Multiple sequence alignment - TraesCS4A01G064100

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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 TraesCS4A01G064100 chr4A 100.000 2471 0 0 1 2471 60891411 60893881 0.000000e+00 4564
1 TraesCS4A01G064100 chr4A 89.974 1935 153 12 1 1908 19186144 19184224 0.000000e+00 2460
2 TraesCS4A01G064100 chr4B 91.079 1928 132 16 1 1899 551784515 551786431 0.000000e+00 2571
3 TraesCS4A01G064100 chr4B 90.824 1929 135 18 1 1899 551729907 551731823 0.000000e+00 2543
4 TraesCS4A01G064100 chr4B 90.831 349 24 6 2127 2471 500111098 500111442 6.230000e-126 460
5 TraesCS4A01G064100 chr4B 94.521 146 8 0 1985 2130 500110924 500111069 2.470000e-55 226
6 TraesCS4A01G064100 chr2A 90.947 1922 144 10 2 1906 504065758 504067666 0.000000e+00 2558
7 TraesCS4A01G064100 chr2A 89.112 1938 151 21 1 1909 779811664 779813570 0.000000e+00 2355
8 TraesCS4A01G064100 chr2A 86.038 530 59 10 1 530 769258167 769258681 2.780000e-154 555
9 TraesCS4A01G064100 chr7B 90.975 1928 131 18 1 1899 150841909 150843822 0.000000e+00 2556
10 TraesCS4A01G064100 chr6D 90.961 1925 128 14 1 1899 450905769 450907673 0.000000e+00 2549
11 TraesCS4A01G064100 chr7D 90.412 1940 142 12 1 1905 463976035 463974105 0.000000e+00 2512
12 TraesCS4A01G064100 chr7D 87.382 317 25 4 1 302 182353139 182353455 1.410000e-92 350
13 TraesCS4A01G064100 chr4D 90.067 1933 145 18 3 1906 414225398 414227312 0.000000e+00 2462
14 TraesCS4A01G064100 chr4D 91.466 1582 116 8 336 1908 102106757 102105186 0.000000e+00 2156
15 TraesCS4A01G064100 chr4D 89.404 906 63 10 3 884 508924510 508925406 0.000000e+00 1110
16 TraesCS4A01G064100 chr4D 89.863 365 13 4 2127 2471 403292303 403292663 4.850000e-122 448
17 TraesCS4A01G064100 chr4D 86.364 264 19 7 1 247 56941401 56941664 3.130000e-69 272
18 TraesCS4A01G064100 chr4D 94.697 132 7 0 1999 2130 403292141 403292272 3.220000e-49 206
19 TraesCS4A01G064100 chr3D 89.928 1946 139 18 1 1909 593766553 593764628 0.000000e+00 2455
20 TraesCS4A01G064100 chr3D 90.490 715 37 4 1 693 575956258 575955553 0.000000e+00 915
21 TraesCS4A01G064100 chr3D 88.235 595 46 7 3 594 448601859 448602432 0.000000e+00 689
22 TraesCS4A01G064100 chr5D 88.220 1961 136 37 1 1907 492733012 492731093 0.000000e+00 2254
23 TraesCS4A01G064100 chr2D 91.160 1629 127 6 279 1899 469180817 469182436 0.000000e+00 2194
24 TraesCS4A01G064100 chr2D 91.723 1474 95 6 1 1456 487337356 487335892 0.000000e+00 2021
25 TraesCS4A01G064100 chr6B 87.403 1929 177 30 3 1899 81980875 81982769 0.000000e+00 2156
26 TraesCS4A01G064100 chr6B 87.848 1078 99 9 1 1057 690430500 690431566 0.000000e+00 1236
27 TraesCS4A01G064100 chr1D 90.642 1122 82 5 1 1109 338633394 338634505 0.000000e+00 1469


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 TraesCS4A01G064100 chr4A 60891411 60893881 2470 False 4564 4564 100.000 1 2471 1 chr4A.!!$F1 2470
1 TraesCS4A01G064100 chr4A 19184224 19186144 1920 True 2460 2460 89.974 1 1908 1 chr4A.!!$R1 1907
2 TraesCS4A01G064100 chr4B 551784515 551786431 1916 False 2571 2571 91.079 1 1899 1 chr4B.!!$F2 1898
3 TraesCS4A01G064100 chr4B 551729907 551731823 1916 False 2543 2543 90.824 1 1899 1 chr4B.!!$F1 1898
4 TraesCS4A01G064100 chr4B 500110924 500111442 518 False 343 460 92.676 1985 2471 2 chr4B.!!$F3 486
5 TraesCS4A01G064100 chr2A 504065758 504067666 1908 False 2558 2558 90.947 2 1906 1 chr2A.!!$F1 1904
6 TraesCS4A01G064100 chr2A 779811664 779813570 1906 False 2355 2355 89.112 1 1909 1 chr2A.!!$F3 1908
7 TraesCS4A01G064100 chr2A 769258167 769258681 514 False 555 555 86.038 1 530 1 chr2A.!!$F2 529
8 TraesCS4A01G064100 chr7B 150841909 150843822 1913 False 2556 2556 90.975 1 1899 1 chr7B.!!$F1 1898
9 TraesCS4A01G064100 chr6D 450905769 450907673 1904 False 2549 2549 90.961 1 1899 1 chr6D.!!$F1 1898
10 TraesCS4A01G064100 chr7D 463974105 463976035 1930 True 2512 2512 90.412 1 1905 1 chr7D.!!$R1 1904
11 TraesCS4A01G064100 chr4D 414225398 414227312 1914 False 2462 2462 90.067 3 1906 1 chr4D.!!$F2 1903
12 TraesCS4A01G064100 chr4D 102105186 102106757 1571 True 2156 2156 91.466 336 1908 1 chr4D.!!$R1 1572
13 TraesCS4A01G064100 chr4D 508924510 508925406 896 False 1110 1110 89.404 3 884 1 chr4D.!!$F3 881
14 TraesCS4A01G064100 chr4D 403292141 403292663 522 False 327 448 92.280 1999 2471 2 chr4D.!!$F4 472
15 TraesCS4A01G064100 chr3D 593764628 593766553 1925 True 2455 2455 89.928 1 1909 1 chr3D.!!$R2 1908
16 TraesCS4A01G064100 chr3D 575955553 575956258 705 True 915 915 90.490 1 693 1 chr3D.!!$R1 692
17 TraesCS4A01G064100 chr3D 448601859 448602432 573 False 689 689 88.235 3 594 1 chr3D.!!$F1 591
18 TraesCS4A01G064100 chr5D 492731093 492733012 1919 True 2254 2254 88.220 1 1907 1 chr5D.!!$R1 1906
19 TraesCS4A01G064100 chr2D 469180817 469182436 1619 False 2194 2194 91.160 279 1899 1 chr2D.!!$F1 1620
20 TraesCS4A01G064100 chr2D 487335892 487337356 1464 True 2021 2021 91.723 1 1456 1 chr2D.!!$R1 1455
21 TraesCS4A01G064100 chr6B 81980875 81982769 1894 False 2156 2156 87.403 3 1899 1 chr6B.!!$F1 1896
22 TraesCS4A01G064100 chr6B 690430500 690431566 1066 False 1236 1236 87.848 1 1057 1 chr6B.!!$F2 1056
23 TraesCS4A01G064100 chr1D 338633394 338634505 1111 False 1469 1469 90.642 1 1109 1 chr1D.!!$F1 1108

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
911 1035 0.035317 TGTGATGTGTCTGGCTCCAC 59.965 55.0 0.0 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2118 2306 0.029834 GTTTCGATAGGGAGCGCGTA 59.97 55.0 8.43 0.0 33.48 4.42 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
149 228 0.480796 AAGGGGGATTGGGGGTACAA 60.481 55.000 0.00 0.00 34.41 2.41
160 239 1.133730 GGGGGTACAAAACAGACACCA 60.134 52.381 0.00 0.00 38.50 4.17
355 455 2.238319 TAGGCTCCCCACCGATGACT 62.238 60.000 0.00 0.00 0.00 3.41
367 467 3.649277 GATGACTGTCGGCGGCACT 62.649 63.158 11.51 0.17 0.00 4.40
411 511 1.515954 CACGGCGGTCATTAGGAGT 59.484 57.895 13.24 0.00 0.00 3.85
447 547 3.858135 ACTTGGACCACTTCTTCCTCTA 58.142 45.455 0.00 0.00 32.55 2.43
465 565 2.938451 TCTATTTAGCGTCGTCGGAGAA 59.062 45.455 3.90 0.00 39.69 2.87
613 722 2.358939 GCATGGAGCCAAAGTTTGAG 57.641 50.000 17.33 8.25 37.23 3.02
614 723 1.670967 GCATGGAGCCAAAGTTTGAGC 60.671 52.381 17.33 16.94 37.23 4.26
615 724 1.614903 CATGGAGCCAAAGTTTGAGCA 59.385 47.619 22.71 9.55 31.84 4.26
616 725 1.032014 TGGAGCCAAAGTTTGAGCAC 58.968 50.000 22.71 18.31 31.84 4.40
617 726 0.315251 GGAGCCAAAGTTTGAGCACC 59.685 55.000 22.71 21.70 33.41 5.01
618 727 0.315251 GAGCCAAAGTTTGAGCACCC 59.685 55.000 22.71 12.48 31.84 4.61
619 728 1.007387 GCCAAAGTTTGAGCACCCG 60.007 57.895 17.33 0.00 0.00 5.28
620 729 1.452145 GCCAAAGTTTGAGCACCCGA 61.452 55.000 17.33 0.00 0.00 5.14
626 737 3.842925 TTTGAGCACCCGAGGCACC 62.843 63.158 0.00 0.00 0.00 5.01
701 812 2.386935 GCCCTCCAGCCAATACCCT 61.387 63.158 0.00 0.00 0.00 4.34
704 815 2.065799 CCCTCCAGCCAATACCCTAAT 58.934 52.381 0.00 0.00 0.00 1.73
764 881 2.883026 CGATGGAGAGGAGGAAGGTAT 58.117 52.381 0.00 0.00 0.00 2.73
784 901 6.795507 AGGTATATAGTGAGAGAAGAGAGGGA 59.204 42.308 0.00 0.00 0.00 4.20
833 952 4.822026 AGTAAATATAGGCACGATGGAGC 58.178 43.478 0.00 0.00 0.00 4.70
844 967 1.103987 CGATGGAGCGGAGGAAGAGA 61.104 60.000 0.00 0.00 0.00 3.10
862 986 3.119316 AGAGAGACAGTCATGCCGTTTAG 60.119 47.826 2.66 0.00 0.00 1.85
870 994 2.936498 GTCATGCCGTTTAGCTACATGT 59.064 45.455 16.52 2.69 39.27 3.21
905 1029 3.391506 TGAACTCTGTGATGTGTCTGG 57.608 47.619 0.00 0.00 0.00 3.86
911 1035 0.035317 TGTGATGTGTCTGGCTCCAC 59.965 55.000 0.00 0.00 0.00 4.02
934 1058 0.247460 TTGTGTGCAGATCGAGGAGG 59.753 55.000 0.00 0.00 0.00 4.30
1049 1179 0.244178 GAGGAAGAACCGAAGACGCT 59.756 55.000 0.00 0.00 44.74 5.07
1289 1429 2.350522 GGTGAAGCTGATGAACGACAT 58.649 47.619 0.00 0.00 42.47 3.06
1505 1647 6.328672 ACCTCCTTCCTAAGTACTATCGAGTA 59.671 42.308 0.00 0.00 37.10 2.59
1512 1654 9.565090 TTCCTAAGTACTATCGAGTATGCTTTA 57.435 33.333 0.00 0.00 40.32 1.85
1513 1655 9.217278 TCCTAAGTACTATCGAGTATGCTTTAG 57.783 37.037 0.00 0.00 40.32 1.85
1525 1679 6.292381 CGAGTATGCTTTAGACTGTTTATGGC 60.292 42.308 0.00 0.00 29.22 4.40
1647 1834 1.295357 TGGTTGTGCCGAAGTATGCG 61.295 55.000 0.00 0.00 41.21 4.73
1673 1860 2.307098 AGCTCACCAACTAGCCAAAGAT 59.693 45.455 0.00 0.00 39.64 2.40
1678 1865 5.815581 TCACCAACTAGCCAAAGATGTTAT 58.184 37.500 0.00 0.00 0.00 1.89
1702 1889 2.483877 CACACCAGACGTTGCATACAAT 59.516 45.455 0.00 0.00 38.27 2.71
1744 1931 2.954989 TGTTCACTAACATGCAGGCAAA 59.045 40.909 0.00 0.00 40.69 3.68
1758 1945 0.809636 GGCAAACAAACACCAGGCAC 60.810 55.000 0.00 0.00 0.00 5.01
1794 1981 2.362120 GGCAAGAGGGCATGCAGT 60.362 61.111 21.36 5.20 44.32 4.40
1802 1989 0.896940 AGGGCATGCAGTCAACCAAG 60.897 55.000 21.36 0.00 0.00 3.61
1899 2087 2.353269 TGTTCACTACTGCAACCAAACG 59.647 45.455 0.00 0.00 0.00 3.60
1909 2097 1.000394 GCAACCAAACGCACCCTAAAT 60.000 47.619 0.00 0.00 0.00 1.40
1910 2098 2.229302 GCAACCAAACGCACCCTAAATA 59.771 45.455 0.00 0.00 0.00 1.40
1911 2099 3.305471 GCAACCAAACGCACCCTAAATAA 60.305 43.478 0.00 0.00 0.00 1.40
1912 2100 4.796618 GCAACCAAACGCACCCTAAATAAA 60.797 41.667 0.00 0.00 0.00 1.40
1913 2101 5.290386 CAACCAAACGCACCCTAAATAAAA 58.710 37.500 0.00 0.00 0.00 1.52
1914 2102 5.128992 ACCAAACGCACCCTAAATAAAAG 57.871 39.130 0.00 0.00 0.00 2.27
1915 2103 4.828387 ACCAAACGCACCCTAAATAAAAGA 59.172 37.500 0.00 0.00 0.00 2.52
1916 2104 5.302313 ACCAAACGCACCCTAAATAAAAGAA 59.698 36.000 0.00 0.00 0.00 2.52
1917 2105 5.631929 CCAAACGCACCCTAAATAAAAGAAC 59.368 40.000 0.00 0.00 0.00 3.01
1918 2106 6.443792 CAAACGCACCCTAAATAAAAGAACT 58.556 36.000 0.00 0.00 0.00 3.01
1919 2107 6.644248 AACGCACCCTAAATAAAAGAACTT 57.356 33.333 0.00 0.00 0.00 2.66
1920 2108 6.009115 ACGCACCCTAAATAAAAGAACTTG 57.991 37.500 0.00 0.00 0.00 3.16
1921 2109 5.766174 ACGCACCCTAAATAAAAGAACTTGA 59.234 36.000 0.00 0.00 0.00 3.02
1922 2110 6.072673 ACGCACCCTAAATAAAAGAACTTGAG 60.073 38.462 0.00 0.00 0.00 3.02
1923 2111 6.621613 GCACCCTAAATAAAAGAACTTGAGG 58.378 40.000 0.00 0.00 0.00 3.86
1924 2112 6.621613 CACCCTAAATAAAAGAACTTGAGGC 58.378 40.000 0.00 0.00 0.00 4.70
1925 2113 5.715279 ACCCTAAATAAAAGAACTTGAGGCC 59.285 40.000 0.00 0.00 0.00 5.19
1926 2114 5.952347 CCCTAAATAAAAGAACTTGAGGCCT 59.048 40.000 3.86 3.86 0.00 5.19
1927 2115 6.095580 CCCTAAATAAAAGAACTTGAGGCCTC 59.904 42.308 26.78 26.78 0.00 4.70
1928 2116 6.887002 CCTAAATAAAAGAACTTGAGGCCTCT 59.113 38.462 32.28 13.46 0.00 3.69
1929 2117 6.581171 AAATAAAAGAACTTGAGGCCTCTG 57.419 37.500 32.28 25.36 0.00 3.35
1930 2118 3.584733 AAAAGAACTTGAGGCCTCTGT 57.415 42.857 32.28 25.98 0.00 3.41
1931 2119 2.557920 AAGAACTTGAGGCCTCTGTG 57.442 50.000 32.28 22.72 0.00 3.66
1932 2120 1.428869 AGAACTTGAGGCCTCTGTGT 58.571 50.000 32.28 23.33 0.00 3.72
1933 2121 1.346068 AGAACTTGAGGCCTCTGTGTC 59.654 52.381 32.28 24.36 0.00 3.67
1934 2122 1.346068 GAACTTGAGGCCTCTGTGTCT 59.654 52.381 32.28 16.07 0.00 3.41
1935 2123 0.972883 ACTTGAGGCCTCTGTGTCTC 59.027 55.000 32.28 5.83 0.00 3.36
1936 2124 1.265236 CTTGAGGCCTCTGTGTCTCT 58.735 55.000 32.28 0.00 0.00 3.10
1937 2125 0.972134 TTGAGGCCTCTGTGTCTCTG 59.028 55.000 32.28 0.00 0.00 3.35
1938 2126 0.902048 TGAGGCCTCTGTGTCTCTGG 60.902 60.000 32.28 0.00 0.00 3.86
1939 2127 1.611851 AGGCCTCTGTGTCTCTGGG 60.612 63.158 0.00 0.00 0.00 4.45
1940 2128 1.610673 GGCCTCTGTGTCTCTGGGA 60.611 63.158 0.00 0.00 0.00 4.37
1941 2129 1.594310 GCCTCTGTGTCTCTGGGAC 59.406 63.158 0.00 0.00 44.70 4.46
1942 2130 1.893919 GCCTCTGTGTCTCTGGGACC 61.894 65.000 5.00 0.00 43.89 4.46
1943 2131 1.599606 CCTCTGTGTCTCTGGGACCG 61.600 65.000 5.00 0.00 43.89 4.79
1944 2132 1.599606 CTCTGTGTCTCTGGGACCGG 61.600 65.000 5.00 0.00 43.89 5.28
1945 2133 1.606601 CTGTGTCTCTGGGACCGGA 60.607 63.158 9.46 0.00 43.89 5.14
1946 2134 0.972983 CTGTGTCTCTGGGACCGGAT 60.973 60.000 9.46 0.00 43.89 4.18
1947 2135 0.970937 TGTGTCTCTGGGACCGGATC 60.971 60.000 9.46 1.18 43.89 3.36
1948 2136 0.970937 GTGTCTCTGGGACCGGATCA 60.971 60.000 9.46 1.77 43.89 2.92
1949 2137 0.970937 TGTCTCTGGGACCGGATCAC 60.971 60.000 9.46 3.48 43.89 3.06
1950 2138 1.381327 TCTCTGGGACCGGATCACC 60.381 63.158 9.46 4.85 0.00 4.02
1960 2148 4.057224 GGATCACCGCACACACAA 57.943 55.556 0.00 0.00 0.00 3.33
1961 2149 1.868997 GGATCACCGCACACACAAG 59.131 57.895 0.00 0.00 0.00 3.16
1962 2150 1.207593 GATCACCGCACACACAAGC 59.792 57.895 0.00 0.00 0.00 4.01
1963 2151 1.506309 GATCACCGCACACACAAGCA 61.506 55.000 0.00 0.00 0.00 3.91
1964 2152 1.509644 ATCACCGCACACACAAGCAG 61.510 55.000 0.00 0.00 0.00 4.24
1965 2153 3.585990 ACCGCACACACAAGCAGC 61.586 61.111 0.00 0.00 0.00 5.25
1966 2154 4.332637 CCGCACACACAAGCAGCC 62.333 66.667 0.00 0.00 0.00 4.85
1967 2155 3.282157 CGCACACACAAGCAGCCT 61.282 61.111 0.00 0.00 0.00 4.58
1968 2156 1.960763 CGCACACACAAGCAGCCTA 60.961 57.895 0.00 0.00 0.00 3.93
1969 2157 1.576421 GCACACACAAGCAGCCTAC 59.424 57.895 0.00 0.00 0.00 3.18
1970 2158 0.886490 GCACACACAAGCAGCCTACT 60.886 55.000 0.00 0.00 0.00 2.57
1971 2159 1.597742 CACACACAAGCAGCCTACTT 58.402 50.000 0.00 0.00 0.00 2.24
1972 2160 1.532868 CACACACAAGCAGCCTACTTC 59.467 52.381 0.00 0.00 0.00 3.01
1973 2161 0.792640 CACACAAGCAGCCTACTTCG 59.207 55.000 0.00 0.00 0.00 3.79
1974 2162 0.951040 ACACAAGCAGCCTACTTCGC 60.951 55.000 0.00 0.00 0.00 4.70
1975 2163 0.671781 CACAAGCAGCCTACTTCGCT 60.672 55.000 0.00 0.00 36.91 4.93
1979 2167 3.791539 CAGCCTACTTCGCTGCTG 58.208 61.111 0.00 0.00 46.54 4.41
1980 2168 2.125350 AGCCTACTTCGCTGCTGC 60.125 61.111 5.34 5.34 34.56 5.25
1981 2169 2.125350 GCCTACTTCGCTGCTGCT 60.125 61.111 14.03 0.00 36.97 4.24
1982 2170 2.170434 GCCTACTTCGCTGCTGCTC 61.170 63.158 14.03 0.00 36.97 4.26
1983 2171 1.520342 CCTACTTCGCTGCTGCTCC 60.520 63.158 14.03 0.00 36.97 4.70
1987 2175 3.954465 CTTCGCTGCTGCTCCTGCT 62.954 63.158 14.03 0.00 40.48 4.24
1997 2185 2.676463 GCTGCTCCTGCTATATGCCTAC 60.676 54.545 0.00 0.00 42.00 3.18
2073 2261 5.483583 AGTCTGAGCTAACCATCTCTTTCTT 59.516 40.000 0.00 0.00 0.00 2.52
2075 2263 4.256920 TGAGCTAACCATCTCTTTCTTGC 58.743 43.478 0.00 0.00 0.00 4.01
2114 2302 3.206964 CTTTCCCTTCTCCCGATAAAGC 58.793 50.000 0.00 0.00 0.00 3.51
2118 2306 2.158755 CCCTTCTCCCGATAAAGCACAT 60.159 50.000 0.00 0.00 0.00 3.21
2123 2311 0.506932 CCCGATAAAGCACATACGCG 59.493 55.000 3.53 3.53 36.85 6.01
2129 2351 2.521958 AAAGCACATACGCGCTCCCT 62.522 55.000 5.73 0.00 37.54 4.20
2217 2460 1.017387 GTATGCAGGCCTGTAAGTGC 58.983 55.000 32.81 19.41 34.40 4.40
2263 2506 3.883489 CTGCTAACCCAGTTAATTAGGCC 59.117 47.826 0.00 0.00 0.00 5.19
2356 2599 1.290203 ATATTGCCGACACAGAAGCG 58.710 50.000 0.00 0.00 0.00 4.68
2374 2617 0.388520 CGTCTGCGAGTTCCATCACA 60.389 55.000 0.00 0.00 41.33 3.58
2437 2680 9.346725 CTTTTGTCCTGAAAGATTATTGTTAGC 57.653 33.333 0.00 0.00 36.45 3.09
2443 2686 6.194796 TGAAAGATTATTGTTAGCCTGTGC 57.805 37.500 0.00 0.00 37.95 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
95 137 6.349777 CCACATCTACCTCTATTCCGATCTTC 60.350 46.154 0.00 0.00 0.00 2.87
149 228 2.076863 GCGATTAGCTGGTGTCTGTTT 58.923 47.619 0.00 0.00 44.04 2.83
355 455 1.447140 GACAATAGTGCCGCCGACA 60.447 57.895 0.00 0.00 0.00 4.35
367 467 3.442625 CAGTGTACTGGGAGACGACAATA 59.557 47.826 4.10 0.00 40.20 1.90
411 511 4.282703 GGTCCAAGTACAAGAACTACTGGA 59.717 45.833 0.00 0.00 0.00 3.86
447 547 1.202268 CCTTCTCCGACGACGCTAAAT 60.202 52.381 0.64 0.00 38.29 1.40
617 726 4.181010 CATGGAGGGGTGCCTCGG 62.181 72.222 0.00 0.00 37.68 4.63
618 727 4.181010 CCATGGAGGGGTGCCTCG 62.181 72.222 5.56 0.00 37.68 4.63
619 728 3.017581 ACCATGGAGGGGTGCCTC 61.018 66.667 21.47 0.00 43.89 4.70
626 737 0.613260 TTCGAGAACACCATGGAGGG 59.387 55.000 21.47 10.02 43.89 4.30
701 812 0.406361 AACGCCAACCCCTTCCATTA 59.594 50.000 0.00 0.00 0.00 1.90
704 815 2.203422 CAACGCCAACCCCTTCCA 60.203 61.111 0.00 0.00 0.00 3.53
764 881 5.163141 CCACTCCCTCTCTTCTCTCACTATA 60.163 48.000 0.00 0.00 0.00 1.31
784 901 1.652947 CCCACCACTACTTACCCACT 58.347 55.000 0.00 0.00 0.00 4.00
833 952 1.827681 TGACTGTCTCTCTTCCTCCG 58.172 55.000 9.51 0.00 0.00 4.63
844 967 1.276421 AGCTAAACGGCATGACTGTCT 59.724 47.619 9.51 0.00 36.64 3.41
862 986 5.818136 TGGCTTATTGAAGAACATGTAGC 57.182 39.130 0.00 0.22 34.25 3.58
870 994 6.149973 CACAGAGTTCATGGCTTATTGAAGAA 59.850 38.462 0.00 0.00 34.25 2.52
911 1035 1.325640 CCTCGATCTGCACACAATTCG 59.674 52.381 0.00 0.00 33.68 3.34
934 1058 2.484062 CCGTGCCCATCTCATTGCC 61.484 63.158 0.00 0.00 0.00 4.52
985 1112 0.465460 GGCATTGGATGAACGGGCTA 60.465 55.000 0.00 0.00 0.00 3.93
1049 1179 4.394078 CGTCGTCGCCAACCTCGA 62.394 66.667 0.00 0.00 0.00 4.04
1162 1292 0.391661 GGGATGCACTCAAGCTTCGA 60.392 55.000 0.00 0.00 38.98 3.71
1505 1647 7.469181 GCATAAGCCATAAACAGTCTAAAGCAT 60.469 37.037 0.00 0.00 33.58 3.79
1512 1654 5.887598 TCAATGCATAAGCCATAAACAGTCT 59.112 36.000 0.00 0.00 41.13 3.24
1513 1655 6.135290 TCAATGCATAAGCCATAAACAGTC 57.865 37.500 0.00 0.00 41.13 3.51
1525 1679 8.239314 ACACTTCATAACAGTTCAATGCATAAG 58.761 33.333 0.00 0.00 0.00 1.73
1647 1834 1.407025 GGCTAGTTGGTGAGCTTACCC 60.407 57.143 23.81 10.24 40.09 3.69
1653 1840 2.185004 TCTTTGGCTAGTTGGTGAGC 57.815 50.000 0.00 0.00 38.00 4.26
1673 1860 3.127589 CAACGTCTGGTGTGTGATAACA 58.872 45.455 0.00 0.00 0.00 2.41
1678 1865 0.179059 ATGCAACGTCTGGTGTGTGA 60.179 50.000 0.00 0.00 0.00 3.58
1744 1931 1.037030 CCACAGTGCCTGGTGTTTGT 61.037 55.000 0.00 0.00 35.51 2.83
1758 1945 1.162698 CTGCATGAGGTGAACCACAG 58.837 55.000 0.00 0.27 39.88 3.66
1794 1981 1.761449 TCTGCAAGTTGCTTGGTTGA 58.239 45.000 27.17 12.97 45.31 3.18
1899 2087 6.621613 CCTCAAGTTCTTTTATTTAGGGTGC 58.378 40.000 0.00 0.00 0.00 5.01
1909 2097 4.141482 ACACAGAGGCCTCAAGTTCTTTTA 60.141 41.667 33.90 0.00 0.00 1.52
1910 2098 3.217626 CACAGAGGCCTCAAGTTCTTTT 58.782 45.455 33.90 7.59 0.00 2.27
1911 2099 2.173569 ACACAGAGGCCTCAAGTTCTTT 59.826 45.455 33.90 8.39 0.00 2.52
1912 2100 1.771255 ACACAGAGGCCTCAAGTTCTT 59.229 47.619 33.90 14.90 0.00 2.52
1913 2101 1.346068 GACACAGAGGCCTCAAGTTCT 59.654 52.381 33.90 17.79 0.00 3.01
1914 2102 1.346068 AGACACAGAGGCCTCAAGTTC 59.654 52.381 33.90 25.14 0.00 3.01
1915 2103 1.346068 GAGACACAGAGGCCTCAAGTT 59.654 52.381 33.90 19.94 0.00 2.66
1916 2104 0.972883 GAGACACAGAGGCCTCAAGT 59.027 55.000 33.90 27.07 0.00 3.16
1917 2105 1.067000 CAGAGACACAGAGGCCTCAAG 60.067 57.143 33.90 26.41 0.00 3.02
1918 2106 0.972134 CAGAGACACAGAGGCCTCAA 59.028 55.000 33.90 0.00 0.00 3.02
1919 2107 0.902048 CCAGAGACACAGAGGCCTCA 60.902 60.000 33.90 0.00 0.00 3.86
1920 2108 1.612395 CCCAGAGACACAGAGGCCTC 61.612 65.000 26.22 26.22 0.00 4.70
1921 2109 1.611851 CCCAGAGACACAGAGGCCT 60.612 63.158 3.86 3.86 0.00 5.19
1922 2110 1.610673 TCCCAGAGACACAGAGGCC 60.611 63.158 0.00 0.00 0.00 5.19
1923 2111 1.594310 GTCCCAGAGACACAGAGGC 59.406 63.158 0.00 0.00 45.55 4.70
1931 2119 1.677637 GGTGATCCGGTCCCAGAGAC 61.678 65.000 0.00 0.00 45.51 3.36
1932 2120 1.381327 GGTGATCCGGTCCCAGAGA 60.381 63.158 0.00 0.00 0.00 3.10
1933 2121 3.221222 GGTGATCCGGTCCCAGAG 58.779 66.667 0.00 0.00 0.00 3.35
1943 2131 1.868997 CTTGTGTGTGCGGTGATCC 59.131 57.895 0.00 0.00 0.00 3.36
1944 2132 1.207593 GCTTGTGTGTGCGGTGATC 59.792 57.895 0.00 0.00 0.00 2.92
1945 2133 1.509644 CTGCTTGTGTGTGCGGTGAT 61.510 55.000 0.00 0.00 0.00 3.06
1946 2134 2.124942 TGCTTGTGTGTGCGGTGA 60.125 55.556 0.00 0.00 0.00 4.02
1947 2135 2.328989 CTGCTTGTGTGTGCGGTG 59.671 61.111 0.00 0.00 0.00 4.94
1948 2136 3.585990 GCTGCTTGTGTGTGCGGT 61.586 61.111 0.00 0.00 37.82 5.68
1949 2137 4.332637 GGCTGCTTGTGTGTGCGG 62.333 66.667 0.00 0.00 38.49 5.69
1950 2138 1.960763 TAGGCTGCTTGTGTGTGCG 60.961 57.895 0.00 0.00 0.00 5.34
1951 2139 0.886490 AGTAGGCTGCTTGTGTGTGC 60.886 55.000 0.00 0.00 0.00 4.57
1952 2140 1.532868 GAAGTAGGCTGCTTGTGTGTG 59.467 52.381 22.82 0.00 0.00 3.82
1953 2141 1.873903 CGAAGTAGGCTGCTTGTGTGT 60.874 52.381 22.82 0.00 0.00 3.72
1954 2142 0.792640 CGAAGTAGGCTGCTTGTGTG 59.207 55.000 22.82 5.91 0.00 3.82
1955 2143 0.951040 GCGAAGTAGGCTGCTTGTGT 60.951 55.000 22.82 0.00 0.00 3.72
1956 2144 0.671781 AGCGAAGTAGGCTGCTTGTG 60.672 55.000 22.82 14.93 39.77 3.33
1957 2145 1.674057 AGCGAAGTAGGCTGCTTGT 59.326 52.632 22.82 0.00 39.77 3.16
1958 2146 4.606071 AGCGAAGTAGGCTGCTTG 57.394 55.556 22.82 14.82 39.77 4.01
1963 2151 2.125350 GCAGCAGCGAAGTAGGCT 60.125 61.111 0.00 0.00 42.61 4.58
1973 2161 1.440708 CATATAGCAGGAGCAGCAGC 58.559 55.000 0.00 0.00 45.49 5.25
1974 2162 1.440708 GCATATAGCAGGAGCAGCAG 58.559 55.000 0.00 0.00 45.49 4.24
1975 2163 3.620061 GCATATAGCAGGAGCAGCA 57.380 52.632 0.00 0.00 45.49 4.41
1977 2165 6.959456 CATATGTAGGCATATAGCAGGAGCAG 60.959 46.154 0.00 0.00 44.12 4.24
1978 2166 5.163374 CATATGTAGGCATATAGCAGGAGCA 60.163 44.000 0.00 0.00 44.12 4.26
1979 2167 5.163364 ACATATGTAGGCATATAGCAGGAGC 60.163 44.000 6.56 0.00 44.12 4.70
1980 2168 6.127225 ACACATATGTAGGCATATAGCAGGAG 60.127 42.308 8.32 0.00 44.12 3.69
1981 2169 5.721480 ACACATATGTAGGCATATAGCAGGA 59.279 40.000 8.32 0.00 44.12 3.86
1982 2170 5.982356 ACACATATGTAGGCATATAGCAGG 58.018 41.667 8.32 0.00 44.12 4.85
1983 2171 7.547227 TGTACACATATGTAGGCATATAGCAG 58.453 38.462 8.32 0.00 44.12 4.24
1987 2175 9.030452 TCACATGTACACATATGTAGGCATATA 57.970 33.333 8.32 0.00 44.12 0.86
1997 2185 8.702163 TTAGTTCAGTCACATGTACACATATG 57.298 34.615 0.00 0.00 34.26 1.78
2073 2261 1.000060 GTTGGAAGCAAAGCATGAGCA 60.000 47.619 0.00 0.00 45.49 4.26
2075 2263 3.655276 AAGTTGGAAGCAAAGCATGAG 57.345 42.857 0.00 0.00 0.00 2.90
2114 2302 0.729478 CGATAGGGAGCGCGTATGTG 60.729 60.000 8.43 0.00 0.00 3.21
2118 2306 0.029834 GTTTCGATAGGGAGCGCGTA 59.970 55.000 8.43 0.00 33.48 4.42
2129 2351 0.671163 ACGCAAAGCCCGTTTCGATA 60.671 50.000 0.00 0.00 34.96 2.92
2217 2460 0.668706 CTGGTTCTGCTCAGTGGACG 60.669 60.000 0.00 0.00 0.00 4.79
2356 2599 1.071605 GTGTGATGGAACTCGCAGAC 58.928 55.000 0.00 0.00 36.39 3.51
2393 2636 4.483476 AAAGAAAGAATCGTTCGTTGGG 57.517 40.909 8.88 0.00 31.54 4.12
2437 2680 2.030185 ACAACTGAGTAGTACGCACAGG 60.030 50.000 20.40 9.11 35.69 4.00
2443 2686 8.182881 AGAGCTAATTAACAACTGAGTAGTACG 58.817 37.037 0.00 0.00 35.69 3.67


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

AutoCloner maintained by Alex Coulton.