Locus 8652

Sequence ID X_DroMel_CAF1
Location 21,863,777 – 21,863,980
Length 203
Max. P 0.980853
window14216 window14217 window14218 window14219 window14220

overview

Window 6

Location 21,863,777 – 21,863,873
Length 96
Sequences 4
Columns 98
Reading direction forward
Mean pairwise identity 89.18
Mean single sequence MFE -39.45
Consensus MFE -32.62
Energy contribution -32.50
Covariance contribution -0.12
Combinations/Pair 1.14
Mean z-score -2.25
Structure conservation index 0.83
SVM decision value 1.35
SVM RNA-class probability 0.945032
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21863777 96 + 22224390
ACAGUGGGGCAAAACAGUCGGCGGGGGGCGGAUACCGAGACUGUGCUCACGUGAGUACCAGGACAUC--GACUUAGUGUCCUGGGAUUGGUAAUUGCA
.((((.((((...((((((..(((..........))).))))))))))((....)).(((((((((.--......))))))))).))))......... ( -36.00)
>DroSec_CAF1 55289 96 + 1
ACAGUGGGGCAAAAUAGUCGGCGGGGGGCGGAUGCGGAGACUGUGCUCACGUUAGUGCCAGGACAUC--GACUUAGUGUCCUGGGAUUGGUAAUUGCA
........((((..((((((((((((.((((.........)))).))).))))....(((((((((.--......))))))))))))))....)))). ( -32.70)
>DroEre_CAF1 26631 95 + 1
ACAGUGGGGCAAAGCCGUCGGCG-GAGGCGGAUGCCGAGCCUGUGCUCACGUGAGUGCCAGGACACC--GACUUGGUGUCCUGGGAUUGGUAAUUGCA
........((((.((((((((((-.((((.........)))).))))(((....)))((((((((((--.....)))))))))))).))))..)))). ( -44.30)
>DroYak_CAF1 28823 98 + 1
ACAGUGAGGCAAAGCAGUCGGCGGGAGGCGGAUACCGAGCCUGUGCUCACGUGAUUGCCAGGACACCAGGUCUUGGUGUCCUGGGACUGGCAAUUGCA
...(((((((...)).....(((((...(((...)))..))))).)))))(..((((((((....(((((.(.....).)))))..))))))))..). ( -44.80)
>consensus
ACAGUGGGGCAAAACAGUCGGCGGGAGGCGGAUACCGAGACUGUGCUCACGUGAGUGCCAGGACACC__GACUUAGUGUCCUGGGAUUGGUAAUUGCA
........((((..(((((.(((.(((((((.........)))).))).))).....((((((((((.......)))))))))))))))....)))). (-32.62 = -32.50 +  -0.12)

alignment

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secondary structure

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Window 7

Location 21,863,777 – 21,863,873
Length 96
Sequences 4
Columns 98
Reading direction reverse
Mean pairwise identity 89.18
Mean single sequence MFE -31.40
Consensus MFE -25.12
Energy contribution -25.12
Covariance contribution 0.00
Combinations/Pair 1.12
Mean z-score -2.30
Structure conservation index 0.80
SVM decision value 1.23
SVM RNA-class probability 0.933632
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21863777 96 - 22224390
UGCAAUUACCAAUCCCAGGACACUAAGUC--GAUGUCCUGGUACUCACGUGAGCACAGUCUCGGUAUCCGCCCCCCGCCGACUGUUUUGCCCCACUGU
.((((.........(((((((((......--).))))))))..(((....))).((((((.(((..........)))..)))))).))))........ ( -25.80)
>DroSec_CAF1 55289 96 - 1
UGCAAUUACCAAUCCCAGGACACUAAGUC--GAUGUCCUGGCACUAACGUGAGCACAGUCUCCGCAUCCGCCCCCCGCCGACUAUUUUGCCCCACUGU
.((...........(((((((((......--).))))))))(((....))).))(((((....(((((.((.....)).))......)))...))))) ( -24.20)
>DroEre_CAF1 26631 95 - 1
UGCAAUUACCAAUCCCAGGACACCAAGUC--GGUGUCCUGGCACUCACGUGAGCACAGGCUCGGCAUCCGCCUC-CGCCGACGGCUUUGCCCCACUGU
.((...........((((((((((.....--))))))))))(((....))).))((((....((((...(((((-....)).)))..))))...)))) ( -37.20)
>DroYak_CAF1 28823 98 - 1
UGCAAUUGCCAGUCCCAGGACACCAAGACCUGGUGUCCUGGCAAUCACGUGAGCACAGGCUCGGUAUCCGCCUCCCGCCGACUGCUUUGCCUCACUGU
.((((..((.((((..(((((((((.....)))))))))(((........((((....))))(((....)))....))))))))).))))........ ( -38.40)
>consensus
UGCAAUUACCAAUCCCAGGACACCAAGUC__GAUGUCCUGGCACUCACGUGAGCACAGGCUCGGCAUCCGCCCCCCGCCGACUGCUUUGCCCCACUGU
.(((..........((((((((((.......)))))))))).......(((.(((.((..(((((...........)))))...)).)))..)))))) (-25.12 = -25.12 +   0.00)

alignment

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secondary structure

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dotplot

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Window 8

Location 21,863,835 – 21,863,953
Length 118
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 90.20
Mean single sequence MFE -44.72
Consensus MFE -33.56
Energy contribution -34.56
Covariance contribution 1.00
Combinations/Pair 1.15
Mean z-score -3.06
Structure conservation index 0.75
SVM decision value 1.19
SVM RNA-class probability 0.928597
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21863835 118 + 22224390
CAGGACAUC--GACUUAGUGUCCUGGGAUUGGUAAUUGCAUUGCCAUGGAUACGCCAACUACGUCUUCGAGUGCAUUACCCGUAGACAACCAGUUGCAUUUGCGUAGGUGGCGCAAUUAA
((((((((.--......)))))))).......(((((((...(((((...((((((((((..((((.((.(((...))).)).))))....))))).....))))).)))))))))))). ( -39.00)
>DroSec_CAF1 55347 118 + 1
CAGGACAUC--GACUUAGUGUCCUGGGAUUGGUAAUUGCAUUGCCAUGGAUACGCCAACUGCGUCUUCGAGUGCAUUACUCGUAGACAACCAGUUGCAUUUGCGUAGGUGGCGCAAUUAA
((((((((.--......)))))))).......(((((((...(((((...(((((((((((.((((.((((((...)))))).))))...)))))).....))))).)))))))))))). ( -46.90)
>DroEre_CAF1 26688 115 + 1
CAGGACACC--GACUUGGUGUCCUGGGAUUGGUAAUUGCAUUGCCAUGGAUACGC--ACUGCGUCU-CGAGUGCAUUACGCAUAGGCAACCAGUUGCAUUUGCGUAGGUGCCGCAAUUAG
(((((((((--.....))))))))).......(((((((..((((........((--(((.((...-)))))))..((((((...((((....))))...))))))))))..))))))). ( -47.80)
>DroYak_CAF1 28881 120 + 1
CAGGACACCAGGUCUUGGUGUCCUGGGACUGGCAAUUGCAUUGCCAUGGAUACGACAACUGCGUCUUCAAGUGCAUUACGCGUAGACAACCAGUUGCAUUUGCAUGUGUGGCGCACUUAA
(((((((((((...)))))))))))....(((((((...))))))).(((.(((.(....)))).)))((((((.((((((((.(((.....)))((....)))))))))).)))))).. ( -45.20)
>consensus
CAGGACACC__GACUUAGUGUCCUGGGAUUGGUAAUUGCAUUGCCAUGGAUACGCCAACUGCGUCUUCGAGUGCAUUACGCGUAGACAACCAGUUGCAUUUGCGUAGGUGGCGCAAUUAA
(((((((((.......)))))))))....(((((((...)))))))......(((((.(((((....((((((((...................))))))))))))).)))))....... (-33.56 = -34.56 +   1.00)

alignment

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secondary structure

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dotplot

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Window 9

Location 21,863,835 – 21,863,953
Length 118
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 90.20
Mean single sequence MFE -42.30
Consensus MFE -34.20
Energy contribution -35.70
Covariance contribution 1.50
Combinations/Pair 1.17
Mean z-score -3.37
Structure conservation index 0.81
SVM decision value 1.87
SVM RNA-class probability 0.980853
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21863835 118 - 22224390
UUAAUUGCGCCACCUACGCAAAUGCAACUGGUUGUCUACGGGUAAUGCACUCGAAGACGUAGUUGGCGUAUCCAUGGCAAUGCAAUUACCAAUCCCAGGACACUAAGUC--GAUGUCCUG
.(((((((((((..(((((.....((((((..(((((.(((((.....))))).))))))))))))))))....))))...))))))).......((((((((......--).))))))) ( -39.70)
>DroSec_CAF1 55347 118 - 1
UUAAUUGCGCCACCUACGCAAAUGCAACUGGUUGUCUACGAGUAAUGCACUCGAAGACGCAGUUGGCGUAUCCAUGGCAAUGCAAUUACCAAUCCCAGGACACUAAGUC--GAUGUCCUG
.(((((((((((..(((((.....((((((..(((((.(((((.....))))).))))))))))))))))....))))...))))))).......((((((((......--).))))))) ( -42.20)
>DroEre_CAF1 26688 115 - 1
CUAAUUGCGGCACCUACGCAAAUGCAACUGGUUGCCUAUGCGUAAUGCACUCG-AGACGCAGU--GCGUAUCCAUGGCAAUGCAAUUACCAAUCCCAGGACACCAAGUC--GGUGUCCUG
.((((((((...((((((((...((((....))))...))))))(((((((((-...)).)))--))))......))...)))))))).......(((((((((.....--))))))))) ( -45.20)
>DroYak_CAF1 28881 120 - 1
UUAAGUGCGCCACACAUGCAAAUGCAACUGGUUGUCUACGCGUAAUGCACUUGAAGACGCAGUUGUCGUAUCCAUGGCAAUGCAAUUGCCAGUCCCAGGACACCAAGACCUGGUGUCCUG
....(((.....))).(((....)))((((((.((((.((.((.....)).)).))))(((.(((((((....))))))))))....))))))..((((((((((.....)))))))))) ( -42.10)
>consensus
UUAAUUGCGCCACCUACGCAAAUGCAACUGGUUGUCUACGCGUAAUGCACUCGAAGACGCAGUUGGCGUAUCCAUGGCAAUGCAAUUACCAAUCCCAGGACACCAAGUC__GAUGUCCUG
.(((((((((((..(((((.....((((((..(((((.(((((.....))))).))))))))))))))))....))))...))))))).......(((((((((.......))))))))) (-34.20 = -35.70 +   1.50)

alignment

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secondary structure

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dotplot

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Window 0

Location 21,863,873 – 21,863,980
Length 107
Sequences 4
Columns 107
Reading direction reverse
Mean pairwise identity 88.16
Mean single sequence MFE -33.64
Consensus MFE -21.24
Energy contribution -22.05
Covariance contribution 0.81
Combinations/Pair 1.21
Mean z-score -2.18
Structure conservation index 0.63
SVM decision value 0.02
SVM RNA-class probability 0.542250
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21863873 107 - 22224390
CCAGCUUAGUGCUGUAAGCAACACUUCUUAAUUGCGCCACCUACGCAAAUGCAACUGGUUGUCUACGGGUAAUGCACUCGAAGACGUAGUUGGCGUAUCCAUGGCAA
...(((.((((.((....)).)))).......(((((((.((((((....))........((((.(((((.....))))).)))))))).))))))).....))).. ( -35.10)
>DroSec_CAF1 55385 107 - 1
CAAGCUUAGUGCCGUAAGCAACACUUGUUAAUUGCGCCACCUACGCAAAUGCAACUGGUUGUCUACGAGUAAUGCACUCGAAGACGCAGUUGGCGUAUCCAUGGCAA
.........((((((.((((.....))))...((((((......((....))(((((..(((((.(((((.....))))).))))))))))))))))...)))))). ( -35.30)
>DroEre_CAF1 26726 104 - 1
CCAGCUUCAUGCCGCAAGCAACACUUCCUAAUUGCGGCACCUACGCAAAUGCAACUGGUUGCCUAUGCGUAAUGCACUCG-AGACGCAGU--GCGUAUCCAUGGCAA
((((.....((((((((..............)))))))).....((....))..))))(((((.(((.(((.((((((((-...)).)))--)))))).)))))))) ( -34.74)
>DroYak_CAF1 28921 107 - 1
CCAGCUUCAUGCGGCUAGCAACUCUUCUUAAGUGCGCCACACAUGCAAAUGCAACUGGUUGUCUACGCGUAAUGCACUUGAAGACGCAGUUGUCGUAUCCAUGGCAA
...(((..(((((((.(((..((((((..((((((((((....(((....)))..)))).((....)).....))))))))))).)..))))))))))....))).. ( -29.40)
>consensus
CCAGCUUAAUGCCGCAAGCAACACUUCUUAAUUGCGCCACCUACGCAAAUGCAACUGGUUGUCUACGCGUAAUGCACUCGAAGACGCAGUUGGCGUAUCCAUGGCAA
.........(((((.................(((((.......)))))(((((((((..(((((.(((((.....))))).))))))))))).))).....))))). (-21.24 = -22.05 +   0.81)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:09:26 2006