Locus 930

Sequence ID 3R_DroMel_CAF1
Location 3,117,676 – 3,117,812
Length 136
Max. P 0.961602
window1470 window1471

overview

Window 0

Location 3,117,676 – 3,117,772
Length 96
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 78.62
Mean single sequence MFE -44.32
Consensus MFE -31.27
Energy contribution -30.27
Covariance contribution -1.00
Combinations/Pair 1.19
Mean z-score -2.30
Structure conservation index 0.71
SVM decision value 1.53
SVM RNA-class probability 0.961602
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3117676 96 - 27905053
C---------------------GCCGUCGCCGCCGCCCACCAUCACAACCAGGCGGUGGCAGCUGCUUCGGCGGCCGCUU---UACUGGUGGUGCCCCAGCCGAUCAAUGCCAGCAAAAU
.---------------------......(((((((((..............))))))))).(((((.((((((((((((.---....)))))....)).))))).....).))))..... ( -39.24)
>DroPse_CAF1 5039 120 - 1
UGGGAAUCAUGUGAGCGCAGCAGCCGCUGCUGCUGCCCAUCAUCACAGUUCUGCAGUGGCAGCUGCCUCGGCGGCGGCUUCUCUUCUCGUCGUGCCCCAACCCAUCAAUGCCAGCAAAAU
((((........(((.(((((.((((((((.((((..........))))...)))))))).))))))))((((.((((..........))))))))....))))................ ( -48.10)
>DroSim_CAF1 10660 96 - 1
C---------------------GCCGUCGCCGCCGCCCACCAUCACAACCAGGCGGUGGCAGCUGCUUCGGCGGCCGCUU---UGCUGGUGGUGCCCCAGCCGAUCAAUGCCAGCAAAAU
.---------------------((....(((((((((..............))))))))).(((((....))))).))((---((((((((((......))).......))))))))).. ( -44.85)
>DroPer_CAF1 5034 120 - 1
UGGGAAUCAUGUGAGCGCCGCAGCCGCUGCUGCUGCCCAUCAUCACAGCUCUGCAGUGGCAGCUGCCUCGGCGGCGGCUUCUCUUCUCGUCGUGCCCCAACCCAUCAAUGCCAGCAAAAU
((((.((.(((.(((.(((...((((((((.((((..........))))...)))))))).(((((....))))))))..)))....))).))..))))..................... ( -45.10)
>DroEre_CAF1 5172 96 - 1
C---------------------GCCGUCGCCGCCGCCCACCAUCACAACCAGGCGGUGGCGGCUGCCUCGGCGGCCGCUU---UGCUGGUGGUGCCCCAGCCGAUCAAUGCCAGCAAAAU
.---------------------((....(((((((((..............)))))))))((((((....))))))))((---((((((((((......))).......))))))))).. ( -47.25)
>DroYak_CAF1 8925 96 - 1
C---------------------GCCGUCGCCGCCGCCCACCAUCACAACCAAGCGGUGGCAGCUGCUUCGGCGGCCGCUU---UGCUGGUGGUGCCCCAGCCGAUCAAUGCCAGCAAAAU
.---------------------((....((((((((................)))))))).(((((....))))).))((---((((((((((......))).......))))))))).. ( -41.40)
>consensus
C_____________________GCCGUCGCCGCCGCCCACCAUCACAACCAGGCGGUGGCAGCUGCCUCGGCGGCCGCUU___UGCUGGUGGUGCCCCAGCCGAUCAAUGCCAGCAAAAU
......................((.((.((((((((................)))))))).)).))...((((.(((((........)))))))))........................ (-31.27 = -30.27 +  -1.00)

alignment

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secondary structure

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dotplot

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Window 1

Location 3,117,713 – 3,117,812
Length 99
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 82.77
Mean single sequence MFE -49.54
Consensus MFE -35.43
Energy contribution -35.76
Covariance contribution 0.34
Combinations/Pair 1.17
Mean z-score -2.36
Structure conservation index 0.72
SVM decision value 0.61
SVM RNA-class probability 0.798431
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3117713 99 - 27905053
CCGUGGUUGGAAAUUCCAGUCUGGGCGCCAGCUCCCACCAC---------------------GCCGUCGCCGCCGCCCACCAUCACAACCAGGCGGUGGCAGCUGCUUCGGCGGCCGCUU
..((((((((.....)))....(((.(....).))))))))---------------------((....(((((((((..............))))))))).(((((....))))).)).. ( -45.64)
>DroSec_CAF1 5396 99 - 1
CGGUGGGUGGAAAUUCCAGCCUGGGCGCCAGCUCCCACCAC---------------------GCCGUCGCCGCCGCCCACCAUCACAACCAGGCGGUGGCAGCUGCUUCGGCGGCCGCUU
((((((((((.....((.....))((....))..))))).)---------------------))))..(((((((((..............))))))))).(((((....)))))..... ( -49.14)
>DroSim_CAF1 10697 99 - 1
CGGUGGGUGGAAAUUCCAGCCUGGGCGCCAGCUCCCACCAC---------------------GCCGUCGCCGCCGCCCACCAUCACAACCAGGCGGUGGCAGCUGCUUCGGCGGCCGCUU
((((((((((.....((.....))((....))..))))).)---------------------))))..(((((((((..............))))))))).(((((....)))))..... ( -49.14)
>DroPer_CAF1 5074 120 - 1
CUGGCGGAGGCAACUCCAGCCUGGGCGCCCCAUCACAUCAUGGGAAUCAUGUGAGCGCCGCAGCCGCUGCUGCUGCCCAUCAUCACAGCUCUGCAGUGGCAGCUGCCUCGGCGGCGGCUU
..(((((((....)))).)))((((((((((((......)))))..((....))))))).))((((((((.((((..........))))...))))))))(((((((.....))))))). ( -62.00)
>DroEre_CAF1 5209 99 - 1
CUGUGGGCGGCAAUUCCAGCCUGGGCGCCAGCUCCCACCAC---------------------GCCGUCGCCGCCGCCCACCAUCACAACCAGGCGGUGGCGGCUGCCUCGGCGGCCGCUU
....(((((((..........((((.(....).))))...(---------------------((((..((.((((((.(((..(.......)..))))))))).))..)))))))))))) ( -49.70)
>DroYak_CAF1 8962 99 - 1
CUGUAGGUGGCAAUUCCAGCCUCGGCGCCAGUUCCCACCAC---------------------GCCGUCGCCGCCGCCCACCAUCACAACCAAGCGGUGGCAGCUGCUUCGGCGGCCGCUU
..((.(((((.((((...((....))...)))).)))))))---------------------((....((((((((................)))))))).(((((....))))).)).. ( -41.59)
>consensus
CUGUGGGUGGAAAUUCCAGCCUGGGCGCCAGCUCCCACCAC_____________________GCCGUCGCCGCCGCCCACCAUCACAACCAGGCGGUGGCAGCUGCUUCGGCGGCCGCUU
.....(((((........((....))........))))).......................((....(((((((((..............))))))))).(((((....))))).)).. (-35.43 = -35.76 +   0.34)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:55:38 2006