Multiple sequence alignment - TraesCS3B01G161700

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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 TraesCS3B01G161700 chr3B 100.000 2720 0 0 1 2720 158220161 158217442 0.000000e+00 5024.0
1 TraesCS3B01G161700 chr3B 90.756 1309 98 11 1 1294 158237701 158236401 0.000000e+00 1725.0
2 TraesCS3B01G161700 chr3B 88.889 54 5 1 1052 1105 701124262 701124210 6.290000e-07 65.8
3 TraesCS3B01G161700 chr3D 93.889 1080 42 11 855 1921 107441675 107440607 0.000000e+00 1607.0
4 TraesCS3B01G161700 chr3D 79.825 342 45 9 2101 2424 107440529 107440194 7.580000e-56 228.0
5 TraesCS3B01G161700 chr3A 92.518 1136 50 21 774 1887 124655369 124656491 0.000000e+00 1594.0
6 TraesCS3B01G161700 chr3A 96.970 33 1 0 2616 2648 25763197 25763165 3.780000e-04 56.5
7 TraesCS3B01G161700 chrUn 82.138 683 92 20 1 678 2430294 2430951 2.370000e-155 558.0
8 TraesCS3B01G161700 chr6B 83.755 554 60 13 2101 2625 260104547 260103995 5.230000e-137 497.0
9 TraesCS3B01G161700 chr5D 80.115 523 71 15 2106 2601 369325644 369326160 2.580000e-95 359.0
10 TraesCS3B01G161700 chr2A 87.500 256 25 6 1011 1260 675937632 675937886 3.430000e-74 289.0
11 TraesCS3B01G161700 chr4B 90.741 54 4 1 1052 1105 267356510 267356458 1.350000e-08 71.3
12 TraesCS3B01G161700 chr4B 90.741 54 4 1 1052 1105 614206807 614206755 1.350000e-08 71.3
13 TraesCS3B01G161700 chr2B 90.741 54 4 1 1052 1105 96276369 96276421 1.350000e-08 71.3
14 TraesCS3B01G161700 chr1B 88.889 54 5 1 1052 1105 127374013 127373961 6.290000e-07 65.8
15 TraesCS3B01G161700 chr7A 91.111 45 3 1 2616 2660 452062633 452062676 2.920000e-05 60.2


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3B01G161700 chr3B 158217442 158220161 2719 True 5024.0 5024 100.000 1 2720 1 chr3B.!!$R1 2719
1 TraesCS3B01G161700 chr3B 158236401 158237701 1300 True 1725.0 1725 90.756 1 1294 1 chr3B.!!$R2 1293
2 TraesCS3B01G161700 chr3D 107440194 107441675 1481 True 917.5 1607 86.857 855 2424 2 chr3D.!!$R1 1569
3 TraesCS3B01G161700 chr3A 124655369 124656491 1122 False 1594.0 1594 92.518 774 1887 1 chr3A.!!$F1 1113
4 TraesCS3B01G161700 chrUn 2430294 2430951 657 False 558.0 558 82.138 1 678 1 chrUn.!!$F1 677
5 TraesCS3B01G161700 chr6B 260103995 260104547 552 True 497.0 497 83.755 2101 2625 1 chr6B.!!$R1 524
6 TraesCS3B01G161700 chr5D 369325644 369326160 516 False 359.0 359 80.115 2106 2601 1 chr5D.!!$F1 495

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
403 408 0.031857 CAACAAAATGGTCGCTGCCA 59.968 50.0 0.0 0.0 43.48 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1974 2020 0.030504 CAAATGTCAAGTGCGGCACA 59.969 50.0 32.29 13.92 36.74 4.57 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
109 110 6.205784 TCCAACAAAATGAAAGACGATTGTC 58.794 36.000 4.78 4.78 45.86 3.18
241 246 5.778862 GCTTTCCAGCAAAACAATAACCTA 58.221 37.500 0.00 0.00 46.49 3.08
257 262 7.092174 ACAATAACCTACTTGTATCATCCCCAA 60.092 37.037 0.00 0.00 33.96 4.12
303 308 3.736252 CGGAGGTTGTAGCTTTATCATCG 59.264 47.826 0.00 0.00 0.00 3.84
305 310 5.542779 GGAGGTTGTAGCTTTATCATCGAT 58.457 41.667 0.00 0.00 0.00 3.59
306 311 5.406780 GGAGGTTGTAGCTTTATCATCGATG 59.593 44.000 19.61 19.61 0.00 3.84
307 312 5.300752 AGGTTGTAGCTTTATCATCGATGG 58.699 41.667 24.61 9.70 0.00 3.51
334 339 3.063915 TTTTTGCCAGCTGCCCATA 57.936 47.368 8.66 0.00 40.16 2.74
355 360 3.050275 GACAGCCGGTTCCAGCAC 61.050 66.667 1.90 0.00 0.00 4.40
372 377 2.591429 CGCCTCTGGTGTTGCACA 60.591 61.111 1.61 0.00 35.86 4.57
396 401 1.726248 GCCGATTGCAACAAAATGGTC 59.274 47.619 0.00 0.00 40.77 4.02
401 406 0.597118 TGCAACAAAATGGTCGCTGC 60.597 50.000 0.00 0.00 0.00 5.25
403 408 0.031857 CAACAAAATGGTCGCTGCCA 59.968 50.000 0.00 0.00 43.48 4.92
437 442 0.310854 GTTGCCAGTTGTAGCACCAC 59.689 55.000 0.00 0.00 39.10 4.16
459 464 0.733729 CCGACTAGTGGGTCTTCTCG 59.266 60.000 15.41 2.01 34.38 4.04
474 479 3.729965 CTCGAGCGCCATCAGCCTT 62.730 63.158 2.29 0.00 38.78 4.35
499 505 2.029743 GCAAAACGCTCCCTGTTCA 58.970 52.632 0.00 0.00 37.77 3.18
502 508 1.782028 AAAACGCTCCCTGTTCACGC 61.782 55.000 0.00 0.00 0.00 5.34
512 518 3.723348 GTTCACGCCAACCCTCGC 61.723 66.667 0.00 0.00 0.00 5.03
593 599 2.159599 GCTGCATCGTGAGGAAGAAAAG 60.160 50.000 0.00 0.00 0.00 2.27
596 602 2.615493 GCATCGTGAGGAAGAAAAGGGA 60.615 50.000 0.00 0.00 0.00 4.20
646 653 2.768492 GCATGGGGAAAGAGCTGCG 61.768 63.158 0.00 0.00 0.00 5.18
649 656 4.722700 GGGGAAAGAGCTGCGGCA 62.723 66.667 21.93 1.29 41.70 5.69
668 675 1.071699 CACAGAAAGGGGGAGAACGAA 59.928 52.381 0.00 0.00 0.00 3.85
672 679 1.280998 GAAAGGGGGAGAACGAATGGA 59.719 52.381 0.00 0.00 0.00 3.41
681 688 0.177141 GAACGAATGGATGGGGACGA 59.823 55.000 0.00 0.00 0.00 4.20
690 697 1.618143 ATGGGGACGATGGGTTGGA 60.618 57.895 0.00 0.00 0.00 3.53
726 733 2.418746 CCCAGATCAAACAGTAGGGTCG 60.419 54.545 0.00 0.00 0.00 4.79
730 737 0.390124 TCAAACAGTAGGGTCGCGTT 59.610 50.000 5.77 0.00 0.00 4.84
733 740 2.202570 CAGTAGGGTCGCGTTCGG 60.203 66.667 5.77 0.00 36.13 4.30
749 756 2.263540 GGCCGAAGTGTAAGCCGA 59.736 61.111 0.00 0.00 35.30 5.54
750 757 2.098831 GGCCGAAGTGTAAGCCGAC 61.099 63.158 0.00 0.00 35.30 4.79
765 772 2.388232 CGACCTGCCGGCAGTAAAC 61.388 63.158 44.92 31.85 42.15 2.01
829 841 7.122204 GGGAATAACCAGCTACTATTGTTTTGT 59.878 37.037 0.00 0.00 41.20 2.83
846 858 1.954146 GTGTTTGGCTCGCTCGTGA 60.954 57.895 0.00 0.00 0.00 4.35
1112 1153 1.038130 ATCCTCGTCGTCTCCCCAAG 61.038 60.000 0.00 0.00 0.00 3.61
1218 1259 0.043334 CTTCCCTCCTCCTCCCAGAA 59.957 60.000 0.00 0.00 0.00 3.02
1233 1274 2.156098 AGAACTCCCCCTGCAGCAA 61.156 57.895 8.66 0.00 0.00 3.91
1450 1491 1.613630 GAGGGGAAGCTGGAGACCA 60.614 63.158 0.00 0.00 0.00 4.02
1756 1802 2.369860 ACTTCTCTGTGCTCATGGTTCA 59.630 45.455 0.00 0.00 0.00 3.18
1762 1808 2.418976 CTGTGCTCATGGTTCATCAGTG 59.581 50.000 0.00 0.00 0.00 3.66
1765 1811 1.741706 GCTCATGGTTCATCAGTGGTG 59.258 52.381 0.00 0.00 0.00 4.17
1778 1824 1.476085 CAGTGGTGTTGTTTGGCTTGA 59.524 47.619 0.00 0.00 0.00 3.02
1779 1825 2.101249 CAGTGGTGTTGTTTGGCTTGAT 59.899 45.455 0.00 0.00 0.00 2.57
1781 1827 2.100584 GTGGTGTTGTTTGGCTTGATCA 59.899 45.455 0.00 0.00 0.00 2.92
1782 1828 2.964464 TGGTGTTGTTTGGCTTGATCAT 59.036 40.909 0.00 0.00 0.00 2.45
1783 1829 3.005684 TGGTGTTGTTTGGCTTGATCATC 59.994 43.478 0.00 0.00 0.00 2.92
1787 1833 4.022935 TGTTGTTTGGCTTGATCATCTGAC 60.023 41.667 0.00 0.00 0.00 3.51
1788 1834 2.743664 TGTTTGGCTTGATCATCTGACG 59.256 45.455 0.00 0.00 0.00 4.35
1799 1845 6.030548 TGATCATCTGACGAGAGAAGTTTT 57.969 37.500 0.00 0.00 0.00 2.43
1844 1890 7.893124 ATCAGGAATTCAGTATTCAGCAATT 57.107 32.000 7.93 0.00 43.72 2.32
1854 1900 5.343058 CAGTATTCAGCAATTTTGTGTTCGG 59.657 40.000 0.00 0.00 0.00 4.30
1892 1938 7.032580 CAGGATTATGGACACGCAAATTTAAA 58.967 34.615 0.00 0.00 0.00 1.52
1921 1967 7.335924 ACATTTCAGTGTTAACTTGTGTGTAGT 59.664 33.333 7.22 0.00 32.98 2.73
1922 1968 7.675962 TTTCAGTGTTAACTTGTGTGTAGTT 57.324 32.000 7.22 0.00 39.13 2.24
1923 1969 6.656314 TCAGTGTTAACTTGTGTGTAGTTG 57.344 37.500 7.22 0.00 36.56 3.16
1924 1970 5.064198 TCAGTGTTAACTTGTGTGTAGTTGC 59.936 40.000 7.22 0.00 36.56 4.17
1925 1971 4.334481 AGTGTTAACTTGTGTGTAGTTGCC 59.666 41.667 7.22 0.00 36.56 4.52
1926 1972 3.310227 TGTTAACTTGTGTGTAGTTGCCG 59.690 43.478 7.22 0.00 36.56 5.69
1927 1973 2.032680 AACTTGTGTGTAGTTGCCGT 57.967 45.000 0.00 0.00 34.68 5.68
1928 1974 1.578583 ACTTGTGTGTAGTTGCCGTC 58.421 50.000 0.00 0.00 0.00 4.79
1929 1975 1.138266 ACTTGTGTGTAGTTGCCGTCT 59.862 47.619 0.00 0.00 0.00 4.18
1930 1976 1.792949 CTTGTGTGTAGTTGCCGTCTC 59.207 52.381 0.00 0.00 0.00 3.36
1931 1977 1.037493 TGTGTGTAGTTGCCGTCTCT 58.963 50.000 0.00 0.00 0.00 3.10
1932 1978 1.269569 TGTGTGTAGTTGCCGTCTCTG 60.270 52.381 0.00 0.00 0.00 3.35
1933 1979 0.319555 TGTGTAGTTGCCGTCTCTGC 60.320 55.000 0.00 0.00 0.00 4.26
1934 1980 1.080772 TGTAGTTGCCGTCTCTGCG 60.081 57.895 0.00 0.00 0.00 5.18
1935 1981 1.080705 GTAGTTGCCGTCTCTGCGT 60.081 57.895 0.00 0.00 0.00 5.24
1936 1982 0.666577 GTAGTTGCCGTCTCTGCGTT 60.667 55.000 0.00 0.00 0.00 4.84
1937 1983 0.666274 TAGTTGCCGTCTCTGCGTTG 60.666 55.000 0.00 0.00 0.00 4.10
1938 1984 1.954146 GTTGCCGTCTCTGCGTTGA 60.954 57.895 0.00 0.00 0.00 3.18
1939 1985 1.664649 TTGCCGTCTCTGCGTTGAG 60.665 57.895 1.27 1.27 35.52 3.02
1940 1986 2.082629 TTGCCGTCTCTGCGTTGAGA 62.083 55.000 5.60 5.60 40.39 3.27
1941 1987 1.372997 GCCGTCTCTGCGTTGAGAA 60.373 57.895 10.25 0.00 43.68 2.87
1942 1988 1.618640 GCCGTCTCTGCGTTGAGAAC 61.619 60.000 10.25 5.63 43.68 3.01
1943 1989 0.039074 CCGTCTCTGCGTTGAGAACT 60.039 55.000 10.25 0.00 43.68 3.01
1944 1990 1.603172 CCGTCTCTGCGTTGAGAACTT 60.603 52.381 10.25 0.00 43.68 2.66
1945 1991 1.453524 CGTCTCTGCGTTGAGAACTTG 59.546 52.381 10.25 0.41 43.68 3.16
1946 1992 1.193426 GTCTCTGCGTTGAGAACTTGC 59.807 52.381 10.25 0.00 43.68 4.01
1947 1993 1.069204 TCTCTGCGTTGAGAACTTGCT 59.931 47.619 6.97 0.00 39.80 3.91
1948 1994 1.194098 CTCTGCGTTGAGAACTTGCTG 59.806 52.381 1.43 0.00 36.23 4.41
1949 1995 0.385223 CTGCGTTGAGAACTTGCTGC 60.385 55.000 0.00 0.00 0.00 5.25
1950 1996 1.081840 GCGTTGAGAACTTGCTGCC 60.082 57.895 0.00 0.00 0.00 4.85
1951 1997 1.510480 GCGTTGAGAACTTGCTGCCT 61.510 55.000 0.00 0.00 0.00 4.75
1952 1998 1.795768 CGTTGAGAACTTGCTGCCTA 58.204 50.000 0.00 0.00 0.00 3.93
1953 1999 2.350522 CGTTGAGAACTTGCTGCCTAT 58.649 47.619 0.00 0.00 0.00 2.57
1954 2000 2.094894 CGTTGAGAACTTGCTGCCTATG 59.905 50.000 0.00 0.00 0.00 2.23
1955 2001 3.077359 GTTGAGAACTTGCTGCCTATGT 58.923 45.455 0.00 0.00 0.00 2.29
1956 2002 2.703416 TGAGAACTTGCTGCCTATGTG 58.297 47.619 0.00 0.00 0.00 3.21
1957 2003 2.038952 TGAGAACTTGCTGCCTATGTGT 59.961 45.455 0.00 0.00 0.00 3.72
1958 2004 3.077359 GAGAACTTGCTGCCTATGTGTT 58.923 45.455 0.00 0.00 0.00 3.32
1959 2005 2.816087 AGAACTTGCTGCCTATGTGTTG 59.184 45.455 0.00 0.00 0.00 3.33
1960 2006 2.276732 ACTTGCTGCCTATGTGTTGT 57.723 45.000 0.00 0.00 0.00 3.32
1961 2007 2.586425 ACTTGCTGCCTATGTGTTGTT 58.414 42.857 0.00 0.00 0.00 2.83
1962 2008 2.958355 ACTTGCTGCCTATGTGTTGTTT 59.042 40.909 0.00 0.00 0.00 2.83
1963 2009 3.384467 ACTTGCTGCCTATGTGTTGTTTT 59.616 39.130 0.00 0.00 0.00 2.43
1964 2010 3.367992 TGCTGCCTATGTGTTGTTTTG 57.632 42.857 0.00 0.00 0.00 2.44
1965 2011 2.954989 TGCTGCCTATGTGTTGTTTTGA 59.045 40.909 0.00 0.00 0.00 2.69
1966 2012 3.004629 TGCTGCCTATGTGTTGTTTTGAG 59.995 43.478 0.00 0.00 0.00 3.02
1967 2013 3.253188 GCTGCCTATGTGTTGTTTTGAGA 59.747 43.478 0.00 0.00 0.00 3.27
1968 2014 4.787598 CTGCCTATGTGTTGTTTTGAGAC 58.212 43.478 0.00 0.00 0.00 3.36
1969 2015 3.568007 TGCCTATGTGTTGTTTTGAGACC 59.432 43.478 0.00 0.00 0.00 3.85
1970 2016 3.057526 GCCTATGTGTTGTTTTGAGACCC 60.058 47.826 0.00 0.00 0.00 4.46
1971 2017 4.398319 CCTATGTGTTGTTTTGAGACCCT 58.602 43.478 0.00 0.00 0.00 4.34
1972 2018 4.216257 CCTATGTGTTGTTTTGAGACCCTG 59.784 45.833 0.00 0.00 0.00 4.45
1973 2019 1.748493 TGTGTTGTTTTGAGACCCTGC 59.252 47.619 0.00 0.00 0.00 4.85
1974 2020 2.024414 GTGTTGTTTTGAGACCCTGCT 58.976 47.619 0.00 0.00 0.00 4.24
1975 2021 2.023673 TGTTGTTTTGAGACCCTGCTG 58.976 47.619 0.00 0.00 0.00 4.41
1976 2022 2.024414 GTTGTTTTGAGACCCTGCTGT 58.976 47.619 0.00 0.00 0.00 4.40
1977 2023 1.679139 TGTTTTGAGACCCTGCTGTG 58.321 50.000 0.00 0.00 0.00 3.66
1978 2024 0.312102 GTTTTGAGACCCTGCTGTGC 59.688 55.000 0.00 0.00 0.00 4.57
1979 2025 0.823356 TTTTGAGACCCTGCTGTGCC 60.823 55.000 0.00 0.00 0.00 5.01
1980 2026 3.535629 TTGAGACCCTGCTGTGCCG 62.536 63.158 0.00 0.00 0.00 5.69
1986 2032 4.034258 CCTGCTGTGCCGCACTTG 62.034 66.667 23.52 16.66 35.74 3.16
1987 2033 2.974148 CTGCTGTGCCGCACTTGA 60.974 61.111 23.52 3.49 35.74 3.02
1988 2034 3.245948 CTGCTGTGCCGCACTTGAC 62.246 63.158 23.52 11.00 35.74 3.18
1989 2035 3.279116 GCTGTGCCGCACTTGACA 61.279 61.111 23.52 2.81 35.11 3.58
1990 2036 2.620112 GCTGTGCCGCACTTGACAT 61.620 57.895 23.52 0.00 35.11 3.06
1991 2037 1.951510 CTGTGCCGCACTTGACATT 59.048 52.632 23.52 0.00 35.11 2.71
1992 2038 0.311790 CTGTGCCGCACTTGACATTT 59.688 50.000 23.52 0.00 35.11 2.32
1993 2039 0.030504 TGTGCCGCACTTGACATTTG 59.969 50.000 23.52 0.00 35.11 2.32
1994 2040 0.310543 GTGCCGCACTTGACATTTGA 59.689 50.000 16.51 0.00 0.00 2.69
1995 2041 1.068333 GTGCCGCACTTGACATTTGAT 60.068 47.619 16.51 0.00 0.00 2.57
1996 2042 1.199789 TGCCGCACTTGACATTTGATC 59.800 47.619 0.00 0.00 0.00 2.92
1997 2043 1.199789 GCCGCACTTGACATTTGATCA 59.800 47.619 0.00 0.00 0.00 2.92
1998 2044 2.351641 GCCGCACTTGACATTTGATCAA 60.352 45.455 3.38 3.38 34.89 2.57
1999 2045 3.674138 GCCGCACTTGACATTTGATCAAT 60.674 43.478 9.40 0.00 35.57 2.57
2001 2047 4.379708 CCGCACTTGACATTTGATCAATGA 60.380 41.667 9.40 0.00 44.78 2.57
2002 2048 5.337554 CGCACTTGACATTTGATCAATGAT 58.662 37.500 9.40 0.00 44.78 2.45
2003 2049 5.454554 CGCACTTGACATTTGATCAATGATC 59.545 40.000 15.86 15.86 44.78 2.92
2004 2050 6.327154 GCACTTGACATTTGATCAATGATCA 58.673 36.000 20.85 20.85 45.78 2.92
2005 2051 6.978659 GCACTTGACATTTGATCAATGATCAT 59.021 34.615 24.53 11.33 46.52 2.45
2006 2052 7.043391 GCACTTGACATTTGATCAATGATCATG 60.043 37.037 24.53 21.76 46.52 3.07
2007 2053 6.978659 ACTTGACATTTGATCAATGATCATGC 59.021 34.615 24.53 16.36 46.52 4.06
2008 2054 6.458232 TGACATTTGATCAATGATCATGCA 57.542 33.333 24.53 18.21 46.52 3.96
2009 2055 6.270064 TGACATTTGATCAATGATCATGCAC 58.730 36.000 24.53 17.42 46.52 4.57
2010 2056 6.127591 TGACATTTGATCAATGATCATGCACA 60.128 34.615 24.53 19.24 46.52 4.57
2011 2057 6.635755 ACATTTGATCAATGATCATGCACAA 58.364 32.000 24.53 16.19 46.52 3.33
2012 2058 6.533723 ACATTTGATCAATGATCATGCACAAC 59.466 34.615 24.53 0.00 46.52 3.32
2013 2059 5.907866 TTGATCAATGATCATGCACAACT 57.092 34.783 24.53 0.00 46.52 3.16
2014 2060 5.243426 TGATCAATGATCATGCACAACTG 57.757 39.130 20.85 1.83 43.11 3.16
2015 2061 3.497297 TCAATGATCATGCACAACTGC 57.503 42.857 9.46 0.00 44.52 4.40
2016 2062 2.164827 TCAATGATCATGCACAACTGCC 59.835 45.455 9.46 0.00 43.51 4.85
2017 2063 1.108776 ATGATCATGCACAACTGCCC 58.891 50.000 7.59 0.00 43.51 5.36
2018 2064 1.307355 TGATCATGCACAACTGCCCG 61.307 55.000 0.00 0.00 43.51 6.13
2019 2065 1.303561 ATCATGCACAACTGCCCGT 60.304 52.632 0.00 0.00 43.51 5.28
2020 2066 0.895100 ATCATGCACAACTGCCCGTT 60.895 50.000 0.00 0.00 43.51 4.44
2021 2067 1.081242 CATGCACAACTGCCCGTTC 60.081 57.895 0.00 0.00 43.51 3.95
2022 2068 2.268076 ATGCACAACTGCCCGTTCC 61.268 57.895 0.00 0.00 43.51 3.62
2023 2069 3.670377 GCACAACTGCCCGTTCCC 61.670 66.667 0.00 0.00 37.45 3.97
2024 2070 2.983592 CACAACTGCCCGTTCCCC 60.984 66.667 0.00 0.00 32.27 4.81
2025 2071 3.175710 ACAACTGCCCGTTCCCCT 61.176 61.111 0.00 0.00 32.27 4.79
2026 2072 2.115266 CAACTGCCCGTTCCCCTT 59.885 61.111 0.00 0.00 32.27 3.95
2027 2073 1.530655 CAACTGCCCGTTCCCCTTT 60.531 57.895 0.00 0.00 32.27 3.11
2028 2074 1.228459 AACTGCCCGTTCCCCTTTC 60.228 57.895 0.00 0.00 0.00 2.62
2029 2075 2.746277 CTGCCCGTTCCCCTTTCG 60.746 66.667 0.00 0.00 0.00 3.46
2030 2076 3.546714 CTGCCCGTTCCCCTTTCGT 62.547 63.158 0.00 0.00 0.00 3.85
2031 2077 3.053896 GCCCGTTCCCCTTTCGTG 61.054 66.667 0.00 0.00 0.00 4.35
2032 2078 2.745037 CCCGTTCCCCTTTCGTGA 59.255 61.111 0.00 0.00 0.00 4.35
2033 2079 1.375523 CCCGTTCCCCTTTCGTGAG 60.376 63.158 0.00 0.00 0.00 3.51
2034 2080 1.669440 CCGTTCCCCTTTCGTGAGA 59.331 57.895 0.00 0.00 39.20 3.27
2035 2081 0.389948 CCGTTCCCCTTTCGTGAGAG 60.390 60.000 0.00 0.00 43.69 3.20
2036 2082 0.601558 CGTTCCCCTTTCGTGAGAGA 59.398 55.000 0.00 0.00 43.69 3.10
2037 2083 1.402984 CGTTCCCCTTTCGTGAGAGAG 60.403 57.143 0.00 0.00 43.69 3.20
2044 2090 2.993545 CTTTCGTGAGAGAGGCGATAG 58.006 52.381 0.00 0.00 43.69 2.08
2045 2091 2.039818 TTCGTGAGAGAGGCGATAGT 57.960 50.000 0.00 0.00 43.69 2.12
2046 2092 2.039818 TCGTGAGAGAGGCGATAGTT 57.960 50.000 0.00 0.00 34.72 2.24
2047 2093 3.189618 TCGTGAGAGAGGCGATAGTTA 57.810 47.619 0.00 0.00 34.72 2.24
2048 2094 3.132160 TCGTGAGAGAGGCGATAGTTAG 58.868 50.000 0.00 0.00 34.72 2.34
2051 2097 1.198178 GAGAGAGGCGATAGTTAGGCG 59.802 57.143 0.00 0.00 38.03 5.52
2060 2106 4.860799 GCGATAGTTAGGCGACAGTTTCG 61.861 52.174 0.00 0.00 45.31 3.46
2067 2113 4.496898 CGACAGTTTCGTGCTTGC 57.503 55.556 0.00 0.00 43.24 4.01
2150 2222 7.676468 AGTTCATAGATTAGGGATAGGTCTTCC 59.324 40.741 0.00 0.00 0.00 3.46
2208 2286 1.306997 TGGCCTCGGATTCTCCCTT 60.307 57.895 3.32 0.00 31.13 3.95
2263 2341 1.869574 CGATGGTCTCGTGTGCTCG 60.870 63.158 0.00 0.00 42.56 5.03
2266 2344 1.524008 ATGGTCTCGTGTGCTCGTCA 61.524 55.000 0.00 0.00 0.00 4.35
2275 2353 0.039888 TGTGCTCGTCATTCGTTCGA 60.040 50.000 0.00 0.00 40.80 3.71
2306 2385 4.681744 CTTTATGTGCCTGTTTGTGTTGT 58.318 39.130 0.00 0.00 0.00 3.32
2319 2398 2.270257 TGTTGTGATGCTGCTGCCC 61.270 57.895 13.47 5.68 38.71 5.36
2320 2399 2.677524 TTGTGATGCTGCTGCCCC 60.678 61.111 13.47 5.32 38.71 5.80
2321 2400 3.214190 TTGTGATGCTGCTGCCCCT 62.214 57.895 13.47 0.00 38.71 4.79
2323 2402 1.821332 GTGATGCTGCTGCCCCTAC 60.821 63.158 13.47 3.67 38.71 3.18
2325 2404 2.693864 ATGCTGCTGCCCCTACCT 60.694 61.111 13.47 0.00 38.71 3.08
2326 2405 1.384502 ATGCTGCTGCCCCTACCTA 60.385 57.895 13.47 0.00 38.71 3.08
2328 2407 3.108288 GCTGCTGCCCCTACCTACC 62.108 68.421 3.85 0.00 0.00 3.18
2336 2429 0.107214 CCCCTACCTACCGTCGTGTA 60.107 60.000 0.00 0.00 0.00 2.90
2350 2443 1.000607 TCGTGTACTTGGAGCACAGAC 60.001 52.381 0.00 0.00 33.70 3.51
2367 2460 2.113139 CGGAGGTTTGGTGGCAGT 59.887 61.111 0.00 0.00 0.00 4.40
2389 2482 0.323451 ATTTGGCTTTCCTCCCCGTC 60.323 55.000 0.00 0.00 0.00 4.79
2399 2492 2.762043 TCCCCGTCATCATCGGCA 60.762 61.111 0.00 0.00 45.71 5.69
2401 2494 2.501128 CCCGTCATCATCGGCAGT 59.499 61.111 0.00 0.00 45.71 4.40
2426 2527 0.529773 GCGGATCCAGATACAACGCA 60.530 55.000 13.41 0.00 44.32 5.24
2431 2532 1.496060 TCCAGATACAACGCAGGGAT 58.504 50.000 0.00 0.00 0.00 3.85
2454 2556 2.125713 CAGCCGACGTGCCACATA 60.126 61.111 0.00 0.00 0.00 2.29
2472 2574 3.133003 ACATAGTCAAGCGCCTGTTCTAT 59.867 43.478 2.29 11.52 0.00 1.98
2474 2576 3.887621 AGTCAAGCGCCTGTTCTATAA 57.112 42.857 2.29 0.00 0.00 0.98
2479 2581 0.179056 GCGCCTGTTCTATAAGCCCA 60.179 55.000 0.00 0.00 0.00 5.36
2495 2597 0.250234 CCCAGTCATCGGCTCTCAAA 59.750 55.000 0.00 0.00 0.00 2.69
2544 2646 2.531771 TCGTGGGATTGTGGAAGTCTA 58.468 47.619 0.00 0.00 0.00 2.59
2616 2718 2.357009 CTGTGTTGATTATCTGCAGGGC 59.643 50.000 15.13 0.00 0.00 5.19
2617 2719 1.678101 GTGTTGATTATCTGCAGGGCC 59.322 52.381 15.13 0.00 0.00 5.80
2620 2722 0.698886 TGATTATCTGCAGGGCCCCT 60.699 55.000 21.43 0.00 0.00 4.79
2621 2723 1.362224 GATTATCTGCAGGGCCCCTA 58.638 55.000 21.43 3.71 29.64 3.53
2623 2725 1.140312 TTATCTGCAGGGCCCCTAAG 58.860 55.000 21.43 13.83 29.64 2.18
2624 2726 0.267658 TATCTGCAGGGCCCCTAAGA 59.732 55.000 21.43 19.13 32.47 2.10
2625 2727 1.059006 ATCTGCAGGGCCCCTAAGAG 61.059 60.000 21.43 7.92 31.77 2.85
2626 2728 3.411517 TGCAGGGCCCCTAAGAGC 61.412 66.667 21.43 13.87 29.64 4.09
2627 2729 3.411517 GCAGGGCCCCTAAGAGCA 61.412 66.667 21.43 0.00 29.64 4.26
2628 2730 2.761465 GCAGGGCCCCTAAGAGCAT 61.761 63.158 21.43 0.00 29.64 3.79
2629 2731 1.453669 CAGGGCCCCTAAGAGCATC 59.546 63.158 21.43 0.00 29.64 3.91
2641 2743 3.364277 GAGCATCTACAACCGGACC 57.636 57.895 9.46 0.00 0.00 4.46
2642 2744 0.179081 GAGCATCTACAACCGGACCC 60.179 60.000 9.46 0.00 0.00 4.46
2643 2745 0.617820 AGCATCTACAACCGGACCCT 60.618 55.000 9.46 0.00 0.00 4.34
2644 2746 0.252197 GCATCTACAACCGGACCCTT 59.748 55.000 9.46 0.00 0.00 3.95
2645 2747 1.742750 GCATCTACAACCGGACCCTTC 60.743 57.143 9.46 0.00 0.00 3.46
2646 2748 1.553248 CATCTACAACCGGACCCTTCA 59.447 52.381 9.46 0.00 0.00 3.02
2647 2749 1.946984 TCTACAACCGGACCCTTCAT 58.053 50.000 9.46 0.00 0.00 2.57
2648 2750 3.104519 TCTACAACCGGACCCTTCATA 57.895 47.619 9.46 0.00 0.00 2.15
2649 2751 2.762327 TCTACAACCGGACCCTTCATAC 59.238 50.000 9.46 0.00 0.00 2.39
2650 2752 0.616891 ACAACCGGACCCTTCATACC 59.383 55.000 9.46 0.00 0.00 2.73
2651 2753 0.909623 CAACCGGACCCTTCATACCT 59.090 55.000 9.46 0.00 0.00 3.08
2652 2754 0.909623 AACCGGACCCTTCATACCTG 59.090 55.000 9.46 0.00 0.00 4.00
2653 2755 1.146263 CCGGACCCTTCATACCTGC 59.854 63.158 0.00 0.00 0.00 4.85
2654 2756 1.146263 CGGACCCTTCATACCTGCC 59.854 63.158 0.00 0.00 0.00 4.85
2655 2757 1.532238 GGACCCTTCATACCTGCCC 59.468 63.158 0.00 0.00 0.00 5.36
2656 2758 1.532238 GACCCTTCATACCTGCCCC 59.468 63.158 0.00 0.00 0.00 5.80
2657 2759 1.230149 ACCCTTCATACCTGCCCCA 60.230 57.895 0.00 0.00 0.00 4.96
2658 2760 0.849094 ACCCTTCATACCTGCCCCAA 60.849 55.000 0.00 0.00 0.00 4.12
2659 2761 0.334676 CCCTTCATACCTGCCCCAAA 59.665 55.000 0.00 0.00 0.00 3.28
2660 2762 1.474330 CCTTCATACCTGCCCCAAAC 58.526 55.000 0.00 0.00 0.00 2.93
2661 2763 1.094785 CTTCATACCTGCCCCAAACG 58.905 55.000 0.00 0.00 0.00 3.60
2662 2764 0.402504 TTCATACCTGCCCCAAACGT 59.597 50.000 0.00 0.00 0.00 3.99
2663 2765 0.035820 TCATACCTGCCCCAAACGTC 60.036 55.000 0.00 0.00 0.00 4.34
2664 2766 0.035439 CATACCTGCCCCAAACGTCT 60.035 55.000 0.00 0.00 0.00 4.18
2665 2767 1.208535 CATACCTGCCCCAAACGTCTA 59.791 52.381 0.00 0.00 0.00 2.59
2666 2768 0.899720 TACCTGCCCCAAACGTCTAG 59.100 55.000 0.00 0.00 0.00 2.43
2667 2769 0.834687 ACCTGCCCCAAACGTCTAGA 60.835 55.000 0.00 0.00 0.00 2.43
2668 2770 0.391263 CCTGCCCCAAACGTCTAGAC 60.391 60.000 13.18 13.18 0.00 2.59
2669 2771 0.320374 CTGCCCCAAACGTCTAGACA 59.680 55.000 22.37 0.00 0.00 3.41
2670 2772 0.034337 TGCCCCAAACGTCTAGACAC 59.966 55.000 22.37 0.00 0.00 3.67
2671 2773 1.012486 GCCCCAAACGTCTAGACACG 61.012 60.000 22.37 12.64 45.65 4.49
2672 2774 0.389426 CCCCAAACGTCTAGACACGG 60.389 60.000 22.37 14.92 44.41 4.94
2673 2775 0.316204 CCCAAACGTCTAGACACGGT 59.684 55.000 22.37 9.65 43.09 4.83
2676 2778 3.190337 AACGTCTAGACACGGTTGC 57.810 52.632 22.37 0.00 44.41 4.17
2677 2779 0.319297 AACGTCTAGACACGGTTGCC 60.319 55.000 22.37 0.00 44.41 4.52
2678 2780 1.445582 CGTCTAGACACGGTTGCCC 60.446 63.158 22.37 0.00 36.07 5.36
2690 2792 4.593864 TTGCCCGGGCGCAAAAAC 62.594 61.111 39.00 12.45 45.46 2.43
2699 2801 2.105128 CGCAAAAACCGCACCCAA 59.895 55.556 0.00 0.00 0.00 4.12
2700 2802 2.234335 CGCAAAAACCGCACCCAAC 61.234 57.895 0.00 0.00 0.00 3.77
2701 2803 1.153549 GCAAAAACCGCACCCAACA 60.154 52.632 0.00 0.00 0.00 3.33
2702 2804 1.151172 GCAAAAACCGCACCCAACAG 61.151 55.000 0.00 0.00 0.00 3.16
2703 2805 0.174617 CAAAAACCGCACCCAACAGT 59.825 50.000 0.00 0.00 0.00 3.55
2704 2806 1.405821 CAAAAACCGCACCCAACAGTA 59.594 47.619 0.00 0.00 0.00 2.74
2705 2807 1.026584 AAAACCGCACCCAACAGTAC 58.973 50.000 0.00 0.00 0.00 2.73
2706 2808 0.820482 AAACCGCACCCAACAGTACC 60.820 55.000 0.00 0.00 0.00 3.34
2707 2809 1.985460 AACCGCACCCAACAGTACCA 61.985 55.000 0.00 0.00 0.00 3.25
2708 2810 1.964373 CCGCACCCAACAGTACCAC 60.964 63.158 0.00 0.00 0.00 4.16
2709 2811 1.070786 CGCACCCAACAGTACCACT 59.929 57.895 0.00 0.00 0.00 4.00
2710 2812 0.534203 CGCACCCAACAGTACCACTT 60.534 55.000 0.00 0.00 0.00 3.16
2711 2813 1.270412 CGCACCCAACAGTACCACTTA 60.270 52.381 0.00 0.00 0.00 2.24
2712 2814 2.807472 CGCACCCAACAGTACCACTTAA 60.807 50.000 0.00 0.00 0.00 1.85
2713 2815 3.215975 GCACCCAACAGTACCACTTAAA 58.784 45.455 0.00 0.00 0.00 1.52
2714 2816 3.824443 GCACCCAACAGTACCACTTAAAT 59.176 43.478 0.00 0.00 0.00 1.40
2715 2817 4.082949 GCACCCAACAGTACCACTTAAATC 60.083 45.833 0.00 0.00 0.00 2.17
2716 2818 4.457949 CACCCAACAGTACCACTTAAATCC 59.542 45.833 0.00 0.00 0.00 3.01
2717 2819 3.687698 CCCAACAGTACCACTTAAATCCG 59.312 47.826 0.00 0.00 0.00 4.18
2718 2820 3.687698 CCAACAGTACCACTTAAATCCGG 59.312 47.826 0.00 0.00 0.00 5.14
2719 2821 4.320870 CAACAGTACCACTTAAATCCGGT 58.679 43.478 0.00 0.00 35.46 5.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 5.423610 TGATTTTTCTGGAACCACCTCAAAA 59.576 36.000 0.00 0.00 39.86 2.44
109 110 3.911868 TGGAACCATCTCAAAATTTGCG 58.088 40.909 0.00 0.00 0.00 4.85
215 219 0.103937 TTGTTTTGCTGGAAAGCCGG 59.896 50.000 0.00 0.00 43.89 6.13
236 241 4.079958 GGTTGGGGATGATACAAGTAGGTT 60.080 45.833 0.00 0.00 0.00 3.50
241 246 2.919602 AGTGGTTGGGGATGATACAAGT 59.080 45.455 0.00 0.00 0.00 3.16
257 262 4.074970 CTGAATTTGCTGGAACTAGTGGT 58.925 43.478 0.00 0.00 0.00 4.16
323 328 0.106335 CTGTCTCCTATGGGCAGCTG 59.894 60.000 10.11 10.11 0.00 4.24
324 329 1.694133 GCTGTCTCCTATGGGCAGCT 61.694 60.000 15.82 0.00 46.20 4.24
334 339 2.203788 TGGAACCGGCTGTCTCCT 60.204 61.111 0.00 0.00 0.00 3.69
355 360 2.591429 TGTGCAACACCAGAGGCG 60.591 61.111 0.00 0.00 45.67 5.52
380 385 2.406130 CAGCGACCATTTTGTTGCAAT 58.594 42.857 0.59 0.00 46.19 3.56
396 401 2.180017 GTTGCTGGAATGGCAGCG 59.820 61.111 0.00 0.00 46.60 5.18
401 406 1.000060 CAACCACTGTTGCTGGAATGG 60.000 52.381 0.00 0.00 44.86 3.16
414 419 0.182537 TGCTACAACTGGCAACCACT 59.817 50.000 0.00 0.00 35.40 4.00
437 442 2.280823 GAAGACCCACTAGTCGGCCG 62.281 65.000 22.12 22.12 41.83 6.13
459 464 0.590195 CATAAAGGCTGATGGCGCTC 59.410 55.000 7.64 0.00 44.18 5.03
512 518 0.931005 GCGCCATAACTTCTTCTCCG 59.069 55.000 0.00 0.00 0.00 4.63
514 520 1.922570 TCGCGCCATAACTTCTTCTC 58.077 50.000 0.00 0.00 0.00 2.87
515 521 2.380084 TTCGCGCCATAACTTCTTCT 57.620 45.000 0.00 0.00 0.00 2.85
593 599 2.124942 CGCAGCTCCTCCTTTCCC 60.125 66.667 0.00 0.00 0.00 3.97
596 602 4.416738 GCCCGCAGCTCCTCCTTT 62.417 66.667 0.00 0.00 38.99 3.11
635 641 1.230635 TTCTGTGCCGCAGCTCTTTC 61.231 55.000 0.00 0.00 44.66 2.62
646 653 0.609406 GTTCTCCCCCTTTCTGTGCC 60.609 60.000 0.00 0.00 0.00 5.01
649 656 1.430992 TTCGTTCTCCCCCTTTCTGT 58.569 50.000 0.00 0.00 0.00 3.41
652 659 1.280998 TCCATTCGTTCTCCCCCTTTC 59.719 52.381 0.00 0.00 0.00 2.62
668 675 0.993509 AACCCATCGTCCCCATCCAT 60.994 55.000 0.00 0.00 0.00 3.41
672 679 1.211567 TTCCAACCCATCGTCCCCAT 61.212 55.000 0.00 0.00 0.00 4.00
681 688 1.506028 ATCCCACGGTTCCAACCCAT 61.506 55.000 2.78 0.00 46.53 4.00
716 723 2.202570 CCGAACGCGACCCTACTG 60.203 66.667 15.93 0.00 40.82 2.74
717 724 4.125695 GCCGAACGCGACCCTACT 62.126 66.667 15.93 0.00 40.82 2.57
726 733 1.952266 CTTACACTTCGGCCGAACGC 61.952 60.000 35.81 0.00 0.00 4.84
730 737 2.263540 GGCTTACACTTCGGCCGA 59.736 61.111 27.28 27.28 35.08 5.54
733 740 2.098831 GGTCGGCTTACACTTCGGC 61.099 63.158 0.00 0.00 0.00 5.54
829 841 1.954146 GTCACGAGCGAGCCAAACA 60.954 57.895 0.00 0.00 0.00 2.83
846 858 4.712337 AGGTAAACTCTTCCATCTCATCGT 59.288 41.667 0.00 0.00 0.00 3.73
894 906 1.973812 GTGGGTCAAGGGCTCAAGC 60.974 63.158 0.00 0.00 41.14 4.01
976 1009 2.186903 GATGCGATCGGTGGTGGT 59.813 61.111 18.30 0.00 0.00 4.16
1218 1259 2.679716 GATTGCTGCAGGGGGAGT 59.320 61.111 17.12 0.00 34.49 3.85
1756 1802 2.071778 AGCCAAACAACACCACTGAT 57.928 45.000 0.00 0.00 0.00 2.90
1762 1808 3.256631 AGATGATCAAGCCAAACAACACC 59.743 43.478 0.00 0.00 0.00 4.16
1765 1811 4.479619 GTCAGATGATCAAGCCAAACAAC 58.520 43.478 0.00 0.00 0.00 3.32
1778 1824 7.831753 TCTTAAAACTTCTCTCGTCAGATGAT 58.168 34.615 0.00 0.00 0.00 2.45
1779 1825 7.175119 TCTCTTAAAACTTCTCTCGTCAGATGA 59.825 37.037 0.00 0.00 0.00 2.92
1781 1827 7.455641 TCTCTTAAAACTTCTCTCGTCAGAT 57.544 36.000 0.00 0.00 0.00 2.90
1782 1828 6.879276 TCTCTTAAAACTTCTCTCGTCAGA 57.121 37.500 0.00 0.00 0.00 3.27
1783 1829 7.932120 TTTCTCTTAAAACTTCTCTCGTCAG 57.068 36.000 0.00 0.00 0.00 3.51
1810 1856 4.651503 ACTGAATTCCTGATACATCTCGGT 59.348 41.667 2.27 0.00 0.00 4.69
1844 1890 0.958091 CAGATTGCCCCGAACACAAA 59.042 50.000 0.00 0.00 0.00 2.83
1854 1900 1.188863 AATCCTGTTGCAGATTGCCC 58.811 50.000 0.00 0.00 44.23 5.36
1892 1938 8.682710 ACACACAAGTTAACACTGAAATGTAAT 58.317 29.630 8.61 0.00 31.60 1.89
1921 1967 1.664649 CTCAACGCAGAGACGGCAA 60.665 57.895 0.00 0.00 37.87 4.52
1922 1968 2.049156 CTCAACGCAGAGACGGCA 60.049 61.111 0.00 0.00 37.87 5.69
1923 1969 1.372997 TTCTCAACGCAGAGACGGC 60.373 57.895 6.89 0.00 43.91 5.68
1924 1970 0.039074 AGTTCTCAACGCAGAGACGG 60.039 55.000 6.89 0.00 43.91 4.79
1925 1971 1.453524 CAAGTTCTCAACGCAGAGACG 59.546 52.381 6.89 0.00 43.91 4.18
1926 1972 1.193426 GCAAGTTCTCAACGCAGAGAC 59.807 52.381 6.89 3.86 43.91 3.36
1927 1973 1.069204 AGCAAGTTCTCAACGCAGAGA 59.931 47.619 3.51 3.51 42.62 3.10
1928 1974 1.194098 CAGCAAGTTCTCAACGCAGAG 59.806 52.381 0.00 0.00 36.97 3.35
1929 1975 1.220529 CAGCAAGTTCTCAACGCAGA 58.779 50.000 0.00 0.00 36.23 4.26
1930 1976 0.385223 GCAGCAAGTTCTCAACGCAG 60.385 55.000 0.00 0.00 36.23 5.18
1931 1977 1.648720 GCAGCAAGTTCTCAACGCA 59.351 52.632 0.00 0.00 36.23 5.24
1932 1978 1.081840 GGCAGCAAGTTCTCAACGC 60.082 57.895 0.00 0.00 36.23 4.84
1933 1979 1.795768 TAGGCAGCAAGTTCTCAACG 58.204 50.000 0.00 0.00 36.23 4.10
1934 1980 3.077359 ACATAGGCAGCAAGTTCTCAAC 58.923 45.455 0.00 0.00 0.00 3.18
1935 1981 3.076621 CACATAGGCAGCAAGTTCTCAA 58.923 45.455 0.00 0.00 0.00 3.02
1936 1982 2.038952 ACACATAGGCAGCAAGTTCTCA 59.961 45.455 0.00 0.00 0.00 3.27
1937 1983 2.704572 ACACATAGGCAGCAAGTTCTC 58.295 47.619 0.00 0.00 0.00 2.87
1938 1984 2.816087 CAACACATAGGCAGCAAGTTCT 59.184 45.455 0.00 0.00 0.00 3.01
1939 1985 2.554032 ACAACACATAGGCAGCAAGTTC 59.446 45.455 0.00 0.00 0.00 3.01
1940 1986 2.586425 ACAACACATAGGCAGCAAGTT 58.414 42.857 0.00 0.00 0.00 2.66
1941 1987 2.276732 ACAACACATAGGCAGCAAGT 57.723 45.000 0.00 0.00 0.00 3.16
1942 1988 3.648339 AAACAACACATAGGCAGCAAG 57.352 42.857 0.00 0.00 0.00 4.01
1943 1989 3.382865 TCAAAACAACACATAGGCAGCAA 59.617 39.130 0.00 0.00 0.00 3.91
1944 1990 2.954989 TCAAAACAACACATAGGCAGCA 59.045 40.909 0.00 0.00 0.00 4.41
1945 1991 3.253188 TCTCAAAACAACACATAGGCAGC 59.747 43.478 0.00 0.00 0.00 5.25
1946 1992 4.320494 GGTCTCAAAACAACACATAGGCAG 60.320 45.833 0.00 0.00 0.00 4.85
1947 1993 3.568007 GGTCTCAAAACAACACATAGGCA 59.432 43.478 0.00 0.00 0.00 4.75
1948 1994 3.057526 GGGTCTCAAAACAACACATAGGC 60.058 47.826 0.00 0.00 0.00 3.93
1949 1995 4.216257 CAGGGTCTCAAAACAACACATAGG 59.784 45.833 0.00 0.00 0.00 2.57
1950 1996 4.320494 GCAGGGTCTCAAAACAACACATAG 60.320 45.833 0.00 0.00 0.00 2.23
1951 1997 3.568007 GCAGGGTCTCAAAACAACACATA 59.432 43.478 0.00 0.00 0.00 2.29
1952 1998 2.362077 GCAGGGTCTCAAAACAACACAT 59.638 45.455 0.00 0.00 0.00 3.21
1953 1999 1.748493 GCAGGGTCTCAAAACAACACA 59.252 47.619 0.00 0.00 0.00 3.72
1954 2000 2.024414 AGCAGGGTCTCAAAACAACAC 58.976 47.619 0.00 0.00 0.00 3.32
1955 2001 2.023673 CAGCAGGGTCTCAAAACAACA 58.976 47.619 0.00 0.00 0.00 3.33
1956 2002 2.024414 ACAGCAGGGTCTCAAAACAAC 58.976 47.619 0.00 0.00 0.00 3.32
1957 2003 2.023673 CACAGCAGGGTCTCAAAACAA 58.976 47.619 0.00 0.00 0.00 2.83
1958 2004 1.679139 CACAGCAGGGTCTCAAAACA 58.321 50.000 0.00 0.00 0.00 2.83
1959 2005 0.312102 GCACAGCAGGGTCTCAAAAC 59.688 55.000 0.00 0.00 0.00 2.43
1960 2006 0.823356 GGCACAGCAGGGTCTCAAAA 60.823 55.000 0.00 0.00 0.00 2.44
1961 2007 1.228245 GGCACAGCAGGGTCTCAAA 60.228 57.895 0.00 0.00 0.00 2.69
1962 2008 2.431683 GGCACAGCAGGGTCTCAA 59.568 61.111 0.00 0.00 0.00 3.02
1963 2009 4.007644 CGGCACAGCAGGGTCTCA 62.008 66.667 0.00 0.00 0.00 3.27
1971 2017 3.279116 GTCAAGTGCGGCACAGCA 61.279 61.111 32.29 14.01 45.96 4.41
1972 2018 2.133742 AATGTCAAGTGCGGCACAGC 62.134 55.000 32.29 19.18 36.74 4.40
1973 2019 0.311790 AAATGTCAAGTGCGGCACAG 59.688 50.000 32.29 23.85 36.74 3.66
1974 2020 0.030504 CAAATGTCAAGTGCGGCACA 59.969 50.000 32.29 13.92 36.74 4.57
1975 2021 0.310543 TCAAATGTCAAGTGCGGCAC 59.689 50.000 25.00 25.00 34.10 5.01
1976 2022 1.199789 GATCAAATGTCAAGTGCGGCA 59.800 47.619 0.00 0.00 0.00 5.69
1977 2023 1.199789 TGATCAAATGTCAAGTGCGGC 59.800 47.619 0.00 0.00 0.00 6.53
1978 2024 3.557577 TTGATCAAATGTCAAGTGCGG 57.442 42.857 5.45 0.00 32.23 5.69
1979 2025 4.725359 TCATTGATCAAATGTCAAGTGCG 58.275 39.130 13.09 0.00 45.14 5.34
1980 2026 6.327154 TGATCATTGATCAAATGTCAAGTGC 58.673 36.000 23.72 0.00 44.70 4.40
2007 2053 2.976494 AAGGGGAACGGGCAGTTGTG 62.976 60.000 7.99 0.00 44.35 3.33
2008 2054 2.292785 AAAGGGGAACGGGCAGTTGT 62.293 55.000 7.99 0.00 44.35 3.32
2009 2055 1.524008 GAAAGGGGAACGGGCAGTTG 61.524 60.000 7.99 0.00 44.35 3.16
2011 2057 2.434774 GAAAGGGGAACGGGCAGT 59.565 61.111 0.00 0.00 0.00 4.40
2012 2058 2.746277 CGAAAGGGGAACGGGCAG 60.746 66.667 0.00 0.00 0.00 4.85
2013 2059 3.562232 ACGAAAGGGGAACGGGCA 61.562 61.111 0.00 0.00 0.00 5.36
2014 2060 3.053896 CACGAAAGGGGAACGGGC 61.054 66.667 0.00 0.00 0.00 6.13
2015 2061 1.375523 CTCACGAAAGGGGAACGGG 60.376 63.158 0.00 0.00 33.12 5.28
2016 2062 0.389948 CTCTCACGAAAGGGGAACGG 60.390 60.000 0.00 0.00 33.12 4.44
2017 2063 0.601558 TCTCTCACGAAAGGGGAACG 59.398 55.000 0.00 0.00 33.12 3.95
2018 2064 1.066787 CCTCTCTCACGAAAGGGGAAC 60.067 57.143 0.00 0.00 33.12 3.62
2019 2065 1.267121 CCTCTCTCACGAAAGGGGAA 58.733 55.000 0.00 0.00 33.12 3.97
2020 2066 1.258445 GCCTCTCTCACGAAAGGGGA 61.258 60.000 0.00 0.00 33.12 4.81
2021 2067 1.219393 GCCTCTCTCACGAAAGGGG 59.781 63.158 0.00 0.00 33.12 4.79
2022 2068 1.153745 CGCCTCTCTCACGAAAGGG 60.154 63.158 0.00 0.00 0.00 3.95
2023 2069 0.457851 ATCGCCTCTCTCACGAAAGG 59.542 55.000 0.00 0.00 39.56 3.11
2024 2070 2.356382 ACTATCGCCTCTCTCACGAAAG 59.644 50.000 0.00 0.00 39.56 2.62
2025 2071 2.366533 ACTATCGCCTCTCTCACGAAA 58.633 47.619 0.00 0.00 39.56 3.46
2026 2072 2.039818 ACTATCGCCTCTCTCACGAA 57.960 50.000 0.00 0.00 39.56 3.85
2027 2073 2.039818 AACTATCGCCTCTCTCACGA 57.960 50.000 0.00 0.00 40.53 4.35
2028 2074 2.224549 CCTAACTATCGCCTCTCTCACG 59.775 54.545 0.00 0.00 0.00 4.35
2029 2075 2.030628 GCCTAACTATCGCCTCTCTCAC 60.031 54.545 0.00 0.00 0.00 3.51
2030 2076 2.231529 GCCTAACTATCGCCTCTCTCA 58.768 52.381 0.00 0.00 0.00 3.27
2031 2077 1.198178 CGCCTAACTATCGCCTCTCTC 59.802 57.143 0.00 0.00 0.00 3.20
2032 2078 1.202782 TCGCCTAACTATCGCCTCTCT 60.203 52.381 0.00 0.00 0.00 3.10
2033 2079 1.069091 GTCGCCTAACTATCGCCTCTC 60.069 57.143 0.00 0.00 0.00 3.20
2034 2080 0.953003 GTCGCCTAACTATCGCCTCT 59.047 55.000 0.00 0.00 0.00 3.69
2035 2081 0.666913 TGTCGCCTAACTATCGCCTC 59.333 55.000 0.00 0.00 0.00 4.70
2036 2082 0.669077 CTGTCGCCTAACTATCGCCT 59.331 55.000 0.00 0.00 0.00 5.52
2037 2083 0.384669 ACTGTCGCCTAACTATCGCC 59.615 55.000 0.00 0.00 0.00 5.54
2038 2084 2.205307 AACTGTCGCCTAACTATCGC 57.795 50.000 0.00 0.00 0.00 4.58
2039 2085 2.782192 CGAAACTGTCGCCTAACTATCG 59.218 50.000 0.00 0.00 44.14 2.92
2051 2097 0.512952 ATCGCAAGCACGAAACTGTC 59.487 50.000 0.59 0.00 46.59 3.51
2060 2106 2.806856 CGCCAGAGATCGCAAGCAC 61.807 63.158 10.44 0.00 37.18 4.40
2062 2108 2.202797 TCGCCAGAGATCGCAAGC 60.203 61.111 0.00 0.00 37.18 4.01
2182 2260 4.646572 GAGAATCCGAGGCCAGATTATTT 58.353 43.478 5.01 0.27 32.91 1.40
2208 2286 3.376078 GAGGGCGTCACCGTGGTA 61.376 66.667 1.64 0.00 40.62 3.25
2222 2300 2.124901 TTTACGCCGCCATGGAGG 60.125 61.111 28.87 28.87 42.78 4.30
2228 2306 4.770874 GGCTCCTTTACGCCGCCA 62.771 66.667 0.00 0.00 40.41 5.69
2263 2341 1.993370 CTCAACCCTCGAACGAATGAC 59.007 52.381 0.00 0.00 0.00 3.06
2266 2344 0.608640 AGCTCAACCCTCGAACGAAT 59.391 50.000 0.00 0.00 0.00 3.34
2275 2353 1.355720 AGGCACATAAAGCTCAACCCT 59.644 47.619 0.00 0.00 0.00 4.34
2276 2354 1.474077 CAGGCACATAAAGCTCAACCC 59.526 52.381 0.00 0.00 0.00 4.11
2306 2385 2.591753 GTAGGGGCAGCAGCATCA 59.408 61.111 2.65 0.00 44.61 3.07
2319 2398 2.029838 AGTACACGACGGTAGGTAGG 57.970 55.000 0.00 0.00 0.00 3.18
2320 2399 2.096496 CCAAGTACACGACGGTAGGTAG 59.904 54.545 0.00 0.00 0.00 3.18
2321 2400 2.083774 CCAAGTACACGACGGTAGGTA 58.916 52.381 0.00 0.00 0.00 3.08
2323 2402 1.131883 CTCCAAGTACACGACGGTAGG 59.868 57.143 0.00 0.00 0.00 3.18
2325 2404 0.523072 GCTCCAAGTACACGACGGTA 59.477 55.000 0.00 0.00 0.00 4.02
2326 2405 1.288127 GCTCCAAGTACACGACGGT 59.712 57.895 0.00 0.00 0.00 4.83
2328 2407 0.318360 TGTGCTCCAAGTACACGACG 60.318 55.000 0.00 0.00 35.91 5.12
2336 2429 1.668294 CTCCGTCTGTGCTCCAAGT 59.332 57.895 0.00 0.00 0.00 3.16
2350 2443 2.113139 ACTGCCACCAAACCTCCG 59.887 61.111 0.00 0.00 0.00 4.63
2367 2460 0.041090 GGGGAGGAAAGCCAAATCCA 59.959 55.000 0.00 0.00 38.23 3.41
2389 2482 1.434622 GCCACTCACTGCCGATGATG 61.435 60.000 0.00 0.00 0.00 3.07
2399 2492 0.689080 ATCTGGATCCGCCACTCACT 60.689 55.000 7.39 0.00 43.33 3.41
2401 2494 1.040646 GTATCTGGATCCGCCACTCA 58.959 55.000 7.39 0.00 43.33 3.41
2431 2532 2.185867 GCACGTCGGCTGGGAATA 59.814 61.111 0.00 0.00 0.00 1.75
2438 2539 2.184322 CTATGTGGCACGTCGGCT 59.816 61.111 17.00 0.00 41.89 5.52
2454 2556 3.786635 CTTATAGAACAGGCGCTTGACT 58.213 45.455 27.58 23.63 0.00 3.41
2479 2581 3.450028 GCTTTGAGAGCCGATGACT 57.550 52.632 0.00 0.00 46.01 3.41
2501 2603 4.473643 GCCAACGCCATAGCCATA 57.526 55.556 0.00 0.00 34.57 2.74
2544 2646 1.596895 GACTCGCCGGAAGAAGAGGT 61.597 60.000 5.05 0.00 38.25 3.85
2591 2693 5.163683 CCCTGCAGATAATCAACACAGAAAG 60.164 44.000 17.39 0.00 0.00 2.62
2603 2705 1.707427 CTTAGGGGCCCTGCAGATAAT 59.293 52.381 35.70 8.00 34.61 1.28
2611 2713 1.059006 AGATGCTCTTAGGGGCCCTG 61.059 60.000 35.70 19.77 34.61 4.45
2616 2718 2.224066 CGGTTGTAGATGCTCTTAGGGG 60.224 54.545 0.00 0.00 0.00 4.79
2617 2719 2.224066 CCGGTTGTAGATGCTCTTAGGG 60.224 54.545 0.00 0.00 0.00 3.53
2620 2722 2.429610 GGTCCGGTTGTAGATGCTCTTA 59.570 50.000 0.00 0.00 0.00 2.10
2621 2723 1.207329 GGTCCGGTTGTAGATGCTCTT 59.793 52.381 0.00 0.00 0.00 2.85
2623 2725 0.179081 GGGTCCGGTTGTAGATGCTC 60.179 60.000 0.00 0.00 0.00 4.26
2624 2726 0.617820 AGGGTCCGGTTGTAGATGCT 60.618 55.000 0.00 0.00 0.00 3.79
2625 2727 0.252197 AAGGGTCCGGTTGTAGATGC 59.748 55.000 0.00 0.00 0.00 3.91
2626 2728 1.553248 TGAAGGGTCCGGTTGTAGATG 59.447 52.381 0.00 0.00 0.00 2.90
2627 2729 1.946984 TGAAGGGTCCGGTTGTAGAT 58.053 50.000 0.00 0.00 0.00 1.98
2628 2730 1.946984 ATGAAGGGTCCGGTTGTAGA 58.053 50.000 0.00 0.00 0.00 2.59
2629 2731 2.159000 GGTATGAAGGGTCCGGTTGTAG 60.159 54.545 0.00 0.00 0.00 2.74
2630 2732 1.832998 GGTATGAAGGGTCCGGTTGTA 59.167 52.381 0.00 0.00 0.00 2.41
2631 2733 0.616891 GGTATGAAGGGTCCGGTTGT 59.383 55.000 0.00 0.00 0.00 3.32
2632 2734 0.909623 AGGTATGAAGGGTCCGGTTG 59.090 55.000 0.00 0.00 0.00 3.77
2633 2735 0.909623 CAGGTATGAAGGGTCCGGTT 59.090 55.000 0.00 0.00 0.00 4.44
2634 2736 1.623542 GCAGGTATGAAGGGTCCGGT 61.624 60.000 0.00 0.00 0.00 5.28
2635 2737 1.146263 GCAGGTATGAAGGGTCCGG 59.854 63.158 0.00 0.00 0.00 5.14
2636 2738 1.146263 GGCAGGTATGAAGGGTCCG 59.854 63.158 0.00 0.00 0.00 4.79
2637 2739 1.532238 GGGCAGGTATGAAGGGTCC 59.468 63.158 0.00 0.00 0.00 4.46
2638 2740 1.279025 TGGGGCAGGTATGAAGGGTC 61.279 60.000 0.00 0.00 0.00 4.46
2639 2741 0.849094 TTGGGGCAGGTATGAAGGGT 60.849 55.000 0.00 0.00 0.00 4.34
2640 2742 0.334676 TTTGGGGCAGGTATGAAGGG 59.665 55.000 0.00 0.00 0.00 3.95
2641 2743 1.474330 GTTTGGGGCAGGTATGAAGG 58.526 55.000 0.00 0.00 0.00 3.46
2642 2744 1.094785 CGTTTGGGGCAGGTATGAAG 58.905 55.000 0.00 0.00 0.00 3.02
2643 2745 0.402504 ACGTTTGGGGCAGGTATGAA 59.597 50.000 0.00 0.00 0.00 2.57
2644 2746 0.035820 GACGTTTGGGGCAGGTATGA 60.036 55.000 0.00 0.00 0.00 2.15
2645 2747 0.035439 AGACGTTTGGGGCAGGTATG 60.035 55.000 0.00 0.00 0.00 2.39
2646 2748 1.485066 CTAGACGTTTGGGGCAGGTAT 59.515 52.381 0.00 0.00 0.00 2.73
2647 2749 0.899720 CTAGACGTTTGGGGCAGGTA 59.100 55.000 0.00 0.00 0.00 3.08
2648 2750 0.834687 TCTAGACGTTTGGGGCAGGT 60.835 55.000 0.00 0.00 0.00 4.00
2649 2751 0.391263 GTCTAGACGTTTGGGGCAGG 60.391 60.000 7.22 0.00 0.00 4.85
2650 2752 0.320374 TGTCTAGACGTTTGGGGCAG 59.680 55.000 17.85 0.00 0.00 4.85
2651 2753 0.034337 GTGTCTAGACGTTTGGGGCA 59.966 55.000 17.85 0.00 0.00 5.36
2652 2754 1.012486 CGTGTCTAGACGTTTGGGGC 61.012 60.000 17.85 0.62 34.56 5.80
2653 2755 0.389426 CCGTGTCTAGACGTTTGGGG 60.389 60.000 17.85 8.47 37.66 4.96
2654 2756 0.316204 ACCGTGTCTAGACGTTTGGG 59.684 55.000 17.85 14.98 37.66 4.12
2655 2757 1.790623 CAACCGTGTCTAGACGTTTGG 59.209 52.381 17.85 17.04 37.89 3.28
2656 2758 1.191647 GCAACCGTGTCTAGACGTTTG 59.808 52.381 17.85 16.62 42.63 2.93
2657 2759 1.494824 GCAACCGTGTCTAGACGTTT 58.505 50.000 17.85 5.47 37.66 3.60
2658 2760 0.319297 GGCAACCGTGTCTAGACGTT 60.319 55.000 17.85 12.66 37.66 3.99
2659 2761 1.288127 GGCAACCGTGTCTAGACGT 59.712 57.895 17.85 7.20 37.66 4.34
2660 2762 4.164252 GGCAACCGTGTCTAGACG 57.836 61.111 17.85 7.66 39.13 4.18
2681 2783 4.577246 TGGGTGCGGTTTTTGCGC 62.577 61.111 0.00 0.00 41.98 6.09
2682 2784 2.105128 TTGGGTGCGGTTTTTGCG 59.895 55.556 0.00 0.00 34.24 4.85
2683 2785 1.151172 CTGTTGGGTGCGGTTTTTGC 61.151 55.000 0.00 0.00 0.00 3.68
2684 2786 0.174617 ACTGTTGGGTGCGGTTTTTG 59.825 50.000 0.00 0.00 0.00 2.44
2685 2787 1.406180 GTACTGTTGGGTGCGGTTTTT 59.594 47.619 0.00 0.00 0.00 1.94
2686 2788 1.026584 GTACTGTTGGGTGCGGTTTT 58.973 50.000 0.00 0.00 0.00 2.43
2687 2789 0.820482 GGTACTGTTGGGTGCGGTTT 60.820 55.000 0.00 0.00 0.00 3.27
2688 2790 1.228033 GGTACTGTTGGGTGCGGTT 60.228 57.895 0.00 0.00 0.00 4.44
2689 2791 2.428622 GGTACTGTTGGGTGCGGT 59.571 61.111 0.00 0.00 0.00 5.68
2690 2792 1.964373 GTGGTACTGTTGGGTGCGG 60.964 63.158 0.00 0.00 0.00 5.69
2691 2793 0.534203 AAGTGGTACTGTTGGGTGCG 60.534 55.000 0.00 0.00 0.00 5.34
2692 2794 2.554370 TAAGTGGTACTGTTGGGTGC 57.446 50.000 0.00 0.00 0.00 5.01
2693 2795 4.457949 GGATTTAAGTGGTACTGTTGGGTG 59.542 45.833 0.00 0.00 0.00 4.61
2694 2796 4.659115 GGATTTAAGTGGTACTGTTGGGT 58.341 43.478 0.00 0.00 0.00 4.51
2695 2797 3.687698 CGGATTTAAGTGGTACTGTTGGG 59.312 47.826 0.00 0.00 0.00 4.12
2696 2798 3.687698 CCGGATTTAAGTGGTACTGTTGG 59.312 47.826 0.00 0.00 0.00 3.77
2697 2799 4.320870 ACCGGATTTAAGTGGTACTGTTG 58.679 43.478 9.46 0.00 31.60 3.33
2698 2800 4.628963 ACCGGATTTAAGTGGTACTGTT 57.371 40.909 9.46 0.00 31.60 3.16


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

AutoCloner maintained by Alex Coulton.