Multiple sequence alignment - TraesCS5A01G530900

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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 TraesCS5A01G530900 chr5A 100.000 2549 0 0 1 2549 689447108 689444560 0.000000e+00 4708.0
1 TraesCS5A01G530900 chr5A 95.054 1961 72 12 594 2549 689409588 689407648 0.000000e+00 3061.0
2 TraesCS5A01G530900 chr5A 93.964 497 22 5 1 496 671997738 671997249 0.000000e+00 745.0
3 TraesCS5A01G530900 chr5A 80.077 261 16 10 172 424 689482872 689482640 7.300000e-36 161.0
4 TraesCS5A01G530900 chr5A 89.744 78 5 1 527 601 671997254 671997177 2.090000e-16 97.1
5 TraesCS5A01G530900 chr7A 96.061 1955 67 6 602 2549 36946200 36948151 0.000000e+00 3175.0
6 TraesCS5A01G530900 chr2A 95.910 1956 70 6 602 2549 677958469 677956516 0.000000e+00 3160.0
7 TraesCS5A01G530900 chr2A 95.812 1958 73 7 600 2549 744582027 744583983 0.000000e+00 3153.0
8 TraesCS5A01G530900 chr2A 94.353 1948 98 10 602 2541 677413606 677411663 0.000000e+00 2977.0
9 TraesCS5A01G530900 chr2A 92.378 1968 122 19 601 2549 213959518 213957560 0.000000e+00 2778.0
10 TraesCS5A01G530900 chr1B 94.699 1943 76 10 601 2532 645321436 645323362 0.000000e+00 2992.0
11 TraesCS5A01G530900 chr7D 94.238 1961 93 15 600 2549 63995388 63997339 0.000000e+00 2977.0
12 TraesCS5A01G530900 chr3D 94.031 1960 97 16 601 2549 475106680 475108630 0.000000e+00 2953.0
13 TraesCS5A01G530900 chr4D 91.928 607 30 7 1 601 505243425 505242832 0.000000e+00 832.0
14 TraesCS5A01G530900 chr4D 90.397 604 26 10 1 601 490418896 490418322 0.000000e+00 765.0
15 TraesCS5A01G530900 chr4B 92.832 572 25 6 1 572 630086621 630086066 0.000000e+00 815.0
16 TraesCS5A01G530900 chr4B 91.142 429 27 6 1 426 651806506 651806926 2.850000e-159 571.0
17 TraesCS5A01G530900 chr4B 84.932 584 41 28 28 601 651868751 651869297 4.790000e-152 547.0
18 TraesCS5A01G530900 chr6B 95.116 389 19 0 583 971 64173037 64173425 4.660000e-172 614.0


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 TraesCS5A01G530900 chr5A 689444560 689447108 2548 True 4708.00 4708 100.000 1 2549 1 chr5A.!!$R2 2548
1 TraesCS5A01G530900 chr5A 689407648 689409588 1940 True 3061.00 3061 95.054 594 2549 1 chr5A.!!$R1 1955
2 TraesCS5A01G530900 chr5A 671997177 671997738 561 True 421.05 745 91.854 1 601 2 chr5A.!!$R4 600
3 TraesCS5A01G530900 chr7A 36946200 36948151 1951 False 3175.00 3175 96.061 602 2549 1 chr7A.!!$F1 1947
4 TraesCS5A01G530900 chr2A 677956516 677958469 1953 True 3160.00 3160 95.910 602 2549 1 chr2A.!!$R3 1947
5 TraesCS5A01G530900 chr2A 744582027 744583983 1956 False 3153.00 3153 95.812 600 2549 1 chr2A.!!$F1 1949
6 TraesCS5A01G530900 chr2A 677411663 677413606 1943 True 2977.00 2977 94.353 602 2541 1 chr2A.!!$R2 1939
7 TraesCS5A01G530900 chr2A 213957560 213959518 1958 True 2778.00 2778 92.378 601 2549 1 chr2A.!!$R1 1948
8 TraesCS5A01G530900 chr1B 645321436 645323362 1926 False 2992.00 2992 94.699 601 2532 1 chr1B.!!$F1 1931
9 TraesCS5A01G530900 chr7D 63995388 63997339 1951 False 2977.00 2977 94.238 600 2549 1 chr7D.!!$F1 1949
10 TraesCS5A01G530900 chr3D 475106680 475108630 1950 False 2953.00 2953 94.031 601 2549 1 chr3D.!!$F1 1948
11 TraesCS5A01G530900 chr4D 505242832 505243425 593 True 832.00 832 91.928 1 601 1 chr4D.!!$R2 600
12 TraesCS5A01G530900 chr4D 490418322 490418896 574 True 765.00 765 90.397 1 601 1 chr4D.!!$R1 600
13 TraesCS5A01G530900 chr4B 630086066 630086621 555 True 815.00 815 92.832 1 572 1 chr4B.!!$R1 571
14 TraesCS5A01G530900 chr4B 651868751 651869297 546 False 547.00 547 84.932 28 601 1 chr4B.!!$F2 573

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
131 141 0.172803 CGTCTCCTCCAAACTACCCG 59.827 60.0 0.0 0.0 0.0 5.28 F
479 493 0.178990 GCCACCTCCAGTTCCAGTTT 60.179 55.0 0.0 0.0 0.0 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1182 1231 1.029947 ATCCCGACCACGAAAATGGC 61.030 55.0 0.00 0.0 44.33 4.40 R
2306 2377 0.316937 ACGCGTGTGCAAACATTCAG 60.317 50.0 12.93 0.0 42.97 3.02 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
23 24 0.540923 GCTCAGATGAGGAACAGGCT 59.459 55.000 11.63 0.00 42.29 4.58
33 34 1.743252 GAACAGGCTCCTTCCAGCG 60.743 63.158 0.00 0.00 40.68 5.18
131 141 0.172803 CGTCTCCTCCAAACTACCCG 59.827 60.000 0.00 0.00 0.00 5.28
399 413 1.600916 GAACCCCAACGCTTGCTCT 60.601 57.895 0.00 0.00 0.00 4.09
438 452 4.408821 GACCCAGCGGCACCATCA 62.409 66.667 1.45 0.00 0.00 3.07
439 453 3.918253 GACCCAGCGGCACCATCAA 62.918 63.158 1.45 0.00 0.00 2.57
440 454 3.443045 CCCAGCGGCACCATCAAC 61.443 66.667 1.45 0.00 0.00 3.18
441 455 3.803082 CCAGCGGCACCATCAACG 61.803 66.667 1.45 0.00 0.00 4.10
442 456 3.049674 CAGCGGCACCATCAACGT 61.050 61.111 1.45 0.00 0.00 3.99
443 457 2.742372 AGCGGCACCATCAACGTC 60.742 61.111 1.45 0.00 0.00 4.34
444 458 2.742372 GCGGCACCATCAACGTCT 60.742 61.111 0.00 0.00 0.00 4.18
445 459 3.027170 GCGGCACCATCAACGTCTG 62.027 63.158 0.00 0.00 0.00 3.51
446 460 2.870372 GGCACCATCAACGTCTGC 59.130 61.111 0.00 0.00 0.00 4.26
447 461 2.476051 GCACCATCAACGTCTGCG 59.524 61.111 0.00 0.00 44.93 5.18
457 471 4.337060 CGTCTGCGTCCACGTCCA 62.337 66.667 0.36 0.00 42.22 4.02
458 472 2.028484 GTCTGCGTCCACGTCCAA 59.972 61.111 0.36 0.00 42.22 3.53
459 473 2.028484 TCTGCGTCCACGTCCAAC 59.972 61.111 0.36 0.00 42.22 3.77
469 483 4.308458 CGTCCAACGCCACCTCCA 62.308 66.667 0.00 0.00 33.65 3.86
470 484 2.358737 GTCCAACGCCACCTCCAG 60.359 66.667 0.00 0.00 0.00 3.86
471 485 2.847234 TCCAACGCCACCTCCAGT 60.847 61.111 0.00 0.00 0.00 4.00
472 486 2.113139 CCAACGCCACCTCCAGTT 59.887 61.111 0.00 0.00 0.00 3.16
473 487 1.966451 CCAACGCCACCTCCAGTTC 60.966 63.158 0.00 0.00 0.00 3.01
474 488 1.966451 CAACGCCACCTCCAGTTCC 60.966 63.158 0.00 0.00 0.00 3.62
475 489 2.448582 AACGCCACCTCCAGTTCCA 61.449 57.895 0.00 0.00 0.00 3.53
476 490 2.046892 CGCCACCTCCAGTTCCAG 60.047 66.667 0.00 0.00 0.00 3.86
477 491 2.883828 CGCCACCTCCAGTTCCAGT 61.884 63.158 0.00 0.00 0.00 4.00
478 492 1.456287 GCCACCTCCAGTTCCAGTT 59.544 57.895 0.00 0.00 0.00 3.16
479 493 0.178990 GCCACCTCCAGTTCCAGTTT 60.179 55.000 0.00 0.00 0.00 2.66
480 494 1.754201 GCCACCTCCAGTTCCAGTTTT 60.754 52.381 0.00 0.00 0.00 2.43
481 495 2.488347 GCCACCTCCAGTTCCAGTTTTA 60.488 50.000 0.00 0.00 0.00 1.52
482 496 3.814316 GCCACCTCCAGTTCCAGTTTTAT 60.814 47.826 0.00 0.00 0.00 1.40
483 497 4.407365 CCACCTCCAGTTCCAGTTTTATT 58.593 43.478 0.00 0.00 0.00 1.40
484 498 5.566469 CCACCTCCAGTTCCAGTTTTATTA 58.434 41.667 0.00 0.00 0.00 0.98
485 499 5.648092 CCACCTCCAGTTCCAGTTTTATTAG 59.352 44.000 0.00 0.00 0.00 1.73
486 500 5.123979 CACCTCCAGTTCCAGTTTTATTAGC 59.876 44.000 0.00 0.00 0.00 3.09
487 501 4.640647 CCTCCAGTTCCAGTTTTATTAGCC 59.359 45.833 0.00 0.00 0.00 3.93
488 502 4.595986 TCCAGTTCCAGTTTTATTAGCCC 58.404 43.478 0.00 0.00 0.00 5.19
489 503 4.291249 TCCAGTTCCAGTTTTATTAGCCCT 59.709 41.667 0.00 0.00 0.00 5.19
490 504 4.640647 CCAGTTCCAGTTTTATTAGCCCTC 59.359 45.833 0.00 0.00 0.00 4.30
491 505 4.640647 CAGTTCCAGTTTTATTAGCCCTCC 59.359 45.833 0.00 0.00 0.00 4.30
492 506 4.540502 AGTTCCAGTTTTATTAGCCCTCCT 59.459 41.667 0.00 0.00 0.00 3.69
493 507 5.729718 AGTTCCAGTTTTATTAGCCCTCCTA 59.270 40.000 0.00 0.00 0.00 2.94
494 508 6.390165 AGTTCCAGTTTTATTAGCCCTCCTAT 59.610 38.462 0.00 0.00 0.00 2.57
495 509 7.571357 AGTTCCAGTTTTATTAGCCCTCCTATA 59.429 37.037 0.00 0.00 0.00 1.31
496 510 8.383947 GTTCCAGTTTTATTAGCCCTCCTATAT 58.616 37.037 0.00 0.00 0.00 0.86
497 511 9.624037 TTCCAGTTTTATTAGCCCTCCTATATA 57.376 33.333 0.00 0.00 0.00 0.86
498 512 9.799223 TCCAGTTTTATTAGCCCTCCTATATAT 57.201 33.333 0.00 0.00 0.00 0.86
508 522 7.899648 AGCCCTCCTATATATATACACACAC 57.100 40.000 0.00 0.00 0.00 3.82
509 523 6.546403 AGCCCTCCTATATATATACACACACG 59.454 42.308 0.00 0.00 0.00 4.49
510 524 6.544931 GCCCTCCTATATATATACACACACGA 59.455 42.308 0.00 0.00 0.00 4.35
511 525 7.230913 GCCCTCCTATATATATACACACACGAT 59.769 40.741 0.00 0.00 0.00 3.73
512 526 9.788889 CCCTCCTATATATATACACACACGATA 57.211 37.037 0.00 0.00 0.00 2.92
526 540 3.043635 CACGATATGTGCAAGCAGAAC 57.956 47.619 0.00 0.00 42.70 3.01
527 541 2.674852 CACGATATGTGCAAGCAGAACT 59.325 45.455 0.00 0.00 42.70 3.01
528 542 2.932614 ACGATATGTGCAAGCAGAACTC 59.067 45.455 0.00 0.00 0.00 3.01
529 543 2.931969 CGATATGTGCAAGCAGAACTCA 59.068 45.455 0.00 0.00 0.00 3.41
530 544 3.558829 CGATATGTGCAAGCAGAACTCAT 59.441 43.478 0.00 0.00 0.00 2.90
531 545 4.552184 CGATATGTGCAAGCAGAACTCATG 60.552 45.833 0.00 0.00 0.00 3.07
532 546 2.259266 TGTGCAAGCAGAACTCATGA 57.741 45.000 0.00 0.00 0.00 3.07
533 547 2.148768 TGTGCAAGCAGAACTCATGAG 58.851 47.619 21.37 21.37 0.00 2.90
534 548 1.467734 GTGCAAGCAGAACTCATGAGG 59.532 52.381 26.08 9.79 0.00 3.86
535 549 1.072806 TGCAAGCAGAACTCATGAGGT 59.927 47.619 26.08 21.22 0.00 3.85
536 550 1.467734 GCAAGCAGAACTCATGAGGTG 59.532 52.381 26.08 19.57 0.00 4.00
537 551 1.467734 CAAGCAGAACTCATGAGGTGC 59.532 52.381 27.13 27.13 35.37 5.01
538 552 0.982704 AGCAGAACTCATGAGGTGCT 59.017 50.000 29.60 29.60 38.46 4.40
539 553 2.182827 AGCAGAACTCATGAGGTGCTA 58.817 47.619 31.99 0.00 40.19 3.49
540 554 2.770802 AGCAGAACTCATGAGGTGCTAT 59.229 45.455 31.99 18.77 40.19 2.97
541 555 3.129871 GCAGAACTCATGAGGTGCTATC 58.870 50.000 27.12 12.35 33.60 2.08
542 556 3.379240 CAGAACTCATGAGGTGCTATCG 58.621 50.000 26.08 5.01 0.00 2.92
543 557 3.027412 AGAACTCATGAGGTGCTATCGT 58.973 45.455 26.08 0.00 0.00 3.73
544 558 3.067461 AGAACTCATGAGGTGCTATCGTC 59.933 47.826 26.08 5.72 0.00 4.20
545 559 1.335182 ACTCATGAGGTGCTATCGTCG 59.665 52.381 26.08 0.00 0.00 5.12
546 560 1.335182 CTCATGAGGTGCTATCGTCGT 59.665 52.381 15.38 0.00 0.00 4.34
547 561 1.749063 TCATGAGGTGCTATCGTCGTT 59.251 47.619 0.00 0.00 0.00 3.85
548 562 2.165641 TCATGAGGTGCTATCGTCGTTT 59.834 45.455 0.00 0.00 0.00 3.60
549 563 3.379057 TCATGAGGTGCTATCGTCGTTTA 59.621 43.478 0.00 0.00 0.00 2.01
550 564 3.416119 TGAGGTGCTATCGTCGTTTAG 57.584 47.619 0.00 0.00 0.00 1.85
551 565 2.751259 TGAGGTGCTATCGTCGTTTAGT 59.249 45.455 0.00 0.00 0.00 2.24
552 566 3.192001 TGAGGTGCTATCGTCGTTTAGTT 59.808 43.478 0.00 0.00 0.00 2.24
553 567 3.767278 AGGTGCTATCGTCGTTTAGTTC 58.233 45.455 0.00 0.00 0.00 3.01
554 568 2.856557 GGTGCTATCGTCGTTTAGTTCC 59.143 50.000 0.00 0.05 0.00 3.62
555 569 3.504863 GTGCTATCGTCGTTTAGTTCCA 58.495 45.455 0.00 0.00 0.00 3.53
556 570 3.922240 GTGCTATCGTCGTTTAGTTCCAA 59.078 43.478 0.00 0.00 0.00 3.53
557 571 3.922240 TGCTATCGTCGTTTAGTTCCAAC 59.078 43.478 0.00 0.00 0.00 3.77
558 572 4.171754 GCTATCGTCGTTTAGTTCCAACT 58.828 43.478 0.00 0.00 42.91 3.16
559 573 4.031426 GCTATCGTCGTTTAGTTCCAACTG 59.969 45.833 2.01 0.00 40.07 3.16
560 574 3.713858 TCGTCGTTTAGTTCCAACTGA 57.286 42.857 2.01 0.00 40.07 3.41
561 575 4.247267 TCGTCGTTTAGTTCCAACTGAT 57.753 40.909 2.01 0.00 40.07 2.90
562 576 3.985279 TCGTCGTTTAGTTCCAACTGATG 59.015 43.478 2.01 0.00 40.07 3.07
563 577 3.985279 CGTCGTTTAGTTCCAACTGATGA 59.015 43.478 2.01 0.01 40.07 2.92
564 578 4.143389 CGTCGTTTAGTTCCAACTGATGAC 60.143 45.833 14.22 14.22 40.07 3.06
565 579 4.748102 GTCGTTTAGTTCCAACTGATGACA 59.252 41.667 16.96 0.00 39.53 3.58
566 580 5.408604 GTCGTTTAGTTCCAACTGATGACAT 59.591 40.000 16.96 0.00 39.53 3.06
567 581 6.588756 GTCGTTTAGTTCCAACTGATGACATA 59.411 38.462 16.96 0.00 39.53 2.29
568 582 6.811665 TCGTTTAGTTCCAACTGATGACATAG 59.188 38.462 2.01 0.00 40.07 2.23
569 583 6.590292 CGTTTAGTTCCAACTGATGACATAGT 59.410 38.462 2.01 0.00 40.07 2.12
570 584 7.758076 CGTTTAGTTCCAACTGATGACATAGTA 59.242 37.037 2.01 0.00 40.07 1.82
571 585 8.870879 GTTTAGTTCCAACTGATGACATAGTAC 58.129 37.037 2.01 0.00 40.07 2.73
572 586 6.605471 AGTTCCAACTGATGACATAGTACA 57.395 37.500 0.00 0.00 37.98 2.90
573 587 7.004555 AGTTCCAACTGATGACATAGTACAA 57.995 36.000 0.00 0.00 37.98 2.41
574 588 7.624549 AGTTCCAACTGATGACATAGTACAAT 58.375 34.615 0.00 0.00 37.98 2.71
575 589 7.550551 AGTTCCAACTGATGACATAGTACAATG 59.449 37.037 0.00 0.00 37.98 2.82
576 590 6.946340 TCCAACTGATGACATAGTACAATGT 58.054 36.000 0.00 0.00 42.75 2.71
577 591 8.073467 TCCAACTGATGACATAGTACAATGTA 57.927 34.615 0.00 0.00 40.17 2.29
578 592 8.536175 TCCAACTGATGACATAGTACAATGTAA 58.464 33.333 0.00 0.00 40.17 2.41
579 593 9.161629 CCAACTGATGACATAGTACAATGTAAA 57.838 33.333 0.00 0.00 40.17 2.01
581 595 8.425577 ACTGATGACATAGTACAATGTAAAGC 57.574 34.615 0.00 0.00 40.17 3.51
582 596 8.260818 ACTGATGACATAGTACAATGTAAAGCT 58.739 33.333 0.00 0.00 40.17 3.74
583 597 8.424274 TGATGACATAGTACAATGTAAAGCTG 57.576 34.615 0.00 0.00 40.17 4.24
584 598 6.662414 TGACATAGTACAATGTAAAGCTGC 57.338 37.500 0.00 0.00 40.17 5.25
585 599 6.169800 TGACATAGTACAATGTAAAGCTGCA 58.830 36.000 1.02 0.00 40.17 4.41
586 600 6.652900 TGACATAGTACAATGTAAAGCTGCAA 59.347 34.615 1.02 0.00 40.17 4.08
587 601 6.842163 ACATAGTACAATGTAAAGCTGCAAC 58.158 36.000 1.02 0.00 38.31 4.17
588 602 6.655003 ACATAGTACAATGTAAAGCTGCAACT 59.345 34.615 1.02 0.00 38.31 3.16
589 603 5.613358 AGTACAATGTAAAGCTGCAACTC 57.387 39.130 1.02 0.00 0.00 3.01
590 604 5.063204 AGTACAATGTAAAGCTGCAACTCA 58.937 37.500 1.02 0.00 0.00 3.41
591 605 4.228912 ACAATGTAAAGCTGCAACTCAC 57.771 40.909 1.02 0.00 0.00 3.51
592 606 3.885297 ACAATGTAAAGCTGCAACTCACT 59.115 39.130 1.02 0.00 0.00 3.41
593 607 5.063204 ACAATGTAAAGCTGCAACTCACTA 58.937 37.500 1.02 0.00 0.00 2.74
594 608 5.530915 ACAATGTAAAGCTGCAACTCACTAA 59.469 36.000 1.02 0.00 0.00 2.24
595 609 6.207417 ACAATGTAAAGCTGCAACTCACTAAT 59.793 34.615 1.02 0.00 0.00 1.73
596 610 7.390440 ACAATGTAAAGCTGCAACTCACTAATA 59.610 33.333 1.02 0.00 0.00 0.98
597 611 7.921786 ATGTAAAGCTGCAACTCACTAATAA 57.078 32.000 1.02 0.00 0.00 1.40
627 641 7.340999 GGGTTAATTATCTTTTTGCCCTCAGTA 59.659 37.037 0.00 0.00 0.00 2.74
632 646 4.164843 TCTTTTTGCCCTCAGTAGTGTT 57.835 40.909 0.00 0.00 0.00 3.32
658 672 3.515602 ACTCAGTTTTGCCCTCAGATT 57.484 42.857 0.00 0.00 0.00 2.40
840 869 2.047844 GCAGAGAGCCGTTGAGCA 60.048 61.111 0.00 0.00 37.23 4.26
841 870 2.099431 GCAGAGAGCCGTTGAGCAG 61.099 63.158 0.00 0.00 37.23 4.24
842 871 1.588597 CAGAGAGCCGTTGAGCAGA 59.411 57.895 0.00 0.00 34.23 4.26
843 872 0.458197 CAGAGAGCCGTTGAGCAGAG 60.458 60.000 0.00 0.00 34.23 3.35
844 873 0.610509 AGAGAGCCGTTGAGCAGAGA 60.611 55.000 0.00 0.00 34.23 3.10
845 874 0.179140 GAGAGCCGTTGAGCAGAGAG 60.179 60.000 0.00 0.00 34.23 3.20
846 875 0.897863 AGAGCCGTTGAGCAGAGAGT 60.898 55.000 0.00 0.00 34.23 3.24
929 974 2.711922 GGTGACCACGGCGAGAGAT 61.712 63.158 16.62 0.00 0.00 2.75
1182 1231 1.021202 TAAGAATCGGGGCAATTGCG 58.979 50.000 23.48 10.69 43.26 4.85
1441 1491 4.944317 GGATGTTGAAGAAGAAGGTTAGGG 59.056 45.833 0.00 0.00 0.00 3.53
1443 1493 5.640158 TGTTGAAGAAGAAGGTTAGGGAA 57.360 39.130 0.00 0.00 0.00 3.97
1482 1532 5.362430 ACGACCAATACCCATTTGCAAATAT 59.638 36.000 23.69 14.58 0.00 1.28
2010 2072 9.967346 TCAAATACACCGTGATTTAAATCAAAA 57.033 25.926 28.02 12.93 46.13 2.44
2038 2100 1.811965 TGTCATGGAAAATGTGCCTCG 59.188 47.619 0.00 0.00 0.00 4.63
2045 2107 1.589716 AAAATGTGCCTCGGCTCTGC 61.590 55.000 9.65 0.00 42.51 4.26
2242 2307 4.383118 GCTAGGACAGATGGCAAGACTTTA 60.383 45.833 0.00 0.00 0.00 1.85
2396 2468 7.466746 AGGTTGAAAATGTATGTTGCACTAT 57.533 32.000 0.00 0.00 0.00 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 0.473694 TGGAAGGAGCCTGTTCCTCA 60.474 55.000 2.83 0.00 46.90 3.86
23 24 4.087892 GGAGCAGCGCTGGAAGGA 62.088 66.667 36.47 0.00 39.88 3.36
238 252 0.877649 CGGCGCGTAGTAGGAGTAGA 60.878 60.000 8.43 0.00 0.00 2.59
332 346 2.110420 GCACGTAGTATGGCCCCC 59.890 66.667 0.00 0.00 41.61 5.40
333 347 2.110420 GGCACGTAGTATGGCCCC 59.890 66.667 0.00 0.00 41.61 5.80
339 353 1.202336 GCGTAGTTGGGCACGTAGTAT 60.202 52.381 0.00 0.00 41.61 2.12
399 413 3.251004 CGTCATCGATCAGTCACTGGATA 59.749 47.826 4.57 0.00 39.71 2.59
440 454 3.834447 TTGGACGTGGACGCAGACG 62.834 63.158 0.00 0.00 44.43 4.18
441 455 2.028484 TTGGACGTGGACGCAGAC 59.972 61.111 0.00 0.00 44.43 3.51
442 456 2.028484 GTTGGACGTGGACGCAGA 59.972 61.111 0.00 0.00 44.43 4.26
443 457 3.403057 CGTTGGACGTGGACGCAG 61.403 66.667 0.00 0.00 44.43 5.18
446 460 4.953868 TGGCGTTGGACGTGGACG 62.954 66.667 0.00 0.97 44.73 4.79
447 461 3.343421 GTGGCGTTGGACGTGGAC 61.343 66.667 0.00 0.00 44.73 4.02
448 462 4.612412 GGTGGCGTTGGACGTGGA 62.612 66.667 0.00 0.00 44.73 4.02
449 463 4.619227 AGGTGGCGTTGGACGTGG 62.619 66.667 0.00 0.00 44.73 4.94
450 464 3.041940 GAGGTGGCGTTGGACGTG 61.042 66.667 0.00 0.00 44.73 4.49
451 465 4.309950 GGAGGTGGCGTTGGACGT 62.310 66.667 0.00 0.00 44.73 4.34
452 466 4.308458 TGGAGGTGGCGTTGGACG 62.308 66.667 0.00 0.00 45.88 4.79
453 467 2.358737 CTGGAGGTGGCGTTGGAC 60.359 66.667 0.00 0.00 0.00 4.02
454 468 2.391724 GAACTGGAGGTGGCGTTGGA 62.392 60.000 0.00 0.00 0.00 3.53
455 469 1.966451 GAACTGGAGGTGGCGTTGG 60.966 63.158 0.00 0.00 0.00 3.77
456 470 1.966451 GGAACTGGAGGTGGCGTTG 60.966 63.158 0.00 0.00 0.00 4.10
457 471 2.397413 CTGGAACTGGAGGTGGCGTT 62.397 60.000 0.00 0.00 0.00 4.84
458 472 2.847234 TGGAACTGGAGGTGGCGT 60.847 61.111 0.00 0.00 0.00 5.68
459 473 2.046892 CTGGAACTGGAGGTGGCG 60.047 66.667 0.00 0.00 0.00 5.69
460 474 0.178990 AAACTGGAACTGGAGGTGGC 60.179 55.000 0.00 0.00 0.00 5.01
461 475 2.364972 AAAACTGGAACTGGAGGTGG 57.635 50.000 0.00 0.00 0.00 4.61
462 476 5.123979 GCTAATAAAACTGGAACTGGAGGTG 59.876 44.000 0.00 0.00 0.00 4.00
463 477 5.254115 GCTAATAAAACTGGAACTGGAGGT 58.746 41.667 0.00 0.00 0.00 3.85
464 478 4.640647 GGCTAATAAAACTGGAACTGGAGG 59.359 45.833 0.00 0.00 0.00 4.30
465 479 4.640647 GGGCTAATAAAACTGGAACTGGAG 59.359 45.833 0.00 0.00 0.00 3.86
466 480 4.291249 AGGGCTAATAAAACTGGAACTGGA 59.709 41.667 0.00 0.00 0.00 3.86
467 481 4.600062 AGGGCTAATAAAACTGGAACTGG 58.400 43.478 0.00 0.00 0.00 4.00
468 482 4.640647 GGAGGGCTAATAAAACTGGAACTG 59.359 45.833 0.00 0.00 0.00 3.16
469 483 4.540502 AGGAGGGCTAATAAAACTGGAACT 59.459 41.667 0.00 0.00 0.00 3.01
470 484 4.856509 AGGAGGGCTAATAAAACTGGAAC 58.143 43.478 0.00 0.00 0.00 3.62
471 485 6.841781 ATAGGAGGGCTAATAAAACTGGAA 57.158 37.500 0.00 0.00 0.00 3.53
472 486 9.799223 ATATATAGGAGGGCTAATAAAACTGGA 57.201 33.333 0.00 0.00 0.00 3.86
482 496 9.417561 GTGTGTGTATATATATAGGAGGGCTAA 57.582 37.037 2.53 0.00 0.00 3.09
483 497 7.718314 CGTGTGTGTATATATATAGGAGGGCTA 59.282 40.741 2.53 0.00 0.00 3.93
484 498 6.546403 CGTGTGTGTATATATATAGGAGGGCT 59.454 42.308 2.53 0.00 0.00 5.19
485 499 6.544931 TCGTGTGTGTATATATATAGGAGGGC 59.455 42.308 2.53 0.00 0.00 5.19
486 500 8.693120 ATCGTGTGTGTATATATATAGGAGGG 57.307 38.462 2.53 0.00 0.00 4.30
507 521 2.932614 GAGTTCTGCTTGCACATATCGT 59.067 45.455 0.00 0.00 0.00 3.73
508 522 2.931969 TGAGTTCTGCTTGCACATATCG 59.068 45.455 0.00 0.00 0.00 2.92
509 523 4.573607 TCATGAGTTCTGCTTGCACATATC 59.426 41.667 0.00 0.00 0.00 1.63
510 524 4.520179 TCATGAGTTCTGCTTGCACATAT 58.480 39.130 0.00 0.00 0.00 1.78
511 525 3.937079 CTCATGAGTTCTGCTTGCACATA 59.063 43.478 14.95 0.00 0.00 2.29
512 526 2.747989 CTCATGAGTTCTGCTTGCACAT 59.252 45.455 14.95 0.00 0.00 3.21
513 527 2.148768 CTCATGAGTTCTGCTTGCACA 58.851 47.619 14.95 0.00 0.00 4.57
514 528 1.467734 CCTCATGAGTTCTGCTTGCAC 59.532 52.381 21.11 0.00 0.00 4.57
515 529 1.072806 ACCTCATGAGTTCTGCTTGCA 59.927 47.619 21.11 0.00 0.00 4.08
516 530 1.467734 CACCTCATGAGTTCTGCTTGC 59.532 52.381 21.11 0.00 0.00 4.01
517 531 1.467734 GCACCTCATGAGTTCTGCTTG 59.532 52.381 21.11 5.94 0.00 4.01
518 532 1.350351 AGCACCTCATGAGTTCTGCTT 59.650 47.619 24.05 14.05 31.65 3.91
519 533 0.982704 AGCACCTCATGAGTTCTGCT 59.017 50.000 24.05 24.05 31.15 4.24
520 534 2.680312 TAGCACCTCATGAGTTCTGC 57.320 50.000 21.11 21.26 0.00 4.26
521 535 3.181482 ACGATAGCACCTCATGAGTTCTG 60.181 47.826 21.11 13.53 42.67 3.02
522 536 3.027412 ACGATAGCACCTCATGAGTTCT 58.973 45.455 21.11 15.65 42.67 3.01
523 537 3.376540 GACGATAGCACCTCATGAGTTC 58.623 50.000 21.11 9.56 42.67 3.01
524 538 2.223595 CGACGATAGCACCTCATGAGTT 60.224 50.000 21.11 4.13 42.67 3.01
525 539 1.335182 CGACGATAGCACCTCATGAGT 59.665 52.381 21.11 6.95 42.67 3.41
526 540 1.335182 ACGACGATAGCACCTCATGAG 59.665 52.381 16.24 16.24 42.67 2.90
527 541 1.389555 ACGACGATAGCACCTCATGA 58.610 50.000 0.00 0.00 42.67 3.07
528 542 2.209838 AACGACGATAGCACCTCATG 57.790 50.000 0.00 0.00 42.67 3.07
529 543 2.961526 AAACGACGATAGCACCTCAT 57.038 45.000 0.00 0.00 42.67 2.90
530 544 2.751259 ACTAAACGACGATAGCACCTCA 59.249 45.455 0.00 0.00 42.67 3.86
531 545 3.417690 ACTAAACGACGATAGCACCTC 57.582 47.619 0.00 0.00 42.67 3.85
532 546 3.428589 GGAACTAAACGACGATAGCACCT 60.429 47.826 0.00 0.00 42.67 4.00
533 547 2.856557 GGAACTAAACGACGATAGCACC 59.143 50.000 0.00 7.18 42.67 5.01
534 548 3.504863 TGGAACTAAACGACGATAGCAC 58.495 45.455 0.00 2.17 42.67 4.40
535 549 3.853831 TGGAACTAAACGACGATAGCA 57.146 42.857 0.00 0.00 42.67 3.49
536 550 4.031426 CAGTTGGAACTAAACGACGATAGC 59.969 45.833 0.00 0.00 37.08 2.97
537 551 5.396484 TCAGTTGGAACTAAACGACGATAG 58.604 41.667 0.00 6.38 37.08 2.08
538 552 5.375417 TCAGTTGGAACTAAACGACGATA 57.625 39.130 0.00 0.00 37.08 2.92
539 553 4.247267 TCAGTTGGAACTAAACGACGAT 57.753 40.909 0.00 0.00 37.08 3.73
540 554 3.713858 TCAGTTGGAACTAAACGACGA 57.286 42.857 0.00 0.00 37.08 4.20
541 555 3.985279 TCATCAGTTGGAACTAAACGACG 59.015 43.478 0.00 0.00 37.08 5.12
542 556 4.748102 TGTCATCAGTTGGAACTAAACGAC 59.252 41.667 0.00 0.00 37.08 4.34
543 557 4.951254 TGTCATCAGTTGGAACTAAACGA 58.049 39.130 0.00 0.00 37.08 3.85
544 558 5.862924 ATGTCATCAGTTGGAACTAAACG 57.137 39.130 0.00 0.00 37.08 3.60
545 559 7.907214 ACTATGTCATCAGTTGGAACTAAAC 57.093 36.000 0.00 0.00 37.08 2.01
546 560 8.590204 TGTACTATGTCATCAGTTGGAACTAAA 58.410 33.333 0.00 0.00 37.08 1.85
547 561 8.129496 TGTACTATGTCATCAGTTGGAACTAA 57.871 34.615 0.00 0.00 37.08 2.24
548 562 7.712204 TGTACTATGTCATCAGTTGGAACTA 57.288 36.000 0.00 0.00 37.08 2.24
549 563 6.605471 TGTACTATGTCATCAGTTGGAACT 57.395 37.500 0.00 0.00 40.60 3.01
550 564 7.334421 ACATTGTACTATGTCATCAGTTGGAAC 59.666 37.037 15.90 0.00 33.58 3.62
551 565 7.394016 ACATTGTACTATGTCATCAGTTGGAA 58.606 34.615 15.90 0.00 33.58 3.53
552 566 6.946340 ACATTGTACTATGTCATCAGTTGGA 58.054 36.000 15.90 0.00 33.58 3.53
553 567 8.716646 TTACATTGTACTATGTCATCAGTTGG 57.283 34.615 23.30 0.00 39.39 3.77
555 569 8.883731 GCTTTACATTGTACTATGTCATCAGTT 58.116 33.333 23.30 2.76 39.39 3.16
556 570 8.260818 AGCTTTACATTGTACTATGTCATCAGT 58.739 33.333 23.30 5.93 39.39 3.41
557 571 8.546244 CAGCTTTACATTGTACTATGTCATCAG 58.454 37.037 23.30 15.91 39.39 2.90
558 572 7.011389 GCAGCTTTACATTGTACTATGTCATCA 59.989 37.037 23.30 6.40 39.39 3.07
559 573 7.011389 TGCAGCTTTACATTGTACTATGTCATC 59.989 37.037 23.30 12.70 39.39 2.92
560 574 6.823182 TGCAGCTTTACATTGTACTATGTCAT 59.177 34.615 23.30 5.37 39.39 3.06
561 575 6.169800 TGCAGCTTTACATTGTACTATGTCA 58.830 36.000 23.30 12.35 39.39 3.58
562 576 6.662414 TGCAGCTTTACATTGTACTATGTC 57.338 37.500 23.30 11.34 39.39 3.06
563 577 6.655003 AGTTGCAGCTTTACATTGTACTATGT 59.345 34.615 23.19 23.19 41.43 2.29
564 578 7.076842 AGTTGCAGCTTTACATTGTACTATG 57.923 36.000 14.63 14.63 0.00 2.23
565 579 6.878923 TGAGTTGCAGCTTTACATTGTACTAT 59.121 34.615 3.97 0.00 0.00 2.12
566 580 6.147164 GTGAGTTGCAGCTTTACATTGTACTA 59.853 38.462 3.97 0.00 0.00 1.82
567 581 5.049405 GTGAGTTGCAGCTTTACATTGTACT 60.049 40.000 3.97 0.00 0.00 2.73
568 582 5.049405 AGTGAGTTGCAGCTTTACATTGTAC 60.049 40.000 16.92 0.00 0.00 2.90
569 583 5.063204 AGTGAGTTGCAGCTTTACATTGTA 58.937 37.500 16.92 0.00 0.00 2.41
570 584 3.885297 AGTGAGTTGCAGCTTTACATTGT 59.115 39.130 16.92 0.00 0.00 2.71
571 585 4.494350 AGTGAGTTGCAGCTTTACATTG 57.506 40.909 16.92 0.00 0.00 2.82
572 586 6.824305 ATTAGTGAGTTGCAGCTTTACATT 57.176 33.333 16.92 6.40 0.00 2.71
573 587 7.921786 TTATTAGTGAGTTGCAGCTTTACAT 57.078 32.000 16.92 8.41 0.00 2.29
574 588 7.737972 TTTATTAGTGAGTTGCAGCTTTACA 57.262 32.000 16.92 4.44 0.00 2.41
575 589 9.118236 CTTTTTATTAGTGAGTTGCAGCTTTAC 57.882 33.333 3.97 7.60 0.00 2.01
576 590 8.296713 CCTTTTTATTAGTGAGTTGCAGCTTTA 58.703 33.333 3.97 0.00 0.00 1.85
577 591 7.147976 CCTTTTTATTAGTGAGTTGCAGCTTT 58.852 34.615 3.97 0.00 0.00 3.51
578 592 6.294731 CCCTTTTTATTAGTGAGTTGCAGCTT 60.295 38.462 3.97 0.00 0.00 3.74
579 593 5.183904 CCCTTTTTATTAGTGAGTTGCAGCT 59.816 40.000 1.30 1.30 0.00 4.24
580 594 5.048013 ACCCTTTTTATTAGTGAGTTGCAGC 60.048 40.000 0.00 0.00 0.00 5.25
581 595 6.575162 ACCCTTTTTATTAGTGAGTTGCAG 57.425 37.500 0.00 0.00 0.00 4.41
582 596 6.969993 AACCCTTTTTATTAGTGAGTTGCA 57.030 33.333 0.00 0.00 0.00 4.08
583 597 9.923143 AATTAACCCTTTTTATTAGTGAGTTGC 57.077 29.630 0.00 0.00 0.00 4.17
595 609 9.727859 GGGCAAAAAGATAATTAACCCTTTTTA 57.272 29.630 22.09 0.00 43.06 1.52
596 610 8.444783 AGGGCAAAAAGATAATTAACCCTTTTT 58.555 29.630 19.53 19.53 42.56 1.94
597 611 7.984475 AGGGCAAAAAGATAATTAACCCTTTT 58.016 30.769 13.36 13.36 42.56 2.27
627 641 4.275936 GGCAAAACTGAGTACATGAACACT 59.724 41.667 0.00 0.00 0.00 3.55
632 646 3.072330 TGAGGGCAAAACTGAGTACATGA 59.928 43.478 0.00 0.00 0.00 3.07
658 672 2.287547 GGCAAAACTGAGCACAATTCGA 60.288 45.455 0.00 0.00 0.00 3.71
706 720 1.001597 ACGAAGACGACAGAGTTCACC 60.002 52.381 0.00 0.00 42.66 4.02
832 861 1.056103 CAACGACTCTCTGCTCAACG 58.944 55.000 0.00 0.00 0.00 4.10
833 862 1.423395 CCAACGACTCTCTGCTCAAC 58.577 55.000 0.00 0.00 0.00 3.18
834 863 0.319900 GCCAACGACTCTCTGCTCAA 60.320 55.000 0.00 0.00 0.00 3.02
835 864 1.290324 GCCAACGACTCTCTGCTCA 59.710 57.895 0.00 0.00 0.00 4.26
836 865 1.803519 CGCCAACGACTCTCTGCTC 60.804 63.158 0.00 0.00 43.93 4.26
837 866 2.259818 CGCCAACGACTCTCTGCT 59.740 61.111 0.00 0.00 43.93 4.24
838 867 2.811317 CCGCCAACGACTCTCTGC 60.811 66.667 0.00 0.00 43.93 4.26
839 868 2.125912 CCCGCCAACGACTCTCTG 60.126 66.667 0.00 0.00 43.93 3.35
840 869 2.600769 ACCCGCCAACGACTCTCT 60.601 61.111 0.00 0.00 43.93 3.10
841 870 2.432628 CACCCGCCAACGACTCTC 60.433 66.667 0.00 0.00 43.93 3.20
842 871 3.231736 ACACCCGCCAACGACTCT 61.232 61.111 0.00 0.00 43.93 3.24
843 872 3.041940 CACACCCGCCAACGACTC 61.042 66.667 0.00 0.00 43.93 3.36
845 874 3.750077 TATAGCACACCCGCCAACGAC 62.750 57.143 0.00 0.00 43.93 4.34
846 875 1.605971 TATAGCACACCCGCCAACGA 61.606 55.000 0.00 0.00 43.93 3.85
887 930 2.126307 CTCTCTGTCGCCGTGGTG 60.126 66.667 0.00 0.00 0.00 4.17
1099 1148 1.353091 GGTGTCTGAGAAACCCTCCT 58.647 55.000 10.88 0.00 41.25 3.69
1182 1231 1.029947 ATCCCGACCACGAAAATGGC 61.030 55.000 0.00 0.00 44.33 4.40
1460 1510 8.504812 AAAATATTTGCAAATGGGTATTGGTC 57.495 30.769 30.43 0.00 0.00 4.02
1482 1532 4.841246 ACCATACCTACAAATGCCCAAAAA 59.159 37.500 0.00 0.00 0.00 1.94
2010 2072 5.239087 GCACATTTTCCATGACATTTTGGTT 59.761 36.000 0.00 0.00 34.48 3.67
2038 2100 1.803252 GCGTAAACCTCTAGCAGAGCC 60.803 57.143 7.44 0.00 40.98 4.70
2045 2107 1.739371 GCACCTGGCGTAAACCTCTAG 60.739 57.143 0.00 0.00 0.00 2.43
2242 2307 1.923148 CCTTCCTTCCCTACCCATGTT 59.077 52.381 0.00 0.00 0.00 2.71
2297 2364 2.229792 GCAAACATTCAGGGTCTCACA 58.770 47.619 0.00 0.00 0.00 3.58
2306 2377 0.316937 ACGCGTGTGCAAACATTCAG 60.317 50.000 12.93 0.00 42.97 3.02
2396 2468 4.074259 CCACTCTGACCAAAATCATGTGA 58.926 43.478 0.00 0.00 36.16 3.58
2514 2591 0.252742 AATCGGAGGGGGTGAGAAGT 60.253 55.000 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.