Locus 12082

Sequence ID dm3.chr3R
Location 25,575,232 – 25,575,340
Length 108
Max. P 0.686446
window16612 window16613

overview

Window 2

Location 25,575,232 – 25,575,340
Length 108
Sequences 6
Columns 108
Reading direction forward
Mean pairwise identity 75.00
Shannon entropy 0.49101
G+C content 0.51026
Mean single sequence MFE -32.31
Consensus MFE -17.99
Energy contribution -20.48
Covariance contribution 2.49
Combinations/Pair 1.26
Mean z-score -1.26
Structure conservation index 0.56
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.42
SVM RNA-class probability 0.686446
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 25575232 108 + 27905053
CUGGAUUGGCAUGAGGAGGAUAGGGCUCAAGCCAAGGCUAAAGACAGAGGCAUAGUGCUUGAGGAUAAACCGAGAAUCGGGGCUCCACCGAUUUCAGUGCCUUUGUGU
.(((.(((((.((((..........)))).)))))..)))...((((((((((....((((.(......)))))(((((((....).))))))...)))))))))).. ( -36.90, z-score =  -1.58, R)
>droSim1.chr3R 25248266 107 + 27517382
CUGGAUUGGCAUGAGGAGGAUAAGGCUCAAGCCAAGGCUAAAGACAGAGGCAUAGAGCUUGAGGAUAAACCGAGAAUCGGG-CUCCACCGAUUUCAGUGCCUUUGUGU
.(((.(((((.((((..........)))).)))))..)))...((((((((((.((.((((.(......)))))((((((.-.....)))))))).)))))))))).. ( -38.40, z-score =  -2.68, R)
>droSec1.super_4 4427946 108 + 6179234
CUGGAUUGGCAUGAGGAGGAUAAGGCUCAAGCCAAGGCUAAAGACAGAGGCAUAGAGCUUGAGGAUAAACCGAGAAUCGGGGCUCCACCGAUUUCAGUGCCUUUGUGU
.(((.(((((.((((..........)))).)))))..)))...((((((((((.((.((((.(......)))))(((((((....).)))))))).)))))))))).. ( -38.20, z-score =  -2.38, R)
>droYak2.chr3R 7937596 108 - 28832112
CUGGAUUGGCAUGACGAGGAUAAAGCUAAAGCCAAGGCUAAAGACAGAGGCAUAGAGCUUGAGGAUAAACCGAGAAUCGGGGCUCCACUGAUUUCAGUGCCUUUGUGU
.(((.(((((....................)))))..)))...((((((((...(((((..........(((.....)))))))).((((....)))))))))))).. ( -30.15, z-score =  -0.84, R)
>droEre2.scaffold_4820 8043089 108 - 10470090
CUGGAUUGGCAUGACGAGGAUAAAGCUAAAGCCAAGGCUAAAGACAGCGGCAUAGAGCUUGAGGAUAAACCGAGAAUCGGGGCUUCACCGAUUCCAGUGCCUUUGUGU
.......(((((..........(((((...(((...(((......))))))....)))))..((.....))(.(((((((.......)))))))).)))))....... ( -28.70, z-score =  -0.01, R)
>droAna3.scaffold_12911 5277986 84 + 5364042
AAAGAUUGAAAUAUUGAAAGUGCAUCAUAGUCGUGUGGCAGCAGUAGGCGCA--------GAGGCGAGGCGGCGGGCUGACACACCACGGAG----------------
........................((...((.(((((.((((....(.(((.--------........))).)..)))).))))).)).)).---------------- ( -21.50, z-score =  -0.06, R)
>consensus
CUGGAUUGGCAUGAGGAGGAUAAAGCUCAAGCCAAGGCUAAAGACAGAGGCAUAGAGCUUGAGGAUAAACCGAGAAUCGGGGCUCCACCGAUUUCAGUGCCUUUGUGU
.....(((((.(((............))).)))))........((((((((((.........((.....))..(((((((.......)))))))..)))))))))).. (-17.99 = -20.48 +   2.49)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 25,575,232 – 25,575,340
Length 108
Sequences 6
Columns 108
Reading direction reverse
Mean pairwise identity 75.00
Shannon entropy 0.49101
G+C content 0.51026
Mean single sequence MFE -26.18
Consensus MFE -13.32
Energy contribution -15.05
Covariance contribution 1.73
Combinations/Pair 1.28
Mean z-score -1.35
Structure conservation index 0.51
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.18
SVM RNA-class probability 0.581824
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 25575232 108 - 27905053
ACACAAAGGCACUGAAAUCGGUGGAGCCCCGAUUCUCGGUUUAUCCUCAAGCACUAUGCCUCUGUCUUUAGCCUUGGCUUGAGCCCUAUCCUCCUCAUGCCAAUCCAG
.....((((((((((((((((.(....))))))).)))))..........((.....))...........)))))(((.((((..........)))).)))....... ( -28.20, z-score =  -1.36, R)
>droSim1.chr3R 25248266 107 - 27517382
ACACAAAGGCACUGAAAUCGGUGGAG-CCCGAUUCUCGGUUUAUCCUCAAGCUCUAUGCCUCUGUCUUUAGCCUUGGCUUGAGCCUUAUCCUCCUCAUGCCAAUCCAG
..(((.((((((((....)))(((((-((((.....)))...........))))))))))).))).....(..(((((.((((..........)))).)))))..).. ( -28.40, z-score =  -1.50, R)
>droSec1.super_4 4427946 108 - 6179234
ACACAAAGGCACUGAAAUCGGUGGAGCCCCGAUUCUCGGUUUAUCCUCAAGCUCUAUGCCUCUGUCUUUAGCCUUGGCUUGAGCCUUAUCCUCCUCAUGCCAAUCCAG
.....((((((((((((((((.(....))))))).)))))..........((.....))...........)))))(((.((((..........)))).)))....... ( -28.40, z-score =  -1.44, R)
>droYak2.chr3R 7937596 108 + 28832112
ACACAAAGGCACUGAAAUCAGUGGAGCCCCGAUUCUCGGUUUAUCCUCAAGCUCUAUGCCUCUGUCUUUAGCCUUGGCUUUAGCUUUAUCCUCGUCAUGCCAAUCCAG
.......((((.(((.....(.(((...(((.....)))....))).)(((((....(((.(((....)))....)))...)))))........)))))))....... ( -24.60, z-score =  -1.01, R)
>droEre2.scaffold_4820 8043089 108 + 10470090
ACACAAAGGCACUGGAAUCGGUGAAGCCCCGAUUCUCGGUUUAUCCUCAAGCUCUAUGCCGCUGUCUUUAGCCUUGGCUUUAGCUUUAUCCUCGUCAUGCCAAUCCAG
.......((((((((((((((.(....)))))))).))))........(((((....(((((((....))))...)))...)))))............)))....... ( -29.90, z-score =  -1.93, R)
>droAna3.scaffold_12911 5277986 84 - 5364042
----------------CUCCGUGGUGUGUCAGCCCGCCGCCUCGCCUC--------UGCGCCUACUGCUGCCACACGACUAUGAUGCACUUUCAAUAUUUCAAUCUUU
----------------....((.(((((.((((..(.(((........--------.))).)....)))).))))).))..(((.......))).............. ( -17.60, z-score =  -0.86, R)
>consensus
ACACAAAGGCACUGAAAUCGGUGGAGCCCCGAUUCUCGGUUUAUCCUCAAGCUCUAUGCCUCUGUCUUUAGCCUUGGCUUGAGCCUUAUCCUCCUCAUGCCAAUCCAG
..(((.(((((..((.....(.(((...(((.....)))....))).)....))..))))).)))........(((((.(((............))).)))))..... (-13.32 = -15.05 +   1.73)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:55:24 2011