Multiple sequence alignment - TraesCS7B01G193000

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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 TraesCS7B01G193000 chr7B 100.000 5255 0 0 1 5255 332010055 332015309 0.000000e+00 9705.0
1 TraesCS7B01G193000 chr7B 96.552 58 2 0 2101 2158 417293177 417293120 4.330000e-16 97.1
2 TraesCS7B01G193000 chr7D 93.967 2188 90 26 2177 4357 188161410 188163562 0.000000e+00 3271.0
3 TraesCS7B01G193000 chr7D 97.122 973 27 1 802 1774 188159988 188160959 0.000000e+00 1640.0
4 TraesCS7B01G193000 chr7D 94.054 185 5 1 4341 4525 188163597 188163775 5.180000e-70 276.0
5 TraesCS7B01G193000 chr7D 97.222 36 1 0 1838 1873 188161272 188161307 1.580000e-05 62.1
6 TraesCS7B01G193000 chr7A 93.139 1749 68 26 2783 4514 195839880 195838167 0.000000e+00 2518.0
7 TraesCS7B01G193000 chr7A 95.566 1060 37 7 805 1860 195841878 195840825 0.000000e+00 1688.0
8 TraesCS7B01G193000 chr7A 88.624 756 59 7 4527 5255 306223621 306224376 0.000000e+00 894.0
9 TraesCS7B01G193000 chr7A 90.514 622 40 12 2178 2794 195840735 195840128 0.000000e+00 804.0
10 TraesCS7B01G193000 chr7A 100.000 28 0 0 2152 2179 195840773 195840746 1.000000e-02 52.8
11 TraesCS7B01G193000 chr3B 97.406 771 19 1 1 771 27474407 27473638 0.000000e+00 1312.0
12 TraesCS7B01G193000 chr3B 96.936 359 11 0 410 768 15031957 15032315 2.090000e-168 603.0
13 TraesCS7B01G193000 chr1B 96.248 773 28 1 1 772 12318683 12317911 0.000000e+00 1266.0
14 TraesCS7B01G193000 chr1B 85.375 759 82 13 4525 5255 563469355 563470112 0.000000e+00 760.0
15 TraesCS7B01G193000 chr3A 91.797 768 59 3 1 767 588142352 588141588 0.000000e+00 1066.0
16 TraesCS7B01G193000 chr3A 90.950 221 13 6 4525 4740 455226797 455226579 1.850000e-74 291.0
17 TraesCS7B01G193000 chr6A 91.525 767 45 9 1 767 558916662 558917408 0.000000e+00 1038.0
18 TraesCS7B01G193000 chr4B 89.791 764 48 4 1 764 312670926 312670193 0.000000e+00 952.0
19 TraesCS7B01G193000 chr5B 86.934 773 94 2 1 773 659478439 659479204 0.000000e+00 861.0
20 TraesCS7B01G193000 chr1D 87.887 743 76 8 4524 5255 416681241 416681980 0.000000e+00 861.0
21 TraesCS7B01G193000 chr1D 86.012 672 86 7 1 670 216720008 216720673 0.000000e+00 713.0
22 TraesCS7B01G193000 chr1D 100.000 52 0 0 2101 2152 51824686 51824737 4.330000e-16 97.1
23 TraesCS7B01G193000 chr1D 96.552 58 2 0 2101 2158 254466683 254466626 4.330000e-16 97.1
24 TraesCS7B01G193000 chr1D 98.077 52 1 0 2101 2152 180378963 180379014 2.020000e-14 91.6
25 TraesCS7B01G193000 chr1D 96.364 55 2 0 2104 2158 244191210 244191156 2.020000e-14 91.6
26 TraesCS7B01G193000 chr1A 86.701 767 100 2 1 766 504065955 504066720 0.000000e+00 850.0
27 TraesCS7B01G193000 chr1A 87.254 761 70 11 4522 5255 514030790 514031550 0.000000e+00 843.0
28 TraesCS7B01G193000 chr1A 85.696 769 75 23 1 766 25887950 25887214 0.000000e+00 778.0
29 TraesCS7B01G193000 chr4D 80.670 388 60 14 383 766 94382111 94381735 2.390000e-73 287.0
30 TraesCS7B01G193000 chr4D 94.828 58 2 1 2101 2158 19907952 19907896 7.250000e-14 89.8
31 TraesCS7B01G193000 chr3D 73.046 371 90 8 4525 4891 81732473 81732109 7.150000e-24 122.0
32 TraesCS7B01G193000 chr5D 98.077 52 1 0 2101 2152 58692536 58692587 2.020000e-14 91.6
33 TraesCS7B01G193000 chr5D 94.595 37 1 1 4545 4581 87848826 87848791 7.350000e-04 56.5
34 TraesCS7B01G193000 chr2A 94.828 58 3 0 2101 2158 359074767 359074710 2.020000e-14 91.6
35 TraesCS7B01G193000 chr6D 98.077 52 0 1 2101 2152 19329869 19329919 7.250000e-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 TraesCS7B01G193000 chr7B 332010055 332015309 5254 False 9705.000 9705 100.00000 1 5255 1 chr7B.!!$F1 5254
1 TraesCS7B01G193000 chr7D 188159988 188163775 3787 False 1312.275 3271 95.59125 802 4525 4 chr7D.!!$F1 3723
2 TraesCS7B01G193000 chr7A 195838167 195841878 3711 True 1265.700 2518 94.80475 805 4514 4 chr7A.!!$R1 3709
3 TraesCS7B01G193000 chr7A 306223621 306224376 755 False 894.000 894 88.62400 4527 5255 1 chr7A.!!$F1 728
4 TraesCS7B01G193000 chr3B 27473638 27474407 769 True 1312.000 1312 97.40600 1 771 1 chr3B.!!$R1 770
5 TraesCS7B01G193000 chr1B 12317911 12318683 772 True 1266.000 1266 96.24800 1 772 1 chr1B.!!$R1 771
6 TraesCS7B01G193000 chr1B 563469355 563470112 757 False 760.000 760 85.37500 4525 5255 1 chr1B.!!$F1 730
7 TraesCS7B01G193000 chr3A 588141588 588142352 764 True 1066.000 1066 91.79700 1 767 1 chr3A.!!$R2 766
8 TraesCS7B01G193000 chr6A 558916662 558917408 746 False 1038.000 1038 91.52500 1 767 1 chr6A.!!$F1 766
9 TraesCS7B01G193000 chr4B 312670193 312670926 733 True 952.000 952 89.79100 1 764 1 chr4B.!!$R1 763
10 TraesCS7B01G193000 chr5B 659478439 659479204 765 False 861.000 861 86.93400 1 773 1 chr5B.!!$F1 772
11 TraesCS7B01G193000 chr1D 416681241 416681980 739 False 861.000 861 87.88700 4524 5255 1 chr1D.!!$F4 731
12 TraesCS7B01G193000 chr1D 216720008 216720673 665 False 713.000 713 86.01200 1 670 1 chr1D.!!$F3 669
13 TraesCS7B01G193000 chr1A 504065955 504066720 765 False 850.000 850 86.70100 1 766 1 chr1A.!!$F1 765
14 TraesCS7B01G193000 chr1A 514030790 514031550 760 False 843.000 843 87.25400 4522 5255 1 chr1A.!!$F2 733
15 TraesCS7B01G193000 chr1A 25887214 25887950 736 True 778.000 778 85.69600 1 766 1 chr1A.!!$R1 765

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
802 814 2.477863 CCGGGTCAATCGATTTTTCAGC 60.478 50.0 8.21 2.65 0.00 4.26 F
1146 1159 0.033920 TCATGAAGATCATCGGGCGG 59.966 55.0 0.00 0.00 34.28 6.13 F
1706 1722 0.178953 ATGCCAGAAACAGCCAGGTT 60.179 50.0 0.00 0.00 0.00 3.50 F
2775 3060 0.029834 CGCCATCATAAGGTTGCTGC 59.970 55.0 0.00 0.00 0.00 5.25 F
2832 3379 0.246635 TCGTCAAGTTGCCTAGCTCC 59.753 55.0 0.00 0.00 0.00 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2080 2344 0.243095 AGACTACGGTTTGCCTCGTC 59.757 55.000 0.0 0.0 40.31 4.20 R
2515 2799 0.527565 AATCAATGCGGTGACTTGCC 59.472 50.000 0.0 0.0 0.00 4.52 R
3249 3804 0.179004 TAAACCTGCACCACCACCAG 60.179 55.000 0.0 0.0 0.00 4.00 R
4233 4788 1.024579 ATACAGAAAAGCGGTGCGGG 61.025 55.000 0.0 0.0 0.00 6.13 R
4352 4960 2.851195 ACCATGCGGGAAATCTACATC 58.149 47.619 0.6 0.0 41.15 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
797 809 4.857509 TTTTTCCGGGTCAATCGATTTT 57.142 36.364 8.21 0.00 0.00 1.82
798 810 4.857509 TTTTCCGGGTCAATCGATTTTT 57.142 36.364 8.21 0.00 0.00 1.94
799 811 4.428615 TTTCCGGGTCAATCGATTTTTC 57.571 40.909 8.21 1.86 0.00 2.29
800 812 3.060736 TCCGGGTCAATCGATTTTTCA 57.939 42.857 8.21 0.00 0.00 2.69
801 813 3.006940 TCCGGGTCAATCGATTTTTCAG 58.993 45.455 8.21 0.00 0.00 3.02
802 814 2.477863 CCGGGTCAATCGATTTTTCAGC 60.478 50.000 8.21 2.65 0.00 4.26
803 815 2.477863 CGGGTCAATCGATTTTTCAGCC 60.478 50.000 8.21 10.48 0.00 4.85
1146 1159 0.033920 TCATGAAGATCATCGGGCGG 59.966 55.000 0.00 0.00 34.28 6.13
1440 1453 2.799371 GGAGACTACCCGCTGTCG 59.201 66.667 0.00 0.00 38.16 4.35
1620 1633 3.710722 CCGGAGGCTGCTGACCTT 61.711 66.667 4.02 0.00 46.14 3.50
1706 1722 0.178953 ATGCCAGAAACAGCCAGGTT 60.179 50.000 0.00 0.00 0.00 3.50
1714 1730 2.432628 CAGCCAGGTTCGTCGGTC 60.433 66.667 0.00 0.00 0.00 4.79
1723 1739 0.455126 GTTCGTCGGTCGTCCTAACC 60.455 60.000 0.00 0.00 40.80 2.85
1733 1749 1.001269 GTCCTAACCCCCAACTGGC 60.001 63.158 0.00 0.00 0.00 4.85
1764 1780 2.157668 GTCTCTTCGACCACGTACGTTA 59.842 50.000 20.23 0.00 40.69 3.18
1816 1995 3.724478 AGGAGTGACATTCATACAGGGA 58.276 45.455 0.00 0.00 0.00 4.20
1829 2008 6.327279 TCATACAGGGAGTTATCATGTACG 57.673 41.667 0.00 0.00 34.11 3.67
1830 2009 3.454371 ACAGGGAGTTATCATGTACGC 57.546 47.619 0.00 0.00 0.00 4.42
1831 2010 2.764010 ACAGGGAGTTATCATGTACGCA 59.236 45.455 0.00 0.00 0.00 5.24
1832 2011 3.388024 ACAGGGAGTTATCATGTACGCAT 59.612 43.478 0.00 0.00 35.32 4.73
1875 2139 9.893305 ATTGTCAGTACACAGTAAAAATTTAGC 57.107 29.630 0.00 0.00 34.61 3.09
1876 2140 8.671384 TGTCAGTACACAGTAAAAATTTAGCT 57.329 30.769 0.00 0.00 0.00 3.32
1877 2141 9.767228 TGTCAGTACACAGTAAAAATTTAGCTA 57.233 29.630 0.00 0.00 0.00 3.32
1891 2155 9.686683 AAAAATTTAGCTATGTCTAGGACACAT 57.313 29.630 2.34 1.62 45.65 3.21
1892 2156 8.894768 AAATTTAGCTATGTCTAGGACACATC 57.105 34.615 2.34 0.00 45.65 3.06
1893 2157 7.847711 ATTTAGCTATGTCTAGGACACATCT 57.152 36.000 2.34 0.00 45.65 2.90
1894 2158 8.941995 ATTTAGCTATGTCTAGGACACATCTA 57.058 34.615 2.34 0.00 45.65 1.98
1895 2159 7.987750 TTAGCTATGTCTAGGACACATCTAG 57.012 40.000 2.34 2.86 45.65 2.43
1896 2160 6.194285 AGCTATGTCTAGGACACATCTAGA 57.806 41.667 2.34 0.00 45.65 2.43
1897 2161 6.237901 AGCTATGTCTAGGACACATCTAGAG 58.762 44.000 0.00 0.00 45.65 2.43
1898 2162 6.001460 GCTATGTCTAGGACACATCTAGAGT 58.999 44.000 0.00 0.00 45.65 3.24
1899 2163 6.488683 GCTATGTCTAGGACACATCTAGAGTT 59.511 42.308 0.00 0.00 45.65 3.01
1900 2164 7.662258 GCTATGTCTAGGACACATCTAGAGTTA 59.338 40.741 0.00 0.00 45.65 2.24
1901 2165 9.733556 CTATGTCTAGGACACATCTAGAGTTAT 57.266 37.037 0.00 0.00 45.65 1.89
1902 2166 7.809546 TGTCTAGGACACATCTAGAGTTATG 57.190 40.000 0.00 0.00 42.45 1.90
1903 2167 7.347252 TGTCTAGGACACATCTAGAGTTATGT 58.653 38.462 0.00 0.00 42.45 2.29
1904 2168 7.499563 TGTCTAGGACACATCTAGAGTTATGTC 59.500 40.741 15.18 15.18 42.45 3.06
1905 2169 7.499563 GTCTAGGACACATCTAGAGTTATGTCA 59.500 40.741 20.91 8.43 42.45 3.58
1906 2170 6.458232 AGGACACATCTAGAGTTATGTCAC 57.542 41.667 20.91 14.11 38.54 3.67
1907 2171 5.952347 AGGACACATCTAGAGTTATGTCACA 59.048 40.000 20.91 0.00 38.54 3.58
1908 2172 6.609212 AGGACACATCTAGAGTTATGTCACAT 59.391 38.462 20.91 0.00 38.54 3.21
1909 2173 6.920758 GGACACATCTAGAGTTATGTCACATC 59.079 42.308 20.91 7.65 38.54 3.06
1910 2174 7.201866 GGACACATCTAGAGTTATGTCACATCT 60.202 40.741 20.91 0.00 38.54 2.90
1911 2175 8.753497 ACACATCTAGAGTTATGTCACATCTA 57.247 34.615 0.00 0.00 34.12 1.98
1912 2176 9.190317 ACACATCTAGAGTTATGTCACATCTAA 57.810 33.333 0.00 0.00 34.12 2.10
1917 2181 8.191446 TCTAGAGTTATGTCACATCTAAACTGC 58.809 37.037 8.84 2.60 0.00 4.40
1918 2182 6.940739 AGAGTTATGTCACATCTAAACTGCT 58.059 36.000 8.84 4.41 0.00 4.24
1919 2183 6.815641 AGAGTTATGTCACATCTAAACTGCTG 59.184 38.462 8.84 0.00 0.00 4.41
1920 2184 6.467677 AGTTATGTCACATCTAAACTGCTGT 58.532 36.000 3.98 0.00 0.00 4.40
1921 2185 6.591834 AGTTATGTCACATCTAAACTGCTGTC 59.408 38.462 3.98 0.00 0.00 3.51
1922 2186 3.664107 TGTCACATCTAAACTGCTGTCC 58.336 45.455 0.00 0.00 0.00 4.02
1923 2187 3.070878 TGTCACATCTAAACTGCTGTCCA 59.929 43.478 0.00 0.00 0.00 4.02
1924 2188 3.433615 GTCACATCTAAACTGCTGTCCAC 59.566 47.826 0.00 0.00 0.00 4.02
1925 2189 3.324846 TCACATCTAAACTGCTGTCCACT 59.675 43.478 0.00 0.00 0.00 4.00
1926 2190 4.067896 CACATCTAAACTGCTGTCCACTT 58.932 43.478 0.00 0.00 0.00 3.16
1927 2191 4.516698 CACATCTAAACTGCTGTCCACTTT 59.483 41.667 0.00 0.00 0.00 2.66
1928 2192 4.516698 ACATCTAAACTGCTGTCCACTTTG 59.483 41.667 0.00 0.00 0.00 2.77
1929 2193 4.150897 TCTAAACTGCTGTCCACTTTGT 57.849 40.909 0.00 0.00 0.00 2.83
1930 2194 4.523083 TCTAAACTGCTGTCCACTTTGTT 58.477 39.130 0.00 0.00 0.00 2.83
1931 2195 4.947388 TCTAAACTGCTGTCCACTTTGTTT 59.053 37.500 0.00 0.00 0.00 2.83
1932 2196 3.508744 AACTGCTGTCCACTTTGTTTG 57.491 42.857 0.00 0.00 0.00 2.93
1933 2197 2.446435 ACTGCTGTCCACTTTGTTTGT 58.554 42.857 0.00 0.00 0.00 2.83
1934 2198 2.164219 ACTGCTGTCCACTTTGTTTGTG 59.836 45.455 0.00 0.00 35.39 3.33
1968 2232 5.597813 TTTTTGTTTCATGTTGTTGCGTT 57.402 30.435 0.00 0.00 0.00 4.84
1969 2233 6.706055 TTTTTGTTTCATGTTGTTGCGTTA 57.294 29.167 0.00 0.00 0.00 3.18
1970 2234 6.893958 TTTTGTTTCATGTTGTTGCGTTAT 57.106 29.167 0.00 0.00 0.00 1.89
1971 2235 7.987268 TTTTGTTTCATGTTGTTGCGTTATA 57.013 28.000 0.00 0.00 0.00 0.98
1972 2236 8.581057 TTTTGTTTCATGTTGTTGCGTTATAT 57.419 26.923 0.00 0.00 0.00 0.86
1973 2237 9.678941 TTTTGTTTCATGTTGTTGCGTTATATA 57.321 25.926 0.00 0.00 0.00 0.86
1974 2238 9.847706 TTTGTTTCATGTTGTTGCGTTATATAT 57.152 25.926 0.00 0.00 0.00 0.86
1975 2239 9.847706 TTGTTTCATGTTGTTGCGTTATATATT 57.152 25.926 0.00 0.00 0.00 1.28
1976 2240 9.847706 TGTTTCATGTTGTTGCGTTATATATTT 57.152 25.926 0.00 0.00 0.00 1.40
1978 2242 9.847706 TTTCATGTTGTTGCGTTATATATTTGT 57.152 25.926 0.00 0.00 0.00 2.83
1979 2243 8.833976 TCATGTTGTTGCGTTATATATTTGTG 57.166 30.769 0.00 0.00 0.00 3.33
1980 2244 8.669243 TCATGTTGTTGCGTTATATATTTGTGA 58.331 29.630 0.00 0.00 0.00 3.58
1981 2245 8.946935 CATGTTGTTGCGTTATATATTTGTGAG 58.053 33.333 0.00 0.00 0.00 3.51
1982 2246 8.257830 TGTTGTTGCGTTATATATTTGTGAGA 57.742 30.769 0.00 0.00 0.00 3.27
1983 2247 8.387354 TGTTGTTGCGTTATATATTTGTGAGAG 58.613 33.333 0.00 0.00 0.00 3.20
1984 2248 8.600625 GTTGTTGCGTTATATATTTGTGAGAGA 58.399 33.333 0.00 0.00 0.00 3.10
1985 2249 8.887036 TGTTGCGTTATATATTTGTGAGAGAT 57.113 30.769 0.00 0.00 0.00 2.75
1986 2250 9.325198 TGTTGCGTTATATATTTGTGAGAGATT 57.675 29.630 0.00 0.00 0.00 2.40
1999 2263 8.853077 TTTGTGAGAGATTAGATGTGACATTT 57.147 30.769 0.00 0.00 0.00 2.32
2000 2264 8.853077 TTGTGAGAGATTAGATGTGACATTTT 57.147 30.769 0.00 0.00 0.00 1.82
2001 2265 8.853077 TGTGAGAGATTAGATGTGACATTTTT 57.147 30.769 0.00 0.00 0.00 1.94
2002 2266 9.942850 TGTGAGAGATTAGATGTGACATTTTTA 57.057 29.630 0.00 0.00 0.00 1.52
2067 2331 4.419200 TCCCTCTAGGCACCTTAGAGATTA 59.581 45.833 17.65 6.47 39.61 1.75
2086 2350 7.045126 AGATTACTCTAATTTCCAGACGAGG 57.955 40.000 0.00 0.00 0.00 4.63
2101 2365 0.458025 CGAGGCAAACCGTAGTCTCC 60.458 60.000 0.00 0.00 42.76 3.71
2102 2366 0.458025 GAGGCAAACCGTAGTCTCCG 60.458 60.000 0.00 0.00 42.76 4.63
2103 2367 2.098831 GGCAAACCGTAGTCTCCGC 61.099 63.158 0.00 0.00 0.00 5.54
2104 2368 1.373748 GCAAACCGTAGTCTCCGCA 60.374 57.895 0.00 0.00 0.00 5.69
2105 2369 1.352156 GCAAACCGTAGTCTCCGCAG 61.352 60.000 0.00 0.00 0.00 5.18
2106 2370 0.242825 CAAACCGTAGTCTCCGCAGA 59.757 55.000 0.00 0.00 0.00 4.26
2107 2371 1.135083 CAAACCGTAGTCTCCGCAGAT 60.135 52.381 0.00 0.00 0.00 2.90
2108 2372 1.183549 AACCGTAGTCTCCGCAGATT 58.816 50.000 0.00 0.00 0.00 2.40
2109 2373 1.183549 ACCGTAGTCTCCGCAGATTT 58.816 50.000 0.00 0.00 0.00 2.17
2110 2374 1.549170 ACCGTAGTCTCCGCAGATTTT 59.451 47.619 0.00 0.00 0.00 1.82
2111 2375 2.028385 ACCGTAGTCTCCGCAGATTTTT 60.028 45.455 0.00 0.00 0.00 1.94
2132 2396 6.587206 TTTTTAGTCCATCACATTCATGCA 57.413 33.333 0.00 0.00 0.00 3.96
2133 2397 6.778834 TTTTAGTCCATCACATTCATGCAT 57.221 33.333 0.00 0.00 0.00 3.96
2134 2398 6.778834 TTTAGTCCATCACATTCATGCATT 57.221 33.333 0.00 0.00 0.00 3.56
2135 2399 6.778834 TTAGTCCATCACATTCATGCATTT 57.221 33.333 0.00 0.00 0.00 2.32
2136 2400 7.878547 TTAGTCCATCACATTCATGCATTTA 57.121 32.000 0.00 0.00 0.00 1.40
2137 2401 6.140303 AGTCCATCACATTCATGCATTTAC 57.860 37.500 0.00 0.00 0.00 2.01
2138 2402 5.068198 AGTCCATCACATTCATGCATTTACC 59.932 40.000 0.00 0.00 0.00 2.85
2139 2403 4.954826 TCCATCACATTCATGCATTTACCA 59.045 37.500 0.00 0.00 0.00 3.25
2140 2404 5.599242 TCCATCACATTCATGCATTTACCAT 59.401 36.000 0.00 0.00 0.00 3.55
2141 2405 6.776603 TCCATCACATTCATGCATTTACCATA 59.223 34.615 0.00 0.00 0.00 2.74
2142 2406 6.864685 CCATCACATTCATGCATTTACCATAC 59.135 38.462 0.00 0.00 0.00 2.39
2143 2407 7.427214 CATCACATTCATGCATTTACCATACA 58.573 34.615 0.00 0.00 0.00 2.29
2144 2408 7.585579 TCACATTCATGCATTTACCATACAT 57.414 32.000 0.00 0.00 0.00 2.29
2145 2409 7.427214 TCACATTCATGCATTTACCATACATG 58.573 34.615 0.00 0.00 39.53 3.21
2146 2410 7.068470 TCACATTCATGCATTTACCATACATGT 59.932 33.333 2.69 2.69 39.27 3.21
2147 2411 7.168469 CACATTCATGCATTTACCATACATGTG 59.832 37.037 9.11 1.08 39.27 3.21
2148 2412 7.068470 ACATTCATGCATTTACCATACATGTGA 59.932 33.333 9.11 0.00 39.27 3.58
2149 2413 6.375945 TCATGCATTTACCATACATGTGAC 57.624 37.500 9.11 0.00 39.27 3.67
2150 2414 6.121590 TCATGCATTTACCATACATGTGACT 58.878 36.000 9.11 0.00 39.27 3.41
2219 2495 5.163195 ACCCGGATTTAAGCTGATACATCTT 60.163 40.000 0.73 0.00 0.00 2.40
2252 2530 4.468095 AAATGAACGGTTCAAGAGTTCG 57.532 40.909 25.64 0.00 45.04 3.95
2260 2538 0.392706 TTCAAGAGTTCGAGGCTGCA 59.607 50.000 0.50 0.00 0.00 4.41
2366 2650 0.794473 CGAAGTACCTTTGAACGGCC 59.206 55.000 0.00 0.00 0.00 6.13
2515 2799 2.241722 CGCCTTGCACTAAACATTTCG 58.758 47.619 0.00 0.00 0.00 3.46
2524 2808 4.219033 CACTAAACATTTCGGCAAGTCAC 58.781 43.478 0.00 0.00 0.00 3.67
2600 2884 1.164411 ATCTCAAACAAATGGCGCGA 58.836 45.000 12.10 0.00 0.00 5.87
2699 2983 1.301874 CCGTAAACGAACCTGGGCA 60.302 57.895 3.65 0.00 43.02 5.36
2723 3007 8.458843 GCACAGTTTGCCTAATTATTTTCTCTA 58.541 33.333 0.00 0.00 46.63 2.43
2728 3012 6.861065 TGCCTAATTATTTTCTCTAAGCCG 57.139 37.500 0.00 0.00 0.00 5.52
2729 3013 5.763204 TGCCTAATTATTTTCTCTAAGCCGG 59.237 40.000 0.00 0.00 0.00 6.13
2744 3029 1.007580 GCCGGAGCTTAACTAAGTGC 58.992 55.000 5.05 0.00 35.75 4.40
2775 3060 0.029834 CGCCATCATAAGGTTGCTGC 59.970 55.000 0.00 0.00 0.00 5.25
2799 3343 9.953565 TGCTTATACTTGTCTAGTTTTGGTATT 57.046 29.630 0.00 0.00 38.33 1.89
2832 3379 0.246635 TCGTCAAGTTGCCTAGCTCC 59.753 55.000 0.00 0.00 0.00 4.70
2936 3483 7.192676 CATACTTAAACAAGTTTGCATACGC 57.807 36.000 8.37 0.00 34.37 4.42
3051 3606 3.857157 ATTGAAGTGGCATATACCGGT 57.143 42.857 13.98 13.98 0.00 5.28
3052 3607 2.613026 TGAAGTGGCATATACCGGTG 57.387 50.000 19.93 0.19 0.00 4.94
3078 3633 6.061441 TGAATCTGGCTCACTTTAGTTTTCA 58.939 36.000 0.00 0.00 0.00 2.69
3118 3673 1.757118 GGTCGATCAGGAGGTGATTCA 59.243 52.381 0.00 0.00 46.64 2.57
3145 3700 7.797038 ACACCAAAAGATAAAGTAGAAACGT 57.203 32.000 0.00 0.00 0.00 3.99
3146 3701 8.891671 ACACCAAAAGATAAAGTAGAAACGTA 57.108 30.769 0.00 0.00 0.00 3.57
3147 3702 8.768019 ACACCAAAAGATAAAGTAGAAACGTAC 58.232 33.333 0.00 0.00 0.00 3.67
3214 3769 7.506328 ACCAACTAAAGTTCAGTAATTGACC 57.494 36.000 0.00 0.00 35.83 4.02
3225 3780 8.524870 GTTCAGTAATTGACCGAACTAACTAA 57.475 34.615 0.00 0.00 40.79 2.24
3226 3781 8.430828 GTTCAGTAATTGACCGAACTAACTAAC 58.569 37.037 0.00 0.00 40.79 2.34
3227 3782 7.889469 TCAGTAATTGACCGAACTAACTAACT 58.111 34.615 0.00 0.00 0.00 2.24
3228 3783 7.811236 TCAGTAATTGACCGAACTAACTAACTG 59.189 37.037 0.00 0.00 0.00 3.16
3232 3787 3.057033 TGACCGAACTAACTAACTGCTCC 60.057 47.826 0.00 0.00 0.00 4.70
3234 3789 3.251571 CCGAACTAACTAACTGCTCCAC 58.748 50.000 0.00 0.00 0.00 4.02
3251 3806 2.439701 CCTGATGGGTGCTGGCTG 60.440 66.667 0.00 0.00 0.00 4.85
3252 3807 2.439701 CTGATGGGTGCTGGCTGG 60.440 66.667 0.00 0.00 0.00 4.85
3553 4108 1.952102 GATCTACCGGCCGTGGTTCA 61.952 60.000 26.12 6.01 43.56 3.18
3554 4109 1.546589 ATCTACCGGCCGTGGTTCAA 61.547 55.000 26.12 5.14 43.56 2.69
4104 4659 4.194720 ACGATGAGGCGGTCGCTC 62.195 66.667 15.04 10.67 41.31 5.03
4128 4683 3.127352 GAACGAGAGCGAGCGGGAT 62.127 63.158 0.00 0.00 41.64 3.85
4141 4696 1.899437 GCGGGATCAGAACCAGGACA 61.899 60.000 0.00 0.00 0.00 4.02
4233 4788 0.101759 TTAGCACGTCGCCTATCCAC 59.898 55.000 6.39 0.00 44.04 4.02
4272 4827 8.352201 TCTGTATGATGGAACTTTGAAAACTTG 58.648 33.333 0.00 0.00 0.00 3.16
4395 5004 3.003275 TGCTTCGTTTGATTGGTTGAGAC 59.997 43.478 0.00 0.00 0.00 3.36
4435 5046 4.885325 TCAAACTTTGTAAAGGTCTGGTCC 59.115 41.667 9.00 0.00 33.74 4.46
4459 5071 9.749340 TCCTATGTAACTAGCTATGCTATTACA 57.251 33.333 21.59 21.59 42.11 2.41
4462 5074 8.651589 ATGTAACTAGCTATGCTATTACAGGA 57.348 34.615 22.54 11.70 41.74 3.86
4463 5075 8.112016 TGTAACTAGCTATGCTATTACAGGAG 57.888 38.462 18.75 5.78 40.54 3.69
4499 5111 2.106338 TGATGGTGATTGTGGTGTCACT 59.894 45.455 2.35 0.00 43.23 3.41
4525 5137 8.908903 TCAAAACACAAATATGTTAGTCAGGTT 58.091 29.630 0.00 0.00 42.01 3.50
4526 5138 9.528018 CAAAACACAAATATGTTAGTCAGGTTT 57.472 29.630 0.00 0.00 42.01 3.27
4682 5294 7.588512 AGCATCAGAATTCAAACTACAACTTC 58.411 34.615 8.44 0.00 0.00 3.01
4699 5311 7.406799 ACAACTTCCAAAAATAAATTCGCAG 57.593 32.000 0.00 0.00 0.00 5.18
4703 5315 5.384063 TCCAAAAATAAATTCGCAGCTCA 57.616 34.783 0.00 0.00 0.00 4.26
4839 5451 4.811024 GTCGAGTGATAGATCCAATGCAAA 59.189 41.667 0.00 0.00 0.00 3.68
4887 5499 4.112341 CAGGGTCGTCGGGTCGTC 62.112 72.222 0.00 0.00 0.00 4.20
4928 5540 1.434188 TGAGGAGCCCAAGAACAGAA 58.566 50.000 0.00 0.00 0.00 3.02
4930 5542 1.072331 GAGGAGCCCAAGAACAGAACA 59.928 52.381 0.00 0.00 0.00 3.18
4933 5545 1.876156 GAGCCCAAGAACAGAACAGTG 59.124 52.381 0.00 0.00 0.00 3.66
4941 5553 2.103263 AGAACAGAACAGTGTGGTCTCC 59.897 50.000 0.00 0.00 41.32 3.71
4989 5601 0.398664 CCGTCCCTTGATAGTCCCCT 60.399 60.000 0.00 0.00 0.00 4.79
4996 5608 2.840651 CCTTGATAGTCCCCTGTCAACT 59.159 50.000 0.00 0.00 41.97 3.16
5034 5663 3.215151 CTGGACTAGGAGCAATCGAGTA 58.785 50.000 0.00 0.00 0.00 2.59
5058 5712 2.222596 GCACATCTCGAATGTCGTTGAC 60.223 50.000 9.38 0.00 41.35 3.18
5165 5819 1.454276 GTGAATCGCTTTTCGTCACGA 59.546 47.619 0.00 0.00 35.49 4.35
5242 5897 7.458409 AGTTCATCAATCAGTGCAAATAACT 57.542 32.000 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
538 542 3.941188 CTCGGTGCTGGGTGTGGT 61.941 66.667 0.00 0.00 0.00 4.16
776 788 4.857509 AAAATCGATTGACCCGGAAAAA 57.142 36.364 12.25 0.00 0.00 1.94
777 789 4.278669 TGAAAAATCGATTGACCCGGAAAA 59.721 37.500 12.25 0.00 0.00 2.29
778 790 3.821600 TGAAAAATCGATTGACCCGGAAA 59.178 39.130 12.25 0.00 0.00 3.13
779 791 3.413327 TGAAAAATCGATTGACCCGGAA 58.587 40.909 12.25 0.00 0.00 4.30
780 792 3.006940 CTGAAAAATCGATTGACCCGGA 58.993 45.455 12.25 0.00 0.00 5.14
781 793 2.477863 GCTGAAAAATCGATTGACCCGG 60.478 50.000 12.25 7.80 0.00 5.73
782 794 2.477863 GGCTGAAAAATCGATTGACCCG 60.478 50.000 12.25 2.27 0.00 5.28
783 795 2.159240 GGGCTGAAAAATCGATTGACCC 60.159 50.000 12.25 12.09 0.00 4.46
784 796 2.491693 TGGGCTGAAAAATCGATTGACC 59.508 45.455 12.25 10.82 0.00 4.02
785 797 3.501950 GTGGGCTGAAAAATCGATTGAC 58.498 45.455 12.25 6.94 0.00 3.18
786 798 2.161410 CGTGGGCTGAAAAATCGATTGA 59.839 45.455 12.25 0.00 0.00 2.57
787 799 2.518949 CGTGGGCTGAAAAATCGATTG 58.481 47.619 12.25 0.00 0.00 2.67
788 800 1.472480 CCGTGGGCTGAAAAATCGATT 59.528 47.619 4.39 4.39 0.00 3.34
789 801 1.094785 CCGTGGGCTGAAAAATCGAT 58.905 50.000 0.00 0.00 0.00 3.59
790 802 1.582610 GCCGTGGGCTGAAAAATCGA 61.583 55.000 0.00 0.00 46.69 3.59
791 803 1.154035 GCCGTGGGCTGAAAAATCG 60.154 57.895 0.00 0.00 46.69 3.34
792 804 4.889427 GCCGTGGGCTGAAAAATC 57.111 55.556 0.00 0.00 46.69 2.17
802 814 0.604511 AGTAAAGAAACGGCCGTGGG 60.605 55.000 34.95 1.63 0.00 4.61
803 815 0.794473 GAGTAAAGAAACGGCCGTGG 59.206 55.000 34.95 2.10 0.00 4.94
961 974 3.593794 GCTACCGATCGGCCGAGT 61.594 66.667 33.87 26.57 39.32 4.18
1620 1633 3.716539 GAGTATGACGCGCCAGGCA 62.717 63.158 13.30 0.00 43.84 4.75
1706 1722 2.040544 GGGTTAGGACGACCGACGA 61.041 63.158 0.00 0.00 45.77 4.20
1714 1730 1.298667 CCAGTTGGGGGTTAGGACG 59.701 63.158 0.00 0.00 0.00 4.79
1764 1780 6.803366 ACTGGAACTACGTTAGGGAAATAT 57.197 37.500 0.00 0.00 0.00 1.28
1796 1975 3.452627 ACTCCCTGTATGAATGTCACTCC 59.547 47.826 0.00 0.00 0.00 3.85
1829 2008 1.198867 TGTGCCGAAACATGTACATGC 59.801 47.619 31.19 18.77 42.39 4.06
1830 2009 3.763097 ATGTGCCGAAACATGTACATG 57.237 42.857 29.97 29.97 39.32 3.21
1831 2010 3.505680 ACAATGTGCCGAAACATGTACAT 59.494 39.130 1.41 1.41 39.89 2.29
1832 2011 2.881513 ACAATGTGCCGAAACATGTACA 59.118 40.909 0.00 0.00 39.89 2.90
1833 2012 3.058570 TGACAATGTGCCGAAACATGTAC 60.059 43.478 0.00 0.00 39.89 2.90
1835 2014 1.952990 TGACAATGTGCCGAAACATGT 59.047 42.857 0.00 0.00 39.89 3.21
1836 2015 2.030893 ACTGACAATGTGCCGAAACATG 60.031 45.455 0.00 0.00 39.89 3.21
1844 2108 2.494059 ACTGTGTACTGACAATGTGCC 58.506 47.619 0.00 0.00 37.31 5.01
1874 2138 6.001460 ACTCTAGATGTGTCCTAGACATAGC 58.999 44.000 0.05 1.13 44.63 2.97
1875 2139 9.733556 ATAACTCTAGATGTGTCCTAGACATAG 57.266 37.037 0.05 0.00 44.63 2.23
1876 2140 9.508642 CATAACTCTAGATGTGTCCTAGACATA 57.491 37.037 0.05 0.00 44.63 2.29
1877 2141 8.001875 ACATAACTCTAGATGTGTCCTAGACAT 58.998 37.037 0.05 0.00 44.63 3.06
1878 2142 7.347252 ACATAACTCTAGATGTGTCCTAGACA 58.653 38.462 0.00 0.00 40.50 3.41
1879 2143 7.499563 TGACATAACTCTAGATGTGTCCTAGAC 59.500 40.741 16.22 0.00 38.08 2.59
1880 2144 7.499563 GTGACATAACTCTAGATGTGTCCTAGA 59.500 40.741 16.22 0.00 40.00 2.43
1881 2145 7.283354 TGTGACATAACTCTAGATGTGTCCTAG 59.717 40.741 16.22 0.00 36.42 3.02
1882 2146 7.116736 TGTGACATAACTCTAGATGTGTCCTA 58.883 38.462 16.22 6.60 36.42 2.94
1883 2147 5.952347 TGTGACATAACTCTAGATGTGTCCT 59.048 40.000 16.22 0.00 36.42 3.85
1884 2148 6.208988 TGTGACATAACTCTAGATGTGTCC 57.791 41.667 16.22 10.50 36.42 4.02
1885 2149 7.711846 AGATGTGACATAACTCTAGATGTGTC 58.288 38.462 13.47 13.47 36.42 3.67
1886 2150 7.652524 AGATGTGACATAACTCTAGATGTGT 57.347 36.000 0.00 0.00 36.42 3.72
1891 2155 8.191446 GCAGTTTAGATGTGACATAACTCTAGA 58.809 37.037 8.77 0.00 0.00 2.43
1892 2156 8.194104 AGCAGTTTAGATGTGACATAACTCTAG 58.806 37.037 8.77 1.75 0.00 2.43
1893 2157 7.976175 CAGCAGTTTAGATGTGACATAACTCTA 59.024 37.037 8.77 0.18 0.00 2.43
1894 2158 6.815641 CAGCAGTTTAGATGTGACATAACTCT 59.184 38.462 8.77 7.25 0.00 3.24
1895 2159 6.591834 ACAGCAGTTTAGATGTGACATAACTC 59.408 38.462 8.77 5.59 36.67 3.01
1896 2160 6.467677 ACAGCAGTTTAGATGTGACATAACT 58.532 36.000 0.00 2.03 36.67 2.24
1897 2161 6.183360 GGACAGCAGTTTAGATGTGACATAAC 60.183 42.308 0.00 0.00 38.41 1.89
1898 2162 5.874810 GGACAGCAGTTTAGATGTGACATAA 59.125 40.000 0.00 0.00 38.41 1.90
1899 2163 5.046663 TGGACAGCAGTTTAGATGTGACATA 60.047 40.000 0.00 0.00 38.41 2.29
1900 2164 4.256920 GGACAGCAGTTTAGATGTGACAT 58.743 43.478 0.00 0.00 38.41 3.06
1901 2165 3.070878 TGGACAGCAGTTTAGATGTGACA 59.929 43.478 0.00 0.00 38.41 3.58
1902 2166 3.433615 GTGGACAGCAGTTTAGATGTGAC 59.566 47.826 0.00 0.00 38.41 3.67
1903 2167 3.324846 AGTGGACAGCAGTTTAGATGTGA 59.675 43.478 0.00 0.00 38.41 3.58
1904 2168 3.668447 AGTGGACAGCAGTTTAGATGTG 58.332 45.455 0.00 0.00 38.41 3.21
1905 2169 4.357918 AAGTGGACAGCAGTTTAGATGT 57.642 40.909 0.00 0.00 41.46 3.06
1906 2170 4.516698 ACAAAGTGGACAGCAGTTTAGATG 59.483 41.667 0.00 0.00 0.00 2.90
1907 2171 4.718961 ACAAAGTGGACAGCAGTTTAGAT 58.281 39.130 0.00 0.00 0.00 1.98
1908 2172 4.150897 ACAAAGTGGACAGCAGTTTAGA 57.849 40.909 0.00 0.00 0.00 2.10
1909 2173 4.900635 AACAAAGTGGACAGCAGTTTAG 57.099 40.909 0.00 0.00 0.00 1.85
1910 2174 4.461081 ACAAACAAAGTGGACAGCAGTTTA 59.539 37.500 0.00 0.00 0.00 2.01
1911 2175 3.258123 ACAAACAAAGTGGACAGCAGTTT 59.742 39.130 0.00 0.00 0.00 2.66
1912 2176 2.825532 ACAAACAAAGTGGACAGCAGTT 59.174 40.909 0.00 0.00 0.00 3.16
1913 2177 2.164219 CACAAACAAAGTGGACAGCAGT 59.836 45.455 0.00 0.00 33.43 4.40
1914 2178 2.801063 CACAAACAAAGTGGACAGCAG 58.199 47.619 0.00 0.00 33.43 4.24
1915 2179 2.937469 CACAAACAAAGTGGACAGCA 57.063 45.000 0.00 0.00 33.43 4.41
1946 2210 5.597813 AACGCAACAACATGAAACAAAAA 57.402 30.435 0.00 0.00 0.00 1.94
1947 2211 6.893958 ATAACGCAACAACATGAAACAAAA 57.106 29.167 0.00 0.00 0.00 2.44
1948 2212 9.847706 ATATATAACGCAACAACATGAAACAAA 57.152 25.926 0.00 0.00 0.00 2.83
1949 2213 9.847706 AATATATAACGCAACAACATGAAACAA 57.152 25.926 0.00 0.00 0.00 2.83
1950 2214 9.847706 AAATATATAACGCAACAACATGAAACA 57.152 25.926 0.00 0.00 0.00 2.83
1952 2216 9.847706 ACAAATATATAACGCAACAACATGAAA 57.152 25.926 0.00 0.00 0.00 2.69
1953 2217 9.283420 CACAAATATATAACGCAACAACATGAA 57.717 29.630 0.00 0.00 0.00 2.57
1954 2218 8.669243 TCACAAATATATAACGCAACAACATGA 58.331 29.630 0.00 0.00 0.00 3.07
1955 2219 8.833976 TCACAAATATATAACGCAACAACATG 57.166 30.769 0.00 0.00 0.00 3.21
1956 2220 8.888716 TCTCACAAATATATAACGCAACAACAT 58.111 29.630 0.00 0.00 0.00 2.71
1957 2221 8.257830 TCTCACAAATATATAACGCAACAACA 57.742 30.769 0.00 0.00 0.00 3.33
1958 2222 8.600625 TCTCTCACAAATATATAACGCAACAAC 58.399 33.333 0.00 0.00 0.00 3.32
1959 2223 8.710835 TCTCTCACAAATATATAACGCAACAA 57.289 30.769 0.00 0.00 0.00 2.83
1960 2224 8.887036 ATCTCTCACAAATATATAACGCAACA 57.113 30.769 0.00 0.00 0.00 3.33
1973 2237 9.458727 AAATGTCACATCTAATCTCTCACAAAT 57.541 29.630 0.00 0.00 0.00 2.32
1974 2238 8.853077 AAATGTCACATCTAATCTCTCACAAA 57.147 30.769 0.00 0.00 0.00 2.83
1975 2239 8.853077 AAAATGTCACATCTAATCTCTCACAA 57.147 30.769 0.00 0.00 0.00 3.33
1976 2240 8.853077 AAAAATGTCACATCTAATCTCTCACA 57.147 30.769 0.00 0.00 0.00 3.58
2036 2300 2.728007 GTGCCTAGAGGGAGCATTTTT 58.272 47.619 0.00 0.00 39.04 1.94
2037 2301 2.426842 GTGCCTAGAGGGAGCATTTT 57.573 50.000 0.00 0.00 39.04 1.82
2067 2331 2.832129 TGCCTCGTCTGGAAATTAGAGT 59.168 45.455 0.00 0.00 0.00 3.24
2077 2341 0.736325 CTACGGTTTGCCTCGTCTGG 60.736 60.000 0.00 0.00 40.31 3.86
2080 2344 0.243095 AGACTACGGTTTGCCTCGTC 59.757 55.000 0.00 0.00 40.31 4.20
2086 2350 1.352156 CTGCGGAGACTACGGTTTGC 61.352 60.000 9.61 0.00 0.00 3.68
2109 2373 6.587206 TGCATGAATGTGATGGACTAAAAA 57.413 33.333 0.00 0.00 0.00 1.94
2110 2374 6.778834 ATGCATGAATGTGATGGACTAAAA 57.221 33.333 0.00 0.00 0.00 1.52
2111 2375 6.778834 AATGCATGAATGTGATGGACTAAA 57.221 33.333 0.00 0.00 0.00 1.85
2112 2376 6.778834 AAATGCATGAATGTGATGGACTAA 57.221 33.333 0.00 0.00 0.00 2.24
2113 2377 6.262944 GGTAAATGCATGAATGTGATGGACTA 59.737 38.462 0.00 0.00 0.00 2.59
2114 2378 5.068198 GGTAAATGCATGAATGTGATGGACT 59.932 40.000 0.00 0.00 0.00 3.85
2115 2379 5.163530 TGGTAAATGCATGAATGTGATGGAC 60.164 40.000 0.00 0.00 0.00 4.02
2116 2380 4.954826 TGGTAAATGCATGAATGTGATGGA 59.045 37.500 0.00 0.00 0.00 3.41
2117 2381 5.265350 TGGTAAATGCATGAATGTGATGG 57.735 39.130 0.00 0.00 0.00 3.51
2118 2382 7.427214 TGTATGGTAAATGCATGAATGTGATG 58.573 34.615 0.00 0.00 0.00 3.07
2119 2383 7.585579 TGTATGGTAAATGCATGAATGTGAT 57.414 32.000 0.00 0.00 0.00 3.06
2120 2384 7.068470 ACATGTATGGTAAATGCATGAATGTGA 59.932 33.333 19.04 0.00 42.26 3.58
2121 2385 7.168469 CACATGTATGGTAAATGCATGAATGTG 59.832 37.037 19.04 6.72 42.26 3.21
2122 2386 7.068470 TCACATGTATGGTAAATGCATGAATGT 59.932 33.333 19.04 0.00 42.26 2.71
2123 2387 7.380333 GTCACATGTATGGTAAATGCATGAATG 59.620 37.037 19.04 10.43 42.26 2.67
2124 2388 7.286087 AGTCACATGTATGGTAAATGCATGAAT 59.714 33.333 19.04 0.00 42.26 2.57
2125 2389 6.602803 AGTCACATGTATGGTAAATGCATGAA 59.397 34.615 19.04 7.44 42.26 2.57
2126 2390 6.038492 CAGTCACATGTATGGTAAATGCATGA 59.962 38.462 19.04 0.81 42.26 3.07
2127 2391 6.203647 CAGTCACATGTATGGTAAATGCATG 58.796 40.000 0.00 12.86 44.22 4.06
2128 2392 5.300034 CCAGTCACATGTATGGTAAATGCAT 59.700 40.000 13.32 0.00 0.00 3.96
2129 2393 4.639755 CCAGTCACATGTATGGTAAATGCA 59.360 41.667 13.32 0.00 0.00 3.96
2130 2394 4.881273 TCCAGTCACATGTATGGTAAATGC 59.119 41.667 18.42 0.00 34.32 3.56
2131 2395 6.115446 ACTCCAGTCACATGTATGGTAAATG 58.885 40.000 18.42 10.41 34.32 2.32
2132 2396 6.313519 ACTCCAGTCACATGTATGGTAAAT 57.686 37.500 18.42 5.53 34.32 1.40
2133 2397 5.755409 ACTCCAGTCACATGTATGGTAAA 57.245 39.130 18.42 4.54 34.32 2.01
2134 2398 6.439375 AGTTACTCCAGTCACATGTATGGTAA 59.561 38.462 18.42 11.02 34.32 2.85
2135 2399 5.955959 AGTTACTCCAGTCACATGTATGGTA 59.044 40.000 18.42 6.87 34.32 3.25
2136 2400 4.777896 AGTTACTCCAGTCACATGTATGGT 59.222 41.667 18.42 7.61 34.32 3.55
2137 2401 5.344743 AGTTACTCCAGTCACATGTATGG 57.655 43.478 14.77 14.77 0.00 2.74
2138 2402 6.873605 TCAAAGTTACTCCAGTCACATGTATG 59.126 38.462 0.00 0.00 0.00 2.39
2139 2403 7.004555 TCAAAGTTACTCCAGTCACATGTAT 57.995 36.000 0.00 0.00 0.00 2.29
2140 2404 6.413783 TCAAAGTTACTCCAGTCACATGTA 57.586 37.500 0.00 0.00 0.00 2.29
2141 2405 5.290493 TCAAAGTTACTCCAGTCACATGT 57.710 39.130 0.00 0.00 0.00 3.21
2142 2406 5.934043 TGATCAAAGTTACTCCAGTCACATG 59.066 40.000 0.00 0.00 0.00 3.21
2143 2407 6.114187 TGATCAAAGTTACTCCAGTCACAT 57.886 37.500 0.00 0.00 0.00 3.21
2144 2408 5.545063 TGATCAAAGTTACTCCAGTCACA 57.455 39.130 0.00 0.00 0.00 3.58
2145 2409 6.861065 TTTGATCAAAGTTACTCCAGTCAC 57.139 37.500 16.91 0.00 0.00 3.67
2146 2410 9.739276 ATATTTTGATCAAAGTTACTCCAGTCA 57.261 29.630 19.71 2.57 0.00 3.41
2239 2517 1.433534 CAGCCTCGAACTCTTGAACC 58.566 55.000 0.00 0.00 0.00 3.62
2252 2530 3.243839 TGAAAACTTCCAAATGCAGCCTC 60.244 43.478 0.00 0.00 0.00 4.70
2366 2650 7.174946 CAGCTGGTATTATTAACTTACCATGGG 59.825 40.741 18.09 0.00 43.23 4.00
2393 2677 2.098117 GGATTAACAGTCATGGCAGCAC 59.902 50.000 0.00 0.00 0.00 4.40
2496 2780 2.595386 CCGAAATGTTTAGTGCAAGGC 58.405 47.619 0.00 0.00 0.00 4.35
2515 2799 0.527565 AATCAATGCGGTGACTTGCC 59.472 50.000 0.00 0.00 0.00 4.52
2524 2808 4.876107 AGTTTAGTCTACCAATCAATGCGG 59.124 41.667 0.00 0.00 0.00 5.69
2600 2884 4.771054 AGTATCCCGCGGTATATTCTTCTT 59.229 41.667 26.12 0.00 0.00 2.52
2728 3012 2.633488 CCTGGCACTTAGTTAAGCTCC 58.367 52.381 0.00 1.98 36.79 4.70
2729 3013 2.010497 GCCTGGCACTTAGTTAAGCTC 58.990 52.381 15.17 0.00 36.79 4.09
2737 3021 4.950479 CCAGAGCCTGGCACTTAG 57.050 61.111 22.65 9.83 45.13 2.18
2757 3042 1.396653 AGCAGCAACCTTATGATGGC 58.603 50.000 0.00 0.00 37.20 4.40
2832 3379 1.512926 AGCTAGTGCAAGGTCAAACG 58.487 50.000 0.00 0.00 42.74 3.60
2924 3471 6.027749 GCTTATTTTACAGCGTATGCAAACT 58.972 36.000 10.11 0.00 46.23 2.66
2936 3483 9.443283 GATATGCTCAACTTGCTTATTTTACAG 57.557 33.333 0.00 0.00 33.07 2.74
3051 3606 2.574006 AAAGTGAGCCAGATTCAGCA 57.426 45.000 2.12 0.00 0.00 4.41
3052 3607 3.604582 ACTAAAGTGAGCCAGATTCAGC 58.395 45.455 0.00 0.00 0.00 4.26
3078 3633 5.351948 ACCTGGTTTGTTAACTGCAAAAT 57.648 34.783 7.22 0.00 37.54 1.82
3144 3699 5.862924 TTGACACTACAGTAGTACGGTAC 57.137 43.478 13.12 10.29 37.23 3.34
3145 3700 6.875948 TTTTGACACTACAGTAGTACGGTA 57.124 37.500 13.12 11.98 37.23 4.02
3146 3701 5.772825 TTTTGACACTACAGTAGTACGGT 57.227 39.130 13.12 10.94 37.23 4.83
3211 3766 3.057033 TGGAGCAGTTAGTTAGTTCGGTC 60.057 47.826 0.00 0.00 0.00 4.79
3214 3769 3.056749 AGGTGGAGCAGTTAGTTAGTTCG 60.057 47.826 0.00 0.00 0.00 3.95
3234 3789 2.439701 CAGCCAGCACCCATCAGG 60.440 66.667 0.00 0.00 43.78 3.86
3246 3801 4.584518 CTGCACCACCACCAGCCA 62.585 66.667 0.00 0.00 0.00 4.75
3248 3803 4.586235 ACCTGCACCACCACCAGC 62.586 66.667 0.00 0.00 0.00 4.85
3249 3804 0.179004 TAAACCTGCACCACCACCAG 60.179 55.000 0.00 0.00 0.00 4.00
3250 3805 0.466555 GTAAACCTGCACCACCACCA 60.467 55.000 0.00 0.00 0.00 4.17
3251 3806 1.512156 CGTAAACCTGCACCACCACC 61.512 60.000 0.00 0.00 0.00 4.61
3252 3807 1.512156 CCGTAAACCTGCACCACCAC 61.512 60.000 0.00 0.00 0.00 4.16
3327 3882 2.126031 GCGTTCAGGTCGAGGTCC 60.126 66.667 0.00 0.00 0.00 4.46
3687 4242 3.984193 GAAGCCGGCCATCTGCAGT 62.984 63.158 26.15 0.00 43.89 4.40
3978 4533 4.155733 TACCCGGCCTGCACATCG 62.156 66.667 0.00 0.00 0.00 3.84
4104 4659 1.350319 CTCGCTCTCGTTCTCCTCG 59.650 63.158 0.00 0.00 36.96 4.63
4128 4683 1.666011 GTCGCTGTCCTGGTTCTGA 59.334 57.895 0.00 0.00 0.00 3.27
4233 4788 1.024579 ATACAGAAAAGCGGTGCGGG 61.025 55.000 0.00 0.00 0.00 6.13
4352 4960 2.851195 ACCATGCGGGAAATCTACATC 58.149 47.619 0.60 0.00 41.15 3.06
4458 5070 5.598416 TCACCAACTCACATATACTCCTG 57.402 43.478 0.00 0.00 0.00 3.86
4459 5071 5.070981 CCATCACCAACTCACATATACTCCT 59.929 44.000 0.00 0.00 0.00 3.69
4460 5072 5.163301 ACCATCACCAACTCACATATACTCC 60.163 44.000 0.00 0.00 0.00 3.85
4461 5073 5.755375 CACCATCACCAACTCACATATACTC 59.245 44.000 0.00 0.00 0.00 2.59
4462 5074 5.425217 TCACCATCACCAACTCACATATACT 59.575 40.000 0.00 0.00 0.00 2.12
4463 5075 5.670485 TCACCATCACCAACTCACATATAC 58.330 41.667 0.00 0.00 0.00 1.47
4499 5111 8.458573 ACCTGACTAACATATTTGTGTTTTGA 57.541 30.769 0.00 0.00 42.08 2.69
4526 5138 9.198475 TCAATAAAGTGTGGTTTACCCTAAAAA 57.802 29.630 0.00 0.00 34.29 1.94
4527 5139 8.763984 TCAATAAAGTGTGGTTTACCCTAAAA 57.236 30.769 0.00 0.00 34.29 1.52
4528 5140 8.943594 ATCAATAAAGTGTGGTTTACCCTAAA 57.056 30.769 0.00 0.00 34.29 1.85
4529 5141 8.798402 CAATCAATAAAGTGTGGTTTACCCTAA 58.202 33.333 0.00 0.00 34.29 2.69
4530 5142 7.094118 GCAATCAATAAAGTGTGGTTTACCCTA 60.094 37.037 0.00 0.00 34.29 3.53
4531 5143 6.295067 GCAATCAATAAAGTGTGGTTTACCCT 60.295 38.462 0.00 0.00 34.29 4.34
4619 5231 6.357367 AGTTTTCTTCTTCTTTAGCTGGTGA 58.643 36.000 0.00 0.00 0.00 4.02
4682 5294 5.863397 TCTTGAGCTGCGAATTTATTTTTGG 59.137 36.000 0.00 0.00 0.00 3.28
4703 5315 3.441572 CGTGCCCAATCAAGAGATTTCTT 59.558 43.478 0.00 0.00 42.46 2.52
4758 5370 3.137360 AGAGGAGATAAAGAATGGCACCC 59.863 47.826 0.00 0.00 0.00 4.61
4859 5471 2.990479 GACCCTGGAGGCATTCGT 59.010 61.111 0.00 0.00 40.58 3.85
4863 5475 3.461773 CGACGACCCTGGAGGCAT 61.462 66.667 0.00 0.00 40.58 4.40
4902 5514 0.036010 CTTGGGCTCCTCAACGATGT 60.036 55.000 0.00 0.00 0.00 3.06
4908 5520 1.434188 TCTGTTCTTGGGCTCCTCAA 58.566 50.000 0.00 0.00 0.00 3.02
4945 5557 2.034066 GGGGCAGCTGCAACAGTA 59.966 61.111 37.63 0.00 44.36 2.74
4989 5601 4.022935 GCATGACAAAGATCCAAGTTGACA 60.023 41.667 3.87 0.00 32.92 3.58
4996 5608 2.041485 TCCAGGCATGACAAAGATCCAA 59.959 45.455 0.00 0.00 0.00 3.53
5030 5642 4.085363 CGACATTCGAGATGTGCAATACTC 60.085 45.833 15.02 0.00 43.74 2.59
5034 5663 2.621338 ACGACATTCGAGATGTGCAAT 58.379 42.857 15.02 0.00 43.74 3.56
5042 5671 2.035449 ACAAGGTCAACGACATTCGAGA 59.965 45.455 1.94 0.00 43.74 4.04
5058 5712 6.112734 TGAAACTATACATGCACCTACAAGG 58.887 40.000 0.00 0.00 42.49 3.61


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

AutoCloner maintained by Alex Coulton.