Multiple sequence alignment - TraesCS3A01G176100

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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 TraesCS3A01G176100 chr3A 100.000 2321 0 0 1 2321 196763260 196760940 0.000000e+00 4287
1 TraesCS3A01G176100 chr3A 87.266 267 32 2 1942 2207 743686131 743686396 1.040000e-78 303
2 TraesCS3A01G176100 chr3D 95.755 1225 45 6 882 2103 164546915 164545695 0.000000e+00 1967
3 TraesCS3A01G176100 chr3D 96.778 900 26 3 1 897 164547854 164546955 0.000000e+00 1498
4 TraesCS3A01G176100 chr3B 96.997 899 25 2 1 897 240532976 240532078 0.000000e+00 1509
5 TraesCS3A01G176100 chr3B 94.712 832 32 7 882 1709 240532038 240531215 0.000000e+00 1282
6 TraesCS3A01G176100 chr3B 85.926 270 36 2 1942 2210 564250197 564249929 1.050000e-73 287
7 TraesCS3A01G176100 chrUn 88.312 308 36 0 1007 1314 296339372 296339679 1.010000e-98 370
8 TraesCS3A01G176100 chr1B 88.525 305 35 0 1010 1314 21383951 21383647 1.010000e-98 370
9 TraesCS3A01G176100 chr1B 88.525 305 35 0 1010 1314 21390741 21390437 1.010000e-98 370
10 TraesCS3A01G176100 chr1B 87.869 305 37 0 1010 1314 21409318 21409014 2.190000e-95 359
11 TraesCS3A01G176100 chr6D 86.296 270 33 4 1942 2207 436730978 436730709 8.110000e-75 291
12 TraesCS3A01G176100 chr5A 85.932 263 36 1 1942 2203 410800620 410800882 1.760000e-71 279
13 TraesCS3A01G176100 chr4D 85.714 266 37 1 1939 2203 16920419 16920684 1.760000e-71 279
14 TraesCS3A01G176100 chr7A 85.606 264 37 1 1942 2204 176271806 176272069 2.270000e-70 276
15 TraesCS3A01G176100 chr2B 85.227 264 37 2 1942 2203 24511962 24512225 1.060000e-68 270
16 TraesCS3A01G176100 chr2B 79.167 192 36 4 1134 1323 100024867 100025056 1.870000e-26 130
17 TraesCS3A01G176100 chr2B 75.197 254 59 4 1082 1333 100030113 100029862 1.460000e-22 117
18 TraesCS3A01G176100 chr5B 84.502 271 41 1 1938 2207 430743950 430743680 1.370000e-67 267
19 TraesCS3A01G176100 chr1A 86.250 160 19 1 1165 1321 16093936 16094095 1.100000e-38 171
20 TraesCS3A01G176100 chr2D 78.421 190 39 2 1134 1322 64011106 64011294 3.130000e-24 122


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 TraesCS3A01G176100 chr3A 196760940 196763260 2320 True 4287.0 4287 100.0000 1 2321 1 chr3A.!!$R1 2320
1 TraesCS3A01G176100 chr3D 164545695 164547854 2159 True 1732.5 1967 96.2665 1 2103 2 chr3D.!!$R1 2102
2 TraesCS3A01G176100 chr3B 240531215 240532976 1761 True 1395.5 1509 95.8545 1 1709 2 chr3B.!!$R2 1708

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
907 966 0.459237 CCAGTGCTAGCTCGACCAAG 60.459 60.0 17.23 0.0 0.0 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1948 2012 0.10104 TACACTTATTCGCGGACGGG 59.899 55.0 6.13 2.09 40.63 5.28 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
93 95 4.813697 GGAAAAACAATGCTGCAAAAGGTA 59.186 37.500 6.36 0.00 0.00 3.08
160 162 1.139058 ACTGTATGGCGAGTGAATCCC 59.861 52.381 0.00 0.00 0.00 3.85
351 353 3.063997 CGCCATCAGTTAATGTCCTGTTC 59.936 47.826 0.00 0.00 0.00 3.18
498 501 5.776208 AGCTACCTACCTAGCTAGAATTTCC 59.224 44.000 22.70 3.64 46.35 3.13
596 599 5.445939 CGCGCACTACTCAAGTTTAATGAAT 60.446 40.000 8.75 0.00 35.76 2.57
637 640 1.683025 CCCATCCCTGTGCATGCAA 60.683 57.895 24.58 6.73 0.00 4.08
734 737 5.727135 GCGTATATCGACGTACTAATCACTG 59.273 44.000 0.00 0.00 44.74 3.66
771 774 5.050769 CGCAGTCGCATAAGAAATCTATGTT 60.051 40.000 0.00 0.00 38.40 2.71
822 825 3.578716 CTCTACCCCACACCATCGATAAT 59.421 47.826 0.00 0.00 0.00 1.28
907 966 0.459237 CCAGTGCTAGCTCGACCAAG 60.459 60.000 17.23 0.00 0.00 3.61
953 1012 4.524714 CCCTCAATCTCTAAGCCGATAGAA 59.475 45.833 0.00 0.00 39.76 2.10
1029 1090 0.253610 TGTGGGTGTTCAAGAACGGT 59.746 50.000 8.28 0.00 43.94 4.83
1230 1291 1.358402 CTGCCTCGACCTCATCTCG 59.642 63.158 0.00 0.00 0.00 4.04
1296 1357 2.609491 CGTCGTCATCAAGAACAGGGAA 60.609 50.000 0.00 0.00 0.00 3.97
1356 1417 1.955778 CCATGCAGTCTCTCGATCTCT 59.044 52.381 0.00 0.00 0.00 3.10
1364 1425 4.815846 CAGTCTCTCGATCTCTTCTCATCA 59.184 45.833 0.00 0.00 0.00 3.07
1475 1536 0.890683 GTGCCTGATTTGGTTGGGAG 59.109 55.000 0.00 0.00 0.00 4.30
1498 1559 3.319972 GTGTAGTGTGGTAGTGGAGTGAA 59.680 47.826 0.00 0.00 0.00 3.18
1513 1574 3.315418 GAGTGAACGAGGGTACTGTTTC 58.685 50.000 0.00 0.00 0.00 2.78
1637 1700 4.537135 AATTAGTGTCCGTGTGATGACT 57.463 40.909 0.00 0.00 32.67 3.41
1638 1701 5.654603 AATTAGTGTCCGTGTGATGACTA 57.345 39.130 0.00 0.00 32.67 2.59
1728 1791 5.317600 TGTTGCATGCCTAGGGAAATATA 57.682 39.130 16.68 0.00 0.00 0.86
1826 1890 6.767902 TGATGAAAACATAGGGAATAGACAGC 59.232 38.462 0.00 0.00 0.00 4.40
1836 1900 3.561313 GGGAATAGACAGCCACTCCAAAA 60.561 47.826 0.00 0.00 0.00 2.44
1876 1940 3.997021 GGGAATAATAGGCTGACACGATG 59.003 47.826 0.00 0.00 0.00 3.84
1948 2012 2.548480 GCAAGACAACCACTTACTCCAC 59.452 50.000 0.00 0.00 0.00 4.02
1994 2058 8.990163 TTCTACCTTTTGTCCTAAATCAAACT 57.010 30.769 0.00 0.00 34.05 2.66
1997 2061 9.463443 CTACCTTTTGTCCTAAATCAAACTTTG 57.537 33.333 0.00 0.00 34.05 2.77
2000 2065 9.377312 CCTTTTGTCCTAAATCAAACTTTGAAA 57.623 29.630 8.28 0.00 43.95 2.69
2087 2152 8.488651 AGGTACATTTTAAAACGGATCTACTG 57.511 34.615 1.97 0.00 0.00 2.74
2115 2180 8.980481 ACTAATTTAGTACCATAAATGCTGCT 57.020 30.769 7.31 0.00 37.23 4.24
2179 2244 8.671384 AACTTAGTACAAAAACTAGATGTGCA 57.329 30.769 0.00 0.00 33.62 4.57
2180 2245 8.848474 ACTTAGTACAAAAACTAGATGTGCAT 57.152 30.769 0.00 0.00 33.62 3.96
2181 2246 9.284968 ACTTAGTACAAAAACTAGATGTGCATT 57.715 29.630 0.00 0.00 33.62 3.56
2188 2253 9.762933 ACAAAAACTAGATGTGCATTTATTTGT 57.237 25.926 0.00 0.00 32.93 2.83
2190 2255 8.761575 AAAACTAGATGTGCATTTATTTGTGG 57.238 30.769 0.00 0.00 0.00 4.17
2191 2256 7.701539 AACTAGATGTGCATTTATTTGTGGA 57.298 32.000 0.00 0.00 0.00 4.02
2192 2257 7.088589 ACTAGATGTGCATTTATTTGTGGAC 57.911 36.000 0.00 0.00 37.22 4.02
2193 2258 4.985413 AGATGTGCATTTATTTGTGGACG 58.015 39.130 0.00 0.00 39.22 4.79
2194 2259 3.567576 TGTGCATTTATTTGTGGACGG 57.432 42.857 0.00 0.00 39.22 4.79
2195 2260 3.149981 TGTGCATTTATTTGTGGACGGA 58.850 40.909 0.00 0.00 39.22 4.69
2196 2261 3.190327 TGTGCATTTATTTGTGGACGGAG 59.810 43.478 0.00 0.00 39.22 4.63
2197 2262 2.752354 TGCATTTATTTGTGGACGGAGG 59.248 45.455 0.00 0.00 0.00 4.30
2198 2263 2.099098 GCATTTATTTGTGGACGGAGGG 59.901 50.000 0.00 0.00 0.00 4.30
2199 2264 3.616219 CATTTATTTGTGGACGGAGGGA 58.384 45.455 0.00 0.00 0.00 4.20
2200 2265 3.343941 TTTATTTGTGGACGGAGGGAG 57.656 47.619 0.00 0.00 0.00 4.30
2201 2266 1.946984 TATTTGTGGACGGAGGGAGT 58.053 50.000 0.00 0.00 0.00 3.85
2202 2267 1.946984 ATTTGTGGACGGAGGGAGTA 58.053 50.000 0.00 0.00 0.00 2.59
2203 2268 0.971386 TTTGTGGACGGAGGGAGTAC 59.029 55.000 0.00 0.00 0.00 2.73
2204 2269 0.113776 TTGTGGACGGAGGGAGTACT 59.886 55.000 0.00 0.00 0.00 2.73
2205 2270 0.113776 TGTGGACGGAGGGAGTACTT 59.886 55.000 0.00 0.00 0.00 2.24
2206 2271 1.264295 GTGGACGGAGGGAGTACTTT 58.736 55.000 0.00 0.00 0.00 2.66
2207 2272 1.067071 GTGGACGGAGGGAGTACTTTG 60.067 57.143 0.00 0.00 0.00 2.77
2208 2273 0.108281 GGACGGAGGGAGTACTTTGC 60.108 60.000 0.00 0.00 0.00 3.68
2209 2274 0.896226 GACGGAGGGAGTACTTTGCT 59.104 55.000 0.00 0.00 0.00 3.91
2210 2275 0.608640 ACGGAGGGAGTACTTTGCTG 59.391 55.000 0.00 0.00 0.00 4.41
2211 2276 0.108138 CGGAGGGAGTACTTTGCTGG 60.108 60.000 0.00 0.00 0.00 4.85
2212 2277 0.393132 GGAGGGAGTACTTTGCTGGC 60.393 60.000 0.00 0.00 0.00 4.85
2213 2278 0.324943 GAGGGAGTACTTTGCTGGCA 59.675 55.000 0.00 0.00 0.00 4.92
2214 2279 0.995024 AGGGAGTACTTTGCTGGCAT 59.005 50.000 0.00 0.00 0.00 4.40
2215 2280 1.065126 AGGGAGTACTTTGCTGGCATC 60.065 52.381 0.00 0.00 0.00 3.91
2216 2281 1.383523 GGAGTACTTTGCTGGCATCC 58.616 55.000 0.00 0.00 0.00 3.51
2217 2282 1.340017 GGAGTACTTTGCTGGCATCCA 60.340 52.381 0.00 0.00 0.00 3.41
2218 2283 2.436417 GAGTACTTTGCTGGCATCCAA 58.564 47.619 0.00 0.00 30.80 3.53
2219 2284 2.819608 GAGTACTTTGCTGGCATCCAAA 59.180 45.455 0.00 11.40 30.80 3.28
2220 2285 3.230134 AGTACTTTGCTGGCATCCAAAA 58.770 40.909 12.53 1.05 30.80 2.44
2221 2286 3.834231 AGTACTTTGCTGGCATCCAAAAT 59.166 39.130 12.53 7.22 30.80 1.82
2222 2287 3.775261 ACTTTGCTGGCATCCAAAATT 57.225 38.095 12.53 3.23 30.80 1.82
2223 2288 3.404899 ACTTTGCTGGCATCCAAAATTG 58.595 40.909 12.53 6.15 30.80 2.32
2224 2289 3.071312 ACTTTGCTGGCATCCAAAATTGA 59.929 39.130 12.53 0.00 30.80 2.57
2225 2290 3.766068 TTGCTGGCATCCAAAATTGAA 57.234 38.095 0.00 0.00 30.80 2.69
2226 2291 3.985019 TGCTGGCATCCAAAATTGAAT 57.015 38.095 0.00 0.00 30.80 2.57
2227 2292 3.864243 TGCTGGCATCCAAAATTGAATC 58.136 40.909 0.00 0.00 30.80 2.52
2228 2293 2.861935 GCTGGCATCCAAAATTGAATCG 59.138 45.455 0.00 0.00 30.80 3.34
2229 2294 2.861935 CTGGCATCCAAAATTGAATCGC 59.138 45.455 0.00 0.00 30.80 4.58
2230 2295 2.496871 TGGCATCCAAAATTGAATCGCT 59.503 40.909 0.00 0.00 0.00 4.93
2231 2296 2.861935 GGCATCCAAAATTGAATCGCTG 59.138 45.455 0.00 0.00 0.00 5.18
2232 2297 3.429272 GGCATCCAAAATTGAATCGCTGA 60.429 43.478 0.00 0.00 0.00 4.26
2233 2298 4.175516 GCATCCAAAATTGAATCGCTGAA 58.824 39.130 0.00 0.00 0.00 3.02
2234 2299 4.266976 GCATCCAAAATTGAATCGCTGAAG 59.733 41.667 0.00 0.00 0.00 3.02
2235 2300 3.836949 TCCAAAATTGAATCGCTGAAGC 58.163 40.909 0.00 0.00 37.78 3.86
2236 2301 3.507233 TCCAAAATTGAATCGCTGAAGCT 59.493 39.130 0.10 0.00 39.32 3.74
2237 2302 4.699735 TCCAAAATTGAATCGCTGAAGCTA 59.300 37.500 0.10 0.00 39.32 3.32
2238 2303 4.795278 CCAAAATTGAATCGCTGAAGCTAC 59.205 41.667 0.10 0.00 39.32 3.58
2239 2304 5.393124 CAAAATTGAATCGCTGAAGCTACA 58.607 37.500 0.10 0.00 39.32 2.74
2240 2305 4.871993 AATTGAATCGCTGAAGCTACAG 57.128 40.909 0.10 0.00 40.43 2.74
2251 2316 3.635510 GCTACAGCTACTGGGCCT 58.364 61.111 4.53 0.00 35.51 5.19
2252 2317 1.908483 GCTACAGCTACTGGGCCTT 59.092 57.895 4.53 0.00 35.51 4.35
2253 2318 0.179070 GCTACAGCTACTGGGCCTTC 60.179 60.000 4.53 0.00 35.51 3.46
2254 2319 0.103208 CTACAGCTACTGGGCCTTCG 59.897 60.000 4.53 0.00 35.51 3.79
2255 2320 0.613853 TACAGCTACTGGGCCTTCGT 60.614 55.000 4.53 1.72 35.51 3.85
2256 2321 1.296715 CAGCTACTGGGCCTTCGTT 59.703 57.895 4.53 0.00 0.00 3.85
2257 2322 0.321653 CAGCTACTGGGCCTTCGTTT 60.322 55.000 4.53 0.00 0.00 3.60
2258 2323 0.321653 AGCTACTGGGCCTTCGTTTG 60.322 55.000 4.53 0.00 0.00 2.93
2259 2324 0.321298 GCTACTGGGCCTTCGTTTGA 60.321 55.000 4.53 0.00 0.00 2.69
2260 2325 1.880646 GCTACTGGGCCTTCGTTTGAA 60.881 52.381 4.53 0.00 0.00 2.69
2261 2326 2.711542 CTACTGGGCCTTCGTTTGAAT 58.288 47.619 4.53 0.00 32.61 2.57
2262 2327 1.534729 ACTGGGCCTTCGTTTGAATC 58.465 50.000 4.53 0.00 32.61 2.52
2263 2328 1.202879 ACTGGGCCTTCGTTTGAATCA 60.203 47.619 4.53 0.00 32.61 2.57
2264 2329 1.200020 CTGGGCCTTCGTTTGAATCAC 59.800 52.381 4.53 0.00 32.61 3.06
2265 2330 0.526211 GGGCCTTCGTTTGAATCACC 59.474 55.000 0.84 0.00 32.61 4.02
2266 2331 1.243902 GGCCTTCGTTTGAATCACCA 58.756 50.000 0.00 0.00 32.61 4.17
2267 2332 1.068541 GGCCTTCGTTTGAATCACCAC 60.069 52.381 0.00 0.00 32.61 4.16
2268 2333 1.606668 GCCTTCGTTTGAATCACCACA 59.393 47.619 0.00 0.00 32.61 4.17
2269 2334 2.350772 GCCTTCGTTTGAATCACCACAG 60.351 50.000 0.00 0.00 32.61 3.66
2270 2335 3.138304 CCTTCGTTTGAATCACCACAGA 58.862 45.455 0.00 0.00 32.61 3.41
2271 2336 3.753272 CCTTCGTTTGAATCACCACAGAT 59.247 43.478 0.00 0.00 32.61 2.90
2272 2337 4.216257 CCTTCGTTTGAATCACCACAGATT 59.784 41.667 0.00 0.00 40.75 2.40
2273 2338 5.411361 CCTTCGTTTGAATCACCACAGATTA 59.589 40.000 0.00 0.00 38.30 1.75
2274 2339 6.072728 CCTTCGTTTGAATCACCACAGATTAA 60.073 38.462 0.00 0.00 38.30 1.40
2275 2340 6.236017 TCGTTTGAATCACCACAGATTAAC 57.764 37.500 0.00 0.00 38.30 2.01
2276 2341 5.760743 TCGTTTGAATCACCACAGATTAACA 59.239 36.000 0.00 0.00 38.30 2.41
2277 2342 6.429692 TCGTTTGAATCACCACAGATTAACAT 59.570 34.615 0.00 0.00 38.30 2.71
2278 2343 7.040755 TCGTTTGAATCACCACAGATTAACATT 60.041 33.333 0.00 0.00 38.30 2.71
2279 2344 7.594758 CGTTTGAATCACCACAGATTAACATTT 59.405 33.333 0.00 0.00 38.30 2.32
2280 2345 9.260002 GTTTGAATCACCACAGATTAACATTTT 57.740 29.630 0.00 0.00 38.30 1.82
2281 2346 8.815141 TTGAATCACCACAGATTAACATTTTG 57.185 30.769 0.00 0.00 38.30 2.44
2282 2347 8.175925 TGAATCACCACAGATTAACATTTTGA 57.824 30.769 0.00 0.00 38.30 2.69
2283 2348 8.298854 TGAATCACCACAGATTAACATTTTGAG 58.701 33.333 0.00 0.00 38.30 3.02
2284 2349 6.012658 TCACCACAGATTAACATTTTGAGC 57.987 37.500 0.00 0.00 0.00 4.26
2285 2350 5.048083 TCACCACAGATTAACATTTTGAGCC 60.048 40.000 0.00 0.00 0.00 4.70
2286 2351 4.832266 ACCACAGATTAACATTTTGAGCCA 59.168 37.500 0.00 0.00 0.00 4.75
2287 2352 5.163513 CCACAGATTAACATTTTGAGCCAC 58.836 41.667 0.00 0.00 0.00 5.01
2288 2353 5.278907 CCACAGATTAACATTTTGAGCCACA 60.279 40.000 0.00 0.00 0.00 4.17
2289 2354 5.860182 CACAGATTAACATTTTGAGCCACAG 59.140 40.000 0.00 0.00 0.00 3.66
2290 2355 5.536161 ACAGATTAACATTTTGAGCCACAGT 59.464 36.000 0.00 0.00 0.00 3.55
2291 2356 6.714810 ACAGATTAACATTTTGAGCCACAGTA 59.285 34.615 0.00 0.00 0.00 2.74
2292 2357 7.230510 ACAGATTAACATTTTGAGCCACAGTAA 59.769 33.333 0.00 0.00 0.00 2.24
2293 2358 7.752239 CAGATTAACATTTTGAGCCACAGTAAG 59.248 37.037 0.00 0.00 0.00 2.34
2294 2359 6.952773 TTAACATTTTGAGCCACAGTAAGT 57.047 33.333 0.00 0.00 0.00 2.24
2295 2360 8.630054 ATTAACATTTTGAGCCACAGTAAGTA 57.370 30.769 0.00 0.00 0.00 2.24
2296 2361 5.941948 ACATTTTGAGCCACAGTAAGTAC 57.058 39.130 0.00 0.00 0.00 2.73
2297 2362 5.373222 ACATTTTGAGCCACAGTAAGTACA 58.627 37.500 0.00 0.00 0.00 2.90
2298 2363 6.003950 ACATTTTGAGCCACAGTAAGTACAT 58.996 36.000 0.00 0.00 0.00 2.29
2299 2364 5.940192 TTTTGAGCCACAGTAAGTACATG 57.060 39.130 0.00 0.00 0.00 3.21
2300 2365 2.972625 TGAGCCACAGTAAGTACATGC 58.027 47.619 0.00 0.00 0.00 4.06
2301 2366 2.567169 TGAGCCACAGTAAGTACATGCT 59.433 45.455 0.00 0.00 0.00 3.79
2302 2367 3.007940 TGAGCCACAGTAAGTACATGCTT 59.992 43.478 0.00 0.00 0.00 3.91
2303 2368 3.600388 AGCCACAGTAAGTACATGCTTC 58.400 45.455 0.00 0.00 0.00 3.86
2304 2369 2.348666 GCCACAGTAAGTACATGCTTCG 59.651 50.000 0.00 0.00 0.00 3.79
2305 2370 3.585862 CCACAGTAAGTACATGCTTCGT 58.414 45.455 0.00 0.00 0.00 3.85
2306 2371 3.612860 CCACAGTAAGTACATGCTTCGTC 59.387 47.826 0.00 0.00 0.00 4.20
2307 2372 4.234574 CACAGTAAGTACATGCTTCGTCA 58.765 43.478 0.00 0.00 0.00 4.35
2308 2373 4.090066 CACAGTAAGTACATGCTTCGTCAC 59.910 45.833 0.00 0.00 0.00 3.67
2309 2374 4.234574 CAGTAAGTACATGCTTCGTCACA 58.765 43.478 0.00 0.00 0.00 3.58
2310 2375 4.684242 CAGTAAGTACATGCTTCGTCACAA 59.316 41.667 0.00 0.00 0.00 3.33
2311 2376 5.176774 CAGTAAGTACATGCTTCGTCACAAA 59.823 40.000 0.00 0.00 0.00 2.83
2312 2377 5.932303 AGTAAGTACATGCTTCGTCACAAAT 59.068 36.000 0.00 0.00 0.00 2.32
2313 2378 5.689383 AAGTACATGCTTCGTCACAAATT 57.311 34.783 0.00 0.00 0.00 1.82
2314 2379 5.283060 AGTACATGCTTCGTCACAAATTC 57.717 39.130 0.00 0.00 0.00 2.17
2315 2380 3.187478 ACATGCTTCGTCACAAATTCG 57.813 42.857 0.00 0.00 0.00 3.34
2316 2381 2.095768 ACATGCTTCGTCACAAATTCGG 60.096 45.455 0.00 0.00 0.00 4.30
2317 2382 0.237235 TGCTTCGTCACAAATTCGGC 59.763 50.000 0.00 0.00 0.00 5.54
2318 2383 0.454452 GCTTCGTCACAAATTCGGCC 60.454 55.000 0.00 0.00 0.00 6.13
2319 2384 0.168128 CTTCGTCACAAATTCGGCCC 59.832 55.000 0.00 0.00 0.00 5.80
2320 2385 0.535328 TTCGTCACAAATTCGGCCCA 60.535 50.000 0.00 0.00 0.00 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 0.035598 TTTCTGGCCGGTCGATCAAA 59.964 50.000 12.43 0.08 0.00 2.69
93 95 6.520272 AGAAATATGAGAGCTATCTTTGCGT 58.480 36.000 10.18 0.00 35.30 5.24
160 162 3.872459 AGCCTAATTCTCAGGGGAATG 57.128 47.619 0.00 0.00 36.24 2.67
214 216 1.899814 TGTTGTGCGAGGAATCCTACT 59.100 47.619 0.00 0.00 31.76 2.57
268 270 2.221981 GCGTAATCTATGGCTTGAGCAC 59.778 50.000 5.24 0.00 44.36 4.40
637 640 1.209019 CAGGAAGATGCTGTAGCTGGT 59.791 52.381 5.38 0.00 42.66 4.00
734 737 2.852748 CGACTGCGATACTATACTGCC 58.147 52.381 0.00 0.00 40.82 4.85
822 825 2.435805 GGTGGATGTGGATGAAGCTAGA 59.564 50.000 0.00 0.00 0.00 2.43
907 966 5.739161 GGAAAACAAACGATAGATGATGCAC 59.261 40.000 0.00 0.00 41.38 4.57
953 1012 2.541466 CTACCCCTCAACTCTCACCTT 58.459 52.381 0.00 0.00 0.00 3.50
1230 1291 1.002011 GTTGAAGTCCCTGGGGAGC 60.002 63.158 14.00 3.81 46.16 4.70
1296 1357 3.129502 TCGACGACGCGGAAGGAT 61.130 61.111 12.47 0.00 39.58 3.24
1475 1536 2.029290 CACTCCACTACCACACTACACC 60.029 54.545 0.00 0.00 0.00 4.16
1498 1559 1.045407 TGCAGAAACAGTACCCTCGT 58.955 50.000 0.00 0.00 0.00 4.18
1697 1760 2.413963 GCATGCAACATGGCCGGTA 61.414 57.895 14.21 0.00 0.00 4.02
1788 1852 0.404040 TTCATCAGAACCCCCACACC 59.596 55.000 0.00 0.00 0.00 4.16
1795 1859 4.855340 TCCCTATGTTTTCATCAGAACCC 58.145 43.478 0.00 0.00 41.25 4.11
1855 1919 4.883083 TCATCGTGTCAGCCTATTATTCC 58.117 43.478 0.00 0.00 0.00 3.01
1897 1961 7.652105 GCATCAGTCGGTCTAAATATTTGTCTA 59.348 37.037 11.05 0.00 0.00 2.59
1914 1978 1.134995 TGTCTTGCCTAGCATCAGTCG 60.135 52.381 0.00 0.00 38.76 4.18
1948 2012 0.101040 TACACTTATTCGCGGACGGG 59.899 55.000 6.13 2.09 40.63 5.28
2063 2128 8.483307 TCAGTAGATCCGTTTTAAAATGTACC 57.517 34.615 16.89 6.98 0.00 3.34
2153 2218 9.767228 TGCACATCTAGTTTTTGTACTAAGTTA 57.233 29.630 0.00 0.00 30.63 2.24
2154 2219 8.671384 TGCACATCTAGTTTTTGTACTAAGTT 57.329 30.769 0.00 0.00 30.63 2.66
2155 2220 8.848474 ATGCACATCTAGTTTTTGTACTAAGT 57.152 30.769 0.00 0.00 30.63 2.24
2162 2227 9.762933 ACAAATAAATGCACATCTAGTTTTTGT 57.237 25.926 0.00 0.00 0.00 2.83
2164 2229 9.206870 CCACAAATAAATGCACATCTAGTTTTT 57.793 29.630 0.00 0.00 0.00 1.94
2165 2230 8.584157 TCCACAAATAAATGCACATCTAGTTTT 58.416 29.630 0.00 0.00 0.00 2.43
2166 2231 8.028938 GTCCACAAATAAATGCACATCTAGTTT 58.971 33.333 0.00 0.00 0.00 2.66
2167 2232 7.538575 GTCCACAAATAAATGCACATCTAGTT 58.461 34.615 0.00 0.00 0.00 2.24
2168 2233 6.183360 CGTCCACAAATAAATGCACATCTAGT 60.183 38.462 0.00 0.00 0.00 2.57
2169 2234 6.194463 CGTCCACAAATAAATGCACATCTAG 58.806 40.000 0.00 0.00 0.00 2.43
2170 2235 5.065859 CCGTCCACAAATAAATGCACATCTA 59.934 40.000 0.00 0.00 0.00 1.98
2171 2236 4.142403 CCGTCCACAAATAAATGCACATCT 60.142 41.667 0.00 0.00 0.00 2.90
2172 2237 4.104776 CCGTCCACAAATAAATGCACATC 58.895 43.478 0.00 0.00 0.00 3.06
2173 2238 3.761218 TCCGTCCACAAATAAATGCACAT 59.239 39.130 0.00 0.00 0.00 3.21
2174 2239 3.149981 TCCGTCCACAAATAAATGCACA 58.850 40.909 0.00 0.00 0.00 4.57
2175 2240 3.427503 CCTCCGTCCACAAATAAATGCAC 60.428 47.826 0.00 0.00 0.00 4.57
2176 2241 2.752354 CCTCCGTCCACAAATAAATGCA 59.248 45.455 0.00 0.00 0.00 3.96
2177 2242 2.099098 CCCTCCGTCCACAAATAAATGC 59.901 50.000 0.00 0.00 0.00 3.56
2178 2243 3.616219 TCCCTCCGTCCACAAATAAATG 58.384 45.455 0.00 0.00 0.00 2.32
2179 2244 3.265995 ACTCCCTCCGTCCACAAATAAAT 59.734 43.478 0.00 0.00 0.00 1.40
2180 2245 2.640826 ACTCCCTCCGTCCACAAATAAA 59.359 45.455 0.00 0.00 0.00 1.40
2181 2246 2.262637 ACTCCCTCCGTCCACAAATAA 58.737 47.619 0.00 0.00 0.00 1.40
2182 2247 1.946984 ACTCCCTCCGTCCACAAATA 58.053 50.000 0.00 0.00 0.00 1.40
2183 2248 1.553704 GTACTCCCTCCGTCCACAAAT 59.446 52.381 0.00 0.00 0.00 2.32
2184 2249 0.971386 GTACTCCCTCCGTCCACAAA 59.029 55.000 0.00 0.00 0.00 2.83
2185 2250 0.113776 AGTACTCCCTCCGTCCACAA 59.886 55.000 0.00 0.00 0.00 3.33
2186 2251 0.113776 AAGTACTCCCTCCGTCCACA 59.886 55.000 0.00 0.00 0.00 4.17
2187 2252 1.067071 CAAAGTACTCCCTCCGTCCAC 60.067 57.143 0.00 0.00 0.00 4.02
2188 2253 1.263356 CAAAGTACTCCCTCCGTCCA 58.737 55.000 0.00 0.00 0.00 4.02
2189 2254 0.108281 GCAAAGTACTCCCTCCGTCC 60.108 60.000 0.00 0.00 0.00 4.79
2190 2255 0.896226 AGCAAAGTACTCCCTCCGTC 59.104 55.000 0.00 0.00 0.00 4.79
2191 2256 0.608640 CAGCAAAGTACTCCCTCCGT 59.391 55.000 0.00 0.00 0.00 4.69
2192 2257 0.108138 CCAGCAAAGTACTCCCTCCG 60.108 60.000 0.00 0.00 0.00 4.63
2193 2258 0.393132 GCCAGCAAAGTACTCCCTCC 60.393 60.000 0.00 0.00 0.00 4.30
2194 2259 0.324943 TGCCAGCAAAGTACTCCCTC 59.675 55.000 0.00 0.00 0.00 4.30
2195 2260 0.995024 ATGCCAGCAAAGTACTCCCT 59.005 50.000 0.00 0.00 0.00 4.20
2196 2261 1.383523 GATGCCAGCAAAGTACTCCC 58.616 55.000 0.00 0.00 0.00 4.30
2197 2262 1.340017 TGGATGCCAGCAAAGTACTCC 60.340 52.381 0.00 0.00 0.00 3.85
2198 2263 2.113860 TGGATGCCAGCAAAGTACTC 57.886 50.000 0.00 0.00 0.00 2.59
2199 2264 2.584835 TTGGATGCCAGCAAAGTACT 57.415 45.000 0.00 0.00 33.81 2.73
2200 2265 3.658757 TTTTGGATGCCAGCAAAGTAC 57.341 42.857 0.00 0.00 33.81 2.73
2201 2266 4.282957 TCAATTTTGGATGCCAGCAAAGTA 59.717 37.500 0.00 0.00 33.81 2.24
2202 2267 3.071312 TCAATTTTGGATGCCAGCAAAGT 59.929 39.130 0.00 0.00 33.81 2.66
2203 2268 3.666274 TCAATTTTGGATGCCAGCAAAG 58.334 40.909 0.00 0.00 33.81 2.77
2204 2269 3.766068 TCAATTTTGGATGCCAGCAAA 57.234 38.095 0.00 0.00 33.81 3.68
2205 2270 3.766068 TTCAATTTTGGATGCCAGCAA 57.234 38.095 0.00 0.00 33.81 3.91
2206 2271 3.676598 CGATTCAATTTTGGATGCCAGCA 60.677 43.478 0.00 0.00 33.81 4.41
2207 2272 2.861935 CGATTCAATTTTGGATGCCAGC 59.138 45.455 0.00 0.00 33.81 4.85
2208 2273 2.861935 GCGATTCAATTTTGGATGCCAG 59.138 45.455 0.00 0.00 33.81 4.85
2209 2274 2.496871 AGCGATTCAATTTTGGATGCCA 59.503 40.909 0.00 0.00 0.00 4.92
2210 2275 2.861935 CAGCGATTCAATTTTGGATGCC 59.138 45.455 0.00 0.00 0.00 4.40
2211 2276 3.772932 TCAGCGATTCAATTTTGGATGC 58.227 40.909 0.00 0.00 0.00 3.91
2212 2277 4.266976 GCTTCAGCGATTCAATTTTGGATG 59.733 41.667 0.00 0.00 0.00 3.51
2213 2278 4.427312 GCTTCAGCGATTCAATTTTGGAT 58.573 39.130 0.00 0.00 0.00 3.41
2214 2279 3.836949 GCTTCAGCGATTCAATTTTGGA 58.163 40.909 0.00 0.00 0.00 3.53
2234 2299 0.179070 GAAGGCCCAGTAGCTGTAGC 60.179 60.000 0.00 0.00 42.49 3.58
2235 2300 0.103208 CGAAGGCCCAGTAGCTGTAG 59.897 60.000 0.00 0.00 0.00 2.74
2236 2301 0.613853 ACGAAGGCCCAGTAGCTGTA 60.614 55.000 0.00 0.00 0.00 2.74
2237 2302 1.481056 AACGAAGGCCCAGTAGCTGT 61.481 55.000 0.00 0.00 0.00 4.40
2238 2303 0.321653 AAACGAAGGCCCAGTAGCTG 60.322 55.000 0.00 0.00 0.00 4.24
2239 2304 0.321653 CAAACGAAGGCCCAGTAGCT 60.322 55.000 0.00 0.00 0.00 3.32
2240 2305 0.321298 TCAAACGAAGGCCCAGTAGC 60.321 55.000 0.00 0.00 0.00 3.58
2241 2306 2.178912 TTCAAACGAAGGCCCAGTAG 57.821 50.000 0.00 0.00 0.00 2.57
2242 2307 2.039216 TGATTCAAACGAAGGCCCAGTA 59.961 45.455 0.00 0.00 0.00 2.74
2243 2308 1.202879 TGATTCAAACGAAGGCCCAGT 60.203 47.619 0.00 0.00 0.00 4.00
2244 2309 1.200020 GTGATTCAAACGAAGGCCCAG 59.800 52.381 0.00 0.00 0.00 4.45
2245 2310 1.243902 GTGATTCAAACGAAGGCCCA 58.756 50.000 0.00 0.00 0.00 5.36
2246 2311 0.526211 GGTGATTCAAACGAAGGCCC 59.474 55.000 0.00 0.00 0.00 5.80
2247 2312 1.068541 GTGGTGATTCAAACGAAGGCC 60.069 52.381 0.00 0.00 0.00 5.19
2248 2313 1.606668 TGTGGTGATTCAAACGAAGGC 59.393 47.619 0.00 0.00 0.00 4.35
2249 2314 3.138304 TCTGTGGTGATTCAAACGAAGG 58.862 45.455 0.00 0.00 0.00 3.46
2250 2315 5.362556 AATCTGTGGTGATTCAAACGAAG 57.637 39.130 0.00 0.00 31.72 3.79
2251 2316 6.261158 TGTTAATCTGTGGTGATTCAAACGAA 59.739 34.615 0.00 0.00 37.73 3.85
2252 2317 5.760743 TGTTAATCTGTGGTGATTCAAACGA 59.239 36.000 0.00 0.00 37.73 3.85
2253 2318 5.996219 TGTTAATCTGTGGTGATTCAAACG 58.004 37.500 0.00 0.00 37.73 3.60
2254 2319 8.816640 AAATGTTAATCTGTGGTGATTCAAAC 57.183 30.769 0.00 0.00 37.73 2.93
2255 2320 9.258826 CAAAATGTTAATCTGTGGTGATTCAAA 57.741 29.630 0.00 0.00 37.73 2.69
2256 2321 8.637099 TCAAAATGTTAATCTGTGGTGATTCAA 58.363 29.630 0.00 0.00 37.73 2.69
2257 2322 8.175925 TCAAAATGTTAATCTGTGGTGATTCA 57.824 30.769 0.00 0.00 37.73 2.57
2258 2323 7.274250 GCTCAAAATGTTAATCTGTGGTGATTC 59.726 37.037 0.00 0.00 37.73 2.52
2259 2324 7.092716 GCTCAAAATGTTAATCTGTGGTGATT 58.907 34.615 0.00 0.00 39.63 2.57
2260 2325 6.350445 GGCTCAAAATGTTAATCTGTGGTGAT 60.350 38.462 0.00 0.00 0.00 3.06
2261 2326 5.048083 GGCTCAAAATGTTAATCTGTGGTGA 60.048 40.000 0.00 0.00 0.00 4.02
2262 2327 5.163513 GGCTCAAAATGTTAATCTGTGGTG 58.836 41.667 0.00 0.00 0.00 4.17
2263 2328 4.832266 TGGCTCAAAATGTTAATCTGTGGT 59.168 37.500 0.00 0.00 0.00 4.16
2264 2329 5.163513 GTGGCTCAAAATGTTAATCTGTGG 58.836 41.667 0.00 0.00 0.00 4.17
2265 2330 5.771469 TGTGGCTCAAAATGTTAATCTGTG 58.229 37.500 0.00 0.00 0.00 3.66
2266 2331 5.536161 ACTGTGGCTCAAAATGTTAATCTGT 59.464 36.000 0.00 0.00 0.00 3.41
2267 2332 6.017400 ACTGTGGCTCAAAATGTTAATCTG 57.983 37.500 0.00 0.00 0.00 2.90
2268 2333 7.448469 ACTTACTGTGGCTCAAAATGTTAATCT 59.552 33.333 0.00 0.00 0.00 2.40
2269 2334 7.593825 ACTTACTGTGGCTCAAAATGTTAATC 58.406 34.615 0.00 0.00 0.00 1.75
2270 2335 7.524717 ACTTACTGTGGCTCAAAATGTTAAT 57.475 32.000 0.00 0.00 0.00 1.40
2271 2336 6.952773 ACTTACTGTGGCTCAAAATGTTAA 57.047 33.333 0.00 0.00 0.00 2.01
2272 2337 6.993308 TGTACTTACTGTGGCTCAAAATGTTA 59.007 34.615 0.00 0.00 0.00 2.41
2273 2338 5.825679 TGTACTTACTGTGGCTCAAAATGTT 59.174 36.000 0.00 0.00 0.00 2.71
2274 2339 5.373222 TGTACTTACTGTGGCTCAAAATGT 58.627 37.500 0.00 0.00 0.00 2.71
2275 2340 5.940192 TGTACTTACTGTGGCTCAAAATG 57.060 39.130 0.00 0.00 0.00 2.32
2276 2341 5.106157 GCATGTACTTACTGTGGCTCAAAAT 60.106 40.000 0.00 0.00 0.00 1.82
2277 2342 4.215399 GCATGTACTTACTGTGGCTCAAAA 59.785 41.667 0.00 0.00 0.00 2.44
2278 2343 3.751175 GCATGTACTTACTGTGGCTCAAA 59.249 43.478 0.00 0.00 0.00 2.69
2279 2344 3.007940 AGCATGTACTTACTGTGGCTCAA 59.992 43.478 0.00 0.00 0.00 3.02
2280 2345 2.567169 AGCATGTACTTACTGTGGCTCA 59.433 45.455 0.00 0.00 0.00 4.26
2281 2346 3.252974 AGCATGTACTTACTGTGGCTC 57.747 47.619 0.00 0.00 0.00 4.70
2282 2347 3.600388 GAAGCATGTACTTACTGTGGCT 58.400 45.455 0.00 0.00 0.00 4.75
2283 2348 2.348666 CGAAGCATGTACTTACTGTGGC 59.651 50.000 0.00 0.00 0.00 5.01
2284 2349 3.585862 ACGAAGCATGTACTTACTGTGG 58.414 45.455 0.00 0.00 0.00 4.17
2285 2350 4.090066 GTGACGAAGCATGTACTTACTGTG 59.910 45.833 0.00 0.00 0.00 3.66
2286 2351 4.235360 GTGACGAAGCATGTACTTACTGT 58.765 43.478 0.00 0.00 0.00 3.55
2287 2352 4.234574 TGTGACGAAGCATGTACTTACTG 58.765 43.478 0.00 0.00 0.00 2.74
2288 2353 4.514781 TGTGACGAAGCATGTACTTACT 57.485 40.909 0.00 0.00 0.00 2.24
2289 2354 5.585500 TTTGTGACGAAGCATGTACTTAC 57.415 39.130 0.00 0.00 0.00 2.34
2290 2355 6.400621 CGAATTTGTGACGAAGCATGTACTTA 60.401 38.462 0.00 0.00 0.00 2.24
2291 2356 5.614668 CGAATTTGTGACGAAGCATGTACTT 60.615 40.000 0.00 0.00 0.00 2.24
2292 2357 4.143115 CGAATTTGTGACGAAGCATGTACT 60.143 41.667 0.00 0.00 0.00 2.73
2293 2358 4.081761 CGAATTTGTGACGAAGCATGTAC 58.918 43.478 0.00 0.00 0.00 2.90
2294 2359 3.124466 CCGAATTTGTGACGAAGCATGTA 59.876 43.478 0.00 0.00 0.00 2.29
2295 2360 2.095768 CCGAATTTGTGACGAAGCATGT 60.096 45.455 0.00 0.00 0.00 3.21
2296 2361 2.508867 CCGAATTTGTGACGAAGCATG 58.491 47.619 0.00 0.00 0.00 4.06
2297 2362 1.135689 GCCGAATTTGTGACGAAGCAT 60.136 47.619 0.00 0.00 0.00 3.79
2298 2363 0.237235 GCCGAATTTGTGACGAAGCA 59.763 50.000 0.00 0.00 0.00 3.91
2299 2364 0.454452 GGCCGAATTTGTGACGAAGC 60.454 55.000 0.00 0.00 0.00 3.86
2300 2365 0.168128 GGGCCGAATTTGTGACGAAG 59.832 55.000 0.00 0.00 0.00 3.79
2301 2366 0.535328 TGGGCCGAATTTGTGACGAA 60.535 50.000 0.00 0.00 0.00 3.85
2302 2367 1.071642 TGGGCCGAATTTGTGACGA 59.928 52.632 0.00 0.00 0.00 4.20
2303 2368 3.661911 TGGGCCGAATTTGTGACG 58.338 55.556 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.