Multiple sequence alignment - TraesCS7A01G270100

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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 TraesCS7A01G270100 chr7A 100.000 3453 0 0 1 3453 276187319 276183867 0.000000e+00 6377.0
1 TraesCS7A01G270100 chr7A 87.619 105 13 0 1 105 584030568 584030672 4.680000e-24 122.0
2 TraesCS7A01G270100 chr7B 96.635 2110 62 6 265 2369 235451030 235448925 0.000000e+00 3494.0
3 TraesCS7A01G270100 chr7B 95.370 108 4 1 2469 2575 235448540 235448433 1.650000e-38 171.0
4 TraesCS7A01G270100 chr7B 95.238 63 2 1 2668 2729 235448074 235448012 7.890000e-17 99.0
5 TraesCS7A01G270100 chr7D 95.072 1948 53 12 426 2369 256445291 256443383 0.000000e+00 3025.0
6 TraesCS7A01G270100 chr7D 85.244 698 86 16 2766 3452 597703368 597702677 0.000000e+00 702.0
7 TraesCS7A01G270100 chr7D 84.848 693 90 11 2767 3451 489451482 489452167 0.000000e+00 684.0
8 TraesCS7A01G270100 chr7D 89.728 331 20 10 106 434 256448682 256448364 8.920000e-111 411.0
9 TraesCS7A01G270100 chr7D 89.252 214 15 8 2535 2745 256443147 256442939 9.510000e-66 261.0
10 TraesCS7A01G270100 chr7D 93.243 74 5 0 2415 2488 256443373 256443300 3.640000e-20 110.0
11 TraesCS7A01G270100 chr4D 85.206 703 88 12 2760 3452 318591721 318592417 0.000000e+00 708.0
12 TraesCS7A01G270100 chr6D 85.201 696 89 12 2766 3452 58834470 58833780 0.000000e+00 702.0
13 TraesCS7A01G270100 chr5D 85.303 694 85 14 2768 3452 412713368 412714053 0.000000e+00 701.0
14 TraesCS7A01G270100 chr5D 84.870 694 89 11 2767 3452 76211599 76210914 0.000000e+00 686.0
15 TraesCS7A01G270100 chr5D 89.109 101 11 0 1465 1565 413058646 413058546 3.620000e-25 126.0
16 TraesCS7A01G270100 chr5D 77.619 210 39 8 1154 1361 558247773 558247570 1.680000e-23 121.0
17 TraesCS7A01G270100 chr4B 85.159 694 91 10 2767 3452 203210125 203210814 0.000000e+00 701.0
18 TraesCS7A01G270100 chr2D 85.100 698 85 12 2766 3452 592373046 592373735 0.000000e+00 695.0
19 TraesCS7A01G270100 chr2D 84.748 695 92 10 2767 3452 574977714 574978403 0.000000e+00 684.0
20 TraesCS7A01G270100 chr2D 87.736 106 11 2 1 105 649556163 649556059 4.680000e-24 122.0
21 TraesCS7A01G270100 chr4A 90.476 105 10 0 1 105 614128292 614128188 4.650000e-29 139.0
22 TraesCS7A01G270100 chr4A 87.619 105 13 0 1 105 555931233 555931337 4.680000e-24 122.0
23 TraesCS7A01G270100 chr4A 76.777 211 41 8 1153 1361 610490465 610490261 1.010000e-20 111.0
24 TraesCS7A01G270100 chr1A 89.815 108 11 0 1 108 459176706 459176813 4.650000e-29 139.0
25 TraesCS7A01G270100 chr1A 87.736 106 13 0 1 106 498406303 498406198 1.300000e-24 124.0
26 TraesCS7A01G270100 chr1A 84.404 109 15 2 1 108 586066663 586066556 4.710000e-19 106.0
27 TraesCS7A01G270100 chr6A 88.571 105 12 0 1 105 448047571 448047675 1.010000e-25 128.0
28 TraesCS7A01G270100 chr5B 89.109 101 11 0 1465 1565 497757637 497757537 3.620000e-25 126.0
29 TraesCS7A01G270100 chr5B 77.725 211 39 8 1153 1361 704878529 704878733 4.680000e-24 122.0
30 TraesCS7A01G270100 chr5A 89.109 101 11 0 1465 1565 525078933 525078833 3.620000e-25 126.0
31 TraesCS7A01G270100 chr3B 86.792 106 13 1 1 106 245057143 245057039 2.180000e-22 117.0
32 TraesCS7A01G270100 chr3D 91.379 58 5 0 1308 1365 120908536 120908593 2.860000e-11 80.5


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 TraesCS7A01G270100 chr7A 276183867 276187319 3452 True 6377.000000 6377 100.000000 1 3453 1 chr7A.!!$R1 3452
1 TraesCS7A01G270100 chr7B 235448012 235451030 3018 True 1254.666667 3494 95.747667 265 2729 3 chr7B.!!$R1 2464
2 TraesCS7A01G270100 chr7D 256442939 256448682 5743 True 951.750000 3025 91.823750 106 2745 4 chr7D.!!$R2 2639
3 TraesCS7A01G270100 chr7D 597702677 597703368 691 True 702.000000 702 85.244000 2766 3452 1 chr7D.!!$R1 686
4 TraesCS7A01G270100 chr7D 489451482 489452167 685 False 684.000000 684 84.848000 2767 3451 1 chr7D.!!$F1 684
5 TraesCS7A01G270100 chr4D 318591721 318592417 696 False 708.000000 708 85.206000 2760 3452 1 chr4D.!!$F1 692
6 TraesCS7A01G270100 chr6D 58833780 58834470 690 True 702.000000 702 85.201000 2766 3452 1 chr6D.!!$R1 686
7 TraesCS7A01G270100 chr5D 412713368 412714053 685 False 701.000000 701 85.303000 2768 3452 1 chr5D.!!$F1 684
8 TraesCS7A01G270100 chr5D 76210914 76211599 685 True 686.000000 686 84.870000 2767 3452 1 chr5D.!!$R1 685
9 TraesCS7A01G270100 chr4B 203210125 203210814 689 False 701.000000 701 85.159000 2767 3452 1 chr4B.!!$F1 685
10 TraesCS7A01G270100 chr2D 592373046 592373735 689 False 695.000000 695 85.100000 2766 3452 1 chr2D.!!$F2 686
11 TraesCS7A01G270100 chr2D 574977714 574978403 689 False 684.000000 684 84.748000 2767 3452 1 chr2D.!!$F1 685

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
196 197 0.252197 GAGTTTGGGTACGGCCATCT 59.748 55.0 2.24 0.0 39.65 2.90 F
1026 4112 0.673985 GAAGGTTGCTTTGACACCCC 59.326 55.0 0.00 0.0 0.00 4.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1822 4911 0.107945 GCTTCTTCATCTGCCCGAGT 60.108 55.0 0.00 0.00 0.0 4.18 R
2674 6414 0.254462 TTATTCGGGGTGATGCTGCA 59.746 50.0 4.13 4.13 0.0 4.41 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
23 24 6.576662 CTTTAGTCTCAGTTACTCCACTCA 57.423 41.667 0.00 0.00 0.00 3.41
24 25 7.164230 CTTTAGTCTCAGTTACTCCACTCAT 57.836 40.000 0.00 0.00 0.00 2.90
25 26 8.282455 CTTTAGTCTCAGTTACTCCACTCATA 57.718 38.462 0.00 0.00 0.00 2.15
26 27 8.824756 TTTAGTCTCAGTTACTCCACTCATAT 57.175 34.615 0.00 0.00 0.00 1.78
27 28 6.707440 AGTCTCAGTTACTCCACTCATATG 57.293 41.667 0.00 0.00 0.00 1.78
28 29 6.191315 AGTCTCAGTTACTCCACTCATATGT 58.809 40.000 1.90 0.00 0.00 2.29
29 30 6.096141 AGTCTCAGTTACTCCACTCATATGTG 59.904 42.308 1.90 2.63 37.66 3.21
30 31 5.952347 TCTCAGTTACTCCACTCATATGTGT 59.048 40.000 4.59 4.59 36.30 3.72
31 32 5.965922 TCAGTTACTCCACTCATATGTGTG 58.034 41.667 24.52 24.52 38.75 3.82
32 33 4.568359 CAGTTACTCCACTCATATGTGTGC 59.432 45.833 25.59 14.49 37.99 4.57
33 34 4.222810 AGTTACTCCACTCATATGTGTGCA 59.777 41.667 25.59 14.98 37.99 4.57
34 35 3.920231 ACTCCACTCATATGTGTGCAT 57.080 42.857 25.59 13.81 37.99 3.96
35 36 3.538591 ACTCCACTCATATGTGTGCATG 58.461 45.455 25.59 19.68 37.99 4.06
36 37 3.198417 ACTCCACTCATATGTGTGCATGA 59.802 43.478 25.59 18.27 37.99 3.07
37 38 4.193865 CTCCACTCATATGTGTGCATGAA 58.806 43.478 25.59 11.38 37.99 2.57
38 39 4.784177 TCCACTCATATGTGTGCATGAAT 58.216 39.130 25.59 0.00 37.99 2.57
39 40 4.577283 TCCACTCATATGTGTGCATGAATG 59.423 41.667 25.59 14.06 37.99 2.67
40 41 4.577283 CCACTCATATGTGTGCATGAATGA 59.423 41.667 25.59 0.00 37.99 2.57
41 42 5.277828 CCACTCATATGTGTGCATGAATGAG 60.278 44.000 25.59 18.21 45.15 2.90
42 43 4.275196 ACTCATATGTGTGCATGAATGAGC 59.725 41.667 19.08 0.00 44.36 4.26
43 44 3.566742 TCATATGTGTGCATGAATGAGCC 59.433 43.478 1.90 0.00 36.58 4.70
44 45 1.842052 ATGTGTGCATGAATGAGCCA 58.158 45.000 0.00 0.00 33.37 4.75
45 46 1.618487 TGTGTGCATGAATGAGCCAA 58.382 45.000 0.00 0.00 0.00 4.52
46 47 1.962100 TGTGTGCATGAATGAGCCAAA 59.038 42.857 0.00 0.00 0.00 3.28
47 48 2.364647 TGTGTGCATGAATGAGCCAAAA 59.635 40.909 0.00 0.00 0.00 2.44
48 49 2.991190 GTGTGCATGAATGAGCCAAAAG 59.009 45.455 0.00 0.00 0.00 2.27
49 50 2.892215 TGTGCATGAATGAGCCAAAAGA 59.108 40.909 0.00 0.00 0.00 2.52
50 51 3.321396 TGTGCATGAATGAGCCAAAAGAA 59.679 39.130 0.00 0.00 0.00 2.52
51 52 4.020928 TGTGCATGAATGAGCCAAAAGAAT 60.021 37.500 0.00 0.00 0.00 2.40
52 53 4.933400 GTGCATGAATGAGCCAAAAGAATT 59.067 37.500 0.00 0.00 0.00 2.17
53 54 5.410439 GTGCATGAATGAGCCAAAAGAATTT 59.590 36.000 0.00 0.00 42.41 1.82
78 79 6.835819 AGAATTTTAGTTGGACTTTAGGCC 57.164 37.500 0.00 0.00 0.00 5.19
79 80 6.311735 AGAATTTTAGTTGGACTTTAGGCCA 58.688 36.000 5.01 0.00 0.00 5.36
80 81 6.780522 AGAATTTTAGTTGGACTTTAGGCCAA 59.219 34.615 13.08 13.08 41.61 4.52
81 82 6.987403 ATTTTAGTTGGACTTTAGGCCAAA 57.013 33.333 18.40 3.47 45.03 3.28
82 83 6.399639 TTTTAGTTGGACTTTAGGCCAAAG 57.600 37.500 18.40 19.79 45.03 2.77
83 84 2.876581 AGTTGGACTTTAGGCCAAAGG 58.123 47.619 18.40 8.04 46.77 3.11
101 102 7.599171 GCCAAAGGCTTACTAGTAAAATTTCA 58.401 34.615 15.95 0.00 46.69 2.69
102 103 8.085909 GCCAAAGGCTTACTAGTAAAATTTCAA 58.914 33.333 15.95 0.00 46.69 2.69
103 104 9.406828 CCAAAGGCTTACTAGTAAAATTTCAAC 57.593 33.333 15.95 0.00 0.00 3.18
104 105 9.959749 CAAAGGCTTACTAGTAAAATTTCAACA 57.040 29.630 15.95 0.00 0.00 3.33
188 189 3.288809 AGTCGTAACGAGTTTGGGTAC 57.711 47.619 0.00 0.00 35.97 3.34
196 197 0.252197 GAGTTTGGGTACGGCCATCT 59.748 55.000 2.24 0.00 39.65 2.90
198 199 1.208776 AGTTTGGGTACGGCCATCTAC 59.791 52.381 2.24 0.00 39.65 2.59
204 205 3.712733 TGGGTACGGCCATCTACTTTAAT 59.287 43.478 2.24 0.00 39.65 1.40
205 206 4.202284 TGGGTACGGCCATCTACTTTAATC 60.202 45.833 2.24 0.00 39.65 1.75
206 207 4.202284 GGGTACGGCCATCTACTTTAATCA 60.202 45.833 2.24 0.00 39.65 2.57
207 208 4.989168 GGTACGGCCATCTACTTTAATCAG 59.011 45.833 2.24 0.00 37.17 2.90
208 209 5.221382 GGTACGGCCATCTACTTTAATCAGA 60.221 44.000 2.24 0.00 37.17 3.27
209 210 4.950050 ACGGCCATCTACTTTAATCAGAG 58.050 43.478 2.24 0.00 0.00 3.35
210 211 4.202264 ACGGCCATCTACTTTAATCAGAGG 60.202 45.833 2.24 0.00 0.00 3.69
211 212 4.068599 GGCCATCTACTTTAATCAGAGGC 58.931 47.826 0.00 0.00 34.54 4.70
212 213 3.743396 GCCATCTACTTTAATCAGAGGCG 59.257 47.826 0.00 0.00 0.00 5.52
236 237 6.039493 CGTGAGGGTGACAAGACTATAGTAAT 59.961 42.308 5.09 0.00 0.00 1.89
276 277 2.450609 ACCAACGAACTAATCAGCGT 57.549 45.000 0.00 0.00 38.81 5.07
316 318 1.625616 AAGCTAAACGACCGATCACG 58.374 50.000 0.00 0.00 39.43 4.35
391 393 4.783764 ATCTTCAAAACAATTCCGGGAC 57.216 40.909 0.00 0.00 0.00 4.46
451 3534 7.985476 AGATAATTTCCCTCGTGTACATTTTG 58.015 34.615 0.00 0.00 0.00 2.44
475 3558 2.819550 CAACGGACGGGATAGGGG 59.180 66.667 0.00 0.00 0.00 4.79
497 3583 3.131396 AGCTCCGCGGATATTTGTTTAG 58.869 45.455 31.19 13.99 0.00 1.85
498 3584 2.870411 GCTCCGCGGATATTTGTTTAGT 59.130 45.455 31.19 0.00 0.00 2.24
499 3585 3.311596 GCTCCGCGGATATTTGTTTAGTT 59.688 43.478 31.19 0.00 0.00 2.24
500 3586 4.201881 GCTCCGCGGATATTTGTTTAGTTT 60.202 41.667 31.19 0.00 0.00 2.66
501 3587 5.224562 TCCGCGGATATTTGTTTAGTTTG 57.775 39.130 27.28 0.00 0.00 2.93
541 3627 2.045438 TGCCGCCCACCACAATAG 60.045 61.111 0.00 0.00 0.00 1.73
639 3725 4.593956 CCTTGAACCTTCCAGAATAAGCT 58.406 43.478 0.00 0.00 0.00 3.74
646 3732 6.694445 ACCTTCCAGAATAAGCTATAGCAT 57.306 37.500 26.07 17.28 45.16 3.79
742 3828 2.683465 CCACCCACATCCCTCCAGG 61.683 68.421 0.00 0.00 0.00 4.45
971 4057 3.500014 CGTTTCCGTCTCTAACTTCCTC 58.500 50.000 0.00 0.00 0.00 3.71
1026 4112 0.673985 GAAGGTTGCTTTGACACCCC 59.326 55.000 0.00 0.00 0.00 4.95
1457 4546 4.415150 AGGTGCTCATGGGCGTGG 62.415 66.667 14.07 0.00 34.52 4.94
1747 4836 3.584052 CCGTCCTACTCCGGCTCG 61.584 72.222 0.00 0.00 37.43 5.03
2007 5117 2.034687 GCTCTTGCCTTCCTGCCA 59.965 61.111 0.00 0.00 0.00 4.92
2200 5310 1.005512 CGGAATGGACGGTCACACA 60.006 57.895 10.76 0.00 0.00 3.72
2228 5338 1.257055 GCAAGCCTGGCCCATTTACA 61.257 55.000 16.57 0.00 0.00 2.41
2248 5358 2.886134 GCCCAGACCCGTGTACCAA 61.886 63.158 0.00 0.00 0.00 3.67
2369 5483 2.360475 GGTGAGCTGGGTTCAGGC 60.360 66.667 0.00 0.00 41.19 4.85
2370 5484 2.753029 GTGAGCTGGGTTCAGGCT 59.247 61.111 0.00 0.00 41.19 4.58
2371 5485 1.073897 GTGAGCTGGGTTCAGGCTT 59.926 57.895 0.00 0.00 41.19 4.35
2372 5486 0.324943 GTGAGCTGGGTTCAGGCTTA 59.675 55.000 0.00 0.00 41.19 3.09
2373 5487 1.064003 TGAGCTGGGTTCAGGCTTAA 58.936 50.000 0.00 0.00 41.19 1.85
2374 5488 1.003580 TGAGCTGGGTTCAGGCTTAAG 59.996 52.381 0.00 0.00 41.19 1.85
2375 5489 0.329596 AGCTGGGTTCAGGCTTAAGG 59.670 55.000 4.29 0.00 41.19 2.69
2385 5499 1.549170 CAGGCTTAAGGGTCGTGTACT 59.451 52.381 4.29 0.00 0.00 2.73
2386 5500 1.549170 AGGCTTAAGGGTCGTGTACTG 59.451 52.381 4.29 0.00 0.00 2.74
2387 5501 1.405121 GGCTTAAGGGTCGTGTACTGG 60.405 57.143 4.29 0.00 0.00 4.00
2388 5502 1.274447 GCTTAAGGGTCGTGTACTGGT 59.726 52.381 4.29 0.00 0.00 4.00
2389 5503 2.493278 GCTTAAGGGTCGTGTACTGGTA 59.507 50.000 4.29 0.00 0.00 3.25
2390 5504 3.674410 GCTTAAGGGTCGTGTACTGGTAC 60.674 52.174 4.29 4.15 36.63 3.34
2391 5505 1.260544 AAGGGTCGTGTACTGGTACC 58.739 55.000 4.43 4.43 35.26 3.34
2392 5506 0.962356 AGGGTCGTGTACTGGTACCG 60.962 60.000 7.57 4.79 35.26 4.02
2393 5507 1.244019 GGGTCGTGTACTGGTACCGT 61.244 60.000 7.57 10.74 35.26 4.83
2394 5508 1.448985 GGTCGTGTACTGGTACCGTA 58.551 55.000 7.57 9.72 35.26 4.02
2395 5509 1.130561 GGTCGTGTACTGGTACCGTAC 59.869 57.143 26.55 26.55 38.13 3.67
2396 5510 2.076863 GTCGTGTACTGGTACCGTACT 58.923 52.381 29.85 10.58 38.39 2.73
2397 5511 2.484264 GTCGTGTACTGGTACCGTACTT 59.516 50.000 29.85 10.59 38.39 2.24
2398 5512 3.058224 GTCGTGTACTGGTACCGTACTTT 60.058 47.826 29.85 9.22 38.39 2.66
2399 5513 3.568007 TCGTGTACTGGTACCGTACTTTT 59.432 43.478 29.85 8.13 38.39 2.27
2400 5514 4.037446 TCGTGTACTGGTACCGTACTTTTT 59.963 41.667 29.85 7.31 38.39 1.94
2424 5544 1.488390 TGAGGGGATTGGTACCGTAC 58.512 55.000 7.57 0.00 0.00 3.67
2427 5547 1.835531 AGGGGATTGGTACCGTACTTG 59.164 52.381 7.57 0.00 0.00 3.16
2507 5943 6.150318 TGTACGTAGAGAGAAAGAAAGCAAG 58.850 40.000 0.00 0.00 0.00 4.01
2550 6125 1.076332 CCGTAAGTTTCTCGGCAAGG 58.924 55.000 0.00 0.00 37.90 3.61
2575 6150 6.262273 GCCCGAGTATTTTATCATCTCCAAAA 59.738 38.462 0.00 0.00 0.00 2.44
2576 6151 7.639945 CCCGAGTATTTTATCATCTCCAAAAC 58.360 38.462 0.00 0.00 0.00 2.43
2577 6152 7.255139 CCCGAGTATTTTATCATCTCCAAAACC 60.255 40.741 0.00 0.00 0.00 3.27
2578 6153 7.499232 CCGAGTATTTTATCATCTCCAAAACCT 59.501 37.037 0.00 0.00 0.00 3.50
2579 6154 9.542462 CGAGTATTTTATCATCTCCAAAACCTA 57.458 33.333 0.00 0.00 0.00 3.08
2610 6347 9.606631 TTGTACATAAAACAAGCCAGAAAAATT 57.393 25.926 0.00 0.00 33.13 1.82
2632 6369 1.728971 GAGCAGTGATGACAAGTTCGG 59.271 52.381 0.00 0.00 0.00 4.30
2654 6392 5.147162 GGTGATGTGATCTTCGTTCAAAAC 58.853 41.667 0.00 0.00 0.00 2.43
2674 6414 8.508875 TCAAAACGAGTTTCTTTTTGAGTACTT 58.491 29.630 15.25 0.00 44.33 2.24
2686 6528 1.339055 TGAGTACTTGCAGCATCACCC 60.339 52.381 0.00 0.00 0.00 4.61
2720 6562 2.052782 TAGCATGTCCACTCGAGCTA 57.947 50.000 13.61 3.31 33.83 3.32
2730 6572 3.451540 TCCACTCGAGCTAGAGAGTTCTA 59.548 47.826 27.99 8.81 44.46 2.10
2731 6573 4.081031 TCCACTCGAGCTAGAGAGTTCTAA 60.081 45.833 27.99 5.53 44.46 2.10
2732 6574 4.636648 CCACTCGAGCTAGAGAGTTCTAAA 59.363 45.833 27.99 0.00 44.46 1.85
2747 6589 9.968743 GAGAGTTCTAAACATAAAACATTACGG 57.031 33.333 0.00 0.00 0.00 4.02
2748 6590 8.943002 AGAGTTCTAAACATAAAACATTACGGG 58.057 33.333 0.00 0.00 0.00 5.28
2749 6591 8.625786 AGTTCTAAACATAAAACATTACGGGT 57.374 30.769 0.00 0.00 0.00 5.28
2750 6592 9.070179 AGTTCTAAACATAAAACATTACGGGTT 57.930 29.630 0.00 0.00 0.00 4.11
2755 6597 8.523523 AAACATAAAACATTACGGGTTAAAGC 57.476 30.769 0.00 0.00 0.00 3.51
2756 6598 7.457024 ACATAAAACATTACGGGTTAAAGCT 57.543 32.000 0.00 0.00 0.00 3.74
2757 6599 7.888424 ACATAAAACATTACGGGTTAAAGCTT 58.112 30.769 0.00 0.00 0.00 3.74
2758 6600 7.810759 ACATAAAACATTACGGGTTAAAGCTTG 59.189 33.333 0.00 0.00 0.00 4.01
2764 6606 6.698329 ACATTACGGGTTAAAGCTTGTTTTTC 59.302 34.615 0.00 0.00 0.00 2.29
2796 6638 2.096169 CGCTTACACGTGTGGCATTTTA 60.096 45.455 31.92 12.79 34.19 1.52
2810 6652 7.212976 TGTGGCATTTTACACATTGTTTACAT 58.787 30.769 0.00 0.00 42.20 2.29
2833 6675 6.839124 TGCCTTCATCATCACTTATTTTGT 57.161 33.333 0.00 0.00 0.00 2.83
2871 6713 9.017509 AGATGACATTAGCAGAAATCTTTTTGA 57.982 29.630 0.00 0.00 0.00 2.69
2956 6799 6.749139 TCATTAAATCCGTCTCGATGAGATT 58.251 36.000 0.00 0.00 40.98 2.40
2959 6802 7.843490 TTAAATCCGTCTCGATGAGATTTTT 57.157 32.000 14.23 1.96 40.98 1.94
2964 6807 7.843490 TCCGTCTCGATGAGATTTTTAAAAT 57.157 32.000 2.23 2.23 40.98 1.82
3070 6920 5.897377 ACTAAAGTGGTAATGTGGCAATC 57.103 39.130 0.00 0.00 0.00 2.67
3092 6942 4.695455 TCTTAGTTTGTAGAGCATGGCAAC 59.305 41.667 0.00 0.00 0.00 4.17
3181 7035 6.392354 CAATTTCAAGTGCATGTCTTATGGT 58.608 36.000 0.00 0.00 0.00 3.55
3334 7190 7.497579 TGGTAATTTATACGCAACAGACATGAT 59.502 33.333 0.00 0.00 0.00 2.45
3346 7202 7.573096 CGCAACAGACATGATAACTTTTAACCT 60.573 37.037 0.00 0.00 0.00 3.50
3347 7203 8.082242 GCAACAGACATGATAACTTTTAACCTT 58.918 33.333 0.00 0.00 0.00 3.50
3351 7209 9.831737 CAGACATGATAACTTTTAACCTTCAAG 57.168 33.333 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.576662 TGAGTGGAGTAACTGAGACTAAAG 57.423 41.667 0.00 0.00 0.00 1.85
1 2 8.687242 CATATGAGTGGAGTAACTGAGACTAAA 58.313 37.037 0.00 0.00 0.00 1.85
2 3 7.834681 ACATATGAGTGGAGTAACTGAGACTAA 59.165 37.037 10.38 0.00 0.00 2.24
3 4 7.283354 CACATATGAGTGGAGTAACTGAGACTA 59.717 40.741 10.38 0.00 35.88 2.59
4 5 6.096141 CACATATGAGTGGAGTAACTGAGACT 59.904 42.308 10.38 0.00 35.88 3.24
5 6 6.127591 ACACATATGAGTGGAGTAACTGAGAC 60.128 42.308 10.38 0.00 43.72 3.36
6 7 5.952347 ACACATATGAGTGGAGTAACTGAGA 59.048 40.000 10.38 0.00 43.72 3.27
7 8 6.038985 CACACATATGAGTGGAGTAACTGAG 58.961 44.000 21.52 0.00 43.72 3.35
8 9 5.624509 GCACACATATGAGTGGAGTAACTGA 60.625 44.000 27.51 0.00 43.72 3.41
9 10 4.568359 GCACACATATGAGTGGAGTAACTG 59.432 45.833 27.51 7.51 43.72 3.16
10 11 4.222810 TGCACACATATGAGTGGAGTAACT 59.777 41.667 27.51 0.00 43.72 2.24
11 12 4.503910 TGCACACATATGAGTGGAGTAAC 58.496 43.478 27.51 14.42 43.72 2.50
12 13 4.817318 TGCACACATATGAGTGGAGTAA 57.183 40.909 27.51 0.74 43.72 2.24
13 14 4.405358 TCATGCACACATATGAGTGGAGTA 59.595 41.667 27.51 17.31 43.72 2.59
14 15 3.198417 TCATGCACACATATGAGTGGAGT 59.802 43.478 27.51 15.67 43.72 3.85
15 16 3.800531 TCATGCACACATATGAGTGGAG 58.199 45.455 27.51 19.81 43.72 3.86
16 17 3.910568 TCATGCACACATATGAGTGGA 57.089 42.857 27.51 26.23 43.72 4.02
17 18 4.577283 TCATTCATGCACACATATGAGTGG 59.423 41.667 27.51 15.37 43.72 4.00
18 19 5.744666 TCATTCATGCACACATATGAGTG 57.255 39.130 23.99 23.99 44.93 3.51
19 20 4.275196 GCTCATTCATGCACACATATGAGT 59.725 41.667 10.38 4.57 44.36 3.41
20 21 4.320275 GGCTCATTCATGCACACATATGAG 60.320 45.833 10.38 15.99 44.84 2.90
21 22 3.566742 GGCTCATTCATGCACACATATGA 59.433 43.478 10.38 0.00 33.67 2.15
22 23 3.316868 TGGCTCATTCATGCACACATATG 59.683 43.478 0.00 0.00 33.67 1.78
23 24 3.558033 TGGCTCATTCATGCACACATAT 58.442 40.909 0.00 0.00 33.67 1.78
24 25 3.002038 TGGCTCATTCATGCACACATA 57.998 42.857 0.00 0.00 33.67 2.29
25 26 1.842052 TGGCTCATTCATGCACACAT 58.158 45.000 0.00 0.00 36.79 3.21
26 27 1.618487 TTGGCTCATTCATGCACACA 58.382 45.000 0.00 0.00 0.00 3.72
27 28 2.728690 TTTGGCTCATTCATGCACAC 57.271 45.000 0.00 0.00 0.00 3.82
28 29 2.892215 TCTTTTGGCTCATTCATGCACA 59.108 40.909 0.00 0.00 0.00 4.57
29 30 3.581024 TCTTTTGGCTCATTCATGCAC 57.419 42.857 0.00 0.00 0.00 4.57
30 31 4.811969 ATTCTTTTGGCTCATTCATGCA 57.188 36.364 0.00 0.00 0.00 3.96
31 32 6.490566 AAAATTCTTTTGGCTCATTCATGC 57.509 33.333 0.00 0.00 0.00 4.06
32 33 8.991243 TCTAAAATTCTTTTGGCTCATTCATG 57.009 30.769 0.00 0.00 34.19 3.07
52 53 8.799367 GGCCTAAAGTCCAACTAAAATTCTAAA 58.201 33.333 0.00 0.00 0.00 1.85
53 54 7.945664 TGGCCTAAAGTCCAACTAAAATTCTAA 59.054 33.333 3.32 0.00 0.00 2.10
54 55 7.463431 TGGCCTAAAGTCCAACTAAAATTCTA 58.537 34.615 3.32 0.00 0.00 2.10
55 56 6.311735 TGGCCTAAAGTCCAACTAAAATTCT 58.688 36.000 3.32 0.00 0.00 2.40
56 57 6.584185 TGGCCTAAAGTCCAACTAAAATTC 57.416 37.500 3.32 0.00 0.00 2.17
57 58 6.987403 TTGGCCTAAAGTCCAACTAAAATT 57.013 33.333 3.32 0.00 37.43 1.82
58 59 6.014584 CCTTTGGCCTAAAGTCCAACTAAAAT 60.015 38.462 19.68 0.00 43.45 1.82
59 60 5.303333 CCTTTGGCCTAAAGTCCAACTAAAA 59.697 40.000 19.68 2.11 43.45 1.52
60 61 4.830600 CCTTTGGCCTAAAGTCCAACTAAA 59.169 41.667 19.68 2.47 43.45 1.85
61 62 4.403734 CCTTTGGCCTAAAGTCCAACTAA 58.596 43.478 19.68 0.00 43.45 2.24
62 63 3.812882 GCCTTTGGCCTAAAGTCCAACTA 60.813 47.826 19.68 0.00 44.06 2.24
63 64 2.876581 CCTTTGGCCTAAAGTCCAACT 58.123 47.619 19.68 0.00 43.45 3.16
64 65 1.272490 GCCTTTGGCCTAAAGTCCAAC 59.728 52.381 19.68 6.56 44.06 3.77
65 66 1.627864 GCCTTTGGCCTAAAGTCCAA 58.372 50.000 19.68 0.00 44.06 3.53
66 67 3.356814 GCCTTTGGCCTAAAGTCCA 57.643 52.632 19.68 0.00 44.06 4.02
77 78 9.406828 GTTGAAATTTTACTAGTAAGCCTTTGG 57.593 33.333 14.73 0.00 0.00 3.28
78 79 9.959749 TGTTGAAATTTTACTAGTAAGCCTTTG 57.040 29.630 14.73 0.00 0.00 2.77
151 152 9.035607 CGTTACGACTTACTACCTCTATTCTAA 57.964 37.037 0.00 0.00 0.00 2.10
152 153 8.414003 TCGTTACGACTTACTACCTCTATTCTA 58.586 37.037 2.33 0.00 0.00 2.10
155 156 7.044798 ACTCGTTACGACTTACTACCTCTATT 58.955 38.462 2.33 0.00 0.00 1.73
157 158 5.967088 ACTCGTTACGACTTACTACCTCTA 58.033 41.667 2.33 0.00 0.00 2.43
159 160 5.538067 AACTCGTTACGACTTACTACCTC 57.462 43.478 2.33 0.00 0.00 3.85
160 161 5.335191 CCAAACTCGTTACGACTTACTACCT 60.335 44.000 2.33 0.00 0.00 3.08
161 162 4.853743 CCAAACTCGTTACGACTTACTACC 59.146 45.833 2.33 0.00 0.00 3.18
162 163 4.853743 CCCAAACTCGTTACGACTTACTAC 59.146 45.833 2.33 0.00 0.00 2.73
188 189 4.310769 CCTCTGATTAAAGTAGATGGCCG 58.689 47.826 0.00 0.00 0.00 6.13
196 197 3.132289 CCCTCACGCCTCTGATTAAAGTA 59.868 47.826 0.00 0.00 0.00 2.24
198 199 2.093447 ACCCTCACGCCTCTGATTAAAG 60.093 50.000 0.00 0.00 0.00 1.85
204 205 2.117423 TCACCCTCACGCCTCTGA 59.883 61.111 0.00 0.00 0.00 3.27
205 206 2.099652 TTGTCACCCTCACGCCTCTG 62.100 60.000 0.00 0.00 0.00 3.35
206 207 1.821061 CTTGTCACCCTCACGCCTCT 61.821 60.000 0.00 0.00 0.00 3.69
207 208 1.374758 CTTGTCACCCTCACGCCTC 60.375 63.158 0.00 0.00 0.00 4.70
208 209 1.837051 TCTTGTCACCCTCACGCCT 60.837 57.895 0.00 0.00 0.00 5.52
209 210 1.668151 GTCTTGTCACCCTCACGCC 60.668 63.158 0.00 0.00 0.00 5.68
210 211 0.601558 TAGTCTTGTCACCCTCACGC 59.398 55.000 0.00 0.00 0.00 5.34
211 212 3.695060 ACTATAGTCTTGTCACCCTCACG 59.305 47.826 0.00 0.00 0.00 4.35
212 213 6.770746 TTACTATAGTCTTGTCACCCTCAC 57.229 41.667 9.12 0.00 0.00 3.51
236 237 1.444250 GAGTCCAACCCACGTGTCA 59.556 57.895 15.65 0.00 0.00 3.58
391 393 4.491676 TCCCAGTTACTCGAGATTTTTCG 58.508 43.478 21.68 1.42 41.79 3.46
451 3534 0.390735 ATCCCGTCCGTTGCAGTAAC 60.391 55.000 0.00 0.00 35.90 2.50
499 3585 1.067821 GCAACCGTTGGATCAAACCAA 59.932 47.619 13.12 0.00 46.02 3.67
500 3586 0.671251 GCAACCGTTGGATCAAACCA 59.329 50.000 13.12 0.00 38.24 3.67
501 3587 0.386731 CGCAACCGTTGGATCAAACC 60.387 55.000 13.12 0.00 0.00 3.27
971 4057 1.583967 CGTAGCGTGGAGAGAAGCG 60.584 63.158 0.00 0.00 34.34 4.68
1053 4139 3.842923 AGCGCAGATCTGTCCCGG 61.843 66.667 23.38 9.46 0.00 5.73
1155 4244 4.463879 CAGCGACCTCTGCCCCAG 62.464 72.222 0.00 0.00 0.00 4.45
1346 4435 2.298163 CCCACTTACGTAGGTGTTGAGT 59.702 50.000 29.12 11.68 32.07 3.41
1457 4546 2.026262 TCTTCCTAAATCCCTGCACCAC 60.026 50.000 0.00 0.00 0.00 4.16
1609 4698 4.884257 GCTACCGGAATCGCGGCA 62.884 66.667 9.46 0.00 34.56 5.69
1822 4911 0.107945 GCTTCTTCATCTGCCCGAGT 60.108 55.000 0.00 0.00 0.00 4.18
2007 5117 2.639327 GCAGCCGTGGGAGCATTTT 61.639 57.895 0.00 0.00 0.00 1.82
2200 5310 4.988598 CAGGCTTGCACGTCCGGT 62.989 66.667 0.00 0.00 0.00 5.28
2228 5338 3.001406 GTACACGGGTCTGGGCCT 61.001 66.667 4.53 0.00 0.00 5.19
2369 5483 3.119352 GGTACCAGTACACGACCCTTAAG 60.119 52.174 7.15 0.00 37.78 1.85
2370 5484 2.825532 GGTACCAGTACACGACCCTTAA 59.174 50.000 7.15 0.00 37.78 1.85
2371 5485 2.446435 GGTACCAGTACACGACCCTTA 58.554 52.381 7.15 0.00 37.78 2.69
2372 5486 1.260544 GGTACCAGTACACGACCCTT 58.739 55.000 7.15 0.00 37.78 3.95
2373 5487 0.962356 CGGTACCAGTACACGACCCT 60.962 60.000 13.54 0.00 37.78 4.34
2374 5488 1.244019 ACGGTACCAGTACACGACCC 61.244 60.000 13.54 0.00 37.78 4.46
2375 5489 1.130561 GTACGGTACCAGTACACGACC 59.869 57.143 27.50 10.83 42.77 4.79
2401 5515 2.108601 ACGGTACCAATCCCCTCAAAAA 59.891 45.455 13.54 0.00 0.00 1.94
2402 5516 1.706305 ACGGTACCAATCCCCTCAAAA 59.294 47.619 13.54 0.00 0.00 2.44
2403 5517 1.364269 ACGGTACCAATCCCCTCAAA 58.636 50.000 13.54 0.00 0.00 2.69
2404 5518 1.832998 GTACGGTACCAATCCCCTCAA 59.167 52.381 13.54 0.00 0.00 3.02
2405 5519 1.007479 AGTACGGTACCAATCCCCTCA 59.993 52.381 13.54 0.00 0.00 3.86
2406 5520 1.785647 AGTACGGTACCAATCCCCTC 58.214 55.000 13.54 0.00 0.00 4.30
2407 5521 1.835531 CAAGTACGGTACCAATCCCCT 59.164 52.381 13.54 0.00 0.00 4.79
2408 5522 1.832998 TCAAGTACGGTACCAATCCCC 59.167 52.381 13.54 0.00 0.00 4.81
2409 5523 2.498885 ACTCAAGTACGGTACCAATCCC 59.501 50.000 13.54 0.00 0.00 3.85
2410 5524 3.881937 ACTCAAGTACGGTACCAATCC 57.118 47.619 13.54 0.00 0.00 3.01
2411 5525 7.838771 AATTAACTCAAGTACGGTACCAATC 57.161 36.000 13.54 0.79 0.00 2.67
2412 5526 9.723601 TTTAATTAACTCAAGTACGGTACCAAT 57.276 29.630 13.54 1.32 0.00 3.16
2413 5527 9.723601 ATTTAATTAACTCAAGTACGGTACCAA 57.276 29.630 13.54 0.00 0.00 3.67
2467 5587 5.801350 ACGTACATGCGACTTACTACTAA 57.199 39.130 0.00 0.00 35.59 2.24
2480 5915 5.004916 GCTTTCTTTCTCTCTACGTACATGC 59.995 44.000 0.00 0.00 0.00 4.06
2507 5943 6.349363 GGAGAAACTGGAATTCCACATACAAC 60.349 42.308 23.63 11.54 42.01 3.32
2550 6125 4.894784 TGGAGATGATAAAATACTCGGGC 58.105 43.478 0.00 0.00 0.00 6.13
2575 6150 8.139350 GGCTTGTTTTATGTACAAAAACTAGGT 58.861 33.333 29.89 10.46 43.56 3.08
2576 6151 8.138712 TGGCTTGTTTTATGTACAAAAACTAGG 58.861 33.333 29.89 23.25 43.56 3.02
2577 6152 9.180678 CTGGCTTGTTTTATGTACAAAAACTAG 57.819 33.333 27.94 27.94 44.84 2.57
2578 6153 8.904834 TCTGGCTTGTTTTATGTACAAAAACTA 58.095 29.630 27.41 23.15 43.82 2.24
2579 6154 7.777095 TCTGGCTTGTTTTATGTACAAAAACT 58.223 30.769 27.41 8.75 43.82 2.66
2580 6155 7.995463 TCTGGCTTGTTTTATGTACAAAAAC 57.005 32.000 24.26 24.26 43.77 2.43
2610 6347 3.367395 CCGAACTTGTCATCACTGCTCTA 60.367 47.826 0.00 0.00 0.00 2.43
2654 6392 5.806286 TGCAAGTACTCAAAAAGAAACTCG 58.194 37.500 0.00 0.00 0.00 4.18
2674 6414 0.254462 TTATTCGGGGTGATGCTGCA 59.746 50.000 4.13 4.13 0.00 4.41
2686 6528 8.230486 GTGGACATGCTAAAATATCTTATTCGG 58.770 37.037 0.00 0.00 0.00 4.30
2730 6572 8.361889 AGCTTTAACCCGTAATGTTTTATGTTT 58.638 29.630 0.00 0.00 0.00 2.83
2731 6573 7.888424 AGCTTTAACCCGTAATGTTTTATGTT 58.112 30.769 0.00 0.00 0.00 2.71
2732 6574 7.457024 AGCTTTAACCCGTAATGTTTTATGT 57.543 32.000 0.00 0.00 0.00 2.29
2745 6587 6.410243 TTTTGAAAAACAAGCTTTAACCCG 57.590 33.333 0.00 0.00 39.77 5.28
2778 6620 3.626217 TGTGTAAAATGCCACACGTGTAA 59.374 39.130 22.90 10.65 46.42 2.41
2779 6621 3.203716 TGTGTAAAATGCCACACGTGTA 58.796 40.909 22.90 6.47 46.42 2.90
2796 6638 5.243507 TGATGAAGGCATGTAAACAATGTGT 59.756 36.000 0.00 0.00 34.11 3.72
2802 6644 5.255687 AGTGATGATGAAGGCATGTAAACA 58.744 37.500 0.00 0.00 34.11 2.83
2806 6648 8.407832 CAAAATAAGTGATGATGAAGGCATGTA 58.592 33.333 0.00 0.00 34.11 2.29
2810 6652 6.839124 ACAAAATAAGTGATGATGAAGGCA 57.161 33.333 0.00 0.00 0.00 4.75
2833 6675 7.262048 TGCTAATGTCATCTGTTCATACGTAA 58.738 34.615 0.00 0.00 0.00 3.18
3040 6890 7.576856 GCCACATTACCACTTTAGTTTAAGCAT 60.577 37.037 0.00 0.00 0.00 3.79
3056 6906 6.267496 ACAAACTAAGATTGCCACATTACC 57.733 37.500 0.00 0.00 0.00 2.85
3059 6909 6.127897 GCTCTACAAACTAAGATTGCCACATT 60.128 38.462 0.00 0.00 0.00 2.71
3070 6920 4.697352 AGTTGCCATGCTCTACAAACTAAG 59.303 41.667 0.00 0.00 0.00 2.18
3106 6956 6.073276 TGGTCAAAGTACTGAAATTGTCATCG 60.073 38.462 0.00 0.00 35.07 3.84
3144 6998 6.593382 GCACTTGAAATTGCCATGGTTTATAA 59.407 34.615 14.67 4.82 32.21 0.98
3148 7002 3.140623 GCACTTGAAATTGCCATGGTTT 58.859 40.909 14.67 6.03 32.21 3.27
3163 7017 9.507280 CTAAAATTACCATAAGACATGCACTTG 57.493 33.333 13.65 0.00 0.00 3.16
3316 7172 8.487313 AAAAGTTATCATGTCTGTTGCGTATA 57.513 30.769 0.00 0.00 0.00 1.47
3320 7176 6.523201 GGTTAAAAGTTATCATGTCTGTTGCG 59.477 38.462 0.00 0.00 0.00 4.85
3325 7181 9.831737 CTTGAAGGTTAAAAGTTATCATGTCTG 57.168 33.333 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.