Multiple sequence alignment - TraesCS6A01G209700

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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 TraesCS6A01G209700 chr6A 100.000 2393 0 0 1 2393 379679232 379676840 0.000000e+00 4420
1 TraesCS6A01G209700 chr7A 93.523 2146 121 7 14 2142 300157948 300160092 0.000000e+00 3177
2 TraesCS6A01G209700 chr7A 92.179 2148 149 10 10 2142 221854881 221857024 0.000000e+00 3018
3 TraesCS6A01G209700 chr7A 92.052 2139 150 11 17 2142 484264552 484262421 0.000000e+00 2990
4 TraesCS6A01G209700 chr7A 96.850 254 8 0 2139 2392 528098932 528099185 2.200000e-115 425
5 TraesCS6A01G209700 chr4A 92.821 2145 137 10 10 2142 466512600 466510461 0.000000e+00 3092
6 TraesCS6A01G209700 chr4A 92.787 2135 137 11 19 2142 254267014 254269142 0.000000e+00 3073
7 TraesCS6A01G209700 chr4A 91.944 2135 154 7 22 2140 137854590 137852458 0.000000e+00 2974
8 TraesCS6A01G209700 chr4A 91.601 2143 155 15 19 2142 330368828 330366692 0.000000e+00 2937
9 TraesCS6A01G209700 chr4A 96.457 254 9 0 2139 2392 32255484 32255231 1.020000e-113 420
10 TraesCS6A01G209700 chr3A 92.265 2146 146 12 10 2140 585453108 585455248 0.000000e+00 3025
11 TraesCS6A01G209700 chr3A 97.244 254 7 0 2139 2392 593740306 593740053 4.730000e-117 431
12 TraesCS6A01G209700 chr5A 91.822 2140 150 21 19 2142 487149071 487151201 0.000000e+00 2959
13 TraesCS6A01G209700 chr5A 96.863 255 7 1 2139 2393 128951987 128952240 2.200000e-115 425
14 TraesCS6A01G209700 chr5A 96.850 254 8 0 2139 2392 567681210 567680957 2.200000e-115 425
15 TraesCS6A01G209700 chr2A 96.863 255 8 0 2139 2393 652488403 652488657 6.110000e-116 427
16 TraesCS6A01G209700 chr1A 96.471 255 9 0 2139 2393 443918175 443918429 2.840000e-114 422
17 TraesCS6A01G209700 chr1A 96.471 255 8 1 2139 2393 24368801 24369054 1.020000e-113 420
18 TraesCS6A01G209700 chr1A 96.457 254 9 0 2139 2392 272121445 272121698 1.020000e-113 420


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 TraesCS6A01G209700 chr6A 379676840 379679232 2392 True 4420 4420 100.000 1 2393 1 chr6A.!!$R1 2392
1 TraesCS6A01G209700 chr7A 300157948 300160092 2144 False 3177 3177 93.523 14 2142 1 chr7A.!!$F2 2128
2 TraesCS6A01G209700 chr7A 221854881 221857024 2143 False 3018 3018 92.179 10 2142 1 chr7A.!!$F1 2132
3 TraesCS6A01G209700 chr7A 484262421 484264552 2131 True 2990 2990 92.052 17 2142 1 chr7A.!!$R1 2125
4 TraesCS6A01G209700 chr4A 466510461 466512600 2139 True 3092 3092 92.821 10 2142 1 chr4A.!!$R4 2132
5 TraesCS6A01G209700 chr4A 254267014 254269142 2128 False 3073 3073 92.787 19 2142 1 chr4A.!!$F1 2123
6 TraesCS6A01G209700 chr4A 137852458 137854590 2132 True 2974 2974 91.944 22 2140 1 chr4A.!!$R2 2118
7 TraesCS6A01G209700 chr4A 330366692 330368828 2136 True 2937 2937 91.601 19 2142 1 chr4A.!!$R3 2123
8 TraesCS6A01G209700 chr3A 585453108 585455248 2140 False 3025 3025 92.265 10 2140 1 chr3A.!!$F1 2130
9 TraesCS6A01G209700 chr5A 487149071 487151201 2130 False 2959 2959 91.822 19 2142 1 chr5A.!!$F2 2123

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
931 938 1.006878 TCACCATGGGATGCATTGGAA 59.993 47.619 19.7 6.53 0.0 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1809 1851 0.811281 GCATCCTGCAGTGGTTAACC 59.189 55.0 18.27 18.27 44.26 2.85 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
223 229 5.519927 GTGTTATTTTGCCAGCATATTCCAC 59.480 40.000 0.00 0.00 0.00 4.02
230 236 3.085208 AGCATATTCCACGTGCTGG 57.915 52.632 10.91 0.00 46.60 4.85
469 476 8.732531 GCTACTCTGTTATAAATCCTCGAGTAT 58.267 37.037 12.31 5.15 33.74 2.12
594 601 4.053295 GTTGAACACGACCACTAAGCTAA 58.947 43.478 0.00 0.00 0.00 3.09
717 724 2.158871 AGCACCTTTTGGACGACACTTA 60.159 45.455 0.00 0.00 44.07 2.24
804 811 2.242926 CCAGAAGAGGAGCGATGGATA 58.757 52.381 0.00 0.00 0.00 2.59
805 812 2.230992 CCAGAAGAGGAGCGATGGATAG 59.769 54.545 0.00 0.00 0.00 2.08
868 875 6.940298 CACTAAACCCATAGAGTTTTCCTTCA 59.060 38.462 0.00 0.00 38.37 3.02
931 938 1.006878 TCACCATGGGATGCATTGGAA 59.993 47.619 19.70 6.53 0.00 3.53
934 941 3.116959 ACCATGGGATGCATTGGAAAAT 58.883 40.909 19.70 0.00 0.00 1.82
1007 1014 3.937778 TGAGCAATGGGAGATGATCAA 57.062 42.857 0.00 0.00 38.85 2.57
1017 1024 3.308402 GGGAGATGATCAACACCAGGAAA 60.308 47.826 18.62 0.00 0.00 3.13
1166 1174 5.223382 ACTCAAGTCTACACGTGAAGATTG 58.777 41.667 25.01 18.25 40.06 2.67
1168 1176 6.016527 ACTCAAGTCTACACGTGAAGATTGTA 60.017 38.462 25.01 0.61 40.06 2.41
1194 1202 5.068723 GGAGGAAATCGTCATACTAGTGGAA 59.931 44.000 5.39 0.00 32.79 3.53
1220 1228 8.729805 AAGAATGATGACCTGATTAAGAAGAC 57.270 34.615 0.00 0.00 0.00 3.01
1285 1293 2.731571 CCCAAGGAGATTCGCCCGA 61.732 63.158 2.46 0.00 0.00 5.14
1320 1328 2.747822 CGACGACACCGACTCCGAT 61.748 63.158 0.00 0.00 39.50 4.18
1357 1365 0.610174 TGAAGACGAAGCTGGAGCAT 59.390 50.000 0.65 0.00 45.16 3.79
1398 1406 9.384764 GCAACTGAGGAATATTTTTAGTAGACT 57.615 33.333 0.00 0.00 0.00 3.24
1444 1452 6.183360 CCACCATGTAAATAGAGTAGTCCGAA 60.183 42.308 0.00 0.00 0.00 4.30
1586 1606 2.281345 CCCATCAGATGCCTCCGC 60.281 66.667 4.68 0.00 0.00 5.54
1615 1636 1.631405 CCAGATTTGCTTTCCCACCA 58.369 50.000 0.00 0.00 0.00 4.17
1699 1735 3.241932 GCAACAACAACAACAACAATCCG 60.242 43.478 0.00 0.00 0.00 4.18
1713 1755 2.351924 AATCCGCCACCACCAGTTGT 62.352 55.000 0.00 0.00 0.00 3.32
1714 1756 2.351924 ATCCGCCACCACCAGTTGTT 62.352 55.000 0.00 0.00 0.00 2.83
1786 1828 4.344102 ACCGAGCCTATAGTAGCAAATGAA 59.656 41.667 0.00 0.00 0.00 2.57
2142 2184 4.226427 TGGAAGGGTTGAATGATGAGAG 57.774 45.455 0.00 0.00 0.00 3.20
2143 2185 3.588842 TGGAAGGGTTGAATGATGAGAGT 59.411 43.478 0.00 0.00 0.00 3.24
2144 2186 4.782691 TGGAAGGGTTGAATGATGAGAGTA 59.217 41.667 0.00 0.00 0.00 2.59
2145 2187 5.250543 TGGAAGGGTTGAATGATGAGAGTAA 59.749 40.000 0.00 0.00 0.00 2.24
2146 2188 6.069440 TGGAAGGGTTGAATGATGAGAGTAAT 60.069 38.462 0.00 0.00 0.00 1.89
2147 2189 7.127186 TGGAAGGGTTGAATGATGAGAGTAATA 59.873 37.037 0.00 0.00 0.00 0.98
2148 2190 7.993183 GGAAGGGTTGAATGATGAGAGTAATAA 59.007 37.037 0.00 0.00 0.00 1.40
2149 2191 9.396022 GAAGGGTTGAATGATGAGAGTAATAAA 57.604 33.333 0.00 0.00 0.00 1.40
2150 2192 9.753674 AAGGGTTGAATGATGAGAGTAATAAAA 57.246 29.630 0.00 0.00 0.00 1.52
2151 2193 9.927081 AGGGTTGAATGATGAGAGTAATAAAAT 57.073 29.630 0.00 0.00 0.00 1.82
2223 2265 8.867112 ATTGTTGAATTCATTCATGATGCTAC 57.133 30.769 9.40 0.33 45.30 3.58
2224 2266 7.634671 TGTTGAATTCATTCATGATGCTACT 57.365 32.000 9.40 0.00 45.30 2.57
2225 2267 7.477494 TGTTGAATTCATTCATGATGCTACTG 58.523 34.615 9.40 0.00 45.30 2.74
2226 2268 7.337436 TGTTGAATTCATTCATGATGCTACTGA 59.663 33.333 9.40 0.00 45.30 3.41
2227 2269 7.868906 TGAATTCATTCATGATGCTACTGAA 57.131 32.000 3.38 0.58 41.51 3.02
2228 2270 8.283699 TGAATTCATTCATGATGCTACTGAAA 57.716 30.769 3.38 0.00 41.51 2.69
2229 2271 8.741841 TGAATTCATTCATGATGCTACTGAAAA 58.258 29.630 3.38 0.00 41.51 2.29
2230 2272 9.745880 GAATTCATTCATGATGCTACTGAAAAT 57.254 29.630 0.00 0.00 36.56 1.82
2241 2283 9.288576 TGATGCTACTGAAAATTATTATGAGGG 57.711 33.333 0.00 0.00 0.00 4.30
2242 2284 9.507329 GATGCTACTGAAAATTATTATGAGGGA 57.493 33.333 0.00 0.00 0.00 4.20
2243 2285 8.908786 TGCTACTGAAAATTATTATGAGGGAG 57.091 34.615 0.00 0.00 0.00 4.30
2244 2286 7.939039 TGCTACTGAAAATTATTATGAGGGAGG 59.061 37.037 0.00 0.00 0.00 4.30
2245 2287 8.157476 GCTACTGAAAATTATTATGAGGGAGGA 58.843 37.037 0.00 0.00 0.00 3.71
2247 2289 8.753497 ACTGAAAATTATTATGAGGGAGGAAC 57.247 34.615 0.00 0.00 0.00 3.62
2248 2290 8.336235 ACTGAAAATTATTATGAGGGAGGAACA 58.664 33.333 0.00 0.00 0.00 3.18
2249 2291 9.359653 CTGAAAATTATTATGAGGGAGGAACAT 57.640 33.333 0.00 0.00 0.00 2.71
2253 2295 8.814038 AATTATTATGAGGGAGGAACATATGC 57.186 34.615 1.58 0.00 0.00 3.14
2254 2296 7.574021 TTATTATGAGGGAGGAACATATGCT 57.426 36.000 1.58 0.00 0.00 3.79
2255 2297 5.912149 TTATGAGGGAGGAACATATGCTT 57.088 39.130 1.58 0.00 0.00 3.91
2256 2298 3.565764 TGAGGGAGGAACATATGCTTG 57.434 47.619 1.58 0.00 0.00 4.01
2257 2299 2.846206 TGAGGGAGGAACATATGCTTGT 59.154 45.455 1.58 0.00 0.00 3.16
2258 2300 4.037222 TGAGGGAGGAACATATGCTTGTA 58.963 43.478 1.58 0.00 0.00 2.41
2259 2301 4.101585 TGAGGGAGGAACATATGCTTGTAG 59.898 45.833 1.58 0.00 0.00 2.74
2260 2302 3.392616 AGGGAGGAACATATGCTTGTAGG 59.607 47.826 1.58 0.00 0.00 3.18
2261 2303 3.391296 GGGAGGAACATATGCTTGTAGGA 59.609 47.826 1.58 0.00 0.00 2.94
2262 2304 4.141482 GGGAGGAACATATGCTTGTAGGAA 60.141 45.833 1.58 0.00 0.00 3.36
2263 2305 5.456763 GGGAGGAACATATGCTTGTAGGAAT 60.457 44.000 1.58 0.00 0.00 3.01
2264 2306 6.064717 GGAGGAACATATGCTTGTAGGAATT 58.935 40.000 1.58 0.00 0.00 2.17
2265 2307 6.016777 GGAGGAACATATGCTTGTAGGAATTG 60.017 42.308 1.58 0.00 0.00 2.32
2266 2308 5.300286 AGGAACATATGCTTGTAGGAATTGC 59.700 40.000 1.58 0.00 0.00 3.56
2267 2309 5.067674 GGAACATATGCTTGTAGGAATTGCA 59.932 40.000 1.58 0.00 38.05 4.08
2268 2310 6.405731 GGAACATATGCTTGTAGGAATTGCAA 60.406 38.462 0.00 0.00 37.20 4.08
2269 2311 6.720112 ACATATGCTTGTAGGAATTGCAAT 57.280 33.333 5.99 5.99 37.20 3.56
2270 2312 7.822161 ACATATGCTTGTAGGAATTGCAATA 57.178 32.000 13.39 0.00 37.20 1.90
2271 2313 8.236585 ACATATGCTTGTAGGAATTGCAATAA 57.763 30.769 13.39 0.93 37.20 1.40
2272 2314 8.863086 ACATATGCTTGTAGGAATTGCAATAAT 58.137 29.630 13.39 4.32 37.20 1.28
2276 2318 8.462589 TGCTTGTAGGAATTGCAATAATATCA 57.537 30.769 13.39 7.32 30.73 2.15
2277 2319 8.911965 TGCTTGTAGGAATTGCAATAATATCAA 58.088 29.630 13.39 13.85 30.73 2.57
2278 2320 9.403110 GCTTGTAGGAATTGCAATAATATCAAG 57.597 33.333 25.16 25.16 30.73 3.02
2282 2324 9.899226 GTAGGAATTGCAATAATATCAAGTTCC 57.101 33.333 13.39 12.20 33.13 3.62
2283 2325 7.955918 AGGAATTGCAATAATATCAAGTTCCC 58.044 34.615 13.39 0.00 33.25 3.97
2284 2326 7.786464 AGGAATTGCAATAATATCAAGTTCCCT 59.214 33.333 13.39 0.77 33.25 4.20
2285 2327 8.424133 GGAATTGCAATAATATCAAGTTCCCTT 58.576 33.333 13.39 0.00 30.34 3.95
2286 2328 9.822185 GAATTGCAATAATATCAAGTTCCCTTT 57.178 29.630 13.39 0.00 0.00 3.11
2287 2329 9.822185 AATTGCAATAATATCAAGTTCCCTTTC 57.178 29.630 13.39 0.00 0.00 2.62
2288 2330 8.593945 TTGCAATAATATCAAGTTCCCTTTCT 57.406 30.769 0.00 0.00 0.00 2.52
2289 2331 9.693739 TTGCAATAATATCAAGTTCCCTTTCTA 57.306 29.630 0.00 0.00 0.00 2.10
2290 2332 9.866655 TGCAATAATATCAAGTTCCCTTTCTAT 57.133 29.630 0.00 0.00 0.00 1.98
2293 2335 6.867662 AATATCAAGTTCCCTTTCTATGCG 57.132 37.500 0.00 0.00 0.00 4.73
2294 2336 2.356135 TCAAGTTCCCTTTCTATGCGC 58.644 47.619 0.00 0.00 0.00 6.09
2295 2337 2.027192 TCAAGTTCCCTTTCTATGCGCT 60.027 45.455 9.73 0.00 0.00 5.92
2296 2338 2.749621 CAAGTTCCCTTTCTATGCGCTT 59.250 45.455 9.73 4.59 0.00 4.68
2297 2339 3.906720 AGTTCCCTTTCTATGCGCTTA 57.093 42.857 9.73 5.78 0.00 3.09
2298 2340 4.216411 AGTTCCCTTTCTATGCGCTTAA 57.784 40.909 9.73 0.00 0.00 1.85
2299 2341 4.585879 AGTTCCCTTTCTATGCGCTTAAA 58.414 39.130 9.73 0.00 0.00 1.52
2300 2342 5.007682 AGTTCCCTTTCTATGCGCTTAAAA 58.992 37.500 9.73 9.18 0.00 1.52
2301 2343 5.652452 AGTTCCCTTTCTATGCGCTTAAAAT 59.348 36.000 9.73 0.00 0.00 1.82
2302 2344 5.751243 TCCCTTTCTATGCGCTTAAAATC 57.249 39.130 9.73 0.00 0.00 2.17
2303 2345 5.437060 TCCCTTTCTATGCGCTTAAAATCT 58.563 37.500 9.73 0.00 0.00 2.40
2304 2346 5.885912 TCCCTTTCTATGCGCTTAAAATCTT 59.114 36.000 9.73 0.00 0.00 2.40
2305 2347 5.973565 CCCTTTCTATGCGCTTAAAATCTTG 59.026 40.000 9.73 0.00 0.00 3.02
2306 2348 6.183360 CCCTTTCTATGCGCTTAAAATCTTGA 60.183 38.462 9.73 0.00 0.00 3.02
2307 2349 7.250569 CCTTTCTATGCGCTTAAAATCTTGAA 58.749 34.615 9.73 2.01 0.00 2.69
2308 2350 7.430502 CCTTTCTATGCGCTTAAAATCTTGAAG 59.569 37.037 9.73 0.00 0.00 3.02
2309 2351 6.985188 TCTATGCGCTTAAAATCTTGAAGT 57.015 33.333 9.73 0.00 0.00 3.01
2310 2352 7.005062 TCTATGCGCTTAAAATCTTGAAGTC 57.995 36.000 9.73 0.00 0.00 3.01
2311 2353 5.627499 ATGCGCTTAAAATCTTGAAGTCA 57.373 34.783 9.73 0.00 0.00 3.41
2312 2354 5.627499 TGCGCTTAAAATCTTGAAGTCAT 57.373 34.783 9.73 0.00 0.00 3.06
2313 2355 5.393124 TGCGCTTAAAATCTTGAAGTCATG 58.607 37.500 9.73 0.00 0.00 3.07
2314 2356 4.263911 GCGCTTAAAATCTTGAAGTCATGC 59.736 41.667 0.00 0.00 0.00 4.06
2315 2357 5.634896 CGCTTAAAATCTTGAAGTCATGCT 58.365 37.500 0.00 0.00 0.00 3.79
2316 2358 6.088824 CGCTTAAAATCTTGAAGTCATGCTT 58.911 36.000 2.57 2.57 40.76 3.91
2317 2359 6.033196 CGCTTAAAATCTTGAAGTCATGCTTG 59.967 38.462 7.05 0.00 37.59 4.01
2318 2360 6.865205 GCTTAAAATCTTGAAGTCATGCTTGT 59.135 34.615 7.05 0.00 37.59 3.16
2319 2361 7.383300 GCTTAAAATCTTGAAGTCATGCTTGTT 59.617 33.333 7.05 0.00 37.59 2.83
2320 2362 9.252962 CTTAAAATCTTGAAGTCATGCTTGTTT 57.747 29.630 7.05 0.00 37.59 2.83
2321 2363 9.598517 TTAAAATCTTGAAGTCATGCTTGTTTT 57.401 25.926 7.05 8.34 37.59 2.43
2322 2364 7.473027 AAATCTTGAAGTCATGCTTGTTTTG 57.527 32.000 7.05 0.00 37.59 2.44
2323 2365 4.362279 TCTTGAAGTCATGCTTGTTTTGC 58.638 39.130 7.05 0.00 37.59 3.68
2324 2366 4.098349 TCTTGAAGTCATGCTTGTTTTGCT 59.902 37.500 7.05 0.00 37.59 3.91
2325 2367 4.389890 TGAAGTCATGCTTGTTTTGCTT 57.610 36.364 7.05 0.00 37.59 3.91
2326 2368 4.757594 TGAAGTCATGCTTGTTTTGCTTT 58.242 34.783 7.05 0.00 37.59 3.51
2327 2369 4.805192 TGAAGTCATGCTTGTTTTGCTTTC 59.195 37.500 7.05 0.00 37.59 2.62
2328 2370 3.721035 AGTCATGCTTGTTTTGCTTTCC 58.279 40.909 0.00 0.00 0.00 3.13
2329 2371 3.385755 AGTCATGCTTGTTTTGCTTTCCT 59.614 39.130 0.00 0.00 0.00 3.36
2330 2372 4.584325 AGTCATGCTTGTTTTGCTTTCCTA 59.416 37.500 0.00 0.00 0.00 2.94
2331 2373 5.244626 AGTCATGCTTGTTTTGCTTTCCTAT 59.755 36.000 0.00 0.00 0.00 2.57
2332 2374 5.346822 GTCATGCTTGTTTTGCTTTCCTATG 59.653 40.000 0.00 0.00 0.00 2.23
2333 2375 3.652274 TGCTTGTTTTGCTTTCCTATGC 58.348 40.909 0.00 0.00 0.00 3.14
2334 2376 3.321682 TGCTTGTTTTGCTTTCCTATGCT 59.678 39.130 0.00 0.00 0.00 3.79
2335 2377 4.522405 TGCTTGTTTTGCTTTCCTATGCTA 59.478 37.500 0.00 0.00 0.00 3.49
2336 2378 5.098211 GCTTGTTTTGCTTTCCTATGCTAG 58.902 41.667 0.00 0.00 0.00 3.42
2337 2379 5.335976 GCTTGTTTTGCTTTCCTATGCTAGT 60.336 40.000 0.00 0.00 0.00 2.57
2338 2380 6.648879 TTGTTTTGCTTTCCTATGCTAGTT 57.351 33.333 0.00 0.00 0.00 2.24
2339 2381 6.012658 TGTTTTGCTTTCCTATGCTAGTTG 57.987 37.500 0.00 0.00 0.00 3.16
2340 2382 5.767665 TGTTTTGCTTTCCTATGCTAGTTGA 59.232 36.000 0.00 0.00 0.00 3.18
2341 2383 6.434028 TGTTTTGCTTTCCTATGCTAGTTGAT 59.566 34.615 0.00 0.00 0.00 2.57
2342 2384 7.039784 TGTTTTGCTTTCCTATGCTAGTTGATT 60.040 33.333 0.00 0.00 0.00 2.57
2343 2385 8.458843 GTTTTGCTTTCCTATGCTAGTTGATTA 58.541 33.333 0.00 0.00 0.00 1.75
2344 2386 8.752005 TTTGCTTTCCTATGCTAGTTGATTAT 57.248 30.769 0.00 0.00 0.00 1.28
2345 2387 8.752005 TTGCTTTCCTATGCTAGTTGATTATT 57.248 30.769 0.00 0.00 0.00 1.40
2346 2388 9.845740 TTGCTTTCCTATGCTAGTTGATTATTA 57.154 29.630 0.00 0.00 0.00 0.98
2351 2393 9.959721 TTCCTATGCTAGTTGATTATTATTCCC 57.040 33.333 0.00 0.00 0.00 3.97
2352 2394 9.111519 TCCTATGCTAGTTGATTATTATTCCCA 57.888 33.333 0.00 0.00 0.00 4.37
2353 2395 9.911788 CCTATGCTAGTTGATTATTATTCCCAT 57.088 33.333 0.00 0.00 0.00 4.00
2368 2410 8.947055 ATTATTCCCATAAATTGTTTGCTCAC 57.053 30.769 0.00 0.00 0.00 3.51
2369 2411 5.798125 TTCCCATAAATTGTTTGCTCACA 57.202 34.783 0.00 0.00 0.00 3.58
2370 2412 5.798125 TCCCATAAATTGTTTGCTCACAA 57.202 34.783 4.07 4.07 40.92 3.33
2371 2413 6.166984 TCCCATAAATTGTTTGCTCACAAA 57.833 33.333 5.52 0.00 43.45 2.83
2372 2414 6.586344 TCCCATAAATTGTTTGCTCACAAAA 58.414 32.000 5.52 0.00 46.94 2.44
2373 2415 7.222872 TCCCATAAATTGTTTGCTCACAAAAT 58.777 30.769 5.52 1.59 46.94 1.82
2374 2416 7.387397 TCCCATAAATTGTTTGCTCACAAAATC 59.613 33.333 5.52 0.00 46.94 2.17
2375 2417 7.361116 CCCATAAATTGTTTGCTCACAAAATCC 60.361 37.037 5.52 0.00 46.94 3.01
2376 2418 7.361116 CCATAAATTGTTTGCTCACAAAATCCC 60.361 37.037 5.52 0.00 46.94 3.85
2377 2419 4.961438 ATTGTTTGCTCACAAAATCCCT 57.039 36.364 5.52 0.00 46.94 4.20
2378 2420 6.418057 AATTGTTTGCTCACAAAATCCCTA 57.582 33.333 5.52 0.00 46.94 3.53
2379 2421 6.610075 ATTGTTTGCTCACAAAATCCCTAT 57.390 33.333 5.52 0.00 46.94 2.57
2380 2422 5.389859 TGTTTGCTCACAAAATCCCTATG 57.610 39.130 0.00 0.00 46.94 2.23
2381 2423 4.176271 GTTTGCTCACAAAATCCCTATGC 58.824 43.478 0.00 0.00 46.94 3.14
2382 2424 3.084536 TGCTCACAAAATCCCTATGCA 57.915 42.857 0.00 0.00 0.00 3.96
2383 2425 3.634504 TGCTCACAAAATCCCTATGCAT 58.365 40.909 3.79 3.79 0.00 3.96
2384 2426 4.790937 TGCTCACAAAATCCCTATGCATA 58.209 39.130 6.20 6.20 0.00 3.14
2385 2427 4.823442 TGCTCACAAAATCCCTATGCATAG 59.177 41.667 24.33 24.33 0.00 2.23
2386 2428 7.637743 TTGCTCACAAAATCCCTATGCATAGG 61.638 42.308 36.50 36.50 40.27 2.57
2387 2429 9.708066 TTGCTCACAAAATCCCTATGCATAGGA 62.708 40.741 42.12 30.58 41.70 2.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.881937 GGTAACTAGTCATCAACCCGT 57.118 47.619 0.00 0.00 0.00 5.28
15 16 6.661805 TCCAACTCAATCCCAATTAAGGTAAC 59.338 38.462 0.00 0.00 0.00 2.50
191 197 4.455877 GCTGGCAAAATAACACAGTAGAGT 59.544 41.667 0.00 0.00 0.00 3.24
261 268 4.487019 CTTACTCCTCGTCTGAAAAGTCC 58.513 47.826 0.00 0.00 0.00 3.85
469 476 1.870402 CGGTAATGCTGACACACACAA 59.130 47.619 0.00 0.00 0.00 3.33
568 575 2.396590 AGTGGTCGTGTTCAACACTT 57.603 45.000 18.49 0.00 46.46 3.16
574 581 4.325028 TTTAGCTTAGTGGTCGTGTTCA 57.675 40.909 0.00 0.00 0.00 3.18
576 583 3.497262 GCTTTTAGCTTAGTGGTCGTGTT 59.503 43.478 0.00 0.00 38.45 3.32
594 601 8.261349 AGAAGAGAATAGTGATCTATGGCTTT 57.739 34.615 0.00 0.00 37.02 3.51
717 724 4.748701 TCAGGTACCTAGTGACTTCCTTT 58.251 43.478 15.80 0.00 0.00 3.11
804 811 4.503714 TCCTGGAACTTGAACTTGAACT 57.496 40.909 0.00 0.00 0.00 3.01
805 812 4.036852 CCTTCCTGGAACTTGAACTTGAAC 59.963 45.833 4.68 0.00 38.35 3.18
868 875 2.086610 AAACTCCAGGTTGGTGCATT 57.913 45.000 0.00 0.00 39.03 3.56
931 938 9.914131 GTCTTTAAGCTCCTTGTGATAAAATTT 57.086 29.630 0.00 0.00 0.00 1.82
934 941 7.719633 AGTGTCTTTAAGCTCCTTGTGATAAAA 59.280 33.333 0.00 0.00 0.00 1.52
1007 1014 5.591877 GCAATTGATCTATCTTTCCTGGTGT 59.408 40.000 10.34 0.00 0.00 4.16
1017 1024 6.207025 GGATGAAAGCTGCAATTGATCTATCT 59.793 38.462 10.34 0.00 0.00 1.98
1166 1174 7.140048 CACTAGTATGACGATTTCCTCCTTAC 58.860 42.308 0.00 0.00 0.00 2.34
1168 1176 5.069251 CCACTAGTATGACGATTTCCTCCTT 59.931 44.000 0.00 0.00 0.00 3.36
1194 1202 9.171877 GTCTTCTTAATCAGGTCATCATTCTTT 57.828 33.333 0.00 0.00 0.00 2.52
1220 1228 2.290323 GGGTCTCCCATGAATATTCCGG 60.290 54.545 12.90 12.48 44.65 5.14
1285 1293 5.163652 TGTCGTCGATGATGATGTAGTCTTT 60.164 40.000 11.16 0.00 29.93 2.52
1320 1328 6.566753 CGTCTTCATAGTCATCATCGCTAAGA 60.567 42.308 0.00 0.00 0.00 2.10
1357 1365 5.011431 CCTCAGTTGCAGACTCCATGATATA 59.989 44.000 0.00 0.00 36.10 0.86
1398 1406 6.548622 GGTGGAATACTACTACTGATGTGGTA 59.451 42.308 0.00 0.00 38.78 3.25
1444 1452 4.890088 TGGTCTAACTATCGCAAAAGTGT 58.110 39.130 0.00 0.00 0.00 3.55
1586 1606 1.635663 GCAAATCTGGGGTCACGTCG 61.636 60.000 0.00 0.00 0.00 5.12
1615 1636 2.496871 CTGGATCAACTGAGTGAGCTCT 59.503 50.000 16.19 0.00 42.13 4.09
1699 1735 1.687563 AGTTAACAACTGGTGGTGGC 58.312 50.000 8.61 0.00 41.01 5.01
1713 1755 5.868454 ACCTTAGAAAACGGGCTAAGTTAA 58.132 37.500 0.00 0.00 41.10 2.01
1714 1756 5.488262 ACCTTAGAAAACGGGCTAAGTTA 57.512 39.130 0.00 0.00 41.10 2.24
1809 1851 0.811281 GCATCCTGCAGTGGTTAACC 59.189 55.000 18.27 18.27 44.26 2.85
1828 1870 1.085091 GCACCTTCTCAGCATCAGTG 58.915 55.000 0.00 0.00 0.00 3.66
2044 2086 2.472695 ACTTGCTAAACTCATCCGCA 57.527 45.000 0.00 0.00 0.00 5.69
2071 2113 3.181430 TGGCCACATTATCAGGTGCATAT 60.181 43.478 0.00 0.00 33.72 1.78
2077 2119 1.915489 TCTGTGGCCACATTATCAGGT 59.085 47.619 37.66 0.00 41.01 4.00
2204 2246 9.745880 ATTTTCAGTAGCATCATGAATGAATTC 57.254 29.630 0.00 0.00 40.69 2.17
2215 2257 9.288576 CCCTCATAATAATTTTCAGTAGCATCA 57.711 33.333 0.00 0.00 0.00 3.07
2216 2258 9.507329 TCCCTCATAATAATTTTCAGTAGCATC 57.493 33.333 0.00 0.00 0.00 3.91
2217 2259 9.512588 CTCCCTCATAATAATTTTCAGTAGCAT 57.487 33.333 0.00 0.00 0.00 3.79
2218 2260 7.939039 CCTCCCTCATAATAATTTTCAGTAGCA 59.061 37.037 0.00 0.00 0.00 3.49
2219 2261 8.157476 TCCTCCCTCATAATAATTTTCAGTAGC 58.843 37.037 0.00 0.00 0.00 3.58
2221 2263 9.847224 GTTCCTCCCTCATAATAATTTTCAGTA 57.153 33.333 0.00 0.00 0.00 2.74
2222 2264 8.336235 TGTTCCTCCCTCATAATAATTTTCAGT 58.664 33.333 0.00 0.00 0.00 3.41
2223 2265 8.752005 TGTTCCTCCCTCATAATAATTTTCAG 57.248 34.615 0.00 0.00 0.00 3.02
2227 2269 9.247861 GCATATGTTCCTCCCTCATAATAATTT 57.752 33.333 4.29 0.00 0.00 1.82
2228 2270 8.618385 AGCATATGTTCCTCCCTCATAATAATT 58.382 33.333 4.29 0.00 0.00 1.40
2229 2271 8.167691 AGCATATGTTCCTCCCTCATAATAAT 57.832 34.615 4.29 0.00 0.00 1.28
2230 2272 7.574021 AGCATATGTTCCTCCCTCATAATAA 57.426 36.000 4.29 0.00 0.00 1.40
2231 2273 7.017551 ACAAGCATATGTTCCTCCCTCATAATA 59.982 37.037 4.29 0.00 0.00 0.98
2232 2274 6.183361 ACAAGCATATGTTCCTCCCTCATAAT 60.183 38.462 4.29 0.00 0.00 1.28
2233 2275 5.132648 ACAAGCATATGTTCCTCCCTCATAA 59.867 40.000 4.29 0.00 0.00 1.90
2234 2276 4.660303 ACAAGCATATGTTCCTCCCTCATA 59.340 41.667 4.29 0.00 0.00 2.15
2235 2277 3.461085 ACAAGCATATGTTCCTCCCTCAT 59.539 43.478 4.29 0.00 0.00 2.90
2236 2278 2.846206 ACAAGCATATGTTCCTCCCTCA 59.154 45.455 4.29 0.00 0.00 3.86
2237 2279 3.567478 ACAAGCATATGTTCCTCCCTC 57.433 47.619 4.29 0.00 0.00 4.30
2238 2280 3.392616 CCTACAAGCATATGTTCCTCCCT 59.607 47.826 4.29 0.00 34.75 4.20
2239 2281 3.391296 TCCTACAAGCATATGTTCCTCCC 59.609 47.826 4.29 0.00 34.75 4.30
2240 2282 4.689612 TCCTACAAGCATATGTTCCTCC 57.310 45.455 4.29 0.00 34.75 4.30
2241 2283 6.514048 GCAATTCCTACAAGCATATGTTCCTC 60.514 42.308 4.29 0.00 34.75 3.71
2242 2284 5.300286 GCAATTCCTACAAGCATATGTTCCT 59.700 40.000 4.29 0.00 34.75 3.36
2243 2285 5.067674 TGCAATTCCTACAAGCATATGTTCC 59.932 40.000 4.29 0.00 34.75 3.62
2244 2286 6.135290 TGCAATTCCTACAAGCATATGTTC 57.865 37.500 4.29 0.00 34.75 3.18
2245 2287 6.528537 TTGCAATTCCTACAAGCATATGTT 57.471 33.333 4.29 0.00 34.87 2.71
2246 2288 6.720112 ATTGCAATTCCTACAAGCATATGT 57.280 33.333 5.99 0.00 34.87 2.29
2250 2292 9.081204 TGATATTATTGCAATTCCTACAAGCAT 57.919 29.630 18.75 2.59 34.87 3.79
2251 2293 8.462589 TGATATTATTGCAATTCCTACAAGCA 57.537 30.769 18.75 3.20 0.00 3.91
2252 2294 9.403110 CTTGATATTATTGCAATTCCTACAAGC 57.597 33.333 18.75 0.62 0.00 4.01
2256 2298 9.899226 GGAACTTGATATTATTGCAATTCCTAC 57.101 33.333 18.75 7.81 31.22 3.18
2257 2299 9.077885 GGGAACTTGATATTATTGCAATTCCTA 57.922 33.333 18.75 7.43 33.81 2.94
2258 2300 7.786464 AGGGAACTTGATATTATTGCAATTCCT 59.214 33.333 18.75 0.00 37.44 3.36
2259 2301 7.955918 AGGGAACTTGATATTATTGCAATTCC 58.044 34.615 18.75 14.12 37.44 3.01
2278 2320 4.957759 TTTAAGCGCATAGAAAGGGAAC 57.042 40.909 11.47 0.00 0.00 3.62
2279 2321 5.885912 AGATTTTAAGCGCATAGAAAGGGAA 59.114 36.000 11.47 0.00 0.00 3.97
2280 2322 5.437060 AGATTTTAAGCGCATAGAAAGGGA 58.563 37.500 11.47 0.00 0.00 4.20
2281 2323 5.757850 AGATTTTAAGCGCATAGAAAGGG 57.242 39.130 11.47 0.00 0.00 3.95
2282 2324 6.785191 TCAAGATTTTAAGCGCATAGAAAGG 58.215 36.000 11.47 0.00 0.00 3.11
2283 2325 7.965107 ACTTCAAGATTTTAAGCGCATAGAAAG 59.035 33.333 11.47 0.00 0.00 2.62
2284 2326 7.816640 ACTTCAAGATTTTAAGCGCATAGAAA 58.183 30.769 11.47 5.41 0.00 2.52
2285 2327 7.119116 TGACTTCAAGATTTTAAGCGCATAGAA 59.881 33.333 11.47 3.68 0.00 2.10
2286 2328 6.593770 TGACTTCAAGATTTTAAGCGCATAGA 59.406 34.615 11.47 0.00 0.00 1.98
2287 2329 6.775088 TGACTTCAAGATTTTAAGCGCATAG 58.225 36.000 11.47 0.00 0.00 2.23
2288 2330 6.735678 TGACTTCAAGATTTTAAGCGCATA 57.264 33.333 11.47 0.00 0.00 3.14
2289 2331 5.627499 TGACTTCAAGATTTTAAGCGCAT 57.373 34.783 11.47 0.00 0.00 4.73
2290 2332 5.393124 CATGACTTCAAGATTTTAAGCGCA 58.607 37.500 11.47 0.00 0.00 6.09
2291 2333 4.263911 GCATGACTTCAAGATTTTAAGCGC 59.736 41.667 0.00 0.00 0.00 5.92
2292 2334 5.634896 AGCATGACTTCAAGATTTTAAGCG 58.365 37.500 0.00 0.00 0.00 4.68
2293 2335 6.865205 ACAAGCATGACTTCAAGATTTTAAGC 59.135 34.615 0.00 0.00 36.04 3.09
2294 2336 8.807667 AACAAGCATGACTTCAAGATTTTAAG 57.192 30.769 0.00 0.00 36.04 1.85
2295 2337 9.598517 AAAACAAGCATGACTTCAAGATTTTAA 57.401 25.926 0.00 0.00 36.04 1.52
2296 2338 9.033481 CAAAACAAGCATGACTTCAAGATTTTA 57.967 29.630 0.00 0.00 36.04 1.52
2297 2339 7.466320 GCAAAACAAGCATGACTTCAAGATTTT 60.466 33.333 0.00 0.00 36.04 1.82
2298 2340 6.018507 GCAAAACAAGCATGACTTCAAGATTT 60.019 34.615 0.00 0.00 36.04 2.17
2299 2341 5.464389 GCAAAACAAGCATGACTTCAAGATT 59.536 36.000 0.00 0.00 36.04 2.40
2300 2342 4.986659 GCAAAACAAGCATGACTTCAAGAT 59.013 37.500 0.00 0.00 36.04 2.40
2301 2343 4.098349 AGCAAAACAAGCATGACTTCAAGA 59.902 37.500 0.00 0.00 36.04 3.02
2302 2344 4.365723 AGCAAAACAAGCATGACTTCAAG 58.634 39.130 0.00 0.00 36.04 3.02
2303 2345 4.389890 AGCAAAACAAGCATGACTTCAA 57.610 36.364 0.00 0.00 36.04 2.69
2304 2346 4.389890 AAGCAAAACAAGCATGACTTCA 57.610 36.364 0.00 0.00 36.04 3.02
2305 2347 4.209911 GGAAAGCAAAACAAGCATGACTTC 59.790 41.667 0.00 0.00 36.04 3.01
2306 2348 4.122046 GGAAAGCAAAACAAGCATGACTT 58.878 39.130 0.00 0.00 40.05 3.01
2307 2349 3.385755 AGGAAAGCAAAACAAGCATGACT 59.614 39.130 0.00 0.00 0.00 3.41
2308 2350 3.721035 AGGAAAGCAAAACAAGCATGAC 58.279 40.909 0.00 0.00 0.00 3.06
2309 2351 5.472148 CATAGGAAAGCAAAACAAGCATGA 58.528 37.500 0.00 0.00 0.00 3.07
2310 2352 4.092383 GCATAGGAAAGCAAAACAAGCATG 59.908 41.667 0.00 0.00 0.00 4.06
2311 2353 4.020839 AGCATAGGAAAGCAAAACAAGCAT 60.021 37.500 0.00 0.00 0.00 3.79
2312 2354 3.321682 AGCATAGGAAAGCAAAACAAGCA 59.678 39.130 0.00 0.00 0.00 3.91
2313 2355 3.917988 AGCATAGGAAAGCAAAACAAGC 58.082 40.909 0.00 0.00 0.00 4.01
2314 2356 6.259550 ACTAGCATAGGAAAGCAAAACAAG 57.740 37.500 0.00 0.00 44.97 3.16
2315 2357 6.264292 TCAACTAGCATAGGAAAGCAAAACAA 59.736 34.615 0.00 0.00 44.97 2.83
2316 2358 5.767665 TCAACTAGCATAGGAAAGCAAAACA 59.232 36.000 0.00 0.00 44.97 2.83
2317 2359 6.254281 TCAACTAGCATAGGAAAGCAAAAC 57.746 37.500 0.00 0.00 44.97 2.43
2318 2360 7.466746 AATCAACTAGCATAGGAAAGCAAAA 57.533 32.000 0.00 0.00 44.97 2.44
2319 2361 8.752005 ATAATCAACTAGCATAGGAAAGCAAA 57.248 30.769 0.00 0.00 44.97 3.68
2320 2362 8.752005 AATAATCAACTAGCATAGGAAAGCAA 57.248 30.769 0.00 0.00 44.97 3.91
2325 2367 9.959721 GGGAATAATAATCAACTAGCATAGGAA 57.040 33.333 0.00 0.00 44.97 3.36
2326 2368 9.111519 TGGGAATAATAATCAACTAGCATAGGA 57.888 33.333 0.00 0.00 44.97 2.94
2327 2369 9.911788 ATGGGAATAATAATCAACTAGCATAGG 57.088 33.333 0.00 0.00 44.97 2.57
2343 2385 8.538701 TGTGAGCAAACAATTTATGGGAATAAT 58.461 29.630 0.00 0.00 0.00 1.28
2344 2386 7.901029 TGTGAGCAAACAATTTATGGGAATAA 58.099 30.769 0.00 0.00 0.00 1.40
2345 2387 7.473735 TGTGAGCAAACAATTTATGGGAATA 57.526 32.000 0.00 0.00 0.00 1.75
2346 2388 6.357579 TGTGAGCAAACAATTTATGGGAAT 57.642 33.333 0.00 0.00 0.00 3.01
2347 2389 5.798125 TGTGAGCAAACAATTTATGGGAA 57.202 34.783 0.00 0.00 0.00 3.97
2348 2390 5.798125 TTGTGAGCAAACAATTTATGGGA 57.202 34.783 0.47 0.00 35.16 4.37
2349 2391 6.857777 TTTTGTGAGCAAACAATTTATGGG 57.142 33.333 5.21 0.00 43.47 4.00
2350 2392 7.361116 GGGATTTTGTGAGCAAACAATTTATGG 60.361 37.037 5.21 0.00 43.47 2.74
2351 2393 7.388500 AGGGATTTTGTGAGCAAACAATTTATG 59.612 33.333 5.21 0.00 43.47 1.90
2352 2394 7.452562 AGGGATTTTGTGAGCAAACAATTTAT 58.547 30.769 5.21 1.18 43.47 1.40
2353 2395 6.825610 AGGGATTTTGTGAGCAAACAATTTA 58.174 32.000 5.21 0.00 43.47 1.40
2354 2396 5.683681 AGGGATTTTGTGAGCAAACAATTT 58.316 33.333 5.21 0.00 43.47 1.82
2355 2397 5.294734 AGGGATTTTGTGAGCAAACAATT 57.705 34.783 5.21 0.00 43.47 2.32
2356 2398 4.961438 AGGGATTTTGTGAGCAAACAAT 57.039 36.364 5.21 0.00 43.47 2.71
2357 2399 5.782047 CATAGGGATTTTGTGAGCAAACAA 58.218 37.500 0.47 0.47 43.47 2.83
2358 2400 4.321899 GCATAGGGATTTTGTGAGCAAACA 60.322 41.667 0.00 0.00 43.47 2.83
2359 2401 4.176271 GCATAGGGATTTTGTGAGCAAAC 58.824 43.478 0.00 0.00 43.47 2.93
2360 2402 3.831333 TGCATAGGGATTTTGTGAGCAAA 59.169 39.130 0.00 0.00 42.25 3.68
2361 2403 3.429492 TGCATAGGGATTTTGTGAGCAA 58.571 40.909 0.00 0.00 0.00 3.91
2362 2404 3.084536 TGCATAGGGATTTTGTGAGCA 57.915 42.857 0.00 0.00 0.00 4.26
2363 2405 4.217118 CCTATGCATAGGGATTTTGTGAGC 59.783 45.833 36.06 0.00 44.97 4.26
2364 2406 5.954296 CCTATGCATAGGGATTTTGTGAG 57.046 43.478 36.06 12.91 44.97 3.51


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

AutoCloner maintained by Alex Coulton.