Multiple sequence alignment - TraesCS4B01G300400

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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 TraesCS4B01G300400 chr4B 100.000 4966 0 0 1 4966 586867655 586872620 0.000000e+00 9171.0
1 TraesCS4B01G300400 chr4B 94.382 178 7 2 1853 2030 586869449 586869623 2.280000e-68 270.0
2 TraesCS4B01G300400 chr4B 94.382 178 7 2 1795 1969 586869507 586869684 2.280000e-68 270.0
3 TraesCS4B01G300400 chr4B 91.667 120 7 2 1911 2030 586869449 586869565 3.980000e-36 163.0
4 TraesCS4B01G300400 chr4B 91.667 120 7 2 1795 1911 586869565 586869684 3.980000e-36 163.0
5 TraesCS4B01G300400 chr4B 87.097 62 5 2 1969 2030 586869449 586869507 3.210000e-07 67.6
6 TraesCS4B01G300400 chr4B 87.097 62 5 2 1795 1853 586869623 586869684 3.210000e-07 67.6
7 TraesCS4B01G300400 chr4A 92.383 2442 137 22 1977 4403 3111956 3109549 0.000000e+00 3434.0
8 TraesCS4B01G300400 chr4A 94.441 1871 80 14 1 1861 3113788 3111932 0.000000e+00 2857.0
9 TraesCS4B01G300400 chr4A 95.588 68 2 1 1853 1919 3111999 3111932 1.890000e-19 108.0
10 TraesCS4B01G300400 chr4A 98.361 61 1 0 1911 1971 3111999 3111939 1.890000e-19 108.0
11 TraesCS4B01G300400 chr4A 88.710 62 4 2 1969 2030 3111999 3111941 6.900000e-09 73.1
12 TraesCS4B01G300400 chr4D 92.101 2418 159 18 1977 4380 468295954 468298353 0.000000e+00 3378.0
13 TraesCS4B01G300400 chr4D 95.358 1874 68 10 1 1861 468294111 468295978 0.000000e+00 2961.0
14 TraesCS4B01G300400 chr4D 83.627 397 37 13 4554 4935 468298561 468298944 1.020000e-91 348.0
15 TraesCS4B01G300400 chr4D 94.118 68 3 1 1853 1919 468295911 468295978 8.790000e-18 102.0
16 TraesCS4B01G300400 chr4D 98.276 58 1 0 1911 1968 468295911 468295968 8.790000e-18 102.0
17 TraesCS4B01G300400 chr4D 88.525 61 4 2 1969 2029 468295911 468295968 2.480000e-08 71.3


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 TraesCS4B01G300400 chr4B 586867655 586872620 4965 False 1453.171429 9171 92.327429 1 4966 7 chr4B.!!$F1 4965
1 TraesCS4B01G300400 chr4A 3109549 3113788 4239 True 1316.020000 3434 93.896600 1 4403 5 chr4A.!!$R1 4402
2 TraesCS4B01G300400 chr4D 468294111 468298944 4833 False 1160.383333 3378 92.000833 1 4935 6 chr4D.!!$F1 4934

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
587 599 3.262420 GTTTGCATGTCCAGATCGTACT 58.738 45.455 0.00 0.0 0.0 2.73 F
1234 1251 0.313987 GGTTGAACAAAAGGCTCCCG 59.686 55.000 0.00 0.0 0.0 5.14 F
2168 2186 1.205893 GAGGTCGGTCTGCTGAAGAAT 59.794 52.381 0.00 0.0 36.4 2.40 F
2370 2388 0.397816 GGAGGAAGGAGGAGCTAGCA 60.398 60.000 18.83 0.0 0.0 3.49 F
2977 2995 1.277557 AGATGAAGTCTGTGCCCTGAC 59.722 52.381 0.00 0.0 39.2 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1737 1754 0.100503 GCACTGGTTCTGTTTTGCGT 59.899 50.0 0.00 0.00 0.00 5.24 R
2276 2294 0.107312 CATGTTCTGCCCTCTCCAGG 60.107 60.0 0.00 0.00 39.98 4.45 R
3440 3458 0.038251 TGAGAGACGCGTGCTCATTT 60.038 50.0 27.78 14.64 34.02 2.32 R
3518 3536 0.038744 CCTTGGCCATCTCAACCTGT 59.961 55.0 6.09 0.00 0.00 4.00 R
4515 4569 0.102844 GCAGCAAGCAAAACCACTGA 59.897 50.0 0.00 0.00 44.79 3.41 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
54 55 8.740616 ACCAAATATTGCATTAGGGGAATAAT 57.259 30.769 0.00 0.00 35.21 1.28
240 242 5.446473 CGTTTTGAAGATCCTTCATCCTTCG 60.446 44.000 9.83 7.62 30.71 3.79
250 252 6.985188 TCCTTCATCCTTCGATTACAAAAG 57.015 37.500 0.00 0.00 0.00 2.27
261 263 5.483811 TCGATTACAAAAGATACAGGCACA 58.516 37.500 0.00 0.00 0.00 4.57
367 371 7.327032 GCTCAGTTGTAATCATGTTTTCCTTTC 59.673 37.037 0.00 0.00 0.00 2.62
369 373 8.690884 TCAGTTGTAATCATGTTTTCCTTTCAA 58.309 29.630 0.00 0.00 0.00 2.69
370 380 8.755018 CAGTTGTAATCATGTTTTCCTTTCAAC 58.245 33.333 0.00 0.00 0.00 3.18
462 473 8.546597 AGTTGGATTATTTTGTTTAACCATGC 57.453 30.769 0.00 0.00 0.00 4.06
529 540 6.738114 AGCAATATTGGTTTTACATGGATCG 58.262 36.000 14.31 0.00 34.89 3.69
587 599 3.262420 GTTTGCATGTCCAGATCGTACT 58.738 45.455 0.00 0.00 0.00 2.73
588 600 3.610040 TTGCATGTCCAGATCGTACTT 57.390 42.857 0.00 0.00 0.00 2.24
825 842 6.449698 TGAAGACCTTCATTGAAAAATCTGC 58.550 36.000 8.27 3.53 43.90 4.26
866 883 6.299023 TGCTGAGTTTATTGTAGTTGTGTG 57.701 37.500 0.00 0.00 0.00 3.82
867 884 5.820423 TGCTGAGTTTATTGTAGTTGTGTGT 59.180 36.000 0.00 0.00 0.00 3.72
868 885 6.136071 GCTGAGTTTATTGTAGTTGTGTGTG 58.864 40.000 0.00 0.00 0.00 3.82
876 893 4.671880 TGTAGTTGTGTGTGTGTGTTTC 57.328 40.909 0.00 0.00 0.00 2.78
877 894 4.065789 TGTAGTTGTGTGTGTGTGTTTCA 58.934 39.130 0.00 0.00 0.00 2.69
881 898 3.500558 TGTGTGTGTGTGTTTCAATGG 57.499 42.857 0.00 0.00 0.00 3.16
899 916 9.566432 TTTCAATGGTTTACTTTATTTGGCAAT 57.434 25.926 0.00 0.00 0.00 3.56
1025 1042 4.712337 GGTAGAGGAGAATCTTGAAGTGGA 59.288 45.833 0.00 0.00 33.73 4.02
1075 1092 5.124457 TCTGTGCAAAATTCATTAGAGCCTC 59.876 40.000 0.00 0.00 0.00 4.70
1104 1121 5.181748 ACTGAAGGCACTAATGAAGATGAC 58.818 41.667 0.00 0.00 38.49 3.06
1109 1126 5.316167 AGGCACTAATGAAGATGACAACAA 58.684 37.500 0.00 0.00 36.02 2.83
1234 1251 0.313987 GGTTGAACAAAAGGCTCCCG 59.686 55.000 0.00 0.00 0.00 5.14
1266 1283 7.395190 TTCCATAATTGGTTCATCAGAAGTG 57.605 36.000 0.00 0.00 44.06 3.16
1316 1333 6.814506 AGAAGATTCTCACAGTTTTCCATG 57.185 37.500 0.00 0.00 29.94 3.66
1375 1392 6.345096 TCAGTGACTTGATGACAGTTCATA 57.655 37.500 0.00 0.00 42.95 2.15
1428 1445 5.160641 CAGACTTCAGTTAGCTCAAGAGAC 58.839 45.833 0.00 0.00 0.00 3.36
1686 1703 2.675844 CGATACAACGAAGCCCATTGAA 59.324 45.455 0.00 0.00 35.09 2.69
1737 1754 3.568007 GTGGTAGCATCAACTGGAAAACA 59.432 43.478 0.00 0.00 0.00 2.83
1844 1861 9.525409 AAATTATCTTTCATTTGCATCAGCTAC 57.475 29.630 0.00 0.00 42.74 3.58
1845 1862 7.628769 TTATCTTTCATTTGCATCAGCTACA 57.371 32.000 0.00 0.00 42.74 2.74
1846 1863 5.963176 TCTTTCATTTGCATCAGCTACAA 57.037 34.783 0.00 0.00 42.74 2.41
1847 1864 5.702865 TCTTTCATTTGCATCAGCTACAAC 58.297 37.500 0.00 0.00 42.74 3.32
1848 1865 5.474532 TCTTTCATTTGCATCAGCTACAACT 59.525 36.000 0.00 0.00 42.74 3.16
1849 1866 5.710513 TTCATTTGCATCAGCTACAACTT 57.289 34.783 0.00 0.00 42.74 2.66
1850 1867 6.816134 TTCATTTGCATCAGCTACAACTTA 57.184 33.333 0.00 0.00 42.74 2.24
1851 1868 6.816134 TCATTTGCATCAGCTACAACTTAA 57.184 33.333 0.00 0.00 42.74 1.85
1852 1869 7.395190 TCATTTGCATCAGCTACAACTTAAT 57.605 32.000 0.00 0.00 42.74 1.40
1853 1870 8.504812 TCATTTGCATCAGCTACAACTTAATA 57.495 30.769 0.00 0.00 42.74 0.98
1854 1871 8.955388 TCATTTGCATCAGCTACAACTTAATAA 58.045 29.630 0.00 0.00 42.74 1.40
1855 1872 9.740239 CATTTGCATCAGCTACAACTTAATAAT 57.260 29.630 0.00 0.00 42.74 1.28
1857 1874 9.787532 TTTGCATCAGCTACAACTTAATAATTC 57.212 29.630 0.00 0.00 42.74 2.17
1858 1875 8.737168 TGCATCAGCTACAACTTAATAATTCT 57.263 30.769 0.00 0.00 42.74 2.40
1859 1876 8.830580 TGCATCAGCTACAACTTAATAATTCTC 58.169 33.333 0.00 0.00 42.74 2.87
1860 1877 9.050601 GCATCAGCTACAACTTAATAATTCTCT 57.949 33.333 0.00 0.00 37.91 3.10
1863 1880 9.809096 TCAGCTACAACTTAATAATTCTCTCAG 57.191 33.333 0.00 0.00 0.00 3.35
1864 1881 8.547069 CAGCTACAACTTAATAATTCTCTCAGC 58.453 37.037 0.00 0.00 0.00 4.26
1865 1882 8.482128 AGCTACAACTTAATAATTCTCTCAGCT 58.518 33.333 0.00 0.00 0.00 4.24
1866 1883 9.751542 GCTACAACTTAATAATTCTCTCAGCTA 57.248 33.333 0.00 0.00 0.00 3.32
1869 1886 9.944376 ACAACTTAATAATTCTCTCAGCTACAA 57.056 29.630 0.00 0.00 0.00 2.41
1902 1919 9.525409 AAATTATCTTTCATTTGCATCAGCTAC 57.475 29.630 0.00 0.00 42.74 3.58
1903 1920 7.628769 TTATCTTTCATTTGCATCAGCTACA 57.371 32.000 0.00 0.00 42.74 2.74
1904 1921 5.963176 TCTTTCATTTGCATCAGCTACAA 57.037 34.783 0.00 0.00 42.74 2.41
1905 1922 5.702865 TCTTTCATTTGCATCAGCTACAAC 58.297 37.500 0.00 0.00 42.74 3.32
1906 1923 5.474532 TCTTTCATTTGCATCAGCTACAACT 59.525 36.000 0.00 0.00 42.74 3.16
1907 1924 5.710513 TTCATTTGCATCAGCTACAACTT 57.289 34.783 0.00 0.00 42.74 2.66
1908 1925 6.816134 TTCATTTGCATCAGCTACAACTTA 57.184 33.333 0.00 0.00 42.74 2.24
1909 1926 6.816134 TCATTTGCATCAGCTACAACTTAA 57.184 33.333 0.00 0.00 42.74 1.85
1910 1927 7.395190 TCATTTGCATCAGCTACAACTTAAT 57.605 32.000 0.00 0.00 42.74 1.40
1911 1928 8.504812 TCATTTGCATCAGCTACAACTTAATA 57.495 30.769 0.00 0.00 42.74 0.98
1912 1929 8.955388 TCATTTGCATCAGCTACAACTTAATAA 58.045 29.630 0.00 0.00 42.74 1.40
1913 1930 9.740239 CATTTGCATCAGCTACAACTTAATAAT 57.260 29.630 0.00 0.00 42.74 1.28
1915 1932 9.787532 TTTGCATCAGCTACAACTTAATAATTC 57.212 29.630 0.00 0.00 42.74 2.17
1916 1933 8.737168 TGCATCAGCTACAACTTAATAATTCT 57.263 30.769 0.00 0.00 42.74 2.40
1917 1934 8.830580 TGCATCAGCTACAACTTAATAATTCTC 58.169 33.333 0.00 0.00 42.74 2.87
1918 1935 9.050601 GCATCAGCTACAACTTAATAATTCTCT 57.949 33.333 0.00 0.00 37.91 3.10
1921 1938 9.809096 TCAGCTACAACTTAATAATTCTCTCAG 57.191 33.333 0.00 0.00 0.00 3.35
1922 1939 8.547069 CAGCTACAACTTAATAATTCTCTCAGC 58.453 37.037 0.00 0.00 0.00 4.26
1923 1940 8.482128 AGCTACAACTTAATAATTCTCTCAGCT 58.518 33.333 0.00 0.00 0.00 4.24
1924 1941 9.751542 GCTACAACTTAATAATTCTCTCAGCTA 57.248 33.333 0.00 0.00 0.00 3.32
1927 1944 9.944376 ACAACTTAATAATTCTCTCAGCTACAA 57.056 29.630 0.00 0.00 0.00 2.41
1960 1977 9.525409 AAATTATCTTTCATTTGCATCAGCTAC 57.475 29.630 0.00 0.00 42.74 3.58
1961 1978 7.628769 TTATCTTTCATTTGCATCAGCTACA 57.371 32.000 0.00 0.00 42.74 2.74
1962 1979 5.963176 TCTTTCATTTGCATCAGCTACAA 57.037 34.783 0.00 0.00 42.74 2.41
1963 1980 5.702865 TCTTTCATTTGCATCAGCTACAAC 58.297 37.500 0.00 0.00 42.74 3.32
1964 1981 5.474532 TCTTTCATTTGCATCAGCTACAACT 59.525 36.000 0.00 0.00 42.74 3.16
1965 1982 5.710513 TTCATTTGCATCAGCTACAACTT 57.289 34.783 0.00 0.00 42.74 2.66
1966 1983 6.816134 TTCATTTGCATCAGCTACAACTTA 57.184 33.333 0.00 0.00 42.74 2.24
1967 1984 6.816134 TCATTTGCATCAGCTACAACTTAA 57.184 33.333 0.00 0.00 42.74 1.85
1968 1985 7.395190 TCATTTGCATCAGCTACAACTTAAT 57.605 32.000 0.00 0.00 42.74 1.40
1969 1986 8.504812 TCATTTGCATCAGCTACAACTTAATA 57.495 30.769 0.00 0.00 42.74 0.98
1970 1987 8.955388 TCATTTGCATCAGCTACAACTTAATAA 58.045 29.630 0.00 0.00 42.74 1.40
1971 1988 9.740239 CATTTGCATCAGCTACAACTTAATAAT 57.260 29.630 0.00 0.00 42.74 1.28
1973 1990 9.787532 TTTGCATCAGCTACAACTTAATAATTC 57.212 29.630 0.00 0.00 42.74 2.17
1974 1991 8.737168 TGCATCAGCTACAACTTAATAATTCT 57.263 30.769 0.00 0.00 42.74 2.40
1975 1992 8.830580 TGCATCAGCTACAACTTAATAATTCTC 58.169 33.333 0.00 0.00 42.74 2.87
1976 1993 9.050601 GCATCAGCTACAACTTAATAATTCTCT 57.949 33.333 0.00 0.00 37.91 3.10
2082 2099 6.481984 GCTTGAGCACTTACAGACATATTTC 58.518 40.000 0.00 0.00 41.59 2.17
2154 2172 1.336887 ACCATGTCAAACTCGAGGTCG 60.337 52.381 18.41 0.00 41.45 4.79
2168 2186 1.205893 GAGGTCGGTCTGCTGAAGAAT 59.794 52.381 0.00 0.00 36.40 2.40
2276 2294 7.147976 AGCTTATTGAAAACCTGAAACATGAC 58.852 34.615 0.00 0.00 0.00 3.06
2330 2348 4.223700 GCCAAGGAGGATTTGGATTTCTTT 59.776 41.667 8.13 0.00 46.42 2.52
2370 2388 0.397816 GGAGGAAGGAGGAGCTAGCA 60.398 60.000 18.83 0.00 0.00 3.49
2453 2471 4.082463 GTGTCCAAACTGAAGTTGGTCAAA 60.082 41.667 4.99 0.00 38.44 2.69
2522 2540 6.514947 TGAACAGGACATTTCCATTGAAAAG 58.485 36.000 0.00 0.00 45.72 2.27
2573 2591 2.093553 GTCTGAGAAGCAAGCAGAGGAT 60.094 50.000 0.00 0.00 39.15 3.24
2643 2661 2.029288 ACGTGCCGTGATGCTGAAG 61.029 57.895 0.00 0.00 39.18 3.02
2699 2717 3.585732 AGGACCGTCTTAAATGGGAGAAA 59.414 43.478 0.00 0.00 38.50 2.52
2771 2789 6.617782 TCCTCTGTTGAAGATCTGAAATCT 57.382 37.500 0.00 0.00 33.29 2.40
2777 2795 5.642491 TGTTGAAGATCTGAAATCTGAGCTG 59.358 40.000 8.53 0.00 39.81 4.24
2782 2800 5.184711 AGATCTGAAATCTGAGCTGGAAAC 58.815 41.667 7.19 0.00 38.75 2.78
2831 2849 6.292865 GCAACGAAGAGCTAAATGCATATGTA 60.293 38.462 0.00 0.00 45.94 2.29
2903 2921 4.154942 AGACCATGCAAGAAGAAACCATT 58.845 39.130 0.00 0.00 0.00 3.16
2904 2922 4.219288 AGACCATGCAAGAAGAAACCATTC 59.781 41.667 0.00 0.00 35.70 2.67
2924 2942 8.954350 ACCATTCTTCTATCAAGAAATGAACTG 58.046 33.333 1.09 0.00 42.54 3.16
2977 2995 1.277557 AGATGAAGTCTGTGCCCTGAC 59.722 52.381 0.00 0.00 39.20 3.51
2982 3000 1.717032 AGTCTGTGCCCTGACAGTTA 58.283 50.000 8.76 0.00 43.38 2.24
2993 3011 2.354503 CCTGACAGTTACTGCTGCATCT 60.355 50.000 12.80 0.00 39.96 2.90
3149 3167 2.171341 AGGAGAAGAAAACCTGCGAC 57.829 50.000 0.00 0.00 32.39 5.19
3156 3174 2.154462 AGAAAACCTGCGACAGAATGG 58.846 47.619 8.20 0.00 43.62 3.16
3181 3199 2.282745 GCCTGGGCTTCTGCAAGT 60.283 61.111 4.12 0.00 41.91 3.16
3230 3248 3.199508 AGTCTCTTGCTATGAAGGCACAT 59.800 43.478 3.08 3.08 39.55 3.21
3325 3343 1.536943 GCAGTCCTGAAGGAGACGGT 61.537 60.000 0.00 0.00 46.49 4.83
3353 3371 2.300956 AAGAGTCTGAGAGGCTGTCA 57.699 50.000 14.20 14.20 24.78 3.58
3434 3452 3.740764 GCTCTCCTGGAATGATCACACTC 60.741 52.174 0.00 0.00 0.00 3.51
3440 3458 4.142160 CCTGGAATGATCACACTCGACTTA 60.142 45.833 0.00 0.00 0.00 2.24
3441 3459 5.400066 TGGAATGATCACACTCGACTTAA 57.600 39.130 0.00 0.00 0.00 1.85
3446 3464 7.254252 GGAATGATCACACTCGACTTAAATGAG 60.254 40.741 0.00 0.00 35.85 2.90
3489 3507 1.340795 CCCATCAGGCAGAAGAGCTTT 60.341 52.381 0.00 0.00 34.17 3.51
3518 3536 6.016024 ACAAGAAGATATCTTTTGCAGTTGCA 60.016 34.615 24.71 2.03 46.39 4.08
3551 3569 1.551452 CCAAGGACTCCGAGTCTCTT 58.449 55.000 24.45 21.32 44.46 2.85
3633 3651 2.887360 CCCAAAAGCAGGCCGATG 59.113 61.111 0.00 0.00 0.00 3.84
3665 3683 1.980232 CAAGCTGGCCATGGAGCAA 60.980 57.895 23.41 0.00 37.70 3.91
3668 3686 2.119655 GCTGGCCATGGAGCAAGAG 61.120 63.158 18.40 1.87 35.67 2.85
3733 3751 1.131883 CGCTGAGGCTTTGAAATCTGG 59.868 52.381 0.00 0.00 36.09 3.86
3753 3771 6.234920 TCTGGAACTAAACATTCAAATCCGA 58.765 36.000 0.00 0.00 0.00 4.55
3758 3776 6.834168 ACTAAACATTCAAATCCGATGGTT 57.166 33.333 0.00 0.00 0.00 3.67
3761 3779 8.966868 ACTAAACATTCAAATCCGATGGTTATT 58.033 29.630 0.00 0.00 0.00 1.40
3886 3904 3.681835 AGGTTCGCGCGAGAAGGT 61.682 61.111 32.74 12.83 0.00 3.50
3896 3914 0.036858 GCGAGAAGGTGAAGAAGGCT 60.037 55.000 0.00 0.00 0.00 4.58
3927 3945 1.069090 TTCCTCCGCCGTATGATGC 59.931 57.895 0.00 0.00 0.00 3.91
3936 3954 1.743772 GCCGTATGATGCTGTTCCTGT 60.744 52.381 0.00 0.00 0.00 4.00
3997 4015 0.321564 TCCTTCTGGCGGATGTGTTG 60.322 55.000 0.00 0.00 0.00 3.33
3998 4016 0.321564 CCTTCTGGCGGATGTGTTGA 60.322 55.000 0.00 0.00 0.00 3.18
4025 4043 3.897141 TTCCCCGCAAAAAGAAAAAGT 57.103 38.095 0.00 0.00 0.00 2.66
4141 4170 3.149196 GGCTGTGAAGTCTTCATGGAAA 58.851 45.455 18.08 2.46 42.47 3.13
4179 4222 6.809196 AGAAAACGTGAACTTGTAAATTTGCA 59.191 30.769 4.71 4.71 0.00 4.08
4188 4231 8.035394 TGAACTTGTAAATTTGCAAAGGTGTAA 58.965 29.630 20.05 8.96 32.49 2.41
4190 4233 8.419076 ACTTGTAAATTTGCAAAGGTGTAAAG 57.581 30.769 20.05 16.71 41.75 1.85
4263 4309 3.318017 CTGTAACTTTGACCGACTCCAG 58.682 50.000 0.00 0.00 0.00 3.86
4273 4319 1.364626 CCGACTCCAGTGCTTGATGC 61.365 60.000 0.00 0.00 43.25 3.91
4289 4335 4.025040 TGATGCACTGGATCTTGAGTTT 57.975 40.909 11.42 0.00 0.00 2.66
4294 4340 4.937620 TGCACTGGATCTTGAGTTTGATAC 59.062 41.667 0.00 0.00 0.00 2.24
4354 4408 2.203112 TGCATGCATCCGGCTCTC 60.203 61.111 18.46 0.00 45.15 3.20
4385 4439 5.124457 GGATCTGATGCTGTTAACATTGTGT 59.876 40.000 9.13 0.00 0.00 3.72
4386 4440 5.361135 TCTGATGCTGTTAACATTGTGTG 57.639 39.130 9.13 0.00 0.00 3.82
4390 4444 2.424956 TGCTGTTAACATTGTGTGTGCA 59.575 40.909 9.13 9.60 41.14 4.57
4392 4446 3.243035 GCTGTTAACATTGTGTGTGCAGA 60.243 43.478 9.13 0.00 41.14 4.26
4394 4448 3.314913 TGTTAACATTGTGTGTGCAGAGG 59.685 43.478 3.59 0.00 41.14 3.69
4407 4461 0.606673 GCAGAGGGTTTCAGTGGGTC 60.607 60.000 0.00 0.00 0.00 4.46
4423 4477 1.081175 GTCTTGCAAGGCGCTTTCC 60.081 57.895 25.73 0.00 43.06 3.13
4424 4478 1.228245 TCTTGCAAGGCGCTTTCCT 60.228 52.632 25.73 0.00 43.06 3.36
4425 4479 1.211190 CTTGCAAGGCGCTTTCCTC 59.789 57.895 19.14 0.00 43.06 3.71
4426 4480 1.228245 TTGCAAGGCGCTTTCCTCT 60.228 52.632 7.64 0.00 43.06 3.69
4427 4481 1.518056 TTGCAAGGCGCTTTCCTCTG 61.518 55.000 7.64 0.00 43.06 3.35
4428 4482 1.672356 GCAAGGCGCTTTCCTCTGA 60.672 57.895 7.64 0.00 34.82 3.27
4429 4483 1.028868 GCAAGGCGCTTTCCTCTGAT 61.029 55.000 7.64 0.00 34.82 2.90
4430 4484 1.457346 CAAGGCGCTTTCCTCTGATT 58.543 50.000 7.64 0.00 34.82 2.57
4431 4485 1.815003 CAAGGCGCTTTCCTCTGATTT 59.185 47.619 7.64 0.00 34.82 2.17
4432 4486 1.743996 AGGCGCTTTCCTCTGATTTC 58.256 50.000 7.64 0.00 0.00 2.17
4437 4491 3.181512 GCGCTTTCCTCTGATTTCTTCTG 60.182 47.826 0.00 0.00 0.00 3.02
4448 4502 4.389374 TGATTTCTTCTGGAGTGTGAACC 58.611 43.478 0.00 0.00 0.00 3.62
4458 4512 2.033424 GGAGTGTGAACCTTGCTCAAAC 59.967 50.000 0.00 0.00 32.07 2.93
4461 4515 2.423538 GTGTGAACCTTGCTCAAACTGT 59.576 45.455 0.00 0.00 29.72 3.55
4462 4516 3.088532 TGTGAACCTTGCTCAAACTGTT 58.911 40.909 0.00 0.00 0.00 3.16
4463 4517 3.128589 TGTGAACCTTGCTCAAACTGTTC 59.871 43.478 0.00 10.09 34.25 3.18
4464 4518 3.128589 GTGAACCTTGCTCAAACTGTTCA 59.871 43.478 13.35 13.35 39.59 3.18
4468 4522 2.551459 CCTTGCTCAAACTGTTCAGAGG 59.449 50.000 18.57 8.17 0.00 3.69
4471 4525 2.224378 TGCTCAAACTGTTCAGAGGAGG 60.224 50.000 18.57 2.19 0.00 4.30
4472 4526 2.873649 GCTCAAACTGTTCAGAGGAGGG 60.874 54.545 18.57 1.92 0.00 4.30
4473 4527 2.370189 CTCAAACTGTTCAGAGGAGGGT 59.630 50.000 6.83 0.00 0.00 4.34
4475 4529 3.971305 TCAAACTGTTCAGAGGAGGGTTA 59.029 43.478 6.83 0.00 0.00 2.85
4476 4530 4.065789 CAAACTGTTCAGAGGAGGGTTAC 58.934 47.826 6.83 0.00 0.00 2.50
4478 4532 2.900546 ACTGTTCAGAGGAGGGTTACTG 59.099 50.000 6.83 0.00 0.00 2.74
4479 4533 2.900546 CTGTTCAGAGGAGGGTTACTGT 59.099 50.000 0.00 0.00 0.00 3.55
4480 4534 2.897969 TGTTCAGAGGAGGGTTACTGTC 59.102 50.000 0.00 0.00 0.00 3.51
4481 4535 2.233305 TCAGAGGAGGGTTACTGTCC 57.767 55.000 0.00 0.00 0.00 4.02
4482 4536 1.717077 TCAGAGGAGGGTTACTGTCCT 59.283 52.381 5.89 5.89 43.76 3.85
4483 4537 1.827969 CAGAGGAGGGTTACTGTCCTG 59.172 57.143 10.07 0.00 41.00 3.86
4484 4538 1.433592 AGAGGAGGGTTACTGTCCTGT 59.566 52.381 10.07 4.52 41.00 4.00
4485 4539 1.550976 GAGGAGGGTTACTGTCCTGTG 59.449 57.143 10.07 0.00 41.00 3.66
4495 4549 5.105310 GGTTACTGTCCTGTGTACATCTGAT 60.105 44.000 0.00 0.00 0.00 2.90
4502 4556 5.048782 GTCCTGTGTACATCTGATTGCAAAA 60.049 40.000 1.71 0.00 0.00 2.44
4503 4557 5.181811 TCCTGTGTACATCTGATTGCAAAAG 59.818 40.000 1.71 4.55 0.00 2.27
4504 4558 5.375417 TGTGTACATCTGATTGCAAAAGG 57.625 39.130 1.71 0.00 0.00 3.11
4505 4559 4.826733 TGTGTACATCTGATTGCAAAAGGT 59.173 37.500 1.71 0.00 0.00 3.50
4506 4560 5.301551 TGTGTACATCTGATTGCAAAAGGTT 59.698 36.000 1.71 0.00 0.00 3.50
4507 4561 6.183360 TGTGTACATCTGATTGCAAAAGGTTT 60.183 34.615 1.71 0.00 0.00 3.27
4508 4562 6.363357 GTGTACATCTGATTGCAAAAGGTTTC 59.637 38.462 1.71 0.00 0.00 2.78
4509 4563 5.534207 ACATCTGATTGCAAAAGGTTTCA 57.466 34.783 1.71 0.00 0.00 2.69
4510 4564 5.535333 ACATCTGATTGCAAAAGGTTTCAG 58.465 37.500 16.05 16.05 33.55 3.02
4511 4565 5.302568 ACATCTGATTGCAAAAGGTTTCAGA 59.697 36.000 23.36 23.36 42.50 3.27
4512 4566 5.186996 TCTGATTGCAAAAGGTTTCAGAC 57.813 39.130 19.36 0.00 35.82 3.51
4513 4567 4.889409 TCTGATTGCAAAAGGTTTCAGACT 59.111 37.500 19.36 0.00 35.82 3.24
4514 4568 5.360714 TCTGATTGCAAAAGGTTTCAGACTT 59.639 36.000 19.36 0.00 35.82 3.01
4515 4569 5.976458 TGATTGCAAAAGGTTTCAGACTTT 58.024 33.333 1.71 0.00 38.48 2.66
4516 4570 6.042143 TGATTGCAAAAGGTTTCAGACTTTC 58.958 36.000 1.71 0.00 35.99 2.62
4517 4571 5.398603 TTGCAAAAGGTTTCAGACTTTCA 57.601 34.783 0.00 0.00 35.99 2.69
4518 4572 4.997565 TGCAAAAGGTTTCAGACTTTCAG 58.002 39.130 0.00 0.00 35.99 3.02
4523 4577 4.236527 AGGTTTCAGACTTTCAGTGGTT 57.763 40.909 0.00 0.00 0.00 3.67
4524 4578 4.600062 AGGTTTCAGACTTTCAGTGGTTT 58.400 39.130 0.00 0.00 0.00 3.27
4528 4582 3.620488 TCAGACTTTCAGTGGTTTTGCT 58.380 40.909 0.00 0.00 0.00 3.91
4557 4693 7.370383 TGCAAGTATTCTTCTGAATTTTGGTC 58.630 34.615 12.80 0.00 42.37 4.02
4561 4697 2.790433 TCTTCTGAATTTTGGTCCCGG 58.210 47.619 0.00 0.00 0.00 5.73
4563 4699 0.958382 TCTGAATTTTGGTCCCGGCG 60.958 55.000 0.00 0.00 0.00 6.46
4564 4700 2.180769 GAATTTTGGTCCCGGCGC 59.819 61.111 0.00 0.00 0.00 6.53
4581 4717 4.680237 CCGGCGCTCAACACCTCA 62.680 66.667 7.64 0.00 0.00 3.86
4583 4719 2.034879 CGGCGCTCAACACCTCAAT 61.035 57.895 7.64 0.00 0.00 2.57
4584 4720 0.739462 CGGCGCTCAACACCTCAATA 60.739 55.000 7.64 0.00 0.00 1.90
4585 4721 1.668419 GGCGCTCAACACCTCAATAT 58.332 50.000 7.64 0.00 0.00 1.28
4587 4723 2.032178 GGCGCTCAACACCTCAATATTC 59.968 50.000 7.64 0.00 0.00 1.75
4588 4724 2.677836 GCGCTCAACACCTCAATATTCA 59.322 45.455 0.00 0.00 0.00 2.57
4589 4725 3.242543 GCGCTCAACACCTCAATATTCAG 60.243 47.826 0.00 0.00 0.00 3.02
4590 4726 3.310774 CGCTCAACACCTCAATATTCAGG 59.689 47.826 3.44 3.44 35.69 3.86
4591 4727 3.065925 GCTCAACACCTCAATATTCAGGC 59.934 47.826 5.11 0.00 32.32 4.85
4593 4729 4.264253 TCAACACCTCAATATTCAGGCTG 58.736 43.478 8.58 8.58 32.32 4.85
4594 4730 4.019411 TCAACACCTCAATATTCAGGCTGA 60.019 41.667 14.43 14.43 32.32 4.26
4595 4731 4.148128 ACACCTCAATATTCAGGCTGAG 57.852 45.455 17.91 5.82 35.99 3.35
4596 4732 2.877168 CACCTCAATATTCAGGCTGAGC 59.123 50.000 17.91 0.00 35.09 4.26
4597 4733 2.141517 CCTCAATATTCAGGCTGAGCG 58.858 52.381 17.91 5.91 35.09 5.03
4598 4734 2.224137 CCTCAATATTCAGGCTGAGCGA 60.224 50.000 17.91 3.26 35.09 4.93
4639 4776 2.513666 GGATTGTCGGCGGCATGA 60.514 61.111 17.58 0.08 0.00 3.07
4640 4777 2.112198 GGATTGTCGGCGGCATGAA 61.112 57.895 17.58 0.00 0.00 2.57
4642 4779 2.322999 GATTGTCGGCGGCATGAACC 62.323 60.000 17.58 0.00 0.00 3.62
4650 4787 2.358247 GGCATGAACCGTGGACGT 60.358 61.111 0.00 0.00 37.74 4.34
4652 4789 1.959226 GCATGAACCGTGGACGTGT 60.959 57.895 0.00 0.00 37.74 4.49
4653 4790 1.897398 GCATGAACCGTGGACGTGTC 61.897 60.000 0.00 0.00 37.74 3.67
4678 4817 2.568090 CGCCAACCAACATGCTCC 59.432 61.111 0.00 0.00 0.00 4.70
4717 4856 4.323792 CCTGGCATATCATATTCCTTCCGT 60.324 45.833 0.00 0.00 0.00 4.69
4721 4860 5.338056 GGCATATCATATTCCTTCCGTGGTA 60.338 44.000 0.00 0.00 0.00 3.25
4745 4884 3.567797 GCCATTGTCGGCGCTCTC 61.568 66.667 7.64 0.00 43.52 3.20
4746 4885 2.892425 CCATTGTCGGCGCTCTCC 60.892 66.667 7.64 0.00 0.00 3.71
4747 4886 2.892425 CATTGTCGGCGCTCTCCC 60.892 66.667 7.64 0.00 0.00 4.30
4789 4931 1.172180 CCCTCAACTTGCCGCAAGAA 61.172 55.000 34.38 19.53 43.42 2.52
4806 4948 4.647615 AGAAGCTGTCGCGCACGT 62.648 61.111 8.75 0.00 42.32 4.49
4807 4949 4.122515 GAAGCTGTCGCGCACGTC 62.123 66.667 8.75 2.85 42.32 4.34
4864 5010 1.027357 ATTTCCATGCCATCGTGAGC 58.973 50.000 0.00 0.00 0.00 4.26
4888 5034 6.470235 GCGAGAATTGTGATAAACCATTTCTG 59.530 38.462 0.00 0.00 0.00 3.02
4891 5037 9.994432 GAGAATTGTGATAAACCATTTCTGTAG 57.006 33.333 0.00 0.00 0.00 2.74
4901 5047 3.758554 ACCATTTCTGTAGGCACACATTC 59.241 43.478 0.00 0.00 0.00 2.67
4926 5072 9.768662 TCCACCGTTTATTTAGTTAATATCCTC 57.231 33.333 0.00 0.00 0.00 3.71
4927 5073 8.996271 CCACCGTTTATTTAGTTAATATCCTCC 58.004 37.037 0.00 0.00 0.00 4.30
4938 5084 9.976511 TTAGTTAATATCCTCCGTAAACTGATG 57.023 33.333 0.00 0.00 0.00 3.07
4939 5085 8.019656 AGTTAATATCCTCCGTAAACTGATGT 57.980 34.615 0.00 0.00 0.00 3.06
4940 5086 9.139734 AGTTAATATCCTCCGTAAACTGATGTA 57.860 33.333 0.00 0.00 0.00 2.29
4941 5087 9.754382 GTTAATATCCTCCGTAAACTGATGTAA 57.246 33.333 0.00 0.00 0.00 2.41
4942 5088 9.976511 TTAATATCCTCCGTAAACTGATGTAAG 57.023 33.333 0.00 0.00 0.00 2.34
4943 5089 7.834881 ATATCCTCCGTAAACTGATGTAAGA 57.165 36.000 0.00 0.00 0.00 2.10
4944 5090 6.732896 ATCCTCCGTAAACTGATGTAAGAT 57.267 37.500 0.00 0.00 0.00 2.40
4945 5091 6.145338 TCCTCCGTAAACTGATGTAAGATC 57.855 41.667 0.00 0.00 0.00 2.75
4946 5092 5.892119 TCCTCCGTAAACTGATGTAAGATCT 59.108 40.000 0.00 0.00 0.00 2.75
4947 5093 6.380274 TCCTCCGTAAACTGATGTAAGATCTT 59.620 38.462 13.56 13.56 0.00 2.40
4948 5094 7.042335 CCTCCGTAAACTGATGTAAGATCTTT 58.958 38.462 14.36 0.00 0.00 2.52
4949 5095 7.222999 CCTCCGTAAACTGATGTAAGATCTTTC 59.777 40.741 14.36 9.34 0.00 2.62
4950 5096 7.837863 TCCGTAAACTGATGTAAGATCTTTCT 58.162 34.615 14.36 0.00 0.00 2.52
4951 5097 8.311836 TCCGTAAACTGATGTAAGATCTTTCTT 58.688 33.333 14.36 6.73 44.44 2.52
4952 5098 8.383619 CCGTAAACTGATGTAAGATCTTTCTTG 58.616 37.037 14.36 5.66 42.25 3.02
4953 5099 9.140286 CGTAAACTGATGTAAGATCTTTCTTGA 57.860 33.333 14.36 0.17 42.25 3.02
4956 5102 9.566432 AAACTGATGTAAGATCTTTCTTGAACT 57.434 29.630 14.36 0.00 42.25 3.01
4957 5103 8.545229 ACTGATGTAAGATCTTTCTTGAACTG 57.455 34.615 14.36 6.24 42.25 3.16
4958 5104 7.118971 ACTGATGTAAGATCTTTCTTGAACTGC 59.881 37.037 14.36 2.15 42.25 4.40
4959 5105 6.936335 TGATGTAAGATCTTTCTTGAACTGCA 59.064 34.615 14.36 4.54 42.25 4.41
4960 5106 7.445096 TGATGTAAGATCTTTCTTGAACTGCAA 59.555 33.333 14.36 0.00 42.25 4.08
4961 5107 7.566760 TGTAAGATCTTTCTTGAACTGCAAA 57.433 32.000 14.36 0.00 42.25 3.68
4962 5108 7.995289 TGTAAGATCTTTCTTGAACTGCAAAA 58.005 30.769 14.36 0.00 42.25 2.44
4963 5109 8.632679 TGTAAGATCTTTCTTGAACTGCAAAAT 58.367 29.630 14.36 0.00 42.25 1.82
4964 5110 9.122613 GTAAGATCTTTCTTGAACTGCAAAATC 57.877 33.333 14.36 0.00 42.25 2.17
4965 5111 6.376978 AGATCTTTCTTGAACTGCAAAATCG 58.623 36.000 0.00 0.00 35.74 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 55 3.849574 TCATATGTGGGGAAGACTTGGAA 59.150 43.478 1.90 0.00 0.00 3.53
240 242 6.151144 ACCTTGTGCCTGTATCTTTTGTAATC 59.849 38.462 0.00 0.00 0.00 1.75
250 252 3.003480 GTTGAGACCTTGTGCCTGTATC 58.997 50.000 0.00 0.00 0.00 2.24
261 263 6.487299 AACTTACTGAAGAGTTGAGACCTT 57.513 37.500 0.00 0.00 34.96 3.50
462 473 7.988737 TGAGGTCTTCATATGTAAGCAAATTG 58.011 34.615 1.90 0.00 0.00 2.32
529 540 9.772973 ACACCTCTAAATTTTGGTTTAATTTCC 57.227 29.630 0.00 0.00 36.75 3.13
593 605 7.531857 TTGGCTAAATGTTCTTGGACATAAA 57.468 32.000 0.00 0.00 39.25 1.40
748 760 7.228706 TCAGGAAAGGTTTGAACTTGATAAGAC 59.771 37.037 0.00 0.00 0.00 3.01
866 883 8.865590 ATAAAGTAAACCATTGAAACACACAC 57.134 30.769 0.00 0.00 0.00 3.82
867 884 9.877178 AAATAAAGTAAACCATTGAAACACACA 57.123 25.926 0.00 0.00 0.00 3.72
987 1004 2.761208 CTCTACCATTCTTCCGGTCACT 59.239 50.000 0.00 0.00 36.69 3.41
993 1010 4.586841 AGATTCTCCTCTACCATTCTTCCG 59.413 45.833 0.00 0.00 0.00 4.30
1025 1042 3.069586 TGGTGAAGACAAAGACGAGTCAT 59.930 43.478 5.99 0.00 37.23 3.06
1104 1121 6.272318 TGCTGTTTTCTCAAGGTTATTGTTG 58.728 36.000 0.00 0.00 0.00 3.33
1109 1126 5.565439 GCACATGCTGTTTTCTCAAGGTTAT 60.565 40.000 0.00 0.00 38.21 1.89
1266 1283 2.597510 GGCAACCCACTGTGGTCC 60.598 66.667 24.32 15.41 37.76 4.46
1316 1333 3.585862 TCATCAACTTCGTTAGAGGCAC 58.414 45.455 0.00 0.00 0.00 5.01
1341 1358 2.681848 CAAGTCACTGATGGCATCCTTC 59.318 50.000 23.92 10.28 30.46 3.46
1369 1386 7.693952 TGTGTGTTTTCTTCTGAAGTATGAAC 58.306 34.615 16.43 15.31 33.28 3.18
1371 1388 7.520453 GCATGTGTGTTTTCTTCTGAAGTATGA 60.520 37.037 16.43 0.00 33.28 2.15
1375 1392 4.398988 TGCATGTGTGTTTTCTTCTGAAGT 59.601 37.500 16.43 0.00 33.28 3.01
1457 1474 1.901591 ACAGGAAGCACCATCTTGTG 58.098 50.000 2.96 0.00 42.04 3.33
1458 1475 2.107204 AGAACAGGAAGCACCATCTTGT 59.893 45.455 2.96 0.00 38.58 3.16
1686 1703 1.001641 GGCAGCCACCTTCACTGAT 60.002 57.895 6.55 0.00 33.10 2.90
1737 1754 0.100503 GCACTGGTTCTGTTTTGCGT 59.899 50.000 0.00 0.00 0.00 5.24
1838 1855 8.547069 GCTGAGAGAATTATTAAGTTGTAGCTG 58.453 37.037 0.00 0.00 0.00 4.24
1839 1856 8.482128 AGCTGAGAGAATTATTAAGTTGTAGCT 58.518 33.333 0.00 0.00 0.00 3.32
1840 1857 8.655651 AGCTGAGAGAATTATTAAGTTGTAGC 57.344 34.615 0.00 0.00 0.00 3.58
1843 1860 9.944376 TTGTAGCTGAGAGAATTATTAAGTTGT 57.056 29.630 0.00 0.00 0.00 3.32
1876 1893 9.525409 GTAGCTGATGCAAATGAAAGATAATTT 57.475 29.630 0.00 0.00 42.74 1.82
1877 1894 8.689061 TGTAGCTGATGCAAATGAAAGATAATT 58.311 29.630 0.00 0.00 42.74 1.40
1878 1895 8.229253 TGTAGCTGATGCAAATGAAAGATAAT 57.771 30.769 0.00 0.00 42.74 1.28
1879 1896 7.628769 TGTAGCTGATGCAAATGAAAGATAA 57.371 32.000 0.00 0.00 42.74 1.75
1880 1897 7.337689 AGTTGTAGCTGATGCAAATGAAAGATA 59.662 33.333 0.00 0.00 42.74 1.98
1881 1898 6.152323 AGTTGTAGCTGATGCAAATGAAAGAT 59.848 34.615 0.00 0.00 42.74 2.40
1882 1899 5.474532 AGTTGTAGCTGATGCAAATGAAAGA 59.525 36.000 0.00 0.00 42.74 2.52
1883 1900 5.706916 AGTTGTAGCTGATGCAAATGAAAG 58.293 37.500 0.00 0.00 42.74 2.62
1884 1901 5.710513 AGTTGTAGCTGATGCAAATGAAA 57.289 34.783 0.00 0.00 42.74 2.69
1885 1902 5.710513 AAGTTGTAGCTGATGCAAATGAA 57.289 34.783 0.00 0.00 42.74 2.57
1886 1903 6.816134 TTAAGTTGTAGCTGATGCAAATGA 57.184 33.333 0.00 0.00 42.74 2.57
1887 1904 9.740239 ATTATTAAGTTGTAGCTGATGCAAATG 57.260 29.630 0.00 0.00 42.74 2.32
1889 1906 9.787532 GAATTATTAAGTTGTAGCTGATGCAAA 57.212 29.630 0.00 0.00 42.74 3.68
1890 1907 9.177608 AGAATTATTAAGTTGTAGCTGATGCAA 57.822 29.630 0.00 0.00 42.74 4.08
1891 1908 8.737168 AGAATTATTAAGTTGTAGCTGATGCA 57.263 30.769 0.00 0.00 42.74 3.96
1892 1909 9.050601 AGAGAATTATTAAGTTGTAGCTGATGC 57.949 33.333 0.00 0.00 40.05 3.91
1895 1912 9.809096 CTGAGAGAATTATTAAGTTGTAGCTGA 57.191 33.333 0.00 0.00 0.00 4.26
1896 1913 8.547069 GCTGAGAGAATTATTAAGTTGTAGCTG 58.453 37.037 0.00 0.00 0.00 4.24
1897 1914 8.482128 AGCTGAGAGAATTATTAAGTTGTAGCT 58.518 33.333 0.00 0.00 0.00 3.32
1898 1915 8.655651 AGCTGAGAGAATTATTAAGTTGTAGC 57.344 34.615 0.00 0.00 0.00 3.58
1901 1918 9.944376 TTGTAGCTGAGAGAATTATTAAGTTGT 57.056 29.630 0.00 0.00 0.00 3.32
1934 1951 9.525409 GTAGCTGATGCAAATGAAAGATAATTT 57.475 29.630 0.00 0.00 42.74 1.82
1935 1952 8.689061 TGTAGCTGATGCAAATGAAAGATAATT 58.311 29.630 0.00 0.00 42.74 1.40
1936 1953 8.229253 TGTAGCTGATGCAAATGAAAGATAAT 57.771 30.769 0.00 0.00 42.74 1.28
1937 1954 7.628769 TGTAGCTGATGCAAATGAAAGATAA 57.371 32.000 0.00 0.00 42.74 1.75
1938 1955 7.337689 AGTTGTAGCTGATGCAAATGAAAGATA 59.662 33.333 0.00 0.00 42.74 1.98
1939 1956 6.152323 AGTTGTAGCTGATGCAAATGAAAGAT 59.848 34.615 0.00 0.00 42.74 2.40
1940 1957 5.474532 AGTTGTAGCTGATGCAAATGAAAGA 59.525 36.000 0.00 0.00 42.74 2.52
1941 1958 5.706916 AGTTGTAGCTGATGCAAATGAAAG 58.293 37.500 0.00 0.00 42.74 2.62
1942 1959 5.710513 AGTTGTAGCTGATGCAAATGAAA 57.289 34.783 0.00 0.00 42.74 2.69
1943 1960 5.710513 AAGTTGTAGCTGATGCAAATGAA 57.289 34.783 0.00 0.00 42.74 2.57
1944 1961 6.816134 TTAAGTTGTAGCTGATGCAAATGA 57.184 33.333 0.00 0.00 42.74 2.57
1945 1962 9.740239 ATTATTAAGTTGTAGCTGATGCAAATG 57.260 29.630 0.00 0.00 42.74 2.32
1947 1964 9.787532 GAATTATTAAGTTGTAGCTGATGCAAA 57.212 29.630 0.00 0.00 42.74 3.68
1948 1965 9.177608 AGAATTATTAAGTTGTAGCTGATGCAA 57.822 29.630 0.00 0.00 42.74 4.08
1949 1966 8.737168 AGAATTATTAAGTTGTAGCTGATGCA 57.263 30.769 0.00 0.00 42.74 3.96
1950 1967 9.050601 AGAGAATTATTAAGTTGTAGCTGATGC 57.949 33.333 0.00 0.00 40.05 3.91
1953 1970 9.809096 CTGAGAGAATTATTAAGTTGTAGCTGA 57.191 33.333 0.00 0.00 0.00 4.26
1954 1971 8.547069 GCTGAGAGAATTATTAAGTTGTAGCTG 58.453 37.037 0.00 0.00 0.00 4.24
1955 1972 8.482128 AGCTGAGAGAATTATTAAGTTGTAGCT 58.518 33.333 0.00 0.00 0.00 3.32
1956 1973 8.655651 AGCTGAGAGAATTATTAAGTTGTAGC 57.344 34.615 0.00 0.00 0.00 3.58
1959 1976 9.944376 TTGTAGCTGAGAGAATTATTAAGTTGT 57.056 29.630 0.00 0.00 0.00 3.32
2058 2075 6.314896 AGAAATATGTCTGTAAGTGCTCAAGC 59.685 38.462 0.00 0.00 42.50 4.01
2114 2131 3.433173 GGTCACCCACCTGATATACCAAC 60.433 52.174 0.00 0.00 42.84 3.77
2154 2172 6.017400 TGAAATTTCATTCTTCAGCAGACC 57.983 37.500 16.91 0.00 31.01 3.85
2168 2186 5.910637 GCTGTTTGCAATCTGAAATTTCA 57.089 34.783 19.45 19.45 42.31 2.69
2262 2280 2.711009 TCTCCAGGTCATGTTTCAGGTT 59.289 45.455 0.00 0.00 0.00 3.50
2276 2294 0.107312 CATGTTCTGCCCTCTCCAGG 60.107 60.000 0.00 0.00 39.98 4.45
2330 2348 7.127186 TCCTCCATCTCTGGTACAATAAATTGA 59.873 37.037 9.60 0.00 43.61 2.57
2370 2388 2.283298 CTCGCCTGCAACACTATCATT 58.717 47.619 0.00 0.00 0.00 2.57
2411 2429 1.134340 ACCAGTACTTTGTGCCGTTCA 60.134 47.619 0.00 0.00 0.00 3.18
2453 2471 4.601857 TCCTGAACCCCTTTTAACTCATCT 59.398 41.667 0.00 0.00 0.00 2.90
2522 2540 5.126384 GGATACTATGATGGCTACCTGAGAC 59.874 48.000 0.00 0.00 0.00 3.36
2573 2591 6.042777 CAGTTTGTTCAACTCTACAGTGAGA 58.957 40.000 0.00 0.00 44.60 3.27
2586 2604 5.336372 CCAACACTTCCTTCAGTTTGTTCAA 60.336 40.000 0.00 0.00 0.00 2.69
2588 2606 4.398044 TCCAACACTTCCTTCAGTTTGTTC 59.602 41.667 0.00 0.00 0.00 3.18
2632 2650 2.351157 GCCTTGTGTTCTTCAGCATCAC 60.351 50.000 0.00 0.00 0.00 3.06
2660 2678 2.552315 GTCCTCATCTCGAGCTAAGGAG 59.448 54.545 22.21 15.38 40.78 3.69
2699 2717 2.699846 CTCTTCTGCTTGCCCTAGATCT 59.300 50.000 0.00 0.00 0.00 2.75
2777 2795 2.097825 AGCAAGCTGGATGATGTTTCC 58.902 47.619 0.00 0.00 0.00 3.13
2831 2849 5.711976 TGCTTCTTTAATTAGCTTTGCCTCT 59.288 36.000 0.00 0.00 35.93 3.69
2903 2921 7.180946 TCCTCCAGTTCATTTCTTGATAGAAGA 59.819 37.037 0.00 0.00 41.25 2.87
2904 2922 7.334090 TCCTCCAGTTCATTTCTTGATAGAAG 58.666 38.462 0.00 0.00 41.25 2.85
2905 2923 7.257790 TCCTCCAGTTCATTTCTTGATAGAA 57.742 36.000 0.00 0.00 38.61 2.10
2921 2939 2.178580 CTCTTCTTCTGCTCCTCCAGT 58.821 52.381 0.00 0.00 34.47 4.00
2924 2942 0.901124 TGCTCTTCTTCTGCTCCTCC 59.099 55.000 0.00 0.00 0.00 4.30
2977 2995 3.593096 TGAAGAGATGCAGCAGTAACTG 58.407 45.455 4.07 0.00 40.80 3.16
2982 3000 1.622312 TGACTGAAGAGATGCAGCAGT 59.378 47.619 4.07 0.00 42.03 4.40
2993 3011 6.040955 TCTCTTTGCTTAACTCTGACTGAAGA 59.959 38.462 0.00 0.00 0.00 2.87
3032 3050 0.393402 CTTCCAGCTGCTGCATGGTA 60.393 55.000 23.86 17.18 42.74 3.25
3072 3090 2.151502 ATCTCCGCCTTGAGAGAAGA 57.848 50.000 0.00 0.00 44.19 2.87
3116 3134 2.479566 TCTCCTTGGCATGAACTGTC 57.520 50.000 0.00 0.00 0.00 3.51
3125 3143 2.586425 CAGGTTTTCTTCTCCTTGGCA 58.414 47.619 0.00 0.00 0.00 4.92
3191 3209 2.305343 AGACTTTGCCTCATCAGCTTCT 59.695 45.455 0.00 0.00 0.00 2.85
3325 3343 2.421775 CTCTCAGACTCTTTCGCTGCTA 59.578 50.000 0.00 0.00 0.00 3.49
3400 3418 2.503356 CCAGGAGAGCCTTGTTCTGTAT 59.497 50.000 0.00 0.00 43.90 2.29
3402 3420 0.689623 CCAGGAGAGCCTTGTTCTGT 59.310 55.000 0.00 0.00 43.90 3.41
3434 3452 0.713883 ACGCGTGCTCATTTAAGTCG 59.286 50.000 12.93 0.00 0.00 4.18
3440 3458 0.038251 TGAGAGACGCGTGCTCATTT 60.038 50.000 27.78 14.64 34.02 2.32
3441 3459 0.174389 ATGAGAGACGCGTGCTCATT 59.826 50.000 32.26 22.35 44.55 2.57
3446 3464 2.100410 TCGATGAGAGACGCGTGC 59.900 61.111 20.70 8.85 0.00 5.34
3518 3536 0.038744 CCTTGGCCATCTCAACCTGT 59.961 55.000 6.09 0.00 0.00 4.00
3551 3569 1.509644 CGCTGAGCTTTGCCAAGACA 61.510 55.000 1.78 0.29 30.57 3.41
3662 3680 0.251354 TCCATGTCCTCAGCTCTTGC 59.749 55.000 0.00 0.00 40.05 4.01
3665 3683 0.690411 CCCTCCATGTCCTCAGCTCT 60.690 60.000 0.00 0.00 0.00 4.09
3668 3686 1.694133 CCTCCCTCCATGTCCTCAGC 61.694 65.000 0.00 0.00 0.00 4.26
3733 3751 6.852664 ACCATCGGATTTGAATGTTTAGTTC 58.147 36.000 0.00 0.00 0.00 3.01
3749 3767 3.517602 CTCAACGACAATAACCATCGGA 58.482 45.455 0.00 0.00 40.16 4.55
3874 3892 1.678269 CTTCTTCACCTTCTCGCGCG 61.678 60.000 26.76 26.76 0.00 6.86
3896 3914 1.217244 GAGGAACGGCGGCTTCTTA 59.783 57.895 13.24 0.00 0.00 2.10
3920 3938 3.548745 CTGGACAGGAACAGCATCATA 57.451 47.619 0.00 0.00 0.00 2.15
3936 3954 1.305633 CTGTGAGCCTCCTCCTGGA 60.306 63.158 0.00 0.00 40.69 3.86
3997 4015 5.128992 TCTTTTTGCGGGGAAATAGTTTC 57.871 39.130 3.85 0.00 38.94 2.78
3998 4016 5.538849 TTCTTTTTGCGGGGAAATAGTTT 57.461 34.783 3.85 0.00 0.00 2.66
4025 4043 8.421784 ACAAATCTGACAGTTCTAACACTTCTA 58.578 33.333 1.59 0.00 0.00 2.10
4141 4170 8.411683 AGTTCACGTTTTCTCCGTAGATATAAT 58.588 33.333 0.00 0.00 36.65 1.28
4162 4205 6.402222 ACACCTTTGCAAATTTACAAGTTCA 58.598 32.000 13.23 0.00 0.00 3.18
4273 4319 6.169094 AGTGTATCAAACTCAAGATCCAGTG 58.831 40.000 0.00 0.00 0.00 3.66
4289 4335 5.524511 CGAAATTCGTCCAAAGTGTATCA 57.475 39.130 7.29 0.00 34.72 2.15
4354 4408 1.202348 ACAGCATCAGATCCGAGAACG 60.202 52.381 0.00 0.00 39.43 3.95
4385 4439 0.179020 CCACTGAAACCCTCTGCACA 60.179 55.000 0.00 0.00 0.00 4.57
4386 4440 0.890996 CCCACTGAAACCCTCTGCAC 60.891 60.000 0.00 0.00 0.00 4.57
4390 4444 1.421646 CAAGACCCACTGAAACCCTCT 59.578 52.381 0.00 0.00 0.00 3.69
4392 4446 0.178990 GCAAGACCCACTGAAACCCT 60.179 55.000 0.00 0.00 0.00 4.34
4394 4448 1.338020 CTTGCAAGACCCACTGAAACC 59.662 52.381 22.31 0.00 0.00 3.27
4423 4477 5.144692 TCACACTCCAGAAGAAATCAGAG 57.855 43.478 0.00 0.00 36.98 3.35
4424 4478 5.300752 GTTCACACTCCAGAAGAAATCAGA 58.699 41.667 0.00 0.00 0.00 3.27
4425 4479 4.453819 GGTTCACACTCCAGAAGAAATCAG 59.546 45.833 0.00 0.00 0.00 2.90
4426 4480 4.103153 AGGTTCACACTCCAGAAGAAATCA 59.897 41.667 0.00 0.00 0.00 2.57
4427 4481 4.646572 AGGTTCACACTCCAGAAGAAATC 58.353 43.478 0.00 0.00 0.00 2.17
4428 4482 4.713792 AGGTTCACACTCCAGAAGAAAT 57.286 40.909 0.00 0.00 0.00 2.17
4429 4483 4.199310 CAAGGTTCACACTCCAGAAGAAA 58.801 43.478 0.00 0.00 0.00 2.52
4430 4484 3.808728 CAAGGTTCACACTCCAGAAGAA 58.191 45.455 0.00 0.00 0.00 2.52
4431 4485 2.485479 GCAAGGTTCACACTCCAGAAGA 60.485 50.000 0.00 0.00 0.00 2.87
4432 4486 1.876156 GCAAGGTTCACACTCCAGAAG 59.124 52.381 0.00 0.00 0.00 2.85
4437 4491 1.967319 TTGAGCAAGGTTCACACTCC 58.033 50.000 0.00 0.00 0.00 3.85
4448 4502 3.470709 TCCTCTGAACAGTTTGAGCAAG 58.529 45.455 10.23 1.17 0.00 4.01
4458 4512 2.900546 ACAGTAACCCTCCTCTGAACAG 59.099 50.000 0.00 0.00 0.00 3.16
4461 4515 2.111972 AGGACAGTAACCCTCCTCTGAA 59.888 50.000 0.00 0.00 27.04 3.02
4462 4516 1.717077 AGGACAGTAACCCTCCTCTGA 59.283 52.381 0.00 0.00 27.04 3.27
4463 4517 1.827969 CAGGACAGTAACCCTCCTCTG 59.172 57.143 0.00 0.00 31.58 3.35
4464 4518 1.433592 ACAGGACAGTAACCCTCCTCT 59.566 52.381 0.00 0.00 31.58 3.69
4468 4522 2.895404 TGTACACAGGACAGTAACCCTC 59.105 50.000 0.00 0.00 0.00 4.30
4471 4525 4.219944 TCAGATGTACACAGGACAGTAACC 59.780 45.833 0.00 0.00 0.00 2.85
4472 4526 5.386958 TCAGATGTACACAGGACAGTAAC 57.613 43.478 0.00 0.00 0.00 2.50
4473 4527 6.398095 CAATCAGATGTACACAGGACAGTAA 58.602 40.000 0.00 0.00 0.00 2.24
4475 4529 4.825422 CAATCAGATGTACACAGGACAGT 58.175 43.478 0.00 0.00 0.00 3.55
4476 4530 3.620374 GCAATCAGATGTACACAGGACAG 59.380 47.826 0.00 0.00 0.00 3.51
4478 4532 3.599343 TGCAATCAGATGTACACAGGAC 58.401 45.455 0.00 0.00 0.00 3.85
4479 4533 3.979101 TGCAATCAGATGTACACAGGA 57.021 42.857 0.00 0.00 0.00 3.86
4480 4534 5.375417 TTTTGCAATCAGATGTACACAGG 57.625 39.130 0.00 0.00 0.00 4.00
4481 4535 5.048504 ACCTTTTGCAATCAGATGTACACAG 60.049 40.000 0.00 0.00 0.00 3.66
4482 4536 4.826733 ACCTTTTGCAATCAGATGTACACA 59.173 37.500 0.00 0.00 0.00 3.72
4483 4537 5.376854 ACCTTTTGCAATCAGATGTACAC 57.623 39.130 0.00 0.00 0.00 2.90
4484 4538 6.040278 TGAAACCTTTTGCAATCAGATGTACA 59.960 34.615 0.00 0.00 0.00 2.90
4485 4539 6.446318 TGAAACCTTTTGCAATCAGATGTAC 58.554 36.000 0.00 0.00 0.00 2.90
4495 4549 5.398603 TGAAAGTCTGAAACCTTTTGCAA 57.601 34.783 0.00 0.00 0.00 4.08
4512 4566 2.861935 CAGCAAGCAAAACCACTGAAAG 59.138 45.455 0.00 0.00 42.29 2.62
4513 4567 2.891112 CAGCAAGCAAAACCACTGAAA 58.109 42.857 0.00 0.00 0.00 2.69
4514 4568 1.471327 GCAGCAAGCAAAACCACTGAA 60.471 47.619 0.00 0.00 44.79 3.02
4515 4569 0.102844 GCAGCAAGCAAAACCACTGA 59.897 50.000 0.00 0.00 44.79 3.41
4516 4570 2.596875 GCAGCAAGCAAAACCACTG 58.403 52.632 0.00 0.00 44.79 3.66
4528 4582 6.579666 AATTCAGAAGAATACTTGCAGCAA 57.420 33.333 7.81 7.81 43.52 3.91
4537 4591 5.163652 CCGGGACCAAAATTCAGAAGAATAC 60.164 44.000 0.00 0.00 43.52 1.89
4576 4712 2.484417 CGCTCAGCCTGAATATTGAGGT 60.484 50.000 20.41 6.54 37.97 3.85
4579 4715 2.804572 GCTCGCTCAGCCTGAATATTGA 60.805 50.000 0.00 0.00 43.17 2.57
4580 4716 1.530293 GCTCGCTCAGCCTGAATATTG 59.470 52.381 0.00 0.00 43.17 1.90
4581 4717 1.876322 GCTCGCTCAGCCTGAATATT 58.124 50.000 0.00 0.00 43.17 1.28
4618 4755 4.814294 GCCGCCGACAATCCGTCT 62.814 66.667 0.00 0.00 42.98 4.18
4620 4757 4.467084 ATGCCGCCGACAATCCGT 62.467 61.111 0.00 0.00 0.00 4.69
4636 4773 4.667420 GACACGTCCACGGTTCAT 57.333 55.556 3.81 0.00 44.95 2.57
4663 4802 1.228831 TGGGGAGCATGTTGGTTGG 60.229 57.895 0.00 0.00 0.00 3.77
4667 4806 1.228521 TGTGTGGGGAGCATGTTGG 60.229 57.895 0.00 0.00 0.00 3.77
4693 4832 3.950395 GGAAGGAATATGATATGCCAGGC 59.050 47.826 12.00 3.66 0.00 4.85
4694 4833 4.194640 CGGAAGGAATATGATATGCCAGG 58.805 47.826 12.00 0.00 0.00 4.45
4695 4834 4.633126 CACGGAAGGAATATGATATGCCAG 59.367 45.833 12.00 3.11 0.00 4.85
4696 4835 4.565444 CCACGGAAGGAATATGATATGCCA 60.565 45.833 12.00 0.00 0.00 4.92
4697 4836 3.941483 CCACGGAAGGAATATGATATGCC 59.059 47.826 0.79 0.79 0.00 4.40
4698 4837 4.579869 ACCACGGAAGGAATATGATATGC 58.420 43.478 0.00 0.00 0.00 3.14
4699 4838 5.812642 GCTACCACGGAAGGAATATGATATG 59.187 44.000 0.00 0.00 0.00 1.78
4700 4839 5.483937 TGCTACCACGGAAGGAATATGATAT 59.516 40.000 0.00 0.00 0.00 1.63
4701 4840 4.836175 TGCTACCACGGAAGGAATATGATA 59.164 41.667 0.00 0.00 0.00 2.15
4717 4856 0.677731 GACAATGGCAGCTGCTACCA 60.678 55.000 35.82 26.02 41.70 3.25
4721 4860 2.749044 CCGACAATGGCAGCTGCT 60.749 61.111 35.82 18.07 41.70 4.24
4742 4881 3.059982 CACCAACGAGCAGGGAGA 58.940 61.111 0.00 0.00 0.00 3.71
4743 4882 2.743928 GCACCAACGAGCAGGGAG 60.744 66.667 0.00 0.00 0.00 4.30
4744 4883 3.555324 TGCACCAACGAGCAGGGA 61.555 61.111 0.00 0.00 35.51 4.20
4789 4931 4.647615 ACGTGCGCGACAGCTTCT 62.648 61.111 28.73 0.00 42.32 2.85
4811 4953 3.711541 ATAACGTGCCCGGCGAGTC 62.712 63.158 9.30 0.00 38.78 3.36
4812 4954 2.791501 AAATAACGTGCCCGGCGAGT 62.792 55.000 9.30 4.23 38.78 4.18
4813 4955 1.641123 AAAATAACGTGCCCGGCGAG 61.641 55.000 9.30 0.00 38.78 5.03
4864 5010 7.530010 ACAGAAATGGTTTATCACAATTCTCG 58.470 34.615 0.00 0.00 27.51 4.04
4872 5018 5.414454 TGTGCCTACAGAAATGGTTTATCAC 59.586 40.000 0.00 0.00 31.91 3.06
4888 5034 0.321298 ACGGTGGAATGTGTGCCTAC 60.321 55.000 0.00 0.00 0.00 3.18
4891 5037 1.240256 TAAACGGTGGAATGTGTGCC 58.760 50.000 0.00 0.00 0.00 5.01
4901 5047 8.996271 GGAGGATATTAACTAAATAAACGGTGG 58.004 37.037 0.00 0.00 33.76 4.61
4922 5068 5.892119 AGATCTTACATCAGTTTACGGAGGA 59.108 40.000 1.93 0.00 0.00 3.71
4924 5070 7.976734 AGAAAGATCTTACATCAGTTTACGGAG 59.023 37.037 8.75 0.00 29.15 4.63
4925 5071 7.837863 AGAAAGATCTTACATCAGTTTACGGA 58.162 34.615 8.75 0.00 29.15 4.69
4926 5072 8.383619 CAAGAAAGATCTTACATCAGTTTACGG 58.616 37.037 8.75 0.00 44.11 4.02
4927 5073 9.140286 TCAAGAAAGATCTTACATCAGTTTACG 57.860 33.333 8.75 0.00 44.11 3.18
4935 5081 7.369803 TGCAGTTCAAGAAAGATCTTACATC 57.630 36.000 8.75 2.81 44.11 3.06
4936 5082 7.750229 TTGCAGTTCAAGAAAGATCTTACAT 57.250 32.000 8.75 0.00 44.11 2.29
4937 5083 7.566760 TTTGCAGTTCAAGAAAGATCTTACA 57.433 32.000 8.75 0.00 44.11 2.41
4938 5084 9.122613 GATTTTGCAGTTCAAGAAAGATCTTAC 57.877 33.333 8.75 1.89 44.11 2.34
4939 5085 8.017373 CGATTTTGCAGTTCAAGAAAGATCTTA 58.983 33.333 8.75 0.00 44.11 2.10
4940 5086 6.860023 CGATTTTGCAGTTCAAGAAAGATCTT 59.140 34.615 0.88 0.88 46.91 2.40
4941 5087 6.376978 CGATTTTGCAGTTCAAGAAAGATCT 58.623 36.000 0.00 0.00 35.84 2.75
4942 5088 6.608435 CGATTTTGCAGTTCAAGAAAGATC 57.392 37.500 0.00 0.00 35.84 2.75


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

AutoCloner maintained by Alex Coulton.