Multiple sequence alignment - TraesCS7B01G115900

Loading Multiple Alignment...

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 TraesCS7B01G115900 chr7B 100.000 5418 0 0 1 5418 134553551 134558968 0.000000e+00 10006
1 TraesCS7B01G115900 chr7B 88.745 231 23 2 1939 2167 43246661 43246432 4.130000e-71 279
2 TraesCS7B01G115900 chr7D 92.348 4809 213 71 687 5418 169382265 169386995 0.000000e+00 6698
3 TraesCS7B01G115900 chr7D 86.916 2033 182 31 1756 3742 638149214 638151208 0.000000e+00 2204
4 TraesCS7B01G115900 chr7D 85.197 304 22 10 1173 1476 638148827 638149107 1.910000e-74 291
5 TraesCS7B01G115900 chr7D 88.462 234 24 2 1936 2167 91688672 91688904 4.130000e-71 279
6 TraesCS7B01G115900 chr7D 82.500 320 23 16 14 308 169381861 169382172 3.240000e-62 250
7 TraesCS7B01G115900 chr7A 94.547 1522 57 9 3901 5418 171383817 171385316 0.000000e+00 2327
8 TraesCS7B01G115900 chr7A 91.249 1497 114 9 2368 3852 171382322 171383813 0.000000e+00 2023
9 TraesCS7B01G115900 chr7A 87.544 1694 108 54 687 2316 171380674 171382328 0.000000e+00 1864
10 TraesCS7B01G115900 chr7A 94.815 270 13 1 421 689 463707875 463707606 2.330000e-113 420
11 TraesCS7B01G115900 chr7A 87.137 241 21 3 1936 2166 93255379 93255619 1.160000e-66 265
12 TraesCS7B01G115900 chr3D 86.335 1932 192 21 1794 3690 570094447 570092553 0.000000e+00 2039
13 TraesCS7B01G115900 chr2B 97.368 266 7 0 424 689 779958554 779958819 2.300000e-123 453
14 TraesCS7B01G115900 chr5A 96.981 265 8 0 425 689 51668750 51669014 3.850000e-121 446
15 TraesCS7B01G115900 chr5A 95.522 268 12 0 422 689 9765870 9766137 3.880000e-116 429
16 TraesCS7B01G115900 chr5A 95.802 262 11 0 428 689 665445845 665445584 1.800000e-114 424
17 TraesCS7B01G115900 chr6A 95.522 268 12 0 422 689 511118737 511119004 3.880000e-116 429
18 TraesCS7B01G115900 chr6A 95.522 268 12 0 422 689 511149638 511149905 3.880000e-116 429
19 TraesCS7B01G115900 chr3A 95.149 268 13 0 422 689 58274808 58275075 1.800000e-114 424
20 TraesCS7B01G115900 chr1A 94.815 270 13 1 421 689 107407961 107407692 2.330000e-113 420


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 TraesCS7B01G115900 chr7B 134553551 134558968 5417 False 10006.000000 10006 100.000000 1 5418 1 chr7B.!!$F1 5417
1 TraesCS7B01G115900 chr7D 169381861 169386995 5134 False 3474.000000 6698 87.424000 14 5418 2 chr7D.!!$F2 5404
2 TraesCS7B01G115900 chr7D 638148827 638151208 2381 False 1247.500000 2204 86.056500 1173 3742 2 chr7D.!!$F3 2569
3 TraesCS7B01G115900 chr7A 171380674 171385316 4642 False 2071.333333 2327 91.113333 687 5418 3 chr7A.!!$F2 4731
4 TraesCS7B01G115900 chr3D 570092553 570094447 1894 True 2039.000000 2039 86.335000 1794 3690 1 chr3D.!!$R1 1896

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
883 924 0.041576 CAACCAGCATCGCATCATCG 60.042 55.0 0.00 0.0 0.00 3.84 F
943 1005 0.419459 ACCACCATCTTCTCCTCCCT 59.581 55.0 0.00 0.0 0.00 4.20 F
2469 2625 0.240945 AGCCCGCGAAAGAAAACATG 59.759 50.0 8.23 0.0 0.00 3.21 F
2586 2742 0.107945 GAAGCTCATCTGCCGGAGTT 60.108 55.0 5.05 0.0 33.66 3.01 F
3189 3347 0.752658 AAACTTTGCCCAACTGCTCC 59.247 50.0 0.00 0.0 0.00 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2448 2604 0.030101 TGTTTTCTTTCGCGGGCTTG 59.970 50.0 6.13 0.0 0.00 4.01 R
2556 2712 0.032678 ATGAGCTTCGGTCCGCATAG 59.967 55.0 6.34 5.0 0.00 2.23 R
3410 3572 0.458543 AACTGCAGTCAGATACGCGG 60.459 55.0 21.95 0.0 42.95 6.46 R
4317 4488 0.689623 AGCCCATCCGATCTGATTCC 59.310 55.0 0.00 0.0 0.00 3.01 R
4882 5055 0.109342 ACTCTGCTCAAAGGTGTGGG 59.891 55.0 0.00 0.0 0.00 4.61 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
55 56 5.564048 AGCAAAACAACGTGGTAGTTTTA 57.436 34.783 16.03 0.00 41.86 1.52
56 57 5.952033 AGCAAAACAACGTGGTAGTTTTAA 58.048 33.333 16.03 0.00 41.86 1.52
76 77 3.591695 AAAAACCATGGCCCAAATTGT 57.408 38.095 13.04 0.00 0.00 2.71
141 163 8.084590 AGTTAAGATAAAAGAAAGTGTCACGG 57.915 34.615 0.00 0.00 0.00 4.94
143 165 6.541111 AAGATAAAAGAAAGTGTCACGGAC 57.459 37.500 0.00 0.00 0.00 4.79
146 168 0.179094 AAGAAAGTGTCACGGACGCA 60.179 50.000 16.42 0.00 44.42 5.24
148 170 1.149361 GAAAGTGTCACGGACGCACA 61.149 55.000 16.42 0.00 44.42 4.57
149 171 0.741574 AAAGTGTCACGGACGCACAA 60.742 50.000 16.42 0.00 44.42 3.33
154 176 1.007336 GTCACGGACGCACAAGTAGG 61.007 60.000 0.00 0.00 0.00 3.18
158 180 1.592400 CGGACGCACAAGTAGGAGGA 61.592 60.000 0.00 0.00 0.00 3.71
165 187 3.617531 CGCACAAGTAGGAGGATGAAAGT 60.618 47.826 0.00 0.00 0.00 2.66
177 199 5.003096 AGGATGAAAGTTGGAATTCACCT 57.997 39.130 7.93 0.00 38.29 4.00
191 214 1.105167 TCACCTCGGTCGACACTTGT 61.105 55.000 18.91 6.06 0.00 3.16
200 223 1.856597 GTCGACACTTGTACCACACAC 59.143 52.381 11.55 0.00 36.69 3.82
287 310 1.881925 CGGCCTCCAGATCAACAACAA 60.882 52.381 0.00 0.00 0.00 2.83
290 313 2.622942 GCCTCCAGATCAACAACAACAA 59.377 45.455 0.00 0.00 0.00 2.83
304 327 0.588730 CAACAACAACACAGACGCGG 60.589 55.000 12.47 0.00 0.00 6.46
305 328 2.052237 CAACAACACAGACGCGGC 60.052 61.111 12.47 7.86 0.00 6.53
306 329 3.276846 AACAACACAGACGCGGCC 61.277 61.111 9.25 0.00 0.00 6.13
307 330 4.539083 ACAACACAGACGCGGCCA 62.539 61.111 9.25 0.00 0.00 5.36
308 331 4.012895 CAACACAGACGCGGCCAC 62.013 66.667 9.25 0.00 0.00 5.01
320 343 4.704833 GGCCACGCTTGCAGGAGA 62.705 66.667 6.56 0.00 0.00 3.71
321 344 3.123620 GCCACGCTTGCAGGAGAG 61.124 66.667 6.56 0.00 0.00 3.20
322 345 3.123620 CCACGCTTGCAGGAGAGC 61.124 66.667 6.56 1.84 35.58 4.09
334 357 2.383527 GGAGAGCGCCAACGACAAG 61.384 63.158 2.29 0.00 43.93 3.16
340 363 3.723348 GCCAACGACAAGGACCGC 61.723 66.667 0.00 0.00 0.00 5.68
375 406 3.334078 GCACCAACATGCAGCATAC 57.666 52.632 7.82 0.00 45.39 2.39
376 407 0.523968 GCACCAACATGCAGCATACG 60.524 55.000 7.82 0.00 45.39 3.06
377 408 0.804364 CACCAACATGCAGCATACGT 59.196 50.000 7.82 0.00 0.00 3.57
378 409 2.006169 CACCAACATGCAGCATACGTA 58.994 47.619 7.82 0.00 0.00 3.57
379 410 2.030823 CACCAACATGCAGCATACGTAG 59.969 50.000 7.82 0.00 0.00 3.51
380 411 1.599071 CCAACATGCAGCATACGTAGG 59.401 52.381 7.82 2.16 0.00 3.18
381 412 2.549926 CAACATGCAGCATACGTAGGA 58.450 47.619 12.12 0.00 0.00 2.94
382 413 2.225068 ACATGCAGCATACGTAGGAC 57.775 50.000 12.12 2.49 0.00 3.85
383 414 1.480545 ACATGCAGCATACGTAGGACA 59.519 47.619 12.12 5.98 0.00 4.02
384 415 2.130395 CATGCAGCATACGTAGGACAG 58.870 52.381 12.12 0.59 0.00 3.51
385 416 0.179111 TGCAGCATACGTAGGACAGC 60.179 55.000 12.12 11.20 0.00 4.40
386 417 0.876342 GCAGCATACGTAGGACAGCC 60.876 60.000 12.12 0.00 0.00 4.85
387 418 0.249489 CAGCATACGTAGGACAGCCC 60.249 60.000 12.12 0.00 33.31 5.19
388 419 0.686441 AGCATACGTAGGACAGCCCA 60.686 55.000 12.12 0.00 37.41 5.36
389 420 0.249489 GCATACGTAGGACAGCCCAG 60.249 60.000 12.12 0.00 37.41 4.45
390 421 0.249489 CATACGTAGGACAGCCCAGC 60.249 60.000 0.00 0.00 37.41 4.85
391 422 1.735376 ATACGTAGGACAGCCCAGCG 61.735 60.000 0.08 0.00 39.23 5.18
393 424 4.840005 GTAGGACAGCCCAGCGCC 62.840 72.222 2.29 0.00 38.78 6.53
430 461 5.007724 GTGCTGCAAACTTCACTTTACTACT 59.992 40.000 2.77 0.00 0.00 2.57
431 462 5.236478 TGCTGCAAACTTCACTTTACTACTC 59.764 40.000 0.00 0.00 0.00 2.59
432 463 5.334182 GCTGCAAACTTCACTTTACTACTCC 60.334 44.000 0.00 0.00 0.00 3.85
433 464 5.061179 TGCAAACTTCACTTTACTACTCCC 58.939 41.667 0.00 0.00 0.00 4.30
434 465 5.163237 TGCAAACTTCACTTTACTACTCCCT 60.163 40.000 0.00 0.00 0.00 4.20
435 466 5.408909 GCAAACTTCACTTTACTACTCCCTC 59.591 44.000 0.00 0.00 0.00 4.30
436 467 5.741962 AACTTCACTTTACTACTCCCTCC 57.258 43.478 0.00 0.00 0.00 4.30
437 468 3.762823 ACTTCACTTTACTACTCCCTCCG 59.237 47.826 0.00 0.00 0.00 4.63
438 469 2.731572 TCACTTTACTACTCCCTCCGG 58.268 52.381 0.00 0.00 0.00 5.14
439 470 2.042162 TCACTTTACTACTCCCTCCGGT 59.958 50.000 0.00 0.00 0.00 5.28
440 471 2.426381 CACTTTACTACTCCCTCCGGTC 59.574 54.545 0.00 0.00 0.00 4.79
441 472 2.030371 CTTTACTACTCCCTCCGGTCC 58.970 57.143 0.00 0.00 0.00 4.46
442 473 1.302907 TTACTACTCCCTCCGGTCCT 58.697 55.000 0.00 0.00 0.00 3.85
443 474 1.302907 TACTACTCCCTCCGGTCCTT 58.697 55.000 0.00 0.00 0.00 3.36
444 475 0.412640 ACTACTCCCTCCGGTCCTTT 59.587 55.000 0.00 0.00 0.00 3.11
445 476 1.203275 ACTACTCCCTCCGGTCCTTTT 60.203 52.381 0.00 0.00 0.00 2.27
446 477 1.907255 CTACTCCCTCCGGTCCTTTTT 59.093 52.381 0.00 0.00 0.00 1.94
447 478 2.034436 ACTCCCTCCGGTCCTTTTTA 57.966 50.000 0.00 0.00 0.00 1.52
448 479 1.627329 ACTCCCTCCGGTCCTTTTTAC 59.373 52.381 0.00 0.00 0.00 2.01
449 480 1.907255 CTCCCTCCGGTCCTTTTTACT 59.093 52.381 0.00 0.00 0.00 2.24
450 481 2.305052 CTCCCTCCGGTCCTTTTTACTT 59.695 50.000 0.00 0.00 0.00 2.24
451 482 2.712627 TCCCTCCGGTCCTTTTTACTTT 59.287 45.455 0.00 0.00 0.00 2.66
452 483 2.817844 CCCTCCGGTCCTTTTTACTTTG 59.182 50.000 0.00 0.00 0.00 2.77
453 484 2.228103 CCTCCGGTCCTTTTTACTTTGC 59.772 50.000 0.00 0.00 0.00 3.68
454 485 2.882137 CTCCGGTCCTTTTTACTTTGCA 59.118 45.455 0.00 0.00 0.00 4.08
455 486 3.492337 TCCGGTCCTTTTTACTTTGCAT 58.508 40.909 0.00 0.00 0.00 3.96
456 487 4.653868 TCCGGTCCTTTTTACTTTGCATA 58.346 39.130 0.00 0.00 0.00 3.14
457 488 5.258051 TCCGGTCCTTTTTACTTTGCATAT 58.742 37.500 0.00 0.00 0.00 1.78
458 489 5.712917 TCCGGTCCTTTTTACTTTGCATATT 59.287 36.000 0.00 0.00 0.00 1.28
459 490 6.885376 TCCGGTCCTTTTTACTTTGCATATTA 59.115 34.615 0.00 0.00 0.00 0.98
460 491 7.066525 TCCGGTCCTTTTTACTTTGCATATTAG 59.933 37.037 0.00 0.00 0.00 1.73
461 492 7.193595 CGGTCCTTTTTACTTTGCATATTAGG 58.806 38.462 0.00 0.00 0.00 2.69
462 493 7.148137 CGGTCCTTTTTACTTTGCATATTAGGT 60.148 37.037 0.00 0.00 0.00 3.08
463 494 8.528643 GGTCCTTTTTACTTTGCATATTAGGTT 58.471 33.333 0.00 0.00 0.00 3.50
464 495 9.923143 GTCCTTTTTACTTTGCATATTAGGTTT 57.077 29.630 0.00 0.00 0.00 3.27
465 496 9.921637 TCCTTTTTACTTTGCATATTAGGTTTG 57.078 29.630 0.00 0.00 0.00 2.93
466 497 9.705290 CCTTTTTACTTTGCATATTAGGTTTGT 57.295 29.630 0.00 0.00 0.00 2.83
468 499 9.699703 TTTTTACTTTGCATATTAGGTTTGTCC 57.300 29.630 0.00 0.00 0.00 4.02
469 500 5.560966 ACTTTGCATATTAGGTTTGTCCG 57.439 39.130 0.00 0.00 41.99 4.79
470 501 5.250200 ACTTTGCATATTAGGTTTGTCCGA 58.750 37.500 0.00 0.00 41.99 4.55
471 502 5.708230 ACTTTGCATATTAGGTTTGTCCGAA 59.292 36.000 0.00 0.00 41.99 4.30
472 503 5.811399 TTGCATATTAGGTTTGTCCGAAG 57.189 39.130 0.00 0.00 41.99 3.79
473 504 4.839121 TGCATATTAGGTTTGTCCGAAGT 58.161 39.130 0.00 0.00 41.99 3.01
474 505 4.873827 TGCATATTAGGTTTGTCCGAAGTC 59.126 41.667 0.00 0.00 41.99 3.01
475 506 4.873827 GCATATTAGGTTTGTCCGAAGTCA 59.126 41.667 0.00 0.00 41.99 3.41
476 507 5.353123 GCATATTAGGTTTGTCCGAAGTCAA 59.647 40.000 0.00 0.00 41.99 3.18
477 508 6.038271 GCATATTAGGTTTGTCCGAAGTCAAT 59.962 38.462 0.00 0.00 41.99 2.57
478 509 7.415206 GCATATTAGGTTTGTCCGAAGTCAATT 60.415 37.037 0.00 0.00 41.99 2.32
479 510 6.894339 ATTAGGTTTGTCCGAAGTCAATTT 57.106 33.333 0.00 0.00 41.99 1.82
480 511 7.989416 ATTAGGTTTGTCCGAAGTCAATTTA 57.011 32.000 0.00 0.00 41.99 1.40
481 512 7.804843 TTAGGTTTGTCCGAAGTCAATTTAA 57.195 32.000 0.00 0.00 41.99 1.52
482 513 6.894339 AGGTTTGTCCGAAGTCAATTTAAT 57.106 33.333 0.00 0.00 41.99 1.40
483 514 6.909909 AGGTTTGTCCGAAGTCAATTTAATC 58.090 36.000 0.00 0.00 41.99 1.75
484 515 6.072119 AGGTTTGTCCGAAGTCAATTTAATCC 60.072 38.462 0.00 0.00 41.99 3.01
485 516 6.294286 GGTTTGTCCGAAGTCAATTTAATCCA 60.294 38.462 0.00 0.00 0.00 3.41
486 517 6.885952 TTGTCCGAAGTCAATTTAATCCAA 57.114 33.333 0.00 0.00 0.00 3.53
487 518 6.249035 TGTCCGAAGTCAATTTAATCCAAC 57.751 37.500 0.00 0.00 0.00 3.77
488 519 6.001460 TGTCCGAAGTCAATTTAATCCAACT 58.999 36.000 0.00 0.00 0.00 3.16
489 520 6.488683 TGTCCGAAGTCAATTTAATCCAACTT 59.511 34.615 0.00 0.00 0.00 2.66
490 521 7.013846 TGTCCGAAGTCAATTTAATCCAACTTT 59.986 33.333 0.00 0.00 0.00 2.66
491 522 7.326063 GTCCGAAGTCAATTTAATCCAACTTTG 59.674 37.037 0.00 0.00 0.00 2.77
492 523 7.229707 TCCGAAGTCAATTTAATCCAACTTTGA 59.770 33.333 12.16 0.00 32.33 2.69
493 524 7.326063 CCGAAGTCAATTTAATCCAACTTTGAC 59.674 37.037 12.16 5.67 38.56 3.18
494 525 7.326063 CGAAGTCAATTTAATCCAACTTTGACC 59.674 37.037 9.31 0.00 38.81 4.02
495 526 7.595819 AGTCAATTTAATCCAACTTTGACCA 57.404 32.000 9.31 0.00 38.81 4.02
496 527 8.017418 AGTCAATTTAATCCAACTTTGACCAA 57.983 30.769 9.31 0.00 38.81 3.67
497 528 8.143835 AGTCAATTTAATCCAACTTTGACCAAG 58.856 33.333 9.31 0.00 38.81 3.61
498 529 7.384932 GTCAATTTAATCCAACTTTGACCAAGG 59.615 37.037 0.00 0.00 35.44 3.61
499 530 6.994421 ATTTAATCCAACTTTGACCAAGGT 57.006 33.333 0.00 0.00 36.72 3.50
500 531 6.800072 TTTAATCCAACTTTGACCAAGGTT 57.200 33.333 4.69 4.69 40.57 3.50
501 532 7.899648 TTTAATCCAACTTTGACCAAGGTTA 57.100 32.000 9.41 0.00 38.34 2.85
502 533 8.485578 TTTAATCCAACTTTGACCAAGGTTAT 57.514 30.769 9.41 0.08 38.34 1.89
503 534 9.589461 TTTAATCCAACTTTGACCAAGGTTATA 57.411 29.630 9.41 2.89 38.34 0.98
504 535 9.762381 TTAATCCAACTTTGACCAAGGTTATAT 57.238 29.630 9.41 4.72 38.34 0.86
506 537 9.762381 AATCCAACTTTGACCAAGGTTATATAA 57.238 29.630 9.41 0.00 38.34 0.98
507 538 9.762381 ATCCAACTTTGACCAAGGTTATATAAA 57.238 29.630 9.41 0.00 38.34 1.40
508 539 9.589461 TCCAACTTTGACCAAGGTTATATAAAA 57.411 29.630 9.41 0.00 38.34 1.52
536 567 9.679661 ATTATAGACATTCACATAACAACACCA 57.320 29.630 0.00 0.00 0.00 4.17
537 568 7.994425 ATAGACATTCACATAACAACACCAA 57.006 32.000 0.00 0.00 0.00 3.67
538 569 6.899393 AGACATTCACATAACAACACCAAT 57.101 33.333 0.00 0.00 0.00 3.16
539 570 7.994425 AGACATTCACATAACAACACCAATA 57.006 32.000 0.00 0.00 0.00 1.90
540 571 8.579850 AGACATTCACATAACAACACCAATAT 57.420 30.769 0.00 0.00 0.00 1.28
541 572 8.677300 AGACATTCACATAACAACACCAATATC 58.323 33.333 0.00 0.00 0.00 1.63
542 573 8.347004 ACATTCACATAACAACACCAATATCA 57.653 30.769 0.00 0.00 0.00 2.15
543 574 8.970020 ACATTCACATAACAACACCAATATCAT 58.030 29.630 0.00 0.00 0.00 2.45
544 575 9.806203 CATTCACATAACAACACCAATATCATT 57.194 29.630 0.00 0.00 0.00 2.57
547 578 9.898152 TCACATAACAACACCAATATCATTAGA 57.102 29.630 0.00 0.00 0.00 2.10
554 585 9.857656 ACAACACCAATATCATTAGATTCATCT 57.142 29.630 0.00 0.00 40.86 2.90
648 679 4.598062 ACTTAGCAAAGTTTGACTTTCGC 58.402 39.130 19.82 14.44 44.47 4.70
649 680 2.492019 AGCAAAGTTTGACTTTCGCC 57.508 45.000 19.82 0.00 44.47 5.54
650 681 1.748493 AGCAAAGTTTGACTTTCGCCA 59.252 42.857 19.82 0.00 44.47 5.69
651 682 2.165437 AGCAAAGTTTGACTTTCGCCAA 59.835 40.909 19.82 0.00 44.47 4.52
652 683 2.926838 GCAAAGTTTGACTTTCGCCAAA 59.073 40.909 19.82 0.00 44.47 3.28
653 684 3.555547 GCAAAGTTTGACTTTCGCCAAAT 59.444 39.130 19.82 0.00 44.47 2.32
654 685 4.318050 GCAAAGTTTGACTTTCGCCAAATC 60.318 41.667 19.82 0.00 44.47 2.17
655 686 3.643159 AGTTTGACTTTCGCCAAATCC 57.357 42.857 0.00 0.00 35.14 3.01
656 687 2.955660 AGTTTGACTTTCGCCAAATCCA 59.044 40.909 0.00 0.00 35.14 3.41
657 688 3.383185 AGTTTGACTTTCGCCAAATCCAA 59.617 39.130 0.00 0.00 35.14 3.53
658 689 4.039124 AGTTTGACTTTCGCCAAATCCAAT 59.961 37.500 0.00 0.00 35.14 3.16
659 690 3.574284 TGACTTTCGCCAAATCCAATG 57.426 42.857 0.00 0.00 0.00 2.82
660 691 2.890311 TGACTTTCGCCAAATCCAATGT 59.110 40.909 0.00 0.00 0.00 2.71
661 692 3.244976 GACTTTCGCCAAATCCAATGTG 58.755 45.455 0.00 0.00 0.00 3.21
662 693 1.994779 CTTTCGCCAAATCCAATGTGC 59.005 47.619 0.00 0.00 0.00 4.57
663 694 0.964700 TTCGCCAAATCCAATGTGCA 59.035 45.000 0.00 0.00 0.00 4.57
664 695 0.964700 TCGCCAAATCCAATGTGCAA 59.035 45.000 0.00 0.00 0.00 4.08
665 696 1.342496 TCGCCAAATCCAATGTGCAAA 59.658 42.857 0.00 0.00 0.00 3.68
666 697 1.727880 CGCCAAATCCAATGTGCAAAG 59.272 47.619 0.00 0.00 0.00 2.77
667 698 2.769893 GCCAAATCCAATGTGCAAAGT 58.230 42.857 0.00 0.00 0.00 2.66
668 699 3.613671 CGCCAAATCCAATGTGCAAAGTA 60.614 43.478 0.00 0.00 0.00 2.24
669 700 4.314121 GCCAAATCCAATGTGCAAAGTAA 58.686 39.130 0.00 0.00 0.00 2.24
670 701 4.754114 GCCAAATCCAATGTGCAAAGTAAA 59.246 37.500 0.00 0.00 0.00 2.01
671 702 5.238214 GCCAAATCCAATGTGCAAAGTAAAA 59.762 36.000 0.00 0.00 0.00 1.52
672 703 6.238593 GCCAAATCCAATGTGCAAAGTAAAAA 60.239 34.615 0.00 0.00 0.00 1.94
709 742 0.914417 TTCCAATTCCGCCCTCCTCT 60.914 55.000 0.00 0.00 0.00 3.69
714 747 0.543749 ATTCCGCCCTCCTCTTCTTG 59.456 55.000 0.00 0.00 0.00 3.02
758 794 3.426568 GCTCAAGCCCAGTCGCAC 61.427 66.667 0.00 0.00 34.31 5.34
759 795 2.031012 CTCAAGCCCAGTCGCACA 59.969 61.111 0.00 0.00 0.00 4.57
852 892 0.829990 CCAAACCCAAACCAAGCACT 59.170 50.000 0.00 0.00 0.00 4.40
853 893 1.209261 CCAAACCCAAACCAAGCACTT 59.791 47.619 0.00 0.00 0.00 3.16
854 894 2.549926 CAAACCCAAACCAAGCACTTC 58.450 47.619 0.00 0.00 0.00 3.01
858 898 1.480137 CCCAAACCAAGCACTTCACAA 59.520 47.619 0.00 0.00 0.00 3.33
859 899 2.539476 CCAAACCAAGCACTTCACAAC 58.461 47.619 0.00 0.00 0.00 3.32
863 904 1.110442 CCAAGCACTTCACAACCCAA 58.890 50.000 0.00 0.00 0.00 4.12
881 922 1.133598 CAACAACCAGCATCGCATCAT 59.866 47.619 0.00 0.00 0.00 2.45
883 924 0.041576 CAACCAGCATCGCATCATCG 60.042 55.000 0.00 0.00 0.00 3.84
884 925 1.779025 AACCAGCATCGCATCATCGC 61.779 55.000 0.00 0.00 0.00 4.58
886 927 1.959738 CAGCATCGCATCATCGCCT 60.960 57.895 0.00 0.00 0.00 5.52
887 928 1.227764 AGCATCGCATCATCGCCTT 60.228 52.632 0.00 0.00 0.00 4.35
888 929 1.206072 GCATCGCATCATCGCCTTC 59.794 57.895 0.00 0.00 0.00 3.46
889 930 1.864862 CATCGCATCATCGCCTTCC 59.135 57.895 0.00 0.00 0.00 3.46
890 931 0.881600 CATCGCATCATCGCCTTCCA 60.882 55.000 0.00 0.00 0.00 3.53
891 932 0.882042 ATCGCATCATCGCCTTCCAC 60.882 55.000 0.00 0.00 0.00 4.02
892 933 2.874694 CGCATCATCGCCTTCCACG 61.875 63.158 0.00 0.00 0.00 4.94
893 934 1.521457 GCATCATCGCCTTCCACGA 60.521 57.895 0.00 0.00 44.75 4.35
926 988 1.671379 GCCTTCCTTCGTGTCCACC 60.671 63.158 0.00 0.00 0.00 4.61
934 996 0.762418 TTCGTGTCCACCACCATCTT 59.238 50.000 0.00 0.00 41.26 2.40
942 1004 0.543749 CACCACCATCTTCTCCTCCC 59.456 60.000 0.00 0.00 0.00 4.30
943 1005 0.419459 ACCACCATCTTCTCCTCCCT 59.581 55.000 0.00 0.00 0.00 4.20
945 1007 0.749649 CACCATCTTCTCCTCCCTCG 59.250 60.000 0.00 0.00 0.00 4.63
947 1009 0.758685 CCATCTTCTCCTCCCTCGCT 60.759 60.000 0.00 0.00 0.00 4.93
950 1012 1.032657 TCTTCTCCTCCCTCGCTTCG 61.033 60.000 0.00 0.00 0.00 3.79
951 1013 2.621371 CTTCTCCTCCCTCGCTTCGC 62.621 65.000 0.00 0.00 0.00 4.70
952 1014 3.144193 CTCCTCCCTCGCTTCGCT 61.144 66.667 0.00 0.00 0.00 4.93
953 1015 2.680352 TCCTCCCTCGCTTCGCTT 60.680 61.111 0.00 0.00 0.00 4.68
954 1016 2.510238 CCTCCCTCGCTTCGCTTG 60.510 66.667 0.00 0.00 0.00 4.01
956 1018 3.939837 CTCCCTCGCTTCGCTTGCA 62.940 63.158 0.00 0.00 0.00 4.08
958 1020 1.521457 CCCTCGCTTCGCTTGCATA 60.521 57.895 0.00 0.00 0.00 3.14
959 1021 1.493950 CCCTCGCTTCGCTTGCATAG 61.494 60.000 0.00 0.00 0.00 2.23
968 1034 1.069204 TCGCTTGCATAGAAGCCTAGG 59.931 52.381 3.67 3.67 44.73 3.02
977 1045 6.736581 TGCATAGAAGCCTAGGACTATCTAT 58.263 40.000 14.75 14.96 31.97 1.98
978 1046 6.831353 TGCATAGAAGCCTAGGACTATCTATC 59.169 42.308 14.75 12.11 29.96 2.08
986 1054 6.097839 AGCCTAGGACTATCTATCTCTCTACG 59.902 46.154 14.75 0.00 0.00 3.51
1005 1073 3.838271 GCCTCGCCGGAGATGTCA 61.838 66.667 8.83 0.00 43.27 3.58
1009 1077 3.842923 CGCCGGAGATGTCAGCCT 61.843 66.667 5.05 0.00 0.00 4.58
1032 1112 4.069232 TTGCTGTCGGCGGAGGAG 62.069 66.667 7.21 0.00 45.43 3.69
1460 1558 0.893727 AATTTGCTCCTTTCCGCCGT 60.894 50.000 0.00 0.00 0.00 5.68
1597 1700 2.280628 GACTTCGGTTGGATCACCATC 58.719 52.381 3.35 0.00 46.34 3.51
1625 1728 8.378172 TGTCACTTTAACCTGAATCTGTTTAG 57.622 34.615 0.00 0.00 0.00 1.85
1818 1937 2.158475 TGAGTTGAACCCTTCCTTGCAT 60.158 45.455 0.00 0.00 0.00 3.96
1890 2014 2.880268 TGTTGCATTTCTGTCCTGTCAG 59.120 45.455 0.00 0.00 36.85 3.51
1974 2100 8.406297 TGTATTTAGATATAGGCATGTCGCTAG 58.594 37.037 0.00 0.00 41.91 3.42
1982 2111 6.680874 ATAGGCATGTCGCTAGTAGTATAC 57.319 41.667 0.00 0.00 40.92 1.47
2064 2193 5.872635 TCAATCTTTCTGTTCGCATGATTC 58.127 37.500 0.00 0.00 0.00 2.52
2294 2436 3.645687 ACAAATTGCACAAAGGTGGGTAT 59.354 39.130 0.00 0.00 45.38 2.73
2410 2563 4.278170 TCAAAATTCACAGCGTTCCTGATT 59.722 37.500 0.00 0.00 44.64 2.57
2469 2625 0.240945 AGCCCGCGAAAGAAAACATG 59.759 50.000 8.23 0.00 0.00 3.21
2474 2630 2.031157 CCGCGAAAGAAAACATGGTTCT 60.031 45.455 8.23 1.97 36.90 3.01
2489 2645 1.290134 GTTCTCCCCAGGGATTCACT 58.710 55.000 7.25 0.00 44.24 3.41
2494 2650 1.075374 TCCCCAGGGATTCACTTTGTG 59.925 52.381 7.25 0.00 39.76 3.33
2541 2697 2.098614 TGTGACACCTGCAAACAATGT 58.901 42.857 2.45 0.00 0.00 2.71
2544 2700 2.757314 TGACACCTGCAAACAATGTGAA 59.243 40.909 0.00 0.00 34.38 3.18
2556 2712 5.679734 AACAATGTGAATATGAGATCGCC 57.320 39.130 0.00 0.00 0.00 5.54
2574 2730 1.437573 CTATGCGGACCGAAGCTCA 59.562 57.895 20.50 5.75 0.00 4.26
2583 2739 2.496341 CGAAGCTCATCTGCCGGA 59.504 61.111 5.05 0.00 0.00 5.14
2586 2742 0.107945 GAAGCTCATCTGCCGGAGTT 60.108 55.000 5.05 0.00 33.66 3.01
2598 2754 1.517832 CGGAGTTCTTGCGAGGGAT 59.482 57.895 0.00 0.00 44.18 3.85
2604 2760 4.202223 GGAGTTCTTGCGAGGGATAACATA 60.202 45.833 0.00 0.00 0.00 2.29
2605 2761 5.353394 AGTTCTTGCGAGGGATAACATAA 57.647 39.130 0.00 0.00 0.00 1.90
2633 2789 4.803426 CGCAGACGGTGAGAGGGC 62.803 72.222 0.00 0.00 34.97 5.19
2982 3140 2.926242 ACATGGGTTCCCGTCCGT 60.926 61.111 0.00 0.00 0.00 4.69
3040 3198 3.482156 AGATTATTCTCACATGCGGCT 57.518 42.857 0.00 0.00 0.00 5.52
3086 3244 2.264480 CCCACATCGTCTTCGGCA 59.736 61.111 0.00 0.00 37.69 5.69
3189 3347 0.752658 AAACTTTGCCCAACTGCTCC 59.247 50.000 0.00 0.00 0.00 4.70
3289 3449 5.049198 CAGCCGTAGCAATTGATATCACATT 60.049 40.000 10.34 6.16 43.56 2.71
3319 3479 6.251589 CGTCGAACTAGATTATATCCATGCAC 59.748 42.308 0.00 0.00 0.00 4.57
3410 3572 8.188139 TGAAAATTCACTTTGTTGAGGTTAGAC 58.812 33.333 0.00 0.00 31.01 2.59
3614 3776 3.558505 CTGATTGCTTCCGTGAGTTTTG 58.441 45.455 0.00 0.00 0.00 2.44
3620 3782 2.664916 CTTCCGTGAGTTTTGGCATTG 58.335 47.619 0.00 0.00 0.00 2.82
3666 3837 5.871396 TCAGTTCCATCCTTATACCTGAC 57.129 43.478 0.00 0.00 0.00 3.51
3673 3844 8.598041 GTTCCATCCTTATACCTGACTATGATT 58.402 37.037 0.00 0.00 0.00 2.57
3763 3934 6.627953 GCCTTTCTGCATGAAGCCTAATTTTA 60.628 38.462 0.00 0.00 44.83 1.52
3879 4050 5.837829 TCATTAGAAATAACCCTGCCCTTT 58.162 37.500 0.00 0.00 0.00 3.11
3880 4051 5.891551 TCATTAGAAATAACCCTGCCCTTTC 59.108 40.000 0.00 0.00 0.00 2.62
3881 4052 5.530176 TTAGAAATAACCCTGCCCTTTCT 57.470 39.130 0.00 0.00 39.03 2.52
3882 4053 3.969553 AGAAATAACCCTGCCCTTTCTC 58.030 45.455 0.00 0.00 32.23 2.87
3883 4054 3.593780 AGAAATAACCCTGCCCTTTCTCT 59.406 43.478 0.00 0.00 32.23 3.10
3984 4155 2.905415 TGGCTTGTGATCCCAAGAAT 57.095 45.000 20.49 0.00 43.65 2.40
3990 4161 3.417069 TGTGATCCCAAGAATGTTCGT 57.583 42.857 0.00 0.00 0.00 3.85
4100 4271 5.882000 TCATCACCATCATACTTTTCCTGTG 59.118 40.000 0.00 0.00 0.00 3.66
4257 4428 2.037772 TCTGTCAAGCTCACCTTTCTCC 59.962 50.000 0.00 0.00 0.00 3.71
4317 4488 0.092351 GTTGCGTATGACAACGACGG 59.908 55.000 12.35 0.00 45.68 4.79
4354 4525 0.602060 CTCAGTCAGACTGCAGCAGA 59.398 55.000 29.70 6.43 45.54 4.26
4378 4549 0.185901 AGAAAGCAAGCAGGGTTCCA 59.814 50.000 0.00 0.00 0.00 3.53
4401 4572 2.027745 TCTTCCTTTCGAGAGCATTGCT 60.028 45.455 11.79 11.79 43.88 3.91
4539 4710 8.101419 GGATGTAGTTAAACAAGGGATATAGGG 58.899 40.741 0.00 0.00 32.02 3.53
4794 4967 1.647346 GTTGGTGGAATATCGCGTGA 58.353 50.000 5.77 0.00 0.00 4.35
4805 4978 0.736325 ATCGCGTGAAGGCTACACAC 60.736 55.000 5.77 8.62 38.04 3.82
4853 5026 2.702478 TCATGTCCAAACAATGCCCAAA 59.298 40.909 0.00 0.00 39.30 3.28
4860 5033 3.012518 CAAACAATGCCCAAACAAACCA 58.987 40.909 0.00 0.00 0.00 3.67
4883 5056 2.153366 CAACACATGGAAAGCAACCC 57.847 50.000 0.00 0.00 0.00 4.11
4903 5076 0.590195 CACACCTTTGAGCAGAGTGC 59.410 55.000 0.00 0.00 45.46 4.40
5315 5490 2.360475 GTGGAGGGACCTTGCAGC 60.360 66.667 0.00 0.00 39.86 5.25
5362 5537 4.098960 AGCCCAACAGATCTGCATATTTTG 59.901 41.667 22.83 16.70 0.00 2.44
5370 5545 4.274459 AGATCTGCATATTTTGGCGAGAAC 59.726 41.667 0.00 0.00 0.00 3.01
5385 5560 1.823899 GAACCCCGCCATCATCCAC 60.824 63.158 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.050295 GCCTACCGACTTGAGTATAATTTGC 60.050 44.000 0.00 0.00 0.00 3.68
1 2 6.046593 TGCCTACCGACTTGAGTATAATTTG 58.953 40.000 0.00 0.00 0.00 2.32
2 3 6.229936 TGCCTACCGACTTGAGTATAATTT 57.770 37.500 0.00 0.00 0.00 1.82
3 4 5.864418 TGCCTACCGACTTGAGTATAATT 57.136 39.130 0.00 0.00 0.00 1.40
4 5 5.538813 TGATGCCTACCGACTTGAGTATAAT 59.461 40.000 0.00 0.00 0.00 1.28
5 6 4.891168 TGATGCCTACCGACTTGAGTATAA 59.109 41.667 0.00 0.00 0.00 0.98
6 7 4.466827 TGATGCCTACCGACTTGAGTATA 58.533 43.478 0.00 0.00 0.00 1.47
7 8 3.296854 TGATGCCTACCGACTTGAGTAT 58.703 45.455 0.00 0.00 0.00 2.12
8 9 2.688446 CTGATGCCTACCGACTTGAGTA 59.312 50.000 0.00 0.00 0.00 2.59
9 10 1.478510 CTGATGCCTACCGACTTGAGT 59.521 52.381 0.00 0.00 0.00 3.41
10 11 1.804372 GCTGATGCCTACCGACTTGAG 60.804 57.143 0.00 0.00 0.00 3.02
11 12 0.175760 GCTGATGCCTACCGACTTGA 59.824 55.000 0.00 0.00 0.00 3.02
12 13 2.682893 GCTGATGCCTACCGACTTG 58.317 57.895 0.00 0.00 0.00 3.16
56 57 3.220940 CACAATTTGGGCCATGGTTTTT 58.779 40.909 14.67 0.00 0.00 1.94
116 118 7.929785 TCCGTGACACTTTCTTTTATCTTAACT 59.070 33.333 3.68 0.00 0.00 2.24
126 148 0.935196 GCGTCCGTGACACTTTCTTT 59.065 50.000 3.68 0.00 32.09 2.52
134 156 0.318360 CTACTTGTGCGTCCGTGACA 60.318 55.000 5.15 0.00 32.09 3.58
140 162 0.824759 ATCCTCCTACTTGTGCGTCC 59.175 55.000 0.00 0.00 0.00 4.79
141 163 1.476891 TCATCCTCCTACTTGTGCGTC 59.523 52.381 0.00 0.00 0.00 5.19
143 165 2.672961 TTCATCCTCCTACTTGTGCG 57.327 50.000 0.00 0.00 0.00 5.34
146 168 4.597507 TCCAACTTTCATCCTCCTACTTGT 59.402 41.667 0.00 0.00 0.00 3.16
148 170 5.843019 TTCCAACTTTCATCCTCCTACTT 57.157 39.130 0.00 0.00 0.00 2.24
149 171 6.012508 TGAATTCCAACTTTCATCCTCCTACT 60.013 38.462 2.27 0.00 0.00 2.57
154 176 5.012893 AGGTGAATTCCAACTTTCATCCTC 58.987 41.667 2.27 0.00 40.69 3.71
158 180 3.758554 CCGAGGTGAATTCCAACTTTCAT 59.241 43.478 2.27 0.00 44.35 2.57
165 187 0.970640 TCGACCGAGGTGAATTCCAA 59.029 50.000 0.00 0.00 0.00 3.53
177 199 0.311790 GTGGTACAAGTGTCGACCGA 59.688 55.000 14.12 0.00 44.16 4.69
191 214 1.812686 GACCGCTGGAGTGTGTGGTA 61.813 60.000 1.50 0.00 45.76 3.25
200 223 2.187946 GGTGGATGACCGCTGGAG 59.812 66.667 1.50 0.00 45.13 3.86
275 298 5.182950 TCTGTGTTGTTGTTGTTGTTGATCT 59.817 36.000 0.00 0.00 0.00 2.75
287 310 2.819552 GCCGCGTCTGTGTTGTTGT 61.820 57.895 4.92 0.00 0.00 3.32
290 313 4.539083 TGGCCGCGTCTGTGTTGT 62.539 61.111 4.92 0.00 0.00 3.32
304 327 3.123620 CTCTCCTGCAAGCGTGGC 61.124 66.667 0.79 0.00 0.00 5.01
305 328 3.123620 GCTCTCCTGCAAGCGTGG 61.124 66.667 0.79 0.00 0.00 4.94
310 333 2.359107 TTGGCGCTCTCCTGCAAG 60.359 61.111 7.64 0.00 0.00 4.01
311 334 2.669569 GTTGGCGCTCTCCTGCAA 60.670 61.111 7.64 0.00 0.00 4.08
313 336 4.742201 TCGTTGGCGCTCTCCTGC 62.742 66.667 7.64 0.00 38.14 4.85
314 337 2.811317 GTCGTTGGCGCTCTCCTG 60.811 66.667 7.64 0.00 38.14 3.86
315 338 2.771763 CTTGTCGTTGGCGCTCTCCT 62.772 60.000 7.64 0.00 38.14 3.69
316 339 2.357034 TTGTCGTTGGCGCTCTCC 60.357 61.111 7.64 0.00 38.14 3.71
317 340 2.383527 CCTTGTCGTTGGCGCTCTC 61.384 63.158 7.64 0.00 38.14 3.20
318 341 2.357517 CCTTGTCGTTGGCGCTCT 60.358 61.111 7.64 0.00 38.14 4.09
319 342 2.357034 TCCTTGTCGTTGGCGCTC 60.357 61.111 7.64 0.00 38.14 5.03
320 343 2.665185 GTCCTTGTCGTTGGCGCT 60.665 61.111 7.64 0.00 38.14 5.92
321 344 3.723348 GGTCCTTGTCGTTGGCGC 61.723 66.667 0.00 0.00 38.14 6.53
322 345 3.411351 CGGTCCTTGTCGTTGGCG 61.411 66.667 0.00 0.00 39.92 5.69
349 372 1.870055 GCATGTTGGTGCCAGTGAGG 61.870 60.000 0.00 0.00 39.18 3.86
350 373 1.174078 TGCATGTTGGTGCCAGTGAG 61.174 55.000 0.00 0.00 44.43 3.51
351 374 1.152798 TGCATGTTGGTGCCAGTGA 60.153 52.632 0.00 0.00 44.43 3.41
352 375 1.287815 CTGCATGTTGGTGCCAGTG 59.712 57.895 0.00 0.00 44.43 3.66
353 376 2.567497 GCTGCATGTTGGTGCCAGT 61.567 57.895 0.00 0.00 44.43 4.00
355 386 0.611340 TATGCTGCATGTTGGTGCCA 60.611 50.000 24.59 0.00 44.43 4.92
360 391 1.599071 CCTACGTATGCTGCATGTTGG 59.401 52.381 24.59 19.18 0.00 3.77
372 403 1.735376 CGCTGGGCTGTCCTACGTAT 61.735 60.000 0.00 0.00 36.20 3.06
373 404 2.412323 CGCTGGGCTGTCCTACGTA 61.412 63.158 0.00 0.00 36.20 3.57
374 405 3.760035 CGCTGGGCTGTCCTACGT 61.760 66.667 0.00 0.00 36.20 3.57
376 407 4.840005 GGCGCTGGGCTGTCCTAC 62.840 72.222 16.51 0.00 42.94 3.18
391 422 4.052229 CACCAGCAGCAGCAAGGC 62.052 66.667 11.63 0.00 45.49 4.35
392 423 4.052229 GCACCAGCAGCAGCAAGG 62.052 66.667 3.17 7.47 45.49 3.61
393 424 2.984155 AGCACCAGCAGCAGCAAG 60.984 61.111 3.17 0.00 45.49 4.01
394 425 3.292159 CAGCACCAGCAGCAGCAA 61.292 61.111 3.17 0.00 45.49 3.91
406 437 4.292977 AGTAAAGTGAAGTTTGCAGCAC 57.707 40.909 0.00 0.00 0.00 4.40
433 464 2.882137 TGCAAAGTAAAAAGGACCGGAG 59.118 45.455 9.46 0.00 0.00 4.63
434 465 2.933573 TGCAAAGTAAAAAGGACCGGA 58.066 42.857 9.46 0.00 0.00 5.14
435 466 3.934457 ATGCAAAGTAAAAAGGACCGG 57.066 42.857 0.00 0.00 0.00 5.28
436 467 7.148137 ACCTAATATGCAAAGTAAAAAGGACCG 60.148 37.037 0.00 0.00 0.00 4.79
437 468 8.063200 ACCTAATATGCAAAGTAAAAAGGACC 57.937 34.615 0.00 0.00 0.00 4.46
438 469 9.923143 AAACCTAATATGCAAAGTAAAAAGGAC 57.077 29.630 0.00 0.00 0.00 3.85
439 470 9.921637 CAAACCTAATATGCAAAGTAAAAAGGA 57.078 29.630 0.00 0.00 0.00 3.36
440 471 9.705290 ACAAACCTAATATGCAAAGTAAAAAGG 57.295 29.630 0.00 0.00 0.00 3.11
442 473 9.699703 GGACAAACCTAATATGCAAAGTAAAAA 57.300 29.630 0.00 0.00 35.41 1.94
443 474 8.024285 CGGACAAACCTAATATGCAAAGTAAAA 58.976 33.333 0.00 0.00 36.31 1.52
444 475 7.390996 TCGGACAAACCTAATATGCAAAGTAAA 59.609 33.333 0.00 0.00 36.31 2.01
445 476 6.879993 TCGGACAAACCTAATATGCAAAGTAA 59.120 34.615 0.00 0.00 36.31 2.24
446 477 6.408035 TCGGACAAACCTAATATGCAAAGTA 58.592 36.000 0.00 0.00 36.31 2.24
447 478 5.250200 TCGGACAAACCTAATATGCAAAGT 58.750 37.500 0.00 0.00 36.31 2.66
448 479 5.811399 TCGGACAAACCTAATATGCAAAG 57.189 39.130 0.00 0.00 36.31 2.77
449 480 5.708230 ACTTCGGACAAACCTAATATGCAAA 59.292 36.000 0.00 0.00 36.31 3.68
450 481 5.250200 ACTTCGGACAAACCTAATATGCAA 58.750 37.500 0.00 0.00 36.31 4.08
451 482 4.839121 ACTTCGGACAAACCTAATATGCA 58.161 39.130 0.00 0.00 36.31 3.96
452 483 4.873827 TGACTTCGGACAAACCTAATATGC 59.126 41.667 0.00 0.00 36.31 3.14
453 484 6.978343 TTGACTTCGGACAAACCTAATATG 57.022 37.500 0.00 0.00 36.31 1.78
454 485 8.575649 AAATTGACTTCGGACAAACCTAATAT 57.424 30.769 0.00 0.00 33.90 1.28
455 486 7.989416 AAATTGACTTCGGACAAACCTAATA 57.011 32.000 0.00 0.00 33.90 0.98
456 487 6.894339 AAATTGACTTCGGACAAACCTAAT 57.106 33.333 0.00 0.00 33.90 1.73
457 488 7.804843 TTAAATTGACTTCGGACAAACCTAA 57.195 32.000 0.00 0.00 33.90 2.69
458 489 7.120138 GGATTAAATTGACTTCGGACAAACCTA 59.880 37.037 0.00 0.00 33.90 3.08
459 490 6.072119 GGATTAAATTGACTTCGGACAAACCT 60.072 38.462 0.00 0.00 33.90 3.50
460 491 6.090783 GGATTAAATTGACTTCGGACAAACC 58.909 40.000 0.00 0.00 33.90 3.27
461 492 6.674066 TGGATTAAATTGACTTCGGACAAAC 58.326 36.000 0.00 0.00 33.90 2.93
462 493 6.885952 TGGATTAAATTGACTTCGGACAAA 57.114 33.333 0.00 0.00 33.90 2.83
463 494 6.488683 AGTTGGATTAAATTGACTTCGGACAA 59.511 34.615 0.00 0.00 34.59 3.18
464 495 6.001460 AGTTGGATTAAATTGACTTCGGACA 58.999 36.000 0.00 0.00 0.00 4.02
465 496 6.496338 AGTTGGATTAAATTGACTTCGGAC 57.504 37.500 0.00 0.00 0.00 4.79
466 497 7.229707 TCAAAGTTGGATTAAATTGACTTCGGA 59.770 33.333 0.00 0.00 0.00 4.55
467 498 7.326063 GTCAAAGTTGGATTAAATTGACTTCGG 59.674 37.037 8.70 0.00 40.58 4.30
468 499 7.326063 GGTCAAAGTTGGATTAAATTGACTTCG 59.674 37.037 13.97 0.00 41.91 3.79
469 500 8.141268 TGGTCAAAGTTGGATTAAATTGACTTC 58.859 33.333 13.97 2.43 41.91 3.01
470 501 8.017418 TGGTCAAAGTTGGATTAAATTGACTT 57.983 30.769 13.97 0.00 41.91 3.01
471 502 7.595819 TGGTCAAAGTTGGATTAAATTGACT 57.404 32.000 13.97 0.00 41.91 3.41
472 503 7.384932 CCTTGGTCAAAGTTGGATTAAATTGAC 59.615 37.037 7.68 7.68 41.72 3.18
473 504 7.070571 ACCTTGGTCAAAGTTGGATTAAATTGA 59.929 33.333 0.00 0.00 33.66 2.57
474 505 7.216494 ACCTTGGTCAAAGTTGGATTAAATTG 58.784 34.615 0.00 0.00 33.66 2.32
475 506 7.373617 ACCTTGGTCAAAGTTGGATTAAATT 57.626 32.000 0.00 0.00 33.66 1.82
476 507 6.994421 ACCTTGGTCAAAGTTGGATTAAAT 57.006 33.333 0.00 0.00 33.66 1.40
477 508 6.800072 AACCTTGGTCAAAGTTGGATTAAA 57.200 33.333 0.00 0.00 33.66 1.52
478 509 9.762381 ATATAACCTTGGTCAAAGTTGGATTAA 57.238 29.630 7.67 0.00 33.66 1.40
480 511 9.762381 TTATATAACCTTGGTCAAAGTTGGATT 57.238 29.630 7.67 0.00 33.66 3.01
481 512 9.762381 TTTATATAACCTTGGTCAAAGTTGGAT 57.238 29.630 7.67 4.40 33.66 3.41
482 513 9.589461 TTTTATATAACCTTGGTCAAAGTTGGA 57.411 29.630 7.67 0.00 33.66 3.53
510 541 9.679661 TGGTGTTGTTATGTGAATGTCTATAAT 57.320 29.630 0.00 0.00 0.00 1.28
511 542 9.508642 TTGGTGTTGTTATGTGAATGTCTATAA 57.491 29.630 0.00 0.00 0.00 0.98
512 543 9.679661 ATTGGTGTTGTTATGTGAATGTCTATA 57.320 29.630 0.00 0.00 0.00 1.31
513 544 7.994425 TTGGTGTTGTTATGTGAATGTCTAT 57.006 32.000 0.00 0.00 0.00 1.98
514 545 7.994425 ATTGGTGTTGTTATGTGAATGTCTA 57.006 32.000 0.00 0.00 0.00 2.59
515 546 6.899393 ATTGGTGTTGTTATGTGAATGTCT 57.101 33.333 0.00 0.00 0.00 3.41
516 547 8.458052 TGATATTGGTGTTGTTATGTGAATGTC 58.542 33.333 0.00 0.00 0.00 3.06
517 548 8.347004 TGATATTGGTGTTGTTATGTGAATGT 57.653 30.769 0.00 0.00 0.00 2.71
518 549 9.806203 AATGATATTGGTGTTGTTATGTGAATG 57.194 29.630 0.00 0.00 0.00 2.67
521 552 9.898152 TCTAATGATATTGGTGTTGTTATGTGA 57.102 29.630 0.00 0.00 0.00 3.58
528 559 9.857656 AGATGAATCTAATGATATTGGTGTTGT 57.142 29.630 0.00 0.00 34.85 3.32
640 671 3.244976 CACATTGGATTTGGCGAAAGTC 58.755 45.455 0.00 0.00 0.00 3.01
641 672 2.610232 GCACATTGGATTTGGCGAAAGT 60.610 45.455 0.00 0.00 0.00 2.66
642 673 1.994779 GCACATTGGATTTGGCGAAAG 59.005 47.619 0.00 0.00 0.00 2.62
643 674 1.342496 TGCACATTGGATTTGGCGAAA 59.658 42.857 0.00 0.00 0.00 3.46
644 675 0.964700 TGCACATTGGATTTGGCGAA 59.035 45.000 0.00 0.00 0.00 4.70
645 676 0.964700 TTGCACATTGGATTTGGCGA 59.035 45.000 0.00 0.00 0.00 5.54
646 677 1.727880 CTTTGCACATTGGATTTGGCG 59.272 47.619 0.00 0.00 0.00 5.69
647 678 2.769893 ACTTTGCACATTGGATTTGGC 58.230 42.857 0.00 0.00 0.00 4.52
648 679 6.857777 TTTTACTTTGCACATTGGATTTGG 57.142 33.333 0.00 0.00 0.00 3.28
671 702 1.738474 AGGTACTCCCTCCGGTTTTT 58.262 50.000 0.00 0.00 40.71 1.94
672 703 1.627329 GAAGGTACTCCCTCCGGTTTT 59.373 52.381 0.00 0.00 45.47 2.43
673 704 1.273759 GAAGGTACTCCCTCCGGTTT 58.726 55.000 0.00 0.00 45.47 3.27
674 705 0.616964 GGAAGGTACTCCCTCCGGTT 60.617 60.000 0.00 0.00 45.47 4.44
675 706 1.001376 GGAAGGTACTCCCTCCGGT 59.999 63.158 0.00 0.00 45.47 5.28
676 707 0.616679 TTGGAAGGTACTCCCTCCGG 60.617 60.000 0.00 0.00 45.47 5.14
677 708 1.497161 ATTGGAAGGTACTCCCTCCG 58.503 55.000 0.00 0.00 45.47 4.63
678 709 2.172930 GGAATTGGAAGGTACTCCCTCC 59.827 54.545 0.00 0.00 45.47 4.30
679 710 2.158943 CGGAATTGGAAGGTACTCCCTC 60.159 54.545 0.00 0.00 45.47 4.30
681 712 1.746171 GCGGAATTGGAAGGTACTCCC 60.746 57.143 0.00 0.00 38.49 4.30
682 713 1.664873 GCGGAATTGGAAGGTACTCC 58.335 55.000 0.00 0.00 38.49 3.85
683 714 1.664873 GGCGGAATTGGAAGGTACTC 58.335 55.000 0.00 0.00 38.49 2.59
685 716 0.255033 AGGGCGGAATTGGAAGGTAC 59.745 55.000 0.00 0.00 0.00 3.34
709 742 3.045634 TGGGTTGACCTCTTCTCAAGAA 58.954 45.455 0.00 0.00 41.11 2.52
714 747 1.814793 GCTTGGGTTGACCTCTTCTC 58.185 55.000 0.00 0.00 41.11 2.87
785 821 2.179018 CGGCTGCGGGTTTGATTG 59.821 61.111 0.00 0.00 0.00 2.67
786 822 3.747976 GCGGCTGCGGGTTTGATT 61.748 61.111 0.00 0.00 0.00 2.57
852 892 0.820871 GCTGGTTGTTGGGTTGTGAA 59.179 50.000 0.00 0.00 0.00 3.18
853 893 0.323816 TGCTGGTTGTTGGGTTGTGA 60.324 50.000 0.00 0.00 0.00 3.58
854 894 0.752054 ATGCTGGTTGTTGGGTTGTG 59.248 50.000 0.00 0.00 0.00 3.33
858 898 2.268076 GCGATGCTGGTTGTTGGGT 61.268 57.895 0.00 0.00 0.00 4.51
859 899 1.597797 ATGCGATGCTGGTTGTTGGG 61.598 55.000 0.00 0.00 0.00 4.12
863 904 1.019673 GATGATGCGATGCTGGTTGT 58.980 50.000 0.00 0.00 0.00 3.32
908 949 1.671379 GGTGGACACGAAGGAAGGC 60.671 63.158 0.00 0.00 0.00 4.35
926 988 0.749649 CGAGGGAGGAGAAGATGGTG 59.250 60.000 0.00 0.00 0.00 4.17
950 1012 2.103941 AGTCCTAGGCTTCTATGCAAGC 59.896 50.000 2.96 0.00 46.99 4.01
951 1013 5.480073 AGATAGTCCTAGGCTTCTATGCAAG 59.520 44.000 18.72 0.00 34.04 4.01
952 1014 5.398236 AGATAGTCCTAGGCTTCTATGCAA 58.602 41.667 18.72 0.33 34.04 4.08
953 1015 5.004361 AGATAGTCCTAGGCTTCTATGCA 57.996 43.478 18.72 0.00 34.04 3.96
954 1016 7.060421 AGATAGATAGTCCTAGGCTTCTATGC 58.940 42.308 23.27 18.49 0.00 3.14
956 1018 8.638570 AGAGATAGATAGTCCTAGGCTTCTAT 57.361 38.462 21.15 21.15 0.00 1.98
958 1020 6.735704 AGAGAGATAGATAGTCCTAGGCTTCT 59.264 42.308 2.96 11.79 0.00 2.85
959 1021 6.958767 AGAGAGATAGATAGTCCTAGGCTTC 58.041 44.000 2.96 5.78 0.00 3.86
968 1034 4.080751 AGGCCCGTAGAGAGATAGATAGTC 60.081 50.000 0.00 0.00 0.00 2.59
977 1045 2.516460 GCGAGGCCCGTAGAGAGA 60.516 66.667 13.97 0.00 41.15 3.10
978 1046 3.597728 GGCGAGGCCCGTAGAGAG 61.598 72.222 13.97 0.00 44.06 3.20
1136 1216 2.678580 TCCACGCCCGTCTCATCA 60.679 61.111 0.00 0.00 0.00 3.07
1137 1217 2.105128 CTCCACGCCCGTCTCATC 59.895 66.667 0.00 0.00 0.00 2.92
1138 1218 3.461773 CCTCCACGCCCGTCTCAT 61.462 66.667 0.00 0.00 0.00 2.90
1460 1558 7.148540 CGTCGTAGGATACAAAAAGAATCCAAA 60.149 37.037 3.61 0.00 43.24 3.28
1597 1700 7.264373 ACAGATTCAGGTTAAAGTGACAAAG 57.736 36.000 0.00 0.00 0.00 2.77
1625 1728 9.558396 AATCCAGAATGAAGATGAGAAGTTATC 57.442 33.333 0.00 0.00 39.69 1.75
1750 1854 9.685276 AGGTCATTCATGTGAAACTATTATTCA 57.315 29.630 0.00 0.00 37.61 2.57
1759 1864 5.437289 TTGACAGGTCATTCATGTGAAAC 57.563 39.130 2.52 0.00 41.28 2.78
1788 1898 1.069227 GGGTTCAACTCATTCACGTGC 60.069 52.381 11.67 0.00 0.00 5.34
1792 1904 3.756117 AGGAAGGGTTCAACTCATTCAC 58.244 45.455 0.00 0.00 0.00 3.18
1818 1937 6.406400 CCAGTTGGTTACCTTTGACAAATTCA 60.406 38.462 2.07 0.00 0.00 2.57
1890 2014 1.825622 GCTTATGACCCAGCAGGCC 60.826 63.158 0.00 0.00 40.58 5.19
1974 2100 6.649557 AGTCTTTGCTTGTTGGTGTATACTAC 59.350 38.462 4.17 1.04 0.00 2.73
1982 2111 4.351192 GTGTAAGTCTTTGCTTGTTGGTG 58.649 43.478 0.00 0.00 0.00 4.17
2064 2193 6.382869 AAGAACAGGACTTTGTCAAAGATG 57.617 37.500 28.07 22.86 41.02 2.90
2294 2436 5.392272 CGAGATGAAATGTGGCTGAAAATGA 60.392 40.000 0.00 0.00 0.00 2.57
2410 2563 4.534500 TCCCTGTAACAAGATAAGAAGCCA 59.466 41.667 0.00 0.00 0.00 4.75
2448 2604 0.030101 TGTTTTCTTTCGCGGGCTTG 59.970 50.000 6.13 0.00 0.00 4.01
2474 2630 1.075374 CACAAAGTGAATCCCTGGGGA 59.925 52.381 14.00 11.11 41.54 4.81
2489 2645 2.037901 TGCCTTGCAATTCCTCACAAA 58.962 42.857 0.00 0.00 34.76 2.83
2556 2712 0.032678 ATGAGCTTCGGTCCGCATAG 59.967 55.000 6.34 5.00 0.00 2.23
2574 2730 1.448540 CGCAAGAACTCCGGCAGAT 60.449 57.895 0.00 0.00 43.02 2.90
2598 2754 3.867857 TGCGGTGATCAGCTTTATGTTA 58.132 40.909 21.73 0.00 35.86 2.41
2604 2760 1.016130 CGTCTGCGGTGATCAGCTTT 61.016 55.000 21.73 0.00 35.86 3.51
2605 2761 1.446792 CGTCTGCGGTGATCAGCTT 60.447 57.895 21.73 0.00 35.86 3.74
2633 2789 3.304659 CCCGAAGACAAAGTCCATGTTTG 60.305 47.826 5.89 5.89 40.18 2.93
2982 3140 2.434428 GAGACTCACTCTGGACCGTTA 58.566 52.381 0.00 0.00 41.94 3.18
3072 3230 1.067212 GTATCCTGCCGAAGACGATGT 59.933 52.381 0.00 0.00 42.66 3.06
3086 3244 2.831770 CAGGGCATGCCGTATCCT 59.168 61.111 30.23 18.35 36.85 3.24
3265 3425 3.809279 TGTGATATCAATTGCTACGGCTG 59.191 43.478 7.07 0.00 39.59 4.85
3289 3449 6.936335 TGGATATAATCTAGTTCGACGGTGTA 59.064 38.462 0.00 0.00 0.00 2.90
3319 3479 4.511527 AGGAAATCTGTGTCACAGCATAG 58.488 43.478 25.45 5.53 45.54 2.23
3410 3572 0.458543 AACTGCAGTCAGATACGCGG 60.459 55.000 21.95 0.00 42.95 6.46
3604 3766 2.549754 AGAGTCAATGCCAAAACTCACG 59.450 45.455 4.39 0.00 40.45 4.35
3614 3776 2.996249 TCTGATGGAGAGTCAATGCC 57.004 50.000 0.00 0.00 0.00 4.40
3620 3782 4.141528 ACCCATTTCATCTGATGGAGAGTC 60.142 45.833 17.06 0.00 44.49 3.36
3666 3837 7.329962 TCAAGCTGTTGAATTGCAAAATCATAG 59.670 33.333 16.26 16.76 39.85 2.23
3763 3934 4.908601 TTCCATCACATTACCTCACTGT 57.091 40.909 0.00 0.00 0.00 3.55
3869 4040 3.282885 GTCATTTAGAGAAAGGGCAGGG 58.717 50.000 0.00 0.00 31.35 4.45
3879 4050 7.445096 TGAAAAATGCTCAGTGTCATTTAGAGA 59.555 33.333 18.97 7.72 40.73 3.10
3880 4051 7.587629 TGAAAAATGCTCAGTGTCATTTAGAG 58.412 34.615 18.97 0.00 40.73 2.43
3881 4052 7.308770 CCTGAAAAATGCTCAGTGTCATTTAGA 60.309 37.037 18.97 10.14 40.73 2.10
3882 4053 6.805271 CCTGAAAAATGCTCAGTGTCATTTAG 59.195 38.462 18.97 14.68 40.73 1.85
3883 4054 6.265196 ACCTGAAAAATGCTCAGTGTCATTTA 59.735 34.615 18.97 8.98 40.73 1.40
3984 4155 4.524316 TTCTCGGGAGAAATTACGAACA 57.476 40.909 8.61 0.00 43.79 3.18
4100 4271 1.821136 CCCTTGTCCTGAAAATGAGGC 59.179 52.381 0.00 0.00 0.00 4.70
4317 4488 0.689623 AGCCCATCCGATCTGATTCC 59.310 55.000 0.00 0.00 0.00 3.01
4354 4525 0.825010 CCCTGCTTGCTTTCTGTGGT 60.825 55.000 0.00 0.00 0.00 4.16
4378 4549 3.376546 GCAATGCTCTCGAAAGGAAGAAT 59.623 43.478 0.00 0.00 0.00 2.40
4401 4572 4.023536 GTGCCATTTAAAGAAGTTGACCGA 60.024 41.667 0.00 0.00 0.00 4.69
4403 4574 5.009610 TCTGTGCCATTTAAAGAAGTTGACC 59.990 40.000 0.00 0.00 0.00 4.02
4539 4710 5.912892 TCACCTTTCTTCCAATTTGGTTTC 58.087 37.500 14.98 0.00 39.03 2.78
4605 4776 3.892918 CAGAGTTCTGCTTCTTTGGTG 57.107 47.619 0.00 0.00 37.15 4.17
4633 4804 8.512966 TGAGATATACTCTACAGCATATCCAC 57.487 38.462 0.00 0.00 45.13 4.02
4769 4942 3.366476 CGCGATATTCCACCAACCAAAAA 60.366 43.478 0.00 0.00 0.00 1.94
4770 4943 2.162608 CGCGATATTCCACCAACCAAAA 59.837 45.455 0.00 0.00 0.00 2.44
4771 4944 1.740585 CGCGATATTCCACCAACCAAA 59.259 47.619 0.00 0.00 0.00 3.28
4772 4945 1.339247 ACGCGATATTCCACCAACCAA 60.339 47.619 15.93 0.00 0.00 3.67
4773 4946 0.250793 ACGCGATATTCCACCAACCA 59.749 50.000 15.93 0.00 0.00 3.67
4779 4952 0.582005 GCCTTCACGCGATATTCCAC 59.418 55.000 15.93 0.00 0.00 4.02
4794 4967 5.825679 TGAGTTAAACATTGTGTGTAGCCTT 59.174 36.000 0.00 0.00 41.14 4.35
4805 4978 8.801715 ACTTATGTTGCTTGAGTTAAACATTG 57.198 30.769 5.32 3.01 41.94 2.82
4853 5026 1.480137 CCATGTGTTGGTGTGGTTTGT 59.520 47.619 0.00 0.00 40.99 2.83
4860 5033 1.774110 TGCTTTCCATGTGTTGGTGT 58.226 45.000 0.00 0.00 46.52 4.16
4882 5055 0.109342 ACTCTGCTCAAAGGTGTGGG 59.891 55.000 0.00 0.00 0.00 4.61
4883 5056 1.233019 CACTCTGCTCAAAGGTGTGG 58.767 55.000 0.00 0.00 0.00 4.17
5276 5451 1.239347 GGAAACCTTGCCACTCACTC 58.761 55.000 0.00 0.00 0.00 3.51
5285 5460 0.895559 CCTCCACCTGGAAACCTTGC 60.896 60.000 0.00 0.00 44.91 4.01
5315 5490 1.840741 GAGTTGACATCGACGATGACG 59.159 52.381 37.26 16.95 42.09 4.35


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

AutoCloner maintained by Alex Coulton.