Multiple sequence alignment - TraesCS7D01G532900

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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 TraesCS7D01G532900 chr7D 100.000 2840 0 0 1 2840 626535870 626533031 0.000000e+00 5245
1 TraesCS7D01G532900 chr7D 84.670 424 35 18 2324 2724 181006968 181006552 2.050000e-106 396
2 TraesCS7D01G532900 chr7A 90.578 1921 99 39 161 2035 722211152 722213036 0.000000e+00 2470
3 TraesCS7D01G532900 chr7A 91.252 503 30 5 2225 2723 722213102 722213594 0.000000e+00 673
4 TraesCS7D01G532900 chr7A 85.882 170 9 8 2 162 722210958 722211121 1.750000e-37 167
5 TraesCS7D01G532900 chr7B 90.252 1867 108 37 187 2012 726863215 726865048 0.000000e+00 2372
6 TraesCS7D01G532900 chr7B 91.304 115 9 1 3 116 726863101 726863215 3.790000e-34 156
7 TraesCS7D01G532900 chr2D 83.962 424 38 18 2324 2724 58999952 58999536 2.060000e-101 379


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 TraesCS7D01G532900 chr7D 626533031 626535870 2839 True 5245.000000 5245 100.000000 1 2840 1 chr7D.!!$R2 2839
1 TraesCS7D01G532900 chr7A 722210958 722213594 2636 False 1103.333333 2470 89.237333 2 2723 3 chr7A.!!$F1 2721
2 TraesCS7D01G532900 chr7B 726863101 726865048 1947 False 1264.000000 2372 90.778000 3 2012 2 chr7B.!!$F1 2009

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
710 780 0.029567 GTACGTGGATCGAGCTCCAG 59.97 60.0 8.02 5.69 45.87 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2220 2340 0.03213 TGAAGAGACGACAGTGTGGC 59.968 55.0 0.0 0.0 0.0 5.01 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
33 34 9.245962 AGTAAATTATATGTACGCTTGTCACTC 57.754 33.333 0.00 0.00 0.00 3.51
128 138 2.045926 GGTGATGCACGGCTCCTT 60.046 61.111 0.00 0.00 34.83 3.36
129 139 1.675641 GGTGATGCACGGCTCCTTT 60.676 57.895 0.00 0.00 34.83 3.11
130 140 1.648467 GGTGATGCACGGCTCCTTTC 61.648 60.000 0.00 0.00 34.83 2.62
131 141 1.377202 TGATGCACGGCTCCTTTCC 60.377 57.895 0.00 0.00 0.00 3.13
136 146 1.377333 CACGGCTCCTTTCCTTCCC 60.377 63.158 0.00 0.00 0.00 3.97
158 168 2.337583 TCCTTTGTGAAGCGATCGAAG 58.662 47.619 21.57 11.22 0.00 3.79
172 214 2.495409 TCGAAGACGTACAAGCACAA 57.505 45.000 0.00 0.00 40.69 3.33
176 218 3.603857 CGAAGACGTACAAGCACAAAAGG 60.604 47.826 0.00 0.00 34.56 3.11
226 268 0.457337 AAGCCGTCGTTGGATCGTAC 60.457 55.000 0.00 0.00 0.00 3.67
262 304 1.132834 CAATGCATGGCGTGTACACAT 59.867 47.619 24.98 9.08 0.00 3.21
461 515 2.745884 CATGGCGACCAAGCGGAA 60.746 61.111 2.68 0.00 36.95 4.30
489 553 3.146182 GCTCCAGGCGAGATCCAT 58.854 61.111 0.00 0.00 41.63 3.41
690 760 3.449227 ACGCGCTGCAGGTAGCTA 61.449 61.111 17.12 0.00 45.94 3.32
691 761 2.656651 CGCGCTGCAGGTAGCTAG 60.657 66.667 17.12 0.00 45.94 3.42
692 762 2.496817 GCGCTGCAGGTAGCTAGT 59.503 61.111 17.12 0.00 45.94 2.57
693 763 1.734137 GCGCTGCAGGTAGCTAGTA 59.266 57.895 17.12 0.00 45.94 1.82
694 764 0.595310 GCGCTGCAGGTAGCTAGTAC 60.595 60.000 17.12 0.00 45.94 2.73
695 765 0.317103 CGCTGCAGGTAGCTAGTACG 60.317 60.000 17.12 2.03 45.94 3.67
696 766 0.739561 GCTGCAGGTAGCTAGTACGT 59.260 55.000 17.12 0.00 45.94 3.57
708 778 1.532007 CTAGTACGTGGATCGAGCTCC 59.468 57.143 8.47 0.00 42.86 4.70
709 779 0.393944 AGTACGTGGATCGAGCTCCA 60.394 55.000 8.47 3.55 43.09 3.86
710 780 0.029567 GTACGTGGATCGAGCTCCAG 59.970 60.000 8.02 5.69 45.87 3.86
711 781 1.725557 TACGTGGATCGAGCTCCAGC 61.726 60.000 8.02 0.00 45.87 4.85
712 782 2.895680 GTGGATCGAGCTCCAGCA 59.104 61.111 8.02 0.00 45.87 4.41
713 783 1.227205 GTGGATCGAGCTCCAGCAG 60.227 63.158 8.02 0.00 45.87 4.24
714 784 2.420890 GGATCGAGCTCCAGCAGG 59.579 66.667 8.47 0.00 45.16 4.85
715 785 2.280052 GATCGAGCTCCAGCAGGC 60.280 66.667 8.47 0.00 45.16 4.85
716 786 3.079478 ATCGAGCTCCAGCAGGCA 61.079 61.111 8.47 0.00 45.16 4.75
717 787 2.974935 GATCGAGCTCCAGCAGGCAG 62.975 65.000 8.47 0.00 45.16 4.85
809 880 2.865308 CACATGCACAGAGCCACG 59.135 61.111 0.00 0.00 44.83 4.94
902 978 2.492484 CCGCTCTCCCGCTTTATATACT 59.508 50.000 0.00 0.00 0.00 2.12
907 983 5.258051 CTCTCCCGCTTTATATACTCCTCT 58.742 45.833 0.00 0.00 0.00 3.69
939 1015 3.433173 CCCTCTCATCATTCATCACAGCA 60.433 47.826 0.00 0.00 0.00 4.41
940 1016 4.196971 CCTCTCATCATTCATCACAGCAA 58.803 43.478 0.00 0.00 0.00 3.91
951 1027 1.589461 CACAGCAAAGCAAGCGCAA 60.589 52.632 11.47 0.00 42.27 4.85
952 1028 1.299620 ACAGCAAAGCAAGCGCAAG 60.300 52.632 11.47 1.56 42.27 4.01
1134 1227 2.043450 CTCCTCTCCCACCTCGCT 60.043 66.667 0.00 0.00 0.00 4.93
1300 1393 3.062466 CCGACTGCCTCCTCGACA 61.062 66.667 0.00 0.00 31.24 4.35
1343 1436 4.394712 CGGCGCCTTCCAGGAGTT 62.395 66.667 26.68 0.00 37.67 3.01
1541 1634 2.675772 GGAGGTCGAGGTGTCCGT 60.676 66.667 0.00 0.00 0.00 4.69
1855 1954 3.317406 TGCTGATCCAATCCCTAGCTAA 58.683 45.455 0.00 0.00 32.66 3.09
1875 1977 7.507733 GCTAATGTAGCCTAGTGTAGTCTTA 57.492 40.000 0.00 0.00 45.95 2.10
1890 1992 8.207545 AGTGTAGTCTTATTTTGGAGGATCATC 58.792 37.037 0.00 0.00 36.25 2.92
1925 2029 4.553330 AACCCTCAAGTGTACATACCAG 57.447 45.455 0.00 0.00 0.00 4.00
1964 2073 4.725359 AGCAAAGCAAAAGCTTTTGTTTG 58.275 34.783 37.21 37.21 46.23 2.93
1965 2074 4.216042 AGCAAAGCAAAAGCTTTTGTTTGT 59.784 33.333 38.40 31.43 46.23 2.83
1967 2076 5.059587 GCAAAGCAAAAGCTTTTGTTTGTTC 59.940 36.000 38.40 30.69 46.23 3.18
1968 2077 4.944962 AGCAAAAGCTTTTGTTTGTTCC 57.055 36.364 38.57 25.80 46.92 3.62
1969 2078 4.322567 AGCAAAAGCTTTTGTTTGTTCCA 58.677 34.783 38.57 0.00 46.92 3.53
1970 2079 4.943093 AGCAAAAGCTTTTGTTTGTTCCAT 59.057 33.333 38.57 18.88 46.92 3.41
1971 2080 5.415389 AGCAAAAGCTTTTGTTTGTTCCATT 59.585 32.000 38.57 17.41 46.92 3.16
1973 2082 6.251163 GCAAAAGCTTTTGTTTGTTCCATTTC 59.749 34.615 38.57 21.40 46.92 2.17
1974 2083 6.435430 AAAGCTTTTGTTTGTTCCATTTCC 57.565 33.333 5.69 0.00 0.00 3.13
1986 2095 4.263462 TGTTCCATTTCCATAGCAGACTGT 60.263 41.667 3.99 0.00 0.00 3.55
2004 2117 6.585702 CAGACTGTTGATGTCTCTTTACTCTG 59.414 42.308 0.00 0.00 42.21 3.35
2054 2174 3.781079 ACACAAACACATGGTGAACTG 57.219 42.857 2.98 0.39 36.96 3.16
2061 2181 3.674997 ACACATGGTGAACTGTCATACC 58.325 45.455 2.98 0.00 36.96 2.73
2062 2182 3.072330 ACACATGGTGAACTGTCATACCA 59.928 43.478 11.49 11.49 35.13 3.25
2063 2183 4.071423 CACATGGTGAACTGTCATACCAA 58.929 43.478 12.65 1.06 34.52 3.67
2064 2184 4.518590 CACATGGTGAACTGTCATACCAAA 59.481 41.667 12.65 0.00 34.52 3.28
2065 2185 4.761739 ACATGGTGAACTGTCATACCAAAG 59.238 41.667 12.65 11.09 34.52 2.77
2066 2186 3.750371 TGGTGAACTGTCATACCAAAGG 58.250 45.455 7.91 0.00 35.80 3.11
2067 2187 2.488153 GGTGAACTGTCATACCAAAGGC 59.512 50.000 0.00 0.00 35.80 4.35
2068 2188 3.146066 GTGAACTGTCATACCAAAGGCA 58.854 45.455 0.00 0.00 35.80 4.75
2069 2189 3.758554 GTGAACTGTCATACCAAAGGCAT 59.241 43.478 0.00 0.00 35.80 4.40
2070 2190 3.758023 TGAACTGTCATACCAAAGGCATG 59.242 43.478 0.00 0.00 0.00 4.06
2071 2191 3.719268 ACTGTCATACCAAAGGCATGA 57.281 42.857 0.00 0.00 0.00 3.07
2072 2192 4.032960 ACTGTCATACCAAAGGCATGAA 57.967 40.909 0.00 0.00 30.85 2.57
2073 2193 4.012374 ACTGTCATACCAAAGGCATGAAG 58.988 43.478 0.00 4.47 30.85 3.02
2074 2194 3.355378 TGTCATACCAAAGGCATGAAGG 58.645 45.455 0.00 0.00 30.85 3.46
2075 2195 3.245229 TGTCATACCAAAGGCATGAAGGT 60.245 43.478 0.00 0.00 36.40 3.50
2076 2196 3.763897 GTCATACCAAAGGCATGAAGGTT 59.236 43.478 0.00 0.00 33.91 3.50
2077 2197 4.220602 GTCATACCAAAGGCATGAAGGTTT 59.779 41.667 0.00 0.00 33.91 3.27
2078 2198 4.462483 TCATACCAAAGGCATGAAGGTTTC 59.538 41.667 0.00 0.00 33.91 2.78
2079 2199 1.970640 ACCAAAGGCATGAAGGTTTCC 59.029 47.619 0.00 0.00 0.00 3.13
2080 2200 1.276138 CCAAAGGCATGAAGGTTTCCC 59.724 52.381 0.00 0.00 0.00 3.97
2081 2201 1.969923 CAAAGGCATGAAGGTTTCCCA 59.030 47.619 0.00 0.00 0.00 4.37
2082 2202 2.568509 CAAAGGCATGAAGGTTTCCCAT 59.431 45.455 0.00 0.00 0.00 4.00
2083 2203 3.756082 AAGGCATGAAGGTTTCCCATA 57.244 42.857 0.00 0.00 0.00 2.74
2084 2204 3.979501 AGGCATGAAGGTTTCCCATAT 57.020 42.857 0.00 0.00 0.00 1.78
2085 2205 5.402054 AAGGCATGAAGGTTTCCCATATA 57.598 39.130 0.00 0.00 0.00 0.86
2086 2206 4.990526 AGGCATGAAGGTTTCCCATATAG 58.009 43.478 0.00 0.00 0.00 1.31
2087 2207 3.507622 GGCATGAAGGTTTCCCATATAGC 59.492 47.826 0.00 0.00 0.00 2.97
2088 2208 4.401925 GCATGAAGGTTTCCCATATAGCT 58.598 43.478 0.00 0.00 0.00 3.32
2089 2209 4.457257 GCATGAAGGTTTCCCATATAGCTC 59.543 45.833 0.00 0.00 0.00 4.09
2090 2210 5.747248 GCATGAAGGTTTCCCATATAGCTCT 60.747 44.000 0.00 0.00 0.00 4.09
2091 2211 5.975988 TGAAGGTTTCCCATATAGCTCTT 57.024 39.130 0.00 0.00 0.00 2.85
2092 2212 5.684704 TGAAGGTTTCCCATATAGCTCTTG 58.315 41.667 0.00 0.00 0.00 3.02
2093 2213 5.428457 TGAAGGTTTCCCATATAGCTCTTGA 59.572 40.000 0.00 0.00 0.00 3.02
2094 2214 6.101734 TGAAGGTTTCCCATATAGCTCTTGAT 59.898 38.462 0.00 0.00 0.00 2.57
2095 2215 6.120507 AGGTTTCCCATATAGCTCTTGATC 57.879 41.667 0.00 0.00 0.00 2.92
2096 2216 5.608437 AGGTTTCCCATATAGCTCTTGATCA 59.392 40.000 0.00 0.00 0.00 2.92
2104 2224 7.601886 CCCATATAGCTCTTGATCAAAGTGTAG 59.398 40.741 9.88 3.77 37.18 2.74
2127 2247 6.982852 AGATCGTAATCGTATCAGGTGATTT 58.017 36.000 0.00 0.00 36.97 2.17
2128 2248 7.434492 AGATCGTAATCGTATCAGGTGATTTT 58.566 34.615 0.00 0.00 36.97 1.82
2129 2249 7.926555 AGATCGTAATCGTATCAGGTGATTTTT 59.073 33.333 0.00 0.00 36.97 1.94
2130 2250 7.229228 TCGTAATCGTATCAGGTGATTTTTG 57.771 36.000 0.00 0.00 38.33 2.44
2131 2251 6.256975 TCGTAATCGTATCAGGTGATTTTTGG 59.743 38.462 0.00 0.00 38.33 3.28
2132 2252 6.256975 CGTAATCGTATCAGGTGATTTTTGGA 59.743 38.462 0.00 0.00 36.05 3.53
2133 2253 7.042051 CGTAATCGTATCAGGTGATTTTTGGAT 60.042 37.037 0.00 0.00 36.05 3.41
2134 2254 6.624352 ATCGTATCAGGTGATTTTTGGATG 57.376 37.500 0.00 0.00 36.05 3.51
2135 2255 4.335315 TCGTATCAGGTGATTTTTGGATGC 59.665 41.667 0.00 0.00 36.05 3.91
2136 2256 3.788333 ATCAGGTGATTTTTGGATGCG 57.212 42.857 0.00 0.00 0.00 4.73
2137 2257 1.818060 TCAGGTGATTTTTGGATGCGG 59.182 47.619 0.00 0.00 0.00 5.69
2138 2258 1.545582 CAGGTGATTTTTGGATGCGGT 59.454 47.619 0.00 0.00 0.00 5.68
2139 2259 2.029110 CAGGTGATTTTTGGATGCGGTT 60.029 45.455 0.00 0.00 0.00 4.44
2140 2260 3.192422 CAGGTGATTTTTGGATGCGGTTA 59.808 43.478 0.00 0.00 0.00 2.85
2141 2261 4.023291 AGGTGATTTTTGGATGCGGTTAT 58.977 39.130 0.00 0.00 0.00 1.89
2142 2262 4.097892 AGGTGATTTTTGGATGCGGTTATC 59.902 41.667 0.00 0.00 0.00 1.75
2143 2263 4.097892 GGTGATTTTTGGATGCGGTTATCT 59.902 41.667 0.00 0.00 0.00 1.98
2144 2264 5.394115 GGTGATTTTTGGATGCGGTTATCTT 60.394 40.000 0.00 0.00 0.00 2.40
2145 2265 5.743872 GTGATTTTTGGATGCGGTTATCTTC 59.256 40.000 0.00 0.00 0.00 2.87
2146 2266 4.712122 TTTTTGGATGCGGTTATCTTCC 57.288 40.909 0.00 0.00 0.00 3.46
2147 2267 2.341846 TTGGATGCGGTTATCTTCCC 57.658 50.000 0.00 0.00 0.00 3.97
2148 2268 1.507140 TGGATGCGGTTATCTTCCCT 58.493 50.000 0.00 0.00 0.00 4.20
2149 2269 1.843851 TGGATGCGGTTATCTTCCCTT 59.156 47.619 0.00 0.00 0.00 3.95
2150 2270 2.222027 GGATGCGGTTATCTTCCCTTG 58.778 52.381 0.00 0.00 0.00 3.61
2151 2271 2.222027 GATGCGGTTATCTTCCCTTGG 58.778 52.381 0.00 0.00 0.00 3.61
2152 2272 0.254747 TGCGGTTATCTTCCCTTGGG 59.745 55.000 0.00 0.00 0.00 4.12
2153 2273 0.544697 GCGGTTATCTTCCCTTGGGA 59.455 55.000 3.91 3.91 0.00 4.37
2154 2274 1.143073 GCGGTTATCTTCCCTTGGGAT 59.857 52.381 9.48 0.00 0.00 3.85
2155 2275 2.370849 GCGGTTATCTTCCCTTGGGATA 59.629 50.000 9.48 1.58 0.00 2.59
2156 2276 3.806157 GCGGTTATCTTCCCTTGGGATAC 60.806 52.174 9.48 3.65 0.00 2.24
2184 2304 5.254339 GATTTCAATCCATGTTGGTCCTC 57.746 43.478 0.00 0.00 39.03 3.71
2185 2305 4.387026 TTTCAATCCATGTTGGTCCTCT 57.613 40.909 0.00 0.00 39.03 3.69
2186 2306 4.387026 TTCAATCCATGTTGGTCCTCTT 57.613 40.909 0.00 0.00 39.03 2.85
2187 2307 3.955471 TCAATCCATGTTGGTCCTCTTC 58.045 45.455 0.00 0.00 39.03 2.87
2188 2308 3.330405 TCAATCCATGTTGGTCCTCTTCA 59.670 43.478 0.00 0.00 39.03 3.02
2189 2309 4.081406 CAATCCATGTTGGTCCTCTTCAA 58.919 43.478 0.00 0.00 39.03 2.69
2190 2310 3.140325 TCCATGTTGGTCCTCTTCAAC 57.860 47.619 0.00 0.00 42.38 3.18
2194 2314 3.924114 TGTTGGTCCTCTTCAACAAGA 57.076 42.857 6.44 0.00 46.69 3.02
2195 2315 4.437682 TGTTGGTCCTCTTCAACAAGAT 57.562 40.909 6.44 0.00 46.69 2.40
2196 2316 4.389374 TGTTGGTCCTCTTCAACAAGATC 58.611 43.478 6.44 0.00 46.69 2.75
2197 2317 3.319137 TGGTCCTCTTCAACAAGATCG 57.681 47.619 0.00 0.00 38.02 3.69
2198 2318 2.003301 GGTCCTCTTCAACAAGATCGC 58.997 52.381 0.00 0.00 38.02 4.58
2199 2319 1.656095 GTCCTCTTCAACAAGATCGCG 59.344 52.381 0.00 0.00 38.02 5.87
2200 2320 1.544246 TCCTCTTCAACAAGATCGCGA 59.456 47.619 13.09 13.09 38.02 5.87
2201 2321 1.656095 CCTCTTCAACAAGATCGCGAC 59.344 52.381 12.93 5.67 38.02 5.19
2202 2322 2.328473 CTCTTCAACAAGATCGCGACA 58.672 47.619 12.93 0.00 38.02 4.35
2203 2323 2.058798 TCTTCAACAAGATCGCGACAC 58.941 47.619 12.93 9.24 33.38 3.67
2204 2324 1.126846 CTTCAACAAGATCGCGACACC 59.873 52.381 12.93 3.54 0.00 4.16
2205 2325 0.669318 TCAACAAGATCGCGACACCC 60.669 55.000 12.93 0.56 0.00 4.61
2206 2326 0.948623 CAACAAGATCGCGACACCCA 60.949 55.000 12.93 0.00 0.00 4.51
2207 2327 0.250124 AACAAGATCGCGACACCCAA 60.250 50.000 12.93 0.00 0.00 4.12
2208 2328 0.250124 ACAAGATCGCGACACCCAAA 60.250 50.000 12.93 0.00 0.00 3.28
2209 2329 0.165944 CAAGATCGCGACACCCAAAC 59.834 55.000 12.93 0.00 0.00 2.93
2210 2330 1.289109 AAGATCGCGACACCCAAACG 61.289 55.000 12.93 0.00 0.00 3.60
2240 2360 1.932604 GCCACACTGTCGTCTCTTCAG 60.933 57.143 0.00 0.00 35.60 3.02
2254 2374 4.220821 GTCTCTTCAGTCTTCACCCACATA 59.779 45.833 0.00 0.00 0.00 2.29
2268 2388 3.646162 ACCCACATAAGAGTTCACTCACA 59.354 43.478 9.62 0.00 45.21 3.58
2288 2408 3.871594 ACAGAAAGTGAAAGTCAACTCCG 59.128 43.478 0.00 0.00 0.00 4.63
2307 2427 1.534028 GAAGTGTGTGTGTGTTTGCG 58.466 50.000 0.00 0.00 0.00 4.85
2372 2492 3.583086 GCCATTAGGTTCCGCCGC 61.583 66.667 0.00 0.00 43.70 6.53
2373 2493 2.189521 CCATTAGGTTCCGCCGCT 59.810 61.111 0.00 0.00 43.70 5.52
2374 2494 2.180204 CCATTAGGTTCCGCCGCTG 61.180 63.158 0.00 0.00 43.70 5.18
2375 2495 2.513897 ATTAGGTTCCGCCGCTGC 60.514 61.111 0.00 0.00 43.70 5.25
2376 2496 3.031417 ATTAGGTTCCGCCGCTGCT 62.031 57.895 0.00 0.00 43.70 4.24
2377 2497 2.925162 ATTAGGTTCCGCCGCTGCTC 62.925 60.000 0.00 0.00 43.70 4.26
2389 2509 2.187424 CTGCTCTCCTGCTGCCTC 59.813 66.667 0.00 0.00 0.00 4.70
2430 2566 3.357079 GACCCAGGTGCTGCAACG 61.357 66.667 12.67 7.27 0.00 4.10
2502 2641 6.935208 ACACTATCCAGTAACCTGTCTTTTTC 59.065 38.462 0.00 0.00 36.95 2.29
2527 2666 6.018669 CCTTTTCTTGCGTGGAGTAATCTATC 60.019 42.308 0.00 0.00 0.00 2.08
2561 2700 8.919777 TGTATAATAATCTCTCTCCGTTCTCA 57.080 34.615 0.00 0.00 0.00 3.27
2562 2701 9.521841 TGTATAATAATCTCTCTCCGTTCTCAT 57.478 33.333 0.00 0.00 0.00 2.90
2563 2702 9.997482 GTATAATAATCTCTCTCCGTTCTCATC 57.003 37.037 0.00 0.00 0.00 2.92
2564 2703 5.975693 ATAATCTCTCTCCGTTCTCATCC 57.024 43.478 0.00 0.00 0.00 3.51
2565 2704 2.060050 TCTCTCTCCGTTCTCATCCC 57.940 55.000 0.00 0.00 0.00 3.85
2566 2705 1.566703 TCTCTCTCCGTTCTCATCCCT 59.433 52.381 0.00 0.00 0.00 4.20
2567 2706 2.024846 TCTCTCTCCGTTCTCATCCCTT 60.025 50.000 0.00 0.00 0.00 3.95
2568 2707 2.763448 CTCTCTCCGTTCTCATCCCTTT 59.237 50.000 0.00 0.00 0.00 3.11
2569 2708 2.761208 TCTCTCCGTTCTCATCCCTTTC 59.239 50.000 0.00 0.00 0.00 2.62
2570 2709 1.476891 TCTCCGTTCTCATCCCTTTCG 59.523 52.381 0.00 0.00 0.00 3.46
2586 2725 7.931578 TCCCTTTCGTGTCAAATTTATACAT 57.068 32.000 8.34 0.00 0.00 2.29
2664 2803 6.650807 ACGAGACACTGTAAACATCAATTCAT 59.349 34.615 0.00 0.00 0.00 2.57
2693 2832 1.776662 TCCTTGGACGTCCCATCTAG 58.223 55.000 31.19 18.54 46.10 2.43
2723 2862 3.954258 GTGGCAGACTTTTTAGGGCATAT 59.046 43.478 0.00 0.00 36.41 1.78
2724 2863 3.953612 TGGCAGACTTTTTAGGGCATATG 59.046 43.478 0.00 0.00 0.00 1.78
2725 2864 3.319122 GGCAGACTTTTTAGGGCATATGG 59.681 47.826 4.56 0.00 0.00 2.74
2726 2865 3.243535 GCAGACTTTTTAGGGCATATGGC 60.244 47.826 20.55 20.55 43.74 4.40
2736 2875 2.532186 GCATATGGCATCGCTTCGA 58.468 52.632 1.65 0.00 43.97 3.71
2738 2877 1.061711 GCATATGGCATCGCTTCGATC 59.938 52.381 1.65 0.00 45.19 3.69
2739 2878 1.322637 CATATGGCATCGCTTCGATCG 59.677 52.381 9.36 9.36 45.19 3.69
2740 2879 0.313987 TATGGCATCGCTTCGATCGT 59.686 50.000 15.94 0.00 45.19 3.73
2741 2880 0.941463 ATGGCATCGCTTCGATCGTC 60.941 55.000 15.94 4.95 45.19 4.20
2742 2881 1.299468 GGCATCGCTTCGATCGTCT 60.299 57.895 15.94 0.00 45.19 4.18
2743 2882 1.272114 GGCATCGCTTCGATCGTCTC 61.272 60.000 15.94 4.23 45.19 3.36
2744 2883 0.592500 GCATCGCTTCGATCGTCTCA 60.593 55.000 15.94 0.00 45.19 3.27
2745 2884 1.116436 CATCGCTTCGATCGTCTCAC 58.884 55.000 15.94 0.91 45.19 3.51
2746 2885 1.018148 ATCGCTTCGATCGTCTCACT 58.982 50.000 15.94 0.00 43.45 3.41
2747 2886 1.648504 TCGCTTCGATCGTCTCACTA 58.351 50.000 15.94 0.00 0.00 2.74
2748 2887 1.326852 TCGCTTCGATCGTCTCACTAC 59.673 52.381 15.94 0.00 0.00 2.73
2749 2888 1.595003 CGCTTCGATCGTCTCACTACC 60.595 57.143 15.94 0.00 0.00 3.18
2750 2889 1.671845 GCTTCGATCGTCTCACTACCT 59.328 52.381 15.94 0.00 0.00 3.08
2751 2890 2.286536 GCTTCGATCGTCTCACTACCTC 60.287 54.545 15.94 0.00 0.00 3.85
2752 2891 2.685850 TCGATCGTCTCACTACCTCA 57.314 50.000 15.94 0.00 0.00 3.86
2753 2892 3.195471 TCGATCGTCTCACTACCTCAT 57.805 47.619 15.94 0.00 0.00 2.90
2754 2893 4.332428 TCGATCGTCTCACTACCTCATA 57.668 45.455 15.94 0.00 0.00 2.15
2755 2894 4.056740 TCGATCGTCTCACTACCTCATAC 58.943 47.826 15.94 0.00 0.00 2.39
2756 2895 3.120957 CGATCGTCTCACTACCTCATACG 60.121 52.174 7.03 0.00 0.00 3.06
2757 2896 3.257469 TCGTCTCACTACCTCATACGT 57.743 47.619 0.00 0.00 0.00 3.57
2758 2897 3.193263 TCGTCTCACTACCTCATACGTC 58.807 50.000 0.00 0.00 0.00 4.34
2759 2898 2.934553 CGTCTCACTACCTCATACGTCA 59.065 50.000 0.00 0.00 0.00 4.35
2760 2899 3.560481 CGTCTCACTACCTCATACGTCAT 59.440 47.826 0.00 0.00 0.00 3.06
2761 2900 4.552961 CGTCTCACTACCTCATACGTCATG 60.553 50.000 0.00 0.00 35.81 3.07
2762 2901 3.315470 TCTCACTACCTCATACGTCATGC 59.685 47.826 0.00 0.00 34.35 4.06
2763 2902 3.020984 TCACTACCTCATACGTCATGCA 58.979 45.455 0.00 0.00 34.35 3.96
2764 2903 3.636764 TCACTACCTCATACGTCATGCAT 59.363 43.478 0.00 0.00 34.35 3.96
2765 2904 3.737774 CACTACCTCATACGTCATGCATG 59.262 47.826 21.07 21.07 34.35 4.06
2766 2905 1.586422 ACCTCATACGTCATGCATGC 58.414 50.000 22.25 11.82 34.35 4.06
2767 2906 0.870393 CCTCATACGTCATGCATGCC 59.130 55.000 22.25 10.13 34.35 4.40
2768 2907 0.509929 CTCATACGTCATGCATGCCG 59.490 55.000 26.87 26.87 35.01 5.69
2769 2908 1.082561 CATACGTCATGCATGCCGC 60.083 57.895 28.20 15.92 42.89 6.53
2770 2909 2.253758 ATACGTCATGCATGCCGCC 61.254 57.895 28.20 11.79 41.33 6.13
2771 2910 2.939133 ATACGTCATGCATGCCGCCA 62.939 55.000 28.20 17.45 41.33 5.69
2772 2911 2.939133 TACGTCATGCATGCCGCCAT 62.939 55.000 28.20 12.97 41.33 4.40
2779 2918 4.136511 CATGCCGCCATGCAAGCA 62.137 61.111 12.06 0.00 45.84 3.91
2780 2919 4.137872 ATGCCGCCATGCAAGCAC 62.138 61.111 12.06 4.45 45.84 4.40
2782 2921 4.137872 GCCGCCATGCAAGCACAT 62.138 61.111 12.06 0.00 0.00 3.21
2783 2922 2.202690 CCGCCATGCAAGCACATG 60.203 61.111 12.06 7.25 45.74 3.21
2784 2923 2.883730 CGCCATGCAAGCACATGC 60.884 61.111 12.06 5.68 44.98 4.06
2792 2931 1.556564 GCAAGCACATGCATGATCAC 58.443 50.000 32.75 17.31 45.70 3.06
2793 2932 1.134367 GCAAGCACATGCATGATCACT 59.866 47.619 32.75 19.12 45.70 3.41
2794 2933 2.356695 GCAAGCACATGCATGATCACTA 59.643 45.455 32.75 0.00 45.70 2.74
2795 2934 3.548214 GCAAGCACATGCATGATCACTAG 60.548 47.826 32.75 15.73 45.70 2.57
2796 2935 3.555527 AGCACATGCATGATCACTAGT 57.444 42.857 32.75 4.93 45.16 2.57
2797 2936 4.677673 AGCACATGCATGATCACTAGTA 57.322 40.909 32.75 0.00 45.16 1.82
2798 2937 4.375272 AGCACATGCATGATCACTAGTAC 58.625 43.478 32.75 2.74 45.16 2.73
2799 2938 4.122046 GCACATGCATGATCACTAGTACA 58.878 43.478 32.75 0.00 41.59 2.90
2800 2939 4.753610 GCACATGCATGATCACTAGTACAT 59.246 41.667 32.75 2.54 41.59 2.29
2801 2940 5.928264 GCACATGCATGATCACTAGTACATA 59.072 40.000 32.75 0.00 41.59 2.29
2802 2941 6.090493 GCACATGCATGATCACTAGTACATAG 59.910 42.308 32.75 0.18 41.59 2.23
2803 2942 6.090493 CACATGCATGATCACTAGTACATAGC 59.910 42.308 32.75 8.94 34.56 2.97
2804 2943 5.789643 TGCATGATCACTAGTACATAGCA 57.210 39.130 0.00 17.99 34.56 3.49
2805 2944 5.532557 TGCATGATCACTAGTACATAGCAC 58.467 41.667 0.00 8.74 34.56 4.40
2806 2945 4.618912 GCATGATCACTAGTACATAGCACG 59.381 45.833 0.00 0.00 34.56 5.34
2807 2946 4.224715 TGATCACTAGTACATAGCACGC 57.775 45.455 0.00 0.00 34.56 5.34
2808 2947 3.630312 TGATCACTAGTACATAGCACGCA 59.370 43.478 0.00 0.00 34.56 5.24
2809 2948 4.097286 TGATCACTAGTACATAGCACGCAA 59.903 41.667 0.00 0.00 34.56 4.85
2810 2949 4.443913 TCACTAGTACATAGCACGCAAA 57.556 40.909 0.00 0.00 34.56 3.68
2811 2950 5.006153 TCACTAGTACATAGCACGCAAAT 57.994 39.130 0.00 0.00 34.56 2.32
2812 2951 4.803613 TCACTAGTACATAGCACGCAAATG 59.196 41.667 0.00 0.00 34.56 2.32
2813 2952 4.803613 CACTAGTACATAGCACGCAAATGA 59.196 41.667 10.31 0.00 34.56 2.57
2814 2953 5.290885 CACTAGTACATAGCACGCAAATGAA 59.709 40.000 10.31 0.00 34.56 2.57
2815 2954 4.864916 AGTACATAGCACGCAAATGAAG 57.135 40.909 10.31 0.00 0.00 3.02
2816 2955 4.503910 AGTACATAGCACGCAAATGAAGA 58.496 39.130 10.31 0.00 0.00 2.87
2817 2956 3.747099 ACATAGCACGCAAATGAAGAC 57.253 42.857 10.31 0.00 0.00 3.01
2818 2957 2.094258 ACATAGCACGCAAATGAAGACG 59.906 45.455 10.31 0.00 0.00 4.18
2819 2958 0.442310 TAGCACGCAAATGAAGACGC 59.558 50.000 0.00 0.00 0.00 5.19
2820 2959 1.207593 GCACGCAAATGAAGACGCT 59.792 52.632 0.00 0.00 0.00 5.07
2821 2960 0.385974 GCACGCAAATGAAGACGCTT 60.386 50.000 0.00 0.00 0.00 4.68
2822 2961 1.321016 CACGCAAATGAAGACGCTTG 58.679 50.000 0.00 0.00 0.00 4.01
2823 2962 0.385974 ACGCAAATGAAGACGCTTGC 60.386 50.000 0.00 0.00 40.58 4.01
2824 2963 0.385849 CGCAAATGAAGACGCTTGCA 60.386 50.000 6.46 0.00 43.43 4.08
2825 2964 1.730121 CGCAAATGAAGACGCTTGCAT 60.730 47.619 6.46 0.00 43.43 3.96
2826 2965 1.652124 GCAAATGAAGACGCTTGCATG 59.348 47.619 0.00 0.00 42.91 4.06
2827 2966 2.256174 CAAATGAAGACGCTTGCATGG 58.744 47.619 1.34 0.00 0.00 3.66
2828 2967 1.538047 AATGAAGACGCTTGCATGGT 58.462 45.000 1.34 0.00 0.00 3.55
2829 2968 1.089920 ATGAAGACGCTTGCATGGTC 58.910 50.000 11.03 11.03 0.00 4.02
2830 2969 1.291184 TGAAGACGCTTGCATGGTCG 61.291 55.000 1.34 0.23 35.87 4.79
2831 2970 1.970917 GAAGACGCTTGCATGGTCGG 61.971 60.000 1.34 0.00 35.87 4.79
2832 2971 4.166011 GACGCTTGCATGGTCGGC 62.166 66.667 1.34 0.00 0.00 5.54
2839 2978 1.007964 TGCATGGTCGGCAAAAACG 60.008 52.632 0.00 0.00 38.54 3.60
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 63 4.021456 ACACCTGAATACAGTGACAATCGA 60.021 41.667 0.00 0.00 42.05 3.59
128 138 3.832527 CTTCACAAAGGAAGGGAAGGAA 58.167 45.455 0.00 0.00 40.44 3.36
129 139 2.489073 GCTTCACAAAGGAAGGGAAGGA 60.489 50.000 7.23 0.00 43.54 3.36
130 140 1.889170 GCTTCACAAAGGAAGGGAAGG 59.111 52.381 7.23 0.00 43.54 3.46
136 146 2.337583 TCGATCGCTTCACAAAGGAAG 58.662 47.619 11.09 0.00 45.58 3.46
158 168 3.955771 TTCCTTTTGTGCTTGTACGTC 57.044 42.857 0.00 0.00 0.00 4.34
172 214 6.540189 CAGCACTGTACTAAGCATATTCCTTT 59.460 38.462 0.00 0.00 0.00 3.11
176 218 5.601662 TCCAGCACTGTACTAAGCATATTC 58.398 41.667 0.00 0.00 0.00 1.75
185 227 3.969553 AGATCACTCCAGCACTGTACTA 58.030 45.455 0.00 0.00 0.00 1.82
186 228 2.813907 AGATCACTCCAGCACTGTACT 58.186 47.619 0.00 0.00 0.00 2.73
226 268 1.739466 CATTGTCAATCTCACCACCCG 59.261 52.381 0.00 0.00 0.00 5.28
415 460 2.027625 CCCTTTCCTCGTGCACGAC 61.028 63.158 36.40 0.00 44.22 4.34
417 462 1.301401 TTCCCTTTCCTCGTGCACG 60.301 57.895 32.76 32.76 41.45 5.34
418 463 1.235281 GGTTCCCTTTCCTCGTGCAC 61.235 60.000 6.82 6.82 0.00 4.57
479 543 1.153939 CCCGATCGATGGATCTCGC 60.154 63.158 18.66 0.00 45.66 5.03
481 545 1.068194 GTGTCCCGATCGATGGATCTC 60.068 57.143 18.66 4.75 45.66 2.75
482 546 0.962489 GTGTCCCGATCGATGGATCT 59.038 55.000 18.66 0.00 45.66 2.75
483 547 0.038159 GGTGTCCCGATCGATGGATC 60.038 60.000 18.66 12.14 44.63 3.36
484 548 2.050269 GGTGTCCCGATCGATGGAT 58.950 57.895 18.66 0.00 34.96 3.41
485 549 3.533720 GGTGTCCCGATCGATGGA 58.466 61.111 18.66 13.08 0.00 3.41
541 605 0.027979 CCATACGCGTGGATGCTTTG 59.972 55.000 24.59 1.82 42.02 2.77
542 606 1.714899 GCCATACGCGTGGATGCTTT 61.715 55.000 24.59 0.00 42.02 3.51
544 608 2.588877 GCCATACGCGTGGATGCT 60.589 61.111 24.59 0.00 42.02 3.79
686 756 0.945813 GCTCGATCCACGTACTAGCT 59.054 55.000 0.00 0.00 43.13 3.32
687 757 0.945813 AGCTCGATCCACGTACTAGC 59.054 55.000 0.00 0.00 43.13 3.42
688 758 1.532007 GGAGCTCGATCCACGTACTAG 59.468 57.143 7.83 0.00 43.13 2.57
689 759 1.134310 TGGAGCTCGATCCACGTACTA 60.134 52.381 7.83 0.00 44.56 1.82
690 760 0.393944 TGGAGCTCGATCCACGTACT 60.394 55.000 7.83 0.00 44.56 2.73
691 761 0.029567 CTGGAGCTCGATCCACGTAC 59.970 60.000 7.83 0.00 44.56 3.67
692 762 1.725557 GCTGGAGCTCGATCCACGTA 61.726 60.000 7.83 0.00 44.56 3.57
693 763 3.069980 GCTGGAGCTCGATCCACGT 62.070 63.158 7.83 0.00 44.56 4.49
694 764 2.279120 GCTGGAGCTCGATCCACG 60.279 66.667 7.83 2.69 44.56 4.94
695 765 1.227205 CTGCTGGAGCTCGATCCAC 60.227 63.158 7.83 2.93 44.56 4.02
720 790 2.181021 GACGCGTGGACCTGTAGG 59.819 66.667 20.70 0.00 42.17 3.18
721 791 2.181021 GGACGCGTGGACCTGTAG 59.819 66.667 20.70 0.00 0.00 2.74
722 792 3.376078 GGGACGCGTGGACCTGTA 61.376 66.667 20.70 0.00 0.00 2.74
902 978 2.257541 GAGGGATGGGGTGGAGAGGA 62.258 65.000 0.00 0.00 0.00 3.71
907 983 0.400525 GATGAGAGGGATGGGGTGGA 60.401 60.000 0.00 0.00 0.00 4.02
939 1015 2.355481 GCTGCTTGCGCTTGCTTT 60.355 55.556 21.48 0.00 40.12 3.51
940 1016 3.553437 CTGCTGCTTGCGCTTGCTT 62.553 57.895 21.48 0.00 46.63 3.91
953 1029 1.792118 TTGACTTGCTGCTGCTGCTG 61.792 55.000 27.67 22.10 40.48 4.41
1092 1185 4.459089 GAGTGGCAGGGGAGCGAC 62.459 72.222 0.00 0.00 42.62 5.19
1134 1227 2.363276 ACGGCGGAGATGTGGGTA 60.363 61.111 13.24 0.00 0.00 3.69
1617 1710 4.344865 TTCTTGGAGGTGGCGGCC 62.345 66.667 13.32 13.32 0.00 6.13
1720 1813 3.522731 CTCGACCTCCTCCAGCCG 61.523 72.222 0.00 0.00 0.00 5.52
1806 1899 0.543749 GGGTCTGGATGTTGAGGAGG 59.456 60.000 0.00 0.00 0.00 4.30
1855 1954 8.204836 CCAAAATAAGACTACACTAGGCTACAT 58.795 37.037 0.00 0.00 45.46 2.29
1862 1964 8.696374 TGATCCTCCAAAATAAGACTACACTAG 58.304 37.037 0.00 0.00 0.00 2.57
1890 1992 0.995024 AGGGTTTGGACAGGATCAGG 59.005 55.000 0.00 0.00 0.00 3.86
1925 2029 4.593597 TTGCTTTAATCCGTTGATCGAC 57.406 40.909 2.65 2.65 42.86 4.20
1964 2073 4.265073 ACAGTCTGCTATGGAAATGGAAC 58.735 43.478 0.00 0.00 0.00 3.62
1965 2074 4.574674 ACAGTCTGCTATGGAAATGGAA 57.425 40.909 0.00 0.00 0.00 3.53
1967 2076 4.264253 TCAACAGTCTGCTATGGAAATGG 58.736 43.478 0.00 0.00 0.00 3.16
1968 2077 5.356190 ACATCAACAGTCTGCTATGGAAATG 59.644 40.000 0.00 0.81 0.00 2.32
1969 2078 5.503927 ACATCAACAGTCTGCTATGGAAAT 58.496 37.500 0.00 0.00 0.00 2.17
1970 2079 4.910195 ACATCAACAGTCTGCTATGGAAA 58.090 39.130 0.00 0.00 0.00 3.13
1971 2080 4.223700 AGACATCAACAGTCTGCTATGGAA 59.776 41.667 0.00 0.00 44.23 3.53
1973 2082 4.118410 GAGACATCAACAGTCTGCTATGG 58.882 47.826 0.00 0.00 45.79 2.74
1974 2083 5.008619 AGAGACATCAACAGTCTGCTATG 57.991 43.478 0.00 4.15 45.79 2.23
1986 2095 7.329471 CGATTTGTCAGAGTAAAGAGACATCAA 59.671 37.037 0.00 0.00 40.32 2.57
2004 2117 4.375235 GCGAGCGAAATATACGATTTGTC 58.625 43.478 6.44 0.00 0.00 3.18
2045 2165 3.750371 CCTTTGGTATGACAGTTCACCA 58.250 45.455 0.00 0.00 33.38 4.17
2047 2167 3.146066 TGCCTTTGGTATGACAGTTCAC 58.854 45.455 0.00 0.00 33.38 3.18
2073 2193 7.040823 CTTTGATCAAGAGCTATATGGGAAACC 60.041 40.741 8.41 0.00 43.09 3.27
2074 2194 7.500559 ACTTTGATCAAGAGCTATATGGGAAAC 59.499 37.037 8.41 0.00 36.21 2.78
2075 2195 7.500227 CACTTTGATCAAGAGCTATATGGGAAA 59.500 37.037 8.41 0.00 36.21 3.13
2076 2196 6.994496 CACTTTGATCAAGAGCTATATGGGAA 59.006 38.462 8.41 0.00 36.21 3.97
2077 2197 6.100279 ACACTTTGATCAAGAGCTATATGGGA 59.900 38.462 8.41 0.00 36.21 4.37
2078 2198 6.294473 ACACTTTGATCAAGAGCTATATGGG 58.706 40.000 8.41 0.00 36.21 4.00
2079 2199 8.363390 TCTACACTTTGATCAAGAGCTATATGG 58.637 37.037 8.41 0.00 36.21 2.74
2080 2200 9.926158 ATCTACACTTTGATCAAGAGCTATATG 57.074 33.333 8.41 6.10 36.21 1.78
2082 2202 8.293157 CGATCTACACTTTGATCAAGAGCTATA 58.707 37.037 8.41 0.00 39.06 1.31
2083 2203 7.144661 CGATCTACACTTTGATCAAGAGCTAT 58.855 38.462 8.41 0.00 39.06 2.97
2084 2204 6.095580 ACGATCTACACTTTGATCAAGAGCTA 59.904 38.462 8.41 0.00 39.06 3.32
2085 2205 5.105554 ACGATCTACACTTTGATCAAGAGCT 60.106 40.000 8.41 0.00 39.06 4.09
2086 2206 5.105752 ACGATCTACACTTTGATCAAGAGC 58.894 41.667 8.41 3.24 39.06 4.09
2087 2207 8.864069 ATTACGATCTACACTTTGATCAAGAG 57.136 34.615 8.41 11.26 39.06 2.85
2088 2208 7.644157 CGATTACGATCTACACTTTGATCAAGA 59.356 37.037 8.41 1.45 42.66 3.02
2089 2209 7.432545 ACGATTACGATCTACACTTTGATCAAG 59.567 37.037 8.41 5.87 42.66 3.02
2090 2210 7.255569 ACGATTACGATCTACACTTTGATCAA 58.744 34.615 3.38 3.38 42.66 2.57
2091 2211 6.792326 ACGATTACGATCTACACTTTGATCA 58.208 36.000 0.00 0.00 42.66 2.92
2092 2212 8.951954 ATACGATTACGATCTACACTTTGATC 57.048 34.615 0.00 0.00 42.66 2.92
2093 2213 8.565416 TGATACGATTACGATCTACACTTTGAT 58.435 33.333 0.00 0.00 42.66 2.57
2094 2214 7.922837 TGATACGATTACGATCTACACTTTGA 58.077 34.615 0.00 0.00 42.66 2.69
2095 2215 7.323895 CCTGATACGATTACGATCTACACTTTG 59.676 40.741 0.00 0.00 42.66 2.77
2096 2216 7.013083 ACCTGATACGATTACGATCTACACTTT 59.987 37.037 0.00 0.00 42.66 2.66
2104 2224 7.639162 AAAATCACCTGATACGATTACGATC 57.361 36.000 0.00 0.00 37.05 3.69
2127 2247 2.241176 AGGGAAGATAACCGCATCCAAA 59.759 45.455 0.00 0.00 31.63 3.28
2128 2248 1.843851 AGGGAAGATAACCGCATCCAA 59.156 47.619 0.00 0.00 31.63 3.53
2129 2249 1.507140 AGGGAAGATAACCGCATCCA 58.493 50.000 0.00 0.00 31.63 3.41
2130 2250 2.222027 CAAGGGAAGATAACCGCATCC 58.778 52.381 0.00 0.00 0.00 3.51
2131 2251 2.222027 CCAAGGGAAGATAACCGCATC 58.778 52.381 0.00 0.00 0.00 3.91
2132 2252 1.133792 CCCAAGGGAAGATAACCGCAT 60.134 52.381 0.00 0.00 37.50 4.73
2133 2253 0.254747 CCCAAGGGAAGATAACCGCA 59.745 55.000 0.00 0.00 37.50 5.69
2134 2254 0.544697 TCCCAAGGGAAGATAACCGC 59.455 55.000 5.09 0.00 42.05 5.68
2138 2258 8.788885 TCCCAAGGTATCCCAAGGGAAGATAA 62.789 46.154 12.67 0.00 46.98 1.75
2139 2259 7.393583 TCCCAAGGTATCCCAAGGGAAGATA 62.394 48.000 12.67 0.00 46.98 1.98
2140 2260 6.714634 TCCCAAGGTATCCCAAGGGAAGAT 62.715 50.000 12.67 0.00 46.98 2.40
2141 2261 5.469852 TCCCAAGGTATCCCAAGGGAAGA 62.470 52.174 12.67 0.11 46.98 2.87
2142 2262 3.170622 TCCCAAGGTATCCCAAGGGAAG 61.171 54.545 12.67 0.00 46.98 3.46
2143 2263 1.203635 TCCCAAGGTATCCCAAGGGAA 60.204 52.381 12.67 0.00 46.98 3.97
2144 2264 3.036865 CCCAAGGTATCCCAAGGGA 57.963 57.895 10.86 10.86 45.42 4.20
2145 2265 1.534338 ATCCCAAGGTATCCCAAGGG 58.466 55.000 0.00 0.00 44.47 3.95
2146 2266 3.052944 TGAAATCCCAAGGTATCCCAAGG 60.053 47.826 0.00 0.00 0.00 3.61
2147 2267 4.249638 TGAAATCCCAAGGTATCCCAAG 57.750 45.455 0.00 0.00 0.00 3.61
2148 2268 4.683766 TTGAAATCCCAAGGTATCCCAA 57.316 40.909 0.00 0.00 0.00 4.12
2149 2269 4.803452 GATTGAAATCCCAAGGTATCCCA 58.197 43.478 0.00 0.00 0.00 4.37
2162 2282 4.952335 AGAGGACCAACATGGATTGAAATC 59.048 41.667 2.85 0.00 40.96 2.17
2163 2283 4.939255 AGAGGACCAACATGGATTGAAAT 58.061 39.130 2.85 0.00 40.96 2.17
2164 2284 4.387026 AGAGGACCAACATGGATTGAAA 57.613 40.909 2.85 0.00 40.96 2.69
2165 2285 4.202556 TGAAGAGGACCAACATGGATTGAA 60.203 41.667 2.85 0.00 40.96 2.69
2166 2286 3.330405 TGAAGAGGACCAACATGGATTGA 59.670 43.478 2.85 0.00 40.96 2.57
2167 2287 3.689347 TGAAGAGGACCAACATGGATTG 58.311 45.455 2.85 0.00 40.96 2.67
2168 2288 4.082125 GTTGAAGAGGACCAACATGGATT 58.918 43.478 2.85 0.00 40.96 3.01
2169 2289 3.074390 TGTTGAAGAGGACCAACATGGAT 59.926 43.478 2.85 0.00 45.13 3.41
2170 2290 2.441375 TGTTGAAGAGGACCAACATGGA 59.559 45.455 2.85 0.00 45.13 3.41
2171 2291 2.862541 TGTTGAAGAGGACCAACATGG 58.137 47.619 0.00 0.00 45.13 3.66
2175 2295 3.433615 CGATCTTGTTGAAGAGGACCAAC 59.566 47.826 0.00 0.00 41.62 3.77
2176 2296 3.664107 CGATCTTGTTGAAGAGGACCAA 58.336 45.455 0.00 0.00 41.62 3.67
2177 2297 2.612972 GCGATCTTGTTGAAGAGGACCA 60.613 50.000 0.00 0.00 41.62 4.02
2178 2298 2.003301 GCGATCTTGTTGAAGAGGACC 58.997 52.381 0.00 0.00 41.62 4.46
2179 2299 1.656095 CGCGATCTTGTTGAAGAGGAC 59.344 52.381 0.00 0.00 41.62 3.85
2180 2300 1.544246 TCGCGATCTTGTTGAAGAGGA 59.456 47.619 3.71 0.00 41.62 3.71
2181 2301 1.656095 GTCGCGATCTTGTTGAAGAGG 59.344 52.381 14.06 0.00 41.62 3.69
2182 2302 2.091277 GTGTCGCGATCTTGTTGAAGAG 59.909 50.000 14.06 0.00 41.62 2.85
2183 2303 2.058798 GTGTCGCGATCTTGTTGAAGA 58.941 47.619 14.06 0.00 42.53 2.87
2184 2304 1.126846 GGTGTCGCGATCTTGTTGAAG 59.873 52.381 14.06 0.00 0.00 3.02
2185 2305 1.144969 GGTGTCGCGATCTTGTTGAA 58.855 50.000 14.06 0.00 0.00 2.69
2186 2306 0.669318 GGGTGTCGCGATCTTGTTGA 60.669 55.000 14.06 0.00 0.00 3.18
2187 2307 0.948623 TGGGTGTCGCGATCTTGTTG 60.949 55.000 14.06 0.00 0.00 3.33
2188 2308 0.250124 TTGGGTGTCGCGATCTTGTT 60.250 50.000 14.06 0.00 0.00 2.83
2189 2309 0.250124 TTTGGGTGTCGCGATCTTGT 60.250 50.000 14.06 0.00 0.00 3.16
2190 2310 0.165944 GTTTGGGTGTCGCGATCTTG 59.834 55.000 14.06 0.00 0.00 3.02
2191 2311 1.289109 CGTTTGGGTGTCGCGATCTT 61.289 55.000 14.06 0.00 0.00 2.40
2192 2312 1.736645 CGTTTGGGTGTCGCGATCT 60.737 57.895 14.06 0.00 0.00 2.75
2193 2313 2.776072 CGTTTGGGTGTCGCGATC 59.224 61.111 14.06 9.02 0.00 3.69
2194 2314 3.419759 GCGTTTGGGTGTCGCGAT 61.420 61.111 14.06 0.00 40.51 4.58
2220 2340 0.032130 TGAAGAGACGACAGTGTGGC 59.968 55.000 0.00 0.00 0.00 5.01
2221 2341 1.338337 ACTGAAGAGACGACAGTGTGG 59.662 52.381 0.00 0.79 42.18 4.17
2222 2342 2.292016 AGACTGAAGAGACGACAGTGTG 59.708 50.000 0.00 0.00 43.49 3.82
2223 2343 2.577700 AGACTGAAGAGACGACAGTGT 58.422 47.619 0.00 0.00 43.49 3.55
2240 2360 4.691216 GTGAACTCTTATGTGGGTGAAGAC 59.309 45.833 0.00 0.00 0.00 3.01
2268 2388 4.402056 TCGGAGTTGACTTTCACTTTCT 57.598 40.909 0.00 0.00 0.00 2.52
2279 2399 1.593006 CACACACACTTCGGAGTTGAC 59.407 52.381 11.49 0.00 32.54 3.18
2288 2408 1.129624 TCGCAAACACACACACACTTC 59.870 47.619 0.00 0.00 0.00 3.01
2307 2427 2.476619 CACAGACACATCGAGGTTGTTC 59.523 50.000 0.00 0.00 0.00 3.18
2372 2492 2.187424 GAGGCAGCAGGAGAGCAG 59.813 66.667 0.00 0.00 36.85 4.24
2373 2493 3.397439 GGAGGCAGCAGGAGAGCA 61.397 66.667 0.00 0.00 36.85 4.26
2374 2494 3.082701 AGGAGGCAGCAGGAGAGC 61.083 66.667 0.00 0.00 0.00 4.09
2375 2495 2.901813 CAGGAGGCAGCAGGAGAG 59.098 66.667 0.00 0.00 0.00 3.20
2376 2496 3.397439 GCAGGAGGCAGCAGGAGA 61.397 66.667 0.00 0.00 43.97 3.71
2386 2506 2.547595 TTTTGGGGAGGGCAGGAGG 61.548 63.158 0.00 0.00 0.00 4.30
2387 2507 1.304464 GTTTTGGGGAGGGCAGGAG 60.304 63.158 0.00 0.00 0.00 3.69
2388 2508 1.778383 AGTTTTGGGGAGGGCAGGA 60.778 57.895 0.00 0.00 0.00 3.86
2389 2509 1.607467 CAGTTTTGGGGAGGGCAGG 60.607 63.158 0.00 0.00 0.00 4.85
2399 2519 1.007387 GGGTCGCAAGCAGTTTTGG 60.007 57.895 0.00 0.00 37.18 3.28
2442 2578 2.616510 GGAGTGTGGAGAATTGGTGAGG 60.617 54.545 0.00 0.00 0.00 3.86
2502 2641 4.003648 AGATTACTCCACGCAAGAAAAGG 58.996 43.478 0.00 0.00 43.62 3.11
2561 2700 7.931578 TGTATAAATTTGACACGAAAGGGAT 57.068 32.000 0.00 0.00 38.45 3.85
2562 2701 7.608376 TGATGTATAAATTTGACACGAAAGGGA 59.392 33.333 9.24 0.00 38.45 4.20
2563 2702 7.757526 TGATGTATAAATTTGACACGAAAGGG 58.242 34.615 9.24 0.00 43.28 3.95
2564 2703 8.664798 TCTGATGTATAAATTTGACACGAAAGG 58.335 33.333 9.24 0.77 0.00 3.11
2568 2707 9.599866 AGAATCTGATGTATAAATTTGACACGA 57.400 29.630 9.24 7.51 0.00 4.35
2586 2725 9.155975 GCTACAAATCTCAAAACTAGAATCTGA 57.844 33.333 0.00 0.00 0.00 3.27
2611 2750 7.757097 TTCTCTTCATAATTAACTGTCGAGC 57.243 36.000 0.00 0.00 0.00 5.03
2708 2847 3.569701 CGATGCCATATGCCCTAAAAAGT 59.430 43.478 0.00 0.00 40.16 2.66
2723 2862 1.588932 GACGATCGAAGCGATGCCA 60.589 57.895 24.34 0.00 47.00 4.92
2724 2863 1.272114 GAGACGATCGAAGCGATGCC 61.272 60.000 24.34 0.00 47.00 4.40
2725 2864 0.592500 TGAGACGATCGAAGCGATGC 60.593 55.000 24.34 2.63 47.00 3.91
2726 2865 1.116436 GTGAGACGATCGAAGCGATG 58.884 55.000 24.34 2.97 47.00 3.84
2728 2867 1.326852 GTAGTGAGACGATCGAAGCGA 59.673 52.381 24.34 0.00 41.13 4.93
2729 2868 1.595003 GGTAGTGAGACGATCGAAGCG 60.595 57.143 24.34 9.17 0.00 4.68
2730 2869 1.671845 AGGTAGTGAGACGATCGAAGC 59.328 52.381 24.34 10.58 0.00 3.86
2731 2870 2.937149 TGAGGTAGTGAGACGATCGAAG 59.063 50.000 24.34 0.00 0.00 3.79
2732 2871 2.981898 TGAGGTAGTGAGACGATCGAA 58.018 47.619 24.34 0.98 0.00 3.71
2733 2872 2.685850 TGAGGTAGTGAGACGATCGA 57.314 50.000 24.34 0.00 0.00 3.59
2734 2873 3.120957 CGTATGAGGTAGTGAGACGATCG 60.121 52.174 14.88 14.88 0.00 3.69
2735 2874 3.808726 ACGTATGAGGTAGTGAGACGATC 59.191 47.826 0.00 0.00 33.30 3.69
2736 2875 3.806380 ACGTATGAGGTAGTGAGACGAT 58.194 45.455 0.00 0.00 33.30 3.73
2737 2876 3.193263 GACGTATGAGGTAGTGAGACGA 58.807 50.000 0.00 0.00 33.30 4.20
2738 2877 2.934553 TGACGTATGAGGTAGTGAGACG 59.065 50.000 0.00 0.00 35.10 4.18
2739 2878 4.790123 GCATGACGTATGAGGTAGTGAGAC 60.790 50.000 0.00 0.00 39.21 3.36
2740 2879 3.315470 GCATGACGTATGAGGTAGTGAGA 59.685 47.826 0.00 0.00 39.21 3.27
2741 2880 3.066760 TGCATGACGTATGAGGTAGTGAG 59.933 47.826 0.00 0.00 39.21 3.51
2742 2881 3.020984 TGCATGACGTATGAGGTAGTGA 58.979 45.455 0.00 0.00 39.21 3.41
2743 2882 3.436700 TGCATGACGTATGAGGTAGTG 57.563 47.619 0.00 0.00 39.21 2.74
2744 2883 3.800261 GCATGCATGACGTATGAGGTAGT 60.800 47.826 30.64 0.00 39.91 2.73
2745 2884 2.733552 GCATGCATGACGTATGAGGTAG 59.266 50.000 30.64 0.00 39.91 3.18
2746 2885 2.547855 GGCATGCATGACGTATGAGGTA 60.548 50.000 30.64 0.00 39.91 3.08
2747 2886 1.586422 GCATGCATGACGTATGAGGT 58.414 50.000 30.64 0.00 39.91 3.85
2748 2887 0.870393 GGCATGCATGACGTATGAGG 59.130 55.000 30.64 0.00 39.91 3.86
2762 2901 4.136511 TGCTTGCATGGCGGCATG 62.137 61.111 39.08 39.08 44.48 4.06
2763 2902 4.137872 GTGCTTGCATGGCGGCAT 62.138 61.111 20.18 20.18 44.48 4.40
2765 2904 4.137872 ATGTGCTTGCATGGCGGC 62.138 61.111 0.00 0.00 0.00 6.53
2766 2905 2.202690 CATGTGCTTGCATGGCGG 60.203 61.111 0.00 0.00 41.70 6.13
2767 2906 2.883730 GCATGTGCTTGCATGGCG 60.884 61.111 14.77 0.00 44.58 5.69
2773 2912 1.134367 AGTGATCATGCATGTGCTTGC 59.866 47.619 25.43 12.26 43.38 4.01
2774 2913 3.626217 ACTAGTGATCATGCATGTGCTTG 59.374 43.478 25.43 19.14 44.56 4.01
2775 2914 3.882444 ACTAGTGATCATGCATGTGCTT 58.118 40.909 25.43 9.84 42.66 3.91
2776 2915 3.555527 ACTAGTGATCATGCATGTGCT 57.444 42.857 25.43 19.21 42.66 4.40
2777 2916 4.122046 TGTACTAGTGATCATGCATGTGC 58.878 43.478 25.43 18.19 42.50 4.57
2778 2917 6.090493 GCTATGTACTAGTGATCATGCATGTG 59.910 42.308 25.43 3.46 0.00 3.21
2779 2918 6.162079 GCTATGTACTAGTGATCATGCATGT 58.838 40.000 25.43 13.42 0.00 3.21
2780 2919 6.090493 GTGCTATGTACTAGTGATCATGCATG 59.910 42.308 21.07 21.07 32.25 4.06
2781 2920 6.162079 GTGCTATGTACTAGTGATCATGCAT 58.838 40.000 21.15 0.00 32.25 3.96
2782 2921 5.532557 GTGCTATGTACTAGTGATCATGCA 58.467 41.667 5.39 14.63 0.00 3.96
2783 2922 4.618912 CGTGCTATGTACTAGTGATCATGC 59.381 45.833 5.39 12.74 0.00 4.06
2784 2923 4.618912 GCGTGCTATGTACTAGTGATCATG 59.381 45.833 5.39 2.11 0.00 3.07
2785 2924 4.278419 TGCGTGCTATGTACTAGTGATCAT 59.722 41.667 5.39 9.93 0.00 2.45
2786 2925 3.630312 TGCGTGCTATGTACTAGTGATCA 59.370 43.478 5.39 2.73 0.00 2.92
2787 2926 4.224715 TGCGTGCTATGTACTAGTGATC 57.775 45.455 5.39 0.00 0.00 2.92
2788 2927 4.649088 TTGCGTGCTATGTACTAGTGAT 57.351 40.909 5.39 0.00 0.00 3.06
2789 2928 4.443913 TTTGCGTGCTATGTACTAGTGA 57.556 40.909 5.39 0.00 0.00 3.41
2790 2929 4.803613 TCATTTGCGTGCTATGTACTAGTG 59.196 41.667 5.39 0.00 0.00 2.74
2791 2930 5.006153 TCATTTGCGTGCTATGTACTAGT 57.994 39.130 0.00 0.00 0.00 2.57
2792 2931 5.748630 TCTTCATTTGCGTGCTATGTACTAG 59.251 40.000 0.00 0.00 0.00 2.57
2793 2932 5.518847 GTCTTCATTTGCGTGCTATGTACTA 59.481 40.000 0.00 0.00 0.00 1.82
2794 2933 4.330074 GTCTTCATTTGCGTGCTATGTACT 59.670 41.667 0.00 0.00 0.00 2.73
2795 2934 4.578601 GTCTTCATTTGCGTGCTATGTAC 58.421 43.478 0.00 0.00 0.00 2.90
2796 2935 3.305897 CGTCTTCATTTGCGTGCTATGTA 59.694 43.478 0.00 0.00 0.00 2.29
2797 2936 2.094258 CGTCTTCATTTGCGTGCTATGT 59.906 45.455 0.00 0.00 0.00 2.29
2798 2937 2.697363 CGTCTTCATTTGCGTGCTATG 58.303 47.619 0.00 0.00 0.00 2.23
2799 2938 1.062587 GCGTCTTCATTTGCGTGCTAT 59.937 47.619 0.00 0.00 0.00 2.97
2800 2939 0.442310 GCGTCTTCATTTGCGTGCTA 59.558 50.000 0.00 0.00 0.00 3.49
2801 2940 1.207593 GCGTCTTCATTTGCGTGCT 59.792 52.632 0.00 0.00 0.00 4.40
2802 2941 0.385974 AAGCGTCTTCATTTGCGTGC 60.386 50.000 0.00 0.00 0.00 5.34
2803 2942 1.321016 CAAGCGTCTTCATTTGCGTG 58.679 50.000 0.00 0.00 0.00 5.34
2804 2943 0.385974 GCAAGCGTCTTCATTTGCGT 60.386 50.000 0.00 0.00 36.89 5.24
2805 2944 0.385849 TGCAAGCGTCTTCATTTGCG 60.386 50.000 3.95 0.00 46.61 4.85
2806 2945 1.652124 CATGCAAGCGTCTTCATTTGC 59.348 47.619 0.00 1.39 44.56 3.68
2807 2946 2.256174 CCATGCAAGCGTCTTCATTTG 58.744 47.619 0.00 0.00 0.00 2.32
2808 2947 1.888512 ACCATGCAAGCGTCTTCATTT 59.111 42.857 0.00 0.00 0.00 2.32
2809 2948 1.470098 GACCATGCAAGCGTCTTCATT 59.530 47.619 0.00 0.00 0.00 2.57
2810 2949 1.089920 GACCATGCAAGCGTCTTCAT 58.910 50.000 0.00 0.00 0.00 2.57
2811 2950 1.291184 CGACCATGCAAGCGTCTTCA 61.291 55.000 0.00 0.00 0.00 3.02
2812 2951 1.421485 CGACCATGCAAGCGTCTTC 59.579 57.895 0.00 0.00 0.00 2.87
2813 2952 2.034879 CCGACCATGCAAGCGTCTT 61.035 57.895 0.00 0.00 0.00 3.01
2814 2953 2.434884 CCGACCATGCAAGCGTCT 60.435 61.111 0.00 0.00 0.00 4.18
2815 2954 4.166011 GCCGACCATGCAAGCGTC 62.166 66.667 0.00 0.00 0.00 5.19
2817 2956 3.736100 TTGCCGACCATGCAAGCG 61.736 61.111 0.00 0.00 43.36 4.68
2820 2959 0.596083 CGTTTTTGCCGACCATGCAA 60.596 50.000 0.00 0.00 46.30 4.08
2821 2960 1.007964 CGTTTTTGCCGACCATGCA 60.008 52.632 0.00 0.00 36.84 3.96
2822 2961 3.841222 CGTTTTTGCCGACCATGC 58.159 55.556 0.00 0.00 0.00 4.06


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

AutoCloner maintained by Alex Coulton.