Locus 5961

Sequence ID dm3.chr3L
Location 2,807,683 – 2,807,778
Length 95
Max. P 0.978547
window8200 window8201

overview

Window 0

Location 2,807,683 – 2,807,778
Length 95
Sequences 3
Columns 95
Reading direction forward
Mean pairwise identity 92.83
Shannon entropy 0.09666
G+C content 0.43623
Mean single sequence MFE -23.00
Consensus MFE -21.47
Energy contribution -21.80
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.07
Structure conservation index 0.93
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.56
SVM RNA-class probability 0.950158
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 2807683 95 + 24543557
UAAAUUGGCGACAGACAUUAAGUGACUUGUCUUGUUAGCCCGAUUCCGAUUCCAAUCCCAAUUCCGAUUUAGAUUCGAAUUCGAAUUCGGACUCG
......(((((((((((..........)))).)))).)))(((.(((((....((((........))))...(((((....)))))))))).))) ( -22.80, z-score =  -1.65, R)
>droSim1.chr3L 2360285 89 + 22553184
UAAAUUGGCGACAGACAUUAAGUGACUUGUCUUGUUAGCCCGAUUCCGAUUCCAAUCCCAAUUCCGAUUCAGAUUCGAAUUCGGACUCG------
......(((((((((((..........)))).)))).)))(((.((((((((.((((..(((....)))..)))).))).))))).)))------ ( -23.10, z-score =  -2.25, R)
>droSec1.super_2 2828302 89 + 7591821
UAAAUUGGCGACAGACAUUAAGUGACUUGUCUUGUUAGCCCGAUUCCGAUUCCAAUCCCAAUUCCGAUUCAGAUUCGAACUCGGACUCG------
......(((((((((((..........)))).)))).)))(((.((((((((.((((..(((....)))..)))).))).))))).)))------ ( -23.10, z-score =  -2.30, R)
>consensus
UAAAUUGGCGACAGACAUUAAGUGACUUGUCUUGUUAGCCCGAUUCCGAUUCCAAUCCCAAUUCCGAUUCAGAUUCGAAUUCGGACUCG______
......(((((((((((..........)))).)))).)))(((.((((((((.((((..(((....)))..)))).))).))))).)))...... (-21.47 = -21.80 +   0.33)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 2,807,683 – 2,807,778
Length 95
Sequences 3
Columns 95
Reading direction reverse
Mean pairwise identity 92.83
Shannon entropy 0.09666
G+C content 0.43623
Mean single sequence MFE -28.10
Consensus MFE -26.87
Energy contribution -26.43
Covariance contribution -0.44
Combinations/Pair 1.07
Mean z-score -2.20
Structure conservation index 0.96
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.00
SVM RNA-class probability 0.978547
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 2807683 95 - 24543557
CGAGUCCGAAUUCGAAUUCGAAUCUAAAUCGGAAUUGGGAUUGGAAUCGGAAUCGGGCUAACAAGACAAGUCACUUAAUGUCUGUCGCCAAUUUA
..(((((((.(((((.(((.(((((.(((....))).))))).)))))))).))))))).....((((.(.((.....)).)))))......... ( -27.90, z-score =  -2.06, R)
>droSim1.chr3L 2360285 89 - 22553184
------CGAGUCCGAAUUCGAAUCUGAAUCGGAAUUGGGAUUGGAAUCGGAAUCGGGCUAACAAGACAAGUCACUUAAUGUCUGUCGCCAAUUUA
------(((.(((((.(((.(((((.(((....))).))))).)))))))).)))(((..(((.((((..........))))))).)))...... ( -28.20, z-score =  -2.39, R)
>droSec1.super_2 2828302 89 - 7591821
------CGAGUCCGAGUUCGAAUCUGAAUCGGAAUUGGGAUUGGAAUCGGAAUCGGGCUAACAAGACAAGUCACUUAAUGUCUGUCGCCAAUUUA
------(((.(((((.(((.(((((.(((....))).))))).)))))))).)))(((..(((.((((..........))))))).)))...... ( -28.20, z-score =  -2.14, R)
>consensus
______CGAGUCCGAAUUCGAAUCUGAAUCGGAAUUGGGAUUGGAAUCGGAAUCGGGCUAACAAGACAAGUCACUUAAUGUCUGUCGCCAAUUUA
......(((.((((.((((.(((((.(((....))).))))).)))))))).)))(((..(((.((((..........))))))).)))...... (-26.87 = -26.43 +  -0.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:58:36 2011