Multiple sequence alignment - TraesCS6D01G397100

Loading Multiple Alignment...

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 TraesCS6D01G397100 chr6D 100.000 2288 0 0 1 2288 469235211 469237498 0.000000e+00 4226.0
1 TraesCS6D01G397100 chr6D 93.801 1710 85 4 1 1690 450905953 450907661 0.000000e+00 2551.0
2 TraesCS6D01G397100 chr6D 92.212 1605 111 5 1 1601 305745358 305746952 0.000000e+00 2259.0
3 TraesCS6D01G397100 chr6D 81.028 253 20 14 1764 2001 469207668 469207907 2.340000e-40 176.0
4 TraesCS6D01G397100 chr6D 79.070 129 15 8 1913 2033 469214153 469214277 6.780000e-11 78.7
5 TraesCS6D01G397100 chr4B 91.633 1709 117 9 1 1684 551784706 551786413 0.000000e+00 2340.0
6 TraesCS6D01G397100 chr7B 91.472 1712 118 9 1 1690 150842105 150843810 0.000000e+00 2327.0
7 TraesCS6D01G397100 chr7D 91.370 1715 122 10 1 1690 463975836 463974123 0.000000e+00 2324.0
8 TraesCS6D01G397100 chr7D 90.983 1719 126 7 1 1690 107722777 107721059 0.000000e+00 2289.0
9 TraesCS6D01G397100 chr7D 90.000 210 4 3 1497 1690 182493704 182493912 2.920000e-64 255.0
10 TraesCS6D01G397100 chr4A 90.409 1710 137 10 1 1690 19185948 19184246 0.000000e+00 2224.0
11 TraesCS6D01G397100 chr2B 90.338 1718 131 17 1 1690 459481030 459479320 0.000000e+00 2220.0
12 TraesCS6D01G397100 chr3A 89.977 1716 139 13 2 1690 418765665 418763956 0.000000e+00 2185.0
13 TraesCS6D01G397100 chr4D 91.394 1592 106 11 127 1690 56941670 56943258 0.000000e+00 2152.0
14 TraesCS6D01G397100 chr4D 89.284 1717 145 16 1 1690 116524563 116522859 0.000000e+00 2115.0
15 TraesCS6D01G397100 chr5B 89.558 1695 154 16 1 1680 407222536 407224222 0.000000e+00 2128.0
16 TraesCS6D01G397100 chr1D 89.750 839 58 11 877 1690 429021017 429021852 0.000000e+00 1048.0
17 TraesCS6D01G397100 chr1B 92.530 415 14 3 1292 1690 684578734 684579147 1.520000e-161 579.0
18 TraesCS6D01G397100 chr6A 87.108 287 11 6 1689 1961 614404859 614405133 3.690000e-78 302.0
19 TraesCS6D01G397100 chr6A 87.907 215 9 9 1727 1927 614390791 614391002 1.060000e-58 237.0
20 TraesCS6D01G397100 chr6A 83.065 248 18 15 1697 1933 614385810 614386044 1.070000e-48 204.0
21 TraesCS6D01G397100 chr6A 92.742 124 9 0 2088 2211 614405253 614405376 1.810000e-41 180.0
22 TraesCS6D01G397100 chr6A 100.000 29 0 0 1965 1993 614391030 614391058 1.000000e-03 54.7
23 TraesCS6D01G397100 chr6B 90.066 151 13 2 2089 2238 715511508 715511657 6.450000e-46 195.0


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 TraesCS6D01G397100 chr6D 469235211 469237498 2287 False 4226 4226 100.000 1 2288 1 chr6D.!!$F5 2287
1 TraesCS6D01G397100 chr6D 450905953 450907661 1708 False 2551 2551 93.801 1 1690 1 chr6D.!!$F2 1689
2 TraesCS6D01G397100 chr6D 305745358 305746952 1594 False 2259 2259 92.212 1 1601 1 chr6D.!!$F1 1600
3 TraesCS6D01G397100 chr4B 551784706 551786413 1707 False 2340 2340 91.633 1 1684 1 chr4B.!!$F1 1683
4 TraesCS6D01G397100 chr7B 150842105 150843810 1705 False 2327 2327 91.472 1 1690 1 chr7B.!!$F1 1689
5 TraesCS6D01G397100 chr7D 463974123 463975836 1713 True 2324 2324 91.370 1 1690 1 chr7D.!!$R2 1689
6 TraesCS6D01G397100 chr7D 107721059 107722777 1718 True 2289 2289 90.983 1 1690 1 chr7D.!!$R1 1689
7 TraesCS6D01G397100 chr4A 19184246 19185948 1702 True 2224 2224 90.409 1 1690 1 chr4A.!!$R1 1689
8 TraesCS6D01G397100 chr2B 459479320 459481030 1710 True 2220 2220 90.338 1 1690 1 chr2B.!!$R1 1689
9 TraesCS6D01G397100 chr3A 418763956 418765665 1709 True 2185 2185 89.977 2 1690 1 chr3A.!!$R1 1688
10 TraesCS6D01G397100 chr4D 56941670 56943258 1588 False 2152 2152 91.394 127 1690 1 chr4D.!!$F1 1563
11 TraesCS6D01G397100 chr4D 116522859 116524563 1704 True 2115 2115 89.284 1 1690 1 chr4D.!!$R1 1689
12 TraesCS6D01G397100 chr5B 407222536 407224222 1686 False 2128 2128 89.558 1 1680 1 chr5B.!!$F1 1679
13 TraesCS6D01G397100 chr1D 429021017 429021852 835 False 1048 1048 89.750 877 1690 1 chr1D.!!$F1 813
14 TraesCS6D01G397100 chr6A 614404859 614405376 517 False 241 302 89.925 1689 2211 2 chr6A.!!$F3 522

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
875 892 0.250295 CCAAAGACGCCTGAGGTTGA 60.25 55.0 0.0 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2050 2125 0.031994 CTTTTGAACCTTGGTGGGCG 59.968 55.0 0.0 0.0 41.11 6.13 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
34 35 0.976641 TCGAGTGTCTGGCCTTCATT 59.023 50.000 3.32 0.00 0.00 2.57
78 82 1.659794 GCGGGTCATTGTTGCTGTT 59.340 52.632 0.00 0.00 0.00 3.16
213 217 3.136763 CGATAGCCGTCTCCTAGTACAA 58.863 50.000 0.00 0.00 0.00 2.41
266 270 3.400255 GTCTTGTACTTGGACCACTTCC 58.600 50.000 0.00 0.00 46.13 3.46
324 328 1.293924 GCCCAGTGAATGATGTCGAG 58.706 55.000 0.00 0.00 0.00 4.04
391 396 2.226315 TGCAGTGGCCCTCATGAGT 61.226 57.895 21.11 0.00 40.13 3.41
405 410 5.366460 CCTCATGAGTACTGCATCAGATTT 58.634 41.667 21.11 0.00 35.18 2.17
436 444 1.091771 CAGGCATGGCGAAGTTCGAT 61.092 55.000 28.66 11.39 43.74 3.59
468 476 1.295792 GTGTTCTCGAACTTGGTGCA 58.704 50.000 10.75 0.00 41.67 4.57
472 480 0.750249 TCTCGAACTTGGTGCAGTCA 59.250 50.000 0.00 0.00 0.00 3.41
473 481 0.861837 CTCGAACTTGGTGCAGTCAC 59.138 55.000 0.00 0.00 42.40 3.67
474 482 0.464036 TCGAACTTGGTGCAGTCACT 59.536 50.000 0.00 0.00 42.72 3.41
485 496 1.878656 GCAGTCACTAGCCGACCACT 61.879 60.000 8.83 0.00 33.70 4.00
541 553 2.268920 GGGTCGCATTGGAGCTGA 59.731 61.111 0.00 0.00 34.90 4.26
640 652 3.583086 AGGGTGAGTAAATATAGGCGCAT 59.417 43.478 10.83 3.98 0.00 4.73
649 661 1.717032 TATAGGCGCATTGGAGAGGT 58.283 50.000 10.83 0.00 0.00 3.85
655 669 0.745845 CGCATTGGAGAGGTGGAAGG 60.746 60.000 0.00 0.00 0.00 3.46
706 720 4.036144 GCTCTTCAATAAGCCATGAACTCC 59.964 45.833 0.00 0.00 32.46 3.85
712 726 0.674895 AAGCCATGAACTCCGTGCTC 60.675 55.000 0.00 0.00 0.00 4.26
875 892 0.250295 CCAAAGACGCCTGAGGTTGA 60.250 55.000 0.00 0.00 0.00 3.18
940 962 1.341679 ACTACGGCCACTACCATCAGA 60.342 52.381 2.24 0.00 0.00 3.27
999 1022 1.462616 CGAAGGTTGAATGCATCCCA 58.537 50.000 0.00 0.00 34.95 4.37
1160 1183 2.606725 CAGCCGTTCATCAGATCAAGAC 59.393 50.000 0.00 0.00 0.00 3.01
1288 1311 1.945354 CTTCGCCGCCAAGGACTAGA 61.945 60.000 0.00 0.00 45.00 2.43
1292 1316 2.105128 CGCCAAGGACTAGAGCCG 59.895 66.667 0.00 0.00 0.00 5.52
1325 1350 6.099413 TCCTTCCTAAGTACTATCGAGTCTGA 59.901 42.308 0.00 0.00 37.10 3.27
1406 1450 9.371136 TCTGAATTATGCTGTTAAGTAGTTGAG 57.629 33.333 0.00 0.00 0.00 3.02
1588 1634 0.469917 ACCAGACAGTGTGGTTCAGG 59.530 55.000 16.80 0.00 46.73 3.86
1674 1736 3.944015 GAGTTGAGAAGGCTATGCAATGT 59.056 43.478 0.00 0.00 0.00 2.71
1690 1752 6.961360 TGCAATGTAGCTACTGTAGACTAT 57.039 37.500 23.84 4.47 34.99 2.12
1691 1753 8.637196 ATGCAATGTAGCTACTGTAGACTATA 57.363 34.615 23.84 15.50 34.99 1.31
1692 1754 8.637196 TGCAATGTAGCTACTGTAGACTATAT 57.363 34.615 23.84 16.75 34.99 0.86
1809 1871 2.285256 CGAATGAATCGCGACCTTTCTG 60.285 50.000 12.93 12.02 45.89 3.02
1810 1872 1.656652 ATGAATCGCGACCTTTCTGG 58.343 50.000 12.93 0.00 42.93 3.86
1823 1885 3.718434 ACCTTTCTGGGCATGATGATAGA 59.282 43.478 0.00 0.00 41.11 1.98
1824 1886 4.353191 ACCTTTCTGGGCATGATGATAGAT 59.647 41.667 0.00 0.00 41.11 1.98
1825 1887 5.549228 ACCTTTCTGGGCATGATGATAGATA 59.451 40.000 0.00 0.00 41.11 1.98
1826 1888 6.114089 CCTTTCTGGGCATGATGATAGATAG 58.886 44.000 0.00 1.32 0.00 2.08
1827 1889 6.070366 CCTTTCTGGGCATGATGATAGATAGA 60.070 42.308 0.00 0.00 0.00 1.98
1828 1890 7.365742 CCTTTCTGGGCATGATGATAGATAGAT 60.366 40.741 0.00 0.00 0.00 1.98
1829 1891 8.613922 TTTCTGGGCATGATGATAGATAGATA 57.386 34.615 0.00 0.00 0.00 1.98
1830 1892 8.794364 TTCTGGGCATGATGATAGATAGATAT 57.206 34.615 0.00 0.00 0.00 1.63
1831 1893 9.887862 TTCTGGGCATGATGATAGATAGATATA 57.112 33.333 0.00 0.00 0.00 0.86
1853 1915 5.886960 ATATAATCTGGCATCTTTTCCGC 57.113 39.130 0.00 0.00 0.00 5.54
1868 1930 2.249535 CCGCGCTGGATGGATTCAG 61.250 63.158 12.11 0.00 42.00 3.02
1898 1968 4.384247 TGTCTGCTTGTTTTGTTTGTTTCG 59.616 37.500 0.00 0.00 0.00 3.46
1903 1973 3.026630 TGTTTTGTTTGTTTCGGTGCA 57.973 38.095 0.00 0.00 0.00 4.57
1929 1999 3.990318 AACTGTTGCCTGAAGCTTTAC 57.010 42.857 0.00 0.00 44.23 2.01
1961 2036 3.678548 GCAGTAGTAAACCTTTCGTCTGG 59.321 47.826 0.00 0.00 0.00 3.86
1963 2038 4.684703 CAGTAGTAAACCTTTCGTCTGGTG 59.315 45.833 0.00 0.00 36.57 4.17
1964 2039 3.832615 AGTAAACCTTTCGTCTGGTGT 57.167 42.857 0.00 0.00 36.57 4.16
1966 2041 1.578583 AAACCTTTCGTCTGGTGTCG 58.421 50.000 0.00 0.00 36.57 4.35
1968 2043 0.031721 ACCTTTCGTCTGGTGTCGTC 59.968 55.000 0.00 0.00 34.90 4.20
1970 2045 1.666311 CCTTTCGTCTGGTGTCGTCTC 60.666 57.143 0.00 0.00 0.00 3.36
1971 2046 0.040692 TTTCGTCTGGTGTCGTCTCG 60.041 55.000 0.00 0.00 0.00 4.04
1974 2049 1.566882 CGTCTGGTGTCGTCTCGTCT 61.567 60.000 0.00 0.00 0.00 4.18
1976 2051 0.250166 TCTGGTGTCGTCTCGTCTCA 60.250 55.000 0.00 0.00 0.00 3.27
1978 2053 0.250166 TGGTGTCGTCTCGTCTCAGA 60.250 55.000 0.00 0.00 0.00 3.27
1979 2054 1.088306 GGTGTCGTCTCGTCTCAGAT 58.912 55.000 0.00 0.00 0.00 2.90
1980 2055 1.202087 GGTGTCGTCTCGTCTCAGATG 60.202 57.143 0.00 0.00 0.00 2.90
1981 2056 1.465387 GTGTCGTCTCGTCTCAGATGT 59.535 52.381 0.00 0.00 32.06 3.06
1982 2057 2.095668 GTGTCGTCTCGTCTCAGATGTT 60.096 50.000 0.00 0.00 32.06 2.71
1983 2058 2.159824 TGTCGTCTCGTCTCAGATGTTC 59.840 50.000 0.00 0.00 32.06 3.18
1984 2059 2.159824 GTCGTCTCGTCTCAGATGTTCA 59.840 50.000 0.00 0.00 32.06 3.18
1985 2060 2.159824 TCGTCTCGTCTCAGATGTTCAC 59.840 50.000 0.00 0.00 32.06 3.18
1987 2062 3.238441 GTCTCGTCTCAGATGTTCACAC 58.762 50.000 0.00 0.00 0.00 3.82
1988 2063 2.229062 TCTCGTCTCAGATGTTCACACC 59.771 50.000 0.00 0.00 0.00 4.16
1991 2066 2.693069 GTCTCAGATGTTCACACCAGG 58.307 52.381 0.00 0.00 0.00 4.45
1992 2067 2.037772 GTCTCAGATGTTCACACCAGGT 59.962 50.000 0.00 0.00 0.00 4.00
1995 2070 2.172505 TCAGATGTTCACACCAGGTGTT 59.827 45.455 23.68 8.15 45.08 3.32
1997 2072 1.531149 GATGTTCACACCAGGTGTTCG 59.469 52.381 23.68 13.02 45.08 3.95
1998 2073 0.250793 TGTTCACACCAGGTGTTCGT 59.749 50.000 23.68 0.00 45.08 3.85
1999 2074 1.481363 TGTTCACACCAGGTGTTCGTA 59.519 47.619 23.68 7.42 45.08 3.43
2000 2075 2.093606 TGTTCACACCAGGTGTTCGTAA 60.094 45.455 23.68 11.84 45.08 3.18
2001 2076 2.937799 GTTCACACCAGGTGTTCGTAAA 59.062 45.455 23.68 9.44 45.08 2.01
2003 2078 2.937799 TCACACCAGGTGTTCGTAAAAC 59.062 45.455 23.68 0.00 45.08 2.43
2005 2080 1.262151 CACCAGGTGTTCGTAAAACGG 59.738 52.381 11.99 0.00 42.81 4.44
2007 2082 1.540797 CCAGGTGTTCGTAAAACGGGA 60.541 52.381 0.00 0.00 42.81 5.14
2008 2083 2.419667 CAGGTGTTCGTAAAACGGGAT 58.580 47.619 0.00 0.00 42.81 3.85
2010 2085 3.368843 CAGGTGTTCGTAAAACGGGATAC 59.631 47.826 0.00 0.00 42.81 2.24
2032 2107 1.117994 GTAGTACTACCAGCACCCCC 58.882 60.000 20.47 0.00 0.00 5.40
2034 2109 1.986210 GTACTACCAGCACCCCCGT 60.986 63.158 0.00 0.00 0.00 5.28
2035 2110 1.683365 TACTACCAGCACCCCCGTC 60.683 63.158 0.00 0.00 0.00 4.79
2036 2111 2.444004 TACTACCAGCACCCCCGTCA 62.444 60.000 0.00 0.00 0.00 4.35
2037 2112 2.285069 TACCAGCACCCCCGTCAT 60.285 61.111 0.00 0.00 0.00 3.06
2038 2113 2.311688 CTACCAGCACCCCCGTCATC 62.312 65.000 0.00 0.00 0.00 2.92
2039 2114 4.838152 CCAGCACCCCCGTCATCG 62.838 72.222 0.00 0.00 0.00 3.84
2040 2115 3.770040 CAGCACCCCCGTCATCGA 61.770 66.667 0.00 0.00 39.71 3.59
2042 2117 2.588877 GCACCCCCGTCATCGATG 60.589 66.667 19.61 19.61 39.71 3.84
2043 2118 2.108976 CACCCCCGTCATCGATGG 59.891 66.667 24.61 10.45 38.38 3.51
2048 2123 4.954933 CCGTCATCGATGGGGTTT 57.045 55.556 24.61 0.00 39.71 3.27
2050 2125 1.714899 CCGTCATCGATGGGGTTTGC 61.715 60.000 24.61 6.39 39.71 3.68
2051 2126 1.721487 GTCATCGATGGGGTTTGCG 59.279 57.895 24.61 0.00 0.00 4.85
2053 2128 2.828549 ATCGATGGGGTTTGCGCC 60.829 61.111 4.18 0.00 46.74 6.53
2061 2136 3.989787 GGTTTGCGCCCACCAAGG 61.990 66.667 17.96 0.00 32.74 3.61
2062 2137 3.223589 GTTTGCGCCCACCAAGGT 61.224 61.111 4.18 0.00 34.66 3.50
2063 2138 2.443016 TTTGCGCCCACCAAGGTT 60.443 55.556 4.18 0.00 34.66 3.50
2064 2139 2.494530 TTTGCGCCCACCAAGGTTC 61.495 57.895 4.18 0.00 34.66 3.62
2065 2140 3.723097 TTGCGCCCACCAAGGTTCA 62.723 57.895 4.18 0.00 34.66 3.18
2066 2141 2.909965 GCGCCCACCAAGGTTCAA 60.910 61.111 0.00 0.00 34.66 2.69
2067 2142 2.494530 GCGCCCACCAAGGTTCAAA 61.495 57.895 0.00 0.00 34.66 2.69
2068 2143 2.022240 GCGCCCACCAAGGTTCAAAA 62.022 55.000 0.00 0.00 34.66 2.44
2069 2144 0.031994 CGCCCACCAAGGTTCAAAAG 59.968 55.000 0.00 0.00 34.66 2.27
2071 2146 1.413118 CCCACCAAGGTTCAAAAGCT 58.587 50.000 0.00 0.00 41.85 3.74
2072 2147 2.593026 CCCACCAAGGTTCAAAAGCTA 58.407 47.619 0.00 0.00 38.49 3.32
2073 2148 3.165071 CCCACCAAGGTTCAAAAGCTAT 58.835 45.455 0.00 0.00 38.49 2.97
2075 2150 3.119849 CCACCAAGGTTCAAAAGCTATCG 60.120 47.826 0.00 0.00 38.49 2.92
2076 2151 2.488153 ACCAAGGTTCAAAAGCTATCGC 59.512 45.455 0.00 0.00 38.49 4.58
2077 2152 2.476185 CCAAGGTTCAAAAGCTATCGCG 60.476 50.000 0.00 0.00 42.32 5.87
2080 2155 0.446222 GTTCAAAAGCTATCGCGGCA 59.554 50.000 6.13 0.00 42.32 5.69
2081 2156 0.726827 TTCAAAAGCTATCGCGGCAG 59.273 50.000 6.13 4.72 42.32 4.85
2082 2157 1.089481 TCAAAAGCTATCGCGGCAGG 61.089 55.000 6.13 0.00 42.32 4.85
2083 2158 1.078426 AAAAGCTATCGCGGCAGGT 60.078 52.632 6.13 6.51 42.32 4.00
2084 2159 1.369091 AAAAGCTATCGCGGCAGGTG 61.369 55.000 6.13 0.00 42.32 4.00
2085 2160 2.521958 AAAGCTATCGCGGCAGGTGT 62.522 55.000 6.13 1.11 42.32 4.16
2086 2161 1.672854 AAGCTATCGCGGCAGGTGTA 61.673 55.000 6.13 0.00 42.32 2.90
2130 2205 2.202919 CATCTCATCACGCCGGCA 60.203 61.111 28.98 7.49 0.00 5.69
2140 2215 2.114670 ACGCCGGCAATGATTCCTG 61.115 57.895 28.98 8.28 0.00 3.86
2154 2229 0.472471 TTCCTGGCGGAAAAGTCTGT 59.528 50.000 8.09 0.00 46.11 3.41
2161 2236 1.876416 GCGGAAAAGTCTGTACCTGCA 60.876 52.381 0.00 0.00 32.14 4.41
2162 2237 1.798813 CGGAAAAGTCTGTACCTGCAC 59.201 52.381 0.00 0.00 0.00 4.57
2189 2264 2.885113 CTGTCGACCGCTCCATCA 59.115 61.111 14.12 0.00 0.00 3.07
2196 2271 4.598894 CCGCTCCATCAGGCTCGG 62.599 72.222 0.00 0.00 40.95 4.63
2200 2275 3.781770 CTCCATCAGGCTCGGCGTC 62.782 68.421 6.85 0.00 33.74 5.19
2215 2290 3.994853 GTCCGTCCGTTTCCCCGT 61.995 66.667 0.00 0.00 0.00 5.28
2216 2291 3.993584 TCCGTCCGTTTCCCCGTG 61.994 66.667 0.00 0.00 0.00 4.94
2223 2298 3.781162 GTTTCCCCGTGCGCGTAC 61.781 66.667 17.94 17.94 36.15 3.67
2257 2332 9.229784 GTACTACTGTACGTACGTAGTATTACA 57.770 37.037 37.38 27.87 42.77 2.41
2267 2342 4.125703 ACGTAGTATTACAGAGGAGTCGG 58.874 47.826 0.00 0.00 41.94 4.79
2268 2343 3.497640 CGTAGTATTACAGAGGAGTCGGG 59.502 52.174 0.00 0.00 0.00 5.14
2269 2344 2.946785 AGTATTACAGAGGAGTCGGGG 58.053 52.381 0.00 0.00 0.00 5.73
2270 2345 2.244252 AGTATTACAGAGGAGTCGGGGT 59.756 50.000 0.00 0.00 0.00 4.95
2271 2346 1.777941 ATTACAGAGGAGTCGGGGTC 58.222 55.000 0.00 0.00 0.00 4.46
2272 2347 0.324091 TTACAGAGGAGTCGGGGTCC 60.324 60.000 0.00 0.00 0.00 4.46
2274 2349 1.305381 CAGAGGAGTCGGGGTCCTT 60.305 63.158 3.10 0.00 45.00 3.36
2275 2350 0.905337 CAGAGGAGTCGGGGTCCTTT 60.905 60.000 3.10 0.00 45.00 3.11
2276 2351 0.615261 AGAGGAGTCGGGGTCCTTTC 60.615 60.000 3.10 0.00 45.00 2.62
2277 2352 1.612739 AGGAGTCGGGGTCCTTTCC 60.613 63.158 0.00 0.00 42.12 3.13
2278 2353 1.612739 GGAGTCGGGGTCCTTTCCT 60.613 63.158 0.00 0.00 0.00 3.36
2279 2354 1.597461 GAGTCGGGGTCCTTTCCTG 59.403 63.158 0.00 0.00 0.00 3.86
2280 2355 1.152096 AGTCGGGGTCCTTTCCTGT 60.152 57.895 0.00 0.00 32.62 4.00
2281 2356 0.115745 AGTCGGGGTCCTTTCCTGTA 59.884 55.000 0.00 0.00 32.62 2.74
2282 2357 0.978907 GTCGGGGTCCTTTCCTGTAA 59.021 55.000 0.00 0.00 32.62 2.41
2283 2358 1.348696 GTCGGGGTCCTTTCCTGTAAA 59.651 52.381 0.00 0.00 32.62 2.01
2284 2359 1.348696 TCGGGGTCCTTTCCTGTAAAC 59.651 52.381 0.00 0.00 32.62 2.01
2285 2360 1.072648 CGGGGTCCTTTCCTGTAAACA 59.927 52.381 0.00 0.00 0.00 2.83
2286 2361 2.290705 CGGGGTCCTTTCCTGTAAACAT 60.291 50.000 0.00 0.00 0.00 2.71
2287 2362 3.054948 CGGGGTCCTTTCCTGTAAACATA 60.055 47.826 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 3.157087 GGACAAGAAAATGAAGGCCAGA 58.843 45.455 5.01 0.00 0.00 3.86
34 35 1.811965 CACATGGCGATGGACAAGAAA 59.188 47.619 13.62 0.00 32.52 2.52
69 70 0.249868 CGACTCCTCCAACAGCAACA 60.250 55.000 0.00 0.00 0.00 3.33
72 73 1.536073 CCTCGACTCCTCCAACAGCA 61.536 60.000 0.00 0.00 0.00 4.41
78 82 3.075186 TCGACCTCGACTCCTCCA 58.925 61.111 0.00 0.00 44.22 3.86
134 138 0.674895 GAAGAACCGGTGCAGATGCT 60.675 55.000 16.99 0.00 42.66 3.79
213 217 2.566057 TAATGACCGTCGTGCCGCAT 62.566 55.000 0.00 0.00 0.00 4.73
266 270 0.784778 GACGACGCAAAACAGAGGAG 59.215 55.000 0.00 0.00 0.00 3.69
347 351 1.734465 GCTGAAGACGTTGATTCCTGG 59.266 52.381 0.00 0.00 0.00 4.45
468 476 1.306642 CGAGTGGTCGGCTAGTGACT 61.307 60.000 14.32 0.00 42.87 3.41
472 480 1.749638 CCTCGAGTGGTCGGCTAGT 60.750 63.158 12.31 0.00 46.80 2.57
473 481 1.030488 TTCCTCGAGTGGTCGGCTAG 61.030 60.000 12.31 0.00 46.80 3.42
474 482 1.001764 TTCCTCGAGTGGTCGGCTA 60.002 57.895 12.31 0.00 46.80 3.93
485 496 4.035843 GAGGGCCTTCTTCCTCGA 57.964 61.111 7.89 0.00 39.95 4.04
640 652 0.104672 TCACCCTTCCACCTCTCCAA 60.105 55.000 0.00 0.00 0.00 3.53
649 661 0.036732 GCATGACTGTCACCCTTCCA 59.963 55.000 13.50 0.00 0.00 3.53
655 669 0.951558 AAAACGGCATGACTGTCACC 59.048 50.000 13.50 9.88 36.64 4.02
706 720 2.125753 GGAGTCAGGCAGAGCACG 60.126 66.667 0.00 0.00 0.00 5.34
712 726 2.422479 CACAATTCATGGAGTCAGGCAG 59.578 50.000 0.00 0.00 0.00 4.85
847 864 0.611714 GGCGTCTTTGGGTCTTCCTA 59.388 55.000 0.00 0.00 36.20 2.94
875 892 4.129737 CCATGCCCTCGTCGTCGT 62.130 66.667 1.33 0.00 38.33 4.34
940 962 0.779997 AAGTGAGTTGGGCCATCCTT 59.220 50.000 7.26 6.09 36.20 3.36
999 1022 1.384191 GGTGAAGTCCAGGGGCATT 59.616 57.895 0.00 0.00 0.00 3.56
1121 1144 4.770874 CGTAGGTGGCCCAACCCG 62.771 72.222 8.63 2.90 41.54 5.28
1160 1183 0.462047 GAAGGTCACCATGTAGCCGG 60.462 60.000 0.00 0.00 0.00 6.13
1292 1316 0.914902 ACTTAGGAAGGAGGTGCCCC 60.915 60.000 0.00 0.00 37.37 5.80
1325 1350 7.375053 ACGCATAAACCATAAACAGTTCAAAT 58.625 30.769 0.00 0.00 0.00 2.32
1406 1450 4.367450 CAGAGCAGAGTATAAACAGAGCC 58.633 47.826 0.00 0.00 0.00 4.70
1690 1752 5.407387 CGTCTGCATGACAATCATCATCATA 59.593 40.000 14.09 0.00 45.60 2.15
1691 1753 4.213482 CGTCTGCATGACAATCATCATCAT 59.787 41.667 14.09 0.00 45.60 2.45
1692 1754 3.558418 CGTCTGCATGACAATCATCATCA 59.442 43.478 14.09 0.00 45.60 3.07
1742 1804 1.280998 GGCCCAGCTTTCTACCACTTA 59.719 52.381 0.00 0.00 0.00 2.24
1746 1808 0.480690 TTTGGCCCAGCTTTCTACCA 59.519 50.000 0.00 0.00 0.00 3.25
1801 1863 3.718434 TCTATCATCATGCCCAGAAAGGT 59.282 43.478 0.00 0.00 34.66 3.50
1827 1889 9.277783 GCGGAAAAGATGCCAGATTATATATAT 57.722 33.333 0.00 0.00 0.00 0.86
1828 1890 7.438160 CGCGGAAAAGATGCCAGATTATATATA 59.562 37.037 0.00 0.00 0.00 0.86
1829 1891 6.258727 CGCGGAAAAGATGCCAGATTATATAT 59.741 38.462 0.00 0.00 0.00 0.86
1830 1892 5.580691 CGCGGAAAAGATGCCAGATTATATA 59.419 40.000 0.00 0.00 0.00 0.86
1831 1893 4.393062 CGCGGAAAAGATGCCAGATTATAT 59.607 41.667 0.00 0.00 0.00 0.86
1832 1894 3.745975 CGCGGAAAAGATGCCAGATTATA 59.254 43.478 0.00 0.00 0.00 0.98
1851 1913 2.890109 GCTGAATCCATCCAGCGCG 61.890 63.158 0.00 0.00 44.99 6.86
1852 1914 3.028969 GCTGAATCCATCCAGCGC 58.971 61.111 0.00 0.00 44.99 5.92
1868 1930 3.111098 CAAAACAAGCAGACAGACAAGC 58.889 45.455 0.00 0.00 0.00 4.01
1898 1968 2.100749 AGGCAACAGTTAAACTTGCACC 59.899 45.455 12.57 0.00 34.52 5.01
1903 1973 3.954258 AGCTTCAGGCAACAGTTAAACTT 59.046 39.130 0.00 0.00 44.79 2.66
1929 1999 3.124636 GGTTTACTACTGCGGTGTGATTG 59.875 47.826 8.92 0.00 0.00 2.67
1961 2036 1.465387 ACATCTGAGACGAGACGACAC 59.535 52.381 0.00 0.00 0.00 3.67
1963 2038 2.159824 TGAACATCTGAGACGAGACGAC 59.840 50.000 0.00 0.00 0.00 4.34
1964 2039 2.159824 GTGAACATCTGAGACGAGACGA 59.840 50.000 0.00 0.00 0.00 4.20
1966 2041 3.238441 GTGTGAACATCTGAGACGAGAC 58.762 50.000 0.00 0.00 0.00 3.36
1968 2043 2.029918 TGGTGTGAACATCTGAGACGAG 60.030 50.000 0.00 0.00 0.00 4.18
1970 2045 2.332104 CTGGTGTGAACATCTGAGACG 58.668 52.381 0.00 0.00 0.00 4.18
1971 2046 2.037772 ACCTGGTGTGAACATCTGAGAC 59.962 50.000 0.00 0.00 0.00 3.36
1974 2049 2.172505 AACACCTGGTGTGAACATCTGA 59.827 45.455 31.55 0.00 46.79 3.27
1976 2051 2.806745 CGAACACCTGGTGTGAACATCT 60.807 50.000 31.55 15.13 46.79 2.90
1978 2053 1.134220 ACGAACACCTGGTGTGAACAT 60.134 47.619 31.55 16.63 46.79 2.71
1979 2054 0.250793 ACGAACACCTGGTGTGAACA 59.749 50.000 31.55 0.00 46.79 3.18
1980 2055 2.228138 TACGAACACCTGGTGTGAAC 57.772 50.000 31.55 22.73 46.79 3.18
1981 2056 2.983907 TTACGAACACCTGGTGTGAA 57.016 45.000 31.55 19.68 46.79 3.18
1982 2057 2.937799 GTTTTACGAACACCTGGTGTGA 59.062 45.455 31.55 15.27 46.79 3.58
1983 2058 2.285950 CGTTTTACGAACACCTGGTGTG 60.286 50.000 31.55 22.06 44.28 3.82
1984 2059 1.935199 CGTTTTACGAACACCTGGTGT 59.065 47.619 26.28 26.28 46.05 4.16
1985 2060 1.262151 CCGTTTTACGAACACCTGGTG 59.738 52.381 24.80 24.80 46.05 4.17
1987 2062 0.869730 CCCGTTTTACGAACACCTGG 59.130 55.000 0.05 0.00 46.05 4.45
1988 2063 1.868469 TCCCGTTTTACGAACACCTG 58.132 50.000 0.05 0.00 46.05 4.00
1991 2066 3.368843 CCAGTATCCCGTTTTACGAACAC 59.631 47.826 0.05 0.00 46.05 3.32
1992 2067 3.006752 ACCAGTATCCCGTTTTACGAACA 59.993 43.478 0.05 0.00 46.05 3.18
1993 2068 3.588955 ACCAGTATCCCGTTTTACGAAC 58.411 45.455 0.05 0.00 46.05 3.95
1994 2069 3.959535 ACCAGTATCCCGTTTTACGAA 57.040 42.857 0.05 0.00 46.05 3.85
1995 2070 4.016444 ACTACCAGTATCCCGTTTTACGA 58.984 43.478 0.05 0.00 46.05 3.43
1997 2072 6.456795 AGTACTACCAGTATCCCGTTTTAC 57.543 41.667 0.00 0.00 32.65 2.01
1998 2073 7.568199 GTAGTACTACCAGTATCCCGTTTTA 57.432 40.000 20.47 0.00 32.65 1.52
1999 2074 6.456795 GTAGTACTACCAGTATCCCGTTTT 57.543 41.667 20.47 0.00 32.65 2.43
2013 2088 1.117994 GGGGGTGCTGGTAGTACTAC 58.882 60.000 22.53 22.53 31.18 2.73
2015 2090 1.684734 CGGGGGTGCTGGTAGTACT 60.685 63.158 0.00 0.00 31.18 2.73
2016 2091 1.953231 GACGGGGGTGCTGGTAGTAC 61.953 65.000 0.00 0.00 0.00 2.73
2018 2093 3.001406 GACGGGGGTGCTGGTAGT 61.001 66.667 0.00 0.00 0.00 2.73
2020 2095 2.285069 ATGACGGGGGTGCTGGTA 60.285 61.111 0.00 0.00 0.00 3.25
2021 2096 3.717294 GATGACGGGGGTGCTGGT 61.717 66.667 0.00 0.00 0.00 4.00
2022 2097 4.838152 CGATGACGGGGGTGCTGG 62.838 72.222 0.00 0.00 35.72 4.85
2024 2099 2.764128 ATCGATGACGGGGGTGCT 60.764 61.111 0.00 0.00 40.21 4.40
2025 2100 2.588877 CATCGATGACGGGGGTGC 60.589 66.667 21.02 0.00 40.21 5.01
2026 2101 2.108976 CCATCGATGACGGGGGTG 59.891 66.667 26.86 3.28 40.21 4.61
2027 2102 3.161450 CCCATCGATGACGGGGGT 61.161 66.667 26.86 0.00 43.83 4.95
2030 2105 1.095228 CAAACCCCATCGATGACGGG 61.095 60.000 28.48 28.48 40.21 5.28
2031 2106 1.714899 GCAAACCCCATCGATGACGG 61.715 60.000 26.86 24.43 40.21 4.79
2032 2107 1.721487 GCAAACCCCATCGATGACG 59.279 57.895 26.86 17.09 41.26 4.35
2034 2109 2.112198 GCGCAAACCCCATCGATGA 61.112 57.895 26.86 0.00 0.00 2.92
2035 2110 2.408835 GCGCAAACCCCATCGATG 59.591 61.111 18.76 18.76 0.00 3.84
2036 2111 2.828549 GGCGCAAACCCCATCGAT 60.829 61.111 10.83 0.00 0.00 3.59
2044 2119 3.989787 CCTTGGTGGGCGCAAACC 61.990 66.667 20.59 20.59 36.96 3.27
2045 2120 2.693250 GAACCTTGGTGGGCGCAAAC 62.693 60.000 10.83 6.42 41.11 2.93
2046 2121 2.443016 AACCTTGGTGGGCGCAAA 60.443 55.556 10.83 0.00 41.11 3.68
2048 2123 3.723097 TTGAACCTTGGTGGGCGCA 62.723 57.895 10.83 0.00 41.11 6.09
2050 2125 0.031994 CTTTTGAACCTTGGTGGGCG 59.968 55.000 0.00 0.00 41.11 6.13
2051 2126 0.249868 GCTTTTGAACCTTGGTGGGC 60.250 55.000 0.00 0.00 41.11 5.36
2053 2128 3.119849 CGATAGCTTTTGAACCTTGGTGG 60.120 47.826 0.00 0.00 42.93 4.61
2054 2129 4.083581 CGATAGCTTTTGAACCTTGGTG 57.916 45.455 0.00 0.00 0.00 4.17
2071 2146 0.878523 GCATTACACCTGCCGCGATA 60.879 55.000 8.23 0.00 33.44 2.92
2072 2147 2.180204 GCATTACACCTGCCGCGAT 61.180 57.895 8.23 0.00 33.44 4.58
2073 2148 2.817834 GCATTACACCTGCCGCGA 60.818 61.111 8.23 0.00 33.44 5.87
2075 2150 1.064621 CATGCATTACACCTGCCGC 59.935 57.895 0.00 0.00 38.89 6.53
2076 2151 1.064621 GCATGCATTACACCTGCCG 59.935 57.895 14.21 0.00 38.89 5.69
2077 2152 1.064621 CGCATGCATTACACCTGCC 59.935 57.895 19.57 0.00 38.89 4.85
2140 2215 1.439679 CAGGTACAGACTTTTCCGCC 58.560 55.000 0.00 0.00 0.00 6.13
2151 2226 2.167219 CATCGGCGTGCAGGTACAG 61.167 63.158 6.85 0.00 0.00 2.74
2211 2286 3.094661 TAGTACGTACGCGCACGGG 62.095 63.158 32.63 9.70 46.12 5.28
2212 2287 1.929714 GTAGTACGTACGCGCACGG 60.930 63.158 32.63 16.61 46.12 4.94
2231 2306 9.229784 TGTAATACTACGTACGTACAGTAGTAC 57.770 37.037 37.54 34.68 43.12 2.73
2232 2307 9.447040 CTGTAATACTACGTACGTACAGTAGTA 57.553 37.037 37.22 37.22 43.66 1.82
2233 2308 8.188799 TCTGTAATACTACGTACGTACAGTAGT 58.811 37.037 36.28 36.28 42.78 2.73
2234 2309 8.561932 TCTGTAATACTACGTACGTACAGTAG 57.438 38.462 32.33 32.33 39.02 2.57
2235 2310 7.648112 CCTCTGTAATACTACGTACGTACAGTA 59.352 40.741 30.69 28.21 39.02 2.74
2236 2311 6.477033 CCTCTGTAATACTACGTACGTACAGT 59.523 42.308 30.69 27.32 39.02 3.55
2237 2312 6.697455 TCCTCTGTAATACTACGTACGTACAG 59.303 42.308 28.40 28.40 39.15 2.74
2238 2313 6.569780 TCCTCTGTAATACTACGTACGTACA 58.430 40.000 23.60 19.39 0.00 2.90
2239 2314 6.697892 ACTCCTCTGTAATACTACGTACGTAC 59.302 42.308 23.60 15.90 0.00 3.67
2240 2315 6.806751 ACTCCTCTGTAATACTACGTACGTA 58.193 40.000 25.41 25.41 0.00 3.57
2241 2316 5.665459 ACTCCTCTGTAATACTACGTACGT 58.335 41.667 25.98 25.98 0.00 3.57
2242 2317 5.108065 CGACTCCTCTGTAATACTACGTACG 60.108 48.000 15.01 15.01 0.00 3.67
2243 2318 5.176590 CCGACTCCTCTGTAATACTACGTAC 59.823 48.000 0.00 0.00 0.00 3.67
2244 2319 5.292765 CCGACTCCTCTGTAATACTACGTA 58.707 45.833 0.00 0.00 0.00 3.57
2245 2320 4.125703 CCGACTCCTCTGTAATACTACGT 58.874 47.826 0.00 0.00 0.00 3.57
2246 2321 3.497640 CCCGACTCCTCTGTAATACTACG 59.502 52.174 0.00 0.00 0.00 3.51
2247 2322 3.819902 CCCCGACTCCTCTGTAATACTAC 59.180 52.174 0.00 0.00 0.00 2.73
2248 2323 3.461085 ACCCCGACTCCTCTGTAATACTA 59.539 47.826 0.00 0.00 0.00 1.82
2249 2324 2.244252 ACCCCGACTCCTCTGTAATACT 59.756 50.000 0.00 0.00 0.00 2.12
2250 2325 2.622470 GACCCCGACTCCTCTGTAATAC 59.378 54.545 0.00 0.00 0.00 1.89
2251 2326 2.423947 GGACCCCGACTCCTCTGTAATA 60.424 54.545 0.00 0.00 0.00 0.98
2252 2327 1.688627 GGACCCCGACTCCTCTGTAAT 60.689 57.143 0.00 0.00 0.00 1.89
2253 2328 0.324091 GGACCCCGACTCCTCTGTAA 60.324 60.000 0.00 0.00 0.00 2.41
2254 2329 1.212934 AGGACCCCGACTCCTCTGTA 61.213 60.000 0.00 0.00 32.06 2.74
2255 2330 2.037527 GGACCCCGACTCCTCTGT 59.962 66.667 0.00 0.00 0.00 3.41
2256 2331 0.905337 AAAGGACCCCGACTCCTCTG 60.905 60.000 0.00 0.00 37.13 3.35
2257 2332 0.615261 GAAAGGACCCCGACTCCTCT 60.615 60.000 0.00 0.00 37.13 3.69
2258 2333 1.615165 GGAAAGGACCCCGACTCCTC 61.615 65.000 0.00 0.00 37.13 3.71
2259 2334 1.612739 GGAAAGGACCCCGACTCCT 60.613 63.158 0.00 0.00 40.11 3.69
2260 2335 1.612739 AGGAAAGGACCCCGACTCC 60.613 63.158 0.00 0.00 0.00 3.85
2261 2336 1.192803 ACAGGAAAGGACCCCGACTC 61.193 60.000 0.00 0.00 0.00 3.36
2262 2337 0.115745 TACAGGAAAGGACCCCGACT 59.884 55.000 0.00 0.00 0.00 4.18
2263 2338 0.978907 TTACAGGAAAGGACCCCGAC 59.021 55.000 0.00 0.00 0.00 4.79
2264 2339 1.348696 GTTTACAGGAAAGGACCCCGA 59.651 52.381 0.00 0.00 0.00 5.14
2265 2340 1.072648 TGTTTACAGGAAAGGACCCCG 59.927 52.381 0.00 0.00 0.00 5.73
2266 2341 2.963599 TGTTTACAGGAAAGGACCCC 57.036 50.000 0.00 0.00 0.00 4.95


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

AutoCloner maintained by Alex Coulton.