Locus 4778

Sequence ID 3L_DroMel_CAF1
Location 13,398,644 – 13,398,844
Length 200
Max. P 0.685787
window7522 window7523

overview

Window 2

Location 13,398,644 – 13,398,764
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.33
Mean single sequence MFE -37.38
Consensus MFE -30.34
Energy contribution -31.14
Covariance contribution 0.80
Combinations/Pair 1.18
Mean z-score -1.35
Structure conservation index 0.81
SVM decision value 0.00
SVM RNA-class probability 0.535767
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13398644 120 - 23771897
GAAUGGUGCUAAUGGAUGCCGUCCGUAAGCGGCAAAAUCAAUUGAUUGCGGAAUACAACCGAUUGCCACUUACCGUGGGCACAUUGCGAGUCCGGAAUCUCAAGAGACAACUGGAGCAGC
.....(((((...((((...))))(((((.(((((((((....)))).(((.......))).))))).)))))....))))).((((...(((((..(((....)))...))))))))). ( -36.10)
>DroSec_CAF1 14236 120 - 1
GAAUGAUGCUUAUGGAUGCCGUCCGUAAGCGGCAAAAUCAAUUGAUUGCGGAAUACAACCGUUUGCCACUUUCCGUAGGCACAUUACGAGUCCGGAAUCUCAAGAGACAACUGGAGCAGC
.((((.((((((((((((((((......)))))).((((....))))((((.......)))).........)))))))))))))).....(((((..(((....)))...)))))..... ( -36.60)
>DroSim_CAF1 11215 120 - 1
GAAUGAUGCUUAUGGAUGCCGUUCGUAAGCGGCAAAAUCAAUUGAUUGCGGAAUACAACCGUUUGCCACUUUCCGUGGGCACAUUGCGAGUCCGGAAUCUCAAGAGACAACUGGAGCAGC
.((((.((((((((((((((((......)))))).((((....))))((((.......)))).........))))))))))))))((...(((((..(((....)))...)))))...)) ( -37.90)
>DroEre_CAF1 11792 120 - 1
GAAUGCUCCUCAUGGAUGCCGCCCGUAAGCGGCAAAACCAAUUGAUUGCCGAAUACAACCGCUUGCCGCUUUCCAUGGGCACAUUGCGAGUCCGGAAUCUCAAGAGACAACUGGAGCAGC
...((((((...((((((..(((((((((((((((......((((((....))).)))....)))))))))...)))))).))))..(((........)))......))...)))))).. ( -37.90)
>DroYak_CAF1 11429 120 - 1
GAAUGCUGCUUAUGGAGUCCGCCCGUAAGCGGCAAAACCAAUUAAUUGCCGAAUACAACCGUUUGCCGCUUUCCAUGGGCACAUUGCGAGUCCGGAAUCUUAAGAGACAAUUGGAGCAGC
....(((((((.....((((((((((((((((((((..(((....))).((........))))))))))))...))))))..(((.((....)).))).....).))).....))))))) ( -38.40)
>consensus
GAAUGAUGCUUAUGGAUGCCGUCCGUAAGCGGCAAAAUCAAUUGAUUGCGGAAUACAACCGUUUGCCACUUUCCGUGGGCACAUUGCGAGUCCGGAAUCUCAAGAGACAACUGGAGCAGC
.((((.((((((((((((((((......)))))).............((((.......)))).........))))))))))))))((...(((((..(((....)))...)))))...)) (-30.34 = -31.14 +   0.80)

alignment

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secondary structure

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dotplot

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Window 3

Location 13,398,724 – 13,398,844
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 79.33
Mean single sequence MFE -38.28
Consensus MFE -18.72
Energy contribution -19.52
Covariance contribution 0.80
Combinations/Pair 1.16
Mean z-score -2.04
Structure conservation index 0.49
SVM decision value 0.32
SVM RNA-class probability 0.685787
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13398724 120 - 23771897
AGCGGAAGUCCAACUACCGGAGAAUUCUCAAACGGAUUCACCUGAGGAAUCCCAACCUAUUCUGCUAACCAGUGAGCAGAGAAUGGUGCUAAUGGAUGCCGUCCGUAAGCGGCAAAAUCA
(((((.((.....)).))((.((.((((((...((.....)))))))).)))).(((..(((((((........)))))))...))))))......((((((......))))))...... ( -35.50)
>DroSec_CAF1 14316 108 - 1
------------ACCGGCGGAAAAUUCCCAAACGGAGUCACCUGAGGAUUCGCAACCAAUUCUGCUAACCAGUGAACAGAGAAUGAUGCUUAUGGAUGCCGUCCGUAAGCGGCAAAAUCA
------------...(((((((.(((((.....))))).......((........))..)))))))............((...((.(((((((((((...))))))))))).))...)). ( -28.20)
>DroSim_CAF1 11295 111 - 1
AGCGGAGGUUCAACCGGCGGAGAAUUCCCAAACGG---------AGGAUUCCCAGCCAAUUCUGCUAAACAGUGAGCAGAGAAUGAUGCUUAUGGAUGCCGUUCGUAAGCGGCAAAAUCA
((((((((.....))(((((.((((((((....))---------.)))))))).)))...)))))).....(((((((........)))))))...((((((......))))))...... ( -41.80)
>DroEre_CAF1 11872 120 - 1
AGCUGAGGUCCAACCACAGGAGAACUCCCAGACGGAGUCAGGUGAGGAGUCCCAGCCCAUCCUGCUUACCAGUGAGCAGAGAAUGCUCCUCAUGGAUGCCGCCCGUAAGCGGCAAAACCA
..(((.((.....)).)))..((.((((.....))))))..(((((((((.........(((((((((....))))))).))..)))))))))((.((((((......))))))...)). ( -44.20)
>DroYak_CAF1 11509 120 - 1
AGCGGAGAUCCAAUCACCGGAGAAUUCUCAGGCGGAGUCACAUGAGGAGUCCCAACCCAUCCUGCUUUCCAGUGAGCAGAGAAUGCUGCUUAUGGAGUCCGCCCGUAAGCGGCAAAACCA
.(.(((..(((..((.((.(((....))).)).))..((....))))).))))......((((((((......)))))).)).((((((((((((.(....)))))))))))))...... ( -41.70)
>consensus
AGCGGAGGUCCAACCACCGGAGAAUUCCCAAACGGAGUCACCUGAGGAGUCCCAACCAAUUCUGCUAACCAGUGAGCAGAGAAUGAUGCUUAUGGAUGCCGUCCGUAAGCGGCAAAAUCA
.............(((..((...((((......(((.((.......)).))).........(((((........))))).))))....))..))).((((((......))))))...... (-18.72 = -19.52 +   0.80)

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 11:33:00 2006