Locus 6178

Sequence ID 3R_DroMel_CAF1
Location 16,172,746 – 16,172,841
Length 95
Max. P 0.992843
window10068 window10069

overview

Window 8

Location 16,172,746 – 16,172,841
Length 95
Sequences 4
Columns 96
Reading direction forward
Mean pairwise identity 80.14
Mean single sequence MFE -29.20
Consensus MFE -21.75
Energy contribution -23.00
Covariance contribution 1.25
Combinations/Pair 1.15
Mean z-score -1.46
Structure conservation index 0.74
SVM decision value -0.05
SVM RNA-class probability 0.508563
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16172746 95 + 27905053
CAGCAAACAUGCCCCCCCCCCACAUCCGCUCCACCCCUUAACUUGCCCCCUUUUCAGAAGAGGGUUUUAGGGGUGCACGGAAUGCAGGGGUUGCC-
..(((....)))....((((..((((((...(((((((......((((.((((...)))).))))...)))))))..))).)))..)))).....- ( -35.50)
>DroSec_CAF1 1932 92 + 1
CAGCAAACAUGCCCCCUCC---CAUCCGCUCCACCACUAAACUUGCCCCCUUUUCAAAAGAGGGUUUUCGGGGUGCACGGAAUGCAGGGGUUGCC-
..((((......(((((..---..((((...((((.(..((...((((.(((.....))).)))).))..)))))..))))....))))))))).- ( -28.80)
>DroEre_CAF1 781 85 + 1
CAGCAAACAUGCCCCGCCC----------ACCACCCCCAAGCCUGCCCCCU-UUGAAAAGAGUGUUUUGGGGGCGUGCGGCAUGCAGGGGUUGCCU
..(((.....(((((((((----------((..((((((((...((...((-((....)))).)))))))))).))).))).....)))))))).. ( -31.90)
>DroYak_CAF1 1979 86 + 1
CAGCAAACAUGCCCCGCUC----------CCUACCCCUAAACUUGCCCCCUUUUGAAAAGAGUGUUUUCGGGGUGUUCCGAAUGCAGGGGUUGCCU
..(((.....(((((((((----------..((((((.((((.....................))))..))))))....))..)).)))))))).. ( -20.60)
>consensus
CAGCAAACAUGCCCCCCCC__________UCCACCCCUAAACUUGCCCCCUUUUCAAAAGAGGGUUUUCGGGGUGCACGGAAUGCAGGGGUUGCC_
..(((.....(((((.................(((((((((...((((.((((...)))).)))))))))))))((.......)).)))))))).. (-21.75 = -23.00 +   1.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 16,172,746 – 16,172,841
Length 95
Sequences 4
Columns 96
Reading direction reverse
Mean pairwise identity 80.14
Mean single sequence MFE -39.55
Consensus MFE -24.91
Energy contribution -26.72
Covariance contribution 1.81
Combinations/Pair 1.14
Mean z-score -2.85
Structure conservation index 0.63
SVM decision value 2.36
SVM RNA-class probability 0.992843
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16172746 95 - 27905053
-GGCAACCCCUGCAUUCCGUGCACCCCUAAAACCCUCUUCUGAAAAGGGGGCAAGUUAAGGGGUGGAGCGGAUGUGGGGGGGGGGCAUGUUUGCUG
-..(..((((..(((.((((.(((((((.((.(((((((.....)))))))....)).)))))))..)))))))..))))..)((((....)))). ( -49.90)
>DroSec_CAF1 1932 92 - 1
-GGCAACCCCUGCAUUCCGUGCACCCCGAAAACCCUCUUUUGAAAAGGGGGCAAGUUUAGUGGUGGAGCGGAUG---GGAGGGGGCAUGUUUGCUG
-.....(((((.(..(((((.(((((..((..(((((((.....)))))))....))..).))))..)))))..---).)))))(((....))).. ( -38.40)
>DroEre_CAF1 781 85 - 1
AGGCAACCCCUGCAUGCCGCACGCCCCCAAAACACUCUUUUCAA-AGGGGGCAGGCUUGGGGGUGGU----------GGGCGGGGCAUGUUUGCUG
.(((((.((((((...((((.(((((((((..(.((((((....-))))))..)..)))))))))))----------)))))))).....))))). ( -40.80)
>DroYak_CAF1 1979 86 - 1
AGGCAACCCCUGCAUUCGGAACACCCCGAAAACACUCUUUUCAAAAGGGGGCAAGUUUAGGGGUAGG----------GAGCGGGGCAUGUUUGCUG
.(((((.((((((.(((.....(((((..((((.((((((....))))))....)))).))))).))----------).)))))).....))))). ( -29.10)
>consensus
_GGCAACCCCUGCAUUCCGUACACCCCGAAAACACUCUUUUCAAAAGGGGGCAAGUUUAGGGGUGGA__________GGGCGGGGCAUGUUUGCUG
.((((((((((((.....)))((((((((((.(((((((.....)))))))....))))))))))................)))).....))))). (-24.91 = -26.72 +   1.81)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:14:39 2006