Multiple sequence alignment - TraesCS7D01G242000

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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 TraesCS7D01G242000 chr7D 100.000 2414 0 0 1 2414 205952816 205955229 0.000000e+00 4458
1 TraesCS7D01G242000 chr7D 88.942 208 19 3 2203 2408 394256728 394256523 1.110000e-63 254
2 TraesCS7D01G242000 chr7D 86.512 215 21 4 2205 2413 577909417 577909629 1.870000e-56 230
3 TraesCS7D01G242000 chr7D 81.818 253 32 11 2169 2413 498600455 498600209 1.460000e-47 200
4 TraesCS7D01G242000 chr7A 94.313 2110 84 12 88 2167 218264468 218266571 0.000000e+00 3199
5 TraesCS7D01G242000 chr7A 83.412 211 27 8 2202 2407 54876326 54876119 3.170000e-44 189
6 TraesCS7D01G242000 chr7B 94.540 2088 72 15 88 2148 196277741 196275669 0.000000e+00 3186
7 TraesCS7D01G242000 chr7B 86.192 239 22 10 2169 2402 437763327 437763095 5.150000e-62 248
8 TraesCS7D01G242000 chr7B 85.306 245 26 6 2175 2413 52614447 52614207 6.670000e-61 244
9 TraesCS7D01G242000 chr7B 87.500 176 20 2 2203 2376 710331859 710332034 4.070000e-48 202
10 TraesCS7D01G242000 chr6D 90.400 250 20 1 2169 2414 327985469 327985718 2.310000e-85 326
11 TraesCS7D01G242000 chr4B 87.500 176 20 2 2203 2376 551945602 551945427 4.070000e-48 202
12 TraesCS7D01G242000 chr3B 87.179 156 19 1 2222 2376 465968513 465968668 2.470000e-40 176


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 TraesCS7D01G242000 chr7D 205952816 205955229 2413 False 4458 4458 100.000 1 2414 1 chr7D.!!$F1 2413
1 TraesCS7D01G242000 chr7A 218264468 218266571 2103 False 3199 3199 94.313 88 2167 1 chr7A.!!$F1 2079
2 TraesCS7D01G242000 chr7B 196275669 196277741 2072 True 3186 3186 94.540 88 2148 1 chr7B.!!$R2 2060

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
60 61 0.459759 GGAAACCCTAACGAGAGCGG 60.460 60.0 0.0 0.0 43.17 5.52 F
1065 1084 0.038166 ACCGAATGATGCCCAGTTGT 59.962 50.0 0.0 0.0 0.00 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1293 1312 0.380378 TTGCGGCACTGTTTTGACTC 59.620 50.0 0.05 0.00 0.0 3.36 R
2196 2244 0.037605 GTGGGATCGGTCGACTGTTT 60.038 55.0 23.27 12.66 0.0 2.83 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
59 60 3.046280 GGAAACCCTAACGAGAGCG 57.954 57.895 0.00 0.00 44.79 5.03
60 61 0.459759 GGAAACCCTAACGAGAGCGG 60.460 60.000 0.00 0.00 43.17 5.52
61 62 0.459759 GAAACCCTAACGAGAGCGGG 60.460 60.000 0.00 0.00 43.17 6.13
62 63 1.896122 AAACCCTAACGAGAGCGGGG 61.896 60.000 0.00 0.00 43.17 5.73
63 64 4.222847 CCCTAACGAGAGCGGGGC 62.223 72.222 0.00 0.00 43.17 5.80
64 65 4.570663 CCTAACGAGAGCGGGGCG 62.571 72.222 0.00 0.00 43.17 6.13
65 66 4.570663 CTAACGAGAGCGGGGCGG 62.571 72.222 0.00 0.00 43.17 6.13
122 123 7.287696 GGATATACATGACAAGGAAAAACCCAT 59.712 37.037 0.00 0.00 40.05 4.00
201 203 5.875224 TCACAGGTCCATGAAATGTTTCTA 58.125 37.500 6.99 0.00 44.81 2.10
296 298 3.211045 AGTGCCAATACAACTTCGTGTT 58.789 40.909 0.00 0.00 39.92 3.32
455 460 6.028131 TCTTCCTAGATGGCAATGGATATCT 58.972 40.000 2.05 0.00 35.26 1.98
565 570 5.614308 TCTTATATGCACTGCTAGCACATT 58.386 37.500 20.51 12.68 45.95 2.71
610 629 8.108364 GTCTAGGCTACTATAATCCCTCAGTTA 58.892 40.741 0.00 0.00 0.00 2.24
629 648 6.830324 TCAGTTAGCAGCCAGAAATGATAAAT 59.170 34.615 0.00 0.00 29.91 1.40
637 656 9.565213 GCAGCCAGAAATGATAAATATGATAAC 57.435 33.333 0.00 0.00 0.00 1.89
716 735 4.463891 CCAACAGCAAATAATCAACTCCCT 59.536 41.667 0.00 0.00 0.00 4.20
804 823 1.873591 CAGTTTGTCTTGAACCCCTCG 59.126 52.381 0.00 0.00 0.00 4.63
1062 1081 0.180406 GGTACCGAATGATGCCCAGT 59.820 55.000 0.00 0.00 0.00 4.00
1065 1084 0.038166 ACCGAATGATGCCCAGTTGT 59.962 50.000 0.00 0.00 0.00 3.32
1120 1139 2.829741 AGGAACAGAAGTGAGACAGC 57.170 50.000 0.00 0.00 0.00 4.40
1143 1162 5.698545 GCTCACACTTGAAGAACTTCTGTAT 59.301 40.000 14.31 2.37 40.14 2.29
1172 1191 2.440247 CTGGGAAATGGGGGCGAC 60.440 66.667 0.00 0.00 0.00 5.19
1293 1312 2.357517 GGTGGAGTGTCTGTGCGG 60.358 66.667 0.00 0.00 0.00 5.69
1530 1556 6.396829 AGAAGGAAAATCTTGTGGAGTTTG 57.603 37.500 0.00 0.00 41.45 2.93
1627 1653 4.794278 TGCATACTTGAGGTTTACGAGA 57.206 40.909 0.00 0.00 0.00 4.04
1629 1655 4.927425 TGCATACTTGAGGTTTACGAGAAC 59.073 41.667 0.00 0.00 0.00 3.01
1772 1801 5.017294 TGTATCATGCGTAGGATTGACAA 57.983 39.130 5.87 0.00 35.32 3.18
1877 1911 1.778027 GAACGGGTGTTGGGTGTTCG 61.778 60.000 0.00 0.00 38.78 3.95
1883 1917 2.223745 GGTGTTGGGTGTTCGTACAAT 58.776 47.619 0.00 0.00 35.69 2.71
1928 1962 1.959226 TGGGCACGAGCGAACTTTC 60.959 57.895 0.00 0.00 43.41 2.62
1947 1981 6.688554 ACTTTCTGGAGATAGGATACCTTCT 58.311 40.000 0.00 0.00 34.61 2.85
2169 2217 2.970639 CGAGGGGAGTTTCGCAGA 59.029 61.111 0.00 0.00 0.00 4.26
2170 2218 1.292223 CGAGGGGAGTTTCGCAGAA 59.708 57.895 0.00 0.00 45.90 3.02
2171 2219 0.320421 CGAGGGGAGTTTCGCAGAAA 60.320 55.000 0.55 0.55 45.90 2.52
2172 2220 1.876416 CGAGGGGAGTTTCGCAGAAAA 60.876 52.381 5.51 0.00 45.90 2.29
2173 2221 1.535896 GAGGGGAGTTTCGCAGAAAAC 59.464 52.381 5.51 2.52 45.90 2.43
2174 2222 0.596577 GGGGAGTTTCGCAGAAAACC 59.403 55.000 5.51 10.63 45.90 3.27
2175 2223 0.596577 GGGAGTTTCGCAGAAAACCC 59.403 55.000 19.95 19.95 45.90 4.11
2176 2224 1.605753 GGAGTTTCGCAGAAAACCCT 58.394 50.000 5.51 0.55 45.90 4.34
2177 2225 2.551504 GGGAGTTTCGCAGAAAACCCTA 60.552 50.000 23.33 0.21 45.90 3.53
2178 2226 3.344515 GGAGTTTCGCAGAAAACCCTAT 58.655 45.455 5.51 0.00 45.90 2.57
2179 2227 3.756963 GGAGTTTCGCAGAAAACCCTATT 59.243 43.478 5.51 0.00 45.90 1.73
2180 2228 4.217767 GGAGTTTCGCAGAAAACCCTATTT 59.782 41.667 5.51 0.00 45.90 1.40
2181 2229 5.121221 AGTTTCGCAGAAAACCCTATTTG 57.879 39.130 5.51 0.00 45.90 2.32
2182 2230 4.825085 AGTTTCGCAGAAAACCCTATTTGA 59.175 37.500 5.51 0.00 45.90 2.69
2183 2231 4.759516 TTCGCAGAAAACCCTATTTGAC 57.240 40.909 0.00 0.00 45.90 3.18
2184 2232 2.739913 TCGCAGAAAACCCTATTTGACG 59.260 45.455 0.00 0.00 0.00 4.35
2185 2233 2.727916 CGCAGAAAACCCTATTTGACGC 60.728 50.000 0.00 0.00 0.00 5.19
2186 2234 2.488153 GCAGAAAACCCTATTTGACGCT 59.512 45.455 0.00 0.00 0.00 5.07
2187 2235 3.426292 GCAGAAAACCCTATTTGACGCTC 60.426 47.826 0.00 0.00 0.00 5.03
2188 2236 4.003648 CAGAAAACCCTATTTGACGCTCT 58.996 43.478 0.00 0.00 0.00 4.09
2189 2237 4.093556 CAGAAAACCCTATTTGACGCTCTC 59.906 45.833 0.00 0.00 0.00 3.20
2190 2238 3.983044 AAACCCTATTTGACGCTCTCT 57.017 42.857 0.00 0.00 0.00 3.10
2191 2239 2.969628 ACCCTATTTGACGCTCTCTG 57.030 50.000 0.00 0.00 0.00 3.35
2192 2240 1.134670 ACCCTATTTGACGCTCTCTGC 60.135 52.381 0.00 0.00 38.57 4.26
2202 2250 2.906047 GCTCTCTGCGTCAAACAGT 58.094 52.632 0.00 0.00 36.50 3.55
2203 2251 0.787183 GCTCTCTGCGTCAAACAGTC 59.213 55.000 0.00 0.00 36.50 3.51
2204 2252 1.056103 CTCTCTGCGTCAAACAGTCG 58.944 55.000 0.00 0.00 36.50 4.18
2205 2253 0.666374 TCTCTGCGTCAAACAGTCGA 59.334 50.000 0.00 0.00 36.50 4.20
2206 2254 0.778815 CTCTGCGTCAAACAGTCGAC 59.221 55.000 7.70 7.70 36.50 4.20
2207 2255 0.596600 TCTGCGTCAAACAGTCGACC 60.597 55.000 13.01 0.00 36.50 4.79
2208 2256 1.876453 CTGCGTCAAACAGTCGACCG 61.876 60.000 13.01 4.15 0.00 4.79
2209 2257 1.659335 GCGTCAAACAGTCGACCGA 60.659 57.895 13.01 0.00 0.00 4.69
2210 2258 1.007336 GCGTCAAACAGTCGACCGAT 61.007 55.000 13.01 0.00 0.00 4.18
2211 2259 0.982673 CGTCAAACAGTCGACCGATC 59.017 55.000 13.01 0.00 0.00 3.69
2212 2260 1.347320 GTCAAACAGTCGACCGATCC 58.653 55.000 13.01 0.00 0.00 3.36
2213 2261 0.245539 TCAAACAGTCGACCGATCCC 59.754 55.000 13.01 0.00 0.00 3.85
2214 2262 0.037697 CAAACAGTCGACCGATCCCA 60.038 55.000 13.01 0.00 0.00 4.37
2215 2263 0.037605 AAACAGTCGACCGATCCCAC 60.038 55.000 13.01 0.00 0.00 4.61
2216 2264 1.183030 AACAGTCGACCGATCCCACA 61.183 55.000 13.01 0.00 0.00 4.17
2217 2265 1.139734 CAGTCGACCGATCCCACAG 59.860 63.158 13.01 0.00 0.00 3.66
2218 2266 2.052690 AGTCGACCGATCCCACAGG 61.053 63.158 13.01 0.00 0.00 4.00
2219 2267 2.758327 TCGACCGATCCCACAGGG 60.758 66.667 0.00 0.00 46.11 4.45
2229 2277 2.124901 CCACAGGGGCGCGATAAA 60.125 61.111 12.10 0.00 0.00 1.40
2230 2278 2.180204 CCACAGGGGCGCGATAAAG 61.180 63.158 12.10 0.00 0.00 1.85
2231 2279 1.449601 CACAGGGGCGCGATAAAGT 60.450 57.895 12.10 0.00 0.00 2.66
2232 2280 1.449601 ACAGGGGCGCGATAAAGTG 60.450 57.895 12.10 0.58 0.00 3.16
2233 2281 2.180204 CAGGGGCGCGATAAAGTGG 61.180 63.158 12.10 0.00 0.00 4.00
2234 2282 2.900337 GGGGCGCGATAAAGTGGG 60.900 66.667 12.10 0.00 0.00 4.61
2235 2283 3.583086 GGGCGCGATAAAGTGGGC 61.583 66.667 12.10 0.00 42.67 5.36
2237 2285 3.937062 GCGCGATAAAGTGGGCCG 61.937 66.667 12.10 0.00 38.02 6.13
2238 2286 3.269347 CGCGATAAAGTGGGCCGG 61.269 66.667 0.00 0.00 0.00 6.13
2239 2287 2.188469 GCGATAAAGTGGGCCGGA 59.812 61.111 5.05 0.00 0.00 5.14
2240 2288 2.178235 GCGATAAAGTGGGCCGGAC 61.178 63.158 5.05 0.00 0.00 4.79
2241 2289 1.523032 CGATAAAGTGGGCCGGACC 60.523 63.158 23.70 23.70 37.93 4.46
2242 2290 1.605453 GATAAAGTGGGCCGGACCA 59.395 57.895 30.39 30.39 42.05 4.02
2243 2291 0.182775 GATAAAGTGGGCCGGACCAT 59.817 55.000 36.84 20.93 43.59 3.55
2244 2292 0.182775 ATAAAGTGGGCCGGACCATC 59.817 55.000 36.84 25.90 43.59 3.51
2245 2293 0.912487 TAAAGTGGGCCGGACCATCT 60.912 55.000 36.84 27.81 43.59 2.90
2246 2294 2.198304 AAAGTGGGCCGGACCATCTC 62.198 60.000 36.84 21.32 43.59 2.75
2247 2295 4.176752 GTGGGCCGGACCATCTCC 62.177 72.222 36.84 17.12 43.59 3.71
2252 2300 4.227134 CCGGACCATCTCCCGCTG 62.227 72.222 0.00 0.00 44.07 5.18
2253 2301 3.461773 CGGACCATCTCCCGCTGT 61.462 66.667 0.00 0.00 39.22 4.40
2254 2302 2.125326 CGGACCATCTCCCGCTGTA 61.125 63.158 0.00 0.00 39.22 2.74
2255 2303 1.742768 GGACCATCTCCCGCTGTAG 59.257 63.158 0.00 0.00 31.83 2.74
2256 2304 1.742768 GACCATCTCCCGCTGTAGG 59.257 63.158 0.00 0.00 0.00 3.18
2257 2305 2.370647 GACCATCTCCCGCTGTAGGC 62.371 65.000 0.00 0.00 37.64 3.93
2258 2306 2.434843 CCATCTCCCGCTGTAGGCA 61.435 63.158 0.00 0.00 41.91 4.75
2259 2307 1.068753 CATCTCCCGCTGTAGGCAG 59.931 63.158 0.00 0.00 45.23 4.85
2260 2308 1.381872 ATCTCCCGCTGTAGGCAGT 60.382 57.895 0.00 0.00 44.32 4.40
2261 2309 0.978146 ATCTCCCGCTGTAGGCAGTT 60.978 55.000 0.00 0.00 44.32 3.16
2262 2310 1.153549 CTCCCGCTGTAGGCAGTTC 60.154 63.158 0.00 0.00 44.32 3.01
2263 2311 2.125106 CCCGCTGTAGGCAGTTCC 60.125 66.667 0.00 0.00 44.32 3.62
2264 2312 2.509336 CCGCTGTAGGCAGTTCCG 60.509 66.667 0.00 0.00 44.32 4.30
2265 2313 2.509336 CGCTGTAGGCAGTTCCGG 60.509 66.667 0.00 0.00 44.32 5.14
2266 2314 2.663196 GCTGTAGGCAGTTCCGGT 59.337 61.111 0.00 0.00 44.32 5.28
2267 2315 1.003718 GCTGTAGGCAGTTCCGGTT 60.004 57.895 0.00 0.00 44.32 4.44
2268 2316 0.605589 GCTGTAGGCAGTTCCGGTTT 60.606 55.000 0.00 0.00 44.32 3.27
2269 2317 1.892209 CTGTAGGCAGTTCCGGTTTT 58.108 50.000 0.00 0.00 40.77 2.43
2270 2318 1.535462 CTGTAGGCAGTTCCGGTTTTG 59.465 52.381 0.00 0.00 40.77 2.44
2271 2319 0.879090 GTAGGCAGTTCCGGTTTTGG 59.121 55.000 0.00 0.00 40.77 3.28
2272 2320 0.250989 TAGGCAGTTCCGGTTTTGGG 60.251 55.000 0.00 0.00 40.77 4.12
2273 2321 1.529713 GGCAGTTCCGGTTTTGGGA 60.530 57.895 0.00 0.00 0.00 4.37
2274 2322 1.110518 GGCAGTTCCGGTTTTGGGAA 61.111 55.000 0.00 0.00 41.14 3.97
2280 2328 2.740506 TCCGGTTTTGGGAACTTTCT 57.259 45.000 0.00 0.00 0.00 2.52
2281 2329 3.860968 TCCGGTTTTGGGAACTTTCTA 57.139 42.857 0.00 0.00 0.00 2.10
2282 2330 3.746940 TCCGGTTTTGGGAACTTTCTAG 58.253 45.455 0.00 0.00 0.00 2.43
2283 2331 3.391955 TCCGGTTTTGGGAACTTTCTAGA 59.608 43.478 0.00 0.00 0.00 2.43
2284 2332 4.139038 CCGGTTTTGGGAACTTTCTAGAA 58.861 43.478 0.00 0.00 0.00 2.10
2285 2333 4.215613 CCGGTTTTGGGAACTTTCTAGAAG 59.784 45.833 5.12 3.14 0.00 2.85
2286 2334 4.820173 CGGTTTTGGGAACTTTCTAGAAGT 59.180 41.667 5.12 3.76 0.00 3.01
2287 2335 5.298527 CGGTTTTGGGAACTTTCTAGAAGTT 59.701 40.000 15.68 15.68 42.62 2.66
2288 2336 6.183360 CGGTTTTGGGAACTTTCTAGAAGTTT 60.183 38.462 16.40 9.87 40.27 2.66
2289 2337 7.201145 GGTTTTGGGAACTTTCTAGAAGTTTC 58.799 38.462 16.40 15.80 40.27 2.78
2292 2340 4.981812 GGGAACTTTCTAGAAGTTTCCCA 58.018 43.478 35.27 13.31 45.89 4.37
2293 2341 5.004448 GGGAACTTTCTAGAAGTTTCCCAG 58.996 45.833 35.27 21.16 45.89 4.45
2294 2342 5.221864 GGGAACTTTCTAGAAGTTTCCCAGA 60.222 44.000 35.27 12.20 45.89 3.86
2295 2343 5.701750 GGAACTTTCTAGAAGTTTCCCAGAC 59.298 44.000 24.28 10.98 40.27 3.51
2296 2344 4.884247 ACTTTCTAGAAGTTTCCCAGACG 58.116 43.478 5.12 0.00 0.00 4.18
2297 2345 3.955650 TTCTAGAAGTTTCCCAGACGG 57.044 47.619 0.00 0.00 0.00 4.79
2298 2346 2.885616 TCTAGAAGTTTCCCAGACGGT 58.114 47.619 0.00 0.00 0.00 4.83
2299 2347 3.236896 TCTAGAAGTTTCCCAGACGGTT 58.763 45.455 0.00 0.00 0.00 4.44
2300 2348 3.644738 TCTAGAAGTTTCCCAGACGGTTT 59.355 43.478 0.00 0.00 0.00 3.27
2301 2349 3.292492 AGAAGTTTCCCAGACGGTTTT 57.708 42.857 0.00 0.00 0.00 2.43
2302 2350 3.628008 AGAAGTTTCCCAGACGGTTTTT 58.372 40.909 0.00 0.00 0.00 1.94
2303 2351 4.784177 AGAAGTTTCCCAGACGGTTTTTA 58.216 39.130 0.00 0.00 0.00 1.52
2304 2352 5.382616 AGAAGTTTCCCAGACGGTTTTTAT 58.617 37.500 0.00 0.00 0.00 1.40
2305 2353 5.472478 AGAAGTTTCCCAGACGGTTTTTATC 59.528 40.000 0.00 0.00 0.00 1.75
2306 2354 4.077108 AGTTTCCCAGACGGTTTTTATCC 58.923 43.478 0.00 0.00 0.00 2.59
2318 2366 5.557388 CGGTTTTTATCCGTTTCTAGAAGC 58.443 41.667 9.14 9.14 42.62 3.86
2319 2367 5.350640 CGGTTTTTATCCGTTTCTAGAAGCT 59.649 40.000 16.13 1.89 42.62 3.74
2320 2368 6.128363 CGGTTTTTATCCGTTTCTAGAAGCTT 60.128 38.462 16.13 0.00 42.62 3.74
2321 2369 7.242079 GGTTTTTATCCGTTTCTAGAAGCTTC 58.758 38.462 19.11 19.11 0.00 3.86
2322 2370 6.980051 TTTTATCCGTTTCTAGAAGCTTCC 57.020 37.500 22.81 5.49 0.00 3.46
2323 2371 5.934402 TTATCCGTTTCTAGAAGCTTCCT 57.066 39.130 22.81 12.48 0.00 3.36
2324 2372 7.414222 TTTATCCGTTTCTAGAAGCTTCCTA 57.586 36.000 22.81 12.93 0.00 2.94
2325 2373 5.934402 ATCCGTTTCTAGAAGCTTCCTAA 57.066 39.130 22.81 11.68 0.00 2.69
2326 2374 5.733620 TCCGTTTCTAGAAGCTTCCTAAA 57.266 39.130 22.81 16.55 0.00 1.85
2327 2375 5.721232 TCCGTTTCTAGAAGCTTCCTAAAG 58.279 41.667 22.81 14.61 35.47 1.85
2339 2387 4.895224 CTTCCTAAAGCGGGGTATTTTC 57.105 45.455 0.00 0.00 0.00 2.29
2340 2388 3.286329 TCCTAAAGCGGGGTATTTTCC 57.714 47.619 0.00 0.00 0.00 3.13
2341 2389 2.848071 TCCTAAAGCGGGGTATTTTCCT 59.152 45.455 0.00 0.00 0.00 3.36
2342 2390 3.267551 TCCTAAAGCGGGGTATTTTCCTT 59.732 43.478 0.00 0.00 0.00 3.36
2343 2391 4.021229 CCTAAAGCGGGGTATTTTCCTTT 58.979 43.478 0.00 0.00 0.00 3.11
2344 2392 4.464951 CCTAAAGCGGGGTATTTTCCTTTT 59.535 41.667 0.00 0.00 0.00 2.27
2345 2393 5.653330 CCTAAAGCGGGGTATTTTCCTTTTA 59.347 40.000 0.00 0.00 0.00 1.52
2346 2394 6.322969 CCTAAAGCGGGGTATTTTCCTTTTAT 59.677 38.462 0.00 0.00 0.00 1.40
2347 2395 6.614694 AAAGCGGGGTATTTTCCTTTTATT 57.385 33.333 0.00 0.00 0.00 1.40
2348 2396 6.614694 AAGCGGGGTATTTTCCTTTTATTT 57.385 33.333 0.00 0.00 0.00 1.40
2349 2397 6.614694 AGCGGGGTATTTTCCTTTTATTTT 57.385 33.333 0.00 0.00 0.00 1.82
2350 2398 6.636705 AGCGGGGTATTTTCCTTTTATTTTC 58.363 36.000 0.00 0.00 0.00 2.29
2351 2399 6.439375 AGCGGGGTATTTTCCTTTTATTTTCT 59.561 34.615 0.00 0.00 0.00 2.52
2352 2400 6.533723 GCGGGGTATTTTCCTTTTATTTTCTG 59.466 38.462 0.00 0.00 0.00 3.02
2353 2401 7.608153 CGGGGTATTTTCCTTTTATTTTCTGT 58.392 34.615 0.00 0.00 0.00 3.41
2354 2402 8.092068 CGGGGTATTTTCCTTTTATTTTCTGTT 58.908 33.333 0.00 0.00 0.00 3.16
2355 2403 9.787435 GGGGTATTTTCCTTTTATTTTCTGTTT 57.213 29.630 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 0.459759 CGCTCTCGTTAGGGTTTCCC 60.460 60.000 0.00 0.00 45.90 3.97
41 42 0.459759 CCGCTCTCGTTAGGGTTTCC 60.460 60.000 3.90 0.00 0.00 3.13
42 43 0.459759 CCCGCTCTCGTTAGGGTTTC 60.460 60.000 0.00 0.00 39.05 2.78
43 44 1.595357 CCCGCTCTCGTTAGGGTTT 59.405 57.895 0.00 0.00 39.05 3.27
44 45 2.356780 CCCCGCTCTCGTTAGGGTT 61.357 63.158 0.00 0.00 42.26 4.11
45 46 2.758737 CCCCGCTCTCGTTAGGGT 60.759 66.667 0.00 0.00 42.26 4.34
46 47 4.222847 GCCCCGCTCTCGTTAGGG 62.223 72.222 0.00 0.00 43.41 3.53
47 48 4.570663 CGCCCCGCTCTCGTTAGG 62.571 72.222 0.00 0.00 0.00 2.69
48 49 4.570663 CCGCCCCGCTCTCGTTAG 62.571 72.222 0.00 0.00 0.00 2.34
73 74 4.360405 TTTTGGCCCCGCTCCCTC 62.360 66.667 0.00 0.00 0.00 4.30
74 75 4.366684 CTTTTGGCCCCGCTCCCT 62.367 66.667 0.00 0.00 0.00 4.20
77 78 3.286915 CTTGCTTTTGGCCCCGCTC 62.287 63.158 0.00 0.00 40.92 5.03
78 79 3.305516 CTTGCTTTTGGCCCCGCT 61.306 61.111 0.00 0.00 40.92 5.52
79 80 4.377708 CCTTGCTTTTGGCCCCGC 62.378 66.667 0.00 0.00 40.92 6.13
80 81 3.694538 CCCTTGCTTTTGGCCCCG 61.695 66.667 0.00 0.00 40.92 5.73
81 82 0.325203 TATCCCTTGCTTTTGGCCCC 60.325 55.000 0.00 0.00 40.92 5.80
82 83 1.793414 ATATCCCTTGCTTTTGGCCC 58.207 50.000 0.00 0.00 40.92 5.80
83 84 3.295973 TGTATATCCCTTGCTTTTGGCC 58.704 45.455 0.00 0.00 40.92 5.36
84 85 4.584325 TCATGTATATCCCTTGCTTTTGGC 59.416 41.667 0.00 0.00 42.22 4.52
85 86 5.593909 TGTCATGTATATCCCTTGCTTTTGG 59.406 40.000 0.00 0.00 0.00 3.28
86 87 6.698008 TGTCATGTATATCCCTTGCTTTTG 57.302 37.500 0.00 0.00 0.00 2.44
122 123 7.663493 TGACACAATTATGTTGTATCTTGACCA 59.337 33.333 0.00 0.00 37.82 4.02
201 203 3.828451 AGTTGCCAACTTGCTATTCATGT 59.172 39.130 3.74 0.00 39.04 3.21
360 362 7.406031 TGTTGTTTACACCATCCTTTGTAAA 57.594 32.000 3.40 3.40 42.93 2.01
367 372 4.821805 CACTCTTGTTGTTTACACCATCCT 59.178 41.667 0.00 0.00 36.21 3.24
402 407 7.329717 ACGAGAAACTCAAAATATGACTCTGTC 59.670 37.037 0.00 0.00 33.47 3.51
565 570 7.201920 GCCTAGACTATGTCTGGACTTTATTGA 60.202 40.741 11.71 0.00 42.49 2.57
610 629 9.524496 TTATCATATTTATCATTTCTGGCTGCT 57.476 29.630 0.00 0.00 0.00 4.24
637 656 9.683069 ATTCAAAACTAGCACTTGTTATTTCAG 57.317 29.630 0.00 0.00 0.00 3.02
716 735 0.106669 TAGCTGCCGAGAGAAGCCTA 60.107 55.000 0.00 0.00 40.21 3.93
785 804 1.814248 GCGAGGGGTTCAAGACAAACT 60.814 52.381 0.00 0.00 0.00 2.66
804 823 1.816835 TCGATATCACAGGGATACGGC 59.183 52.381 3.12 0.00 41.17 5.68
1120 1139 6.367422 GGATACAGAAGTTCTTCAAGTGTGAG 59.633 42.308 1.56 0.00 34.49 3.51
1143 1162 2.632602 TTTCCCAGCTTGGTTGCGGA 62.633 55.000 3.35 0.00 35.17 5.54
1172 1191 2.434359 GAGCCGGTGTTCCTTCGG 60.434 66.667 1.90 0.00 45.84 4.30
1179 1198 1.183676 AGTACCTTCGAGCCGGTGTT 61.184 55.000 1.90 0.00 34.76 3.32
1185 1204 1.728672 CGGAGAGTACCTTCGAGCC 59.271 63.158 6.26 0.00 46.85 4.70
1275 1294 2.421314 CGCACAGACACTCCACCA 59.579 61.111 0.00 0.00 0.00 4.17
1293 1312 0.380378 TTGCGGCACTGTTTTGACTC 59.620 50.000 0.05 0.00 0.00 3.36
1355 1374 1.938577 CTGAATCTCGTGCAGGAATGG 59.061 52.381 10.76 0.00 0.00 3.16
1627 1653 6.995686 TGAATTTCGGGTACTGCATATATGTT 59.004 34.615 14.14 2.30 32.53 2.71
1629 1655 6.873605 TCTGAATTTCGGGTACTGCATATATG 59.126 38.462 8.45 8.45 32.53 1.78
1772 1801 3.009033 TCAGACGGGGTCATTTCTTCATT 59.991 43.478 0.00 0.00 34.60 2.57
1877 1911 8.635983 GCTTGAAAATCCGAGTAAAAATTGTAC 58.364 33.333 0.00 0.00 0.00 2.90
1883 1917 7.758495 GGATAGCTTGAAAATCCGAGTAAAAA 58.242 34.615 0.00 0.00 30.50 1.94
1928 1962 5.047377 GCAGAAGAAGGTATCCTATCTCCAG 60.047 48.000 0.00 0.00 31.13 3.86
2019 2060 3.314331 CTCGGTGGTGGGTGAGCT 61.314 66.667 0.00 0.00 0.00 4.09
2128 2169 4.671590 TCCCTGTCCGCTCGACCA 62.672 66.667 0.00 0.00 41.18 4.02
2129 2170 4.131088 GTCCCTGTCCGCTCGACC 62.131 72.222 0.00 0.00 41.18 4.79
2161 2209 4.319911 CGTCAAATAGGGTTTTCTGCGAAA 60.320 41.667 0.00 0.55 0.00 3.46
2164 2212 2.727916 GCGTCAAATAGGGTTTTCTGCG 60.728 50.000 0.00 0.00 0.00 5.18
2165 2213 2.488153 AGCGTCAAATAGGGTTTTCTGC 59.512 45.455 0.00 0.00 0.00 4.26
2166 2214 4.003648 AGAGCGTCAAATAGGGTTTTCTG 58.996 43.478 0.00 0.00 0.00 3.02
2167 2215 4.020128 AGAGAGCGTCAAATAGGGTTTTCT 60.020 41.667 0.00 0.00 0.00 2.52
2168 2216 4.093556 CAGAGAGCGTCAAATAGGGTTTTC 59.906 45.833 0.00 0.00 0.00 2.29
2169 2217 4.003648 CAGAGAGCGTCAAATAGGGTTTT 58.996 43.478 0.00 0.00 0.00 2.43
2170 2218 3.600388 CAGAGAGCGTCAAATAGGGTTT 58.400 45.455 0.00 0.00 0.00 3.27
2171 2219 2.678190 GCAGAGAGCGTCAAATAGGGTT 60.678 50.000 0.00 0.00 0.00 4.11
2172 2220 1.134670 GCAGAGAGCGTCAAATAGGGT 60.135 52.381 0.00 0.00 0.00 4.34
2173 2221 1.576356 GCAGAGAGCGTCAAATAGGG 58.424 55.000 0.00 0.00 0.00 3.53
2184 2232 0.787183 GACTGTTTGACGCAGAGAGC 59.213 55.000 0.00 0.00 37.40 4.09
2185 2233 1.056103 CGACTGTTTGACGCAGAGAG 58.944 55.000 0.00 0.00 37.40 3.20
2186 2234 0.666374 TCGACTGTTTGACGCAGAGA 59.334 50.000 0.00 0.00 37.40 3.10
2187 2235 0.778815 GTCGACTGTTTGACGCAGAG 59.221 55.000 8.70 0.00 37.40 3.35
2188 2236 0.596600 GGTCGACTGTTTGACGCAGA 60.597 55.000 16.46 0.00 37.04 4.26
2189 2237 1.853319 GGTCGACTGTTTGACGCAG 59.147 57.895 16.46 0.00 37.04 5.18
2190 2238 1.947146 CGGTCGACTGTTTGACGCA 60.947 57.895 16.54 0.00 37.04 5.24
2191 2239 1.007336 ATCGGTCGACTGTTTGACGC 61.007 55.000 23.27 0.00 37.04 5.19
2192 2240 0.982673 GATCGGTCGACTGTTTGACG 59.017 55.000 23.27 12.50 37.04 4.35
2193 2241 1.347320 GGATCGGTCGACTGTTTGAC 58.653 55.000 23.27 11.16 35.57 3.18
2194 2242 0.245539 GGGATCGGTCGACTGTTTGA 59.754 55.000 23.27 5.09 0.00 2.69
2195 2243 0.037697 TGGGATCGGTCGACTGTTTG 60.038 55.000 23.27 5.27 0.00 2.93
2196 2244 0.037605 GTGGGATCGGTCGACTGTTT 60.038 55.000 23.27 12.66 0.00 2.83
2197 2245 1.183030 TGTGGGATCGGTCGACTGTT 61.183 55.000 23.27 15.78 0.00 3.16
2198 2246 1.595993 CTGTGGGATCGGTCGACTGT 61.596 60.000 23.27 11.31 0.00 3.55
2199 2247 1.139734 CTGTGGGATCGGTCGACTG 59.860 63.158 18.66 18.66 0.00 3.51
2200 2248 2.052690 CCTGTGGGATCGGTCGACT 61.053 63.158 16.46 0.00 33.58 4.18
2201 2249 2.494918 CCTGTGGGATCGGTCGAC 59.505 66.667 7.13 7.13 33.58 4.20
2212 2260 2.124901 TTTATCGCGCCCCTGTGG 60.125 61.111 0.00 0.00 37.09 4.17
2213 2261 1.449601 ACTTTATCGCGCCCCTGTG 60.450 57.895 0.00 0.00 0.00 3.66
2214 2262 1.449601 CACTTTATCGCGCCCCTGT 60.450 57.895 0.00 0.00 0.00 4.00
2215 2263 2.180204 CCACTTTATCGCGCCCCTG 61.180 63.158 0.00 0.00 0.00 4.45
2216 2264 2.189521 CCACTTTATCGCGCCCCT 59.810 61.111 0.00 0.00 0.00 4.79
2217 2265 2.900337 CCCACTTTATCGCGCCCC 60.900 66.667 0.00 0.00 0.00 5.80
2218 2266 3.583086 GCCCACTTTATCGCGCCC 61.583 66.667 0.00 0.00 0.00 6.13
2219 2267 3.583086 GGCCCACTTTATCGCGCC 61.583 66.667 0.00 0.00 0.00 6.53
2220 2268 3.937062 CGGCCCACTTTATCGCGC 61.937 66.667 0.00 0.00 0.00 6.86
2221 2269 3.269347 CCGGCCCACTTTATCGCG 61.269 66.667 0.00 0.00 0.00 5.87
2222 2270 2.178235 GTCCGGCCCACTTTATCGC 61.178 63.158 0.00 0.00 0.00 4.58
2223 2271 1.523032 GGTCCGGCCCACTTTATCG 60.523 63.158 0.00 0.00 0.00 2.92
2224 2272 0.182775 ATGGTCCGGCCCACTTTATC 59.817 55.000 6.24 0.00 37.31 1.75
2225 2273 0.182775 GATGGTCCGGCCCACTTTAT 59.817 55.000 6.24 0.00 37.31 1.40
2226 2274 0.912487 AGATGGTCCGGCCCACTTTA 60.912 55.000 6.24 0.00 37.31 1.85
2227 2275 2.198304 GAGATGGTCCGGCCCACTTT 62.198 60.000 6.24 0.00 37.31 2.66
2228 2276 2.610859 AGATGGTCCGGCCCACTT 60.611 61.111 6.24 0.00 37.31 3.16
2229 2277 3.083997 GAGATGGTCCGGCCCACT 61.084 66.667 6.24 6.32 37.31 4.00
2230 2278 4.176752 GGAGATGGTCCGGCCCAC 62.177 72.222 6.24 0.36 37.31 4.61
2251 2299 1.600023 CAAAACCGGAACTGCCTACA 58.400 50.000 9.46 0.00 0.00 2.74
2252 2300 0.879090 CCAAAACCGGAACTGCCTAC 59.121 55.000 9.46 0.00 0.00 3.18
2253 2301 0.250989 CCCAAAACCGGAACTGCCTA 60.251 55.000 9.46 0.00 0.00 3.93
2254 2302 1.530655 CCCAAAACCGGAACTGCCT 60.531 57.895 9.46 0.00 0.00 4.75
2255 2303 1.110518 TTCCCAAAACCGGAACTGCC 61.111 55.000 9.46 0.00 34.40 4.85
2256 2304 2.421220 TTCCCAAAACCGGAACTGC 58.579 52.632 9.46 0.00 34.40 4.40
2260 2308 3.021177 AGAAAGTTCCCAAAACCGGAA 57.979 42.857 9.46 0.00 37.04 4.30
2261 2309 2.740506 AGAAAGTTCCCAAAACCGGA 57.259 45.000 9.46 0.00 0.00 5.14
2262 2310 3.746940 TCTAGAAAGTTCCCAAAACCGG 58.253 45.455 0.00 0.00 0.00 5.28
2263 2311 4.820173 ACTTCTAGAAAGTTCCCAAAACCG 59.180 41.667 6.63 0.00 0.00 4.44
2264 2312 6.710597 AACTTCTAGAAAGTTCCCAAAACC 57.289 37.500 6.63 0.00 35.76 3.27
2265 2313 7.201145 GGAAACTTCTAGAAAGTTCCCAAAAC 58.799 38.462 24.26 8.54 39.36 2.43
2266 2314 6.322969 GGGAAACTTCTAGAAAGTTCCCAAAA 59.677 38.462 35.35 6.59 41.70 2.44
2267 2315 5.831525 GGGAAACTTCTAGAAAGTTCCCAAA 59.168 40.000 35.35 7.01 41.70 3.28
2268 2316 5.103855 TGGGAAACTTCTAGAAAGTTCCCAA 60.104 40.000 37.90 28.85 44.69 4.12
2269 2317 4.414182 TGGGAAACTTCTAGAAAGTTCCCA 59.586 41.667 37.19 37.19 45.02 4.37
2270 2318 4.981812 TGGGAAACTTCTAGAAAGTTCCC 58.018 43.478 34.59 34.59 42.03 3.97
2271 2319 5.701750 GTCTGGGAAACTTCTAGAAAGTTCC 59.298 44.000 25.57 25.57 39.36 3.62
2272 2320 5.405873 CGTCTGGGAAACTTCTAGAAAGTTC 59.594 44.000 15.90 15.48 39.36 3.01
2273 2321 5.298347 CGTCTGGGAAACTTCTAGAAAGTT 58.702 41.667 6.63 9.95 41.82 2.66
2274 2322 4.262506 CCGTCTGGGAAACTTCTAGAAAGT 60.263 45.833 6.63 4.39 38.47 2.66
2275 2323 4.246458 CCGTCTGGGAAACTTCTAGAAAG 58.754 47.826 6.63 3.77 38.47 2.62
2276 2324 3.644738 ACCGTCTGGGAAACTTCTAGAAA 59.355 43.478 6.63 0.00 40.75 2.52
2277 2325 3.236896 ACCGTCTGGGAAACTTCTAGAA 58.763 45.455 4.81 4.81 40.75 2.10
2278 2326 2.885616 ACCGTCTGGGAAACTTCTAGA 58.114 47.619 0.00 0.00 40.75 2.43
2279 2327 3.679824 AACCGTCTGGGAAACTTCTAG 57.320 47.619 0.00 0.00 40.75 2.43
2280 2328 4.426736 AAAACCGTCTGGGAAACTTCTA 57.573 40.909 0.00 0.00 40.75 2.10
2281 2329 3.292492 AAAACCGTCTGGGAAACTTCT 57.708 42.857 0.00 0.00 40.75 2.85
2282 2330 5.335426 GGATAAAAACCGTCTGGGAAACTTC 60.335 44.000 0.00 0.00 40.75 3.01
2283 2331 4.521639 GGATAAAAACCGTCTGGGAAACTT 59.478 41.667 0.00 0.00 40.75 2.66
2284 2332 4.077108 GGATAAAAACCGTCTGGGAAACT 58.923 43.478 0.00 0.00 40.75 2.66
2285 2333 3.120095 CGGATAAAAACCGTCTGGGAAAC 60.120 47.826 0.00 0.00 44.57 2.78
2286 2334 3.075884 CGGATAAAAACCGTCTGGGAAA 58.924 45.455 0.00 0.00 44.57 3.13
2287 2335 2.702261 CGGATAAAAACCGTCTGGGAA 58.298 47.619 0.00 0.00 44.57 3.97
2288 2336 2.389962 CGGATAAAAACCGTCTGGGA 57.610 50.000 0.00 0.00 44.57 4.37
2296 2344 6.738832 AGCTTCTAGAAACGGATAAAAACC 57.261 37.500 6.63 0.00 0.00 3.27
2297 2345 7.119407 AGGAAGCTTCTAGAAACGGATAAAAAC 59.881 37.037 25.05 2.79 0.00 2.43
2298 2346 7.166167 AGGAAGCTTCTAGAAACGGATAAAAA 58.834 34.615 25.05 0.00 0.00 1.94
2299 2347 6.708285 AGGAAGCTTCTAGAAACGGATAAAA 58.292 36.000 25.05 0.00 0.00 1.52
2300 2348 6.295719 AGGAAGCTTCTAGAAACGGATAAA 57.704 37.500 25.05 0.00 0.00 1.40
2301 2349 5.934402 AGGAAGCTTCTAGAAACGGATAA 57.066 39.130 25.05 0.00 0.00 1.75
2302 2350 7.414222 TTTAGGAAGCTTCTAGAAACGGATA 57.586 36.000 25.05 0.04 0.00 2.59
2303 2351 5.934402 TTAGGAAGCTTCTAGAAACGGAT 57.066 39.130 25.05 0.00 0.00 4.18
2304 2352 5.721232 CTTTAGGAAGCTTCTAGAAACGGA 58.279 41.667 25.05 2.83 0.00 4.69
2318 2366 3.630769 GGAAAATACCCCGCTTTAGGAAG 59.369 47.826 0.00 0.00 35.92 3.46
2319 2367 3.267551 AGGAAAATACCCCGCTTTAGGAA 59.732 43.478 0.00 0.00 0.00 3.36
2320 2368 2.848071 AGGAAAATACCCCGCTTTAGGA 59.152 45.455 0.00 0.00 0.00 2.94
2321 2369 3.292492 AGGAAAATACCCCGCTTTAGG 57.708 47.619 0.00 0.00 0.00 2.69
2322 2370 5.654603 AAAAGGAAAATACCCCGCTTTAG 57.345 39.130 0.00 0.00 0.00 1.85
2323 2371 7.721409 AATAAAAGGAAAATACCCCGCTTTA 57.279 32.000 0.00 0.00 0.00 1.85
2324 2372 6.614694 AATAAAAGGAAAATACCCCGCTTT 57.385 33.333 0.00 0.00 0.00 3.51
2325 2373 6.614694 AAATAAAAGGAAAATACCCCGCTT 57.385 33.333 0.00 0.00 0.00 4.68
2326 2374 6.439375 AGAAAATAAAAGGAAAATACCCCGCT 59.561 34.615 0.00 0.00 0.00 5.52
2327 2375 6.533723 CAGAAAATAAAAGGAAAATACCCCGC 59.466 38.462 0.00 0.00 0.00 6.13
2328 2376 7.608153 ACAGAAAATAAAAGGAAAATACCCCG 58.392 34.615 0.00 0.00 0.00 5.73
2329 2377 9.787435 AAACAGAAAATAAAAGGAAAATACCCC 57.213 29.630 0.00 0.00 0.00 4.95


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

AutoCloner maintained by Alex Coulton.