Multiple sequence alignment - TraesCS5A01G492400

Loading Multiple Alignment...

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 TraesCS5A01G492400 chr5A 100.000 2895 0 0 1 2895 661220751 661223645 0.000000e+00 5347.0
1 TraesCS5A01G492400 chr4D 88.314 1797 95 47 78 1825 481449211 481447481 0.000000e+00 2049.0
2 TraesCS5A01G492400 chr4D 85.342 730 36 32 2058 2771 481447314 481446640 0.000000e+00 689.0
3 TraesCS5A01G492400 chr4D 99.174 121 1 0 2775 2895 481440495 481440375 4.860000e-53 219.0
4 TraesCS5A01G492400 chr4B 87.466 1827 127 56 49 1825 610436227 610434453 0.000000e+00 2012.0
5 TraesCS5A01G492400 chr4B 89.556 450 30 11 2058 2492 610434291 610433844 3.260000e-154 555.0
6 TraesCS5A01G492400 chr4B 92.141 369 23 2 2530 2895 610433839 610433474 1.540000e-142 516.0
7 TraesCS5A01G492400 chr4B 96.429 112 4 0 1943 2054 562324376 562324265 4.930000e-43 185.0
8 TraesCS5A01G492400 chr4B 91.000 100 6 1 1853 1952 610434385 610434289 6.510000e-27 132.0
9 TraesCS5A01G492400 chr4B 74.554 224 44 13 1411 1627 531094066 531094283 5.140000e-13 86.1
10 TraesCS5A01G492400 chr5B 98.198 111 2 0 1947 2057 134582561 134582451 8.190000e-46 195.0
11 TraesCS5A01G492400 chr2B 97.248 109 3 0 1947 2055 620631486 620631594 4.930000e-43 185.0
12 TraesCS5A01G492400 chr2B 96.429 112 4 0 1943 2054 662485291 662485402 4.930000e-43 185.0
13 TraesCS5A01G492400 chr2B 94.783 115 6 0 1940 2054 460807284 460807170 2.290000e-41 180.0
14 TraesCS5A01G492400 chr4A 95.614 114 5 0 1941 2054 16982524 16982637 1.770000e-42 183.0
15 TraesCS5A01G492400 chr4A 96.396 111 4 0 1945 2055 610483274 610483384 1.770000e-42 183.0
16 TraesCS5A01G492400 chr4A 75.000 224 41 15 1412 1627 34294909 34295125 3.970000e-14 89.8
17 TraesCS5A01G492400 chr3D 95.575 113 5 0 1943 2055 419583114 419583002 6.370000e-42 182.0
18 TraesCS5A01G492400 chr3D 92.623 122 8 1 1943 2064 614541911 614541791 1.070000e-39 174.0


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 TraesCS5A01G492400 chr5A 661220751 661223645 2894 False 5347.00 5347 100.00000 1 2895 1 chr5A.!!$F1 2894
1 TraesCS5A01G492400 chr4D 481446640 481449211 2571 True 1369.00 2049 86.82800 78 2771 2 chr4D.!!$R2 2693
2 TraesCS5A01G492400 chr4B 610433474 610436227 2753 True 803.75 2012 90.04075 49 2895 4 chr4B.!!$R2 2846

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
207 226 0.039911 AGCGACAGTAGGACCCTTCT 59.96 55.0 0.0 0.0 0.0 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2036 2162 0.038744 AGTACTCCCTCCGTTCGGAA 59.961 55.0 14.79 0.04 33.41 4.3 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
23 24 6.420913 AAGTTGAGGTATATATGCCGAAGT 57.579 37.500 13.49 10.53 37.65 3.01
24 25 5.784177 AGTTGAGGTATATATGCCGAAGTG 58.216 41.667 13.49 0.00 37.65 3.16
25 26 5.538813 AGTTGAGGTATATATGCCGAAGTGA 59.461 40.000 13.49 0.00 37.65 3.41
26 27 6.041637 AGTTGAGGTATATATGCCGAAGTGAA 59.958 38.462 13.49 0.00 37.65 3.18
27 28 6.025749 TGAGGTATATATGCCGAAGTGAAG 57.974 41.667 13.49 0.00 37.65 3.02
28 29 4.822026 AGGTATATATGCCGAAGTGAAGC 58.178 43.478 13.49 0.00 37.65 3.86
29 30 3.612860 GGTATATATGCCGAAGTGAAGCG 59.387 47.826 3.90 0.00 0.00 4.68
30 31 3.660501 ATATATGCCGAAGTGAAGCGA 57.339 42.857 0.00 0.00 0.00 4.93
31 32 1.571919 ATATGCCGAAGTGAAGCGAC 58.428 50.000 0.00 0.00 0.00 5.19
32 33 0.800683 TATGCCGAAGTGAAGCGACG 60.801 55.000 0.00 0.00 0.00 5.12
33 34 2.430244 GCCGAAGTGAAGCGACGA 60.430 61.111 0.00 0.00 0.00 4.20
34 35 2.437343 GCCGAAGTGAAGCGACGAG 61.437 63.158 0.00 0.00 0.00 4.18
35 36 1.209383 CCGAAGTGAAGCGACGAGA 59.791 57.895 0.00 0.00 0.00 4.04
36 37 0.794981 CCGAAGTGAAGCGACGAGAG 60.795 60.000 0.00 0.00 0.00 3.20
37 38 0.166161 CGAAGTGAAGCGACGAGAGA 59.834 55.000 0.00 0.00 0.00 3.10
38 39 1.788699 CGAAGTGAAGCGACGAGAGAG 60.789 57.143 0.00 0.00 0.00 3.20
39 40 1.465387 GAAGTGAAGCGACGAGAGAGA 59.535 52.381 0.00 0.00 0.00 3.10
40 41 1.083489 AGTGAAGCGACGAGAGAGAG 58.917 55.000 0.00 0.00 0.00 3.20
41 42 1.080298 GTGAAGCGACGAGAGAGAGA 58.920 55.000 0.00 0.00 0.00 3.10
42 43 1.062002 GTGAAGCGACGAGAGAGAGAG 59.938 57.143 0.00 0.00 0.00 3.20
43 44 1.066787 TGAAGCGACGAGAGAGAGAGA 60.067 52.381 0.00 0.00 0.00 3.10
44 45 1.593006 GAAGCGACGAGAGAGAGAGAG 59.407 57.143 0.00 0.00 0.00 3.20
45 46 0.821517 AGCGACGAGAGAGAGAGAGA 59.178 55.000 0.00 0.00 0.00 3.10
46 47 0.928229 GCGACGAGAGAGAGAGAGAC 59.072 60.000 0.00 0.00 0.00 3.36
47 48 1.197055 CGACGAGAGAGAGAGAGACG 58.803 60.000 0.00 0.00 0.00 4.18
64 65 0.171679 ACGCAACGGATCGACACATA 59.828 50.000 0.00 0.00 0.00 2.29
66 67 1.635844 GCAACGGATCGACACATACA 58.364 50.000 0.00 0.00 0.00 2.29
67 68 2.201732 GCAACGGATCGACACATACAT 58.798 47.619 0.00 0.00 0.00 2.29
68 69 2.033747 GCAACGGATCGACACATACATG 60.034 50.000 0.00 0.00 0.00 3.21
69 70 1.852942 ACGGATCGACACATACATGC 58.147 50.000 0.00 0.00 0.00 4.06
70 71 0.778223 CGGATCGACACATACATGCG 59.222 55.000 0.00 0.00 0.00 4.73
71 72 1.139989 GGATCGACACATACATGCGG 58.860 55.000 0.00 0.00 0.00 5.69
72 73 1.269569 GGATCGACACATACATGCGGA 60.270 52.381 0.00 0.00 0.00 5.54
73 74 2.610479 GGATCGACACATACATGCGGAT 60.610 50.000 0.00 0.00 0.00 4.18
74 75 1.851658 TCGACACATACATGCGGATG 58.148 50.000 16.07 16.07 35.49 3.51
75 76 1.407258 TCGACACATACATGCGGATGA 59.593 47.619 24.66 7.69 33.36 2.92
76 77 2.159170 TCGACACATACATGCGGATGAA 60.159 45.455 24.66 0.00 33.36 2.57
81 82 4.639755 ACACATACATGCGGATGAAATGAA 59.360 37.500 28.86 10.11 33.92 2.57
93 94 7.010645 TGCGGATGAAATGAAATGAAATGAATG 59.989 33.333 0.00 0.00 0.00 2.67
159 166 0.454957 CGCGTTTCTTCCAAGGCATG 60.455 55.000 0.00 0.00 37.39 4.06
161 168 1.810151 GCGTTTCTTCCAAGGCATGTA 59.190 47.619 0.00 0.00 37.47 2.29
162 169 2.159517 GCGTTTCTTCCAAGGCATGTAG 60.160 50.000 0.00 0.00 37.47 2.74
164 171 3.941483 CGTTTCTTCCAAGGCATGTAGAT 59.059 43.478 0.00 0.00 0.00 1.98
204 223 0.330604 TGTAGCGACAGTAGGACCCT 59.669 55.000 0.00 0.00 0.00 4.34
207 226 0.039911 AGCGACAGTAGGACCCTTCT 59.960 55.000 0.00 0.00 0.00 2.85
229 248 6.487828 TCTCCTCTGATCCACAAATCAAATT 58.512 36.000 0.00 0.00 35.32 1.82
250 276 4.280436 TGGTTATGTATAATCAGGCCCG 57.720 45.455 0.00 0.00 30.40 6.13
252 278 4.839550 TGGTTATGTATAATCAGGCCCGTA 59.160 41.667 0.00 0.00 30.40 4.02
253 279 5.486063 TGGTTATGTATAATCAGGCCCGTAT 59.514 40.000 0.00 0.00 30.40 3.06
255 281 3.861276 TGTATAATCAGGCCCGTATCG 57.139 47.619 0.00 0.00 0.00 2.92
257 283 4.334552 TGTATAATCAGGCCCGTATCGTA 58.665 43.478 0.00 0.00 0.00 3.43
258 284 3.863142 ATAATCAGGCCCGTATCGTAC 57.137 47.619 0.00 0.00 0.00 3.67
284 310 3.682292 AAATCTCCCGCCACCTCGC 62.682 63.158 0.00 0.00 0.00 5.03
305 331 3.764466 CTGGCGCTTCCCTCGTCT 61.764 66.667 7.64 0.00 32.08 4.18
306 332 3.302347 CTGGCGCTTCCCTCGTCTT 62.302 63.158 7.64 0.00 32.08 3.01
307 333 2.815647 GGCGCTTCCCTCGTCTTG 60.816 66.667 7.64 0.00 0.00 3.02
308 334 3.491652 GCGCTTCCCTCGTCTTGC 61.492 66.667 0.00 0.00 0.00 4.01
311 337 1.448717 GCTTCCCTCGTCTTGCTCC 60.449 63.158 0.00 0.00 0.00 4.70
364 390 2.456119 GCAAGCGTCGTGGATCAGG 61.456 63.158 0.00 0.00 0.00 3.86
365 391 1.215382 CAAGCGTCGTGGATCAGGA 59.785 57.895 0.00 0.00 0.00 3.86
711 771 2.359850 TGGTGGCATTCAGTCGGC 60.360 61.111 0.00 0.00 0.00 5.54
728 788 1.797025 GGCTTACCAGACAGTGACAC 58.203 55.000 0.00 0.00 35.26 3.67
821 881 0.455972 GCGTGTCTCTCTCTCTGCAC 60.456 60.000 0.00 0.00 0.00 4.57
885 945 0.752658 TGTGTGACACTAGTGCTGCT 59.247 50.000 22.90 2.78 35.11 4.24
939 1002 0.108138 GCTCTTCTTAAGCCCGAGCA 60.108 55.000 23.62 0.00 44.74 4.26
983 1046 1.749634 TCTTCCTCGCTAGCCAAGTAC 59.250 52.381 9.66 0.00 0.00 2.73
986 1049 1.065928 CTCGCTAGCCAAGTACCCG 59.934 63.158 9.66 0.00 0.00 5.28
1067 1132 2.360475 GTGGAGACTGCCAAGCCC 60.360 66.667 0.00 0.00 40.20 5.19
1188 1253 2.589492 AAGTCGTCGTCGTCGTCGT 61.589 57.895 18.44 2.14 45.27 4.34
1189 1254 2.472061 AAGTCGTCGTCGTCGTCGTC 62.472 60.000 18.44 14.10 45.27 4.20
1190 1255 4.108437 TCGTCGTCGTCGTCGTCG 62.108 66.667 20.39 20.39 45.27 5.12
1529 1594 2.356780 GGAGAACGGGATCACGGGT 61.357 63.158 23.42 9.15 38.39 5.28
1575 1640 1.006102 CGGTTCCTGTCGCTCAACT 60.006 57.895 0.00 0.00 0.00 3.16
1657 1725 4.457496 CGACCCCACGCAGATGCT 62.457 66.667 2.95 0.00 39.32 3.79
1694 1762 4.106925 CCTGCTGTCTCCCCTGCC 62.107 72.222 0.00 0.00 0.00 4.85
1732 1800 3.680525 CAGCTAGCTGCACGTACG 58.319 61.111 30.62 15.01 45.94 3.67
1733 1801 2.202623 AGCTAGCTGCACGTACGC 60.203 61.111 18.57 0.00 45.94 4.42
1734 1802 2.506217 GCTAGCTGCACGTACGCA 60.506 61.111 16.72 5.12 42.31 5.24
1745 1821 2.844146 GTACGCACGCACTGACAC 59.156 61.111 0.00 0.00 0.00 3.67
1825 1905 1.670295 CCGATCCGATGAAAACATGCA 59.330 47.619 0.00 0.00 0.00 3.96
1826 1906 2.097304 CCGATCCGATGAAAACATGCAA 59.903 45.455 0.00 0.00 0.00 4.08
1828 1908 3.181507 CGATCCGATGAAAACATGCAACT 60.182 43.478 0.00 0.00 0.00 3.16
1831 1911 2.508867 CGATGAAAACATGCAACTCGG 58.491 47.619 0.00 0.00 0.00 4.63
1832 1912 2.253603 GATGAAAACATGCAACTCGGC 58.746 47.619 0.00 0.00 0.00 5.54
1834 1914 0.598065 GAAAACATGCAACTCGGCCT 59.402 50.000 0.00 0.00 0.00 5.19
1835 1915 0.598065 AAAACATGCAACTCGGCCTC 59.402 50.000 0.00 0.00 0.00 4.70
1836 1916 0.537143 AAACATGCAACTCGGCCTCA 60.537 50.000 0.00 0.00 0.00 3.86
1837 1917 0.322816 AACATGCAACTCGGCCTCAT 60.323 50.000 0.00 0.00 0.00 2.90
1838 1918 1.028330 ACATGCAACTCGGCCTCATG 61.028 55.000 0.00 7.23 40.07 3.07
1840 1920 1.028330 ATGCAACTCGGCCTCATGTG 61.028 55.000 0.00 0.00 0.00 3.21
1841 1921 1.375908 GCAACTCGGCCTCATGTGA 60.376 57.895 0.00 0.00 0.00 3.58
1845 1971 0.176680 ACTCGGCCTCATGTGATGAC 59.823 55.000 0.00 0.00 35.06 3.06
1847 1973 0.977627 TCGGCCTCATGTGATGACCT 60.978 55.000 0.00 0.00 35.06 3.85
1851 1977 1.209019 GCCTCATGTGATGACCTGAGT 59.791 52.381 14.51 0.00 41.09 3.41
1889 2015 6.040616 TCTCCTCCGTTAATCCTGTAAAGATC 59.959 42.308 0.00 0.00 0.00 2.75
1901 2027 6.051074 TCCTGTAAAGATCTCATCGTACGTA 58.949 40.000 16.05 2.34 31.41 3.57
1902 2028 6.018425 TCCTGTAAAGATCTCATCGTACGTAC 60.018 42.308 15.90 15.90 31.41 3.67
1920 2046 3.000476 CGTACGTACATTTCCCGTGAATG 60.000 47.826 24.50 0.18 39.73 2.67
1935 2061 1.068281 TGAATGTTGCGTGCCATTGTT 59.932 42.857 1.82 0.00 31.67 2.83
1939 2065 1.007502 TTGCGTGCCATTGTTGCTC 60.008 52.632 0.00 0.00 0.00 4.26
1946 2072 1.142474 GCCATTGTTGCTCTGTTTGC 58.858 50.000 0.00 0.00 0.00 3.68
1947 2073 1.269936 GCCATTGTTGCTCTGTTTGCT 60.270 47.619 0.00 0.00 0.00 3.91
1948 2074 2.030007 GCCATTGTTGCTCTGTTTGCTA 60.030 45.455 0.00 0.00 0.00 3.49
1949 2075 3.568538 CCATTGTTGCTCTGTTTGCTAC 58.431 45.455 0.00 0.00 36.87 3.58
1950 2076 3.254166 CCATTGTTGCTCTGTTTGCTACT 59.746 43.478 0.00 0.00 37.15 2.57
1951 2077 4.470462 CATTGTTGCTCTGTTTGCTACTC 58.530 43.478 0.00 0.00 37.15 2.59
1952 2078 2.494059 TGTTGCTCTGTTTGCTACTCC 58.506 47.619 0.00 0.00 37.15 3.85
1953 2079 1.807142 GTTGCTCTGTTTGCTACTCCC 59.193 52.381 0.00 0.00 34.37 4.30
1954 2080 1.352083 TGCTCTGTTTGCTACTCCCT 58.648 50.000 0.00 0.00 0.00 4.20
1955 2081 1.276421 TGCTCTGTTTGCTACTCCCTC 59.724 52.381 0.00 0.00 0.00 4.30
1956 2082 1.406205 GCTCTGTTTGCTACTCCCTCC 60.406 57.143 0.00 0.00 0.00 4.30
1957 2083 0.895530 TCTGTTTGCTACTCCCTCCG 59.104 55.000 0.00 0.00 0.00 4.63
1958 2084 0.608640 CTGTTTGCTACTCCCTCCGT 59.391 55.000 0.00 0.00 0.00 4.69
1959 2085 1.002087 CTGTTTGCTACTCCCTCCGTT 59.998 52.381 0.00 0.00 0.00 4.44
1960 2086 1.001633 TGTTTGCTACTCCCTCCGTTC 59.998 52.381 0.00 0.00 0.00 3.95
1961 2087 0.245539 TTTGCTACTCCCTCCGTTCG 59.754 55.000 0.00 0.00 0.00 3.95
1962 2088 0.609957 TTGCTACTCCCTCCGTTCGA 60.610 55.000 0.00 0.00 0.00 3.71
1963 2089 0.609957 TGCTACTCCCTCCGTTCGAA 60.610 55.000 0.00 0.00 0.00 3.71
1964 2090 0.529378 GCTACTCCCTCCGTTCGAAA 59.471 55.000 0.00 0.00 0.00 3.46
1965 2091 1.136500 GCTACTCCCTCCGTTCGAAAT 59.864 52.381 0.00 0.00 0.00 2.17
1966 2092 2.418334 GCTACTCCCTCCGTTCGAAATT 60.418 50.000 0.00 0.00 0.00 1.82
1967 2093 3.181483 GCTACTCCCTCCGTTCGAAATTA 60.181 47.826 0.00 0.00 0.00 1.40
1968 2094 3.242549 ACTCCCTCCGTTCGAAATTAC 57.757 47.619 0.00 0.00 0.00 1.89
1969 2095 2.830321 ACTCCCTCCGTTCGAAATTACT 59.170 45.455 0.00 0.00 0.00 2.24
1970 2096 3.260128 ACTCCCTCCGTTCGAAATTACTT 59.740 43.478 0.00 0.00 0.00 2.24
1971 2097 3.592059 TCCCTCCGTTCGAAATTACTTG 58.408 45.455 0.00 0.00 0.00 3.16
1972 2098 3.007182 TCCCTCCGTTCGAAATTACTTGT 59.993 43.478 0.00 0.00 0.00 3.16
1973 2099 3.370061 CCCTCCGTTCGAAATTACTTGTC 59.630 47.826 0.00 0.00 0.00 3.18
1974 2100 4.243270 CCTCCGTTCGAAATTACTTGTCT 58.757 43.478 0.00 0.00 0.00 3.41
1975 2101 4.326548 CCTCCGTTCGAAATTACTTGTCTC 59.673 45.833 0.00 0.00 0.00 3.36
1976 2102 3.916172 TCCGTTCGAAATTACTTGTCTCG 59.084 43.478 0.00 0.00 0.00 4.04
1977 2103 3.060363 CCGTTCGAAATTACTTGTCTCGG 59.940 47.826 0.00 0.00 0.00 4.63
1978 2104 3.916172 CGTTCGAAATTACTTGTCTCGGA 59.084 43.478 0.00 0.00 0.00 4.55
1979 2105 4.383649 CGTTCGAAATTACTTGTCTCGGAA 59.616 41.667 0.00 0.00 0.00 4.30
1980 2106 5.107760 CGTTCGAAATTACTTGTCTCGGAAA 60.108 40.000 0.00 0.00 0.00 3.13
1981 2107 6.400727 CGTTCGAAATTACTTGTCTCGGAAAT 60.401 38.462 0.00 0.00 0.00 2.17
1982 2108 7.201376 CGTTCGAAATTACTTGTCTCGGAAATA 60.201 37.037 0.00 0.00 0.00 1.40
1983 2109 7.751047 TCGAAATTACTTGTCTCGGAAATAG 57.249 36.000 0.00 0.00 0.00 1.73
1984 2110 7.541162 TCGAAATTACTTGTCTCGGAAATAGA 58.459 34.615 0.00 0.00 0.00 1.98
1985 2111 8.195436 TCGAAATTACTTGTCTCGGAAATAGAT 58.805 33.333 0.00 0.00 0.00 1.98
1986 2112 8.269424 CGAAATTACTTGTCTCGGAAATAGATG 58.731 37.037 0.00 0.00 0.00 2.90
1987 2113 9.099454 GAAATTACTTGTCTCGGAAATAGATGT 57.901 33.333 0.00 0.00 0.00 3.06
1993 2119 9.751542 ACTTGTCTCGGAAATAGATGTATTTAG 57.248 33.333 7.77 6.04 38.70 1.85
1994 2120 9.967346 CTTGTCTCGGAAATAGATGTATTTAGA 57.033 33.333 7.77 9.42 38.70 2.10
1996 2122 9.745880 TGTCTCGGAAATAGATGTATTTAGAAC 57.254 33.333 7.77 10.74 38.70 3.01
1997 2123 9.968870 GTCTCGGAAATAGATGTATTTAGAACT 57.031 33.333 7.77 0.00 38.70 3.01
2029 2155 9.900710 ACATCTAGATACATTCATTTCTACGAC 57.099 33.333 4.54 0.00 0.00 4.34
2030 2156 9.899226 CATCTAGATACATTCATTTCTACGACA 57.101 33.333 4.54 0.00 0.00 4.35
2032 2158 9.952188 TCTAGATACATTCATTTCTACGACAAG 57.048 33.333 0.00 0.00 0.00 3.16
2033 2159 9.737427 CTAGATACATTCATTTCTACGACAAGT 57.263 33.333 0.00 0.00 0.00 3.16
2039 2165 8.665685 ACATTCATTTCTACGACAAGTAATTCC 58.334 33.333 0.00 0.00 34.45 3.01
2040 2166 6.880822 TCATTTCTACGACAAGTAATTCCG 57.119 37.500 0.00 0.00 34.45 4.30
2041 2167 6.623486 TCATTTCTACGACAAGTAATTCCGA 58.377 36.000 0.00 0.00 34.45 4.55
2042 2168 7.092079 TCATTTCTACGACAAGTAATTCCGAA 58.908 34.615 0.00 0.00 34.45 4.30
2043 2169 6.695292 TTTCTACGACAAGTAATTCCGAAC 57.305 37.500 0.00 0.00 34.45 3.95
2044 2170 4.406069 TCTACGACAAGTAATTCCGAACG 58.594 43.478 0.00 0.00 34.45 3.95
2045 2171 2.331194 ACGACAAGTAATTCCGAACGG 58.669 47.619 6.94 6.94 0.00 4.44
2046 2172 2.030007 ACGACAAGTAATTCCGAACGGA 60.030 45.455 12.04 12.04 43.52 4.69
2047 2173 2.597305 CGACAAGTAATTCCGAACGGAG 59.403 50.000 15.34 5.60 46.06 4.63
2048 2174 2.928116 GACAAGTAATTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
2049 2175 2.277084 CAAGTAATTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
2050 2176 1.856629 AGTAATTCCGAACGGAGGGA 58.143 50.000 15.34 2.49 46.06 4.20
2051 2177 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
2052 2178 1.479730 GTAATTCCGAACGGAGGGAGT 59.520 52.381 15.34 4.12 46.06 3.85
2053 2179 1.856629 AATTCCGAACGGAGGGAGTA 58.143 50.000 15.34 1.05 46.06 2.59
2056 2182 0.038744 TCCGAACGGAGGGAGTACTT 59.961 55.000 12.04 0.00 39.76 2.24
2061 2187 1.836802 ACGGAGGGAGTACTTCTCAC 58.163 55.000 21.13 13.23 46.26 3.51
2066 2192 0.243095 GGGAGTACTTCTCACGCGTT 59.757 55.000 10.22 0.00 44.40 4.84
2102 2243 3.690487 TGGTCGACCAAACACGAAT 57.310 47.368 34.60 0.00 44.35 3.34
2104 2245 0.437295 GGTCGACCAAACACGAATCG 59.563 55.000 29.75 0.00 40.12 3.34
2105 2246 1.411394 GTCGACCAAACACGAATCGA 58.589 50.000 10.55 0.00 40.12 3.59
2106 2247 1.411394 TCGACCAAACACGAATCGAC 58.589 50.000 10.55 0.00 36.92 4.20
2107 2248 1.133407 CGACCAAACACGAATCGACA 58.867 50.000 10.55 0.00 34.77 4.35
2108 2249 1.124297 CGACCAAACACGAATCGACAG 59.876 52.381 10.55 1.08 34.77 3.51
2109 2250 1.459592 GACCAAACACGAATCGACAGG 59.540 52.381 10.55 6.26 0.00 4.00
2114 2255 1.445410 CACGAATCGACAGGCGGAA 60.445 57.895 10.55 0.00 41.33 4.30
2151 2292 1.233285 GCTGATCGCCATGGATCCAC 61.233 60.000 18.99 3.30 41.71 4.02
2176 2317 2.110967 CATGAGGCCGAGTTGCTGG 61.111 63.158 0.00 0.00 0.00 4.85
2213 2366 4.057428 GTGGTCTGCTCGTCGCCT 62.057 66.667 0.00 0.00 38.05 5.52
2214 2367 3.749064 TGGTCTGCTCGTCGCCTC 61.749 66.667 0.00 0.00 38.05 4.70
2215 2368 4.838486 GGTCTGCTCGTCGCCTCG 62.838 72.222 0.00 0.00 38.05 4.63
2216 2369 4.104417 GTCTGCTCGTCGCCTCGT 62.104 66.667 0.00 0.00 38.05 4.18
2217 2370 3.800863 TCTGCTCGTCGCCTCGTC 61.801 66.667 0.00 0.00 38.05 4.20
2327 2480 5.579904 CGAATTGATTGACTGACTGACTGAT 59.420 40.000 0.00 0.00 0.00 2.90
2340 2497 5.640783 TGACTGACTGATTGATTGATGTGAC 59.359 40.000 0.00 0.00 0.00 3.67
2395 2556 1.271379 CCTCACCCCGTGACTGAAAAT 60.271 52.381 0.00 0.00 37.67 1.82
2486 2647 4.933064 CGATCGCCCCTCTGACGC 62.933 72.222 0.26 0.00 0.00 5.19
2494 2655 3.449227 CCTCTGACGCCCGTGCTA 61.449 66.667 0.00 0.00 34.43 3.49
2495 2656 2.103143 CTCTGACGCCCGTGCTAG 59.897 66.667 0.00 0.00 34.43 3.42
2496 2657 2.675423 TCTGACGCCCGTGCTAGT 60.675 61.111 0.00 0.00 34.43 2.57
2497 2658 2.202623 CTGACGCCCGTGCTAGTC 60.203 66.667 0.00 0.00 34.43 2.59
2498 2659 3.701604 CTGACGCCCGTGCTAGTCC 62.702 68.421 0.00 0.00 34.43 3.85
2499 2660 4.849329 GACGCCCGTGCTAGTCCG 62.849 72.222 0.00 0.00 34.43 4.79
2507 2668 2.865343 CGTGCTAGTCCGGAAATACT 57.135 50.000 5.23 1.27 0.00 2.12
2508 2669 3.160777 CGTGCTAGTCCGGAAATACTT 57.839 47.619 5.23 0.00 0.00 2.24
2509 2670 2.858344 CGTGCTAGTCCGGAAATACTTG 59.142 50.000 5.23 1.38 0.00 3.16
2510 2671 3.675228 CGTGCTAGTCCGGAAATACTTGT 60.675 47.826 5.23 0.00 0.00 3.16
2511 2672 3.864003 GTGCTAGTCCGGAAATACTTGTC 59.136 47.826 5.23 0.00 0.00 3.18
2512 2673 3.512329 TGCTAGTCCGGAAATACTTGTCA 59.488 43.478 5.23 1.00 0.00 3.58
2574 2737 1.203523 CCTCTGTGTCTGTAGGTGCTC 59.796 57.143 0.00 0.00 0.00 4.26
2588 2751 3.798202 AGGTGCTCGACATAGAAATTCC 58.202 45.455 0.00 0.00 0.00 3.01
2613 2776 2.969300 TTTTCCCGGGTGTCACCTGC 62.969 60.000 23.63 6.75 43.40 4.85
2625 2788 4.643387 ACCTGCCACGGGTGCTTC 62.643 66.667 0.00 0.00 42.23 3.86
2636 2799 3.938963 CACGGGTGCTTCACAAATACTAT 59.061 43.478 0.00 0.00 35.86 2.12
2637 2800 5.113383 CACGGGTGCTTCACAAATACTATA 58.887 41.667 0.00 0.00 35.86 1.31
2639 2802 5.583457 ACGGGTGCTTCACAAATACTATAAC 59.417 40.000 0.00 0.00 35.86 1.89
2642 2805 7.361371 CGGGTGCTTCACAAATACTATAACAAA 60.361 37.037 0.00 0.00 35.86 2.83
2643 2806 7.753580 GGGTGCTTCACAAATACTATAACAAAC 59.246 37.037 0.00 0.00 35.86 2.93
2644 2807 8.512138 GGTGCTTCACAAATACTATAACAAACT 58.488 33.333 0.00 0.00 35.86 2.66
2870 3036 0.176449 TGCCACATGATCTCCGTCTG 59.824 55.000 0.00 0.00 0.00 3.51
2882 3048 2.490509 TCTCCGTCTGATGAAACGCTTA 59.509 45.455 0.00 0.00 37.56 3.09
2887 3053 4.804139 CCGTCTGATGAAACGCTTAGTTAT 59.196 41.667 0.00 0.00 43.37 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.041637 TCACTTCGGCATATATACCTCAACTT 59.958 38.462 0.44 0.00 0.00 2.66
1 2 5.538813 TCACTTCGGCATATATACCTCAACT 59.461 40.000 0.44 0.00 0.00 3.16
2 3 5.779922 TCACTTCGGCATATATACCTCAAC 58.220 41.667 0.44 0.00 0.00 3.18
3 4 6.413783 TTCACTTCGGCATATATACCTCAA 57.586 37.500 0.44 0.00 0.00 3.02
4 5 5.566826 GCTTCACTTCGGCATATATACCTCA 60.567 44.000 0.44 0.00 0.00 3.86
5 6 4.865365 GCTTCACTTCGGCATATATACCTC 59.135 45.833 0.44 0.00 0.00 3.85
6 7 4.618460 CGCTTCACTTCGGCATATATACCT 60.618 45.833 0.44 0.00 0.00 3.08
7 8 3.612860 CGCTTCACTTCGGCATATATACC 59.387 47.826 0.00 0.00 0.00 2.73
8 9 4.323868 GTCGCTTCACTTCGGCATATATAC 59.676 45.833 0.00 0.00 0.00 1.47
9 10 4.482386 GTCGCTTCACTTCGGCATATATA 58.518 43.478 0.00 0.00 0.00 0.86
10 11 3.318017 GTCGCTTCACTTCGGCATATAT 58.682 45.455 0.00 0.00 0.00 0.86
11 12 2.739292 GTCGCTTCACTTCGGCATATA 58.261 47.619 0.00 0.00 0.00 0.86
12 13 1.571919 GTCGCTTCACTTCGGCATAT 58.428 50.000 0.00 0.00 0.00 1.78
13 14 0.800683 CGTCGCTTCACTTCGGCATA 60.801 55.000 0.00 0.00 0.00 3.14
14 15 2.094659 CGTCGCTTCACTTCGGCAT 61.095 57.895 0.00 0.00 0.00 4.40
15 16 2.733218 CGTCGCTTCACTTCGGCA 60.733 61.111 0.00 0.00 0.00 5.69
16 17 2.430244 TCGTCGCTTCACTTCGGC 60.430 61.111 0.00 0.00 0.00 5.54
17 18 0.794981 CTCTCGTCGCTTCACTTCGG 60.795 60.000 0.00 0.00 0.00 4.30
18 19 0.166161 TCTCTCGTCGCTTCACTTCG 59.834 55.000 0.00 0.00 0.00 3.79
19 20 1.465387 TCTCTCTCGTCGCTTCACTTC 59.535 52.381 0.00 0.00 0.00 3.01
20 21 1.466950 CTCTCTCTCGTCGCTTCACTT 59.533 52.381 0.00 0.00 0.00 3.16
21 22 1.083489 CTCTCTCTCGTCGCTTCACT 58.917 55.000 0.00 0.00 0.00 3.41
22 23 1.062002 CTCTCTCTCTCGTCGCTTCAC 59.938 57.143 0.00 0.00 0.00 3.18
23 24 1.066787 TCTCTCTCTCTCGTCGCTTCA 60.067 52.381 0.00 0.00 0.00 3.02
24 25 1.593006 CTCTCTCTCTCTCGTCGCTTC 59.407 57.143 0.00 0.00 0.00 3.86
25 26 1.206132 TCTCTCTCTCTCTCGTCGCTT 59.794 52.381 0.00 0.00 0.00 4.68
26 27 0.821517 TCTCTCTCTCTCTCGTCGCT 59.178 55.000 0.00 0.00 0.00 4.93
27 28 0.928229 GTCTCTCTCTCTCTCGTCGC 59.072 60.000 0.00 0.00 0.00 5.19
28 29 1.197055 CGTCTCTCTCTCTCTCGTCG 58.803 60.000 0.00 0.00 0.00 5.12
29 30 0.928229 GCGTCTCTCTCTCTCTCGTC 59.072 60.000 0.00 0.00 0.00 4.20
30 31 0.248012 TGCGTCTCTCTCTCTCTCGT 59.752 55.000 0.00 0.00 0.00 4.18
31 32 1.062002 GTTGCGTCTCTCTCTCTCTCG 59.938 57.143 0.00 0.00 0.00 4.04
32 33 1.062002 CGTTGCGTCTCTCTCTCTCTC 59.938 57.143 0.00 0.00 0.00 3.20
33 34 1.083489 CGTTGCGTCTCTCTCTCTCT 58.917 55.000 0.00 0.00 0.00 3.10
34 35 0.098025 CCGTTGCGTCTCTCTCTCTC 59.902 60.000 0.00 0.00 0.00 3.20
35 36 0.321741 TCCGTTGCGTCTCTCTCTCT 60.322 55.000 0.00 0.00 0.00 3.10
36 37 0.736053 ATCCGTTGCGTCTCTCTCTC 59.264 55.000 0.00 0.00 0.00 3.20
37 38 0.736053 GATCCGTTGCGTCTCTCTCT 59.264 55.000 0.00 0.00 0.00 3.10
38 39 0.590230 CGATCCGTTGCGTCTCTCTC 60.590 60.000 0.00 0.00 0.00 3.20
39 40 1.025113 TCGATCCGTTGCGTCTCTCT 61.025 55.000 0.00 0.00 0.00 3.10
40 41 0.862283 GTCGATCCGTTGCGTCTCTC 60.862 60.000 0.00 0.00 0.00 3.20
41 42 1.136984 GTCGATCCGTTGCGTCTCT 59.863 57.895 0.00 0.00 0.00 3.10
42 43 1.154093 TGTCGATCCGTTGCGTCTC 60.154 57.895 0.00 0.00 0.00 3.36
43 44 1.443872 GTGTCGATCCGTTGCGTCT 60.444 57.895 0.00 0.00 0.00 4.18
44 45 1.076533 ATGTGTCGATCCGTTGCGTC 61.077 55.000 0.00 0.00 0.00 5.19
45 46 0.171679 TATGTGTCGATCCGTTGCGT 59.828 50.000 0.00 0.00 0.00 5.24
46 47 0.570734 GTATGTGTCGATCCGTTGCG 59.429 55.000 0.00 0.00 0.00 4.85
47 48 1.635844 TGTATGTGTCGATCCGTTGC 58.364 50.000 0.00 0.00 0.00 4.17
64 65 4.987408 TCATTTCATTTCATCCGCATGT 57.013 36.364 0.00 0.00 0.00 3.21
66 67 6.575267 TCATTTCATTTCATTTCATCCGCAT 58.425 32.000 0.00 0.00 0.00 4.73
67 68 5.963594 TCATTTCATTTCATTTCATCCGCA 58.036 33.333 0.00 0.00 0.00 5.69
68 69 6.890663 TTCATTTCATTTCATTTCATCCGC 57.109 33.333 0.00 0.00 0.00 5.54
69 70 7.042321 CCCATTCATTTCATTTCATTTCATCCG 60.042 37.037 0.00 0.00 0.00 4.18
70 71 7.988599 TCCCATTCATTTCATTTCATTTCATCC 59.011 33.333 0.00 0.00 0.00 3.51
71 72 8.823818 GTCCCATTCATTTCATTTCATTTCATC 58.176 33.333 0.00 0.00 0.00 2.92
72 73 8.322828 TGTCCCATTCATTTCATTTCATTTCAT 58.677 29.630 0.00 0.00 0.00 2.57
73 74 7.677892 TGTCCCATTCATTTCATTTCATTTCA 58.322 30.769 0.00 0.00 0.00 2.69
74 75 7.201582 GCTGTCCCATTCATTTCATTTCATTTC 60.202 37.037 0.00 0.00 0.00 2.17
75 76 6.596497 GCTGTCCCATTCATTTCATTTCATTT 59.404 34.615 0.00 0.00 0.00 2.32
76 77 6.110707 GCTGTCCCATTCATTTCATTTCATT 58.889 36.000 0.00 0.00 0.00 2.57
81 82 4.622220 GCTTGCTGTCCCATTCATTTCATT 60.622 41.667 0.00 0.00 0.00 2.57
93 94 0.598419 GTTTGCTTGCTTGCTGTCCC 60.598 55.000 3.47 0.00 0.00 4.46
204 223 5.503634 TTGATTTGTGGATCAGAGGAGAA 57.496 39.130 0.00 0.00 37.35 2.87
207 226 5.419788 CCAATTTGATTTGTGGATCAGAGGA 59.580 40.000 0.00 0.00 37.35 3.71
229 248 3.649023 ACGGGCCTGATTATACATAACCA 59.351 43.478 21.41 0.00 0.00 3.67
250 276 4.916249 GGAGATTTGGATCACGTACGATAC 59.084 45.833 24.41 7.29 34.60 2.24
252 278 3.243771 GGGAGATTTGGATCACGTACGAT 60.244 47.826 24.41 5.58 34.60 3.73
253 279 2.100252 GGGAGATTTGGATCACGTACGA 59.900 50.000 24.41 0.00 34.60 3.43
255 281 2.470821 CGGGAGATTTGGATCACGTAC 58.529 52.381 0.00 0.00 34.60 3.67
257 283 0.462047 GCGGGAGATTTGGATCACGT 60.462 55.000 0.00 0.00 34.60 4.49
258 284 1.160329 GGCGGGAGATTTGGATCACG 61.160 60.000 0.00 0.00 34.60 4.35
259 285 0.107214 TGGCGGGAGATTTGGATCAC 60.107 55.000 0.00 0.00 34.60 3.06
288 314 3.302347 AAGACGAGGGAAGCGCCAG 62.302 63.158 2.29 0.00 38.95 4.85
305 331 4.344865 GGGCGGAACAGGGAGCAA 62.345 66.667 0.00 0.00 0.00 3.91
343 369 2.789203 GATCCACGACGCTTGCGTC 61.789 63.158 30.61 30.61 40.44 5.19
344 370 2.809601 GATCCACGACGCTTGCGT 60.810 61.111 20.76 20.76 43.67 5.24
345 371 2.792290 CTGATCCACGACGCTTGCG 61.792 63.158 13.70 13.70 0.00 4.85
346 372 2.456119 CCTGATCCACGACGCTTGC 61.456 63.158 0.00 0.00 0.00 4.01
361 387 1.086634 GGCAAAGCTAGCGTCTCCTG 61.087 60.000 9.55 2.25 0.00 3.86
364 390 1.014564 AACGGCAAAGCTAGCGTCTC 61.015 55.000 9.55 1.35 0.00 3.36
365 391 1.004918 AACGGCAAAGCTAGCGTCT 60.005 52.632 9.55 0.00 0.00 4.18
523 567 0.234884 AACTAAAACTCAGCGCGCAC 59.765 50.000 35.10 4.34 0.00 5.34
527 571 3.959943 TCCAAAAACTAAAACTCAGCGC 58.040 40.909 0.00 0.00 0.00 5.92
534 578 6.073927 ACGATCGAGTCTCCAAAAACTAAAAC 60.074 38.462 24.34 0.00 0.00 2.43
650 701 9.136952 GAACCAGATGAAATGAAATGAAAGAAG 57.863 33.333 0.00 0.00 0.00 2.85
655 706 6.380995 CACGAACCAGATGAAATGAAATGAA 58.619 36.000 0.00 0.00 0.00 2.57
657 708 4.560035 GCACGAACCAGATGAAATGAAATG 59.440 41.667 0.00 0.00 0.00 2.32
658 709 4.460382 AGCACGAACCAGATGAAATGAAAT 59.540 37.500 0.00 0.00 0.00 2.17
664 716 7.624360 AATAATTAGCACGAACCAGATGAAA 57.376 32.000 0.00 0.00 0.00 2.69
702 762 1.272490 CTGTCTGGTAAGCCGACTGAA 59.728 52.381 7.14 0.00 38.33 3.02
711 771 3.553096 GGTCAGTGTCACTGTCTGGTAAG 60.553 52.174 27.97 4.11 46.03 2.34
728 788 3.957260 CAGCTGTTCGGTGGTCAG 58.043 61.111 5.25 0.00 37.47 3.51
759 819 7.748847 TGGATTTCAATCGACTAAAAACTAGC 58.251 34.615 0.00 0.00 36.27 3.42
821 881 0.457509 CTCTAGTGGCGTGTGCAGAG 60.458 60.000 0.00 0.00 45.35 3.35
891 951 4.980805 AAACCGAGCGCGCAGGAA 62.981 61.111 39.31 0.00 35.83 3.36
894 954 4.430423 GTGAAACCGAGCGCGCAG 62.430 66.667 35.10 25.61 35.83 5.18
895 955 4.961511 AGTGAAACCGAGCGCGCA 62.962 61.111 35.10 6.63 37.80 6.09
939 1002 5.548446 AGCTAAGGGAAGAAAAGGAACTAGT 59.452 40.000 0.00 0.00 38.49 2.57
1067 1132 1.677217 CCGGCCTTCTTCCTCTTCTTG 60.677 57.143 0.00 0.00 0.00 3.02
1619 1684 3.225235 GCGAAGAGCTCCTCCCAT 58.775 61.111 10.93 0.00 44.04 4.00
1657 1725 0.250038 ACGCTTCTGCTTCTGCTTCA 60.250 50.000 0.00 0.00 40.48 3.02
1729 1797 2.728015 CGTGTCAGTGCGTGCGTA 60.728 61.111 0.00 0.00 0.00 4.42
1730 1798 2.940250 TAACGTGTCAGTGCGTGCGT 62.940 55.000 0.00 0.00 41.42 5.24
1731 1799 1.813212 TTAACGTGTCAGTGCGTGCG 61.813 55.000 0.00 0.00 41.42 5.34
1732 1800 0.382636 GTTAACGTGTCAGTGCGTGC 60.383 55.000 0.00 0.00 41.42 5.34
1733 1801 1.205657 AGTTAACGTGTCAGTGCGTG 58.794 50.000 0.00 0.00 41.42 5.34
1734 1802 2.223548 TGTAGTTAACGTGTCAGTGCGT 60.224 45.455 0.00 0.00 43.64 5.24
1745 1821 4.853743 GGAGTTTACGGACTGTAGTTAACG 59.146 45.833 0.00 0.00 35.73 3.18
1784 1864 3.056328 GCAACAACTCCCGAGGGC 61.056 66.667 2.58 0.00 34.68 5.19
1794 1874 2.736682 CGGATCGGACGGCAACAAC 61.737 63.158 0.00 0.00 0.00 3.32
1825 1905 0.904649 TCATCACATGAGGCCGAGTT 59.095 50.000 0.00 0.00 33.59 3.01
1826 1906 0.176680 GTCATCACATGAGGCCGAGT 59.823 55.000 0.00 0.00 40.53 4.18
1828 1908 0.977627 AGGTCATCACATGAGGCCGA 60.978 55.000 0.00 0.00 40.53 5.54
1834 1914 3.434309 TCAGACTCAGGTCATCACATGA 58.566 45.455 0.00 0.00 44.36 3.07
1835 1915 3.881937 TCAGACTCAGGTCATCACATG 57.118 47.619 0.00 0.00 44.36 3.21
1836 1916 4.468868 TGATTCAGACTCAGGTCATCACAT 59.531 41.667 0.00 0.00 44.36 3.21
1837 1917 3.834231 TGATTCAGACTCAGGTCATCACA 59.166 43.478 0.00 0.00 44.36 3.58
1838 1918 4.081752 ACTGATTCAGACTCAGGTCATCAC 60.082 45.833 20.33 0.00 43.58 3.06
1840 1920 4.734398 ACTGATTCAGACTCAGGTCATC 57.266 45.455 20.33 0.00 43.58 2.92
1845 1971 4.142182 GGAGAGAACTGATTCAGACTCAGG 60.142 50.000 28.25 4.74 43.58 3.86
1847 1973 4.671831 AGGAGAGAACTGATTCAGACTCA 58.328 43.478 28.25 0.00 39.04 3.41
1851 1977 3.020274 CGGAGGAGAGAACTGATTCAGA 58.980 50.000 20.33 0.00 37.29 3.27
1901 2027 3.048337 ACATTCACGGGAAATGTACGT 57.952 42.857 3.14 0.00 42.17 3.57
1902 2028 3.742786 CAACATTCACGGGAAATGTACG 58.257 45.455 3.14 1.70 36.43 3.67
1903 2029 3.498082 GCAACATTCACGGGAAATGTAC 58.502 45.455 3.14 2.71 36.43 2.90
1920 2046 1.277495 GAGCAACAATGGCACGCAAC 61.277 55.000 0.00 0.00 0.00 4.17
1935 2061 1.276421 GAGGGAGTAGCAAACAGAGCA 59.724 52.381 0.00 0.00 0.00 4.26
1939 2065 0.608640 ACGGAGGGAGTAGCAAACAG 59.391 55.000 0.00 0.00 0.00 3.16
1946 2072 3.521947 AATTTCGAACGGAGGGAGTAG 57.478 47.619 0.00 0.00 0.00 2.57
1947 2073 4.019174 AGTAATTTCGAACGGAGGGAGTA 58.981 43.478 0.00 0.00 0.00 2.59
1948 2074 2.830321 AGTAATTTCGAACGGAGGGAGT 59.170 45.455 0.00 0.00 0.00 3.85
1949 2075 3.521947 AGTAATTTCGAACGGAGGGAG 57.478 47.619 0.00 0.00 0.00 4.30
1950 2076 3.007182 ACAAGTAATTTCGAACGGAGGGA 59.993 43.478 0.00 0.00 0.00 4.20
1951 2077 3.332034 ACAAGTAATTTCGAACGGAGGG 58.668 45.455 0.00 0.00 0.00 4.30
1952 2078 4.243270 AGACAAGTAATTTCGAACGGAGG 58.757 43.478 0.00 0.00 0.00 4.30
1953 2079 4.030306 CGAGACAAGTAATTTCGAACGGAG 59.970 45.833 0.00 0.00 33.38 4.63
1954 2080 3.916172 CGAGACAAGTAATTTCGAACGGA 59.084 43.478 0.00 0.00 33.38 4.69
1955 2081 3.060363 CCGAGACAAGTAATTTCGAACGG 59.940 47.826 0.00 0.00 33.38 4.44
1956 2082 3.916172 TCCGAGACAAGTAATTTCGAACG 59.084 43.478 0.00 0.00 33.38 3.95
1957 2083 5.834239 TTCCGAGACAAGTAATTTCGAAC 57.166 39.130 0.00 0.00 33.38 3.95
1958 2084 8.030692 TCTATTTCCGAGACAAGTAATTTCGAA 58.969 33.333 0.00 0.00 33.38 3.71
1959 2085 7.541162 TCTATTTCCGAGACAAGTAATTTCGA 58.459 34.615 0.00 0.00 33.38 3.71
1960 2086 7.751047 TCTATTTCCGAGACAAGTAATTTCG 57.249 36.000 0.00 0.00 0.00 3.46
1961 2087 9.099454 ACATCTATTTCCGAGACAAGTAATTTC 57.901 33.333 0.00 0.00 0.00 2.17
1967 2093 9.751542 CTAAATACATCTATTTCCGAGACAAGT 57.248 33.333 0.00 0.00 34.83 3.16
1968 2094 9.967346 TCTAAATACATCTATTTCCGAGACAAG 57.033 33.333 0.00 0.00 34.83 3.16
1970 2096 9.745880 GTTCTAAATACATCTATTTCCGAGACA 57.254 33.333 0.00 0.00 34.83 3.41
1971 2097 9.968870 AGTTCTAAATACATCTATTTCCGAGAC 57.031 33.333 0.00 0.00 34.83 3.36
2003 2129 9.900710 GTCGTAGAAATGAATGTATCTAGATGT 57.099 33.333 15.79 0.00 39.69 3.06
2004 2130 9.899226 TGTCGTAGAAATGAATGTATCTAGATG 57.101 33.333 15.79 0.00 39.69 2.90
2006 2132 9.952188 CTTGTCGTAGAAATGAATGTATCTAGA 57.048 33.333 0.00 0.00 39.69 2.43
2007 2133 9.737427 ACTTGTCGTAGAAATGAATGTATCTAG 57.263 33.333 0.00 0.00 39.69 2.43
2013 2139 8.665685 GGAATTACTTGTCGTAGAAATGAATGT 58.334 33.333 0.00 0.00 39.69 2.71
2014 2140 7.846107 CGGAATTACTTGTCGTAGAAATGAATG 59.154 37.037 0.00 0.00 39.69 2.67
2015 2141 7.762615 TCGGAATTACTTGTCGTAGAAATGAAT 59.237 33.333 0.00 0.00 39.69 2.57
2016 2142 7.092079 TCGGAATTACTTGTCGTAGAAATGAA 58.908 34.615 0.00 0.00 39.69 2.57
2017 2143 6.623486 TCGGAATTACTTGTCGTAGAAATGA 58.377 36.000 0.00 0.00 39.69 2.57
2018 2144 6.880822 TCGGAATTACTTGTCGTAGAAATG 57.119 37.500 0.00 0.00 39.69 2.32
2019 2145 6.034256 CGTTCGGAATTACTTGTCGTAGAAAT 59.966 38.462 0.00 0.00 39.69 2.17
2020 2146 5.343058 CGTTCGGAATTACTTGTCGTAGAAA 59.657 40.000 0.00 0.00 39.69 2.52
2021 2147 4.853196 CGTTCGGAATTACTTGTCGTAGAA 59.147 41.667 0.00 0.00 39.69 2.10
2022 2148 4.406069 CGTTCGGAATTACTTGTCGTAGA 58.594 43.478 0.00 0.00 0.00 2.59
2023 2149 3.545078 CCGTTCGGAATTACTTGTCGTAG 59.455 47.826 5.19 0.00 0.00 3.51
2024 2150 3.190327 TCCGTTCGGAATTACTTGTCGTA 59.810 43.478 11.66 0.00 0.00 3.43
2025 2151 2.030007 TCCGTTCGGAATTACTTGTCGT 60.030 45.455 11.66 0.00 0.00 4.34
2026 2152 2.597305 CTCCGTTCGGAATTACTTGTCG 59.403 50.000 14.79 0.00 33.41 4.35
2027 2153 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
2028 2154 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
2029 2155 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
2030 2156 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
2031 2157 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
2032 2158 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
2033 2159 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
2034 2160 1.479730 GTACTCCCTCCGTTCGGAATT 59.520 52.381 14.79 0.00 33.41 2.17
2035 2161 1.109609 GTACTCCCTCCGTTCGGAAT 58.890 55.000 14.79 2.09 33.41 3.01
2036 2162 0.038744 AGTACTCCCTCCGTTCGGAA 59.961 55.000 14.79 0.04 33.41 4.30
2037 2163 0.038744 AAGTACTCCCTCCGTTCGGA 59.961 55.000 13.34 13.34 0.00 4.55
2038 2164 0.455005 GAAGTACTCCCTCCGTTCGG 59.545 60.000 4.74 4.74 0.00 4.30
2039 2165 1.401199 GAGAAGTACTCCCTCCGTTCG 59.599 57.143 12.00 0.00 39.53 3.95
2040 2166 2.164017 GTGAGAAGTACTCCCTCCGTTC 59.836 54.545 17.51 1.79 44.34 3.95
2041 2167 2.169330 GTGAGAAGTACTCCCTCCGTT 58.831 52.381 17.51 0.00 44.34 4.44
2042 2168 1.836802 GTGAGAAGTACTCCCTCCGT 58.163 55.000 17.51 0.00 44.34 4.69
2043 2169 0.733729 CGTGAGAAGTACTCCCTCCG 59.266 60.000 17.51 16.07 44.34 4.63
2044 2170 0.456628 GCGTGAGAAGTACTCCCTCC 59.543 60.000 17.51 10.78 44.34 4.30
2045 2171 0.099082 CGCGTGAGAAGTACTCCCTC 59.901 60.000 14.83 14.83 44.34 4.30
2046 2172 0.608582 ACGCGTGAGAAGTACTCCCT 60.609 55.000 12.93 0.00 44.34 4.20
2047 2173 0.243095 AACGCGTGAGAAGTACTCCC 59.757 55.000 14.98 0.00 44.34 4.30
2048 2174 1.337821 CAACGCGTGAGAAGTACTCC 58.662 55.000 14.98 0.00 44.34 3.85
2049 2175 0.708918 GCAACGCGTGAGAAGTACTC 59.291 55.000 14.98 0.00 45.11 2.59
2050 2176 2.810486 GCAACGCGTGAGAAGTACT 58.190 52.632 14.98 0.00 0.00 2.73
2097 2238 1.153823 CTTCCGCCTGTCGATTCGT 60.154 57.895 5.89 0.00 41.67 3.85
2098 2239 2.517450 GCTTCCGCCTGTCGATTCG 61.517 63.158 0.00 0.00 41.67 3.34
2100 2241 1.448540 CTGCTTCCGCCTGTCGATT 60.449 57.895 0.00 0.00 41.67 3.34
2101 2242 2.185350 CTGCTTCCGCCTGTCGAT 59.815 61.111 0.00 0.00 41.67 3.59
2102 2243 4.742201 GCTGCTTCCGCCTGTCGA 62.742 66.667 0.00 0.00 41.67 4.20
2109 2250 4.537433 ATCTCCCGCTGCTTCCGC 62.537 66.667 0.00 0.00 0.00 5.54
2176 2317 1.225704 CCCTCTCCCACCAAGCATC 59.774 63.158 0.00 0.00 0.00 3.91
2277 2430 6.057533 TCCCGTTTAAGTACTCGATATCTCA 58.942 40.000 0.00 0.00 0.00 3.27
2327 2480 2.076100 GACGCAGGTCACATCAATCAA 58.924 47.619 0.00 0.00 42.91 2.57
2340 2497 4.498520 ATCTCGCACCGACGCAGG 62.499 66.667 0.00 0.00 37.30 4.85
2381 2542 1.501741 CGGCATTTTCAGTCACGGG 59.498 57.895 0.00 0.00 0.00 5.28
2492 2653 5.290386 GGATGACAAGTATTTCCGGACTAG 58.710 45.833 1.83 0.00 0.00 2.57
2494 2655 3.430374 CGGATGACAAGTATTTCCGGACT 60.430 47.826 1.83 0.00 44.24 3.85
2495 2656 2.864343 CGGATGACAAGTATTTCCGGAC 59.136 50.000 1.83 0.00 44.24 4.79
2496 2657 3.173668 CGGATGACAAGTATTTCCGGA 57.826 47.619 0.00 0.00 44.24 5.14
2499 2660 3.270877 AGCACGGATGACAAGTATTTCC 58.729 45.455 0.00 0.00 0.00 3.13
2500 2661 5.109903 ACTAGCACGGATGACAAGTATTTC 58.890 41.667 0.00 0.00 0.00 2.17
2501 2662 5.086104 ACTAGCACGGATGACAAGTATTT 57.914 39.130 0.00 0.00 0.00 1.40
2502 2663 4.737855 ACTAGCACGGATGACAAGTATT 57.262 40.909 0.00 0.00 0.00 1.89
2503 2664 6.406692 AATACTAGCACGGATGACAAGTAT 57.593 37.500 0.00 0.00 32.38 2.12
2504 2665 5.847111 AATACTAGCACGGATGACAAGTA 57.153 39.130 0.00 0.00 0.00 2.24
2505 2666 4.737855 AATACTAGCACGGATGACAAGT 57.262 40.909 0.00 0.00 0.00 3.16
2506 2667 4.870426 ACAAATACTAGCACGGATGACAAG 59.130 41.667 0.00 0.00 0.00 3.16
2507 2668 4.827692 ACAAATACTAGCACGGATGACAA 58.172 39.130 0.00 0.00 0.00 3.18
2508 2669 4.465632 ACAAATACTAGCACGGATGACA 57.534 40.909 0.00 0.00 0.00 3.58
2509 2670 6.040878 ACTAACAAATACTAGCACGGATGAC 58.959 40.000 0.00 0.00 0.00 3.06
2510 2671 6.216801 ACTAACAAATACTAGCACGGATGA 57.783 37.500 0.00 0.00 0.00 2.92
2511 2672 6.312918 ACAACTAACAAATACTAGCACGGATG 59.687 38.462 0.00 0.00 0.00 3.51
2512 2673 6.403878 ACAACTAACAAATACTAGCACGGAT 58.596 36.000 0.00 0.00 0.00 4.18
2574 2737 7.189512 GGAAAAGTCATGGAATTTCTATGTCG 58.810 38.462 18.69 0.00 36.80 4.35
2588 2751 1.165270 GACACCCGGGAAAAGTCATG 58.835 55.000 32.02 15.30 0.00 3.07
2613 2776 1.199097 GTATTTGTGAAGCACCCGTGG 59.801 52.381 0.00 0.00 32.73 4.94
2616 2779 5.583061 TGTTATAGTATTTGTGAAGCACCCG 59.417 40.000 0.00 0.00 32.73 5.28
2636 2799 6.828273 AGCCATATGAAGTGCATAGTTTGTTA 59.172 34.615 3.65 0.00 42.45 2.41
2637 2800 5.653769 AGCCATATGAAGTGCATAGTTTGTT 59.346 36.000 3.65 0.00 42.45 2.83
2639 2802 5.506815 CCAGCCATATGAAGTGCATAGTTTG 60.507 44.000 3.65 0.00 42.45 2.93
2642 2805 3.497405 CCCAGCCATATGAAGTGCATAGT 60.497 47.826 3.65 0.00 42.45 2.12
2643 2806 3.079578 CCCAGCCATATGAAGTGCATAG 58.920 50.000 3.65 0.00 42.45 2.23
2644 2807 2.442878 ACCCAGCCATATGAAGTGCATA 59.557 45.455 3.65 0.00 43.28 3.14
2647 2810 1.312815 GACCCAGCCATATGAAGTGC 58.687 55.000 3.65 0.00 0.00 4.40
2648 2811 2.715749 TGACCCAGCCATATGAAGTG 57.284 50.000 3.65 0.00 0.00 3.16
2650 2813 4.217118 GCTAATTGACCCAGCCATATGAAG 59.783 45.833 3.65 0.00 0.00 3.02
2779 2945 1.824444 GCATGCATCCACCCACCATAT 60.824 52.381 14.21 0.00 0.00 1.78
2782 2948 2.362760 GCATGCATCCACCCACCA 60.363 61.111 14.21 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.