Locus 3710

Sequence ID 3L_DroMel_CAF1
Location 10,774,989 – 10,775,118
Length 129
Max. P 0.976630
window5800 window5801

overview

Window 0

Location 10,774,989 – 10,775,092
Length 103
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 84.47
Mean single sequence MFE -42.70
Consensus MFE -30.03
Energy contribution -30.92
Covariance contribution 0.89
Combinations/Pair 1.07
Mean z-score -2.73
Structure conservation index 0.70
SVM decision value 0.33
SVM RNA-class probability 0.691972
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10774989 103 - 23771897
--------AUUCGAGGCAAUA---CGGCCUUGUCCGGAAGCACCACGCAAGUGGUGCA----GUGCACUUCGAACACCCCCGGGCGAGUUAAAAGCAUUAACACAGGCU--CGAGUGGCU
--------(((((((.(....---.....((((((((..(((((((....))))))).----(((.........)))..))))))))(((((.....)))))...).))--))))).... ( -42.50)
>DroSec_CAF1 108563 103 - 1
--------AUUCGAGGCACCA---CGGCCUUGUGCGGAAGCACCACGCAAGUGGUGCA----GUGCACUUCGAACACCCCCGGGCGAGUUAACAGCAUUAACACAGGCU--CGAGUGGCU
--------.((((((((....---..)))..(((((...(((((((....))))))).----.))))).)))))(((...(((((..(((((.....)))))....)))--)).)))... ( -40.20)
>DroSim_CAF1 111520 103 - 1
--------AUUCGAGGCACCA---CGGCCUUGUCCGGAAGCACCACGCAAGUGGUGCA----GUGCACUUCGAACACCCCCGGGCGAGUUAACAGCAUUAACACAGGCU--CGAGUGGCU
--------.....((.(((..---(((((((((((((..(((((((....))))))).----(((.........)))..))))))))(((((.....)))))...))).--)).))).)) ( -43.10)
>DroEre_CAF1 113842 114 - 1
CCACCGCCAUCCGAGGCACCACCGCGGCCUUGUCCGGAAGCACCACGCAAGUGGUGCA----CUGCACUUCGAACACCCCCGGGCCAGUUAACAGUAUUAACACAGGCU--CGAGUGGCU
.....(((......))).((((((.(((((.((((((..(((((((....))))))).----(........).......))))))..(((((.....)))))..)))))--)).)))).. ( -45.60)
>DroYak_CAF1 125185 106 - 1
--------AUUCGCGGCUCCACCGCGGCCUUGUCCGGAAGCACCACGCAAGUGGUGCA----CUGCACUUCGAACACCCCCGGGCCAGUUAACAGCAUUAACACAGGCU--CGAGUGGCU
--------...(((((.....)))))(((..((.(((..(((((((....))))))).----))).))............((((((.(((((.....)))))...))))--))...))). ( -42.50)
>DroAna_CAF1 109295 103 - 1
--------AUUCGAG-----A---CGGCCUUGUGCGGAAGC-CAACGCAAGUGGUGCAAGUGAUGCACUACGACACCCCCGGGGCAAGUUGGCCAAGUUAACACAGGCUCUCGAGAGCCU
--------.((((((-----(---..((((.(((..((.((-((((((..((((((((.....))))))))....((....))))..))))))....))..))))))))))))))..... ( -42.30)
>consensus
________AUUCGAGGCACCA___CGGCCUUGUCCGGAAGCACCACGCAAGUGGUGCA____GUGCACUUCGAACACCCCCGGGCGAGUUAACAGCAUUAACACAGGCU__CGAGUGGCU
..............(((........(((((.((((((..(((((((....)))))))........(.....).......))))))..(((((.....)))))..)))))........))) (-30.03 = -30.92 +   0.89)

alignment

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secondary structure

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dotplot

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Window 1

Location 10,775,027 – 10,775,118
Length 91
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 79.04
Mean single sequence MFE -35.82
Consensus MFE -19.73
Energy contribution -20.57
Covariance contribution 0.83
Combinations/Pair 1.00
Mean z-score -3.01
Structure conservation index 0.55
SVM decision value 1.77
SVM RNA-class probability 0.976630
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10775027 91 - 23771897
ACACUUUUAU-AGAG--------CGCACCACCG---CG----------AUUCGAGGCAAUA---CGGCCUUGUCCGGAAGCACCACGCAAGUGGUGCA----GUGCACUUCGAACACCCC
..........-.(((--------.((((..(((---.(----------(..((((((....---..)))))))))))..(((((((....))))))).----)))).))).......... ( -38.00)
>DroSec_CAF1 108601 91 - 1
ACACUUUUAU-AGAG--------CGCACCACCG---CG----------AUUCGAGGCACCA---CGGCCUUGUGCGGAAGCACCACGCAAGUGGUGCA----GUGCACUUCGAACACCCC
..........-.(((--------.((((..(((---((----------...((((((....---..)))))))))))..(((((((....))))))).----)))).))).......... ( -40.50)
>DroSim_CAF1 111558 92 - 1
ACACUUUUAUGAGAG--------CGCACCACCG---CG----------AUUCGAGGCACCA---CGGCCUUGUCCGGAAGCACCACGCAAGUGGUGCA----GUGCACUUCGAACACCCC
.........(((.((--------.((((..(((---.(----------(..((((((....---..)))))))))))..(((((((....))))))).----)))).)))))........ ( -38.30)
>DroEre_CAF1 113880 104 - 1
ACACUUUUAU-AGAG--------CGAACCACCG---CGAACCACCGCCAUCCGAGGCACCACCGCGGCCUUGUCCGGAAGCACCACGCAAGUGGUGCA----CUGCACUUCGAACACCCC
..........-.(..--------((((...(((---((.......(((......))).....)))))....((.(((..(((((((....))))))).----))).))))))..)..... ( -32.90)
>DroYak_CAF1 125223 94 - 1
ACACUUUUAU-AGAG--------CGAACCACCG---CG----------AUUCGCGGCUCCACCGCGGCCUUGUCCGGAAGCACCACGCAAGUGGUGCA----CUGCACUUCGAACACCCC
..........-.(..--------((((...(((---.(----------((((((((.....))))))....))))))..(((((((....))))))).----......))))..)..... ( -34.30)
>DroAna_CAF1 109335 100 - 1
GCAUUUAUAU-AGCUGUAUGUUUCCAGUUGCGGUGAUG----------AUUCGAG-----A---CGGCCUUGUGCGGAAGC-CAACGCAAGUGGUGCAAGUGAUGCACUACGACACCCCC
.........(-(((((........)))))).((((...----------.......-----.---..((.(((.((....))-))).))..((((((((.....))))))))..))))... ( -30.90)
>consensus
ACACUUUUAU_AGAG________CGAACCACCG___CG__________AUUCGAGGCACCA___CGGCCUUGUCCGGAAGCACCACGCAAGUGGUGCA____GUGCACUUCGAACACCCC
...................................................((((((.........)))))).......(((((((....)))))))....................... (-19.73 = -20.57 +   0.83)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:04:57 2006