Multiple sequence alignment - TraesCS5A01G379900

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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 TraesCS5A01G379900 chr5A 100.000 2504 0 0 1 2504 577791112 577788609 0.000000e+00 4625.0
1 TraesCS5A01G379900 chr5A 87.153 288 35 2 435 721 436888072 436887786 2.400000e-85 326.0
2 TraesCS5A01G379900 chr5A 88.889 81 3 3 2406 2480 577731815 577731735 7.370000e-16 95.3
3 TraesCS5A01G379900 chr5D 89.449 1289 72 35 708 1973 458747447 458746200 0.000000e+00 1568.0
4 TraesCS5A01G379900 chr5D 82.941 340 27 14 1 331 458747897 458747580 6.820000e-71 278.0
5 TraesCS5A01G379900 chr5D 84.906 159 10 6 2242 2399 458745920 458745775 5.580000e-32 148.0
6 TraesCS5A01G379900 chr5D 87.387 111 8 6 2384 2490 458709210 458709102 3.380000e-24 122.0
7 TraesCS5A01G379900 chr5D 90.000 80 3 1 2406 2480 458727143 458727064 5.700000e-17 99.0
8 TraesCS5A01G379900 chr5B 89.405 1227 72 25 737 1940 562371715 562370524 0.000000e+00 1493.0
9 TraesCS5A01G379900 chr5B 82.774 447 38 19 1 426 562372160 562371732 1.830000e-96 363.0
10 TraesCS5A01G379900 chr5B 85.393 178 11 8 2242 2405 562370214 562370038 1.190000e-38 171.0
11 TraesCS5A01G379900 chr5B 87.654 81 4 4 2406 2480 562269072 562268992 3.430000e-14 89.8
12 TraesCS5A01G379900 chr5B 93.333 60 4 0 2421 2480 562369989 562369930 3.430000e-14 89.8
13 TraesCS5A01G379900 chr2A 89.510 286 28 2 433 717 623089755 623089471 6.580000e-96 361.0
14 TraesCS5A01G379900 chr3A 89.855 276 27 1 439 713 21148100 21148375 1.100000e-93 353.0
15 TraesCS5A01G379900 chr3A 84.000 200 23 4 1039 1229 233025337 233025138 1.530000e-42 183.0
16 TraesCS5A01G379900 chr6A 89.091 275 29 1 440 713 494914483 494914757 8.580000e-90 340.0
17 TraesCS5A01G379900 chr6A 88.489 278 31 1 440 716 544677875 544677598 3.990000e-88 335.0
18 TraesCS5A01G379900 chrUn 88.571 280 31 1 439 717 231014490 231014769 3.090000e-89 339.0
19 TraesCS5A01G379900 chrUn 88.448 277 31 1 440 715 351169300 351169576 1.440000e-87 333.0
20 TraesCS5A01G379900 chr7A 88.809 277 30 1 440 715 45687491 45687215 3.090000e-89 339.0
21 TraesCS5A01G379900 chr4A 87.676 284 34 1 440 722 121150613 121150330 1.860000e-86 329.0


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 TraesCS5A01G379900 chr5A 577788609 577791112 2503 True 4625.000000 4625 100.000000 1 2504 1 chr5A.!!$R3 2503
1 TraesCS5A01G379900 chr5D 458745775 458747897 2122 True 664.666667 1568 85.765333 1 2399 3 chr5D.!!$R3 2398
2 TraesCS5A01G379900 chr5B 562369930 562372160 2230 True 529.200000 1493 87.726250 1 2480 4 chr5B.!!$R2 2479

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
905 975 0.105194 TCACTCCTCCCCACAAGACA 60.105 55.0 0.0 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1840 1938 0.097674 GCAGTGCTGGACATTAAGCG 59.902 55.0 8.18 0.0 42.54 4.68 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
131 139 0.390078 TTGCTTTGCCCAATGATGCG 60.390 50.000 0.00 0.00 0.00 4.73
153 161 3.677601 CAGCACACACGATCAAATGATC 58.322 45.455 12.40 12.40 45.60 2.92
162 170 1.224069 ATCAAATGATCTCGCCGGCG 61.224 55.000 42.13 42.13 41.35 6.46
184 192 3.609103 AAAAGAAGCATCACACGACAC 57.391 42.857 0.00 0.00 0.00 3.67
205 213 4.265556 CACAATGTAGTAGTAGCGCTTCAC 59.734 45.833 18.68 9.17 0.00 3.18
206 214 4.158025 ACAATGTAGTAGTAGCGCTTCACT 59.842 41.667 18.68 17.39 0.00 3.41
260 282 2.268802 ACTCGCCTTCAGCTCGTGA 61.269 57.895 1.49 0.00 40.39 4.35
262 284 1.927608 CTCGCCTTCAGCTCGTGAGA 61.928 60.000 0.00 0.00 40.39 3.27
263 285 1.140589 CGCCTTCAGCTCGTGAGAT 59.859 57.895 0.00 0.00 40.84 2.75
264 286 0.382158 CGCCTTCAGCTCGTGAGATA 59.618 55.000 0.00 0.00 40.84 1.98
265 287 1.202302 CGCCTTCAGCTCGTGAGATAA 60.202 52.381 0.00 0.00 40.84 1.75
272 294 0.574454 GCTCGTGAGATAAAGCAGCG 59.426 55.000 0.00 0.00 40.84 5.18
291 313 4.687215 TCTGCTCCTGTGCACGCC 62.687 66.667 13.13 0.00 38.12 5.68
305 327 2.207924 ACGCCCGTCCTCTGTTTCT 61.208 57.895 0.00 0.00 0.00 2.52
306 328 1.446272 CGCCCGTCCTCTGTTTCTC 60.446 63.158 0.00 0.00 0.00 2.87
307 329 1.079057 GCCCGTCCTCTGTTTCTCC 60.079 63.158 0.00 0.00 0.00 3.71
308 330 1.597461 CCCGTCCTCTGTTTCTCCC 59.403 63.158 0.00 0.00 0.00 4.30
309 331 1.215647 CCGTCCTCTGTTTCTCCCG 59.784 63.158 0.00 0.00 0.00 5.14
322 344 4.539083 TCCCGCACGCACACAGTT 62.539 61.111 0.00 0.00 0.00 3.16
324 346 2.549282 CCGCACGCACACAGTTAC 59.451 61.111 0.00 0.00 0.00 2.50
325 347 1.954146 CCGCACGCACACAGTTACT 60.954 57.895 0.00 0.00 0.00 2.24
326 348 0.665068 CCGCACGCACACAGTTACTA 60.665 55.000 0.00 0.00 0.00 1.82
327 349 0.433492 CGCACGCACACAGTTACTAC 59.567 55.000 0.00 0.00 0.00 2.73
328 350 1.493772 GCACGCACACAGTTACTACA 58.506 50.000 0.00 0.00 0.00 2.74
329 351 1.191647 GCACGCACACAGTTACTACAC 59.808 52.381 0.00 0.00 0.00 2.90
330 352 2.465855 CACGCACACAGTTACTACACA 58.534 47.619 0.00 0.00 0.00 3.72
332 354 3.493129 CACGCACACAGTTACTACACAAT 59.507 43.478 0.00 0.00 0.00 2.71
334 356 3.493129 CGCACACAGTTACTACACAATGT 59.507 43.478 0.00 0.00 0.00 2.71
335 357 4.608222 CGCACACAGTTACTACACAATGTG 60.608 45.833 12.40 12.40 42.78 3.21
337 359 5.220777 GCACACAGTTACTACACAATGTGTT 60.221 40.000 24.78 10.13 46.58 3.32
339 361 7.342194 CACACAGTTACTACACAATGTGTTAC 58.658 38.462 24.78 16.12 46.58 2.50
424 482 2.731721 CACAACGCGACGCTGGTA 60.732 61.111 15.93 0.00 0.00 3.25
426 484 2.731721 CAACGCGACGCTGGTACA 60.732 61.111 15.93 0.00 0.00 2.90
433 491 0.524862 CGACGCTGGTACAAGTAGGT 59.475 55.000 0.00 0.00 38.70 3.08
438 496 5.278169 CGACGCTGGTACAAGTAGGTTATAT 60.278 44.000 0.00 0.00 38.70 0.86
439 497 6.073058 CGACGCTGGTACAAGTAGGTTATATA 60.073 42.308 0.00 0.00 38.70 0.86
440 498 7.211966 ACGCTGGTACAAGTAGGTTATATAG 57.788 40.000 0.00 0.00 38.70 1.31
441 499 7.000472 ACGCTGGTACAAGTAGGTTATATAGA 59.000 38.462 0.00 0.00 38.70 1.98
442 500 7.040823 ACGCTGGTACAAGTAGGTTATATAGAC 60.041 40.741 0.00 0.00 38.70 2.59
443 501 7.174599 CGCTGGTACAAGTAGGTTATATAGACT 59.825 40.741 0.00 0.00 38.70 3.24
444 502 9.512588 GCTGGTACAAGTAGGTTATATAGACTA 57.487 37.037 0.00 0.00 38.70 2.59
446 504 9.512588 TGGTACAAGTAGGTTATATAGACTAGC 57.487 37.037 0.00 0.00 31.92 3.42
447 505 8.955388 GGTACAAGTAGGTTATATAGACTAGCC 58.045 40.741 0.00 0.00 0.00 3.93
448 506 9.512588 GTACAAGTAGGTTATATAGACTAGCCA 57.487 37.037 0.00 0.00 0.00 4.75
449 507 8.406730 ACAAGTAGGTTATATAGACTAGCCAC 57.593 38.462 0.00 0.00 0.00 5.01
450 508 8.003044 ACAAGTAGGTTATATAGACTAGCCACA 58.997 37.037 0.00 0.00 0.00 4.17
451 509 8.857098 CAAGTAGGTTATATAGACTAGCCACAA 58.143 37.037 0.00 0.00 0.00 3.33
452 510 9.603189 AAGTAGGTTATATAGACTAGCCACAAT 57.397 33.333 0.00 0.00 0.00 2.71
453 511 9.026121 AGTAGGTTATATAGACTAGCCACAATG 57.974 37.037 0.00 0.00 0.00 2.82
454 512 9.021807 GTAGGTTATATAGACTAGCCACAATGA 57.978 37.037 0.00 0.00 0.00 2.57
455 513 8.492415 AGGTTATATAGACTAGCCACAATGAA 57.508 34.615 0.00 0.00 0.00 2.57
456 514 8.934697 AGGTTATATAGACTAGCCACAATGAAA 58.065 33.333 0.00 0.00 0.00 2.69
457 515 9.555727 GGTTATATAGACTAGCCACAATGAAAA 57.444 33.333 0.00 0.00 0.00 2.29
462 520 6.803154 AGACTAGCCACAATGAAAAGTAAC 57.197 37.500 0.00 0.00 0.00 2.50
463 521 6.296026 AGACTAGCCACAATGAAAAGTAACA 58.704 36.000 0.00 0.00 0.00 2.41
464 522 6.942576 AGACTAGCCACAATGAAAAGTAACAT 59.057 34.615 0.00 0.00 0.00 2.71
465 523 8.100791 AGACTAGCCACAATGAAAAGTAACATA 58.899 33.333 0.00 0.00 0.00 2.29
466 524 8.807948 ACTAGCCACAATGAAAAGTAACATAT 57.192 30.769 0.00 0.00 0.00 1.78
467 525 9.899661 ACTAGCCACAATGAAAAGTAACATATA 57.100 29.630 0.00 0.00 0.00 0.86
469 527 8.807948 AGCCACAATGAAAAGTAACATATACT 57.192 30.769 0.00 0.00 0.00 2.12
470 528 9.899661 AGCCACAATGAAAAGTAACATATACTA 57.100 29.630 0.00 0.00 0.00 1.82
534 592 8.849543 ATAGAGGGTAATAACTTAAGTGTGGA 57.150 34.615 9.34 0.00 0.00 4.02
535 593 7.563724 AGAGGGTAATAACTTAAGTGTGGAA 57.436 36.000 9.34 0.00 0.00 3.53
536 594 7.981142 AGAGGGTAATAACTTAAGTGTGGAAA 58.019 34.615 9.34 0.00 0.00 3.13
537 595 7.881751 AGAGGGTAATAACTTAAGTGTGGAAAC 59.118 37.037 9.34 3.55 0.00 2.78
538 596 7.519927 AGGGTAATAACTTAAGTGTGGAAACA 58.480 34.615 9.34 0.00 38.70 2.83
539 597 8.168058 AGGGTAATAACTTAAGTGTGGAAACAT 58.832 33.333 9.34 0.00 46.14 2.71
540 598 8.241367 GGGTAATAACTTAAGTGTGGAAACATG 58.759 37.037 9.34 0.00 46.14 3.21
541 599 8.789762 GGTAATAACTTAAGTGTGGAAACATGT 58.210 33.333 9.34 0.00 46.14 3.21
546 604 8.514330 AACTTAAGTGTGGAAACATGTAAAGA 57.486 30.769 9.34 0.00 46.14 2.52
547 605 8.691661 ACTTAAGTGTGGAAACATGTAAAGAT 57.308 30.769 7.48 0.00 46.14 2.40
548 606 9.131791 ACTTAAGTGTGGAAACATGTAAAGATT 57.868 29.630 7.48 0.00 46.14 2.40
549 607 9.612620 CTTAAGTGTGGAAACATGTAAAGATTC 57.387 33.333 0.00 0.00 46.14 2.52
550 608 7.581213 AAGTGTGGAAACATGTAAAGATTCA 57.419 32.000 0.00 0.00 46.14 2.57
551 609 7.765695 AGTGTGGAAACATGTAAAGATTCAT 57.234 32.000 0.00 0.00 46.14 2.57
552 610 8.181904 AGTGTGGAAACATGTAAAGATTCATT 57.818 30.769 0.00 0.00 46.14 2.57
553 611 8.641541 AGTGTGGAAACATGTAAAGATTCATTT 58.358 29.630 0.00 0.00 46.14 2.32
554 612 9.906660 GTGTGGAAACATGTAAAGATTCATTTA 57.093 29.630 0.00 0.00 46.14 1.40
589 647 8.613060 AGACTTATATTGCATTAGGACATGTG 57.387 34.615 1.15 0.00 0.00 3.21
590 648 8.432013 AGACTTATATTGCATTAGGACATGTGA 58.568 33.333 1.15 0.00 0.00 3.58
591 649 9.224267 GACTTATATTGCATTAGGACATGTGAT 57.776 33.333 1.15 0.00 0.00 3.06
592 650 9.006839 ACTTATATTGCATTAGGACATGTGATG 57.993 33.333 1.15 3.48 0.00 3.07
594 652 7.828508 ATATTGCATTAGGACATGTGATGTT 57.171 32.000 1.15 0.00 45.03 2.71
595 653 8.922931 ATATTGCATTAGGACATGTGATGTTA 57.077 30.769 1.15 0.00 45.03 2.41
596 654 6.435430 TTGCATTAGGACATGTGATGTTAC 57.565 37.500 1.15 0.00 45.03 2.50
597 655 5.495640 TGCATTAGGACATGTGATGTTACA 58.504 37.500 1.15 0.00 45.03 2.41
598 656 5.585844 TGCATTAGGACATGTGATGTTACAG 59.414 40.000 1.15 0.00 45.03 2.74
599 657 5.586243 GCATTAGGACATGTGATGTTACAGT 59.414 40.000 1.15 0.00 45.03 3.55
600 658 6.761242 GCATTAGGACATGTGATGTTACAGTA 59.239 38.462 1.15 0.00 45.03 2.74
601 659 7.279981 GCATTAGGACATGTGATGTTACAGTAA 59.720 37.037 1.15 0.00 45.03 2.24
602 660 8.604035 CATTAGGACATGTGATGTTACAGTAAC 58.396 37.037 15.58 15.58 45.03 2.50
603 661 6.360370 AGGACATGTGATGTTACAGTAACT 57.640 37.500 21.56 9.41 45.03 2.24
604 662 7.476540 AGGACATGTGATGTTACAGTAACTA 57.523 36.000 21.56 10.50 45.03 2.24
605 663 7.548097 AGGACATGTGATGTTACAGTAACTAG 58.452 38.462 21.56 8.25 45.03 2.57
606 664 6.255887 GGACATGTGATGTTACAGTAACTAGC 59.744 42.308 21.56 12.59 45.03 3.42
607 665 6.936279 ACATGTGATGTTACAGTAACTAGCT 58.064 36.000 21.56 6.57 41.63 3.32
608 666 8.063200 ACATGTGATGTTACAGTAACTAGCTA 57.937 34.615 21.56 4.25 41.63 3.32
609 667 8.528643 ACATGTGATGTTACAGTAACTAGCTAA 58.471 33.333 21.56 3.59 41.63 3.09
610 668 9.366216 CATGTGATGTTACAGTAACTAGCTAAA 57.634 33.333 21.56 2.93 39.38 1.85
612 670 9.938280 TGTGATGTTACAGTAACTAGCTAAATT 57.062 29.630 21.56 0.00 39.38 1.82
627 685 9.411189 ACTAGCTAAATTACTACAACTAGCTCT 57.589 33.333 7.19 0.00 40.82 4.09
628 686 9.887406 CTAGCTAAATTACTACAACTAGCTCTC 57.113 37.037 7.19 0.00 40.82 3.20
629 687 8.528044 AGCTAAATTACTACAACTAGCTCTCT 57.472 34.615 0.00 0.00 38.07 3.10
630 688 8.626526 AGCTAAATTACTACAACTAGCTCTCTC 58.373 37.037 0.00 0.00 38.07 3.20
631 689 7.863877 GCTAAATTACTACAACTAGCTCTCTCC 59.136 40.741 0.00 0.00 31.23 3.71
632 690 7.964666 AAATTACTACAACTAGCTCTCTCCT 57.035 36.000 0.00 0.00 0.00 3.69
633 691 7.964666 AATTACTACAACTAGCTCTCTCCTT 57.035 36.000 0.00 0.00 0.00 3.36
634 692 9.476928 AAATTACTACAACTAGCTCTCTCCTTA 57.523 33.333 0.00 0.00 0.00 2.69
635 693 9.649316 AATTACTACAACTAGCTCTCTCCTTAT 57.351 33.333 0.00 0.00 0.00 1.73
636 694 9.649316 ATTACTACAACTAGCTCTCTCCTTATT 57.351 33.333 0.00 0.00 0.00 1.40
639 697 9.649316 ACTACAACTAGCTCTCTCCTTATTAAT 57.351 33.333 0.00 0.00 0.00 1.40
642 700 8.138712 ACAACTAGCTCTCTCCTTATTAATTCG 58.861 37.037 0.00 0.00 0.00 3.34
643 701 7.826918 ACTAGCTCTCTCCTTATTAATTCGT 57.173 36.000 0.00 0.00 0.00 3.85
644 702 8.240267 ACTAGCTCTCTCCTTATTAATTCGTT 57.760 34.615 0.00 0.00 0.00 3.85
645 703 8.138712 ACTAGCTCTCTCCTTATTAATTCGTTG 58.861 37.037 0.00 0.00 0.00 4.10
646 704 6.879400 AGCTCTCTCCTTATTAATTCGTTGT 58.121 36.000 0.00 0.00 0.00 3.32
647 705 6.981559 AGCTCTCTCCTTATTAATTCGTTGTC 59.018 38.462 0.00 0.00 0.00 3.18
648 706 6.757010 GCTCTCTCCTTATTAATTCGTTGTCA 59.243 38.462 0.00 0.00 0.00 3.58
649 707 7.254151 GCTCTCTCCTTATTAATTCGTTGTCAC 60.254 40.741 0.00 0.00 0.00 3.67
650 708 7.608153 TCTCTCCTTATTAATTCGTTGTCACA 58.392 34.615 0.00 0.00 0.00 3.58
651 709 8.258007 TCTCTCCTTATTAATTCGTTGTCACAT 58.742 33.333 0.00 0.00 0.00 3.21
652 710 9.529325 CTCTCCTTATTAATTCGTTGTCACATA 57.471 33.333 0.00 0.00 0.00 2.29
653 711 9.878667 TCTCCTTATTAATTCGTTGTCACATAA 57.121 29.630 0.00 0.00 0.00 1.90
655 713 8.609176 TCCTTATTAATTCGTTGTCACATAAGC 58.391 33.333 0.00 0.00 0.00 3.09
656 714 8.394877 CCTTATTAATTCGTTGTCACATAAGCA 58.605 33.333 0.00 0.00 0.00 3.91
657 715 9.767684 CTTATTAATTCGTTGTCACATAAGCAA 57.232 29.630 0.00 0.00 0.00 3.91
660 718 9.638239 ATTAATTCGTTGTCACATAAGCAAATT 57.362 25.926 0.00 0.00 0.00 1.82
661 719 7.945033 AATTCGTTGTCACATAAGCAAATTT 57.055 28.000 0.00 0.00 0.00 1.82
662 720 7.945033 ATTCGTTGTCACATAAGCAAATTTT 57.055 28.000 0.00 0.00 0.00 1.82
663 721 6.984740 TCGTTGTCACATAAGCAAATTTTC 57.015 33.333 0.00 0.00 0.00 2.29
664 722 6.734137 TCGTTGTCACATAAGCAAATTTTCT 58.266 32.000 0.00 0.00 0.00 2.52
665 723 6.636447 TCGTTGTCACATAAGCAAATTTTCTG 59.364 34.615 0.00 0.00 0.00 3.02
666 724 6.129115 CGTTGTCACATAAGCAAATTTTCTGG 60.129 38.462 0.00 0.00 0.00 3.86
667 725 5.782047 TGTCACATAAGCAAATTTTCTGGG 58.218 37.500 0.00 0.00 0.00 4.45
668 726 5.304101 TGTCACATAAGCAAATTTTCTGGGT 59.696 36.000 0.00 0.00 0.00 4.51
669 727 6.183360 TGTCACATAAGCAAATTTTCTGGGTT 60.183 34.615 0.00 0.00 0.00 4.11
670 728 6.146021 GTCACATAAGCAAATTTTCTGGGTTG 59.854 38.462 0.00 0.00 0.00 3.77
671 729 5.409214 CACATAAGCAAATTTTCTGGGTTGG 59.591 40.000 0.00 0.00 0.00 3.77
672 730 5.306678 ACATAAGCAAATTTTCTGGGTTGGA 59.693 36.000 0.00 0.00 0.00 3.53
673 731 3.751479 AGCAAATTTTCTGGGTTGGAC 57.249 42.857 0.00 0.00 0.00 4.02
674 732 2.368548 AGCAAATTTTCTGGGTTGGACC 59.631 45.455 0.00 0.00 37.60 4.46
687 745 4.296621 GGTTGGACCCAATGTTACTAGT 57.703 45.455 4.63 0.00 38.28 2.57
688 746 4.007659 GGTTGGACCCAATGTTACTAGTG 58.992 47.826 5.39 0.00 38.28 2.74
689 747 4.263156 GGTTGGACCCAATGTTACTAGTGA 60.263 45.833 5.39 0.00 38.28 3.41
690 748 5.310451 GTTGGACCCAATGTTACTAGTGAA 58.690 41.667 5.39 0.00 38.28 3.18
691 749 5.160607 TGGACCCAATGTTACTAGTGAAG 57.839 43.478 5.39 0.00 0.00 3.02
692 750 4.595781 TGGACCCAATGTTACTAGTGAAGT 59.404 41.667 5.39 0.00 42.62 3.01
693 751 5.072600 TGGACCCAATGTTACTAGTGAAGTT 59.927 40.000 5.39 0.00 39.80 2.66
694 752 6.270463 TGGACCCAATGTTACTAGTGAAGTTA 59.730 38.462 5.39 0.00 39.80 2.24
695 753 6.592994 GGACCCAATGTTACTAGTGAAGTTAC 59.407 42.308 5.39 0.00 39.80 2.50
696 754 7.312415 ACCCAATGTTACTAGTGAAGTTACT 57.688 36.000 5.39 0.00 38.33 2.24
697 755 7.384477 ACCCAATGTTACTAGTGAAGTTACTC 58.616 38.462 5.39 0.00 38.33 2.59
698 756 6.530534 CCCAATGTTACTAGTGAAGTTACTCG 59.469 42.308 5.39 0.00 38.33 4.18
699 757 6.034683 CCAATGTTACTAGTGAAGTTACTCGC 59.965 42.308 5.39 0.00 38.33 5.03
700 758 5.694231 TGTTACTAGTGAAGTTACTCGCA 57.306 39.130 5.39 0.00 38.33 5.10
701 759 5.455392 TGTTACTAGTGAAGTTACTCGCAC 58.545 41.667 5.39 9.37 38.33 5.34
702 760 5.240183 TGTTACTAGTGAAGTTACTCGCACT 59.760 40.000 19.46 19.46 43.40 4.40
703 761 4.850347 ACTAGTGAAGTTACTCGCACTT 57.150 40.909 20.31 6.48 41.43 3.16
704 762 4.547532 ACTAGTGAAGTTACTCGCACTTG 58.452 43.478 20.31 19.78 41.43 3.16
705 763 2.755650 AGTGAAGTTACTCGCACTTGG 58.244 47.619 12.86 0.00 38.34 3.61
706 764 1.194772 GTGAAGTTACTCGCACTTGGC 59.805 52.381 9.92 0.00 34.49 4.52
707 765 1.070134 TGAAGTTACTCGCACTTGGCT 59.930 47.619 0.00 0.00 41.67 4.75
708 766 2.297880 TGAAGTTACTCGCACTTGGCTA 59.702 45.455 0.00 0.00 41.67 3.93
709 767 2.656560 AGTTACTCGCACTTGGCTAG 57.343 50.000 0.00 0.00 40.92 3.42
713 771 0.244994 ACTCGCACTTGGCTAGTCTG 59.755 55.000 0.00 0.00 44.47 3.51
731 789 2.377531 TCTGAGGTGGTGTACTCTACCA 59.622 50.000 26.21 14.84 45.52 3.25
757 815 0.326264 ACGTCCCTAGGTACACGTCT 59.674 55.000 19.78 4.40 41.51 4.18
836 895 2.066393 TTGGCATCCTCCTCCTCCG 61.066 63.158 0.00 0.00 0.00 4.63
901 971 2.224159 GGCTCACTCCTCCCCACAA 61.224 63.158 0.00 0.00 0.00 3.33
902 972 1.298014 GCTCACTCCTCCCCACAAG 59.702 63.158 0.00 0.00 0.00 3.16
903 973 1.194781 GCTCACTCCTCCCCACAAGA 61.195 60.000 0.00 0.00 0.00 3.02
904 974 0.610687 CTCACTCCTCCCCACAAGAC 59.389 60.000 0.00 0.00 0.00 3.01
905 975 0.105194 TCACTCCTCCCCACAAGACA 60.105 55.000 0.00 0.00 0.00 3.41
950 1025 4.048696 AGCTCTGCTCCTCCCTTC 57.951 61.111 0.00 0.00 30.62 3.46
966 1041 5.163237 CCTCCCTTCACCTCGGATTAATAAA 60.163 44.000 0.00 0.00 0.00 1.40
975 1050 2.540931 TCGGATTAATAAACTTCGGCGC 59.459 45.455 0.00 0.00 0.00 6.53
994 1072 6.591062 TCGGCGCCGATTTTTACTATAATATT 59.409 34.615 45.37 0.00 44.01 1.28
1529 1626 3.933722 CTGGCCGGCGAGATGGAT 61.934 66.667 32.52 0.00 0.00 3.41
1530 1627 3.873026 CTGGCCGGCGAGATGGATC 62.873 68.421 32.52 9.73 0.00 3.36
1532 1629 3.978491 GCCGGCGAGATGGATCGA 61.978 66.667 12.58 0.00 45.56 3.59
1536 1633 2.552819 GGCGAGATGGATCGACCGA 61.553 63.158 0.00 0.00 45.21 4.69
1537 1634 1.359117 GCGAGATGGATCGACCGAA 59.641 57.895 0.00 0.00 45.56 4.30
1539 1636 0.317938 CGAGATGGATCGACCGAACC 60.318 60.000 11.13 11.13 45.56 3.62
1601 1699 8.239314 TGTAGAGTTACGTGTAAACTAATCCAG 58.761 37.037 0.00 0.00 32.21 3.86
1602 1700 7.224522 AGAGTTACGTGTAAACTAATCCAGT 57.775 36.000 0.00 0.00 40.05 4.00
1644 1742 9.803315 TTGACTAATGCTAATCTAGTGTAGTTG 57.197 33.333 0.00 0.00 0.00 3.16
1695 1793 2.552585 TAGCTACTGCCGCACGTTCC 62.553 60.000 0.00 0.00 40.80 3.62
1700 1798 4.539083 TGCCGCACGTTCCAGTGT 62.539 61.111 0.00 0.00 43.61 3.55
1702 1800 2.380410 GCCGCACGTTCCAGTGTAG 61.380 63.158 0.00 0.00 43.61 2.74
1703 1801 1.006571 CCGCACGTTCCAGTGTAGT 60.007 57.895 0.00 0.00 43.61 2.73
1704 1802 1.282248 CCGCACGTTCCAGTGTAGTG 61.282 60.000 0.00 0.00 43.61 2.74
1706 1804 1.886861 GCACGTTCCAGTGTAGTGCG 61.887 60.000 11.69 2.30 46.54 5.34
1707 1805 1.663702 ACGTTCCAGTGTAGTGCGC 60.664 57.895 0.00 0.00 0.00 6.09
1708 1806 1.663388 CGTTCCAGTGTAGTGCGCA 60.663 57.895 5.66 5.66 0.00 6.09
1709 1807 1.014044 CGTTCCAGTGTAGTGCGCAT 61.014 55.000 15.91 5.37 0.00 4.73
1710 1808 0.443869 GTTCCAGTGTAGTGCGCATG 59.556 55.000 15.91 6.38 0.00 4.06
1711 1809 0.034756 TTCCAGTGTAGTGCGCATGT 59.965 50.000 15.91 6.96 0.00 3.21
1778 1876 1.521681 CTGATTCCGTCGAAGGGCC 60.522 63.158 17.69 0.00 0.00 5.80
1816 1914 2.436646 GCCATGGTCTCCCGTGTG 60.437 66.667 14.67 0.00 44.96 3.82
1846 1944 2.658422 GGGTCCCACGACGCTTAA 59.342 61.111 1.78 0.00 45.89 1.85
1852 1950 0.390603 CCCACGACGCTTAATGTCCA 60.391 55.000 0.00 0.00 32.68 4.02
1857 1955 1.726853 GACGCTTAATGTCCAGCACT 58.273 50.000 0.00 0.00 35.60 4.40
1859 1957 0.097674 CGCTTAATGTCCAGCACTGC 59.902 55.000 0.00 0.00 35.60 4.40
1860 1958 0.453390 GCTTAATGTCCAGCACTGCC 59.547 55.000 0.00 0.00 35.95 4.85
1861 1959 0.729116 CTTAATGTCCAGCACTGCCG 59.271 55.000 0.00 0.00 0.00 5.69
1901 1999 0.179258 GACGAAATGACGTGCCGAAC 60.179 55.000 0.00 0.00 46.52 3.95
1942 2040 0.941542 TGCGCCCATCGTATTAAAGC 59.058 50.000 4.18 0.00 41.07 3.51
1948 2046 2.289547 CCCATCGTATTAAAGCCGTTGG 59.710 50.000 11.79 11.79 39.80 3.77
1967 2065 6.090129 CGTTGGTAAATGGAGTGTATTTTGG 58.910 40.000 0.00 0.00 0.00 3.28
1968 2066 6.294286 CGTTGGTAAATGGAGTGTATTTTGGT 60.294 38.462 0.00 0.00 0.00 3.67
1969 2067 7.094720 CGTTGGTAAATGGAGTGTATTTTGGTA 60.095 37.037 0.00 0.00 0.00 3.25
1970 2068 7.690952 TGGTAAATGGAGTGTATTTTGGTAC 57.309 36.000 0.00 0.00 0.00 3.34
1971 2069 6.372103 TGGTAAATGGAGTGTATTTTGGTACG 59.628 38.462 0.00 0.00 0.00 3.67
1972 2070 4.957759 AATGGAGTGTATTTTGGTACGC 57.042 40.909 0.00 0.00 35.77 4.42
1975 2073 3.514706 TGGAGTGTATTTTGGTACGCCTA 59.485 43.478 0.00 0.00 36.07 3.93
1990 2088 1.211181 GCCTACGCGTTAATCCGGTC 61.211 60.000 20.78 2.19 0.00 4.79
1995 2093 1.689352 CGCGTTAATCCGGTCGCTTT 61.689 55.000 20.17 5.74 45.25 3.51
1996 2094 0.445043 GCGTTAATCCGGTCGCTTTT 59.555 50.000 17.40 2.24 44.28 2.27
1997 2095 1.135888 GCGTTAATCCGGTCGCTTTTT 60.136 47.619 17.40 0.88 44.28 1.94
1998 2096 2.501881 CGTTAATCCGGTCGCTTTTTG 58.498 47.619 0.00 0.00 0.00 2.44
1999 2097 2.247637 GTTAATCCGGTCGCTTTTTGC 58.752 47.619 0.00 0.00 38.57 3.68
2011 2109 3.673746 GCTTTTTGCGCCTTTTCTTTT 57.326 38.095 4.18 0.00 0.00 2.27
2012 2110 4.787381 GCTTTTTGCGCCTTTTCTTTTA 57.213 36.364 4.18 0.00 0.00 1.52
2013 2111 5.150342 GCTTTTTGCGCCTTTTCTTTTAA 57.850 34.783 4.18 0.00 0.00 1.52
2014 2112 5.564768 GCTTTTTGCGCCTTTTCTTTTAAA 58.435 33.333 4.18 0.00 0.00 1.52
2015 2113 6.024664 GCTTTTTGCGCCTTTTCTTTTAAAA 58.975 32.000 4.18 0.00 0.00 1.52
2016 2114 6.524933 GCTTTTTGCGCCTTTTCTTTTAAAAA 59.475 30.769 4.18 6.24 0.00 1.94
2058 2192 0.485099 TTGCCCCTGGTATTTGTGGT 59.515 50.000 0.00 0.00 0.00 4.16
2062 2196 1.544724 CCCTGGTATTTGTGGTGGTG 58.455 55.000 0.00 0.00 0.00 4.17
2063 2197 0.887933 CCTGGTATTTGTGGTGGTGC 59.112 55.000 0.00 0.00 0.00 5.01
2072 2206 3.579302 TGGTGGTGCCTTGGGAGG 61.579 66.667 0.00 0.00 46.50 4.30
2074 2208 3.256960 GTGGTGCCTTGGGAGGGA 61.257 66.667 0.00 0.00 43.75 4.20
2088 2227 4.840005 GGGAAGGAGAAGCGCGGG 62.840 72.222 8.83 0.00 0.00 6.13
2095 2234 3.140225 GAGAAGCGCGGGGAGGTAG 62.140 68.421 8.83 0.00 0.00 3.18
2141 2284 1.135460 GTACGAGGAAGACGACAAGGG 60.135 57.143 0.00 0.00 34.70 3.95
2143 2286 1.597461 GAGGAAGACGACAAGGGGG 59.403 63.158 0.00 0.00 0.00 5.40
2163 2306 3.491342 GGGACCTTTTCTCAGCTTTTCT 58.509 45.455 0.00 0.00 0.00 2.52
2178 2321 3.553917 GCTTTTCTGTCTAATCCTCTCGC 59.446 47.826 0.00 0.00 0.00 5.03
2305 2499 0.179100 ATTCCACGGATGAGCTGACG 60.179 55.000 0.00 0.00 0.00 4.35
2366 2573 3.365364 GCTTTATTATCTCGCCATGCACC 60.365 47.826 0.00 0.00 0.00 5.01
2388 2595 2.125106 GACTGGTCGATGTGCCCC 60.125 66.667 0.00 0.00 0.00 5.80
2396 2603 3.499737 GATGTGCCCCGCGAACAG 61.500 66.667 8.23 0.00 0.00 3.16
2417 2645 0.523968 TTCGTTCGTCCGGATAAGCG 60.524 55.000 7.81 13.12 0.00 4.68
2418 2646 2.574222 CGTTCGTCCGGATAAGCGC 61.574 63.158 7.81 0.00 0.00 5.92
2419 2647 1.517694 GTTCGTCCGGATAAGCGCA 60.518 57.895 7.81 0.00 0.00 6.09
2472 2712 2.919043 GGGTCCGGATCCAATGCT 59.081 61.111 29.68 0.00 0.00 3.79
2480 2720 2.941064 CCGGATCCAATGCTATGCTATG 59.059 50.000 13.41 0.00 0.00 2.23
2481 2721 2.353889 CGGATCCAATGCTATGCTATGC 59.646 50.000 13.41 0.00 0.00 3.14
2482 2722 3.618351 GGATCCAATGCTATGCTATGCT 58.382 45.455 6.95 0.00 0.00 3.79
2483 2723 4.681512 CGGATCCAATGCTATGCTATGCTA 60.682 45.833 13.41 0.00 0.00 3.49
2484 2724 5.374921 GGATCCAATGCTATGCTATGCTAT 58.625 41.667 6.95 0.00 0.00 2.97
2485 2725 5.469421 GGATCCAATGCTATGCTATGCTATC 59.531 44.000 6.95 0.00 0.00 2.08
2486 2726 5.688814 TCCAATGCTATGCTATGCTATCT 57.311 39.130 0.00 0.00 0.00 1.98
2487 2727 5.425630 TCCAATGCTATGCTATGCTATCTG 58.574 41.667 0.00 0.00 0.00 2.90
2488 2728 5.188359 TCCAATGCTATGCTATGCTATCTGA 59.812 40.000 0.00 0.00 0.00 3.27
2489 2729 5.524281 CCAATGCTATGCTATGCTATCTGAG 59.476 44.000 0.00 0.00 0.00 3.35
2490 2730 4.732672 TGCTATGCTATGCTATCTGAGG 57.267 45.455 0.00 0.00 0.00 3.86
2491 2731 3.118847 TGCTATGCTATGCTATCTGAGGC 60.119 47.826 0.00 0.00 0.00 4.70
2492 2732 2.669300 ATGCTATGCTATCTGAGGCG 57.331 50.000 0.00 0.00 0.00 5.52
2493 2733 0.605083 TGCTATGCTATCTGAGGCGG 59.395 55.000 0.00 0.00 0.00 6.13
2494 2734 0.891373 GCTATGCTATCTGAGGCGGA 59.109 55.000 0.00 0.00 0.00 5.54
2495 2735 1.480137 GCTATGCTATCTGAGGCGGAT 59.520 52.381 0.00 0.00 33.63 4.18
2496 2736 2.481104 GCTATGCTATCTGAGGCGGATC 60.481 54.545 0.00 0.00 31.33 3.36
2497 2737 1.935799 ATGCTATCTGAGGCGGATCT 58.064 50.000 0.00 0.00 31.33 2.75
2498 2738 0.964700 TGCTATCTGAGGCGGATCTG 59.035 55.000 0.00 0.00 31.33 2.90
2499 2739 0.965439 GCTATCTGAGGCGGATCTGT 59.035 55.000 2.89 0.00 31.33 3.41
2500 2740 1.342819 GCTATCTGAGGCGGATCTGTT 59.657 52.381 2.89 0.00 31.33 3.16
2501 2741 2.558795 GCTATCTGAGGCGGATCTGTTA 59.441 50.000 2.89 0.00 31.33 2.41
2502 2742 3.612955 GCTATCTGAGGCGGATCTGTTAC 60.613 52.174 2.89 0.00 31.33 2.50
2503 2743 1.847328 TCTGAGGCGGATCTGTTACA 58.153 50.000 2.89 0.56 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
113 121 1.215912 CGCATCATTGGGCAAAGCA 59.784 52.632 0.00 0.00 0.00 3.91
131 139 1.197492 TCATTTGATCGTGTGTGCTGC 59.803 47.619 0.00 0.00 0.00 5.25
146 154 2.499205 TCGCCGGCGAGATCATTT 59.501 55.556 45.37 0.00 44.01 2.32
162 170 3.968724 GTGTCGTGTGATGCTTCTTTTTC 59.031 43.478 0.88 0.00 0.00 2.29
184 192 4.673441 AGTGAAGCGCTACTACTACATTG 58.327 43.478 12.05 0.00 0.00 2.82
205 213 0.868406 GTCAAGTCCCAAGCACGAAG 59.132 55.000 0.00 0.00 0.00 3.79
206 214 0.179234 TGTCAAGTCCCAAGCACGAA 59.821 50.000 0.00 0.00 0.00 3.85
272 294 3.117171 CGTGCACAGGAGCAGAGC 61.117 66.667 18.64 0.00 46.69 4.09
287 309 2.156051 GAGAAACAGAGGACGGGCGT 62.156 60.000 0.00 0.00 0.00 5.68
291 313 1.215647 CGGGAGAAACAGAGGACGG 59.784 63.158 0.00 0.00 0.00 4.79
294 316 1.671742 GTGCGGGAGAAACAGAGGA 59.328 57.895 0.00 0.00 0.00 3.71
305 327 3.153270 TAACTGTGTGCGTGCGGGA 62.153 57.895 0.00 0.00 0.00 5.14
306 328 2.663520 TAACTGTGTGCGTGCGGG 60.664 61.111 0.00 0.00 0.00 6.13
307 329 0.665068 TAGTAACTGTGTGCGTGCGG 60.665 55.000 0.00 0.00 0.00 5.69
308 330 0.433492 GTAGTAACTGTGTGCGTGCG 59.567 55.000 0.00 0.00 0.00 5.34
309 331 1.191647 GTGTAGTAACTGTGTGCGTGC 59.808 52.381 0.00 0.00 0.00 5.34
335 357 1.301401 TGGCTGCTGACGTGGTAAC 60.301 57.895 0.00 0.00 0.00 2.50
336 358 1.301401 GTGGCTGCTGACGTGGTAA 60.301 57.895 0.00 0.00 0.00 2.85
337 359 2.207229 AGTGGCTGCTGACGTGGTA 61.207 57.895 0.00 0.00 0.00 3.25
339 361 2.994387 TTCAGTGGCTGCTGACGTGG 62.994 60.000 10.88 0.00 44.23 4.94
421 472 8.955388 GGCTAGTCTATATAACCTACTTGTACC 58.045 40.741 0.00 0.00 0.00 3.34
424 482 8.003044 TGTGGCTAGTCTATATAACCTACTTGT 58.997 37.037 0.00 0.00 0.00 3.16
426 484 9.603189 ATTGTGGCTAGTCTATATAACCTACTT 57.397 33.333 0.00 0.00 0.00 2.24
438 496 7.446769 TGTTACTTTTCATTGTGGCTAGTCTA 58.553 34.615 0.00 0.00 0.00 2.59
439 497 6.296026 TGTTACTTTTCATTGTGGCTAGTCT 58.704 36.000 0.00 0.00 0.00 3.24
440 498 6.554334 TGTTACTTTTCATTGTGGCTAGTC 57.446 37.500 0.00 0.00 0.00 2.59
441 499 8.807948 ATATGTTACTTTTCATTGTGGCTAGT 57.192 30.769 0.00 0.00 0.00 2.57
443 501 9.899661 AGTATATGTTACTTTTCATTGTGGCTA 57.100 29.630 0.00 0.00 0.00 3.93
444 502 8.807948 AGTATATGTTACTTTTCATTGTGGCT 57.192 30.769 0.00 0.00 0.00 4.75
508 566 9.940974 TCCACACTTAAGTTATTACCCTCTATA 57.059 33.333 5.07 0.00 0.00 1.31
509 567 8.849543 TCCACACTTAAGTTATTACCCTCTAT 57.150 34.615 5.07 0.00 0.00 1.98
510 568 8.669055 TTCCACACTTAAGTTATTACCCTCTA 57.331 34.615 5.07 0.00 0.00 2.43
511 569 7.563724 TTCCACACTTAAGTTATTACCCTCT 57.436 36.000 5.07 0.00 0.00 3.69
512 570 7.662669 TGTTTCCACACTTAAGTTATTACCCTC 59.337 37.037 5.07 0.00 0.00 4.30
513 571 7.519927 TGTTTCCACACTTAAGTTATTACCCT 58.480 34.615 5.07 0.00 0.00 4.34
514 572 7.748691 TGTTTCCACACTTAAGTTATTACCC 57.251 36.000 5.07 0.00 0.00 3.69
515 573 8.789762 ACATGTTTCCACACTTAAGTTATTACC 58.210 33.333 5.07 0.00 35.03 2.85
520 578 9.616156 TCTTTACATGTTTCCACACTTAAGTTA 57.384 29.630 5.07 0.00 35.03 2.24
521 579 8.514330 TCTTTACATGTTTCCACACTTAAGTT 57.486 30.769 5.07 0.00 35.03 2.66
522 580 8.691661 ATCTTTACATGTTTCCACACTTAAGT 57.308 30.769 2.30 1.12 35.03 2.24
523 581 9.612620 GAATCTTTACATGTTTCCACACTTAAG 57.387 33.333 2.30 0.00 35.03 1.85
524 582 9.126151 TGAATCTTTACATGTTTCCACACTTAA 57.874 29.630 2.30 0.00 35.03 1.85
525 583 8.684386 TGAATCTTTACATGTTTCCACACTTA 57.316 30.769 2.30 0.00 35.03 2.24
526 584 7.581213 TGAATCTTTACATGTTTCCACACTT 57.419 32.000 2.30 0.00 35.03 3.16
527 585 7.765695 ATGAATCTTTACATGTTTCCACACT 57.234 32.000 2.30 0.00 35.03 3.55
528 586 8.816640 AAATGAATCTTTACATGTTTCCACAC 57.183 30.769 2.30 0.00 35.03 3.82
563 621 9.710900 CACATGTCCTAATGCAATATAAGTCTA 57.289 33.333 0.00 0.00 0.00 2.59
564 622 8.432013 TCACATGTCCTAATGCAATATAAGTCT 58.568 33.333 0.00 0.00 0.00 3.24
565 623 8.607441 TCACATGTCCTAATGCAATATAAGTC 57.393 34.615 0.00 0.00 0.00 3.01
566 624 9.006839 CATCACATGTCCTAATGCAATATAAGT 57.993 33.333 0.00 0.00 0.00 2.24
567 625 9.006839 ACATCACATGTCCTAATGCAATATAAG 57.993 33.333 0.00 0.00 39.92 1.73
568 626 8.922931 ACATCACATGTCCTAATGCAATATAA 57.077 30.769 0.00 0.00 39.92 0.98
569 627 8.922931 AACATCACATGTCCTAATGCAATATA 57.077 30.769 0.00 0.00 44.07 0.86
570 628 7.828508 AACATCACATGTCCTAATGCAATAT 57.171 32.000 0.00 0.00 44.07 1.28
571 629 7.772757 TGTAACATCACATGTCCTAATGCAATA 59.227 33.333 0.00 0.00 44.07 1.90
572 630 6.602803 TGTAACATCACATGTCCTAATGCAAT 59.397 34.615 0.00 0.00 44.07 3.56
573 631 5.942826 TGTAACATCACATGTCCTAATGCAA 59.057 36.000 0.00 0.00 44.07 4.08
574 632 5.495640 TGTAACATCACATGTCCTAATGCA 58.504 37.500 0.00 0.00 44.07 3.96
575 633 5.586243 ACTGTAACATCACATGTCCTAATGC 59.414 40.000 0.00 0.00 44.07 3.56
576 634 8.604035 GTTACTGTAACATCACATGTCCTAATG 58.396 37.037 22.30 0.45 44.07 1.90
577 635 8.540388 AGTTACTGTAACATCACATGTCCTAAT 58.460 33.333 27.12 3.45 44.07 1.73
578 636 7.903145 AGTTACTGTAACATCACATGTCCTAA 58.097 34.615 27.12 0.00 44.07 2.69
579 637 7.476540 AGTTACTGTAACATCACATGTCCTA 57.523 36.000 27.12 0.00 44.07 2.94
580 638 6.360370 AGTTACTGTAACATCACATGTCCT 57.640 37.500 27.12 4.57 44.07 3.85
581 639 6.255887 GCTAGTTACTGTAACATCACATGTCC 59.744 42.308 27.12 1.73 44.07 4.02
582 640 7.036220 AGCTAGTTACTGTAACATCACATGTC 58.964 38.462 27.12 9.51 44.07 3.06
584 642 8.926715 TTAGCTAGTTACTGTAACATCACATG 57.073 34.615 27.12 12.57 41.07 3.21
586 644 9.938280 AATTTAGCTAGTTACTGTAACATCACA 57.062 29.630 27.12 10.61 41.07 3.58
601 659 9.411189 AGAGCTAGTTGTAGTAATTTAGCTAGT 57.589 33.333 4.46 0.00 42.64 2.57
602 660 9.887406 GAGAGCTAGTTGTAGTAATTTAGCTAG 57.113 37.037 4.46 0.00 42.64 3.42
603 661 9.629878 AGAGAGCTAGTTGTAGTAATTTAGCTA 57.370 33.333 4.46 0.00 42.64 3.32
604 662 8.528044 AGAGAGCTAGTTGTAGTAATTTAGCT 57.472 34.615 4.17 4.17 44.57 3.32
605 663 7.863877 GGAGAGAGCTAGTTGTAGTAATTTAGC 59.136 40.741 0.00 0.00 35.06 3.09
606 664 9.127277 AGGAGAGAGCTAGTTGTAGTAATTTAG 57.873 37.037 0.00 0.00 0.00 1.85
607 665 9.476928 AAGGAGAGAGCTAGTTGTAGTAATTTA 57.523 33.333 0.00 0.00 0.00 1.40
608 666 7.964666 AGGAGAGAGCTAGTTGTAGTAATTT 57.035 36.000 0.00 0.00 0.00 1.82
609 667 7.964666 AAGGAGAGAGCTAGTTGTAGTAATT 57.035 36.000 0.00 0.00 0.00 1.40
610 668 9.649316 AATAAGGAGAGAGCTAGTTGTAGTAAT 57.351 33.333 0.00 0.00 0.00 1.89
613 671 9.649316 ATTAATAAGGAGAGAGCTAGTTGTAGT 57.351 33.333 0.00 0.00 0.00 2.73
616 674 8.138712 CGAATTAATAAGGAGAGAGCTAGTTGT 58.861 37.037 0.00 0.00 0.00 3.32
617 675 8.138712 ACGAATTAATAAGGAGAGAGCTAGTTG 58.861 37.037 0.00 0.00 0.00 3.16
618 676 8.240267 ACGAATTAATAAGGAGAGAGCTAGTT 57.760 34.615 0.00 0.00 0.00 2.24
619 677 7.826918 ACGAATTAATAAGGAGAGAGCTAGT 57.173 36.000 0.00 0.00 0.00 2.57
620 678 8.138712 ACAACGAATTAATAAGGAGAGAGCTAG 58.861 37.037 0.00 0.00 0.00 3.42
621 679 8.008513 ACAACGAATTAATAAGGAGAGAGCTA 57.991 34.615 0.00 0.00 0.00 3.32
622 680 6.879400 ACAACGAATTAATAAGGAGAGAGCT 58.121 36.000 0.00 0.00 0.00 4.09
623 681 6.757010 TGACAACGAATTAATAAGGAGAGAGC 59.243 38.462 0.00 0.00 0.00 4.09
624 682 7.759886 TGTGACAACGAATTAATAAGGAGAGAG 59.240 37.037 0.00 0.00 0.00 3.20
625 683 7.608153 TGTGACAACGAATTAATAAGGAGAGA 58.392 34.615 0.00 0.00 0.00 3.10
626 684 7.827819 TGTGACAACGAATTAATAAGGAGAG 57.172 36.000 0.00 0.00 0.00 3.20
627 685 9.878667 TTATGTGACAACGAATTAATAAGGAGA 57.121 29.630 0.00 0.00 0.00 3.71
629 687 8.609176 GCTTATGTGACAACGAATTAATAAGGA 58.391 33.333 0.00 0.00 30.56 3.36
630 688 8.394877 TGCTTATGTGACAACGAATTAATAAGG 58.605 33.333 0.00 0.00 30.56 2.69
631 689 9.767684 TTGCTTATGTGACAACGAATTAATAAG 57.232 29.630 0.00 0.00 32.20 1.73
634 692 9.638239 AATTTGCTTATGTGACAACGAATTAAT 57.362 25.926 0.00 0.00 0.00 1.40
635 693 9.469807 AAATTTGCTTATGTGACAACGAATTAA 57.530 25.926 0.00 0.00 0.00 1.40
636 694 9.469807 AAAATTTGCTTATGTGACAACGAATTA 57.530 25.926 0.00 0.00 0.00 1.40
637 695 7.945033 AAATTTGCTTATGTGACAACGAATT 57.055 28.000 0.00 0.00 0.00 2.17
638 696 7.867403 AGAAAATTTGCTTATGTGACAACGAAT 59.133 29.630 0.00 0.00 0.00 3.34
639 697 7.167302 CAGAAAATTTGCTTATGTGACAACGAA 59.833 33.333 0.00 0.00 0.00 3.85
640 698 6.636447 CAGAAAATTTGCTTATGTGACAACGA 59.364 34.615 0.00 0.00 0.00 3.85
641 699 6.129115 CCAGAAAATTTGCTTATGTGACAACG 60.129 38.462 0.00 0.00 0.00 4.10
642 700 6.146021 CCCAGAAAATTTGCTTATGTGACAAC 59.854 38.462 0.00 0.00 0.00 3.32
643 701 6.183360 ACCCAGAAAATTTGCTTATGTGACAA 60.183 34.615 0.00 0.00 0.00 3.18
644 702 5.304101 ACCCAGAAAATTTGCTTATGTGACA 59.696 36.000 0.00 0.00 0.00 3.58
645 703 5.783111 ACCCAGAAAATTTGCTTATGTGAC 58.217 37.500 0.00 0.00 0.00 3.67
646 704 6.222389 CAACCCAGAAAATTTGCTTATGTGA 58.778 36.000 0.00 0.00 0.00 3.58
647 705 5.409214 CCAACCCAGAAAATTTGCTTATGTG 59.591 40.000 0.00 0.00 0.00 3.21
648 706 5.306678 TCCAACCCAGAAAATTTGCTTATGT 59.693 36.000 0.00 0.00 0.00 2.29
649 707 5.639082 GTCCAACCCAGAAAATTTGCTTATG 59.361 40.000 0.00 0.00 0.00 1.90
650 708 5.279960 GGTCCAACCCAGAAAATTTGCTTAT 60.280 40.000 0.00 0.00 30.04 1.73
651 709 4.039852 GGTCCAACCCAGAAAATTTGCTTA 59.960 41.667 0.00 0.00 30.04 3.09
652 710 3.181455 GGTCCAACCCAGAAAATTTGCTT 60.181 43.478 0.00 0.00 30.04 3.91
653 711 2.368548 GGTCCAACCCAGAAAATTTGCT 59.631 45.455 0.00 0.00 30.04 3.91
654 712 2.766313 GGTCCAACCCAGAAAATTTGC 58.234 47.619 0.00 0.00 30.04 3.68
666 724 4.007659 CACTAGTAACATTGGGTCCAACC 58.992 47.826 4.37 0.00 38.88 3.77
667 725 4.901868 TCACTAGTAACATTGGGTCCAAC 58.098 43.478 4.37 0.00 38.88 3.77
668 726 5.072600 ACTTCACTAGTAACATTGGGTCCAA 59.927 40.000 4.78 4.78 36.40 3.53
669 727 4.595781 ACTTCACTAGTAACATTGGGTCCA 59.404 41.667 0.00 0.00 34.56 4.02
670 728 5.161943 ACTTCACTAGTAACATTGGGTCC 57.838 43.478 0.00 0.00 34.56 4.46
671 729 7.384477 AGTAACTTCACTAGTAACATTGGGTC 58.616 38.462 0.00 0.00 35.54 4.46
672 730 7.312415 AGTAACTTCACTAGTAACATTGGGT 57.688 36.000 0.00 0.00 35.54 4.51
673 731 6.530534 CGAGTAACTTCACTAGTAACATTGGG 59.469 42.308 0.00 0.00 35.54 4.12
674 732 6.034683 GCGAGTAACTTCACTAGTAACATTGG 59.965 42.308 0.00 0.00 35.54 3.16
675 733 6.584942 TGCGAGTAACTTCACTAGTAACATTG 59.415 38.462 0.00 0.00 35.54 2.82
676 734 6.585322 GTGCGAGTAACTTCACTAGTAACATT 59.415 38.462 0.00 0.00 35.54 2.71
677 735 6.072064 AGTGCGAGTAACTTCACTAGTAACAT 60.072 38.462 0.00 0.00 37.94 2.71
678 736 5.240183 AGTGCGAGTAACTTCACTAGTAACA 59.760 40.000 0.00 0.00 37.94 2.41
679 737 5.697826 AGTGCGAGTAACTTCACTAGTAAC 58.302 41.667 0.00 0.00 37.94 2.50
680 738 5.954296 AGTGCGAGTAACTTCACTAGTAA 57.046 39.130 0.00 0.00 37.94 2.24
681 739 5.335426 CCAAGTGCGAGTAACTTCACTAGTA 60.335 44.000 0.00 0.00 38.68 1.82
682 740 4.547532 CAAGTGCGAGTAACTTCACTAGT 58.452 43.478 0.00 0.00 38.68 2.57
683 741 3.921021 CCAAGTGCGAGTAACTTCACTAG 59.079 47.826 4.93 0.00 38.68 2.57
684 742 3.859627 GCCAAGTGCGAGTAACTTCACTA 60.860 47.826 4.93 0.00 38.68 2.74
685 743 2.755650 CCAAGTGCGAGTAACTTCACT 58.244 47.619 0.00 0.00 41.08 3.41
686 744 1.194772 GCCAAGTGCGAGTAACTTCAC 59.805 52.381 0.00 0.00 35.70 3.18
687 745 1.508632 GCCAAGTGCGAGTAACTTCA 58.491 50.000 0.00 0.00 35.70 3.02
695 753 0.528017 TCAGACTAGCCAAGTGCGAG 59.472 55.000 0.00 0.00 46.95 5.03
698 756 0.610687 ACCTCAGACTAGCCAAGTGC 59.389 55.000 0.00 0.00 39.07 4.40
699 757 1.066573 CCACCTCAGACTAGCCAAGTG 60.067 57.143 0.00 0.00 39.07 3.16
700 758 1.270907 CCACCTCAGACTAGCCAAGT 58.729 55.000 0.00 0.00 42.80 3.16
701 759 1.066573 CACCACCTCAGACTAGCCAAG 60.067 57.143 0.00 0.00 0.00 3.61
702 760 0.976641 CACCACCTCAGACTAGCCAA 59.023 55.000 0.00 0.00 0.00 4.52
703 761 0.178932 ACACCACCTCAGACTAGCCA 60.179 55.000 0.00 0.00 0.00 4.75
704 762 1.477295 GTACACCACCTCAGACTAGCC 59.523 57.143 0.00 0.00 0.00 3.93
705 763 2.424246 GAGTACACCACCTCAGACTAGC 59.576 54.545 0.00 0.00 0.00 3.42
706 764 3.958018 AGAGTACACCACCTCAGACTAG 58.042 50.000 0.00 0.00 0.00 2.57
707 765 4.324099 GGTAGAGTACACCACCTCAGACTA 60.324 50.000 0.83 0.00 36.01 2.59
708 766 2.982339 AGAGTACACCACCTCAGACT 57.018 50.000 0.00 0.00 0.00 3.24
709 767 2.754002 GGTAGAGTACACCACCTCAGAC 59.246 54.545 0.83 0.00 36.01 3.51
710 768 2.377531 TGGTAGAGTACACCACCTCAGA 59.622 50.000 9.10 0.00 41.17 3.27
713 771 2.754002 GTCTGGTAGAGTACACCACCTC 59.246 54.545 9.10 0.00 41.17 3.85
748 806 1.853319 GCACTGTGCAGACGTGTAC 59.147 57.895 26.70 0.00 44.26 2.90
901 971 3.857038 ACGGCGGTGGTTGTGTCT 61.857 61.111 13.24 0.00 0.00 3.41
902 972 3.645975 CACGGCGGTGGTTGTGTC 61.646 66.667 16.16 0.00 40.58 3.67
938 1013 1.984570 CGAGGTGAAGGGAGGAGCA 60.985 63.158 0.00 0.00 0.00 4.26
939 1014 2.726351 CCGAGGTGAAGGGAGGAGC 61.726 68.421 0.00 0.00 0.00 4.70
946 1021 6.018994 CGAAGTTTATTAATCCGAGGTGAAGG 60.019 42.308 0.00 0.00 0.00 3.46
947 1022 6.018994 CCGAAGTTTATTAATCCGAGGTGAAG 60.019 42.308 0.00 0.00 0.00 3.02
948 1023 5.813672 CCGAAGTTTATTAATCCGAGGTGAA 59.186 40.000 0.00 0.00 0.00 3.18
949 1024 5.353938 CCGAAGTTTATTAATCCGAGGTGA 58.646 41.667 0.00 0.00 0.00 4.02
950 1025 4.025145 GCCGAAGTTTATTAATCCGAGGTG 60.025 45.833 0.00 0.00 0.00 4.00
994 1072 3.436055 GCACGCGCCCATGGTAAA 61.436 61.111 11.73 0.00 0.00 2.01
1518 1615 2.049985 CGGTCGATCCATCTCGCC 60.050 66.667 0.00 0.00 38.52 5.54
1521 1618 0.317938 CGGTTCGGTCGATCCATCTC 60.318 60.000 17.26 0.00 34.54 2.75
1522 1619 1.734137 CGGTTCGGTCGATCCATCT 59.266 57.895 17.26 0.00 34.54 2.90
1524 1621 2.812499 CCGGTTCGGTCGATCCAT 59.188 61.111 17.26 0.00 42.73 3.41
1558 1655 5.105432 ACTCTACACTCGGGTTATTTTCCTC 60.105 44.000 0.00 0.00 0.00 3.71
1561 1658 6.252228 CGTAACTCTACACTCGGGTTATTTTC 59.748 42.308 0.00 0.00 0.00 2.29
1601 1699 2.820197 GTCAAACCAAATCTCCCTCCAC 59.180 50.000 0.00 0.00 0.00 4.02
1602 1700 2.716424 AGTCAAACCAAATCTCCCTCCA 59.284 45.455 0.00 0.00 0.00 3.86
1686 1784 1.886861 GCACTACACTGGAACGTGCG 61.887 60.000 0.00 0.00 41.06 5.34
1695 1793 0.867746 ACAACATGCGCACTACACTG 59.132 50.000 14.90 8.89 0.00 3.66
1700 1798 3.033368 TCTTGTACAACATGCGCACTA 57.967 42.857 14.90 0.00 0.00 2.74
1702 1800 2.679355 TTCTTGTACAACATGCGCAC 57.321 45.000 14.90 0.00 0.00 5.34
1703 1801 2.875317 TCTTTCTTGTACAACATGCGCA 59.125 40.909 14.96 14.96 0.00 6.09
1704 1802 3.226347 GTCTTTCTTGTACAACATGCGC 58.774 45.455 3.59 0.00 0.00 6.09
1705 1803 3.469629 CGTCTTTCTTGTACAACATGCG 58.530 45.455 3.59 1.64 0.00 4.73
1706 1804 3.226347 GCGTCTTTCTTGTACAACATGC 58.774 45.455 3.59 0.37 0.00 4.06
1707 1805 3.059868 ACGCGTCTTTCTTGTACAACATG 60.060 43.478 5.58 0.00 0.00 3.21
1708 1806 3.128349 ACGCGTCTTTCTTGTACAACAT 58.872 40.909 5.58 0.00 0.00 2.71
1709 1807 2.542597 ACGCGTCTTTCTTGTACAACA 58.457 42.857 5.58 0.00 0.00 3.33
1710 1808 3.120782 CCTACGCGTCTTTCTTGTACAAC 59.879 47.826 18.63 0.00 0.00 3.32
1711 1809 3.311106 CCTACGCGTCTTTCTTGTACAA 58.689 45.455 18.63 8.28 0.00 2.41
1751 1849 3.932822 TCGACGGAATCAGGATCAAAAA 58.067 40.909 0.00 0.00 0.00 1.94
1761 1859 2.582436 GGCCCTTCGACGGAATCA 59.418 61.111 10.00 0.00 0.00 2.57
1762 1860 2.585247 CGGCCCTTCGACGGAATC 60.585 66.667 10.00 0.00 0.00 2.52
1764 1862 4.060038 GACGGCCCTTCGACGGAA 62.060 66.667 10.00 0.00 0.00 4.30
1768 1866 0.391263 ATTTCAGACGGCCCTTCGAC 60.391 55.000 0.00 0.00 0.00 4.20
1770 1868 0.108138 AGATTTCAGACGGCCCTTCG 60.108 55.000 0.00 0.00 0.00 3.79
1778 1876 2.611518 GTCCAGTCCAGATTTCAGACG 58.388 52.381 0.00 0.00 35.65 4.18
1816 1914 4.699522 GACCCACCCGTCAGCCAC 62.700 72.222 0.00 0.00 32.74 5.01
1840 1938 0.097674 GCAGTGCTGGACATTAAGCG 59.902 55.000 8.18 0.00 42.54 4.68
1843 1941 1.305219 GCGGCAGTGCTGGACATTAA 61.305 55.000 25.02 0.00 35.15 1.40
1852 1950 2.749044 CATTCTGGCGGCAGTGCT 60.749 61.111 34.57 19.32 34.52 4.40
1861 1959 1.657751 GAAGAACGCCCCATTCTGGC 61.658 60.000 0.00 0.00 45.70 4.85
1863 1961 1.089920 CAGAAGAACGCCCCATTCTG 58.910 55.000 0.00 0.00 41.76 3.02
1864 1962 0.984230 TCAGAAGAACGCCCCATTCT 59.016 50.000 0.00 0.00 38.05 2.40
1872 1970 2.470781 CGTCATTTCGTCAGAAGAACGC 60.471 50.000 0.00 0.00 37.70 4.84
1873 1971 2.724690 ACGTCATTTCGTCAGAAGAACG 59.275 45.455 0.00 2.87 40.04 3.95
1901 1999 1.287730 GCTAAGCATCGATCTGGCCG 61.288 60.000 0.00 0.00 0.00 6.13
1942 2040 5.890424 AAATACACTCCATTTACCAACGG 57.110 39.130 0.00 0.00 0.00 4.44
1948 2046 6.253013 GCGTACCAAAATACACTCCATTTAC 58.747 40.000 0.00 0.00 0.00 2.01
1971 2069 1.211181 GACCGGATTAACGCGTAGGC 61.211 60.000 14.46 2.03 0.00 3.93
1972 2070 0.931662 CGACCGGATTAACGCGTAGG 60.932 60.000 14.46 11.94 0.00 3.18
1975 2073 2.882301 GCGACCGGATTAACGCGT 60.882 61.111 9.46 5.58 41.49 6.01
2033 2131 1.488390 AATACCAGGGGCAAATGCAG 58.512 50.000 7.80 0.00 44.36 4.41
2058 2192 2.451493 TTCCCTCCCAAGGCACCA 60.451 61.111 0.00 0.00 41.85 4.17
2062 2196 1.208165 TTCTCCTTCCCTCCCAAGGC 61.208 60.000 0.00 0.00 41.85 4.35
2063 2197 0.915364 CTTCTCCTTCCCTCCCAAGG 59.085 60.000 0.00 0.00 41.81 3.61
2072 2206 4.840005 CCCCGCGCTTCTCCTTCC 62.840 72.222 5.56 0.00 0.00 3.46
2074 2208 3.775654 CTCCCCGCGCTTCTCCTT 61.776 66.667 5.56 0.00 0.00 3.36
2088 2227 0.178301 GCTTAGCCCACACTACCTCC 59.822 60.000 0.00 0.00 0.00 4.30
2093 2232 1.613255 GCCTTTGCTTAGCCCACACTA 60.613 52.381 0.29 0.00 33.53 2.74
2095 2234 1.586541 GCCTTTGCTTAGCCCACAC 59.413 57.895 0.29 0.00 33.53 3.82
2141 2284 2.294449 AAAGCTGAGAAAAGGTCCCC 57.706 50.000 0.00 0.00 0.00 4.81
2163 2306 1.355563 CGCGCGAGAGGATTAGACA 59.644 57.895 28.94 0.00 0.00 3.41
2323 2517 1.676303 GCCCCGGGAAAACGAATCA 60.676 57.895 26.32 0.00 35.47 2.57
2345 2552 3.189287 GGGTGCATGGCGAGATAATAAAG 59.811 47.826 0.00 0.00 0.00 1.85
2396 2603 1.785430 GCTTATCCGGACGAACGAATC 59.215 52.381 6.12 0.00 35.47 2.52
2417 2645 2.269172 GTACGGCCTTCTTTCTACTGC 58.731 52.381 0.00 0.00 0.00 4.40
2418 2646 2.094854 ACGTACGGCCTTCTTTCTACTG 60.095 50.000 21.06 0.00 0.00 2.74
2419 2647 2.163211 GACGTACGGCCTTCTTTCTACT 59.837 50.000 21.06 0.00 0.00 2.57
2462 2702 6.203145 CAGATAGCATAGCATAGCATTGGATC 59.797 42.308 0.00 0.00 0.00 3.36
2472 2712 2.428530 CCGCCTCAGATAGCATAGCATA 59.571 50.000 0.00 0.00 0.00 3.14
2480 2720 0.965439 ACAGATCCGCCTCAGATAGC 59.035 55.000 0.00 0.00 0.00 2.97
2481 2721 3.570125 TGTAACAGATCCGCCTCAGATAG 59.430 47.826 0.00 0.00 0.00 2.08
2482 2722 3.562182 TGTAACAGATCCGCCTCAGATA 58.438 45.455 0.00 0.00 0.00 1.98
2483 2723 2.388735 TGTAACAGATCCGCCTCAGAT 58.611 47.619 0.00 0.00 0.00 2.90
2484 2724 1.847328 TGTAACAGATCCGCCTCAGA 58.153 50.000 0.00 0.00 0.00 3.27


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

AutoCloner maintained by Alex Coulton.