Multiple sequence alignment - TraesCS4D01G205400

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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 TraesCS4D01G205400 chr4D 100.000 2636 0 0 1 2636 352806990 352809625 0.000000e+00 4868.0
1 TraesCS4D01G205400 chr4D 88.318 214 17 8 1 208 352807290 352807501 1.570000e-62 250.0
2 TraesCS4D01G205400 chr4A 97.535 1136 20 4 736 1867 112697628 112696497 0.000000e+00 1936.0
3 TraesCS4D01G205400 chr4A 93.897 426 22 4 2213 2636 112696262 112695839 7.960000e-180 640.0
4 TraesCS4D01G205400 chr4B 95.739 1150 29 13 735 1877 436318947 436320083 0.000000e+00 1834.0
5 TraesCS4D01G205400 chr4B 84.375 256 28 9 468 717 440917914 440917665 9.430000e-60 241.0
6 TraesCS4D01G205400 chr4B 87.283 173 19 3 2467 2636 436341432 436341604 7.440000e-46 195.0
7 TraesCS4D01G205400 chr4B 91.026 78 7 0 2190 2267 436324853 436324930 3.590000e-19 106.0
8 TraesCS4D01G205400 chr2D 91.389 720 41 9 1 718 623953590 623952890 0.000000e+00 966.0
9 TraesCS4D01G205400 chr2D 89.720 214 13 9 1 208 623953305 623953095 5.590000e-67 265.0
10 TraesCS4D01G205400 chr3B 83.662 710 61 23 11 718 705562330 705562986 3.730000e-173 617.0
11 TraesCS4D01G205400 chr1B 85.185 513 64 11 205 714 91384234 91384737 1.400000e-142 516.0
12 TraesCS4D01G205400 chr1B 80.870 345 47 16 370 706 25433534 25433201 1.210000e-63 254.0
13 TraesCS4D01G205400 chr6B 82.702 607 58 29 115 719 36377919 36377358 1.820000e-136 496.0
14 TraesCS4D01G205400 chr6B 79.564 367 55 18 363 717 6613461 6613819 7.290000e-61 244.0
15 TraesCS4D01G205400 chr5B 87.600 250 25 6 469 717 37054157 37053913 4.290000e-73 285.0
16 TraesCS4D01G205400 chr5B 80.299 401 50 20 334 719 655211609 655211995 2.580000e-70 276.0
17 TraesCS4D01G205400 chr5B 86.694 248 25 8 472 718 87140040 87140280 4.320000e-68 268.0
18 TraesCS4D01G205400 chr2B 94.444 54 3 0 2038 2091 89325267 89325214 1.680000e-12 84.2


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 TraesCS4D01G205400 chr4D 352806990 352809625 2635 False 2559.0 4868 94.1590 1 2636 2 chr4D.!!$F1 2635
1 TraesCS4D01G205400 chr4A 112695839 112697628 1789 True 1288.0 1936 95.7160 736 2636 2 chr4A.!!$R1 1900
2 TraesCS4D01G205400 chr4B 436318947 436320083 1136 False 1834.0 1834 95.7390 735 1877 1 chr4B.!!$F1 1142
3 TraesCS4D01G205400 chr2D 623952890 623953590 700 True 615.5 966 90.5545 1 718 2 chr2D.!!$R1 717
4 TraesCS4D01G205400 chr3B 705562330 705562986 656 False 617.0 617 83.6620 11 718 1 chr3B.!!$F1 707
5 TraesCS4D01G205400 chr1B 91384234 91384737 503 False 516.0 516 85.1850 205 714 1 chr1B.!!$F1 509
6 TraesCS4D01G205400 chr6B 36377358 36377919 561 True 496.0 496 82.7020 115 719 1 chr6B.!!$R1 604

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
627 655 0.179235 CGGTATCGGTGCAAACGTTG 60.179 55.0 0.0 0.0 0.0 4.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2164 2272 0.106708 TGCCGCCTTTGCTATAGGAG 59.893 55.0 1.04 0.82 34.56 3.69 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
193 202 9.471084 AAAAGAAACAGAGAAAACGAAAAGAAA 57.529 25.926 0.00 0.00 0.00 2.52
194 203 9.471084 AAAGAAACAGAGAAAACGAAAAGAAAA 57.529 25.926 0.00 0.00 0.00 2.29
195 204 8.675040 AGAAACAGAGAAAACGAAAAGAAAAG 57.325 30.769 0.00 0.00 0.00 2.27
196 205 8.512138 AGAAACAGAGAAAACGAAAAGAAAAGA 58.488 29.630 0.00 0.00 0.00 2.52
197 206 9.124807 GAAACAGAGAAAACGAAAAGAAAAGAA 57.875 29.630 0.00 0.00 0.00 2.52
198 207 9.471084 AAACAGAGAAAACGAAAAGAAAAGAAA 57.529 25.926 0.00 0.00 0.00 2.52
199 208 9.471084 AACAGAGAAAACGAAAAGAAAAGAAAA 57.529 25.926 0.00 0.00 0.00 2.29
200 209 9.471084 ACAGAGAAAACGAAAAGAAAAGAAAAA 57.529 25.926 0.00 0.00 0.00 1.94
201 210 9.727403 CAGAGAAAACGAAAAGAAAAGAAAAAC 57.273 29.630 0.00 0.00 0.00 2.43
202 211 8.635983 AGAGAAAACGAAAAGAAAAGAAAAACG 58.364 29.630 0.00 0.00 0.00 3.60
203 212 7.726079 AGAAAACGAAAAGAAAAGAAAAACGG 58.274 30.769 0.00 0.00 0.00 4.44
239 248 7.973601 AGAACAAAATTTTGAAAAGCGAACAT 58.026 26.923 32.20 7.11 40.55 2.71
571 599 2.613595 AGAACGTTCCCAAAACCGTAAC 59.386 45.455 24.22 0.00 32.49 2.50
601 629 4.564769 GCTAGAAACATCAGAGAAGGTTCG 59.435 45.833 0.00 0.00 33.03 3.95
606 634 3.070018 ACATCAGAGAAGGTTCGCAAAG 58.930 45.455 0.00 0.00 0.00 2.77
627 655 0.179235 CGGTATCGGTGCAAACGTTG 60.179 55.000 0.00 0.00 0.00 4.10
719 749 1.235724 GGCGAATAGGATTTTCCCCG 58.764 55.000 0.00 0.00 37.19 5.73
720 750 1.202722 GGCGAATAGGATTTTCCCCGA 60.203 52.381 0.00 0.00 37.19 5.14
721 751 1.871676 GCGAATAGGATTTTCCCCGAC 59.128 52.381 0.00 0.00 37.19 4.79
722 752 2.743838 GCGAATAGGATTTTCCCCGACA 60.744 50.000 0.00 0.00 37.19 4.35
723 753 2.870411 CGAATAGGATTTTCCCCGACAC 59.130 50.000 0.00 0.00 37.19 3.67
724 754 3.431766 CGAATAGGATTTTCCCCGACACT 60.432 47.826 0.00 0.00 37.19 3.55
725 755 4.202182 CGAATAGGATTTTCCCCGACACTA 60.202 45.833 0.00 0.00 37.19 2.74
726 756 5.510861 CGAATAGGATTTTCCCCGACACTAT 60.511 44.000 0.00 0.00 37.19 2.12
727 757 5.906772 ATAGGATTTTCCCCGACACTATT 57.093 39.130 0.00 0.00 37.19 1.73
728 758 4.586306 AGGATTTTCCCCGACACTATTT 57.414 40.909 0.00 0.00 37.19 1.40
729 759 4.270008 AGGATTTTCCCCGACACTATTTG 58.730 43.478 0.00 0.00 37.19 2.32
730 760 4.014406 GGATTTTCCCCGACACTATTTGT 58.986 43.478 0.00 0.00 43.10 2.83
731 761 6.092358 AGGATTTTCCCCGACACTATTTGTC 61.092 44.000 0.00 0.00 43.79 3.18
732 762 8.221058 AGGATTTTCCCCGACACTATTTGTCT 62.221 42.308 3.11 0.00 44.47 3.41
733 763 9.599504 AGGATTTTCCCCGACACTATTTGTCTT 62.600 40.741 3.11 0.00 44.47 3.01
789 830 4.052518 GCACTGGGTCATGGGCCT 62.053 66.667 4.53 0.00 0.00 5.19
790 831 2.273449 CACTGGGTCATGGGCCTC 59.727 66.667 4.53 0.00 0.00 4.70
791 832 3.017581 ACTGGGTCATGGGCCTCC 61.018 66.667 4.53 1.97 0.00 4.30
803 844 3.015383 GCCTCCATTGGGCCCTTA 58.985 61.111 25.70 11.93 43.49 2.69
842 883 3.749609 GGTTATAATATCGGCAGGCGTTT 59.250 43.478 17.01 11.04 0.00 3.60
1479 1520 2.915659 ACGACCACGGAGCTGGAA 60.916 61.111 0.00 0.00 44.46 3.53
1825 1873 6.718294 TGTACACTACTCTGTCCTGAATCTA 58.282 40.000 0.00 0.00 0.00 1.98
1880 1963 3.005367 AGAACCCAAGGCAAAAATGTACG 59.995 43.478 0.00 0.00 0.00 3.67
1940 2037 8.480643 AGCATTACCGTAATAGAATCATTAGC 57.519 34.615 3.42 0.22 0.00 3.09
1947 2044 6.531948 CCGTAATAGAATCATTAGCCTAGCAC 59.468 42.308 0.00 0.00 0.00 4.40
1956 2053 2.820728 TAGCCTAGCACTAGACCACA 57.179 50.000 6.25 0.00 35.21 4.17
1960 2057 2.287668 GCCTAGCACTAGACCACATACG 60.288 54.545 6.25 0.00 35.21 3.06
1977 2074 6.756542 CCACATACGACATGATTAACAGAGAA 59.243 38.462 0.00 0.00 0.00 2.87
2020 2117 1.065126 AGTAAAGTCCCATGCCTGCTC 60.065 52.381 0.00 0.00 0.00 4.26
2042 2150 2.884827 GTGTAACCCATGGTCGTACTC 58.115 52.381 11.73 6.96 33.12 2.59
2043 2151 1.826720 TGTAACCCATGGTCGTACTCC 59.173 52.381 11.73 0.00 33.12 3.85
2044 2152 2.105766 GTAACCCATGGTCGTACTCCT 58.894 52.381 11.73 0.00 33.12 3.69
2045 2153 1.652947 AACCCATGGTCGTACTCCTT 58.347 50.000 11.73 0.00 33.12 3.36
2046 2154 1.192428 ACCCATGGTCGTACTCCTTC 58.808 55.000 11.73 0.00 0.00 3.46
2047 2155 1.273098 ACCCATGGTCGTACTCCTTCT 60.273 52.381 11.73 0.00 0.00 2.85
2048 2156 1.137086 CCCATGGTCGTACTCCTTCTG 59.863 57.143 11.73 0.00 0.00 3.02
2049 2157 1.825474 CCATGGTCGTACTCCTTCTGT 59.175 52.381 2.57 0.00 0.00 3.41
2050 2158 2.159226 CCATGGTCGTACTCCTTCTGTC 60.159 54.545 2.57 0.00 0.00 3.51
2051 2159 1.542492 TGGTCGTACTCCTTCTGTCC 58.458 55.000 5.74 0.00 0.00 4.02
2052 2160 0.450983 GGTCGTACTCCTTCTGTCCG 59.549 60.000 0.00 0.00 0.00 4.79
2053 2161 1.446907 GTCGTACTCCTTCTGTCCGA 58.553 55.000 0.00 0.00 0.00 4.55
2054 2162 1.808945 GTCGTACTCCTTCTGTCCGAA 59.191 52.381 0.00 0.00 0.00 4.30
2055 2163 2.227388 GTCGTACTCCTTCTGTCCGAAA 59.773 50.000 0.00 0.00 0.00 3.46
2056 2164 2.886523 TCGTACTCCTTCTGTCCGAAAA 59.113 45.455 0.00 0.00 0.00 2.29
2057 2165 3.318839 TCGTACTCCTTCTGTCCGAAAAA 59.681 43.478 0.00 0.00 0.00 1.94
2058 2166 3.673809 CGTACTCCTTCTGTCCGAAAAAG 59.326 47.826 0.00 0.00 0.00 2.27
2059 2167 2.495084 ACTCCTTCTGTCCGAAAAAGC 58.505 47.619 0.00 0.00 0.00 3.51
2060 2168 2.158813 ACTCCTTCTGTCCGAAAAAGCA 60.159 45.455 0.00 0.00 0.00 3.91
2061 2169 3.077359 CTCCTTCTGTCCGAAAAAGCAT 58.923 45.455 0.00 0.00 0.00 3.79
2062 2170 2.813754 TCCTTCTGTCCGAAAAAGCATG 59.186 45.455 0.00 0.00 0.00 4.06
2063 2171 2.554032 CCTTCTGTCCGAAAAAGCATGT 59.446 45.455 0.00 0.00 0.00 3.21
2064 2172 3.365364 CCTTCTGTCCGAAAAAGCATGTC 60.365 47.826 0.00 0.00 0.00 3.06
2065 2173 3.126001 TCTGTCCGAAAAAGCATGTCT 57.874 42.857 0.00 0.00 0.00 3.41
2066 2174 3.067106 TCTGTCCGAAAAAGCATGTCTC 58.933 45.455 0.00 0.00 0.00 3.36
2067 2175 3.070018 CTGTCCGAAAAAGCATGTCTCT 58.930 45.455 0.00 0.00 0.00 3.10
2068 2176 3.067106 TGTCCGAAAAAGCATGTCTCTC 58.933 45.455 0.00 0.00 0.00 3.20
2069 2177 3.067106 GTCCGAAAAAGCATGTCTCTCA 58.933 45.455 0.00 0.00 0.00 3.27
2070 2178 3.498397 GTCCGAAAAAGCATGTCTCTCAA 59.502 43.478 0.00 0.00 0.00 3.02
2071 2179 4.024048 GTCCGAAAAAGCATGTCTCTCAAA 60.024 41.667 0.00 0.00 0.00 2.69
2072 2180 4.761739 TCCGAAAAAGCATGTCTCTCAAAT 59.238 37.500 0.00 0.00 0.00 2.32
2073 2181 4.855388 CCGAAAAAGCATGTCTCTCAAATG 59.145 41.667 0.00 0.00 0.00 2.32
2074 2182 4.855388 CGAAAAAGCATGTCTCTCAAATGG 59.145 41.667 0.00 0.00 0.00 3.16
2075 2183 5.335113 CGAAAAAGCATGTCTCTCAAATGGA 60.335 40.000 0.00 0.00 0.00 3.41
2076 2184 6.600882 AAAAAGCATGTCTCTCAAATGGAT 57.399 33.333 0.00 0.00 0.00 3.41
2077 2185 7.414429 CGAAAAAGCATGTCTCTCAAATGGATA 60.414 37.037 0.00 0.00 0.00 2.59
2078 2186 7.893124 AAAAGCATGTCTCTCAAATGGATAT 57.107 32.000 0.00 0.00 0.00 1.63
2079 2187 8.985315 AAAAGCATGTCTCTCAAATGGATATA 57.015 30.769 0.00 0.00 0.00 0.86
2080 2188 9.584008 AAAAGCATGTCTCTCAAATGGATATAT 57.416 29.630 0.00 0.00 0.00 0.86
2081 2189 8.789825 AAGCATGTCTCTCAAATGGATATATC 57.210 34.615 3.96 3.96 0.00 1.63
2082 2190 8.148437 AGCATGTCTCTCAAATGGATATATCT 57.852 34.615 12.42 0.00 0.00 1.98
2083 2191 9.264653 AGCATGTCTCTCAAATGGATATATCTA 57.735 33.333 12.42 6.97 0.00 1.98
2084 2192 9.531942 GCATGTCTCTCAAATGGATATATCTAG 57.468 37.037 12.42 0.00 0.00 2.43
2085 2193 9.531942 CATGTCTCTCAAATGGATATATCTAGC 57.468 37.037 12.42 0.00 0.00 3.42
2086 2194 8.655935 TGTCTCTCAAATGGATATATCTAGCA 57.344 34.615 12.42 2.95 0.00 3.49
2087 2195 9.264653 TGTCTCTCAAATGGATATATCTAGCAT 57.735 33.333 12.42 5.11 0.00 3.79
2088 2196 9.748708 GTCTCTCAAATGGATATATCTAGCATC 57.251 37.037 12.42 0.00 0.00 3.91
2089 2197 9.484806 TCTCTCAAATGGATATATCTAGCATCA 57.515 33.333 12.42 1.56 0.00 3.07
2097 2205 8.877808 TGGATATATCTAGCATCAATTAAGCG 57.122 34.615 12.42 0.00 0.00 4.68
2098 2206 7.439356 TGGATATATCTAGCATCAATTAAGCGC 59.561 37.037 12.42 0.00 0.00 5.92
2099 2207 7.655328 GGATATATCTAGCATCAATTAAGCGCT 59.345 37.037 2.64 2.64 36.72 5.92
2100 2208 9.684448 GATATATCTAGCATCAATTAAGCGCTA 57.316 33.333 12.05 0.00 34.18 4.26
2102 2210 8.777865 ATATCTAGCATCAATTAAGCGCTAAA 57.222 30.769 12.05 0.00 34.94 1.85
2103 2211 7.678947 ATCTAGCATCAATTAAGCGCTAAAT 57.321 32.000 12.05 0.00 34.94 1.40
2104 2212 8.777865 ATCTAGCATCAATTAAGCGCTAAATA 57.222 30.769 12.05 0.00 34.94 1.40
2105 2213 8.018677 TCTAGCATCAATTAAGCGCTAAATAC 57.981 34.615 12.05 0.00 34.94 1.89
2106 2214 6.618287 AGCATCAATTAAGCGCTAAATACA 57.382 33.333 12.05 0.00 0.00 2.29
2107 2215 7.206981 AGCATCAATTAAGCGCTAAATACAT 57.793 32.000 12.05 0.00 0.00 2.29
2108 2216 7.301054 AGCATCAATTAAGCGCTAAATACATC 58.699 34.615 12.05 0.00 0.00 3.06
2109 2217 6.524586 GCATCAATTAAGCGCTAAATACATCC 59.475 38.462 12.05 0.00 0.00 3.51
2110 2218 7.584108 CATCAATTAAGCGCTAAATACATCCA 58.416 34.615 12.05 0.00 0.00 3.41
2111 2219 7.744087 TCAATTAAGCGCTAAATACATCCAT 57.256 32.000 12.05 0.00 0.00 3.41
2112 2220 8.165239 TCAATTAAGCGCTAAATACATCCATT 57.835 30.769 12.05 0.00 0.00 3.16
2113 2221 8.629158 TCAATTAAGCGCTAAATACATCCATTT 58.371 29.630 12.05 0.00 32.91 2.32
2114 2222 8.693504 CAATTAAGCGCTAAATACATCCATTTG 58.306 33.333 12.05 0.00 30.84 2.32
2115 2223 7.561021 TTAAGCGCTAAATACATCCATTTGA 57.439 32.000 12.05 0.00 30.84 2.69
2116 2224 5.679734 AGCGCTAAATACATCCATTTGAG 57.320 39.130 8.99 0.00 30.84 3.02
2117 2225 5.368145 AGCGCTAAATACATCCATTTGAGA 58.632 37.500 8.99 0.00 30.84 3.27
2118 2226 5.468072 AGCGCTAAATACATCCATTTGAGAG 59.532 40.000 8.99 0.00 30.84 3.20
2119 2227 5.334414 GCGCTAAATACATCCATTTGAGAGG 60.334 44.000 0.00 0.00 30.84 3.69
2120 2228 5.334414 CGCTAAATACATCCATTTGAGAGGC 60.334 44.000 0.00 0.00 30.84 4.70
2121 2229 5.532406 GCTAAATACATCCATTTGAGAGGCA 59.468 40.000 0.00 0.00 30.84 4.75
2122 2230 6.039717 GCTAAATACATCCATTTGAGAGGCAA 59.960 38.462 0.00 0.00 33.88 4.52
2130 2238 4.935125 TCCATTTGAGAGGCAAACTTGGAA 60.935 41.667 9.62 0.00 45.66 3.53
2131 2239 6.957671 TCCATTTGAGAGGCAAACTTGGAAC 61.958 44.000 9.62 0.00 45.66 3.62
2132 2240 2.727123 TGAGAGGCAAACTTGGAACA 57.273 45.000 0.00 0.00 0.00 3.18
2133 2241 3.360867 TTGAGAGGCAAACTTGGAACAA 58.639 40.909 0.00 0.00 37.18 2.83
2134 2242 3.381272 TTGAGAGGCAAACTTGGAACAAG 59.619 43.478 7.41 7.41 37.18 3.16
2135 2243 6.232513 TTGAGAGGCAAACTTGGAACAAGC 62.233 45.833 8.79 0.00 37.18 4.01
2147 2255 4.589216 TGGAACAAGCTTTTTCAGATGG 57.411 40.909 23.09 0.80 31.92 3.51
2148 2256 4.214310 TGGAACAAGCTTTTTCAGATGGA 58.786 39.130 23.09 1.41 31.92 3.41
2149 2257 4.279169 TGGAACAAGCTTTTTCAGATGGAG 59.721 41.667 23.09 0.00 31.92 3.86
2150 2258 4.520492 GGAACAAGCTTTTTCAGATGGAGA 59.480 41.667 23.09 0.00 0.00 3.71
2151 2259 5.335504 GGAACAAGCTTTTTCAGATGGAGAG 60.336 44.000 23.09 0.00 0.00 3.20
2152 2260 4.978099 ACAAGCTTTTTCAGATGGAGAGA 58.022 39.130 0.00 0.00 0.00 3.10
2153 2261 5.002516 ACAAGCTTTTTCAGATGGAGAGAG 58.997 41.667 0.00 0.00 0.00 3.20
2154 2262 4.906747 AGCTTTTTCAGATGGAGAGAGT 57.093 40.909 0.00 0.00 0.00 3.24
2155 2263 6.169094 CAAGCTTTTTCAGATGGAGAGAGTA 58.831 40.000 0.00 0.00 0.00 2.59
2156 2264 5.729510 AGCTTTTTCAGATGGAGAGAGTAC 58.270 41.667 0.00 0.00 0.00 2.73
2157 2265 5.483583 AGCTTTTTCAGATGGAGAGAGTACT 59.516 40.000 0.00 0.00 0.00 2.73
2158 2266 6.013812 AGCTTTTTCAGATGGAGAGAGTACTT 60.014 38.462 0.00 0.00 0.00 2.24
2159 2267 6.312672 GCTTTTTCAGATGGAGAGAGTACTTC 59.687 42.308 0.00 0.00 0.00 3.01
2160 2268 5.568685 TTTCAGATGGAGAGAGTACTTCG 57.431 43.478 0.00 0.00 0.00 3.79
2161 2269 3.546724 TCAGATGGAGAGAGTACTTCGG 58.453 50.000 0.00 0.00 0.00 4.30
2162 2270 3.200165 TCAGATGGAGAGAGTACTTCGGA 59.800 47.826 0.00 0.00 0.00 4.55
2163 2271 4.141287 CAGATGGAGAGAGTACTTCGGAT 58.859 47.826 0.00 0.00 0.00 4.18
2164 2272 4.215399 CAGATGGAGAGAGTACTTCGGATC 59.785 50.000 0.00 0.00 0.00 3.36
2165 2273 3.935818 TGGAGAGAGTACTTCGGATCT 57.064 47.619 0.00 0.00 0.00 2.75
2166 2274 3.811083 TGGAGAGAGTACTTCGGATCTC 58.189 50.000 0.00 5.76 38.77 2.75
2167 2275 3.143728 GGAGAGAGTACTTCGGATCTCC 58.856 54.545 18.27 18.27 44.28 3.71
2168 2276 3.181448 GGAGAGAGTACTTCGGATCTCCT 60.181 52.174 22.15 5.19 46.09 3.69
2169 2277 4.040706 GGAGAGAGTACTTCGGATCTCCTA 59.959 50.000 22.15 0.00 46.09 2.94
2170 2278 5.280317 GGAGAGAGTACTTCGGATCTCCTAT 60.280 48.000 22.15 3.19 46.09 2.57
2171 2279 6.070653 GGAGAGAGTACTTCGGATCTCCTATA 60.071 46.154 22.15 0.00 46.09 1.31
2172 2280 6.942976 AGAGAGTACTTCGGATCTCCTATAG 58.057 44.000 0.00 0.00 39.19 1.31
2173 2281 5.493809 AGAGTACTTCGGATCTCCTATAGC 58.506 45.833 0.00 0.00 0.00 2.97
2174 2282 5.013287 AGAGTACTTCGGATCTCCTATAGCA 59.987 44.000 0.00 0.00 0.00 3.49
2175 2283 5.632118 AGTACTTCGGATCTCCTATAGCAA 58.368 41.667 0.00 0.00 0.00 3.91
2176 2284 6.069331 AGTACTTCGGATCTCCTATAGCAAA 58.931 40.000 0.00 0.00 0.00 3.68
2177 2285 5.461032 ACTTCGGATCTCCTATAGCAAAG 57.539 43.478 0.00 0.00 0.00 2.77
2178 2286 4.282195 ACTTCGGATCTCCTATAGCAAAGG 59.718 45.833 0.00 0.00 35.26 3.11
2179 2287 2.563179 TCGGATCTCCTATAGCAAAGGC 59.437 50.000 0.00 0.00 41.61 4.35
2190 2298 2.962089 GCAAAGGCGGCAATATGTG 58.038 52.632 13.08 0.00 0.00 3.21
2191 2299 0.173255 GCAAAGGCGGCAATATGTGT 59.827 50.000 13.08 0.00 0.00 3.72
2192 2300 1.912001 CAAAGGCGGCAATATGTGTG 58.088 50.000 13.08 0.00 0.00 3.82
2193 2301 0.817013 AAAGGCGGCAATATGTGTGG 59.183 50.000 13.08 0.00 0.00 4.17
2194 2302 0.323360 AAGGCGGCAATATGTGTGGT 60.323 50.000 13.08 0.00 0.00 4.16
2195 2303 1.031571 AGGCGGCAATATGTGTGGTG 61.032 55.000 13.08 0.00 0.00 4.17
2196 2304 1.433064 GCGGCAATATGTGTGGTGG 59.567 57.895 0.00 0.00 0.00 4.61
2197 2305 1.312371 GCGGCAATATGTGTGGTGGT 61.312 55.000 0.00 0.00 0.00 4.16
2198 2306 1.173043 CGGCAATATGTGTGGTGGTT 58.827 50.000 0.00 0.00 0.00 3.67
2199 2307 1.135431 CGGCAATATGTGTGGTGGTTG 60.135 52.381 0.00 0.00 0.00 3.77
2200 2308 1.204467 GGCAATATGTGTGGTGGTTGG 59.796 52.381 0.00 0.00 0.00 3.77
2201 2309 1.404047 GCAATATGTGTGGTGGTTGGC 60.404 52.381 0.00 0.00 0.00 4.52
2202 2310 1.135431 CAATATGTGTGGTGGTTGGCG 60.135 52.381 0.00 0.00 0.00 5.69
2203 2311 0.679640 ATATGTGTGGTGGTTGGCGG 60.680 55.000 0.00 0.00 0.00 6.13
2204 2312 2.058125 TATGTGTGGTGGTTGGCGGT 62.058 55.000 0.00 0.00 0.00 5.68
2205 2313 3.591835 GTGTGGTGGTTGGCGGTG 61.592 66.667 0.00 0.00 0.00 4.94
2206 2314 4.885270 TGTGGTGGTTGGCGGTGG 62.885 66.667 0.00 0.00 0.00 4.61
2207 2315 4.887190 GTGGTGGTTGGCGGTGGT 62.887 66.667 0.00 0.00 0.00 4.16
2208 2316 3.169242 TGGTGGTTGGCGGTGGTA 61.169 61.111 0.00 0.00 0.00 3.25
2209 2317 2.359478 GGTGGTTGGCGGTGGTAG 60.359 66.667 0.00 0.00 0.00 3.18
2210 2318 2.745037 GTGGTTGGCGGTGGTAGA 59.255 61.111 0.00 0.00 0.00 2.59
2211 2319 1.670083 GTGGTTGGCGGTGGTAGAC 60.670 63.158 0.00 0.00 0.00 2.59
2259 2367 2.364579 ATCGGGCGTTAGGGGTGA 60.365 61.111 0.00 0.00 0.00 4.02
2284 2392 9.561069 GAAACCTACATTATCATGTGGATAGTT 57.439 33.333 5.04 0.00 43.06 2.24
2302 2410 1.345415 GTTAGTTTCTGACGGTGGGGA 59.655 52.381 0.00 0.00 0.00 4.81
2326 2434 5.715279 ACCCTTTTCCTTTTATGCTAGGTTC 59.285 40.000 0.00 0.00 33.15 3.62
2374 2482 2.876550 GTTGGTACGATGCCCCTTATTC 59.123 50.000 0.00 0.00 0.00 1.75
2377 2485 0.682852 TACGATGCCCCTTATTCGGG 59.317 55.000 0.00 0.00 44.20 5.14
2386 2494 1.202604 CCCTTATTCGGGCACATACGT 60.203 52.381 0.00 0.00 37.41 3.57
2387 2495 2.132762 CCTTATTCGGGCACATACGTC 58.867 52.381 0.00 0.00 0.00 4.34
2395 2505 1.068127 GGGCACATACGTCGAGGTATT 59.932 52.381 24.22 14.66 30.86 1.89
2426 2536 8.433421 TTTCTCTTTCTGGTTGTTACAACTAG 57.567 34.615 28.01 28.01 0.00 2.57
2545 2655 4.450757 TGGTCAATGAAATGTCACTGTACG 59.549 41.667 0.00 0.00 36.31 3.67
2547 2657 5.389516 GGTCAATGAAATGTCACTGTACGTC 60.390 44.000 0.00 0.00 36.31 4.34
2560 2670 9.382275 TGTCACTGTACGTCAATACTTATAGTA 57.618 33.333 0.00 0.00 32.40 1.82
2622 2732 5.122869 GGAGTTGGTTTATTTAACGGTCCTC 59.877 44.000 0.00 0.00 37.64 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
179 188 7.722336 TCCGTTTTTCTTTTCTTTTCGTTTTC 58.278 30.769 0.00 0.00 0.00 2.29
571 599 3.334691 TCTGATGTTTCTAGCCGGTTTG 58.665 45.455 1.90 0.00 0.00 2.93
747 777 2.166459 GCTTTTAATGAGTTGGGCCTCC 59.834 50.000 4.53 0.00 0.00 4.30
748 778 2.166459 GGCTTTTAATGAGTTGGGCCTC 59.834 50.000 4.53 0.00 35.92 4.70
789 830 1.616930 TCGGTAAGGGCCCAATGGA 60.617 57.895 27.56 11.66 0.00 3.41
790 831 1.453197 GTCGGTAAGGGCCCAATGG 60.453 63.158 27.56 9.17 0.00 3.16
791 832 1.817941 CGTCGGTAAGGGCCCAATG 60.818 63.158 27.56 8.99 0.00 2.82
792 833 2.587889 CGTCGGTAAGGGCCCAAT 59.412 61.111 27.56 15.58 0.00 3.16
793 834 4.397832 GCGTCGGTAAGGGCCCAA 62.398 66.667 27.56 9.05 0.00 4.12
798 839 2.751357 TTTTGGGGCGTCGGTAAGGG 62.751 60.000 0.00 0.00 0.00 3.95
799 840 1.302671 TTTTGGGGCGTCGGTAAGG 60.303 57.895 0.00 0.00 0.00 2.69
800 841 0.885596 TGTTTTGGGGCGTCGGTAAG 60.886 55.000 0.00 0.00 0.00 2.34
801 842 0.885596 CTGTTTTGGGGCGTCGGTAA 60.886 55.000 0.00 0.00 0.00 2.85
802 843 1.301874 CTGTTTTGGGGCGTCGGTA 60.302 57.895 0.00 0.00 0.00 4.02
803 844 2.593436 CTGTTTTGGGGCGTCGGT 60.593 61.111 0.00 0.00 0.00 4.69
842 883 4.371590 TCGCGCTTGCTGCCACTA 62.372 61.111 5.56 0.00 38.78 2.74
932 973 4.394712 CCGTGTGGTGGGGAGAGC 62.395 72.222 0.00 0.00 0.00 4.09
1185 1226 3.083349 TCCATCTCCACGGCCAGG 61.083 66.667 2.24 3.74 0.00 4.45
1479 1520 3.816524 CCCTCGTCGAGCTTCGCT 61.817 66.667 17.02 0.00 43.88 4.93
1680 1721 8.943909 ACTAGAAATCTTTACTATGAAACGGG 57.056 34.615 0.00 0.00 0.00 5.28
1825 1873 4.692523 ATTGGGGATTAAAGGACCACTT 57.307 40.909 0.00 0.00 42.52 3.16
1880 1963 6.157904 GTCTAACAAGGGACAGTCTACTTTC 58.842 44.000 0.00 0.00 0.00 2.62
1889 1972 8.567285 AAAGAATAATGTCTAACAAGGGACAG 57.433 34.615 0.00 0.00 0.00 3.51
1923 2020 7.316640 AGTGCTAGGCTAATGATTCTATTACG 58.683 38.462 0.00 0.00 0.00 3.18
1931 2028 4.901849 TGGTCTAGTGCTAGGCTAATGATT 59.098 41.667 10.21 0.00 37.87 2.57
1940 2037 3.003482 GTCGTATGTGGTCTAGTGCTAGG 59.997 52.174 6.41 0.00 34.06 3.02
1944 2041 2.933495 TGTCGTATGTGGTCTAGTGC 57.067 50.000 0.00 0.00 0.00 4.40
1947 2044 7.200455 TGTTAATCATGTCGTATGTGGTCTAG 58.800 38.462 0.00 0.00 0.00 2.43
1956 2053 6.098409 ACCCTTCTCTGTTAATCATGTCGTAT 59.902 38.462 0.00 0.00 0.00 3.06
1960 2057 5.292101 CGAACCCTTCTCTGTTAATCATGTC 59.708 44.000 0.00 0.00 0.00 3.06
1998 2095 2.019156 GCAGGCATGGGACTTTACTCC 61.019 57.143 0.00 0.00 0.00 3.85
2020 2117 0.531657 TACGACCATGGGTTACACCG 59.468 55.000 18.09 9.67 39.83 4.94
2034 2142 1.446907 TCGGACAGAAGGAGTACGAC 58.553 55.000 0.00 0.00 46.52 4.34
2036 2144 3.293311 TTTTCGGACAGAAGGAGTACG 57.707 47.619 0.00 0.00 44.48 3.67
2037 2145 3.432592 GCTTTTTCGGACAGAAGGAGTAC 59.567 47.826 0.00 0.00 40.40 2.73
2042 2150 2.554032 ACATGCTTTTTCGGACAGAAGG 59.446 45.455 0.00 0.00 40.40 3.46
2043 2151 3.499918 AGACATGCTTTTTCGGACAGAAG 59.500 43.478 0.00 0.00 40.40 2.85
2044 2152 3.476552 AGACATGCTTTTTCGGACAGAA 58.523 40.909 0.00 0.00 37.01 3.02
2045 2153 3.067106 GAGACATGCTTTTTCGGACAGA 58.933 45.455 0.00 0.00 0.00 3.41
2046 2154 3.070018 AGAGACATGCTTTTTCGGACAG 58.930 45.455 0.00 0.00 0.00 3.51
2047 2155 3.067106 GAGAGACATGCTTTTTCGGACA 58.933 45.455 0.00 0.00 0.00 4.02
2048 2156 3.067106 TGAGAGACATGCTTTTTCGGAC 58.933 45.455 0.00 0.00 0.00 4.79
2049 2157 3.401033 TGAGAGACATGCTTTTTCGGA 57.599 42.857 0.00 0.00 0.00 4.55
2050 2158 4.488126 TTTGAGAGACATGCTTTTTCGG 57.512 40.909 0.00 0.00 0.00 4.30
2051 2159 4.855388 CCATTTGAGAGACATGCTTTTTCG 59.145 41.667 0.00 0.00 0.00 3.46
2052 2160 6.017400 TCCATTTGAGAGACATGCTTTTTC 57.983 37.500 0.00 0.00 0.00 2.29
2053 2161 6.600882 ATCCATTTGAGAGACATGCTTTTT 57.399 33.333 0.00 0.00 0.00 1.94
2054 2162 7.893124 ATATCCATTTGAGAGACATGCTTTT 57.107 32.000 0.00 0.00 0.00 2.27
2055 2163 9.228949 GATATATCCATTTGAGAGACATGCTTT 57.771 33.333 0.81 0.00 0.00 3.51
2056 2164 8.604184 AGATATATCCATTTGAGAGACATGCTT 58.396 33.333 9.18 0.00 0.00 3.91
2057 2165 8.148437 AGATATATCCATTTGAGAGACATGCT 57.852 34.615 9.18 0.00 0.00 3.79
2058 2166 9.531942 CTAGATATATCCATTTGAGAGACATGC 57.468 37.037 9.18 0.00 0.00 4.06
2059 2167 9.531942 GCTAGATATATCCATTTGAGAGACATG 57.468 37.037 9.18 0.00 0.00 3.21
2060 2168 9.264653 TGCTAGATATATCCATTTGAGAGACAT 57.735 33.333 9.18 0.00 0.00 3.06
2061 2169 8.655935 TGCTAGATATATCCATTTGAGAGACA 57.344 34.615 9.18 0.00 0.00 3.41
2062 2170 9.748708 GATGCTAGATATATCCATTTGAGAGAC 57.251 37.037 9.18 0.00 0.00 3.36
2063 2171 9.484806 TGATGCTAGATATATCCATTTGAGAGA 57.515 33.333 9.18 0.00 0.00 3.10
2071 2179 9.486497 CGCTTAATTGATGCTAGATATATCCAT 57.514 33.333 9.18 5.95 0.00 3.41
2072 2180 7.439356 GCGCTTAATTGATGCTAGATATATCCA 59.561 37.037 9.18 1.11 0.00 3.41
2073 2181 7.655328 AGCGCTTAATTGATGCTAGATATATCC 59.345 37.037 2.64 0.00 33.37 2.59
2074 2182 8.586570 AGCGCTTAATTGATGCTAGATATATC 57.413 34.615 2.64 4.42 33.37 1.63
2076 2184 9.869757 TTTAGCGCTTAATTGATGCTAGATATA 57.130 29.630 18.68 0.00 39.13 0.86
2077 2185 8.777865 TTTAGCGCTTAATTGATGCTAGATAT 57.222 30.769 18.68 0.00 39.13 1.63
2078 2186 8.777865 ATTTAGCGCTTAATTGATGCTAGATA 57.222 30.769 18.68 0.00 39.13 1.98
2079 2187 7.678947 ATTTAGCGCTTAATTGATGCTAGAT 57.321 32.000 18.68 0.00 39.13 1.98
2080 2188 7.655732 TGTATTTAGCGCTTAATTGATGCTAGA 59.344 33.333 24.82 3.11 39.13 2.43
2081 2189 7.796838 TGTATTTAGCGCTTAATTGATGCTAG 58.203 34.615 24.82 0.00 39.13 3.42
2082 2190 7.722795 TGTATTTAGCGCTTAATTGATGCTA 57.277 32.000 24.82 4.35 37.12 3.49
2083 2191 6.618287 TGTATTTAGCGCTTAATTGATGCT 57.382 33.333 24.82 4.34 39.59 3.79
2084 2192 6.524586 GGATGTATTTAGCGCTTAATTGATGC 59.475 38.462 24.82 17.55 0.00 3.91
2085 2193 7.584108 TGGATGTATTTAGCGCTTAATTGATG 58.416 34.615 24.82 0.00 0.00 3.07
2086 2194 7.744087 TGGATGTATTTAGCGCTTAATTGAT 57.256 32.000 24.82 16.82 0.00 2.57
2087 2195 7.744087 ATGGATGTATTTAGCGCTTAATTGA 57.256 32.000 24.82 13.21 0.00 2.57
2088 2196 8.693504 CAAATGGATGTATTTAGCGCTTAATTG 58.306 33.333 24.82 11.84 0.00 2.32
2089 2197 8.629158 TCAAATGGATGTATTTAGCGCTTAATT 58.371 29.630 24.82 9.07 0.00 1.40
2090 2198 8.165239 TCAAATGGATGTATTTAGCGCTTAAT 57.835 30.769 23.42 23.42 0.00 1.40
2091 2199 7.497579 TCTCAAATGGATGTATTTAGCGCTTAA 59.502 33.333 18.68 14.75 0.00 1.85
2092 2200 6.989759 TCTCAAATGGATGTATTTAGCGCTTA 59.010 34.615 18.68 2.28 0.00 3.09
2093 2201 5.822519 TCTCAAATGGATGTATTTAGCGCTT 59.177 36.000 18.68 0.00 0.00 4.68
2094 2202 5.368145 TCTCAAATGGATGTATTTAGCGCT 58.632 37.500 17.26 17.26 0.00 5.92
2095 2203 5.334414 CCTCTCAAATGGATGTATTTAGCGC 60.334 44.000 0.00 0.00 0.00 5.92
2096 2204 5.334414 GCCTCTCAAATGGATGTATTTAGCG 60.334 44.000 0.00 0.00 0.00 4.26
2097 2205 5.532406 TGCCTCTCAAATGGATGTATTTAGC 59.468 40.000 0.00 0.00 0.00 3.09
2098 2206 7.572523 TTGCCTCTCAAATGGATGTATTTAG 57.427 36.000 0.00 0.00 0.00 1.85
2099 2207 7.615365 AGTTTGCCTCTCAAATGGATGTATTTA 59.385 33.333 0.00 0.00 45.43 1.40
2100 2208 6.438425 AGTTTGCCTCTCAAATGGATGTATTT 59.562 34.615 0.00 0.00 45.43 1.40
2101 2209 5.954150 AGTTTGCCTCTCAAATGGATGTATT 59.046 36.000 0.00 0.00 45.43 1.89
2102 2210 5.513233 AGTTTGCCTCTCAAATGGATGTAT 58.487 37.500 0.00 0.00 45.43 2.29
2103 2211 4.922206 AGTTTGCCTCTCAAATGGATGTA 58.078 39.130 0.00 0.00 45.43 2.29
2104 2212 3.771216 AGTTTGCCTCTCAAATGGATGT 58.229 40.909 0.00 0.00 45.43 3.06
2105 2213 4.491676 CAAGTTTGCCTCTCAAATGGATG 58.508 43.478 0.00 0.00 45.43 3.51
2106 2214 3.512724 CCAAGTTTGCCTCTCAAATGGAT 59.487 43.478 4.77 0.00 42.98 3.41
2107 2215 2.892852 CCAAGTTTGCCTCTCAAATGGA 59.107 45.455 4.77 0.00 42.98 3.41
2108 2216 2.892852 TCCAAGTTTGCCTCTCAAATGG 59.107 45.455 4.49 4.49 45.43 3.16
2109 2217 4.202141 TGTTCCAAGTTTGCCTCTCAAATG 60.202 41.667 0.00 0.00 45.43 2.32
2110 2218 3.960102 TGTTCCAAGTTTGCCTCTCAAAT 59.040 39.130 0.00 0.00 45.43 2.32
2111 2219 3.360867 TGTTCCAAGTTTGCCTCTCAAA 58.639 40.909 0.00 0.00 42.01 2.69
2112 2220 3.011566 TGTTCCAAGTTTGCCTCTCAA 57.988 42.857 0.00 0.00 0.00 3.02
2113 2221 2.727123 TGTTCCAAGTTTGCCTCTCA 57.273 45.000 0.00 0.00 0.00 3.27
2114 2222 2.287849 GCTTGTTCCAAGTTTGCCTCTC 60.288 50.000 5.92 0.00 0.00 3.20
2115 2223 1.683385 GCTTGTTCCAAGTTTGCCTCT 59.317 47.619 5.92 0.00 0.00 3.69
2116 2224 1.683385 AGCTTGTTCCAAGTTTGCCTC 59.317 47.619 5.92 0.00 0.00 4.70
2117 2225 1.780503 AGCTTGTTCCAAGTTTGCCT 58.219 45.000 5.92 0.00 0.00 4.75
2118 2226 2.602257 AAGCTTGTTCCAAGTTTGCC 57.398 45.000 0.00 0.00 0.00 4.52
2119 2227 4.391523 TGAAAAAGCTTGTTCCAAGTTTGC 59.608 37.500 23.66 0.20 0.00 3.68
2120 2228 5.868801 TCTGAAAAAGCTTGTTCCAAGTTTG 59.131 36.000 23.66 7.77 0.00 2.93
2121 2229 6.036577 TCTGAAAAAGCTTGTTCCAAGTTT 57.963 33.333 23.66 7.47 0.00 2.66
2122 2230 5.659440 TCTGAAAAAGCTTGTTCCAAGTT 57.341 34.783 23.66 0.00 0.00 2.66
2123 2231 5.452356 CCATCTGAAAAAGCTTGTTCCAAGT 60.452 40.000 23.66 7.24 0.00 3.16
2124 2232 4.986659 CCATCTGAAAAAGCTTGTTCCAAG 59.013 41.667 23.66 16.22 0.00 3.61
2125 2233 4.648762 TCCATCTGAAAAAGCTTGTTCCAA 59.351 37.500 23.66 13.56 0.00 3.53
2126 2234 4.214310 TCCATCTGAAAAAGCTTGTTCCA 58.786 39.130 23.66 12.59 0.00 3.53
2127 2235 4.520492 TCTCCATCTGAAAAAGCTTGTTCC 59.480 41.667 23.66 8.90 0.00 3.62
2128 2236 5.471456 TCTCTCCATCTGAAAAAGCTTGTTC 59.529 40.000 20.63 20.63 0.00 3.18
2129 2237 5.380043 TCTCTCCATCTGAAAAAGCTTGTT 58.620 37.500 0.10 0.10 0.00 2.83
2130 2238 4.978099 TCTCTCCATCTGAAAAAGCTTGT 58.022 39.130 0.00 0.00 0.00 3.16
2131 2239 5.002516 ACTCTCTCCATCTGAAAAAGCTTG 58.997 41.667 0.00 0.00 0.00 4.01
2132 2240 5.240013 ACTCTCTCCATCTGAAAAAGCTT 57.760 39.130 0.00 0.00 0.00 3.74
2133 2241 4.906747 ACTCTCTCCATCTGAAAAAGCT 57.093 40.909 0.00 0.00 0.00 3.74
2134 2242 5.729510 AGTACTCTCTCCATCTGAAAAAGC 58.270 41.667 0.00 0.00 0.00 3.51
2135 2243 6.529829 CGAAGTACTCTCTCCATCTGAAAAAG 59.470 42.308 0.00 0.00 0.00 2.27
2136 2244 6.390721 CGAAGTACTCTCTCCATCTGAAAAA 58.609 40.000 0.00 0.00 0.00 1.94
2137 2245 5.105716 CCGAAGTACTCTCTCCATCTGAAAA 60.106 44.000 0.00 0.00 0.00 2.29
2138 2246 4.399618 CCGAAGTACTCTCTCCATCTGAAA 59.600 45.833 0.00 0.00 0.00 2.69
2139 2247 3.948473 CCGAAGTACTCTCTCCATCTGAA 59.052 47.826 0.00 0.00 0.00 3.02
2140 2248 3.200165 TCCGAAGTACTCTCTCCATCTGA 59.800 47.826 0.00 0.00 0.00 3.27
2141 2249 3.546724 TCCGAAGTACTCTCTCCATCTG 58.453 50.000 0.00 0.00 0.00 2.90
2142 2250 3.935818 TCCGAAGTACTCTCTCCATCT 57.064 47.619 0.00 0.00 0.00 2.90
2143 2251 4.394729 AGATCCGAAGTACTCTCTCCATC 58.605 47.826 0.00 0.00 0.00 3.51
2144 2252 4.394729 GAGATCCGAAGTACTCTCTCCAT 58.605 47.826 0.00 0.00 33.05 3.41
2145 2253 3.433882 GGAGATCCGAAGTACTCTCTCCA 60.434 52.174 21.52 0.19 45.25 3.86
2146 2254 3.143728 GGAGATCCGAAGTACTCTCTCC 58.856 54.545 16.24 16.24 41.30 3.71
2147 2255 4.081322 AGGAGATCCGAAGTACTCTCTC 57.919 50.000 0.00 3.68 42.08 3.20
2148 2256 5.836024 ATAGGAGATCCGAAGTACTCTCT 57.164 43.478 0.00 0.00 42.08 3.10
2149 2257 5.583457 GCTATAGGAGATCCGAAGTACTCTC 59.417 48.000 0.00 0.00 42.08 3.20
2150 2258 5.013287 TGCTATAGGAGATCCGAAGTACTCT 59.987 44.000 0.00 0.00 42.08 3.24
2151 2259 5.247084 TGCTATAGGAGATCCGAAGTACTC 58.753 45.833 0.00 0.00 42.08 2.59
2152 2260 5.244189 TGCTATAGGAGATCCGAAGTACT 57.756 43.478 1.04 0.00 42.08 2.73
2153 2261 5.961396 TTGCTATAGGAGATCCGAAGTAC 57.039 43.478 1.04 0.00 42.08 2.73
2154 2262 5.477291 CCTTTGCTATAGGAGATCCGAAGTA 59.523 44.000 1.04 0.00 42.08 2.24
2155 2263 4.282195 CCTTTGCTATAGGAGATCCGAAGT 59.718 45.833 1.04 0.00 42.08 3.01
2156 2264 4.815269 CCTTTGCTATAGGAGATCCGAAG 58.185 47.826 1.04 0.00 42.08 3.79
2157 2265 3.006967 GCCTTTGCTATAGGAGATCCGAA 59.993 47.826 1.04 0.00 36.27 4.30
2158 2266 2.563179 GCCTTTGCTATAGGAGATCCGA 59.437 50.000 1.04 0.00 36.27 4.55
2159 2267 2.672478 CGCCTTTGCTATAGGAGATCCG 60.672 54.545 1.04 0.00 34.87 4.18
2160 2268 2.354203 CCGCCTTTGCTATAGGAGATCC 60.354 54.545 1.04 0.00 34.87 3.36
2161 2269 2.933056 GCCGCCTTTGCTATAGGAGATC 60.933 54.545 1.04 0.00 34.87 2.75
2162 2270 1.002544 GCCGCCTTTGCTATAGGAGAT 59.997 52.381 1.04 0.00 34.87 2.75
2163 2271 0.393077 GCCGCCTTTGCTATAGGAGA 59.607 55.000 1.04 0.00 34.87 3.71
2164 2272 0.106708 TGCCGCCTTTGCTATAGGAG 59.893 55.000 1.04 0.82 34.56 3.69
2165 2273 0.544223 TTGCCGCCTTTGCTATAGGA 59.456 50.000 1.04 0.00 34.56 2.94
2166 2274 1.609208 ATTGCCGCCTTTGCTATAGG 58.391 50.000 1.04 0.00 35.80 2.57
2167 2275 3.753272 ACATATTGCCGCCTTTGCTATAG 59.247 43.478 0.00 0.00 31.72 1.31
2168 2276 3.501828 CACATATTGCCGCCTTTGCTATA 59.498 43.478 0.00 0.00 32.51 1.31
2169 2277 2.294233 CACATATTGCCGCCTTTGCTAT 59.706 45.455 0.00 0.00 34.43 2.97
2170 2278 1.675483 CACATATTGCCGCCTTTGCTA 59.325 47.619 0.00 0.00 34.43 3.49
2171 2279 0.457035 CACATATTGCCGCCTTTGCT 59.543 50.000 0.00 0.00 34.43 3.91
2172 2280 0.173255 ACACATATTGCCGCCTTTGC 59.827 50.000 0.00 0.00 0.00 3.68
2173 2281 1.469595 CCACACATATTGCCGCCTTTG 60.470 52.381 0.00 0.00 0.00 2.77
2174 2282 0.817013 CCACACATATTGCCGCCTTT 59.183 50.000 0.00 0.00 0.00 3.11
2175 2283 0.323360 ACCACACATATTGCCGCCTT 60.323 50.000 0.00 0.00 0.00 4.35
2176 2284 1.031571 CACCACACATATTGCCGCCT 61.032 55.000 0.00 0.00 0.00 5.52
2177 2285 1.433064 CACCACACATATTGCCGCC 59.567 57.895 0.00 0.00 0.00 6.13
2178 2286 1.312371 ACCACCACACATATTGCCGC 61.312 55.000 0.00 0.00 0.00 6.53
2179 2287 1.135431 CAACCACCACACATATTGCCG 60.135 52.381 0.00 0.00 0.00 5.69
2180 2288 1.204467 CCAACCACCACACATATTGCC 59.796 52.381 0.00 0.00 0.00 4.52
2181 2289 1.404047 GCCAACCACCACACATATTGC 60.404 52.381 0.00 0.00 0.00 3.56
2182 2290 1.135431 CGCCAACCACCACACATATTG 60.135 52.381 0.00 0.00 0.00 1.90
2183 2291 1.173043 CGCCAACCACCACACATATT 58.827 50.000 0.00 0.00 0.00 1.28
2184 2292 0.679640 CCGCCAACCACCACACATAT 60.680 55.000 0.00 0.00 0.00 1.78
2185 2293 1.302913 CCGCCAACCACCACACATA 60.303 57.895 0.00 0.00 0.00 2.29
2186 2294 2.597217 CCGCCAACCACCACACAT 60.597 61.111 0.00 0.00 0.00 3.21
2187 2295 4.116585 ACCGCCAACCACCACACA 62.117 61.111 0.00 0.00 0.00 3.72
2188 2296 3.591835 CACCGCCAACCACCACAC 61.592 66.667 0.00 0.00 0.00 3.82
2189 2297 4.885270 CCACCGCCAACCACCACA 62.885 66.667 0.00 0.00 0.00 4.17
2190 2298 3.479127 TACCACCGCCAACCACCAC 62.479 63.158 0.00 0.00 0.00 4.16
2191 2299 3.169242 TACCACCGCCAACCACCA 61.169 61.111 0.00 0.00 0.00 4.17
2192 2300 2.359478 CTACCACCGCCAACCACC 60.359 66.667 0.00 0.00 0.00 4.61
2193 2301 1.670083 GTCTACCACCGCCAACCAC 60.670 63.158 0.00 0.00 0.00 4.16
2194 2302 2.745037 GTCTACCACCGCCAACCA 59.255 61.111 0.00 0.00 0.00 3.67
2195 2303 2.433664 CGTCTACCACCGCCAACC 60.434 66.667 0.00 0.00 0.00 3.77
2196 2304 1.735559 GTCGTCTACCACCGCCAAC 60.736 63.158 0.00 0.00 0.00 3.77
2197 2305 2.652530 GTCGTCTACCACCGCCAA 59.347 61.111 0.00 0.00 0.00 4.52
2273 2381 5.187186 ACCGTCAGAAACTAACTATCCACAT 59.813 40.000 0.00 0.00 0.00 3.21
2284 2392 0.971386 GTCCCCACCGTCAGAAACTA 59.029 55.000 0.00 0.00 0.00 2.24
2291 2399 2.059345 GAAAAGGGTCCCCACCGTCA 62.059 60.000 3.51 0.00 44.91 4.35
2302 2410 5.270979 ACCTAGCATAAAAGGAAAAGGGT 57.729 39.130 0.00 0.00 36.66 4.34
2304 2412 8.624776 CATAGAACCTAGCATAAAAGGAAAAGG 58.375 37.037 0.00 0.00 36.66 3.11
2318 2426 0.318762 CCGCCTCCATAGAACCTAGC 59.681 60.000 0.00 0.00 0.00 3.42
2326 2434 2.520982 TCGGTCCCGCCTCCATAG 60.521 66.667 0.00 0.00 39.59 2.23
2374 2482 1.717791 TACCTCGACGTATGTGCCCG 61.718 60.000 0.00 0.00 0.00 6.13
2377 2485 2.787680 GTGAATACCTCGACGTATGTGC 59.212 50.000 7.68 2.88 0.00 4.57
2395 2505 4.855340 ACAACCAGAAAGAGAAAAGGTGA 58.145 39.130 0.00 0.00 0.00 4.02
2447 2557 5.885912 GCTTGTTAACCTAATGATCAAGGGA 59.114 40.000 16.24 3.00 37.18 4.20
2563 2673 9.480053 CATGCTACCCATTTTAAAATAGAATGG 57.520 33.333 12.98 11.09 45.96 3.16
2615 2725 0.179108 GATCCTGGAAACGAGGACCG 60.179 60.000 0.00 0.00 39.42 4.79


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

AutoCloner maintained by Alex Coulton.