Multiple sequence alignment - TraesCS3B01G066900

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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 TraesCS3B01G066900 chr3B 100.000 2420 0 0 1 2420 39815617 39818036 0.000000e+00 4470
1 TraesCS3B01G066900 chr3B 96.058 1725 63 5 697 2420 173888307 173890027 0.000000e+00 2804
2 TraesCS3B01G066900 chr3B 97.583 331 3 3 1 326 173887998 173888328 1.620000e-156 562
3 TraesCS3B01G066900 chr2B 96.870 1725 51 3 697 2420 357429724 357431446 0.000000e+00 2883
4 TraesCS3B01G066900 chr2B 97.444 1604 37 3 820 2420 357718974 357717372 0.000000e+00 2732
5 TraesCS3B01G066900 chr2B 96.324 1605 52 4 820 2420 357344747 357343146 0.000000e+00 2630
6 TraesCS3B01G066900 chr6B 96.524 1726 57 3 697 2420 625641641 625639917 0.000000e+00 2852
7 TraesCS3B01G066900 chr5A 96.294 1727 57 5 698 2420 534933337 534935060 0.000000e+00 2828
8 TraesCS3B01G066900 chr5A 96.979 1324 39 1 1098 2420 647029609 647030932 0.000000e+00 2222
9 TraesCS3B01G066900 chr5A 96.800 375 11 1 326 699 315501175 315500801 2.040000e-175 625
10 TraesCS3B01G066900 chr7A 96.060 1726 57 3 697 2420 211291846 211293562 0.000000e+00 2800
11 TraesCS3B01G066900 chr7B 95.362 1725 64 7 697 2420 139542643 139540934 0.000000e+00 2728
12 TraesCS3B01G066900 chr7B 97.059 374 11 0 322 695 720994360 720994733 4.390000e-177 630
13 TraesCS3B01G066900 chr7B 96.809 376 10 2 320 693 24403361 24403736 5.680000e-176 627
14 TraesCS3B01G066900 chr7B 97.561 328 5 1 2 326 139542949 139542622 2.100000e-155 558
15 TraesCS3B01G066900 chr4D 97.988 994 20 0 1427 2420 123507853 123506860 0.000000e+00 1725
16 TraesCS3B01G066900 chr4D 97.872 329 4 1 1 326 123738419 123738091 1.260000e-157 566
17 TraesCS3B01G066900 chr4D 97.568 329 5 1 1 326 123508922 123508594 5.840000e-156 560
18 TraesCS3B01G066900 chr5B 99.451 364 2 0 324 687 222365429 222365792 0.000000e+00 662
19 TraesCS3B01G066900 chr6A 97.312 372 10 0 323 694 158065766 158065395 1.220000e-177 632
20 TraesCS3B01G066900 chr6A 96.809 376 11 1 322 697 208511498 208511872 5.680000e-176 627
21 TraesCS3B01G066900 chr4B 97.561 369 9 0 326 694 306604682 306604314 1.220000e-177 632
22 TraesCS3B01G066900 chr3A 97.814 366 8 0 324 689 631290042 631289677 1.220000e-177 632
23 TraesCS3B01G066900 chr1A 96.834 379 11 1 325 703 45799846 45800223 1.220000e-177 632
24 TraesCS3B01G066900 chrUn 97.872 329 4 1 1 326 415353960 415354288 1.260000e-157 566
25 TraesCS3B01G066900 chr7D 97.872 329 4 1 1 326 579028959 579029287 1.260000e-157 566
26 TraesCS3B01G066900 chr6D 97.872 329 4 1 1 326 108466943 108467271 1.260000e-157 566
27 TraesCS3B01G066900 chr2D 97.872 329 4 1 1 326 637318534 637318206 1.260000e-157 566
28 TraesCS3B01G066900 chr1D 97.872 329 4 1 1 326 212468628 212468300 1.260000e-157 566


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 TraesCS3B01G066900 chr3B 39815617 39818036 2419 False 4470.0 4470 100.0000 1 2420 1 chr3B.!!$F1 2419
1 TraesCS3B01G066900 chr3B 173887998 173890027 2029 False 1683.0 2804 96.8205 1 2420 2 chr3B.!!$F2 2419
2 TraesCS3B01G066900 chr2B 357429724 357431446 1722 False 2883.0 2883 96.8700 697 2420 1 chr2B.!!$F1 1723
3 TraesCS3B01G066900 chr2B 357717372 357718974 1602 True 2732.0 2732 97.4440 820 2420 1 chr2B.!!$R2 1600
4 TraesCS3B01G066900 chr2B 357343146 357344747 1601 True 2630.0 2630 96.3240 820 2420 1 chr2B.!!$R1 1600
5 TraesCS3B01G066900 chr6B 625639917 625641641 1724 True 2852.0 2852 96.5240 697 2420 1 chr6B.!!$R1 1723
6 TraesCS3B01G066900 chr5A 534933337 534935060 1723 False 2828.0 2828 96.2940 698 2420 1 chr5A.!!$F1 1722
7 TraesCS3B01G066900 chr5A 647029609 647030932 1323 False 2222.0 2222 96.9790 1098 2420 1 chr5A.!!$F2 1322
8 TraesCS3B01G066900 chr7A 211291846 211293562 1716 False 2800.0 2800 96.0600 697 2420 1 chr7A.!!$F1 1723
9 TraesCS3B01G066900 chr7B 139540934 139542949 2015 True 1643.0 2728 96.4615 2 2420 2 chr7B.!!$R1 2418
10 TraesCS3B01G066900 chr4D 123506860 123508922 2062 True 1142.5 1725 97.7780 1 2420 2 chr4D.!!$R2 2419

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
397 403 0.034089 AGGGTTGTGATAGGCTTGGC 60.034 55.0 0.0 0.0 0.0 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2003 2046 1.167851 CAGGTCCACGCATGTTGAAT 58.832 50.0 0.0 0.0 0.0 2.57 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
178 179 7.400599 TCTTCTCTTCCAGCGTTTAGTATTA 57.599 36.000 0.00 0.00 0.00 0.98
292 296 3.635373 TCCACTACCCGCTTTACTATCTG 59.365 47.826 0.00 0.00 0.00 2.90
332 338 8.667076 TTAAGTTTCCCTTAATATAACTCCGC 57.333 34.615 0.00 0.00 40.02 5.54
333 339 5.618236 AGTTTCCCTTAATATAACTCCGCC 58.382 41.667 0.00 0.00 0.00 6.13
334 340 5.368816 AGTTTCCCTTAATATAACTCCGCCT 59.631 40.000 0.00 0.00 0.00 5.52
335 341 6.556116 AGTTTCCCTTAATATAACTCCGCCTA 59.444 38.462 0.00 0.00 0.00 3.93
336 342 7.237055 AGTTTCCCTTAATATAACTCCGCCTAT 59.763 37.037 0.00 0.00 0.00 2.57
337 343 6.540438 TCCCTTAATATAACTCCGCCTATG 57.460 41.667 0.00 0.00 0.00 2.23
338 344 6.021030 TCCCTTAATATAACTCCGCCTATGT 58.979 40.000 0.00 0.00 0.00 2.29
339 345 6.154021 TCCCTTAATATAACTCCGCCTATGTC 59.846 42.308 0.00 0.00 0.00 3.06
340 346 6.154706 CCCTTAATATAACTCCGCCTATGTCT 59.845 42.308 0.00 0.00 0.00 3.41
341 347 7.310485 CCCTTAATATAACTCCGCCTATGTCTT 60.310 40.741 0.00 0.00 0.00 3.01
342 348 7.760340 CCTTAATATAACTCCGCCTATGTCTTC 59.240 40.741 0.00 0.00 0.00 2.87
343 349 6.919775 AATATAACTCCGCCTATGTCTTCT 57.080 37.500 0.00 0.00 0.00 2.85
344 350 9.524496 TTAATATAACTCCGCCTATGTCTTCTA 57.476 33.333 0.00 0.00 0.00 2.10
345 351 5.968528 ATAACTCCGCCTATGTCTTCTAG 57.031 43.478 0.00 0.00 0.00 2.43
346 352 2.588620 ACTCCGCCTATGTCTTCTAGG 58.411 52.381 0.00 0.00 39.06 3.02
362 368 2.203209 GGCATAGCCGGTCCCAAG 60.203 66.667 1.90 0.00 39.62 3.61
363 369 2.902343 GCATAGCCGGTCCCAAGC 60.902 66.667 1.90 0.00 0.00 4.01
364 370 2.203209 CATAGCCGGTCCCAAGCC 60.203 66.667 1.90 0.00 0.00 4.35
365 371 3.489513 ATAGCCGGTCCCAAGCCC 61.490 66.667 1.90 0.00 0.00 5.19
374 380 2.044352 CCCAAGCCCGGGTAAAGG 60.044 66.667 24.63 18.41 41.83 3.11
375 381 2.608550 CCCAAGCCCGGGTAAAGGA 61.609 63.158 24.63 0.00 41.83 3.36
376 382 1.077716 CCAAGCCCGGGTAAAGGAG 60.078 63.158 24.63 5.31 0.00 3.69
377 383 1.077716 CAAGCCCGGGTAAAGGAGG 60.078 63.158 24.63 0.00 0.00 4.30
378 384 1.229723 AAGCCCGGGTAAAGGAGGA 60.230 57.895 24.63 0.00 0.00 3.71
379 385 1.272554 AAGCCCGGGTAAAGGAGGAG 61.273 60.000 24.63 0.00 0.00 3.69
380 386 2.743179 GCCCGGGTAAAGGAGGAGG 61.743 68.421 24.63 0.00 0.00 4.30
381 387 2.070650 CCCGGGTAAAGGAGGAGGG 61.071 68.421 14.18 0.00 0.00 4.30
382 388 1.306739 CCGGGTAAAGGAGGAGGGT 60.307 63.158 0.00 0.00 0.00 4.34
383 389 0.912968 CCGGGTAAAGGAGGAGGGTT 60.913 60.000 0.00 0.00 0.00 4.11
384 390 0.252197 CGGGTAAAGGAGGAGGGTTG 59.748 60.000 0.00 0.00 0.00 3.77
385 391 1.369403 GGGTAAAGGAGGAGGGTTGT 58.631 55.000 0.00 0.00 0.00 3.32
386 392 1.004394 GGGTAAAGGAGGAGGGTTGTG 59.996 57.143 0.00 0.00 0.00 3.33
387 393 1.982958 GGTAAAGGAGGAGGGTTGTGA 59.017 52.381 0.00 0.00 0.00 3.58
388 394 2.576648 GGTAAAGGAGGAGGGTTGTGAT 59.423 50.000 0.00 0.00 0.00 3.06
389 395 3.778629 GGTAAAGGAGGAGGGTTGTGATA 59.221 47.826 0.00 0.00 0.00 2.15
390 396 4.141688 GGTAAAGGAGGAGGGTTGTGATAG 60.142 50.000 0.00 0.00 0.00 2.08
391 397 2.182516 AGGAGGAGGGTTGTGATAGG 57.817 55.000 0.00 0.00 0.00 2.57
392 398 0.470341 GGAGGAGGGTTGTGATAGGC 59.530 60.000 0.00 0.00 0.00 3.93
393 399 1.501582 GAGGAGGGTTGTGATAGGCT 58.498 55.000 0.00 0.00 0.00 4.58
394 400 1.840635 GAGGAGGGTTGTGATAGGCTT 59.159 52.381 0.00 0.00 0.00 4.35
395 401 1.561542 AGGAGGGTTGTGATAGGCTTG 59.438 52.381 0.00 0.00 0.00 4.01
396 402 1.408822 GGAGGGTTGTGATAGGCTTGG 60.409 57.143 0.00 0.00 0.00 3.61
397 403 0.034089 AGGGTTGTGATAGGCTTGGC 60.034 55.000 0.00 0.00 0.00 4.52
398 404 1.376609 GGGTTGTGATAGGCTTGGCG 61.377 60.000 0.00 0.00 0.00 5.69
399 405 0.392461 GGTTGTGATAGGCTTGGCGA 60.392 55.000 0.00 0.00 0.00 5.54
400 406 1.009829 GTTGTGATAGGCTTGGCGAG 58.990 55.000 0.00 0.00 0.00 5.03
411 417 4.458666 TGGCGAGCCAACGTAAAA 57.541 50.000 15.24 0.00 44.12 1.52
412 418 2.935505 TGGCGAGCCAACGTAAAAT 58.064 47.368 15.24 0.00 44.12 1.82
413 419 0.800012 TGGCGAGCCAACGTAAAATC 59.200 50.000 15.24 0.00 44.12 2.17
414 420 1.084289 GGCGAGCCAACGTAAAATCT 58.916 50.000 9.58 0.00 35.81 2.40
415 421 2.273557 GGCGAGCCAACGTAAAATCTA 58.726 47.619 9.58 0.00 35.81 1.98
416 422 2.284417 GGCGAGCCAACGTAAAATCTAG 59.716 50.000 9.58 0.00 35.81 2.43
417 423 2.285660 GCGAGCCAACGTAAAATCTAGC 60.286 50.000 0.00 0.00 35.59 3.42
418 424 2.284417 CGAGCCAACGTAAAATCTAGCC 59.716 50.000 0.00 0.00 0.00 3.93
419 425 3.267483 GAGCCAACGTAAAATCTAGCCA 58.733 45.455 0.00 0.00 0.00 4.75
420 426 3.270877 AGCCAACGTAAAATCTAGCCAG 58.729 45.455 0.00 0.00 0.00 4.85
421 427 3.007635 GCCAACGTAAAATCTAGCCAGT 58.992 45.455 0.00 0.00 0.00 4.00
422 428 3.063588 GCCAACGTAAAATCTAGCCAGTC 59.936 47.826 0.00 0.00 0.00 3.51
423 429 3.621715 CCAACGTAAAATCTAGCCAGTCC 59.378 47.826 0.00 0.00 0.00 3.85
424 430 3.538634 ACGTAAAATCTAGCCAGTCCC 57.461 47.619 0.00 0.00 0.00 4.46
425 431 2.835764 ACGTAAAATCTAGCCAGTCCCA 59.164 45.455 0.00 0.00 0.00 4.37
426 432 3.454812 ACGTAAAATCTAGCCAGTCCCAT 59.545 43.478 0.00 0.00 0.00 4.00
427 433 3.809832 CGTAAAATCTAGCCAGTCCCATG 59.190 47.826 0.00 0.00 0.00 3.66
428 434 3.303351 AAAATCTAGCCAGTCCCATGG 57.697 47.619 4.14 4.14 43.72 3.66
429 435 1.143813 AATCTAGCCAGTCCCATGGG 58.856 55.000 26.30 26.30 40.97 4.00
433 439 4.907457 GCCAGTCCCATGGGTATG 57.093 61.111 30.28 26.25 40.97 2.39
434 440 2.230664 GCCAGTCCCATGGGTATGA 58.769 57.895 30.28 8.41 40.97 2.15
435 441 0.550914 GCCAGTCCCATGGGTATGAA 59.449 55.000 30.28 7.98 40.97 2.57
436 442 1.064017 GCCAGTCCCATGGGTATGAAA 60.064 52.381 30.28 7.14 40.97 2.69
437 443 2.654863 CCAGTCCCATGGGTATGAAAC 58.345 52.381 30.28 19.33 36.36 2.78
448 454 3.420839 GGTATGAAACCCATTTGAGCG 57.579 47.619 0.00 0.00 43.16 5.03
449 455 3.013921 GGTATGAAACCCATTTGAGCGA 58.986 45.455 0.00 0.00 43.16 4.93
450 456 3.065371 GGTATGAAACCCATTTGAGCGAG 59.935 47.826 0.00 0.00 43.16 5.03
451 457 2.559698 TGAAACCCATTTGAGCGAGA 57.440 45.000 0.00 0.00 0.00 4.04
452 458 2.426522 TGAAACCCATTTGAGCGAGAG 58.573 47.619 0.00 0.00 0.00 3.20
453 459 2.224523 TGAAACCCATTTGAGCGAGAGT 60.225 45.455 0.00 0.00 0.00 3.24
454 460 3.007506 TGAAACCCATTTGAGCGAGAGTA 59.992 43.478 0.00 0.00 0.00 2.59
455 461 2.969628 ACCCATTTGAGCGAGAGTAG 57.030 50.000 0.00 0.00 0.00 2.57
456 462 2.180276 ACCCATTTGAGCGAGAGTAGT 58.820 47.619 0.00 0.00 0.00 2.73
457 463 3.362706 ACCCATTTGAGCGAGAGTAGTA 58.637 45.455 0.00 0.00 0.00 1.82
458 464 3.130693 ACCCATTTGAGCGAGAGTAGTAC 59.869 47.826 0.00 0.00 0.00 2.73
459 465 3.381908 CCCATTTGAGCGAGAGTAGTACT 59.618 47.826 1.37 1.37 0.00 2.73
460 466 4.579340 CCCATTTGAGCGAGAGTAGTACTA 59.421 45.833 1.88 0.00 0.00 1.82
461 467 5.278071 CCCATTTGAGCGAGAGTAGTACTAG 60.278 48.000 1.87 0.00 0.00 2.57
462 468 5.278071 CCATTTGAGCGAGAGTAGTACTAGG 60.278 48.000 1.87 0.00 0.00 3.02
463 469 4.750021 TTGAGCGAGAGTAGTACTAGGA 57.250 45.455 1.87 0.00 0.00 2.94
464 470 4.959560 TGAGCGAGAGTAGTACTAGGAT 57.040 45.455 1.87 0.00 0.00 3.24
465 471 4.633175 TGAGCGAGAGTAGTACTAGGATG 58.367 47.826 1.87 0.00 0.00 3.51
466 472 3.998341 GAGCGAGAGTAGTACTAGGATGG 59.002 52.174 1.87 0.00 0.00 3.51
467 473 3.075884 GCGAGAGTAGTACTAGGATGGG 58.924 54.545 1.87 0.00 0.00 4.00
468 474 3.496515 GCGAGAGTAGTACTAGGATGGGT 60.497 52.174 1.87 0.00 0.00 4.51
469 475 4.066490 CGAGAGTAGTACTAGGATGGGTG 58.934 52.174 1.87 0.00 0.00 4.61
470 476 4.202336 CGAGAGTAGTACTAGGATGGGTGA 60.202 50.000 1.87 0.00 0.00 4.02
471 477 5.051409 AGAGTAGTACTAGGATGGGTGAC 57.949 47.826 1.87 0.00 0.00 3.67
483 489 4.234673 GGTGACCTCCTGGGAAGT 57.765 61.111 0.00 0.00 38.76 3.01
484 490 1.984020 GGTGACCTCCTGGGAAGTC 59.016 63.158 10.52 10.52 36.44 3.01
485 491 1.554583 GGTGACCTCCTGGGAAGTCC 61.555 65.000 13.79 6.97 35.38 3.85
486 492 0.545548 GTGACCTCCTGGGAAGTCCT 60.546 60.000 13.79 0.00 35.38 3.85
487 493 0.193574 TGACCTCCTGGGAAGTCCTT 59.806 55.000 13.79 0.00 35.38 3.36
488 494 0.615850 GACCTCCTGGGAAGTCCTTG 59.384 60.000 7.04 0.00 38.76 3.61
489 495 0.104409 ACCTCCTGGGAAGTCCTTGT 60.104 55.000 0.00 0.00 38.76 3.16
490 496 0.326264 CCTCCTGGGAAGTCCTTGTG 59.674 60.000 0.00 0.00 37.23 3.33
491 497 1.352083 CTCCTGGGAAGTCCTTGTGA 58.648 55.000 0.00 0.00 36.20 3.58
492 498 1.699634 CTCCTGGGAAGTCCTTGTGAA 59.300 52.381 0.00 0.00 36.20 3.18
493 499 2.106511 CTCCTGGGAAGTCCTTGTGAAA 59.893 50.000 0.00 0.00 36.20 2.69
494 500 2.106511 TCCTGGGAAGTCCTTGTGAAAG 59.893 50.000 0.00 0.00 36.20 2.62
495 501 2.508526 CTGGGAAGTCCTTGTGAAAGG 58.491 52.381 0.00 0.00 41.35 3.11
496 502 1.144913 TGGGAAGTCCTTGTGAAAGGG 59.855 52.381 4.73 0.00 40.38 3.95
497 503 1.145119 GGGAAGTCCTTGTGAAAGGGT 59.855 52.381 4.73 0.00 40.38 4.34
498 504 2.424379 GGGAAGTCCTTGTGAAAGGGTT 60.424 50.000 4.73 0.00 40.38 4.11
499 505 3.296854 GGAAGTCCTTGTGAAAGGGTTT 58.703 45.455 4.73 0.44 40.38 3.27
500 506 3.318275 GGAAGTCCTTGTGAAAGGGTTTC 59.682 47.826 4.73 8.41 40.38 2.78
501 507 3.662759 AGTCCTTGTGAAAGGGTTTCA 57.337 42.857 4.73 0.00 46.68 2.69
512 518 6.652205 TGAAAGGGTTTCATATCTAAGGGT 57.348 37.500 0.00 0.00 44.21 4.34
513 519 7.039722 TGAAAGGGTTTCATATCTAAGGGTT 57.960 36.000 0.00 0.00 44.21 4.11
514 520 6.889722 TGAAAGGGTTTCATATCTAAGGGTTG 59.110 38.462 0.00 0.00 44.21 3.77
515 521 6.402981 AAGGGTTTCATATCTAAGGGTTGT 57.597 37.500 0.00 0.00 0.00 3.32
516 522 5.755849 AGGGTTTCATATCTAAGGGTTGTG 58.244 41.667 0.00 0.00 0.00 3.33
517 523 5.491078 AGGGTTTCATATCTAAGGGTTGTGA 59.509 40.000 0.00 0.00 0.00 3.58
518 524 6.160459 AGGGTTTCATATCTAAGGGTTGTGAT 59.840 38.462 0.00 0.00 0.00 3.06
519 525 7.349859 AGGGTTTCATATCTAAGGGTTGTGATA 59.650 37.037 0.00 0.00 0.00 2.15
520 526 7.661847 GGGTTTCATATCTAAGGGTTGTGATAG 59.338 40.741 0.00 0.00 0.00 2.08
521 527 7.661847 GGTTTCATATCTAAGGGTTGTGATAGG 59.338 40.741 0.00 0.00 0.00 2.57
522 528 6.360370 TCATATCTAAGGGTTGTGATAGGC 57.640 41.667 0.00 0.00 0.00 3.93
523 529 6.084738 TCATATCTAAGGGTTGTGATAGGCT 58.915 40.000 0.00 0.00 0.00 4.58
524 530 6.558775 TCATATCTAAGGGTTGTGATAGGCTT 59.441 38.462 0.00 0.00 0.00 4.35
525 531 4.487714 TCTAAGGGTTGTGATAGGCTTG 57.512 45.455 0.00 0.00 0.00 4.01
526 532 2.514458 AAGGGTTGTGATAGGCTTGG 57.486 50.000 0.00 0.00 0.00 3.61
527 533 0.034089 AGGGTTGTGATAGGCTTGGC 60.034 55.000 0.00 0.00 0.00 4.52
528 534 1.376609 GGGTTGTGATAGGCTTGGCG 61.377 60.000 0.00 0.00 0.00 5.69
529 535 0.392461 GGTTGTGATAGGCTTGGCGA 60.392 55.000 0.00 0.00 0.00 5.54
530 536 1.009829 GTTGTGATAGGCTTGGCGAG 58.990 55.000 0.00 0.00 0.00 5.03
541 547 4.458666 TGGCGAGCCAACGTAAAA 57.541 50.000 15.24 0.00 44.12 1.52
542 548 2.704108 TGGCGAGCCAACGTAAAAA 58.296 47.368 15.24 0.00 44.12 1.94
543 549 0.308376 TGGCGAGCCAACGTAAAAAC 59.692 50.000 15.24 0.00 44.12 2.43
544 550 0.589708 GGCGAGCCAACGTAAAAACT 59.410 50.000 9.58 0.00 35.81 2.66
545 551 1.799994 GGCGAGCCAACGTAAAAACTA 59.200 47.619 9.58 0.00 35.81 2.24
546 552 2.159747 GGCGAGCCAACGTAAAAACTAG 60.160 50.000 9.58 0.00 35.81 2.57
547 553 2.723923 GCGAGCCAACGTAAAAACTAGC 60.724 50.000 0.00 0.00 35.59 3.42
548 554 2.159747 CGAGCCAACGTAAAAACTAGCC 60.160 50.000 0.00 0.00 0.00 3.93
549 555 2.809696 GAGCCAACGTAAAAACTAGCCA 59.190 45.455 0.00 0.00 0.00 4.75
550 556 2.812011 AGCCAACGTAAAAACTAGCCAG 59.188 45.455 0.00 0.00 0.00 4.85
551 557 2.551032 GCCAACGTAAAAACTAGCCAGT 59.449 45.455 0.00 0.00 36.19 4.00
552 558 3.364664 GCCAACGTAAAAACTAGCCAGTC 60.365 47.826 0.00 0.00 32.29 3.51
553 559 3.187842 CCAACGTAAAAACTAGCCAGTCC 59.812 47.826 0.00 0.00 32.29 3.85
554 560 4.062991 CAACGTAAAAACTAGCCAGTCCT 58.937 43.478 0.00 0.00 32.29 3.85
555 561 4.347360 ACGTAAAAACTAGCCAGTCCTT 57.653 40.909 0.00 0.00 32.29 3.36
556 562 4.711399 ACGTAAAAACTAGCCAGTCCTTT 58.289 39.130 0.00 0.00 32.29 3.11
557 563 4.514066 ACGTAAAAACTAGCCAGTCCTTTG 59.486 41.667 0.00 0.00 32.29 2.77
558 564 4.083484 CGTAAAAACTAGCCAGTCCTTTGG 60.083 45.833 0.00 0.00 41.35 3.28
559 565 2.586648 AAACTAGCCAGTCCTTTGGG 57.413 50.000 0.00 0.00 38.72 4.12
561 567 2.337359 ACTAGCCAGTCCTTTGGGTA 57.663 50.000 4.17 4.17 46.57 3.69
562 568 2.846950 ACTAGCCAGTCCTTTGGGTAT 58.153 47.619 4.61 0.00 46.74 2.73
563 569 2.505819 ACTAGCCAGTCCTTTGGGTATG 59.494 50.000 4.61 2.96 46.74 2.39
564 570 1.668826 AGCCAGTCCTTTGGGTATGA 58.331 50.000 0.00 0.00 46.57 2.15
565 571 1.992557 AGCCAGTCCTTTGGGTATGAA 59.007 47.619 0.00 0.00 46.57 2.57
566 572 2.378547 AGCCAGTCCTTTGGGTATGAAA 59.621 45.455 0.00 0.00 46.57 2.69
567 573 2.492088 GCCAGTCCTTTGGGTATGAAAC 59.508 50.000 0.00 0.00 38.72 2.78
568 574 6.882412 AGCCAGTCCTTTGGGTATGAAACC 62.882 50.000 0.00 0.00 46.57 3.27
589 595 4.073293 CCATTTGGGCGAGAATAGTACT 57.927 45.455 0.00 0.00 0.00 2.73
590 596 5.209818 CCATTTGGGCGAGAATAGTACTA 57.790 43.478 4.77 4.77 0.00 1.82
591 597 5.230942 CCATTTGGGCGAGAATAGTACTAG 58.769 45.833 8.85 0.00 0.00 2.57
592 598 4.931661 TTTGGGCGAGAATAGTACTAGG 57.068 45.455 8.85 0.00 0.00 3.02
593 599 3.870538 TGGGCGAGAATAGTACTAGGA 57.129 47.619 8.85 0.00 0.00 2.94
594 600 4.383931 TGGGCGAGAATAGTACTAGGAT 57.616 45.455 8.85 0.00 0.00 3.24
595 601 4.079970 TGGGCGAGAATAGTACTAGGATG 58.920 47.826 8.85 0.00 0.00 3.51
596 602 3.444388 GGGCGAGAATAGTACTAGGATGG 59.556 52.174 8.85 0.00 0.00 3.51
597 603 3.444388 GGCGAGAATAGTACTAGGATGGG 59.556 52.174 8.85 0.00 0.00 4.00
598 604 4.080687 GCGAGAATAGTACTAGGATGGGT 58.919 47.826 8.85 0.00 0.00 4.51
599 605 4.082679 GCGAGAATAGTACTAGGATGGGTG 60.083 50.000 8.85 0.00 0.00 4.61
600 606 5.314529 CGAGAATAGTACTAGGATGGGTGA 58.685 45.833 8.85 0.00 0.00 4.02
601 607 5.181622 CGAGAATAGTACTAGGATGGGTGAC 59.818 48.000 8.85 0.00 0.00 3.67
613 619 4.234673 GGTGACCTCCTGGGAAGT 57.765 61.111 0.00 0.00 38.76 3.01
614 620 1.984020 GGTGACCTCCTGGGAAGTC 59.016 63.158 10.52 10.52 36.44 3.01
615 621 1.554583 GGTGACCTCCTGGGAAGTCC 61.555 65.000 13.79 6.97 35.38 3.85
616 622 0.545548 GTGACCTCCTGGGAAGTCCT 60.546 60.000 13.79 0.00 35.38 3.85
617 623 0.252284 TGACCTCCTGGGAAGTCCTC 60.252 60.000 13.79 0.00 35.38 3.71
618 624 1.305381 ACCTCCTGGGAAGTCCTCG 60.305 63.158 0.00 0.00 38.76 4.63
619 625 1.305381 CCTCCTGGGAAGTCCTCGT 60.305 63.158 0.00 0.00 37.23 4.18
620 626 1.608717 CCTCCTGGGAAGTCCTCGTG 61.609 65.000 0.00 0.00 37.23 4.35
621 627 0.612174 CTCCTGGGAAGTCCTCGTGA 60.612 60.000 0.00 0.00 36.20 4.35
622 628 0.178944 TCCTGGGAAGTCCTCGTGAA 60.179 55.000 0.00 0.00 36.20 3.18
623 629 0.685097 CCTGGGAAGTCCTCGTGAAA 59.315 55.000 0.00 0.00 36.20 2.69
624 630 1.338200 CCTGGGAAGTCCTCGTGAAAG 60.338 57.143 0.00 0.00 36.20 2.62
625 631 0.685097 TGGGAAGTCCTCGTGAAAGG 59.315 55.000 0.00 0.00 37.81 3.11
626 632 0.036294 GGGAAGTCCTCGTGAAAGGG 60.036 60.000 0.00 0.00 37.02 3.95
627 633 0.685660 GGAAGTCCTCGTGAAAGGGT 59.314 55.000 0.00 0.00 37.02 4.34
628 634 1.071857 GGAAGTCCTCGTGAAAGGGTT 59.928 52.381 0.00 0.00 37.02 4.11
629 635 2.486727 GGAAGTCCTCGTGAAAGGGTTT 60.487 50.000 0.00 0.00 37.02 3.27
630 636 2.545537 AGTCCTCGTGAAAGGGTTTC 57.454 50.000 0.00 0.00 40.08 2.78
631 637 1.766496 AGTCCTCGTGAAAGGGTTTCA 59.234 47.619 0.00 0.00 46.68 2.69
641 647 5.975988 TGAAAGGGTTTCATATCTAGCCT 57.024 39.130 0.00 0.00 44.21 4.58
643 649 6.827727 TGAAAGGGTTTCATATCTAGCCTAC 58.172 40.000 0.00 0.00 44.21 3.18
644 650 5.827326 AAGGGTTTCATATCTAGCCTACC 57.173 43.478 0.00 0.00 38.75 3.18
645 651 4.168883 AGGGTTTCATATCTAGCCTACCC 58.831 47.826 0.00 0.00 43.42 3.69
646 652 3.263681 GGGTTTCATATCTAGCCTACCCC 59.736 52.174 0.00 0.00 38.39 4.95
647 653 3.908103 GGTTTCATATCTAGCCTACCCCA 59.092 47.826 0.00 0.00 0.00 4.96
648 654 4.349930 GGTTTCATATCTAGCCTACCCCAA 59.650 45.833 0.00 0.00 0.00 4.12
649 655 5.306394 GTTTCATATCTAGCCTACCCCAAC 58.694 45.833 0.00 0.00 0.00 3.77
650 656 4.487282 TCATATCTAGCCTACCCCAACT 57.513 45.455 0.00 0.00 0.00 3.16
651 657 4.827789 TCATATCTAGCCTACCCCAACTT 58.172 43.478 0.00 0.00 0.00 2.66
652 658 4.593206 TCATATCTAGCCTACCCCAACTTG 59.407 45.833 0.00 0.00 0.00 3.16
653 659 2.337359 TCTAGCCTACCCCAACTTGT 57.663 50.000 0.00 0.00 0.00 3.16
654 660 2.627933 TCTAGCCTACCCCAACTTGTT 58.372 47.619 0.00 0.00 0.00 2.83
655 661 2.983898 TCTAGCCTACCCCAACTTGTTT 59.016 45.455 0.00 0.00 0.00 2.83
656 662 1.995376 AGCCTACCCCAACTTGTTTG 58.005 50.000 0.00 0.00 34.63 2.93
676 682 4.717279 TGGGACAAAAGGCTTAGTAAGT 57.283 40.909 11.51 0.00 31.92 2.24
677 683 5.829062 TGGGACAAAAGGCTTAGTAAGTA 57.171 39.130 11.51 0.00 31.92 2.24
678 684 6.190346 TGGGACAAAAGGCTTAGTAAGTAA 57.810 37.500 11.51 0.00 31.92 2.24
679 685 6.235664 TGGGACAAAAGGCTTAGTAAGTAAG 58.764 40.000 11.51 0.00 37.30 2.34
680 686 6.183361 TGGGACAAAAGGCTTAGTAAGTAAGT 60.183 38.462 11.51 2.81 36.83 2.24
681 687 7.016465 TGGGACAAAAGGCTTAGTAAGTAAGTA 59.984 37.037 11.51 0.00 36.83 2.24
682 688 7.879677 GGGACAAAAGGCTTAGTAAGTAAGTAA 59.120 37.037 11.51 0.00 40.47 2.24
683 689 8.933807 GGACAAAAGGCTTAGTAAGTAAGTAAG 58.066 37.037 11.51 0.50 42.04 2.34
684 690 9.486497 GACAAAAGGCTTAGTAAGTAAGTAAGT 57.514 33.333 11.51 3.37 41.44 2.24
901 907 4.100189 GCAGGGCTAAACTTCTATCTGAGA 59.900 45.833 0.00 0.00 0.00 3.27
930 936 1.136828 CAGGATCCGGGATGGGTTAA 58.863 55.000 15.70 0.00 38.76 2.01
967 974 3.785887 AGCTTAATCACAATACCCCCTGA 59.214 43.478 0.00 0.00 0.00 3.86
982 989 1.916181 CCCTGAAAGACATACCTGGGT 59.084 52.381 0.00 0.00 34.07 4.51
1110 1117 1.207089 CCCTACTTGGTCGATGAAGCA 59.793 52.381 6.35 0.00 0.00 3.91
1560 1603 6.874278 TTGGGACTCTCTATTTCATCTTCA 57.126 37.500 0.00 0.00 0.00 3.02
1722 1765 0.953471 TATGGTTATGCCGGCGATGC 60.953 55.000 23.90 12.11 41.21 3.91
1750 1793 6.463755 GGTGGATTTGGTAATTGGTTTGTTCT 60.464 38.462 0.00 0.00 0.00 3.01
1865 1908 2.846827 AGCCTTAGTAGAAGTGGGCAAT 59.153 45.455 0.00 0.00 41.71 3.56
1903 1946 3.005578 GTCTATCCGCCCTTAAGTGGTAG 59.994 52.174 0.97 5.66 38.61 3.18
2266 2311 5.995282 TGCCTGGATTTGGTATTATTAGTCG 59.005 40.000 0.00 0.00 0.00 4.18
2292 2337 7.611213 ATCGTATCGACCTTTTCAAGAAAAT 57.389 32.000 8.28 0.00 39.18 1.82
2391 2436 4.634012 ATGTTTACTGTGGGCTTAGACA 57.366 40.909 0.00 0.00 0.00 3.41
2401 2446 2.169561 TGGGCTTAGACATTGATACGCA 59.830 45.455 0.00 0.00 0.00 5.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
178 179 2.224892 GGGGCTGGAAGAGAAGAACTTT 60.225 50.000 0.00 0.00 34.07 2.66
308 314 7.071572 AGGCGGAGTTATATTAAGGGAAACTTA 59.928 37.037 0.00 0.00 40.64 2.24
309 315 6.060136 GGCGGAGTTATATTAAGGGAAACTT 58.940 40.000 0.00 0.00 43.28 2.66
310 316 5.368816 AGGCGGAGTTATATTAAGGGAAACT 59.631 40.000 0.00 0.00 33.26 2.66
311 317 5.618236 AGGCGGAGTTATATTAAGGGAAAC 58.382 41.667 0.00 0.00 0.00 2.78
312 318 5.899631 AGGCGGAGTTATATTAAGGGAAA 57.100 39.130 0.00 0.00 0.00 3.13
313 319 6.499350 ACATAGGCGGAGTTATATTAAGGGAA 59.501 38.462 0.00 0.00 0.00 3.97
314 320 6.021030 ACATAGGCGGAGTTATATTAAGGGA 58.979 40.000 0.00 0.00 0.00 4.20
315 321 6.154706 AGACATAGGCGGAGTTATATTAAGGG 59.845 42.308 0.00 0.00 0.00 3.95
316 322 7.171630 AGACATAGGCGGAGTTATATTAAGG 57.828 40.000 0.00 0.00 0.00 2.69
317 323 8.524487 AGAAGACATAGGCGGAGTTATATTAAG 58.476 37.037 0.00 0.00 0.00 1.85
318 324 8.418597 AGAAGACATAGGCGGAGTTATATTAA 57.581 34.615 0.00 0.00 0.00 1.40
319 325 9.175312 CTAGAAGACATAGGCGGAGTTATATTA 57.825 37.037 0.00 0.00 0.00 0.98
320 326 6.919775 AGAAGACATAGGCGGAGTTATATT 57.080 37.500 0.00 0.00 0.00 1.28
321 327 6.603997 CCTAGAAGACATAGGCGGAGTTATAT 59.396 42.308 0.00 0.00 33.76 0.86
322 328 5.944599 CCTAGAAGACATAGGCGGAGTTATA 59.055 44.000 0.00 0.00 33.76 0.98
323 329 4.767928 CCTAGAAGACATAGGCGGAGTTAT 59.232 45.833 0.00 0.00 33.76 1.89
324 330 4.142790 CCTAGAAGACATAGGCGGAGTTA 58.857 47.826 0.00 0.00 33.76 2.24
325 331 2.959707 CCTAGAAGACATAGGCGGAGTT 59.040 50.000 0.00 0.00 33.76 3.01
326 332 2.588620 CCTAGAAGACATAGGCGGAGT 58.411 52.381 0.00 0.00 33.76 3.85
332 338 4.464069 GGCTATGCCTAGAAGACATAGG 57.536 50.000 16.76 0.00 46.69 2.57
345 351 2.203209 CTTGGGACCGGCTATGCC 60.203 66.667 0.00 0.00 46.75 4.40
346 352 2.902343 GCTTGGGACCGGCTATGC 60.902 66.667 0.00 0.00 0.00 3.14
347 353 2.203209 GGCTTGGGACCGGCTATG 60.203 66.667 0.00 0.00 0.00 2.23
348 354 3.489513 GGGCTTGGGACCGGCTAT 61.490 66.667 0.00 0.00 0.00 2.97
358 364 1.077716 CTCCTTTACCCGGGCTTGG 60.078 63.158 24.08 17.99 0.00 3.61
359 365 1.077716 CCTCCTTTACCCGGGCTTG 60.078 63.158 24.08 8.51 0.00 4.01
360 366 1.229723 TCCTCCTTTACCCGGGCTT 60.230 57.895 24.08 4.08 0.00 4.35
361 367 1.689582 CTCCTCCTTTACCCGGGCT 60.690 63.158 24.08 10.93 0.00 5.19
362 368 2.743179 CCTCCTCCTTTACCCGGGC 61.743 68.421 24.08 0.00 0.00 6.13
363 369 2.070650 CCCTCCTCCTTTACCCGGG 61.071 68.421 22.25 22.25 0.00 5.73
364 370 0.912968 AACCCTCCTCCTTTACCCGG 60.913 60.000 0.00 0.00 0.00 5.73
365 371 0.252197 CAACCCTCCTCCTTTACCCG 59.748 60.000 0.00 0.00 0.00 5.28
366 372 1.004394 CACAACCCTCCTCCTTTACCC 59.996 57.143 0.00 0.00 0.00 3.69
367 373 1.982958 TCACAACCCTCCTCCTTTACC 59.017 52.381 0.00 0.00 0.00 2.85
368 374 4.141688 CCTATCACAACCCTCCTCCTTTAC 60.142 50.000 0.00 0.00 0.00 2.01
369 375 4.037927 CCTATCACAACCCTCCTCCTTTA 58.962 47.826 0.00 0.00 0.00 1.85
370 376 2.846827 CCTATCACAACCCTCCTCCTTT 59.153 50.000 0.00 0.00 0.00 3.11
371 377 2.482494 CCTATCACAACCCTCCTCCTT 58.518 52.381 0.00 0.00 0.00 3.36
372 378 1.972207 GCCTATCACAACCCTCCTCCT 60.972 57.143 0.00 0.00 0.00 3.69
373 379 0.470341 GCCTATCACAACCCTCCTCC 59.530 60.000 0.00 0.00 0.00 4.30
374 380 1.501582 AGCCTATCACAACCCTCCTC 58.498 55.000 0.00 0.00 0.00 3.71
375 381 1.561542 CAAGCCTATCACAACCCTCCT 59.438 52.381 0.00 0.00 0.00 3.69
376 382 1.408822 CCAAGCCTATCACAACCCTCC 60.409 57.143 0.00 0.00 0.00 4.30
377 383 2.019156 GCCAAGCCTATCACAACCCTC 61.019 57.143 0.00 0.00 0.00 4.30
378 384 0.034089 GCCAAGCCTATCACAACCCT 60.034 55.000 0.00 0.00 0.00 4.34
379 385 1.376609 CGCCAAGCCTATCACAACCC 61.377 60.000 0.00 0.00 0.00 4.11
380 386 0.392461 TCGCCAAGCCTATCACAACC 60.392 55.000 0.00 0.00 0.00 3.77
381 387 1.009829 CTCGCCAAGCCTATCACAAC 58.990 55.000 0.00 0.00 0.00 3.32
382 388 0.744414 GCTCGCCAAGCCTATCACAA 60.744 55.000 0.00 0.00 45.92 3.33
383 389 1.153369 GCTCGCCAAGCCTATCACA 60.153 57.895 0.00 0.00 45.92 3.58
384 390 3.724494 GCTCGCCAAGCCTATCAC 58.276 61.111 0.00 0.00 45.92 3.06
394 400 0.800012 GATTTTACGTTGGCTCGCCA 59.200 50.000 6.52 6.52 45.63 5.69
395 401 1.084289 AGATTTTACGTTGGCTCGCC 58.916 50.000 0.00 0.00 0.00 5.54
396 402 2.285660 GCTAGATTTTACGTTGGCTCGC 60.286 50.000 0.00 0.00 0.00 5.03
397 403 2.284417 GGCTAGATTTTACGTTGGCTCG 59.716 50.000 0.00 1.70 0.00 5.03
398 404 3.267483 TGGCTAGATTTTACGTTGGCTC 58.733 45.455 0.00 0.00 0.00 4.70
399 405 3.270877 CTGGCTAGATTTTACGTTGGCT 58.729 45.455 0.00 0.00 0.00 4.75
400 406 3.007635 ACTGGCTAGATTTTACGTTGGC 58.992 45.455 3.17 0.00 0.00 4.52
401 407 3.621715 GGACTGGCTAGATTTTACGTTGG 59.378 47.826 3.17 0.00 0.00 3.77
402 408 3.621715 GGGACTGGCTAGATTTTACGTTG 59.378 47.826 3.17 0.00 0.00 4.10
403 409 3.262405 TGGGACTGGCTAGATTTTACGTT 59.738 43.478 3.17 0.00 0.00 3.99
404 410 2.835764 TGGGACTGGCTAGATTTTACGT 59.164 45.455 3.17 0.00 0.00 3.57
405 411 3.536956 TGGGACTGGCTAGATTTTACG 57.463 47.619 3.17 0.00 0.00 3.18
406 412 4.137543 CCATGGGACTGGCTAGATTTTAC 58.862 47.826 3.17 0.00 0.00 2.01
407 413 3.138283 CCCATGGGACTGGCTAGATTTTA 59.862 47.826 28.27 0.00 37.50 1.52
408 414 2.091665 CCCATGGGACTGGCTAGATTTT 60.092 50.000 28.27 0.00 37.50 1.82
409 415 1.496429 CCCATGGGACTGGCTAGATTT 59.504 52.381 28.27 0.00 37.50 2.17
410 416 1.143813 CCCATGGGACTGGCTAGATT 58.856 55.000 28.27 0.00 37.50 2.40
411 417 0.029681 ACCCATGGGACTGGCTAGAT 60.030 55.000 38.07 7.69 38.96 1.98
412 418 0.639943 TACCCATGGGACTGGCTAGA 59.360 55.000 38.07 7.33 38.96 2.43
413 419 1.349026 CATACCCATGGGACTGGCTAG 59.651 57.143 38.07 13.17 38.96 3.42
414 420 1.061735 TCATACCCATGGGACTGGCTA 60.062 52.381 38.07 18.16 38.96 3.93
415 421 0.327480 TCATACCCATGGGACTGGCT 60.327 55.000 38.07 16.38 38.96 4.75
416 422 0.550914 TTCATACCCATGGGACTGGC 59.449 55.000 38.07 0.00 38.96 4.85
417 423 2.654863 GTTTCATACCCATGGGACTGG 58.345 52.381 38.07 21.65 38.96 4.00
418 424 2.654863 GGTTTCATACCCATGGGACTG 58.345 52.381 38.07 29.36 41.43 3.51
428 434 3.013921 TCGCTCAAATGGGTTTCATACC 58.986 45.455 0.00 0.00 46.99 2.73
429 435 3.938963 TCTCGCTCAAATGGGTTTCATAC 59.061 43.478 0.00 0.00 34.44 2.39
430 436 4.191544 CTCTCGCTCAAATGGGTTTCATA 58.808 43.478 0.00 0.00 34.44 2.15
431 437 3.012518 CTCTCGCTCAAATGGGTTTCAT 58.987 45.455 0.00 0.00 37.79 2.57
432 438 2.224523 ACTCTCGCTCAAATGGGTTTCA 60.225 45.455 0.00 0.00 0.00 2.69
433 439 2.427506 ACTCTCGCTCAAATGGGTTTC 58.572 47.619 0.00 0.00 0.00 2.78
434 440 2.568623 ACTCTCGCTCAAATGGGTTT 57.431 45.000 0.00 0.00 0.00 3.27
435 441 2.567615 ACTACTCTCGCTCAAATGGGTT 59.432 45.455 0.00 0.00 0.00 4.11
436 442 2.180276 ACTACTCTCGCTCAAATGGGT 58.820 47.619 0.00 0.00 0.00 4.51
437 443 2.969628 ACTACTCTCGCTCAAATGGG 57.030 50.000 0.00 0.00 0.00 4.00
438 444 4.640789 AGTACTACTCTCGCTCAAATGG 57.359 45.455 0.00 0.00 0.00 3.16
439 445 5.527951 TCCTAGTACTACTCTCGCTCAAATG 59.472 44.000 0.00 0.00 0.00 2.32
440 446 5.682659 TCCTAGTACTACTCTCGCTCAAAT 58.317 41.667 0.00 0.00 0.00 2.32
441 447 5.095145 TCCTAGTACTACTCTCGCTCAAA 57.905 43.478 0.00 0.00 0.00 2.69
442 448 4.750021 TCCTAGTACTACTCTCGCTCAA 57.250 45.455 0.00 0.00 0.00 3.02
443 449 4.503469 CCATCCTAGTACTACTCTCGCTCA 60.503 50.000 0.00 0.00 0.00 4.26
444 450 3.998341 CCATCCTAGTACTACTCTCGCTC 59.002 52.174 0.00 0.00 0.00 5.03
445 451 3.244630 CCCATCCTAGTACTACTCTCGCT 60.245 52.174 0.00 0.00 0.00 4.93
446 452 3.075884 CCCATCCTAGTACTACTCTCGC 58.924 54.545 0.00 0.00 0.00 5.03
447 453 4.066490 CACCCATCCTAGTACTACTCTCG 58.934 52.174 0.00 0.00 0.00 4.04
448 454 5.065235 GTCACCCATCCTAGTACTACTCTC 58.935 50.000 0.00 0.00 0.00 3.20
449 455 4.141205 GGTCACCCATCCTAGTACTACTCT 60.141 50.000 0.00 0.00 0.00 3.24
450 456 4.141205 AGGTCACCCATCCTAGTACTACTC 60.141 50.000 0.00 0.00 31.66 2.59
451 457 3.792684 AGGTCACCCATCCTAGTACTACT 59.207 47.826 0.00 0.00 31.66 2.57
452 458 4.143543 GAGGTCACCCATCCTAGTACTAC 58.856 52.174 0.00 0.00 33.83 2.73
453 459 3.139770 GGAGGTCACCCATCCTAGTACTA 59.860 52.174 1.89 1.89 33.83 1.82
454 460 2.091222 GGAGGTCACCCATCCTAGTACT 60.091 54.545 0.00 0.00 33.83 2.73
455 461 2.091222 AGGAGGTCACCCATCCTAGTAC 60.091 54.545 2.60 0.00 36.91 2.73
456 462 2.091278 CAGGAGGTCACCCATCCTAGTA 60.091 54.545 4.27 0.00 36.69 1.82
457 463 1.019650 AGGAGGTCACCCATCCTAGT 58.980 55.000 2.60 0.00 36.91 2.57
458 464 1.418334 CAGGAGGTCACCCATCCTAG 58.582 60.000 4.27 0.00 36.69 3.02
459 465 0.031111 CCAGGAGGTCACCCATCCTA 60.031 60.000 4.27 0.00 36.69 2.94
460 466 1.307343 CCAGGAGGTCACCCATCCT 60.307 63.158 0.00 0.00 38.30 3.24
461 467 2.378634 CCCAGGAGGTCACCCATCC 61.379 68.421 0.00 0.00 0.00 3.51
462 468 0.914417 TTCCCAGGAGGTCACCCATC 60.914 60.000 0.00 0.00 36.75 3.51
463 469 0.916358 CTTCCCAGGAGGTCACCCAT 60.916 60.000 0.00 0.00 36.75 4.00
464 470 1.538876 CTTCCCAGGAGGTCACCCA 60.539 63.158 0.00 0.00 36.75 4.51
465 471 1.539124 ACTTCCCAGGAGGTCACCC 60.539 63.158 0.00 0.00 36.75 4.61
466 472 1.984020 GACTTCCCAGGAGGTCACC 59.016 63.158 20.66 0.00 46.32 4.02
469 475 0.615850 CAAGGACTTCCCAGGAGGTC 59.384 60.000 18.15 18.15 46.33 3.85
470 476 0.104409 ACAAGGACTTCCCAGGAGGT 60.104 55.000 0.31 0.31 37.15 3.85
471 477 0.326264 CACAAGGACTTCCCAGGAGG 59.674 60.000 0.00 0.00 37.41 4.30
472 478 1.352083 TCACAAGGACTTCCCAGGAG 58.648 55.000 0.00 0.00 37.41 3.69
473 479 1.814429 TTCACAAGGACTTCCCAGGA 58.186 50.000 0.00 0.00 37.41 3.86
474 480 2.508526 CTTTCACAAGGACTTCCCAGG 58.491 52.381 0.00 0.00 37.41 4.45
490 496 6.890268 ACAACCCTTAGATATGAAACCCTTTC 59.110 38.462 0.00 0.00 40.08 2.62
491 497 6.663523 CACAACCCTTAGATATGAAACCCTTT 59.336 38.462 0.00 0.00 0.00 3.11
492 498 6.011981 TCACAACCCTTAGATATGAAACCCTT 60.012 38.462 0.00 0.00 0.00 3.95
493 499 5.491078 TCACAACCCTTAGATATGAAACCCT 59.509 40.000 0.00 0.00 0.00 4.34
494 500 5.751586 TCACAACCCTTAGATATGAAACCC 58.248 41.667 0.00 0.00 0.00 4.11
495 501 7.661847 CCTATCACAACCCTTAGATATGAAACC 59.338 40.741 0.00 0.00 0.00 3.27
496 502 7.173390 GCCTATCACAACCCTTAGATATGAAAC 59.827 40.741 0.00 0.00 0.00 2.78
497 503 7.072454 AGCCTATCACAACCCTTAGATATGAAA 59.928 37.037 0.00 0.00 0.00 2.69
498 504 6.558775 AGCCTATCACAACCCTTAGATATGAA 59.441 38.462 0.00 0.00 0.00 2.57
499 505 6.084738 AGCCTATCACAACCCTTAGATATGA 58.915 40.000 0.00 0.00 0.00 2.15
500 506 6.365970 AGCCTATCACAACCCTTAGATATG 57.634 41.667 0.00 0.00 0.00 1.78
501 507 6.240002 CCAAGCCTATCACAACCCTTAGATAT 60.240 42.308 0.00 0.00 0.00 1.63
502 508 5.071788 CCAAGCCTATCACAACCCTTAGATA 59.928 44.000 0.00 0.00 0.00 1.98
503 509 4.141390 CCAAGCCTATCACAACCCTTAGAT 60.141 45.833 0.00 0.00 0.00 1.98
504 510 3.199946 CCAAGCCTATCACAACCCTTAGA 59.800 47.826 0.00 0.00 0.00 2.10
505 511 3.545703 CCAAGCCTATCACAACCCTTAG 58.454 50.000 0.00 0.00 0.00 2.18
506 512 2.356741 GCCAAGCCTATCACAACCCTTA 60.357 50.000 0.00 0.00 0.00 2.69
507 513 1.616994 GCCAAGCCTATCACAACCCTT 60.617 52.381 0.00 0.00 0.00 3.95
508 514 0.034089 GCCAAGCCTATCACAACCCT 60.034 55.000 0.00 0.00 0.00 4.34
509 515 1.376609 CGCCAAGCCTATCACAACCC 61.377 60.000 0.00 0.00 0.00 4.11
510 516 0.392461 TCGCCAAGCCTATCACAACC 60.392 55.000 0.00 0.00 0.00 3.77
511 517 1.009829 CTCGCCAAGCCTATCACAAC 58.990 55.000 0.00 0.00 0.00 3.32
512 518 0.744414 GCTCGCCAAGCCTATCACAA 60.744 55.000 0.00 0.00 45.92 3.33
513 519 1.153369 GCTCGCCAAGCCTATCACA 60.153 57.895 0.00 0.00 45.92 3.58
514 520 3.724494 GCTCGCCAAGCCTATCAC 58.276 61.111 0.00 0.00 45.92 3.06
524 530 0.308376 GTTTTTACGTTGGCTCGCCA 59.692 50.000 6.52 6.52 45.63 5.69
525 531 0.589708 AGTTTTTACGTTGGCTCGCC 59.410 50.000 0.00 0.00 0.00 5.54
526 532 2.723923 GCTAGTTTTTACGTTGGCTCGC 60.724 50.000 0.00 0.00 0.00 5.03
527 533 2.159747 GGCTAGTTTTTACGTTGGCTCG 60.160 50.000 0.00 1.70 0.00 5.03
528 534 2.809696 TGGCTAGTTTTTACGTTGGCTC 59.190 45.455 0.00 0.00 0.00 4.70
529 535 2.812011 CTGGCTAGTTTTTACGTTGGCT 59.188 45.455 0.00 0.00 0.00 4.75
530 536 2.551032 ACTGGCTAGTTTTTACGTTGGC 59.449 45.455 0.00 0.00 31.66 4.52
531 537 3.187842 GGACTGGCTAGTTTTTACGTTGG 59.812 47.826 3.47 0.00 37.25 3.77
532 538 4.062991 AGGACTGGCTAGTTTTTACGTTG 58.937 43.478 3.47 0.00 37.25 4.10
533 539 4.347360 AGGACTGGCTAGTTTTTACGTT 57.653 40.909 3.47 0.00 37.25 3.99
534 540 4.347360 AAGGACTGGCTAGTTTTTACGT 57.653 40.909 3.47 0.00 37.25 3.57
535 541 4.083484 CCAAAGGACTGGCTAGTTTTTACG 60.083 45.833 3.47 0.00 37.25 3.18
536 542 4.217767 CCCAAAGGACTGGCTAGTTTTTAC 59.782 45.833 3.47 0.00 37.25 2.01
537 543 4.141111 ACCCAAAGGACTGGCTAGTTTTTA 60.141 41.667 3.47 0.00 37.25 1.52
538 544 3.230976 CCCAAAGGACTGGCTAGTTTTT 58.769 45.455 3.47 6.04 37.25 1.94
539 545 2.177016 ACCCAAAGGACTGGCTAGTTTT 59.823 45.455 3.47 0.00 37.25 2.43
540 546 1.780919 ACCCAAAGGACTGGCTAGTTT 59.219 47.619 3.47 0.00 37.25 2.66
541 547 1.446016 ACCCAAAGGACTGGCTAGTT 58.554 50.000 3.47 0.00 37.25 2.24
542 548 2.337359 TACCCAAAGGACTGGCTAGT 57.663 50.000 0.69 0.69 40.66 2.57
543 549 2.771943 TCATACCCAAAGGACTGGCTAG 59.228 50.000 0.00 0.00 34.88 3.42
544 550 2.840511 TCATACCCAAAGGACTGGCTA 58.159 47.619 0.00 0.00 34.88 3.93
545 551 1.668826 TCATACCCAAAGGACTGGCT 58.331 50.000 0.00 0.00 34.88 4.75
546 552 2.492088 GTTTCATACCCAAAGGACTGGC 59.508 50.000 0.00 0.00 34.88 4.85
547 553 3.089284 GGTTTCATACCCAAAGGACTGG 58.911 50.000 0.00 0.00 41.43 4.00
568 574 4.073293 AGTACTATTCTCGCCCAAATGG 57.927 45.455 0.00 0.00 37.09 3.16
569 575 5.010719 TCCTAGTACTATTCTCGCCCAAATG 59.989 44.000 2.33 0.00 0.00 2.32
570 576 5.145564 TCCTAGTACTATTCTCGCCCAAAT 58.854 41.667 2.33 0.00 0.00 2.32
571 577 4.539726 TCCTAGTACTATTCTCGCCCAAA 58.460 43.478 2.33 0.00 0.00 3.28
572 578 4.174704 TCCTAGTACTATTCTCGCCCAA 57.825 45.455 2.33 0.00 0.00 4.12
573 579 3.870538 TCCTAGTACTATTCTCGCCCA 57.129 47.619 2.33 0.00 0.00 5.36
574 580 3.444388 CCATCCTAGTACTATTCTCGCCC 59.556 52.174 2.33 0.00 0.00 6.13
575 581 3.444388 CCCATCCTAGTACTATTCTCGCC 59.556 52.174 2.33 0.00 0.00 5.54
576 582 4.080687 ACCCATCCTAGTACTATTCTCGC 58.919 47.826 2.33 0.00 0.00 5.03
577 583 5.181622 GTCACCCATCCTAGTACTATTCTCG 59.818 48.000 2.33 0.00 0.00 4.04
578 584 5.477637 GGTCACCCATCCTAGTACTATTCTC 59.522 48.000 2.33 0.00 0.00 2.87
579 585 5.136392 AGGTCACCCATCCTAGTACTATTCT 59.864 44.000 2.33 0.00 31.66 2.40
580 586 5.395611 AGGTCACCCATCCTAGTACTATTC 58.604 45.833 2.33 0.00 31.66 1.75
581 587 5.395611 GAGGTCACCCATCCTAGTACTATT 58.604 45.833 2.33 0.00 33.83 1.73
582 588 4.202695 GGAGGTCACCCATCCTAGTACTAT 60.203 50.000 2.33 0.00 33.83 2.12
583 589 3.139770 GGAGGTCACCCATCCTAGTACTA 59.860 52.174 1.89 1.89 33.83 1.82
584 590 2.091222 GGAGGTCACCCATCCTAGTACT 60.091 54.545 0.00 0.00 33.83 2.73
585 591 2.091222 AGGAGGTCACCCATCCTAGTAC 60.091 54.545 2.60 0.00 36.91 2.73
586 592 2.091278 CAGGAGGTCACCCATCCTAGTA 60.091 54.545 4.27 0.00 36.69 1.82
587 593 1.019650 AGGAGGTCACCCATCCTAGT 58.980 55.000 2.60 0.00 36.91 2.57
588 594 1.418334 CAGGAGGTCACCCATCCTAG 58.582 60.000 4.27 0.00 36.69 3.02
589 595 0.031111 CCAGGAGGTCACCCATCCTA 60.031 60.000 4.27 0.00 36.69 2.94
590 596 1.307343 CCAGGAGGTCACCCATCCT 60.307 63.158 0.00 0.00 38.30 3.24
591 597 2.378634 CCCAGGAGGTCACCCATCC 61.379 68.421 0.00 0.00 0.00 3.51
592 598 0.914417 TTCCCAGGAGGTCACCCATC 60.914 60.000 0.00 0.00 36.75 3.51
593 599 0.916358 CTTCCCAGGAGGTCACCCAT 60.916 60.000 0.00 0.00 36.75 4.00
594 600 1.538876 CTTCCCAGGAGGTCACCCA 60.539 63.158 0.00 0.00 36.75 4.51
595 601 1.539124 ACTTCCCAGGAGGTCACCC 60.539 63.158 0.00 0.00 36.75 4.61
596 602 1.984020 GACTTCCCAGGAGGTCACC 59.016 63.158 20.66 0.00 46.32 4.02
599 605 1.324005 CGAGGACTTCCCAGGAGGTC 61.324 65.000 18.15 18.15 46.33 3.85
600 606 1.305381 CGAGGACTTCCCAGGAGGT 60.305 63.158 0.31 0.31 37.15 3.85
601 607 1.305381 ACGAGGACTTCCCAGGAGG 60.305 63.158 0.00 0.00 37.41 4.30
602 608 0.612174 TCACGAGGACTTCCCAGGAG 60.612 60.000 0.00 0.00 37.41 3.69
603 609 0.178944 TTCACGAGGACTTCCCAGGA 60.179 55.000 0.00 0.00 37.41 3.86
604 610 0.685097 TTTCACGAGGACTTCCCAGG 59.315 55.000 0.00 0.00 37.41 4.45
605 611 1.338200 CCTTTCACGAGGACTTCCCAG 60.338 57.143 0.00 0.00 39.25 4.45
606 612 0.685097 CCTTTCACGAGGACTTCCCA 59.315 55.000 0.00 0.00 39.25 4.37
607 613 0.036294 CCCTTTCACGAGGACTTCCC 60.036 60.000 0.00 0.00 39.25 3.97
608 614 0.685660 ACCCTTTCACGAGGACTTCC 59.314 55.000 0.00 0.00 39.25 3.46
609 615 2.545537 AACCCTTTCACGAGGACTTC 57.454 50.000 0.00 0.00 39.25 3.01
610 616 2.171870 TGAAACCCTTTCACGAGGACTT 59.828 45.455 0.00 0.00 44.21 3.01
611 617 1.766496 TGAAACCCTTTCACGAGGACT 59.234 47.619 0.00 0.00 44.21 3.85
612 618 2.249844 TGAAACCCTTTCACGAGGAC 57.750 50.000 0.00 0.00 44.21 3.85
620 626 6.231951 GGTAGGCTAGATATGAAACCCTTTC 58.768 44.000 0.00 0.00 40.08 2.62
621 627 5.073280 GGGTAGGCTAGATATGAAACCCTTT 59.927 44.000 8.73 0.00 41.75 3.11
622 628 4.597940 GGGTAGGCTAGATATGAAACCCTT 59.402 45.833 8.73 0.00 41.75 3.95
623 629 4.168883 GGGTAGGCTAGATATGAAACCCT 58.831 47.826 8.73 0.00 41.75 4.34
624 630 3.263681 GGGGTAGGCTAGATATGAAACCC 59.736 52.174 7.65 7.65 43.82 4.11
625 631 3.908103 TGGGGTAGGCTAGATATGAAACC 59.092 47.826 0.00 0.00 0.00 3.27
626 632 5.071923 AGTTGGGGTAGGCTAGATATGAAAC 59.928 44.000 0.00 0.00 0.00 2.78
627 633 5.224441 AGTTGGGGTAGGCTAGATATGAAA 58.776 41.667 0.00 0.00 0.00 2.69
628 634 4.827789 AGTTGGGGTAGGCTAGATATGAA 58.172 43.478 0.00 0.00 0.00 2.57
629 635 4.487282 AGTTGGGGTAGGCTAGATATGA 57.513 45.455 0.00 0.00 0.00 2.15
630 636 4.348168 ACAAGTTGGGGTAGGCTAGATATG 59.652 45.833 7.96 0.00 0.00 1.78
631 637 4.567857 ACAAGTTGGGGTAGGCTAGATAT 58.432 43.478 7.96 0.00 0.00 1.63
632 638 4.003584 ACAAGTTGGGGTAGGCTAGATA 57.996 45.455 7.96 0.00 0.00 1.98
633 639 2.846950 ACAAGTTGGGGTAGGCTAGAT 58.153 47.619 7.96 0.00 0.00 1.98
634 640 2.337359 ACAAGTTGGGGTAGGCTAGA 57.663 50.000 7.96 0.00 0.00 2.43
635 641 3.081804 CAAACAAGTTGGGGTAGGCTAG 58.918 50.000 7.96 0.00 33.18 3.42
636 642 3.149005 CAAACAAGTTGGGGTAGGCTA 57.851 47.619 7.96 0.00 33.18 3.93
637 643 1.995376 CAAACAAGTTGGGGTAGGCT 58.005 50.000 7.96 0.00 33.18 4.58
650 656 4.027437 ACTAAGCCTTTTGTCCCAAACAA 58.973 39.130 0.00 0.00 46.11 2.83
651 657 3.637769 ACTAAGCCTTTTGTCCCAAACA 58.362 40.909 0.00 0.00 35.59 2.83
652 658 5.301045 ACTTACTAAGCCTTTTGTCCCAAAC 59.699 40.000 0.00 0.00 0.00 2.93
653 659 5.451354 ACTTACTAAGCCTTTTGTCCCAAA 58.549 37.500 0.00 0.00 0.00 3.28
654 660 5.056553 ACTTACTAAGCCTTTTGTCCCAA 57.943 39.130 0.00 0.00 0.00 4.12
655 661 4.717279 ACTTACTAAGCCTTTTGTCCCA 57.283 40.909 0.00 0.00 0.00 4.37
656 662 6.236409 ACTTACTTACTAAGCCTTTTGTCCC 58.764 40.000 0.00 0.00 36.04 4.46
657 663 8.837788 TTACTTACTTACTAAGCCTTTTGTCC 57.162 34.615 0.00 0.00 36.04 4.02
658 664 9.486497 ACTTACTTACTTACTAAGCCTTTTGTC 57.514 33.333 0.00 0.00 36.04 3.18
790 796 6.056428 ACGAAGCACGAACTAAAAAGATTT 57.944 33.333 10.05 0.00 45.77 2.17
930 936 7.078228 GTGATTAAGCTCGTTTTGAATGAACT 58.922 34.615 0.00 0.00 0.00 3.01
967 974 1.372501 AGCCACCCAGGTATGTCTTT 58.627 50.000 0.00 0.00 40.61 2.52
982 989 3.780294 TCCATTAGGAAGAGCTTAAGCCA 59.220 43.478 23.71 0.00 42.23 4.75
1449 1491 5.600669 AACTTTCCTTATCAAAGAGGGGT 57.399 39.130 0.00 0.00 35.24 4.95
1722 1765 6.210584 ACAAACCAATTACCAAATCCACCTAG 59.789 38.462 0.00 0.00 0.00 3.02
1750 1793 3.106827 TCAGGTGCACCTATCAGAATCA 58.893 45.455 37.27 7.01 46.65 2.57
1865 1908 2.772191 ACTGTCCACCCAGTGCCA 60.772 61.111 0.00 0.00 43.86 4.92
2003 2046 1.167851 CAGGTCCACGCATGTTGAAT 58.832 50.000 0.00 0.00 0.00 2.57
2266 2311 7.515957 TTTCTTGAAAAGGTCGATACGATAC 57.484 36.000 0.00 0.00 46.24 2.24
2292 2337 1.816961 GCCTAGATACCCGAAGACCGA 60.817 57.143 0.00 0.00 41.76 4.69
2391 2436 3.809832 GTGAAGTAGGCATGCGTATCAAT 59.190 43.478 21.86 9.53 0.00 2.57
2401 2446 1.450312 GCTGCGGTGAAGTAGGCAT 60.450 57.895 0.00 0.00 34.49 4.40


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

AutoCloner maintained by Alex Coulton.