Locus 954

Sequence ID	3R_DroMel_CAF1
Location	3,135,694 – 3,135,847
Length	153
Max. P	0.790705

overview

Window 9

Location	3,135,694 – 3,135,807
Length	113
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	96.14
Mean single sequence MFE	-26.15
Consensus MFE	-23.44
Energy contribution	-24.12
Covariance contribution	0.69
Combinations/Pair	1.00
Mean z-score	-1.89
Structure conservation index	0.90
SVM decision value	0.59
SVM RNA-class probability	0.790705
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3135694 113 - 27905053
CCGCGCAACGAGCAGCGUGCAAC-------GUGCAGCAUGCAACUCGCAAUAUGCUCAUUCAUGCUCAAAGUCAAGAGAAAAGAAAAGCCACUCAGGCAAAAAGCCCGAAAUCAAAUCAA
.((.((...(((((((((((...-------.....)))))).....((.....)).......)))))....................(((.....))).....)).))............ ( -27.10)
>DroSec_CAF1 11353 113 - 1
CCGCGCAACGAACAGCGUGCAAC-------GUGCAGCAUGCAACUCGCAAUAUGCUCAUUCAUGCUCAAAGUCAAGAGAAAAGAAAAGCCACUCAGGCAAAAAGCCCGAAAUCAAAUCAA
.((.((...((..((((((.((.-------(.(((...(((.....)))...))).).)))))))).....))..............(((.....))).....)).))............ ( -22.60)
>DroSim_CAF1 11916 113 - 1
CCGCGCAACGAGCAGCGUGCAAC-------GUGCAGCAUGCAACUCGCAAUAUGCUCAUUCAUGCUCAAAGUCAAGAGAAAAGAAAAGCCACUCAGGCAAAAAGCCCGAAAUCAAAUCAA
.((.((...(((((((((((...-------.....)))))).....((.....)).......)))))....................(((.....))).....)).))............ ( -27.10)
>DroEre_CAF1 11931 120 - 1
CCGCGCAACGAGCAGCGUGCAACGUGCAACGUGCAACAUGCAACUCGCAAUAUGCUCAUUCAUGCUCAAAGUCAAGAGAAAAGAAAAGCCACUCAGGCAAAAAGCCCGAAAUCAAAUCAA
.((.((...((((((((((((...(((.....)))...))))...)))....))))).(((...(((........)))....)))..(((.....))).....)).))............ ( -27.80)
>consensus
CCGCGCAACGAGCAGCGUGCAAC_______GUGCAGCAUGCAACUCGCAAUAUGCUCAUUCAUGCUCAAAGUCAAGAGAAAAGAAAAGCCACUCAGGCAAAAAGCCCGAAAUCAAAUCAA
.((.((...(((((((((((.(((.....)))...)))))).....((.....)).......)))))....................(((.....))).....)).))............ (-23.44 = -24.12 +   0.69)

alignment

secondary structure

dotplot

Window 0

Location	3,135,734 – 3,135,847
Length	113
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	94.42
Mean single sequence MFE	-33.25
Consensus MFE	-28.98
Energy contribution	-29.72
Covariance contribution	0.75
Combinations/Pair	1.03
Mean z-score	-1.61
Structure conservation index	0.87
SVM decision value	0.23
SVM RNA-class probability	0.644984
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3135734 113 - 27905053
AGAUUGAGCUAUAAAAACGGAGUGCCGCAUUAACCGUUCGCCGCGCAACGAGCAGCGUGCAAC-------GUGCAGCAUGCAACUCGCAAUAUGCUCAUUCAUGCUCAAAGUCAAGAGAA
.((.(((((.(((........((((.((...........)).))))..((((..((((((...-------.....))))))..))))...)))))))).))...(((........))).. ( -32.90)
>DroSec_CAF1 11393 113 - 1
AGAUUGAGCUAUAAAAACGGGGUGCCGCAUUAACCGUUCGCCGCGCAACGAACAGCGUGCAAC-------GUGCAGCAUGCAACUCGCAAUAUGCUCAUUCAUGCUCAAAGUCAAGAGAA
.((.(((((.(((....((..((((.((...........)).))))..))....((((((...-------.....)))))).........)))))))).))...(((........))).. ( -31.80)
>DroSim_CAF1 11956 113 - 1
AGAUUGAGCUAUAAAAACGGGGUGCCGCAUUAACCGUUCGCCGCGCAACGAGCAGCGUGCAAC-------GUGCAGCAUGCAACUCGCAAUAUGCUCAUUCAUGCUCAAAGUCAAGAGAA
.((((((((.........(..((((.((...........)).))))..)(((((...(((...-------.(((.....)))....)))...)))))......)))))..)))....... ( -33.40)
>DroEre_CAF1 11971 119 - 1
AGAUUGAGCUAUAAAAACGGGGCGCCACAUUAA-CGUUCGCCGCGCAACGAGCAGCGUGCAACGUGCAACGUGCAACAUGCAACUCGCAAUAUGCUCAUUCAUGCUCAAAGUCAAGAGAA
.((((((((........((.((((..((.....-.)).)))).))....((((((((((((...(((.....)))...))))...)))....)))))......)))))..)))....... ( -34.90)
>consensus
AGAUUGAGCUAUAAAAACGGGGUGCCGCAUUAACCGUUCGCCGCGCAACGAGCAGCGUGCAAC_______GUGCAGCAUGCAACUCGCAAUAUGCUCAUUCAUGCUCAAAGUCAAGAGAA
.((.(((((.(((.....(..((((.((...........)).))))..)(((..((((((.(((.....)))...))))))..)))....)))))))).))...(((........))).. (-28.98 = -29.72 +   0.75)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:56:33 2006