Multiple sequence alignment - TraesCS3B01G206200

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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 TraesCS3B01G206200 chr3B 100.000 2388 0 0 1 2388 241399568 241401955 0.000000e+00 4410.0
1 TraesCS3B01G206200 chr3B 92.268 194 13 2 2197 2388 345712025 345711832 8.410000e-70 274.0
2 TraesCS3B01G206200 chr3B 85.492 193 26 2 2197 2388 707451852 707452043 1.450000e-47 200.0
3 TraesCS3B01G206200 chr3A 94.196 2188 87 17 9 2182 203660966 203663127 0.000000e+00 3301.0
4 TraesCS3B01G206200 chr3A 82.353 68 7 2 361 428 495001612 495001550 1.000000e-03 54.7
5 TraesCS3B01G206200 chr3D 93.803 1904 71 18 312 2182 165758331 165760220 0.000000e+00 2819.0
6 TraesCS3B01G206200 chr3D 92.790 319 21 2 1 317 165740718 165741036 6.010000e-126 460.0
7 TraesCS3B01G206200 chr3D 83.607 61 6 3 330 388 373478340 373478282 1.000000e-03 54.7
8 TraesCS3B01G206200 chr6B 91.710 193 15 1 2197 2388 42598130 42597938 1.410000e-67 267.0
9 TraesCS3B01G206200 chr4A 91.753 194 13 3 2197 2388 676452976 676452784 1.410000e-67 267.0
10 TraesCS3B01G206200 chr5B 89.744 195 17 3 2197 2388 87243546 87243740 1.830000e-61 246.0
11 TraesCS3B01G206200 chrUn 88.265 196 19 3 2197 2388 3920801 3920996 5.130000e-57 231.0
12 TraesCS3B01G206200 chr7B 85.128 195 26 2 2197 2388 41433769 41433963 1.870000e-46 196.0
13 TraesCS3B01G206200 chr1B 80.682 264 39 10 730 986 537464110 537464368 6.740000e-46 195.0
14 TraesCS3B01G206200 chr1B 82.558 86 13 2 733 817 16604959 16605043 9.150000e-10 75.0
15 TraesCS3B01G206200 chr2A 80.000 125 20 5 874 994 591751525 591751402 1.180000e-13 87.9
16 TraesCS3B01G206200 chr7D 86.567 67 8 1 753 818 611216137 611216071 3.290000e-09 73.1
17 TraesCS3B01G206200 chr5A 77.692 130 21 6 733 859 680925042 680924918 3.290000e-09 73.1


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 TraesCS3B01G206200 chr3B 241399568 241401955 2387 False 4410 4410 100.000 1 2388 1 chr3B.!!$F1 2387
1 TraesCS3B01G206200 chr3A 203660966 203663127 2161 False 3301 3301 94.196 9 2182 1 chr3A.!!$F1 2173
2 TraesCS3B01G206200 chr3D 165758331 165760220 1889 False 2819 2819 93.803 312 2182 1 chr3D.!!$F2 1870

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
413 415 0.038892 ACGCAAGGCTCTGCATTTTG 60.039 50.0 17.54 7.03 42.77 2.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2210 2259 0.253327 CAGAGGCTGGAGTAAACCCC 59.747 60.0 0.0 0.0 0.0 4.95 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
37 38 1.867363 AGTCCTTATTGTCCGGCTCT 58.133 50.000 0.00 0.00 0.00 4.09
38 39 1.757699 AGTCCTTATTGTCCGGCTCTC 59.242 52.381 0.00 0.00 0.00 3.20
44 45 0.389948 ATTGTCCGGCTCTCGTCAAC 60.390 55.000 0.00 0.00 35.20 3.18
54 55 0.387929 TCTCGTCAACGGCAAGTCTT 59.612 50.000 2.31 0.00 40.29 3.01
108 109 6.791867 ACTCAGCTTACATAGTCATTACCA 57.208 37.500 0.00 0.00 0.00 3.25
115 116 4.423625 ACATAGTCATTACCAAGAGCCC 57.576 45.455 0.00 0.00 0.00 5.19
121 122 1.468520 CATTACCAAGAGCCCGTGTTG 59.531 52.381 0.00 0.00 0.00 3.33
150 151 1.005294 GCGAAACGGTAAGCACTCGA 61.005 55.000 0.00 0.00 0.00 4.04
186 187 4.349365 TCCAGTAGTGTATGGACATGTCA 58.651 43.478 26.47 13.45 40.70 3.58
187 188 4.962362 TCCAGTAGTGTATGGACATGTCAT 59.038 41.667 26.47 18.82 40.70 3.06
227 228 1.295423 GCCCGACTCACTTTAGCCA 59.705 57.895 0.00 0.00 0.00 4.75
249 250 4.762289 ACCTCCTTGACAATATCCAGTC 57.238 45.455 0.00 0.00 35.37 3.51
388 390 7.992754 ACAAACTCTTCTTTCTATCAATGCT 57.007 32.000 0.00 0.00 0.00 3.79
391 393 8.509690 CAAACTCTTCTTTCTATCAATGCTTCA 58.490 33.333 0.00 0.00 0.00 3.02
413 415 0.038892 ACGCAAGGCTCTGCATTTTG 60.039 50.000 17.54 7.03 42.77 2.44
416 418 1.670967 GCAAGGCTCTGCATTTTGTCC 60.671 52.381 14.15 0.00 42.17 4.02
451 454 2.865119 TGGACGTCTAGTACTGGTCA 57.135 50.000 16.46 0.00 33.83 4.02
790 800 2.010544 GCTTAGTGCCGTTTACCTCCC 61.011 57.143 0.00 0.00 35.15 4.30
822 832 3.031736 TCATGGAGCTTAGGTGTCCTAC 58.968 50.000 0.00 0.00 35.63 3.18
869 879 5.254115 GGCCTACCTATGTGTTCTTTTCTT 58.746 41.667 0.00 0.00 0.00 2.52
877 887 7.713942 ACCTATGTGTTCTTTTCTTAGAAACGT 59.286 33.333 6.93 0.01 36.01 3.99
965 981 0.791422 CGTTCGGCCGTGTATTTTGA 59.209 50.000 27.15 0.00 0.00 2.69
991 1007 6.321821 TGTGCTTTATCTATAAAGTGGGGT 57.678 37.500 18.85 0.00 46.78 4.95
999 1015 5.609533 TCTATAAAGTGGGGTAAGAGCAC 57.390 43.478 0.00 0.00 0.00 4.40
1119 1135 1.138661 GACCTCCTGAGAGCCAATGAG 59.861 57.143 0.00 0.00 38.96 2.90
1191 1207 7.919091 TGAACTACGTACTTACCAATGATGATC 59.081 37.037 0.00 0.00 0.00 2.92
1216 1232 3.827876 TCTGTTCGTAGTGTAATGGTCCA 59.172 43.478 0.00 0.00 0.00 4.02
1245 1261 1.485838 CTCCAGCGCGCACATAGAAG 61.486 60.000 35.10 15.67 0.00 2.85
1246 1262 1.519234 CCAGCGCGCACATAGAAGA 60.519 57.895 35.10 0.00 0.00 2.87
1354 1371 3.203716 GACGGAGGTTCTGAAGTGTTTT 58.796 45.455 0.00 0.00 0.00 2.43
1355 1372 4.141892 TGACGGAGGTTCTGAAGTGTTTTA 60.142 41.667 0.00 0.00 0.00 1.52
1356 1373 4.969484 ACGGAGGTTCTGAAGTGTTTTAT 58.031 39.130 0.00 0.00 0.00 1.40
1357 1374 5.374071 ACGGAGGTTCTGAAGTGTTTTATT 58.626 37.500 0.00 0.00 0.00 1.40
1358 1375 5.826208 ACGGAGGTTCTGAAGTGTTTTATTT 59.174 36.000 0.00 0.00 0.00 1.40
1362 1379 9.459640 GGAGGTTCTGAAGTGTTTTATTTTAAC 57.540 33.333 0.00 0.00 0.00 2.01
1399 1416 4.006780 TGCTTGCTGATCTCAAGTGTTA 57.993 40.909 21.11 9.47 42.06 2.41
1401 1418 4.453478 TGCTTGCTGATCTCAAGTGTTAAG 59.547 41.667 21.11 6.47 42.06 1.85
1402 1419 4.453819 GCTTGCTGATCTCAAGTGTTAAGT 59.546 41.667 21.11 0.00 42.06 2.24
1403 1420 5.390356 GCTTGCTGATCTCAAGTGTTAAGTC 60.390 44.000 21.11 6.44 42.06 3.01
1404 1421 5.213891 TGCTGATCTCAAGTGTTAAGTCA 57.786 39.130 0.00 0.00 0.00 3.41
1405 1422 5.610398 TGCTGATCTCAAGTGTTAAGTCAA 58.390 37.500 0.00 0.00 0.00 3.18
1412 1430 7.915293 TCTCAAGTGTTAAGTCAAAAACTCA 57.085 32.000 0.00 0.00 37.17 3.41
1422 1440 9.620660 GTTAAGTCAAAAACTCAAAACAGAGAA 57.379 29.630 0.00 0.00 37.17 2.87
1545 1581 9.781425 ATGATAGAATGATACCAGTATCTTCCT 57.219 33.333 16.59 8.11 41.80 3.36
1546 1582 9.607333 TGATAGAATGATACCAGTATCTTCCTT 57.393 33.333 16.59 7.09 41.80 3.36
1551 1587 8.511604 AATGATACCAGTATCTTCCTTTTGTG 57.488 34.615 16.59 0.00 41.80 3.33
1847 1891 2.358267 AGCGTCTTAACATCCTCTACGG 59.642 50.000 0.00 0.00 0.00 4.02
1923 1972 2.700897 GGTGGTGGTATCAGTGAGCTAT 59.299 50.000 0.00 0.00 0.00 2.97
1929 1978 2.103094 GGTATCAGTGAGCTATGCACCA 59.897 50.000 0.00 0.00 36.95 4.17
2064 2113 6.070021 AGTGGATTTTGAGATCATACTGGTGA 60.070 38.462 0.00 0.00 0.00 4.02
2182 2231 2.993899 CGAATTACTGGAGCAACGACTT 59.006 45.455 0.00 0.00 0.00 3.01
2183 2232 3.181530 CGAATTACTGGAGCAACGACTTG 60.182 47.826 0.00 0.00 0.00 3.16
2184 2233 2.902705 TTACTGGAGCAACGACTTGT 57.097 45.000 0.00 0.00 0.00 3.16
2185 2234 2.902705 TACTGGAGCAACGACTTGTT 57.097 45.000 0.00 0.00 43.09 2.83
2186 2235 2.038387 ACTGGAGCAACGACTTGTTT 57.962 45.000 0.00 0.00 39.29 2.83
2187 2236 2.365582 ACTGGAGCAACGACTTGTTTT 58.634 42.857 0.00 0.00 39.29 2.43
2188 2237 2.752903 ACTGGAGCAACGACTTGTTTTT 59.247 40.909 0.00 0.00 39.29 1.94
2189 2238 3.181500 ACTGGAGCAACGACTTGTTTTTC 60.181 43.478 0.00 0.00 39.29 2.29
2190 2239 3.013921 TGGAGCAACGACTTGTTTTTCT 58.986 40.909 0.00 0.00 39.29 2.52
2191 2240 3.181501 TGGAGCAACGACTTGTTTTTCTG 60.182 43.478 0.00 0.00 39.29 3.02
2192 2241 3.064820 GGAGCAACGACTTGTTTTTCTGA 59.935 43.478 0.00 0.00 39.29 3.27
2193 2242 4.438200 GGAGCAACGACTTGTTTTTCTGAA 60.438 41.667 0.00 0.00 39.29 3.02
2194 2243 4.662145 AGCAACGACTTGTTTTTCTGAAG 58.338 39.130 0.00 0.00 39.29 3.02
2195 2244 3.791353 GCAACGACTTGTTTTTCTGAAGG 59.209 43.478 0.00 0.00 39.29 3.46
2196 2245 4.674362 GCAACGACTTGTTTTTCTGAAGGT 60.674 41.667 0.00 0.00 39.29 3.50
2197 2246 5.399013 CAACGACTTGTTTTTCTGAAGGTT 58.601 37.500 0.00 0.00 39.29 3.50
2198 2247 5.638596 ACGACTTGTTTTTCTGAAGGTTT 57.361 34.783 0.00 0.00 0.00 3.27
2199 2248 6.020971 ACGACTTGTTTTTCTGAAGGTTTT 57.979 33.333 0.00 0.00 0.00 2.43
2200 2249 6.452242 ACGACTTGTTTTTCTGAAGGTTTTT 58.548 32.000 0.00 0.00 0.00 1.94
2220 2269 5.518848 TTTTTCGAAAAGGGGGTTTACTC 57.481 39.130 21.53 0.00 0.00 2.59
2221 2270 2.865119 TCGAAAAGGGGGTTTACTCC 57.135 50.000 0.00 0.00 0.00 3.85
2222 2271 2.056359 TCGAAAAGGGGGTTTACTCCA 58.944 47.619 0.46 0.00 0.00 3.86
2223 2272 2.039348 TCGAAAAGGGGGTTTACTCCAG 59.961 50.000 0.46 0.00 0.00 3.86
2224 2273 2.168496 GAAAAGGGGGTTTACTCCAGC 58.832 52.381 0.46 0.00 0.00 4.85
2225 2274 0.408309 AAAGGGGGTTTACTCCAGCC 59.592 55.000 0.46 0.00 0.00 4.85
2226 2275 0.477795 AAGGGGGTTTACTCCAGCCT 60.478 55.000 0.46 0.00 31.96 4.58
2227 2276 0.914902 AGGGGGTTTACTCCAGCCTC 60.915 60.000 0.46 0.00 31.77 4.70
2228 2277 0.914902 GGGGGTTTACTCCAGCCTCT 60.915 60.000 0.46 0.00 31.96 3.69
2229 2278 0.253327 GGGGTTTACTCCAGCCTCTG 59.747 60.000 0.00 0.00 31.96 3.35
2230 2279 0.393132 GGGTTTACTCCAGCCTCTGC 60.393 60.000 0.00 0.00 37.95 4.26
2231 2280 0.324943 GGTTTACTCCAGCCTCTGCA 59.675 55.000 0.00 0.00 41.13 4.41
2232 2281 1.065126 GGTTTACTCCAGCCTCTGCAT 60.065 52.381 0.00 0.00 41.13 3.96
2233 2282 2.284190 GTTTACTCCAGCCTCTGCATC 58.716 52.381 0.00 0.00 41.13 3.91
2234 2283 1.571955 TTACTCCAGCCTCTGCATCA 58.428 50.000 0.00 0.00 41.13 3.07
2235 2284 1.798626 TACTCCAGCCTCTGCATCAT 58.201 50.000 0.00 0.00 41.13 2.45
2236 2285 0.917533 ACTCCAGCCTCTGCATCATT 59.082 50.000 0.00 0.00 41.13 2.57
2237 2286 1.134159 ACTCCAGCCTCTGCATCATTC 60.134 52.381 0.00 0.00 41.13 2.67
2238 2287 1.141254 CTCCAGCCTCTGCATCATTCT 59.859 52.381 0.00 0.00 41.13 2.40
2239 2288 1.134189 TCCAGCCTCTGCATCATTCTG 60.134 52.381 0.00 0.00 41.13 3.02
2240 2289 1.134189 CCAGCCTCTGCATCATTCTGA 60.134 52.381 0.00 0.00 41.13 3.27
2241 2290 2.487445 CCAGCCTCTGCATCATTCTGAT 60.487 50.000 0.00 0.00 41.13 2.90
2250 2299 3.466712 CATCATTCTGATGCATACGGC 57.533 47.619 0.00 0.00 46.37 5.68
2251 2300 1.882912 TCATTCTGATGCATACGGCC 58.117 50.000 0.00 0.00 43.89 6.13
2252 2301 1.140652 TCATTCTGATGCATACGGCCA 59.859 47.619 2.24 0.00 43.89 5.36
2253 2302 1.948834 CATTCTGATGCATACGGCCAA 59.051 47.619 2.24 0.00 43.89 4.52
2254 2303 2.346766 TTCTGATGCATACGGCCAAT 57.653 45.000 2.24 0.00 43.89 3.16
2255 2304 3.483808 TTCTGATGCATACGGCCAATA 57.516 42.857 2.24 0.00 43.89 1.90
2256 2305 3.701205 TCTGATGCATACGGCCAATAT 57.299 42.857 2.24 0.00 43.89 1.28
2257 2306 4.019792 TCTGATGCATACGGCCAATATT 57.980 40.909 2.24 0.00 43.89 1.28
2258 2307 5.159273 TCTGATGCATACGGCCAATATTA 57.841 39.130 2.24 0.00 43.89 0.98
2259 2308 5.744171 TCTGATGCATACGGCCAATATTAT 58.256 37.500 2.24 0.00 43.89 1.28
2260 2309 6.179756 TCTGATGCATACGGCCAATATTATT 58.820 36.000 2.24 0.00 43.89 1.40
2261 2310 7.334858 TCTGATGCATACGGCCAATATTATTA 58.665 34.615 2.24 0.00 43.89 0.98
2262 2311 7.826744 TCTGATGCATACGGCCAATATTATTAA 59.173 33.333 2.24 0.00 43.89 1.40
2263 2312 8.518430 TGATGCATACGGCCAATATTATTAAT 57.482 30.769 2.24 0.00 43.89 1.40
2264 2313 9.620259 TGATGCATACGGCCAATATTATTAATA 57.380 29.630 2.24 0.00 43.89 0.98
2288 2337 5.397142 AAAAAGATCCAGCAACAATCTCC 57.603 39.130 0.00 0.00 0.00 3.71
2289 2338 3.726557 AAGATCCAGCAACAATCTCCA 57.273 42.857 0.00 0.00 0.00 3.86
2290 2339 3.726557 AGATCCAGCAACAATCTCCAA 57.273 42.857 0.00 0.00 0.00 3.53
2291 2340 3.618351 AGATCCAGCAACAATCTCCAAG 58.382 45.455 0.00 0.00 0.00 3.61
2292 2341 2.957402 TCCAGCAACAATCTCCAAGT 57.043 45.000 0.00 0.00 0.00 3.16
2293 2342 2.783135 TCCAGCAACAATCTCCAAGTC 58.217 47.619 0.00 0.00 0.00 3.01
2294 2343 2.373169 TCCAGCAACAATCTCCAAGTCT 59.627 45.455 0.00 0.00 0.00 3.24
2295 2344 2.746362 CCAGCAACAATCTCCAAGTCTC 59.254 50.000 0.00 0.00 0.00 3.36
2296 2345 2.414481 CAGCAACAATCTCCAAGTCTCG 59.586 50.000 0.00 0.00 0.00 4.04
2297 2346 1.129437 GCAACAATCTCCAAGTCTCGC 59.871 52.381 0.00 0.00 0.00 5.03
2298 2347 2.416747 CAACAATCTCCAAGTCTCGCA 58.583 47.619 0.00 0.00 0.00 5.10
2299 2348 2.376808 ACAATCTCCAAGTCTCGCAG 57.623 50.000 0.00 0.00 0.00 5.18
2300 2349 1.895798 ACAATCTCCAAGTCTCGCAGA 59.104 47.619 0.00 0.00 0.00 4.26
2301 2350 2.300152 ACAATCTCCAAGTCTCGCAGAA 59.700 45.455 0.00 0.00 34.09 3.02
2302 2351 2.928757 CAATCTCCAAGTCTCGCAGAAG 59.071 50.000 0.00 0.00 34.09 2.85
2303 2352 0.891373 TCTCCAAGTCTCGCAGAAGG 59.109 55.000 0.00 0.00 34.09 3.46
2304 2353 0.891373 CTCCAAGTCTCGCAGAAGGA 59.109 55.000 0.00 0.00 34.09 3.36
2305 2354 1.273606 CTCCAAGTCTCGCAGAAGGAA 59.726 52.381 0.00 0.00 34.09 3.36
2306 2355 1.273606 TCCAAGTCTCGCAGAAGGAAG 59.726 52.381 0.00 0.00 34.09 3.46
2307 2356 1.001406 CCAAGTCTCGCAGAAGGAAGT 59.999 52.381 0.00 0.00 34.09 3.01
2308 2357 2.231478 CCAAGTCTCGCAGAAGGAAGTA 59.769 50.000 0.00 0.00 34.09 2.24
2309 2358 3.306088 CCAAGTCTCGCAGAAGGAAGTAA 60.306 47.826 0.00 0.00 34.09 2.24
2310 2359 4.307432 CAAGTCTCGCAGAAGGAAGTAAA 58.693 43.478 0.00 0.00 34.09 2.01
2311 2360 3.915536 AGTCTCGCAGAAGGAAGTAAAC 58.084 45.455 0.00 0.00 34.09 2.01
2312 2361 3.321111 AGTCTCGCAGAAGGAAGTAAACA 59.679 43.478 0.00 0.00 34.09 2.83
2313 2362 4.056050 GTCTCGCAGAAGGAAGTAAACAA 58.944 43.478 0.00 0.00 34.09 2.83
2314 2363 4.510340 GTCTCGCAGAAGGAAGTAAACAAA 59.490 41.667 0.00 0.00 34.09 2.83
2315 2364 5.179555 GTCTCGCAGAAGGAAGTAAACAAAT 59.820 40.000 0.00 0.00 34.09 2.32
2316 2365 5.179368 TCTCGCAGAAGGAAGTAAACAAATG 59.821 40.000 0.00 0.00 34.09 2.32
2317 2366 3.914364 CGCAGAAGGAAGTAAACAAATGC 59.086 43.478 0.00 0.00 0.00 3.56
2318 2367 4.320494 CGCAGAAGGAAGTAAACAAATGCT 60.320 41.667 0.00 0.00 0.00 3.79
2319 2368 5.157067 GCAGAAGGAAGTAAACAAATGCTC 58.843 41.667 0.00 0.00 0.00 4.26
2320 2369 5.278463 GCAGAAGGAAGTAAACAAATGCTCA 60.278 40.000 0.00 0.00 0.00 4.26
2321 2370 6.145535 CAGAAGGAAGTAAACAAATGCTCAC 58.854 40.000 0.00 0.00 0.00 3.51
2322 2371 5.827797 AGAAGGAAGTAAACAAATGCTCACA 59.172 36.000 0.00 0.00 0.00 3.58
2323 2372 6.321181 AGAAGGAAGTAAACAAATGCTCACAA 59.679 34.615 0.00 0.00 0.00 3.33
2324 2373 6.076981 AGGAAGTAAACAAATGCTCACAAG 57.923 37.500 0.00 0.00 0.00 3.16
2325 2374 5.827797 AGGAAGTAAACAAATGCTCACAAGA 59.172 36.000 0.00 0.00 0.00 3.02
2326 2375 6.016777 AGGAAGTAAACAAATGCTCACAAGAG 60.017 38.462 0.00 0.00 44.96 2.85
2358 2407 2.594592 GCCAAGCCACAACCGACT 60.595 61.111 0.00 0.00 0.00 4.18
2359 2408 2.908073 GCCAAGCCACAACCGACTG 61.908 63.158 0.00 0.00 0.00 3.51
2360 2409 2.260869 CCAAGCCACAACCGACTGG 61.261 63.158 0.00 0.00 42.84 4.00
2364 2413 3.834726 CCACAACCGACTGGCAAA 58.165 55.556 0.00 0.00 39.70 3.68
2365 2414 2.111162 CCACAACCGACTGGCAAAA 58.889 52.632 0.00 0.00 39.70 2.44
2366 2415 0.457851 CCACAACCGACTGGCAAAAA 59.542 50.000 0.00 0.00 39.70 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.344968 AGGACTTGGCAAGCAAAATAAACT 59.655 37.500 26.45 3.17 0.00 2.66
1 2 4.631131 AGGACTTGGCAAGCAAAATAAAC 58.369 39.130 26.45 6.82 0.00 2.01
2 3 4.953940 AGGACTTGGCAAGCAAAATAAA 57.046 36.364 26.45 0.00 0.00 1.40
3 4 4.953940 AAGGACTTGGCAAGCAAAATAA 57.046 36.364 26.45 0.00 0.00 1.40
4 5 6.014669 ACAATAAGGACTTGGCAAGCAAAATA 60.015 34.615 26.45 13.62 0.00 1.40
5 6 5.221702 ACAATAAGGACTTGGCAAGCAAAAT 60.222 36.000 26.45 7.10 0.00 1.82
6 7 4.100808 ACAATAAGGACTTGGCAAGCAAAA 59.899 37.500 26.45 9.48 0.00 2.44
7 8 3.640967 ACAATAAGGACTTGGCAAGCAAA 59.359 39.130 26.45 8.77 0.00 3.68
17 18 2.168728 GAGAGCCGGACAATAAGGACTT 59.831 50.000 5.05 0.00 0.00 3.01
37 38 0.934496 CAAAGACTTGCCGTTGACGA 59.066 50.000 4.91 0.00 43.02 4.20
38 39 3.437845 CAAAGACTTGCCGTTGACG 57.562 52.632 0.00 0.00 39.44 4.35
54 55 2.129607 GTAACAGTTCGAACTCGGCAA 58.870 47.619 27.54 9.24 37.08 4.52
115 116 3.047877 GCCGAGTTCCCCAACACG 61.048 66.667 0.00 0.00 43.73 4.49
121 122 3.116531 CGTTTCGCCGAGTTCCCC 61.117 66.667 0.00 0.00 0.00 4.81
150 151 3.910627 ACTACTGGAAAATCCCTCTGTGT 59.089 43.478 0.00 0.00 35.03 3.72
186 187 5.729454 GCGTTGTCGAAATGCCTATGTAAAT 60.729 40.000 11.25 0.00 39.71 1.40
187 188 4.436317 GCGTTGTCGAAATGCCTATGTAAA 60.436 41.667 11.25 0.00 39.71 2.01
227 228 4.383118 CGACTGGATATTGTCAAGGAGGTT 60.383 45.833 0.00 0.00 31.59 3.50
249 250 0.539986 TTGCCCCTAGCCTAACTTCG 59.460 55.000 0.00 0.00 42.71 3.79
333 335 5.707298 TCAAAGATGAAAGACACCCAGAATC 59.293 40.000 0.00 0.00 30.99 2.52
388 390 1.230635 GCAGAGCCTTGCGTCTTGAA 61.231 55.000 0.00 0.00 33.90 2.69
776 786 2.652095 CCTCGGGAGGTAAACGGCA 61.652 63.158 6.56 0.00 43.61 5.69
790 800 1.811266 CTCCATGACAACGCCCTCG 60.811 63.158 0.00 0.00 42.43 4.63
877 887 1.461512 CAACATAAACGCACACGCCTA 59.538 47.619 0.00 0.00 45.53 3.93
884 894 0.453782 GCCGGACAACATAAACGCAC 60.454 55.000 5.05 0.00 0.00 5.34
999 1015 5.008316 TGGATCATCATTTTCTCGAAGCATG 59.992 40.000 0.00 0.00 0.00 4.06
1041 1057 2.224606 CATTCTTGGTGTGCAGACAGT 58.775 47.619 16.68 0.00 30.74 3.55
1086 1102 0.698818 GGAGGTCCCTGTCCAACAAT 59.301 55.000 0.00 0.00 32.55 2.71
1119 1135 3.627732 TTCGATCTTACCGAGCAGATC 57.372 47.619 7.33 7.33 41.43 2.75
1191 1207 5.291128 GGACCATTACACTACGAACAGAATG 59.709 44.000 0.00 0.00 46.00 2.67
1216 1232 2.042831 GCGCTGGAGGCAAGTTGAT 61.043 57.895 7.16 0.00 41.91 2.57
1233 1249 1.756375 CGCTGGTCTTCTATGTGCGC 61.756 60.000 0.00 0.00 35.77 6.09
1245 1261 1.423845 CGTTGCAATACCGCTGGTC 59.576 57.895 0.59 0.00 37.09 4.02
1246 1262 2.686816 GCGTTGCAATACCGCTGGT 61.687 57.895 21.47 5.58 43.81 4.00
1336 1353 9.459640 GTTAAAATAAAACACTTCAGAACCTCC 57.540 33.333 0.00 0.00 0.00 4.30
1357 1374 9.515020 CAAGCAAGAAACAATTCTACTGTTAAA 57.485 29.630 0.00 0.00 45.19 1.52
1358 1375 7.647715 GCAAGCAAGAAACAATTCTACTGTTAA 59.352 33.333 0.00 0.00 45.19 2.01
1362 1379 5.628193 CAGCAAGCAAGAAACAATTCTACTG 59.372 40.000 0.00 0.00 45.19 2.74
1401 1418 9.950680 TCATATTCTCTGTTTTGAGTTTTTGAC 57.049 29.630 0.00 0.00 35.68 3.18
1405 1422 9.342308 TGTCTCATATTCTCTGTTTTGAGTTTT 57.658 29.630 0.00 0.00 35.68 2.43
1428 1446 6.366877 ACAGCTGCAATGTGATTAATTTTGTC 59.633 34.615 15.27 0.00 0.00 3.18
1440 1458 7.430211 CACATAGTATAAAACAGCTGCAATGTG 59.570 37.037 15.27 14.79 35.08 3.21
1534 1561 6.486657 TGAAAGACCACAAAAGGAAGATACTG 59.513 38.462 0.00 0.00 0.00 2.74
1863 1912 8.909671 GCAATGTGTCATCTAAAGAAAAAGAAG 58.090 33.333 0.00 0.00 0.00 2.85
1884 1933 4.083003 ACCACCGTATTAACACAAGCAATG 60.083 41.667 0.00 0.00 0.00 2.82
1886 1935 3.251245 CACCACCGTATTAACACAAGCAA 59.749 43.478 0.00 0.00 0.00 3.91
1923 1972 2.358582 CTCATGTTGTCTGTTTGGTGCA 59.641 45.455 0.00 0.00 0.00 4.57
1929 1978 4.101585 TCTGTCCTCTCATGTTGTCTGTTT 59.898 41.667 0.00 0.00 0.00 2.83
2064 2113 2.329267 TCAGATCTCCGGCCACATAAT 58.671 47.619 2.24 0.00 0.00 1.28
2111 2160 4.345547 AGGAAACTATAGGGCTACAGAAGC 59.654 45.833 4.43 0.00 45.95 3.86
2198 2247 4.341806 GGAGTAAACCCCCTTTTCGAAAAA 59.658 41.667 22.67 8.37 0.00 1.94
2199 2248 3.890756 GGAGTAAACCCCCTTTTCGAAAA 59.109 43.478 21.35 21.35 0.00 2.29
2200 2249 3.117587 TGGAGTAAACCCCCTTTTCGAAA 60.118 43.478 6.47 6.47 0.00 3.46
2201 2250 2.442502 TGGAGTAAACCCCCTTTTCGAA 59.557 45.455 0.00 0.00 0.00 3.71
2202 2251 2.039348 CTGGAGTAAACCCCCTTTTCGA 59.961 50.000 0.00 0.00 0.00 3.71
2203 2252 2.433436 CTGGAGTAAACCCCCTTTTCG 58.567 52.381 0.00 0.00 0.00 3.46
2204 2253 2.168496 GCTGGAGTAAACCCCCTTTTC 58.832 52.381 0.00 0.00 0.00 2.29
2205 2254 1.203137 GGCTGGAGTAAACCCCCTTTT 60.203 52.381 0.00 0.00 0.00 2.27
2206 2255 0.408309 GGCTGGAGTAAACCCCCTTT 59.592 55.000 0.00 0.00 0.00 3.11
2207 2256 0.477795 AGGCTGGAGTAAACCCCCTT 60.478 55.000 0.00 0.00 30.18 3.95
2208 2257 0.914902 GAGGCTGGAGTAAACCCCCT 60.915 60.000 0.00 0.00 34.76 4.79
2209 2258 0.914902 AGAGGCTGGAGTAAACCCCC 60.915 60.000 0.00 0.00 0.00 5.40
2210 2259 0.253327 CAGAGGCTGGAGTAAACCCC 59.747 60.000 0.00 0.00 0.00 4.95
2211 2260 0.393132 GCAGAGGCTGGAGTAAACCC 60.393 60.000 0.00 0.00 36.96 4.11
2212 2261 0.324943 TGCAGAGGCTGGAGTAAACC 59.675 55.000 0.00 0.00 41.91 3.27
2213 2262 2.284190 GATGCAGAGGCTGGAGTAAAC 58.716 52.381 0.00 0.00 41.91 2.01
2214 2263 1.908619 TGATGCAGAGGCTGGAGTAAA 59.091 47.619 0.00 0.00 41.91 2.01
2215 2264 1.571955 TGATGCAGAGGCTGGAGTAA 58.428 50.000 0.00 0.00 41.91 2.24
2216 2265 1.798626 ATGATGCAGAGGCTGGAGTA 58.201 50.000 0.00 0.00 41.91 2.59
2217 2266 0.917533 AATGATGCAGAGGCTGGAGT 59.082 50.000 0.00 0.00 41.91 3.85
2218 2267 1.141254 AGAATGATGCAGAGGCTGGAG 59.859 52.381 0.00 0.00 41.91 3.86
2219 2268 1.134189 CAGAATGATGCAGAGGCTGGA 60.134 52.381 0.00 0.00 39.69 3.86
2220 2269 1.134189 TCAGAATGATGCAGAGGCTGG 60.134 52.381 0.00 0.00 42.56 4.85
2221 2270 2.327200 TCAGAATGATGCAGAGGCTG 57.673 50.000 0.00 0.00 42.56 4.85
2232 2281 1.140652 TGGCCGTATGCATCAGAATGA 59.859 47.619 0.19 0.00 44.08 2.57
2233 2282 1.596603 TGGCCGTATGCATCAGAATG 58.403 50.000 0.19 0.00 43.89 2.67
2234 2283 2.346766 TTGGCCGTATGCATCAGAAT 57.653 45.000 0.19 0.00 43.89 2.40
2235 2284 2.346766 ATTGGCCGTATGCATCAGAA 57.653 45.000 0.19 0.00 43.89 3.02
2236 2285 3.701205 ATATTGGCCGTATGCATCAGA 57.299 42.857 0.19 0.00 43.89 3.27
2237 2286 6.441093 AATAATATTGGCCGTATGCATCAG 57.559 37.500 0.19 0.00 43.89 2.90
2238 2287 7.929941 TTAATAATATTGGCCGTATGCATCA 57.070 32.000 0.19 0.00 43.89 3.07
2266 2315 4.834496 TGGAGATTGTTGCTGGATCTTTTT 59.166 37.500 0.00 0.00 30.64 1.94
2267 2316 4.410099 TGGAGATTGTTGCTGGATCTTTT 58.590 39.130 0.00 0.00 30.64 2.27
2268 2317 4.038271 TGGAGATTGTTGCTGGATCTTT 57.962 40.909 0.00 0.00 30.64 2.52
2269 2318 3.726557 TGGAGATTGTTGCTGGATCTT 57.273 42.857 0.00 0.00 30.64 2.40
2270 2319 3.009916 ACTTGGAGATTGTTGCTGGATCT 59.990 43.478 0.00 0.00 33.05 2.75
2271 2320 3.350833 ACTTGGAGATTGTTGCTGGATC 58.649 45.455 0.00 0.00 0.00 3.36
2272 2321 3.009916 AGACTTGGAGATTGTTGCTGGAT 59.990 43.478 0.00 0.00 0.00 3.41
2273 2322 2.373169 AGACTTGGAGATTGTTGCTGGA 59.627 45.455 0.00 0.00 0.00 3.86
2274 2323 2.746362 GAGACTTGGAGATTGTTGCTGG 59.254 50.000 0.00 0.00 0.00 4.85
2275 2324 2.414481 CGAGACTTGGAGATTGTTGCTG 59.586 50.000 0.00 0.00 0.00 4.41
2276 2325 2.693069 CGAGACTTGGAGATTGTTGCT 58.307 47.619 0.00 0.00 0.00 3.91
2277 2326 1.129437 GCGAGACTTGGAGATTGTTGC 59.871 52.381 0.00 0.00 0.00 4.17
2278 2327 2.414481 CTGCGAGACTTGGAGATTGTTG 59.586 50.000 5.27 0.00 0.00 3.33
2279 2328 2.300152 TCTGCGAGACTTGGAGATTGTT 59.700 45.455 9.75 0.00 0.00 2.83
2280 2329 1.895798 TCTGCGAGACTTGGAGATTGT 59.104 47.619 9.75 0.00 0.00 2.71
2281 2330 2.662006 TCTGCGAGACTTGGAGATTG 57.338 50.000 9.75 0.00 0.00 2.67
2282 2331 2.093764 CCTTCTGCGAGACTTGGAGATT 60.094 50.000 14.15 0.00 33.63 2.40
2283 2332 1.480137 CCTTCTGCGAGACTTGGAGAT 59.520 52.381 14.15 0.00 33.63 2.75
2284 2333 0.891373 CCTTCTGCGAGACTTGGAGA 59.109 55.000 9.75 9.75 31.50 3.71
2285 2334 0.891373 TCCTTCTGCGAGACTTGGAG 59.109 55.000 4.85 4.85 0.00 3.86
2286 2335 1.273606 CTTCCTTCTGCGAGACTTGGA 59.726 52.381 0.00 0.00 0.00 3.53
2287 2336 1.001406 ACTTCCTTCTGCGAGACTTGG 59.999 52.381 0.00 0.00 0.00 3.61
2288 2337 2.447244 ACTTCCTTCTGCGAGACTTG 57.553 50.000 0.00 0.00 0.00 3.16
2289 2338 4.202223 TGTTTACTTCCTTCTGCGAGACTT 60.202 41.667 0.00 0.00 0.00 3.01
2290 2339 3.321111 TGTTTACTTCCTTCTGCGAGACT 59.679 43.478 0.00 0.00 0.00 3.24
2291 2340 3.650139 TGTTTACTTCCTTCTGCGAGAC 58.350 45.455 0.00 0.00 0.00 3.36
2292 2341 4.330944 TTGTTTACTTCCTTCTGCGAGA 57.669 40.909 0.00 0.00 0.00 4.04
2293 2342 5.385617 CATTTGTTTACTTCCTTCTGCGAG 58.614 41.667 0.00 0.00 0.00 5.03
2294 2343 4.320202 GCATTTGTTTACTTCCTTCTGCGA 60.320 41.667 0.00 0.00 0.00 5.10
2295 2344 3.914364 GCATTTGTTTACTTCCTTCTGCG 59.086 43.478 0.00 0.00 0.00 5.18
2296 2345 5.126396 AGCATTTGTTTACTTCCTTCTGC 57.874 39.130 0.00 0.00 0.00 4.26
2297 2346 6.145535 GTGAGCATTTGTTTACTTCCTTCTG 58.854 40.000 0.00 0.00 0.00 3.02
2298 2347 5.827797 TGTGAGCATTTGTTTACTTCCTTCT 59.172 36.000 0.00 0.00 0.00 2.85
2299 2348 6.072112 TGTGAGCATTTGTTTACTTCCTTC 57.928 37.500 0.00 0.00 0.00 3.46
2300 2349 6.321181 TCTTGTGAGCATTTGTTTACTTCCTT 59.679 34.615 0.00 0.00 0.00 3.36
2301 2350 5.827797 TCTTGTGAGCATTTGTTTACTTCCT 59.172 36.000 0.00 0.00 0.00 3.36
2302 2351 6.072112 TCTTGTGAGCATTTGTTTACTTCC 57.928 37.500 0.00 0.00 0.00 3.46
2341 2390 2.594592 AGTCGGTTGTGGCTTGGC 60.595 61.111 0.00 0.00 0.00 4.52
2342 2391 2.260869 CCAGTCGGTTGTGGCTTGG 61.261 63.158 0.00 0.00 0.00 3.61
2343 2392 3.343972 CCAGTCGGTTGTGGCTTG 58.656 61.111 0.00 0.00 0.00 4.01
2347 2396 0.457851 TTTTTGCCAGTCGGTTGTGG 59.542 50.000 0.00 0.00 36.85 4.17


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

AutoCloner maintained by Alex Coulton.