Multiple sequence alignment - TraesCS5B01G205200

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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 TraesCS5B01G205200 chr5B 100.000 3252 0 0 1 3252 373527697 373524446 0.000000e+00 6006.0
1 TraesCS5B01G205200 chr5B 85.859 99 10 4 129 224 680768288 680768191 5.740000e-18 102.0
2 TraesCS5B01G205200 chr5D 93.543 1905 80 14 1 1884 322181478 322179596 0.000000e+00 2796.0
3 TraesCS5B01G205200 chr5D 87.333 821 68 20 2055 2858 322179599 322178798 0.000000e+00 907.0
4 TraesCS5B01G205200 chr5D 94.382 178 10 0 1883 2060 75415156 75415333 1.150000e-69 274.0
5 TraesCS5B01G205200 chr5D 92.553 188 13 1 1872 2059 20965452 20965638 5.350000e-68 268.0
6 TraesCS5B01G205200 chr5D 89.552 201 11 1 3062 3252 322178211 322178011 2.510000e-61 246.0
7 TraesCS5B01G205200 chr5D 80.328 183 29 6 11 191 9495480 9495303 7.320000e-27 132.0
8 TraesCS5B01G205200 chr5D 78.616 159 29 4 323 478 478806130 478806286 2.060000e-17 100.0
9 TraesCS5B01G205200 chr5A 90.696 1236 74 14 654 1880 417314034 417312831 0.000000e+00 1607.0
10 TraesCS5B01G205200 chr5A 88.363 1057 81 27 2059 3081 417312826 417311778 0.000000e+00 1232.0
11 TraesCS5B01G205200 chr2D 94.350 177 10 0 1883 2059 503882026 503882202 4.130000e-69 272.0
12 TraesCS5B01G205200 chr2D 94.253 174 10 0 1879 2052 458715801 458715974 1.920000e-67 267.0
13 TraesCS5B01G205200 chr2D 84.043 94 14 1 324 416 586594864 586594957 4.470000e-14 89.8
14 TraesCS5B01G205200 chr2D 97.297 37 1 0 556 592 412830535 412830571 2.710000e-06 63.9
15 TraesCS5B01G205200 chr2D 92.857 42 1 2 146 186 618654790 618654830 3.500000e-05 60.2
16 TraesCS5B01G205200 chr3D 94.767 172 9 0 1884 2055 240009470 240009299 5.350000e-68 268.0
17 TraesCS5B01G205200 chr3D 93.750 176 11 0 1883 2058 253591563 253591388 6.920000e-67 265.0
18 TraesCS5B01G205200 chr1D 94.767 172 9 0 1884 2055 326157573 326157744 5.350000e-68 268.0
19 TraesCS5B01G205200 chr1D 79.630 108 20 2 145 250 357460974 357460867 3.480000e-10 76.8
20 TraesCS5B01G205200 chr3B 93.785 177 10 1 1883 2059 670148728 670148553 6.920000e-67 265.0
21 TraesCS5B01G205200 chr7D 93.220 177 12 0 1879 2055 307433381 307433557 8.950000e-66 261.0
22 TraesCS5B01G205200 chr7D 85.263 95 13 1 323 416 526381892 526381986 2.670000e-16 97.1
23 TraesCS5B01G205200 chr4B 88.350 103 11 1 145 246 13392686 13392788 4.410000e-24 122.0
24 TraesCS5B01G205200 chr4B 77.143 175 27 6 323 495 26483604 26483441 4.470000e-14 89.8
25 TraesCS5B01G205200 chr7A 85.859 99 10 3 321 417 29287906 29287810 5.740000e-18 102.0
26 TraesCS5B01G205200 chr6A 89.041 73 8 0 149 221 449394705 449394633 1.240000e-14 91.6
27 TraesCS5B01G205200 chr6A 87.838 74 8 1 149 221 449389477 449389404 5.780000e-13 86.1
28 TraesCS5B01G205200 chr7B 80.000 120 16 7 313 429 677713976 677713862 7.480000e-12 82.4
29 TraesCS5B01G205200 chr3A 82.828 99 9 7 323 417 63826693 63826787 7.480000e-12 82.4
30 TraesCS5B01G205200 chr6B 76.250 160 27 7 323 479 380549915 380549764 1.250000e-09 75.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5B01G205200 chr5B 373524446 373527697 3251 True 6006.000000 6006 100.000000 1 3252 1 chr5B.!!$R1 3251
1 TraesCS5B01G205200 chr5D 322178011 322181478 3467 True 1316.333333 2796 90.142667 1 3252 3 chr5D.!!$R2 3251
2 TraesCS5B01G205200 chr5A 417311778 417314034 2256 True 1419.500000 1607 89.529500 654 3081 2 chr5A.!!$R1 2427

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
436 441 0.034059 GTCACTGTACACTGGCTGCT 59.966 55.0 0.0 0.0 0.0 4.24 F
630 635 0.453793 TTGGTCCACTGCAAACAACG 59.546 50.0 0.0 0.0 0.0 4.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1706 1736 0.106918 TCTTGGGTTGGCGTGTTCTT 60.107 50.0 0.00 0.0 0.0 2.52 R
2579 2660 0.033228 CGCTAAGATGGAGGCTCAGG 59.967 60.0 17.69 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
23 24 6.168164 GTAATGTTAAAAATCCGACGTCCA 57.832 37.500 10.58 0.00 0.00 4.02
43 44 6.402011 CGTCCAATTTTTAACCATGGCAAATC 60.402 38.462 13.04 0.00 0.00 2.17
45 46 7.121020 GTCCAATTTTTAACCATGGCAAATCAT 59.879 33.333 13.04 5.41 0.00 2.45
113 114 0.899720 ACAAGCATGGCAAATCCTGG 59.100 50.000 0.00 0.00 35.26 4.45
122 123 2.531522 GCAAATCCTGGCAAAACACT 57.468 45.000 0.00 0.00 0.00 3.55
154 155 5.920193 AAAGGATTTGCTATGCTTGCTAA 57.080 34.783 6.85 0.00 36.60 3.09
156 157 5.511234 AGGATTTGCTATGCTTGCTAAAG 57.489 39.130 0.00 0.00 36.41 1.85
159 160 6.153340 AGGATTTGCTATGCTTGCTAAAGAAA 59.847 34.615 0.00 0.00 35.19 2.52
176 177 5.613358 AAGAAAATTGTCATCCTCACGAC 57.387 39.130 0.00 0.00 0.00 4.34
187 188 7.156000 TGTCATCCTCACGACAACTAAATTTA 58.844 34.615 0.00 0.00 39.14 1.40
257 259 5.768317 TGTAGCGAAATCTTTTCTTTTGGG 58.232 37.500 0.00 0.00 0.00 4.12
258 260 4.937201 AGCGAAATCTTTTCTTTTGGGT 57.063 36.364 0.00 0.00 0.00 4.51
272 274 6.778834 TCTTTTGGGTAGTCATGTATCGTA 57.221 37.500 0.00 0.00 0.00 3.43
277 279 6.778834 TGGGTAGTCATGTATCGTAAAGAA 57.221 37.500 0.00 0.00 0.00 2.52
308 310 8.862325 TTAGAACACAATACATTTGAGGATGT 57.138 30.769 0.00 0.00 42.57 3.06
395 400 3.938963 CCAACTGCCTTCGTGTATTGTAT 59.061 43.478 0.00 0.00 0.00 2.29
400 405 6.817184 ACTGCCTTCGTGTATTGTATAGAAT 58.183 36.000 0.29 0.29 0.00 2.40
406 411 9.181805 CCTTCGTGTATTGTATAGAATACTGTG 57.818 37.037 25.01 17.30 38.91 3.66
436 441 0.034059 GTCACTGTACACTGGCTGCT 59.966 55.000 0.00 0.00 0.00 4.24
438 443 1.151668 CACTGTACACTGGCTGCTTC 58.848 55.000 0.00 0.00 0.00 3.86
441 446 1.741770 GTACACTGGCTGCTTCGGG 60.742 63.158 0.00 0.00 0.00 5.14
442 447 2.214216 TACACTGGCTGCTTCGGGT 61.214 57.895 0.00 0.00 0.00 5.28
508 513 7.758980 GCACATACTCATCTCTATGAACATAGG 59.241 40.741 17.97 11.01 41.57 2.57
509 514 8.801299 CACATACTCATCTCTATGAACATAGGT 58.199 37.037 17.97 11.11 41.57 3.08
534 539 4.238761 TCATATTCGACCGAACATCTCC 57.761 45.455 7.02 0.00 36.91 3.71
539 544 1.211212 TCGACCGAACATCTCCTCCTA 59.789 52.381 0.00 0.00 0.00 2.94
609 614 6.183360 GCAAGCACTGATGTTAAAGTCTAGAG 60.183 42.308 0.00 0.00 0.00 2.43
630 635 0.453793 TTGGTCCACTGCAAACAACG 59.546 50.000 0.00 0.00 0.00 4.10
634 639 2.292292 GGTCCACTGCAAACAACGTAAT 59.708 45.455 0.00 0.00 0.00 1.89
652 657 2.469274 ATCATCTTGAGCTATGCCCG 57.531 50.000 0.00 0.00 0.00 6.13
836 841 1.034838 AGTCCTGCTACCTCGCTCTG 61.035 60.000 0.00 0.00 0.00 3.35
855 860 1.206849 TGTGCATACGCTTCCATCAGA 59.793 47.619 0.00 0.00 39.64 3.27
885 890 9.283768 TGGCTTCCATATGTGTAGTATAAATTG 57.716 33.333 1.24 0.00 0.00 2.32
954 959 7.772757 CCAACTTTTAGCCTTCTTCAGAGATAT 59.227 37.037 0.00 0.00 0.00 1.63
955 960 9.823647 CAACTTTTAGCCTTCTTCAGAGATATA 57.176 33.333 0.00 0.00 0.00 0.86
964 969 7.179338 GCCTTCTTCAGAGATATATAGTTCCCA 59.821 40.741 0.00 0.00 0.00 4.37
969 980 9.650539 CTTCAGAGATATATAGTTCCCACATTG 57.349 37.037 0.00 0.00 0.00 2.82
971 982 7.235399 TCAGAGATATATAGTTCCCACATTGCA 59.765 37.037 0.00 0.00 0.00 4.08
1316 1346 8.450578 TGTTGAAATCTGAACTCTTATGTGTT 57.549 30.769 0.00 0.00 33.26 3.32
1317 1347 8.902806 TGTTGAAATCTGAACTCTTATGTGTTT 58.097 29.630 0.00 0.00 31.09 2.83
1318 1348 9.736023 GTTGAAATCTGAACTCTTATGTGTTTT 57.264 29.630 0.00 0.00 31.09 2.43
1320 1350 9.734620 TGAAATCTGAACTCTTATGTGTTTTTG 57.265 29.630 0.00 0.00 31.09 2.44
1321 1351 9.736023 GAAATCTGAACTCTTATGTGTTTTTGT 57.264 29.630 0.00 0.00 31.09 2.83
1322 1352 9.520204 AAATCTGAACTCTTATGTGTTTTTGTG 57.480 29.630 0.00 0.00 31.09 3.33
1323 1353 7.624360 TCTGAACTCTTATGTGTTTTTGTGT 57.376 32.000 0.00 0.00 31.09 3.72
1407 1437 2.038659 GGACATCAAGGAGGAGGAGAG 58.961 57.143 0.00 0.00 0.00 3.20
1432 1462 2.628178 CGTCAAGATATGGCTCCAGGTA 59.372 50.000 0.00 0.00 0.00 3.08
1702 1732 1.070134 GGGTTTGGGAAGAAAAGCACC 59.930 52.381 0.00 0.00 36.88 5.01
1703 1733 1.760029 GGTTTGGGAAGAAAAGCACCA 59.240 47.619 0.00 0.00 35.58 4.17
1706 1736 0.260230 TGGGAAGAAAAGCACCACCA 59.740 50.000 0.00 0.00 0.00 4.17
1718 1748 1.077357 ACCACCAAGAACACGCCAA 60.077 52.632 0.00 0.00 0.00 4.52
1732 1762 1.832167 GCCAACCCAAGACAAGCCA 60.832 57.895 0.00 0.00 0.00 4.75
1748 1778 0.038251 GCCAAGCTTAAACAGTGCCC 60.038 55.000 0.00 0.00 0.00 5.36
1749 1779 1.327303 CCAAGCTTAAACAGTGCCCA 58.673 50.000 0.00 0.00 0.00 5.36
1750 1780 1.686052 CCAAGCTTAAACAGTGCCCAA 59.314 47.619 0.00 0.00 0.00 4.12
1751 1781 2.288395 CCAAGCTTAAACAGTGCCCAAG 60.288 50.000 0.00 0.00 0.00 3.61
1752 1782 1.620822 AGCTTAAACAGTGCCCAAGG 58.379 50.000 0.00 0.00 0.00 3.61
1753 1783 1.144913 AGCTTAAACAGTGCCCAAGGA 59.855 47.619 0.00 0.00 0.00 3.36
1769 1799 1.377987 GGACAAGGTAATGGCGCCA 60.378 57.895 34.80 34.80 0.00 5.69
1777 1807 2.036006 TAATGGCGCCACACCGAAC 61.036 57.895 35.50 0.00 0.00 3.95
1834 1864 3.620761 CGTTTTTCCCTTTTCGTGTACC 58.379 45.455 0.00 0.00 0.00 3.34
1846 1887 3.443145 TCGTGTACCCATTTCCCATTT 57.557 42.857 0.00 0.00 0.00 2.32
1863 1904 8.438676 TTCCCATTTTTCTTTTGCGAAATAAA 57.561 26.923 0.00 2.76 33.33 1.40
1871 1912 8.635877 TTTCTTTTGCGAAATAAACAGCTTAA 57.364 26.923 0.00 0.00 0.00 1.85
1884 1925 9.696917 AATAAACAGCTTAAGTTTGAAATGAGG 57.303 29.630 13.74 0.00 39.36 3.86
1885 1926 5.712152 ACAGCTTAAGTTTGAAATGAGGG 57.288 39.130 13.74 0.00 0.00 4.30
1886 1927 4.524328 ACAGCTTAAGTTTGAAATGAGGGG 59.476 41.667 13.74 0.00 0.00 4.79
1887 1928 4.082026 CAGCTTAAGTTTGAAATGAGGGGG 60.082 45.833 4.02 0.00 0.00 5.40
1888 1929 3.832490 GCTTAAGTTTGAAATGAGGGGGT 59.168 43.478 4.02 0.00 0.00 4.95
1889 1930 4.321974 GCTTAAGTTTGAAATGAGGGGGTG 60.322 45.833 4.02 0.00 0.00 4.61
1890 1931 3.328535 AAGTTTGAAATGAGGGGGTGT 57.671 42.857 0.00 0.00 0.00 4.16
1891 1932 3.328535 AGTTTGAAATGAGGGGGTGTT 57.671 42.857 0.00 0.00 0.00 3.32
1892 1933 3.653164 AGTTTGAAATGAGGGGGTGTTT 58.347 40.909 0.00 0.00 0.00 2.83
1893 1934 3.387699 AGTTTGAAATGAGGGGGTGTTTG 59.612 43.478 0.00 0.00 0.00 2.93
1894 1935 2.008242 TGAAATGAGGGGGTGTTTGG 57.992 50.000 0.00 0.00 0.00 3.28
1895 1936 1.219213 TGAAATGAGGGGGTGTTTGGT 59.781 47.619 0.00 0.00 0.00 3.67
1896 1937 2.325484 GAAATGAGGGGGTGTTTGGTT 58.675 47.619 0.00 0.00 0.00 3.67
1897 1938 2.009681 AATGAGGGGGTGTTTGGTTC 57.990 50.000 0.00 0.00 0.00 3.62
1898 1939 0.856982 ATGAGGGGGTGTTTGGTTCA 59.143 50.000 0.00 0.00 0.00 3.18
1899 1940 0.184933 TGAGGGGGTGTTTGGTTCAG 59.815 55.000 0.00 0.00 0.00 3.02
1900 1941 0.539669 GAGGGGGTGTTTGGTTCAGG 60.540 60.000 0.00 0.00 0.00 3.86
1901 1942 1.533033 GGGGGTGTTTGGTTCAGGG 60.533 63.158 0.00 0.00 0.00 4.45
1902 1943 1.539665 GGGGTGTTTGGTTCAGGGA 59.460 57.895 0.00 0.00 0.00 4.20
1903 1944 0.826256 GGGGTGTTTGGTTCAGGGAC 60.826 60.000 0.00 0.00 0.00 4.46
1904 1945 0.185175 GGGTGTTTGGTTCAGGGACT 59.815 55.000 0.00 0.00 43.88 3.85
1905 1946 1.411074 GGGTGTTTGGTTCAGGGACTT 60.411 52.381 0.00 0.00 34.60 3.01
1906 1947 2.384828 GGTGTTTGGTTCAGGGACTTT 58.615 47.619 0.00 0.00 34.60 2.66
1907 1948 2.764010 GGTGTTTGGTTCAGGGACTTTT 59.236 45.455 0.00 0.00 34.60 2.27
1908 1949 3.196901 GGTGTTTGGTTCAGGGACTTTTT 59.803 43.478 0.00 0.00 34.60 1.94
1909 1950 4.403113 GGTGTTTGGTTCAGGGACTTTTTA 59.597 41.667 0.00 0.00 34.60 1.52
1910 1951 5.451381 GGTGTTTGGTTCAGGGACTTTTTAG 60.451 44.000 0.00 0.00 34.60 1.85
1911 1952 5.126545 GTGTTTGGTTCAGGGACTTTTTAGT 59.873 40.000 0.00 0.00 34.60 2.24
1912 1953 5.358725 TGTTTGGTTCAGGGACTTTTTAGTC 59.641 40.000 0.00 0.00 34.60 2.59
1913 1954 5.382664 TTGGTTCAGGGACTTTTTAGTCT 57.617 39.130 5.40 0.00 34.60 3.24
1914 1955 4.969484 TGGTTCAGGGACTTTTTAGTCTC 58.031 43.478 5.40 1.37 39.50 3.36
1915 1956 4.410883 TGGTTCAGGGACTTTTTAGTCTCA 59.589 41.667 7.82 0.00 41.56 3.27
1916 1957 4.998033 GGTTCAGGGACTTTTTAGTCTCAG 59.002 45.833 7.82 0.09 41.56 3.35
1917 1958 5.221661 GGTTCAGGGACTTTTTAGTCTCAGA 60.222 44.000 7.82 2.47 41.56 3.27
1918 1959 5.730296 TCAGGGACTTTTTAGTCTCAGAG 57.270 43.478 7.82 0.00 41.56 3.35
1919 1960 5.394738 TCAGGGACTTTTTAGTCTCAGAGA 58.605 41.667 7.82 0.00 41.56 3.10
1920 1961 5.244178 TCAGGGACTTTTTAGTCTCAGAGAC 59.756 44.000 21.47 21.47 41.56 3.36
1922 1963 6.434652 CAGGGACTTTTTAGTCTCAGAGACTA 59.565 42.308 29.49 29.49 46.80 2.59
1923 1964 6.661805 AGGGACTTTTTAGTCTCAGAGACTAG 59.338 42.308 30.60 25.27 46.53 2.57
1924 1965 7.476520 AGGGACTTTTTAGTCTCAGAGACTAGA 60.477 40.741 30.60 26.25 46.53 2.43
1934 1975 6.988522 GTCTCAGAGACTAGAAAAAGTTCCT 58.011 40.000 21.67 0.00 41.88 3.36
1935 1976 8.113173 GTCTCAGAGACTAGAAAAAGTTCCTA 57.887 38.462 21.67 0.00 41.88 2.94
1936 1977 8.241367 GTCTCAGAGACTAGAAAAAGTTCCTAG 58.759 40.741 21.67 0.00 41.88 3.02
1937 1978 8.164733 TCTCAGAGACTAGAAAAAGTTCCTAGA 58.835 37.037 0.00 0.00 33.92 2.43
1938 1979 8.707796 TCAGAGACTAGAAAAAGTTCCTAGAA 57.292 34.615 0.00 0.00 33.92 2.10
1939 1980 9.144298 TCAGAGACTAGAAAAAGTTCCTAGAAA 57.856 33.333 0.00 0.00 33.92 2.52
1940 1981 9.198837 CAGAGACTAGAAAAAGTTCCTAGAAAC 57.801 37.037 0.00 0.00 33.92 2.78
1941 1982 8.369424 AGAGACTAGAAAAAGTTCCTAGAAACC 58.631 37.037 0.00 0.00 33.92 3.27
1942 1983 8.030913 AGACTAGAAAAAGTTCCTAGAAACCA 57.969 34.615 0.00 0.00 33.92 3.67
1943 1984 8.491958 AGACTAGAAAAAGTTCCTAGAAACCAA 58.508 33.333 0.00 0.00 33.92 3.67
1944 1985 9.117183 GACTAGAAAAAGTTCCTAGAAACCAAA 57.883 33.333 0.00 0.00 33.92 3.28
1945 1986 8.900781 ACTAGAAAAAGTTCCTAGAAACCAAAC 58.099 33.333 0.00 0.00 33.92 2.93
1946 1987 6.792326 AGAAAAAGTTCCTAGAAACCAAACG 58.208 36.000 0.00 0.00 33.92 3.60
1947 1988 5.509716 AAAAGTTCCTAGAAACCAAACGG 57.490 39.130 0.00 0.00 0.00 4.44
1948 1989 3.136009 AGTTCCTAGAAACCAAACGGG 57.864 47.619 0.00 0.00 44.81 5.28
1949 1990 2.707257 AGTTCCTAGAAACCAAACGGGA 59.293 45.455 0.00 0.00 41.15 5.14
1950 1991 3.072211 GTTCCTAGAAACCAAACGGGAG 58.928 50.000 0.00 0.00 41.15 4.30
1951 1992 1.626825 TCCTAGAAACCAAACGGGAGG 59.373 52.381 0.00 0.00 41.15 4.30
1952 1993 1.626825 CCTAGAAACCAAACGGGAGGA 59.373 52.381 0.00 0.00 41.15 3.71
1953 1994 2.039348 CCTAGAAACCAAACGGGAGGAA 59.961 50.000 0.00 0.00 41.15 3.36
1954 1995 1.977056 AGAAACCAAACGGGAGGAAC 58.023 50.000 0.00 0.00 41.15 3.62
1956 1997 2.092049 AGAAACCAAACGGGAGGAACTT 60.092 45.455 0.00 0.00 41.55 2.66
1957 1998 2.447408 AACCAAACGGGAGGAACTTT 57.553 45.000 0.00 0.00 41.55 2.66
1958 1999 2.447408 ACCAAACGGGAGGAACTTTT 57.553 45.000 0.00 0.00 41.55 2.27
1959 2000 2.742348 ACCAAACGGGAGGAACTTTTT 58.258 42.857 0.00 0.00 41.55 1.94
1960 2001 2.691526 ACCAAACGGGAGGAACTTTTTC 59.308 45.455 0.00 0.00 41.55 2.29
1961 2002 2.956333 CCAAACGGGAGGAACTTTTTCT 59.044 45.455 0.00 0.00 41.55 2.52
1962 2003 4.139038 CCAAACGGGAGGAACTTTTTCTA 58.861 43.478 0.00 0.00 41.55 2.10
1963 2004 4.023450 CCAAACGGGAGGAACTTTTTCTAC 60.023 45.833 0.00 0.00 41.55 2.59
1964 2005 4.426736 AACGGGAGGAACTTTTTCTACA 57.573 40.909 0.00 0.00 41.55 2.74
1965 2006 4.426736 ACGGGAGGAACTTTTTCTACAA 57.573 40.909 0.00 0.00 41.55 2.41
1966 2007 4.981812 ACGGGAGGAACTTTTTCTACAAT 58.018 39.130 0.00 0.00 41.55 2.71
1967 2008 4.760204 ACGGGAGGAACTTTTTCTACAATG 59.240 41.667 0.00 0.00 41.55 2.82
1968 2009 5.001232 CGGGAGGAACTTTTTCTACAATGA 58.999 41.667 0.00 0.00 41.55 2.57
1969 2010 5.648092 CGGGAGGAACTTTTTCTACAATGAT 59.352 40.000 0.00 0.00 41.55 2.45
1970 2011 6.151144 CGGGAGGAACTTTTTCTACAATGATT 59.849 38.462 0.00 0.00 41.55 2.57
1971 2012 7.335924 CGGGAGGAACTTTTTCTACAATGATTA 59.664 37.037 0.00 0.00 41.55 1.75
1972 2013 8.678199 GGGAGGAACTTTTTCTACAATGATTAG 58.322 37.037 0.00 0.00 41.55 1.73
1973 2014 9.449719 GGAGGAACTTTTTCTACAATGATTAGA 57.550 33.333 0.00 0.00 41.55 2.10
1988 2029 9.442047 ACAATGATTAGAAAAAGACTCTACTGG 57.558 33.333 0.00 0.00 0.00 4.00
1989 2030 9.658799 CAATGATTAGAAAAAGACTCTACTGGA 57.341 33.333 0.00 0.00 0.00 3.86
1990 2031 9.883142 AATGATTAGAAAAAGACTCTACTGGAG 57.117 33.333 0.00 0.00 46.87 3.86
1991 2032 8.651589 TGATTAGAAAAAGACTCTACTGGAGA 57.348 34.615 0.00 0.00 44.45 3.71
2039 2080 8.751302 GACTAGAAAAAGTCCTAGAACTTCTG 57.249 38.462 0.00 0.00 40.06 3.02
2040 2081 8.480133 ACTAGAAAAAGTCCTAGAACTTCTGA 57.520 34.615 0.00 0.00 38.52 3.27
2041 2082 8.925338 ACTAGAAAAAGTCCTAGAACTTCTGAA 58.075 33.333 0.00 0.00 38.52 3.02
2042 2083 9.198837 CTAGAAAAAGTCCTAGAACTTCTGAAC 57.801 37.037 0.00 0.00 38.52 3.18
2043 2084 6.993308 AGAAAAAGTCCTAGAACTTCTGAACC 59.007 38.462 0.00 0.00 38.52 3.62
2044 2085 5.888982 AAAGTCCTAGAACTTCTGAACCA 57.111 39.130 0.00 0.00 38.52 3.67
2045 2086 5.888982 AAGTCCTAGAACTTCTGAACCAA 57.111 39.130 1.17 0.00 34.37 3.67
2046 2087 5.888982 AGTCCTAGAACTTCTGAACCAAA 57.111 39.130 1.17 0.00 0.00 3.28
2047 2088 5.612351 AGTCCTAGAACTTCTGAACCAAAC 58.388 41.667 1.17 0.00 0.00 2.93
2048 2089 5.130477 AGTCCTAGAACTTCTGAACCAAACA 59.870 40.000 1.17 0.00 0.00 2.83
2049 2090 5.236695 GTCCTAGAACTTCTGAACCAAACAC 59.763 44.000 1.17 0.00 0.00 3.32
2050 2091 4.515567 CCTAGAACTTCTGAACCAAACACC 59.484 45.833 1.17 0.00 0.00 4.16
2051 2092 3.288092 AGAACTTCTGAACCAAACACCC 58.712 45.455 0.00 0.00 0.00 4.61
2052 2093 2.067365 ACTTCTGAACCAAACACCCC 57.933 50.000 0.00 0.00 0.00 4.95
2053 2094 1.328279 CTTCTGAACCAAACACCCCC 58.672 55.000 0.00 0.00 0.00 5.40
2054 2095 0.930726 TTCTGAACCAAACACCCCCT 59.069 50.000 0.00 0.00 0.00 4.79
2055 2096 0.184933 TCTGAACCAAACACCCCCTG 59.815 55.000 0.00 0.00 0.00 4.45
2056 2097 0.184933 CTGAACCAAACACCCCCTGA 59.815 55.000 0.00 0.00 0.00 3.86
2057 2098 0.631753 TGAACCAAACACCCCCTGAA 59.368 50.000 0.00 0.00 0.00 3.02
2070 2111 0.179048 CCCTGAATGATGCACCGCTA 60.179 55.000 0.00 0.00 0.00 4.26
2113 2154 4.277174 TGTGCGTATGGAGATTGTTTGTTT 59.723 37.500 0.00 0.00 0.00 2.83
2135 2176 9.554724 TGTTTAAAATTGAGCTCTTTTATAGCG 57.445 29.630 16.19 0.00 44.87 4.26
2302 2349 2.197605 TCCACGACCACGAGCTTCA 61.198 57.895 0.00 0.00 42.66 3.02
2303 2350 1.300620 CCACGACCACGAGCTTCAA 60.301 57.895 0.00 0.00 42.66 2.69
2315 2362 1.268079 GAGCTTCAACTTCAAGGGCAC 59.732 52.381 0.00 0.00 0.00 5.01
2328 2375 1.937191 AGGGCACGATTTGGGAAAAT 58.063 45.000 0.00 0.00 0.00 1.82
2331 2378 1.731709 GGCACGATTTGGGAAAATTGC 59.268 47.619 0.00 0.35 0.00 3.56
2334 2381 2.916716 CACGATTTGGGAAAATTGCGAG 59.083 45.455 0.00 0.00 0.00 5.03
2340 2389 0.108662 GGGAAAATTGCGAGCCAAGG 60.109 55.000 0.00 0.00 36.76 3.61
2356 2405 2.096496 CCAAGGCGCTAAGAAGTTGATG 59.904 50.000 7.64 0.00 0.00 3.07
2357 2406 1.373570 AGGCGCTAAGAAGTTGATGC 58.626 50.000 7.64 0.00 0.00 3.91
2358 2407 1.086696 GGCGCTAAGAAGTTGATGCA 58.913 50.000 7.64 0.00 0.00 3.96
2359 2408 1.202076 GGCGCTAAGAAGTTGATGCAC 60.202 52.381 7.64 0.00 0.00 4.57
2371 2445 0.249826 TGATGCACTGCTCGTTGTGA 60.250 50.000 1.98 0.00 36.38 3.58
2376 2450 0.110509 CACTGCTCGTTGTGATGTGC 60.111 55.000 0.00 0.00 36.38 4.57
2382 2456 1.660607 CTCGTTGTGATGTGCGCTATT 59.339 47.619 9.73 0.00 0.00 1.73
2385 2459 2.347150 CGTTGTGATGTGCGCTATTGTA 59.653 45.455 9.73 0.00 0.00 2.41
2387 2461 4.518217 GTTGTGATGTGCGCTATTGTATC 58.482 43.478 9.73 4.24 0.00 2.24
2398 2472 5.103000 GCGCTATTGTATCCGTATGAGATT 58.897 41.667 0.00 0.00 0.00 2.40
2399 2473 6.127842 TGCGCTATTGTATCCGTATGAGATTA 60.128 38.462 9.73 0.00 0.00 1.75
2419 2493 8.243289 AGATTATTGGTTTGAAATTCGCAAAG 57.757 30.769 6.67 0.00 36.06 2.77
2432 2506 8.707839 TGAAATTCGCAAAGTCATTTATTTTCC 58.292 29.630 0.00 0.00 0.00 3.13
2528 2603 3.287222 CAAGTCTCTGGGGTTGTTGAAA 58.713 45.455 0.00 0.00 0.00 2.69
2534 2612 4.104738 TCTCTGGGGTTGTTGAAATCTTCT 59.895 41.667 0.00 0.00 0.00 2.85
2556 2634 4.965119 TCCTATATCCATCGATGACACG 57.035 45.455 26.86 9.92 0.00 4.49
2573 2654 3.229652 CGCTGTACGCAATACTCGA 57.770 52.632 9.69 0.00 39.08 4.04
2575 2656 1.448308 CGCTGTACGCAATACTCGATG 59.552 52.381 9.69 0.00 39.08 3.84
2576 2657 1.190323 GCTGTACGCAATACTCGATGC 59.810 52.381 0.00 0.00 38.92 3.91
2578 2659 0.776451 GTACGCAATACTCGATGCCG 59.224 55.000 3.28 2.02 39.39 5.69
2579 2660 0.937699 TACGCAATACTCGATGCCGC 60.938 55.000 3.28 0.00 39.39 6.53
2658 2740 0.669318 GTCGGAAGTCGGTGATGCAA 60.669 55.000 0.00 0.00 39.77 4.08
2715 2797 1.616865 TCACCACCCTGTAGAACGAAG 59.383 52.381 0.00 0.00 0.00 3.79
2812 2894 6.281848 GACAAAAGTCGACAACATTCACTA 57.718 37.500 19.50 0.00 0.00 2.74
2819 2901 5.124138 AGTCGACAACATTCACTAGTAGGAG 59.876 44.000 19.50 0.00 0.00 3.69
2829 2911 1.775459 ACTAGTAGGAGCCGGAGATGA 59.225 52.381 5.05 0.00 0.00 2.92
2847 2929 6.371595 AGATGAAGGATCAAGACAGAAAGT 57.628 37.500 0.00 0.00 39.49 2.66
2849 2931 5.174395 ATGAAGGATCAAGACAGAAAGTCG 58.826 41.667 0.00 0.00 44.02 4.18
2893 2975 2.070262 TCGAGACAGACATGCACAAG 57.930 50.000 0.00 0.00 0.00 3.16
2897 2979 3.363378 CGAGACAGACATGCACAAGAAAC 60.363 47.826 0.00 0.00 0.00 2.78
2911 2994 6.096705 TGCACAAGAAACCCAATCCATATAAG 59.903 38.462 0.00 0.00 0.00 1.73
2928 3011 8.781951 TCCATATAAGAAGAAGAAGGGACAAAT 58.218 33.333 0.00 0.00 0.00 2.32
2958 3041 2.100605 AACACCGGCAGAGAAGATTC 57.899 50.000 0.00 0.00 0.00 2.52
2961 3044 0.173708 ACCGGCAGAGAAGATTCGAC 59.826 55.000 0.00 0.00 0.00 4.20
2980 3063 2.663196 GGGAGTTACCGCACTGCT 59.337 61.111 0.00 0.00 40.11 4.24
3026 3109 1.003464 GGGAGGGGCGTAACAACTAAA 59.997 52.381 0.00 0.00 0.00 1.85
3141 3654 7.849904 ACCCTTCAAAGAGTCTTTATATAGGGA 59.150 37.037 33.53 19.93 39.83 4.20
3159 3672 4.855340 AGGGAAAATTCATTTCGGCTCTA 58.145 39.130 0.00 0.00 46.93 2.43
3164 3677 2.981859 TTCATTTCGGCTCTAGGTCC 57.018 50.000 0.00 0.00 0.00 4.46
3171 3684 2.184533 TCGGCTCTAGGTCCAAATGAA 58.815 47.619 0.00 0.00 0.00 2.57
3174 3687 2.026262 GGCTCTAGGTCCAAATGAACCA 60.026 50.000 0.00 0.00 0.00 3.67
3180 3693 7.335422 GCTCTAGGTCCAAATGAACCATATATG 59.665 40.741 5.68 5.68 0.00 1.78
3186 3699 6.667661 TCCAAATGAACCATATATGTGGACA 58.332 36.000 23.95 20.71 42.02 4.02
3190 3703 7.991084 AATGAACCATATATGTGGACATCTG 57.009 36.000 23.95 0.00 42.02 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 9.683870 ACATATGATTTGCCATGGTTAAAAATT 57.316 25.926 14.67 1.17 0.00 1.82
43 44 9.976255 CAACTGAATTTGCCATAAAAACATATG 57.024 29.630 0.00 0.00 33.85 1.78
45 46 7.118971 GCCAACTGAATTTGCCATAAAAACATA 59.881 33.333 0.00 0.00 0.00 2.29
113 114 2.535934 TGTCGTGTTCAGTGTTTTGC 57.464 45.000 0.00 0.00 0.00 3.68
122 123 2.948979 AGCAAATCCTTTGTCGTGTTCA 59.051 40.909 1.97 0.00 42.56 3.18
153 154 5.530915 TGTCGTGAGGATGACAATTTTCTTT 59.469 36.000 0.00 0.00 43.74 2.52
154 155 5.063204 TGTCGTGAGGATGACAATTTTCTT 58.937 37.500 0.00 0.00 43.74 2.52
187 188 6.072563 GCATGGCAAATCAAACTTTTTATGGT 60.073 34.615 0.00 0.00 0.00 3.55
373 378 2.151202 ACAATACACGAAGGCAGTTGG 58.849 47.619 0.00 0.00 0.00 3.77
376 381 5.847111 TCTATACAATACACGAAGGCAGT 57.153 39.130 0.00 0.00 0.00 4.40
483 488 8.801299 ACCTATGTTCATAGAGATGAGTATGTG 58.199 37.037 18.03 3.13 43.03 3.21
484 489 8.801299 CACCTATGTTCATAGAGATGAGTATGT 58.199 37.037 18.03 4.17 43.03 2.29
508 513 2.927477 TGTTCGGTCGAATATGAAGCAC 59.073 45.455 9.06 0.00 36.45 4.40
509 514 3.239587 TGTTCGGTCGAATATGAAGCA 57.760 42.857 9.06 0.00 36.45 3.91
575 580 3.570975 ACATCAGTGCTTGCATTTTCTGA 59.429 39.130 13.40 13.40 36.58 3.27
609 614 0.820871 TTGTTTGCAGTGGACCAACC 59.179 50.000 0.00 0.00 39.54 3.77
630 635 3.681897 CGGGCATAGCTCAAGATGATTAC 59.318 47.826 0.00 0.00 0.00 1.89
634 639 0.394192 CCGGGCATAGCTCAAGATGA 59.606 55.000 0.00 0.00 0.00 2.92
652 657 2.798976 TCTTGTTGATGCAGCAAACC 57.201 45.000 20.56 8.73 34.48 3.27
741 746 7.398829 GGAGGGAATAAAGAGAGAAGAAAACT 58.601 38.462 0.00 0.00 0.00 2.66
836 841 1.863454 CTCTGATGGAAGCGTATGCAC 59.137 52.381 10.11 2.67 46.23 4.57
855 860 0.921896 ACACATATGGAAGCCAGGCT 59.078 50.000 8.70 8.70 42.56 4.58
885 890 1.134560 CTACTAGTGTGAGGCGGTTCC 59.865 57.143 5.39 0.00 0.00 3.62
923 928 7.228706 TCTGAAGAAGGCTAAAAGTTGGTTTAG 59.771 37.037 0.00 1.22 41.88 1.85
954 959 5.122707 TGGATTGCAATGTGGGAACTATA 57.877 39.130 18.59 0.00 0.00 1.31
955 960 3.956199 CTGGATTGCAATGTGGGAACTAT 59.044 43.478 18.59 0.00 0.00 2.12
956 961 3.355378 CTGGATTGCAATGTGGGAACTA 58.645 45.455 18.59 0.00 0.00 2.24
957 962 2.173519 CTGGATTGCAATGTGGGAACT 58.826 47.619 18.59 0.00 0.00 3.01
964 969 1.754803 CCTGATGCTGGATTGCAATGT 59.245 47.619 18.59 0.00 46.61 2.71
969 980 2.818432 CCTTATCCTGATGCTGGATTGC 59.182 50.000 10.47 0.00 41.36 3.56
971 982 2.444388 TGCCTTATCCTGATGCTGGATT 59.556 45.455 10.47 0.00 41.36 3.01
1098 1118 4.847444 GGCCTCCAAGAGCGGCTC 62.847 72.222 22.13 22.13 43.29 4.70
1316 1346 2.359214 ACACACACACACACACACAAAA 59.641 40.909 0.00 0.00 0.00 2.44
1317 1347 1.950216 ACACACACACACACACACAAA 59.050 42.857 0.00 0.00 0.00 2.83
1318 1348 1.265365 CACACACACACACACACACAA 59.735 47.619 0.00 0.00 0.00 3.33
1319 1349 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1320 1350 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1321 1351 1.533299 GAACACACACACACACACACA 59.467 47.619 0.00 0.00 0.00 3.72
1322 1352 1.533299 TGAACACACACACACACACAC 59.467 47.619 0.00 0.00 0.00 3.82
1323 1353 1.803555 CTGAACACACACACACACACA 59.196 47.619 0.00 0.00 0.00 3.72
1407 1437 1.221414 GAGCCATATCTTGACGTGCC 58.779 55.000 0.00 0.00 0.00 5.01
1702 1732 1.358759 GGTTGGCGTGTTCTTGGTG 59.641 57.895 0.00 0.00 0.00 4.17
1703 1733 1.826487 GGGTTGGCGTGTTCTTGGT 60.826 57.895 0.00 0.00 0.00 3.67
1706 1736 0.106918 TCTTGGGTTGGCGTGTTCTT 60.107 50.000 0.00 0.00 0.00 2.52
1718 1748 1.538666 AGCTTGGCTTGTCTTGGGT 59.461 52.632 0.00 0.00 33.89 4.51
1732 1762 1.963515 CCTTGGGCACTGTTTAAGCTT 59.036 47.619 3.48 3.48 0.00 3.74
1737 1767 2.582052 CTTGTCCTTGGGCACTGTTTA 58.418 47.619 0.00 0.00 0.00 2.01
1743 1773 1.818674 CATTACCTTGTCCTTGGGCAC 59.181 52.381 0.00 0.00 0.00 5.01
1748 1778 0.451783 GCGCCATTACCTTGTCCTTG 59.548 55.000 0.00 0.00 0.00 3.61
1749 1779 0.679960 GGCGCCATTACCTTGTCCTT 60.680 55.000 24.80 0.00 0.00 3.36
1750 1780 1.077716 GGCGCCATTACCTTGTCCT 60.078 57.895 24.80 0.00 0.00 3.85
1751 1781 1.377987 TGGCGCCATTACCTTGTCC 60.378 57.895 29.03 0.00 0.00 4.02
1752 1782 0.958382 TGTGGCGCCATTACCTTGTC 60.958 55.000 35.23 16.90 0.00 3.18
1753 1783 1.074072 TGTGGCGCCATTACCTTGT 59.926 52.632 35.23 0.00 0.00 3.16
1769 1799 3.131396 GTCACTTCTGATTGTTCGGTGT 58.869 45.455 0.00 0.00 0.00 4.16
1777 1807 1.026718 GGGCCGGTCACTTCTGATTG 61.027 60.000 9.07 0.00 0.00 2.67
1834 1864 4.754114 TCGCAAAAGAAAAATGGGAAATGG 59.246 37.500 0.00 0.00 33.74 3.16
1846 1887 8.635877 TTAAGCTGTTTATTTCGCAAAAGAAA 57.364 26.923 0.00 0.00 43.28 2.52
1863 1904 4.524328 CCCCTCATTTCAAACTTAAGCTGT 59.476 41.667 1.29 0.00 0.00 4.40
1871 1912 3.328535 AACACCCCCTCATTTCAAACT 57.671 42.857 0.00 0.00 0.00 2.66
1884 1925 0.826256 GTCCCTGAACCAAACACCCC 60.826 60.000 0.00 0.00 0.00 4.95
1885 1926 0.185175 AGTCCCTGAACCAAACACCC 59.815 55.000 0.00 0.00 0.00 4.61
1886 1927 2.067365 AAGTCCCTGAACCAAACACC 57.933 50.000 0.00 0.00 0.00 4.16
1887 1928 4.465632 AAAAAGTCCCTGAACCAAACAC 57.534 40.909 0.00 0.00 0.00 3.32
1888 1929 5.265989 ACTAAAAAGTCCCTGAACCAAACA 58.734 37.500 0.00 0.00 0.00 2.83
1889 1930 5.593095 AGACTAAAAAGTCCCTGAACCAAAC 59.407 40.000 2.00 0.00 39.50 2.93
1890 1931 5.762279 AGACTAAAAAGTCCCTGAACCAAA 58.238 37.500 2.00 0.00 39.50 3.28
1891 1932 5.104277 TGAGACTAAAAAGTCCCTGAACCAA 60.104 40.000 2.00 0.00 39.50 3.67
1892 1933 4.410883 TGAGACTAAAAAGTCCCTGAACCA 59.589 41.667 2.00 0.00 39.50 3.67
1893 1934 4.969484 TGAGACTAAAAAGTCCCTGAACC 58.031 43.478 2.00 0.00 39.50 3.62
1894 1935 5.855045 TCTGAGACTAAAAAGTCCCTGAAC 58.145 41.667 2.00 0.00 39.50 3.18
1895 1936 5.839063 TCTCTGAGACTAAAAAGTCCCTGAA 59.161 40.000 2.58 0.00 39.50 3.02
1896 1937 5.244178 GTCTCTGAGACTAAAAAGTCCCTGA 59.756 44.000 26.44 0.16 41.88 3.86
1897 1938 5.474825 GTCTCTGAGACTAAAAAGTCCCTG 58.525 45.833 26.44 0.00 41.88 4.45
1898 1939 5.731957 GTCTCTGAGACTAAAAAGTCCCT 57.268 43.478 26.44 0.00 41.88 4.20
1908 1949 7.945664 AGGAACTTTTTCTAGTCTCTGAGACTA 59.054 37.037 33.75 33.75 46.53 2.59
1910 1951 6.988522 AGGAACTTTTTCTAGTCTCTGAGAC 58.011 40.000 26.43 26.43 40.30 3.36
1911 1952 8.164733 TCTAGGAACTTTTTCTAGTCTCTGAGA 58.835 37.037 2.58 2.58 41.75 3.27
1912 1953 8.343168 TCTAGGAACTTTTTCTAGTCTCTGAG 57.657 38.462 0.00 0.00 41.75 3.35
1913 1954 8.707796 TTCTAGGAACTTTTTCTAGTCTCTGA 57.292 34.615 1.92 0.00 41.75 3.27
1914 1955 9.198837 GTTTCTAGGAACTTTTTCTAGTCTCTG 57.801 37.037 6.66 0.00 41.75 3.35
1915 1956 8.369424 GGTTTCTAGGAACTTTTTCTAGTCTCT 58.631 37.037 13.68 0.00 41.75 3.10
1916 1957 8.148999 TGGTTTCTAGGAACTTTTTCTAGTCTC 58.851 37.037 13.68 0.00 41.75 3.36
1917 1958 8.030913 TGGTTTCTAGGAACTTTTTCTAGTCT 57.969 34.615 13.68 0.00 41.75 3.24
1918 1959 8.672823 TTGGTTTCTAGGAACTTTTTCTAGTC 57.327 34.615 13.68 0.00 41.75 2.59
1919 1960 8.900781 GTTTGGTTTCTAGGAACTTTTTCTAGT 58.099 33.333 13.68 0.00 41.75 2.57
1920 1961 8.068380 CGTTTGGTTTCTAGGAACTTTTTCTAG 58.932 37.037 13.68 0.00 41.75 2.43
1921 1962 7.012610 CCGTTTGGTTTCTAGGAACTTTTTCTA 59.987 37.037 13.68 0.00 41.75 2.10
1922 1963 6.183360 CCGTTTGGTTTCTAGGAACTTTTTCT 60.183 38.462 13.68 0.00 41.75 2.52
1923 1964 5.975344 CCGTTTGGTTTCTAGGAACTTTTTC 59.025 40.000 13.68 0.00 41.75 2.29
1924 1965 5.163488 CCCGTTTGGTTTCTAGGAACTTTTT 60.163 40.000 13.68 0.00 41.75 1.94
1925 1966 4.340097 CCCGTTTGGTTTCTAGGAACTTTT 59.660 41.667 13.68 0.00 41.75 2.27
1926 1967 3.887110 CCCGTTTGGTTTCTAGGAACTTT 59.113 43.478 13.68 0.00 41.75 2.66
1927 1968 3.136992 TCCCGTTTGGTTTCTAGGAACTT 59.863 43.478 13.68 0.00 35.86 2.66
1928 1969 2.707257 TCCCGTTTGGTTTCTAGGAACT 59.293 45.455 13.68 0.00 37.79 3.01
1929 1970 3.072211 CTCCCGTTTGGTTTCTAGGAAC 58.928 50.000 5.21 5.21 34.77 3.62
1930 1971 2.039348 CCTCCCGTTTGGTTTCTAGGAA 59.961 50.000 0.00 0.00 34.77 3.36
1931 1972 1.626825 CCTCCCGTTTGGTTTCTAGGA 59.373 52.381 0.00 0.00 34.77 2.94
1932 1973 1.626825 TCCTCCCGTTTGGTTTCTAGG 59.373 52.381 0.00 0.00 34.77 3.02
1933 1974 3.072211 GTTCCTCCCGTTTGGTTTCTAG 58.928 50.000 0.00 0.00 34.77 2.43
1934 1975 2.707257 AGTTCCTCCCGTTTGGTTTCTA 59.293 45.455 0.00 0.00 34.77 2.10
1935 1976 1.493446 AGTTCCTCCCGTTTGGTTTCT 59.507 47.619 0.00 0.00 34.77 2.52
1936 1977 1.977056 AGTTCCTCCCGTTTGGTTTC 58.023 50.000 0.00 0.00 34.77 2.78
1937 1978 2.447408 AAGTTCCTCCCGTTTGGTTT 57.553 45.000 0.00 0.00 34.77 3.27
1938 1979 2.447408 AAAGTTCCTCCCGTTTGGTT 57.553 45.000 0.00 0.00 34.77 3.67
1939 1980 2.447408 AAAAGTTCCTCCCGTTTGGT 57.553 45.000 0.00 0.00 34.77 3.67
1940 1981 2.956333 AGAAAAAGTTCCTCCCGTTTGG 59.044 45.455 0.00 0.00 33.92 3.28
1941 1982 4.577283 TGTAGAAAAAGTTCCTCCCGTTTG 59.423 41.667 0.00 0.00 33.92 2.93
1942 1983 4.784177 TGTAGAAAAAGTTCCTCCCGTTT 58.216 39.130 0.00 0.00 33.92 3.60
1943 1984 4.426736 TGTAGAAAAAGTTCCTCCCGTT 57.573 40.909 0.00 0.00 33.92 4.44
1944 1985 4.426736 TTGTAGAAAAAGTTCCTCCCGT 57.573 40.909 0.00 0.00 33.92 5.28
1945 1986 5.001232 TCATTGTAGAAAAAGTTCCTCCCG 58.999 41.667 0.00 0.00 33.92 5.14
1946 1987 7.468141 AATCATTGTAGAAAAAGTTCCTCCC 57.532 36.000 0.00 0.00 33.92 4.30
1947 1988 9.449719 TCTAATCATTGTAGAAAAAGTTCCTCC 57.550 33.333 0.00 0.00 33.92 4.30
1962 2003 9.442047 CCAGTAGAGTCTTTTTCTAATCATTGT 57.558 33.333 0.00 0.00 0.00 2.71
1963 2004 9.658799 TCCAGTAGAGTCTTTTTCTAATCATTG 57.341 33.333 0.00 0.00 0.00 2.82
1964 2005 9.883142 CTCCAGTAGAGTCTTTTTCTAATCATT 57.117 33.333 0.00 0.00 37.87 2.57
1965 2006 9.261035 TCTCCAGTAGAGTCTTTTTCTAATCAT 57.739 33.333 0.00 0.00 43.71 2.45
1966 2007 8.651589 TCTCCAGTAGAGTCTTTTTCTAATCA 57.348 34.615 0.00 0.00 43.71 2.57
2014 2055 8.578151 TCAGAAGTTCTAGGACTTTTTCTAGTC 58.422 37.037 17.72 2.66 39.84 2.59
2015 2056 8.480133 TCAGAAGTTCTAGGACTTTTTCTAGT 57.520 34.615 17.72 0.00 39.84 2.57
2016 2057 9.198837 GTTCAGAAGTTCTAGGACTTTTTCTAG 57.801 37.037 17.72 6.26 39.84 2.43
2017 2058 8.148999 GGTTCAGAAGTTCTAGGACTTTTTCTA 58.851 37.037 17.72 0.94 39.84 2.10
2018 2059 6.993308 GGTTCAGAAGTTCTAGGACTTTTTCT 59.007 38.462 17.72 7.89 39.84 2.52
2019 2060 6.766467 TGGTTCAGAAGTTCTAGGACTTTTTC 59.234 38.462 17.72 5.59 39.84 2.29
2020 2061 6.659824 TGGTTCAGAAGTTCTAGGACTTTTT 58.340 36.000 17.72 6.93 39.84 1.94
2021 2062 6.248569 TGGTTCAGAAGTTCTAGGACTTTT 57.751 37.500 17.72 9.52 39.84 2.27
2022 2063 5.888982 TGGTTCAGAAGTTCTAGGACTTT 57.111 39.130 17.72 5.47 39.84 2.66
2023 2064 5.888982 TTGGTTCAGAAGTTCTAGGACTT 57.111 39.130 16.69 16.69 42.31 3.01
2024 2065 5.130477 TGTTTGGTTCAGAAGTTCTAGGACT 59.870 40.000 4.74 0.00 0.00 3.85
2025 2066 5.236695 GTGTTTGGTTCAGAAGTTCTAGGAC 59.763 44.000 4.74 5.28 0.00 3.85
2026 2067 5.365619 GTGTTTGGTTCAGAAGTTCTAGGA 58.634 41.667 4.74 0.00 0.00 2.94
2027 2068 4.515567 GGTGTTTGGTTCAGAAGTTCTAGG 59.484 45.833 4.74 0.00 0.00 3.02
2028 2069 4.515567 GGGTGTTTGGTTCAGAAGTTCTAG 59.484 45.833 4.74 0.69 0.00 2.43
2029 2070 4.457466 GGGTGTTTGGTTCAGAAGTTCTA 58.543 43.478 4.74 0.00 0.00 2.10
2030 2071 3.288092 GGGTGTTTGGTTCAGAAGTTCT 58.712 45.455 0.00 0.00 0.00 3.01
2031 2072 2.361119 GGGGTGTTTGGTTCAGAAGTTC 59.639 50.000 0.00 0.00 0.00 3.01
2032 2073 2.384828 GGGGTGTTTGGTTCAGAAGTT 58.615 47.619 0.00 0.00 0.00 2.66
2033 2074 1.411074 GGGGGTGTTTGGTTCAGAAGT 60.411 52.381 0.00 0.00 0.00 3.01
2034 2075 1.133482 AGGGGGTGTTTGGTTCAGAAG 60.133 52.381 0.00 0.00 0.00 2.85
2035 2076 0.930726 AGGGGGTGTTTGGTTCAGAA 59.069 50.000 0.00 0.00 0.00 3.02
2036 2077 0.184933 CAGGGGGTGTTTGGTTCAGA 59.815 55.000 0.00 0.00 0.00 3.27
2037 2078 0.184933 TCAGGGGGTGTTTGGTTCAG 59.815 55.000 0.00 0.00 0.00 3.02
2038 2079 0.631753 TTCAGGGGGTGTTTGGTTCA 59.368 50.000 0.00 0.00 0.00 3.18
2039 2080 1.618343 CATTCAGGGGGTGTTTGGTTC 59.382 52.381 0.00 0.00 0.00 3.62
2040 2081 1.219213 TCATTCAGGGGGTGTTTGGTT 59.781 47.619 0.00 0.00 0.00 3.67
2041 2082 0.856982 TCATTCAGGGGGTGTTTGGT 59.143 50.000 0.00 0.00 0.00 3.67
2042 2083 1.826720 CATCATTCAGGGGGTGTTTGG 59.173 52.381 0.00 0.00 0.00 3.28
2043 2084 1.205417 GCATCATTCAGGGGGTGTTTG 59.795 52.381 0.00 0.00 0.00 2.93
2044 2085 1.203162 TGCATCATTCAGGGGGTGTTT 60.203 47.619 0.00 0.00 0.00 2.83
2045 2086 0.409092 TGCATCATTCAGGGGGTGTT 59.591 50.000 0.00 0.00 0.00 3.32
2046 2087 0.323725 GTGCATCATTCAGGGGGTGT 60.324 55.000 0.00 0.00 0.00 4.16
2047 2088 1.039233 GGTGCATCATTCAGGGGGTG 61.039 60.000 0.00 0.00 0.00 4.61
2048 2089 1.307647 GGTGCATCATTCAGGGGGT 59.692 57.895 0.00 0.00 0.00 4.95
2049 2090 1.825191 CGGTGCATCATTCAGGGGG 60.825 63.158 0.00 0.00 0.00 5.40
2050 2091 2.484062 GCGGTGCATCATTCAGGGG 61.484 63.158 0.00 0.00 0.00 4.79
2051 2092 0.179048 TAGCGGTGCATCATTCAGGG 60.179 55.000 0.00 0.00 0.00 4.45
2052 2093 1.224075 CTAGCGGTGCATCATTCAGG 58.776 55.000 0.00 0.00 0.00 3.86
2053 2094 1.945387 ACTAGCGGTGCATCATTCAG 58.055 50.000 0.00 0.00 0.00 3.02
2054 2095 2.009051 CAACTAGCGGTGCATCATTCA 58.991 47.619 0.00 0.00 0.00 2.57
2055 2096 2.009774 ACAACTAGCGGTGCATCATTC 58.990 47.619 0.00 0.00 0.00 2.67
2056 2097 1.739466 CACAACTAGCGGTGCATCATT 59.261 47.619 0.00 0.00 0.00 2.57
2057 2098 1.372582 CACAACTAGCGGTGCATCAT 58.627 50.000 0.00 0.00 0.00 2.45
2131 2172 7.541091 CGGACTATATTAATTTCTGAAGCGCTA 59.459 37.037 12.05 0.00 0.00 4.26
2135 2176 9.042008 TGAACGGACTATATTAATTTCTGAAGC 57.958 33.333 0.00 0.00 0.00 3.86
2239 2285 3.118408 TGGTGAGCTTTCAAGTGTAGTGT 60.118 43.478 0.00 0.00 0.00 3.55
2302 2349 1.613437 CCAAATCGTGCCCTTGAAGTT 59.387 47.619 0.00 0.00 0.00 2.66
2303 2350 1.247567 CCAAATCGTGCCCTTGAAGT 58.752 50.000 0.00 0.00 0.00 3.01
2315 2362 1.919918 GCTCGCAATTTTCCCAAATCG 59.080 47.619 0.00 0.00 30.80 3.34
2331 2378 1.424493 CTTCTTAGCGCCTTGGCTCG 61.424 60.000 2.29 0.00 43.54 5.03
2334 2381 0.169009 CAACTTCTTAGCGCCTTGGC 59.831 55.000 2.29 0.75 0.00 4.52
2340 2389 1.734465 AGTGCATCAACTTCTTAGCGC 59.266 47.619 0.00 0.00 0.00 5.92
2356 2405 0.110509 CACATCACAACGAGCAGTGC 60.111 55.000 7.13 7.13 35.76 4.40
2357 2406 0.110509 GCACATCACAACGAGCAGTG 60.111 55.000 0.00 0.00 37.10 3.66
2358 2407 1.560004 CGCACATCACAACGAGCAGT 61.560 55.000 0.00 0.00 0.00 4.40
2359 2408 1.131218 CGCACATCACAACGAGCAG 59.869 57.895 0.00 0.00 0.00 4.24
2371 2445 2.526304 ACGGATACAATAGCGCACAT 57.474 45.000 11.47 0.00 0.00 3.21
2376 2450 8.746751 CAATAATCTCATACGGATACAATAGCG 58.253 37.037 0.00 0.00 0.00 4.26
2382 2456 8.425703 TCAAACCAATAATCTCATACGGATACA 58.574 33.333 0.00 0.00 0.00 2.29
2385 2459 8.746052 TTTCAAACCAATAATCTCATACGGAT 57.254 30.769 0.00 0.00 0.00 4.18
2387 2461 9.450807 GAATTTCAAACCAATAATCTCATACGG 57.549 33.333 0.00 0.00 0.00 4.02
2398 2472 6.507900 TGACTTTGCGAATTTCAAACCAATA 58.492 32.000 0.00 0.00 31.05 1.90
2399 2473 5.355596 TGACTTTGCGAATTTCAAACCAAT 58.644 33.333 0.00 0.00 31.05 3.16
2419 2493 7.275560 CCATTGGTCTTTCGGAAAATAAATGAC 59.724 37.037 19.11 14.61 0.00 3.06
2432 2506 7.226720 ACTTAATGTATAGCCATTGGTCTTTCG 59.773 37.037 4.26 0.00 35.85 3.46
2502 2577 1.352352 CAACCCCAGAGACTTGGATGT 59.648 52.381 5.53 1.27 40.87 3.06
2513 2588 4.453480 AGAAGATTTCAACAACCCCAGA 57.547 40.909 0.00 0.00 0.00 3.86
2528 2603 7.617329 TGTCATCGATGGATATAGGAAGAAGAT 59.383 37.037 24.61 0.00 0.00 2.40
2534 2612 4.380550 GCGTGTCATCGATGGATATAGGAA 60.381 45.833 24.61 0.00 0.00 3.36
2567 2648 3.120105 CTCAGGCGGCATCGAGTA 58.880 61.111 13.08 0.00 39.00 2.59
2568 2649 4.521062 GCTCAGGCGGCATCGAGT 62.521 66.667 13.08 0.00 39.00 4.18
2572 2653 4.925861 GGAGGCTCAGGCGGCATC 62.926 72.222 17.69 0.00 39.38 3.91
2575 2656 4.925861 GATGGAGGCTCAGGCGGC 62.926 72.222 17.69 0.00 39.81 6.53
2576 2657 1.402896 TAAGATGGAGGCTCAGGCGG 61.403 60.000 17.69 0.00 39.81 6.13
2578 2659 0.250252 GCTAAGATGGAGGCTCAGGC 60.250 60.000 17.69 4.23 37.82 4.85
2579 2660 0.033228 CGCTAAGATGGAGGCTCAGG 59.967 60.000 17.69 0.00 0.00 3.86
2658 2740 0.320771 AATGCCGACGTCTTCTGCTT 60.321 50.000 14.70 6.43 35.54 3.91
2703 2785 2.097629 TCTCCGATGCTTCGTTCTACAG 59.902 50.000 19.21 3.95 43.97 2.74
2711 2793 2.279784 GCCCTCTCCGATGCTTCG 60.280 66.667 14.61 14.61 45.08 3.79
2715 2797 4.247380 CCAGGCCCTCTCCGATGC 62.247 72.222 0.00 0.00 0.00 3.91
2765 2847 0.250467 AGCATGTGAGGTTTGCGTCT 60.250 50.000 0.00 0.00 41.22 4.18
2805 2887 2.175069 TCTCCGGCTCCTACTAGTGAAT 59.825 50.000 5.39 0.00 0.00 2.57
2812 2894 1.698506 CTTCATCTCCGGCTCCTACT 58.301 55.000 0.00 0.00 0.00 2.57
2819 2901 1.414181 TCTTGATCCTTCATCTCCGGC 59.586 52.381 0.00 0.00 31.92 6.13
2829 2911 3.330267 GCGACTTTCTGTCTTGATCCTT 58.670 45.455 0.00 0.00 43.25 3.36
2859 2941 3.243873 TGTCTCGATGGCATTGTCCTATC 60.244 47.826 14.28 0.00 0.00 2.08
2865 2947 1.276138 TGTCTGTCTCGATGGCATTGT 59.724 47.619 14.28 0.00 0.00 2.71
2867 2949 2.558378 CATGTCTGTCTCGATGGCATT 58.442 47.619 0.00 0.00 0.00 3.56
2868 2950 1.809271 GCATGTCTGTCTCGATGGCAT 60.809 52.381 0.00 0.00 0.00 4.40
2893 2975 8.980481 TCTTCTTCTTATATGGATTGGGTTTC 57.020 34.615 0.00 0.00 0.00 2.78
2897 2979 6.944862 CCCTTCTTCTTCTTATATGGATTGGG 59.055 42.308 0.00 0.00 0.00 4.12
2911 2994 2.493675 GGCCATTTGTCCCTTCTTCTTC 59.506 50.000 0.00 0.00 0.00 2.87
2928 3011 2.594303 CGGTGTTTCTGCTGGCCA 60.594 61.111 4.71 4.71 0.00 5.36
3003 3086 3.876255 TTGTTACGCCCCTCCCCCT 62.876 63.158 0.00 0.00 0.00 4.79
3008 3091 3.376234 GGATTTTAGTTGTTACGCCCCTC 59.624 47.826 0.00 0.00 0.00 4.30
3009 3092 3.244981 TGGATTTTAGTTGTTACGCCCCT 60.245 43.478 0.00 0.00 0.00 4.79
3141 3654 4.640647 GGACCTAGAGCCGAAATGAATTTT 59.359 41.667 0.00 0.00 0.00 1.82
3152 3665 2.280628 GTTCATTTGGACCTAGAGCCG 58.719 52.381 0.00 0.00 0.00 5.52
3159 3672 6.070656 CCACATATATGGTTCATTTGGACCT 58.929 40.000 16.96 0.00 34.77 3.85
3164 3677 8.294577 CAGATGTCCACATATATGGTTCATTTG 58.705 37.037 16.96 14.47 40.95 2.32
3171 3684 6.753913 AACTCAGATGTCCACATATATGGT 57.246 37.500 16.96 0.28 40.95 3.55
3180 3693 6.214191 TCTCTATGAAACTCAGATGTCCAC 57.786 41.667 0.00 0.00 0.00 4.02
3186 3699 9.365906 AGACACATATCTCTATGAAACTCAGAT 57.634 33.333 0.00 0.00 38.49 2.90
3190 3703 9.677567 GAGAAGACACATATCTCTATGAAACTC 57.322 37.037 0.00 0.00 38.49 3.01


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

AutoCloner maintained by Alex Coulton.