Multiple sequence alignment - TraesCS2D01G276400

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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 TraesCS2D01G276400 chr2D 100.000 2324 0 0 1 2324 346077626 346079949 0.000000e+00 4292.0
1 TraesCS2D01G276400 chr2D 85.616 146 18 3 2105 2250 503572382 503572524 1.440000e-32 150.0
2 TraesCS2D01G276400 chr2D 93.846 65 4 0 2251 2315 631993196 631993132 5.280000e-17 99.0
3 TraesCS2D01G276400 chr2D 92.308 65 5 0 2251 2315 316142258 316142194 2.460000e-15 93.5
4 TraesCS2D01G276400 chr2A 92.939 1133 49 11 674 1786 457441354 457440233 0.000000e+00 1620.0
5 TraesCS2D01G276400 chr2A 86.560 625 57 15 1 625 457446926 457446329 0.000000e+00 664.0
6 TraesCS2D01G276400 chr2A 87.075 147 17 2 2105 2251 277608616 277608472 5.140000e-37 165.0
7 TraesCS2D01G276400 chr2A 85.034 147 17 5 2105 2250 32943500 32943642 6.690000e-31 145.0
8 TraesCS2D01G276400 chr2A 100.000 73 0 0 618 690 457444915 457444843 4.030000e-28 135.0
9 TraesCS2D01G276400 chr2A 93.056 72 4 1 2248 2319 5108597 5108667 1.140000e-18 104.0
10 TraesCS2D01G276400 chr2B 93.432 1081 39 5 1 1073 411973856 411974912 0.000000e+00 1574.0
11 TraesCS2D01G276400 chr2B 91.296 494 15 9 1113 1597 411974915 411975389 0.000000e+00 649.0
12 TraesCS2D01G276400 chr2B 90.106 283 24 2 1581 1859 411975399 411975681 4.720000e-97 364.0
13 TraesCS2D01G276400 chr1D 87.075 147 17 2 2105 2251 224397233 224397377 5.140000e-37 165.0
14 TraesCS2D01G276400 chr1D 98.667 75 1 0 2250 2324 408745086 408745012 1.450000e-27 134.0
15 TraesCS2D01G276400 chr5D 86.395 147 18 2 2105 2251 46088740 46088884 2.390000e-35 159.0
16 TraesCS2D01G276400 chr6D 85.714 147 19 2 2105 2251 365733915 365733771 1.110000e-33 154.0
17 TraesCS2D01G276400 chr6D 85.714 147 16 5 2105 2250 365733840 365733698 1.440000e-32 150.0
18 TraesCS2D01G276400 chr6D 92.754 69 4 1 2247 2315 385992697 385992764 5.280000e-17 99.0
19 TraesCS2D01G276400 chr1A 85.616 146 18 3 2105 2250 219383839 219383981 1.440000e-32 150.0
20 TraesCS2D01G276400 chr4A 85.034 147 20 2 2105 2251 56265623 56265479 5.170000e-32 148.0
21 TraesCS2D01G276400 chr3B 82.353 153 23 3 375 523 810628755 810628907 1.870000e-26 130.0
22 TraesCS2D01G276400 chr3A 95.890 73 3 0 2252 2324 730905276 730905348 4.060000e-23 119.0
23 TraesCS2D01G276400 chr7D 94.595 74 4 0 2251 2324 8415375 8415302 5.250000e-22 115.0
24 TraesCS2D01G276400 chr7D 90.909 55 5 0 1677 1731 535569984 535569930 8.910000e-10 75.0
25 TraesCS2D01G276400 chrUn 96.296 54 2 0 2252 2305 95404543 95404490 3.180000e-14 89.8


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 TraesCS2D01G276400 chr2D 346077626 346079949 2323 False 4292.000000 4292 100.000000 1 2324 1 chr2D.!!$F1 2323
1 TraesCS2D01G276400 chr2A 457440233 457446926 6693 True 806.333333 1620 93.166333 1 1786 3 chr2A.!!$R2 1785
2 TraesCS2D01G276400 chr2B 411973856 411975681 1825 False 862.333333 1574 91.611333 1 1859 3 chr2B.!!$F1 1858

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
613 637 1.375908 ATACACAGGCACGCACAGG 60.376 57.895 0.0 0.0 0.0 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2256 7256 0.035598 TCGACCCGAATTTCTGGCAA 59.964 50.0 6.76 0.0 31.06 4.52 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
47 48 6.073548 GCAATCGGACTGGACAGATAATTAAG 60.074 42.308 6.29 0.00 0.00 1.85
232 233 9.884814 ACTAACCAGGAGATATAATACAACTCT 57.115 33.333 0.00 0.00 0.00 3.24
338 339 7.534239 GCACTTCTATCCGTTTGTTTAGAAAAG 59.466 37.037 0.00 0.00 32.07 2.27
341 342 7.429636 TCTATCCGTTTGTTTAGAAAAGTGG 57.570 36.000 0.00 0.00 0.00 4.00
401 402 5.841237 AGACCATGGCTTCTGTATACTATGT 59.159 40.000 13.04 0.00 0.00 2.29
429 453 4.695217 AAACTTCAGTTTTTGCTGACGA 57.305 36.364 0.00 0.00 45.07 4.20
430 454 3.675467 ACTTCAGTTTTTGCTGACGAC 57.325 42.857 6.58 0.00 44.23 4.34
431 455 3.006940 ACTTCAGTTTTTGCTGACGACA 58.993 40.909 6.58 0.00 44.23 4.35
432 456 3.438781 ACTTCAGTTTTTGCTGACGACAA 59.561 39.130 6.58 0.00 44.23 3.18
433 457 4.083003 ACTTCAGTTTTTGCTGACGACAAA 60.083 37.500 6.58 0.00 44.23 2.83
434 458 3.753842 TCAGTTTTTGCTGACGACAAAC 58.246 40.909 0.00 0.00 40.23 2.93
435 459 3.189495 TCAGTTTTTGCTGACGACAAACA 59.811 39.130 0.00 0.00 40.23 2.83
443 467 3.127721 TGCTGACGACAAACACATCAAAA 59.872 39.130 0.00 0.00 0.00 2.44
576 600 3.009033 TGTTATTGGGAGGGAGTGAACAG 59.991 47.826 0.00 0.00 0.00 3.16
613 637 1.375908 ATACACAGGCACGCACAGG 60.376 57.895 0.00 0.00 0.00 4.00
764 5714 4.893608 TGAATCAGTTTTCGTGATCTCCA 58.106 39.130 0.00 0.00 33.34 3.86
849 5799 2.641305 AGCTGATGATCTGTTTCAGGC 58.359 47.619 13.58 8.48 37.84 4.85
1043 6001 2.232452 TCTCTCTGCTTGTAGTTGGAGC 59.768 50.000 0.00 0.00 36.95 4.70
1386 6344 4.166888 ACTCGATGGCATGCCGCT 62.167 61.111 30.87 21.10 41.91 5.52
1399 6357 0.600518 TGCCGCTAAACTTGTACGCA 60.601 50.000 0.00 0.00 0.00 5.24
1576 6543 2.617274 GCCAGCGGCGAGTTTTCTT 61.617 57.895 12.98 0.00 39.62 2.52
1659 6658 8.978874 AGAATATTGTAGATGGTGTGCATTTA 57.021 30.769 0.00 0.00 0.00 1.40
1663 6662 5.621197 TGTAGATGGTGTGCATTTAACAC 57.379 39.130 0.00 0.00 45.81 3.32
1709 6708 5.477291 TGGTTTATTTTCAACCGGCTGATAA 59.523 36.000 8.68 10.73 46.01 1.75
1816 6816 2.493675 TCGATTCCCTTGTCTCTCACTG 59.506 50.000 0.00 0.00 0.00 3.66
1839 6839 6.816136 TGCTCATCACTAAAATCTTATCCGA 58.184 36.000 0.00 0.00 0.00 4.55
1846 6846 7.145985 TCACTAAAATCTTATCCGATCCTTCG 58.854 38.462 0.00 0.00 45.08 3.79
1859 6859 3.669536 GATCCTTCGAATCCCAATCTCC 58.330 50.000 0.00 0.00 0.00 3.71
1860 6860 2.764269 TCCTTCGAATCCCAATCTCCT 58.236 47.619 0.00 0.00 0.00 3.69
1861 6861 3.115390 TCCTTCGAATCCCAATCTCCTT 58.885 45.455 0.00 0.00 0.00 3.36
1862 6862 3.134804 TCCTTCGAATCCCAATCTCCTTC 59.865 47.826 0.00 0.00 0.00 3.46
1863 6863 3.135530 CCTTCGAATCCCAATCTCCTTCT 59.864 47.826 0.00 0.00 0.00 2.85
1864 6864 3.827008 TCGAATCCCAATCTCCTTCTG 57.173 47.619 0.00 0.00 0.00 3.02
1865 6865 2.158900 TCGAATCCCAATCTCCTTCTGC 60.159 50.000 0.00 0.00 0.00 4.26
1866 6866 2.580962 GAATCCCAATCTCCTTCTGCC 58.419 52.381 0.00 0.00 0.00 4.85
1867 6867 0.471617 ATCCCAATCTCCTTCTGCCG 59.528 55.000 0.00 0.00 0.00 5.69
1868 6868 0.617535 TCCCAATCTCCTTCTGCCGA 60.618 55.000 0.00 0.00 0.00 5.54
1869 6869 0.471617 CCCAATCTCCTTCTGCCGAT 59.528 55.000 0.00 0.00 0.00 4.18
1870 6870 1.590932 CCAATCTCCTTCTGCCGATG 58.409 55.000 0.00 0.00 0.00 3.84
1871 6871 0.942962 CAATCTCCTTCTGCCGATGC 59.057 55.000 0.00 0.00 38.26 3.91
1880 6880 3.985877 TGCCGATGCAGGAACAAG 58.014 55.556 0.00 0.00 44.23 3.16
1881 6881 1.374568 TGCCGATGCAGGAACAAGA 59.625 52.632 0.00 0.00 44.23 3.02
1882 6882 0.250684 TGCCGATGCAGGAACAAGAA 60.251 50.000 0.00 0.00 44.23 2.52
1883 6883 0.449388 GCCGATGCAGGAACAAGAAG 59.551 55.000 0.00 0.00 37.47 2.85
1884 6884 0.449388 CCGATGCAGGAACAAGAAGC 59.551 55.000 0.00 0.00 0.00 3.86
1885 6885 0.449388 CGATGCAGGAACAAGAAGCC 59.551 55.000 0.00 0.00 0.00 4.35
1886 6886 1.831580 GATGCAGGAACAAGAAGCCT 58.168 50.000 0.00 0.00 0.00 4.58
1887 6887 1.742268 GATGCAGGAACAAGAAGCCTC 59.258 52.381 0.00 0.00 0.00 4.70
1888 6888 0.250901 TGCAGGAACAAGAAGCCTCC 60.251 55.000 0.00 0.00 0.00 4.30
1889 6889 0.250901 GCAGGAACAAGAAGCCTCCA 60.251 55.000 0.00 0.00 0.00 3.86
1890 6890 1.528129 CAGGAACAAGAAGCCTCCAC 58.472 55.000 0.00 0.00 0.00 4.02
1891 6891 0.402121 AGGAACAAGAAGCCTCCACC 59.598 55.000 0.00 0.00 0.00 4.61
1892 6892 0.955919 GGAACAAGAAGCCTCCACCG 60.956 60.000 0.00 0.00 0.00 4.94
1893 6893 0.955919 GAACAAGAAGCCTCCACCGG 60.956 60.000 0.00 0.00 0.00 5.28
1913 6913 4.640855 ACGTGCCTGTCGTGACCG 62.641 66.667 0.00 0.00 40.07 4.79
1932 6932 3.716006 CGACAGCCACCGTTGCAG 61.716 66.667 0.00 0.00 0.00 4.41
1933 6933 3.357079 GACAGCCACCGTTGCAGG 61.357 66.667 0.00 0.00 37.30 4.85
1934 6934 3.825160 GACAGCCACCGTTGCAGGA 62.825 63.158 0.00 0.00 34.73 3.86
1935 6935 3.052082 CAGCCACCGTTGCAGGAG 61.052 66.667 0.00 0.00 34.73 3.69
1938 6938 4.641645 CCACCGTTGCAGGAGCCA 62.642 66.667 0.00 0.00 41.13 4.75
1939 6939 3.052082 CACCGTTGCAGGAGCCAG 61.052 66.667 0.00 0.00 41.13 4.85
1943 6943 2.598394 GTTGCAGGAGCCAGCCAA 60.598 61.111 1.26 0.00 41.13 4.52
1944 6944 1.980772 GTTGCAGGAGCCAGCCAAT 60.981 57.895 1.26 0.00 41.13 3.16
1945 6945 1.679977 TTGCAGGAGCCAGCCAATC 60.680 57.895 1.26 0.00 41.13 2.67
1946 6946 3.207669 GCAGGAGCCAGCCAATCG 61.208 66.667 0.00 0.00 33.58 3.34
1947 6947 3.207669 CAGGAGCCAGCCAATCGC 61.208 66.667 0.00 0.00 37.98 4.58
1956 6956 2.493030 GCCAATCGCTGCTGCAAT 59.507 55.556 16.29 0.00 39.64 3.56
1957 6957 1.588139 GCCAATCGCTGCTGCAATC 60.588 57.895 16.29 0.00 39.64 2.67
1958 6958 1.298116 CCAATCGCTGCTGCAATCG 60.298 57.895 16.29 15.07 39.64 3.34
1959 6959 1.937846 CAATCGCTGCTGCAATCGC 60.938 57.895 16.29 10.02 39.64 4.58
1960 6960 2.110967 AATCGCTGCTGCAATCGCT 61.111 52.632 16.29 6.75 39.64 4.93
1961 6961 2.044832 AATCGCTGCTGCAATCGCTC 62.045 55.000 16.29 0.00 39.64 5.03
1962 6962 4.233635 CGCTGCTGCAATCGCTCC 62.234 66.667 16.29 0.00 39.64 4.70
1963 6963 3.129502 GCTGCTGCAATCGCTCCA 61.130 61.111 11.11 0.00 39.64 3.86
1964 6964 2.789917 CTGCTGCAATCGCTCCAC 59.210 61.111 3.02 0.00 39.64 4.02
1965 6965 1.744368 CTGCTGCAATCGCTCCACT 60.744 57.895 3.02 0.00 39.64 4.00
1966 6966 1.302752 TGCTGCAATCGCTCCACTT 60.303 52.632 0.00 0.00 39.64 3.16
1967 6967 1.136147 GCTGCAATCGCTCCACTTG 59.864 57.895 0.00 0.00 39.64 3.16
1968 6968 1.136147 CTGCAATCGCTCCACTTGC 59.864 57.895 0.00 0.00 44.25 4.01
1969 6969 1.302752 TGCAATCGCTCCACTTGCT 60.303 52.632 7.85 0.00 44.29 3.91
1970 6970 0.890542 TGCAATCGCTCCACTTGCTT 60.891 50.000 7.85 0.00 44.29 3.91
1971 6971 0.242017 GCAATCGCTCCACTTGCTTT 59.758 50.000 0.00 0.00 41.52 3.51
1972 6972 1.336240 GCAATCGCTCCACTTGCTTTT 60.336 47.619 0.00 0.00 41.52 2.27
1973 6973 2.863704 GCAATCGCTCCACTTGCTTTTT 60.864 45.455 0.00 0.00 41.52 1.94
1996 6996 4.992381 TTCTTTTCTTCTAGACGCAAGC 57.008 40.909 0.00 0.00 45.62 4.01
1997 6997 3.990092 TCTTTTCTTCTAGACGCAAGCA 58.010 40.909 0.00 0.00 45.62 3.91
1998 6998 3.741344 TCTTTTCTTCTAGACGCAAGCAC 59.259 43.478 0.00 0.00 45.62 4.40
1999 6999 2.812358 TTCTTCTAGACGCAAGCACA 57.188 45.000 0.00 0.00 45.62 4.57
2000 7000 2.812358 TCTTCTAGACGCAAGCACAA 57.188 45.000 0.00 0.00 45.62 3.33
2001 7001 2.404215 TCTTCTAGACGCAAGCACAAC 58.596 47.619 0.00 0.00 45.62 3.32
2002 7002 1.125021 CTTCTAGACGCAAGCACAACG 59.875 52.381 0.00 0.00 45.62 4.10
2003 7003 0.666274 TCTAGACGCAAGCACAACGG 60.666 55.000 0.00 0.00 45.62 4.44
2004 7004 2.227968 CTAGACGCAAGCACAACGGC 62.228 60.000 0.00 0.00 45.62 5.68
2008 7008 3.722295 GCAAGCACAACGGCGCTA 61.722 61.111 6.90 0.00 37.54 4.26
2009 7009 2.173382 CAAGCACAACGGCGCTAC 59.827 61.111 6.90 0.00 37.54 3.58
2010 7010 3.411351 AAGCACAACGGCGCTACG 61.411 61.111 6.90 5.82 37.54 3.51
2011 7011 3.851845 AAGCACAACGGCGCTACGA 62.852 57.895 13.02 0.00 37.54 3.43
2012 7012 4.130281 GCACAACGGCGCTACGAC 62.130 66.667 13.02 0.00 37.61 4.34
2013 7013 3.475774 CACAACGGCGCTACGACC 61.476 66.667 13.02 0.00 37.61 4.79
2014 7014 4.729856 ACAACGGCGCTACGACCC 62.730 66.667 13.02 0.00 37.61 4.46
2015 7015 4.728102 CAACGGCGCTACGACCCA 62.728 66.667 13.02 0.00 37.61 4.51
2016 7016 4.729856 AACGGCGCTACGACCCAC 62.730 66.667 13.02 0.00 37.61 4.61
2018 7018 4.728102 CGGCGCTACGACCCACAA 62.728 66.667 7.64 0.00 35.47 3.33
2019 7019 2.125269 GGCGCTACGACCCACAAT 60.125 61.111 7.64 0.00 0.00 2.71
2020 7020 2.171725 GGCGCTACGACCCACAATC 61.172 63.158 7.64 0.00 0.00 2.67
2021 7021 1.153628 GCGCTACGACCCACAATCT 60.154 57.895 0.00 0.00 0.00 2.40
2022 7022 1.146358 GCGCTACGACCCACAATCTC 61.146 60.000 0.00 0.00 0.00 2.75
2023 7023 0.866061 CGCTACGACCCACAATCTCG 60.866 60.000 0.00 0.00 0.00 4.04
2024 7024 1.146358 GCTACGACCCACAATCTCGC 61.146 60.000 0.00 0.00 0.00 5.03
2025 7025 0.527817 CTACGACCCACAATCTCGCC 60.528 60.000 0.00 0.00 0.00 5.54
2026 7026 2.274232 TACGACCCACAATCTCGCCG 62.274 60.000 0.00 0.00 0.00 6.46
2027 7027 3.195698 GACCCACAATCTCGCCGC 61.196 66.667 0.00 0.00 0.00 6.53
2028 7028 3.665675 GACCCACAATCTCGCCGCT 62.666 63.158 0.00 0.00 0.00 5.52
2029 7029 3.197790 CCCACAATCTCGCCGCTG 61.198 66.667 0.00 0.00 0.00 5.18
2030 7030 2.125552 CCACAATCTCGCCGCTGA 60.126 61.111 0.00 0.00 0.00 4.26
2031 7031 2.456119 CCACAATCTCGCCGCTGAC 61.456 63.158 0.00 0.00 0.00 3.51
2032 7032 2.125512 ACAATCTCGCCGCTGACC 60.126 61.111 0.00 0.00 0.00 4.02
2033 7033 2.125552 CAATCTCGCCGCTGACCA 60.126 61.111 0.00 0.00 0.00 4.02
2034 7034 2.169789 CAATCTCGCCGCTGACCAG 61.170 63.158 0.00 0.00 0.00 4.00
2035 7035 3.376935 AATCTCGCCGCTGACCAGG 62.377 63.158 0.00 0.00 0.00 4.45
2059 7059 2.574212 GCAACGCGATTCTTGCCG 60.574 61.111 15.93 0.00 37.41 5.69
2127 7127 4.824166 GCTGTCGGCGCTGCATTG 62.824 66.667 12.58 3.65 34.18 2.82
2128 7128 4.170062 CTGTCGGCGCTGCATTGG 62.170 66.667 12.58 0.00 0.00 3.16
2129 7129 4.695993 TGTCGGCGCTGCATTGGA 62.696 61.111 12.58 0.00 0.00 3.53
2130 7130 3.869272 GTCGGCGCTGCATTGGAG 61.869 66.667 12.58 0.03 0.00 3.86
2131 7131 4.393155 TCGGCGCTGCATTGGAGT 62.393 61.111 12.58 0.00 0.00 3.85
2132 7132 3.434319 CGGCGCTGCATTGGAGTT 61.434 61.111 7.64 0.00 0.00 3.01
2133 7133 2.486966 GGCGCTGCATTGGAGTTC 59.513 61.111 7.64 0.00 0.00 3.01
2134 7134 2.042831 GGCGCTGCATTGGAGTTCT 61.043 57.895 7.64 0.00 0.00 3.01
2135 7135 1.136147 GCGCTGCATTGGAGTTCTG 59.864 57.895 0.00 0.00 0.00 3.02
2136 7136 1.136147 CGCTGCATTGGAGTTCTGC 59.864 57.895 7.05 0.00 36.45 4.26
2137 7137 1.509923 GCTGCATTGGAGTTCTGCC 59.490 57.895 7.05 0.00 35.02 4.85
2138 7138 1.798735 CTGCATTGGAGTTCTGCCG 59.201 57.895 0.00 0.00 35.02 5.69
2139 7139 1.651240 CTGCATTGGAGTTCTGCCGG 61.651 60.000 0.00 0.00 35.02 6.13
2140 7140 2.409870 GCATTGGAGTTCTGCCGGG 61.410 63.158 2.18 0.00 0.00 5.73
2141 7141 1.750399 CATTGGAGTTCTGCCGGGG 60.750 63.158 2.18 0.00 0.00 5.73
2142 7142 3.645268 ATTGGAGTTCTGCCGGGGC 62.645 63.158 2.18 1.86 42.35 5.80
2144 7144 4.785453 GGAGTTCTGCCGGGGCTG 62.785 72.222 11.55 10.74 42.51 4.85
2148 7148 4.365111 TTCTGCCGGGGCTGCAAT 62.365 61.111 11.55 0.00 42.51 3.56
2154 7154 4.431131 CGGGGCTGCAATGGACCT 62.431 66.667 0.50 0.00 31.26 3.85
2155 7155 2.440980 GGGGCTGCAATGGACCTC 60.441 66.667 0.50 0.00 31.26 3.85
2156 7156 2.825836 GGGCTGCAATGGACCTCG 60.826 66.667 0.50 0.00 0.00 4.63
2157 7157 2.825836 GGCTGCAATGGACCTCGG 60.826 66.667 0.50 0.00 0.00 4.63
2158 7158 3.512516 GCTGCAATGGACCTCGGC 61.513 66.667 0.00 0.00 0.00 5.54
2159 7159 2.825836 CTGCAATGGACCTCGGCC 60.826 66.667 0.00 0.00 0.00 6.13
2160 7160 4.776322 TGCAATGGACCTCGGCCG 62.776 66.667 22.12 22.12 0.00 6.13
2162 7162 3.781307 CAATGGACCTCGGCCGGA 61.781 66.667 27.83 11.38 0.00 5.14
2163 7163 3.470888 AATGGACCTCGGCCGGAG 61.471 66.667 27.83 20.31 42.75 4.63
2164 7164 4.779733 ATGGACCTCGGCCGGAGT 62.780 66.667 27.83 22.87 41.46 3.85
2166 7166 4.452733 GGACCTCGGCCGGAGTTG 62.453 72.222 27.83 11.82 41.46 3.16
2169 7169 4.697756 CCTCGGCCGGAGTTGCAA 62.698 66.667 27.83 1.15 41.46 4.08
2170 7170 2.436646 CTCGGCCGGAGTTGCAAT 60.437 61.111 27.83 0.00 38.02 3.56
2171 7171 2.745884 TCGGCCGGAGTTGCAATG 60.746 61.111 27.83 0.00 0.00 2.82
2172 7172 3.814268 CGGCCGGAGTTGCAATGG 61.814 66.667 20.10 3.96 0.00 3.16
2173 7173 2.361104 GGCCGGAGTTGCAATGGA 60.361 61.111 5.05 0.00 0.00 3.41
2174 7174 2.409870 GGCCGGAGTTGCAATGGAG 61.410 63.158 5.05 0.00 0.00 3.86
2175 7175 3.056313 GCCGGAGTTGCAATGGAGC 62.056 63.158 5.05 0.00 0.00 4.70
2176 7176 1.377725 CCGGAGTTGCAATGGAGCT 60.378 57.895 0.59 0.00 34.99 4.09
2177 7177 0.962356 CCGGAGTTGCAATGGAGCTT 60.962 55.000 0.59 0.00 34.99 3.74
2178 7178 0.449388 CGGAGTTGCAATGGAGCTTC 59.551 55.000 0.59 0.00 34.99 3.86
2179 7179 0.449388 GGAGTTGCAATGGAGCTTCG 59.551 55.000 0.59 0.00 34.99 3.79
2180 7180 0.179179 GAGTTGCAATGGAGCTTCGC 60.179 55.000 0.59 0.00 34.99 4.70
2181 7181 1.153958 GTTGCAATGGAGCTTCGCC 60.154 57.895 0.59 0.00 34.99 5.54
2182 7182 2.689785 TTGCAATGGAGCTTCGCCG 61.690 57.895 0.00 0.00 34.99 6.46
2183 7183 3.880846 GCAATGGAGCTTCGCCGG 61.881 66.667 0.00 0.00 0.00 6.13
2184 7184 2.125147 CAATGGAGCTTCGCCGGA 60.125 61.111 5.05 0.00 0.00 5.14
2185 7185 2.176273 CAATGGAGCTTCGCCGGAG 61.176 63.158 5.05 0.00 0.00 4.63
2186 7186 4.537433 ATGGAGCTTCGCCGGAGC 62.537 66.667 10.01 10.01 0.00 4.70
2197 7197 4.778415 CCGGAGCCGTCGACACTG 62.778 72.222 17.16 8.39 37.81 3.66
2198 7198 4.039357 CGGAGCCGTCGACACTGT 62.039 66.667 17.16 0.00 34.35 3.55
2199 7199 2.430921 GGAGCCGTCGACACTGTG 60.431 66.667 17.16 6.19 0.00 3.66
2200 7200 2.335369 GAGCCGTCGACACTGTGT 59.665 61.111 14.23 14.23 0.00 3.72
2201 7201 1.299926 GAGCCGTCGACACTGTGTT 60.300 57.895 15.54 0.00 0.00 3.32
2202 7202 1.548973 GAGCCGTCGACACTGTGTTG 61.549 60.000 19.91 19.91 33.03 3.33
2203 7203 2.594962 GCCGTCGACACTGTGTTGG 61.595 63.158 24.13 18.75 32.62 3.77
2204 7204 1.066752 CCGTCGACACTGTGTTGGA 59.933 57.895 24.13 17.09 32.62 3.53
2205 7205 1.213094 CCGTCGACACTGTGTTGGAC 61.213 60.000 24.13 24.25 32.62 4.02
2206 7206 1.213094 CGTCGACACTGTGTTGGACC 61.213 60.000 26.31 16.19 33.42 4.46
2207 7207 0.104304 GTCGACACTGTGTTGGACCT 59.896 55.000 24.13 0.00 32.62 3.85
2208 7208 0.387929 TCGACACTGTGTTGGACCTC 59.612 55.000 24.13 5.99 32.62 3.85
2209 7209 0.389391 CGACACTGTGTTGGACCTCT 59.611 55.000 18.52 0.00 0.00 3.69
2210 7210 1.869754 CGACACTGTGTTGGACCTCTG 60.870 57.143 18.52 0.00 0.00 3.35
2211 7211 0.179045 ACACTGTGTTGGACCTCTGC 60.179 55.000 7.80 0.00 0.00 4.26
2212 7212 0.886490 CACTGTGTTGGACCTCTGCC 60.886 60.000 0.00 0.00 0.00 4.85
2213 7213 1.344953 ACTGTGTTGGACCTCTGCCA 61.345 55.000 0.00 0.00 0.00 4.92
2214 7214 0.604780 CTGTGTTGGACCTCTGCCAG 60.605 60.000 0.00 0.00 36.64 4.85
2222 7222 4.355720 CCTCTGCCAGGGCTGCAA 62.356 66.667 12.19 0.00 42.51 4.08
2223 7223 2.044252 CTCTGCCAGGGCTGCAAT 60.044 61.111 12.19 0.00 42.51 3.56
2224 7224 2.361992 TCTGCCAGGGCTGCAATG 60.362 61.111 12.19 0.00 42.51 2.82
2225 7225 3.458163 CTGCCAGGGCTGCAATGG 61.458 66.667 15.70 15.70 42.51 3.16
2226 7226 3.949885 CTGCCAGGGCTGCAATGGA 62.950 63.158 22.12 9.37 42.51 3.41
2227 7227 3.145551 GCCAGGGCTGCAATGGAG 61.146 66.667 22.12 0.00 36.09 3.86
2228 7228 3.145551 CCAGGGCTGCAATGGAGC 61.146 66.667 18.67 18.67 36.09 4.70
2229 7229 2.044252 CAGGGCTGCAATGGAGCT 60.044 61.111 25.07 4.62 36.63 4.09
2230 7230 2.119655 CAGGGCTGCAATGGAGCTC 61.120 63.158 25.07 22.40 37.17 4.09
2231 7231 3.207669 GGGCTGCAATGGAGCTCG 61.208 66.667 25.07 0.00 36.63 5.03
2232 7232 2.124983 GGCTGCAATGGAGCTCGA 60.125 61.111 25.07 3.70 36.63 4.04
2233 7233 2.467826 GGCTGCAATGGAGCTCGAC 61.468 63.158 25.07 5.86 36.63 4.20
2234 7234 2.467826 GCTGCAATGGAGCTCGACC 61.468 63.158 19.55 0.00 33.37 4.79
2235 7235 2.125552 TGCAATGGAGCTCGACCG 60.126 61.111 7.83 0.00 34.99 4.79
2236 7236 2.892425 GCAATGGAGCTCGACCGG 60.892 66.667 7.83 0.00 0.00 5.28
2237 7237 2.892640 CAATGGAGCTCGACCGGA 59.107 61.111 9.46 0.00 0.00 5.14
2238 7238 1.443407 CAATGGAGCTCGACCGGAT 59.557 57.895 9.46 0.00 0.00 4.18
2239 7239 0.179073 CAATGGAGCTCGACCGGATT 60.179 55.000 9.46 0.00 0.00 3.01
2240 7240 0.541863 AATGGAGCTCGACCGGATTT 59.458 50.000 9.46 0.00 0.00 2.17
2241 7241 0.179073 ATGGAGCTCGACCGGATTTG 60.179 55.000 9.46 0.00 0.00 2.32
2242 7242 2.174319 GGAGCTCGACCGGATTTGC 61.174 63.158 9.46 7.35 0.00 3.68
2243 7243 1.447838 GAGCTCGACCGGATTTGCA 60.448 57.895 9.46 0.00 0.00 4.08
2244 7244 1.003839 AGCTCGACCGGATTTGCAA 60.004 52.632 9.46 0.00 0.00 4.08
2245 7245 0.392998 AGCTCGACCGGATTTGCAAT 60.393 50.000 9.46 0.00 0.00 3.56
2246 7246 0.248215 GCTCGACCGGATTTGCAATG 60.248 55.000 9.46 0.00 0.00 2.82
2247 7247 0.378257 CTCGACCGGATTTGCAATGG 59.622 55.000 9.46 2.86 0.00 3.16
2248 7248 0.035915 TCGACCGGATTTGCAATGGA 60.036 50.000 9.46 0.00 0.00 3.41
2249 7249 0.378257 CGACCGGATTTGCAATGGAG 59.622 55.000 9.46 0.00 0.00 3.86
2250 7250 0.101219 GACCGGATTTGCAATGGAGC 59.899 55.000 9.46 0.00 0.00 4.70
2251 7251 1.322538 ACCGGATTTGCAATGGAGCC 61.323 55.000 9.46 0.00 0.00 4.70
2252 7252 1.321805 CCGGATTTGCAATGGAGCCA 61.322 55.000 0.00 0.00 0.00 4.75
2253 7253 0.748450 CGGATTTGCAATGGAGCCAT 59.252 50.000 0.00 0.00 38.46 4.40
2254 7254 1.955778 CGGATTTGCAATGGAGCCATA 59.044 47.619 0.00 0.00 35.31 2.74
2255 7255 2.030540 CGGATTTGCAATGGAGCCATAG 60.031 50.000 0.00 0.00 35.31 2.23
2256 7256 2.961062 GGATTTGCAATGGAGCCATAGT 59.039 45.455 0.00 0.00 35.31 2.12
2257 7257 3.385755 GGATTTGCAATGGAGCCATAGTT 59.614 43.478 0.00 0.00 35.31 2.24
2258 7258 3.872511 TTTGCAATGGAGCCATAGTTG 57.127 42.857 0.00 0.00 35.31 3.16
2259 7259 1.105457 TGCAATGGAGCCATAGTTGC 58.895 50.000 15.79 15.79 37.87 4.17
2260 7260 0.386838 GCAATGGAGCCATAGTTGCC 59.613 55.000 12.93 0.00 33.82 4.52
2261 7261 1.766494 CAATGGAGCCATAGTTGCCA 58.234 50.000 1.81 0.00 35.31 4.92
2262 7262 1.679680 CAATGGAGCCATAGTTGCCAG 59.320 52.381 1.81 0.00 35.31 4.85
2263 7263 1.216064 ATGGAGCCATAGTTGCCAGA 58.784 50.000 0.00 0.00 34.49 3.86
2264 7264 0.991146 TGGAGCCATAGTTGCCAGAA 59.009 50.000 0.00 0.00 0.00 3.02
2265 7265 1.354031 TGGAGCCATAGTTGCCAGAAA 59.646 47.619 0.00 0.00 0.00 2.52
2266 7266 2.025037 TGGAGCCATAGTTGCCAGAAAT 60.025 45.455 0.00 0.00 0.00 2.17
2267 7267 3.026694 GGAGCCATAGTTGCCAGAAATT 58.973 45.455 0.00 0.00 0.00 1.82
2268 7268 3.067320 GGAGCCATAGTTGCCAGAAATTC 59.933 47.826 0.00 0.00 0.00 2.17
2269 7269 2.684881 AGCCATAGTTGCCAGAAATTCG 59.315 45.455 0.00 0.00 0.00 3.34
2270 7270 2.223572 GCCATAGTTGCCAGAAATTCGG 60.224 50.000 0.64 0.64 0.00 4.30
2271 7271 2.358898 CCATAGTTGCCAGAAATTCGGG 59.641 50.000 7.82 7.82 34.70 5.14
2272 7272 2.871096 TAGTTGCCAGAAATTCGGGT 57.129 45.000 13.39 0.00 34.05 5.28
2273 7273 1.534729 AGTTGCCAGAAATTCGGGTC 58.465 50.000 13.39 6.80 34.05 4.46
2274 7274 0.168128 GTTGCCAGAAATTCGGGTCG 59.832 55.000 13.39 0.00 34.05 4.79
2275 7275 0.035598 TTGCCAGAAATTCGGGTCGA 59.964 50.000 13.39 3.76 34.05 4.20
2276 7276 0.251916 TGCCAGAAATTCGGGTCGAT 59.748 50.000 13.39 0.00 35.23 3.59
2277 7277 0.938008 GCCAGAAATTCGGGTCGATC 59.062 55.000 13.39 0.00 35.23 3.69
2278 7278 1.209128 CCAGAAATTCGGGTCGATCG 58.791 55.000 9.36 9.36 35.23 3.69
2279 7279 1.209128 CAGAAATTCGGGTCGATCGG 58.791 55.000 16.41 4.17 35.23 4.18
2280 7280 0.104304 AGAAATTCGGGTCGATCGGG 59.896 55.000 16.41 2.71 35.23 5.14
2281 7281 0.179092 GAAATTCGGGTCGATCGGGT 60.179 55.000 16.41 0.00 35.23 5.28
2282 7282 0.179092 AAATTCGGGTCGATCGGGTC 60.179 55.000 16.41 6.31 35.23 4.46
2291 7291 2.412112 GATCGGGTCGAGGAACGG 59.588 66.667 0.00 0.00 39.91 4.44
2292 7292 3.135056 GATCGGGTCGAGGAACGGG 62.135 68.421 0.00 0.00 39.91 5.28
2295 7295 3.767806 GGGTCGAGGAACGGGGTC 61.768 72.222 0.00 0.00 42.82 4.46
2296 7296 4.125695 GGTCGAGGAACGGGGTCG 62.126 72.222 0.00 0.00 42.82 4.79
2297 7297 4.790861 GTCGAGGAACGGGGTCGC 62.791 72.222 0.00 0.00 42.82 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 7.036220 CCTCTATGATGTACAATATTCCGTCC 58.964 42.308 0.00 0.00 0.00 4.79
314 315 8.557029 CACTTTTCTAAACAAACGGATAGAAGT 58.443 33.333 0.00 0.00 36.18 3.01
413 437 3.189495 TGTTTGTCGTCAGCAAAAACTGA 59.811 39.130 0.00 0.00 44.32 3.41
414 438 3.300590 GTGTTTGTCGTCAGCAAAAACTG 59.699 43.478 0.00 0.00 39.61 3.16
415 439 3.057876 TGTGTTTGTCGTCAGCAAAAACT 60.058 39.130 10.99 0.00 41.89 2.66
416 440 3.238441 TGTGTTTGTCGTCAGCAAAAAC 58.762 40.909 4.63 4.63 41.79 2.43
417 441 3.560902 TGTGTTTGTCGTCAGCAAAAA 57.439 38.095 0.00 0.00 37.54 1.94
418 442 3.127721 TGATGTGTTTGTCGTCAGCAAAA 59.872 39.130 0.00 0.00 37.54 2.44
419 443 2.680339 TGATGTGTTTGTCGTCAGCAAA 59.320 40.909 0.00 0.00 33.96 3.68
420 444 2.284190 TGATGTGTTTGTCGTCAGCAA 58.716 42.857 0.00 0.00 0.00 3.91
421 445 1.946745 TGATGTGTTTGTCGTCAGCA 58.053 45.000 0.00 0.00 0.00 4.41
422 446 3.332761 TTTGATGTGTTTGTCGTCAGC 57.667 42.857 0.00 0.00 33.32 4.26
423 447 7.802720 TGAATATTTTGATGTGTTTGTCGTCAG 59.197 33.333 0.00 0.00 33.32 3.51
424 448 7.643579 TGAATATTTTGATGTGTTTGTCGTCA 58.356 30.769 0.00 0.00 0.00 4.35
425 449 8.500837 TTGAATATTTTGATGTGTTTGTCGTC 57.499 30.769 0.00 0.00 0.00 4.20
426 450 8.864069 TTTGAATATTTTGATGTGTTTGTCGT 57.136 26.923 0.00 0.00 0.00 4.34
427 451 9.566624 GTTTTGAATATTTTGATGTGTTTGTCG 57.433 29.630 0.00 0.00 0.00 4.35
428 452 9.862585 GGTTTTGAATATTTTGATGTGTTTGTC 57.137 29.630 0.00 0.00 0.00 3.18
429 453 9.388506 TGGTTTTGAATATTTTGATGTGTTTGT 57.611 25.926 0.00 0.00 0.00 2.83
432 456 9.001542 CCATGGTTTTGAATATTTTGATGTGTT 57.998 29.630 2.57 0.00 0.00 3.32
433 457 8.156165 ACCATGGTTTTGAATATTTTGATGTGT 58.844 29.630 13.00 0.00 0.00 3.72
434 458 8.550710 ACCATGGTTTTGAATATTTTGATGTG 57.449 30.769 13.00 0.00 0.00 3.21
435 459 9.571816 AAACCATGGTTTTGAATATTTTGATGT 57.428 25.926 32.77 8.70 44.84 3.06
464 488 1.404986 CGGAGAATGCCGTGGTTTCTA 60.405 52.381 0.00 0.00 46.07 2.10
576 600 0.387622 TGTGCGGTGTACTAGTTCGC 60.388 55.000 18.78 18.78 45.60 4.70
613 637 1.001745 GGCAATCACCAAAACGTCGC 61.002 55.000 0.00 0.00 0.00 5.19
764 5714 1.348036 CCTTCTCTTCCAACCGGTCTT 59.652 52.381 8.04 0.00 0.00 3.01
849 5799 3.803778 GTGCAACTTTTGGTCCAAAGATG 59.196 43.478 16.47 16.26 34.72 2.90
1386 6344 3.316071 TTCGGGATGCGTACAAGTTTA 57.684 42.857 0.00 0.00 0.00 2.01
1399 6357 1.027357 ACGCACGTACTATTCGGGAT 58.973 50.000 0.00 0.00 33.17 3.85
1425 6383 9.578439 CCAACTAGTACTATAACAACTACCAAC 57.422 37.037 2.33 0.00 0.00 3.77
1576 6543 7.428826 TGTGTAAACATATGCACACATTTTGA 58.571 30.769 23.93 9.36 44.59 2.69
1628 6624 9.712305 GCACACCATCTACAATATTCTTACTAT 57.288 33.333 0.00 0.00 0.00 2.12
1630 6626 7.564793 TGCACACCATCTACAATATTCTTACT 58.435 34.615 0.00 0.00 0.00 2.24
1641 6637 5.621197 GTGTTAAATGCACACCATCTACA 57.379 39.130 0.00 0.00 38.95 2.74
1659 6658 4.832266 TCCTAAATCAACTGCATTGGTGTT 59.168 37.500 8.40 0.00 38.98 3.32
1663 6662 5.813672 CCATTTCCTAAATCAACTGCATTGG 59.186 40.000 8.40 0.00 38.98 3.16
1709 6708 2.654912 GCAACTTACGCGTCGCTGT 61.655 57.895 18.63 16.43 0.00 4.40
1816 6816 7.064016 GGATCGGATAAGATTTTAGTGATGAGC 59.936 40.741 0.00 0.00 0.00 4.26
1839 6839 3.321950 AGGAGATTGGGATTCGAAGGAT 58.678 45.455 3.35 0.00 0.00 3.24
1846 6846 2.580962 GGCAGAAGGAGATTGGGATTC 58.419 52.381 0.00 0.00 0.00 2.52
1864 6864 0.449388 CTTCTTGTTCCTGCATCGGC 59.551 55.000 0.00 0.00 41.68 5.54
1865 6865 0.449388 GCTTCTTGTTCCTGCATCGG 59.551 55.000 0.00 0.00 0.00 4.18
1866 6866 0.449388 GGCTTCTTGTTCCTGCATCG 59.551 55.000 0.00 0.00 0.00 3.84
1867 6867 1.742268 GAGGCTTCTTGTTCCTGCATC 59.258 52.381 0.00 0.00 0.00 3.91
1868 6868 1.615384 GGAGGCTTCTTGTTCCTGCAT 60.615 52.381 0.00 0.00 38.10 3.96
1869 6869 0.250901 GGAGGCTTCTTGTTCCTGCA 60.251 55.000 0.00 0.00 38.10 4.41
1870 6870 0.250901 TGGAGGCTTCTTGTTCCTGC 60.251 55.000 0.00 0.00 38.60 4.85
1871 6871 1.528129 GTGGAGGCTTCTTGTTCCTG 58.472 55.000 0.00 0.00 0.00 3.86
1872 6872 0.402121 GGTGGAGGCTTCTTGTTCCT 59.598 55.000 0.00 0.00 0.00 3.36
1873 6873 0.955919 CGGTGGAGGCTTCTTGTTCC 60.956 60.000 0.00 0.00 0.00 3.62
1874 6874 0.955919 CCGGTGGAGGCTTCTTGTTC 60.956 60.000 0.00 0.00 0.00 3.18
1875 6875 1.073199 CCGGTGGAGGCTTCTTGTT 59.927 57.895 0.00 0.00 0.00 2.83
1876 6876 2.750350 CCGGTGGAGGCTTCTTGT 59.250 61.111 0.00 0.00 0.00 3.16
1896 6896 4.640855 CGGTCACGACAGGCACGT 62.641 66.667 0.00 0.00 44.60 4.49
1915 6915 3.716006 CTGCAACGGTGGCTGTCG 61.716 66.667 9.26 0.00 0.00 4.35
1916 6916 3.357079 CCTGCAACGGTGGCTGTC 61.357 66.667 9.26 0.00 0.00 3.51
1917 6917 3.832237 CTCCTGCAACGGTGGCTGT 62.832 63.158 9.26 0.00 0.00 4.40
1918 6918 3.052082 CTCCTGCAACGGTGGCTG 61.052 66.667 9.26 8.25 0.00 4.85
1921 6921 4.641645 TGGCTCCTGCAACGGTGG 62.642 66.667 0.90 0.00 41.91 4.61
1922 6922 3.052082 CTGGCTCCTGCAACGGTG 61.052 66.667 0.00 0.00 41.91 4.94
1926 6926 1.941999 GATTGGCTGGCTCCTGCAAC 61.942 60.000 17.54 4.15 41.69 4.17
1927 6927 1.679977 GATTGGCTGGCTCCTGCAA 60.680 57.895 17.54 5.52 41.69 4.08
1928 6928 2.044650 GATTGGCTGGCTCCTGCA 60.045 61.111 17.54 0.96 41.69 4.41
1929 6929 3.207669 CGATTGGCTGGCTCCTGC 61.208 66.667 9.01 9.01 39.65 4.85
1930 6930 3.207669 GCGATTGGCTGGCTCCTG 61.208 66.667 2.00 0.00 39.11 3.86
1939 6939 1.588139 GATTGCAGCAGCGATTGGC 60.588 57.895 5.17 0.00 44.95 4.52
1940 6940 1.298116 CGATTGCAGCAGCGATTGG 60.298 57.895 12.87 0.72 44.95 3.16
1941 6941 1.937846 GCGATTGCAGCAGCGATTG 60.938 57.895 20.11 13.10 44.95 2.67
1942 6942 2.044832 GAGCGATTGCAGCAGCGATT 62.045 55.000 20.11 9.49 44.95 3.34
1944 6944 3.190849 GAGCGATTGCAGCAGCGA 61.191 61.111 20.11 0.00 46.23 4.93
1945 6945 4.233635 GGAGCGATTGCAGCAGCG 62.234 66.667 7.90 13.62 46.23 5.18
1946 6946 3.129502 TGGAGCGATTGCAGCAGC 61.130 61.111 7.90 0.00 46.23 5.25
1947 6947 1.303799 AAGTGGAGCGATTGCAGCAG 61.304 55.000 7.90 0.00 46.23 4.24
1948 6948 1.302752 AAGTGGAGCGATTGCAGCA 60.303 52.632 7.90 0.00 46.23 4.41
1949 6949 1.136147 CAAGTGGAGCGATTGCAGC 59.864 57.895 7.90 0.00 46.23 5.25
1950 6950 1.136147 GCAAGTGGAGCGATTGCAG 59.864 57.895 7.90 0.00 46.64 4.41
1951 6951 3.266964 GCAAGTGGAGCGATTGCA 58.733 55.556 7.90 0.00 46.64 4.08
1953 6953 2.712057 AAAAGCAAGTGGAGCGATTG 57.288 45.000 0.00 0.00 37.01 2.67
1972 6972 6.183360 TGCTTGCGTCTAGAAGAAAAGAAAAA 60.183 34.615 18.88 5.06 0.00 1.94
1973 6973 5.295787 TGCTTGCGTCTAGAAGAAAAGAAAA 59.704 36.000 18.88 6.74 0.00 2.29
1974 6974 4.814234 TGCTTGCGTCTAGAAGAAAAGAAA 59.186 37.500 18.88 8.44 0.00 2.52
1975 6975 4.211374 GTGCTTGCGTCTAGAAGAAAAGAA 59.789 41.667 18.88 10.33 0.00 2.52
1976 6976 3.741344 GTGCTTGCGTCTAGAAGAAAAGA 59.259 43.478 18.88 0.98 0.00 2.52
1977 6977 3.494626 TGTGCTTGCGTCTAGAAGAAAAG 59.505 43.478 10.08 12.22 0.00 2.27
1978 6978 3.462982 TGTGCTTGCGTCTAGAAGAAAA 58.537 40.909 10.08 2.40 0.00 2.29
1979 6979 3.106242 TGTGCTTGCGTCTAGAAGAAA 57.894 42.857 10.08 4.29 0.00 2.52
1980 6980 2.800544 GTTGTGCTTGCGTCTAGAAGAA 59.199 45.455 10.08 0.00 0.00 2.52
1981 6981 2.404215 GTTGTGCTTGCGTCTAGAAGA 58.596 47.619 10.08 0.00 0.00 2.87
1982 6982 1.125021 CGTTGTGCTTGCGTCTAGAAG 59.875 52.381 0.74 0.74 0.00 2.85
1983 6983 1.136690 CGTTGTGCTTGCGTCTAGAA 58.863 50.000 0.00 0.00 0.00 2.10
1984 6984 0.666274 CCGTTGTGCTTGCGTCTAGA 60.666 55.000 0.00 0.00 0.00 2.43
1985 6985 1.781555 CCGTTGTGCTTGCGTCTAG 59.218 57.895 0.00 0.00 0.00 2.43
1986 6986 2.314647 GCCGTTGTGCTTGCGTCTA 61.315 57.895 0.00 0.00 0.00 2.59
1987 6987 3.649986 GCCGTTGTGCTTGCGTCT 61.650 61.111 0.00 0.00 0.00 4.18
1996 6996 3.475774 GGTCGTAGCGCCGTTGTG 61.476 66.667 2.29 0.00 0.00 3.33
1997 6997 4.729856 GGGTCGTAGCGCCGTTGT 62.730 66.667 2.29 0.00 0.00 3.32
1998 6998 4.728102 TGGGTCGTAGCGCCGTTG 62.728 66.667 2.29 0.00 0.00 4.10
1999 6999 4.729856 GTGGGTCGTAGCGCCGTT 62.730 66.667 2.29 0.00 0.00 4.44
2001 7001 4.728102 TTGTGGGTCGTAGCGCCG 62.728 66.667 2.29 0.45 0.00 6.46
2002 7002 2.125269 ATTGTGGGTCGTAGCGCC 60.125 61.111 2.29 0.00 0.00 6.53
2003 7003 1.146358 GAGATTGTGGGTCGTAGCGC 61.146 60.000 0.00 0.00 0.00 5.92
2004 7004 0.866061 CGAGATTGTGGGTCGTAGCG 60.866 60.000 0.00 0.00 0.00 4.26
2005 7005 1.146358 GCGAGATTGTGGGTCGTAGC 61.146 60.000 0.00 0.00 36.09 3.58
2006 7006 0.527817 GGCGAGATTGTGGGTCGTAG 60.528 60.000 0.00 0.00 36.09 3.51
2007 7007 1.514087 GGCGAGATTGTGGGTCGTA 59.486 57.895 0.00 0.00 36.09 3.43
2008 7008 2.264794 GGCGAGATTGTGGGTCGT 59.735 61.111 0.00 0.00 36.09 4.34
2009 7009 2.885644 CGGCGAGATTGTGGGTCG 60.886 66.667 0.00 0.00 36.77 4.79
2010 7010 3.195698 GCGGCGAGATTGTGGGTC 61.196 66.667 12.98 0.00 0.00 4.46
2011 7011 3.706373 AGCGGCGAGATTGTGGGT 61.706 61.111 12.98 0.00 0.00 4.51
2012 7012 3.197790 CAGCGGCGAGATTGTGGG 61.198 66.667 12.98 0.00 0.00 4.61
2013 7013 2.125552 TCAGCGGCGAGATTGTGG 60.126 61.111 12.98 0.00 0.00 4.17
2014 7014 2.456119 GGTCAGCGGCGAGATTGTG 61.456 63.158 12.98 0.00 0.00 3.33
2015 7015 2.125512 GGTCAGCGGCGAGATTGT 60.126 61.111 12.98 0.00 0.00 2.71
2016 7016 2.125552 TGGTCAGCGGCGAGATTG 60.126 61.111 12.98 2.64 0.00 2.67
2017 7017 2.185350 CTGGTCAGCGGCGAGATT 59.815 61.111 12.98 0.00 0.00 2.40
2018 7018 3.842923 CCTGGTCAGCGGCGAGAT 61.843 66.667 12.98 0.00 0.00 2.75
2042 7042 2.574212 CGGCAAGAATCGCGTTGC 60.574 61.111 20.21 20.21 46.88 4.17
2043 7043 2.574212 GCGGCAAGAATCGCGTTG 60.574 61.111 5.77 4.15 42.48 4.10
2068 7068 4.099170 CTTGCCGCAGTGCAGCTC 62.099 66.667 23.11 5.52 43.21 4.09
2110 7110 4.824166 CAATGCAGCGCCGACAGC 62.824 66.667 2.29 1.03 38.52 4.40
2111 7111 4.170062 CCAATGCAGCGCCGACAG 62.170 66.667 2.29 0.00 0.00 3.51
2112 7112 4.695993 TCCAATGCAGCGCCGACA 62.696 61.111 2.29 0.00 0.00 4.35
2113 7113 3.869272 CTCCAATGCAGCGCCGAC 61.869 66.667 2.29 0.00 0.00 4.79
2114 7114 3.899981 AACTCCAATGCAGCGCCGA 62.900 57.895 2.29 0.00 0.00 5.54
2115 7115 3.386867 GAACTCCAATGCAGCGCCG 62.387 63.158 2.29 0.00 0.00 6.46
2116 7116 2.042831 AGAACTCCAATGCAGCGCC 61.043 57.895 2.29 0.00 0.00 6.53
2117 7117 1.136147 CAGAACTCCAATGCAGCGC 59.864 57.895 0.00 0.00 0.00 5.92
2118 7118 1.136147 GCAGAACTCCAATGCAGCG 59.864 57.895 0.00 0.00 39.75 5.18
2119 7119 1.509923 GGCAGAACTCCAATGCAGC 59.490 57.895 0.00 0.00 41.78 5.25
2120 7120 1.651240 CCGGCAGAACTCCAATGCAG 61.651 60.000 0.00 0.00 41.78 4.41
2121 7121 1.675310 CCGGCAGAACTCCAATGCA 60.675 57.895 0.00 0.00 41.78 3.96
2122 7122 2.409870 CCCGGCAGAACTCCAATGC 61.410 63.158 0.00 0.00 39.25 3.56
2123 7123 1.750399 CCCCGGCAGAACTCCAATG 60.750 63.158 0.00 0.00 0.00 2.82
2124 7124 2.677228 CCCCGGCAGAACTCCAAT 59.323 61.111 0.00 0.00 0.00 3.16
2125 7125 4.344865 GCCCCGGCAGAACTCCAA 62.345 66.667 0.00 0.00 41.49 3.53
2127 7127 4.785453 CAGCCCCGGCAGAACTCC 62.785 72.222 8.74 0.00 44.88 3.85
2131 7131 4.365111 ATTGCAGCCCCGGCAGAA 62.365 61.111 8.74 0.00 43.05 3.02
2137 7137 4.431131 AGGTCCATTGCAGCCCCG 62.431 66.667 0.00 0.00 0.00 5.73
2138 7138 2.440980 GAGGTCCATTGCAGCCCC 60.441 66.667 0.00 0.00 0.00 5.80
2139 7139 2.825836 CGAGGTCCATTGCAGCCC 60.826 66.667 0.00 0.00 0.00 5.19
2140 7140 2.825836 CCGAGGTCCATTGCAGCC 60.826 66.667 0.00 0.00 0.00 4.85
2141 7141 3.512516 GCCGAGGTCCATTGCAGC 61.513 66.667 0.00 0.00 0.00 5.25
2142 7142 2.825836 GGCCGAGGTCCATTGCAG 60.826 66.667 0.00 0.00 0.00 4.41
2143 7143 4.776322 CGGCCGAGGTCCATTGCA 62.776 66.667 24.07 0.00 0.00 4.08
2145 7145 3.740128 CTCCGGCCGAGGTCCATTG 62.740 68.421 30.73 6.27 34.67 2.82
2146 7146 3.470888 CTCCGGCCGAGGTCCATT 61.471 66.667 30.73 0.00 34.67 3.16
2147 7147 4.779733 ACTCCGGCCGAGGTCCAT 62.780 66.667 30.73 0.85 43.57 3.41
2149 7149 4.452733 CAACTCCGGCCGAGGTCC 62.453 72.222 30.73 0.00 43.57 4.46
2152 7152 3.976701 ATTGCAACTCCGGCCGAGG 62.977 63.158 30.73 20.88 43.57 4.63
2153 7153 2.436646 ATTGCAACTCCGGCCGAG 60.437 61.111 30.73 23.54 44.95 4.63
2154 7154 2.745884 CATTGCAACTCCGGCCGA 60.746 61.111 30.73 12.25 0.00 5.54
2155 7155 3.814268 CCATTGCAACTCCGGCCG 61.814 66.667 21.04 21.04 0.00 6.13
2156 7156 2.361104 TCCATTGCAACTCCGGCC 60.361 61.111 0.00 0.00 0.00 6.13
2157 7157 3.056313 GCTCCATTGCAACTCCGGC 62.056 63.158 0.00 0.00 0.00 6.13
2158 7158 0.962356 AAGCTCCATTGCAACTCCGG 60.962 55.000 0.00 0.00 34.99 5.14
2159 7159 0.449388 GAAGCTCCATTGCAACTCCG 59.551 55.000 0.00 0.00 34.99 4.63
2160 7160 0.449388 CGAAGCTCCATTGCAACTCC 59.551 55.000 0.00 0.00 34.99 3.85
2161 7161 3.984292 CGAAGCTCCATTGCAACTC 57.016 52.632 0.00 0.00 34.99 3.01
2180 7180 4.778415 CAGTGTCGACGGCTCCGG 62.778 72.222 11.62 0.00 44.69 5.14
2181 7181 4.039357 ACAGTGTCGACGGCTCCG 62.039 66.667 11.62 6.79 46.03 4.63
2182 7182 2.430921 CACAGTGTCGACGGCTCC 60.431 66.667 11.62 0.00 0.00 4.70
2183 7183 1.299926 AACACAGTGTCGACGGCTC 60.300 57.895 11.62 0.00 0.00 4.70
2184 7184 1.591594 CAACACAGTGTCGACGGCT 60.592 57.895 11.62 8.84 0.00 5.52
2185 7185 2.594962 CCAACACAGTGTCGACGGC 61.595 63.158 11.62 6.45 0.00 5.68
2186 7186 1.066752 TCCAACACAGTGTCGACGG 59.933 57.895 11.62 5.91 0.00 4.79
2187 7187 1.213094 GGTCCAACACAGTGTCGACG 61.213 60.000 20.03 0.00 33.10 5.12
2188 7188 0.104304 AGGTCCAACACAGTGTCGAC 59.896 55.000 19.17 19.17 32.15 4.20
2189 7189 0.387929 GAGGTCCAACACAGTGTCGA 59.612 55.000 6.67 2.90 0.00 4.20
2190 7190 0.389391 AGAGGTCCAACACAGTGTCG 59.611 55.000 6.67 0.00 0.00 4.35
2191 7191 1.871080 CAGAGGTCCAACACAGTGTC 58.129 55.000 6.67 0.00 0.00 3.67
2192 7192 0.179045 GCAGAGGTCCAACACAGTGT 60.179 55.000 0.00 0.00 0.00 3.55
2193 7193 0.886490 GGCAGAGGTCCAACACAGTG 60.886 60.000 0.00 0.00 0.00 3.66
2194 7194 1.344953 TGGCAGAGGTCCAACACAGT 61.345 55.000 0.00 0.00 0.00 3.55
2195 7195 0.604780 CTGGCAGAGGTCCAACACAG 60.605 60.000 9.42 0.00 32.41 3.66
2196 7196 1.451504 CTGGCAGAGGTCCAACACA 59.548 57.895 9.42 0.00 32.41 3.72
2197 7197 1.302832 CCTGGCAGAGGTCCAACAC 60.303 63.158 17.94 0.00 37.02 3.32
2198 7198 2.528818 CCCTGGCAGAGGTCCAACA 61.529 63.158 17.94 0.00 40.87 3.33
2199 7199 2.352805 CCCTGGCAGAGGTCCAAC 59.647 66.667 17.94 0.00 40.87 3.77
2200 7200 3.650950 GCCCTGGCAGAGGTCCAA 61.651 66.667 17.94 0.00 40.87 3.53
2201 7201 4.664267 AGCCCTGGCAGAGGTCCA 62.664 66.667 17.94 0.00 44.88 4.02
2202 7202 4.106925 CAGCCCTGGCAGAGGTCC 62.107 72.222 17.94 4.01 44.88 4.46
2203 7203 4.792804 GCAGCCCTGGCAGAGGTC 62.793 72.222 17.94 11.28 44.88 3.85
2205 7205 3.657038 ATTGCAGCCCTGGCAGAGG 62.657 63.158 17.94 16.34 43.05 3.69
2206 7206 2.044252 ATTGCAGCCCTGGCAGAG 60.044 61.111 17.94 3.04 43.05 3.35
2207 7207 2.361992 CATTGCAGCCCTGGCAGA 60.362 61.111 17.94 0.00 43.05 4.26
2208 7208 3.458163 CCATTGCAGCCCTGGCAG 61.458 66.667 11.38 7.75 43.05 4.85
2209 7209 3.949885 CTCCATTGCAGCCCTGGCA 62.950 63.158 11.38 0.00 44.88 4.92
2210 7210 3.145551 CTCCATTGCAGCCCTGGC 61.146 66.667 0.00 0.00 42.33 4.85
2211 7211 3.145551 GCTCCATTGCAGCCCTGG 61.146 66.667 4.28 4.28 0.00 4.45
2212 7212 2.044252 AGCTCCATTGCAGCCCTG 60.044 61.111 0.00 0.00 37.63 4.45
2213 7213 2.274760 GAGCTCCATTGCAGCCCT 59.725 61.111 0.87 0.00 37.63 5.19
2214 7214 3.207669 CGAGCTCCATTGCAGCCC 61.208 66.667 8.47 0.00 37.63 5.19
2215 7215 2.124983 TCGAGCTCCATTGCAGCC 60.125 61.111 8.47 0.00 37.63 4.85
2216 7216 2.467826 GGTCGAGCTCCATTGCAGC 61.468 63.158 8.47 0.00 37.12 5.25
2217 7217 2.169789 CGGTCGAGCTCCATTGCAG 61.170 63.158 13.48 0.00 34.99 4.41
2218 7218 2.125552 CGGTCGAGCTCCATTGCA 60.126 61.111 13.48 0.00 34.99 4.08
2219 7219 2.650813 ATCCGGTCGAGCTCCATTGC 62.651 60.000 13.48 0.00 0.00 3.56
2220 7220 0.179073 AATCCGGTCGAGCTCCATTG 60.179 55.000 13.48 0.00 0.00 2.82
2221 7221 0.541863 AAATCCGGTCGAGCTCCATT 59.458 50.000 13.48 5.03 0.00 3.16
2222 7222 0.179073 CAAATCCGGTCGAGCTCCAT 60.179 55.000 13.48 0.00 0.00 3.41
2223 7223 1.218047 CAAATCCGGTCGAGCTCCA 59.782 57.895 13.48 0.00 0.00 3.86
2224 7224 2.174319 GCAAATCCGGTCGAGCTCC 61.174 63.158 13.48 0.00 0.00 4.70
2225 7225 1.019278 TTGCAAATCCGGTCGAGCTC 61.019 55.000 13.48 2.73 0.00 4.09
2226 7226 0.392998 ATTGCAAATCCGGTCGAGCT 60.393 50.000 13.48 0.00 0.00 4.09
2227 7227 0.248215 CATTGCAAATCCGGTCGAGC 60.248 55.000 1.71 4.06 0.00 5.03
2228 7228 0.378257 CCATTGCAAATCCGGTCGAG 59.622 55.000 1.71 0.00 0.00 4.04
2229 7229 0.035915 TCCATTGCAAATCCGGTCGA 60.036 50.000 1.71 0.00 0.00 4.20
2230 7230 0.378257 CTCCATTGCAAATCCGGTCG 59.622 55.000 1.71 0.00 0.00 4.79
2231 7231 0.101219 GCTCCATTGCAAATCCGGTC 59.899 55.000 1.71 0.00 0.00 4.79
2232 7232 1.322538 GGCTCCATTGCAAATCCGGT 61.323 55.000 1.71 0.00 34.04 5.28
2233 7233 1.321805 TGGCTCCATTGCAAATCCGG 61.322 55.000 1.71 0.00 34.04 5.14
2234 7234 0.748450 ATGGCTCCATTGCAAATCCG 59.252 50.000 1.71 0.00 31.82 4.18
2235 7235 2.961062 ACTATGGCTCCATTGCAAATCC 59.039 45.455 1.71 1.02 37.82 3.01
2236 7236 4.365723 CAACTATGGCTCCATTGCAAATC 58.634 43.478 1.71 0.00 37.82 2.17
2237 7237 3.431207 GCAACTATGGCTCCATTGCAAAT 60.431 43.478 16.54 0.00 37.53 2.32
2238 7238 2.094078 GCAACTATGGCTCCATTGCAAA 60.094 45.455 16.54 0.00 37.53 3.68
2239 7239 1.477700 GCAACTATGGCTCCATTGCAA 59.522 47.619 16.54 0.00 37.53 4.08
2240 7240 1.105457 GCAACTATGGCTCCATTGCA 58.895 50.000 16.54 0.00 37.53 4.08
2241 7241 3.953201 GCAACTATGGCTCCATTGC 57.047 52.632 6.73 8.17 37.82 3.56
2250 7250 2.358898 CCCGAATTTCTGGCAACTATGG 59.641 50.000 0.00 0.00 37.61 2.74
2251 7251 3.016736 ACCCGAATTTCTGGCAACTATG 58.983 45.455 6.76 0.00 37.61 2.23
2252 7252 3.279434 GACCCGAATTTCTGGCAACTAT 58.721 45.455 6.76 0.00 37.61 2.12
2253 7253 2.706890 GACCCGAATTTCTGGCAACTA 58.293 47.619 6.76 0.00 37.61 2.24
2254 7254 1.534729 GACCCGAATTTCTGGCAACT 58.465 50.000 6.76 0.00 37.61 3.16
2255 7255 0.168128 CGACCCGAATTTCTGGCAAC 59.832 55.000 6.76 0.00 0.00 4.17
2256 7256 0.035598 TCGACCCGAATTTCTGGCAA 59.964 50.000 6.76 0.00 31.06 4.52
2257 7257 0.251916 ATCGACCCGAATTTCTGGCA 59.748 50.000 6.76 0.00 39.99 4.92
2258 7258 0.938008 GATCGACCCGAATTTCTGGC 59.062 55.000 6.76 0.33 39.99 4.85
2259 7259 1.209128 CGATCGACCCGAATTTCTGG 58.791 55.000 10.26 5.40 39.99 3.86
2260 7260 1.209128 CCGATCGACCCGAATTTCTG 58.791 55.000 18.66 0.00 39.99 3.02
2261 7261 0.104304 CCCGATCGACCCGAATTTCT 59.896 55.000 18.66 0.00 39.99 2.52
2262 7262 0.179092 ACCCGATCGACCCGAATTTC 60.179 55.000 18.66 0.00 39.99 2.17
2263 7263 0.179092 GACCCGATCGACCCGAATTT 60.179 55.000 18.66 0.00 39.99 1.82
2264 7264 1.440476 GACCCGATCGACCCGAATT 59.560 57.895 18.66 0.00 39.99 2.17
2265 7265 3.126528 GACCCGATCGACCCGAAT 58.873 61.111 18.66 0.00 39.99 3.34
2274 7274 2.412112 CCGTTCCTCGACCCGATC 59.588 66.667 0.00 0.00 42.86 3.69
2275 7275 3.145551 CCCGTTCCTCGACCCGAT 61.146 66.667 0.00 0.00 42.86 4.18
2278 7278 3.767806 GACCCCGTTCCTCGACCC 61.768 72.222 0.00 0.00 42.86 4.46
2279 7279 4.125695 CGACCCCGTTCCTCGACC 62.126 72.222 0.00 0.00 42.86 4.79
2280 7280 4.790861 GCGACCCCGTTCCTCGAC 62.791 72.222 0.00 0.00 42.86 4.20


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

AutoCloner maintained by Alex Coulton.