 57.778 39.130 0.00 0.00 0.00 1.90
2241 2390 0.673333 CAGGCGTGCCACTGTCATTA 60.673 55.000 14.29 0.00 38.92 1.90
2262 2411 3.821421 TCTATTTCTTCTCCGGGCTTC 57.179 47.619 0.00 0.00 0.00 3.86
2388 2537 0.745845 CATTTCCTCGGCCAGTCCAG 60.746 60.000 2.24 0.00 34.01 3.86
2494 2643 1.434696 GACCGCATGCCCAATTCAG 59.565 57.895 13.15 0.00 0.00 3.02
2746 2898 2.416431 CCAAAGCCAGTAATGAAGCAGC 60.416 50.000 0.00 0.00 0.00 5.25
2793 2945 6.394809 TCTGCGAATGTAGACTTACAATTGA 58.605 36.000 13.59 0.00 42.72 2.57
2804 2956 6.587608 CAGCACATATTATCTGCGAATGTAGA 59.412 38.462 0.00 0.00 41.27 2.59
2810 2962 4.948847 AGTCAGCACATATTATCTGCGAA 58.051 39.130 0.00 0.00 35.98 4.70
2812 2964 5.222631 TGTAGTCAGCACATATTATCTGCG 58.777 41.667 0.00 0.00 35.98 5.18
2818 2970 9.313118 CATAAACACTGTAGTCAGCACATATTA 57.687 33.333 0.00 0.00 44.77 0.98
3042 3263 8.991026 CATGATTAGGCATTCAAAAGTCAAAAA 58.009 29.630 0.00 0.00 0.00 1.94
3104 3325 6.947464 ACCTAACAGATTTTAGCTAGAAGCA 58.053 36.000 13.95 0.00 45.56 3.91
3221 3468 7.928307 TGCAGAACTAGCAAATAAGAAGAAT 57.072 32.000 0.00 0.00 39.39 2.40
3312 3562 9.878667 AAATTGTTCTCATATGATTCATGCAAA 57.121 25.926 5.72 0.00 0.00 3.68
3447 3697 3.323979 ACGAGGATCACAACTGGTTTAGT 59.676 43.478 0.00 0.00 36.56 2.24
3574 3824 4.345257 GGGAAGATTATCCAGCTGACACTA 59.655 45.833 17.39 0.00 41.55 2.74
3596 3846 6.730960 AGCAAAGCAATACAAAATCATTGG 57.269 33.333 0.00 0.00 33.61 3.16
3719 4030 4.732285 AGTTAGTGCAAACTGTTGATCG 57.268 40.909 2.97 0.00 38.28 3.69
3851 4177 2.749441 GGAAGCACAGGGAGCAGC 60.749 66.667 0.00 0.00 0.00 5.25
3882 4208 5.067273 TCCGAAAAATCACAGAAAGCCTAA 58.933 37.500 0.00 0.00 0.00 2.69
3884 4210 3.486383 TCCGAAAAATCACAGAAAGCCT 58.514 40.909 0.00 0.00 0.00 4.58
3899 4225 0.601558 AACTAGAGCGTGCTCCGAAA 59.398 50.000 17.76 1.53 43.70 3.46
3961 4287 5.505181 ACATCAGAACATTACTGGTTCCT 57.495 39.130 0.00 0.00 44.40 3.36
3984 4310 1.004745 CCTACTGCCACCTTTCACCAT 59.995 52.381 0.00 0.00 0.00 3.55
4031 4357 2.696506 CAGCGATGCACATCCATAGAT 58.303 47.619 5.09 0.00 34.40 1.98
4035 4361 2.540228 CGCAGCGATGCACATCCAT 61.540 57.895 26.87 0.00 34.40 3.41
4098 4424 1.204704 CAGTTAGAGACCACATCGGCA 59.795 52.381 0.00 0.00 39.03 5.69
4100 4426 2.881074 CACAGTTAGAGACCACATCGG 58.119 52.381 0.00 0.00 42.50 4.18
4102 4428 3.056536 TGAGCACAGTTAGAGACCACATC 60.057 47.826 0.00 0.00 0.00 3.06
4103 4429 2.899900 TGAGCACAGTTAGAGACCACAT 59.100 45.455 0.00 0.00 0.00 3.21
4106 4432 3.435275 AGATGAGCACAGTTAGAGACCA 58.565 45.455 0.00 0.00 0.00 4.02
4107 4433 4.464069 AAGATGAGCACAGTTAGAGACC 57.536 45.455 0.00 0.00 0.00 3.85
4108 4434 6.529829 CAGTAAAGATGAGCACAGTTAGAGAC 59.470 42.308 0.00 0.00 0.00 3.36
4175 4501 4.409574 TCGCCTACTAATAACCAATCCCAA 59.590 41.667 0.00 0.00 0.00 4.12
4177 4503 4.040095 ACTCGCCTACTAATAACCAATCCC 59.960 45.833 0.00 0.00 0.00 3.85
4178 4504 5.211174 ACTCGCCTACTAATAACCAATCC 57.789 43.478 0.00 0.00 0.00 3.01
4181 4507 9.754382 CTAAAATACTCGCCTACTAATAACCAA 57.246 33.333 0.00 0.00 0.00 3.67
4185 4511 9.820725 TTTGCTAAAATACTCGCCTACTAATAA 57.179 29.630 0.00 0.00 0.00 1.40
4186 4512 9.252962 GTTTGCTAAAATACTCGCCTACTAATA 57.747 33.333 0.00 0.00 0.00 0.98
4187 4513 7.226128 GGTTTGCTAAAATACTCGCCTACTAAT 59.774 37.037 0.00 0.00 0.00 1.73
4188 4514 6.536224 GGTTTGCTAAAATACTCGCCTACTAA 59.464 38.462 0.00 0.00 0.00 2.24
4190 4516 4.874396 GGTTTGCTAAAATACTCGCCTACT 59.126 41.667 0.00 0.00 0.00 2.57
4191 4517 4.034858 GGGTTTGCTAAAATACTCGCCTAC 59.965 45.833 0.00 0.00 0.00 3.18
4194 4520 3.014623 AGGGTTTGCTAAAATACTCGCC 58.985 45.455 0.00 0.00 0.00 5.54
4195 4521 4.412207 CAAGGGTTTGCTAAAATACTCGC 58.588 43.478 0.00 0.00 0.00 5.03
4196 4522 4.142469 CCCAAGGGTTTGCTAAAATACTCG 60.142 45.833 0.00 0.00 32.79 4.18
4197 4523 5.014202 TCCCAAGGGTTTGCTAAAATACTC 58.986 41.667 4.80 0.00 36.47 2.59
4199 4525 4.159693 CCTCCCAAGGGTTTGCTAAAATAC 59.840 45.833 4.80 0.00 39.21 1.89
4201 4527 3.173151 CCTCCCAAGGGTTTGCTAAAAT 58.827 45.455 4.80 0.00 39.21 1.82
4203 4529 1.825641 GCCTCCCAAGGGTTTGCTAAA 60.826 52.381 4.80 0.00 43.58 1.85
4206 4532 2.118294 GCCTCCCAAGGGTTTGCT 59.882 61.111 4.80 0.00 43.58 3.91
4207 4533 2.203625 TGCCTCCCAAGGGTTTGC 60.204 61.111 4.80 7.13 43.58 3.68
4208 4534 1.607467 CCTGCCTCCCAAGGGTTTG 60.607 63.158 4.80 0.00 43.58 2.93
4209 4535 2.091283 ACCTGCCTCCCAAGGGTTT 61.091 57.895 4.80 0.00 43.58 3.27
4210 4536 2.452491 ACCTGCCTCCCAAGGGTT 60.452 61.111 4.80 0.00 43.58 4.11
4211 4537 3.260100 CACCTGCCTCCCAAGGGT 61.260 66.667 4.80 0.00 43.58 4.34
4214 4540 0.918983 TAATCCACCTGCCTCCCAAG 59.081 55.000 0.00 0.00 0.00 3.61
4215 4541 1.494721 GATAATCCACCTGCCTCCCAA 59.505 52.381 0.00 0.00 0.00 4.12
4217 4543 1.140312 TGATAATCCACCTGCCTCCC 58.860 55.000 0.00 0.00 0.00 4.30
4218 4544 1.490490 TGTGATAATCCACCTGCCTCC 59.510 52.381 0.00 0.00 36.26 4.30
4219 4545 3.144506 CATGTGATAATCCACCTGCCTC 58.855 50.000 0.00 0.00 36.26 4.70
4220 4546 2.158564 CCATGTGATAATCCACCTGCCT 60.159 50.000 0.00 0.00 36.26 4.75
4221 4547 2.233271 CCATGTGATAATCCACCTGCC 58.767 52.381 0.00 0.00 36.26 4.85
4222 4548 2.233271 CCCATGTGATAATCCACCTGC 58.767 52.381 0.00 0.00 36.26 4.85
4223 4549 3.582998 ACCCATGTGATAATCCACCTG 57.417 47.619 0.00 0.00 36.26 4.00
4224 4550 3.269381 ACAACCCATGTGATAATCCACCT 59.731 43.478 0.00 0.00 41.93 4.00
4225 4551 3.631250 ACAACCCATGTGATAATCCACC 58.369 45.455 0.00 0.00 41.93 4.61
4226 4552 5.067283 GGTTACAACCCATGTGATAATCCAC 59.933 44.000 0.00 0.00 43.77 4.02
4227 4553 5.197451 GGTTACAACCCATGTGATAATCCA 58.803 41.667 0.00 0.00 43.77 3.41
4228 4554 5.767816 GGTTACAACCCATGTGATAATCC 57.232 43.478 0.00 0.00 43.77 3.01
4242 4568 6.077838 GTGAATGAAACGATGAGGTTACAAC 58.922 40.000 0.00 0.00 0.00 3.32
4243 4569 5.180492 GGTGAATGAAACGATGAGGTTACAA 59.820 40.000 0.00 0.00 0.00 2.41
4348 4775 6.436843 AACAGTTGAAGTTCGAGAAAATGT 57.563 33.333 0.00 0.02 31.09 2.71
4357 4784 9.028185 ACTAGTAAAACTAACAGTTGAAGTTCG 57.972 33.333 0.00 0.00 38.66 3.95
4650 5115 7.649306 GTGCACACTTACAATTGAAAGATTCTT 59.351 33.333 13.17 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.