Multiple sequence alignment - TraesCS7B01G452200

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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 TraesCS7B01G452200 chr7B 100.000 2264 0 0 1 2264 713544130 713541867 0.000000e+00 4096
1 TraesCS7B01G452200 chr7B 98.117 1646 25 3 617 2262 95041357 95039718 0.000000e+00 2863
2 TraesCS7B01G452200 chr7B 97.934 1646 34 0 617 2262 687041238 687042883 0.000000e+00 2852
3 TraesCS7B01G452200 chr7B 90.753 584 31 16 1 568 687040778 687041354 0.000000e+00 758
4 TraesCS7B01G452200 chr7B 91.416 233 14 2 340 566 577211925 577212157 4.690000e-82 315
5 TraesCS7B01G452200 chr7B 98.592 142 2 0 427 568 713543539 713543398 3.730000e-63 252
6 TraesCS7B01G452200 chr1B 97.268 1647 31 2 617 2262 38184007 38185640 0.000000e+00 2780
7 TraesCS7B01G452200 chr1B 87.727 717 48 16 1 697 550439972 550439276 0.000000e+00 815
8 TraesCS7B01G452200 chr1B 90.223 583 34 21 1 567 357901975 357901400 0.000000e+00 739
9 TraesCS7B01G452200 chr1B 90.258 349 34 0 1914 2262 357900217 357899869 7.370000e-125 457
10 TraesCS7B01G452200 chr1B 94.298 228 13 0 340 567 550439564 550439337 1.290000e-92 350
11 TraesCS7B01G452200 chr3B 94.253 1653 80 13 617 2262 28617541 28619185 0.000000e+00 2512
12 TraesCS7B01G452200 chr3B 96.447 1351 24 3 617 1943 16123821 16122471 0.000000e+00 2207
13 TraesCS7B01G452200 chr3B 98.063 568 11 0 1 568 803584818 803584251 0.000000e+00 989
14 TraesCS7B01G452200 chr3B 98.592 142 2 0 427 568 803584140 803583999 3.730000e-63 252
15 TraesCS7B01G452200 chr4B 96.177 1491 30 4 617 2083 402786587 402785100 0.000000e+00 2412
16 TraesCS7B01G452200 chr4B 97.359 568 15 0 1 568 49105839 49106406 0.000000e+00 966
17 TraesCS7B01G452200 chr6B 95.488 1485 36 6 595 2049 687513841 687512358 0.000000e+00 2342
18 TraesCS7B01G452200 chr6B 90.550 582 32 14 1 568 114144638 114144066 0.000000e+00 749
19 TraesCS7B01G452200 chr6B 95.067 223 11 0 340 562 114144234 114144012 3.580000e-93 351
20 TraesCS7B01G452200 chr5B 96.447 1351 24 3 617 1943 464634722 464636072 0.000000e+00 2207
21 TraesCS7B01G452200 chr5B 91.050 581 35 14 1 568 464634262 464634838 0.000000e+00 769
22 TraesCS7B01G452200 chr5B 90.104 576 38 16 1 562 426532979 426533549 0.000000e+00 730
23 TraesCS7B01G452200 chr5B 83.717 565 55 14 1733 2262 433000814 433000252 1.210000e-137 499
24 TraesCS7B01G452200 chr5B 83.186 565 58 14 1733 2262 471293235 471292673 1.220000e-132 483
25 TraesCS7B01G452200 chr2B 96.513 1348 24 3 617 1943 563916524 563915179 0.000000e+00 2207
26 TraesCS7B01G452200 chr2B 96.797 562 18 0 1 562 45596213 45596774 0.000000e+00 939
27 TraesCS7B01G452200 chr2B 96.491 228 8 0 340 567 717652586 717652813 5.900000e-101 377
28 TraesCS7B01G452200 chr2B 95.067 223 11 0 340 562 178345489 178345267 3.580000e-93 351
29 TraesCS7B01G452200 chr4A 91.050 581 35 15 1 568 712877634 712878210 0.000000e+00 769
30 TraesCS7B01G452200 chr4A 92.797 236 17 0 327 562 712878029 712878264 2.150000e-90 342
31 TraesCS7B01G452200 chr5A 90.087 575 37 12 1 562 288268933 288268366 0.000000e+00 728
32 TraesCS7B01G452200 chrUn 83.186 565 57 15 1733 2262 416567433 416566872 1.220000e-132 483
33 TraesCS7B01G452200 chr7A 83.186 565 57 15 1733 2262 16006710 16007271 1.220000e-132 483
34 TraesCS7B01G452200 chr2A 83.186 565 58 14 1733 2262 728935370 728935932 1.220000e-132 483
35 TraesCS7B01G452200 chr5D 85.514 214 19 5 599 800 485078399 485078186 1.760000e-51 213


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 TraesCS7B01G452200 chr7B 713541867 713544130 2263 True 2174.0 4096 99.2960 1 2264 2 chr7B.!!$R2 2263
1 TraesCS7B01G452200 chr7B 95039718 95041357 1639 True 2863.0 2863 98.1170 617 2262 1 chr7B.!!$R1 1645
2 TraesCS7B01G452200 chr7B 687040778 687042883 2105 False 1805.0 2852 94.3435 1 2262 2 chr7B.!!$F2 2261
3 TraesCS7B01G452200 chr1B 38184007 38185640 1633 False 2780.0 2780 97.2680 617 2262 1 chr1B.!!$F1 1645
4 TraesCS7B01G452200 chr1B 357899869 357901975 2106 True 598.0 739 90.2405 1 2262 2 chr1B.!!$R1 2261
5 TraesCS7B01G452200 chr1B 550439276 550439972 696 True 582.5 815 91.0125 1 697 2 chr1B.!!$R2 696
6 TraesCS7B01G452200 chr3B 28617541 28619185 1644 False 2512.0 2512 94.2530 617 2262 1 chr3B.!!$F1 1645
7 TraesCS7B01G452200 chr3B 16122471 16123821 1350 True 2207.0 2207 96.4470 617 1943 1 chr3B.!!$R1 1326
8 TraesCS7B01G452200 chr3B 803583999 803584818 819 True 620.5 989 98.3275 1 568 2 chr3B.!!$R2 567
9 TraesCS7B01G452200 chr4B 402785100 402786587 1487 True 2412.0 2412 96.1770 617 2083 1 chr4B.!!$R1 1466
10 TraesCS7B01G452200 chr4B 49105839 49106406 567 False 966.0 966 97.3590 1 568 1 chr4B.!!$F1 567
11 TraesCS7B01G452200 chr6B 687512358 687513841 1483 True 2342.0 2342 95.4880 595 2049 1 chr6B.!!$R1 1454
12 TraesCS7B01G452200 chr6B 114144012 114144638 626 True 550.0 749 92.8085 1 568 2 chr6B.!!$R2 567
13 TraesCS7B01G452200 chr5B 464634262 464636072 1810 False 1488.0 2207 93.7485 1 1943 2 chr5B.!!$F2 1942
14 TraesCS7B01G452200 chr5B 426532979 426533549 570 False 730.0 730 90.1040 1 562 1 chr5B.!!$F1 561
15 TraesCS7B01G452200 chr5B 433000252 433000814 562 True 499.0 499 83.7170 1733 2262 1 chr5B.!!$R1 529
16 TraesCS7B01G452200 chr5B 471292673 471293235 562 True 483.0 483 83.1860 1733 2262 1 chr5B.!!$R2 529
17 TraesCS7B01G452200 chr2B 563915179 563916524 1345 True 2207.0 2207 96.5130 617 1943 1 chr2B.!!$R2 1326
18 TraesCS7B01G452200 chr2B 45596213 45596774 561 False 939.0 939 96.7970 1 562 1 chr2B.!!$F1 561
19 TraesCS7B01G452200 chr4A 712877634 712878264 630 False 555.5 769 91.9235 1 568 2 chr4A.!!$F1 567
20 TraesCS7B01G452200 chr5A 288268366 288268933 567 True 728.0 728 90.0870 1 562 1 chr5A.!!$R1 561
21 TraesCS7B01G452200 chrUn 416566872 416567433 561 True 483.0 483 83.1860 1733 2262 1 chrUn.!!$R1 529
22 TraesCS7B01G452200 chr7A 16006710 16007271 561 False 483.0 483 83.1860 1733 2262 1 chr7A.!!$F1 529
23 TraesCS7B01G452200 chr2A 728935370 728935932 562 False 483.0 483 83.1860 1733 2262 1 chr2A.!!$F1 529

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
447 637 0.03438 CTAGAGGTGGTGGTCGAGGA 60.034 60.0 0.0 0.0 0.0 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2148 2951 0.320697 GACCTTAGCGTCTGGGTGTT 59.679 55.0 9.57 0.0 31.6 3.32 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
153 154 5.082425 ACGAAGGGTAGAAGGAGAACTAAA 58.918 41.667 0.00 0.00 0.00 1.85
419 609 3.077556 AGGTGGTGGCCGAGCTAG 61.078 66.667 0.00 0.00 0.00 3.42
420 610 4.840005 GGTGGTGGCCGAGCTAGC 62.840 72.222 6.62 6.62 38.00 3.42
421 611 4.082523 GTGGTGGCCGAGCTAGCA 62.083 66.667 18.83 9.37 44.45 3.49
422 612 3.318384 TGGTGGCCGAGCTAGCAA 61.318 61.111 18.83 0.00 43.77 3.91
423 613 2.046314 GGTGGCCGAGCTAGCAAA 60.046 61.111 18.83 0.00 37.47 3.68
424 614 1.674322 GGTGGCCGAGCTAGCAAAA 60.674 57.895 18.83 0.00 37.47 2.44
425 615 1.648467 GGTGGCCGAGCTAGCAAAAG 61.648 60.000 18.83 3.53 37.47 2.27
426 616 0.955919 GTGGCCGAGCTAGCAAAAGT 60.956 55.000 18.83 0.00 0.00 2.66
427 617 0.955428 TGGCCGAGCTAGCAAAAGTG 60.955 55.000 18.83 0.00 0.00 3.16
440 630 2.154462 CAAAAGTGCTAGAGGTGGTGG 58.846 52.381 0.00 0.00 0.00 4.61
441 631 1.435256 AAAGTGCTAGAGGTGGTGGT 58.565 50.000 0.00 0.00 0.00 4.16
442 632 0.977395 AAGTGCTAGAGGTGGTGGTC 59.023 55.000 0.00 0.00 0.00 4.02
443 633 1.215647 GTGCTAGAGGTGGTGGTCG 59.784 63.158 0.00 0.00 0.00 4.79
444 634 1.076014 TGCTAGAGGTGGTGGTCGA 59.924 57.895 0.00 0.00 0.00 4.20
445 635 0.965866 TGCTAGAGGTGGTGGTCGAG 60.966 60.000 0.00 0.00 0.00 4.04
446 636 1.668101 GCTAGAGGTGGTGGTCGAGG 61.668 65.000 0.00 0.00 0.00 4.63
447 637 0.034380 CTAGAGGTGGTGGTCGAGGA 60.034 60.000 0.00 0.00 0.00 3.71
448 638 0.406750 TAGAGGTGGTGGTCGAGGAA 59.593 55.000 0.00 0.00 0.00 3.36
449 639 0.900647 AGAGGTGGTGGTCGAGGAAG 60.901 60.000 0.00 0.00 0.00 3.46
450 640 2.047179 GGTGGTGGTCGAGGAAGC 60.047 66.667 0.00 0.00 0.00 3.86
451 641 2.741092 GTGGTGGTCGAGGAAGCA 59.259 61.111 0.00 0.00 0.00 3.91
452 642 1.668151 GTGGTGGTCGAGGAAGCAC 60.668 63.158 8.07 8.07 44.83 4.40
453 643 2.137528 TGGTGGTCGAGGAAGCACA 61.138 57.895 8.29 0.00 46.81 4.57
454 644 1.070786 GGTGGTCGAGGAAGCACAA 59.929 57.895 8.29 0.00 46.81 3.33
455 645 0.951040 GGTGGTCGAGGAAGCACAAG 60.951 60.000 8.29 0.00 46.81 3.16
456 646 0.249911 GTGGTCGAGGAAGCACAAGT 60.250 55.000 1.66 0.00 44.90 3.16
457 647 0.249868 TGGTCGAGGAAGCACAAGTG 60.250 55.000 0.00 0.00 0.00 3.16
468 658 3.706055 CACAAGTGCTAGTGGTGGT 57.294 52.632 0.00 0.00 32.24 4.16
469 659 1.229428 CACAAGTGCTAGTGGTGGTG 58.771 55.000 0.00 0.00 32.24 4.17
470 660 0.108585 ACAAGTGCTAGTGGTGGTGG 59.891 55.000 0.00 0.00 0.00 4.61
471 661 0.108585 CAAGTGCTAGTGGTGGTGGT 59.891 55.000 0.00 0.00 0.00 4.16
472 662 0.396811 AAGTGCTAGTGGTGGTGGTC 59.603 55.000 0.00 0.00 0.00 4.02
473 663 1.374252 GTGCTAGTGGTGGTGGTCG 60.374 63.158 0.00 0.00 0.00 4.79
474 664 1.532078 TGCTAGTGGTGGTGGTCGA 60.532 57.895 0.00 0.00 0.00 4.20
475 665 1.215647 GCTAGTGGTGGTGGTCGAG 59.784 63.158 0.00 0.00 0.00 4.04
476 666 1.215647 CTAGTGGTGGTGGTCGAGC 59.784 63.158 7.89 7.89 0.00 5.03
477 667 1.228769 TAGTGGTGGTGGTCGAGCT 60.229 57.895 16.64 0.00 0.00 4.09
478 668 0.038599 TAGTGGTGGTGGTCGAGCTA 59.961 55.000 16.64 0.00 0.00 3.32
479 669 1.215647 GTGGTGGTGGTCGAGCTAG 59.784 63.158 16.64 0.00 0.00 3.42
480 670 2.184579 GGTGGTGGTCGAGCTAGC 59.815 66.667 16.64 6.62 0.00 3.42
481 671 2.646175 GGTGGTGGTCGAGCTAGCA 61.646 63.158 18.83 14.25 33.68 3.49
482 672 1.446272 GTGGTGGTCGAGCTAGCAC 60.446 63.158 23.19 23.19 46.59 4.40
484 674 4.988065 GTGGTCGAGCTAGCACAA 57.012 55.556 18.83 0.00 45.11 3.33
485 675 2.743195 GTGGTCGAGCTAGCACAAG 58.257 57.895 18.83 4.97 45.11 3.16
486 676 0.038159 GTGGTCGAGCTAGCACAAGT 60.038 55.000 18.83 0.00 45.11 3.16
487 677 0.038251 TGGTCGAGCTAGCACAAGTG 60.038 55.000 18.83 0.00 0.00 3.16
499 689 1.800805 CACAAGTGCTAGAGGTGGTG 58.199 55.000 0.00 0.00 0.00 4.17
500 690 0.687354 ACAAGTGCTAGAGGTGGTGG 59.313 55.000 0.00 0.00 0.00 4.61
501 691 0.687354 CAAGTGCTAGAGGTGGTGGT 59.313 55.000 0.00 0.00 0.00 4.16
502 692 0.977395 AAGTGCTAGAGGTGGTGGTC 59.023 55.000 0.00 0.00 0.00 4.02
503 693 1.215647 GTGCTAGAGGTGGTGGTCG 59.784 63.158 0.00 0.00 0.00 4.79
504 694 1.076014 TGCTAGAGGTGGTGGTCGA 59.924 57.895 0.00 0.00 0.00 4.20
505 695 0.965866 TGCTAGAGGTGGTGGTCGAG 60.966 60.000 0.00 0.00 0.00 4.04
506 696 1.668101 GCTAGAGGTGGTGGTCGAGG 61.668 65.000 0.00 0.00 0.00 4.63
507 697 0.034380 CTAGAGGTGGTGGTCGAGGA 60.034 60.000 0.00 0.00 0.00 3.71
508 698 0.406750 TAGAGGTGGTGGTCGAGGAA 59.593 55.000 0.00 0.00 0.00 3.36
509 699 0.900647 AGAGGTGGTGGTCGAGGAAG 60.901 60.000 0.00 0.00 0.00 3.46
510 700 2.047179 GGTGGTGGTCGAGGAAGC 60.047 66.667 0.00 0.00 0.00 3.86
511 701 2.741092 GTGGTGGTCGAGGAAGCA 59.259 61.111 0.00 0.00 0.00 3.91
512 702 1.668151 GTGGTGGTCGAGGAAGCAC 60.668 63.158 8.07 8.07 44.83 4.40
513 703 2.137528 TGGTGGTCGAGGAAGCACA 61.138 57.895 8.29 0.00 46.81 4.57
514 704 1.070786 GGTGGTCGAGGAAGCACAA 59.929 57.895 8.29 0.00 46.81 3.33
515 705 0.951040 GGTGGTCGAGGAAGCACAAG 60.951 60.000 8.29 0.00 46.81 3.16
516 706 0.249911 GTGGTCGAGGAAGCACAAGT 60.250 55.000 1.66 0.00 44.90 3.16
517 707 0.249868 TGGTCGAGGAAGCACAAGTG 60.250 55.000 0.00 0.00 0.00 3.16
530 720 2.688507 CACAAGTGCTAGTGGTAGTGG 58.311 52.381 0.00 0.00 32.24 4.00
531 721 2.037251 CACAAGTGCTAGTGGTAGTGGT 59.963 50.000 0.00 0.00 32.24 4.16
532 722 2.299297 ACAAGTGCTAGTGGTAGTGGTC 59.701 50.000 0.00 0.00 0.00 4.02
533 723 1.174783 AGTGCTAGTGGTAGTGGTCG 58.825 55.000 0.00 0.00 0.00 4.79
534 724 1.171308 GTGCTAGTGGTAGTGGTCGA 58.829 55.000 0.00 0.00 0.00 4.20
535 725 1.132643 GTGCTAGTGGTAGTGGTCGAG 59.867 57.143 0.00 0.00 0.00 4.04
536 726 0.100861 GCTAGTGGTAGTGGTCGAGC 59.899 60.000 7.89 7.89 0.00 5.03
537 727 1.752683 CTAGTGGTAGTGGTCGAGCT 58.247 55.000 16.64 2.77 0.00 4.09
538 728 2.915349 CTAGTGGTAGTGGTCGAGCTA 58.085 52.381 16.64 1.75 0.00 3.32
539 729 1.752683 AGTGGTAGTGGTCGAGCTAG 58.247 55.000 16.64 0.00 0.00 3.42
540 730 0.100861 GTGGTAGTGGTCGAGCTAGC 59.899 60.000 16.64 6.62 36.55 3.42
541 731 0.323087 TGGTAGTGGTCGAGCTAGCA 60.323 55.000 18.83 15.74 41.53 3.49
542 732 0.100861 GGTAGTGGTCGAGCTAGCAC 59.899 60.000 18.83 10.18 45.91 4.40
544 734 4.988065 GTGGTCGAGCTAGCACAA 57.012 55.556 18.83 0.00 45.11 3.33
545 735 2.743195 GTGGTCGAGCTAGCACAAG 58.257 57.895 18.83 4.97 45.11 3.16
546 736 0.038159 GTGGTCGAGCTAGCACAAGT 60.038 55.000 18.83 0.00 45.11 3.16
547 737 0.038251 TGGTCGAGCTAGCACAAGTG 60.038 55.000 18.83 0.00 0.00 3.16
559 749 1.800805 CACAAGTGCTAGAGGTGGTG 58.199 55.000 0.00 0.00 0.00 4.17
560 750 0.687354 ACAAGTGCTAGAGGTGGTGG 59.313 55.000 0.00 0.00 0.00 4.61
561 751 0.687354 CAAGTGCTAGAGGTGGTGGT 59.313 55.000 0.00 0.00 0.00 4.16
562 752 0.977395 AAGTGCTAGAGGTGGTGGTC 59.023 55.000 0.00 0.00 0.00 4.02
563 753 1.215647 GTGCTAGAGGTGGTGGTCG 59.784 63.158 0.00 0.00 0.00 4.79
564 754 1.076014 TGCTAGAGGTGGTGGTCGA 59.924 57.895 0.00 0.00 0.00 4.20
565 755 0.965866 TGCTAGAGGTGGTGGTCGAG 60.966 60.000 0.00 0.00 0.00 4.04
566 756 1.810532 CTAGAGGTGGTGGTCGAGC 59.189 63.158 7.89 7.89 0.00 5.03
567 757 0.681564 CTAGAGGTGGTGGTCGAGCT 60.682 60.000 16.64 0.00 33.17 4.09
612 802 0.034380 CTAGAGGTGGTGGTCGAGGA 60.034 60.000 0.00 0.00 0.00 3.71
613 803 0.323178 TAGAGGTGGTGGTCGAGGAC 60.323 60.000 0.00 0.00 0.00 3.85
638 828 1.374252 GTGCTAGTGGTGGTGGTCG 60.374 63.158 0.00 0.00 0.00 4.79
639 829 1.532078 TGCTAGTGGTGGTGGTCGA 60.532 57.895 0.00 0.00 0.00 4.20
640 830 1.215647 GCTAGTGGTGGTGGTCGAG 59.784 63.158 0.00 0.00 0.00 4.04
641 831 1.215647 CTAGTGGTGGTGGTCGAGC 59.784 63.158 7.89 7.89 0.00 5.03
642 832 1.228769 TAGTGGTGGTGGTCGAGCT 60.229 57.895 16.64 0.00 0.00 4.09
643 833 0.038599 TAGTGGTGGTGGTCGAGCTA 59.961 55.000 16.64 0.00 0.00 3.32
644 834 1.215647 GTGGTGGTGGTCGAGCTAG 59.784 63.158 16.64 0.00 0.00 3.42
645 835 2.184579 GGTGGTGGTCGAGCTAGC 59.815 66.667 16.64 6.62 0.00 3.42
646 836 2.646175 GGTGGTGGTCGAGCTAGCA 61.646 63.158 18.83 14.25 33.68 3.49
647 837 1.446272 GTGGTGGTCGAGCTAGCAC 60.446 63.158 23.19 23.19 46.59 4.40
649 839 4.988065 GTGGTCGAGCTAGCACAA 57.012 55.556 18.83 0.00 45.11 3.33
650 840 2.743195 GTGGTCGAGCTAGCACAAG 58.257 57.895 18.83 4.97 45.11 3.16
651 841 0.038159 GTGGTCGAGCTAGCACAAGT 60.038 55.000 18.83 0.00 45.11 3.16
652 842 0.038251 TGGTCGAGCTAGCACAAGTG 60.038 55.000 18.83 0.00 0.00 3.16
664 854 1.800805 CACAAGTGCTAGAGGTGGTG 58.199 55.000 0.00 0.00 0.00 4.17
665 855 0.687354 ACAAGTGCTAGAGGTGGTGG 59.313 55.000 0.00 0.00 0.00 4.61
666 856 0.687354 CAAGTGCTAGAGGTGGTGGT 59.313 55.000 0.00 0.00 0.00 4.16
667 857 0.977395 AAGTGCTAGAGGTGGTGGTC 59.023 55.000 0.00 0.00 0.00 4.02
1058 1374 0.460987 GACCAAGAGGACATGCCGAG 60.461 60.000 0.00 0.00 43.43 4.63
1148 1464 3.753272 GCTGATGTTTGTAAGCTGAAGGA 59.247 43.478 0.00 0.00 32.82 3.36
1460 1776 0.468226 GTCCTATGCACGGGGATTGA 59.532 55.000 0.00 0.00 0.00 2.57
1493 1809 0.251386 TGAGAAGGAGGCTCGTGAGT 60.251 55.000 10.92 0.00 35.15 3.41
2148 2951 2.498885 CCCTGTCTGATGTGTCTGATGA 59.501 50.000 0.00 0.00 35.22 2.92
2161 2964 0.036952 CTGATGAACACCCAGACGCT 60.037 55.000 0.00 0.00 0.00 5.07
2262 3065 2.889512 ACACCCTGTCTGATGTGTCTA 58.110 47.619 0.00 0.00 37.37 2.59
2263 3066 3.239449 ACACCCTGTCTGATGTGTCTAA 58.761 45.455 0.00 0.00 37.37 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
153 154 2.858644 TCCATATCACCCCTGAACCTT 58.141 47.619 0.00 0.00 0.00 3.50
313 314 0.245539 CCGCCTCCACGACTTCTTTA 59.754 55.000 0.00 0.00 34.06 1.85
317 318 4.373116 TGCCGCCTCCACGACTTC 62.373 66.667 0.00 0.00 34.06 3.01
420 610 2.154462 CCACCACCTCTAGCACTTTTG 58.846 52.381 0.00 0.00 0.00 2.44
421 611 1.774856 ACCACCACCTCTAGCACTTTT 59.225 47.619 0.00 0.00 0.00 2.27
422 612 1.348036 GACCACCACCTCTAGCACTTT 59.652 52.381 0.00 0.00 0.00 2.66
423 613 0.977395 GACCACCACCTCTAGCACTT 59.023 55.000 0.00 0.00 0.00 3.16
424 614 1.251527 CGACCACCACCTCTAGCACT 61.252 60.000 0.00 0.00 0.00 4.40
425 615 1.215647 CGACCACCACCTCTAGCAC 59.784 63.158 0.00 0.00 0.00 4.40
426 616 0.965866 CTCGACCACCACCTCTAGCA 60.966 60.000 0.00 0.00 0.00 3.49
427 617 1.668101 CCTCGACCACCACCTCTAGC 61.668 65.000 0.00 0.00 0.00 3.42
428 618 0.034380 TCCTCGACCACCACCTCTAG 60.034 60.000 0.00 0.00 0.00 2.43
429 619 0.406750 TTCCTCGACCACCACCTCTA 59.593 55.000 0.00 0.00 0.00 2.43
430 620 0.900647 CTTCCTCGACCACCACCTCT 60.901 60.000 0.00 0.00 0.00 3.69
431 621 1.592223 CTTCCTCGACCACCACCTC 59.408 63.158 0.00 0.00 0.00 3.85
432 622 2.584391 GCTTCCTCGACCACCACCT 61.584 63.158 0.00 0.00 0.00 4.00
433 623 2.047179 GCTTCCTCGACCACCACC 60.047 66.667 0.00 0.00 0.00 4.61
434 624 1.668151 GTGCTTCCTCGACCACCAC 60.668 63.158 0.00 0.00 0.00 4.16
435 625 1.691195 TTGTGCTTCCTCGACCACCA 61.691 55.000 0.00 0.00 0.00 4.17
436 626 0.951040 CTTGTGCTTCCTCGACCACC 60.951 60.000 0.00 0.00 0.00 4.61
437 627 0.249911 ACTTGTGCTTCCTCGACCAC 60.250 55.000 0.00 0.00 0.00 4.16
438 628 0.249868 CACTTGTGCTTCCTCGACCA 60.250 55.000 0.00 0.00 0.00 4.02
439 629 1.569479 GCACTTGTGCTTCCTCGACC 61.569 60.000 17.36 0.00 0.00 4.79
440 630 0.601311 AGCACTTGTGCTTCCTCGAC 60.601 55.000 20.95 0.00 43.52 4.20
441 631 0.966179 TAGCACTTGTGCTTCCTCGA 59.034 50.000 29.37 10.97 43.52 4.04
442 632 1.337260 ACTAGCACTTGTGCTTCCTCG 60.337 52.381 29.37 16.38 43.52 4.63
443 633 2.072298 CACTAGCACTTGTGCTTCCTC 58.928 52.381 29.37 0.08 43.52 3.71
444 634 1.271054 CCACTAGCACTTGTGCTTCCT 60.271 52.381 29.37 11.29 43.52 3.36
445 635 1.160137 CCACTAGCACTTGTGCTTCC 58.840 55.000 29.37 1.14 43.52 3.46
446 636 1.532868 CACCACTAGCACTTGTGCTTC 59.467 52.381 29.37 1.49 43.52 3.86
447 637 1.597742 CACCACTAGCACTTGTGCTT 58.402 50.000 29.37 13.03 43.52 3.91
449 639 0.535102 ACCACCACTAGCACTTGTGC 60.535 55.000 16.98 16.98 35.51 4.57
450 640 1.229428 CACCACCACTAGCACTTGTG 58.771 55.000 5.41 5.41 36.36 3.33
451 641 0.108585 CCACCACCACTAGCACTTGT 59.891 55.000 0.00 0.00 0.00 3.16
452 642 0.108585 ACCACCACCACTAGCACTTG 59.891 55.000 0.00 0.00 0.00 3.16
453 643 0.396811 GACCACCACCACTAGCACTT 59.603 55.000 0.00 0.00 0.00 3.16
454 644 1.816863 CGACCACCACCACTAGCACT 61.817 60.000 0.00 0.00 0.00 4.40
455 645 1.374252 CGACCACCACCACTAGCAC 60.374 63.158 0.00 0.00 0.00 4.40
456 646 1.532078 TCGACCACCACCACTAGCA 60.532 57.895 0.00 0.00 0.00 3.49
457 647 1.215647 CTCGACCACCACCACTAGC 59.784 63.158 0.00 0.00 0.00 3.42
458 648 1.215647 GCTCGACCACCACCACTAG 59.784 63.158 0.00 0.00 0.00 2.57
459 649 0.038599 TAGCTCGACCACCACCACTA 59.961 55.000 0.00 0.00 0.00 2.74
460 650 1.228769 TAGCTCGACCACCACCACT 60.229 57.895 0.00 0.00 0.00 4.00
461 651 1.215647 CTAGCTCGACCACCACCAC 59.784 63.158 0.00 0.00 0.00 4.16
462 652 2.646175 GCTAGCTCGACCACCACCA 61.646 63.158 7.70 0.00 0.00 4.17
463 653 2.184579 GCTAGCTCGACCACCACC 59.815 66.667 7.70 0.00 0.00 4.61
464 654 1.446272 GTGCTAGCTCGACCACCAC 60.446 63.158 17.23 0.00 0.00 4.16
465 655 1.468506 TTGTGCTAGCTCGACCACCA 61.469 55.000 17.23 0.00 0.00 4.17
466 656 0.737715 CTTGTGCTAGCTCGACCACC 60.738 60.000 17.23 0.00 0.00 4.61
467 657 0.038159 ACTTGTGCTAGCTCGACCAC 60.038 55.000 17.23 4.92 0.00 4.16
468 658 0.038251 CACTTGTGCTAGCTCGACCA 60.038 55.000 17.23 2.09 0.00 4.02
469 659 1.355066 GCACTTGTGCTAGCTCGACC 61.355 60.000 17.23 0.00 0.00 4.79
470 660 0.389166 AGCACTTGTGCTAGCTCGAC 60.389 55.000 24.50 6.50 44.28 4.20
471 661 1.173913 TAGCACTTGTGCTAGCTCGA 58.826 50.000 25.81 11.44 44.28 4.04
472 662 3.721625 TAGCACTTGTGCTAGCTCG 57.278 52.632 25.81 3.24 44.28 5.03
477 667 1.550524 CCACCTCTAGCACTTGTGCTA 59.449 52.381 27.11 27.11 44.28 3.49
479 669 0.035458 ACCACCTCTAGCACTTGTGC 59.965 55.000 16.98 16.98 0.00 4.57
480 670 1.609061 CCACCACCTCTAGCACTTGTG 60.609 57.143 0.00 0.00 0.00 3.33
481 671 0.687354 CCACCACCTCTAGCACTTGT 59.313 55.000 0.00 0.00 0.00 3.16
482 672 0.687354 ACCACCACCTCTAGCACTTG 59.313 55.000 0.00 0.00 0.00 3.16
483 673 0.977395 GACCACCACCTCTAGCACTT 59.023 55.000 0.00 0.00 0.00 3.16
484 674 1.251527 CGACCACCACCTCTAGCACT 61.252 60.000 0.00 0.00 0.00 4.40
485 675 1.215647 CGACCACCACCTCTAGCAC 59.784 63.158 0.00 0.00 0.00 4.40
486 676 0.965866 CTCGACCACCACCTCTAGCA 60.966 60.000 0.00 0.00 0.00 3.49
487 677 1.668101 CCTCGACCACCACCTCTAGC 61.668 65.000 0.00 0.00 0.00 3.42
488 678 0.034380 TCCTCGACCACCACCTCTAG 60.034 60.000 0.00 0.00 0.00 2.43
489 679 0.406750 TTCCTCGACCACCACCTCTA 59.593 55.000 0.00 0.00 0.00 2.43
490 680 0.900647 CTTCCTCGACCACCACCTCT 60.901 60.000 0.00 0.00 0.00 3.69
491 681 1.592223 CTTCCTCGACCACCACCTC 59.408 63.158 0.00 0.00 0.00 3.85
492 682 2.584391 GCTTCCTCGACCACCACCT 61.584 63.158 0.00 0.00 0.00 4.00
493 683 2.047179 GCTTCCTCGACCACCACC 60.047 66.667 0.00 0.00 0.00 4.61
494 684 1.668151 GTGCTTCCTCGACCACCAC 60.668 63.158 0.00 0.00 0.00 4.16
495 685 1.691195 TTGTGCTTCCTCGACCACCA 61.691 55.000 0.00 0.00 0.00 4.17
496 686 0.951040 CTTGTGCTTCCTCGACCACC 60.951 60.000 0.00 0.00 0.00 4.61
497 687 0.249911 ACTTGTGCTTCCTCGACCAC 60.250 55.000 0.00 0.00 0.00 4.16
498 688 0.249868 CACTTGTGCTTCCTCGACCA 60.250 55.000 0.00 0.00 0.00 4.02
499 689 1.569479 GCACTTGTGCTTCCTCGACC 61.569 60.000 17.36 0.00 0.00 4.79
500 690 0.601311 AGCACTTGTGCTTCCTCGAC 60.601 55.000 20.95 0.00 43.52 4.20
501 691 0.966179 TAGCACTTGTGCTTCCTCGA 59.034 50.000 29.37 10.97 43.52 4.04
502 692 1.337260 ACTAGCACTTGTGCTTCCTCG 60.337 52.381 29.37 16.38 43.52 4.63
503 693 2.072298 CACTAGCACTTGTGCTTCCTC 58.928 52.381 29.37 0.08 43.52 3.71
504 694 1.271054 CCACTAGCACTTGTGCTTCCT 60.271 52.381 29.37 11.29 43.52 3.36
505 695 1.160137 CCACTAGCACTTGTGCTTCC 58.840 55.000 29.37 1.14 43.52 3.46
506 696 1.884235 ACCACTAGCACTTGTGCTTC 58.116 50.000 29.37 1.49 43.52 3.86
507 697 2.368875 ACTACCACTAGCACTTGTGCTT 59.631 45.455 29.37 15.83 43.52 3.91
509 699 2.069273 CACTACCACTAGCACTTGTGC 58.931 52.381 16.98 16.98 35.51 4.57
510 700 2.037251 ACCACTACCACTAGCACTTGTG 59.963 50.000 5.41 5.41 36.36 3.33
511 701 2.299297 GACCACTACCACTAGCACTTGT 59.701 50.000 0.00 0.00 0.00 3.16
512 702 2.671351 CGACCACTACCACTAGCACTTG 60.671 54.545 0.00 0.00 0.00 3.16
513 703 1.544691 CGACCACTACCACTAGCACTT 59.455 52.381 0.00 0.00 0.00 3.16
514 704 1.174783 CGACCACTACCACTAGCACT 58.825 55.000 0.00 0.00 0.00 4.40
515 705 1.132643 CTCGACCACTACCACTAGCAC 59.867 57.143 0.00 0.00 0.00 4.40
516 706 1.460504 CTCGACCACTACCACTAGCA 58.539 55.000 0.00 0.00 0.00 3.49
517 707 0.100861 GCTCGACCACTACCACTAGC 59.899 60.000 0.00 0.00 0.00 3.42
518 708 1.752683 AGCTCGACCACTACCACTAG 58.247 55.000 0.00 0.00 0.00 2.57
519 709 2.915349 CTAGCTCGACCACTACCACTA 58.085 52.381 0.00 0.00 0.00 2.74
520 710 1.752683 CTAGCTCGACCACTACCACT 58.247 55.000 0.00 0.00 0.00 4.00
521 711 0.100861 GCTAGCTCGACCACTACCAC 59.899 60.000 7.70 0.00 0.00 4.16
522 712 0.323087 TGCTAGCTCGACCACTACCA 60.323 55.000 17.23 0.00 0.00 3.25
523 713 0.100861 GTGCTAGCTCGACCACTACC 59.899 60.000 17.23 0.00 0.00 3.18
524 714 0.809385 TGTGCTAGCTCGACCACTAC 59.191 55.000 17.23 2.58 0.00 2.73
525 715 1.472878 CTTGTGCTAGCTCGACCACTA 59.527 52.381 17.23 0.49 0.00 2.74
526 716 0.244994 CTTGTGCTAGCTCGACCACT 59.755 55.000 17.23 0.00 0.00 4.00
527 717 0.038159 ACTTGTGCTAGCTCGACCAC 60.038 55.000 17.23 4.92 0.00 4.16
528 718 0.038251 CACTTGTGCTAGCTCGACCA 60.038 55.000 17.23 2.09 0.00 4.02
529 719 1.355066 GCACTTGTGCTAGCTCGACC 61.355 60.000 17.23 0.00 0.00 4.79
530 720 0.389166 AGCACTTGTGCTAGCTCGAC 60.389 55.000 24.50 6.50 44.28 4.20
531 721 1.173913 TAGCACTTGTGCTAGCTCGA 58.826 50.000 25.81 11.44 44.28 4.04
532 722 3.721625 TAGCACTTGTGCTAGCTCG 57.278 52.632 25.81 3.24 44.28 5.03
537 727 1.550524 CCACCTCTAGCACTTGTGCTA 59.449 52.381 27.11 27.11 44.28 3.49
539 729 0.035458 ACCACCTCTAGCACTTGTGC 59.965 55.000 16.98 16.98 0.00 4.57
540 730 1.609061 CCACCACCTCTAGCACTTGTG 60.609 57.143 0.00 0.00 0.00 3.33
541 731 0.687354 CCACCACCTCTAGCACTTGT 59.313 55.000 0.00 0.00 0.00 3.16
542 732 0.687354 ACCACCACCTCTAGCACTTG 59.313 55.000 0.00 0.00 0.00 3.16
543 733 0.977395 GACCACCACCTCTAGCACTT 59.023 55.000 0.00 0.00 0.00 3.16
544 734 1.251527 CGACCACCACCTCTAGCACT 61.252 60.000 0.00 0.00 0.00 4.40
545 735 1.215647 CGACCACCACCTCTAGCAC 59.784 63.158 0.00 0.00 0.00 4.40
546 736 0.965866 CTCGACCACCACCTCTAGCA 60.966 60.000 0.00 0.00 0.00 3.49
547 737 1.810532 CTCGACCACCACCTCTAGC 59.189 63.158 0.00 0.00 0.00 3.42
548 738 0.681564 AGCTCGACCACCACCTCTAG 60.682 60.000 0.00 0.00 0.00 2.43
549 739 1.383019 AGCTCGACCACCACCTCTA 59.617 57.895 0.00 0.00 0.00 2.43
550 740 2.118513 AGCTCGACCACCACCTCT 59.881 61.111 0.00 0.00 0.00 3.69
591 781 0.965866 CTCGACCACCACCTCTAGCA 60.966 60.000 0.00 0.00 0.00 3.49
592 782 1.668101 CCTCGACCACCACCTCTAGC 61.668 65.000 0.00 0.00 0.00 3.42
593 783 0.034380 TCCTCGACCACCACCTCTAG 60.034 60.000 0.00 0.00 0.00 2.43
594 784 0.323178 GTCCTCGACCACCACCTCTA 60.323 60.000 0.00 0.00 0.00 2.43
595 785 1.606889 GTCCTCGACCACCACCTCT 60.607 63.158 0.00 0.00 0.00 3.69
596 786 2.971452 GTCCTCGACCACCACCTC 59.029 66.667 0.00 0.00 0.00 3.85
597 787 2.989824 CGTCCTCGACCACCACCT 60.990 66.667 0.00 0.00 39.71 4.00
598 788 4.736896 GCGTCCTCGACCACCACC 62.737 72.222 0.00 0.00 39.71 4.61
602 792 2.022129 CTTGTGCGTCCTCGACCAC 61.022 63.158 6.50 6.50 39.71 4.16
604 794 2.022129 CACTTGTGCGTCCTCGACC 61.022 63.158 0.00 0.00 39.71 4.79
607 797 1.073216 CTAGCACTTGTGCGTCCTCG 61.073 60.000 18.32 3.22 40.27 4.63
612 802 0.880278 CACCACTAGCACTTGTGCGT 60.880 55.000 18.32 9.73 40.27 5.24
613 803 1.568612 CCACCACTAGCACTTGTGCG 61.569 60.000 18.32 9.14 40.27 5.34
627 817 2.646175 GCTAGCTCGACCACCACCA 61.646 63.158 7.70 0.00 0.00 4.17
642 832 1.550524 CCACCTCTAGCACTTGTGCTA 59.449 52.381 27.11 27.11 44.28 3.49
644 834 0.035458 ACCACCTCTAGCACTTGTGC 59.965 55.000 16.98 16.98 0.00 4.57
645 835 1.609061 CCACCACCTCTAGCACTTGTG 60.609 57.143 0.00 0.00 0.00 3.33
646 836 0.687354 CCACCACCTCTAGCACTTGT 59.313 55.000 0.00 0.00 0.00 3.16
647 837 0.687354 ACCACCACCTCTAGCACTTG 59.313 55.000 0.00 0.00 0.00 3.16
648 838 0.977395 GACCACCACCTCTAGCACTT 59.023 55.000 0.00 0.00 0.00 3.16
649 839 1.251527 CGACCACCACCTCTAGCACT 61.252 60.000 0.00 0.00 0.00 4.40
650 840 1.215647 CGACCACCACCTCTAGCAC 59.784 63.158 0.00 0.00 0.00 4.40
651 841 0.965866 CTCGACCACCACCTCTAGCA 60.966 60.000 0.00 0.00 0.00 3.49
652 842 1.668101 CCTCGACCACCACCTCTAGC 61.668 65.000 0.00 0.00 0.00 3.42
653 843 0.034380 TCCTCGACCACCACCTCTAG 60.034 60.000 0.00 0.00 0.00 2.43
654 844 0.406750 TTCCTCGACCACCACCTCTA 59.593 55.000 0.00 0.00 0.00 2.43
655 845 0.900647 CTTCCTCGACCACCACCTCT 60.901 60.000 0.00 0.00 0.00 3.69
656 846 1.592223 CTTCCTCGACCACCACCTC 59.408 63.158 0.00 0.00 0.00 3.85
657 847 2.584391 GCTTCCTCGACCACCACCT 61.584 63.158 0.00 0.00 0.00 4.00
658 848 2.047179 GCTTCCTCGACCACCACC 60.047 66.667 0.00 0.00 0.00 4.61
659 849 1.668151 GTGCTTCCTCGACCACCAC 60.668 63.158 0.00 0.00 0.00 4.16
660 850 1.691195 TTGTGCTTCCTCGACCACCA 61.691 55.000 0.00 0.00 0.00 4.17
661 851 0.951040 CTTGTGCTTCCTCGACCACC 60.951 60.000 0.00 0.00 0.00 4.61
662 852 0.249911 ACTTGTGCTTCCTCGACCAC 60.250 55.000 0.00 0.00 0.00 4.16
663 853 0.249868 CACTTGTGCTTCCTCGACCA 60.250 55.000 0.00 0.00 0.00 4.02
664 854 1.569479 GCACTTGTGCTTCCTCGACC 61.569 60.000 17.36 0.00 0.00 4.79
665 855 0.601311 AGCACTTGTGCTTCCTCGAC 60.601 55.000 20.95 0.00 43.52 4.20
666 856 0.966179 TAGCACTTGTGCTTCCTCGA 59.034 50.000 29.37 10.97 43.52 4.04
667 857 1.337260 ACTAGCACTTGTGCTTCCTCG 60.337 52.381 29.37 16.38 43.52 4.63
1038 1354 0.904865 TCGGCATGTCCTCTTGGTCT 60.905 55.000 0.00 0.00 34.23 3.85
1058 1374 3.391665 CTGGCCTCCATCCACGTCC 62.392 68.421 3.32 0.00 30.82 4.79
1148 1464 0.532862 CTTGTTGCGGTCAGTGGACT 60.533 55.000 0.00 0.00 43.77 3.85
1460 1776 4.421479 CTCACGACGCTCCCGCTT 62.421 66.667 0.00 0.00 38.22 4.68
1493 1809 0.392706 TCTTCCTCACGCTTCTTGCA 59.607 50.000 0.00 0.00 43.06 4.08
2148 2951 0.320697 GACCTTAGCGTCTGGGTGTT 59.679 55.000 9.57 0.00 31.60 3.32
2161 2964 2.967397 CAGACGCCACGGACCTTA 59.033 61.111 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.