Multiple sequence alignment - TraesCS2A01G420900

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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 TraesCS2A01G420900 chr2A 100.000 5439 0 0 1 5439 676393755 676388317 0.000000e+00 10045
1 TraesCS2A01G420900 chr2A 80.193 207 29 9 4193 4393 676389521 676389321 1.580000e-30 145
2 TraesCS2A01G420900 chr2A 80.193 207 29 9 4235 4435 676389563 676389363 1.580000e-30 145
3 TraesCS2A01G420900 chr2B 95.219 2719 81 18 2075 4752 631803468 631800758 0.000000e+00 4255
4 TraesCS2A01G420900 chr2B 94.747 1999 63 13 2 1967 631805459 631803470 0.000000e+00 3072
5 TraesCS2A01G420900 chr2D 94.847 1999 64 11 2 1966 531940979 531938986 0.000000e+00 3085
6 TraesCS2A01G420900 chr2D 96.307 1083 33 4 3730 4810 531936972 531935895 0.000000e+00 1772
7 TraesCS2A01G420900 chr2D 97.672 902 19 2 2832 3732 531937975 531937075 0.000000e+00 1548
8 TraesCS2A01G420900 chr2D 96.892 547 14 2 2289 2835 531938630 531938087 0.000000e+00 913
9 TraesCS2A01G420900 chr2D 88.868 530 26 18 4796 5317 531935882 531935378 5.980000e-174 621
10 TraesCS2A01G420900 chr2D 92.857 224 14 2 2071 2292 531938987 531938764 1.890000e-84 324
11 TraesCS2A01G420900 chr2D 90.678 118 8 3 5323 5439 534403725 534403610 2.620000e-33 154
12 TraesCS2A01G420900 chr6A 95.070 142 5 1 4611 4752 378253997 378253858 7.090000e-54 222
13 TraesCS2A01G420900 chr6A 92.254 142 9 1 4611 4752 349888610 349888471 3.320000e-47 200
14 TraesCS2A01G420900 chr6A 92.035 113 8 1 5327 5439 60495172 60495061 2.030000e-34 158
15 TraesCS2A01G420900 chr3A 94.366 142 6 1 4611 4752 702415807 702415946 3.300000e-52 217
16 TraesCS2A01G420900 chr3A 91.667 108 8 1 1965 2072 156231329 156231223 1.220000e-31 148
17 TraesCS2A01G420900 chr3D 93.662 142 7 1 4611 4752 551129586 551129725 1.530000e-50 211
18 TraesCS2A01G420900 chr3D 92.857 112 6 1 5328 5439 597833744 597833853 1.570000e-35 161
19 TraesCS2A01G420900 chr3D 92.035 113 8 1 5327 5439 104099029 104098918 2.030000e-34 158
20 TraesCS2A01G420900 chr3D 92.035 113 8 1 5327 5439 506177311 506177200 2.030000e-34 158
21 TraesCS2A01G420900 chr6D 90.756 119 8 3 5322 5439 376939129 376939013 7.290000e-34 156
22 TraesCS2A01G420900 chr6D 91.150 113 9 1 5327 5439 31964825 31964714 9.440000e-33 152
23 TraesCS2A01G420900 chr5D 91.892 111 8 1 5327 5437 429353715 429353606 2.620000e-33 154
24 TraesCS2A01G420900 chr5D 88.710 124 13 1 5316 5439 521487797 521487919 3.390000e-32 150
25 TraesCS2A01G420900 chr5D 89.286 112 12 0 1961 2072 56805507 56805618 2.040000e-29 141
26 TraesCS2A01G420900 chr5D 88.889 108 11 1 1965 2072 371831360 371831466 1.230000e-26 132
27 TraesCS2A01G420900 chr4A 91.071 112 10 0 1961 2072 675970296 675970185 9.440000e-33 152
28 TraesCS2A01G420900 chr4A 89.091 110 12 0 1964 2073 274596289 274596180 2.640000e-28 137
29 TraesCS2A01G420900 chr5B 90.517 116 8 3 1965 2080 349086812 349086924 3.390000e-32 150
30 TraesCS2A01G420900 chr4D 89.286 112 12 0 1961 2072 128641912 128641801 2.040000e-29 141
31 TraesCS2A01G420900 chr7A 89.815 108 10 1 1965 2072 57873683 57873577 2.640000e-28 137
32 TraesCS2A01G420900 chr4B 87.719 114 14 0 1962 2075 621807 621920 3.420000e-27 134


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 TraesCS2A01G420900 chr2A 676388317 676393755 5438 True 10045.000000 10045 100.000000 1 5439 1 chr2A.!!$R1 5438
1 TraesCS2A01G420900 chr2B 631800758 631805459 4701 True 3663.500000 4255 94.983000 2 4752 2 chr2B.!!$R1 4750
2 TraesCS2A01G420900 chr2D 531935378 531940979 5601 True 1377.166667 3085 94.573833 2 5317 6 chr2D.!!$R2 5315

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
309 328 0.392327 GGCTGGAACAAGGAGAGAGC 60.392 60.000 0.00 0.00 38.70 4.09 F
1359 1412 0.319641 AGCGTTTCAGTCTCGGAACC 60.320 55.000 0.00 0.00 0.00 3.62 F
2029 2083 1.066002 TGAGCTGTTTTGCAAGCTGTC 59.934 47.619 15.16 3.25 37.79 3.51 F
2338 2531 0.042431 TAACAATTGGGCCCCTGCAT 59.958 50.000 22.27 9.27 40.13 3.96 F
2692 2885 1.474330 GGCCTGGTGTTTATCTTGGG 58.526 55.000 0.00 0.00 0.00 4.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1835 1889 0.322648 TAGCAGTGCATGTCTGTGCT 59.677 50.000 19.20 16.05 46.10 4.40 R
2254 2310 0.814812 ACGCTCTAGAGACTACCGGC 60.815 60.000 24.24 5.10 0.00 6.13 R
3433 3748 1.529948 ACCAACGACGAGGAGGTCA 60.530 57.895 15.92 0.00 36.73 4.02 R
3696 4011 3.068024 TGGAACATGAAGGAAACTGTTGC 59.932 43.478 0.00 0.00 42.68 4.17 R
4472 4917 0.321564 TTTGATCGTCCACAGGGCAG 60.322 55.000 0.00 0.00 0.00 4.85 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
96 97 4.123506 CTCTTCTTATTTCCTTCCGCCTC 58.876 47.826 0.00 0.00 0.00 4.70
155 156 3.453070 CTTAGCAGCTCGGCCTCCC 62.453 68.421 0.00 0.00 0.00 4.30
166 167 1.617018 CGGCCTCCCAAGACTCATCA 61.617 60.000 0.00 0.00 0.00 3.07
170 171 1.209019 CCTCCCAAGACTCATCACCAG 59.791 57.143 0.00 0.00 0.00 4.00
171 172 1.209019 CTCCCAAGACTCATCACCAGG 59.791 57.143 0.00 0.00 0.00 4.45
175 176 1.065854 CAAGACTCATCACCAGGGGAC 60.066 57.143 0.00 0.00 0.00 4.46
180 181 1.221840 CATCACCAGGGGACTTCCG 59.778 63.158 0.00 0.00 40.21 4.30
195 196 3.423154 CCGTTGCCGCTCTGTTCC 61.423 66.667 0.00 0.00 0.00 3.62
240 241 2.740055 CTCGCGTGCCTTCAGCTT 60.740 61.111 5.77 0.00 44.23 3.74
244 263 2.684843 GCGTGCCTTCAGCTTCAGG 61.685 63.158 3.78 3.78 44.23 3.86
246 265 0.886490 CGTGCCTTCAGCTTCAGGTT 60.886 55.000 9.33 0.00 44.23 3.50
252 271 3.570125 GCCTTCAGCTTCAGGTTAAAGTT 59.430 43.478 9.33 0.00 38.99 2.66
309 328 0.392327 GGCTGGAACAAGGAGAGAGC 60.392 60.000 0.00 0.00 38.70 4.09
436 455 2.639327 GGTGCCGCCTGCTGAATTT 61.639 57.895 0.00 0.00 42.00 1.82
438 457 2.507769 GCCGCCTGCTGAATTTGC 60.508 61.111 0.00 0.00 36.87 3.68
441 460 1.512734 CGCCTGCTGAATTTGCGTC 60.513 57.895 0.00 0.00 40.33 5.19
509 530 4.989279 AGTTGTGATGTGGATTTATGCC 57.011 40.909 0.00 0.00 0.00 4.40
516 537 2.676748 TGTGGATTTATGCCCATTCCC 58.323 47.619 0.00 0.00 34.58 3.97
582 603 0.618968 ATGGAGACTTCCTTCGCCCT 60.619 55.000 0.00 0.00 44.36 5.19
607 628 2.494870 GCTTTTGCAGATTCCACCATCT 59.505 45.455 0.00 0.00 46.58 2.90
609 630 4.158394 GCTTTTGCAGATTCCACCATCTTA 59.842 41.667 0.00 0.00 46.58 2.10
614 635 6.438186 TGCAGATTCCACCATCTTATGATA 57.562 37.500 0.00 0.00 30.50 2.15
617 638 7.392393 TGCAGATTCCACCATCTTATGATATTG 59.608 37.037 0.00 0.00 30.50 1.90
618 639 7.627939 GCAGATTCCACCATCTTATGATATTGC 60.628 40.741 0.00 0.00 30.50 3.56
631 652 3.018856 TGATATTGCCTGCTTGGTTCTG 58.981 45.455 0.00 0.00 38.35 3.02
636 657 4.093952 CTGCTTGGTTCTGCGGCG 62.094 66.667 0.51 0.51 0.00 6.46
800 821 6.204688 CCAGCACTTGTTTATTCTCTTGTGTA 59.795 38.462 0.00 0.00 0.00 2.90
801 822 7.094634 CCAGCACTTGTTTATTCTCTTGTGTAT 60.095 37.037 0.00 0.00 0.00 2.29
802 823 8.935844 CAGCACTTGTTTATTCTCTTGTGTATA 58.064 33.333 0.00 0.00 0.00 1.47
1004 1057 1.872952 TCAACTGTTCGGCACAATGAG 59.127 47.619 0.00 0.00 33.87 2.90
1056 1109 3.759544 ACGCAGTCGGAAGAGTCA 58.240 55.556 0.00 0.00 43.20 3.41
1089 1142 2.048603 GGGGCATTGCTCTCACCAC 61.049 63.158 8.71 0.00 0.00 4.16
1122 1175 1.003003 TGTTCTCCATCGATGCAACCA 59.997 47.619 20.25 9.05 0.00 3.67
1359 1412 0.319641 AGCGTTTCAGTCTCGGAACC 60.320 55.000 0.00 0.00 0.00 3.62
1473 1526 1.508088 GAACCAATGCCTTCCTGCG 59.492 57.895 0.00 0.00 0.00 5.18
1545 1598 2.035066 CAGGCTTGTTTTCAGACTTGGG 59.965 50.000 0.00 0.00 0.00 4.12
1546 1599 2.091885 AGGCTTGTTTTCAGACTTGGGA 60.092 45.455 0.00 0.00 0.00 4.37
1547 1600 2.294512 GGCTTGTTTTCAGACTTGGGAG 59.705 50.000 0.00 0.00 0.00 4.30
1548 1601 2.952310 GCTTGTTTTCAGACTTGGGAGT 59.048 45.455 0.00 0.00 39.32 3.85
1652 1706 7.223971 GTCGTAGAATTTTCATACTATGGTGCA 59.776 37.037 0.00 0.00 39.69 4.57
1835 1889 6.461370 GCTGCCATGTGTATAAATTGGATTGA 60.461 38.462 0.00 0.00 0.00 2.57
1932 1986 6.922957 GGACAAAGTGAATAAAATTGCAGTGA 59.077 34.615 0.00 0.00 0.00 3.41
1934 1988 6.417635 ACAAAGTGAATAAAATTGCAGTGACG 59.582 34.615 0.00 0.00 0.00 4.35
1967 2021 3.629087 ACACGGGCTGATAGTTACTACT 58.371 45.455 0.00 0.00 38.44 2.57
1968 2022 3.631227 ACACGGGCTGATAGTTACTACTC 59.369 47.826 0.00 0.00 35.78 2.59
1969 2023 3.004524 CACGGGCTGATAGTTACTACTCC 59.995 52.174 0.00 0.00 35.78 3.85
1970 2024 2.557490 CGGGCTGATAGTTACTACTCCC 59.443 54.545 0.00 2.59 35.78 4.30
1971 2025 3.751245 CGGGCTGATAGTTACTACTCCCT 60.751 52.174 13.95 0.00 33.34 4.20
1972 2026 3.827876 GGGCTGATAGTTACTACTCCCTC 59.172 52.174 0.00 0.00 32.95 4.30
1973 2027 3.827876 GGCTGATAGTTACTACTCCCTCC 59.172 52.174 0.00 0.00 35.78 4.30
1974 2028 3.502979 GCTGATAGTTACTACTCCCTCCG 59.497 52.174 0.00 0.00 35.78 4.63
1975 2029 4.716794 CTGATAGTTACTACTCCCTCCGT 58.283 47.826 0.00 0.00 35.78 4.69
1976 2030 5.121380 TGATAGTTACTACTCCCTCCGTT 57.879 43.478 0.00 0.00 35.78 4.44
1977 2031 5.128919 TGATAGTTACTACTCCCTCCGTTC 58.871 45.833 0.00 0.00 35.78 3.95
1978 2032 3.446442 AGTTACTACTCCCTCCGTTCA 57.554 47.619 0.00 0.00 0.00 3.18
1979 2033 3.978610 AGTTACTACTCCCTCCGTTCAT 58.021 45.455 0.00 0.00 0.00 2.57
1980 2034 4.351127 AGTTACTACTCCCTCCGTTCATT 58.649 43.478 0.00 0.00 0.00 2.57
1981 2035 4.776308 AGTTACTACTCCCTCCGTTCATTT 59.224 41.667 0.00 0.00 0.00 2.32
1982 2036 5.247792 AGTTACTACTCCCTCCGTTCATTTT 59.752 40.000 0.00 0.00 0.00 1.82
1983 2037 4.635699 ACTACTCCCTCCGTTCATTTTT 57.364 40.909 0.00 0.00 0.00 1.94
1984 2038 5.750352 ACTACTCCCTCCGTTCATTTTTA 57.250 39.130 0.00 0.00 0.00 1.52
1985 2039 6.309389 ACTACTCCCTCCGTTCATTTTTAT 57.691 37.500 0.00 0.00 0.00 1.40
1986 2040 7.427989 ACTACTCCCTCCGTTCATTTTTATA 57.572 36.000 0.00 0.00 0.00 0.98
1987 2041 7.854337 ACTACTCCCTCCGTTCATTTTTATAA 58.146 34.615 0.00 0.00 0.00 0.98
1988 2042 7.985752 ACTACTCCCTCCGTTCATTTTTATAAG 59.014 37.037 0.00 0.00 0.00 1.73
1989 2043 6.718294 ACTCCCTCCGTTCATTTTTATAAGT 58.282 36.000 0.00 0.00 0.00 2.24
1990 2044 6.822170 ACTCCCTCCGTTCATTTTTATAAGTC 59.178 38.462 0.00 0.00 0.00 3.01
1991 2045 5.813672 TCCCTCCGTTCATTTTTATAAGTCG 59.186 40.000 0.00 0.00 0.00 4.18
1992 2046 5.583457 CCCTCCGTTCATTTTTATAAGTCGT 59.417 40.000 0.00 0.00 0.00 4.34
1993 2047 6.093082 CCCTCCGTTCATTTTTATAAGTCGTT 59.907 38.462 0.00 0.00 0.00 3.85
1994 2048 7.361457 CCCTCCGTTCATTTTTATAAGTCGTTT 60.361 37.037 0.00 0.00 0.00 3.60
1995 2049 7.691050 CCTCCGTTCATTTTTATAAGTCGTTTC 59.309 37.037 0.00 0.00 0.00 2.78
1996 2050 8.085720 TCCGTTCATTTTTATAAGTCGTTTCA 57.914 30.769 0.00 0.00 0.00 2.69
1997 2051 8.557864 TCCGTTCATTTTTATAAGTCGTTTCAA 58.442 29.630 0.00 0.00 0.00 2.69
1998 2052 9.171701 CCGTTCATTTTTATAAGTCGTTTCAAA 57.828 29.630 0.00 0.00 0.00 2.69
1999 2053 9.968620 CGTTCATTTTTATAAGTCGTTTCAAAC 57.031 29.630 0.00 0.00 0.00 2.93
2010 2064 6.869421 AGTCGTTTCAAACAACTGAAATTG 57.131 33.333 0.22 0.11 44.76 2.32
2011 2065 6.616947 AGTCGTTTCAAACAACTGAAATTGA 58.383 32.000 0.22 2.16 44.76 2.57
2012 2066 6.747280 AGTCGTTTCAAACAACTGAAATTGAG 59.253 34.615 0.22 0.00 44.76 3.02
2013 2067 5.514914 TCGTTTCAAACAACTGAAATTGAGC 59.485 36.000 0.22 0.00 44.76 4.26
2014 2068 5.516339 CGTTTCAAACAACTGAAATTGAGCT 59.484 36.000 0.22 0.00 44.76 4.09
2015 2069 6.506827 CGTTTCAAACAACTGAAATTGAGCTG 60.507 38.462 0.22 0.00 44.76 4.24
2016 2070 5.581126 TCAAACAACTGAAATTGAGCTGT 57.419 34.783 0.00 0.00 33.57 4.40
2017 2071 5.964758 TCAAACAACTGAAATTGAGCTGTT 58.035 33.333 0.00 0.00 33.57 3.16
2018 2072 6.397272 TCAAACAACTGAAATTGAGCTGTTT 58.603 32.000 7.88 7.88 36.29 2.83
2019 2073 6.873076 TCAAACAACTGAAATTGAGCTGTTTT 59.127 30.769 10.40 0.00 34.28 2.43
2020 2074 6.651755 AACAACTGAAATTGAGCTGTTTTG 57.348 33.333 0.00 0.00 33.57 2.44
2021 2075 4.567959 ACAACTGAAATTGAGCTGTTTTGC 59.432 37.500 0.00 0.00 33.57 3.68
2022 2076 4.389890 ACTGAAATTGAGCTGTTTTGCA 57.610 36.364 0.00 0.00 34.99 4.08
2023 2077 4.757594 ACTGAAATTGAGCTGTTTTGCAA 58.242 34.783 0.00 0.00 34.99 4.08
2024 2078 4.807304 ACTGAAATTGAGCTGTTTTGCAAG 59.193 37.500 0.00 0.00 34.99 4.01
2025 2079 3.556775 TGAAATTGAGCTGTTTTGCAAGC 59.443 39.130 0.00 0.00 34.99 4.01
2026 2080 3.464111 AATTGAGCTGTTTTGCAAGCT 57.536 38.095 10.36 10.36 40.68 3.74
2027 2081 2.212869 TTGAGCTGTTTTGCAAGCTG 57.787 45.000 15.16 9.84 37.79 4.24
2028 2082 1.105457 TGAGCTGTTTTGCAAGCTGT 58.895 45.000 15.16 0.00 37.79 4.40
2029 2083 1.066002 TGAGCTGTTTTGCAAGCTGTC 59.934 47.619 15.16 3.25 37.79 3.51
2030 2084 1.336125 GAGCTGTTTTGCAAGCTGTCT 59.664 47.619 15.16 9.80 37.79 3.41
2031 2085 1.066605 AGCTGTTTTGCAAGCTGTCTG 59.933 47.619 9.80 1.60 36.15 3.51
2032 2086 1.066002 GCTGTTTTGCAAGCTGTCTGA 59.934 47.619 0.00 0.00 0.00 3.27
2033 2087 2.480073 GCTGTTTTGCAAGCTGTCTGAA 60.480 45.455 0.00 0.00 0.00 3.02
2034 2088 3.772932 CTGTTTTGCAAGCTGTCTGAAA 58.227 40.909 0.00 0.00 0.00 2.69
2035 2089 4.365723 CTGTTTTGCAAGCTGTCTGAAAT 58.634 39.130 0.00 0.00 0.00 2.17
2036 2090 4.114073 TGTTTTGCAAGCTGTCTGAAATG 58.886 39.130 0.00 0.00 0.00 2.32
2037 2091 4.114794 GTTTTGCAAGCTGTCTGAAATGT 58.885 39.130 0.00 0.00 0.00 2.71
2038 2092 5.163571 TGTTTTGCAAGCTGTCTGAAATGTA 60.164 36.000 0.00 0.00 0.00 2.29
2039 2093 5.710513 TTTGCAAGCTGTCTGAAATGTAT 57.289 34.783 0.00 0.00 0.00 2.29
2040 2094 6.816134 TTTGCAAGCTGTCTGAAATGTATA 57.184 33.333 0.00 0.00 0.00 1.47
2041 2095 5.801350 TGCAAGCTGTCTGAAATGTATAC 57.199 39.130 0.00 0.00 0.00 1.47
2042 2096 5.244755 TGCAAGCTGTCTGAAATGTATACA 58.755 37.500 8.27 8.27 0.00 2.29
2043 2097 5.704978 TGCAAGCTGTCTGAAATGTATACAA 59.295 36.000 10.14 0.00 0.00 2.41
2044 2098 6.375174 TGCAAGCTGTCTGAAATGTATACAAT 59.625 34.615 10.14 0.00 0.00 2.71
2045 2099 7.094248 TGCAAGCTGTCTGAAATGTATACAATT 60.094 33.333 10.14 7.87 0.00 2.32
2046 2100 7.430502 GCAAGCTGTCTGAAATGTATACAATTC 59.569 37.037 21.76 21.76 36.55 2.17
2047 2101 7.559590 AGCTGTCTGAAATGTATACAATTCC 57.440 36.000 24.31 13.54 35.47 3.01
2048 2102 7.341805 AGCTGTCTGAAATGTATACAATTCCT 58.658 34.615 24.31 13.70 35.47 3.36
2049 2103 7.831193 AGCTGTCTGAAATGTATACAATTCCTT 59.169 33.333 24.31 6.96 35.47 3.36
2050 2104 9.109393 GCTGTCTGAAATGTATACAATTCCTTA 57.891 33.333 24.31 11.49 35.47 2.69
2066 2120 9.014297 ACAATTCCTTATAAAAGTGAACAGAGG 57.986 33.333 4.77 0.00 30.04 3.69
2067 2121 8.462016 CAATTCCTTATAAAAGTGAACAGAGGG 58.538 37.037 0.00 0.00 30.04 4.30
2068 2122 6.945636 TCCTTATAAAAGTGAACAGAGGGA 57.054 37.500 0.00 0.00 0.00 4.20
2069 2123 6.947464 TCCTTATAAAAGTGAACAGAGGGAG 58.053 40.000 0.00 0.00 0.00 4.30
2070 2124 6.500751 TCCTTATAAAAGTGAACAGAGGGAGT 59.499 38.462 0.00 0.00 0.00 3.85
2071 2125 7.676893 TCCTTATAAAAGTGAACAGAGGGAGTA 59.323 37.037 0.00 0.00 0.00 2.59
2072 2126 8.487028 CCTTATAAAAGTGAACAGAGGGAGTAT 58.513 37.037 0.00 0.00 0.00 2.12
2081 2135 2.755655 ACAGAGGGAGTATGTCAGTTCG 59.244 50.000 0.00 0.00 0.00 3.95
2189 2244 2.171840 TCTTGTGGTGGTCTCTAGAGC 58.828 52.381 15.35 9.94 42.48 4.09
2208 2263 1.135689 GCGCCAACTGGATGTAACTTG 60.136 52.381 0.00 0.00 37.39 3.16
2220 2276 6.591935 TGGATGTAACTTGAGTTATCCCATC 58.408 40.000 17.13 16.91 40.18 3.51
2254 2310 5.635280 TCAGCAATCAGAAGTAACTTTCTCG 59.365 40.000 0.00 0.00 35.28 4.04
2258 2314 1.993370 CAGAAGTAACTTTCTCGCCGG 59.007 52.381 0.00 0.00 35.28 6.13
2271 2327 0.532417 TCGCCGGTAGTCTCTAGAGC 60.532 60.000 15.35 10.15 0.00 4.09
2274 2330 1.666054 CCGGTAGTCTCTAGAGCGTT 58.334 55.000 15.35 5.41 32.42 4.84
2338 2531 0.042431 TAACAATTGGGCCCCTGCAT 59.958 50.000 22.27 9.27 40.13 3.96
2355 2548 5.053145 CCTGCATAAATCTAGTCACCACTC 58.947 45.833 0.00 0.00 33.62 3.51
2447 2640 5.244851 TCCAGAAGTTAGAGCAGCATATAGG 59.755 44.000 0.00 0.00 0.00 2.57
2511 2704 4.246458 GAGAGTTCTCCATACGCTGTTTT 58.754 43.478 0.00 0.00 37.02 2.43
2692 2885 1.474330 GGCCTGGTGTTTATCTTGGG 58.526 55.000 0.00 0.00 0.00 4.12
2755 2948 5.514169 TGGTATGGAATTTATGCTGGAACA 58.486 37.500 0.00 0.00 0.00 3.18
2867 3175 9.905713 ATAGAGAAATGCCTAGTTAATGTTTCA 57.094 29.630 0.00 0.00 0.00 2.69
2988 3296 4.839121 TGTACCAGTTTTTGTCAGTCAGT 58.161 39.130 0.00 0.00 0.00 3.41
3116 3431 3.669536 AGCTTCTCCTTCTGTTTAGTGC 58.330 45.455 0.00 0.00 0.00 4.40
3117 3432 3.071602 AGCTTCTCCTTCTGTTTAGTGCA 59.928 43.478 0.00 0.00 0.00 4.57
3433 3748 6.715280 TGAGAAAGGAATATGCTTCTTCACT 58.285 36.000 1.08 0.00 0.00 3.41
3724 4039 4.580580 AGTTTCCTTCATGTTCCAGTGTTC 59.419 41.667 0.00 0.00 0.00 3.18
3761 4206 8.747471 TCATGTTATTGGCATTTCATACTTGAA 58.253 29.630 0.00 0.00 40.09 2.69
3844 4289 3.504021 GCAGGAGCAAAGAAAAGCC 57.496 52.632 0.00 0.00 41.58 4.35
3927 4372 3.322466 CACCCCGGCAGAGAAGGT 61.322 66.667 0.00 0.00 0.00 3.50
3986 4431 1.153489 CTGCCTCGTCATGACCTGG 60.153 63.158 20.03 20.65 0.00 4.45
4318 4763 2.654079 CCTGGAGAAGCAGCCTCGT 61.654 63.158 0.00 0.00 0.00 4.18
4423 4868 3.224324 GACCCGGAGCCGAGCATA 61.224 66.667 11.05 0.00 42.83 3.14
4472 4917 2.425143 TGACATTTCTGGGATGAGCC 57.575 50.000 0.00 0.00 0.00 4.70
4473 4918 1.918262 TGACATTTCTGGGATGAGCCT 59.082 47.619 0.00 0.00 36.66 4.58
4474 4919 2.295885 GACATTTCTGGGATGAGCCTG 58.704 52.381 0.00 0.00 36.66 4.85
4475 4920 1.030457 CATTTCTGGGATGAGCCTGC 58.970 55.000 0.00 0.00 36.66 4.85
4476 4921 0.106318 ATTTCTGGGATGAGCCTGCC 60.106 55.000 0.00 0.00 36.66 4.85
4477 4922 2.215451 TTTCTGGGATGAGCCTGCCC 62.215 60.000 0.00 0.00 42.38 5.36
4573 5019 1.941325 ACTGCTACTATTGGCTTCGC 58.059 50.000 0.00 0.00 0.00 4.70
4574 5020 1.207089 ACTGCTACTATTGGCTTCGCA 59.793 47.619 0.00 0.00 0.00 5.10
4766 5212 1.279271 CTCTGGTTCACCCCTTGTAGG 59.721 57.143 0.00 0.00 34.29 3.18
4791 5237 7.444792 GGATGTTGCTAGATGATTGATCTTTCT 59.555 37.037 0.00 0.00 41.94 2.52
4794 5240 9.842775 TGTTGCTAGATGATTGATCTTTCTATT 57.157 29.630 0.00 0.00 41.94 1.73
4853 5331 6.513180 TGTTCACTCGTTACTCAGATTTCTT 58.487 36.000 0.00 0.00 0.00 2.52
4952 5431 4.633980 GCAGTTTTGCTGTTCCCG 57.366 55.556 0.00 0.00 46.95 5.14
5001 5480 6.430962 TGGATCTGAATCTCTTCTATTGGG 57.569 41.667 0.00 0.00 32.29 4.12
5022 5501 8.519799 TTGGGAAAGAATGTAATAGGATTGAC 57.480 34.615 0.00 0.00 0.00 3.18
5051 5530 8.280258 AGAACCTGGGATGATTGATCTTATAA 57.720 34.615 0.00 0.00 0.00 0.98
5080 5559 5.990668 ACTGAATCTTAGATGTGTTACCCC 58.009 41.667 0.00 0.00 0.00 4.95
5081 5560 5.726793 ACTGAATCTTAGATGTGTTACCCCT 59.273 40.000 0.00 0.00 0.00 4.79
5082 5561 6.901300 ACTGAATCTTAGATGTGTTACCCCTA 59.099 38.462 0.00 0.00 0.00 3.53
5106 5585 4.079253 TCTTAAAAGGACATGGAAGCCAC 58.921 43.478 0.00 0.00 35.80 5.01
5116 5595 0.034896 TGGAAGCCACTTTCGAGGTC 59.965 55.000 0.00 0.00 0.00 3.85
5134 5613 3.089284 GGTCGAAAGAATCCCCAATTGT 58.911 45.455 4.43 0.00 45.01 2.71
5230 5712 8.750515 TTAAGCATATGACATTGAAAGATCCA 57.249 30.769 6.97 0.00 0.00 3.41
5231 5713 7.649533 AAGCATATGACATTGAAAGATCCAA 57.350 32.000 6.97 0.00 0.00 3.53
5232 5714 7.834881 AGCATATGACATTGAAAGATCCAAT 57.165 32.000 6.97 0.00 34.83 3.16
5272 5754 9.934190 AAAATGCTGTTCAAAATTGTAAATGTC 57.066 25.926 0.00 0.00 0.00 3.06
5273 5755 7.656707 ATGCTGTTCAAAATTGTAAATGTCC 57.343 32.000 0.00 0.00 0.00 4.02
5286 5768 5.730550 TGTAAATGTCCGACTGAAGCTATT 58.269 37.500 0.00 0.00 0.00 1.73
5292 5774 4.021456 TGTCCGACTGAAGCTATTGAAAGA 60.021 41.667 0.00 0.00 0.00 2.52
5322 5804 6.030228 GGAATCTTCCACTCTTATTTTTGCG 58.970 40.000 4.05 0.00 46.76 4.85
5323 5805 6.128007 GGAATCTTCCACTCTTATTTTTGCGA 60.128 38.462 4.05 0.00 46.76 5.10
5324 5806 6.817765 ATCTTCCACTCTTATTTTTGCGAA 57.182 33.333 0.00 0.00 0.00 4.70
5325 5807 6.817765 TCTTCCACTCTTATTTTTGCGAAT 57.182 33.333 0.00 0.00 0.00 3.34
5326 5808 7.915293 TCTTCCACTCTTATTTTTGCGAATA 57.085 32.000 0.00 0.00 0.00 1.75
5327 5809 7.974675 TCTTCCACTCTTATTTTTGCGAATAG 58.025 34.615 0.00 0.00 0.00 1.73
5328 5810 7.606456 TCTTCCACTCTTATTTTTGCGAATAGT 59.394 33.333 0.00 0.00 0.00 2.12
5329 5811 7.681939 TCCACTCTTATTTTTGCGAATAGTT 57.318 32.000 0.00 0.00 0.00 2.24
5330 5812 8.106247 TCCACTCTTATTTTTGCGAATAGTTT 57.894 30.769 0.00 0.00 0.00 2.66
5331 5813 8.020819 TCCACTCTTATTTTTGCGAATAGTTTG 58.979 33.333 0.00 0.00 0.00 2.93
5332 5814 7.807907 CCACTCTTATTTTTGCGAATAGTTTGT 59.192 33.333 0.00 0.00 0.00 2.83
5333 5815 8.840867 CACTCTTATTTTTGCGAATAGTTTGTC 58.159 33.333 0.00 0.00 0.00 3.18
5334 5816 8.784043 ACTCTTATTTTTGCGAATAGTTTGTCT 58.216 29.630 0.00 0.00 0.00 3.41
5340 5822 9.906660 ATTTTTGCGAATAGTTTGTCTAATTCA 57.093 25.926 0.00 0.00 31.94 2.57
5341 5823 8.722342 TTTTGCGAATAGTTTGTCTAATTCAC 57.278 30.769 0.00 0.00 31.94 3.18
5342 5824 7.428282 TTGCGAATAGTTTGTCTAATTCACA 57.572 32.000 0.00 0.00 31.94 3.58
5343 5825 7.609760 TGCGAATAGTTTGTCTAATTCACAT 57.390 32.000 0.00 0.00 31.94 3.21
5344 5826 7.684670 TGCGAATAGTTTGTCTAATTCACATC 58.315 34.615 0.00 0.00 31.94 3.06
5345 5827 7.549134 TGCGAATAGTTTGTCTAATTCACATCT 59.451 33.333 0.00 0.00 31.94 2.90
5346 5828 9.031360 GCGAATAGTTTGTCTAATTCACATCTA 57.969 33.333 0.00 0.00 31.94 1.98
5378 5860 9.567776 TTTTTAAGGATGTCACATCTAAACTCA 57.432 29.630 17.46 0.00 0.00 3.41
5379 5861 8.547967 TTTAAGGATGTCACATCTAAACTCAC 57.452 34.615 17.46 0.00 0.00 3.51
5380 5862 5.745312 AGGATGTCACATCTAAACTCACA 57.255 39.130 17.46 0.00 0.00 3.58
5381 5863 5.482908 AGGATGTCACATCTAAACTCACAC 58.517 41.667 17.46 0.00 0.00 3.82
5382 5864 5.012046 AGGATGTCACATCTAAACTCACACA 59.988 40.000 17.46 0.00 0.00 3.72
5383 5865 5.700832 GGATGTCACATCTAAACTCACACAA 59.299 40.000 17.46 0.00 0.00 3.33
5384 5866 6.204688 GGATGTCACATCTAAACTCACACAAA 59.795 38.462 17.46 0.00 0.00 2.83
5385 5867 7.094634 GGATGTCACATCTAAACTCACACAAAT 60.095 37.037 17.46 0.00 0.00 2.32
5386 5868 8.846943 ATGTCACATCTAAACTCACACAAATA 57.153 30.769 0.00 0.00 0.00 1.40
5387 5869 8.310406 TGTCACATCTAAACTCACACAAATAG 57.690 34.615 0.00 0.00 0.00 1.73
5388 5870 8.147704 TGTCACATCTAAACTCACACAAATAGA 58.852 33.333 0.00 0.00 0.00 1.98
5389 5871 9.155975 GTCACATCTAAACTCACACAAATAGAT 57.844 33.333 0.00 0.00 31.97 1.98
5398 5880 9.448438 AAACTCACACAAATAGATAATACAGCA 57.552 29.630 0.00 0.00 0.00 4.41
5399 5881 8.425577 ACTCACACAAATAGATAATACAGCAC 57.574 34.615 0.00 0.00 0.00 4.40
5400 5882 7.495934 ACTCACACAAATAGATAATACAGCACC 59.504 37.037 0.00 0.00 0.00 5.01
5401 5883 7.334858 TCACACAAATAGATAATACAGCACCA 58.665 34.615 0.00 0.00 0.00 4.17
5402 5884 7.826744 TCACACAAATAGATAATACAGCACCAA 59.173 33.333 0.00 0.00 0.00 3.67
5403 5885 8.124823 CACACAAATAGATAATACAGCACCAAG 58.875 37.037 0.00 0.00 0.00 3.61
5404 5886 8.046708 ACACAAATAGATAATACAGCACCAAGA 58.953 33.333 0.00 0.00 0.00 3.02
5405 5887 8.892723 CACAAATAGATAATACAGCACCAAGAA 58.107 33.333 0.00 0.00 0.00 2.52
5406 5888 9.113838 ACAAATAGATAATACAGCACCAAGAAG 57.886 33.333 0.00 0.00 0.00 2.85
5407 5889 9.113838 CAAATAGATAATACAGCACCAAGAAGT 57.886 33.333 0.00 0.00 0.00 3.01
5412 5894 9.515226 AGATAATACAGCACCAAGAAGTAAAAA 57.485 29.630 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.710809 AGGGAGCAACAACCTGGTATT 59.289 47.619 0.00 0.00 32.26 1.89
5 6 0.400213 TGGTAGGGAGCAACAACCTG 59.600 55.000 0.00 0.00 35.84 4.00
155 156 1.065854 GTCCCCTGGTGATGAGTCTTG 60.066 57.143 0.00 0.00 0.00 3.02
180 181 2.035442 GGAGGAACAGAGCGGCAAC 61.035 63.158 1.45 0.00 0.00 4.17
195 196 1.160137 GTGCTGGTTGCTTGTAGGAG 58.840 55.000 0.00 0.00 43.37 3.69
238 239 4.874970 AGCAATGCAACTTTAACCTGAAG 58.125 39.130 8.35 0.00 0.00 3.02
240 241 3.255642 GGAGCAATGCAACTTTAACCTGA 59.744 43.478 8.35 0.00 0.00 3.86
244 263 2.989166 GCTGGAGCAATGCAACTTTAAC 59.011 45.455 8.35 0.00 41.59 2.01
309 328 1.007387 GGGGAACAAACAGCAAGCG 60.007 57.895 0.00 0.00 0.00 4.68
337 356 4.699522 AGAAGCAACCCGCCGACC 62.700 66.667 0.00 0.00 44.04 4.79
436 455 2.443390 GGGTAGGGCCTAGACGCA 60.443 66.667 15.05 0.00 37.43 5.24
438 457 1.201424 AAAAGGGTAGGGCCTAGACG 58.799 55.000 15.05 0.00 37.43 4.18
441 460 1.763968 GCAAAAAGGGTAGGGCCTAG 58.236 55.000 15.05 0.17 37.43 3.02
509 530 1.135112 GCCTTTAAACAGCGGGAATGG 60.135 52.381 0.00 0.00 0.00 3.16
516 537 4.148696 CACAAATTCTGCCTTTAAACAGCG 59.851 41.667 1.81 0.00 33.80 5.18
582 603 1.888512 GTGGAATCTGCAAAAGCCAGA 59.111 47.619 0.00 0.00 42.91 3.86
603 624 5.475909 ACCAAGCAGGCAATATCATAAGATG 59.524 40.000 0.00 0.00 43.14 2.90
604 625 5.638133 ACCAAGCAGGCAATATCATAAGAT 58.362 37.500 0.00 0.00 43.14 2.40
607 628 5.300034 CAGAACCAAGCAGGCAATATCATAA 59.700 40.000 0.00 0.00 43.14 1.90
609 630 3.635373 CAGAACCAAGCAGGCAATATCAT 59.365 43.478 0.00 0.00 43.14 2.45
614 635 1.870055 CGCAGAACCAAGCAGGCAAT 61.870 55.000 0.00 0.00 43.14 3.56
617 638 3.741476 CCGCAGAACCAAGCAGGC 61.741 66.667 0.00 0.00 43.14 4.85
618 639 3.741476 GCCGCAGAACCAAGCAGG 61.741 66.667 0.00 0.00 45.67 4.85
636 657 2.807967 TGTATATTCTTGCTGCGCATCC 59.192 45.455 12.24 5.81 38.76 3.51
658 679 7.704271 ACGACGAATATGACCCACTATATATG 58.296 38.462 0.00 0.00 0.00 1.78
662 683 5.997129 TGTACGACGAATATGACCCACTATA 59.003 40.000 0.00 0.00 0.00 1.31
664 685 4.198530 TGTACGACGAATATGACCCACTA 58.801 43.478 0.00 0.00 0.00 2.74
665 686 3.018856 TGTACGACGAATATGACCCACT 58.981 45.455 0.00 0.00 0.00 4.00
666 687 3.065786 TCTGTACGACGAATATGACCCAC 59.934 47.826 0.00 0.00 0.00 4.61
708 729 0.179113 CCACGCAAACAAAAGCTGGT 60.179 50.000 0.00 0.00 0.00 4.00
711 732 1.639280 CAACCACGCAAACAAAAGCT 58.361 45.000 0.00 0.00 0.00 3.74
802 823 9.343539 GAAACTAAGAGCATCCAGGTTATTATT 57.656 33.333 0.00 0.00 28.79 1.40
1004 1057 1.964552 CATCCTGTCATCTGAAGGCC 58.035 55.000 0.00 0.00 0.00 5.19
1056 1109 2.579201 CCCTCCACGTCAAGCGAT 59.421 61.111 0.00 0.00 44.77 4.58
1122 1175 1.893808 CACGCACCCAGAAGCAACT 60.894 57.895 0.00 0.00 0.00 3.16
1137 1190 1.869503 CGCTATTTTCTGTGTGCACG 58.130 50.000 13.13 0.00 0.00 5.34
1473 1526 1.925185 GGTTCTCGTACCGCAAGAATC 59.075 52.381 0.00 0.00 43.02 2.52
1548 1601 6.317088 AGATATTAGTCGACGACAAAAACGA 58.683 36.000 28.31 12.49 34.60 3.85
1549 1602 6.550371 AGATATTAGTCGACGACAAAAACG 57.450 37.500 28.31 0.00 34.60 3.60
1550 1603 8.430063 TGAAAGATATTAGTCGACGACAAAAAC 58.570 33.333 28.31 14.76 34.60 2.43
1551 1604 8.430063 GTGAAAGATATTAGTCGACGACAAAAA 58.570 33.333 28.31 18.96 34.60 1.94
1652 1706 1.418637 TCTTTAGGTGTTTGAGCCGGT 59.581 47.619 1.90 0.00 0.00 5.28
1835 1889 0.322648 TAGCAGTGCATGTCTGTGCT 59.677 50.000 19.20 16.05 46.10 4.40
1932 1986 2.482490 GCCCGTGTCATAACCTTATCGT 60.482 50.000 0.00 0.00 0.00 3.73
1934 1988 3.131396 CAGCCCGTGTCATAACCTTATC 58.869 50.000 0.00 0.00 0.00 1.75
1967 2021 5.813672 CGACTTATAAAAATGAACGGAGGGA 59.186 40.000 0.00 0.00 0.00 4.20
1968 2022 5.583457 ACGACTTATAAAAATGAACGGAGGG 59.417 40.000 0.00 0.00 0.00 4.30
1969 2023 6.657836 ACGACTTATAAAAATGAACGGAGG 57.342 37.500 0.00 0.00 0.00 4.30
1970 2024 8.225107 TGAAACGACTTATAAAAATGAACGGAG 58.775 33.333 0.00 0.00 0.00 4.63
1971 2025 8.085720 TGAAACGACTTATAAAAATGAACGGA 57.914 30.769 0.00 0.00 0.00 4.69
1972 2026 8.716619 TTGAAACGACTTATAAAAATGAACGG 57.283 30.769 0.00 0.00 0.00 4.44
1973 2027 9.968620 GTTTGAAACGACTTATAAAAATGAACG 57.031 29.630 0.00 0.00 0.00 3.95
1988 2042 6.506357 GCTCAATTTCAGTTGTTTGAAACGAC 60.506 38.462 18.41 18.41 46.44 4.34
1989 2043 5.514914 GCTCAATTTCAGTTGTTTGAAACGA 59.485 36.000 3.37 0.00 46.44 3.85
1990 2044 5.516339 AGCTCAATTTCAGTTGTTTGAAACG 59.484 36.000 3.37 0.00 46.44 3.60
1991 2045 6.311200 ACAGCTCAATTTCAGTTGTTTGAAAC 59.689 34.615 0.14 0.14 46.44 2.78
1993 2047 5.964758 ACAGCTCAATTTCAGTTGTTTGAA 58.035 33.333 0.00 0.00 31.86 2.69
1994 2048 5.581126 ACAGCTCAATTTCAGTTGTTTGA 57.419 34.783 0.00 0.00 31.86 2.69
1997 2051 5.063817 GCAAAACAGCTCAATTTCAGTTGTT 59.936 36.000 9.44 9.44 44.43 2.83
1998 2052 4.567959 GCAAAACAGCTCAATTTCAGTTGT 59.432 37.500 0.00 0.00 36.94 3.32
1999 2053 4.567558 TGCAAAACAGCTCAATTTCAGTTG 59.432 37.500 0.00 0.00 34.99 3.16
2000 2054 4.757594 TGCAAAACAGCTCAATTTCAGTT 58.242 34.783 0.00 0.00 34.99 3.16
2001 2055 4.389890 TGCAAAACAGCTCAATTTCAGT 57.610 36.364 0.00 0.00 34.99 3.41
2002 2056 4.318546 GCTTGCAAAACAGCTCAATTTCAG 60.319 41.667 0.00 0.00 34.99 3.02
2003 2057 3.556775 GCTTGCAAAACAGCTCAATTTCA 59.443 39.130 0.00 0.00 34.99 2.69
2004 2058 3.805971 AGCTTGCAAAACAGCTCAATTTC 59.194 39.130 4.77 0.00 30.05 2.17
2005 2059 3.558418 CAGCTTGCAAAACAGCTCAATTT 59.442 39.130 7.67 0.00 32.57 1.82
2006 2060 3.128349 CAGCTTGCAAAACAGCTCAATT 58.872 40.909 7.67 0.00 32.57 2.32
2007 2061 2.101917 ACAGCTTGCAAAACAGCTCAAT 59.898 40.909 7.67 0.00 32.57 2.57
2008 2062 1.477700 ACAGCTTGCAAAACAGCTCAA 59.522 42.857 7.67 0.00 32.57 3.02
2009 2063 1.066002 GACAGCTTGCAAAACAGCTCA 59.934 47.619 7.67 0.00 32.57 4.26
2010 2064 1.336125 AGACAGCTTGCAAAACAGCTC 59.664 47.619 7.67 0.00 32.57 4.09
2011 2065 1.066605 CAGACAGCTTGCAAAACAGCT 59.933 47.619 4.77 4.77 34.40 4.24
2012 2066 1.066002 TCAGACAGCTTGCAAAACAGC 59.934 47.619 0.00 0.00 0.00 4.40
2013 2067 3.425577 TTCAGACAGCTTGCAAAACAG 57.574 42.857 0.00 0.00 0.00 3.16
2014 2068 3.865011 TTTCAGACAGCTTGCAAAACA 57.135 38.095 0.00 0.00 0.00 2.83
2015 2069 4.114794 ACATTTCAGACAGCTTGCAAAAC 58.885 39.130 0.00 0.00 0.00 2.43
2016 2070 4.389890 ACATTTCAGACAGCTTGCAAAA 57.610 36.364 0.00 0.00 0.00 2.44
2017 2071 5.710513 ATACATTTCAGACAGCTTGCAAA 57.289 34.783 0.00 0.00 0.00 3.68
2018 2072 5.704978 TGTATACATTTCAGACAGCTTGCAA 59.295 36.000 0.08 0.00 0.00 4.08
2019 2073 5.244755 TGTATACATTTCAGACAGCTTGCA 58.755 37.500 0.08 0.00 0.00 4.08
2020 2074 5.801350 TGTATACATTTCAGACAGCTTGC 57.199 39.130 0.08 0.00 0.00 4.01
2021 2075 7.912250 GGAATTGTATACATTTCAGACAGCTTG 59.088 37.037 28.50 0.00 37.74 4.01
2022 2076 7.831193 AGGAATTGTATACATTTCAGACAGCTT 59.169 33.333 28.50 7.13 37.74 3.74
2023 2077 7.341805 AGGAATTGTATACATTTCAGACAGCT 58.658 34.615 28.50 18.26 37.74 4.24
2024 2078 7.559590 AGGAATTGTATACATTTCAGACAGC 57.440 36.000 28.50 16.93 37.74 4.40
2040 2094 9.014297 CCTCTGTTCACTTTTATAAGGAATTGT 57.986 33.333 0.00 0.00 35.61 2.71
2041 2095 8.462016 CCCTCTGTTCACTTTTATAAGGAATTG 58.538 37.037 0.00 0.00 35.61 2.32
2042 2096 8.390921 TCCCTCTGTTCACTTTTATAAGGAATT 58.609 33.333 0.00 0.00 35.61 2.17
2043 2097 7.928873 TCCCTCTGTTCACTTTTATAAGGAAT 58.071 34.615 0.00 0.00 35.61 3.01
2044 2098 7.017254 ACTCCCTCTGTTCACTTTTATAAGGAA 59.983 37.037 0.00 0.00 35.61 3.36
2045 2099 6.500751 ACTCCCTCTGTTCACTTTTATAAGGA 59.499 38.462 0.00 0.00 35.61 3.36
2046 2100 6.712276 ACTCCCTCTGTTCACTTTTATAAGG 58.288 40.000 0.00 0.00 35.61 2.69
2047 2101 9.319143 CATACTCCCTCTGTTCACTTTTATAAG 57.681 37.037 0.00 0.00 37.40 1.73
2048 2102 8.822805 ACATACTCCCTCTGTTCACTTTTATAA 58.177 33.333 0.00 0.00 0.00 0.98
2049 2103 8.375493 ACATACTCCCTCTGTTCACTTTTATA 57.625 34.615 0.00 0.00 0.00 0.98
2050 2104 7.038302 TGACATACTCCCTCTGTTCACTTTTAT 60.038 37.037 0.00 0.00 0.00 1.40
2051 2105 6.269077 TGACATACTCCCTCTGTTCACTTTTA 59.731 38.462 0.00 0.00 0.00 1.52
2052 2106 5.071788 TGACATACTCCCTCTGTTCACTTTT 59.928 40.000 0.00 0.00 0.00 2.27
2053 2107 4.593206 TGACATACTCCCTCTGTTCACTTT 59.407 41.667 0.00 0.00 0.00 2.66
2054 2108 4.160329 TGACATACTCCCTCTGTTCACTT 58.840 43.478 0.00 0.00 0.00 3.16
2055 2109 3.766591 CTGACATACTCCCTCTGTTCACT 59.233 47.826 0.00 0.00 0.00 3.41
2056 2110 3.511934 ACTGACATACTCCCTCTGTTCAC 59.488 47.826 0.00 0.00 0.00 3.18
2057 2111 3.779444 ACTGACATACTCCCTCTGTTCA 58.221 45.455 0.00 0.00 0.00 3.18
2058 2112 4.675671 CGAACTGACATACTCCCTCTGTTC 60.676 50.000 0.00 0.00 38.51 3.18
2059 2113 3.193691 CGAACTGACATACTCCCTCTGTT 59.806 47.826 0.00 0.00 0.00 3.16
2060 2114 2.755655 CGAACTGACATACTCCCTCTGT 59.244 50.000 0.00 0.00 0.00 3.41
2061 2115 2.480416 GCGAACTGACATACTCCCTCTG 60.480 54.545 0.00 0.00 0.00 3.35
2062 2116 1.751924 GCGAACTGACATACTCCCTCT 59.248 52.381 0.00 0.00 0.00 3.69
2063 2117 1.476891 TGCGAACTGACATACTCCCTC 59.523 52.381 0.00 0.00 0.00 4.30
2064 2118 1.204941 GTGCGAACTGACATACTCCCT 59.795 52.381 0.00 0.00 0.00 4.20
2065 2119 1.204941 AGTGCGAACTGACATACTCCC 59.795 52.381 0.00 0.00 0.00 4.30
2066 2120 2.263077 CAGTGCGAACTGACATACTCC 58.737 52.381 19.55 0.00 39.99 3.85
2067 2121 2.947852 ACAGTGCGAACTGACATACTC 58.052 47.619 30.50 0.00 39.99 2.59
2068 2122 3.386768 AACAGTGCGAACTGACATACT 57.613 42.857 30.50 3.07 39.99 2.12
2069 2123 4.492570 GCATAACAGTGCGAACTGACATAC 60.493 45.833 30.50 12.62 39.99 2.39
2070 2124 3.616821 GCATAACAGTGCGAACTGACATA 59.383 43.478 30.50 18.41 39.99 2.29
2071 2125 2.416547 GCATAACAGTGCGAACTGACAT 59.583 45.455 30.50 18.02 39.99 3.06
2072 2126 1.798223 GCATAACAGTGCGAACTGACA 59.202 47.619 30.50 16.55 39.99 3.58
2150 2205 8.318167 CCACAAGAAAAACGAACAAAGATTTAC 58.682 33.333 0.00 0.00 0.00 2.01
2189 2244 2.416547 CTCAAGTTACATCCAGTTGGCG 59.583 50.000 0.00 0.00 34.44 5.69
2208 2263 4.386867 TCAGTTCACGATGGGATAACTC 57.613 45.455 0.00 0.00 0.00 3.01
2254 2310 0.814812 ACGCTCTAGAGACTACCGGC 60.815 60.000 24.24 5.10 0.00 6.13
2258 2314 3.436015 TGACACAACGCTCTAGAGACTAC 59.564 47.826 24.24 4.49 0.00 2.73
2338 2531 6.585695 AAAGACGAGTGGTGACTAGATTTA 57.414 37.500 0.00 0.00 30.16 1.40
2355 2548 9.298113 CAAAATAGTACGTGAGTTTTAAAGACG 57.702 33.333 0.00 0.00 46.40 4.18
2511 2704 1.270839 GGCTTGCAACCTGAGACAGTA 60.271 52.381 0.00 0.00 0.00 2.74
2692 2885 2.435059 GTTGCCCTCTCGACAGCC 60.435 66.667 0.00 0.00 0.00 4.85
2755 2948 1.555533 GTAGCTGCTCTACCTGGGTTT 59.444 52.381 4.91 0.00 41.40 3.27
2778 2971 9.965902 ATGAATTCCCTATATCAACCAGATAAC 57.034 33.333 2.27 0.00 42.27 1.89
3097 3412 4.636249 ACTGCACTAAACAGAAGGAGAAG 58.364 43.478 0.00 0.00 38.55 2.85
3433 3748 1.529948 ACCAACGACGAGGAGGTCA 60.530 57.895 15.92 0.00 36.73 4.02
3664 3979 4.201685 CCTTTGAGCGATTCGTCGTTTATT 60.202 41.667 8.03 0.00 35.26 1.40
3695 4010 3.300009 GAACATGAAGGAAACTGTTGCG 58.700 45.455 0.00 0.00 42.68 4.85
3696 4011 3.068024 TGGAACATGAAGGAAACTGTTGC 59.932 43.478 0.00 0.00 42.68 4.17
3724 4039 4.999950 GCCAATAACATGATACTCCAGGAG 59.000 45.833 15.72 15.72 35.52 3.69
3759 4204 5.457140 TGGAGCAAACGTAATTCAACATTC 58.543 37.500 0.00 0.00 0.00 2.67
3761 4206 5.446143 TTGGAGCAAACGTAATTCAACAT 57.554 34.783 0.00 0.00 0.00 2.71
3844 4289 4.232221 CAGAGTTAATTGCAGCCACAAAG 58.768 43.478 0.00 0.00 32.27 2.77
3916 4361 3.197549 AGATCTCTTCAACCTTCTCTGCC 59.802 47.826 0.00 0.00 0.00 4.85
3927 4372 5.243981 CAAGAGGCTCAAAGATCTCTTCAA 58.756 41.667 18.26 0.00 42.56 2.69
3986 4431 3.879351 CTTCGGTTGTGGCGCTTGC 62.879 63.158 7.64 0.00 38.11 4.01
4066 4511 4.758251 CGCACGGGAGACATGCCA 62.758 66.667 0.00 0.00 39.98 4.92
4423 4868 1.677217 GCGCTTCATTTCTCCAGGTCT 60.677 52.381 0.00 0.00 0.00 3.85
4472 4917 0.321564 TTTGATCGTCCACAGGGCAG 60.322 55.000 0.00 0.00 0.00 4.85
4473 4918 0.321564 CTTTGATCGTCCACAGGGCA 60.322 55.000 0.00 0.00 0.00 5.36
4474 4919 1.648467 GCTTTGATCGTCCACAGGGC 61.648 60.000 0.00 0.00 0.00 5.19
4475 4920 1.361668 CGCTTTGATCGTCCACAGGG 61.362 60.000 0.00 0.00 0.00 4.45
4476 4921 0.389817 TCGCTTTGATCGTCCACAGG 60.390 55.000 0.00 0.00 0.00 4.00
4477 4922 0.994995 CTCGCTTTGATCGTCCACAG 59.005 55.000 0.00 0.00 0.00 3.66
4573 5019 5.473039 TGACATGATACGATATGCTTCCTG 58.527 41.667 0.00 0.00 0.00 3.86
4574 5020 5.728637 TGACATGATACGATATGCTTCCT 57.271 39.130 0.00 0.00 0.00 3.36
4766 5212 8.380743 AGAAAGATCAATCATCTAGCAACATC 57.619 34.615 0.00 0.00 41.47 3.06
4911 5389 5.643348 CAGTGCTACAATCCAACATCTAACA 59.357 40.000 0.00 0.00 0.00 2.41
4969 5448 6.436738 AGAGATTCAGATCCAGCATTATGT 57.563 37.500 0.00 0.00 32.44 2.29
5022 5501 4.160642 TCAATCATCCCAGGTTCTCATG 57.839 45.455 0.00 0.00 0.00 3.07
5070 5549 8.572195 TGTCCTTTTAAGACTAGGGGTAACACA 61.572 40.741 0.00 0.00 37.57 3.72
5071 5550 6.169094 GTCCTTTTAAGACTAGGGGTAACAC 58.831 44.000 0.00 0.00 44.66 3.32
5072 5551 5.845614 TGTCCTTTTAAGACTAGGGGTAACA 59.154 40.000 0.00 0.00 35.21 2.41
5073 5552 6.364568 TGTCCTTTTAAGACTAGGGGTAAC 57.635 41.667 0.00 0.00 35.21 2.50
5074 5553 6.069847 CCATGTCCTTTTAAGACTAGGGGTAA 60.070 42.308 0.00 0.00 35.21 2.85
5075 5554 5.427481 CCATGTCCTTTTAAGACTAGGGGTA 59.573 44.000 0.00 0.00 35.21 3.69
5076 5555 4.227527 CCATGTCCTTTTAAGACTAGGGGT 59.772 45.833 0.00 0.00 35.21 4.95
5077 5556 4.473559 TCCATGTCCTTTTAAGACTAGGGG 59.526 45.833 0.00 0.00 35.21 4.79
5078 5557 5.693769 TCCATGTCCTTTTAAGACTAGGG 57.306 43.478 0.00 0.00 35.21 3.53
5079 5558 5.586643 GCTTCCATGTCCTTTTAAGACTAGG 59.413 44.000 0.00 0.00 35.21 3.02
5080 5559 5.586643 GGCTTCCATGTCCTTTTAAGACTAG 59.413 44.000 0.00 0.00 35.21 2.57
5081 5560 5.013704 TGGCTTCCATGTCCTTTTAAGACTA 59.986 40.000 0.00 0.00 35.21 2.59
5082 5561 4.202567 TGGCTTCCATGTCCTTTTAAGACT 60.203 41.667 0.00 0.00 35.21 3.24
5116 5595 5.897377 ACTTACAATTGGGGATTCTTTCG 57.103 39.130 10.83 0.00 0.00 3.46
5118 5597 7.441836 GTCAAACTTACAATTGGGGATTCTTT 58.558 34.615 10.83 0.00 0.00 2.52
5246 5728 9.934190 GACATTTACAATTTTGAACAGCATTTT 57.066 25.926 0.00 0.00 0.00 1.82
5252 5734 7.113404 CAGTCGGACATTTACAATTTTGAACAG 59.887 37.037 11.27 0.00 0.00 3.16
5257 5739 6.088085 GCTTCAGTCGGACATTTACAATTTTG 59.912 38.462 11.27 0.00 0.00 2.44
5272 5754 4.932200 ACTTCTTTCAATAGCTTCAGTCGG 59.068 41.667 0.00 0.00 0.00 4.79
5273 5755 6.473397 AACTTCTTTCAATAGCTTCAGTCG 57.527 37.500 0.00 0.00 0.00 4.18
5314 5796 9.906660 TGAATTAGACAAACTATTCGCAAAAAT 57.093 25.926 0.00 0.00 0.00 1.82
5315 5797 9.176181 GTGAATTAGACAAACTATTCGCAAAAA 57.824 29.630 0.00 0.00 34.00 1.94
5318 5800 7.428282 TGTGAATTAGACAAACTATTCGCAA 57.572 32.000 0.00 0.00 36.88 4.85
5319 5801 7.549134 AGATGTGAATTAGACAAACTATTCGCA 59.451 33.333 11.00 11.00 39.77 5.10
5320 5802 7.910304 AGATGTGAATTAGACAAACTATTCGC 58.090 34.615 0.00 0.00 34.17 4.70
5352 5834 9.567776 TGAGTTTAGATGTGACATCCTTAAAAA 57.432 29.630 21.05 11.39 0.00 1.94
5353 5835 8.999431 GTGAGTTTAGATGTGACATCCTTAAAA 58.001 33.333 21.05 13.52 0.00 1.52
5354 5836 8.154203 TGTGAGTTTAGATGTGACATCCTTAAA 58.846 33.333 21.05 16.39 0.00 1.52
5355 5837 7.602644 GTGTGAGTTTAGATGTGACATCCTTAA 59.397 37.037 21.05 11.73 0.00 1.85
5356 5838 7.097192 GTGTGAGTTTAGATGTGACATCCTTA 58.903 38.462 21.05 6.22 0.00 2.69
5357 5839 5.934625 GTGTGAGTTTAGATGTGACATCCTT 59.065 40.000 21.05 7.22 0.00 3.36
5358 5840 5.012046 TGTGTGAGTTTAGATGTGACATCCT 59.988 40.000 21.05 11.37 0.00 3.24
5359 5841 5.237815 TGTGTGAGTTTAGATGTGACATCC 58.762 41.667 21.05 6.69 0.00 3.51
5360 5842 6.785488 TTGTGTGAGTTTAGATGTGACATC 57.215 37.500 17.46 17.46 0.00 3.06
5361 5843 7.750229 ATTTGTGTGAGTTTAGATGTGACAT 57.250 32.000 0.00 0.00 0.00 3.06
5362 5844 8.147704 TCTATTTGTGTGAGTTTAGATGTGACA 58.852 33.333 0.00 0.00 0.00 3.58
5363 5845 8.534333 TCTATTTGTGTGAGTTTAGATGTGAC 57.466 34.615 0.00 0.00 0.00 3.67
5372 5854 9.448438 TGCTGTATTATCTATTTGTGTGAGTTT 57.552 29.630 0.00 0.00 0.00 2.66
5373 5855 8.883731 GTGCTGTATTATCTATTTGTGTGAGTT 58.116 33.333 0.00 0.00 0.00 3.01
5374 5856 7.495934 GGTGCTGTATTATCTATTTGTGTGAGT 59.504 37.037 0.00 0.00 0.00 3.41
5375 5857 7.495606 TGGTGCTGTATTATCTATTTGTGTGAG 59.504 37.037 0.00 0.00 0.00 3.51
5376 5858 7.334858 TGGTGCTGTATTATCTATTTGTGTGA 58.665 34.615 0.00 0.00 0.00 3.58
5377 5859 7.552458 TGGTGCTGTATTATCTATTTGTGTG 57.448 36.000 0.00 0.00 0.00 3.82
5378 5860 8.046708 TCTTGGTGCTGTATTATCTATTTGTGT 58.953 33.333 0.00 0.00 0.00 3.72
5379 5861 8.437360 TCTTGGTGCTGTATTATCTATTTGTG 57.563 34.615 0.00 0.00 0.00 3.33
5380 5862 9.113838 CTTCTTGGTGCTGTATTATCTATTTGT 57.886 33.333 0.00 0.00 0.00 2.83
5381 5863 9.113838 ACTTCTTGGTGCTGTATTATCTATTTG 57.886 33.333 0.00 0.00 0.00 2.32
5386 5868 9.515226 TTTTTACTTCTTGGTGCTGTATTATCT 57.485 29.630 0.00 0.00 0.00 1.98


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

AutoCloner maintained by Alex Coulton.