Multiple sequence alignment - TraesCS5D01G290700

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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 TraesCS5D01G290700 chr5D 100.000 3196 0 0 1 3196 388592566 388595761 0.000000e+00 5903
1 TraesCS5D01G290700 chr5D 91.031 1416 79 10 608 2008 406899477 406900859 0.000000e+00 1868
2 TraesCS5D01G290700 chr5D 91.296 540 29 11 1 531 388412488 388413018 0.000000e+00 721
3 TraesCS5D01G290700 chr5D 89.493 552 33 9 1 535 388381420 388381963 0.000000e+00 675
4 TraesCS5D01G290700 chr5D 89.579 499 33 6 10 501 353954507 353954993 1.630000e-172 616
5 TraesCS5D01G290700 chr7D 94.571 1934 86 9 609 2531 525733739 525735664 0.000000e+00 2972
6 TraesCS5D01G290700 chr7D 93.023 688 33 5 2522 3196 525762931 525763616 0.000000e+00 990
7 TraesCS5D01G290700 chr7D 88.293 410 35 7 1 404 437592820 437593222 2.230000e-131 479
8 TraesCS5D01G290700 chr1D 93.933 1945 97 10 607 2531 42897257 42895314 0.000000e+00 2918
9 TraesCS5D01G290700 chr1D 95.190 998 36 6 1545 2531 7181412 7182408 0.000000e+00 1567
10 TraesCS5D01G290700 chr3B 92.824 1951 109 13 608 2532 726424352 726426297 0.000000e+00 2798
11 TraesCS5D01G290700 chr3B 91.189 681 43 3 2522 3190 575280146 575280821 0.000000e+00 909
12 TraesCS5D01G290700 chr3B 89.229 687 49 10 2522 3196 13522634 13523307 0.000000e+00 835
13 TraesCS5D01G290700 chr2B 94.247 1825 91 5 608 2425 80552660 80550843 0.000000e+00 2776
14 TraesCS5D01G290700 chr2B 91.266 687 35 5 2522 3196 80545025 80544352 0.000000e+00 913
15 TraesCS5D01G290700 chr3A 92.820 1936 100 16 608 2531 22779068 22777160 0.000000e+00 2769
16 TraesCS5D01G290700 chr7A 92.680 1940 104 15 608 2525 689936403 689938326 0.000000e+00 2761
17 TraesCS5D01G290700 chr5A 92.596 1945 105 19 608 2531 573012214 573010288 0.000000e+00 2758
18 TraesCS5D01G290700 chr5A 92.285 687 40 2 2522 3196 113805878 113805193 0.000000e+00 963
19 TraesCS5D01G290700 chr6A 92.184 1932 118 15 608 2525 116690038 116691950 0.000000e+00 2700
20 TraesCS5D01G290700 chr6A 89.362 705 45 8 2522 3196 116696918 116697622 0.000000e+00 859
21 TraesCS5D01G290700 chr6A 87.464 694 66 4 2522 3196 117578999 117579690 0.000000e+00 780
22 TraesCS5D01G290700 chr6A 89.194 546 35 15 1 534 130413464 130413997 0.000000e+00 660
23 TraesCS5D01G290700 chr2D 91.795 1950 98 16 605 2531 380678112 380680022 0.000000e+00 2658
24 TraesCS5D01G290700 chr1B 93.467 1546 90 3 609 2147 548830933 548829392 0.000000e+00 2285
25 TraesCS5D01G290700 chr1B 91.581 677 41 3 2532 3196 548683182 548682510 0.000000e+00 920
26 TraesCS5D01G290700 chr1B 89.971 688 42 8 2522 3196 539844559 539843886 0.000000e+00 863
27 TraesCS5D01G290700 chr2A 91.774 1471 90 16 782 2237 773340879 773339425 0.000000e+00 2017
28 TraesCS5D01G290700 chr3D 95.391 998 32 7 1545 2531 590154237 590155231 0.000000e+00 1576
29 TraesCS5D01G290700 chr6D 94.349 814 44 2 607 1419 45675921 45676733 0.000000e+00 1247
30 TraesCS5D01G290700 chr6D 92.868 687 35 3 2522 3196 45802732 45803416 0.000000e+00 985
31 TraesCS5D01G290700 chr6D 88.278 546 35 11 1 534 106952376 106952904 7.530000e-176 627
32 TraesCS5D01G290700 chr4D 92.163 689 37 3 2522 3196 488871816 488872501 0.000000e+00 957
33 TraesCS5D01G290700 chr1A 88.369 705 46 11 2522 3196 571994390 571993692 0.000000e+00 815
34 TraesCS5D01G290700 chr5B 90.348 632 37 13 1 613 467020021 467020647 0.000000e+00 808
35 TraesCS5D01G290700 chr6B 91.590 547 33 2 2662 3196 130319221 130318676 0.000000e+00 743
36 TraesCS5D01G290700 chr7B 90.000 410 29 6 1 404 456502019 456501616 1.310000e-143 520
37 TraesCS5D01G290700 chr4A 89.258 391 34 2 1 388 45871671 45872056 1.720000e-132 483


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 TraesCS5D01G290700 chr5D 388592566 388595761 3195 False 5903 5903 100.000 1 3196 1 chr5D.!!$F4 3195
1 TraesCS5D01G290700 chr5D 406899477 406900859 1382 False 1868 1868 91.031 608 2008 1 chr5D.!!$F5 1400
2 TraesCS5D01G290700 chr5D 388412488 388413018 530 False 721 721 91.296 1 531 1 chr5D.!!$F3 530
3 TraesCS5D01G290700 chr5D 388381420 388381963 543 False 675 675 89.493 1 535 1 chr5D.!!$F2 534
4 TraesCS5D01G290700 chr7D 525733739 525735664 1925 False 2972 2972 94.571 609 2531 1 chr7D.!!$F2 1922
5 TraesCS5D01G290700 chr7D 525762931 525763616 685 False 990 990 93.023 2522 3196 1 chr7D.!!$F3 674
6 TraesCS5D01G290700 chr1D 42895314 42897257 1943 True 2918 2918 93.933 607 2531 1 chr1D.!!$R1 1924
7 TraesCS5D01G290700 chr1D 7181412 7182408 996 False 1567 1567 95.190 1545 2531 1 chr1D.!!$F1 986
8 TraesCS5D01G290700 chr3B 726424352 726426297 1945 False 2798 2798 92.824 608 2532 1 chr3B.!!$F3 1924
9 TraesCS5D01G290700 chr3B 575280146 575280821 675 False 909 909 91.189 2522 3190 1 chr3B.!!$F2 668
10 TraesCS5D01G290700 chr3B 13522634 13523307 673 False 835 835 89.229 2522 3196 1 chr3B.!!$F1 674
11 TraesCS5D01G290700 chr2B 80550843 80552660 1817 True 2776 2776 94.247 608 2425 1 chr2B.!!$R2 1817
12 TraesCS5D01G290700 chr2B 80544352 80545025 673 True 913 913 91.266 2522 3196 1 chr2B.!!$R1 674
13 TraesCS5D01G290700 chr3A 22777160 22779068 1908 True 2769 2769 92.820 608 2531 1 chr3A.!!$R1 1923
14 TraesCS5D01G290700 chr7A 689936403 689938326 1923 False 2761 2761 92.680 608 2525 1 chr7A.!!$F1 1917
15 TraesCS5D01G290700 chr5A 573010288 573012214 1926 True 2758 2758 92.596 608 2531 1 chr5A.!!$R2 1923
16 TraesCS5D01G290700 chr5A 113805193 113805878 685 True 963 963 92.285 2522 3196 1 chr5A.!!$R1 674
17 TraesCS5D01G290700 chr6A 116690038 116691950 1912 False 2700 2700 92.184 608 2525 1 chr6A.!!$F1 1917
18 TraesCS5D01G290700 chr6A 116696918 116697622 704 False 859 859 89.362 2522 3196 1 chr6A.!!$F2 674
19 TraesCS5D01G290700 chr6A 117578999 117579690 691 False 780 780 87.464 2522 3196 1 chr6A.!!$F3 674
20 TraesCS5D01G290700 chr6A 130413464 130413997 533 False 660 660 89.194 1 534 1 chr6A.!!$F4 533
21 TraesCS5D01G290700 chr2D 380678112 380680022 1910 False 2658 2658 91.795 605 2531 1 chr2D.!!$F1 1926
22 TraesCS5D01G290700 chr1B 548829392 548830933 1541 True 2285 2285 93.467 609 2147 1 chr1B.!!$R3 1538
23 TraesCS5D01G290700 chr1B 548682510 548683182 672 True 920 920 91.581 2532 3196 1 chr1B.!!$R2 664
24 TraesCS5D01G290700 chr1B 539843886 539844559 673 True 863 863 89.971 2522 3196 1 chr1B.!!$R1 674
25 TraesCS5D01G290700 chr2A 773339425 773340879 1454 True 2017 2017 91.774 782 2237 1 chr2A.!!$R1 1455
26 TraesCS5D01G290700 chr3D 590154237 590155231 994 False 1576 1576 95.391 1545 2531 1 chr3D.!!$F1 986
27 TraesCS5D01G290700 chr6D 45675921 45676733 812 False 1247 1247 94.349 607 1419 1 chr6D.!!$F1 812
28 TraesCS5D01G290700 chr6D 45802732 45803416 684 False 985 985 92.868 2522 3196 1 chr6D.!!$F2 674
29 TraesCS5D01G290700 chr6D 106952376 106952904 528 False 627 627 88.278 1 534 1 chr6D.!!$F3 533
30 TraesCS5D01G290700 chr4D 488871816 488872501 685 False 957 957 92.163 2522 3196 1 chr4D.!!$F1 674
31 TraesCS5D01G290700 chr1A 571993692 571994390 698 True 815 815 88.369 2522 3196 1 chr1A.!!$R1 674
32 TraesCS5D01G290700 chr5B 467020021 467020647 626 False 808 808 90.348 1 613 1 chr5B.!!$F1 612
33 TraesCS5D01G290700 chr6B 130318676 130319221 545 True 743 743 91.590 2662 3196 1 chr6B.!!$R1 534

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
471 476 0.107268 TCTTCTGCTGCTGCTGAACA 59.893 50.000 26.43 17.81 46.93 3.18 F
957 977 0.455410 CTCTGTTCCTCTGCTCTCCG 59.545 60.000 0.00 0.00 0.00 4.63 F
1698 1884 1.152881 GGTAGATGCCCCTTGCCTG 60.153 63.158 0.00 0.00 40.16 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1943 2146 0.767375 TCTTTGCCTGCTCCTCAAGT 59.233 50.000 0.00 0.00 0.00 3.16 R
2008 2226 0.982704 AGCTTGACTCTGCAGGATGT 59.017 50.000 15.13 10.62 39.31 3.06 R
3097 3414 4.019513 TCGTCCTCCCCACCCCAT 62.020 66.667 0.00 0.00 0.00 4.00 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
99 100 1.289109 CCAACACTACGCCTCCAACG 61.289 60.000 0.00 0.00 0.00 4.10
205 206 1.739049 GTGCTCGAGATGGAGAGGG 59.261 63.158 18.75 0.00 36.08 4.30
300 301 1.263217 GACAACTTGTTGCGACGGATT 59.737 47.619 12.76 0.00 0.00 3.01
314 315 1.827969 ACGGATTGGACTCTTCCTCAG 59.172 52.381 0.00 0.00 43.31 3.35
331 332 2.201022 AGGCTTGACGACCACGACT 61.201 57.895 0.00 0.00 42.66 4.18
348 349 1.743958 GACTTGAAGCAGCAGCATCAT 59.256 47.619 9.89 0.00 46.50 2.45
349 350 2.941064 GACTTGAAGCAGCAGCATCATA 59.059 45.455 9.89 1.32 46.50 2.15
350 351 3.349927 ACTTGAAGCAGCAGCATCATAA 58.650 40.909 9.89 0.00 46.50 1.90
351 352 3.952323 ACTTGAAGCAGCAGCATCATAAT 59.048 39.130 9.89 0.00 46.50 1.28
352 353 4.036498 ACTTGAAGCAGCAGCATCATAATC 59.964 41.667 9.89 0.00 46.50 1.75
353 354 3.547746 TGAAGCAGCAGCATCATAATCA 58.452 40.909 4.80 0.00 42.90 2.57
354 355 3.949113 TGAAGCAGCAGCATCATAATCAA 59.051 39.130 4.80 0.00 42.90 2.57
355 356 4.399934 TGAAGCAGCAGCATCATAATCAAA 59.600 37.500 4.80 0.00 42.90 2.69
356 357 4.569761 AGCAGCAGCATCATAATCAAAG 57.430 40.909 3.17 0.00 45.49 2.77
357 358 3.050619 GCAGCAGCATCATAATCAAAGC 58.949 45.455 0.00 0.00 41.58 3.51
358 359 3.243434 GCAGCAGCATCATAATCAAAGCT 60.243 43.478 0.00 0.00 41.58 3.74
359 360 4.736759 GCAGCAGCATCATAATCAAAGCTT 60.737 41.667 0.00 0.00 41.58 3.74
360 361 4.976731 CAGCAGCATCATAATCAAAGCTTC 59.023 41.667 0.00 0.00 0.00 3.86
408 409 1.136446 CGGTTGTGATCGTCGTTTTCC 60.136 52.381 0.00 0.00 0.00 3.13
411 412 3.002965 GGTTGTGATCGTCGTTTTCCTTT 59.997 43.478 0.00 0.00 0.00 3.11
451 456 8.319146 TGGCTAGTAGAAAGCTTGTAATAGTTT 58.681 33.333 17.96 0.00 39.97 2.66
471 476 0.107268 TCTTCTGCTGCTGCTGAACA 59.893 50.000 26.43 17.81 46.93 3.18
496 501 9.914923 CATGATTGAAAATGTATGAAATTGCTG 57.085 29.630 0.00 0.00 0.00 4.41
497 502 9.878667 ATGATTGAAAATGTATGAAATTGCTGA 57.121 25.926 0.00 0.00 0.00 4.26
498 503 9.878667 TGATTGAAAATGTATGAAATTGCTGAT 57.121 25.926 0.00 0.00 0.00 2.90
501 506 9.708092 TTGAAAATGTATGAAATTGCTGATTCA 57.292 25.926 2.05 2.05 39.66 2.57
502 507 9.878667 TGAAAATGTATGAAATTGCTGATTCAT 57.121 25.926 13.34 13.34 45.54 2.57
505 510 8.570096 AATGTATGAAATTGCTGATTCATTCG 57.430 30.769 13.82 0.00 42.12 3.34
506 511 7.319142 TGTATGAAATTGCTGATTCATTCGA 57.681 32.000 13.82 0.00 42.12 3.71
507 512 7.412063 TGTATGAAATTGCTGATTCATTCGAG 58.588 34.615 13.82 0.00 42.12 4.04
508 513 5.885230 TGAAATTGCTGATTCATTCGAGT 57.115 34.783 0.00 0.00 30.94 4.18
509 514 5.872635 TGAAATTGCTGATTCATTCGAGTC 58.127 37.500 0.00 0.00 30.94 3.36
510 515 5.645067 TGAAATTGCTGATTCATTCGAGTCT 59.355 36.000 0.00 0.00 30.94 3.24
511 516 5.731599 AATTGCTGATTCATTCGAGTCTC 57.268 39.130 0.00 0.00 0.00 3.36
512 517 4.462508 TTGCTGATTCATTCGAGTCTCT 57.537 40.909 0.00 0.00 0.00 3.10
513 518 3.778618 TGCTGATTCATTCGAGTCTCTG 58.221 45.455 0.00 0.00 0.00 3.35
514 519 2.539274 GCTGATTCATTCGAGTCTCTGC 59.461 50.000 0.00 0.00 0.00 4.26
515 520 3.737663 GCTGATTCATTCGAGTCTCTGCT 60.738 47.826 0.00 0.00 0.00 4.24
516 521 4.039151 TGATTCATTCGAGTCTCTGCTC 57.961 45.455 0.00 0.00 0.00 4.26
517 522 3.445096 TGATTCATTCGAGTCTCTGCTCA 59.555 43.478 0.00 0.00 35.33 4.26
518 523 3.942130 TTCATTCGAGTCTCTGCTCAA 57.058 42.857 0.00 0.00 35.33 3.02
519 524 4.462508 TTCATTCGAGTCTCTGCTCAAT 57.537 40.909 0.00 0.00 35.33 2.57
520 525 4.462508 TCATTCGAGTCTCTGCTCAATT 57.537 40.909 0.00 0.00 35.33 2.32
521 526 5.582689 TCATTCGAGTCTCTGCTCAATTA 57.417 39.130 0.00 0.00 35.33 1.40
522 527 5.586339 TCATTCGAGTCTCTGCTCAATTAG 58.414 41.667 0.00 0.00 35.33 1.73
523 528 5.126222 TCATTCGAGTCTCTGCTCAATTAGT 59.874 40.000 0.00 0.00 35.33 2.24
524 529 4.362932 TCGAGTCTCTGCTCAATTAGTG 57.637 45.455 0.00 0.00 35.33 2.74
525 530 4.010349 TCGAGTCTCTGCTCAATTAGTGA 58.990 43.478 0.00 0.00 35.33 3.41
526 531 4.642437 TCGAGTCTCTGCTCAATTAGTGAT 59.358 41.667 0.00 0.00 35.07 3.06
527 532 5.126222 TCGAGTCTCTGCTCAATTAGTGATT 59.874 40.000 0.00 0.00 35.07 2.57
528 533 5.809562 CGAGTCTCTGCTCAATTAGTGATTT 59.190 40.000 0.00 0.00 35.07 2.17
529 534 6.312426 CGAGTCTCTGCTCAATTAGTGATTTT 59.688 38.462 0.00 0.00 35.07 1.82
530 535 7.148507 CGAGTCTCTGCTCAATTAGTGATTTTT 60.149 37.037 0.00 0.00 35.07 1.94
551 556 4.478206 TTTTCAACTGATTTGGTTGCCA 57.522 36.364 0.00 0.00 42.40 4.92
552 557 4.686191 TTTCAACTGATTTGGTTGCCAT 57.314 36.364 0.00 0.00 42.40 4.40
553 558 3.940209 TCAACTGATTTGGTTGCCATC 57.060 42.857 0.00 0.00 42.40 3.51
554 559 3.499338 TCAACTGATTTGGTTGCCATCT 58.501 40.909 0.00 0.00 42.40 2.90
555 560 3.896888 TCAACTGATTTGGTTGCCATCTT 59.103 39.130 0.00 0.00 42.40 2.40
556 561 3.947910 ACTGATTTGGTTGCCATCTTG 57.052 42.857 0.00 0.00 31.53 3.02
557 562 3.233507 ACTGATTTGGTTGCCATCTTGT 58.766 40.909 0.00 0.00 31.53 3.16
558 563 3.256631 ACTGATTTGGTTGCCATCTTGTC 59.743 43.478 0.00 0.00 31.53 3.18
559 564 3.499338 TGATTTGGTTGCCATCTTGTCT 58.501 40.909 0.00 0.00 31.53 3.41
560 565 4.661222 TGATTTGGTTGCCATCTTGTCTA 58.339 39.130 0.00 0.00 31.53 2.59
561 566 4.701651 TGATTTGGTTGCCATCTTGTCTAG 59.298 41.667 0.00 0.00 31.53 2.43
562 567 2.113860 TGGTTGCCATCTTGTCTAGC 57.886 50.000 0.00 0.00 0.00 3.42
563 568 1.350684 TGGTTGCCATCTTGTCTAGCA 59.649 47.619 0.00 0.00 0.00 3.49
564 569 2.224744 TGGTTGCCATCTTGTCTAGCAA 60.225 45.455 0.00 0.00 40.89 3.91
566 571 2.857186 TGCCATCTTGTCTAGCAACA 57.143 45.000 0.00 0.00 32.90 3.33
567 572 3.354948 TGCCATCTTGTCTAGCAACAT 57.645 42.857 0.00 0.00 32.90 2.71
568 573 4.486125 TGCCATCTTGTCTAGCAACATA 57.514 40.909 0.00 0.00 32.90 2.29
569 574 4.842574 TGCCATCTTGTCTAGCAACATAA 58.157 39.130 0.00 0.00 32.90 1.90
570 575 4.635765 TGCCATCTTGTCTAGCAACATAAC 59.364 41.667 0.00 0.00 32.90 1.89
571 576 4.878397 GCCATCTTGTCTAGCAACATAACT 59.122 41.667 0.00 0.00 32.90 2.24
572 577 5.220739 GCCATCTTGTCTAGCAACATAACTG 60.221 44.000 0.00 0.00 32.90 3.16
573 578 6.108687 CCATCTTGTCTAGCAACATAACTGA 58.891 40.000 0.00 0.00 32.90 3.41
574 579 6.036517 CCATCTTGTCTAGCAACATAACTGAC 59.963 42.308 0.00 0.00 32.90 3.51
575 580 6.096673 TCTTGTCTAGCAACATAACTGACA 57.903 37.500 0.00 0.00 32.90 3.58
576 581 5.926542 TCTTGTCTAGCAACATAACTGACAC 59.073 40.000 0.00 0.00 33.53 3.67
577 582 5.468540 TGTCTAGCAACATAACTGACACT 57.531 39.130 0.00 0.00 0.00 3.55
578 583 5.853936 TGTCTAGCAACATAACTGACACTT 58.146 37.500 0.00 0.00 0.00 3.16
579 584 5.696270 TGTCTAGCAACATAACTGACACTTG 59.304 40.000 0.00 0.00 0.00 3.16
580 585 5.926542 GTCTAGCAACATAACTGACACTTGA 59.073 40.000 0.00 0.00 0.00 3.02
581 586 6.591834 GTCTAGCAACATAACTGACACTTGAT 59.408 38.462 0.00 0.00 0.00 2.57
582 587 5.618056 AGCAACATAACTGACACTTGATG 57.382 39.130 0.00 0.00 0.00 3.07
584 589 5.532406 AGCAACATAACTGACACTTGATGTT 59.468 36.000 0.00 0.00 43.56 2.71
586 591 6.728200 CAACATAACTGACACTTGATGTTGT 58.272 36.000 14.42 0.00 44.50 3.32
587 592 6.942532 ACATAACTGACACTTGATGTTGTT 57.057 33.333 0.00 0.00 43.56 2.83
588 593 6.959361 ACATAACTGACACTTGATGTTGTTC 58.041 36.000 0.00 0.00 43.56 3.18
589 594 6.767902 ACATAACTGACACTTGATGTTGTTCT 59.232 34.615 0.00 0.00 43.56 3.01
590 595 7.283127 ACATAACTGACACTTGATGTTGTTCTT 59.717 33.333 0.00 0.00 43.56 2.52
591 596 5.490139 ACTGACACTTGATGTTGTTCTTG 57.510 39.130 0.00 0.00 43.56 3.02
592 597 5.185454 ACTGACACTTGATGTTGTTCTTGA 58.815 37.500 0.00 0.00 43.56 3.02
593 598 5.295292 ACTGACACTTGATGTTGTTCTTGAG 59.705 40.000 0.00 0.00 43.56 3.02
594 599 4.576053 TGACACTTGATGTTGTTCTTGAGG 59.424 41.667 0.00 0.00 43.56 3.86
595 600 4.526970 ACACTTGATGTTGTTCTTGAGGT 58.473 39.130 0.00 0.00 38.98 3.85
596 601 4.576463 ACACTTGATGTTGTTCTTGAGGTC 59.424 41.667 0.00 0.00 38.98 3.85
597 602 4.818546 CACTTGATGTTGTTCTTGAGGTCT 59.181 41.667 0.00 0.00 0.00 3.85
598 603 5.049818 CACTTGATGTTGTTCTTGAGGTCTC 60.050 44.000 0.00 0.00 0.00 3.36
599 604 4.687901 TGATGTTGTTCTTGAGGTCTCA 57.312 40.909 0.00 0.00 37.91 3.27
600 605 4.635223 TGATGTTGTTCTTGAGGTCTCAG 58.365 43.478 0.75 0.00 41.13 3.35
601 606 4.344968 TGATGTTGTTCTTGAGGTCTCAGA 59.655 41.667 0.75 0.00 41.13 3.27
602 607 4.327982 TGTTGTTCTTGAGGTCTCAGAG 57.672 45.455 0.75 0.00 41.13 3.35
603 608 3.960755 TGTTGTTCTTGAGGTCTCAGAGA 59.039 43.478 0.00 0.00 41.13 3.10
604 609 4.405680 TGTTGTTCTTGAGGTCTCAGAGAA 59.594 41.667 0.20 15.10 41.13 2.87
605 610 4.862902 TGTTCTTGAGGTCTCAGAGAAG 57.137 45.455 17.46 0.00 41.13 2.85
741 748 5.763698 ACTAGATCGAGTTGATGACCGATTA 59.236 40.000 2.18 0.00 39.83 1.75
791 798 3.622826 CCCACCGGTCAGGACGTT 61.623 66.667 14.08 0.00 45.00 3.99
792 799 2.277591 CCCACCGGTCAGGACGTTA 61.278 63.158 14.08 0.00 45.00 3.18
824 831 4.371590 TAACAGCGCTCGCCTGCA 62.372 61.111 7.13 0.00 43.17 4.41
900 907 2.951745 GGCTCGCTCGTCGTCATG 60.952 66.667 0.00 0.00 39.67 3.07
957 977 0.455410 CTCTGTTCCTCTGCTCTCCG 59.545 60.000 0.00 0.00 0.00 4.63
978 1001 3.745458 CGCTGCTTCTTTTCTTCTTCTCT 59.255 43.478 0.00 0.00 0.00 3.10
1235 1417 6.989169 GCAAACTCCAGATACTGTGATAGATT 59.011 38.462 0.00 0.00 0.00 2.40
1697 1883 2.386935 GGGTAGATGCCCCTTGCCT 61.387 63.158 0.00 0.00 42.89 4.75
1698 1884 1.152881 GGTAGATGCCCCTTGCCTG 60.153 63.158 0.00 0.00 40.16 4.85
1741 1938 4.141756 GCTCTGGGATATGTATCATGAGGG 60.142 50.000 0.09 0.00 34.40 4.30
1943 2146 6.533730 TGAACTTAAGGAGAAGAAGCATCAA 58.466 36.000 7.53 0.00 0.00 2.57
2008 2226 5.552870 AAGCTCAAGAAAGAACAGAGGTA 57.447 39.130 0.00 0.00 36.17 3.08
2315 2539 3.910627 ACTCCCTATTAACTGCCTATGGG 59.089 47.826 0.00 0.00 34.98 4.00
2404 2628 4.169856 TCCTATTTGTAATGCCCCCTGAAT 59.830 41.667 0.00 0.00 0.00 2.57
2457 2681 0.986992 GCAATTTGTTGCTGCTAGCG 59.013 50.000 10.77 6.22 46.26 4.26
2715 2942 4.895668 ATTCCCATTGTGCTCAAACATT 57.104 36.364 5.15 0.00 37.11 2.71
2730 2957 9.979578 TGCTCAAACATTGTTCTAATGTAAATT 57.020 25.926 1.83 0.00 39.73 1.82
2818 3047 0.833287 ATCTGTTGCCATACCTCGCT 59.167 50.000 0.00 0.00 0.00 4.93
2840 3069 1.676967 CCAGCAGGACAAGGAAGCC 60.677 63.158 0.00 0.00 36.89 4.35
2842 3071 0.615331 CAGCAGGACAAGGAAGCCTA 59.385 55.000 0.00 0.00 31.13 3.93
3037 3332 3.262686 GATTCGGCGCCGGAGTTC 61.263 66.667 44.95 30.24 40.25 3.01
3097 3414 1.984570 CAGTGAGCTCGGGGGAGAA 60.985 63.158 9.64 0.00 0.00 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
180 181 1.326213 CCATCTCGAGCACCTCCTGT 61.326 60.000 7.81 0.00 0.00 4.00
250 251 1.198408 CGTGTTGTGCTGATCAATGCT 59.802 47.619 8.27 0.00 0.00 3.79
279 280 0.460459 TCCGTCGCAACAAGTTGTCA 60.460 50.000 9.40 0.00 42.31 3.58
314 315 1.300697 AAGTCGTGGTCGTCAAGCC 60.301 57.895 0.00 0.00 38.33 4.35
348 349 9.739276 TCTAAATCTTCTTGGAAGCTTTGATTA 57.261 29.630 15.05 0.69 0.00 1.75
349 350 8.641498 TCTAAATCTTCTTGGAAGCTTTGATT 57.359 30.769 15.05 0.57 0.00 2.57
350 351 7.338957 CCTCTAAATCTTCTTGGAAGCTTTGAT 59.661 37.037 15.05 0.00 0.00 2.57
351 352 6.656693 CCTCTAAATCTTCTTGGAAGCTTTGA 59.343 38.462 15.05 10.90 0.00 2.69
352 353 6.656693 TCCTCTAAATCTTCTTGGAAGCTTTG 59.343 38.462 15.05 8.39 0.00 2.77
353 354 6.784031 TCCTCTAAATCTTCTTGGAAGCTTT 58.216 36.000 0.00 11.83 0.00 3.51
354 355 6.380079 TCCTCTAAATCTTCTTGGAAGCTT 57.620 37.500 0.00 0.00 0.00 3.74
355 356 6.380079 TTCCTCTAAATCTTCTTGGAAGCT 57.620 37.500 2.74 0.00 0.00 3.74
356 357 5.588246 CCTTCCTCTAAATCTTCTTGGAAGC 59.412 44.000 11.94 0.00 44.36 3.86
357 358 6.118852 CCCTTCCTCTAAATCTTCTTGGAAG 58.881 44.000 10.79 10.79 44.94 3.46
358 359 5.044846 CCCCTTCCTCTAAATCTTCTTGGAA 60.045 44.000 0.00 0.00 0.00 3.53
359 360 4.475016 CCCCTTCCTCTAAATCTTCTTGGA 59.525 45.833 0.00 0.00 0.00 3.53
360 361 4.475016 TCCCCTTCCTCTAAATCTTCTTGG 59.525 45.833 0.00 0.00 0.00 3.61
408 409 2.993899 AGCCACGACGATCACTAAAAAG 59.006 45.455 0.00 0.00 0.00 2.27
411 412 2.751259 ACTAGCCACGACGATCACTAAA 59.249 45.455 0.00 0.00 0.00 1.85
451 456 1.233019 GTTCAGCAGCAGCAGAAGAA 58.767 50.000 9.18 2.17 45.27 2.52
454 459 0.879090 CATGTTCAGCAGCAGCAGAA 59.121 50.000 4.79 4.79 42.94 3.02
456 461 1.095600 ATCATGTTCAGCAGCAGCAG 58.904 50.000 3.17 0.00 45.49 4.24
457 462 1.201414 CAATCATGTTCAGCAGCAGCA 59.799 47.619 3.17 0.00 45.49 4.41
458 463 1.471287 TCAATCATGTTCAGCAGCAGC 59.529 47.619 0.00 0.00 42.56 5.25
471 476 9.878667 TCAGCAATTTCATACATTTTCAATCAT 57.121 25.926 0.00 0.00 0.00 2.45
491 496 4.179298 CAGAGACTCGAATGAATCAGCAA 58.821 43.478 0.00 0.00 0.00 3.91
493 498 2.539274 GCAGAGACTCGAATGAATCAGC 59.461 50.000 0.00 0.00 0.00 4.26
496 501 4.039151 TGAGCAGAGACTCGAATGAATC 57.961 45.455 0.00 0.00 39.68 2.52
497 502 4.462508 TTGAGCAGAGACTCGAATGAAT 57.537 40.909 0.00 0.00 39.68 2.57
498 503 3.942130 TTGAGCAGAGACTCGAATGAA 57.058 42.857 0.00 0.00 39.68 2.57
499 504 4.462508 AATTGAGCAGAGACTCGAATGA 57.537 40.909 0.00 0.00 39.68 2.57
500 505 5.231779 CACTAATTGAGCAGAGACTCGAATG 59.768 44.000 0.00 0.00 39.68 2.67
501 506 5.126222 TCACTAATTGAGCAGAGACTCGAAT 59.874 40.000 0.00 0.00 39.68 3.34
502 507 4.459337 TCACTAATTGAGCAGAGACTCGAA 59.541 41.667 0.00 0.00 39.68 3.71
503 508 4.010349 TCACTAATTGAGCAGAGACTCGA 58.990 43.478 0.00 0.00 39.68 4.04
504 509 4.362932 TCACTAATTGAGCAGAGACTCG 57.637 45.455 0.00 0.00 39.68 4.18
505 510 7.608308 AAAATCACTAATTGAGCAGAGACTC 57.392 36.000 0.00 0.00 37.77 3.36
506 511 7.992754 AAAAATCACTAATTGAGCAGAGACT 57.007 32.000 0.00 0.00 37.77 3.24
529 534 4.836825 TGGCAACCAAATCAGTTGAAAAA 58.163 34.783 7.77 0.00 46.03 1.94
530 535 4.478206 TGGCAACCAAATCAGTTGAAAA 57.522 36.364 7.77 0.00 46.03 2.29
531 536 4.344679 AGATGGCAACCAAATCAGTTGAAA 59.655 37.500 7.77 0.00 46.03 2.69
532 537 3.896888 AGATGGCAACCAAATCAGTTGAA 59.103 39.130 7.77 0.00 46.03 2.69
533 538 3.499338 AGATGGCAACCAAATCAGTTGA 58.501 40.909 7.77 0.00 46.03 3.18
534 539 3.947910 AGATGGCAACCAAATCAGTTG 57.052 42.857 0.00 0.00 45.92 3.16
535 540 3.642848 ACAAGATGGCAACCAAATCAGTT 59.357 39.130 0.00 0.00 36.95 3.16
536 541 3.233507 ACAAGATGGCAACCAAATCAGT 58.766 40.909 0.00 0.00 36.95 3.41
537 542 3.508793 AGACAAGATGGCAACCAAATCAG 59.491 43.478 0.00 0.00 36.95 2.90
538 543 3.499338 AGACAAGATGGCAACCAAATCA 58.501 40.909 0.00 0.00 36.95 2.57
539 544 4.439289 GCTAGACAAGATGGCAACCAAATC 60.439 45.833 0.00 0.00 36.95 2.17
540 545 3.445096 GCTAGACAAGATGGCAACCAAAT 59.555 43.478 0.00 0.00 36.95 2.32
541 546 2.819608 GCTAGACAAGATGGCAACCAAA 59.180 45.455 0.00 0.00 36.95 3.28
542 547 2.224744 TGCTAGACAAGATGGCAACCAA 60.225 45.455 0.00 0.00 36.95 3.67
543 548 1.350684 TGCTAGACAAGATGGCAACCA 59.649 47.619 0.00 0.00 38.19 3.67
544 549 2.113860 TGCTAGACAAGATGGCAACC 57.886 50.000 0.00 0.00 0.00 3.77
546 551 3.138884 TGTTGCTAGACAAGATGGCAA 57.861 42.857 0.00 0.00 39.50 4.52
547 552 2.857186 TGTTGCTAGACAAGATGGCA 57.143 45.000 0.00 0.00 39.50 4.92
548 553 4.878397 AGTTATGTTGCTAGACAAGATGGC 59.122 41.667 15.16 9.93 41.97 4.40
549 554 6.036517 GTCAGTTATGTTGCTAGACAAGATGG 59.963 42.308 15.16 6.63 41.97 3.51
550 555 6.591448 TGTCAGTTATGTTGCTAGACAAGATG 59.409 38.462 15.16 5.16 41.97 2.90
551 556 6.591834 GTGTCAGTTATGTTGCTAGACAAGAT 59.408 38.462 12.01 12.01 44.04 2.40
552 557 5.926542 GTGTCAGTTATGTTGCTAGACAAGA 59.073 40.000 0.00 0.00 39.50 3.02
553 558 5.928839 AGTGTCAGTTATGTTGCTAGACAAG 59.071 40.000 0.00 0.00 39.50 3.16
554 559 5.853936 AGTGTCAGTTATGTTGCTAGACAA 58.146 37.500 0.00 0.00 36.43 3.18
555 560 5.468540 AGTGTCAGTTATGTTGCTAGACA 57.531 39.130 0.00 0.00 32.70 3.41
556 561 5.926542 TCAAGTGTCAGTTATGTTGCTAGAC 59.073 40.000 0.00 0.00 0.00 2.59
557 562 6.096673 TCAAGTGTCAGTTATGTTGCTAGA 57.903 37.500 0.00 0.00 0.00 2.43
558 563 6.369890 ACATCAAGTGTCAGTTATGTTGCTAG 59.630 38.462 0.00 0.00 35.77 3.42
559 564 6.230472 ACATCAAGTGTCAGTTATGTTGCTA 58.770 36.000 0.00 0.00 35.77 3.49
560 565 5.065914 ACATCAAGTGTCAGTTATGTTGCT 58.934 37.500 0.00 0.00 35.77 3.91
561 566 5.362556 ACATCAAGTGTCAGTTATGTTGC 57.637 39.130 0.00 0.00 35.77 4.17
563 568 6.942532 ACAACATCAAGTGTCAGTTATGTT 57.057 33.333 15.33 15.33 41.14 2.71
564 569 6.767902 AGAACAACATCAAGTGTCAGTTATGT 59.232 34.615 0.00 2.08 41.14 2.29
565 570 7.194607 AGAACAACATCAAGTGTCAGTTATG 57.805 36.000 0.00 1.54 41.14 1.90
566 571 7.498900 TCAAGAACAACATCAAGTGTCAGTTAT 59.501 33.333 0.00 0.00 41.14 1.89
567 572 6.821160 TCAAGAACAACATCAAGTGTCAGTTA 59.179 34.615 0.00 0.00 41.14 2.24
568 573 5.647658 TCAAGAACAACATCAAGTGTCAGTT 59.352 36.000 0.00 0.00 41.14 3.16
569 574 5.185454 TCAAGAACAACATCAAGTGTCAGT 58.815 37.500 0.00 0.00 41.14 3.41
570 575 5.277683 CCTCAAGAACAACATCAAGTGTCAG 60.278 44.000 0.00 0.00 41.14 3.51
571 576 4.576053 CCTCAAGAACAACATCAAGTGTCA 59.424 41.667 0.00 0.00 41.14 3.58
572 577 4.576463 ACCTCAAGAACAACATCAAGTGTC 59.424 41.667 0.00 0.00 41.14 3.67
573 578 4.526970 ACCTCAAGAACAACATCAAGTGT 58.473 39.130 0.00 0.00 44.84 3.55
574 579 4.818546 AGACCTCAAGAACAACATCAAGTG 59.181 41.667 0.00 0.00 0.00 3.16
575 580 5.041191 AGACCTCAAGAACAACATCAAGT 57.959 39.130 0.00 0.00 0.00 3.16
576 581 5.059161 TGAGACCTCAAGAACAACATCAAG 58.941 41.667 0.00 0.00 36.53 3.02
577 582 5.034852 TGAGACCTCAAGAACAACATCAA 57.965 39.130 0.00 0.00 36.53 2.57
578 583 4.344968 TCTGAGACCTCAAGAACAACATCA 59.655 41.667 1.08 0.00 39.39 3.07
579 584 4.887748 TCTGAGACCTCAAGAACAACATC 58.112 43.478 1.08 0.00 39.39 3.06
580 585 4.590647 TCTCTGAGACCTCAAGAACAACAT 59.409 41.667 2.58 0.00 39.39 2.71
581 586 3.960755 TCTCTGAGACCTCAAGAACAACA 59.039 43.478 2.58 0.00 39.39 3.33
582 587 4.592485 TCTCTGAGACCTCAAGAACAAC 57.408 45.455 2.58 0.00 39.39 3.32
583 588 4.039730 CCTTCTCTGAGACCTCAAGAACAA 59.960 45.833 6.92 0.00 39.39 2.83
584 589 3.576118 CCTTCTCTGAGACCTCAAGAACA 59.424 47.826 6.92 0.00 39.39 3.18
585 590 3.056179 CCCTTCTCTGAGACCTCAAGAAC 60.056 52.174 6.92 0.00 39.39 3.01
586 591 3.169099 CCCTTCTCTGAGACCTCAAGAA 58.831 50.000 6.92 16.28 39.39 2.52
587 592 2.380249 TCCCTTCTCTGAGACCTCAAGA 59.620 50.000 6.92 4.94 39.39 3.02
588 593 2.760092 CTCCCTTCTCTGAGACCTCAAG 59.240 54.545 6.92 1.59 39.39 3.02
589 594 2.110899 ACTCCCTTCTCTGAGACCTCAA 59.889 50.000 6.92 0.00 39.39 3.02
590 595 1.713647 ACTCCCTTCTCTGAGACCTCA 59.286 52.381 6.92 0.00 38.06 3.86
591 596 2.525105 ACTCCCTTCTCTGAGACCTC 57.475 55.000 6.92 0.00 32.84 3.85
592 597 4.618378 ATTACTCCCTTCTCTGAGACCT 57.382 45.455 6.92 0.00 32.84 3.85
593 598 4.712337 TCAATTACTCCCTTCTCTGAGACC 59.288 45.833 6.92 0.00 32.84 3.85
594 599 5.186021 TGTCAATTACTCCCTTCTCTGAGAC 59.814 44.000 6.92 0.00 32.84 3.36
595 600 5.333581 TGTCAATTACTCCCTTCTCTGAGA 58.666 41.667 2.58 2.58 32.84 3.27
596 601 5.667539 TGTCAATTACTCCCTTCTCTGAG 57.332 43.478 0.00 0.00 34.73 3.35
597 602 6.433847 TTTGTCAATTACTCCCTTCTCTGA 57.566 37.500 0.00 0.00 0.00 3.27
598 603 7.510549 TTTTTGTCAATTACTCCCTTCTCTG 57.489 36.000 0.00 0.00 0.00 3.35
719 726 6.628919 TTAATCGGTCATCAACTCGATCTA 57.371 37.500 0.00 0.00 39.08 1.98
760 767 3.083349 TGGGCCGGATCTGTCAGG 61.083 66.667 5.05 0.00 41.98 3.86
898 905 2.616458 GGAAGAGTGGGGTGGGCAT 61.616 63.158 0.00 0.00 0.00 4.40
900 907 4.048470 GGGAAGAGTGGGGTGGGC 62.048 72.222 0.00 0.00 0.00 5.36
957 977 4.754114 TGAGAGAAGAAGAAAAGAAGCAGC 59.246 41.667 0.00 0.00 0.00 5.25
1255 1437 2.353803 GCACCTACGGTCAGATTCAGTT 60.354 50.000 0.00 0.00 31.02 3.16
1293 1475 2.028733 GCCACAAATTTGCCTGCCG 61.029 57.895 18.12 0.27 0.00 5.69
1651 1837 2.435372 ACACCACAGTTCACACCATT 57.565 45.000 0.00 0.00 0.00 3.16
1943 2146 0.767375 TCTTTGCCTGCTCCTCAAGT 59.233 50.000 0.00 0.00 0.00 3.16
2008 2226 0.982704 AGCTTGACTCTGCAGGATGT 59.017 50.000 15.13 10.62 39.31 3.06
2315 2539 6.042143 ACAACACAACCAAAATGATCTGAAC 58.958 36.000 0.00 0.00 0.00 3.18
2457 2681 8.936864 AGATTCAAGTGTAAGTATTAGCAACAC 58.063 33.333 0.00 0.00 40.53 3.32
2594 2821 8.560355 ACTGTCATACACTAAATATTGTGCAA 57.440 30.769 5.97 0.00 37.68 4.08
2730 2957 8.406297 CGATATATAGGCTAGTTGCATAGTCAA 58.594 37.037 0.00 0.00 41.42 3.18
2732 2959 7.858382 CACGATATATAGGCTAGTTGCATAGTC 59.142 40.741 0.00 0.00 41.42 2.59
2818 3047 4.020617 CCTTGTCCTGCTGGCGGA 62.021 66.667 4.42 2.83 0.00 5.54
3097 3414 4.019513 TCGTCCTCCCCACCCCAT 62.020 66.667 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.