Locus 991

Sequence ID 3R_DroMel_CAF1
Location 3,169,788 – 3,169,948
Length 160
Max. P 0.898664
window1605 window1606 window1607

overview

Window 5

Location 3,169,788 – 3,169,908
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 98.33
Mean single sequence MFE -31.33
Consensus MFE -29.55
Energy contribution -29.67
Covariance contribution 0.11
Combinations/Pair 1.03
Mean z-score -2.16
Structure conservation index 0.94
SVM decision value 0.87
SVM RNA-class probability 0.872039
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3169788 120 + 27905053
CUAAACAUUUGAUGCAGGUCAUUUCGACACCGAAACGGUUGCCCCAUGACUCGGCAGCUUCCACUAACGAAUUAUGCGCUCUAGCGCCUCAUGUUCUCCGUCCAAAUCUUCUGUCAUCAU
.........(((((((((..((((.(((........(((((((.........))))))).........((((...((((....)))).....))))...))).))))..)))).))))). ( -32.00)
>DroSim_CAF1 928 120 + 1
CGAAACAUUUGAUGCAGGUCAUUUCGACACCGAAACGGUUGCCCCAUGACUCGGCAGCUUCCACUAACGAAUUAUGCGCUCUAGCGCCUCAUGUUCUCCGGCCAAAUCUUCUGUCAUCAU
.........(((((((((((.....))).(((....(((((((.........))))))).........((((...((((....)))).....))))..))).........))).))))). ( -30.80)
>DroYak_CAF1 1181 120 + 1
CGAAACAUUUGAUGCAGGUCAUUUCGACACCGAAACGGUUGCCCCAUGACUCGGCAGCUUCCACUAACGAAUUAUGCGCUCUAGCGCCUCAUGUUCUCCAGCCAAAUCUUCUGUCAUCAU
.........(((((((((...(((((....))))).(((((...(((((.(((..((......))..))).....((((....)))).))))).....)))))......)))).))))). ( -31.20)
>consensus
CGAAACAUUUGAUGCAGGUCAUUUCGACACCGAAACGGUUGCCCCAUGACUCGGCAGCUUCCACUAACGAAUUAUGCGCUCUAGCGCCUCAUGUUCUCCGGCCAAAUCUUCUGUCAUCAU
.........(((((((((...(((((....))))).(((((...(((((.(((..((......))..))).....((((....)))).))))).....)))))......)))).))))). (-29.55 = -29.67 +   0.11) 

alignment

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secondary structure

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dotplot

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Window 6

Location 3,169,788 – 3,169,908
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 98.33
Mean single sequence MFE -39.53
Consensus MFE -37.32
Energy contribution -37.43
Covariance contribution 0.11
Combinations/Pair 1.03
Mean z-score -1.92
Structure conservation index 0.94
SVM decision value 0.55
SVM RNA-class probability 0.778328
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3169788 120 - 27905053
AUGAUGACAGAAGAUUUGGACGGAGAACAUGAGGCGCUAGAGCGCAUAAUUCGUUAGUGGAAGCUGCCGAGUCAUGGGGCAACCGUUUCGGUGUCGAAAUGACCUGCAUCAAAUGUUUAG
.(((((.(((...((((.((((..((((((((.((((....))))....((((.((((....)))).)))))))))((....))..)))..)))).))))...))))))))......... ( -40.10)
>DroSim_CAF1 928 120 - 1
AUGAUGACAGAAGAUUUGGCCGGAGAACAUGAGGCGCUAGAGCGCAUAAUUCGUUAGUGGAAGCUGCCGAGUCAUGGGGCAACCGUUUCGGUGUCGAAAUGACCUGCAUCAAAUGUUUCG
.(((((.(((........(((((((..(((((.((((....))))....((((.((((....)))).)))))))))((....)).)))))))(((.....)))))))))))......... ( -40.10)
>DroYak_CAF1 1181 120 - 1
AUGAUGACAGAAGAUUUGGCUGGAGAACAUGAGGCGCUAGAGCGCAUAAUUCGUUAGUGGAAGCUGCCGAGUCAUGGGGCAACCGUUUCGGUGUCGAAAUGACCUGCAUCAAAUGUUUCG
.........((((((((((.((.((..(((..(((((..((((.(((.(((((.((((....)))).))))).)))((....))))))..)))))...)))..)).)))))))).)))). ( -38.40)
>consensus
AUGAUGACAGAAGAUUUGGCCGGAGAACAUGAGGCGCUAGAGCGCAUAAUUCGUUAGUGGAAGCUGCCGAGUCAUGGGGCAACCGUUUCGGUGUCGAAAUGACCUGCAUCAAAUGUUUCG
.(((((.(((........(((((((..(((((.((((....))))....((((.((((....)))).)))))))))((....)).)))))))(((.....)))))))))))......... (-37.32 = -37.43 +   0.11) 

alignment

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secondary structure

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dotplot

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Window 7

Location 3,169,828 – 3,169,948
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 98.89
Mean single sequence MFE -36.93
Consensus MFE -36.50
Energy contribution -36.50
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.01
Structure conservation index 0.99
SVM decision value 1.00
SVM RNA-class probability 0.898664
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3169828 120 - 27905053
GGCAAUUGCUAUUGAUUAAAUCGGCUUAAAGCUUUGACUAAUGAUGACAGAAGAUUUGGACGGAGAACAUGAGGCGCUAGAGCGCAUAAUUCGUUAGUGGAAGCUGCCGAGUCAUGGGGC
.......(((..((((....(((((....((((((.((((((((...((((...))))...............((((....)))).....)))))))).)))))))))))))))...))) ( -36.50)
>DroSim_CAF1 968 120 - 1
GGCAAUUGCUAUUGAUUAAAUCGGCUUAAAGCUUUGACUAAUGAUGACAGAAGAUUUGGCCGGAGAACAUGAGGCGCUAGAGCGCAUAAUUCGUUAGUGGAAGCUGCCGAGUCAUGGGGC
.......(((..((((....(((((....((((((.((((((((...((((...))))...............((((....)))).....)))))))).)))))))))))))))...))) ( -36.50)
>DroYak_CAF1 1221 120 - 1
GGCAAUUGCUAUUGAUUAAAUCGGCUUAAAGCUUUGACUAAUGAUGACAGAAGAUUUGGCUGGAGAACAUGAGGCGCUAGAGCGCAUAAUUCGUUAGUGGAAGCUGCCGAGUCAUGGGGC
.......(((..((((....(((((....((((((.((((((((...(((.........)))...........((((....)))).....)))))))).)))))))))))))))...))) ( -37.80)
>consensus
GGCAAUUGCUAUUGAUUAAAUCGGCUUAAAGCUUUGACUAAUGAUGACAGAAGAUUUGGCCGGAGAACAUGAGGCGCUAGAGCGCAUAAUUCGUUAGUGGAAGCUGCCGAGUCAUGGGGC
.......(((..((((....(((((....((((((.((((((((...((((...))))...............((((....)))).....)))))))).)))))))))))))))...))) (-36.50 = -36.50 +   0.00) 

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 09:57:49 2006