Multiple sequence alignment - TraesCS6B01G273500

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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 TraesCS6B01G273500 chr6B 100.000 2913 0 0 1 2913 493983243 493986155 0.000000e+00 5380
1 TraesCS6B01G273500 chr6B 93.123 349 13 5 1892 2232 701069466 701069121 4.330000e-138 501
2 TraesCS6B01G273500 chr6D 89.583 1920 89 37 2 1886 327373894 327372051 0.000000e+00 2335
3 TraesCS6B01G273500 chr6D 93.033 689 33 10 2232 2913 327372057 327371377 0.000000e+00 992
4 TraesCS6B01G273500 chr6A 88.616 1915 123 38 2 1886 466484970 466483121 0.000000e+00 2241
5 TraesCS6B01G273500 chr6A 91.115 529 33 8 2235 2750 466483083 466482556 0.000000e+00 704
6 TraesCS6B01G273500 chr6A 91.667 156 10 1 2748 2903 466482500 466482348 2.270000e-51 213
7 TraesCS6B01G273500 chr4B 93.296 358 13 5 1892 2239 633150088 633150444 4.300000e-143 518
8 TraesCS6B01G273500 chr4B 94.444 324 14 4 1886 2207 601188671 601188992 2.020000e-136 496
9 TraesCS6B01G273500 chr1B 93.447 351 11 6 1892 2232 43326280 43325932 7.200000e-141 510
10 TraesCS6B01G273500 chr1A 91.620 358 20 4 1886 2233 346462546 346462903 1.210000e-133 486
11 TraesCS6B01G273500 chr5B 91.808 354 16 4 1892 2232 583185155 583184802 5.650000e-132 481
12 TraesCS6B01G273500 chr5B 91.292 356 19 5 1886 2232 493285863 493285511 2.630000e-130 475
13 TraesCS6B01G273500 chr4A 91.573 356 16 7 1892 2234 713367141 713367495 2.030000e-131 479
14 TraesCS6B01G273500 chr3B 93.458 321 16 4 1892 2207 707937827 707937507 3.400000e-129 472


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 TraesCS6B01G273500 chr6B 493983243 493986155 2912 False 5380.000000 5380 100.000 1 2913 1 chr6B.!!$F1 2912
1 TraesCS6B01G273500 chr6D 327371377 327373894 2517 True 1663.500000 2335 91.308 2 2913 2 chr6D.!!$R1 2911
2 TraesCS6B01G273500 chr6A 466482348 466484970 2622 True 1052.666667 2241 90.466 2 2903 3 chr6A.!!$R1 2901

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
919 963 0.251787 ATTTGGAGACAGTTGGGGGC 60.252 55.000 0.0 0.0 44.54 5.8 F
1772 1836 1.418264 GCTGGTTAATCCTCCTCCTCC 59.582 57.143 0.0 0.0 37.07 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1775 1839 0.105555 AGCTGATGGAGGAGGAGGAG 60.106 60.0 0.0 0.0 0.00 3.69 R
2666 2794 0.112995 TGCTCCATTTTGCTCTGGGT 59.887 50.0 0.0 0.0 33.13 4.51 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
40 46 1.066587 CAAGAGAGGCCGATCCGAC 59.933 63.158 0.00 0.00 40.77 4.79
83 89 6.037940 TGACGGTTATGAGTAGTAGTTAGCTG 59.962 42.308 0.00 0.00 0.00 4.24
87 93 7.255520 CGGTTATGAGTAGTAGTTAGCTGGAAT 60.256 40.741 0.00 0.00 0.00 3.01
91 97 5.186992 TGAGTAGTAGTTAGCTGGAATTGCA 59.813 40.000 0.00 0.00 0.00 4.08
94 100 4.848357 AGTAGTTAGCTGGAATTGCATGT 58.152 39.130 0.00 0.00 0.00 3.21
102 111 6.720112 AGCTGGAATTGCATGTATGTTATT 57.280 33.333 0.00 0.00 0.00 1.40
103 112 6.742109 AGCTGGAATTGCATGTATGTTATTC 58.258 36.000 0.00 0.00 33.23 1.75
240 258 1.915141 CTGAAAGGGACAGCAATGGT 58.085 50.000 0.00 0.00 0.00 3.55
247 265 1.686115 GGGACAGCAATGGTAATGCCT 60.686 52.381 0.29 0.00 44.91 4.75
249 267 2.648059 GACAGCAATGGTAATGCCTCT 58.352 47.619 0.00 0.00 44.91 3.69
250 268 2.615912 GACAGCAATGGTAATGCCTCTC 59.384 50.000 0.00 0.00 44.91 3.20
252 270 3.018856 CAGCAATGGTAATGCCTCTCAA 58.981 45.455 0.00 0.00 44.91 3.02
254 272 3.698040 AGCAATGGTAATGCCTCTCAAAG 59.302 43.478 0.00 0.00 44.91 2.77
255 273 3.736126 GCAATGGTAATGCCTCTCAAAGC 60.736 47.826 0.00 0.00 37.85 3.51
256 274 2.128771 TGGTAATGCCTCTCAAAGCC 57.871 50.000 0.00 0.00 38.35 4.35
257 275 1.635487 TGGTAATGCCTCTCAAAGCCT 59.365 47.619 0.00 0.00 38.35 4.58
258 276 2.019984 GGTAATGCCTCTCAAAGCCTG 58.980 52.381 0.00 0.00 0.00 4.85
259 277 1.403323 GTAATGCCTCTCAAAGCCTGC 59.597 52.381 0.00 0.00 0.00 4.85
260 278 1.310933 AATGCCTCTCAAAGCCTGCG 61.311 55.000 0.00 0.00 0.00 5.18
261 279 2.046892 GCCTCTCAAAGCCTGCGA 60.047 61.111 0.00 0.00 0.00 5.10
262 280 1.451028 GCCTCTCAAAGCCTGCGAT 60.451 57.895 0.00 0.00 0.00 4.58
282 300 1.134995 TCGATCGAGCATTGCAGAGTT 60.135 47.619 15.15 0.00 0.00 3.01
301 319 1.830279 TGAGCCTCCTGCATTTCAAG 58.170 50.000 0.00 0.00 44.83 3.02
311 329 2.230508 CTGCATTTCAAGACCATGCACT 59.769 45.455 10.56 0.00 46.53 4.40
326 348 1.349627 CACTGCTAATTCGCCAGCG 59.650 57.895 5.50 5.50 40.79 5.18
345 367 2.722201 CCTCCAGACCCCGTGCTAC 61.722 68.421 0.00 0.00 0.00 3.58
387 409 6.096423 CCCTACACTACACAGTACACATACAT 59.904 42.308 0.00 0.00 33.30 2.29
388 410 6.972901 CCTACACTACACAGTACACATACATG 59.027 42.308 0.00 0.00 33.30 3.21
389 411 6.340962 ACACTACACAGTACACATACATGT 57.659 37.500 2.69 2.69 36.99 3.21
391 413 5.062183 CACTACACAGTACACATACATGTGC 59.938 44.000 19.70 6.98 46.66 4.57
392 414 7.065778 CACTACACAGTACACATACATGTGCT 61.066 42.308 19.70 8.93 46.66 4.40
427 449 1.530441 CGTACTACCACCACACGATCG 60.530 57.143 14.88 14.88 34.66 3.69
444 473 0.939419 TCGCGATCGAACTTATCCGA 59.061 50.000 21.57 12.62 42.44 4.55
502 532 0.544697 AGGGTGTCCGTGTCAAACTT 59.455 50.000 0.00 0.00 38.33 2.66
629 659 1.079819 CGTCCCAATGACTGCGAGT 60.080 57.895 0.00 0.00 42.13 4.18
660 690 2.995283 TGTGAGGCATCCATTTCTCTG 58.005 47.619 0.00 0.00 0.00 3.35
777 807 4.818546 AGCAGCATTGATCCATGTTAGTAC 59.181 41.667 8.45 0.00 0.00 2.73
778 808 4.576053 GCAGCATTGATCCATGTTAGTACA 59.424 41.667 8.45 0.00 38.95 2.90
864 908 4.416738 GAGCCAGGTCCCCACTGC 62.417 72.222 0.00 0.00 34.65 4.40
900 944 1.133294 TCAGTGACCTGAGGTGGTGTA 60.133 52.381 9.89 0.00 42.80 2.90
912 956 2.979678 AGGTGGTGTATTTGGAGACAGT 59.020 45.455 0.00 0.00 44.54 3.55
913 957 3.394606 AGGTGGTGTATTTGGAGACAGTT 59.605 43.478 0.00 0.00 44.54 3.16
914 958 3.502211 GGTGGTGTATTTGGAGACAGTTG 59.498 47.826 0.00 0.00 44.54 3.16
915 959 3.502211 GTGGTGTATTTGGAGACAGTTGG 59.498 47.826 0.00 0.00 44.54 3.77
916 960 3.081804 GGTGTATTTGGAGACAGTTGGG 58.918 50.000 0.00 0.00 44.54 4.12
917 961 3.081804 GTGTATTTGGAGACAGTTGGGG 58.918 50.000 0.00 0.00 44.54 4.96
918 962 2.041081 TGTATTTGGAGACAGTTGGGGG 59.959 50.000 0.00 0.00 44.54 5.40
919 963 0.251787 ATTTGGAGACAGTTGGGGGC 60.252 55.000 0.00 0.00 44.54 5.80
1092 1138 3.204526 GAAGGACTGAGCGCTACTACTA 58.795 50.000 11.50 0.00 0.00 1.82
1255 1310 4.641645 CACCAGTCCAAGGCGGCA 62.642 66.667 13.08 0.00 33.14 5.69
1257 1312 4.020617 CCAGTCCAAGGCGGCAGA 62.021 66.667 13.08 1.38 33.14 4.26
1259 1314 4.400961 AGTCCAAGGCGGCAGAGC 62.401 66.667 13.08 0.00 33.14 4.09
1339 1394 2.380410 GGTGCGCGTCAAGATCGTT 61.380 57.895 8.43 0.00 0.00 3.85
1600 1658 5.448904 CGAGGAGGTTTACTGAGTTACTAGC 60.449 48.000 0.00 0.00 0.00 3.42
1604 1662 4.525874 AGGTTTACTGAGTTACTAGCGGTT 59.474 41.667 0.00 0.00 0.00 4.44
1620 1678 2.802057 GCGGTTTAGTAGATGATGGCGT 60.802 50.000 0.00 0.00 0.00 5.68
1722 1786 6.262944 TGTGTACAATGCTCTTGATTTGTTCT 59.737 34.615 0.00 0.00 34.39 3.01
1770 1834 2.122768 CTGCTGGTTAATCCTCCTCCT 58.877 52.381 0.00 0.00 37.07 3.69
1771 1835 2.103941 CTGCTGGTTAATCCTCCTCCTC 59.896 54.545 0.00 0.00 37.07 3.71
1772 1836 1.418264 GCTGGTTAATCCTCCTCCTCC 59.582 57.143 0.00 0.00 37.07 4.30
1773 1837 2.961977 GCTGGTTAATCCTCCTCCTCCT 60.962 54.545 0.00 0.00 37.07 3.69
1774 1838 2.969262 CTGGTTAATCCTCCTCCTCCTC 59.031 54.545 0.00 0.00 37.07 3.71
1775 1839 2.331166 GGTTAATCCTCCTCCTCCTCC 58.669 57.143 0.00 0.00 0.00 4.30
1776 1840 2.090437 GGTTAATCCTCCTCCTCCTCCT 60.090 54.545 0.00 0.00 0.00 3.69
1777 1841 3.236047 GTTAATCCTCCTCCTCCTCCTC 58.764 54.545 0.00 0.00 0.00 3.71
1832 1896 4.687483 CCTGTGAAATTTTGGAGATTGTGC 59.313 41.667 0.00 0.00 0.00 4.57
1892 1956 4.754372 CAAGAGCTGCATTCAACAGTAA 57.246 40.909 1.02 0.00 37.47 2.24
1893 1957 5.112220 CAAGAGCTGCATTCAACAGTAAA 57.888 39.130 1.02 0.00 37.47 2.01
1894 1958 5.522456 CAAGAGCTGCATTCAACAGTAAAA 58.478 37.500 1.02 0.00 37.47 1.52
1895 1959 5.972107 AGAGCTGCATTCAACAGTAAAAT 57.028 34.783 1.02 0.00 37.47 1.82
1896 1960 5.947443 AGAGCTGCATTCAACAGTAAAATC 58.053 37.500 1.02 0.00 37.47 2.17
1897 1961 5.474532 AGAGCTGCATTCAACAGTAAAATCA 59.525 36.000 1.02 0.00 37.47 2.57
1898 1962 6.016024 AGAGCTGCATTCAACAGTAAAATCAA 60.016 34.615 1.02 0.00 37.47 2.57
1899 1963 6.514947 AGCTGCATTCAACAGTAAAATCAAA 58.485 32.000 1.02 0.00 37.47 2.69
1900 1964 6.985645 AGCTGCATTCAACAGTAAAATCAAAA 59.014 30.769 1.02 0.00 37.47 2.44
1901 1965 7.495279 AGCTGCATTCAACAGTAAAATCAAAAA 59.505 29.630 1.02 0.00 37.47 1.94
1947 2011 8.925161 TTTCTTGGTAGAAACATTGACAAAAG 57.075 30.769 0.00 0.00 43.63 2.27
1948 2012 7.639113 TCTTGGTAGAAACATTGACAAAAGT 57.361 32.000 0.00 0.00 0.00 2.66
1949 2013 8.062065 TCTTGGTAGAAACATTGACAAAAGTT 57.938 30.769 0.00 0.00 0.00 2.66
1950 2014 8.527810 TCTTGGTAGAAACATTGACAAAAGTTT 58.472 29.630 17.09 17.09 39.28 2.66
1951 2015 9.150348 CTTGGTAGAAACATTGACAAAAGTTTT 57.850 29.630 17.76 0.00 37.33 2.43
1957 2021 9.366216 AGAAACATTGACAAAAGTTTTAAGTCC 57.634 29.630 17.76 8.51 37.33 3.85
1958 2022 9.366216 GAAACATTGACAAAAGTTTTAAGTCCT 57.634 29.630 17.76 2.52 37.33 3.85
1959 2023 9.719355 AAACATTGACAAAAGTTTTAAGTCCTT 57.281 25.926 13.39 2.39 34.43 3.36
1960 2024 8.702163 ACATTGACAAAAGTTTTAAGTCCTTG 57.298 30.769 13.39 12.64 0.00 3.61
1961 2025 7.277760 ACATTGACAAAAGTTTTAAGTCCTTGC 59.722 33.333 13.39 0.00 0.00 4.01
1962 2026 6.274157 TGACAAAAGTTTTAAGTCCTTGCA 57.726 33.333 13.39 0.00 0.00 4.08
1963 2027 6.692486 TGACAAAAGTTTTAAGTCCTTGCAA 58.308 32.000 13.39 0.00 0.00 4.08
1964 2028 7.155328 TGACAAAAGTTTTAAGTCCTTGCAAA 58.845 30.769 13.39 0.00 0.00 3.68
1965 2029 7.657761 TGACAAAAGTTTTAAGTCCTTGCAAAA 59.342 29.630 13.39 0.00 0.00 2.44
1966 2030 8.384607 ACAAAAGTTTTAAGTCCTTGCAAAAA 57.615 26.923 0.00 0.00 0.00 1.94
1967 2031 9.008965 ACAAAAGTTTTAAGTCCTTGCAAAAAT 57.991 25.926 0.00 0.00 0.00 1.82
1968 2032 9.838975 CAAAAGTTTTAAGTCCTTGCAAAAATT 57.161 25.926 0.00 0.00 31.70 1.82
1970 2034 7.463469 AGTTTTAAGTCCTTGCAAAAATTCG 57.537 32.000 0.00 0.00 0.00 3.34
1971 2035 7.039270 AGTTTTAAGTCCTTGCAAAAATTCGT 58.961 30.769 0.00 0.00 0.00 3.85
1972 2036 7.222031 AGTTTTAAGTCCTTGCAAAAATTCGTC 59.778 33.333 0.00 0.00 0.00 4.20
1973 2037 4.647424 AAGTCCTTGCAAAAATTCGTCA 57.353 36.364 0.00 0.00 0.00 4.35
1974 2038 4.853924 AGTCCTTGCAAAAATTCGTCAT 57.146 36.364 0.00 0.00 0.00 3.06
1975 2039 4.549458 AGTCCTTGCAAAAATTCGTCATG 58.451 39.130 0.00 0.00 0.00 3.07
1976 2040 4.278170 AGTCCTTGCAAAAATTCGTCATGA 59.722 37.500 0.00 0.00 0.00 3.07
1977 2041 4.981674 GTCCTTGCAAAAATTCGTCATGAA 59.018 37.500 0.00 0.00 41.81 2.57
1978 2042 5.461737 GTCCTTGCAAAAATTCGTCATGAAA 59.538 36.000 0.00 0.00 40.71 2.69
1979 2043 6.146021 GTCCTTGCAAAAATTCGTCATGAAAT 59.854 34.615 0.00 0.00 40.71 2.17
1980 2044 6.365789 TCCTTGCAAAAATTCGTCATGAAATC 59.634 34.615 0.00 0.00 40.71 2.17
1981 2045 6.145858 CCTTGCAAAAATTCGTCATGAAATCA 59.854 34.615 0.00 0.00 40.71 2.57
1982 2046 6.450845 TGCAAAAATTCGTCATGAAATCAC 57.549 33.333 0.00 0.00 40.71 3.06
1983 2047 5.116831 TGCAAAAATTCGTCATGAAATCACG 59.883 36.000 0.00 0.00 40.71 4.35
1984 2048 5.116983 GCAAAAATTCGTCATGAAATCACGT 59.883 36.000 0.00 0.00 40.71 4.49
1985 2049 6.345723 GCAAAAATTCGTCATGAAATCACGTT 60.346 34.615 0.00 0.00 40.71 3.99
1986 2050 7.554732 CAAAAATTCGTCATGAAATCACGTTT 58.445 30.769 0.00 0.00 40.71 3.60
1987 2051 6.911484 AAATTCGTCATGAAATCACGTTTC 57.089 33.333 0.00 0.00 45.21 2.78
1988 2052 5.862924 ATTCGTCATGAAATCACGTTTCT 57.137 34.783 0.00 0.00 45.22 2.52
1989 2053 6.961359 ATTCGTCATGAAATCACGTTTCTA 57.039 33.333 0.00 0.00 45.22 2.10
1990 2054 6.389622 TTCGTCATGAAATCACGTTTCTAG 57.610 37.500 0.00 0.00 45.22 2.43
1991 2055 5.705902 TCGTCATGAAATCACGTTTCTAGA 58.294 37.500 0.00 0.00 45.22 2.43
1992 2056 6.153756 TCGTCATGAAATCACGTTTCTAGAA 58.846 36.000 0.00 0.00 45.22 2.10
1993 2057 6.308041 TCGTCATGAAATCACGTTTCTAGAAG 59.692 38.462 5.12 0.00 45.22 2.85
1994 2058 6.454318 CGTCATGAAATCACGTTTCTAGAAGG 60.454 42.308 5.12 4.80 45.22 3.46
1995 2059 5.351465 TCATGAAATCACGTTTCTAGAAGGC 59.649 40.000 5.12 2.48 45.22 4.35
1996 2060 3.678072 TGAAATCACGTTTCTAGAAGGCG 59.322 43.478 21.85 21.85 45.22 5.52
1997 2061 3.314541 AATCACGTTTCTAGAAGGCGT 57.685 42.857 22.82 22.82 35.38 5.68
1998 2062 2.060326 TCACGTTTCTAGAAGGCGTG 57.940 50.000 34.19 34.19 44.60 5.34
1999 2063 1.068474 CACGTTTCTAGAAGGCGTGG 58.932 55.000 33.33 23.39 42.24 4.94
2000 2064 0.669625 ACGTTTCTAGAAGGCGTGGC 60.670 55.000 25.73 6.10 34.38 5.01
2001 2065 0.669318 CGTTTCTAGAAGGCGTGGCA 60.669 55.000 17.78 0.00 0.00 4.92
2002 2066 1.519408 GTTTCTAGAAGGCGTGGCAA 58.481 50.000 5.12 0.00 0.00 4.52
2003 2067 1.877443 GTTTCTAGAAGGCGTGGCAAA 59.123 47.619 5.12 0.00 0.00 3.68
2004 2068 2.264005 TTCTAGAAGGCGTGGCAAAA 57.736 45.000 0.00 0.00 0.00 2.44
2005 2069 2.264005 TCTAGAAGGCGTGGCAAAAA 57.736 45.000 0.00 0.00 0.00 1.94
2029 2093 8.574196 AAAACAAAATCGGTACTCTGAAAATG 57.426 30.769 0.00 0.00 32.29 2.32
2030 2094 5.699839 ACAAAATCGGTACTCTGAAAATGC 58.300 37.500 0.00 0.00 32.29 3.56
2031 2095 5.473504 ACAAAATCGGTACTCTGAAAATGCT 59.526 36.000 0.00 0.00 32.29 3.79
2032 2096 6.653320 ACAAAATCGGTACTCTGAAAATGCTA 59.347 34.615 0.00 0.00 32.29 3.49
2033 2097 6.663944 AAATCGGTACTCTGAAAATGCTAC 57.336 37.500 0.00 0.00 32.29 3.58
2034 2098 5.599999 ATCGGTACTCTGAAAATGCTACT 57.400 39.130 0.00 0.00 32.29 2.57
2035 2099 5.401531 TCGGTACTCTGAAAATGCTACTT 57.598 39.130 0.00 0.00 0.00 2.24
2036 2100 5.790593 TCGGTACTCTGAAAATGCTACTTT 58.209 37.500 0.00 0.00 0.00 2.66
2037 2101 5.867716 TCGGTACTCTGAAAATGCTACTTTC 59.132 40.000 0.00 0.00 34.09 2.62
2038 2102 5.637810 CGGTACTCTGAAAATGCTACTTTCA 59.362 40.000 7.77 7.77 39.79 2.69
2039 2103 6.147164 CGGTACTCTGAAAATGCTACTTTCAA 59.853 38.462 8.91 2.50 41.10 2.69
2040 2104 7.307751 CGGTACTCTGAAAATGCTACTTTCAAA 60.308 37.037 8.91 0.00 41.10 2.69
2041 2105 8.349983 GGTACTCTGAAAATGCTACTTTCAAAA 58.650 33.333 8.91 2.31 41.10 2.44
2042 2106 9.387123 GTACTCTGAAAATGCTACTTTCAAAAG 57.613 33.333 0.97 0.97 41.10 2.27
2043 2107 6.920210 ACTCTGAAAATGCTACTTTCAAAAGC 59.080 34.615 2.43 0.00 41.10 3.51
2060 2124 4.628963 AAAGCATTTTGGAGGCTGAATT 57.371 36.364 0.00 0.00 31.62 2.17
2061 2125 4.628963 AAGCATTTTGGAGGCTGAATTT 57.371 36.364 0.00 0.00 38.04 1.82
2062 2126 5.743636 AAGCATTTTGGAGGCTGAATTTA 57.256 34.783 0.00 0.00 38.04 1.40
2063 2127 5.945144 AGCATTTTGGAGGCTGAATTTAT 57.055 34.783 0.00 0.00 36.34 1.40
2064 2128 6.303903 AGCATTTTGGAGGCTGAATTTATT 57.696 33.333 0.00 0.00 36.34 1.40
2065 2129 6.714278 AGCATTTTGGAGGCTGAATTTATTT 58.286 32.000 0.00 0.00 36.34 1.40
2066 2130 7.170277 AGCATTTTGGAGGCTGAATTTATTTT 58.830 30.769 0.00 0.00 36.34 1.82
2067 2131 7.666804 AGCATTTTGGAGGCTGAATTTATTTTT 59.333 29.630 0.00 0.00 36.34 1.94
2082 2146 3.926003 TTTTTGCCACGCCTCACA 58.074 50.000 0.00 0.00 0.00 3.58
2083 2147 1.732917 TTTTTGCCACGCCTCACAG 59.267 52.632 0.00 0.00 0.00 3.66
2084 2148 1.733402 TTTTTGCCACGCCTCACAGG 61.733 55.000 0.00 0.00 38.80 4.00
2085 2149 2.616797 TTTTGCCACGCCTCACAGGA 62.617 55.000 0.00 0.00 37.67 3.86
2086 2150 2.616797 TTTGCCACGCCTCACAGGAA 62.617 55.000 0.00 0.00 37.67 3.36
2087 2151 2.045926 GCCACGCCTCACAGGAAT 60.046 61.111 0.00 0.00 37.67 3.01
2088 2152 2.401766 GCCACGCCTCACAGGAATG 61.402 63.158 0.00 0.00 37.67 2.67
2089 2153 1.003355 CCACGCCTCACAGGAATGT 60.003 57.895 0.00 0.00 37.67 2.71
2090 2154 1.300971 CCACGCCTCACAGGAATGTG 61.301 60.000 1.95 1.95 37.67 3.21
2091 2155 0.320683 CACGCCTCACAGGAATGTGA 60.321 55.000 10.40 10.40 45.41 3.58
2092 2156 0.615331 ACGCCTCACAGGAATGTGAT 59.385 50.000 11.19 0.00 46.24 3.06
2093 2157 1.003580 ACGCCTCACAGGAATGTGATT 59.996 47.619 11.19 0.00 46.24 2.57
2094 2158 2.086869 CGCCTCACAGGAATGTGATTT 58.913 47.619 11.19 0.00 46.24 2.17
2095 2159 2.489329 CGCCTCACAGGAATGTGATTTT 59.511 45.455 11.19 0.00 46.24 1.82
2096 2160 3.689161 CGCCTCACAGGAATGTGATTTTA 59.311 43.478 11.19 0.00 46.24 1.52
2097 2161 4.336433 CGCCTCACAGGAATGTGATTTTAT 59.664 41.667 11.19 0.00 46.24 1.40
2098 2162 5.585390 GCCTCACAGGAATGTGATTTTATG 58.415 41.667 11.19 0.00 46.24 1.90
2099 2163 5.357878 GCCTCACAGGAATGTGATTTTATGA 59.642 40.000 11.19 0.00 46.24 2.15
2100 2164 6.040166 GCCTCACAGGAATGTGATTTTATGAT 59.960 38.462 11.19 0.00 46.24 2.45
2101 2165 7.423199 CCTCACAGGAATGTGATTTTATGATG 58.577 38.462 11.19 0.00 46.24 3.07
2102 2166 7.283807 CCTCACAGGAATGTGATTTTATGATGA 59.716 37.037 11.19 0.00 46.24 2.92
2103 2167 8.578448 TCACAGGAATGTGATTTTATGATGAA 57.422 30.769 6.97 0.00 43.09 2.57
2104 2168 9.192642 TCACAGGAATGTGATTTTATGATGAAT 57.807 29.630 6.97 0.00 43.09 2.57
2105 2169 9.811995 CACAGGAATGTGATTTTATGATGAATT 57.188 29.630 2.18 0.00 42.02 2.17
2114 2178 9.269415 GTGATTTTATGATGAATTTTTGCAAGC 57.731 29.630 0.00 0.00 0.00 4.01
2115 2179 9.000486 TGATTTTATGATGAATTTTTGCAAGCA 58.000 25.926 0.00 0.00 0.00 3.91
2116 2180 9.269415 GATTTTATGATGAATTTTTGCAAGCAC 57.731 29.630 0.00 0.00 0.00 4.40
2117 2181 7.966246 TTTATGATGAATTTTTGCAAGCACT 57.034 28.000 0.00 0.00 0.00 4.40
2118 2182 7.966246 TTATGATGAATTTTTGCAAGCACTT 57.034 28.000 0.00 0.00 0.00 3.16
2119 2183 9.486497 TTTATGATGAATTTTTGCAAGCACTTA 57.514 25.926 0.00 0.00 0.00 2.24
2120 2184 7.591006 ATGATGAATTTTTGCAAGCACTTAG 57.409 32.000 0.00 0.00 0.00 2.18
2121 2185 6.747125 TGATGAATTTTTGCAAGCACTTAGA 58.253 32.000 0.00 0.00 0.00 2.10
2122 2186 7.208777 TGATGAATTTTTGCAAGCACTTAGAA 58.791 30.769 0.00 0.00 0.00 2.10
2123 2187 6.826893 TGAATTTTTGCAAGCACTTAGAAC 57.173 33.333 0.00 0.00 0.00 3.01
2124 2188 6.572519 TGAATTTTTGCAAGCACTTAGAACT 58.427 32.000 0.00 0.00 0.00 3.01
2125 2189 7.041107 TGAATTTTTGCAAGCACTTAGAACTT 58.959 30.769 0.00 0.00 0.00 2.66
2126 2190 7.548780 TGAATTTTTGCAAGCACTTAGAACTTT 59.451 29.630 0.00 0.00 0.00 2.66
2127 2191 7.848223 ATTTTTGCAAGCACTTAGAACTTTT 57.152 28.000 0.00 0.00 0.00 2.27
2128 2192 6.645700 TTTTGCAAGCACTTAGAACTTTTG 57.354 33.333 0.00 0.00 0.00 2.44
2129 2193 4.981806 TGCAAGCACTTAGAACTTTTGT 57.018 36.364 0.00 0.00 0.00 2.83
2130 2194 4.920376 TGCAAGCACTTAGAACTTTTGTC 58.080 39.130 0.00 0.00 0.00 3.18
2131 2195 4.397730 TGCAAGCACTTAGAACTTTTGTCA 59.602 37.500 0.00 0.00 0.00 3.58
2132 2196 5.105957 TGCAAGCACTTAGAACTTTTGTCAA 60.106 36.000 0.00 0.00 0.00 3.18
2133 2197 5.979517 GCAAGCACTTAGAACTTTTGTCAAT 59.020 36.000 0.00 0.00 0.00 2.57
2134 2198 7.138736 GCAAGCACTTAGAACTTTTGTCAATA 58.861 34.615 0.00 0.00 0.00 1.90
2135 2199 7.809806 GCAAGCACTTAGAACTTTTGTCAATAT 59.190 33.333 0.00 0.00 0.00 1.28
2136 2200 9.683069 CAAGCACTTAGAACTTTTGTCAATATT 57.317 29.630 0.00 0.00 0.00 1.28
2138 2202 9.899226 AGCACTTAGAACTTTTGTCAATATTTC 57.101 29.630 0.00 0.00 0.00 2.17
2139 2203 9.899226 GCACTTAGAACTTTTGTCAATATTTCT 57.101 29.630 11.47 11.47 0.00 2.52
2145 2209 9.784531 AGAACTTTTGTCAATATTTCTCTGAGA 57.215 29.630 2.58 2.58 0.00 3.27
2203 2267 5.987777 TTTTCGATTTTACTGTTCACCGA 57.012 34.783 0.00 0.00 0.00 4.69
2204 2268 5.585500 TTTCGATTTTACTGTTCACCGAG 57.415 39.130 0.00 0.00 0.00 4.63
2205 2269 2.991190 TCGATTTTACTGTTCACCGAGC 59.009 45.455 0.00 0.00 0.00 5.03
2206 2270 2.993899 CGATTTTACTGTTCACCGAGCT 59.006 45.455 0.00 0.00 0.00 4.09
2207 2271 3.181530 CGATTTTACTGTTCACCGAGCTG 60.182 47.826 0.00 0.00 0.00 4.24
2208 2272 1.508632 TTTACTGTTCACCGAGCTGC 58.491 50.000 0.00 0.00 0.00 5.25
2209 2273 0.679505 TTACTGTTCACCGAGCTGCT 59.320 50.000 0.00 0.00 0.00 4.24
2210 2274 0.243907 TACTGTTCACCGAGCTGCTC 59.756 55.000 19.53 19.53 0.00 4.26
2225 2289 4.701663 CTCGGAAGCAGAAAGGCA 57.298 55.556 0.00 0.00 35.83 4.75
2226 2290 2.166270 CTCGGAAGCAGAAAGGCAC 58.834 57.895 0.00 0.00 35.83 5.01
2267 2372 9.922305 GAAATACTTTCACTATCTGTTATGTGC 57.078 33.333 0.00 0.00 39.45 4.57
2274 2379 5.350365 TCACTATCTGTTATGTGCGGAAAAC 59.650 40.000 0.00 0.00 0.00 2.43
2318 2424 2.803956 GCCGCTGTCAAGTTAAACTGTA 59.196 45.455 0.00 0.00 0.00 2.74
2664 2792 6.514048 CGACCTGCTTCTTTTTCTGAATTTCT 60.514 38.462 0.00 0.00 0.00 2.52
2666 2794 6.322201 ACCTGCTTCTTTTTCTGAATTTCTCA 59.678 34.615 0.00 0.00 0.00 3.27
2688 2816 2.621998 CCCAGAGCAAAATGGAGCATAG 59.378 50.000 0.00 0.00 39.02 2.23
2697 2825 5.695816 GCAAAATGGAGCATAGTTTGTCAAA 59.304 36.000 0.00 0.00 29.50 2.69
2706 2834 4.672801 GCATAGTTTGTCAAACAGCCTAGC 60.673 45.833 26.19 17.35 43.79 3.42
2725 2853 6.073711 GCCTAGCGTAAATCCATACTTTCTTC 60.074 42.308 0.00 0.00 0.00 2.87
2726 2854 7.210873 CCTAGCGTAAATCCATACTTTCTTCT 58.789 38.462 0.00 0.00 0.00 2.85
2760 2946 8.447833 CCAAAATTAGAGTGTACTATTTTCGCA 58.552 33.333 0.00 0.00 30.69 5.10
2761 2947 9.262472 CAAAATTAGAGTGTACTATTTTCGCAC 57.738 33.333 0.00 0.00 30.69 5.34
2815 3001 0.514255 GAACGGGTGTTACGGCTTTC 59.486 55.000 0.00 0.00 38.78 2.62
2877 3063 4.389890 TCTCTGCAAAGCAACAAACATT 57.610 36.364 0.00 0.00 38.41 2.71
2878 3064 5.512753 TCTCTGCAAAGCAACAAACATTA 57.487 34.783 0.00 0.00 38.41 1.90
2879 3065 5.522456 TCTCTGCAAAGCAACAAACATTAG 58.478 37.500 0.00 0.00 38.41 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
83 89 8.158169 TCTGAGAATAACATACATGCAATTCC 57.842 34.615 0.00 6.30 34.94 3.01
87 93 7.209475 TCGATCTGAGAATAACATACATGCAA 58.791 34.615 0.00 0.00 0.00 4.08
127 136 8.605354 CGTAAAAGACGTTGATACATACTGTA 57.395 34.615 0.00 0.00 46.86 2.74
128 137 7.502177 CGTAAAAGACGTTGATACATACTGT 57.498 36.000 0.00 0.00 46.86 3.55
233 251 3.736126 GCTTTGAGAGGCATTACCATTGC 60.736 47.826 0.00 0.00 43.14 3.56
247 265 0.461548 ATCGATCGCAGGCTTTGAGA 59.538 50.000 11.09 0.00 40.01 3.27
249 267 0.871592 CGATCGATCGCAGGCTTTGA 60.872 55.000 32.34 0.00 43.84 2.69
250 268 1.561730 CGATCGATCGCAGGCTTTG 59.438 57.895 32.34 5.85 43.84 2.77
260 278 1.720316 CTCTGCAATGCTCGATCGATC 59.280 52.381 19.78 15.57 0.00 3.69
261 279 1.068281 ACTCTGCAATGCTCGATCGAT 59.932 47.619 19.78 0.00 0.00 3.59
262 280 0.457443 ACTCTGCAATGCTCGATCGA 59.543 50.000 18.32 18.32 0.00 3.59
282 300 1.352017 TCTTGAAATGCAGGAGGCTCA 59.648 47.619 17.69 0.00 45.15 4.26
301 319 1.268234 GCGAATTAGCAGTGCATGGTC 60.268 52.381 19.20 8.25 40.89 4.02
311 329 3.202001 GGCGCTGGCGAATTAGCA 61.202 61.111 19.31 0.00 42.83 3.49
345 367 3.510388 AGGGATGTATGTATGATCGCG 57.490 47.619 0.00 0.00 34.98 5.87
387 409 0.250814 TGCATCCACACATCAGCACA 60.251 50.000 0.00 0.00 0.00 4.57
388 410 0.169672 GTGCATCCACACATCAGCAC 59.830 55.000 0.00 0.00 44.31 4.40
389 411 1.300266 CGTGCATCCACACATCAGCA 61.300 55.000 0.00 0.00 42.17 4.41
390 412 1.300971 ACGTGCATCCACACATCAGC 61.301 55.000 0.00 0.00 42.17 4.26
391 413 1.660607 GTACGTGCATCCACACATCAG 59.339 52.381 0.00 0.00 42.17 2.90
392 414 1.275010 AGTACGTGCATCCACACATCA 59.725 47.619 6.38 0.00 42.17 3.07
399 421 0.533491 GGTGGTAGTACGTGCATCCA 59.467 55.000 13.60 13.60 0.00 3.41
427 449 3.301116 GCTATTCGGATAAGTTCGATCGC 59.699 47.826 11.09 0.00 35.25 4.58
444 473 2.852449 TCCCATGTTCCCTCTTGCTATT 59.148 45.455 0.00 0.00 0.00 1.73
502 532 0.457166 CGTTCTGGTTACGATGGCGA 60.457 55.000 0.00 0.00 41.33 5.54
867 911 2.448542 ACTGACCAGTGGGCCAGT 60.449 61.111 25.06 25.06 40.75 4.00
884 928 2.039746 CCAAATACACCACCTCAGGTCA 59.960 50.000 0.00 0.00 40.77 4.02
900 944 0.251787 GCCCCCAACTGTCTCCAAAT 60.252 55.000 0.00 0.00 0.00 2.32
1177 1232 1.212751 CATCGATCTGGCCGCGATA 59.787 57.895 18.08 2.04 42.23 2.92
1259 1314 4.834453 CAGCTGCTCGAGGGCCTG 62.834 72.222 12.95 3.26 0.00 4.85
1264 1319 4.383861 TGGTGCAGCTGCTCGAGG 62.384 66.667 36.61 0.00 42.66 4.63
1339 1394 4.669842 AGCTCGCGCTTGCTGACA 62.670 61.111 20.30 0.00 46.47 3.58
1405 1460 4.862092 CGATCAGCAGACGCCGCT 62.862 66.667 0.00 0.00 41.47 5.52
1585 1640 6.824305 ACTAAACCGCTAGTAACTCAGTAA 57.176 37.500 0.00 0.00 30.13 2.24
1600 1658 3.050619 GACGCCATCATCTACTAAACCG 58.949 50.000 0.00 0.00 0.00 4.44
1604 1662 2.032290 CGACGACGCCATCATCTACTAA 60.032 50.000 0.00 0.00 0.00 2.24
1705 1769 5.537674 AGGAACAAGAACAAATCAAGAGCAT 59.462 36.000 0.00 0.00 0.00 3.79
1722 1786 8.442374 AGTTTAACCCTCATAGTTAAGGAACAA 58.558 33.333 0.00 0.00 39.96 2.83
1770 1834 0.631998 ATGGAGGAGGAGGAGGAGGA 60.632 60.000 0.00 0.00 0.00 3.71
1771 1835 0.178935 GATGGAGGAGGAGGAGGAGG 60.179 65.000 0.00 0.00 0.00 4.30
1772 1836 0.560193 TGATGGAGGAGGAGGAGGAG 59.440 60.000 0.00 0.00 0.00 3.69
1773 1837 0.560193 CTGATGGAGGAGGAGGAGGA 59.440 60.000 0.00 0.00 0.00 3.71
1774 1838 1.120795 GCTGATGGAGGAGGAGGAGG 61.121 65.000 0.00 0.00 0.00 4.30
1775 1839 0.105555 AGCTGATGGAGGAGGAGGAG 60.106 60.000 0.00 0.00 0.00 3.69
1776 1840 0.341258 AAGCTGATGGAGGAGGAGGA 59.659 55.000 0.00 0.00 0.00 3.71
1777 1841 0.469070 CAAGCTGATGGAGGAGGAGG 59.531 60.000 0.00 0.00 0.00 4.30
1810 1874 4.383649 CGCACAATCTCCAAAATTTCACAG 59.616 41.667 0.00 0.00 0.00 3.66
1811 1875 4.037327 TCGCACAATCTCCAAAATTTCACA 59.963 37.500 0.00 0.00 0.00 3.58
1832 1896 6.073058 TCACCTCTCATTTTTCATCTGTTTCG 60.073 38.462 0.00 0.00 0.00 3.46
1922 1986 8.527810 ACTTTTGTCAATGTTTCTACCAAGAAA 58.472 29.630 0.00 0.00 46.96 2.52
1923 1987 8.062065 ACTTTTGTCAATGTTTCTACCAAGAA 57.938 30.769 0.00 0.00 40.03 2.52
1924 1988 7.639113 ACTTTTGTCAATGTTTCTACCAAGA 57.361 32.000 0.00 0.00 0.00 3.02
1925 1989 8.702163 AAACTTTTGTCAATGTTTCTACCAAG 57.298 30.769 9.87 0.14 36.13 3.61
1931 1995 9.366216 GGACTTAAAACTTTTGTCAATGTTTCT 57.634 29.630 13.86 9.23 38.61 2.52
1932 1996 9.366216 AGGACTTAAAACTTTTGTCAATGTTTC 57.634 29.630 13.86 5.49 38.61 2.78
1933 1997 9.719355 AAGGACTTAAAACTTTTGTCAATGTTT 57.281 25.926 9.87 9.87 40.32 2.83
1934 1998 9.150348 CAAGGACTTAAAACTTTTGTCAATGTT 57.850 29.630 0.00 0.00 32.90 2.71
1935 1999 7.277760 GCAAGGACTTAAAACTTTTGTCAATGT 59.722 33.333 0.00 0.00 0.00 2.71
1936 2000 7.277539 TGCAAGGACTTAAAACTTTTGTCAATG 59.722 33.333 0.00 2.36 0.00 2.82
1937 2001 7.327214 TGCAAGGACTTAAAACTTTTGTCAAT 58.673 30.769 0.00 0.00 0.00 2.57
1938 2002 6.692486 TGCAAGGACTTAAAACTTTTGTCAA 58.308 32.000 0.00 0.00 0.00 3.18
1939 2003 6.274157 TGCAAGGACTTAAAACTTTTGTCA 57.726 33.333 0.00 0.00 0.00 3.58
1940 2004 7.589574 TTTGCAAGGACTTAAAACTTTTGTC 57.410 32.000 0.00 0.00 0.00 3.18
1941 2005 7.971183 TTTTGCAAGGACTTAAAACTTTTGT 57.029 28.000 0.00 0.00 0.00 2.83
1942 2006 9.838975 AATTTTTGCAAGGACTTAAAACTTTTG 57.161 25.926 0.00 0.00 0.00 2.44
1944 2008 8.387354 CGAATTTTTGCAAGGACTTAAAACTTT 58.613 29.630 0.00 0.00 0.00 2.66
1945 2009 7.547722 ACGAATTTTTGCAAGGACTTAAAACTT 59.452 29.630 0.00 0.00 0.00 2.66
1946 2010 7.039270 ACGAATTTTTGCAAGGACTTAAAACT 58.961 30.769 0.00 0.00 0.00 2.66
1947 2011 7.009723 TGACGAATTTTTGCAAGGACTTAAAAC 59.990 33.333 0.00 0.00 0.00 2.43
1948 2012 7.036220 TGACGAATTTTTGCAAGGACTTAAAA 58.964 30.769 0.00 0.00 0.00 1.52
1949 2013 6.565234 TGACGAATTTTTGCAAGGACTTAAA 58.435 32.000 0.00 0.00 0.00 1.52
1950 2014 6.137794 TGACGAATTTTTGCAAGGACTTAA 57.862 33.333 0.00 0.00 0.00 1.85
1951 2015 5.759506 TGACGAATTTTTGCAAGGACTTA 57.240 34.783 0.00 0.00 0.00 2.24
1952 2016 4.647424 TGACGAATTTTTGCAAGGACTT 57.353 36.364 0.00 0.00 0.00 3.01
1953 2017 4.278170 TCATGACGAATTTTTGCAAGGACT 59.722 37.500 0.00 0.00 0.00 3.85
1954 2018 4.545610 TCATGACGAATTTTTGCAAGGAC 58.454 39.130 0.00 0.00 0.00 3.85
1955 2019 4.844998 TCATGACGAATTTTTGCAAGGA 57.155 36.364 0.00 0.00 0.00 3.36
1956 2020 5.903764 TTTCATGACGAATTTTTGCAAGG 57.096 34.783 0.00 0.00 32.32 3.61
1957 2021 7.005380 GTGATTTCATGACGAATTTTTGCAAG 58.995 34.615 0.00 0.00 32.32 4.01
1958 2022 6.345644 CGTGATTTCATGACGAATTTTTGCAA 60.346 34.615 0.00 0.00 35.05 4.08
1959 2023 5.116831 CGTGATTTCATGACGAATTTTTGCA 59.883 36.000 0.00 0.00 35.05 4.08
1960 2024 5.116983 ACGTGATTTCATGACGAATTTTTGC 59.883 36.000 10.46 0.00 36.90 3.68
1961 2025 6.674005 ACGTGATTTCATGACGAATTTTTG 57.326 33.333 10.46 0.00 36.90 2.44
1962 2026 7.692908 AAACGTGATTTCATGACGAATTTTT 57.307 28.000 10.46 0.00 36.90 1.94
1963 2027 7.320499 GAAACGTGATTTCATGACGAATTTT 57.680 32.000 10.46 1.79 45.32 1.82
1964 2028 6.911484 GAAACGTGATTTCATGACGAATTT 57.089 33.333 10.46 2.40 45.32 1.82
1975 2039 3.678548 ACGCCTTCTAGAAACGTGATTTC 59.321 43.478 24.52 0.00 46.21 2.17
1976 2040 3.432252 CACGCCTTCTAGAAACGTGATTT 59.568 43.478 35.00 14.55 45.69 2.17
1977 2041 2.993899 CACGCCTTCTAGAAACGTGATT 59.006 45.455 35.00 14.83 45.69 2.57
1978 2042 2.607187 CACGCCTTCTAGAAACGTGAT 58.393 47.619 35.00 15.09 45.69 3.06
1979 2043 1.336517 CCACGCCTTCTAGAAACGTGA 60.337 52.381 37.43 10.00 45.69 4.35
1980 2044 1.068474 CCACGCCTTCTAGAAACGTG 58.932 55.000 33.18 33.18 44.05 4.49
1981 2045 0.669625 GCCACGCCTTCTAGAAACGT 60.670 55.000 21.35 21.35 34.73 3.99
1982 2046 0.669318 TGCCACGCCTTCTAGAAACG 60.669 55.000 20.30 20.30 0.00 3.60
1983 2047 1.519408 TTGCCACGCCTTCTAGAAAC 58.481 50.000 6.63 0.98 0.00 2.78
1984 2048 2.264005 TTTGCCACGCCTTCTAGAAA 57.736 45.000 6.63 0.00 0.00 2.52
1985 2049 2.264005 TTTTGCCACGCCTTCTAGAA 57.736 45.000 4.81 4.81 0.00 2.10
1986 2050 2.264005 TTTTTGCCACGCCTTCTAGA 57.736 45.000 0.00 0.00 0.00 2.43
2003 2067 9.030301 CATTTTCAGAGTACCGATTTTGTTTTT 57.970 29.630 0.00 0.00 0.00 1.94
2004 2068 7.169140 GCATTTTCAGAGTACCGATTTTGTTTT 59.831 33.333 0.00 0.00 0.00 2.43
2005 2069 6.640907 GCATTTTCAGAGTACCGATTTTGTTT 59.359 34.615 0.00 0.00 0.00 2.83
2006 2070 6.016276 AGCATTTTCAGAGTACCGATTTTGTT 60.016 34.615 0.00 0.00 0.00 2.83
2007 2071 5.473504 AGCATTTTCAGAGTACCGATTTTGT 59.526 36.000 0.00 0.00 0.00 2.83
2008 2072 5.942872 AGCATTTTCAGAGTACCGATTTTG 58.057 37.500 0.00 0.00 0.00 2.44
2009 2073 6.879458 AGTAGCATTTTCAGAGTACCGATTTT 59.121 34.615 0.00 0.00 0.00 1.82
2010 2074 6.407202 AGTAGCATTTTCAGAGTACCGATTT 58.593 36.000 0.00 0.00 0.00 2.17
2011 2075 5.978814 AGTAGCATTTTCAGAGTACCGATT 58.021 37.500 0.00 0.00 0.00 3.34
2012 2076 5.599999 AGTAGCATTTTCAGAGTACCGAT 57.400 39.130 0.00 0.00 0.00 4.18
2013 2077 5.401531 AAGTAGCATTTTCAGAGTACCGA 57.598 39.130 0.00 0.00 0.00 4.69
2014 2078 5.637810 TGAAAGTAGCATTTTCAGAGTACCG 59.362 40.000 6.29 0.00 39.05 4.02
2015 2079 7.435068 TTGAAAGTAGCATTTTCAGAGTACC 57.565 36.000 9.30 0.00 43.22 3.34
2016 2080 9.387123 CTTTTGAAAGTAGCATTTTCAGAGTAC 57.613 33.333 9.30 0.00 43.22 2.73
2017 2081 8.076178 GCTTTTGAAAGTAGCATTTTCAGAGTA 58.924 33.333 5.47 0.00 43.22 2.59
2018 2082 6.920210 GCTTTTGAAAGTAGCATTTTCAGAGT 59.080 34.615 5.47 0.00 43.22 3.24
2019 2083 6.919662 TGCTTTTGAAAGTAGCATTTTCAGAG 59.080 34.615 0.45 11.39 43.22 3.35
2020 2084 6.804677 TGCTTTTGAAAGTAGCATTTTCAGA 58.195 32.000 0.45 4.38 43.22 3.27
2038 2102 4.628963 ATTCAGCCTCCAAAATGCTTTT 57.371 36.364 0.00 0.00 31.77 2.27
2039 2103 4.628963 AATTCAGCCTCCAAAATGCTTT 57.371 36.364 0.00 0.00 31.77 3.51
2040 2104 4.628963 AAATTCAGCCTCCAAAATGCTT 57.371 36.364 0.00 0.00 31.77 3.91
2041 2105 5.945144 ATAAATTCAGCCTCCAAAATGCT 57.055 34.783 0.00 0.00 35.25 3.79
2042 2106 6.990341 AAATAAATTCAGCCTCCAAAATGC 57.010 33.333 0.00 0.00 0.00 3.56
2065 2129 1.732917 CTGTGAGGCGTGGCAAAAA 59.267 52.632 0.00 0.00 0.00 1.94
2066 2130 2.192861 CCTGTGAGGCGTGGCAAAA 61.193 57.895 0.00 0.00 0.00 2.44
2067 2131 2.594303 CCTGTGAGGCGTGGCAAA 60.594 61.111 0.00 0.00 0.00 3.68
2068 2132 2.410322 ATTCCTGTGAGGCGTGGCAA 62.410 55.000 0.00 0.00 34.61 4.52
2069 2133 2.894257 ATTCCTGTGAGGCGTGGCA 61.894 57.895 0.00 0.00 34.61 4.92
2070 2134 2.045926 ATTCCTGTGAGGCGTGGC 60.046 61.111 0.00 0.00 34.61 5.01
2071 2135 1.003355 ACATTCCTGTGAGGCGTGG 60.003 57.895 0.00 0.00 34.61 4.94
2072 2136 4.701663 ACATTCCTGTGAGGCGTG 57.298 55.556 0.00 0.00 34.61 5.34
2088 2152 9.269415 GCTTGCAAAAATTCATCATAAAATCAC 57.731 29.630 0.00 0.00 0.00 3.06
2089 2153 9.000486 TGCTTGCAAAAATTCATCATAAAATCA 58.000 25.926 0.00 0.00 0.00 2.57
2090 2154 9.269415 GTGCTTGCAAAAATTCATCATAAAATC 57.731 29.630 0.00 0.00 0.00 2.17
2091 2155 9.005777 AGTGCTTGCAAAAATTCATCATAAAAT 57.994 25.926 0.00 0.00 0.00 1.82
2092 2156 8.380743 AGTGCTTGCAAAAATTCATCATAAAA 57.619 26.923 0.00 0.00 0.00 1.52
2093 2157 7.966246 AGTGCTTGCAAAAATTCATCATAAA 57.034 28.000 0.00 0.00 0.00 1.40
2094 2158 7.966246 AAGTGCTTGCAAAAATTCATCATAA 57.034 28.000 0.00 0.00 0.00 1.90
2095 2159 8.522003 TCTAAGTGCTTGCAAAAATTCATCATA 58.478 29.630 0.00 0.00 0.00 2.15
2096 2160 7.380536 TCTAAGTGCTTGCAAAAATTCATCAT 58.619 30.769 0.00 0.00 0.00 2.45
2097 2161 6.747125 TCTAAGTGCTTGCAAAAATTCATCA 58.253 32.000 0.00 0.00 0.00 3.07
2098 2162 7.383300 AGTTCTAAGTGCTTGCAAAAATTCATC 59.617 33.333 0.00 0.00 0.00 2.92
2099 2163 7.212274 AGTTCTAAGTGCTTGCAAAAATTCAT 58.788 30.769 0.00 0.00 0.00 2.57
2100 2164 6.572519 AGTTCTAAGTGCTTGCAAAAATTCA 58.427 32.000 0.00 0.00 0.00 2.57
2101 2165 7.468922 AAGTTCTAAGTGCTTGCAAAAATTC 57.531 32.000 0.00 0.00 0.00 2.17
2102 2166 7.848223 AAAGTTCTAAGTGCTTGCAAAAATT 57.152 28.000 0.00 0.00 0.00 1.82
2103 2167 7.334171 ACAAAAGTTCTAAGTGCTTGCAAAAAT 59.666 29.630 0.00 0.00 0.00 1.82
2104 2168 6.648725 ACAAAAGTTCTAAGTGCTTGCAAAAA 59.351 30.769 0.00 0.00 0.00 1.94
2105 2169 6.162777 ACAAAAGTTCTAAGTGCTTGCAAAA 58.837 32.000 0.00 0.00 0.00 2.44
2106 2170 5.719173 ACAAAAGTTCTAAGTGCTTGCAAA 58.281 33.333 0.00 0.00 0.00 3.68
2107 2171 5.105957 TGACAAAAGTTCTAAGTGCTTGCAA 60.106 36.000 0.00 0.00 0.00 4.08
2108 2172 4.397730 TGACAAAAGTTCTAAGTGCTTGCA 59.602 37.500 0.00 0.00 0.00 4.08
2109 2173 4.920376 TGACAAAAGTTCTAAGTGCTTGC 58.080 39.130 0.00 0.00 0.00 4.01
2110 2174 9.683069 AATATTGACAAAAGTTCTAAGTGCTTG 57.317 29.630 0.00 0.00 0.00 4.01
2112 2176 9.899226 GAAATATTGACAAAAGTTCTAAGTGCT 57.101 29.630 0.00 0.00 0.00 4.40
2113 2177 9.899226 AGAAATATTGACAAAAGTTCTAAGTGC 57.101 29.630 8.19 0.00 0.00 4.40
2119 2183 9.784531 TCTCAGAGAAATATTGACAAAAGTTCT 57.215 29.630 0.00 9.24 0.00 3.01
2180 2244 6.360844 TCGGTGAACAGTAAAATCGAAAAA 57.639 33.333 0.00 0.00 0.00 1.94
2181 2245 5.559417 GCTCGGTGAACAGTAAAATCGAAAA 60.559 40.000 0.00 0.00 0.00 2.29
2182 2246 4.084223 GCTCGGTGAACAGTAAAATCGAAA 60.084 41.667 0.00 0.00 0.00 3.46
2183 2247 3.430895 GCTCGGTGAACAGTAAAATCGAA 59.569 43.478 0.00 0.00 0.00 3.71
2184 2248 2.991190 GCTCGGTGAACAGTAAAATCGA 59.009 45.455 0.00 0.00 0.00 3.59
2185 2249 2.993899 AGCTCGGTGAACAGTAAAATCG 59.006 45.455 0.00 0.00 0.00 3.34
2186 2250 3.424962 GCAGCTCGGTGAACAGTAAAATC 60.425 47.826 0.00 0.00 0.00 2.17
2187 2251 2.484264 GCAGCTCGGTGAACAGTAAAAT 59.516 45.455 0.00 0.00 0.00 1.82
2188 2252 1.871039 GCAGCTCGGTGAACAGTAAAA 59.129 47.619 0.00 0.00 0.00 1.52
2189 2253 1.070134 AGCAGCTCGGTGAACAGTAAA 59.930 47.619 0.00 0.00 0.00 2.01
2190 2254 0.679505 AGCAGCTCGGTGAACAGTAA 59.320 50.000 0.00 0.00 0.00 2.24
2191 2255 0.243907 GAGCAGCTCGGTGAACAGTA 59.756 55.000 6.67 0.00 0.00 2.74
2192 2256 1.005630 GAGCAGCTCGGTGAACAGT 60.006 57.895 6.67 0.00 0.00 3.55
2193 2257 3.867771 GAGCAGCTCGGTGAACAG 58.132 61.111 6.67 0.00 0.00 3.16
2208 2272 0.321122 AGTGCCTTTCTGCTTCCGAG 60.321 55.000 0.00 0.00 0.00 4.63
2209 2273 0.108585 AAGTGCCTTTCTGCTTCCGA 59.891 50.000 0.00 0.00 0.00 4.55
2210 2274 0.954452 AAAGTGCCTTTCTGCTTCCG 59.046 50.000 0.00 0.00 0.00 4.30
2211 2275 1.068954 CGAAAGTGCCTTTCTGCTTCC 60.069 52.381 19.11 0.67 45.19 3.46
2212 2276 1.664302 GCGAAAGTGCCTTTCTGCTTC 60.664 52.381 21.80 9.04 45.19 3.86
2213 2277 0.312102 GCGAAAGTGCCTTTCTGCTT 59.688 50.000 21.80 0.00 45.19 3.91
2214 2278 0.819259 TGCGAAAGTGCCTTTCTGCT 60.819 50.000 25.10 2.83 45.19 4.24
2215 2279 0.242017 ATGCGAAAGTGCCTTTCTGC 59.758 50.000 22.03 22.03 45.19 4.26
2216 2280 2.030893 TGAATGCGAAAGTGCCTTTCTG 60.031 45.455 19.11 14.97 45.19 3.02
2217 2281 2.229792 TGAATGCGAAAGTGCCTTTCT 58.770 42.857 19.11 6.52 45.19 2.52
2218 2282 2.704725 TGAATGCGAAAGTGCCTTTC 57.295 45.000 14.28 14.28 44.29 2.62
2219 2283 2.821969 AGATGAATGCGAAAGTGCCTTT 59.178 40.909 0.46 0.46 36.29 3.11
2220 2284 2.163010 CAGATGAATGCGAAAGTGCCTT 59.837 45.455 0.00 0.00 0.00 4.35
2221 2285 1.741706 CAGATGAATGCGAAAGTGCCT 59.258 47.619 0.00 0.00 0.00 4.75
2222 2286 1.739466 TCAGATGAATGCGAAAGTGCC 59.261 47.619 0.00 0.00 0.00 5.01
2223 2287 3.476295 TTCAGATGAATGCGAAAGTGC 57.524 42.857 0.00 0.00 0.00 4.40
2224 2288 6.779117 AGTATTTCAGATGAATGCGAAAGTG 58.221 36.000 0.00 0.00 33.54 3.16
2225 2289 6.992063 AGTATTTCAGATGAATGCGAAAGT 57.008 33.333 0.00 0.00 33.54 2.66
2260 2365 3.745799 TCCTGAAGTTTTCCGCACATAA 58.254 40.909 0.00 0.00 0.00 1.90
2267 2372 6.126568 TGTTTTTACTCCTGAAGTTTTCCG 57.873 37.500 0.00 0.00 39.55 4.30
2274 2379 5.514279 CAGCACTTGTTTTTACTCCTGAAG 58.486 41.667 0.00 0.00 0.00 3.02
2318 2424 1.812708 GCCACGAACCCACAGTTTACT 60.813 52.381 0.00 0.00 39.40 2.24
2581 2708 1.834263 AGGAGGAGAAAATGACCCTCG 59.166 52.381 0.00 0.00 44.60 4.63
2646 2773 7.013655 TCTGGGTGAGAAATTCAGAAAAAGAAG 59.986 37.037 0.00 0.00 36.21 2.85
2664 2792 1.887956 GCTCCATTTTGCTCTGGGTGA 60.888 52.381 0.00 0.00 33.13 4.02
2666 2794 0.112995 TGCTCCATTTTGCTCTGGGT 59.887 50.000 0.00 0.00 33.13 4.51
2688 2816 1.602377 ACGCTAGGCTGTTTGACAAAC 59.398 47.619 21.68 21.68 41.73 2.93
2697 2825 3.641906 AGTATGGATTTACGCTAGGCTGT 59.358 43.478 0.00 0.00 0.00 4.40
2742 2870 3.508762 CGGTGCGAAAATAGTACACTCT 58.491 45.455 0.00 0.00 0.00 3.24
2750 2936 0.378257 ATGCTGCGGTGCGAAAATAG 59.622 50.000 0.00 0.00 35.36 1.73
2877 3063 1.411246 CGGGCAGCAGGTATGTTACTA 59.589 52.381 0.00 0.00 0.00 1.82
2878 3064 0.178068 CGGGCAGCAGGTATGTTACT 59.822 55.000 0.00 0.00 0.00 2.24
2879 3065 2.690326 CGGGCAGCAGGTATGTTAC 58.310 57.895 0.00 0.00 0.00 2.50


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

AutoCloner maintained by Alex Coulton.