Locus 9922

Sequence ID dm3.chr3R
Location 9,825,317 – 9,825,391
Length 74
Max. P 0.986879
window13632 window13633

overview

Window 2

Location 9,825,317 – 9,825,391
Length 74
Sequences 6
Columns 77
Reading direction forward
Mean pairwise identity 91.42
Shannon entropy 0.16262
G+C content 0.50111
Mean single sequence MFE -16.63
Consensus MFE -14.94
Energy contribution -14.80
Covariance contribution -0.14
Combinations/Pair 1.06
Mean z-score -1.86
Structure conservation index 0.90
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.28
SVM RNA-class probability 0.919970
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 9825317 74 + 27905053
GCCAGCGUCUUGGUUUGGUGAUAUCGCCUGAGCAUAUCACCGCAUAACGAUUUCCCA---ACCCCCCAAUUACACUG
..(((.((.((((...((((((((.((....)))))))))).......(......).---.....))))..)).))) ( -16.40, z-score =  -2.02, R)
>droSim1.chr3R 15913940 73 - 27517382
GCCAGCGUCUUGGUUUGGUGAUAUCGCCUGAGCAUAUCACCGCAUAACGAUUUCCCA---ACCCCC-AAUUACACUG
..(((.((.((((...((((((((.((....)))))))))).......(......).---....))-))..)).))) ( -16.40, z-score =  -1.90, R)
>droSec1.super_0 8932652 73 - 21120651
GCCAGCGUCUUGGUUUGGUGAUAUCGCCUGAGCAUAUCACCGCAUAACGAUUUCCCA---AACUCC-AAUUACACUG
..(((.((.(((((((((.((.((((..((.((........)).)).)))).)))))---))..))-))..)).))) ( -16.60, z-score =  -1.88, R)
>droYak2.chr3R 12226258 73 - 28832112
GCCAGCGUCUUGGUUUGGUGAUAUCGCCUGAGCAUAUCACCGCAUAACGAUUUCCCA---ACCCCC-AAUUACACUG
..(((.((.((((...((((((((.((....)))))))))).......(......).---....))-))..)).))) ( -16.40, z-score =  -1.90, R)
>droEre2.scaffold_4770 9368933 73 + 17746568
GCCAGCGUCUUGGUUUGGUGAUAUCGCCUGAGCAUAUCACCGCAUAACGAUUUCCCA---ACCCCC-AAUUACACUG
..(((.((.((((...((((((((.((....)))))))))).......(......).---....))-))..)).))) ( -16.40, z-score =  -1.90, R)
>droAna3.scaffold_13340 3051014 73 - 23697760
----GUGUCUUGGUUUGGUGAUAUCGCCUGAGCAUAUCACCGCAUAACGAUUUCCCCCAUAGCUCCAUGCCACACUA
----(((.(.(((...((((((((.((....))))))))))((..................)).))).).))).... ( -17.57, z-score =  -1.58, R)
>consensus
GCCAGCGUCUUGGUUUGGUGAUAUCGCCUGAGCAUAUCACCGCAUAACGAUUUCCCA___ACCCCC_AAUUACACUG
.....(((..((...(((((((((.((....)))))))))))))..)))............................ (-14.94 = -14.80 +  -0.14)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 9,825,317 – 9,825,391
Length 74
Sequences 6
Columns 77
Reading direction reverse
Mean pairwise identity 91.42
Shannon entropy 0.16262
G+C content 0.50111
Mean single sequence MFE -25.80
Consensus MFE -20.00
Energy contribution -20.20
Covariance contribution 0.20
Combinations/Pair 1.05
Mean z-score -3.11
Structure conservation index 0.78
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.26
SVM RNA-class probability 0.986879
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 9825317 74 - 27905053
CAGUGUAAUUGGGGGGU---UGGGAAAUCGUUAUGCGGUGAUAUGCUCAGGCGAUAUCACCAAACCAAGACGCUGGC
((((((..((((..(((---(....)))).......((((((((((....)).))))))))...)))).)))))).. ( -26.60, z-score =  -3.25, R)
>droSim1.chr3R 15913940 73 + 27517382
CAGUGUAAUU-GGGGGU---UGGGAAAUCGUUAUGCGGUGAUAUGCUCAGGCGAUAUCACCAAACCAAGACGCUGGC
((((((..((-((...(---(((((.((((((..(((......)))...)))))).)).)))).)))).)))))).. ( -26.90, z-score =  -3.44, R)
>droSec1.super_0 8932652 73 + 21120651
CAGUGUAAUU-GGAGUU---UGGGAAAUCGUUAUGCGGUGAUAUGCUCAGGCGAUAUCACCAAACCAAGACGCUGGC
((((((....-.(.(((---(((((.((((((..(((......)))...)))))).)).)))))))...)))))).. ( -25.80, z-score =  -3.35, R)
>droYak2.chr3R 12226258 73 + 28832112
CAGUGUAAUU-GGGGGU---UGGGAAAUCGUUAUGCGGUGAUAUGCUCAGGCGAUAUCACCAAACCAAGACGCUGGC
((((((..((-((...(---(((((.((((((..(((......)))...)))))).)).)))).)))).)))))).. ( -26.90, z-score =  -3.44, R)
>droEre2.scaffold_4770 9368933 73 - 17746568
CAGUGUAAUU-GGGGGU---UGGGAAAUCGUUAUGCGGUGAUAUGCUCAGGCGAUAUCACCAAACCAAGACGCUGGC
((((((..((-((...(---(((((.((((((..(((......)))...)))))).)).)))).)))).)))))).. ( -26.90, z-score =  -3.44, R)
>droAna3.scaffold_13340 3051014 73 + 23697760
UAGUGUGGCAUGGAGCUAUGGGGGAAAUCGUUAUGCGGUGAUAUGCUCAGGCGAUAUCACCAAACCAAGACAC----
....(((.(.(((.((.((((......))))...))((((((((((....)).))))))))...))).).)))---- ( -21.70, z-score =  -1.71, R)
>consensus
CAGUGUAAUU_GGGGGU___UGGGAAAUCGUUAUGCGGUGAUAUGCUCAGGCGAUAUCACCAAACCAAGACGCUGGC
((((((.....((................(.....)((((((((((....)).))))))))...))...)))))).. (-20.00 = -20.20 +   0.20)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:13:57 2011