Multiple sequence alignment - TraesCS7A01G538200

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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 TraesCS7A01G538200 chr7A 100.000 1976 0 0 1 1976 715437349 715435374 0.000000e+00 3650
1 TraesCS7A01G538200 chr7A 98.186 1819 30 2 1 1816 715578718 715576900 0.000000e+00 3173
2 TraesCS7A01G538200 chr7A 97.590 1701 36 3 121 1816 715246798 715245098 0.000000e+00 2909
3 TraesCS7A01G538200 chr7A 99.555 899 4 0 1 899 715334684 715333786 0.000000e+00 1639
4 TraesCS7A01G538200 chr7A 97.839 833 16 1 986 1816 715333786 715332954 0.000000e+00 1437
5 TraesCS7A01G538200 chr7A 97.236 832 21 1 987 1816 715662730 715661899 0.000000e+00 1408
6 TraesCS7A01G538200 chr7A 100.000 164 0 0 2350 2513 715435000 715434837 1.130000e-78 303
7 TraesCS7A01G538200 chr7A 94.578 166 7 2 2350 2513 721937304 721937469 3.210000e-64 255
8 TraesCS7A01G538200 chr7A 90.244 164 9 2 1817 1974 179763570 179763732 9.110000e-50 207
9 TraesCS7A01G538200 chr7B 90.643 855 39 18 982 1816 716977322 716978155 0.000000e+00 1098
10 TraesCS7A01G538200 chr7B 90.414 845 33 19 987 1806 716699889 716699068 0.000000e+00 1068
11 TraesCS7A01G538200 chr7B 91.979 187 12 2 1 184 587458283 587458097 2.480000e-65 259
12 TraesCS7A01G538200 chrUn 94.972 179 8 1 1 178 110541296 110541474 1.900000e-71 279
13 TraesCS7A01G538200 chr5B 93.855 179 10 1 1 178 538919338 538919160 4.120000e-68 268
14 TraesCS7A01G538200 chr5A 95.783 166 5 2 2350 2513 47967053 47967218 1.480000e-67 267
15 TraesCS7A01G538200 chr5A 95.210 167 5 3 2350 2513 470135705 470135539 6.890000e-66 261
16 TraesCS7A01G538200 chr5A 95.181 166 6 2 2350 2513 612176641 612176476 6.890000e-66 261
17 TraesCS7A01G538200 chr5A 94.048 168 6 3 2350 2513 599426610 599426777 4.150000e-63 252
18 TraesCS7A01G538200 chr5D 93.296 179 11 1 1 178 22963271 22963093 1.920000e-66 263
19 TraesCS7A01G538200 chr3D 93.296 179 11 1 1 178 593049168 593048990 1.920000e-66 263
20 TraesCS7A01G538200 chr6A 91.579 190 11 4 1 188 24063130 24062944 8.920000e-65 257
21 TraesCS7A01G538200 chr6A 90.244 164 10 1 1817 1974 415693164 415693327 2.530000e-50 209
22 TraesCS7A01G538200 chr1D 92.737 179 12 1 1 178 366646810 366646988 8.920000e-65 257
23 TraesCS7A01G538200 chr6B 94.578 166 7 2 2350 2513 586545797 586545632 3.210000e-64 255
24 TraesCS7A01G538200 chr3A 94.611 167 6 3 2350 2513 720910372 720910206 3.210000e-64 255
25 TraesCS7A01G538200 chr3A 94.578 166 7 2 2350 2513 720996226 720996061 3.210000e-64 255
26 TraesCS7A01G538200 chr1A 93.976 166 8 2 2350 2513 511248579 511248744 1.490000e-62 250
27 TraesCS7A01G538200 chr1A 90.244 164 10 1 1817 1974 551940904 551941067 2.530000e-50 209
28 TraesCS7A01G538200 chr2A 89.349 169 10 3 1814 1974 109983656 109983488 3.280000e-49 206
29 TraesCS7A01G538200 chr2A 89.697 165 10 2 1817 1974 706556577 706556413 1.180000e-48 204
30 TraesCS7A01G538200 chr2A 89.634 164 10 2 1817 1974 629221321 629221159 4.240000e-48 202
31 TraesCS7A01G538200 chr2A 89.634 164 10 2 1817 1974 760214231 760214393 4.240000e-48 202
32 TraesCS7A01G538200 chr2A 89.024 164 12 2 1817 1974 633186659 633186822 5.480000e-47 198
33 TraesCS7A01G538200 chr4A 89.634 164 11 1 1817 1974 564132739 564132576 1.180000e-48 204


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 TraesCS7A01G538200 chr7A 715434837 715437349 2512 True 1976.5 3650 100.000 1 2513 2 chr7A.!!$R5 2512
1 TraesCS7A01G538200 chr7A 715576900 715578718 1818 True 3173.0 3173 98.186 1 1816 1 chr7A.!!$R2 1815
2 TraesCS7A01G538200 chr7A 715245098 715246798 1700 True 2909.0 2909 97.590 121 1816 1 chr7A.!!$R1 1695
3 TraesCS7A01G538200 chr7A 715332954 715334684 1730 True 1538.0 1639 98.697 1 1816 2 chr7A.!!$R4 1815
4 TraesCS7A01G538200 chr7A 715661899 715662730 831 True 1408.0 1408 97.236 987 1816 1 chr7A.!!$R3 829
5 TraesCS7A01G538200 chr7B 716977322 716978155 833 False 1098.0 1098 90.643 982 1816 1 chr7B.!!$F1 834
6 TraesCS7A01G538200 chr7B 716699068 716699889 821 True 1068.0 1068 90.414 987 1806 1 chr7B.!!$R2 819

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
1004 1096 2.284263 TATGCAGATCGATCGATGGC 57.716 50.0 33.86 31.64 34.6 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1931 2051 0.095245 CACGTGATGGCACTTTAGCG 59.905 55.0 10.9 0.0 42.93 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
1004 1096 2.284263 TATGCAGATCGATCGATGGC 57.716 50.000 33.86 31.64 34.60 4.40
1643 1756 5.009410 GTGATTCTTCATGGGCCATCTAAAG 59.991 44.000 18.16 19.12 33.56 1.85
1692 1807 9.453572 CTGGTAAGATGTAATAATACCATGCAT 57.546 33.333 0.00 0.00 42.93 3.96
1699 1814 9.831737 GATGTAATAATACCATGCATTGTTCTC 57.168 33.333 8.93 0.00 0.00 2.87
1820 1940 8.786826 TTGTGTACAATGGGATCTAAAACTAG 57.213 34.615 0.00 0.00 0.00 2.57
1821 1941 7.913789 TGTGTACAATGGGATCTAAAACTAGT 58.086 34.615 0.00 0.00 0.00 2.57
1822 1942 9.038072 TGTGTACAATGGGATCTAAAACTAGTA 57.962 33.333 0.00 0.00 0.00 1.82
1823 1943 9.530633 GTGTACAATGGGATCTAAAACTAGTAG 57.469 37.037 0.00 0.00 0.00 2.57
1824 1944 9.483489 TGTACAATGGGATCTAAAACTAGTAGA 57.517 33.333 3.59 0.00 32.28 2.59
1829 1949 8.943909 ATGGGATCTAAAACTAGTAGAAAACG 57.056 34.615 3.59 0.00 31.52 3.60
1830 1950 7.325694 TGGGATCTAAAACTAGTAGAAAACGG 58.674 38.462 3.59 0.00 31.52 4.44
1831 1951 7.178983 TGGGATCTAAAACTAGTAGAAAACGGA 59.821 37.037 3.59 0.00 31.52 4.69
1832 1952 7.705752 GGGATCTAAAACTAGTAGAAAACGGAG 59.294 40.741 3.59 0.00 31.52 4.63
1833 1953 8.249638 GGATCTAAAACTAGTAGAAAACGGAGT 58.750 37.037 3.59 0.00 34.59 3.85
1834 1954 9.636879 GATCTAAAACTAGTAGAAAACGGAGTT 57.363 33.333 3.59 0.00 40.03 3.01
1848 1968 2.907393 CGGAGTTTTAAAACCGGTTCG 58.093 47.619 22.53 12.55 41.41 3.95
1849 1969 2.287644 CGGAGTTTTAAAACCGGTTCGT 59.712 45.455 22.53 14.40 41.41 3.85
1850 1970 3.492756 CGGAGTTTTAAAACCGGTTCGTA 59.507 43.478 22.53 13.30 41.41 3.43
1851 1971 4.025313 CGGAGTTTTAAAACCGGTTCGTAA 60.025 41.667 22.53 18.41 41.41 3.18
1852 1972 5.443261 GGAGTTTTAAAACCGGTTCGTAAG 58.557 41.667 22.53 0.00 39.71 2.34
1853 1973 5.422666 AGTTTTAAAACCGGTTCGTAAGG 57.577 39.130 22.53 0.00 39.71 2.69
1854 1974 4.275689 AGTTTTAAAACCGGTTCGTAAGGG 59.724 41.667 22.53 0.00 39.71 3.95
1855 1975 1.807139 TAAAACCGGTTCGTAAGGGC 58.193 50.000 22.53 0.00 38.47 5.19
1856 1976 0.890542 AAAACCGGTTCGTAAGGGCC 60.891 55.000 22.53 0.00 38.47 5.80
1857 1977 1.771783 AAACCGGTTCGTAAGGGCCT 61.772 55.000 22.53 0.00 38.47 5.19
1858 1978 1.771783 AACCGGTTCGTAAGGGCCTT 61.772 55.000 24.44 24.44 38.47 4.35
1859 1979 1.002990 CCGGTTCGTAAGGGCCTTT 60.003 57.895 26.29 5.08 38.47 3.11
1860 1980 0.249955 CCGGTTCGTAAGGGCCTTTA 59.750 55.000 26.29 2.60 38.47 1.85
1861 1981 1.648504 CGGTTCGTAAGGGCCTTTAG 58.351 55.000 26.29 18.30 38.47 1.85
1862 1982 1.066645 CGGTTCGTAAGGGCCTTTAGT 60.067 52.381 26.29 1.50 38.47 2.24
1863 1983 2.353323 GGTTCGTAAGGGCCTTTAGTG 58.647 52.381 26.29 11.88 38.47 2.74
1864 1984 2.027837 GGTTCGTAAGGGCCTTTAGTGA 60.028 50.000 26.29 14.04 38.47 3.41
1865 1985 3.557686 GGTTCGTAAGGGCCTTTAGTGAA 60.558 47.826 26.29 18.79 38.47 3.18
1866 1986 3.604875 TCGTAAGGGCCTTTAGTGAAG 57.395 47.619 26.29 8.38 38.47 3.02
1883 2003 8.801882 TTAGTGAAGGTTCCATAACTAATTGG 57.198 34.615 1.26 0.00 35.81 3.16
1884 2004 6.790319 AGTGAAGGTTCCATAACTAATTGGT 58.210 36.000 0.00 0.00 35.81 3.67
1885 2005 6.659242 AGTGAAGGTTCCATAACTAATTGGTG 59.341 38.462 0.00 0.00 35.81 4.17
1886 2006 5.949354 TGAAGGTTCCATAACTAATTGGTGG 59.051 40.000 0.00 0.00 35.81 4.61
1887 2007 4.867086 AGGTTCCATAACTAATTGGTGGG 58.133 43.478 0.00 0.00 35.81 4.61
1888 2008 3.383505 GGTTCCATAACTAATTGGTGGGC 59.616 47.826 0.00 0.00 35.81 5.36
1889 2009 4.020543 GTTCCATAACTAATTGGTGGGCA 58.979 43.478 0.00 0.00 34.48 5.36
1890 2010 3.626930 TCCATAACTAATTGGTGGGCAC 58.373 45.455 0.00 0.00 34.48 5.01
1891 2011 3.268334 TCCATAACTAATTGGTGGGCACT 59.732 43.478 0.00 0.00 34.48 4.40
1892 2012 4.475381 TCCATAACTAATTGGTGGGCACTA 59.525 41.667 0.00 0.00 34.48 2.74
1893 2013 5.044772 TCCATAACTAATTGGTGGGCACTAA 60.045 40.000 0.00 0.00 36.25 2.24
1894 2014 5.654650 CCATAACTAATTGGTGGGCACTAAA 59.345 40.000 0.00 0.00 35.44 1.85
1895 2015 6.183360 CCATAACTAATTGGTGGGCACTAAAG 60.183 42.308 0.00 0.00 35.44 1.85
1896 2016 3.697166 ACTAATTGGTGGGCACTAAAGG 58.303 45.455 0.00 0.00 35.44 3.11
1897 2017 1.937191 AATTGGTGGGCACTAAAGGG 58.063 50.000 0.00 0.00 35.44 3.95
1898 2018 1.080638 ATTGGTGGGCACTAAAGGGA 58.919 50.000 0.00 0.00 35.44 4.20
1899 2019 0.111639 TTGGTGGGCACTAAAGGGAC 59.888 55.000 0.00 0.00 0.00 4.46
1900 2020 1.001269 GGTGGGCACTAAAGGGACC 60.001 63.158 0.00 0.00 0.00 4.46
1901 2021 1.001269 GTGGGCACTAAAGGGACCC 60.001 63.158 0.59 0.59 41.24 4.46
1902 2022 2.235761 TGGGCACTAAAGGGACCCC 61.236 63.158 7.00 1.17 40.04 4.95
1903 2023 2.681591 GGCACTAAAGGGACCCCC 59.318 66.667 7.00 0.00 45.90 5.40
1919 2039 0.176449 CCCCCTTTAGTACCGGTTCG 59.824 60.000 15.04 0.00 0.00 3.95
1920 2040 1.185315 CCCCTTTAGTACCGGTTCGA 58.815 55.000 15.04 0.00 0.00 3.71
1921 2041 1.134995 CCCCTTTAGTACCGGTTCGAC 60.135 57.143 15.04 4.79 0.00 4.20
1922 2042 1.545582 CCCTTTAGTACCGGTTCGACA 59.454 52.381 15.04 0.00 0.00 4.35
1923 2043 2.599659 CCTTTAGTACCGGTTCGACAC 58.400 52.381 15.04 3.84 0.00 3.67
1924 2044 2.245096 CTTTAGTACCGGTTCGACACG 58.755 52.381 15.04 1.21 0.00 4.49
1925 2045 1.518325 TTAGTACCGGTTCGACACGA 58.482 50.000 15.04 0.00 0.00 4.35
1926 2046 1.518325 TAGTACCGGTTCGACACGAA 58.482 50.000 15.04 2.48 43.75 3.85
1935 2055 4.764336 CGACACGAACCGGCGCTA 62.764 66.667 7.64 0.00 33.86 4.26
1936 2056 2.431260 GACACGAACCGGCGCTAA 60.431 61.111 7.64 0.00 33.86 3.09
1937 2057 2.023223 GACACGAACCGGCGCTAAA 61.023 57.895 7.64 0.00 33.86 1.85
1938 2058 1.952266 GACACGAACCGGCGCTAAAG 61.952 60.000 7.64 0.00 33.86 1.85
1939 2059 2.025418 CACGAACCGGCGCTAAAGT 61.025 57.895 7.64 0.00 33.86 2.66
1940 2060 2.025418 ACGAACCGGCGCTAAAGTG 61.025 57.895 7.64 0.00 33.86 3.16
1969 2089 3.730761 CGTGAGCTTGTGCCCTGC 61.731 66.667 0.00 0.00 40.80 4.85
1970 2090 2.282040 GTGAGCTTGTGCCCTGCT 60.282 61.111 0.00 0.00 40.80 4.24
1971 2091 1.003355 GTGAGCTTGTGCCCTGCTA 60.003 57.895 0.00 0.00 40.80 3.49
1972 2092 0.393537 GTGAGCTTGTGCCCTGCTAT 60.394 55.000 0.00 0.00 40.80 2.97
1973 2093 0.393402 TGAGCTTGTGCCCTGCTATG 60.393 55.000 0.00 0.00 40.80 2.23
1974 2094 0.107508 GAGCTTGTGCCCTGCTATGA 60.108 55.000 0.00 0.00 40.80 2.15
1975 2095 0.107312 AGCTTGTGCCCTGCTATGAG 60.107 55.000 0.00 0.00 40.80 2.90
2366 2486 2.255252 CCGTTTTTGCCGGCTCTG 59.745 61.111 29.70 11.12 38.85 3.35
2367 2487 2.255252 CGTTTTTGCCGGCTCTGG 59.745 61.111 29.70 8.20 0.00 3.86
2378 2498 4.181051 GCTCTGGCCAAAACTGGT 57.819 55.556 7.01 0.00 0.00 4.00
2379 2499 1.662044 GCTCTGGCCAAAACTGGTG 59.338 57.895 7.01 0.00 0.00 4.17
2380 2500 0.823356 GCTCTGGCCAAAACTGGTGA 60.823 55.000 7.01 0.00 0.00 4.02
2381 2501 0.954452 CTCTGGCCAAAACTGGTGAC 59.046 55.000 7.01 0.00 0.00 3.67
2382 2502 0.817634 TCTGGCCAAAACTGGTGACG 60.818 55.000 7.01 0.00 0.00 4.35
2383 2503 1.795170 CTGGCCAAAACTGGTGACGG 61.795 60.000 7.01 0.00 44.60 4.79
2384 2504 2.335011 GCCAAAACTGGTGACGGC 59.665 61.111 0.00 0.00 41.93 5.68
2385 2505 2.637025 CCAAAACTGGTGACGGCG 59.363 61.111 4.80 4.80 41.93 6.46
2386 2506 2.637025 CAAAACTGGTGACGGCGG 59.363 61.111 13.24 0.00 41.93 6.13
2387 2507 1.890041 CAAAACTGGTGACGGCGGA 60.890 57.895 13.24 0.00 41.93 5.54
2388 2508 1.890510 AAAACTGGTGACGGCGGAC 60.891 57.895 13.24 7.37 41.93 4.79
2389 2509 3.819877 AAACTGGTGACGGCGGACC 62.820 63.158 19.97 19.97 41.93 4.46
2401 2521 4.410400 CGGACCCAGGCAGAACCC 62.410 72.222 0.00 0.00 40.58 4.11
2402 2522 4.410400 GGACCCAGGCAGAACCCG 62.410 72.222 0.00 0.00 40.58 5.28
2433 2553 4.659172 CTTGGGGAGCCGGCACAA 62.659 66.667 31.54 24.29 0.00 3.33
2434 2554 4.659172 TTGGGGAGCCGGCACAAG 62.659 66.667 31.54 0.00 0.00 3.16
2439 2559 3.353836 GAGCCGGCACAAGCGAAA 61.354 61.111 31.54 0.00 43.41 3.46
2440 2560 2.903547 GAGCCGGCACAAGCGAAAA 61.904 57.895 31.54 0.00 43.41 2.29
2441 2561 2.026879 GCCGGCACAAGCGAAAAA 59.973 55.556 24.80 0.00 43.41 1.94
2442 2562 2.016165 GCCGGCACAAGCGAAAAAG 61.016 57.895 24.80 0.00 43.41 2.27
2443 2563 1.371635 CCGGCACAAGCGAAAAAGG 60.372 57.895 0.00 0.00 43.41 3.11
2444 2564 2.016165 CGGCACAAGCGAAAAAGGC 61.016 57.895 0.00 0.00 43.41 4.35
2445 2565 2.016165 GGCACAAGCGAAAAAGGCG 61.016 57.895 0.00 0.00 43.41 5.52
2481 2601 4.717313 GCGACCCGAGGGCCTTTT 62.717 66.667 7.89 0.00 39.32 2.27
2482 2602 2.033602 CGACCCGAGGGCCTTTTT 59.966 61.111 7.89 0.00 39.32 1.94
2483 2603 2.038837 CGACCCGAGGGCCTTTTTC 61.039 63.158 7.89 1.14 39.32 2.29
2484 2604 1.677966 GACCCGAGGGCCTTTTTCC 60.678 63.158 7.89 0.00 39.32 3.13
2485 2605 2.420466 GACCCGAGGGCCTTTTTCCA 62.420 60.000 7.89 0.00 39.32 3.53
2486 2606 1.977009 CCCGAGGGCCTTTTTCCAC 60.977 63.158 7.89 0.00 0.00 4.02
2487 2607 1.977009 CCGAGGGCCTTTTTCCACC 60.977 63.158 7.89 0.00 0.00 4.61
2488 2608 2.332654 CGAGGGCCTTTTTCCACCG 61.333 63.158 7.89 0.00 0.00 4.94
2489 2609 2.600470 AGGGCCTTTTTCCACCGC 60.600 61.111 0.00 0.00 0.00 5.68
2490 2610 2.600470 GGGCCTTTTTCCACCGCT 60.600 61.111 0.84 0.00 0.00 5.52
2491 2611 2.207229 GGGCCTTTTTCCACCGCTT 61.207 57.895 0.84 0.00 0.00 4.68
2492 2612 1.289066 GGCCTTTTTCCACCGCTTC 59.711 57.895 0.00 0.00 0.00 3.86
2493 2613 1.179174 GGCCTTTTTCCACCGCTTCT 61.179 55.000 0.00 0.00 0.00 2.85
2494 2614 0.673985 GCCTTTTTCCACCGCTTCTT 59.326 50.000 0.00 0.00 0.00 2.52
2495 2615 1.602920 GCCTTTTTCCACCGCTTCTTG 60.603 52.381 0.00 0.00 0.00 3.02
2496 2616 1.953686 CCTTTTTCCACCGCTTCTTGA 59.046 47.619 0.00 0.00 0.00 3.02
2497 2617 2.287608 CCTTTTTCCACCGCTTCTTGAC 60.288 50.000 0.00 0.00 0.00 3.18
2498 2618 0.941542 TTTTCCACCGCTTCTTGACG 59.058 50.000 0.00 0.00 0.00 4.35
2499 2619 1.503818 TTTCCACCGCTTCTTGACGC 61.504 55.000 0.00 0.00 0.00 5.19
2500 2620 2.357517 CCACCGCTTCTTGACGCT 60.358 61.111 0.00 0.00 0.00 5.07
2501 2621 1.961277 CCACCGCTTCTTGACGCTT 60.961 57.895 0.00 0.00 0.00 4.68
2502 2622 1.507141 CCACCGCTTCTTGACGCTTT 61.507 55.000 0.00 0.00 0.00 3.51
2503 2623 0.307760 CACCGCTTCTTGACGCTTTT 59.692 50.000 0.00 0.00 0.00 2.27
2504 2624 0.586802 ACCGCTTCTTGACGCTTTTC 59.413 50.000 0.00 0.00 0.00 2.29
2505 2625 0.110192 CCGCTTCTTGACGCTTTTCC 60.110 55.000 0.00 0.00 0.00 3.13
2506 2626 0.110192 CGCTTCTTGACGCTTTTCCC 60.110 55.000 0.00 0.00 0.00 3.97
2507 2627 1.239347 GCTTCTTGACGCTTTTCCCT 58.761 50.000 0.00 0.00 0.00 4.20
2508 2628 1.197949 GCTTCTTGACGCTTTTCCCTC 59.802 52.381 0.00 0.00 0.00 4.30
2509 2629 1.461127 CTTCTTGACGCTTTTCCCTCG 59.539 52.381 0.00 0.00 0.00 4.63
2510 2630 0.949105 TCTTGACGCTTTTCCCTCGC 60.949 55.000 0.00 0.00 0.00 5.03
2511 2631 1.227704 TTGACGCTTTTCCCTCGCA 60.228 52.632 0.00 0.00 0.00 5.10
2512 2632 0.605319 TTGACGCTTTTCCCTCGCAT 60.605 50.000 0.00 0.00 0.00 4.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
447 452 6.850234 TGTTAGTAATGGTTTTGTTCCCCTA 58.150 36.000 0.00 0.00 0.00 3.53
962 1054 1.659233 CATGCACCGGAAAAGCACA 59.341 52.632 9.46 0.00 41.60 4.57
1004 1096 2.553247 GGGGTTGGGAACTTCTCTGAAG 60.553 54.545 5.85 5.85 0.00 3.02
1080 1172 1.443828 GAAGACGGGCTCCAGGATC 59.556 63.158 0.00 0.00 0.00 3.36
1643 1756 9.736023 CCAGAAATAATACTTTTAATGGAGCAC 57.264 33.333 0.00 0.00 30.20 4.40
1692 1807 5.239306 ACGAGAAATGAAATGCAGAGAACAA 59.761 36.000 0.00 0.00 0.00 2.83
1699 1814 5.396484 ACATGAACGAGAAATGAAATGCAG 58.604 37.500 0.00 0.00 0.00 4.41
1816 1936 8.830580 GGTTTTAAAACTCCGTTTTCTACTAGT 58.169 33.333 25.89 0.00 43.43 2.57
1817 1937 8.006027 CGGTTTTAAAACTCCGTTTTCTACTAG 58.994 37.037 25.89 0.00 43.43 2.57
1818 1938 7.042119 CCGGTTTTAAAACTCCGTTTTCTACTA 60.042 37.037 25.89 0.00 43.43 1.82
1819 1939 6.238456 CCGGTTTTAAAACTCCGTTTTCTACT 60.238 38.462 25.89 0.00 43.43 2.57
1820 1940 5.909054 CCGGTTTTAAAACTCCGTTTTCTAC 59.091 40.000 25.89 7.91 43.43 2.59
1821 1941 5.588246 ACCGGTTTTAAAACTCCGTTTTCTA 59.412 36.000 25.89 0.00 43.43 2.10
1822 1942 4.398988 ACCGGTTTTAAAACTCCGTTTTCT 59.601 37.500 25.89 4.17 43.43 2.52
1823 1943 4.671377 ACCGGTTTTAAAACTCCGTTTTC 58.329 39.130 25.89 9.56 43.43 2.29
1824 1944 4.717233 ACCGGTTTTAAAACTCCGTTTT 57.283 36.364 25.89 9.35 45.80 2.43
1825 1945 4.671377 GAACCGGTTTTAAAACTCCGTTT 58.329 39.130 23.22 18.29 41.17 3.60
1826 1946 3.242706 CGAACCGGTTTTAAAACTCCGTT 60.243 43.478 23.22 22.87 41.17 4.44
1827 1947 2.287644 CGAACCGGTTTTAAAACTCCGT 59.712 45.455 23.22 17.50 41.17 4.69
1828 1948 2.287644 ACGAACCGGTTTTAAAACTCCG 59.712 45.455 23.22 21.95 42.22 4.63
1829 1949 3.969117 ACGAACCGGTTTTAAAACTCC 57.031 42.857 23.22 12.95 38.89 3.85
1830 1950 5.443261 CCTTACGAACCGGTTTTAAAACTC 58.557 41.667 23.22 16.37 38.89 3.01
1831 1951 4.275689 CCCTTACGAACCGGTTTTAAAACT 59.724 41.667 23.22 10.12 38.89 2.66
1832 1952 4.536065 CCCTTACGAACCGGTTTTAAAAC 58.464 43.478 23.22 20.58 38.17 2.43
1833 1953 3.004210 GCCCTTACGAACCGGTTTTAAAA 59.996 43.478 23.22 12.46 0.00 1.52
1834 1954 2.551887 GCCCTTACGAACCGGTTTTAAA 59.448 45.455 23.22 14.20 0.00 1.52
1835 1955 2.150390 GCCCTTACGAACCGGTTTTAA 58.850 47.619 23.22 19.35 0.00 1.52
1836 1956 1.610363 GGCCCTTACGAACCGGTTTTA 60.610 52.381 23.22 13.17 0.00 1.52
1837 1957 0.890542 GGCCCTTACGAACCGGTTTT 60.891 55.000 23.22 14.26 0.00 2.43
1838 1958 1.302752 GGCCCTTACGAACCGGTTT 60.303 57.895 23.22 9.26 0.00 3.27
1839 1959 1.771783 AAGGCCCTTACGAACCGGTT 61.772 55.000 22.50 22.50 0.00 4.44
1840 1960 1.771783 AAAGGCCCTTACGAACCGGT 61.772 55.000 0.00 0.00 0.00 5.28
1841 1961 0.249955 TAAAGGCCCTTACGAACCGG 59.750 55.000 0.00 0.00 0.00 5.28
1842 1962 1.066645 ACTAAAGGCCCTTACGAACCG 60.067 52.381 0.00 0.00 0.00 4.44
1843 1963 2.027837 TCACTAAAGGCCCTTACGAACC 60.028 50.000 0.00 0.00 0.00 3.62
1844 1964 3.323751 TCACTAAAGGCCCTTACGAAC 57.676 47.619 0.00 0.00 0.00 3.95
1845 1965 3.934068 CTTCACTAAAGGCCCTTACGAA 58.066 45.455 0.00 0.12 0.00 3.85
1846 1966 3.604875 CTTCACTAAAGGCCCTTACGA 57.395 47.619 0.00 0.00 0.00 3.43
1857 1977 9.238368 CCAATTAGTTATGGAACCTTCACTAAA 57.762 33.333 13.52 3.51 39.12 1.85
1858 1978 8.387813 ACCAATTAGTTATGGAACCTTCACTAA 58.612 33.333 12.53 12.53 39.12 2.24
1859 1979 7.827236 CACCAATTAGTTATGGAACCTTCACTA 59.173 37.037 0.00 0.00 39.12 2.74
1860 1980 6.659242 CACCAATTAGTTATGGAACCTTCACT 59.341 38.462 0.00 0.00 39.12 3.41
1861 1981 6.127730 CCACCAATTAGTTATGGAACCTTCAC 60.128 42.308 0.00 0.00 39.12 3.18
1862 1982 5.949354 CCACCAATTAGTTATGGAACCTTCA 59.051 40.000 0.00 0.00 39.12 3.02
1863 1983 5.359860 CCCACCAATTAGTTATGGAACCTTC 59.640 44.000 0.00 0.00 39.12 3.46
1864 1984 5.269189 CCCACCAATTAGTTATGGAACCTT 58.731 41.667 0.00 0.00 39.12 3.50
1865 1985 4.867086 CCCACCAATTAGTTATGGAACCT 58.133 43.478 0.00 0.00 39.12 3.50
1866 1986 3.383505 GCCCACCAATTAGTTATGGAACC 59.616 47.826 0.00 0.00 39.12 3.62
1867 1987 4.020543 TGCCCACCAATTAGTTATGGAAC 58.979 43.478 0.00 0.00 39.12 3.62
1868 1988 4.020543 GTGCCCACCAATTAGTTATGGAA 58.979 43.478 0.00 0.00 39.12 3.53
1869 1989 3.268334 AGTGCCCACCAATTAGTTATGGA 59.732 43.478 0.00 0.00 39.12 3.41
1870 1990 3.631250 AGTGCCCACCAATTAGTTATGG 58.369 45.455 0.00 0.00 42.60 2.74
1871 1991 6.183360 CCTTTAGTGCCCACCAATTAGTTATG 60.183 42.308 0.00 0.00 0.00 1.90
1872 1992 5.891551 CCTTTAGTGCCCACCAATTAGTTAT 59.108 40.000 0.00 0.00 0.00 1.89
1873 1993 5.258051 CCTTTAGTGCCCACCAATTAGTTA 58.742 41.667 0.00 0.00 0.00 2.24
1874 1994 4.086457 CCTTTAGTGCCCACCAATTAGTT 58.914 43.478 0.00 0.00 0.00 2.24
1875 1995 3.563479 CCCTTTAGTGCCCACCAATTAGT 60.563 47.826 0.00 0.00 0.00 2.24
1876 1996 3.023832 CCCTTTAGTGCCCACCAATTAG 58.976 50.000 0.00 0.00 0.00 1.73
1877 1997 2.650322 TCCCTTTAGTGCCCACCAATTA 59.350 45.455 0.00 0.00 0.00 1.40
1878 1998 1.431243 TCCCTTTAGTGCCCACCAATT 59.569 47.619 0.00 0.00 0.00 2.32
1879 1999 1.080638 TCCCTTTAGTGCCCACCAAT 58.919 50.000 0.00 0.00 0.00 3.16
1880 2000 0.111639 GTCCCTTTAGTGCCCACCAA 59.888 55.000 0.00 0.00 0.00 3.67
1881 2001 1.765074 GTCCCTTTAGTGCCCACCA 59.235 57.895 0.00 0.00 0.00 4.17
1882 2002 1.001269 GGTCCCTTTAGTGCCCACC 60.001 63.158 0.00 0.00 0.00 4.61
1883 2003 1.001269 GGGTCCCTTTAGTGCCCAC 60.001 63.158 0.00 0.00 39.13 4.61
1884 2004 2.235761 GGGGTCCCTTTAGTGCCCA 61.236 63.158 8.15 0.00 41.02 5.36
1885 2005 2.681591 GGGGTCCCTTTAGTGCCC 59.318 66.667 8.15 0.00 38.61 5.36
1886 2006 2.681591 GGGGGTCCCTTTAGTGCC 59.318 66.667 8.15 0.00 41.34 5.01
1900 2020 0.176449 CGAACCGGTACTAAAGGGGG 59.824 60.000 8.00 0.00 0.00 5.40
1901 2021 1.134995 GTCGAACCGGTACTAAAGGGG 60.135 57.143 8.00 0.00 0.00 4.79
1902 2022 1.545582 TGTCGAACCGGTACTAAAGGG 59.454 52.381 8.00 0.00 0.00 3.95
1903 2023 2.599659 GTGTCGAACCGGTACTAAAGG 58.400 52.381 8.00 0.00 0.00 3.11
1904 2024 2.095768 TCGTGTCGAACCGGTACTAAAG 60.096 50.000 8.00 0.00 31.06 1.85
1905 2025 1.876799 TCGTGTCGAACCGGTACTAAA 59.123 47.619 8.00 0.00 31.06 1.85
1906 2026 1.518325 TCGTGTCGAACCGGTACTAA 58.482 50.000 8.00 0.00 31.06 2.24
1907 2027 1.518325 TTCGTGTCGAACCGGTACTA 58.482 50.000 8.00 0.00 41.05 1.82
1908 2028 2.330254 TTCGTGTCGAACCGGTACT 58.670 52.632 8.00 0.00 41.05 2.73
1909 2029 4.942090 TTCGTGTCGAACCGGTAC 57.058 55.556 8.00 2.48 41.05 3.34
1918 2038 4.764336 TAGCGCCGGTTCGTGTCG 62.764 66.667 2.29 0.00 0.00 4.35
1919 2039 1.952266 CTTTAGCGCCGGTTCGTGTC 61.952 60.000 2.29 0.00 0.00 3.67
1920 2040 2.025418 CTTTAGCGCCGGTTCGTGT 61.025 57.895 2.29 0.00 0.00 4.49
1921 2041 2.025418 ACTTTAGCGCCGGTTCGTG 61.025 57.895 2.29 0.00 0.00 4.35
1922 2042 2.025418 CACTTTAGCGCCGGTTCGT 61.025 57.895 2.29 0.00 0.00 3.85
1923 2043 2.776072 CACTTTAGCGCCGGTTCG 59.224 61.111 2.29 0.00 0.00 3.95
1924 2044 2.479198 GCACTTTAGCGCCGGTTC 59.521 61.111 2.29 0.00 0.00 3.62
1925 2045 3.053896 GGCACTTTAGCGCCGGTT 61.054 61.111 2.29 0.00 38.82 4.44
1930 2050 1.060937 CGTGATGGCACTTTAGCGC 59.939 57.895 0.00 0.00 42.93 5.92
1931 2051 0.095245 CACGTGATGGCACTTTAGCG 59.905 55.000 10.90 0.00 42.93 4.26
1932 2052 0.447801 CCACGTGATGGCACTTTAGC 59.552 55.000 19.30 0.00 43.24 3.09
1946 2066 2.967076 CACAAGCTCACGCCACGT 60.967 61.111 0.00 0.00 42.36 4.49
1947 2067 4.374702 GCACAAGCTCACGCCACG 62.375 66.667 0.00 0.00 37.91 4.94
1948 2068 4.030452 GGCACAAGCTCACGCCAC 62.030 66.667 13.73 0.00 44.25 5.01
1951 2071 3.730761 CAGGGCACAAGCTCACGC 61.731 66.667 0.00 0.00 46.43 5.34
1952 2072 2.786539 TAGCAGGGCACAAGCTCACG 62.787 60.000 9.35 0.00 46.43 4.35
1953 2073 0.393537 ATAGCAGGGCACAAGCTCAC 60.394 55.000 9.35 0.00 46.43 3.51
1954 2074 0.393402 CATAGCAGGGCACAAGCTCA 60.393 55.000 9.35 0.00 46.43 4.26
1955 2075 0.107508 TCATAGCAGGGCACAAGCTC 60.108 55.000 9.35 0.00 43.44 4.09
1956 2076 0.107312 CTCATAGCAGGGCACAAGCT 60.107 55.000 10.86 10.86 41.70 3.74
1957 2077 2.401967 CTCATAGCAGGGCACAAGC 58.598 57.895 0.00 0.00 41.10 4.01
2350 2470 2.255252 CCAGAGCCGGCAAAAACG 59.745 61.111 31.54 10.27 0.00 3.60
2369 2489 1.890041 TCCGCCGTCACCAGTTTTG 60.890 57.895 0.00 0.00 0.00 2.44
2370 2490 1.890510 GTCCGCCGTCACCAGTTTT 60.891 57.895 0.00 0.00 0.00 2.43
2371 2491 2.280592 GTCCGCCGTCACCAGTTT 60.281 61.111 0.00 0.00 0.00 2.66
2372 2492 4.309950 GGTCCGCCGTCACCAGTT 62.310 66.667 0.00 0.00 32.33 3.16
2384 2504 4.410400 GGGTTCTGCCTGGGTCCG 62.410 72.222 0.00 0.00 37.43 4.79
2385 2505 4.410400 CGGGTTCTGCCTGGGTCC 62.410 72.222 0.00 0.00 40.02 4.46
2416 2536 4.659172 TTGTGCCGGCTCCCCAAG 62.659 66.667 29.70 0.00 0.00 3.61
2417 2537 4.659172 CTTGTGCCGGCTCCCCAA 62.659 66.667 29.70 21.61 0.00 4.12
2422 2542 2.400896 TTTTTCGCTTGTGCCGGCTC 62.401 55.000 29.70 25.38 35.36 4.70
2423 2543 2.406452 CTTTTTCGCTTGTGCCGGCT 62.406 55.000 29.70 0.00 35.36 5.52
2424 2544 2.016165 CTTTTTCGCTTGTGCCGGC 61.016 57.895 22.73 22.73 35.36 6.13
2425 2545 1.371635 CCTTTTTCGCTTGTGCCGG 60.372 57.895 0.00 0.00 35.36 6.13
2426 2546 2.016165 GCCTTTTTCGCTTGTGCCG 61.016 57.895 0.00 0.00 35.36 5.69
2427 2547 2.016165 CGCCTTTTTCGCTTGTGCC 61.016 57.895 0.00 0.00 35.36 5.01
2428 2548 3.526029 CGCCTTTTTCGCTTGTGC 58.474 55.556 0.00 0.00 0.00 4.57
2436 2556 4.717629 GGCCCACGCGCCTTTTTC 62.718 66.667 5.73 0.00 46.10 2.29
2464 2584 4.717313 AAAAGGCCCTCGGGTCGC 62.717 66.667 0.00 0.00 46.16 5.19
2465 2585 2.033602 AAAAAGGCCCTCGGGTCG 59.966 61.111 0.00 0.00 46.16 4.79
2466 2586 1.677966 GGAAAAAGGCCCTCGGGTC 60.678 63.158 0.00 0.00 40.91 4.46
2467 2587 2.439245 GGAAAAAGGCCCTCGGGT 59.561 61.111 0.00 0.00 37.65 5.28
2468 2588 1.977009 GTGGAAAAAGGCCCTCGGG 60.977 63.158 0.00 0.00 38.57 5.14
2469 2589 1.977009 GGTGGAAAAAGGCCCTCGG 60.977 63.158 0.00 0.00 0.00 4.63
2470 2590 2.332654 CGGTGGAAAAAGGCCCTCG 61.333 63.158 0.00 0.00 0.00 4.63
2471 2591 2.636412 GCGGTGGAAAAAGGCCCTC 61.636 63.158 0.00 0.00 0.00 4.30
2472 2592 2.600470 GCGGTGGAAAAAGGCCCT 60.600 61.111 0.00 0.00 0.00 5.19
2473 2593 2.154798 GAAGCGGTGGAAAAAGGCCC 62.155 60.000 0.00 0.00 0.00 5.80
2474 2594 1.179174 AGAAGCGGTGGAAAAAGGCC 61.179 55.000 0.00 0.00 0.00 5.19
2475 2595 0.673985 AAGAAGCGGTGGAAAAAGGC 59.326 50.000 0.00 0.00 0.00 4.35
2476 2596 1.953686 TCAAGAAGCGGTGGAAAAAGG 59.046 47.619 0.00 0.00 0.00 3.11
2477 2597 2.602217 CGTCAAGAAGCGGTGGAAAAAG 60.602 50.000 0.00 0.00 0.00 2.27
2478 2598 1.332375 CGTCAAGAAGCGGTGGAAAAA 59.668 47.619 0.00 0.00 0.00 1.94
2479 2599 0.941542 CGTCAAGAAGCGGTGGAAAA 59.058 50.000 0.00 0.00 0.00 2.29
2480 2600 1.503818 GCGTCAAGAAGCGGTGGAAA 61.504 55.000 0.00 0.00 0.00 3.13
2481 2601 1.959226 GCGTCAAGAAGCGGTGGAA 60.959 57.895 0.00 0.00 0.00 3.53
2482 2602 2.357034 GCGTCAAGAAGCGGTGGA 60.357 61.111 0.00 0.00 0.00 4.02
2483 2603 1.507141 AAAGCGTCAAGAAGCGGTGG 61.507 55.000 2.49 0.00 40.72 4.61
2484 2604 0.307760 AAAAGCGTCAAGAAGCGGTG 59.692 50.000 2.49 0.00 40.72 4.94
2485 2605 0.586802 GAAAAGCGTCAAGAAGCGGT 59.413 50.000 2.49 0.00 40.72 5.68
2486 2606 0.110192 GGAAAAGCGTCAAGAAGCGG 60.110 55.000 2.49 0.00 40.72 5.52
2487 2607 0.110192 GGGAAAAGCGTCAAGAAGCG 60.110 55.000 2.49 0.00 40.72 4.68
2488 2608 1.197949 GAGGGAAAAGCGTCAAGAAGC 59.802 52.381 0.00 0.00 36.04 3.86
2489 2609 1.461127 CGAGGGAAAAGCGTCAAGAAG 59.539 52.381 0.00 0.00 0.00 2.85
2490 2610 1.508632 CGAGGGAAAAGCGTCAAGAA 58.491 50.000 0.00 0.00 0.00 2.52
2491 2611 0.949105 GCGAGGGAAAAGCGTCAAGA 60.949 55.000 0.00 0.00 0.00 3.02
2492 2612 1.227999 TGCGAGGGAAAAGCGTCAAG 61.228 55.000 0.00 0.00 0.00 3.02
2493 2613 0.605319 ATGCGAGGGAAAAGCGTCAA 60.605 50.000 0.00 0.00 0.00 3.18
2494 2614 1.003839 ATGCGAGGGAAAAGCGTCA 60.004 52.632 0.00 0.00 0.00 4.35
2495 2615 3.890674 ATGCGAGGGAAAAGCGTC 58.109 55.556 0.00 0.00 0.00 5.19


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

AutoCloner maintained by Alex Coulton.