Locus 10235

Sequence ID dm3.chr3R
Location 12,332,833 – 12,332,985
Length 152
Max. P 0.937023
window14072 window14073

overview

Window 2

Location 12,332,833 – 12,332,945
Length 112
Sequences 5
Columns 112
Reading direction forward
Mean pairwise identity 71.48
Shannon entropy 0.49829
G+C content 0.41071
Mean single sequence MFE -28.72
Consensus MFE -13.50
Energy contribution -14.98
Covariance contribution 1.48
Combinations/Pair 1.13
Mean z-score -1.52
Structure conservation index 0.47
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.24
SVM RNA-class probability 0.608753
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 12332833 112 + 27905053
GGACGGAUUAAAAUGGUCAGCUUAAUUCCCGGAUUAUCGAUACUUUGAGUCUUGGGACUUAUGGGCAGAUUAUCUCUGCCUGAUGAGUAAUGGUUGUUUCGGUUCUUAAGUA
....((((..((((..(((........(((((((..((((....))))))).))))(((((((((((((.....))))))).))))))..)))..))))..))))....... ( -33.90, z-score =  -2.17, R)
>droSim1.chr3R 18383262 93 - 27517382
UGUAGGAUCAAAAUGGUCAGCUUAAUUCCUGGAUUAUCGAUACUUUAAGUCUUGGGACUUAUGGGCAGAUUAUCUCUGCCUGGUUUUUAAGUA-------------------
.....((((.....)))).((((((..((................((((((....)))))).(((((((.....)))))))))...)))))).------------------- ( -25.60, z-score =  -1.93, R)
>droSec1.super_12 308699 85 - 2123299
UGUCGGAUCAAAAUGGUCAGUUUAAUUCCUGGAUUAACGAUACUUUAAGUCUUGGGAC--------AGAUUAUCUCUGCCUGGUUUUUAAGUA-------------------
(((((((((.....))))...((((((....))))))))))).((((((..(..((.(--------(((.....))))))..)..))))))..------------------- ( -20.20, z-score =  -1.32, R)
>droYak2.chr3R 16770459 112 - 28832112
UGUCGGAUCAAAGCGGUCACCUUGGUUCCGGGAUAAUCAAUACUUUGAGCCUUGGGACUUAUGGGCAGAUUAUCUCUGCCUGAAGGGUAAUGUAAGCUUCGGAUUUUAAACG
....(((((.((((.((.((((((((((((((....((((....))))..)))))))))...(((((((.....)))))))..))))).))....))))..)))))...... ( -33.10, z-score =  -1.34, R)
>droEre2.scaffold_4770 8441017 112 - 17746568
UGUCAGAUCAAAGCGGUCAGCUUAAUUCCGGGAUUGUCAAUACUUUGGGUCUGGGGACUUAUGGCCAGAUUAUCGCUGCCUGAUGAGUAAUGGCUAUUUCGGAUUUUAAACG
.....((((.....)))).(.((((.((((..((.((((.(((((((((((....)))))).(((.((.......)))))....))))).)))).))..))))..)))).). ( -30.80, z-score =  -0.83, R)
>consensus
UGUCGGAUCAAAAUGGUCAGCUUAAUUCCGGGAUUAUCGAUACUUUGAGUCUUGGGACUUAUGGGCAGAUUAUCUCUGCCUGAUGAGUAAUGA____UUCGG_U_UUAA___
.....((((.....)))).......((((.((((..((((....)))))))).)))).....(((((((.....)))))))............................... (-13.50 = -14.98 +   1.48)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 12,332,865 – 12,332,985
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 72.53
Shannon entropy 0.46850
G+C content 0.33136
Mean single sequence MFE -26.46
Consensus MFE -14.22
Energy contribution -16.42
Covariance contribution 2.20
Combinations/Pair 1.29
Mean z-score -1.96
Structure conservation index 0.54
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.41
SVM RNA-class probability 0.937023
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 12332865 120 + 27905053
AUUAUCGAUACUUUGAGUCUUGGGACUUAUGGGCAGAUUAUCUCUGCCUGAUGAGUAAUGGUUGUUUCGGUUCUUAAGUAAAUAAUUUCUUGAGAAAUUUGUUUGAGAAUAUGAGGUAAU
.(((((.......((((((....)))))).(((((((.....))))))))))))......((((..((((((((((((.....((((((....))))))..))))))))).)))..)))) ( -32.80, z-score =  -2.97, R)
>droSim1.chr3R 18383294 101 - 27517382
AUUAUCGAUACUUUAAGUCUUGGGACUUAUGGGCAGAUUAUCUCUGCCUG-------------------GUUUUUAAGUAAAUCAUUUCUUGGGAAAUUUGUUGUAGAAUAUGAGGUAAU
........(((((((..(((..(((.....(((((((.....)))))))(-------------------((((......)))))...)))..))).((((......)))).))))))).. ( -24.60, z-score =  -1.97, R)
>droSec1.super_12 308731 93 - 2123299
AUUAACGAUACUUUAAGUCUUGGGAC--------AGAUUAUCUCUGCCUG-------------------GUUUUUAAGUAAAUCAUUUCUUGAGAAAUUUGUUUGAGAAUAUGAGGUAAU
........(((((((..(((..(.((--------(((((.((((....((-------------------((((......))))))......))))))))))))..)))...))))))).. ( -22.30, z-score =  -2.17, R)
>droYak2.chr3R 16770491 115 - 28832112
AUAAUCAAUACUUUGAGCCUUGGGACUUAUGGGCAGAUUAUCUCUGCCUGAAGGGUAAUGUAAGCUUCGGAUUUUAAACGA-----UUCUUGAGAAAUUUGUUUGAAAGAACAAAAUAAU
....((((....))))..((..((((((.((((((((.....)))))))).)))............(((.........)))-----.)))..))...(((((((....)))))))..... ( -27.80, z-score =  -2.04, R)
>droEre2.scaffold_4770 8441049 115 - 17746568
AUUGUCAAUACUUUGGGUCUGGGGACUUAUGGCCAGAUUAUCGCUGCCUGAUGAGUAAUGGCUAUUUCGGAUUUUAAACGA-----UUCUUGAGAAAUUUGUUUGAAAGAAAAGAAUAAU
.............((((((....))))))((((((..((((((.....))))))....)))))).(((...((((((((((-----(((....)))..)))))))))).....))).... ( -24.80, z-score =  -0.67, R)
>consensus
AUUAUCGAUACUUUGAGUCUUGGGACUUAUGGGCAGAUUAUCUCUGCCUGA_G_GUAAUG_____UUCGGUUUUUAAGUAAAU_AUUUCUUGAGAAAUUUGUUUGAGAAUAUGAGGUAAU
........(((((((((((....)))))..(((((((.....)))))))....................((((((((((((((...(((....)))))))))))))))))..)))))).. (-14.22 = -16.42 +   2.20)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:20:03 2011