Multiple sequence alignment - TraesCS6B01G043200

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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 TraesCS6B01G043200 chr6B 100.000 2798 0 0 1 2798 26305804 26303007 0.000000e+00 5168.0
1 TraesCS6B01G043200 chr6B 80.418 766 140 7 1034 1792 26399270 26398508 2.420000e-160 575.0
2 TraesCS6B01G043200 chr6B 79.877 651 113 13 1063 1701 143660868 143661512 7.060000e-126 460.0
3 TraesCS6B01G043200 chr6D 94.050 1664 87 5 1145 2798 14468965 14467304 0.000000e+00 2514.0
4 TraesCS6B01G043200 chr6D 92.199 987 71 4 689 1672 14479960 14478977 0.000000e+00 1391.0
5 TraesCS6B01G043200 chr6D 90.973 565 43 6 589 1149 14478058 14477498 0.000000e+00 754.0
6 TraesCS6B01G043200 chr6D 79.719 784 142 12 1022 1792 14900503 14901282 4.070000e-153 551.0
7 TraesCS6B01G043200 chr6A 93.036 1120 70 7 808 1922 15916056 15917172 0.000000e+00 1629.0
8 TraesCS6B01G043200 chr6A 81.638 806 140 7 994 1793 15656176 15655373 0.000000e+00 662.0
9 TraesCS6B01G043200 chr6A 92.442 172 13 0 589 760 15915892 15916063 2.150000e-61 246.0
10 TraesCS6B01G043200 chr6A 96.667 60 2 0 1944 2003 15917570 15917629 1.770000e-17 100.0
11 TraesCS6B01G043200 chr2D 92.607 798 54 4 2005 2798 550680652 550681448 0.000000e+00 1142.0
12 TraesCS6B01G043200 chrUn 92.365 799 55 5 2005 2798 89173840 89174637 0.000000e+00 1133.0
13 TraesCS6B01G043200 chrUn 92.115 799 57 5 2005 2798 90644360 90643563 0.000000e+00 1122.0
14 TraesCS6B01G043200 chr5D 92.365 799 55 4 2005 2798 438087975 438088772 0.000000e+00 1133.0
15 TraesCS6B01G043200 chr5D 92.115 799 57 5 2005 2798 174785177 174785974 0.000000e+00 1122.0
16 TraesCS6B01G043200 chr5D 93.489 599 24 11 1 589 498552061 498552654 0.000000e+00 876.0
17 TraesCS6B01G043200 chr3D 92.365 799 55 5 2005 2798 510987041 510986244 0.000000e+00 1133.0
18 TraesCS6B01G043200 chr3D 79.130 690 132 8 1109 1793 554056715 554056033 1.520000e-127 466.0
19 TraesCS6B01G043200 chr7D 92.240 799 56 5 2005 2798 566143819 566143022 0.000000e+00 1127.0
20 TraesCS6B01G043200 chr4D 92.240 799 56 4 2005 2798 496924587 496923790 0.000000e+00 1127.0
21 TraesCS6B01G043200 chr5A 91.869 578 26 6 1 559 18660806 18660231 0.000000e+00 787.0
22 TraesCS6B01G043200 chr5B 80.000 730 136 9 1072 1793 457930885 457930158 5.310000e-147 531.0
23 TraesCS6B01G043200 chr3B 78.543 741 141 12 1063 1793 735814845 735814113 3.260000e-129 472.0
24 TraesCS6B01G043200 chr4A 90.566 53 5 0 3 55 657891700 657891648 1.390000e-08 71.3
25 TraesCS6B01G043200 chr4B 87.097 62 7 1 3 64 377688987 377689047 5.000000e-08 69.4


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 TraesCS6B01G043200 chr6B 26303007 26305804 2797 True 5168.000000 5168 100.000000 1 2798 1 chr6B.!!$R1 2797
1 TraesCS6B01G043200 chr6B 26398508 26399270 762 True 575.000000 575 80.418000 1034 1792 1 chr6B.!!$R2 758
2 TraesCS6B01G043200 chr6B 143660868 143661512 644 False 460.000000 460 79.877000 1063 1701 1 chr6B.!!$F1 638
3 TraesCS6B01G043200 chr6D 14467304 14468965 1661 True 2514.000000 2514 94.050000 1145 2798 1 chr6D.!!$R1 1653
4 TraesCS6B01G043200 chr6D 14477498 14479960 2462 True 1072.500000 1391 91.586000 589 1672 2 chr6D.!!$R2 1083
5 TraesCS6B01G043200 chr6D 14900503 14901282 779 False 551.000000 551 79.719000 1022 1792 1 chr6D.!!$F1 770
6 TraesCS6B01G043200 chr6A 15655373 15656176 803 True 662.000000 662 81.638000 994 1793 1 chr6A.!!$R1 799
7 TraesCS6B01G043200 chr6A 15915892 15917629 1737 False 658.333333 1629 94.048333 589 2003 3 chr6A.!!$F1 1414
8 TraesCS6B01G043200 chr2D 550680652 550681448 796 False 1142.000000 1142 92.607000 2005 2798 1 chr2D.!!$F1 793
9 TraesCS6B01G043200 chrUn 89173840 89174637 797 False 1133.000000 1133 92.365000 2005 2798 1 chrUn.!!$F1 793
10 TraesCS6B01G043200 chrUn 90643563 90644360 797 True 1122.000000 1122 92.115000 2005 2798 1 chrUn.!!$R1 793
11 TraesCS6B01G043200 chr5D 438087975 438088772 797 False 1133.000000 1133 92.365000 2005 2798 1 chr5D.!!$F2 793
12 TraesCS6B01G043200 chr5D 174785177 174785974 797 False 1122.000000 1122 92.115000 2005 2798 1 chr5D.!!$F1 793
13 TraesCS6B01G043200 chr5D 498552061 498552654 593 False 876.000000 876 93.489000 1 589 1 chr5D.!!$F3 588
14 TraesCS6B01G043200 chr3D 510986244 510987041 797 True 1133.000000 1133 92.365000 2005 2798 1 chr3D.!!$R1 793
15 TraesCS6B01G043200 chr3D 554056033 554056715 682 True 466.000000 466 79.130000 1109 1793 1 chr3D.!!$R2 684
16 TraesCS6B01G043200 chr7D 566143022 566143819 797 True 1127.000000 1127 92.240000 2005 2798 1 chr7D.!!$R1 793
17 TraesCS6B01G043200 chr4D 496923790 496924587 797 True 1127.000000 1127 92.240000 2005 2798 1 chr4D.!!$R1 793
18 TraesCS6B01G043200 chr5A 18660231 18660806 575 True 787.000000 787 91.869000 1 559 1 chr5A.!!$R1 558
19 TraesCS6B01G043200 chr5B 457930158 457930885 727 True 531.000000 531 80.000000 1072 1793 1 chr5B.!!$R1 721
20 TraesCS6B01G043200 chr3B 735814113 735814845 732 True 472.000000 472 78.543000 1063 1793 1 chr3B.!!$R1 730

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
535 555 0.171231 TGAAGACCAGCACTCGATCG 59.829 55.0 9.36 9.36 0.0 3.69 F
538 558 0.171455 AGACCAGCACTCGATCGAAC 59.829 55.0 19.92 11.47 0.0 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1428 1459 0.245266 TCAATCTTGTACCGCTCGCA 59.755 50.0 0.0 0.0 0.0 5.10 R
2209 2713 0.738389 ATATTTTTGACTGCGGCCCG 59.262 50.0 0.0 0.0 0.0 6.13 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
194 214 5.977129 CAGTTGGTACTTTCTTTTGCGAATT 59.023 36.000 0.00 0.00 30.26 2.17
239 259 5.876357 TGACATTATAAGAACCATAGCCCC 58.124 41.667 0.00 0.00 0.00 5.80
389 409 4.142752 TGGACTCGTGATCTACAGTAAACG 60.143 45.833 0.00 0.00 0.00 3.60
415 435 0.819582 CATGTGCCAACCCATCCTTC 59.180 55.000 0.00 0.00 0.00 3.46
480 500 7.390718 TGACAAAGAGGAGAATTAAGCTAAACC 59.609 37.037 0.00 0.00 0.00 3.27
485 505 6.154706 AGAGGAGAATTAAGCTAAACCGAGAA 59.845 38.462 0.00 0.00 0.00 2.87
486 506 6.708285 AGGAGAATTAAGCTAAACCGAGAAA 58.292 36.000 0.00 0.00 0.00 2.52
487 507 7.339482 AGGAGAATTAAGCTAAACCGAGAAAT 58.661 34.615 0.00 0.00 0.00 2.17
488 508 7.829706 AGGAGAATTAAGCTAAACCGAGAAATT 59.170 33.333 0.00 0.00 0.00 1.82
489 509 8.459635 GGAGAATTAAGCTAAACCGAGAAATTT 58.540 33.333 0.00 0.00 0.00 1.82
490 510 9.278734 GAGAATTAAGCTAAACCGAGAAATTTG 57.721 33.333 0.00 0.00 0.00 2.32
491 511 9.010029 AGAATTAAGCTAAACCGAGAAATTTGA 57.990 29.630 0.00 0.00 0.00 2.69
492 512 9.620660 GAATTAAGCTAAACCGAGAAATTTGAA 57.379 29.630 0.00 0.00 0.00 2.69
494 514 8.964420 TTAAGCTAAACCGAGAAATTTGAATG 57.036 30.769 0.00 0.00 0.00 2.67
495 515 5.402398 AGCTAAACCGAGAAATTTGAATGC 58.598 37.500 0.00 0.00 0.00 3.56
496 516 5.183904 AGCTAAACCGAGAAATTTGAATGCT 59.816 36.000 0.00 0.00 0.00 3.79
497 517 6.374333 AGCTAAACCGAGAAATTTGAATGCTA 59.626 34.615 0.00 0.00 0.00 3.49
498 518 7.027161 GCTAAACCGAGAAATTTGAATGCTAA 58.973 34.615 0.00 0.00 0.00 3.09
499 519 7.008357 GCTAAACCGAGAAATTTGAATGCTAAC 59.992 37.037 0.00 0.00 0.00 2.34
500 520 6.575162 AACCGAGAAATTTGAATGCTAACT 57.425 33.333 0.00 0.00 0.00 2.24
501 521 7.681939 AACCGAGAAATTTGAATGCTAACTA 57.318 32.000 0.00 0.00 0.00 2.24
502 522 7.865706 ACCGAGAAATTTGAATGCTAACTAT 57.134 32.000 0.00 0.00 0.00 2.12
503 523 7.697691 ACCGAGAAATTTGAATGCTAACTATG 58.302 34.615 0.00 0.00 0.00 2.23
504 524 6.634436 CCGAGAAATTTGAATGCTAACTATGC 59.366 38.462 0.00 0.00 0.00 3.14
505 525 7.188834 CGAGAAATTTGAATGCTAACTATGCA 58.811 34.615 0.00 0.00 44.95 3.96
506 526 7.164826 CGAGAAATTTGAATGCTAACTATGCAC 59.835 37.037 0.00 0.00 43.59 4.57
507 527 7.829725 AGAAATTTGAATGCTAACTATGCACA 58.170 30.769 0.00 0.00 43.59 4.57
508 528 8.306038 AGAAATTTGAATGCTAACTATGCACAA 58.694 29.630 0.00 0.00 43.59 3.33
509 529 8.830201 AAATTTGAATGCTAACTATGCACAAA 57.170 26.923 0.00 0.00 43.59 2.83
510 530 9.439500 AAATTTGAATGCTAACTATGCACAAAT 57.561 25.926 9.77 9.77 42.96 2.32
511 531 8.638685 ATTTGAATGCTAACTATGCACAAATC 57.361 30.769 9.77 1.07 40.12 2.17
512 532 6.135290 TGAATGCTAACTATGCACAAATCC 57.865 37.500 0.00 0.00 43.59 3.01
513 533 5.651576 TGAATGCTAACTATGCACAAATCCA 59.348 36.000 0.00 0.00 43.59 3.41
514 534 4.963276 TGCTAACTATGCACAAATCCAC 57.037 40.909 0.00 0.00 35.31 4.02
515 535 4.331108 TGCTAACTATGCACAAATCCACA 58.669 39.130 0.00 0.00 35.31 4.17
516 536 4.949238 TGCTAACTATGCACAAATCCACAT 59.051 37.500 0.00 0.00 35.31 3.21
517 537 5.163632 TGCTAACTATGCACAAATCCACATG 60.164 40.000 0.00 0.00 35.31 3.21
518 538 5.066375 GCTAACTATGCACAAATCCACATGA 59.934 40.000 0.00 0.00 0.00 3.07
519 539 5.981088 AACTATGCACAAATCCACATGAA 57.019 34.783 0.00 0.00 0.00 2.57
520 540 5.571784 ACTATGCACAAATCCACATGAAG 57.428 39.130 0.00 0.00 0.00 3.02
521 541 5.255687 ACTATGCACAAATCCACATGAAGA 58.744 37.500 0.00 0.00 0.00 2.87
522 542 3.921119 TGCACAAATCCACATGAAGAC 57.079 42.857 0.00 0.00 0.00 3.01
523 543 2.557924 TGCACAAATCCACATGAAGACC 59.442 45.455 0.00 0.00 0.00 3.85
524 544 2.557924 GCACAAATCCACATGAAGACCA 59.442 45.455 0.00 0.00 0.00 4.02
525 545 3.366679 GCACAAATCCACATGAAGACCAG 60.367 47.826 0.00 0.00 0.00 4.00
526 546 2.821969 ACAAATCCACATGAAGACCAGC 59.178 45.455 0.00 0.00 0.00 4.85
527 547 2.821378 CAAATCCACATGAAGACCAGCA 59.179 45.455 0.00 0.00 0.00 4.41
528 548 2.119801 ATCCACATGAAGACCAGCAC 57.880 50.000 0.00 0.00 0.00 4.40
529 549 1.059098 TCCACATGAAGACCAGCACT 58.941 50.000 0.00 0.00 0.00 4.40
530 550 1.002430 TCCACATGAAGACCAGCACTC 59.998 52.381 0.00 0.00 0.00 3.51
531 551 1.073964 CACATGAAGACCAGCACTCG 58.926 55.000 0.00 0.00 0.00 4.18
532 552 0.969149 ACATGAAGACCAGCACTCGA 59.031 50.000 0.00 0.00 0.00 4.04
533 553 1.552337 ACATGAAGACCAGCACTCGAT 59.448 47.619 0.00 0.00 0.00 3.59
534 554 2.200067 CATGAAGACCAGCACTCGATC 58.800 52.381 0.00 0.00 0.00 3.69
535 555 0.171231 TGAAGACCAGCACTCGATCG 59.829 55.000 9.36 9.36 0.00 3.69
536 556 0.452184 GAAGACCAGCACTCGATCGA 59.548 55.000 18.32 18.32 0.00 3.59
537 557 0.888619 AAGACCAGCACTCGATCGAA 59.111 50.000 19.92 3.18 0.00 3.71
538 558 0.171455 AGACCAGCACTCGATCGAAC 59.829 55.000 19.92 11.47 0.00 3.95
539 559 1.134530 GACCAGCACTCGATCGAACG 61.135 60.000 19.92 13.65 0.00 3.95
540 560 1.874019 CCAGCACTCGATCGAACGG 60.874 63.158 19.92 10.25 0.00 4.44
541 561 2.202623 AGCACTCGATCGAACGGC 60.203 61.111 19.92 20.60 0.00 5.68
542 562 2.506217 GCACTCGATCGAACGGCA 60.506 61.111 19.92 0.00 0.00 5.69
543 563 2.789203 GCACTCGATCGAACGGCAC 61.789 63.158 19.92 2.10 0.00 5.01
544 564 2.158959 CACTCGATCGAACGGCACC 61.159 63.158 19.92 0.00 0.00 5.01
545 565 2.582498 CTCGATCGAACGGCACCC 60.582 66.667 19.92 0.00 0.00 4.61
546 566 3.350909 CTCGATCGAACGGCACCCA 62.351 63.158 19.92 0.00 0.00 4.51
547 567 3.186047 CGATCGAACGGCACCCAC 61.186 66.667 10.26 0.00 0.00 4.61
548 568 2.818274 GATCGAACGGCACCCACC 60.818 66.667 0.00 0.00 0.00 4.61
549 569 3.599285 GATCGAACGGCACCCACCA 62.599 63.158 0.00 0.00 0.00 4.17
550 570 2.869503 GATCGAACGGCACCCACCAT 62.870 60.000 0.00 0.00 0.00 3.55
551 571 3.430862 CGAACGGCACCCACCATG 61.431 66.667 0.00 0.00 0.00 3.66
552 572 3.061848 GAACGGCACCCACCATGG 61.062 66.667 11.19 11.19 37.25 3.66
561 581 2.819595 CCACCATGGGTTCGAGCG 60.820 66.667 18.09 0.00 31.02 5.03
562 582 2.819595 CACCATGGGTTCGAGCGG 60.820 66.667 18.09 0.00 31.02 5.52
563 583 3.000819 ACCATGGGTTCGAGCGGA 61.001 61.111 18.09 0.00 27.29 5.54
564 584 2.511600 CCATGGGTTCGAGCGGAC 60.512 66.667 2.85 0.00 0.00 4.79
565 585 2.511600 CATGGGTTCGAGCGGACC 60.512 66.667 11.88 11.88 0.00 4.46
566 586 3.000819 ATGGGTTCGAGCGGACCA 61.001 61.111 20.91 12.00 35.39 4.02
567 587 2.367202 ATGGGTTCGAGCGGACCAT 61.367 57.895 20.91 13.54 37.12 3.55
568 588 2.511600 GGGTTCGAGCGGACCATG 60.512 66.667 20.91 0.00 0.00 3.66
569 589 2.511600 GGTTCGAGCGGACCATGG 60.512 66.667 15.20 11.19 0.00 3.66
570 590 2.264794 GTTCGAGCGGACCATGGT 59.735 61.111 19.89 19.89 0.00 3.55
571 591 1.810030 GTTCGAGCGGACCATGGTC 60.810 63.158 33.14 33.14 43.87 4.02
580 600 2.695314 GACCATGGTCCTGAATCGC 58.305 57.895 31.37 6.14 39.08 4.58
581 601 0.179000 GACCATGGTCCTGAATCGCT 59.821 55.000 31.37 0.00 39.08 4.93
582 602 0.620556 ACCATGGTCCTGAATCGCTT 59.379 50.000 13.00 0.00 0.00 4.68
583 603 1.019673 CCATGGTCCTGAATCGCTTG 58.980 55.000 2.57 0.00 0.00 4.01
584 604 1.679944 CCATGGTCCTGAATCGCTTGT 60.680 52.381 2.57 0.00 0.00 3.16
585 605 1.667724 CATGGTCCTGAATCGCTTGTC 59.332 52.381 0.00 0.00 0.00 3.18
586 606 0.976641 TGGTCCTGAATCGCTTGTCT 59.023 50.000 0.00 0.00 0.00 3.41
587 607 1.066858 TGGTCCTGAATCGCTTGTCTC 60.067 52.381 0.00 0.00 0.00 3.36
604 624 3.450817 TGTCTCGAAAATCATCAGGCCTA 59.549 43.478 3.98 0.00 0.00 3.93
605 625 4.054671 GTCTCGAAAATCATCAGGCCTAG 58.945 47.826 3.98 0.00 0.00 3.02
619 639 3.320541 CAGGCCTAGAGTACCTTCATGAG 59.679 52.174 3.98 0.00 0.00 2.90
655 675 3.009140 CACCGTCATCAGCGCATC 58.991 61.111 11.47 0.00 0.00 3.91
657 677 3.333189 CCGTCATCAGCGCATCCG 61.333 66.667 11.47 2.35 37.57 4.18
662 682 1.457303 GTCATCAGCGCATCCGTATTC 59.543 52.381 11.47 0.00 36.67 1.75
733 753 1.583054 AAGGTCTCGCTTTGTGTCAC 58.417 50.000 0.00 0.00 0.00 3.67
753 773 2.492088 ACATGCTGATATGGCATCATGC 59.508 45.455 20.01 0.00 46.94 4.06
760 780 5.587443 GCTGATATGGCATCATGCTATACAA 59.413 40.000 17.24 8.25 46.90 2.41
763 783 8.584063 TGATATGGCATCATGCTATACAATTT 57.416 30.769 17.24 1.97 46.90 1.82
766 786 4.281435 TGGCATCATGCTATACAATTTGGG 59.719 41.667 10.11 0.00 44.28 4.12
804 824 9.403583 ACTAGGTACACTCAAAATCAAAAGAAA 57.596 29.630 0.00 0.00 0.00 2.52
954 977 5.572252 AGCTCCCAGTATAGATAGTACCAC 58.428 45.833 0.00 0.00 0.00 4.16
984 1007 5.938710 ACTAAGCTTTTCTTTACCAGCCTAC 59.061 40.000 3.20 0.00 36.25 3.18
999 1022 1.613255 GCCTACCTTACTTGCCTTGCA 60.613 52.381 0.00 0.00 36.47 4.08
1011 1034 4.099266 ACTTGCCTTGCAACACAGAAATAA 59.901 37.500 0.00 0.00 43.99 1.40
1055 1078 0.607489 GGATGGCAGCAAGTGTGACT 60.607 55.000 4.64 0.00 0.00 3.41
1060 1083 0.319555 GCAGCAAGTGTGACTACCGA 60.320 55.000 0.00 0.00 0.00 4.69
1103 1126 2.949106 CTCACAACGCTGCTTGGG 59.051 61.111 13.62 10.72 0.00 4.12
1115 1138 1.561542 CTGCTTGGGGAGGAGTACAAT 59.438 52.381 0.00 0.00 38.87 2.71
1155 1180 5.091261 GAAGCAAGTATCCTTCCTCAAGA 57.909 43.478 0.00 0.00 33.13 3.02
1173 1198 1.783031 GAATGAGCTCAGCGCCATGG 61.783 60.000 22.96 7.63 40.39 3.66
1385 1416 2.938451 GCATCATCAGATTGTCAACCGA 59.062 45.455 0.00 0.00 30.20 4.69
1428 1459 1.675641 GTGGAGGCAAATGCTCGGT 60.676 57.895 5.25 0.00 41.70 4.69
1512 1543 1.620819 AGGTGTCAGCGATCTTCAAGT 59.379 47.619 0.00 0.00 0.00 3.16
1577 1611 6.371809 GTCAGTTGGTTGACAGATAAACAA 57.628 37.500 1.54 0.00 45.32 2.83
1623 1659 1.340114 GGTTCTGGAGGCTTGGGTAAG 60.340 57.143 0.00 0.00 36.97 2.34
1869 1960 8.903820 ACAATTAGCAGGGTAAATAATTGACTC 58.096 33.333 18.37 0.00 43.47 3.36
1898 1989 7.071950 TCCTTATCTAAGCCCTGCATAGTAAAA 59.928 37.037 0.00 0.00 32.57 1.52
1966 2434 1.001597 CGTCTACTAAGATCCGCCACC 60.002 57.143 0.00 0.00 33.30 4.61
2063 2532 2.749621 GCAAAAATCAGTGTCCTCGGAT 59.250 45.455 0.00 0.00 0.00 4.18
2091 2560 5.005682 CGATGAGCGAGTACAAATGAATGAA 59.994 40.000 0.00 0.00 44.57 2.57
2194 2698 2.162681 GCAGCAGGTACCAAAGTGATT 58.837 47.619 15.94 0.00 0.00 2.57
2196 2700 2.416547 CAGCAGGTACCAAAGTGATTCG 59.583 50.000 15.94 0.00 0.00 3.34
2209 2713 1.743394 GTGATTCGGGATTGGAACACC 59.257 52.381 0.00 0.00 39.29 4.16
2266 2770 7.182026 TCAGAAGGACCAATGATTTACTCCTTA 59.818 37.037 7.45 0.00 38.08 2.69
2534 3041 4.083862 GCTGGACCCGGTGGAGAC 62.084 72.222 0.00 0.00 34.81 3.36
2562 3070 2.093181 TGATAATAGTGGCACGTGGCTT 60.093 45.455 37.33 27.93 44.01 4.35
2573 3082 2.746375 CGTGGCTTGGGCTAGGGAT 61.746 63.158 0.00 0.00 38.73 3.85
2581 3090 2.212752 TGGGCTAGGGATCCATCTTT 57.787 50.000 15.23 0.00 0.00 2.52
2604 3113 6.682423 TGCACCATAAGACAAGACATATTG 57.318 37.500 0.00 0.00 36.22 1.90
2679 3960 2.288579 ACGCAAAGTTCACACGGATCTA 60.289 45.455 0.00 0.00 0.00 1.98
2756 4039 5.011738 ACCGGATAGTCATTGGTATTAGTGG 59.988 44.000 9.46 0.00 0.00 4.00
2772 4055 1.985159 AGTGGAGCCATGTAACTGGAA 59.015 47.619 0.00 0.00 38.69 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 3.428870 ACGTTATTCAACAGAACAGCTCG 59.571 43.478 0.00 0.00 34.05 5.03
118 120 9.672673 AGCAGTTTACTGTTCTTATAATCACAT 57.327 29.630 11.23 0.00 45.45 3.21
135 155 6.535508 AGAATATTCTTCCACGAGCAGTTTAC 59.464 38.462 12.37 0.00 32.55 2.01
235 255 2.622064 AGTTCTTATCATGTCGGGGC 57.378 50.000 0.00 0.00 0.00 5.80
359 379 0.460987 GATCACGAGTCCAAGCCTGG 60.461 60.000 0.00 0.00 45.08 4.45
369 389 5.064452 CCTACGTTTACTGTAGATCACGAGT 59.936 44.000 14.02 1.21 41.44 4.18
373 393 4.735873 GCCCCTACGTTTACTGTAGATCAC 60.736 50.000 0.00 0.00 41.44 3.06
415 435 4.141620 TGCCTAGGCTCATCTTTTTAGGAG 60.142 45.833 33.07 0.00 42.51 3.69
480 500 7.164826 GTGCATAGTTAGCATTCAAATTTCTCG 59.835 37.037 0.00 0.00 44.79 4.04
485 505 9.090692 GATTTGTGCATAGTTAGCATTCAAATT 57.909 29.630 13.99 3.73 43.07 1.82
486 506 7.707893 GGATTTGTGCATAGTTAGCATTCAAAT 59.292 33.333 13.16 13.16 44.38 2.32
487 507 7.035004 GGATTTGTGCATAGTTAGCATTCAAA 58.965 34.615 0.00 0.00 44.79 2.69
488 508 6.152492 TGGATTTGTGCATAGTTAGCATTCAA 59.848 34.615 0.00 0.00 44.79 2.69
489 509 5.651576 TGGATTTGTGCATAGTTAGCATTCA 59.348 36.000 0.00 0.00 44.79 2.57
490 510 5.973565 GTGGATTTGTGCATAGTTAGCATTC 59.026 40.000 0.00 0.00 44.79 2.67
491 511 5.418524 TGTGGATTTGTGCATAGTTAGCATT 59.581 36.000 0.00 0.00 44.79 3.56
492 512 4.949238 TGTGGATTTGTGCATAGTTAGCAT 59.051 37.500 0.00 0.00 44.79 3.79
493 513 4.331108 TGTGGATTTGTGCATAGTTAGCA 58.669 39.130 0.00 0.00 40.19 3.49
494 514 4.963276 TGTGGATTTGTGCATAGTTAGC 57.037 40.909 0.00 0.00 0.00 3.09
495 515 6.682423 TCATGTGGATTTGTGCATAGTTAG 57.318 37.500 0.00 0.00 0.00 2.34
496 516 6.883756 TCTTCATGTGGATTTGTGCATAGTTA 59.116 34.615 0.00 0.00 0.00 2.24
497 517 5.711506 TCTTCATGTGGATTTGTGCATAGTT 59.288 36.000 0.00 0.00 0.00 2.24
498 518 5.124457 GTCTTCATGTGGATTTGTGCATAGT 59.876 40.000 0.00 0.00 0.00 2.12
499 519 5.449588 GGTCTTCATGTGGATTTGTGCATAG 60.450 44.000 0.00 0.00 0.00 2.23
500 520 4.398988 GGTCTTCATGTGGATTTGTGCATA 59.601 41.667 0.00 0.00 0.00 3.14
501 521 3.194116 GGTCTTCATGTGGATTTGTGCAT 59.806 43.478 0.00 0.00 0.00 3.96
502 522 2.557924 GGTCTTCATGTGGATTTGTGCA 59.442 45.455 0.00 0.00 0.00 4.57
503 523 2.557924 TGGTCTTCATGTGGATTTGTGC 59.442 45.455 0.00 0.00 0.00 4.57
504 524 3.366679 GCTGGTCTTCATGTGGATTTGTG 60.367 47.826 0.00 0.00 0.00 3.33
505 525 2.821969 GCTGGTCTTCATGTGGATTTGT 59.178 45.455 0.00 0.00 0.00 2.83
506 526 2.821378 TGCTGGTCTTCATGTGGATTTG 59.179 45.455 0.00 0.00 0.00 2.32
507 527 2.821969 GTGCTGGTCTTCATGTGGATTT 59.178 45.455 0.00 0.00 0.00 2.17
508 528 2.040813 AGTGCTGGTCTTCATGTGGATT 59.959 45.455 0.00 0.00 0.00 3.01
509 529 1.632409 AGTGCTGGTCTTCATGTGGAT 59.368 47.619 0.00 0.00 0.00 3.41
510 530 1.002430 GAGTGCTGGTCTTCATGTGGA 59.998 52.381 0.00 0.00 0.00 4.02
511 531 1.446907 GAGTGCTGGTCTTCATGTGG 58.553 55.000 0.00 0.00 0.00 4.17
512 532 1.073964 CGAGTGCTGGTCTTCATGTG 58.926 55.000 0.00 0.00 0.00 3.21
513 533 0.969149 TCGAGTGCTGGTCTTCATGT 59.031 50.000 0.00 0.00 0.00 3.21
514 534 2.200067 GATCGAGTGCTGGTCTTCATG 58.800 52.381 0.00 0.00 0.00 3.07
515 535 1.202348 CGATCGAGTGCTGGTCTTCAT 60.202 52.381 10.26 0.00 0.00 2.57
516 536 0.171231 CGATCGAGTGCTGGTCTTCA 59.829 55.000 10.26 0.00 0.00 3.02
517 537 0.452184 TCGATCGAGTGCTGGTCTTC 59.548 55.000 15.15 0.00 0.00 2.87
518 538 0.888619 TTCGATCGAGTGCTGGTCTT 59.111 50.000 18.54 0.00 0.00 3.01
519 539 0.171455 GTTCGATCGAGTGCTGGTCT 59.829 55.000 18.54 0.00 0.00 3.85
520 540 1.134530 CGTTCGATCGAGTGCTGGTC 61.135 60.000 18.54 2.53 0.00 4.02
521 541 1.154016 CGTTCGATCGAGTGCTGGT 60.154 57.895 18.54 0.00 0.00 4.00
522 542 1.874019 CCGTTCGATCGAGTGCTGG 60.874 63.158 18.54 12.42 0.00 4.85
523 543 2.508891 GCCGTTCGATCGAGTGCTG 61.509 63.158 18.54 10.04 0.00 4.41
524 544 2.202623 GCCGTTCGATCGAGTGCT 60.203 61.111 18.54 0.00 0.00 4.40
525 545 2.506217 TGCCGTTCGATCGAGTGC 60.506 61.111 18.54 20.32 0.00 4.40
526 546 2.158959 GGTGCCGTTCGATCGAGTG 61.159 63.158 18.54 14.07 0.00 3.51
527 547 2.181021 GGTGCCGTTCGATCGAGT 59.819 61.111 18.54 0.00 0.00 4.18
528 548 2.582498 GGGTGCCGTTCGATCGAG 60.582 66.667 18.54 8.21 0.00 4.04
529 549 3.375239 TGGGTGCCGTTCGATCGA 61.375 61.111 15.15 15.15 0.00 3.59
530 550 3.186047 GTGGGTGCCGTTCGATCG 61.186 66.667 9.36 9.36 0.00 3.69
531 551 2.818274 GGTGGGTGCCGTTCGATC 60.818 66.667 0.00 0.00 0.00 3.69
532 552 2.966732 ATGGTGGGTGCCGTTCGAT 61.967 57.895 0.00 0.00 0.00 3.59
533 553 3.632080 ATGGTGGGTGCCGTTCGA 61.632 61.111 0.00 0.00 0.00 3.71
534 554 3.430862 CATGGTGGGTGCCGTTCG 61.431 66.667 0.00 0.00 0.00 3.95
535 555 3.061848 CCATGGTGGGTGCCGTTC 61.062 66.667 2.57 0.00 32.67 3.95
544 564 2.819595 CGCTCGAACCCATGGTGG 60.820 66.667 11.73 0.00 35.34 4.61
545 565 2.819595 CCGCTCGAACCCATGGTG 60.820 66.667 11.73 4.77 35.34 4.17
546 566 3.000819 TCCGCTCGAACCCATGGT 61.001 61.111 11.73 0.00 37.65 3.55
547 567 2.511600 GTCCGCTCGAACCCATGG 60.512 66.667 4.14 4.14 0.00 3.66
548 568 2.511600 GGTCCGCTCGAACCCATG 60.512 66.667 0.00 0.00 0.00 3.66
549 569 2.367202 ATGGTCCGCTCGAACCCAT 61.367 57.895 1.62 0.00 34.47 4.00
550 570 3.000819 ATGGTCCGCTCGAACCCA 61.001 61.111 1.62 0.00 34.47 4.51
551 571 2.511600 CATGGTCCGCTCGAACCC 60.512 66.667 1.62 0.00 34.47 4.11
552 572 2.511600 CCATGGTCCGCTCGAACC 60.512 66.667 2.57 0.00 36.03 3.62
553 573 1.810030 GACCATGGTCCGCTCGAAC 60.810 63.158 31.37 6.14 39.08 3.95
554 574 2.577059 GACCATGGTCCGCTCGAA 59.423 61.111 31.37 0.00 39.08 3.71
562 582 0.179000 AGCGATTCAGGACCATGGTC 59.821 55.000 33.14 33.14 43.87 4.02
563 583 0.620556 AAGCGATTCAGGACCATGGT 59.379 50.000 19.89 19.89 0.00 3.55
564 584 1.019673 CAAGCGATTCAGGACCATGG 58.980 55.000 11.19 11.19 0.00 3.66
565 585 1.667724 GACAAGCGATTCAGGACCATG 59.332 52.381 0.00 0.00 0.00 3.66
566 586 1.556911 AGACAAGCGATTCAGGACCAT 59.443 47.619 0.00 0.00 0.00 3.55
567 587 0.976641 AGACAAGCGATTCAGGACCA 59.023 50.000 0.00 0.00 0.00 4.02
568 588 1.646189 GAGACAAGCGATTCAGGACC 58.354 55.000 0.00 0.00 0.00 4.46
569 589 1.135373 TCGAGACAAGCGATTCAGGAC 60.135 52.381 0.00 0.00 32.09 3.85
570 590 1.173913 TCGAGACAAGCGATTCAGGA 58.826 50.000 0.00 0.00 32.09 3.86
571 591 1.996292 TTCGAGACAAGCGATTCAGG 58.004 50.000 0.00 0.00 37.64 3.86
572 592 4.091945 TGATTTTCGAGACAAGCGATTCAG 59.908 41.667 0.00 0.00 37.64 3.02
573 593 3.993736 TGATTTTCGAGACAAGCGATTCA 59.006 39.130 0.00 0.00 37.64 2.57
574 594 4.584029 TGATTTTCGAGACAAGCGATTC 57.416 40.909 0.00 0.00 37.64 2.52
575 595 4.631377 TGATGATTTTCGAGACAAGCGATT 59.369 37.500 0.00 0.00 37.64 3.34
576 596 4.183865 TGATGATTTTCGAGACAAGCGAT 58.816 39.130 0.00 0.00 37.64 4.58
577 597 3.584834 TGATGATTTTCGAGACAAGCGA 58.415 40.909 0.00 0.00 35.76 4.93
578 598 3.242220 CCTGATGATTTTCGAGACAAGCG 60.242 47.826 0.00 0.00 0.00 4.68
579 599 3.486542 GCCTGATGATTTTCGAGACAAGC 60.487 47.826 0.00 0.00 0.00 4.01
580 600 3.064545 GGCCTGATGATTTTCGAGACAAG 59.935 47.826 0.00 0.00 0.00 3.16
581 601 3.009723 GGCCTGATGATTTTCGAGACAA 58.990 45.455 0.00 0.00 0.00 3.18
582 602 2.237143 AGGCCTGATGATTTTCGAGACA 59.763 45.455 3.11 0.00 0.00 3.41
583 603 2.911484 AGGCCTGATGATTTTCGAGAC 58.089 47.619 3.11 0.00 0.00 3.36
584 604 3.960755 TCTAGGCCTGATGATTTTCGAGA 59.039 43.478 17.99 1.85 0.00 4.04
585 605 4.202202 ACTCTAGGCCTGATGATTTTCGAG 60.202 45.833 17.99 0.00 0.00 4.04
586 606 3.706594 ACTCTAGGCCTGATGATTTTCGA 59.293 43.478 17.99 0.00 0.00 3.71
587 607 4.065321 ACTCTAGGCCTGATGATTTTCG 57.935 45.455 17.99 1.59 0.00 3.46
604 624 3.840666 TGCCTTTCTCATGAAGGTACTCT 59.159 43.478 12.50 0.00 38.49 3.24
605 625 3.935828 GTGCCTTTCTCATGAAGGTACTC 59.064 47.826 20.04 3.96 38.49 2.59
643 663 1.341209 AGAATACGGATGCGCTGATGA 59.659 47.619 9.73 0.00 0.00 2.92
644 664 1.788258 AGAATACGGATGCGCTGATG 58.212 50.000 9.73 0.00 0.00 3.07
655 675 6.055231 TCAAGAACAACAACAAGAATACGG 57.945 37.500 0.00 0.00 0.00 4.02
662 682 9.105206 CAAAACAAAATCAAGAACAACAACAAG 57.895 29.630 0.00 0.00 0.00 3.16
715 735 0.464036 TGTGACACAAAGCGAGACCT 59.536 50.000 5.62 0.00 0.00 3.85
753 773 4.260212 CGTTCTCGTGCCCAAATTGTATAG 60.260 45.833 0.00 0.00 0.00 1.31
814 834 6.712547 GCATATCTAAGCTATTGGGTTCAAGT 59.287 38.462 0.00 0.00 36.19 3.16
907 930 8.430431 GCTACCCCTACTATAGACTTTGAAAAT 58.570 37.037 6.78 0.00 0.00 1.82
912 935 5.477637 GGAGCTACCCCTACTATAGACTTTG 59.522 48.000 6.78 0.00 0.00 2.77
954 977 3.626028 AAAGAAAAGCTTAGTGTGCGG 57.374 42.857 0.00 0.00 35.24 5.69
999 1022 5.865085 TGGTGAGCTAGTTATTTCTGTGTT 58.135 37.500 0.00 0.00 0.00 3.32
1011 1034 1.203187 TGAGGAGGTTGGTGAGCTAGT 60.203 52.381 0.00 0.00 35.91 2.57
1055 1078 2.758979 GAGAGGGTTCATCACTTCGGTA 59.241 50.000 0.00 0.00 0.00 4.02
1060 1083 2.907892 TGAGGAGAGGGTTCATCACTT 58.092 47.619 0.00 0.00 33.41 3.16
1103 1126 3.491104 CCGTGAGCTTATTGTACTCCTCC 60.491 52.174 0.00 0.00 0.00 4.30
1385 1416 2.183679 AGAACCTTGAGCTCCTCGATT 58.816 47.619 12.15 0.00 32.35 3.34
1428 1459 0.245266 TCAATCTTGTACCGCTCGCA 59.755 50.000 0.00 0.00 0.00 5.10
1512 1543 3.134623 TCAATACCGACGAGACCTACCTA 59.865 47.826 0.00 0.00 0.00 3.08
1782 1860 2.238646 TCCGCCACTGAGGTCAATAATT 59.761 45.455 0.00 0.00 40.61 1.40
1869 1960 2.968574 TGCAGGGCTTAGATAAGGAGAG 59.031 50.000 2.00 0.00 33.95 3.20
1947 2415 1.001597 CGGTGGCGGATCTTAGTAGAC 60.002 57.143 0.00 0.00 31.99 2.59
1966 2434 1.134491 GGTCCCTAAGGTGGTCAATCG 60.134 57.143 0.00 0.00 0.00 3.34
2091 2560 5.130477 ACCAACTACCGAATCATATGGAACT 59.870 40.000 2.13 0.00 0.00 3.01
2179 2683 2.262637 TCCCGAATCACTTTGGTACCT 58.737 47.619 14.36 0.00 34.45 3.08
2194 2698 2.666207 CCGGTGTTCCAATCCCGA 59.334 61.111 0.00 0.00 43.01 5.14
2196 2700 2.754254 GCCCGGTGTTCCAATCCC 60.754 66.667 0.00 0.00 0.00 3.85
2209 2713 0.738389 ATATTTTTGACTGCGGCCCG 59.262 50.000 0.00 0.00 0.00 6.13
2266 2770 2.101582 GCTCTTCATCACCTCCGTACAT 59.898 50.000 0.00 0.00 0.00 2.29
2330 2834 8.489489 AGCCTAATTGAGATTTGAAGTCATCTA 58.511 33.333 0.00 0.00 29.41 1.98
2410 2917 2.361119 CCTCCATCGTAGAATCCGTCAA 59.639 50.000 0.00 0.00 43.58 3.18
2463 2970 1.982073 GCTTGATCCAAACCGCCTCG 61.982 60.000 0.00 0.00 0.00 4.63
2534 3041 5.177511 CACGTGCCACTATTATCACAATAGG 59.822 44.000 0.82 0.00 35.18 2.57
2562 3070 1.776667 CAAAGATGGATCCCTAGCCCA 59.223 52.381 9.90 0.00 0.00 5.36
2573 3082 4.299586 TGTCTTATGGTGCAAAGATGGA 57.700 40.909 2.07 0.00 34.43 3.41
2581 3090 6.413892 TCAATATGTCTTGTCTTATGGTGCA 58.586 36.000 0.00 0.00 0.00 4.57
2604 3113 7.177407 TGTCGAATGAGTTTATATTTGCGTTC 58.823 34.615 0.00 0.00 0.00 3.95
2679 3960 4.753516 TGTCATCGGGTCTGATATGTTT 57.246 40.909 0.00 0.00 0.00 2.83
2756 4039 5.615289 AGTCATATTCCAGTTACATGGCTC 58.385 41.667 0.00 0.00 40.41 4.70
2772 4055 4.290093 TCCCACTTGCACTAGAGTCATAT 58.710 43.478 0.00 0.00 0.00 1.78


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

AutoCloner maintained by Alex Coulton.