Locus 6749

Sequence ID 3L_DroMel_CAF1
Location 18,092,561 – 18,092,741
Length 180
Max. P 0.845612
window10972 window10973 window10974 window10975 window10976

overview

Window 2

Location 18,092,561 – 18,092,669
Length 108
Sequences 4
Columns 115
Reading direction reverse
Mean pairwise identity 90.65
Mean single sequence MFE -30.83
Consensus MFE -25.45
Energy contribution -25.45
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.55
Structure conservation index 0.83
SVM decision value 0.24
SVM RNA-class probability 0.649754
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18092561 108 - 23771897
CUGCAAGUUUGCGGCCAACUUGGCCGCAGCUCAUAUGCUAAUUAGUGUGGCAUACUUUAAGGCCGCUCACCGAUACGCAUUAAAUCGCAAAACU-------UUACGACGUGAAAA
.(((.((((.((((((.....))))))))))...((((..((..(((((((..........)))))..))..))..))))......)))....(-------((((...))))).. ( -28.90)
>DroSec_CAF1 18937 107 - 1
CUGCAAGUUUGCGGCCAACUUGGCCGCAGCUCAUAUGCUAAUUAGUGUGGCAUACUUUAAGGCGGCCCACCGAUACGCAUUAAAUCGGAAAACU-------UUACGACGUGAA-A
.(((......((((((.....))))))(((......))).((..(((.(((...(.....)...))))))..))..)))(((..(((.......-------...)))..))).-. ( -30.60)
>DroEre_CAF1 19444 104 - 1
CUGCAAGUUUGCGGCCAACUUGGCCGCAGCUCAUAUGCUAAUUAGUGUGGCAUACUUUAAGGC---GCACGGCUAGGCAUUAAAUCGGAAAAGU-------UUACGACGUGAA-A
........((((((((.....)))))))).(((((((((.....(((((.(.........).)---)))).....)))))....(((.......-------...))).)))).-. ( -29.90)
>DroYak_CAF1 26262 111 - 1
CUGCAAGUUUGCGGCCAACUUGGCCGCAGCUCAUAUGCUAAUUAGUGUGGCAUACUUUAAGGC---UCACCAAUAGGCAUUAAAUCGGAAAAGUUUCACGUUUACGACGUGAA-A
(((..((((.((((((.....))))))))))...(((((.(((.(((.(((..........))---)))).))).))))).....))).....(((((((((...))))))))-) ( -33.90)
>consensus
CUGCAAGUUUGCGGCCAACUUGGCCGCAGCUCAUAUGCUAAUUAGUGUGGCAUACUUUAAGGC___UCACCGAUACGCAUUAAAUCGGAAAACU_______UUACGACGUGAA_A
.(((.((((.((((((.....))))))))))..(((((((.......)))))))......................)))(((..(((.................)))..)))... (-25.45 = -25.45 +   0.00)

alignment

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secondary structure

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Window 3

Location 18,092,594 – 18,092,708
Length 114
Sequences 4
Columns 115
Reading direction forward
Mean pairwise identity 93.42
Mean single sequence MFE -35.22
Consensus MFE -27.02
Energy contribution -28.40
Covariance contribution 1.38
Combinations/Pair 1.04
Mean z-score -2.34
Structure conservation index 0.77
SVM decision value 0.40
SVM RNA-class probability 0.719194
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18092594 114 + 23771897
UAUCGGUGAGCGGCCUUAAAGUAUGCCACACUAAUUAGCAUAUGAGCUGCGGCCAAGUUGGCCGCAAACUUGCAGCUUAUCGCAAAUAUGCAUUCUCAAACCCCGGAUG-CGAUC
...((((((((.((......((((((...........))))))(((.(((((((.....)))))))..))))).))))))))......(((((((.........)))))-))... ( -38.20)
>DroSec_CAF1 18969 114 + 1
UAUCGGUGGGCCGCCUUAAAGUAUGCCACACUAAUUAGCAUAUGAGCUGCGGCCAAGUUGGCCGCAAACUUGCAGCUUAUCGCAAAUAUGCAUUCUCAAACCCCGGAUG-CGAUC
...((((((((.((......((((((...........))))))(((.(((((((.....)))))))..))))).))))))))......(((((((.........)))))-))... ( -37.40)
>DroEre_CAF1 19476 111 + 1
UAGCCGUGC---GCCUUAAAGUAUGCCACACUAAUUAGCAUAUGAGCUGCGGCCAAGUUGGCCGCAAACUUGCAGCUUAUCGCAAAUAUGCAUUCUCAAACCCCGGAUG-CGAUC
......(((---(.......((((((...........))))))(((((((((((.....))))(....)..)))))))..))))....(((((((.........)))))-))... ( -32.00)
>DroYak_CAF1 26301 112 + 1
UAUUGGUGA---GCCUUAAAGUAUGCCACACUAAUUAGCAUAUGAGCUGCGGCCAAGUUGGCCGCAAACUUGCAGCUUAUCGCAAAUAUGCAUUCUCAAACCCCCACCGAGGAUC
....(((((---((......((((((...........))))))..(((((((((.....))))))).....)).)))))))(((....)))((((((...........)))))). ( -33.30)
>consensus
UAUCGGUGA___GCCUUAAAGUAUGCCACACUAAUUAGCAUAUGAGCUGCGGCCAAGUUGGCCGCAAACUUGCAGCUUAUCGCAAAUAUGCAUUCUCAAACCCCGGAUG_CGAUC
....(((((((.((......((((((...........))))))(((.(((((((.....)))))))..))))).)))))))(((....)))........................ (-27.02 = -28.40 +   1.38)

alignment

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secondary structure

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dotplot

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Window 4

Location 18,092,594 – 18,092,708
Length 114
Sequences 4
Columns 115
Reading direction reverse
Mean pairwise identity 93.42
Mean single sequence MFE -38.10
Consensus MFE -31.29
Energy contribution -32.73
Covariance contribution 1.44
Combinations/Pair 1.11
Mean z-score -1.88
Structure conservation index 0.82
SVM decision value 0.45
SVM RNA-class probability 0.740198
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18092594 114 - 23771897
GAUCG-CAUCCGGGGUUUGAGAAUGCAUAUUUGCGAUAAGCUGCAAGUUUGCGGCCAACUUGGCCGCAGCUCAUAUGCUAAUUAGUGUGGCAUACUUUAAGGCCGCUCACCGAUA
.....-....((((((.((((.......(((((((......)))))))((((((((.....))))))))))))...))).....(.(((((..........))))).).)))... ( -37.40)
>DroSec_CAF1 18969 114 - 1
GAUCG-CAUCCGGGGUUUGAGAAUGCAUAUUUGCGAUAAGCUGCAAGUUUGCGGCCAACUUGGCCGCAGCUCAUAUGCUAAUUAGUGUGGCAUACUUUAAGGCGGCCCACCGAUA
.....-....(((((........((((....))))....(((((.((((.((((((.....))))))))))..(((((((.......))))))).......))))))).)))... ( -38.70)
>DroEre_CAF1 19476 111 - 1
GAUCG-CAUCCGGGGUUUGAGAAUGCAUAUUUGCGAUAAGCUGCAAGUUUGCGGCCAACUUGGCCGCAGCUCAUAUGCUAAUUAGUGUGGCAUACUUUAAGGC---GCACGGCUA
.((((-((....(.(((....))).).....)))))).(((((((((((.((((((.....))))))))))....)))......(((((.(.........).)---)))))))). ( -37.30)
>DroYak_CAF1 26301 112 - 1
GAUCCUCGGUGGGGGUUUGAGAAUGCAUAUUUGCGAUAAGCUGCAAGUUUGCGGCCAACUUGGCCGCAGCUCAUAUGCUAAUUAGUGUGGCAUACUUUAAGGC---UCACCAAUA
.......((((((..((.(((.((((..(((((((......)))))))((((((((.....))))))))..(((((........))))))))).))).))..)---))))).... ( -39.00)
>consensus
GAUCG_CAUCCGGGGUUUGAGAAUGCAUAUUUGCGAUAAGCUGCAAGUUUGCGGCCAACUUGGCCGCAGCUCAUAUGCUAAUUAGUGUGGCAUACUUUAAGGC___UCACCGAUA
.......(((((((((.((((.......(((((((......)))))))((((((((.....))))))))))))(((((((.......)))))))..........)))).))))). (-31.29 = -32.73 +   1.44)

alignment

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secondary structure

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dotplot

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Window 5

Location 18,092,634 – 18,092,741
Length 107
Sequences 4
Columns 115
Reading direction forward
Mean pairwise identity 93.24
Mean single sequence MFE -32.17
Consensus MFE -25.70
Energy contribution -26.95
Covariance contribution 1.25
Combinations/Pair 1.00
Mean z-score -2.34
Structure conservation index 0.80
SVM decision value 0.77
SVM RNA-class probability 0.845612
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18092634 107 + 23771897
UAUGAGCUGCGGCCAAGUUGGCCGCAAACUUGCAGCUUAUCGCAAAUAUGCAUUCUCAAACCCCGGAUG-CGAUCCAGAAGCAAAUGGGCACCAUCCAUUAGC-------CAUUA
.(((.(((((((((.....)))))).....(((.((.....)).....(((((((.........)))))-))........)))((((((.....)))))))))-------))).. ( -31.80)
>DroSec_CAF1 19009 107 + 1
UAUGAGCUGCGGCCAAGUUGGCCGCAAACUUGCAGCUUAUCGCAAAUAUGCAUUCUCAAACCCCGGAUG-CGAUCCAGAAGCAAAUGGGCACCAUCCAUUAGC-------CAUUA
.(((.(((((((((.....)))))).....(((.((.....)).....(((((((.........)))))-))........)))((((((.....)))))))))-------))).. ( -31.80)
>DroEre_CAF1 19513 114 + 1
UAUGAGCUGCGGCCAAGUUGGCCGCAAACUUGCAGCUUAUCGCAAAUAUGCAUUCUCAAACCCCGGAUG-CGAUCCAGAAGCAAAUGGGCACCAUCCAUUAGCCAUUAGCCAUUA
.(((((((((((((.....))))(....)..))))))))).((.....(((((((.........)))))-))........((.((((((.....)))))).)).....))..... ( -33.50)
>DroYak_CAF1 26338 108 + 1
UAUGAGCUGCGGCCAAGUUGGCCGCAAACUUGCAGCUUAUCGCAAAUAUGCAUUCUCAAACCCCCACCGAGGAUCCAGCAGCAAAUUGGCACCAUCCAUUAGC-------CAUUA
.....(((((((((.....))))(((.(.((((........)))).).)))((((((...........))))))...)))))....((((...........))-------))... ( -31.60)
>consensus
UAUGAGCUGCGGCCAAGUUGGCCGCAAACUUGCAGCUUAUCGCAAAUAUGCAUUCUCAAACCCCGGAUG_CGAUCCAGAAGCAAAUGGGCACCAUCCAUUAGC_______CAUUA
.(((((((((((((.....))))(....)..))))))))).(((....))).............((((....))))....((.((((((.....)))))).))............ (-25.70 = -26.95 +   1.25)

alignment

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secondary structure

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Window 6

Location 18,092,634 – 18,092,741
Length 107
Sequences 4
Columns 115
Reading direction reverse
Mean pairwise identity 93.24
Mean single sequence MFE -37.30
Consensus MFE -32.35
Energy contribution -32.48
Covariance contribution 0.13
Combinations/Pair 1.06
Mean z-score -1.78
Structure conservation index 0.87
SVM decision value 0.64
SVM RNA-class probability 0.807543
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18092634 107 - 23771897
UAAUG-------GCUAAUGGAUGGUGCCCAUUUGCUUCUGGAUCG-CAUCCGGGGUUUGAGAAUGCAUAUUUGCGAUAAGCUGCAAGUUUGCGGCCAACUUGGCCGCAGCUCAUA
....(-------((.(((((.......))))).)))(((((((..-.)))))))...((((.......(((((((......)))))))((((((((.....)))))))))))).. ( -36.50)
>DroSec_CAF1 19009 107 - 1
UAAUG-------GCUAAUGGAUGGUGCCCAUUUGCUUCUGGAUCG-CAUCCGGGGUUUGAGAAUGCAUAUUUGCGAUAAGCUGCAAGUUUGCGGCCAACUUGGCCGCAGCUCAUA
....(-------((.(((((.......))))).)))(((((((..-.)))))))...((((.......(((((((......)))))))((((((((.....)))))))))))).. ( -36.50)
>DroEre_CAF1 19513 114 - 1
UAAUGGCUAAUGGCUAAUGGAUGGUGCCCAUUUGCUUCUGGAUCG-CAUCCGGGGUUUGAGAAUGCAUAUUUGCGAUAAGCUGCAAGUUUGCGGCCAACUUGGCCGCAGCUCAUA
...((((.....))))....((((.((..((((((..((..((((-((....(.(((....))).).....)))))).))..)))))).(((((((.....))))))))))))). ( -37.30)
>DroYak_CAF1 26338 108 - 1
UAAUG-------GCUAAUGGAUGGUGCCAAUUUGCUGCUGGAUCCUCGGUGGGGGUUUGAGAAUGCAUAUUUGCGAUAAGCUGCAAGUUUGCGGCCAACUUGGCCGCAGCUCAUA
...((-------((...........))))....(((((.(((((((.....)))))))......(((.(((((((......))))))).)))((((.....)))))))))..... ( -38.90)
>consensus
UAAUG_______GCUAAUGGAUGGUGCCCAUUUGCUUCUGGAUCG_CAUCCGGGGUUUGAGAAUGCAUAUUUGCGAUAAGCUGCAAGUUUGCGGCCAACUUGGCCGCAGCUCAUA
....................((((.((..((((((..((((((....))))))((((((....((((....)))).)))))))))))).(((((((.....))))))))))))). (-32.35 = -32.48 +   0.13)

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 12:29:07 2006