Multiple sequence alignment - TraesCS3A01G250800

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 TraesCS3A01G250800 chr3A 100.000 2726 0 0 1 2726 469833574 469830849 0.000000e+00 5035
1 TraesCS3A01G250800 chr3D 93.936 1814 59 30 571 2374 352109256 352107484 0.000000e+00 2693
2 TraesCS3A01G250800 chr3D 92.748 262 18 1 1 261 352109774 352109513 7.130000e-101 377
3 TraesCS3A01G250800 chr3B 91.748 1854 82 28 597 2437 450365982 450364187 0.000000e+00 2510
4 TraesCS3A01G250800 chr3B 90.496 242 15 6 28 261 450372283 450372042 2.040000e-81 313
5 TraesCS3A01G250800 chr3B 93.939 198 12 0 2529 2726 450364182 450363985 1.590000e-77 300
6 TraesCS3A01G250800 chr1D 91.818 110 8 1 1613 1722 446800993 446800885 4.700000e-33 152
7 TraesCS3A01G250800 chr1B 91.818 110 8 1 1613 1722 612403536 612403428 4.700000e-33 152
8 TraesCS3A01G250800 chr1B 89.247 93 10 0 1214 1306 612404302 612404210 1.720000e-22 117
9 TraesCS3A01G250800 chr1A 91.818 110 8 1 1613 1722 542825477 542825369 4.700000e-33 152
10 TraesCS3A01G250800 chr1A 89.247 93 10 0 1214 1306 542826270 542826178 1.720000e-22 117
11 TraesCS3A01G250800 chrUn 78.924 223 34 10 2510 2726 234158330 234158545 3.660000e-29 139
12 TraesCS3A01G250800 chr6B 79.091 220 33 10 2513 2726 41386923 41386711 3.660000e-29 139
13 TraesCS3A01G250800 chr6B 77.626 219 36 10 2510 2722 41319781 41319992 1.330000e-23 121


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 TraesCS3A01G250800 chr3A 469830849 469833574 2725 True 5035 5035 100.0000 1 2726 1 chr3A.!!$R1 2725
1 TraesCS3A01G250800 chr3D 352107484 352109774 2290 True 1535 2693 93.3420 1 2374 2 chr3D.!!$R1 2373
2 TraesCS3A01G250800 chr3B 450363985 450365982 1997 True 1405 2510 92.8435 597 2726 2 chr3B.!!$R2 2129

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
639 708 0.108898 GCGATGCTCAGTGAGTCAGT 60.109 55.0 21.06 9.61 31.39 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2299 2396 0.106918 TCCTGTGTTCTGGCGGTTTT 60.107 50.0 0.0 0.0 33.5 2.43 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
26 27 8.004344 CGTGCTTCGGAATCTTACTAAATAATG 58.996 37.037 0.00 0.00 35.71 1.90
48 49 4.160814 TGGATTGAAATTGAAGGGCATCTG 59.839 41.667 0.00 0.00 0.00 2.90
60 61 1.340405 GGGCATCTGTCTTGTCCATGT 60.340 52.381 0.00 0.00 38.76 3.21
69 70 5.412594 TCTGTCTTGTCCATGTTAAAGATGC 59.587 40.000 4.97 0.00 31.73 3.91
85 86 2.330393 GCGCATGTGCATAGGCTG 59.670 61.111 25.87 12.09 42.21 4.85
111 112 1.154225 CGTCCCAACAGCGCAATTC 60.154 57.895 11.47 0.00 0.00 2.17
120 121 1.250476 CAGCGCAATTCACGTTAAGC 58.750 50.000 11.47 0.00 0.00 3.09
139 140 2.761195 CGCGGTGGATCGAGTCAGA 61.761 63.158 0.00 0.00 0.00 3.27
169 170 2.124695 GGTTCCGATCTGGCCACC 60.125 66.667 0.00 0.00 37.80 4.61
218 219 1.526575 AAGGCACAATCGGCAAGTGG 61.527 55.000 0.00 0.00 33.98 4.00
261 263 1.348064 TCTCCACGTGGTTCCTTCAT 58.652 50.000 32.74 0.00 36.34 2.57
263 265 1.276421 CTCCACGTGGTTCCTTCATCT 59.724 52.381 32.74 0.00 36.34 2.90
264 266 1.001974 TCCACGTGGTTCCTTCATCTG 59.998 52.381 32.74 3.84 36.34 2.90
265 267 1.001974 CCACGTGGTTCCTTCATCTGA 59.998 52.381 26.95 0.00 0.00 3.27
274 302 4.323104 GGTTCCTTCATCTGACTAGCTTGT 60.323 45.833 0.00 0.00 0.00 3.16
282 310 2.231235 TCTGACTAGCTTGTTGCATCGA 59.769 45.455 1.43 0.00 45.94 3.59
295 323 6.018589 TGTTGCATCGAAATGATAAACCAA 57.981 33.333 0.00 0.00 34.83 3.67
296 324 5.861251 TGTTGCATCGAAATGATAAACCAAC 59.139 36.000 0.00 0.00 34.83 3.77
297 325 5.635417 TGCATCGAAATGATAAACCAACA 57.365 34.783 0.00 0.00 34.83 3.33
298 326 5.398169 TGCATCGAAATGATAAACCAACAC 58.602 37.500 0.00 0.00 34.83 3.32
299 327 5.048434 TGCATCGAAATGATAAACCAACACA 60.048 36.000 0.00 0.00 34.83 3.72
301 329 5.365403 TCGAAATGATAAACCAACACACC 57.635 39.130 0.00 0.00 0.00 4.16
302 330 5.067273 TCGAAATGATAAACCAACACACCT 58.933 37.500 0.00 0.00 0.00 4.00
304 332 5.049060 CGAAATGATAAACCAACACACCTCA 60.049 40.000 0.00 0.00 0.00 3.86
305 333 5.705609 AATGATAAACCAACACACCTCAC 57.294 39.130 0.00 0.00 0.00 3.51
306 334 3.135225 TGATAAACCAACACACCTCACG 58.865 45.455 0.00 0.00 0.00 4.35
307 335 1.956297 TAAACCAACACACCTCACGG 58.044 50.000 0.00 0.00 0.00 4.94
308 336 1.381165 AAACCAACACACCTCACGGC 61.381 55.000 0.00 0.00 0.00 5.68
309 337 2.203139 CCAACACACCTCACGGCA 60.203 61.111 0.00 0.00 0.00 5.69
310 338 2.542907 CCAACACACCTCACGGCAC 61.543 63.158 0.00 0.00 0.00 5.01
311 339 2.203153 AACACACCTCACGGCACC 60.203 61.111 0.00 0.00 0.00 5.01
312 340 3.037686 AACACACCTCACGGCACCA 62.038 57.895 0.00 0.00 0.00 4.17
313 341 2.032528 CACACCTCACGGCACCAT 59.967 61.111 0.00 0.00 0.00 3.55
314 342 1.600636 CACACCTCACGGCACCATT 60.601 57.895 0.00 0.00 0.00 3.16
326 354 0.242017 GCACCATTCAAGCTGGTCAC 59.758 55.000 0.00 0.00 45.23 3.67
330 358 1.002134 ATTCAAGCTGGTCACGGGG 60.002 57.895 0.00 0.00 0.00 5.73
331 359 3.842925 TTCAAGCTGGTCACGGGGC 62.843 63.158 0.00 0.00 0.00 5.80
343 371 1.086696 CACGGGGCTATTGTTGTGAG 58.913 55.000 0.00 0.00 0.00 3.51
351 379 5.106277 GGGGCTATTGTTGTGAGAAGTAAAC 60.106 44.000 0.00 0.00 0.00 2.01
358 386 8.603242 ATTGTTGTGAGAAGTAAACGAGTTAT 57.397 30.769 0.00 0.00 0.00 1.89
360 388 6.073980 TGTTGTGAGAAGTAAACGAGTTATGC 60.074 38.462 0.00 0.00 0.00 3.14
361 389 5.534407 TGTGAGAAGTAAACGAGTTATGCA 58.466 37.500 0.00 0.00 0.00 3.96
365 393 7.063544 GTGAGAAGTAAACGAGTTATGCATCTT 59.936 37.037 0.19 0.00 0.00 2.40
366 394 7.063426 TGAGAAGTAAACGAGTTATGCATCTTG 59.937 37.037 0.19 1.27 0.00 3.02
367 395 7.097192 AGAAGTAAACGAGTTATGCATCTTGA 58.903 34.615 0.19 0.00 0.00 3.02
368 396 7.766278 AGAAGTAAACGAGTTATGCATCTTGAT 59.234 33.333 0.19 0.00 0.00 2.57
369 397 7.849804 AGTAAACGAGTTATGCATCTTGATT 57.150 32.000 0.19 3.01 0.00 2.57
370 398 7.910304 AGTAAACGAGTTATGCATCTTGATTC 58.090 34.615 0.19 0.00 0.00 2.52
371 399 6.992063 AAACGAGTTATGCATCTTGATTCT 57.008 33.333 0.19 0.00 0.00 2.40
372 400 6.595772 AACGAGTTATGCATCTTGATTCTC 57.404 37.500 0.19 1.53 0.00 2.87
373 401 5.664457 ACGAGTTATGCATCTTGATTCTCA 58.336 37.500 0.19 0.00 0.00 3.27
374 402 5.752472 ACGAGTTATGCATCTTGATTCTCAG 59.248 40.000 0.19 2.43 0.00 3.35
375 403 5.981915 CGAGTTATGCATCTTGATTCTCAGA 59.018 40.000 0.19 0.00 0.00 3.27
376 404 6.074409 CGAGTTATGCATCTTGATTCTCAGAC 60.074 42.308 0.19 0.00 0.00 3.51
377 405 6.887013 AGTTATGCATCTTGATTCTCAGACT 58.113 36.000 0.19 0.00 0.00 3.24
378 406 6.985645 AGTTATGCATCTTGATTCTCAGACTC 59.014 38.462 0.19 0.00 0.00 3.36
379 407 5.617528 ATGCATCTTGATTCTCAGACTCT 57.382 39.130 0.00 0.00 0.00 3.24
380 408 5.008619 TGCATCTTGATTCTCAGACTCTC 57.991 43.478 0.00 0.00 0.00 3.20
381 409 4.141981 TGCATCTTGATTCTCAGACTCTCC 60.142 45.833 0.00 0.00 0.00 3.71
382 410 4.141981 GCATCTTGATTCTCAGACTCTCCA 60.142 45.833 0.00 0.00 0.00 3.86
398 426 8.986847 CAGACTCTCCATACACATAATTGAATC 58.013 37.037 0.00 0.00 0.00 2.52
417 445 9.918630 ATTGAATCAATCGACTCTTTCAAAAAT 57.081 25.926 15.17 2.42 36.85 1.82
418 446 8.955061 TGAATCAATCGACTCTTTCAAAAATC 57.045 30.769 0.00 0.00 0.00 2.17
419 447 8.567104 TGAATCAATCGACTCTTTCAAAAATCA 58.433 29.630 0.00 0.00 0.00 2.57
420 448 9.398170 GAATCAATCGACTCTTTCAAAAATCAA 57.602 29.630 0.00 0.00 0.00 2.57
421 449 9.748708 AATCAATCGACTCTTTCAAAAATCAAA 57.251 25.926 0.00 0.00 0.00 2.69
422 450 9.748708 ATCAATCGACTCTTTCAAAAATCAAAA 57.251 25.926 0.00 0.00 0.00 2.44
423 451 9.748708 TCAATCGACTCTTTCAAAAATCAAAAT 57.251 25.926 0.00 0.00 0.00 1.82
427 455 9.878599 TCGACTCTTTCAAAAATCAAAATAGTC 57.121 29.630 0.00 0.00 34.94 2.59
428 456 9.663904 CGACTCTTTCAAAAATCAAAATAGTCA 57.336 29.630 10.94 0.00 36.60 3.41
458 492 6.127479 ACACTCTAGCTCTCTTGTTTGGATAG 60.127 42.308 0.00 0.00 0.00 2.08
466 500 4.342378 TCTCTTGTTTGGATAGATCGGGAG 59.658 45.833 0.00 0.00 0.00 4.30
481 515 1.536922 CGGGAGATGTGGATTGACGAG 60.537 57.143 0.00 0.00 0.00 4.18
482 516 1.202580 GGGAGATGTGGATTGACGAGG 60.203 57.143 0.00 0.00 0.00 4.63
484 518 2.693591 GGAGATGTGGATTGACGAGGTA 59.306 50.000 0.00 0.00 0.00 3.08
485 519 3.243569 GGAGATGTGGATTGACGAGGTAG 60.244 52.174 0.00 0.00 0.00 3.18
486 520 3.632333 AGATGTGGATTGACGAGGTAGA 58.368 45.455 0.00 0.00 0.00 2.59
487 521 3.634448 AGATGTGGATTGACGAGGTAGAG 59.366 47.826 0.00 0.00 0.00 2.43
488 522 2.803956 TGTGGATTGACGAGGTAGAGT 58.196 47.619 0.00 0.00 0.00 3.24
489 523 2.492088 TGTGGATTGACGAGGTAGAGTG 59.508 50.000 0.00 0.00 0.00 3.51
490 524 2.492484 GTGGATTGACGAGGTAGAGTGT 59.508 50.000 0.00 0.00 0.00 3.55
491 525 3.056749 GTGGATTGACGAGGTAGAGTGTT 60.057 47.826 0.00 0.00 0.00 3.32
492 526 3.192844 TGGATTGACGAGGTAGAGTGTTC 59.807 47.826 0.00 0.00 0.00 3.18
493 527 3.444388 GGATTGACGAGGTAGAGTGTTCT 59.556 47.826 0.00 0.00 37.46 3.01
494 528 4.082136 GGATTGACGAGGTAGAGTGTTCTT 60.082 45.833 0.00 0.00 34.79 2.52
495 529 4.931661 TTGACGAGGTAGAGTGTTCTTT 57.068 40.909 0.00 0.00 34.79 2.52
496 530 4.931661 TGACGAGGTAGAGTGTTCTTTT 57.068 40.909 0.00 0.00 34.79 2.27
497 531 4.868067 TGACGAGGTAGAGTGTTCTTTTC 58.132 43.478 0.00 0.00 34.79 2.29
498 532 4.583489 TGACGAGGTAGAGTGTTCTTTTCT 59.417 41.667 0.00 0.00 34.79 2.52
499 533 5.068723 TGACGAGGTAGAGTGTTCTTTTCTT 59.931 40.000 0.00 0.00 34.79 2.52
500 534 5.530712 ACGAGGTAGAGTGTTCTTTTCTTC 58.469 41.667 0.00 0.00 34.79 2.87
501 535 5.302313 ACGAGGTAGAGTGTTCTTTTCTTCT 59.698 40.000 0.00 0.00 34.79 2.85
502 536 6.489361 ACGAGGTAGAGTGTTCTTTTCTTCTA 59.511 38.462 0.00 0.00 34.79 2.10
503 537 6.802834 CGAGGTAGAGTGTTCTTTTCTTCTAC 59.197 42.308 0.00 0.00 34.79 2.59
504 538 7.521748 CGAGGTAGAGTGTTCTTTTCTTCTACA 60.522 40.741 10.51 0.00 34.79 2.74
505 539 7.435305 AGGTAGAGTGTTCTTTTCTTCTACAC 58.565 38.462 10.51 0.00 39.41 2.90
506 540 6.645827 GGTAGAGTGTTCTTTTCTTCTACACC 59.354 42.308 10.51 0.00 39.83 4.16
507 541 6.235231 AGAGTGTTCTTTTCTTCTACACCA 57.765 37.500 0.00 0.00 39.83 4.17
508 542 6.650120 AGAGTGTTCTTTTCTTCTACACCAA 58.350 36.000 0.00 0.00 39.83 3.67
509 543 6.763610 AGAGTGTTCTTTTCTTCTACACCAAG 59.236 38.462 0.00 0.00 39.83 3.61
510 544 5.297029 AGTGTTCTTTTCTTCTACACCAAGC 59.703 40.000 0.00 0.00 39.83 4.01
511 545 4.272504 TGTTCTTTTCTTCTACACCAAGCG 59.727 41.667 0.00 0.00 0.00 4.68
512 546 2.806244 TCTTTTCTTCTACACCAAGCGC 59.194 45.455 0.00 0.00 0.00 5.92
513 547 2.543777 TTTCTTCTACACCAAGCGCT 57.456 45.000 2.64 2.64 0.00 5.92
514 548 2.080286 TTCTTCTACACCAAGCGCTC 57.920 50.000 12.06 0.00 0.00 5.03
515 549 0.966179 TCTTCTACACCAAGCGCTCA 59.034 50.000 12.06 0.00 0.00 4.26
516 550 1.067565 TCTTCTACACCAAGCGCTCAG 60.068 52.381 12.06 7.90 0.00 3.35
536 570 4.040645 TGGCAAGCCACCAACAAA 57.959 50.000 10.24 0.00 41.89 2.83
537 571 2.290847 TGGCAAGCCACCAACAAAA 58.709 47.368 10.24 0.00 41.89 2.44
538 572 0.615331 TGGCAAGCCACCAACAAAAA 59.385 45.000 10.24 0.00 41.89 1.94
539 573 1.211457 TGGCAAGCCACCAACAAAAAT 59.789 42.857 10.24 0.00 41.89 1.82
540 574 2.296792 GGCAAGCCACCAACAAAAATT 58.703 42.857 6.14 0.00 35.81 1.82
541 575 2.033174 GGCAAGCCACCAACAAAAATTG 59.967 45.455 6.14 0.00 35.81 2.32
542 576 2.541383 GCAAGCCACCAACAAAAATTGC 60.541 45.455 0.00 0.00 35.55 3.56
543 577 2.681848 CAAGCCACCAACAAAAATTGCA 59.318 40.909 0.00 0.00 0.00 4.08
544 578 2.996631 AGCCACCAACAAAAATTGCAA 58.003 38.095 0.00 0.00 0.00 4.08
545 579 3.553904 AGCCACCAACAAAAATTGCAAT 58.446 36.364 5.99 5.99 0.00 3.56
546 580 3.565063 AGCCACCAACAAAAATTGCAATC 59.435 39.130 13.38 0.00 0.00 2.67
547 581 3.314635 GCCACCAACAAAAATTGCAATCA 59.685 39.130 13.38 0.00 0.00 2.57
548 582 4.201990 GCCACCAACAAAAATTGCAATCAA 60.202 37.500 13.38 0.00 36.51 2.57
549 583 5.512473 CCACCAACAAAAATTGCAATCAAG 58.488 37.500 13.38 6.03 35.37 3.02
550 584 5.296283 CCACCAACAAAAATTGCAATCAAGA 59.704 36.000 13.38 0.00 35.37 3.02
551 585 6.423862 CACCAACAAAAATTGCAATCAAGAG 58.576 36.000 13.38 4.97 35.37 2.85
552 586 6.037391 CACCAACAAAAATTGCAATCAAGAGT 59.963 34.615 13.38 5.60 35.37 3.24
553 587 6.037391 ACCAACAAAAATTGCAATCAAGAGTG 59.963 34.615 13.38 7.62 35.37 3.51
554 588 6.037391 CCAACAAAAATTGCAATCAAGAGTGT 59.963 34.615 13.38 8.56 35.37 3.55
555 589 7.414319 CCAACAAAAATTGCAATCAAGAGTGTT 60.414 33.333 13.38 13.51 35.37 3.32
556 590 7.237920 ACAAAAATTGCAATCAAGAGTGTTC 57.762 32.000 13.38 0.00 35.37 3.18
557 591 7.043565 ACAAAAATTGCAATCAAGAGTGTTCT 58.956 30.769 13.38 0.00 35.37 3.01
558 592 7.550196 ACAAAAATTGCAATCAAGAGTGTTCTT 59.450 29.630 13.38 0.00 44.45 2.52
559 593 8.392612 CAAAAATTGCAATCAAGAGTGTTCTTT 58.607 29.630 13.38 2.05 41.71 2.52
560 594 8.496707 AAAATTGCAATCAAGAGTGTTCTTTT 57.503 26.923 13.38 2.69 41.71 2.27
561 595 8.496707 AAATTGCAATCAAGAGTGTTCTTTTT 57.503 26.923 13.38 0.00 41.71 1.94
579 613 2.649331 TTTACGAGCTAGAGTGCCAC 57.351 50.000 0.00 0.00 0.00 5.01
580 614 1.835494 TTACGAGCTAGAGTGCCACT 58.165 50.000 0.00 0.00 0.00 4.00
583 617 1.950909 ACGAGCTAGAGTGCCACTATC 59.049 52.381 0.00 0.00 0.00 2.08
584 618 1.950216 CGAGCTAGAGTGCCACTATCA 59.050 52.381 0.00 0.00 0.00 2.15
587 621 4.216472 CGAGCTAGAGTGCCACTATCATTA 59.784 45.833 0.00 0.00 0.00 1.90
591 625 7.512992 AGCTAGAGTGCCACTATCATTATTTT 58.487 34.615 0.00 0.00 0.00 1.82
593 627 7.227512 GCTAGAGTGCCACTATCATTATTTTGT 59.772 37.037 0.00 0.00 0.00 2.83
594 628 7.944729 AGAGTGCCACTATCATTATTTTGTT 57.055 32.000 0.00 0.00 0.00 2.83
596 630 9.632638 AGAGTGCCACTATCATTATTTTGTTAT 57.367 29.630 0.00 0.00 0.00 1.89
633 702 2.202479 CGACGCGATGCTCAGTGA 60.202 61.111 15.93 0.00 0.00 3.41
634 703 2.220224 CGACGCGATGCTCAGTGAG 61.220 63.158 15.93 16.21 0.00 3.51
635 704 1.153939 GACGCGATGCTCAGTGAGT 60.154 57.895 21.06 2.23 31.39 3.41
636 705 1.136872 GACGCGATGCTCAGTGAGTC 61.137 60.000 21.06 13.62 31.39 3.36
637 706 1.153958 CGCGATGCTCAGTGAGTCA 60.154 57.895 21.06 18.36 31.39 3.41
638 707 1.138636 CGCGATGCTCAGTGAGTCAG 61.139 60.000 21.06 11.33 31.39 3.51
639 708 0.108898 GCGATGCTCAGTGAGTCAGT 60.109 55.000 21.06 9.61 31.39 3.41
640 709 1.626747 CGATGCTCAGTGAGTCAGTG 58.373 55.000 20.14 20.14 36.25 3.66
646 715 0.398522 TCAGTGAGTCAGTGGTGGGT 60.399 55.000 24.47 0.00 35.69 4.51
672 747 1.648504 GGCTTGCATTGAATTGAGCC 58.351 50.000 6.06 6.06 42.35 4.70
705 780 0.907704 ATCTCCAACCTGGCACGGTA 60.908 55.000 8.70 0.00 37.47 4.02
718 793 0.387929 CACGGTACATGGTCGGCTAT 59.612 55.000 0.00 0.00 0.00 2.97
853 931 5.646793 TCCTTCTCCTCGTATATTATCACCG 59.353 44.000 0.00 0.00 0.00 4.94
900 979 1.159285 ACATCATCAGCACACCAACG 58.841 50.000 0.00 0.00 0.00 4.10
915 994 2.359107 ACGCACCGACGTCTCCTA 60.359 61.111 14.70 0.00 44.43 2.94
916 995 2.396955 ACGCACCGACGTCTCCTAG 61.397 63.158 14.70 4.91 44.43 3.02
1315 1394 2.824341 CCTCCCGAGTACAACTACAACT 59.176 50.000 0.00 0.00 0.00 3.16
1321 1400 4.217983 CCGAGTACAACTACAACTCTTCCT 59.782 45.833 0.00 0.00 37.97 3.36
1323 1402 5.619533 CGAGTACAACTACAACTCTTCCTCC 60.620 48.000 0.00 0.00 37.97 4.30
1872 1962 0.173481 TGTATGAGACGCTGCAGGTC 59.827 55.000 21.10 21.10 34.62 3.85
1890 1980 4.706476 CAGGTCAATTTGGATCCTGCTAAA 59.294 41.667 14.23 5.33 39.02 1.85
1891 1981 5.185635 CAGGTCAATTTGGATCCTGCTAAAA 59.814 40.000 14.23 4.93 39.02 1.52
1892 1982 5.779771 AGGTCAATTTGGATCCTGCTAAAAA 59.220 36.000 14.23 4.16 0.00 1.94
1964 2057 9.316730 GGTGAATCCAAACAATAGTACGTATAA 57.683 33.333 0.00 0.00 35.97 0.98
2046 2139 0.172578 TCCTACGATGAACACGCCAG 59.827 55.000 0.00 0.00 0.00 4.85
2047 2140 1.421410 CCTACGATGAACACGCCAGC 61.421 60.000 0.00 0.00 0.00 4.85
2048 2141 1.421410 CTACGATGAACACGCCAGCC 61.421 60.000 0.00 0.00 0.00 4.85
2049 2142 2.161078 TACGATGAACACGCCAGCCA 62.161 55.000 0.00 0.00 0.00 4.75
2135 2228 0.110192 GACGAAAAGAAGCCCGCTTG 60.110 55.000 6.68 0.00 36.26 4.01
2136 2229 0.818040 ACGAAAAGAAGCCCGCTTGT 60.818 50.000 6.68 0.00 36.26 3.16
2137 2230 1.153353 CGAAAAGAAGCCCGCTTGTA 58.847 50.000 6.68 0.00 36.26 2.41
2167 2260 3.609853 CAACTCTTGCATAACTAGGCCA 58.390 45.455 5.01 0.00 30.87 5.36
2255 2350 6.991531 ACAAAAGCTTTGCCTCATTTCATTAA 59.008 30.769 13.54 0.00 0.00 1.40
2256 2351 7.662669 ACAAAAGCTTTGCCTCATTTCATTAAT 59.337 29.630 13.54 0.00 0.00 1.40
2257 2352 8.508875 CAAAAGCTTTGCCTCATTTCATTAATT 58.491 29.630 13.54 0.00 0.00 1.40
2258 2353 7.605410 AAGCTTTGCCTCATTTCATTAATTG 57.395 32.000 0.00 0.00 0.00 2.32
2299 2396 6.128227 CCTGTTATTTACGGAAAATCGGACAA 60.128 38.462 0.00 0.00 38.71 3.18
2377 2474 0.248907 CACACACGTCGTCAAGGAGT 60.249 55.000 0.00 0.00 0.00 3.85
2419 2516 2.433436 GCCATCAAACTTTAGGGTCGT 58.567 47.619 0.00 0.00 0.00 4.34
2439 2536 1.358046 GCTCATGATCCAAAGCGCC 59.642 57.895 2.29 0.00 0.00 6.53
2441 2538 2.025156 CATGATCCAAAGCGCCGC 59.975 61.111 2.29 0.00 0.00 6.53
2442 2539 3.211963 ATGATCCAAAGCGCCGCC 61.212 61.111 4.98 0.00 0.00 6.13
2443 2540 3.704231 ATGATCCAAAGCGCCGCCT 62.704 57.895 4.98 0.00 0.00 5.52
2444 2541 3.880846 GATCCAAAGCGCCGCCTG 61.881 66.667 4.98 3.20 0.00 4.85
2454 2551 4.996434 GCCGCCTGCGCCATAGAT 62.996 66.667 4.18 0.00 38.24 1.98
2455 2552 2.281070 CCGCCTGCGCCATAGATT 60.281 61.111 4.18 0.00 38.24 2.40
2456 2553 1.893808 CCGCCTGCGCCATAGATTT 60.894 57.895 4.18 0.00 38.24 2.17
2457 2554 1.280746 CGCCTGCGCCATAGATTTG 59.719 57.895 4.18 0.00 0.00 2.32
2458 2555 1.008079 GCCTGCGCCATAGATTTGC 60.008 57.895 4.18 0.00 0.00 3.68
2462 2559 4.141144 CGCCATAGATTTGCGGGT 57.859 55.556 0.00 0.00 44.29 5.28
2463 2560 2.404083 CGCCATAGATTTGCGGGTT 58.596 52.632 0.00 0.00 44.29 4.11
2464 2561 1.588674 CGCCATAGATTTGCGGGTTA 58.411 50.000 0.00 0.00 44.29 2.85
2465 2562 1.263217 CGCCATAGATTTGCGGGTTAC 59.737 52.381 0.00 0.00 44.29 2.50
2466 2563 2.294074 GCCATAGATTTGCGGGTTACA 58.706 47.619 0.00 0.00 0.00 2.41
2467 2564 2.685897 GCCATAGATTTGCGGGTTACAA 59.314 45.455 0.00 0.00 0.00 2.41
2468 2565 3.243068 GCCATAGATTTGCGGGTTACAAG 60.243 47.826 0.00 0.00 0.00 3.16
2469 2566 3.315191 CCATAGATTTGCGGGTTACAAGG 59.685 47.826 0.00 0.00 0.00 3.61
2470 2567 2.579410 AGATTTGCGGGTTACAAGGT 57.421 45.000 0.00 0.00 0.00 3.50
2471 2568 2.871453 AGATTTGCGGGTTACAAGGTT 58.129 42.857 0.00 0.00 0.00 3.50
2472 2569 2.817844 AGATTTGCGGGTTACAAGGTTC 59.182 45.455 0.00 0.00 0.00 3.62
2473 2570 1.320507 TTTGCGGGTTACAAGGTTCC 58.679 50.000 0.00 0.00 0.00 3.62
2474 2571 0.475044 TTGCGGGTTACAAGGTTCCT 59.525 50.000 0.00 0.00 0.00 3.36
2475 2572 1.350071 TGCGGGTTACAAGGTTCCTA 58.650 50.000 0.00 0.00 0.00 2.94
2476 2573 1.002315 TGCGGGTTACAAGGTTCCTAC 59.998 52.381 0.00 0.00 0.00 3.18
2477 2574 1.002315 GCGGGTTACAAGGTTCCTACA 59.998 52.381 0.00 0.00 0.00 2.74
2478 2575 2.691927 CGGGTTACAAGGTTCCTACAC 58.308 52.381 0.00 0.00 0.00 2.90
2479 2576 2.613725 CGGGTTACAAGGTTCCTACACC 60.614 54.545 0.00 0.00 37.04 4.16
2480 2577 2.372837 GGGTTACAAGGTTCCTACACCA 59.627 50.000 0.00 0.00 39.62 4.17
2481 2578 3.181441 GGGTTACAAGGTTCCTACACCAA 60.181 47.826 0.00 0.00 39.62 3.67
2482 2579 4.463070 GGTTACAAGGTTCCTACACCAAA 58.537 43.478 0.00 0.00 39.62 3.28
2483 2580 5.074804 GGTTACAAGGTTCCTACACCAAAT 58.925 41.667 0.00 0.00 39.62 2.32
2484 2581 6.240145 GGTTACAAGGTTCCTACACCAAATA 58.760 40.000 0.00 0.00 39.62 1.40
2485 2582 6.716173 GGTTACAAGGTTCCTACACCAAATAA 59.284 38.462 0.00 0.00 39.62 1.40
2486 2583 7.231115 GGTTACAAGGTTCCTACACCAAATAAA 59.769 37.037 0.00 0.00 39.62 1.40
2487 2584 8.631797 GTTACAAGGTTCCTACACCAAATAAAA 58.368 33.333 0.00 0.00 39.62 1.52
2488 2585 7.046292 ACAAGGTTCCTACACCAAATAAAAC 57.954 36.000 0.00 0.00 39.62 2.43
2489 2586 6.837048 ACAAGGTTCCTACACCAAATAAAACT 59.163 34.615 0.00 0.00 39.62 2.66
2490 2587 7.343574 ACAAGGTTCCTACACCAAATAAAACTT 59.656 33.333 0.00 0.00 39.62 2.66
2491 2588 7.907841 AGGTTCCTACACCAAATAAAACTTT 57.092 32.000 0.00 0.00 39.62 2.66
2492 2589 8.313944 AGGTTCCTACACCAAATAAAACTTTT 57.686 30.769 0.00 0.00 39.62 2.27
2493 2590 8.418662 AGGTTCCTACACCAAATAAAACTTTTC 58.581 33.333 0.00 0.00 39.62 2.29
2494 2591 7.380333 GGTTCCTACACCAAATAAAACTTTTCG 59.620 37.037 0.00 0.00 36.73 3.46
2495 2592 6.440436 TCCTACACCAAATAAAACTTTTCGC 58.560 36.000 0.00 0.00 0.00 4.70
2496 2593 6.263617 TCCTACACCAAATAAAACTTTTCGCT 59.736 34.615 0.00 0.00 0.00 4.93
2497 2594 6.921307 CCTACACCAAATAAAACTTTTCGCTT 59.079 34.615 0.00 0.00 0.00 4.68
2498 2595 6.582437 ACACCAAATAAAACTTTTCGCTTG 57.418 33.333 0.00 0.00 0.00 4.01
2499 2596 6.103330 ACACCAAATAAAACTTTTCGCTTGT 58.897 32.000 0.00 0.00 0.00 3.16
2500 2597 6.035542 ACACCAAATAAAACTTTTCGCTTGTG 59.964 34.615 0.00 0.00 0.00 3.33
2501 2598 5.006261 ACCAAATAAAACTTTTCGCTTGTGC 59.994 36.000 0.00 0.00 0.00 4.57
2502 2599 5.431309 CAAATAAAACTTTTCGCTTGTGCC 58.569 37.500 0.00 0.00 35.36 5.01
2503 2600 1.555477 AAAACTTTTCGCTTGTGCCG 58.445 45.000 0.00 0.00 35.36 5.69
2504 2601 0.869880 AAACTTTTCGCTTGTGCCGC 60.870 50.000 0.00 0.00 35.36 6.53
2505 2602 1.999071 AACTTTTCGCTTGTGCCGCA 61.999 50.000 0.00 0.00 35.36 5.69
2506 2603 1.299014 CTTTTCGCTTGTGCCGCAA 60.299 52.632 0.00 0.00 35.36 4.85
2507 2604 1.539776 CTTTTCGCTTGTGCCGCAAC 61.540 55.000 0.00 0.00 35.36 4.17
2508 2605 2.271607 TTTTCGCTTGTGCCGCAACA 62.272 50.000 0.00 0.00 35.36 3.33
2509 2606 2.271607 TTTCGCTTGTGCCGCAACAA 62.272 50.000 0.00 1.50 37.71 2.83
2510 2607 2.928313 TTCGCTTGTGCCGCAACAAC 62.928 55.000 0.00 0.00 35.16 3.32
2511 2608 2.103934 GCTTGTGCCGCAACAACA 59.896 55.556 0.00 0.00 35.16 3.33
2512 2609 2.230264 GCTTGTGCCGCAACAACAC 61.230 57.895 0.00 0.00 35.16 3.32
2513 2610 1.433064 CTTGTGCCGCAACAACACT 59.567 52.632 0.00 0.00 35.16 3.55
2514 2611 0.660488 CTTGTGCCGCAACAACACTA 59.340 50.000 0.00 0.00 35.16 2.74
2515 2612 1.064803 CTTGTGCCGCAACAACACTAA 59.935 47.619 0.00 0.00 35.16 2.24
2516 2613 0.378962 TGTGCCGCAACAACACTAAC 59.621 50.000 0.00 0.00 35.33 2.34
2517 2614 0.378962 GTGCCGCAACAACACTAACA 59.621 50.000 0.00 0.00 0.00 2.41
2518 2615 1.095600 TGCCGCAACAACACTAACAA 58.904 45.000 0.00 0.00 0.00 2.83
2519 2616 1.064803 TGCCGCAACAACACTAACAAG 59.935 47.619 0.00 0.00 0.00 3.16
2520 2617 1.599419 GCCGCAACAACACTAACAAGG 60.599 52.381 0.00 0.00 0.00 3.61
2521 2618 1.001815 CCGCAACAACACTAACAAGGG 60.002 52.381 0.00 0.00 0.00 3.95
2522 2619 1.673920 CGCAACAACACTAACAAGGGT 59.326 47.619 0.00 0.00 0.00 4.34
2523 2620 2.540769 CGCAACAACACTAACAAGGGTG 60.541 50.000 0.00 0.00 0.00 4.61
2524 2621 2.425668 GCAACAACACTAACAAGGGTGT 59.574 45.455 0.00 0.00 40.75 4.16
2526 2623 4.096682 GCAACAACACTAACAAGGGTGTTA 59.903 41.667 10.42 0.00 46.33 2.41
2527 2624 5.393243 GCAACAACACTAACAAGGGTGTTAA 60.393 40.000 10.42 0.00 46.91 2.01
2538 2635 1.710809 AGGGTGTTAACCTTGATGGCT 59.289 47.619 2.48 0.00 46.70 4.75
2551 2648 4.142600 CCTTGATGGCTTTGCTAGTTGTAC 60.143 45.833 0.00 0.00 0.00 2.90
2561 2658 8.889717 GGCTTTGCTAGTTGTACAAGATATTAA 58.110 33.333 8.98 0.00 0.00 1.40
2678 2775 0.103026 GCTCAAAATTGGATCGGGGC 59.897 55.000 0.00 0.00 0.00 5.80
2690 2787 1.275573 GATCGGGGCTTATAGGTCACC 59.724 57.143 0.00 0.00 0.00 4.02
2694 2791 2.755549 CGGGGCTTATAGGTCACCTAGT 60.756 54.545 10.07 0.61 39.70 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 7.631933 TGCCCTTCAATTTCAATCCATTATTT 58.368 30.769 0.00 0.00 0.00 1.40
26 27 4.161001 ACAGATGCCCTTCAATTTCAATCC 59.839 41.667 0.00 0.00 0.00 3.01
33 34 3.760684 GACAAGACAGATGCCCTTCAATT 59.239 43.478 0.00 0.00 0.00 2.32
48 49 4.651994 CGCATCTTTAACATGGACAAGAC 58.348 43.478 0.00 0.00 0.00 3.01
69 70 0.237498 CATCAGCCTATGCACATGCG 59.763 55.000 0.00 0.00 45.83 4.73
111 112 3.784412 CCACCGCGGCTTAACGTG 61.784 66.667 28.58 14.31 43.45 4.49
120 121 3.758088 CTGACTCGATCCACCGCGG 62.758 68.421 26.86 26.86 0.00 6.46
139 140 2.746277 GAACCGCGGCAGGTCAAT 60.746 61.111 28.58 0.00 45.21 2.57
218 219 2.480416 CCGTCCAGCTAGTGATCAAGTC 60.480 54.545 0.00 0.00 0.00 3.01
223 224 2.166664 AGAAACCGTCCAGCTAGTGATC 59.833 50.000 0.00 0.00 0.00 2.92
261 263 2.231235 TCGATGCAACAAGCTAGTCAGA 59.769 45.455 0.00 0.00 45.94 3.27
263 265 2.741759 TCGATGCAACAAGCTAGTCA 57.258 45.000 0.00 0.00 45.94 3.41
264 266 4.093408 TCATTTCGATGCAACAAGCTAGTC 59.907 41.667 0.00 0.00 45.94 2.59
265 267 4.002982 TCATTTCGATGCAACAAGCTAGT 58.997 39.130 0.00 0.00 45.94 2.57
274 302 5.861251 GTGTTGGTTTATCATTTCGATGCAA 59.139 36.000 0.00 0.00 35.39 4.08
282 310 5.278266 CGTGAGGTGTGTTGGTTTATCATTT 60.278 40.000 0.00 0.00 0.00 2.32
301 329 0.957395 AGCTTGAATGGTGCCGTGAG 60.957 55.000 0.00 0.00 0.00 3.51
302 330 1.073025 AGCTTGAATGGTGCCGTGA 59.927 52.632 0.00 0.00 0.00 4.35
304 332 1.973281 CCAGCTTGAATGGTGCCGT 60.973 57.895 0.00 0.00 34.47 5.68
305 333 2.879907 CCAGCTTGAATGGTGCCG 59.120 61.111 0.00 0.00 34.47 5.69
310 338 1.308069 CCCGTGACCAGCTTGAATGG 61.308 60.000 0.00 0.00 43.87 3.16
311 339 1.308069 CCCCGTGACCAGCTTGAATG 61.308 60.000 0.00 0.00 0.00 2.67
312 340 1.002134 CCCCGTGACCAGCTTGAAT 60.002 57.895 0.00 0.00 0.00 2.57
313 341 2.429930 CCCCGTGACCAGCTTGAA 59.570 61.111 0.00 0.00 0.00 2.69
314 342 4.329545 GCCCCGTGACCAGCTTGA 62.330 66.667 0.00 0.00 0.00 3.02
326 354 2.009774 CTTCTCACAACAATAGCCCCG 58.990 52.381 0.00 0.00 0.00 5.73
330 358 6.145696 ACTCGTTTACTTCTCACAACAATAGC 59.854 38.462 0.00 0.00 0.00 2.97
331 359 7.639162 ACTCGTTTACTTCTCACAACAATAG 57.361 36.000 0.00 0.00 0.00 1.73
343 371 7.290857 TCAAGATGCATAACTCGTTTACTTC 57.709 36.000 0.00 0.00 0.00 3.01
366 394 5.843673 TGTGTATGGAGAGTCTGAGAATC 57.156 43.478 0.95 0.95 0.00 2.52
367 395 7.904558 TTATGTGTATGGAGAGTCTGAGAAT 57.095 36.000 0.00 0.00 0.00 2.40
368 396 7.904558 ATTATGTGTATGGAGAGTCTGAGAA 57.095 36.000 0.00 0.00 0.00 2.87
369 397 7.561356 TCAATTATGTGTATGGAGAGTCTGAGA 59.439 37.037 0.00 0.00 0.00 3.27
370 398 7.720442 TCAATTATGTGTATGGAGAGTCTGAG 58.280 38.462 0.00 0.00 0.00 3.35
371 399 7.660030 TCAATTATGTGTATGGAGAGTCTGA 57.340 36.000 0.00 0.00 0.00 3.27
372 400 8.899427 ATTCAATTATGTGTATGGAGAGTCTG 57.101 34.615 0.00 0.00 0.00 3.51
373 401 8.708378 TGATTCAATTATGTGTATGGAGAGTCT 58.292 33.333 0.00 0.00 0.00 3.24
374 402 8.893219 TGATTCAATTATGTGTATGGAGAGTC 57.107 34.615 0.00 0.00 0.00 3.36
375 403 9.857656 ATTGATTCAATTATGTGTATGGAGAGT 57.142 29.630 6.06 0.00 28.76 3.24
377 405 8.992073 CGATTGATTCAATTATGTGTATGGAGA 58.008 33.333 12.96 0.00 33.90 3.71
378 406 8.992073 TCGATTGATTCAATTATGTGTATGGAG 58.008 33.333 12.96 0.00 33.90 3.86
379 407 8.773645 GTCGATTGATTCAATTATGTGTATGGA 58.226 33.333 12.96 0.00 33.90 3.41
380 408 8.777413 AGTCGATTGATTCAATTATGTGTATGG 58.223 33.333 12.96 0.00 33.90 2.74
381 409 9.803130 GAGTCGATTGATTCAATTATGTGTATG 57.197 33.333 12.96 0.00 33.90 2.39
382 410 9.770097 AGAGTCGATTGATTCAATTATGTGTAT 57.230 29.630 12.96 0.00 33.90 2.29
417 445 7.612244 AGCTAGAGTGTAGAGTGACTATTTTGA 59.388 37.037 0.00 0.00 33.39 2.69
418 446 7.767261 AGCTAGAGTGTAGAGTGACTATTTTG 58.233 38.462 0.00 0.00 33.39 2.44
419 447 7.832187 AGAGCTAGAGTGTAGAGTGACTATTTT 59.168 37.037 0.00 0.00 33.39 1.82
420 448 7.343357 AGAGCTAGAGTGTAGAGTGACTATTT 58.657 38.462 0.00 0.00 33.39 1.40
421 449 6.895782 AGAGCTAGAGTGTAGAGTGACTATT 58.104 40.000 0.00 0.00 33.39 1.73
422 450 6.326583 AGAGAGCTAGAGTGTAGAGTGACTAT 59.673 42.308 0.00 0.00 33.39 2.12
423 451 5.659525 AGAGAGCTAGAGTGTAGAGTGACTA 59.340 44.000 0.00 0.00 0.00 2.59
425 453 4.766375 AGAGAGCTAGAGTGTAGAGTGAC 58.234 47.826 0.00 0.00 0.00 3.67
426 454 5.182487 CAAGAGAGCTAGAGTGTAGAGTGA 58.818 45.833 0.00 0.00 0.00 3.41
427 455 4.941263 ACAAGAGAGCTAGAGTGTAGAGTG 59.059 45.833 0.00 0.00 0.00 3.51
428 456 5.174037 ACAAGAGAGCTAGAGTGTAGAGT 57.826 43.478 0.00 0.00 0.00 3.24
429 457 6.321717 CAAACAAGAGAGCTAGAGTGTAGAG 58.678 44.000 0.00 0.00 0.00 2.43
430 458 5.184096 CCAAACAAGAGAGCTAGAGTGTAGA 59.816 44.000 0.00 0.00 0.00 2.59
431 459 5.184096 TCCAAACAAGAGAGCTAGAGTGTAG 59.816 44.000 0.00 0.00 0.00 2.74
432 460 5.077564 TCCAAACAAGAGAGCTAGAGTGTA 58.922 41.667 0.00 0.00 0.00 2.90
433 461 3.898123 TCCAAACAAGAGAGCTAGAGTGT 59.102 43.478 0.00 0.00 0.00 3.55
434 462 4.527509 TCCAAACAAGAGAGCTAGAGTG 57.472 45.455 0.00 0.00 0.00 3.51
435 463 6.191315 TCTATCCAAACAAGAGAGCTAGAGT 58.809 40.000 0.00 0.00 0.00 3.24
436 464 6.707440 TCTATCCAAACAAGAGAGCTAGAG 57.293 41.667 0.00 0.00 0.00 2.43
458 492 2.760374 GTCAATCCACATCTCCCGATC 58.240 52.381 0.00 0.00 0.00 3.69
466 500 3.381908 ACTCTACCTCGTCAATCCACATC 59.618 47.826 0.00 0.00 0.00 3.06
478 512 5.774630 AGAAGAAAAGAACACTCTACCTCG 58.225 41.667 0.00 0.00 0.00 4.63
481 515 6.645827 GGTGTAGAAGAAAAGAACACTCTACC 59.354 42.308 0.00 0.00 40.18 3.18
482 516 7.208080 TGGTGTAGAAGAAAAGAACACTCTAC 58.792 38.462 0.00 0.00 40.18 2.59
484 518 6.235231 TGGTGTAGAAGAAAAGAACACTCT 57.765 37.500 0.00 0.00 40.18 3.24
485 519 6.511929 GCTTGGTGTAGAAGAAAAGAACACTC 60.512 42.308 0.00 0.00 40.18 3.51
486 520 5.297029 GCTTGGTGTAGAAGAAAAGAACACT 59.703 40.000 0.00 0.00 40.18 3.55
487 521 5.511571 GCTTGGTGTAGAAGAAAAGAACAC 58.488 41.667 0.00 0.00 39.72 3.32
488 522 4.272504 CGCTTGGTGTAGAAGAAAAGAACA 59.727 41.667 0.00 0.00 0.00 3.18
489 523 4.773510 CGCTTGGTGTAGAAGAAAAGAAC 58.226 43.478 0.00 0.00 0.00 3.01
490 524 3.250040 GCGCTTGGTGTAGAAGAAAAGAA 59.750 43.478 0.00 0.00 0.00 2.52
491 525 2.806244 GCGCTTGGTGTAGAAGAAAAGA 59.194 45.455 0.00 0.00 0.00 2.52
492 526 2.808543 AGCGCTTGGTGTAGAAGAAAAG 59.191 45.455 2.64 0.00 0.00 2.27
493 527 2.806244 GAGCGCTTGGTGTAGAAGAAAA 59.194 45.455 13.26 0.00 0.00 2.29
494 528 2.224185 TGAGCGCTTGGTGTAGAAGAAA 60.224 45.455 13.26 0.00 0.00 2.52
495 529 1.343142 TGAGCGCTTGGTGTAGAAGAA 59.657 47.619 13.26 0.00 0.00 2.52
496 530 0.966179 TGAGCGCTTGGTGTAGAAGA 59.034 50.000 13.26 0.00 0.00 2.87
497 531 1.354040 CTGAGCGCTTGGTGTAGAAG 58.646 55.000 13.26 0.00 0.00 2.85
498 532 0.670546 GCTGAGCGCTTGGTGTAGAA 60.671 55.000 13.26 0.00 35.14 2.10
499 533 1.079819 GCTGAGCGCTTGGTGTAGA 60.080 57.895 13.26 0.00 35.14 2.59
500 534 3.479370 GCTGAGCGCTTGGTGTAG 58.521 61.111 13.26 4.92 35.14 2.74
517 551 0.177604 TTTGTTGGTGGCTTGCCAAG 59.822 50.000 16.55 0.00 45.50 3.61
518 552 0.615331 TTTTGTTGGTGGCTTGCCAA 59.385 45.000 16.55 0.00 43.04 4.52
519 553 0.615331 TTTTTGTTGGTGGCTTGCCA 59.385 45.000 10.65 10.65 0.00 4.92
520 554 1.965935 ATTTTTGTTGGTGGCTTGCC 58.034 45.000 4.43 4.43 0.00 4.52
521 555 2.541383 GCAATTTTTGTTGGTGGCTTGC 60.541 45.455 0.00 0.00 0.00 4.01
522 556 2.681848 TGCAATTTTTGTTGGTGGCTTG 59.318 40.909 0.00 0.00 0.00 4.01
523 557 2.996631 TGCAATTTTTGTTGGTGGCTT 58.003 38.095 0.00 0.00 0.00 4.35
524 558 2.706339 TGCAATTTTTGTTGGTGGCT 57.294 40.000 0.00 0.00 0.00 4.75
525 559 3.314635 TGATTGCAATTTTTGTTGGTGGC 59.685 39.130 14.33 0.00 0.00 5.01
526 560 5.296283 TCTTGATTGCAATTTTTGTTGGTGG 59.704 36.000 14.33 0.00 32.68 4.61
527 561 6.037391 ACTCTTGATTGCAATTTTTGTTGGTG 59.963 34.615 14.33 2.93 32.68 4.17
528 562 6.037391 CACTCTTGATTGCAATTTTTGTTGGT 59.963 34.615 14.33 3.35 32.68 3.67
529 563 6.037391 ACACTCTTGATTGCAATTTTTGTTGG 59.963 34.615 14.33 3.46 32.68 3.77
530 564 7.007313 ACACTCTTGATTGCAATTTTTGTTG 57.993 32.000 14.33 9.89 32.68 3.33
531 565 7.550196 AGAACACTCTTGATTGCAATTTTTGTT 59.450 29.630 14.33 15.55 32.68 2.83
532 566 7.043565 AGAACACTCTTGATTGCAATTTTTGT 58.956 30.769 14.33 8.50 32.68 2.83
533 567 7.473027 AGAACACTCTTGATTGCAATTTTTG 57.527 32.000 14.33 7.91 32.68 2.44
534 568 8.496707 AAAGAACACTCTTGATTGCAATTTTT 57.503 26.923 14.33 0.00 41.23 1.94
535 569 8.496707 AAAAGAACACTCTTGATTGCAATTTT 57.503 26.923 14.33 3.21 41.23 1.82
536 570 8.496707 AAAAAGAACACTCTTGATTGCAATTT 57.503 26.923 14.33 0.53 41.23 1.82
558 592 3.006537 AGTGGCACTCTAGCTCGTAAAAA 59.993 43.478 15.88 0.00 34.17 1.94
559 593 2.561419 AGTGGCACTCTAGCTCGTAAAA 59.439 45.455 15.88 0.00 34.17 1.52
560 594 2.168496 AGTGGCACTCTAGCTCGTAAA 58.832 47.619 15.88 0.00 34.17 2.01
561 595 1.835494 AGTGGCACTCTAGCTCGTAA 58.165 50.000 15.88 0.00 34.17 3.18
562 596 2.704464 TAGTGGCACTCTAGCTCGTA 57.296 50.000 25.80 0.00 32.87 3.43
587 621 8.939929 CCTAGCGTCATCATCATATAACAAAAT 58.060 33.333 0.00 0.00 0.00 1.82
591 625 5.624509 GCCCTAGCGTCATCATCATATAACA 60.625 44.000 0.00 0.00 0.00 2.41
593 627 4.141937 GGCCCTAGCGTCATCATCATATAA 60.142 45.833 0.00 0.00 41.24 0.98
594 628 3.384789 GGCCCTAGCGTCATCATCATATA 59.615 47.826 0.00 0.00 41.24 0.86
596 630 1.550524 GGCCCTAGCGTCATCATCATA 59.449 52.381 0.00 0.00 41.24 2.15
598 632 1.748403 GGCCCTAGCGTCATCATCA 59.252 57.895 0.00 0.00 41.24 3.07
600 634 1.832608 TCGGCCCTAGCGTCATCAT 60.833 57.895 0.00 0.00 41.24 2.45
601 635 2.441348 TCGGCCCTAGCGTCATCA 60.441 61.111 0.00 0.00 41.24 3.07
633 702 2.044806 GCTGTGACCCACCACTGACT 62.045 60.000 0.00 0.00 37.96 3.41
634 703 1.598130 GCTGTGACCCACCACTGAC 60.598 63.158 0.00 0.00 37.96 3.51
635 704 2.828868 GCTGTGACCCACCACTGA 59.171 61.111 0.00 0.00 37.96 3.41
636 705 2.666190 CGCTGTGACCCACCACTG 60.666 66.667 0.00 0.00 37.89 3.66
637 706 3.941188 CCGCTGTGACCCACCACT 61.941 66.667 0.00 0.00 37.89 4.00
640 709 4.643387 AAGCCGCTGTGACCCACC 62.643 66.667 0.00 0.00 32.73 4.61
646 715 1.171549 TTCAATGCAAGCCGCTGTGA 61.172 50.000 0.00 0.00 43.06 3.58
653 728 1.648504 GGCTCAATTCAATGCAAGCC 58.351 50.000 6.06 6.06 42.17 4.35
672 747 1.422161 GGAGATCCCCAGACCCATGG 61.422 65.000 4.14 4.14 40.29 3.66
705 780 1.526887 CACCCATAGCCGACCATGT 59.473 57.895 0.00 0.00 0.00 3.21
825 900 6.663953 TGATAATATACGAGGAGAAGGAAGGG 59.336 42.308 0.00 0.00 0.00 3.95
826 901 7.363094 GGTGATAATATACGAGGAGAAGGAAGG 60.363 44.444 0.00 0.00 0.00 3.46
827 902 7.540299 GGTGATAATATACGAGGAGAAGGAAG 58.460 42.308 0.00 0.00 0.00 3.46
828 903 6.150641 CGGTGATAATATACGAGGAGAAGGAA 59.849 42.308 0.00 0.00 0.00 3.36
829 904 5.646793 CGGTGATAATATACGAGGAGAAGGA 59.353 44.000 0.00 0.00 0.00 3.36
830 905 5.676584 GCGGTGATAATATACGAGGAGAAGG 60.677 48.000 0.00 0.00 0.00 3.46
900 979 0.376502 GTACTAGGAGACGTCGGTGC 59.623 60.000 10.46 0.00 0.00 5.01
914 993 1.485066 GCTAAGCCAAGCCAGGTACTA 59.515 52.381 0.00 0.00 34.29 1.82
915 994 0.253327 GCTAAGCCAAGCCAGGTACT 59.747 55.000 0.00 0.00 36.45 2.73
916 995 0.253327 AGCTAAGCCAAGCCAGGTAC 59.747 55.000 4.35 0.00 43.86 3.34
994 1073 3.131478 CGGGGCGTCCATTTGTCC 61.131 66.667 9.07 0.00 34.36 4.02
996 1075 3.642503 TCCGGGGCGTCCATTTGT 61.643 61.111 9.07 0.00 34.36 2.83
1164 1243 2.113774 TCCTTGTGCTGGTGCTGG 59.886 61.111 0.00 0.00 40.48 4.85
1315 1394 4.388499 GTTGCCGGCGGAGGAAGA 62.388 66.667 33.44 4.56 0.00 2.87
1357 1436 1.919956 CTGTACTGCTGCTGCTTGCC 61.920 60.000 17.00 3.43 42.00 4.52
1473 1552 1.977544 CCTCACCTCCGTCTCCGTT 60.978 63.158 0.00 0.00 0.00 4.44
1746 1825 4.457496 CATCTGCTCCCCGTGCGT 62.457 66.667 0.00 0.00 0.00 5.24
1753 1832 0.885596 GCTGATCTGCATCTGCTCCC 60.886 60.000 18.67 0.00 45.84 4.30
1872 1962 7.910441 AATGTTTTTAGCAGGATCCAAATTG 57.090 32.000 15.82 4.26 0.00 2.32
1890 1980 7.530426 AATGGAAGCTTCTTCTGTAATGTTT 57.470 32.000 25.05 1.82 0.00 2.83
1891 1981 7.309438 GGAAATGGAAGCTTCTTCTGTAATGTT 60.309 37.037 25.05 6.15 0.00 2.71
1892 1982 6.151817 GGAAATGGAAGCTTCTTCTGTAATGT 59.848 38.462 25.05 4.36 0.00 2.71
1964 2057 1.076777 CCACGCCTCCATTCCCATT 60.077 57.895 0.00 0.00 0.00 3.16
2046 2139 5.163874 TGCTTTTTGAAATATGCGAATTGGC 60.164 36.000 5.36 5.36 0.00 4.52
2047 2140 6.406093 TGCTTTTTGAAATATGCGAATTGG 57.594 33.333 0.00 0.00 0.00 3.16
2048 2141 8.620641 GTTTTGCTTTTTGAAATATGCGAATTG 58.379 29.630 0.00 0.00 0.00 2.32
2049 2142 7.530190 CGTTTTGCTTTTTGAAATATGCGAATT 59.470 29.630 0.00 0.00 0.00 2.17
2135 2228 5.567138 ATGCAAGAGTTGGCAAATACTAC 57.433 39.130 0.00 0.00 44.20 2.73
2136 2229 6.884295 AGTTATGCAAGAGTTGGCAAATACTA 59.116 34.615 0.00 0.00 44.20 1.82
2137 2230 5.711976 AGTTATGCAAGAGTTGGCAAATACT 59.288 36.000 0.00 0.00 44.20 2.12
2167 2260 3.137913 CAGTCATGGGAGGATGGAATCTT 59.862 47.826 0.00 0.00 44.71 2.40
2230 2325 4.405116 TGAAATGAGGCAAAGCTTTTGT 57.595 36.364 9.53 0.00 0.00 2.83
2231 2326 5.934935 AATGAAATGAGGCAAAGCTTTTG 57.065 34.783 9.53 6.62 0.00 2.44
2232 2327 8.508875 CAATTAATGAAATGAGGCAAAGCTTTT 58.491 29.630 9.53 0.00 0.00 2.27
2276 2373 6.798315 TTGTCCGATTTTCCGTAAATAACA 57.202 33.333 0.00 0.00 36.59 2.41
2299 2396 0.106918 TCCTGTGTTCTGGCGGTTTT 60.107 50.000 0.00 0.00 33.50 2.43
2307 2404 0.890996 GTGCCCCTTCCTGTGTTCTG 60.891 60.000 0.00 0.00 0.00 3.02
2309 2406 1.603739 GGTGCCCCTTCCTGTGTTC 60.604 63.158 0.00 0.00 0.00 3.18
2393 2490 2.556622 CCTAAAGTTTGATGGCCGTTGT 59.443 45.455 0.00 0.00 0.00 3.32
2403 2500 1.342174 AGCGACGACCCTAAAGTTTGA 59.658 47.619 0.00 0.00 0.00 2.69
2441 2538 1.280746 CGCAAATCTATGGCGCAGG 59.719 57.895 10.83 0.00 44.49 4.85
2442 2539 4.907946 CGCAAATCTATGGCGCAG 57.092 55.556 10.83 0.00 44.49 5.18
2446 2543 2.294074 TGTAACCCGCAAATCTATGGC 58.706 47.619 0.00 0.00 0.00 4.40
2447 2544 3.315191 CCTTGTAACCCGCAAATCTATGG 59.685 47.826 0.00 0.00 0.00 2.74
2448 2545 3.945285 ACCTTGTAACCCGCAAATCTATG 59.055 43.478 0.00 0.00 0.00 2.23
2449 2546 4.230745 ACCTTGTAACCCGCAAATCTAT 57.769 40.909 0.00 0.00 0.00 1.98
2450 2547 3.706600 ACCTTGTAACCCGCAAATCTA 57.293 42.857 0.00 0.00 0.00 1.98
2451 2548 2.579410 ACCTTGTAACCCGCAAATCT 57.421 45.000 0.00 0.00 0.00 2.40
2452 2549 2.094906 GGAACCTTGTAACCCGCAAATC 60.095 50.000 0.00 0.00 0.00 2.17
2453 2550 1.890489 GGAACCTTGTAACCCGCAAAT 59.110 47.619 0.00 0.00 0.00 2.32
2454 2551 1.133730 AGGAACCTTGTAACCCGCAAA 60.134 47.619 0.00 0.00 0.00 3.68
2455 2552 0.475044 AGGAACCTTGTAACCCGCAA 59.525 50.000 0.00 0.00 0.00 4.85
2456 2553 1.002315 GTAGGAACCTTGTAACCCGCA 59.998 52.381 0.00 0.00 0.00 5.69
2457 2554 1.002315 TGTAGGAACCTTGTAACCCGC 59.998 52.381 0.00 0.00 0.00 6.13
2458 2555 2.613725 GGTGTAGGAACCTTGTAACCCG 60.614 54.545 0.00 0.00 37.24 5.28
2459 2556 2.372837 TGGTGTAGGAACCTTGTAACCC 59.627 50.000 0.00 0.00 41.16 4.11
2460 2557 3.775261 TGGTGTAGGAACCTTGTAACC 57.225 47.619 0.00 3.37 41.16 2.85
2461 2558 7.748691 TTATTTGGTGTAGGAACCTTGTAAC 57.251 36.000 0.00 0.00 41.16 2.50
2462 2559 8.631797 GTTTTATTTGGTGTAGGAACCTTGTAA 58.368 33.333 0.00 0.00 41.16 2.41
2463 2560 8.000127 AGTTTTATTTGGTGTAGGAACCTTGTA 59.000 33.333 0.00 0.00 41.16 2.41
2464 2561 6.837048 AGTTTTATTTGGTGTAGGAACCTTGT 59.163 34.615 0.00 0.00 41.16 3.16
2465 2562 7.284919 AGTTTTATTTGGTGTAGGAACCTTG 57.715 36.000 0.00 0.00 41.16 3.61
2466 2563 7.907841 AAGTTTTATTTGGTGTAGGAACCTT 57.092 32.000 0.00 0.00 41.16 3.50
2467 2564 7.907841 AAAGTTTTATTTGGTGTAGGAACCT 57.092 32.000 0.00 0.00 41.16 3.50
2468 2565 7.380333 CGAAAAGTTTTATTTGGTGTAGGAACC 59.620 37.037 0.00 0.00 40.94 3.62
2469 2566 7.096353 GCGAAAAGTTTTATTTGGTGTAGGAAC 60.096 37.037 0.00 0.00 0.00 3.62
2470 2567 6.919115 GCGAAAAGTTTTATTTGGTGTAGGAA 59.081 34.615 0.00 0.00 0.00 3.36
2471 2568 6.263617 AGCGAAAAGTTTTATTTGGTGTAGGA 59.736 34.615 0.00 0.00 0.00 2.94
2472 2569 6.443792 AGCGAAAAGTTTTATTTGGTGTAGG 58.556 36.000 0.00 0.00 0.00 3.18
2473 2570 7.434013 ACAAGCGAAAAGTTTTATTTGGTGTAG 59.566 33.333 16.72 6.04 0.00 2.74
2474 2571 7.221067 CACAAGCGAAAAGTTTTATTTGGTGTA 59.779 33.333 16.72 0.00 0.00 2.90
2475 2572 6.035542 CACAAGCGAAAAGTTTTATTTGGTGT 59.964 34.615 16.72 8.76 0.00 4.16
2476 2573 6.410038 CACAAGCGAAAAGTTTTATTTGGTG 58.590 36.000 16.72 12.29 0.00 4.17
2477 2574 5.006261 GCACAAGCGAAAAGTTTTATTTGGT 59.994 36.000 16.72 6.37 0.00 3.67
2478 2575 5.431309 GCACAAGCGAAAAGTTTTATTTGG 58.569 37.500 16.72 10.45 0.00 3.28
2479 2576 5.431309 GGCACAAGCGAAAAGTTTTATTTG 58.569 37.500 0.00 8.67 43.41 2.32
2480 2577 4.208253 CGGCACAAGCGAAAAGTTTTATTT 59.792 37.500 0.00 0.00 43.41 1.40
2481 2578 3.733727 CGGCACAAGCGAAAAGTTTTATT 59.266 39.130 0.00 0.00 43.41 1.40
2482 2579 3.305110 CGGCACAAGCGAAAAGTTTTAT 58.695 40.909 0.00 0.00 43.41 1.40
2483 2580 2.722071 CGGCACAAGCGAAAAGTTTTA 58.278 42.857 0.00 0.00 43.41 1.52
2484 2581 1.555477 CGGCACAAGCGAAAAGTTTT 58.445 45.000 0.00 0.00 43.41 2.43
2485 2582 0.869880 GCGGCACAAGCGAAAAGTTT 60.870 50.000 0.00 0.00 43.41 2.66
2486 2583 1.299089 GCGGCACAAGCGAAAAGTT 60.299 52.632 0.00 0.00 43.41 2.66
2487 2584 1.999071 TTGCGGCACAAGCGAAAAGT 61.999 50.000 0.05 0.00 43.41 2.66
2488 2585 1.299014 TTGCGGCACAAGCGAAAAG 60.299 52.632 0.05 0.00 43.41 2.27
2489 2586 1.587613 GTTGCGGCACAAGCGAAAA 60.588 52.632 0.05 0.00 43.41 2.29
2490 2587 2.025441 GTTGCGGCACAAGCGAAA 59.975 55.556 0.05 0.00 43.41 3.46
2491 2588 2.765356 TTGTTGCGGCACAAGCGAA 61.765 52.632 0.05 0.00 43.41 4.70
2492 2589 3.205536 TTGTTGCGGCACAAGCGA 61.206 55.556 0.05 0.00 43.41 4.93
2493 2590 3.024043 GTTGTTGCGGCACAAGCG 61.024 61.111 15.06 0.00 43.41 4.68
2494 2591 2.103934 TGTTGTTGCGGCACAAGC 59.896 55.556 15.06 11.57 39.50 4.01
2495 2592 0.660488 TAGTGTTGTTGCGGCACAAG 59.340 50.000 15.06 0.00 39.50 3.16
2496 2593 1.095600 TTAGTGTTGTTGCGGCACAA 58.904 45.000 0.05 8.01 35.75 3.33
2497 2594 0.378962 GTTAGTGTTGTTGCGGCACA 59.621 50.000 0.05 1.24 35.75 4.57
2498 2595 0.378962 TGTTAGTGTTGTTGCGGCAC 59.621 50.000 0.05 0.00 0.00 5.01
2499 2596 1.064803 CTTGTTAGTGTTGTTGCGGCA 59.935 47.619 0.00 0.00 0.00 5.69
2500 2597 1.599419 CCTTGTTAGTGTTGTTGCGGC 60.599 52.381 0.00 0.00 0.00 6.53
2501 2598 1.001815 CCCTTGTTAGTGTTGTTGCGG 60.002 52.381 0.00 0.00 0.00 5.69
2502 2599 1.673920 ACCCTTGTTAGTGTTGTTGCG 59.326 47.619 0.00 0.00 0.00 4.85
2503 2600 2.425668 ACACCCTTGTTAGTGTTGTTGC 59.574 45.455 0.00 0.00 44.65 4.17
2509 2606 4.783560 AGGTTAACACCCTTGTTAGTGT 57.216 40.909 8.10 0.00 46.53 3.55
2517 2614 2.110011 AGCCATCAAGGTTAACACCCTT 59.890 45.455 8.10 0.00 45.63 3.95
2518 2615 1.710809 AGCCATCAAGGTTAACACCCT 59.289 47.619 8.10 0.00 45.63 4.34
2519 2616 2.215942 AGCCATCAAGGTTAACACCC 57.784 50.000 8.10 0.00 45.63 4.61
2520 2617 3.860754 GCAAAGCCATCAAGGTTAACACC 60.861 47.826 8.10 0.00 44.67 4.16
2521 2618 3.005791 AGCAAAGCCATCAAGGTTAACAC 59.994 43.478 8.10 0.00 40.61 3.32
2522 2619 3.230134 AGCAAAGCCATCAAGGTTAACA 58.770 40.909 8.10 0.00 40.61 2.41
2523 2620 3.942130 AGCAAAGCCATCAAGGTTAAC 57.058 42.857 0.00 0.00 40.61 2.01
2524 2621 4.662278 ACTAGCAAAGCCATCAAGGTTAA 58.338 39.130 0.00 0.00 40.61 2.01
2525 2622 4.301072 ACTAGCAAAGCCATCAAGGTTA 57.699 40.909 0.00 0.00 40.61 2.85
2526 2623 3.160679 ACTAGCAAAGCCATCAAGGTT 57.839 42.857 0.00 0.00 40.61 3.50
2527 2624 2.821969 CAACTAGCAAAGCCATCAAGGT 59.178 45.455 0.00 0.00 40.61 3.50
2535 2632 6.927294 ATATCTTGTACAACTAGCAAAGCC 57.073 37.500 3.59 0.00 0.00 4.35
2643 2740 8.490355 CAATTTTGAGCTTAATGAAACACTTCC 58.510 33.333 0.00 0.00 0.00 3.46
2678 2775 9.357161 AGAGAATTACACTAGGTGACCTATAAG 57.643 37.037 12.49 4.99 35.36 1.73


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

AutoCloner maintained by Alex Coulton.