Locus 2258

Sequence ID dm3.chr2L
Location 17,346,127 – 17,346,254
Length 127
Max. P 0.993026
window3110 window3111

overview

Window 0

Location 17,346,127 – 17,346,218
Length 91
Sequences 12
Columns 121
Reading direction reverse
Mean pairwise identity 82.06
Shannon entropy 0.35834
G+C content 0.40375
Mean single sequence MFE -24.51
Consensus MFE -21.58
Energy contribution -21.45
Covariance contribution -0.13
Combinations/Pair 1.08
Mean z-score -2.30
Structure conservation index 0.88
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.58
SVM RNA-class probability 0.993026
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 17346127 91 - 23011544
AAUGACAAUUUAUUGGUGGUUUUUACUAUUCGCAAUUUAUUUUAACUCCGCAAGGAAAUGCAUUGCGGAUGUAACACCCCGUCGGCACCCA------------------------------
..((((........((.(((..((((.(((((((((.((((.....(((....))))))).))))))))))))).))))))))).......------------------------------ ( -24.60, z-score =  -2.14, R)
>droSim1.chr2L 17044362 91 - 22036055
AAUGACAAUUUAUUGGUGGUUUUUACUAUUCGCAAUUUAUUUUAACUCCGCAAGGAAAUGCAUUGCGGAUGUAACACCCCGUCGGCACCCA------------------------------
..((((........((.(((..((((.(((((((((.((((.....(((....))))))).))))))))))))).))))))))).......------------------------------ ( -24.60, z-score =  -2.14, R)
>droSec1.super_7 978702 91 - 3727775
AAUGACAAUUUAUUGGUGGUUUUUACUAUUCGCAAUUUAUUUUAACUCCGCAAGGAAAUGCAUUGCGGAUGUAACACCCCGUCGGCACCCA------------------------------
..((((........((.(((..((((.(((((((((.((((.....(((....))))))).))))))))))))).))))))))).......------------------------------ ( -24.60, z-score =  -2.14, R)
>droYak2.chr2R 17379256 91 + 21139217
AAUGACAAUUUAUUGGUGGUUUUUACUAUUCGCAAUUUAUUUUAACUCCGCAAGGAAAUGCAUUGCGGAUGUAACACCCCGACGGCGCCCU------------------------------
.........(..((((.(((..((((.(((((((((.((((.....(((....))))))).))))))))))))).)))))))..)......------------------------------ ( -25.90, z-score =  -2.52, R)
>droEre2.scaffold_4845 15681431 91 + 22589142
AAUGACAAUUUAUUGGUGGUUUUUACUAUUCGCAAUUUAUUUUAACUCCGCAAGGAAAUGCAUUGCGGAUGUAACACCCCGUCGGCCUCCU------------------------------
..((((........((.(((..((((.(((((((((.((((.....(((....))))))).))))))))))))).))))))))).......------------------------------ ( -24.60, z-score =  -2.37, R)
>droAna3.scaffold_12916 12656613 93 + 16180835
AAUGACAAUUUAUUGGUGGUUUUUACUAUUCGCAAUUUAUUUUAACUCCGCAAGGAAAUGCAUUGCGGAUGUAACACCCCGCUCUGGCCAGCU----------------------------
..............((.(((..((((.(((((((((.((((.....(((....))))))).))))))))))))).)))))(((......))).---------------------------- ( -26.10, z-score =  -2.44, R)
>dp4.chr4_group4 282632 91 - 6586962
AAUGACAAUUUAUUGGUGGUUUUUACUAUUCGCAAUUUAUUUUAACUCCGCAAGGAAAUGCAUUGCGGAUGUAACACCCGUCUCUCUCUCU------------------------------
..............((((....((((.(((((((((.((((.....(((....))))))).))))))))))))))))).............------------------------------ ( -22.40, z-score =  -3.23, R)
>droPer1.super_68 178001 91 + 338515
AAUGACAAUUUAUUGGUGGUUUUUACUAUUCGCAAUUUAUUUUAACUCCGCAAGGAAAUGCAUUGCGGAUGUAACACCCGUCUCUCUCUCU------------------------------
..............((((....((((.(((((((((.((((.....(((....))))))).))))))))))))))))).............------------------------------ ( -22.40, z-score =  -3.23, R)
>droWil1.scaffold_180703 3191632 91 + 3946847
AAUGACAAUUUAUUGGUGGUUUUUACUAUUCGCAAUUUAUUUUAACUCCGCAAGGAAAUGCAUUGCGGAUGUAACGCCCAAACCGUAGCGA------------------------------
..............((((((..((((.(((((((((.((((.....(((....))))))).))))))))))))).)))...))).......------------------------------ ( -23.70, z-score =  -1.95, R)
>droVir3.scaffold_13246 2026402 95 + 2672878
AAUGACAAUUUAUUGGUGGUUUUUACUAUUCGCAAUUUAUUUCAACUCCGCAAGGAAAUGCAUUGCGGAUGUAACGCCCCAUAACCUCACCCCGA--------------------------
.............(((.(((..((((.(((((((((.((((.....(((....))))))).))))))))))))).))))))..............-------------------------- ( -25.40, z-score =  -2.88, R)
>droMoj3.scaffold_6500 5326811 118 - 32352404
AAUGACAAUUUAUUGGUGGUUUUUACUAUUCGCAAUUUAUUUCAACUCCGCAAGGAAAUGCAUUGCGGAUGUAACGCCCCAC---AGCCAGCGCUCAAAACUCAAACUCAAACGAAGCCAA
..(((........(((.(((..((((.(((((((((.((((.....(((....))))))).))))))))))))).)))))).---(((....)))......)))................. ( -26.60, z-score =  -1.35, R)
>droGri2.scaffold_15252 16584643 115 - 17193109
AAUGACAAUUUAUUGGUGGUUUUUACUAUUCACAAUUUAUUUCAACUCCGCAAGGAAAUACAUUGCGGAUAUAACGCCCCAUAACCAUGCCCCGUGCCCCUUCCUCACGGCCCUU------
.............(((.(((.((...(((((.((((.((((.....(((....))))))).)))).))))).)).))))))..........(((((.........))))).....------ ( -23.20, z-score =  -1.17, R)
>consensus
AAUGACAAUUUAUUGGUGGUUUUUACUAUUCGCAAUUUAUUUUAACUCCGCAAGGAAAUGCAUUGCGGAUGUAACACCCCGUCGGCACCCA______________________________
..............((((....((((.(((((((((.((((.....(((....))))))).)))))))))))))))))........................................... (-21.58 = -21.45 +  -0.13)

alignment

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secondary structure

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dotplot

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Window 1

Location 17,346,138 – 17,346,254
Length 116
Sequences 12
Columns 120
Reading direction reverse
Mean pairwise identity 97.86
Shannon entropy 0.04723
G+C content 0.33156
Mean single sequence MFE -25.66
Consensus MFE -24.88
Energy contribution -24.75
Covariance contribution -0.13
Combinations/Pair 1.06
Mean z-score -2.32
Structure conservation index 0.97
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.05
SVM RNA-class probability 0.980640
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 17346138 116 - 23011544
----UCAUAAAUUUAAAAAAUGUAAUAUCCCUCUUACGGAAAUGACAAUUUAUUGGUGGUUUUUACUAUUCGCAAUUUAUUUUAACUCCGCAAGGAAAUGCAUUGCGGAUGUAACACCCC
----................(((.((.(((.......))).)).))).......((.(((..((((.(((((((((.((((.....(((....))))))).))))))))))))).))))) ( -26.00, z-score =  -2.50, R)
>droSim1.chr2L 17044373 116 - 22036055
----UCAUAAAUUUAAAAAAUGUAAUAUCCCUCUUACGGAAAUGACAAUUUAUUGGUGGUUUUUACUAUUCGCAAUUUAUUUUAACUCCGCAAGGAAAUGCAUUGCGGAUGUAACACCCC
----................(((.((.(((.......))).)).))).......((.(((..((((.(((((((((.((((.....(((....))))))).))))))))))))).))))) ( -26.00, z-score =  -2.50, R)
>droSec1.super_7 978713 116 - 3727775
----UCAUAAAUUUAAAAAAUGUAAUAUCCCUCUUACGGAAAUGACAAUUUAUUGGUGGUUUUUACUAUUCGCAAUUUAUUUUAACUCCGCAAGGAAAUGCAUUGCGGAUGUAACACCCC
----................(((.((.(((.......))).)).))).......((.(((..((((.(((((((((.((((.....(((....))))))).))))))))))))).))))) ( -26.00, z-score =  -2.50, R)
>droYak2.chr2R 17379267 116 + 21139217
----UCAUAAAUUUAAAAAAUGUAAUAUCCCUCUUACGGAAAUGACAAUUUAUUGGUGGUUUUUACUAUUCGCAAUUUAUUUUAACUCCGCAAGGAAAUGCAUUGCGGAUGUAACACCCC
----................(((.((.(((.......))).)).))).......((.(((..((((.(((((((((.((((.....(((....))))))).))))))))))))).))))) ( -26.00, z-score =  -2.50, R)
>droEre2.scaffold_4845 15681442 116 + 22589142
----UCAUAAAUUUAAAAAAUGUAAUAUCCCUCUUACGGAAAUGACAAUUUAUUGGUGGUUUUUACUAUUCGCAAUUUAUUUUAACUCCGCAAGGAAAUGCAUUGCGGAUGUAACACCCC
----................(((.((.(((.......))).)).))).......((.(((..((((.(((((((((.((((.....(((....))))))).))))))))))))).))))) ( -26.00, z-score =  -2.50, R)
>droAna3.scaffold_12916 12656626 116 + 16180835
----UCAUAAAUUUAAAAAAUGUAAUAUCCCUCUUACGGAAAUGACAAUUUAUUGGUGGUUUUUACUAUUCGCAAUUUAUUUUAACUCCGCAAGGAAAUGCAUUGCGGAUGUAACACCCC
----................(((.((.(((.......))).)).))).......((.(((..((((.(((((((((.((((.....(((....))))))).))))))))))))).))))) ( -26.00, z-score =  -2.50, R)
>dp4.chr4_group4 282643 116 - 6586962
----UCAUAAAUUUAAAAAAUGUAAUAUCCCUCUUACGGAAAUGACAAUUUAUUGGUGGUUUUUACUAUUCGCAAUUUAUUUUAACUCCGCAAGGAAAUGCAUUGCGGAUGUAACACCCG
----................(((.((.(((.......))).)).))).......((((....((((.(((((((((.((((.....(((....))))))).))))))))))))))))).. ( -25.70, z-score =  -2.49, R)
>droPer1.super_68 178012 116 + 338515
----UCAUAAAUUUAAAAAAUGUAAUAUCCCUCUUACGGAAAUGACAAUUUAUUGGUGGUUUUUACUAUUCGCAAUUUAUUUUAACUCCGCAAGGAAAUGCAUUGCGGAUGUAACACCCG
----................(((.((.(((.......))).)).))).......((((....((((.(((((((((.((((.....(((....))))))).))))))))))))))))).. ( -25.70, z-score =  -2.49, R)
>droWil1.scaffold_180703 3191643 116 + 3946847
----UCAUAAAUUUAAAAAAUGUAAUAUCCCUCUUACGGAAAUGACAAUUUAUUGGUGGUUUUUACUAUUCGCAAUUUAUUUUAACUCCGCAAGGAAAUGCAUUGCGGAUGUAACGCCCA
----................(((.((.(((.......))).)).))).......((((....((((.(((((((((.((((.....(((....))))))).))))))))))))))))).. ( -25.30, z-score =  -1.97, R)
>droVir3.scaffold_13246 2026417 116 + 2672878
----UCAUAAAUUUAAAAAAUGUAAUAUCCCUCUUACGGAAAUGACAAUUUAUUGGUGGUUUUUACUAUUCGCAAUUUAUUUCAACUCCGCAAGGAAAUGCAUUGCGGAUGUAACGCCCC
----................(((.((.(((.......))).)).))).......((.(((..((((.(((((((((.((((.....(((....))))))).))))))))))))).))))) ( -26.30, z-score =  -2.27, R)
>droMoj3.scaffold_6500 5326849 120 - 32352404
GCGCUCAUAAAUUUAAAAAAUGUAAUAUCCCUCUUACGGAAAUGACAAUUUAUUGGUGGUUUUUACUAUUCGCAAUUUAUUUCAACUCCGCAAGGAAAUGCAUUGCGGAUGUAACGCCCC
..(((.(((((((.......(((((........)))))........))))))).)))(((..((((.(((((((((.((((.....(((....))))))).))))))))))))).))).. ( -27.36, z-score =  -1.93, R)
>droGri2.scaffold_15252 16584678 116 - 17193109
----UCAUAAAUUUAAAAAAUGUAAUAUCCCUCUUACGGAAAUGACAAUUUAUUGGUGGUUUUUACUAUUCACAAUUUAUUUCAACUCCGCAAGGAAAUACAUUGCGGAUAUAACGCCCC
----.................((.((((((.......(((..(((.(((..(((((((((....)))))...))))..))))))..)))(((((......).)))))))))).))..... ( -21.50, z-score =  -1.69, R)
>consensus
____UCAUAAAUUUAAAAAAUGUAAUAUCCCUCUUACGGAAAUGACAAUUUAUUGGUGGUUUUUACUAUUCGCAAUUUAUUUUAACUCCGCAAGGAAAUGCAUUGCGGAUGUAACACCCC
....................(((.((.(((.......))).)).))).......((((....((((.(((((((((.((((.....(((....))))))).))))))))))))))))).. (-24.88 = -24.75 +  -0.13)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:47:50 2011