Multiple sequence alignment - TraesCS3D01G543800

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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 TraesCS3D01G543800 chr3D 100.000 7097 0 0 1 7097 613731672 613738768 0.000000e+00 13106.0
1 TraesCS3D01G543800 chr3D 79.128 963 170 24 4621 5566 613736238 613737186 2.790000e-178 636.0
2 TraesCS3D01G543800 chr3D 79.084 961 174 21 4567 5515 613736292 613737237 2.790000e-178 636.0
3 TraesCS3D01G543800 chr3D 82.265 733 95 26 2290 2994 613733784 613734509 1.020000e-167 601.0
4 TraesCS3D01G543800 chr3D 82.265 733 95 26 2113 2838 613733961 613734665 1.020000e-167 601.0
5 TraesCS3D01G543800 chr3D 86.719 512 29 22 6534 7012 5569046 5568541 3.770000e-147 532.0
6 TraesCS3D01G543800 chr3D 83.585 597 47 27 6528 7097 584374621 584375193 4.910000e-141 512.0
7 TraesCS3D01G543800 chr3D 85.221 521 28 26 6528 7016 558905446 558905949 2.300000e-134 490.0
8 TraesCS3D01G543800 chr3D 84.872 509 34 22 6534 7012 215740804 215740309 2.320000e-129 473.0
9 TraesCS3D01G543800 chr3D 91.358 243 6 7 6781 7012 344157046 344157284 1.150000e-82 318.0
10 TraesCS3D01G543800 chr3D 82.692 364 49 8 4675 5028 613736238 613736597 1.920000e-80 311.0
11 TraesCS3D01G543800 chr3D 82.692 364 49 8 4567 4926 613736346 613736699 1.920000e-80 311.0
12 TraesCS3D01G543800 chr3D 77.778 378 70 6 5104 5477 613736337 613736704 3.330000e-53 220.0
13 TraesCS3D01G543800 chr3D 77.778 378 70 6 4666 5033 613736775 613737148 3.330000e-53 220.0
14 TraesCS3D01G543800 chr3D 82.800 250 26 12 6528 6766 344143947 344144190 2.590000e-49 207.0
15 TraesCS3D01G543800 chr3D 79.705 271 31 15 4778 5033 613736239 613736500 2.630000e-39 174.0
16 TraesCS3D01G543800 chr3D 79.705 271 31 15 4568 4829 613736449 613736704 2.630000e-39 174.0
17 TraesCS3D01G543800 chr3D 79.310 261 43 8 5326 5576 613736238 613736497 9.460000e-39 172.0
18 TraesCS3D01G543800 chr3D 79.310 261 43 8 4567 4826 613736997 613737247 9.460000e-39 172.0
19 TraesCS3D01G543800 chr3D 97.500 80 2 0 6528 6607 504820932 504821011 3.450000e-28 137.0
20 TraesCS3D01G543800 chr3A 94.626 4336 156 14 1892 6154 749402860 749407191 0.000000e+00 6645.0
21 TraesCS3D01G543800 chr3A 89.176 2051 120 22 1 1988 749400849 749402860 0.000000e+00 2464.0
22 TraesCS3D01G543800 chr3A 79.495 990 154 26 4621 5572 749405553 749406531 0.000000e+00 658.0
23 TraesCS3D01G543800 chr3A 80.234 855 128 29 2113 2960 749403264 749404084 7.870000e-169 604.0
24 TraesCS3D01G543800 chr3A 82.201 736 96 24 2290 2997 749403087 749403815 1.020000e-167 601.0
25 TraesCS3D01G543800 chr3A 77.647 935 155 28 4675 5567 749405553 749406475 2.930000e-143 520.0
26 TraesCS3D01G543800 chr3A 82.253 648 27 36 6405 7020 749407363 749407954 4.980000e-131 479.0
27 TraesCS3D01G543800 chr3A 76.014 863 152 30 4568 5419 749405764 749406582 5.160000e-106 396.0
28 TraesCS3D01G543800 chr3A 75.532 846 143 36 4778 5576 749405554 749406382 2.430000e-94 357.0
29 TraesCS3D01G543800 chr3A 80.556 468 81 7 5053 5515 749406114 749406576 1.130000e-92 351.0
30 TraesCS3D01G543800 chr3A 82.796 279 33 10 6534 6805 262004726 262004456 1.190000e-57 235.0
31 TraesCS3D01G543800 chr3A 82.034 295 31 13 6528 6805 263483774 263484063 1.540000e-56 231.0
32 TraesCS3D01G543800 chr3A 91.566 166 3 6 6268 6425 181281212 181281050 1.200000e-52 219.0
33 TraesCS3D01G543800 chr3A 93.571 140 2 2 6194 6327 749407188 749407326 1.210000e-47 202.0
34 TraesCS3D01G543800 chr3A 78.846 260 46 6 5326 5576 749405553 749405812 4.400000e-37 167.0
35 TraesCS3D01G543800 chr3A 96.364 55 0 2 7044 7097 749407945 749407998 9.810000e-14 89.8
36 TraesCS3D01G543800 chr3B 91.875 2966 163 28 1 2917 822967004 822969940 0.000000e+00 4071.0
37 TraesCS3D01G543800 chr3B 93.455 2674 109 12 2965 5572 822969937 822972610 0.000000e+00 3908.0
38 TraesCS3D01G543800 chr3B 80.947 2556 265 130 4564 7020 822971728 822974160 0.000000e+00 1818.0
39 TraesCS3D01G543800 chr3B 78.926 1006 148 35 4621 5576 822971572 822972563 6.040000e-175 625.0
40 TraesCS3D01G543800 chr3B 82.648 657 87 19 2113 2768 822969316 822969946 2.240000e-154 556.0
41 TraesCS3D01G543800 chr3B 85.256 468 60 5 4567 5028 822971626 822972090 2.320000e-129 473.0
42 TraesCS3D01G543800 chr3B 82.008 528 82 9 5053 5572 822972139 822972661 3.040000e-118 436.0
43 TraesCS3D01G543800 chr3B 75.413 484 93 16 5109 5577 822971832 822972304 2.010000e-50 211.0
44 TraesCS3D01G543800 chr3B 94.366 71 2 1 7029 7097 822974134 822974204 2.710000e-19 108.0
45 TraesCS3D01G543800 chrUn 86.719 512 29 22 6534 7012 287762178 287761673 3.770000e-147 532.0
46 TraesCS3D01G543800 chrUn 85.603 514 35 21 6528 7012 30176847 30177350 2.960000e-138 503.0
47 TraesCS3D01G543800 chrUn 82.463 268 28 15 6528 6782 150825629 150825890 4.310000e-52 217.0
48 TraesCS3D01G543800 chr2D 85.992 514 32 22 6534 7012 151644423 151643915 1.370000e-141 514.0
49 TraesCS3D01G543800 chr5D 85.380 513 38 20 6528 7012 487766252 487766755 1.370000e-136 497.0
50 TraesCS3D01G543800 chr4D 85.214 514 38 18 6528 7012 279518874 279519378 1.780000e-135 494.0
51 TraesCS3D01G543800 chr4D 85.207 507 32 20 6534 7012 381523195 381522704 1.380000e-131 481.0
52 TraesCS3D01G543800 chr1A 82.993 294 28 14 6528 6805 508089927 508090214 5.500000e-61 246.0
53 TraesCS3D01G543800 chr7D 92.683 164 3 5 6268 6425 158431245 158431085 1.990000e-55 228.0
54 TraesCS3D01G543800 chr7D 92.073 164 4 5 6268 6425 366417619 366417459 9.270000e-54 222.0
55 TraesCS3D01G543800 chr7A 92.073 164 4 5 6268 6425 81941608 81941448 9.270000e-54 222.0
56 TraesCS3D01G543800 chr7A 90.964 166 4 6 6268 6425 668633979 668633817 5.580000e-51 213.0
57 TraesCS3D01G543800 chr7A 100.000 28 0 0 1803 1830 279182479 279182506 1.300000e-02 52.8
58 TraesCS3D01G543800 chr5A 81.944 288 29 13 6534 6805 424336800 424336520 9.270000e-54 222.0
59 TraesCS3D01G543800 chr5A 90.361 166 5 6 6268 6425 583493991 583493829 2.590000e-49 207.0
60 TraesCS3D01G543800 chr5A 90.798 163 4 7 6268 6423 696287235 696287077 2.590000e-49 207.0
61 TraesCS3D01G543800 chr2A 91.463 164 5 5 6268 6425 214138024 214137864 4.310000e-52 217.0
62 TraesCS3D01G543800 chr2A 93.846 65 3 1 7033 7097 109857251 109857314 5.860000e-16 97.1
63 TraesCS3D01G543800 chr5B 100.000 28 0 0 1803 1830 616698876 616698849 1.300000e-02 52.8


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 TraesCS3D01G543800 chr3D 613731672 613738768 7096 False 13106.000000 13106 100.000000 1 7097 1 chr3D.!!$F6 7096
1 TraesCS3D01G543800 chr3D 5568541 5569046 505 True 532.000000 532 86.719000 6534 7012 1 chr3D.!!$R1 478
2 TraesCS3D01G543800 chr3D 584374621 584375193 572 False 512.000000 512 83.585000 6528 7097 1 chr3D.!!$F5 569
3 TraesCS3D01G543800 chr3D 558905446 558905949 503 False 490.000000 490 85.221000 6528 7016 1 chr3D.!!$F4 488
4 TraesCS3D01G543800 chr3D 613733784 613737247 3463 False 352.333333 636 80.142667 2113 5576 12 chr3D.!!$F7 3463
5 TraesCS3D01G543800 chr3A 749400849 749407191 6342 False 4554.500000 6645 91.901000 1 6154 2 chr3A.!!$F2 6153
6 TraesCS3D01G543800 chr3A 749403087 749407998 4911 False 402.254545 658 82.064818 2113 7097 11 chr3A.!!$F3 4984
7 TraesCS3D01G543800 chr3B 822967004 822974204 7200 False 1356.222222 4071 84.988222 1 7097 9 chr3B.!!$F1 7096
8 TraesCS3D01G543800 chrUn 287761673 287762178 505 True 532.000000 532 86.719000 6534 7012 1 chrUn.!!$R1 478
9 TraesCS3D01G543800 chrUn 30176847 30177350 503 False 503.000000 503 85.603000 6528 7012 1 chrUn.!!$F1 484
10 TraesCS3D01G543800 chr2D 151643915 151644423 508 True 514.000000 514 85.992000 6534 7012 1 chr2D.!!$R1 478
11 TraesCS3D01G543800 chr5D 487766252 487766755 503 False 497.000000 497 85.380000 6528 7012 1 chr5D.!!$F1 484
12 TraesCS3D01G543800 chr4D 279518874 279519378 504 False 494.000000 494 85.214000 6528 7012 1 chr4D.!!$F1 484

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
903 963 0.460987 CTCGGAATGAAAGCTCGGCT 60.461 55.000 0.00 0.0 42.56 5.52 F
1203 1265 0.033991 TCCAGGACGAGGAGAAGGAG 60.034 60.000 0.00 0.0 0.00 3.69 F
1929 2105 0.689080 AGAGATCGAGGCATGGTGGT 60.689 55.000 0.00 0.0 0.00 4.16 F
1957 2133 1.226802 TCGCGCAAGAGAGATGCTC 60.227 57.895 8.75 0.0 42.76 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2085 2261 0.912486 GCATAGGGGTGTCCTCAACT 59.088 55.000 0.0 0.0 44.06 3.16 R
5608 5985 7.716560 CCAGTAATTGTCCTTCATATCATCACA 59.283 37.037 0.0 0.0 0.00 3.58 R
5758 6135 1.447489 CGTTCTCTGCCTCTGCCAG 60.447 63.158 0.0 0.0 36.33 4.85 R
6347 6796 0.846693 AGAGACCACCACAAAGCCTT 59.153 50.000 0.0 0.0 0.00 4.35 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
165 166 5.514274 AGTGAACCAGTAAAACACAATGG 57.486 39.130 0.00 0.00 37.07 3.16
265 266 2.546645 TACACCGTCCGTTCATCCGC 62.547 60.000 0.00 0.00 0.00 5.54
379 384 3.695830 ACTGGAATCAATACACACCGT 57.304 42.857 0.00 0.00 0.00 4.83
420 425 7.589395 TGACAAATTACGTTGCATATCTGTTT 58.411 30.769 0.00 0.00 31.29 2.83
426 431 2.419673 CGTTGCATATCTGTTTCCAGCA 59.580 45.455 0.00 0.00 38.66 4.41
428 433 3.632643 TGCATATCTGTTTCCAGCAGA 57.367 42.857 0.00 0.00 45.59 4.26
608 632 3.977427 GTGTGATTGAACACCCCTTTTC 58.023 45.455 0.00 0.00 43.84 2.29
622 646 3.128764 CCCCTTTTCGAAAATACAGGAGC 59.871 47.826 22.73 0.00 0.00 4.70
628 652 5.607119 TTCGAAAATACAGGAGCAAGAAC 57.393 39.130 0.00 0.00 0.00 3.01
647 671 1.085893 CGGGGCCAAATTGCAAAATC 58.914 50.000 4.39 0.00 0.00 2.17
697 726 1.376812 GTGGCCCCTTGTCCTAACG 60.377 63.158 0.00 0.00 0.00 3.18
717 746 0.710588 AGAATTCCCCAAACCCTCCC 59.289 55.000 0.65 0.00 0.00 4.30
721 750 1.725169 TTCCCCAAACCCTCCCACTG 61.725 60.000 0.00 0.00 0.00 3.66
898 958 0.543749 CCCTCCTCGGAATGAAAGCT 59.456 55.000 0.00 0.00 33.16 3.74
903 963 0.460987 CTCGGAATGAAAGCTCGGCT 60.461 55.000 0.00 0.00 42.56 5.52
927 987 1.418373 ATCGCGCCTTTTTCTTTTGC 58.582 45.000 0.00 0.00 0.00 3.68
930 990 0.581529 GCGCCTTTTTCTTTTGCACC 59.418 50.000 0.00 0.00 0.00 5.01
932 992 1.801025 CGCCTTTTTCTTTTGCACCGT 60.801 47.619 0.00 0.00 0.00 4.83
1198 1260 1.677966 CCGTTCCAGGACGAGGAGA 60.678 63.158 11.67 0.00 45.47 3.71
1199 1261 1.248785 CCGTTCCAGGACGAGGAGAA 61.249 60.000 11.67 0.00 45.47 2.87
1200 1262 0.171455 CGTTCCAGGACGAGGAGAAG 59.829 60.000 5.73 0.00 45.47 2.85
1201 1263 0.533032 GTTCCAGGACGAGGAGAAGG 59.467 60.000 0.00 0.00 36.33 3.46
1202 1264 0.408309 TTCCAGGACGAGGAGAAGGA 59.592 55.000 0.00 0.00 36.33 3.36
1203 1265 0.033991 TCCAGGACGAGGAGAAGGAG 60.034 60.000 0.00 0.00 0.00 3.69
1385 1447 2.365635 CTGGATGGACCCCTCCGT 60.366 66.667 6.00 0.00 39.88 4.69
1453 1515 3.506096 TCTCCAGCTACGTCGCCG 61.506 66.667 8.64 0.00 40.83 6.46
1551 1613 1.380524 CCAGGAAGCAGCAGATTCAG 58.619 55.000 9.40 1.10 41.82 3.02
1555 1617 2.039480 AGGAAGCAGCAGATTCAGAACA 59.961 45.455 9.40 0.00 41.82 3.18
1569 1631 0.978146 AGAACACCGGGATCAGGGAG 60.978 60.000 6.32 3.15 0.00 4.30
1656 1718 2.822255 TACATTTCGGCGCTGGGC 60.822 61.111 17.88 8.35 42.51 5.36
1659 1721 4.408821 ATTTCGGCGCTGGGCAGA 62.409 61.111 17.88 16.76 46.16 4.26
1824 1898 2.187424 GCTGAGGCTGAGGCTGAG 59.813 66.667 17.72 17.72 41.76 3.35
1923 2099 2.364970 CAAGGAGAAGAGATCGAGGCAT 59.635 50.000 0.00 0.00 0.00 4.40
1924 2100 1.962807 AGGAGAAGAGATCGAGGCATG 59.037 52.381 0.00 0.00 0.00 4.06
1929 2105 0.689080 AGAGATCGAGGCATGGTGGT 60.689 55.000 0.00 0.00 0.00 4.16
1957 2133 1.226802 TCGCGCAAGAGAGATGCTC 60.227 57.895 8.75 0.00 42.76 4.26
2085 2261 2.561858 TGCAAACAAAGATGCTGCCATA 59.438 40.909 0.00 0.00 42.97 2.74
5614 5991 3.422303 CGCCGGTGGTGTGTGATG 61.422 66.667 7.26 0.00 0.00 3.07
5626 6003 4.224818 TGGTGTGTGATGATATGAAGGACA 59.775 41.667 0.00 0.00 0.00 4.02
5919 6350 2.750637 GAGGCGAGGACGGAGACA 60.751 66.667 0.00 0.00 40.15 3.41
6115 6552 3.324930 CAGGGCTGCTGGAGGTGA 61.325 66.667 0.00 0.00 0.00 4.02
6159 6596 7.884816 ATGATGATTTATTTATTGCTGCTGC 57.115 32.000 8.89 8.89 40.20 5.25
6160 6597 7.046292 TGATGATTTATTTATTGCTGCTGCT 57.954 32.000 17.00 0.00 40.48 4.24
6161 6598 6.921307 TGATGATTTATTTATTGCTGCTGCTG 59.079 34.615 17.00 0.77 40.48 4.41
6244 6687 0.949397 CTGATGCTGTGTTGCTGTGT 59.051 50.000 0.00 0.00 0.00 3.72
6328 6777 6.769341 GGTTGTGTTAAAAGGAGGAGTAAGAA 59.231 38.462 0.00 0.00 0.00 2.52
6337 6786 7.712204 AAAGGAGGAGTAAGAAGAGTAAGAG 57.288 40.000 0.00 0.00 0.00 2.85
6338 6787 6.397217 AGGAGGAGTAAGAAGAGTAAGAGT 57.603 41.667 0.00 0.00 0.00 3.24
6339 6788 7.513560 AGGAGGAGTAAGAAGAGTAAGAGTA 57.486 40.000 0.00 0.00 0.00 2.59
6340 6789 7.931046 AGGAGGAGTAAGAAGAGTAAGAGTAA 58.069 38.462 0.00 0.00 0.00 2.24
6341 6790 8.050930 AGGAGGAGTAAGAAGAGTAAGAGTAAG 58.949 40.741 0.00 0.00 0.00 2.34
6343 6792 9.452287 GAGGAGTAAGAAGAGTAAGAGTAAGAA 57.548 37.037 0.00 0.00 0.00 2.52
6344 6793 9.810870 AGGAGTAAGAAGAGTAAGAGTAAGAAA 57.189 33.333 0.00 0.00 0.00 2.52
6346 6795 9.563898 GAGTAAGAAGAGTAAGAGTAAGAAAGC 57.436 37.037 0.00 0.00 0.00 3.51
6347 6796 9.080097 AGTAAGAAGAGTAAGAGTAAGAAAGCA 57.920 33.333 0.00 0.00 0.00 3.91
6348 6797 9.694137 GTAAGAAGAGTAAGAGTAAGAAAGCAA 57.306 33.333 0.00 0.00 0.00 3.91
6349 6798 8.825667 AAGAAGAGTAAGAGTAAGAAAGCAAG 57.174 34.615 0.00 0.00 0.00 4.01
6351 6800 5.483811 AGAGTAAGAGTAAGAAAGCAAGGC 58.516 41.667 0.00 0.00 0.00 4.35
6352 6801 5.247337 AGAGTAAGAGTAAGAAAGCAAGGCT 59.753 40.000 0.00 0.00 42.56 4.58
6363 6812 1.109323 AGCAAGGCTTTGTGGTGGTC 61.109 55.000 10.54 0.00 33.89 4.02
6375 6824 2.507886 TGTGGTGGTCTCTTTTTGGAGA 59.492 45.455 0.00 0.00 39.69 3.71
6438 6909 7.386848 TGCTGAGAGGTGTTTGTTATTAAGTAC 59.613 37.037 0.00 0.00 0.00 2.73
6440 6911 9.141400 CTGAGAGGTGTTTGTTATTAAGTACTC 57.859 37.037 0.00 0.00 0.00 2.59
6441 6912 8.092687 TGAGAGGTGTTTGTTATTAAGTACTCC 58.907 37.037 0.00 0.00 0.00 3.85
6442 6913 7.970102 AGAGGTGTTTGTTATTAAGTACTCCA 58.030 34.615 0.00 0.00 0.00 3.86
6443 6914 8.095169 AGAGGTGTTTGTTATTAAGTACTCCAG 58.905 37.037 0.00 0.00 0.00 3.86
6530 7012 2.158667 CCTGGTGACTTTGTTGGTACCT 60.159 50.000 14.36 0.00 0.00 3.08
6607 7098 4.986054 ATTGGTTGGTGGTCACTAGTTA 57.014 40.909 0.00 0.00 0.00 2.24
6608 7099 4.774660 TTGGTTGGTGGTCACTAGTTAA 57.225 40.909 0.00 0.00 0.00 2.01
6609 7100 4.075963 TGGTTGGTGGTCACTAGTTAAC 57.924 45.455 0.00 0.00 0.00 2.01
6610 7101 3.712733 TGGTTGGTGGTCACTAGTTAACT 59.287 43.478 13.68 13.68 0.00 2.24
6611 7102 4.202284 TGGTTGGTGGTCACTAGTTAACTC 60.202 45.833 12.39 0.00 0.00 3.01
6612 7103 4.040095 GGTTGGTGGTCACTAGTTAACTCT 59.960 45.833 12.39 0.00 0.00 3.24
6613 7104 5.244626 GGTTGGTGGTCACTAGTTAACTCTA 59.755 44.000 12.39 0.00 0.00 2.43
6614 7105 6.388278 GTTGGTGGTCACTAGTTAACTCTAG 58.612 44.000 12.39 7.64 41.99 2.43
6616 7107 6.073314 TGGTGGTCACTAGTTAACTCTAGTT 58.927 40.000 12.39 0.39 45.43 2.24
6617 7108 6.015688 TGGTGGTCACTAGTTAACTCTAGTTG 60.016 42.308 12.39 6.53 45.43 3.16
6618 7109 6.015603 GGTGGTCACTAGTTAACTCTAGTTGT 60.016 42.308 12.39 0.48 45.43 3.32
6619 7110 7.432059 GTGGTCACTAGTTAACTCTAGTTGTT 58.568 38.462 12.39 8.43 45.43 2.83
6620 7111 8.571336 GTGGTCACTAGTTAACTCTAGTTGTTA 58.429 37.037 12.39 6.89 45.43 2.41
6638 7133 6.811170 AGTTGTTATTCTTGTTGTTGTGGTTG 59.189 34.615 0.00 0.00 0.00 3.77
6639 7134 5.655488 TGTTATTCTTGTTGTTGTGGTTGG 58.345 37.500 0.00 0.00 0.00 3.77
6640 7135 5.186021 TGTTATTCTTGTTGTTGTGGTTGGT 59.814 36.000 0.00 0.00 0.00 3.67
6641 7136 3.859411 TTCTTGTTGTTGTGGTTGGTC 57.141 42.857 0.00 0.00 0.00 4.02
6647 7159 7.001674 TCTTGTTGTTGTGGTTGGTCTAATAT 58.998 34.615 0.00 0.00 0.00 1.28
6648 7160 6.567687 TGTTGTTGTGGTTGGTCTAATATG 57.432 37.500 0.00 0.00 0.00 1.78
6653 7165 5.023533 TGTGGTTGGTCTAATATGAGAGC 57.976 43.478 11.81 11.81 42.99 4.09
6682 7207 4.160736 CATTGATGCATCTATGTGCTGG 57.839 45.455 30.95 13.68 45.27 4.85
6684 7209 3.286329 TGATGCATCTATGTGCTGGTT 57.714 42.857 26.32 0.00 45.27 3.67
6685 7210 4.420522 TGATGCATCTATGTGCTGGTTA 57.579 40.909 26.32 0.00 45.27 2.85
6686 7211 4.383173 TGATGCATCTATGTGCTGGTTAG 58.617 43.478 26.32 0.00 45.27 2.34
6687 7212 9.839167 CATTGATGCATCTATGTGCTGGTTAGC 62.839 44.444 30.95 3.58 45.27 3.09
6766 7297 7.012138 ACTGGTAGTAACTGATAGTGTGATACG 59.988 40.741 0.00 0.00 0.00 3.06
6965 7554 8.662781 TGTAAACTAAACATGCTCATCTATCC 57.337 34.615 0.00 0.00 0.00 2.59
6966 7555 8.264347 TGTAAACTAAACATGCTCATCTATCCA 58.736 33.333 0.00 0.00 0.00 3.41
6967 7556 9.277783 GTAAACTAAACATGCTCATCTATCCAT 57.722 33.333 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 3.326006 TCAGACTCTTTGACATTGGCTCT 59.674 43.478 0.00 0.00 0.00 4.09
111 112 6.642707 TTCACCGTCCATTGTAAGAATTTT 57.357 33.333 0.00 0.00 0.00 1.82
113 114 5.943416 TCATTCACCGTCCATTGTAAGAATT 59.057 36.000 0.00 0.00 0.00 2.17
114 115 5.496556 TCATTCACCGTCCATTGTAAGAAT 58.503 37.500 0.00 0.00 0.00 2.40
123 124 4.216257 CACTTTTCTTCATTCACCGTCCAT 59.784 41.667 0.00 0.00 0.00 3.41
231 232 5.368256 ACGGTGTATATCGATTCCAGTAC 57.632 43.478 1.71 0.92 33.73 2.73
265 266 7.166307 CCATACGCAACAATAATTTGTCTGATG 59.834 37.037 0.00 0.00 45.30 3.07
291 292 4.498323 GGTGTGTATCGATTCAAGTCGTAC 59.502 45.833 1.71 0.00 42.07 3.67
299 300 1.202211 CGGACGGTGTGTATCGATTCA 60.202 52.381 1.71 0.71 33.73 2.57
379 384 3.012934 TGTCAGATACAGATGGACGGA 57.987 47.619 0.00 0.00 33.01 4.69
420 425 7.828508 ATAGCATTTATTGATTTCTGCTGGA 57.171 32.000 5.18 0.00 40.01 3.86
452 463 5.107133 GGCGCAATATAACTACGGATACAT 58.893 41.667 10.83 0.00 0.00 2.29
460 471 3.921081 CGCGGCGCAATATAACTAC 57.079 52.632 32.61 0.00 0.00 2.73
552 566 3.492137 GCCTGCCTGATGATGAAATTTCC 60.492 47.826 15.48 1.80 0.00 3.13
608 632 3.181520 CCGTTCTTGCTCCTGTATTTTCG 60.182 47.826 0.00 0.00 0.00 3.46
622 646 0.670239 GCAATTTGGCCCCGTTCTTG 60.670 55.000 0.00 0.00 0.00 3.02
628 652 1.085893 GATTTTGCAATTTGGCCCCG 58.914 50.000 0.00 0.00 0.00 5.73
647 671 1.002868 CACCCTCTGCCTCTGGTTG 60.003 63.158 0.00 0.00 0.00 3.77
697 726 1.342076 GGGAGGGTTTGGGGAATTCTC 60.342 57.143 5.23 0.00 0.00 2.87
717 746 1.974236 AGAGGAGGAACAGGAACAGTG 59.026 52.381 0.00 0.00 0.00 3.66
721 750 4.830600 CCTATAGAGAGGAGGAACAGGAAC 59.169 50.000 0.00 0.00 39.15 3.62
839 891 0.549950 TTACCGTCGGGGAGATCTCT 59.450 55.000 21.81 2.51 39.97 3.10
898 958 3.095032 GGCGCGATTTTTAGCCGA 58.905 55.556 12.10 0.00 40.17 5.54
903 963 5.557325 GCAAAAGAAAAAGGCGCGATTTTTA 60.557 36.000 25.37 0.00 39.34 1.52
927 987 2.322081 CGCTGGGGTTTGTACGGTG 61.322 63.158 0.00 0.00 0.00 4.94
930 990 3.784412 CGCGCTGGGGTTTGTACG 61.784 66.667 5.56 0.00 0.00 3.67
1180 1242 1.248785 TTCTCCTCGTCCTGGAACGG 61.249 60.000 15.28 9.08 42.80 4.44
1201 1263 4.432741 GAACCCCTGCTGCCCCTC 62.433 72.222 0.00 0.00 0.00 4.30
1525 1587 4.379243 CTGCTTCCTGGCGACGGT 62.379 66.667 0.00 0.00 33.66 4.83
1551 1613 1.522569 CTCCCTGATCCCGGTGTTC 59.477 63.158 0.00 0.00 0.00 3.18
1555 1617 4.499116 CCCCTCCCTGATCCCGGT 62.499 72.222 0.00 0.00 0.00 5.28
1891 1968 2.203126 CTCCTTGGCCGGAGCATC 60.203 66.667 13.13 0.00 43.69 3.91
1923 2099 1.893062 CGATGAGCTCTCACCACCA 59.107 57.895 16.19 0.00 43.11 4.17
1924 2100 1.520342 GCGATGAGCTCTCACCACC 60.520 63.158 16.19 0.00 43.11 4.61
1929 2105 1.517913 CTTGCGCGATGAGCTCTCA 60.518 57.895 12.10 1.67 45.59 3.27
1957 2133 1.610522 CACTTCTGGTTCCTTTGCAGG 59.389 52.381 0.00 0.00 42.50 4.85
2085 2261 0.912486 GCATAGGGGTGTCCTCAACT 59.088 55.000 0.00 0.00 44.06 3.16
5608 5985 7.716560 CCAGTAATTGTCCTTCATATCATCACA 59.283 37.037 0.00 0.00 0.00 3.58
5614 5991 7.439655 GTCAGACCAGTAATTGTCCTTCATATC 59.560 40.741 0.00 0.00 31.76 1.63
5626 6003 9.167311 GTTTATGAGAATGTCAGACCAGTAATT 57.833 33.333 0.00 0.00 39.07 1.40
5756 6133 2.219164 TTCTCTGCCTCTGCCAGCA 61.219 57.895 0.00 0.00 36.33 4.41
5757 6134 1.744741 GTTCTCTGCCTCTGCCAGC 60.745 63.158 0.00 0.00 36.33 4.85
5758 6135 1.447489 CGTTCTCTGCCTCTGCCAG 60.447 63.158 0.00 0.00 36.33 4.85
5759 6136 2.659016 CGTTCTCTGCCTCTGCCA 59.341 61.111 0.00 0.00 36.33 4.92
5817 6248 3.664495 CTGAAGTGCAGCACCAGG 58.336 61.111 22.41 6.47 37.90 4.45
5898 6329 4.478371 TCCGTCCTCGCCTCGCTA 62.478 66.667 0.00 0.00 35.54 4.26
6071 6508 4.388499 GCTTCGGCCCGTCCTCAA 62.388 66.667 1.63 0.00 34.32 3.02
6115 6552 7.736691 TCATCATATCCAATTACCTCTCTCCTT 59.263 37.037 0.00 0.00 0.00 3.36
6244 6687 3.699038 CCTCTTCACCTGAAACCAACAAA 59.301 43.478 0.00 0.00 33.07 2.83
6328 6777 5.247337 AGCCTTGCTTTCTTACTCTTACTCT 59.753 40.000 0.00 0.00 33.89 3.24
6344 6793 1.076044 ACCACCACAAAGCCTTGCT 60.076 52.632 0.00 0.00 42.56 3.91
6345 6794 1.109323 AGACCACCACAAAGCCTTGC 61.109 55.000 0.00 0.00 35.84 4.01
6346 6795 0.954452 GAGACCACCACAAAGCCTTG 59.046 55.000 0.00 0.00 38.61 3.61
6347 6796 0.846693 AGAGACCACCACAAAGCCTT 59.153 50.000 0.00 0.00 0.00 4.35
6348 6797 0.846693 AAGAGACCACCACAAAGCCT 59.153 50.000 0.00 0.00 0.00 4.58
6349 6798 1.692411 AAAGAGACCACCACAAAGCC 58.308 50.000 0.00 0.00 0.00 4.35
6351 6800 3.699038 TCCAAAAAGAGACCACCACAAAG 59.301 43.478 0.00 0.00 0.00 2.77
6352 6801 3.699038 CTCCAAAAAGAGACCACCACAAA 59.301 43.478 0.00 0.00 35.82 2.83
6354 6803 2.507886 TCTCCAAAAAGAGACCACCACA 59.492 45.455 0.00 0.00 37.98 4.17
6355 6804 3.208747 TCTCCAAAAAGAGACCACCAC 57.791 47.619 0.00 0.00 37.98 4.16
6363 6812 2.517959 TGCCACCATCTCCAAAAAGAG 58.482 47.619 0.00 0.00 35.04 2.85
6391 6840 0.535328 CAGCATCAGCATCCAGGGAG 60.535 60.000 0.00 0.00 45.49 4.30
6392 6841 0.984432 TCAGCATCAGCATCCAGGGA 60.984 55.000 0.00 0.00 45.49 4.20
6393 6842 0.110678 ATCAGCATCAGCATCCAGGG 59.889 55.000 0.00 0.00 45.49 4.45
6394 6843 1.239347 CATCAGCATCAGCATCCAGG 58.761 55.000 0.00 0.00 45.49 4.45
6395 6844 0.593618 GCATCAGCATCAGCATCCAG 59.406 55.000 0.00 0.00 45.49 3.86
6396 6845 0.182775 AGCATCAGCATCAGCATCCA 59.817 50.000 0.00 0.00 45.49 3.41
6397 6846 0.593618 CAGCATCAGCATCAGCATCC 59.406 55.000 0.00 0.00 45.49 3.51
6442 6913 9.819267 GCCATAGTCTTTTTACATCTTACTACT 57.181 33.333 0.00 0.00 0.00 2.57
6443 6914 9.595823 TGCCATAGTCTTTTTACATCTTACTAC 57.404 33.333 0.00 0.00 0.00 2.73
6530 7012 5.116180 CAACACAGACAGACTTTCAGGTAA 58.884 41.667 0.00 0.00 0.00 2.85
6607 7098 9.174166 ACAACAACAAGAATAACAACTAGAGTT 57.826 29.630 0.00 3.61 39.12 3.01
6608 7099 8.612619 CACAACAACAAGAATAACAACTAGAGT 58.387 33.333 0.00 0.00 0.00 3.24
6609 7100 8.070171 CCACAACAACAAGAATAACAACTAGAG 58.930 37.037 0.00 0.00 0.00 2.43
6610 7101 7.554835 ACCACAACAACAAGAATAACAACTAGA 59.445 33.333 0.00 0.00 0.00 2.43
6611 7102 7.703328 ACCACAACAACAAGAATAACAACTAG 58.297 34.615 0.00 0.00 0.00 2.57
6612 7103 7.633193 ACCACAACAACAAGAATAACAACTA 57.367 32.000 0.00 0.00 0.00 2.24
6613 7104 6.524101 ACCACAACAACAAGAATAACAACT 57.476 33.333 0.00 0.00 0.00 3.16
6614 7105 6.035542 CCAACCACAACAACAAGAATAACAAC 59.964 38.462 0.00 0.00 0.00 3.32
6615 7106 6.102663 CCAACCACAACAACAAGAATAACAA 58.897 36.000 0.00 0.00 0.00 2.83
6616 7107 5.186021 ACCAACCACAACAACAAGAATAACA 59.814 36.000 0.00 0.00 0.00 2.41
6617 7108 5.656480 ACCAACCACAACAACAAGAATAAC 58.344 37.500 0.00 0.00 0.00 1.89
6618 7109 5.654650 AGACCAACCACAACAACAAGAATAA 59.345 36.000 0.00 0.00 0.00 1.40
6619 7110 5.197451 AGACCAACCACAACAACAAGAATA 58.803 37.500 0.00 0.00 0.00 1.75
6620 7111 4.023291 AGACCAACCACAACAACAAGAAT 58.977 39.130 0.00 0.00 0.00 2.40
6623 7114 4.974368 TTAGACCAACCACAACAACAAG 57.026 40.909 0.00 0.00 0.00 3.16
6638 7133 4.082245 GCTCCTCTGCTCTCATATTAGACC 60.082 50.000 0.00 0.00 0.00 3.85
6639 7134 4.522405 TGCTCCTCTGCTCTCATATTAGAC 59.478 45.833 0.00 0.00 0.00 2.59
6640 7135 4.734266 TGCTCCTCTGCTCTCATATTAGA 58.266 43.478 0.00 0.00 0.00 2.10
6641 7136 5.664294 ATGCTCCTCTGCTCTCATATTAG 57.336 43.478 0.00 0.00 0.00 1.73
6647 7159 1.565067 TCAATGCTCCTCTGCTCTCA 58.435 50.000 0.00 0.00 0.00 3.27
6648 7160 2.485903 CATCAATGCTCCTCTGCTCTC 58.514 52.381 0.00 0.00 0.00 3.20
6681 7206 8.314751 TCCTCATCATATAAAAGCTAGCTAACC 58.685 37.037 19.70 0.00 0.00 2.85
6682 7207 9.364989 CTCCTCATCATATAAAAGCTAGCTAAC 57.635 37.037 19.70 0.00 0.00 2.34
6684 7209 7.895962 TCCTCCTCATCATATAAAAGCTAGCTA 59.104 37.037 19.70 2.19 0.00 3.32
6685 7210 6.728164 TCCTCCTCATCATATAAAAGCTAGCT 59.272 38.462 12.68 12.68 0.00 3.32
6686 7211 6.940739 TCCTCCTCATCATATAAAAGCTAGC 58.059 40.000 6.62 6.62 0.00 3.42
6687 7212 8.133024 ACTCCTCCTCATCATATAAAAGCTAG 57.867 38.462 0.00 0.00 0.00 3.42
6688 7213 9.775539 ATACTCCTCCTCATCATATAAAAGCTA 57.224 33.333 0.00 0.00 0.00 3.32
6689 7214 8.677870 ATACTCCTCCTCATCATATAAAAGCT 57.322 34.615 0.00 0.00 0.00 3.74
6690 7215 8.757877 AGATACTCCTCCTCATCATATAAAAGC 58.242 37.037 0.00 0.00 0.00 3.51
6738 7269 6.243148 TCACACTATCAGTTACTACCAGTGA 58.757 40.000 19.37 11.23 36.34 3.41
6948 7501 8.148437 AGATAGATGGATAGATGAGCATGTTT 57.852 34.615 0.00 0.00 0.00 2.83
7018 7607 9.260002 CACACACACATACATACATACATACAT 57.740 33.333 0.00 0.00 0.00 2.29
7019 7608 8.254508 ACACACACACATACATACATACATACA 58.745 33.333 0.00 0.00 0.00 2.29
7020 7609 8.642908 ACACACACACATACATACATACATAC 57.357 34.615 0.00 0.00 0.00 2.39
7022 7611 9.830975 AATACACACACACATACATACATACAT 57.169 29.630 0.00 0.00 0.00 2.29
7023 7612 9.092876 CAATACACACACACATACATACATACA 57.907 33.333 0.00 0.00 0.00 2.29
7024 7613 9.093970 ACAATACACACACACATACATACATAC 57.906 33.333 0.00 0.00 0.00 2.39
7026 7615 9.830975 ATACAATACACACACACATACATACAT 57.169 29.630 0.00 0.00 0.00 2.29
7027 7616 9.660180 AATACAATACACACACACATACATACA 57.340 29.630 0.00 0.00 0.00 2.29
7037 7626 9.197694 GGCAAATAAAAATACAATACACACACA 57.802 29.630 0.00 0.00 0.00 3.72
7038 7627 9.418045 AGGCAAATAAAAATACAATACACACAC 57.582 29.630 0.00 0.00 0.00 3.82
7039 7628 9.988815 AAGGCAAATAAAAATACAATACACACA 57.011 25.926 0.00 0.00 0.00 3.72


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

AutoCloner maintained by Alex Coulton.