Locus 2661

Sequence ID dm3.chr2L
Location 20,809,852 – 20,809,944
Length 92
Max. P 0.968289
window3647 window3648

overview

Window 7

Location 20,809,852 – 20,809,944
Length 92
Sequences 8
Columns 109
Reading direction forward
Mean pairwise identity 86.84
Shannon entropy 0.23046
G+C content 0.49602
Mean single sequence MFE -35.79
Consensus MFE -34.00
Energy contribution -33.14
Covariance contribution -0.86
Combinations/Pair 1.17
Mean z-score -1.78
Structure conservation index 0.95
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.80
SVM RNA-class probability 0.968289
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 20809852 92 + 23011544
-----------UUUGGUUAGCUGCUGCAAAUGAGGAAGCCUAAAAUAGCGA----GCCAAACGCGUUACGUGUUGGCGUCGCACU--GCACAAAGUUGCAGCAGCGGCA
-----------....(((.((((((((((.(((((...)))......((((----(((((.((((...))))))))).))))...--...))...))))))))))))). ( -37.40, z-score =  -1.98, R)
>droSim1.chr2L 20416881 92 + 22036055
-----------UUUGGUUAGCUGCUGCAAAUGAGGAAGCCUAAAAUAGCGA----GCCAAACGCGUUACGUGUUGGCGUCGCACU--GCACAAAGUUGCAGCAGCAGCA
-----------....(((.((((((((((.(((((...)))......((((----(((((.((((...))))))))).))))...--...))...))))))))))))). ( -38.20, z-score =  -2.49, R)
>droSec1.super_18 720643 92 + 1342155
-----------UUUGGUUAGCUGCUGCAAAUGAGGAAGCCUAAAAUAGCGA----GCCAAACGCGUUACGUGUUGGCGUCGCACU--GCACAAAGUUGCAGCAGCAGCA
-----------....(((.((((((((((.(((((...)))......((((----(((((.((((...))))))))).))))...--...))...))))))))))))). ( -38.20, z-score =  -2.49, R)
>droYak2.chr2R 11387587 92 - 21139217
-----------UUUGGUUAGCUGCUGCAAAUGAGGAAGCCUAAAAUAGCAA----GCCAAACGCGUUACGUGUUGGCGUCGCACU--GCACAAAGUUGCAGCAGCAGCA
-----------....(((.((((((((((.(((((...)))......((..----(((((.((((...)))))))))...))...--...))...))))))))))))). ( -33.90, z-score =  -1.24, R)
>droEre2.scaffold_4845 18929377 92 - 22589142
-----------UUUGGUUAGCUGCUGCAAAUGAGGAAGCCUAAAAUAGCAA----GCCAAACGCGUUACGUGUUGGCGUCGCACU--GCACAAAGUUGCAGCAGCAGCA
-----------....(((.((((((((((.(((((...)))......((..----(((((.((((...)))))))))...))...--...))...))))))))))))). ( -33.90, z-score =  -1.24, R)
>droAna3.scaffold_12943 1125544 90 - 5039921
-----------UUUGGUUAGCUGCUGCAAAUGAGGAAGCCUAAAAUAGCAA----GCCAAACGCGUUACGUGUUGGCGUUGCA----GCACAAACUUGCAGCAGCAGCA
-----------....(((.((((((((((...(((...)))......((((----(((((.((((...))))))))).)))).----........))))))))))))). ( -36.10, z-score =  -2.35, R)
>dp4.chr4_group3 4219086 109 - 11692001
UUUGGGAUGGGGAUACAUAGUGGCUGCAAAUGAGGAAGCCUAAAAUAGCAAAAAAGCCAAACGCGUUACGUGUUGGCGUUGCACUCUGCACAAAGUUGCAGCAGCUACA
......(((......))).((((((((....................((((....(((((.((((...))))))))).))))....((((......)))))))))))). ( -34.30, z-score =  -1.23, R)
>droPer1.super_1 1360283 109 - 10282868
UUUGGGAUGGGGAUACAUAGUGGCUGCAAAUGAGGAAGCCUAAAAUAGCAAAAAAGCCAAACGCGUUACGUGUUGGCGUUGCACUCUGCACAAAGUUGCAGCAGCUACA
......(((......))).((((((((....................((((....(((((.((((...))))))))).))))....((((......)))))))))))). ( -34.30, z-score =  -1.23, R)
>consensus
___________UUUGGUUAGCUGCUGCAAAUGAGGAAGCCUAAAAUAGCAA____GCCAAACGCGUUACGUGUUGGCGUCGCACU__GCACAAAGUUGCAGCAGCAGCA
...................((((((((....................((((....(((((.((((...))))))))).)))).....(((......))).)))))))). (-34.00 = -33.14 +  -0.86)

alignment

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secondary structure

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dotplot

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Window 8

Location 20,809,852 – 20,809,944
Length 92
Sequences 8
Columns 109
Reading direction reverse
Mean pairwise identity 86.84
Shannon entropy 0.23046
G+C content 0.49602
Mean single sequence MFE -32.36
Consensus MFE -28.82
Energy contribution -28.85
Covariance contribution 0.03
Combinations/Pair 1.08
Mean z-score -1.91
Structure conservation index 0.89
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.59
SVM RNA-class probability 0.952889
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 20809852 92 - 23011544
UGCCGCUGCUGCAACUUUGUGC--AGUGCGACGCCAACACGUAACGCGUUUGGC----UCGCUAUUUUAGGCUUCCUCAUUUGCAGCAGCUAACCAAA-----------
....((((((((((........--...((((.(((((.(((.....))))))))----))))......(((...)))...))))))))))........----------- ( -33.90, z-score =  -2.28, R)
>droSim1.chr2L 20416881 92 - 22036055
UGCUGCUGCUGCAACUUUGUGC--AGUGCGACGCCAACACGUAACGCGUUUGGC----UCGCUAUUUUAGGCUUCCUCAUUUGCAGCAGCUAACCAAA-----------
.((((((((((((......)))--)..((((.(((((.(((.....))))))))----))))....................))))))))........----------- ( -35.00, z-score =  -2.58, R)
>droSec1.super_18 720643 92 - 1342155
UGCUGCUGCUGCAACUUUGUGC--AGUGCGACGCCAACACGUAACGCGUUUGGC----UCGCUAUUUUAGGCUUCCUCAUUUGCAGCAGCUAACCAAA-----------
.((((((((((((......)))--)..((((.(((((.(((.....))))))))----))))....................))))))))........----------- ( -35.00, z-score =  -2.58, R)
>droYak2.chr2R 11387587 92 + 21139217
UGCUGCUGCUGCAACUUUGUGC--AGUGCGACGCCAACACGUAACGCGUUUGGC----UUGCUAUUUUAGGCUUCCUCAUUUGCAGCAGCUAACCAAA-----------
.((((((((((((......)))--)..((((.(((((.(((.....))))))))----))))....................))))))))........----------- ( -32.90, z-score =  -1.78, R)
>droEre2.scaffold_4845 18929377 92 + 22589142
UGCUGCUGCUGCAACUUUGUGC--AGUGCGACGCCAACACGUAACGCGUUUGGC----UUGCUAUUUUAGGCUUCCUCAUUUGCAGCAGCUAACCAAA-----------
.((((((((((((......)))--)..((((.(((((.(((.....))))))))----))))....................))))))))........----------- ( -32.90, z-score =  -1.78, R)
>droAna3.scaffold_12943 1125544 90 + 5039921
UGCUGCUGCUGCAAGUUUGUGC----UGCAACGCCAACACGUAACGCGUUUGGC----UUGCUAUUUUAGGCUUCCUCAUUUGCAGCAGCUAACCAAA-----------
....((((((((((((..(.((----(((((.(((((.(((.....))))))))----)))).......)))...)..))))))))))))........----------- ( -34.71, z-score =  -2.79, R)
>dp4.chr4_group3 4219086 109 + 11692001
UGUAGCUGCUGCAACUUUGUGCAGAGUGCAACGCCAACACGUAACGCGUUUGGCUUUUUUGCUAUUUUAGGCUUCCUCAUUUGCAGCCACUAUGUAUCCCCAUCCCAAA
.((((..(((((((......((.((((((((.(((((.(((.....))))))))....)))).))))...))........)))))))..))))................ ( -27.24, z-score =  -0.73, R)
>droPer1.super_1 1360283 109 + 10282868
UGUAGCUGCUGCAACUUUGUGCAGAGUGCAACGCCAACACGUAACGCGUUUGGCUUUUUUGCUAUUUUAGGCUUCCUCAUUUGCAGCCACUAUGUAUCCCCAUCCCAAA
.((((..(((((((......((.((((((((.(((((.(((.....))))))))....)))).))))...))........)))))))..))))................ ( -27.24, z-score =  -0.73, R)
>consensus
UGCUGCUGCUGCAACUUUGUGC__AGUGCGACGCCAACACGUAACGCGUUUGGC____UUGCUAUUUUAGGCUUCCUCAUUUGCAGCAGCUAACCAAA___________
....((((((((((.............((((.(((((.(((.....))))))))....))))......(((...)))...))))))))))................... (-28.82 = -28.85 +   0.03)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:55:22 2011