Multiple sequence alignment - TraesCS1D01G381000

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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 TraesCS1D01G381000 chr1D 100.000 1600 0 0 1 1600 456195407 456197006 0.000000e+00 2955.0
1 TraesCS1D01G381000 chr1D 99.077 758 5 2 1 757 365293980 365293224 0.000000e+00 1360.0
2 TraesCS1D01G381000 chr1D 97.092 791 19 4 3 791 182573776 182572988 0.000000e+00 1330.0
3 TraesCS1D01G381000 chr1D 95.041 847 39 2 756 1600 4203635 4202790 0.000000e+00 1328.0
4 TraesCS1D01G381000 chr1D 100.000 550 0 0 1802 2351 456197208 456197757 0.000000e+00 1016.0
5 TraesCS1D01G381000 chr1D 95.652 92 4 0 1817 1908 473644569 473644660 5.230000e-32 148.0
6 TraesCS1D01G381000 chr1D 90.566 106 10 0 1802 1907 20713727 20713622 8.760000e-30 141.0
7 TraesCS1D01G381000 chr1D 84.545 110 13 3 1912 2018 114158407 114158515 3.200000e-19 106.0
8 TraesCS1D01G381000 chr6D 99.078 759 5 2 1 757 67528420 67527662 0.000000e+00 1362.0
9 TraesCS1D01G381000 chr2D 99.078 759 5 2 1 757 368084732 368085490 0.000000e+00 1362.0
10 TraesCS1D01G381000 chr2D 98.947 760 7 1 1 759 131091625 131090866 0.000000e+00 1358.0
11 TraesCS1D01G381000 chr2D 95.159 847 39 1 756 1600 593127294 593128140 0.000000e+00 1336.0
12 TraesCS1D01G381000 chr2D 95.030 845 41 1 756 1600 305960348 305959505 0.000000e+00 1327.0
13 TraesCS1D01G381000 chr2D 84.545 110 13 3 1912 2018 69264002 69263894 3.200000e-19 106.0
14 TraesCS1D01G381000 chr2D 96.970 33 0 1 2304 2336 358119436 358119405 1.000000e-03 54.7
15 TraesCS1D01G381000 chr3D 98.949 761 6 2 1 759 597424163 597423403 0.000000e+00 1360.0
16 TraesCS1D01G381000 chr3D 97.727 88 2 0 1821 1908 553355201 553355114 4.050000e-33 152.0
17 TraesCS1D01G381000 chr5D 98.819 762 7 2 1 761 276445102 276444342 0.000000e+00 1356.0
18 TraesCS1D01G381000 chr5D 97.753 89 2 0 1821 1909 395721001 395721089 1.130000e-33 154.0
19 TraesCS1D01G381000 chr5D 84.545 110 13 3 1912 2018 515688604 515688496 3.200000e-19 106.0
20 TraesCS1D01G381000 chr7D 98.945 758 6 2 1 756 64644204 64644961 0.000000e+00 1354.0
21 TraesCS1D01G381000 chr7D 95.035 846 40 2 756 1600 242795316 242794472 0.000000e+00 1328.0
22 TraesCS1D01G381000 chr7D 94.563 846 45 1 756 1600 41573145 41572300 0.000000e+00 1306.0
23 TraesCS1D01G381000 chr7D 94.563 846 42 2 756 1600 31419574 31420416 0.000000e+00 1304.0
24 TraesCS1D01G381000 chr7D 94.563 846 43 3 756 1600 33633616 33634459 0.000000e+00 1304.0
25 TraesCS1D01G381000 chr7D 94.563 846 43 3 756 1600 262288910 262288067 0.000000e+00 1304.0
26 TraesCS1D01G381000 chr7D 92.982 114 8 0 1802 1915 100666650 100666537 1.450000e-37 167.0
27 TraesCS1D01G381000 chr7D 98.837 86 1 0 1823 1908 177987405 177987320 1.130000e-33 154.0
28 TraesCS1D01G381000 chr7D 98.810 84 1 0 1825 1908 31420418 31420501 1.460000e-32 150.0
29 TraesCS1D01G381000 chr7D 97.674 86 1 1 1824 1908 481003232 481003147 1.880000e-31 147.0
30 TraesCS1D01G381000 chr4D 98.945 758 7 1 1 757 78765522 78764765 0.000000e+00 1354.0
31 TraesCS1D01G381000 chrUn 95.154 846 40 1 756 1600 241759996 241759151 0.000000e+00 1334.0
32 TraesCS1D01G381000 chrUn 83.486 109 14 3 1913 2018 67085277 67085170 5.350000e-17 99.0
33 TraesCS1D01G381000 chrUn 83.486 109 14 3 1913 2018 439250474 439250581 5.350000e-17 99.0
34 TraesCS1D01G381000 chr1B 94.815 135 6 1 2130 2264 626600119 626600252 2.370000e-50 209.0
35 TraesCS1D01G381000 chr4B 95.327 107 5 0 1802 1908 52592691 52592585 1.120000e-38 171.0
36 TraesCS1D01G381000 chr7B 84.545 110 13 3 1912 2018 709509668 709509560 3.200000e-19 106.0
37 TraesCS1D01G381000 chr7B 83.636 110 14 3 1912 2018 532033554 532033662 1.490000e-17 100.0
38 TraesCS1D01G381000 chr2B 84.071 113 13 3 1908 2016 584823468 584823357 1.150000e-18 104.0
39 TraesCS1D01G381000 chr3B 83.636 110 14 3 1912 2018 773728209 773728101 1.490000e-17 100.0


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 TraesCS1D01G381000 chr1D 456195407 456197757 2350 False 1985.5 2955 100.0000 1 2351 2 chr1D.!!$F3 2350
1 TraesCS1D01G381000 chr1D 365293224 365293980 756 True 1360.0 1360 99.0770 1 757 1 chr1D.!!$R4 756
2 TraesCS1D01G381000 chr1D 182572988 182573776 788 True 1330.0 1330 97.0920 3 791 1 chr1D.!!$R3 788
3 TraesCS1D01G381000 chr1D 4202790 4203635 845 True 1328.0 1328 95.0410 756 1600 1 chr1D.!!$R1 844
4 TraesCS1D01G381000 chr6D 67527662 67528420 758 True 1362.0 1362 99.0780 1 757 1 chr6D.!!$R1 756
5 TraesCS1D01G381000 chr2D 368084732 368085490 758 False 1362.0 1362 99.0780 1 757 1 chr2D.!!$F1 756
6 TraesCS1D01G381000 chr2D 131090866 131091625 759 True 1358.0 1358 98.9470 1 759 1 chr2D.!!$R2 758
7 TraesCS1D01G381000 chr2D 593127294 593128140 846 False 1336.0 1336 95.1590 756 1600 1 chr2D.!!$F2 844
8 TraesCS1D01G381000 chr2D 305959505 305960348 843 True 1327.0 1327 95.0300 756 1600 1 chr2D.!!$R3 844
9 TraesCS1D01G381000 chr3D 597423403 597424163 760 True 1360.0 1360 98.9490 1 759 1 chr3D.!!$R2 758
10 TraesCS1D01G381000 chr5D 276444342 276445102 760 True 1356.0 1356 98.8190 1 761 1 chr5D.!!$R1 760
11 TraesCS1D01G381000 chr7D 64644204 64644961 757 False 1354.0 1354 98.9450 1 756 1 chr7D.!!$F2 755
12 TraesCS1D01G381000 chr7D 242794472 242795316 844 True 1328.0 1328 95.0350 756 1600 1 chr7D.!!$R4 844
13 TraesCS1D01G381000 chr7D 41572300 41573145 845 True 1306.0 1306 94.5630 756 1600 1 chr7D.!!$R1 844
14 TraesCS1D01G381000 chr7D 33633616 33634459 843 False 1304.0 1304 94.5630 756 1600 1 chr7D.!!$F1 844
15 TraesCS1D01G381000 chr7D 262288067 262288910 843 True 1304.0 1304 94.5630 756 1600 1 chr7D.!!$R5 844
16 TraesCS1D01G381000 chr7D 31419574 31420501 927 False 727.0 1304 96.6865 756 1908 2 chr7D.!!$F3 1152
17 TraesCS1D01G381000 chr4D 78764765 78765522 757 True 1354.0 1354 98.9450 1 757 1 chr4D.!!$R1 756
18 TraesCS1D01G381000 chrUn 241759151 241759996 845 True 1334.0 1334 95.1540 756 1600 1 chrUn.!!$R2 844

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
984 990 0.865769 CGCGCCAGAACAAGTAGTTT 59.134 50.0 0.0 0.0 41.51 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1971 1980 0.107312 CTCCTGATGAGCACCAAGGG 60.107 60.0 0.0 0.0 33.47 3.95 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
111 113 3.745799 TGTTACTTGCCCGAGATTTGAA 58.254 40.909 0.00 0.00 0.00 2.69
320 323 3.028130 CAACCCAACAAGTACCTTTGGT 58.972 45.455 13.83 0.00 38.53 3.67
432 435 9.311916 GCATAATCTCATAGTCATAGGAACATC 57.688 37.037 0.00 0.00 0.00 3.06
765 771 2.424842 ATTTCCTTCAGGTGGCGGCA 62.425 55.000 7.97 7.97 36.34 5.69
984 990 0.865769 CGCGCCAGAACAAGTAGTTT 59.134 50.000 0.00 0.00 41.51 2.66
1067 1073 2.437359 AGCAGCAGGGACGATTGC 60.437 61.111 0.00 0.00 40.57 3.56
1071 1077 4.778143 GCAGGGACGATTGCCGGT 62.778 66.667 1.90 0.00 43.93 5.28
1091 1097 3.371097 GAGCCGCGACAGGATCCAA 62.371 63.158 15.82 0.00 40.60 3.53
1143 1149 2.833582 ACGATCGGGATCACGGCT 60.834 61.111 18.99 5.16 37.69 5.52
1144 1150 1.512996 GACGATCGGGATCACGGCTA 61.513 60.000 18.99 0.00 37.69 3.93
1161 1167 1.899437 CTATGGGTGGTGCCGTGAGT 61.899 60.000 0.00 0.00 38.44 3.41
1886 1895 7.744678 ATAAGGTATGGTTTACACAGTAGGT 57.255 36.000 0.00 0.00 0.00 3.08
1908 1917 5.736358 GGTCTACAATACGAAGTCTAACACG 59.264 44.000 0.00 0.00 43.93 4.49
1909 1918 5.226772 GTCTACAATACGAAGTCTAACACGC 59.773 44.000 0.00 0.00 43.93 5.34
1910 1919 3.248266 ACAATACGAAGTCTAACACGCC 58.752 45.455 0.00 0.00 43.93 5.68
1911 1920 2.573941 ATACGAAGTCTAACACGCCC 57.426 50.000 0.00 0.00 43.93 6.13
1912 1921 1.538047 TACGAAGTCTAACACGCCCT 58.462 50.000 0.00 0.00 43.93 5.19
1913 1922 0.038526 ACGAAGTCTAACACGCCCTG 60.039 55.000 0.00 0.00 29.74 4.45
1914 1923 1.352156 CGAAGTCTAACACGCCCTGC 61.352 60.000 0.00 0.00 0.00 4.85
1915 1924 0.320421 GAAGTCTAACACGCCCTGCA 60.320 55.000 0.00 0.00 0.00 4.41
1916 1925 0.320771 AAGTCTAACACGCCCTGCAG 60.321 55.000 6.78 6.78 0.00 4.41
1917 1926 2.047274 TCTAACACGCCCTGCAGC 60.047 61.111 8.66 0.00 0.00 5.25
1918 1927 3.127533 CTAACACGCCCTGCAGCC 61.128 66.667 8.66 0.00 0.00 4.85
1943 1952 3.775654 CCGCCTCTGGTCACCCTC 61.776 72.222 0.00 0.00 0.00 4.30
1944 1953 4.135153 CGCCTCTGGTCACCCTCG 62.135 72.222 0.00 0.00 0.00 4.63
1945 1954 3.775654 GCCTCTGGTCACCCTCGG 61.776 72.222 0.00 0.00 0.00 4.63
1946 1955 3.077556 CCTCTGGTCACCCTCGGG 61.078 72.222 0.00 0.00 42.03 5.14
1947 1956 3.775654 CTCTGGTCACCCTCGGGC 61.776 72.222 0.82 0.00 39.32 6.13
1961 1970 3.195698 GGGCCGTCGCATTGTCTC 61.196 66.667 0.00 0.00 36.38 3.36
1962 1971 3.195698 GGCCGTCGCATTGTCTCC 61.196 66.667 0.00 0.00 36.38 3.71
1963 1972 2.125512 GCCGTCGCATTGTCTCCT 60.126 61.111 0.00 0.00 34.03 3.69
1964 1973 2.167861 GCCGTCGCATTGTCTCCTC 61.168 63.158 0.00 0.00 34.03 3.71
1965 1974 1.519455 CCGTCGCATTGTCTCCTCC 60.519 63.158 0.00 0.00 0.00 4.30
1966 1975 1.215382 CGTCGCATTGTCTCCTCCA 59.785 57.895 0.00 0.00 0.00 3.86
1967 1976 1.078759 CGTCGCATTGTCTCCTCCAC 61.079 60.000 0.00 0.00 0.00 4.02
1968 1977 1.078759 GTCGCATTGTCTCCTCCACG 61.079 60.000 0.00 0.00 0.00 4.94
1969 1978 2.456119 CGCATTGTCTCCTCCACGC 61.456 63.158 0.00 0.00 0.00 5.34
1970 1979 2.109126 GCATTGTCTCCTCCACGCC 61.109 63.158 0.00 0.00 0.00 5.68
1971 1980 1.450312 CATTGTCTCCTCCACGCCC 60.450 63.158 0.00 0.00 0.00 6.13
1972 1981 2.670148 ATTGTCTCCTCCACGCCCC 61.670 63.158 0.00 0.00 0.00 5.80
1975 1984 4.332543 TCTCCTCCACGCCCCCTT 62.333 66.667 0.00 0.00 0.00 3.95
1976 1985 4.101448 CTCCTCCACGCCCCCTTG 62.101 72.222 0.00 0.00 0.00 3.61
1984 1993 4.431131 CGCCCCCTTGGTGCTCAT 62.431 66.667 0.00 0.00 37.93 2.90
1985 1994 2.440980 GCCCCCTTGGTGCTCATC 60.441 66.667 0.00 0.00 36.04 2.92
1986 1995 3.089838 CCCCCTTGGTGCTCATCA 58.910 61.111 0.00 0.00 0.00 3.07
1987 1996 1.077212 CCCCCTTGGTGCTCATCAG 60.077 63.158 0.00 0.00 0.00 2.90
1988 1997 1.077212 CCCCTTGGTGCTCATCAGG 60.077 63.158 0.00 0.00 0.00 3.86
1989 1998 1.565390 CCCCTTGGTGCTCATCAGGA 61.565 60.000 0.00 0.00 0.00 3.86
1990 1999 0.107312 CCCTTGGTGCTCATCAGGAG 60.107 60.000 0.00 0.00 46.93 3.69
1991 2000 0.107312 CCTTGGTGCTCATCAGGAGG 60.107 60.000 0.00 0.00 44.22 4.30
1992 2001 0.907486 CTTGGTGCTCATCAGGAGGA 59.093 55.000 0.00 0.00 44.22 3.71
1993 2002 0.907486 TTGGTGCTCATCAGGAGGAG 59.093 55.000 6.60 6.60 45.37 3.69
1998 2007 1.440893 CTCATCAGGAGGAGCACGG 59.559 63.158 0.00 0.00 40.13 4.94
1999 2008 2.202987 CATCAGGAGGAGCACGGC 60.203 66.667 0.00 0.00 0.00 5.68
2000 2009 2.364842 ATCAGGAGGAGCACGGCT 60.365 61.111 0.00 0.00 43.88 5.52
2027 2036 4.379243 CCCTCGCGCACTTCCACT 62.379 66.667 8.75 0.00 0.00 4.00
2028 2037 3.114616 CCTCGCGCACTTCCACTG 61.115 66.667 8.75 0.00 0.00 3.66
2029 2038 3.782244 CTCGCGCACTTCCACTGC 61.782 66.667 8.75 0.00 0.00 4.40
2030 2039 4.299547 TCGCGCACTTCCACTGCT 62.300 61.111 8.75 0.00 32.03 4.24
2031 2040 3.782244 CGCGCACTTCCACTGCTC 61.782 66.667 8.75 0.00 32.03 4.26
2032 2041 2.358003 GCGCACTTCCACTGCTCT 60.358 61.111 0.30 0.00 32.03 4.09
2033 2042 2.386660 GCGCACTTCCACTGCTCTC 61.387 63.158 0.30 0.00 32.03 3.20
2034 2043 1.739562 CGCACTTCCACTGCTCTCC 60.740 63.158 0.00 0.00 32.03 3.71
2035 2044 1.376553 GCACTTCCACTGCTCTCCC 60.377 63.158 0.00 0.00 0.00 4.30
2036 2045 1.298014 CACTTCCACTGCTCTCCCC 59.702 63.158 0.00 0.00 0.00 4.81
2037 2046 1.152030 ACTTCCACTGCTCTCCCCA 60.152 57.895 0.00 0.00 0.00 4.96
2038 2047 0.548682 ACTTCCACTGCTCTCCCCAT 60.549 55.000 0.00 0.00 0.00 4.00
2039 2048 0.179936 CTTCCACTGCTCTCCCCATC 59.820 60.000 0.00 0.00 0.00 3.51
2040 2049 0.547471 TTCCACTGCTCTCCCCATCA 60.547 55.000 0.00 0.00 0.00 3.07
2041 2050 0.547471 TCCACTGCTCTCCCCATCAA 60.547 55.000 0.00 0.00 0.00 2.57
2042 2051 0.107312 CCACTGCTCTCCCCATCAAG 60.107 60.000 0.00 0.00 0.00 3.02
2043 2052 0.107312 CACTGCTCTCCCCATCAAGG 60.107 60.000 0.00 0.00 37.03 3.61
2044 2053 0.548682 ACTGCTCTCCCCATCAAGGT 60.549 55.000 0.00 0.00 34.66 3.50
2045 2054 0.622665 CTGCTCTCCCCATCAAGGTT 59.377 55.000 0.00 0.00 34.66 3.50
2046 2055 1.005215 CTGCTCTCCCCATCAAGGTTT 59.995 52.381 0.00 0.00 34.66 3.27
2047 2056 1.004745 TGCTCTCCCCATCAAGGTTTC 59.995 52.381 0.00 0.00 34.66 2.78
2048 2057 1.683319 GCTCTCCCCATCAAGGTTTCC 60.683 57.143 0.00 0.00 34.66 3.13
2049 2058 0.999712 TCTCCCCATCAAGGTTTCCC 59.000 55.000 0.00 0.00 34.66 3.97
2050 2059 0.033109 CTCCCCATCAAGGTTTCCCC 60.033 60.000 0.00 0.00 34.66 4.81
2052 2061 0.033109 CCCCATCAAGGTTTCCCCTC 60.033 60.000 0.00 0.00 45.47 4.30
2053 2062 0.704076 CCCATCAAGGTTTCCCCTCA 59.296 55.000 0.00 0.00 45.47 3.86
2054 2063 1.616994 CCCATCAAGGTTTCCCCTCAC 60.617 57.143 0.00 0.00 45.47 3.51
2055 2064 1.616994 CCATCAAGGTTTCCCCTCACC 60.617 57.143 0.00 0.00 45.47 4.02
2056 2065 1.075374 CATCAAGGTTTCCCCTCACCA 59.925 52.381 0.00 0.00 45.47 4.17
2057 2066 1.455822 TCAAGGTTTCCCCTCACCAT 58.544 50.000 0.00 0.00 45.47 3.55
2058 2067 1.354368 TCAAGGTTTCCCCTCACCATC 59.646 52.381 0.00 0.00 45.47 3.51
2059 2068 0.328258 AAGGTTTCCCCTCACCATCG 59.672 55.000 0.00 0.00 45.47 3.84
2060 2069 0.546747 AGGTTTCCCCTCACCATCGA 60.547 55.000 0.00 0.00 40.71 3.59
2061 2070 0.546598 GGTTTCCCCTCACCATCGAT 59.453 55.000 0.00 0.00 32.74 3.59
2062 2071 1.668419 GTTTCCCCTCACCATCGATG 58.332 55.000 18.76 18.76 0.00 3.84
2063 2072 1.065418 GTTTCCCCTCACCATCGATGT 60.065 52.381 23.27 9.39 0.00 3.06
2064 2073 0.541392 TTCCCCTCACCATCGATGTG 59.459 55.000 23.27 19.61 0.00 3.21
2065 2074 0.325203 TCCCCTCACCATCGATGTGA 60.325 55.000 23.27 22.16 0.00 3.58
2066 2075 0.761187 CCCCTCACCATCGATGTGAT 59.239 55.000 23.27 6.46 38.01 3.06
2074 2083 3.551796 ATCGATGTGATGGTCGTCG 57.448 52.632 0.00 0.00 43.08 5.12
2075 2084 0.738975 ATCGATGTGATGGTCGTCGT 59.261 50.000 0.00 0.00 42.55 4.34
2076 2085 1.371595 TCGATGTGATGGTCGTCGTA 58.628 50.000 7.27 0.00 42.55 3.43
2077 2086 1.063027 TCGATGTGATGGTCGTCGTAC 59.937 52.381 7.27 0.00 42.55 3.67
2078 2087 1.836383 GATGTGATGGTCGTCGTACC 58.164 55.000 6.85 6.85 40.19 3.34
2092 2101 3.437746 GTACCAAACGGAGCTCCTC 57.562 57.895 29.73 5.50 0.00 3.71
2093 2102 0.108281 GTACCAAACGGAGCTCCTCC 60.108 60.000 29.73 5.73 46.44 4.30
2100 2109 3.453988 GGAGCTCCTCCTGATCCG 58.546 66.667 26.25 0.00 46.41 4.18
2101 2110 2.733945 GAGCTCCTCCTGATCCGC 59.266 66.667 0.87 0.00 0.00 5.54
2102 2111 2.841988 AGCTCCTCCTGATCCGCC 60.842 66.667 0.00 0.00 0.00 6.13
2103 2112 4.292178 GCTCCTCCTGATCCGCCG 62.292 72.222 0.00 0.00 0.00 6.46
2104 2113 2.519541 CTCCTCCTGATCCGCCGA 60.520 66.667 0.00 0.00 0.00 5.54
2105 2114 2.833582 TCCTCCTGATCCGCCGAC 60.834 66.667 0.00 0.00 0.00 4.79
2106 2115 2.835431 CCTCCTGATCCGCCGACT 60.835 66.667 0.00 0.00 0.00 4.18
2107 2116 2.415010 CTCCTGATCCGCCGACTG 59.585 66.667 0.00 0.00 0.00 3.51
2108 2117 3.144120 CTCCTGATCCGCCGACTGG 62.144 68.421 0.00 0.00 38.77 4.00
2118 2127 4.821589 CCGACTGGCGCTCTTCCC 62.822 72.222 7.64 0.00 39.11 3.97
2119 2128 4.821589 CGACTGGCGCTCTTCCCC 62.822 72.222 7.64 0.00 0.00 4.81
2120 2129 3.706373 GACTGGCGCTCTTCCCCA 61.706 66.667 7.64 0.00 0.00 4.96
2121 2130 3.959991 GACTGGCGCTCTTCCCCAC 62.960 68.421 7.64 0.00 0.00 4.61
2122 2131 4.785453 CTGGCGCTCTTCCCCACC 62.785 72.222 7.64 0.00 0.00 4.61
2145 2154 3.436001 CGATGTCGCCCTTTACACT 57.564 52.632 0.00 0.00 0.00 3.55
2146 2155 1.278238 CGATGTCGCCCTTTACACTC 58.722 55.000 0.00 0.00 0.00 3.51
2147 2156 1.135083 CGATGTCGCCCTTTACACTCT 60.135 52.381 0.00 0.00 0.00 3.24
2148 2157 2.541556 GATGTCGCCCTTTACACTCTC 58.458 52.381 0.00 0.00 0.00 3.20
2149 2158 1.629043 TGTCGCCCTTTACACTCTCT 58.371 50.000 0.00 0.00 0.00 3.10
2150 2159 1.544691 TGTCGCCCTTTACACTCTCTC 59.455 52.381 0.00 0.00 0.00 3.20
2151 2160 1.819903 GTCGCCCTTTACACTCTCTCT 59.180 52.381 0.00 0.00 0.00 3.10
2152 2161 2.093106 TCGCCCTTTACACTCTCTCTC 58.907 52.381 0.00 0.00 0.00 3.20
2153 2162 1.135333 CGCCCTTTACACTCTCTCTCC 59.865 57.143 0.00 0.00 0.00 3.71
2154 2163 2.180276 GCCCTTTACACTCTCTCTCCA 58.820 52.381 0.00 0.00 0.00 3.86
2155 2164 2.769095 GCCCTTTACACTCTCTCTCCAT 59.231 50.000 0.00 0.00 0.00 3.41
2156 2165 3.198853 GCCCTTTACACTCTCTCTCCATT 59.801 47.826 0.00 0.00 0.00 3.16
2157 2166 4.406003 GCCCTTTACACTCTCTCTCCATTA 59.594 45.833 0.00 0.00 0.00 1.90
2158 2167 5.071115 GCCCTTTACACTCTCTCTCCATTAT 59.929 44.000 0.00 0.00 0.00 1.28
2159 2168 6.740122 GCCCTTTACACTCTCTCTCCATTATC 60.740 46.154 0.00 0.00 0.00 1.75
2160 2169 6.325028 CCCTTTACACTCTCTCTCCATTATCA 59.675 42.308 0.00 0.00 0.00 2.15
2161 2170 7.206687 CCTTTACACTCTCTCTCCATTATCAC 58.793 42.308 0.00 0.00 0.00 3.06
2162 2171 7.147828 CCTTTACACTCTCTCTCCATTATCACA 60.148 40.741 0.00 0.00 0.00 3.58
2163 2172 7.904558 TTACACTCTCTCTCCATTATCACAT 57.095 36.000 0.00 0.00 0.00 3.21
2164 2173 8.996651 TTACACTCTCTCTCCATTATCACATA 57.003 34.615 0.00 0.00 0.00 2.29
2165 2174 9.593565 TTACACTCTCTCTCCATTATCACATAT 57.406 33.333 0.00 0.00 0.00 1.78
2166 2175 7.894708 ACACTCTCTCTCCATTATCACATATG 58.105 38.462 0.00 0.00 0.00 1.78
2167 2176 7.727634 ACACTCTCTCTCCATTATCACATATGA 59.272 37.037 10.38 0.00 39.83 2.15
2168 2177 8.583296 CACTCTCTCTCCATTATCACATATGAA 58.417 37.037 10.38 0.00 38.69 2.57
2169 2178 8.584157 ACTCTCTCTCCATTATCACATATGAAC 58.416 37.037 10.38 0.00 38.69 3.18
2170 2179 8.482852 TCTCTCTCCATTATCACATATGAACA 57.517 34.615 10.38 0.00 38.69 3.18
2171 2180 8.363390 TCTCTCTCCATTATCACATATGAACAC 58.637 37.037 10.38 0.00 38.69 3.32
2172 2181 7.147976 TCTCTCCATTATCACATATGAACACG 58.852 38.462 10.38 0.00 38.69 4.49
2173 2182 6.816136 TCTCCATTATCACATATGAACACGT 58.184 36.000 10.38 0.00 38.69 4.49
2174 2183 6.923508 TCTCCATTATCACATATGAACACGTC 59.076 38.462 10.38 0.00 38.69 4.34
2175 2184 6.816136 TCCATTATCACATATGAACACGTCT 58.184 36.000 10.38 0.00 38.69 4.18
2176 2185 7.947282 TCCATTATCACATATGAACACGTCTA 58.053 34.615 10.38 0.00 38.69 2.59
2177 2186 8.585018 TCCATTATCACATATGAACACGTCTAT 58.415 33.333 10.38 0.00 38.69 1.98
2178 2187 9.208022 CCATTATCACATATGAACACGTCTATT 57.792 33.333 10.38 0.00 38.69 1.73
2181 2190 6.344572 TCACATATGAACACGTCTATTTGC 57.655 37.500 10.38 0.00 0.00 3.68
2182 2191 6.106003 TCACATATGAACACGTCTATTTGCT 58.894 36.000 10.38 0.00 0.00 3.91
2183 2192 6.035975 TCACATATGAACACGTCTATTTGCTG 59.964 38.462 10.38 0.00 0.00 4.41
2184 2193 5.294306 ACATATGAACACGTCTATTTGCTGG 59.706 40.000 10.38 0.00 0.00 4.85
2185 2194 3.120321 TGAACACGTCTATTTGCTGGT 57.880 42.857 0.00 0.00 0.00 4.00
2186 2195 2.805671 TGAACACGTCTATTTGCTGGTG 59.194 45.455 0.00 0.00 0.00 4.17
2187 2196 2.831685 ACACGTCTATTTGCTGGTGA 57.168 45.000 0.00 0.00 0.00 4.02
2188 2197 2.688507 ACACGTCTATTTGCTGGTGAG 58.311 47.619 0.00 0.00 0.00 3.51
2189 2198 2.299013 ACACGTCTATTTGCTGGTGAGA 59.701 45.455 0.00 0.00 0.00 3.27
2190 2199 3.244078 ACACGTCTATTTGCTGGTGAGAA 60.244 43.478 0.00 0.00 0.00 2.87
2191 2200 3.745975 CACGTCTATTTGCTGGTGAGAAA 59.254 43.478 0.00 0.00 0.00 2.52
2192 2201 3.997021 ACGTCTATTTGCTGGTGAGAAAG 59.003 43.478 0.00 0.00 0.00 2.62
2193 2202 3.372206 CGTCTATTTGCTGGTGAGAAAGG 59.628 47.826 0.00 0.00 0.00 3.11
2194 2203 4.579869 GTCTATTTGCTGGTGAGAAAGGA 58.420 43.478 0.00 0.00 0.00 3.36
2195 2204 4.393371 GTCTATTTGCTGGTGAGAAAGGAC 59.607 45.833 0.00 0.00 0.00 3.85
2196 2205 2.727123 TTTGCTGGTGAGAAAGGACA 57.273 45.000 0.00 0.00 0.00 4.02
2197 2206 1.967319 TTGCTGGTGAGAAAGGACAC 58.033 50.000 0.00 0.00 36.44 3.67
2198 2207 0.836606 TGCTGGTGAGAAAGGACACA 59.163 50.000 0.00 0.00 38.57 3.72
2199 2208 1.230324 GCTGGTGAGAAAGGACACAC 58.770 55.000 0.00 0.00 38.57 3.82
2200 2209 1.202698 GCTGGTGAGAAAGGACACACT 60.203 52.381 0.00 0.00 38.57 3.55
2201 2210 2.487934 CTGGTGAGAAAGGACACACTG 58.512 52.381 0.00 0.00 38.57 3.66
2202 2211 1.140852 TGGTGAGAAAGGACACACTGG 59.859 52.381 0.00 0.00 38.57 4.00
2203 2212 1.543429 GGTGAGAAAGGACACACTGGG 60.543 57.143 0.00 0.00 38.57 4.45
2204 2213 0.108585 TGAGAAAGGACACACTGGGC 59.891 55.000 0.00 0.00 0.00 5.36
2205 2214 0.108585 GAGAAAGGACACACTGGGCA 59.891 55.000 0.00 0.00 0.00 5.36
2206 2215 0.109342 AGAAAGGACACACTGGGCAG 59.891 55.000 0.00 0.00 0.00 4.85
2207 2216 0.179018 GAAAGGACACACTGGGCAGT 60.179 55.000 0.00 0.00 43.61 4.40
2208 2217 1.071699 GAAAGGACACACTGGGCAGTA 59.928 52.381 0.00 0.00 40.20 2.74
2209 2218 0.687354 AAGGACACACTGGGCAGTAG 59.313 55.000 0.00 0.00 40.20 2.57
2210 2219 1.376037 GGACACACTGGGCAGTAGC 60.376 63.158 0.00 0.00 40.20 3.58
2220 2229 3.755628 GCAGTAGCCCGTCGGTGA 61.756 66.667 11.06 0.00 33.58 4.02
2221 2230 2.490217 CAGTAGCCCGTCGGTGAG 59.510 66.667 11.06 0.00 0.00 3.51
2222 2231 2.754658 AGTAGCCCGTCGGTGAGG 60.755 66.667 11.06 0.00 0.00 3.86
2227 2236 3.760035 CCCGTCGGTGAGGGTGAG 61.760 72.222 11.06 0.00 42.67 3.51
2228 2237 2.989824 CCGTCGGTGAGGGTGAGT 60.990 66.667 2.08 0.00 33.46 3.41
2229 2238 1.676635 CCGTCGGTGAGGGTGAGTA 60.677 63.158 2.08 0.00 33.46 2.59
2230 2239 1.654954 CCGTCGGTGAGGGTGAGTAG 61.655 65.000 2.08 0.00 33.46 2.57
2231 2240 0.675837 CGTCGGTGAGGGTGAGTAGA 60.676 60.000 0.00 0.00 0.00 2.59
2232 2241 1.096416 GTCGGTGAGGGTGAGTAGAG 58.904 60.000 0.00 0.00 0.00 2.43
2233 2242 0.697079 TCGGTGAGGGTGAGTAGAGT 59.303 55.000 0.00 0.00 0.00 3.24
2234 2243 1.075050 TCGGTGAGGGTGAGTAGAGTT 59.925 52.381 0.00 0.00 0.00 3.01
2235 2244 1.893801 CGGTGAGGGTGAGTAGAGTTT 59.106 52.381 0.00 0.00 0.00 2.66
2236 2245 2.094649 CGGTGAGGGTGAGTAGAGTTTC 60.095 54.545 0.00 0.00 0.00 2.78
2237 2246 3.166679 GGTGAGGGTGAGTAGAGTTTCT 58.833 50.000 0.00 0.00 0.00 2.52
2238 2247 3.193903 GGTGAGGGTGAGTAGAGTTTCTC 59.806 52.174 0.00 0.00 0.00 2.87
2239 2248 4.083565 GTGAGGGTGAGTAGAGTTTCTCT 58.916 47.826 4.69 4.69 43.83 3.10
2240 2249 4.157105 GTGAGGGTGAGTAGAGTTTCTCTC 59.843 50.000 2.41 0.00 40.34 3.20
2250 2259 3.569250 GAGTTTCTCTCTGCTTCGTCT 57.431 47.619 0.00 0.00 39.86 4.18
2251 2260 3.908213 GAGTTTCTCTCTGCTTCGTCTT 58.092 45.455 0.00 0.00 39.86 3.01
2252 2261 5.049398 GAGTTTCTCTCTGCTTCGTCTTA 57.951 43.478 0.00 0.00 39.86 2.10
2253 2262 5.455056 AGTTTCTCTCTGCTTCGTCTTAA 57.545 39.130 0.00 0.00 0.00 1.85
2254 2263 5.844004 AGTTTCTCTCTGCTTCGTCTTAAA 58.156 37.500 0.00 0.00 0.00 1.52
2255 2264 6.281405 AGTTTCTCTCTGCTTCGTCTTAAAA 58.719 36.000 0.00 0.00 0.00 1.52
2256 2265 6.422400 AGTTTCTCTCTGCTTCGTCTTAAAAG 59.578 38.462 0.00 0.00 0.00 2.27
2257 2266 4.810790 TCTCTCTGCTTCGTCTTAAAAGG 58.189 43.478 0.00 0.00 0.00 3.11
2258 2267 4.281182 TCTCTCTGCTTCGTCTTAAAAGGT 59.719 41.667 0.00 0.00 0.00 3.50
2259 2268 4.307432 TCTCTGCTTCGTCTTAAAAGGTG 58.693 43.478 0.00 0.00 0.00 4.00
2260 2269 3.399330 TCTGCTTCGTCTTAAAAGGTGG 58.601 45.455 0.00 0.00 0.00 4.61
2261 2270 1.877443 TGCTTCGTCTTAAAAGGTGGC 59.123 47.619 0.00 0.00 0.00 5.01
2262 2271 1.877443 GCTTCGTCTTAAAAGGTGGCA 59.123 47.619 0.00 0.00 0.00 4.92
2263 2272 2.488153 GCTTCGTCTTAAAAGGTGGCAT 59.512 45.455 0.00 0.00 0.00 4.40
2264 2273 3.670627 GCTTCGTCTTAAAAGGTGGCATG 60.671 47.826 0.00 0.00 0.00 4.06
2265 2274 3.410631 TCGTCTTAAAAGGTGGCATGA 57.589 42.857 0.00 0.00 0.00 3.07
2266 2275 3.334691 TCGTCTTAAAAGGTGGCATGAG 58.665 45.455 0.00 0.00 0.00 2.90
2267 2276 2.420022 CGTCTTAAAAGGTGGCATGAGG 59.580 50.000 0.00 0.00 0.00 3.86
2268 2277 2.755103 GTCTTAAAAGGTGGCATGAGGG 59.245 50.000 0.00 0.00 0.00 4.30
2269 2278 1.478105 CTTAAAAGGTGGCATGAGGGC 59.522 52.381 0.00 0.00 43.73 5.19
2281 2290 2.203126 GAGGGCATCTCAAGGCGG 60.203 66.667 0.00 0.00 42.02 6.13
2282 2291 2.688666 AGGGCATCTCAAGGCGGA 60.689 61.111 0.00 0.00 31.44 5.54
2283 2292 2.514824 GGGCATCTCAAGGCGGAC 60.515 66.667 0.00 0.00 31.44 4.79
2284 2293 2.514824 GGCATCTCAAGGCGGACC 60.515 66.667 0.00 0.00 31.44 4.46
2293 2302 2.681778 AGGCGGACCTCAGACTGG 60.682 66.667 1.81 0.00 46.34 4.00
2294 2303 2.997897 GGCGGACCTCAGACTGGT 60.998 66.667 1.81 0.00 41.07 4.00
2300 2309 2.633199 GACCTCAGACTGGTCGTAAC 57.367 55.000 1.81 0.00 43.55 2.50
2301 2310 1.201880 GACCTCAGACTGGTCGTAACC 59.798 57.143 1.81 0.00 43.55 2.85
2309 2318 2.179267 GGTCGTAACCGTCCGGAC 59.821 66.667 25.28 25.28 35.36 4.79
2310 2319 2.179267 GTCGTAACCGTCCGGACC 59.821 66.667 28.52 13.11 38.96 4.46
2311 2320 3.430862 TCGTAACCGTCCGGACCG 61.431 66.667 28.52 23.87 38.96 4.79
2313 2322 4.054825 GTAACCGTCCGGACCGCA 62.055 66.667 28.52 11.02 38.96 5.69
2314 2323 4.054825 TAACCGTCCGGACCGCAC 62.055 66.667 28.52 2.09 38.96 5.34
2327 2336 4.735132 CGCACGGTCCGGACATGT 62.735 66.667 34.40 27.76 0.00 3.21
2328 2337 2.358247 GCACGGTCCGGACATGTT 60.358 61.111 34.40 13.36 0.00 2.71
2329 2338 2.677003 GCACGGTCCGGACATGTTG 61.677 63.158 34.40 23.91 0.00 3.33
2330 2339 1.301401 CACGGTCCGGACATGTTGT 60.301 57.895 34.40 20.57 0.00 3.32
2331 2340 1.301401 ACGGTCCGGACATGTTGTG 60.301 57.895 34.40 16.67 0.00 3.33
2332 2341 1.301401 CGGTCCGGACATGTTGTGT 60.301 57.895 34.40 0.00 45.83 3.72
2342 2351 3.319137 ACATGTTGTGTCATCTAGCGT 57.681 42.857 0.00 0.00 35.77 5.07
2343 2352 2.995939 ACATGTTGTGTCATCTAGCGTG 59.004 45.455 0.00 0.00 35.77 5.34
2344 2353 2.078849 TGTTGTGTCATCTAGCGTGG 57.921 50.000 0.00 0.00 0.00 4.94
2345 2354 1.337728 TGTTGTGTCATCTAGCGTGGG 60.338 52.381 0.00 0.00 0.00 4.61
2346 2355 0.391130 TTGTGTCATCTAGCGTGGGC 60.391 55.000 0.00 0.00 40.37 5.36
2347 2356 1.521681 GTGTCATCTAGCGTGGGCC 60.522 63.158 0.00 0.00 41.24 5.80
2348 2357 1.685765 TGTCATCTAGCGTGGGCCT 60.686 57.895 4.53 0.00 41.24 5.19
2349 2358 1.068250 GTCATCTAGCGTGGGCCTC 59.932 63.158 4.53 0.00 41.24 4.70
2350 2359 1.075970 TCATCTAGCGTGGGCCTCT 60.076 57.895 4.53 1.66 41.24 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 6.666113 TCGTAGAATATGTGGGAGCCAATATA 59.334 38.462 0.00 0.00 34.18 0.86
320 323 1.717032 AAGGTGCTCTACAGGTGTCA 58.283 50.000 0.00 0.00 0.00 3.58
432 435 9.049523 TGCTATTGCTTTCTTCATGACTTATAG 57.950 33.333 0.00 0.00 40.48 1.31
765 771 1.986882 CCACTGGCCTTTGTCTCTTT 58.013 50.000 3.32 0.00 0.00 2.52
806 812 1.470996 GGCGATCCTCTCTGCCATCT 61.471 60.000 2.54 0.00 40.81 2.90
1071 1077 3.838271 GATCCTGTCGCGGCTCCA 61.838 66.667 13.81 0.05 0.00 3.86
1143 1149 1.916273 ACTCACGGCACCACCCATA 60.916 57.895 0.00 0.00 33.26 2.74
1144 1150 3.249189 ACTCACGGCACCACCCAT 61.249 61.111 0.00 0.00 33.26 4.00
1196 1202 4.807631 TCATCCCGGCGACCTCGA 62.808 66.667 9.30 0.00 43.02 4.04
1341 1347 1.541233 CCGTCAGTGCCTCAGTTCTTT 60.541 52.381 0.00 0.00 0.00 2.52
1461 1470 1.279025 CCTAAACCCTAGGGCTGCCA 61.279 60.000 28.88 7.83 39.32 4.92
1886 1895 5.327091 GCGTGTTAGACTTCGTATTGTAGA 58.673 41.667 0.00 0.00 0.00 2.59
1944 1953 3.195698 GAGACAATGCGACGGCCC 61.196 66.667 0.00 0.00 38.85 5.80
1945 1954 3.195698 GGAGACAATGCGACGGCC 61.196 66.667 0.00 0.00 38.85 6.13
1946 1955 2.125512 AGGAGACAATGCGACGGC 60.126 61.111 0.00 0.00 40.52 5.68
1947 1956 1.519455 GGAGGAGACAATGCGACGG 60.519 63.158 0.00 0.00 0.00 4.79
1948 1957 1.078759 GTGGAGGAGACAATGCGACG 61.079 60.000 0.00 0.00 0.00 5.12
1949 1958 1.078759 CGTGGAGGAGACAATGCGAC 61.079 60.000 0.00 0.00 0.00 5.19
1950 1959 1.215382 CGTGGAGGAGACAATGCGA 59.785 57.895 0.00 0.00 0.00 5.10
1951 1960 2.456119 GCGTGGAGGAGACAATGCG 61.456 63.158 0.00 0.00 0.00 4.73
1952 1961 2.109126 GGCGTGGAGGAGACAATGC 61.109 63.158 0.00 0.00 0.00 3.56
1953 1962 1.450312 GGGCGTGGAGGAGACAATG 60.450 63.158 0.00 0.00 0.00 2.82
1954 1963 2.670148 GGGGCGTGGAGGAGACAAT 61.670 63.158 0.00 0.00 0.00 2.71
1955 1964 3.319198 GGGGCGTGGAGGAGACAA 61.319 66.667 0.00 0.00 0.00 3.18
1958 1967 4.332543 AAGGGGGCGTGGAGGAGA 62.333 66.667 0.00 0.00 0.00 3.71
1959 1968 4.101448 CAAGGGGGCGTGGAGGAG 62.101 72.222 0.00 0.00 0.00 3.69
1962 1971 4.722700 CACCAAGGGGGCGTGGAG 62.723 72.222 0.00 0.00 42.05 3.86
1969 1978 1.077212 CTGATGAGCACCAAGGGGG 60.077 63.158 0.00 0.00 44.81 5.40
1970 1979 1.077212 CCTGATGAGCACCAAGGGG 60.077 63.158 0.00 0.00 41.29 4.79
1971 1980 0.107312 CTCCTGATGAGCACCAAGGG 60.107 60.000 0.00 0.00 33.47 3.95
1972 1981 0.107312 CCTCCTGATGAGCACCAAGG 60.107 60.000 0.00 0.00 39.98 3.61
1973 1982 0.907486 TCCTCCTGATGAGCACCAAG 59.093 55.000 0.00 0.00 39.98 3.61
1974 1983 0.907486 CTCCTCCTGATGAGCACCAA 59.093 55.000 0.00 0.00 39.98 3.67
1975 1984 2.600439 CTCCTCCTGATGAGCACCA 58.400 57.895 0.00 0.00 39.98 4.17
1980 1989 1.440893 CCGTGCTCCTCCTGATGAG 59.559 63.158 0.00 0.00 41.07 2.90
1981 1990 2.725312 GCCGTGCTCCTCCTGATGA 61.725 63.158 0.00 0.00 0.00 2.92
1982 1991 2.202987 GCCGTGCTCCTCCTGATG 60.203 66.667 0.00 0.00 0.00 3.07
1983 1992 2.364842 AGCCGTGCTCCTCCTGAT 60.365 61.111 0.00 0.00 30.62 2.90
2010 2019 4.379243 AGTGGAAGTGCGCGAGGG 62.379 66.667 12.10 0.00 0.00 4.30
2011 2020 3.114616 CAGTGGAAGTGCGCGAGG 61.115 66.667 12.10 0.00 0.00 4.63
2018 2027 1.298014 GGGGAGAGCAGTGGAAGTG 59.702 63.158 0.00 0.00 41.28 3.16
2019 2028 0.548682 ATGGGGAGAGCAGTGGAAGT 60.549 55.000 0.00 0.00 0.00 3.01
2020 2029 0.179936 GATGGGGAGAGCAGTGGAAG 59.820 60.000 0.00 0.00 0.00 3.46
2021 2030 0.547471 TGATGGGGAGAGCAGTGGAA 60.547 55.000 0.00 0.00 0.00 3.53
2022 2031 0.547471 TTGATGGGGAGAGCAGTGGA 60.547 55.000 0.00 0.00 0.00 4.02
2023 2032 0.107312 CTTGATGGGGAGAGCAGTGG 60.107 60.000 0.00 0.00 0.00 4.00
2024 2033 0.107312 CCTTGATGGGGAGAGCAGTG 60.107 60.000 0.00 0.00 0.00 3.66
2025 2034 0.548682 ACCTTGATGGGGAGAGCAGT 60.549 55.000 0.00 0.00 41.11 4.40
2026 2035 0.622665 AACCTTGATGGGGAGAGCAG 59.377 55.000 0.00 0.00 41.11 4.24
2027 2036 1.004745 GAAACCTTGATGGGGAGAGCA 59.995 52.381 0.00 0.00 41.11 4.26
2028 2037 1.683319 GGAAACCTTGATGGGGAGAGC 60.683 57.143 0.00 0.00 41.11 4.09
2029 2038 2.426842 GGAAACCTTGATGGGGAGAG 57.573 55.000 0.00 0.00 41.11 3.20
2043 2052 1.065418 ACATCGATGGTGAGGGGAAAC 60.065 52.381 28.09 0.00 0.00 2.78
2044 2053 1.065491 CACATCGATGGTGAGGGGAAA 60.065 52.381 28.09 0.00 38.54 3.13
2045 2054 0.541392 CACATCGATGGTGAGGGGAA 59.459 55.000 28.09 0.00 38.54 3.97
2046 2055 0.325203 TCACATCGATGGTGAGGGGA 60.325 55.000 28.09 4.64 40.16 4.81
2047 2056 2.211375 TCACATCGATGGTGAGGGG 58.789 57.895 28.09 2.00 40.16 4.79
2056 2065 0.738975 ACGACGACCATCACATCGAT 59.261 50.000 0.00 0.00 40.86 3.59
2057 2066 1.063027 GTACGACGACCATCACATCGA 59.937 52.381 0.00 0.00 40.86 3.59
2058 2067 1.463805 GTACGACGACCATCACATCG 58.536 55.000 0.00 0.00 43.97 3.84
2059 2068 1.133598 TGGTACGACGACCATCACATC 59.866 52.381 13.06 0.00 44.79 3.06
2060 2069 1.179152 TGGTACGACGACCATCACAT 58.821 50.000 13.06 0.00 44.79 3.21
2061 2070 2.643655 TGGTACGACGACCATCACA 58.356 52.632 13.06 0.00 44.79 3.58
2074 2083 0.108281 GGAGGAGCTCCGTTTGGTAC 60.108 60.000 26.95 5.42 41.08 3.34
2075 2084 2.283824 GGAGGAGCTCCGTTTGGTA 58.716 57.895 26.95 0.00 41.08 3.25
2076 2085 3.069778 GGAGGAGCTCCGTTTGGT 58.930 61.111 26.95 8.53 41.08 3.67
2084 2093 2.733945 GCGGATCAGGAGGAGCTC 59.266 66.667 4.71 4.71 30.93 4.09
2085 2094 2.841988 GGCGGATCAGGAGGAGCT 60.842 66.667 0.00 0.00 30.93 4.09
2086 2095 4.292178 CGGCGGATCAGGAGGAGC 62.292 72.222 0.00 0.00 0.00 4.70
2087 2096 2.519541 TCGGCGGATCAGGAGGAG 60.520 66.667 7.21 0.00 0.00 3.69
2088 2097 2.833582 GTCGGCGGATCAGGAGGA 60.834 66.667 7.21 0.00 0.00 3.71
2089 2098 2.835431 AGTCGGCGGATCAGGAGG 60.835 66.667 7.21 0.00 0.00 4.30
2090 2099 2.415010 CAGTCGGCGGATCAGGAG 59.585 66.667 7.21 0.00 0.00 3.69
2091 2100 3.147595 CCAGTCGGCGGATCAGGA 61.148 66.667 7.21 0.00 0.00 3.86
2101 2110 4.821589 GGGAAGAGCGCCAGTCGG 62.822 72.222 2.29 0.00 38.94 4.79
2127 2136 1.135083 AGAGTGTAAAGGGCGACATCG 60.135 52.381 0.00 0.00 43.27 3.84
2128 2137 2.166664 AGAGAGTGTAAAGGGCGACATC 59.833 50.000 0.00 0.00 0.00 3.06
2129 2138 2.166664 GAGAGAGTGTAAAGGGCGACAT 59.833 50.000 0.00 0.00 0.00 3.06
2130 2139 1.544691 GAGAGAGTGTAAAGGGCGACA 59.455 52.381 0.00 0.00 0.00 4.35
2131 2140 1.819903 AGAGAGAGTGTAAAGGGCGAC 59.180 52.381 0.00 0.00 0.00 5.19
2132 2141 2.093106 GAGAGAGAGTGTAAAGGGCGA 58.907 52.381 0.00 0.00 0.00 5.54
2133 2142 1.135333 GGAGAGAGAGTGTAAAGGGCG 59.865 57.143 0.00 0.00 0.00 6.13
2134 2143 2.180276 TGGAGAGAGAGTGTAAAGGGC 58.820 52.381 0.00 0.00 0.00 5.19
2135 2144 6.325028 TGATAATGGAGAGAGAGTGTAAAGGG 59.675 42.308 0.00 0.00 0.00 3.95
2136 2145 7.147828 TGTGATAATGGAGAGAGAGTGTAAAGG 60.148 40.741 0.00 0.00 0.00 3.11
2137 2146 7.776107 TGTGATAATGGAGAGAGAGTGTAAAG 58.224 38.462 0.00 0.00 0.00 1.85
2138 2147 7.718334 TGTGATAATGGAGAGAGAGTGTAAA 57.282 36.000 0.00 0.00 0.00 2.01
2139 2148 7.904558 ATGTGATAATGGAGAGAGAGTGTAA 57.095 36.000 0.00 0.00 0.00 2.41
2140 2149 9.018582 CATATGTGATAATGGAGAGAGAGTGTA 57.981 37.037 0.00 0.00 0.00 2.90
2141 2150 7.727634 TCATATGTGATAATGGAGAGAGAGTGT 59.272 37.037 1.90 0.00 0.00 3.55
2142 2151 8.120140 TCATATGTGATAATGGAGAGAGAGTG 57.880 38.462 1.90 0.00 0.00 3.51
2143 2152 8.584157 GTTCATATGTGATAATGGAGAGAGAGT 58.416 37.037 1.90 0.00 33.56 3.24
2144 2153 8.583296 TGTTCATATGTGATAATGGAGAGAGAG 58.417 37.037 1.90 0.00 33.56 3.20
2145 2154 8.363390 GTGTTCATATGTGATAATGGAGAGAGA 58.637 37.037 1.90 0.00 33.56 3.10
2146 2155 7.328005 CGTGTTCATATGTGATAATGGAGAGAG 59.672 40.741 1.90 0.00 33.56 3.20
2147 2156 7.147976 CGTGTTCATATGTGATAATGGAGAGA 58.852 38.462 1.90 0.00 33.56 3.10
2148 2157 6.925718 ACGTGTTCATATGTGATAATGGAGAG 59.074 38.462 1.90 0.00 33.56 3.20
2149 2158 6.816136 ACGTGTTCATATGTGATAATGGAGA 58.184 36.000 1.90 0.00 33.56 3.71
2150 2159 6.925718 AGACGTGTTCATATGTGATAATGGAG 59.074 38.462 1.90 0.00 33.56 3.86
2151 2160 6.816136 AGACGTGTTCATATGTGATAATGGA 58.184 36.000 1.90 0.00 33.56 3.41
2152 2161 8.763049 ATAGACGTGTTCATATGTGATAATGG 57.237 34.615 1.90 0.00 33.56 3.16
2155 2164 8.547894 GCAAATAGACGTGTTCATATGTGATAA 58.452 33.333 1.90 0.00 33.56 1.75
2156 2165 7.926018 AGCAAATAGACGTGTTCATATGTGATA 59.074 33.333 1.90 0.00 33.56 2.15
2157 2166 6.763135 AGCAAATAGACGTGTTCATATGTGAT 59.237 34.615 1.90 0.00 33.56 3.06
2158 2167 6.035975 CAGCAAATAGACGTGTTCATATGTGA 59.964 38.462 1.90 0.00 0.00 3.58
2159 2168 6.187480 CAGCAAATAGACGTGTTCATATGTG 58.813 40.000 1.90 0.00 0.00 3.21
2160 2169 5.294306 CCAGCAAATAGACGTGTTCATATGT 59.706 40.000 1.90 0.00 0.00 2.29
2161 2170 5.294306 ACCAGCAAATAGACGTGTTCATATG 59.706 40.000 0.00 0.00 0.00 1.78
2162 2171 5.294306 CACCAGCAAATAGACGTGTTCATAT 59.706 40.000 0.00 0.00 0.00 1.78
2163 2172 4.629634 CACCAGCAAATAGACGTGTTCATA 59.370 41.667 0.00 0.00 0.00 2.15
2164 2173 3.436704 CACCAGCAAATAGACGTGTTCAT 59.563 43.478 0.00 0.00 0.00 2.57
2165 2174 2.805671 CACCAGCAAATAGACGTGTTCA 59.194 45.455 0.00 0.00 0.00 3.18
2166 2175 3.064207 TCACCAGCAAATAGACGTGTTC 58.936 45.455 0.00 0.00 0.00 3.18
2167 2176 3.067106 CTCACCAGCAAATAGACGTGTT 58.933 45.455 0.00 0.00 0.00 3.32
2168 2177 2.299013 TCTCACCAGCAAATAGACGTGT 59.701 45.455 0.00 0.00 0.00 4.49
2169 2178 2.959516 TCTCACCAGCAAATAGACGTG 58.040 47.619 0.00 0.00 0.00 4.49
2170 2179 3.678056 TTCTCACCAGCAAATAGACGT 57.322 42.857 0.00 0.00 0.00 4.34
2171 2180 3.372206 CCTTTCTCACCAGCAAATAGACG 59.628 47.826 0.00 0.00 0.00 4.18
2172 2181 4.393371 GTCCTTTCTCACCAGCAAATAGAC 59.607 45.833 0.00 0.00 0.00 2.59
2173 2182 4.041567 TGTCCTTTCTCACCAGCAAATAGA 59.958 41.667 0.00 0.00 0.00 1.98
2174 2183 4.154918 GTGTCCTTTCTCACCAGCAAATAG 59.845 45.833 0.00 0.00 0.00 1.73
2175 2184 4.072131 GTGTCCTTTCTCACCAGCAAATA 58.928 43.478 0.00 0.00 0.00 1.40
2176 2185 2.887152 GTGTCCTTTCTCACCAGCAAAT 59.113 45.455 0.00 0.00 0.00 2.32
2177 2186 2.297701 GTGTCCTTTCTCACCAGCAAA 58.702 47.619 0.00 0.00 0.00 3.68
2178 2187 1.211703 TGTGTCCTTTCTCACCAGCAA 59.788 47.619 0.00 0.00 34.14 3.91
2179 2188 0.836606 TGTGTCCTTTCTCACCAGCA 59.163 50.000 0.00 0.00 34.14 4.41
2180 2189 1.202698 AGTGTGTCCTTTCTCACCAGC 60.203 52.381 0.00 0.00 33.89 4.85
2181 2190 2.487934 CAGTGTGTCCTTTCTCACCAG 58.512 52.381 0.00 0.00 33.89 4.00
2182 2191 1.140852 CCAGTGTGTCCTTTCTCACCA 59.859 52.381 0.00 0.00 33.89 4.17
2183 2192 1.543429 CCCAGTGTGTCCTTTCTCACC 60.543 57.143 0.00 0.00 33.89 4.02
2184 2193 1.884235 CCCAGTGTGTCCTTTCTCAC 58.116 55.000 0.00 0.00 35.43 3.51
2185 2194 0.108585 GCCCAGTGTGTCCTTTCTCA 59.891 55.000 0.00 0.00 0.00 3.27
2186 2195 0.108585 TGCCCAGTGTGTCCTTTCTC 59.891 55.000 0.00 0.00 0.00 2.87
2187 2196 0.109342 CTGCCCAGTGTGTCCTTTCT 59.891 55.000 0.00 0.00 0.00 2.52
2188 2197 0.179018 ACTGCCCAGTGTGTCCTTTC 60.179 55.000 0.00 0.00 40.75 2.62
2189 2198 1.072331 CTACTGCCCAGTGTGTCCTTT 59.928 52.381 11.02 0.00 42.52 3.11
2190 2199 0.687354 CTACTGCCCAGTGTGTCCTT 59.313 55.000 11.02 0.00 42.52 3.36
2191 2200 1.831652 GCTACTGCCCAGTGTGTCCT 61.832 60.000 11.02 0.00 42.52 3.85
2192 2201 1.376037 GCTACTGCCCAGTGTGTCC 60.376 63.158 11.02 0.00 42.52 4.02
2193 2202 4.285851 GCTACTGCCCAGTGTGTC 57.714 61.111 11.02 0.00 42.52 3.67
2203 2212 3.701604 CTCACCGACGGGCTACTGC 62.702 68.421 20.00 0.00 36.48 4.40
2204 2213 2.490217 CTCACCGACGGGCTACTG 59.510 66.667 20.00 6.99 36.48 2.74
2205 2214 2.754658 CCTCACCGACGGGCTACT 60.755 66.667 20.00 0.00 36.48 2.57
2206 2215 3.834799 CCCTCACCGACGGGCTAC 61.835 72.222 20.00 0.00 36.48 3.58
2207 2216 4.371417 ACCCTCACCGACGGGCTA 62.371 66.667 20.00 1.66 44.63 3.93
2210 2219 3.760035 CTCACCCTCACCGACGGG 61.760 72.222 20.00 7.45 46.26 5.28
2211 2220 1.654954 CTACTCACCCTCACCGACGG 61.655 65.000 13.61 13.61 0.00 4.79
2212 2221 0.675837 TCTACTCACCCTCACCGACG 60.676 60.000 0.00 0.00 0.00 5.12
2213 2222 1.096416 CTCTACTCACCCTCACCGAC 58.904 60.000 0.00 0.00 0.00 4.79
2214 2223 0.697079 ACTCTACTCACCCTCACCGA 59.303 55.000 0.00 0.00 0.00 4.69
2215 2224 1.546961 AACTCTACTCACCCTCACCG 58.453 55.000 0.00 0.00 0.00 4.94
2216 2225 3.166679 AGAAACTCTACTCACCCTCACC 58.833 50.000 0.00 0.00 0.00 4.02
2217 2226 4.083565 AGAGAAACTCTACTCACCCTCAC 58.916 47.826 0.00 0.00 39.28 3.51
2218 2227 4.337145 GAGAGAAACTCTACTCACCCTCA 58.663 47.826 1.12 0.00 41.35 3.86
2219 2228 4.976224 GAGAGAAACTCTACTCACCCTC 57.024 50.000 1.12 0.00 41.35 4.30
2230 2239 3.569250 AGACGAAGCAGAGAGAAACTC 57.431 47.619 0.00 0.00 45.22 3.01
2231 2240 5.455056 TTAAGACGAAGCAGAGAGAAACT 57.545 39.130 0.00 0.00 0.00 2.66
2232 2241 6.346999 CCTTTTAAGACGAAGCAGAGAGAAAC 60.347 42.308 0.00 0.00 0.00 2.78
2233 2242 5.696724 CCTTTTAAGACGAAGCAGAGAGAAA 59.303 40.000 0.00 0.00 0.00 2.52
2234 2243 5.221461 ACCTTTTAAGACGAAGCAGAGAGAA 60.221 40.000 0.00 0.00 0.00 2.87
2235 2244 4.281182 ACCTTTTAAGACGAAGCAGAGAGA 59.719 41.667 0.00 0.00 0.00 3.10
2236 2245 4.387256 CACCTTTTAAGACGAAGCAGAGAG 59.613 45.833 0.00 0.00 0.00 3.20
2237 2246 4.307432 CACCTTTTAAGACGAAGCAGAGA 58.693 43.478 0.00 0.00 0.00 3.10
2238 2247 3.433615 CCACCTTTTAAGACGAAGCAGAG 59.566 47.826 0.00 0.00 0.00 3.35
2239 2248 3.399330 CCACCTTTTAAGACGAAGCAGA 58.601 45.455 0.00 0.00 0.00 4.26
2240 2249 2.095718 GCCACCTTTTAAGACGAAGCAG 60.096 50.000 0.00 0.00 0.00 4.24
2241 2250 1.877443 GCCACCTTTTAAGACGAAGCA 59.123 47.619 0.00 0.00 0.00 3.91
2242 2251 1.877443 TGCCACCTTTTAAGACGAAGC 59.123 47.619 0.00 0.00 0.00 3.86
2243 2252 3.751175 TCATGCCACCTTTTAAGACGAAG 59.249 43.478 0.00 0.00 0.00 3.79
2244 2253 3.745799 TCATGCCACCTTTTAAGACGAA 58.254 40.909 0.00 0.00 0.00 3.85
2245 2254 3.334691 CTCATGCCACCTTTTAAGACGA 58.665 45.455 0.00 0.00 0.00 4.20
2246 2255 2.420022 CCTCATGCCACCTTTTAAGACG 59.580 50.000 0.00 0.00 0.00 4.18
2247 2256 2.755103 CCCTCATGCCACCTTTTAAGAC 59.245 50.000 0.00 0.00 0.00 3.01
2248 2257 2.883888 GCCCTCATGCCACCTTTTAAGA 60.884 50.000 0.00 0.00 0.00 2.10
2249 2258 1.478105 GCCCTCATGCCACCTTTTAAG 59.522 52.381 0.00 0.00 0.00 1.85
2250 2259 1.203112 TGCCCTCATGCCACCTTTTAA 60.203 47.619 0.00 0.00 0.00 1.52
2251 2260 0.407528 TGCCCTCATGCCACCTTTTA 59.592 50.000 0.00 0.00 0.00 1.52
2252 2261 0.252375 ATGCCCTCATGCCACCTTTT 60.252 50.000 0.00 0.00 0.00 2.27
2253 2262 0.685458 GATGCCCTCATGCCACCTTT 60.685 55.000 0.00 0.00 31.96 3.11
2254 2263 1.076485 GATGCCCTCATGCCACCTT 60.076 57.895 0.00 0.00 31.96 3.50
2255 2264 1.992519 GAGATGCCCTCATGCCACCT 61.993 60.000 0.00 0.00 41.58 4.00
2256 2265 1.527844 GAGATGCCCTCATGCCACC 60.528 63.158 0.00 0.00 41.58 4.61
2257 2266 1.225426 TGAGATGCCCTCATGCCAC 59.775 57.895 2.19 0.00 46.38 5.01
2258 2267 3.744137 TGAGATGCCCTCATGCCA 58.256 55.556 2.19 0.00 46.38 4.92
2264 2273 2.203126 CCGCCTTGAGATGCCCTC 60.203 66.667 0.00 0.00 42.30 4.30
2265 2274 2.688666 TCCGCCTTGAGATGCCCT 60.689 61.111 0.00 0.00 0.00 5.19
2266 2275 2.514824 GTCCGCCTTGAGATGCCC 60.515 66.667 0.00 0.00 0.00 5.36
2267 2276 2.514824 GGTCCGCCTTGAGATGCC 60.515 66.667 0.00 0.00 0.00 4.40
2268 2277 2.586792 AGGTCCGCCTTGAGATGC 59.413 61.111 0.00 0.00 44.18 3.91
2277 2286 2.997897 ACCAGTCTGAGGTCCGCC 60.998 66.667 0.00 0.00 32.90 6.13
2282 2291 1.254954 GGTTACGACCAGTCTGAGGT 58.745 55.000 0.00 0.00 45.77 3.85
2283 2292 0.170561 CGGTTACGACCAGTCTGAGG 59.829 60.000 0.00 0.00 46.91 3.86
2284 2293 0.879765 ACGGTTACGACCAGTCTGAG 59.120 55.000 0.00 0.00 46.91 3.35
2285 2294 0.877071 GACGGTTACGACCAGTCTGA 59.123 55.000 0.00 0.00 46.91 3.27
2286 2295 3.396491 GACGGTTACGACCAGTCTG 57.604 57.895 0.00 0.00 46.91 3.51
2293 2302 2.179267 GGTCCGGACGGTTACGAC 59.821 66.667 27.68 7.98 44.60 4.34
2294 2303 3.430862 CGGTCCGGACGGTTACGA 61.431 66.667 28.79 0.00 44.60 3.43
2296 2305 4.054825 TGCGGTCCGGACGGTTAC 62.055 66.667 34.25 22.30 36.47 2.50
2297 2306 4.054825 GTGCGGTCCGGACGGTTA 62.055 66.667 34.25 24.08 38.53 2.85
2310 2319 4.735132 ACATGTCCGGACCGTGCG 62.735 66.667 31.19 16.62 0.00 5.34
2311 2320 2.358247 AACATGTCCGGACCGTGC 60.358 61.111 31.19 7.14 0.00 5.34
2312 2321 1.301401 ACAACATGTCCGGACCGTG 60.301 57.895 31.19 28.49 0.00 4.94
2313 2322 1.301401 CACAACATGTCCGGACCGT 60.301 57.895 31.19 24.30 0.00 4.83
2314 2323 1.301401 ACACAACATGTCCGGACCG 60.301 57.895 31.19 23.63 36.54 4.79
2315 2324 4.792087 ACACAACATGTCCGGACC 57.208 55.556 31.19 14.15 36.54 4.46
2323 2332 2.349580 CCACGCTAGATGACACAACATG 59.650 50.000 0.00 0.00 0.00 3.21
2324 2333 2.621338 CCACGCTAGATGACACAACAT 58.379 47.619 0.00 0.00 0.00 2.71
2325 2334 1.337728 CCCACGCTAGATGACACAACA 60.338 52.381 0.00 0.00 0.00 3.33
2326 2335 1.359848 CCCACGCTAGATGACACAAC 58.640 55.000 0.00 0.00 0.00 3.32
2327 2336 0.391130 GCCCACGCTAGATGACACAA 60.391 55.000 0.00 0.00 0.00 3.33
2328 2337 1.218047 GCCCACGCTAGATGACACA 59.782 57.895 0.00 0.00 0.00 3.72
2329 2338 1.521681 GGCCCACGCTAGATGACAC 60.522 63.158 0.00 0.00 34.44 3.67
2330 2339 1.676678 GAGGCCCACGCTAGATGACA 61.677 60.000 0.00 0.00 34.44 3.58
2331 2340 1.068250 GAGGCCCACGCTAGATGAC 59.932 63.158 0.00 0.00 34.44 3.06
2332 2341 1.075970 AGAGGCCCACGCTAGATGA 60.076 57.895 0.00 0.00 34.44 2.92
2333 2342 3.543537 AGAGGCCCACGCTAGATG 58.456 61.111 0.00 0.00 34.44 2.90


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

AutoCloner maintained by Alex Coulton.