Multiple sequence alignment - TraesCS6A01G042200

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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 TraesCS6A01G042200 chr6A 100.000 3278 0 0 1 3278 22201977 22198700 0.000000e+00 6054.0
1 TraesCS6A01G042200 chr6A 88.390 1335 141 10 971 2304 22193484 22192163 0.000000e+00 1594.0
2 TraesCS6A01G042200 chr6A 84.516 155 20 4 237 389 416679840 416679688 2.040000e-32 150.0
3 TraesCS6A01G042200 chr6A 82.036 167 26 3 69 233 416828791 416828627 4.410000e-29 139.0
4 TraesCS6A01G042200 chr6D 94.887 1682 61 12 776 2441 23642420 23640748 0.000000e+00 2606.0
5 TraesCS6A01G042200 chr6D 88.847 1336 133 11 971 2304 23632172 23630851 0.000000e+00 1628.0
6 TraesCS6A01G042200 chr6D 85.255 746 58 24 2575 3278 23640730 23639995 0.000000e+00 721.0
7 TraesCS6A01G042200 chr6B 94.696 1678 64 12 776 2437 37653187 37651519 0.000000e+00 2582.0
8 TraesCS6A01G042200 chr6B 92.835 1605 92 10 775 2364 46653739 46655335 0.000000e+00 2305.0
9 TraesCS6A01G042200 chr6B 88.914 1335 139 7 971 2304 37645005 37643679 0.000000e+00 1637.0
10 TraesCS6A01G042200 chr6B 88.556 1337 136 13 971 2304 38541468 38540146 0.000000e+00 1605.0
11 TraesCS6A01G042200 chr6B 87.795 1270 130 13 958 2225 46661919 46663165 0.000000e+00 1463.0
12 TraesCS6A01G042200 chr6B 86.930 1293 152 11 979 2267 38625775 38624496 0.000000e+00 1435.0
13 TraesCS6A01G042200 chr6B 95.362 345 15 1 2935 3278 38563647 38563303 6.180000e-152 547.0
14 TraesCS6A01G042200 chr6B 95.087 346 15 2 2935 3278 37651426 37651081 8.000000e-151 544.0
15 TraesCS6A01G042200 chr6B 84.594 357 46 8 14 364 23346635 23346988 2.420000e-91 346.0
16 TraesCS6A01G042200 chr6B 82.569 327 48 7 10 332 152709323 152709002 2.490000e-71 279.0
17 TraesCS6A01G042200 chr6B 93.370 181 11 1 2759 2938 38563867 38563687 1.940000e-67 267.0
18 TraesCS6A01G042200 chr6B 85.657 251 32 4 114 361 156523830 156523581 9.020000e-66 261.0
19 TraesCS6A01G042200 chr6B 93.814 97 5 1 2831 2926 46655782 46655878 9.480000e-31 145.0
20 TraesCS6A01G042200 chr6B 93.846 65 3 1 2240 2304 46670080 46670143 2.690000e-16 97.1
21 TraesCS6A01G042200 chr6B 78.286 175 18 18 602 774 438390138 438390294 9.680000e-16 95.3
22 TraesCS6A01G042200 chr6B 77.143 175 24 16 603 774 370147761 370147600 1.620000e-13 87.9
23 TraesCS6A01G042200 chr1A 88.931 786 50 15 1 751 473413854 473414637 0.000000e+00 935.0
24 TraesCS6A01G042200 chr3B 84.607 916 85 26 2012 2911 744916146 744915271 0.000000e+00 859.0
25 TraesCS6A01G042200 chr3B 77.966 177 21 18 602 774 427341989 427342151 9.680000e-16 95.3
26 TraesCS6A01G042200 chr2B 82.825 361 49 12 25 379 707727234 707727587 8.830000e-81 311.0
27 TraesCS6A01G042200 chr2B 84.375 256 34 6 36 288 728371198 728370946 2.530000e-61 246.0
28 TraesCS6A01G042200 chr2B 77.222 180 27 12 596 774 505804816 505804982 3.480000e-15 93.5
29 TraesCS6A01G042200 chr2B 77.273 176 24 16 602 774 58872252 58872414 4.510000e-14 89.8
30 TraesCS6A01G042200 chr2D 81.132 371 54 14 13 377 39105533 39105173 1.930000e-72 283.0
31 TraesCS6A01G042200 chr2D 78.313 166 22 10 617 774 18168272 18168431 9.680000e-16 95.3
32 TraesCS6A01G042200 chr7D 88.660 194 17 5 174 364 48827288 48827097 7.070000e-57 231.0
33 TraesCS6A01G042200 chr2A 82.014 278 38 9 6 275 451875825 451876098 3.290000e-55 226.0
34 TraesCS6A01G042200 chr5A 77.841 176 23 15 602 774 707655344 707655506 9.680000e-16 95.3
35 TraesCS6A01G042200 chr4B 77.143 175 26 14 602 774 608387243 608387081 4.510000e-14 89.8
36 TraesCS6A01G042200 chr1B 77.273 176 24 16 602 774 630514673 630514511 4.510000e-14 89.8


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 TraesCS6A01G042200 chr6A 22198700 22201977 3277 True 6054.0 6054 100.0000 1 3278 1 chr6A.!!$R2 3277
1 TraesCS6A01G042200 chr6A 22192163 22193484 1321 True 1594.0 1594 88.3900 971 2304 1 chr6A.!!$R1 1333
2 TraesCS6A01G042200 chr6D 23639995 23642420 2425 True 1663.5 2606 90.0710 776 3278 2 chr6D.!!$R2 2502
3 TraesCS6A01G042200 chr6D 23630851 23632172 1321 True 1628.0 1628 88.8470 971 2304 1 chr6D.!!$R1 1333
4 TraesCS6A01G042200 chr6B 37643679 37645005 1326 True 1637.0 1637 88.9140 971 2304 1 chr6B.!!$R1 1333
5 TraesCS6A01G042200 chr6B 38540146 38541468 1322 True 1605.0 1605 88.5560 971 2304 1 chr6B.!!$R2 1333
6 TraesCS6A01G042200 chr6B 37651081 37653187 2106 True 1563.0 2582 94.8915 776 3278 2 chr6B.!!$R7 2502
7 TraesCS6A01G042200 chr6B 46661919 46663165 1246 False 1463.0 1463 87.7950 958 2225 1 chr6B.!!$F2 1267
8 TraesCS6A01G042200 chr6B 38624496 38625775 1279 True 1435.0 1435 86.9300 979 2267 1 chr6B.!!$R3 1288
9 TraesCS6A01G042200 chr6B 46653739 46655878 2139 False 1225.0 2305 93.3245 775 2926 2 chr6B.!!$F5 2151
10 TraesCS6A01G042200 chr6B 38563303 38563867 564 True 407.0 547 94.3660 2759 3278 2 chr6B.!!$R8 519
11 TraesCS6A01G042200 chr1A 473413854 473414637 783 False 935.0 935 88.9310 1 751 1 chr1A.!!$F1 750
12 TraesCS6A01G042200 chr3B 744915271 744916146 875 True 859.0 859 84.6070 2012 2911 1 chr3B.!!$R1 899

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
823 827 0.175989 GCTCTCCCGGTCTGTTTAGG 59.824 60.0 0.0 0.0 0.0 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2586 2780 0.46729 TTATGGCCCGGCTTTGATCC 60.467 55.0 9.86 0.0 0.0 3.36 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
100 101 5.645624 TGAAAGTGCGAACATTTCTCAAAA 58.354 33.333 15.21 0.00 34.70 2.44
142 143 9.434420 TTCAAGACATGAACACTTTTTGAATTT 57.566 25.926 0.00 0.00 43.08 1.82
166 167 5.417580 TCCCTGAACATTTTTCGAATTAGGG 59.582 40.000 14.79 14.79 41.92 3.53
214 215 6.580963 TTTTGACGATGTGAACAAATTTGG 57.419 33.333 21.74 4.42 33.38 3.28
219 220 4.744631 ACGATGTGAACAAATTTGGAAAGC 59.255 37.500 21.74 8.65 0.00 3.51
224 225 3.323403 TGAACAAATTTGGAAAGCGGGAT 59.677 39.130 21.74 0.00 0.00 3.85
299 302 5.065731 GTGAACATTTTTCCAATGTGCCAAA 59.934 36.000 1.05 0.00 40.43 3.28
376 379 4.332268 TGAACAAATTTGCAAAGCTGGAAC 59.668 37.500 18.19 11.84 31.86 3.62
395 398 7.548196 TGGAACATATATTGGAAACGAGAAC 57.452 36.000 0.00 0.00 0.00 3.01
396 399 6.256975 TGGAACATATATTGGAAACGAGAACG 59.743 38.462 0.00 0.00 45.75 3.95
424 427 9.678260 TTTTTGAAATCCCAGAATTTCTTGAAA 57.322 25.926 9.88 0.00 43.17 2.69
428 431 8.263640 TGAAATCCCAGAATTTCTTGAAAAACA 58.736 29.630 9.88 0.00 43.17 2.83
466 470 9.688592 AAAGTGCAAACAAAATTTTGAAAATGA 57.311 22.222 32.20 12.00 40.55 2.57
467 471 8.898983 AGTGCAAACAAAATTTTGAAAATGAG 57.101 26.923 32.20 16.67 40.55 2.90
468 472 8.728833 AGTGCAAACAAAATTTTGAAAATGAGA 58.271 25.926 32.20 14.13 40.55 3.27
469 473 9.339492 GTGCAAACAAAATTTTGAAAATGAGAA 57.661 25.926 32.20 10.26 40.55 2.87
579 583 9.587772 TGAAATTTTCGAACAAAATAAACAGGA 57.412 25.926 0.00 0.00 30.38 3.86
585 589 7.995463 TCGAACAAAATAAACAGGAAAAAGG 57.005 32.000 0.00 0.00 0.00 3.11
586 590 6.981559 TCGAACAAAATAAACAGGAAAAAGGG 59.018 34.615 0.00 0.00 0.00 3.95
587 591 6.981559 CGAACAAAATAAACAGGAAAAAGGGA 59.018 34.615 0.00 0.00 0.00 4.20
588 592 7.492994 CGAACAAAATAAACAGGAAAAAGGGAA 59.507 33.333 0.00 0.00 0.00 3.97
589 593 9.168451 GAACAAAATAAACAGGAAAAAGGGAAA 57.832 29.630 0.00 0.00 0.00 3.13
590 594 8.731275 ACAAAATAAACAGGAAAAAGGGAAAG 57.269 30.769 0.00 0.00 0.00 2.62
591 595 8.544622 ACAAAATAAACAGGAAAAAGGGAAAGA 58.455 29.630 0.00 0.00 0.00 2.52
592 596 9.389755 CAAAATAAACAGGAAAAAGGGAAAGAA 57.610 29.630 0.00 0.00 0.00 2.52
593 597 9.967451 AAAATAAACAGGAAAAAGGGAAAGAAA 57.033 25.926 0.00 0.00 0.00 2.52
594 598 9.613428 AAATAAACAGGAAAAAGGGAAAGAAAG 57.387 29.630 0.00 0.00 0.00 2.62
595 599 6.867519 AAACAGGAAAAAGGGAAAGAAAGA 57.132 33.333 0.00 0.00 0.00 2.52
596 600 6.867519 AACAGGAAAAAGGGAAAGAAAGAA 57.132 33.333 0.00 0.00 0.00 2.52
597 601 6.867519 ACAGGAAAAAGGGAAAGAAAGAAA 57.132 33.333 0.00 0.00 0.00 2.52
598 602 7.252612 ACAGGAAAAAGGGAAAGAAAGAAAA 57.747 32.000 0.00 0.00 0.00 2.29
599 603 7.103641 ACAGGAAAAAGGGAAAGAAAGAAAAC 58.896 34.615 0.00 0.00 0.00 2.43
600 604 6.538742 CAGGAAAAAGGGAAAGAAAGAAAACC 59.461 38.462 0.00 0.00 0.00 3.27
601 605 6.214615 AGGAAAAAGGGAAAGAAAGAAAACCA 59.785 34.615 0.00 0.00 0.00 3.67
602 606 6.882140 GGAAAAAGGGAAAGAAAGAAAACCAA 59.118 34.615 0.00 0.00 0.00 3.67
603 607 7.392113 GGAAAAAGGGAAAGAAAGAAAACCAAA 59.608 33.333 0.00 0.00 0.00 3.28
604 608 8.698973 AAAAAGGGAAAGAAAGAAAACCAAAA 57.301 26.923 0.00 0.00 0.00 2.44
605 609 8.877864 AAAAGGGAAAGAAAGAAAACCAAAAT 57.122 26.923 0.00 0.00 0.00 1.82
606 610 9.967451 AAAAGGGAAAGAAAGAAAACCAAAATA 57.033 25.926 0.00 0.00 0.00 1.40
607 611 9.967451 AAAGGGAAAGAAAGAAAACCAAAATAA 57.033 25.926 0.00 0.00 0.00 1.40
608 612 9.967451 AAGGGAAAGAAAGAAAACCAAAATAAA 57.033 25.926 0.00 0.00 0.00 1.40
609 613 9.967451 AGGGAAAGAAAGAAAACCAAAATAAAA 57.033 25.926 0.00 0.00 0.00 1.52
610 614 9.997482 GGGAAAGAAAGAAAACCAAAATAAAAC 57.003 29.630 0.00 0.00 0.00 2.43
615 619 9.952030 AGAAAGAAAACCAAAATAAAACTTGGA 57.048 25.926 7.80 0.00 44.16 3.53
632 636 6.529463 ACTTGGAAAAAGAAAATGAATGCG 57.471 33.333 0.00 0.00 0.00 4.73
633 637 6.279882 ACTTGGAAAAAGAAAATGAATGCGA 58.720 32.000 0.00 0.00 0.00 5.10
634 638 6.760770 ACTTGGAAAAAGAAAATGAATGCGAA 59.239 30.769 0.00 0.00 0.00 4.70
635 639 7.442062 ACTTGGAAAAAGAAAATGAATGCGAAT 59.558 29.630 0.00 0.00 0.00 3.34
636 640 8.824159 TTGGAAAAAGAAAATGAATGCGAATA 57.176 26.923 0.00 0.00 0.00 1.75
637 641 8.824159 TGGAAAAAGAAAATGAATGCGAATAA 57.176 26.923 0.00 0.00 0.00 1.40
638 642 9.265901 TGGAAAAAGAAAATGAATGCGAATAAA 57.734 25.926 0.00 0.00 0.00 1.40
667 671 9.438228 AAGGAAAAACGGAAAGAAAAATAAACA 57.562 25.926 0.00 0.00 0.00 2.83
668 672 9.093970 AGGAAAAACGGAAAGAAAAATAAACAG 57.906 29.630 0.00 0.00 0.00 3.16
669 673 9.089601 GGAAAAACGGAAAGAAAAATAAACAGA 57.910 29.630 0.00 0.00 0.00 3.41
741 745 8.209917 AGGTAGCAAGAAGAAAATATAAACCG 57.790 34.615 0.00 0.00 0.00 4.44
742 746 7.282450 AGGTAGCAAGAAGAAAATATAAACCGG 59.718 37.037 0.00 0.00 0.00 5.28
743 747 5.891451 AGCAAGAAGAAAATATAAACCGGC 58.109 37.500 0.00 0.00 0.00 6.13
744 748 5.652452 AGCAAGAAGAAAATATAAACCGGCT 59.348 36.000 0.00 0.00 0.00 5.52
745 749 5.971792 GCAAGAAGAAAATATAAACCGGCTC 59.028 40.000 0.00 0.00 0.00 4.70
746 750 6.404293 GCAAGAAGAAAATATAAACCGGCTCA 60.404 38.462 0.00 0.00 0.00 4.26
747 751 6.927294 AGAAGAAAATATAAACCGGCTCAG 57.073 37.500 0.00 0.00 0.00 3.35
748 752 5.823045 AGAAGAAAATATAAACCGGCTCAGG 59.177 40.000 0.00 0.00 37.30 3.86
749 753 5.367945 AGAAAATATAAACCGGCTCAGGA 57.632 39.130 0.00 0.00 34.73 3.86
750 754 5.751586 AGAAAATATAAACCGGCTCAGGAA 58.248 37.500 0.00 0.00 34.73 3.36
751 755 5.589050 AGAAAATATAAACCGGCTCAGGAAC 59.411 40.000 0.00 0.00 34.73 3.62
752 756 2.994186 TATAAACCGGCTCAGGAACC 57.006 50.000 0.00 0.00 34.73 3.62
753 757 1.286248 ATAAACCGGCTCAGGAACCT 58.714 50.000 0.00 0.00 34.73 3.50
754 758 1.061546 TAAACCGGCTCAGGAACCTT 58.938 50.000 0.00 0.00 34.73 3.50
755 759 0.250770 AAACCGGCTCAGGAACCTTC 60.251 55.000 0.00 0.00 34.73 3.46
756 760 1.128188 AACCGGCTCAGGAACCTTCT 61.128 55.000 0.00 0.00 34.73 2.85
757 761 0.252103 ACCGGCTCAGGAACCTTCTA 60.252 55.000 0.00 0.00 34.73 2.10
758 762 0.461961 CCGGCTCAGGAACCTTCTAG 59.538 60.000 0.00 0.00 0.00 2.43
759 763 1.475403 CGGCTCAGGAACCTTCTAGA 58.525 55.000 0.00 0.00 0.00 2.43
760 764 1.825474 CGGCTCAGGAACCTTCTAGAA 59.175 52.381 4.81 4.81 0.00 2.10
761 765 2.159170 CGGCTCAGGAACCTTCTAGAAG 60.159 54.545 23.31 23.31 38.14 2.85
823 827 0.175989 GCTCTCCCGGTCTGTTTAGG 59.824 60.000 0.00 0.00 0.00 2.69
953 957 3.665675 ATCTCCGGCGCTCAACCAC 62.666 63.158 7.64 0.00 0.00 4.16
964 968 1.405526 GCTCAACCACTGCGATCCTAA 60.406 52.381 0.00 0.00 0.00 2.69
1731 1742 0.036388 CAGGCCGGTCACAGTACATT 60.036 55.000 9.71 0.00 0.00 2.71
2109 2130 2.352032 GGTGGACGAGCTAGGCACT 61.352 63.158 0.85 0.00 46.37 4.40
2304 2332 3.940209 TGTGGAATCATTTGGCTGTTC 57.060 42.857 0.00 0.00 0.00 3.18
2307 2335 4.240096 GTGGAATCATTTGGCTGTTCTTG 58.760 43.478 0.00 0.00 0.00 3.02
2311 2339 6.436847 TGGAATCATTTGGCTGTTCTTGAATA 59.563 34.615 0.00 0.00 0.00 1.75
2312 2340 6.976925 GGAATCATTTGGCTGTTCTTGAATAG 59.023 38.462 3.27 3.27 0.00 1.73
2313 2341 5.902613 TCATTTGGCTGTTCTTGAATAGG 57.097 39.130 8.73 0.00 0.00 2.57
2337 2365 8.739972 AGGAGTAAATATTTGAACATTGGTCAC 58.260 33.333 11.05 0.00 0.00 3.67
2338 2366 8.739972 GGAGTAAATATTTGAACATTGGTCACT 58.260 33.333 11.05 1.64 0.00 3.41
2364 2393 2.338809 AGATTTGGTCACTCCTGTCCA 58.661 47.619 0.00 0.00 34.19 4.02
2365 2394 2.711009 AGATTTGGTCACTCCTGTCCAA 59.289 45.455 0.00 0.00 41.96 3.53
2366 2395 2.341846 TTTGGTCACTCCTGTCCAAC 57.658 50.000 0.00 0.00 42.94 3.77
2372 2415 3.636764 GGTCACTCCTGTCCAACAAATTT 59.363 43.478 0.00 0.00 0.00 1.82
2386 2579 2.494870 ACAAATTTGAGGATGCAGGAGC 59.505 45.455 24.64 0.00 42.57 4.70
2404 2597 1.411977 AGCGAGTCCTGATCTCCATTG 59.588 52.381 0.00 0.00 0.00 2.82
2479 2673 7.020010 CAGTAGAAAAGTGAATGCAGATCAAC 58.980 38.462 6.56 0.95 0.00 3.18
2484 2678 6.492007 AAAGTGAATGCAGATCAACTACAG 57.508 37.500 6.56 0.00 0.00 2.74
2493 2687 4.511527 CAGATCAACTACAGTGGAGCATT 58.488 43.478 0.91 0.00 36.87 3.56
2502 2696 5.643777 ACTACAGTGGAGCATTGTAATTCAC 59.356 40.000 0.91 0.00 36.44 3.18
2503 2697 4.655963 ACAGTGGAGCATTGTAATTCACT 58.344 39.130 0.00 0.00 32.72 3.41
2512 2706 5.352569 AGCATTGTAATTCACTCTGTACTGC 59.647 40.000 0.00 0.00 0.00 4.40
2541 2735 7.031372 TGTGAGCTGAATGAAATGAATTTAGC 58.969 34.615 0.00 5.13 43.38 3.09
2542 2736 6.195983 GTGAGCTGAATGAAATGAATTTAGCG 59.804 38.462 0.00 0.00 46.00 4.26
2543 2737 5.039333 AGCTGAATGAAATGAATTTAGCGC 58.961 37.500 0.00 0.00 46.00 5.92
2544 2738 4.207841 GCTGAATGAAATGAATTTAGCGCC 59.792 41.667 2.29 0.00 37.04 6.53
2545 2739 5.581126 TGAATGAAATGAATTTAGCGCCT 57.419 34.783 2.29 0.00 0.00 5.52
2546 2740 5.342433 TGAATGAAATGAATTTAGCGCCTG 58.658 37.500 2.29 0.00 0.00 4.85
2547 2741 4.989279 ATGAAATGAATTTAGCGCCTGT 57.011 36.364 2.29 0.00 0.00 4.00
2548 2742 4.782019 TGAAATGAATTTAGCGCCTGTT 57.218 36.364 2.29 0.00 0.00 3.16
2561 2755 2.335712 CCTGTTGGCGCCTTTCTCC 61.336 63.158 29.70 9.18 0.00 3.71
2565 2759 1.964373 TTGGCGCCTTTCTCCGTTC 60.964 57.895 29.70 0.00 0.00 3.95
2622 2816 5.102313 GCCATAAGTATGACTTTGCAAACC 58.898 41.667 8.05 3.85 39.51 3.27
2660 2858 4.530161 AGAGGCTCTTGTATTCAGTCTGTT 59.470 41.667 12.24 0.00 0.00 3.16
2668 2867 3.745975 TGTATTCAGTCTGTTTCTTGGCG 59.254 43.478 0.00 0.00 0.00 5.69
2671 2870 1.134220 TCAGTCTGTTTCTTGGCGGTT 60.134 47.619 0.00 0.00 0.00 4.44
2711 2910 7.938563 TTAACAGCAAAATGTATTGTTCCAC 57.061 32.000 0.00 0.00 34.22 4.02
2713 2912 5.772521 ACAGCAAAATGTATTGTTCCACTC 58.227 37.500 0.00 0.00 32.80 3.51
2719 2918 8.011106 GCAAAATGTATTGTTCCACTCAAAATG 58.989 33.333 0.00 0.00 32.80 2.32
2720 2919 9.044150 CAAAATGTATTGTTCCACTCAAAATGT 57.956 29.630 0.00 0.00 0.00 2.71
2724 2923 9.859427 ATGTATTGTTCCACTCAAAATGTATTG 57.141 29.630 0.00 0.00 0.00 1.90
2725 2924 9.072375 TGTATTGTTCCACTCAAAATGTATTGA 57.928 29.630 0.00 0.00 37.70 2.57
2726 2925 9.341899 GTATTGTTCCACTCAAAATGTATTGAC 57.658 33.333 0.00 0.00 35.55 3.18
2772 2992 3.557228 ATTCAGGATTCTCAGACAGGC 57.443 47.619 0.00 0.00 0.00 4.85
2926 3147 2.448926 ATGACGATCCAACACGAACA 57.551 45.000 0.00 0.00 0.00 3.18
2964 3228 5.914085 CAGTGAACTGGAGTACTTTTGAG 57.086 43.478 0.00 0.00 40.20 3.02
3043 3308 3.364023 CACGTTTATGTTCTGTCTCGGAC 59.636 47.826 0.00 0.00 0.00 4.79
3059 3324 0.889306 GGACGCTCTGGAGTTACACT 59.111 55.000 0.00 0.00 0.00 3.55
3136 3402 5.304614 TCTTTCTAACCTAGCAGTGTGTCTT 59.695 40.000 0.00 0.00 0.00 3.01
3176 3442 6.324819 CCAACTGTACTTTCATTTGGCATAG 58.675 40.000 0.00 0.00 39.78 2.23
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 6.667007 AAATGTTTTGCACTTTCAAGGAAG 57.333 33.333 0.00 0.00 0.00 3.46
34 35 5.502220 CGGAAAATGTTTTGCACTTTCAAGG 60.502 40.000 9.78 0.00 42.97 3.61
42 43 3.308323 TGCTTTCGGAAAATGTTTTGCAC 59.692 39.130 4.53 0.00 38.24 4.57
82 83 8.226543 TCATAAATTTTGAGAAATGTTCGCAC 57.773 30.769 0.00 0.00 39.21 5.34
83 84 8.698854 GTTCATAAATTTTGAGAAATGTTCGCA 58.301 29.630 0.00 0.00 37.71 5.10
142 143 5.417580 CCCTAATTCGAAAAATGTTCAGGGA 59.582 40.000 0.00 0.00 41.31 4.20
166 167 9.786105 AATGTTCATGTTTTTCAAAATTTGACC 57.214 25.926 8.06 0.00 39.87 4.02
197 198 4.143556 CGCTTTCCAAATTTGTTCACATCG 60.144 41.667 16.73 7.54 0.00 3.84
329 332 7.170151 TCACAAATTCAAGAAATGCTCATGTTG 59.830 33.333 0.00 0.00 0.00 3.33
443 447 8.892887 TCTCATTTTCAAAATTTTGTTTGCAC 57.107 26.923 25.98 0.00 38.20 4.57
553 557 9.587772 TCCTGTTTATTTTGTTCGAAAATTTCA 57.412 25.926 0.00 0.00 32.64 2.69
559 563 8.874816 CCTTTTTCCTGTTTATTTTGTTCGAAA 58.125 29.630 0.00 0.00 0.00 3.46
560 564 7.492994 CCCTTTTTCCTGTTTATTTTGTTCGAA 59.507 33.333 0.00 0.00 0.00 3.71
561 565 6.981559 CCCTTTTTCCTGTTTATTTTGTTCGA 59.018 34.615 0.00 0.00 0.00 3.71
562 566 6.981559 TCCCTTTTTCCTGTTTATTTTGTTCG 59.018 34.615 0.00 0.00 0.00 3.95
563 567 8.725405 TTCCCTTTTTCCTGTTTATTTTGTTC 57.275 30.769 0.00 0.00 0.00 3.18
564 568 9.173021 CTTTCCCTTTTTCCTGTTTATTTTGTT 57.827 29.630 0.00 0.00 0.00 2.83
565 569 8.544622 TCTTTCCCTTTTTCCTGTTTATTTTGT 58.455 29.630 0.00 0.00 0.00 2.83
566 570 8.956533 TCTTTCCCTTTTTCCTGTTTATTTTG 57.043 30.769 0.00 0.00 0.00 2.44
567 571 9.967451 TTTCTTTCCCTTTTTCCTGTTTATTTT 57.033 25.926 0.00 0.00 0.00 1.82
568 572 9.613428 CTTTCTTTCCCTTTTTCCTGTTTATTT 57.387 29.630 0.00 0.00 0.00 1.40
569 573 8.988060 TCTTTCTTTCCCTTTTTCCTGTTTATT 58.012 29.630 0.00 0.00 0.00 1.40
570 574 8.547481 TCTTTCTTTCCCTTTTTCCTGTTTAT 57.453 30.769 0.00 0.00 0.00 1.40
571 575 7.964666 TCTTTCTTTCCCTTTTTCCTGTTTA 57.035 32.000 0.00 0.00 0.00 2.01
572 576 6.867519 TCTTTCTTTCCCTTTTTCCTGTTT 57.132 33.333 0.00 0.00 0.00 2.83
573 577 6.867519 TTCTTTCTTTCCCTTTTTCCTGTT 57.132 33.333 0.00 0.00 0.00 3.16
574 578 6.867519 TTTCTTTCTTTCCCTTTTTCCTGT 57.132 33.333 0.00 0.00 0.00 4.00
575 579 6.538742 GGTTTTCTTTCTTTCCCTTTTTCCTG 59.461 38.462 0.00 0.00 0.00 3.86
576 580 6.214615 TGGTTTTCTTTCTTTCCCTTTTTCCT 59.785 34.615 0.00 0.00 0.00 3.36
577 581 6.411376 TGGTTTTCTTTCTTTCCCTTTTTCC 58.589 36.000 0.00 0.00 0.00 3.13
578 582 7.915293 TTGGTTTTCTTTCTTTCCCTTTTTC 57.085 32.000 0.00 0.00 0.00 2.29
579 583 8.698973 TTTTGGTTTTCTTTCTTTCCCTTTTT 57.301 26.923 0.00 0.00 0.00 1.94
580 584 8.877864 ATTTTGGTTTTCTTTCTTTCCCTTTT 57.122 26.923 0.00 0.00 0.00 2.27
581 585 9.967451 TTATTTTGGTTTTCTTTCTTTCCCTTT 57.033 25.926 0.00 0.00 0.00 3.11
582 586 9.967451 TTTATTTTGGTTTTCTTTCTTTCCCTT 57.033 25.926 0.00 0.00 0.00 3.95
583 587 9.967451 TTTTATTTTGGTTTTCTTTCTTTCCCT 57.033 25.926 0.00 0.00 0.00 4.20
584 588 9.997482 GTTTTATTTTGGTTTTCTTTCTTTCCC 57.003 29.630 0.00 0.00 0.00 3.97
589 593 9.952030 TCCAAGTTTTATTTTGGTTTTCTTTCT 57.048 25.926 3.46 0.00 43.43 2.52
606 610 7.909641 CGCATTCATTTTCTTTTTCCAAGTTTT 59.090 29.630 0.00 0.00 0.00 2.43
607 611 7.279758 TCGCATTCATTTTCTTTTTCCAAGTTT 59.720 29.630 0.00 0.00 0.00 2.66
608 612 6.760770 TCGCATTCATTTTCTTTTTCCAAGTT 59.239 30.769 0.00 0.00 0.00 2.66
609 613 6.279882 TCGCATTCATTTTCTTTTTCCAAGT 58.720 32.000 0.00 0.00 0.00 3.16
610 614 6.768029 TCGCATTCATTTTCTTTTTCCAAG 57.232 33.333 0.00 0.00 0.00 3.61
611 615 7.727331 ATTCGCATTCATTTTCTTTTTCCAA 57.273 28.000 0.00 0.00 0.00 3.53
612 616 8.824159 TTATTCGCATTCATTTTCTTTTTCCA 57.176 26.923 0.00 0.00 0.00 3.53
641 645 9.438228 TGTTTATTTTTCTTTCCGTTTTTCCTT 57.562 25.926 0.00 0.00 0.00 3.36
642 646 9.093970 CTGTTTATTTTTCTTTCCGTTTTTCCT 57.906 29.630 0.00 0.00 0.00 3.36
643 647 9.089601 TCTGTTTATTTTTCTTTCCGTTTTTCC 57.910 29.630 0.00 0.00 0.00 3.13
715 719 8.674607 CGGTTTATATTTTCTTCTTGCTACCTT 58.325 33.333 0.00 0.00 0.00 3.50
716 720 7.282450 CCGGTTTATATTTTCTTCTTGCTACCT 59.718 37.037 0.00 0.00 0.00 3.08
717 721 7.415229 CCGGTTTATATTTTCTTCTTGCTACC 58.585 38.462 0.00 0.00 0.00 3.18
718 722 6.910972 GCCGGTTTATATTTTCTTCTTGCTAC 59.089 38.462 1.90 0.00 0.00 3.58
719 723 6.826741 AGCCGGTTTATATTTTCTTCTTGCTA 59.173 34.615 1.90 0.00 0.00 3.49
720 724 5.652452 AGCCGGTTTATATTTTCTTCTTGCT 59.348 36.000 1.90 0.00 0.00 3.91
721 725 5.891451 AGCCGGTTTATATTTTCTTCTTGC 58.109 37.500 1.90 0.00 0.00 4.01
722 726 7.083875 TGAGCCGGTTTATATTTTCTTCTTG 57.916 36.000 1.90 0.00 0.00 3.02
723 727 6.318900 CCTGAGCCGGTTTATATTTTCTTCTT 59.681 38.462 1.90 0.00 0.00 2.52
724 728 5.823045 CCTGAGCCGGTTTATATTTTCTTCT 59.177 40.000 1.90 0.00 0.00 2.85
725 729 5.820947 TCCTGAGCCGGTTTATATTTTCTTC 59.179 40.000 1.90 0.00 0.00 2.87
726 730 5.751586 TCCTGAGCCGGTTTATATTTTCTT 58.248 37.500 1.90 0.00 0.00 2.52
727 731 5.367945 TCCTGAGCCGGTTTATATTTTCT 57.632 39.130 1.90 0.00 0.00 2.52
728 732 5.220989 GGTTCCTGAGCCGGTTTATATTTTC 60.221 44.000 1.90 0.00 0.00 2.29
729 733 4.643334 GGTTCCTGAGCCGGTTTATATTTT 59.357 41.667 1.90 0.00 0.00 1.82
730 734 4.079958 AGGTTCCTGAGCCGGTTTATATTT 60.080 41.667 1.90 0.00 36.74 1.40
731 735 3.458487 AGGTTCCTGAGCCGGTTTATATT 59.542 43.478 1.90 0.00 36.74 1.28
732 736 3.046374 AGGTTCCTGAGCCGGTTTATAT 58.954 45.455 1.90 0.00 36.74 0.86
733 737 2.474112 AGGTTCCTGAGCCGGTTTATA 58.526 47.619 1.90 0.00 36.74 0.98
734 738 1.286248 AGGTTCCTGAGCCGGTTTAT 58.714 50.000 1.90 0.00 36.74 1.40
735 739 1.002773 GAAGGTTCCTGAGCCGGTTTA 59.997 52.381 1.90 0.00 36.74 2.01
736 740 0.250770 GAAGGTTCCTGAGCCGGTTT 60.251 55.000 1.90 0.00 36.74 3.27
737 741 1.128188 AGAAGGTTCCTGAGCCGGTT 61.128 55.000 1.90 0.00 36.74 4.44
738 742 0.252103 TAGAAGGTTCCTGAGCCGGT 60.252 55.000 1.90 0.00 36.74 5.28
739 743 0.461961 CTAGAAGGTTCCTGAGCCGG 59.538 60.000 0.00 0.00 36.74 6.13
740 744 1.475403 TCTAGAAGGTTCCTGAGCCG 58.525 55.000 0.00 0.00 36.74 5.52
741 745 3.535280 CTTCTAGAAGGTTCCTGAGCC 57.465 52.381 22.67 0.00 34.87 4.70
762 766 2.288579 CGGGCTAAAAGGTTTTGGGAAC 60.289 50.000 0.00 0.00 0.00 3.62
763 767 1.964933 CGGGCTAAAAGGTTTTGGGAA 59.035 47.619 0.00 0.00 0.00 3.97
764 768 1.133419 ACGGGCTAAAAGGTTTTGGGA 60.133 47.619 0.00 0.00 0.00 4.37
765 769 1.000394 CACGGGCTAAAAGGTTTTGGG 60.000 52.381 0.00 0.00 0.00 4.12
766 770 1.684450 ACACGGGCTAAAAGGTTTTGG 59.316 47.619 0.00 0.00 0.00 3.28
767 771 2.603652 CGACACGGGCTAAAAGGTTTTG 60.604 50.000 0.00 0.00 0.00 2.44
768 772 1.605232 CGACACGGGCTAAAAGGTTTT 59.395 47.619 0.00 0.00 0.00 2.43
769 773 1.232119 CGACACGGGCTAAAAGGTTT 58.768 50.000 0.00 0.00 0.00 3.27
770 774 0.107268 ACGACACGGGCTAAAAGGTT 59.893 50.000 0.00 0.00 0.00 3.50
771 775 0.601841 CACGACACGGGCTAAAAGGT 60.602 55.000 0.00 0.00 0.00 3.50
772 776 2.159181 CACGACACGGGCTAAAAGG 58.841 57.895 0.00 0.00 0.00 3.11
953 957 2.802787 AGATTCGGTTAGGATCGCAG 57.197 50.000 0.00 0.00 0.00 5.18
956 960 4.296690 GTGGTAAGATTCGGTTAGGATCG 58.703 47.826 0.00 0.00 0.00 3.69
964 968 1.066645 GGGTTCGTGGTAAGATTCGGT 60.067 52.381 0.00 0.00 0.00 4.69
999 1003 1.226859 CTTCCCGAAGCGCGACATA 60.227 57.895 12.10 0.00 44.57 2.29
1705 1716 3.680786 TGACCGGCCTGTCGTCAG 61.681 66.667 20.74 2.40 38.11 3.51
1731 1742 2.038975 AAGCCCGGGTAGAGAGCA 59.961 61.111 24.63 0.00 0.00 4.26
2065 2086 2.203209 GGCCTTATGGAGCACCCG 60.203 66.667 0.00 0.00 37.93 5.28
2311 2339 8.739972 GTGACCAATGTTCAAATATTTACTCCT 58.260 33.333 0.00 0.00 0.00 3.69
2312 2340 8.739972 AGTGACCAATGTTCAAATATTTACTCC 58.260 33.333 0.00 0.00 0.00 3.85
2337 2365 4.153117 CAGGAGTGACCAAATCTTCGAAAG 59.847 45.833 0.00 0.00 42.04 2.62
2338 2366 4.065088 CAGGAGTGACCAAATCTTCGAAA 58.935 43.478 0.00 0.00 42.04 3.46
2364 2393 3.056322 GCTCCTGCATCCTCAAATTTGTT 60.056 43.478 17.47 0.00 39.41 2.83
2365 2394 2.494870 GCTCCTGCATCCTCAAATTTGT 59.505 45.455 17.47 0.00 39.41 2.83
2366 2395 2.479049 CGCTCCTGCATCCTCAAATTTG 60.479 50.000 12.15 12.15 39.64 2.32
2372 2415 1.670949 GACTCGCTCCTGCATCCTCA 61.671 60.000 0.00 0.00 39.64 3.86
2386 2579 3.808466 TTCAATGGAGATCAGGACTCG 57.192 47.619 0.00 0.00 35.49 4.18
2431 2625 0.685097 ACCGCTTGTTGCTCTTAGGA 59.315 50.000 0.00 0.00 40.11 2.94
2454 2648 6.732531 TGATCTGCATTCACTTTTCTACTG 57.267 37.500 0.00 0.00 0.00 2.74
2479 2673 5.877012 AGTGAATTACAATGCTCCACTGTAG 59.123 40.000 0.00 0.00 28.10 2.74
2484 2678 4.697352 ACAGAGTGAATTACAATGCTCCAC 59.303 41.667 0.00 0.00 0.00 4.02
2493 2687 4.514781 ACGCAGTACAGAGTGAATTACA 57.485 40.909 0.00 0.00 41.94 2.41
2512 2706 5.723492 TCATTTCATTCAGCTCACATACG 57.277 39.130 0.00 0.00 0.00 3.06
2542 2736 2.982744 GAGAAAGGCGCCAACAGGC 61.983 63.158 31.54 11.37 45.19 4.85
2543 2737 2.335712 GGAGAAAGGCGCCAACAGG 61.336 63.158 31.54 0.00 36.33 4.00
2544 2738 2.680913 CGGAGAAAGGCGCCAACAG 61.681 63.158 31.54 11.27 36.02 3.16
2545 2739 2.668212 CGGAGAAAGGCGCCAACA 60.668 61.111 31.54 0.00 36.02 3.33
2546 2740 2.183858 GAACGGAGAAAGGCGCCAAC 62.184 60.000 31.54 18.84 36.02 3.77
2547 2741 1.964373 GAACGGAGAAAGGCGCCAA 60.964 57.895 31.54 0.00 36.02 4.52
2548 2742 2.358247 GAACGGAGAAAGGCGCCA 60.358 61.111 31.54 0.00 36.02 5.69
2586 2780 0.467290 TTATGGCCCGGCTTTGATCC 60.467 55.000 9.86 0.00 0.00 3.36
2600 2794 5.331902 CGGTTTGCAAAGTCATACTTATGG 58.668 41.667 13.26 0.00 37.47 2.74
2637 2831 4.093011 ACAGACTGAATACAAGAGCCTCT 58.907 43.478 10.08 0.00 0.00 3.69
2689 2888 6.160576 AGTGGAACAATACATTTTGCTGTT 57.839 33.333 0.00 0.00 44.16 3.16
2700 2899 9.341899 GTCAATACATTTTGAGTGGAACAATAC 57.658 33.333 0.00 0.00 36.00 1.89
2702 2901 7.950512 TGTCAATACATTTTGAGTGGAACAAT 58.049 30.769 0.00 0.00 42.06 2.71
2707 2906 5.316167 AGCTGTCAATACATTTTGAGTGGA 58.684 37.500 0.00 0.00 36.34 4.02
2711 2910 7.977904 TCATGTAGCTGTCAATACATTTTGAG 58.022 34.615 0.00 0.00 39.91 3.02
2713 2912 9.229784 GAATCATGTAGCTGTCAATACATTTTG 57.770 33.333 0.00 1.30 39.91 2.44
2719 2918 6.051717 ACAGGAATCATGTAGCTGTCAATAC 58.948 40.000 0.00 0.00 0.00 1.89
2720 2919 6.239217 ACAGGAATCATGTAGCTGTCAATA 57.761 37.500 0.00 0.00 0.00 1.90
2722 2921 4.507710 GACAGGAATCATGTAGCTGTCAA 58.492 43.478 0.00 0.00 39.36 3.18
2723 2922 3.118629 GGACAGGAATCATGTAGCTGTCA 60.119 47.826 0.00 0.00 40.76 3.58
2724 2923 3.118629 TGGACAGGAATCATGTAGCTGTC 60.119 47.826 0.00 0.00 38.98 3.51
2725 2924 2.840038 TGGACAGGAATCATGTAGCTGT 59.160 45.455 0.00 0.00 0.00 4.40
2726 2925 3.548745 TGGACAGGAATCATGTAGCTG 57.451 47.619 0.00 0.00 0.00 4.24
2772 2992 0.807496 GCCTAGCTGCCTTGTCAAAG 59.193 55.000 0.00 0.00 0.00 2.77
2822 3042 8.143193 CAGAGCAAGAAGATCTCTGTACATATT 58.857 37.037 0.00 0.00 42.09 1.28
2911 3132 0.665068 TCCGTGTTCGTGTTGGATCG 60.665 55.000 0.00 0.00 35.01 3.69
2926 3147 1.000955 CACTGGCTAGAACTGTTCCGT 59.999 52.381 16.48 2.39 0.00 4.69
2964 3228 1.295792 TGTTTTGTCGACTCACCTGC 58.704 50.000 17.92 1.54 0.00 4.85
3028 3293 0.171455 GAGCGTCCGAGACAGAACAT 59.829 55.000 5.15 0.00 32.09 2.71
3059 3324 4.884668 ACCGGAGAGAAAAATGAGTGTA 57.115 40.909 9.46 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.