Locus 5420

Sequence ID 3R_DroMel_CAF1
Location 14,279,062 – 14,279,153
Length 91
Max. P 0.933087
window8820 window8821

overview

Window 0

Location 14,279,062 – 14,279,153
Length 91
Sequences 6
Columns 99
Reading direction forward
Mean pairwise identity 79.22
Mean single sequence MFE -16.58
Consensus MFE -13.01
Energy contribution -13.45
Covariance contribution 0.44
Combinations/Pair 1.06
Mean z-score -1.95
Structure conservation index 0.78
SVM decision value 1.23
SVM RNA-class probability 0.933087
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14279062 91 + 27905053
CCGUGUGGCAAUGCGAAAAUGUG-AAUGUGAAAAU-------GUGGAAAUGUGAAAAUGUGCAAUGUGCACAUUAAAAUCAAUUAAAUGACAAAUUGAA
(((..(..((...((......))-....))...).-------.))).........(((((((.....)))))))....((((((........)))))). ( -15.70)
>DroSec_CAF1 58433 69 + 1
CCGUGUGGCAAUGCGAAAA------------------------------UGUGGAAAUGUGCAAUGUGCACAUUAAAAUCAAUUAAAUGACAAAUUGAA
.(((((....)))))....------------------------------......(((((((.....)))))))....((((((........)))))). ( -14.60)
>DroSim_CAF1 50121 77 + 1
CCGUGUGGCAAUGCGAAAAUGUG-A---------------------AAAUGUGGAAAUGUGCAAUGUGCACAUUAAAAUCAAUUAAAUGACAAAUUGAA
.(((((....)))))...((((.-.---------------------..))))...(((((((.....)))))))....((((((........)))))). ( -14.90)
>DroEre_CAF1 60567 98 + 1
CCGUGUGGCAAUGCGAAAAUGUGCAAUGUGGAAAUGUGCAAUGUGGAAAUGUGC-AAUGUGCAAUGUGCACAUUAAAAUCAAUUAAAUGACAAAUUGAA
.(((((....)))))..((((((((...((.(....((((.(((....))))))-)...).))...))))))))....((((((........)))))). ( -24.10)
>DroYak_CAF1 55389 76 + 1
CCGUGUGGCAAUGCGAAAAU----------------------GUGGAAGUAUGC-AAUGUGCAAUGUGCACAUUAAAAUCAAUUAAAUGACAAAUUGAA
..((((((((.((((....(----------------------(((......)))-)...)))).))).))))).....((((((........)))))). ( -14.90)
>DroAna_CAF1 50199 77 + 1
CCGUGUGGAAAUGCGAAAAUGUG-A---------------------AAAUGCGACUGUGUUCGGUGUGCACAUUAAAAUCAAUUAAAUGACAAAUUGAA
.(((((....)))))..((((((-.---------------------....((.((((....)))))).))))))....((((((........)))))). ( -15.30)
>consensus
CCGUGUGGCAAUGCGAAAAUGUG_A_____________________AAAUGUGAAAAUGUGCAAUGUGCACAUUAAAAUCAAUUAAAUGACAAAUUGAA
.(((((....)))))........................................(((((((.....)))))))....((((((........)))))). (-13.01 = -13.45 +   0.44)

alignment

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secondary structure

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dotplot

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Window 1

Location 14,279,062 – 14,279,153
Length 91
Sequences 6
Columns 99
Reading direction reverse
Mean pairwise identity 79.22
Mean single sequence MFE -11.20
Consensus MFE -8.82
Energy contribution -9.32
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -1.36
Structure conservation index 0.79
SVM decision value 0.60
SVM RNA-class probability 0.796512
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14279062 91 - 27905053
UUCAAUUUGUCAUUUAAUUGAUUUUAAUGUGCACAUUGCACAUUUUCACAUUUCCAC-------AUUUUCACAUU-CACAUUUUCGCAUUGCCACACGG
.((((((........))))))....(((((((.....))))))).............-------...........-....................... ( -10.70)
>DroSec_CAF1 58433 69 - 1
UUCAAUUUGUCAUUUAAUUGAUUUUAAUGUGCACAUUGCACAUUUCCACA------------------------------UUUUCGCAUUGCCACACGG
.((((((........))))))....(((((((.....)))))))......------------------------------................... ( -10.70)
>DroSim_CAF1 50121 77 - 1
UUCAAUUUGUCAUUUAAUUGAUUUUAAUGUGCACAUUGCACAUUUCCACAUUU---------------------U-CACAUUUUCGCAUUGCCACACGG
.((((((........))))))....(((((((.....))))))).........---------------------.-....................... ( -10.70)
>DroEre_CAF1 60567 98 - 1
UUCAAUUUGUCAUUUAAUUGAUUUUAAUGUGCACAUUGCACAUU-GCACAUUUCCACAUUGCACAUUUCCACAUUGCACAUUUUCGCAUUGCCACACGG
.((((((........))))))...((((((((.....)))))))-).........................((.(((........))).))........ ( -15.30)
>DroYak_CAF1 55389 76 - 1
UUCAAUUUGUCAUUUAAUUGAUUUUAAUGUGCACAUUGCACAUU-GCAUACUUCCAC----------------------AUUUUCGCAUUGCCACACGG
.((((((........))))))...((((((((.....)))))))-)...........----------------------.................... ( -12.10)
>DroAna_CAF1 50199 77 - 1
UUCAAUUUGUCAUUUAAUUGAUUUUAAUGUGCACACCGAACACAGUCGCAUUU---------------------U-CACAUUUUCGCAUUUCCACACGG
.((((((........))))))....((((((.....(((......))).....---------------------.-))))))................. (  -7.70)
>consensus
UUCAAUUUGUCAUUUAAUUGAUUUUAAUGUGCACAUUGCACAUUUCCACAUUU_____________________U_CACAUUUUCGCAUUGCCACACGG
.((((((........))))))....(((((((.....)))))))....................................................... ( -8.82 =  -9.32 +   0.50)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:54:14 2006