Locus 10352

Sequence ID dm3.chr3R
Location 13,240,772 – 13,240,864
Length 92
Max. P 0.955314
window14236 window14237

overview

Window 6

Location 13,240,772 – 13,240,864
Length 92
Sequences 3
Columns 111
Reading direction forward
Mean pairwise identity 80.78
Shannon entropy 0.26473
G+C content 0.27399
Mean single sequence MFE -20.90
Consensus MFE -17.54
Energy contribution -19.10
Covariance contribution 1.56
Combinations/Pair 1.08
Mean z-score -2.02
Structure conservation index 0.84
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.62
SVM RNA-class probability 0.955314
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 13240772 92 + 27905053
UCUAAAUAGAUAUAU-AUCUUCUUCAGUG-------AUCCCUUUCUUAACAGGAACUUAACAUUUUAUUUUAAUAUGAAACGUGAAU-AAAAAGCUGAAGA----------
.......((((....-))))((((((((.-------...(((........)))......((.((((((......)))))).))....-.....))))))))---------- ( -13.90, z-score =  -0.99, R)
>droSec1.super_12 1217402 110 - 2123299
UCUAAAUAGAUAUAUUAUCUUCUUUAGUAUACGGUAAUCCCACUCUUAAUGGGAAUUUUACAUUUUAUUUGGAUAUGAAACGUGAAUUAAAAA-CUGAAGAAGACAGCAGA
.................(((((((((((.........(((((.......)))))..(((((.((((((......)))))).)))))......)-))))))))))....... ( -24.70, z-score =  -2.82, R)
>droSim1.chr3R 19286594 111 - 27517382
UCUAAAUAUAUAUAUUAUCUUCUUCAGUGUACGGUAAUCCUUCUCUUAAUAGGAAUUUUACAUUUUAUUUGGAUAUGAAACGUGAAUUAAAAAGCUGAAGAAGACAGCAGA
.................(((((((((((.........((((.........))))..(((((.((((((......)))))).))))).......)))))))))))....... ( -24.10, z-score =  -2.25, R)
>consensus
UCUAAAUAGAUAUAUUAUCUUCUUCAGUGUACGGUAAUCCCUCUCUUAAUAGGAAUUUUACAUUUUAUUUGGAUAUGAAACGUGAAUUAAAAAGCUGAAGAAGACAGCAGA
.................(((((((((((.........((((.........))))..(((((.((((((......)))))).))))).......)))))))))))....... (-17.54 = -19.10 +   1.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 13,240,772 – 13,240,864
Length 92
Sequences 3
Columns 111
Reading direction reverse
Mean pairwise identity 80.78
Shannon entropy 0.26473
G+C content 0.27399
Mean single sequence MFE -19.50
Consensus MFE -15.39
Energy contribution -16.70
Covariance contribution 1.31
Combinations/Pair 1.08
Mean z-score -1.88
Structure conservation index 0.79
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.08
SVM RNA-class probability 0.886688
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 13240772 92 - 27905053
----------UCUUCAGCUUUUU-AUUCACGUUUCAUAUUAAAAUAAAAUGUUAAGUUCCUGUUAAGAAAGGGAU-------CACUGAAGAAGAU-AUAUAUCUAUUUAGA
----------(((((((......-....((((((.((......)).))))))...((((((........))))))-------..)))))))((((-....))))....... ( -16.10, z-score =  -1.05, R)
>droSec1.super_12 1217402 110 + 2123299
UCUGCUGUCUUCUUCAG-UUUUUAAUUCACGUUUCAUAUCCAAAUAAAAUGUAAAAUUCCCAUUAAGAGUGGGAUUACCGUAUACUAAAGAAGAUAAUAUAUCUAUUUAGA
.....(((((((((.((-(.........((((((.((......)).)))))).....((((((.....)))))).........))).)))))))))............... ( -21.00, z-score =  -2.33, R)
>droSim1.chr3R 19286594 111 + 27517382
UCUGCUGUCUUCUUCAGCUUUUUAAUUCACGUUUCAUAUCCAAAUAAAAUGUAAAAUUCCUAUUAAGAGAAGGAUUACCGUACACUGAAGAAGAUAAUAUAUAUAUUUAGA
.....((((((((((((.....((((((((((((.((......)).))))))....(((((....)).))))))))).......))))))))))))............... ( -21.40, z-score =  -2.25, R)
>consensus
UCUGCUGUCUUCUUCAGCUUUUUAAUUCACGUUUCAUAUCCAAAUAAAAUGUAAAAUUCCUAUUAAGAGAGGGAUUACCGUACACUGAAGAAGAUAAUAUAUCUAUUUAGA
.....((((((((((((...........((((((.((......)).)))))).....((((.........))))..........))))))))))))............... (-15.39 = -16.70 +   1.31)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:22:20 2011