Multiple sequence alignment - TraesCS1B01G320300

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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 TraesCS1B01G320300 chr1B 100.000 2297 0 0 1 2297 544613002 544615298 0.000000e+00 4242
1 TraesCS1B01G320300 chr1B 99.321 2062 12 1 1 2062 544593697 544595756 0.000000e+00 3729
2 TraesCS1B01G320300 chr1B 99.224 2062 16 0 1 2062 544623636 544625697 0.000000e+00 3720
3 TraesCS1B01G320300 chrUn 99.370 2062 13 0 1 2062 229310227 229308166 0.000000e+00 3736
4 TraesCS1B01G320300 chrUn 99.321 2062 14 0 1 2062 199874824 199876885 0.000000e+00 3731
5 TraesCS1B01G320300 chrUn 99.321 2062 14 0 1 2062 291535440 291537501 0.000000e+00 3731
6 TraesCS1B01G320300 chrUn 99.224 2063 15 1 1 2062 274341282 274339220 0.000000e+00 3720
7 TraesCS1B01G320300 chrUn 99.224 2062 15 1 1 2062 245706068 245708128 0.000000e+00 3718
8 TraesCS1B01G320300 chrUn 99.176 2062 17 0 1 2062 199904744 199906805 0.000000e+00 3714
9 TraesCS1B01G320300 chrUn 99.127 2062 18 0 1 2062 3845814 3843753 0.000000e+00 3709
10 TraesCS1B01G320300 chrUn 100.000 224 0 0 2074 2297 237320527 237320750 4.570000e-112 414
11 TraesCS1B01G320300 chrUn 100.000 224 0 0 2074 2297 274341153 274340930 4.570000e-112 414
12 TraesCS1B01G320300 chrUn 100.000 224 0 0 2074 2297 342573974 342573751 4.570000e-112 414
13 TraesCS1B01G320300 chrUn 100.000 224 0 0 2074 2297 402044345 402044568 4.570000e-112 414
14 TraesCS1B01G320300 chrUn 100.000 224 0 0 2074 2297 416971039 416971262 4.570000e-112 414
15 TraesCS1B01G320300 chrUn 100.000 224 0 0 2074 2297 450280287 450280064 4.570000e-112 414
16 TraesCS1B01G320300 chrUn 100.000 224 0 0 2074 2297 453574162 453574385 4.570000e-112 414
17 TraesCS1B01G320300 chrUn 99.554 224 1 0 2074 2297 245706197 245706420 2.120000e-110 409
18 TraesCS1B01G320300 chrUn 99.554 224 1 0 2074 2297 395173183 395172960 2.120000e-110 409


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 TraesCS1B01G320300 chr1B 544613002 544615298 2296 False 4242.0 4242 100.000 1 2297 1 chr1B.!!$F2 2296
1 TraesCS1B01G320300 chr1B 544593697 544595756 2059 False 3729.0 3729 99.321 1 2062 1 chr1B.!!$F1 2061
2 TraesCS1B01G320300 chr1B 544623636 544625697 2061 False 3720.0 3720 99.224 1 2062 1 chr1B.!!$F3 2061
3 TraesCS1B01G320300 chrUn 229308166 229310227 2061 True 3736.0 3736 99.370 1 2062 1 chrUn.!!$R2 2061
4 TraesCS1B01G320300 chrUn 199874824 199876885 2061 False 3731.0 3731 99.321 1 2062 1 chrUn.!!$F1 2061
5 TraesCS1B01G320300 chrUn 291535440 291537501 2061 False 3731.0 3731 99.321 1 2062 1 chrUn.!!$F4 2061
6 TraesCS1B01G320300 chrUn 199904744 199906805 2061 False 3714.0 3714 99.176 1 2062 1 chrUn.!!$F2 2061
7 TraesCS1B01G320300 chrUn 3843753 3845814 2061 True 3709.0 3709 99.127 1 2062 1 chrUn.!!$R1 2061
8 TraesCS1B01G320300 chrUn 274339220 274341282 2062 True 2067.0 3720 99.612 1 2297 2 chrUn.!!$R6 2296
9 TraesCS1B01G320300 chrUn 245706068 245708128 2060 False 2063.5 3718 99.389 1 2297 2 chrUn.!!$F8 2296

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
886 887 1.371389 GAAGAGAACCGCACGTCGT 60.371 57.895 0.0 0.0 36.19 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2075 2078 0.179018 GCGTCCCCAATGCCTCTAAT 60.179 55.0 0.0 0.0 33.47 1.73 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
146 147 3.655276 CAATGATTAGAGGCATTGGGC 57.345 47.619 0.00 0.00 44.62 5.36
753 754 2.033448 GGGATGTGGCGGTTGACA 59.967 61.111 0.00 0.00 0.00 3.58
874 875 2.119611 TCCAGTGGCCGGAAGAGA 59.880 61.111 5.05 0.00 0.00 3.10
886 887 1.371389 GAAGAGAACCGCACGTCGT 60.371 57.895 0.00 0.00 36.19 4.34
1033 1034 0.603065 GCAAGGGAAGTCGGCAAAAT 59.397 50.000 0.00 0.00 0.00 1.82
1364 1365 1.526455 AACCAAGCGCGGGTAAACA 60.526 52.632 23.98 0.00 37.77 2.83
1423 1424 4.401202 TGCCTCGTCATCTAATTAGTGACA 59.599 41.667 28.21 20.45 41.69 3.58
2074 2077 2.805845 CCAATAGGTTAGACCGTCGTG 58.194 52.381 0.00 0.00 44.90 4.35
2075 2078 2.424601 CCAATAGGTTAGACCGTCGTGA 59.575 50.000 0.00 0.00 44.90 4.35
2076 2079 3.067742 CCAATAGGTTAGACCGTCGTGAT 59.932 47.826 0.00 0.00 44.90 3.06
2077 2080 4.441079 CCAATAGGTTAGACCGTCGTGATT 60.441 45.833 0.00 0.00 44.90 2.57
2078 2081 5.221106 CCAATAGGTTAGACCGTCGTGATTA 60.221 44.000 0.00 0.00 44.90 1.75
2079 2082 5.686159 ATAGGTTAGACCGTCGTGATTAG 57.314 43.478 0.00 0.00 44.90 1.73
2080 2083 3.614092 AGGTTAGACCGTCGTGATTAGA 58.386 45.455 0.00 0.00 44.90 2.10
2081 2084 3.626670 AGGTTAGACCGTCGTGATTAGAG 59.373 47.826 0.00 0.00 44.90 2.43
2082 2085 3.243002 GGTTAGACCGTCGTGATTAGAGG 60.243 52.174 0.00 0.00 0.00 3.69
2083 2086 0.739561 AGACCGTCGTGATTAGAGGC 59.260 55.000 0.00 0.00 0.00 4.70
2084 2087 0.454600 GACCGTCGTGATTAGAGGCA 59.545 55.000 0.00 0.00 0.00 4.75
2085 2088 1.067212 GACCGTCGTGATTAGAGGCAT 59.933 52.381 0.00 0.00 0.00 4.40
2086 2089 1.480954 ACCGTCGTGATTAGAGGCATT 59.519 47.619 0.00 0.00 0.00 3.56
2087 2090 1.860950 CCGTCGTGATTAGAGGCATTG 59.139 52.381 0.00 0.00 0.00 2.82
2088 2091 1.860950 CGTCGTGATTAGAGGCATTGG 59.139 52.381 0.00 0.00 0.00 3.16
2089 2092 2.213499 GTCGTGATTAGAGGCATTGGG 58.787 52.381 0.00 0.00 0.00 4.12
2090 2093 1.140852 TCGTGATTAGAGGCATTGGGG 59.859 52.381 0.00 0.00 0.00 4.96
2091 2094 1.140852 CGTGATTAGAGGCATTGGGGA 59.859 52.381 0.00 0.00 0.00 4.81
2092 2095 2.576615 GTGATTAGAGGCATTGGGGAC 58.423 52.381 0.00 0.00 0.00 4.46
2093 2096 1.140852 TGATTAGAGGCATTGGGGACG 59.859 52.381 0.00 0.00 0.00 4.79
2094 2097 0.179018 ATTAGAGGCATTGGGGACGC 60.179 55.000 0.00 0.00 0.00 5.19
2095 2098 1.558167 TTAGAGGCATTGGGGACGCA 61.558 55.000 0.00 0.00 0.00 5.24
2096 2099 1.558167 TAGAGGCATTGGGGACGCAA 61.558 55.000 4.25 4.25 0.00 4.85
2097 2100 2.676471 AGGCATTGGGGACGCAAC 60.676 61.111 3.84 0.00 0.00 4.17
2098 2101 4.114997 GGCATTGGGGACGCAACG 62.115 66.667 3.84 0.00 0.00 4.10
2099 2102 3.361977 GCATTGGGGACGCAACGT 61.362 61.111 3.84 0.00 45.10 3.99
2108 2111 3.292936 ACGCAACGTCCTCGACCT 61.293 61.111 10.31 0.00 33.69 3.85
2109 2112 1.968017 ACGCAACGTCCTCGACCTA 60.968 57.895 10.31 0.00 33.69 3.08
2110 2113 1.310933 ACGCAACGTCCTCGACCTAT 61.311 55.000 10.31 0.00 33.69 2.57
2111 2114 0.179145 CGCAACGTCCTCGACCTATT 60.179 55.000 0.00 0.00 40.62 1.73
2112 2115 1.557651 GCAACGTCCTCGACCTATTC 58.442 55.000 0.00 0.00 40.62 1.75
2113 2116 1.134560 GCAACGTCCTCGACCTATTCT 59.865 52.381 0.00 0.00 40.62 2.40
2114 2117 2.795331 GCAACGTCCTCGACCTATTCTC 60.795 54.545 0.00 0.00 40.62 2.87
2115 2118 2.414994 ACGTCCTCGACCTATTCTCA 57.585 50.000 0.00 0.00 40.62 3.27
2116 2119 2.719739 ACGTCCTCGACCTATTCTCAA 58.280 47.619 0.00 0.00 40.62 3.02
2117 2120 3.087031 ACGTCCTCGACCTATTCTCAAA 58.913 45.455 0.00 0.00 40.62 2.69
2118 2121 3.119566 ACGTCCTCGACCTATTCTCAAAC 60.120 47.826 0.00 0.00 40.62 2.93
2119 2122 3.128938 CGTCCTCGACCTATTCTCAAACT 59.871 47.826 0.00 0.00 39.71 2.66
2120 2123 4.380655 CGTCCTCGACCTATTCTCAAACTT 60.381 45.833 0.00 0.00 39.71 2.66
2121 2124 5.480205 GTCCTCGACCTATTCTCAAACTTT 58.520 41.667 0.00 0.00 0.00 2.66
2122 2125 6.624423 CGTCCTCGACCTATTCTCAAACTTTA 60.624 42.308 0.00 0.00 39.71 1.85
2123 2126 7.095270 GTCCTCGACCTATTCTCAAACTTTAA 58.905 38.462 0.00 0.00 0.00 1.52
2124 2127 7.601508 GTCCTCGACCTATTCTCAAACTTTAAA 59.398 37.037 0.00 0.00 0.00 1.52
2125 2128 8.319146 TCCTCGACCTATTCTCAAACTTTAAAT 58.681 33.333 0.00 0.00 0.00 1.40
2126 2129 9.595823 CCTCGACCTATTCTCAAACTTTAAATA 57.404 33.333 0.00 0.00 0.00 1.40
2136 2139 9.681062 TTCTCAAACTTTAAATAGGTAGGATGG 57.319 33.333 0.00 0.00 0.00 3.51
2137 2140 8.832735 TCTCAAACTTTAAATAGGTAGGATGGT 58.167 33.333 0.00 0.00 0.00 3.55
2138 2141 8.801882 TCAAACTTTAAATAGGTAGGATGGTG 57.198 34.615 0.00 0.00 0.00 4.17
2139 2142 7.338449 TCAAACTTTAAATAGGTAGGATGGTGC 59.662 37.037 0.00 0.00 0.00 5.01
2140 2143 5.365619 ACTTTAAATAGGTAGGATGGTGCG 58.634 41.667 0.00 0.00 0.00 5.34
2141 2144 2.930826 AAATAGGTAGGATGGTGCGG 57.069 50.000 0.00 0.00 0.00 5.69
2142 2145 0.396811 AATAGGTAGGATGGTGCGGC 59.603 55.000 0.00 0.00 0.00 6.53
2143 2146 0.471971 ATAGGTAGGATGGTGCGGCT 60.472 55.000 0.00 0.00 0.00 5.52
2144 2147 1.399744 TAGGTAGGATGGTGCGGCTG 61.400 60.000 0.00 0.00 0.00 4.85
2145 2148 2.897350 GTAGGATGGTGCGGCTGC 60.897 66.667 11.65 11.65 43.20 5.25
2146 2149 3.083349 TAGGATGGTGCGGCTGCT 61.083 61.111 20.27 0.00 43.34 4.24
2147 2150 2.669133 TAGGATGGTGCGGCTGCTT 61.669 57.895 20.27 0.42 43.34 3.91
2148 2151 2.593468 TAGGATGGTGCGGCTGCTTC 62.593 60.000 20.27 11.66 43.34 3.86
2149 2152 3.869272 GATGGTGCGGCTGCTTCG 61.869 66.667 20.27 0.00 43.34 3.79
2173 2176 4.752879 CGTGCCACGGAATCGGGT 62.753 66.667 9.90 0.00 38.30 5.28
2174 2177 3.124921 GTGCCACGGAATCGGGTG 61.125 66.667 0.00 0.00 38.30 4.61
2176 2179 4.778143 GCCACGGAATCGGGTGCT 62.778 66.667 0.00 0.00 38.30 4.40
2177 2180 2.511600 CCACGGAATCGGGTGCTC 60.512 66.667 0.00 0.00 38.30 4.26
2178 2181 2.511600 CACGGAATCGGGTGCTCC 60.512 66.667 0.00 0.00 41.39 4.70
2179 2182 3.000819 ACGGAATCGGGTGCTCCA 61.001 61.111 7.20 0.00 41.39 3.86
2180 2183 2.267642 CGGAATCGGGTGCTCCAA 59.732 61.111 7.20 0.00 34.36 3.53
2181 2184 1.815421 CGGAATCGGGTGCTCCAAG 60.815 63.158 7.20 0.08 34.36 3.61
2182 2185 1.299976 GGAATCGGGTGCTCCAAGT 59.700 57.895 7.20 0.00 34.36 3.16
2183 2186 1.026718 GGAATCGGGTGCTCCAAGTG 61.027 60.000 7.20 0.00 34.36 3.16
2184 2187 1.002134 AATCGGGTGCTCCAAGTGG 60.002 57.895 7.20 0.00 34.36 4.00
2185 2188 2.484287 AATCGGGTGCTCCAAGTGGG 62.484 60.000 7.20 0.00 35.41 4.61
2188 2191 4.284550 GGTGCTCCAAGTGGGCCA 62.285 66.667 0.00 0.00 36.21 5.36
2189 2192 2.036256 GTGCTCCAAGTGGGCCAT 59.964 61.111 10.70 0.00 36.21 4.40
2190 2193 1.607467 GTGCTCCAAGTGGGCCATT 60.607 57.895 10.70 0.91 36.21 3.16
2191 2194 1.155859 TGCTCCAAGTGGGCCATTT 59.844 52.632 10.70 9.58 36.21 2.32
2192 2195 0.471591 TGCTCCAAGTGGGCCATTTT 60.472 50.000 10.70 4.76 36.21 1.82
2193 2196 0.686789 GCTCCAAGTGGGCCATTTTT 59.313 50.000 10.70 1.81 36.21 1.94
2194 2197 1.608801 GCTCCAAGTGGGCCATTTTTG 60.609 52.381 10.70 14.78 36.21 2.44
2195 2198 1.002315 CTCCAAGTGGGCCATTTTTGG 59.998 52.381 27.91 27.91 39.66 3.28
2196 2199 0.764271 CCAAGTGGGCCATTTTTGGT 59.236 50.000 26.55 2.45 34.88 3.67
2197 2200 1.974236 CCAAGTGGGCCATTTTTGGTA 59.026 47.619 26.55 0.00 34.88 3.25
2198 2201 2.370189 CCAAGTGGGCCATTTTTGGTAA 59.630 45.455 26.55 0.00 34.88 2.85
2199 2202 3.556843 CCAAGTGGGCCATTTTTGGTAAG 60.557 47.826 26.55 11.01 34.88 2.34
2200 2203 1.623311 AGTGGGCCATTTTTGGTAAGC 59.377 47.619 10.70 0.00 0.00 3.09
2201 2204 1.346068 GTGGGCCATTTTTGGTAAGCA 59.654 47.619 10.70 0.00 0.00 3.91
2202 2205 1.622811 TGGGCCATTTTTGGTAAGCAG 59.377 47.619 0.00 0.00 0.00 4.24
2203 2206 1.899142 GGGCCATTTTTGGTAAGCAGA 59.101 47.619 4.39 0.00 0.00 4.26
2204 2207 2.301583 GGGCCATTTTTGGTAAGCAGAA 59.698 45.455 4.39 0.00 0.00 3.02
2205 2208 3.325870 GGCCATTTTTGGTAAGCAGAAC 58.674 45.455 0.00 0.00 0.00 3.01
2206 2209 3.006859 GGCCATTTTTGGTAAGCAGAACT 59.993 43.478 0.00 0.00 0.00 3.01
2207 2210 3.989817 GCCATTTTTGGTAAGCAGAACTG 59.010 43.478 0.00 0.00 0.00 3.16
2208 2211 4.559153 CCATTTTTGGTAAGCAGAACTGG 58.441 43.478 3.99 0.00 0.00 4.00
2209 2212 3.726291 TTTTTGGTAAGCAGAACTGGC 57.274 42.857 3.99 0.00 0.00 4.85
2210 2213 1.234821 TTTGGTAAGCAGAACTGGCG 58.765 50.000 3.99 0.00 36.08 5.69
2211 2214 0.394938 TTGGTAAGCAGAACTGGCGA 59.605 50.000 3.99 0.00 36.08 5.54
2212 2215 0.613260 TGGTAAGCAGAACTGGCGAT 59.387 50.000 3.99 0.00 36.08 4.58
2213 2216 1.009829 GGTAAGCAGAACTGGCGATG 58.990 55.000 3.99 0.00 36.08 3.84
2214 2217 0.375106 GTAAGCAGAACTGGCGATGC 59.625 55.000 3.99 0.00 38.97 3.91
2215 2218 1.083806 TAAGCAGAACTGGCGATGCG 61.084 55.000 3.99 0.00 43.41 4.73
2216 2219 3.869272 GCAGAACTGGCGATGCGG 61.869 66.667 3.99 0.00 0.00 5.69
2217 2220 3.197790 CAGAACTGGCGATGCGGG 61.198 66.667 0.00 0.00 0.00 6.13
2218 2221 3.390521 AGAACTGGCGATGCGGGA 61.391 61.111 0.00 0.00 0.00 5.14
2219 2222 2.203070 GAACTGGCGATGCGGGAT 60.203 61.111 0.00 0.00 0.00 3.85
2220 2223 2.514592 AACTGGCGATGCGGGATG 60.515 61.111 0.00 0.00 0.00 3.51
2221 2224 2.923426 GAACTGGCGATGCGGGATGA 62.923 60.000 0.00 0.00 0.00 2.92
2222 2225 2.203056 CTGGCGATGCGGGATGAA 60.203 61.111 0.00 0.00 0.00 2.57
2223 2226 2.513666 TGGCGATGCGGGATGAAC 60.514 61.111 0.00 0.00 0.00 3.18
2224 2227 3.279875 GGCGATGCGGGATGAACC 61.280 66.667 0.00 0.00 38.08 3.62
2248 2251 3.051479 CGGGTTACGGTGCCCAAC 61.051 66.667 18.44 3.74 45.07 3.77
2249 2252 2.433004 GGGTTACGGTGCCCAACT 59.567 61.111 15.03 0.00 44.23 3.16
2250 2253 1.969589 GGGTTACGGTGCCCAACTG 60.970 63.158 15.03 0.00 44.23 3.16
2251 2254 2.622962 GGTTACGGTGCCCAACTGC 61.623 63.158 0.00 0.00 38.92 4.40
2252 2255 2.666862 TTACGGTGCCCAACTGCG 60.667 61.111 0.00 0.00 38.92 5.18
2258 2261 4.998400 TGCCCAACTGCGCGCTAA 62.998 61.111 33.29 12.42 0.00 3.09
2259 2262 4.460873 GCCCAACTGCGCGCTAAC 62.461 66.667 33.29 10.69 0.00 2.34
2260 2263 3.799755 CCCAACTGCGCGCTAACC 61.800 66.667 33.29 2.60 0.00 2.85
2261 2264 2.742372 CCAACTGCGCGCTAACCT 60.742 61.111 33.29 9.31 0.00 3.50
2262 2265 1.447140 CCAACTGCGCGCTAACCTA 60.447 57.895 33.29 9.83 0.00 3.08
2263 2266 1.421410 CCAACTGCGCGCTAACCTAG 61.421 60.000 33.29 21.88 0.00 3.02
2264 2267 0.457853 CAACTGCGCGCTAACCTAGA 60.458 55.000 33.29 8.12 0.00 2.43
2265 2268 0.245539 AACTGCGCGCTAACCTAGAA 59.754 50.000 33.29 7.29 0.00 2.10
2266 2269 0.458025 ACTGCGCGCTAACCTAGAAC 60.458 55.000 33.29 0.00 0.00 3.01
2267 2270 1.146358 CTGCGCGCTAACCTAGAACC 61.146 60.000 33.29 0.00 0.00 3.62
2268 2271 1.881709 GCGCGCTAACCTAGAACCC 60.882 63.158 26.67 0.00 0.00 4.11
2269 2272 1.514087 CGCGCTAACCTAGAACCCA 59.486 57.895 5.56 0.00 0.00 4.51
2270 2273 0.804933 CGCGCTAACCTAGAACCCAC 60.805 60.000 5.56 0.00 0.00 4.61
2271 2274 0.248289 GCGCTAACCTAGAACCCACA 59.752 55.000 0.00 0.00 0.00 4.17
2272 2275 1.338389 GCGCTAACCTAGAACCCACAA 60.338 52.381 0.00 0.00 0.00 3.33
2273 2276 2.872842 GCGCTAACCTAGAACCCACAAA 60.873 50.000 0.00 0.00 0.00 2.83
2274 2277 3.000727 CGCTAACCTAGAACCCACAAAG 58.999 50.000 0.00 0.00 0.00 2.77
2275 2278 3.344515 GCTAACCTAGAACCCACAAAGG 58.655 50.000 0.00 0.00 37.03 3.11
2285 2288 2.029743 CCACAAAGGGTGTTGGTCG 58.970 57.895 0.00 0.00 46.44 4.79
2286 2289 0.464735 CCACAAAGGGTGTTGGTCGA 60.465 55.000 0.00 0.00 46.44 4.20
2287 2290 1.604604 CACAAAGGGTGTTGGTCGAT 58.395 50.000 0.00 0.00 42.75 3.59
2288 2291 1.953686 CACAAAGGGTGTTGGTCGATT 59.046 47.619 0.00 0.00 42.75 3.34
2289 2292 3.142951 CACAAAGGGTGTTGGTCGATTA 58.857 45.455 0.00 0.00 42.75 1.75
2290 2293 3.566322 CACAAAGGGTGTTGGTCGATTAA 59.434 43.478 0.00 0.00 42.75 1.40
2291 2294 3.818773 ACAAAGGGTGTTGGTCGATTAAG 59.181 43.478 0.00 0.00 37.01 1.85
2292 2295 4.069304 CAAAGGGTGTTGGTCGATTAAGA 58.931 43.478 0.00 0.00 0.00 2.10
2293 2296 3.329929 AGGGTGTTGGTCGATTAAGAC 57.670 47.619 0.00 0.00 40.25 3.01
2294 2297 2.635915 AGGGTGTTGGTCGATTAAGACA 59.364 45.455 11.90 1.56 42.62 3.41
2295 2298 3.000727 GGGTGTTGGTCGATTAAGACAG 58.999 50.000 11.90 0.00 42.62 3.51
2296 2299 2.415512 GGTGTTGGTCGATTAAGACAGC 59.584 50.000 11.90 8.29 42.62 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
146 147 2.191354 TAGGTCGAGGACGTTGCGTG 62.191 60.000 0.00 0.00 41.37 5.34
550 551 1.746615 CCACCAAGATCTGCACCGG 60.747 63.158 0.00 0.00 0.00 5.28
753 754 1.505353 CGGACTTCCTAACGTCGCT 59.495 57.895 0.00 0.00 0.00 4.93
1364 1365 3.117813 AGAGAGTCATAGTTACTCCCGCT 60.118 47.826 0.00 0.00 43.64 5.52
1423 1424 3.792401 TCTCGTTAATCCATTCATGCGT 58.208 40.909 0.00 0.00 0.00 5.24
2062 2065 2.357009 GCCTCTAATCACGACGGTCTAA 59.643 50.000 6.57 0.00 0.00 2.10
2063 2066 1.945394 GCCTCTAATCACGACGGTCTA 59.055 52.381 6.57 0.00 0.00 2.59
2064 2067 0.739561 GCCTCTAATCACGACGGTCT 59.260 55.000 6.57 0.00 0.00 3.85
2065 2068 0.454600 TGCCTCTAATCACGACGGTC 59.545 55.000 0.00 0.00 0.00 4.79
2066 2069 1.112113 ATGCCTCTAATCACGACGGT 58.888 50.000 0.00 0.00 0.00 4.83
2067 2070 1.860950 CAATGCCTCTAATCACGACGG 59.139 52.381 0.00 0.00 0.00 4.79
2068 2071 1.860950 CCAATGCCTCTAATCACGACG 59.139 52.381 0.00 0.00 0.00 5.12
2069 2072 2.213499 CCCAATGCCTCTAATCACGAC 58.787 52.381 0.00 0.00 0.00 4.34
2070 2073 1.140852 CCCCAATGCCTCTAATCACGA 59.859 52.381 0.00 0.00 0.00 4.35
2071 2074 1.140852 TCCCCAATGCCTCTAATCACG 59.859 52.381 0.00 0.00 0.00 4.35
2072 2075 2.576615 GTCCCCAATGCCTCTAATCAC 58.423 52.381 0.00 0.00 0.00 3.06
2073 2076 1.140852 CGTCCCCAATGCCTCTAATCA 59.859 52.381 0.00 0.00 0.00 2.57
2074 2077 1.884235 CGTCCCCAATGCCTCTAATC 58.116 55.000 0.00 0.00 0.00 1.75
2075 2078 0.179018 GCGTCCCCAATGCCTCTAAT 60.179 55.000 0.00 0.00 33.47 1.73
2076 2079 1.223487 GCGTCCCCAATGCCTCTAA 59.777 57.895 0.00 0.00 33.47 2.10
2077 2080 1.558167 TTGCGTCCCCAATGCCTCTA 61.558 55.000 0.00 0.00 39.30 2.43
2078 2081 2.905996 TTGCGTCCCCAATGCCTCT 61.906 57.895 0.00 0.00 39.30 3.69
2079 2082 2.361104 TTGCGTCCCCAATGCCTC 60.361 61.111 0.00 0.00 39.30 4.70
2080 2083 2.676471 GTTGCGTCCCCAATGCCT 60.676 61.111 0.00 0.00 39.30 4.75
2081 2084 4.114997 CGTTGCGTCCCCAATGCC 62.115 66.667 0.00 0.00 39.30 4.40
2082 2085 3.361977 ACGTTGCGTCCCCAATGC 61.362 61.111 0.00 0.00 33.69 3.56
2091 2094 1.310933 ATAGGTCGAGGACGTTGCGT 61.311 55.000 0.00 0.00 45.10 5.24
2092 2095 0.179145 AATAGGTCGAGGACGTTGCG 60.179 55.000 0.00 0.00 40.69 4.85
2093 2096 1.134560 AGAATAGGTCGAGGACGTTGC 59.865 52.381 0.00 0.00 40.69 4.17
2094 2097 2.422479 TGAGAATAGGTCGAGGACGTTG 59.578 50.000 0.00 0.00 40.69 4.10
2095 2098 2.719739 TGAGAATAGGTCGAGGACGTT 58.280 47.619 0.00 0.00 40.69 3.99
2096 2099 2.414994 TGAGAATAGGTCGAGGACGT 57.585 50.000 0.00 0.00 40.69 4.34
2097 2100 3.128938 AGTTTGAGAATAGGTCGAGGACG 59.871 47.826 0.00 0.00 41.26 4.79
2098 2101 4.722361 AGTTTGAGAATAGGTCGAGGAC 57.278 45.455 0.00 0.00 0.00 3.85
2099 2102 5.740290 AAAGTTTGAGAATAGGTCGAGGA 57.260 39.130 0.00 0.00 0.00 3.71
2100 2103 7.900782 TTTAAAGTTTGAGAATAGGTCGAGG 57.099 36.000 0.00 0.00 0.00 4.63
2102 2105 9.595823 CCTATTTAAAGTTTGAGAATAGGTCGA 57.404 33.333 23.12 0.00 41.92 4.20
2110 2113 9.681062 CCATCCTACCTATTTAAAGTTTGAGAA 57.319 33.333 0.00 0.00 0.00 2.87
2111 2114 8.832735 ACCATCCTACCTATTTAAAGTTTGAGA 58.167 33.333 0.00 0.00 0.00 3.27
2112 2115 8.893727 CACCATCCTACCTATTTAAAGTTTGAG 58.106 37.037 0.00 0.00 0.00 3.02
2113 2116 7.338449 GCACCATCCTACCTATTTAAAGTTTGA 59.662 37.037 0.00 0.00 0.00 2.69
2114 2117 7.480810 GCACCATCCTACCTATTTAAAGTTTG 58.519 38.462 0.00 0.00 0.00 2.93
2115 2118 6.317893 CGCACCATCCTACCTATTTAAAGTTT 59.682 38.462 0.00 0.00 0.00 2.66
2116 2119 5.820947 CGCACCATCCTACCTATTTAAAGTT 59.179 40.000 0.00 0.00 0.00 2.66
2117 2120 5.365619 CGCACCATCCTACCTATTTAAAGT 58.634 41.667 0.00 0.00 0.00 2.66
2118 2121 4.755123 CCGCACCATCCTACCTATTTAAAG 59.245 45.833 0.00 0.00 0.00 1.85
2119 2122 4.710324 CCGCACCATCCTACCTATTTAAA 58.290 43.478 0.00 0.00 0.00 1.52
2120 2123 3.495453 GCCGCACCATCCTACCTATTTAA 60.495 47.826 0.00 0.00 0.00 1.52
2121 2124 2.038033 GCCGCACCATCCTACCTATTTA 59.962 50.000 0.00 0.00 0.00 1.40
2122 2125 1.202770 GCCGCACCATCCTACCTATTT 60.203 52.381 0.00 0.00 0.00 1.40
2123 2126 0.396811 GCCGCACCATCCTACCTATT 59.603 55.000 0.00 0.00 0.00 1.73
2124 2127 0.471971 AGCCGCACCATCCTACCTAT 60.472 55.000 0.00 0.00 0.00 2.57
2125 2128 1.075525 AGCCGCACCATCCTACCTA 60.076 57.895 0.00 0.00 0.00 3.08
2126 2129 2.365635 AGCCGCACCATCCTACCT 60.366 61.111 0.00 0.00 0.00 3.08
2127 2130 2.203070 CAGCCGCACCATCCTACC 60.203 66.667 0.00 0.00 0.00 3.18
2128 2131 2.876368 AAGCAGCCGCACCATCCTAC 62.876 60.000 0.00 0.00 42.27 3.18
2129 2132 2.593468 GAAGCAGCCGCACCATCCTA 62.593 60.000 0.00 0.00 42.27 2.94
2130 2133 3.984193 GAAGCAGCCGCACCATCCT 62.984 63.158 0.00 0.00 42.27 3.24
2131 2134 3.512516 GAAGCAGCCGCACCATCC 61.513 66.667 0.00 0.00 42.27 3.51
2132 2135 3.869272 CGAAGCAGCCGCACCATC 61.869 66.667 0.00 0.00 42.27 3.51
2156 2159 4.752879 ACCCGATTCCGTGGCACG 62.753 66.667 31.78 31.78 42.11 5.34
2157 2160 3.124921 CACCCGATTCCGTGGCAC 61.125 66.667 7.79 7.79 31.93 5.01
2159 2162 4.778143 AGCACCCGATTCCGTGGC 62.778 66.667 0.00 0.00 31.93 5.01
2160 2163 2.511600 GAGCACCCGATTCCGTGG 60.512 66.667 0.00 0.00 33.98 4.94
2161 2164 2.511600 GGAGCACCCGATTCCGTG 60.512 66.667 0.00 0.00 0.00 4.94
2162 2165 2.521958 CTTGGAGCACCCGATTCCGT 62.522 60.000 0.00 0.00 37.93 4.69
2163 2166 1.815421 CTTGGAGCACCCGATTCCG 60.815 63.158 0.00 0.00 37.93 4.30
2164 2167 1.026718 CACTTGGAGCACCCGATTCC 61.027 60.000 0.00 0.00 37.93 3.01
2165 2168 1.026718 CCACTTGGAGCACCCGATTC 61.027 60.000 0.00 0.00 37.93 2.52
2166 2169 1.002134 CCACTTGGAGCACCCGATT 60.002 57.895 0.00 0.00 37.93 3.34
2167 2170 2.671070 CCACTTGGAGCACCCGAT 59.329 61.111 0.00 0.00 37.93 4.18
2168 2171 3.636231 CCCACTTGGAGCACCCGA 61.636 66.667 0.00 0.00 37.93 5.14
2171 2174 3.590466 ATGGCCCACTTGGAGCACC 62.590 63.158 0.00 0.00 37.39 5.01
2172 2175 1.187567 AAATGGCCCACTTGGAGCAC 61.188 55.000 0.00 0.00 37.39 4.40
2173 2176 0.471591 AAAATGGCCCACTTGGAGCA 60.472 50.000 0.00 0.00 37.39 4.26
2174 2177 0.686789 AAAAATGGCCCACTTGGAGC 59.313 50.000 0.00 0.00 37.39 4.70
2175 2178 1.002315 CCAAAAATGGCCCACTTGGAG 59.998 52.381 13.44 0.00 39.12 3.86
2176 2179 1.055040 CCAAAAATGGCCCACTTGGA 58.945 50.000 13.44 0.00 39.12 3.53
2177 2180 0.764271 ACCAAAAATGGCCCACTTGG 59.236 50.000 16.01 16.01 41.91 3.61
2178 2181 3.663025 CTTACCAAAAATGGCCCACTTG 58.337 45.455 0.00 0.00 0.00 3.16
2179 2182 2.038426 GCTTACCAAAAATGGCCCACTT 59.962 45.455 0.00 0.00 0.00 3.16
2180 2183 1.623311 GCTTACCAAAAATGGCCCACT 59.377 47.619 0.00 0.00 0.00 4.00
2181 2184 1.346068 TGCTTACCAAAAATGGCCCAC 59.654 47.619 0.00 0.00 0.00 4.61
2182 2185 1.622811 CTGCTTACCAAAAATGGCCCA 59.377 47.619 0.00 0.00 0.00 5.36
2183 2186 1.899142 TCTGCTTACCAAAAATGGCCC 59.101 47.619 0.00 0.00 0.00 5.80
2184 2187 3.006859 AGTTCTGCTTACCAAAAATGGCC 59.993 43.478 0.00 0.00 0.00 5.36
2185 2188 3.989817 CAGTTCTGCTTACCAAAAATGGC 59.010 43.478 0.00 0.00 0.00 4.40
2186 2189 4.559153 CCAGTTCTGCTTACCAAAAATGG 58.441 43.478 0.00 0.00 0.00 3.16
2187 2190 3.989817 GCCAGTTCTGCTTACCAAAAATG 59.010 43.478 0.00 0.00 0.00 2.32
2188 2191 3.305335 CGCCAGTTCTGCTTACCAAAAAT 60.305 43.478 0.00 0.00 0.00 1.82
2189 2192 2.034053 CGCCAGTTCTGCTTACCAAAAA 59.966 45.455 0.00 0.00 0.00 1.94
2190 2193 1.606668 CGCCAGTTCTGCTTACCAAAA 59.393 47.619 0.00 0.00 0.00 2.44
2191 2194 1.202710 TCGCCAGTTCTGCTTACCAAA 60.203 47.619 0.00 0.00 0.00 3.28
2192 2195 0.394938 TCGCCAGTTCTGCTTACCAA 59.605 50.000 0.00 0.00 0.00 3.67
2193 2196 0.613260 ATCGCCAGTTCTGCTTACCA 59.387 50.000 0.00 0.00 0.00 3.25
2194 2197 1.009829 CATCGCCAGTTCTGCTTACC 58.990 55.000 0.00 0.00 0.00 2.85
2195 2198 0.375106 GCATCGCCAGTTCTGCTTAC 59.625 55.000 0.00 0.00 0.00 2.34
2196 2199 1.083806 CGCATCGCCAGTTCTGCTTA 61.084 55.000 0.00 0.00 32.48 3.09
2197 2200 2.393768 CGCATCGCCAGTTCTGCTT 61.394 57.895 0.00 0.00 32.48 3.91
2198 2201 2.816958 CGCATCGCCAGTTCTGCT 60.817 61.111 0.00 0.00 32.48 4.24
2199 2202 3.869272 CCGCATCGCCAGTTCTGC 61.869 66.667 0.00 0.00 0.00 4.26
2200 2203 2.930385 ATCCCGCATCGCCAGTTCTG 62.930 60.000 0.00 0.00 0.00 3.02
2201 2204 2.735772 ATCCCGCATCGCCAGTTCT 61.736 57.895 0.00 0.00 0.00 3.01
2202 2205 2.203070 ATCCCGCATCGCCAGTTC 60.203 61.111 0.00 0.00 0.00 3.01
2203 2206 2.514592 CATCCCGCATCGCCAGTT 60.515 61.111 0.00 0.00 0.00 3.16
2204 2207 3.030168 TTCATCCCGCATCGCCAGT 62.030 57.895 0.00 0.00 0.00 4.00
2205 2208 2.203056 TTCATCCCGCATCGCCAG 60.203 61.111 0.00 0.00 0.00 4.85
2206 2209 2.513666 GTTCATCCCGCATCGCCA 60.514 61.111 0.00 0.00 0.00 5.69
2207 2210 3.279875 GGTTCATCCCGCATCGCC 61.280 66.667 0.00 0.00 0.00 5.54
2208 2211 3.640000 CGGTTCATCCCGCATCGC 61.640 66.667 0.00 0.00 41.78 4.58
2209 2212 2.916502 TTCCGGTTCATCCCGCATCG 62.917 60.000 0.00 0.00 46.71 3.84
2210 2213 1.153249 TTCCGGTTCATCCCGCATC 60.153 57.895 0.00 0.00 46.71 3.91
2211 2214 1.153168 CTTCCGGTTCATCCCGCAT 60.153 57.895 0.00 0.00 46.71 4.73
2212 2215 2.267642 CTTCCGGTTCATCCCGCA 59.732 61.111 0.00 0.00 46.71 5.69
2213 2216 3.202706 GCTTCCGGTTCATCCCGC 61.203 66.667 0.00 0.00 46.71 6.13
2215 2218 2.513897 CGGCTTCCGGTTCATCCC 60.514 66.667 0.00 0.00 44.15 3.85
2243 2246 2.845752 TAGGTTAGCGCGCAGTTGGG 62.846 60.000 35.10 0.00 0.00 4.12
2244 2247 1.421410 CTAGGTTAGCGCGCAGTTGG 61.421 60.000 35.10 12.68 0.00 3.77
2245 2248 0.457853 TCTAGGTTAGCGCGCAGTTG 60.458 55.000 35.10 15.65 0.00 3.16
2246 2249 0.245539 TTCTAGGTTAGCGCGCAGTT 59.754 50.000 35.10 16.01 0.00 3.16
2247 2250 0.458025 GTTCTAGGTTAGCGCGCAGT 60.458 55.000 35.10 16.87 0.00 4.40
2248 2251 1.146358 GGTTCTAGGTTAGCGCGCAG 61.146 60.000 35.10 20.64 0.00 5.18
2249 2252 1.153706 GGTTCTAGGTTAGCGCGCA 60.154 57.895 35.10 16.82 0.00 6.09
2250 2253 1.881709 GGGTTCTAGGTTAGCGCGC 60.882 63.158 26.66 26.66 0.00 6.86
2251 2254 0.804933 GTGGGTTCTAGGTTAGCGCG 60.805 60.000 0.00 0.00 0.00 6.86
2252 2255 0.248289 TGTGGGTTCTAGGTTAGCGC 59.752 55.000 0.00 0.00 0.00 5.92
2253 2256 2.754946 TTGTGGGTTCTAGGTTAGCG 57.245 50.000 0.00 0.00 0.00 4.26
2254 2257 3.344515 CCTTTGTGGGTTCTAGGTTAGC 58.655 50.000 0.00 0.00 0.00 3.09
2269 2272 2.358322 AATCGACCAACACCCTTTGT 57.642 45.000 0.00 0.00 41.74 2.83
2270 2273 4.069304 TCTTAATCGACCAACACCCTTTG 58.931 43.478 0.00 0.00 0.00 2.77
2271 2274 4.070009 GTCTTAATCGACCAACACCCTTT 58.930 43.478 0.00 0.00 0.00 3.11
2272 2275 3.071892 TGTCTTAATCGACCAACACCCTT 59.928 43.478 0.00 0.00 32.97 3.95
2273 2276 2.635915 TGTCTTAATCGACCAACACCCT 59.364 45.455 0.00 0.00 32.97 4.34
2274 2277 3.000727 CTGTCTTAATCGACCAACACCC 58.999 50.000 0.00 0.00 32.97 4.61
2275 2278 2.415512 GCTGTCTTAATCGACCAACACC 59.584 50.000 0.00 0.00 32.97 4.16
2276 2279 3.724295 GCTGTCTTAATCGACCAACAC 57.276 47.619 0.00 0.00 32.97 3.32


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

AutoCloner maintained by Alex Coulton.