Multiple sequence alignment - TraesCS1A01G403800

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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 TraesCS1A01G403800 chr1A 100.000 3000 0 0 1 3000 566687744 566690743 0.000000e+00 5541
1 TraesCS1A01G403800 chr1A 84.316 899 129 8 935 1828 547216708 547215817 0.000000e+00 869
2 TraesCS1A01G403800 chr1B 92.684 2310 106 18 574 2850 657506200 657508479 0.000000e+00 3271
3 TraesCS1A01G403800 chr1B 84.436 257 22 10 57 308 657505904 657506147 1.390000e-58 237
4 TraesCS1A01G403800 chr1B 95.122 123 5 1 1 122 657505792 657505914 3.050000e-45 193
5 TraesCS1A01G403800 chr1D 94.960 1369 48 2 569 1937 473033704 473035051 0.000000e+00 2126
6 TraesCS1A01G403800 chr1D 86.885 793 101 1 1036 1828 452265065 452264276 0.000000e+00 885
7 TraesCS1A01G403800 chr1D 86.507 793 104 2 1036 1828 452262191 452261402 0.000000e+00 869
8 TraesCS1A01G403800 chr1D 90.232 604 30 11 2403 2992 473035517 473036105 0.000000e+00 761
9 TraesCS1A01G403800 chr1D 93.603 469 30 0 1918 2386 473035060 473035528 0.000000e+00 701
10 TraesCS1A01G403800 chr1D 90.314 382 32 3 1 378 473033331 473033711 2.080000e-136 496
11 TraesCS1A01G403800 chr7D 86.609 814 107 2 1036 1848 156455339 156456151 0.000000e+00 898
12 TraesCS1A01G403800 chr7B 86.364 814 109 2 1036 1848 118891407 118892219 0.000000e+00 887
13 TraesCS1A01G403800 chr7B 84.434 848 128 4 1002 1848 118821339 118822183 0.000000e+00 832
14 TraesCS1A01G403800 chrUn 84.316 899 129 8 935 1828 246249635 246248744 0.000000e+00 869
15 TraesCS1A01G403800 chr6D 85.326 184 27 0 2206 2389 449782429 449782246 1.100000e-44 191
16 TraesCS1A01G403800 chr7A 87.143 140 18 0 398 537 35439233 35439094 3.100000e-35 159


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 TraesCS1A01G403800 chr1A 566687744 566690743 2999 False 5541.000000 5541 100.000000 1 3000 1 chr1A.!!$F1 2999
1 TraesCS1A01G403800 chr1A 547215817 547216708 891 True 869.000000 869 84.316000 935 1828 1 chr1A.!!$R1 893
2 TraesCS1A01G403800 chr1B 657505792 657508479 2687 False 1233.666667 3271 90.747333 1 2850 3 chr1B.!!$F1 2849
3 TraesCS1A01G403800 chr1D 473033331 473036105 2774 False 1021.000000 2126 92.277250 1 2992 4 chr1D.!!$F1 2991
4 TraesCS1A01G403800 chr1D 452261402 452265065 3663 True 877.000000 885 86.696000 1036 1828 2 chr1D.!!$R1 792
5 TraesCS1A01G403800 chr7D 156455339 156456151 812 False 898.000000 898 86.609000 1036 1848 1 chr7D.!!$F1 812
6 TraesCS1A01G403800 chr7B 118891407 118892219 812 False 887.000000 887 86.364000 1036 1848 1 chr7B.!!$F2 812
7 TraesCS1A01G403800 chr7B 118821339 118822183 844 False 832.000000 832 84.434000 1002 1848 1 chr7B.!!$F1 846
8 TraesCS1A01G403800 chrUn 246248744 246249635 891 True 869.000000 869 84.316000 935 1828 1 chrUn.!!$R1 893

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
480 541 0.042431 AGCATGGCCCAATTTACCCA 59.958 50.0 0.0 0.0 0.0 4.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2400 5372 0.108138 CTCAACCGAGACCATCCACC 60.108 60.0 0.0 0.0 42.34 4.61 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
93 150 1.285962 AGGGGATGGACAATCACAAGG 59.714 52.381 0.00 0.00 40.89 3.61
161 219 4.142773 GCCGACCGTATGAAAATTTTCTGA 60.143 41.667 26.73 14.63 38.02 3.27
173 231 8.925161 TGAAAATTTTCTGAAACGATCAAACT 57.075 26.923 26.73 0.00 37.67 2.66
180 238 2.220824 TGAAACGATCAAACTCAGCGTG 59.779 45.455 0.00 0.00 34.30 5.34
195 253 2.510948 CGTGCAGTCGCCAGATATC 58.489 57.895 0.00 0.00 37.32 1.63
308 369 1.202879 ACCGACACAAACCCATCACAT 60.203 47.619 0.00 0.00 0.00 3.21
312 373 2.884012 GACACAAACCCATCACATGTGA 59.116 45.455 29.67 29.67 43.01 3.58
318 379 3.350219 ACCCATCACATGTGAACTACC 57.650 47.619 31.00 0.00 43.58 3.18
323 384 3.847671 TCACATGTGAACTACCCACAA 57.152 42.857 26.02 0.00 46.12 3.33
334 395 3.295973 ACTACCCACAAAACATGCAACT 58.704 40.909 0.00 0.00 0.00 3.16
342 403 5.177327 CCACAAAACATGCAACTCCATAAAC 59.823 40.000 0.00 0.00 0.00 2.01
346 407 2.754552 ACATGCAACTCCATAAACGCAT 59.245 40.909 0.00 0.00 40.55 4.73
352 413 4.787563 GCAACTCCATAAACGCATGATCAG 60.788 45.833 0.09 0.00 0.00 2.90
356 417 3.118445 TCCATAAACGCATGATCAGTCCA 60.118 43.478 0.09 0.00 0.00 4.02
373 434 3.132111 AGTCCAACAATCAAACCCAACAC 59.868 43.478 0.00 0.00 0.00 3.32
374 435 2.099921 TCCAACAATCAAACCCAACACG 59.900 45.455 0.00 0.00 0.00 4.49
375 436 1.857837 CAACAATCAAACCCAACACGC 59.142 47.619 0.00 0.00 0.00 5.34
376 437 1.107114 ACAATCAAACCCAACACGCA 58.893 45.000 0.00 0.00 0.00 5.24
377 438 1.478510 ACAATCAAACCCAACACGCAA 59.521 42.857 0.00 0.00 0.00 4.85
378 439 2.102252 ACAATCAAACCCAACACGCAAT 59.898 40.909 0.00 0.00 0.00 3.56
379 440 2.437200 ATCAAACCCAACACGCAATG 57.563 45.000 0.00 0.00 0.00 2.82
380 441 1.393603 TCAAACCCAACACGCAATGA 58.606 45.000 0.00 0.00 0.00 2.57
381 442 1.066303 TCAAACCCAACACGCAATGAC 59.934 47.619 0.00 0.00 0.00 3.06
382 443 0.387565 AAACCCAACACGCAATGACC 59.612 50.000 0.00 0.00 0.00 4.02
383 444 0.753479 AACCCAACACGCAATGACCA 60.753 50.000 0.00 0.00 0.00 4.02
384 445 1.285641 CCCAACACGCAATGACCAC 59.714 57.895 0.00 0.00 0.00 4.16
385 446 1.285641 CCAACACGCAATGACCACC 59.714 57.895 0.00 0.00 0.00 4.61
386 447 1.451337 CCAACACGCAATGACCACCA 61.451 55.000 0.00 0.00 0.00 4.17
387 448 0.383590 CAACACGCAATGACCACCAA 59.616 50.000 0.00 0.00 0.00 3.67
388 449 0.383949 AACACGCAATGACCACCAAC 59.616 50.000 0.00 0.00 0.00 3.77
389 450 1.285641 CACGCAATGACCACCAACC 59.714 57.895 0.00 0.00 0.00 3.77
390 451 1.901464 ACGCAATGACCACCAACCC 60.901 57.895 0.00 0.00 0.00 4.11
391 452 1.603455 CGCAATGACCACCAACCCT 60.603 57.895 0.00 0.00 0.00 4.34
392 453 1.586154 CGCAATGACCACCAACCCTC 61.586 60.000 0.00 0.00 0.00 4.30
393 454 0.539438 GCAATGACCACCAACCCTCA 60.539 55.000 0.00 0.00 0.00 3.86
394 455 1.247567 CAATGACCACCAACCCTCAC 58.752 55.000 0.00 0.00 0.00 3.51
395 456 0.850100 AATGACCACCAACCCTCACA 59.150 50.000 0.00 0.00 0.00 3.58
396 457 0.110486 ATGACCACCAACCCTCACAC 59.890 55.000 0.00 0.00 0.00 3.82
397 458 1.228154 GACCACCAACCCTCACACC 60.228 63.158 0.00 0.00 0.00 4.16
398 459 1.990160 GACCACCAACCCTCACACCA 61.990 60.000 0.00 0.00 0.00 4.17
399 460 1.228245 CCACCAACCCTCACACCAG 60.228 63.158 0.00 0.00 0.00 4.00
400 461 1.531748 CACCAACCCTCACACCAGT 59.468 57.895 0.00 0.00 0.00 4.00
402 463 1.228245 CCAACCCTCACACCAGTGG 60.228 63.158 7.91 7.91 45.91 4.00
403 464 1.898574 CAACCCTCACACCAGTGGC 60.899 63.158 9.78 0.00 45.91 5.01
404 465 3.476031 AACCCTCACACCAGTGGCG 62.476 63.158 9.78 1.17 45.91 5.69
405 466 4.704833 CCCTCACACCAGTGGCGG 62.705 72.222 9.78 4.24 45.91 6.13
406 467 3.625897 CCTCACACCAGTGGCGGA 61.626 66.667 9.78 3.33 45.91 5.54
407 468 2.047844 CTCACACCAGTGGCGGAG 60.048 66.667 9.78 9.92 45.91 4.63
427 488 1.981256 CTACAACAGCAAACCTGGGT 58.019 50.000 0.00 0.00 46.14 4.51
428 489 1.608590 CTACAACAGCAAACCTGGGTG 59.391 52.381 0.00 0.00 46.14 4.61
429 490 1.042559 ACAACAGCAAACCTGGGTGG 61.043 55.000 0.00 0.00 46.14 4.61
430 491 1.457455 AACAGCAAACCTGGGTGGG 60.457 57.895 0.00 0.00 46.14 4.61
431 492 3.305516 CAGCAAACCTGGGTGGGC 61.306 66.667 0.00 0.00 41.11 5.36
432 493 4.621087 AGCAAACCTGGGTGGGCC 62.621 66.667 0.00 0.00 41.11 5.80
433 494 4.932105 GCAAACCTGGGTGGGCCA 62.932 66.667 0.00 0.00 41.11 5.36
434 495 2.120274 CAAACCTGGGTGGGCCAT 59.880 61.111 10.70 0.00 41.11 4.40
435 496 1.536174 CAAACCTGGGTGGGCCATT 60.536 57.895 10.70 0.00 41.11 3.16
436 497 0.252012 CAAACCTGGGTGGGCCATTA 60.252 55.000 10.70 0.00 41.11 1.90
437 498 0.252057 AAACCTGGGTGGGCCATTAC 60.252 55.000 10.70 3.52 41.11 1.89
438 499 1.439524 AACCTGGGTGGGCCATTACA 61.440 55.000 10.70 8.60 41.11 2.41
439 500 1.386155 CCTGGGTGGGCCATTACAA 59.614 57.895 10.70 0.00 36.17 2.41
440 501 0.252012 CCTGGGTGGGCCATTACAAA 60.252 55.000 10.70 0.00 36.17 2.83
441 502 1.185315 CTGGGTGGGCCATTACAAAG 58.815 55.000 10.70 1.70 36.17 2.77
442 503 0.780637 TGGGTGGGCCATTACAAAGA 59.219 50.000 10.70 0.00 36.17 2.52
443 504 1.148027 TGGGTGGGCCATTACAAAGAA 59.852 47.619 10.70 0.00 36.17 2.52
444 505 2.252714 GGGTGGGCCATTACAAAGAAA 58.747 47.619 10.70 0.00 36.17 2.52
445 506 2.233676 GGGTGGGCCATTACAAAGAAAG 59.766 50.000 10.70 0.00 36.17 2.62
446 507 2.353704 GGTGGGCCATTACAAAGAAAGC 60.354 50.000 10.70 0.00 34.09 3.51
447 508 2.562738 GTGGGCCATTACAAAGAAAGCT 59.437 45.455 10.70 0.00 0.00 3.74
448 509 3.761752 GTGGGCCATTACAAAGAAAGCTA 59.238 43.478 10.70 0.00 0.00 3.32
449 510 4.219725 GTGGGCCATTACAAAGAAAGCTAA 59.780 41.667 10.70 0.00 0.00 3.09
450 511 4.219725 TGGGCCATTACAAAGAAAGCTAAC 59.780 41.667 0.00 0.00 0.00 2.34
451 512 4.462834 GGGCCATTACAAAGAAAGCTAACT 59.537 41.667 4.39 0.00 0.00 2.24
452 513 5.650703 GGGCCATTACAAAGAAAGCTAACTA 59.349 40.000 4.39 0.00 0.00 2.24
453 514 6.321435 GGGCCATTACAAAGAAAGCTAACTAT 59.679 38.462 4.39 0.00 0.00 2.12
454 515 7.147897 GGGCCATTACAAAGAAAGCTAACTATT 60.148 37.037 4.39 0.00 0.00 1.73
455 516 8.251026 GGCCATTACAAAGAAAGCTAACTATTT 58.749 33.333 0.00 0.00 0.00 1.40
456 517 9.639601 GCCATTACAAAGAAAGCTAACTATTTT 57.360 29.630 0.00 0.00 0.00 1.82
462 523 9.899226 ACAAAGAAAGCTAACTATTTTTGCTAG 57.101 29.630 0.00 0.00 33.28 3.42
463 524 8.854312 CAAAGAAAGCTAACTATTTTTGCTAGC 58.146 33.333 8.10 8.10 36.13 3.42
464 525 7.687941 AGAAAGCTAACTATTTTTGCTAGCA 57.312 32.000 14.93 14.93 37.93 3.49
465 526 8.286191 AGAAAGCTAACTATTTTTGCTAGCAT 57.714 30.769 20.13 5.96 37.93 3.79
466 527 8.186821 AGAAAGCTAACTATTTTTGCTAGCATG 58.813 33.333 20.13 7.43 37.93 4.06
467 528 6.382869 AGCTAACTATTTTTGCTAGCATGG 57.617 37.500 20.13 8.10 37.93 3.66
468 529 4.978580 GCTAACTATTTTTGCTAGCATGGC 59.021 41.667 20.13 10.72 46.05 4.40
469 530 4.391405 AACTATTTTTGCTAGCATGGCC 57.609 40.909 20.13 0.00 44.77 5.36
470 531 2.695147 ACTATTTTTGCTAGCATGGCCC 59.305 45.455 20.13 0.00 44.77 5.80
471 532 1.570803 ATTTTTGCTAGCATGGCCCA 58.429 45.000 20.13 0.00 44.77 5.36
472 533 1.346062 TTTTTGCTAGCATGGCCCAA 58.654 45.000 20.13 5.63 44.77 4.12
473 534 1.570803 TTTTGCTAGCATGGCCCAAT 58.429 45.000 20.13 0.00 44.77 3.16
474 535 1.570803 TTTGCTAGCATGGCCCAATT 58.429 45.000 20.13 0.00 44.77 2.32
475 536 1.570803 TTGCTAGCATGGCCCAATTT 58.429 45.000 20.13 0.00 44.77 1.82
476 537 2.450867 TGCTAGCATGGCCCAATTTA 57.549 45.000 14.93 0.00 44.77 1.40
477 538 2.031120 TGCTAGCATGGCCCAATTTAC 58.969 47.619 14.93 0.00 44.77 2.01
478 539 1.341209 GCTAGCATGGCCCAATTTACC 59.659 52.381 10.63 0.00 36.10 2.85
479 540 1.963515 CTAGCATGGCCCAATTTACCC 59.036 52.381 0.00 0.00 0.00 3.69
480 541 0.042431 AGCATGGCCCAATTTACCCA 59.958 50.000 0.00 0.00 0.00 4.51
481 542 1.130777 GCATGGCCCAATTTACCCAT 58.869 50.000 0.00 0.00 38.56 4.00
482 543 1.070601 GCATGGCCCAATTTACCCATC 59.929 52.381 0.00 0.00 35.97 3.51
483 544 2.396608 CATGGCCCAATTTACCCATCA 58.603 47.619 0.00 0.00 35.97 3.07
484 545 2.630889 TGGCCCAATTTACCCATCAA 57.369 45.000 0.00 0.00 0.00 2.57
485 546 3.127791 TGGCCCAATTTACCCATCAAT 57.872 42.857 0.00 0.00 0.00 2.57
486 547 3.037549 TGGCCCAATTTACCCATCAATC 58.962 45.455 0.00 0.00 0.00 2.67
487 548 3.308401 GGCCCAATTTACCCATCAATCT 58.692 45.455 0.00 0.00 0.00 2.40
488 549 3.711190 GGCCCAATTTACCCATCAATCTT 59.289 43.478 0.00 0.00 0.00 2.40
489 550 4.202253 GGCCCAATTTACCCATCAATCTTC 60.202 45.833 0.00 0.00 0.00 2.87
490 551 4.405358 GCCCAATTTACCCATCAATCTTCA 59.595 41.667 0.00 0.00 0.00 3.02
491 552 5.070847 GCCCAATTTACCCATCAATCTTCAT 59.929 40.000 0.00 0.00 0.00 2.57
492 553 6.408434 GCCCAATTTACCCATCAATCTTCATT 60.408 38.462 0.00 0.00 0.00 2.57
493 554 7.201992 GCCCAATTTACCCATCAATCTTCATTA 60.202 37.037 0.00 0.00 0.00 1.90
494 555 8.703743 CCCAATTTACCCATCAATCTTCATTAA 58.296 33.333 0.00 0.00 0.00 1.40
500 561 6.633856 ACCCATCAATCTTCATTAAACTTGC 58.366 36.000 0.00 0.00 0.00 4.01
501 562 6.438425 ACCCATCAATCTTCATTAAACTTGCT 59.562 34.615 0.00 0.00 0.00 3.91
502 563 7.615365 ACCCATCAATCTTCATTAAACTTGCTA 59.385 33.333 0.00 0.00 0.00 3.49
503 564 8.133627 CCCATCAATCTTCATTAAACTTGCTAG 58.866 37.037 0.00 0.00 0.00 3.42
504 565 8.896744 CCATCAATCTTCATTAAACTTGCTAGA 58.103 33.333 1.04 0.00 0.00 2.43
505 566 9.932699 CATCAATCTTCATTAAACTTGCTAGAG 57.067 33.333 1.04 0.00 0.00 2.43
506 567 8.498054 TCAATCTTCATTAAACTTGCTAGAGG 57.502 34.615 1.04 0.00 0.00 3.69
507 568 8.321353 TCAATCTTCATTAAACTTGCTAGAGGA 58.679 33.333 1.04 0.00 0.00 3.71
508 569 9.118300 CAATCTTCATTAAACTTGCTAGAGGAT 57.882 33.333 1.04 0.00 0.00 3.24
509 570 8.674263 ATCTTCATTAAACTTGCTAGAGGATG 57.326 34.615 1.04 1.47 0.00 3.51
510 571 7.624549 TCTTCATTAAACTTGCTAGAGGATGT 58.375 34.615 1.04 0.00 0.00 3.06
511 572 7.550551 TCTTCATTAAACTTGCTAGAGGATGTG 59.449 37.037 1.04 0.00 0.00 3.21
512 573 5.586243 TCATTAAACTTGCTAGAGGATGTGC 59.414 40.000 1.04 0.00 0.00 4.57
513 574 3.423539 AAACTTGCTAGAGGATGTGCA 57.576 42.857 1.04 0.00 0.00 4.57
514 575 2.687700 ACTTGCTAGAGGATGTGCAG 57.312 50.000 1.04 0.00 36.75 4.41
515 576 2.182827 ACTTGCTAGAGGATGTGCAGA 58.817 47.619 1.04 0.00 36.75 4.26
516 577 2.093764 ACTTGCTAGAGGATGTGCAGAC 60.094 50.000 1.04 0.00 36.75 3.51
517 578 1.857965 TGCTAGAGGATGTGCAGACT 58.142 50.000 0.00 0.00 0.00 3.24
518 579 3.018423 TGCTAGAGGATGTGCAGACTA 57.982 47.619 0.00 0.00 0.00 2.59
519 580 3.570540 TGCTAGAGGATGTGCAGACTAT 58.429 45.455 0.00 0.00 0.00 2.12
520 581 4.729868 TGCTAGAGGATGTGCAGACTATA 58.270 43.478 0.00 0.00 0.00 1.31
521 582 4.764308 TGCTAGAGGATGTGCAGACTATAG 59.236 45.833 0.00 0.00 0.00 1.31
522 583 4.380444 GCTAGAGGATGTGCAGACTATAGC 60.380 50.000 10.88 10.88 41.59 2.97
523 584 2.896685 AGAGGATGTGCAGACTATAGCC 59.103 50.000 0.00 0.00 0.00 3.93
524 585 2.896685 GAGGATGTGCAGACTATAGCCT 59.103 50.000 0.00 0.00 0.00 4.58
525 586 4.082845 GAGGATGTGCAGACTATAGCCTA 58.917 47.826 0.00 0.00 0.00 3.93
526 587 3.829601 AGGATGTGCAGACTATAGCCTAC 59.170 47.826 0.00 0.00 0.00 3.18
527 588 3.829601 GGATGTGCAGACTATAGCCTACT 59.170 47.826 0.00 0.00 0.00 2.57
528 589 4.282195 GGATGTGCAGACTATAGCCTACTT 59.718 45.833 0.00 0.00 0.00 2.24
529 590 5.221541 GGATGTGCAGACTATAGCCTACTTT 60.222 44.000 0.00 0.00 0.00 2.66
530 591 5.011090 TGTGCAGACTATAGCCTACTTTG 57.989 43.478 0.00 0.00 0.00 2.77
531 592 3.804873 GTGCAGACTATAGCCTACTTTGC 59.195 47.826 0.00 0.00 0.00 3.68
532 593 3.706594 TGCAGACTATAGCCTACTTTGCT 59.293 43.478 0.00 0.00 42.81 3.91
533 594 4.893524 TGCAGACTATAGCCTACTTTGCTA 59.106 41.667 0.00 0.00 44.78 3.49
534 595 5.362717 TGCAGACTATAGCCTACTTTGCTAA 59.637 40.000 0.00 0.00 43.96 3.09
535 596 5.692654 GCAGACTATAGCCTACTTTGCTAAC 59.307 44.000 0.00 0.00 43.96 2.34
536 597 6.683110 GCAGACTATAGCCTACTTTGCTAACA 60.683 42.308 0.00 0.00 43.96 2.41
537 598 6.697892 CAGACTATAGCCTACTTTGCTAACAC 59.302 42.308 0.00 0.00 43.96 3.32
538 599 6.380274 AGACTATAGCCTACTTTGCTAACACA 59.620 38.462 0.00 0.00 43.96 3.72
539 600 7.070074 AGACTATAGCCTACTTTGCTAACACAT 59.930 37.037 0.00 0.00 43.96 3.21
540 601 8.246430 ACTATAGCCTACTTTGCTAACACATA 57.754 34.615 0.00 0.00 43.96 2.29
541 602 8.361139 ACTATAGCCTACTTTGCTAACACATAG 58.639 37.037 0.00 0.00 43.96 2.23
542 603 5.677319 AGCCTACTTTGCTAACACATAGA 57.323 39.130 0.00 0.00 37.28 1.98
543 604 6.240549 AGCCTACTTTGCTAACACATAGAT 57.759 37.500 0.00 0.00 37.28 1.98
544 605 6.284459 AGCCTACTTTGCTAACACATAGATC 58.716 40.000 0.00 0.00 37.28 2.75
545 606 5.467063 GCCTACTTTGCTAACACATAGATCC 59.533 44.000 0.00 0.00 33.04 3.36
546 607 5.692204 CCTACTTTGCTAACACATAGATCCG 59.308 44.000 0.00 0.00 33.04 4.18
547 608 3.871594 ACTTTGCTAACACATAGATCCGC 59.128 43.478 0.00 0.00 33.04 5.54
548 609 2.526304 TGCTAACACATAGATCCGCC 57.474 50.000 0.00 0.00 33.04 6.13
549 610 1.760029 TGCTAACACATAGATCCGCCA 59.240 47.619 0.00 0.00 33.04 5.69
550 611 2.224042 TGCTAACACATAGATCCGCCAG 60.224 50.000 0.00 0.00 33.04 4.85
551 612 2.224066 GCTAACACATAGATCCGCCAGT 60.224 50.000 0.00 0.00 33.04 4.00
552 613 2.315925 AACACATAGATCCGCCAGTG 57.684 50.000 0.00 0.00 0.00 3.66
553 614 0.179073 ACACATAGATCCGCCAGTGC 60.179 55.000 0.00 0.00 0.00 4.40
554 615 0.105593 CACATAGATCCGCCAGTGCT 59.894 55.000 0.00 0.00 34.43 4.40
555 616 0.390860 ACATAGATCCGCCAGTGCTC 59.609 55.000 0.00 0.00 34.43 4.26
556 617 0.320247 CATAGATCCGCCAGTGCTCC 60.320 60.000 0.00 0.00 34.43 4.70
557 618 0.760567 ATAGATCCGCCAGTGCTCCA 60.761 55.000 0.00 0.00 34.43 3.86
558 619 1.676678 TAGATCCGCCAGTGCTCCAC 61.677 60.000 0.00 0.00 34.43 4.02
559 620 3.315142 GATCCGCCAGTGCTCCACA 62.315 63.158 0.00 0.00 36.74 4.17
569 630 1.997669 GTGCTCCACACTGCTAGTAC 58.002 55.000 0.00 0.00 46.41 2.73
570 631 1.272490 GTGCTCCACACTGCTAGTACA 59.728 52.381 0.00 0.00 46.41 2.90
571 632 2.093973 GTGCTCCACACTGCTAGTACAT 60.094 50.000 0.00 0.00 46.41 2.29
635 700 3.775261 ATCAAATTTGTTGGGCAAGCT 57.225 38.095 17.47 0.00 38.47 3.74
662 727 3.312973 GTGTGATGTACGTTGGGAAAACA 59.687 43.478 0.00 0.00 0.00 2.83
685 750 1.039233 AAGAGGATGCGGCCAAATGG 61.039 55.000 2.24 0.00 38.53 3.16
751 816 2.095364 GCGGTCTCTTTCGACTTGTCTA 60.095 50.000 0.00 0.00 34.38 2.59
754 819 4.320348 CGGTCTCTTTCGACTTGTCTAACT 60.320 45.833 0.00 0.00 34.38 2.24
900 965 1.338973 CAGCTGTCAGCAAACACCAAT 59.661 47.619 26.23 0.00 45.56 3.16
992 1058 2.847327 AACCATCTCCACACACTCAG 57.153 50.000 0.00 0.00 0.00 3.35
1074 1142 3.244700 ACCACCATGTCTCTTTCCTCTTG 60.245 47.826 0.00 0.00 0.00 3.02
1183 1251 6.293407 CGAAAGCCAAACAAGTTTCATCTAGA 60.293 38.462 0.00 0.00 0.00 2.43
1830 4772 1.154225 CATTCGCCACCAACTTCGC 60.154 57.895 0.00 0.00 0.00 4.70
1848 4790 1.520666 CGCCGGGGAAGTAAGACAT 59.479 57.895 14.46 0.00 0.00 3.06
1858 4800 5.440610 GGGAAGTAAGACATGAATGATGGT 58.559 41.667 0.00 0.00 36.23 3.55
1861 4803 6.183360 GGAAGTAAGACATGAATGATGGTTGG 60.183 42.308 0.00 0.00 36.23 3.77
1864 4806 3.894759 AGACATGAATGATGGTTGGGAG 58.105 45.455 0.00 0.00 36.23 4.30
1907 4849 9.088512 GTTGAATTGTAACACCAACATGTAAAA 57.911 29.630 0.00 0.00 37.59 1.52
1982 4952 1.202879 TGCTCCCCGTCTTGTTTTCAT 60.203 47.619 0.00 0.00 0.00 2.57
2008 4978 5.483685 TCACTAAGCACTCATTGGTAGTT 57.516 39.130 0.00 0.00 33.68 2.24
2043 5013 8.554528 CAGAATATCCATAACTTGTGATGACAC 58.445 37.037 0.00 0.00 46.09 3.67
2098 5069 1.151668 GCTTGCTGACATTGTCGAGT 58.848 50.000 11.97 0.00 34.95 4.18
2117 5088 4.601019 GAGTGTCAAGTGGATTGTTTGTG 58.399 43.478 0.00 0.00 40.05 3.33
2137 5108 3.373439 GTGGTGATGTGATTGCTCTTCTC 59.627 47.826 0.00 0.00 0.00 2.87
2169 5140 0.107831 CTTCTTCGGGTGTGGTTCCA 59.892 55.000 0.00 0.00 0.00 3.53
2205 5176 1.674817 CCTTCTGCGATTACGGTGGTT 60.675 52.381 0.00 0.00 40.15 3.67
2235 5206 1.478510 AGTGAAGCGATCTGGGTGTAG 59.521 52.381 0.00 0.00 0.00 2.74
2238 5209 1.476891 GAAGCGATCTGGGTGTAGACA 59.523 52.381 0.00 0.00 0.00 3.41
2250 5222 0.601558 TGTAGACACGGCTCCTTGTC 59.398 55.000 15.30 15.30 42.98 3.18
2312 5284 2.365617 ACTCGGATGTGTGTGACTCTTT 59.634 45.455 0.00 0.00 0.00 2.52
2317 5289 3.466836 GATGTGTGTGACTCTTTGTCCA 58.533 45.455 0.00 0.00 44.75 4.02
2319 5291 2.499693 TGTGTGTGACTCTTTGTCCAGA 59.500 45.455 0.00 0.00 44.75 3.86
2342 5314 0.674895 GGACTTGGTCGCTCATTGCT 60.675 55.000 0.00 0.00 40.11 3.91
2386 5358 2.560542 GAGGCATCATAGATGGTCTCGT 59.439 50.000 8.87 0.00 0.00 4.18
2389 5361 4.130118 GGCATCATAGATGGTCTCGTTTT 58.870 43.478 8.87 0.00 0.00 2.43
2390 5362 4.212214 GGCATCATAGATGGTCTCGTTTTC 59.788 45.833 8.87 0.00 0.00 2.29
2391 5363 5.053145 GCATCATAGATGGTCTCGTTTTCT 58.947 41.667 8.87 0.00 0.00 2.52
2392 5364 5.525378 GCATCATAGATGGTCTCGTTTTCTT 59.475 40.000 8.87 0.00 0.00 2.52
2393 5365 6.037610 GCATCATAGATGGTCTCGTTTTCTTT 59.962 38.462 8.87 0.00 0.00 2.52
2394 5366 7.414540 GCATCATAGATGGTCTCGTTTTCTTTT 60.415 37.037 8.87 0.00 0.00 2.27
2395 5367 7.364522 TCATAGATGGTCTCGTTTTCTTTTG 57.635 36.000 0.00 0.00 0.00 2.44
2396 5368 4.489679 AGATGGTCTCGTTTTCTTTTGC 57.510 40.909 0.00 0.00 0.00 3.68
2397 5369 3.882888 AGATGGTCTCGTTTTCTTTTGCA 59.117 39.130 0.00 0.00 0.00 4.08
2398 5370 3.414549 TGGTCTCGTTTTCTTTTGCAC 57.585 42.857 0.00 0.00 0.00 4.57
2399 5371 2.098443 TGGTCTCGTTTTCTTTTGCACC 59.902 45.455 0.00 0.00 0.00 5.01
2400 5372 2.372350 GTCTCGTTTTCTTTTGCACCG 58.628 47.619 0.00 0.00 0.00 4.94
2401 5373 1.332375 TCTCGTTTTCTTTTGCACCGG 59.668 47.619 0.00 0.00 0.00 5.28
2415 5387 3.075005 CCGGTGGATGGTCTCGGT 61.075 66.667 0.00 0.00 36.38 4.69
2417 5389 1.447838 CGGTGGATGGTCTCGGTTG 60.448 63.158 0.00 0.00 0.00 3.77
2418 5390 1.884075 CGGTGGATGGTCTCGGTTGA 61.884 60.000 0.00 0.00 0.00 3.18
2419 5391 0.108138 GGTGGATGGTCTCGGTTGAG 60.108 60.000 0.00 0.00 43.99 3.02
2425 5397 0.391597 TGGTCTCGGTTGAGTTGGAC 59.608 55.000 0.00 0.00 43.09 4.02
2431 5403 1.766496 TCGGTTGAGTTGGACCTCTTT 59.234 47.619 0.00 0.00 33.69 2.52
2486 5458 1.586564 CGCGAGGACGATGGAAGAC 60.587 63.158 0.00 0.00 42.66 3.01
2489 5461 0.028242 CGAGGACGATGGAAGACGAG 59.972 60.000 0.00 0.00 42.66 4.18
2505 5477 1.303282 GAGGGCATTCCGGTCCTTT 59.697 57.895 0.00 0.00 44.66 3.11
2506 5478 0.323451 GAGGGCATTCCGGTCCTTTT 60.323 55.000 0.00 0.00 44.66 2.27
2557 5534 6.865726 CAGGTGTAATCTATTTCCTCTCATCG 59.134 42.308 0.00 0.00 0.00 3.84
2563 5540 5.440234 TCTATTTCCTCTCATCGCTGTAC 57.560 43.478 0.00 0.00 0.00 2.90
2572 5549 1.745653 TCATCGCTGTACTCCTCTGTG 59.254 52.381 0.00 0.00 0.00 3.66
2616 5593 7.486232 GTGCCTTCTTAATGAATGAAAAGTAGC 59.514 37.037 0.00 0.00 33.71 3.58
2630 5607 0.599558 AGTAGCGCTGGTACGTTTCA 59.400 50.000 22.90 0.00 40.83 2.69
2632 5609 2.424601 AGTAGCGCTGGTACGTTTCATA 59.575 45.455 22.90 0.00 40.83 2.15
2723 5721 6.553476 AGCCCAGTTTAAACCTCTAATTTTGT 59.447 34.615 14.72 0.00 0.00 2.83
2842 5840 6.047870 CCAACTCTTCTCATACATCCTTCTG 58.952 44.000 0.00 0.00 0.00 3.02
2847 5845 8.378565 ACTCTTCTCATACATCCTTCTGAAAAA 58.621 33.333 0.00 0.00 0.00 1.94
2944 5942 3.997681 CTCGGCTATGATTCTCTCTCGTA 59.002 47.826 0.00 0.00 0.00 3.43
2960 5958 7.879677 TCTCTCTCGTATTATTTCATACCGGTA 59.120 37.037 18.46 18.46 0.00 4.02
2966 5964 8.845227 TCGTATTATTTCATACCGGTAACTGTA 58.155 33.333 20.22 4.32 40.73 2.74
2996 5994 6.596309 GAAGAAATCCAAAGAGTCCCATTT 57.404 37.500 0.00 0.00 0.00 2.32
2997 5995 6.997655 GAAGAAATCCAAAGAGTCCCATTTT 58.002 36.000 0.00 0.00 0.00 1.82
2998 5996 7.379059 AAGAAATCCAAAGAGTCCCATTTTT 57.621 32.000 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
93 150 7.158099 AGAGTAAATATGTGTTTCTTTGCCC 57.842 36.000 0.00 0.00 0.00 5.36
161 219 1.069906 GCACGCTGAGTTTGATCGTTT 60.070 47.619 0.00 0.00 0.00 3.60
180 238 4.558538 AAAATTGATATCTGGCGACTGC 57.441 40.909 3.98 0.00 41.71 4.40
212 270 8.814038 ACTGATTAGGCAAATATTTTGTCTCT 57.186 30.769 10.12 0.77 35.73 3.10
281 340 1.477295 GGGTTTGTGTCGGTTTTTCCA 59.523 47.619 0.00 0.00 35.57 3.53
283 342 2.943449 TGGGTTTGTGTCGGTTTTTC 57.057 45.000 0.00 0.00 0.00 2.29
308 369 3.067461 GCATGTTTTGTGGGTAGTTCACA 59.933 43.478 0.00 0.00 42.57 3.58
312 373 3.704061 AGTTGCATGTTTTGTGGGTAGTT 59.296 39.130 0.00 0.00 0.00 2.24
318 379 2.886862 TGGAGTTGCATGTTTTGTGG 57.113 45.000 0.00 0.00 0.00 4.17
323 384 3.005261 TGCGTTTATGGAGTTGCATGTTT 59.995 39.130 0.00 0.00 0.00 2.83
334 395 3.118445 TGGACTGATCATGCGTTTATGGA 60.118 43.478 0.00 0.00 0.00 3.41
342 403 2.679336 TGATTGTTGGACTGATCATGCG 59.321 45.455 0.00 0.00 0.00 4.73
346 407 3.826157 GGGTTTGATTGTTGGACTGATCA 59.174 43.478 0.00 0.00 0.00 2.92
352 413 3.453424 GTGTTGGGTTTGATTGTTGGAC 58.547 45.455 0.00 0.00 0.00 4.02
356 417 1.478510 TGCGTGTTGGGTTTGATTGTT 59.521 42.857 0.00 0.00 0.00 2.83
373 434 1.586154 GAGGGTTGGTGGTCATTGCG 61.586 60.000 0.00 0.00 0.00 4.85
374 435 0.539438 TGAGGGTTGGTGGTCATTGC 60.539 55.000 0.00 0.00 0.00 3.56
375 436 1.247567 GTGAGGGTTGGTGGTCATTG 58.752 55.000 0.00 0.00 0.00 2.82
376 437 0.850100 TGTGAGGGTTGGTGGTCATT 59.150 50.000 0.00 0.00 0.00 2.57
377 438 0.110486 GTGTGAGGGTTGGTGGTCAT 59.890 55.000 0.00 0.00 0.00 3.06
378 439 1.529796 GTGTGAGGGTTGGTGGTCA 59.470 57.895 0.00 0.00 0.00 4.02
379 440 1.228154 GGTGTGAGGGTTGGTGGTC 60.228 63.158 0.00 0.00 0.00 4.02
380 441 1.994885 CTGGTGTGAGGGTTGGTGGT 61.995 60.000 0.00 0.00 0.00 4.16
381 442 1.228245 CTGGTGTGAGGGTTGGTGG 60.228 63.158 0.00 0.00 0.00 4.61
382 443 0.819259 CACTGGTGTGAGGGTTGGTG 60.819 60.000 0.00 0.00 46.55 4.17
383 444 1.531748 CACTGGTGTGAGGGTTGGT 59.468 57.895 0.00 0.00 46.55 3.67
384 445 1.228245 CCACTGGTGTGAGGGTTGG 60.228 63.158 0.00 0.00 46.55 3.77
385 446 1.898574 GCCACTGGTGTGAGGGTTG 60.899 63.158 0.00 0.00 46.55 3.77
386 447 2.515901 GCCACTGGTGTGAGGGTT 59.484 61.111 0.00 0.00 46.55 4.11
387 448 3.941188 CGCCACTGGTGTGAGGGT 61.941 66.667 0.00 0.00 46.55 4.34
388 449 4.704833 CCGCCACTGGTGTGAGGG 62.705 72.222 7.86 0.00 46.55 4.30
389 450 3.596066 CTCCGCCACTGGTGTGAGG 62.596 68.421 14.72 6.56 46.55 3.86
390 451 2.047844 CTCCGCCACTGGTGTGAG 60.048 66.667 7.86 9.59 46.55 3.51
391 452 4.314440 GCTCCGCCACTGGTGTGA 62.314 66.667 7.86 4.17 46.55 3.58
392 453 2.942796 TAGCTCCGCCACTGGTGTG 61.943 63.158 7.86 1.78 43.45 3.82
393 454 2.603473 TAGCTCCGCCACTGGTGT 60.603 61.111 7.86 0.00 0.00 4.16
394 455 2.125512 GTAGCTCCGCCACTGGTG 60.126 66.667 1.13 1.13 0.00 4.17
395 456 2.214216 TTGTAGCTCCGCCACTGGT 61.214 57.895 0.00 0.00 0.00 4.00
396 457 1.741770 GTTGTAGCTCCGCCACTGG 60.742 63.158 0.00 0.00 0.00 4.00
397 458 1.005037 TGTTGTAGCTCCGCCACTG 60.005 57.895 0.00 0.00 0.00 3.66
398 459 1.293498 CTGTTGTAGCTCCGCCACT 59.707 57.895 0.00 0.00 0.00 4.00
399 460 3.876300 CTGTTGTAGCTCCGCCAC 58.124 61.111 0.00 0.00 0.00 5.01
408 469 1.608590 CACCCAGGTTTGCTGTTGTAG 59.391 52.381 0.00 0.00 0.00 2.74
409 470 1.686355 CACCCAGGTTTGCTGTTGTA 58.314 50.000 0.00 0.00 0.00 2.41
410 471 1.042559 CCACCCAGGTTTGCTGTTGT 61.043 55.000 0.00 0.00 0.00 3.32
411 472 1.741525 CCACCCAGGTTTGCTGTTG 59.258 57.895 0.00 0.00 0.00 3.33
412 473 1.457455 CCCACCCAGGTTTGCTGTT 60.457 57.895 0.00 0.00 34.66 3.16
413 474 2.198426 CCCACCCAGGTTTGCTGT 59.802 61.111 0.00 0.00 34.66 4.40
414 475 3.305516 GCCCACCCAGGTTTGCTG 61.306 66.667 0.00 0.00 34.66 4.41
415 476 4.621087 GGCCCACCCAGGTTTGCT 62.621 66.667 0.00 0.00 34.66 3.91
416 477 4.932105 TGGCCCACCCAGGTTTGC 62.932 66.667 0.00 0.00 39.18 3.68
424 485 1.931635 TTCTTTGTAATGGCCCACCC 58.068 50.000 0.00 0.00 33.59 4.61
425 486 2.353704 GCTTTCTTTGTAATGGCCCACC 60.354 50.000 0.00 0.00 0.00 4.61
426 487 2.562738 AGCTTTCTTTGTAATGGCCCAC 59.437 45.455 0.00 0.00 0.00 4.61
427 488 2.888212 AGCTTTCTTTGTAATGGCCCA 58.112 42.857 0.00 0.00 0.00 5.36
428 489 4.462834 AGTTAGCTTTCTTTGTAATGGCCC 59.537 41.667 0.00 0.00 0.00 5.80
429 490 5.644977 AGTTAGCTTTCTTTGTAATGGCC 57.355 39.130 0.00 0.00 0.00 5.36
430 491 9.639601 AAAATAGTTAGCTTTCTTTGTAATGGC 57.360 29.630 0.00 0.00 0.00 4.40
436 497 9.899226 CTAGCAAAAATAGTTAGCTTTCTTTGT 57.101 29.630 7.88 0.00 36.80 2.83
437 498 8.854312 GCTAGCAAAAATAGTTAGCTTTCTTTG 58.146 33.333 10.63 0.00 41.01 2.77
438 499 8.576442 TGCTAGCAAAAATAGTTAGCTTTCTTT 58.424 29.630 16.84 0.00 43.50 2.52
439 500 8.110860 TGCTAGCAAAAATAGTTAGCTTTCTT 57.889 30.769 16.84 0.00 43.50 2.52
440 501 7.687941 TGCTAGCAAAAATAGTTAGCTTTCT 57.312 32.000 16.84 0.00 43.50 2.52
441 502 7.433425 CCATGCTAGCAAAAATAGTTAGCTTTC 59.567 37.037 23.54 2.73 43.50 2.62
442 503 7.260603 CCATGCTAGCAAAAATAGTTAGCTTT 58.739 34.615 23.54 0.00 43.50 3.51
443 504 6.681368 GCCATGCTAGCAAAAATAGTTAGCTT 60.681 38.462 23.54 0.00 43.50 3.74
444 505 5.221126 GCCATGCTAGCAAAAATAGTTAGCT 60.221 40.000 23.54 7.73 43.50 3.32
445 506 4.978580 GCCATGCTAGCAAAAATAGTTAGC 59.021 41.667 23.54 3.25 43.43 3.09
446 507 5.507985 GGGCCATGCTAGCAAAAATAGTTAG 60.508 44.000 23.54 0.00 0.00 2.34
447 508 4.340950 GGGCCATGCTAGCAAAAATAGTTA 59.659 41.667 23.54 0.00 0.00 2.24
448 509 3.132824 GGGCCATGCTAGCAAAAATAGTT 59.867 43.478 23.54 0.00 0.00 2.24
449 510 2.695147 GGGCCATGCTAGCAAAAATAGT 59.305 45.455 23.54 0.00 0.00 2.12
450 511 2.694628 TGGGCCATGCTAGCAAAAATAG 59.305 45.455 23.54 7.97 0.00 1.73
451 512 2.744760 TGGGCCATGCTAGCAAAAATA 58.255 42.857 23.54 4.16 0.00 1.40
452 513 1.570803 TGGGCCATGCTAGCAAAAAT 58.429 45.000 23.54 1.20 0.00 1.82
453 514 1.346062 TTGGGCCATGCTAGCAAAAA 58.654 45.000 23.54 7.20 0.00 1.94
454 515 1.570803 ATTGGGCCATGCTAGCAAAA 58.429 45.000 23.54 9.78 0.00 2.44
455 516 1.570803 AATTGGGCCATGCTAGCAAA 58.429 45.000 23.54 10.76 0.00 3.68
456 517 1.570803 AAATTGGGCCATGCTAGCAA 58.429 45.000 23.54 3.02 0.00 3.91
457 518 2.031120 GTAAATTGGGCCATGCTAGCA 58.969 47.619 21.85 21.85 0.00 3.49
458 519 1.341209 GGTAAATTGGGCCATGCTAGC 59.659 52.381 7.26 8.10 0.00 3.42
459 520 1.963515 GGGTAAATTGGGCCATGCTAG 59.036 52.381 7.26 0.00 0.00 3.42
460 521 1.289231 TGGGTAAATTGGGCCATGCTA 59.711 47.619 7.26 0.00 0.00 3.49
461 522 0.042431 TGGGTAAATTGGGCCATGCT 59.958 50.000 7.26 0.00 0.00 3.79
462 523 1.070601 GATGGGTAAATTGGGCCATGC 59.929 52.381 7.26 0.00 0.00 4.06
463 524 2.396608 TGATGGGTAAATTGGGCCATG 58.603 47.619 7.26 0.00 0.00 3.66
464 525 2.864885 TGATGGGTAAATTGGGCCAT 57.135 45.000 7.26 0.00 0.00 4.40
465 526 2.630889 TTGATGGGTAAATTGGGCCA 57.369 45.000 0.00 0.00 0.00 5.36
466 527 3.308401 AGATTGATGGGTAAATTGGGCC 58.692 45.455 0.00 0.00 0.00 5.80
467 528 4.405358 TGAAGATTGATGGGTAAATTGGGC 59.595 41.667 0.00 0.00 0.00 5.36
468 529 6.736110 ATGAAGATTGATGGGTAAATTGGG 57.264 37.500 0.00 0.00 0.00 4.12
474 535 8.250332 GCAAGTTTAATGAAGATTGATGGGTAA 58.750 33.333 0.00 0.00 0.00 2.85
475 536 7.615365 AGCAAGTTTAATGAAGATTGATGGGTA 59.385 33.333 0.00 0.00 0.00 3.69
476 537 6.438425 AGCAAGTTTAATGAAGATTGATGGGT 59.562 34.615 0.00 0.00 0.00 4.51
477 538 6.870769 AGCAAGTTTAATGAAGATTGATGGG 58.129 36.000 0.00 0.00 0.00 4.00
478 539 8.896744 TCTAGCAAGTTTAATGAAGATTGATGG 58.103 33.333 0.00 0.00 0.00 3.51
479 540 9.932699 CTCTAGCAAGTTTAATGAAGATTGATG 57.067 33.333 0.00 0.00 0.00 3.07
480 541 9.118300 CCTCTAGCAAGTTTAATGAAGATTGAT 57.882 33.333 0.00 0.00 0.00 2.57
481 542 8.321353 TCCTCTAGCAAGTTTAATGAAGATTGA 58.679 33.333 0.00 0.00 0.00 2.57
482 543 8.498054 TCCTCTAGCAAGTTTAATGAAGATTG 57.502 34.615 0.00 0.00 0.00 2.67
483 544 9.118300 CATCCTCTAGCAAGTTTAATGAAGATT 57.882 33.333 0.00 0.00 0.00 2.40
484 545 8.270744 ACATCCTCTAGCAAGTTTAATGAAGAT 58.729 33.333 0.00 0.00 0.00 2.40
485 546 7.550551 CACATCCTCTAGCAAGTTTAATGAAGA 59.449 37.037 0.00 0.00 0.00 2.87
486 547 7.678218 GCACATCCTCTAGCAAGTTTAATGAAG 60.678 40.741 0.00 0.00 0.00 3.02
487 548 6.094048 GCACATCCTCTAGCAAGTTTAATGAA 59.906 38.462 0.00 0.00 0.00 2.57
488 549 5.586243 GCACATCCTCTAGCAAGTTTAATGA 59.414 40.000 0.00 0.00 0.00 2.57
489 550 5.355071 TGCACATCCTCTAGCAAGTTTAATG 59.645 40.000 0.00 0.00 33.48 1.90
490 551 5.500234 TGCACATCCTCTAGCAAGTTTAAT 58.500 37.500 0.00 0.00 33.48 1.40
491 552 4.905429 TGCACATCCTCTAGCAAGTTTAA 58.095 39.130 0.00 0.00 33.48 1.52
492 553 4.222810 TCTGCACATCCTCTAGCAAGTTTA 59.777 41.667 0.00 0.00 36.44 2.01
493 554 3.008375 TCTGCACATCCTCTAGCAAGTTT 59.992 43.478 0.00 0.00 36.44 2.66
494 555 2.568956 TCTGCACATCCTCTAGCAAGTT 59.431 45.455 0.00 0.00 36.44 2.66
495 556 2.093764 GTCTGCACATCCTCTAGCAAGT 60.094 50.000 0.00 0.00 36.44 3.16
496 557 2.168106 AGTCTGCACATCCTCTAGCAAG 59.832 50.000 0.00 0.00 36.44 4.01
497 558 2.182827 AGTCTGCACATCCTCTAGCAA 58.817 47.619 0.00 0.00 36.44 3.91
498 559 1.857965 AGTCTGCACATCCTCTAGCA 58.142 50.000 0.00 0.00 35.43 3.49
499 560 4.380444 GCTATAGTCTGCACATCCTCTAGC 60.380 50.000 0.84 0.00 0.00 3.42
500 561 4.157656 GGCTATAGTCTGCACATCCTCTAG 59.842 50.000 0.84 0.00 0.00 2.43
501 562 4.082845 GGCTATAGTCTGCACATCCTCTA 58.917 47.826 0.84 0.00 0.00 2.43
502 563 2.896685 GGCTATAGTCTGCACATCCTCT 59.103 50.000 0.84 0.00 0.00 3.69
503 564 2.896685 AGGCTATAGTCTGCACATCCTC 59.103 50.000 5.94 0.00 0.00 3.71
504 565 2.969628 AGGCTATAGTCTGCACATCCT 58.030 47.619 5.94 0.00 0.00 3.24
505 566 3.829601 AGTAGGCTATAGTCTGCACATCC 59.170 47.826 22.24 2.59 34.73 3.51
506 567 5.461032 AAGTAGGCTATAGTCTGCACATC 57.539 43.478 22.24 4.80 34.73 3.06
507 568 5.605534 CAAAGTAGGCTATAGTCTGCACAT 58.394 41.667 22.24 7.28 34.73 3.21
508 569 4.680708 GCAAAGTAGGCTATAGTCTGCACA 60.681 45.833 22.24 0.00 34.73 4.57
509 570 3.804873 GCAAAGTAGGCTATAGTCTGCAC 59.195 47.826 22.24 11.50 34.73 4.57
510 571 3.706594 AGCAAAGTAGGCTATAGTCTGCA 59.293 43.478 22.24 0.00 40.47 4.41
511 572 4.329462 AGCAAAGTAGGCTATAGTCTGC 57.671 45.455 17.30 15.58 40.47 4.26
512 573 6.697892 GTGTTAGCAAAGTAGGCTATAGTCTG 59.302 42.308 17.30 1.63 42.91 3.51
513 574 6.380274 TGTGTTAGCAAAGTAGGCTATAGTCT 59.620 38.462 12.37 12.37 42.91 3.24
514 575 6.570692 TGTGTTAGCAAAGTAGGCTATAGTC 58.429 40.000 0.00 0.00 42.91 2.59
515 576 6.540438 TGTGTTAGCAAAGTAGGCTATAGT 57.460 37.500 0.00 0.00 42.91 2.12
516 577 8.577296 TCTATGTGTTAGCAAAGTAGGCTATAG 58.423 37.037 0.00 0.00 42.91 1.31
517 578 8.473358 TCTATGTGTTAGCAAAGTAGGCTATA 57.527 34.615 0.00 0.00 42.91 1.31
518 579 7.361457 TCTATGTGTTAGCAAAGTAGGCTAT 57.639 36.000 0.00 0.00 42.91 2.97
519 580 6.785337 TCTATGTGTTAGCAAAGTAGGCTA 57.215 37.500 0.00 0.00 42.62 3.93
520 581 5.677319 TCTATGTGTTAGCAAAGTAGGCT 57.323 39.130 0.00 0.00 45.18 4.58
521 582 5.467063 GGATCTATGTGTTAGCAAAGTAGGC 59.533 44.000 0.00 0.00 0.00 3.93
522 583 5.692204 CGGATCTATGTGTTAGCAAAGTAGG 59.308 44.000 0.00 0.00 0.00 3.18
523 584 5.175856 GCGGATCTATGTGTTAGCAAAGTAG 59.824 44.000 0.00 0.00 0.00 2.57
524 585 5.047847 GCGGATCTATGTGTTAGCAAAGTA 58.952 41.667 0.00 0.00 0.00 2.24
525 586 3.871594 GCGGATCTATGTGTTAGCAAAGT 59.128 43.478 0.00 0.00 0.00 2.66
526 587 3.248602 GGCGGATCTATGTGTTAGCAAAG 59.751 47.826 0.00 0.00 0.00 2.77
527 588 3.202906 GGCGGATCTATGTGTTAGCAAA 58.797 45.455 0.00 0.00 0.00 3.68
528 589 2.169561 TGGCGGATCTATGTGTTAGCAA 59.830 45.455 0.00 0.00 0.00 3.91
529 590 1.760029 TGGCGGATCTATGTGTTAGCA 59.240 47.619 0.00 0.00 0.00 3.49
530 591 2.224066 ACTGGCGGATCTATGTGTTAGC 60.224 50.000 0.00 0.00 0.00 3.09
531 592 3.384668 CACTGGCGGATCTATGTGTTAG 58.615 50.000 0.00 0.00 0.00 2.34
532 593 2.483013 GCACTGGCGGATCTATGTGTTA 60.483 50.000 0.00 0.00 0.00 2.41
533 594 1.743772 GCACTGGCGGATCTATGTGTT 60.744 52.381 0.00 0.00 0.00 3.32
534 595 0.179073 GCACTGGCGGATCTATGTGT 60.179 55.000 0.00 0.00 0.00 3.72
535 596 2.609825 GCACTGGCGGATCTATGTG 58.390 57.895 0.00 0.00 0.00 3.21
551 612 1.627864 TGTACTAGCAGTGTGGAGCA 58.372 50.000 0.00 0.00 0.00 4.26
552 613 2.796383 CGATGTACTAGCAGTGTGGAGC 60.796 54.545 0.00 0.00 0.00 4.70
553 614 2.796383 GCGATGTACTAGCAGTGTGGAG 60.796 54.545 0.00 0.00 0.00 3.86
554 615 1.134367 GCGATGTACTAGCAGTGTGGA 59.866 52.381 0.00 0.00 0.00 4.02
555 616 1.135112 TGCGATGTACTAGCAGTGTGG 60.135 52.381 6.42 0.00 35.81 4.17
556 617 2.278026 TGCGATGTACTAGCAGTGTG 57.722 50.000 6.42 0.00 35.81 3.82
557 618 3.056821 TCTTTGCGATGTACTAGCAGTGT 60.057 43.478 9.59 0.00 42.19 3.55
558 619 3.511699 TCTTTGCGATGTACTAGCAGTG 58.488 45.455 9.59 7.64 42.19 3.66
559 620 3.868757 TCTTTGCGATGTACTAGCAGT 57.131 42.857 9.59 0.00 42.19 4.40
560 621 5.107104 TGTTTTCTTTGCGATGTACTAGCAG 60.107 40.000 9.59 2.22 42.19 4.24
561 622 4.752604 TGTTTTCTTTGCGATGTACTAGCA 59.247 37.500 6.42 6.42 39.33 3.49
562 623 5.277601 TGTTTTCTTTGCGATGTACTAGC 57.722 39.130 0.00 0.00 0.00 3.42
563 624 5.734498 GCATGTTTTCTTTGCGATGTACTAG 59.266 40.000 0.00 0.00 0.00 2.57
564 625 5.180304 TGCATGTTTTCTTTGCGATGTACTA 59.820 36.000 0.00 0.00 0.00 1.82
565 626 4.023279 TGCATGTTTTCTTTGCGATGTACT 60.023 37.500 0.00 0.00 0.00 2.73
566 627 4.225984 TGCATGTTTTCTTTGCGATGTAC 58.774 39.130 0.00 0.00 0.00 2.90
567 628 4.495911 TGCATGTTTTCTTTGCGATGTA 57.504 36.364 0.00 0.00 0.00 2.29
568 629 3.367992 TGCATGTTTTCTTTGCGATGT 57.632 38.095 0.00 0.00 0.00 3.06
569 630 3.982701 TCTTGCATGTTTTCTTTGCGATG 59.017 39.130 0.00 0.00 0.00 3.84
570 631 4.241590 TCTTGCATGTTTTCTTTGCGAT 57.758 36.364 0.00 0.00 0.00 4.58
571 632 3.706802 TCTTGCATGTTTTCTTTGCGA 57.293 38.095 0.00 0.00 0.00 5.10
612 677 6.406849 GGAGCTTGCCCAACAAATTTGATATA 60.407 38.462 24.64 3.28 37.96 0.86
635 700 1.001520 CCAACGTACATCACACTGGGA 59.998 52.381 0.00 0.00 0.00 4.37
662 727 2.517875 GGCCGCATCCTCTTGCAT 60.518 61.111 0.00 0.00 42.91 3.96
677 742 2.243810 TGGTTTACCAGTCCATTTGGC 58.756 47.619 0.00 0.00 42.01 4.52
729 794 0.387929 ACAAGTCGAAAGAGACCGCA 59.612 50.000 0.00 0.00 43.49 5.69
751 816 2.548067 CGTGACTGGACCAGCTTTAGTT 60.548 50.000 21.95 0.00 34.37 2.24
754 819 1.272490 CTCGTGACTGGACCAGCTTTA 59.728 52.381 21.95 2.48 34.37 1.85
992 1058 2.084546 GTGTTCTCCAATAGTGTGGCC 58.915 52.381 0.00 0.00 38.68 5.36
1118 1186 0.179032 ACACGTGCCTCACCAATGAA 60.179 50.000 17.22 0.00 33.30 2.57
1162 1230 5.048434 GCTTCTAGATGAAACTTGTTTGGCT 60.048 40.000 9.72 1.50 33.79 4.75
1294 1362 1.379176 CTCAGGGTCAGCCGAGAGA 60.379 63.158 11.70 0.00 38.08 3.10
1830 4772 0.810031 CATGTCTTACTTCCCCGGCG 60.810 60.000 0.00 0.00 0.00 6.46
1834 4776 4.823989 CCATCATTCATGTCTTACTTCCCC 59.176 45.833 0.00 0.00 0.00 4.81
1848 4790 3.524095 ACAACTCCCAACCATCATTCA 57.476 42.857 0.00 0.00 0.00 2.57
1858 4800 3.389656 TGACACTCACATACAACTCCCAA 59.610 43.478 0.00 0.00 0.00 4.12
1861 4803 4.258702 ACTGACACTCACATACAACTCC 57.741 45.455 0.00 0.00 0.00 3.85
1864 4806 5.984233 TTCAACTGACACTCACATACAAC 57.016 39.130 0.00 0.00 0.00 3.32
1907 4849 6.822667 TGTCTTTGCACACAATTCTCATAT 57.177 33.333 0.00 0.00 35.21 1.78
1982 4952 7.620880 ACTACCAATGAGTGCTTAGTGATTTA 58.379 34.615 0.00 0.00 0.00 1.40
2043 5013 2.290641 GCTCCCCAACGCTAATTGTATG 59.709 50.000 0.00 0.00 0.00 2.39
2098 5069 3.130164 CACCACAAACAATCCACTTGACA 59.870 43.478 0.00 0.00 38.29 3.58
2117 5088 2.941720 GGAGAAGAGCAATCACATCACC 59.058 50.000 0.00 0.00 0.00 4.02
2137 5108 1.337260 CGAAGAAGACACCACCAGAGG 60.337 57.143 0.00 0.00 0.00 3.69
2169 5140 0.251341 AAGGAAAACTCCGGCAGCAT 60.251 50.000 0.00 0.00 34.28 3.79
2205 5176 1.595109 CGCTTCACTGTGCTCACCA 60.595 57.895 2.12 0.00 0.00 4.17
2235 5206 1.733399 GACGACAAGGAGCCGTGTC 60.733 63.158 20.91 20.91 46.63 3.67
2238 5209 2.156051 GAAGGACGACAAGGAGCCGT 62.156 60.000 0.00 0.00 39.41 5.68
2279 5251 4.245660 CACATCCGAGTCTACAACACAAT 58.754 43.478 0.00 0.00 0.00 2.71
2317 5289 0.247736 GAGCGACCAAGTCCACATCT 59.752 55.000 0.00 0.00 0.00 2.90
2319 5291 0.615331 ATGAGCGACCAAGTCCACAT 59.385 50.000 0.00 0.00 0.00 3.21
2342 5314 2.596904 GCTATTGGTGTAGCCGAAGA 57.403 50.000 0.00 0.00 40.92 2.87
2375 5347 3.882888 TGCAAAAGAAAACGAGACCATCT 59.117 39.130 0.00 0.00 0.00 2.90
2386 5358 1.475403 TCCACCGGTGCAAAAGAAAA 58.525 45.000 29.75 2.20 0.00 2.29
2389 5361 0.893270 CCATCCACCGGTGCAAAAGA 60.893 55.000 29.75 20.13 0.00 2.52
2390 5362 1.178534 ACCATCCACCGGTGCAAAAG 61.179 55.000 29.75 15.17 34.69 2.27
2391 5363 1.152652 ACCATCCACCGGTGCAAAA 60.153 52.632 29.75 13.90 34.69 2.44
2392 5364 1.602323 GACCATCCACCGGTGCAAA 60.602 57.895 29.75 16.50 36.69 3.68
2393 5365 2.033448 GACCATCCACCGGTGCAA 59.967 61.111 29.75 19.15 36.69 4.08
2394 5366 2.927856 AGACCATCCACCGGTGCA 60.928 61.111 29.75 16.74 36.69 4.57
2395 5367 2.125106 GAGACCATCCACCGGTGC 60.125 66.667 29.75 14.22 36.69 5.01
2396 5368 2.184322 CGAGACCATCCACCGGTG 59.816 66.667 28.26 28.26 36.69 4.94
2397 5369 3.075005 CCGAGACCATCCACCGGT 61.075 66.667 0.00 0.00 40.30 5.28
2398 5370 2.656069 AACCGAGACCATCCACCGG 61.656 63.158 0.00 0.00 45.09 5.28
2399 5371 1.447838 CAACCGAGACCATCCACCG 60.448 63.158 0.00 0.00 0.00 4.94
2400 5372 0.108138 CTCAACCGAGACCATCCACC 60.108 60.000 0.00 0.00 42.34 4.61
2401 5373 0.608640 ACTCAACCGAGACCATCCAC 59.391 55.000 0.00 0.00 42.34 4.02
2415 5387 3.808728 CAGACAAAGAGGTCCAACTCAA 58.191 45.455 0.00 0.00 39.97 3.02
2417 5389 2.147150 GCAGACAAAGAGGTCCAACTC 58.853 52.381 0.00 0.00 38.59 3.01
2418 5390 1.490490 TGCAGACAAAGAGGTCCAACT 59.510 47.619 0.00 0.00 38.59 3.16
2419 5391 1.876156 CTGCAGACAAAGAGGTCCAAC 59.124 52.381 8.42 0.00 38.59 3.77
2425 5397 1.233019 CACCACTGCAGACAAAGAGG 58.767 55.000 23.35 11.94 0.00 3.69
2431 5403 0.463654 GAACACCACCACTGCAGACA 60.464 55.000 23.35 0.00 0.00 3.41
2486 5458 2.536997 AAAGGACCGGAATGCCCTCG 62.537 60.000 9.46 0.00 0.00 4.63
2489 5461 0.323451 AGAAAAGGACCGGAATGCCC 60.323 55.000 9.46 0.49 0.00 5.36
2505 5477 8.977412 ACACAATAGAAGGGAAAAAGAAAAGAA 58.023 29.630 0.00 0.00 0.00 2.52
2506 5478 8.533569 ACACAATAGAAGGGAAAAAGAAAAGA 57.466 30.769 0.00 0.00 0.00 2.52
2557 5534 3.526534 GGAAATCACAGAGGAGTACAGC 58.473 50.000 0.00 0.00 0.00 4.40
2563 5540 0.462759 GCCGGGAAATCACAGAGGAG 60.463 60.000 2.18 0.00 0.00 3.69
2592 5569 6.688813 CGCTACTTTTCATTCATTAAGAAGGC 59.311 38.462 0.00 0.00 40.15 4.35
2687 5685 2.348411 AACTGGGCTAATTGGATCCG 57.652 50.000 7.39 0.00 0.00 4.18
2688 5686 5.163447 GGTTTAAACTGGGCTAATTGGATCC 60.163 44.000 17.50 4.20 0.00 3.36
2723 5721 3.366724 GCGTGTTGAATGATCGTTAGACA 59.633 43.478 0.00 5.89 0.00 3.41
2893 5891 9.729281 AATCAAATCAAACAAATTGGAAGCTAT 57.271 25.926 0.00 0.00 39.62 2.97
2896 5894 7.804600 GGAAATCAAATCAAACAAATTGGAAGC 59.195 33.333 0.00 0.00 39.62 3.86
2907 5905 4.440839 AGCCGAGGAAATCAAATCAAAC 57.559 40.909 0.00 0.00 0.00 2.93
2944 5942 6.932960 GCCTACAGTTACCGGTATGAAATAAT 59.067 38.462 19.67 0.00 0.00 1.28
2960 5958 3.308473 GGATTTCTTCCCTGCCTACAGTT 60.308 47.826 0.00 0.00 42.81 3.16
2966 5964 2.379907 TCTTTGGATTTCTTCCCTGCCT 59.620 45.455 0.00 0.00 44.77 4.75


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

AutoCloner maintained by Alex Coulton.