Multiple sequence alignment - TraesCS5A01G074700

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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 TraesCS5A01G074700 chr5A 100.000 4162 0 0 1 4162 87985833 87981672 0.000000e+00 7686.0
1 TraesCS5A01G074700 chr5A 94.578 332 13 5 308 636 653049632 653049303 3.710000e-140 508.0
2 TraesCS5A01G074700 chr5A 87.282 401 44 6 231 628 690430063 690429667 6.340000e-123 451.0
3 TraesCS5A01G074700 chr5D 95.135 1994 87 7 637 2620 94060498 94058505 0.000000e+00 3136.0
4 TraesCS5A01G074700 chr5D 97.172 778 22 0 2607 3384 94051939 94051162 0.000000e+00 1315.0
5 TraesCS5A01G074700 chr5D 86.111 792 31 23 3376 4162 94048363 94047646 0.000000e+00 780.0
6 TraesCS5A01G074700 chr5D 93.991 233 10 4 1 230 94060720 94060489 2.380000e-92 350.0
7 TraesCS5A01G074700 chr5B 94.347 1875 98 3 637 2509 101410912 101409044 0.000000e+00 2868.0
8 TraesCS5A01G074700 chr5B 96.596 1087 28 3 2542 3626 101409045 101407966 0.000000e+00 1794.0
9 TraesCS5A01G074700 chr5B 88.383 439 29 8 3673 4107 101407965 101407545 3.710000e-140 508.0
10 TraesCS5A01G074700 chr5B 95.652 230 8 2 1 230 101411130 101410903 6.570000e-98 368.0
11 TraesCS5A01G074700 chr4A 95.086 407 17 3 231 637 136645859 136645456 4.540000e-179 638.0
12 TraesCS5A01G074700 chr4A 80.460 87 14 3 4078 4162 696544297 696544382 3.470000e-06 63.9
13 TraesCS5A01G074700 chr2A 95.522 402 12 5 230 628 163850592 163850990 4.540000e-179 638.0
14 TraesCS5A01G074700 chr2A 88.732 71 8 0 4089 4159 644060241 644060311 2.060000e-13 87.9
15 TraesCS5A01G074700 chr6D 93.171 410 24 4 231 636 355101016 355100607 2.140000e-167 599.0
16 TraesCS5A01G074700 chr6D 89.189 74 8 0 4089 4162 82643201 82643274 4.430000e-15 93.5
17 TraesCS5A01G074700 chr4D 86.783 401 45 7 231 626 434981856 434981459 1.370000e-119 440.0
18 TraesCS5A01G074700 chr4D 87.671 73 9 0 4088 4160 508263377 508263449 7.410000e-13 86.1
19 TraesCS5A01G074700 chr2D 86.500 400 49 5 231 626 155775417 155775815 6.390000e-118 435.0
20 TraesCS5A01G074700 chr2D 88.462 78 9 0 4085 4162 333218819 333218896 1.230000e-15 95.3
21 TraesCS5A01G074700 chr2D 85.507 69 10 0 4090 4158 108629784 108629852 5.770000e-09 73.1
22 TraesCS5A01G074700 chr3B 86.352 403 44 11 231 626 285350 284952 2.970000e-116 429.0
23 TraesCS5A01G074700 chr3B 85.135 74 10 1 4089 4162 6674622 6674694 1.600000e-09 75.0
24 TraesCS5A01G074700 chr3D 85.372 417 51 9 227 638 184141566 184141155 1.380000e-114 424.0
25 TraesCS5A01G074700 chr7D 86.842 76 9 1 4088 4162 136117833 136117758 2.670000e-12 84.2


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 TraesCS5A01G074700 chr5A 87981672 87985833 4161 True 7686.0 7686 100.0000 1 4162 1 chr5A.!!$R1 4161
1 TraesCS5A01G074700 chr5D 94058505 94060720 2215 True 1743.0 3136 94.5630 1 2620 2 chr5D.!!$R2 2619
2 TraesCS5A01G074700 chr5D 94047646 94051939 4293 True 1047.5 1315 91.6415 2607 4162 2 chr5D.!!$R1 1555
3 TraesCS5A01G074700 chr5B 101407545 101411130 3585 True 1384.5 2868 93.7445 1 4107 4 chr5B.!!$R1 4106

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
267 271 0.179089 CCCGAGCTCCATGACTCTTG 60.179 60.0 8.47 0.00 0.00 3.02 F
268 272 0.179089 CCGAGCTCCATGACTCTTGG 60.179 60.0 8.47 4.82 35.45 3.61 F
2022 2027 0.108186 CACCAGCTAGCGTGATGGAA 60.108 55.0 23.49 0.00 45.53 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2022 2027 0.036164 TAGCAGGTTTGGCACACGAT 59.964 50.00 0.0 0.0 39.29 3.73 R
2131 2136 3.966665 TCTTCTCCCTTGTTTTGCCAAAT 59.033 39.13 0.0 0.0 0.00 2.32 R
3768 6591 0.035630 GCCTGCCTGATTCTGTCTGT 60.036 55.00 0.0 0.0 0.00 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
83 84 7.380536 TCTAAAGAAACATGATTGCAGCAAAT 58.619 30.769 12.97 0.00 0.00 2.32
97 98 3.614870 GCAGCAAATCCAAAAGACGGAAT 60.615 43.478 0.00 0.00 35.77 3.01
139 140 2.028203 GGGCTTTGCTTGATTGGCTAAA 60.028 45.455 0.00 0.00 0.00 1.85
140 141 2.995939 GGCTTTGCTTGATTGGCTAAAC 59.004 45.455 0.00 0.00 0.00 2.01
227 231 9.787532 CAAATAGGTGTTATAACATGTTTGAGG 57.212 33.333 23.49 10.05 41.59 3.86
228 232 9.747898 AAATAGGTGTTATAACATGTTTGAGGA 57.252 29.630 20.72 0.00 41.59 3.71
229 233 8.964476 ATAGGTGTTATAACATGTTTGAGGAG 57.036 34.615 20.72 0.00 41.59 3.69
230 234 5.648092 AGGTGTTATAACATGTTTGAGGAGC 59.352 40.000 20.72 8.31 41.59 4.70
231 235 5.447279 GGTGTTATAACATGTTTGAGGAGCG 60.447 44.000 20.72 0.00 41.59 5.03
232 236 5.350365 GTGTTATAACATGTTTGAGGAGCGA 59.650 40.000 20.72 0.00 41.59 4.93
233 237 5.935206 TGTTATAACATGTTTGAGGAGCGAA 59.065 36.000 17.78 0.00 33.17 4.70
234 238 6.428465 TGTTATAACATGTTTGAGGAGCGAAA 59.572 34.615 17.78 0.00 33.17 3.46
235 239 5.957842 ATAACATGTTTGAGGAGCGAAAA 57.042 34.783 17.78 0.00 0.00 2.29
236 240 3.904136 ACATGTTTGAGGAGCGAAAAG 57.096 42.857 0.00 0.00 0.00 2.27
237 241 3.214328 ACATGTTTGAGGAGCGAAAAGT 58.786 40.909 0.00 0.00 0.00 2.66
238 242 3.003689 ACATGTTTGAGGAGCGAAAAGTG 59.996 43.478 0.00 0.00 0.00 3.16
239 243 1.333619 TGTTTGAGGAGCGAAAAGTGC 59.666 47.619 0.00 0.00 0.00 4.40
240 244 1.333619 GTTTGAGGAGCGAAAAGTGCA 59.666 47.619 0.00 0.00 33.85 4.57
241 245 1.674359 TTGAGGAGCGAAAAGTGCAA 58.326 45.000 0.00 0.00 33.85 4.08
242 246 1.229428 TGAGGAGCGAAAAGTGCAAG 58.771 50.000 0.00 0.00 33.85 4.01
243 247 1.230324 GAGGAGCGAAAAGTGCAAGT 58.770 50.000 0.00 0.00 33.85 3.16
244 248 2.224185 TGAGGAGCGAAAAGTGCAAGTA 60.224 45.455 0.00 0.00 33.85 2.24
245 249 2.413453 GAGGAGCGAAAAGTGCAAGTAG 59.587 50.000 0.00 0.00 33.85 2.57
246 250 1.135944 GGAGCGAAAAGTGCAAGTAGC 60.136 52.381 0.00 0.00 45.96 3.58
247 251 1.801178 GAGCGAAAAGTGCAAGTAGCT 59.199 47.619 0.00 0.00 45.94 3.32
248 252 1.801178 AGCGAAAAGTGCAAGTAGCTC 59.199 47.619 0.00 0.00 45.94 4.09
249 253 1.135944 GCGAAAAGTGCAAGTAGCTCC 60.136 52.381 0.00 0.00 45.94 4.70
250 254 1.464997 CGAAAAGTGCAAGTAGCTCCC 59.535 52.381 0.00 0.00 45.94 4.30
251 255 1.464997 GAAAAGTGCAAGTAGCTCCCG 59.535 52.381 0.00 0.00 45.94 5.14
252 256 0.685097 AAAGTGCAAGTAGCTCCCGA 59.315 50.000 0.00 0.00 45.94 5.14
253 257 0.247736 AAGTGCAAGTAGCTCCCGAG 59.752 55.000 0.00 0.00 45.94 4.63
263 267 3.947173 CTCCCGAGCTCCATGACT 58.053 61.111 8.47 0.00 0.00 3.41
264 268 1.739049 CTCCCGAGCTCCATGACTC 59.261 63.158 8.47 0.00 0.00 3.36
265 269 0.754957 CTCCCGAGCTCCATGACTCT 60.755 60.000 8.47 0.00 0.00 3.24
266 270 0.324738 TCCCGAGCTCCATGACTCTT 60.325 55.000 8.47 0.00 0.00 2.85
267 271 0.179089 CCCGAGCTCCATGACTCTTG 60.179 60.000 8.47 0.00 0.00 3.02
268 272 0.179089 CCGAGCTCCATGACTCTTGG 60.179 60.000 8.47 4.82 35.45 3.61
269 273 0.534412 CGAGCTCCATGACTCTTGGT 59.466 55.000 8.47 0.00 35.64 3.67
270 274 1.751351 CGAGCTCCATGACTCTTGGTA 59.249 52.381 8.47 0.00 35.64 3.25
271 275 2.363680 CGAGCTCCATGACTCTTGGTAT 59.636 50.000 8.47 0.00 35.64 2.73
272 276 3.181471 CGAGCTCCATGACTCTTGGTATT 60.181 47.826 8.47 0.00 35.64 1.89
273 277 4.681781 CGAGCTCCATGACTCTTGGTATTT 60.682 45.833 8.47 0.00 35.64 1.40
274 278 4.521146 AGCTCCATGACTCTTGGTATTTG 58.479 43.478 10.10 0.94 35.64 2.32
275 279 4.225942 AGCTCCATGACTCTTGGTATTTGA 59.774 41.667 10.10 0.00 35.64 2.69
276 280 4.943705 GCTCCATGACTCTTGGTATTTGAA 59.056 41.667 10.10 0.00 35.64 2.69
277 281 5.415701 GCTCCATGACTCTTGGTATTTGAAA 59.584 40.000 10.10 0.00 35.64 2.69
278 282 6.096001 GCTCCATGACTCTTGGTATTTGAAAT 59.904 38.462 10.10 0.00 35.64 2.17
279 283 7.363268 GCTCCATGACTCTTGGTATTTGAAATT 60.363 37.037 10.10 0.00 35.64 1.82
280 284 8.421249 TCCATGACTCTTGGTATTTGAAATTT 57.579 30.769 10.10 0.00 35.64 1.82
281 285 8.869109 TCCATGACTCTTGGTATTTGAAATTTT 58.131 29.630 10.10 0.00 35.64 1.82
282 286 9.492973 CCATGACTCTTGGTATTTGAAATTTTT 57.507 29.630 0.00 0.00 0.00 1.94
316 320 8.539770 CACTTCTAGTGCTCAGAAAAATCTAA 57.460 34.615 0.00 0.00 39.62 2.10
317 321 8.993121 CACTTCTAGTGCTCAGAAAAATCTAAA 58.007 33.333 0.00 0.00 39.62 1.85
318 322 9.561069 ACTTCTAGTGCTCAGAAAAATCTAAAA 57.439 29.630 0.00 0.00 31.84 1.52
355 359 5.740290 ATACACATATTCCTAAGACCCGG 57.260 43.478 0.00 0.00 0.00 5.73
356 360 3.381335 ACACATATTCCTAAGACCCGGT 58.619 45.455 0.00 0.00 0.00 5.28
357 361 4.549668 ACACATATTCCTAAGACCCGGTA 58.450 43.478 0.00 0.00 0.00 4.02
358 362 4.964262 ACACATATTCCTAAGACCCGGTAA 59.036 41.667 0.00 0.00 0.00 2.85
359 363 5.426185 ACACATATTCCTAAGACCCGGTAAA 59.574 40.000 0.00 0.00 0.00 2.01
360 364 6.070078 ACACATATTCCTAAGACCCGGTAAAA 60.070 38.462 0.00 0.00 0.00 1.52
361 365 6.824704 CACATATTCCTAAGACCCGGTAAAAA 59.175 38.462 0.00 0.00 0.00 1.94
362 366 7.501225 CACATATTCCTAAGACCCGGTAAAAAT 59.499 37.037 0.00 0.00 0.00 1.82
363 367 7.718314 ACATATTCCTAAGACCCGGTAAAAATC 59.282 37.037 0.00 0.00 0.00 2.17
364 368 5.767277 TTCCTAAGACCCGGTAAAAATCT 57.233 39.130 0.00 0.00 0.00 2.40
365 369 5.093849 TCCTAAGACCCGGTAAAAATCTG 57.906 43.478 0.00 0.00 0.00 2.90
366 370 4.778958 TCCTAAGACCCGGTAAAAATCTGA 59.221 41.667 0.00 0.00 0.00 3.27
367 371 5.427481 TCCTAAGACCCGGTAAAAATCTGAT 59.573 40.000 0.00 0.00 0.00 2.90
368 372 6.612456 TCCTAAGACCCGGTAAAAATCTGATA 59.388 38.462 0.00 0.00 0.00 2.15
369 373 7.126115 TCCTAAGACCCGGTAAAAATCTGATAA 59.874 37.037 0.00 0.00 0.00 1.75
370 374 7.771826 CCTAAGACCCGGTAAAAATCTGATAAA 59.228 37.037 0.00 0.00 0.00 1.40
371 375 9.169592 CTAAGACCCGGTAAAAATCTGATAAAA 57.830 33.333 0.00 0.00 0.00 1.52
372 376 8.411991 AAGACCCGGTAAAAATCTGATAAAAA 57.588 30.769 0.00 0.00 0.00 1.94
432 436 6.698008 TTCTGACAGAAATGACACAATTGT 57.302 33.333 15.58 4.92 32.46 2.71
433 437 6.698008 TCTGACAGAAATGACACAATTGTT 57.302 33.333 8.77 0.41 35.47 2.83
434 438 6.728200 TCTGACAGAAATGACACAATTGTTC 58.272 36.000 8.77 10.55 35.47 3.18
435 439 6.543465 TCTGACAGAAATGACACAATTGTTCT 59.457 34.615 8.77 5.35 35.47 3.01
436 440 6.728200 TGACAGAAATGACACAATTGTTCTC 58.272 36.000 8.77 7.19 35.47 2.87
437 441 6.543465 TGACAGAAATGACACAATTGTTCTCT 59.457 34.615 8.77 6.74 35.47 3.10
438 442 7.067372 TGACAGAAATGACACAATTGTTCTCTT 59.933 33.333 8.77 7.67 35.47 2.85
439 443 8.450578 ACAGAAATGACACAATTGTTCTCTTA 57.549 30.769 8.77 0.00 35.47 2.10
440 444 9.071276 ACAGAAATGACACAATTGTTCTCTTAT 57.929 29.630 8.77 3.47 35.47 1.73
445 449 9.507329 AATGACACAATTGTTCTCTTATACACT 57.493 29.630 8.77 0.00 35.47 3.55
446 450 8.310406 TGACACAATTGTTCTCTTATACACTG 57.690 34.615 8.77 0.00 35.47 3.66
447 451 7.931407 TGACACAATTGTTCTCTTATACACTGT 59.069 33.333 8.77 0.00 35.47 3.55
448 452 8.311650 ACACAATTGTTCTCTTATACACTGTC 57.688 34.615 8.77 0.00 28.43 3.51
449 453 7.931407 ACACAATTGTTCTCTTATACACTGTCA 59.069 33.333 8.77 0.00 28.43 3.58
450 454 8.438513 CACAATTGTTCTCTTATACACTGTCAG 58.561 37.037 8.77 0.00 0.00 3.51
451 455 8.367911 ACAATTGTTCTCTTATACACTGTCAGA 58.632 33.333 4.92 0.00 0.00 3.27
452 456 9.208022 CAATTGTTCTCTTATACACTGTCAGAA 57.792 33.333 6.91 0.00 0.00 3.02
453 457 9.778741 AATTGTTCTCTTATACACTGTCAGAAA 57.221 29.630 6.91 0.00 0.00 2.52
454 458 9.950496 ATTGTTCTCTTATACACTGTCAGAAAT 57.050 29.630 6.91 0.00 0.00 2.17
455 459 9.778741 TTGTTCTCTTATACACTGTCAGAAATT 57.221 29.630 6.91 0.00 0.00 1.82
456 460 9.778741 TGTTCTCTTATACACTGTCAGAAATTT 57.221 29.630 6.91 0.00 0.00 1.82
458 462 9.778741 TTCTCTTATACACTGTCAGAAATTTGT 57.221 29.630 6.91 2.53 0.00 2.83
459 463 9.778741 TCTCTTATACACTGTCAGAAATTTGTT 57.221 29.630 6.91 0.00 0.00 2.83
485 489 7.701809 TTTTTCTATAGCCCAAAACAAAACG 57.298 32.000 0.00 0.00 0.00 3.60
486 490 6.636562 TTTCTATAGCCCAAAACAAAACGA 57.363 33.333 0.00 0.00 0.00 3.85
487 491 6.827586 TTCTATAGCCCAAAACAAAACGAT 57.172 33.333 0.00 0.00 0.00 3.73
488 492 7.925043 TTCTATAGCCCAAAACAAAACGATA 57.075 32.000 0.00 0.00 0.00 2.92
489 493 8.514330 TTCTATAGCCCAAAACAAAACGATAT 57.486 30.769 0.00 0.00 0.00 1.63
490 494 8.514330 TCTATAGCCCAAAACAAAACGATATT 57.486 30.769 0.00 0.00 0.00 1.28
491 495 8.962679 TCTATAGCCCAAAACAAAACGATATTT 58.037 29.630 0.00 0.00 0.00 1.40
492 496 9.233232 CTATAGCCCAAAACAAAACGATATTTC 57.767 33.333 0.00 0.00 0.00 2.17
493 497 6.096673 AGCCCAAAACAAAACGATATTTCT 57.903 33.333 0.00 0.00 0.00 2.52
494 498 7.222000 AGCCCAAAACAAAACGATATTTCTA 57.778 32.000 0.00 0.00 0.00 2.10
495 499 7.088272 AGCCCAAAACAAAACGATATTTCTAC 58.912 34.615 0.00 0.00 0.00 2.59
496 500 6.309494 GCCCAAAACAAAACGATATTTCTACC 59.691 38.462 0.00 0.00 0.00 3.18
497 501 6.525280 CCCAAAACAAAACGATATTTCTACCG 59.475 38.462 0.00 0.00 0.00 4.02
498 502 7.299586 CCAAAACAAAACGATATTTCTACCGA 58.700 34.615 0.00 0.00 0.00 4.69
499 503 7.804129 CCAAAACAAAACGATATTTCTACCGAA 59.196 33.333 0.00 0.00 0.00 4.30
500 504 9.171701 CAAAACAAAACGATATTTCTACCGAAA 57.828 29.630 0.00 0.00 42.83 3.46
501 505 8.718047 AAACAAAACGATATTTCTACCGAAAC 57.282 30.769 0.00 0.00 41.58 2.78
502 506 7.662604 ACAAAACGATATTTCTACCGAAACT 57.337 32.000 0.00 0.00 41.58 2.66
503 507 8.091385 ACAAAACGATATTTCTACCGAAACTT 57.909 30.769 0.00 0.00 41.58 2.66
504 508 8.013378 ACAAAACGATATTTCTACCGAAACTTG 58.987 33.333 0.00 0.00 41.58 3.16
505 509 5.713822 ACGATATTTCTACCGAAACTTGC 57.286 39.130 0.00 0.00 41.58 4.01
506 510 4.569564 ACGATATTTCTACCGAAACTTGCC 59.430 41.667 0.00 0.00 41.58 4.52
507 511 4.569162 CGATATTTCTACCGAAACTTGCCA 59.431 41.667 0.00 0.00 41.58 4.92
508 512 5.501897 CGATATTTCTACCGAAACTTGCCAC 60.502 44.000 0.00 0.00 41.58 5.01
509 513 1.504359 TTCTACCGAAACTTGCCACG 58.496 50.000 0.00 0.00 0.00 4.94
512 516 2.593436 CCGAAACTTGCCACGGGT 60.593 61.111 0.00 0.00 41.41 5.28
513 517 1.301874 CCGAAACTTGCCACGGGTA 60.302 57.895 0.00 0.00 41.41 3.69
514 518 0.675522 CCGAAACTTGCCACGGGTAT 60.676 55.000 0.00 0.00 41.41 2.73
515 519 1.161843 CGAAACTTGCCACGGGTATT 58.838 50.000 0.00 0.00 0.00 1.89
516 520 1.129811 CGAAACTTGCCACGGGTATTC 59.870 52.381 0.00 0.00 0.00 1.75
517 521 1.129811 GAAACTTGCCACGGGTATTCG 59.870 52.381 0.00 0.00 0.00 3.34
518 522 0.675522 AACTTGCCACGGGTATTCGG 60.676 55.000 0.00 0.00 0.00 4.30
519 523 1.219664 CTTGCCACGGGTATTCGGA 59.780 57.895 0.00 0.00 0.00 4.55
520 524 0.391927 CTTGCCACGGGTATTCGGAA 60.392 55.000 0.00 0.00 0.00 4.30
521 525 0.253610 TTGCCACGGGTATTCGGAAT 59.746 50.000 8.49 8.49 0.00 3.01
522 526 0.462937 TGCCACGGGTATTCGGAATG 60.463 55.000 13.37 0.00 0.00 2.67
523 527 0.463116 GCCACGGGTATTCGGAATGT 60.463 55.000 13.37 0.00 0.00 2.71
524 528 1.295792 CCACGGGTATTCGGAATGTG 58.704 55.000 13.37 11.64 0.00 3.21
525 529 1.406341 CCACGGGTATTCGGAATGTGT 60.406 52.381 13.37 3.79 0.00 3.72
526 530 2.159071 CCACGGGTATTCGGAATGTGTA 60.159 50.000 13.37 0.00 0.00 2.90
527 531 3.493699 CCACGGGTATTCGGAATGTGTAT 60.494 47.826 13.37 0.00 0.00 2.29
528 532 3.493129 CACGGGTATTCGGAATGTGTATG 59.507 47.826 13.37 3.20 0.00 2.39
529 533 2.478894 CGGGTATTCGGAATGTGTATGC 59.521 50.000 13.37 0.00 0.00 3.14
530 534 2.478894 GGGTATTCGGAATGTGTATGCG 59.521 50.000 13.37 0.00 0.00 4.73
531 535 3.128349 GGTATTCGGAATGTGTATGCGT 58.872 45.455 13.37 0.00 33.08 5.24
532 536 4.300803 GGTATTCGGAATGTGTATGCGTA 58.699 43.478 13.37 0.00 33.08 4.42
533 537 4.927425 GGTATTCGGAATGTGTATGCGTAT 59.073 41.667 13.37 0.00 33.08 3.06
534 538 5.061808 GGTATTCGGAATGTGTATGCGTATC 59.938 44.000 13.37 0.00 33.08 2.24
535 539 3.021269 TCGGAATGTGTATGCGTATCC 57.979 47.619 0.00 0.00 33.08 2.59
536 540 2.066262 CGGAATGTGTATGCGTATCCC 58.934 52.381 0.00 0.00 0.00 3.85
537 541 2.423577 GGAATGTGTATGCGTATCCCC 58.576 52.381 0.00 0.00 0.00 4.81
538 542 2.066262 GAATGTGTATGCGTATCCCCG 58.934 52.381 0.00 0.00 0.00 5.73
539 543 0.320374 ATGTGTATGCGTATCCCCGG 59.680 55.000 0.00 0.00 0.00 5.73
540 544 1.005394 GTGTATGCGTATCCCCGGG 60.005 63.158 15.80 15.80 0.00 5.73
541 545 1.152504 TGTATGCGTATCCCCGGGA 60.153 57.895 26.32 9.16 35.55 5.14
542 546 0.759812 TGTATGCGTATCCCCGGGAA 60.760 55.000 26.32 0.00 34.34 3.97
543 547 0.393820 GTATGCGTATCCCCGGGAAA 59.606 55.000 26.32 10.61 34.34 3.13
544 548 1.129917 TATGCGTATCCCCGGGAAAA 58.870 50.000 26.32 7.47 34.34 2.29
545 549 0.256464 ATGCGTATCCCCGGGAAAAA 59.744 50.000 26.32 4.40 34.34 1.94
546 550 0.677414 TGCGTATCCCCGGGAAAAAC 60.677 55.000 26.32 13.49 34.34 2.43
547 551 0.393402 GCGTATCCCCGGGAAAAACT 60.393 55.000 26.32 1.55 34.34 2.66
548 552 1.951895 GCGTATCCCCGGGAAAAACTT 60.952 52.381 26.32 0.17 34.34 2.66
549 553 2.011947 CGTATCCCCGGGAAAAACTTC 58.988 52.381 26.32 2.74 34.34 3.01
550 554 2.616001 CGTATCCCCGGGAAAAACTTCA 60.616 50.000 26.32 0.00 34.34 3.02
551 555 1.919240 ATCCCCGGGAAAAACTTCAC 58.081 50.000 26.32 0.00 34.34 3.18
552 556 0.551879 TCCCCGGGAAAAACTTCACA 59.448 50.000 26.32 0.00 0.00 3.58
553 557 1.146152 TCCCCGGGAAAAACTTCACAT 59.854 47.619 26.32 0.00 0.00 3.21
554 558 1.967779 CCCCGGGAAAAACTTCACATT 59.032 47.619 26.32 0.00 0.00 2.71
555 559 2.367241 CCCCGGGAAAAACTTCACATTT 59.633 45.455 26.32 0.00 0.00 2.32
556 560 3.181459 CCCCGGGAAAAACTTCACATTTT 60.181 43.478 26.32 0.00 0.00 1.82
557 561 4.447290 CCCGGGAAAAACTTCACATTTTT 58.553 39.130 18.48 0.00 40.94 1.94
568 572 9.487790 AAAACTTCACATTTTTCTGAAACTTCA 57.512 25.926 1.58 0.00 35.57 3.02
569 573 9.487790 AAACTTCACATTTTTCTGAAACTTCAA 57.512 25.926 1.58 0.00 36.64 2.69
570 574 9.487790 AACTTCACATTTTTCTGAAACTTCAAA 57.512 25.926 1.58 0.00 36.64 2.69
571 575 9.487790 ACTTCACATTTTTCTGAAACTTCAAAA 57.512 25.926 1.58 0.00 36.64 2.44
572 576 9.962759 CTTCACATTTTTCTGAAACTTCAAAAG 57.037 29.630 1.58 0.71 36.64 2.27
573 577 7.962917 TCACATTTTTCTGAAACTTCAAAAGC 58.037 30.769 1.58 0.00 36.64 3.51
574 578 7.601886 TCACATTTTTCTGAAACTTCAAAAGCA 59.398 29.630 1.58 0.00 36.64 3.91
575 579 8.392612 CACATTTTTCTGAAACTTCAAAAGCAT 58.607 29.630 1.58 0.00 36.64 3.79
576 580 8.392612 ACATTTTTCTGAAACTTCAAAAGCATG 58.607 29.630 1.58 0.00 36.64 4.06
577 581 8.605746 CATTTTTCTGAAACTTCAAAAGCATGA 58.394 29.630 1.58 0.00 36.64 3.07
578 582 8.545229 TTTTTCTGAAACTTCAAAAGCATGAA 57.455 26.923 1.58 0.00 36.64 2.57
579 583 8.721019 TTTTCTGAAACTTCAAAAGCATGAAT 57.279 26.923 1.58 0.00 38.55 2.57
580 584 8.721019 TTTCTGAAACTTCAAAAGCATGAATT 57.279 26.923 0.00 0.00 38.55 2.17
581 585 8.721019 TTCTGAAACTTCAAAAGCATGAATTT 57.279 26.923 0.00 0.00 38.55 1.82
582 586 8.356533 TCTGAAACTTCAAAAGCATGAATTTC 57.643 30.769 0.00 16.58 38.55 2.17
583 587 7.980662 TCTGAAACTTCAAAAGCATGAATTTCA 59.019 29.630 20.18 20.18 40.10 2.69
584 588 8.489990 TGAAACTTCAAAAGCATGAATTTCAA 57.510 26.923 19.75 0.00 39.85 2.69
585 589 8.944029 TGAAACTTCAAAAGCATGAATTTCAAA 58.056 25.926 19.75 0.00 39.85 2.69
586 590 9.771915 GAAACTTCAAAAGCATGAATTTCAAAA 57.228 25.926 2.68 0.00 38.55 2.44
612 616 9.442047 ATATTTAAATATAGAGAGCACTGGTGC 57.558 33.333 17.32 16.81 41.82 5.01
629 633 4.950479 CTCGGGAGCTGCAAATCT 57.050 55.556 7.79 0.00 0.00 2.40
630 634 2.391469 CTCGGGAGCTGCAAATCTG 58.609 57.895 7.79 0.00 0.00 2.90
747 751 0.620556 TGAACTGGAGGGAGAATGGC 59.379 55.000 0.00 0.00 0.00 4.40
1053 1058 2.076100 TCAACAACTCCTGCATTAGCG 58.924 47.619 0.00 0.00 46.23 4.26
1164 1169 2.093973 AGTTCCACATTACCAGAGAGCG 60.094 50.000 0.00 0.00 0.00 5.03
1343 1348 5.591877 ACAAAGCAAGAAACAAGAGTCAGAT 59.408 36.000 0.00 0.00 0.00 2.90
1350 1355 5.558818 AGAAACAAGAGTCAGATGCTGAAT 58.441 37.500 0.00 0.00 42.46 2.57
1376 1381 4.183865 TCTCATGTAAAAGATGACGCTGG 58.816 43.478 0.00 0.00 0.00 4.85
1404 1409 4.219725 GGTAAGCCTGAATTTACCAAGCAA 59.780 41.667 8.19 0.00 45.22 3.91
1548 1553 5.473066 TCATCTCACTTGATGACTTGTCA 57.527 39.130 5.89 5.89 45.29 3.58
1696 1701 3.854666 TCAGAGAACATGACTAAGCAGC 58.145 45.455 0.00 0.00 0.00 5.25
1735 1740 3.618690 AGCACAGACAAGATAAGGACC 57.381 47.619 0.00 0.00 0.00 4.46
1752 1757 2.633481 GGACCTGACTAAACCACAGAGT 59.367 50.000 0.00 0.00 34.07 3.24
1763 1768 0.326264 CCACAGAGTTTCTCCCAGGG 59.674 60.000 0.00 0.00 0.00 4.45
1775 1780 0.696143 TCCCAGGGGTCTGTGAAACA 60.696 55.000 5.33 0.00 39.95 2.83
1790 1795 4.105486 GTGAAACAGAACAGGAAAGCAAC 58.895 43.478 0.00 0.00 36.32 4.17
1791 1796 3.761218 TGAAACAGAACAGGAAAGCAACA 59.239 39.130 0.00 0.00 0.00 3.33
1792 1797 3.782889 AACAGAACAGGAAAGCAACAC 57.217 42.857 0.00 0.00 0.00 3.32
1794 1799 2.023673 CAGAACAGGAAAGCAACACCA 58.976 47.619 0.00 0.00 0.00 4.17
1796 1801 2.689983 AGAACAGGAAAGCAACACCAAG 59.310 45.455 0.00 0.00 0.00 3.61
1808 1813 5.003804 AGCAACACCAAGTATAACCAGAAG 58.996 41.667 0.00 0.00 0.00 2.85
1811 1816 4.579869 ACACCAAGTATAACCAGAAGCAG 58.420 43.478 0.00 0.00 0.00 4.24
1812 1817 4.041691 ACACCAAGTATAACCAGAAGCAGT 59.958 41.667 0.00 0.00 0.00 4.40
1827 1832 5.049198 CAGAAGCAGTATGTCAAAGCAGAAA 60.049 40.000 0.00 0.00 39.31 2.52
1832 1837 2.712057 ATGTCAAAGCAGAAAAGCGG 57.288 45.000 0.00 0.00 40.15 5.52
1853 1858 5.118990 CGGAATAACATCACATGAGAAGGT 58.881 41.667 0.00 0.00 0.00 3.50
1899 1904 2.063015 ATGGACCAAGGACAACGGCA 62.063 55.000 0.00 0.00 0.00 5.69
1921 1926 4.844349 AAAAAGGCAGATCCTAGTGCTA 57.156 40.909 4.84 0.00 46.94 3.49
1934 1939 6.268825 TCCTAGTGCTACTAACAAGTTCAG 57.731 41.667 0.00 0.00 29.00 3.02
1936 1941 3.665190 AGTGCTACTAACAAGTTCAGCC 58.335 45.455 9.95 4.40 0.00 4.85
1937 1942 2.742589 GTGCTACTAACAAGTTCAGCCC 59.257 50.000 9.95 0.00 0.00 5.19
2022 2027 0.108186 CACCAGCTAGCGTGATGGAA 60.108 55.000 23.49 0.00 45.53 3.53
2131 2136 4.339872 AATGTTGCCAAGAATGCTCAAA 57.660 36.364 0.00 0.00 0.00 2.69
2200 2205 3.127895 GCTGTCTCGTTCTACAGTGAGAT 59.872 47.826 0.00 0.00 44.03 2.75
2245 2250 3.173965 TCCCCAGTGAAGAGTAAGAAGG 58.826 50.000 0.00 0.00 0.00 3.46
2289 2294 6.012337 TCTGGGTGCAAGGATAAAATATCA 57.988 37.500 0.00 0.00 0.00 2.15
2303 2308 5.627499 AAAATATCAAAGACAGCTTCGCA 57.373 34.783 0.00 0.00 31.82 5.10
2379 2384 9.886132 GGTACATCTTATCTTTACCTTCTGAAA 57.114 33.333 0.00 0.00 31.19 2.69
2454 2468 8.931385 ACAATATTATGAATTTCACTGGCAAC 57.069 30.769 0.15 0.00 0.00 4.17
2498 2512 9.578576 AACTTGTATGGCATGATTGATTATAGT 57.421 29.630 10.98 0.00 0.00 2.12
2517 2531 4.978083 AGTGCTGCCTTAAATTGATCAG 57.022 40.909 0.00 0.00 0.00 2.90
2558 2572 5.959652 ACAAAAACGTCTTGTATTTTGGC 57.040 34.783 19.47 0.00 39.79 4.52
2567 2581 2.279935 TGTATTTTGGCACGGAGGTT 57.720 45.000 0.00 0.00 0.00 3.50
2814 2828 1.662044 CTGAACCTTGGCAGCAACC 59.338 57.895 0.00 0.00 0.00 3.77
2872 2886 1.478105 TGCAGATGCTACAGATGACGT 59.522 47.619 6.35 0.00 42.66 4.34
3230 3244 5.515008 GGAGTTTCCATGTTAGAGGTTTCCT 60.515 44.000 0.00 0.00 36.28 3.36
3370 3384 7.865706 TTACCTAATTCCAAGAGAGATTTGC 57.134 36.000 0.00 0.00 0.00 3.68
3520 6342 9.845740 ATGCCATAACAACATACAAACTATCTA 57.154 29.630 0.00 0.00 0.00 1.98
3594 6417 1.731433 ATTCATCAGTGGCATGCCGC 61.731 55.000 37.67 37.67 46.30 6.53
3665 6488 1.270274 GGTGACATTGTTGATGCAGCA 59.730 47.619 0.00 0.00 39.47 4.41
3680 6503 1.674221 GCAGCAATCGAGAAGTCACCT 60.674 52.381 0.00 0.00 0.00 4.00
3681 6504 2.417379 GCAGCAATCGAGAAGTCACCTA 60.417 50.000 0.00 0.00 0.00 3.08
3720 6543 0.992802 GCGACAACGAACTGAGGATC 59.007 55.000 0.00 0.00 42.66 3.36
3722 6545 2.672714 CGACAACGAACTGAGGATCAA 58.327 47.619 0.00 0.00 43.73 2.57
3767 6590 1.005215 ACAAGGAGGGCAGAAATCCAG 59.995 52.381 0.00 0.00 35.45 3.86
3768 6591 1.283029 CAAGGAGGGCAGAAATCCAGA 59.717 52.381 0.00 0.00 35.45 3.86
3832 6658 1.302511 TTGAACCTGGCTCCGCTTC 60.303 57.895 0.00 0.00 0.00 3.86
3860 6686 2.767505 GGAGAAGAAGCCGAAAGACAA 58.232 47.619 0.00 0.00 0.00 3.18
3861 6687 3.139077 GGAGAAGAAGCCGAAAGACAAA 58.861 45.455 0.00 0.00 0.00 2.83
3864 6690 4.921547 AGAAGAAGCCGAAAGACAAAAAC 58.078 39.130 0.00 0.00 0.00 2.43
3875 6701 1.001815 AGACAAAAACATGAACCGCCG 60.002 47.619 0.00 0.00 0.00 6.46
3994 6820 0.813184 CTTTGCCGATGCCAATCAGT 59.187 50.000 0.00 0.00 36.33 3.41
4031 6857 5.788450 GGACATGATGTTAGAGTCCCTATG 58.212 45.833 0.00 0.00 42.21 2.23
4064 6890 5.721960 ACTCACAAGTACCAGGATTACAGAT 59.278 40.000 0.00 0.00 32.59 2.90
4138 6969 8.732746 ATATTGCGAAGATACCAATAATACCC 57.267 34.615 0.00 0.00 35.71 3.69
4141 6972 5.046878 TGCGAAGATACCAATAATACCCGAT 60.047 40.000 0.00 0.00 0.00 4.18
4145 6976 7.817962 CGAAGATACCAATAATACCCGATCTTT 59.182 37.037 0.00 0.00 33.65 2.52
4146 6977 8.848474 AAGATACCAATAATACCCGATCTTTG 57.152 34.615 0.00 0.00 30.20 2.77
4149 6980 9.148104 GATACCAATAATACCCGATCTTTGTAC 57.852 37.037 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
69 70 4.933400 GTCTTTTGGATTTGCTGCAATCAT 59.067 37.500 16.77 7.62 34.90 2.45
83 84 6.071616 CCCTTTGAATTATTCCGTCTTTTGGA 60.072 38.462 2.22 0.00 0.00 3.53
97 98 5.104235 GCCCTACTTACTCCCCTTTGAATTA 60.104 44.000 0.00 0.00 0.00 1.40
226 230 1.135944 GCTACTTGCACTTTTCGCTCC 60.136 52.381 0.00 0.00 42.31 4.70
227 231 1.801178 AGCTACTTGCACTTTTCGCTC 59.199 47.619 0.00 0.00 45.94 5.03
228 232 1.801178 GAGCTACTTGCACTTTTCGCT 59.199 47.619 0.00 0.00 45.94 4.93
229 233 1.135944 GGAGCTACTTGCACTTTTCGC 60.136 52.381 0.00 0.00 45.94 4.70
230 234 1.464997 GGGAGCTACTTGCACTTTTCG 59.535 52.381 0.00 0.00 45.94 3.46
231 235 1.464997 CGGGAGCTACTTGCACTTTTC 59.535 52.381 0.00 0.00 45.94 2.29
232 236 1.071699 TCGGGAGCTACTTGCACTTTT 59.928 47.619 0.00 0.00 45.94 2.27
233 237 0.685097 TCGGGAGCTACTTGCACTTT 59.315 50.000 0.00 0.00 45.94 2.66
234 238 0.247736 CTCGGGAGCTACTTGCACTT 59.752 55.000 0.00 0.00 45.94 3.16
235 239 1.893786 CTCGGGAGCTACTTGCACT 59.106 57.895 0.00 0.00 45.94 4.40
236 240 4.504132 CTCGGGAGCTACTTGCAC 57.496 61.111 0.00 0.00 45.94 4.57
246 250 0.754957 AGAGTCATGGAGCTCGGGAG 60.755 60.000 7.83 0.00 36.88 4.30
247 251 0.324738 AAGAGTCATGGAGCTCGGGA 60.325 55.000 7.83 1.89 36.88 5.14
248 252 0.179089 CAAGAGTCATGGAGCTCGGG 60.179 60.000 7.83 0.00 36.88 5.14
249 253 0.179089 CCAAGAGTCATGGAGCTCGG 60.179 60.000 8.81 0.00 40.56 4.63
250 254 0.534412 ACCAAGAGTCATGGAGCTCG 59.466 55.000 20.95 0.00 40.56 5.03
251 255 4.414337 AATACCAAGAGTCATGGAGCTC 57.586 45.455 20.95 4.71 40.56 4.09
252 256 4.225942 TCAAATACCAAGAGTCATGGAGCT 59.774 41.667 20.95 1.39 40.56 4.09
253 257 4.517285 TCAAATACCAAGAGTCATGGAGC 58.483 43.478 20.95 0.00 40.56 4.70
254 258 7.636150 ATTTCAAATACCAAGAGTCATGGAG 57.364 36.000 20.95 5.54 40.56 3.86
255 259 8.421249 AAATTTCAAATACCAAGAGTCATGGA 57.579 30.769 20.95 5.33 40.56 3.41
256 260 9.492973 AAAAATTTCAAATACCAAGAGTCATGG 57.507 29.630 12.86 12.86 43.84 3.66
292 296 9.561069 TTTTAGATTTTTCTGAGCACTAGAAGT 57.439 29.630 0.00 0.00 35.74 3.01
329 333 9.144298 CCGGGTCTTAGGAATATGTGTATATAT 57.856 37.037 0.00 0.00 0.00 0.86
330 334 8.117956 ACCGGGTCTTAGGAATATGTGTATATA 58.882 37.037 6.32 0.00 0.00 0.86
331 335 6.958192 ACCGGGTCTTAGGAATATGTGTATAT 59.042 38.462 6.32 0.00 0.00 0.86
332 336 6.317312 ACCGGGTCTTAGGAATATGTGTATA 58.683 40.000 6.32 0.00 0.00 1.47
333 337 5.152934 ACCGGGTCTTAGGAATATGTGTAT 58.847 41.667 6.32 0.00 0.00 2.29
334 338 4.549668 ACCGGGTCTTAGGAATATGTGTA 58.450 43.478 6.32 0.00 0.00 2.90
335 339 3.381335 ACCGGGTCTTAGGAATATGTGT 58.619 45.455 6.32 0.00 0.00 3.72
336 340 5.540400 TTACCGGGTCTTAGGAATATGTG 57.460 43.478 6.32 0.00 0.00 3.21
337 341 6.564557 TTTTACCGGGTCTTAGGAATATGT 57.435 37.500 6.32 0.00 0.00 2.29
338 342 7.937394 AGATTTTTACCGGGTCTTAGGAATATG 59.063 37.037 6.32 0.00 0.00 1.78
339 343 7.937394 CAGATTTTTACCGGGTCTTAGGAATAT 59.063 37.037 6.32 0.00 0.00 1.28
340 344 7.126115 TCAGATTTTTACCGGGTCTTAGGAATA 59.874 37.037 6.32 0.00 0.00 1.75
341 345 6.069847 TCAGATTTTTACCGGGTCTTAGGAAT 60.070 38.462 6.32 0.00 0.00 3.01
342 346 5.248934 TCAGATTTTTACCGGGTCTTAGGAA 59.751 40.000 6.32 0.00 0.00 3.36
343 347 4.778958 TCAGATTTTTACCGGGTCTTAGGA 59.221 41.667 6.32 0.00 0.00 2.94
344 348 5.093849 TCAGATTTTTACCGGGTCTTAGG 57.906 43.478 6.32 0.00 0.00 2.69
345 349 8.726870 TTTATCAGATTTTTACCGGGTCTTAG 57.273 34.615 6.32 0.00 0.00 2.18
346 350 9.517868 TTTTTATCAGATTTTTACCGGGTCTTA 57.482 29.630 6.32 0.00 0.00 2.10
347 351 8.411991 TTTTTATCAGATTTTTACCGGGTCTT 57.588 30.769 6.32 0.00 0.00 3.01
407 411 8.199449 AACAATTGTGTCATTTCTGTCAGAAAT 58.801 29.630 27.88 27.88 44.99 2.17
408 412 7.099266 ACAATTGTGTCATTTCTGTCAGAAA 57.901 32.000 26.17 26.17 40.15 2.52
409 413 6.698008 ACAATTGTGTCATTTCTGTCAGAA 57.302 33.333 11.07 11.36 29.49 3.02
410 414 6.543465 AGAACAATTGTGTCATTTCTGTCAGA 59.457 34.615 12.82 0.00 36.80 3.27
411 415 6.732154 AGAACAATTGTGTCATTTCTGTCAG 58.268 36.000 12.82 0.00 36.80 3.51
412 416 6.543465 AGAGAACAATTGTGTCATTTCTGTCA 59.457 34.615 12.82 0.00 36.80 3.58
413 417 6.963796 AGAGAACAATTGTGTCATTTCTGTC 58.036 36.000 12.82 1.83 36.80 3.51
414 418 6.949352 AGAGAACAATTGTGTCATTTCTGT 57.051 33.333 12.82 5.72 36.80 3.41
419 423 9.507329 AGTGTATAAGAGAACAATTGTGTCATT 57.493 29.630 12.82 12.12 36.80 2.57
420 424 8.939929 CAGTGTATAAGAGAACAATTGTGTCAT 58.060 33.333 12.82 7.89 36.80 3.06
421 425 7.931407 ACAGTGTATAAGAGAACAATTGTGTCA 59.069 33.333 12.82 0.00 36.80 3.58
422 426 8.311650 ACAGTGTATAAGAGAACAATTGTGTC 57.688 34.615 12.82 12.08 36.80 3.67
423 427 7.931407 TGACAGTGTATAAGAGAACAATTGTGT 59.069 33.333 12.82 2.24 40.75 3.72
424 428 8.310406 TGACAGTGTATAAGAGAACAATTGTG 57.690 34.615 12.82 0.00 30.39 3.33
425 429 8.367911 TCTGACAGTGTATAAGAGAACAATTGT 58.632 33.333 4.92 4.92 31.92 2.71
426 430 8.763049 TCTGACAGTGTATAAGAGAACAATTG 57.237 34.615 3.24 3.24 0.00 2.32
427 431 9.778741 TTTCTGACAGTGTATAAGAGAACAATT 57.221 29.630 1.59 0.00 0.00 2.32
428 432 9.950496 ATTTCTGACAGTGTATAAGAGAACAAT 57.050 29.630 1.59 0.00 0.00 2.71
429 433 9.778741 AATTTCTGACAGTGTATAAGAGAACAA 57.221 29.630 1.59 0.00 0.00 2.83
430 434 9.778741 AAATTTCTGACAGTGTATAAGAGAACA 57.221 29.630 1.59 0.00 0.00 3.18
432 436 9.778741 ACAAATTTCTGACAGTGTATAAGAGAA 57.221 29.630 1.59 0.00 0.00 2.87
433 437 9.778741 AACAAATTTCTGACAGTGTATAAGAGA 57.221 29.630 1.59 0.00 0.00 3.10
461 465 7.490000 TCGTTTTGTTTTGGGCTATAGAAAAA 58.510 30.769 3.21 4.36 0.00 1.94
462 466 7.040473 TCGTTTTGTTTTGGGCTATAGAAAA 57.960 32.000 3.21 0.00 0.00 2.29
463 467 6.636562 TCGTTTTGTTTTGGGCTATAGAAA 57.363 33.333 3.21 0.00 0.00 2.52
464 468 6.827586 ATCGTTTTGTTTTGGGCTATAGAA 57.172 33.333 3.21 0.00 0.00 2.10
465 469 8.514330 AATATCGTTTTGTTTTGGGCTATAGA 57.486 30.769 3.21 0.00 0.00 1.98
466 470 9.233232 GAAATATCGTTTTGTTTTGGGCTATAG 57.767 33.333 0.00 0.00 0.00 1.31
467 471 8.962679 AGAAATATCGTTTTGTTTTGGGCTATA 58.037 29.630 0.00 0.00 0.00 1.31
468 472 7.836842 AGAAATATCGTTTTGTTTTGGGCTAT 58.163 30.769 0.00 0.00 0.00 2.97
469 473 7.222000 AGAAATATCGTTTTGTTTTGGGCTA 57.778 32.000 0.00 0.00 0.00 3.93
470 474 6.096673 AGAAATATCGTTTTGTTTTGGGCT 57.903 33.333 0.00 0.00 0.00 5.19
471 475 6.309494 GGTAGAAATATCGTTTTGTTTTGGGC 59.691 38.462 0.00 0.00 0.00 5.36
472 476 6.525280 CGGTAGAAATATCGTTTTGTTTTGGG 59.475 38.462 0.00 0.00 0.00 4.12
473 477 7.299586 TCGGTAGAAATATCGTTTTGTTTTGG 58.700 34.615 0.00 0.00 0.00 3.28
474 478 8.716619 TTCGGTAGAAATATCGTTTTGTTTTG 57.283 30.769 0.00 0.00 32.65 2.44
475 479 9.172820 GTTTCGGTAGAAATATCGTTTTGTTTT 57.827 29.630 0.00 0.00 46.64 2.43
476 480 8.562052 AGTTTCGGTAGAAATATCGTTTTGTTT 58.438 29.630 0.00 0.00 46.64 2.83
477 481 8.091385 AGTTTCGGTAGAAATATCGTTTTGTT 57.909 30.769 0.00 0.00 46.64 2.83
478 482 7.662604 AGTTTCGGTAGAAATATCGTTTTGT 57.337 32.000 0.00 0.00 46.64 2.83
479 483 7.007099 GCAAGTTTCGGTAGAAATATCGTTTTG 59.993 37.037 0.00 0.00 46.64 2.44
480 484 7.019418 GCAAGTTTCGGTAGAAATATCGTTTT 58.981 34.615 0.00 0.00 46.64 2.43
481 485 6.402875 GGCAAGTTTCGGTAGAAATATCGTTT 60.403 38.462 0.00 0.00 46.64 3.60
482 486 5.064325 GGCAAGTTTCGGTAGAAATATCGTT 59.936 40.000 0.00 0.00 46.64 3.85
483 487 4.569564 GGCAAGTTTCGGTAGAAATATCGT 59.430 41.667 0.00 0.00 46.64 3.73
484 488 4.569162 TGGCAAGTTTCGGTAGAAATATCG 59.431 41.667 0.00 0.00 46.64 2.92
485 489 5.501897 CGTGGCAAGTTTCGGTAGAAATATC 60.502 44.000 0.00 0.00 46.64 1.63
486 490 4.331717 CGTGGCAAGTTTCGGTAGAAATAT 59.668 41.667 0.00 0.00 46.64 1.28
487 491 3.680937 CGTGGCAAGTTTCGGTAGAAATA 59.319 43.478 0.00 0.00 46.64 1.40
488 492 2.482721 CGTGGCAAGTTTCGGTAGAAAT 59.517 45.455 0.00 0.00 46.64 2.17
489 493 1.868498 CGTGGCAAGTTTCGGTAGAAA 59.132 47.619 0.00 0.00 43.44 2.52
490 494 1.504359 CGTGGCAAGTTTCGGTAGAA 58.496 50.000 0.00 0.00 33.98 2.10
491 495 0.320073 CCGTGGCAAGTTTCGGTAGA 60.320 55.000 5.40 0.00 38.45 2.59
492 496 1.296056 CCCGTGGCAAGTTTCGGTAG 61.296 60.000 11.81 0.00 41.17 3.18
493 497 1.301874 CCCGTGGCAAGTTTCGGTA 60.302 57.895 11.81 0.00 41.17 4.02
494 498 2.042404 TACCCGTGGCAAGTTTCGGT 62.042 55.000 11.81 8.21 41.17 4.69
495 499 0.675522 ATACCCGTGGCAAGTTTCGG 60.676 55.000 6.51 6.51 42.22 4.30
496 500 1.129811 GAATACCCGTGGCAAGTTTCG 59.870 52.381 0.00 0.00 0.00 3.46
497 501 1.129811 CGAATACCCGTGGCAAGTTTC 59.870 52.381 0.00 0.00 0.00 2.78
498 502 1.161843 CGAATACCCGTGGCAAGTTT 58.838 50.000 0.00 0.00 0.00 2.66
499 503 0.675522 CCGAATACCCGTGGCAAGTT 60.676 55.000 0.00 0.00 0.00 2.66
500 504 1.078708 CCGAATACCCGTGGCAAGT 60.079 57.895 0.00 0.00 0.00 3.16
501 505 0.391927 TTCCGAATACCCGTGGCAAG 60.392 55.000 0.00 0.00 0.00 4.01
502 506 0.253610 ATTCCGAATACCCGTGGCAA 59.746 50.000 0.00 0.00 0.00 4.52
503 507 0.462937 CATTCCGAATACCCGTGGCA 60.463 55.000 0.00 0.00 0.00 4.92
504 508 0.463116 ACATTCCGAATACCCGTGGC 60.463 55.000 0.00 0.00 0.00 5.01
505 509 1.295792 CACATTCCGAATACCCGTGG 58.704 55.000 0.00 0.00 0.00 4.94
506 510 2.018542 ACACATTCCGAATACCCGTG 57.981 50.000 7.45 7.45 0.00 4.94
507 511 3.724374 CATACACATTCCGAATACCCGT 58.276 45.455 0.00 0.00 0.00 5.28
508 512 2.478894 GCATACACATTCCGAATACCCG 59.521 50.000 0.00 0.00 0.00 5.28
509 513 2.478894 CGCATACACATTCCGAATACCC 59.521 50.000 0.00 0.00 0.00 3.69
510 514 3.128349 ACGCATACACATTCCGAATACC 58.872 45.455 0.00 0.00 0.00 2.73
511 515 5.061808 GGATACGCATACACATTCCGAATAC 59.938 44.000 0.00 0.00 0.00 1.89
512 516 5.165676 GGATACGCATACACATTCCGAATA 58.834 41.667 0.00 0.00 0.00 1.75
513 517 3.994392 GGATACGCATACACATTCCGAAT 59.006 43.478 0.00 0.00 0.00 3.34
514 518 3.386486 GGATACGCATACACATTCCGAA 58.614 45.455 0.00 0.00 0.00 4.30
515 519 2.288579 GGGATACGCATACACATTCCGA 60.289 50.000 0.00 0.00 37.60 4.55
516 520 2.066262 GGGATACGCATACACATTCCG 58.934 52.381 0.00 0.00 37.60 4.30
529 533 2.011947 GAAGTTTTTCCCGGGGATACG 58.988 52.381 23.50 0.00 37.60 3.06
530 534 2.751259 GTGAAGTTTTTCCCGGGGATAC 59.249 50.000 23.50 13.73 32.09 2.24
531 535 2.375845 TGTGAAGTTTTTCCCGGGGATA 59.624 45.455 23.50 9.75 32.09 2.59
532 536 1.146152 TGTGAAGTTTTTCCCGGGGAT 59.854 47.619 23.50 0.00 32.09 3.85
533 537 0.551879 TGTGAAGTTTTTCCCGGGGA 59.448 50.000 23.50 12.99 32.09 4.81
534 538 1.627864 ATGTGAAGTTTTTCCCGGGG 58.372 50.000 23.50 6.77 32.09 5.73
535 539 3.744238 AAATGTGAAGTTTTTCCCGGG 57.256 42.857 16.85 16.85 32.09 5.73
536 540 5.651172 GAAAAATGTGAAGTTTTTCCCGG 57.349 39.130 11.15 0.00 44.13 5.73
542 546 9.487790 TGAAGTTTCAGAAAAATGTGAAGTTTT 57.512 25.926 0.00 0.00 34.25 2.43
543 547 9.487790 TTGAAGTTTCAGAAAAATGTGAAGTTT 57.512 25.926 0.00 0.00 38.61 2.66
544 548 9.487790 TTTGAAGTTTCAGAAAAATGTGAAGTT 57.512 25.926 0.00 0.00 38.61 2.66
545 549 9.487790 TTTTGAAGTTTCAGAAAAATGTGAAGT 57.512 25.926 0.00 0.00 38.61 3.01
546 550 9.962759 CTTTTGAAGTTTCAGAAAAATGTGAAG 57.037 29.630 0.00 0.00 38.61 3.02
547 551 8.442384 GCTTTTGAAGTTTCAGAAAAATGTGAA 58.558 29.630 0.00 0.00 38.61 3.18
548 552 7.601886 TGCTTTTGAAGTTTCAGAAAAATGTGA 59.398 29.630 0.00 0.00 38.61 3.58
549 553 7.741198 TGCTTTTGAAGTTTCAGAAAAATGTG 58.259 30.769 0.00 0.00 38.61 3.21
550 554 7.903995 TGCTTTTGAAGTTTCAGAAAAATGT 57.096 28.000 0.00 0.00 38.61 2.71
551 555 8.605746 TCATGCTTTTGAAGTTTCAGAAAAATG 58.394 29.630 0.00 10.40 38.61 2.32
552 556 8.721019 TCATGCTTTTGAAGTTTCAGAAAAAT 57.279 26.923 0.00 0.00 38.61 1.82
553 557 8.545229 TTCATGCTTTTGAAGTTTCAGAAAAA 57.455 26.923 0.00 0.00 38.61 1.94
554 558 8.721019 ATTCATGCTTTTGAAGTTTCAGAAAA 57.279 26.923 0.00 0.00 38.90 2.29
555 559 8.721019 AATTCATGCTTTTGAAGTTTCAGAAA 57.279 26.923 0.00 0.00 38.90 2.52
556 560 8.721019 AAATTCATGCTTTTGAAGTTTCAGAA 57.279 26.923 5.05 0.00 39.98 3.02
557 561 7.980662 TGAAATTCATGCTTTTGAAGTTTCAGA 59.019 29.630 17.77 0.00 42.16 3.27
558 562 8.133754 TGAAATTCATGCTTTTGAAGTTTCAG 57.866 30.769 17.77 0.00 42.16 3.02
559 563 8.489990 TTGAAATTCATGCTTTTGAAGTTTCA 57.510 26.923 17.77 17.77 42.16 2.69
560 564 9.771915 TTTTGAAATTCATGCTTTTGAAGTTTC 57.228 25.926 0.00 13.26 42.16 2.78
612 616 2.391469 CAGATTTGCAGCTCCCGAG 58.609 57.895 0.00 0.00 0.00 4.63
613 617 4.623814 CAGATTTGCAGCTCCCGA 57.376 55.556 0.00 0.00 0.00 5.14
623 627 2.807967 TCCTCAAACGAGTGCAGATTTG 59.192 45.455 0.00 0.00 34.11 2.32
624 628 3.070018 CTCCTCAAACGAGTGCAGATTT 58.930 45.455 0.00 0.00 0.00 2.17
625 629 2.037772 ACTCCTCAAACGAGTGCAGATT 59.962 45.455 0.00 0.00 39.14 2.40
626 630 1.620819 ACTCCTCAAACGAGTGCAGAT 59.379 47.619 0.00 0.00 39.14 2.90
627 631 1.040646 ACTCCTCAAACGAGTGCAGA 58.959 50.000 0.00 0.00 39.14 4.26
628 632 1.871080 AACTCCTCAAACGAGTGCAG 58.129 50.000 0.00 0.00 39.69 4.41
629 633 3.678056 ATAACTCCTCAAACGAGTGCA 57.322 42.857 0.00 0.00 39.69 4.57
630 634 7.095607 CCATATTATAACTCCTCAAACGAGTGC 60.096 40.741 0.00 0.00 39.69 4.40
631 635 8.141909 TCCATATTATAACTCCTCAAACGAGTG 58.858 37.037 0.00 0.00 39.69 3.51
632 636 8.246430 TCCATATTATAACTCCTCAAACGAGT 57.754 34.615 0.00 0.00 42.41 4.18
633 637 9.542462 TTTCCATATTATAACTCCTCAAACGAG 57.458 33.333 0.00 0.00 0.00 4.18
636 640 9.899226 GCATTTCCATATTATAACTCCTCAAAC 57.101 33.333 0.00 0.00 0.00 2.93
637 641 9.866655 AGCATTTCCATATTATAACTCCTCAAA 57.133 29.630 0.00 0.00 0.00 2.69
638 642 9.866655 AAGCATTTCCATATTATAACTCCTCAA 57.133 29.630 0.00 0.00 0.00 3.02
639 643 9.866655 AAAGCATTTCCATATTATAACTCCTCA 57.133 29.630 0.00 0.00 27.08 3.86
700 704 6.994421 ATTCTCACCAAACCCAACTAATTT 57.006 33.333 0.00 0.00 0.00 1.82
747 751 5.526479 CCAAGAATATGCATAGATGGATCCG 59.474 44.000 18.14 0.00 39.62 4.18
1053 1058 4.678622 GGAGATCTTCTTTCTTCGACTCC 58.321 47.826 0.00 0.00 35.43 3.85
1176 1181 1.755959 AGTTTGCAGTTGTCATGGCAA 59.244 42.857 9.09 9.09 43.79 4.52
1350 1355 7.011389 CCAGCGTCATCTTTTACATGAGAAATA 59.989 37.037 0.00 0.00 30.72 1.40
1370 1375 2.663196 GCTTACCAGGACCAGCGT 59.337 61.111 0.00 0.00 0.00 5.07
1376 1381 3.945921 GGTAAATTCAGGCTTACCAGGAC 59.054 47.826 7.33 0.00 44.38 3.85
1404 1409 3.515602 ACTCCTTTCAGTGATGGCTTT 57.484 42.857 0.00 0.00 0.00 3.51
1519 1524 2.591571 TCAAGTGAGATGATGAGGCG 57.408 50.000 0.00 0.00 0.00 5.52
1548 1553 3.087031 CAATTGTCCATCTCCACAGCTT 58.913 45.455 0.00 0.00 0.00 3.74
1696 1701 0.178767 TTCTCCGATGCCATCACAGG 59.821 55.000 5.40 0.00 0.00 4.00
1710 1715 4.081420 TCCTTATCTTGTCTGTGCTTCTCC 60.081 45.833 0.00 0.00 0.00 3.71
1721 1726 6.107343 GGTTTAGTCAGGTCCTTATCTTGTC 58.893 44.000 0.00 0.00 0.00 3.18
1735 1740 4.991687 GGAGAAACTCTGTGGTTTAGTCAG 59.008 45.833 0.00 0.00 39.20 3.51
1752 1757 2.463441 CACAGACCCCTGGGAGAAA 58.537 57.895 16.20 0.00 46.73 2.52
1775 1780 2.435372 TGGTGTTGCTTTCCTGTTCT 57.565 45.000 0.00 0.00 0.00 3.01
1776 1781 2.427095 ACTTGGTGTTGCTTTCCTGTTC 59.573 45.455 0.00 0.00 0.00 3.18
1790 1795 4.579869 ACTGCTTCTGGTTATACTTGGTG 58.420 43.478 0.00 0.00 0.00 4.17
1791 1796 4.910458 ACTGCTTCTGGTTATACTTGGT 57.090 40.909 0.00 0.00 0.00 3.67
1792 1797 6.349300 ACATACTGCTTCTGGTTATACTTGG 58.651 40.000 0.00 0.00 0.00 3.61
1794 1799 7.182817 TGACATACTGCTTCTGGTTATACTT 57.817 36.000 0.00 0.00 0.00 2.24
1796 1801 7.466050 GCTTTGACATACTGCTTCTGGTTATAC 60.466 40.741 0.00 0.00 0.00 1.47
1808 1813 3.916776 GCTTTTCTGCTTTGACATACTGC 59.083 43.478 0.00 0.00 0.00 4.40
1811 1816 3.188460 TCCGCTTTTCTGCTTTGACATAC 59.812 43.478 0.00 0.00 0.00 2.39
1812 1817 3.407698 TCCGCTTTTCTGCTTTGACATA 58.592 40.909 0.00 0.00 0.00 2.29
1827 1832 4.769688 TCTCATGTGATGTTATTCCGCTT 58.230 39.130 0.00 0.00 0.00 4.68
1832 1837 6.127925 TGCAACCTTCTCATGTGATGTTATTC 60.128 38.462 10.86 6.46 0.00 1.75
1853 1858 0.983467 TCCAGCTGATGTACCTGCAA 59.017 50.000 17.39 0.00 34.07 4.08
1917 1922 2.611971 CGGGCTGAACTTGTTAGTAGCA 60.612 50.000 14.30 0.00 37.60 3.49
1919 1924 2.232941 TCCGGGCTGAACTTGTTAGTAG 59.767 50.000 0.00 0.00 33.17 2.57
1921 1926 1.002087 CTCCGGGCTGAACTTGTTAGT 59.998 52.381 0.00 0.00 35.68 2.24
1934 1939 0.673956 GTTGAGTTTCCTCTCCGGGC 60.674 60.000 0.00 0.00 38.61 6.13
1936 1941 2.037251 TCAAGTTGAGTTTCCTCTCCGG 59.963 50.000 0.08 0.00 38.61 5.14
1937 1942 3.386768 TCAAGTTGAGTTTCCTCTCCG 57.613 47.619 0.08 0.00 38.61 4.63
1955 1960 4.971939 TGGAAGAGTTGATGTGACAATCA 58.028 39.130 0.00 0.00 34.75 2.57
1956 1961 5.106396 CCTTGGAAGAGTTGATGTGACAATC 60.106 44.000 0.00 0.00 32.36 2.67
2022 2027 0.036164 TAGCAGGTTTGGCACACGAT 59.964 50.000 0.00 0.00 39.29 3.73
2131 2136 3.966665 TCTTCTCCCTTGTTTTGCCAAAT 59.033 39.130 0.00 0.00 0.00 2.32
2200 2205 4.130118 GCAGAAGTTTCTTTCCTGACTGA 58.870 43.478 0.00 0.00 34.74 3.41
2245 2250 8.251026 CCCAGAAAAACTTTCTATCCCATAAAC 58.749 37.037 1.48 0.00 0.00 2.01
2379 2384 9.640952 ACCTAAGGTGCAATTATATGTTTATGT 57.359 29.630 0.00 0.00 32.98 2.29
2517 2531 2.704065 TGTAGGCTAAACTAGGATGGCC 59.296 50.000 14.19 14.19 39.82 5.36
2558 2572 4.562082 TGTTAGATGTTACAACCTCCGTG 58.438 43.478 0.00 0.00 0.00 4.94
2567 2581 7.013178 CCATACATTGCCATGTTAGATGTTACA 59.987 37.037 8.93 0.00 41.16 2.41
2633 2647 2.224281 TGTCTTGCGATGAACTCCAAGT 60.224 45.455 0.00 0.00 35.43 3.16
2646 2660 3.187022 TGATGTCTTGTCATTGTCTTGCG 59.813 43.478 0.00 0.00 0.00 4.85
2814 2828 0.604780 CTGGGAGTGCTGTTGTCAGG 60.605 60.000 0.00 0.00 41.57 3.86
3075 3089 2.335712 GGGCCTTCACTTTGCTCCG 61.336 63.158 0.84 0.00 0.00 4.63
3230 3244 4.458989 GGAATGTGCACAAGAACTCCAATA 59.541 41.667 25.72 0.00 0.00 1.90
3370 3384 8.277713 CAGCTCAAATGTAAAAGACAATTTTGG 58.722 33.333 0.00 0.00 42.78 3.28
3544 6367 1.684734 GGGCGTCCCTAGGAGTGAA 60.685 63.158 11.48 0.00 41.34 3.18
3567 6390 1.022735 CCACTGATGAATGCAGGAGC 58.977 55.000 0.00 0.00 37.69 4.70
3665 6488 3.087031 TCCGTTAGGTGACTTCTCGATT 58.913 45.455 0.00 0.00 43.67 3.34
3680 6503 0.249398 GGCTTCTTCTGCCTCCGTTA 59.751 55.000 0.00 0.00 46.38 3.18
3681 6504 1.003233 GGCTTCTTCTGCCTCCGTT 60.003 57.895 0.00 0.00 46.38 4.44
3720 6543 0.463654 TTCTCCGGGATGGCGATTTG 60.464 55.000 0.00 0.00 37.80 2.32
3722 6545 1.048724 TCTTCTCCGGGATGGCGATT 61.049 55.000 0.00 0.00 37.80 3.34
3730 6553 0.762418 TGTTGCTTTCTTCTCCGGGA 59.238 50.000 0.00 0.00 0.00 5.14
3767 6590 2.011046 GCCTGCCTGATTCTGTCTGTC 61.011 57.143 0.00 0.00 0.00 3.51
3768 6591 0.035630 GCCTGCCTGATTCTGTCTGT 60.036 55.000 0.00 0.00 0.00 3.41
3796 6619 3.596214 TCAACTTCGTTGGGAATCTAGC 58.404 45.455 6.86 0.00 42.99 3.42
3832 6658 2.445438 GCTTCTTCTCCGTTCGGCG 61.445 63.158 0.00 0.00 40.95 6.46
3840 6666 2.457366 TGTCTTTCGGCTTCTTCTCC 57.543 50.000 0.00 0.00 0.00 3.71
3858 6684 1.404477 GACGGCGGTTCATGTTTTTG 58.596 50.000 13.24 0.00 0.00 2.44
3860 6686 1.161563 ACGACGGCGGTTCATGTTTT 61.162 50.000 18.49 0.00 43.17 2.43
3861 6687 1.562575 GACGACGGCGGTTCATGTTT 61.563 55.000 18.49 0.00 43.17 2.83
3864 6690 3.186047 GGACGACGGCGGTTCATG 61.186 66.667 18.49 0.00 43.17 3.07
3934 6760 0.768609 GGCTAGATTAGGGGCCCTGT 60.769 60.000 35.70 23.19 38.77 4.00
3994 6820 1.000843 CATGTCCTCATTCCGGCGATA 59.999 52.381 9.30 0.00 31.15 2.92
4031 6857 7.553334 TCCTGGTACTTGTGAGTGAAATATAC 58.447 38.462 0.00 0.00 36.60 1.47
4064 6890 6.707290 AGAACAAGTGTAGTTGTGGCATATA 58.293 36.000 5.90 0.00 39.82 0.86


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

AutoCloner maintained by Alex Coulton.