Multiple sequence alignment - TraesCS2A01G031700

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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 TraesCS2A01G031700 chr2A 100.000 2264 0 0 1 2264 14629505 14627242 0.000000e+00 4181.0
1 TraesCS2A01G031700 chr2A 87.805 246 22 8 1976 2217 14627289 14627530 4.760000e-72 281.0
2 TraesCS2A01G031700 chr3B 93.119 2049 99 27 1 2031 558278366 558276342 0.000000e+00 2964.0
3 TraesCS2A01G031700 chr3B 92.750 2069 98 32 1 2031 604266036 604263982 0.000000e+00 2942.0
4 TraesCS2A01G031700 chr3B 87.382 1276 113 23 698 1954 548879796 548881042 0.000000e+00 1421.0
5 TraesCS2A01G031700 chr3B 83.095 349 45 10 1918 2264 420919155 420918819 2.830000e-79 305.0
6 TraesCS2A01G031700 chr3B 78.242 455 55 30 1673 2092 420919509 420919064 3.730000e-63 252.0
7 TraesCS2A01G031700 chr3B 81.522 276 35 6 1974 2234 760825831 760825557 1.760000e-51 213.0
8 TraesCS2A01G031700 chr3B 76.923 169 30 9 2067 2228 558276323 558276489 1.110000e-13 87.9
9 TraesCS2A01G031700 chr6B 93.115 2048 90 32 1 2031 679251638 679253651 0.000000e+00 2953.0
10 TraesCS2A01G031700 chr6B 85.265 1432 162 31 701 2110 702991738 702990334 0.000000e+00 1430.0
11 TraesCS2A01G031700 chr6B 87.590 1249 117 24 737 1968 702946742 702945515 0.000000e+00 1413.0
12 TraesCS2A01G031700 chr4B 92.881 2065 91 35 1 2030 551060044 551062087 0.000000e+00 2948.0
13 TraesCS2A01G031700 chr2B 92.788 2066 99 32 1 2031 454449232 454451282 0.000000e+00 2944.0
14 TraesCS2A01G031700 chr2B 92.788 2066 99 32 1 2031 454473365 454475415 0.000000e+00 2944.0
15 TraesCS2A01G031700 chr2B 92.736 2065 98 35 1 2029 549352852 549354900 0.000000e+00 2935.0
16 TraesCS2A01G031700 chr1B 93.560 2003 85 27 1 1970 571422397 571420406 0.000000e+00 2944.0
17 TraesCS2A01G031700 chr5B 92.684 2064 99 33 3 2031 506965552 506967598 0.000000e+00 2928.0
18 TraesCS2A01G031700 chr5B 78.107 169 28 9 2067 2228 709184715 709184881 5.150000e-17 99.0
19 TraesCS2A01G031700 chr2D 92.958 1278 52 20 781 2030 152001843 152003110 0.000000e+00 1827.0
20 TraesCS2A01G031700 chr2D 86.755 151 15 5 1981 2126 619855557 619855707 1.800000e-36 163.0
21 TraesCS2A01G031700 chr2D 84.127 63 10 0 1884 1946 166960814 166960876 6.750000e-06 62.1
22 TraesCS2A01G031700 chr7D 92.493 1039 55 15 1008 2030 460800797 460801828 0.000000e+00 1465.0
23 TraesCS2A01G031700 chr7D 89.270 904 55 25 1095 1970 610729345 610728456 0.000000e+00 1094.0
24 TraesCS2A01G031700 chr7D 86.683 811 64 25 1256 2030 72155657 72156459 0.000000e+00 859.0
25 TraesCS2A01G031700 chr4D 84.083 289 32 13 1974 2253 470194600 470194317 1.330000e-67 267.0
26 TraesCS2A01G031700 chr4D 88.800 125 10 4 1974 2095 470194717 470194594 1.400000e-32 150.0
27 TraesCS2A01G031700 chrUn 82.353 255 40 5 1975 2227 86408938 86409189 1.360000e-52 217.0
28 TraesCS2A01G031700 chr6D 87.805 123 11 3 1974 2092 62143148 62143270 8.430000e-30 141.0
29 TraesCS2A01G031700 chr5D 78.333 180 28 9 2057 2228 445781656 445781832 3.080000e-19 106.0


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 TraesCS2A01G031700 chr2A 14627242 14629505 2263 True 4181.0 4181 100.0000 1 2264 1 chr2A.!!$R1 2263
1 TraesCS2A01G031700 chr3B 558276342 558278366 2024 True 2964.0 2964 93.1190 1 2031 1 chr3B.!!$R1 2030
2 TraesCS2A01G031700 chr3B 604263982 604266036 2054 True 2942.0 2942 92.7500 1 2031 1 chr3B.!!$R2 2030
3 TraesCS2A01G031700 chr3B 548879796 548881042 1246 False 1421.0 1421 87.3820 698 1954 1 chr3B.!!$F1 1256
4 TraesCS2A01G031700 chr3B 420918819 420919509 690 True 278.5 305 80.6685 1673 2264 2 chr3B.!!$R4 591
5 TraesCS2A01G031700 chr6B 679251638 679253651 2013 False 2953.0 2953 93.1150 1 2031 1 chr6B.!!$F1 2030
6 TraesCS2A01G031700 chr6B 702990334 702991738 1404 True 1430.0 1430 85.2650 701 2110 1 chr6B.!!$R2 1409
7 TraesCS2A01G031700 chr6B 702945515 702946742 1227 True 1413.0 1413 87.5900 737 1968 1 chr6B.!!$R1 1231
8 TraesCS2A01G031700 chr4B 551060044 551062087 2043 False 2948.0 2948 92.8810 1 2030 1 chr4B.!!$F1 2029
9 TraesCS2A01G031700 chr2B 454449232 454451282 2050 False 2944.0 2944 92.7880 1 2031 1 chr2B.!!$F1 2030
10 TraesCS2A01G031700 chr2B 454473365 454475415 2050 False 2944.0 2944 92.7880 1 2031 1 chr2B.!!$F2 2030
11 TraesCS2A01G031700 chr2B 549352852 549354900 2048 False 2935.0 2935 92.7360 1 2029 1 chr2B.!!$F3 2028
12 TraesCS2A01G031700 chr1B 571420406 571422397 1991 True 2944.0 2944 93.5600 1 1970 1 chr1B.!!$R1 1969
13 TraesCS2A01G031700 chr5B 506965552 506967598 2046 False 2928.0 2928 92.6840 3 2031 1 chr5B.!!$F1 2028
14 TraesCS2A01G031700 chr2D 152001843 152003110 1267 False 1827.0 1827 92.9580 781 2030 1 chr2D.!!$F1 1249
15 TraesCS2A01G031700 chr7D 460800797 460801828 1031 False 1465.0 1465 92.4930 1008 2030 1 chr7D.!!$F2 1022
16 TraesCS2A01G031700 chr7D 610728456 610729345 889 True 1094.0 1094 89.2700 1095 1970 1 chr7D.!!$R1 875
17 TraesCS2A01G031700 chr7D 72155657 72156459 802 False 859.0 859 86.6830 1256 2030 1 chr7D.!!$F1 774

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
241 242 1.142965 AAAAACCGTTGGTGCCAGC 59.857 52.632 0.0 0.0 35.34 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1897 1961 0.037975 ACAACAACCTACCGCCGTAG 60.038 55.0 5.35 5.35 41.55 3.51 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
241 242 1.142965 AAAAACCGTTGGTGCCAGC 59.857 52.632 0.00 0.00 35.34 4.85
242 243 1.326951 AAAAACCGTTGGTGCCAGCT 61.327 50.000 3.70 0.00 35.34 4.24
276 277 3.758023 CACACAAGTATCATTGGCCTTGA 59.242 43.478 3.32 7.96 38.11 3.02
369 370 5.277154 CGAGTTTACATTGGAACGAACAAGT 60.277 40.000 0.00 0.00 0.00 3.16
607 608 3.423749 TGTGGAGAATGCAATGACACAT 58.576 40.909 9.55 0.00 39.09 3.21
635 636 2.812011 ACGTTAGGACATGCAAGAAACC 59.188 45.455 0.00 0.00 0.00 3.27
676 677 1.594293 CAAACACGTGGACGGAGCT 60.594 57.895 21.57 0.00 44.95 4.09
864 877 1.683418 GGGGAAGGCCTATCGACGTT 61.683 60.000 5.16 0.00 0.00 3.99
1154 1168 1.067295 TGCAAGGTGAAGGAGTCCAT 58.933 50.000 12.86 0.00 0.00 3.41
1160 1174 0.895530 GTGAAGGAGTCCATCGACCA 59.104 55.000 12.86 0.00 40.12 4.02
1296 1310 6.203530 ACATGTTACTCTCAAATGTGTGTCAG 59.796 38.462 0.00 0.00 30.53 3.51
1352 1366 5.201243 TCCTCTATGCAAGTACTTCAGCTA 58.799 41.667 16.32 6.17 0.00 3.32
1550 1566 0.988063 AGGAGGAGAGGGCAAGAAAC 59.012 55.000 0.00 0.00 0.00 2.78
1664 1682 1.468736 GGACTCGTCATGTAACCGGAC 60.469 57.143 9.46 0.00 0.00 4.79
1847 1906 1.308998 AAACTGTTGTGCCGAGAAGG 58.691 50.000 0.00 0.00 44.97 3.46
1852 1911 0.390472 GTTGTGCCGAGAAGGAGAGG 60.390 60.000 0.00 0.00 45.00 3.69
1855 1914 3.855853 GCCGAGAAGGAGAGGGGC 61.856 72.222 0.00 0.00 45.00 5.80
1857 1916 2.430610 CCGAGAAGGAGAGGGGCAG 61.431 68.421 0.00 0.00 45.00 4.85
1860 1919 0.539518 GAGAAGGAGAGGGGCAGAAC 59.460 60.000 0.00 0.00 0.00 3.01
1887 1951 8.199176 GAGGATTACTCTGTTTTTAAGCCTAC 57.801 38.462 0.00 0.00 40.80 3.18
1888 1952 7.110810 AGGATTACTCTGTTTTTAAGCCTACC 58.889 38.462 0.00 0.00 39.32 3.18
1889 1953 6.036844 GGATTACTCTGTTTTTAAGCCTACCG 59.963 42.308 0.00 0.00 30.14 4.02
1890 1954 3.072211 ACTCTGTTTTTAAGCCTACCGC 58.928 45.455 0.00 0.00 37.98 5.68
1891 1955 2.418976 CTCTGTTTTTAAGCCTACCGCC 59.581 50.000 0.00 0.00 38.78 6.13
1892 1956 2.156098 CTGTTTTTAAGCCTACCGCCA 58.844 47.619 0.00 0.00 38.78 5.69
1893 1957 2.752903 CTGTTTTTAAGCCTACCGCCAT 59.247 45.455 0.00 0.00 38.78 4.40
1894 1958 3.942748 CTGTTTTTAAGCCTACCGCCATA 59.057 43.478 0.00 0.00 38.78 2.74
1895 1959 3.942748 TGTTTTTAAGCCTACCGCCATAG 59.057 43.478 0.00 0.00 38.78 2.23
1896 1960 3.918294 TTTTAAGCCTACCGCCATAGT 57.082 42.857 0.00 0.00 38.78 2.12
1897 1961 3.464111 TTTAAGCCTACCGCCATAGTC 57.536 47.619 0.00 0.00 38.78 2.59
1898 1962 2.376695 TAAGCCTACCGCCATAGTCT 57.623 50.000 0.00 0.00 38.78 3.24
1899 1963 2.376695 AAGCCTACCGCCATAGTCTA 57.623 50.000 0.00 0.00 38.78 2.59
1900 1964 1.618487 AGCCTACCGCCATAGTCTAC 58.382 55.000 0.00 0.00 38.78 2.59
1901 1965 0.240411 GCCTACCGCCATAGTCTACG 59.760 60.000 0.00 0.00 0.00 3.51
1906 1970 3.126528 GCCATAGTCTACGGCGGT 58.873 61.111 13.24 1.39 35.79 5.68
1907 1971 2.334307 GCCATAGTCTACGGCGGTA 58.666 57.895 13.24 3.91 35.79 4.02
1911 1975 1.952296 CATAGTCTACGGCGGTAGGTT 59.048 52.381 25.82 17.97 45.10 3.50
1912 1977 1.382522 TAGTCTACGGCGGTAGGTTG 58.617 55.000 25.82 6.80 45.10 3.77
1950 2017 4.096003 CCCTGGCGGTAGGTGGTG 62.096 72.222 0.00 0.00 36.02 4.17
1951 2018 4.096003 CCTGGCGGTAGGTGGTGG 62.096 72.222 0.00 0.00 32.99 4.61
1952 2019 4.778143 CTGGCGGTAGGTGGTGGC 62.778 72.222 0.00 0.00 0.00 5.01
1954 2021 4.338710 GGCGGTAGGTGGTGGCAA 62.339 66.667 0.00 0.00 0.00 4.52
1955 2022 2.281900 GCGGTAGGTGGTGGCAAA 60.282 61.111 0.00 0.00 0.00 3.68
1956 2023 2.332654 GCGGTAGGTGGTGGCAAAG 61.333 63.158 0.00 0.00 0.00 2.77
1957 2024 1.072505 CGGTAGGTGGTGGCAAAGT 59.927 57.895 0.00 0.00 0.00 2.66
1958 2025 0.536460 CGGTAGGTGGTGGCAAAGTT 60.536 55.000 0.00 0.00 0.00 2.66
1959 2026 1.699730 GGTAGGTGGTGGCAAAGTTT 58.300 50.000 0.00 0.00 0.00 2.66
1960 2027 1.611977 GGTAGGTGGTGGCAAAGTTTC 59.388 52.381 0.00 0.00 0.00 2.78
1961 2028 2.583143 GTAGGTGGTGGCAAAGTTTCT 58.417 47.619 0.00 0.00 0.00 2.52
1962 2029 1.402787 AGGTGGTGGCAAAGTTTCTG 58.597 50.000 0.00 0.00 0.00 3.02
1963 2030 1.111277 GGTGGTGGCAAAGTTTCTGT 58.889 50.000 0.00 0.00 0.00 3.41
1964 2031 1.202405 GGTGGTGGCAAAGTTTCTGTG 60.202 52.381 0.00 0.00 0.00 3.66
1965 2032 1.748493 GTGGTGGCAAAGTTTCTGTGA 59.252 47.619 0.00 0.00 0.00 3.58
1966 2033 1.748493 TGGTGGCAAAGTTTCTGTGAC 59.252 47.619 0.00 0.00 0.00 3.67
1967 2034 1.268539 GGTGGCAAAGTTTCTGTGACG 60.269 52.381 0.00 0.00 26.80 4.35
1968 2035 1.668751 GTGGCAAAGTTTCTGTGACGA 59.331 47.619 0.00 0.00 26.80 4.20
1969 2036 2.096819 GTGGCAAAGTTTCTGTGACGAA 59.903 45.455 0.00 0.00 26.80 3.85
1970 2037 2.750166 TGGCAAAGTTTCTGTGACGAAA 59.250 40.909 0.00 0.00 26.80 3.46
1971 2038 3.191581 TGGCAAAGTTTCTGTGACGAAAA 59.808 39.130 0.00 0.00 34.93 2.29
1972 2039 3.791353 GGCAAAGTTTCTGTGACGAAAAG 59.209 43.478 0.00 0.00 34.93 2.27
1973 2040 3.791353 GCAAAGTTTCTGTGACGAAAAGG 59.209 43.478 0.00 0.00 34.93 3.11
1974 2041 3.692791 AAGTTTCTGTGACGAAAAGGC 57.307 42.857 0.00 0.00 34.93 4.35
1975 2042 1.947456 AGTTTCTGTGACGAAAAGGCC 59.053 47.619 0.00 0.00 34.93 5.19
1976 2043 1.673920 GTTTCTGTGACGAAAAGGCCA 59.326 47.619 5.01 0.00 34.93 5.36
1977 2044 1.305201 TTCTGTGACGAAAAGGCCAC 58.695 50.000 5.01 0.00 0.00 5.01
1978 2045 0.179234 TCTGTGACGAAAAGGCCACA 59.821 50.000 5.01 0.00 36.57 4.17
1979 2046 1.021202 CTGTGACGAAAAGGCCACAA 58.979 50.000 5.01 0.00 37.19 3.33
1980 2047 1.002468 CTGTGACGAAAAGGCCACAAG 60.002 52.381 5.01 0.00 37.19 3.16
1981 2048 0.317854 GTGACGAAAAGGCCACAAGC 60.318 55.000 5.01 0.00 42.60 4.01
1990 2057 4.410400 GCCACAAGCCCTAGCGGT 62.410 66.667 0.00 0.00 46.67 5.68
1991 2058 3.026431 GCCACAAGCCCTAGCGGTA 62.026 63.158 0.00 0.00 46.67 4.02
1992 2059 1.144057 CCACAAGCCCTAGCGGTAG 59.856 63.158 14.73 14.73 46.67 3.18
1993 2060 1.144057 CACAAGCCCTAGCGGTAGG 59.856 63.158 29.84 29.84 46.67 3.18
1994 2061 2.109181 CAAGCCCTAGCGGTAGGC 59.891 66.667 31.08 25.20 44.39 3.93
2015 2082 0.251922 ACTGTACCCTACCGCCAGAA 60.252 55.000 0.00 0.00 0.00 3.02
2037 2104 4.424867 TGGCGGTAGGGGGTCCAT 62.425 66.667 0.00 0.00 34.83 3.41
2038 2105 2.122725 GGCGGTAGGGGGTCCATA 60.123 66.667 0.00 0.00 34.83 2.74
2039 2106 1.538135 GGCGGTAGGGGGTCCATAT 60.538 63.158 0.00 0.00 34.83 1.78
2040 2107 1.551019 GGCGGTAGGGGGTCCATATC 61.551 65.000 0.00 0.00 34.83 1.63
2059 2130 0.784778 CTTCTGTGACGAGAAACGCC 59.215 55.000 0.00 0.00 46.94 5.68
2062 2133 1.891060 CTGTGACGAGAAACGCCAGC 61.891 60.000 0.00 0.00 46.94 4.85
2082 2153 4.162690 CCTGGCGGTAGGGCTGAC 62.163 72.222 0.00 0.00 41.85 3.51
2083 2154 4.162690 CTGGCGGTAGGGCTGACC 62.163 72.222 0.00 0.00 41.85 4.02
2093 2164 3.702048 GGCTGACCTACCGCCACA 61.702 66.667 0.00 0.00 45.99 4.17
2094 2165 2.125512 GCTGACCTACCGCCACAG 60.126 66.667 0.00 0.00 0.00 3.66
2095 2166 2.125512 CTGACCTACCGCCACAGC 60.126 66.667 0.00 0.00 0.00 4.40
2096 2167 3.665675 CTGACCTACCGCCACAGCC 62.666 68.421 0.00 0.00 34.57 4.85
2097 2168 4.814294 GACCTACCGCCACAGCCG 62.814 72.222 0.00 0.00 34.57 5.52
2099 2170 4.814294 CCTACCGCCACAGCCGAC 62.814 72.222 0.00 0.00 34.57 4.79
2114 2185 2.202531 GACGGCGGTAAGGTCGAC 60.203 66.667 13.24 7.13 38.63 4.20
2115 2186 3.690108 GACGGCGGTAAGGTCGACC 62.690 68.421 27.67 27.67 38.63 4.79
2116 2187 4.503314 CGGCGGTAAGGTCGACCC 62.503 72.222 30.82 15.66 37.14 4.46
2118 2189 1.754234 GGCGGTAAGGTCGACCCTA 60.754 63.158 30.82 20.14 45.47 3.53
2119 2190 1.435105 GCGGTAAGGTCGACCCTAC 59.565 63.158 28.23 28.23 45.47 3.18
2120 2191 2.009424 GCGGTAAGGTCGACCCTACC 62.009 65.000 37.35 37.35 45.47 3.18
2121 2192 1.718757 CGGTAAGGTCGACCCTACCG 61.719 65.000 45.93 45.93 45.47 4.02
2122 2193 1.435105 GTAAGGTCGACCCTACCGC 59.565 63.158 30.82 11.66 45.47 5.68
2123 2194 1.754234 TAAGGTCGACCCTACCGCC 60.754 63.158 30.82 3.34 45.47 6.13
2124 2195 2.497792 TAAGGTCGACCCTACCGCCA 62.498 60.000 30.82 0.00 45.47 5.69
2125 2196 3.834799 GGTCGACCCTACCGCCAG 61.835 72.222 24.75 0.00 0.00 4.85
2126 2197 3.834799 GTCGACCCTACCGCCAGG 61.835 72.222 3.51 0.00 45.13 4.45
2139 2210 2.746277 CCAGGGCGCTAGCGTTTT 60.746 61.111 35.21 19.30 46.35 2.43
2140 2211 2.750888 CCAGGGCGCTAGCGTTTTC 61.751 63.158 35.21 19.98 46.35 2.29
2141 2212 1.741770 CAGGGCGCTAGCGTTTTCT 60.742 57.895 35.21 23.56 46.35 2.52
2142 2213 1.741770 AGGGCGCTAGCGTTTTCTG 60.742 57.895 35.21 9.05 46.35 3.02
2143 2214 2.033194 GGGCGCTAGCGTTTTCTGT 61.033 57.895 35.21 0.00 46.35 3.41
2144 2215 1.420312 GGCGCTAGCGTTTTCTGTC 59.580 57.895 35.21 17.48 46.35 3.51
2145 2216 1.289109 GGCGCTAGCGTTTTCTGTCA 61.289 55.000 35.21 0.00 46.35 3.58
2146 2217 0.179248 GCGCTAGCGTTTTCTGTCAC 60.179 55.000 35.21 13.13 42.09 3.67
2147 2218 1.136690 CGCTAGCGTTTTCTGTCACA 58.863 50.000 28.66 0.00 34.35 3.58
2148 2219 1.525197 CGCTAGCGTTTTCTGTCACAA 59.475 47.619 28.66 0.00 34.35 3.33
2149 2220 2.033236 CGCTAGCGTTTTCTGTCACAAA 60.033 45.455 28.66 0.00 34.35 2.83
2150 2221 3.545228 CGCTAGCGTTTTCTGTCACAAAA 60.545 43.478 28.66 0.00 34.35 2.44
2151 2222 3.968724 GCTAGCGTTTTCTGTCACAAAAG 59.031 43.478 0.00 0.00 0.00 2.27
2152 2223 4.260620 GCTAGCGTTTTCTGTCACAAAAGA 60.261 41.667 0.00 0.00 0.00 2.52
2153 2224 4.900635 AGCGTTTTCTGTCACAAAAGAT 57.099 36.364 0.00 0.00 0.00 2.40
2154 2225 6.347402 GCTAGCGTTTTCTGTCACAAAAGATA 60.347 38.462 0.00 0.00 0.00 1.98
2155 2226 6.560253 AGCGTTTTCTGTCACAAAAGATAT 57.440 33.333 0.00 0.00 0.00 1.63
2156 2227 6.373779 AGCGTTTTCTGTCACAAAAGATATG 58.626 36.000 0.00 0.00 0.00 1.78
2157 2228 5.569059 GCGTTTTCTGTCACAAAAGATATGG 59.431 40.000 0.00 0.00 0.00 2.74
2158 2229 6.567701 GCGTTTTCTGTCACAAAAGATATGGA 60.568 38.462 0.00 0.00 0.00 3.41
2159 2230 6.797033 CGTTTTCTGTCACAAAAGATATGGAC 59.203 38.462 0.00 0.00 0.00 4.02
2160 2231 6.817765 TTTCTGTCACAAAAGATATGGACC 57.182 37.500 0.00 0.00 0.00 4.46
2161 2232 4.843728 TCTGTCACAAAAGATATGGACCC 58.156 43.478 0.00 0.00 0.00 4.46
2162 2233 3.947834 CTGTCACAAAAGATATGGACCCC 59.052 47.826 0.00 0.00 0.00 4.95
2163 2234 3.288092 GTCACAAAAGATATGGACCCCC 58.712 50.000 0.00 0.00 0.00 5.40
2164 2235 3.053619 GTCACAAAAGATATGGACCCCCT 60.054 47.826 0.00 0.00 0.00 4.79
2165 2236 4.165372 GTCACAAAAGATATGGACCCCCTA 59.835 45.833 0.00 0.00 0.00 3.53
2166 2237 4.165372 TCACAAAAGATATGGACCCCCTAC 59.835 45.833 0.00 0.00 0.00 3.18
2167 2238 3.462205 ACAAAAGATATGGACCCCCTACC 59.538 47.826 0.00 0.00 0.00 3.18
2168 2239 2.025636 AAGATATGGACCCCCTACCG 57.974 55.000 0.00 0.00 0.00 4.02
2169 2240 0.544595 AGATATGGACCCCCTACCGC 60.545 60.000 0.00 0.00 0.00 5.68
2170 2241 1.538135 ATATGGACCCCCTACCGCC 60.538 63.158 0.00 0.00 0.00 6.13
2171 2242 2.335134 ATATGGACCCCCTACCGCCA 62.335 60.000 0.00 0.00 0.00 5.69
2190 2261 4.078516 GCGTTCTGGCGGTAGGGT 62.079 66.667 0.00 0.00 0.00 4.34
2197 2541 3.480133 GGCGGTAGGGTCCAGCAT 61.480 66.667 0.00 0.00 0.00 3.79
2227 2571 2.590114 GGCCTGTGACGGTAGGGTT 61.590 63.158 0.00 0.00 34.58 4.11
2244 2588 2.515854 GGTTTGGTCCCTCCTTTTCTC 58.484 52.381 0.00 0.00 37.07 2.87
2246 2590 1.073098 TTGGTCCCTCCTTTTCTCCC 58.927 55.000 0.00 0.00 37.07 4.30
2256 2600 2.091333 TCCTTTTCTCCCCTGTTTTGCT 60.091 45.455 0.00 0.00 0.00 3.91
2261 2605 1.180029 CTCCCCTGTTTTGCTCCATG 58.820 55.000 0.00 0.00 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
240 241 2.427320 TGTGGCCTCTCACACAGC 59.573 61.111 3.32 0.00 42.20 4.40
276 277 0.659427 CTGCGGTCATCAAATGCGAT 59.341 50.000 0.00 0.00 0.00 4.58
573 574 6.183360 TGCATTCTCCACAATTGTTGTTTACT 60.183 34.615 8.77 0.00 43.23 2.24
575 576 6.154203 TGCATTCTCCACAATTGTTGTTTA 57.846 33.333 8.77 0.00 43.23 2.01
607 608 2.139917 GCATGTCCTAACGTTGTGTCA 58.860 47.619 11.99 6.19 0.00 3.58
635 636 1.101049 AGTGCCCGTGTTGGTTCTTG 61.101 55.000 0.00 0.00 35.15 3.02
676 677 3.015145 GCCCCCTCCAAGGCTACA 61.015 66.667 0.00 0.00 46.14 2.74
864 877 1.818060 CAACCATCCGGATTGAGCAAA 59.182 47.619 21.66 0.00 35.59 3.68
917 930 5.636121 GGCAAATATATCAACACATGCATGG 59.364 40.000 29.41 20.05 34.37 3.66
981 995 5.012561 AGCCATGCCCTACAACAAATAAAAA 59.987 36.000 0.00 0.00 0.00 1.94
982 996 4.530161 AGCCATGCCCTACAACAAATAAAA 59.470 37.500 0.00 0.00 0.00 1.52
1154 1168 3.399330 GTCCATGACTTCTTTTGGTCGA 58.601 45.455 0.00 0.00 35.45 4.20
1160 1174 3.072476 TCCTTCGGTCCATGACTTCTTTT 59.928 43.478 0.00 0.00 32.47 2.27
1296 1310 6.055231 TGCATATAAAACGGATGTTAGTGC 57.945 37.500 0.00 0.00 37.31 4.40
1352 1366 6.656902 TCTTTTGGCACTTCATGATCTATCT 58.343 36.000 0.00 0.00 0.00 1.98
1423 1438 3.304726 GCCTCTTTGAAACCTTTCTTCGG 60.305 47.826 0.00 0.00 38.02 4.30
1664 1682 4.044336 TGATAAATTTGGCATGGCTTCG 57.956 40.909 21.08 0.00 0.00 3.79
1774 1827 9.362539 GACAAATCATAGAAATTGCTGACAAAT 57.637 29.630 0.00 0.00 39.77 2.32
1840 1898 0.972983 TTCTGCCCCTCTCCTTCTCG 60.973 60.000 0.00 0.00 0.00 4.04
1847 1906 0.616111 TCCTCTGTTCTGCCCCTCTC 60.616 60.000 0.00 0.00 0.00 3.20
1852 1911 3.186702 GAGTAATCCTCTGTTCTGCCC 57.813 52.381 0.00 0.00 37.22 5.36
1880 1944 1.962100 GTAGACTATGGCGGTAGGCTT 59.038 52.381 9.96 0.00 40.51 4.35
1881 1945 1.618487 GTAGACTATGGCGGTAGGCT 58.382 55.000 9.65 9.65 42.63 4.58
1882 1946 0.240411 CGTAGACTATGGCGGTAGGC 59.760 60.000 0.00 0.00 44.11 3.93
1883 1947 0.879765 CCGTAGACTATGGCGGTAGG 59.120 60.000 7.82 0.00 39.41 3.18
1890 1954 0.879765 CCTACCGCCGTAGACTATGG 59.120 60.000 15.47 15.47 44.18 2.74
1891 1955 1.602311 ACCTACCGCCGTAGACTATG 58.398 55.000 13.05 0.00 44.18 2.23
1892 1956 1.952296 CAACCTACCGCCGTAGACTAT 59.048 52.381 13.05 0.00 44.18 2.12
1893 1957 1.340017 ACAACCTACCGCCGTAGACTA 60.340 52.381 13.05 0.00 44.18 2.59
1894 1958 0.610232 ACAACCTACCGCCGTAGACT 60.610 55.000 13.05 0.00 44.18 3.24
1895 1959 0.244721 AACAACCTACCGCCGTAGAC 59.755 55.000 13.05 0.00 44.18 2.59
1896 1960 0.244450 CAACAACCTACCGCCGTAGA 59.756 55.000 13.05 0.00 44.18 2.59
1897 1961 0.037975 ACAACAACCTACCGCCGTAG 60.038 55.000 5.35 5.35 41.55 3.51
1898 1962 1.067915 GTACAACAACCTACCGCCGTA 60.068 52.381 0.00 0.00 0.00 4.02
1899 1963 0.319813 GTACAACAACCTACCGCCGT 60.320 55.000 0.00 0.00 0.00 5.68
1900 1964 1.015607 GGTACAACAACCTACCGCCG 61.016 60.000 0.00 0.00 36.53 6.46
1901 1965 0.674581 GGGTACAACAACCTACCGCC 60.675 60.000 0.00 0.00 39.65 6.13
1902 1966 0.322648 AGGGTACAACAACCTACCGC 59.677 55.000 0.00 0.00 39.65 5.68
1906 1970 1.550072 GCGGTAGGGTACAACAACCTA 59.450 52.381 0.00 0.00 39.65 3.08
1907 1971 0.322648 GCGGTAGGGTACAACAACCT 59.677 55.000 0.00 0.00 39.65 3.50
1911 1975 0.542467 TCTGGCGGTAGGGTACAACA 60.542 55.000 0.00 0.00 0.00 3.33
1912 1977 0.108472 GTCTGGCGGTAGGGTACAAC 60.108 60.000 0.00 0.00 0.00 3.32
1947 2014 1.268539 CGTCACAGAAACTTTGCCACC 60.269 52.381 0.00 0.00 0.00 4.61
1949 2016 2.031258 TCGTCACAGAAACTTTGCCA 57.969 45.000 0.00 0.00 0.00 4.92
1950 2017 3.414549 TTTCGTCACAGAAACTTTGCC 57.585 42.857 0.00 0.00 35.44 4.52
1951 2018 3.791353 CCTTTTCGTCACAGAAACTTTGC 59.209 43.478 0.00 0.00 39.53 3.68
1952 2019 3.791353 GCCTTTTCGTCACAGAAACTTTG 59.209 43.478 0.00 0.00 39.53 2.77
1953 2020 3.181490 GGCCTTTTCGTCACAGAAACTTT 60.181 43.478 0.00 0.00 39.53 2.66
1954 2021 2.357952 GGCCTTTTCGTCACAGAAACTT 59.642 45.455 0.00 0.00 39.53 2.66
1955 2022 1.947456 GGCCTTTTCGTCACAGAAACT 59.053 47.619 0.00 0.00 39.53 2.66
1956 2023 1.673920 TGGCCTTTTCGTCACAGAAAC 59.326 47.619 3.32 0.00 39.53 2.78
1957 2024 1.673920 GTGGCCTTTTCGTCACAGAAA 59.326 47.619 3.32 0.00 38.23 2.52
1958 2025 1.305201 GTGGCCTTTTCGTCACAGAA 58.695 50.000 3.32 0.00 0.00 3.02
1959 2026 0.179234 TGTGGCCTTTTCGTCACAGA 59.821 50.000 3.32 0.00 35.52 3.41
1960 2027 1.002468 CTTGTGGCCTTTTCGTCACAG 60.002 52.381 3.32 0.00 40.55 3.66
1961 2028 1.021202 CTTGTGGCCTTTTCGTCACA 58.979 50.000 3.32 0.00 38.21 3.58
1962 2029 0.317854 GCTTGTGGCCTTTTCGTCAC 60.318 55.000 3.32 0.00 34.27 3.67
1963 2030 2.029743 GCTTGTGGCCTTTTCGTCA 58.970 52.632 3.32 0.00 34.27 4.35
1964 2031 4.944249 GCTTGTGGCCTTTTCGTC 57.056 55.556 3.32 0.00 34.27 4.20
1973 2040 2.925162 CTACCGCTAGGGCTTGTGGC 62.925 65.000 0.19 0.00 43.47 5.01
1974 2041 1.144057 CTACCGCTAGGGCTTGTGG 59.856 63.158 0.19 0.00 43.47 4.17
1975 2042 1.144057 CCTACCGCTAGGGCTTGTG 59.856 63.158 0.19 0.00 43.47 3.33
1976 2043 2.732619 GCCTACCGCTAGGGCTTGT 61.733 63.158 5.94 0.00 40.26 3.16
1977 2044 2.109181 GCCTACCGCTAGGGCTTG 59.891 66.667 5.94 0.00 40.26 4.01
1986 2053 1.738432 GGGTACAGTAGCCTACCGC 59.262 63.158 19.97 0.00 42.93 5.68
1992 2059 1.738432 GCGGTAGGGTACAGTAGCC 59.262 63.158 19.70 19.70 46.53 3.93
1993 2060 1.039233 TGGCGGTAGGGTACAGTAGC 61.039 60.000 0.69 0.69 0.00 3.58
1994 2061 1.030457 CTGGCGGTAGGGTACAGTAG 58.970 60.000 0.00 0.00 0.00 2.57
1995 2062 0.625316 TCTGGCGGTAGGGTACAGTA 59.375 55.000 0.00 0.00 0.00 2.74
1996 2063 0.251922 TTCTGGCGGTAGGGTACAGT 60.252 55.000 0.00 0.00 0.00 3.55
2000 2067 2.713967 GCGTTCTGGCGGTAGGGTA 61.714 63.158 0.00 0.00 0.00 3.69
2034 2101 4.500837 CGTTTCTCGTCACAGAAGATATGG 59.499 45.833 0.00 0.00 33.85 2.74
2035 2102 4.027295 GCGTTTCTCGTCACAGAAGATATG 60.027 45.833 0.00 0.00 42.13 1.78
2036 2103 4.106197 GCGTTTCTCGTCACAGAAGATAT 58.894 43.478 0.00 0.00 42.13 1.63
2037 2104 3.499048 GCGTTTCTCGTCACAGAAGATA 58.501 45.455 0.00 0.00 42.13 1.98
2038 2105 2.329379 GCGTTTCTCGTCACAGAAGAT 58.671 47.619 0.00 0.00 42.13 2.40
2039 2106 1.602165 GGCGTTTCTCGTCACAGAAGA 60.602 52.381 0.00 0.00 44.22 2.87
2040 2107 0.784778 GGCGTTTCTCGTCACAGAAG 59.215 55.000 0.00 0.00 44.22 2.85
2065 2136 4.162690 GTCAGCCCTACCGCCAGG 62.163 72.222 0.00 0.00 45.13 4.45
2077 2148 2.125512 CTGTGGCGGTAGGTCAGC 60.126 66.667 0.00 0.00 36.55 4.26
2078 2149 2.125512 GCTGTGGCGGTAGGTCAG 60.126 66.667 0.00 0.00 0.00 3.51
2079 2150 3.702048 GGCTGTGGCGGTAGGTCA 61.702 66.667 0.00 0.00 39.81 4.02
2097 2168 2.202531 GTCGACCTTACCGCCGTC 60.203 66.667 3.51 0.00 0.00 4.79
2098 2169 3.752339 GGTCGACCTTACCGCCGT 61.752 66.667 27.64 0.00 0.00 5.68
2099 2170 4.503314 GGGTCGACCTTACCGCCG 62.503 72.222 32.52 0.00 37.93 6.46
2108 2179 3.834799 CTGGCGGTAGGGTCGACC 61.835 72.222 27.04 27.04 34.20 4.79
2109 2180 3.834799 CCTGGCGGTAGGGTCGAC 61.835 72.222 7.13 7.13 34.06 4.20
2122 2193 2.746277 AAAACGCTAGCGCCCTGG 60.746 61.111 35.63 10.34 44.19 4.45
2123 2194 1.741770 AGAAAACGCTAGCGCCCTG 60.742 57.895 35.63 11.13 44.19 4.45
2124 2195 1.741770 CAGAAAACGCTAGCGCCCT 60.742 57.895 35.63 22.96 44.19 5.19
2125 2196 1.967597 GACAGAAAACGCTAGCGCCC 61.968 60.000 35.63 21.20 44.19 6.13
2126 2197 1.289109 TGACAGAAAACGCTAGCGCC 61.289 55.000 35.63 21.54 44.19 6.53
2127 2198 0.179248 GTGACAGAAAACGCTAGCGC 60.179 55.000 35.63 19.85 44.19 5.92
2128 2199 1.136690 TGTGACAGAAAACGCTAGCG 58.863 50.000 34.27 34.27 46.03 4.26
2129 2200 3.602390 TTTGTGACAGAAAACGCTAGC 57.398 42.857 4.06 4.06 0.00 3.42
2130 2201 5.403897 TCTTTTGTGACAGAAAACGCTAG 57.596 39.130 6.41 0.00 0.00 3.42
2131 2202 7.360861 CCATATCTTTTGTGACAGAAAACGCTA 60.361 37.037 6.41 0.58 0.00 4.26
2132 2203 4.900635 ATCTTTTGTGACAGAAAACGCT 57.099 36.364 6.41 0.00 0.00 5.07
2133 2204 5.569059 CCATATCTTTTGTGACAGAAAACGC 59.431 40.000 6.41 0.00 0.00 4.84
2134 2205 6.797033 GTCCATATCTTTTGTGACAGAAAACG 59.203 38.462 6.41 4.27 0.00 3.60
2135 2206 7.084486 GGTCCATATCTTTTGTGACAGAAAAC 58.916 38.462 6.41 0.00 0.00 2.43
2136 2207 6.208599 GGGTCCATATCTTTTGTGACAGAAAA 59.791 38.462 9.84 9.84 0.00 2.29
2137 2208 5.710099 GGGTCCATATCTTTTGTGACAGAAA 59.290 40.000 0.00 0.00 0.00 2.52
2138 2209 5.253330 GGGTCCATATCTTTTGTGACAGAA 58.747 41.667 0.00 0.00 0.00 3.02
2139 2210 4.324254 GGGGTCCATATCTTTTGTGACAGA 60.324 45.833 0.00 0.00 0.00 3.41
2140 2211 3.947834 GGGGTCCATATCTTTTGTGACAG 59.052 47.826 0.00 0.00 0.00 3.51
2141 2212 3.308832 GGGGGTCCATATCTTTTGTGACA 60.309 47.826 0.00 0.00 0.00 3.58
2142 2213 3.053619 AGGGGGTCCATATCTTTTGTGAC 60.054 47.826 0.00 0.00 34.83 3.67
2143 2214 3.197983 AGGGGGTCCATATCTTTTGTGA 58.802 45.455 0.00 0.00 34.83 3.58
2144 2215 3.669939 AGGGGGTCCATATCTTTTGTG 57.330 47.619 0.00 0.00 34.83 3.33
2145 2216 3.462205 GGTAGGGGGTCCATATCTTTTGT 59.538 47.826 0.00 0.00 34.83 2.83
2146 2217 3.496160 CGGTAGGGGGTCCATATCTTTTG 60.496 52.174 0.00 0.00 34.83 2.44
2147 2218 2.709397 CGGTAGGGGGTCCATATCTTTT 59.291 50.000 0.00 0.00 34.83 2.27
2148 2219 2.335933 CGGTAGGGGGTCCATATCTTT 58.664 52.381 0.00 0.00 34.83 2.52
2149 2220 2.025636 CGGTAGGGGGTCCATATCTT 57.974 55.000 0.00 0.00 34.83 2.40
2150 2221 0.544595 GCGGTAGGGGGTCCATATCT 60.545 60.000 0.00 0.00 34.83 1.98
2151 2222 1.551019 GGCGGTAGGGGGTCCATATC 61.551 65.000 0.00 0.00 34.83 1.63
2152 2223 1.538135 GGCGGTAGGGGGTCCATAT 60.538 63.158 0.00 0.00 34.83 1.78
2153 2224 2.122725 GGCGGTAGGGGGTCCATA 60.123 66.667 0.00 0.00 34.83 2.74
2154 2225 4.424867 TGGCGGTAGGGGGTCCAT 62.425 66.667 0.00 0.00 34.83 3.41
2173 2244 4.078516 ACCCTACCGCCAGAACGC 62.079 66.667 0.00 0.00 0.00 4.84
2174 2245 2.183555 GACCCTACCGCCAGAACG 59.816 66.667 0.00 0.00 0.00 3.95
2175 2246 2.288025 TGGACCCTACCGCCAGAAC 61.288 63.158 0.00 0.00 0.00 3.01
2176 2247 2.120940 TGGACCCTACCGCCAGAA 59.879 61.111 0.00 0.00 0.00 3.02
2180 2251 3.462199 GATGCTGGACCCTACCGCC 62.462 68.421 0.00 0.00 0.00 6.13
2181 2252 2.109181 GATGCTGGACCCTACCGC 59.891 66.667 0.00 0.00 0.00 5.68
2182 2253 0.469331 TAGGATGCTGGACCCTACCG 60.469 60.000 0.00 0.00 0.00 4.02
2183 2254 1.049402 GTAGGATGCTGGACCCTACC 58.951 60.000 8.50 0.00 44.02 3.18
2185 2256 0.469331 CGGTAGGATGCTGGACCCTA 60.469 60.000 0.00 0.00 0.00 3.53
2186 2257 1.762460 CGGTAGGATGCTGGACCCT 60.762 63.158 0.00 0.00 0.00 4.34
2187 2258 2.822399 CGGTAGGATGCTGGACCC 59.178 66.667 0.00 0.00 0.00 4.46
2188 2259 2.109181 GCGGTAGGATGCTGGACC 59.891 66.667 0.00 0.00 0.00 4.46
2189 2260 2.109181 GGCGGTAGGATGCTGGAC 59.891 66.667 0.00 0.00 0.00 4.02
2190 2261 2.364973 TGGCGGTAGGATGCTGGA 60.365 61.111 0.00 0.00 0.00 3.86
2217 2561 3.487211 GGGACCAAACCCTACCGT 58.513 61.111 0.00 0.00 45.90 4.83
2227 2571 1.073098 GGGAGAAAAGGAGGGACCAA 58.927 55.000 0.00 0.00 42.04 3.67
2238 2582 2.316108 GGAGCAAAACAGGGGAGAAAA 58.684 47.619 0.00 0.00 0.00 2.29
2239 2583 1.216678 TGGAGCAAAACAGGGGAGAAA 59.783 47.619 0.00 0.00 0.00 2.52
2240 2584 0.850100 TGGAGCAAAACAGGGGAGAA 59.150 50.000 0.00 0.00 0.00 2.87
2244 2588 0.604578 CACATGGAGCAAAACAGGGG 59.395 55.000 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.