Locus 1164

Sequence ID 3L_DroMel_CAF1
Location 3,358,774 – 3,358,894
Length 120
Max. P 0.821915
window1812 window1813

overview

Window 2

Location 3,358,774 – 3,358,894
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 90.33
Mean single sequence MFE -30.70
Consensus MFE -24.14
Energy contribution -24.62
Covariance contribution 0.48
Combinations/Pair 1.16
Mean z-score -1.40
Structure conservation index 0.79
SVM decision value -0.03
SVM RNA-class probability 0.515817
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3358774 120 + 23771897
UAAUCCUCAUUGAGGAUCUGGAGCUGCUCUGCCCCUCAACGGCUGUCGCAGAUGCAAAAAACUCUAGCAAUAGCCUACGAAUUUCAGCUGAGCUCUACAAACUGCUAGACGCACUUCCUC
...........(((((..(((((((...(((....((...((((((.(((((..........))).)).))))))...))....)))...))))))).....(((.....)))..))))) ( -29.50)
>DroSec_CAF1 25958 120 + 1
UAAUCCUCAUUGAGGAUCUGGAGCUGCUCUGCCCCUCUACGGCUGUCGCAGAUGCAAAAAACUCUAGCAAUAGCCUACGAAUUUCAGCUCAGCUCUACAAACUGCUGGACGCACUUCCUC
...........(((((..((((((((..(((....((...((((((.(((((..........))).)).))))))...))....)))..)))))))).....(((.....)))..))))) ( -33.20)
>DroSim_CAF1 23647 120 + 1
UAAUCCUUAUUGAGGAUCUGGAGCUGCUCUGCCCCUCUACGGCUGUCGCAGAUGCAAAAAACUCUAGCAAUAGCCUACGAAUUUCAGCUGAGCUCUACAAACUGCUAGACGCACUUCCUC
...........(((((..(((((((...(((....((...((((((.(((((..........))).)).))))))...))....)))...))))))).....(((.....)))..))))) ( -29.50)
>DroEre_CAF1 24523 120 + 1
UGAUACUUAUUGAGGAUCUGGAGCUGCUCUGCCCCCUAACGGGUGUCGCAGAUACAAAAAACUCAAGCAAUUCUCUACGAAUUUCAGCUCAGCUAUACAAACUGAUAGACGCACUUCCUC
...........(((((..((((((((.(((((((((....))).)..)))))................(((((.....))))).)))))).(((((........)))).).))..))))) ( -30.80)
>DroYak_CAF1 24511 120 + 1
UGAUACUUAUUGAGGAUCUGGAGCUGCUCUGUCCCCUUACGGGUGUCGCGGACACAAAAAACUCUAGCAAUUCUCUGCGGAUAUCAGCUCAGCUCUACAAACUGCUAGACGCACUUCCGC
...........((((((((((((.....((((......))))(((((...)))))......))))))..)))))).(((((.....(((((((..........))).)).))...))))) ( -30.50)
>consensus
UAAUCCUUAUUGAGGAUCUGGAGCUGCUCUGCCCCUCUACGGCUGUCGCAGAUGCAAAAAACUCUAGCAAUAGCCUACGAAUUUCAGCUCAGCUCUACAAACUGCUAGACGCACUUCCUC
...........(((((..((((((((..(((....((...((((((.(((((..........))).)).))))))...))....)))..)))))))).....(((.....)))..))))) (-24.14 = -24.62 +   0.48)

alignment

Postscript

secondary structure

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dotplot

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Window 3

Location 3,358,774 – 3,358,894
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 90.33
Mean single sequence MFE -40.12
Consensus MFE -31.00
Energy contribution -30.64
Covariance contribution -0.36
Combinations/Pair 1.15
Mean z-score -1.86
Structure conservation index 0.77
SVM decision value 0.68
SVM RNA-class probability 0.821915
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3358774 120 - 23771897
GAGGAAGUGCGUCUAGCAGUUUGUAGAGCUCAGCUGAAAUUCGUAGGCUAUUGCUAGAGUUUUUUGCAUCUGCGACAGCCGUUGAGGGGCAGAGCAGCUCCAGAUCCUCAAUGAGGAUUA
.(.(((.(((.....))).))).).(((((...(((...((((..((((.((((.(((((.....)).))))))).))))..))))...)))...)))))..(((((((...))))))). ( -40.80)
>DroSec_CAF1 25958 120 - 1
GAGGAAGUGCGUCCAGCAGUUUGUAGAGCUGAGCUGAAAUUCGUAGGCUAUUGCUAGAGUUUUUUGCAUCUGCGACAGCCGUAGAGGGGCAGAGCAGCUCCAGAUCCUCAAUGAGGAUUA
.(.(((.(((.....))).))).).((((((..(((...(((...((((.((((.(((((.....)).))))))).))))...)))...)))..))))))..(((((((...))))))). ( -46.40)
>DroSim_CAF1 23647 120 - 1
GAGGAAGUGCGUCUAGCAGUUUGUAGAGCUCAGCUGAAAUUCGUAGGCUAUUGCUAGAGUUUUUUGCAUCUGCGACAGCCGUAGAGGGGCAGAGCAGCUCCAGAUCCUCAAUAAGGAUUA
..(((..(((.((((((((((((..((..((....))..))..)))))...)))))))....(((((.((((((.....))))))...))))))))..))).((((((.....)))))). ( -40.20)
>DroEre_CAF1 24523 120 - 1
GAGGAAGUGCGUCUAUCAGUUUGUAUAGCUGAGCUGAAAUUCGUAGAGAAUUGCUUGAGUUUUUUGUAUCUGCGACACCCGUUAGGGGGCAGAGCAGCUCCAGAUCCUCAAUAAGUAUCA
(((((..((((....(((((((........)))))))....))))........((.((((....(((.(((((....(((....))).)))))))))))).)).)))))........... ( -35.20)
>DroYak_CAF1 24511 120 - 1
GCGGAAGUGCGUCUAGCAGUUUGUAGAGCUGAGCUGAUAUCCGCAGAGAAUUGCUAGAGUUUUUUGUGUCCGCGACACCCGUAAGGGGACAGAGCAGCUCCAGAUCCUCAAUAAGUAUCA
(((((..(((.....))).))))).((((((..(((.....(((((((((((.....))))))))))).........(((....)))..)))..))))))..(((.((.....)).))). ( -38.00)
>consensus
GAGGAAGUGCGUCUAGCAGUUUGUAGAGCUGAGCUGAAAUUCGUAGGCUAUUGCUAGAGUUUUUUGCAUCUGCGACAGCCGUAGAGGGGCAGAGCAGCUCCAGAUCCUCAAUAAGGAUUA
(((((..((((.....((((((........)))))).....))))........((.(((((((((((.((((((.....)))..))).)))))).))))).)).)))))........... (-31.00 = -30.64 +  -0.36)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:00:48 2006