Multiple sequence alignment - TraesCS6B01G306200

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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 TraesCS6B01G306200 chr6B 100.000 2405 0 0 1 2405 549415407 549413003 0.000000e+00 4442.0
1 TraesCS6B01G306200 chr6B 94.909 275 12 2 2132 2405 438362700 438362427 1.710000e-116 429.0
2 TraesCS6B01G306200 chr6B 73.799 874 185 34 669 1523 20667979 20667131 3.000000e-79 305.0
3 TraesCS6B01G306200 chr6B 71.570 809 177 35 751 1524 20625201 20624411 1.140000e-38 171.0
4 TraesCS6B01G306200 chr6D 93.052 2130 133 10 1 2123 364438402 364436281 0.000000e+00 3099.0
5 TraesCS6B01G306200 chr6D 95.238 273 11 2 2134 2405 310208295 310208024 4.750000e-117 431.0
6 TraesCS6B01G306200 chr6D 94.265 279 14 2 2128 2405 373645439 373645716 2.210000e-115 425.0
7 TraesCS6B01G306200 chr6D 74.230 877 180 35 669 1523 10815598 10814746 2.310000e-85 326.0
8 TraesCS6B01G306200 chr6A 92.448 2145 148 9 1 2138 505898541 505896404 0.000000e+00 3051.0
9 TraesCS6B01G306200 chr5D 95.273 275 11 2 2132 2405 293318182 293317909 3.670000e-118 435.0
10 TraesCS6B01G306200 chr5D 94.604 278 13 2 2129 2405 281160286 281160562 1.710000e-116 429.0
11 TraesCS6B01G306200 chr5D 94.604 278 13 2 2129 2405 424717758 424718034 1.710000e-116 429.0
12 TraesCS6B01G306200 chr2D 95.290 276 10 3 2132 2405 521466062 521465788 3.670000e-118 435.0
13 TraesCS6B01G306200 chr2D 94.928 276 11 3 2132 2405 185172201 185171927 1.710000e-116 429.0
14 TraesCS6B01G306200 chr2B 94.909 275 12 2 2132 2405 638834502 638834229 1.710000e-116 429.0
15 TraesCS6B01G306200 chr2A 75.242 723 143 30 990 1695 704058534 704057831 6.460000e-81 311.0
16 TraesCS6B01G306200 chr2A 95.556 45 2 0 1307 1351 5404986 5404942 3.320000e-09 73.1
17 TraesCS6B01G306200 chr3A 72.862 807 167 34 750 1523 133684283 133683496 1.860000e-56 230.0
18 TraesCS6B01G306200 chr3A 78.289 152 26 5 656 803 133684453 133684305 9.160000e-15 91.6
19 TraesCS6B01G306200 chr3D 78.443 167 34 2 1700 1864 575754911 575754745 9.090000e-20 108.0


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 TraesCS6B01G306200 chr6B 549413003 549415407 2404 True 4442 4442 100.000 1 2405 1 chr6B.!!$R4 2404
1 TraesCS6B01G306200 chr6B 20667131 20667979 848 True 305 305 73.799 669 1523 1 chr6B.!!$R2 854
2 TraesCS6B01G306200 chr6D 364436281 364438402 2121 True 3099 3099 93.052 1 2123 1 chr6D.!!$R3 2122
3 TraesCS6B01G306200 chr6D 10814746 10815598 852 True 326 326 74.230 669 1523 1 chr6D.!!$R1 854
4 TraesCS6B01G306200 chr6A 505896404 505898541 2137 True 3051 3051 92.448 1 2138 1 chr6A.!!$R1 2137
5 TraesCS6B01G306200 chr2A 704057831 704058534 703 True 311 311 75.242 990 1695 1 chr2A.!!$R2 705

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
128 129 0.763223 CGGCCTAACCCTGGGTAGAT 60.763 60.0 20.91 6.26 33.12 1.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2099 2129 0.308684 CCATTCATCGGGCATTCACG 59.691 55.0 0.0 0.0 0.0 4.35 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
37 38 1.343465 ACACTACACTTCCCGTTCCAG 59.657 52.381 0.00 0.00 0.00 3.86
72 73 5.360591 AGCTCTCTATCCACCAAATAAACG 58.639 41.667 0.00 0.00 0.00 3.60
78 79 5.872617 TCTATCCACCAAATAAACGACACAG 59.127 40.000 0.00 0.00 0.00 3.66
117 118 2.489751 GCAACCATGCGGCCTAAC 59.510 61.111 0.00 0.00 43.83 2.34
128 129 0.763223 CGGCCTAACCCTGGGTAGAT 60.763 60.000 20.91 6.26 33.12 1.98
130 131 1.694693 GGCCTAACCCTGGGTAGATCA 60.695 57.143 20.91 1.40 33.12 2.92
181 182 4.740822 ATCCACGCCTTGCACCCC 62.741 66.667 0.00 0.00 0.00 4.95
202 203 3.372954 CGTCTATGAATCGACAAGGGAC 58.627 50.000 0.00 0.00 0.00 4.46
294 295 5.396772 CCTTGAGTATCCACAAATCTAGGCA 60.397 44.000 0.00 0.00 0.00 4.75
319 320 2.708861 TGTCCTTGTTTCCTAGCTTCCA 59.291 45.455 0.00 0.00 0.00 3.53
320 321 3.137544 TGTCCTTGTTTCCTAGCTTCCAA 59.862 43.478 0.00 0.00 0.00 3.53
335 336 3.745797 GCTTCCAACCTTCACTCACTCTT 60.746 47.826 0.00 0.00 0.00 2.85
351 352 4.277423 TCACTCTTGATCTAACACGTGTCA 59.723 41.667 23.61 12.45 0.00 3.58
353 354 5.635280 CACTCTTGATCTAACACGTGTCAAT 59.365 40.000 23.61 15.26 0.00 2.57
384 385 1.212935 ACCCATGCATCCTCCACTAAC 59.787 52.381 0.00 0.00 0.00 2.34
439 442 9.791801 TGTATTGCCATAATCAACACTATACAT 57.208 29.630 0.00 0.00 0.00 2.29
571 575 3.305335 GGTCAACAATTAGGTGGCAACTG 60.305 47.826 17.03 0.83 42.90 3.16
614 618 5.346551 CCATATGCACATGTCAACAACTTTG 59.653 40.000 3.92 0.00 0.00 2.77
615 619 3.162202 TGCACATGTCAACAACTTTGG 57.838 42.857 0.00 0.00 0.00 3.28
809 817 7.874940 TGATTCATGTCTTTTAGAACCACTTG 58.125 34.615 0.00 0.00 0.00 3.16
812 820 5.592282 TCATGTCTTTTAGAACCACTTGCAA 59.408 36.000 0.00 0.00 0.00 4.08
933 941 8.445493 GTCTCGTCTTTCTAGGCTATAAGATAC 58.555 40.741 17.17 11.76 0.00 2.24
969 982 2.418197 GGGTGTGCATCTACTCGCTTAA 60.418 50.000 0.00 0.00 0.00 1.85
973 986 4.566759 GTGTGCATCTACTCGCTTAATTGA 59.433 41.667 0.00 0.00 0.00 2.57
1064 1077 4.457257 GCTCATGCCACTTCTTTTAGTTCT 59.543 41.667 0.00 0.00 0.00 3.01
1071 1084 6.603997 TGCCACTTCTTTTAGTTCTTGGTAAA 59.396 34.615 0.00 0.00 0.00 2.01
1072 1085 7.139392 GCCACTTCTTTTAGTTCTTGGTAAAG 58.861 38.462 0.00 0.00 34.45 1.85
1174 1192 4.595350 ACTCCAGGCTACTTCTTTCTTTCT 59.405 41.667 0.00 0.00 0.00 2.52
1175 1193 5.072464 ACTCCAGGCTACTTCTTTCTTTCTT 59.928 40.000 0.00 0.00 0.00 2.52
1176 1194 5.941788 TCCAGGCTACTTCTTTCTTTCTTT 58.058 37.500 0.00 0.00 0.00 2.52
1177 1195 5.998363 TCCAGGCTACTTCTTTCTTTCTTTC 59.002 40.000 0.00 0.00 0.00 2.62
1287 1309 5.615289 GTTGAACATAGCAGGACCTATCAT 58.385 41.667 0.00 0.00 0.00 2.45
1435 1458 4.949856 TCATGCTGCGACTATCATAGGATA 59.050 41.667 0.00 0.00 34.89 2.59
1491 1516 4.957327 TGATGAATTGAGAATGGGCAATGA 59.043 37.500 0.00 0.00 35.11 2.57
1504 1529 2.227388 GGGCAATGACAGAAGTTGAGTG 59.773 50.000 0.00 0.00 0.00 3.51
1565 1591 1.065854 AGGACTACTCACAATGCAGGC 60.066 52.381 0.00 0.00 0.00 4.85
1580 1606 2.159212 TGCAGGCACATCAAACATATGC 60.159 45.455 1.58 0.00 35.51 3.14
1626 1655 5.005779 GCTAGAAATGTGAGATGTGGTTACG 59.994 44.000 0.00 0.00 0.00 3.18
1627 1656 3.684788 AGAAATGTGAGATGTGGTTACGC 59.315 43.478 0.00 0.00 0.00 4.42
1643 1672 4.442472 GGTTACGCTGATTACCATACACCT 60.442 45.833 0.00 0.00 0.00 4.00
1649 1678 5.583061 CGCTGATTACCATACACCTACAAAA 59.417 40.000 0.00 0.00 0.00 2.44
1713 1743 8.545229 TTTGGTGATGCTTGTTAAAAATATGG 57.455 30.769 0.00 0.00 0.00 2.74
1945 1975 5.047519 CCGACTCATTAATTACCGGGAGTAT 60.048 44.000 6.32 0.00 35.88 2.12
1947 1977 6.110411 ACTCATTAATTACCGGGAGTATGG 57.890 41.667 6.32 0.00 34.13 2.74
1959 1989 1.067212 GGAGTATGGCGAGACGTCAAT 59.933 52.381 19.50 0.00 46.66 2.57
2083 2113 1.649664 CAACGAGGAGAGCATCAAGG 58.350 55.000 0.00 0.00 37.82 3.61
2089 2119 0.883814 GGAGAGCATCAAGGCATCCG 60.884 60.000 0.00 0.00 37.82 4.18
2091 2121 2.890109 GAGCATCAAGGCATCCGCG 61.890 63.158 0.00 0.00 34.68 6.46
2112 2142 1.227943 CATCCCGTGAATGCCCGAT 60.228 57.895 0.00 0.00 0.00 4.18
2131 2161 0.539518 TGAATGGGATTCCGCGAAGA 59.460 50.000 8.23 0.00 38.50 2.87
2146 2176 2.537401 CGAAGAGGTCGTTGATAACCC 58.463 52.381 0.00 0.00 45.09 4.11
2147 2177 2.094390 CGAAGAGGTCGTTGATAACCCA 60.094 50.000 0.00 0.00 45.09 4.51
2148 2178 3.259902 GAAGAGGTCGTTGATAACCCAC 58.740 50.000 0.00 0.00 36.11 4.61
2149 2179 2.253610 AGAGGTCGTTGATAACCCACA 58.746 47.619 0.00 0.00 36.11 4.17
2150 2180 2.635915 AGAGGTCGTTGATAACCCACAA 59.364 45.455 0.00 0.00 36.11 3.33
2151 2181 3.000727 GAGGTCGTTGATAACCCACAAG 58.999 50.000 0.00 0.00 36.11 3.16
2152 2182 2.370849 AGGTCGTTGATAACCCACAAGT 59.629 45.455 0.00 0.00 36.11 3.16
2153 2183 3.579586 AGGTCGTTGATAACCCACAAGTA 59.420 43.478 0.00 0.00 36.11 2.24
2154 2184 4.224370 AGGTCGTTGATAACCCACAAGTAT 59.776 41.667 0.00 0.00 36.11 2.12
2155 2185 5.422970 AGGTCGTTGATAACCCACAAGTATA 59.577 40.000 0.00 0.00 36.11 1.47
2156 2186 5.751990 GGTCGTTGATAACCCACAAGTATAG 59.248 44.000 0.00 0.00 0.00 1.31
2157 2187 5.751990 GTCGTTGATAACCCACAAGTATAGG 59.248 44.000 0.00 0.00 0.00 2.57
2168 2198 6.601332 CCCACAAGTATAGGGTATCAATTGT 58.399 40.000 5.13 0.00 37.81 2.71
2169 2199 7.741785 CCCACAAGTATAGGGTATCAATTGTA 58.258 38.462 5.13 0.00 37.81 2.41
2170 2200 7.878127 CCCACAAGTATAGGGTATCAATTGTAG 59.122 40.741 5.13 0.00 37.81 2.74
2171 2201 7.387948 CCACAAGTATAGGGTATCAATTGTAGC 59.612 40.741 5.13 6.96 0.00 3.58
2172 2202 7.387948 CACAAGTATAGGGTATCAATTGTAGCC 59.612 40.741 19.85 19.85 39.44 3.93
2174 2204 7.483580 AGTATAGGGTATCAATTGTAGCCTC 57.516 40.000 27.32 19.05 44.48 4.70
2175 2205 7.249715 AGTATAGGGTATCAATTGTAGCCTCT 58.750 38.462 27.32 22.79 44.48 3.69
2176 2206 8.399529 AGTATAGGGTATCAATTGTAGCCTCTA 58.600 37.037 27.32 22.13 44.48 2.43
2177 2207 9.203163 GTATAGGGTATCAATTGTAGCCTCTAT 57.797 37.037 27.32 21.66 44.48 1.98
2178 2208 6.613153 AGGGTATCAATTGTAGCCTCTATC 57.387 41.667 22.41 6.54 44.48 2.08
2179 2209 5.186021 AGGGTATCAATTGTAGCCTCTATCG 59.814 44.000 22.41 0.00 44.48 2.92
2180 2210 5.185249 GGGTATCAATTGTAGCCTCTATCGA 59.815 44.000 20.03 0.00 36.89 3.59
2181 2211 6.127310 GGGTATCAATTGTAGCCTCTATCGAT 60.127 42.308 20.03 2.16 36.89 3.59
2182 2212 7.068348 GGGTATCAATTGTAGCCTCTATCGATA 59.932 40.741 20.03 4.78 36.89 2.92
2183 2213 8.467598 GGTATCAATTGTAGCCTCTATCGATAA 58.532 37.037 6.58 0.00 0.00 1.75
2184 2214 9.509855 GTATCAATTGTAGCCTCTATCGATAAG 57.490 37.037 6.58 7.04 0.00 1.73
2185 2215 7.526142 TCAATTGTAGCCTCTATCGATAAGT 57.474 36.000 6.58 0.00 0.00 2.24
2186 2216 8.631480 TCAATTGTAGCCTCTATCGATAAGTA 57.369 34.615 6.58 0.00 0.00 2.24
2187 2217 9.074576 TCAATTGTAGCCTCTATCGATAAGTAA 57.925 33.333 6.58 0.00 0.00 2.24
2188 2218 9.347934 CAATTGTAGCCTCTATCGATAAGTAAG 57.652 37.037 6.58 0.00 0.00 2.34
2189 2219 8.865420 ATTGTAGCCTCTATCGATAAGTAAGA 57.135 34.615 6.58 0.59 0.00 2.10
2190 2220 7.908827 TGTAGCCTCTATCGATAAGTAAGAG 57.091 40.000 13.12 13.12 34.71 2.85
2191 2221 7.451732 TGTAGCCTCTATCGATAAGTAAGAGT 58.548 38.462 16.98 6.13 33.38 3.24
2192 2222 6.811253 AGCCTCTATCGATAAGTAAGAGTG 57.189 41.667 16.98 11.37 33.38 3.51
2193 2223 6.300703 AGCCTCTATCGATAAGTAAGAGTGT 58.699 40.000 16.98 5.10 33.38 3.55
2194 2224 6.428771 AGCCTCTATCGATAAGTAAGAGTGTC 59.571 42.308 16.98 8.72 33.38 3.67
2195 2225 6.619018 GCCTCTATCGATAAGTAAGAGTGTCG 60.619 46.154 16.98 6.59 33.38 4.35
2196 2226 6.645827 CCTCTATCGATAAGTAAGAGTGTCGA 59.354 42.308 16.98 0.00 41.52 4.20
2197 2227 7.332430 CCTCTATCGATAAGTAAGAGTGTCGAT 59.668 40.741 16.98 11.94 46.57 3.59
2198 2228 8.242085 TCTATCGATAAGTAAGAGTGTCGATC 57.758 38.462 6.58 0.00 44.62 3.69
2199 2229 5.670149 TCGATAAGTAAGAGTGTCGATCC 57.330 43.478 0.00 0.00 33.73 3.36
2200 2230 4.514441 TCGATAAGTAAGAGTGTCGATCCC 59.486 45.833 0.00 0.00 33.73 3.85
2201 2231 4.275196 CGATAAGTAAGAGTGTCGATCCCA 59.725 45.833 0.00 0.00 0.00 4.37
2202 2232 5.220989 CGATAAGTAAGAGTGTCGATCCCAA 60.221 44.000 0.00 0.00 0.00 4.12
2203 2233 3.870633 AGTAAGAGTGTCGATCCCAAC 57.129 47.619 0.00 0.00 0.00 3.77
2204 2234 2.163815 AGTAAGAGTGTCGATCCCAACG 59.836 50.000 0.00 0.00 0.00 4.10
2205 2235 1.254026 AAGAGTGTCGATCCCAACGA 58.746 50.000 0.00 0.00 37.43 3.85
2206 2236 0.811915 AGAGTGTCGATCCCAACGAG 59.188 55.000 0.00 0.00 40.37 4.18
2207 2237 0.179134 GAGTGTCGATCCCAACGAGG 60.179 60.000 0.00 0.00 40.37 4.63
2208 2238 0.611062 AGTGTCGATCCCAACGAGGA 60.611 55.000 0.00 0.00 41.22 3.71
2209 2239 0.179134 GTGTCGATCCCAACGAGGAG 60.179 60.000 0.00 0.00 39.95 3.69
2210 2240 1.227002 GTCGATCCCAACGAGGAGC 60.227 63.158 0.00 0.00 39.95 4.70
2211 2241 1.379977 TCGATCCCAACGAGGAGCT 60.380 57.895 7.37 0.00 40.30 4.09
2212 2242 0.106868 TCGATCCCAACGAGGAGCTA 60.107 55.000 7.37 0.00 40.30 3.32
2213 2243 0.744874 CGATCCCAACGAGGAGCTAA 59.255 55.000 7.37 0.00 40.30 3.09
2214 2244 1.136305 CGATCCCAACGAGGAGCTAAA 59.864 52.381 7.37 0.00 40.30 1.85
2215 2245 2.799917 CGATCCCAACGAGGAGCTAAAG 60.800 54.545 7.37 0.00 40.30 1.85
2216 2246 0.902531 TCCCAACGAGGAGCTAAAGG 59.097 55.000 0.00 0.00 41.22 3.11
2217 2247 0.613777 CCCAACGAGGAGCTAAAGGT 59.386 55.000 0.00 0.00 41.22 3.50
2218 2248 1.829222 CCCAACGAGGAGCTAAAGGTA 59.171 52.381 0.00 0.00 41.22 3.08
2219 2249 2.159085 CCCAACGAGGAGCTAAAGGTAG 60.159 54.545 0.00 0.00 41.22 3.18
2220 2250 2.758979 CCAACGAGGAGCTAAAGGTAGA 59.241 50.000 0.00 0.00 41.22 2.59
2221 2251 3.194968 CCAACGAGGAGCTAAAGGTAGAA 59.805 47.826 0.00 0.00 41.22 2.10
2222 2252 4.174762 CAACGAGGAGCTAAAGGTAGAAC 58.825 47.826 0.00 0.00 0.00 3.01
2223 2253 3.428532 ACGAGGAGCTAAAGGTAGAACA 58.571 45.455 0.00 0.00 0.00 3.18
2224 2254 3.830755 ACGAGGAGCTAAAGGTAGAACAA 59.169 43.478 0.00 0.00 0.00 2.83
2225 2255 4.082136 ACGAGGAGCTAAAGGTAGAACAAG 60.082 45.833 0.00 0.00 0.00 3.16
2226 2256 4.082136 CGAGGAGCTAAAGGTAGAACAAGT 60.082 45.833 0.00 0.00 0.00 3.16
2227 2257 5.125097 CGAGGAGCTAAAGGTAGAACAAGTA 59.875 44.000 0.00 0.00 0.00 2.24
2228 2258 6.183360 CGAGGAGCTAAAGGTAGAACAAGTAT 60.183 42.308 0.00 0.00 0.00 2.12
2229 2259 7.497773 AGGAGCTAAAGGTAGAACAAGTATT 57.502 36.000 0.00 0.00 0.00 1.89
2230 2260 7.557724 AGGAGCTAAAGGTAGAACAAGTATTC 58.442 38.462 0.00 0.00 0.00 1.75
2231 2261 6.762187 GGAGCTAAAGGTAGAACAAGTATTCC 59.238 42.308 0.00 0.00 0.00 3.01
2232 2262 6.651086 AGCTAAAGGTAGAACAAGTATTCCC 58.349 40.000 0.00 0.00 0.00 3.97
2233 2263 6.444171 AGCTAAAGGTAGAACAAGTATTCCCT 59.556 38.462 0.00 0.00 0.00 4.20
2234 2264 7.037514 AGCTAAAGGTAGAACAAGTATTCCCTT 60.038 37.037 0.00 0.00 33.90 3.95
2235 2265 8.262933 GCTAAAGGTAGAACAAGTATTCCCTTA 58.737 37.037 0.00 0.00 32.30 2.69
2238 2268 7.809880 AGGTAGAACAAGTATTCCCTTAAGT 57.190 36.000 0.97 0.00 0.00 2.24
2239 2269 8.215954 AGGTAGAACAAGTATTCCCTTAAGTT 57.784 34.615 0.97 0.00 0.00 2.66
2240 2270 8.319881 AGGTAGAACAAGTATTCCCTTAAGTTC 58.680 37.037 0.97 0.00 32.04 3.01
2241 2271 8.319881 GGTAGAACAAGTATTCCCTTAAGTTCT 58.680 37.037 0.00 0.00 39.29 3.01
2245 2275 8.943909 AACAAGTATTCCCTTAAGTTCTATCG 57.056 34.615 0.97 0.00 0.00 2.92
2246 2276 8.302515 ACAAGTATTCCCTTAAGTTCTATCGA 57.697 34.615 0.97 0.00 0.00 3.59
2247 2277 8.196103 ACAAGTATTCCCTTAAGTTCTATCGAC 58.804 37.037 0.97 0.00 0.00 4.20
2248 2278 7.287512 AGTATTCCCTTAAGTTCTATCGACC 57.712 40.000 0.97 0.00 0.00 4.79
2249 2279 6.837568 AGTATTCCCTTAAGTTCTATCGACCA 59.162 38.462 0.97 0.00 0.00 4.02
2250 2280 4.996788 TCCCTTAAGTTCTATCGACCAC 57.003 45.455 0.97 0.00 0.00 4.16
2251 2281 3.703052 TCCCTTAAGTTCTATCGACCACC 59.297 47.826 0.97 0.00 0.00 4.61
2252 2282 3.490419 CCCTTAAGTTCTATCGACCACCG 60.490 52.174 0.97 0.00 40.25 4.94
2261 2291 3.564262 TCGACCACCGATACACTCT 57.436 52.632 0.00 0.00 43.23 3.24
2262 2292 2.696989 TCGACCACCGATACACTCTA 57.303 50.000 0.00 0.00 43.23 2.43
2263 2293 3.204306 TCGACCACCGATACACTCTAT 57.796 47.619 0.00 0.00 43.23 1.98
2264 2294 2.876550 TCGACCACCGATACACTCTATG 59.123 50.000 0.00 0.00 43.23 2.23
2265 2295 2.604855 CGACCACCGATACACTCTATGC 60.605 54.545 0.00 0.00 41.76 3.14
2266 2296 2.361119 GACCACCGATACACTCTATGCA 59.639 50.000 0.00 0.00 0.00 3.96
2267 2297 2.100916 ACCACCGATACACTCTATGCAC 59.899 50.000 0.00 0.00 0.00 4.57
2268 2298 2.385315 CACCGATACACTCTATGCACG 58.615 52.381 0.00 0.00 0.00 5.34
2269 2299 1.269102 ACCGATACACTCTATGCACGC 60.269 52.381 0.00 0.00 0.00 5.34
2270 2300 1.001268 CCGATACACTCTATGCACGCT 60.001 52.381 0.00 0.00 0.00 5.07
2271 2301 2.543861 CCGATACACTCTATGCACGCTT 60.544 50.000 0.00 0.00 0.00 4.68
2272 2302 3.304458 CCGATACACTCTATGCACGCTTA 60.304 47.826 0.00 0.00 0.00 3.09
2273 2303 4.287720 CGATACACTCTATGCACGCTTAA 58.712 43.478 0.00 0.00 0.00 1.85
2274 2304 4.146616 CGATACACTCTATGCACGCTTAAC 59.853 45.833 0.00 0.00 0.00 2.01
2275 2305 3.313012 ACACTCTATGCACGCTTAACA 57.687 42.857 0.00 0.00 0.00 2.41
2276 2306 3.861840 ACACTCTATGCACGCTTAACAT 58.138 40.909 0.00 0.00 0.00 2.71
2277 2307 4.253685 ACACTCTATGCACGCTTAACATT 58.746 39.130 0.00 0.00 0.00 2.71
2278 2308 4.330074 ACACTCTATGCACGCTTAACATTC 59.670 41.667 0.00 0.00 0.00 2.67
2279 2309 4.329801 CACTCTATGCACGCTTAACATTCA 59.670 41.667 0.00 0.00 0.00 2.57
2280 2310 4.330074 ACTCTATGCACGCTTAACATTCAC 59.670 41.667 0.00 0.00 0.00 3.18
2281 2311 4.503910 TCTATGCACGCTTAACATTCACT 58.496 39.130 0.00 0.00 0.00 3.41
2282 2312 4.935205 TCTATGCACGCTTAACATTCACTT 59.065 37.500 0.00 0.00 0.00 3.16
2283 2313 3.980646 TGCACGCTTAACATTCACTTT 57.019 38.095 0.00 0.00 0.00 2.66
2284 2314 5.621197 ATGCACGCTTAACATTCACTTTA 57.379 34.783 0.00 0.00 0.00 1.85
2285 2315 4.778904 TGCACGCTTAACATTCACTTTAC 58.221 39.130 0.00 0.00 0.00 2.01
2286 2316 4.156182 GCACGCTTAACATTCACTTTACC 58.844 43.478 0.00 0.00 0.00 2.85
2287 2317 4.083484 GCACGCTTAACATTCACTTTACCT 60.083 41.667 0.00 0.00 0.00 3.08
2288 2318 5.121142 GCACGCTTAACATTCACTTTACCTA 59.879 40.000 0.00 0.00 0.00 3.08
2289 2319 6.672357 GCACGCTTAACATTCACTTTACCTAG 60.672 42.308 0.00 0.00 0.00 3.02
2290 2320 6.588756 CACGCTTAACATTCACTTTACCTAGA 59.411 38.462 0.00 0.00 0.00 2.43
2291 2321 7.117236 CACGCTTAACATTCACTTTACCTAGAA 59.883 37.037 0.00 0.00 0.00 2.10
2292 2322 7.117379 ACGCTTAACATTCACTTTACCTAGAAC 59.883 37.037 0.00 0.00 0.00 3.01
2293 2323 7.117236 CGCTTAACATTCACTTTACCTAGAACA 59.883 37.037 0.00 0.00 0.00 3.18
2294 2324 8.780249 GCTTAACATTCACTTTACCTAGAACAA 58.220 33.333 0.00 0.00 0.00 2.83
2296 2326 9.841295 TTAACATTCACTTTACCTAGAACAAGT 57.159 29.630 0.00 0.00 0.00 3.16
2299 2329 9.436957 ACATTCACTTTACCTAGAACAAGTATG 57.563 33.333 0.00 1.19 0.00 2.39
2300 2330 9.653287 CATTCACTTTACCTAGAACAAGTATGA 57.347 33.333 0.00 0.00 0.00 2.15
2303 2333 9.485206 TCACTTTACCTAGAACAAGTATGAAAC 57.515 33.333 0.00 0.00 0.00 2.78
2304 2334 9.490379 CACTTTACCTAGAACAAGTATGAAACT 57.510 33.333 0.00 0.00 41.49 2.66
2310 2340 9.091220 ACCTAGAACAAGTATGAAACTAGAAGT 57.909 33.333 0.00 0.00 37.50 3.01
2323 2353 8.015185 TGAAACTAGAAGTACTTTGTAGGTGT 57.985 34.615 21.29 11.44 37.05 4.16
2324 2354 8.480501 TGAAACTAGAAGTACTTTGTAGGTGTT 58.519 33.333 21.29 15.01 37.05 3.32
2325 2355 8.658499 AAACTAGAAGTACTTTGTAGGTGTTG 57.342 34.615 21.29 5.55 37.05 3.33
2326 2356 7.357429 ACTAGAAGTACTTTGTAGGTGTTGT 57.643 36.000 21.29 6.00 37.05 3.32
2327 2357 7.789026 ACTAGAAGTACTTTGTAGGTGTTGTT 58.211 34.615 21.29 4.92 37.05 2.83
2328 2358 6.920569 AGAAGTACTTTGTAGGTGTTGTTG 57.079 37.500 10.02 0.00 0.00 3.33
2329 2359 5.820947 AGAAGTACTTTGTAGGTGTTGTTGG 59.179 40.000 10.02 0.00 0.00 3.77
2330 2360 5.362105 AGTACTTTGTAGGTGTTGTTGGA 57.638 39.130 0.00 0.00 0.00 3.53
2331 2361 5.937111 AGTACTTTGTAGGTGTTGTTGGAT 58.063 37.500 0.00 0.00 0.00 3.41
2332 2362 7.069877 AGTACTTTGTAGGTGTTGTTGGATA 57.930 36.000 0.00 0.00 0.00 2.59
2333 2363 7.159372 AGTACTTTGTAGGTGTTGTTGGATAG 58.841 38.462 0.00 0.00 0.00 2.08
2334 2364 5.313712 ACTTTGTAGGTGTTGTTGGATAGG 58.686 41.667 0.00 0.00 0.00 2.57
2335 2365 4.986054 TTGTAGGTGTTGTTGGATAGGT 57.014 40.909 0.00 0.00 0.00 3.08
2336 2366 4.986054 TGTAGGTGTTGTTGGATAGGTT 57.014 40.909 0.00 0.00 0.00 3.50
2337 2367 5.313280 TGTAGGTGTTGTTGGATAGGTTT 57.687 39.130 0.00 0.00 0.00 3.27
2338 2368 5.067273 TGTAGGTGTTGTTGGATAGGTTTG 58.933 41.667 0.00 0.00 0.00 2.93
2339 2369 2.890945 AGGTGTTGTTGGATAGGTTTGC 59.109 45.455 0.00 0.00 0.00 3.68
2340 2370 2.625790 GGTGTTGTTGGATAGGTTTGCA 59.374 45.455 0.00 0.00 0.00 4.08
2341 2371 3.068873 GGTGTTGTTGGATAGGTTTGCAA 59.931 43.478 0.00 0.00 0.00 4.08
2342 2372 4.298332 GTGTTGTTGGATAGGTTTGCAAG 58.702 43.478 0.00 0.00 0.00 4.01
2343 2373 4.037446 GTGTTGTTGGATAGGTTTGCAAGA 59.963 41.667 0.00 0.00 0.00 3.02
2344 2374 4.646945 TGTTGTTGGATAGGTTTGCAAGAA 59.353 37.500 0.00 0.00 29.78 2.52
2345 2375 5.304101 TGTTGTTGGATAGGTTTGCAAGAAT 59.696 36.000 0.00 0.00 33.86 2.40
2346 2376 6.491745 TGTTGTTGGATAGGTTTGCAAGAATA 59.508 34.615 0.00 0.00 33.86 1.75
2347 2377 7.178274 TGTTGTTGGATAGGTTTGCAAGAATAT 59.822 33.333 0.00 0.00 33.86 1.28
2348 2378 8.682710 GTTGTTGGATAGGTTTGCAAGAATATA 58.317 33.333 0.00 0.00 33.86 0.86
2349 2379 8.815565 TGTTGGATAGGTTTGCAAGAATATAA 57.184 30.769 0.00 0.00 0.00 0.98
2350 2380 9.249053 TGTTGGATAGGTTTGCAAGAATATAAA 57.751 29.630 0.00 0.00 0.00 1.40
2351 2381 9.736023 GTTGGATAGGTTTGCAAGAATATAAAG 57.264 33.333 0.00 0.00 0.00 1.85
2352 2382 9.693739 TTGGATAGGTTTGCAAGAATATAAAGA 57.306 29.630 0.00 0.00 0.00 2.52
2353 2383 9.342308 TGGATAGGTTTGCAAGAATATAAAGAG 57.658 33.333 0.00 0.00 0.00 2.85
2354 2384 8.293157 GGATAGGTTTGCAAGAATATAAAGAGC 58.707 37.037 0.00 0.00 0.00 4.09
2355 2385 8.752005 ATAGGTTTGCAAGAATATAAAGAGCA 57.248 30.769 0.00 0.00 0.00 4.26
2356 2386 6.856895 AGGTTTGCAAGAATATAAAGAGCAC 58.143 36.000 0.00 0.00 0.00 4.40
2357 2387 6.434028 AGGTTTGCAAGAATATAAAGAGCACA 59.566 34.615 0.00 0.00 0.00 4.57
2358 2388 7.123247 AGGTTTGCAAGAATATAAAGAGCACAT 59.877 33.333 0.00 0.00 0.00 3.21
2359 2389 8.405531 GGTTTGCAAGAATATAAAGAGCACATA 58.594 33.333 0.00 0.00 0.00 2.29
2360 2390 9.787532 GTTTGCAAGAATATAAAGAGCACATAA 57.212 29.630 0.00 0.00 0.00 1.90
2374 2404 9.574516 AAAGAGCACATAAATATAAACTAGGGG 57.425 33.333 0.00 0.00 0.00 4.79
2375 2405 7.168905 AGAGCACATAAATATAAACTAGGGGC 58.831 38.462 0.00 0.00 0.00 5.80
2376 2406 7.017651 AGAGCACATAAATATAAACTAGGGGCT 59.982 37.037 0.00 0.00 38.69 5.19
2377 2407 6.942576 AGCACATAAATATAAACTAGGGGCTG 59.057 38.462 0.00 0.00 34.96 4.85
2378 2408 6.715264 GCACATAAATATAAACTAGGGGCTGT 59.285 38.462 0.00 0.00 0.00 4.40
2379 2409 7.230712 GCACATAAATATAAACTAGGGGCTGTT 59.769 37.037 0.00 0.00 0.00 3.16
2380 2410 9.131791 CACATAAATATAAACTAGGGGCTGTTT 57.868 33.333 0.00 0.00 39.37 2.83
2389 2419 6.886178 AACTAGGGGCTGTTTAGATAAAGA 57.114 37.500 0.00 0.00 0.00 2.52
2390 2420 6.886178 ACTAGGGGCTGTTTAGATAAAGAA 57.114 37.500 0.00 0.00 0.00 2.52
2391 2421 6.890293 ACTAGGGGCTGTTTAGATAAAGAAG 58.110 40.000 0.00 0.00 0.00 2.85
2392 2422 4.527944 AGGGGCTGTTTAGATAAAGAAGC 58.472 43.478 9.78 9.78 36.27 3.86
2393 2423 4.018415 AGGGGCTGTTTAGATAAAGAAGCA 60.018 41.667 16.11 0.24 37.60 3.91
2394 2424 4.705023 GGGGCTGTTTAGATAAAGAAGCAA 59.295 41.667 16.11 0.00 37.60 3.91
2395 2425 5.360999 GGGGCTGTTTAGATAAAGAAGCAAT 59.639 40.000 16.11 0.00 37.60 3.56
2396 2426 6.546034 GGGGCTGTTTAGATAAAGAAGCAATA 59.454 38.462 16.11 0.00 37.60 1.90
2397 2427 7.068226 GGGGCTGTTTAGATAAAGAAGCAATAA 59.932 37.037 16.11 0.00 37.60 1.40
2398 2428 8.466798 GGGCTGTTTAGATAAAGAAGCAATAAA 58.533 33.333 16.11 0.00 37.60 1.40
2399 2429 9.508567 GGCTGTTTAGATAAAGAAGCAATAAAG 57.491 33.333 16.11 0.00 37.60 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 73 4.082136 CACCCTACTCCTAGTTTCTGTGTC 60.082 50.000 0.00 0.00 0.00 3.67
78 79 5.105064 TGCATAACACCCTACTCCTAGTTTC 60.105 44.000 0.00 0.00 0.00 2.78
115 116 3.967987 GACACTATGATCTACCCAGGGTT 59.032 47.826 19.18 0.00 37.09 4.11
117 118 3.850752 AGACACTATGATCTACCCAGGG 58.149 50.000 2.85 2.85 0.00 4.45
128 129 8.237949 CGAGAAAAGAGTAGAAAGACACTATGA 58.762 37.037 0.00 0.00 0.00 2.15
130 131 8.113173 ACGAGAAAAGAGTAGAAAGACACTAT 57.887 34.615 0.00 0.00 0.00 2.12
181 182 3.372954 GTCCCTTGTCGATTCATAGACG 58.627 50.000 0.00 0.00 40.05 4.18
240 241 0.390603 TAACCGGGTGTCTTCATGCG 60.391 55.000 0.00 0.00 0.00 4.73
243 244 1.975680 AGTGTAACCGGGTGTCTTCAT 59.024 47.619 0.00 0.00 37.80 2.57
244 245 1.342174 GAGTGTAACCGGGTGTCTTCA 59.658 52.381 0.00 0.00 37.80 3.02
245 246 1.617357 AGAGTGTAACCGGGTGTCTTC 59.383 52.381 0.00 0.00 37.80 2.87
246 247 1.713297 AGAGTGTAACCGGGTGTCTT 58.287 50.000 0.00 0.00 37.80 3.01
247 248 2.592102 TAGAGTGTAACCGGGTGTCT 57.408 50.000 0.00 0.96 37.80 3.41
294 295 4.851639 AGCTAGGAAACAAGGACATGAT 57.148 40.909 0.00 0.00 0.00 2.45
319 320 6.042093 TGTTAGATCAAGAGTGAGTGAAGGTT 59.958 38.462 0.00 0.00 37.14 3.50
320 321 5.540337 TGTTAGATCAAGAGTGAGTGAAGGT 59.460 40.000 0.00 0.00 37.14 3.50
335 336 3.369052 GGGGATTGACACGTGTTAGATCA 60.369 47.826 24.26 12.88 0.00 2.92
351 352 0.251742 CATGGGTGTGTGTGGGGATT 60.252 55.000 0.00 0.00 0.00 3.01
353 354 2.842801 CATGGGTGTGTGTGGGGA 59.157 61.111 0.00 0.00 0.00 4.81
502 505 6.202954 GCACAAGGCCACATATTACTACTTAG 59.797 42.308 5.01 0.00 36.11 2.18
506 509 4.813296 GCACAAGGCCACATATTACTAC 57.187 45.455 5.01 0.00 36.11 2.73
571 575 5.712152 ATGGATTTTCAACAACCTCAGAC 57.288 39.130 0.00 0.00 0.00 3.51
809 817 3.672808 AGATGTGGCTATATCTGCTTGC 58.327 45.455 8.55 0.00 34.00 4.01
812 820 6.252233 TCTAGAAGATGTGGCTATATCTGCT 58.748 40.000 19.23 19.23 41.70 4.24
904 912 2.096248 AGCCTAGAAAGACGAGACCTG 58.904 52.381 0.00 0.00 0.00 4.00
948 956 0.108138 AAGCGAGTAGATGCACACCC 60.108 55.000 0.00 0.00 0.00 4.61
950 958 4.566759 TCAATTAAGCGAGTAGATGCACAC 59.433 41.667 0.00 0.00 0.00 3.82
1064 1077 8.848474 TGAAATTTTCAAACAACCTTTACCAA 57.152 26.923 9.36 0.00 36.59 3.67
1071 1084 9.883142 TGTTTATCTGAAATTTTCAAACAACCT 57.117 25.926 18.13 0.00 39.58 3.50
1157 1174 7.265647 ACAAGAAAGAAAGAAAGAAGTAGCC 57.734 36.000 0.00 0.00 0.00 3.93
1287 1309 5.784906 TGGATCCACCTTGCATGATATAGTA 59.215 40.000 11.44 0.00 39.86 1.82
1491 1516 5.353394 TTTGGTAGACACTCAACTTCTGT 57.647 39.130 0.00 0.00 0.00 3.41
1504 1529 8.683615 CCAAAAGGTAAGGAATATTTGGTAGAC 58.316 37.037 6.87 0.00 41.02 2.59
1557 1583 4.689071 CATATGTTTGATGTGCCTGCATT 58.311 39.130 0.00 0.00 0.00 3.56
1565 1591 2.847959 TGCGGCATATGTTTGATGTG 57.152 45.000 0.00 0.00 0.00 3.21
1626 1655 6.995511 TTTTGTAGGTGTATGGTAATCAGC 57.004 37.500 0.00 0.00 0.00 4.26
1649 1678 6.319911 GCTAGAGCAGATGTTAGGGAATTTTT 59.680 38.462 0.00 0.00 41.59 1.94
1651 1680 5.372373 GCTAGAGCAGATGTTAGGGAATTT 58.628 41.667 0.00 0.00 41.59 1.82
1652 1681 4.502259 CGCTAGAGCAGATGTTAGGGAATT 60.502 45.833 1.89 0.00 42.21 2.17
1653 1682 3.006323 CGCTAGAGCAGATGTTAGGGAAT 59.994 47.826 1.89 0.00 42.21 3.01
1661 1691 2.294791 GGACATACGCTAGAGCAGATGT 59.705 50.000 14.82 14.82 44.00 3.06
1667 1697 1.000052 GGGAAGGACATACGCTAGAGC 60.000 57.143 0.00 0.00 37.78 4.09
1766 1796 9.731819 TTGCGTTTATAACACAACAAGATAAAA 57.268 25.926 0.00 0.00 29.25 1.52
1772 1802 5.918011 ACCATTGCGTTTATAACACAACAAG 59.082 36.000 0.00 0.00 36.39 3.16
1789 1819 6.863126 CGAATCCCATATTTAAGAACCATTGC 59.137 38.462 0.00 0.00 0.00 3.56
1823 1853 1.955778 CTTTTCACACATGCCACTGGA 59.044 47.619 0.00 0.00 0.00 3.86
1901 1931 2.217038 ACGACCCACATGCTGGAGT 61.217 57.895 13.86 10.40 43.95 3.85
1945 1975 1.135199 GGTTCTATTGACGTCTCGCCA 60.135 52.381 17.92 0.00 0.00 5.69
1947 1977 2.159421 TCAGGTTCTATTGACGTCTCGC 60.159 50.000 17.92 0.20 0.00 5.03
1959 1989 4.077108 TCTTGTACGAGCTTCAGGTTCTA 58.923 43.478 5.12 0.00 0.00 2.10
2037 2067 0.597568 TGCAAGGGTGATGCTTTTCG 59.402 50.000 0.00 0.00 44.14 3.46
2089 2119 3.585990 CATTCACGGGATGGGCGC 61.586 66.667 0.00 0.00 0.00 6.53
2091 2121 3.219198 GGCATTCACGGGATGGGC 61.219 66.667 0.00 0.00 0.00 5.36
2099 2129 0.308684 CCATTCATCGGGCATTCACG 59.691 55.000 0.00 0.00 0.00 4.35
2101 2131 0.550432 TCCCATTCATCGGGCATTCA 59.450 50.000 0.00 0.00 44.11 2.57
2112 2142 0.539518 TCTTCGCGGAATCCCATTCA 59.460 50.000 6.13 0.00 41.03 2.57
2131 2161 2.370849 ACTTGTGGGTTATCAACGACCT 59.629 45.455 0.00 0.00 36.18 3.85
2144 2174 6.601332 ACAATTGATACCCTATACTTGTGGG 58.399 40.000 13.59 0.00 46.07 4.61
2145 2175 7.387948 GCTACAATTGATACCCTATACTTGTGG 59.612 40.741 13.59 0.00 0.00 4.17
2146 2176 7.387948 GGCTACAATTGATACCCTATACTTGTG 59.612 40.741 13.59 0.00 0.00 3.33
2147 2177 7.292591 AGGCTACAATTGATACCCTATACTTGT 59.707 37.037 13.59 0.00 0.00 3.16
2148 2178 7.680730 AGGCTACAATTGATACCCTATACTTG 58.319 38.462 13.59 0.00 0.00 3.16
2149 2179 7.735321 AGAGGCTACAATTGATACCCTATACTT 59.265 37.037 13.59 0.00 0.00 2.24
2150 2180 7.249715 AGAGGCTACAATTGATACCCTATACT 58.750 38.462 13.59 3.44 0.00 2.12
2151 2181 7.483580 AGAGGCTACAATTGATACCCTATAC 57.516 40.000 13.59 1.38 0.00 1.47
2152 2182 9.422681 GATAGAGGCTACAATTGATACCCTATA 57.577 37.037 13.59 12.74 0.00 1.31
2153 2183 7.068839 CGATAGAGGCTACAATTGATACCCTAT 59.931 40.741 13.59 15.55 39.76 2.57
2154 2184 6.377429 CGATAGAGGCTACAATTGATACCCTA 59.623 42.308 13.59 12.26 39.76 3.53
2155 2185 5.186021 CGATAGAGGCTACAATTGATACCCT 59.814 44.000 13.59 11.39 39.76 4.34
2156 2186 5.185249 TCGATAGAGGCTACAATTGATACCC 59.815 44.000 13.59 6.75 42.67 3.69
2157 2187 6.268825 TCGATAGAGGCTACAATTGATACC 57.731 41.667 13.59 9.66 42.67 2.73
2174 2204 7.413219 GGGATCGACACTCTTACTTATCGATAG 60.413 44.444 5.09 3.13 46.21 2.08
2175 2205 6.370994 GGGATCGACACTCTTACTTATCGATA 59.629 42.308 0.00 0.00 46.21 2.92
2177 2207 4.514441 GGGATCGACACTCTTACTTATCGA 59.486 45.833 0.00 0.00 42.18 3.59
2178 2208 4.275196 TGGGATCGACACTCTTACTTATCG 59.725 45.833 0.00 0.00 0.00 2.92
2179 2209 5.769484 TGGGATCGACACTCTTACTTATC 57.231 43.478 0.00 0.00 0.00 1.75
2180 2210 5.450137 CGTTGGGATCGACACTCTTACTTAT 60.450 44.000 0.00 0.00 0.00 1.73
2181 2211 4.142534 CGTTGGGATCGACACTCTTACTTA 60.143 45.833 0.00 0.00 0.00 2.24
2182 2212 3.367087 CGTTGGGATCGACACTCTTACTT 60.367 47.826 0.00 0.00 0.00 2.24
2183 2213 2.163815 CGTTGGGATCGACACTCTTACT 59.836 50.000 0.00 0.00 0.00 2.24
2184 2214 2.163010 TCGTTGGGATCGACACTCTTAC 59.837 50.000 0.00 0.00 32.30 2.34
2185 2215 2.422479 CTCGTTGGGATCGACACTCTTA 59.578 50.000 0.00 0.00 33.71 2.10
2186 2216 1.202582 CTCGTTGGGATCGACACTCTT 59.797 52.381 0.00 0.00 33.71 2.85
2187 2217 0.811915 CTCGTTGGGATCGACACTCT 59.188 55.000 0.00 0.00 33.71 3.24
2188 2218 0.179134 CCTCGTTGGGATCGACACTC 60.179 60.000 0.00 0.00 33.71 3.51
2189 2219 0.611062 TCCTCGTTGGGATCGACACT 60.611 55.000 0.00 0.00 36.20 3.55
2190 2220 0.179134 CTCCTCGTTGGGATCGACAC 60.179 60.000 0.00 0.00 34.56 3.67
2191 2221 1.945354 GCTCCTCGTTGGGATCGACA 61.945 60.000 0.00 0.00 34.56 4.35
2192 2222 1.227002 GCTCCTCGTTGGGATCGAC 60.227 63.158 0.00 0.00 34.56 4.20
2193 2223 0.106868 TAGCTCCTCGTTGGGATCGA 60.107 55.000 0.00 0.00 34.56 3.59
2194 2224 0.744874 TTAGCTCCTCGTTGGGATCG 59.255 55.000 0.00 0.00 34.56 3.69
2195 2225 2.483889 CCTTTAGCTCCTCGTTGGGATC 60.484 54.545 0.00 0.00 34.56 3.36
2196 2226 1.486726 CCTTTAGCTCCTCGTTGGGAT 59.513 52.381 0.00 0.00 34.56 3.85
2197 2227 0.902531 CCTTTAGCTCCTCGTTGGGA 59.097 55.000 0.00 0.00 36.20 4.37
2198 2228 0.613777 ACCTTTAGCTCCTCGTTGGG 59.386 55.000 0.00 0.00 36.20 4.12
2199 2229 2.758979 TCTACCTTTAGCTCCTCGTTGG 59.241 50.000 0.00 0.00 37.10 3.77
2200 2230 4.174762 GTTCTACCTTTAGCTCCTCGTTG 58.825 47.826 0.00 0.00 0.00 4.10
2201 2231 3.830755 TGTTCTACCTTTAGCTCCTCGTT 59.169 43.478 0.00 0.00 0.00 3.85
2202 2232 3.428532 TGTTCTACCTTTAGCTCCTCGT 58.571 45.455 0.00 0.00 0.00 4.18
2203 2233 4.082136 ACTTGTTCTACCTTTAGCTCCTCG 60.082 45.833 0.00 0.00 0.00 4.63
2204 2234 5.408880 ACTTGTTCTACCTTTAGCTCCTC 57.591 43.478 0.00 0.00 0.00 3.71
2205 2235 7.364851 GGAATACTTGTTCTACCTTTAGCTCCT 60.365 40.741 0.00 0.00 0.00 3.69
2206 2236 6.762187 GGAATACTTGTTCTACCTTTAGCTCC 59.238 42.308 0.00 0.00 0.00 4.70
2207 2237 6.762187 GGGAATACTTGTTCTACCTTTAGCTC 59.238 42.308 0.00 0.00 0.00 4.09
2208 2238 6.444171 AGGGAATACTTGTTCTACCTTTAGCT 59.556 38.462 0.00 0.00 0.00 3.32
2209 2239 6.651086 AGGGAATACTTGTTCTACCTTTAGC 58.349 40.000 0.00 0.00 0.00 3.09
2212 2242 8.666821 ACTTAAGGGAATACTTGTTCTACCTTT 58.333 33.333 7.53 0.00 34.08 3.11
2213 2243 8.215954 ACTTAAGGGAATACTTGTTCTACCTT 57.784 34.615 7.53 0.00 35.40 3.50
2214 2244 7.809880 ACTTAAGGGAATACTTGTTCTACCT 57.190 36.000 7.53 0.00 32.02 3.08
2215 2245 8.319881 AGAACTTAAGGGAATACTTGTTCTACC 58.680 37.037 7.53 0.00 39.71 3.18
2219 2249 9.032420 CGATAGAACTTAAGGGAATACTTGTTC 57.968 37.037 7.53 0.00 35.38 3.18
2220 2250 8.755977 TCGATAGAACTTAAGGGAATACTTGTT 58.244 33.333 7.53 0.00 46.15 2.83
2221 2251 8.302515 TCGATAGAACTTAAGGGAATACTTGT 57.697 34.615 7.53 0.00 46.15 3.16
2244 2274 2.604855 GCATAGAGTGTATCGGTGGTCG 60.605 54.545 0.00 0.00 40.90 4.79
2245 2275 2.361119 TGCATAGAGTGTATCGGTGGTC 59.639 50.000 0.00 0.00 0.00 4.02
2246 2276 2.100916 GTGCATAGAGTGTATCGGTGGT 59.899 50.000 0.00 0.00 0.00 4.16
2247 2277 2.743938 GTGCATAGAGTGTATCGGTGG 58.256 52.381 0.00 0.00 0.00 4.61
2248 2278 2.385315 CGTGCATAGAGTGTATCGGTG 58.615 52.381 0.00 0.00 0.00 4.94
2249 2279 1.269102 GCGTGCATAGAGTGTATCGGT 60.269 52.381 0.00 0.00 0.00 4.69
2250 2280 1.001268 AGCGTGCATAGAGTGTATCGG 60.001 52.381 0.00 0.00 0.00 4.18
2251 2281 2.407521 AGCGTGCATAGAGTGTATCG 57.592 50.000 0.00 0.00 0.00 2.92
2252 2282 5.041287 TGTTAAGCGTGCATAGAGTGTATC 58.959 41.667 0.00 0.00 0.00 2.24
2253 2283 5.006153 TGTTAAGCGTGCATAGAGTGTAT 57.994 39.130 0.00 0.00 0.00 2.29
2254 2284 4.443913 TGTTAAGCGTGCATAGAGTGTA 57.556 40.909 0.00 0.00 0.00 2.90
2255 2285 3.313012 TGTTAAGCGTGCATAGAGTGT 57.687 42.857 0.00 0.00 0.00 3.55
2256 2286 4.329801 TGAATGTTAAGCGTGCATAGAGTG 59.670 41.667 0.00 0.00 0.00 3.51
2257 2287 4.330074 GTGAATGTTAAGCGTGCATAGAGT 59.670 41.667 0.00 0.00 0.00 3.24
2258 2288 4.568359 AGTGAATGTTAAGCGTGCATAGAG 59.432 41.667 0.00 0.00 0.00 2.43
2259 2289 4.503910 AGTGAATGTTAAGCGTGCATAGA 58.496 39.130 0.00 0.00 0.00 1.98
2260 2290 4.864916 AGTGAATGTTAAGCGTGCATAG 57.135 40.909 0.00 0.00 0.00 2.23
2261 2291 5.621197 AAAGTGAATGTTAAGCGTGCATA 57.379 34.783 0.00 0.00 0.00 3.14
2262 2292 4.503741 AAAGTGAATGTTAAGCGTGCAT 57.496 36.364 0.00 0.00 0.00 3.96
2263 2293 3.980646 AAAGTGAATGTTAAGCGTGCA 57.019 38.095 0.00 0.00 0.00 4.57
2264 2294 4.083484 AGGTAAAGTGAATGTTAAGCGTGC 60.083 41.667 0.00 0.00 0.00 5.34
2265 2295 5.607119 AGGTAAAGTGAATGTTAAGCGTG 57.393 39.130 0.00 0.00 0.00 5.34
2266 2296 6.694447 TCTAGGTAAAGTGAATGTTAAGCGT 58.306 36.000 0.00 0.00 0.00 5.07
2267 2297 7.117236 TGTTCTAGGTAAAGTGAATGTTAAGCG 59.883 37.037 0.00 0.00 0.00 4.68
2268 2298 8.319143 TGTTCTAGGTAAAGTGAATGTTAAGC 57.681 34.615 0.00 0.00 0.00 3.09
2270 2300 9.841295 ACTTGTTCTAGGTAAAGTGAATGTTAA 57.159 29.630 4.66 0.00 31.82 2.01
2273 2303 9.436957 CATACTTGTTCTAGGTAAAGTGAATGT 57.563 33.333 12.36 0.00 34.76 2.71
2274 2304 9.653287 TCATACTTGTTCTAGGTAAAGTGAATG 57.347 33.333 12.36 9.89 34.76 2.67
2277 2307 9.485206 GTTTCATACTTGTTCTAGGTAAAGTGA 57.515 33.333 12.36 3.36 34.76 3.41
2278 2308 9.490379 AGTTTCATACTTGTTCTAGGTAAAGTG 57.510 33.333 12.36 1.63 34.76 3.16
2284 2314 9.091220 ACTTCTAGTTTCATACTTGTTCTAGGT 57.909 33.333 0.00 0.00 38.33 3.08
2297 2327 8.648693 ACACCTACAAAGTACTTCTAGTTTCAT 58.351 33.333 8.95 0.00 0.00 2.57
2298 2328 8.015185 ACACCTACAAAGTACTTCTAGTTTCA 57.985 34.615 8.95 0.00 0.00 2.69
2299 2329 8.762426 CAACACCTACAAAGTACTTCTAGTTTC 58.238 37.037 8.95 0.00 0.00 2.78
2300 2330 8.262933 ACAACACCTACAAAGTACTTCTAGTTT 58.737 33.333 8.95 2.14 0.00 2.66
2301 2331 7.789026 ACAACACCTACAAAGTACTTCTAGTT 58.211 34.615 8.95 4.93 0.00 2.24
2302 2332 7.357429 ACAACACCTACAAAGTACTTCTAGT 57.643 36.000 8.95 10.55 0.00 2.57
2303 2333 7.170998 CCAACAACACCTACAAAGTACTTCTAG 59.829 40.741 8.95 10.33 0.00 2.43
2304 2334 6.987992 CCAACAACACCTACAAAGTACTTCTA 59.012 38.462 8.95 0.94 0.00 2.10
2305 2335 5.820947 CCAACAACACCTACAAAGTACTTCT 59.179 40.000 8.95 0.00 0.00 2.85
2306 2336 5.818857 TCCAACAACACCTACAAAGTACTTC 59.181 40.000 8.95 0.00 0.00 3.01
2307 2337 5.747342 TCCAACAACACCTACAAAGTACTT 58.253 37.500 1.12 1.12 0.00 2.24
2308 2338 5.362105 TCCAACAACACCTACAAAGTACT 57.638 39.130 0.00 0.00 0.00 2.73
2309 2339 6.370718 CCTATCCAACAACACCTACAAAGTAC 59.629 42.308 0.00 0.00 0.00 2.73
2310 2340 6.043474 ACCTATCCAACAACACCTACAAAGTA 59.957 38.462 0.00 0.00 0.00 2.24
2311 2341 5.163131 ACCTATCCAACAACACCTACAAAGT 60.163 40.000 0.00 0.00 0.00 2.66
2312 2342 5.313712 ACCTATCCAACAACACCTACAAAG 58.686 41.667 0.00 0.00 0.00 2.77
2313 2343 5.313280 ACCTATCCAACAACACCTACAAA 57.687 39.130 0.00 0.00 0.00 2.83
2314 2344 4.986054 ACCTATCCAACAACACCTACAA 57.014 40.909 0.00 0.00 0.00 2.41
2315 2345 4.986054 AACCTATCCAACAACACCTACA 57.014 40.909 0.00 0.00 0.00 2.74
2316 2346 4.082949 GCAAACCTATCCAACAACACCTAC 60.083 45.833 0.00 0.00 0.00 3.18
2317 2347 4.076394 GCAAACCTATCCAACAACACCTA 58.924 43.478 0.00 0.00 0.00 3.08
2318 2348 2.890945 GCAAACCTATCCAACAACACCT 59.109 45.455 0.00 0.00 0.00 4.00
2319 2349 2.625790 TGCAAACCTATCCAACAACACC 59.374 45.455 0.00 0.00 0.00 4.16
2320 2350 4.037446 TCTTGCAAACCTATCCAACAACAC 59.963 41.667 0.00 0.00 0.00 3.32
2321 2351 4.211125 TCTTGCAAACCTATCCAACAACA 58.789 39.130 0.00 0.00 0.00 3.33
2322 2352 4.846779 TCTTGCAAACCTATCCAACAAC 57.153 40.909 0.00 0.00 0.00 3.32
2323 2353 7.716799 ATATTCTTGCAAACCTATCCAACAA 57.283 32.000 0.00 0.00 0.00 2.83
2324 2354 8.815565 TTATATTCTTGCAAACCTATCCAACA 57.184 30.769 0.00 0.00 0.00 3.33
2325 2355 9.736023 CTTTATATTCTTGCAAACCTATCCAAC 57.264 33.333 0.00 0.00 0.00 3.77
2326 2356 9.693739 TCTTTATATTCTTGCAAACCTATCCAA 57.306 29.630 0.00 0.00 0.00 3.53
2327 2357 9.342308 CTCTTTATATTCTTGCAAACCTATCCA 57.658 33.333 0.00 0.00 0.00 3.41
2328 2358 8.293157 GCTCTTTATATTCTTGCAAACCTATCC 58.707 37.037 0.00 0.00 0.00 2.59
2329 2359 8.840321 TGCTCTTTATATTCTTGCAAACCTATC 58.160 33.333 0.00 0.00 0.00 2.08
2330 2360 8.624776 GTGCTCTTTATATTCTTGCAAACCTAT 58.375 33.333 0.00 0.38 0.00 2.57
2331 2361 7.609918 TGTGCTCTTTATATTCTTGCAAACCTA 59.390 33.333 0.00 0.00 0.00 3.08
2332 2362 6.434028 TGTGCTCTTTATATTCTTGCAAACCT 59.566 34.615 0.00 0.00 0.00 3.50
2333 2363 6.620678 TGTGCTCTTTATATTCTTGCAAACC 58.379 36.000 0.00 0.00 0.00 3.27
2334 2364 9.787532 TTATGTGCTCTTTATATTCTTGCAAAC 57.212 29.630 0.00 0.00 0.00 2.93
2348 2378 9.574516 CCCCTAGTTTATATTTATGTGCTCTTT 57.425 33.333 0.00 0.00 0.00 2.52
2349 2379 7.665974 GCCCCTAGTTTATATTTATGTGCTCTT 59.334 37.037 0.00 0.00 0.00 2.85
2350 2380 7.017651 AGCCCCTAGTTTATATTTATGTGCTCT 59.982 37.037 0.00 0.00 0.00 4.09
2351 2381 7.119846 CAGCCCCTAGTTTATATTTATGTGCTC 59.880 40.741 0.00 0.00 0.00 4.26
2352 2382 6.942576 CAGCCCCTAGTTTATATTTATGTGCT 59.057 38.462 0.00 0.00 0.00 4.40
2353 2383 6.715264 ACAGCCCCTAGTTTATATTTATGTGC 59.285 38.462 0.00 0.00 0.00 4.57
2354 2384 8.691661 AACAGCCCCTAGTTTATATTTATGTG 57.308 34.615 0.00 0.00 0.00 3.21
2363 2393 8.999895 TCTTTATCTAAACAGCCCCTAGTTTAT 58.000 33.333 0.00 0.00 38.91 1.40
2364 2394 8.383374 TCTTTATCTAAACAGCCCCTAGTTTA 57.617 34.615 0.00 0.00 38.71 2.01
2365 2395 7.266905 TCTTTATCTAAACAGCCCCTAGTTT 57.733 36.000 0.00 0.00 40.68 2.66
2366 2396 6.886178 TCTTTATCTAAACAGCCCCTAGTT 57.114 37.500 0.00 0.00 0.00 2.24
2367 2397 6.632900 GCTTCTTTATCTAAACAGCCCCTAGT 60.633 42.308 0.00 0.00 0.00 2.57
2368 2398 5.760743 GCTTCTTTATCTAAACAGCCCCTAG 59.239 44.000 0.00 0.00 0.00 3.02
2369 2399 5.190925 TGCTTCTTTATCTAAACAGCCCCTA 59.809 40.000 6.64 0.00 30.61 3.53
2370 2400 4.018415 TGCTTCTTTATCTAAACAGCCCCT 60.018 41.667 6.64 0.00 30.61 4.79
2371 2401 4.270008 TGCTTCTTTATCTAAACAGCCCC 58.730 43.478 6.64 0.00 30.61 5.80
2372 2402 5.897377 TTGCTTCTTTATCTAAACAGCCC 57.103 39.130 6.64 0.00 30.61 5.19
2373 2403 9.508567 CTTTATTGCTTCTTTATCTAAACAGCC 57.491 33.333 6.64 0.00 30.61 4.85


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

AutoCloner maintained by Alex Coulton.