Locus 5594

Sequence ID dm3.chr3LHet
Location 1,654,358 – 1,654,444
Length 86
Max. P 0.976393
window7683 window7684

overview

Window 3

Location 1,654,358 – 1,654,444
Length 86
Sequences 3
Columns 102
Reading direction forward
Mean pairwise identity 69.31
Shannon entropy 0.40266
G+C content 0.36572
Mean single sequence MFE -16.90
Consensus MFE -11.88
Energy contribution -11.00
Covariance contribution -0.88
Combinations/Pair 1.29
Mean z-score -1.16
Structure conservation index 0.70
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.30
SVM RNA-class probability 0.633289
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3LHet 1654358 86 + 2555491
--------AGUAGUGUUGGGUAAACCUAGUUCAAUUUGGGGAAUAAGUUCGUUCGUUCGUUUAAAAUCAAUGAACUAGGUCGUUCAUUUAGUUC--------
--------........((..(..((((((((((..((((.(((..((........))..)))....)))))))))))))).)..))........-------- ( -16.20, z-score =  -1.76, R)
>droSim1.chrU 8887157 86 - 15797150
--------GGUAGUGUUGGGUAAUCCUAGUUCAAUUUGAGGAAUAAGUUCGUUCGUUCGUUUAAAAUCAAUGAACUAGGUCGUUCAUUUAGUUC--------
--------........((..(...(((((((((..((((.(((..((........))..)))....)))))))))))))..)..))........-------- ( -16.40, z-score =  -1.97, R)
>droVir3.scaffold_13036 877321 101 + 1135500
UGGUAUUUGGUA-CAGUGGGGAUUUCUAGUUCAAUUUGCUGAAUAAGUUUACUCGUUCAUUUUCUGGCCGAGAACUAAAUCUGUCAUUAAGUUCACUCGUUC
(((.((((((((-(((...((....((.(((((......))))).))....((((..((.....))..))))..))....)))).))))))))))....... ( -18.10, z-score =   0.25, R)
>consensus
________GGUAGUGUUGGGUAAUCCUAGUUCAAUUUGAGGAAUAAGUUCGUUCGUUCGUUUAAAAUCAAUGAACUAGGUCGUUCAUUUAGUUC________
................((..(...(((((((((..((((.(((..((....))..)))........)))))))))))))..)..))................ (-11.88 = -11.00 +  -0.88)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 1,654,358 – 1,654,444
Length 86
Sequences 3
Columns 102
Reading direction reverse
Mean pairwise identity 69.31
Shannon entropy 0.40266
G+C content 0.36572
Mean single sequence MFE -13.61
Consensus MFE -8.91
Energy contribution -8.58
Covariance contribution -0.33
Combinations/Pair 1.15
Mean z-score -2.22
Structure conservation index 0.65
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.95
SVM RNA-class probability 0.976393
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3LHet 1654358 86 - 2555491
--------GAACUAAAUGAACGACCUAGUUCAUUGAUUUUAAACGAACGAACGAACUUAUUCCCCAAAUUGAACUAGGUUUACCCAACACUACU--------
--------.............(((((((((((...((((.....(((..(......)..)))...)))))))))))))))..............-------- ( -13.20, z-score =  -2.92, R)
>droSim1.chrU 8887157 86 + 15797150
--------GAACUAAAUGAACGACCUAGUUCAUUGAUUUUAAACGAACGAACGAACUUAUUCCUCAAAUUGAACUAGGAUUACCCAACACUACC--------
--------...............(((((((((((((...(((.((......))...)))....))))..)))))))))................-------- ( -13.10, z-score =  -3.14, R)
>droVir3.scaffold_13036 877321 101 - 1135500
GAACGAGUGAACUUAAUGACAGAUUUAGUUCUCGGCCAGAAAAUGAACGAGUAAACUUAUUCAGCAAAUUGAACUAGAAAUCCCCACUG-UACCAAAUACCA
....(((....)))....((((......((((.(..(((....((((..((....))..)))).....)))..).)))).......)))-)........... ( -14.52, z-score =  -0.60, R)
>consensus
________GAACUAAAUGAACGACCUAGUUCAUUGAUUUUAAACGAACGAACGAACUUAUUCCCCAAAUUGAACUAGGAUUACCCAACACUACC________
.......................(((((((((............(((..(......)..))).......)))))))))........................ ( -8.91 =  -8.58 +  -0.33)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:51:26 2011