Multiple sequence alignment - TraesCS2A01G088200

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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 TraesCS2A01G088200 chr2A 100.000 2939 0 0 1 2939 41620622 41623560 0.000000e+00 5428.0
1 TraesCS2A01G088200 chr2A 91.837 49 3 1 2735 2783 21812855 21812808 1.890000e-07 67.6
2 TraesCS2A01G088200 chr2B 93.444 2044 116 10 1 2042 63864905 63862878 0.000000e+00 3016.0
3 TraesCS2A01G088200 chr2B 87.397 2063 227 19 1 2046 64191194 64193240 0.000000e+00 2338.0
4 TraesCS2A01G088200 chr2B 86.129 2069 242 21 1 2039 64091356 64089303 0.000000e+00 2189.0
5 TraesCS2A01G088200 chr2B 80.556 180 21 6 2769 2939 63860712 63860538 3.070000e-25 126.0
6 TraesCS2A01G088200 chr2D 93.376 2053 107 16 1 2046 36911251 36913281 0.000000e+00 3011.0
7 TraesCS2A01G088200 chr2D 85.907 2072 244 22 1 2046 36886262 36888311 0.000000e+00 2165.0
8 TraesCS2A01G088200 chr2D 87.282 401 34 6 2554 2939 36890036 36890434 2.690000e-120 442.0
9 TraesCS2A01G088200 chr2D 86.284 401 38 6 2554 2939 36915003 36915401 1.260000e-113 420.0
10 TraesCS2A01G088200 chr2D 82.143 196 35 0 2125 2320 634561449 634561254 5.040000e-38 169.0
11 TraesCS2A01G088200 chr2D 97.222 36 1 0 2039 2074 36888321 36888356 8.790000e-06 62.1
12 TraesCS2A01G088200 chr5D 89.362 188 18 2 2125 2312 267821730 267821545 4.900000e-58 235.0
13 TraesCS2A01G088200 chr5D 87.845 181 18 3 2125 2304 220707707 220707530 2.970000e-50 209.0
14 TraesCS2A01G088200 chr6A 88.398 181 21 0 2126 2306 559398330 559398150 4.930000e-53 219.0
15 TraesCS2A01G088200 chr6D 85.326 184 27 0 2124 2307 438404123 438403940 1.080000e-44 191.0
16 TraesCS2A01G088200 chr3D 85.556 180 26 0 2125 2304 395665851 395665672 3.870000e-44 189.0
17 TraesCS2A01G088200 chr5A 85.393 178 24 2 2128 2304 217004407 217004231 1.800000e-42 183.0
18 TraesCS2A01G088200 chr5A 86.452 155 21 0 2119 2273 472902079 472902233 1.400000e-38 171.0
19 TraesCS2A01G088200 chr3B 86.982 169 14 4 2149 2316 39446410 39446571 1.800000e-42 183.0


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 TraesCS2A01G088200 chr2A 41620622 41623560 2938 False 5428.0 5428 100.000 1 2939 1 chr2A.!!$F1 2938
1 TraesCS2A01G088200 chr2B 64191194 64193240 2046 False 2338.0 2338 87.397 1 2046 1 chr2B.!!$F1 2045
2 TraesCS2A01G088200 chr2B 64089303 64091356 2053 True 2189.0 2189 86.129 1 2039 1 chr2B.!!$R1 2038
3 TraesCS2A01G088200 chr2B 63860538 63864905 4367 True 1571.0 3016 87.000 1 2939 2 chr2B.!!$R2 2938
4 TraesCS2A01G088200 chr2D 36911251 36915401 4150 False 1715.5 3011 89.830 1 2939 2 chr2D.!!$F2 2938
5 TraesCS2A01G088200 chr2D 36886262 36890434 4172 False 889.7 2165 90.137 1 2939 3 chr2D.!!$F1 2938

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
144 145 1.026182 TTGCCTCATCGTGATGTGCC 61.026 55.0 17.78 5.63 39.72 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2116 2183 0.023732 CGCGTCACTAAATGTGCTCG 59.976 55.0 0.0 0.0 45.81 5.03 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
144 145 1.026182 TTGCCTCATCGTGATGTGCC 61.026 55.000 17.78 5.63 39.72 5.01
171 172 1.425066 AGGCAGGATGGTTGAAGTTCA 59.575 47.619 0.08 0.08 35.86 3.18
493 509 4.124351 GTCCGACCATGGCGACGA 62.124 66.667 24.22 14.00 0.00 4.20
713 729 2.383527 GGACGAGCTCTGGTTTGCG 61.384 63.158 12.85 0.00 0.00 4.85
834 850 2.365582 GCGTGGGAGTGGTTTATCAAT 58.634 47.619 0.00 0.00 0.00 2.57
1088 1116 1.668751 GGAAACAGTGTTGCGTCTCAA 59.331 47.619 9.79 0.00 0.00 3.02
1245 1282 2.743752 CGTGAAGGATGCGGTGCTG 61.744 63.158 0.00 0.00 0.00 4.41
1247 1284 0.955428 GTGAAGGATGCGGTGCTGAA 60.955 55.000 0.00 0.00 0.00 3.02
1288 1325 0.955919 GGGACTGGACAAAGGAAGCG 60.956 60.000 0.00 0.00 0.00 4.68
1410 1453 0.817229 TTGCTTGTCACATCGGCACA 60.817 50.000 0.88 0.00 32.47 4.57
1434 1477 3.378742 GGCTCTTCGAGATCAAGTACTCA 59.621 47.826 0.00 0.00 33.86 3.41
1439 1482 2.418976 TCGAGATCAAGTACTCACACGG 59.581 50.000 0.00 0.00 33.86 4.94
1440 1483 2.531206 GAGATCAAGTACTCACACGGC 58.469 52.381 0.00 0.00 33.86 5.68
1649 1692 2.740826 GGCGCAAAGGTACGAGCA 60.741 61.111 10.83 0.00 0.00 4.26
1654 1697 1.802880 CGCAAAGGTACGAGCAGCTAT 60.803 52.381 0.00 0.00 0.00 2.97
1669 1712 0.463295 GCTATGCAAGGAGCTGAGCA 60.463 55.000 7.39 0.00 45.31 4.26
1670 1713 2.015588 GCTATGCAAGGAGCTGAGCAA 61.016 52.381 7.39 0.00 45.31 3.91
1729 1772 2.680352 GGAGACGCCTGGTGGAGA 60.680 66.667 12.58 0.00 36.60 3.71
1911 1954 3.311110 GTCACGGACAGGCCTGGA 61.311 66.667 35.42 20.12 32.09 3.86
1929 1972 0.311790 GAACACGTGACGGTAGTGGA 59.688 55.000 25.01 0.00 39.95 4.02
1935 1978 0.611340 GTGACGGTAGTGGAGTCCCT 60.611 60.000 6.74 6.06 34.24 4.20
1976 2026 8.903059 ACCATGTATAATTTGGTTCCCTTTTA 57.097 30.769 0.00 0.00 40.87 1.52
2008 2058 5.697178 ACCTTTCTCGTTTTAGAAGCTTCTC 59.303 40.000 31.67 16.56 36.85 2.87
2014 2064 6.421202 TCTCGTTTTAGAAGCTTCTCTTGTTC 59.579 38.462 31.67 16.51 38.70 3.18
2015 2065 6.046593 TCGTTTTAGAAGCTTCTCTTGTTCA 58.953 36.000 31.67 10.51 38.70 3.18
2033 2084 9.193133 TCTTGTTCACTTTTTAGACTAGAATCG 57.807 33.333 0.00 0.00 0.00 3.34
2035 2086 8.882415 TGTTCACTTTTTAGACTAGAATCGTT 57.118 30.769 0.00 0.00 0.00 3.85
2036 2087 8.761497 TGTTCACTTTTTAGACTAGAATCGTTG 58.239 33.333 0.00 0.00 0.00 4.10
2037 2088 8.762426 GTTCACTTTTTAGACTAGAATCGTTGT 58.238 33.333 0.00 0.00 0.00 3.32
2122 2189 9.769093 AAATTATTTTTAGACATGTACGAGCAC 57.231 29.630 0.00 0.00 0.00 4.40
2123 2190 7.892778 TTATTTTTAGACATGTACGAGCACA 57.107 32.000 0.00 0.00 0.00 4.57
2124 2191 6.985188 ATTTTTAGACATGTACGAGCACAT 57.015 33.333 0.00 0.00 39.76 3.21
2125 2192 6.795098 TTTTTAGACATGTACGAGCACATT 57.205 33.333 0.00 0.00 37.02 2.71
2126 2193 6.795098 TTTTAGACATGTACGAGCACATTT 57.205 33.333 0.00 0.00 37.02 2.32
2127 2194 7.892778 TTTTAGACATGTACGAGCACATTTA 57.107 32.000 0.00 0.00 37.02 1.40
2128 2195 7.520119 TTTAGACATGTACGAGCACATTTAG 57.480 36.000 0.00 0.00 37.02 1.85
2129 2196 5.073311 AGACATGTACGAGCACATTTAGT 57.927 39.130 0.00 0.00 37.02 2.24
2140 2207 2.961526 ACATTTAGTGACGCGAGGAT 57.038 45.000 15.93 0.00 0.00 3.24
2141 2208 2.540515 ACATTTAGTGACGCGAGGATG 58.459 47.619 15.93 9.22 0.00 3.51
2142 2209 1.860950 CATTTAGTGACGCGAGGATGG 59.139 52.381 15.93 0.00 0.00 3.51
2143 2210 0.892755 TTTAGTGACGCGAGGATGGT 59.107 50.000 15.93 0.00 0.00 3.55
2144 2211 1.753930 TTAGTGACGCGAGGATGGTA 58.246 50.000 15.93 0.00 0.00 3.25
2145 2212 1.753930 TAGTGACGCGAGGATGGTAA 58.246 50.000 15.93 0.00 0.00 2.85
2146 2213 0.172803 AGTGACGCGAGGATGGTAAC 59.827 55.000 15.93 0.00 0.00 2.50
2147 2214 0.172803 GTGACGCGAGGATGGTAACT 59.827 55.000 15.93 0.00 37.61 2.24
2148 2215 0.892755 TGACGCGAGGATGGTAACTT 59.107 50.000 15.93 0.00 37.61 2.66
2149 2216 1.274167 TGACGCGAGGATGGTAACTTT 59.726 47.619 15.93 0.00 37.61 2.66
2150 2217 2.492881 TGACGCGAGGATGGTAACTTTA 59.507 45.455 15.93 0.00 37.61 1.85
2151 2218 3.056678 TGACGCGAGGATGGTAACTTTAA 60.057 43.478 15.93 0.00 37.61 1.52
2152 2219 4.117685 GACGCGAGGATGGTAACTTTAAT 58.882 43.478 15.93 0.00 37.61 1.40
2153 2220 4.510571 ACGCGAGGATGGTAACTTTAATT 58.489 39.130 15.93 0.00 37.61 1.40
2154 2221 4.331717 ACGCGAGGATGGTAACTTTAATTG 59.668 41.667 15.93 0.00 37.61 2.32
2155 2222 4.598062 GCGAGGATGGTAACTTTAATTGC 58.402 43.478 0.00 0.00 37.61 3.56
2156 2223 4.497507 GCGAGGATGGTAACTTTAATTGCC 60.498 45.833 0.00 0.00 35.08 4.52
2157 2224 4.638421 CGAGGATGGTAACTTTAATTGCCA 59.362 41.667 1.71 1.71 46.65 4.92
2158 2225 5.124776 CGAGGATGGTAACTTTAATTGCCAA 59.875 40.000 3.18 0.00 45.87 4.52
2159 2226 6.530019 AGGATGGTAACTTTAATTGCCAAG 57.470 37.500 3.18 0.00 45.87 3.61
2160 2227 5.105351 AGGATGGTAACTTTAATTGCCAAGC 60.105 40.000 3.18 0.14 45.87 4.01
2161 2228 5.337169 GGATGGTAACTTTAATTGCCAAGCA 60.337 40.000 3.18 0.00 45.87 3.91
2162 2229 5.736951 TGGTAACTTTAATTGCCAAGCAT 57.263 34.783 0.00 0.00 40.86 3.79
2163 2230 5.477510 TGGTAACTTTAATTGCCAAGCATG 58.522 37.500 0.00 0.00 40.86 4.06
2164 2231 5.244851 TGGTAACTTTAATTGCCAAGCATGA 59.755 36.000 0.00 0.00 40.86 3.07
2165 2232 5.576774 GGTAACTTTAATTGCCAAGCATGAC 59.423 40.000 0.00 0.00 38.76 3.06
2166 2233 4.870123 ACTTTAATTGCCAAGCATGACA 57.130 36.364 0.00 0.00 38.76 3.58
2167 2234 5.212532 ACTTTAATTGCCAAGCATGACAA 57.787 34.783 0.00 0.00 38.76 3.18
2168 2235 5.232463 ACTTTAATTGCCAAGCATGACAAG 58.768 37.500 0.00 0.00 38.76 3.16
2169 2236 4.870123 TTAATTGCCAAGCATGACAAGT 57.130 36.364 0.00 0.00 38.76 3.16
2170 2237 3.756933 AATTGCCAAGCATGACAAGTT 57.243 38.095 0.00 0.00 38.76 2.66
2171 2238 3.756933 ATTGCCAAGCATGACAAGTTT 57.243 38.095 0.00 0.00 38.76 2.66
2172 2239 2.798976 TGCCAAGCATGACAAGTTTC 57.201 45.000 0.00 0.00 31.71 2.78
2173 2240 1.001487 TGCCAAGCATGACAAGTTTCG 60.001 47.619 0.00 0.00 31.71 3.46
2174 2241 1.001378 GCCAAGCATGACAAGTTTCGT 60.001 47.619 0.00 0.00 0.00 3.85
2175 2242 2.653890 CCAAGCATGACAAGTTTCGTG 58.346 47.619 0.00 0.00 35.85 4.35
2180 2247 3.607422 CATGACAAGTTTCGTGCTTCA 57.393 42.857 0.00 0.00 0.00 3.02
2181 2248 3.548587 CATGACAAGTTTCGTGCTTCAG 58.451 45.455 0.00 0.00 0.00 3.02
2182 2249 2.627945 TGACAAGTTTCGTGCTTCAGT 58.372 42.857 0.00 0.00 0.00 3.41
2183 2250 3.006940 TGACAAGTTTCGTGCTTCAGTT 58.993 40.909 0.00 0.00 0.00 3.16
2184 2251 3.438781 TGACAAGTTTCGTGCTTCAGTTT 59.561 39.130 0.00 0.00 0.00 2.66
2185 2252 4.632251 TGACAAGTTTCGTGCTTCAGTTTA 59.368 37.500 0.00 0.00 0.00 2.01
2186 2253 5.295787 TGACAAGTTTCGTGCTTCAGTTTAT 59.704 36.000 0.00 0.00 0.00 1.40
2187 2254 6.131544 ACAAGTTTCGTGCTTCAGTTTATT 57.868 33.333 0.00 0.00 0.00 1.40
2188 2255 6.199393 ACAAGTTTCGTGCTTCAGTTTATTC 58.801 36.000 0.00 0.00 0.00 1.75
2189 2256 6.038271 ACAAGTTTCGTGCTTCAGTTTATTCT 59.962 34.615 0.00 0.00 0.00 2.40
2190 2257 6.619801 AGTTTCGTGCTTCAGTTTATTCTT 57.380 33.333 0.00 0.00 0.00 2.52
2191 2258 6.430451 AGTTTCGTGCTTCAGTTTATTCTTG 58.570 36.000 0.00 0.00 0.00 3.02
2192 2259 6.260050 AGTTTCGTGCTTCAGTTTATTCTTGA 59.740 34.615 0.00 0.00 0.00 3.02
2193 2260 5.591643 TCGTGCTTCAGTTTATTCTTGAC 57.408 39.130 0.00 0.00 0.00 3.18
2194 2261 5.053811 TCGTGCTTCAGTTTATTCTTGACA 58.946 37.500 0.00 0.00 0.00 3.58
2195 2262 5.177511 TCGTGCTTCAGTTTATTCTTGACAG 59.822 40.000 0.00 0.00 0.00 3.51
2196 2263 5.177511 CGTGCTTCAGTTTATTCTTGACAGA 59.822 40.000 0.00 0.00 0.00 3.41
2197 2264 6.292865 CGTGCTTCAGTTTATTCTTGACAGAA 60.293 38.462 0.00 0.00 43.45 3.02
2198 2265 7.417612 GTGCTTCAGTTTATTCTTGACAGAAA 58.582 34.615 0.00 0.00 42.53 2.52
2199 2266 7.377131 GTGCTTCAGTTTATTCTTGACAGAAAC 59.623 37.037 0.00 0.00 42.53 2.78
2200 2267 7.283127 TGCTTCAGTTTATTCTTGACAGAAACT 59.717 33.333 0.00 0.00 42.53 2.66
2201 2268 8.131731 GCTTCAGTTTATTCTTGACAGAAACTT 58.868 33.333 0.00 0.00 42.53 2.66
2202 2269 9.443283 CTTCAGTTTATTCTTGACAGAAACTTG 57.557 33.333 0.00 0.00 42.53 3.16
2203 2270 7.417612 TCAGTTTATTCTTGACAGAAACTTGC 58.582 34.615 0.00 0.00 42.53 4.01
2204 2271 6.638468 CAGTTTATTCTTGACAGAAACTTGCC 59.362 38.462 0.00 0.00 42.53 4.52
2205 2272 3.904136 ATTCTTGACAGAAACTTGCCG 57.096 42.857 0.00 0.00 42.53 5.69
2206 2273 2.325583 TCTTGACAGAAACTTGCCGT 57.674 45.000 0.00 0.00 0.00 5.68
2207 2274 1.939934 TCTTGACAGAAACTTGCCGTG 59.060 47.619 0.00 0.00 0.00 4.94
2208 2275 1.670811 CTTGACAGAAACTTGCCGTGT 59.329 47.619 0.00 0.00 0.00 4.49
2209 2276 1.013596 TGACAGAAACTTGCCGTGTG 58.986 50.000 0.00 0.00 0.00 3.82
2210 2277 1.014352 GACAGAAACTTGCCGTGTGT 58.986 50.000 0.00 0.00 0.00 3.72
2211 2278 1.003866 GACAGAAACTTGCCGTGTGTC 60.004 52.381 0.00 0.00 0.00 3.67
2212 2279 1.013596 CAGAAACTTGCCGTGTGTCA 58.986 50.000 0.00 0.00 0.00 3.58
2213 2280 1.014352 AGAAACTTGCCGTGTGTCAC 58.986 50.000 0.00 0.00 0.00 3.67
2214 2281 1.014352 GAAACTTGCCGTGTGTCACT 58.986 50.000 4.27 0.00 31.34 3.41
2215 2282 0.732571 AAACTTGCCGTGTGTCACTG 59.267 50.000 4.27 0.00 31.34 3.66
2216 2283 0.107897 AACTTGCCGTGTGTCACTGA 60.108 50.000 4.27 0.00 31.34 3.41
2217 2284 0.107897 ACTTGCCGTGTGTCACTGAA 60.108 50.000 4.27 0.00 31.34 3.02
2218 2285 1.013596 CTTGCCGTGTGTCACTGAAA 58.986 50.000 4.27 0.00 31.34 2.69
2219 2286 1.400142 CTTGCCGTGTGTCACTGAAAA 59.600 47.619 4.27 0.00 31.34 2.29
2220 2287 1.674359 TGCCGTGTGTCACTGAAAAT 58.326 45.000 4.27 0.00 31.34 1.82
2221 2288 2.020720 TGCCGTGTGTCACTGAAAATT 58.979 42.857 4.27 0.00 31.34 1.82
2222 2289 2.223456 TGCCGTGTGTCACTGAAAATTG 60.223 45.455 4.27 0.00 31.34 2.32
2223 2290 2.384382 CCGTGTGTCACTGAAAATTGC 58.616 47.619 4.27 0.00 31.34 3.56
2224 2291 2.384382 CGTGTGTCACTGAAAATTGCC 58.616 47.619 4.27 0.00 31.34 4.52
2225 2292 2.223456 CGTGTGTCACTGAAAATTGCCA 60.223 45.455 4.27 0.00 31.34 4.92
2226 2293 3.550639 CGTGTGTCACTGAAAATTGCCAT 60.551 43.478 4.27 0.00 31.34 4.40
2227 2294 3.983344 GTGTGTCACTGAAAATTGCCATC 59.017 43.478 4.27 0.00 0.00 3.51
2228 2295 3.890756 TGTGTCACTGAAAATTGCCATCT 59.109 39.130 4.27 0.00 0.00 2.90
2229 2296 4.341806 TGTGTCACTGAAAATTGCCATCTT 59.658 37.500 4.27 0.00 0.00 2.40
2230 2297 5.163426 TGTGTCACTGAAAATTGCCATCTTT 60.163 36.000 4.27 0.00 0.00 2.52
2231 2298 5.176223 GTGTCACTGAAAATTGCCATCTTTG 59.824 40.000 0.00 0.00 0.00 2.77
2232 2299 4.151157 GTCACTGAAAATTGCCATCTTTGC 59.849 41.667 0.00 0.00 0.00 3.68
2233 2300 3.122278 CACTGAAAATTGCCATCTTTGCG 59.878 43.478 0.00 0.00 0.00 4.85
2234 2301 3.243839 ACTGAAAATTGCCATCTTTGCGT 60.244 39.130 0.00 0.00 0.00 5.24
2235 2302 3.058450 TGAAAATTGCCATCTTTGCGTG 58.942 40.909 0.00 0.00 0.00 5.34
2236 2303 3.243670 TGAAAATTGCCATCTTTGCGTGA 60.244 39.130 0.00 0.00 0.00 4.35
2237 2304 2.352503 AATTGCCATCTTTGCGTGAC 57.647 45.000 0.00 0.00 0.00 3.67
2238 2305 1.538047 ATTGCCATCTTTGCGTGACT 58.462 45.000 0.00 0.00 0.00 3.41
2239 2306 0.592637 TTGCCATCTTTGCGTGACTG 59.407 50.000 0.00 0.00 0.00 3.51
2240 2307 0.250252 TGCCATCTTTGCGTGACTGA 60.250 50.000 0.00 0.00 0.00 3.41
2241 2308 0.874390 GCCATCTTTGCGTGACTGAA 59.126 50.000 0.00 0.00 0.00 3.02
2242 2309 1.266718 GCCATCTTTGCGTGACTGAAA 59.733 47.619 0.00 0.00 0.00 2.69
2243 2310 2.095059 GCCATCTTTGCGTGACTGAAAT 60.095 45.455 0.00 0.00 0.00 2.17
2244 2311 3.612479 GCCATCTTTGCGTGACTGAAATT 60.612 43.478 0.00 0.00 0.00 1.82
2245 2312 3.916172 CCATCTTTGCGTGACTGAAATTG 59.084 43.478 0.00 0.00 0.00 2.32
2246 2313 2.998772 TCTTTGCGTGACTGAAATTGC 58.001 42.857 0.00 0.00 0.00 3.56
2247 2314 2.053627 CTTTGCGTGACTGAAATTGCC 58.946 47.619 0.00 0.00 0.00 4.52
2248 2315 1.028130 TTGCGTGACTGAAATTGCCA 58.972 45.000 0.00 0.00 0.00 4.92
2249 2316 1.246649 TGCGTGACTGAAATTGCCAT 58.753 45.000 0.00 0.00 0.00 4.40
2250 2317 1.199789 TGCGTGACTGAAATTGCCATC 59.800 47.619 0.00 0.00 0.00 3.51
2251 2318 1.791555 GCGTGACTGAAATTGCCATCG 60.792 52.381 0.00 0.00 0.00 3.84
2252 2319 1.731709 CGTGACTGAAATTGCCATCGA 59.268 47.619 0.00 0.00 0.00 3.59
2253 2320 2.159430 CGTGACTGAAATTGCCATCGAA 59.841 45.455 0.00 0.00 0.00 3.71
2254 2321 3.364864 CGTGACTGAAATTGCCATCGAAA 60.365 43.478 0.00 0.00 0.00 3.46
2255 2322 4.545610 GTGACTGAAATTGCCATCGAAAA 58.454 39.130 0.00 0.00 0.00 2.29
2256 2323 4.981674 GTGACTGAAATTGCCATCGAAAAA 59.018 37.500 0.00 0.00 0.00 1.94
2257 2324 4.981674 TGACTGAAATTGCCATCGAAAAAC 59.018 37.500 0.00 0.00 0.00 2.43
2258 2325 3.980775 ACTGAAATTGCCATCGAAAAACG 59.019 39.130 0.00 0.00 44.09 3.60
2259 2326 3.971150 TGAAATTGCCATCGAAAAACGT 58.029 36.364 0.00 0.00 43.13 3.99
2260 2327 3.978217 TGAAATTGCCATCGAAAAACGTC 59.022 39.130 0.00 0.00 43.13 4.34
2261 2328 3.634568 AATTGCCATCGAAAAACGTCA 57.365 38.095 0.00 0.00 43.13 4.35
2262 2329 2.679355 TTGCCATCGAAAAACGTCAG 57.321 45.000 0.00 0.00 43.13 3.51
2263 2330 0.871722 TGCCATCGAAAAACGTCAGG 59.128 50.000 0.00 0.00 43.13 3.86
2264 2331 0.168128 GCCATCGAAAAACGTCAGGG 59.832 55.000 0.00 0.00 43.13 4.45
2265 2332 0.168128 CCATCGAAAAACGTCAGGGC 59.832 55.000 0.00 0.00 43.13 5.19
2266 2333 1.156736 CATCGAAAAACGTCAGGGCT 58.843 50.000 0.00 0.00 43.13 5.19
2267 2334 2.343101 CATCGAAAAACGTCAGGGCTA 58.657 47.619 0.00 0.00 43.13 3.93
2268 2335 2.074547 TCGAAAAACGTCAGGGCTAG 57.925 50.000 0.00 0.00 43.13 3.42
2269 2336 1.614903 TCGAAAAACGTCAGGGCTAGA 59.385 47.619 0.00 0.00 43.13 2.43
2270 2337 1.993370 CGAAAAACGTCAGGGCTAGAG 59.007 52.381 0.00 0.00 37.22 2.43
2271 2338 2.609737 CGAAAAACGTCAGGGCTAGAGT 60.610 50.000 0.00 0.00 37.22 3.24
2272 2339 2.457366 AAAACGTCAGGGCTAGAGTG 57.543 50.000 0.00 0.00 0.00 3.51
2273 2340 0.037232 AAACGTCAGGGCTAGAGTGC 60.037 55.000 0.00 0.00 0.00 4.40
2274 2341 1.185618 AACGTCAGGGCTAGAGTGCA 61.186 55.000 0.00 0.00 34.04 4.57
2275 2342 1.185618 ACGTCAGGGCTAGAGTGCAA 61.186 55.000 0.00 0.00 34.04 4.08
2276 2343 0.737715 CGTCAGGGCTAGAGTGCAAC 60.738 60.000 0.00 0.00 34.04 4.17
2277 2344 0.737715 GTCAGGGCTAGAGTGCAACG 60.738 60.000 0.00 0.00 45.86 4.10
2278 2345 2.103042 CAGGGCTAGAGTGCAACGC 61.103 63.158 0.00 0.00 45.86 4.84
2279 2346 2.047274 GGGCTAGAGTGCAACGCA 60.047 61.111 0.00 0.00 45.86 5.24
2288 2355 3.342909 TGCAACGCACCTGACATG 58.657 55.556 0.00 0.00 31.71 3.21
2289 2356 1.525765 TGCAACGCACCTGACATGT 60.526 52.632 0.00 0.00 31.71 3.21
2290 2357 1.081906 GCAACGCACCTGACATGTG 60.082 57.895 1.15 6.51 36.79 3.21
2291 2358 1.506309 GCAACGCACCTGACATGTGA 61.506 55.000 14.26 0.00 35.74 3.58
2292 2359 0.235665 CAACGCACCTGACATGTGAC 59.764 55.000 14.26 5.42 35.74 3.67
2293 2360 0.179059 AACGCACCTGACATGTGACA 60.179 50.000 14.26 0.00 35.74 3.58
2294 2361 0.880278 ACGCACCTGACATGTGACAC 60.880 55.000 14.26 0.00 35.74 3.67
2295 2362 0.601046 CGCACCTGACATGTGACACT 60.601 55.000 14.26 0.00 35.74 3.55
2296 2363 1.597742 GCACCTGACATGTGACACTT 58.402 50.000 14.26 0.00 35.74 3.16
2297 2364 2.766313 GCACCTGACATGTGACACTTA 58.234 47.619 14.26 0.00 35.74 2.24
2298 2365 3.338249 GCACCTGACATGTGACACTTAT 58.662 45.455 14.26 0.00 35.74 1.73
2299 2366 3.372206 GCACCTGACATGTGACACTTATC 59.628 47.826 14.26 0.00 35.74 1.75
2300 2367 4.568956 CACCTGACATGTGACACTTATCA 58.431 43.478 1.15 4.75 35.74 2.15
2301 2368 5.181009 CACCTGACATGTGACACTTATCAT 58.819 41.667 1.15 0.00 35.74 2.45
2302 2369 5.645067 CACCTGACATGTGACACTTATCATT 59.355 40.000 1.15 0.00 35.74 2.57
2303 2370 6.149973 CACCTGACATGTGACACTTATCATTT 59.850 38.462 1.15 0.00 35.74 2.32
2304 2371 6.149973 ACCTGACATGTGACACTTATCATTTG 59.850 38.462 1.15 0.92 0.00 2.32
2305 2372 6.403964 CCTGACATGTGACACTTATCATTTGG 60.404 42.308 1.15 0.27 0.00 3.28
2306 2373 6.237154 TGACATGTGACACTTATCATTTGGA 58.763 36.000 1.15 0.00 0.00 3.53
2307 2374 6.885918 TGACATGTGACACTTATCATTTGGAT 59.114 34.615 1.15 0.00 40.14 3.41
2308 2375 7.394077 TGACATGTGACACTTATCATTTGGATT 59.606 33.333 1.15 0.00 37.44 3.01
2309 2376 8.806429 ACATGTGACACTTATCATTTGGATTA 57.194 30.769 7.20 0.00 37.44 1.75
2310 2377 9.412460 ACATGTGACACTTATCATTTGGATTAT 57.588 29.630 7.20 0.00 37.44 1.28
2313 2380 9.685276 TGTGACACTTATCATTTGGATTATTCT 57.315 29.630 7.20 0.00 37.44 2.40
2359 2426 9.453572 TTCTGACATGAAAATCTGCTTTACTAT 57.546 29.630 0.00 0.00 0.00 2.12
2364 2431 9.678260 ACATGAAAATCTGCTTTACTATTCTCT 57.322 29.630 0.00 0.00 0.00 3.10
2375 2442 6.922957 GCTTTACTATTCTCTCCATGTCTGAG 59.077 42.308 0.00 0.00 0.00 3.35
2401 2468 4.149598 AGGCCTAAAATTTTGTCGGAAGT 58.850 39.130 1.29 0.00 0.00 3.01
2417 2484 9.315341 TTGTCGGAAGTCAAATAGTGCAACTTC 62.315 40.741 14.15 14.15 39.26 3.01
2434 2501 7.538678 GTGCAACTTCGATCAAATTTGTAGATT 59.461 33.333 17.47 5.92 0.00 2.40
2502 2629 9.431887 ACACAATAAATATATGGCCTAACTACG 57.568 33.333 3.32 0.00 0.00 3.51
2532 2659 9.687717 CGATTGGTTTCATGCAAAAATTTATAC 57.312 29.630 0.00 0.00 0.00 1.47
2568 4130 2.043248 GGGGGTAGAGCGAGGTGA 60.043 66.667 0.00 0.00 0.00 4.02
2596 4158 0.537188 CTAGCCACAACGGATCTGGT 59.463 55.000 6.47 0.00 36.56 4.00
2606 4168 2.606587 GGATCTGGTGCCCCTGTGT 61.607 63.158 0.00 0.00 0.00 3.72
2611 4173 3.570212 GGTGCCCCTGTGTGGACT 61.570 66.667 0.00 0.00 38.35 3.85
2634 4201 2.259204 CATGGTGGCCTTGTTGCG 59.741 61.111 3.32 0.00 0.00 4.85
2658 4225 3.736252 CGACCCGACTTCATGTTATGATC 59.264 47.826 0.00 0.00 39.39 2.92
2674 4241 0.392998 GATCGGGCAAGAAGCTCCAA 60.393 55.000 0.00 0.00 42.29 3.53
2704 4271 9.893305 GGTCCTTTGCATATAAACAACATATAC 57.107 33.333 0.00 0.00 0.00 1.47
2762 4329 1.627864 AAAGGACATTGAAACCCCCG 58.372 50.000 0.00 0.00 0.00 5.73
2789 4640 3.016031 TGTATCATTGTGATGTGTGGGC 58.984 45.455 2.82 0.00 37.70 5.36
2790 4641 2.219080 ATCATTGTGATGTGTGGGCA 57.781 45.000 0.00 0.00 35.43 5.36
2870 4731 6.984740 TGACAACGAAACAAATCTAATTGC 57.015 33.333 0.00 0.00 33.52 3.56
2923 4784 9.101655 GCATAGGATTTGAAATGCTTTAACAAT 57.898 29.630 16.93 1.16 41.16 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
144 145 1.915078 AACCATCCTGCCTCGGGAAG 61.915 60.000 0.00 0.00 42.74 3.46
171 172 2.743183 CGATGAAGATCGCCTTTCCCTT 60.743 50.000 0.00 0.00 44.75 3.95
361 362 1.118838 CTCCTTGCTCTCCCCTACTG 58.881 60.000 0.00 0.00 0.00 2.74
362 363 0.689412 GCTCCTTGCTCTCCCCTACT 60.689 60.000 0.00 0.00 38.95 2.57
713 729 6.038936 GGAGTGGAGAGTAGTAGAAATCACTC 59.961 46.154 0.00 0.00 44.33 3.51
834 850 2.871096 AGGCGATTACCCTTTTGTCA 57.129 45.000 0.00 0.00 0.00 3.58
1061 1089 1.453015 AACACTGTTTCCAGCGCCA 60.453 52.632 2.29 0.00 42.81 5.69
1203 1240 1.009389 GCGAGACTTCCACCGACTTG 61.009 60.000 0.00 0.00 0.00 3.16
1205 1242 2.637383 GGCGAGACTTCCACCGACT 61.637 63.158 0.00 0.00 0.00 4.18
1245 1282 2.470983 AGCTGCTCTTCAAGGACTTC 57.529 50.000 0.00 0.00 0.00 3.01
1247 1284 2.170187 CCATAGCTGCTCTTCAAGGACT 59.830 50.000 4.91 0.00 0.00 3.85
1392 1435 0.817229 TTGTGCCGATGTGACAAGCA 60.817 50.000 4.49 4.49 0.00 3.91
1398 1441 1.375908 GAGCCTTGTGCCGATGTGA 60.376 57.895 0.00 0.00 42.71 3.58
1654 1697 0.604780 GTCTTGCTCAGCTCCTTGCA 60.605 55.000 0.00 0.00 45.94 4.08
1669 1712 2.286523 CCTCGTCCCTGCTGGTCTT 61.287 63.158 9.00 0.00 34.77 3.01
1670 1713 2.681778 CCTCGTCCCTGCTGGTCT 60.682 66.667 9.00 0.00 34.77 3.85
1729 1772 3.494336 CTCGTCCTCGGCGTACGT 61.494 66.667 23.17 0.00 44.69 3.57
1911 1954 0.313043 CTCCACTACCGTCACGTGTT 59.687 55.000 16.51 1.27 0.00 3.32
1976 2026 4.853924 AAAACGAGAAAGGTGCATGAAT 57.146 36.364 0.00 0.00 0.00 2.57
2008 2058 8.979574 ACGATTCTAGTCTAAAAAGTGAACAAG 58.020 33.333 0.00 0.00 0.00 3.16
2015 2065 9.978044 ACTTACAACGATTCTAGTCTAAAAAGT 57.022 29.630 0.00 0.00 0.00 2.66
2096 2163 9.769093 GTGCTCGTACATGTCTAAAAATAATTT 57.231 29.630 0.00 0.00 0.00 1.82
2097 2164 8.941977 TGTGCTCGTACATGTCTAAAAATAATT 58.058 29.630 0.00 0.00 0.00 1.40
2098 2165 8.487313 TGTGCTCGTACATGTCTAAAAATAAT 57.513 30.769 0.00 0.00 0.00 1.28
2099 2166 7.892778 TGTGCTCGTACATGTCTAAAAATAA 57.107 32.000 0.00 0.00 0.00 1.40
2100 2167 8.487313 AATGTGCTCGTACATGTCTAAAAATA 57.513 30.769 0.00 0.00 40.24 1.40
2101 2168 6.985188 ATGTGCTCGTACATGTCTAAAAAT 57.015 33.333 0.00 0.00 39.68 1.82
2102 2169 6.795098 AATGTGCTCGTACATGTCTAAAAA 57.205 33.333 0.00 0.00 40.24 1.94
2103 2170 6.795098 AAATGTGCTCGTACATGTCTAAAA 57.205 33.333 0.00 0.00 40.24 1.52
2104 2171 7.062956 CACTAAATGTGCTCGTACATGTCTAAA 59.937 37.037 0.00 0.00 40.24 1.85
2105 2172 6.530181 CACTAAATGTGCTCGTACATGTCTAA 59.470 38.462 0.00 0.00 40.24 2.10
2106 2173 6.033966 CACTAAATGTGCTCGTACATGTCTA 58.966 40.000 0.00 0.00 40.24 2.59
2107 2174 4.864806 CACTAAATGTGCTCGTACATGTCT 59.135 41.667 0.00 0.00 40.24 3.41
2108 2175 4.862574 TCACTAAATGTGCTCGTACATGTC 59.137 41.667 0.00 0.00 45.81 3.06
2109 2176 4.625742 GTCACTAAATGTGCTCGTACATGT 59.374 41.667 2.69 2.69 45.81 3.21
2110 2177 4.259411 CGTCACTAAATGTGCTCGTACATG 60.259 45.833 1.43 0.00 45.81 3.21
2111 2178 3.857665 CGTCACTAAATGTGCTCGTACAT 59.142 43.478 0.00 0.00 45.81 2.29
2112 2179 3.239254 CGTCACTAAATGTGCTCGTACA 58.761 45.455 0.00 0.00 45.81 2.90
2113 2180 2.027688 GCGTCACTAAATGTGCTCGTAC 59.972 50.000 0.00 0.00 45.81 3.67
2114 2181 2.256174 GCGTCACTAAATGTGCTCGTA 58.744 47.619 0.00 0.00 45.81 3.43
2115 2182 1.068474 GCGTCACTAAATGTGCTCGT 58.932 50.000 0.00 0.00 45.81 4.18
2116 2183 0.023732 CGCGTCACTAAATGTGCTCG 59.976 55.000 0.00 0.00 45.81 5.03
2117 2184 1.321743 CTCGCGTCACTAAATGTGCTC 59.678 52.381 5.77 0.00 45.81 4.26
2118 2185 1.350193 CTCGCGTCACTAAATGTGCT 58.650 50.000 5.77 0.00 45.81 4.40
2119 2186 0.370273 CCTCGCGTCACTAAATGTGC 59.630 55.000 5.77 0.00 45.81 4.57
2121 2188 2.540515 CATCCTCGCGTCACTAAATGT 58.459 47.619 5.77 0.00 0.00 2.71
2122 2189 1.860950 CCATCCTCGCGTCACTAAATG 59.139 52.381 5.77 2.01 0.00 2.32
2123 2190 1.480954 ACCATCCTCGCGTCACTAAAT 59.519 47.619 5.77 0.00 0.00 1.40
2124 2191 0.892755 ACCATCCTCGCGTCACTAAA 59.107 50.000 5.77 0.00 0.00 1.85
2125 2192 1.753930 TACCATCCTCGCGTCACTAA 58.246 50.000 5.77 0.00 0.00 2.24
2126 2193 1.402968 GTTACCATCCTCGCGTCACTA 59.597 52.381 5.77 0.00 0.00 2.74
2127 2194 0.172803 GTTACCATCCTCGCGTCACT 59.827 55.000 5.77 0.00 0.00 3.41
2128 2195 0.172803 AGTTACCATCCTCGCGTCAC 59.827 55.000 5.77 0.00 0.00 3.67
2129 2196 0.892755 AAGTTACCATCCTCGCGTCA 59.107 50.000 5.77 0.00 0.00 4.35
2130 2197 2.005971 AAAGTTACCATCCTCGCGTC 57.994 50.000 5.77 0.00 0.00 5.19
2131 2198 3.598019 TTAAAGTTACCATCCTCGCGT 57.402 42.857 5.77 0.00 0.00 6.01
2132 2199 4.785341 GCAATTAAAGTTACCATCCTCGCG 60.785 45.833 0.00 0.00 0.00 5.87
2133 2200 4.497507 GGCAATTAAAGTTACCATCCTCGC 60.498 45.833 0.00 0.00 0.00 5.03
2134 2201 4.638421 TGGCAATTAAAGTTACCATCCTCG 59.362 41.667 0.00 0.00 0.00 4.63
2135 2202 6.524101 TTGGCAATTAAAGTTACCATCCTC 57.476 37.500 0.00 0.00 0.00 3.71
2136 2203 5.105351 GCTTGGCAATTAAAGTTACCATCCT 60.105 40.000 0.00 0.00 0.00 3.24
2137 2204 5.109210 GCTTGGCAATTAAAGTTACCATCC 58.891 41.667 0.00 0.00 0.00 3.51
2138 2205 5.719173 TGCTTGGCAATTAAAGTTACCATC 58.281 37.500 0.00 0.00 34.76 3.51
2139 2206 5.736951 TGCTTGGCAATTAAAGTTACCAT 57.263 34.783 0.00 0.00 34.76 3.55
2140 2207 5.244851 TCATGCTTGGCAATTAAAGTTACCA 59.755 36.000 0.00 0.00 43.62 3.25
2141 2208 5.576774 GTCATGCTTGGCAATTAAAGTTACC 59.423 40.000 0.00 0.00 43.62 2.85
2142 2209 6.155827 TGTCATGCTTGGCAATTAAAGTTAC 58.844 36.000 4.13 0.00 43.62 2.50
2143 2210 6.338214 TGTCATGCTTGGCAATTAAAGTTA 57.662 33.333 4.13 0.00 43.62 2.24
2144 2211 5.212532 TGTCATGCTTGGCAATTAAAGTT 57.787 34.783 4.13 0.00 43.62 2.66
2145 2212 4.870123 TGTCATGCTTGGCAATTAAAGT 57.130 36.364 4.13 0.00 43.62 2.66
2146 2213 5.232463 ACTTGTCATGCTTGGCAATTAAAG 58.768 37.500 18.63 10.06 45.85 1.85
2147 2214 5.212532 ACTTGTCATGCTTGGCAATTAAA 57.787 34.783 18.63 0.00 45.85 1.52
2148 2215 4.870123 ACTTGTCATGCTTGGCAATTAA 57.130 36.364 18.63 0.00 45.85 1.40
2149 2216 4.870123 AACTTGTCATGCTTGGCAATTA 57.130 36.364 18.63 0.00 45.85 1.40
2150 2217 3.756933 AACTTGTCATGCTTGGCAATT 57.243 38.095 18.63 11.43 45.85 2.32
2151 2218 3.656559 GAAACTTGTCATGCTTGGCAAT 58.343 40.909 18.63 5.73 45.85 3.56
2152 2219 2.543445 CGAAACTTGTCATGCTTGGCAA 60.543 45.455 17.51 17.51 44.90 4.52
2153 2220 1.001487 CGAAACTTGTCATGCTTGGCA 60.001 47.619 2.24 2.24 44.86 4.92
2154 2221 1.001378 ACGAAACTTGTCATGCTTGGC 60.001 47.619 0.00 0.00 0.00 4.52
2155 2222 2.653890 CACGAAACTTGTCATGCTTGG 58.346 47.619 0.00 0.00 0.00 3.61
2156 2223 2.046313 GCACGAAACTTGTCATGCTTG 58.954 47.619 0.00 0.00 0.00 4.01
2157 2224 1.949525 AGCACGAAACTTGTCATGCTT 59.050 42.857 0.00 0.00 40.39 3.91
2158 2225 1.597742 AGCACGAAACTTGTCATGCT 58.402 45.000 0.00 0.00 38.55 3.79
2159 2226 2.286950 TGAAGCACGAAACTTGTCATGC 60.287 45.455 0.00 0.00 0.00 4.06
2160 2227 3.002656 ACTGAAGCACGAAACTTGTCATG 59.997 43.478 0.00 0.00 0.00 3.07
2161 2228 3.206150 ACTGAAGCACGAAACTTGTCAT 58.794 40.909 0.00 0.00 0.00 3.06
2162 2229 2.627945 ACTGAAGCACGAAACTTGTCA 58.372 42.857 0.00 0.00 0.00 3.58
2163 2230 3.675467 AACTGAAGCACGAAACTTGTC 57.325 42.857 0.00 0.00 0.00 3.18
2164 2231 5.751243 ATAAACTGAAGCACGAAACTTGT 57.249 34.783 0.00 0.00 0.00 3.16
2165 2232 6.430451 AGAATAAACTGAAGCACGAAACTTG 58.570 36.000 0.00 0.00 0.00 3.16
2166 2233 6.619801 AGAATAAACTGAAGCACGAAACTT 57.380 33.333 0.00 0.00 0.00 2.66
2167 2234 6.260050 TCAAGAATAAACTGAAGCACGAAACT 59.740 34.615 0.00 0.00 0.00 2.66
2168 2235 6.357240 GTCAAGAATAAACTGAAGCACGAAAC 59.643 38.462 0.00 0.00 0.00 2.78
2169 2236 6.037720 TGTCAAGAATAAACTGAAGCACGAAA 59.962 34.615 0.00 0.00 0.00 3.46
2170 2237 5.525745 TGTCAAGAATAAACTGAAGCACGAA 59.474 36.000 0.00 0.00 0.00 3.85
2171 2238 5.053811 TGTCAAGAATAAACTGAAGCACGA 58.946 37.500 0.00 0.00 0.00 4.35
2172 2239 5.177511 TCTGTCAAGAATAAACTGAAGCACG 59.822 40.000 0.00 0.00 0.00 5.34
2173 2240 6.545504 TCTGTCAAGAATAAACTGAAGCAC 57.454 37.500 0.00 0.00 0.00 4.40
2174 2241 7.283127 AGTTTCTGTCAAGAATAAACTGAAGCA 59.717 33.333 0.00 0.00 42.04 3.91
2175 2242 7.643579 AGTTTCTGTCAAGAATAAACTGAAGC 58.356 34.615 0.00 0.00 42.04 3.86
2176 2243 9.443283 CAAGTTTCTGTCAAGAATAAACTGAAG 57.557 33.333 0.00 0.00 42.04 3.02
2177 2244 7.915397 GCAAGTTTCTGTCAAGAATAAACTGAA 59.085 33.333 0.00 0.00 42.04 3.02
2178 2245 7.417612 GCAAGTTTCTGTCAAGAATAAACTGA 58.582 34.615 0.00 0.00 42.04 3.41
2179 2246 6.638468 GGCAAGTTTCTGTCAAGAATAAACTG 59.362 38.462 0.00 0.00 42.04 3.16
2180 2247 6.513393 CGGCAAGTTTCTGTCAAGAATAAACT 60.513 38.462 0.00 0.00 42.04 2.66
2181 2248 5.625311 CGGCAAGTTTCTGTCAAGAATAAAC 59.375 40.000 0.00 0.00 42.04 2.01
2182 2249 5.298276 ACGGCAAGTTTCTGTCAAGAATAAA 59.702 36.000 0.00 0.00 42.04 1.40
2183 2250 4.819630 ACGGCAAGTTTCTGTCAAGAATAA 59.180 37.500 0.00 0.00 42.04 1.40
2184 2251 4.213270 CACGGCAAGTTTCTGTCAAGAATA 59.787 41.667 0.00 0.00 42.04 1.75
2185 2252 3.003689 CACGGCAAGTTTCTGTCAAGAAT 59.996 43.478 0.00 0.00 42.04 2.40
2186 2253 2.354510 CACGGCAAGTTTCTGTCAAGAA 59.645 45.455 0.00 0.00 40.76 2.52
2187 2254 1.939934 CACGGCAAGTTTCTGTCAAGA 59.060 47.619 0.00 0.00 0.00 3.02
2188 2255 1.670811 ACACGGCAAGTTTCTGTCAAG 59.329 47.619 0.00 0.00 0.00 3.02
2189 2256 1.400142 CACACGGCAAGTTTCTGTCAA 59.600 47.619 0.00 0.00 0.00 3.18
2190 2257 1.013596 CACACGGCAAGTTTCTGTCA 58.986 50.000 0.00 0.00 0.00 3.58
2191 2258 1.003866 GACACACGGCAAGTTTCTGTC 60.004 52.381 0.00 0.00 0.00 3.51
2192 2259 1.014352 GACACACGGCAAGTTTCTGT 58.986 50.000 0.00 0.00 0.00 3.41
2193 2260 1.013596 TGACACACGGCAAGTTTCTG 58.986 50.000 0.00 0.00 0.00 3.02
2194 2261 1.014352 GTGACACACGGCAAGTTTCT 58.986 50.000 0.00 0.00 0.00 2.52
2195 2262 1.014352 AGTGACACACGGCAAGTTTC 58.986 50.000 8.59 0.00 39.64 2.78
2196 2263 0.732571 CAGTGACACACGGCAAGTTT 59.267 50.000 8.59 0.00 39.64 2.66
2197 2264 0.107897 TCAGTGACACACGGCAAGTT 60.108 50.000 8.59 0.00 39.64 2.66
2198 2265 0.107897 TTCAGTGACACACGGCAAGT 60.108 50.000 8.59 0.00 39.64 3.16
2199 2266 1.013596 TTTCAGTGACACACGGCAAG 58.986 50.000 8.59 0.00 39.64 4.01
2200 2267 1.454201 TTTTCAGTGACACACGGCAA 58.546 45.000 8.59 0.00 39.64 4.52
2201 2268 1.674359 ATTTTCAGTGACACACGGCA 58.326 45.000 8.59 0.00 39.64 5.69
2202 2269 2.384382 CAATTTTCAGTGACACACGGC 58.616 47.619 8.59 0.00 39.64 5.68
2203 2270 2.384382 GCAATTTTCAGTGACACACGG 58.616 47.619 8.59 1.20 39.64 4.94
2204 2271 2.223456 TGGCAATTTTCAGTGACACACG 60.223 45.455 8.59 0.00 39.64 4.49
2205 2272 3.435105 TGGCAATTTTCAGTGACACAC 57.565 42.857 8.59 0.00 28.41 3.82
2206 2273 3.890756 AGATGGCAATTTTCAGTGACACA 59.109 39.130 8.59 0.00 39.34 3.72
2207 2274 4.510038 AGATGGCAATTTTCAGTGACAC 57.490 40.909 0.00 0.00 39.34 3.67
2208 2275 5.291178 CAAAGATGGCAATTTTCAGTGACA 58.709 37.500 0.00 0.00 41.25 3.58
2209 2276 4.151157 GCAAAGATGGCAATTTTCAGTGAC 59.849 41.667 0.00 0.00 0.00 3.67
2210 2277 4.309099 GCAAAGATGGCAATTTTCAGTGA 58.691 39.130 0.00 0.00 0.00 3.41
2211 2278 3.122278 CGCAAAGATGGCAATTTTCAGTG 59.878 43.478 0.00 0.00 0.00 3.66
2212 2279 3.243839 ACGCAAAGATGGCAATTTTCAGT 60.244 39.130 0.00 0.00 0.00 3.41
2213 2280 3.122278 CACGCAAAGATGGCAATTTTCAG 59.878 43.478 0.00 0.00 0.00 3.02
2214 2281 3.058450 CACGCAAAGATGGCAATTTTCA 58.942 40.909 0.00 0.00 0.00 2.69
2215 2282 3.121778 GTCACGCAAAGATGGCAATTTTC 59.878 43.478 0.00 0.00 0.00 2.29
2216 2283 3.059166 GTCACGCAAAGATGGCAATTTT 58.941 40.909 0.00 0.00 0.00 1.82
2217 2284 2.297033 AGTCACGCAAAGATGGCAATTT 59.703 40.909 0.00 0.00 0.00 1.82
2218 2285 1.888512 AGTCACGCAAAGATGGCAATT 59.111 42.857 0.00 0.00 0.00 2.32
2219 2286 1.200716 CAGTCACGCAAAGATGGCAAT 59.799 47.619 0.00 0.00 0.00 3.56
2220 2287 0.592637 CAGTCACGCAAAGATGGCAA 59.407 50.000 0.00 0.00 0.00 4.52
2221 2288 0.250252 TCAGTCACGCAAAGATGGCA 60.250 50.000 0.00 0.00 0.00 4.92
2222 2289 0.874390 TTCAGTCACGCAAAGATGGC 59.126 50.000 0.00 0.00 0.00 4.40
2223 2290 3.837213 ATTTCAGTCACGCAAAGATGG 57.163 42.857 0.00 0.00 0.00 3.51
2224 2291 3.362831 GCAATTTCAGTCACGCAAAGATG 59.637 43.478 0.00 0.00 0.00 2.90
2225 2292 3.568538 GCAATTTCAGTCACGCAAAGAT 58.431 40.909 0.00 0.00 0.00 2.40
2226 2293 2.287547 GGCAATTTCAGTCACGCAAAGA 60.288 45.455 0.00 0.00 0.00 2.52
2227 2294 2.053627 GGCAATTTCAGTCACGCAAAG 58.946 47.619 0.00 0.00 0.00 2.77
2228 2295 1.406898 TGGCAATTTCAGTCACGCAAA 59.593 42.857 0.00 0.00 0.00 3.68
2229 2296 1.028130 TGGCAATTTCAGTCACGCAA 58.972 45.000 0.00 0.00 0.00 4.85
2230 2297 1.199789 GATGGCAATTTCAGTCACGCA 59.800 47.619 0.00 0.00 0.00 5.24
2231 2298 1.791555 CGATGGCAATTTCAGTCACGC 60.792 52.381 0.00 0.00 0.00 5.34
2232 2299 1.731709 TCGATGGCAATTTCAGTCACG 59.268 47.619 0.00 0.00 0.00 4.35
2233 2300 3.829886 TTCGATGGCAATTTCAGTCAC 57.170 42.857 0.00 0.00 0.00 3.67
2234 2301 4.844998 TTTTCGATGGCAATTTCAGTCA 57.155 36.364 0.00 0.00 0.00 3.41
2235 2302 4.088496 CGTTTTTCGATGGCAATTTCAGTC 59.912 41.667 0.00 0.00 42.86 3.51
2236 2303 3.980775 CGTTTTTCGATGGCAATTTCAGT 59.019 39.130 0.00 0.00 42.86 3.41
2237 2304 3.980775 ACGTTTTTCGATGGCAATTTCAG 59.019 39.130 0.00 0.00 42.86 3.02
2238 2305 3.971150 ACGTTTTTCGATGGCAATTTCA 58.029 36.364 0.00 0.00 42.86 2.69
2239 2306 3.978217 TGACGTTTTTCGATGGCAATTTC 59.022 39.130 0.00 0.00 42.86 2.17
2240 2307 3.971150 TGACGTTTTTCGATGGCAATTT 58.029 36.364 0.00 0.00 42.86 1.82
2241 2308 3.564511 CTGACGTTTTTCGATGGCAATT 58.435 40.909 0.00 0.00 42.86 2.32
2242 2309 2.095263 CCTGACGTTTTTCGATGGCAAT 60.095 45.455 0.00 0.00 42.86 3.56
2243 2310 1.265635 CCTGACGTTTTTCGATGGCAA 59.734 47.619 0.00 0.00 42.86 4.52
2244 2311 0.871722 CCTGACGTTTTTCGATGGCA 59.128 50.000 0.00 0.00 42.86 4.92
2245 2312 0.168128 CCCTGACGTTTTTCGATGGC 59.832 55.000 0.00 0.00 42.86 4.40
2246 2313 0.168128 GCCCTGACGTTTTTCGATGG 59.832 55.000 0.00 0.00 42.86 3.51
2247 2314 1.156736 AGCCCTGACGTTTTTCGATG 58.843 50.000 0.00 0.00 42.86 3.84
2248 2315 2.232941 TCTAGCCCTGACGTTTTTCGAT 59.767 45.455 0.00 0.00 42.86 3.59
2249 2316 1.614903 TCTAGCCCTGACGTTTTTCGA 59.385 47.619 0.00 0.00 42.86 3.71
2250 2317 1.993370 CTCTAGCCCTGACGTTTTTCG 59.007 52.381 0.00 0.00 46.00 3.46
2251 2318 2.737252 CACTCTAGCCCTGACGTTTTTC 59.263 50.000 0.00 0.00 0.00 2.29
2252 2319 2.767505 CACTCTAGCCCTGACGTTTTT 58.232 47.619 0.00 0.00 0.00 1.94
2253 2320 1.608283 GCACTCTAGCCCTGACGTTTT 60.608 52.381 0.00 0.00 0.00 2.43
2254 2321 0.037232 GCACTCTAGCCCTGACGTTT 60.037 55.000 0.00 0.00 0.00 3.60
2255 2322 1.185618 TGCACTCTAGCCCTGACGTT 61.186 55.000 0.00 0.00 0.00 3.99
2256 2323 1.185618 TTGCACTCTAGCCCTGACGT 61.186 55.000 0.00 0.00 0.00 4.34
2257 2324 0.737715 GTTGCACTCTAGCCCTGACG 60.738 60.000 0.00 0.00 0.00 4.35
2258 2325 0.737715 CGTTGCACTCTAGCCCTGAC 60.738 60.000 0.00 0.00 0.00 3.51
2259 2326 1.591703 CGTTGCACTCTAGCCCTGA 59.408 57.895 0.00 0.00 0.00 3.86
2260 2327 2.103042 GCGTTGCACTCTAGCCCTG 61.103 63.158 0.00 0.00 0.00 4.45
2261 2328 2.266055 GCGTTGCACTCTAGCCCT 59.734 61.111 0.00 0.00 0.00 5.19
2262 2329 2.047274 TGCGTTGCACTCTAGCCC 60.047 61.111 0.00 0.00 31.71 5.19
2271 2338 1.525765 ACATGTCAGGTGCGTTGCA 60.526 52.632 0.00 0.00 35.60 4.08
2272 2339 1.081906 CACATGTCAGGTGCGTTGC 60.082 57.895 4.45 0.00 0.00 4.17
2273 2340 0.235665 GTCACATGTCAGGTGCGTTG 59.764 55.000 12.74 0.00 36.22 4.10
2274 2341 0.179059 TGTCACATGTCAGGTGCGTT 60.179 50.000 12.74 0.00 36.22 4.84
2275 2342 0.880278 GTGTCACATGTCAGGTGCGT 60.880 55.000 12.74 0.00 36.22 5.24
2276 2343 0.601046 AGTGTCACATGTCAGGTGCG 60.601 55.000 12.74 0.00 36.22 5.34
2277 2344 1.597742 AAGTGTCACATGTCAGGTGC 58.402 50.000 12.74 8.60 36.22 5.01
2278 2345 4.568956 TGATAAGTGTCACATGTCAGGTG 58.431 43.478 11.39 11.39 37.60 4.00
2279 2346 4.890158 TGATAAGTGTCACATGTCAGGT 57.110 40.909 5.62 0.00 0.00 4.00
2280 2347 6.403964 CCAAATGATAAGTGTCACATGTCAGG 60.404 42.308 12.26 5.81 0.00 3.86
2281 2348 6.372381 TCCAAATGATAAGTGTCACATGTCAG 59.628 38.462 12.26 1.19 0.00 3.51
2282 2349 6.237154 TCCAAATGATAAGTGTCACATGTCA 58.763 36.000 9.63 9.63 0.00 3.58
2283 2350 6.741992 TCCAAATGATAAGTGTCACATGTC 57.258 37.500 5.62 1.73 0.00 3.06
2284 2351 7.707624 AATCCAAATGATAAGTGTCACATGT 57.292 32.000 5.62 0.00 31.83 3.21
2287 2354 9.685276 AGAATAATCCAAATGATAAGTGTCACA 57.315 29.630 5.62 0.00 31.83 3.58
2337 2404 9.928236 GAGAATAGTAAAGCAGATTTTCATGTC 57.072 33.333 0.00 0.00 32.01 3.06
2350 2417 6.810911 TCAGACATGGAGAGAATAGTAAAGC 58.189 40.000 0.00 0.00 0.00 3.51
2359 2426 4.564406 GCCTTTTCTCAGACATGGAGAGAA 60.564 45.833 17.44 17.44 44.20 2.87
2364 2431 1.988107 AGGCCTTTTCTCAGACATGGA 59.012 47.619 0.00 0.00 0.00 3.41
2365 2432 2.503895 AGGCCTTTTCTCAGACATGG 57.496 50.000 0.00 0.00 0.00 3.66
2375 2442 5.534407 TCCGACAAAATTTTAGGCCTTTTC 58.466 37.500 12.58 0.00 0.00 2.29
2401 2468 6.552859 TTTGATCGAAGTTGCACTATTTGA 57.447 33.333 0.00 0.00 0.00 2.69
2434 2501 6.065374 TGGTGCCAGAGTTTTTGATAGTTTA 58.935 36.000 0.00 0.00 0.00 2.01
2486 2553 2.229543 CGGTGCGTAGTTAGGCCATATA 59.770 50.000 5.01 0.00 36.33 0.86
2487 2554 1.000506 CGGTGCGTAGTTAGGCCATAT 59.999 52.381 5.01 0.00 36.33 1.78
2488 2555 0.386476 CGGTGCGTAGTTAGGCCATA 59.614 55.000 5.01 0.00 36.33 2.74
2513 2640 9.709495 AGAAGCTGTATAAATTTTTGCATGAAA 57.291 25.926 0.00 0.00 0.00 2.69
2525 2652 7.103641 TCCGTCTCAAAAGAAGCTGTATAAAT 58.896 34.615 0.00 0.00 31.93 1.40
2532 2659 2.072298 CCTCCGTCTCAAAAGAAGCTG 58.928 52.381 0.00 0.00 31.93 4.24
2534 2661 1.443802 CCCTCCGTCTCAAAAGAAGC 58.556 55.000 0.00 0.00 31.93 3.86
2547 2674 2.907917 CTCGCTCTACCCCCTCCG 60.908 72.222 0.00 0.00 0.00 4.63
2596 4158 3.569210 CCAGTCCACACAGGGGCA 61.569 66.667 0.00 0.00 38.24 5.36
2606 4168 1.303948 CCACCATGCATCCAGTCCA 59.696 57.895 0.00 0.00 0.00 4.02
2611 4173 1.683025 CAAGGCCACCATGCATCCA 60.683 57.895 5.01 0.00 0.00 3.41
2634 4201 0.108520 TAACATGAAGTCGGGTCGGC 60.109 55.000 0.00 0.00 0.00 5.54
2636 4203 3.159353 TCATAACATGAAGTCGGGTCG 57.841 47.619 0.00 0.00 36.11 4.79
2658 4225 0.036388 TACTTGGAGCTTCTTGCCCG 60.036 55.000 0.00 0.00 44.23 6.13
2674 4241 7.172342 TGTTGTTTATATGCAAAGGACCTACT 58.828 34.615 0.00 0.00 0.00 2.57
2704 4271 3.794138 GCCCACACAAAAACTTTACTCGG 60.794 47.826 0.00 0.00 0.00 4.63
2749 4316 2.037208 AGGCCGGGGGTTTCAATG 59.963 61.111 2.18 0.00 0.00 2.82
2750 4317 2.238701 AGAGGCCGGGGGTTTCAAT 61.239 57.895 2.18 0.00 0.00 2.57
2762 4329 3.562973 CACATCACAATGATACAGAGGCC 59.437 47.826 0.00 0.00 34.28 5.19
2896 4757 7.609960 TGTTAAAGCATTTCAAATCCTATGCA 58.390 30.769 0.00 0.00 44.38 3.96


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

AutoCloner maintained by Alex Coulton.