Locus 3666

Sequence ID dm3.chr2R
Location 6,972,597 – 6,972,685
Length 88
Max. P 0.970897
window5027 window5028

overview

Window 7

Location 6,972,597 – 6,972,685
Length 88
Sequences 4
Columns 90
Reading direction forward
Mean pairwise identity 85.77
Shannon entropy 0.21708
G+C content 0.62511
Mean single sequence MFE -37.25
Consensus MFE -23.16
Energy contribution -23.91
Covariance contribution 0.75
Combinations/Pair 1.04
Mean z-score -3.18
Structure conservation index 0.62
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.84
SVM RNA-class probability 0.970897
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 6972597 88 + 21146708
CAGAAGGGGG--CUUGACGGUGUUUAGGCCAAGUCGAGCUCAACGUGGCUCAGAUCGGCUCAAGUGAGCCCCAAUGCACUGAGCCACUCG
..((...(((--(((((((((......)))..)))))))))...(((((((((...(((((....)))))........))))))))))). ( -39.60, z-score =  -3.19, R)
>droSim1.chr2R 5513563 80 + 19596830
CAGAAGGGGGGGCUUGGCGGGGUUUAGGCCAAGUCGAGCUCAACGUGGCUCAGAUCGGCUCA-GUG---------GCACUGAGCCACUCG
..((..(..(((((((((..(((....)))..)))))))))..)(((((((((....(((..-..)---------)).))))))))))). ( -39.60, z-score =  -3.98, R)
>droSec1.super_1 4539815 78 + 14215200
CAGAAGGGGG--CUUGGCGGGGUUUAGGCCAAGUCGAGCUCAACGUGGCUCAGAUCGGCUCA-GUG---------GCACUGAGCCACUCG
..((...(((--((((((..(((....)))..)))))))))...(((((((((....(((..-..)---------)).))))))))))). ( -38.00, z-score =  -3.73, R)
>droYak2.chr2R 18968538 73 - 21139217
CAGAAGGGGG--CUUGACGCGGUUUGGGCCAAGUCGAGCUCAACGUGGCUCCGAUCGGCUCAGGUG---------------AGCCACUCG
..((...(((--((((((..(((....)))..)))))))))...(((((((..(((......))))---------------)))))))). ( -31.80, z-score =  -1.82, R)
>consensus
CAGAAGGGGG__CUUGACGGGGUUUAGGCCAAGUCGAGCUCAACGUGGCUCAGAUCGGCUCA_GUG_________GCACUGAGCCACUCG
..((...(((..((((((..(((....)))..)))))))))...(((((((((.........................))))))))))). (-23.16 = -23.91 +   0.75)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 6,972,597 – 6,972,685
Length 88
Sequences 4
Columns 90
Reading direction reverse
Mean pairwise identity 85.77
Shannon entropy 0.21708
G+C content 0.62511
Mean single sequence MFE -28.27
Consensus MFE -20.73
Energy contribution -21.73
Covariance contribution 1.00
Combinations/Pair 1.04
Mean z-score -2.46
Structure conservation index 0.73
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.33
SVM RNA-class probability 0.927335
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 6972597 88 - 21146708
CGAGUGGCUCAGUGCAUUGGGGCUCACUUGAGCCGAUCUGAGCCACGUUGAGCUCGACUUGGCCUAAACACCGUCAAG--CCCCCUUCUG
((((((((((((........(((((....)))))...))))))))).))).(((.(((..((........))))).))--)......... ( -30.80, z-score =  -1.29, R)
>droSim1.chr2R 5513563 80 - 19596830
CGAGUGGCUCAGUGC---------CAC-UGAGCCGAUCUGAGCCACGUUGAGCUCGACUUGGCCUAAACCCCGCCAAGCCCCCCCUUCUG
.((.((((((((...---------..)-))))))).))((((((.....).))))).((((((.........))))))............ ( -27.90, z-score =  -3.31, R)
>droSec1.super_1 4539815 78 - 14215200
CGAGUGGCUCAGUGC---------CAC-UGAGCCGAUCUGAGCCACGUUGAGCUCGACUUGGCCUAAACCCCGCCAAG--CCCCCUUCUG
.((.((((((((...---------..)-))))))).))((((((.....).))))).((((((.........))))))--.......... ( -27.90, z-score =  -3.10, R)
>droYak2.chr2R 18968538 73 + 21139217
CGAGUGGCU---------------CACCUGAGCCGAUCGGAGCCACGUUGAGCUCGACUUGGCCCAAACCGCGUCAAG--CCCCCUUCUG
.((.(((((---------------(....)))))).))((.((((.((((....)))).)))))).....((.....)--)......... ( -26.50, z-score =  -2.11, R)
>consensus
CGAGUGGCUCAGUGC_________CAC_UGAGCCGAUCUGAGCCACGUUGAGCUCGACUUGGCCUAAACCCCGCCAAG__CCCCCUUCUG
.((.((((((((((..........))).))))))).)).(((((.....).))))..((((((.........))))))............ (-20.73 = -21.73 +   1.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:14:27 2011