Locus 1179

Sequence ID 3R_DroMel_CAF1
Location 3,568,074 – 3,568,171
Length 97
Max. P 0.932254
window1929 window1930

overview

Window 9

Location 3,568,074 – 3,568,171
Length 97
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 78.25
Mean single sequence MFE -37.20
Consensus MFE -24.02
Energy contribution -25.94
Covariance contribution 1.92
Combinations/Pair 1.08
Mean z-score -2.06
Structure conservation index 0.65
SVM decision value 1.22
SVM RNA-class probability 0.932254
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3568074 97 + 27905053
UGCACCACUGUUGCUUAUCCUGGUGAAAAAUGCACGAGUUGC----CCGGAAGCGGCGGCCACCAGCUGGGUUGGCCUGAACCCAGCUAAAGGGCCAACGC-------------------
.((......((((((..(((.((..(............)..)----).)))))))))((((...(((((((((......)))))))))....))))...))------------------- ( -39.10)
>DroSec_CAF1 19035 97 + 1
UGCACCACUGUUGCUUAUCCUGGUGAAAAAUGCACGAGUUGC----CCGGAAGCGGCGGCCACCAGCUGGGUUGGCCUGAACCCAGCUAAAGGGCCAACGC-------------------
.((......((((((..(((.((..(............)..)----).)))))))))((((...(((((((((......)))))))))....))))...))------------------- ( -39.10)
>DroSim_CAF1 19344 97 + 1
UGCACCACUGUUGCUUAUCCUGGUGAAAAAUGCACGAGUUGC----CCGGAAGCGGCGGCCACCAGCUGGGUUGGCCUGAACCCAGCUAAAGGGCCAACGC-------------------
.((......((((((..(((.((..(............)..)----).)))))))))((((...(((((((((......)))))))))....))))...))------------------- ( -39.10)
>DroEre_CAF1 24122 91 + 1
UACAGCACUGUUGCUUAUCCUGGUGAAAAAUGCACGAGUUGC-----CGGAAGCGGCGACCACCAGCUGGGUUGGCCUGAACCCAGCUAAAGGUCC------------------------
....(((...(..((......))..)....)))..(.(((((-----((....))))))))((((((((((((......)))))))))...)))..------------------------ ( -35.00)
>DroAna_CAF1 15129 113 + 1
CGCACC-CAGUU------GCUGGUGAAAAAUGCAUGAGCUCUCCAACCGGAAGCGCCAACCACCAGCUGUGUUGGCGUGAUCCCAGCCAAAGGGGUAAAAGGAGCAAAAAAUAUCAAAAG
...(((-(..((------(((((.((...........(((.(((....))))))((((((((.....)).))))))....)))))).)))..))))........................ ( -33.70)
>consensus
UGCACCACUGUUGCUUAUCCUGGUGAAAAAUGCACGAGUUGC____CCGGAAGCGGCGGCCACCAGCUGGGUUGGCCUGAACCCAGCUAAAGGGCCAACGC___________________
.........(((((((...((((........((....)).......)))))))))))((((...(((((((((......)))))))))....))))........................ (-24.02 = -25.94 +   1.92)

alignment

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secondary structure

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dotplot

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Window 0

Location 3,568,074 – 3,568,171
Length 97
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 78.25
Mean single sequence MFE -37.64
Consensus MFE -22.50
Energy contribution -24.58
Covariance contribution 2.08
Combinations/Pair 1.15
Mean z-score -1.75
Structure conservation index 0.60
SVM decision value 0.22
SVM RNA-class probability 0.638419
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3568074 97 - 27905053
-------------------GCGUUGGCCCUUUAGCUGGGUUCAGGCCAACCCAGCUGGUGGCCGCCGCUUCCGG----GCAACUCGUGCAUUUUUCACCAGGAUAAGCAACAGUGGUGCA
-------------------((...((((..(((((((((((......))))))))))).))))((((((..(((----....).))(((.((.(((....))).)))))..)))))))). ( -39.50)
>DroSec_CAF1 19035 97 - 1
-------------------GCGUUGGCCCUUUAGCUGGGUUCAGGCCAACCCAGCUGGUGGCCGCCGCUUCCGG----GCAACUCGUGCAUUUUUCACCAGGAUAAGCAACAGUGGUGCA
-------------------((...((((..(((((((((((......))))))))))).))))((((((..(((----....).))(((.((.(((....))).)))))..)))))))). ( -39.50)
>DroSim_CAF1 19344 97 - 1
-------------------GCGUUGGCCCUUUAGCUGGGUUCAGGCCAACCCAGCUGGUGGCCGCCGCUUCCGG----GCAACUCGUGCAUUUUUCACCAGGAUAAGCAACAGUGGUGCA
-------------------((...((((..(((((((((((......))))))))))).))))((((((..(((----....).))(((.((.(((....))).)))))..)))))))). ( -39.50)
>DroEre_CAF1 24122 91 - 1
------------------------GGACCUUUAGCUGGGUUCAGGCCAACCCAGCUGGUGGUCGCCGCUUCCG-----GCAACUCGUGCAUUUUUCACCAGGAUAAGCAACAGUGCUGUA
------------------------.((((.(((((((((((......))))))))))).))))((((....))-----))..((.(((.......))).))....((((....))))... ( -34.80)
>DroAna_CAF1 15129 113 - 1
CUUUUGAUAUUUUUUGCUCCUUUUACCCCUUUGGCUGGGAUCACGCCAACACAGCUGGUGGUUGGCGCUUCCGGUUGGAGAGCUCAUGCAUUUUUCACCAGC------AACUG-GGUGCG
.......................((((((((..(((((((...(((((((((.....)).))))))).)))))))..))).((....)).............------....)-)))).. ( -34.90)
>consensus
___________________GCGUUGGCCCUUUAGCUGGGUUCAGGCCAACCCAGCUGGUGGCCGCCGCUUCCGG____GCAACUCGUGCAUUUUUCACCAGGAUAAGCAACAGUGGUGCA
...................(((.(((((..(((((((((((......))))))))))).))))).)))..........(((.....)))......(((((.............))))).. (-22.50 = -24.58 +   2.08)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:02:55 2006