Multiple sequence alignment - TraesCS6A01G281800

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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 TraesCS6A01G281800 chr6A 100.000 2315 0 0 1 2315 511536374 511538688 0.000000e+00 4276.0
1 TraesCS6A01G281800 chr6A 97.546 1345 29 2 1 1343 97342671 97341329 0.000000e+00 2298.0
2 TraesCS6A01G281800 chr6A 97.103 1346 27 6 1 1344 543212680 543214015 0.000000e+00 2259.0
3 TraesCS6A01G281800 chr4A 96.808 1347 36 4 1 1342 494000386 494001730 0.000000e+00 2242.0
4 TraesCS6A01G281800 chr2A 97.604 1127 27 0 216 1342 48221206 48222332 0.000000e+00 1932.0
5 TraesCS6A01G281800 chr5B 92.148 1350 97 4 6 1346 281242805 281244154 0.000000e+00 1897.0
6 TraesCS6A01G281800 chr1B 90.246 1343 128 2 4 1343 533811579 533812921 0.000000e+00 1751.0
7 TraesCS6A01G281800 chr1B 89.227 1346 139 3 4 1343 510814671 510813326 0.000000e+00 1677.0
8 TraesCS6A01G281800 chr2B 90.171 1343 127 3 4 1343 751294002 751292662 0.000000e+00 1744.0
9 TraesCS6A01G281800 chr2B 89.563 709 72 2 1396 2103 690213019 690213726 0.000000e+00 898.0
10 TraesCS6A01G281800 chr7B 89.822 1346 133 3 4 1345 74304276 74302931 0.000000e+00 1724.0
11 TraesCS6A01G281800 chr3A 89.912 684 67 2 1400 2083 584027973 584028654 0.000000e+00 880.0
12 TraesCS6A01G281800 chr3A 86.827 706 89 4 1401 2106 672583991 672583290 0.000000e+00 785.0
13 TraesCS6A01G281800 chr6D 88.593 675 74 2 1410 2083 431855149 431854477 0.000000e+00 817.0
14 TraesCS6A01G281800 chr6D 87.725 668 79 3 1400 2065 451958363 451957697 0.000000e+00 776.0
15 TraesCS6A01G281800 chr6D 94.444 126 7 0 2146 2271 370692772 370692897 6.530000e-46 195.0
16 TraesCS6A01G281800 chr6D 97.826 46 1 0 2270 2315 370692922 370692967 1.910000e-11 80.5
17 TraesCS6A01G281800 chr3D 88.006 692 79 3 1403 2092 340702874 340702185 0.000000e+00 815.0
18 TraesCS6A01G281800 chrUn 87.032 694 84 4 1391 2083 92406745 92407433 0.000000e+00 778.0
19 TraesCS6A01G281800 chr6B 87.228 689 81 6 1401 2086 671720396 671719712 0.000000e+00 778.0
20 TraesCS6A01G281800 chr6B 95.385 130 6 0 2142 2271 555808925 555809054 8.380000e-50 207.0
21 TraesCS6A01G281800 chr7D 86.763 695 84 5 1391 2083 207314064 207314752 0.000000e+00 767.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6A01G281800 chr6A 511536374 511538688 2314 False 4276 4276 100.000 1 2315 1 chr6A.!!$F1 2314
1 TraesCS6A01G281800 chr6A 97341329 97342671 1342 True 2298 2298 97.546 1 1343 1 chr6A.!!$R1 1342
2 TraesCS6A01G281800 chr6A 543212680 543214015 1335 False 2259 2259 97.103 1 1344 1 chr6A.!!$F2 1343
3 TraesCS6A01G281800 chr4A 494000386 494001730 1344 False 2242 2242 96.808 1 1342 1 chr4A.!!$F1 1341
4 TraesCS6A01G281800 chr2A 48221206 48222332 1126 False 1932 1932 97.604 216 1342 1 chr2A.!!$F1 1126
5 TraesCS6A01G281800 chr5B 281242805 281244154 1349 False 1897 1897 92.148 6 1346 1 chr5B.!!$F1 1340
6 TraesCS6A01G281800 chr1B 533811579 533812921 1342 False 1751 1751 90.246 4 1343 1 chr1B.!!$F1 1339
7 TraesCS6A01G281800 chr1B 510813326 510814671 1345 True 1677 1677 89.227 4 1343 1 chr1B.!!$R1 1339
8 TraesCS6A01G281800 chr2B 751292662 751294002 1340 True 1744 1744 90.171 4 1343 1 chr2B.!!$R1 1339
9 TraesCS6A01G281800 chr2B 690213019 690213726 707 False 898 898 89.563 1396 2103 1 chr2B.!!$F1 707
10 TraesCS6A01G281800 chr7B 74302931 74304276 1345 True 1724 1724 89.822 4 1345 1 chr7B.!!$R1 1341
11 TraesCS6A01G281800 chr3A 584027973 584028654 681 False 880 880 89.912 1400 2083 1 chr3A.!!$F1 683
12 TraesCS6A01G281800 chr3A 672583290 672583991 701 True 785 785 86.827 1401 2106 1 chr3A.!!$R1 705
13 TraesCS6A01G281800 chr6D 431854477 431855149 672 True 817 817 88.593 1410 2083 1 chr6D.!!$R1 673
14 TraesCS6A01G281800 chr6D 451957697 451958363 666 True 776 776 87.725 1400 2065 1 chr6D.!!$R2 665
15 TraesCS6A01G281800 chr3D 340702185 340702874 689 True 815 815 88.006 1403 2092 1 chr3D.!!$R1 689
16 TraesCS6A01G281800 chrUn 92406745 92407433 688 False 778 778 87.032 1391 2083 1 chrUn.!!$F1 692
17 TraesCS6A01G281800 chr6B 671719712 671720396 684 True 778 778 87.228 1401 2086 1 chr6B.!!$R1 685
18 TraesCS6A01G281800 chr7D 207314064 207314752 688 False 767 767 86.763 1391 2083 1 chr7D.!!$F1 692

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
735 741 0.387929 CCATTAAGCTGGCTGCATGG 59.612 55.0 18.84 17.3 45.94 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2233 2260 0.036732 GTGACTGAGGATTGGCCACA 59.963 55.0 3.88 0.0 40.02 4.17 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
28 29 2.173356 TCCGTCCGATAACTCCTAAGGA 59.827 50.000 0.00 0.00 0.00 3.36
278 281 2.037367 TGCCTCGAGTACTGCCCT 59.963 61.111 12.31 0.00 0.00 5.19
328 331 3.274823 TGGAAGTCCAGGGTTCCTT 57.725 52.632 17.96 3.08 42.51 3.36
490 493 0.737804 TTGCTCACATGCACGTTTGT 59.262 45.000 0.00 0.00 43.20 2.83
625 628 7.834181 AGGACATGCTACTTATGTTTATTTGGT 59.166 33.333 0.00 0.00 38.78 3.67
735 741 0.387929 CCATTAAGCTGGCTGCATGG 59.612 55.000 18.84 17.30 45.94 3.66
911 917 1.937546 GCTGCTGTTGGTATGGTGCC 61.938 60.000 0.00 0.00 0.00 5.01
932 944 4.036144 GCCTAGAAATGACAAAGGAGATGC 59.964 45.833 0.00 0.00 0.00 3.91
1061 1077 0.106149 GTGGTGGTTCAGACGGACTT 59.894 55.000 0.00 0.00 0.00 3.01
1107 1123 4.275689 ACAAATGATGCACTTCTTCGTTCA 59.724 37.500 0.00 0.00 30.49 3.18
1364 1381 7.576861 AAAAAGTCGGTGGAATCTCTAAAAA 57.423 32.000 0.00 0.00 0.00 1.94
1563 1582 0.919981 CGTCAATCTCTGCTCGAAGC 59.080 55.000 0.00 0.00 42.82 3.86
1581 1600 3.477210 AGCAAAACTCCGAAGACTTCT 57.523 42.857 13.22 0.00 0.00 2.85
1614 1633 3.496884 TGTAATTTGACTGGAGCAACGAC 59.503 43.478 0.00 0.00 0.00 4.34
1615 1634 2.254546 ATTTGACTGGAGCAACGACA 57.745 45.000 0.00 0.00 0.00 4.35
1675 1694 3.186909 GTTTTTGAAAGCGCCTTGAGTT 58.813 40.909 2.29 0.00 0.00 3.01
1686 1705 1.856629 CCTTGAGTTGCCCATCCAAT 58.143 50.000 0.00 0.00 0.00 3.16
1712 1731 2.173356 TGGGAAGCCTTGATCGATGAAT 59.827 45.455 0.54 0.00 0.00 2.57
1750 1770 2.988859 TGATCCCCTATAAATGCAGGCT 59.011 45.455 0.00 0.00 0.00 4.58
1786 1808 9.281371 CTATATCTTCACCATGTTGTTGATGAT 57.719 33.333 9.55 11.26 0.00 2.45
1798 1820 8.464404 CATGTTGTTGATGATAGATTTCACCTT 58.536 33.333 0.00 0.00 0.00 3.50
1817 1839 7.405292 TCACCTTCATAAAGAATCAGACCAAT 58.595 34.615 0.00 0.00 35.25 3.16
2092 2119 4.515567 CACAAGAAACCCTAGTTGAAGACC 59.484 45.833 0.00 0.00 35.97 3.85
2096 2123 6.954352 AGAAACCCTAGTTGAAGACCTATT 57.046 37.500 0.00 0.00 35.97 1.73
2106 2133 3.334691 TGAAGACCTATTTTGCGTGGAG 58.665 45.455 0.00 0.00 0.00 3.86
2117 2144 4.192000 CGTGGAGCAGCAGTTAGG 57.808 61.111 0.00 0.00 0.00 2.69
2118 2145 1.591703 CGTGGAGCAGCAGTTAGGA 59.408 57.895 0.00 0.00 0.00 2.94
2119 2146 0.459237 CGTGGAGCAGCAGTTAGGAG 60.459 60.000 0.00 0.00 0.00 3.69
2120 2147 0.742635 GTGGAGCAGCAGTTAGGAGC 60.743 60.000 0.00 0.00 0.00 4.70
2121 2148 1.153269 GGAGCAGCAGTTAGGAGCC 60.153 63.158 0.00 0.00 0.00 4.70
2122 2149 1.520342 GAGCAGCAGTTAGGAGCCG 60.520 63.158 0.00 0.00 0.00 5.52
2123 2150 2.512515 GCAGCAGTTAGGAGCCGG 60.513 66.667 0.00 0.00 0.00 6.13
2124 2151 3.019003 GCAGCAGTTAGGAGCCGGA 62.019 63.158 5.05 0.00 0.00 5.14
2125 2152 1.142748 CAGCAGTTAGGAGCCGGAG 59.857 63.158 5.05 0.00 0.00 4.63
2126 2153 1.305381 AGCAGTTAGGAGCCGGAGT 60.305 57.895 5.05 0.00 0.00 3.85
2127 2154 1.142097 GCAGTTAGGAGCCGGAGTC 59.858 63.158 5.05 0.00 0.00 3.36
2128 2155 1.433879 CAGTTAGGAGCCGGAGTCG 59.566 63.158 5.05 0.00 0.00 4.18
2138 2165 2.799371 CGGAGTCGGAGTAGGTGC 59.201 66.667 0.00 0.00 0.00 5.01
2139 2166 1.749638 CGGAGTCGGAGTAGGTGCT 60.750 63.158 0.00 0.00 0.00 4.40
2140 2167 1.716826 CGGAGTCGGAGTAGGTGCTC 61.717 65.000 0.00 0.00 34.89 4.26
2141 2168 0.680280 GGAGTCGGAGTAGGTGCTCA 60.680 60.000 0.00 0.00 37.24 4.26
2142 2169 0.452585 GAGTCGGAGTAGGTGCTCAC 59.547 60.000 0.00 0.00 37.24 3.51
2143 2170 1.136984 GTCGGAGTAGGTGCTCACG 59.863 63.158 0.00 0.00 37.24 4.35
2144 2171 2.044555 TCGGAGTAGGTGCTCACGG 61.045 63.158 0.00 0.00 37.24 4.94
2145 2172 2.044555 CGGAGTAGGTGCTCACGGA 61.045 63.158 0.00 0.00 37.24 4.69
2146 2173 1.810532 GGAGTAGGTGCTCACGGAG 59.189 63.158 0.00 0.00 37.24 4.63
2147 2174 1.668101 GGAGTAGGTGCTCACGGAGG 61.668 65.000 0.00 0.00 37.24 4.30
2148 2175 1.668101 GAGTAGGTGCTCACGGAGGG 61.668 65.000 3.56 0.00 35.67 4.30
2149 2176 1.681327 GTAGGTGCTCACGGAGGGA 60.681 63.158 3.56 0.00 0.00 4.20
2150 2177 1.379977 TAGGTGCTCACGGAGGGAG 60.380 63.158 0.00 0.00 35.47 4.30
2151 2178 2.151307 TAGGTGCTCACGGAGGGAGT 62.151 60.000 1.03 0.00 34.83 3.85
2152 2179 1.681327 GGTGCTCACGGAGGGAGTA 60.681 63.158 1.03 0.00 34.83 2.59
2153 2180 1.511768 GTGCTCACGGAGGGAGTAC 59.488 63.158 4.89 4.89 40.02 2.73
2154 2181 0.966370 GTGCTCACGGAGGGAGTACT 60.966 60.000 12.19 0.00 42.46 2.73
2155 2182 0.622136 TGCTCACGGAGGGAGTACTA 59.378 55.000 0.00 0.00 34.83 1.82
2156 2183 1.214673 TGCTCACGGAGGGAGTACTAT 59.785 52.381 0.00 0.00 34.83 2.12
2157 2184 2.440627 TGCTCACGGAGGGAGTACTATA 59.559 50.000 0.00 0.00 34.83 1.31
2158 2185 3.074094 TGCTCACGGAGGGAGTACTATAT 59.926 47.826 0.00 0.00 34.83 0.86
2159 2186 4.080687 GCTCACGGAGGGAGTACTATATT 58.919 47.826 0.00 0.00 34.83 1.28
2160 2187 4.523558 GCTCACGGAGGGAGTACTATATTT 59.476 45.833 0.00 0.00 34.83 1.40
2161 2188 5.709164 GCTCACGGAGGGAGTACTATATTTA 59.291 44.000 0.00 0.00 34.83 1.40
2162 2189 6.377712 GCTCACGGAGGGAGTACTATATTTAT 59.622 42.308 0.00 0.00 34.83 1.40
2163 2190 7.093858 GCTCACGGAGGGAGTACTATATTTATT 60.094 40.741 0.00 0.00 34.83 1.40
2164 2191 8.716674 TCACGGAGGGAGTACTATATTTATTT 57.283 34.615 0.00 0.00 0.00 1.40
2165 2192 8.800332 TCACGGAGGGAGTACTATATTTATTTC 58.200 37.037 0.00 0.00 0.00 2.17
2166 2193 8.804204 CACGGAGGGAGTACTATATTTATTTCT 58.196 37.037 0.00 0.00 0.00 2.52
2167 2194 8.804204 ACGGAGGGAGTACTATATTTATTTCTG 58.196 37.037 0.00 0.00 0.00 3.02
2168 2195 9.021807 CGGAGGGAGTACTATATTTATTTCTGA 57.978 37.037 0.00 0.00 0.00 3.27
2188 2215 7.572523 TCTGAATCTTATTGGCTTTACATGG 57.427 36.000 0.00 0.00 0.00 3.66
2189 2216 7.118723 TCTGAATCTTATTGGCTTTACATGGT 58.881 34.615 0.00 0.00 0.00 3.55
2190 2217 8.271458 TCTGAATCTTATTGGCTTTACATGGTA 58.729 33.333 0.00 0.00 0.00 3.25
2191 2218 8.450578 TGAATCTTATTGGCTTTACATGGTAG 57.549 34.615 0.00 0.00 0.00 3.18
2192 2219 6.884280 ATCTTATTGGCTTTACATGGTAGC 57.116 37.500 0.00 2.44 0.00 3.58
2199 2226 2.356069 GCTTTACATGGTAGCCTTCAGC 59.644 50.000 0.00 0.00 44.25 4.26
2212 2239 4.676849 GCCTTCAGCTGTTCTCTTAAAG 57.323 45.455 14.67 7.06 38.99 1.85
2213 2240 4.068599 GCCTTCAGCTGTTCTCTTAAAGT 58.931 43.478 14.67 0.00 38.99 2.66
2214 2241 4.083590 GCCTTCAGCTGTTCTCTTAAAGTG 60.084 45.833 14.67 3.24 38.99 3.16
2215 2242 5.300752 CCTTCAGCTGTTCTCTTAAAGTGA 58.699 41.667 14.67 0.00 0.00 3.41
2216 2243 5.407995 CCTTCAGCTGTTCTCTTAAAGTGAG 59.592 44.000 14.67 0.00 0.00 3.51
2217 2244 5.537300 TCAGCTGTTCTCTTAAAGTGAGT 57.463 39.130 14.67 0.00 33.59 3.41
2218 2245 5.918608 TCAGCTGTTCTCTTAAAGTGAGTT 58.081 37.500 14.67 0.00 33.59 3.01
2219 2246 5.986135 TCAGCTGTTCTCTTAAAGTGAGTTC 59.014 40.000 14.67 0.00 33.59 3.01
2220 2247 5.178438 CAGCTGTTCTCTTAAAGTGAGTTCC 59.822 44.000 5.25 0.00 33.59 3.62
2221 2248 5.057149 GCTGTTCTCTTAAAGTGAGTTCCA 58.943 41.667 0.00 0.00 33.59 3.53
2222 2249 5.703130 GCTGTTCTCTTAAAGTGAGTTCCAT 59.297 40.000 0.00 0.00 33.59 3.41
2223 2250 6.874134 GCTGTTCTCTTAAAGTGAGTTCCATA 59.126 38.462 0.00 0.00 33.59 2.74
2224 2251 7.064016 GCTGTTCTCTTAAAGTGAGTTCCATAG 59.936 40.741 0.00 0.00 33.59 2.23
2225 2252 8.190326 TGTTCTCTTAAAGTGAGTTCCATAGA 57.810 34.615 0.00 0.00 33.59 1.98
2226 2253 8.816894 TGTTCTCTTAAAGTGAGTTCCATAGAT 58.183 33.333 0.00 0.00 33.59 1.98
2235 2262 9.965902 AAAGTGAGTTCCATAGATAATTCTTGT 57.034 29.630 0.00 0.00 33.17 3.16
2236 2263 8.954950 AGTGAGTTCCATAGATAATTCTTGTG 57.045 34.615 0.00 0.00 33.17 3.33
2237 2264 7.989741 AGTGAGTTCCATAGATAATTCTTGTGG 59.010 37.037 0.00 0.00 37.65 4.17
2238 2265 6.767902 TGAGTTCCATAGATAATTCTTGTGGC 59.232 38.462 0.00 0.00 36.88 5.01
2239 2266 6.064717 AGTTCCATAGATAATTCTTGTGGCC 58.935 40.000 0.00 0.00 36.88 5.36
2240 2267 5.645056 TCCATAGATAATTCTTGTGGCCA 57.355 39.130 0.00 0.00 36.88 5.36
2241 2268 6.012337 TCCATAGATAATTCTTGTGGCCAA 57.988 37.500 7.24 0.00 36.88 4.52
2242 2269 6.613699 TCCATAGATAATTCTTGTGGCCAAT 58.386 36.000 7.24 0.00 36.88 3.16
2243 2270 6.716628 TCCATAGATAATTCTTGTGGCCAATC 59.283 38.462 7.24 4.01 36.88 2.67
2244 2271 6.071728 CCATAGATAATTCTTGTGGCCAATCC 60.072 42.308 7.24 0.00 32.89 3.01
2245 2272 5.134725 AGATAATTCTTGTGGCCAATCCT 57.865 39.130 7.24 0.00 35.26 3.24
2246 2273 5.136105 AGATAATTCTTGTGGCCAATCCTC 58.864 41.667 7.24 0.00 35.26 3.71
2247 2274 2.905415 ATTCTTGTGGCCAATCCTCA 57.095 45.000 7.24 0.00 36.62 3.86
2248 2275 2.205022 TTCTTGTGGCCAATCCTCAG 57.795 50.000 7.24 0.00 39.29 3.35
2249 2276 1.067295 TCTTGTGGCCAATCCTCAGT 58.933 50.000 7.24 0.00 39.29 3.41
2250 2277 1.003580 TCTTGTGGCCAATCCTCAGTC 59.996 52.381 7.24 0.00 39.29 3.51
2251 2278 0.770499 TTGTGGCCAATCCTCAGTCA 59.230 50.000 7.24 0.00 39.29 3.41
2252 2279 0.036732 TGTGGCCAATCCTCAGTCAC 59.963 55.000 7.24 0.00 33.69 3.67
2253 2280 0.036732 GTGGCCAATCCTCAGTCACA 59.963 55.000 7.24 0.00 35.26 3.58
2254 2281 0.994247 TGGCCAATCCTCAGTCACAT 59.006 50.000 0.61 0.00 35.26 3.21
2255 2282 1.340308 TGGCCAATCCTCAGTCACATG 60.340 52.381 0.61 0.00 35.26 3.21
2256 2283 1.386533 GCCAATCCTCAGTCACATGG 58.613 55.000 0.00 0.00 0.00 3.66
2257 2284 1.340405 GCCAATCCTCAGTCACATGGT 60.340 52.381 0.00 0.00 0.00 3.55
2258 2285 2.362736 CCAATCCTCAGTCACATGGTG 58.637 52.381 0.00 0.00 34.45 4.17
2259 2286 1.741706 CAATCCTCAGTCACATGGTGC 59.258 52.381 0.00 0.00 32.98 5.01
2260 2287 0.107993 ATCCTCAGTCACATGGTGCG 60.108 55.000 0.00 0.00 32.98 5.34
2261 2288 1.004560 CCTCAGTCACATGGTGCGT 60.005 57.895 0.00 0.00 32.98 5.24
2262 2289 1.293963 CCTCAGTCACATGGTGCGTG 61.294 60.000 0.00 0.00 32.98 5.34
2263 2290 1.904852 CTCAGTCACATGGTGCGTGC 61.905 60.000 0.00 0.00 34.27 5.34
2264 2291 2.110835 AGTCACATGGTGCGTGCA 59.889 55.556 0.00 0.00 34.27 4.57
2265 2292 2.252260 GTCACATGGTGCGTGCAC 59.748 61.111 16.40 16.40 45.49 4.57
2266 2293 2.110835 TCACATGGTGCGTGCACT 59.889 55.556 22.82 2.94 45.52 4.40
2267 2294 1.960763 TCACATGGTGCGTGCACTC 60.961 57.895 22.82 7.74 45.52 3.51
2268 2295 2.110835 ACATGGTGCGTGCACTCA 59.889 55.556 22.82 18.60 45.52 3.41
2269 2296 2.253758 ACATGGTGCGTGCACTCAC 61.254 57.895 27.73 27.73 45.52 3.51
2270 2297 2.110835 ATGGTGCGTGCACTCACA 59.889 55.556 33.76 22.72 45.52 3.58
2271 2298 2.253758 ATGGTGCGTGCACTCACAC 61.254 57.895 33.76 26.65 45.52 3.82
2272 2299 2.588877 GGTGCGTGCACTCACACT 60.589 61.111 33.76 0.00 45.52 3.55
2273 2300 1.300620 GGTGCGTGCACTCACACTA 60.301 57.895 33.76 0.95 45.52 2.74
2274 2301 0.878523 GGTGCGTGCACTCACACTAA 60.879 55.000 33.76 0.20 45.52 2.24
2275 2302 0.232303 GTGCGTGCACTCACACTAAC 59.768 55.000 29.92 6.13 43.28 2.34
2276 2303 0.878523 TGCGTGCACTCACACTAACC 60.879 55.000 16.19 0.00 43.28 2.85
2277 2304 0.878523 GCGTGCACTCACACTAACCA 60.879 55.000 16.19 0.00 43.28 3.67
2278 2305 1.139989 CGTGCACTCACACTAACCAG 58.860 55.000 16.19 0.00 43.28 4.00
2279 2306 1.538204 CGTGCACTCACACTAACCAGT 60.538 52.381 16.19 0.00 43.28 4.00
2299 2326 5.968254 CAGTGGAGATGATCTGGAGATATG 58.032 45.833 0.00 0.00 34.37 1.78
2300 2327 5.481122 CAGTGGAGATGATCTGGAGATATGT 59.519 44.000 0.00 0.00 34.37 2.29
2301 2328 6.014413 CAGTGGAGATGATCTGGAGATATGTT 60.014 42.308 0.00 0.00 34.37 2.71
2302 2329 6.558014 AGTGGAGATGATCTGGAGATATGTTT 59.442 38.462 0.00 0.00 34.37 2.83
2303 2330 6.873076 GTGGAGATGATCTGGAGATATGTTTC 59.127 42.308 0.00 0.00 34.37 2.78
2304 2331 6.786461 TGGAGATGATCTGGAGATATGTTTCT 59.214 38.462 0.00 0.00 34.37 2.52
2305 2332 7.291885 TGGAGATGATCTGGAGATATGTTTCTT 59.708 37.037 0.00 0.00 34.37 2.52
2306 2333 8.811017 GGAGATGATCTGGAGATATGTTTCTTA 58.189 37.037 0.00 0.00 34.37 2.10
2311 2338 9.770097 TGATCTGGAGATATGTTTCTTATTGTC 57.230 33.333 0.00 0.00 34.37 3.18
2312 2339 9.995003 GATCTGGAGATATGTTTCTTATTGTCT 57.005 33.333 0.00 0.00 34.37 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
278 281 0.337082 TCCTGACCGGTTCCCATCTA 59.663 55.000 9.42 0.00 0.00 1.98
328 331 5.879777 TCCATGCGTTGATCTTCATTTTCTA 59.120 36.000 0.00 0.00 0.00 2.10
490 493 1.401552 GCAGCGCATGTTAATCCAGAA 59.598 47.619 11.47 0.00 0.00 3.02
625 628 2.352388 GTTACGTAGCTGCCAAATCCA 58.648 47.619 1.72 0.00 0.00 3.41
735 741 8.091449 CCTTTAATGATCTCCTCCATAGTGTAC 58.909 40.741 0.00 0.00 0.00 2.90
911 917 4.578105 GGGCATCTCCTTTGTCATTTCTAG 59.422 45.833 0.00 0.00 34.39 2.43
932 944 1.071471 CGGTAGGCAGCCATTAGGG 59.929 63.158 15.80 0.00 40.85 3.53
1181 1197 5.163854 CGATCGGCAACTCTATTTTGAAGTT 60.164 40.000 7.38 0.00 0.00 2.66
1365 1382 9.533831 ACTCCCTTCATTCATAAATACAAGTTT 57.466 29.630 0.00 0.00 0.00 2.66
1367 1384 9.614792 GTACTCCCTTCATTCATAAATACAAGT 57.385 33.333 0.00 0.00 0.00 3.16
1368 1385 9.838339 AGTACTCCCTTCATTCATAAATACAAG 57.162 33.333 0.00 0.00 0.00 3.16
1473 1491 8.576442 CATGGGAGTTACTTTGTATTTTCTTGT 58.424 33.333 0.00 0.00 0.00 3.16
1530 1549 0.675083 TTGACGCCGTGAAGAAGGTA 59.325 50.000 0.00 0.00 0.00 3.08
1563 1582 6.479001 TCTTTACAGAAGTCTTCGGAGTTTTG 59.521 38.462 18.15 6.91 42.02 2.44
1572 1591 8.834749 ATTACAACCTCTTTACAGAAGTCTTC 57.165 34.615 4.26 4.26 0.00 2.87
1581 1600 7.284074 TCCAGTCAAATTACAACCTCTTTACA 58.716 34.615 0.00 0.00 0.00 2.41
1614 1633 1.197721 GCGGGTGAAAGAGTGACAATG 59.802 52.381 0.00 0.00 0.00 2.82
1615 1634 1.202758 TGCGGGTGAAAGAGTGACAAT 60.203 47.619 0.00 0.00 0.00 2.71
1686 1705 1.139654 CGATCAAGGCTTCCCATCTCA 59.860 52.381 0.00 0.00 0.00 3.27
1712 1731 0.548926 TCATCCCTGGCCCAAGTACA 60.549 55.000 0.00 0.00 0.00 2.90
1750 1770 6.709018 TGGTGAAGATATAGTGATTCGACA 57.291 37.500 0.00 0.00 0.00 4.35
2026 2053 0.790993 AGTTAGGTCCCCTCACCTCA 59.209 55.000 0.00 0.00 44.08 3.86
2106 2133 2.512515 CCGGCTCCTAACTGCTGC 60.513 66.667 0.00 0.00 34.48 5.25
2107 2134 1.142748 CTCCGGCTCCTAACTGCTG 59.857 63.158 0.00 0.00 35.50 4.41
2108 2135 1.305381 ACTCCGGCTCCTAACTGCT 60.305 57.895 0.00 0.00 0.00 4.24
2109 2136 1.142097 GACTCCGGCTCCTAACTGC 59.858 63.158 0.00 0.00 0.00 4.40
2110 2137 1.433879 CGACTCCGGCTCCTAACTG 59.566 63.158 0.00 0.00 0.00 3.16
2111 2138 3.921521 CGACTCCGGCTCCTAACT 58.078 61.111 0.00 0.00 0.00 2.24
2121 2148 1.716826 GAGCACCTACTCCGACTCCG 61.717 65.000 0.00 0.00 0.00 4.63
2122 2149 0.680280 TGAGCACCTACTCCGACTCC 60.680 60.000 0.00 0.00 35.72 3.85
2123 2150 0.452585 GTGAGCACCTACTCCGACTC 59.547 60.000 0.00 0.00 35.72 3.36
2124 2151 1.306642 CGTGAGCACCTACTCCGACT 61.307 60.000 0.00 0.00 35.72 4.18
2125 2152 1.136984 CGTGAGCACCTACTCCGAC 59.863 63.158 0.00 0.00 35.72 4.79
2126 2153 2.044555 CCGTGAGCACCTACTCCGA 61.045 63.158 0.00 0.00 35.72 4.55
2127 2154 1.994507 CTCCGTGAGCACCTACTCCG 61.995 65.000 0.00 0.00 35.72 4.63
2128 2155 1.668101 CCTCCGTGAGCACCTACTCC 61.668 65.000 0.00 0.00 35.72 3.85
2129 2156 1.668101 CCCTCCGTGAGCACCTACTC 61.668 65.000 0.00 0.00 37.19 2.59
2130 2157 1.682684 CCCTCCGTGAGCACCTACT 60.683 63.158 0.00 0.00 0.00 2.57
2131 2158 1.668101 CTCCCTCCGTGAGCACCTAC 61.668 65.000 0.00 0.00 0.00 3.18
2132 2159 1.379977 CTCCCTCCGTGAGCACCTA 60.380 63.158 0.00 0.00 0.00 3.08
2133 2160 2.151307 TACTCCCTCCGTGAGCACCT 62.151 60.000 0.00 0.00 32.98 4.00
2134 2161 1.681327 TACTCCCTCCGTGAGCACC 60.681 63.158 0.00 0.00 32.98 5.01
2135 2162 0.966370 AGTACTCCCTCCGTGAGCAC 60.966 60.000 0.00 0.00 32.98 4.40
2136 2163 0.622136 TAGTACTCCCTCCGTGAGCA 59.378 55.000 0.00 0.00 32.98 4.26
2137 2164 1.984066 ATAGTACTCCCTCCGTGAGC 58.016 55.000 0.00 0.00 32.98 4.26
2138 2165 7.941431 ATAAATATAGTACTCCCTCCGTGAG 57.059 40.000 0.00 0.00 35.92 3.51
2139 2166 8.716674 AAATAAATATAGTACTCCCTCCGTGA 57.283 34.615 0.00 0.00 0.00 4.35
2140 2167 8.804204 AGAAATAAATATAGTACTCCCTCCGTG 58.196 37.037 0.00 0.00 0.00 4.94
2141 2168 8.804204 CAGAAATAAATATAGTACTCCCTCCGT 58.196 37.037 0.00 0.00 0.00 4.69
2142 2169 9.021807 TCAGAAATAAATATAGTACTCCCTCCG 57.978 37.037 0.00 0.00 0.00 4.63
2162 2189 8.469200 CCATGTAAAGCCAATAAGATTCAGAAA 58.531 33.333 0.00 0.00 0.00 2.52
2163 2190 7.615365 ACCATGTAAAGCCAATAAGATTCAGAA 59.385 33.333 0.00 0.00 0.00 3.02
2164 2191 7.118723 ACCATGTAAAGCCAATAAGATTCAGA 58.881 34.615 0.00 0.00 0.00 3.27
2165 2192 7.338800 ACCATGTAAAGCCAATAAGATTCAG 57.661 36.000 0.00 0.00 0.00 3.02
2166 2193 7.013274 GCTACCATGTAAAGCCAATAAGATTCA 59.987 37.037 0.00 0.00 0.00 2.57
2167 2194 7.363431 GCTACCATGTAAAGCCAATAAGATTC 58.637 38.462 0.00 0.00 0.00 2.52
2168 2195 7.277174 GCTACCATGTAAAGCCAATAAGATT 57.723 36.000 0.00 0.00 0.00 2.40
2169 2196 6.884280 GCTACCATGTAAAGCCAATAAGAT 57.116 37.500 0.00 0.00 0.00 2.40
2178 2205 2.356069 GCTGAAGGCTACCATGTAAAGC 59.644 50.000 0.00 3.28 38.06 3.51
2191 2218 4.068599 ACTTTAAGAGAACAGCTGAAGGC 58.931 43.478 23.35 7.00 42.19 4.35
2192 2219 5.300752 TCACTTTAAGAGAACAGCTGAAGG 58.699 41.667 23.35 5.15 0.00 3.46
2193 2220 5.988561 ACTCACTTTAAGAGAACAGCTGAAG 59.011 40.000 23.35 13.08 36.91 3.02
2194 2221 5.918608 ACTCACTTTAAGAGAACAGCTGAA 58.081 37.500 23.35 0.00 36.91 3.02
2195 2222 5.537300 ACTCACTTTAAGAGAACAGCTGA 57.463 39.130 23.35 0.00 36.91 4.26
2196 2223 5.178438 GGAACTCACTTTAAGAGAACAGCTG 59.822 44.000 13.48 13.48 36.91 4.24
2197 2224 5.163301 TGGAACTCACTTTAAGAGAACAGCT 60.163 40.000 0.00 0.00 36.91 4.24
2198 2225 5.057149 TGGAACTCACTTTAAGAGAACAGC 58.943 41.667 0.00 0.00 36.91 4.40
2199 2226 8.307483 TCTATGGAACTCACTTTAAGAGAACAG 58.693 37.037 0.00 0.00 36.91 3.16
2200 2227 8.190326 TCTATGGAACTCACTTTAAGAGAACA 57.810 34.615 0.00 0.00 36.91 3.18
2209 2236 9.965902 ACAAGAATTATCTATGGAACTCACTTT 57.034 29.630 0.00 0.00 33.77 2.66
2210 2237 9.388506 CACAAGAATTATCTATGGAACTCACTT 57.611 33.333 0.00 0.00 33.77 3.16
2211 2238 7.989741 CCACAAGAATTATCTATGGAACTCACT 59.010 37.037 3.96 0.00 33.77 3.41
2212 2239 7.254932 GCCACAAGAATTATCTATGGAACTCAC 60.255 40.741 11.35 0.00 33.77 3.51
2213 2240 6.767902 GCCACAAGAATTATCTATGGAACTCA 59.232 38.462 11.35 0.00 33.77 3.41
2214 2241 6.205658 GGCCACAAGAATTATCTATGGAACTC 59.794 42.308 0.00 0.00 33.77 3.01
2215 2242 6.064717 GGCCACAAGAATTATCTATGGAACT 58.935 40.000 0.00 0.00 33.77 3.01
2216 2243 5.827797 TGGCCACAAGAATTATCTATGGAAC 59.172 40.000 0.00 5.71 33.77 3.62
2217 2244 6.012337 TGGCCACAAGAATTATCTATGGAA 57.988 37.500 0.00 0.00 33.77 3.53
2218 2245 5.645056 TGGCCACAAGAATTATCTATGGA 57.355 39.130 0.00 0.00 33.77 3.41
2219 2246 6.071728 GGATTGGCCACAAGAATTATCTATGG 60.072 42.308 3.88 5.21 40.49 2.74
2220 2247 6.718454 AGGATTGGCCACAAGAATTATCTATG 59.282 38.462 3.88 0.00 40.49 2.23
2221 2248 6.856757 AGGATTGGCCACAAGAATTATCTAT 58.143 36.000 3.88 0.00 40.49 1.98
2222 2249 6.126507 TGAGGATTGGCCACAAGAATTATCTA 60.127 38.462 3.88 0.00 40.49 1.98
2223 2250 5.134725 AGGATTGGCCACAAGAATTATCT 57.865 39.130 3.88 0.00 40.49 1.98
2224 2251 4.889409 TGAGGATTGGCCACAAGAATTATC 59.111 41.667 3.88 2.53 40.49 1.75
2225 2252 4.870636 TGAGGATTGGCCACAAGAATTAT 58.129 39.130 3.88 0.00 40.49 1.28
2226 2253 4.263905 ACTGAGGATTGGCCACAAGAATTA 60.264 41.667 3.88 0.00 40.49 1.40
2227 2254 3.094572 CTGAGGATTGGCCACAAGAATT 58.905 45.455 3.88 0.00 40.49 2.17
2228 2255 2.042162 ACTGAGGATTGGCCACAAGAAT 59.958 45.455 3.88 0.00 40.49 2.40
2229 2256 1.425066 ACTGAGGATTGGCCACAAGAA 59.575 47.619 3.88 0.00 40.49 2.52
2230 2257 1.003580 GACTGAGGATTGGCCACAAGA 59.996 52.381 3.88 0.00 40.49 3.02
2231 2258 1.271543 TGACTGAGGATTGGCCACAAG 60.272 52.381 3.88 0.00 40.49 3.16
2232 2259 0.770499 TGACTGAGGATTGGCCACAA 59.230 50.000 3.88 0.00 36.78 3.33
2233 2260 0.036732 GTGACTGAGGATTGGCCACA 59.963 55.000 3.88 0.00 40.02 4.17
2234 2261 0.036732 TGTGACTGAGGATTGGCCAC 59.963 55.000 3.88 0.00 40.02 5.01
2235 2262 0.994247 ATGTGACTGAGGATTGGCCA 59.006 50.000 0.00 0.00 40.02 5.36
2236 2263 1.386533 CATGTGACTGAGGATTGGCC 58.613 55.000 0.00 0.00 0.00 5.36
2237 2264 1.340405 ACCATGTGACTGAGGATTGGC 60.340 52.381 0.00 0.00 0.00 4.52
2238 2265 2.362736 CACCATGTGACTGAGGATTGG 58.637 52.381 0.00 0.00 35.23 3.16
2239 2266 1.741706 GCACCATGTGACTGAGGATTG 59.258 52.381 0.00 0.00 35.23 2.67
2240 2267 1.676916 CGCACCATGTGACTGAGGATT 60.677 52.381 0.00 0.00 35.23 3.01
2241 2268 0.107993 CGCACCATGTGACTGAGGAT 60.108 55.000 0.00 0.00 35.23 3.24
2242 2269 1.293179 CGCACCATGTGACTGAGGA 59.707 57.895 0.00 0.00 35.23 3.71
2243 2270 1.004560 ACGCACCATGTGACTGAGG 60.005 57.895 0.00 0.00 35.23 3.86
2244 2271 1.904852 GCACGCACCATGTGACTGAG 61.905 60.000 0.00 0.00 39.73 3.35
2245 2272 1.960763 GCACGCACCATGTGACTGA 60.961 57.895 0.00 0.00 39.73 3.41
2246 2273 2.253051 TGCACGCACCATGTGACTG 61.253 57.895 0.00 0.00 39.73 3.51
2247 2274 2.110835 TGCACGCACCATGTGACT 59.889 55.556 0.00 0.00 39.73 3.41
2248 2275 2.252260 GTGCACGCACCATGTGAC 59.748 61.111 11.13 0.00 40.79 3.67
2260 2287 2.240493 ACTGGTTAGTGTGAGTGCAC 57.760 50.000 9.40 9.40 45.35 4.57
2270 2297 3.708631 CCAGATCATCTCCACTGGTTAGT 59.291 47.826 0.00 0.00 43.16 2.24
2271 2298 3.963374 TCCAGATCATCTCCACTGGTTAG 59.037 47.826 0.00 0.00 46.68 2.34
2272 2299 3.963374 CTCCAGATCATCTCCACTGGTTA 59.037 47.826 0.00 0.00 46.68 2.85
2273 2300 2.770802 CTCCAGATCATCTCCACTGGTT 59.229 50.000 0.00 0.00 46.68 3.67
2274 2301 2.023598 TCTCCAGATCATCTCCACTGGT 60.024 50.000 0.00 0.00 46.68 4.00
2276 2303 5.481122 ACATATCTCCAGATCATCTCCACTG 59.519 44.000 0.00 0.00 36.05 3.66
2277 2304 5.653346 ACATATCTCCAGATCATCTCCACT 58.347 41.667 0.00 0.00 36.05 4.00
2278 2305 5.999205 ACATATCTCCAGATCATCTCCAC 57.001 43.478 0.00 0.00 36.05 4.02
2279 2306 6.786461 AGAAACATATCTCCAGATCATCTCCA 59.214 38.462 0.00 0.00 36.05 3.86
2280 2307 7.243604 AGAAACATATCTCCAGATCATCTCC 57.756 40.000 0.00 0.00 36.05 3.71
2285 2312 9.770097 GACAATAAGAAACATATCTCCAGATCA 57.230 33.333 0.00 0.00 36.05 2.92
2286 2313 9.995003 AGACAATAAGAAACATATCTCCAGATC 57.005 33.333 0.00 0.00 36.05 2.75


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

AutoCloner maintained by Alex Coulton.