Multiple sequence alignment - TraesCS5B01G309000

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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 TraesCS5B01G309000 chr5B 100.000 3388 0 0 1 3388 491585435 491582048 0.000000e+00 6257.0
1 TraesCS5B01G309000 chr5B 100.000 113 0 0 1828 1940 491583497 491583385 3.430000e-50 209.0
2 TraesCS5B01G309000 chr5B 100.000 113 0 0 1939 2051 491583608 491583496 3.430000e-50 209.0
3 TraesCS5B01G309000 chr5D 90.707 1894 109 36 1 1868 409940911 409939059 0.000000e+00 2460.0
4 TraesCS5B01G309000 chr5D 90.097 414 30 5 1437 1849 79989472 79989875 8.330000e-146 527.0
5 TraesCS5B01G309000 chr5D 84.950 505 52 16 2230 2716 409938711 409938213 1.090000e-134 490.0
6 TraesCS5B01G309000 chr5D 79.159 547 61 26 2813 3323 409938200 409937671 2.520000e-86 329.0
7 TraesCS5B01G309000 chr5D 93.814 97 6 0 2714 2810 395699606 395699702 2.720000e-31 147.0
8 TraesCS5B01G309000 chr5A 87.945 1966 160 31 1 1940 521024014 521022100 0.000000e+00 2246.0
9 TraesCS5B01G309000 chr5A 88.974 780 37 12 1940 2717 521022209 521021477 0.000000e+00 918.0
10 TraesCS5B01G309000 chr5A 90.476 588 37 6 2797 3371 521021480 521020899 0.000000e+00 758.0
11 TraesCS5B01G309000 chr3B 88.835 412 37 4 1439 1849 290616457 290616860 6.530000e-137 497.0
12 TraesCS5B01G309000 chr3B 97.500 40 1 0 1939 1978 828460936 828460975 6.070000e-08 69.4
13 TraesCS5B01G309000 chr7A 88.647 414 38 5 1437 1849 397427662 397427257 2.350000e-136 496.0
14 TraesCS5B01G309000 chr7A 91.940 335 23 3 1534 1867 474142841 474142510 1.840000e-127 466.0
15 TraesCS5B01G309000 chr7A 97.500 40 1 0 1939 1978 474142549 474142510 6.070000e-08 69.4
16 TraesCS5B01G309000 chr4B 93.433 335 18 3 1534 1867 235739075 235739406 8.450000e-136 494.0
17 TraesCS5B01G309000 chr4B 91.566 332 24 3 1534 1864 199055892 199056220 3.990000e-124 455.0
18 TraesCS5B01G309000 chr4B 87.781 401 32 8 1437 1827 397268326 397267933 1.430000e-123 453.0
19 TraesCS5B01G309000 chr4B 93.878 98 6 0 2703 2800 610796091 610796188 7.570000e-32 148.0
20 TraesCS5B01G309000 chr4B 97.297 37 1 0 1939 1975 199056184 199056220 2.820000e-06 63.9
21 TraesCS5B01G309000 chr7B 92.836 335 20 3 1534 1867 604278722 604279053 1.830000e-132 483.0
22 TraesCS5B01G309000 chr7B 89.474 114 8 4 2714 2824 167622235 167622347 1.270000e-29 141.0
23 TraesCS5B01G309000 chr7B 97.500 40 1 0 1939 1978 604279014 604279053 6.070000e-08 69.4
24 TraesCS5B01G309000 chr2A 88.136 177 14 4 1156 1326 739439862 739439687 1.590000e-48 204.0
25 TraesCS5B01G309000 chr2A 95.699 93 4 0 2714 2806 177665201 177665293 2.110000e-32 150.0
26 TraesCS5B01G309000 chr6A 95.699 93 4 0 2714 2806 553003194 553003286 2.110000e-32 150.0
27 TraesCS5B01G309000 chr6A 96.667 90 3 0 2714 2803 563127910 563127999 2.110000e-32 150.0
28 TraesCS5B01G309000 chrUn 91.589 107 7 1 2714 2818 132121232 132121126 2.720000e-31 147.0
29 TraesCS5B01G309000 chr7D 90.741 108 9 1 2696 2802 210052517 210052624 3.520000e-30 143.0
30 TraesCS5B01G309000 chr6D 90.654 107 9 1 2714 2820 271233443 271233548 1.270000e-29 141.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5B01G309000 chr5B 491582048 491585435 3387 True 2225.000000 6257 100.000000 1 3388 3 chr5B.!!$R1 3387
1 TraesCS5B01G309000 chr5D 409937671 409940911 3240 True 1093.000000 2460 84.938667 1 3323 3 chr5D.!!$R1 3322
2 TraesCS5B01G309000 chr5A 521020899 521024014 3115 True 1307.333333 2246 89.131667 1 3371 3 chr5A.!!$R1 3370

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
939 989 0.037882 ACACTGACTGATGCGTCCAG 60.038 55.0 2.83 6.31 37.64 3.86 F
1416 1481 0.045623 TGAAGGGATGGAAGGGCCTA 59.954 55.0 6.41 0.00 37.63 3.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1960 2028 0.112995 TCAGCAAAGGGGATGCAACT 59.887 50.0 0.0 0.0 46.22 3.16 R
3149 3404 0.179000 GATGCTTGACCTCCCGACAT 59.821 55.0 0.0 0.0 0.00 3.06 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
25 26 3.987220 GCATTAAGCATGAACCGTTTTGT 59.013 39.130 0.00 0.00 44.79 2.83
43 44 7.265286 CCGTTTTGTTTATTCGCTTTTAAATGC 59.735 33.333 14.42 14.42 0.00 3.56
49 50 8.821894 TGTTTATTCGCTTTTAAATGCAACTTT 58.178 25.926 21.72 7.64 0.00 2.66
102 103 4.380678 CGTTTTGTCTTAATCTCGTCACGA 59.619 41.667 0.00 0.00 0.00 4.35
116 117 3.001634 TCGTCACGATATCACGGAGTAAC 59.998 47.826 12.50 0.00 41.61 2.50
117 118 3.286576 GTCACGATATCACGGAGTAACG 58.713 50.000 3.12 0.00 41.61 3.18
121 122 3.247173 ACGATATCACGGAGTAACGTCTC 59.753 47.826 3.12 0.00 46.75 3.36
125 126 3.549299 TCACGGAGTAACGTCTCTTTC 57.451 47.619 4.47 0.00 46.75 2.62
134 135 7.008992 CGGAGTAACGTCTCTTTCGAAAATTAT 59.991 37.037 12.41 0.00 35.11 1.28
154 155 8.433421 AATTATAGTTACATGTGTTTCGAGGG 57.567 34.615 9.11 0.00 0.00 4.30
177 178 3.437049 GGCTTATTCAGACGAAGCACTTT 59.563 43.478 14.67 0.00 45.97 2.66
223 224 6.787170 ACCATATATGATGGACTCTGCAATT 58.213 36.000 14.54 0.00 41.64 2.32
242 243 5.514204 GCAATTACAGCATCATCACTTGTTC 59.486 40.000 0.00 0.00 0.00 3.18
369 372 3.733443 ATGGTCCAAGAAAACACAAGC 57.267 42.857 0.00 0.00 0.00 4.01
370 373 2.451490 TGGTCCAAGAAAACACAAGCA 58.549 42.857 0.00 0.00 0.00 3.91
405 408 2.825836 CTGGGCTGGATCAACGGC 60.826 66.667 0.00 0.00 42.02 5.68
419 422 3.220110 TCAACGGCCGATATACTTCTCT 58.780 45.455 35.90 0.00 0.00 3.10
424 427 2.164624 GGCCGATATACTTCTCTGCGAT 59.835 50.000 0.00 0.00 0.00 4.58
472 475 0.322546 AGAACAACCCGATCCTTGGC 60.323 55.000 0.00 0.00 0.00 4.52
495 498 1.645034 AAGATGACGATTGCAGACCG 58.355 50.000 0.00 3.47 0.00 4.79
528 536 0.681733 TGCCAAGTGAGAGAGACCAC 59.318 55.000 0.00 0.00 0.00 4.16
530 538 1.248486 CCAAGTGAGAGAGACCACGA 58.752 55.000 0.00 0.00 38.26 4.35
564 572 2.095461 TCTGGATCCTTGTCACTCTCG 58.905 52.381 14.23 0.00 0.00 4.04
609 617 9.485591 GGAAATATATGTCTGTGTAACGTTTTG 57.514 33.333 5.91 0.00 42.39 2.44
662 670 8.040132 AGTTGATTCTGACAGAAGATAGAAAGG 58.960 37.037 21.78 0.00 37.69 3.11
750 758 9.460019 TGTGACAAAAATGATAATATCCACTCA 57.540 29.630 0.00 0.00 0.00 3.41
813 824 8.807581 GTTGCAAACTAGAATGGCAATAATAAC 58.192 33.333 15.01 2.74 45.32 1.89
814 825 8.060931 TGCAAACTAGAATGGCAATAATAACA 57.939 30.769 0.00 0.00 0.00 2.41
838 861 5.661056 TCTCGGAGTACATCTCATTTTGT 57.339 39.130 4.69 0.00 44.40 2.83
858 881 5.078411 TGTTTGTAAGGCAGCTTGAAAAA 57.922 34.783 0.00 0.00 0.00 1.94
861 884 7.268586 TGTTTGTAAGGCAGCTTGAAAAATAA 58.731 30.769 0.00 0.00 0.00 1.40
862 885 7.223777 TGTTTGTAAGGCAGCTTGAAAAATAAC 59.776 33.333 0.00 0.00 0.00 1.89
863 886 5.778862 TGTAAGGCAGCTTGAAAAATAACC 58.221 37.500 0.00 0.00 0.00 2.85
864 887 4.953940 AAGGCAGCTTGAAAAATAACCA 57.046 36.364 0.00 0.00 0.00 3.67
908 940 2.818130 TTTGTGGTACAGGTACGGTC 57.182 50.000 3.70 0.00 41.80 4.79
936 986 2.947852 AGTTACACTGACTGATGCGTC 58.052 47.619 0.00 0.00 34.52 5.19
937 987 1.993370 GTTACACTGACTGATGCGTCC 59.007 52.381 2.83 0.00 32.97 4.79
938 988 1.253100 TACACTGACTGATGCGTCCA 58.747 50.000 2.83 0.00 32.97 4.02
939 989 0.037882 ACACTGACTGATGCGTCCAG 60.038 55.000 2.83 6.31 37.64 3.86
940 990 0.037882 CACTGACTGATGCGTCCAGT 60.038 55.000 9.69 9.69 46.51 4.00
941 991 0.681733 ACTGACTGATGCGTCCAGTT 59.318 50.000 9.69 0.00 44.14 3.16
942 992 1.073964 CTGACTGATGCGTCCAGTTG 58.926 55.000 2.83 1.93 44.14 3.16
943 993 0.392706 TGACTGATGCGTCCAGTTGT 59.607 50.000 2.83 0.00 44.14 3.32
944 994 1.616374 TGACTGATGCGTCCAGTTGTA 59.384 47.619 2.83 0.00 44.14 2.41
945 995 1.993370 GACTGATGCGTCCAGTTGTAC 59.007 52.381 2.83 0.00 44.14 2.90
983 1033 1.065600 GTGAACGCCAAGCAAAGCA 59.934 52.632 0.00 0.00 0.00 3.91
1253 1318 1.156736 GAGTGGTACGCACATGCTTT 58.843 50.000 14.39 0.00 44.14 3.51
1256 1321 1.535462 GTGGTACGCACATGCTTTCTT 59.465 47.619 1.82 0.00 39.55 2.52
1343 1408 1.004745 GAGTGAGGAGGGGAATTGCAA 59.995 52.381 0.00 0.00 0.00 4.08
1416 1481 0.045623 TGAAGGGATGGAAGGGCCTA 59.954 55.000 6.41 0.00 37.63 3.93
1419 1484 0.476611 AGGGATGGAAGGGCCTATCC 60.477 60.000 21.15 21.15 40.63 2.59
1449 1514 6.146021 GGATGGTAAGTGCAAACTTTTTGATG 59.854 38.462 2.80 0.00 0.00 3.07
1587 1654 1.243902 GATTTGGTTCGCTTCACCCA 58.756 50.000 0.00 0.00 32.71 4.51
1596 1663 2.789213 TCGCTTCACCCAATGATTTCA 58.211 42.857 0.00 0.00 37.11 2.69
1609 1676 4.536364 ATGATTTCATCGCCGTAAACTG 57.464 40.909 0.00 0.00 28.78 3.16
1615 1682 1.665679 CATCGCCGTAAACTGAGCATT 59.334 47.619 0.00 0.00 0.00 3.56
1630 1697 3.318839 TGAGCATTTGTGTTTCTTCAGGG 59.681 43.478 0.00 0.00 0.00 4.45
1876 1944 1.635487 TCCCCTTTGCTGATTGCTACT 59.365 47.619 0.00 0.00 43.37 2.57
1905 1973 8.256356 AGTTGCTTGATAGTATCATCTACCTT 57.744 34.615 13.58 0.45 39.39 3.50
1909 1977 7.290014 TGCTTGATAGTATCATCTACCTTTCCA 59.710 37.037 13.58 0.00 39.39 3.53
1911 1979 9.703892 CTTGATAGTATCATCTACCTTTCCAAG 57.296 37.037 13.58 0.18 39.39 3.61
1912 1980 8.783660 TGATAGTATCATCTACCTTTCCAAGT 57.216 34.615 8.84 0.00 33.59 3.16
1916 1984 8.567285 AGTATCATCTACCTTTCCAAGTTTTG 57.433 34.615 0.00 0.00 0.00 2.44
1917 1985 8.164070 AGTATCATCTACCTTTCCAAGTTTTGT 58.836 33.333 0.00 0.00 0.00 2.83
1918 1986 9.444600 GTATCATCTACCTTTCCAAGTTTTGTA 57.555 33.333 0.00 0.00 0.00 2.41
1919 1987 7.739498 TCATCTACCTTTCCAAGTTTTGTAC 57.261 36.000 0.00 0.00 0.00 2.90
1920 1988 7.514721 TCATCTACCTTTCCAAGTTTTGTACT 58.485 34.615 0.00 0.00 39.32 2.73
1922 1990 9.280174 CATCTACCTTTCCAAGTTTTGTACTTA 57.720 33.333 0.00 0.00 45.29 2.24
1923 1991 8.897872 TCTACCTTTCCAAGTTTTGTACTTAG 57.102 34.615 0.00 0.00 45.29 2.18
1924 1992 6.387041 ACCTTTCCAAGTTTTGTACTTAGC 57.613 37.500 0.00 0.00 45.29 3.09
1925 1993 6.127101 ACCTTTCCAAGTTTTGTACTTAGCT 58.873 36.000 0.00 0.00 45.29 3.32
1926 1994 6.039382 ACCTTTCCAAGTTTTGTACTTAGCTG 59.961 38.462 0.00 0.00 45.29 4.24
1927 1995 6.039382 CCTTTCCAAGTTTTGTACTTAGCTGT 59.961 38.462 0.00 0.00 45.29 4.40
1928 1996 6.613755 TTCCAAGTTTTGTACTTAGCTGTC 57.386 37.500 0.00 0.00 45.29 3.51
1929 1997 5.925509 TCCAAGTTTTGTACTTAGCTGTCT 58.074 37.500 0.00 0.00 45.29 3.41
1930 1998 6.354130 TCCAAGTTTTGTACTTAGCTGTCTT 58.646 36.000 0.00 0.00 45.29 3.01
1931 1999 6.482308 TCCAAGTTTTGTACTTAGCTGTCTTC 59.518 38.462 0.00 0.00 45.29 2.87
1932 2000 6.260050 CCAAGTTTTGTACTTAGCTGTCTTCA 59.740 38.462 0.00 0.00 45.29 3.02
1933 2001 6.846325 AGTTTTGTACTTAGCTGTCTTCAC 57.154 37.500 0.00 0.00 31.29 3.18
1934 2002 6.583562 AGTTTTGTACTTAGCTGTCTTCACT 58.416 36.000 0.00 0.00 31.29 3.41
1935 2003 7.048512 AGTTTTGTACTTAGCTGTCTTCACTT 58.951 34.615 0.00 0.00 31.29 3.16
1936 2004 6.844696 TTTGTACTTAGCTGTCTTCACTTG 57.155 37.500 0.00 0.00 0.00 3.16
1937 2005 5.531122 TGTACTTAGCTGTCTTCACTTGT 57.469 39.130 0.00 0.00 0.00 3.16
1938 2006 5.529791 TGTACTTAGCTGTCTTCACTTGTC 58.470 41.667 0.00 0.00 0.00 3.18
1939 2007 4.672587 ACTTAGCTGTCTTCACTTGTCA 57.327 40.909 0.00 0.00 0.00 3.58
1940 2008 5.220710 ACTTAGCTGTCTTCACTTGTCAT 57.779 39.130 0.00 0.00 0.00 3.06
1941 2009 6.346477 ACTTAGCTGTCTTCACTTGTCATA 57.654 37.500 0.00 0.00 0.00 2.15
1942 2010 6.940739 ACTTAGCTGTCTTCACTTGTCATAT 58.059 36.000 0.00 0.00 0.00 1.78
1943 2011 7.390027 ACTTAGCTGTCTTCACTTGTCATATT 58.610 34.615 0.00 0.00 0.00 1.28
1944 2012 8.531982 ACTTAGCTGTCTTCACTTGTCATATTA 58.468 33.333 0.00 0.00 0.00 0.98
1945 2013 9.371136 CTTAGCTGTCTTCACTTGTCATATTAA 57.629 33.333 0.00 0.00 0.00 1.40
1946 2014 7.602517 AGCTGTCTTCACTTGTCATATTAAC 57.397 36.000 0.00 0.00 0.00 2.01
1947 2015 6.595716 AGCTGTCTTCACTTGTCATATTAACC 59.404 38.462 0.00 0.00 0.00 2.85
1948 2016 6.595716 GCTGTCTTCACTTGTCATATTAACCT 59.404 38.462 0.00 0.00 0.00 3.50
1949 2017 7.413438 GCTGTCTTCACTTGTCATATTAACCTG 60.413 40.741 0.00 0.00 0.00 4.00
1950 2018 7.676004 TGTCTTCACTTGTCATATTAACCTGA 58.324 34.615 0.00 0.00 0.00 3.86
1951 2019 8.154203 TGTCTTCACTTGTCATATTAACCTGAA 58.846 33.333 0.00 0.00 0.00 3.02
1952 2020 8.660373 GTCTTCACTTGTCATATTAACCTGAAG 58.340 37.037 0.00 0.00 35.47 3.02
1953 2021 7.824289 TCTTCACTTGTCATATTAACCTGAAGG 59.176 37.037 0.00 0.00 42.17 3.46
1954 2022 5.880332 TCACTTGTCATATTAACCTGAAGGC 59.120 40.000 0.00 0.00 39.32 4.35
1955 2023 5.647658 CACTTGTCATATTAACCTGAAGGCA 59.352 40.000 0.00 0.00 39.32 4.75
1956 2024 6.150976 CACTTGTCATATTAACCTGAAGGCAA 59.849 38.462 0.00 0.00 39.32 4.52
1957 2025 6.719370 ACTTGTCATATTAACCTGAAGGCAAA 59.281 34.615 0.00 0.00 39.32 3.68
1958 2026 6.757897 TGTCATATTAACCTGAAGGCAAAG 57.242 37.500 0.00 0.00 39.32 2.77
1959 2027 5.125417 TGTCATATTAACCTGAAGGCAAAGC 59.875 40.000 0.00 0.00 39.32 3.51
1960 2028 5.125417 GTCATATTAACCTGAAGGCAAAGCA 59.875 40.000 0.00 0.00 39.32 3.91
1961 2029 5.357878 TCATATTAACCTGAAGGCAAAGCAG 59.642 40.000 0.00 0.00 39.32 4.24
1962 2030 2.656947 TAACCTGAAGGCAAAGCAGT 57.343 45.000 0.00 0.00 39.32 4.40
1963 2031 1.780503 AACCTGAAGGCAAAGCAGTT 58.219 45.000 0.00 0.00 39.32 3.16
1964 2032 1.035139 ACCTGAAGGCAAAGCAGTTG 58.965 50.000 0.00 0.00 40.50 3.16
1972 2040 2.662309 CAAAGCAGTTGCATCCCCT 58.338 52.632 6.90 0.00 45.16 4.79
1973 2041 0.971386 CAAAGCAGTTGCATCCCCTT 59.029 50.000 6.90 0.00 45.16 3.95
1974 2042 1.345415 CAAAGCAGTTGCATCCCCTTT 59.655 47.619 6.90 0.00 45.16 3.11
1975 2043 0.971386 AAGCAGTTGCATCCCCTTTG 59.029 50.000 6.90 0.00 45.16 2.77
1976 2044 1.079612 GCAGTTGCATCCCCTTTGC 60.080 57.895 0.00 0.00 41.59 3.68
1977 2045 1.538687 GCAGTTGCATCCCCTTTGCT 61.539 55.000 0.00 0.00 40.77 3.91
1978 2046 0.245539 CAGTTGCATCCCCTTTGCTG 59.754 55.000 0.00 0.00 40.77 4.41
1979 2047 0.112995 AGTTGCATCCCCTTTGCTGA 59.887 50.000 0.00 0.00 40.77 4.26
1980 2048 1.188863 GTTGCATCCCCTTTGCTGAT 58.811 50.000 0.00 0.00 40.77 2.90
1981 2049 1.551883 GTTGCATCCCCTTTGCTGATT 59.448 47.619 0.00 0.00 40.77 2.57
1982 2050 1.187974 TGCATCCCCTTTGCTGATTG 58.812 50.000 0.00 0.00 40.77 2.67
1983 2051 0.179092 GCATCCCCTTTGCTGATTGC 60.179 55.000 0.00 0.00 43.25 3.56
1984 2052 1.481871 CATCCCCTTTGCTGATTGCT 58.518 50.000 0.00 0.00 43.37 3.91
1985 2053 2.658285 CATCCCCTTTGCTGATTGCTA 58.342 47.619 0.00 0.00 43.37 3.49
1986 2054 2.128771 TCCCCTTTGCTGATTGCTAC 57.871 50.000 0.00 0.00 43.37 3.58
1987 2055 1.635487 TCCCCTTTGCTGATTGCTACT 59.365 47.619 0.00 0.00 43.37 2.57
1988 2056 2.843730 TCCCCTTTGCTGATTGCTACTA 59.156 45.455 0.00 0.00 43.37 1.82
1989 2057 2.945668 CCCCTTTGCTGATTGCTACTAC 59.054 50.000 0.00 0.00 43.37 2.73
1990 2058 3.370953 CCCCTTTGCTGATTGCTACTACT 60.371 47.826 0.00 0.00 43.37 2.57
1991 2059 4.141711 CCCCTTTGCTGATTGCTACTACTA 60.142 45.833 0.00 0.00 43.37 1.82
1992 2060 5.053145 CCCTTTGCTGATTGCTACTACTAG 58.947 45.833 0.00 0.00 43.37 2.57
1993 2061 5.395768 CCCTTTGCTGATTGCTACTACTAGT 60.396 44.000 0.00 0.00 43.37 2.57
1994 2062 6.109359 CCTTTGCTGATTGCTACTACTAGTT 58.891 40.000 0.00 0.00 43.37 2.24
1995 2063 6.036517 CCTTTGCTGATTGCTACTACTAGTTG 59.963 42.308 0.00 0.59 43.37 3.16
1996 2064 4.433615 TGCTGATTGCTACTACTAGTTGC 58.566 43.478 13.80 13.80 45.06 4.17
1997 2065 4.160439 TGCTGATTGCTACTACTAGTTGCT 59.840 41.667 19.25 4.66 45.07 3.91
1998 2066 5.112686 GCTGATTGCTACTACTAGTTGCTT 58.887 41.667 19.25 9.96 45.07 3.91
1999 2067 5.006165 GCTGATTGCTACTACTAGTTGCTTG 59.994 44.000 19.25 9.04 45.07 4.01
2000 2068 6.280855 TGATTGCTACTACTAGTTGCTTGA 57.719 37.500 19.25 9.16 45.07 3.02
2001 2069 6.878317 TGATTGCTACTACTAGTTGCTTGAT 58.122 36.000 19.25 12.38 45.07 2.57
2002 2070 8.007405 TGATTGCTACTACTAGTTGCTTGATA 57.993 34.615 19.25 1.24 45.07 2.15
2003 2071 8.138074 TGATTGCTACTACTAGTTGCTTGATAG 58.862 37.037 19.25 0.00 45.07 2.08
2004 2072 7.406031 TTGCTACTACTAGTTGCTTGATAGT 57.594 36.000 19.25 0.00 45.07 2.12
2005 2073 8.515695 TTGCTACTACTAGTTGCTTGATAGTA 57.484 34.615 19.25 0.00 45.07 1.82
2006 2074 8.693120 TGCTACTACTAGTTGCTTGATAGTAT 57.307 34.615 19.25 0.00 45.07 2.12
2007 2075 8.784994 TGCTACTACTAGTTGCTTGATAGTATC 58.215 37.037 19.25 2.97 45.07 2.24
2008 2076 8.784994 GCTACTACTAGTTGCTTGATAGTATCA 58.215 37.037 8.84 8.84 42.32 2.15
2011 2079 9.581289 ACTACTAGTTGCTTGATAGTATCATCT 57.419 33.333 13.58 9.55 39.39 2.90
2014 2082 8.798402 ACTAGTTGCTTGATAGTATCATCTACC 58.202 37.037 13.58 3.23 39.39 3.18
2015 2083 7.847711 AGTTGCTTGATAGTATCATCTACCT 57.152 36.000 13.58 5.28 39.39 3.08
2016 2084 8.256356 AGTTGCTTGATAGTATCATCTACCTT 57.744 34.615 13.58 0.45 39.39 3.50
2017 2085 8.709308 AGTTGCTTGATAGTATCATCTACCTTT 58.291 33.333 13.58 0.00 39.39 3.11
2018 2086 8.983724 GTTGCTTGATAGTATCATCTACCTTTC 58.016 37.037 13.58 0.00 39.39 2.62
2019 2087 7.671302 TGCTTGATAGTATCATCTACCTTTCC 58.329 38.462 13.58 0.00 39.39 3.13
2020 2088 7.290014 TGCTTGATAGTATCATCTACCTTTCCA 59.710 37.037 13.58 0.00 39.39 3.53
2021 2089 8.150945 GCTTGATAGTATCATCTACCTTTCCAA 58.849 37.037 13.58 0.00 39.39 3.53
2022 2090 9.703892 CTTGATAGTATCATCTACCTTTCCAAG 57.296 37.037 13.58 0.18 39.39 3.61
2023 2091 8.783660 TGATAGTATCATCTACCTTTCCAAGT 57.216 34.615 8.84 0.00 33.59 3.16
2024 2092 9.213777 TGATAGTATCATCTACCTTTCCAAGTT 57.786 33.333 8.84 0.00 33.59 2.66
2027 2095 8.567285 AGTATCATCTACCTTTCCAAGTTTTG 57.433 34.615 0.00 0.00 0.00 2.44
2028 2096 8.164070 AGTATCATCTACCTTTCCAAGTTTTGT 58.836 33.333 0.00 0.00 0.00 2.83
2029 2097 9.444600 GTATCATCTACCTTTCCAAGTTTTGTA 57.555 33.333 0.00 0.00 0.00 2.41
2030 2098 7.739498 TCATCTACCTTTCCAAGTTTTGTAC 57.261 36.000 0.00 0.00 0.00 2.90
2031 2099 7.514721 TCATCTACCTTTCCAAGTTTTGTACT 58.485 34.615 0.00 0.00 39.32 2.73
2033 2101 9.280174 CATCTACCTTTCCAAGTTTTGTACTTA 57.720 33.333 0.00 0.00 45.29 2.24
2057 2125 3.186909 TGTCTTCACTTGTCAACTGTCG 58.813 45.455 0.00 0.00 0.00 4.35
2068 2136 1.817941 AACTGTCGTTGTGCGCCTT 60.818 52.632 4.18 0.00 41.07 4.35
2070 2138 2.512745 TGTCGTTGTGCGCCTTGT 60.513 55.556 4.18 0.00 41.07 3.16
2090 2158 5.367945 TGTCTACCCTGAATATTTCCACC 57.632 43.478 0.00 0.00 0.00 4.61
2094 2177 4.675063 ACCCTGAATATTTCCACCAACT 57.325 40.909 0.00 0.00 0.00 3.16
2125 2327 1.266989 GCACTTGATAATTAGCGGGCC 59.733 52.381 0.00 0.00 0.00 5.80
2130 2332 1.270094 TGATAATTAGCGGGCCAGACG 60.270 52.381 7.23 0.17 0.00 4.18
2170 2372 5.472820 AGCAGCTATATCCTGAATTCTTTGC 59.527 40.000 7.05 2.51 32.03 3.68
2294 2496 1.234615 TACTTGTGGCGCTTCAAGGC 61.235 55.000 31.23 9.60 43.40 4.35
2469 2673 6.503560 TTCCTTGTTACTAAGAGGTGGAAA 57.496 37.500 0.00 0.00 0.00 3.13
2478 2682 6.248569 ACTAAGAGGTGGAAACTTCTTGAA 57.751 37.500 12.04 0.00 0.00 2.69
2484 2688 4.823989 AGGTGGAAACTTCTTGAATGACAG 59.176 41.667 0.00 0.00 0.00 3.51
2486 2690 5.049129 GGTGGAAACTTCTTGAATGACAGAG 60.049 44.000 0.00 0.00 0.00 3.35
2487 2691 5.529060 GTGGAAACTTCTTGAATGACAGAGT 59.471 40.000 0.00 0.00 0.00 3.24
2535 2739 8.385898 ACCGTTCTTAATTTGTAATTCTGTCA 57.614 30.769 0.00 0.00 0.00 3.58
2548 2752 3.836365 TTCTGTCACACACCTGATTCA 57.164 42.857 0.00 0.00 0.00 2.57
2618 2823 2.755103 CAGAGGGTCACCATAAAAAGGC 59.245 50.000 0.00 0.00 40.13 4.35
2619 2824 2.100197 GAGGGTCACCATAAAAAGGCC 58.900 52.381 0.00 0.00 40.13 5.19
2646 2851 7.852516 ACTGACAGAACGAAAGAAACTTATTC 58.147 34.615 10.08 0.00 0.00 1.75
2654 2859 6.956047 ACGAAAGAAACTTATTCTTGTCCAC 58.044 36.000 4.36 0.00 38.62 4.02
2674 2888 7.552687 TGTCCACCTATAATTCAAATGTCAGTC 59.447 37.037 0.00 0.00 0.00 3.51
2710 2926 6.918022 CACCCTGAAATTTGTGTAAGAAGAAC 59.082 38.462 0.00 0.00 0.00 3.01
2716 2932 9.403583 TGAAATTTGTGTAAGAAGAACCTTACT 57.596 29.630 12.99 0.00 45.28 2.24
2717 2933 9.880064 GAAATTTGTGTAAGAAGAACCTTACTC 57.120 33.333 12.99 10.53 45.28 2.59
2718 2934 7.981102 ATTTGTGTAAGAAGAACCTTACTCC 57.019 36.000 12.99 6.35 45.28 3.85
2719 2935 5.479124 TGTGTAAGAAGAACCTTACTCCC 57.521 43.478 12.99 4.54 45.28 4.30
2723 2939 2.458620 AGAAGAACCTTACTCCCTCCG 58.541 52.381 0.00 0.00 0.00 4.63
2725 2941 3.011032 AGAAGAACCTTACTCCCTCCGTA 59.989 47.826 0.00 0.00 0.00 4.02
2726 2942 3.463048 AGAACCTTACTCCCTCCGTAA 57.537 47.619 0.00 0.00 0.00 3.18
2727 2943 3.782992 AGAACCTTACTCCCTCCGTAAA 58.217 45.455 0.00 0.00 0.00 2.01
2728 2944 3.513119 AGAACCTTACTCCCTCCGTAAAC 59.487 47.826 0.00 0.00 0.00 2.01
2729 2945 3.181393 ACCTTACTCCCTCCGTAAACT 57.819 47.619 0.00 0.00 0.00 2.66
2730 2946 4.322057 ACCTTACTCCCTCCGTAAACTA 57.678 45.455 0.00 0.00 0.00 2.24
2731 2947 4.677182 ACCTTACTCCCTCCGTAAACTAA 58.323 43.478 0.00 0.00 0.00 2.24
2732 2948 5.275630 ACCTTACTCCCTCCGTAAACTAAT 58.724 41.667 0.00 0.00 0.00 1.73
2733 2949 6.435164 ACCTTACTCCCTCCGTAAACTAATA 58.565 40.000 0.00 0.00 0.00 0.98
2734 2950 7.071917 ACCTTACTCCCTCCGTAAACTAATAT 58.928 38.462 0.00 0.00 0.00 1.28
2735 2951 8.227507 ACCTTACTCCCTCCGTAAACTAATATA 58.772 37.037 0.00 0.00 0.00 0.86
2736 2952 9.082313 CCTTACTCCCTCCGTAAACTAATATAA 57.918 37.037 0.00 0.00 0.00 0.98
2738 2954 9.866655 TTACTCCCTCCGTAAACTAATATAAGA 57.133 33.333 0.00 0.00 0.00 2.10
2739 2955 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
2740 2956 7.039853 ACTCCCTCCGTAAACTAATATAAGAGC 60.040 40.741 0.00 0.00 0.00 4.09
2741 2957 6.072286 TCCCTCCGTAAACTAATATAAGAGCG 60.072 42.308 0.00 0.00 0.00 5.03
2742 2958 6.294397 CCCTCCGTAAACTAATATAAGAGCGT 60.294 42.308 0.00 0.00 0.00 5.07
2743 2959 7.144000 CCTCCGTAAACTAATATAAGAGCGTT 58.856 38.462 0.00 0.00 0.00 4.84
2744 2960 7.650903 CCTCCGTAAACTAATATAAGAGCGTTT 59.349 37.037 0.00 0.00 0.00 3.60
2745 2961 9.669353 CTCCGTAAACTAATATAAGAGCGTTTA 57.331 33.333 0.00 0.00 0.00 2.01
2746 2962 9.669353 TCCGTAAACTAATATAAGAGCGTTTAG 57.331 33.333 0.00 0.00 30.36 1.85
2747 2963 9.669353 CCGTAAACTAATATAAGAGCGTTTAGA 57.331 33.333 0.00 0.00 30.36 2.10
2762 2978 6.642683 GCGTTTAGAATGCTAAAGTACTGA 57.357 37.500 6.11 0.00 44.78 3.41
2763 2979 7.235430 GCGTTTAGAATGCTAAAGTACTGAT 57.765 36.000 6.11 0.00 44.78 2.90
2764 2980 7.685594 GCGTTTAGAATGCTAAAGTACTGATT 58.314 34.615 6.11 0.00 44.78 2.57
2765 2981 8.175716 GCGTTTAGAATGCTAAAGTACTGATTT 58.824 33.333 6.11 0.00 44.78 2.17
2771 2987 8.175716 AGAATGCTAAAGTACTGATTTAAACGC 58.824 33.333 0.00 0.00 0.00 4.84
2772 2988 7.611213 ATGCTAAAGTACTGATTTAAACGCT 57.389 32.000 0.00 0.00 0.00 5.07
2773 2989 7.057149 TGCTAAAGTACTGATTTAAACGCTC 57.943 36.000 0.00 0.00 0.00 5.03
2774 2990 6.872020 TGCTAAAGTACTGATTTAAACGCTCT 59.128 34.615 0.00 0.00 0.00 4.09
2775 2991 7.386848 TGCTAAAGTACTGATTTAAACGCTCTT 59.613 33.333 0.00 0.00 0.00 2.85
2776 2992 8.866956 GCTAAAGTACTGATTTAAACGCTCTTA 58.133 33.333 0.00 0.00 0.00 2.10
2792 3008 9.530633 AAACGCTCTTATATTAGTTTACAGAGG 57.469 33.333 0.00 0.00 31.14 3.69
2793 3009 7.659186 ACGCTCTTATATTAGTTTACAGAGGG 58.341 38.462 8.36 8.36 42.53 4.30
2794 3010 7.504911 ACGCTCTTATATTAGTTTACAGAGGGA 59.495 37.037 14.96 0.00 40.49 4.20
2795 3011 8.024285 CGCTCTTATATTAGTTTACAGAGGGAG 58.976 40.741 4.76 0.00 40.49 4.30
2796 3012 8.862085 GCTCTTATATTAGTTTACAGAGGGAGT 58.138 37.037 0.00 0.00 0.00 3.85
2810 3026 5.477637 ACAGAGGGAGTACTAAACTTCTCAC 59.522 44.000 0.00 0.00 39.07 3.51
2811 3027 5.712917 CAGAGGGAGTACTAAACTTCTCACT 59.287 44.000 0.00 0.00 42.39 3.41
2893 3124 8.465999 CACCTTTGCATACTTTATCCATTGTTA 58.534 33.333 0.00 0.00 0.00 2.41
2911 3143 8.236586 CCATTGTTAAGAGATTGAATCGTTTCA 58.763 33.333 4.80 4.80 40.09 2.69
2926 3158 4.930963 TCGTTTCAATGTGAAATTGCTGT 58.069 34.783 6.69 0.00 46.55 4.40
3016 3249 9.638239 TGCTAATTTAGTAAATTTTGAGCCAAG 57.362 29.630 25.14 16.45 38.38 3.61
3098 3353 0.249405 ATTGCCAAACAACGGTGCAG 60.249 50.000 0.00 0.00 42.27 4.41
3118 3373 1.672356 AGGACAGGTTCATGCACGC 60.672 57.895 0.00 0.00 0.00 5.34
3149 3404 1.236616 CGCTGGTGCCTTGTCAATGA 61.237 55.000 0.00 0.00 35.36 2.57
3150 3405 1.180029 GCTGGTGCCTTGTCAATGAT 58.820 50.000 0.00 0.00 0.00 2.45
3152 3407 2.165167 CTGGTGCCTTGTCAATGATGT 58.835 47.619 0.00 0.00 0.00 3.06
3153 3408 2.161855 TGGTGCCTTGTCAATGATGTC 58.838 47.619 0.00 0.00 0.00 3.06
3188 3443 6.467677 GCATCTAGCATAGGAATGAAACCTA 58.532 40.000 0.00 0.00 44.79 3.08
3198 3453 3.756963 GGAATGAAACCTACACTTGGGTC 59.243 47.826 0.00 0.00 34.35 4.46
3212 3467 4.754667 GGTCGACGCAGGAACCCC 62.755 72.222 9.92 0.00 0.00 4.95
3217 3472 3.236003 GACGCAGGAACCCCGACTT 62.236 63.158 8.13 0.00 37.58 3.01
3319 3574 6.371548 TGAAAGTGATAATACAGAGCCAACAC 59.628 38.462 0.00 0.00 0.00 3.32
3323 3578 2.969821 AATACAGAGCCAACACCCAA 57.030 45.000 0.00 0.00 0.00 4.12
3349 3604 0.881118 CAGCAAACCTTACGTGCCAT 59.119 50.000 0.00 0.00 39.13 4.40
3378 3633 2.858745 GGAAACCTTACAGAGCCAACA 58.141 47.619 0.00 0.00 0.00 3.33
3379 3634 2.814336 GGAAACCTTACAGAGCCAACAG 59.186 50.000 0.00 0.00 0.00 3.16
3380 3635 3.477530 GAAACCTTACAGAGCCAACAGT 58.522 45.455 0.00 0.00 0.00 3.55
3381 3636 2.550830 ACCTTACAGAGCCAACAGTG 57.449 50.000 0.00 0.00 0.00 3.66
3382 3637 2.047061 ACCTTACAGAGCCAACAGTGA 58.953 47.619 0.00 0.00 0.00 3.41
3383 3638 2.438021 ACCTTACAGAGCCAACAGTGAA 59.562 45.455 0.00 0.00 0.00 3.18
3384 3639 2.808543 CCTTACAGAGCCAACAGTGAAC 59.191 50.000 0.00 0.00 0.00 3.18
3385 3640 3.495100 CCTTACAGAGCCAACAGTGAACT 60.495 47.826 0.00 0.00 0.00 3.01
3386 3641 2.717639 ACAGAGCCAACAGTGAACTT 57.282 45.000 0.00 0.00 0.00 2.66
3387 3642 2.565841 ACAGAGCCAACAGTGAACTTC 58.434 47.619 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 6.071108 AGCTGCTCTTTAGATGAAAGTCACTA 60.071 38.462 0.00 0.00 44.35 2.74
102 103 5.503683 CGAAAGAGACGTTACTCCGTGATAT 60.504 44.000 0.89 0.00 41.98 1.63
125 126 9.961266 TCGAAACACATGTAACTATAATTTTCG 57.039 29.630 0.00 8.19 41.65 3.46
134 135 3.055675 CCCCCTCGAAACACATGTAACTA 60.056 47.826 0.00 0.00 0.00 2.24
154 155 1.666189 GTGCTTCGTCTGAATAAGCCC 59.334 52.381 17.59 7.17 43.93 5.19
223 224 5.173664 CAGAGAACAAGTGATGATGCTGTA 58.826 41.667 0.00 0.00 0.00 2.74
296 299 2.013400 CAGCACAACCTACACACACAA 58.987 47.619 0.00 0.00 0.00 3.33
298 301 1.948104 TCAGCACAACCTACACACAC 58.052 50.000 0.00 0.00 0.00 3.82
369 372 1.451927 TGGCTTTGCGGAGGCTATG 60.452 57.895 12.74 0.00 42.29 2.23
370 373 1.452108 GTGGCTTTGCGGAGGCTAT 60.452 57.895 12.74 0.00 42.29 2.97
400 403 2.288273 GCAGAGAAGTATATCGGCCGTT 60.288 50.000 27.15 20.39 31.48 4.44
405 408 6.771188 AAAAATCGCAGAGAAGTATATCGG 57.229 37.500 0.00 0.00 43.63 4.18
472 475 2.029728 GTCTGCAATCGTCATCTTTCCG 59.970 50.000 0.00 0.00 0.00 4.30
517 525 0.378962 CGGTGATCGTGGTCTCTCTC 59.621 60.000 0.00 0.00 0.00 3.20
518 526 2.483441 CGGTGATCGTGGTCTCTCT 58.517 57.895 0.00 0.00 0.00 3.10
564 572 3.496331 TCCACCAAGGATCAAAGGAAAC 58.504 45.455 0.00 0.00 43.07 2.78
588 596 5.875910 CCCCAAAACGTTACACAGACATATA 59.124 40.000 0.00 0.00 0.00 0.86
589 597 4.698304 CCCCAAAACGTTACACAGACATAT 59.302 41.667 0.00 0.00 0.00 1.78
590 598 4.066490 CCCCAAAACGTTACACAGACATA 58.934 43.478 0.00 0.00 0.00 2.29
609 617 4.439860 AGAGGTTATCCCTATGAATCCCC 58.560 47.826 0.00 0.00 46.51 4.81
662 670 2.338500 CAGCACGTAGGTTTCTTCTCC 58.662 52.381 0.00 0.00 0.00 3.71
714 722 6.831727 TCATTTTTGTCACAAGAAATGCAG 57.168 33.333 21.35 8.86 38.64 4.41
784 795 3.485394 TGCCATTCTAGTTTGCAACTCA 58.515 40.909 0.00 0.00 41.77 3.41
797 808 6.998074 TCCGAGATTGTTATTATTGCCATTCT 59.002 34.615 0.00 0.00 0.00 2.40
799 810 6.772716 ACTCCGAGATTGTTATTATTGCCATT 59.227 34.615 1.33 0.00 0.00 3.16
803 814 7.709269 TGTACTCCGAGATTGTTATTATTGC 57.291 36.000 1.33 0.00 0.00 3.56
804 815 9.698309 AGATGTACTCCGAGATTGTTATTATTG 57.302 33.333 1.33 0.00 0.00 1.90
805 816 9.915629 GAGATGTACTCCGAGATTGTTATTATT 57.084 33.333 1.33 0.00 39.53 1.40
808 819 7.348080 TGAGATGTACTCCGAGATTGTTATT 57.652 36.000 1.33 0.00 44.34 1.40
811 822 5.860941 ATGAGATGTACTCCGAGATTGTT 57.139 39.130 1.33 0.00 44.34 2.83
813 824 6.536582 ACAAAATGAGATGTACTCCGAGATTG 59.463 38.462 1.33 0.00 44.34 2.67
814 825 6.644347 ACAAAATGAGATGTACTCCGAGATT 58.356 36.000 1.33 0.00 44.34 2.40
838 861 6.704050 GGTTATTTTTCAAGCTGCCTTACAAA 59.296 34.615 0.00 0.00 0.00 2.83
888 920 2.433604 TGACCGTACCTGTACCACAAAA 59.566 45.455 2.04 0.00 32.61 2.44
928 978 1.616374 TCTGTACAACTGGACGCATCA 59.384 47.619 0.00 0.00 0.00 3.07
929 979 2.363788 TCTGTACAACTGGACGCATC 57.636 50.000 0.00 0.00 0.00 3.91
930 980 2.688507 CTTCTGTACAACTGGACGCAT 58.311 47.619 0.00 0.00 0.00 4.73
931 981 1.872237 GCTTCTGTACAACTGGACGCA 60.872 52.381 0.00 0.00 0.00 5.24
932 982 0.790814 GCTTCTGTACAACTGGACGC 59.209 55.000 0.00 0.00 0.00 5.19
933 983 2.440539 AGCTTCTGTACAACTGGACG 57.559 50.000 0.00 0.00 0.00 4.79
934 984 4.865365 GTGATAGCTTCTGTACAACTGGAC 59.135 45.833 0.00 0.00 0.00 4.02
935 985 4.380550 CGTGATAGCTTCTGTACAACTGGA 60.381 45.833 0.00 0.00 0.00 3.86
936 986 3.859961 CGTGATAGCTTCTGTACAACTGG 59.140 47.826 0.00 0.00 0.00 4.00
937 987 4.733850 TCGTGATAGCTTCTGTACAACTG 58.266 43.478 0.00 0.00 0.00 3.16
938 988 4.459685 ACTCGTGATAGCTTCTGTACAACT 59.540 41.667 0.00 0.00 0.00 3.16
939 989 4.734917 ACTCGTGATAGCTTCTGTACAAC 58.265 43.478 0.00 0.00 0.00 3.32
940 990 5.183331 AGAACTCGTGATAGCTTCTGTACAA 59.817 40.000 0.00 0.00 0.00 2.41
941 991 4.700692 AGAACTCGTGATAGCTTCTGTACA 59.299 41.667 0.00 0.00 0.00 2.90
942 992 5.031578 CAGAACTCGTGATAGCTTCTGTAC 58.968 45.833 0.00 0.00 34.03 2.90
943 993 4.700692 ACAGAACTCGTGATAGCTTCTGTA 59.299 41.667 14.87 0.00 41.15 2.74
944 994 3.508012 ACAGAACTCGTGATAGCTTCTGT 59.492 43.478 12.12 12.12 39.84 3.41
945 995 3.856521 CACAGAACTCGTGATAGCTTCTG 59.143 47.826 11.16 11.16 38.79 3.02
983 1033 2.800250 CCATGAAGTGGGAAGAGCTTT 58.200 47.619 0.00 0.00 44.79 3.51
1244 1303 2.223876 ACTGTGGCAAAGAAAGCATGTG 60.224 45.455 12.68 0.00 0.00 3.21
1253 1318 0.108585 GGAGTGGACTGTGGCAAAGA 59.891 55.000 12.68 0.00 0.00 2.52
1256 1321 1.555075 GATAGGAGTGGACTGTGGCAA 59.445 52.381 0.00 0.00 0.00 4.52
1343 1408 3.329542 ATCGCCGTCACCCTGCAAT 62.330 57.895 0.00 0.00 0.00 3.56
1404 1469 0.773700 CCCAGGATAGGCCCTTCCAT 60.774 60.000 20.68 6.15 37.37 3.41
1419 1484 0.331278 TTGCACTTACCATCCCCCAG 59.669 55.000 0.00 0.00 0.00 4.45
1449 1514 3.317993 TGGCTTCTTTACCAAAACTCTGC 59.682 43.478 0.00 0.00 31.46 4.26
1587 1654 4.634004 TCAGTTTACGGCGATGAAATCATT 59.366 37.500 16.62 0.00 45.97 2.57
1596 1663 2.024176 AATGCTCAGTTTACGGCGAT 57.976 45.000 16.62 0.00 0.00 4.58
1609 1676 3.569701 TCCCTGAAGAAACACAAATGCTC 59.430 43.478 0.00 0.00 0.00 4.26
1615 1682 1.850345 AGGGTCCCTGAAGAAACACAA 59.150 47.619 10.61 0.00 29.57 3.33
1630 1697 3.010420 GCACACTTCAATAAGGAGGGTC 58.990 50.000 0.00 0.00 37.01 4.46
1905 1973 6.354130 AGACAGCTAAGTACAAAACTTGGAA 58.646 36.000 5.56 0.00 46.68 3.53
1911 1979 6.846325 AGTGAAGACAGCTAAGTACAAAAC 57.154 37.500 0.00 0.00 0.00 2.43
1912 1980 6.821665 ACAAGTGAAGACAGCTAAGTACAAAA 59.178 34.615 0.00 0.00 0.00 2.44
1916 1984 5.529791 TGACAAGTGAAGACAGCTAAGTAC 58.470 41.667 0.00 0.00 0.00 2.73
1917 1985 5.784578 TGACAAGTGAAGACAGCTAAGTA 57.215 39.130 0.00 0.00 0.00 2.24
1918 1986 4.672587 TGACAAGTGAAGACAGCTAAGT 57.327 40.909 0.00 0.00 0.00 2.24
1919 1987 7.840342 AATATGACAAGTGAAGACAGCTAAG 57.160 36.000 0.00 0.00 0.00 2.18
1920 1988 9.151471 GTTAATATGACAAGTGAAGACAGCTAA 57.849 33.333 0.00 0.00 0.00 3.09
1921 1989 7.764443 GGTTAATATGACAAGTGAAGACAGCTA 59.236 37.037 0.00 0.00 0.00 3.32
1922 1990 6.595716 GGTTAATATGACAAGTGAAGACAGCT 59.404 38.462 0.00 0.00 0.00 4.24
1923 1991 6.595716 AGGTTAATATGACAAGTGAAGACAGC 59.404 38.462 0.00 0.00 0.00 4.40
1924 1992 7.819415 TCAGGTTAATATGACAAGTGAAGACAG 59.181 37.037 0.00 0.00 0.00 3.51
1925 1993 7.676004 TCAGGTTAATATGACAAGTGAAGACA 58.324 34.615 0.00 0.00 0.00 3.41
1926 1994 8.547967 TTCAGGTTAATATGACAAGTGAAGAC 57.452 34.615 0.00 0.00 0.00 3.01
1927 1995 7.824289 CCTTCAGGTTAATATGACAAGTGAAGA 59.176 37.037 18.30 0.00 40.42 2.87
1928 1996 7.414540 GCCTTCAGGTTAATATGACAAGTGAAG 60.415 40.741 14.16 14.16 38.61 3.02
1929 1997 6.374333 GCCTTCAGGTTAATATGACAAGTGAA 59.626 38.462 0.00 0.00 37.57 3.18
1930 1998 5.880332 GCCTTCAGGTTAATATGACAAGTGA 59.120 40.000 0.00 0.00 37.57 3.41
1931 1999 5.647658 TGCCTTCAGGTTAATATGACAAGTG 59.352 40.000 0.00 0.00 37.57 3.16
1932 2000 5.815581 TGCCTTCAGGTTAATATGACAAGT 58.184 37.500 0.00 0.00 37.57 3.16
1933 2001 6.757897 TTGCCTTCAGGTTAATATGACAAG 57.242 37.500 0.00 0.00 37.57 3.16
1934 2002 6.350110 GCTTTGCCTTCAGGTTAATATGACAA 60.350 38.462 0.00 0.00 37.57 3.18
1935 2003 5.125417 GCTTTGCCTTCAGGTTAATATGACA 59.875 40.000 0.00 0.00 37.57 3.58
1936 2004 5.125417 TGCTTTGCCTTCAGGTTAATATGAC 59.875 40.000 0.00 0.00 37.57 3.06
1937 2005 5.260424 TGCTTTGCCTTCAGGTTAATATGA 58.740 37.500 0.00 0.00 37.57 2.15
1938 2006 5.126061 ACTGCTTTGCCTTCAGGTTAATATG 59.874 40.000 0.00 0.00 37.57 1.78
1939 2007 5.264395 ACTGCTTTGCCTTCAGGTTAATAT 58.736 37.500 0.00 0.00 37.57 1.28
1940 2008 4.662278 ACTGCTTTGCCTTCAGGTTAATA 58.338 39.130 0.00 0.00 37.57 0.98
1941 2009 3.500343 ACTGCTTTGCCTTCAGGTTAAT 58.500 40.909 0.00 0.00 37.57 1.40
1942 2010 2.944129 ACTGCTTTGCCTTCAGGTTAA 58.056 42.857 0.00 0.00 37.57 2.01
1943 2011 2.622942 CAACTGCTTTGCCTTCAGGTTA 59.377 45.455 0.00 0.00 37.57 2.85
1944 2012 1.410153 CAACTGCTTTGCCTTCAGGTT 59.590 47.619 0.00 0.00 37.57 3.50
1945 2013 1.035139 CAACTGCTTTGCCTTCAGGT 58.965 50.000 0.00 0.00 37.57 4.00
1946 2014 3.879912 CAACTGCTTTGCCTTCAGG 57.120 52.632 0.00 0.00 38.53 3.86
1954 2022 0.971386 AAGGGGATGCAACTGCTTTG 59.029 50.000 2.95 0.00 42.66 2.77
1955 2023 1.345415 CAAAGGGGATGCAACTGCTTT 59.655 47.619 2.95 0.00 42.66 3.51
1956 2024 0.971386 CAAAGGGGATGCAACTGCTT 59.029 50.000 2.95 0.00 42.66 3.91
1957 2025 1.538687 GCAAAGGGGATGCAACTGCT 61.539 55.000 2.95 0.00 43.29 4.24
1958 2026 1.079612 GCAAAGGGGATGCAACTGC 60.080 57.895 0.00 0.00 43.29 4.40
1959 2027 0.245539 CAGCAAAGGGGATGCAACTG 59.754 55.000 0.00 0.00 46.22 3.16
1960 2028 0.112995 TCAGCAAAGGGGATGCAACT 59.887 50.000 0.00 0.00 46.22 3.16
1961 2029 1.188863 ATCAGCAAAGGGGATGCAAC 58.811 50.000 0.00 0.00 46.22 4.17
1962 2030 1.551430 CAATCAGCAAAGGGGATGCAA 59.449 47.619 0.00 0.00 46.22 4.08
1963 2031 1.187974 CAATCAGCAAAGGGGATGCA 58.812 50.000 0.00 0.00 46.22 3.96
1964 2032 0.179092 GCAATCAGCAAAGGGGATGC 60.179 55.000 0.00 0.00 44.79 3.91
1975 2043 4.688021 AGCAACTAGTAGTAGCAATCAGC 58.312 43.478 2.50 1.01 46.19 4.26
1976 2044 6.333416 TCAAGCAACTAGTAGTAGCAATCAG 58.667 40.000 2.50 0.00 0.00 2.90
1977 2045 6.280855 TCAAGCAACTAGTAGTAGCAATCA 57.719 37.500 2.50 0.00 0.00 2.57
1978 2046 8.138712 ACTATCAAGCAACTAGTAGTAGCAATC 58.861 37.037 2.50 0.00 0.00 2.67
1979 2047 8.012957 ACTATCAAGCAACTAGTAGTAGCAAT 57.987 34.615 2.50 0.00 0.00 3.56
1980 2048 7.406031 ACTATCAAGCAACTAGTAGTAGCAA 57.594 36.000 2.50 0.00 0.00 3.91
1981 2049 8.693120 ATACTATCAAGCAACTAGTAGTAGCA 57.307 34.615 2.50 0.00 32.95 3.49
1982 2050 8.784994 TGATACTATCAAGCAACTAGTAGTAGC 58.215 37.037 2.50 1.17 36.11 3.58
1985 2053 9.581289 AGATGATACTATCAAGCAACTAGTAGT 57.419 33.333 2.79 0.00 43.50 2.73
1988 2056 8.798402 GGTAGATGATACTATCAAGCAACTAGT 58.202 37.037 2.79 0.00 43.50 2.57
1989 2057 9.019656 AGGTAGATGATACTATCAAGCAACTAG 57.980 37.037 2.79 0.00 43.50 2.57
1990 2058 8.941995 AGGTAGATGATACTATCAAGCAACTA 57.058 34.615 2.79 1.33 43.50 2.24
1991 2059 7.847711 AGGTAGATGATACTATCAAGCAACT 57.152 36.000 2.79 0.00 43.50 3.16
1992 2060 8.894768 AAAGGTAGATGATACTATCAAGCAAC 57.105 34.615 2.79 0.74 43.50 4.17
1993 2061 8.150945 GGAAAGGTAGATGATACTATCAAGCAA 58.849 37.037 2.79 0.00 43.50 3.91
1994 2062 7.290014 TGGAAAGGTAGATGATACTATCAAGCA 59.710 37.037 2.79 0.00 43.50 3.91
1995 2063 7.671302 TGGAAAGGTAGATGATACTATCAAGC 58.329 38.462 2.79 0.00 43.50 4.01
1996 2064 9.703892 CTTGGAAAGGTAGATGATACTATCAAG 57.296 37.037 2.79 0.00 40.89 3.02
1998 2066 9.213777 AACTTGGAAAGGTAGATGATACTATCA 57.786 33.333 1.10 1.10 46.27 2.15
2015 2083 6.826741 AGACAGCTAAGTACAAAACTTGGAAA 59.173 34.615 5.56 0.00 46.68 3.13
2016 2084 6.354130 AGACAGCTAAGTACAAAACTTGGAA 58.646 36.000 5.56 0.00 46.68 3.53
2017 2085 5.925509 AGACAGCTAAGTACAAAACTTGGA 58.074 37.500 5.56 0.00 46.68 3.53
2021 2089 6.583562 AGTGAAGACAGCTAAGTACAAAACT 58.416 36.000 0.00 0.00 41.49 2.66
2022 2090 6.846325 AGTGAAGACAGCTAAGTACAAAAC 57.154 37.500 0.00 0.00 0.00 2.43
2023 2091 6.821665 ACAAGTGAAGACAGCTAAGTACAAAA 59.178 34.615 0.00 0.00 0.00 2.44
2024 2092 6.346096 ACAAGTGAAGACAGCTAAGTACAAA 58.654 36.000 0.00 0.00 0.00 2.83
2025 2093 5.914033 ACAAGTGAAGACAGCTAAGTACAA 58.086 37.500 0.00 0.00 0.00 2.41
2026 2094 5.068591 TGACAAGTGAAGACAGCTAAGTACA 59.931 40.000 0.00 0.00 0.00 2.90
2027 2095 5.529791 TGACAAGTGAAGACAGCTAAGTAC 58.470 41.667 0.00 0.00 0.00 2.73
2028 2096 5.784578 TGACAAGTGAAGACAGCTAAGTA 57.215 39.130 0.00 0.00 0.00 2.24
2029 2097 4.672587 TGACAAGTGAAGACAGCTAAGT 57.327 40.909 0.00 0.00 0.00 2.24
2030 2098 5.050499 CAGTTGACAAGTGAAGACAGCTAAG 60.050 44.000 16.64 0.00 33.58 2.18
2031 2099 4.811024 CAGTTGACAAGTGAAGACAGCTAA 59.189 41.667 16.64 0.00 33.58 3.09
2032 2100 4.141937 ACAGTTGACAAGTGAAGACAGCTA 60.142 41.667 26.16 0.00 35.76 3.32
2033 2101 3.201290 CAGTTGACAAGTGAAGACAGCT 58.799 45.455 16.64 0.00 33.58 4.24
2057 2125 1.574702 GGGTAGACAAGGCGCACAAC 61.575 60.000 10.83 0.00 0.00 3.32
2068 2136 4.785914 TGGTGGAAATATTCAGGGTAGACA 59.214 41.667 0.00 0.00 0.00 3.41
2070 2138 5.491078 AGTTGGTGGAAATATTCAGGGTAGA 59.509 40.000 0.00 0.00 0.00 2.59
2090 2158 8.969121 TTATCAAGTGCATTGTGATTAAGTTG 57.031 30.769 13.03 0.00 40.05 3.16
2094 2177 9.734620 GCTAATTATCAAGTGCATTGTGATTAA 57.265 29.630 13.03 7.71 40.05 1.40
2125 2327 4.143305 GCTGAAAGTAGTTAGCAACGTCTG 60.143 45.833 0.00 0.00 36.24 3.51
2170 2372 4.536065 TCATTCAGCAAAACTAACAAGCG 58.464 39.130 0.00 0.00 0.00 4.68
2215 2417 5.603170 AAAGGAACATGGGCAGAATAATG 57.397 39.130 0.00 0.00 0.00 1.90
2294 2496 0.659427 TACCGATCACCGTTAGAGCG 59.341 55.000 0.00 0.00 43.78 5.03
2443 2647 6.531021 TCCACCTCTTAGTAACAAGGAAAAG 58.469 40.000 11.81 0.00 32.99 2.27
2534 2738 4.682860 GCATTTTCTTGAATCAGGTGTGTG 59.317 41.667 0.00 0.00 0.00 3.82
2535 2739 4.341806 TGCATTTTCTTGAATCAGGTGTGT 59.658 37.500 0.00 0.00 0.00 3.72
2548 2752 5.492895 TGCATCCATCATTTGCATTTTCTT 58.507 33.333 0.00 0.00 41.18 2.52
2618 2823 5.290386 AGTTTCTTTCGTTCTGTCAGTAGG 58.710 41.667 0.00 0.00 0.00 3.18
2619 2824 6.830114 AAGTTTCTTTCGTTCTGTCAGTAG 57.170 37.500 0.00 0.00 0.00 2.57
2646 2851 8.279970 TGACATTTGAATTATAGGTGGACAAG 57.720 34.615 0.00 0.00 0.00 3.16
2710 2926 5.866159 ATTAGTTTACGGAGGGAGTAAGG 57.134 43.478 0.00 0.00 35.75 2.69
2716 2932 6.072286 CGCTCTTATATTAGTTTACGGAGGGA 60.072 42.308 0.00 0.00 34.63 4.20
2717 2933 6.091437 CGCTCTTATATTAGTTTACGGAGGG 58.909 44.000 0.00 0.00 0.00 4.30
2718 2934 6.675987 ACGCTCTTATATTAGTTTACGGAGG 58.324 40.000 0.00 0.00 0.00 4.30
2719 2935 8.571461 AAACGCTCTTATATTAGTTTACGGAG 57.429 34.615 0.00 0.00 31.14 4.63
2726 2942 9.765795 AGCATTCTAAACGCTCTTATATTAGTT 57.234 29.630 0.00 0.00 0.00 2.24
2731 2947 9.765795 ACTTTAGCATTCTAAACGCTCTTATAT 57.234 29.630 0.00 0.00 39.23 0.86
2733 2949 9.032420 GTACTTTAGCATTCTAAACGCTCTTAT 57.968 33.333 0.00 0.00 39.23 1.73
2734 2950 8.248945 AGTACTTTAGCATTCTAAACGCTCTTA 58.751 33.333 0.00 0.00 39.23 2.10
2735 2951 7.063544 CAGTACTTTAGCATTCTAAACGCTCTT 59.936 37.037 0.00 0.00 39.23 2.85
2736 2952 6.531948 CAGTACTTTAGCATTCTAAACGCTCT 59.468 38.462 0.00 0.00 39.23 4.09
2737 2953 6.530534 TCAGTACTTTAGCATTCTAAACGCTC 59.469 38.462 0.00 0.00 39.23 5.03
2738 2954 6.395629 TCAGTACTTTAGCATTCTAAACGCT 58.604 36.000 0.00 0.00 39.23 5.07
2739 2955 6.642683 TCAGTACTTTAGCATTCTAAACGC 57.357 37.500 0.00 0.00 39.23 4.84
2745 2961 8.175716 GCGTTTAAATCAGTACTTTAGCATTCT 58.824 33.333 0.00 0.00 0.00 2.40
2746 2962 8.175716 AGCGTTTAAATCAGTACTTTAGCATTC 58.824 33.333 0.00 0.00 0.00 2.67
2747 2963 8.040716 AGCGTTTAAATCAGTACTTTAGCATT 57.959 30.769 0.00 0.00 0.00 3.56
2748 2964 7.549488 AGAGCGTTTAAATCAGTACTTTAGCAT 59.451 33.333 0.00 0.00 0.00 3.79
2749 2965 6.872020 AGAGCGTTTAAATCAGTACTTTAGCA 59.128 34.615 0.00 0.00 0.00 3.49
2750 2966 7.292129 AGAGCGTTTAAATCAGTACTTTAGC 57.708 36.000 0.00 0.00 0.00 3.09
2766 2982 9.530633 CCTCTGTAAACTAATATAAGAGCGTTT 57.469 33.333 0.00 0.00 0.00 3.60
2767 2983 8.142551 CCCTCTGTAAACTAATATAAGAGCGTT 58.857 37.037 0.00 0.00 0.00 4.84
2768 2984 7.504911 TCCCTCTGTAAACTAATATAAGAGCGT 59.495 37.037 0.00 0.00 0.00 5.07
2769 2985 7.883217 TCCCTCTGTAAACTAATATAAGAGCG 58.117 38.462 0.00 0.00 0.00 5.03
2770 2986 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
2778 2994 9.544579 AGTTTAGTACTCCCTCTGTAAACTAAT 57.455 33.333 12.31 0.00 38.38 1.73
2779 2995 8.946797 AGTTTAGTACTCCCTCTGTAAACTAA 57.053 34.615 12.31 0.00 38.38 2.24
2780 2996 8.946797 AAGTTTAGTACTCCCTCTGTAAACTA 57.053 34.615 13.69 0.00 38.92 2.24
2781 2997 7.729431 AGAAGTTTAGTACTCCCTCTGTAAACT 59.271 37.037 0.00 4.48 40.64 2.66
2782 2998 7.894708 AGAAGTTTAGTACTCCCTCTGTAAAC 58.105 38.462 0.00 1.96 35.54 2.01
2783 2999 7.727186 TGAGAAGTTTAGTACTCCCTCTGTAAA 59.273 37.037 0.00 0.00 37.37 2.01
2784 3000 7.176340 GTGAGAAGTTTAGTACTCCCTCTGTAA 59.824 40.741 0.00 0.00 37.37 2.41
2785 3001 6.658391 GTGAGAAGTTTAGTACTCCCTCTGTA 59.342 42.308 0.00 0.00 37.37 2.74
2786 3002 5.477637 GTGAGAAGTTTAGTACTCCCTCTGT 59.522 44.000 0.00 0.00 37.37 3.41
2787 3003 5.712917 AGTGAGAAGTTTAGTACTCCCTCTG 59.287 44.000 0.00 0.00 37.37 3.35
2788 3004 5.894653 AGTGAGAAGTTTAGTACTCCCTCT 58.105 41.667 0.00 0.00 37.37 3.69
2789 3005 6.593268 AAGTGAGAAGTTTAGTACTCCCTC 57.407 41.667 0.00 0.00 35.54 4.30
2790 3006 6.997942 AAAGTGAGAAGTTTAGTACTCCCT 57.002 37.500 0.00 0.00 35.54 4.20
2791 3007 7.215085 TCAAAAGTGAGAAGTTTAGTACTCCC 58.785 38.462 0.00 0.00 35.54 4.30
2792 3008 8.658499 TTCAAAAGTGAGAAGTTTAGTACTCC 57.342 34.615 0.00 0.00 33.26 3.85
2794 3010 9.832445 TCATTCAAAAGTGAGAAGTTTAGTACT 57.168 29.630 0.00 0.00 34.98 2.73
2795 3011 9.865484 GTCATTCAAAAGTGAGAAGTTTAGTAC 57.135 33.333 0.00 0.00 34.49 2.73
2796 3012 9.607988 TGTCATTCAAAAGTGAGAAGTTTAGTA 57.392 29.630 0.00 0.00 34.49 1.82
2797 3013 8.506168 TGTCATTCAAAAGTGAGAAGTTTAGT 57.494 30.769 0.00 0.00 34.49 2.24
2798 3014 9.390795 CATGTCATTCAAAAGTGAGAAGTTTAG 57.609 33.333 0.00 0.00 34.49 1.85
2810 3026 3.120616 CACGCTTGCATGTCATTCAAAAG 59.879 43.478 0.00 0.07 0.00 2.27
2811 3027 3.051327 CACGCTTGCATGTCATTCAAAA 58.949 40.909 0.00 0.00 0.00 2.44
2911 3143 4.669206 TGGTTCACAGCAATTTCACATT 57.331 36.364 0.00 0.00 0.00 2.71
2922 3154 1.527433 GGGCCTCTTTGGTTCACAGC 61.527 60.000 0.84 0.00 38.35 4.40
2926 3158 0.850100 TCAAGGGCCTCTTTGGTTCA 59.150 50.000 6.46 0.00 38.35 3.18
3012 3245 5.805728 AGTACCAGGAAGTGTTTATCTTGG 58.194 41.667 0.00 2.76 45.52 3.61
3016 3249 6.465084 AGTCAAGTACCAGGAAGTGTTTATC 58.535 40.000 0.00 0.00 0.00 1.75
3098 3353 1.878775 GTGCATGAACCTGTCCTGC 59.121 57.895 0.00 0.00 45.34 4.85
3118 3373 3.282157 CCAGCGATCATTGCCGGG 61.282 66.667 2.18 0.00 0.00 5.73
3149 3404 0.179000 GATGCTTGACCTCCCGACAT 59.821 55.000 0.00 0.00 0.00 3.06
3150 3405 0.904865 AGATGCTTGACCTCCCGACA 60.905 55.000 0.00 0.00 0.00 4.35
3152 3407 1.403814 CTAGATGCTTGACCTCCCGA 58.596 55.000 0.00 0.00 0.00 5.14
3153 3408 0.249657 GCTAGATGCTTGACCTCCCG 60.250 60.000 0.00 0.00 38.95 5.14
3175 3430 3.397955 ACCCAAGTGTAGGTTTCATTCCT 59.602 43.478 0.00 0.00 38.91 3.36
3188 3443 2.029073 CTGCGTCGACCCAAGTGT 59.971 61.111 10.58 0.00 0.00 3.55
3217 3472 2.443811 CGATGCGCGACACATGTCA 61.444 57.895 12.10 0.00 44.99 3.58
3283 3538 7.823799 TGTATTATCACTTTCAGCAATGACTCA 59.176 33.333 0.00 0.00 0.00 3.41
3319 3574 3.541996 AGGTTTGCTGAAAAACTTGGG 57.458 42.857 0.00 0.00 43.58 4.12
3349 3604 5.533528 GCTCTGTAAGGTTTCCCAGTTTTAA 59.466 40.000 0.00 0.00 0.00 1.52
3364 3619 3.733337 AGTTCACTGTTGGCTCTGTAAG 58.267 45.455 0.00 0.00 0.00 2.34
3365 3620 3.838244 AGTTCACTGTTGGCTCTGTAA 57.162 42.857 0.00 0.00 0.00 2.41
3366 3621 3.728845 GAAGTTCACTGTTGGCTCTGTA 58.271 45.455 0.00 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.