Locus 3633

Sequence ID 3L_DroMel_CAF1
Location 10,682,966 – 10,683,126
Length 160
Max. P 0.997801
window5667 window5668 window5669

overview

Window 7

Location 10,682,966 – 10,683,086
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 94.01
Mean single sequence MFE -45.20
Consensus MFE -40.78
Energy contribution -40.65
Covariance contribution -0.13
Combinations/Pair 1.17
Mean z-score -2.49
Structure conservation index 0.90
SVM decision value 2.93
SVM RNA-class probability 0.997801
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10682966 120 + 23771897
CUACGGCGGUGGCGCGUCGUCGUUGUGUGUUAUACAAUAAUUAAGUUUUCAGCACCUGCGUGAGUCCAAGUUGGAGCCGCUACCGCUGCAGCUGCUCGUUUGCAGCUCUUAAGCUUGUCC
...(((((((((((.((....(((((((...))))))).........((((((....((....))....))))))))))))))))))).((((((......))))))............. ( -42.40)
>DroSec_CAF1 17297 117 + 1
CUGCGGCGGUGGCGCGU---CGUUGUGUGUUAUACAAUAAUUAAGUUUUCAGCACCUGCGUGACUCCAAGUUGGAGCCUCUACCGCUGCAGCUGCUCGUUUGCAGCUCUUAAGCUUGUCC
.((((((((((((((((---....((((.....((.........)).....))))..))))).((((.....))))...)))))))))))(((((......))))).............. ( -42.00)
>DroSim_CAF1 18538 117 + 1
CUGCGGCGGUGGCGCGU---CGUUGUGUGUUAUACAAUAAUUAAGUUUUCAGCACCUGCGUGAGUCCAAGUUGGAUCCGCUACCGCUGCAGCUGCUCGUUUGCAGCUCUUAAGCUUGUCC
.(((((((((((((.((---((((((((...)))))))...........((((....((....))....))))))).)))))))))))))(((((......))))).............. ( -47.40)
>DroEre_CAF1 17932 117 + 1
UUGCGGCGGUGGCGCGU---CGUUGUGUGUUAUACAAUAAUUAAGUUUUCAGCACCUGCGUGAGUCCAAGUUGGAGCCGCUACCGCUGCAGCUGCUCGUUUGCAGCGCUUAAGCUUGUCC
.(((((((((((((.((---.(((((((...))))))).........((((((....((....))....)))))))))))))))))))))(((((......)))))((....))...... ( -48.40)
>DroYak_CAF1 29341 117 + 1
UUGCGGCGGUGGCGCGU---CGUUGUGUGUUAUACAAUAAUUAAGUUUUCAGCACCUGCGUGAGUCCAAGUUGGAGCCGCUACCGCUGCAGCUGCUCGUUUGCAGCUCUUGAGCUUGUCC
.(((((((((((((.((---.(((((((...))))))).........((((((....((....))....)))))))))))))))))))))(((((......))))).............. ( -46.90)
>DroAna_CAF1 17698 116 + 1
-AGCGGUGGCAGCGCGU---CGUUGUAUGUUAUACAAUAAUUAAGUUUUCAGCACCUGCGUGAGUCCAAGUUGGAGCUGCUGUCGCUGCAGCUGCUCGUGUGCAGCUCUUAAGCCUGUCC
-.(((((((((((((..---.(((((((...))))))).........((((((....((....))....)))))))).)))))))))))((((((......))))))............. ( -44.10)
>consensus
CUGCGGCGGUGGCGCGU___CGUUGUGUGUUAUACAAUAAUUAAGUUUUCAGCACCUGCGUGAGUCCAAGUUGGAGCCGCUACCGCUGCAGCUGCUCGUUUGCAGCUCUUAAGCUUGUCC
.(((((((((((((.((....(((((((...))))))).........((((((....)).))))(((.....))))))))))))))))))(((((......))))).............. (-40.78 = -40.65 +  -0.13)

alignment

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secondary structure

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dotplot

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Window 8

Location 10,682,966 – 10,683,086
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 94.01
Mean single sequence MFE -36.15
Consensus MFE -30.74
Energy contribution -31.02
Covariance contribution 0.28
Combinations/Pair 1.10
Mean z-score -1.47
Structure conservation index 0.85
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10682966 120 - 23771897
GGACAAGCUUAAGAGCUGCAAACGAGCAGCUGCAGCGGUAGCGGCUCCAACUUGGACUCACGCAGGUGCUGAAAACUUAAUUAUUGUAUAACACACAACGACGACGCGCCACCGCCGUAG
.............((((((......))))))((.(((((.(((..(((.....)))....))).((((((((....))).(..((((.......))))..)....)))))))))).)).. ( -33.70)
>DroSec_CAF1 17297 117 - 1
GGACAAGCUUAAGAGCUGCAAACGAGCAGCUGCAGCGGUAGAGGCUCCAACUUGGAGUCACGCAGGUGCUGAAAACUUAAUUAUUGUAUAACACACAACG---ACGCGCCACCGCCGCAG
.............((((((......))))))((.(((((...((((((.....)))))).....((((((((....))).(..((((.......))))..---).)))))))))).)).. ( -38.80)
>DroSim_CAF1 18538 117 - 1
GGACAAGCUUAAGAGCUGCAAACGAGCAGCUGCAGCGGUAGCGGAUCCAACUUGGACUCACGCAGGUGCUGAAAACUUAAUUAUUGUAUAACACACAACG---ACGCGCCACCGCCGCAG
.............((((((......))))))((.(((((.((((((((.....))).)).))).((((((((....))).(..((((.......))))..---).)))))))))).)).. ( -37.70)
>DroEre_CAF1 17932 117 - 1
GGACAAGCUUAAGCGCUGCAAACGAGCAGCUGCAGCGGUAGCGGCUCCAACUUGGACUCACGCAGGUGCUGAAAACUUAAUUAUUGUAUAACACACAACG---ACGCGCCACCGCCGCAA
......((....))(((((......)))))(((.(((((.(((..(((.....)))....))).((((((((....))).(..((((.......))))..---).)))))))))).))). ( -36.90)
>DroYak_CAF1 29341 117 - 1
GGACAAGCUCAAGAGCUGCAAACGAGCAGCUGCAGCGGUAGCGGCUCCAACUUGGACUCACGCAGGUGCUGAAAACUUAAUUAUUGUAUAACACACAACG---ACGCGCCACCGCCGCAA
.............((((((......))))))((.(((((.(((..(((.....)))....))).((((((((....))).(..((((.......))))..---).)))))))))).)).. ( -35.90)
>DroAna_CAF1 17698 116 - 1
GGACAGGCUUAAGAGCUGCACACGAGCAGCUGCAGCGACAGCAGCUCCAACUUGGACUCACGCAGGUGCUGAAAACUUAAUUAUUGUAUAACAUACAACG---ACGCGCUGCCACCGCU-
.....(((.....((((((......))))))((((((.(((((.((((.....)))........).))))).........(..((((((...))))))..---)..))))))....)))- ( -33.90)
>consensus
GGACAAGCUUAAGAGCUGCAAACGAGCAGCUGCAGCGGUAGCGGCUCCAACUUGGACUCACGCAGGUGCUGAAAACUUAAUUAUUGUAUAACACACAACG___ACGCGCCACCGCCGCAG
.............((((((......))))))((.(((((.(((..(((.....)))....))).((((((((....)))....((((.......)))).......)))))))))).)).. (-30.74 = -31.02 +   0.28)

alignment

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secondary structure

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dotplot

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Window 9

Location 10,683,006 – 10,683,126
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 91.69
Mean single sequence MFE -40.10
Consensus MFE -36.62
Energy contribution -36.65
Covariance contribution 0.03
Combinations/Pair 1.16
Mean z-score -1.44
Structure conservation index 0.91
SVM decision value 0.88
SVM RNA-class probability 0.872711
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10683006 120 + 23771897
UUAAGUUUUCAGCACCUGCGUGAGUCCAAGUUGGAGCCGCUACCGCUGCAGCUGCUCGUUUGCAGCUCUUAAGCUUGUCCAGACAACCAGCCCGAUGAGCCAAUGAGCGGCUCCAAAGAU
....(..((((((....)).))))..)...(((((((((((...(((((((........)))))))......(((..((..(........)..))..))).....))))))))))).... ( -42.50)
>DroSec_CAF1 17334 118 + 1
UUAAGUUUUCAGCACCUGCGUGACUCCAAGUUGGAGCCUCUACCGCUGCAGCUGCUCGUUUGCAGCUCUUAAGCUUGUCCAGACAACCAGCCCGAU--GCCAAUGAGCGGCUCCAAAGAU
...((((....((....))..)))).....((((((((......((....)).(((((((.((((((....)))((((....)))).........)--)).))))))))))))))).... ( -35.20)
>DroSim_CAF1 18575 118 + 1
UUAAGUUUUCAGCACCUGCGUGAGUCCAAGUUGGAUCCGCUACCGCUGCAGCUGCUCGUUUGCAGCUCUUAAGCUUGUCCAGACAACCAGCCCGAU--GCCAAUGAGCGGCUCCAAAGAU
.........((((....(((.((.(((.....))))))))....)))).(((((((((((.((((((....)))((((....)))).........)--)).)))))))))))........ ( -36.70)
>DroEre_CAF1 17969 118 + 1
UUAAGUUUUCAGCACCUGCGUGAGUCCAAGUUGGAGCCGCUACCGCUGCAGCUGCUCGUUUGCAGCGCUUAAGCUUGUCCAGACAACCAGCCCGAU--GCCAAUGAGCGGCUCCAAAGAC
....(..((((((....)).))))..)...(((((((((((......((((((((......)))))(((...(.((((....)))).))))....)--)).....))))))))))).... ( -41.90)
>DroYak_CAF1 29378 118 + 1
UUAAGUUUUCAGCACCUGCGUGAGUCCAAGUUGGAGCCGCUACCGCUGCAGCUGCUCGUUUGCAGCUCUUGAGCUUGUCCAGACAACCAGCCCGAU--GCCAAUGAGCGGCUCCAAAGAU
....(..((((((....)).))))..)...(((((((((((......((((((((......)))))..(((.((((((....)))...))).))))--)).....))))))))))).... ( -42.60)
>DroAna_CAF1 17734 118 + 1
UUAAGUUUUCAGCACCUGCGUGAGUCCAAGUUGGAGCUGCUGUCGCUGCAGCUGCUCGUGUGCAGCUCUUAAGCCUGUCCAGACAGCGAGCCACAA--AAGCAGGAGCGGUUCGGGACUC
...((((((..((.(((((.((..(((.....)))((((((((((((..((((((......))))))....))).......)))))).)))..)).--..))))).)).....)))))). ( -41.71)
>consensus
UUAAGUUUUCAGCACCUGCGUGAGUCCAAGUUGGAGCCGCUACCGCUGCAGCUGCUCGUUUGCAGCUCUUAAGCUUGUCCAGACAACCAGCCCGAU__GCCAAUGAGCGGCUCCAAAGAU
....(..((((((....)).))))..)...(((((((((((...(((..((((((......))))))....)))((((....))))...................))))))))))).... (-36.62 = -36.65 +   0.03)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:02:50 2006