Locus 2193

Sequence ID 3R_DroMel_CAF1
Location 6,266,346 – 6,266,458
Length 112
Max. P 0.941984
window3564 window3565

overview

Window 4

Location 6,266,346 – 6,266,438
Length 92
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 81.00
Mean single sequence MFE -19.08
Consensus MFE -15.60
Energy contribution -15.60
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -2.48
Structure conservation index 0.82
SVM decision value 1.32
SVM RNA-class probability 0.941984
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6266346 92 + 27905053
C------CCGAGCUGU---A-------------------UGUGCAUCCUCAAUUUCCCUUUUAUGUUAUUUUAAUUUUAUGUUAUUGUUAUGACACAAUGAAAAUAAAAUUGAAUUGACA
.------..(((.(((---.-------------------...)))..))).............(((((.(((((((((((.(((((((......)))))))..))))))))))).))))) ( -18.90)
>DroVir_CAF1 33732 95 + 1
A------GCGAACUGUUUUC-------------------UGUGCAUCCUCAAUUUCCUUUUUAUGUUAUUUUAAUUUUAUGUUAUUGUUAUGACACAAUGAAAAUAAAAUUGAAUUGACA
.------(((....(....)-------------------..)))...................(((((.(((((((((((.(((((((......)))))))..))))))))))).))))) ( -16.30)
>DroPse_CAF1 28202 102 + 1
CCCUCCCUUCAGCCAU---A---------------CGAGUAUGCAUCCUCAAUUUCCUUUUUAUGUUAUUUUAAUUUUAUGUUAUUGUUAUGACACAAUGAAAAUAAAAUUGAAUUGACA
...........((.((---(---------------....)))))...................(((((.(((((((((((.(((((((......)))))))..))))))))))).))))) ( -17.50)
>DroGri_CAF1 48092 114 + 1
C------GGGAACUGUUUGCUGUUCAACUGUUCUAUAGCUGUGCAUCCUCAAUUUCCUUUUUAUGUUAUUUUAAUUUUAUGUUAUUGUUAUGACACAAUGAAAAUAAAAUUGAAUUGACA
.------(((((.((..(((....((.((((...)))).)).)))....)).)))))......(((((.(((((((((((.(((((((......)))))))..))))))))))).))))) ( -25.10)
>DroWil_CAF1 42933 87 + 1
-----------GCAGU---C-------------------CCUGCAUCCUCAAUUUCCUUUUUAUGUUAUUUUAAUUUUAUGUUAUUGUUAUGACACAAUGAAAAUAAAAUUGAAUUGACA
-----------((((.---.-------------------.))))...................(((((.(((((((((((.(((((((......)))))))..))))))))))).))))) ( -19.20)
>DroPer_CAF1 33536 102 + 1
CUCUCCCUUCAGCCAU---A---------------CGAGUAUGCAUCCUCAAUUUCCUUUUUAUGUUAUUUUAAUUUUAUGUUAUUGUUAUGACACAAUGAAAAUAAAAUUGAAUUGACA
...........((.((---(---------------....)))))...................(((((.(((((((((((.(((((((......)))))))..))))))))))).))))) ( -17.50)
>consensus
C______GCGAGCUGU___A___________________UGUGCAUCCUCAAUUUCCUUUUUAUGUUAUUUUAAUUUUAUGUUAUUGUUAUGACACAAUGAAAAUAAAAUUGAAUUGACA
...............................................................(((((.(((((((((((.(((((((......)))))))..))))))))))).))))) (-15.60 = -15.60 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 5

Location 6,266,358 – 6,266,458
Length 100
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 80.92
Mean single sequence MFE -19.38
Consensus MFE -16.10
Energy contribution -16.10
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -2.10
Structure conservation index 0.83
SVM decision value 1.11
SVM RNA-class probability 0.917119
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6266358 100 + 27905053
GUGCAUCCUCAAUUUCCCUUUUAUGUUAUUUUAAUUUUAUGUUAUUGUUAUGACACAAUGAAAAUAAAAUUGAAUUGACACUGAUGUCCU----UGCUUCCUU---U-------------
(..((((...((........)).(((((.(((((((((((.(((((((......)))))))..))))))))))).)))))..))))..).----.........---.------------- ( -17.90)
>DroVir_CAF1 33747 113 + 1
GUGCAUCCUCAAUUUCCUUUUUAUGUUAUUUUAAUUUUAUGUUAUUGUUAUGACACAAUGAAAAUAAAAUUGAAUUGACACUGAAGCAUCUCGACAAUGCCUGUACGCCCCGA-------
(((((..............(((((((((.(((((((((((.(((((((......)))))))..))))))))))).))))).))))((((.......)))).))))).......------- ( -23.80)
>DroGri_CAF1 48126 103 + 1
GUGCAUCCUCAAUUUCCUUUUUAUGUUAUUUUAAUUUUAUGUUAUUGUUAUGACACAAUGAAAAUAAAAUUGAAUUGACACUGAAGCAUCUCGGCACCGCCUG-----------------
((((............((((...(((((.(((((((((((.(((((((......)))))))..))))))))))).)))))..)))).......))))......----------------- ( -21.01)
>DroWil_CAF1 42940 113 + 1
CUGCAUCCUCAAUUUCCUUUUUAUGUUAUUUUAAUUUUAUGUUAUUGUUAUGACACAAUGAAAAUAAAAUUGAAUUGACACUGAUGUCCU----UGGCCCAAC---CCCCCAAUCCCCCC
..(((((...((........)).(((((.(((((((((((.(((((((......)))))))..))))))))))).)))))..)))))..(----(((......---...))))....... ( -17.90)
>DroMoj_CAF1 52385 99 + 1
GUGCAUCCUCAAUUUCCUUUUUAUGUUAUUUUAAUUUUAUGUUAUUGUUAUGACACAAUGAAAAUAAAAUUGAAUUGACACUGAAGCGUCUCGACAACG---------------------
................((((...(((((.(((((((((((.(((((((......)))))))..))))))))))).)))))..)))).............--------------------- ( -17.80)
>DroPer_CAF1 33558 108 + 1
AUGCAUCCUCAAUUUCCUUUUUAUGUUAUUUUAAUUUUAUGUUAUUGUUAUGACACAAUGAAAAUAAAAUUGAAUUGACACUGAUGUCCU----UACUUCCUU---C-----AGCCCUUA
.......................(((((.(((((((((((.(((((((......)))))))..))))))))))).)))))((((......----........)---)-----))...... ( -17.84)
>consensus
GUGCAUCCUCAAUUUCCUUUUUAUGUUAUUUUAAUUUUAUGUUAUUGUUAUGACACAAUGAAAAUAAAAUUGAAUUGACACUGAAGCCCC____CACCGCCUG_________________
.......................(((((.(((((((((((.(((((((......)))))))..))))))))))).)))))........................................ (-16.10 = -16.10 +  -0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:29:33 2006