Locus 2309

Sequence ID dm3.chr2L
Location 17,858,301 – 17,858,459
Length 158
Max. P 0.992317
window3183 window3184 window3185

overview

Window 3

Location 17,858,301 – 17,858,353
Length 52
Sequences 4
Columns 52
Reading direction reverse
Mean pairwise identity 85.58
Shannon entropy 0.23402
G+C content 0.42996
Mean single sequence MFE -7.98
Consensus MFE -4.70
Energy contribution -5.45
Covariance contribution 0.75
Combinations/Pair 1.00
Mean z-score -2.36
Structure conservation index 0.59
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.28
SVM RNA-class probability 0.625968
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 17858301 52 - 23011544
ACACAUUCACUAAGGAAAUUCACAGCAGAAUUCCGCAUCAUAUUUCCCAGAC
.............((((((.....((.(....).)).....))))))..... (  -6.60, z-score =  -2.90, R)
>droSim1.chr2L 17536473 52 - 22036055
ACACAUUCACUAAGGGAAUUCACAGCAGAAUUCCGCAGCAUAUUUCCCAGAC
..............(((((((......))))))).................. (  -8.80, z-score =  -3.06, R)
>droSec1.super_7 1491212 52 - 3727775
ACACAUUCACUAAGGGAAUUCACAGCAGAAUUCCGCAGCAUAUUUCCCAGAC
..............(((((((......))))))).................. (  -8.80, z-score =  -3.06, R)
>droEre2.scaffold_4845 16185231 51 + 22589142
-CAAAUCCACUAAGGGAAUUUAAAGCCUAAUGCCUCAGCAUUUCUCUCGGAC
-........(..((((((...........((((....))))))))))..).. (  -7.70, z-score =  -0.42, R)
>consensus
ACACAUUCACUAAGGGAAUUCACAGCAGAAUUCCGCAGCAUAUUUCCCAGAC
..............(((((((......))))))).................. ( -4.70 =  -5.45 +   0.75)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 17,858,353 – 17,858,459
Length 106
Sequences 3
Columns 106
Reading direction forward
Mean pairwise identity 94.34
Shannon entropy 0.07797
G+C content 0.31447
Mean single sequence MFE -20.33
Consensus MFE -18.59
Energy contribution -18.27
Covariance contribution -0.33
Combinations/Pair 1.10
Mean z-score -3.05
Structure conservation index 0.91
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.53
SVM RNA-class probability 0.992317
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 17858353 106 + 23011544
UAAAUACCAAGAGAUAUGGGCUGUUUCGAAAUUAACCAGCAUUGUAGCCAAUUACUGAAAUUUUACUUUUGUAAUUAGUCCUACUAUUCCUAUCUAUAUUUCAUAG
..........(((((((((((((((........)).))))...((((.(((((((.(((.......))).)))))).)..)))).........))))))))).... ( -18.70, z-score =  -1.62, R)
>droSim1.chr2L 17536525 106 + 22036055
UAAAUACCAUGAGAUAUGGACUGUUUCGAAAUUAACCAGCAUUGUAGCCGAUUACUGAAAUUUUACUUUCGUAAUUACUCCUACUAUUCCAAACCAUAUUUCAUAG
........(((((((((((.(((((........)).)))....((((..((((((.((((......))))))))))....)))).........))))))))))).. ( -21.10, z-score =  -3.75, R)
>droSec1.super_7 1491264 106 + 3727775
UAAAUACCAUGAGAUAUGGACUGUUUCGAAAUUAACCAGCAUUGUAGCCGAUUACUGAAAUUUUACUUUCGUAAUUACUCCUACUAAUCCUAACCAUAUUUCAUAG
........(((((((((((...(((........))).((.(((((((..((((((.((((......))))))))))....)))).))).))..))))))))))).. ( -21.20, z-score =  -3.79, R)
>consensus
UAAAUACCAUGAGAUAUGGACUGUUUCGAAAUUAACCAGCAUUGUAGCCGAUUACUGAAAUUUUACUUUCGUAAUUACUCCUACUAUUCCUAACCAUAUUUCAUAG
........(((((((((((.(((((........)).)))....((((..((((((.((((......))))))))))....)))).........))))))))))).. (-18.59 = -18.27 +  -0.33)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 17,858,353 – 17,858,459
Length 106
Sequences 3
Columns 106
Reading direction reverse
Mean pairwise identity 94.34
Shannon entropy 0.07797
G+C content 0.31447
Mean single sequence MFE -26.97
Consensus MFE -22.29
Energy contribution -23.07
Covariance contribution 0.78
Combinations/Pair 1.03
Mean z-score -3.27
Structure conservation index 0.83
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.27
SVM RNA-class probability 0.987286
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 17858353 106 - 23011544
CUAUGAAAUAUAGAUAGGAAUAGUAGGACUAAUUACAAAAGUAAAAUUUCAGUAAUUGGCUACAAUGCUGGUUAAUUUCGAAACAGCCCAUAUCUCUUGGUAUUUA
.....(((((((((((((....((((..((((((((..((((...))))..))))))))))))...((((.............)))))).)))))....)))))). ( -20.22, z-score =  -0.98, R)
>droSim1.chr2L 17536525 106 - 22036055
CUAUGAAAUAUGGUUUGGAAUAGUAGGAGUAAUUACGAAAGUAAAAUUUCAGUAAUCGGCUACAAUGCUGGUUAAUUUCGAAACAGUCCAUAUCUCAUGGUAUUUA
((((((.((((((((((((((....(((((..((((....)))).)))))..((((((((......)))))))))))))))).....)))))).))))))...... ( -32.20, z-score =  -5.05, R)
>droSec1.super_7 1491264 106 - 3727775
CUAUGAAAUAUGGUUAGGAUUAGUAGGAGUAAUUACGAAAGUAAAAUUUCAGUAAUCGGCUACAAUGCUGGUUAAUUUCGAAACAGUCCAUAUCUCAUGGUAUUUA
((((((.((((((....(.......(((((..((((....)))).)))))..((((((((......)))))))).........)...)))))).))))))...... ( -28.50, z-score =  -3.79, R)
>consensus
CUAUGAAAUAUGGUUAGGAAUAGUAGGAGUAAUUACGAAAGUAAAAUUUCAGUAAUCGGCUACAAUGCUGGUUAAUUUCGAAACAGUCCAUAUCUCAUGGUAUUUA
((((((.((((((............(((((..((((....)))).)))))..((((((((......)))))))).............)))))).))))))...... (-22.29 = -23.07 +   0.78)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:48:51 2011