Locus 3665

Sequence ID dm3.chr2R
Location 6,970,335 – 6,970,456
Length 121
Max. P 0.994399
window5024 window5025 window5026

overview

Window 4

Location 6,970,335 – 6,970,425
Length 90
Sequences 4
Columns 96
Reading direction forward
Mean pairwise identity 84.64
Shannon entropy 0.23800
G+C content 0.46681
Mean single sequence MFE -27.30
Consensus MFE -23.08
Energy contribution -24.70
Covariance contribution 1.62
Combinations/Pair 1.04
Mean z-score -2.89
Structure conservation index 0.85
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.70
SVM RNA-class probability 0.994399
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 6970335 90 + 21146708
------AAUCGGCAUCUUUCAAAAAGCGAAAAUCUCACAUUCCGCCAUCAAGUGGUUGCAAAUGAGAUUUUUGCCUGCCACCACCUCUCGCUGGCG
------...................((((((((((((....(.(((((...))))).)....))))))))))))..((((.(.......).)))). ( -23.90, z-score =  -2.18, R)
>droYak2.chr2R 18966198 87 - 21139217
AAUCGUUCGUGGAAUCUUUCAAAAAGCGAAAAUCUCACAUUCCGCCAUCAAGUGGUUGCAAAUGAGAUUUUUGCCUGCCAGCGG---ACG------
...(((((((((.............((((((((((((....(.(((((...))))).)....))))))))))))...))).)))---)))------ ( -26.69, z-score =  -2.65, R)
>droSec1.super_1 4537564 85 + 14215200
------AAUCGGCAUCUUUCAAAAAGCGAAAAUCUCACAUUCCGCCAUCAAGUGGUUGCAAAUGAGAUUUUUGCCCGCCAGC-----UUGCUGGCG
------...................((((((((((((....(.(((((...))))).)....)))))))))))).((((((.-----...)))))) ( -29.30, z-score =  -3.37, R)
>droSim1.chr2R 5511311 85 + 19596830
------AAUCGGCAUCUUUCAAAAAGCGAAAAUCUCACAUUCCGCCAUCAAGUGGUUGCAAAUGAGAUUUUUGCCCGCCAGC-----UUGCUGGCG
------...................((((((((((((....(.(((((...))))).)....)))))))))))).((((((.-----...)))))) ( -29.30, z-score =  -3.37, R)
>consensus
______AAUCGGCAUCUUUCAAAAAGCGAAAAUCUCACAUUCCGCCAUCAAGUGGUUGCAAAUGAGAUUUUUGCCCGCCAGC_____UCGCUGGCG
.........................((((((((((((....(.(((((...))))).)....)))))))))))).(((((((.......))))))) (-23.08 = -24.70 +   1.62)

alignment

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secondary structure

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dotplot

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Window 5

Location 6,970,335 – 6,970,425
Length 90
Sequences 4
Columns 96
Reading direction reverse
Mean pairwise identity 84.64
Shannon entropy 0.23800
G+C content 0.46681
Mean single sequence MFE -29.30
Consensus MFE -23.55
Energy contribution -24.80
Covariance contribution 1.25
Combinations/Pair 1.04
Mean z-score -2.30
Structure conservation index 0.80
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.66
SVM RNA-class probability 0.958553
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 6970335 90 - 21146708
CGCCAGCGAGAGGUGGUGGCAGGCAAAAAUCUCAUUUGCAACCACUUGAUGGCGGAAUGUGAGAUUUUCGCUUUUUGAAAGAUGCCGAUU------
.((((.(....).))))(((((((.((((((((((...(..(((.....)))..)...)))))))))).)))..((....))))))....------ ( -31.50, z-score =  -2.40, R)
>droYak2.chr2R 18966198 87 + 21139217
------CGU---CCGCUGGCAGGCAAAAAUCUCAUUUGCAACCACUUGAUGGCGGAAUGUGAGAUUUUCGCUUUUUGAAAGAUUCCACGAACGAUU
------(((---.((.(((.((((.((((((((((...(..(((.....)))..)...)))))))))).)))).((....))..))))).)))... ( -24.30, z-score =  -1.45, R)
>droSec1.super_1 4537564 85 - 14215200
CGCCAGCAA-----GCUGGCGGGCAAAAAUCUCAUUUGCAACCACUUGAUGGCGGAAUGUGAGAUUUUCGCUUUUUGAAAGAUGCCGAUU------
((((((...-----.))))))((((((((((((((...(..(((.....)))..)...))))))))))..(((.....))).))))....------ ( -30.70, z-score =  -2.68, R)
>droSim1.chr2R 5511311 85 - 19596830
CGCCAGCAA-----GCUGGCGGGCAAAAAUCUCAUUUGCAACCACUUGAUGGCGGAAUGUGAGAUUUUCGCUUUUUGAAAGAUGCCGAUU------
((((((...-----.))))))((((((((((((((...(..(((.....)))..)...))))))))))..(((.....))).))))....------ ( -30.70, z-score =  -2.68, R)
>consensus
CGCCAGCAA_____GCUGGCAGGCAAAAAUCUCAUUUGCAACCACUUGAUGGCGGAAUGUGAGAUUUUCGCUUUUUGAAAGAUGCCGAUU______
.((((((.......))))))((((.((((((((((...(..(((.....)))..)...)))))))))).))))....................... (-23.55 = -24.80 +   1.25)

alignment

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secondary structure

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dotplot

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Window 6

Location 6,970,356 – 6,970,456
Length 100
Sequences 5
Columns 107
Reading direction reverse
Mean pairwise identity 68.81
Shannon entropy 0.51936
G+C content 0.47925
Mean single sequence MFE -28.54
Consensus MFE -12.66
Energy contribution -13.06
Covariance contribution 0.40
Combinations/Pair 1.45
Mean z-score -1.49
Structure conservation index 0.44
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.10
SVM RNA-class probability 0.542298
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 6970356 100 - 21146708
-------CAUUUUCCGUGUUUUACGAGAGCAAUGAGUUCGCCAGCGAGAGGUGGUGGCAGGCAAAAAUCUCAUUUGCAACCACUUGAUGGCGGAAUGUGAGAUUUUC
-------(((((((((((...)))).))).)))).((.(((((.(....).))))))).....((((((((((...(..(((.....)))..)...)))))))))). ( -29.40, z-score =  -1.19, R)
>dp4.chr3 1002063 78 + 19779522
-------CAUUUUCCCCCCUUGACUGCUGUCGUACACGUGUC----------AGUGCAGGAUUCAGUGCUCGCUGG---------GCUGGCGGCUUAUGAAAUC---
-------.....(((......(((....)))((((.......----------.)))).)))((((..((.((((..---------...))))))...))))...--- ( -19.40, z-score =   0.87, R)
>droYak2.chr2R 18966225 98 + 21139217
CAUUUUACGUGUUCCGUGUUUUACGAGAGCAAUGAGUCCGUCC---------GCUGGCAGGCAAAAAUCUCAUUUGCAACCACUUGAUGGCGGAAUGUGAGAUUUUC
.(((((((((((((((((...)))).))))......((((((.---------..(((...(((((.......)))))..)))......))))))))))))))).... ( -26.10, z-score =  -0.72, R)
>droSec1.super_1 4537585 95 - 14215200
-------AAUUUUCCGUGUUUUACGAGAGCAAUGAGUUCGCCAGCAA-----GCUGGCGGGCAAAAAUCUCAUUUGCAACCACUUGAUGGCGGAAUGUGAGAUUUUC
-------.....((..(((((.....)))))..))(((((((((...-----.))))))))).((((((((((...(..(((.....)))..)...)))))))))). ( -32.90, z-score =  -2.88, R)
>droSim1.chr2R 5511332 95 - 19596830
-------CAUUUUCCGUGUUUUACGAGAGCAAUGAGUUCGCCAGCAA-----GCUGGCGGGCAAAAAUCUCAUUUGCAACCACUUGAUGGCGGAAUGUGAGAUUUUC
-------(((((((((((...)))).))).)))).(((((((((...-----.))))))))).((((((((((...(..(((.....)))..)...)))))))))). ( -34.90, z-score =  -3.51, R)
>consensus
_______CAUUUUCCGUGUUUUACGAGAGCAAUGAGUUCGCCAGC_A_____GCUGGCGGGCAAAAAUCUCAUUUGCAACCACUUGAUGGCGGAAUGUGAGAUUUUC
.......(((.((((((...........((((((((...(((.((...........)).)))......))))).)))............)))))).)))........ (-12.66 = -13.06 +   0.40)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:14:26 2011