Locus 8096

Sequence ID dm3.chr3L
Location 20,166,712 – 20,166,829
Length 117
Max. P 0.998458
window11141 window11142

overview

Window 1

Location 20,166,712 – 20,166,829
Length 117
Sequences 3
Columns 117
Reading direction forward
Mean pairwise identity 76.47
Shannon entropy 0.29825
G+C content 0.39038
Mean single sequence MFE -25.30
Consensus MFE -19.33
Energy contribution -20.00
Covariance contribution 0.67
Combinations/Pair 1.12
Mean z-score -3.42
Structure conservation index 0.76
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.26
SVM RNA-class probability 0.998115
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 20166712 117 + 24543557
UGAACGUCCCUUUAUAGCAAUGAAAUCAUCCAACUUCAUGCAAUUGCAAUUGCAUGAGGAUAACCCGAUAACCGCAUUAGAUAAGCAUUUGAAAUAUGCUUAACCAACGUGAGACAC
.....(((.........................(((((((((((....))))))))))).............(((.((.(.(((((((.......))))))).).)).))).))).. ( -25.90, z-score =  -2.97, R)
>droSec1.super_11 76733 89 + 2888827
----------------------------UCCAACUUCGUGCAAUUGCAAUUGCAUGAUAAUACCCGGAUAACCGUAUUAGUUAAGCAUUUGAAAUAUGCUUAACCAACGUGAGACAC
----------------------------.......(((((((((....)))))))))((((((..((....))))))))(((((((((.......)))))))))...(....).... ( -24.30, z-score =  -4.18, R)
>droSim1.chr3L 19454483 89 + 22553184
----------------------------UCCAACUUCAUGCAAUUGCAAUUGCUUGGGGAUAACCGGAUAACCGUGUUAGUUAAGCAUUUGAAAUAUGCUUAACCAACGUGAGACAC
----------------------------.....(((((.(((((....))))).))))).(((((((....))).))))(((((((((.......)))))))))...(....).... ( -25.70, z-score =  -3.10, R)
>consensus
____________________________UCCAACUUCAUGCAAUUGCAAUUGCAUGAGGAUAACCGGAUAACCGUAUUAGUUAAGCAUUUGAAAUAUGCUUAACCAACGUGAGACAC
.................................(((((((((((....))))))))))).............(((.((.(((((((((.......))))))))).)).)))...... (-19.33 = -20.00 +   0.67)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 20,166,712 – 20,166,829
Length 117
Sequences 3
Columns 117
Reading direction reverse
Mean pairwise identity 76.47
Shannon entropy 0.29825
G+C content 0.39038
Mean single sequence MFE -30.70
Consensus MFE -23.12
Energy contribution -24.57
Covariance contribution 1.45
Combinations/Pair 1.03
Mean z-score -3.55
Structure conservation index 0.75
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.37
SVM RNA-class probability 0.998458
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 20166712 117 - 24543557
GUGUCUCACGUUGGUUAAGCAUAUUUCAAAUGCUUAUCUAAUGCGGUUAUCGGGUUAUCCUCAUGCAAUUGCAAUUGCAUGAAGUUGGAUGAUUUCAUUGCUAUAAAGGGACGUUCA
..(((((.((((((.(((((((.......))))))).)))))).(((.((..(((((((((((((((((....)))))))))....))))))))..)).))).....)))))..... ( -39.70, z-score =  -4.61, R)
>droSec1.super_11 76733 89 - 2888827
GUGUCUCACGUUGGUUAAGCAUAUUUCAAAUGCUUAACUAAUACGGUUAUCCGGGUAUUAUCAUGCAAUUGCAAUUGCACGAAGUUGGA----------------------------
...(((.(((((((((((((((.......))))))))))))).(((....))).......((.((((((....)))))).)).)).)))---------------------------- ( -25.70, z-score =  -2.96, R)
>droSim1.chr3L 19454483 89 - 22553184
GUGUCUCACGUUGGUUAAGCAUAUUUCAAAUGCUUAACUAACACGGUUAUCCGGUUAUCCCCAAGCAAUUGCAAUUGCAUGAAGUUGGA----------------------------
(((...)))(((((((((((((.......))))))))))))).(((....))).......((((.....(((....))).....)))).---------------------------- ( -26.70, z-score =  -3.09, R)
>consensus
GUGUCUCACGUUGGUUAAGCAUAUUUCAAAUGCUUAACUAAUACGGUUAUCCGGUUAUCCUCAUGCAAUUGCAAUUGCAUGAAGUUGGA____________________________
...(((.(((((((((((((((.......))))))))))))).(((....))).......(((((((((....))))))))).)).)))............................ (-23.12 = -24.57 +   1.45)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:39:22 2011