Multiple sequence alignment - TraesCS2A01G077000

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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 TraesCS2A01G077000 chr2A 100.000 2473 0 0 1 2473 34831006 34833478 0.000000e+00 4567
1 TraesCS2A01G077000 chr2A 93.701 127 8 0 1 127 41999920 41999794 9.030000e-45 191
2 TraesCS2A01G077000 chr7A 95.549 2067 79 8 1 2067 727828392 727830445 0.000000e+00 3295
3 TraesCS2A01G077000 chr7A 93.828 2074 118 7 1 2067 7721967 7724037 0.000000e+00 3112
4 TraesCS2A01G077000 chr7A 90.179 112 9 2 1956 2066 559405025 559404915 7.130000e-31 145
5 TraesCS2A01G077000 chr1D 94.211 2073 97 6 1 2065 28017871 28019928 0.000000e+00 3142
6 TraesCS2A01G077000 chr5A 93.600 2078 115 10 1 2070 311293661 311291594 0.000000e+00 3085
7 TraesCS2A01G077000 chr5A 92.926 2078 135 7 1 2070 77082314 77080241 0.000000e+00 3013
8 TraesCS2A01G077000 chr5A 93.627 204 7 4 2078 2276 50774481 50774279 1.440000e-77 300
9 TraesCS2A01G077000 chr5A 94.792 192 7 1 2077 2265 483514291 483514482 1.860000e-76 296
10 TraesCS2A01G077000 chr5A 92.308 78 6 0 2078 2155 1523218 1523141 7.230000e-21 111
11 TraesCS2A01G077000 chr1A 93.542 2075 119 12 1 2067 548953955 548956022 0.000000e+00 3075
12 TraesCS2A01G077000 chr6A 93.481 2071 126 7 1 2067 94342166 94344231 0.000000e+00 3068
13 TraesCS2A01G077000 chr6A 100.000 75 0 0 2266 2340 15004663 15004737 3.320000e-29 139
14 TraesCS2A01G077000 chr6A 100.000 75 0 0 2266 2340 15116143 15116217 3.320000e-29 139
15 TraesCS2A01G077000 chr4A 93.088 2069 131 9 3 2066 522257288 522259349 0.000000e+00 3018
16 TraesCS2A01G077000 chr4A 93.677 1961 116 6 112 2067 117881718 117883675 0.000000e+00 2928
17 TraesCS2A01G077000 chr4A 95.610 205 9 0 2269 2473 713173077 713172873 1.830000e-86 329
18 TraesCS2A01G077000 chr4A 95.652 138 6 0 2336 2473 134637627 134637490 3.200000e-54 222
19 TraesCS2A01G077000 chr4A 95.652 138 6 0 2336 2473 597472631 597472768 3.200000e-54 222
20 TraesCS2A01G077000 chr3A 95.074 203 9 1 2077 2278 708093490 708093288 3.970000e-83 318
21 TraesCS2A01G077000 chr3A 92.208 77 5 1 2079 2155 6662939 6663014 9.350000e-20 108
22 TraesCS2A01G077000 chr7D 96.809 188 6 0 2078 2265 493955445 493955632 5.130000e-82 315
23 TraesCS2A01G077000 chr7B 95.652 138 6 0 2336 2473 703986179 703986042 3.200000e-54 222
24 TraesCS2A01G077000 chr7B 98.750 80 1 0 2261 2340 189384600 189384679 2.560000e-30 143
25 TraesCS2A01G077000 chr7B 98.734 79 1 0 2262 2340 123046882 123046804 9.220000e-30 141
26 TraesCS2A01G077000 chr7B 97.561 82 1 1 2259 2340 448461607 448461687 3.320000e-29 139
27 TraesCS2A01G077000 chr6B 95.652 138 6 0 2336 2473 482530533 482530670 3.200000e-54 222
28 TraesCS2A01G077000 chr6B 98.795 83 1 0 2258 2340 117779267 117779349 5.510000e-32 148
29 TraesCS2A01G077000 chr1B 95.652 138 6 0 2336 2473 526349651 526349514 3.200000e-54 222
30 TraesCS2A01G077000 chr1B 96.386 83 2 1 2258 2340 628614783 628614702 4.290000e-28 135
31 TraesCS2A01G077000 chrUn 94.928 138 7 0 2336 2473 351391786 351391923 1.490000e-52 217
32 TraesCS2A01G077000 chr4B 94.928 138 7 0 2336 2473 64790548 64790411 1.490000e-52 217
33 TraesCS2A01G077000 chr4B 94.928 138 7 0 2336 2473 580807681 580807544 1.490000e-52 217
34 TraesCS2A01G077000 chr5B 98.718 78 1 0 2266 2343 678669366 678669289 3.320000e-29 139
35 TraesCS2A01G077000 chr3B 91.667 72 4 2 2077 2146 370159486 370159415 5.630000e-17 99


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 TraesCS2A01G077000 chr2A 34831006 34833478 2472 False 4567 4567 100.000 1 2473 1 chr2A.!!$F1 2472
1 TraesCS2A01G077000 chr7A 727828392 727830445 2053 False 3295 3295 95.549 1 2067 1 chr7A.!!$F2 2066
2 TraesCS2A01G077000 chr7A 7721967 7724037 2070 False 3112 3112 93.828 1 2067 1 chr7A.!!$F1 2066
3 TraesCS2A01G077000 chr1D 28017871 28019928 2057 False 3142 3142 94.211 1 2065 1 chr1D.!!$F1 2064
4 TraesCS2A01G077000 chr5A 311291594 311293661 2067 True 3085 3085 93.600 1 2070 1 chr5A.!!$R4 2069
5 TraesCS2A01G077000 chr5A 77080241 77082314 2073 True 3013 3013 92.926 1 2070 1 chr5A.!!$R3 2069
6 TraesCS2A01G077000 chr1A 548953955 548956022 2067 False 3075 3075 93.542 1 2067 1 chr1A.!!$F1 2066
7 TraesCS2A01G077000 chr6A 94342166 94344231 2065 False 3068 3068 93.481 1 2067 1 chr6A.!!$F3 2066
8 TraesCS2A01G077000 chr4A 522257288 522259349 2061 False 3018 3018 93.088 3 2066 1 chr4A.!!$F2 2063
9 TraesCS2A01G077000 chr4A 117881718 117883675 1957 False 2928 2928 93.677 112 2067 1 chr4A.!!$F1 1955

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
321 325 0.319555 TTCGCTACTTTGTCTGCGCT 60.32 50.0 9.73 0.0 46.73 5.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2172 2212 0.037697 AGCGATGTACGTGCCAGAAA 60.038 50.0 0.0 0.0 44.6 2.52 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
128 129 2.434359 GTGACGCCCTTCCTTCCG 60.434 66.667 0.00 0.00 0.00 4.30
199 203 4.554363 CGCTCGCTCGATCCCGTT 62.554 66.667 0.00 0.00 37.05 4.44
321 325 0.319555 TTCGCTACTTTGTCTGCGCT 60.320 50.000 9.73 0.00 46.73 5.92
333 337 2.259618 GTCTGCGCTAACGAGATCAAA 58.740 47.619 9.73 0.00 43.93 2.69
452 457 1.221840 CTAGGGCGCCATTGACACT 59.778 57.895 30.85 16.57 0.00 3.55
626 632 4.479993 GCCCATGCTCGAGCCTGT 62.480 66.667 31.90 18.63 41.18 4.00
638 644 4.996976 GCCTGTCGCTCTTCTTCA 57.003 55.556 0.00 0.00 0.00 3.02
720 726 4.831307 CGCTACCTTCGCGCTCGT 62.831 66.667 5.56 0.00 44.33 4.18
769 775 4.935495 CACACACCCTGGCTGCGT 62.935 66.667 0.00 0.00 0.00 5.24
1032 1040 0.464554 TGTCGTGGACAAATGTGGCA 60.465 50.000 0.00 0.00 39.78 4.92
1115 1124 3.702048 GGCGGTGTCACCTGGCTA 61.702 66.667 23.58 0.00 35.66 3.93
1180 1192 4.398319 AGGTCACAATTGGAAAGAATCGT 58.602 39.130 10.83 0.00 0.00 3.73
1391 1411 0.533308 GTACCTGCCCGTTTGTGACA 60.533 55.000 0.00 0.00 0.00 3.58
2067 2107 5.873179 CTCGTCCATTAGGAGTAGAGATC 57.127 47.826 0.00 0.00 46.92 2.75
2070 2110 4.400120 GTCCATTAGGAGTAGAGATCCGT 58.600 47.826 0.00 0.00 46.92 4.69
2071 2111 4.828387 GTCCATTAGGAGTAGAGATCCGTT 59.172 45.833 0.00 0.00 46.92 4.44
2072 2112 5.048573 GTCCATTAGGAGTAGAGATCCGTTC 60.049 48.000 0.00 0.00 46.92 3.95
2073 2113 4.827835 CCATTAGGAGTAGAGATCCGTTCA 59.172 45.833 0.00 0.00 42.02 3.18
2074 2114 5.302059 CCATTAGGAGTAGAGATCCGTTCAA 59.698 44.000 0.00 0.00 42.02 2.69
2075 2115 6.015010 CCATTAGGAGTAGAGATCCGTTCAAT 60.015 42.308 0.00 0.00 42.02 2.57
2076 2116 7.437748 CATTAGGAGTAGAGATCCGTTCAATT 58.562 38.462 0.00 0.00 42.02 2.32
2077 2117 5.941555 AGGAGTAGAGATCCGTTCAATTT 57.058 39.130 0.00 0.00 42.02 1.82
2078 2118 6.301169 AGGAGTAGAGATCCGTTCAATTTT 57.699 37.500 0.00 0.00 42.02 1.82
2079 2119 6.712276 AGGAGTAGAGATCCGTTCAATTTTT 58.288 36.000 0.00 0.00 42.02 1.94
2120 2160 2.765689 TTTCCAACATCCAAGGTGGT 57.234 45.000 0.00 0.00 39.03 4.16
2121 2161 3.885976 TTTCCAACATCCAAGGTGGTA 57.114 42.857 0.00 0.00 39.03 3.25
2122 2162 2.871096 TCCAACATCCAAGGTGGTAC 57.129 50.000 0.00 0.00 39.03 3.34
2123 2163 2.344592 TCCAACATCCAAGGTGGTACT 58.655 47.619 0.00 0.00 39.03 2.73
2124 2164 3.522759 TCCAACATCCAAGGTGGTACTA 58.477 45.455 0.00 0.00 39.03 1.82
2125 2165 3.911260 TCCAACATCCAAGGTGGTACTAA 59.089 43.478 0.00 0.00 39.03 2.24
2126 2166 4.538490 TCCAACATCCAAGGTGGTACTAAT 59.462 41.667 0.00 0.00 39.03 1.73
2127 2167 4.881850 CCAACATCCAAGGTGGTACTAATC 59.118 45.833 0.00 0.00 39.03 1.75
2128 2168 5.339200 CCAACATCCAAGGTGGTACTAATCT 60.339 44.000 0.00 0.00 39.03 2.40
2129 2169 6.126883 CCAACATCCAAGGTGGTACTAATCTA 60.127 42.308 0.00 0.00 39.03 1.98
2130 2170 7.420214 CCAACATCCAAGGTGGTACTAATCTAT 60.420 40.741 0.00 0.00 39.03 1.98
2131 2171 7.691993 ACATCCAAGGTGGTACTAATCTATT 57.308 36.000 0.00 0.00 39.03 1.73
2132 2172 8.102484 ACATCCAAGGTGGTACTAATCTATTT 57.898 34.615 0.00 0.00 39.03 1.40
2133 2173 9.220906 ACATCCAAGGTGGTACTAATCTATTTA 57.779 33.333 0.00 0.00 39.03 1.40
2157 2197 9.970395 TTATATATCACGTCCTACAAAATTCGT 57.030 29.630 0.00 0.00 0.00 3.85
2158 2198 6.823678 ATATCACGTCCTACAAAATTCGTC 57.176 37.500 0.00 0.00 0.00 4.20
2159 2199 3.319755 TCACGTCCTACAAAATTCGTCC 58.680 45.455 0.00 0.00 0.00 4.79
2160 2200 2.091588 CACGTCCTACAAAATTCGTCCG 59.908 50.000 0.00 0.00 0.00 4.79
2161 2201 2.288395 ACGTCCTACAAAATTCGTCCGT 60.288 45.455 0.00 0.00 0.00 4.69
2162 2202 2.343544 CGTCCTACAAAATTCGTCCGTC 59.656 50.000 0.00 0.00 0.00 4.79
2163 2203 3.319755 GTCCTACAAAATTCGTCCGTCA 58.680 45.455 0.00 0.00 0.00 4.35
2164 2204 3.122445 GTCCTACAAAATTCGTCCGTCAC 59.878 47.826 0.00 0.00 0.00 3.67
2165 2205 3.006110 TCCTACAAAATTCGTCCGTCACT 59.994 43.478 0.00 0.00 0.00 3.41
2166 2206 3.744426 CCTACAAAATTCGTCCGTCACTT 59.256 43.478 0.00 0.00 0.00 3.16
2167 2207 4.212636 CCTACAAAATTCGTCCGTCACTTT 59.787 41.667 0.00 0.00 0.00 2.66
2168 2208 4.205323 ACAAAATTCGTCCGTCACTTTC 57.795 40.909 0.00 0.00 0.00 2.62
2169 2209 3.215244 CAAAATTCGTCCGTCACTTTCG 58.785 45.455 0.00 0.00 0.00 3.46
2170 2210 2.427232 AATTCGTCCGTCACTTTCGA 57.573 45.000 0.00 0.00 0.00 3.71
2171 2211 2.649331 ATTCGTCCGTCACTTTCGAT 57.351 45.000 0.00 0.00 0.00 3.59
2172 2212 2.427232 TTCGTCCGTCACTTTCGATT 57.573 45.000 0.00 0.00 0.00 3.34
2173 2213 2.427232 TCGTCCGTCACTTTCGATTT 57.573 45.000 0.00 0.00 0.00 2.17
2174 2214 2.746269 TCGTCCGTCACTTTCGATTTT 58.254 42.857 0.00 0.00 0.00 1.82
2175 2215 2.727798 TCGTCCGTCACTTTCGATTTTC 59.272 45.455 0.00 0.00 0.00 2.29
2176 2216 2.729882 CGTCCGTCACTTTCGATTTTCT 59.270 45.455 0.00 0.00 0.00 2.52
2177 2217 3.421826 CGTCCGTCACTTTCGATTTTCTG 60.422 47.826 0.00 0.00 0.00 3.02
2178 2218 3.064207 TCCGTCACTTTCGATTTTCTGG 58.936 45.455 0.00 0.00 0.00 3.86
2179 2219 2.412847 CCGTCACTTTCGATTTTCTGGC 60.413 50.000 0.00 0.00 0.00 4.85
2180 2220 2.223144 CGTCACTTTCGATTTTCTGGCA 59.777 45.455 0.00 0.00 0.00 4.92
2181 2221 3.555518 GTCACTTTCGATTTTCTGGCAC 58.444 45.455 0.00 0.00 0.00 5.01
2182 2222 2.223144 TCACTTTCGATTTTCTGGCACG 59.777 45.455 0.00 0.00 0.00 5.34
2183 2223 2.032030 CACTTTCGATTTTCTGGCACGT 60.032 45.455 0.00 0.00 0.00 4.49
2184 2224 3.185594 CACTTTCGATTTTCTGGCACGTA 59.814 43.478 0.00 0.00 0.00 3.57
2185 2225 3.185797 ACTTTCGATTTTCTGGCACGTAC 59.814 43.478 0.00 0.00 0.00 3.67
2186 2226 2.442212 TCGATTTTCTGGCACGTACA 57.558 45.000 0.00 0.00 0.00 2.90
2187 2227 2.967362 TCGATTTTCTGGCACGTACAT 58.033 42.857 0.00 0.00 0.00 2.29
2188 2228 2.927477 TCGATTTTCTGGCACGTACATC 59.073 45.455 0.00 0.00 0.00 3.06
2189 2229 2.285026 CGATTTTCTGGCACGTACATCG 60.285 50.000 0.00 0.00 46.00 3.84
2190 2230 0.793861 TTTTCTGGCACGTACATCGC 59.206 50.000 0.00 0.00 44.19 4.58
2191 2231 0.037697 TTTCTGGCACGTACATCGCT 60.038 50.000 0.00 0.00 44.19 4.93
2192 2232 0.457853 TTCTGGCACGTACATCGCTC 60.458 55.000 0.00 0.00 44.19 5.03
2193 2233 1.153842 CTGGCACGTACATCGCTCA 60.154 57.895 0.00 0.00 44.19 4.26
2194 2234 0.528466 CTGGCACGTACATCGCTCAT 60.528 55.000 0.00 0.00 44.19 2.90
2195 2235 0.527600 TGGCACGTACATCGCTCATC 60.528 55.000 0.00 0.00 44.19 2.92
2196 2236 0.527600 GGCACGTACATCGCTCATCA 60.528 55.000 0.00 0.00 44.19 3.07
2197 2237 0.572590 GCACGTACATCGCTCATCAC 59.427 55.000 0.00 0.00 44.19 3.06
2198 2238 1.908065 CACGTACATCGCTCATCACA 58.092 50.000 0.00 0.00 44.19 3.58
2199 2239 2.463876 CACGTACATCGCTCATCACAT 58.536 47.619 0.00 0.00 44.19 3.21
2200 2240 2.217167 CACGTACATCGCTCATCACATG 59.783 50.000 0.00 0.00 44.19 3.21
2201 2241 1.788886 CGTACATCGCTCATCACATGG 59.211 52.381 0.00 0.00 0.00 3.66
2202 2242 2.138320 GTACATCGCTCATCACATGGG 58.862 52.381 0.00 0.00 0.00 4.00
2207 2247 4.573210 CTCATCACATGGGCCTGG 57.427 61.111 4.53 0.00 0.00 4.45
2208 2248 1.826921 CTCATCACATGGGCCTGGC 60.827 63.158 11.05 11.05 0.00 4.85
2209 2249 2.277737 CATCACATGGGCCTGGCT 59.722 61.111 19.68 0.00 0.00 4.75
2210 2250 0.987613 TCATCACATGGGCCTGGCTA 60.988 55.000 19.68 8.66 0.00 3.93
2211 2251 0.536687 CATCACATGGGCCTGGCTAG 60.537 60.000 19.68 8.50 0.00 3.42
2234 2274 2.935481 CCAGGGCCCTCTCCACAA 60.935 66.667 25.77 0.00 0.00 3.33
2235 2275 2.311854 CCAGGGCCCTCTCCACAAT 61.312 63.158 25.77 0.00 0.00 2.71
2236 2276 1.693640 CAGGGCCCTCTCCACAATT 59.306 57.895 25.77 0.00 0.00 2.32
2237 2277 0.040204 CAGGGCCCTCTCCACAATTT 59.960 55.000 25.77 0.00 0.00 1.82
2238 2278 0.786435 AGGGCCCTCTCCACAATTTT 59.214 50.000 22.28 0.00 0.00 1.82
2239 2279 1.149923 AGGGCCCTCTCCACAATTTTT 59.850 47.619 22.28 0.00 0.00 1.94
2284 2324 6.830873 ATATTATACTAGAAGAACGCCCGT 57.169 37.500 0.00 0.00 0.00 5.28
2285 2325 2.865343 ATACTAGAAGAACGCCCGTG 57.135 50.000 0.00 0.00 0.00 4.94
2286 2326 0.171903 TACTAGAAGAACGCCCGTGC 59.828 55.000 0.00 0.00 0.00 5.34
2304 2344 3.302344 GTTGCAACGGGGCCACAT 61.302 61.111 14.90 0.00 30.39 3.21
2305 2345 2.522923 TTGCAACGGGGCCACATT 60.523 55.556 5.46 0.00 0.00 2.71
2306 2346 1.228583 TTGCAACGGGGCCACATTA 60.229 52.632 5.46 0.00 0.00 1.90
2307 2347 0.827925 TTGCAACGGGGCCACATTAA 60.828 50.000 5.46 0.00 0.00 1.40
2308 2348 1.214325 GCAACGGGGCCACATTAAC 59.786 57.895 5.46 0.00 0.00 2.01
2309 2349 1.248101 GCAACGGGGCCACATTAACT 61.248 55.000 5.46 0.00 0.00 2.24
2310 2350 1.253100 CAACGGGGCCACATTAACTT 58.747 50.000 5.46 0.00 0.00 2.66
2311 2351 1.616374 CAACGGGGCCACATTAACTTT 59.384 47.619 5.46 0.00 0.00 2.66
2312 2352 2.820787 CAACGGGGCCACATTAACTTTA 59.179 45.455 5.46 0.00 0.00 1.85
2313 2353 3.157750 ACGGGGCCACATTAACTTTAA 57.842 42.857 5.46 0.00 0.00 1.52
2314 2354 3.086282 ACGGGGCCACATTAACTTTAAG 58.914 45.455 5.46 0.00 0.00 1.85
2315 2355 3.244981 ACGGGGCCACATTAACTTTAAGA 60.245 43.478 5.46 0.00 0.00 2.10
2316 2356 3.377172 CGGGGCCACATTAACTTTAAGAG 59.623 47.826 5.46 0.00 0.00 2.85
2317 2357 4.341487 GGGGCCACATTAACTTTAAGAGT 58.659 43.478 4.39 0.00 41.47 3.24
2319 2359 5.105877 GGGGCCACATTAACTTTAAGAGTTC 60.106 44.000 4.39 0.00 45.40 3.01
2320 2360 5.475564 GGGCCACATTAACTTTAAGAGTTCA 59.524 40.000 4.39 0.00 45.40 3.18
2321 2361 6.015772 GGGCCACATTAACTTTAAGAGTTCAA 60.016 38.462 4.39 2.81 45.40 2.69
2322 2362 7.309805 GGGCCACATTAACTTTAAGAGTTCAAT 60.310 37.037 4.39 4.32 45.40 2.57
2323 2363 8.736244 GGCCACATTAACTTTAAGAGTTCAATA 58.264 33.333 0.00 0.00 45.40 1.90
2351 2391 3.892527 TGTTAATAACATGCGACGACG 57.107 42.857 1.08 2.12 38.37 5.12
2352 2392 3.500014 TGTTAATAACATGCGACGACGA 58.500 40.909 12.29 0.00 37.90 4.20
2353 2393 3.301379 TGTTAATAACATGCGACGACGAC 59.699 43.478 12.29 3.11 37.90 4.34
2354 2394 2.273370 AATAACATGCGACGACGACT 57.727 45.000 12.29 0.00 42.66 4.18
2355 2395 2.273370 ATAACATGCGACGACGACTT 57.727 45.000 12.29 0.00 42.66 3.01
2356 2396 2.898181 TAACATGCGACGACGACTTA 57.102 45.000 12.29 0.00 42.66 2.24
2357 2397 1.614385 AACATGCGACGACGACTTAG 58.386 50.000 12.29 0.00 42.66 2.18
2358 2398 0.797249 ACATGCGACGACGACTTAGC 60.797 55.000 12.29 0.00 42.66 3.09
2359 2399 1.582937 ATGCGACGACGACTTAGCG 60.583 57.895 12.29 0.00 42.66 4.26
2360 2400 1.974249 ATGCGACGACGACTTAGCGA 61.974 55.000 12.29 0.00 42.66 4.93
2361 2401 1.928769 GCGACGACGACTTAGCGAG 60.929 63.158 12.29 0.72 42.66 5.03
2362 2402 1.928769 CGACGACGACTTAGCGAGC 60.929 63.158 0.00 0.00 42.66 5.03
2363 2403 1.928769 GACGACGACTTAGCGAGCG 60.929 63.158 0.00 8.17 38.07 5.03
2364 2404 2.648102 CGACGACTTAGCGAGCGG 60.648 66.667 0.00 0.00 34.83 5.52
2365 2405 2.789917 GACGACTTAGCGAGCGGA 59.210 61.111 0.00 0.00 34.83 5.54
2366 2406 1.583194 GACGACTTAGCGAGCGGAC 60.583 63.158 0.00 0.00 34.83 4.79
2367 2407 2.278013 CGACTTAGCGAGCGGACC 60.278 66.667 0.00 0.00 0.00 4.46
2368 2408 2.104530 GACTTAGCGAGCGGACCC 59.895 66.667 0.00 0.00 0.00 4.46
2369 2409 3.427598 GACTTAGCGAGCGGACCCC 62.428 68.421 0.00 0.00 0.00 4.95
2370 2410 4.222847 CTTAGCGAGCGGACCCCC 62.223 72.222 0.00 0.00 0.00 5.40
2371 2411 4.772231 TTAGCGAGCGGACCCCCT 62.772 66.667 0.00 0.00 0.00 4.79
2372 2412 4.772231 TAGCGAGCGGACCCCCTT 62.772 66.667 0.00 0.00 0.00 3.95
2373 2413 2.859525 TTAGCGAGCGGACCCCCTTA 62.860 60.000 0.00 0.00 0.00 2.69
2374 2414 2.859525 TAGCGAGCGGACCCCCTTAA 62.860 60.000 0.00 0.00 0.00 1.85
2375 2415 2.983791 CGAGCGGACCCCCTTAAA 59.016 61.111 0.00 0.00 0.00 1.52
2376 2416 1.297364 CGAGCGGACCCCCTTAAAA 59.703 57.895 0.00 0.00 0.00 1.52
2377 2417 0.321830 CGAGCGGACCCCCTTAAAAA 60.322 55.000 0.00 0.00 0.00 1.94
2397 2437 6.749923 AAAAAGACATAGTGAGCAGATTCC 57.250 37.500 0.00 0.00 0.00 3.01
2398 2438 4.414337 AAGACATAGTGAGCAGATTCCC 57.586 45.455 0.00 0.00 0.00 3.97
2399 2439 3.652055 AGACATAGTGAGCAGATTCCCT 58.348 45.455 0.00 0.00 0.00 4.20
2400 2440 4.036518 AGACATAGTGAGCAGATTCCCTT 58.963 43.478 0.00 0.00 0.00 3.95
2401 2441 5.211973 AGACATAGTGAGCAGATTCCCTTA 58.788 41.667 0.00 0.00 0.00 2.69
2402 2442 5.663106 AGACATAGTGAGCAGATTCCCTTAA 59.337 40.000 0.00 0.00 0.00 1.85
2403 2443 6.156949 AGACATAGTGAGCAGATTCCCTTAAA 59.843 38.462 0.00 0.00 0.00 1.52
2404 2444 6.721318 ACATAGTGAGCAGATTCCCTTAAAA 58.279 36.000 0.00 0.00 0.00 1.52
2405 2445 6.599638 ACATAGTGAGCAGATTCCCTTAAAAC 59.400 38.462 0.00 0.00 0.00 2.43
2406 2446 5.248380 AGTGAGCAGATTCCCTTAAAACT 57.752 39.130 0.00 0.00 0.00 2.66
2407 2447 5.006386 AGTGAGCAGATTCCCTTAAAACTG 58.994 41.667 0.00 0.00 0.00 3.16
2408 2448 4.156739 GTGAGCAGATTCCCTTAAAACTGG 59.843 45.833 0.00 0.00 0.00 4.00
2409 2449 4.202567 TGAGCAGATTCCCTTAAAACTGGT 60.203 41.667 0.00 0.00 38.25 4.00
2410 2450 5.013704 TGAGCAGATTCCCTTAAAACTGGTA 59.986 40.000 0.00 0.00 36.84 3.25
2411 2451 5.501156 AGCAGATTCCCTTAAAACTGGTAG 58.499 41.667 0.00 0.00 35.81 3.18
2412 2452 4.640647 GCAGATTCCCTTAAAACTGGTAGG 59.359 45.833 0.00 0.00 0.00 3.18
2413 2453 5.572885 GCAGATTCCCTTAAAACTGGTAGGA 60.573 44.000 0.00 0.00 0.00 2.94
2414 2454 6.481643 CAGATTCCCTTAAAACTGGTAGGAA 58.518 40.000 0.00 0.00 36.43 3.36
2415 2455 7.119387 CAGATTCCCTTAAAACTGGTAGGAAT 58.881 38.462 0.00 0.00 43.51 3.01
2416 2456 7.067494 CAGATTCCCTTAAAACTGGTAGGAATG 59.933 40.741 6.12 0.00 41.49 2.67
2417 2457 5.187621 TCCCTTAAAACTGGTAGGAATGG 57.812 43.478 0.00 0.00 0.00 3.16
2418 2458 4.853276 TCCCTTAAAACTGGTAGGAATGGA 59.147 41.667 0.00 0.00 0.00 3.41
2419 2459 5.494706 TCCCTTAAAACTGGTAGGAATGGAT 59.505 40.000 0.00 0.00 0.00 3.41
2420 2460 6.679303 TCCCTTAAAACTGGTAGGAATGGATA 59.321 38.462 0.00 0.00 0.00 2.59
2421 2461 6.771267 CCCTTAAAACTGGTAGGAATGGATAC 59.229 42.308 0.00 0.00 0.00 2.24
2422 2462 6.482308 CCTTAAAACTGGTAGGAATGGATACG 59.518 42.308 0.00 0.00 42.51 3.06
2423 2463 5.687166 AAAACTGGTAGGAATGGATACGA 57.313 39.130 0.00 0.00 42.51 3.43
2424 2464 5.888982 AAACTGGTAGGAATGGATACGAT 57.111 39.130 0.00 0.00 42.51 3.73
2425 2465 5.888982 AACTGGTAGGAATGGATACGATT 57.111 39.130 0.00 0.00 42.51 3.34
2426 2466 5.215252 ACTGGTAGGAATGGATACGATTG 57.785 43.478 0.00 0.00 42.51 2.67
2427 2467 4.899457 ACTGGTAGGAATGGATACGATTGA 59.101 41.667 0.00 0.00 42.51 2.57
2428 2468 5.544176 ACTGGTAGGAATGGATACGATTGAT 59.456 40.000 0.00 0.00 42.51 2.57
2429 2469 5.793817 TGGTAGGAATGGATACGATTGATG 58.206 41.667 0.00 0.00 42.51 3.07
2430 2470 5.542251 TGGTAGGAATGGATACGATTGATGA 59.458 40.000 0.00 0.00 42.51 2.92
2431 2471 5.869888 GGTAGGAATGGATACGATTGATGAC 59.130 44.000 0.00 0.00 42.51 3.06
2432 2472 5.551305 AGGAATGGATACGATTGATGACA 57.449 39.130 0.00 0.00 42.51 3.58
2433 2473 6.119240 AGGAATGGATACGATTGATGACAT 57.881 37.500 0.00 0.00 42.51 3.06
2434 2474 6.537355 AGGAATGGATACGATTGATGACATT 58.463 36.000 0.00 0.00 42.51 2.71
2435 2475 6.429078 AGGAATGGATACGATTGATGACATTG 59.571 38.462 0.00 0.00 42.51 2.82
2436 2476 6.427853 GGAATGGATACGATTGATGACATTGA 59.572 38.462 0.00 0.00 42.51 2.57
2437 2477 7.120285 GGAATGGATACGATTGATGACATTGAT 59.880 37.037 0.00 0.00 42.51 2.57
2438 2478 9.154847 GAATGGATACGATTGATGACATTGATA 57.845 33.333 0.00 0.00 42.51 2.15
2439 2479 9.506018 AATGGATACGATTGATGACATTGATAA 57.494 29.630 0.00 0.00 42.51 1.75
2440 2480 8.900983 TGGATACGATTGATGACATTGATAAA 57.099 30.769 0.00 0.00 42.51 1.40
2441 2481 9.506018 TGGATACGATTGATGACATTGATAAAT 57.494 29.630 0.00 0.00 42.51 1.40
2446 2486 8.777413 ACGATTGATGACATTGATAAATAGTGG 58.223 33.333 0.00 0.00 0.00 4.00
2447 2487 7.747799 CGATTGATGACATTGATAAATAGTGGC 59.252 37.037 0.00 0.00 0.00 5.01
2448 2488 6.544038 TGATGACATTGATAAATAGTGGCG 57.456 37.500 0.00 0.00 0.00 5.69
2449 2489 5.469760 TGATGACATTGATAAATAGTGGCGG 59.530 40.000 0.00 0.00 0.00 6.13
2450 2490 5.029807 TGACATTGATAAATAGTGGCGGA 57.970 39.130 0.00 0.00 0.00 5.54
2451 2491 5.620206 TGACATTGATAAATAGTGGCGGAT 58.380 37.500 0.00 0.00 0.00 4.18
2452 2492 5.469760 TGACATTGATAAATAGTGGCGGATG 59.530 40.000 0.00 0.00 0.00 3.51
2453 2493 5.376625 ACATTGATAAATAGTGGCGGATGT 58.623 37.500 0.00 0.00 0.00 3.06
2454 2494 5.827797 ACATTGATAAATAGTGGCGGATGTT 59.172 36.000 0.00 0.00 0.00 2.71
2455 2495 5.749596 TTGATAAATAGTGGCGGATGTTG 57.250 39.130 0.00 0.00 0.00 3.33
2456 2496 4.133820 TGATAAATAGTGGCGGATGTTGG 58.866 43.478 0.00 0.00 0.00 3.77
2457 2497 2.507407 AAATAGTGGCGGATGTTGGT 57.493 45.000 0.00 0.00 0.00 3.67
2458 2498 2.038387 AATAGTGGCGGATGTTGGTC 57.962 50.000 0.00 0.00 0.00 4.02
2459 2499 1.204146 ATAGTGGCGGATGTTGGTCT 58.796 50.000 0.00 0.00 0.00 3.85
2460 2500 1.855295 TAGTGGCGGATGTTGGTCTA 58.145 50.000 0.00 0.00 0.00 2.59
2461 2501 0.981183 AGTGGCGGATGTTGGTCTAA 59.019 50.000 0.00 0.00 0.00 2.10
2462 2502 1.559682 AGTGGCGGATGTTGGTCTAAT 59.440 47.619 0.00 0.00 0.00 1.73
2463 2503 2.026262 AGTGGCGGATGTTGGTCTAATT 60.026 45.455 0.00 0.00 0.00 1.40
2464 2504 2.752903 GTGGCGGATGTTGGTCTAATTT 59.247 45.455 0.00 0.00 0.00 1.82
2465 2505 3.942748 GTGGCGGATGTTGGTCTAATTTA 59.057 43.478 0.00 0.00 0.00 1.40
2466 2506 3.942748 TGGCGGATGTTGGTCTAATTTAC 59.057 43.478 0.00 0.00 0.00 2.01
2467 2507 4.196971 GGCGGATGTTGGTCTAATTTACT 58.803 43.478 0.00 0.00 0.00 2.24
2468 2508 5.104859 TGGCGGATGTTGGTCTAATTTACTA 60.105 40.000 0.00 0.00 0.00 1.82
2469 2509 5.995897 GGCGGATGTTGGTCTAATTTACTAT 59.004 40.000 0.00 0.00 0.00 2.12
2470 2510 6.147328 GGCGGATGTTGGTCTAATTTACTATC 59.853 42.308 0.00 0.00 0.00 2.08
2471 2511 6.704493 GCGGATGTTGGTCTAATTTACTATCA 59.296 38.462 0.00 0.00 0.00 2.15
2472 2512 7.387948 GCGGATGTTGGTCTAATTTACTATCAT 59.612 37.037 0.00 0.00 0.00 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
91 92 1.073923 CCCTTATCCATTCCCCTTCGG 59.926 57.143 0.00 0.00 0.00 4.30
199 203 1.468914 CGTCTGACTTCGTCCAGATCA 59.531 52.381 6.21 0.00 0.00 2.92
321 325 3.531538 GGTGCTGGATTTGATCTCGTTA 58.468 45.455 0.00 0.00 0.00 3.18
333 337 4.195334 GATGCGGGGGTGCTGGAT 62.195 66.667 0.00 0.00 35.36 3.41
414 418 0.107459 GGGAAGACATGGGAGCTCAC 60.107 60.000 17.19 13.72 0.00 3.51
452 457 3.794737 GCAAGAGGAGATCATGGCA 57.205 52.632 0.00 0.00 0.00 4.92
537 542 2.042741 CCCTGCAATGGCCATGGA 60.043 61.111 25.26 15.62 40.13 3.41
941 948 2.036733 AGTAGGAAGCAACACGCAGTAA 59.963 45.455 0.00 0.00 41.61 2.24
1032 1040 4.960469 TCGTACTCCATTAACAATCCCTCT 59.040 41.667 0.00 0.00 0.00 3.69
1115 1124 1.280710 TCGCATAAACACCTCCACCAT 59.719 47.619 0.00 0.00 0.00 3.55
1195 1213 4.617253 TTTTTGAACTGAGATCTCCGGA 57.383 40.909 20.03 2.93 0.00 5.14
1391 1411 6.403866 TTTGCAAACTTCCTAATCACACAT 57.596 33.333 8.05 0.00 0.00 3.21
1968 2006 2.863988 CCCCCTTCCACCCTGGTT 60.864 66.667 0.00 0.00 39.03 3.67
2018 2058 3.061563 TGAATCGTCTTCGCGGTTTATTG 59.938 43.478 6.13 0.00 35.12 1.90
2099 2139 3.379452 ACCACCTTGGATGTTGGAAAAA 58.621 40.909 0.00 0.00 40.96 1.94
2100 2140 3.039252 ACCACCTTGGATGTTGGAAAA 57.961 42.857 0.00 0.00 40.96 2.29
2101 2141 2.765689 ACCACCTTGGATGTTGGAAA 57.234 45.000 0.00 0.00 40.96 3.13
2102 2142 2.714250 AGTACCACCTTGGATGTTGGAA 59.286 45.455 0.00 0.00 40.96 3.53
2103 2143 2.344592 AGTACCACCTTGGATGTTGGA 58.655 47.619 0.00 0.00 40.96 3.53
2104 2144 2.879103 AGTACCACCTTGGATGTTGG 57.121 50.000 0.00 0.00 40.96 3.77
2105 2145 5.745227 AGATTAGTACCACCTTGGATGTTG 58.255 41.667 0.00 0.00 40.96 3.33
2106 2146 7.691993 ATAGATTAGTACCACCTTGGATGTT 57.308 36.000 0.00 0.00 40.96 2.71
2107 2147 7.691993 AATAGATTAGTACCACCTTGGATGT 57.308 36.000 0.00 0.00 40.96 3.06
2131 2171 9.970395 ACGAATTTTGTAGGACGTGATATATAA 57.030 29.630 0.00 0.00 32.93 0.98
2132 2172 9.616634 GACGAATTTTGTAGGACGTGATATATA 57.383 33.333 0.00 0.00 34.26 0.86
2133 2173 7.597743 GGACGAATTTTGTAGGACGTGATATAT 59.402 37.037 0.00 0.00 34.26 0.86
2134 2174 6.919662 GGACGAATTTTGTAGGACGTGATATA 59.080 38.462 0.00 0.00 34.26 0.86
2135 2175 5.751990 GGACGAATTTTGTAGGACGTGATAT 59.248 40.000 0.00 0.00 34.26 1.63
2136 2176 5.104374 GGACGAATTTTGTAGGACGTGATA 58.896 41.667 0.00 0.00 34.26 2.15
2137 2177 3.930848 GGACGAATTTTGTAGGACGTGAT 59.069 43.478 0.00 0.00 34.26 3.06
2138 2178 3.319755 GGACGAATTTTGTAGGACGTGA 58.680 45.455 0.00 0.00 34.26 4.35
2139 2179 2.091588 CGGACGAATTTTGTAGGACGTG 59.908 50.000 0.00 0.00 34.26 4.49
2140 2180 2.288395 ACGGACGAATTTTGTAGGACGT 60.288 45.455 0.00 0.00 36.71 4.34
2141 2181 2.331194 ACGGACGAATTTTGTAGGACG 58.669 47.619 0.00 0.00 0.00 4.79
2142 2182 3.122445 GTGACGGACGAATTTTGTAGGAC 59.878 47.826 0.00 0.00 0.00 3.85
2143 2183 3.006110 AGTGACGGACGAATTTTGTAGGA 59.994 43.478 0.00 0.00 0.00 2.94
2144 2184 3.323243 AGTGACGGACGAATTTTGTAGG 58.677 45.455 0.00 0.00 0.00 3.18
2145 2185 4.985044 AAGTGACGGACGAATTTTGTAG 57.015 40.909 0.00 0.00 0.00 2.74
2146 2186 4.084952 CGAAAGTGACGGACGAATTTTGTA 60.085 41.667 0.00 0.00 0.00 2.41
2147 2187 3.302870 CGAAAGTGACGGACGAATTTTGT 60.303 43.478 0.00 0.00 0.00 2.83
2148 2188 3.060138 TCGAAAGTGACGGACGAATTTTG 60.060 43.478 0.00 0.00 0.00 2.44
2149 2189 3.125316 TCGAAAGTGACGGACGAATTTT 58.875 40.909 0.00 0.00 0.00 1.82
2150 2190 2.746269 TCGAAAGTGACGGACGAATTT 58.254 42.857 0.00 0.00 0.00 1.82
2151 2191 2.427232 TCGAAAGTGACGGACGAATT 57.573 45.000 0.00 0.00 0.00 2.17
2152 2192 2.649331 ATCGAAAGTGACGGACGAAT 57.351 45.000 0.00 0.00 36.62 3.34
2153 2193 2.427232 AATCGAAAGTGACGGACGAA 57.573 45.000 0.00 0.00 36.62 3.85
2154 2194 2.427232 AAATCGAAAGTGACGGACGA 57.573 45.000 0.00 0.00 37.39 4.20
2155 2195 2.729882 AGAAAATCGAAAGTGACGGACG 59.270 45.455 0.00 0.00 0.00 4.79
2156 2196 3.120649 CCAGAAAATCGAAAGTGACGGAC 60.121 47.826 0.00 0.00 0.00 4.79
2157 2197 3.064207 CCAGAAAATCGAAAGTGACGGA 58.936 45.455 0.00 0.00 0.00 4.69
2158 2198 2.412847 GCCAGAAAATCGAAAGTGACGG 60.413 50.000 0.00 0.00 0.00 4.79
2159 2199 2.223144 TGCCAGAAAATCGAAAGTGACG 59.777 45.455 0.00 0.00 0.00 4.35
2160 2200 3.555518 GTGCCAGAAAATCGAAAGTGAC 58.444 45.455 0.00 0.00 0.00 3.67
2161 2201 2.223144 CGTGCCAGAAAATCGAAAGTGA 59.777 45.455 0.00 0.00 0.00 3.41
2162 2202 2.032030 ACGTGCCAGAAAATCGAAAGTG 60.032 45.455 0.00 0.00 0.00 3.16
2163 2203 2.218603 ACGTGCCAGAAAATCGAAAGT 58.781 42.857 0.00 0.00 0.00 2.66
2164 2204 2.969443 ACGTGCCAGAAAATCGAAAG 57.031 45.000 0.00 0.00 0.00 2.62
2165 2205 3.132160 TGTACGTGCCAGAAAATCGAAA 58.868 40.909 0.00 0.00 0.00 3.46
2166 2206 2.756829 TGTACGTGCCAGAAAATCGAA 58.243 42.857 0.00 0.00 0.00 3.71
2167 2207 2.442212 TGTACGTGCCAGAAAATCGA 57.558 45.000 0.00 0.00 0.00 3.59
2168 2208 2.285026 CGATGTACGTGCCAGAAAATCG 60.285 50.000 0.00 2.66 37.22 3.34
2169 2209 2.536928 GCGATGTACGTGCCAGAAAATC 60.537 50.000 0.00 0.00 44.60 2.17
2170 2210 1.396996 GCGATGTACGTGCCAGAAAAT 59.603 47.619 0.00 0.00 44.60 1.82
2171 2211 0.793861 GCGATGTACGTGCCAGAAAA 59.206 50.000 0.00 0.00 44.60 2.29
2172 2212 0.037697 AGCGATGTACGTGCCAGAAA 60.038 50.000 0.00 0.00 44.60 2.52
2173 2213 0.457853 GAGCGATGTACGTGCCAGAA 60.458 55.000 0.00 0.00 44.60 3.02
2174 2214 1.138883 GAGCGATGTACGTGCCAGA 59.861 57.895 0.00 0.00 44.60 3.86
2175 2215 0.528466 ATGAGCGATGTACGTGCCAG 60.528 55.000 0.00 0.00 44.60 4.85
2176 2216 0.527600 GATGAGCGATGTACGTGCCA 60.528 55.000 0.00 0.00 44.60 4.92
2177 2217 0.527600 TGATGAGCGATGTACGTGCC 60.528 55.000 0.00 0.00 44.60 5.01
2178 2218 0.572590 GTGATGAGCGATGTACGTGC 59.427 55.000 0.00 0.00 44.60 5.34
2179 2219 1.908065 TGTGATGAGCGATGTACGTG 58.092 50.000 0.00 0.00 44.60 4.49
2180 2220 2.463876 CATGTGATGAGCGATGTACGT 58.536 47.619 0.00 0.00 44.60 3.57
2181 2221 1.788886 CCATGTGATGAGCGATGTACG 59.211 52.381 0.00 0.00 45.66 3.67
2182 2222 2.138320 CCCATGTGATGAGCGATGTAC 58.862 52.381 0.00 0.00 0.00 2.90
2183 2223 1.541015 GCCCATGTGATGAGCGATGTA 60.541 52.381 0.00 0.00 0.00 2.29
2184 2224 0.816825 GCCCATGTGATGAGCGATGT 60.817 55.000 0.00 0.00 0.00 3.06
2185 2225 1.512996 GGCCCATGTGATGAGCGATG 61.513 60.000 0.00 0.00 34.49 3.84
2186 2226 1.228063 GGCCCATGTGATGAGCGAT 60.228 57.895 0.00 0.00 34.49 4.58
2187 2227 2.190313 GGCCCATGTGATGAGCGA 59.810 61.111 0.00 0.00 34.49 4.93
2188 2228 2.184830 CAGGCCCATGTGATGAGCG 61.185 63.158 0.00 0.00 34.49 5.03
2189 2229 1.826921 CCAGGCCCATGTGATGAGC 60.827 63.158 0.00 0.00 32.69 4.26
2190 2230 1.826921 GCCAGGCCCATGTGATGAG 60.827 63.158 0.00 0.00 0.00 2.90
2191 2231 0.987613 TAGCCAGGCCCATGTGATGA 60.988 55.000 8.22 0.00 0.00 2.92
2192 2232 0.536687 CTAGCCAGGCCCATGTGATG 60.537 60.000 8.22 0.00 0.00 3.07
2193 2233 1.713005 CCTAGCCAGGCCCATGTGAT 61.713 60.000 8.22 0.00 34.35 3.06
2194 2234 2.377810 CCTAGCCAGGCCCATGTGA 61.378 63.158 8.22 0.00 34.35 3.58
2195 2235 2.194056 CCTAGCCAGGCCCATGTG 59.806 66.667 8.22 0.00 34.35 3.21
2217 2257 1.867595 AATTGTGGAGAGGGCCCTGG 61.868 60.000 34.59 0.00 0.00 4.45
2218 2258 0.040204 AAATTGTGGAGAGGGCCCTG 59.960 55.000 34.59 0.00 0.00 4.45
2219 2259 0.786435 AAAATTGTGGAGAGGGCCCT 59.214 50.000 29.18 29.18 0.00 5.19
2220 2260 1.644509 AAAAATTGTGGAGAGGGCCC 58.355 50.000 16.46 16.46 0.00 5.80
2258 2298 9.618890 ACGGGCGTTCTTCTAGTATAATATATA 57.381 33.333 0.00 0.00 0.00 0.86
2259 2299 8.404000 CACGGGCGTTCTTCTAGTATAATATAT 58.596 37.037 0.00 0.00 0.00 0.86
2260 2300 7.627088 GCACGGGCGTTCTTCTAGTATAATATA 60.627 40.741 0.00 0.00 0.00 0.86
2261 2301 6.618811 CACGGGCGTTCTTCTAGTATAATAT 58.381 40.000 0.00 0.00 0.00 1.28
2262 2302 5.563475 GCACGGGCGTTCTTCTAGTATAATA 60.563 44.000 0.00 0.00 0.00 0.98
2263 2303 4.795308 GCACGGGCGTTCTTCTAGTATAAT 60.795 45.833 0.00 0.00 0.00 1.28
2264 2304 3.489738 GCACGGGCGTTCTTCTAGTATAA 60.490 47.826 0.00 0.00 0.00 0.98
2265 2305 2.033801 GCACGGGCGTTCTTCTAGTATA 59.966 50.000 0.00 0.00 0.00 1.47
2266 2306 1.202382 GCACGGGCGTTCTTCTAGTAT 60.202 52.381 0.00 0.00 0.00 2.12
2267 2307 0.171903 GCACGGGCGTTCTTCTAGTA 59.828 55.000 0.00 0.00 0.00 1.82
2268 2308 1.080025 GCACGGGCGTTCTTCTAGT 60.080 57.895 0.00 0.00 0.00 2.57
2269 2309 3.782042 GCACGGGCGTTCTTCTAG 58.218 61.111 0.00 0.00 0.00 2.43
2287 2327 1.528292 TAATGTGGCCCCGTTGCAAC 61.528 55.000 19.89 19.89 35.65 4.17
2288 2328 0.827925 TTAATGTGGCCCCGTTGCAA 60.828 50.000 0.00 0.00 0.00 4.08
2289 2329 1.228583 TTAATGTGGCCCCGTTGCA 60.229 52.632 0.00 0.00 0.00 4.08
2290 2330 1.214325 GTTAATGTGGCCCCGTTGC 59.786 57.895 0.00 0.00 0.00 4.17
2291 2331 1.253100 AAGTTAATGTGGCCCCGTTG 58.747 50.000 0.00 0.00 0.00 4.10
2292 2332 2.003937 AAAGTTAATGTGGCCCCGTT 57.996 45.000 0.00 0.00 0.00 4.44
2293 2333 2.883122 TAAAGTTAATGTGGCCCCGT 57.117 45.000 0.00 0.00 0.00 5.28
2294 2334 3.349022 TCTTAAAGTTAATGTGGCCCCG 58.651 45.455 0.00 0.00 0.00 5.73
2295 2335 4.341487 ACTCTTAAAGTTAATGTGGCCCC 58.659 43.478 0.00 0.00 33.03 5.80
2296 2336 5.977489 AACTCTTAAAGTTAATGTGGCCC 57.023 39.130 0.00 0.00 46.55 5.80
2330 2370 4.027132 GTCGTCGTCGCATGTTATTAACAT 60.027 41.667 14.87 14.87 43.19 2.71
2331 2371 3.301379 GTCGTCGTCGCATGTTATTAACA 59.699 43.478 11.47 11.47 40.39 2.41
2332 2372 3.545078 AGTCGTCGTCGCATGTTATTAAC 59.455 43.478 0.00 0.00 36.96 2.01
2333 2373 3.761657 AGTCGTCGTCGCATGTTATTAA 58.238 40.909 0.00 0.00 36.96 1.40
2334 2374 3.409851 AGTCGTCGTCGCATGTTATTA 57.590 42.857 0.00 0.00 36.96 0.98
2335 2375 2.273370 AGTCGTCGTCGCATGTTATT 57.727 45.000 0.00 0.00 36.96 1.40
2336 2376 2.273370 AAGTCGTCGTCGCATGTTAT 57.727 45.000 0.00 0.00 36.96 1.89
2337 2377 2.777494 CTAAGTCGTCGTCGCATGTTA 58.223 47.619 0.00 0.00 36.96 2.41
2338 2378 1.614385 CTAAGTCGTCGTCGCATGTT 58.386 50.000 0.00 0.00 36.96 2.71
2339 2379 0.797249 GCTAAGTCGTCGTCGCATGT 60.797 55.000 0.00 0.00 36.96 3.21
2340 2380 1.788621 CGCTAAGTCGTCGTCGCATG 61.789 60.000 0.00 0.00 36.96 4.06
2341 2381 1.582937 CGCTAAGTCGTCGTCGCAT 60.583 57.895 0.00 0.00 36.96 4.73
2342 2382 2.202260 CGCTAAGTCGTCGTCGCA 60.202 61.111 0.00 0.00 36.96 5.10
2343 2383 1.928769 CTCGCTAAGTCGTCGTCGC 60.929 63.158 0.00 0.00 36.96 5.19
2344 2384 1.928769 GCTCGCTAAGTCGTCGTCG 60.929 63.158 0.00 0.00 38.55 5.12
2345 2385 1.928769 CGCTCGCTAAGTCGTCGTC 60.929 63.158 0.00 0.00 0.00 4.20
2346 2386 2.097918 CGCTCGCTAAGTCGTCGT 59.902 61.111 0.00 0.00 0.00 4.34
2347 2387 2.648102 CCGCTCGCTAAGTCGTCG 60.648 66.667 0.00 0.00 0.00 5.12
2348 2388 1.583194 GTCCGCTCGCTAAGTCGTC 60.583 63.158 0.00 0.00 0.00 4.20
2349 2389 2.484203 GTCCGCTCGCTAAGTCGT 59.516 61.111 0.00 0.00 0.00 4.34
2350 2390 2.278013 GGTCCGCTCGCTAAGTCG 60.278 66.667 0.00 0.00 0.00 4.18
2351 2391 2.104530 GGGTCCGCTCGCTAAGTC 59.895 66.667 0.00 0.00 0.00 3.01
2352 2392 3.459063 GGGGTCCGCTCGCTAAGT 61.459 66.667 0.00 0.00 0.00 2.24
2353 2393 4.222847 GGGGGTCCGCTCGCTAAG 62.223 72.222 5.82 0.00 0.00 2.18
2354 2394 2.859525 TAAGGGGGTCCGCTCGCTAA 62.860 60.000 7.05 0.00 37.40 3.09
2355 2395 2.859525 TTAAGGGGGTCCGCTCGCTA 62.860 60.000 7.05 0.00 37.40 4.26
2356 2396 4.772231 TAAGGGGGTCCGCTCGCT 62.772 66.667 7.05 0.00 40.38 4.93
2357 2397 2.808181 TTTTAAGGGGGTCCGCTCGC 62.808 60.000 7.05 0.00 38.30 5.03
2358 2398 0.321830 TTTTTAAGGGGGTCCGCTCG 60.322 55.000 7.05 0.00 38.30 5.03
2359 2399 3.656457 TTTTTAAGGGGGTCCGCTC 57.344 52.632 7.05 0.00 38.30 5.03
2374 2414 5.649831 GGGAATCTGCTCACTATGTCTTTTT 59.350 40.000 0.00 0.00 0.00 1.94
2375 2415 5.045286 AGGGAATCTGCTCACTATGTCTTTT 60.045 40.000 0.00 0.00 0.00 2.27
2376 2416 4.472833 AGGGAATCTGCTCACTATGTCTTT 59.527 41.667 0.00 0.00 0.00 2.52
2377 2417 4.036518 AGGGAATCTGCTCACTATGTCTT 58.963 43.478 0.00 0.00 0.00 3.01
2378 2418 3.652055 AGGGAATCTGCTCACTATGTCT 58.348 45.455 0.00 0.00 0.00 3.41
2379 2419 4.414337 AAGGGAATCTGCTCACTATGTC 57.586 45.455 0.00 0.00 0.00 3.06
2380 2420 5.957771 TTAAGGGAATCTGCTCACTATGT 57.042 39.130 0.00 0.00 0.00 2.29
2381 2421 6.825721 AGTTTTAAGGGAATCTGCTCACTATG 59.174 38.462 0.00 0.00 0.00 2.23
2382 2422 6.825721 CAGTTTTAAGGGAATCTGCTCACTAT 59.174 38.462 0.00 0.00 0.00 2.12
2383 2423 6.173339 CAGTTTTAAGGGAATCTGCTCACTA 58.827 40.000 0.00 0.00 0.00 2.74
2384 2424 5.006386 CAGTTTTAAGGGAATCTGCTCACT 58.994 41.667 0.00 0.00 0.00 3.41
2385 2425 4.156739 CCAGTTTTAAGGGAATCTGCTCAC 59.843 45.833 0.00 0.00 0.00 3.51
2386 2426 4.202567 ACCAGTTTTAAGGGAATCTGCTCA 60.203 41.667 0.00 0.00 0.00 4.26
2387 2427 4.336280 ACCAGTTTTAAGGGAATCTGCTC 58.664 43.478 0.00 0.00 0.00 4.26
2388 2428 4.388577 ACCAGTTTTAAGGGAATCTGCT 57.611 40.909 0.00 0.00 0.00 4.24
2389 2429 4.640647 CCTACCAGTTTTAAGGGAATCTGC 59.359 45.833 0.00 0.00 0.00 4.26
2390 2430 6.062258 TCCTACCAGTTTTAAGGGAATCTG 57.938 41.667 0.00 0.00 0.00 2.90
2391 2431 6.713731 TTCCTACCAGTTTTAAGGGAATCT 57.286 37.500 0.00 0.00 0.00 2.40
2392 2432 6.321435 CCATTCCTACCAGTTTTAAGGGAATC 59.679 42.308 0.00 0.00 39.23 2.52
2393 2433 6.011096 TCCATTCCTACCAGTTTTAAGGGAAT 60.011 38.462 0.00 0.00 41.09 3.01
2394 2434 5.313772 TCCATTCCTACCAGTTTTAAGGGAA 59.686 40.000 0.00 0.00 36.11 3.97
2395 2435 4.853276 TCCATTCCTACCAGTTTTAAGGGA 59.147 41.667 0.00 0.00 0.00 4.20
2396 2436 5.187621 TCCATTCCTACCAGTTTTAAGGG 57.812 43.478 0.00 0.00 0.00 3.95
2397 2437 6.482308 CGTATCCATTCCTACCAGTTTTAAGG 59.518 42.308 0.00 0.00 0.00 2.69
2398 2438 7.270047 TCGTATCCATTCCTACCAGTTTTAAG 58.730 38.462 0.00 0.00 0.00 1.85
2399 2439 7.185318 TCGTATCCATTCCTACCAGTTTTAA 57.815 36.000 0.00 0.00 0.00 1.52
2400 2440 6.795144 TCGTATCCATTCCTACCAGTTTTA 57.205 37.500 0.00 0.00 0.00 1.52
2401 2441 5.687166 TCGTATCCATTCCTACCAGTTTT 57.313 39.130 0.00 0.00 0.00 2.43
2402 2442 5.888982 ATCGTATCCATTCCTACCAGTTT 57.111 39.130 0.00 0.00 0.00 2.66
2403 2443 5.365605 TCAATCGTATCCATTCCTACCAGTT 59.634 40.000 0.00 0.00 0.00 3.16
2404 2444 4.899457 TCAATCGTATCCATTCCTACCAGT 59.101 41.667 0.00 0.00 0.00 4.00
2405 2445 5.468540 TCAATCGTATCCATTCCTACCAG 57.531 43.478 0.00 0.00 0.00 4.00
2406 2446 5.542251 TCATCAATCGTATCCATTCCTACCA 59.458 40.000 0.00 0.00 0.00 3.25
2407 2447 5.869888 GTCATCAATCGTATCCATTCCTACC 59.130 44.000 0.00 0.00 0.00 3.18
2408 2448 6.455647 TGTCATCAATCGTATCCATTCCTAC 58.544 40.000 0.00 0.00 0.00 3.18
2409 2449 6.664428 TGTCATCAATCGTATCCATTCCTA 57.336 37.500 0.00 0.00 0.00 2.94
2410 2450 5.551305 TGTCATCAATCGTATCCATTCCT 57.449 39.130 0.00 0.00 0.00 3.36
2411 2451 6.427853 TCAATGTCATCAATCGTATCCATTCC 59.572 38.462 0.00 0.00 0.00 3.01
2412 2452 7.425577 TCAATGTCATCAATCGTATCCATTC 57.574 36.000 0.00 0.00 0.00 2.67
2413 2453 7.991084 ATCAATGTCATCAATCGTATCCATT 57.009 32.000 0.00 0.00 0.00 3.16
2414 2454 9.506018 TTTATCAATGTCATCAATCGTATCCAT 57.494 29.630 0.00 0.00 0.00 3.41
2415 2455 8.900983 TTTATCAATGTCATCAATCGTATCCA 57.099 30.769 0.00 0.00 0.00 3.41
2420 2460 8.777413 CCACTATTTATCAATGTCATCAATCGT 58.223 33.333 0.00 0.00 0.00 3.73
2421 2461 7.747799 GCCACTATTTATCAATGTCATCAATCG 59.252 37.037 0.00 0.00 0.00 3.34
2422 2462 7.747799 CGCCACTATTTATCAATGTCATCAATC 59.252 37.037 0.00 0.00 0.00 2.67
2423 2463 7.308770 CCGCCACTATTTATCAATGTCATCAAT 60.309 37.037 0.00 0.00 0.00 2.57
2424 2464 6.017192 CCGCCACTATTTATCAATGTCATCAA 60.017 38.462 0.00 0.00 0.00 2.57
2425 2465 5.469760 CCGCCACTATTTATCAATGTCATCA 59.530 40.000 0.00 0.00 0.00 3.07
2426 2466 5.700832 TCCGCCACTATTTATCAATGTCATC 59.299 40.000 0.00 0.00 0.00 2.92
2427 2467 5.620206 TCCGCCACTATTTATCAATGTCAT 58.380 37.500 0.00 0.00 0.00 3.06
2428 2468 5.029807 TCCGCCACTATTTATCAATGTCA 57.970 39.130 0.00 0.00 0.00 3.58
2429 2469 5.470098 ACATCCGCCACTATTTATCAATGTC 59.530 40.000 0.00 0.00 0.00 3.06
2430 2470 5.376625 ACATCCGCCACTATTTATCAATGT 58.623 37.500 0.00 0.00 0.00 2.71
2431 2471 5.947228 ACATCCGCCACTATTTATCAATG 57.053 39.130 0.00 0.00 0.00 2.82
2432 2472 5.241506 CCAACATCCGCCACTATTTATCAAT 59.758 40.000 0.00 0.00 0.00 2.57
2433 2473 4.578516 CCAACATCCGCCACTATTTATCAA 59.421 41.667 0.00 0.00 0.00 2.57
2434 2474 4.133820 CCAACATCCGCCACTATTTATCA 58.866 43.478 0.00 0.00 0.00 2.15
2435 2475 4.134563 ACCAACATCCGCCACTATTTATC 58.865 43.478 0.00 0.00 0.00 1.75
2436 2476 4.134563 GACCAACATCCGCCACTATTTAT 58.865 43.478 0.00 0.00 0.00 1.40
2437 2477 3.199071 AGACCAACATCCGCCACTATTTA 59.801 43.478 0.00 0.00 0.00 1.40
2438 2478 2.026262 AGACCAACATCCGCCACTATTT 60.026 45.455 0.00 0.00 0.00 1.40
2439 2479 1.559682 AGACCAACATCCGCCACTATT 59.440 47.619 0.00 0.00 0.00 1.73
2440 2480 1.204146 AGACCAACATCCGCCACTAT 58.796 50.000 0.00 0.00 0.00 2.12
2441 2481 1.855295 TAGACCAACATCCGCCACTA 58.145 50.000 0.00 0.00 0.00 2.74
2442 2482 0.981183 TTAGACCAACATCCGCCACT 59.019 50.000 0.00 0.00 0.00 4.00
2443 2483 2.038387 ATTAGACCAACATCCGCCAC 57.962 50.000 0.00 0.00 0.00 5.01
2444 2484 2.799126 AATTAGACCAACATCCGCCA 57.201 45.000 0.00 0.00 0.00 5.69
2445 2485 4.196971 AGTAAATTAGACCAACATCCGCC 58.803 43.478 0.00 0.00 0.00 6.13
2446 2486 6.704493 TGATAGTAAATTAGACCAACATCCGC 59.296 38.462 0.00 0.00 0.00 5.54
2447 2487 8.833231 ATGATAGTAAATTAGACCAACATCCG 57.167 34.615 0.00 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.