Locus 7498

Sequence ID 3R_DroMel_CAF1
Location 20,043,922 – 20,044,048
Length 126
Max. P 0.950991
window12112 window12113 window12114

overview

Window 2

Location 20,043,922 – 20,044,016
Length 94
Sequences 6
Columns 98
Reading direction forward
Mean pairwise identity 85.80
Mean single sequence MFE -41.97
Consensus MFE -33.73
Energy contribution -33.73
Covariance contribution 0.01
Combinations/Pair 1.34
Mean z-score -1.78
Structure conservation index 0.80
SVM decision value 0.07
SVM RNA-class probability 0.566835
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20043922 94 + 27905053
CGGCGCACUCAUUGAUCCGCUGCUGAUUAACCACUCCAUAGCCAACUGGUUGAGGUGGUUGGCCAGCCGACUG---AGCUGCCCAAUUGGGCGG-UGG
.((((..(.....)...))))((((..(((((((..((..(((....)))))..)))))))..))))......---.(((((((....))))))-).. ( -36.80)
>DroSec_CAF1 32386 94 + 1
CGGCGCACUCAUUGAUCCGCUGCUGGUUGACCACUCCAUAGCCAACAGGCUGAGGUGGUUGGCCAGCCGACUG---AGCUGCCCAAUUGGGCGG-UGG
.((((..(.....)...))))((((((..((((((...(((((....))))).))))))..))))))......---.(((((((....))))))-).. ( -45.80)
>DroSim_CAF1 32113 94 + 1
CGGCGCACUCAUUGAUCCGCUGCUGGUUGACCACUCCAUAGCCAACAGGCUGAGGUGGUUGGCCAGCCGACUG---AGCUGCCCAAUUGGGCGG-UGG
.((((..(.....)...))))((((((..((((((...(((((....))))).))))))..))))))......---.(((((((....))))))-).. ( -45.80)
>DroEre_CAF1 34786 94 + 1
CGGCGCACUCAUUGAUCCGCUGCUGAUUGACCACUCCAUAGCCAGCAGGCUGAGGUGGUUGGCCGGCCGACUG---AACUGCCCAAUUGGGUGG-UGA
.((((..(.....)...))))((((.(..((((((...(((((....))))).))))))..).))))......---.((..(((....)))..)-).. ( -35.40)
>DroYak_CAF1 35300 94 + 1
CGGCGCACUCAUUGAUCCGCUGCUGGUUGACCAUGCCAUAGCCAGCAGGCUGAGGUGGUUGGCUAGCCGACUG---AACUGCCCAAUUGGGCGG-UGG
.((((..(.....)...))))((((((..(((..(((.(((((....))))).))))))..))))))......---.(((((((....))))))-).. ( -42.30)
>DroAna_CAF1 34155 98 + 1
CGGCGCAUUCGUUGAUCCGUUGCUGGUUGACGACGCCGUAGCCACUGGGCUGUGGCGGCGGACCAGUCGCCGGCGAGGUGGUCCAGCUGGGGGGAUGG
((((((..((((..(((.......)))..))))((((((((((....))))))))))))((((((.(((....)))..)))))).))))......... ( -45.70)
>consensus
CGGCGCACUCAUUGAUCCGCUGCUGGUUGACCACUCCAUAGCCAACAGGCUGAGGUGGUUGGCCAGCCGACUG___AGCUGCCCAAUUGGGCGG_UGG
.((((............))))((((((((((((..((.(((((....))))).))))))))))))))...........((((((....)))))).... (-33.73 = -33.73 +   0.01)

alignment

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secondary structure

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dotplot

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Window 3

Location 20,043,956 – 20,044,048
Length 92
Sequences 6
Columns 99
Reading direction forward
Mean pairwise identity 80.42
Mean single sequence MFE -43.73
Consensus MFE -29.17
Energy contribution -30.32
Covariance contribution 1.14
Combinations/Pair 1.33
Mean z-score -2.87
Structure conservation index 0.67
SVM decision value 1.41
SVM RNA-class probability 0.950991
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20043956 92 + 27905053
UCCAUAGCCAACUGGUUGAGGUGGUUGGCCAGCCGACUG---AGCUGCCCAAUUGGGCGG-UGGUGCAGACGGCGGACCAUGAUGCAACCUGUACA---
....(((((....)))))((((.(((((((.((((.(((---.(((((((....))))))-)....))).)))))).)))....)).)))).....--- ( -39.00)
>DroSec_CAF1 32420 92 + 1
UCCAUAGCCAACAGGCUGAGGUGGUUGGCCAGCCGACUG---AGCUGCCCAAUUGGGCGG-UGGUGCAGACGGCCGACCAUGAUGCAGCCUGUACA---
..........((((((((..((((((((((..(.((((.---.(((((((....))))))-)))).).)..))))))))))....))))))))...--- ( -47.30)
>DroSim_CAF1 32147 92 + 1
UCCAUAGCCAACAGGCUGAGGUGGUUGGCCAGCCGACUG---AGCUGCCCAAUUGGGCGG-UGGUGCAGACGGCGGACCAUGAUGCAGCCUGUACA---
..........((((((((..((.((.((((.((((.(((---.(((((((....))))))-)....))).)))))).)))).)).))))))))...--- ( -45.40)
>DroEre_CAF1 34820 92 + 1
UCCAUAGCCAGCAGGCUGAGGUGGUUGGCCGGCCGACUG---AACUGCCCAAUUGGGUGG-UGAUGCCGACGGCGGACCAUGAUGCAGCCUGUACA---
..........((((((((..((((((.((((..((.(..---.((..(((....)))..)-)...).)).)))).))))))....))))))))...--- ( -45.80)
>DroYak_CAF1 35334 92 + 1
GCCAUAGCCAGCAGGCUGAGGUGGUUGGCUAGCCGACUG---AACUGCCCAAUUGGGCGG-UGGUGCAGAAGGUGGACCAUGAUGCAGCCUAUACA---
(((.(((((....))))).)))((((((....)))))).---.(((((((....))))))-)((((((..(((....)).)..)))).))......--- ( -38.40)
>DroAna_CAF1 34189 92 + 1
GCCGUAGCCACUGGGCUGUGGCGGCGGACCAGUCGCCGGCGAGGUGGUCCAGCUGGGGGGAUGG-------GGCGCCGCAUGAUGCAGUCGCUGCAAGU
...(((((.((((.(..(((.(((((..(((.((.(((((..((....)).))))).))..)))-------..))))))))..).)))).))))).... ( -46.50)
>consensus
UCCAUAGCCAACAGGCUGAGGUGGUUGGCCAGCCGACUG___AGCUGCCCAAUUGGGCGG_UGGUGCAGACGGCGGACCAUGAUGCAGCCUGUACA___
..........((((((((..((((((.....((((.(((.....((((((....))))))......))).)))).))))))....))))))))...... (-29.17 = -30.32 +   1.14)

alignment

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secondary structure

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dotplot

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Window 4

Location 20,043,956 – 20,044,048
Length 92
Sequences 6
Columns 99
Reading direction reverse
Mean pairwise identity 80.42
Mean single sequence MFE -35.30
Consensus MFE -23.42
Energy contribution -26.23
Covariance contribution 2.81
Combinations/Pair 1.12
Mean z-score -1.91
Structure conservation index 0.66
SVM decision value 0.67
SVM RNA-class probability 0.817411
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20043956 92 - 27905053
---UGUACAGGUUGCAUCAUGGUCCGCCGUCUGCACCA-CCGCCCAAUUGGGCAGCU---CAGUCGGCUGGCCAACCACCUCAACCAGUUGGCUAUGGA
---......(((.(((..((((....)))).)))))).-((((((....))))....---.((((((((((.............))))))))))..)). ( -33.52)
>DroSec_CAF1 32420 92 - 1
---UGUACAGGCUGCAUCAUGGUCGGCCGUCUGCACCA-CCGCCCAAUUGGGCAGCU---CAGUCGGCUGGCCAACCACCUCAGCCUGUUGGCUAUGGA
---.((((((((((.....((((((((((.(((.....-(.((((....)))).)..---))).)))))))))).......))))))))..))...... ( -41.80)
>DroSim_CAF1 32147 92 - 1
---UGUACAGGCUGCAUCAUGGUCCGCCGUCUGCACCA-CCGCCCAAUUGGGCAGCU---CAGUCGGCUGGCCAACCACCUCAGCCUGUUGGCUAUGGA
---.((((((((((.....(((((.((((.(((.....-(.((((....)))).)..---))).)))).))))).......))))))))..))...... ( -37.90)
>DroEre_CAF1 34820 92 - 1
---UGUACAGGCUGCAUCAUGGUCCGCCGUCGGCAUCA-CCACCCAAUUGGGCAGUU---CAGUCGGCCGGCCAACCACCUCAGCCUGCUGGCUAUGGA
---.((.(((((((.....((((..(((((((((...(-(..(((....)))..)).---..))))).))))..))))...)))))))...))...... ( -35.30)
>DroYak_CAF1 35334 92 - 1
---UGUAUAGGCUGCAUCAUGGUCCACCUUCUGCACCA-CCGCCCAAUUGGGCAGUU---CAGUCGGCUAGCCAACCACCUCAGCCUGCUGGCUAUGGC
---......((.((((....((....))...)))))).-((((((....))))(((.---((((.((((((........)).)))).)))))))..)). ( -29.50)
>DroAna_CAF1 34189 92 - 1
ACUUGCAGCGACUGCAUCAUGCGGCGCC-------CCAUCCCCCCAGCUGGACCACCUCGCCGGCGACUGGUCCGCCGCCACAGCCCAGUGGCUACGGC
...((..(((.((((.....))))))).-------.)).....((.((.((((((..(((....))).)))))))).(((((......)))))...)). ( -33.80)
>consensus
___UGUACAGGCUGCAUCAUGGUCCGCCGUCUGCACCA_CCGCCCAAUUGGGCAGCU___CAGUCGGCUGGCCAACCACCUCAGCCUGUUGGCUAUGGA
....((.(((((((.....(((((.((((.(((........((((....)))).......))).)))).))))).......)))))))...))...... (-23.42 = -26.23 +   2.81)

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 12:47:27 2006