Locus 12030

Sequence ID dm3.chr3R
Location 25,229,899 – 25,230,043
Length 144
Max. P 0.857714
window16536 window16537

overview

Window 6

Location 25,229,899 – 25,230,012
Length 113
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 81.82
Shannon entropy 0.24488
G+C content 0.39757
Mean single sequence MFE -32.31
Consensus MFE -22.39
Energy contribution -22.40
Covariance contribution 0.01
Combinations/Pair 1.11
Mean z-score -2.27
Structure conservation index 0.69
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.94
SVM RNA-class probability 0.857714
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 25229899 113 - 27905053
AUUGUGAUCAAUGUAUUACAUUGG-------CUACUGCAUGGUCACACUGGUGGAAAGUGUGACCAUGCUAACUGUCAAACGCGACGUUUUUGUACCUAAGUAACUUUUUCUUUGCGUGC
...(((..(((((.....))))).-------.))).(((((((((((((.......)))))))))))))..........((((((.(......(((....))).......).)))))).. ( -38.52, z-score =  -3.82, R)
>droSec1.super_4 4090105 112 - 6179234
AUUGCGUUCAAUUUAGUACAUUGGAGUCGUUUUAGUGCAUGGUCGCACUGAUGGAAAGUGUCACCGUGCUAACUGAC--------UGUUUUUUUACUUAAGGAACUUUUUCUUUACGUGU
.....((((.....((((....(.(((((((.....(((((((.(((((.......))))).))))))).))).)))--------).).....))))....))))............... ( -29.20, z-score =  -1.62, R)
>droSim1.chr3R 24904664 112 - 27517382
AUUGCGUUCAAUUUAGUACAUUGGAGUCGUUUUAGUGCAUGGUCGCACUGAUGGAAAGUGUCACCGUGCUAACUGAC--------UGUUUUUUUACUUAAGGAACUUUUUCUUUGCGUGU
.....((((.....((((....(.(((((((.....(((((((.(((((.......))))).))))))).))).)))--------).).....))))....))))............... ( -29.20, z-score =  -1.36, R)
>consensus
AUUGCGUUCAAUUUAGUACAUUGGAGUCGUUUUAGUGCAUGGUCGCACUGAUGGAAAGUGUCACCGUGCUAACUGAC________UGUUUUUUUACUUAAGGAACUUUUUCUUUGCGUGU
......((((((.......))))))...........(((((((.(((((.......))))).)))))))........................(((.(((((((....))))))).))). (-22.39 = -22.40 +   0.01)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 25,229,939 – 25,230,043
Length 104
Sequences 3
Columns 111
Reading direction reverse
Mean pairwise identity 82.12
Shannon entropy 0.24592
G+C content 0.37500
Mean single sequence MFE -27.76
Consensus MFE -20.53
Energy contribution -20.20
Covariance contribution -0.33
Combinations/Pair 1.14
Mean z-score -1.81
Structure conservation index 0.74
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.45
SVM RNA-class probability 0.701702
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 25229939 104 - 27905053
AAAUAUACUUUCAUUACCAAACUUCUGCGUUAUUGUGAUCAAUGUAUUACAUUGG-------CUACUGCAUGGUCACACUGGUGGAAAGUGUGACCAUGCUAACUGUCAAA
............................((((..(((..(((((.....))))).-------.))).(((((((((((((.......)))))))))))))))))....... ( -33.20, z-score =  -4.19, R)
>droSec1.super_4 4090140 108 - 6179234
AAAUUUAAUUUAACAACAAAACUUAUGCGUAAUUGCGUUCAAUUUAGUACAUUGGAGUCGUUUUAGUGCAUGGUCGCACUGAUGGAAAGUGUCACCGUGCUAACUGAC---
...........(((.((........((((....))))((((((.......)))))))).)))((((((((((((.(((((.......))))).)))))))..))))).--- ( -25.00, z-score =  -0.79, R)
>droSim1.chr3R 24904699 108 - 27517382
AAAUGUAAUUUAACAACAAAACUUAUGCGUAAUUGCGUUCAAUUUAGUACAUUGGAGUCGUUUUAGUGCAUGGUCGCACUGAUGGAAAGUGUCACCGUGCUAACUGAC---
.((((((.................(((((....))))).........)))))).........((((((((((((.(((((.......))))).)))))))..))))).--- ( -25.07, z-score =  -0.46, R)
>consensus
AAAUAUAAUUUAACAACAAAACUUAUGCGUAAUUGCGUUCAAUUUAGUACAUUGGAGUCGUUUUAGUGCAUGGUCGCACUGAUGGAAAGUGUCACCGUGCUAACUGAC___
..........................(((....))).((((((.......))))))...........(((((((.(((((.......))))).)))))))........... (-20.53 = -20.20 +  -0.33)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:54:21 2011