Locus 1087

Sequence ID X_DroMel_CAF1
Location 3,205,549 – 3,205,693
Length 144
Max. P 0.810906
window1760 window1761

overview

Window 0

Location 3,205,549 – 3,205,661
Length 112
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 76.52
Mean single sequence MFE -31.65
Consensus MFE -20.75
Energy contribution -21.25
Covariance contribution 0.50
Combinations/Pair 1.07
Mean z-score -1.79
Structure conservation index 0.66
SVM decision value 0.65
SVM RNA-class probability 0.810906
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3205549 112 + 22224390
--------UUUCUUUAAUUGCAACAAUUCCUGCACGCUUUUUAUUGUGGCACCUUUGCGUUGGCUGGCCGCCGCAGAGGCAAACAUCUCUGUUGCAAUUGUCGGUCAUUAGCACGCUGAU
--------..((..(((((((((((.....(((.(((........))))))((((((((.(((....))).))))))))..........)))))))))))..))..(((((....))))) ( -37.30)
>DroSec_CAF1 15002 106 + 1
--------UUUCUUUCAGUGCAACAAUUCCUGCAC----UUUAUUGAGGCACCUUUGCGUUGGCA-GCCGCCGCAGAAGCA-ACAUCUCUGUUGCAAUUGUCGGUCAUUAGCACGCUGAU
--------......(((((((.((((((.((((..----......((.(((....))).))(((.-...)))))))..(((-(((....)))))))))))).)((.....)).)))))). ( -29.60)
>DroEre_CAF1 16717 85 + 1
---------------------------------ACUUUUUCUUUCAGUGCACCUCUGCGUUGGCA-GCCGCCGCAGAAGCG-ACAUCUCUGUUGCAAUUGUCGGUCAUUAGCACGCUGAU
---------------------------------.............(((((((((((((.(((..-.))).)))))).(((-(((....)))))).......))).....))))...... ( -25.20)
>DroYak_CAF1 19337 118 + 1
CGCACAGAUUUCUUCCAGUGCAGCAAUUCCUGCACUCUUUUUAUUGAGGCACCUUUGCGUUGGCA-GCCGCCGCAGAAGCG-ACAUCUCUGUUGCAAUUGUCGGUCAUUAGCACGCUGAU
.((((.((.....))..)))).((((....(((.(((........))))))...))))((..((.-((.(((((((..(((-(((....))))))..))).)))).....))..))..)) ( -34.50)
>consensus
________UUUCUUUCAGUGCAACAAUUCCUGCACUCUUUUUAUUGAGGCACCUUUGCGUUGGCA_GCCGCCGCAGAAGCA_ACAUCUCUGUUGCAAUUGUCGGUCAUUAGCACGCUGAU
.................(((((........))))).............(.(((((((((.(((....))).)))))).(((.(((....)))))).......))))(((((....))))) (-20.75 = -21.25 +   0.50)

alignment

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secondary structure

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dotplot

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Window 1

Location 3,205,581 – 3,205,693
Length 112
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 89.42
Mean single sequence MFE -32.75
Consensus MFE -23.74
Energy contribution -23.80
Covariance contribution 0.06
Combinations/Pair 1.07
Mean z-score -1.86
Structure conservation index 0.72
SVM decision value 0.30
SVM RNA-class probability 0.676522
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3205581 112 + 22224390
UUAUUGUGGCACCUUUGCGUUGGCUGGCCGCCGCAGAGGCAAACAUCUCUGUUGCAAUUGUCGGUCAUUAGCACGCUGAUC--------CUCGACUUGUAACUUGACCUCCCCACUAUAU
.(((.((((..((((((((.(((....))).))))))))......((...(((((((..(((((..(((((....))))).--------.))))))))))))..)).....)))).))). ( -38.20)
>DroSec_CAF1 15030 110 + 1
UUAUUGAGGCACCUUUGCGUUGGCA-GCCGCCGCAGAAGCA-ACAUCUCUGUUGCAAUUGUCGGUCAUUAGCACGCUGAUC--------CUCGACUUGUAACUUGACCUCCCCACUAUAU
.....((((((..((((((.(((..-.))).)))))).(((-(((....))))))....(((((..(((((....))))).--------.)))))........)).)))).......... ( -30.40)
>DroEre_CAF1 16724 110 + 1
CUUUCAGUGCACCUCUGCGUUGGCA-GCCGCCGCAGAAGCG-ACAUCUCUGUUGCAAUUGUCGGUCAUUAGCACGCUGAUC--------CCCGACUUGAAACUUGACCUCCCCACUAUAU
.....((((....((((((.(((..-.))).)))))).(((-(((....))))))....(((((..(((((....))))).--------.))))).................)))).... ( -33.20)
>DroYak_CAF1 19377 118 + 1
UUAUUGAGGCACCUUUGCGUUGGCA-GCCGCCGCAGAAGCG-ACAUCUCUGUUGCAAUUGUCGGUCAUUAGCACGCUGAUCCCCCGAUCCCCUACUUGUAACUUGACCUCCCCACUAUAU
.....((((((..((((((.(((..-.))).)))))).(((-(((....))))))....(((((..(((((....)))))...)))))...............)).)))).......... ( -29.20)
>consensus
UUAUUGAGGCACCUUUGCGUUGGCA_GCCGCCGCAGAAGCA_ACAUCUCUGUUGCAAUUGUCGGUCAUUAGCACGCUGAUC________CCCGACUUGUAACUUGACCUCCCCACUAUAU
........((...((((((.(((....))).)))))).)).....((...(((((((..(((((..(((((....)))))..........))))))))))))..)).............. (-23.74 = -23.80 +   0.06)

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 10:01:13 2006