Locus 12185

Sequence ID	dm3.chr3R
Location	26,308,659 – 26,308,808
Length	149
Max. P	0.949901

overview

Window 8

Location	26,308,659 – 26,308,778
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	70.59
Shannon entropy	0.53783
G+C content	0.42707
Mean single sequence MFE	-33.78
Consensus MFE	-14.66
Energy contribution	-18.90
Covariance contribution	4.24
Combinations/Pair	1.29
Mean z-score	-2.03
Structure conservation index	0.43
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.27
SVM RNA-class probability	0.918915
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 26308659 119 + 27905053
GAAGAAAUUCAUAGAAAACACGUAGCCUGUUAAGUUCGGUGUCU-AAAAGUGUGCAGAGAUUUUAGAAAGUCUUAGUCCUGACUUUUUGGCCCAGCAUUGCAUGCUUUUAGUUGCCUUCU
(((....)))..((((((((.......))))......((((.((-((((((((((((.(...((((((((((........)))))))))).....).)))))))))))))).)))))))) ( -33.60, z-score =  -2.50, R)
>droSim1.chr3R 25952560 119 + 27517382
GAAGAAAUUCAUAGACGACACGUAGCCUGUUAAGUAGGGUGUCUUAAAGGUAUGCAGAGAUUUUAGGAAGU-UUGGUUCAGACUUUUCGGUCCAUCGUUGCAUGCUUUUAGAUAACUUUU
(((....)))......(((((....((((.....)))))))))((((((((((((((.(((.(..((((((-(((...)))))))))..)...))).))))))))))))))......... ( -34.90, z-score =  -2.96, R)
>droSec1.super_4 5130613 120 + 6179234
GAAGAAAUUCACAGAAGACACGUAGCCUGUUAAGUAGGGUGUCUUAAAGGUAUGCAGAGAUUUUAGGAAGUCUUGGUUCAGACUUUUCAGUCCAUCGUUGCAUGCUUUUAGAUACGUUUU
(((....)))....(((((......((((.....))))((((((.((((((((((((.(((.((..(((((((......)))))))..))...))).))))))))))))))))))))))) ( -38.40, z-score =  -3.94, R)
>droYak2.chr3R 27225474 96 + 28832112
GGAGAAAUUGAUGGAAGACACGUGGCCAGUUAAGUUGGGUGUCU-AAAAGUGCGCAGUGAUUUAAGGAAGUCUUAGUCCUG-CUUUUAGAUGCCUUUU----------------------
.....((((..(((....(....).)))....))))((((((((-((((....((((.((((.(((.....))))))))))-)))))))))))))...---------------------- ( -22.50, z-score =  -0.11, R)
>droEre2.scaffold_4820 8766432 114 - 10470090
GCAGAAAUUGGUAGCAGCCACGUAGCCAGUUUAGUUGGCUGGCU------AAUGCGGUGAUUUUGGGCAGGCCUAGUGCCGACUUCUCCGCCCAUCCCUGCAUGCUUUUGGAUACCCUAA
.........((((....(((..(((((((((.....))))))))------)((((((.((...(((((.((...(((....)))...))))))))).)))))).....))).)))).... ( -39.50, z-score =  -0.61, R)
>consensus
GAAGAAAUUCAUAGAAGACACGUAGCCUGUUAAGUUGGGUGUCU_AAAAGUAUGCAGAGAUUUUAGGAAGUCUUAGUCCAGACUUUUCGGUCCAUCGUUGCAUGCUUUUAGAUACCUUUU
................(((((.((((.......)))).)))))..((((((((((((.(((....(((((((........)))))))......))).))))))))))))........... (-14.66 = -18.90 +   4.24)

alignment

secondary structure

dotplot

Window 9

Location	26,308,699 – 26,308,808
Length	109
Sequences	4
Columns	110
Reading direction	forward
Mean pairwise identity	72.38
Shannon entropy	0.45461
G+C content	0.40840
Mean single sequence MFE	-28.07
Consensus MFE	-16.96
Energy contribution	-18.77
Covariance contribution	1.81
Combinations/Pair	1.37
Mean z-score	-1.89
Structure conservation index	0.60
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.56
SVM RNA-class probability	0.949901
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 26308699 109 + 27905053
GUCU-AAAAGUGUGCAGAGAUUUUAGAAAGUCUUAGUCCUGACUUUUUGGCCCAGCAUUGCAUGCUUUUAGUUGCCUUCUUUUAAUUACUGGCACUUUCAAUGCUUUCAA
..((-((((((((((((.(...((((((((((........)))))))))).....).)))))))))))))).((((..............))))................ ( -29.14, z-score =  -2.17, R)
>droSim1.chr3R 25952600 109 + 27517382
GUCUUAAAGGUAUGCAGAGAUUUUAGGAAGU-UUGGUUCAGACUUUUCGGUCCAUCGUUGCAUGCUUUUAGAUAACUUUUUUUAAUUACUAACGCUUUCUAUGCCAUCAA
((((.((((((((((((.(((.(..((((((-(((...)))))))))..)...))).))))))))))))))))....................((.......))...... ( -26.30, z-score =  -2.39, R)
>droSec1.super_4 5130653 110 + 6179234
GUCUUAAAGGUAUGCAGAGAUUUUAGGAAGUCUUGGUUCAGACUUUUCAGUCCAUCGUUGCAUGCUUUUAGAUACGUUUUUUUAAUUACUGGCGCUUUCUAUGCCAUCAA
((((.((((((((((((.(((.((..(((((((......)))))))..))...))).))))))))))))))))................(((((.......))))).... ( -30.80, z-score =  -3.18, R)
>droEre2.scaffold_4820 8766472 97 - 10470090
------GGCUAAUGCGGUGAUUUUGGGCAGGCCUAGUGCCGACUUCUCCGCCCAUCCCUGCAUGCUUUUGGAUACCC-----UAACUGACGG--AUUGCUAUGCCAACAA
------(((..((((((.((...(((((.((...(((....)))...))))))))).))))))((.((((.......-----.......)))--)..))...)))..... ( -26.04, z-score =   0.16, R)
>consensus
GUCU_AAAGGUAUGCAGAGAUUUUAGGAAGUCUUAGUUCAGACUUUUCGGCCCAUCGUUGCAUGCUUUUAGAUACCUUUUUUUAAUUACUGGCGCUUUCUAUGCCAUCAA
...((((((((((((((.(((.((((((((((........))))))))))...))).))))))))))))))....................................... (-16.96 = -18.77 +   1.81)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:57:24 2011