Locus 1921

Sequence ID 3R_DroMel_CAF1
Location 5,441,960 – 5,442,114
Length 154
Max. P 0.993526
window3156 window3157 window3158

overview

Window 6

Location 5,441,960 – 5,442,074
Length 114
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 89.83
Mean single sequence MFE -31.90
Consensus MFE -24.22
Energy contribution -25.33
Covariance contribution 1.11
Combinations/Pair 1.03
Mean z-score -2.40
Structure conservation index 0.76
SVM decision value 0.26
SVM RNA-class probability 0.656937
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5441960 114 + 27905053
GUGGCAUUGCCAUUGUUGUUGGC------GUUGCAGUUGUGCAAACGCAUACAAAACACACAUUAGGCAUCAUUUAGCAUGUUUAGCAUGUUUUGCAUUUUGCGAUUGCCCAAUUAACCC
...(((.(((((.......))))------).)))(((((.((((.((((..(((((((....((((((((........))))))))..))))))).....)))).)))).)))))..... ( -33.30)
>DroEre_CAF1 29173 114 + 1
------UUGCCAUUGUUGUUGGCGGUGCAGUUGCAGUUAUGCAAAUGCAUACAAAACACACAUUAGGCAUCAUUUUGCAUGUUUAGCAUGUUUUGCAUUUUGCUAUUGCCCAAUUAACCC
------..((((.......))))((.(((((.((((..(((((((.((((.(.((((((......)(((......))).))))).).))))))))))).)))).)))))))......... ( -33.70)
>DroYak_CAF1 29714 114 + 1
------UUGGCAUUGUUGUUGGCGUUGCAGUUGCAGUUGUGCAAACGCAUACAAAACACACAUUAGGCAUCAUUUUGCAUGUUUAGCAUGUUUUGCAUUUUGCCAUUGCCCAAUUAACCC
------........((((((((....(((((.((((..(((((((.((((.(.((((((......)(((......))).))))).).))))))))))).)))).))))))))).)))).. ( -28.70)
>consensus
______UUGCCAUUGUUGUUGGCG_UGCAGUUGCAGUUGUGCAAACGCAUACAAAACACACAUUAGGCAUCAUUUUGCAUGUUUAGCAUGUUUUGCAUUUUGCCAUUGCCCAAUUAACCC
..............((((((((....(((((.((((..(((((((.((((.(.((((((......)(((......))).))))).).))))))))))).)))).))))))))).)))).. (-24.22 = -25.33 +   1.11)

alignment

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secondary structure

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dotplot

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Window 7

Location 5,441,960 – 5,442,074
Length 114
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 89.83
Mean single sequence MFE -33.47
Consensus MFE -25.31
Energy contribution -26.20
Covariance contribution 0.89
Combinations/Pair 1.03
Mean z-score -3.31
Structure conservation index 0.76
SVM decision value 0.92
SVM RNA-class probability 0.881430
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5441960 114 - 27905053
GGGUUAAUUGGGCAAUCGCAAAAUGCAAAACAUGCUAAACAUGCUAAAUGAUGCCUAAUGUGUGUUUUGUAUGCGUUUGCACAACUGCAAC------GCCAACAACAAUGGCAAUGCCAC
((((...(((.((((.((((...((((((((((((.......((........)).....)))))))))))))))).)))).)))..))...------((((.......))))....)).. ( -33.00)
>DroEre_CAF1 29173 114 - 1
GGGUUAAUUGGGCAAUAGCAAAAUGCAAAACAUGCUAAACAUGCAAAAUGAUGCCUAAUGUGUGUUUUGUAUGCAUUUGCAUAACUGCAACUGCACCGCCAACAACAAUGGCAA------
.........(((((...(((..(((((((.(((((.(((((((((.............))))))))).)))))..)))))))...)))...))).))((((.......))))..------ ( -32.82)
>DroYak_CAF1 29714 114 - 1
GGGUUAAUUGGGCAAUGGCAAAAUGCAAAACAUGCUAAACAUGCAAAAUGAUGCCUAAUGUGUGUUUUGUAUGCGUUUGCACAACUGCAACUGCAACGCCAACAACAAUGCCAA------
.(((..((((.....((((...(((((((((((((.......(((......))).....)))))))))))))(((.(((((....))))).)))...))))....)))))))..------ ( -34.60)
>consensus
GGGUUAAUUGGGCAAUAGCAAAAUGCAAAACAUGCUAAACAUGCAAAAUGAUGCCUAAUGUGUGUUUUGUAUGCGUUUGCACAACUGCAACUGCA_CGCCAACAACAAUGGCAA______
..(((.....(((.........(((((((((((((.......((........)).....)))))))))))))(((.(((((....))))).)))...)))...))).............. (-25.31 = -26.20 +   0.89)

alignment

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secondary structure

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dotplot

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Window 8

Location 5,441,994 – 5,442,114
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 97.42
Mean single sequence MFE -29.02
Consensus MFE -26.86
Energy contribution -27.26
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -1.94
Structure conservation index 0.93
SVM decision value 2.40
SVM RNA-class probability 0.993526
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5441994 120 - 27905053
CUUGAAAAUUUAUUAGCGCCCAGAAAAAUACCAUAUAAGCGGGUUAAUUGGGCAAUCGCAAAAUGCAAAACAUGCUAAACAUGCUAAAUGAUGCCUAAUGUGUGUUUUGUAUGCGUUUGC
...............((((((((..((...((........)).))..))))))...((((...((((((((((((.......((........)).....))))))))))))))))...)) ( -28.90)
>DroSec_CAF1 28457 120 - 1
CUUGAAAAUUUAUUAGCGCCCAGAAAAAUACCAUAUAAGCGGGUUAAUUGGGCAAUCGCAAAAUGCAAAACAUGCUAAACAUGCAAAAUGAUGCCUAAUGUGUGUUUUGUAUGCGUUUGC
...............((((((((..((...((........)).))..))))))...((((...((((((((((((.......(((......))).....))))))))))))))))...)) ( -29.50)
>DroSim_CAF1 23647 120 - 1
CUUGAAAAUUUAUUAGCGCCCAGAAAAAUACCAUAUAUGCGGGUUAAUUGGGCAAUCGCAAAAUGCAAAACAUGCUAAACAUGCAAAAUGAUGCCUAAUGUGUGUUUUGUAUGCGUUUGC
...............((((((((..((...((........)).))..))))))...((((...((((((((((((.......(((......))).....))))))))))))))))...)) ( -29.50)
>DroEre_CAF1 29207 120 - 1
CUUGCAAAUUUAUUAGCGCCAAGAAAAAUACCAUAUAAGCGGGUUAAUUGGGCAAUAGCAAAAUGCAAAACAUGCUAAACAUGCAAAAUGAUGCCUAAUGUGUGUUUUGUAUGCAUUUGC
...((((((.((((.((.((((..((....((........)).))..))))))))))(((...((((((((((((.......(((......))).....))))))))))))))))))))) ( -28.60)
>DroYak_CAF1 29748 120 - 1
CUCGAAAAUUUAUUAGCGCCCAGAAAAAUACCAUAUAAGCGGGUUAAUUGGGCAAUGGCAAAAUGCAAAACAUGCUAAACAUGCAAAAUGAUGCCUAAUGUGUGUUUUGUAUGCGUUUGC
.................((((((..((...((........)).))..))))))....((((((((((((((((((.......(((......))).....)))))))))))))...))))) ( -28.60)
>consensus
CUUGAAAAUUUAUUAGCGCCCAGAAAAAUACCAUAUAAGCGGGUUAAUUGGGCAAUCGCAAAAUGCAAAACAUGCUAAACAUGCAAAAUGAUGCCUAAUGUGUGUUUUGUAUGCGUUUGC
.................((((((..((...((........)).))..))))))....((((((((((((((((((.......(((......))).....)))))))))))))...))))) (-26.86 = -27.26 +   0.40)

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 10:22:53 2006