Multiple sequence alignment - TraesCS5A01G437000

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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 TraesCS5A01G437000 chr5A 100.000 1479 0 0 1 1479 619274736 619273258 0.000000e+00 2732
1 TraesCS5A01G437000 chr5A 100.000 307 0 0 1838 2144 619272899 619272593 3.090000e-158 568
2 TraesCS5A01G437000 chr5A 96.743 307 10 0 1838 2144 684323616 684323310 1.470000e-141 512
3 TraesCS5A01G437000 chr1D 96.623 918 26 3 566 1479 254488788 254487872 0.000000e+00 1519
4 TraesCS5A01G437000 chr2D 96.522 920 25 4 566 1479 628284764 628283846 0.000000e+00 1515
5 TraesCS5A01G437000 chr2D 96.296 918 28 5 566 1479 334225006 334224091 0.000000e+00 1502
6 TraesCS5A01G437000 chr2D 97.394 307 8 0 1838 2144 628283684 628283378 6.780000e-145 523
7 TraesCS5A01G437000 chr2D 97.394 307 8 0 1838 2144 628286938 628286632 6.780000e-145 523
8 TraesCS5A01G437000 chr3D 96.510 917 28 3 566 1479 21896648 21895733 0.000000e+00 1513
9 TraesCS5A01G437000 chr6D 96.087 920 29 4 566 1479 431399117 431398199 0.000000e+00 1493
10 TraesCS5A01G437000 chr6D 97.720 307 7 0 1838 2144 431398041 431397735 1.460000e-146 529
11 TraesCS5A01G437000 chr1A 96.078 918 29 5 566 1479 256027073 256027987 0.000000e+00 1489
12 TraesCS5A01G437000 chr1A 95.643 918 30 4 566 1479 554465942 554466853 0.000000e+00 1465
13 TraesCS5A01G437000 chr1A 97.068 307 9 0 1838 2144 554467020 554467326 3.150000e-143 518
14 TraesCS5A01G437000 chr2A 95.519 915 36 4 568 1479 335825371 335824459 0.000000e+00 1458
15 TraesCS5A01G437000 chr2A 95.326 920 36 4 566 1479 276441992 276442910 0.000000e+00 1454
16 TraesCS5A01G437000 chr7A 96.000 575 13 5 1 565 160393024 160393598 0.000000e+00 926
17 TraesCS5A01G437000 chr7A 95.280 572 19 6 1 565 706649730 706650300 0.000000e+00 900
18 TraesCS5A01G437000 chr7A 95.096 571 21 6 1 565 595330038 595329469 0.000000e+00 893
19 TraesCS5A01G437000 chr7A 95.088 570 22 5 1 565 700230163 700230731 0.000000e+00 893
20 TraesCS5A01G437000 chr5D 95.423 568 20 4 1 565 334045832 334045268 0.000000e+00 900
21 TraesCS5A01G437000 chr5D 95.238 567 19 6 1 565 512174798 512175358 0.000000e+00 891
22 TraesCS5A01G437000 chr5D 97.068 307 9 0 1838 2144 483797551 483797857 3.150000e-143 518
23 TraesCS5A01G437000 chr4A 95.246 568 22 3 1 563 625193571 625193004 0.000000e+00 894
24 TraesCS5A01G437000 chr3A 95.105 572 20 7 1 565 719175167 719174597 0.000000e+00 894
25 TraesCS5A01G437000 chr7D 95.238 567 20 5 1 565 33834129 33833568 0.000000e+00 891
26 TraesCS5A01G437000 chrUn 97.720 307 7 0 1838 2144 453774476 453774170 1.460000e-146 529
27 TraesCS5A01G437000 chrUn 97.068 307 9 0 1838 2144 463114281 463114587 3.150000e-143 518
28 TraesCS5A01G437000 chr6B 97.368 304 8 0 1841 2144 579205648 579205951 3.150000e-143 518


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 TraesCS5A01G437000 chr5A 619272593 619274736 2143 True 1650.000000 2732 100.000000 1 2144 2 chr5A.!!$R2 2143
1 TraesCS5A01G437000 chr1D 254487872 254488788 916 True 1519.000000 1519 96.623000 566 1479 1 chr1D.!!$R1 913
2 TraesCS5A01G437000 chr2D 334224091 334225006 915 True 1502.000000 1502 96.296000 566 1479 1 chr2D.!!$R1 913
3 TraesCS5A01G437000 chr2D 628283378 628286938 3560 True 853.666667 1515 97.103333 566 2144 3 chr2D.!!$R2 1578
4 TraesCS5A01G437000 chr3D 21895733 21896648 915 True 1513.000000 1513 96.510000 566 1479 1 chr3D.!!$R1 913
5 TraesCS5A01G437000 chr6D 431397735 431399117 1382 True 1011.000000 1493 96.903500 566 2144 2 chr6D.!!$R1 1578
6 TraesCS5A01G437000 chr1A 256027073 256027987 914 False 1489.000000 1489 96.078000 566 1479 1 chr1A.!!$F1 913
7 TraesCS5A01G437000 chr1A 554465942 554467326 1384 False 991.500000 1465 96.355500 566 2144 2 chr1A.!!$F2 1578
8 TraesCS5A01G437000 chr2A 335824459 335825371 912 True 1458.000000 1458 95.519000 568 1479 1 chr2A.!!$R1 911
9 TraesCS5A01G437000 chr2A 276441992 276442910 918 False 1454.000000 1454 95.326000 566 1479 1 chr2A.!!$F1 913
10 TraesCS5A01G437000 chr7A 160393024 160393598 574 False 926.000000 926 96.000000 1 565 1 chr7A.!!$F1 564
11 TraesCS5A01G437000 chr7A 706649730 706650300 570 False 900.000000 900 95.280000 1 565 1 chr7A.!!$F3 564
12 TraesCS5A01G437000 chr7A 595329469 595330038 569 True 893.000000 893 95.096000 1 565 1 chr7A.!!$R1 564
13 TraesCS5A01G437000 chr7A 700230163 700230731 568 False 893.000000 893 95.088000 1 565 1 chr7A.!!$F2 564
14 TraesCS5A01G437000 chr5D 334045268 334045832 564 True 900.000000 900 95.423000 1 565 1 chr5D.!!$R1 564
15 TraesCS5A01G437000 chr5D 512174798 512175358 560 False 891.000000 891 95.238000 1 565 1 chr5D.!!$F2 564
16 TraesCS5A01G437000 chr4A 625193004 625193571 567 True 894.000000 894 95.246000 1 563 1 chr4A.!!$R1 562
17 TraesCS5A01G437000 chr3A 719174597 719175167 570 True 894.000000 894 95.105000 1 565 1 chr3A.!!$R1 564
18 TraesCS5A01G437000 chr7D 33833568 33834129 561 True 891.000000 891 95.238000 1 565 1 chr7D.!!$R1 564

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
458 481 0.031994 GTGCATCCAGTTTTTGCGGT 59.968 50.0 0.0 0.0 39.23 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1911 3535 6.127451 TGCAGGTCTTCTTAATCGTCTATTCA 60.127 38.462 0.0 0.0 0.0 2.57 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
380 403 6.538189 AAAAATGAAATGCCTTTGTAACGG 57.462 33.333 0.00 0.00 0.00 4.44
381 404 5.461032 AAATGAAATGCCTTTGTAACGGA 57.539 34.783 0.00 0.00 0.00 4.69
383 406 4.433186 TGAAATGCCTTTGTAACGGATG 57.567 40.909 0.00 0.00 0.00 3.51
384 407 4.075682 TGAAATGCCTTTGTAACGGATGA 58.924 39.130 0.00 0.00 0.00 2.92
385 408 4.155826 TGAAATGCCTTTGTAACGGATGAG 59.844 41.667 0.00 0.00 0.00 2.90
386 409 2.851263 TGCCTTTGTAACGGATGAGT 57.149 45.000 0.00 0.00 0.00 3.41
388 411 3.482436 TGCCTTTGTAACGGATGAGTTT 58.518 40.909 0.00 0.00 35.70 2.66
390 413 4.023536 TGCCTTTGTAACGGATGAGTTTTC 60.024 41.667 0.00 0.00 35.70 2.29
399 422 3.450893 GGATGAGTTTTCGTCCGAAAC 57.549 47.619 13.86 9.64 46.65 2.78
400 423 2.159037 GGATGAGTTTTCGTCCGAAACC 59.841 50.000 13.86 7.88 46.65 3.27
401 424 1.585297 TGAGTTTTCGTCCGAAACCC 58.415 50.000 13.86 8.27 42.88 4.11
402 425 1.139455 TGAGTTTTCGTCCGAAACCCT 59.861 47.619 13.86 12.36 42.88 4.34
403 426 1.529865 GAGTTTTCGTCCGAAACCCTG 59.470 52.381 13.86 0.00 42.88 4.45
404 427 1.139455 AGTTTTCGTCCGAAACCCTGA 59.861 47.619 13.86 0.00 42.88 3.86
405 428 2.148768 GTTTTCGTCCGAAACCCTGAT 58.851 47.619 13.86 0.00 42.88 2.90
407 430 2.660189 TTCGTCCGAAACCCTGATAC 57.340 50.000 0.00 0.00 0.00 2.24
408 431 1.843368 TCGTCCGAAACCCTGATACT 58.157 50.000 0.00 0.00 0.00 2.12
409 432 2.173519 TCGTCCGAAACCCTGATACTT 58.826 47.619 0.00 0.00 0.00 2.24
410 433 2.165030 TCGTCCGAAACCCTGATACTTC 59.835 50.000 0.00 0.00 0.00 3.01
411 434 2.537401 GTCCGAAACCCTGATACTTCG 58.463 52.381 0.00 0.00 40.18 3.79
415 438 3.617263 CCGAAACCCTGATACTTCGAAAG 59.383 47.826 0.00 0.00 42.44 2.62
417 440 4.563184 CGAAACCCTGATACTTCGAAAGAG 59.437 45.833 0.00 0.00 42.44 2.85
418 441 5.621555 CGAAACCCTGATACTTCGAAAGAGA 60.622 44.000 0.00 0.00 42.44 3.10
419 442 5.941555 AACCCTGATACTTCGAAAGAGAT 57.058 39.130 0.00 0.00 43.69 2.75
420 443 5.941555 ACCCTGATACTTCGAAAGAGATT 57.058 39.130 0.00 0.00 43.69 2.40
421 444 5.665459 ACCCTGATACTTCGAAAGAGATTG 58.335 41.667 0.00 0.00 43.69 2.67
422 445 5.187967 ACCCTGATACTTCGAAAGAGATTGT 59.812 40.000 0.00 0.00 43.69 2.71
423 446 5.751028 CCCTGATACTTCGAAAGAGATTGTC 59.249 44.000 0.00 0.00 43.69 3.18
424 447 5.751028 CCTGATACTTCGAAAGAGATTGTCC 59.249 44.000 0.00 0.00 43.69 4.02
425 448 6.280855 TGATACTTCGAAAGAGATTGTCCA 57.719 37.500 0.00 0.00 43.69 4.02
426 449 6.878317 TGATACTTCGAAAGAGATTGTCCAT 58.122 36.000 0.00 0.00 43.69 3.41
427 450 7.331026 TGATACTTCGAAAGAGATTGTCCATT 58.669 34.615 0.00 0.00 43.69 3.16
428 451 7.824289 TGATACTTCGAAAGAGATTGTCCATTT 59.176 33.333 0.00 0.00 43.69 2.32
429 452 6.884280 ACTTCGAAAGAGATTGTCCATTTT 57.116 33.333 0.00 0.00 43.69 1.82
431 454 6.263168 ACTTCGAAAGAGATTGTCCATTTTGT 59.737 34.615 0.00 0.00 43.69 2.83
432 455 7.444183 ACTTCGAAAGAGATTGTCCATTTTGTA 59.556 33.333 0.00 0.00 43.69 2.41
434 457 6.708502 TCGAAAGAGATTGTCCATTTTGTACA 59.291 34.615 0.00 0.00 34.84 2.90
435 458 6.797033 CGAAAGAGATTGTCCATTTTGTACAC 59.203 38.462 0.00 0.00 0.00 2.90
436 459 5.862924 AGAGATTGTCCATTTTGTACACG 57.137 39.130 0.00 0.00 0.00 4.49
437 460 5.547465 AGAGATTGTCCATTTTGTACACGA 58.453 37.500 0.00 0.00 0.00 4.35
438 461 5.995282 AGAGATTGTCCATTTTGTACACGAA 59.005 36.000 0.00 0.00 0.00 3.85
454 477 3.354089 ACGAAGTGCATCCAGTTTTTG 57.646 42.857 0.00 0.00 42.51 2.44
455 478 2.053627 CGAAGTGCATCCAGTTTTTGC 58.946 47.619 0.00 0.00 34.81 3.68
456 479 2.053627 GAAGTGCATCCAGTTTTTGCG 58.946 47.619 0.00 0.00 39.23 4.85
458 481 0.031994 GTGCATCCAGTTTTTGCGGT 59.968 50.000 0.00 0.00 39.23 5.68
461 484 2.287909 TGCATCCAGTTTTTGCGGTAAC 60.288 45.455 0.00 0.00 39.23 2.50
462 485 2.924880 GCATCCAGTTTTTGCGGTAACC 60.925 50.000 0.00 0.00 0.00 2.85
463 486 1.320507 TCCAGTTTTTGCGGTAACCC 58.679 50.000 0.00 0.00 0.00 4.11
464 487 1.133730 TCCAGTTTTTGCGGTAACCCT 60.134 47.619 0.00 0.00 0.00 4.34
465 488 1.268625 CCAGTTTTTGCGGTAACCCTC 59.731 52.381 0.00 0.00 0.00 4.30
466 489 2.227194 CAGTTTTTGCGGTAACCCTCT 58.773 47.619 0.00 0.00 0.00 3.69
467 490 2.225727 CAGTTTTTGCGGTAACCCTCTC 59.774 50.000 0.00 0.00 0.00 3.20
468 491 2.105993 AGTTTTTGCGGTAACCCTCTCT 59.894 45.455 0.00 0.00 0.00 3.10
469 492 3.325716 AGTTTTTGCGGTAACCCTCTCTA 59.674 43.478 0.00 0.00 0.00 2.43
471 494 2.226962 TTGCGGTAACCCTCTCTACT 57.773 50.000 0.00 0.00 0.00 2.57
472 495 2.226962 TGCGGTAACCCTCTCTACTT 57.773 50.000 0.00 0.00 0.00 2.24
473 496 2.532843 TGCGGTAACCCTCTCTACTTT 58.467 47.619 0.00 0.00 0.00 2.66
474 497 2.901839 TGCGGTAACCCTCTCTACTTTT 59.098 45.455 0.00 0.00 0.00 2.27
475 498 3.325716 TGCGGTAACCCTCTCTACTTTTT 59.674 43.478 0.00 0.00 0.00 1.94
503 526 6.128486 ACATGCTATGTGGGTGAAATTATGA 58.872 36.000 0.00 0.00 43.01 2.15
504 527 6.779049 ACATGCTATGTGGGTGAAATTATGAT 59.221 34.615 0.00 0.00 43.01 2.45
505 528 7.944000 ACATGCTATGTGGGTGAAATTATGATA 59.056 33.333 0.00 0.00 43.01 2.15
506 529 7.744087 TGCTATGTGGGTGAAATTATGATAC 57.256 36.000 0.00 0.00 0.00 2.24
507 530 6.714810 TGCTATGTGGGTGAAATTATGATACC 59.285 38.462 0.00 0.00 0.00 2.73
509 532 7.394359 GCTATGTGGGTGAAATTATGATACCAT 59.606 37.037 0.00 0.00 36.81 3.55
510 533 6.957920 TGTGGGTGAAATTATGATACCATG 57.042 37.500 0.00 0.00 34.31 3.66
512 535 4.832266 TGGGTGAAATTATGATACCATGCC 59.168 41.667 0.00 0.00 34.31 4.40
514 537 5.304101 GGGTGAAATTATGATACCATGCCAA 59.696 40.000 0.00 0.00 34.31 4.52
515 538 6.215845 GGTGAAATTATGATACCATGCCAAC 58.784 40.000 0.00 0.00 34.31 3.77
516 539 6.040842 GGTGAAATTATGATACCATGCCAACT 59.959 38.462 0.00 0.00 34.31 3.16
517 540 7.417797 GGTGAAATTATGATACCATGCCAACTT 60.418 37.037 0.00 0.00 34.31 2.66
518 541 7.981225 GTGAAATTATGATACCATGCCAACTTT 59.019 33.333 0.00 0.00 34.31 2.66
519 542 8.196771 TGAAATTATGATACCATGCCAACTTTC 58.803 33.333 0.00 0.00 34.31 2.62
521 544 7.658525 ATTATGATACCATGCCAACTTTCAA 57.341 32.000 0.00 0.00 34.31 2.69
522 545 4.782019 TGATACCATGCCAACTTTCAAC 57.218 40.909 0.00 0.00 0.00 3.18
523 546 3.509575 TGATACCATGCCAACTTTCAACC 59.490 43.478 0.00 0.00 0.00 3.77
524 547 2.086610 ACCATGCCAACTTTCAACCT 57.913 45.000 0.00 0.00 0.00 3.50
525 548 2.397597 ACCATGCCAACTTTCAACCTT 58.602 42.857 0.00 0.00 0.00 3.50
526 549 2.771372 ACCATGCCAACTTTCAACCTTT 59.229 40.909 0.00 0.00 0.00 3.11
527 550 3.199727 ACCATGCCAACTTTCAACCTTTT 59.800 39.130 0.00 0.00 0.00 2.27
528 551 3.809279 CCATGCCAACTTTCAACCTTTTC 59.191 43.478 0.00 0.00 0.00 2.29
529 552 4.443315 CCATGCCAACTTTCAACCTTTTCT 60.443 41.667 0.00 0.00 0.00 2.52
530 553 4.122143 TGCCAACTTTCAACCTTTTCTG 57.878 40.909 0.00 0.00 0.00 3.02
531 554 3.766591 TGCCAACTTTCAACCTTTTCTGA 59.233 39.130 0.00 0.00 0.00 3.27
532 555 4.142182 TGCCAACTTTCAACCTTTTCTGAG 60.142 41.667 0.00 0.00 0.00 3.35
533 556 4.142160 GCCAACTTTCAACCTTTTCTGAGT 60.142 41.667 0.00 0.00 0.00 3.41
534 557 5.624509 GCCAACTTTCAACCTTTTCTGAGTT 60.625 40.000 0.00 0.00 0.00 3.01
535 558 6.036470 CCAACTTTCAACCTTTTCTGAGTTC 58.964 40.000 0.00 0.00 0.00 3.01
536 559 6.350110 CCAACTTTCAACCTTTTCTGAGTTCA 60.350 38.462 0.00 0.00 0.00 3.18
537 560 7.260603 CAACTTTCAACCTTTTCTGAGTTCAT 58.739 34.615 0.00 0.00 0.00 2.57
540 563 7.761249 ACTTTCAACCTTTTCTGAGTTCATTTG 59.239 33.333 0.00 0.00 0.00 2.32
541 564 7.403312 TTCAACCTTTTCTGAGTTCATTTGA 57.597 32.000 0.00 0.00 0.00 2.69
542 565 7.403312 TCAACCTTTTCTGAGTTCATTTGAA 57.597 32.000 0.00 0.00 0.00 2.69
545 568 8.545420 CAACCTTTTCTGAGTTCATTTGAAATG 58.455 33.333 11.54 11.54 35.58 2.32
546 569 6.703165 ACCTTTTCTGAGTTCATTTGAAATGC 59.297 34.615 12.86 0.56 35.58 3.56
547 570 6.927381 CCTTTTCTGAGTTCATTTGAAATGCT 59.073 34.615 12.86 5.48 35.58 3.79
550 573 8.721019 TTTCTGAGTTCATTTGAAATGCTTTT 57.279 26.923 12.86 0.00 35.58 2.27
551 574 7.935338 TCTGAGTTCATTTGAAATGCTTTTC 57.065 32.000 12.86 16.10 41.39 2.29
563 586 7.961325 TGAAATGCTTTTCAATTTTAGGGTC 57.039 32.000 21.62 0.00 46.26 4.46
565 588 7.440856 TGAAATGCTTTTCAATTTTAGGGTCAC 59.559 33.333 21.62 0.00 46.26 3.67
567 590 4.339814 TGCTTTTCAATTTTAGGGTCACGT 59.660 37.500 0.00 0.00 0.00 4.49
568 591 5.163499 TGCTTTTCAATTTTAGGGTCACGTT 60.163 36.000 0.00 0.00 0.00 3.99
569 592 6.039493 TGCTTTTCAATTTTAGGGTCACGTTA 59.961 34.615 0.00 0.00 0.00 3.18
570 593 6.919115 GCTTTTCAATTTTAGGGTCACGTTAA 59.081 34.615 0.00 0.00 0.00 2.01
571 594 7.597369 GCTTTTCAATTTTAGGGTCACGTTAAT 59.403 33.333 0.00 0.00 0.00 1.40
598 2207 5.704053 ACCGACCGTTTTGATTCTTTAGAAT 59.296 36.000 4.71 4.71 46.54 2.40
679 2288 6.929049 CCTATCCTATTTTTACAGTGCGATGA 59.071 38.462 0.00 0.00 0.00 2.92
701 2310 2.885266 CTGGCTATTCACGGACTAGCTA 59.115 50.000 16.80 12.63 39.62 3.32
1007 2617 6.325545 AGCATGACCAATTGATAAATGTGGAT 59.674 34.615 7.12 0.00 33.39 3.41
1024 2635 4.290985 TGTGGATGAAAGTAGGGGAAATGA 59.709 41.667 0.00 0.00 0.00 2.57
1026 2637 4.540099 TGGATGAAAGTAGGGGAAATGACT 59.460 41.667 0.00 0.00 0.00 3.41
1036 2647 7.823635 AGTAGGGGAAATGACTGATACTACTA 58.176 38.462 0.00 0.00 37.45 1.82
1160 2772 2.376695 TAGTAATCGGAGGGACCAGG 57.623 55.000 0.00 0.00 38.90 4.45
1189 2801 9.000486 GTAAACATGAAAAAGTAGGAGCTTAGT 58.000 33.333 0.00 0.00 0.00 2.24
1235 2847 3.296709 GAGCAGAAAGGACCCGCGA 62.297 63.158 8.23 0.00 0.00 5.87
1246 2858 3.941573 AGGACCCGCGAAATTTTTACTA 58.058 40.909 8.23 0.00 0.00 1.82
1254 2866 8.891720 ACCCGCGAAATTTTTACTATTATAACA 58.108 29.630 8.23 0.00 0.00 2.41
1306 2918 6.949352 TGAAGCAACAAGAAAAAGAGATCT 57.051 33.333 0.00 0.00 0.00 2.75
1332 2944 7.621285 TCTCGAGGATCCAATATCTTATTCCAT 59.379 37.037 15.82 0.00 0.00 3.41
2129 3797 8.601546 TCCAATAAATCAAGGCTTTTTACCAAT 58.398 29.630 0.00 0.00 0.00 3.16
2130 3798 8.667463 CCAATAAATCAAGGCTTTTTACCAATG 58.333 33.333 0.00 0.48 0.00 2.82
2133 3801 4.599047 TCAAGGCTTTTTACCAATGTGG 57.401 40.909 0.00 0.00 45.02 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
357 380 6.284459 TCCGTTACAAAGGCATTTCATTTTT 58.716 32.000 0.00 0.00 0.00 1.94
358 381 5.848406 TCCGTTACAAAGGCATTTCATTTT 58.152 33.333 0.00 0.00 0.00 1.82
359 382 5.461032 TCCGTTACAAAGGCATTTCATTT 57.539 34.783 0.00 0.00 0.00 2.32
360 383 5.184864 TCATCCGTTACAAAGGCATTTCATT 59.815 36.000 0.00 0.00 0.00 2.57
362 385 4.075682 TCATCCGTTACAAAGGCATTTCA 58.924 39.130 0.00 0.00 0.00 2.69
363 386 4.156008 ACTCATCCGTTACAAAGGCATTTC 59.844 41.667 0.00 0.00 0.00 2.17
364 387 4.079253 ACTCATCCGTTACAAAGGCATTT 58.921 39.130 0.00 0.00 0.00 2.32
365 388 3.686016 ACTCATCCGTTACAAAGGCATT 58.314 40.909 0.00 0.00 0.00 3.56
366 389 3.350219 ACTCATCCGTTACAAAGGCAT 57.650 42.857 0.00 0.00 0.00 4.40
367 390 2.851263 ACTCATCCGTTACAAAGGCA 57.149 45.000 0.00 0.00 0.00 4.75
368 391 4.473199 GAAAACTCATCCGTTACAAAGGC 58.527 43.478 0.00 0.00 0.00 4.35
369 392 4.212636 ACGAAAACTCATCCGTTACAAAGG 59.787 41.667 0.00 0.00 30.41 3.11
370 393 5.338614 ACGAAAACTCATCCGTTACAAAG 57.661 39.130 0.00 0.00 30.41 2.77
372 395 3.742369 GGACGAAAACTCATCCGTTACAA 59.258 43.478 0.00 0.00 35.22 2.41
373 396 3.319755 GGACGAAAACTCATCCGTTACA 58.680 45.455 0.00 0.00 35.22 2.41
374 397 3.985912 GGACGAAAACTCATCCGTTAC 57.014 47.619 0.00 0.00 35.22 2.50
379 402 2.159037 GGTTTCGGACGAAAACTCATCC 59.841 50.000 23.46 14.70 45.43 3.51
380 403 3.450893 GGTTTCGGACGAAAACTCATC 57.549 47.619 23.46 10.32 45.43 2.92
386 409 2.554370 ATCAGGGTTTCGGACGAAAA 57.446 45.000 19.84 6.26 44.40 2.29
388 411 2.173519 AGTATCAGGGTTTCGGACGAA 58.826 47.619 2.62 2.62 0.00 3.85
390 413 2.537401 GAAGTATCAGGGTTTCGGACG 58.463 52.381 0.00 0.00 0.00 4.79
394 417 4.491676 TCTTTCGAAGTATCAGGGTTTCG 58.508 43.478 0.00 0.00 42.61 3.46
396 419 5.740290 TCTCTTTCGAAGTATCAGGGTTT 57.260 39.130 0.00 0.00 0.00 3.27
398 421 5.187967 ACAATCTCTTTCGAAGTATCAGGGT 59.812 40.000 0.00 0.00 0.00 4.34
399 422 5.665459 ACAATCTCTTTCGAAGTATCAGGG 58.335 41.667 0.00 0.00 0.00 4.45
400 423 5.751028 GGACAATCTCTTTCGAAGTATCAGG 59.249 44.000 0.00 0.00 0.00 3.86
401 424 6.333416 TGGACAATCTCTTTCGAAGTATCAG 58.667 40.000 0.00 0.00 0.00 2.90
402 425 6.280855 TGGACAATCTCTTTCGAAGTATCA 57.719 37.500 0.00 0.00 0.00 2.15
403 426 7.778470 AATGGACAATCTCTTTCGAAGTATC 57.222 36.000 0.00 0.00 0.00 2.24
404 427 8.454106 CAAAATGGACAATCTCTTTCGAAGTAT 58.546 33.333 0.00 0.00 0.00 2.12
405 428 7.444183 ACAAAATGGACAATCTCTTTCGAAGTA 59.556 33.333 0.00 0.00 0.00 2.24
407 430 6.672147 ACAAAATGGACAATCTCTTTCGAAG 58.328 36.000 0.00 0.00 0.00 3.79
408 431 6.633500 ACAAAATGGACAATCTCTTTCGAA 57.367 33.333 0.00 0.00 0.00 3.71
409 432 6.708502 TGTACAAAATGGACAATCTCTTTCGA 59.291 34.615 0.00 0.00 38.47 3.71
410 433 6.797033 GTGTACAAAATGGACAATCTCTTTCG 59.203 38.462 0.00 0.00 43.90 3.46
411 434 6.797033 CGTGTACAAAATGGACAATCTCTTTC 59.203 38.462 0.00 0.00 43.90 2.62
415 438 5.856126 TCGTGTACAAAATGGACAATCTC 57.144 39.130 0.00 0.00 43.90 2.75
417 440 5.851177 CACTTCGTGTACAAAATGGACAATC 59.149 40.000 0.00 0.00 43.90 2.67
418 441 5.757886 CACTTCGTGTACAAAATGGACAAT 58.242 37.500 0.00 0.00 43.90 2.71
419 442 4.496673 GCACTTCGTGTACAAAATGGACAA 60.497 41.667 0.00 0.00 43.90 3.18
420 443 3.002862 GCACTTCGTGTACAAAATGGACA 59.997 43.478 0.00 0.00 39.27 4.02
421 444 3.002862 TGCACTTCGTGTACAAAATGGAC 59.997 43.478 0.00 0.00 35.75 4.02
422 445 3.206964 TGCACTTCGTGTACAAAATGGA 58.793 40.909 0.00 0.00 35.75 3.41
423 446 3.617540 TGCACTTCGTGTACAAAATGG 57.382 42.857 0.00 0.00 35.75 3.16
424 447 4.158384 GGATGCACTTCGTGTACAAAATG 58.842 43.478 0.00 0.00 35.75 2.32
425 448 3.818210 TGGATGCACTTCGTGTACAAAAT 59.182 39.130 0.00 0.00 35.75 1.82
426 449 3.206964 TGGATGCACTTCGTGTACAAAA 58.793 40.909 0.00 0.00 35.75 2.44
427 450 2.805671 CTGGATGCACTTCGTGTACAAA 59.194 45.455 0.00 0.00 35.75 2.83
428 451 2.224185 ACTGGATGCACTTCGTGTACAA 60.224 45.455 0.00 0.00 35.75 2.41
429 452 1.343142 ACTGGATGCACTTCGTGTACA 59.657 47.619 0.00 0.00 35.75 2.90
431 454 2.831685 AACTGGATGCACTTCGTGTA 57.168 45.000 0.00 0.00 35.75 2.90
432 455 1.967319 AAACTGGATGCACTTCGTGT 58.033 45.000 0.00 0.00 35.75 4.49
434 457 2.543653 GCAAAAACTGGATGCACTTCGT 60.544 45.455 0.00 0.00 39.81 3.85
435 458 2.053627 GCAAAAACTGGATGCACTTCG 58.946 47.619 0.00 0.00 39.81 3.79
436 459 2.053627 CGCAAAAACTGGATGCACTTC 58.946 47.619 0.00 0.00 40.04 3.01
437 460 1.269726 CCGCAAAAACTGGATGCACTT 60.270 47.619 0.00 0.00 40.04 3.16
438 461 0.314935 CCGCAAAAACTGGATGCACT 59.685 50.000 0.00 0.00 40.04 4.40
440 463 1.610363 TACCGCAAAAACTGGATGCA 58.390 45.000 0.00 0.00 40.04 3.96
441 464 2.324860 GTTACCGCAAAAACTGGATGC 58.675 47.619 0.00 0.00 36.74 3.91
443 466 1.890489 GGGTTACCGCAAAAACTGGAT 59.110 47.619 0.00 0.00 0.00 3.41
444 467 1.133730 AGGGTTACCGCAAAAACTGGA 60.134 47.619 0.00 0.00 43.47 3.86
446 469 2.225727 GAGAGGGTTACCGCAAAAACTG 59.774 50.000 0.00 0.00 43.47 3.16
447 470 2.105993 AGAGAGGGTTACCGCAAAAACT 59.894 45.455 0.00 0.00 43.47 2.66
449 472 2.943036 AGAGAGGGTTACCGCAAAAA 57.057 45.000 0.00 0.00 43.47 1.94
450 473 2.901839 AGTAGAGAGGGTTACCGCAAAA 59.098 45.455 0.00 0.00 43.47 2.44
452 475 2.226962 AGTAGAGAGGGTTACCGCAA 57.773 50.000 0.00 0.00 43.47 4.85
454 477 3.606595 AAAAGTAGAGAGGGTTACCGC 57.393 47.619 0.00 0.00 43.47 5.68
479 502 6.128486 TCATAATTTCACCCACATAGCATGT 58.872 36.000 0.00 0.00 46.22 3.21
481 504 7.394359 GGTATCATAATTTCACCCACATAGCAT 59.606 37.037 0.00 0.00 0.00 3.79
482 505 6.714810 GGTATCATAATTTCACCCACATAGCA 59.285 38.462 0.00 0.00 0.00 3.49
487 510 5.301551 GCATGGTATCATAATTTCACCCACA 59.698 40.000 0.00 0.00 31.33 4.17
488 511 5.278957 GGCATGGTATCATAATTTCACCCAC 60.279 44.000 0.00 0.00 31.33 4.61
489 512 4.832266 GGCATGGTATCATAATTTCACCCA 59.168 41.667 0.00 0.00 31.33 4.51
490 513 4.832266 TGGCATGGTATCATAATTTCACCC 59.168 41.667 0.00 0.00 31.33 4.61
491 514 6.040842 AGTTGGCATGGTATCATAATTTCACC 59.959 38.462 0.00 0.00 31.33 4.02
492 515 7.042797 AGTTGGCATGGTATCATAATTTCAC 57.957 36.000 0.00 0.00 31.33 3.18
494 517 8.196771 TGAAAGTTGGCATGGTATCATAATTTC 58.803 33.333 0.00 3.53 31.33 2.17
495 518 8.076910 TGAAAGTTGGCATGGTATCATAATTT 57.923 30.769 0.00 0.00 31.33 1.82
496 519 7.658525 TGAAAGTTGGCATGGTATCATAATT 57.341 32.000 0.00 0.00 31.33 1.40
498 521 6.127479 GGTTGAAAGTTGGCATGGTATCATAA 60.127 38.462 0.00 0.00 31.33 1.90
500 523 4.160252 GGTTGAAAGTTGGCATGGTATCAT 59.840 41.667 0.00 0.00 0.00 2.45
501 524 3.509575 GGTTGAAAGTTGGCATGGTATCA 59.490 43.478 0.00 0.00 0.00 2.15
503 526 3.778265 AGGTTGAAAGTTGGCATGGTAT 58.222 40.909 0.00 0.00 0.00 2.73
504 527 3.237268 AGGTTGAAAGTTGGCATGGTA 57.763 42.857 0.00 0.00 0.00 3.25
505 528 2.086610 AGGTTGAAAGTTGGCATGGT 57.913 45.000 0.00 0.00 0.00 3.55
506 529 3.473923 AAAGGTTGAAAGTTGGCATGG 57.526 42.857 0.00 0.00 0.00 3.66
507 530 4.508861 CAGAAAAGGTTGAAAGTTGGCATG 59.491 41.667 0.00 0.00 0.00 4.06
509 532 3.766591 TCAGAAAAGGTTGAAAGTTGGCA 59.233 39.130 0.00 0.00 0.00 4.92
510 533 4.142160 ACTCAGAAAAGGTTGAAAGTTGGC 60.142 41.667 0.00 0.00 0.00 4.52
512 535 6.620678 TGAACTCAGAAAAGGTTGAAAGTTG 58.379 36.000 0.00 0.00 0.00 3.16
514 537 7.410120 AATGAACTCAGAAAAGGTTGAAAGT 57.590 32.000 0.00 0.00 0.00 2.66
515 538 7.975616 TCAAATGAACTCAGAAAAGGTTGAAAG 59.024 33.333 0.00 0.00 0.00 2.62
516 539 7.835822 TCAAATGAACTCAGAAAAGGTTGAAA 58.164 30.769 0.00 0.00 0.00 2.69
517 540 7.403312 TCAAATGAACTCAGAAAAGGTTGAA 57.597 32.000 0.00 0.00 0.00 2.69
518 541 7.403312 TTCAAATGAACTCAGAAAAGGTTGA 57.597 32.000 0.00 0.00 0.00 3.18
519 542 8.545420 CATTTCAAATGAACTCAGAAAAGGTTG 58.455 33.333 3.82 0.00 33.13 3.77
521 544 6.703165 GCATTTCAAATGAACTCAGAAAAGGT 59.297 34.615 14.65 0.00 33.13 3.50
522 545 6.927381 AGCATTTCAAATGAACTCAGAAAAGG 59.073 34.615 14.65 0.00 33.13 3.11
523 546 7.941795 AGCATTTCAAATGAACTCAGAAAAG 57.058 32.000 14.65 0.00 33.13 2.27
524 547 8.721019 AAAGCATTTCAAATGAACTCAGAAAA 57.279 26.923 14.65 0.00 27.08 2.29
525 548 8.721019 AAAAGCATTTCAAATGAACTCAGAAA 57.279 26.923 14.65 0.00 37.28 2.52
526 549 8.356533 GAAAAGCATTTCAAATGAACTCAGAA 57.643 30.769 14.65 0.00 43.62 3.02
527 550 7.935338 GAAAAGCATTTCAAATGAACTCAGA 57.065 32.000 14.65 0.00 43.62 3.27
540 563 7.359181 CGTGACCCTAAAATTGAAAAGCATTTC 60.359 37.037 7.46 7.46 44.27 2.17
541 564 6.423604 CGTGACCCTAAAATTGAAAAGCATTT 59.576 34.615 0.00 0.00 42.41 2.32
542 565 5.925969 CGTGACCCTAAAATTGAAAAGCATT 59.074 36.000 0.00 0.00 0.00 3.56
545 568 4.866921 ACGTGACCCTAAAATTGAAAAGC 58.133 39.130 0.00 0.00 0.00 3.51
550 573 8.513774 GGTTTATTAACGTGACCCTAAAATTGA 58.486 33.333 0.00 0.00 35.00 2.57
551 574 7.482428 CGGTTTATTAACGTGACCCTAAAATTG 59.518 37.037 0.00 0.00 35.00 2.32
553 576 6.878389 TCGGTTTATTAACGTGACCCTAAAAT 59.122 34.615 0.00 0.00 35.00 1.82
554 577 6.147000 GTCGGTTTATTAACGTGACCCTAAAA 59.853 38.462 0.00 0.00 35.75 1.52
555 578 5.637387 GTCGGTTTATTAACGTGACCCTAAA 59.363 40.000 0.00 0.00 35.75 1.85
556 579 5.167845 GTCGGTTTATTAACGTGACCCTAA 58.832 41.667 0.00 0.00 35.75 2.69
557 580 4.381505 GGTCGGTTTATTAACGTGACCCTA 60.382 45.833 19.19 0.00 45.42 3.53
558 581 3.588955 GTCGGTTTATTAACGTGACCCT 58.411 45.455 0.00 0.00 35.75 4.34
559 582 2.672874 GGTCGGTTTATTAACGTGACCC 59.327 50.000 19.19 8.01 45.42 4.46
560 583 2.345341 CGGTCGGTTTATTAACGTGACC 59.655 50.000 19.63 19.63 46.44 4.02
561 584 2.986479 ACGGTCGGTTTATTAACGTGAC 59.014 45.455 9.03 9.03 38.53 3.67
562 585 3.296322 ACGGTCGGTTTATTAACGTGA 57.704 42.857 0.00 0.00 35.00 4.35
563 586 4.388189 AAACGGTCGGTTTATTAACGTG 57.612 40.909 6.73 0.00 46.76 4.49
572 595 7.255346 ATTCTAAAGAATCAAAACGGTCGGTTT 60.255 33.333 0.09 0.09 44.38 3.27
623 2232 1.141858 GGTCATTGAGGGCCTCCTAAG 59.858 57.143 30.03 17.00 45.05 2.18
679 2288 1.409427 GCTAGTCCGTGAATAGCCAGT 59.591 52.381 17.20 0.00 46.31 4.00
778 2387 5.707764 TCATTCGGGTTTGATTGTGTCATAA 59.292 36.000 0.00 0.00 36.54 1.90
1007 2617 5.779241 ATCAGTCATTTCCCCTACTTTCA 57.221 39.130 0.00 0.00 0.00 2.69
1046 2658 5.395324 GCTACAGTACCTATCAGCCAAAGAA 60.395 44.000 0.00 0.00 0.00 2.52
1128 2740 6.659668 CCTCCGATTACTATAGAGATGAACCA 59.340 42.308 6.78 0.00 0.00 3.67
1160 2772 7.649057 AGCTCCTACTTTTTCATGTTTACAAC 58.351 34.615 0.00 0.00 0.00 3.32
1306 2918 6.954102 TGGAATAAGATATTGGATCCTCGAGA 59.046 38.462 15.71 0.00 0.00 4.04
1347 2959 7.342769 ACTCGAAACTAAACCAAGGATTTTT 57.657 32.000 0.00 0.00 0.00 1.94
1911 3535 6.127451 TGCAGGTCTTCTTAATCGTCTATTCA 60.127 38.462 0.00 0.00 0.00 2.57
2103 3771 7.546250 TGGTAAAAAGCCTTGATTTATTGGA 57.454 32.000 0.00 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.