Multiple sequence alignment - TraesCS1B01G220000

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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 TraesCS1B01G220000 chr1B 100.000 3763 0 0 1 3763 397058108 397054346 0.000000e+00 6950
1 TraesCS1B01G220000 chr1A 95.201 1938 78 7 1 1925 368803539 368801604 0.000000e+00 3049
2 TraesCS1B01G220000 chr1A 92.743 813 42 6 2037 2848 368801568 368800772 0.000000e+00 1158
3 TraesCS1B01G220000 chr1A 86.629 890 82 31 2886 3761 368800773 368799907 0.000000e+00 950
4 TraesCS1B01G220000 chr1D 94.663 1930 85 14 1 1925 295542612 295540696 0.000000e+00 2977
5 TraesCS1B01G220000 chr1D 86.894 1114 88 13 2672 3744 295539508 295538412 0.000000e+00 1195
6 TraesCS1B01G220000 chr1D 94.892 646 30 3 2041 2685 295540663 295540020 0.000000e+00 1007
7 TraesCS1B01G220000 chr4B 86.016 379 45 8 1209 1584 660661768 660662141 2.110000e-107 399
8 TraesCS1B01G220000 chrUn 86.188 362 44 4 1216 1574 110658148 110658506 1.640000e-103 387
9 TraesCS1B01G220000 chr5A 86.141 368 40 10 1209 1574 700663493 700663851 1.640000e-103 387
10 TraesCS1B01G220000 chr5B 90.385 104 8 2 2873 2975 703484631 703484529 6.560000e-28 135


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 TraesCS1B01G220000 chr1B 397054346 397058108 3762 True 6950.000000 6950 100.000000 1 3763 1 chr1B.!!$R1 3762
1 TraesCS1B01G220000 chr1A 368799907 368803539 3632 True 1719.000000 3049 91.524333 1 3761 3 chr1A.!!$R1 3760
2 TraesCS1B01G220000 chr1D 295538412 295542612 4200 True 1726.333333 2977 92.149667 1 3744 3 chr1D.!!$R1 3743

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
804 817 0.250166 AACAGCTTACGGTCCCACAC 60.250 55.0 0.00 0.0 0.00 3.82 F
1011 1024 0.463833 TAGCTCTGATGCTCGACCGA 60.464 55.0 0.00 0.0 42.97 4.69 F
2091 2108 0.109272 GCTCGATGAGTCACCGTTGA 60.109 55.0 6.82 0.0 31.39 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1605 1622 0.029834 AGCAAGCACAGCAAGAAACG 59.970 50.0 0.00 0.00 0.00 3.60 R
2301 2319 0.037790 TGTTGTCGGCGATGATGACA 60.038 50.0 14.79 10.92 40.62 3.58 R
3305 3888 0.110644 GCTGCTCGGAACTTTCAACG 60.111 55.0 0.00 0.00 0.00 4.10 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
212 213 1.298116 CGCTGCCTGCAAATCATCG 60.298 57.895 0.00 0.00 43.06 3.84
397 403 3.542676 TGCCCGTCACCGTGAACT 61.543 61.111 1.88 0.00 0.00 3.01
417 423 4.771356 GACGCGCCGTAGCTGTCA 62.771 66.667 5.73 0.00 41.37 3.58
590 596 4.717629 TGTCAAGCTAGCGCGCGT 62.718 61.111 32.35 20.00 42.32 6.01
804 817 0.250166 AACAGCTTACGGTCCCACAC 60.250 55.000 0.00 0.00 0.00 3.82
878 891 4.063689 CTCACTGTTGTCAGCTTCTCAAT 58.936 43.478 0.00 0.00 44.77 2.57
993 1006 0.970640 TGTCCGCAGCCTAACACTTA 59.029 50.000 0.00 0.00 0.00 2.24
1008 1021 2.159310 ACACTTAGCTCTGATGCTCGAC 60.159 50.000 0.00 0.00 42.97 4.20
1011 1024 0.463833 TAGCTCTGATGCTCGACCGA 60.464 55.000 0.00 0.00 42.97 4.69
1012 1025 1.299014 GCTCTGATGCTCGACCGAG 60.299 63.158 14.45 14.45 44.56 4.63
1173 1186 4.214327 CTCTTCCTCCCGGCGCTC 62.214 72.222 7.64 0.00 0.00 5.03
1234 1247 1.162181 CGTCCGGATCTACGCCTACA 61.162 60.000 7.81 0.00 31.66 2.74
1563 1576 4.408821 TTCGGCGCCTGCTTCCAT 62.409 61.111 26.68 0.00 42.25 3.41
1599 1616 2.503765 TGCTCGATCCAACCTCCAATTA 59.496 45.455 0.00 0.00 0.00 1.40
1605 1622 3.926058 TCCAACCTCCAATTACTAGCC 57.074 47.619 0.00 0.00 0.00 3.93
1615 1632 3.689649 CCAATTACTAGCCGTTTCTTGCT 59.310 43.478 0.00 0.00 41.57 3.91
1667 1684 5.402997 TTTTGCTGCATAATGGTTGATCA 57.597 34.783 1.84 0.00 0.00 2.92
1687 1704 2.621998 CAATCAGGAGGATGTGGCAATC 59.378 50.000 0.00 0.00 36.02 2.67
1693 1710 3.204827 GATGTGGCAATCGCGGCT 61.205 61.111 6.13 0.00 39.92 5.52
1707 1724 2.857744 CGGCTGGTATCCCGGAGTC 61.858 68.421 0.73 0.00 39.78 3.36
1870 1887 2.615493 GGACATCTTTGCCTTCTTCCGA 60.615 50.000 0.00 0.00 0.00 4.55
1925 1942 2.092914 GGCCACTTCTACAGCAGGTAAT 60.093 50.000 0.00 0.00 0.00 1.89
1926 1943 3.610911 GCCACTTCTACAGCAGGTAATT 58.389 45.455 0.00 0.00 0.00 1.40
1927 1944 3.375299 GCCACTTCTACAGCAGGTAATTG 59.625 47.826 0.00 0.00 0.00 2.32
1928 1945 3.375299 CCACTTCTACAGCAGGTAATTGC 59.625 47.826 0.00 0.00 44.41 3.56
1929 1946 4.002982 CACTTCTACAGCAGGTAATTGCA 58.997 43.478 0.52 0.00 46.47 4.08
1932 1949 3.599343 TCTACAGCAGGTAATTGCACAG 58.401 45.455 0.52 0.00 46.47 3.66
1934 1951 2.154462 ACAGCAGGTAATTGCACAGTC 58.846 47.619 0.52 0.00 46.47 3.51
1935 1952 1.470098 CAGCAGGTAATTGCACAGTCC 59.530 52.381 0.52 0.00 46.47 3.85
1936 1953 1.073763 AGCAGGTAATTGCACAGTCCA 59.926 47.619 0.52 0.00 46.47 4.02
1937 1954 2.094675 GCAGGTAATTGCACAGTCCAT 58.905 47.619 0.00 0.00 43.53 3.41
1938 1955 2.493278 GCAGGTAATTGCACAGTCCATT 59.507 45.455 0.00 0.00 43.53 3.16
1939 1956 3.674138 GCAGGTAATTGCACAGTCCATTG 60.674 47.826 0.00 0.00 43.53 2.82
1941 1958 2.825532 GGTAATTGCACAGTCCATTGGT 59.174 45.455 1.86 0.00 0.00 3.67
1942 1959 3.119495 GGTAATTGCACAGTCCATTGGTC 60.119 47.826 1.86 0.00 0.00 4.02
1943 1960 2.291209 ATTGCACAGTCCATTGGTCA 57.709 45.000 1.86 0.00 0.00 4.02
1944 1961 2.064434 TTGCACAGTCCATTGGTCAA 57.936 45.000 1.86 0.00 0.00 3.18
1945 1962 1.317613 TGCACAGTCCATTGGTCAAC 58.682 50.000 1.86 0.00 0.00 3.18
1946 1963 1.133823 TGCACAGTCCATTGGTCAACT 60.134 47.619 1.86 0.00 0.00 3.16
1950 1967 4.142600 GCACAGTCCATTGGTCAACTATTC 60.143 45.833 1.86 0.00 0.00 1.75
1951 1968 5.003160 CACAGTCCATTGGTCAACTATTCA 58.997 41.667 1.86 0.00 0.00 2.57
1952 1969 5.122869 CACAGTCCATTGGTCAACTATTCAG 59.877 44.000 1.86 0.00 0.00 3.02
1953 1970 4.637534 CAGTCCATTGGTCAACTATTCAGG 59.362 45.833 1.86 0.00 0.00 3.86
1955 1972 2.689983 CCATTGGTCAACTATTCAGGCC 59.310 50.000 0.00 0.00 0.00 5.19
1957 1974 0.623723 TGGTCAACTATTCAGGCCCC 59.376 55.000 0.00 0.00 0.00 5.80
1959 1976 1.215423 GGTCAACTATTCAGGCCCCAT 59.785 52.381 0.00 0.00 0.00 4.00
1960 1977 2.358195 GGTCAACTATTCAGGCCCCATT 60.358 50.000 0.00 0.00 0.00 3.16
1961 1978 3.117663 GGTCAACTATTCAGGCCCCATTA 60.118 47.826 0.00 0.00 0.00 1.90
1962 1979 4.137543 GTCAACTATTCAGGCCCCATTAG 58.862 47.826 0.00 0.00 0.00 1.73
1963 1980 3.785887 TCAACTATTCAGGCCCCATTAGT 59.214 43.478 0.00 0.00 0.00 2.24
1964 1981 4.229582 TCAACTATTCAGGCCCCATTAGTT 59.770 41.667 0.00 6.04 31.83 2.24
1965 1982 4.439253 ACTATTCAGGCCCCATTAGTTC 57.561 45.455 0.00 0.00 0.00 3.01
1966 1983 2.348411 ATTCAGGCCCCATTAGTTCG 57.652 50.000 0.00 0.00 0.00 3.95
1967 1984 0.988832 TTCAGGCCCCATTAGTTCGT 59.011 50.000 0.00 0.00 0.00 3.85
1968 1985 1.868713 TCAGGCCCCATTAGTTCGTA 58.131 50.000 0.00 0.00 0.00 3.43
1969 1986 2.189676 TCAGGCCCCATTAGTTCGTAA 58.810 47.619 0.00 0.00 0.00 3.18
1970 1987 2.572556 TCAGGCCCCATTAGTTCGTAAA 59.427 45.455 0.00 0.00 0.00 2.01
1971 1988 2.943033 CAGGCCCCATTAGTTCGTAAAG 59.057 50.000 0.00 0.00 0.00 1.85
1972 1989 2.574824 AGGCCCCATTAGTTCGTAAAGT 59.425 45.455 0.00 0.00 0.00 2.66
1973 1990 2.681344 GGCCCCATTAGTTCGTAAAGTG 59.319 50.000 0.00 0.00 0.00 3.16
1974 1991 2.096980 GCCCCATTAGTTCGTAAAGTGC 59.903 50.000 0.00 0.00 0.00 4.40
1975 1992 3.340034 CCCCATTAGTTCGTAAAGTGCA 58.660 45.455 0.00 0.00 0.00 4.57
1976 1993 3.945285 CCCCATTAGTTCGTAAAGTGCAT 59.055 43.478 0.00 0.00 0.00 3.96
1977 1994 4.035208 CCCCATTAGTTCGTAAAGTGCATC 59.965 45.833 0.00 0.00 0.00 3.91
1978 1995 4.634004 CCCATTAGTTCGTAAAGTGCATCA 59.366 41.667 0.00 0.00 0.00 3.07
1979 1996 5.220662 CCCATTAGTTCGTAAAGTGCATCAG 60.221 44.000 0.00 0.00 0.00 2.90
1980 1997 4.921470 TTAGTTCGTAAAGTGCATCAGC 57.079 40.909 0.00 0.00 42.57 4.26
1993 2010 3.969287 GCATCAGCATATGTAGAGGGA 57.031 47.619 4.29 0.00 41.58 4.20
1994 2011 3.594134 GCATCAGCATATGTAGAGGGAC 58.406 50.000 4.29 0.00 41.58 4.46
1995 2012 3.007290 GCATCAGCATATGTAGAGGGACA 59.993 47.826 4.29 0.00 41.58 4.02
1996 2013 4.503817 GCATCAGCATATGTAGAGGGACAA 60.504 45.833 4.29 0.00 41.58 3.18
1997 2014 5.802465 CATCAGCATATGTAGAGGGACAAT 58.198 41.667 4.29 0.00 31.83 2.71
1998 2015 5.219343 TCAGCATATGTAGAGGGACAATG 57.781 43.478 4.29 0.00 31.83 2.82
1999 2016 3.750130 CAGCATATGTAGAGGGACAATGC 59.250 47.826 4.29 12.01 40.39 3.56
2000 2017 3.649981 AGCATATGTAGAGGGACAATGCT 59.350 43.478 4.29 14.71 42.60 3.79
2001 2018 4.840680 AGCATATGTAGAGGGACAATGCTA 59.159 41.667 17.04 0.00 43.88 3.49
2002 2019 4.932200 GCATATGTAGAGGGACAATGCTAC 59.068 45.833 4.29 0.00 38.89 3.58
2003 2020 5.511373 GCATATGTAGAGGGACAATGCTACA 60.511 44.000 4.29 0.00 44.88 2.74
2005 2022 4.672587 TGTAGAGGGACAATGCTACATC 57.327 45.455 0.00 0.00 38.51 3.06
2006 2023 4.290093 TGTAGAGGGACAATGCTACATCT 58.710 43.478 0.00 0.00 38.51 2.90
2007 2024 5.454966 TGTAGAGGGACAATGCTACATCTA 58.545 41.667 0.00 0.00 38.51 1.98
2008 2025 5.536538 TGTAGAGGGACAATGCTACATCTAG 59.463 44.000 0.00 0.00 38.51 2.43
2009 2026 3.900601 AGAGGGACAATGCTACATCTAGG 59.099 47.826 0.00 0.00 0.00 3.02
2010 2027 3.643792 GAGGGACAATGCTACATCTAGGT 59.356 47.826 0.00 0.00 0.00 3.08
2011 2028 4.816126 AGGGACAATGCTACATCTAGGTA 58.184 43.478 0.00 0.00 0.00 3.08
2012 2029 5.216622 AGGGACAATGCTACATCTAGGTAA 58.783 41.667 0.00 0.00 0.00 2.85
2013 2030 5.846714 AGGGACAATGCTACATCTAGGTAAT 59.153 40.000 0.00 0.00 0.00 1.89
2014 2031 6.014156 AGGGACAATGCTACATCTAGGTAATC 60.014 42.308 0.00 0.00 0.00 1.75
2015 2032 6.239600 GGGACAATGCTACATCTAGGTAATCA 60.240 42.308 0.00 0.00 0.00 2.57
2016 2033 6.870965 GGACAATGCTACATCTAGGTAATCAG 59.129 42.308 0.00 0.00 0.00 2.90
2017 2034 7.366847 ACAATGCTACATCTAGGTAATCAGT 57.633 36.000 0.00 0.00 0.00 3.41
2018 2035 7.796054 ACAATGCTACATCTAGGTAATCAGTT 58.204 34.615 0.00 0.00 0.00 3.16
2019 2036 8.267894 ACAATGCTACATCTAGGTAATCAGTTT 58.732 33.333 0.00 0.00 0.00 2.66
2020 2037 9.113838 CAATGCTACATCTAGGTAATCAGTTTT 57.886 33.333 0.00 0.00 0.00 2.43
2022 2039 9.765795 ATGCTACATCTAGGTAATCAGTTTTAC 57.234 33.333 0.00 0.00 0.00 2.01
2023 2040 8.978472 TGCTACATCTAGGTAATCAGTTTTACT 58.022 33.333 0.00 0.00 33.49 2.24
2024 2041 9.819267 GCTACATCTAGGTAATCAGTTTTACTT 57.181 33.333 0.00 0.00 33.49 2.24
2058 2075 6.178324 TGATTCATCTTGCTCAGAACTTCAT 58.822 36.000 0.00 0.00 34.16 2.57
2059 2076 5.874895 TTCATCTTGCTCAGAACTTCATG 57.125 39.130 0.00 0.00 34.16 3.07
2060 2077 4.903054 TCATCTTGCTCAGAACTTCATGT 58.097 39.130 0.00 0.00 34.16 3.21
2079 2096 6.958255 TCATGTATAACAATTTGGCTCGATG 58.042 36.000 0.78 0.00 0.00 3.84
2091 2108 0.109272 GCTCGATGAGTCACCGTTGA 60.109 55.000 6.82 0.00 31.39 3.18
2147 2165 1.618837 GGTGAGGACTGAACTACTGCA 59.381 52.381 0.00 0.00 0.00 4.41
2217 2235 1.904771 CTACCGGTTGGAGATGGCA 59.095 57.895 15.04 0.00 39.21 4.92
2301 2319 3.160047 CTCCTCGGCTGCATCCCT 61.160 66.667 0.00 0.00 0.00 4.20
2421 2439 3.712881 GTGCTTGACCACGTCGCC 61.713 66.667 0.00 0.00 34.95 5.54
2561 2579 2.669569 GAAGCTGGAGCCGTTGCA 60.670 61.111 0.00 0.00 43.38 4.08
2564 2582 3.286751 GCTGGAGCCGTTGCAACA 61.287 61.111 28.01 7.65 41.13 3.33
2690 3233 3.244700 GCCATATGTGCTCTACTCCCATT 60.245 47.826 1.24 0.00 0.00 3.16
2758 3302 0.870393 CACGCATGCAGGATCCATAC 59.130 55.000 19.57 2.91 0.00 2.39
2772 3316 3.101643 TCCATACCTAGCACTGACAGT 57.898 47.619 1.07 1.07 0.00 3.55
2780 3324 0.603569 AGCACTGACAGTTCCTACCG 59.396 55.000 5.04 0.00 0.00 4.02
2803 3351 4.069232 CCCTCGAAGCCGTGCTGA 62.069 66.667 0.00 0.00 39.62 4.26
2804 3352 2.048222 CCTCGAAGCCGTGCTGAA 60.048 61.111 0.00 0.00 39.62 3.02
2805 3353 1.667830 CCTCGAAGCCGTGCTGAAA 60.668 57.895 0.00 0.00 39.62 2.69
2806 3354 1.630244 CCTCGAAGCCGTGCTGAAAG 61.630 60.000 0.00 0.00 39.62 2.62
2850 3398 5.096443 AGGACAAAGATCTAAGCCTTCTG 57.904 43.478 0.00 0.00 0.00 3.02
2851 3399 4.534103 AGGACAAAGATCTAAGCCTTCTGT 59.466 41.667 0.00 0.00 0.00 3.41
2853 3401 5.234466 ACAAAGATCTAAGCCTTCTGTGT 57.766 39.130 0.00 0.00 33.96 3.72
2861 3409 0.882042 AGCCTTCTGTGTGAACGCTG 60.882 55.000 0.00 0.00 42.51 5.18
2866 3414 0.387565 TCTGTGTGAACGCTGCTACA 59.612 50.000 0.00 0.00 0.00 2.74
2898 3446 0.516877 TTTGCGTTTCATCTGAGCGG 59.483 50.000 7.84 0.00 0.00 5.52
2913 3461 0.107945 AGCGGAGTGATTCCTCAAGC 60.108 55.000 0.00 10.72 44.41 4.01
2966 3514 0.798771 ACGAGAGCAAGCGATCGAAC 60.799 55.000 21.57 1.19 38.50 3.95
2985 3533 2.408565 ACAGGAGGAGAAAGAACCACA 58.591 47.619 0.00 0.00 0.00 4.17
3007 3555 3.694746 TCGGATGTCGAAGCCAGT 58.305 55.556 0.00 0.00 45.86 4.00
3025 3573 4.410492 CAGTTTTCCTGGTTGAGATTCG 57.590 45.455 0.00 0.00 37.54 3.34
3135 3718 1.555075 GCAGGGAAGAGGTGACATACA 59.445 52.381 0.00 0.00 0.00 2.29
3168 3751 3.822192 CCATCGAGGCGACGGTCA 61.822 66.667 9.10 0.00 39.18 4.02
3170 3753 3.823330 ATCGAGGCGACGGTCACC 61.823 66.667 7.10 7.10 39.18 4.02
3183 3766 2.039787 TCACCGCCCTATGGGTCA 59.960 61.111 4.42 0.00 46.51 4.02
3185 3768 1.227943 CACCGCCCTATGGGTCATG 60.228 63.158 4.42 0.00 46.51 3.07
3189 3772 1.410850 CGCCCTATGGGTCATGGACT 61.411 60.000 4.42 0.00 46.51 3.85
3191 3774 1.806496 CCCTATGGGTCATGGACTGA 58.194 55.000 0.00 0.00 38.25 3.41
3201 3784 2.121129 TCATGGACTGATCATGGCTGA 58.879 47.619 0.00 0.00 41.51 4.26
3206 3789 0.904649 ACTGATCATGGCTGAACGGA 59.095 50.000 0.00 0.00 34.91 4.69
3211 3794 0.617935 TCATGGCTGAACGGATTCCA 59.382 50.000 3.09 0.00 33.49 3.53
3226 3809 0.179004 TTCCAATGCCGGTTCACTGT 60.179 50.000 1.90 0.00 0.00 3.55
3230 3813 1.732259 CAATGCCGGTTCACTGTCTAC 59.268 52.381 1.90 0.00 0.00 2.59
3298 3881 2.356313 CAAGCTCTCACGCCGTGT 60.356 61.111 17.83 0.00 34.79 4.49
3305 3888 1.155424 TCTCACGCCGTGTTGTTTCC 61.155 55.000 17.83 0.00 34.79 3.13
3337 3920 2.594592 GCAGCTGGTGGTTTCCGT 60.595 61.111 17.12 0.00 0.00 4.69
3340 3923 2.203294 GCTGGTGGTTTCCGTGGT 60.203 61.111 0.00 0.00 0.00 4.16
3376 3959 4.796231 CCGGGTTGCGACGAGGAG 62.796 72.222 10.09 0.00 0.00 3.69
3386 3969 0.388649 CGACGAGGAGGGTGTTCTTG 60.389 60.000 0.00 0.00 0.00 3.02
3398 3981 0.976641 TGTTCTTGACGCCTGAGGAT 59.023 50.000 0.65 0.00 0.00 3.24
3410 3993 0.468214 CTGAGGATGCCGGTAGGAGA 60.468 60.000 1.90 0.00 41.02 3.71
3454 4044 1.402259 CTAGATGAAGTCACCGTCGCT 59.598 52.381 0.00 0.00 0.00 4.93
3455 4045 0.603569 AGATGAAGTCACCGTCGCTT 59.396 50.000 0.00 0.00 0.00 4.68
3491 4081 5.316987 TCCCTTGTTTCCTGAGAAAAGATC 58.683 41.667 0.00 0.00 43.48 2.75
3558 4161 4.972875 GCAGGAGCTAGTGGCATT 57.027 55.556 0.00 0.00 44.79 3.56
3560 4163 2.557920 GCAGGAGCTAGTGGCATTAT 57.442 50.000 0.00 0.00 44.79 1.28
3561 4164 2.149578 GCAGGAGCTAGTGGCATTATG 58.850 52.381 0.00 0.00 44.79 1.90
3562 4165 2.775890 CAGGAGCTAGTGGCATTATGG 58.224 52.381 0.00 0.00 44.79 2.74
3563 4166 1.072965 AGGAGCTAGTGGCATTATGGC 59.927 52.381 12.03 12.03 44.79 4.40
3583 4188 2.322161 CAAGTTGCTTCTGAAATGGCG 58.678 47.619 0.00 0.00 0.00 5.69
3606 4211 2.301870 TGTTCGGGAGCTCACTGTTTAT 59.698 45.455 15.40 0.00 0.00 1.40
3607 4212 3.512329 TGTTCGGGAGCTCACTGTTTATA 59.488 43.478 15.40 0.00 0.00 0.98
3617 4222 9.595823 GGAGCTCACTGTTTATAGTTAACATAA 57.404 33.333 17.19 7.27 35.18 1.90
3647 4252 4.503910 TCTGGTAGTCGAATTTGTCCATG 58.496 43.478 0.00 0.00 0.00 3.66
3669 4275 3.626028 AGTGGTTTCATTTCGAGCAAC 57.374 42.857 0.00 0.00 0.00 4.17
3680 4286 9.554395 TTTCATTTCGAGCAACCTGATAATATA 57.446 29.630 0.00 0.00 0.00 0.86
3714 4320 1.746220 CTCGACTCTTGTCCCTCGAAT 59.254 52.381 0.00 0.00 39.94 3.34
3720 4326 4.319177 ACTCTTGTCCCTCGAATTGAAAG 58.681 43.478 0.00 0.00 0.00 2.62
3761 4367 2.191815 TGCCAATCGAAATTGATGCG 57.808 45.000 0.26 0.00 44.25 4.73
3762 4368 0.848305 GCCAATCGAAATTGATGCGC 59.152 50.000 0.00 0.00 44.25 6.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
102 103 0.187606 AGGGGGTTTTCAAGGTGGAC 59.812 55.000 0.00 0.00 0.00 4.02
212 213 3.920412 TGATCGACGAATATGTATGCTGC 59.080 43.478 0.00 0.00 0.00 5.25
263 264 1.137086 CTCTAGCACGTACCAGCCATT 59.863 52.381 0.00 0.00 0.00 3.16
590 596 0.174845 CCACTCCACGATAAAGCCGA 59.825 55.000 0.00 0.00 0.00 5.54
679 686 3.352338 CTCTGCCGTACCGACACCC 62.352 68.421 0.00 0.00 0.00 4.61
775 788 0.320697 GTAAGCTGTTGGGTCGTCCT 59.679 55.000 0.00 0.00 36.20 3.85
776 789 1.012486 CGTAAGCTGTTGGGTCGTCC 61.012 60.000 0.00 0.00 0.00 4.79
804 817 1.091771 GTGATGATCACCCACTGGCG 61.092 60.000 14.48 0.00 41.37 5.69
816 829 2.035704 GAGAGGAGATGCGTGTGATGAT 59.964 50.000 0.00 0.00 0.00 2.45
878 891 2.169832 CGGAGCTTTGACTCTTGGAA 57.830 50.000 0.00 0.00 36.87 3.53
1008 1021 4.214327 GGAGAGGGCTTCGCTCGG 62.214 72.222 0.00 0.00 46.03 4.63
1077 1090 4.803426 CTGTCGAGGAGGCGGCAC 62.803 72.222 13.08 4.32 41.44 5.01
1108 1121 0.892755 CACCGCCACCTGTAGAAGTA 59.107 55.000 0.00 0.00 0.00 2.24
1381 1394 1.968017 AGACGTAGACGGGCACGAA 60.968 57.895 19.19 0.00 44.60 3.85
1563 1576 4.408821 GCAGCGGTCACCATGGGA 62.409 66.667 18.09 7.80 0.00 4.37
1599 1616 1.512926 CACAGCAAGAAACGGCTAGT 58.487 50.000 0.00 0.00 38.56 2.57
1605 1622 0.029834 AGCAAGCACAGCAAGAAACG 59.970 50.000 0.00 0.00 0.00 3.60
1667 1684 2.747467 CGATTGCCACATCCTCCTGATT 60.747 50.000 0.00 0.00 0.00 2.57
1870 1887 4.587520 TGGACCTCCATCTTGCCT 57.412 55.556 0.00 0.00 42.01 4.75
1925 1942 1.680735 GTTGACCAATGGACTGTGCAA 59.319 47.619 6.16 0.00 0.00 4.08
1926 1943 1.133823 AGTTGACCAATGGACTGTGCA 60.134 47.619 6.16 4.00 0.00 4.57
1927 1944 1.609208 AGTTGACCAATGGACTGTGC 58.391 50.000 6.16 0.00 0.00 4.57
1928 1945 5.003160 TGAATAGTTGACCAATGGACTGTG 58.997 41.667 6.16 0.00 0.00 3.66
1929 1946 5.241403 TGAATAGTTGACCAATGGACTGT 57.759 39.130 6.16 0.00 0.00 3.55
1932 1949 3.378427 GCCTGAATAGTTGACCAATGGAC 59.622 47.826 6.16 0.00 0.00 4.02
1934 1951 2.689983 GGCCTGAATAGTTGACCAATGG 59.310 50.000 0.00 0.00 0.00 3.16
1935 1952 2.689983 GGGCCTGAATAGTTGACCAATG 59.310 50.000 0.84 0.00 0.00 2.82
1936 1953 2.358195 GGGGCCTGAATAGTTGACCAAT 60.358 50.000 0.84 0.00 0.00 3.16
1937 1954 1.005450 GGGGCCTGAATAGTTGACCAA 59.995 52.381 0.84 0.00 0.00 3.67
1938 1955 0.623723 GGGGCCTGAATAGTTGACCA 59.376 55.000 0.84 0.00 0.00 4.02
1939 1956 0.623723 TGGGGCCTGAATAGTTGACC 59.376 55.000 0.84 0.00 0.00 4.02
1941 1958 3.785887 ACTAATGGGGCCTGAATAGTTGA 59.214 43.478 0.84 0.00 0.00 3.18
1942 1959 4.170468 ACTAATGGGGCCTGAATAGTTG 57.830 45.455 0.84 0.00 0.00 3.16
1943 1960 4.686122 CGAACTAATGGGGCCTGAATAGTT 60.686 45.833 18.13 18.13 36.57 2.24
1944 1961 3.181454 CGAACTAATGGGGCCTGAATAGT 60.181 47.826 0.84 4.36 0.00 2.12
1945 1962 3.181454 ACGAACTAATGGGGCCTGAATAG 60.181 47.826 0.84 3.68 0.00 1.73
1946 1963 2.775384 ACGAACTAATGGGGCCTGAATA 59.225 45.455 0.84 0.00 0.00 1.75
1950 1967 2.702592 TTACGAACTAATGGGGCCTG 57.297 50.000 0.84 0.00 0.00 4.85
1951 1968 2.574824 ACTTTACGAACTAATGGGGCCT 59.425 45.455 0.84 0.00 0.00 5.19
1952 1969 2.681344 CACTTTACGAACTAATGGGGCC 59.319 50.000 0.00 0.00 0.00 5.80
1953 1970 2.096980 GCACTTTACGAACTAATGGGGC 59.903 50.000 0.00 0.00 0.00 5.80
1955 1972 4.634004 TGATGCACTTTACGAACTAATGGG 59.366 41.667 0.00 0.00 0.00 4.00
1957 1974 5.163864 TGCTGATGCACTTTACGAACTAATG 60.164 40.000 0.00 0.00 45.31 1.90
1959 1976 4.311606 TGCTGATGCACTTTACGAACTAA 58.688 39.130 0.00 0.00 45.31 2.24
1960 1977 3.920446 TGCTGATGCACTTTACGAACTA 58.080 40.909 0.00 0.00 45.31 2.24
1961 1978 2.766313 TGCTGATGCACTTTACGAACT 58.234 42.857 0.00 0.00 45.31 3.01
1973 1990 3.007290 TGTCCCTCTACATATGCTGATGC 59.993 47.826 1.58 0.00 40.20 3.91
1974 1991 4.879197 TGTCCCTCTACATATGCTGATG 57.121 45.455 1.58 0.00 0.00 3.07
1975 1992 5.802465 CATTGTCCCTCTACATATGCTGAT 58.198 41.667 1.58 0.00 0.00 2.90
1976 1993 4.503817 GCATTGTCCCTCTACATATGCTGA 60.504 45.833 1.58 0.33 38.89 4.26
1977 1994 3.750130 GCATTGTCCCTCTACATATGCTG 59.250 47.826 1.58 0.00 38.89 4.41
1978 1995 3.649981 AGCATTGTCCCTCTACATATGCT 59.350 43.478 1.58 14.90 42.57 3.79
1979 1996 4.013267 AGCATTGTCCCTCTACATATGC 57.987 45.455 1.58 0.00 40.38 3.14
1980 1997 6.101650 TGTAGCATTGTCCCTCTACATATG 57.898 41.667 0.00 0.00 37.18 1.78
1981 1998 6.728164 AGATGTAGCATTGTCCCTCTACATAT 59.272 38.462 12.09 7.80 46.62 1.78
1982 1999 6.077993 AGATGTAGCATTGTCCCTCTACATA 58.922 40.000 12.09 0.00 46.62 2.29
1984 2001 4.290093 AGATGTAGCATTGTCCCTCTACA 58.710 43.478 3.81 3.81 43.50 2.74
1985 2002 4.946478 AGATGTAGCATTGTCCCTCTAC 57.054 45.455 0.00 0.00 33.80 2.59
1986 2003 5.080337 CCTAGATGTAGCATTGTCCCTCTA 58.920 45.833 0.00 0.00 0.00 2.43
1987 2004 3.900601 CCTAGATGTAGCATTGTCCCTCT 59.099 47.826 0.00 0.00 0.00 3.69
1988 2005 3.643792 ACCTAGATGTAGCATTGTCCCTC 59.356 47.826 0.00 0.00 0.00 4.30
1989 2006 3.658725 ACCTAGATGTAGCATTGTCCCT 58.341 45.455 0.00 0.00 0.00 4.20
1990 2007 5.546621 TTACCTAGATGTAGCATTGTCCC 57.453 43.478 0.00 0.00 0.00 4.46
1991 2008 6.759272 TGATTACCTAGATGTAGCATTGTCC 58.241 40.000 0.00 0.00 0.00 4.02
1992 2009 7.437748 ACTGATTACCTAGATGTAGCATTGTC 58.562 38.462 0.00 0.00 0.00 3.18
1993 2010 7.366847 ACTGATTACCTAGATGTAGCATTGT 57.633 36.000 0.00 0.00 0.00 2.71
1994 2011 8.668510 AAACTGATTACCTAGATGTAGCATTG 57.331 34.615 0.00 0.00 0.00 2.82
1996 2013 9.765795 GTAAAACTGATTACCTAGATGTAGCAT 57.234 33.333 0.00 0.00 31.06 3.79
1997 2014 8.978472 AGTAAAACTGATTACCTAGATGTAGCA 58.022 33.333 0.00 0.00 36.62 3.49
1998 2015 9.819267 AAGTAAAACTGATTACCTAGATGTAGC 57.181 33.333 0.00 0.00 36.62 3.58
2028 2045 9.842775 AGTTCTGAGCAAGATGAATCAATAATA 57.157 29.630 0.00 0.00 33.93 0.98
2029 2046 8.749026 AGTTCTGAGCAAGATGAATCAATAAT 57.251 30.769 0.00 0.00 33.93 1.28
2030 2047 8.571461 AAGTTCTGAGCAAGATGAATCAATAA 57.429 30.769 0.00 0.00 33.93 1.40
2031 2048 7.825761 TGAAGTTCTGAGCAAGATGAATCAATA 59.174 33.333 4.17 0.00 33.93 1.90
2032 2049 6.657966 TGAAGTTCTGAGCAAGATGAATCAAT 59.342 34.615 4.17 0.00 33.93 2.57
2033 2050 5.999600 TGAAGTTCTGAGCAAGATGAATCAA 59.000 36.000 4.17 0.00 33.93 2.57
2034 2051 5.554070 TGAAGTTCTGAGCAAGATGAATCA 58.446 37.500 4.17 0.00 33.93 2.57
2035 2052 6.093771 ACATGAAGTTCTGAGCAAGATGAATC 59.906 38.462 0.00 0.00 33.93 2.52
2043 2060 7.977789 TTGTTATACATGAAGTTCTGAGCAA 57.022 32.000 0.00 0.00 0.00 3.91
2046 2063 9.778993 CCAAATTGTTATACATGAAGTTCTGAG 57.221 33.333 0.00 0.00 0.00 3.35
2058 2075 6.112734 ACTCATCGAGCCAAATTGTTATACA 58.887 36.000 0.00 0.00 32.04 2.29
2059 2076 6.257849 TGACTCATCGAGCCAAATTGTTATAC 59.742 38.462 0.00 0.00 32.04 1.47
2060 2077 6.257849 GTGACTCATCGAGCCAAATTGTTATA 59.742 38.462 0.00 0.00 32.04 0.98
2079 2096 4.829808 GTTGTAAACTTCAACGGTGACTC 58.170 43.478 0.44 0.00 45.32 3.36
2147 2165 2.438434 GGTTGCGGCCATACAGCT 60.438 61.111 2.24 0.00 40.54 4.24
2166 2184 2.386661 TCCGCTTCAGATGGAACTTC 57.613 50.000 0.00 0.00 0.00 3.01
2217 2235 1.004440 GAGGCAGAACAAGGAGCGT 60.004 57.895 0.00 0.00 0.00 5.07
2289 2307 1.890979 GATGACAGGGATGCAGCCG 60.891 63.158 16.15 4.39 0.00 5.52
2301 2319 0.037790 TGTTGTCGGCGATGATGACA 60.038 50.000 14.79 10.92 40.62 3.58
2397 2415 1.072159 GTGGTCAAGCACTGCCTCT 59.928 57.895 5.13 0.00 0.00 3.69
2403 2421 2.661866 GCGACGTGGTCAAGCACT 60.662 61.111 10.29 0.00 32.09 4.40
2421 2439 1.442184 CGTCGTCAGGTTGGTCTCG 60.442 63.158 0.00 0.00 0.00 4.04
2423 2441 1.471684 GTATCGTCGTCAGGTTGGTCT 59.528 52.381 0.00 0.00 0.00 3.85
2727 3270 1.063006 ATGCGTGCAATGTCATCGC 59.937 52.632 8.48 8.48 45.70 4.58
2728 3271 2.849521 CATGCGTGCAATGTCATCG 58.150 52.632 0.00 0.00 0.00 3.84
2758 3302 2.166664 GGTAGGAACTGTCAGTGCTAGG 59.833 54.545 10.93 0.00 41.52 3.02
2772 3316 4.772231 AGGGAGCGCCGGTAGGAA 62.772 66.667 2.29 0.00 41.02 3.36
2803 3351 1.004200 CGGTACCGCCCTTCACTTT 60.004 57.895 23.44 0.00 0.00 2.66
2804 3352 1.474332 TTCGGTACCGCCCTTCACTT 61.474 55.000 29.64 0.00 39.59 3.16
2805 3353 1.262640 ATTCGGTACCGCCCTTCACT 61.263 55.000 29.64 2.24 39.59 3.41
2806 3354 0.808847 GATTCGGTACCGCCCTTCAC 60.809 60.000 29.64 11.69 39.59 3.18
2850 3398 0.934496 TGTTGTAGCAGCGTTCACAC 59.066 50.000 0.00 0.00 0.00 3.82
2851 3399 1.217001 CTGTTGTAGCAGCGTTCACA 58.783 50.000 0.00 0.00 0.00 3.58
2875 3423 2.723010 GCTCAGATGAAACGCAAACGAG 60.723 50.000 0.00 0.00 43.93 4.18
2880 3428 0.320334 TCCGCTCAGATGAAACGCAA 60.320 50.000 0.65 0.00 0.00 4.85
2884 3432 2.370281 TCACTCCGCTCAGATGAAAC 57.630 50.000 0.00 0.00 0.00 2.78
2898 3446 2.235898 ACCTGAGCTTGAGGAATCACTC 59.764 50.000 17.46 0.00 37.99 3.51
2913 3461 6.402550 CCGATGATTCACTTGTTTAACCTGAG 60.403 42.308 0.00 0.00 0.00 3.35
2966 3514 3.492102 TTGTGGTTCTTTCTCCTCCTG 57.508 47.619 0.00 0.00 0.00 3.86
3007 3555 2.857483 TGCGAATCTCAACCAGGAAAA 58.143 42.857 0.00 0.00 0.00 2.29
3025 3573 7.391148 TCTAGTGACCTTTTATTCCAAATGC 57.609 36.000 0.00 0.00 0.00 3.56
3087 3643 2.236146 ACGAATTCCACTGCCACTGATA 59.764 45.455 0.00 0.00 0.00 2.15
3135 3718 2.235016 GATGGAGGAGACGACTATGCT 58.765 52.381 0.00 0.00 0.00 3.79
3174 3757 4.565028 CCATGATCAGTCCATGACCCATAG 60.565 50.000 0.09 0.00 42.89 2.23
3176 3759 2.107726 CCATGATCAGTCCATGACCCAT 59.892 50.000 0.09 0.00 42.89 4.00
3177 3760 1.491754 CCATGATCAGTCCATGACCCA 59.508 52.381 0.09 0.00 42.89 4.51
3183 3766 2.744166 CGTTCAGCCATGATCAGTCCAT 60.744 50.000 0.09 0.00 34.73 3.41
3185 3768 1.293924 CGTTCAGCCATGATCAGTCC 58.706 55.000 0.09 0.00 34.73 3.85
3189 3772 2.564771 GAATCCGTTCAGCCATGATCA 58.435 47.619 0.00 0.00 34.73 2.92
3191 3774 1.212688 TGGAATCCGTTCAGCCATGAT 59.787 47.619 0.00 0.00 36.01 2.45
3201 3784 0.610785 AACCGGCATTGGAATCCGTT 60.611 50.000 0.00 0.00 41.46 4.44
3206 3789 1.176527 CAGTGAACCGGCATTGGAAT 58.823 50.000 0.00 0.00 0.00 3.01
3211 3794 1.346395 TGTAGACAGTGAACCGGCATT 59.654 47.619 0.00 0.00 0.00 3.56
3226 3809 2.187685 CCATGCTGGCGCTGTAGA 59.812 61.111 7.64 0.00 36.97 2.59
3280 3863 2.049156 CACGGCGTGAGAGCTTGA 60.049 61.111 34.85 0.00 35.23 3.02
3298 3881 3.008330 TCGGAACTTTCAACGGAAACAA 58.992 40.909 0.00 0.00 38.07 2.83
3305 3888 0.110644 GCTGCTCGGAACTTTCAACG 60.111 55.000 0.00 0.00 0.00 4.10
3376 3959 0.951040 CTCAGGCGTCAAGAACACCC 60.951 60.000 0.00 0.00 29.63 4.61
3398 3981 1.133294 TCACCATATCTCCTACCGGCA 60.133 52.381 0.00 0.00 0.00 5.69
3410 3993 2.750807 GCCCATGTCAAGCTCACCATAT 60.751 50.000 0.00 0.00 0.00 1.78
3454 4044 1.415672 AAGGGAGGAACAGCGACCAA 61.416 55.000 0.00 0.00 0.00 3.67
3455 4045 1.841556 AAGGGAGGAACAGCGACCA 60.842 57.895 0.00 0.00 0.00 4.02
3463 4053 2.372172 TCTCAGGAAACAAGGGAGGAAC 59.628 50.000 0.00 0.00 0.00 3.62
3491 4081 1.739562 GCACCTCGTCTGCAGGAAG 60.740 63.158 15.13 8.77 34.75 3.46
3556 4159 5.726980 TTTCAGAAGCAACTTGCCATAAT 57.273 34.783 10.25 0.00 46.52 1.28
3557 4160 5.472148 CATTTCAGAAGCAACTTGCCATAA 58.528 37.500 10.25 0.00 46.52 1.90
3558 4161 4.082081 CCATTTCAGAAGCAACTTGCCATA 60.082 41.667 10.25 0.00 46.52 2.74
3559 4162 3.306502 CCATTTCAGAAGCAACTTGCCAT 60.307 43.478 10.25 0.00 46.52 4.40
3560 4163 2.036217 CCATTTCAGAAGCAACTTGCCA 59.964 45.455 10.25 0.00 46.52 4.92
3561 4164 2.680577 CCATTTCAGAAGCAACTTGCC 58.319 47.619 10.25 0.00 46.52 4.52
3562 4165 2.064014 GCCATTTCAGAAGCAACTTGC 58.936 47.619 5.55 5.55 45.46 4.01
3563 4166 2.322161 CGCCATTTCAGAAGCAACTTG 58.678 47.619 0.00 0.00 0.00 3.16
3583 4188 1.374758 CAGTGAGCTCCCGAACACC 60.375 63.158 12.15 0.00 34.33 4.16
3607 4212 8.612145 ACTACCAGAAAGGGAATTATGTTAACT 58.388 33.333 7.22 0.00 43.89 2.24
3617 4222 5.437191 AATTCGACTACCAGAAAGGGAAT 57.563 39.130 0.00 0.00 43.89 3.01
3647 4252 3.896648 TGCTCGAAATGAAACCACTTC 57.103 42.857 0.00 0.00 34.31 3.01
3662 4268 9.599322 GAACAAATTATATTATCAGGTTGCTCG 57.401 33.333 0.00 0.00 0.00 5.03
3680 4286 7.210873 ACAAGAGTCGAGTAAGAGAACAAATT 58.789 34.615 0.00 0.00 0.00 1.82
3714 4320 4.891627 TCTGAATTTGTGTCGCTTTCAA 57.108 36.364 0.00 0.00 0.00 2.69
3720 4326 1.401539 GGCCTTCTGAATTTGTGTCGC 60.402 52.381 0.00 0.00 0.00 5.19


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

AutoCloner maintained by Alex Coulton.