Locus 1049

Sequence ID	dm3.chr2L
Location	7,883,141 – 7,883,203
Length	62
Max. P	0.973068

overview

Window 1

Location	7,883,141 – 7,883,203
Length	62
Sequences	6
Columns	62
Reading direction	forward
Mean pairwise identity	82.58
Shannon entropy	0.33237
G+C content	0.41609
Mean single sequence MFE	-16.35
Consensus MFE	-10.11
Energy contribution	-10.92
Covariance contribution	0.81
Combinations/Pair	1.21
Mean z-score	-2.20
Structure conservation index	0.62
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.11
SVM RNA-class probability	0.892714
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 7883141 62 + 23011544
AAAAUGCUGAAGUGACAGCAUUCGUGCCAGGCACCAUGCUGAAGUAUUUAUUCAGCGAAAAC
....((((((((((.((((((..((((...)))).))))))...)))...)))))))..... ( -18.90, z-score =  -2.80, R)
>droAna3.scaffold_12943 3618513 61 - 5039921
AAAAAGCUAACCUGUCAUCACUUGUACCUGGCACUAAGGGGUGCUAGUUUAAGAAUAAAAC-
....................((((...((((((((....))))))))..))))........- ( -13.30, z-score =  -0.99, R)
>droEre2.scaffold_4929 16805049 62 + 26641161
AAAAUGGUGAAGUGACAGCAUUCGUACCUGGUACCAUGCUGAAGUAUUUAUUCAGCGAAAAC
...((((((.((..((.......))..))..))))))((((((.......))))))...... ( -15.10, z-score =  -1.90, R)
>droYak2.chr2L 17311939 61 - 22324452
AAAAUGCU-AAGUGACAGCAUUCGUACCAGGUACCAAGCUGAAGUAUUUAUUCAGCGAAAAC
..((((((-.......)))))).((((...))))...((((((.......))))))...... ( -13.00, z-score =  -1.90, R)
>droSec1.super_3 3398017 62 + 7220098
AAAAUGCUGAAGUGACAGCAUUCGUGCCAGGCACCAUGCUGAAGUAUUUAUUCAGCGAAAAC
....((((((((((.((((((..((((...)))).))))))...)))...)))))))..... ( -18.90, z-score =  -2.80, R)
>droSim1.chr2L 7680753 62 + 22036055
AAAAUGCUGAAGUGACAGCAUUCGUGCCAGGCACCAUGCUGAAGUAUUUAUUCAGCGAAAAC
....((((((((((.((((((..((((...)))).))))))...)))...)))))))..... ( -18.90, z-score =  -2.80, R)
>consensus
AAAAUGCUGAAGUGACAGCAUUCGUACCAGGCACCAUGCUGAAGUAUUUAUUCAGCGAAAAC
.....(((((((((.((((((..((((...)))).))))))...)))...))))))...... (-10.11 = -10.92 +   0.81)

alignment

secondary structure

dotplot

Window 2

Location	7,883,141 – 7,883,203
Length	62
Sequences	6
Columns	62
Reading direction	reverse
Mean pairwise identity	82.58
Shannon entropy	0.33237
G+C content	0.41609
Mean single sequence MFE	-16.08
Consensus MFE	-12.84
Energy contribution	-13.20
Covariance contribution	0.36
Combinations/Pair	1.33
Mean z-score	-2.07
Structure conservation index	0.80
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.88
SVM RNA-class probability	0.973068
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 7883141 62 - 23011544
GUUUUCGCUGAAUAAAUACUUCAGCAUGGUGCCUGGCACGAAUGCUGUCACUUCAGCAUUUU
......((((((.......))))))...((((...))))((((((((......)))))))). ( -20.00, z-score =  -3.09, R)
>droAna3.scaffold_12943 3618513 61 + 5039921
-GUUUUAUUCUUAAACUAGCACCCCUUAGUGCCAGGUACAAGUGAUGACAGGUUAGCUUUUU
-(((.....(((...((.((((......)))).))....)))....)))............. (  -8.00, z-score =   0.97, R)
>droEre2.scaffold_4929 16805049 62 - 26641161
GUUUUCGCUGAAUAAAUACUUCAGCAUGGUACCAGGUACGAAUGCUGUCACUUCACCAUUUU
......((((((.......))))))(((((...(((((((.....))).)))).)))))... ( -12.70, z-score =  -1.54, R)
>droYak2.chr2L 17311939 61 + 22324452
GUUUUCGCUGAAUAAAUACUUCAGCUUGGUACCUGGUACGAAUGCUGUCACUU-AGCAUUUU
......((((((.......))))))...((((...))))((((((((.....)-))))))). ( -15.80, z-score =  -2.60, R)
>droSec1.super_3 3398017 62 - 7220098
GUUUUCGCUGAAUAAAUACUUCAGCAUGGUGCCUGGCACGAAUGCUGUCACUUCAGCAUUUU
......((((((.......))))))...((((...))))((((((((......)))))))). ( -20.00, z-score =  -3.09, R)
>droSim1.chr2L 7680753 62 - 22036055
GUUUUCGCUGAAUAAAUACUUCAGCAUGGUGCCUGGCACGAAUGCUGUCACUUCAGCAUUUU
......((((((.......))))))...((((...))))((((((((......)))))))). ( -20.00, z-score =  -3.09, R)
>consensus
GUUUUCGCUGAAUAAAUACUUCAGCAUGGUGCCUGGCACGAAUGCUGUCACUUCAGCAUUUU
......((((((.......))))))...((((...))))((((((((......)))))))). (-12.84 = -13.20 +   0.36)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:24:36 2011