Locus 10832

Sequence ID	dm3.chr3R
Location	16,800,839 – 16,800,947
Length	108
Max. P	0.948338

overview

Window 2

Location	16,800,839 – 16,800,947
Length	108
Sequences	7
Columns	114
Reading direction	forward
Mean pairwise identity	80.31
Shannon entropy	0.36924
G+C content	0.46199
Mean single sequence MFE	-25.17
Consensus MFE	-16.42
Energy contribution	-18.63
Covariance contribution	2.21
Combinations/Pair	1.08
Mean z-score	-1.44
Structure conservation index	0.65
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.19
SVM RNA-class probability	0.586071
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 16800839 108 + 27905053
UUUGUGUGCAUUUAAGCCCAAA------AGAACCGAUGCCGAGAUUCGGUGGGAUUAAGUCCCCCGAUGUCGAUAUCGAGAUUCAGAUACAGAUACCAUUACCGAUACCUAGGC
(((((((((......)).....------.(((((((((.(((.((.(((.(((((...)))))))))).))).))))).).)))..)))))))........((........)). ( -29.00, z-score =  -2.49, R)
>dp4.chr2 18158407 81 - 30794189
UUUGUGUGCAUUUAAGCCC---------AAAACAAAUACAGAGAUACAGAGGGGUUAGGUCCCCC----CCGAUAUCG--AUACCGAUACCUAAAU------------------
(((((((............---------.......)))))))((((..(.((((........)))----))..)))).--................------------------ ( -13.81, z-score =  -0.18, R)
>droAna3.scaffold_13340 8058408 100 + 23697760
UUUGUGUGCAUUUAAGCCCGAAAAACCAAAAACAAAUGCAGAGAUACGGAGGGGUUAAGACCCCCGAGAUCGAUAUCG--AUACCGUUACCGAUACCUAAGC------------
..(.(.(((((((....................))))))).).)..(((.(((((....)))))((..((((....))--))..))...)))..........------------ ( -21.85, z-score =  -1.85, R)
>droEre2.scaffold_4770 12890400 108 - 17746568
UUUGUGUGCAUUUAAGCCCAAA------AGAAUCGAUGCCGAGAUUCGGUGGGGUUAAGUCCCCCGAUGUCGAUAUCGAGAUUCAGAUACAGAUACCAUUACCGAUACCUAGGC
(((((((((......)).....------.(((((((((.(((.((.(((.((((.....))))))))).))).))))))..)))..)))))))........((........)). ( -28.40, z-score =  -1.48, R)
>droYak2.chr3R 5591613 108 + 28832112
UUUGUGUGCAUUUAAGCCCAAA------AGAACCGAUGCCGAGAUUCGGUGGGGUUAAGUCCCCCGAUGUCGAUAUCGAGAUUCAGAUACAGAUACCAUUACCGAUACCUAGGC
(((((((((......)).....------.(((((((((.(((.((.(((.((((.....))))))))).))).))))).).)))..)))))))........((........)). ( -27.70, z-score =  -1.41, R)
>droSec1.super_38 75661 108 - 400794
UUUGUGUGCAUUUAAGCCCAAA------AGAACCGAUGCCGAGAUUCGGUGGGGUUAAGUCCCCCGAUGUCGAUAUCGAGAUUCAGAUACAGAUACCAUUACCGAUACCUAGGC
(((((((((......)).....------.(((((((((.(((.((.(((.((((.....))))))))).))).))))).).)))..)))))))........((........)). ( -27.70, z-score =  -1.41, R)
>droSim1.chr3R 22866654 108 - 27517382
UUUGUGUGCAUUUAAGCCCAAA------AGAGCCGAUGCCGAGAUUCGGUGGGGUUAAGUCCCCCGAUGUCGAUAUCGAGAUUCAGAUACAGAUACCAUUACCGAUACCUAGGC
(((((((((......)).....------.(((((((((.(((.((.(((.((((.....))))))))).))).))))).).)))..)))))))........((........)). ( -27.70, z-score =  -1.22, R)
>consensus
UUUGUGUGCAUUUAAGCCCAAA______AGAACCGAUGCCGAGAUUCGGUGGGGUUAAGUCCCCCGAUGUCGAUAUCGAGAUUCAGAUACAGAUACCAUUACCGAUACCUAGGC
(((((((((......))................(((((.(((.((.(((.((((.....))))))))).))).)))))........)))))))..................... (-16.42 = -18.63 +   2.21)

alignment

secondary structure

dotplot

Window 3

Location	16,800,839 – 16,800,947
Length	108
Sequences	7
Columns	114
Reading direction	reverse
Mean pairwise identity	80.31
Shannon entropy	0.36924
G+C content	0.46199
Mean single sequence MFE	-32.00
Consensus MFE	-18.18
Energy contribution	-19.96
Covariance contribution	1.78
Combinations/Pair	1.18
Mean z-score	-2.43
Structure conservation index	0.57
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.54
SVM RNA-class probability	0.948338
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 16800839 108 - 27905053
GCCUAGGUAUCGGUAAUGGUAUCUGUAUCUGAAUCUCGAUAUCGACAUCGGGGGACUUAAUCCCACCGAAUCUCGGCAUCGGUUCU------UUUGGGCUUAAAUGCACACAAA
((((((((((((....))))))).......((((..((((..(((..((((((((.....)))).))))...)))..)))))))).------..)))))............... ( -33.40, z-score =  -2.43, R)
>dp4.chr2 18158407 81 + 30794189
------------------AUUUAGGUAUCGGUAU--CGAUAUCGG----GGGGGACCUAACCCCUCUGUAUCUCUGUAUUUGUUUU---------GGGCUUAAAUGCACACAAA
------------------.....(((((((....--)))))))((----(((((......))))))).......((((((((....---------.....))))))))...... ( -23.70, z-score =  -1.66, R)
>droAna3.scaffold_13340 8058408 100 - 23697760
------------GCUUAGGUAUCGGUAACGGUAU--CGAUAUCGAUCUCGGGGGUCUUAACCCCUCCGUAUCUCUGCAUUUGUUUUUGGUUUUUCGGGCUUAAAUGCACACAAA
------------.....((((((((((....)))--)))))))(((..((((((........)))))).)))..((((((((..(((((....)))))..))))))))...... ( -31.40, z-score =  -3.20, R)
>droEre2.scaffold_4770 12890400 108 + 17746568
GCCUAGGUAUCGGUAAUGGUAUCUGUAUCUGAAUCUCGAUAUCGACAUCGGGGGACUUAACCCCACCGAAUCUCGGCAUCGAUUCU------UUUGGGCUUAAAUGCACACAAA
(((.((((.(((((...(((.((.(((((........))))).)).)))((((.......))))))))))))).))).........------((((.((......))...)))) ( -33.30, z-score =  -2.50, R)
>droYak2.chr3R 5591613 108 - 28832112
GCCUAGGUAUCGGUAAUGGUAUCUGUAUCUGAAUCUCGAUAUCGACAUCGGGGGACUUAACCCCACCGAAUCUCGGCAUCGGUUCU------UUUGGGCUUAAAUGCACACAAA
(((.((((.(((((...(((.((.(((((........))))).)).)))((((.......))))))))))))).))).........------((((.((......))...)))) ( -33.30, z-score =  -2.16, R)
>droSec1.super_38 75661 108 + 400794
GCCUAGGUAUCGGUAAUGGUAUCUGUAUCUGAAUCUCGAUAUCGACAUCGGGGGACUUAACCCCACCGAAUCUCGGCAUCGGUUCU------UUUGGGCUUAAAUGCACACAAA
(((.((((.(((((...(((.((.(((((........))))).)).)))((((.......))))))))))))).))).........------((((.((......))...)))) ( -33.30, z-score =  -2.16, R)
>droSim1.chr3R 22866654 108 + 27517382
GCCUAGGUAUCGGUAAUGGUAUCUGUAUCUGAAUCUCGAUAUCGACAUCGGGGGACUUAACCCCACCGAAUCUCGGCAUCGGCUCU------UUUGGGCUUAAAUGCACACAAA
(((.((((.(((((...(((.((.(((((........))))).)).)))((((.......))))))))))))).)))...(((((.------...))))).............. ( -35.60, z-score =  -2.91, R)
>consensus
GCCUAGGUAUCGGUAAUGGUAUCUGUAUCUGAAUCUCGAUAUCGACAUCGGGGGACUUAACCCCACCGAAUCUCGGCAUCGGUUCU______UUUGGGCUUAAAUGCACACAAA
.........(((((...(((.((.(((((........))))).)).)))((((.......)))))))))......((((.(((((..........)))))...))))....... (-18.18 = -19.96 +   1.78)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:31:16 2011