Locus 8893

Sequence ID 3R_DroMel_CAF1
Location 23,856,693 – 23,856,786
Length 93
Max. P 0.772134
window14269 window14270

overview

Window 9

Location 23,856,693 – 23,856,786
Length 93
Sequences 6
Columns 94
Reading direction forward
Mean pairwise identity 78.93
Mean single sequence MFE -28.40
Consensus MFE -13.27
Energy contribution -13.16
Covariance contribution -0.11
Combinations/Pair 1.31
Mean z-score -2.36
Structure conservation index 0.47
SVM decision value 0.47
SVM RNA-class probability 0.748252
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23856693 93 + 27905053
AGAGCCGCCGCUGUUGAGUAUGCAAUAUUGUCGUUCUCAUUGCAACAUGCAACAUUGCAACAGCACUGGC-GGCAGCAACAAGGCACCUGCUAU
...(((((((.(((((....((((((.((((.((((.....).)))..)))).)))))).))))).))))-)))........(((....))).. ( -31.40)
>DroSec_CAF1 62240 93 + 1
AGAGCAGCCGCUGUUGACUAUGCAACAUUGUCAUUCUCAUUGCAACAUGCAACAUUGCAACAGCACCUGC-GGCAGCAACAAGGCACCUGCUAU
..((((((((((((((....((((...(((.((.......)))))..))))......)))))))...(((-....)))....)))...)))).. ( -26.50)
>DroSim_CAF1 61669 93 + 1
AGAGCAGCCGCUGUUGACUAUGCAACAUUGUCAUUCUCAUUGCAACAUGCAACAUUGCAACAGCACCUGC-GGCAGCAACAAGGCACCUGCUAU
..((((((((((((((....((((...(((.((.......)))))..))))......)))))))...(((-....)))....)))...)))).. ( -26.50)
>DroEre_CAF1 66205 93 + 1
AGAGCAGCCGCUGCUGACUAUGCAACAUUGUCAUUCUCAUUGCAACAUGCAGCAUAGCAAUAACACCGGC-GGCAGCAACAAGGCAUCAGCAAU
...((.(((((((.((.((((((.....((.......)).(((.....)))))))))......)).))))-))).((......))....))... ( -25.60)
>DroYak_CAF1 64098 93 + 1
AGAGCAGCCGCUGCUGACUAUGCAACAUUGUCAUUCGCAUUGCAACAUGCAACAGUGCAACAACACCGGC-GGCAGCAACAAGGCACCUGCUAU
..(((((((((((.((((.(((...))).))))...(((((((.....)))...))))........))))-))).((......))...)))).. ( -29.00)
>DroPer_CAF1 68725 85 + 1
AGUGCAGCCGGUGCAAGCAGUGCGGCACUGCCACACGAAUUGCGGG---------GGAAAUGAGACCUGCAAGCUGCAACAAUGCAGCAAUAGC
.(((..((.(((((..((...)).)))))))..)))...(((((((---------..........)))))))((((((....))))))...... ( -31.40)
>consensus
AGAGCAGCCGCUGCUGACUAUGCAACAUUGUCAUUCUCAUUGCAACAUGCAACAUUGCAACAACACCGGC_GGCAGCAACAAGGCACCUGCUAU
......(((..(((((....(((((..............)))))...(((......)))..............)))))....)))......... (-13.27 = -13.16 +  -0.11)

alignment

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secondary structure

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dotplot

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Window 0

Location 23,856,693 – 23,856,786
Length 93
Sequences 6
Columns 94
Reading direction reverse
Mean pairwise identity 78.93
Mean single sequence MFE -31.82
Consensus MFE -18.01
Energy contribution -20.60
Covariance contribution 2.59
Combinations/Pair 1.32
Mean z-score -1.97
Structure conservation index 0.57
SVM decision value 0.53
SVM RNA-class probability 0.772134
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23856693 93 - 27905053
AUAGCAGGUGCCUUGUUGCUGCC-GCCAGUGCUGUUGCAAUGUUGCAUGUUGCAAUGAGAACGACAAUAUUGCAUACUCAACAGCGGCGGCUCU
.(((((((...)))))))..(((-(((...(((((((((((((((..((((........)))).))))))))))......)))))))))))... ( -33.40)
>DroSec_CAF1 62240 93 - 1
AUAGCAGGUGCCUUGUUGCUGCC-GCAGGUGCUGUUGCAAUGUUGCAUGUUGCAAUGAGAAUGACAAUGUUGCAUAGUCAACAGCGGCUGCUCU
..(((((.(((((..(((((((.-(((..(((....))).))).)))....))))..))..((((.(((...))).))))...))).))))).. ( -32.70)
>DroSim_CAF1 61669 93 - 1
AUAGCAGGUGCCUUGUUGCUGCC-GCAGGUGCUGUUGCAAUGUUGCAUGUUGCAAUGAGAAUGACAAUGUUGCAUAGUCAACAGCGGCUGCUCU
..(((((.(((((..(((((((.-(((..(((....))).))).)))....))))..))..((((.(((...))).))))...))).))))).. ( -32.70)
>DroEre_CAF1 66205 93 - 1
AUUGCUGAUGCCUUGUUGCUGCC-GCCGGUGUUAUUGCUAUGCUGCAUGUUGCAAUGAGAAUGACAAUGUUGCAUAGUCAGCAGCGGCUGCUCU
...((....)).........((.-((((.((((...(((((((.(((((((...........))).)))).))))))).)))).)))).))... ( -29.00)
>DroYak_CAF1 64098 93 - 1
AUAGCAGGUGCCUUGUUGCUGCC-GCCGGUGUUGUUGCACUGUUGCAUGUUGCAAUGCGAAUGACAAUGUUGCAUAGUCAGCAGCGGCUGCUCU
..(((((((((......)).)))-((((.(((((.((((..(((((((.((((...))))))).))))..))))....))))).)))))))).. ( -34.00)
>DroPer_CAF1 68725 85 - 1
GCUAUUGCUGCAUUGUUGCAGCUUGCAGGUCUCAUUUCC---------CCCGCAAUUCGUGUGGCAGUGCCGCACUGCUUGCACCGGCUGCACU
......((((((....)))))).(((((.........((---------...((((...(((((((...)))))))...))))...))))))).. ( -29.10)
>consensus
AUAGCAGGUGCCUUGUUGCUGCC_GCAGGUGCUGUUGCAAUGUUGCAUGUUGCAAUGAGAAUGACAAUGUUGCAUAGUCAACAGCGGCUGCUCU
.((((((........))))))...((((.(((((((((.((((.((((((((.........)))).)))).)))).).)))))))).))))... (-18.01 = -20.60 +   2.59)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:22:11 2006