Locus 3201

Sequence ID X_DroMel_CAF1
Location 8,476,578 – 8,476,735
Length 157
Max. P 0.977367
window5252 window5253 window5254

overview

Window 2

Location 8,476,578 – 8,476,695
Length 117
Sequences 4
Columns 117
Reading direction forward
Mean pairwise identity 92.98
Mean single sequence MFE -29.07
Consensus MFE -24.08
Energy contribution -24.57
Covariance contribution 0.50
Combinations/Pair 1.10
Mean z-score -1.96
Structure conservation index 0.83
SVM decision value 0.66
SVM RNA-class probability 0.815350
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8476578 117 + 22224390
UUCAUAAUGUUAUGUCUUAGUUUGGUUUAAAGAACUUGAAAUUGGAAUUAAGUUUUAGCUUUAUGAUAUGCUGAGCUGGUCCAAACCACCAGUUCUAUGGUGGUGGUGGUGUUGGUG
.((((((.((((...(((((((..((((.((....)).))))..).))))))...)))).))))))........(((..((((.(((((((......)))))))..))).)..))). ( -33.20)
>DroSec_CAF1 19178 111 + 1
UUCGUAAUGUUAUGUCUUAGUUUGGUUUAAAGAACUUGAAAUUUGAAUUAAGUUUUAGCUUUAUGAUAUGCUGAGCUGGUCCGAACCACCAGUUCUAUGGUGAUGGUG------UUG
.((((((.((((...(((((((..((((((.....)))))..)..)))))))...)))).))))))...(((((((((((.......))))))))...))).......------... ( -25.70)
>DroSim_CAF1 28294 111 + 1
UUCGUAAUGUUAUGUCUUAGUUUGGUUUAAAGAACUUGAAAUUGGAAUUAAGUUUUAGCUUUAUGAUAUGCUGAGCUGGUCCAAACCACCAGUUCUAUGCUGAUGGUG------GUG
.((((((.((((...(((((((..((((.((....)).))))..).))))))...)))).))))))...((.((((((((.......))))))))...))........------... ( -27.10)
>DroEre_CAF1 24953 111 + 1
UUCGUAAUGUUAUGUCUUAGUUUGGUUUAAAGAACUUGAAAUUGGAAUUAAGUUUUAGCUUUAUGAUAUGCUGAGCUGGUCCAAGCCACCACUUUUAUGGUGGUGGUG------CUG
.((((((.((((...(((((((..((((.((....)).))))..).))))))...)))).)))))).......(((........(((((((((.....))))))))))------)). ( -30.30)
>consensus
UUCGUAAUGUUAUGUCUUAGUUUGGUUUAAAGAACUUGAAAUUGGAAUUAAGUUUUAGCUUUAUGAUAUGCUGAGCUGGUCCAAACCACCAGUUCUAUGGUGAUGGUG______GUG
............((..((((((..((.((((((((((((........)))))))....)))))......))..))))))..)).(((((((((.....))))))))).......... (-24.08 = -24.57 +   0.50)

alignment

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secondary structure

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dotplot

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Window 3

Location 8,476,618 – 8,476,735
Length 117
Sequences 4
Columns 117
Reading direction forward
Mean pairwise identity 90.01
Mean single sequence MFE -32.83
Consensus MFE -25.83
Energy contribution -26.57
Covariance contribution 0.75
Combinations/Pair 1.11
Mean z-score -1.69
Structure conservation index 0.79
SVM decision value 0.34
SVM RNA-class probability 0.696343
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8476618 117 + 22224390
AUUGGAAUUAAGUUUUAGCUUUAUGAUAUGCUGAGCUGGUCCAAACCACCAGUUCUAUGGUGGUGGUGGUGUUGGUGGUGCAGCUCUGUUCUCCUCUUACUGGCGAUCCCCAAAUGU
.(((((....(((((.(((..........))))))))..)))))(((((((......)))))))((.(((((..((((.(((....)))...))....))..)))..))))...... ( -34.70)
>DroSec_CAF1 19218 110 + 1
AUUUGAAUUAAGUUUUAGCUUUAUGAUAUGCUGAGCUGGUCCGAACCACCAGUUCUAUGGUGAUGGUG------UUGGUGCAGCUCUGUUCUCUUAUUUCUGGCGAUCCCCAAAA-C
....(((.((((....(((..........)))((((((..(((((((((((......))))...))).------))))..))))))......)))).)))(((......)))...-. ( -26.60)
>DroSim_CAF1 28334 110 + 1
AUUGGAAUUAAGUUUUAGCUUUAUGAUAUGCUGAGCUGGUCCAAACCACCAGUUCUAUGCUGAUGGUG------GUGGUGCAGCUCUGUUCUCUUAUUUCUGGCGAUCCCCAAAA-C
.(..(((.((((....(((..........)))((((((..(((.((((.((((.....)))).)))).------.)))..))))))......)))).)))..)............-. ( -31.80)
>DroEre_CAF1 24993 110 + 1
AUUGGAAUUAAGUUUUAGCUUUAUGAUAUGCUGAGCUGGUCCAAGCCACCACUUUUAUGGUGGUGGUG------CUGGUGCAGCUCUGUUUUCUUAUUUCUGGCGAUCCCCAAAG-C
.(..(((.((((....(((..........)))((((((..(((.(((((((((.....))))))))).------.)))..))))))......)))).)))..)............-. ( -38.20)
>consensus
AUUGGAAUUAAGUUUUAGCUUUAUGAUAUGCUGAGCUGGUCCAAACCACCAGUUCUAUGGUGAUGGUG______GUGGUGCAGCUCUGUUCUCUUAUUUCUGGCGAUCCCCAAAA_C
.................(((....((((.((.((((((..(((.(((((((((.....)))))))))........)))..)))))).)).....))))...)))............. (-25.83 = -26.57 +   0.75)

alignment

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secondary structure

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dotplot

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Window 4

Location 8,476,618 – 8,476,735
Length 117
Sequences 4
Columns 117
Reading direction reverse
Mean pairwise identity 90.01
Mean single sequence MFE -30.12
Consensus MFE -25.11
Energy contribution -26.48
Covariance contribution 1.37
Combinations/Pair 1.13
Mean z-score -2.66
Structure conservation index 0.83
SVM decision value 1.79
SVM RNA-class probability 0.977367
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8476618 117 - 22224390
ACAUUUGGGGAUCGCCAGUAAGAGGAGAACAGAGCUGCACCACCAACACCACCACCACCAUAGAACUGGUGGUUUGGACCAGCUCAGCAUAUCAUAAAGCUAAAACUUAAUUCCAAU
....((((......)))).....((((....((((((.....((((.(((((((............)))))))))))..))))))(((..........))).........))))... ( -29.90)
>DroSec_CAF1 19218 110 - 1
G-UUUUGGGGAUCGCCAGAAAUAAGAGAACAGAGCUGCACCAA------CACCAUCACCAUAGAACUGGUGGUUCGGACCAGCUCAGCAUAUCAUAAAGCUAAAACUUAAUUCAAAU
.-...(((......)))(((.((((......((((((..((..------.(((((((.........)))))))..))..))))))(((..........)))....)))).))).... ( -26.60)
>DroSim_CAF1 28334 110 - 1
G-UUUUGGGGAUCGCCAGAAAUAAGAGAACAGAGCUGCACCAC------CACCAUCAGCAUAGAACUGGUGGUUUGGACCAGCUCAGCAUAUCAUAAAGCUAAAACUUAAUUCCAAU
.-((((((......)))))).((((......((((((..(((.------.((((((((.......)))))))).)))..))))))(((..........)))....))))........ ( -31.40)
>DroEre_CAF1 24993 110 - 1
G-CUUUGGGGAUCGCCAGAAAUAAGAAAACAGAGCUGCACCAG------CACCACCACCAUAAAAGUGGUGGCUUGGACCAGCUCAGCAUAUCAUAAAGCUAAAACUUAAUUCCAAU
.-..((((((.((....))..((((......((((((..((((------..(((((((.......))))))).))))..))))))(((..........)))....)))).)))))). ( -32.60)
>consensus
G_UUUUGGGGAUCGCCAGAAAUAAGAGAACAGAGCUGCACCAC______CACCACCACCAUAGAACUGGUGGUUUGGACCAGCUCAGCAUAUCAUAAAGCUAAAACUUAAUUCCAAU
.....(((......)))(((.((((......((((((..((((.......((((((((.......))))))))))))..))))))(((..........)))....)))).))).... (-25.11 = -26.48 +   1.37)

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 10:53:40 2006