Multiple sequence alignment - TraesCS5A01G040400

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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 TraesCS5A01G040400 chr5A 100.000 2713 0 0 1 2713 36367653 36364941 0.000000e+00 5011.0
1 TraesCS5A01G040400 chr5A 78.469 209 35 7 2003 2203 39243445 39243239 7.880000e-26 128.0
2 TraesCS5A01G040400 chr5B 89.862 868 40 9 1468 2301 45538816 45537963 0.000000e+00 1072.0
3 TraesCS5A01G040400 chr5B 89.425 643 44 7 657 1291 45539913 45539287 0.000000e+00 789.0
4 TraesCS5A01G040400 chr5B 84.817 191 16 8 1287 1469 45539262 45539077 2.150000e-41 180.0
5 TraesCS5A01G040400 chr5B 81.383 188 10 10 2454 2639 45537880 45537716 2.190000e-26 130.0
6 TraesCS5A01G040400 chr5B 77.990 209 36 7 2003 2203 52648726 52648520 3.670000e-24 122.0
7 TraesCS5A01G040400 chr5B 78.155 206 35 7 2003 2200 52916218 52916421 3.670000e-24 122.0
8 TraesCS5A01G040400 chr5B 88.889 81 2 7 1936 2015 583738394 583738320 2.880000e-15 93.5
9 TraesCS5A01G040400 chr5D 92.784 485 22 3 1465 1946 45488798 45488324 0.000000e+00 689.0
10 TraesCS5A01G040400 chr5D 93.580 405 20 1 887 1291 45490890 45490492 1.390000e-167 599.0
11 TraesCS5A01G040400 chr5D 91.365 359 16 5 1 348 45491615 45491261 6.800000e-131 477.0
12 TraesCS5A01G040400 chr5D 82.017 595 37 24 2060 2639 45487979 45487440 2.480000e-120 442.0
13 TraesCS5A01G040400 chr5D 90.400 250 12 6 644 888 45491215 45490973 4.360000e-83 318.0
14 TraesCS5A01G040400 chr5D 87.283 173 12 3 1287 1449 45490467 45490295 3.570000e-44 189.0
15 TraesCS5A01G040400 chr5D 77.990 209 36 7 2003 2203 49762795 49762589 3.670000e-24 122.0
16 TraesCS5A01G040400 chr5D 77.990 209 36 7 2003 2203 50038378 50038172 3.670000e-24 122.0
17 TraesCS5A01G040400 chr5D 77.990 209 36 7 2003 2203 50199487 50199281 3.670000e-24 122.0
18 TraesCS5A01G040400 chr5D 80.645 155 25 4 1712 1861 45483418 45483264 6.140000e-22 115.0
19 TraesCS5A01G040400 chr5D 97.059 68 2 0 2646 2713 45487395 45487328 6.140000e-22 115.0
20 TraesCS5A01G040400 chr5D 90.541 74 3 4 1936 2008 476275261 476275191 8.000000e-16 95.3
21 TraesCS5A01G040400 chr5D 100.000 29 0 0 1388 1416 290805487 290805515 1.000000e-03 54.7
22 TraesCS5A01G040400 chrUn 79.012 162 25 6 2050 2203 371433339 371433179 4.780000e-18 102.0
23 TraesCS5A01G040400 chr7B 86.667 90 5 6 1921 2007 165708206 165708291 2.880000e-15 93.5
24 TraesCS5A01G040400 chr6D 91.304 69 4 2 1942 2010 86643238 86643304 2.880000e-15 93.5
25 TraesCS5A01G040400 chr6A 91.429 70 3 3 1942 2010 104308491 104308558 2.880000e-15 93.5
26 TraesCS5A01G040400 chr3D 88.889 81 2 7 1931 2007 564316153 564316230 2.880000e-15 93.5
27 TraesCS5A01G040400 chr1B 89.333 75 7 1 1942 2015 129175006 129174932 2.880000e-15 93.5
28 TraesCS5A01G040400 chr3B 86.207 87 8 3 1942 2027 636452110 636452027 1.030000e-14 91.6


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 TraesCS5A01G040400 chr5A 36364941 36367653 2712 True 5011.00 5011 100.000000 1 2713 1 chr5A.!!$R1 2712
1 TraesCS5A01G040400 chr5B 45537716 45539913 2197 True 542.75 1072 86.371750 657 2639 4 chr5B.!!$R3 1982
2 TraesCS5A01G040400 chr5D 45483264 45491615 8351 True 368.00 689 89.391625 1 2713 8 chr5D.!!$R5 2712

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
644 656 0.259065 TGATAGAGACGTGGAGCCCT 59.741 55.0 0.0 0.0 0.0 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2579 4799 0.249955 TCTCGCCAGCATTCACATGA 59.75 50.0 0.0 0.0 31.07 3.07 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
235 245 9.979578 TTATTAGTTTCACTGTTAGTTACGGAA 57.020 29.630 0.00 0.00 36.57 4.30
253 263 9.148104 GTTACGGAAAACTATCTAATCAGTTGT 57.852 33.333 0.00 0.00 35.23 3.32
254 264 9.715121 TTACGGAAAACTATCTAATCAGTTGTT 57.285 29.630 0.00 0.00 35.23 2.83
296 306 9.083080 CATGAAACAGTACATCGACATAAGTTA 57.917 33.333 0.00 0.00 0.00 2.24
299 309 9.737025 GAAACAGTACATCGACATAAGTTAAAC 57.263 33.333 0.00 0.00 0.00 2.01
355 367 9.658799 TTTTTCTATGTTGGAATTTGTTTCACA 57.341 25.926 0.00 0.00 35.94 3.58
356 368 9.829507 TTTTCTATGTTGGAATTTGTTTCACAT 57.170 25.926 0.00 0.00 35.93 3.21
357 369 9.474920 TTTCTATGTTGGAATTTGTTTCACATC 57.525 29.630 0.00 0.00 34.52 3.06
358 370 8.175925 TCTATGTTGGAATTTGTTTCACATCA 57.824 30.769 0.00 0.00 34.52 3.07
359 371 8.637099 TCTATGTTGGAATTTGTTTCACATCAA 58.363 29.630 0.00 0.00 34.52 2.57
360 372 6.900568 TGTTGGAATTTGTTTCACATCAAC 57.099 33.333 0.00 0.00 35.27 3.18
361 373 6.638610 TGTTGGAATTTGTTTCACATCAACT 58.361 32.000 0.00 0.00 35.52 3.16
365 377 7.499292 TGGAATTTGTTTCACATCAACTGAAT 58.501 30.769 0.00 0.00 35.94 2.57
366 378 7.986320 TGGAATTTGTTTCACATCAACTGAATT 59.014 29.630 0.00 0.00 35.94 2.17
367 379 9.474920 GGAATTTGTTTCACATCAACTGAATTA 57.525 29.630 0.00 0.00 35.94 1.40
372 384 9.814899 TTGTTTCACATCAACTGAATTATTTGT 57.185 25.926 0.00 0.00 0.00 2.83
373 385 9.462174 TGTTTCACATCAACTGAATTATTTGTC 57.538 29.630 0.00 0.00 0.00 3.18
374 386 9.462174 GTTTCACATCAACTGAATTATTTGTCA 57.538 29.630 0.00 0.00 0.00 3.58
375 387 9.462174 TTTCACATCAACTGAATTATTTGTCAC 57.538 29.630 0.00 0.00 0.00 3.67
376 388 8.394971 TCACATCAACTGAATTATTTGTCACT 57.605 30.769 0.00 0.00 0.00 3.41
377 389 8.849168 TCACATCAACTGAATTATTTGTCACTT 58.151 29.630 0.00 0.00 0.00 3.16
378 390 9.121517 CACATCAACTGAATTATTTGTCACTTC 57.878 33.333 0.00 0.00 0.00 3.01
379 391 8.299570 ACATCAACTGAATTATTTGTCACTTCC 58.700 33.333 0.00 0.00 0.00 3.46
380 392 7.815840 TCAACTGAATTATTTGTCACTTCCA 57.184 32.000 0.00 0.00 0.00 3.53
381 393 8.231692 TCAACTGAATTATTTGTCACTTCCAA 57.768 30.769 0.00 0.00 0.00 3.53
382 394 8.690884 TCAACTGAATTATTTGTCACTTCCAAA 58.309 29.630 0.00 0.00 36.34 3.28
383 395 9.480053 CAACTGAATTATTTGTCACTTCCAAAT 57.520 29.630 0.00 0.00 43.14 2.32
395 407 9.883142 TTGTCACTTCCAAATTATTTTGTTTCT 57.117 25.926 8.77 0.00 40.55 2.52
396 408 9.528018 TGTCACTTCCAAATTATTTTGTTTCTC 57.472 29.630 8.77 0.00 40.55 2.87
397 409 9.750125 GTCACTTCCAAATTATTTTGTTTCTCT 57.250 29.630 8.77 0.00 40.55 3.10
457 469 9.733556 AAAGGTTCAAAAGTTACCAAGAATTTT 57.266 25.926 0.00 0.00 34.32 1.82
458 470 9.733556 AAGGTTCAAAAGTTACCAAGAATTTTT 57.266 25.926 0.00 0.00 34.32 1.94
459 471 9.378551 AGGTTCAAAAGTTACCAAGAATTTTTC 57.621 29.630 0.00 0.00 34.32 2.29
460 472 8.609176 GGTTCAAAAGTTACCAAGAATTTTTCC 58.391 33.333 0.00 0.00 28.95 3.13
461 473 9.378551 GTTCAAAAGTTACCAAGAATTTTTCCT 57.621 29.630 0.00 0.00 28.95 3.36
489 501 5.644977 AAAGGTTACCAAGAATTAGCTGC 57.355 39.130 3.51 0.00 0.00 5.25
490 502 3.270877 AGGTTACCAAGAATTAGCTGCG 58.729 45.455 3.51 0.00 0.00 5.18
491 503 3.007635 GGTTACCAAGAATTAGCTGCGT 58.992 45.455 0.00 0.00 0.00 5.24
492 504 3.439129 GGTTACCAAGAATTAGCTGCGTT 59.561 43.478 0.00 0.00 0.00 4.84
493 505 4.082949 GGTTACCAAGAATTAGCTGCGTTT 60.083 41.667 0.00 0.00 0.00 3.60
494 506 5.458015 GTTACCAAGAATTAGCTGCGTTTT 58.542 37.500 0.00 0.00 0.00 2.43
495 507 6.348704 GGTTACCAAGAATTAGCTGCGTTTTA 60.349 38.462 0.00 0.00 0.00 1.52
496 508 5.043189 ACCAAGAATTAGCTGCGTTTTAC 57.957 39.130 0.00 0.00 0.00 2.01
497 509 4.760204 ACCAAGAATTAGCTGCGTTTTACT 59.240 37.500 0.00 0.00 0.00 2.24
498 510 5.106673 ACCAAGAATTAGCTGCGTTTTACTC 60.107 40.000 0.00 0.00 0.00 2.59
499 511 5.106712 CCAAGAATTAGCTGCGTTTTACTCA 60.107 40.000 0.00 0.00 0.00 3.41
500 512 5.532025 AGAATTAGCTGCGTTTTACTCAC 57.468 39.130 0.00 0.00 0.00 3.51
501 513 5.238583 AGAATTAGCTGCGTTTTACTCACT 58.761 37.500 0.00 0.00 0.00 3.41
502 514 6.395629 AGAATTAGCTGCGTTTTACTCACTA 58.604 36.000 0.00 0.00 0.00 2.74
503 515 6.310711 AGAATTAGCTGCGTTTTACTCACTAC 59.689 38.462 0.00 0.00 0.00 2.73
504 516 3.380479 AGCTGCGTTTTACTCACTACA 57.620 42.857 0.00 0.00 0.00 2.74
505 517 3.926616 AGCTGCGTTTTACTCACTACAT 58.073 40.909 0.00 0.00 0.00 2.29
506 518 3.679980 AGCTGCGTTTTACTCACTACATG 59.320 43.478 0.00 0.00 0.00 3.21
507 519 3.678072 GCTGCGTTTTACTCACTACATGA 59.322 43.478 0.00 0.00 35.45 3.07
508 520 4.151689 GCTGCGTTTTACTCACTACATGAA 59.848 41.667 0.00 0.00 36.69 2.57
509 521 5.163854 GCTGCGTTTTACTCACTACATGAAT 60.164 40.000 0.00 0.00 36.69 2.57
510 522 6.035650 GCTGCGTTTTACTCACTACATGAATA 59.964 38.462 0.00 0.00 36.69 1.75
511 523 7.254455 GCTGCGTTTTACTCACTACATGAATAT 60.254 37.037 0.00 0.00 36.69 1.28
512 524 7.905126 TGCGTTTTACTCACTACATGAATATG 58.095 34.615 0.00 0.00 36.69 1.78
513 525 6.846283 GCGTTTTACTCACTACATGAATATGC 59.154 38.462 0.00 0.00 36.69 3.14
514 526 7.465379 GCGTTTTACTCACTACATGAATATGCA 60.465 37.037 0.00 0.00 36.69 3.96
515 527 8.387354 CGTTTTACTCACTACATGAATATGCAA 58.613 33.333 0.00 0.00 36.69 4.08
522 534 9.836076 CTCACTACATGAATATGCAATTTATGG 57.164 33.333 20.05 11.84 36.69 2.74
523 535 9.571816 TCACTACATGAATATGCAATTTATGGA 57.428 29.630 20.05 15.05 37.85 3.41
524 536 9.616634 CACTACATGAATATGCAATTTATGGAC 57.383 33.333 20.05 3.12 37.85 4.02
525 537 9.578576 ACTACATGAATATGCAATTTATGGACT 57.421 29.630 20.05 9.77 37.85 3.85
528 540 9.537192 ACATGAATATGCAATTTATGGACTTTG 57.463 29.630 20.05 5.86 37.85 2.77
529 541 9.537192 CATGAATATGCAATTTATGGACTTTGT 57.463 29.630 13.62 0.00 29.34 2.83
530 542 8.929827 TGAATATGCAATTTATGGACTTTGTG 57.070 30.769 0.00 0.00 29.34 3.33
531 543 8.530311 TGAATATGCAATTTATGGACTTTGTGT 58.470 29.630 0.00 0.00 29.34 3.72
532 544 8.706492 AATATGCAATTTATGGACTTTGTGTG 57.294 30.769 0.00 0.00 29.34 3.82
533 545 4.880759 TGCAATTTATGGACTTTGTGTGG 58.119 39.130 0.00 0.00 0.00 4.17
534 546 4.343526 TGCAATTTATGGACTTTGTGTGGT 59.656 37.500 0.00 0.00 0.00 4.16
535 547 4.685628 GCAATTTATGGACTTTGTGTGGTG 59.314 41.667 0.00 0.00 0.00 4.17
536 548 5.508825 GCAATTTATGGACTTTGTGTGGTGA 60.509 40.000 0.00 0.00 0.00 4.02
537 549 6.511416 CAATTTATGGACTTTGTGTGGTGAA 58.489 36.000 0.00 0.00 0.00 3.18
538 550 6.723298 ATTTATGGACTTTGTGTGGTGAAA 57.277 33.333 0.00 0.00 0.00 2.69
539 551 5.766150 TTATGGACTTTGTGTGGTGAAAG 57.234 39.130 0.00 0.00 35.64 2.62
540 552 3.080300 TGGACTTTGTGTGGTGAAAGT 57.920 42.857 0.00 0.00 43.50 2.66
541 553 2.752354 TGGACTTTGTGTGGTGAAAGTG 59.248 45.455 0.00 0.00 41.43 3.16
542 554 3.013921 GGACTTTGTGTGGTGAAAGTGA 58.986 45.455 0.00 0.00 41.43 3.41
543 555 3.181500 GGACTTTGTGTGGTGAAAGTGAC 60.181 47.826 0.00 0.00 41.43 3.67
544 556 3.417101 ACTTTGTGTGGTGAAAGTGACA 58.583 40.909 0.00 0.00 40.19 3.58
545 557 3.190535 ACTTTGTGTGGTGAAAGTGACAC 59.809 43.478 0.00 0.00 40.19 3.67
546 558 1.364721 TGTGTGGTGAAAGTGACACG 58.635 50.000 0.00 0.00 41.34 4.49
547 559 1.338294 TGTGTGGTGAAAGTGACACGT 60.338 47.619 0.00 0.00 41.34 4.49
548 560 2.094130 TGTGTGGTGAAAGTGACACGTA 60.094 45.455 0.00 0.00 41.34 3.57
549 561 3.128349 GTGTGGTGAAAGTGACACGTAT 58.872 45.455 0.00 0.00 38.90 3.06
550 562 4.202131 TGTGTGGTGAAAGTGACACGTATA 60.202 41.667 0.00 0.00 41.34 1.47
551 563 4.927425 GTGTGGTGAAAGTGACACGTATAT 59.073 41.667 0.00 0.00 38.90 0.86
552 564 5.407387 GTGTGGTGAAAGTGACACGTATATT 59.593 40.000 0.00 0.00 38.90 1.28
553 565 5.636121 TGTGGTGAAAGTGACACGTATATTC 59.364 40.000 0.00 2.73 38.90 1.75
554 566 5.636121 GTGGTGAAAGTGACACGTATATTCA 59.364 40.000 0.00 5.10 38.90 2.57
555 567 5.636121 TGGTGAAAGTGACACGTATATTCAC 59.364 40.000 22.03 22.03 42.56 3.18
561 573 6.954487 AGTGACACGTATATTCACTATCCA 57.046 37.500 15.73 0.00 46.45 3.41
562 574 7.342769 AGTGACACGTATATTCACTATCCAA 57.657 36.000 15.73 0.00 46.45 3.53
563 575 7.426410 AGTGACACGTATATTCACTATCCAAG 58.574 38.462 15.73 0.00 46.45 3.61
564 576 7.068348 AGTGACACGTATATTCACTATCCAAGT 59.932 37.037 15.73 0.00 46.45 3.16
565 577 7.705325 GTGACACGTATATTCACTATCCAAGTT 59.295 37.037 10.10 0.00 35.76 2.66
566 578 7.704899 TGACACGTATATTCACTATCCAAGTTG 59.295 37.037 0.00 0.00 35.76 3.16
591 603 8.208903 TGGCTACCTATTAACCTAGCTAAAAAG 58.791 37.037 0.00 0.00 33.49 2.27
592 604 7.660617 GGCTACCTATTAACCTAGCTAAAAAGG 59.339 40.741 0.00 0.00 38.93 3.11
596 608 8.388589 ACCTATTAACCTAGCTAAAAAGGTGTT 58.611 33.333 6.67 0.00 45.51 3.32
638 650 8.425577 AAAAGAATGTAATGATAGAGACGTGG 57.574 34.615 0.00 0.00 0.00 4.94
639 651 6.961360 AGAATGTAATGATAGAGACGTGGA 57.039 37.500 0.00 0.00 0.00 4.02
640 652 6.976088 AGAATGTAATGATAGAGACGTGGAG 58.024 40.000 0.00 0.00 0.00 3.86
641 653 4.569761 TGTAATGATAGAGACGTGGAGC 57.430 45.455 0.00 0.00 0.00 4.70
642 654 3.318275 TGTAATGATAGAGACGTGGAGCC 59.682 47.826 0.00 0.00 0.00 4.70
643 655 1.333177 ATGATAGAGACGTGGAGCCC 58.667 55.000 0.00 0.00 0.00 5.19
644 656 0.259065 TGATAGAGACGTGGAGCCCT 59.741 55.000 0.00 0.00 0.00 5.19
645 657 1.493446 TGATAGAGACGTGGAGCCCTA 59.507 52.381 0.00 0.00 0.00 3.53
646 658 2.092049 TGATAGAGACGTGGAGCCCTAA 60.092 50.000 0.00 0.00 0.00 2.69
647 659 2.519771 TAGAGACGTGGAGCCCTAAA 57.480 50.000 0.00 0.00 0.00 1.85
648 660 1.640917 AGAGACGTGGAGCCCTAAAA 58.359 50.000 0.00 0.00 0.00 1.52
649 661 1.975680 AGAGACGTGGAGCCCTAAAAA 59.024 47.619 0.00 0.00 0.00 1.94
791 804 8.670521 AAGGGAAAAATTTCAAGAGGTGATAT 57.329 30.769 8.06 0.00 38.92 1.63
792 805 9.768215 AAGGGAAAAATTTCAAGAGGTGATATA 57.232 29.630 8.06 0.00 38.92 0.86
793 806 9.190317 AGGGAAAAATTTCAAGAGGTGATATAC 57.810 33.333 8.06 0.00 38.92 1.47
794 807 9.190317 GGGAAAAATTTCAAGAGGTGATATACT 57.810 33.333 8.06 0.00 38.92 2.12
798 811 8.910351 AAATTTCAAGAGGTGATATACTAGCC 57.090 34.615 0.00 0.00 35.70 3.93
799 812 7.618019 ATTTCAAGAGGTGATATACTAGCCA 57.382 36.000 0.00 0.00 35.70 4.75
800 813 7.618019 TTTCAAGAGGTGATATACTAGCCAT 57.382 36.000 0.00 0.00 35.70 4.40
801 814 6.842437 TCAAGAGGTGATATACTAGCCATC 57.158 41.667 0.00 0.00 0.00 3.51
802 815 5.416013 TCAAGAGGTGATATACTAGCCATCG 59.584 44.000 0.00 0.00 0.00 3.84
1078 1182 2.279517 CACCCTATCCGCAGTCGC 60.280 66.667 0.00 0.00 0.00 5.19
1093 1197 4.767255 CGCCGCCTCTTGCTCCTT 62.767 66.667 0.00 0.00 38.05 3.36
1116 1220 2.550208 CCTGACCTACCTGTTCCAACAC 60.550 54.545 0.00 0.00 34.70 3.32
1233 1337 5.331906 CATCCATCCCTTCTCTCATCTAGA 58.668 45.833 0.00 0.00 0.00 2.43
1263 1367 3.054139 CCATTCAGATTTCAGGTCTCCCA 60.054 47.826 0.00 0.00 0.00 4.37
1267 1371 5.261040 TCAGATTTCAGGTCTCCCATTTT 57.739 39.130 0.00 0.00 0.00 1.82
1334 1469 4.333926 CCTTAACTTCTACTGCATTCAGGC 59.666 45.833 0.00 0.00 44.54 4.85
1338 1473 3.515502 ACTTCTACTGCATTCAGGCACTA 59.484 43.478 0.00 0.00 44.54 2.74
1381 1516 2.097036 ACATATTCCACGTGGTCGAGA 58.903 47.619 32.74 17.91 40.62 4.04
1394 1529 4.315122 CGAGATCGACGAGGGCGG 62.315 72.222 3.01 0.00 43.17 6.13
1438 1585 6.408548 GGAGGATGAAAATGTAGGACAGATGA 60.409 42.308 0.00 0.00 0.00 2.92
1524 3414 6.069963 AGTCTTGGACATATACCTGCTTCTTT 60.070 38.462 0.52 0.00 34.60 2.52
1605 3496 5.273674 TCAGCTCTTAGGTGATGAAGATG 57.726 43.478 4.77 0.00 46.53 2.90
1606 3497 4.958581 TCAGCTCTTAGGTGATGAAGATGA 59.041 41.667 4.77 0.00 46.53 2.92
1607 3498 5.423290 TCAGCTCTTAGGTGATGAAGATGAA 59.577 40.000 4.77 0.00 46.53 2.57
1608 3499 5.754406 CAGCTCTTAGGTGATGAAGATGAAG 59.246 44.000 0.00 0.00 45.98 3.02
1609 3500 5.660417 AGCTCTTAGGTGATGAAGATGAAGA 59.340 40.000 0.00 0.00 31.45 2.87
1630 3521 7.824289 TGAAGATGAAGAAAAACCAGATATCGT 59.176 33.333 0.00 0.00 0.00 3.73
1680 3571 1.251251 ACTGGAATGCAAGAAGCCAC 58.749 50.000 0.00 0.00 44.83 5.01
1725 3616 4.442192 GCCGATTATGAGAAGAACCTGAGT 60.442 45.833 0.00 0.00 0.00 3.41
1731 3622 3.161067 TGAGAAGAACCTGAGTCTGGAG 58.839 50.000 21.84 0.00 0.00 3.86
1766 3660 4.040376 CCTCGCGGTAGTTAGTGATTTAC 58.960 47.826 6.13 0.00 0.00 2.01
1781 3675 5.348724 AGTGATTTACGTGTGCTGTATGAAG 59.651 40.000 0.00 0.00 0.00 3.02
1853 3747 6.820656 AGATGCACTTGTTTATACTCTTGAGG 59.179 38.462 0.00 0.00 0.00 3.86
1923 3817 3.397482 ACTTCAGAGTAAGCTGCAGTTG 58.603 45.455 16.64 0.00 38.88 3.16
1963 3857 8.294954 TCAGTACTCCCTCTGTAAAGAAATAG 57.705 38.462 0.00 0.00 33.89 1.73
1964 3858 7.894364 TCAGTACTCCCTCTGTAAAGAAATAGT 59.106 37.037 0.00 0.00 33.89 2.12
1965 3859 8.192110 CAGTACTCCCTCTGTAAAGAAATAGTC 58.808 40.741 0.00 0.00 0.00 2.59
2135 4342 6.605471 ATGACACCTAGTTCAACATACTCA 57.395 37.500 0.00 0.00 0.00 3.41
2146 4353 7.852263 AGTTCAACATACTCAGGTAGCTTTAT 58.148 34.615 0.00 0.00 0.00 1.40
2155 4362 5.002464 TCAGGTAGCTTTATACGTTGTCC 57.998 43.478 0.00 0.00 0.00 4.02
2289 4509 8.899887 ATTTAAGCATATGGTTTATGGGCTAT 57.100 30.769 24.01 3.40 37.00 2.97
2300 4520 6.099341 GGTTTATGGGCTATGTTGTTTGAAG 58.901 40.000 0.00 0.00 0.00 3.02
2301 4521 3.874392 ATGGGCTATGTTGTTTGAAGC 57.126 42.857 0.00 0.00 0.00 3.86
2307 4527 5.567138 GCTATGTTGTTTGAAGCCTATGT 57.433 39.130 0.00 0.00 0.00 2.29
2308 4528 5.954335 GCTATGTTGTTTGAAGCCTATGTT 58.046 37.500 0.00 0.00 0.00 2.71
2309 4529 5.801947 GCTATGTTGTTTGAAGCCTATGTTG 59.198 40.000 0.00 0.00 0.00 3.33
2310 4530 4.582701 TGTTGTTTGAAGCCTATGTTGG 57.417 40.909 0.00 0.00 0.00 3.77
2311 4531 3.320541 TGTTGTTTGAAGCCTATGTTGGG 59.679 43.478 0.00 0.00 0.00 4.12
2327 4547 3.957497 TGTTGGGCTATGTTGTTTGAAGT 59.043 39.130 0.00 0.00 0.00 3.01
2328 4548 5.133941 TGTTGGGCTATGTTGTTTGAAGTA 58.866 37.500 0.00 0.00 0.00 2.24
2343 4563 6.150976 TGTTTGAAGTATATGGCTTGAGGTTG 59.849 38.462 0.01 0.00 0.00 3.77
2347 4567 3.392616 AGTATATGGCTTGAGGTTGAGGG 59.607 47.826 0.00 0.00 0.00 4.30
2351 4571 1.492993 GGCTTGAGGTTGAGGGTCCT 61.493 60.000 0.00 0.00 36.70 3.85
2368 4588 5.652452 AGGGTCCTGCATAAAGAAAATGTAC 59.348 40.000 0.00 0.00 0.00 2.90
2374 4594 6.183360 CCTGCATAAAGAAAATGTACGGCTTA 60.183 38.462 0.00 0.00 0.00 3.09
2394 4614 0.913451 AGGAGGATCTGCTGCACCTT 60.913 55.000 11.11 0.00 32.31 3.50
2395 4615 0.747283 GGAGGATCTGCTGCACCTTG 60.747 60.000 11.11 0.00 33.73 3.61
2438 4658 3.056536 ACACACAGTGCTGATACCAGTAG 60.057 47.826 6.17 0.00 42.35 2.57
2446 4666 2.693591 GCTGATACCAGTAGTGCCACTA 59.306 50.000 0.00 0.00 42.35 2.74
2448 4668 4.207955 CTGATACCAGTAGTGCCACTAGA 58.792 47.826 4.44 0.00 35.70 2.43
2493 4713 5.603170 CATGCTAATGGGATTTGGAGTTT 57.397 39.130 0.00 0.00 0.00 2.66
2494 4714 5.594926 CATGCTAATGGGATTTGGAGTTTC 58.405 41.667 0.00 0.00 0.00 2.78
2495 4715 4.671831 TGCTAATGGGATTTGGAGTTTCA 58.328 39.130 0.00 0.00 0.00 2.69
2496 4716 4.706476 TGCTAATGGGATTTGGAGTTTCAG 59.294 41.667 0.00 0.00 0.00 3.02
2497 4717 4.098501 GCTAATGGGATTTGGAGTTTCAGG 59.901 45.833 0.00 0.00 0.00 3.86
2498 4718 4.402616 AATGGGATTTGGAGTTTCAGGA 57.597 40.909 0.00 0.00 0.00 3.86
2499 4719 3.439857 TGGGATTTGGAGTTTCAGGAG 57.560 47.619 0.00 0.00 0.00 3.69
2500 4720 2.986019 TGGGATTTGGAGTTTCAGGAGA 59.014 45.455 0.00 0.00 0.00 3.71
2501 4721 3.397618 TGGGATTTGGAGTTTCAGGAGAA 59.602 43.478 0.00 0.00 0.00 2.87
2511 4731 5.365314 GGAGTTTCAGGAGAATCAGGACTAT 59.635 44.000 0.00 0.00 36.25 2.12
2526 4746 2.284190 GACTATGGCCTGCAGTCTTTC 58.716 52.381 13.81 0.00 36.57 2.62
2539 4759 6.429385 CCTGCAGTCTTTCTTTCTTCAGTTAT 59.571 38.462 13.81 0.00 0.00 1.89
2540 4760 7.604164 CCTGCAGTCTTTCTTTCTTCAGTTATA 59.396 37.037 13.81 0.00 0.00 0.98
2551 4771 8.675504 TCTTTCTTCAGTTATAAGTAGACGAGG 58.324 37.037 0.00 0.00 0.00 4.63
2560 4780 8.891720 AGTTATAAGTAGACGAGGTTCAGTTAG 58.108 37.037 0.00 0.00 0.00 2.34
2576 4796 1.463444 GTTAGCGAACGCCTTTGATGT 59.537 47.619 15.44 0.00 43.17 3.06
2577 4797 1.075542 TAGCGAACGCCTTTGATGTG 58.924 50.000 15.44 0.00 43.17 3.21
2578 4798 0.602638 AGCGAACGCCTTTGATGTGA 60.603 50.000 15.44 0.00 43.17 3.58
2579 4799 0.447801 GCGAACGCCTTTGATGTGAT 59.552 50.000 8.03 0.00 34.56 3.06
2580 4800 1.529826 GCGAACGCCTTTGATGTGATC 60.530 52.381 8.03 0.00 34.56 2.92
2581 4801 1.731709 CGAACGCCTTTGATGTGATCA 59.268 47.619 0.00 0.00 37.55 2.92
2582 4802 2.352651 CGAACGCCTTTGATGTGATCAT 59.647 45.455 0.00 0.00 39.39 2.45
2583 4803 3.688272 GAACGCCTTTGATGTGATCATG 58.312 45.455 0.00 0.00 39.39 3.07
2584 4804 2.715046 ACGCCTTTGATGTGATCATGT 58.285 42.857 0.00 0.00 39.39 3.21
2585 4805 2.421073 ACGCCTTTGATGTGATCATGTG 59.579 45.455 0.00 0.00 39.39 3.21
2586 4806 2.679336 CGCCTTTGATGTGATCATGTGA 59.321 45.455 0.00 0.00 39.39 3.58
2602 4822 1.078214 TGAATGCTGGCGAGAAGGG 60.078 57.895 0.00 0.00 0.00 3.95
2614 4834 1.536662 AGAAGGGTCCAACGGCTCT 60.537 57.895 0.00 0.00 0.00 4.09
2639 4861 3.887868 CCCCGCCGCTTAATGCAC 61.888 66.667 0.00 0.00 43.06 4.57
2641 4863 2.709475 CCGCCGCTTAATGCACTC 59.291 61.111 0.00 0.00 43.06 3.51
2642 4864 2.321060 CGCCGCTTAATGCACTCG 59.679 61.111 0.00 0.00 43.06 4.18
2643 4865 2.023320 GCCGCTTAATGCACTCGC 59.977 61.111 0.00 0.00 43.06 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 7.936584 AGCAAAATAAACAAGTAGTAGTTGCA 58.063 30.769 16.19 4.16 39.96 4.08
47 48 9.531942 GTATGTATGCATTCCATGAAAATTTGA 57.468 29.630 17.30 0.00 36.58 2.69
143 144 9.690434 GTAATACAAGATTAGAGCAAAAGTTCG 57.310 33.333 0.00 0.00 0.00 3.95
235 245 9.739276 TTGGATCAACAACTGATTAGATAGTTT 57.261 29.630 0.00 0.00 45.23 2.66
251 261 6.099159 TCATGCTGAAATTTTGGATCAACA 57.901 33.333 0.00 0.00 0.00 3.33
253 263 6.990939 TGTTTCATGCTGAAATTTTGGATCAA 59.009 30.769 12.42 0.00 46.55 2.57
254 264 6.522946 TGTTTCATGCTGAAATTTTGGATCA 58.477 32.000 12.42 3.74 46.55 2.92
348 360 9.462174 TGACAAATAATTCAGTTGATGTGAAAC 57.538 29.630 3.45 0.00 37.46 2.78
349 361 9.462174 GTGACAAATAATTCAGTTGATGTGAAA 57.538 29.630 3.45 0.00 37.46 2.69
350 362 8.849168 AGTGACAAATAATTCAGTTGATGTGAA 58.151 29.630 3.45 0.00 38.28 3.18
351 363 8.394971 AGTGACAAATAATTCAGTTGATGTGA 57.605 30.769 3.45 0.00 35.76 3.58
352 364 9.121517 GAAGTGACAAATAATTCAGTTGATGTG 57.878 33.333 0.00 0.00 35.87 3.21
354 366 8.298854 TGGAAGTGACAAATAATTCAGTTGATG 58.701 33.333 0.00 0.00 35.87 3.07
355 367 8.408043 TGGAAGTGACAAATAATTCAGTTGAT 57.592 30.769 0.00 0.00 35.87 2.57
356 368 7.815840 TGGAAGTGACAAATAATTCAGTTGA 57.184 32.000 0.00 0.00 35.87 3.18
357 369 8.870160 TTTGGAAGTGACAAATAATTCAGTTG 57.130 30.769 0.00 0.00 35.87 3.16
431 443 9.733556 AAAATTCTTGGTAACTTTTGAACCTTT 57.266 25.926 0.00 0.00 34.23 3.11
432 444 9.733556 AAAAATTCTTGGTAACTTTTGAACCTT 57.266 25.926 0.00 0.00 34.23 3.50
433 445 9.378551 GAAAAATTCTTGGTAACTTTTGAACCT 57.621 29.630 0.00 0.00 34.23 3.50
434 446 8.609176 GGAAAAATTCTTGGTAACTTTTGAACC 58.391 33.333 0.00 0.00 37.61 3.62
435 447 9.378551 AGGAAAAATTCTTGGTAACTTTTGAAC 57.621 29.630 0.00 0.00 37.61 3.18
465 477 6.455647 GCAGCTAATTCTTGGTAACCTTTTT 58.544 36.000 0.00 0.00 0.00 1.94
466 478 5.335661 CGCAGCTAATTCTTGGTAACCTTTT 60.336 40.000 0.00 0.00 0.00 2.27
467 479 4.156008 CGCAGCTAATTCTTGGTAACCTTT 59.844 41.667 0.00 0.00 0.00 3.11
468 480 3.689649 CGCAGCTAATTCTTGGTAACCTT 59.310 43.478 0.00 0.00 0.00 3.50
469 481 3.270877 CGCAGCTAATTCTTGGTAACCT 58.729 45.455 0.00 0.00 0.00 3.50
470 482 3.007635 ACGCAGCTAATTCTTGGTAACC 58.992 45.455 0.00 0.00 0.00 2.85
471 483 4.680171 AACGCAGCTAATTCTTGGTAAC 57.320 40.909 0.00 0.00 0.00 2.50
472 484 5.699097 AAAACGCAGCTAATTCTTGGTAA 57.301 34.783 0.00 0.00 0.00 2.85
473 485 5.935789 AGTAAAACGCAGCTAATTCTTGGTA 59.064 36.000 0.00 0.00 0.00 3.25
474 486 4.760204 AGTAAAACGCAGCTAATTCTTGGT 59.240 37.500 0.00 0.00 0.00 3.67
475 487 5.106712 TGAGTAAAACGCAGCTAATTCTTGG 60.107 40.000 0.00 0.00 0.00 3.61
476 488 5.790495 GTGAGTAAAACGCAGCTAATTCTTG 59.210 40.000 0.00 0.00 0.00 3.02
477 489 5.701290 AGTGAGTAAAACGCAGCTAATTCTT 59.299 36.000 0.00 0.00 0.00 2.52
478 490 5.238583 AGTGAGTAAAACGCAGCTAATTCT 58.761 37.500 0.00 0.00 0.00 2.40
479 491 5.532025 AGTGAGTAAAACGCAGCTAATTC 57.468 39.130 0.00 0.00 0.00 2.17
480 492 5.929992 TGTAGTGAGTAAAACGCAGCTAATT 59.070 36.000 0.00 0.00 0.00 1.40
481 493 5.475719 TGTAGTGAGTAAAACGCAGCTAAT 58.524 37.500 0.00 0.00 0.00 1.73
482 494 4.873817 TGTAGTGAGTAAAACGCAGCTAA 58.126 39.130 0.00 0.00 0.00 3.09
483 495 4.508461 TGTAGTGAGTAAAACGCAGCTA 57.492 40.909 0.00 0.00 0.00 3.32
484 496 3.380479 TGTAGTGAGTAAAACGCAGCT 57.620 42.857 0.00 0.00 0.00 4.24
485 497 3.678072 TCATGTAGTGAGTAAAACGCAGC 59.322 43.478 0.00 0.00 31.80 5.25
486 498 5.839262 TTCATGTAGTGAGTAAAACGCAG 57.161 39.130 0.00 0.00 38.29 5.18
487 499 7.465379 GCATATTCATGTAGTGAGTAAAACGCA 60.465 37.037 0.00 0.00 38.29 5.24
488 500 6.846283 GCATATTCATGTAGTGAGTAAAACGC 59.154 38.462 0.00 0.00 38.29 4.84
489 501 7.905126 TGCATATTCATGTAGTGAGTAAAACG 58.095 34.615 0.00 0.00 38.29 3.60
496 508 9.836076 CCATAAATTGCATATTCATGTAGTGAG 57.164 33.333 0.00 0.00 38.29 3.51
497 509 9.571816 TCCATAAATTGCATATTCATGTAGTGA 57.428 29.630 0.00 0.00 34.40 3.41
498 510 9.616634 GTCCATAAATTGCATATTCATGTAGTG 57.383 33.333 0.00 0.00 34.40 2.74
499 511 9.578576 AGTCCATAAATTGCATATTCATGTAGT 57.421 29.630 0.00 0.00 34.40 2.73
502 514 9.537192 CAAAGTCCATAAATTGCATATTCATGT 57.463 29.630 0.00 0.00 34.40 3.21
503 515 9.537192 ACAAAGTCCATAAATTGCATATTCATG 57.463 29.630 0.00 0.00 35.07 3.07
504 516 9.537192 CACAAAGTCCATAAATTGCATATTCAT 57.463 29.630 0.00 0.00 0.00 2.57
505 517 8.530311 ACACAAAGTCCATAAATTGCATATTCA 58.470 29.630 0.00 0.00 0.00 2.57
506 518 8.810427 CACACAAAGTCCATAAATTGCATATTC 58.190 33.333 0.00 0.00 0.00 1.75
507 519 7.765360 CCACACAAAGTCCATAAATTGCATATT 59.235 33.333 0.00 0.00 0.00 1.28
508 520 7.093377 ACCACACAAAGTCCATAAATTGCATAT 60.093 33.333 0.00 0.00 0.00 1.78
509 521 6.210385 ACCACACAAAGTCCATAAATTGCATA 59.790 34.615 0.00 0.00 0.00 3.14
510 522 5.011943 ACCACACAAAGTCCATAAATTGCAT 59.988 36.000 0.00 0.00 0.00 3.96
511 523 4.343526 ACCACACAAAGTCCATAAATTGCA 59.656 37.500 0.00 0.00 0.00 4.08
512 524 4.685628 CACCACACAAAGTCCATAAATTGC 59.314 41.667 0.00 0.00 0.00 3.56
513 525 6.083098 TCACCACACAAAGTCCATAAATTG 57.917 37.500 0.00 0.00 0.00 2.32
514 526 6.723298 TTCACCACACAAAGTCCATAAATT 57.277 33.333 0.00 0.00 0.00 1.82
515 527 6.323739 ACTTTCACCACACAAAGTCCATAAAT 59.676 34.615 0.00 0.00 38.22 1.40
516 528 5.654650 ACTTTCACCACACAAAGTCCATAAA 59.345 36.000 0.00 0.00 38.22 1.40
517 529 5.067153 CACTTTCACCACACAAAGTCCATAA 59.933 40.000 0.00 0.00 40.19 1.90
518 530 4.578516 CACTTTCACCACACAAAGTCCATA 59.421 41.667 0.00 0.00 40.19 2.74
519 531 3.381272 CACTTTCACCACACAAAGTCCAT 59.619 43.478 0.00 0.00 40.19 3.41
520 532 2.752354 CACTTTCACCACACAAAGTCCA 59.248 45.455 0.00 0.00 40.19 4.02
521 533 3.013921 TCACTTTCACCACACAAAGTCC 58.986 45.455 0.00 0.00 40.19 3.85
522 534 3.438781 TGTCACTTTCACCACACAAAGTC 59.561 43.478 0.00 0.00 40.19 3.01
523 535 3.190535 GTGTCACTTTCACCACACAAAGT 59.809 43.478 0.00 0.00 42.39 2.66
524 536 3.727673 CGTGTCACTTTCACCACACAAAG 60.728 47.826 0.65 0.00 39.33 2.77
525 537 2.160615 CGTGTCACTTTCACCACACAAA 59.839 45.455 0.65 0.00 39.33 2.83
526 538 1.735018 CGTGTCACTTTCACCACACAA 59.265 47.619 0.65 0.00 39.33 3.33
527 539 1.338294 ACGTGTCACTTTCACCACACA 60.338 47.619 0.65 0.00 39.33 3.72
528 540 1.365699 ACGTGTCACTTTCACCACAC 58.634 50.000 0.65 0.00 36.57 3.82
529 541 2.963548 TACGTGTCACTTTCACCACA 57.036 45.000 0.00 0.00 32.86 4.17
530 542 5.636121 TGAATATACGTGTCACTTTCACCAC 59.364 40.000 0.00 0.00 32.86 4.16
531 543 5.636121 GTGAATATACGTGTCACTTTCACCA 59.364 40.000 0.00 0.74 38.87 4.17
532 544 6.091123 GTGAATATACGTGTCACTTTCACC 57.909 41.667 0.00 0.00 38.87 4.02
539 551 7.201145 ACTTGGATAGTGAATATACGTGTCAC 58.799 38.462 0.00 6.85 41.62 3.67
540 552 7.342769 ACTTGGATAGTGAATATACGTGTCA 57.657 36.000 0.00 0.00 35.19 3.58
541 553 7.169308 CCAACTTGGATAGTGAATATACGTGTC 59.831 40.741 0.92 0.00 40.96 3.67
542 554 6.984474 CCAACTTGGATAGTGAATATACGTGT 59.016 38.462 0.92 0.00 40.96 4.49
543 555 6.073765 GCCAACTTGGATAGTGAATATACGTG 60.074 42.308 12.37 0.00 40.96 4.49
544 556 5.989777 GCCAACTTGGATAGTGAATATACGT 59.010 40.000 12.37 0.00 40.96 3.57
545 557 6.223852 AGCCAACTTGGATAGTGAATATACG 58.776 40.000 12.37 0.00 40.96 3.06
546 558 7.603024 GGTAGCCAACTTGGATAGTGAATATAC 59.397 40.741 12.37 0.00 39.34 1.47
547 559 7.512746 AGGTAGCCAACTTGGATAGTGAATATA 59.487 37.037 12.37 0.00 39.34 0.86
548 560 6.330250 AGGTAGCCAACTTGGATAGTGAATAT 59.670 38.462 12.37 0.00 39.34 1.28
549 561 5.665812 AGGTAGCCAACTTGGATAGTGAATA 59.334 40.000 12.37 0.00 39.34 1.75
550 562 4.475016 AGGTAGCCAACTTGGATAGTGAAT 59.525 41.667 12.37 0.00 39.34 2.57
551 563 3.844211 AGGTAGCCAACTTGGATAGTGAA 59.156 43.478 12.37 0.00 39.34 3.18
552 564 3.450904 AGGTAGCCAACTTGGATAGTGA 58.549 45.455 12.37 0.00 39.34 3.41
553 565 3.914426 AGGTAGCCAACTTGGATAGTG 57.086 47.619 12.37 0.00 39.34 2.74
554 566 7.419865 GGTTAATAGGTAGCCAACTTGGATAGT 60.420 40.741 12.37 2.90 39.34 2.12
555 567 6.935208 GGTTAATAGGTAGCCAACTTGGATAG 59.065 42.308 12.37 0.00 39.34 2.08
556 568 6.618196 AGGTTAATAGGTAGCCAACTTGGATA 59.382 38.462 12.37 6.86 40.96 2.59
557 569 5.432060 AGGTTAATAGGTAGCCAACTTGGAT 59.568 40.000 12.37 7.99 40.96 3.41
558 570 4.786454 AGGTTAATAGGTAGCCAACTTGGA 59.214 41.667 12.37 0.00 40.96 3.53
559 571 5.112129 AGGTTAATAGGTAGCCAACTTGG 57.888 43.478 3.10 3.10 41.55 3.61
560 572 5.758784 GCTAGGTTAATAGGTAGCCAACTTG 59.241 44.000 0.00 0.00 35.55 3.16
561 573 5.666265 AGCTAGGTTAATAGGTAGCCAACTT 59.334 40.000 0.00 0.00 38.99 2.66
562 574 5.217400 AGCTAGGTTAATAGGTAGCCAACT 58.783 41.667 0.00 0.00 38.99 3.16
563 575 5.548181 AGCTAGGTTAATAGGTAGCCAAC 57.452 43.478 0.00 0.00 38.99 3.77
564 576 7.679732 TTTAGCTAGGTTAATAGGTAGCCAA 57.320 36.000 0.00 0.00 38.99 4.52
565 577 7.679732 TTTTAGCTAGGTTAATAGGTAGCCA 57.320 36.000 0.00 0.00 38.99 4.75
566 578 7.660617 CCTTTTTAGCTAGGTTAATAGGTAGCC 59.339 40.741 17.03 0.00 38.99 3.93
612 624 8.883731 CCACGTCTCTATCATTACATTCTTTTT 58.116 33.333 0.00 0.00 0.00 1.94
613 625 8.258007 TCCACGTCTCTATCATTACATTCTTTT 58.742 33.333 0.00 0.00 0.00 2.27
614 626 7.782049 TCCACGTCTCTATCATTACATTCTTT 58.218 34.615 0.00 0.00 0.00 2.52
615 627 7.348080 TCCACGTCTCTATCATTACATTCTT 57.652 36.000 0.00 0.00 0.00 2.52
616 628 6.515862 GCTCCACGTCTCTATCATTACATTCT 60.516 42.308 0.00 0.00 0.00 2.40
617 629 5.631512 GCTCCACGTCTCTATCATTACATTC 59.368 44.000 0.00 0.00 0.00 2.67
618 630 5.509840 GGCTCCACGTCTCTATCATTACATT 60.510 44.000 0.00 0.00 0.00 2.71
619 631 4.021894 GGCTCCACGTCTCTATCATTACAT 60.022 45.833 0.00 0.00 0.00 2.29
620 632 3.318275 GGCTCCACGTCTCTATCATTACA 59.682 47.826 0.00 0.00 0.00 2.41
621 633 3.305471 GGGCTCCACGTCTCTATCATTAC 60.305 52.174 0.00 0.00 0.00 1.89
622 634 2.891580 GGGCTCCACGTCTCTATCATTA 59.108 50.000 0.00 0.00 0.00 1.90
623 635 1.689273 GGGCTCCACGTCTCTATCATT 59.311 52.381 0.00 0.00 0.00 2.57
624 636 1.133325 AGGGCTCCACGTCTCTATCAT 60.133 52.381 0.00 0.00 0.00 2.45
625 637 0.259065 AGGGCTCCACGTCTCTATCA 59.741 55.000 0.00 0.00 0.00 2.15
626 638 2.273538 TAGGGCTCCACGTCTCTATC 57.726 55.000 0.00 0.00 0.00 2.08
627 639 2.750141 TTAGGGCTCCACGTCTCTAT 57.250 50.000 0.00 0.00 0.00 1.98
628 640 2.519771 TTTAGGGCTCCACGTCTCTA 57.480 50.000 0.00 0.00 0.00 2.43
629 641 1.640917 TTTTAGGGCTCCACGTCTCT 58.359 50.000 0.00 0.00 0.00 3.10
630 642 2.467566 TTTTTAGGGCTCCACGTCTC 57.532 50.000 0.00 0.00 0.00 3.36
648 660 4.579869 ACATGCCACGTCTCTATCTTTTT 58.420 39.130 0.00 0.00 0.00 1.94
649 661 4.207891 ACATGCCACGTCTCTATCTTTT 57.792 40.909 0.00 0.00 0.00 2.27
650 662 3.895232 ACATGCCACGTCTCTATCTTT 57.105 42.857 0.00 0.00 0.00 2.52
651 663 4.207955 TCTACATGCCACGTCTCTATCTT 58.792 43.478 0.00 0.00 0.00 2.40
652 664 3.821748 TCTACATGCCACGTCTCTATCT 58.178 45.455 0.00 0.00 0.00 1.98
653 665 4.569761 TTCTACATGCCACGTCTCTATC 57.430 45.455 0.00 0.00 0.00 2.08
654 666 5.105310 ACTTTTCTACATGCCACGTCTCTAT 60.105 40.000 0.00 0.00 0.00 1.98
655 667 4.219944 ACTTTTCTACATGCCACGTCTCTA 59.780 41.667 0.00 0.00 0.00 2.43
745 758 7.547722 TCCCTTTTTGCAAGTAAGAAAAGAAAC 59.452 33.333 19.33 0.00 40.00 2.78
758 771 7.760437 TCTTGAAATTTTTCCCTTTTTGCAAG 58.240 30.769 0.00 0.00 36.36 4.01
764 777 7.194112 TCACCTCTTGAAATTTTTCCCTTTT 57.806 32.000 0.00 0.00 36.36 2.27
799 812 1.667236 TTTTGCAGCATCCGATCGAT 58.333 45.000 18.66 0.00 0.00 3.59
800 813 1.331447 CATTTTGCAGCATCCGATCGA 59.669 47.619 18.66 2.91 0.00 3.59
801 814 1.598676 CCATTTTGCAGCATCCGATCG 60.599 52.381 8.51 8.51 0.00 3.69
802 815 1.677576 TCCATTTTGCAGCATCCGATC 59.322 47.619 0.00 0.00 0.00 3.69
811 824 4.637483 ATATGAACCGTCCATTTTGCAG 57.363 40.909 0.00 0.00 0.00 4.41
990 1094 3.751246 CCAGCCATGGTTGCCACG 61.751 66.667 22.33 5.66 42.17 4.94
1038 1142 1.401761 AAATCACACTGCAGTTGCCA 58.598 45.000 18.94 1.40 41.18 4.92
1093 1197 0.472925 TGGAACAGGTAGGTCAGGCA 60.473 55.000 0.00 0.00 34.85 4.75
1116 1220 0.807667 CGATCTTGTCCAGGCCGAAG 60.808 60.000 0.00 0.00 0.00 3.79
1233 1337 7.673082 AGACCTGAAATCTGAATGGAAGAAAAT 59.327 33.333 0.00 0.00 0.00 1.82
1334 1469 2.222596 GCACGTTCGAAAGCATCTAGTG 60.223 50.000 11.16 7.28 0.00 2.74
1338 1473 1.071605 GAGCACGTTCGAAAGCATCT 58.928 50.000 11.16 5.63 0.00 2.90
1391 1526 4.933064 CCTCATCCTCGTCGCCGC 62.933 72.222 0.00 0.00 0.00 6.53
1394 1529 2.024871 CGTCCTCATCCTCGTCGC 59.975 66.667 0.00 0.00 0.00 5.19
1398 1533 1.169661 CCTCCTCGTCCTCATCCTCG 61.170 65.000 0.00 0.00 0.00 4.63
1438 1585 8.786826 TTTATGGATCGACTGAAGTTTGTTAT 57.213 30.769 0.00 0.00 0.00 1.89
1530 3420 6.672266 ATTAGAAGCAGGTATTAGCAGCTA 57.328 37.500 12.37 0.00 34.66 3.32
1604 3495 7.824289 ACGATATCTGGTTTTTCTTCATCTTCA 59.176 33.333 0.34 0.00 0.00 3.02
1605 3496 8.119226 CACGATATCTGGTTTTTCTTCATCTTC 58.881 37.037 0.34 0.00 0.00 2.87
1606 3497 7.824289 TCACGATATCTGGTTTTTCTTCATCTT 59.176 33.333 0.34 0.00 0.00 2.40
1607 3498 7.331026 TCACGATATCTGGTTTTTCTTCATCT 58.669 34.615 0.34 0.00 0.00 2.90
1608 3499 7.539712 TCACGATATCTGGTTTTTCTTCATC 57.460 36.000 0.34 0.00 0.00 2.92
1609 3500 7.921786 TTCACGATATCTGGTTTTTCTTCAT 57.078 32.000 0.34 0.00 0.00 2.57
1630 3521 1.971167 GGAGCATGTGGCCGTTTCA 60.971 57.895 0.00 0.00 46.50 2.69
1680 3571 3.931468 CACCTCAAGTCTTGTGCTATCTG 59.069 47.826 12.30 0.00 0.00 2.90
1725 3616 2.045047 AGGAATTCTCTGTCCCTCCAGA 59.955 50.000 5.23 0.00 39.11 3.86
1731 3622 0.528684 CGCGAGGAATTCTCTGTCCC 60.529 60.000 0.00 0.00 40.30 4.46
1781 3675 4.935808 ACTAAGTAAACATAGGCTGTGTGC 59.064 41.667 17.98 10.96 38.39 4.57
1798 3692 6.648879 ATGTTGGTGCAATGTAAACTAAGT 57.351 33.333 0.00 0.00 0.00 2.24
1853 3747 0.598065 ATTGTCCAAACCGCAGCTTC 59.402 50.000 0.00 0.00 0.00 3.86
1890 3784 7.332182 AGCTTACTCTGAAGTATAAACAAGTGC 59.668 37.037 0.00 0.00 37.81 4.40
1923 3817 5.125257 GGAGTACTGAGTAAACTACAGACCC 59.875 48.000 0.00 0.00 35.85 4.46
1963 3857 8.804688 AATATAAGAGCGTTTAGATCACTGAC 57.195 34.615 0.00 0.00 37.82 3.51
1964 3858 9.464714 GAAATATAAGAGCGTTTAGATCACTGA 57.535 33.333 0.00 0.00 37.82 3.41
1965 3859 9.469807 AGAAATATAAGAGCGTTTAGATCACTG 57.530 33.333 0.00 0.00 37.82 3.66
1995 3909 6.415206 TTGGAATAATTAGTACTCCTCCCG 57.585 41.667 0.00 0.00 0.00 5.14
2096 4303 5.648092 AGGTGTCATTTTAACAGCCATCTAC 59.352 40.000 2.16 0.00 44.22 2.59
2135 4342 3.696051 TCGGACAACGTATAAAGCTACCT 59.304 43.478 0.00 0.00 44.69 3.08
2146 4353 1.321474 ACCAGAGTTCGGACAACGTA 58.679 50.000 0.00 0.00 44.69 3.57
2155 4362 4.058817 GGCTTCCATATAACCAGAGTTCG 58.941 47.826 0.00 0.00 37.42 3.95
2289 4509 3.320541 CCCAACATAGGCTTCAAACAACA 59.679 43.478 0.00 0.00 0.00 3.33
2301 4521 4.704540 TCAAACAACATAGCCCAACATAGG 59.295 41.667 0.00 0.00 0.00 2.57
2302 4522 5.895636 TCAAACAACATAGCCCAACATAG 57.104 39.130 0.00 0.00 0.00 2.23
2304 4524 4.588528 ACTTCAAACAACATAGCCCAACAT 59.411 37.500 0.00 0.00 0.00 2.71
2305 4525 3.957497 ACTTCAAACAACATAGCCCAACA 59.043 39.130 0.00 0.00 0.00 3.33
2306 4526 4.584327 ACTTCAAACAACATAGCCCAAC 57.416 40.909 0.00 0.00 0.00 3.77
2307 4527 7.068103 CCATATACTTCAAACAACATAGCCCAA 59.932 37.037 0.00 0.00 0.00 4.12
2308 4528 6.545666 CCATATACTTCAAACAACATAGCCCA 59.454 38.462 0.00 0.00 0.00 5.36
2309 4529 6.515035 GCCATATACTTCAAACAACATAGCCC 60.515 42.308 0.00 0.00 0.00 5.19
2310 4530 6.263168 AGCCATATACTTCAAACAACATAGCC 59.737 38.462 0.00 0.00 0.00 3.93
2311 4531 7.264373 AGCCATATACTTCAAACAACATAGC 57.736 36.000 0.00 0.00 0.00 2.97
2327 4547 3.391296 GACCCTCAACCTCAAGCCATATA 59.609 47.826 0.00 0.00 0.00 0.86
2328 4548 2.173569 GACCCTCAACCTCAAGCCATAT 59.826 50.000 0.00 0.00 0.00 1.78
2343 4563 4.706962 ACATTTTCTTTATGCAGGACCCTC 59.293 41.667 0.00 0.00 0.00 4.30
2347 4567 5.569413 CCGTACATTTTCTTTATGCAGGAC 58.431 41.667 0.00 0.00 0.00 3.85
2351 4571 5.637006 AAGCCGTACATTTTCTTTATGCA 57.363 34.783 0.00 0.00 0.00 3.96
2368 4588 0.755686 AGCAGATCCTCCTTAAGCCG 59.244 55.000 0.00 0.00 0.00 5.52
2374 4594 0.913451 AGGTGCAGCAGATCCTCCTT 60.913 55.000 19.63 0.00 0.00 3.36
2394 4614 2.429930 CGAGGGTGGCCTTCAACA 59.570 61.111 3.32 0.00 33.91 3.33
2395 4615 1.966451 CACGAGGGTGGCCTTCAAC 60.966 63.158 3.32 0.00 40.58 3.18
2421 4641 2.544685 GCACTACTGGTATCAGCACTG 58.455 52.381 1.90 0.00 44.59 3.66
2428 4648 3.952323 TGTCTAGTGGCACTACTGGTATC 59.048 47.826 22.96 8.95 31.80 2.24
2446 4666 3.627395 TCACTTTTGTCCACACTGTCT 57.373 42.857 0.00 0.00 0.00 3.41
2448 4668 4.578928 GGTTATCACTTTTGTCCACACTGT 59.421 41.667 0.00 0.00 0.00 3.55
2492 4712 3.389329 GCCATAGTCCTGATTCTCCTGAA 59.611 47.826 0.00 0.00 36.54 3.02
2493 4713 2.968574 GCCATAGTCCTGATTCTCCTGA 59.031 50.000 0.00 0.00 0.00 3.86
2494 4714 2.038295 GGCCATAGTCCTGATTCTCCTG 59.962 54.545 0.00 0.00 0.00 3.86
2495 4715 2.090267 AGGCCATAGTCCTGATTCTCCT 60.090 50.000 5.01 0.00 31.53 3.69
2496 4716 2.334023 AGGCCATAGTCCTGATTCTCC 58.666 52.381 5.01 0.00 31.53 3.71
2511 4731 1.143684 AGAAAGAAAGACTGCAGGCCA 59.856 47.619 18.28 0.00 0.00 5.36
2526 4746 8.460428 ACCTCGTCTACTTATAACTGAAGAAAG 58.540 37.037 0.00 0.00 0.00 2.62
2539 4759 4.093998 CGCTAACTGAACCTCGTCTACTTA 59.906 45.833 0.00 0.00 0.00 2.24
2540 4760 3.119919 CGCTAACTGAACCTCGTCTACTT 60.120 47.826 0.00 0.00 0.00 2.24
2550 4770 0.669625 AGGCGTTCGCTAACTGAACC 60.670 55.000 16.40 0.00 42.08 3.62
2551 4771 1.145803 AAGGCGTTCGCTAACTGAAC 58.854 50.000 16.40 0.00 41.75 3.18
2560 4780 0.447801 ATCACATCAAAGGCGTTCGC 59.552 50.000 8.75 8.75 0.00 4.70
2576 4796 1.018910 CGCCAGCATTCACATGATCA 58.981 50.000 0.00 0.00 31.07 2.92
2577 4797 1.263484 CTCGCCAGCATTCACATGATC 59.737 52.381 0.00 0.00 31.07 2.92
2578 4798 1.134310 TCTCGCCAGCATTCACATGAT 60.134 47.619 0.00 0.00 31.07 2.45
2579 4799 0.249955 TCTCGCCAGCATTCACATGA 59.750 50.000 0.00 0.00 31.07 3.07
2580 4800 1.063616 CTTCTCGCCAGCATTCACATG 59.936 52.381 0.00 0.00 0.00 3.21
2581 4801 1.376543 CTTCTCGCCAGCATTCACAT 58.623 50.000 0.00 0.00 0.00 3.21
2582 4802 0.674581 CCTTCTCGCCAGCATTCACA 60.675 55.000 0.00 0.00 0.00 3.58
2583 4803 1.372087 CCCTTCTCGCCAGCATTCAC 61.372 60.000 0.00 0.00 0.00 3.18
2584 4804 1.078214 CCCTTCTCGCCAGCATTCA 60.078 57.895 0.00 0.00 0.00 2.57
2585 4805 1.078143 ACCCTTCTCGCCAGCATTC 60.078 57.895 0.00 0.00 0.00 2.67
2586 4806 1.078143 GACCCTTCTCGCCAGCATT 60.078 57.895 0.00 0.00 0.00 3.56
2602 4822 2.095252 GCGAAGAGAGCCGTTGGAC 61.095 63.158 0.00 0.00 0.00 4.02
2639 4861 2.064762 GCATCTTATAGCCAGTGCGAG 58.935 52.381 0.00 0.00 44.33 5.03
2664 4924 0.983467 TGATCCAGCACAAGCCAGTA 59.017 50.000 0.00 0.00 43.56 2.74


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

AutoCloner maintained by Alex Coulton.