Multiple sequence alignment - TraesCS4B01G142200

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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 TraesCS4B01G142200 chr4B 100.000 2417 0 0 1 2417 187727893 187725477 0.000000e+00 4464
1 TraesCS4B01G142200 chr4D 94.042 1796 65 22 1 1784 123142123 123140358 0.000000e+00 2686
2 TraesCS4B01G142200 chr4D 87.168 226 25 3 1865 2086 123101788 123101563 1.110000e-63 254
3 TraesCS4B01G142200 chr4D 87.805 164 17 2 1865 2025 123101962 123101799 3.170000e-44 189
4 TraesCS4B01G142200 chr4A 90.482 1786 97 33 1 1762 446613256 446614992 0.000000e+00 2289
5 TraesCS4B01G142200 chr4A 85.345 232 23 5 1865 2086 446615086 446615316 1.870000e-56 230
6 TraesCS4B01G142200 chr1B 89.376 1826 107 38 26 1808 173123390 173121609 0.000000e+00 2217
7 TraesCS4B01G142200 chr1A 90.783 1085 42 16 746 1808 121130073 121129025 0.000000e+00 1397
8 TraesCS4B01G142200 chr1A 91.517 613 35 10 1 605 121130781 121130178 0.000000e+00 828
9 TraesCS4B01G142200 chr1A 82.960 223 26 3 1865 2084 121129016 121128803 8.820000e-45 191


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 TraesCS4B01G142200 chr4B 187725477 187727893 2416 True 4464.000000 4464 100.0000 1 2417 1 chr4B.!!$R1 2416
1 TraesCS4B01G142200 chr4D 123140358 123142123 1765 True 2686.000000 2686 94.0420 1 1784 1 chr4D.!!$R1 1783
2 TraesCS4B01G142200 chr4A 446613256 446615316 2060 False 1259.500000 2289 87.9135 1 2086 2 chr4A.!!$F1 2085
3 TraesCS4B01G142200 chr1B 173121609 173123390 1781 True 2217.000000 2217 89.3760 26 1808 1 chr1B.!!$R1 1782
4 TraesCS4B01G142200 chr1A 121128803 121130781 1978 True 805.333333 1397 88.4200 1 2084 3 chr1A.!!$R1 2083

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
848 894 0.033405 ACTAGCGTGGCCTCCTCTTA 60.033 55.0 3.32 0.0 0.0 2.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2204 2347 0.036952 AGATGTCTGGCGTTGTGAGG 60.037 55.0 0.0 0.0 0.0 3.86 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
233 236 8.776376 AAAGAAATTTTGAGAAGCAACAAAGA 57.224 26.923 0.00 0.00 37.32 2.52
363 372 0.198696 AAGAAGGGGAAGGGAAGGGA 59.801 55.000 0.00 0.00 0.00 4.20
364 373 0.198696 AGAAGGGGAAGGGAAGGGAA 59.801 55.000 0.00 0.00 0.00 3.97
365 374 0.626382 GAAGGGGAAGGGAAGGGAAG 59.374 60.000 0.00 0.00 0.00 3.46
366 375 0.851332 AAGGGGAAGGGAAGGGAAGG 60.851 60.000 0.00 0.00 0.00 3.46
367 376 2.317378 GGGGAAGGGAAGGGAAGGG 61.317 68.421 0.00 0.00 0.00 3.95
378 387 3.055021 GGAAGGGAAGGGAAGTCAACTAG 60.055 52.174 0.00 0.00 0.00 2.57
451 464 2.093973 ACTGCGAATGTAACCCAGAGAG 60.094 50.000 0.00 0.00 0.00 3.20
501 514 1.395045 TTGGATTTGTTGGCGTGCCA 61.395 50.000 10.06 10.06 45.63 4.92
601 616 5.223449 TGTGCTTAACTTAACCAGCTACT 57.777 39.130 0.00 0.00 33.15 2.57
621 653 4.589908 ACTGCAACCCCTTTTATCACTAG 58.410 43.478 0.00 0.00 0.00 2.57
622 654 4.042934 ACTGCAACCCCTTTTATCACTAGT 59.957 41.667 0.00 0.00 0.00 2.57
623 655 5.249852 ACTGCAACCCCTTTTATCACTAGTA 59.750 40.000 0.00 0.00 0.00 1.82
682 714 2.052782 ATGCAACGGAGGGAATTACC 57.947 50.000 0.00 0.00 38.08 2.85
736 771 4.013728 GAGTGGAGAGCTTTCTGTCTCTA 58.986 47.826 4.01 0.00 39.57 2.43
812 854 4.024143 GCATCGTGCCACGCAACA 62.024 61.111 13.39 0.00 41.47 3.33
848 894 0.033405 ACTAGCGTGGCCTCCTCTTA 60.033 55.000 3.32 0.00 0.00 2.10
954 1001 0.472471 TCATCCCCGATACCAAAGCC 59.528 55.000 0.00 0.00 0.00 4.35
1263 1327 3.706594 GGAAGATGTACCCTGATCTGACA 59.293 47.826 0.38 0.00 0.00 3.58
1464 1532 4.096532 CGTGTGATGGTGTGAGAGTATACT 59.903 45.833 4.68 4.68 0.00 2.12
1578 1657 2.032030 GTCCTTGTGTGTATGTGTGTGC 60.032 50.000 0.00 0.00 0.00 4.57
1585 1664 0.795698 TGTATGTGTGTGCGCATGTC 59.204 50.000 15.91 7.97 44.61 3.06
1688 1767 6.562518 AGTCCTAAATCGCTACTTCAGTTAC 58.437 40.000 0.00 0.00 0.00 2.50
1693 1781 5.599999 AATCGCTACTTCAGTTACCTGAT 57.400 39.130 0.00 0.00 46.80 2.90
1735 1831 6.983307 TCTTCAGCTATTCTCTAACATGAAGC 59.017 38.462 0.00 0.00 41.22 3.86
1761 1895 1.068588 GCGAAGGAATAAATTGCCCCC 59.931 52.381 0.00 0.00 0.00 5.40
1787 1921 9.573133 CAAAAATTGTTGATTCCTCCTATACAC 57.427 33.333 1.78 0.00 0.00 2.90
1808 1942 6.796426 ACACTGAAGATTTCGATCGAGAATA 58.204 36.000 18.54 0.00 0.00 1.75
1809 1943 7.258441 ACACTGAAGATTTCGATCGAGAATAA 58.742 34.615 18.54 10.14 0.00 1.40
1810 1944 7.433719 ACACTGAAGATTTCGATCGAGAATAAG 59.566 37.037 18.54 12.91 0.00 1.73
1811 1945 7.433719 CACTGAAGATTTCGATCGAGAATAAGT 59.566 37.037 18.54 13.49 0.00 2.24
1812 1946 7.976734 ACTGAAGATTTCGATCGAGAATAAGTT 59.023 33.333 18.54 13.35 0.00 2.66
1813 1947 8.120030 TGAAGATTTCGATCGAGAATAAGTTG 57.880 34.615 18.54 0.00 0.00 3.16
1815 1949 5.463724 AGATTTCGATCGAGAATAAGTTGCC 59.536 40.000 18.54 7.44 0.00 4.52
1816 1950 3.093717 TCGATCGAGAATAAGTTGCCC 57.906 47.619 15.15 0.00 0.00 5.36
1817 1951 2.135933 CGATCGAGAATAAGTTGCCCC 58.864 52.381 10.26 0.00 0.00 5.80
1818 1952 2.495084 GATCGAGAATAAGTTGCCCCC 58.505 52.381 0.00 0.00 0.00 5.40
1838 1972 6.316440 CCCCCAAAATTGTTGATTTTCTTG 57.684 37.500 0.00 0.00 44.16 3.02
1839 1973 5.241285 CCCCCAAAATTGTTGATTTTCTTGG 59.759 40.000 0.00 0.00 44.16 3.61
1840 1974 5.278414 CCCCAAAATTGTTGATTTTCTTGGC 60.278 40.000 0.00 0.00 44.16 4.52
1841 1975 5.442402 CCAAAATTGTTGATTTTCTTGGCG 58.558 37.500 0.00 0.00 44.16 5.69
1842 1976 5.442402 CAAAATTGTTGATTTTCTTGGCGG 58.558 37.500 0.00 0.00 44.16 6.13
1843 1977 2.147436 TTGTTGATTTTCTTGGCGGC 57.853 45.000 0.00 0.00 0.00 6.53
1844 1978 0.039617 TGTTGATTTTCTTGGCGGCG 60.040 50.000 0.51 0.51 0.00 6.46
1845 1979 1.080839 TTGATTTTCTTGGCGGCGC 60.081 52.632 26.17 26.17 0.00 6.53
1846 1980 1.800283 TTGATTTTCTTGGCGGCGCA 61.800 50.000 34.36 17.03 0.00 6.09
1847 1981 1.139520 GATTTTCTTGGCGGCGCAT 59.860 52.632 34.36 16.57 0.00 4.73
1848 1982 0.867329 GATTTTCTTGGCGGCGCATC 60.867 55.000 34.36 21.00 0.00 3.91
1849 1983 1.315257 ATTTTCTTGGCGGCGCATCT 61.315 50.000 34.36 5.66 0.00 2.90
1850 1984 1.523154 TTTTCTTGGCGGCGCATCTT 61.523 50.000 34.36 0.00 0.00 2.40
1851 1985 1.523154 TTTCTTGGCGGCGCATCTTT 61.523 50.000 34.36 0.00 0.00 2.52
1852 1986 0.675208 TTCTTGGCGGCGCATCTTTA 60.675 50.000 34.36 10.96 0.00 1.85
1853 1987 1.089481 TCTTGGCGGCGCATCTTTAG 61.089 55.000 34.36 18.81 0.00 1.85
1854 1988 2.652893 CTTGGCGGCGCATCTTTAGC 62.653 60.000 34.36 13.93 0.00 3.09
1855 1989 2.897350 GGCGGCGCATCTTTAGCT 60.897 61.111 34.36 0.00 0.00 3.32
1856 1990 1.594293 GGCGGCGCATCTTTAGCTA 60.594 57.895 34.36 0.00 0.00 3.32
1857 1991 1.565106 GCGGCGCATCTTTAGCTAC 59.435 57.895 29.21 0.00 0.00 3.58
1858 1992 0.876342 GCGGCGCATCTTTAGCTACT 60.876 55.000 29.21 0.00 0.00 2.57
1859 1993 1.132588 CGGCGCATCTTTAGCTACTC 58.867 55.000 10.83 0.00 0.00 2.59
1860 1994 1.269309 CGGCGCATCTTTAGCTACTCT 60.269 52.381 10.83 0.00 0.00 3.24
1861 1995 2.399448 GGCGCATCTTTAGCTACTCTC 58.601 52.381 10.83 0.00 0.00 3.20
1862 1996 2.035321 GGCGCATCTTTAGCTACTCTCT 59.965 50.000 10.83 0.00 0.00 3.10
1863 1997 3.253677 GGCGCATCTTTAGCTACTCTCTA 59.746 47.826 10.83 0.00 0.00 2.43
1871 2005 8.845227 CATCTTTAGCTACTCTCTATCAGAACA 58.155 37.037 0.00 0.00 0.00 3.18
1897 2032 8.964420 TTCAATGTTTCTTAAGCGGAAAATAG 57.036 30.769 0.00 0.00 34.97 1.73
1898 2033 7.535139 TCAATGTTTCTTAAGCGGAAAATAGG 58.465 34.615 0.00 0.00 34.97 2.57
1904 2039 8.912658 GTTTCTTAAGCGGAAAATAGGAAAAAG 58.087 33.333 0.00 0.00 34.97 2.27
1937 2072 2.862436 TGCACGCAAGCAAGATCG 59.138 55.556 0.00 0.00 42.46 3.69
1976 2119 4.626081 AGCGCTCTGTGCCGGTTT 62.626 61.111 2.64 0.00 40.23 3.27
1978 2121 3.023591 GCGCTCTGTGCCGGTTTAC 62.024 63.158 1.90 0.47 38.78 2.01
2031 2174 1.269988 ACATTCGATCGAGATGGCTGG 60.270 52.381 27.95 14.41 0.00 4.85
2047 2190 1.361668 CTGGAACCGTTGGATCTGCG 61.362 60.000 0.00 0.00 0.00 5.18
2055 2198 1.074775 TTGGATCTGCGCCCTTTGT 59.925 52.632 4.18 0.00 0.00 2.83
2057 2200 1.078143 GGATCTGCGCCCTTTGTCT 60.078 57.895 4.18 0.00 0.00 3.41
2072 2215 4.319177 CTTTGTCTTTCCCTTCGTCTCAT 58.681 43.478 0.00 0.00 0.00 2.90
2101 2244 7.667043 AAAAAGAAAGAAAAAGAACCACACC 57.333 32.000 0.00 0.00 0.00 4.16
2102 2245 5.993748 AAGAAAGAAAAAGAACCACACCA 57.006 34.783 0.00 0.00 0.00 4.17
2103 2246 5.324784 AGAAAGAAAAAGAACCACACCAC 57.675 39.130 0.00 0.00 0.00 4.16
2104 2247 4.159693 AGAAAGAAAAAGAACCACACCACC 59.840 41.667 0.00 0.00 0.00 4.61
2105 2248 2.384828 AGAAAAAGAACCACACCACCC 58.615 47.619 0.00 0.00 0.00 4.61
2106 2249 2.104170 GAAAAAGAACCACACCACCCA 58.896 47.619 0.00 0.00 0.00 4.51
2107 2250 1.480789 AAAAGAACCACACCACCCAC 58.519 50.000 0.00 0.00 0.00 4.61
2108 2251 0.333312 AAAGAACCACACCACCCACA 59.667 50.000 0.00 0.00 0.00 4.17
2109 2252 0.395173 AAGAACCACACCACCCACAC 60.395 55.000 0.00 0.00 0.00 3.82
2110 2253 1.077357 GAACCACACCACCCACACA 60.077 57.895 0.00 0.00 0.00 3.72
2111 2254 1.379309 AACCACACCACCCACACAC 60.379 57.895 0.00 0.00 0.00 3.82
2112 2255 2.143575 AACCACACCACCCACACACA 62.144 55.000 0.00 0.00 0.00 3.72
2113 2256 1.823470 CCACACCACCCACACACAG 60.823 63.158 0.00 0.00 0.00 3.66
2114 2257 1.823470 CACACCACCCACACACAGG 60.823 63.158 0.00 0.00 0.00 4.00
2122 2265 3.798794 CCACACACAGGGAAGTGAA 57.201 52.632 0.57 0.00 42.05 3.18
2123 2266 2.276732 CCACACACAGGGAAGTGAAT 57.723 50.000 0.57 0.00 42.05 2.57
2124 2267 1.881973 CCACACACAGGGAAGTGAATG 59.118 52.381 0.57 0.00 42.05 2.67
2125 2268 2.487086 CCACACACAGGGAAGTGAATGA 60.487 50.000 0.57 0.00 42.05 2.57
2126 2269 2.810274 CACACACAGGGAAGTGAATGAG 59.190 50.000 0.57 0.00 42.05 2.90
2127 2270 2.224621 ACACACAGGGAAGTGAATGAGG 60.225 50.000 0.57 0.00 42.05 3.86
2128 2271 1.352352 ACACAGGGAAGTGAATGAGGG 59.648 52.381 0.57 0.00 42.05 4.30
2129 2272 0.329596 ACAGGGAAGTGAATGAGGGC 59.670 55.000 0.00 0.00 0.00 5.19
2130 2273 0.745845 CAGGGAAGTGAATGAGGGCG 60.746 60.000 0.00 0.00 0.00 6.13
2131 2274 2.115291 GGGAAGTGAATGAGGGCGC 61.115 63.158 0.00 0.00 0.00 6.53
2132 2275 1.377202 GGAAGTGAATGAGGGCGCA 60.377 57.895 10.83 0.00 0.00 6.09
2133 2276 0.960364 GGAAGTGAATGAGGGCGCAA 60.960 55.000 10.83 0.00 0.00 4.85
2134 2277 0.881118 GAAGTGAATGAGGGCGCAAA 59.119 50.000 10.83 0.00 0.00 3.68
2135 2278 1.269448 GAAGTGAATGAGGGCGCAAAA 59.731 47.619 10.83 0.00 0.00 2.44
2136 2279 1.327303 AGTGAATGAGGGCGCAAAAA 58.673 45.000 10.83 0.00 0.00 1.94
2155 2298 3.904136 AAAACAGATGAGACTTTGCGG 57.096 42.857 0.00 0.00 0.00 5.69
2156 2299 1.160137 AACAGATGAGACTTTGCGGC 58.840 50.000 0.00 0.00 0.00 6.53
2157 2300 0.322975 ACAGATGAGACTTTGCGGCT 59.677 50.000 0.00 0.00 0.00 5.52
2158 2301 1.271054 ACAGATGAGACTTTGCGGCTT 60.271 47.619 0.00 0.00 0.00 4.35
2159 2302 1.129998 CAGATGAGACTTTGCGGCTTG 59.870 52.381 0.00 0.00 0.00 4.01
2160 2303 0.179179 GATGAGACTTTGCGGCTTGC 60.179 55.000 0.00 0.00 46.70 4.01
2170 2313 4.705519 CGGCTTGCAGCAAACCGG 62.706 66.667 33.39 19.33 45.63 5.28
2173 2316 4.362476 CTTGCAGCAAACCGGCCC 62.362 66.667 9.65 0.00 33.36 5.80
2180 2323 2.989253 CAAACCGGCCCCCAACTC 60.989 66.667 0.00 0.00 0.00 3.01
2181 2324 4.295199 AAACCGGCCCCCAACTCC 62.295 66.667 0.00 0.00 0.00 3.85
2213 2356 3.188786 GCGGCTAGCCTCACAACG 61.189 66.667 30.55 16.58 40.81 4.10
2214 2357 3.188786 CGGCTAGCCTCACAACGC 61.189 66.667 30.55 1.87 0.00 4.84
2215 2358 2.820037 GGCTAGCCTCACAACGCC 60.820 66.667 27.17 0.00 0.00 5.68
2216 2359 2.047274 GCTAGCCTCACAACGCCA 60.047 61.111 2.29 0.00 0.00 5.69
2217 2360 2.103042 GCTAGCCTCACAACGCCAG 61.103 63.158 2.29 0.00 0.00 4.85
2218 2361 1.591703 CTAGCCTCACAACGCCAGA 59.408 57.895 0.00 0.00 0.00 3.86
2219 2362 0.737715 CTAGCCTCACAACGCCAGAC 60.738 60.000 0.00 0.00 0.00 3.51
2220 2363 1.468506 TAGCCTCACAACGCCAGACA 61.469 55.000 0.00 0.00 0.00 3.41
2221 2364 1.672356 GCCTCACAACGCCAGACAT 60.672 57.895 0.00 0.00 0.00 3.06
2222 2365 1.639298 GCCTCACAACGCCAGACATC 61.639 60.000 0.00 0.00 0.00 3.06
2223 2366 0.036952 CCTCACAACGCCAGACATCT 60.037 55.000 0.00 0.00 0.00 2.90
2224 2367 1.354040 CTCACAACGCCAGACATCTC 58.646 55.000 0.00 0.00 0.00 2.75
2225 2368 0.969149 TCACAACGCCAGACATCTCT 59.031 50.000 0.00 0.00 0.00 3.10
2226 2369 1.073964 CACAACGCCAGACATCTCTG 58.926 55.000 0.00 0.00 43.40 3.35
2227 2370 0.671781 ACAACGCCAGACATCTCTGC 60.672 55.000 0.00 0.00 42.55 4.26
2228 2371 0.390866 CAACGCCAGACATCTCTGCT 60.391 55.000 0.00 0.00 42.55 4.24
2229 2372 0.108424 AACGCCAGACATCTCTGCTC 60.108 55.000 0.00 0.00 42.55 4.26
2230 2373 1.588403 CGCCAGACATCTCTGCTCG 60.588 63.158 0.00 0.00 42.55 5.03
2231 2374 1.882167 GCCAGACATCTCTGCTCGC 60.882 63.158 0.00 0.00 42.55 5.03
2232 2375 1.815196 CCAGACATCTCTGCTCGCT 59.185 57.895 0.00 0.00 42.55 4.93
2233 2376 0.528033 CCAGACATCTCTGCTCGCTG 60.528 60.000 0.00 0.00 42.55 5.18
2234 2377 0.528033 CAGACATCTCTGCTCGCTGG 60.528 60.000 0.00 0.00 37.72 4.85
2235 2378 1.227205 GACATCTCTGCTCGCTGGG 60.227 63.158 0.00 0.00 0.00 4.45
2236 2379 2.588314 CATCTCTGCTCGCTGGGC 60.588 66.667 0.00 0.00 0.00 5.36
2237 2380 3.859414 ATCTCTGCTCGCTGGGCC 61.859 66.667 0.00 0.00 0.00 5.80
2241 2384 4.790962 CTGCTCGCTGGGCCACAT 62.791 66.667 0.00 0.00 0.00 3.21
2242 2385 4.783621 TGCTCGCTGGGCCACATC 62.784 66.667 0.00 0.00 0.00 3.06
2244 2387 4.100084 CTCGCTGGGCCACATCCA 62.100 66.667 0.00 0.00 0.00 3.41
2245 2388 3.410628 TCGCTGGGCCACATCCAT 61.411 61.111 0.00 0.00 33.29 3.41
2246 2389 2.903855 CGCTGGGCCACATCCATC 60.904 66.667 0.00 0.00 33.29 3.51
2247 2390 2.520260 GCTGGGCCACATCCATCC 60.520 66.667 0.00 0.00 33.29 3.51
2248 2391 3.009275 CTGGGCCACATCCATCCA 58.991 61.111 0.00 0.00 33.29 3.41
2249 2392 1.540166 CTGGGCCACATCCATCCAT 59.460 57.895 0.00 0.00 33.29 3.41
2250 2393 0.826256 CTGGGCCACATCCATCCATG 60.826 60.000 0.00 0.00 33.29 3.66
2263 2406 4.169059 CCATCCATGGTCATTAGTTCCA 57.831 45.455 12.58 0.00 43.05 3.53
2264 2407 4.733165 CCATCCATGGTCATTAGTTCCAT 58.267 43.478 12.58 0.00 43.05 3.41
2265 2408 4.763793 CCATCCATGGTCATTAGTTCCATC 59.236 45.833 12.58 0.00 43.05 3.51
2266 2409 4.071961 TCCATGGTCATTAGTTCCATCG 57.928 45.455 12.58 0.00 39.57 3.84
2267 2410 3.454447 TCCATGGTCATTAGTTCCATCGT 59.546 43.478 12.58 0.00 39.57 3.73
2268 2411 3.561310 CCATGGTCATTAGTTCCATCGTG 59.439 47.826 2.57 0.00 39.57 4.35
2269 2412 3.260475 TGGTCATTAGTTCCATCGTGG 57.740 47.619 0.00 0.00 39.43 4.94
2270 2413 2.569853 TGGTCATTAGTTCCATCGTGGT 59.430 45.455 4.33 0.00 39.03 4.16
2271 2414 2.936498 GGTCATTAGTTCCATCGTGGTG 59.064 50.000 4.33 0.00 39.03 4.17
2272 2415 3.596214 GTCATTAGTTCCATCGTGGTGT 58.404 45.455 4.33 0.00 39.03 4.16
2273 2416 3.617263 GTCATTAGTTCCATCGTGGTGTC 59.383 47.826 4.33 0.00 39.03 3.67
2274 2417 3.259625 TCATTAGTTCCATCGTGGTGTCA 59.740 43.478 4.33 0.00 39.03 3.58
2275 2418 3.973206 TTAGTTCCATCGTGGTGTCAT 57.027 42.857 4.33 0.00 39.03 3.06
2276 2419 2.386661 AGTTCCATCGTGGTGTCATC 57.613 50.000 4.33 0.00 39.03 2.92
2277 2420 0.999406 GTTCCATCGTGGTGTCATCG 59.001 55.000 4.33 0.00 39.03 3.84
2278 2421 0.739462 TTCCATCGTGGTGTCATCGC 60.739 55.000 4.33 0.00 39.03 4.58
2279 2422 1.447663 CCATCGTGGTGTCATCGCA 60.448 57.895 0.00 0.00 31.35 5.10
2280 2423 1.018752 CCATCGTGGTGTCATCGCAA 61.019 55.000 0.00 0.00 31.35 4.85
2281 2424 0.095245 CATCGTGGTGTCATCGCAAC 59.905 55.000 0.00 0.00 0.00 4.17
2282 2425 1.019278 ATCGTGGTGTCATCGCAACC 61.019 55.000 0.00 0.00 0.00 3.77
2283 2426 2.677003 CGTGGTGTCATCGCAACCC 61.677 63.158 0.00 0.00 0.00 4.11
2284 2427 2.033448 TGGTGTCATCGCAACCCC 59.967 61.111 0.00 0.00 0.00 4.95
2285 2428 3.124921 GGTGTCATCGCAACCCCG 61.125 66.667 0.00 0.00 0.00 5.73
2286 2429 3.799755 GTGTCATCGCAACCCCGC 61.800 66.667 0.00 0.00 0.00 6.13
2287 2430 4.015406 TGTCATCGCAACCCCGCT 62.015 61.111 0.00 0.00 0.00 5.52
2288 2431 3.499737 GTCATCGCAACCCCGCTG 61.500 66.667 0.00 0.00 0.00 5.18
2289 2432 4.776322 TCATCGCAACCCCGCTGG 62.776 66.667 0.00 0.00 41.37 4.85
2295 2438 4.028490 CAACCCCGCTGGCTACCA 62.028 66.667 0.00 0.00 37.83 3.25
2296 2439 3.015145 AACCCCGCTGGCTACCAT 61.015 61.111 0.00 0.00 37.83 3.55
2297 2440 3.344137 AACCCCGCTGGCTACCATG 62.344 63.158 0.00 0.00 37.83 3.66
2298 2441 4.569180 CCCCGCTGGCTACCATGG 62.569 72.222 11.19 11.19 30.82 3.66
2300 2443 4.488136 CCGCTGGCTACCATGGCA 62.488 66.667 13.04 0.00 40.25 4.92
2304 2447 2.591753 TGGCTACCATGGCAGCTC 59.408 61.111 31.36 22.65 37.59 4.09
2305 2448 2.590007 GGCTACCATGGCAGCTCG 60.590 66.667 31.36 7.42 37.91 5.03
2306 2449 2.187946 GCTACCATGGCAGCTCGT 59.812 61.111 27.02 1.68 34.86 4.18
2307 2450 1.884926 GCTACCATGGCAGCTCGTC 60.885 63.158 27.02 0.31 34.86 4.20
2308 2451 1.589993 CTACCATGGCAGCTCGTCG 60.590 63.158 13.04 0.00 0.00 5.12
2309 2452 2.284798 CTACCATGGCAGCTCGTCGT 62.285 60.000 13.04 0.00 0.00 4.34
2310 2453 1.033202 TACCATGGCAGCTCGTCGTA 61.033 55.000 13.04 0.00 0.00 3.43
2311 2454 1.589993 CCATGGCAGCTCGTCGTAG 60.590 63.158 0.00 0.00 0.00 3.51
2312 2455 2.105128 ATGGCAGCTCGTCGTAGC 59.895 61.111 8.15 8.15 43.11 3.58
2313 2456 2.710902 ATGGCAGCTCGTCGTAGCA 61.711 57.895 15.71 0.21 45.30 3.49
2314 2457 2.021068 ATGGCAGCTCGTCGTAGCAT 62.021 55.000 15.71 2.12 45.30 3.79
2315 2458 1.946650 GGCAGCTCGTCGTAGCATC 60.947 63.158 15.71 8.57 45.30 3.91
2316 2459 1.946650 GCAGCTCGTCGTAGCATCC 60.947 63.158 15.71 3.75 45.30 3.51
2317 2460 1.299468 CAGCTCGTCGTAGCATCCC 60.299 63.158 15.71 0.00 45.30 3.85
2318 2461 2.027751 GCTCGTCGTAGCATCCCC 59.972 66.667 10.53 0.00 42.30 4.81
2319 2462 2.782222 GCTCGTCGTAGCATCCCCA 61.782 63.158 10.53 0.00 42.30 4.96
2320 2463 1.065928 CTCGTCGTAGCATCCCCAC 59.934 63.158 0.00 0.00 0.00 4.61
2321 2464 2.106332 CGTCGTAGCATCCCCACC 59.894 66.667 0.00 0.00 0.00 4.61
2322 2465 2.106332 GTCGTAGCATCCCCACCG 59.894 66.667 0.00 0.00 0.00 4.94
2323 2466 3.151710 TCGTAGCATCCCCACCGG 61.152 66.667 0.00 0.00 0.00 5.28
2324 2467 3.467226 CGTAGCATCCCCACCGGT 61.467 66.667 0.00 0.00 0.00 5.28
2325 2468 2.504519 GTAGCATCCCCACCGGTC 59.495 66.667 2.59 0.00 0.00 4.79
2326 2469 2.039787 TAGCATCCCCACCGGTCA 59.960 61.111 2.59 0.00 0.00 4.02
2327 2470 1.383943 TAGCATCCCCACCGGTCAT 60.384 57.895 2.59 0.00 0.00 3.06
2328 2471 0.105401 TAGCATCCCCACCGGTCATA 60.105 55.000 2.59 0.00 0.00 2.15
2329 2472 0.986019 AGCATCCCCACCGGTCATAA 60.986 55.000 2.59 0.00 0.00 1.90
2330 2473 0.106918 GCATCCCCACCGGTCATAAA 60.107 55.000 2.59 0.00 0.00 1.40
2331 2474 1.683629 GCATCCCCACCGGTCATAAAA 60.684 52.381 2.59 0.00 0.00 1.52
2332 2475 2.021457 CATCCCCACCGGTCATAAAAC 58.979 52.381 2.59 0.00 0.00 2.43
2333 2476 0.328926 TCCCCACCGGTCATAAAACC 59.671 55.000 2.59 0.00 35.86 3.27
2334 2477 0.681887 CCCCACCGGTCATAAAACCC 60.682 60.000 2.59 0.00 35.79 4.11
2335 2478 0.038455 CCCACCGGTCATAAAACCCA 59.962 55.000 2.59 0.00 35.79 4.51
2336 2479 1.170442 CCACCGGTCATAAAACCCAC 58.830 55.000 2.59 0.00 35.79 4.61
2337 2480 1.170442 CACCGGTCATAAAACCCACC 58.830 55.000 2.59 0.00 35.79 4.61
2339 2482 1.798087 CGGTCATAAAACCCACCGC 59.202 57.895 0.00 0.00 44.88 5.68
2340 2483 0.675522 CGGTCATAAAACCCACCGCT 60.676 55.000 0.00 0.00 44.88 5.52
2341 2484 1.092348 GGTCATAAAACCCACCGCTC 58.908 55.000 0.00 0.00 32.82 5.03
2342 2485 0.725117 GTCATAAAACCCACCGCTCG 59.275 55.000 0.00 0.00 0.00 5.03
2343 2486 0.609151 TCATAAAACCCACCGCTCGA 59.391 50.000 0.00 0.00 0.00 4.04
2344 2487 0.725117 CATAAAACCCACCGCTCGAC 59.275 55.000 0.00 0.00 0.00 4.20
2345 2488 0.322322 ATAAAACCCACCGCTCGACA 59.678 50.000 0.00 0.00 0.00 4.35
2346 2489 0.322322 TAAAACCCACCGCTCGACAT 59.678 50.000 0.00 0.00 0.00 3.06
2347 2490 0.536460 AAAACCCACCGCTCGACATT 60.536 50.000 0.00 0.00 0.00 2.71
2348 2491 1.234615 AAACCCACCGCTCGACATTG 61.235 55.000 0.00 0.00 0.00 2.82
2349 2492 3.499737 CCCACCGCTCGACATTGC 61.500 66.667 0.00 0.00 0.00 3.56
2350 2493 2.741985 CCACCGCTCGACATTGCA 60.742 61.111 0.00 0.00 0.00 4.08
2351 2494 2.108514 CCACCGCTCGACATTGCAT 61.109 57.895 0.00 0.00 0.00 3.96
2352 2495 1.349627 CACCGCTCGACATTGCATC 59.650 57.895 0.00 0.00 0.00 3.91
2353 2496 1.079197 ACCGCTCGACATTGCATCA 60.079 52.632 0.00 0.00 0.00 3.07
2354 2497 0.462581 ACCGCTCGACATTGCATCAT 60.463 50.000 0.00 0.00 0.00 2.45
2355 2498 0.234106 CCGCTCGACATTGCATCATC 59.766 55.000 0.00 0.00 0.00 2.92
2356 2499 0.932399 CGCTCGACATTGCATCATCA 59.068 50.000 0.00 0.00 0.00 3.07
2357 2500 1.529865 CGCTCGACATTGCATCATCAT 59.470 47.619 0.00 0.00 0.00 2.45
2358 2501 2.411160 CGCTCGACATTGCATCATCATC 60.411 50.000 0.00 0.00 0.00 2.92
2359 2502 2.546789 GCTCGACATTGCATCATCATCA 59.453 45.455 0.00 0.00 0.00 3.07
2360 2503 3.364068 GCTCGACATTGCATCATCATCAG 60.364 47.826 0.00 0.00 0.00 2.90
2361 2504 2.546789 TCGACATTGCATCATCATCAGC 59.453 45.455 0.00 0.00 0.00 4.26
2362 2505 2.661979 CGACATTGCATCATCATCAGCG 60.662 50.000 0.00 0.00 0.00 5.18
2363 2506 1.607148 ACATTGCATCATCATCAGCGG 59.393 47.619 0.00 0.00 0.00 5.52
2364 2507 0.596577 ATTGCATCATCATCAGCGGC 59.403 50.000 0.00 0.00 0.00 6.53
2365 2508 1.778027 TTGCATCATCATCAGCGGCG 61.778 55.000 0.51 0.51 0.00 6.46
2366 2509 2.249535 GCATCATCATCAGCGGCGT 61.250 57.895 9.37 0.00 0.00 5.68
2367 2510 1.858041 CATCATCATCAGCGGCGTC 59.142 57.895 9.37 0.13 0.00 5.19
2368 2511 1.662760 ATCATCATCAGCGGCGTCG 60.663 57.895 4.29 4.29 39.81 5.12
2387 2530 3.047280 GTCCATGGACGCGCAACA 61.047 61.111 28.52 2.56 35.30 3.33
2388 2531 3.047280 TCCATGGACGCGCAACAC 61.047 61.111 11.44 0.00 0.00 3.32
2389 2532 4.101790 CCATGGACGCGCAACACC 62.102 66.667 5.56 5.16 0.00 4.16
2390 2533 4.101790 CATGGACGCGCAACACCC 62.102 66.667 5.73 0.50 0.00 4.61
2409 2552 4.803426 CTCGCGTCCTCACTGCCC 62.803 72.222 5.77 0.00 0.00 5.36
2411 2554 4.379243 CGCGTCCTCACTGCCCTT 62.379 66.667 0.00 0.00 0.00 3.95
2412 2555 2.743928 GCGTCCTCACTGCCCTTG 60.744 66.667 0.00 0.00 0.00 3.61
2413 2556 2.743718 CGTCCTCACTGCCCTTGT 59.256 61.111 0.00 0.00 0.00 3.16
2414 2557 1.669115 CGTCCTCACTGCCCTTGTG 60.669 63.158 0.00 0.00 36.82 3.33
2415 2558 1.968540 GTCCTCACTGCCCTTGTGC 60.969 63.158 0.00 0.00 35.58 4.57
2416 2559 2.113774 CCTCACTGCCCTTGTGCA 59.886 61.111 0.00 0.00 39.37 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
233 236 1.974543 CGGCAAGAAATGGGCCTTT 59.025 52.632 4.53 0.76 45.53 3.11
363 372 5.717119 ATAATGCCTAGTTGACTTCCCTT 57.283 39.130 0.00 0.00 0.00 3.95
364 373 5.398012 GGAATAATGCCTAGTTGACTTCCCT 60.398 44.000 0.00 0.00 0.00 4.20
365 374 4.822350 GGAATAATGCCTAGTTGACTTCCC 59.178 45.833 0.00 0.00 0.00 3.97
366 375 5.685728 AGGAATAATGCCTAGTTGACTTCC 58.314 41.667 0.00 0.00 32.92 3.46
367 376 7.631717 AAAGGAATAATGCCTAGTTGACTTC 57.368 36.000 0.00 0.00 33.76 3.01
378 387 5.408299 GGTTTGTGTCAAAAGGAATAATGCC 59.592 40.000 0.00 0.00 0.00 4.40
451 464 4.959839 ACCTCCTCTACCTTCAAATCTCTC 59.040 45.833 0.00 0.00 0.00 3.20
601 616 4.650972 ACTAGTGATAAAAGGGGTTGCA 57.349 40.909 0.00 0.00 0.00 4.08
656 688 3.469008 TCCCTCCGTTGCATAATACAG 57.531 47.619 0.00 0.00 0.00 2.74
682 714 6.166984 TGATTATCCTTGAGGCAGTTAGAG 57.833 41.667 0.00 0.00 34.44 2.43
689 721 7.719193 TCGATAATTTTGATTATCCTTGAGGCA 59.281 33.333 11.50 0.00 39.27 4.75
954 1001 7.700022 AAAGATTTCAAGGAGAAGAAGATGG 57.300 36.000 0.00 0.00 37.57 3.51
1176 1240 3.221771 TCATCACCACAAAAGGAACTGG 58.778 45.455 0.00 0.00 40.86 4.00
1317 1381 2.592993 CCCCGCCTTGTTCTCAGGA 61.593 63.158 0.00 0.00 0.00 3.86
1464 1532 4.105486 CAGATCAGACGCTCGTTATTCAA 58.895 43.478 0.00 0.00 0.00 2.69
1518 1590 1.364626 CGGAGAGCGAGCAAGCAAAT 61.365 55.000 6.21 0.00 40.15 2.32
1585 1664 6.767456 AGATAGATGAAGCAATTACAGGGAG 58.233 40.000 0.00 0.00 0.00 4.30
1665 1744 5.747675 GGTAACTGAAGTAGCGATTTAGGAC 59.252 44.000 0.00 0.00 0.00 3.85
1688 1767 0.456653 CGCCGCCAAGAAAAATCAGG 60.457 55.000 0.00 0.00 0.00 3.86
1693 1781 1.080839 GATGCGCCGCCAAGAAAAA 60.081 52.632 6.63 0.00 0.00 1.94
1735 1831 5.215160 GGCAATTTATTCCTTCGCTGTATG 58.785 41.667 0.00 0.00 0.00 2.39
1750 1884 5.694995 TCAACAATTTTTGGGGGCAATTTA 58.305 33.333 4.57 0.00 34.12 1.40
1761 1895 9.573133 GTGTATAGGAGGAATCAACAATTTTTG 57.427 33.333 0.00 0.00 0.00 2.44
1787 1921 7.922505 ACTTATTCTCGATCGAAATCTTCAG 57.077 36.000 19.92 11.19 0.00 3.02
1815 1949 5.241285 CCAAGAAAATCAACAATTTTGGGGG 59.759 40.000 0.78 0.00 45.47 5.40
1816 1950 5.278414 GCCAAGAAAATCAACAATTTTGGGG 60.278 40.000 0.78 1.80 45.47 4.96
1817 1951 5.560567 CGCCAAGAAAATCAACAATTTTGGG 60.561 40.000 0.78 2.08 45.47 4.12
1818 1952 5.442402 CGCCAAGAAAATCAACAATTTTGG 58.558 37.500 0.78 0.00 45.47 3.28
1819 1953 5.442402 CCGCCAAGAAAATCAACAATTTTG 58.558 37.500 0.78 0.00 45.47 2.44
1821 1955 3.498018 GCCGCCAAGAAAATCAACAATTT 59.502 39.130 0.00 0.00 39.30 1.82
1822 1956 3.066380 GCCGCCAAGAAAATCAACAATT 58.934 40.909 0.00 0.00 0.00 2.32
1823 1957 2.687370 GCCGCCAAGAAAATCAACAAT 58.313 42.857 0.00 0.00 0.00 2.71
1824 1958 1.601663 CGCCGCCAAGAAAATCAACAA 60.602 47.619 0.00 0.00 0.00 2.83
1825 1959 0.039617 CGCCGCCAAGAAAATCAACA 60.040 50.000 0.00 0.00 0.00 3.33
1826 1960 1.344226 GCGCCGCCAAGAAAATCAAC 61.344 55.000 0.00 0.00 0.00 3.18
1827 1961 1.080839 GCGCCGCCAAGAAAATCAA 60.081 52.632 0.00 0.00 0.00 2.57
1828 1962 1.594194 ATGCGCCGCCAAGAAAATCA 61.594 50.000 6.63 0.00 0.00 2.57
1829 1963 0.867329 GATGCGCCGCCAAGAAAATC 60.867 55.000 6.63 0.00 0.00 2.17
1830 1964 1.139520 GATGCGCCGCCAAGAAAAT 59.860 52.632 6.63 0.00 0.00 1.82
1831 1965 1.523154 AAGATGCGCCGCCAAGAAAA 61.523 50.000 6.63 0.00 0.00 2.29
1832 1966 1.523154 AAAGATGCGCCGCCAAGAAA 61.523 50.000 6.63 0.00 0.00 2.52
1833 1967 0.675208 TAAAGATGCGCCGCCAAGAA 60.675 50.000 6.63 0.00 0.00 2.52
1834 1968 1.078778 TAAAGATGCGCCGCCAAGA 60.079 52.632 6.63 0.00 0.00 3.02
1835 1969 1.353103 CTAAAGATGCGCCGCCAAG 59.647 57.895 6.63 0.00 0.00 3.61
1836 1970 2.760159 GCTAAAGATGCGCCGCCAA 61.760 57.895 6.63 0.00 0.00 4.52
1837 1971 2.304901 TAGCTAAAGATGCGCCGCCA 62.305 55.000 6.63 0.00 35.28 5.69
1838 1972 1.594293 TAGCTAAAGATGCGCCGCC 60.594 57.895 6.63 0.00 35.28 6.13
1839 1973 0.876342 AGTAGCTAAAGATGCGCCGC 60.876 55.000 4.18 0.00 35.28 6.53
1840 1974 1.132588 GAGTAGCTAAAGATGCGCCG 58.867 55.000 4.18 0.00 35.28 6.46
1841 1975 2.035321 AGAGAGTAGCTAAAGATGCGCC 59.965 50.000 4.18 0.00 35.28 6.53
1842 1976 3.363341 AGAGAGTAGCTAAAGATGCGC 57.637 47.619 0.00 0.00 35.28 6.09
1843 1977 6.148645 TCTGATAGAGAGTAGCTAAAGATGCG 59.851 42.308 0.00 0.00 35.28 4.73
1844 1978 7.447374 TCTGATAGAGAGTAGCTAAAGATGC 57.553 40.000 0.00 0.00 0.00 3.91
1845 1979 8.845227 TGTTCTGATAGAGAGTAGCTAAAGATG 58.155 37.037 0.00 0.00 30.18 2.90
1846 1980 8.988546 TGTTCTGATAGAGAGTAGCTAAAGAT 57.011 34.615 0.00 0.00 30.18 2.40
1847 1981 8.988546 ATGTTCTGATAGAGAGTAGCTAAAGA 57.011 34.615 0.00 0.00 30.18 2.52
1848 1982 9.677567 GAATGTTCTGATAGAGAGTAGCTAAAG 57.322 37.037 0.00 0.00 30.18 1.85
1849 1983 9.190317 TGAATGTTCTGATAGAGAGTAGCTAAA 57.810 33.333 0.00 0.00 30.18 1.85
1850 1984 8.753497 TGAATGTTCTGATAGAGAGTAGCTAA 57.247 34.615 0.00 0.00 30.18 3.09
1851 1985 8.753497 TTGAATGTTCTGATAGAGAGTAGCTA 57.247 34.615 0.00 0.00 30.18 3.32
1852 1986 7.652524 TTGAATGTTCTGATAGAGAGTAGCT 57.347 36.000 0.00 0.00 30.18 3.32
1853 1987 7.925483 ACATTGAATGTTCTGATAGAGAGTAGC 59.075 37.037 4.72 0.00 41.63 3.58
1871 2005 9.573133 CTATTTTCCGCTTAAGAAACATTGAAT 57.427 29.630 6.67 0.00 33.11 2.57
1922 2057 0.453282 CAACCGATCTTGCTTGCGTG 60.453 55.000 0.00 0.00 0.00 5.34
1925 2060 4.465413 GCAACCGATCTTGCTTGC 57.535 55.556 11.39 5.40 42.84 4.01
1930 2065 1.603802 ACAACACAGCAACCGATCTTG 59.396 47.619 0.00 0.00 0.00 3.02
1931 2066 1.967319 ACAACACAGCAACCGATCTT 58.033 45.000 0.00 0.00 0.00 2.40
1934 2069 2.033299 CAGAAACAACACAGCAACCGAT 59.967 45.455 0.00 0.00 0.00 4.18
1935 2070 1.400142 CAGAAACAACACAGCAACCGA 59.600 47.619 0.00 0.00 0.00 4.69
1936 2071 1.533756 CCAGAAACAACACAGCAACCG 60.534 52.381 0.00 0.00 0.00 4.44
1937 2072 1.202405 CCCAGAAACAACACAGCAACC 60.202 52.381 0.00 0.00 0.00 3.77
1975 2118 3.365291 CTAGTGCCTGCGCCGGTAA 62.365 63.158 19.63 5.51 0.00 2.85
1976 2119 3.833645 CTAGTGCCTGCGCCGGTA 61.834 66.667 19.63 12.58 0.00 4.02
1978 2121 4.227134 ATCTAGTGCCTGCGCCGG 62.227 66.667 14.29 14.29 0.00 6.13
2031 2174 2.750888 GGCGCAGATCCAACGGTTC 61.751 63.158 10.83 0.00 0.00 3.62
2047 2190 0.881796 CGAAGGGAAAGACAAAGGGC 59.118 55.000 0.00 0.00 0.00 5.19
2055 2198 5.477607 TTTGTATGAGACGAAGGGAAAGA 57.522 39.130 0.00 0.00 0.00 2.52
2081 2224 4.159693 GGTGGTGTGGTTCTTTTTCTTTCT 59.840 41.667 0.00 0.00 0.00 2.52
2086 2229 2.104170 TGGGTGGTGTGGTTCTTTTTC 58.896 47.619 0.00 0.00 0.00 2.29
2087 2230 1.828595 GTGGGTGGTGTGGTTCTTTTT 59.171 47.619 0.00 0.00 0.00 1.94
2088 2231 1.272760 TGTGGGTGGTGTGGTTCTTTT 60.273 47.619 0.00 0.00 0.00 2.27
2089 2232 0.333312 TGTGGGTGGTGTGGTTCTTT 59.667 50.000 0.00 0.00 0.00 2.52
2090 2233 0.395173 GTGTGGGTGGTGTGGTTCTT 60.395 55.000 0.00 0.00 0.00 2.52
2091 2234 1.226262 GTGTGGGTGGTGTGGTTCT 59.774 57.895 0.00 0.00 0.00 3.01
2092 2235 1.077357 TGTGTGGGTGGTGTGGTTC 60.077 57.895 0.00 0.00 0.00 3.62
2093 2236 1.379309 GTGTGTGGGTGGTGTGGTT 60.379 57.895 0.00 0.00 0.00 3.67
2094 2237 2.274104 GTGTGTGGGTGGTGTGGT 59.726 61.111 0.00 0.00 0.00 4.16
2095 2238 1.823470 CTGTGTGTGGGTGGTGTGG 60.823 63.158 0.00 0.00 0.00 4.17
2096 2239 1.823470 CCTGTGTGTGGGTGGTGTG 60.823 63.158 0.00 0.00 0.00 3.82
2097 2240 2.595095 CCTGTGTGTGGGTGGTGT 59.405 61.111 0.00 0.00 0.00 4.16
2098 2241 2.203337 CCCTGTGTGTGGGTGGTG 60.203 66.667 0.00 0.00 39.82 4.17
2099 2242 1.994885 CTTCCCTGTGTGTGGGTGGT 61.995 60.000 0.00 0.00 44.84 4.16
2100 2243 1.228245 CTTCCCTGTGTGTGGGTGG 60.228 63.158 0.00 0.00 44.84 4.61
2101 2244 0.819259 CACTTCCCTGTGTGTGGGTG 60.819 60.000 0.00 0.00 44.84 4.61
2102 2245 0.986019 TCACTTCCCTGTGTGTGGGT 60.986 55.000 0.00 0.00 44.84 4.51
2103 2246 0.182537 TTCACTTCCCTGTGTGTGGG 59.817 55.000 0.00 0.00 45.90 4.61
2104 2247 1.881973 CATTCACTTCCCTGTGTGTGG 59.118 52.381 0.00 0.00 38.90 4.17
2105 2248 2.810274 CTCATTCACTTCCCTGTGTGTG 59.190 50.000 0.00 0.00 38.90 3.82
2106 2249 2.224621 CCTCATTCACTTCCCTGTGTGT 60.225 50.000 0.00 0.00 38.90 3.72
2107 2250 2.430465 CCTCATTCACTTCCCTGTGTG 58.570 52.381 0.00 0.00 38.90 3.82
2108 2251 1.352352 CCCTCATTCACTTCCCTGTGT 59.648 52.381 0.00 0.00 38.90 3.72
2109 2252 1.952367 GCCCTCATTCACTTCCCTGTG 60.952 57.143 0.00 0.00 39.15 3.66
2110 2253 0.329596 GCCCTCATTCACTTCCCTGT 59.670 55.000 0.00 0.00 0.00 4.00
2111 2254 0.745845 CGCCCTCATTCACTTCCCTG 60.746 60.000 0.00 0.00 0.00 4.45
2112 2255 1.604378 CGCCCTCATTCACTTCCCT 59.396 57.895 0.00 0.00 0.00 4.20
2113 2256 2.115291 GCGCCCTCATTCACTTCCC 61.115 63.158 0.00 0.00 0.00 3.97
2114 2257 0.960364 TTGCGCCCTCATTCACTTCC 60.960 55.000 4.18 0.00 0.00 3.46
2115 2258 0.881118 TTTGCGCCCTCATTCACTTC 59.119 50.000 4.18 0.00 0.00 3.01
2116 2259 1.327303 TTTTGCGCCCTCATTCACTT 58.673 45.000 4.18 0.00 0.00 3.16
2117 2260 1.327303 TTTTTGCGCCCTCATTCACT 58.673 45.000 4.18 0.00 0.00 3.41
2118 2261 3.883997 TTTTTGCGCCCTCATTCAC 57.116 47.368 4.18 0.00 0.00 3.18
2134 2277 3.550842 GCCGCAAAGTCTCATCTGTTTTT 60.551 43.478 0.00 0.00 0.00 1.94
2135 2278 2.030805 GCCGCAAAGTCTCATCTGTTTT 60.031 45.455 0.00 0.00 0.00 2.43
2136 2279 1.537202 GCCGCAAAGTCTCATCTGTTT 59.463 47.619 0.00 0.00 0.00 2.83
2137 2280 1.160137 GCCGCAAAGTCTCATCTGTT 58.840 50.000 0.00 0.00 0.00 3.16
2138 2281 0.322975 AGCCGCAAAGTCTCATCTGT 59.677 50.000 0.00 0.00 0.00 3.41
2139 2282 1.129998 CAAGCCGCAAAGTCTCATCTG 59.870 52.381 0.00 0.00 0.00 2.90
2140 2283 1.446907 CAAGCCGCAAAGTCTCATCT 58.553 50.000 0.00 0.00 0.00 2.90
2141 2284 0.179179 GCAAGCCGCAAAGTCTCATC 60.179 55.000 0.00 0.00 41.79 2.92
2142 2285 1.878775 GCAAGCCGCAAAGTCTCAT 59.121 52.632 0.00 0.00 41.79 2.90
2143 2286 3.343972 GCAAGCCGCAAAGTCTCA 58.656 55.556 0.00 0.00 41.79 3.27
2156 2299 4.362476 GGGCCGGTTTGCTGCAAG 62.362 66.667 15.39 5.11 0.00 4.01
2163 2306 2.989253 GAGTTGGGGGCCGGTTTG 60.989 66.667 1.90 0.00 0.00 2.93
2164 2307 4.295199 GGAGTTGGGGGCCGGTTT 62.295 66.667 1.90 0.00 0.00 3.27
2196 2339 3.188786 CGTTGTGAGGCTAGCCGC 61.189 66.667 28.70 28.70 41.95 6.53
2197 2340 3.188786 GCGTTGTGAGGCTAGCCG 61.189 66.667 27.83 14.93 41.95 5.52
2198 2341 2.820037 GGCGTTGTGAGGCTAGCC 60.820 66.667 27.19 27.19 36.89 3.93
2199 2342 2.047274 TGGCGTTGTGAGGCTAGC 60.047 61.111 6.04 6.04 36.89 3.42
2200 2343 0.737715 GTCTGGCGTTGTGAGGCTAG 60.738 60.000 0.00 0.00 43.86 3.42
2201 2344 1.292223 GTCTGGCGTTGTGAGGCTA 59.708 57.895 0.00 0.00 36.89 3.93
2202 2345 2.031163 GTCTGGCGTTGTGAGGCT 59.969 61.111 0.00 0.00 36.89 4.58
2203 2346 1.639298 GATGTCTGGCGTTGTGAGGC 61.639 60.000 0.00 0.00 35.97 4.70
2204 2347 0.036952 AGATGTCTGGCGTTGTGAGG 60.037 55.000 0.00 0.00 0.00 3.86
2205 2348 1.067283 AGAGATGTCTGGCGTTGTGAG 60.067 52.381 0.00 0.00 0.00 3.51
2206 2349 0.969149 AGAGATGTCTGGCGTTGTGA 59.031 50.000 0.00 0.00 0.00 3.58
2207 2350 1.073964 CAGAGATGTCTGGCGTTGTG 58.926 55.000 12.01 0.00 45.85 3.33
2208 2351 3.521995 CAGAGATGTCTGGCGTTGT 57.478 52.632 12.01 0.00 45.85 3.32
2216 2359 1.674764 CCCAGCGAGCAGAGATGTCT 61.675 60.000 0.00 0.00 0.00 3.41
2217 2360 1.227205 CCCAGCGAGCAGAGATGTC 60.227 63.158 0.00 0.00 0.00 3.06
2218 2361 2.898738 CCCAGCGAGCAGAGATGT 59.101 61.111 0.00 0.00 0.00 3.06
2219 2362 2.588314 GCCCAGCGAGCAGAGATG 60.588 66.667 0.00 0.00 0.00 2.90
2220 2363 3.859414 GGCCCAGCGAGCAGAGAT 61.859 66.667 0.00 0.00 0.00 2.75
2224 2367 4.790962 ATGTGGCCCAGCGAGCAG 62.791 66.667 0.00 0.00 0.00 4.24
2225 2368 4.783621 GATGTGGCCCAGCGAGCA 62.784 66.667 0.00 0.00 0.00 4.26
2227 2370 3.411114 ATGGATGTGGCCCAGCGAG 62.411 63.158 0.00 0.00 37.08 5.03
2228 2371 3.405093 GATGGATGTGGCCCAGCGA 62.405 63.158 0.00 0.00 37.08 4.93
2229 2372 2.903855 GATGGATGTGGCCCAGCG 60.904 66.667 0.00 0.00 37.08 5.18
2230 2373 2.520260 GGATGGATGTGGCCCAGC 60.520 66.667 0.00 0.00 39.24 4.85
2231 2374 0.826256 CATGGATGGATGTGGCCCAG 60.826 60.000 0.00 0.00 37.08 4.45
2232 2375 1.230783 CATGGATGGATGTGGCCCA 59.769 57.895 0.00 0.00 38.19 5.36
2233 2376 4.186136 CATGGATGGATGTGGCCC 57.814 61.111 0.00 0.00 0.00 5.80
2243 2386 4.453478 CGATGGAACTAATGACCATGGATG 59.547 45.833 21.47 3.94 43.30 3.51
2244 2387 4.103153 ACGATGGAACTAATGACCATGGAT 59.897 41.667 21.47 1.98 43.30 3.41
2245 2388 3.454447 ACGATGGAACTAATGACCATGGA 59.546 43.478 21.47 0.00 43.30 3.41
2246 2389 3.561310 CACGATGGAACTAATGACCATGG 59.439 47.826 11.19 11.19 43.30 3.66
2247 2390 3.561310 CCACGATGGAACTAATGACCATG 59.439 47.826 0.00 0.00 43.30 3.66
2248 2391 3.199946 ACCACGATGGAACTAATGACCAT 59.800 43.478 10.46 0.00 45.50 3.55
2249 2392 2.569853 ACCACGATGGAACTAATGACCA 59.430 45.455 10.46 0.00 40.96 4.02
2250 2393 2.936498 CACCACGATGGAACTAATGACC 59.064 50.000 10.46 0.00 40.96 4.02
2251 2394 3.596214 ACACCACGATGGAACTAATGAC 58.404 45.455 10.46 0.00 40.96 3.06
2252 2395 3.259625 TGACACCACGATGGAACTAATGA 59.740 43.478 10.46 0.00 40.96 2.57
2253 2396 3.595173 TGACACCACGATGGAACTAATG 58.405 45.455 10.46 1.16 40.96 1.90
2254 2397 3.973206 TGACACCACGATGGAACTAAT 57.027 42.857 10.46 0.00 40.96 1.73
2255 2398 3.674955 CGATGACACCACGATGGAACTAA 60.675 47.826 10.46 0.00 40.96 2.24
2256 2399 2.159296 CGATGACACCACGATGGAACTA 60.159 50.000 10.46 0.00 40.96 2.24
2257 2400 1.404181 CGATGACACCACGATGGAACT 60.404 52.381 10.46 0.00 40.96 3.01
2258 2401 0.999406 CGATGACACCACGATGGAAC 59.001 55.000 10.46 3.23 40.96 3.62
2259 2402 0.739462 GCGATGACACCACGATGGAA 60.739 55.000 10.46 0.00 40.96 3.53
2260 2403 1.153647 GCGATGACACCACGATGGA 60.154 57.895 10.46 0.00 40.96 3.41
2261 2404 1.018752 TTGCGATGACACCACGATGG 61.019 55.000 0.00 0.00 45.02 3.51
2262 2405 0.095245 GTTGCGATGACACCACGATG 59.905 55.000 0.00 0.00 0.00 3.84
2263 2406 1.019278 GGTTGCGATGACACCACGAT 61.019 55.000 0.00 0.00 0.00 3.73
2264 2407 1.666553 GGTTGCGATGACACCACGA 60.667 57.895 0.00 0.00 0.00 4.35
2265 2408 2.677003 GGGTTGCGATGACACCACG 61.677 63.158 0.00 0.00 0.00 4.94
2266 2409 2.332654 GGGGTTGCGATGACACCAC 61.333 63.158 0.31 0.00 40.41 4.16
2267 2410 2.033448 GGGGTTGCGATGACACCA 59.967 61.111 0.31 0.00 40.41 4.17
2268 2411 3.124921 CGGGGTTGCGATGACACC 61.125 66.667 0.00 0.00 37.22 4.16
2269 2412 3.799755 GCGGGGTTGCGATGACAC 61.800 66.667 0.00 0.00 0.00 3.67
2270 2413 4.015406 AGCGGGGTTGCGATGACA 62.015 61.111 0.00 0.00 40.67 3.58
2271 2414 3.499737 CAGCGGGGTTGCGATGAC 61.500 66.667 0.00 0.00 40.67 3.06
2272 2415 4.776322 CCAGCGGGGTTGCGATGA 62.776 66.667 0.00 0.00 40.67 2.92
2278 2421 3.344137 ATGGTAGCCAGCGGGGTTG 62.344 63.158 14.12 0.00 44.14 3.77
2279 2422 3.015145 ATGGTAGCCAGCGGGGTT 61.015 61.111 14.12 2.07 44.14 4.11
2281 2424 4.569180 CCATGGTAGCCAGCGGGG 62.569 72.222 2.57 0.00 36.75 5.73
2283 2426 4.488136 TGCCATGGTAGCCAGCGG 62.488 66.667 14.67 2.94 36.75 5.52
2284 2427 2.898840 CTGCCATGGTAGCCAGCG 60.899 66.667 17.48 0.00 36.75 5.18
2285 2428 3.214845 GCTGCCATGGTAGCCAGC 61.215 66.667 36.85 28.85 45.84 4.85
2290 2433 1.589993 CGACGAGCTGCCATGGTAG 60.590 63.158 24.32 24.32 0.00 3.18
2291 2434 1.033202 TACGACGAGCTGCCATGGTA 61.033 55.000 14.67 8.24 0.00 3.25
2292 2435 2.284798 CTACGACGAGCTGCCATGGT 62.285 60.000 14.67 0.00 0.00 3.55
2293 2436 1.589993 CTACGACGAGCTGCCATGG 60.590 63.158 7.63 7.63 0.00 3.66
2294 2437 2.233654 GCTACGACGAGCTGCCATG 61.234 63.158 0.00 0.00 39.50 3.66
2295 2438 2.021068 ATGCTACGACGAGCTGCCAT 62.021 55.000 16.48 3.62 43.27 4.40
2296 2439 2.613739 GATGCTACGACGAGCTGCCA 62.614 60.000 16.48 1.81 43.27 4.92
2297 2440 1.946650 GATGCTACGACGAGCTGCC 60.947 63.158 16.48 5.95 43.27 4.85
2298 2441 1.946650 GGATGCTACGACGAGCTGC 60.947 63.158 16.48 0.00 43.27 5.25
2299 2442 1.299468 GGGATGCTACGACGAGCTG 60.299 63.158 16.48 0.00 43.27 4.24
2300 2443 2.491022 GGGGATGCTACGACGAGCT 61.491 63.158 16.48 0.00 43.27 4.09
2301 2444 2.027751 GGGGATGCTACGACGAGC 59.972 66.667 0.00 7.10 43.16 5.03
2302 2445 1.065928 GTGGGGATGCTACGACGAG 59.934 63.158 0.00 0.00 0.00 4.18
2303 2446 2.420568 GGTGGGGATGCTACGACGA 61.421 63.158 0.00 0.00 0.00 4.20
2304 2447 2.106332 GGTGGGGATGCTACGACG 59.894 66.667 0.00 0.00 0.00 5.12
2305 2448 2.106332 CGGTGGGGATGCTACGAC 59.894 66.667 0.00 0.00 0.00 4.34
2306 2449 3.151710 CCGGTGGGGATGCTACGA 61.152 66.667 0.00 0.00 38.47 3.43
2307 2450 3.441011 GACCGGTGGGGATGCTACG 62.441 68.421 14.63 0.00 39.97 3.51
2308 2451 1.696097 ATGACCGGTGGGGATGCTAC 61.696 60.000 14.63 0.00 39.97 3.58
2309 2452 0.105401 TATGACCGGTGGGGATGCTA 60.105 55.000 14.63 0.00 39.97 3.49
2310 2453 0.986019 TTATGACCGGTGGGGATGCT 60.986 55.000 14.63 0.00 39.97 3.79
2311 2454 0.106918 TTTATGACCGGTGGGGATGC 60.107 55.000 14.63 0.00 39.97 3.91
2312 2455 2.021457 GTTTTATGACCGGTGGGGATG 58.979 52.381 14.63 0.00 39.97 3.51
2313 2456 1.064240 GGTTTTATGACCGGTGGGGAT 60.064 52.381 14.63 0.38 39.97 3.85
2314 2457 0.328926 GGTTTTATGACCGGTGGGGA 59.671 55.000 14.63 0.00 39.97 4.81
2315 2458 0.681887 GGGTTTTATGACCGGTGGGG 60.682 60.000 14.63 0.00 40.75 4.96
2316 2459 0.038455 TGGGTTTTATGACCGGTGGG 59.962 55.000 14.63 0.00 40.75 4.61
2317 2460 1.170442 GTGGGTTTTATGACCGGTGG 58.830 55.000 14.63 0.00 40.75 4.61
2318 2461 1.170442 GGTGGGTTTTATGACCGGTG 58.830 55.000 14.63 0.00 40.75 4.94
2319 2462 0.321830 CGGTGGGTTTTATGACCGGT 60.322 55.000 6.92 6.92 46.13 5.28
2320 2463 2.473457 CGGTGGGTTTTATGACCGG 58.527 57.895 0.00 0.00 46.13 5.28
2322 2465 1.092348 GAGCGGTGGGTTTTATGACC 58.908 55.000 0.00 0.00 39.04 4.02
2323 2466 0.725117 CGAGCGGTGGGTTTTATGAC 59.275 55.000 0.00 0.00 0.00 3.06
2324 2467 0.609151 TCGAGCGGTGGGTTTTATGA 59.391 50.000 0.00 0.00 0.00 2.15
2325 2468 0.725117 GTCGAGCGGTGGGTTTTATG 59.275 55.000 0.00 0.00 0.00 1.90
2326 2469 0.322322 TGTCGAGCGGTGGGTTTTAT 59.678 50.000 0.00 0.00 0.00 1.40
2327 2470 0.322322 ATGTCGAGCGGTGGGTTTTA 59.678 50.000 0.00 0.00 0.00 1.52
2328 2471 0.536460 AATGTCGAGCGGTGGGTTTT 60.536 50.000 0.00 0.00 0.00 2.43
2329 2472 1.072505 AATGTCGAGCGGTGGGTTT 59.927 52.632 0.00 0.00 0.00 3.27
2330 2473 1.671054 CAATGTCGAGCGGTGGGTT 60.671 57.895 0.00 0.00 0.00 4.11
2331 2474 2.047274 CAATGTCGAGCGGTGGGT 60.047 61.111 0.00 0.00 0.00 4.51
2332 2475 3.499737 GCAATGTCGAGCGGTGGG 61.500 66.667 0.00 0.00 0.00 4.61
2333 2476 2.040213 GATGCAATGTCGAGCGGTGG 62.040 60.000 0.00 0.00 0.00 4.61
2334 2477 1.349627 GATGCAATGTCGAGCGGTG 59.650 57.895 0.00 0.00 0.00 4.94
2335 2478 0.462581 ATGATGCAATGTCGAGCGGT 60.463 50.000 0.00 0.00 0.00 5.68
2336 2479 0.234106 GATGATGCAATGTCGAGCGG 59.766 55.000 0.00 0.00 0.00 5.52
2337 2480 0.932399 TGATGATGCAATGTCGAGCG 59.068 50.000 0.00 0.00 0.00 5.03
2338 2481 2.546789 TGATGATGATGCAATGTCGAGC 59.453 45.455 0.00 0.00 0.00 5.03
2339 2482 3.364068 GCTGATGATGATGCAATGTCGAG 60.364 47.826 0.00 0.00 0.00 4.04
2340 2483 2.546789 GCTGATGATGATGCAATGTCGA 59.453 45.455 0.00 0.00 0.00 4.20
2341 2484 2.661979 CGCTGATGATGATGCAATGTCG 60.662 50.000 0.00 0.00 0.00 4.35
2342 2485 2.350484 CCGCTGATGATGATGCAATGTC 60.350 50.000 0.00 0.00 0.00 3.06
2343 2486 1.607148 CCGCTGATGATGATGCAATGT 59.393 47.619 0.00 0.00 0.00 2.71
2344 2487 1.666023 GCCGCTGATGATGATGCAATG 60.666 52.381 0.00 0.00 0.00 2.82
2345 2488 0.596577 GCCGCTGATGATGATGCAAT 59.403 50.000 0.00 0.00 0.00 3.56
2346 2489 1.778027 CGCCGCTGATGATGATGCAA 61.778 55.000 0.00 0.00 0.00 4.08
2347 2490 2.248835 CGCCGCTGATGATGATGCA 61.249 57.895 0.00 0.00 0.00 3.96
2348 2491 2.167808 GACGCCGCTGATGATGATGC 62.168 60.000 0.00 0.00 0.00 3.91
2349 2492 1.858041 GACGCCGCTGATGATGATG 59.142 57.895 0.00 0.00 0.00 3.07
2350 2493 1.662760 CGACGCCGCTGATGATGAT 60.663 57.895 0.00 0.00 0.00 2.45
2351 2494 2.278792 CGACGCCGCTGATGATGA 60.279 61.111 0.00 0.00 0.00 2.92
2370 2513 3.047280 TGTTGCGCGTCCATGGAC 61.047 61.111 31.59 31.59 41.40 4.02
2371 2514 3.047280 GTGTTGCGCGTCCATGGA 61.047 61.111 11.44 11.44 0.00 3.41
2372 2515 4.101790 GGTGTTGCGCGTCCATGG 62.102 66.667 8.43 4.97 0.00 3.66
2373 2516 4.101790 GGGTGTTGCGCGTCCATG 62.102 66.667 8.43 0.00 0.00 3.66
2392 2535 4.803426 GGGCAGTGAGGACGCGAG 62.803 72.222 15.93 0.00 0.00 5.03
2394 2537 4.379243 AAGGGCAGTGAGGACGCG 62.379 66.667 3.53 3.53 0.00 6.01
2395 2538 2.743928 CAAGGGCAGTGAGGACGC 60.744 66.667 0.00 0.00 0.00 5.19
2396 2539 1.669115 CACAAGGGCAGTGAGGACG 60.669 63.158 0.00 0.00 39.30 4.79
2397 2540 1.968540 GCACAAGGGCAGTGAGGAC 60.969 63.158 7.95 0.00 39.30 3.85
2398 2541 2.431683 GCACAAGGGCAGTGAGGA 59.568 61.111 7.95 0.00 39.30 3.71
2399 2542 2.113774 TGCACAAGGGCAGTGAGG 59.886 61.111 7.95 0.00 39.25 3.86


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

AutoCloner maintained by Alex Coulton.