Multiple sequence alignment - TraesCS4A01G075500

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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 TraesCS4A01G075500 chr4A 100.000 2867 0 0 1 2867 74606577 74603711 0.000000e+00 5295.0
1 TraesCS4A01G075500 chr4A 95.529 1901 71 5 1 1901 213405156 213403270 0.000000e+00 3027.0
2 TraesCS4A01G075500 chr7B 97.733 1897 39 4 1 1895 259716694 259714800 0.000000e+00 3262.0
3 TraesCS4A01G075500 chr7B 89.394 132 8 5 1899 2027 147023439 147023311 8.220000e-36 161.0
4 TraesCS4A01G075500 chr6D 97.065 1329 39 0 1 1329 428459993 428458665 0.000000e+00 2239.0
5 TraesCS4A01G075500 chr6D 96.532 519 16 2 1379 1895 428458663 428458145 0.000000e+00 857.0
6 TraesCS4A01G075500 chr7D 96.559 901 30 1 1002 1902 198617605 198616706 0.000000e+00 1491.0
7 TraesCS4A01G075500 chr7D 91.763 607 28 6 2098 2682 88080860 88081466 0.000000e+00 824.0
8 TraesCS4A01G075500 chr7D 90.769 130 6 6 1899 2025 394833041 394832915 4.910000e-38 169.0
9 TraesCS4A01G075500 chr3B 95.103 633 27 4 834 1464 462888646 462888016 0.000000e+00 994.0
10 TraesCS4A01G075500 chr3B 95.652 460 17 3 1438 1895 462887555 462887097 0.000000e+00 736.0
11 TraesCS4A01G075500 chr2B 86.893 824 57 22 2025 2798 728612019 728612841 0.000000e+00 876.0
12 TraesCS4A01G075500 chr2B 84.341 645 56 18 2023 2623 779191582 779190939 8.850000e-165 590.0
13 TraesCS4A01G075500 chr2B 89.394 132 8 5 1899 2027 21948490 21948618 8.220000e-36 161.0
14 TraesCS4A01G075500 chr2D 88.864 449 30 7 1456 1895 608375417 608375854 4.200000e-148 534.0
15 TraesCS4A01G075500 chr3D 97.287 258 6 1 1416 1672 55749893 55750150 1.220000e-118 436.0
16 TraesCS4A01G075500 chr3D 96.581 234 8 0 1662 1895 55752229 55752462 3.460000e-104 388.0
17 TraesCS4A01G075500 chr1D 93.103 145 10 0 1721 1865 59965079 59965223 2.240000e-51 213.0
18 TraesCS4A01G075500 chr1D 95.652 46 1 1 1851 1895 59965237 59965282 3.960000e-09 73.1
19 TraesCS4A01G075500 chr5B 89.130 138 8 6 1899 2033 43158467 43158334 6.350000e-37 165.0
20 TraesCS4A01G075500 chr5B 91.228 57 4 1 2302 2357 54315510 54315454 3.060000e-10 76.8
21 TraesCS4A01G075500 chr7A 90.000 130 7 5 1899 2025 690026753 690026879 2.290000e-36 163.0
22 TraesCS4A01G075500 chr7A 88.889 135 9 5 1899 2030 98893783 98893652 8.220000e-36 161.0
23 TraesCS4A01G075500 chr1A 90.000 130 7 5 1899 2025 480551963 480551837 2.290000e-36 163.0
24 TraesCS4A01G075500 chr5D 89.394 132 8 5 1899 2027 496563281 496563409 8.220000e-36 161.0
25 TraesCS4A01G075500 chr5D 88.722 133 9 5 1899 2028 233733702 233733831 1.060000e-34 158.0


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 TraesCS4A01G075500 chr4A 74603711 74606577 2866 True 5295 5295 100.0000 1 2867 1 chr4A.!!$R1 2866
1 TraesCS4A01G075500 chr4A 213403270 213405156 1886 True 3027 3027 95.5290 1 1901 1 chr4A.!!$R2 1900
2 TraesCS4A01G075500 chr7B 259714800 259716694 1894 True 3262 3262 97.7330 1 1895 1 chr7B.!!$R2 1894
3 TraesCS4A01G075500 chr6D 428458145 428459993 1848 True 1548 2239 96.7985 1 1895 2 chr6D.!!$R1 1894
4 TraesCS4A01G075500 chr7D 198616706 198617605 899 True 1491 1491 96.5590 1002 1902 1 chr7D.!!$R1 900
5 TraesCS4A01G075500 chr7D 88080860 88081466 606 False 824 824 91.7630 2098 2682 1 chr7D.!!$F1 584
6 TraesCS4A01G075500 chr3B 462887097 462888646 1549 True 865 994 95.3775 834 1895 2 chr3B.!!$R1 1061
7 TraesCS4A01G075500 chr2B 728612019 728612841 822 False 876 876 86.8930 2025 2798 1 chr2B.!!$F2 773
8 TraesCS4A01G075500 chr2B 779190939 779191582 643 True 590 590 84.3410 2023 2623 1 chr2B.!!$R1 600
9 TraesCS4A01G075500 chr3D 55749893 55752462 2569 False 412 436 96.9340 1416 1895 2 chr3D.!!$F1 479

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
526 528 1.993956 TAAGCAAGGCATTGTGTGGT 58.006 45.0 13.3 0.0 38.76 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2019 4598 0.249398 GTCGAGCCCCTTTTAGAGCA 59.751 55.0 0.0 0.0 0.0 4.26 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
202 204 6.205464 TGATCTCACCAAAACTCTTTGTGATC 59.795 38.462 0.00 0.00 40.38 2.92
246 248 2.204136 TGGTGGAGCCAGGTGGAT 60.204 61.111 0.00 0.00 43.61 3.41
526 528 1.993956 TAAGCAAGGCATTGTGTGGT 58.006 45.000 13.30 0.00 38.76 4.16
689 691 4.037089 GGACGTGGAACTTGTAAACCAAAT 59.963 41.667 0.00 0.00 34.11 2.32
887 889 2.386661 ATTACGACAAGCCAGACCAG 57.613 50.000 0.00 0.00 0.00 4.00
1057 1059 2.061509 TGATGAAGATGGTGGCCATG 57.938 50.000 9.72 0.00 45.26 3.66
1178 1180 2.106338 TGGACTGCATCTTCCAGTTTGA 59.894 45.455 7.57 0.00 43.17 2.69
1241 1243 9.109393 GTGTATCTGGTCAGCAAGAAATAAATA 57.891 33.333 0.00 0.00 0.00 1.40
1245 1247 7.816640 TCTGGTCAGCAAGAAATAAATACAAC 58.183 34.615 0.00 0.00 0.00 3.32
1658 2147 1.268285 CGATCTCTCACAGCACGGTAG 60.268 57.143 0.00 0.00 0.00 3.18
1729 4308 0.608130 AGCTGTATCTTGTGTCCGCA 59.392 50.000 0.00 0.00 0.00 5.69
1912 4491 5.708736 AAAAAGAATTGGGTTTGAGGGTT 57.291 34.783 0.00 0.00 0.00 4.11
1913 4492 4.955811 AAAGAATTGGGTTTGAGGGTTC 57.044 40.909 0.00 0.00 0.00 3.62
1914 4493 3.903530 AGAATTGGGTTTGAGGGTTCT 57.096 42.857 0.00 0.00 0.00 3.01
1915 4494 5.333566 AAGAATTGGGTTTGAGGGTTCTA 57.666 39.130 0.00 0.00 0.00 2.10
1916 4495 4.923415 AGAATTGGGTTTGAGGGTTCTAG 58.077 43.478 0.00 0.00 0.00 2.43
1917 4496 4.354087 AGAATTGGGTTTGAGGGTTCTAGT 59.646 41.667 0.00 0.00 0.00 2.57
1918 4497 5.550403 AGAATTGGGTTTGAGGGTTCTAGTA 59.450 40.000 0.00 0.00 0.00 1.82
1919 4498 6.217693 AGAATTGGGTTTGAGGGTTCTAGTAT 59.782 38.462 0.00 0.00 0.00 2.12
1920 4499 5.853572 TTGGGTTTGAGGGTTCTAGTATT 57.146 39.130 0.00 0.00 0.00 1.89
1921 4500 5.853572 TGGGTTTGAGGGTTCTAGTATTT 57.146 39.130 0.00 0.00 0.00 1.40
1922 4501 5.566469 TGGGTTTGAGGGTTCTAGTATTTG 58.434 41.667 0.00 0.00 0.00 2.32
1923 4502 5.073965 TGGGTTTGAGGGTTCTAGTATTTGT 59.926 40.000 0.00 0.00 0.00 2.83
1924 4503 6.008331 GGGTTTGAGGGTTCTAGTATTTGTT 58.992 40.000 0.00 0.00 0.00 2.83
1925 4504 6.150641 GGGTTTGAGGGTTCTAGTATTTGTTC 59.849 42.308 0.00 0.00 0.00 3.18
1926 4505 6.150641 GGTTTGAGGGTTCTAGTATTTGTTCC 59.849 42.308 0.00 0.00 0.00 3.62
1927 4506 6.697641 TTGAGGGTTCTAGTATTTGTTCCT 57.302 37.500 0.00 0.00 0.00 3.36
1928 4507 6.049955 TGAGGGTTCTAGTATTTGTTCCTG 57.950 41.667 0.00 0.00 0.00 3.86
1929 4508 5.546499 TGAGGGTTCTAGTATTTGTTCCTGT 59.454 40.000 0.00 0.00 0.00 4.00
1930 4509 6.043938 TGAGGGTTCTAGTATTTGTTCCTGTT 59.956 38.462 0.00 0.00 0.00 3.16
1931 4510 6.849151 AGGGTTCTAGTATTTGTTCCTGTTT 58.151 36.000 0.00 0.00 0.00 2.83
1932 4511 7.295340 AGGGTTCTAGTATTTGTTCCTGTTTT 58.705 34.615 0.00 0.00 0.00 2.43
1933 4512 7.783119 AGGGTTCTAGTATTTGTTCCTGTTTTT 59.217 33.333 0.00 0.00 0.00 1.94
1934 4513 8.080417 GGGTTCTAGTATTTGTTCCTGTTTTTC 58.920 37.037 0.00 0.00 0.00 2.29
1935 4514 8.626526 GGTTCTAGTATTTGTTCCTGTTTTTCA 58.373 33.333 0.00 0.00 0.00 2.69
1972 4551 6.790285 ATGTCAAAAATGGCATTTCTCAAC 57.210 33.333 24.51 18.88 28.45 3.18
1973 4552 5.055812 TGTCAAAAATGGCATTTCTCAACC 58.944 37.500 24.51 11.72 0.00 3.77
1974 4553 4.452114 GTCAAAAATGGCATTTCTCAACCC 59.548 41.667 24.51 6.95 0.00 4.11
1975 4554 4.347583 TCAAAAATGGCATTTCTCAACCCT 59.652 37.500 24.51 4.89 0.00 4.34
1976 4555 4.980339 AAAATGGCATTTCTCAACCCTT 57.020 36.364 24.51 4.17 0.00 3.95
1977 4556 6.042552 TCAAAAATGGCATTTCTCAACCCTTA 59.957 34.615 24.51 1.07 0.00 2.69
1978 4557 6.432403 AAAATGGCATTTCTCAACCCTTAA 57.568 33.333 24.51 0.00 0.00 1.85
1979 4558 6.432403 AAATGGCATTTCTCAACCCTTAAA 57.568 33.333 19.39 0.00 0.00 1.52
1980 4559 6.432403 AATGGCATTTCTCAACCCTTAAAA 57.568 33.333 6.96 0.00 0.00 1.52
1981 4560 5.208463 TGGCATTTCTCAACCCTTAAAAC 57.792 39.130 0.00 0.00 0.00 2.43
1982 4561 4.898861 TGGCATTTCTCAACCCTTAAAACT 59.101 37.500 0.00 0.00 0.00 2.66
1983 4562 5.221422 TGGCATTTCTCAACCCTTAAAACTG 60.221 40.000 0.00 0.00 0.00 3.16
1984 4563 4.686091 GCATTTCTCAACCCTTAAAACTGC 59.314 41.667 0.00 0.00 0.00 4.40
1985 4564 5.509670 GCATTTCTCAACCCTTAAAACTGCT 60.510 40.000 0.00 0.00 0.00 4.24
1986 4565 6.515832 CATTTCTCAACCCTTAAAACTGCTT 58.484 36.000 0.00 0.00 0.00 3.91
1987 4566 6.538945 TTTCTCAACCCTTAAAACTGCTTT 57.461 33.333 0.00 0.00 0.00 3.51
1988 4567 7.648039 TTTCTCAACCCTTAAAACTGCTTTA 57.352 32.000 0.00 0.00 0.00 1.85
1989 4568 7.648039 TTCTCAACCCTTAAAACTGCTTTAA 57.352 32.000 0.00 0.00 37.18 1.52
1999 4578 8.748380 CTTAAAACTGCTTTAAGGATTTGAGG 57.252 34.615 13.08 0.00 46.98 3.86
2000 4579 5.728637 AAACTGCTTTAAGGATTTGAGGG 57.271 39.130 0.00 0.00 0.00 4.30
2001 4580 4.388577 ACTGCTTTAAGGATTTGAGGGT 57.611 40.909 0.00 0.00 0.00 4.34
2002 4581 4.740902 ACTGCTTTAAGGATTTGAGGGTT 58.259 39.130 0.00 0.00 0.00 4.11
2003 4582 4.767409 ACTGCTTTAAGGATTTGAGGGTTC 59.233 41.667 0.00 0.00 0.00 3.62
2004 4583 3.756434 TGCTTTAAGGATTTGAGGGTTCG 59.244 43.478 0.00 0.00 0.00 3.95
2005 4584 4.007659 GCTTTAAGGATTTGAGGGTTCGA 58.992 43.478 0.00 0.00 0.00 3.71
2006 4585 4.095036 GCTTTAAGGATTTGAGGGTTCGAG 59.905 45.833 0.00 0.00 0.00 4.04
2007 4586 2.789409 AAGGATTTGAGGGTTCGAGG 57.211 50.000 0.00 0.00 0.00 4.63
2008 4587 0.912486 AGGATTTGAGGGTTCGAGGG 59.088 55.000 0.00 0.00 0.00 4.30
2009 4588 0.618981 GGATTTGAGGGTTCGAGGGT 59.381 55.000 0.00 0.00 0.00 4.34
2010 4589 1.004394 GGATTTGAGGGTTCGAGGGTT 59.996 52.381 0.00 0.00 0.00 4.11
2011 4590 2.237893 GGATTTGAGGGTTCGAGGGTTA 59.762 50.000 0.00 0.00 0.00 2.85
2012 4591 3.307904 GGATTTGAGGGTTCGAGGGTTAA 60.308 47.826 0.00 0.00 0.00 2.01
2013 4592 4.524053 GATTTGAGGGTTCGAGGGTTAAT 58.476 43.478 0.00 0.00 0.00 1.40
2014 4593 5.397109 GGATTTGAGGGTTCGAGGGTTAATA 60.397 44.000 0.00 0.00 0.00 0.98
2015 4594 4.748277 TTGAGGGTTCGAGGGTTAATAG 57.252 45.455 0.00 0.00 0.00 1.73
2016 4595 3.716431 TGAGGGTTCGAGGGTTAATAGT 58.284 45.455 0.00 0.00 0.00 2.12
2017 4596 4.870636 TGAGGGTTCGAGGGTTAATAGTA 58.129 43.478 0.00 0.00 0.00 1.82
2018 4597 5.271598 TGAGGGTTCGAGGGTTAATAGTAA 58.728 41.667 0.00 0.00 0.00 2.24
2019 4598 5.901276 TGAGGGTTCGAGGGTTAATAGTAAT 59.099 40.000 0.00 0.00 0.00 1.89
2020 4599 6.170846 AGGGTTCGAGGGTTAATAGTAATG 57.829 41.667 0.00 0.00 0.00 1.90
2021 4600 4.753610 GGGTTCGAGGGTTAATAGTAATGC 59.246 45.833 0.00 0.00 0.00 3.56
2027 4606 8.241497 TCGAGGGTTAATAGTAATGCTCTAAA 57.759 34.615 0.00 0.00 0.00 1.85
2063 4642 3.802948 ACGACACATCCTCACTTATCC 57.197 47.619 0.00 0.00 0.00 2.59
2067 4646 3.861840 ACACATCCTCACTTATCCGTTG 58.138 45.455 0.00 0.00 0.00 4.10
2103 4686 3.305267 CGCTAATCTCTCCCATCTCACAG 60.305 52.174 0.00 0.00 0.00 3.66
2126 4710 1.234821 CTCCTTCTCTCGATCGGAGG 58.765 60.000 24.19 18.54 43.34 4.30
2277 4875 1.686110 GACCAGATCCCCGGTGAGT 60.686 63.158 0.00 0.00 34.99 3.41
2386 5010 1.760086 CATCGGCAGTCTCCTCCCT 60.760 63.158 0.00 0.00 0.00 4.20
2443 5072 2.817396 GCGCTGCTTGAGGAGGTC 60.817 66.667 0.00 0.00 33.79 3.85
2582 5218 1.561643 GGAGGTGGAGATCTGTGACA 58.438 55.000 0.00 0.00 0.00 3.58
2597 5233 2.675423 ACAGAGCCTACGCCGACA 60.675 61.111 0.00 0.00 34.57 4.35
2675 5312 1.296392 CCAGCAAGTGATCCCGACA 59.704 57.895 0.00 0.00 0.00 4.35
2684 5321 0.179048 TGATCCCGACATCACATGCC 60.179 55.000 0.00 0.00 0.00 4.40
2736 5373 1.705256 GTGAGGTACAATTCGTCGCA 58.295 50.000 0.00 0.00 32.72 5.10
2781 5418 5.509670 CGTGGTTGGAGATTGATATAGCAGA 60.510 44.000 0.00 0.00 0.00 4.26
2788 5425 6.112058 GGAGATTGATATAGCAGACCCATTC 58.888 44.000 0.00 0.00 0.00 2.67
2799 5436 4.148128 CAGACCCATTCTTATCTGCAGT 57.852 45.455 14.67 3.75 32.76 4.40
2800 5437 5.282055 CAGACCCATTCTTATCTGCAGTA 57.718 43.478 14.67 2.70 32.76 2.74
2801 5438 5.295950 CAGACCCATTCTTATCTGCAGTAG 58.704 45.833 14.67 9.95 32.76 2.57
2802 5439 4.965532 AGACCCATTCTTATCTGCAGTAGT 59.034 41.667 14.67 3.96 0.00 2.73
2803 5440 5.028549 ACCCATTCTTATCTGCAGTAGTG 57.971 43.478 14.67 3.54 0.00 2.74
2804 5441 4.141620 ACCCATTCTTATCTGCAGTAGTGG 60.142 45.833 14.67 12.89 0.00 4.00
2805 5442 4.101585 CCCATTCTTATCTGCAGTAGTGGA 59.898 45.833 14.67 4.50 0.00 4.02
2806 5443 5.295950 CCATTCTTATCTGCAGTAGTGGAG 58.704 45.833 14.67 12.62 43.37 3.86
2807 5444 4.392921 TTCTTATCTGCAGTAGTGGAGC 57.607 45.455 14.67 0.00 41.79 4.70
2808 5445 3.365472 TCTTATCTGCAGTAGTGGAGCA 58.635 45.455 14.67 4.27 41.79 4.26
2809 5446 3.769300 TCTTATCTGCAGTAGTGGAGCAA 59.231 43.478 14.67 9.33 41.79 3.91
2810 5447 2.393271 ATCTGCAGTAGTGGAGCAAC 57.607 50.000 14.67 0.00 41.79 4.17
2811 5448 1.342074 TCTGCAGTAGTGGAGCAACT 58.658 50.000 14.67 0.00 41.79 3.16
2812 5449 2.525368 TCTGCAGTAGTGGAGCAACTA 58.475 47.619 14.67 0.00 41.79 2.24
2817 5454 1.992170 GTAGTGGAGCAACTACACCG 58.008 55.000 15.54 0.00 45.81 4.94
2818 5455 1.271656 GTAGTGGAGCAACTACACCGT 59.728 52.381 15.54 0.00 45.81 4.83
2819 5456 0.033504 AGTGGAGCAACTACACCGTG 59.966 55.000 6.33 0.00 45.81 4.94
2820 5457 1.301401 TGGAGCAACTACACCGTGC 60.301 57.895 0.00 0.00 0.00 5.34
2821 5458 1.301401 GGAGCAACTACACCGTGCA 60.301 57.895 0.00 0.00 0.00 4.57
2822 5459 1.291877 GGAGCAACTACACCGTGCAG 61.292 60.000 0.00 0.00 0.00 4.41
2824 5461 1.301401 GCAACTACACCGTGCAGGA 60.301 57.895 8.24 0.00 45.00 3.86
2825 5462 0.673644 GCAACTACACCGTGCAGGAT 60.674 55.000 8.24 0.00 45.00 3.24
2826 5463 1.404986 GCAACTACACCGTGCAGGATA 60.405 52.381 8.24 0.00 45.00 2.59
2827 5464 2.741878 GCAACTACACCGTGCAGGATAT 60.742 50.000 8.24 0.00 45.00 1.63
2828 5465 3.491964 GCAACTACACCGTGCAGGATATA 60.492 47.826 8.24 0.00 45.00 0.86
2829 5466 4.049186 CAACTACACCGTGCAGGATATAC 58.951 47.826 8.24 0.00 45.00 1.47
2830 5467 3.293337 ACTACACCGTGCAGGATATACA 58.707 45.455 8.24 0.00 45.00 2.29
2831 5468 2.596904 ACACCGTGCAGGATATACAC 57.403 50.000 8.24 0.00 45.00 2.90
2836 5473 1.767289 GTGCAGGATATACACGACGG 58.233 55.000 0.00 0.00 0.00 4.79
2837 5474 0.031585 TGCAGGATATACACGACGGC 59.968 55.000 0.00 0.00 0.00 5.68
2838 5475 0.666577 GCAGGATATACACGACGGCC 60.667 60.000 0.00 0.00 0.00 6.13
2839 5476 0.386858 CAGGATATACACGACGGCCG 60.387 60.000 26.86 26.86 45.44 6.13
2840 5477 1.080974 GGATATACACGACGGCCGG 60.081 63.158 31.76 15.62 43.93 6.13
2841 5478 1.518056 GGATATACACGACGGCCGGA 61.518 60.000 31.76 7.36 43.93 5.14
2842 5479 0.386478 GATATACACGACGGCCGGAC 60.386 60.000 31.76 21.45 43.93 4.79
2843 5480 2.121564 ATATACACGACGGCCGGACG 62.122 60.000 33.15 33.15 43.93 4.79
2856 5493 4.681978 GGACGTCAAGGCGTGGCT 62.682 66.667 18.91 0.00 45.79 4.75
2857 5494 3.414700 GACGTCAAGGCGTGGCTG 61.415 66.667 11.55 0.00 45.79 4.85
2858 5495 4.235762 ACGTCAAGGCGTGGCTGT 62.236 61.111 0.00 0.24 43.99 4.40
2859 5496 2.972505 CGTCAAGGCGTGGCTGTT 60.973 61.111 3.11 0.00 0.00 3.16
2860 5497 2.639286 GTCAAGGCGTGGCTGTTG 59.361 61.111 0.00 0.00 0.00 3.33
2861 5498 3.286751 TCAAGGCGTGGCTGTTGC 61.287 61.111 0.00 0.00 38.76 4.17
2862 5499 3.289834 CAAGGCGTGGCTGTTGCT 61.290 61.111 0.00 0.00 39.59 3.91
2863 5500 1.965930 CAAGGCGTGGCTGTTGCTA 60.966 57.895 0.00 0.00 39.59 3.49
2864 5501 1.672356 AAGGCGTGGCTGTTGCTAG 60.672 57.895 0.00 0.00 39.59 3.42
2865 5502 2.047274 GGCGTGGCTGTTGCTAGA 60.047 61.111 0.00 0.00 39.59 2.43
2866 5503 2.103042 GGCGTGGCTGTTGCTAGAG 61.103 63.158 0.00 0.00 39.59 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
202 204 4.348656 CGGCAAATCATTGTTGAGATCTG 58.651 43.478 0.00 0.00 38.85 2.90
246 248 6.855763 ATCCAATGCATCTTGTTTTCCTTA 57.144 33.333 0.00 0.00 0.00 2.69
526 528 4.163441 TGTTCTGACCATTTCCAACTCA 57.837 40.909 0.00 0.00 0.00 3.41
689 691 0.880278 GGCGTCTTCAGTGCAGAACA 60.880 55.000 0.00 0.00 0.00 3.18
843 845 1.801178 GCAGTGCTGGTAGAACAGTTC 59.199 52.381 8.18 5.00 40.59 3.01
887 889 2.030274 CAGATTTTTCCCCACCGTGAAC 60.030 50.000 0.00 0.00 0.00 3.18
1178 1180 2.291800 ACTTGCATAGCCAATTGGTCCT 60.292 45.455 25.19 16.71 37.57 3.85
1241 1243 0.748005 AGCACTTTCACCAGCGTTGT 60.748 50.000 0.00 0.00 0.00 3.32
1245 1247 2.328099 GGGAGCACTTTCACCAGCG 61.328 63.158 0.00 0.00 0.00 5.18
1404 1406 0.602638 TGTTGCCTGAGTAAGCACCG 60.603 55.000 0.00 0.00 39.10 4.94
1658 2147 7.334671 GCATATACTTGGCCTTCCTAAAGATAC 59.665 40.741 3.32 0.00 34.14 2.24
1712 4291 3.436704 ACATTTGCGGACACAAGATACAG 59.563 43.478 0.00 0.00 0.00 2.74
1895 4474 4.663334 ACTAGAACCCTCAAACCCAATTC 58.337 43.478 0.00 0.00 0.00 2.17
1897 4476 6.402981 AATACTAGAACCCTCAAACCCAAT 57.597 37.500 0.00 0.00 0.00 3.16
1899 4478 5.073965 ACAAATACTAGAACCCTCAAACCCA 59.926 40.000 0.00 0.00 0.00 4.51
1901 4480 6.150641 GGAACAAATACTAGAACCCTCAAACC 59.849 42.308 0.00 0.00 0.00 3.27
1902 4481 6.940867 AGGAACAAATACTAGAACCCTCAAAC 59.059 38.462 0.00 0.00 0.00 2.93
1903 4482 6.940298 CAGGAACAAATACTAGAACCCTCAAA 59.060 38.462 0.00 0.00 0.00 2.69
1904 4483 6.043938 ACAGGAACAAATACTAGAACCCTCAA 59.956 38.462 0.00 0.00 0.00 3.02
1905 4484 5.546499 ACAGGAACAAATACTAGAACCCTCA 59.454 40.000 0.00 0.00 0.00 3.86
1906 4485 6.051179 ACAGGAACAAATACTAGAACCCTC 57.949 41.667 0.00 0.00 0.00 4.30
1907 4486 6.449830 AACAGGAACAAATACTAGAACCCT 57.550 37.500 0.00 0.00 0.00 4.34
1908 4487 7.520451 AAAACAGGAACAAATACTAGAACCC 57.480 36.000 0.00 0.00 0.00 4.11
1909 4488 8.626526 TGAAAAACAGGAACAAATACTAGAACC 58.373 33.333 0.00 0.00 0.00 3.62
1944 4523 9.334947 TGAGAAATGCCATTTTTGACATTTTTA 57.665 25.926 3.82 0.00 41.48 1.52
1945 4524 8.223177 TGAGAAATGCCATTTTTGACATTTTT 57.777 26.923 3.82 0.00 41.48 1.94
1946 4525 7.804843 TGAGAAATGCCATTTTTGACATTTT 57.195 28.000 3.82 0.00 41.48 1.82
1947 4526 7.255208 GGTTGAGAAATGCCATTTTTGACATTT 60.255 33.333 3.82 0.75 43.45 2.32
1948 4527 6.205270 GGTTGAGAAATGCCATTTTTGACATT 59.795 34.615 3.82 0.00 34.30 2.71
1949 4528 5.702209 GGTTGAGAAATGCCATTTTTGACAT 59.298 36.000 3.82 0.00 31.47 3.06
1950 4529 5.055812 GGTTGAGAAATGCCATTTTTGACA 58.944 37.500 3.82 0.71 31.47 3.58
1951 4530 4.452114 GGGTTGAGAAATGCCATTTTTGAC 59.548 41.667 3.82 0.59 31.47 3.18
1952 4531 4.347583 AGGGTTGAGAAATGCCATTTTTGA 59.652 37.500 3.82 0.00 31.47 2.69
1953 4532 4.644498 AGGGTTGAGAAATGCCATTTTTG 58.356 39.130 3.82 0.00 31.47 2.44
1954 4533 4.980339 AGGGTTGAGAAATGCCATTTTT 57.020 36.364 3.82 0.00 31.47 1.94
1955 4534 4.980339 AAGGGTTGAGAAATGCCATTTT 57.020 36.364 3.82 0.00 31.47 1.82
1956 4535 6.432403 TTTAAGGGTTGAGAAATGCCATTT 57.568 33.333 1.47 1.47 34.64 2.32
1957 4536 6.043127 AGTTTTAAGGGTTGAGAAATGCCATT 59.957 34.615 0.00 0.00 0.00 3.16
1958 4537 5.543790 AGTTTTAAGGGTTGAGAAATGCCAT 59.456 36.000 0.00 0.00 0.00 4.40
1959 4538 4.898861 AGTTTTAAGGGTTGAGAAATGCCA 59.101 37.500 0.00 0.00 0.00 4.92
1960 4539 5.230182 CAGTTTTAAGGGTTGAGAAATGCC 58.770 41.667 0.00 0.00 0.00 4.40
1961 4540 4.686091 GCAGTTTTAAGGGTTGAGAAATGC 59.314 41.667 0.00 0.00 0.00 3.56
1962 4541 6.089249 AGCAGTTTTAAGGGTTGAGAAATG 57.911 37.500 0.00 0.00 0.00 2.32
1963 4542 6.731292 AAGCAGTTTTAAGGGTTGAGAAAT 57.269 33.333 0.00 0.00 0.00 2.17
1964 4543 6.538945 AAAGCAGTTTTAAGGGTTGAGAAA 57.461 33.333 0.00 0.00 0.00 2.52
1965 4544 7.648039 TTAAAGCAGTTTTAAGGGTTGAGAA 57.352 32.000 0.00 0.00 36.55 2.87
1975 4554 7.289084 ACCCTCAAATCCTTAAAGCAGTTTTAA 59.711 33.333 2.57 2.57 38.57 1.52
1976 4555 6.780522 ACCCTCAAATCCTTAAAGCAGTTTTA 59.219 34.615 0.00 0.00 0.00 1.52
1977 4556 5.602561 ACCCTCAAATCCTTAAAGCAGTTTT 59.397 36.000 0.00 0.00 0.00 2.43
1978 4557 5.147767 ACCCTCAAATCCTTAAAGCAGTTT 58.852 37.500 0.00 0.00 0.00 2.66
1979 4558 4.740902 ACCCTCAAATCCTTAAAGCAGTT 58.259 39.130 0.00 0.00 0.00 3.16
1980 4559 4.388577 ACCCTCAAATCCTTAAAGCAGT 57.611 40.909 0.00 0.00 0.00 4.40
1981 4560 4.142600 CGAACCCTCAAATCCTTAAAGCAG 60.143 45.833 0.00 0.00 0.00 4.24
1982 4561 3.756434 CGAACCCTCAAATCCTTAAAGCA 59.244 43.478 0.00 0.00 0.00 3.91
1983 4562 4.007659 TCGAACCCTCAAATCCTTAAAGC 58.992 43.478 0.00 0.00 0.00 3.51
1984 4563 4.636206 CCTCGAACCCTCAAATCCTTAAAG 59.364 45.833 0.00 0.00 0.00 1.85
1985 4564 4.566907 CCCTCGAACCCTCAAATCCTTAAA 60.567 45.833 0.00 0.00 0.00 1.52
1986 4565 3.054655 CCCTCGAACCCTCAAATCCTTAA 60.055 47.826 0.00 0.00 0.00 1.85
1987 4566 2.504175 CCCTCGAACCCTCAAATCCTTA 59.496 50.000 0.00 0.00 0.00 2.69
1988 4567 1.282157 CCCTCGAACCCTCAAATCCTT 59.718 52.381 0.00 0.00 0.00 3.36
1989 4568 0.912486 CCCTCGAACCCTCAAATCCT 59.088 55.000 0.00 0.00 0.00 3.24
1990 4569 0.618981 ACCCTCGAACCCTCAAATCC 59.381 55.000 0.00 0.00 0.00 3.01
1991 4570 2.491675 AACCCTCGAACCCTCAAATC 57.508 50.000 0.00 0.00 0.00 2.17
1992 4571 4.586306 ATTAACCCTCGAACCCTCAAAT 57.414 40.909 0.00 0.00 0.00 2.32
1993 4572 4.533311 ACTATTAACCCTCGAACCCTCAAA 59.467 41.667 0.00 0.00 0.00 2.69
1994 4573 4.098894 ACTATTAACCCTCGAACCCTCAA 58.901 43.478 0.00 0.00 0.00 3.02
1995 4574 3.716431 ACTATTAACCCTCGAACCCTCA 58.284 45.455 0.00 0.00 0.00 3.86
1996 4575 5.859205 TTACTATTAACCCTCGAACCCTC 57.141 43.478 0.00 0.00 0.00 4.30
1997 4576 5.454329 GCATTACTATTAACCCTCGAACCCT 60.454 44.000 0.00 0.00 0.00 4.34
1998 4577 4.753610 GCATTACTATTAACCCTCGAACCC 59.246 45.833 0.00 0.00 0.00 4.11
1999 4578 5.608449 AGCATTACTATTAACCCTCGAACC 58.392 41.667 0.00 0.00 0.00 3.62
2000 4579 6.514063 AGAGCATTACTATTAACCCTCGAAC 58.486 40.000 0.00 0.00 0.00 3.95
2001 4580 6.726490 AGAGCATTACTATTAACCCTCGAA 57.274 37.500 0.00 0.00 0.00 3.71
2002 4581 7.828508 TTAGAGCATTACTATTAACCCTCGA 57.171 36.000 0.00 0.00 0.00 4.04
2003 4582 8.882415 TTTTAGAGCATTACTATTAACCCTCG 57.118 34.615 0.00 0.00 0.00 4.63
2004 4583 9.274206 CCTTTTAGAGCATTACTATTAACCCTC 57.726 37.037 0.00 0.00 0.00 4.30
2005 4584 8.218488 CCCTTTTAGAGCATTACTATTAACCCT 58.782 37.037 0.00 0.00 0.00 4.34
2006 4585 7.447545 CCCCTTTTAGAGCATTACTATTAACCC 59.552 40.741 0.00 0.00 0.00 4.11
2007 4586 7.040617 GCCCCTTTTAGAGCATTACTATTAACC 60.041 40.741 0.00 0.00 0.00 2.85
2008 4587 7.720074 AGCCCCTTTTAGAGCATTACTATTAAC 59.280 37.037 0.00 0.00 0.00 2.01
2009 4588 7.812306 AGCCCCTTTTAGAGCATTACTATTAA 58.188 34.615 0.00 0.00 0.00 1.40
2010 4589 7.388638 AGCCCCTTTTAGAGCATTACTATTA 57.611 36.000 0.00 0.00 0.00 0.98
2011 4590 6.267492 AGCCCCTTTTAGAGCATTACTATT 57.733 37.500 0.00 0.00 0.00 1.73
2012 4591 5.511545 CGAGCCCCTTTTAGAGCATTACTAT 60.512 44.000 0.00 0.00 0.00 2.12
2013 4592 4.202223 CGAGCCCCTTTTAGAGCATTACTA 60.202 45.833 0.00 0.00 0.00 1.82
2014 4593 3.432326 CGAGCCCCTTTTAGAGCATTACT 60.432 47.826 0.00 0.00 0.00 2.24
2015 4594 2.872858 CGAGCCCCTTTTAGAGCATTAC 59.127 50.000 0.00 0.00 0.00 1.89
2016 4595 2.769663 TCGAGCCCCTTTTAGAGCATTA 59.230 45.455 0.00 0.00 0.00 1.90
2017 4596 1.559682 TCGAGCCCCTTTTAGAGCATT 59.440 47.619 0.00 0.00 0.00 3.56
2018 4597 1.134371 GTCGAGCCCCTTTTAGAGCAT 60.134 52.381 0.00 0.00 0.00 3.79
2019 4598 0.249398 GTCGAGCCCCTTTTAGAGCA 59.751 55.000 0.00 0.00 0.00 4.26
2020 4599 0.462225 GGTCGAGCCCCTTTTAGAGC 60.462 60.000 2.39 0.00 0.00 4.09
2021 4600 3.762674 GGTCGAGCCCCTTTTAGAG 57.237 57.895 2.39 0.00 0.00 2.43
2063 4642 0.388649 CGAGTGGGGAGAGAACAACG 60.389 60.000 0.00 0.00 0.00 4.10
2067 4646 1.183549 TTAGCGAGTGGGGAGAGAAC 58.816 55.000 0.00 0.00 0.00 3.01
2189 4773 4.492160 TCGGAGATGCGTGGCGTC 62.492 66.667 1.64 1.64 44.07 5.19
2190 4774 4.796231 GTCGGAGATGCGTGGCGT 62.796 66.667 0.00 0.00 40.67 5.68
2217 4815 1.144057 CCCATGGGTAGCTGTCGAC 59.856 63.158 23.93 9.11 0.00 4.20
2273 4871 4.476361 CGTGTGATGCGCTACTCA 57.524 55.556 9.73 6.36 0.00 3.41
2386 5010 2.678580 TCGAGATGGTGGTCGCCA 60.679 61.111 5.66 5.66 43.48 5.69
2443 5072 1.612442 TCCTCCCCTTCCGTTCCAG 60.612 63.158 0.00 0.00 0.00 3.86
2597 5233 1.077501 CACCCCCGAGCATCAACAT 60.078 57.895 0.00 0.00 33.17 2.71
2665 5302 0.179048 GGCATGTGATGTCGGGATCA 60.179 55.000 0.00 0.00 0.00 2.92
2732 5369 0.976641 AATGAAGGAGAGGTGTGCGA 59.023 50.000 0.00 0.00 0.00 5.10
2734 5371 3.064900 AGAAATGAAGGAGAGGTGTGC 57.935 47.619 0.00 0.00 0.00 4.57
2736 5373 3.118956 CGCTAGAAATGAAGGAGAGGTGT 60.119 47.826 0.00 0.00 0.00 4.16
2781 5418 4.141620 CCACTACTGCAGATAAGAATGGGT 60.142 45.833 23.35 0.00 0.00 4.51
2788 5425 3.808466 TGCTCCACTACTGCAGATAAG 57.192 47.619 23.35 16.35 32.55 1.73
2798 5435 1.271656 ACGGTGTAGTTGCTCCACTAC 59.728 52.381 12.10 12.10 46.54 2.73
2799 5436 1.271379 CACGGTGTAGTTGCTCCACTA 59.729 52.381 0.00 0.00 0.00 2.74
2800 5437 0.033504 CACGGTGTAGTTGCTCCACT 59.966 55.000 0.00 0.00 0.00 4.00
2801 5438 1.566018 GCACGGTGTAGTTGCTCCAC 61.566 60.000 10.24 0.00 0.00 4.02
2802 5439 1.301401 GCACGGTGTAGTTGCTCCA 60.301 57.895 10.24 0.00 0.00 3.86
2803 5440 1.291877 CTGCACGGTGTAGTTGCTCC 61.292 60.000 16.82 0.00 0.00 4.70
2804 5441 1.291877 CCTGCACGGTGTAGTTGCTC 61.292 60.000 21.97 0.00 0.00 4.26
2805 5442 1.301716 CCTGCACGGTGTAGTTGCT 60.302 57.895 21.97 0.00 0.00 3.91
2806 5443 0.673644 ATCCTGCACGGTGTAGTTGC 60.674 55.000 21.97 2.50 0.00 4.17
2807 5444 2.665649 TATCCTGCACGGTGTAGTTG 57.334 50.000 21.97 10.09 0.00 3.16
2808 5445 3.702548 TGTATATCCTGCACGGTGTAGTT 59.297 43.478 21.97 12.99 0.00 2.24
2809 5446 3.067742 GTGTATATCCTGCACGGTGTAGT 59.932 47.826 21.97 9.49 30.55 2.73
2810 5447 3.639538 GTGTATATCCTGCACGGTGTAG 58.360 50.000 17.92 17.92 30.55 2.74
2811 5448 3.720949 GTGTATATCCTGCACGGTGTA 57.279 47.619 10.24 4.14 30.55 2.90
2812 5449 2.596904 GTGTATATCCTGCACGGTGT 57.403 50.000 10.24 0.00 30.55 4.16
2817 5454 1.767289 CCGTCGTGTATATCCTGCAC 58.233 55.000 0.00 0.00 37.14 4.57
2818 5455 0.031585 GCCGTCGTGTATATCCTGCA 59.968 55.000 0.00 0.00 0.00 4.41
2819 5456 0.666577 GGCCGTCGTGTATATCCTGC 60.667 60.000 0.00 0.00 0.00 4.85
2820 5457 0.386858 CGGCCGTCGTGTATATCCTG 60.387 60.000 19.50 0.00 0.00 3.86
2821 5458 1.521450 CCGGCCGTCGTGTATATCCT 61.521 60.000 26.12 0.00 37.11 3.24
2822 5459 1.080974 CCGGCCGTCGTGTATATCC 60.081 63.158 26.12 0.00 37.11 2.59
2823 5460 0.386478 GTCCGGCCGTCGTGTATATC 60.386 60.000 26.12 0.00 37.11 1.63
2824 5461 1.656441 GTCCGGCCGTCGTGTATAT 59.344 57.895 26.12 0.00 37.11 0.86
2825 5462 2.822758 CGTCCGGCCGTCGTGTATA 61.823 63.158 26.12 0.00 37.11 1.47
2826 5463 4.183686 CGTCCGGCCGTCGTGTAT 62.184 66.667 26.12 0.00 37.11 2.29
2839 5476 4.681978 AGCCACGCCTTGACGTCC 62.682 66.667 14.12 0.00 46.34 4.79
2840 5477 3.414700 CAGCCACGCCTTGACGTC 61.415 66.667 9.11 9.11 46.34 4.34
2842 5479 2.972505 AACAGCCACGCCTTGACG 60.973 61.111 0.00 0.00 39.50 4.35
2843 5480 2.639286 CAACAGCCACGCCTTGAC 59.361 61.111 0.00 0.00 0.00 3.18
2844 5481 2.390306 TAGCAACAGCCACGCCTTGA 62.390 55.000 0.00 0.00 0.00 3.02
2845 5482 1.915614 CTAGCAACAGCCACGCCTTG 61.916 60.000 0.00 0.00 0.00 3.61
2846 5483 1.672356 CTAGCAACAGCCACGCCTT 60.672 57.895 0.00 0.00 0.00 4.35
2847 5484 2.046892 CTAGCAACAGCCACGCCT 60.047 61.111 0.00 0.00 0.00 5.52
2848 5485 2.047274 TCTAGCAACAGCCACGCC 60.047 61.111 0.00 0.00 0.00 5.68
2849 5486 3.479370 CTCTAGCAACAGCCACGC 58.521 61.111 0.00 0.00 0.00 5.34


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

AutoCloner maintained by Alex Coulton.