Multiple sequence alignment - TraesCS6B01G224300

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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 TraesCS6B01G224300 chr6B 100.000 2375 0 0 1 2375 341711179 341713553 0.000000e+00 4386
1 TraesCS6B01G224300 chr7B 95.720 2126 85 6 1 2125 399160588 399158468 0.000000e+00 3417
2 TraesCS6B01G224300 chr2B 95.292 2124 96 4 1 2123 395605871 395607991 0.000000e+00 3365
3 TraesCS6B01G224300 chr2B 95.245 2124 97 3 1 2123 345617192 345619312 0.000000e+00 3360
4 TraesCS6B01G224300 chr2B 95.153 2125 98 5 1 2125 591550329 591548210 0.000000e+00 3349
5 TraesCS6B01G224300 chr2B 94.969 2127 102 5 1 2125 71511858 71509735 0.000000e+00 3330
6 TraesCS6B01G224300 chr2B 94.640 2127 103 8 2 2122 294407554 294409675 0.000000e+00 3286
7 TraesCS6B01G224300 chr2B 99.603 252 1 0 2124 2375 576546936 576547187 5.980000e-126 460
8 TraesCS6B01G224300 chr3B 95.200 2125 97 5 1 2122 461815334 461817456 0.000000e+00 3354
9 TraesCS6B01G224300 chr5D 95.110 2127 100 4 1 2125 372676872 372674748 0.000000e+00 3349
10 TraesCS6B01G224300 chr4B 94.729 2125 106 6 1 2122 300655041 300657162 0.000000e+00 3299
11 TraesCS6B01G224300 chr4B 99.602 251 1 0 2125 2375 368296658 368296408 2.150000e-125 459
12 TraesCS6B01G224300 chr4A 99.603 252 1 0 2124 2375 572174411 572174662 5.980000e-126 460
13 TraesCS6B01G224300 chr3A 99.603 252 1 0 2124 2375 315498238 315498489 5.980000e-126 460
14 TraesCS6B01G224300 chr7A 99.216 255 1 1 2122 2375 102681887 102681633 2.150000e-125 459
15 TraesCS6B01G224300 chr6A 99.602 251 1 0 2125 2375 398578529 398578779 2.150000e-125 459
16 TraesCS6B01G224300 chr2A 99.216 255 1 1 2121 2375 644999102 644999355 2.150000e-125 459
17 TraesCS6B01G224300 chr1B 99.602 251 1 0 2125 2375 14710931 14710681 2.150000e-125 459
18 TraesCS6B01G224300 chr1B 99.602 251 1 0 2125 2375 124025381 124025131 2.150000e-125 459


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 TraesCS6B01G224300 chr6B 341711179 341713553 2374 False 4386 4386 100.000 1 2375 1 chr6B.!!$F1 2374
1 TraesCS6B01G224300 chr7B 399158468 399160588 2120 True 3417 3417 95.720 1 2125 1 chr7B.!!$R1 2124
2 TraesCS6B01G224300 chr2B 395605871 395607991 2120 False 3365 3365 95.292 1 2123 1 chr2B.!!$F3 2122
3 TraesCS6B01G224300 chr2B 345617192 345619312 2120 False 3360 3360 95.245 1 2123 1 chr2B.!!$F2 2122
4 TraesCS6B01G224300 chr2B 591548210 591550329 2119 True 3349 3349 95.153 1 2125 1 chr2B.!!$R2 2124
5 TraesCS6B01G224300 chr2B 71509735 71511858 2123 True 3330 3330 94.969 1 2125 1 chr2B.!!$R1 2124
6 TraesCS6B01G224300 chr2B 294407554 294409675 2121 False 3286 3286 94.640 2 2122 1 chr2B.!!$F1 2120
7 TraesCS6B01G224300 chr3B 461815334 461817456 2122 False 3354 3354 95.200 1 2122 1 chr3B.!!$F1 2121
8 TraesCS6B01G224300 chr5D 372674748 372676872 2124 True 3349 3349 95.110 1 2125 1 chr5D.!!$R1 2124
9 TraesCS6B01G224300 chr4B 300655041 300657162 2121 False 3299 3299 94.729 1 2122 1 chr4B.!!$F1 2121

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
312 313 2.40805 CTCTGCTAGTTGTCAGCGTTT 58.592 47.619 0.0 0.0 42.13 3.6 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2182 2198 0.041238 TCTTCCCGTGAGTCCCTGAT 59.959 55.0 0.0 0.0 0.0 2.9 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
312 313 2.408050 CTCTGCTAGTTGTCAGCGTTT 58.592 47.619 0.00 0.00 42.13 3.60
331 332 5.840267 GCGTTTGTTTGCATTATTTTGTCAG 59.160 36.000 0.00 0.00 0.00 3.51
470 474 3.588842 AGGGAGGACATCAAGTGAATTCA 59.411 43.478 3.38 3.38 0.00 2.57
575 580 7.516627 GCTTGATGTTTGTACAAATTGGTGTTC 60.517 37.037 23.11 8.99 37.91 3.18
753 760 2.837591 TGAGCTTATGGTTGGAGCACTA 59.162 45.455 0.00 0.00 38.85 2.74
827 835 7.667043 ACGAGCATAGTCAAACTTCATTTTA 57.333 32.000 0.00 0.00 0.00 1.52
938 949 2.822561 TGAGCTTTGATCAGAGACGTCT 59.177 45.455 20.18 20.18 0.00 4.18
967 978 3.987868 GTCTGAAACACAATCGCAGTCTA 59.012 43.478 0.00 0.00 0.00 2.59
1007 1018 4.289672 AGTTACACAGGATTGGATGGTCTT 59.710 41.667 0.00 0.00 0.00 3.01
1029 1040 4.574892 TGGAACAGCTTCGTCAATATGAA 58.425 39.130 0.00 0.00 0.00 2.57
1217 1228 4.988716 ACCTCGGCGGAGTCCACA 62.989 66.667 18.79 0.00 38.70 4.17
1319 1330 2.684943 TGTCACTGAAGGTCCCAACTA 58.315 47.619 0.00 0.00 0.00 2.24
1367 1378 6.065976 TGATTATGTGAAGGGTGTTCATCT 57.934 37.500 0.00 0.00 0.00 2.90
1377 1388 4.160329 AGGGTGTTCATCTCTTGTAGACA 58.840 43.478 0.00 0.00 36.93 3.41
1411 1422 5.783360 TGGTTCATCTAAGAGTCTACCCAAA 59.217 40.000 0.00 0.00 0.00 3.28
1419 1430 1.071814 GTCTACCCAAACGTGCCCA 59.928 57.895 0.00 0.00 0.00 5.36
1664 1679 7.331026 AGATGATTCTCGATTTAACAAGACCA 58.669 34.615 0.00 0.00 0.00 4.02
1685 1700 2.005370 ACGGTTGTCTCTTCCCACTA 57.995 50.000 0.00 0.00 0.00 2.74
1786 1801 7.857734 TCTGACAGTAAAGAAAAATGTGTCA 57.142 32.000 1.59 0.00 40.26 3.58
1925 1940 2.168521 CCTATGGGACGTCACACTTCAT 59.831 50.000 25.38 9.63 33.58 2.57
1960 1975 2.033407 CAGCGGTCATGATGAATCGTTC 60.033 50.000 16.68 5.57 31.22 3.95
2069 2085 7.125659 TGGAGGAAGATGATTATGTGACTGTTA 59.874 37.037 0.00 0.00 0.00 2.41
2078 2094 7.390823 TGATTATGTGACTGTTAACCTTGCTA 58.609 34.615 2.48 0.00 0.00 3.49
2125 2141 0.469144 AGAATTTGTTGTGCCCCGGT 60.469 50.000 0.00 0.00 0.00 5.28
2126 2142 0.319469 GAATTTGTTGTGCCCCGGTG 60.319 55.000 0.00 0.00 0.00 4.94
2127 2143 1.045911 AATTTGTTGTGCCCCGGTGT 61.046 50.000 0.00 0.00 0.00 4.16
2128 2144 1.743321 ATTTGTTGTGCCCCGGTGTG 61.743 55.000 0.00 0.00 0.00 3.82
2129 2145 2.838748 TTTGTTGTGCCCCGGTGTGA 62.839 55.000 0.00 0.00 0.00 3.58
2130 2146 3.284449 GTTGTGCCCCGGTGTGAC 61.284 66.667 0.00 0.00 0.00 3.67
2131 2147 4.920112 TTGTGCCCCGGTGTGACG 62.920 66.667 0.00 0.00 0.00 4.35
2140 2156 4.404098 GGTGTGACGCCCCCGATT 62.404 66.667 3.20 0.00 38.29 3.34
2141 2157 2.359478 GTGTGACGCCCCCGATTT 60.359 61.111 0.00 0.00 38.29 2.17
2142 2158 1.078988 GTGTGACGCCCCCGATTTA 60.079 57.895 0.00 0.00 38.29 1.40
2143 2159 0.674269 GTGTGACGCCCCCGATTTAA 60.674 55.000 0.00 0.00 38.29 1.52
2144 2160 0.253610 TGTGACGCCCCCGATTTAAT 59.746 50.000 0.00 0.00 38.29 1.40
2145 2161 0.942252 GTGACGCCCCCGATTTAATC 59.058 55.000 0.00 0.00 38.29 1.75
2162 2178 8.919695 GATTTAATCGTACACTAATCATGCAC 57.080 34.615 0.00 0.00 0.00 4.57
2163 2179 6.505039 TTAATCGTACACTAATCATGCACG 57.495 37.500 0.00 0.00 38.02 5.34
2164 2180 2.190161 TCGTACACTAATCATGCACGC 58.810 47.619 0.00 0.00 36.88 5.34
2165 2181 1.923864 CGTACACTAATCATGCACGCA 59.076 47.619 0.00 0.00 30.70 5.24
2166 2182 2.347150 CGTACACTAATCATGCACGCAA 59.653 45.455 0.00 0.00 30.70 4.85
2167 2183 3.181525 CGTACACTAATCATGCACGCAAA 60.182 43.478 0.00 0.00 30.70 3.68
2168 2184 4.494035 CGTACACTAATCATGCACGCAAAT 60.494 41.667 0.00 0.00 30.70 2.32
2169 2185 3.761657 ACACTAATCATGCACGCAAATG 58.238 40.909 0.00 0.00 0.00 2.32
2170 2186 3.191162 ACACTAATCATGCACGCAAATGT 59.809 39.130 0.00 0.00 0.00 2.71
2171 2187 3.544682 CACTAATCATGCACGCAAATGTG 59.455 43.478 0.00 0.00 42.81 3.21
2172 2188 2.728690 AATCATGCACGCAAATGTGT 57.271 40.000 0.00 0.00 41.94 3.72
2173 2189 3.846423 AATCATGCACGCAAATGTGTA 57.154 38.095 0.00 0.00 41.94 2.90
2174 2190 2.610219 TCATGCACGCAAATGTGTAC 57.390 45.000 0.00 0.00 41.94 2.90
2175 2191 1.136113 TCATGCACGCAAATGTGTACG 60.136 47.619 0.00 0.00 41.94 3.67
2176 2192 1.136113 CATGCACGCAAATGTGTACGA 60.136 47.619 0.00 0.00 41.94 3.43
2177 2193 1.152510 TGCACGCAAATGTGTACGAT 58.847 45.000 0.00 0.00 41.94 3.73
2178 2194 1.127766 TGCACGCAAATGTGTACGATC 59.872 47.619 0.00 0.00 41.94 3.69
2179 2195 1.127766 GCACGCAAATGTGTACGATCA 59.872 47.619 0.00 0.00 41.94 2.92
2180 2196 2.412195 GCACGCAAATGTGTACGATCAA 60.412 45.455 0.00 0.00 41.94 2.57
2181 2197 3.804688 CACGCAAATGTGTACGATCAAA 58.195 40.909 0.00 0.00 36.94 2.69
2182 2198 4.215201 CACGCAAATGTGTACGATCAAAA 58.785 39.130 0.00 0.00 36.94 2.44
2183 2199 4.851014 CACGCAAATGTGTACGATCAAAAT 59.149 37.500 0.00 0.00 36.94 1.82
2184 2200 5.002468 CACGCAAATGTGTACGATCAAAATC 59.998 40.000 0.00 0.00 36.94 2.17
2185 2201 5.085390 CGCAAATGTGTACGATCAAAATCA 58.915 37.500 0.00 0.00 31.76 2.57
2186 2202 5.225743 CGCAAATGTGTACGATCAAAATCAG 59.774 40.000 0.00 0.00 31.76 2.90
2187 2203 5.512788 GCAAATGTGTACGATCAAAATCAGG 59.487 40.000 0.00 0.00 31.76 3.86
2188 2204 5.818136 AATGTGTACGATCAAAATCAGGG 57.182 39.130 0.00 0.00 31.76 4.45
2189 2205 4.545208 TGTGTACGATCAAAATCAGGGA 57.455 40.909 0.00 0.00 31.76 4.20
2190 2206 4.250464 TGTGTACGATCAAAATCAGGGAC 58.750 43.478 0.00 0.00 31.76 4.46
2191 2207 4.020573 TGTGTACGATCAAAATCAGGGACT 60.021 41.667 0.00 0.00 43.88 3.85
2192 2208 4.567159 GTGTACGATCAAAATCAGGGACTC 59.433 45.833 0.00 0.00 34.60 3.36
2193 2209 3.981071 ACGATCAAAATCAGGGACTCA 57.019 42.857 0.00 0.00 34.60 3.41
2194 2210 3.600388 ACGATCAAAATCAGGGACTCAC 58.400 45.455 0.00 0.00 34.60 3.51
2195 2211 2.604914 CGATCAAAATCAGGGACTCACG 59.395 50.000 0.00 0.00 34.60 4.35
2196 2212 2.472695 TCAAAATCAGGGACTCACGG 57.527 50.000 0.00 0.00 34.60 4.94
2197 2213 1.003118 TCAAAATCAGGGACTCACGGG 59.997 52.381 0.00 0.00 34.60 5.28
2198 2214 1.003118 CAAAATCAGGGACTCACGGGA 59.997 52.381 0.00 0.00 34.60 5.14
2199 2215 1.358152 AAATCAGGGACTCACGGGAA 58.642 50.000 0.00 0.00 34.60 3.97
2200 2216 0.905357 AATCAGGGACTCACGGGAAG 59.095 55.000 0.00 0.00 34.60 3.46
2201 2217 0.041238 ATCAGGGACTCACGGGAAGA 59.959 55.000 0.00 0.00 34.60 2.87
2202 2218 0.041238 TCAGGGACTCACGGGAAGAT 59.959 55.000 0.00 0.00 34.60 2.40
2203 2219 1.286849 TCAGGGACTCACGGGAAGATA 59.713 52.381 0.00 0.00 34.60 1.98
2204 2220 2.091278 TCAGGGACTCACGGGAAGATAT 60.091 50.000 0.00 0.00 34.60 1.63
2205 2221 2.297597 CAGGGACTCACGGGAAGATATC 59.702 54.545 0.00 0.00 34.60 1.63
2206 2222 2.091278 AGGGACTCACGGGAAGATATCA 60.091 50.000 5.32 0.00 0.00 2.15
2207 2223 2.036089 GGGACTCACGGGAAGATATCAC 59.964 54.545 5.32 0.00 0.00 3.06
2208 2224 2.693591 GGACTCACGGGAAGATATCACA 59.306 50.000 5.32 0.00 0.00 3.58
2209 2225 3.132289 GGACTCACGGGAAGATATCACAA 59.868 47.826 5.32 0.00 0.00 3.33
2210 2226 4.113354 GACTCACGGGAAGATATCACAAC 58.887 47.826 5.32 0.00 0.00 3.32
2211 2227 3.513912 ACTCACGGGAAGATATCACAACA 59.486 43.478 5.32 0.00 0.00 3.33
2212 2228 3.857052 TCACGGGAAGATATCACAACAC 58.143 45.455 5.32 0.00 0.00 3.32
2213 2229 3.259625 TCACGGGAAGATATCACAACACA 59.740 43.478 5.32 0.00 0.00 3.72
2214 2230 4.000325 CACGGGAAGATATCACAACACAA 59.000 43.478 5.32 0.00 0.00 3.33
2215 2231 4.000988 ACGGGAAGATATCACAACACAAC 58.999 43.478 5.32 0.00 0.00 3.32
2216 2232 4.253685 CGGGAAGATATCACAACACAACT 58.746 43.478 5.32 0.00 0.00 3.16
2217 2233 4.330074 CGGGAAGATATCACAACACAACTC 59.670 45.833 5.32 0.00 0.00 3.01
2218 2234 5.491982 GGGAAGATATCACAACACAACTCT 58.508 41.667 5.32 0.00 0.00 3.24
2219 2235 6.627287 CGGGAAGATATCACAACACAACTCTA 60.627 42.308 5.32 0.00 0.00 2.43
2220 2236 6.535508 GGGAAGATATCACAACACAACTCTAC 59.464 42.308 5.32 0.00 0.00 2.59
2221 2237 7.097192 GGAAGATATCACAACACAACTCTACA 58.903 38.462 5.32 0.00 0.00 2.74
2222 2238 7.602644 GGAAGATATCACAACACAACTCTACAA 59.397 37.037 5.32 0.00 0.00 2.41
2223 2239 8.902540 AAGATATCACAACACAACTCTACAAA 57.097 30.769 5.32 0.00 0.00 2.83
2224 2240 9.507329 AAGATATCACAACACAACTCTACAAAT 57.493 29.630 5.32 0.00 0.00 2.32
2256 2272 8.092521 AGTCATACAAGCATCATAATACAAGC 57.907 34.615 0.00 0.00 0.00 4.01
2257 2273 7.173907 AGTCATACAAGCATCATAATACAAGCC 59.826 37.037 0.00 0.00 0.00 4.35
2258 2274 6.997476 TCATACAAGCATCATAATACAAGCCA 59.003 34.615 0.00 0.00 0.00 4.75
2259 2275 5.762825 ACAAGCATCATAATACAAGCCAG 57.237 39.130 0.00 0.00 0.00 4.85
2260 2276 4.581824 ACAAGCATCATAATACAAGCCAGG 59.418 41.667 0.00 0.00 0.00 4.45
2261 2277 3.759581 AGCATCATAATACAAGCCAGGG 58.240 45.455 0.00 0.00 0.00 4.45
2262 2278 2.821969 GCATCATAATACAAGCCAGGGG 59.178 50.000 0.00 0.00 0.00 4.79
2286 2302 1.291132 GAGGGCTCGAATACAAGTGC 58.709 55.000 0.00 0.00 0.00 4.40
2287 2303 0.905357 AGGGCTCGAATACAAGTGCT 59.095 50.000 0.00 0.00 0.00 4.40
2288 2304 1.134670 AGGGCTCGAATACAAGTGCTC 60.135 52.381 0.00 0.00 0.00 4.26
2289 2305 0.924090 GGCTCGAATACAAGTGCTCG 59.076 55.000 0.00 0.00 0.00 5.03
2290 2306 1.469251 GGCTCGAATACAAGTGCTCGA 60.469 52.381 7.80 7.80 37.95 4.04
2291 2307 2.464865 GCTCGAATACAAGTGCTCGAT 58.535 47.619 8.31 0.00 39.39 3.59
2292 2308 2.469516 GCTCGAATACAAGTGCTCGATC 59.530 50.000 8.31 2.80 39.39 3.69
2293 2309 3.695816 CTCGAATACAAGTGCTCGATCA 58.304 45.455 8.31 0.00 39.39 2.92
2294 2310 4.294232 CTCGAATACAAGTGCTCGATCAT 58.706 43.478 8.31 0.00 39.39 2.45
2295 2311 5.432885 TCGAATACAAGTGCTCGATCATA 57.567 39.130 0.00 0.00 35.52 2.15
2296 2312 5.452777 TCGAATACAAGTGCTCGATCATAG 58.547 41.667 0.00 0.00 35.52 2.23
2297 2313 5.238650 TCGAATACAAGTGCTCGATCATAGA 59.761 40.000 0.00 0.00 35.52 1.98
2298 2314 5.340932 CGAATACAAGTGCTCGATCATAGAC 59.659 44.000 0.00 0.00 33.13 2.59
2299 2315 3.071786 ACAAGTGCTCGATCATAGACG 57.928 47.619 0.00 0.00 0.00 4.18
2300 2316 2.683362 ACAAGTGCTCGATCATAGACGA 59.317 45.455 0.00 0.00 37.03 4.20
2306 2322 3.181826 CTCGATCATAGACGAGTCAGC 57.818 52.381 5.99 0.00 46.90 4.26
2307 2323 1.527311 TCGATCATAGACGAGTCAGCG 59.473 52.381 5.99 0.00 34.49 5.18
2308 2324 1.399087 CGATCATAGACGAGTCAGCGG 60.399 57.143 5.99 0.00 35.12 5.52
2309 2325 1.874231 GATCATAGACGAGTCAGCGGA 59.126 52.381 5.99 0.00 35.12 5.54
2310 2326 1.746470 TCATAGACGAGTCAGCGGAA 58.254 50.000 5.99 0.00 35.12 4.30
2311 2327 1.671328 TCATAGACGAGTCAGCGGAAG 59.329 52.381 5.99 0.00 35.12 3.46
2328 2344 5.643339 CGGAAGCAACAATATCTGAGTAC 57.357 43.478 0.00 0.00 0.00 2.73
2329 2345 5.109210 CGGAAGCAACAATATCTGAGTACA 58.891 41.667 0.00 0.00 0.00 2.90
2330 2346 5.233050 CGGAAGCAACAATATCTGAGTACAG 59.767 44.000 0.00 0.00 44.66 2.74
2346 2362 8.304596 TCTGAGTACAGACATAAGTTAAACAGG 58.695 37.037 0.00 0.00 46.55 4.00
2347 2363 7.383687 TGAGTACAGACATAAGTTAAACAGGG 58.616 38.462 0.00 0.00 0.00 4.45
2348 2364 7.015877 TGAGTACAGACATAAGTTAAACAGGGT 59.984 37.037 0.00 0.00 0.00 4.34
2349 2365 7.159372 AGTACAGACATAAGTTAAACAGGGTG 58.841 38.462 0.00 0.00 0.00 4.61
2350 2366 4.760204 ACAGACATAAGTTAAACAGGGTGC 59.240 41.667 0.00 0.00 0.00 5.01
2351 2367 4.156008 CAGACATAAGTTAAACAGGGTGCC 59.844 45.833 0.00 0.00 0.00 5.01
2352 2368 4.076394 GACATAAGTTAAACAGGGTGCCA 58.924 43.478 0.00 0.00 0.00 4.92
2353 2369 4.672899 ACATAAGTTAAACAGGGTGCCAT 58.327 39.130 0.00 0.00 0.00 4.40
2354 2370 5.822204 ACATAAGTTAAACAGGGTGCCATA 58.178 37.500 0.00 0.00 0.00 2.74
2355 2371 6.249951 ACATAAGTTAAACAGGGTGCCATAA 58.750 36.000 0.00 0.00 0.00 1.90
2356 2372 6.377146 ACATAAGTTAAACAGGGTGCCATAAG 59.623 38.462 0.00 0.00 0.00 1.73
2357 2373 4.650972 AGTTAAACAGGGTGCCATAAGA 57.349 40.909 0.00 0.00 0.00 2.10
2358 2374 5.193099 AGTTAAACAGGGTGCCATAAGAT 57.807 39.130 0.00 0.00 0.00 2.40
2359 2375 4.949856 AGTTAAACAGGGTGCCATAAGATG 59.050 41.667 0.00 0.00 0.00 2.90
2371 2387 4.558538 CCATAAGATGGCTAGCACAAAC 57.441 45.455 18.24 10.42 44.70 2.93
2372 2388 4.202441 CCATAAGATGGCTAGCACAAACT 58.798 43.478 18.24 12.26 44.70 2.66
2373 2389 4.036027 CCATAAGATGGCTAGCACAAACTG 59.964 45.833 18.24 5.30 44.70 3.16
2374 2390 2.119801 AGATGGCTAGCACAAACTGG 57.880 50.000 18.24 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 4.127566 ACACAAGCAAAAAGAGCAACAT 57.872 36.364 0.00 0.00 0.00 2.71
194 195 1.486726 CACATACCCTGAACTCCTCCC 59.513 57.143 0.00 0.00 0.00 4.30
312 313 6.154203 TCACCTGACAAAATAATGCAAACA 57.846 33.333 0.00 0.00 0.00 2.83
331 332 9.313118 AGAAAACAGAAATTACAAAACATCACC 57.687 29.630 0.00 0.00 0.00 4.02
470 474 5.131142 ACTTATGGGAGAAGATTCAATCGGT 59.869 40.000 0.00 0.00 0.00 4.69
537 542 5.068987 ACAAACATCAAGCAACCAACATACT 59.931 36.000 0.00 0.00 0.00 2.12
575 580 8.567285 AAATGTCAGACTAGATAAAACAAGGG 57.433 34.615 1.31 0.00 0.00 3.95
776 783 5.799681 AAGTGCACAAAAAGAACAAATGG 57.200 34.783 21.04 0.00 0.00 3.16
827 835 5.475719 CAGCATGGAAAACAGACATTGATT 58.524 37.500 0.00 0.00 0.00 2.57
938 949 4.495679 GCGATTGTGTTTCAGACAAGACAA 60.496 41.667 9.12 9.12 42.31 3.18
967 978 6.013725 TGTGTAACTTCCTCTGTACCATCAAT 60.014 38.462 0.00 0.00 38.04 2.57
1007 1018 4.200838 TCATATTGACGAAGCTGTTCCA 57.799 40.909 0.00 0.00 0.00 3.53
1029 1040 5.526506 ACTTCTTCTTGCTTTGCTTCAAT 57.473 34.783 0.00 0.00 0.00 2.57
1217 1228 5.950549 AGATTCTTCTTCATTCCAGCAACAT 59.049 36.000 0.00 0.00 0.00 2.71
1319 1330 3.603532 AGCACAAAGTCGTCATCATCAT 58.396 40.909 0.00 0.00 0.00 2.45
1367 1378 6.665992 ACCATAGTCTTTGTGTCTACAAGA 57.334 37.500 0.00 0.00 46.63 3.02
1377 1388 8.140112 ACTCTTAGATGAACCATAGTCTTTGT 57.860 34.615 0.00 0.00 0.00 2.83
1411 1422 0.252761 TGACATCATCATGGGCACGT 59.747 50.000 0.00 0.00 33.82 4.49
1419 1430 6.605995 ACCAACATCTTCATTGACATCATCAT 59.394 34.615 0.00 0.00 37.11 2.45
1664 1679 2.537143 AGTGGGAAGAGACAACCGTAT 58.463 47.619 0.00 0.00 0.00 3.06
1675 1690 2.041620 AGCCTTGCAAATAGTGGGAAGA 59.958 45.455 0.00 0.00 34.79 2.87
1728 1743 3.052642 ACCAAATCCAGCATCCCTTACAT 60.053 43.478 0.00 0.00 0.00 2.29
1732 1747 1.077663 ACACCAAATCCAGCATCCCTT 59.922 47.619 0.00 0.00 0.00 3.95
1786 1801 4.948847 TCAGATAGCACATAAGAATGCGT 58.051 39.130 0.00 0.00 46.74 5.24
1849 1864 2.286365 TTCGAAGAACCCTGCCATTT 57.714 45.000 0.00 0.00 45.90 2.32
1898 1913 3.869246 GTGTGACGTCCCATAGGTAAATG 59.131 47.826 14.12 0.00 0.00 2.32
1960 1975 3.473147 CTCATCCTTGAGGGCAGTG 57.527 57.895 0.00 0.00 44.78 3.66
2125 2141 0.253610 ATTAAATCGGGGGCGTCACA 59.746 50.000 0.00 0.00 0.00 3.58
2126 2142 0.942252 GATTAAATCGGGGGCGTCAC 59.058 55.000 0.00 0.00 0.00 3.67
2127 2143 3.390003 GATTAAATCGGGGGCGTCA 57.610 52.632 0.00 0.00 0.00 4.35
2137 2153 8.919695 GTGCATGATTAGTGTACGATTAAATC 57.080 34.615 0.00 0.00 0.00 2.17
2146 2162 4.335082 TTTGCGTGCATGATTAGTGTAC 57.665 40.909 10.93 0.00 0.00 2.90
2147 2163 4.394610 ACATTTGCGTGCATGATTAGTGTA 59.605 37.500 10.93 0.00 0.00 2.90
2148 2164 3.191162 ACATTTGCGTGCATGATTAGTGT 59.809 39.130 10.93 4.47 0.00 3.55
2149 2165 3.544682 CACATTTGCGTGCATGATTAGTG 59.455 43.478 10.93 7.27 0.00 2.74
2150 2166 3.191162 ACACATTTGCGTGCATGATTAGT 59.809 39.130 10.93 0.00 40.73 2.24
2151 2167 3.761657 ACACATTTGCGTGCATGATTAG 58.238 40.909 10.93 0.00 40.73 1.73
2152 2168 3.846423 ACACATTTGCGTGCATGATTA 57.154 38.095 10.93 0.00 40.73 1.75
2153 2169 2.728690 ACACATTTGCGTGCATGATT 57.271 40.000 10.93 0.00 40.73 2.57
2154 2170 2.476018 CGTACACATTTGCGTGCATGAT 60.476 45.455 10.93 0.00 40.73 2.45
2155 2171 1.136113 CGTACACATTTGCGTGCATGA 60.136 47.619 10.93 0.00 40.73 3.07
2156 2172 1.136113 TCGTACACATTTGCGTGCATG 60.136 47.619 0.09 0.09 40.73 4.06
2157 2173 1.152510 TCGTACACATTTGCGTGCAT 58.847 45.000 0.00 0.00 40.73 3.96
2158 2174 1.127766 GATCGTACACATTTGCGTGCA 59.872 47.619 0.00 0.00 40.73 4.57
2159 2175 1.127766 TGATCGTACACATTTGCGTGC 59.872 47.619 0.00 0.00 40.73 5.34
2160 2176 3.447752 TTGATCGTACACATTTGCGTG 57.552 42.857 0.00 0.00 42.81 5.34
2161 2177 4.475763 TTTTGATCGTACACATTTGCGT 57.524 36.364 0.00 0.00 0.00 5.24
2162 2178 5.085390 TGATTTTGATCGTACACATTTGCG 58.915 37.500 0.00 0.00 0.00 4.85
2163 2179 5.512788 CCTGATTTTGATCGTACACATTTGC 59.487 40.000 0.00 0.00 0.00 3.68
2164 2180 6.029607 CCCTGATTTTGATCGTACACATTTG 58.970 40.000 0.00 0.00 0.00 2.32
2165 2181 5.943416 TCCCTGATTTTGATCGTACACATTT 59.057 36.000 0.00 0.00 0.00 2.32
2166 2182 5.354234 GTCCCTGATTTTGATCGTACACATT 59.646 40.000 0.00 0.00 0.00 2.71
2167 2183 4.876107 GTCCCTGATTTTGATCGTACACAT 59.124 41.667 0.00 0.00 0.00 3.21
2168 2184 4.020573 AGTCCCTGATTTTGATCGTACACA 60.021 41.667 0.00 0.00 0.00 3.72
2169 2185 4.504858 AGTCCCTGATTTTGATCGTACAC 58.495 43.478 0.00 0.00 0.00 2.90
2170 2186 4.221924 TGAGTCCCTGATTTTGATCGTACA 59.778 41.667 0.00 0.00 0.00 2.90
2171 2187 4.567159 GTGAGTCCCTGATTTTGATCGTAC 59.433 45.833 0.00 0.00 0.00 3.67
2172 2188 4.676986 CGTGAGTCCCTGATTTTGATCGTA 60.677 45.833 0.00 0.00 0.00 3.43
2173 2189 3.600388 GTGAGTCCCTGATTTTGATCGT 58.400 45.455 0.00 0.00 0.00 3.73
2174 2190 2.604914 CGTGAGTCCCTGATTTTGATCG 59.395 50.000 0.00 0.00 0.00 3.69
2175 2191 2.939103 CCGTGAGTCCCTGATTTTGATC 59.061 50.000 0.00 0.00 0.00 2.92
2176 2192 2.356125 CCCGTGAGTCCCTGATTTTGAT 60.356 50.000 0.00 0.00 0.00 2.57
2177 2193 1.003118 CCCGTGAGTCCCTGATTTTGA 59.997 52.381 0.00 0.00 0.00 2.69
2178 2194 1.003118 TCCCGTGAGTCCCTGATTTTG 59.997 52.381 0.00 0.00 0.00 2.44
2179 2195 1.358152 TCCCGTGAGTCCCTGATTTT 58.642 50.000 0.00 0.00 0.00 1.82
2180 2196 1.279271 CTTCCCGTGAGTCCCTGATTT 59.721 52.381 0.00 0.00 0.00 2.17
2181 2197 0.905357 CTTCCCGTGAGTCCCTGATT 59.095 55.000 0.00 0.00 0.00 2.57
2182 2198 0.041238 TCTTCCCGTGAGTCCCTGAT 59.959 55.000 0.00 0.00 0.00 2.90
2183 2199 0.041238 ATCTTCCCGTGAGTCCCTGA 59.959 55.000 0.00 0.00 0.00 3.86
2184 2200 1.776662 TATCTTCCCGTGAGTCCCTG 58.223 55.000 0.00 0.00 0.00 4.45
2185 2201 2.091278 TGATATCTTCCCGTGAGTCCCT 60.091 50.000 3.98 0.00 0.00 4.20
2186 2202 2.036089 GTGATATCTTCCCGTGAGTCCC 59.964 54.545 3.98 0.00 0.00 4.46
2187 2203 2.693591 TGTGATATCTTCCCGTGAGTCC 59.306 50.000 3.98 0.00 0.00 3.85
2188 2204 4.113354 GTTGTGATATCTTCCCGTGAGTC 58.887 47.826 3.98 0.00 0.00 3.36
2189 2205 3.513912 TGTTGTGATATCTTCCCGTGAGT 59.486 43.478 3.98 0.00 0.00 3.41
2190 2206 3.865745 GTGTTGTGATATCTTCCCGTGAG 59.134 47.826 3.98 0.00 0.00 3.51
2191 2207 3.259625 TGTGTTGTGATATCTTCCCGTGA 59.740 43.478 3.98 0.00 0.00 4.35
2192 2208 3.595173 TGTGTTGTGATATCTTCCCGTG 58.405 45.455 3.98 0.00 0.00 4.94
2193 2209 3.973206 TGTGTTGTGATATCTTCCCGT 57.027 42.857 3.98 0.00 0.00 5.28
2194 2210 4.253685 AGTTGTGTTGTGATATCTTCCCG 58.746 43.478 3.98 0.00 0.00 5.14
2195 2211 5.491982 AGAGTTGTGTTGTGATATCTTCCC 58.508 41.667 3.98 0.00 0.00 3.97
2196 2212 7.097192 TGTAGAGTTGTGTTGTGATATCTTCC 58.903 38.462 3.98 0.00 0.00 3.46
2197 2213 8.534333 TTGTAGAGTTGTGTTGTGATATCTTC 57.466 34.615 3.98 0.00 0.00 2.87
2198 2214 8.902540 TTTGTAGAGTTGTGTTGTGATATCTT 57.097 30.769 3.98 0.00 0.00 2.40
2230 2246 8.562892 GCTTGTATTATGATGCTTGTATGACTT 58.437 33.333 0.00 0.00 0.00 3.01
2231 2247 7.173907 GGCTTGTATTATGATGCTTGTATGACT 59.826 37.037 0.00 0.00 0.00 3.41
2232 2248 7.041167 TGGCTTGTATTATGATGCTTGTATGAC 60.041 37.037 0.00 0.00 0.00 3.06
2233 2249 6.997476 TGGCTTGTATTATGATGCTTGTATGA 59.003 34.615 0.00 0.00 0.00 2.15
2234 2250 7.205737 TGGCTTGTATTATGATGCTTGTATG 57.794 36.000 0.00 0.00 0.00 2.39
2235 2251 6.432162 CCTGGCTTGTATTATGATGCTTGTAT 59.568 38.462 0.00 0.00 0.00 2.29
2236 2252 5.764686 CCTGGCTTGTATTATGATGCTTGTA 59.235 40.000 0.00 0.00 0.00 2.41
2237 2253 4.581824 CCTGGCTTGTATTATGATGCTTGT 59.418 41.667 0.00 0.00 0.00 3.16
2238 2254 4.022589 CCCTGGCTTGTATTATGATGCTTG 60.023 45.833 0.00 0.00 0.00 4.01
2239 2255 4.147321 CCCTGGCTTGTATTATGATGCTT 58.853 43.478 0.00 0.00 0.00 3.91
2240 2256 3.499202 CCCCTGGCTTGTATTATGATGCT 60.499 47.826 0.00 0.00 0.00 3.79
2241 2257 2.821969 CCCCTGGCTTGTATTATGATGC 59.178 50.000 0.00 0.00 0.00 3.91
2242 2258 2.821969 GCCCCTGGCTTGTATTATGATG 59.178 50.000 0.00 0.00 46.69 3.07
2243 2259 3.160679 GCCCCTGGCTTGTATTATGAT 57.839 47.619 0.00 0.00 46.69 2.45
2244 2260 2.656947 GCCCCTGGCTTGTATTATGA 57.343 50.000 0.00 0.00 46.69 2.15
2267 2283 1.134670 AGCACTTGTATTCGAGCCCTC 60.135 52.381 0.00 0.00 0.00 4.30
2268 2284 0.905357 AGCACTTGTATTCGAGCCCT 59.095 50.000 0.00 0.00 0.00 5.19
2269 2285 1.291132 GAGCACTTGTATTCGAGCCC 58.709 55.000 0.00 0.00 0.00 5.19
2270 2286 0.924090 CGAGCACTTGTATTCGAGCC 59.076 55.000 0.00 0.00 35.19 4.70
2271 2287 1.909376 TCGAGCACTTGTATTCGAGC 58.091 50.000 5.19 0.00 37.18 5.03
2272 2288 3.695816 TGATCGAGCACTTGTATTCGAG 58.304 45.455 0.00 0.00 44.14 4.04
2273 2289 3.775661 TGATCGAGCACTTGTATTCGA 57.224 42.857 0.00 9.86 44.88 3.71
2274 2290 5.340932 GTCTATGATCGAGCACTTGTATTCG 59.659 44.000 5.03 0.00 34.56 3.34
2275 2291 5.340932 CGTCTATGATCGAGCACTTGTATTC 59.659 44.000 5.03 0.00 0.00 1.75
2276 2292 5.008712 TCGTCTATGATCGAGCACTTGTATT 59.991 40.000 5.03 0.00 0.00 1.89
2277 2293 4.515567 TCGTCTATGATCGAGCACTTGTAT 59.484 41.667 5.03 0.00 0.00 2.29
2278 2294 3.875134 TCGTCTATGATCGAGCACTTGTA 59.125 43.478 5.03 0.00 0.00 2.41
2279 2295 2.683362 TCGTCTATGATCGAGCACTTGT 59.317 45.455 5.03 0.00 0.00 3.16
2280 2296 3.295785 CTCGTCTATGATCGAGCACTTG 58.704 50.000 5.03 0.00 44.82 3.16
2281 2297 3.617540 CTCGTCTATGATCGAGCACTT 57.382 47.619 5.03 0.00 44.82 3.16
2287 2303 1.527311 CGCTGACTCGTCTATGATCGA 59.473 52.381 0.00 0.00 34.88 3.59
2288 2304 1.399087 CCGCTGACTCGTCTATGATCG 60.399 57.143 0.00 0.00 0.00 3.69
2289 2305 1.874231 TCCGCTGACTCGTCTATGATC 59.126 52.381 0.00 0.00 0.00 2.92
2290 2306 1.968704 TCCGCTGACTCGTCTATGAT 58.031 50.000 0.00 0.00 0.00 2.45
2291 2307 1.671328 CTTCCGCTGACTCGTCTATGA 59.329 52.381 0.00 0.00 0.00 2.15
2292 2308 1.862008 GCTTCCGCTGACTCGTCTATG 60.862 57.143 0.00 0.00 0.00 2.23
2293 2309 0.382515 GCTTCCGCTGACTCGTCTAT 59.617 55.000 0.00 0.00 0.00 1.98
2294 2310 0.958876 TGCTTCCGCTGACTCGTCTA 60.959 55.000 0.00 0.00 36.97 2.59
2295 2311 1.806461 TTGCTTCCGCTGACTCGTCT 61.806 55.000 0.00 0.00 36.97 4.18
2296 2312 1.372997 TTGCTTCCGCTGACTCGTC 60.373 57.895 0.00 0.00 36.97 4.20
2297 2313 1.664965 GTTGCTTCCGCTGACTCGT 60.665 57.895 0.00 0.00 36.97 4.18
2298 2314 1.221466 TTGTTGCTTCCGCTGACTCG 61.221 55.000 0.00 0.00 36.97 4.18
2299 2315 1.160137 ATTGTTGCTTCCGCTGACTC 58.840 50.000 0.00 0.00 36.97 3.36
2300 2316 2.472695 TATTGTTGCTTCCGCTGACT 57.527 45.000 0.00 0.00 36.97 3.41
2301 2317 2.939103 AGATATTGTTGCTTCCGCTGAC 59.061 45.455 0.00 0.00 36.97 3.51
2302 2318 2.938451 CAGATATTGTTGCTTCCGCTGA 59.062 45.455 0.00 0.00 36.97 4.26
2303 2319 2.938451 TCAGATATTGTTGCTTCCGCTG 59.062 45.455 0.00 0.00 36.97 5.18
2304 2320 3.201290 CTCAGATATTGTTGCTTCCGCT 58.799 45.455 0.00 0.00 36.97 5.52
2305 2321 2.939103 ACTCAGATATTGTTGCTTCCGC 59.061 45.455 0.00 0.00 0.00 5.54
2306 2322 5.109210 TGTACTCAGATATTGTTGCTTCCG 58.891 41.667 0.00 0.00 0.00 4.30
2307 2323 6.341316 TCTGTACTCAGATATTGTTGCTTCC 58.659 40.000 0.00 0.00 44.58 3.46
2320 2336 8.304596 CCTGTTTAACTTATGTCTGTACTCAGA 58.695 37.037 0.00 0.00 46.85 3.27
2321 2337 7.545965 CCCTGTTTAACTTATGTCTGTACTCAG 59.454 40.741 0.00 0.00 42.54 3.35
2322 2338 7.015877 ACCCTGTTTAACTTATGTCTGTACTCA 59.984 37.037 0.00 0.00 0.00 3.41
2323 2339 7.331193 CACCCTGTTTAACTTATGTCTGTACTC 59.669 40.741 0.00 0.00 0.00 2.59
2324 2340 7.159372 CACCCTGTTTAACTTATGTCTGTACT 58.841 38.462 0.00 0.00 0.00 2.73
2325 2341 6.128363 GCACCCTGTTTAACTTATGTCTGTAC 60.128 42.308 0.00 0.00 0.00 2.90
2326 2342 5.935789 GCACCCTGTTTAACTTATGTCTGTA 59.064 40.000 0.00 0.00 0.00 2.74
2327 2343 4.760204 GCACCCTGTTTAACTTATGTCTGT 59.240 41.667 0.00 0.00 0.00 3.41
2328 2344 4.156008 GGCACCCTGTTTAACTTATGTCTG 59.844 45.833 0.00 0.00 0.00 3.51
2329 2345 4.202524 TGGCACCCTGTTTAACTTATGTCT 60.203 41.667 0.00 0.00 0.00 3.41
2330 2346 4.076394 TGGCACCCTGTTTAACTTATGTC 58.924 43.478 0.00 0.00 0.00 3.06
2331 2347 4.107127 TGGCACCCTGTTTAACTTATGT 57.893 40.909 0.00 0.00 0.00 2.29
2332 2348 6.601613 TCTTATGGCACCCTGTTTAACTTATG 59.398 38.462 0.00 0.00 0.00 1.90
2333 2349 6.727394 TCTTATGGCACCCTGTTTAACTTAT 58.273 36.000 0.00 0.00 0.00 1.73
2334 2350 6.129414 TCTTATGGCACCCTGTTTAACTTA 57.871 37.500 0.00 0.00 0.00 2.24
2335 2351 4.993028 TCTTATGGCACCCTGTTTAACTT 58.007 39.130 0.00 0.00 0.00 2.66
2336 2352 4.650972 TCTTATGGCACCCTGTTTAACT 57.349 40.909 0.00 0.00 0.00 2.24
2337 2353 4.097892 CCATCTTATGGCACCCTGTTTAAC 59.902 45.833 0.00 0.00 44.70 2.01
2338 2354 4.277476 CCATCTTATGGCACCCTGTTTAA 58.723 43.478 0.00 0.00 44.70 1.52
2339 2355 3.897239 CCATCTTATGGCACCCTGTTTA 58.103 45.455 0.00 0.00 44.70 2.01
2340 2356 2.738743 CCATCTTATGGCACCCTGTTT 58.261 47.619 0.00 0.00 44.70 2.83
2341 2357 2.442236 CCATCTTATGGCACCCTGTT 57.558 50.000 0.00 0.00 44.70 3.16
2351 2367 4.036027 CCAGTTTGTGCTAGCCATCTTATG 59.964 45.833 13.29 3.21 0.00 1.90
2352 2368 4.202441 CCAGTTTGTGCTAGCCATCTTAT 58.798 43.478 13.29 0.00 0.00 1.73
2353 2369 3.609853 CCAGTTTGTGCTAGCCATCTTA 58.390 45.455 13.29 0.00 0.00 2.10
2354 2370 2.440409 CCAGTTTGTGCTAGCCATCTT 58.560 47.619 13.29 0.00 0.00 2.40
2355 2371 2.119801 CCAGTTTGTGCTAGCCATCT 57.880 50.000 13.29 8.50 0.00 2.90


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

AutoCloner maintained by Alex Coulton.