Multiple sequence alignment - TraesCS1A01G349400

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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 TraesCS1A01G349400 chr1A 100.000 2381 0 0 1 2381 534310857 534313237 0.000000e+00 4397.0
1 TraesCS1A01G349400 chr1A 91.095 2201 176 11 1 2187 547860390 547862584 0.000000e+00 2961.0
2 TraesCS1A01G349400 chr1A 99.338 151 1 0 2231 2381 534319835 534319985 8.380000e-70 274.0
3 TraesCS1A01G349400 chr4D 92.577 2196 147 11 1 2188 35486688 35488875 0.000000e+00 3138.0
4 TraesCS1A01G349400 chr4D 92.623 2196 135 16 3 2188 23274066 23271888 0.000000e+00 3133.0
5 TraesCS1A01G349400 chr2D 92.367 2201 148 10 1 2188 549979725 549981918 0.000000e+00 3116.0
6 TraesCS1A01G349400 chr5D 92.220 2198 151 13 1 2188 430529854 430532041 0.000000e+00 3094.0
7 TraesCS1A01G349400 chr5D 88.341 2230 208 22 28 2228 35280728 35278522 0.000000e+00 2630.0
8 TraesCS1A01G349400 chr1D 91.788 2204 158 14 1 2188 453131565 453133761 0.000000e+00 3046.0
9 TraesCS1A01G349400 chr2B 91.413 2201 163 15 1 2188 547943794 547945981 0.000000e+00 2994.0
10 TraesCS1A01G349400 chr2B 90.678 2199 186 12 1 2188 250681505 250679315 0.000000e+00 2907.0
11 TraesCS1A01G349400 chr5B 91.265 2198 172 11 1 2188 292164381 292162194 0.000000e+00 2977.0
12 TraesCS1A01G349400 chr7D 87.231 2279 199 42 1 2228 412230143 412232380 0.000000e+00 2512.0
13 TraesCS1A01G349400 chr2A 86.165 2248 248 36 15 2241 115703887 115701682 0.000000e+00 2370.0
14 TraesCS1A01G349400 chr4B 85.501 1807 213 27 442 2228 652822823 652824600 0.000000e+00 1840.0
15 TraesCS1A01G349400 chr4B 99.338 151 1 0 2231 2381 14855313 14855163 8.380000e-70 274.0
16 TraesCS1A01G349400 chr4B 92.683 41 1 1 2190 2228 519820135 519820175 9.190000e-05 58.4
17 TraesCS1A01G349400 chr5A 87.007 685 71 9 1562 2228 363918536 363919220 0.000000e+00 756.0
18 TraesCS1A01G349400 chr7B 83.863 409 50 5 1835 2228 6063956 6063549 2.230000e-100 375.0
19 TraesCS1A01G349400 chr7B 99.338 151 1 0 2231 2381 133948278 133948428 8.380000e-70 274.0
20 TraesCS1A01G349400 chr7B 99.338 151 1 0 2231 2381 720904303 720904453 8.380000e-70 274.0
21 TraesCS1A01G349400 chr6B 84.518 394 46 5 1850 2228 19543987 19544380 2.230000e-100 375.0
22 TraesCS1A01G349400 chr6B 99.338 151 1 0 2231 2381 64910228 64910078 8.380000e-70 274.0
23 TraesCS1A01G349400 chrUn 99.338 151 1 0 2231 2381 415062959 415063109 8.380000e-70 274.0
24 TraesCS1A01G349400 chrUn 99.338 151 1 0 2231 2381 435675724 435675874 8.380000e-70 274.0
25 TraesCS1A01G349400 chrUn 99.338 151 1 0 2231 2381 452776642 452776792 8.380000e-70 274.0
26 TraesCS1A01G349400 chr4A 99.338 151 1 0 2231 2381 553419693 553419543 8.380000e-70 274.0


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 TraesCS1A01G349400 chr1A 534310857 534313237 2380 False 4397 4397 100.000 1 2381 1 chr1A.!!$F1 2380
1 TraesCS1A01G349400 chr1A 547860390 547862584 2194 False 2961 2961 91.095 1 2187 1 chr1A.!!$F3 2186
2 TraesCS1A01G349400 chr4D 35486688 35488875 2187 False 3138 3138 92.577 1 2188 1 chr4D.!!$F1 2187
3 TraesCS1A01G349400 chr4D 23271888 23274066 2178 True 3133 3133 92.623 3 2188 1 chr4D.!!$R1 2185
4 TraesCS1A01G349400 chr2D 549979725 549981918 2193 False 3116 3116 92.367 1 2188 1 chr2D.!!$F1 2187
5 TraesCS1A01G349400 chr5D 430529854 430532041 2187 False 3094 3094 92.220 1 2188 1 chr5D.!!$F1 2187
6 TraesCS1A01G349400 chr5D 35278522 35280728 2206 True 2630 2630 88.341 28 2228 1 chr5D.!!$R1 2200
7 TraesCS1A01G349400 chr1D 453131565 453133761 2196 False 3046 3046 91.788 1 2188 1 chr1D.!!$F1 2187
8 TraesCS1A01G349400 chr2B 547943794 547945981 2187 False 2994 2994 91.413 1 2188 1 chr2B.!!$F1 2187
9 TraesCS1A01G349400 chr2B 250679315 250681505 2190 True 2907 2907 90.678 1 2188 1 chr2B.!!$R1 2187
10 TraesCS1A01G349400 chr5B 292162194 292164381 2187 True 2977 2977 91.265 1 2188 1 chr5B.!!$R1 2187
11 TraesCS1A01G349400 chr7D 412230143 412232380 2237 False 2512 2512 87.231 1 2228 1 chr7D.!!$F1 2227
12 TraesCS1A01G349400 chr2A 115701682 115703887 2205 True 2370 2370 86.165 15 2241 1 chr2A.!!$R1 2226
13 TraesCS1A01G349400 chr4B 652822823 652824600 1777 False 1840 1840 85.501 442 2228 1 chr4B.!!$F2 1786
14 TraesCS1A01G349400 chr5A 363918536 363919220 684 False 756 756 87.007 1562 2228 1 chr5A.!!$F1 666

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
532 606 0.978151 TTAAACCCTAGCCAGCACGA 59.022 50.0 0.0 0.0 0.0 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2243 2349 0.034896 AAGGCACACTTCAGGTACGG 59.965 55.0 0.0 0.0 32.85 4.02 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
73 74 3.436243 ACCCAATTTTGAGCCGGATTTA 58.564 40.909 5.05 0.00 0.00 1.40
159 183 2.087248 CCACCACCATTTCCCCTCT 58.913 57.895 0.00 0.00 0.00 3.69
423 497 3.473647 CGAGGGATGAGGCTGCCA 61.474 66.667 22.65 0.22 0.00 4.92
532 606 0.978151 TTAAACCCTAGCCAGCACGA 59.022 50.000 0.00 0.00 0.00 4.35
634 708 2.044946 GGCTTGCAACCCGATCCT 60.045 61.111 0.00 0.00 0.00 3.24
1012 1089 1.237285 GGCCTTCATGCGTGTTCAGT 61.237 55.000 5.68 0.00 0.00 3.41
1047 1124 3.787001 GGCTTCCCCCTCGACCAG 61.787 72.222 0.00 0.00 0.00 4.00
1049 1126 2.284699 CTTCCCCCTCGACCAGGT 60.285 66.667 0.00 0.00 41.51 4.00
1131 1208 1.517257 CGAGGACGAGCTCGCAAAT 60.517 57.895 34.83 18.85 44.43 2.32
1178 1256 0.179045 AAGAGCAAGCACACGAAGGT 60.179 50.000 0.00 0.00 0.00 3.50
1200 1278 3.379445 ACGACGGCCGAGGACAAT 61.379 61.111 35.90 7.12 41.76 2.71
1284 1362 4.993029 TTCAACCTTTTGGATTCGTGTT 57.007 36.364 0.00 0.00 44.07 3.32
1294 1372 1.201647 GGATTCGTGTTCACCGAGAGA 59.798 52.381 0.00 0.00 35.49 3.10
1378 1456 1.682684 AAGCGGTGGAGGACGATCT 60.683 57.895 0.00 0.00 0.00 2.75
1567 1652 8.723311 CATGAAAACATTTTGTAGGCATTTCAT 58.277 29.630 9.68 9.68 40.51 2.57
1614 1699 0.681175 AATGGCAAGTGCTTCAACCC 59.319 50.000 2.85 0.00 41.70 4.11
1680 1765 1.133025 GCAATATGCCGCACTCAAGTT 59.867 47.619 0.00 0.00 37.42 2.66
1752 1837 1.738099 CGCGAGGGAAGACCAAGTG 60.738 63.158 0.00 0.00 43.89 3.16
1791 1879 3.670377 GGCCACCAACGCCTTGAC 61.670 66.667 0.00 0.00 43.48 3.18
1915 2006 2.811317 CTTGAGCTGGACGCCGAC 60.811 66.667 0.00 0.00 40.39 4.79
1934 2025 1.615392 ACAAGCAAGCCAAGATGTTCC 59.385 47.619 0.00 0.00 0.00 3.62
1986 2077 4.814294 GATCGAGGCCGCCAACGT 62.814 66.667 21.99 13.21 37.70 3.99
1998 2089 1.523758 GCCAACGTCAAGACCAAGAT 58.476 50.000 0.00 0.00 0.00 2.40
2102 2193 1.402852 CGTGGTTCGAGAAGATGCAGA 60.403 52.381 0.00 0.00 42.86 4.26
2188 2283 1.898094 GTGTGCTGGCATGACCACA 60.898 57.895 6.55 6.55 46.36 4.17
2218 2324 0.478507 ACTCAAGTCCCACCCCTTTG 59.521 55.000 0.00 0.00 0.00 2.77
2223 2329 2.197324 TCCCACCCCTTTGTGTGC 59.803 61.111 0.00 0.00 34.35 4.57
2224 2330 2.917227 CCCACCCCTTTGTGTGCC 60.917 66.667 0.00 0.00 34.35 5.01
2225 2331 3.294493 CCACCCCTTTGTGTGCCG 61.294 66.667 0.00 0.00 34.35 5.69
2241 2347 4.838152 CGGCCGGCTATGCTGTGT 62.838 66.667 28.56 0.00 32.22 3.72
2242 2348 2.504032 GGCCGGCTATGCTGTGTA 59.496 61.111 28.56 0.00 32.22 2.90
2243 2349 1.887707 GGCCGGCTATGCTGTGTAC 60.888 63.158 28.56 0.00 32.22 2.90
2244 2350 1.887707 GCCGGCTATGCTGTGTACC 60.888 63.158 22.15 0.00 32.22 3.34
2245 2351 1.591594 CCGGCTATGCTGTGTACCG 60.592 63.158 0.00 0.00 40.30 4.02
2246 2352 1.141019 CGGCTATGCTGTGTACCGT 59.859 57.895 0.00 0.00 35.99 4.83
2247 2353 0.382873 CGGCTATGCTGTGTACCGTA 59.617 55.000 0.00 0.00 35.99 4.02
2248 2354 1.849097 GGCTATGCTGTGTACCGTAC 58.151 55.000 1.40 1.40 0.00 3.67
2249 2355 1.537562 GGCTATGCTGTGTACCGTACC 60.538 57.143 6.23 0.00 0.00 3.34
2250 2356 1.407979 GCTATGCTGTGTACCGTACCT 59.592 52.381 6.23 0.00 0.00 3.08
2251 2357 2.798499 GCTATGCTGTGTACCGTACCTG 60.798 54.545 6.23 3.68 0.00 4.00
2252 2358 1.552578 ATGCTGTGTACCGTACCTGA 58.447 50.000 6.23 0.00 0.00 3.86
2253 2359 1.330234 TGCTGTGTACCGTACCTGAA 58.670 50.000 6.23 0.00 0.00 3.02
2254 2360 1.271379 TGCTGTGTACCGTACCTGAAG 59.729 52.381 6.23 0.58 0.00 3.02
2255 2361 1.271656 GCTGTGTACCGTACCTGAAGT 59.728 52.381 6.23 0.00 0.00 3.01
2256 2362 2.925306 GCTGTGTACCGTACCTGAAGTG 60.925 54.545 6.23 0.00 0.00 3.16
2257 2363 2.295349 CTGTGTACCGTACCTGAAGTGT 59.705 50.000 6.23 0.00 0.00 3.55
2258 2364 2.034939 TGTGTACCGTACCTGAAGTGTG 59.965 50.000 6.23 0.00 0.00 3.82
2259 2365 1.000060 TGTACCGTACCTGAAGTGTGC 60.000 52.381 6.23 0.00 0.00 4.57
2260 2366 0.604578 TACCGTACCTGAAGTGTGCC 59.395 55.000 0.00 0.00 0.00 5.01
2261 2367 1.119574 ACCGTACCTGAAGTGTGCCT 61.120 55.000 0.00 0.00 0.00 4.75
2262 2368 0.034896 CCGTACCTGAAGTGTGCCTT 59.965 55.000 0.00 0.00 35.59 4.35
2263 2369 1.148310 CGTACCTGAAGTGTGCCTTG 58.852 55.000 0.00 0.00 32.03 3.61
2264 2370 0.875059 GTACCTGAAGTGTGCCTTGC 59.125 55.000 0.00 0.00 32.03 4.01
2265 2371 0.250727 TACCTGAAGTGTGCCTTGCC 60.251 55.000 0.00 0.00 32.03 4.52
2266 2372 1.529010 CCTGAAGTGTGCCTTGCCA 60.529 57.895 0.00 0.00 32.03 4.92
2267 2373 0.896940 CCTGAAGTGTGCCTTGCCAT 60.897 55.000 0.00 0.00 32.03 4.40
2268 2374 0.242825 CTGAAGTGTGCCTTGCCATG 59.757 55.000 0.00 0.00 32.03 3.66
2269 2375 0.178995 TGAAGTGTGCCTTGCCATGA 60.179 50.000 0.00 0.00 32.03 3.07
2270 2376 0.524862 GAAGTGTGCCTTGCCATGAG 59.475 55.000 0.00 0.00 32.03 2.90
2271 2377 0.178981 AAGTGTGCCTTGCCATGAGT 60.179 50.000 0.00 0.00 30.18 3.41
2272 2378 0.607489 AGTGTGCCTTGCCATGAGTC 60.607 55.000 0.00 0.00 0.00 3.36
2273 2379 0.890542 GTGTGCCTTGCCATGAGTCA 60.891 55.000 0.00 0.00 0.00 3.41
2274 2380 0.607217 TGTGCCTTGCCATGAGTCAG 60.607 55.000 0.00 0.00 0.00 3.51
2275 2381 0.607489 GTGCCTTGCCATGAGTCAGT 60.607 55.000 0.00 0.00 0.00 3.41
2276 2382 0.321919 TGCCTTGCCATGAGTCAGTC 60.322 55.000 0.00 0.00 0.00 3.51
2277 2383 0.321919 GCCTTGCCATGAGTCAGTCA 60.322 55.000 0.00 0.00 40.38 3.41
2278 2384 1.883638 GCCTTGCCATGAGTCAGTCAA 60.884 52.381 0.00 2.00 39.19 3.18
2279 2385 2.082231 CCTTGCCATGAGTCAGTCAAG 58.918 52.381 17.84 17.84 39.19 3.02
2280 2386 2.082231 CTTGCCATGAGTCAGTCAAGG 58.918 52.381 17.35 0.00 45.48 3.61
2281 2387 0.325933 TGCCATGAGTCAGTCAAGGG 59.674 55.000 5.90 2.83 43.28 3.95
2282 2388 0.393537 GCCATGAGTCAGTCAAGGGG 60.394 60.000 5.90 0.41 43.28 4.79
2283 2389 0.987294 CCATGAGTCAGTCAAGGGGT 59.013 55.000 0.00 0.00 39.94 4.95
2284 2390 2.187958 CCATGAGTCAGTCAAGGGGTA 58.812 52.381 0.00 0.00 39.94 3.69
2285 2391 2.093447 CCATGAGTCAGTCAAGGGGTAC 60.093 54.545 0.00 0.00 39.94 3.34
2286 2392 2.391926 TGAGTCAGTCAAGGGGTACA 57.608 50.000 0.00 0.00 29.64 2.90
2287 2393 2.684943 TGAGTCAGTCAAGGGGTACAA 58.315 47.619 0.00 0.00 29.64 2.41
2288 2394 2.632996 TGAGTCAGTCAAGGGGTACAAG 59.367 50.000 0.00 0.00 29.64 3.16
2289 2395 2.897969 GAGTCAGTCAAGGGGTACAAGA 59.102 50.000 0.00 0.00 0.00 3.02
2290 2396 2.900546 AGTCAGTCAAGGGGTACAAGAG 59.099 50.000 0.00 0.00 0.00 2.85
2291 2397 2.633481 GTCAGTCAAGGGGTACAAGAGT 59.367 50.000 0.00 0.00 0.00 3.24
2292 2398 2.632996 TCAGTCAAGGGGTACAAGAGTG 59.367 50.000 0.00 0.00 0.00 3.51
2293 2399 2.632996 CAGTCAAGGGGTACAAGAGTGA 59.367 50.000 0.00 0.00 32.74 3.41
2294 2400 3.261897 CAGTCAAGGGGTACAAGAGTGAT 59.738 47.826 0.00 0.00 32.74 3.06
2295 2401 3.515901 AGTCAAGGGGTACAAGAGTGATC 59.484 47.826 0.00 0.00 0.00 2.92
2296 2402 2.838202 TCAAGGGGTACAAGAGTGATCC 59.162 50.000 0.00 0.00 0.00 3.36
2297 2403 2.571653 CAAGGGGTACAAGAGTGATCCA 59.428 50.000 0.00 0.00 0.00 3.41
2298 2404 2.915869 AGGGGTACAAGAGTGATCCAA 58.084 47.619 0.00 0.00 0.00 3.53
2299 2405 2.840651 AGGGGTACAAGAGTGATCCAAG 59.159 50.000 0.00 0.00 0.00 3.61
2300 2406 2.838202 GGGGTACAAGAGTGATCCAAGA 59.162 50.000 0.00 0.00 0.00 3.02
2301 2407 3.263425 GGGGTACAAGAGTGATCCAAGAA 59.737 47.826 0.00 0.00 0.00 2.52
2302 2408 4.080299 GGGGTACAAGAGTGATCCAAGAAT 60.080 45.833 0.00 0.00 0.00 2.40
2303 2409 4.878397 GGGTACAAGAGTGATCCAAGAATG 59.122 45.833 0.00 0.00 0.00 2.67
2308 2414 2.842496 AGAGTGATCCAAGAATGGCTCA 59.158 45.455 0.00 0.00 46.80 4.26
2311 2417 2.995283 TGATCCAAGAATGGCTCACAG 58.005 47.619 0.00 0.00 44.74 3.66
2312 2418 2.356432 TGATCCAAGAATGGCTCACAGG 60.356 50.000 0.00 0.00 44.74 4.00
2313 2419 3.963733 CCAAGAATGGCTCACAGGA 57.036 52.632 0.00 0.00 40.58 3.86
2314 2420 1.457346 CCAAGAATGGCTCACAGGAC 58.543 55.000 0.00 0.00 40.58 3.85
2315 2421 1.271543 CCAAGAATGGCTCACAGGACA 60.272 52.381 0.00 0.00 40.58 4.02
2316 2422 2.082231 CAAGAATGGCTCACAGGACAG 58.918 52.381 0.00 0.00 0.00 3.51
2317 2423 1.356124 AGAATGGCTCACAGGACAGT 58.644 50.000 0.00 0.00 0.00 3.55
2318 2424 1.002888 AGAATGGCTCACAGGACAGTG 59.997 52.381 0.00 0.00 40.85 3.66
2319 2425 0.037303 AATGGCTCACAGGACAGTGG 59.963 55.000 0.00 0.00 39.93 4.00
2320 2426 1.130054 ATGGCTCACAGGACAGTGGT 61.130 55.000 0.00 0.00 39.93 4.16
2321 2427 1.004440 GGCTCACAGGACAGTGGTC 60.004 63.158 0.00 0.00 43.55 4.02
2322 2428 1.748403 GCTCACAGGACAGTGGTCA 59.252 57.895 0.00 0.00 46.17 4.02
2323 2429 0.106708 GCTCACAGGACAGTGGTCAA 59.893 55.000 0.00 0.00 46.17 3.18
2324 2430 1.475034 GCTCACAGGACAGTGGTCAAA 60.475 52.381 0.00 0.00 46.17 2.69
2325 2431 2.487934 CTCACAGGACAGTGGTCAAAG 58.512 52.381 0.00 0.00 46.17 2.77
2326 2432 1.837439 TCACAGGACAGTGGTCAAAGT 59.163 47.619 0.00 0.00 46.17 2.66
2327 2433 2.238646 TCACAGGACAGTGGTCAAAGTT 59.761 45.455 0.00 0.00 46.17 2.66
2328 2434 3.452990 TCACAGGACAGTGGTCAAAGTTA 59.547 43.478 0.00 0.00 46.17 2.24
2329 2435 4.102524 TCACAGGACAGTGGTCAAAGTTAT 59.897 41.667 0.00 0.00 46.17 1.89
2330 2436 4.452455 CACAGGACAGTGGTCAAAGTTATC 59.548 45.833 0.00 0.00 46.17 1.75
2331 2437 4.003648 CAGGACAGTGGTCAAAGTTATCC 58.996 47.826 0.00 0.00 46.17 2.59
2332 2438 3.910627 AGGACAGTGGTCAAAGTTATCCT 59.089 43.478 0.00 0.00 46.17 3.24
2333 2439 4.351111 AGGACAGTGGTCAAAGTTATCCTT 59.649 41.667 0.00 0.00 46.17 3.36
2334 2440 5.546499 AGGACAGTGGTCAAAGTTATCCTTA 59.454 40.000 0.00 0.00 46.17 2.69
2335 2441 5.875359 GGACAGTGGTCAAAGTTATCCTTAG 59.125 44.000 0.00 0.00 46.17 2.18
2336 2442 6.435292 ACAGTGGTCAAAGTTATCCTTAGT 57.565 37.500 0.00 0.00 31.48 2.24
2337 2443 7.310237 GGACAGTGGTCAAAGTTATCCTTAGTA 60.310 40.741 0.00 0.00 46.17 1.82
2338 2444 7.970102 ACAGTGGTCAAAGTTATCCTTAGTAA 58.030 34.615 0.00 0.00 31.48 2.24
2339 2445 7.876582 ACAGTGGTCAAAGTTATCCTTAGTAAC 59.123 37.037 0.00 0.00 31.48 2.50
2340 2446 8.095169 CAGTGGTCAAAGTTATCCTTAGTAACT 58.905 37.037 0.00 0.00 42.53 2.24
2341 2447 9.317827 AGTGGTCAAAGTTATCCTTAGTAACTA 57.682 33.333 0.00 0.00 40.49 2.24
2342 2448 9.583765 GTGGTCAAAGTTATCCTTAGTAACTAG 57.416 37.037 0.00 0.00 40.49 2.57
2343 2449 9.317827 TGGTCAAAGTTATCCTTAGTAACTAGT 57.682 33.333 0.00 0.00 40.49 2.57
2344 2450 9.583765 GGTCAAAGTTATCCTTAGTAACTAGTG 57.416 37.037 0.00 2.50 40.49 2.74
2345 2451 9.583765 GTCAAAGTTATCCTTAGTAACTAGTGG 57.416 37.037 0.00 0.00 40.49 4.00
2346 2452 9.537852 TCAAAGTTATCCTTAGTAACTAGTGGA 57.462 33.333 0.00 0.00 40.49 4.02
2347 2453 9.583765 CAAAGTTATCCTTAGTAACTAGTGGAC 57.416 37.037 0.00 0.00 40.49 4.02
2348 2454 9.544579 AAAGTTATCCTTAGTAACTAGTGGACT 57.455 33.333 13.62 13.62 40.49 3.85
2360 2466 9.102453 AGTAACTAGTGGACTAAGGAATTTTCT 57.898 33.333 8.58 0.00 0.00 2.52
2361 2467 9.368674 GTAACTAGTGGACTAAGGAATTTTCTC 57.631 37.037 0.00 0.00 0.00 2.87
2362 2468 6.631962 ACTAGTGGACTAAGGAATTTTCTCG 58.368 40.000 0.00 0.00 0.00 4.04
2363 2469 5.740290 AGTGGACTAAGGAATTTTCTCGA 57.260 39.130 0.00 0.00 0.00 4.04
2364 2470 6.301169 AGTGGACTAAGGAATTTTCTCGAT 57.699 37.500 0.00 0.00 0.00 3.59
2365 2471 6.712276 AGTGGACTAAGGAATTTTCTCGATT 58.288 36.000 0.00 0.00 0.00 3.34
2366 2472 7.848128 AGTGGACTAAGGAATTTTCTCGATTA 58.152 34.615 0.00 0.00 0.00 1.75
2367 2473 8.487028 AGTGGACTAAGGAATTTTCTCGATTAT 58.513 33.333 0.00 0.00 0.00 1.28
2368 2474 8.552034 GTGGACTAAGGAATTTTCTCGATTATG 58.448 37.037 0.00 0.00 0.00 1.90
2369 2475 7.715249 TGGACTAAGGAATTTTCTCGATTATGG 59.285 37.037 0.00 0.00 0.00 2.74
2370 2476 7.931948 GGACTAAGGAATTTTCTCGATTATGGA 59.068 37.037 0.00 0.00 0.00 3.41
2371 2477 8.894768 ACTAAGGAATTTTCTCGATTATGGAG 57.105 34.615 0.00 0.00 0.00 3.86
2372 2478 7.934120 ACTAAGGAATTTTCTCGATTATGGAGG 59.066 37.037 4.48 0.00 32.34 4.30
2373 2479 6.253946 AGGAATTTTCTCGATTATGGAGGT 57.746 37.500 4.48 0.00 32.34 3.85
2374 2480 6.058183 AGGAATTTTCTCGATTATGGAGGTG 58.942 40.000 4.48 0.00 32.34 4.00
2375 2481 5.239525 GGAATTTTCTCGATTATGGAGGTGG 59.760 44.000 4.48 0.00 32.34 4.61
2376 2482 4.837093 TTTTCTCGATTATGGAGGTGGT 57.163 40.909 4.48 0.00 32.34 4.16
2377 2483 5.943349 TTTTCTCGATTATGGAGGTGGTA 57.057 39.130 4.48 0.00 32.34 3.25
2378 2484 5.943349 TTTCTCGATTATGGAGGTGGTAA 57.057 39.130 4.48 0.00 32.34 2.85
2379 2485 5.943349 TTCTCGATTATGGAGGTGGTAAA 57.057 39.130 4.48 0.00 32.34 2.01
2380 2486 5.943349 TCTCGATTATGGAGGTGGTAAAA 57.057 39.130 4.48 0.00 32.34 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
159 183 1.137282 GCGGGAGTGTTTTGGGAAAAA 59.863 47.619 0.00 0.00 31.13 1.94
300 359 4.078516 GGCGGTCTTGCGTAGGGT 62.079 66.667 0.00 0.00 35.06 4.34
350 409 3.551496 CTCCCTTGCCCGCTGTTCA 62.551 63.158 0.00 0.00 0.00 3.18
532 606 4.003788 CGGTGGCTTGGACGAGGT 62.004 66.667 0.00 0.00 0.00 3.85
576 650 1.962807 CAGCACCATCCAAGGAAACAA 59.037 47.619 0.00 0.00 0.00 2.83
675 750 4.796231 ACGTCGGGCGAGCACATC 62.796 66.667 9.82 0.00 44.77 3.06
822 899 2.342279 CTCGAACAGGTTGCGGGA 59.658 61.111 0.00 0.00 0.00 5.14
1047 1124 0.668401 CGTAGTTGTCCGGGAACACC 60.668 60.000 16.62 1.87 0.00 4.16
1049 1126 1.667151 CCGTAGTTGTCCGGGAACA 59.333 57.895 16.62 6.01 40.54 3.18
1069 1146 2.093106 GCACTCGTCCTCTTCCTCTAA 58.907 52.381 0.00 0.00 0.00 2.10
1128 1205 0.988832 TAGGACCGGTGGCTTGATTT 59.011 50.000 14.63 0.00 0.00 2.17
1131 1208 1.980052 CTTAGGACCGGTGGCTTGA 59.020 57.895 14.63 0.00 0.00 3.02
1178 1256 3.740397 CCTCGGCCGTCGTGTACA 61.740 66.667 27.15 1.04 40.32 2.90
1200 1278 0.944386 GCCAACACTCGCAAAGAAGA 59.056 50.000 0.00 0.00 0.00 2.87
1284 1362 1.066152 CGCTCATGAATCTCTCGGTGA 59.934 52.381 0.00 0.00 0.00 4.02
1294 1372 3.989817 GGAAACTTTTTGCGCTCATGAAT 59.010 39.130 9.73 0.00 0.00 2.57
1372 1450 3.990092 TGTTGCACTCTTGTTAGATCGT 58.010 40.909 0.00 0.00 0.00 3.73
1373 1451 4.449068 ACTTGTTGCACTCTTGTTAGATCG 59.551 41.667 0.00 0.00 0.00 3.69
1567 1652 1.259609 CCTTGAATGCCTCCAAAGCA 58.740 50.000 0.00 0.00 45.94 3.91
1732 1817 2.920912 TTGGTCTTCCCTCGCGGT 60.921 61.111 6.13 0.00 0.00 5.68
1750 1835 1.294659 CTCGCTTGTCCTCCTTGCAC 61.295 60.000 0.00 0.00 0.00 4.57
1752 1837 0.107945 ATCTCGCTTGTCCTCCTTGC 60.108 55.000 0.00 0.00 0.00 4.01
1803 1891 4.101585 AGTCCTTCTTATTCATCATGCCGA 59.898 41.667 0.00 0.00 0.00 5.54
1915 2006 1.614903 TGGAACATCTTGGCTTGCTTG 59.385 47.619 0.00 0.00 0.00 4.01
1934 2025 1.067250 GCTTCTCCGCCTCTAGCTG 59.933 63.158 0.00 0.00 40.39 4.24
1986 2077 5.065914 CCACTTCTTTCATCTTGGTCTTGA 58.934 41.667 0.00 0.00 0.00 3.02
2102 2193 0.317160 TCGAACTTGAGCATGTCGGT 59.683 50.000 0.00 0.00 0.00 4.69
2158 2253 0.673333 CAGCACACCTGCCGACATAA 60.673 55.000 0.00 0.00 45.53 1.90
2188 2283 0.318784 GACTTGAGTTCGACCACGCT 60.319 55.000 0.00 0.00 39.58 5.07
2224 2330 3.439513 TACACAGCATAGCCGGCCG 62.440 63.158 26.15 21.04 0.00 6.13
2225 2331 1.887707 GTACACAGCATAGCCGGCC 60.888 63.158 26.15 7.74 0.00 6.13
2228 2334 0.382873 TACGGTACACAGCATAGCCG 59.617 55.000 0.00 0.00 44.10 5.52
2232 2338 2.725637 TCAGGTACGGTACACAGCATA 58.274 47.619 19.14 0.00 0.00 3.14
2233 2339 1.552578 TCAGGTACGGTACACAGCAT 58.447 50.000 19.14 0.00 0.00 3.79
2234 2340 1.271379 CTTCAGGTACGGTACACAGCA 59.729 52.381 19.14 0.00 0.00 4.41
2235 2341 1.271656 ACTTCAGGTACGGTACACAGC 59.728 52.381 19.14 2.75 0.00 4.40
2236 2342 2.295349 ACACTTCAGGTACGGTACACAG 59.705 50.000 19.14 10.95 0.00 3.66
2239 2345 1.000060 GCACACTTCAGGTACGGTACA 60.000 52.381 19.14 0.00 0.00 2.90
2240 2346 1.670967 GGCACACTTCAGGTACGGTAC 60.671 57.143 9.82 9.82 0.00 3.34
2241 2347 0.604578 GGCACACTTCAGGTACGGTA 59.395 55.000 0.00 0.00 0.00 4.02
2242 2348 1.119574 AGGCACACTTCAGGTACGGT 61.120 55.000 0.00 0.00 0.00 4.83
2243 2349 0.034896 AAGGCACACTTCAGGTACGG 59.965 55.000 0.00 0.00 32.85 4.02
2244 2350 1.148310 CAAGGCACACTTCAGGTACG 58.852 55.000 0.00 0.00 37.29 3.67
2245 2351 0.875059 GCAAGGCACACTTCAGGTAC 59.125 55.000 0.00 0.00 37.29 3.34
2246 2352 0.250727 GGCAAGGCACACTTCAGGTA 60.251 55.000 0.00 0.00 37.29 3.08
2247 2353 1.529244 GGCAAGGCACACTTCAGGT 60.529 57.895 0.00 0.00 37.29 4.00
2248 2354 0.896940 ATGGCAAGGCACACTTCAGG 60.897 55.000 0.00 0.00 37.29 3.86
2249 2355 0.242825 CATGGCAAGGCACACTTCAG 59.757 55.000 0.00 0.00 37.29 3.02
2250 2356 0.178995 TCATGGCAAGGCACACTTCA 60.179 50.000 0.00 0.00 37.29 3.02
2251 2357 0.524862 CTCATGGCAAGGCACACTTC 59.475 55.000 0.00 0.00 37.29 3.01
2252 2358 0.178981 ACTCATGGCAAGGCACACTT 60.179 50.000 0.00 0.00 41.00 3.16
2253 2359 0.607489 GACTCATGGCAAGGCACACT 60.607 55.000 0.00 0.00 0.00 3.55
2254 2360 0.890542 TGACTCATGGCAAGGCACAC 60.891 55.000 0.00 0.00 0.00 3.82
2255 2361 0.607217 CTGACTCATGGCAAGGCACA 60.607 55.000 0.00 0.00 0.00 4.57
2256 2362 0.607489 ACTGACTCATGGCAAGGCAC 60.607 55.000 0.00 0.00 0.00 5.01
2257 2363 0.321919 GACTGACTCATGGCAAGGCA 60.322 55.000 0.00 0.00 0.00 4.75
2258 2364 0.321919 TGACTGACTCATGGCAAGGC 60.322 55.000 0.00 0.00 0.00 4.35
2259 2365 2.082231 CTTGACTGACTCATGGCAAGG 58.918 52.381 12.75 0.00 31.60 3.61
2260 2366 2.082231 CCTTGACTGACTCATGGCAAG 58.918 52.381 13.29 13.29 37.38 4.01
2261 2367 1.271543 CCCTTGACTGACTCATGGCAA 60.272 52.381 0.00 0.00 41.18 4.52
2262 2368 0.325933 CCCTTGACTGACTCATGGCA 59.674 55.000 0.00 0.00 41.18 4.92
2263 2369 0.393537 CCCCTTGACTGACTCATGGC 60.394 60.000 0.00 0.00 41.18 4.40
2264 2370 0.987294 ACCCCTTGACTGACTCATGG 59.013 55.000 0.00 0.00 41.87 3.66
2265 2371 2.567169 TGTACCCCTTGACTGACTCATG 59.433 50.000 0.00 0.00 0.00 3.07
2266 2372 2.902608 TGTACCCCTTGACTGACTCAT 58.097 47.619 0.00 0.00 0.00 2.90
2267 2373 2.391926 TGTACCCCTTGACTGACTCA 57.608 50.000 0.00 0.00 0.00 3.41
2268 2374 2.897969 TCTTGTACCCCTTGACTGACTC 59.102 50.000 0.00 0.00 0.00 3.36
2269 2375 2.900546 CTCTTGTACCCCTTGACTGACT 59.099 50.000 0.00 0.00 0.00 3.41
2270 2376 2.633481 ACTCTTGTACCCCTTGACTGAC 59.367 50.000 0.00 0.00 0.00 3.51
2271 2377 2.632996 CACTCTTGTACCCCTTGACTGA 59.367 50.000 0.00 0.00 0.00 3.41
2272 2378 2.632996 TCACTCTTGTACCCCTTGACTG 59.367 50.000 0.00 0.00 0.00 3.51
2273 2379 2.972348 TCACTCTTGTACCCCTTGACT 58.028 47.619 0.00 0.00 0.00 3.41
2274 2380 3.369576 GGATCACTCTTGTACCCCTTGAC 60.370 52.174 0.00 0.00 0.00 3.18
2275 2381 2.838202 GGATCACTCTTGTACCCCTTGA 59.162 50.000 0.00 0.00 0.00 3.02
2276 2382 2.571653 TGGATCACTCTTGTACCCCTTG 59.428 50.000 0.00 0.00 0.00 3.61
2277 2383 2.915869 TGGATCACTCTTGTACCCCTT 58.084 47.619 0.00 0.00 0.00 3.95
2278 2384 2.642171 TGGATCACTCTTGTACCCCT 57.358 50.000 0.00 0.00 0.00 4.79
2279 2385 2.838202 TCTTGGATCACTCTTGTACCCC 59.162 50.000 0.00 0.00 0.00 4.95
2280 2386 4.553330 TTCTTGGATCACTCTTGTACCC 57.447 45.455 0.00 0.00 0.00 3.69
2281 2387 4.878397 CCATTCTTGGATCACTCTTGTACC 59.122 45.833 0.00 0.00 46.92 3.34
2282 2388 4.333926 GCCATTCTTGGATCACTCTTGTAC 59.666 45.833 0.00 0.00 46.92 2.90
2283 2389 4.225942 AGCCATTCTTGGATCACTCTTGTA 59.774 41.667 0.00 0.00 46.92 2.41
2284 2390 3.009916 AGCCATTCTTGGATCACTCTTGT 59.990 43.478 0.00 0.00 46.92 3.16
2285 2391 3.618351 AGCCATTCTTGGATCACTCTTG 58.382 45.455 0.00 0.00 46.92 3.02
2293 2399 1.918262 TCCTGTGAGCCATTCTTGGAT 59.082 47.619 0.00 0.00 46.72 3.41
2294 2400 1.003580 GTCCTGTGAGCCATTCTTGGA 59.996 52.381 0.00 0.00 46.92 3.53
2295 2401 1.271543 TGTCCTGTGAGCCATTCTTGG 60.272 52.381 0.00 0.00 46.66 3.61
2296 2402 2.082231 CTGTCCTGTGAGCCATTCTTG 58.918 52.381 0.00 0.00 0.00 3.02
2297 2403 1.701847 ACTGTCCTGTGAGCCATTCTT 59.298 47.619 0.00 0.00 0.00 2.52
2298 2404 1.002888 CACTGTCCTGTGAGCCATTCT 59.997 52.381 0.00 0.00 40.12 2.40
2299 2405 1.446907 CACTGTCCTGTGAGCCATTC 58.553 55.000 0.00 0.00 40.12 2.67
2300 2406 0.037303 CCACTGTCCTGTGAGCCATT 59.963 55.000 5.95 0.00 40.12 3.16
2301 2407 1.130054 ACCACTGTCCTGTGAGCCAT 61.130 55.000 5.95 0.00 40.12 4.40
2302 2408 1.758440 GACCACTGTCCTGTGAGCCA 61.758 60.000 5.95 0.00 40.12 4.75
2303 2409 1.004440 GACCACTGTCCTGTGAGCC 60.004 63.158 5.95 0.00 40.12 4.70
2304 2410 0.106708 TTGACCACTGTCCTGTGAGC 59.893 55.000 5.95 0.00 41.01 4.26
2305 2411 2.158900 ACTTTGACCACTGTCCTGTGAG 60.159 50.000 5.95 0.00 41.01 3.51
2306 2412 1.837439 ACTTTGACCACTGTCCTGTGA 59.163 47.619 5.95 0.00 41.01 3.58
2307 2413 2.332063 ACTTTGACCACTGTCCTGTG 57.668 50.000 0.00 0.00 41.01 3.66
2308 2414 4.505039 GGATAACTTTGACCACTGTCCTGT 60.505 45.833 0.00 0.00 41.01 4.00
2309 2415 4.003648 GGATAACTTTGACCACTGTCCTG 58.996 47.826 0.00 0.00 41.01 3.86
2310 2416 3.910627 AGGATAACTTTGACCACTGTCCT 59.089 43.478 0.00 0.00 41.01 3.85
2311 2417 4.287766 AGGATAACTTTGACCACTGTCC 57.712 45.455 0.00 0.00 41.01 4.02
2312 2418 6.465084 ACTAAGGATAACTTTGACCACTGTC 58.535 40.000 0.00 0.00 40.64 3.51
2313 2419 6.435292 ACTAAGGATAACTTTGACCACTGT 57.565 37.500 0.00 0.00 40.64 3.55
2314 2420 8.095169 AGTTACTAAGGATAACTTTGACCACTG 58.905 37.037 0.00 0.00 39.34 3.66
2315 2421 8.203681 AGTTACTAAGGATAACTTTGACCACT 57.796 34.615 0.00 0.00 39.34 4.00
2316 2422 9.583765 CTAGTTACTAAGGATAACTTTGACCAC 57.416 37.037 2.97 0.00 41.84 4.16
2317 2423 9.317827 ACTAGTTACTAAGGATAACTTTGACCA 57.682 33.333 2.97 0.00 41.84 4.02
2318 2424 9.583765 CACTAGTTACTAAGGATAACTTTGACC 57.416 37.037 0.00 0.00 41.84 4.02
2319 2425 9.583765 CCACTAGTTACTAAGGATAACTTTGAC 57.416 37.037 0.00 0.00 41.84 3.18
2320 2426 9.537852 TCCACTAGTTACTAAGGATAACTTTGA 57.462 33.333 8.57 0.00 41.84 2.69
2321 2427 9.583765 GTCCACTAGTTACTAAGGATAACTTTG 57.416 37.037 13.82 2.29 41.84 2.77
2322 2428 9.544579 AGTCCACTAGTTACTAAGGATAACTTT 57.455 33.333 13.82 0.00 41.84 2.66
2334 2440 9.102453 AGAAAATTCCTTAGTCCACTAGTTACT 57.898 33.333 11.41 11.41 0.00 2.24
2335 2441 9.368674 GAGAAAATTCCTTAGTCCACTAGTTAC 57.631 37.037 0.00 0.00 0.00 2.50
2336 2442 8.248945 CGAGAAAATTCCTTAGTCCACTAGTTA 58.751 37.037 0.00 0.00 0.00 2.24
2337 2443 7.039223 TCGAGAAAATTCCTTAGTCCACTAGTT 60.039 37.037 0.00 0.00 0.00 2.24
2338 2444 6.436532 TCGAGAAAATTCCTTAGTCCACTAGT 59.563 38.462 0.00 0.00 0.00 2.57
2339 2445 6.864342 TCGAGAAAATTCCTTAGTCCACTAG 58.136 40.000 0.00 0.00 0.00 2.57
2340 2446 6.845758 TCGAGAAAATTCCTTAGTCCACTA 57.154 37.500 0.00 0.00 0.00 2.74
2341 2447 5.740290 TCGAGAAAATTCCTTAGTCCACT 57.260 39.130 0.00 0.00 0.00 4.00
2342 2448 6.986904 AATCGAGAAAATTCCTTAGTCCAC 57.013 37.500 0.00 0.00 0.00 4.02
2343 2449 7.715249 CCATAATCGAGAAAATTCCTTAGTCCA 59.285 37.037 0.00 0.00 0.00 4.02
2344 2450 7.931948 TCCATAATCGAGAAAATTCCTTAGTCC 59.068 37.037 0.00 0.00 0.00 3.85
2345 2451 8.888579 TCCATAATCGAGAAAATTCCTTAGTC 57.111 34.615 0.00 0.00 0.00 2.59
2346 2452 7.934120 CCTCCATAATCGAGAAAATTCCTTAGT 59.066 37.037 0.00 0.00 0.00 2.24
2347 2453 7.934120 ACCTCCATAATCGAGAAAATTCCTTAG 59.066 37.037 0.00 0.00 0.00 2.18
2348 2454 7.715249 CACCTCCATAATCGAGAAAATTCCTTA 59.285 37.037 0.00 0.00 0.00 2.69
2349 2455 6.543831 CACCTCCATAATCGAGAAAATTCCTT 59.456 38.462 0.00 0.00 0.00 3.36
2350 2456 6.058183 CACCTCCATAATCGAGAAAATTCCT 58.942 40.000 0.00 0.00 0.00 3.36
2351 2457 5.239525 CCACCTCCATAATCGAGAAAATTCC 59.760 44.000 0.00 0.00 0.00 3.01
2352 2458 5.823045 ACCACCTCCATAATCGAGAAAATTC 59.177 40.000 0.00 0.00 0.00 2.17
2353 2459 5.755849 ACCACCTCCATAATCGAGAAAATT 58.244 37.500 0.00 0.00 0.00 1.82
2354 2460 5.373812 ACCACCTCCATAATCGAGAAAAT 57.626 39.130 0.00 0.00 0.00 1.82
2355 2461 4.837093 ACCACCTCCATAATCGAGAAAA 57.163 40.909 0.00 0.00 0.00 2.29
2356 2462 5.943349 TTACCACCTCCATAATCGAGAAA 57.057 39.130 0.00 0.00 0.00 2.52
2357 2463 5.943349 TTTACCACCTCCATAATCGAGAA 57.057 39.130 0.00 0.00 0.00 2.87
2358 2464 5.943349 TTTTACCACCTCCATAATCGAGA 57.057 39.130 0.00 0.00 0.00 4.04


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

AutoCloner maintained by Alex Coulton.