Multiple sequence alignment - TraesCS1D01G363100

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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 TraesCS1D01G363100 chr1D 100.000 3284 0 0 1 3284 444897751 444901034 0.000000e+00 6065
1 TraesCS1D01G363100 chr7D 98.614 2670 37 0 615 3284 625182199 625179530 0.000000e+00 4726
2 TraesCS1D01G363100 chr7D 91.854 2529 124 41 614 3087 93605256 93607757 0.000000e+00 3454
3 TraesCS1D01G363100 chr7D 96.524 1956 45 11 611 2548 393113872 393111922 0.000000e+00 3214
4 TraesCS1D01G363100 chr7D 96.536 1732 39 12 1568 3284 631817586 631815861 0.000000e+00 2846
5 TraesCS1D01G363100 chr7D 92.705 987 45 8 613 1575 92234553 92233570 0.000000e+00 1399
6 TraesCS1D01G363100 chr7D 92.269 983 46 11 614 1575 631818589 631817616 0.000000e+00 1367
7 TraesCS1D01G363100 chr7D 94.391 624 16 5 615 1222 393111299 393111919 0.000000e+00 941
8 TraesCS1D01G363100 chr5D 98.214 2687 29 5 614 3284 545533143 545535826 0.000000e+00 4678
9 TraesCS1D01G363100 chr5D 92.332 2556 128 38 614 3123 494245453 494242920 0.000000e+00 3572
10 TraesCS1D01G363100 chr5D 93.110 987 41 8 613 1575 408555345 408554362 0.000000e+00 1421
11 TraesCS1D01G363100 chr2D 97.579 2685 49 3 615 3284 547546097 547543414 0.000000e+00 4584
12 TraesCS1D01G363100 chr2D 97.507 2687 47 6 614 3284 489934894 489932212 0.000000e+00 4573
13 TraesCS1D01G363100 chr2D 97.472 2690 32 7 615 3284 624287168 624289841 0.000000e+00 4558
14 TraesCS1D01G363100 chr2D 92.347 2535 120 39 610 3087 568357762 568355245 0.000000e+00 3539
15 TraesCS1D01G363100 chrUn 95.742 2701 40 12 615 3284 70158593 70155937 0.000000e+00 4281
16 TraesCS1D01G363100 chr3D 96.420 1732 46 8 1568 3284 45062228 45060498 0.000000e+00 2841
17 TraesCS1D01G363100 chr6B 90.859 1466 79 10 1669 3120 661539903 661541327 0.000000e+00 1914
18 TraesCS1D01G363100 chr1B 91.150 565 34 5 56 614 605440860 605441414 0.000000e+00 752
19 TraesCS1D01G363100 chr7B 92.908 423 24 4 2663 3080 591180864 591181285 7.790000e-171 610
20 TraesCS1D01G363100 chr1A 94.304 316 17 1 103 418 540194972 540195286 1.770000e-132 483
21 TraesCS1D01G363100 chr1A 94.286 175 8 2 440 614 540195383 540195555 1.940000e-67 267
22 TraesCS1D01G363100 chr1A 87.379 103 8 1 11 108 540194711 540194813 2.680000e-21 113
23 TraesCS1D01G363100 chr6D 98.326 239 4 0 3046 3284 137509349 137509111 1.410000e-113 420
24 TraesCS1D01G363100 chr2B 81.702 470 67 16 152 614 114650153 114650610 1.110000e-99 374


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 TraesCS1D01G363100 chr1D 444897751 444901034 3283 False 6065.000000 6065 100.000000 1 3284 1 chr1D.!!$F1 3283
1 TraesCS1D01G363100 chr7D 625179530 625182199 2669 True 4726.000000 4726 98.614000 615 3284 1 chr7D.!!$R3 2669
2 TraesCS1D01G363100 chr7D 93605256 93607757 2501 False 3454.000000 3454 91.854000 614 3087 1 chr7D.!!$F1 2473
3 TraesCS1D01G363100 chr7D 393111922 393113872 1950 True 3214.000000 3214 96.524000 611 2548 1 chr7D.!!$R2 1937
4 TraesCS1D01G363100 chr7D 631815861 631818589 2728 True 2106.500000 2846 94.402500 614 3284 2 chr7D.!!$R4 2670
5 TraesCS1D01G363100 chr7D 92233570 92234553 983 True 1399.000000 1399 92.705000 613 1575 1 chr7D.!!$R1 962
6 TraesCS1D01G363100 chr7D 393111299 393111919 620 False 941.000000 941 94.391000 615 1222 1 chr7D.!!$F2 607
7 TraesCS1D01G363100 chr5D 545533143 545535826 2683 False 4678.000000 4678 98.214000 614 3284 1 chr5D.!!$F1 2670
8 TraesCS1D01G363100 chr5D 494242920 494245453 2533 True 3572.000000 3572 92.332000 614 3123 1 chr5D.!!$R2 2509
9 TraesCS1D01G363100 chr5D 408554362 408555345 983 True 1421.000000 1421 93.110000 613 1575 1 chr5D.!!$R1 962
10 TraesCS1D01G363100 chr2D 547543414 547546097 2683 True 4584.000000 4584 97.579000 615 3284 1 chr2D.!!$R2 2669
11 TraesCS1D01G363100 chr2D 489932212 489934894 2682 True 4573.000000 4573 97.507000 614 3284 1 chr2D.!!$R1 2670
12 TraesCS1D01G363100 chr2D 624287168 624289841 2673 False 4558.000000 4558 97.472000 615 3284 1 chr2D.!!$F1 2669
13 TraesCS1D01G363100 chr2D 568355245 568357762 2517 True 3539.000000 3539 92.347000 610 3087 1 chr2D.!!$R3 2477
14 TraesCS1D01G363100 chrUn 70155937 70158593 2656 True 4281.000000 4281 95.742000 615 3284 1 chrUn.!!$R1 2669
15 TraesCS1D01G363100 chr3D 45060498 45062228 1730 True 2841.000000 2841 96.420000 1568 3284 1 chr3D.!!$R1 1716
16 TraesCS1D01G363100 chr6B 661539903 661541327 1424 False 1914.000000 1914 90.859000 1669 3120 1 chr6B.!!$F1 1451
17 TraesCS1D01G363100 chr1B 605440860 605441414 554 False 752.000000 752 91.150000 56 614 1 chr1B.!!$F1 558
18 TraesCS1D01G363100 chr1A 540194711 540195555 844 False 287.666667 483 91.989667 11 614 3 chr1A.!!$F1 603

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
429 598 0.102481 AAGTTCACTCACAGCGACGT 59.898 50.0 0.00 0.00 0.00 4.34 F
526 777 0.105194 TTGGTGAGTGAGGTCCCAGA 60.105 55.0 0.00 0.00 0.00 3.86 F
527 778 0.117140 TGGTGAGTGAGGTCCCAGAT 59.883 55.0 0.00 0.00 0.00 2.90 F
569 820 0.179004 CTTGTGGCCACCCAGTTGTA 60.179 55.0 32.62 8.94 43.18 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1369 1702 1.283793 CAAGCTCAAGTTGGCCACG 59.716 57.895 3.88 0.0 0.00 4.94 R
2087 2575 2.555325 TGAAAAATGCACCTCTGCTCTG 59.445 45.455 0.00 0.0 44.57 3.35 R
2139 2627 3.439857 TCAACAGCCTTCATAGCCTTT 57.560 42.857 0.00 0.0 0.00 3.11 R
2638 3128 0.244721 GGGTTGCATTTGGTCAGAGC 59.755 55.000 0.00 0.0 0.00 4.09 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
54 60 2.481952 CCTTGTTCAGCTTGCTGACTAC 59.518 50.000 22.92 19.16 32.47 2.73
68 74 5.414360 TGCTGACTACACATCTCAAAGATC 58.586 41.667 0.00 0.00 31.32 2.75
108 114 2.026356 CCCCATGATGACCACAAGTACA 60.026 50.000 0.00 0.00 0.00 2.90
138 307 2.167693 CTGACCATGCAAGCCAATGAAT 59.832 45.455 0.00 0.00 0.00 2.57
218 387 0.179097 GGAGACCGAGACAATGGAGC 60.179 60.000 0.00 0.00 0.00 4.70
222 391 2.169789 CCGAGACAATGGAGCTGCG 61.170 63.158 0.00 0.00 0.00 5.18
225 394 1.661341 GAGACAATGGAGCTGCGATT 58.339 50.000 0.00 0.00 0.00 3.34
306 475 0.690411 CCAGAGAGGCTGTCCCAGAT 60.690 60.000 8.20 0.00 43.33 2.90
355 524 1.596464 GCTACATACCTCGACGAACCG 60.596 57.143 0.00 0.00 0.00 4.44
402 571 0.813610 TGCTTGTCGAACACCACCAG 60.814 55.000 0.00 0.00 0.00 4.00
406 575 1.961277 GTCGAACACCACCAGCAGG 60.961 63.158 0.00 0.00 42.21 4.85
418 587 3.560025 CCACCAGCAGGAATAAGTTCACT 60.560 47.826 0.35 0.00 38.69 3.41
419 588 3.686726 CACCAGCAGGAATAAGTTCACTC 59.313 47.826 0.35 0.00 38.69 3.51
420 589 3.327757 ACCAGCAGGAATAAGTTCACTCA 59.672 43.478 0.35 0.00 38.69 3.41
421 590 3.686726 CCAGCAGGAATAAGTTCACTCAC 59.313 47.826 0.00 0.00 36.01 3.51
423 592 4.391216 CAGCAGGAATAAGTTCACTCACAG 59.609 45.833 0.00 0.00 36.01 3.66
424 593 3.126000 GCAGGAATAAGTTCACTCACAGC 59.874 47.826 0.00 0.00 36.01 4.40
425 594 3.369147 CAGGAATAAGTTCACTCACAGCG 59.631 47.826 0.00 0.00 36.01 5.18
426 595 3.258372 AGGAATAAGTTCACTCACAGCGA 59.742 43.478 0.00 0.00 36.01 4.93
427 596 3.368236 GGAATAAGTTCACTCACAGCGAC 59.632 47.826 0.00 0.00 36.01 5.19
428 597 2.046283 TAAGTTCACTCACAGCGACG 57.954 50.000 0.00 0.00 0.00 5.12
429 598 0.102481 AAGTTCACTCACAGCGACGT 59.898 50.000 0.00 0.00 0.00 4.34
430 599 0.949397 AGTTCACTCACAGCGACGTA 59.051 50.000 0.00 0.00 0.00 3.57
431 600 1.335810 AGTTCACTCACAGCGACGTAA 59.664 47.619 0.00 0.00 0.00 3.18
442 611 7.116662 ACTCACAGCGACGTAAATAAAAATACA 59.883 33.333 0.00 0.00 0.00 2.29
443 612 7.794880 TCACAGCGACGTAAATAAAAATACAA 58.205 30.769 0.00 0.00 0.00 2.41
444 613 7.953173 TCACAGCGACGTAAATAAAAATACAAG 59.047 33.333 0.00 0.00 0.00 3.16
445 614 7.953173 CACAGCGACGTAAATAAAAATACAAGA 59.047 33.333 0.00 0.00 0.00 3.02
446 615 8.166706 ACAGCGACGTAAATAAAAATACAAGAG 58.833 33.333 0.00 0.00 0.00 2.85
487 738 3.719268 TTTCTACACCCACATCATGCT 57.281 42.857 0.00 0.00 0.00 3.79
488 739 2.988010 TCTACACCCACATCATGCTC 57.012 50.000 0.00 0.00 0.00 4.26
489 740 1.136891 TCTACACCCACATCATGCTCG 59.863 52.381 0.00 0.00 0.00 5.03
490 741 0.461870 TACACCCACATCATGCTCGC 60.462 55.000 0.00 0.00 0.00 5.03
491 742 1.746239 CACCCACATCATGCTCGCA 60.746 57.895 0.00 0.00 0.00 5.10
492 743 1.002257 ACCCACATCATGCTCGCAA 60.002 52.632 0.00 0.00 0.00 4.85
493 744 0.608856 ACCCACATCATGCTCGCAAA 60.609 50.000 0.00 0.00 0.00 3.68
494 745 0.742505 CCCACATCATGCTCGCAAAT 59.257 50.000 0.00 0.00 0.00 2.32
495 746 1.535226 CCCACATCATGCTCGCAAATG 60.535 52.381 13.02 13.02 32.74 2.32
496 747 1.535226 CCACATCATGCTCGCAAATGG 60.535 52.381 16.77 8.39 31.57 3.16
497 748 1.402613 CACATCATGCTCGCAAATGGA 59.597 47.619 16.77 5.80 31.57 3.41
498 749 2.034179 CACATCATGCTCGCAAATGGAT 59.966 45.455 16.77 7.39 31.57 3.41
499 750 2.292569 ACATCATGCTCGCAAATGGATC 59.707 45.455 16.77 0.00 31.57 3.36
500 751 0.939419 TCATGCTCGCAAATGGATCG 59.061 50.000 0.00 0.00 0.00 3.69
501 752 0.939419 CATGCTCGCAAATGGATCGA 59.061 50.000 0.00 0.00 0.00 3.59
502 753 1.331447 CATGCTCGCAAATGGATCGAA 59.669 47.619 0.00 0.00 0.00 3.71
503 754 1.667236 TGCTCGCAAATGGATCGAAT 58.333 45.000 0.00 0.00 0.00 3.34
504 755 2.016318 TGCTCGCAAATGGATCGAATT 58.984 42.857 0.00 0.00 0.00 2.17
505 756 2.223317 TGCTCGCAAATGGATCGAATTG 60.223 45.455 1.42 1.42 0.00 2.32
506 757 2.378806 CTCGCAAATGGATCGAATTGC 58.621 47.619 17.69 17.69 43.51 3.56
507 758 2.016318 TCGCAAATGGATCGAATTGCT 58.984 42.857 22.86 0.00 44.47 3.91
508 759 2.423185 TCGCAAATGGATCGAATTGCTT 59.577 40.909 22.86 0.00 44.47 3.91
509 760 2.532723 CGCAAATGGATCGAATTGCTTG 59.467 45.455 22.86 9.19 44.47 4.01
510 761 2.861935 GCAAATGGATCGAATTGCTTGG 59.138 45.455 19.68 0.00 43.58 3.61
511 762 3.676873 GCAAATGGATCGAATTGCTTGGT 60.677 43.478 19.68 0.00 43.58 3.67
512 763 3.788333 AATGGATCGAATTGCTTGGTG 57.212 42.857 0.00 0.00 0.00 4.17
513 764 2.488204 TGGATCGAATTGCTTGGTGA 57.512 45.000 0.00 0.00 0.00 4.02
514 765 2.358957 TGGATCGAATTGCTTGGTGAG 58.641 47.619 0.00 0.00 0.00 3.51
515 766 2.290260 TGGATCGAATTGCTTGGTGAGT 60.290 45.455 0.00 0.00 0.00 3.41
516 767 2.096496 GGATCGAATTGCTTGGTGAGTG 59.904 50.000 0.00 0.00 0.00 3.51
517 768 2.542020 TCGAATTGCTTGGTGAGTGA 57.458 45.000 0.00 0.00 0.00 3.41
518 769 2.416747 TCGAATTGCTTGGTGAGTGAG 58.583 47.619 0.00 0.00 0.00 3.51
519 770 1.466167 CGAATTGCTTGGTGAGTGAGG 59.534 52.381 0.00 0.00 0.00 3.86
520 771 2.508526 GAATTGCTTGGTGAGTGAGGT 58.491 47.619 0.00 0.00 0.00 3.85
521 772 2.191128 ATTGCTTGGTGAGTGAGGTC 57.809 50.000 0.00 0.00 0.00 3.85
522 773 0.108585 TTGCTTGGTGAGTGAGGTCC 59.891 55.000 0.00 0.00 0.00 4.46
523 774 1.003233 GCTTGGTGAGTGAGGTCCC 60.003 63.158 0.00 0.00 0.00 4.46
524 775 1.768684 GCTTGGTGAGTGAGGTCCCA 61.769 60.000 0.00 0.00 0.00 4.37
525 776 0.322975 CTTGGTGAGTGAGGTCCCAG 59.677 60.000 0.00 0.00 0.00 4.45
526 777 0.105194 TTGGTGAGTGAGGTCCCAGA 60.105 55.000 0.00 0.00 0.00 3.86
527 778 0.117140 TGGTGAGTGAGGTCCCAGAT 59.883 55.000 0.00 0.00 0.00 2.90
528 779 0.539051 GGTGAGTGAGGTCCCAGATG 59.461 60.000 0.00 0.00 0.00 2.90
529 780 1.561643 GTGAGTGAGGTCCCAGATGA 58.438 55.000 0.00 0.00 0.00 2.92
530 781 2.114616 GTGAGTGAGGTCCCAGATGAT 58.885 52.381 0.00 0.00 0.00 2.45
531 782 2.113807 TGAGTGAGGTCCCAGATGATG 58.886 52.381 0.00 0.00 0.00 3.07
532 783 2.292455 TGAGTGAGGTCCCAGATGATGA 60.292 50.000 0.00 0.00 0.00 2.92
533 784 2.364970 GAGTGAGGTCCCAGATGATGAG 59.635 54.545 0.00 0.00 0.00 2.90
534 785 2.114616 GTGAGGTCCCAGATGATGAGT 58.885 52.381 0.00 0.00 0.00 3.41
535 786 2.113807 TGAGGTCCCAGATGATGAGTG 58.886 52.381 0.00 0.00 0.00 3.51
536 787 2.114616 GAGGTCCCAGATGATGAGTGT 58.885 52.381 0.00 0.00 0.00 3.55
537 788 2.102252 GAGGTCCCAGATGATGAGTGTC 59.898 54.545 0.00 0.00 0.00 3.67
538 789 2.114616 GGTCCCAGATGATGAGTGTCT 58.885 52.381 0.00 0.00 0.00 3.41
539 790 2.102252 GGTCCCAGATGATGAGTGTCTC 59.898 54.545 0.00 0.00 0.00 3.36
540 791 2.762887 GTCCCAGATGATGAGTGTCTCA 59.237 50.000 1.92 1.92 44.99 3.27
549 800 2.975732 TGAGTGTCTCATCCATGCTC 57.024 50.000 0.00 0.00 35.39 4.26
550 801 1.483827 TGAGTGTCTCATCCATGCTCC 59.516 52.381 0.00 0.00 35.39 4.70
551 802 1.761784 GAGTGTCTCATCCATGCTCCT 59.238 52.381 0.00 0.00 0.00 3.69
552 803 2.170187 GAGTGTCTCATCCATGCTCCTT 59.830 50.000 0.00 0.00 0.00 3.36
553 804 2.093075 AGTGTCTCATCCATGCTCCTTG 60.093 50.000 0.00 0.00 0.00 3.61
554 805 1.911357 TGTCTCATCCATGCTCCTTGT 59.089 47.619 0.00 0.00 0.00 3.16
555 806 2.286872 GTCTCATCCATGCTCCTTGTG 58.713 52.381 0.00 0.00 0.00 3.33
556 807 1.211212 TCTCATCCATGCTCCTTGTGG 59.789 52.381 0.00 0.00 0.00 4.17
557 808 0.394762 TCATCCATGCTCCTTGTGGC 60.395 55.000 0.00 0.00 33.01 5.01
558 809 1.076485 ATCCATGCTCCTTGTGGCC 60.076 57.895 0.00 0.00 33.01 5.36
559 810 1.866483 ATCCATGCTCCTTGTGGCCA 61.866 55.000 0.00 0.00 33.01 5.36
560 811 2.345760 CCATGCTCCTTGTGGCCAC 61.346 63.158 29.67 29.67 0.00 5.01
561 812 2.036256 ATGCTCCTTGTGGCCACC 59.964 61.111 32.62 16.52 0.00 4.61
562 813 3.590466 ATGCTCCTTGTGGCCACCC 62.590 63.158 32.62 10.22 0.00 4.61
563 814 4.284550 GCTCCTTGTGGCCACCCA 62.285 66.667 32.62 18.39 39.32 4.51
564 815 2.034687 CTCCTTGTGGCCACCCAG 59.965 66.667 32.62 25.92 43.18 4.45
565 816 2.776526 TCCTTGTGGCCACCCAGT 60.777 61.111 32.62 0.00 43.18 4.00
566 817 2.198426 CCTTGTGGCCACCCAGTT 59.802 61.111 32.62 0.00 43.18 3.16
567 818 2.202395 CCTTGTGGCCACCCAGTTG 61.202 63.158 32.62 15.09 43.18 3.16
568 819 1.455587 CTTGTGGCCACCCAGTTGT 60.456 57.895 32.62 0.00 43.18 3.32
569 820 0.179004 CTTGTGGCCACCCAGTTGTA 60.179 55.000 32.62 8.94 43.18 2.41
570 821 0.466555 TTGTGGCCACCCAGTTGTAC 60.467 55.000 32.62 4.42 43.18 2.90
571 822 1.602605 GTGGCCACCCAGTTGTACC 60.603 63.158 26.31 0.00 43.18 3.34
572 823 1.772567 TGGCCACCCAGTTGTACCT 60.773 57.895 0.00 0.00 35.79 3.08
573 824 1.303317 GGCCACCCAGTTGTACCTG 60.303 63.158 0.00 0.00 0.00 4.00
574 825 1.971695 GCCACCCAGTTGTACCTGC 60.972 63.158 0.00 0.00 0.00 4.85
575 826 1.454104 CCACCCAGTTGTACCTGCA 59.546 57.895 0.00 0.00 0.00 4.41
576 827 0.606401 CCACCCAGTTGTACCTGCAG 60.606 60.000 6.78 6.78 0.00 4.41
577 828 0.396435 CACCCAGTTGTACCTGCAGA 59.604 55.000 17.39 0.00 0.00 4.26
578 829 0.687354 ACCCAGTTGTACCTGCAGAG 59.313 55.000 17.39 8.04 0.00 3.35
579 830 0.976641 CCCAGTTGTACCTGCAGAGA 59.023 55.000 17.39 0.00 0.00 3.10
580 831 1.347707 CCCAGTTGTACCTGCAGAGAA 59.652 52.381 17.39 0.00 0.00 2.87
581 832 2.417719 CCAGTTGTACCTGCAGAGAAC 58.582 52.381 17.39 11.25 0.00 3.01
582 833 2.224281 CCAGTTGTACCTGCAGAGAACA 60.224 50.000 17.39 13.15 0.00 3.18
583 834 3.062763 CAGTTGTACCTGCAGAGAACAG 58.937 50.000 17.39 4.38 34.82 3.16
588 839 4.709840 CTGCAGAGAACAGGGGTG 57.290 61.111 8.42 0.00 0.00 4.61
589 840 2.061220 CTGCAGAGAACAGGGGTGA 58.939 57.895 8.42 0.00 0.00 4.02
590 841 0.397941 CTGCAGAGAACAGGGGTGAA 59.602 55.000 8.42 0.00 0.00 3.18
591 842 0.397941 TGCAGAGAACAGGGGTGAAG 59.602 55.000 0.00 0.00 0.00 3.02
592 843 0.957888 GCAGAGAACAGGGGTGAAGC 60.958 60.000 0.00 0.00 0.00 3.86
593 844 0.689623 CAGAGAACAGGGGTGAAGCT 59.310 55.000 0.00 0.00 0.00 3.74
594 845 1.902508 CAGAGAACAGGGGTGAAGCTA 59.097 52.381 0.00 0.00 0.00 3.32
595 846 2.093764 CAGAGAACAGGGGTGAAGCTAG 60.094 54.545 0.00 0.00 0.00 3.42
596 847 0.615850 AGAACAGGGGTGAAGCTAGC 59.384 55.000 6.62 6.62 0.00 3.42
597 848 0.615850 GAACAGGGGTGAAGCTAGCT 59.384 55.000 12.68 12.68 0.00 3.32
598 849 1.831736 GAACAGGGGTGAAGCTAGCTA 59.168 52.381 19.70 0.00 0.00 3.32
599 850 1.490574 ACAGGGGTGAAGCTAGCTAG 58.509 55.000 19.70 16.84 0.00 3.42
600 851 0.755686 CAGGGGTGAAGCTAGCTAGG 59.244 60.000 19.70 4.48 0.00 3.02
601 852 0.399233 AGGGGTGAAGCTAGCTAGGG 60.399 60.000 19.70 0.00 0.00 3.53
602 853 0.691413 GGGGTGAAGCTAGCTAGGGT 60.691 60.000 19.70 0.95 0.00 4.34
603 854 0.753867 GGGTGAAGCTAGCTAGGGTC 59.246 60.000 19.70 12.49 0.00 4.46
604 855 1.486211 GGTGAAGCTAGCTAGGGTCA 58.514 55.000 19.70 15.19 0.00 4.02
605 856 1.831736 GGTGAAGCTAGCTAGGGTCAA 59.168 52.381 19.70 0.29 0.00 3.18
606 857 2.436173 GGTGAAGCTAGCTAGGGTCAAT 59.564 50.000 19.70 0.00 0.00 2.57
607 858 3.641906 GGTGAAGCTAGCTAGGGTCAATA 59.358 47.826 19.70 0.00 0.00 1.90
608 859 4.262249 GGTGAAGCTAGCTAGGGTCAATAG 60.262 50.000 19.70 0.00 0.00 1.73
1018 1285 0.321564 CATGCCTTCCTGGAACGACA 60.322 55.000 4.68 4.48 38.35 4.35
1369 1702 0.895559 CACTGTGGAGCCCCTTTTCC 60.896 60.000 0.00 0.00 0.00 3.13
1502 1836 5.829924 CAGTCCAGGTTAGATGCCAATAAAT 59.170 40.000 0.00 0.00 0.00 1.40
2087 2575 3.520569 TGGAAAAGCTCAAACTTGCAAC 58.479 40.909 0.00 0.00 0.00 4.17
2139 2627 5.129980 AGCTGATATCATCAAGAACACCAGA 59.870 40.000 5.72 0.00 39.11 3.86
2638 3128 3.403936 GGCTTAGTGGCCCACTATG 57.596 57.895 23.77 24.57 44.85 2.23
2799 3292 2.031120 GAGATGTCACAGAGGAGGAGG 58.969 57.143 0.00 0.00 0.00 4.30
2957 3475 3.065095 GCAATGATGAAGAACTGGAGCTC 59.935 47.826 4.71 4.71 0.00 4.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 3.522343 AGGGCGTAAGATAAGGGAGTTTT 59.478 43.478 0.00 0.00 43.02 2.43
17 18 2.434702 ACAAGGGCGTAAGATAAGGGAG 59.565 50.000 0.00 0.00 43.02 4.30
25 26 0.685097 AGCTGAACAAGGGCGTAAGA 59.315 50.000 0.00 0.00 43.02 2.10
26 27 1.197721 CAAGCTGAACAAGGGCGTAAG 59.802 52.381 0.00 0.00 43.44 2.34
31 32 1.288127 CAGCAAGCTGAACAAGGGC 59.712 57.895 16.75 0.00 46.30 5.19
54 60 3.340928 TGGCACTGATCTTTGAGATGTG 58.659 45.455 0.00 0.47 34.53 3.21
68 74 1.363744 GATCTCGGAACTTGGCACTG 58.636 55.000 0.00 0.00 0.00 3.66
108 114 3.382546 GCTTGCATGGTCAGGAAATGTAT 59.617 43.478 1.34 0.00 0.00 2.29
138 307 7.606073 TGTTCAAGTGAAAATATCGAGATTGGA 59.394 33.333 5.96 0.00 35.58 3.53
218 387 3.257561 CGTCTCCGCCAATCGCAG 61.258 66.667 0.00 0.00 37.30 5.18
222 391 4.467084 TGGCCGTCTCCGCCAATC 62.467 66.667 0.00 0.00 37.34 2.67
280 449 2.928002 CAGCCTCTCTGGGGATCTT 58.072 57.895 0.00 0.00 39.15 2.40
355 524 4.101448 ACCTGCCTGGCGTGGATC 62.101 66.667 29.13 0.00 40.22 3.36
370 539 4.681978 AAGCAGGACGGCGTGACC 62.682 66.667 21.19 14.39 39.27 4.02
376 545 2.357034 TTCGACAAGCAGGACGGC 60.357 61.111 0.00 0.00 0.00 5.68
391 560 2.489938 TATTCCTGCTGGTGGTGTTC 57.510 50.000 9.73 0.00 34.23 3.18
402 571 3.126000 GCTGTGAGTGAACTTATTCCTGC 59.874 47.826 0.00 0.00 33.49 4.85
406 575 3.059570 CGTCGCTGTGAGTGAACTTATTC 59.940 47.826 0.00 0.00 36.37 1.75
418 587 7.348808 TGTATTTTTATTTACGTCGCTGTGA 57.651 32.000 0.00 0.00 0.00 3.58
419 588 7.953173 TCTTGTATTTTTATTTACGTCGCTGTG 59.047 33.333 0.00 0.00 0.00 3.66
420 589 8.020861 TCTTGTATTTTTATTTACGTCGCTGT 57.979 30.769 0.00 0.00 0.00 4.40
421 590 7.634817 CCTCTTGTATTTTTATTTACGTCGCTG 59.365 37.037 0.00 0.00 0.00 5.18
423 592 7.678226 TCCTCTTGTATTTTTATTTACGTCGC 58.322 34.615 0.00 0.00 0.00 5.19
424 593 9.469239 GTTCCTCTTGTATTTTTATTTACGTCG 57.531 33.333 0.00 0.00 0.00 5.12
425 594 9.764870 GGTTCCTCTTGTATTTTTATTTACGTC 57.235 33.333 0.00 0.00 0.00 4.34
426 595 9.287373 TGGTTCCTCTTGTATTTTTATTTACGT 57.713 29.630 0.00 0.00 0.00 3.57
487 738 2.016318 AGCAATTCGATCCATTTGCGA 58.984 42.857 12.28 0.00 46.84 5.10
488 739 2.480224 AGCAATTCGATCCATTTGCG 57.520 45.000 12.28 0.00 46.84 4.85
489 740 2.861935 CCAAGCAATTCGATCCATTTGC 59.138 45.455 10.73 10.73 43.64 3.68
490 741 3.861113 CACCAAGCAATTCGATCCATTTG 59.139 43.478 0.00 0.00 0.00 2.32
491 742 3.763360 TCACCAAGCAATTCGATCCATTT 59.237 39.130 0.00 0.00 0.00 2.32
492 743 3.355378 TCACCAAGCAATTCGATCCATT 58.645 40.909 0.00 0.00 0.00 3.16
493 744 2.947652 CTCACCAAGCAATTCGATCCAT 59.052 45.455 0.00 0.00 0.00 3.41
494 745 2.290260 ACTCACCAAGCAATTCGATCCA 60.290 45.455 0.00 0.00 0.00 3.41
495 746 2.096496 CACTCACCAAGCAATTCGATCC 59.904 50.000 0.00 0.00 0.00 3.36
496 747 3.002791 TCACTCACCAAGCAATTCGATC 58.997 45.455 0.00 0.00 0.00 3.69
497 748 3.005554 CTCACTCACCAAGCAATTCGAT 58.994 45.455 0.00 0.00 0.00 3.59
498 749 2.416747 CTCACTCACCAAGCAATTCGA 58.583 47.619 0.00 0.00 0.00 3.71
499 750 1.466167 CCTCACTCACCAAGCAATTCG 59.534 52.381 0.00 0.00 0.00 3.34
500 751 2.485814 GACCTCACTCACCAAGCAATTC 59.514 50.000 0.00 0.00 0.00 2.17
501 752 2.508526 GACCTCACTCACCAAGCAATT 58.491 47.619 0.00 0.00 0.00 2.32
502 753 1.271597 GGACCTCACTCACCAAGCAAT 60.272 52.381 0.00 0.00 0.00 3.56
503 754 0.108585 GGACCTCACTCACCAAGCAA 59.891 55.000 0.00 0.00 0.00 3.91
504 755 1.754745 GGACCTCACTCACCAAGCA 59.245 57.895 0.00 0.00 0.00 3.91
505 756 1.003233 GGGACCTCACTCACCAAGC 60.003 63.158 0.00 0.00 0.00 4.01
506 757 0.322975 CTGGGACCTCACTCACCAAG 59.677 60.000 0.00 0.00 0.00 3.61
507 758 0.105194 TCTGGGACCTCACTCACCAA 60.105 55.000 0.00 0.00 0.00 3.67
508 759 0.117140 ATCTGGGACCTCACTCACCA 59.883 55.000 0.00 0.00 0.00 4.17
509 760 0.539051 CATCTGGGACCTCACTCACC 59.461 60.000 0.00 0.00 0.00 4.02
510 761 1.561643 TCATCTGGGACCTCACTCAC 58.438 55.000 0.00 0.00 0.00 3.51
511 762 2.113807 CATCATCTGGGACCTCACTCA 58.886 52.381 0.00 0.00 0.00 3.41
512 763 2.364970 CTCATCATCTGGGACCTCACTC 59.635 54.545 0.00 0.00 0.00 3.51
513 764 2.292785 ACTCATCATCTGGGACCTCACT 60.293 50.000 0.00 0.00 0.00 3.41
514 765 2.114616 ACTCATCATCTGGGACCTCAC 58.885 52.381 0.00 0.00 0.00 3.51
515 766 2.113807 CACTCATCATCTGGGACCTCA 58.886 52.381 0.00 0.00 0.00 3.86
516 767 2.102252 GACACTCATCATCTGGGACCTC 59.898 54.545 0.00 0.00 0.00 3.85
517 768 2.114616 GACACTCATCATCTGGGACCT 58.885 52.381 0.00 0.00 0.00 3.85
518 769 2.102252 GAGACACTCATCATCTGGGACC 59.898 54.545 0.00 0.00 0.00 4.46
519 770 2.762887 TGAGACACTCATCATCTGGGAC 59.237 50.000 0.00 0.00 35.39 4.46
520 771 3.105959 TGAGACACTCATCATCTGGGA 57.894 47.619 0.00 0.00 35.39 4.37
530 781 1.483827 GGAGCATGGATGAGACACTCA 59.516 52.381 3.95 3.95 44.99 3.41
531 782 1.761784 AGGAGCATGGATGAGACACTC 59.238 52.381 0.00 0.00 0.00 3.51
532 783 1.876849 AGGAGCATGGATGAGACACT 58.123 50.000 0.00 0.00 0.00 3.55
533 784 2.286872 CAAGGAGCATGGATGAGACAC 58.713 52.381 0.00 0.00 0.00 3.67
534 785 1.911357 ACAAGGAGCATGGATGAGACA 59.089 47.619 0.00 0.00 0.00 3.41
535 786 2.286872 CACAAGGAGCATGGATGAGAC 58.713 52.381 0.00 0.00 0.00 3.36
536 787 1.211212 CCACAAGGAGCATGGATGAGA 59.789 52.381 0.00 0.00 35.33 3.27
537 788 1.676746 CCACAAGGAGCATGGATGAG 58.323 55.000 0.00 0.00 35.33 2.90
538 789 0.394762 GCCACAAGGAGCATGGATGA 60.395 55.000 0.00 0.00 35.33 2.92
539 790 1.389609 GGCCACAAGGAGCATGGATG 61.390 60.000 0.00 0.00 35.33 3.51
540 791 1.076485 GGCCACAAGGAGCATGGAT 60.076 57.895 0.00 0.00 35.33 3.41
541 792 2.356278 GGCCACAAGGAGCATGGA 59.644 61.111 0.00 0.00 35.33 3.41
542 793 2.036098 TGGCCACAAGGAGCATGG 59.964 61.111 0.00 0.00 36.89 3.66
543 794 2.345760 GGTGGCCACAAGGAGCATG 61.346 63.158 35.78 0.00 36.89 4.06
544 795 2.036256 GGTGGCCACAAGGAGCAT 59.964 61.111 35.78 0.00 36.89 3.79
545 796 4.284550 GGGTGGCCACAAGGAGCA 62.285 66.667 35.78 0.00 36.89 4.26
546 797 4.284550 TGGGTGGCCACAAGGAGC 62.285 66.667 35.78 17.89 36.89 4.70
547 798 2.034687 CTGGGTGGCCACAAGGAG 59.965 66.667 35.78 20.69 36.89 3.69
548 799 2.391130 AACTGGGTGGCCACAAGGA 61.391 57.895 35.78 15.65 36.89 3.36
549 800 2.198426 AACTGGGTGGCCACAAGG 59.802 61.111 35.78 24.87 38.23 3.61
550 801 0.179004 TACAACTGGGTGGCCACAAG 60.179 55.000 35.78 31.17 0.00 3.16
551 802 0.466555 GTACAACTGGGTGGCCACAA 60.467 55.000 35.78 22.54 0.00 3.33
552 803 1.149627 GTACAACTGGGTGGCCACA 59.850 57.895 35.78 16.96 0.00 4.17
553 804 1.602605 GGTACAACTGGGTGGCCAC 60.603 63.158 28.57 28.57 0.00 5.01
554 805 1.772567 AGGTACAACTGGGTGGCCA 60.773 57.895 0.00 0.00 0.00 5.36
555 806 1.303317 CAGGTACAACTGGGTGGCC 60.303 63.158 0.00 0.00 34.84 5.36
556 807 1.971695 GCAGGTACAACTGGGTGGC 60.972 63.158 0.00 0.00 38.90 5.01
557 808 0.606401 CTGCAGGTACAACTGGGTGG 60.606 60.000 5.57 0.00 38.90 4.61
558 809 0.396435 TCTGCAGGTACAACTGGGTG 59.604 55.000 15.13 0.00 38.90 4.61
559 810 0.687354 CTCTGCAGGTACAACTGGGT 59.313 55.000 15.13 0.00 38.90 4.51
560 811 0.976641 TCTCTGCAGGTACAACTGGG 59.023 55.000 15.13 0.00 38.90 4.45
561 812 2.224281 TGTTCTCTGCAGGTACAACTGG 60.224 50.000 15.13 0.00 38.90 4.00
562 813 3.062763 CTGTTCTCTGCAGGTACAACTG 58.937 50.000 15.13 11.12 41.41 3.16
563 814 2.037772 CCTGTTCTCTGCAGGTACAACT 59.962 50.000 15.13 0.00 46.22 3.16
564 815 2.417719 CCTGTTCTCTGCAGGTACAAC 58.582 52.381 15.13 11.67 46.22 3.32
565 816 2.839486 CCTGTTCTCTGCAGGTACAA 57.161 50.000 15.13 0.00 46.22 2.41
571 822 0.397941 TTCACCCCTGTTCTCTGCAG 59.602 55.000 7.63 7.63 0.00 4.41
572 823 0.397941 CTTCACCCCTGTTCTCTGCA 59.602 55.000 0.00 0.00 0.00 4.41
573 824 0.957888 GCTTCACCCCTGTTCTCTGC 60.958 60.000 0.00 0.00 0.00 4.26
574 825 0.689623 AGCTTCACCCCTGTTCTCTG 59.310 55.000 0.00 0.00 0.00 3.35
575 826 2.183679 CTAGCTTCACCCCTGTTCTCT 58.816 52.381 0.00 0.00 0.00 3.10
576 827 1.406205 GCTAGCTTCACCCCTGTTCTC 60.406 57.143 7.70 0.00 0.00 2.87
577 828 0.615850 GCTAGCTTCACCCCTGTTCT 59.384 55.000 7.70 0.00 0.00 3.01
578 829 0.615850 AGCTAGCTTCACCCCTGTTC 59.384 55.000 12.68 0.00 0.00 3.18
579 830 1.834263 CTAGCTAGCTTCACCCCTGTT 59.166 52.381 24.88 0.00 0.00 3.16
580 831 1.490574 CTAGCTAGCTTCACCCCTGT 58.509 55.000 24.88 0.00 0.00 4.00
581 832 0.755686 CCTAGCTAGCTTCACCCCTG 59.244 60.000 24.88 3.51 0.00 4.45
582 833 0.399233 CCCTAGCTAGCTTCACCCCT 60.399 60.000 24.88 0.00 0.00 4.79
583 834 0.691413 ACCCTAGCTAGCTTCACCCC 60.691 60.000 24.88 0.00 0.00 4.95
584 835 0.753867 GACCCTAGCTAGCTTCACCC 59.246 60.000 24.88 6.46 0.00 4.61
585 836 1.486211 TGACCCTAGCTAGCTTCACC 58.514 55.000 24.88 9.46 0.00 4.02
586 837 3.828875 ATTGACCCTAGCTAGCTTCAC 57.171 47.619 24.88 10.80 0.00 3.18
587 838 3.898123 CCTATTGACCCTAGCTAGCTTCA 59.102 47.826 24.88 17.47 0.00 3.02
588 839 4.153411 TCCTATTGACCCTAGCTAGCTTC 58.847 47.826 24.88 14.84 0.00 3.86
589 840 4.200447 TCCTATTGACCCTAGCTAGCTT 57.800 45.455 24.88 4.01 0.00 3.74
590 841 3.905493 TCCTATTGACCCTAGCTAGCT 57.095 47.619 23.12 23.12 0.00 3.32
591 842 3.259625 CCTTCCTATTGACCCTAGCTAGC 59.740 52.174 15.74 6.62 0.00 3.42
592 843 3.835395 CCCTTCCTATTGACCCTAGCTAG 59.165 52.174 14.20 14.20 0.00 3.42
593 844 3.469771 TCCCTTCCTATTGACCCTAGCTA 59.530 47.826 0.00 0.00 0.00 3.32
594 845 2.250273 TCCCTTCCTATTGACCCTAGCT 59.750 50.000 0.00 0.00 0.00 3.32
595 846 2.635427 CTCCCTTCCTATTGACCCTAGC 59.365 54.545 0.00 0.00 0.00 3.42
596 847 3.930035 ACTCCCTTCCTATTGACCCTAG 58.070 50.000 0.00 0.00 0.00 3.02
597 848 5.492565 TTACTCCCTTCCTATTGACCCTA 57.507 43.478 0.00 0.00 0.00 3.53
598 849 2.972153 ACTCCCTTCCTATTGACCCT 57.028 50.000 0.00 0.00 0.00 4.34
599 850 5.648330 ATTTACTCCCTTCCTATTGACCC 57.352 43.478 0.00 0.00 0.00 4.46
600 851 6.183361 TGCTATTTACTCCCTTCCTATTGACC 60.183 42.308 0.00 0.00 0.00 4.02
601 852 6.827727 TGCTATTTACTCCCTTCCTATTGAC 58.172 40.000 0.00 0.00 0.00 3.18
602 853 7.633018 ATGCTATTTACTCCCTTCCTATTGA 57.367 36.000 0.00 0.00 0.00 2.57
603 854 9.793259 TTTATGCTATTTACTCCCTTCCTATTG 57.207 33.333 0.00 0.00 0.00 1.90
605 856 9.794719 GTTTTATGCTATTTACTCCCTTCCTAT 57.205 33.333 0.00 0.00 0.00 2.57
606 857 8.999895 AGTTTTATGCTATTTACTCCCTTCCTA 58.000 33.333 0.00 0.00 0.00 2.94
607 858 7.873195 AGTTTTATGCTATTTACTCCCTTCCT 58.127 34.615 0.00 0.00 0.00 3.36
608 859 9.053840 GTAGTTTTATGCTATTTACTCCCTTCC 57.946 37.037 0.00 0.00 0.00 3.46
683 935 1.268386 CGCGCGACTGATAGGTTTCTA 60.268 52.381 28.94 0.00 0.00 2.10
957 1223 1.372499 CGACCTCAAAGACGGCGAA 60.372 57.895 16.62 0.00 0.00 4.70
1018 1285 0.898789 TCCTCCGAGCTCGTTTCCTT 60.899 55.000 32.41 0.00 37.74 3.36
1369 1702 1.283793 CAAGCTCAAGTTGGCCACG 59.716 57.895 3.88 0.00 0.00 4.94
1502 1836 7.977789 TCAGTGAACATACATAGCAGAAAAA 57.022 32.000 0.00 0.00 0.00 1.94
2087 2575 2.555325 TGAAAAATGCACCTCTGCTCTG 59.445 45.455 0.00 0.00 44.57 3.35
2106 2594 3.644738 TGATGATATCAGCTTGGCTCTGA 59.355 43.478 20.84 7.03 43.79 3.27
2139 2627 3.439857 TCAACAGCCTTCATAGCCTTT 57.560 42.857 0.00 0.00 0.00 3.11
2638 3128 0.244721 GGGTTGCATTTGGTCAGAGC 59.755 55.000 0.00 0.00 0.00 4.09
2735 3227 0.178987 TTTCTTTTGGGTGGCGGCTA 60.179 50.000 11.43 0.00 0.00 3.93
2799 3292 0.618981 CTAACCTCCACAACCTCCCC 59.381 60.000 0.00 0.00 0.00 4.81
2957 3475 1.654220 CCTGCCACCAGTGAAAACG 59.346 57.895 0.00 0.00 37.38 3.60
3022 3540 1.228184 GCTGGATGAGGAGCCATGG 60.228 63.158 7.63 7.63 36.92 3.66


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

AutoCloner maintained by Alex Coulton.