Multiple sequence alignment - TraesCS5B01G478700

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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 TraesCS5B01G478700 chr5B 100.000 3224 0 0 1 3224 650340458 650337235 0.000000e+00 5954.0
1 TraesCS5B01G478700 chr5B 93.701 635 34 4 2596 3224 420865705 420865071 0.000000e+00 946.0
2 TraesCS5B01G478700 chr5D 93.305 1852 86 18 657 2489 517754474 517752642 0.000000e+00 2699.0
3 TraesCS5B01G478700 chr5D 87.788 434 42 5 1 425 517755296 517754865 6.210000e-137 497.0
4 TraesCS5B01G478700 chr5D 86.207 87 7 5 2258 2341 281024790 281024874 4.430000e-14 89.8
5 TraesCS5B01G478700 chr5A 91.213 1673 91 38 631 2285 645128406 645126772 0.000000e+00 2224.0
6 TraesCS5B01G478700 chr5A 87.529 433 33 8 1 425 645128931 645128512 6.260000e-132 481.0
7 TraesCS5B01G478700 chr4B 94.304 632 31 5 2597 3224 627816799 627817429 0.000000e+00 963.0
8 TraesCS5B01G478700 chr4B 93.671 632 32 7 2598 3222 590039026 590039656 0.000000e+00 939.0
9 TraesCS5B01G478700 chr4B 87.500 80 6 4 2264 2341 178077841 178077918 4.430000e-14 89.8
10 TraesCS5B01G478700 chr4B 88.889 72 5 3 2257 2325 41531416 41531487 5.730000e-13 86.1
11 TraesCS5B01G478700 chr2B 93.839 633 35 4 2596 3224 680107016 680106384 0.000000e+00 950.0
12 TraesCS5B01G478700 chr2B 93.701 635 33 6 2596 3224 149031588 149030955 0.000000e+00 944.0
13 TraesCS5B01G478700 chr7B 93.681 633 35 5 2596 3224 664069123 664069754 0.000000e+00 942.0
14 TraesCS5B01G478700 chr7B 73.743 179 31 13 1467 1637 337024231 337024061 4.490000e-04 56.5
15 TraesCS5B01G478700 chr6B 93.523 633 37 4 2596 3224 578449506 578448874 0.000000e+00 939.0
16 TraesCS5B01G478700 chr6B 93.365 633 38 4 2596 3224 571024614 571023982 0.000000e+00 933.0
17 TraesCS5B01G478700 chr3B 93.513 632 37 4 2596 3224 502312185 502311555 0.000000e+00 937.0
18 TraesCS5B01G478700 chr1A 90.789 76 4 2 2267 2341 10076111 10076184 7.360000e-17 99.0
19 TraesCS5B01G478700 chr1A 86.364 88 8 3 2258 2343 11940814 11940899 3.420000e-15 93.5
20 TraesCS5B01G478700 chr1A 96.875 32 0 1 1945 1976 537977645 537977675 6.000000e-03 52.8
21 TraesCS5B01G478700 chr4D 87.342 79 7 3 2264 2341 116276833 116276909 1.590000e-13 87.9
22 TraesCS5B01G478700 chr4A 85.057 87 8 5 2258 2341 467263408 467263324 2.060000e-12 84.2
23 TraesCS5B01G478700 chr7A 84.091 88 10 4 2256 2341 634962435 634962350 7.410000e-12 82.4
24 TraesCS5B01G478700 chr7A 100.000 29 0 0 1609 1637 200509850 200509822 2.000000e-03 54.7
25 TraesCS5B01G478700 chr7D 100.000 29 0 0 1609 1637 191796255 191796227 2.000000e-03 54.7


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 TraesCS5B01G478700 chr5B 650337235 650340458 3223 True 5954.0 5954 100.0000 1 3224 1 chr5B.!!$R2 3223
1 TraesCS5B01G478700 chr5B 420865071 420865705 634 True 946.0 946 93.7010 2596 3224 1 chr5B.!!$R1 628
2 TraesCS5B01G478700 chr5D 517752642 517755296 2654 True 1598.0 2699 90.5465 1 2489 2 chr5D.!!$R1 2488
3 TraesCS5B01G478700 chr5A 645126772 645128931 2159 True 1352.5 2224 89.3710 1 2285 2 chr5A.!!$R1 2284
4 TraesCS5B01G478700 chr4B 627816799 627817429 630 False 963.0 963 94.3040 2597 3224 1 chr4B.!!$F4 627
5 TraesCS5B01G478700 chr4B 590039026 590039656 630 False 939.0 939 93.6710 2598 3222 1 chr4B.!!$F3 624
6 TraesCS5B01G478700 chr2B 680106384 680107016 632 True 950.0 950 93.8390 2596 3224 1 chr2B.!!$R2 628
7 TraesCS5B01G478700 chr2B 149030955 149031588 633 True 944.0 944 93.7010 2596 3224 1 chr2B.!!$R1 628
8 TraesCS5B01G478700 chr7B 664069123 664069754 631 False 942.0 942 93.6810 2596 3224 1 chr7B.!!$F1 628
9 TraesCS5B01G478700 chr6B 578448874 578449506 632 True 939.0 939 93.5230 2596 3224 1 chr6B.!!$R2 628
10 TraesCS5B01G478700 chr6B 571023982 571024614 632 True 933.0 933 93.3650 2596 3224 1 chr6B.!!$R1 628
11 TraesCS5B01G478700 chr3B 502311555 502312185 630 True 937.0 937 93.5130 2596 3224 1 chr3B.!!$R1 628

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
788 1038 0.105039 GATGGATGTCCTCGTCACCC 59.895 60.0 0.09 0.0 36.82 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2341 2614 0.172578 GGCCCTTAACCGCAATCAAC 59.827 55.0 0.0 0.0 0.0 3.18 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
52 53 2.012673 GTGCTGCGGAAGATTGAGAAT 58.987 47.619 0.00 0.00 0.00 2.40
55 56 2.421424 GCTGCGGAAGATTGAGAATGTT 59.579 45.455 0.00 0.00 0.00 2.71
67 68 0.670546 AGAATGTTGCGACTGGACCG 60.671 55.000 5.50 0.00 0.00 4.79
76 77 1.364901 GACTGGACCGAACAACCGA 59.635 57.895 0.00 0.00 0.00 4.69
88 89 2.110213 AACCGACCGAAGCTTGCA 59.890 55.556 2.10 0.00 0.00 4.08
109 110 0.457853 GCGTGATAAGCGAGTGTGGA 60.458 55.000 0.00 0.00 0.00 4.02
126 128 3.194062 GTGGAGAGATGTAGCTTGCTTC 58.806 50.000 0.00 0.00 0.00 3.86
130 132 2.100584 AGAGATGTAGCTTGCTTCTCGG 59.899 50.000 18.93 0.00 40.15 4.63
189 191 6.591935 TGAAAGTACTGAATCACTGGAAACT 58.408 36.000 0.00 0.00 0.00 2.66
192 194 6.174720 AGTACTGAATCACTGGAAACTGAA 57.825 37.500 0.00 0.00 0.00 3.02
201 203 3.999663 CACTGGAAACTGAATGGAGTCTC 59.000 47.826 0.00 0.00 0.00 3.36
246 255 2.857592 ATTGTGAGCATGCGGAATTC 57.142 45.000 13.01 4.35 0.00 2.17
247 256 1.825090 TTGTGAGCATGCGGAATTCT 58.175 45.000 13.01 0.00 0.00 2.40
285 294 3.185188 GCAACATGTATCTGTATCAGCCG 59.815 47.826 0.00 0.00 0.00 5.52
290 299 2.029020 TGTATCTGTATCAGCCGATGCC 60.029 50.000 0.00 0.00 38.69 4.40
302 311 0.462047 CCGATGCCGTAGAGCCTTTT 60.462 55.000 0.00 0.00 0.00 2.27
343 352 8.250332 GGTGTTGAATAATATTGAAAGCAGGAA 58.750 33.333 0.00 0.00 0.00 3.36
344 353 9.807649 GTGTTGAATAATATTGAAAGCAGGAAT 57.192 29.630 0.00 0.00 0.00 3.01
367 376 2.816204 TTGTGCATGTGGTTTGATGG 57.184 45.000 0.00 0.00 0.00 3.51
377 386 1.251251 GGTTTGATGGCTTCACTGCT 58.749 50.000 2.09 0.00 32.84 4.24
381 390 0.958876 TGATGGCTTCACTGCTGCTG 60.959 55.000 4.89 4.89 0.00 4.41
391 401 3.151554 TCACTGCTGCTGATTTGTTGAT 58.848 40.909 13.69 0.00 0.00 2.57
396 406 5.001237 TGCTGCTGATTTGTTGATTATGG 57.999 39.130 0.00 0.00 0.00 2.74
417 427 0.894835 GCCCCCAATTTGTCGTTCAT 59.105 50.000 0.00 0.00 0.00 2.57
422 432 3.987220 CCCCAATTTGTCGTTCATTCAAC 59.013 43.478 0.00 0.00 0.00 3.18
425 435 4.444056 CCAATTTGTCGTTCATTCAACCAC 59.556 41.667 0.00 0.00 0.00 4.16
427 437 3.684103 TTGTCGTTCATTCAACCACAC 57.316 42.857 0.00 0.00 36.01 3.82
429 439 3.275143 TGTCGTTCATTCAACCACACTT 58.725 40.909 0.00 0.00 31.80 3.16
430 440 4.443621 TGTCGTTCATTCAACCACACTTA 58.556 39.130 0.00 0.00 31.80 2.24
431 441 5.060506 TGTCGTTCATTCAACCACACTTAT 58.939 37.500 0.00 0.00 31.80 1.73
432 442 5.529430 TGTCGTTCATTCAACCACACTTATT 59.471 36.000 0.00 0.00 31.80 1.40
433 443 6.038825 TGTCGTTCATTCAACCACACTTATTT 59.961 34.615 0.00 0.00 31.80 1.40
434 444 7.226918 TGTCGTTCATTCAACCACACTTATTTA 59.773 33.333 0.00 0.00 31.80 1.40
435 445 8.234546 GTCGTTCATTCAACCACACTTATTTAT 58.765 33.333 0.00 0.00 0.00 1.40
436 446 8.788806 TCGTTCATTCAACCACACTTATTTATT 58.211 29.630 0.00 0.00 0.00 1.40
437 447 9.405587 CGTTCATTCAACCACACTTATTTATTT 57.594 29.630 0.00 0.00 0.00 1.40
459 469 1.403814 TTTTTGCGGGTGTTCATCCA 58.596 45.000 2.95 0.00 0.00 3.41
460 470 1.403814 TTTTGCGGGTGTTCATCCAA 58.596 45.000 2.95 0.00 0.00 3.53
461 471 0.671251 TTTGCGGGTGTTCATCCAAC 59.329 50.000 2.95 0.00 35.28 3.77
462 472 1.175983 TTGCGGGTGTTCATCCAACC 61.176 55.000 2.95 0.00 38.93 3.77
463 473 1.602323 GCGGGTGTTCATCCAACCA 60.602 57.895 2.95 0.00 42.70 3.67
464 474 1.862602 GCGGGTGTTCATCCAACCAC 61.863 60.000 2.95 0.00 42.70 4.16
465 475 0.536233 CGGGTGTTCATCCAACCACA 60.536 55.000 2.95 0.00 42.70 4.17
466 476 0.958822 GGGTGTTCATCCAACCACAC 59.041 55.000 0.00 0.00 42.10 3.82
467 477 1.478654 GGGTGTTCATCCAACCACACT 60.479 52.381 0.00 0.00 42.10 3.55
468 478 2.306847 GGTGTTCATCCAACCACACTT 58.693 47.619 0.00 0.00 39.63 3.16
485 495 3.134804 ACACTTGCTCTGATATACCACCC 59.865 47.826 0.00 0.00 0.00 4.61
487 497 0.679505 TGCTCTGATATACCACCCGC 59.320 55.000 0.00 0.00 0.00 6.13
488 498 0.969894 GCTCTGATATACCACCCGCT 59.030 55.000 0.00 0.00 0.00 5.52
489 499 1.067495 GCTCTGATATACCACCCGCTC 60.067 57.143 0.00 0.00 0.00 5.03
490 500 1.546476 CTCTGATATACCACCCGCTCC 59.454 57.143 0.00 0.00 0.00 4.70
491 501 1.133294 TCTGATATACCACCCGCTCCA 60.133 52.381 0.00 0.00 0.00 3.86
492 502 1.000955 CTGATATACCACCCGCTCCAC 59.999 57.143 0.00 0.00 0.00 4.02
493 503 1.045407 GATATACCACCCGCTCCACA 58.955 55.000 0.00 0.00 0.00 4.17
494 504 0.756903 ATATACCACCCGCTCCACAC 59.243 55.000 0.00 0.00 0.00 3.82
495 505 0.615261 TATACCACCCGCTCCACACA 60.615 55.000 0.00 0.00 0.00 3.72
496 506 1.899437 ATACCACCCGCTCCACACAG 61.899 60.000 0.00 0.00 0.00 3.66
497 507 3.941188 CCACCCGCTCCACACAGT 61.941 66.667 0.00 0.00 0.00 3.55
498 508 2.111043 CACCCGCTCCACACAGTT 59.889 61.111 0.00 0.00 0.00 3.16
499 509 1.525995 CACCCGCTCCACACAGTTT 60.526 57.895 0.00 0.00 0.00 2.66
500 510 1.101049 CACCCGCTCCACACAGTTTT 61.101 55.000 0.00 0.00 0.00 2.43
501 511 1.101049 ACCCGCTCCACACAGTTTTG 61.101 55.000 0.00 0.00 0.00 2.44
502 512 1.101049 CCCGCTCCACACAGTTTTGT 61.101 55.000 0.00 0.00 38.31 2.83
503 513 0.738389 CCGCTCCACACAGTTTTGTT 59.262 50.000 0.00 0.00 34.62 2.83
504 514 1.134175 CCGCTCCACACAGTTTTGTTT 59.866 47.619 0.00 0.00 34.62 2.83
505 515 2.416701 CCGCTCCACACAGTTTTGTTTT 60.417 45.455 0.00 0.00 34.62 2.43
506 516 3.249917 CGCTCCACACAGTTTTGTTTTT 58.750 40.909 0.00 0.00 34.62 1.94
507 517 3.303229 CGCTCCACACAGTTTTGTTTTTC 59.697 43.478 0.00 0.00 34.62 2.29
508 518 4.494484 GCTCCACACAGTTTTGTTTTTCT 58.506 39.130 0.00 0.00 34.62 2.52
509 519 4.929211 GCTCCACACAGTTTTGTTTTTCTT 59.071 37.500 0.00 0.00 34.62 2.52
510 520 5.062183 GCTCCACACAGTTTTGTTTTTCTTC 59.938 40.000 0.00 0.00 34.62 2.87
511 521 6.339587 TCCACACAGTTTTGTTTTTCTTCT 57.660 33.333 0.00 0.00 34.62 2.85
512 522 6.386654 TCCACACAGTTTTGTTTTTCTTCTC 58.613 36.000 0.00 0.00 34.62 2.87
513 523 6.208599 TCCACACAGTTTTGTTTTTCTTCTCT 59.791 34.615 0.00 0.00 34.62 3.10
514 524 7.392113 TCCACACAGTTTTGTTTTTCTTCTCTA 59.608 33.333 0.00 0.00 34.62 2.43
515 525 8.190784 CCACACAGTTTTGTTTTTCTTCTCTAT 58.809 33.333 0.00 0.00 34.62 1.98
516 526 9.573133 CACACAGTTTTGTTTTTCTTCTCTATT 57.427 29.630 0.00 0.00 34.62 1.73
517 527 9.788960 ACACAGTTTTGTTTTTCTTCTCTATTC 57.211 29.630 0.00 0.00 34.62 1.75
550 561 6.605471 TTTTAGCTCTGTCACTATCTTCCA 57.395 37.500 0.00 0.00 0.00 3.53
553 564 4.348486 AGCTCTGTCACTATCTTCCAAGA 58.652 43.478 0.00 0.00 39.78 3.02
554 565 4.961730 AGCTCTGTCACTATCTTCCAAGAT 59.038 41.667 7.01 7.01 46.85 2.40
556 567 6.782000 AGCTCTGTCACTATCTTCCAAGATAT 59.218 38.462 9.07 0.00 44.54 1.63
558 569 8.580720 GCTCTGTCACTATCTTCCAAGATATAA 58.419 37.037 9.07 0.00 44.54 0.98
570 581 8.705594 TCTTCCAAGATATAATAATCGATCCCC 58.294 37.037 0.00 0.00 0.00 4.81
571 582 8.624019 TTCCAAGATATAATAATCGATCCCCT 57.376 34.615 0.00 0.00 0.00 4.79
573 584 8.068110 TCCAAGATATAATAATCGATCCCCTCT 58.932 37.037 0.00 0.00 0.00 3.69
581 592 4.344359 AATCGATCCCCTCTAAAAGAGC 57.656 45.455 0.00 0.00 40.98 4.09
582 593 2.747177 TCGATCCCCTCTAAAAGAGCA 58.253 47.619 0.00 0.00 40.98 4.26
583 594 3.309296 TCGATCCCCTCTAAAAGAGCAT 58.691 45.455 0.00 0.00 40.98 3.79
584 595 3.070159 TCGATCCCCTCTAAAAGAGCATG 59.930 47.826 0.00 0.00 40.98 4.06
585 596 3.070159 CGATCCCCTCTAAAAGAGCATGA 59.930 47.826 0.00 0.00 40.98 3.07
587 598 5.047021 CGATCCCCTCTAAAAGAGCATGATA 60.047 44.000 0.00 0.00 40.98 2.15
589 600 6.770286 TCCCCTCTAAAAGAGCATGATAAT 57.230 37.500 0.00 0.00 40.98 1.28
590 601 7.154191 TCCCCTCTAAAAGAGCATGATAATT 57.846 36.000 0.00 0.00 40.98 1.40
591 602 8.275187 TCCCCTCTAAAAGAGCATGATAATTA 57.725 34.615 0.00 0.00 40.98 1.40
592 603 8.723365 TCCCCTCTAAAAGAGCATGATAATTAA 58.277 33.333 0.00 0.00 40.98 1.40
637 813 4.074259 ACTGTTCCGGGGTATAACAAAAC 58.926 43.478 0.00 0.00 33.05 2.43
641 817 4.013267 TCCGGGGTATAACAAAACGAAA 57.987 40.909 0.00 0.00 0.00 3.46
642 818 4.587891 TCCGGGGTATAACAAAACGAAAT 58.412 39.130 0.00 0.00 0.00 2.17
649 855 7.652507 GGGGTATAACAAAACGAAATTGTTTGA 59.347 33.333 17.88 6.77 45.97 2.69
651 857 8.696175 GGTATAACAAAACGAAATTGTTTGAGG 58.304 33.333 17.88 0.00 45.97 3.86
665 871 4.601084 TGTTTGAGGTACCAGGAACAAAA 58.399 39.130 15.94 1.03 0.00 2.44
719 966 2.542178 GTCAATATACCGACGCAATGCA 59.458 45.455 5.91 0.00 0.00 3.96
742 989 2.335011 GGCTGCCACGAACAAACC 59.665 61.111 15.17 0.00 0.00 3.27
788 1038 0.105039 GATGGATGTCCTCGTCACCC 59.895 60.000 0.09 0.00 36.82 4.61
789 1039 0.617535 ATGGATGTCCTCGTCACCCA 60.618 55.000 0.09 0.00 36.82 4.51
799 1049 1.745115 CGTCACCCAATCATGCGGT 60.745 57.895 0.00 0.00 32.37 5.68
979 1229 2.229543 CGGGGGTTAAGCTTAAAACACC 59.770 50.000 23.89 23.89 46.54 4.16
1015 1269 0.820482 GTCGAGCTCCTAGGGTCTCC 60.820 65.000 19.10 7.99 0.00 3.71
1025 1279 2.838693 GGGTCTCCCTCTACCGCC 60.839 72.222 0.00 0.00 41.34 6.13
1026 1280 2.043248 GGTCTCCCTCTACCGCCA 60.043 66.667 0.00 0.00 0.00 5.69
1484 1738 2.030562 CGTCACCGGCACCTTCTT 59.969 61.111 0.00 0.00 0.00 2.52
2073 2335 0.701303 CTGTCGTTAGTCGTCGTTGC 59.299 55.000 0.00 0.00 40.80 4.17
2098 2360 4.097286 TCTTTTCTTTTTGGAAGACGTGGG 59.903 41.667 0.00 0.00 0.00 4.61
2176 2445 3.407252 CGCGAACAATCTTGTGTGTATG 58.593 45.455 0.00 0.00 41.31 2.39
2201 2471 7.147794 TGGACTGTGTAAACGGAATCTATACAT 60.148 37.037 0.00 0.00 0.00 2.29
2202 2472 7.169308 GGACTGTGTAAACGGAATCTATACATG 59.831 40.741 0.00 0.00 0.00 3.21
2264 2535 1.829222 TCTCCGTGAACAATACTCCCC 59.171 52.381 0.00 0.00 0.00 4.81
2281 2554 4.019231 ACTCCCCCTCTCAAAATGTAAGAC 60.019 45.833 0.00 0.00 0.00 3.01
2311 2584 9.917129 TTTTAGCCTAAATTAGCCTACAAAAAC 57.083 29.630 0.00 0.00 0.00 2.43
2325 2598 9.005777 AGCCTACAAAAACGTCTTATATTTTGA 57.994 29.630 21.46 9.08 42.48 2.69
2364 2637 0.107165 ATTGCGGTTAAGGGCCTCTC 60.107 55.000 6.46 0.00 0.00 3.20
2366 2639 0.324923 TGCGGTTAAGGGCCTCTCTA 60.325 55.000 6.46 0.00 0.00 2.43
2382 2655 6.928492 GGCCTCTCTAATTCACAAGATTCTAG 59.072 42.308 0.00 0.00 0.00 2.43
2385 2658 8.359642 CCTCTCTAATTCACAAGATTCTAGGAG 58.640 40.741 0.00 0.00 0.00 3.69
2392 2665 5.240891 TCACAAGATTCTAGGAGTGCAAAG 58.759 41.667 0.00 0.00 0.00 2.77
2413 2686 7.384115 GCAAAGATAGGAAAACAAAAGGGTTAC 59.616 37.037 0.00 0.00 0.00 2.50
2421 2694 9.772973 AGGAAAACAAAAGGGTTACAATATTTC 57.227 29.630 0.00 0.00 0.00 2.17
2474 2747 3.874392 ATTTTTGCGGGAGAAATCCTG 57.126 42.857 0.00 0.00 39.14 3.86
2480 2753 3.305720 TGCGGGAGAAATCCTGTAGTAT 58.694 45.455 5.08 0.00 38.40 2.12
2489 2762 9.110502 GGAGAAATCCTGTAGTATTTTAGGTTG 57.889 37.037 0.00 0.00 0.00 3.77
2490 2763 8.507524 AGAAATCCTGTAGTATTTTAGGTTGC 57.492 34.615 0.00 0.00 0.00 4.17
2491 2764 7.556635 AGAAATCCTGTAGTATTTTAGGTTGCC 59.443 37.037 0.00 0.00 0.00 4.52
2492 2765 5.106876 TCCTGTAGTATTTTAGGTTGCCC 57.893 43.478 0.00 0.00 0.00 5.36
2493 2766 4.080186 TCCTGTAGTATTTTAGGTTGCCCC 60.080 45.833 0.00 0.00 0.00 5.80
2494 2767 4.204799 CTGTAGTATTTTAGGTTGCCCCC 58.795 47.826 0.00 0.00 0.00 5.40
2495 2768 3.853784 TGTAGTATTTTAGGTTGCCCCCT 59.146 43.478 0.00 0.00 38.70 4.79
2496 2769 4.292836 TGTAGTATTTTAGGTTGCCCCCTT 59.707 41.667 0.00 0.00 35.97 3.95
2497 2770 4.413641 AGTATTTTAGGTTGCCCCCTTT 57.586 40.909 0.00 0.00 35.97 3.11
2498 2771 4.093743 AGTATTTTAGGTTGCCCCCTTTG 58.906 43.478 0.00 0.00 35.97 2.77
2499 2772 2.480642 TTTTAGGTTGCCCCCTTTGT 57.519 45.000 0.00 0.00 35.97 2.83
2500 2773 2.480642 TTTAGGTTGCCCCCTTTGTT 57.519 45.000 0.00 0.00 35.97 2.83
2501 2774 2.003937 TTAGGTTGCCCCCTTTGTTC 57.996 50.000 0.00 0.00 35.97 3.18
2502 2775 0.250989 TAGGTTGCCCCCTTTGTTCG 60.251 55.000 0.00 0.00 35.97 3.95
2503 2776 2.570284 GGTTGCCCCCTTTGTTCGG 61.570 63.158 0.00 0.00 0.00 4.30
2504 2777 2.203567 TTGCCCCCTTTGTTCGGG 60.204 61.111 0.00 0.00 41.59 5.14
2507 2780 3.083386 CCCCCTTTGTTCGGGCTA 58.917 61.111 0.00 0.00 40.54 3.93
2508 2781 1.378119 CCCCCTTTGTTCGGGCTAC 60.378 63.158 0.00 0.00 40.54 3.58
2509 2782 1.377229 CCCCTTTGTTCGGGCTACA 59.623 57.895 0.00 0.00 40.54 2.74
2510 2783 0.676782 CCCCTTTGTTCGGGCTACAG 60.677 60.000 0.00 0.00 40.54 2.74
2511 2784 0.323629 CCCTTTGTTCGGGCTACAGA 59.676 55.000 0.00 0.00 34.32 3.41
2512 2785 1.065418 CCCTTTGTTCGGGCTACAGAT 60.065 52.381 0.00 0.00 34.32 2.90
2513 2786 2.618045 CCCTTTGTTCGGGCTACAGATT 60.618 50.000 0.00 0.00 34.32 2.40
2514 2787 2.678336 CCTTTGTTCGGGCTACAGATTC 59.322 50.000 0.00 0.00 0.00 2.52
2515 2788 2.396590 TTGTTCGGGCTACAGATTCC 57.603 50.000 0.00 0.00 0.00 3.01
2516 2789 1.568504 TGTTCGGGCTACAGATTCCT 58.431 50.000 0.00 0.00 0.00 3.36
2517 2790 1.207089 TGTTCGGGCTACAGATTCCTG 59.793 52.381 0.00 0.00 45.76 3.86
2518 2791 1.480954 GTTCGGGCTACAGATTCCTGA 59.519 52.381 0.00 0.00 43.02 3.86
2519 2792 1.403814 TCGGGCTACAGATTCCTGAG 58.596 55.000 0.00 0.00 43.02 3.35
2520 2793 1.063942 TCGGGCTACAGATTCCTGAGA 60.064 52.381 0.00 0.00 43.02 3.27
2521 2794 1.757118 CGGGCTACAGATTCCTGAGAA 59.243 52.381 0.00 0.00 43.02 2.87
2522 2795 2.366916 CGGGCTACAGATTCCTGAGAAT 59.633 50.000 0.00 0.00 45.63 2.40
2530 2803 2.131183 GATTCCTGAGAATCGGCTTCG 58.869 52.381 0.39 0.00 46.65 3.79
2531 2804 0.175760 TTCCTGAGAATCGGCTTCGG 59.824 55.000 0.00 0.00 41.22 4.30
2532 2805 1.884926 CCTGAGAATCGGCTTCGGC 60.885 63.158 0.00 0.00 41.22 5.54
2533 2806 1.142748 CTGAGAATCGGCTTCGGCT 59.857 57.895 0.00 0.00 38.61 5.52
2534 2807 0.460987 CTGAGAATCGGCTTCGGCTT 60.461 55.000 0.00 0.00 38.61 4.35
2535 2808 0.740868 TGAGAATCGGCTTCGGCTTG 60.741 55.000 0.00 0.00 38.61 4.01
2536 2809 1.432270 GAGAATCGGCTTCGGCTTGG 61.432 60.000 0.00 0.00 38.98 3.61
2537 2810 1.449601 GAATCGGCTTCGGCTTGGA 60.450 57.895 0.00 0.00 41.44 3.53
2538 2811 0.815615 GAATCGGCTTCGGCTTGGAT 60.816 55.000 0.00 0.00 41.44 3.41
2539 2812 0.394352 AATCGGCTTCGGCTTGGATT 60.394 50.000 0.00 0.00 41.44 3.01
2540 2813 0.815615 ATCGGCTTCGGCTTGGATTC 60.816 55.000 0.00 0.00 41.44 2.52
2541 2814 2.472909 CGGCTTCGGCTTGGATTCC 61.473 63.158 0.00 0.00 41.44 3.01
2542 2815 1.077429 GGCTTCGGCTTGGATTCCT 60.077 57.895 3.95 0.00 41.44 3.36
2543 2816 0.180406 GGCTTCGGCTTGGATTCCTA 59.820 55.000 3.95 0.00 41.44 2.94
2544 2817 1.408266 GGCTTCGGCTTGGATTCCTAA 60.408 52.381 3.95 0.00 41.44 2.69
2545 2818 2.365582 GCTTCGGCTTGGATTCCTAAA 58.634 47.619 3.95 0.00 38.08 1.85
2546 2819 2.752903 GCTTCGGCTTGGATTCCTAAAA 59.247 45.455 3.95 0.00 38.08 1.52
2547 2820 3.381590 GCTTCGGCTTGGATTCCTAAAAT 59.618 43.478 3.95 0.00 38.08 1.82
2548 2821 4.498177 GCTTCGGCTTGGATTCCTAAAATC 60.498 45.833 3.95 0.00 38.08 2.17
2549 2822 4.229304 TCGGCTTGGATTCCTAAAATCA 57.771 40.909 3.95 0.00 0.00 2.57
2550 2823 4.199310 TCGGCTTGGATTCCTAAAATCAG 58.801 43.478 3.95 0.00 0.00 2.90
2551 2824 3.243201 CGGCTTGGATTCCTAAAATCAGC 60.243 47.826 3.95 1.97 0.00 4.26
2552 2825 3.956848 GGCTTGGATTCCTAAAATCAGCT 59.043 43.478 3.95 0.00 30.75 4.24
2553 2826 5.133221 GGCTTGGATTCCTAAAATCAGCTA 58.867 41.667 3.95 0.00 30.75 3.32
2554 2827 5.009110 GGCTTGGATTCCTAAAATCAGCTAC 59.991 44.000 3.95 0.00 30.75 3.58
2555 2828 5.590259 GCTTGGATTCCTAAAATCAGCTACA 59.410 40.000 3.95 0.00 0.00 2.74
2556 2829 6.238593 GCTTGGATTCCTAAAATCAGCTACAG 60.239 42.308 3.95 0.00 0.00 2.74
2557 2830 6.313519 TGGATTCCTAAAATCAGCTACAGT 57.686 37.500 3.95 0.00 0.00 3.55
2558 2831 6.721318 TGGATTCCTAAAATCAGCTACAGTT 58.279 36.000 3.95 0.00 0.00 3.16
2559 2832 6.599244 TGGATTCCTAAAATCAGCTACAGTTG 59.401 38.462 3.95 0.00 0.00 3.16
2560 2833 5.880054 TTCCTAAAATCAGCTACAGTTGC 57.120 39.130 0.00 0.00 0.00 4.17
2561 2834 4.905429 TCCTAAAATCAGCTACAGTTGCA 58.095 39.130 9.75 0.00 0.00 4.08
2562 2835 4.937620 TCCTAAAATCAGCTACAGTTGCAG 59.062 41.667 9.75 1.26 0.00 4.41
2563 2836 4.937620 CCTAAAATCAGCTACAGTTGCAGA 59.062 41.667 9.75 7.14 0.00 4.26
2564 2837 5.587844 CCTAAAATCAGCTACAGTTGCAGAT 59.412 40.000 9.75 9.19 38.09 2.90
2565 2838 5.972107 AAAATCAGCTACAGTTGCAGATT 57.028 34.783 17.77 17.77 44.54 2.40
2566 2839 5.557891 AAATCAGCTACAGTTGCAGATTC 57.442 39.130 21.73 0.00 42.81 2.52
2567 2840 3.969287 TCAGCTACAGTTGCAGATTCT 57.031 42.857 9.75 0.00 0.00 2.40
2568 2841 3.593096 TCAGCTACAGTTGCAGATTCTG 58.407 45.455 9.40 9.40 35.60 3.02
2569 2842 3.259123 TCAGCTACAGTTGCAGATTCTGA 59.741 43.478 17.87 0.47 32.44 3.27
2570 2843 3.617706 CAGCTACAGTTGCAGATTCTGAG 59.382 47.826 17.87 5.04 32.44 3.35
2571 2844 3.513119 AGCTACAGTTGCAGATTCTGAGA 59.487 43.478 17.87 1.75 32.44 3.27
2572 2845 4.020751 AGCTACAGTTGCAGATTCTGAGAA 60.021 41.667 17.87 0.00 32.44 2.87
2573 2846 4.874966 GCTACAGTTGCAGATTCTGAGAAT 59.125 41.667 17.87 7.53 32.44 2.40
2574 2847 5.006552 GCTACAGTTGCAGATTCTGAGAATC 59.993 44.000 23.99 23.99 32.44 2.52
2591 2864 6.591935 TGAGAATCAGAAGTAGGTTGTTTGT 58.408 36.000 0.00 0.00 42.56 2.83
2592 2865 7.054124 TGAGAATCAGAAGTAGGTTGTTTGTT 58.946 34.615 0.00 0.00 42.56 2.83
2593 2866 7.556275 TGAGAATCAGAAGTAGGTTGTTTGTTT 59.444 33.333 0.00 0.00 42.56 2.83
2594 2867 8.974060 AGAATCAGAAGTAGGTTGTTTGTTTA 57.026 30.769 0.00 0.00 0.00 2.01
2645 2921 6.695713 GGGTGAATAGGCGATTTTTACAAATC 59.304 38.462 4.54 4.54 43.49 2.17
2732 3010 7.780745 AGTACTCAGGTATAAGCATAACAGAGT 59.219 37.037 10.64 10.64 46.83 3.24
2750 3028 8.709386 AACAGAGTAACAACATAGTCATCATC 57.291 34.615 0.00 0.00 0.00 2.92
2804 3082 2.420022 CGTGAAAACAGGATAAGCAGGG 59.580 50.000 0.00 0.00 0.00 4.45
2837 3115 9.339850 CTATGAGACTGAAGAAATTGGATTGAT 57.660 33.333 0.00 0.00 0.00 2.57
2923 3201 4.722526 TGAGGAAATGAAAGGGTTGAGA 57.277 40.909 0.00 0.00 0.00 3.27
3038 3317 3.802948 AAACTCGAGAACACACAGTCT 57.197 42.857 21.68 0.00 0.00 3.24
3044 3323 0.311165 AGAACACACAGTCTCGGACG 59.689 55.000 0.00 0.00 37.67 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 1.039785 CGAGCAGACCATCTCCCAGA 61.040 60.000 0.00 0.00 0.00 3.86
52 53 1.593209 GTTCGGTCCAGTCGCAACA 60.593 57.895 0.00 0.00 0.00 3.33
55 56 1.593209 GTTGTTCGGTCCAGTCGCA 60.593 57.895 0.00 0.00 0.00 5.10
67 68 0.234884 CAAGCTTCGGTCGGTTGTTC 59.765 55.000 0.00 0.00 35.70 3.18
76 77 2.669569 ACGCATGCAAGCTTCGGT 60.670 55.556 19.57 1.22 0.00 4.69
88 89 1.280982 CACACTCGCTTATCACGCAT 58.719 50.000 0.00 0.00 0.00 4.73
109 110 2.100584 CCGAGAAGCAAGCTACATCTCT 59.899 50.000 16.07 6.76 35.50 3.10
126 128 4.536687 GAAATTGCCGCGCCCGAG 62.537 66.667 0.00 0.00 36.29 4.63
130 132 2.715624 CTAGGAAATTGCCGCGCC 59.284 61.111 0.00 0.00 0.00 6.53
189 191 3.870274 CAATGCTCTGAGACTCCATTCA 58.130 45.455 9.28 0.00 0.00 2.57
192 194 1.838715 AGCAATGCTCTGAGACTCCAT 59.161 47.619 9.28 0.00 30.62 3.41
201 203 7.959689 AGTAGATTAATACAGCAATGCTCTG 57.040 36.000 4.03 0.00 36.40 3.35
246 255 2.245159 TGCCAGTTTGTCAGAGTCAG 57.755 50.000 0.00 0.00 0.00 3.51
247 256 2.288666 GTTGCCAGTTTGTCAGAGTCA 58.711 47.619 0.00 0.00 0.00 3.41
285 294 4.957759 TTTTAAAAGGCTCTACGGCATC 57.042 40.909 0.00 0.00 41.46 3.91
348 357 1.270199 GCCATCAAACCACATGCACAA 60.270 47.619 0.00 0.00 0.00 3.33
352 361 1.273048 TGAAGCCATCAAACCACATGC 59.727 47.619 0.00 0.00 34.30 4.06
363 372 0.675837 TCAGCAGCAGTGAAGCCATC 60.676 55.000 0.00 0.00 34.23 3.51
367 376 1.268899 ACAAATCAGCAGCAGTGAAGC 59.731 47.619 0.00 0.00 0.00 3.86
377 386 4.098349 GGCTCCATAATCAACAAATCAGCA 59.902 41.667 0.00 0.00 0.00 4.41
381 390 3.321968 GGGGGCTCCATAATCAACAAATC 59.678 47.826 4.16 0.00 35.00 2.17
391 401 2.745968 GACAAATTGGGGGCTCCATAA 58.254 47.619 7.09 0.00 46.52 1.90
396 406 0.526211 GAACGACAAATTGGGGGCTC 59.474 55.000 0.00 0.00 0.00 4.70
440 450 1.403814 TGGATGAACACCCGCAAAAA 58.596 45.000 0.00 0.00 0.00 1.94
441 451 1.067821 GTTGGATGAACACCCGCAAAA 59.932 47.619 0.00 0.00 34.35 2.44
442 452 0.671251 GTTGGATGAACACCCGCAAA 59.329 50.000 0.00 0.00 34.35 3.68
443 453 1.175983 GGTTGGATGAACACCCGCAA 61.176 55.000 0.00 0.00 36.12 4.85
444 454 1.602323 GGTTGGATGAACACCCGCA 60.602 57.895 0.00 0.00 36.12 5.69
445 455 1.602323 TGGTTGGATGAACACCCGC 60.602 57.895 0.00 0.00 36.12 6.13
446 456 0.536233 TGTGGTTGGATGAACACCCG 60.536 55.000 0.00 0.00 36.12 5.28
447 457 0.958822 GTGTGGTTGGATGAACACCC 59.041 55.000 0.00 0.00 37.53 4.61
448 458 1.981256 AGTGTGGTTGGATGAACACC 58.019 50.000 1.41 0.00 43.10 4.16
449 459 2.543653 GCAAGTGTGGTTGGATGAACAC 60.544 50.000 0.00 0.00 42.55 3.32
450 460 1.680735 GCAAGTGTGGTTGGATGAACA 59.319 47.619 0.00 0.00 36.12 3.18
451 461 1.956477 AGCAAGTGTGGTTGGATGAAC 59.044 47.619 0.00 0.00 28.67 3.18
452 462 2.158623 AGAGCAAGTGTGGTTGGATGAA 60.159 45.455 0.00 0.00 35.00 2.57
453 463 1.421268 AGAGCAAGTGTGGTTGGATGA 59.579 47.619 0.00 0.00 35.00 2.92
454 464 1.538512 CAGAGCAAGTGTGGTTGGATG 59.461 52.381 0.00 0.00 35.00 3.51
455 465 1.421268 TCAGAGCAAGTGTGGTTGGAT 59.579 47.619 0.00 0.00 35.00 3.41
456 466 0.836606 TCAGAGCAAGTGTGGTTGGA 59.163 50.000 0.00 0.00 35.00 3.53
457 467 1.901591 ATCAGAGCAAGTGTGGTTGG 58.098 50.000 0.00 0.00 35.00 3.77
458 468 4.572389 GGTATATCAGAGCAAGTGTGGTTG 59.428 45.833 0.00 0.00 35.00 3.77
459 469 4.225042 TGGTATATCAGAGCAAGTGTGGTT 59.775 41.667 0.00 0.00 35.00 3.67
460 470 3.774766 TGGTATATCAGAGCAAGTGTGGT 59.225 43.478 0.00 0.00 38.47 4.16
461 471 4.122776 GTGGTATATCAGAGCAAGTGTGG 58.877 47.826 0.00 0.00 0.00 4.17
462 472 4.122776 GGTGGTATATCAGAGCAAGTGTG 58.877 47.826 0.00 0.00 0.00 3.82
463 473 3.134804 GGGTGGTATATCAGAGCAAGTGT 59.865 47.826 0.00 0.00 0.00 3.55
464 474 3.733337 GGGTGGTATATCAGAGCAAGTG 58.267 50.000 0.00 0.00 0.00 3.16
465 475 2.365617 CGGGTGGTATATCAGAGCAAGT 59.634 50.000 0.00 0.00 0.00 3.16
466 476 2.868044 GCGGGTGGTATATCAGAGCAAG 60.868 54.545 0.00 0.00 0.00 4.01
467 477 1.070134 GCGGGTGGTATATCAGAGCAA 59.930 52.381 0.00 0.00 0.00 3.91
468 478 0.679505 GCGGGTGGTATATCAGAGCA 59.320 55.000 0.00 0.00 0.00 4.26
485 495 2.559998 AAACAAAACTGTGTGGAGCG 57.440 45.000 0.00 0.00 0.00 5.03
487 497 6.389906 AGAAGAAAAACAAAACTGTGTGGAG 58.610 36.000 0.00 0.00 0.00 3.86
488 498 6.208599 AGAGAAGAAAAACAAAACTGTGTGGA 59.791 34.615 0.00 0.00 0.00 4.02
489 499 6.389906 AGAGAAGAAAAACAAAACTGTGTGG 58.610 36.000 0.00 0.00 0.00 4.17
490 500 9.573133 AATAGAGAAGAAAAACAAAACTGTGTG 57.427 29.630 0.00 0.00 0.00 3.82
491 501 9.788960 GAATAGAGAAGAAAAACAAAACTGTGT 57.211 29.630 0.00 0.00 0.00 3.72
498 508 9.396022 ACAGACAGAATAGAGAAGAAAAACAAA 57.604 29.630 0.00 0.00 0.00 2.83
499 509 8.964476 ACAGACAGAATAGAGAAGAAAAACAA 57.036 30.769 0.00 0.00 0.00 2.83
500 510 8.964476 AACAGACAGAATAGAGAAGAAAAACA 57.036 30.769 0.00 0.00 0.00 2.83
545 556 8.709308 AGGGGATCGATTATTATATCTTGGAAG 58.291 37.037 0.00 0.00 0.00 3.46
546 557 8.624019 AGGGGATCGATTATTATATCTTGGAA 57.376 34.615 0.00 0.00 0.00 3.53
548 559 8.256356 AGAGGGGATCGATTATTATATCTTGG 57.744 38.462 0.00 0.00 0.00 3.61
556 567 7.234782 TGCTCTTTTAGAGGGGATCGATTATTA 59.765 37.037 0.00 0.00 42.54 0.98
558 569 5.544176 TGCTCTTTTAGAGGGGATCGATTAT 59.456 40.000 0.00 0.00 42.54 1.28
559 570 4.899457 TGCTCTTTTAGAGGGGATCGATTA 59.101 41.667 0.00 0.00 42.54 1.75
560 571 3.711704 TGCTCTTTTAGAGGGGATCGATT 59.288 43.478 0.00 0.00 42.54 3.34
566 577 6.770286 ATTATCATGCTCTTTTAGAGGGGA 57.230 37.500 5.90 0.00 42.54 4.81
589 600 9.958180 TTCATCCTGAATCACTGTAAGAATTAA 57.042 29.630 0.00 0.00 31.72 1.40
590 601 9.383519 GTTCATCCTGAATCACTGTAAGAATTA 57.616 33.333 0.00 0.00 38.79 1.40
591 602 8.105829 AGTTCATCCTGAATCACTGTAAGAATT 58.894 33.333 0.00 0.00 38.79 2.17
592 603 7.551974 CAGTTCATCCTGAATCACTGTAAGAAT 59.448 37.037 0.00 0.00 38.79 2.40
595 606 6.169094 ACAGTTCATCCTGAATCACTGTAAG 58.831 40.000 10.01 0.00 41.50 2.34
596 607 6.114187 ACAGTTCATCCTGAATCACTGTAA 57.886 37.500 10.01 0.00 41.50 2.41
597 608 5.745312 ACAGTTCATCCTGAATCACTGTA 57.255 39.130 10.01 0.00 41.50 2.74
598 609 4.630644 ACAGTTCATCCTGAATCACTGT 57.369 40.909 7.09 7.09 39.67 3.55
599 610 4.394300 GGAACAGTTCATCCTGAATCACTG 59.606 45.833 15.36 6.10 38.79 3.66
600 611 4.583871 GGAACAGTTCATCCTGAATCACT 58.416 43.478 15.36 0.00 38.79 3.41
601 612 3.372206 CGGAACAGTTCATCCTGAATCAC 59.628 47.826 15.36 0.00 38.79 3.06
602 613 3.599343 CGGAACAGTTCATCCTGAATCA 58.401 45.455 15.36 0.00 38.79 2.57
603 614 2.939103 CCGGAACAGTTCATCCTGAATC 59.061 50.000 15.36 0.00 38.79 2.52
604 615 2.356125 CCCGGAACAGTTCATCCTGAAT 60.356 50.000 15.36 0.00 38.79 2.57
605 616 1.003118 CCCGGAACAGTTCATCCTGAA 59.997 52.381 15.36 0.00 36.30 3.02
606 617 0.613260 CCCGGAACAGTTCATCCTGA 59.387 55.000 15.36 0.00 36.30 3.86
607 618 0.392998 CCCCGGAACAGTTCATCCTG 60.393 60.000 15.36 0.00 38.45 3.86
610 621 4.124970 GTTATACCCCGGAACAGTTCATC 58.875 47.826 15.36 0.00 0.00 2.92
612 623 2.905085 TGTTATACCCCGGAACAGTTCA 59.095 45.455 15.36 0.00 0.00 3.18
613 624 3.615224 TGTTATACCCCGGAACAGTTC 57.385 47.619 0.73 4.52 0.00 3.01
637 813 4.069304 TCCTGGTACCTCAAACAATTTCG 58.931 43.478 14.36 0.00 0.00 3.46
641 817 4.447138 TGTTCCTGGTACCTCAAACAAT 57.553 40.909 14.36 0.00 0.00 2.71
642 818 3.935818 TGTTCCTGGTACCTCAAACAA 57.064 42.857 14.36 3.45 0.00 2.83
649 855 2.781174 TGGACTTTTGTTCCTGGTACCT 59.219 45.455 14.36 0.00 0.00 3.08
651 857 3.816994 ACTGGACTTTTGTTCCTGGTAC 58.183 45.455 0.00 0.00 0.00 3.34
665 871 6.015856 CGATGGATATGTTTCTCTACTGGACT 60.016 42.308 0.00 0.00 0.00 3.85
760 1010 3.737850 GAGGACATCCATCATCACTTCC 58.262 50.000 0.00 0.00 38.89 3.46
788 1038 1.402720 GGTTTGACCACCGCATGATTG 60.403 52.381 0.00 0.00 38.42 2.67
789 1039 0.887933 GGTTTGACCACCGCATGATT 59.112 50.000 0.00 0.00 38.42 2.57
799 1049 1.956043 GCAATCTGCGGTTTGACCA 59.044 52.632 18.52 0.00 38.47 4.02
865 1115 0.818296 AGACACGTACTCATGGGCTC 59.182 55.000 0.00 0.00 0.00 4.70
866 1116 0.818296 GAGACACGTACTCATGGGCT 59.182 55.000 14.35 0.00 34.87 5.19
867 1117 0.525668 CGAGACACGTACTCATGGGC 60.526 60.000 17.73 0.00 37.22 5.36
868 1118 0.100682 CCGAGACACGTACTCATGGG 59.899 60.000 17.73 0.00 40.78 4.00
869 1119 0.809385 ACCGAGACACGTACTCATGG 59.191 55.000 17.73 14.39 40.78 3.66
870 1120 1.199327 ACACCGAGACACGTACTCATG 59.801 52.381 17.73 16.39 40.78 3.07
912 1162 4.980805 TGGTTCGAGGCGGTGCAC 62.981 66.667 8.80 8.80 0.00 4.57
992 1242 3.955101 CCTAGGAGCTCGACCGCG 61.955 72.222 1.05 0.00 39.35 6.46
995 1245 0.820482 GAGACCCTAGGAGCTCGACC 60.820 65.000 11.48 0.00 0.00 4.79
1023 1277 3.365265 CAAAGAGGTGGCGGTGGC 61.365 66.667 0.00 0.00 38.90 5.01
1024 1278 2.672996 CCAAAGAGGTGGCGGTGG 60.673 66.667 0.00 0.00 0.00 4.61
1260 1514 0.173481 CTTTGAGCGTGATCTCGGGA 59.827 55.000 17.94 0.00 35.90 5.14
1263 1517 0.919981 GCTCTTTGAGCGTGATCTCG 59.080 55.000 12.66 12.66 45.85 4.04
1284 1538 1.154016 CTTCTCGTGCGTGGACGAT 60.154 57.895 16.71 0.00 46.72 3.73
1545 1799 4.200283 CCGAGCTCGAGGACCAGC 62.200 72.222 36.59 0.00 43.02 4.85
2033 2294 4.124351 TAACTCTCACCGCCGGCG 62.124 66.667 41.00 41.00 39.44 6.46
2073 2335 5.743872 CCACGTCTTCCAAAAAGAAAAGAAG 59.256 40.000 0.00 0.00 36.19 2.85
2098 2360 3.183775 CACACTTGTTACAGCGAAGGTAC 59.816 47.826 0.00 0.00 35.08 3.34
2176 2445 6.567050 TGTATAGATTCCGTTTACACAGTCC 58.433 40.000 0.00 0.00 0.00 3.85
2291 2564 7.373778 AGACGTTTTTGTAGGCTAATTTAGG 57.626 36.000 0.00 0.00 0.00 2.69
2311 2584 7.437748 ACCTCCATCTCTCAAAATATAAGACG 58.562 38.462 0.00 0.00 0.00 4.18
2324 2597 6.737346 GCAATCAACTACTACCTCCATCTCTC 60.737 46.154 0.00 0.00 0.00 3.20
2325 2598 5.069781 GCAATCAACTACTACCTCCATCTCT 59.930 44.000 0.00 0.00 0.00 3.10
2341 2614 0.172578 GGCCCTTAACCGCAATCAAC 59.827 55.000 0.00 0.00 0.00 3.18
2364 2637 7.044181 TGCACTCCTAGAATCTTGTGAATTAG 58.956 38.462 0.00 0.00 0.00 1.73
2366 2639 5.809001 TGCACTCCTAGAATCTTGTGAATT 58.191 37.500 0.00 0.00 0.00 2.17
2382 2655 5.705609 TTGTTTTCCTATCTTTGCACTCC 57.294 39.130 0.00 0.00 0.00 3.85
2385 2658 5.696270 CCCTTTTGTTTTCCTATCTTTGCAC 59.304 40.000 0.00 0.00 0.00 4.57
2466 2739 7.704271 GGCAACCTAAAATACTACAGGATTTC 58.296 38.462 0.00 0.00 32.25 2.17
2493 2766 2.403252 ATCTGTAGCCCGAACAAAGG 57.597 50.000 0.00 0.00 0.00 3.11
2494 2767 2.678336 GGAATCTGTAGCCCGAACAAAG 59.322 50.000 0.00 0.00 0.00 2.77
2495 2768 2.304761 AGGAATCTGTAGCCCGAACAAA 59.695 45.455 0.00 0.00 0.00 2.83
2496 2769 1.906574 AGGAATCTGTAGCCCGAACAA 59.093 47.619 0.00 0.00 0.00 2.83
2497 2770 1.207089 CAGGAATCTGTAGCCCGAACA 59.793 52.381 0.00 0.00 36.30 3.18
2498 2771 1.480954 TCAGGAATCTGTAGCCCGAAC 59.519 52.381 0.00 0.00 41.59 3.95
2499 2772 1.757118 CTCAGGAATCTGTAGCCCGAA 59.243 52.381 0.00 0.00 41.59 4.30
2500 2773 1.063942 TCTCAGGAATCTGTAGCCCGA 60.064 52.381 0.00 0.00 41.59 5.14
2501 2774 1.403814 TCTCAGGAATCTGTAGCCCG 58.596 55.000 0.00 0.00 41.59 6.13
2511 2784 1.202580 CCGAAGCCGATTCTCAGGAAT 60.203 52.381 0.00 0.00 43.99 3.01
2512 2785 0.175760 CCGAAGCCGATTCTCAGGAA 59.824 55.000 0.00 0.00 38.22 3.36
2513 2786 1.816537 CCGAAGCCGATTCTCAGGA 59.183 57.895 0.00 0.00 38.22 3.86
2514 2787 1.884926 GCCGAAGCCGATTCTCAGG 60.885 63.158 0.00 0.00 38.22 3.86
2515 2788 0.460987 AAGCCGAAGCCGATTCTCAG 60.461 55.000 0.00 0.00 41.25 3.35
2516 2789 0.740868 CAAGCCGAAGCCGATTCTCA 60.741 55.000 0.00 0.00 41.25 3.27
2517 2790 1.432270 CCAAGCCGAAGCCGATTCTC 61.432 60.000 0.00 0.00 41.25 2.87
2518 2791 1.450312 CCAAGCCGAAGCCGATTCT 60.450 57.895 0.00 0.00 41.25 2.40
2519 2792 0.815615 ATCCAAGCCGAAGCCGATTC 60.816 55.000 0.00 0.00 41.25 2.52
2520 2793 0.394352 AATCCAAGCCGAAGCCGATT 60.394 50.000 0.00 0.00 41.25 3.34
2521 2794 0.815615 GAATCCAAGCCGAAGCCGAT 60.816 55.000 0.00 0.00 41.25 4.18
2522 2795 1.449601 GAATCCAAGCCGAAGCCGA 60.450 57.895 0.00 0.00 41.25 5.54
2523 2796 2.472909 GGAATCCAAGCCGAAGCCG 61.473 63.158 0.00 0.00 41.25 5.52
2524 2797 0.180406 TAGGAATCCAAGCCGAAGCC 59.820 55.000 0.61 0.00 41.25 4.35
2525 2798 2.038387 TTAGGAATCCAAGCCGAAGC 57.962 50.000 0.61 0.00 40.32 3.86
2526 2799 4.640201 TGATTTTAGGAATCCAAGCCGAAG 59.360 41.667 0.61 0.00 0.00 3.79
2527 2800 4.594970 TGATTTTAGGAATCCAAGCCGAA 58.405 39.130 0.61 0.00 0.00 4.30
2528 2801 4.199310 CTGATTTTAGGAATCCAAGCCGA 58.801 43.478 0.61 0.00 0.00 5.54
2529 2802 3.243201 GCTGATTTTAGGAATCCAAGCCG 60.243 47.826 0.61 0.00 0.00 5.52
2530 2803 3.956848 AGCTGATTTTAGGAATCCAAGCC 59.043 43.478 0.61 0.00 30.43 4.35
2531 2804 5.590259 TGTAGCTGATTTTAGGAATCCAAGC 59.410 40.000 0.61 0.00 0.00 4.01
2532 2805 6.825721 ACTGTAGCTGATTTTAGGAATCCAAG 59.174 38.462 0.61 0.00 0.00 3.61
2533 2806 6.721318 ACTGTAGCTGATTTTAGGAATCCAA 58.279 36.000 0.61 0.00 0.00 3.53
2534 2807 6.313519 ACTGTAGCTGATTTTAGGAATCCA 57.686 37.500 0.61 0.00 0.00 3.41
2535 2808 6.458888 GCAACTGTAGCTGATTTTAGGAATCC 60.459 42.308 0.00 0.00 0.00 3.01
2536 2809 6.094048 TGCAACTGTAGCTGATTTTAGGAATC 59.906 38.462 0.00 0.00 0.00 2.52
2537 2810 5.945784 TGCAACTGTAGCTGATTTTAGGAAT 59.054 36.000 0.00 0.00 0.00 3.01
2538 2811 5.312895 TGCAACTGTAGCTGATTTTAGGAA 58.687 37.500 0.00 0.00 0.00 3.36
2539 2812 4.905429 TGCAACTGTAGCTGATTTTAGGA 58.095 39.130 0.00 0.00 0.00 2.94
2540 2813 4.937620 TCTGCAACTGTAGCTGATTTTAGG 59.062 41.667 0.00 0.00 35.45 2.69
2541 2814 6.674694 ATCTGCAACTGTAGCTGATTTTAG 57.325 37.500 0.00 0.00 44.77 1.85
2547 2820 3.259123 TCAGAATCTGCAACTGTAGCTGA 59.741 43.478 5.18 0.00 42.73 4.26
2548 2821 3.593096 TCAGAATCTGCAACTGTAGCTG 58.407 45.455 5.18 0.00 33.93 4.24
2549 2822 3.513119 TCTCAGAATCTGCAACTGTAGCT 59.487 43.478 5.18 0.00 33.93 3.32
2550 2823 3.854666 TCTCAGAATCTGCAACTGTAGC 58.145 45.455 5.18 0.00 33.93 3.58
2551 2824 6.104665 TGATTCTCAGAATCTGCAACTGTAG 58.895 40.000 24.80 0.00 33.93 2.74
2552 2825 6.041423 TGATTCTCAGAATCTGCAACTGTA 57.959 37.500 24.80 2.05 33.93 2.74
2553 2826 4.903054 TGATTCTCAGAATCTGCAACTGT 58.097 39.130 24.80 0.00 33.93 3.55
2566 2839 6.708054 ACAAACAACCTACTTCTGATTCTCAG 59.292 38.462 0.00 0.00 45.59 3.35
2567 2840 6.591935 ACAAACAACCTACTTCTGATTCTCA 58.408 36.000 0.00 0.00 0.00 3.27
2568 2841 7.497925 AACAAACAACCTACTTCTGATTCTC 57.502 36.000 0.00 0.00 0.00 2.87
2569 2842 7.881775 AAACAAACAACCTACTTCTGATTCT 57.118 32.000 0.00 0.00 0.00 2.40
2570 2843 9.612620 CATAAACAAACAACCTACTTCTGATTC 57.387 33.333 0.00 0.00 0.00 2.52
2571 2844 9.349713 TCATAAACAAACAACCTACTTCTGATT 57.650 29.630 0.00 0.00 0.00 2.57
2572 2845 8.918202 TCATAAACAAACAACCTACTTCTGAT 57.082 30.769 0.00 0.00 0.00 2.90
2573 2846 8.740123 TTCATAAACAAACAACCTACTTCTGA 57.260 30.769 0.00 0.00 0.00 3.27
2574 2847 9.450807 CTTTCATAAACAAACAACCTACTTCTG 57.549 33.333 0.00 0.00 0.00 3.02
2575 2848 9.185680 ACTTTCATAAACAAACAACCTACTTCT 57.814 29.630 0.00 0.00 0.00 2.85
2576 2849 9.233232 CACTTTCATAAACAAACAACCTACTTC 57.767 33.333 0.00 0.00 0.00 3.01
2577 2850 7.704899 GCACTTTCATAAACAAACAACCTACTT 59.295 33.333 0.00 0.00 0.00 2.24
2578 2851 7.200455 GCACTTTCATAAACAAACAACCTACT 58.800 34.615 0.00 0.00 0.00 2.57
2579 2852 6.141685 CGCACTTTCATAAACAAACAACCTAC 59.858 38.462 0.00 0.00 0.00 3.18
2580 2853 6.183360 ACGCACTTTCATAAACAAACAACCTA 60.183 34.615 0.00 0.00 0.00 3.08
2581 2854 5.040635 CGCACTTTCATAAACAAACAACCT 58.959 37.500 0.00 0.00 0.00 3.50
2582 2855 4.801516 ACGCACTTTCATAAACAAACAACC 59.198 37.500 0.00 0.00 0.00 3.77
2583 2856 5.942325 ACGCACTTTCATAAACAAACAAC 57.058 34.783 0.00 0.00 0.00 3.32
2584 2857 9.900710 ATATAACGCACTTTCATAAACAAACAA 57.099 25.926 0.00 0.00 0.00 2.83
2585 2858 9.549509 GATATAACGCACTTTCATAAACAAACA 57.450 29.630 0.00 0.00 0.00 2.83
2586 2859 8.721476 CGATATAACGCACTTTCATAAACAAAC 58.279 33.333 0.00 0.00 0.00 2.93
2587 2860 8.657729 TCGATATAACGCACTTTCATAAACAAA 58.342 29.630 0.00 0.00 0.00 2.83
2588 2861 8.111836 GTCGATATAACGCACTTTCATAAACAA 58.888 33.333 0.00 0.00 0.00 2.83
2589 2862 7.490079 AGTCGATATAACGCACTTTCATAAACA 59.510 33.333 0.00 0.00 0.00 2.83
2590 2863 7.838498 AGTCGATATAACGCACTTTCATAAAC 58.162 34.615 0.00 0.00 0.00 2.01
2591 2864 7.997107 AGTCGATATAACGCACTTTCATAAA 57.003 32.000 0.00 0.00 0.00 1.40
2592 2865 9.177304 CTTAGTCGATATAACGCACTTTCATAA 57.823 33.333 10.84 2.33 0.00 1.90
2593 2866 7.806487 CCTTAGTCGATATAACGCACTTTCATA 59.194 37.037 10.84 0.00 0.00 2.15
2594 2867 6.641314 CCTTAGTCGATATAACGCACTTTCAT 59.359 38.462 10.84 0.00 0.00 2.57
2645 2921 4.082190 TCACCTAGAAATTCTCAGTGACGG 60.082 45.833 18.36 5.46 35.22 4.79
2750 3028 7.878477 ACTATGTGCTTGTTTTCATTTCATG 57.122 32.000 0.00 0.00 0.00 3.07
2804 3082 8.655092 CAATTTCTTCAGTCTCATAGTCTTCAC 58.345 37.037 0.00 0.00 0.00 3.18
2837 3115 9.265901 CTTTGACTGAAGACTTTCTCTATTTCA 57.734 33.333 0.00 0.00 34.31 2.69
2923 3201 4.039124 CACCAAGCCAACTGGTTCTATTTT 59.961 41.667 0.00 0.00 37.57 1.82
3027 3306 1.299926 GCGTCCGAGACTGTGTGTT 60.300 57.895 0.00 0.00 0.00 3.32
3044 3323 3.462021 GAGAATATGGTGAGGACTGTGC 58.538 50.000 0.00 0.00 0.00 4.57


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

AutoCloner maintained by Alex Coulton.