Multiple sequence alignment - TraesCS1A01G433800

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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 TraesCS1A01G433800 chr1A 100.000 2456 0 0 1 2456 584780605 584778150 0.000000e+00 4536
1 TraesCS1A01G433800 chr1A 91.111 315 20 7 2143 2454 348728304 348727995 1.050000e-113 420
2 TraesCS1A01G433800 chrUn 98.231 2148 22 5 1 2132 93414839 93416986 0.000000e+00 3742
3 TraesCS1A01G433800 chr3B 98.222 2137 32 4 1 2132 201524170 201522035 0.000000e+00 3731
4 TraesCS1A01G433800 chr3A 97.800 2136 40 5 1 2132 672912847 672914979 0.000000e+00 3677
5 TraesCS1A01G433800 chr2D 97.528 2144 37 9 1 2132 272796733 272798872 0.000000e+00 3651
6 TraesCS1A01G433800 chr2D 98.290 1813 20 5 1 1803 635585393 635587204 0.000000e+00 3166
7 TraesCS1A01G433800 chr2D 90.683 322 25 3 2138 2456 6531724 6532043 8.120000e-115 424
8 TraesCS1A01G433800 chr2D 90.506 316 27 2 2143 2456 113478783 113479097 4.890000e-112 414
9 TraesCS1A01G433800 chr6A 97.519 2136 43 6 1 2132 271186937 271184808 0.000000e+00 3642
10 TraesCS1A01G433800 chr4D 97.333 2137 48 7 1 2132 19925957 19923825 0.000000e+00 3622
11 TraesCS1A01G433800 chr4D 92.052 843 62 4 1293 2132 349797059 349797899 0.000000e+00 1181
12 TraesCS1A01G433800 chr7A 94.993 2137 92 9 1 2132 352184643 352186769 0.000000e+00 3339
13 TraesCS1A01G433800 chr2B 97.056 1902 49 4 237 2132 369624971 369623071 0.000000e+00 3195
14 TraesCS1A01G433800 chr1D 91.562 320 19 5 2143 2456 473336485 473336802 3.750000e-118 435
15 TraesCS1A01G433800 chr1D 89.815 324 25 6 2140 2456 403762503 403762825 2.270000e-110 409
16 TraesCS1A01G433800 chr7D 90.823 316 26 2 2143 2456 119561144 119561458 1.050000e-113 420
17 TraesCS1A01G433800 chr7D 90.184 326 22 8 2139 2456 494899308 494898985 1.360000e-112 416
18 TraesCS1A01G433800 chr7D 90.566 318 24 6 2143 2456 579769245 579768930 1.360000e-112 416
19 TraesCS1A01G433800 chr3D 90.312 320 23 7 2143 2456 554031134 554030817 1.760000e-111 412


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 TraesCS1A01G433800 chr1A 584778150 584780605 2455 True 4536 4536 100.000 1 2456 1 chr1A.!!$R2 2455
1 TraesCS1A01G433800 chrUn 93414839 93416986 2147 False 3742 3742 98.231 1 2132 1 chrUn.!!$F1 2131
2 TraesCS1A01G433800 chr3B 201522035 201524170 2135 True 3731 3731 98.222 1 2132 1 chr3B.!!$R1 2131
3 TraesCS1A01G433800 chr3A 672912847 672914979 2132 False 3677 3677 97.800 1 2132 1 chr3A.!!$F1 2131
4 TraesCS1A01G433800 chr2D 272796733 272798872 2139 False 3651 3651 97.528 1 2132 1 chr2D.!!$F3 2131
5 TraesCS1A01G433800 chr2D 635585393 635587204 1811 False 3166 3166 98.290 1 1803 1 chr2D.!!$F4 1802
6 TraesCS1A01G433800 chr6A 271184808 271186937 2129 True 3642 3642 97.519 1 2132 1 chr6A.!!$R1 2131
7 TraesCS1A01G433800 chr4D 19923825 19925957 2132 True 3622 3622 97.333 1 2132 1 chr4D.!!$R1 2131
8 TraesCS1A01G433800 chr4D 349797059 349797899 840 False 1181 1181 92.052 1293 2132 1 chr4D.!!$F1 839
9 TraesCS1A01G433800 chr7A 352184643 352186769 2126 False 3339 3339 94.993 1 2132 1 chr7A.!!$F1 2131
10 TraesCS1A01G433800 chr2B 369623071 369624971 1900 True 3195 3195 97.056 237 2132 1 chr2B.!!$R1 1895

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
497 503 0.816018 TTTTGGAAGCTCCGTTGCGA 60.816 50.0 0.0 0.0 40.17 5.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2414 2462 0.025513 CGATTTTGCTTCCGCGAGAG 59.974 55.0 8.23 5.93 39.65 3.2 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
497 503 0.816018 TTTTGGAAGCTCCGTTGCGA 60.816 50.000 0.00 0.00 40.17 5.10
501 507 1.148759 GGAAGCTCCGTTGCGAGATC 61.149 60.000 0.00 0.00 38.13 2.75
1221 1234 2.032894 AGCAATAACACGATATGCACGC 60.033 45.455 0.00 0.00 0.00 5.34
1254 1267 9.287373 GGAAAAATATGGGTACGTATATTTCCA 57.713 33.333 18.47 9.55 37.59 3.53
1288 1301 2.370849 ACACTAAGACCCACGGAAACAT 59.629 45.455 0.00 0.00 0.00 2.71
1682 1717 6.944557 CGATATGCTCGTATTGGTGATTTA 57.055 37.500 0.00 0.00 42.56 1.40
2132 2180 9.599322 CTATAAGAAATGCGGACATGAATAAAC 57.401 33.333 0.00 0.00 36.36 2.01
2133 2181 6.515272 AAGAAATGCGGACATGAATAAACT 57.485 33.333 0.00 0.00 36.36 2.66
2134 2182 7.624360 AAGAAATGCGGACATGAATAAACTA 57.376 32.000 0.00 0.00 36.36 2.24
2135 2183 7.251704 AGAAATGCGGACATGAATAAACTAG 57.748 36.000 0.00 0.00 36.36 2.57
2136 2184 7.047891 AGAAATGCGGACATGAATAAACTAGA 58.952 34.615 0.00 0.00 36.36 2.43
2137 2185 7.716998 AGAAATGCGGACATGAATAAACTAGAT 59.283 33.333 0.00 0.00 36.36 1.98
2138 2186 8.902540 AAATGCGGACATGAATAAACTAGATA 57.097 30.769 0.00 0.00 36.36 1.98
2139 2187 7.891183 ATGCGGACATGAATAAACTAGATAC 57.109 36.000 0.00 0.00 34.35 2.24
2140 2188 6.220930 TGCGGACATGAATAAACTAGATACC 58.779 40.000 0.00 0.00 0.00 2.73
2141 2189 6.183360 TGCGGACATGAATAAACTAGATACCA 60.183 38.462 0.00 0.00 0.00 3.25
2142 2190 6.874134 GCGGACATGAATAAACTAGATACCAT 59.126 38.462 0.00 0.00 0.00 3.55
2143 2191 7.148573 GCGGACATGAATAAACTAGATACCATG 60.149 40.741 0.00 9.11 36.97 3.66
2144 2192 7.331934 CGGACATGAATAAACTAGATACCATGG 59.668 40.741 11.19 11.19 35.70 3.66
2145 2193 8.375506 GGACATGAATAAACTAGATACCATGGA 58.624 37.037 21.47 2.01 35.70 3.41
2146 2194 9.950496 GACATGAATAAACTAGATACCATGGAT 57.050 33.333 21.47 7.62 35.70 3.41
2152 2200 9.712305 AATAAACTAGATACCATGGATTTCTCG 57.288 33.333 21.47 14.47 0.00 4.04
2153 2201 5.140747 ACTAGATACCATGGATTTCTCGC 57.859 43.478 21.47 0.00 0.00 5.03
2154 2202 3.032017 AGATACCATGGATTTCTCGCG 57.968 47.619 21.47 0.00 0.00 5.87
2155 2203 2.365617 AGATACCATGGATTTCTCGCGT 59.634 45.455 21.47 0.00 0.00 6.01
2156 2204 2.684001 TACCATGGATTTCTCGCGTT 57.316 45.000 21.47 0.00 0.00 4.84
2157 2205 1.086696 ACCATGGATTTCTCGCGTTG 58.913 50.000 21.47 0.00 0.00 4.10
2158 2206 1.338674 ACCATGGATTTCTCGCGTTGA 60.339 47.619 21.47 2.87 0.00 3.18
2159 2207 1.328680 CCATGGATTTCTCGCGTTGAG 59.671 52.381 5.56 0.00 46.72 3.02
2170 2218 3.788434 TCGCGTTGAGATCTTCAAAAC 57.212 42.857 5.77 0.00 46.85 2.43
2171 2219 3.390135 TCGCGTTGAGATCTTCAAAACT 58.610 40.909 5.77 0.00 46.85 2.66
2172 2220 4.552355 TCGCGTTGAGATCTTCAAAACTA 58.448 39.130 5.77 0.00 46.85 2.24
2173 2221 4.621460 TCGCGTTGAGATCTTCAAAACTAG 59.379 41.667 5.77 0.00 46.85 2.57
2174 2222 4.621460 CGCGTTGAGATCTTCAAAACTAGA 59.379 41.667 0.00 0.00 46.85 2.43
2175 2223 5.289675 CGCGTTGAGATCTTCAAAACTAGAT 59.710 40.000 0.00 0.00 46.85 1.98
2176 2224 6.472486 CGCGTTGAGATCTTCAAAACTAGATA 59.528 38.462 0.00 0.00 46.85 1.98
2177 2225 7.513814 CGCGTTGAGATCTTCAAAACTAGATAC 60.514 40.741 0.00 0.00 46.85 2.24
2178 2226 7.254151 GCGTTGAGATCTTCAAAACTAGATACC 60.254 40.741 0.00 0.00 46.85 2.73
2179 2227 7.759886 CGTTGAGATCTTCAAAACTAGATACCA 59.240 37.037 0.00 0.00 46.85 3.25
2180 2228 9.606631 GTTGAGATCTTCAAAACTAGATACCAT 57.393 33.333 0.00 0.00 46.85 3.55
2181 2229 9.605275 TTGAGATCTTCAAAACTAGATACCATG 57.395 33.333 0.00 0.00 42.69 3.66
2182 2230 8.762645 TGAGATCTTCAAAACTAGATACCATGT 58.237 33.333 0.00 0.00 31.34 3.21
2183 2231 9.255304 GAGATCTTCAAAACTAGATACCATGTC 57.745 37.037 0.00 0.00 0.00 3.06
2184 2232 7.923344 AGATCTTCAAAACTAGATACCATGTCG 59.077 37.037 0.00 0.00 0.00 4.35
2185 2233 7.165460 TCTTCAAAACTAGATACCATGTCGA 57.835 36.000 0.00 0.00 0.00 4.20
2186 2234 7.782049 TCTTCAAAACTAGATACCATGTCGAT 58.218 34.615 0.00 0.00 0.00 3.59
2187 2235 8.909923 TCTTCAAAACTAGATACCATGTCGATA 58.090 33.333 0.00 0.00 0.00 2.92
2188 2236 9.186323 CTTCAAAACTAGATACCATGTCGATAG 57.814 37.037 0.00 0.00 0.00 2.08
2189 2237 7.658261 TCAAAACTAGATACCATGTCGATAGG 58.342 38.462 0.00 0.00 0.00 2.57
2190 2238 7.287005 TCAAAACTAGATACCATGTCGATAGGT 59.713 37.037 10.58 10.58 39.41 3.08
2191 2239 7.598759 AAACTAGATACCATGTCGATAGGTT 57.401 36.000 10.95 0.00 36.87 3.50
2192 2240 7.598759 AACTAGATACCATGTCGATAGGTTT 57.401 36.000 10.95 4.54 36.87 3.27
2193 2241 7.598759 ACTAGATACCATGTCGATAGGTTTT 57.401 36.000 10.95 1.53 36.87 2.43
2194 2242 7.434492 ACTAGATACCATGTCGATAGGTTTTG 58.566 38.462 10.95 0.00 36.87 2.44
2195 2243 5.611374 AGATACCATGTCGATAGGTTTTGG 58.389 41.667 10.95 4.69 36.87 3.28
2196 2244 2.365582 ACCATGTCGATAGGTTTTGGC 58.634 47.619 0.00 0.00 29.58 4.52
2197 2245 2.290641 ACCATGTCGATAGGTTTTGGCA 60.291 45.455 0.00 0.00 29.58 4.92
2198 2246 2.752354 CCATGTCGATAGGTTTTGGCAA 59.248 45.455 0.00 0.00 0.00 4.52
2199 2247 3.192422 CCATGTCGATAGGTTTTGGCAAA 59.808 43.478 8.93 8.93 0.00 3.68
2200 2248 3.907894 TGTCGATAGGTTTTGGCAAAC 57.092 42.857 13.10 7.98 41.57 2.93
2201 2249 3.482436 TGTCGATAGGTTTTGGCAAACT 58.518 40.909 13.10 10.11 41.92 2.66
2202 2250 3.886505 TGTCGATAGGTTTTGGCAAACTT 59.113 39.130 13.10 7.21 41.92 2.66
2203 2251 4.339814 TGTCGATAGGTTTTGGCAAACTTT 59.660 37.500 13.10 2.76 41.92 2.66
2204 2252 5.163499 TGTCGATAGGTTTTGGCAAACTTTT 60.163 36.000 13.10 1.65 41.92 2.27
2205 2253 5.751509 GTCGATAGGTTTTGGCAAACTTTTT 59.248 36.000 13.10 0.00 41.92 1.94
2223 2271 1.910688 TTTTCACGAAAAACACCGGC 58.089 45.000 0.00 0.00 37.35 6.13
2224 2272 0.100861 TTTCACGAAAAACACCGGCC 59.899 50.000 0.00 0.00 0.00 6.13
2225 2273 2.049475 TTCACGAAAAACACCGGCCG 62.049 55.000 21.04 21.04 0.00 6.13
2226 2274 2.203042 ACGAAAAACACCGGCCGA 60.203 55.556 30.73 0.00 0.00 5.54
2227 2275 1.818785 ACGAAAAACACCGGCCGAA 60.819 52.632 30.73 0.00 0.00 4.30
2228 2276 1.355916 CGAAAAACACCGGCCGAAA 59.644 52.632 30.73 0.00 0.00 3.46
2229 2277 0.248539 CGAAAAACACCGGCCGAAAA 60.249 50.000 30.73 0.00 0.00 2.29
2230 2278 1.798079 CGAAAAACACCGGCCGAAAAA 60.798 47.619 30.73 0.00 0.00 1.94
2296 2344 1.795768 GTGCCTCTCACGAAATCACA 58.204 50.000 0.00 0.00 35.76 3.58
2297 2345 2.143122 GTGCCTCTCACGAAATCACAA 58.857 47.619 0.00 0.00 35.76 3.33
2298 2346 2.096218 GTGCCTCTCACGAAATCACAAC 60.096 50.000 0.00 0.00 35.76 3.32
2299 2347 1.464997 GCCTCTCACGAAATCACAACC 59.535 52.381 0.00 0.00 0.00 3.77
2300 2348 1.726791 CCTCTCACGAAATCACAACCG 59.273 52.381 0.00 0.00 0.00 4.44
2301 2349 2.404215 CTCTCACGAAATCACAACCGT 58.596 47.619 0.00 0.00 35.46 4.83
2304 2352 2.294479 CACGAAATCACAACCGTGTC 57.706 50.000 0.00 0.00 44.88 3.67
2305 2353 1.864711 CACGAAATCACAACCGTGTCT 59.135 47.619 0.00 0.00 44.88 3.41
2306 2354 2.096909 CACGAAATCACAACCGTGTCTC 60.097 50.000 0.00 0.00 44.88 3.36
2307 2355 2.223971 ACGAAATCACAACCGTGTCTCT 60.224 45.455 0.00 0.00 44.02 3.10
2308 2356 2.408704 CGAAATCACAACCGTGTCTCTC 59.591 50.000 0.00 0.00 44.02 3.20
2309 2357 2.065993 AATCACAACCGTGTCTCTCG 57.934 50.000 0.00 0.00 44.02 4.04
2310 2358 0.388649 ATCACAACCGTGTCTCTCGC 60.389 55.000 0.00 0.00 44.02 5.03
2311 2359 1.299850 CACAACCGTGTCTCTCGCA 60.300 57.895 0.00 0.00 38.41 5.10
2312 2360 1.007271 ACAACCGTGTCTCTCGCAG 60.007 57.895 0.00 0.00 29.49 5.18
2313 2361 1.285950 CAACCGTGTCTCTCGCAGA 59.714 57.895 0.00 0.00 0.00 4.26
2314 2362 0.318699 CAACCGTGTCTCTCGCAGAA 60.319 55.000 0.00 0.00 34.09 3.02
2315 2363 0.039074 AACCGTGTCTCTCGCAGAAG 60.039 55.000 0.00 0.00 34.09 2.85
2316 2364 1.803519 CCGTGTCTCTCGCAGAAGC 60.804 63.158 0.00 0.00 34.09 3.86
2317 2365 1.081175 CGTGTCTCTCGCAGAAGCA 60.081 57.895 0.00 0.00 42.27 3.91
2318 2366 0.664466 CGTGTCTCTCGCAGAAGCAA 60.664 55.000 0.00 0.00 42.27 3.91
2319 2367 1.502231 GTGTCTCTCGCAGAAGCAAA 58.498 50.000 0.00 0.00 42.27 3.68
2320 2368 1.867233 GTGTCTCTCGCAGAAGCAAAA 59.133 47.619 0.00 0.00 42.27 2.44
2321 2369 1.867233 TGTCTCTCGCAGAAGCAAAAC 59.133 47.619 0.00 0.00 42.27 2.43
2322 2370 1.195674 GTCTCTCGCAGAAGCAAAACC 59.804 52.381 0.00 0.00 42.27 3.27
2323 2371 0.164647 CTCTCGCAGAAGCAAAACCG 59.835 55.000 0.00 0.00 42.27 4.44
2324 2372 0.531974 TCTCGCAGAAGCAAAACCGT 60.532 50.000 0.00 0.00 42.27 4.83
2325 2373 0.384725 CTCGCAGAAGCAAAACCGTG 60.385 55.000 0.00 0.00 42.27 4.94
2326 2374 0.812014 TCGCAGAAGCAAAACCGTGA 60.812 50.000 0.00 0.00 42.27 4.35
2327 2375 0.657368 CGCAGAAGCAAAACCGTGAC 60.657 55.000 0.00 0.00 42.27 3.67
2328 2376 0.663153 GCAGAAGCAAAACCGTGACT 59.337 50.000 0.00 0.00 41.58 3.41
2329 2377 1.334149 GCAGAAGCAAAACCGTGACTC 60.334 52.381 0.00 0.00 41.58 3.36
2330 2378 2.213499 CAGAAGCAAAACCGTGACTCT 58.787 47.619 0.00 0.00 0.00 3.24
2331 2379 2.221981 CAGAAGCAAAACCGTGACTCTC 59.778 50.000 0.00 0.00 0.00 3.20
2332 2380 1.192534 GAAGCAAAACCGTGACTCTCG 59.807 52.381 0.00 0.00 0.00 4.04
2333 2381 0.104304 AGCAAAACCGTGACTCTCGT 59.896 50.000 0.24 0.00 0.00 4.18
2334 2382 0.232303 GCAAAACCGTGACTCTCGTG 59.768 55.000 0.24 0.00 0.00 4.35
2335 2383 0.859232 CAAAACCGTGACTCTCGTGG 59.141 55.000 0.24 0.00 0.00 4.94
2336 2384 0.748450 AAAACCGTGACTCTCGTGGA 59.252 50.000 0.24 0.00 0.00 4.02
2337 2385 0.748450 AAACCGTGACTCTCGTGGAA 59.252 50.000 0.24 0.00 0.00 3.53
2338 2386 0.314302 AACCGTGACTCTCGTGGAAG 59.686 55.000 0.24 0.00 0.00 3.46
2339 2387 1.213013 CCGTGACTCTCGTGGAAGG 59.787 63.158 0.24 0.00 0.00 3.46
2340 2388 1.241990 CCGTGACTCTCGTGGAAGGA 61.242 60.000 0.24 0.00 0.00 3.36
2341 2389 0.596577 CGTGACTCTCGTGGAAGGAA 59.403 55.000 0.00 0.00 0.00 3.36
2342 2390 1.000607 CGTGACTCTCGTGGAAGGAAA 60.001 52.381 0.00 0.00 0.00 3.13
2343 2391 2.545113 CGTGACTCTCGTGGAAGGAAAA 60.545 50.000 0.00 0.00 0.00 2.29
2344 2392 3.463944 GTGACTCTCGTGGAAGGAAAAA 58.536 45.455 0.00 0.00 0.00 1.94
2385 2433 1.869690 GTTTTCGAGGAGGCACAGC 59.130 57.895 0.00 0.00 0.00 4.40
2396 2444 3.791539 GCACAGCCATGACTCTCG 58.208 61.111 0.00 0.00 0.00 4.04
2397 2445 2.459442 GCACAGCCATGACTCTCGC 61.459 63.158 0.00 0.00 0.00 5.03
2398 2446 2.163390 CACAGCCATGACTCTCGCG 61.163 63.158 0.00 0.00 0.00 5.87
2399 2447 2.343426 ACAGCCATGACTCTCGCGA 61.343 57.895 9.26 9.26 0.00 5.87
2400 2448 1.153765 CAGCCATGACTCTCGCGAA 60.154 57.895 11.33 0.00 0.00 4.70
2401 2449 0.737367 CAGCCATGACTCTCGCGAAA 60.737 55.000 11.33 0.00 0.00 3.46
2402 2450 0.459237 AGCCATGACTCTCGCGAAAG 60.459 55.000 11.33 9.68 0.00 2.62
2439 2487 2.510615 CGGAAGCAAAATCGTGACTC 57.489 50.000 0.00 0.00 0.00 3.36
2440 2488 2.069273 CGGAAGCAAAATCGTGACTCT 58.931 47.619 0.00 0.00 0.00 3.24
2441 2489 2.092838 CGGAAGCAAAATCGTGACTCTC 59.907 50.000 0.00 0.00 0.00 3.20
2442 2490 2.092838 GGAAGCAAAATCGTGACTCTCG 59.907 50.000 0.00 0.00 0.00 4.04
2443 2491 2.440539 AGCAAAATCGTGACTCTCGT 57.559 45.000 0.76 0.00 0.00 4.18
2444 2492 2.061773 AGCAAAATCGTGACTCTCGTG 58.938 47.619 0.76 0.00 0.00 4.35
2445 2493 2.058798 GCAAAATCGTGACTCTCGTGA 58.941 47.619 0.76 0.00 0.00 4.35
2446 2494 2.475111 GCAAAATCGTGACTCTCGTGAA 59.525 45.455 0.76 0.00 0.00 3.18
2447 2495 3.059868 GCAAAATCGTGACTCTCGTGAAA 60.060 43.478 0.76 0.00 0.00 2.69
2448 2496 4.692135 CAAAATCGTGACTCTCGTGAAAG 58.308 43.478 0.76 0.00 0.00 2.62
2449 2497 2.638556 ATCGTGACTCTCGTGAAAGG 57.361 50.000 0.76 0.00 0.00 3.11
2450 2498 1.601166 TCGTGACTCTCGTGAAAGGA 58.399 50.000 0.76 0.00 0.00 3.36
2451 2499 1.951602 TCGTGACTCTCGTGAAAGGAA 59.048 47.619 0.76 0.00 0.00 3.36
2452 2500 2.359848 TCGTGACTCTCGTGAAAGGAAA 59.640 45.455 0.76 0.00 0.00 3.13
2453 2501 3.120792 CGTGACTCTCGTGAAAGGAAAA 58.879 45.455 0.00 0.00 0.00 2.29
2454 2502 3.554324 CGTGACTCTCGTGAAAGGAAAAA 59.446 43.478 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
220 226 5.952947 TCCCTTTAGTTTTTCTTCACAACCA 59.047 36.000 0.00 0.00 0.00 3.67
497 503 4.164988 CCTTGAATGGTTAGGTCTGGATCT 59.835 45.833 0.00 0.00 0.00 2.75
501 507 3.519510 TCTCCTTGAATGGTTAGGTCTGG 59.480 47.826 0.00 0.00 0.00 3.86
961 974 1.552348 GCTCCTCGCGAATGGAATCG 61.552 60.000 16.83 7.89 45.41 3.34
1221 1234 2.452505 ACCCATATTTTTCCACCACGG 58.547 47.619 0.00 0.00 0.00 4.94
1254 1267 4.502087 GGTCTTAGTGTAACCGGTTTGTCT 60.502 45.833 27.64 21.10 37.80 3.41
1288 1301 1.632018 CCCTTTCCCGAGCCCATACA 61.632 60.000 0.00 0.00 0.00 2.29
1680 1715 6.580791 GCGTCTTTGATTACAGCAACAATTAA 59.419 34.615 0.00 0.00 0.00 1.40
1682 1717 4.917415 GCGTCTTTGATTACAGCAACAATT 59.083 37.500 0.00 0.00 0.00 2.32
2132 2180 4.169508 CGCGAGAAATCCATGGTATCTAG 58.830 47.826 12.58 14.08 0.00 2.43
2133 2181 3.572682 ACGCGAGAAATCCATGGTATCTA 59.427 43.478 15.93 0.00 0.00 1.98
2134 2182 2.365617 ACGCGAGAAATCCATGGTATCT 59.634 45.455 15.93 13.40 0.00 1.98
2135 2183 2.755650 ACGCGAGAAATCCATGGTATC 58.244 47.619 15.93 8.72 0.00 2.24
2136 2184 2.872245 CAACGCGAGAAATCCATGGTAT 59.128 45.455 15.93 0.98 0.00 2.73
2137 2185 2.093921 TCAACGCGAGAAATCCATGGTA 60.094 45.455 15.93 0.00 0.00 3.25
2138 2186 1.086696 CAACGCGAGAAATCCATGGT 58.913 50.000 15.93 0.00 0.00 3.55
2139 2187 1.328680 CTCAACGCGAGAAATCCATGG 59.671 52.381 15.93 4.97 45.45 3.66
2140 2188 2.726555 CTCAACGCGAGAAATCCATG 57.273 50.000 15.93 0.00 45.45 3.66
2149 2197 3.430218 AGTTTTGAAGATCTCAACGCGAG 59.570 43.478 15.93 4.76 43.90 5.03
2150 2198 3.390135 AGTTTTGAAGATCTCAACGCGA 58.610 40.909 15.93 0.00 43.90 5.87
2151 2199 3.795561 AGTTTTGAAGATCTCAACGCG 57.204 42.857 3.53 3.53 43.90 6.01
2152 2200 6.654793 ATCTAGTTTTGAAGATCTCAACGC 57.345 37.500 0.00 0.00 43.90 4.84
2153 2201 7.759886 TGGTATCTAGTTTTGAAGATCTCAACG 59.240 37.037 0.00 0.00 43.90 4.10
2154 2202 9.606631 ATGGTATCTAGTTTTGAAGATCTCAAC 57.393 33.333 0.00 0.00 43.90 3.18
2155 2203 9.605275 CATGGTATCTAGTTTTGAAGATCTCAA 57.395 33.333 0.00 0.00 42.48 3.02
2156 2204 8.762645 ACATGGTATCTAGTTTTGAAGATCTCA 58.237 33.333 0.00 0.00 0.00 3.27
2157 2205 9.255304 GACATGGTATCTAGTTTTGAAGATCTC 57.745 37.037 0.00 0.00 0.00 2.75
2158 2206 7.923344 CGACATGGTATCTAGTTTTGAAGATCT 59.077 37.037 0.00 0.00 0.00 2.75
2159 2207 7.921214 TCGACATGGTATCTAGTTTTGAAGATC 59.079 37.037 0.00 0.00 0.00 2.75
2160 2208 7.782049 TCGACATGGTATCTAGTTTTGAAGAT 58.218 34.615 0.00 0.00 0.00 2.40
2161 2209 7.165460 TCGACATGGTATCTAGTTTTGAAGA 57.835 36.000 0.00 0.00 0.00 2.87
2162 2210 9.186323 CTATCGACATGGTATCTAGTTTTGAAG 57.814 37.037 0.00 0.00 0.00 3.02
2163 2211 8.141909 CCTATCGACATGGTATCTAGTTTTGAA 58.858 37.037 0.00 0.00 0.00 2.69
2164 2212 7.287005 ACCTATCGACATGGTATCTAGTTTTGA 59.713 37.037 0.00 0.00 31.50 2.69
2165 2213 7.434492 ACCTATCGACATGGTATCTAGTTTTG 58.566 38.462 0.00 0.00 31.50 2.44
2166 2214 7.598759 ACCTATCGACATGGTATCTAGTTTT 57.401 36.000 0.00 0.00 31.50 2.43
2167 2215 7.598759 AACCTATCGACATGGTATCTAGTTT 57.401 36.000 6.30 0.00 33.17 2.66
2168 2216 7.598759 AAACCTATCGACATGGTATCTAGTT 57.401 36.000 6.30 0.00 33.17 2.24
2169 2217 7.434492 CAAAACCTATCGACATGGTATCTAGT 58.566 38.462 6.30 0.00 33.17 2.57
2170 2218 6.868864 CCAAAACCTATCGACATGGTATCTAG 59.131 42.308 6.30 0.00 33.17 2.43
2171 2219 6.740401 GCCAAAACCTATCGACATGGTATCTA 60.740 42.308 6.30 0.00 33.17 1.98
2172 2220 5.611374 CCAAAACCTATCGACATGGTATCT 58.389 41.667 6.30 0.00 33.17 1.98
2173 2221 4.213482 GCCAAAACCTATCGACATGGTATC 59.787 45.833 6.30 0.00 33.17 2.24
2174 2222 4.134563 GCCAAAACCTATCGACATGGTAT 58.865 43.478 6.30 0.00 33.17 2.73
2175 2223 3.055021 TGCCAAAACCTATCGACATGGTA 60.055 43.478 6.30 0.00 33.17 3.25
2176 2224 2.290641 TGCCAAAACCTATCGACATGGT 60.291 45.455 0.00 0.00 35.29 3.55
2177 2225 2.364632 TGCCAAAACCTATCGACATGG 58.635 47.619 0.00 0.00 0.00 3.66
2178 2226 4.082787 AGTTTGCCAAAACCTATCGACATG 60.083 41.667 0.00 0.00 45.75 3.21
2179 2227 4.079253 AGTTTGCCAAAACCTATCGACAT 58.921 39.130 0.00 0.00 45.75 3.06
2180 2228 3.482436 AGTTTGCCAAAACCTATCGACA 58.518 40.909 0.00 0.00 45.75 4.35
2181 2229 4.499037 AAGTTTGCCAAAACCTATCGAC 57.501 40.909 0.00 0.00 45.75 4.20
2182 2230 5.523438 AAAAGTTTGCCAAAACCTATCGA 57.477 34.783 0.00 0.00 45.75 3.59
2203 2251 2.260481 GCCGGTGTTTTTCGTGAAAAA 58.740 42.857 14.67 14.67 44.98 1.94
2204 2252 1.469423 GGCCGGTGTTTTTCGTGAAAA 60.469 47.619 1.90 3.74 38.40 2.29
2205 2253 0.100861 GGCCGGTGTTTTTCGTGAAA 59.899 50.000 1.90 0.00 0.00 2.69
2206 2254 1.728672 GGCCGGTGTTTTTCGTGAA 59.271 52.632 1.90 0.00 0.00 3.18
2207 2255 2.535788 CGGCCGGTGTTTTTCGTGA 61.536 57.895 20.10 0.00 0.00 4.35
2208 2256 2.049475 TTCGGCCGGTGTTTTTCGTG 62.049 55.000 27.83 0.00 0.00 4.35
2209 2257 1.375098 TTTCGGCCGGTGTTTTTCGT 61.375 50.000 27.83 0.00 0.00 3.85
2210 2258 0.248539 TTTTCGGCCGGTGTTTTTCG 60.249 50.000 27.83 0.00 0.00 3.46
2211 2259 1.923899 TTTTTCGGCCGGTGTTTTTC 58.076 45.000 27.83 0.00 0.00 2.29
2227 2275 1.152922 TGCTCCCGGTTCGGTTTTT 60.153 52.632 0.00 0.00 46.80 1.94
2228 2276 1.895231 GTGCTCCCGGTTCGGTTTT 60.895 57.895 0.00 0.00 46.80 2.43
2229 2277 2.281276 GTGCTCCCGGTTCGGTTT 60.281 61.111 0.00 0.00 46.80 3.27
2230 2278 4.675029 CGTGCTCCCGGTTCGGTT 62.675 66.667 0.00 0.00 46.80 4.44
2234 2282 3.837570 AAACCCGTGCTCCCGGTTC 62.838 63.158 0.00 0.00 46.66 3.62
2235 2283 2.914756 AAAAACCCGTGCTCCCGGTT 62.915 55.000 0.00 4.62 46.66 4.44
2236 2284 3.424780 AAAAACCCGTGCTCCCGGT 62.425 57.895 0.00 0.00 46.66 5.28
2251 2299 1.144093 TGCCTCTCGGAAAGGGAAAAA 59.856 47.619 0.00 0.00 34.26 1.94
2252 2300 0.768622 TGCCTCTCGGAAAGGGAAAA 59.231 50.000 0.00 0.00 34.26 2.29
2253 2301 0.036306 GTGCCTCTCGGAAAGGGAAA 59.964 55.000 0.00 0.00 35.86 3.13
2254 2302 1.677552 GTGCCTCTCGGAAAGGGAA 59.322 57.895 0.00 0.00 35.86 3.97
2255 2303 2.646175 CGTGCCTCTCGGAAAGGGA 61.646 63.158 0.00 0.00 34.26 4.20
2256 2304 2.125512 CGTGCCTCTCGGAAAGGG 60.126 66.667 0.00 0.00 34.26 3.95
2257 2305 2.815647 GCGTGCCTCTCGGAAAGG 60.816 66.667 0.00 0.00 36.95 3.11
2258 2306 2.815647 GGCGTGCCTCTCGGAAAG 60.816 66.667 2.98 0.00 0.00 2.62
2259 2307 4.388499 GGGCGTGCCTCTCGGAAA 62.388 66.667 11.25 0.00 36.10 3.13
2277 2325 1.795768 TGTGATTTCGTGAGAGGCAC 58.204 50.000 0.00 0.00 43.69 5.01
2278 2326 2.143122 GTTGTGATTTCGTGAGAGGCA 58.857 47.619 0.00 0.00 43.69 4.75
2279 2327 1.464997 GGTTGTGATTTCGTGAGAGGC 59.535 52.381 0.00 0.00 43.69 4.70
2280 2328 1.726791 CGGTTGTGATTTCGTGAGAGG 59.273 52.381 0.00 0.00 43.69 3.69
2281 2329 2.404215 ACGGTTGTGATTTCGTGAGAG 58.596 47.619 0.00 0.00 43.69 3.20
2282 2330 2.519377 ACGGTTGTGATTTCGTGAGA 57.481 45.000 0.00 0.00 34.40 3.27
2294 2342 1.007271 CTGCGAGAGACACGGTTGT 60.007 57.895 0.00 0.00 39.32 3.32
2295 2343 0.318699 TTCTGCGAGAGACACGGTTG 60.319 55.000 0.00 0.00 0.00 3.77
2296 2344 0.039074 CTTCTGCGAGAGACACGGTT 60.039 55.000 0.00 0.00 0.00 4.44
2297 2345 1.581954 CTTCTGCGAGAGACACGGT 59.418 57.895 0.00 0.00 0.00 4.83
2298 2346 1.803519 GCTTCTGCGAGAGACACGG 60.804 63.158 0.00 0.00 0.00 4.94
2299 2347 0.664466 TTGCTTCTGCGAGAGACACG 60.664 55.000 0.00 0.00 43.34 4.49
2300 2348 1.502231 TTTGCTTCTGCGAGAGACAC 58.498 50.000 0.00 0.00 43.34 3.67
2301 2349 1.867233 GTTTTGCTTCTGCGAGAGACA 59.133 47.619 0.00 0.00 43.34 3.41
2302 2350 1.195674 GGTTTTGCTTCTGCGAGAGAC 59.804 52.381 0.00 0.00 43.34 3.36
2303 2351 1.512926 GGTTTTGCTTCTGCGAGAGA 58.487 50.000 0.00 0.00 43.34 3.10
2304 2352 0.164647 CGGTTTTGCTTCTGCGAGAG 59.835 55.000 0.00 0.00 43.34 3.20
2305 2353 0.531974 ACGGTTTTGCTTCTGCGAGA 60.532 50.000 0.00 0.00 43.34 4.04
2306 2354 0.384725 CACGGTTTTGCTTCTGCGAG 60.385 55.000 0.00 0.00 43.34 5.03
2307 2355 0.812014 TCACGGTTTTGCTTCTGCGA 60.812 50.000 0.00 0.00 43.34 5.10
2308 2356 0.657368 GTCACGGTTTTGCTTCTGCG 60.657 55.000 0.00 0.00 43.34 5.18
2309 2357 0.663153 AGTCACGGTTTTGCTTCTGC 59.337 50.000 0.00 0.00 40.20 4.26
2310 2358 2.213499 AGAGTCACGGTTTTGCTTCTG 58.787 47.619 0.00 0.00 0.00 3.02
2311 2359 2.484889 GAGAGTCACGGTTTTGCTTCT 58.515 47.619 0.00 0.00 0.00 2.85
2312 2360 1.192534 CGAGAGTCACGGTTTTGCTTC 59.807 52.381 1.62 0.00 0.00 3.86
2313 2361 1.217882 CGAGAGTCACGGTTTTGCTT 58.782 50.000 1.62 0.00 0.00 3.91
2314 2362 0.104304 ACGAGAGTCACGGTTTTGCT 59.896 50.000 14.49 0.00 44.19 3.91
2315 2363 2.601562 ACGAGAGTCACGGTTTTGC 58.398 52.632 14.49 0.00 44.19 3.68
2361 2409 2.032426 GTGCCTCCTCGAAAACGAAAAA 59.968 45.455 0.00 0.00 0.00 1.94
2362 2410 1.600485 GTGCCTCCTCGAAAACGAAAA 59.400 47.619 0.00 0.00 0.00 2.29
2363 2411 1.223187 GTGCCTCCTCGAAAACGAAA 58.777 50.000 0.00 0.00 0.00 3.46
2364 2412 0.105224 TGTGCCTCCTCGAAAACGAA 59.895 50.000 0.00 0.00 0.00 3.85
2365 2413 0.319555 CTGTGCCTCCTCGAAAACGA 60.320 55.000 0.00 0.00 0.00 3.85
2366 2414 1.901650 GCTGTGCCTCCTCGAAAACG 61.902 60.000 0.00 0.00 0.00 3.60
2367 2415 1.578206 GGCTGTGCCTCCTCGAAAAC 61.578 60.000 0.73 0.00 46.69 2.43
2368 2416 1.302511 GGCTGTGCCTCCTCGAAAA 60.303 57.895 0.73 0.00 46.69 2.29
2369 2417 2.347490 GGCTGTGCCTCCTCGAAA 59.653 61.111 0.73 0.00 46.69 3.46
2379 2427 2.459442 GCGAGAGTCATGGCTGTGC 61.459 63.158 3.48 3.70 0.00 4.57
2380 2428 2.163390 CGCGAGAGTCATGGCTGTG 61.163 63.158 3.48 0.00 0.00 3.66
2381 2429 1.877576 TTCGCGAGAGTCATGGCTGT 61.878 55.000 3.48 0.00 43.69 4.40
2382 2430 0.737367 TTTCGCGAGAGTCATGGCTG 60.737 55.000 3.48 0.00 43.69 4.85
2383 2431 0.459237 CTTTCGCGAGAGTCATGGCT 60.459 55.000 17.92 0.00 43.69 4.75
2384 2432 2.002127 CTTTCGCGAGAGTCATGGC 58.998 57.895 17.92 0.00 43.69 4.40
2385 2433 0.737367 TGCTTTCGCGAGAGTCATGG 60.737 55.000 25.34 2.90 43.69 3.66
2386 2434 0.368227 GTGCTTTCGCGAGAGTCATG 59.632 55.000 25.34 7.32 43.69 3.07
2387 2435 0.038251 TGTGCTTTCGCGAGAGTCAT 60.038 50.000 25.34 0.00 43.69 3.06
2388 2436 0.939577 GTGTGCTTTCGCGAGAGTCA 60.940 55.000 25.34 20.22 43.69 3.41
2389 2437 1.618640 GGTGTGCTTTCGCGAGAGTC 61.619 60.000 25.34 18.16 43.69 3.36
2390 2438 1.664965 GGTGTGCTTTCGCGAGAGT 60.665 57.895 25.34 0.00 43.69 3.24
2391 2439 2.383527 GGGTGTGCTTTCGCGAGAG 61.384 63.158 21.42 21.42 43.69 3.20
2392 2440 2.357034 GGGTGTGCTTTCGCGAGA 60.357 61.111 9.59 3.35 39.65 4.04
2393 2441 3.777925 CGGGTGTGCTTTCGCGAG 61.778 66.667 9.59 0.00 41.28 5.03
2394 2442 4.595538 ACGGGTGTGCTTTCGCGA 62.596 61.111 3.71 3.71 41.28 5.87
2395 2443 4.368808 CACGGGTGTGCTTTCGCG 62.369 66.667 0.00 0.00 39.67 5.87
2413 2461 0.375106 GATTTTGCTTCCGCGAGAGG 59.625 55.000 8.23 4.88 39.65 3.69
2414 2462 0.025513 CGATTTTGCTTCCGCGAGAG 59.974 55.000 8.23 5.93 39.65 3.20
2415 2463 0.669318 ACGATTTTGCTTCCGCGAGA 60.669 50.000 8.23 0.00 39.65 4.04
2416 2464 0.519175 CACGATTTTGCTTCCGCGAG 60.519 55.000 8.23 0.00 39.65 5.03
2417 2465 0.946700 TCACGATTTTGCTTCCGCGA 60.947 50.000 8.23 0.00 39.65 5.87
2418 2466 0.789383 GTCACGATTTTGCTTCCGCG 60.789 55.000 0.00 0.00 39.65 6.46
2419 2467 0.517316 AGTCACGATTTTGCTTCCGC 59.483 50.000 0.00 0.00 0.00 5.54
2420 2468 2.069273 AGAGTCACGATTTTGCTTCCG 58.931 47.619 0.00 0.00 0.00 4.30
2421 2469 2.092838 CGAGAGTCACGATTTTGCTTCC 59.907 50.000 3.68 0.00 0.00 3.46
2422 2470 2.731976 ACGAGAGTCACGATTTTGCTTC 59.268 45.455 17.05 0.00 44.19 3.86
2423 2471 2.755650 ACGAGAGTCACGATTTTGCTT 58.244 42.857 17.05 0.00 44.19 3.91
2424 2472 2.440539 ACGAGAGTCACGATTTTGCT 57.559 45.000 17.05 0.00 44.19 3.91


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

AutoCloner maintained by Alex Coulton.