Multiple sequence alignment - TraesCS3D01G175000

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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 TraesCS3D01G175000 chr3D 100.000 2387 0 0 1 2387 157041392 157039006 0.000000e+00 4409
1 TraesCS3D01G175000 chr3B 92.344 2116 78 30 2 2082 228098889 228096823 0.000000e+00 2933
2 TraesCS3D01G175000 chr3A 92.698 1616 71 17 506 2092 171209187 171210784 0.000000e+00 2287
3 TraesCS3D01G175000 chr3A 91.106 461 23 8 1 451 171208723 171209175 2.030000e-170 608
4 TraesCS3D01G175000 chr3A 91.209 91 6 1 2297 2385 225652197 225652287 3.220000e-24 122
5 TraesCS3D01G175000 chr4D 94.253 87 2 2 2301 2384 8648260 8648174 1.930000e-26 130
6 TraesCS3D01G175000 chr4A 94.186 86 3 1 2302 2385 35510923 35511008 1.930000e-26 130
7 TraesCS3D01G175000 chr7D 93.258 89 3 2 2297 2383 164730668 164730755 6.930000e-26 128
8 TraesCS3D01G175000 chr6D 93.103 87 4 1 2301 2385 350084806 350084892 2.490000e-25 126
9 TraesCS3D01G175000 chr6D 92.308 91 4 2 2300 2387 469962791 469962701 2.490000e-25 126
10 TraesCS3D01G175000 chr2A 92.308 91 4 2 2297 2385 749895068 749895157 2.490000e-25 126
11 TraesCS3D01G175000 chr7A 92.135 89 4 2 2300 2385 648748816 648748728 3.220000e-24 122
12 TraesCS3D01G175000 chr6A 91.304 92 5 2 2295 2383 147956807 147956898 3.220000e-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 TraesCS3D01G175000 chr3D 157039006 157041392 2386 True 4409.0 4409 100.000 1 2387 1 chr3D.!!$R1 2386
1 TraesCS3D01G175000 chr3B 228096823 228098889 2066 True 2933.0 2933 92.344 2 2082 1 chr3B.!!$R1 2080
2 TraesCS3D01G175000 chr3A 171208723 171210784 2061 False 1447.5 2287 91.902 1 2092 2 chr3A.!!$F2 2091

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
32 33 0.109412 GGCAGTGATGCTTCTGTTGC 60.109 55.0 0.00 12.02 34.57 4.17 F
618 630 0.325272 GCCGAGAATATTCCTCCCCC 59.675 60.0 11.92 0.00 0.00 5.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1213 1231 1.301244 AGTGCTCCACGCTTGACAG 60.301 57.895 0.0 0.0 39.64 3.51 R
2099 2148 0.029300 GCTGCTGTGTTCTCGCAAAA 59.971 50.000 0.0 0.0 33.51 2.44 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
32 33 0.109412 GGCAGTGATGCTTCTGTTGC 60.109 55.000 0.00 12.02 34.57 4.17
33 34 0.879765 GCAGTGATGCTTCTGTTGCT 59.120 50.000 0.00 0.00 34.57 3.91
34 35 1.401148 GCAGTGATGCTTCTGTTGCTG 60.401 52.381 0.00 8.90 34.57 4.41
35 36 1.878088 CAGTGATGCTTCTGTTGCTGT 59.122 47.619 0.88 0.00 0.00 4.40
36 37 2.292569 CAGTGATGCTTCTGTTGCTGTT 59.707 45.455 0.88 0.00 0.00 3.16
37 38 2.292569 AGTGATGCTTCTGTTGCTGTTG 59.707 45.455 0.88 0.00 0.00 3.33
145 147 8.355913 CCATTTAAGGCTTCATCTAATTCCTTC 58.644 37.037 1.30 0.00 34.04 3.46
210 218 1.915078 ATCCGAAGCCAGGGGAGTTG 61.915 60.000 0.00 0.00 32.43 3.16
285 297 6.986817 ACCATAGATGAGATGGAAAACTAACG 59.013 38.462 8.62 0.00 45.89 3.18
325 337 4.297510 TCAAACCGAATCAACAATGCTTG 58.702 39.130 0.00 0.00 0.00 4.01
332 344 5.107760 CCGAATCAACAATGCTTGAAAACTG 60.108 40.000 3.37 0.00 33.85 3.16
363 375 1.705337 CTAGACCCATTTGCCGTGCG 61.705 60.000 0.00 0.00 0.00 5.34
618 630 0.325272 GCCGAGAATATTCCTCCCCC 59.675 60.000 11.92 0.00 0.00 5.40
698 714 5.411361 TGAATCATGTTAAAGTTGGACGAGG 59.589 40.000 0.00 0.00 0.00 4.63
729 745 2.826777 AATCAACCAGGAGCCGGCTG 62.827 60.000 38.41 22.65 0.00 4.85
854 871 0.454957 CGCCTTTGACTTTCGCCATG 60.455 55.000 0.00 0.00 0.00 3.66
1213 1231 4.629115 GCACCTGCACCAACACGC 62.629 66.667 0.00 0.00 41.59 5.34
1218 1236 2.124942 TGCACCAACACGCTGTCA 60.125 55.556 0.00 0.00 0.00 3.58
1344 1362 2.594303 TCCAACCAGTGCGCCAAG 60.594 61.111 4.18 0.00 0.00 3.61
1883 1926 8.998277 TTTCTTGTATAGACTAGTAGGCATCT 57.002 34.615 5.63 0.00 30.90 2.90
1899 1942 2.216046 CATCTGTACATGCCATTCGCT 58.784 47.619 0.00 0.00 38.78 4.93
1901 1944 3.535280 TCTGTACATGCCATTCGCTTA 57.465 42.857 0.00 0.00 38.78 3.09
1948 1991 5.880332 TGCCAATTCATAGAACTGGTCTTAC 59.120 40.000 0.00 0.00 37.84 2.34
2034 2077 1.273048 TCAACTCATTTGCATGTGGCC 59.727 47.619 0.00 0.00 43.89 5.36
2035 2078 1.274167 CAACTCATTTGCATGTGGCCT 59.726 47.619 3.32 0.00 43.89 5.19
2036 2079 2.492881 CAACTCATTTGCATGTGGCCTA 59.507 45.455 3.32 0.00 43.89 3.93
2037 2080 2.094675 ACTCATTTGCATGTGGCCTAC 58.905 47.619 3.32 0.69 43.89 3.18
2038 2081 2.093890 CTCATTTGCATGTGGCCTACA 58.906 47.619 3.32 7.45 44.87 2.74
2078 2127 2.427453 GACGTGTCTGTCCAGTATCCAT 59.573 50.000 0.00 0.00 32.61 3.41
2092 2141 5.068636 CAGTATCCATAGCAGCCAAATCTT 58.931 41.667 0.00 0.00 0.00 2.40
2093 2142 5.533903 CAGTATCCATAGCAGCCAAATCTTT 59.466 40.000 0.00 0.00 0.00 2.52
2094 2143 6.040166 CAGTATCCATAGCAGCCAAATCTTTT 59.960 38.462 0.00 0.00 0.00 2.27
2095 2144 5.945144 ATCCATAGCAGCCAAATCTTTTT 57.055 34.783 0.00 0.00 0.00 1.94
2117 2166 2.473530 TTTTTGCGAGAACACAGCAG 57.526 45.000 0.00 0.00 42.19 4.24
2118 2167 0.029300 TTTTGCGAGAACACAGCAGC 59.971 50.000 0.00 0.00 42.19 5.25
2119 2168 1.785041 TTTGCGAGAACACAGCAGCC 61.785 55.000 0.00 0.00 42.19 4.85
2120 2169 2.666190 GCGAGAACACAGCAGCCA 60.666 61.111 0.00 0.00 0.00 4.75
2121 2170 2.253758 GCGAGAACACAGCAGCCAA 61.254 57.895 0.00 0.00 0.00 4.52
2122 2171 1.785041 GCGAGAACACAGCAGCCAAA 61.785 55.000 0.00 0.00 0.00 3.28
2123 2172 0.877071 CGAGAACACAGCAGCCAAAT 59.123 50.000 0.00 0.00 0.00 2.32
2124 2173 1.135859 CGAGAACACAGCAGCCAAATC 60.136 52.381 0.00 0.00 0.00 2.17
2125 2174 2.157738 GAGAACACAGCAGCCAAATCT 58.842 47.619 0.00 0.00 0.00 2.40
2126 2175 1.884579 AGAACACAGCAGCCAAATCTG 59.115 47.619 0.00 0.00 37.15 2.90
2127 2176 1.881973 GAACACAGCAGCCAAATCTGA 59.118 47.619 0.00 0.00 36.19 3.27
2128 2177 1.242076 ACACAGCAGCCAAATCTGAC 58.758 50.000 0.00 0.00 36.19 3.51
2129 2178 1.241165 CACAGCAGCCAAATCTGACA 58.759 50.000 0.00 0.00 36.19 3.58
2130 2179 1.068748 CACAGCAGCCAAATCTGACAC 60.069 52.381 0.00 0.00 36.19 3.67
2131 2180 1.202855 ACAGCAGCCAAATCTGACACT 60.203 47.619 0.00 0.00 36.19 3.55
2132 2181 2.038952 ACAGCAGCCAAATCTGACACTA 59.961 45.455 0.00 0.00 36.19 2.74
2133 2182 2.676839 CAGCAGCCAAATCTGACACTAG 59.323 50.000 0.00 0.00 36.19 2.57
2134 2183 2.304180 AGCAGCCAAATCTGACACTAGT 59.696 45.455 0.00 0.00 36.19 2.57
2135 2184 3.515502 AGCAGCCAAATCTGACACTAGTA 59.484 43.478 0.00 0.00 36.19 1.82
2136 2185 4.020218 AGCAGCCAAATCTGACACTAGTAA 60.020 41.667 0.00 0.00 36.19 2.24
2137 2186 4.878397 GCAGCCAAATCTGACACTAGTAAT 59.122 41.667 0.00 0.00 36.19 1.89
2138 2187 5.355350 GCAGCCAAATCTGACACTAGTAATT 59.645 40.000 0.00 0.00 36.19 1.40
2139 2188 6.127897 GCAGCCAAATCTGACACTAGTAATTT 60.128 38.462 0.00 0.00 36.19 1.82
2140 2189 7.467623 CAGCCAAATCTGACACTAGTAATTTC 58.532 38.462 0.00 0.00 36.19 2.17
2141 2190 6.599638 AGCCAAATCTGACACTAGTAATTTCC 59.400 38.462 0.00 0.00 0.00 3.13
2142 2191 6.599638 GCCAAATCTGACACTAGTAATTTCCT 59.400 38.462 0.00 0.00 0.00 3.36
2143 2192 7.769044 GCCAAATCTGACACTAGTAATTTCCTA 59.231 37.037 0.00 0.00 0.00 2.94
2144 2193 9.667107 CCAAATCTGACACTAGTAATTTCCTAA 57.333 33.333 0.00 0.00 0.00 2.69
2149 2198 9.524496 TCTGACACTAGTAATTTCCTAAGTACA 57.476 33.333 0.00 0.00 37.30 2.90
2150 2199 9.790389 CTGACACTAGTAATTTCCTAAGTACAG 57.210 37.037 0.00 0.00 37.30 2.74
2151 2200 9.305555 TGACACTAGTAATTTCCTAAGTACAGT 57.694 33.333 0.00 0.00 37.30 3.55
2165 2214 9.470399 TCCTAAGTACAGTTTACTATGATCACA 57.530 33.333 0.00 0.00 0.00 3.58
2166 2215 9.737427 CCTAAGTACAGTTTACTATGATCACAG 57.263 37.037 0.00 0.00 0.00 3.66
2167 2216 9.737427 CTAAGTACAGTTTACTATGATCACAGG 57.263 37.037 5.87 0.00 0.00 4.00
2168 2217 7.956328 AGTACAGTTTACTATGATCACAGGA 57.044 36.000 5.87 0.00 0.00 3.86
2169 2218 8.540507 AGTACAGTTTACTATGATCACAGGAT 57.459 34.615 5.87 0.00 36.13 3.24
2170 2219 8.982723 AGTACAGTTTACTATGATCACAGGATT 58.017 33.333 5.87 0.00 32.67 3.01
2171 2220 9.601217 GTACAGTTTACTATGATCACAGGATTT 57.399 33.333 5.87 0.00 32.67 2.17
2172 2221 8.723942 ACAGTTTACTATGATCACAGGATTTC 57.276 34.615 5.87 0.00 32.67 2.17
2173 2222 7.770897 ACAGTTTACTATGATCACAGGATTTCC 59.229 37.037 5.87 0.00 32.67 3.13
2174 2223 7.770433 CAGTTTACTATGATCACAGGATTTCCA 59.230 37.037 5.87 0.00 38.89 3.53
2175 2224 8.328758 AGTTTACTATGATCACAGGATTTCCAA 58.671 33.333 5.87 0.00 38.89 3.53
2176 2225 9.125026 GTTTACTATGATCACAGGATTTCCAAT 57.875 33.333 5.87 0.00 38.89 3.16
2177 2226 8.908786 TTACTATGATCACAGGATTTCCAATC 57.091 34.615 5.87 0.00 38.89 2.67
2178 2227 7.146715 ACTATGATCACAGGATTTCCAATCT 57.853 36.000 5.87 0.00 38.89 2.40
2179 2228 7.580910 ACTATGATCACAGGATTTCCAATCTT 58.419 34.615 5.87 0.00 38.89 2.40
2180 2229 8.057623 ACTATGATCACAGGATTTCCAATCTTT 58.942 33.333 5.87 0.00 38.89 2.52
2181 2230 7.729124 ATGATCACAGGATTTCCAATCTTTT 57.271 32.000 0.00 0.00 38.89 2.27
2182 2231 7.161773 TGATCACAGGATTTCCAATCTTTTC 57.838 36.000 0.00 0.00 38.89 2.29
2183 2232 6.950041 TGATCACAGGATTTCCAATCTTTTCT 59.050 34.615 0.00 0.00 38.89 2.52
2184 2233 7.452501 TGATCACAGGATTTCCAATCTTTTCTT 59.547 33.333 0.00 0.00 38.89 2.52
2185 2234 6.985117 TCACAGGATTTCCAATCTTTTCTTG 58.015 36.000 0.00 0.00 38.89 3.02
2186 2235 6.777091 TCACAGGATTTCCAATCTTTTCTTGA 59.223 34.615 0.00 0.00 38.89 3.02
2187 2236 7.040201 TCACAGGATTTCCAATCTTTTCTTGAG 60.040 37.037 0.00 0.00 38.89 3.02
2188 2237 6.210185 ACAGGATTTCCAATCTTTTCTTGAGG 59.790 38.462 0.00 0.00 38.89 3.86
2189 2238 6.435277 CAGGATTTCCAATCTTTTCTTGAGGA 59.565 38.462 0.00 0.00 38.89 3.71
2190 2239 7.123847 CAGGATTTCCAATCTTTTCTTGAGGAT 59.876 37.037 0.00 0.00 38.89 3.24
2191 2240 7.677319 AGGATTTCCAATCTTTTCTTGAGGATT 59.323 33.333 0.00 0.00 38.89 3.01
2192 2241 8.316946 GGATTTCCAATCTTTTCTTGAGGATTT 58.683 33.333 0.00 0.00 35.64 2.17
2193 2242 9.716531 GATTTCCAATCTTTTCTTGAGGATTTT 57.283 29.630 0.00 0.00 0.00 1.82
2225 2274 6.552445 ACTGTAGAGTTTATCATCTTGGCT 57.448 37.500 0.00 0.00 0.00 4.75
2226 2275 7.661536 ACTGTAGAGTTTATCATCTTGGCTA 57.338 36.000 0.00 0.00 0.00 3.93
2227 2276 7.721402 ACTGTAGAGTTTATCATCTTGGCTAG 58.279 38.462 0.00 0.00 0.00 3.42
2228 2277 7.561722 ACTGTAGAGTTTATCATCTTGGCTAGA 59.438 37.037 0.14 0.14 37.28 2.43
2229 2278 7.946207 TGTAGAGTTTATCATCTTGGCTAGAG 58.054 38.462 4.72 0.00 36.02 2.43
2230 2279 5.852827 AGAGTTTATCATCTTGGCTAGAGC 58.147 41.667 4.72 0.00 36.02 4.09
2231 2280 5.365025 AGAGTTTATCATCTTGGCTAGAGCA 59.635 40.000 4.72 0.00 44.36 4.26
2232 2281 5.994250 AGTTTATCATCTTGGCTAGAGCAA 58.006 37.500 4.72 0.00 44.36 3.91
2233 2282 6.418101 AGTTTATCATCTTGGCTAGAGCAAA 58.582 36.000 4.72 0.00 44.36 3.68
2234 2283 6.886459 AGTTTATCATCTTGGCTAGAGCAAAA 59.114 34.615 4.72 0.73 44.36 2.44
2235 2284 7.394359 AGTTTATCATCTTGGCTAGAGCAAAAA 59.606 33.333 4.72 1.05 44.36 1.94
2257 2306 6.530019 AAAATCAGGGTTTTAGCATAGGTG 57.470 37.500 0.00 0.00 29.96 4.00
2258 2307 4.862641 ATCAGGGTTTTAGCATAGGTGT 57.137 40.909 0.00 0.00 0.00 4.16
2259 2308 5.968676 ATCAGGGTTTTAGCATAGGTGTA 57.031 39.130 0.00 0.00 0.00 2.90
2260 2309 5.968676 TCAGGGTTTTAGCATAGGTGTAT 57.031 39.130 0.00 0.00 0.00 2.29
2261 2310 5.925509 TCAGGGTTTTAGCATAGGTGTATC 58.074 41.667 0.00 0.00 0.00 2.24
2262 2311 5.063880 CAGGGTTTTAGCATAGGTGTATCC 58.936 45.833 0.00 0.00 0.00 2.59
2286 2335 9.691362 TCCTGAACTTTATTTTAAGAAACATGC 57.309 29.630 0.00 0.00 0.00 4.06
2287 2336 9.474920 CCTGAACTTTATTTTAAGAAACATGCA 57.525 29.630 0.00 0.00 0.00 3.96
2289 2338 9.255304 TGAACTTTATTTTAAGAAACATGCACC 57.745 29.630 0.00 0.00 0.00 5.01
2290 2339 8.601845 AACTTTATTTTAAGAAACATGCACCC 57.398 30.769 0.00 0.00 0.00 4.61
2291 2340 6.866248 ACTTTATTTTAAGAAACATGCACCCG 59.134 34.615 0.00 0.00 0.00 5.28
2292 2341 2.715737 TTTAAGAAACATGCACCCGC 57.284 45.000 0.00 0.00 39.24 6.13
2327 2376 7.713764 TTTTTAAGAGAGGCAAAAGATTTGC 57.286 32.000 17.18 17.18 44.22 3.68
2339 2388 7.781548 GCAAAAGATTTGCCTCATTCATTAT 57.218 32.000 15.12 0.00 39.38 1.28
2340 2389 8.876275 GCAAAAGATTTGCCTCATTCATTATA 57.124 30.769 15.12 0.00 39.38 0.98
2341 2390 9.316730 GCAAAAGATTTGCCTCATTCATTATAA 57.683 29.630 15.12 0.00 39.38 0.98
2345 2394 8.632906 AGATTTGCCTCATTCATTATAAGAGG 57.367 34.615 11.58 11.58 46.71 3.69
2346 2395 8.443176 AGATTTGCCTCATTCATTATAAGAGGA 58.557 33.333 17.63 2.00 46.89 3.71
2347 2396 9.071276 GATTTGCCTCATTCATTATAAGAGGAA 57.929 33.333 17.63 7.79 46.89 3.36
2348 2397 9.597681 ATTTGCCTCATTCATTATAAGAGGAAT 57.402 29.630 17.63 11.14 46.89 3.01
2350 2399 9.730705 TTGCCTCATTCATTATAAGAGGAATAG 57.269 33.333 17.63 11.11 46.89 1.73
2351 2400 9.104713 TGCCTCATTCATTATAAGAGGAATAGA 57.895 33.333 17.63 11.88 46.89 1.98
2352 2401 9.598517 GCCTCATTCATTATAAGAGGAATAGAG 57.401 37.037 17.63 17.17 46.89 2.43
2364 2413 7.455641 AAGAGGAATAGAGTATATGGTCGTG 57.544 40.000 0.00 0.00 0.00 4.35
2365 2414 6.544650 AGAGGAATAGAGTATATGGTCGTGT 58.455 40.000 0.00 0.00 0.00 4.49
2366 2415 7.005296 AGAGGAATAGAGTATATGGTCGTGTT 58.995 38.462 0.00 0.00 0.00 3.32
2367 2416 8.162085 AGAGGAATAGAGTATATGGTCGTGTTA 58.838 37.037 0.00 0.00 0.00 2.41
2368 2417 8.108551 AGGAATAGAGTATATGGTCGTGTTAC 57.891 38.462 0.00 0.00 0.00 2.50
2369 2418 7.722728 AGGAATAGAGTATATGGTCGTGTTACA 59.277 37.037 0.00 0.00 0.00 2.41
2370 2419 8.355169 GGAATAGAGTATATGGTCGTGTTACAA 58.645 37.037 0.00 0.00 0.00 2.41
2371 2420 9.178427 GAATAGAGTATATGGTCGTGTTACAAC 57.822 37.037 0.00 0.00 0.00 3.32
2372 2421 6.519679 AGAGTATATGGTCGTGTTACAACA 57.480 37.500 0.00 0.00 36.38 3.33
2382 2431 0.934496 TGTTACAACACAGACAGCGC 59.066 50.000 0.00 0.00 33.17 5.92
2383 2432 0.234884 GTTACAACACAGACAGCGCC 59.765 55.000 2.29 0.00 0.00 6.53
2384 2433 1.218875 TTACAACACAGACAGCGCCG 61.219 55.000 2.29 0.00 0.00 6.46
2385 2434 2.358193 TACAACACAGACAGCGCCGT 62.358 55.000 2.29 0.00 0.00 5.68
2386 2435 1.663388 CAACACAGACAGCGCCGTA 60.663 57.895 2.29 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 2.174639 TGGGGTATAATCCCTGCAACAG 59.825 50.000 12.19 0.00 46.27 3.16
33 34 2.209758 TGGGGTATAATCCCTGCAACA 58.790 47.619 12.19 0.00 46.27 3.33
34 35 3.306472 TTGGGGTATAATCCCTGCAAC 57.694 47.619 12.19 0.00 46.27 4.17
35 36 3.465210 TGATTGGGGTATAATCCCTGCAA 59.535 43.478 12.19 4.07 46.27 4.08
36 37 3.059853 TGATTGGGGTATAATCCCTGCA 58.940 45.455 12.19 0.00 46.27 4.41
37 38 3.806949 TGATTGGGGTATAATCCCTGC 57.193 47.619 12.19 4.36 46.27 4.85
170 172 6.187682 GGATTCCCTTCAGGTTTGATCTAAA 58.812 40.000 0.00 0.00 36.75 1.85
210 218 4.642429 AGTCCACATTCAGACAGGTTTAC 58.358 43.478 0.00 0.00 35.38 2.01
285 297 9.362539 TCGGTTTGAAAGATACAGTAAGTAATC 57.637 33.333 0.00 0.00 36.05 1.75
325 337 6.300356 GTCTAGAAGCACGAAATCAGTTTTC 58.700 40.000 0.00 0.00 40.34 2.29
332 344 3.247006 TGGGTCTAGAAGCACGAAATC 57.753 47.619 0.00 0.00 0.00 2.17
363 375 3.486875 GGCATGTTACTTCGGTATGCAAC 60.487 47.826 0.00 0.00 36.32 4.17
478 490 2.607187 GATTACACGTACTGCTGCTGT 58.393 47.619 16.37 16.37 0.00 4.40
602 614 0.325272 GGCGGGGGAGGAATATTCTC 59.675 60.000 14.95 10.07 0.00 2.87
698 714 2.751806 CTGGTTGATTTCTTCTCTGCCC 59.248 50.000 0.00 0.00 0.00 5.36
1213 1231 1.301244 AGTGCTCCACGCTTGACAG 60.301 57.895 0.00 0.00 39.64 3.51
1344 1362 1.606350 CGAACTCGCACTTGACGGAC 61.606 60.000 0.00 0.00 0.00 4.79
1575 1618 7.481642 ACGAACAGAGAGACGTATAAATCATT 58.518 34.615 0.00 0.00 37.22 2.57
1652 1695 8.780846 ATTCACTTTATTAATACCACGTGACA 57.219 30.769 19.30 4.06 30.79 3.58
1697 1740 8.686334 GGTACCCCAAAAATGATATATATGCTG 58.314 37.037 0.00 0.00 0.00 4.41
1698 1741 8.823220 GGTACCCCAAAAATGATATATATGCT 57.177 34.615 0.00 0.00 0.00 3.79
1861 1904 7.753309 ACAGATGCCTACTAGTCTATACAAG 57.247 40.000 0.00 0.00 0.00 3.16
1862 1905 8.215736 TGTACAGATGCCTACTAGTCTATACAA 58.784 37.037 0.00 0.00 30.26 2.41
1899 1942 5.425577 TTGCAAGCAGTCGTACAAATTAA 57.574 34.783 0.00 0.00 0.00 1.40
1901 1944 3.980646 TTGCAAGCAGTCGTACAAATT 57.019 38.095 0.00 0.00 0.00 1.82
1948 1991 3.220110 TGTACGCATCCTAGGTCCTAAG 58.780 50.000 9.08 0.00 0.00 2.18
1962 2005 2.134346 GTACTTTCCCGTTTGTACGCA 58.866 47.619 0.00 0.00 46.27 5.24
2034 2077 7.391786 GTCACGTACTAATGCAAAGAATGTAG 58.608 38.462 6.45 0.00 0.00 2.74
2035 2078 6.034150 CGTCACGTACTAATGCAAAGAATGTA 59.966 38.462 6.45 0.00 0.00 2.29
2036 2079 5.163992 CGTCACGTACTAATGCAAAGAATGT 60.164 40.000 6.45 0.00 0.00 2.71
2037 2080 5.163992 ACGTCACGTACTAATGCAAAGAATG 60.164 40.000 0.00 0.42 38.73 2.67
2038 2081 4.927425 ACGTCACGTACTAATGCAAAGAAT 59.073 37.500 0.00 0.00 38.73 2.40
2039 2082 4.149221 CACGTCACGTACTAATGCAAAGAA 59.851 41.667 0.41 0.00 38.32 2.52
2040 2083 3.671459 CACGTCACGTACTAATGCAAAGA 59.329 43.478 0.41 0.00 38.32 2.52
2041 2084 3.427528 ACACGTCACGTACTAATGCAAAG 59.572 43.478 0.41 0.00 38.32 2.77
2098 2147 1.533756 GCTGCTGTGTTCTCGCAAAAA 60.534 47.619 0.00 0.00 33.51 1.94
2099 2148 0.029300 GCTGCTGTGTTCTCGCAAAA 59.971 50.000 0.00 0.00 33.51 2.44
2100 2149 1.648720 GCTGCTGTGTTCTCGCAAA 59.351 52.632 0.00 0.00 33.51 3.68
2101 2150 2.253758 GGCTGCTGTGTTCTCGCAA 61.254 57.895 0.00 0.00 33.51 4.85
2102 2151 2.666190 GGCTGCTGTGTTCTCGCA 60.666 61.111 0.00 0.00 0.00 5.10
2103 2152 1.785041 TTTGGCTGCTGTGTTCTCGC 61.785 55.000 0.00 0.00 0.00 5.03
2104 2153 0.877071 ATTTGGCTGCTGTGTTCTCG 59.123 50.000 0.00 0.00 0.00 4.04
2105 2154 2.095364 CAGATTTGGCTGCTGTGTTCTC 60.095 50.000 0.00 0.00 0.00 2.87
2106 2155 1.884579 CAGATTTGGCTGCTGTGTTCT 59.115 47.619 0.00 0.00 0.00 3.01
2107 2156 1.881973 TCAGATTTGGCTGCTGTGTTC 59.118 47.619 0.00 0.00 35.86 3.18
2108 2157 1.610522 GTCAGATTTGGCTGCTGTGTT 59.389 47.619 0.00 0.00 35.86 3.32
2109 2158 1.242076 GTCAGATTTGGCTGCTGTGT 58.758 50.000 0.00 0.00 35.86 3.72
2110 2159 1.068748 GTGTCAGATTTGGCTGCTGTG 60.069 52.381 0.00 0.00 35.86 3.66
2111 2160 1.202855 AGTGTCAGATTTGGCTGCTGT 60.203 47.619 0.00 0.00 35.86 4.40
2112 2161 1.531423 AGTGTCAGATTTGGCTGCTG 58.469 50.000 0.00 0.00 35.86 4.41
2113 2162 2.304180 ACTAGTGTCAGATTTGGCTGCT 59.696 45.455 0.00 0.00 35.86 4.24
2114 2163 2.704572 ACTAGTGTCAGATTTGGCTGC 58.295 47.619 0.00 0.00 35.86 5.25
2115 2164 6.992063 AATTACTAGTGTCAGATTTGGCTG 57.008 37.500 5.39 0.00 37.24 4.85
2116 2165 6.599638 GGAAATTACTAGTGTCAGATTTGGCT 59.400 38.462 5.39 0.00 0.00 4.75
2117 2166 6.599638 AGGAAATTACTAGTGTCAGATTTGGC 59.400 38.462 5.39 0.00 0.00 4.52
2118 2167 9.667107 TTAGGAAATTACTAGTGTCAGATTTGG 57.333 33.333 5.39 0.00 0.00 3.28
2123 2172 9.524496 TGTACTTAGGAAATTACTAGTGTCAGA 57.476 33.333 5.39 0.00 0.00 3.27
2124 2173 9.790389 CTGTACTTAGGAAATTACTAGTGTCAG 57.210 37.037 5.39 0.00 0.00 3.51
2125 2174 9.305555 ACTGTACTTAGGAAATTACTAGTGTCA 57.694 33.333 5.39 0.00 0.00 3.58
2139 2188 9.470399 TGTGATCATAGTAAACTGTACTTAGGA 57.530 33.333 0.00 0.00 0.00 2.94
2140 2189 9.737427 CTGTGATCATAGTAAACTGTACTTAGG 57.263 37.037 11.11 0.00 0.00 2.69
2141 2190 9.737427 CCTGTGATCATAGTAAACTGTACTTAG 57.263 37.037 17.14 0.00 0.00 2.18
2142 2191 9.470399 TCCTGTGATCATAGTAAACTGTACTTA 57.530 33.333 17.14 0.00 0.00 2.24
2143 2192 8.362464 TCCTGTGATCATAGTAAACTGTACTT 57.638 34.615 17.14 0.00 0.00 2.24
2144 2193 7.956328 TCCTGTGATCATAGTAAACTGTACT 57.044 36.000 17.14 0.00 0.00 2.73
2145 2194 9.601217 AAATCCTGTGATCATAGTAAACTGTAC 57.399 33.333 17.14 0.00 0.00 2.90
2146 2195 9.817809 GAAATCCTGTGATCATAGTAAACTGTA 57.182 33.333 17.14 0.00 0.00 2.74
2147 2196 7.770897 GGAAATCCTGTGATCATAGTAAACTGT 59.229 37.037 17.14 0.00 0.00 3.55
2148 2197 7.770433 TGGAAATCCTGTGATCATAGTAAACTG 59.230 37.037 17.14 2.35 36.82 3.16
2149 2198 7.861629 TGGAAATCCTGTGATCATAGTAAACT 58.138 34.615 17.14 0.00 36.82 2.66
2150 2199 8.506168 TTGGAAATCCTGTGATCATAGTAAAC 57.494 34.615 17.14 5.78 36.82 2.01
2151 2200 9.342308 GATTGGAAATCCTGTGATCATAGTAAA 57.658 33.333 17.14 4.21 36.82 2.01
2152 2201 8.717717 AGATTGGAAATCCTGTGATCATAGTAA 58.282 33.333 17.14 6.50 36.82 2.24
2153 2202 8.267620 AGATTGGAAATCCTGTGATCATAGTA 57.732 34.615 17.14 2.91 36.82 1.82
2154 2203 7.146715 AGATTGGAAATCCTGTGATCATAGT 57.853 36.000 17.14 0.00 36.82 2.12
2155 2204 8.461249 AAAGATTGGAAATCCTGTGATCATAG 57.539 34.615 12.27 12.27 36.82 2.23
2156 2205 8.827832 AAAAGATTGGAAATCCTGTGATCATA 57.172 30.769 0.00 0.00 36.82 2.15
2157 2206 7.618512 AGAAAAGATTGGAAATCCTGTGATCAT 59.381 33.333 0.00 0.00 36.82 2.45
2158 2207 6.950041 AGAAAAGATTGGAAATCCTGTGATCA 59.050 34.615 0.44 0.00 36.82 2.92
2159 2208 7.401955 AGAAAAGATTGGAAATCCTGTGATC 57.598 36.000 0.44 0.00 36.82 2.92
2160 2209 7.452501 TCAAGAAAAGATTGGAAATCCTGTGAT 59.547 33.333 0.44 0.00 36.82 3.06
2161 2210 6.777091 TCAAGAAAAGATTGGAAATCCTGTGA 59.223 34.615 0.44 0.00 36.82 3.58
2162 2211 6.985117 TCAAGAAAAGATTGGAAATCCTGTG 58.015 36.000 0.44 0.00 36.82 3.66
2163 2212 6.210185 CCTCAAGAAAAGATTGGAAATCCTGT 59.790 38.462 0.44 0.00 36.82 4.00
2164 2213 6.435277 TCCTCAAGAAAAGATTGGAAATCCTG 59.565 38.462 0.44 0.00 36.82 3.86
2165 2214 6.555711 TCCTCAAGAAAAGATTGGAAATCCT 58.444 36.000 0.44 0.00 36.82 3.24
2166 2215 6.840780 TCCTCAAGAAAAGATTGGAAATCC 57.159 37.500 0.00 0.00 0.00 3.01
2167 2216 9.716531 AAAATCCTCAAGAAAAGATTGGAAATC 57.283 29.630 0.00 0.00 0.00 2.17
2201 2250 6.951971 AGCCAAGATGATAAACTCTACAGTT 58.048 36.000 0.00 0.00 45.43 3.16
2202 2251 6.552445 AGCCAAGATGATAAACTCTACAGT 57.448 37.500 0.00 0.00 0.00 3.55
2203 2252 7.946207 TCTAGCCAAGATGATAAACTCTACAG 58.054 38.462 0.00 0.00 0.00 2.74
2204 2253 7.470702 GCTCTAGCCAAGATGATAAACTCTACA 60.471 40.741 0.00 0.00 32.41 2.74
2205 2254 6.866248 GCTCTAGCCAAGATGATAAACTCTAC 59.134 42.308 0.00 0.00 32.41 2.59
2206 2255 6.551227 TGCTCTAGCCAAGATGATAAACTCTA 59.449 38.462 0.00 0.00 41.18 2.43
2207 2256 5.365025 TGCTCTAGCCAAGATGATAAACTCT 59.635 40.000 0.00 0.00 41.18 3.24
2208 2257 5.605534 TGCTCTAGCCAAGATGATAAACTC 58.394 41.667 0.00 0.00 41.18 3.01
2209 2258 5.620738 TGCTCTAGCCAAGATGATAAACT 57.379 39.130 0.00 0.00 41.18 2.66
2210 2259 6.683974 TTTGCTCTAGCCAAGATGATAAAC 57.316 37.500 0.00 0.00 41.18 2.01
2211 2260 7.701539 TTTTTGCTCTAGCCAAGATGATAAA 57.298 32.000 0.00 0.00 41.18 1.40
2233 2282 6.496911 ACACCTATGCTAAAACCCTGATTTTT 59.503 34.615 0.00 0.00 33.80 1.94
2234 2283 6.016555 ACACCTATGCTAAAACCCTGATTTT 58.983 36.000 0.00 0.00 35.89 1.82
2235 2284 5.580022 ACACCTATGCTAAAACCCTGATTT 58.420 37.500 0.00 0.00 0.00 2.17
2236 2285 5.193099 ACACCTATGCTAAAACCCTGATT 57.807 39.130 0.00 0.00 0.00 2.57
2237 2286 4.862641 ACACCTATGCTAAAACCCTGAT 57.137 40.909 0.00 0.00 0.00 2.90
2238 2287 5.163237 GGATACACCTATGCTAAAACCCTGA 60.163 44.000 0.00 0.00 35.41 3.86
2239 2288 5.063880 GGATACACCTATGCTAAAACCCTG 58.936 45.833 0.00 0.00 35.41 4.45
2240 2289 5.306114 GGATACACCTATGCTAAAACCCT 57.694 43.478 0.00 0.00 35.41 4.34
2260 2309 9.691362 GCATGTTTCTTAAAATAAAGTTCAGGA 57.309 29.630 0.00 0.00 0.00 3.86
2261 2310 9.474920 TGCATGTTTCTTAAAATAAAGTTCAGG 57.525 29.630 0.00 0.00 0.00 3.86
2263 2312 9.255304 GGTGCATGTTTCTTAAAATAAAGTTCA 57.745 29.630 0.00 0.00 0.00 3.18
2264 2313 8.708742 GGGTGCATGTTTCTTAAAATAAAGTTC 58.291 33.333 0.00 0.00 0.00 3.01
2265 2314 7.383843 CGGGTGCATGTTTCTTAAAATAAAGTT 59.616 33.333 0.00 0.00 0.00 2.66
2266 2315 6.866248 CGGGTGCATGTTTCTTAAAATAAAGT 59.134 34.615 0.00 0.00 0.00 2.66
2267 2316 6.183360 GCGGGTGCATGTTTCTTAAAATAAAG 60.183 38.462 0.00 0.00 42.15 1.85
2268 2317 5.635700 GCGGGTGCATGTTTCTTAAAATAAA 59.364 36.000 0.00 0.00 42.15 1.40
2269 2318 5.164954 GCGGGTGCATGTTTCTTAAAATAA 58.835 37.500 0.00 0.00 42.15 1.40
2270 2319 4.739195 GCGGGTGCATGTTTCTTAAAATA 58.261 39.130 0.00 0.00 42.15 1.40
2271 2320 3.584834 GCGGGTGCATGTTTCTTAAAAT 58.415 40.909 0.00 0.00 42.15 1.82
2272 2321 3.019933 GCGGGTGCATGTTTCTTAAAA 57.980 42.857 0.00 0.00 42.15 1.52
2273 2322 2.715737 GCGGGTGCATGTTTCTTAAA 57.284 45.000 0.00 0.00 42.15 1.52
2303 2352 7.713764 GCAAATCTTTTGCCTCTCTTAAAAA 57.286 32.000 12.74 0.00 39.38 1.94
2315 2364 7.781548 ATAATGAATGAGGCAAATCTTTTGC 57.218 32.000 14.88 14.88 44.22 3.68
2319 2368 9.075678 CCTCTTATAATGAATGAGGCAAATCTT 57.924 33.333 5.13 0.00 37.98 2.40
2320 2369 8.443176 TCCTCTTATAATGAATGAGGCAAATCT 58.557 33.333 11.22 0.00 42.77 2.40
2321 2370 8.627208 TCCTCTTATAATGAATGAGGCAAATC 57.373 34.615 11.22 0.00 42.77 2.17
2322 2371 9.597681 ATTCCTCTTATAATGAATGAGGCAAAT 57.402 29.630 11.22 6.07 42.77 2.32
2324 2373 9.730705 CTATTCCTCTTATAATGAATGAGGCAA 57.269 33.333 11.22 8.12 42.77 4.52
2325 2374 9.104713 TCTATTCCTCTTATAATGAATGAGGCA 57.895 33.333 11.22 3.52 42.77 4.75
2326 2375 9.598517 CTCTATTCCTCTTATAATGAATGAGGC 57.401 37.037 11.22 0.00 42.77 4.70
2338 2387 9.179909 CACGACCATATACTCTATTCCTCTTAT 57.820 37.037 0.00 0.00 0.00 1.73
2339 2388 8.162085 ACACGACCATATACTCTATTCCTCTTA 58.838 37.037 0.00 0.00 0.00 2.10
2340 2389 7.005296 ACACGACCATATACTCTATTCCTCTT 58.995 38.462 0.00 0.00 0.00 2.85
2341 2390 6.544650 ACACGACCATATACTCTATTCCTCT 58.455 40.000 0.00 0.00 0.00 3.69
2342 2391 6.821031 ACACGACCATATACTCTATTCCTC 57.179 41.667 0.00 0.00 0.00 3.71
2343 2392 7.722728 TGTAACACGACCATATACTCTATTCCT 59.277 37.037 0.00 0.00 0.00 3.36
2344 2393 7.879070 TGTAACACGACCATATACTCTATTCC 58.121 38.462 0.00 0.00 0.00 3.01
2345 2394 9.178427 GTTGTAACACGACCATATACTCTATTC 57.822 37.037 0.00 0.00 0.00 1.75
2346 2395 8.689061 TGTTGTAACACGACCATATACTCTATT 58.311 33.333 0.00 0.00 33.17 1.73
2347 2396 8.229253 TGTTGTAACACGACCATATACTCTAT 57.771 34.615 0.00 0.00 33.17 1.98
2348 2397 7.628769 TGTTGTAACACGACCATATACTCTA 57.371 36.000 0.00 0.00 33.17 2.43
2349 2398 6.519679 TGTTGTAACACGACCATATACTCT 57.480 37.500 0.00 0.00 33.17 3.24
2363 2412 0.934496 GCGCTGTCTGTGTTGTAACA 59.066 50.000 0.00 0.00 36.38 2.41
2364 2413 0.234884 GGCGCTGTCTGTGTTGTAAC 59.765 55.000 7.64 0.00 0.00 2.50
2365 2414 1.218875 CGGCGCTGTCTGTGTTGTAA 61.219 55.000 8.45 0.00 0.00 2.41
2366 2415 1.663388 CGGCGCTGTCTGTGTTGTA 60.663 57.895 8.45 0.00 0.00 2.41
2367 2416 2.358193 TACGGCGCTGTCTGTGTTGT 62.358 55.000 28.15 0.00 0.00 3.32
2368 2417 1.663388 TACGGCGCTGTCTGTGTTG 60.663 57.895 28.15 0.00 0.00 3.33
2369 2418 2.732016 TACGGCGCTGTCTGTGTT 59.268 55.556 28.15 0.97 0.00 3.32


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

AutoCloner maintained by Alex Coulton.