Locus 3454

Sequence ID 3R_DroMel_CAF1
Location 9,353,493 – 9,353,630
Length 137
Max. P 0.903861
window5543 window5544 window5545

overview

Window 3

Location 9,353,493 – 9,353,611
Length 118
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 75.11
Mean single sequence MFE -22.34
Consensus MFE -8.16
Energy contribution -9.84
Covariance contribution 1.68
Combinations/Pair 1.05
Mean z-score -1.80
Structure conservation index 0.37
SVM decision value 0.18
SVM RNA-class probability 0.622543
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9353493 118 + 27905053
GGUAAAACGAUGCCAACGACCAGAACUGUGUGACUUUUCUGUCUGUCAGUCUGUCCGUCUGUUAAAUUAUUUUUUAAUGUGUCUAUUAAAAAAUACAACAGCUGCAUCAACAACUGCA--
........(((((..(((..((((.(((...(((......)))...)))))))..)))(((((....((((((((((((....)))))))))))).)))))..)))))..........-- ( -30.50)
>DroSec_CAF1 123192 106 + 1
GAUAAAACGAUGCCAACGACCAGGACUGUGUGACUUUUCUGUCUGU------------CCGUUAAAUUAUUUUUUAAUGUGUCUAUUAAAAAAUACAACAGCUGCAUCAACAACUGCA--
........(((((.........((((.....(((......))).))------------))(((....((((((((((((....))))))))))))....))).)))))..........-- ( -22.40)
>DroEre_CAF1 123501 102 + 1
GAUAAAACGAUGCCAACGACGAGGACUCUGUGACUCCGCUGUCUGU----------------CAAAUUAUUUUUUAAUGUGUCUAUUAAAAAAUUCAACAGCUGCAUCAACAACUGCA--
........(((((.........(((.((...)).)))(((((.((.----------------......(((((((((((....))))))))))).))))))).)))))..........-- ( -20.30)
>DroAna_CAF1 118710 94 + 1
GCCAAAACGAAGUAAACGGC--------------UUUCCGUUCUUC------------CCGUUAAAUUAUUUUUUAAUGUGUCUAUUAAAAAAUACAACAGCUGCAUCAACAACUGACAU
.....((((..(..(((((.--------------...)))))..).------------.))))....((((((((((((....))))))))))))...(((.((......)).))).... ( -15.70)
>DroPer_CAF1 122808 106 + 1
ACAAAAACGAGGAG-ACGAACU-GCUUGUGUGACUCUCGGUCCUGU------------CUGUUGAAUUAUUUUUUAAUGUGUCUAUUAAAAAAUACAACAGCUGCAUCAACAACUGACAA
.((...(((((.((-.....))-.))))).))....(((((..(((------------((((((...((((((((((((....))))))))))))))))))..)))......)))))... ( -22.80)
>consensus
GAUAAAACGAUGCCAACGACCAGGACUGUGUGACUUUCCUGUCUGU____________CCGUUAAAUUAUUUUUUAAUGUGUCUAUUAAAAAAUACAACAGCUGCAUCAACAACUGCA__
........(((((..................(((......)))........................((((((((((((....))))))))))))........)))))............ ( -8.16 =  -9.84 +   1.68)

alignment

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secondary structure

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dotplot

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Window 4

Location 9,353,533 – 9,353,630
Length 97
Sequences 4
Columns 100
Reading direction forward
Mean pairwise identity 81.80
Mean single sequence MFE -15.38
Consensus MFE -8.76
Energy contribution -8.32
Covariance contribution -0.44
Combinations/Pair 1.14
Mean z-score -2.41
Structure conservation index 0.57
SVM decision value 0.67
SVM RNA-class probability 0.818966
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9353533 97 + 27905053
GUCUGUCAGUCUGUCCGUCUGUUAAAUUAUUUUUUAAUGUGUCUAUUAAAAAAUACAACAGCUGCAUCAACAACUGCA---GAAACAACUAGAUCAACUA
((..((((((.(((....(((((....((((((((((((....)))))))))))).)))))(((((........))))---)..)))))).)))..)).. ( -19.20)
>DroSec_CAF1 123232 85 + 1
GUCUGU------------CCGUUAAAUUAUUUUUUAAUGUGUCUAUUAAAAAAUACAACAGCUGCAUCAACAACUGCA---GAAACAACUAGAUCAACUA
(((((.------------..(((....((((((((((((....))))))))))))......(((((........))))---).)))...)))))...... ( -14.60)
>DroEre_CAF1 123541 81 + 1
GUCUGU----------------CAAAUUAUUUUUUAAUGUGUCUAUUAAAAAAUUCAACAGCUGCAUCAACAACUGCA---GAAACAACUAGAUCAACUA
..((((----------------......(((((((((((....)))))))))))...))))(((((........))))---).................. ( -12.60)
>DroAna_CAF1 118736 88 + 1
UUCUUC------------CCGUUAAAUUAUUUUUUAAUGUGUCUAUUAAAAAAUACAACAGCUGCAUCAACAACUGACAUUGCAACAACGGCAACAAAGA
......------------(((((....((((((((((((....)))))))))))).....(.(((((((.....)))...)))).))))))......... ( -15.10)
>consensus
GUCUGU____________CCGUUAAAUUAUUUUUUAAUGUGUCUAUUAAAAAAUACAACAGCUGCAUCAACAACUGCA___GAAACAACUAGAUCAACUA
(((((......................((((((((((((....))))))))))))...(((.((......)).))).............)))))...... ( -8.76 =  -8.32 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 5

Location 9,353,533 – 9,353,630
Length 97
Sequences 4
Columns 100
Reading direction reverse
Mean pairwise identity 81.80
Mean single sequence MFE -20.98
Consensus MFE -13.23
Energy contribution -13.73
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -2.30
Structure conservation index 0.63
SVM decision value 1.03
SVM RNA-class probability 0.903861
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9353533 97 - 27905053
UAGUUGAUCUAGUUGUUUC---UGCAGUUGUUGAUGCAGCUGUUGUAUUUUUUAAUAGACACAUUAAAAAAUAAUUUAACAGACGGACAGACUGACAGAC
(((((..(((..(((((..---.((((((((....))))))))..(((((((((((......)))))))))))....)))))..)))..)))))...... ( -24.40)
>DroSec_CAF1 123232 85 - 1
UAGUUGAUCUAGUUGUUUC---UGCAGUUGUUGAUGCAGCUGUUGUAUUUUUUAAUAGACACAUUAAAAAAUAAUUUAACGG------------ACAGAC
..(((..(((.((((....---.((((((((....))))))))..(((((((((((......)))))))))))...))))))------------)..))) ( -19.10)
>DroEre_CAF1 123541 81 - 1
UAGUUGAUCUAGUUGUUUC---UGCAGUUGUUGAUGCAGCUGUUGAAUUUUUUAAUAGACACAUUAAAAAAUAAUUUG----------------ACAGAC
..(((..((.(((((((((---.((((((((....)))))))).))).((((((((......)))))))))))))).)----------------)..))) ( -18.50)
>DroAna_CAF1 118736 88 - 1
UCUUUGUUGCCGUUGUUGCAAUGUCAGUUGUUGAUGCAGCUGUUGUAUUUUUUAAUAGACACAUUAAAAAAUAAUUUAACGG------------GAAGAA
(((((....((((((..((((...(((((((....)))))))))))((((((((((......))))))))))....))))))------------))))). ( -21.90)
>consensus
UAGUUGAUCUAGUUGUUUC___UGCAGUUGUUGAUGCAGCUGUUGUAUUUUUUAAUAGACACAUUAAAAAAUAAUUUAACGG____________ACAGAC
.......................((((((((....))))))))..(((((((((((......)))))))))))........................... (-13.23 = -13.73 +   0.50)

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 11:01:26 2006