Multiple sequence alignment - TraesCS1A01G427900

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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 TraesCS1A01G427900 chr1A 100.000 2549 0 0 1 2549 581941735 581944283 0.000000e+00 4708
1 TraesCS1A01G427900 chr1A 95.829 1990 76 3 567 2549 22791520 22793509 0.000000e+00 3208
2 TraesCS1A01G427900 chr3A 96.274 1986 69 2 568 2549 735555337 735557321 0.000000e+00 3253
3 TraesCS1A01G427900 chr3A 95.976 1988 74 4 567 2549 617401017 617403003 0.000000e+00 3223
4 TraesCS1A01G427900 chr6B 95.890 1995 72 6 561 2549 660437752 660435762 0.000000e+00 3221
5 TraesCS1A01G427900 chr6B 95.856 1979 76 4 576 2549 116269150 116271127 0.000000e+00 3195
6 TraesCS1A01G427900 chr7B 95.974 1987 72 4 571 2549 552932145 552930159 0.000000e+00 3219
7 TraesCS1A01G427900 chr4B 95.956 1978 73 5 563 2533 578529995 578528018 0.000000e+00 3203
8 TraesCS1A01G427900 chr7A 95.819 1985 76 4 572 2549 701581940 701583924 0.000000e+00 3199
9 TraesCS1A01G427900 chr3B 95.861 1981 75 4 575 2549 379294095 379296074 0.000000e+00 3197
10 TraesCS1A01G427900 chr1D 98.424 571 8 1 1 570 484821721 484822291 0.000000e+00 1003
11 TraesCS1A01G427900 chr1D 83.183 553 89 4 23 572 484728529 484729080 1.050000e-138 503
12 TraesCS1A01G427900 chr1B 92.644 571 18 2 1 570 675092069 675091522 0.000000e+00 800
13 TraesCS1A01G427900 chr1B 83.213 554 87 6 23 572 674873637 674874188 1.050000e-138 503
14 TraesCS1A01G427900 chr1B 96.732 153 4 1 419 570 674917681 674917833 1.170000e-63 254


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 TraesCS1A01G427900 chr1A 581941735 581944283 2548 False 4708 4708 100.000 1 2549 1 chr1A.!!$F2 2548
1 TraesCS1A01G427900 chr1A 22791520 22793509 1989 False 3208 3208 95.829 567 2549 1 chr1A.!!$F1 1982
2 TraesCS1A01G427900 chr3A 735555337 735557321 1984 False 3253 3253 96.274 568 2549 1 chr3A.!!$F2 1981
3 TraesCS1A01G427900 chr3A 617401017 617403003 1986 False 3223 3223 95.976 567 2549 1 chr3A.!!$F1 1982
4 TraesCS1A01G427900 chr6B 660435762 660437752 1990 True 3221 3221 95.890 561 2549 1 chr6B.!!$R1 1988
5 TraesCS1A01G427900 chr6B 116269150 116271127 1977 False 3195 3195 95.856 576 2549 1 chr6B.!!$F1 1973
6 TraesCS1A01G427900 chr7B 552930159 552932145 1986 True 3219 3219 95.974 571 2549 1 chr7B.!!$R1 1978
7 TraesCS1A01G427900 chr4B 578528018 578529995 1977 True 3203 3203 95.956 563 2533 1 chr4B.!!$R1 1970
8 TraesCS1A01G427900 chr7A 701581940 701583924 1984 False 3199 3199 95.819 572 2549 1 chr7A.!!$F1 1977
9 TraesCS1A01G427900 chr3B 379294095 379296074 1979 False 3197 3197 95.861 575 2549 1 chr3B.!!$F1 1974
10 TraesCS1A01G427900 chr1D 484821721 484822291 570 False 1003 1003 98.424 1 570 1 chr1D.!!$F2 569
11 TraesCS1A01G427900 chr1D 484728529 484729080 551 False 503 503 83.183 23 572 1 chr1D.!!$F1 549
12 TraesCS1A01G427900 chr1B 675091522 675092069 547 True 800 800 92.644 1 570 1 chr1B.!!$R1 569
13 TraesCS1A01G427900 chr1B 674873637 674874188 551 False 503 503 83.213 23 572 1 chr1B.!!$F1 549

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
460 461 0.108585 ATTATGCTAGTGGGCGGTGG 59.891 55.0 0.0 0.0 34.52 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1751 1803 1.620323 GAATTTGGCCCAAGAGCAACT 59.38 47.619 0.0 0.0 0.0 3.16 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
118 119 1.651987 CCATAACCGCGACAGATGTT 58.348 50.000 8.23 4.29 0.00 2.71
147 148 1.749634 CGATACCGGAGAGTGGACTTT 59.250 52.381 9.46 0.00 0.00 2.66
197 198 1.240256 GGTGTATTGCGGTGAACCAA 58.760 50.000 0.00 0.00 35.14 3.67
322 323 1.682451 CGGGCGGGAATACTTGGAGA 61.682 60.000 0.00 0.00 0.00 3.71
425 426 3.074412 GGTAATGGTTGCCGGATATCAG 58.926 50.000 5.05 0.00 0.00 2.90
426 427 3.496160 GGTAATGGTTGCCGGATATCAGT 60.496 47.826 5.05 0.00 0.00 3.41
427 428 3.297134 AATGGTTGCCGGATATCAGTT 57.703 42.857 5.05 0.00 0.00 3.16
428 429 2.799126 TGGTTGCCGGATATCAGTTT 57.201 45.000 5.05 0.00 0.00 2.66
429 430 2.364632 TGGTTGCCGGATATCAGTTTG 58.635 47.619 5.05 0.00 0.00 2.93
430 431 1.676006 GGTTGCCGGATATCAGTTTGG 59.324 52.381 5.05 0.00 0.00 3.28
431 432 2.639065 GTTGCCGGATATCAGTTTGGA 58.361 47.619 5.05 0.00 0.00 3.53
432 433 3.214328 GTTGCCGGATATCAGTTTGGAT 58.786 45.455 5.05 0.00 0.00 3.41
433 434 3.576078 TGCCGGATATCAGTTTGGATT 57.424 42.857 5.05 0.00 0.00 3.01
434 435 3.476552 TGCCGGATATCAGTTTGGATTC 58.523 45.455 5.05 0.00 0.00 2.52
435 436 3.136443 TGCCGGATATCAGTTTGGATTCT 59.864 43.478 5.05 0.00 0.00 2.40
436 437 4.137543 GCCGGATATCAGTTTGGATTCTT 58.862 43.478 5.05 0.00 0.00 2.52
437 438 4.023707 GCCGGATATCAGTTTGGATTCTTG 60.024 45.833 5.05 0.00 0.00 3.02
438 439 5.368145 CCGGATATCAGTTTGGATTCTTGA 58.632 41.667 0.00 0.00 0.00 3.02
439 440 5.468072 CCGGATATCAGTTTGGATTCTTGAG 59.532 44.000 0.00 0.00 0.00 3.02
440 441 5.468072 CGGATATCAGTTTGGATTCTTGAGG 59.532 44.000 4.83 0.00 0.00 3.86
441 442 6.595682 GGATATCAGTTTGGATTCTTGAGGA 58.404 40.000 4.83 0.00 0.00 3.71
442 443 7.230027 GGATATCAGTTTGGATTCTTGAGGAT 58.770 38.462 4.83 0.00 0.00 3.24
443 444 7.723172 GGATATCAGTTTGGATTCTTGAGGATT 59.277 37.037 4.83 0.00 0.00 3.01
444 445 9.784531 GATATCAGTTTGGATTCTTGAGGATTA 57.215 33.333 0.00 0.00 0.00 1.75
446 447 7.870509 TCAGTTTGGATTCTTGAGGATTATG 57.129 36.000 0.00 0.00 0.00 1.90
447 448 6.319658 TCAGTTTGGATTCTTGAGGATTATGC 59.680 38.462 0.00 0.00 0.00 3.14
448 449 6.320672 CAGTTTGGATTCTTGAGGATTATGCT 59.679 38.462 0.00 0.00 0.00 3.79
449 450 7.500227 CAGTTTGGATTCTTGAGGATTATGCTA 59.500 37.037 0.00 0.00 0.00 3.49
450 451 7.718753 AGTTTGGATTCTTGAGGATTATGCTAG 59.281 37.037 0.00 0.00 0.00 3.42
451 452 6.753913 TGGATTCTTGAGGATTATGCTAGT 57.246 37.500 0.00 0.00 0.00 2.57
452 453 6.528321 TGGATTCTTGAGGATTATGCTAGTG 58.472 40.000 0.00 0.00 0.00 2.74
453 454 5.936956 GGATTCTTGAGGATTATGCTAGTGG 59.063 44.000 0.00 0.00 0.00 4.00
454 455 4.963318 TCTTGAGGATTATGCTAGTGGG 57.037 45.455 0.00 0.00 0.00 4.61
455 456 3.071602 TCTTGAGGATTATGCTAGTGGGC 59.928 47.826 0.00 0.00 0.00 5.36
456 457 1.344438 TGAGGATTATGCTAGTGGGCG 59.656 52.381 0.00 0.00 34.52 6.13
457 458 0.687354 AGGATTATGCTAGTGGGCGG 59.313 55.000 0.00 0.00 34.52 6.13
458 459 0.396811 GGATTATGCTAGTGGGCGGT 59.603 55.000 0.00 0.00 34.52 5.68
459 460 1.512926 GATTATGCTAGTGGGCGGTG 58.487 55.000 0.00 0.00 34.52 4.94
460 461 0.108585 ATTATGCTAGTGGGCGGTGG 59.891 55.000 0.00 0.00 34.52 4.61
461 462 0.978667 TTATGCTAGTGGGCGGTGGA 60.979 55.000 0.00 0.00 34.52 4.02
462 463 1.682451 TATGCTAGTGGGCGGTGGAC 61.682 60.000 0.00 0.00 34.52 4.02
463 464 4.468689 GCTAGTGGGCGGTGGACC 62.469 72.222 0.00 0.00 44.16 4.46
464 465 2.683933 CTAGTGGGCGGTGGACCT 60.684 66.667 0.00 0.00 44.25 3.85
465 466 2.203877 TAGTGGGCGGTGGACCTT 60.204 61.111 0.00 0.00 44.25 3.50
466 467 0.974010 CTAGTGGGCGGTGGACCTTA 60.974 60.000 0.00 0.00 44.25 2.69
467 468 0.544833 TAGTGGGCGGTGGACCTTAA 60.545 55.000 0.00 0.00 44.25 1.85
468 469 1.073548 GTGGGCGGTGGACCTTAAA 59.926 57.895 0.00 0.00 44.25 1.52
469 470 0.958876 GTGGGCGGTGGACCTTAAAG 60.959 60.000 0.00 0.00 44.25 1.85
470 471 2.044555 GGGCGGTGGACCTTAAAGC 61.045 63.158 0.00 0.00 38.83 3.51
471 472 1.302993 GGCGGTGGACCTTAAAGCA 60.303 57.895 0.00 0.00 0.00 3.91
472 473 1.583495 GGCGGTGGACCTTAAAGCAC 61.583 60.000 0.00 0.00 0.00 4.40
473 474 0.887387 GCGGTGGACCTTAAAGCACA 60.887 55.000 0.00 0.00 0.00 4.57
474 475 0.872388 CGGTGGACCTTAAAGCACAC 59.128 55.000 0.00 0.00 0.00 3.82
475 476 1.812324 CGGTGGACCTTAAAGCACACA 60.812 52.381 0.00 0.00 0.00 3.72
476 477 2.303175 GGTGGACCTTAAAGCACACAA 58.697 47.619 0.00 0.00 0.00 3.33
477 478 2.034179 GGTGGACCTTAAAGCACACAAC 59.966 50.000 0.00 0.00 0.00 3.32
478 479 2.034179 GTGGACCTTAAAGCACACAACC 59.966 50.000 0.00 0.00 0.00 3.77
479 480 2.303175 GGACCTTAAAGCACACAACCA 58.697 47.619 0.00 0.00 0.00 3.67
480 481 2.293399 GGACCTTAAAGCACACAACCAG 59.707 50.000 0.00 0.00 0.00 4.00
481 482 1.681264 ACCTTAAAGCACACAACCAGC 59.319 47.619 0.00 0.00 0.00 4.85
482 483 1.680735 CCTTAAAGCACACAACCAGCA 59.319 47.619 0.00 0.00 0.00 4.41
483 484 2.297033 CCTTAAAGCACACAACCAGCAT 59.703 45.455 0.00 0.00 0.00 3.79
484 485 3.243839 CCTTAAAGCACACAACCAGCATT 60.244 43.478 0.00 0.00 0.00 3.56
485 486 2.514205 AAAGCACACAACCAGCATTC 57.486 45.000 0.00 0.00 0.00 2.67
486 487 1.696063 AAGCACACAACCAGCATTCT 58.304 45.000 0.00 0.00 0.00 2.40
487 488 0.956633 AGCACACAACCAGCATTCTG 59.043 50.000 0.00 0.00 40.02 3.02
498 499 2.768698 CAGCATTCTGGATCTGCTAGG 58.231 52.381 6.12 0.00 44.09 3.02
499 500 2.367894 CAGCATTCTGGATCTGCTAGGA 59.632 50.000 6.12 0.00 44.09 2.94
500 501 3.044156 AGCATTCTGGATCTGCTAGGAA 58.956 45.455 4.69 0.00 44.08 3.36
501 502 3.071312 AGCATTCTGGATCTGCTAGGAAG 59.929 47.826 4.69 0.00 44.08 3.46
502 503 3.806507 GCATTCTGGATCTGCTAGGAAGG 60.807 52.174 0.00 0.00 33.15 3.46
503 504 1.418334 TCTGGATCTGCTAGGAAGGC 58.582 55.000 0.00 0.00 0.00 4.35
504 505 0.396060 CTGGATCTGCTAGGAAGGCC 59.604 60.000 0.00 0.00 0.00 5.19
506 507 1.135960 GGATCTGCTAGGAAGGCCTT 58.864 55.000 20.65 20.65 43.90 4.35
507 508 1.202746 GGATCTGCTAGGAAGGCCTTG 60.203 57.143 26.25 9.76 43.90 3.61
508 509 1.488393 GATCTGCTAGGAAGGCCTTGT 59.512 52.381 26.25 12.74 43.90 3.16
509 510 0.905357 TCTGCTAGGAAGGCCTTGTC 59.095 55.000 26.25 15.03 43.90 3.18
510 511 0.908198 CTGCTAGGAAGGCCTTGTCT 59.092 55.000 26.25 21.41 43.90 3.41
511 512 2.111384 CTGCTAGGAAGGCCTTGTCTA 58.889 52.381 26.25 21.38 43.90 2.59
512 513 2.102252 CTGCTAGGAAGGCCTTGTCTAG 59.898 54.545 30.11 30.11 43.90 2.43
513 514 2.292257 TGCTAGGAAGGCCTTGTCTAGA 60.292 50.000 34.43 23.94 43.90 2.43
514 515 2.364002 GCTAGGAAGGCCTTGTCTAGAG 59.636 54.545 34.43 22.84 43.90 2.43
515 516 1.199615 AGGAAGGCCTTGTCTAGAGC 58.800 55.000 26.25 5.23 43.90 4.09
516 517 0.905357 GGAAGGCCTTGTCTAGAGCA 59.095 55.000 26.25 0.00 0.00 4.26
517 518 1.488393 GGAAGGCCTTGTCTAGAGCAT 59.512 52.381 26.25 0.00 0.00 3.79
518 519 2.700897 GGAAGGCCTTGTCTAGAGCATA 59.299 50.000 26.25 0.00 0.00 3.14
519 520 3.244044 GGAAGGCCTTGTCTAGAGCATAG 60.244 52.174 26.25 0.00 0.00 2.23
520 521 3.320610 AGGCCTTGTCTAGAGCATAGA 57.679 47.619 0.00 0.00 0.00 1.98
521 522 3.230134 AGGCCTTGTCTAGAGCATAGAG 58.770 50.000 0.00 0.00 0.00 2.43
522 523 3.117322 AGGCCTTGTCTAGAGCATAGAGA 60.117 47.826 0.00 0.00 0.00 3.10
523 524 3.255642 GGCCTTGTCTAGAGCATAGAGAG 59.744 52.174 0.00 2.05 0.00 3.20
524 525 3.888930 GCCTTGTCTAGAGCATAGAGAGT 59.111 47.826 0.00 0.00 0.00 3.24
525 526 5.067273 GCCTTGTCTAGAGCATAGAGAGTA 58.933 45.833 0.00 0.00 0.00 2.59
526 527 5.048991 GCCTTGTCTAGAGCATAGAGAGTAC 60.049 48.000 0.00 0.00 0.00 2.73
527 528 6.296026 CCTTGTCTAGAGCATAGAGAGTACT 58.704 44.000 0.00 0.00 0.00 2.73
528 529 7.446769 CCTTGTCTAGAGCATAGAGAGTACTA 58.553 42.308 0.00 0.00 0.00 1.82
529 530 7.386848 CCTTGTCTAGAGCATAGAGAGTACTAC 59.613 44.444 0.00 0.00 0.00 2.73
530 531 6.448852 TGTCTAGAGCATAGAGAGTACTACG 58.551 44.000 0.00 0.00 0.00 3.51
531 532 6.040729 TGTCTAGAGCATAGAGAGTACTACGT 59.959 42.308 0.00 0.00 0.00 3.57
532 533 7.230309 TGTCTAGAGCATAGAGAGTACTACGTA 59.770 40.741 0.00 0.00 0.00 3.57
533 534 8.246180 GTCTAGAGCATAGAGAGTACTACGTAT 58.754 40.741 0.00 0.00 0.00 3.06
534 535 8.805175 TCTAGAGCATAGAGAGTACTACGTATT 58.195 37.037 0.00 0.00 0.00 1.89
535 536 9.426837 CTAGAGCATAGAGAGTACTACGTATTT 57.573 37.037 0.00 0.00 0.00 1.40
536 537 8.090250 AGAGCATAGAGAGTACTACGTATTTG 57.910 38.462 0.00 0.00 0.00 2.32
537 538 7.716123 AGAGCATAGAGAGTACTACGTATTTGT 59.284 37.037 0.00 0.00 0.00 2.83
538 539 8.223177 AGCATAGAGAGTACTACGTATTTGTT 57.777 34.615 0.00 0.00 0.00 2.83
539 540 8.129840 AGCATAGAGAGTACTACGTATTTGTTG 58.870 37.037 0.00 0.00 0.00 3.33
540 541 7.096558 GCATAGAGAGTACTACGTATTTGTTGC 60.097 40.741 0.00 0.00 0.00 4.17
541 542 6.263516 AGAGAGTACTACGTATTTGTTGCA 57.736 37.500 0.00 0.00 0.00 4.08
542 543 6.091437 AGAGAGTACTACGTATTTGTTGCAC 58.909 40.000 0.00 0.00 0.00 4.57
543 544 6.022163 AGAGTACTACGTATTTGTTGCACT 57.978 37.500 0.00 0.00 0.00 4.40
544 545 6.091437 AGAGTACTACGTATTTGTTGCACTC 58.909 40.000 0.00 1.74 37.89 3.51
545 546 5.166398 AGTACTACGTATTTGTTGCACTCC 58.834 41.667 0.00 0.00 0.00 3.85
546 547 4.267349 ACTACGTATTTGTTGCACTCCT 57.733 40.909 0.00 0.00 0.00 3.69
547 548 4.243270 ACTACGTATTTGTTGCACTCCTC 58.757 43.478 0.00 0.00 0.00 3.71
548 549 2.423577 ACGTATTTGTTGCACTCCTCC 58.576 47.619 0.00 0.00 0.00 4.30
549 550 2.224426 ACGTATTTGTTGCACTCCTCCA 60.224 45.455 0.00 0.00 0.00 3.86
550 551 2.416547 CGTATTTGTTGCACTCCTCCAG 59.583 50.000 0.00 0.00 0.00 3.86
551 552 2.957402 ATTTGTTGCACTCCTCCAGA 57.043 45.000 0.00 0.00 0.00 3.86
552 553 2.727123 TTTGTTGCACTCCTCCAGAA 57.273 45.000 0.00 0.00 0.00 3.02
553 554 1.967319 TTGTTGCACTCCTCCAGAAC 58.033 50.000 0.00 0.00 0.00 3.01
554 555 0.249868 TGTTGCACTCCTCCAGAACG 60.250 55.000 0.00 0.00 0.00 3.95
555 556 0.249911 GTTGCACTCCTCCAGAACGT 60.250 55.000 0.00 0.00 0.00 3.99
556 557 1.000506 GTTGCACTCCTCCAGAACGTA 59.999 52.381 0.00 0.00 0.00 3.57
557 558 1.334160 TGCACTCCTCCAGAACGTAA 58.666 50.000 0.00 0.00 0.00 3.18
558 559 1.000506 TGCACTCCTCCAGAACGTAAC 59.999 52.381 0.00 0.00 0.00 2.50
559 560 1.672145 GCACTCCTCCAGAACGTAACC 60.672 57.143 0.00 0.00 0.00 2.85
560 561 1.893801 CACTCCTCCAGAACGTAACCT 59.106 52.381 0.00 0.00 0.00 3.50
561 562 2.299297 CACTCCTCCAGAACGTAACCTT 59.701 50.000 0.00 0.00 0.00 3.50
562 563 3.508793 CACTCCTCCAGAACGTAACCTTA 59.491 47.826 0.00 0.00 0.00 2.69
563 564 4.159879 CACTCCTCCAGAACGTAACCTTAT 59.840 45.833 0.00 0.00 0.00 1.73
564 565 4.776308 ACTCCTCCAGAACGTAACCTTATT 59.224 41.667 0.00 0.00 0.00 1.40
565 566 5.247792 ACTCCTCCAGAACGTAACCTTATTT 59.752 40.000 0.00 0.00 0.00 1.40
566 567 6.117975 TCCTCCAGAACGTAACCTTATTTT 57.882 37.500 0.00 0.00 0.00 1.82
567 568 6.536447 TCCTCCAGAACGTAACCTTATTTTT 58.464 36.000 0.00 0.00 0.00 1.94
599 600 7.669722 AGTTAATTATCCTTTTGCCTTCAGTGA 59.330 33.333 0.00 0.00 0.00 3.41
603 604 3.565307 TCCTTTTGCCTTCAGTGATGTT 58.435 40.909 0.00 0.00 0.00 2.71
610 611 4.847198 TGCCTTCAGTGATGTTCATGTAT 58.153 39.130 0.00 0.00 0.00 2.29
612 613 5.711506 TGCCTTCAGTGATGTTCATGTATTT 59.288 36.000 0.00 0.00 0.00 1.40
651 652 2.287788 CGAATTGTGCTCAGTTTTGCCT 60.288 45.455 0.00 0.00 0.00 4.75
676 677 2.429571 GTGCGCACCGACTCGTTA 60.430 61.111 30.12 0.00 0.00 3.18
701 702 2.033602 TCTGCCGTCTCCGTCAGA 59.966 61.111 0.00 0.00 45.80 3.27
717 718 4.310769 CGTCAGATCAACCTTTTGACTCT 58.689 43.478 0.00 0.00 44.66 3.24
837 838 1.674359 CATTGGCGGGTGTGCTATAA 58.326 50.000 0.00 0.00 34.52 0.98
838 839 1.603802 CATTGGCGGGTGTGCTATAAG 59.396 52.381 0.00 0.00 34.52 1.73
839 840 0.746563 TTGGCGGGTGTGCTATAAGC 60.747 55.000 0.00 0.00 42.82 3.09
1076 1077 1.067283 CATGCCTGTCTTCGTCTGTCT 60.067 52.381 0.00 0.00 0.00 3.41
1085 1086 4.662961 CGTCTGTCTGCGGTGCCA 62.663 66.667 0.00 0.00 0.00 4.92
1088 1089 4.320456 CTGTCTGCGGTGCCAGGT 62.320 66.667 0.00 0.00 33.64 4.00
1122 1123 0.966920 GGGTTTCTCAGACACCGAGA 59.033 55.000 3.82 0.00 33.60 4.04
1155 1156 1.272784 CGTTCTACGTGTGCAGCGAA 61.273 55.000 16.16 0.00 36.74 4.70
1161 1162 1.163420 ACGTGTGCAGCGAAAATGGA 61.163 50.000 16.16 0.00 0.00 3.41
1286 1287 0.390998 GCTCTGGCCAAGACTCTGAC 60.391 60.000 7.01 0.00 0.00 3.51
1474 1521 4.523083 TCAAGCACTACCAATACCCATTC 58.477 43.478 0.00 0.00 0.00 2.67
1509 1556 5.772004 TGGGCATTTGTAGGTATGGTAATT 58.228 37.500 0.00 0.00 0.00 1.40
1569 1616 9.768662 GCATGAATTATGGAGGAATTTGTAATT 57.231 29.630 0.00 0.00 37.26 1.40
1813 1865 2.704065 GGCTAGACTAATGGGCCAACTA 59.296 50.000 11.89 4.22 42.08 2.24
1854 1907 2.823747 GGGGGTTCTCTTGCGTATTTTT 59.176 45.455 0.00 0.00 0.00 1.94
2035 2088 4.755629 CCAAAATGTCATGGAAAATGTGCA 59.244 37.500 0.00 0.00 39.12 4.57
2070 2123 1.339929 GGTTTACACCAGGTGCCAAAG 59.660 52.381 20.48 0.00 43.61 2.77
2113 2166 7.319646 TGGGCATTACATTGAGAAAAACATAC 58.680 34.615 0.00 0.00 0.00 2.39
2240 2295 1.474143 GCTAGGACAGATGGCAAGACC 60.474 57.143 0.00 0.00 39.84 3.85
2367 2427 6.644347 TGTTTTGCACTTAAATTTTGGAGGA 58.356 32.000 0.00 0.00 0.00 3.71
2426 2486 0.836606 TTGGTCAGAGTGGCACTTGA 59.163 50.000 22.98 21.67 0.00 3.02
2433 2493 3.582647 TCAGAGTGGCACTTGATTTAGGA 59.417 43.478 22.98 7.82 0.00 2.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
139 140 1.168714 GGCCTGACATGAAAGTCCAC 58.831 55.000 0.00 0.00 37.73 4.02
147 148 2.745308 CCCCATCGGCCTGACATGA 61.745 63.158 0.00 0.00 0.00 3.07
296 297 2.067605 TATTCCCGCCCGTGTCCAT 61.068 57.895 0.00 0.00 0.00 3.41
322 323 2.665185 GGCGGCTGTCGAGTTGTT 60.665 61.111 5.55 0.00 42.43 2.83
425 426 6.705863 AGCATAATCCTCAAGAATCCAAAC 57.294 37.500 0.00 0.00 0.00 2.93
426 427 7.500227 CACTAGCATAATCCTCAAGAATCCAAA 59.500 37.037 0.00 0.00 0.00 3.28
427 428 6.994496 CACTAGCATAATCCTCAAGAATCCAA 59.006 38.462 0.00 0.00 0.00 3.53
428 429 6.464892 CCACTAGCATAATCCTCAAGAATCCA 60.465 42.308 0.00 0.00 0.00 3.41
429 430 5.936956 CCACTAGCATAATCCTCAAGAATCC 59.063 44.000 0.00 0.00 0.00 3.01
430 431 5.936956 CCCACTAGCATAATCCTCAAGAATC 59.063 44.000 0.00 0.00 0.00 2.52
431 432 5.747248 GCCCACTAGCATAATCCTCAAGAAT 60.747 44.000 0.00 0.00 0.00 2.40
432 433 4.444876 GCCCACTAGCATAATCCTCAAGAA 60.445 45.833 0.00 0.00 0.00 2.52
433 434 3.071602 GCCCACTAGCATAATCCTCAAGA 59.928 47.826 0.00 0.00 0.00 3.02
434 435 3.406764 GCCCACTAGCATAATCCTCAAG 58.593 50.000 0.00 0.00 0.00 3.02
435 436 2.224281 CGCCCACTAGCATAATCCTCAA 60.224 50.000 0.00 0.00 0.00 3.02
436 437 1.344438 CGCCCACTAGCATAATCCTCA 59.656 52.381 0.00 0.00 0.00 3.86
437 438 1.338200 CCGCCCACTAGCATAATCCTC 60.338 57.143 0.00 0.00 0.00 3.71
438 439 0.687354 CCGCCCACTAGCATAATCCT 59.313 55.000 0.00 0.00 0.00 3.24
439 440 0.396811 ACCGCCCACTAGCATAATCC 59.603 55.000 0.00 0.00 0.00 3.01
440 441 1.512926 CACCGCCCACTAGCATAATC 58.487 55.000 0.00 0.00 0.00 1.75
441 442 0.108585 CCACCGCCCACTAGCATAAT 59.891 55.000 0.00 0.00 0.00 1.28
442 443 0.978667 TCCACCGCCCACTAGCATAA 60.979 55.000 0.00 0.00 0.00 1.90
443 444 1.382009 TCCACCGCCCACTAGCATA 60.382 57.895 0.00 0.00 0.00 3.14
444 445 2.687200 TCCACCGCCCACTAGCAT 60.687 61.111 0.00 0.00 0.00 3.79
445 446 3.702048 GTCCACCGCCCACTAGCA 61.702 66.667 0.00 0.00 0.00 3.49
446 447 4.468689 GGTCCACCGCCCACTAGC 62.469 72.222 0.00 0.00 0.00 3.42
447 448 0.974010 TAAGGTCCACCGCCCACTAG 60.974 60.000 0.00 0.00 42.08 2.57
448 449 0.544833 TTAAGGTCCACCGCCCACTA 60.545 55.000 0.00 0.00 42.08 2.74
449 450 1.420532 TTTAAGGTCCACCGCCCACT 61.421 55.000 0.00 0.00 42.08 4.00
450 451 0.958876 CTTTAAGGTCCACCGCCCAC 60.959 60.000 0.00 0.00 42.08 4.61
451 452 1.377229 CTTTAAGGTCCACCGCCCA 59.623 57.895 0.00 0.00 42.08 5.36
452 453 2.044555 GCTTTAAGGTCCACCGCCC 61.045 63.158 0.00 0.00 42.08 6.13
453 454 1.302993 TGCTTTAAGGTCCACCGCC 60.303 57.895 0.00 0.00 42.08 6.13
454 455 0.887387 TGTGCTTTAAGGTCCACCGC 60.887 55.000 0.00 0.00 42.08 5.68
455 456 0.872388 GTGTGCTTTAAGGTCCACCG 59.128 55.000 0.00 0.00 42.08 4.94
456 457 1.975660 TGTGTGCTTTAAGGTCCACC 58.024 50.000 0.00 0.00 0.00 4.61
457 458 2.034179 GGTTGTGTGCTTTAAGGTCCAC 59.966 50.000 0.00 0.00 0.00 4.02
458 459 2.303175 GGTTGTGTGCTTTAAGGTCCA 58.697 47.619 0.00 0.00 0.00 4.02
459 460 2.293399 CTGGTTGTGTGCTTTAAGGTCC 59.707 50.000 0.00 0.00 0.00 4.46
460 461 2.287608 GCTGGTTGTGTGCTTTAAGGTC 60.288 50.000 0.00 0.00 0.00 3.85
461 462 1.681264 GCTGGTTGTGTGCTTTAAGGT 59.319 47.619 0.00 0.00 0.00 3.50
462 463 1.680735 TGCTGGTTGTGTGCTTTAAGG 59.319 47.619 0.00 0.00 0.00 2.69
463 464 3.648339 ATGCTGGTTGTGTGCTTTAAG 57.352 42.857 0.00 0.00 0.00 1.85
464 465 3.636300 AGAATGCTGGTTGTGTGCTTTAA 59.364 39.130 0.00 0.00 0.00 1.52
465 466 3.004629 CAGAATGCTGGTTGTGTGCTTTA 59.995 43.478 0.00 0.00 38.51 1.85
466 467 2.034124 AGAATGCTGGTTGTGTGCTTT 58.966 42.857 0.00 0.00 0.00 3.51
467 468 1.338973 CAGAATGCTGGTTGTGTGCTT 59.661 47.619 0.00 0.00 38.51 3.91
468 469 0.956633 CAGAATGCTGGTTGTGTGCT 59.043 50.000 0.00 0.00 38.51 4.40
469 470 3.484524 CAGAATGCTGGTTGTGTGC 57.515 52.632 0.00 0.00 38.51 4.57
480 481 3.401182 CTTCCTAGCAGATCCAGAATGC 58.599 50.000 0.00 0.00 40.29 3.56
481 482 3.806507 GCCTTCCTAGCAGATCCAGAATG 60.807 52.174 0.00 0.00 0.00 2.67
482 483 2.371510 GCCTTCCTAGCAGATCCAGAAT 59.628 50.000 0.00 0.00 0.00 2.40
483 484 1.765314 GCCTTCCTAGCAGATCCAGAA 59.235 52.381 0.00 0.00 0.00 3.02
484 485 1.418334 GCCTTCCTAGCAGATCCAGA 58.582 55.000 0.00 0.00 0.00 3.86
485 486 0.396060 GGCCTTCCTAGCAGATCCAG 59.604 60.000 0.00 0.00 0.00 3.86
486 487 0.030705 AGGCCTTCCTAGCAGATCCA 60.031 55.000 0.00 0.00 42.06 3.41
487 488 1.135960 AAGGCCTTCCTAGCAGATCC 58.864 55.000 13.78 0.00 43.40 3.36
488 489 1.488393 ACAAGGCCTTCCTAGCAGATC 59.512 52.381 17.29 0.00 43.40 2.75
489 490 1.488393 GACAAGGCCTTCCTAGCAGAT 59.512 52.381 17.29 0.00 43.40 2.90
490 491 0.905357 GACAAGGCCTTCCTAGCAGA 59.095 55.000 17.29 0.00 43.40 4.26
491 492 0.908198 AGACAAGGCCTTCCTAGCAG 59.092 55.000 17.29 4.96 43.40 4.24
492 493 2.111384 CTAGACAAGGCCTTCCTAGCA 58.889 52.381 26.33 10.24 43.40 3.49
493 494 2.364002 CTCTAGACAAGGCCTTCCTAGC 59.636 54.545 29.69 15.13 43.40 3.42
494 495 2.364002 GCTCTAGACAAGGCCTTCCTAG 59.636 54.545 29.13 29.13 43.40 3.02
495 496 2.292257 TGCTCTAGACAAGGCCTTCCTA 60.292 50.000 17.29 17.95 43.40 2.94
497 498 0.905357 TGCTCTAGACAAGGCCTTCC 59.095 55.000 17.29 10.80 0.00 3.46
498 499 2.998316 ATGCTCTAGACAAGGCCTTC 57.002 50.000 17.29 5.50 0.00 3.46
499 500 3.640967 CTCTATGCTCTAGACAAGGCCTT 59.359 47.826 13.78 13.78 0.00 4.35
500 501 3.117322 TCTCTATGCTCTAGACAAGGCCT 60.117 47.826 0.00 0.00 0.00 5.19
501 502 3.226777 TCTCTATGCTCTAGACAAGGCC 58.773 50.000 0.00 0.00 0.00 5.19
502 503 3.888930 ACTCTCTATGCTCTAGACAAGGC 59.111 47.826 0.00 0.00 0.00 4.35
503 504 6.296026 AGTACTCTCTATGCTCTAGACAAGG 58.704 44.000 0.00 0.00 0.00 3.61
504 505 7.115805 CGTAGTACTCTCTATGCTCTAGACAAG 59.884 44.444 0.00 0.00 0.00 3.16
505 506 6.924612 CGTAGTACTCTCTATGCTCTAGACAA 59.075 42.308 0.00 0.00 0.00 3.18
506 507 6.040729 ACGTAGTACTCTCTATGCTCTAGACA 59.959 42.308 0.00 0.00 41.94 3.41
507 508 6.449698 ACGTAGTACTCTCTATGCTCTAGAC 58.550 44.000 0.00 0.00 41.94 2.59
508 509 6.653526 ACGTAGTACTCTCTATGCTCTAGA 57.346 41.667 0.00 0.00 41.94 2.43
516 517 7.914346 GTGCAACAAATACGTAGTACTCTCTAT 59.086 37.037 0.00 0.00 41.71 1.98
517 518 7.120285 AGTGCAACAAATACGTAGTACTCTCTA 59.880 37.037 0.00 0.00 44.16 2.43
518 519 6.072064 AGTGCAACAAATACGTAGTACTCTCT 60.072 38.462 0.00 0.00 44.16 3.10
519 520 6.091437 AGTGCAACAAATACGTAGTACTCTC 58.909 40.000 0.00 0.00 44.16 3.20
520 521 6.022163 AGTGCAACAAATACGTAGTACTCT 57.978 37.500 0.00 0.00 44.16 3.24
521 522 5.287992 GGAGTGCAACAAATACGTAGTACTC 59.712 44.000 15.45 15.45 44.16 2.59
522 523 5.047519 AGGAGTGCAACAAATACGTAGTACT 60.048 40.000 0.00 0.00 44.16 2.73
523 524 5.166398 AGGAGTGCAACAAATACGTAGTAC 58.834 41.667 0.08 0.00 44.16 2.73
524 525 5.395682 AGGAGTGCAACAAATACGTAGTA 57.604 39.130 0.08 0.00 45.27 1.82
525 526 4.243270 GAGGAGTGCAACAAATACGTAGT 58.757 43.478 0.08 0.00 43.47 2.73
526 527 3.617263 GGAGGAGTGCAACAAATACGTAG 59.383 47.826 0.08 0.00 41.43 3.51
527 528 3.007074 TGGAGGAGTGCAACAAATACGTA 59.993 43.478 0.00 0.00 41.43 3.57
528 529 2.224426 TGGAGGAGTGCAACAAATACGT 60.224 45.455 0.00 0.00 41.43 3.57
529 530 2.416547 CTGGAGGAGTGCAACAAATACG 59.583 50.000 0.00 0.00 41.43 3.06
530 531 3.674997 TCTGGAGGAGTGCAACAAATAC 58.325 45.455 0.00 0.00 41.43 1.89
531 532 4.072131 GTTCTGGAGGAGTGCAACAAATA 58.928 43.478 0.00 0.00 41.43 1.40
532 533 2.887152 GTTCTGGAGGAGTGCAACAAAT 59.113 45.455 0.00 0.00 41.43 2.32
533 534 2.297701 GTTCTGGAGGAGTGCAACAAA 58.702 47.619 0.00 0.00 41.43 2.83
534 535 1.810031 CGTTCTGGAGGAGTGCAACAA 60.810 52.381 0.00 0.00 41.43 2.83
535 536 0.249868 CGTTCTGGAGGAGTGCAACA 60.250 55.000 0.00 0.00 41.43 3.33
536 537 0.249911 ACGTTCTGGAGGAGTGCAAC 60.250 55.000 0.00 0.00 0.00 4.17
537 538 1.334160 TACGTTCTGGAGGAGTGCAA 58.666 50.000 0.00 0.00 0.00 4.08
538 539 1.000506 GTTACGTTCTGGAGGAGTGCA 59.999 52.381 0.00 0.00 0.00 4.57
539 540 1.672145 GGTTACGTTCTGGAGGAGTGC 60.672 57.143 0.00 0.00 0.00 4.40
540 541 1.893801 AGGTTACGTTCTGGAGGAGTG 59.106 52.381 0.00 0.00 0.00 3.51
541 542 2.305858 AGGTTACGTTCTGGAGGAGT 57.694 50.000 0.00 0.00 0.00 3.85
542 543 5.340439 AATAAGGTTACGTTCTGGAGGAG 57.660 43.478 0.00 0.00 0.00 3.69
543 544 5.750352 AAATAAGGTTACGTTCTGGAGGA 57.250 39.130 0.00 0.00 0.00 3.71
544 545 6.812879 AAAAATAAGGTTACGTTCTGGAGG 57.187 37.500 0.00 0.00 0.00 4.30
569 570 9.747898 TGAAGGCAAAAGGATAATTAACTCTTA 57.252 29.630 0.00 0.00 0.00 2.10
573 574 7.669722 TCACTGAAGGCAAAAGGATAATTAACT 59.330 33.333 0.00 0.00 0.00 2.24
599 600 7.178274 TGAGGGCAAAACTAAATACATGAACAT 59.822 33.333 0.00 0.00 0.00 2.71
603 604 6.480763 TCTGAGGGCAAAACTAAATACATGA 58.519 36.000 0.00 0.00 0.00 3.07
610 611 2.487762 CGCATCTGAGGGCAAAACTAAA 59.512 45.455 5.18 0.00 0.00 1.85
612 613 1.277842 TCGCATCTGAGGGCAAAACTA 59.722 47.619 5.18 0.00 0.00 2.24
651 652 4.111016 CGGTGCGCACGGACTAGA 62.111 66.667 36.33 0.00 36.67 2.43
676 677 1.286260 GAGACGGCAGAGTTCACGT 59.714 57.895 0.00 0.00 42.88 4.49
701 702 2.108952 AGGGCAGAGTCAAAAGGTTGAT 59.891 45.455 0.00 0.00 45.38 2.57
819 820 1.967319 CTTATAGCACACCCGCCAAT 58.033 50.000 0.00 0.00 0.00 3.16
1085 1086 1.528824 CTCCGATCAATGCCCACCT 59.471 57.895 0.00 0.00 0.00 4.00
1088 1089 1.570857 AACCCTCCGATCAATGCCCA 61.571 55.000 0.00 0.00 0.00 5.36
1093 1094 3.107601 TCTGAGAAACCCTCCGATCAAT 58.892 45.455 0.00 0.00 41.25 2.57
1122 1123 2.833631 AGAACGGACGATTCTGGTTT 57.166 45.000 0.00 0.00 35.06 3.27
1155 1156 2.241176 TGCCCCGATTCTTACTCCATTT 59.759 45.455 0.00 0.00 0.00 2.32
1161 1162 2.024414 GCAATTGCCCCGATTCTTACT 58.976 47.619 20.06 0.00 34.31 2.24
1286 1287 2.481568 TGCTCTTCTTGCAGTTCATTCG 59.518 45.455 0.00 0.00 35.31 3.34
1474 1521 4.324974 CAAATGCCCAAAAGTATTTGCG 57.675 40.909 2.86 0.00 43.73 4.85
1509 1556 4.991153 TTTCAACATTACAACCAGTGCA 57.009 36.364 0.00 0.00 0.00 4.57
1695 1744 7.107834 TGCATTTCATTGATCAAAAGTTTCG 57.892 32.000 13.09 0.30 0.00 3.46
1751 1803 1.620323 GAATTTGGCCCAAGAGCAACT 59.380 47.619 0.00 0.00 0.00 3.16
1813 1865 2.586425 CGAATGGGCCTAATTGGATGT 58.414 47.619 4.53 0.00 38.35 3.06
2006 2059 7.774625 ACATTTTCCATGACATTTTGGTCTTTT 59.225 29.630 0.00 0.00 38.61 2.27
2035 2088 4.160626 GTGTAAACCTCTACCAGAGCTGAT 59.839 45.833 0.00 0.00 40.98 2.90
2057 2110 3.237268 TCATTTACTTTGGCACCTGGT 57.763 42.857 0.00 0.00 0.00 4.00
2088 2141 5.798125 TGTTTTTCTCAATGTAATGCCCA 57.202 34.783 0.00 0.00 0.00 5.36
2240 2295 2.196595 TCCTTCCCTACCCATGTCAAG 58.803 52.381 0.00 0.00 0.00 3.02
2299 2359 2.226437 GTGCAAACATTCACGGTCTCAT 59.774 45.455 0.00 0.00 0.00 2.90
2367 2427 6.650390 GCAACATACATTTTCAACCTTCCAAT 59.350 34.615 0.00 0.00 0.00 3.16
2426 2486 5.044846 ACCAAGTGCCACTCTAATCCTAAAT 60.045 40.000 0.00 0.00 0.00 1.40
2433 2493 4.288626 TCCTAAACCAAGTGCCACTCTAAT 59.711 41.667 0.00 0.00 0.00 1.73


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

AutoCloner maintained by Alex Coulton.