Locus 13435

Sequence ID dm3.chrX
Location 6,531,112 – 6,531,180
Length 68
Max. P 0.976449
window18501 window18502

overview

Window 1

Location 6,531,112 – 6,531,180
Length 68
Sequences 5
Columns 69
Reading direction forward
Mean pairwise identity 97.95
Shannon entropy 0.03500
G+C content 0.49557
Mean single sequence MFE -14.92
Consensus MFE -14.61
Energy contribution -14.61
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.37
Structure conservation index 0.98
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.77
SVM RNA-class probability 0.813474
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 6531112 68 + 22422827
GACAACUGCCAGACGGGAACCAACUGGCAGUCCGAAA-CUCUUAACUCUUUUAACUUCGAACUCCCGGA
....((((((((..((...))..))))))))......-.................((((......)))) ( -15.10, z-score =  -1.39, R)
>droSim1.chrX 5133414 68 + 17042790
GACAACUGCCAGACGGGAACCAACUGGCAGUCCGAAA-CUCUUAACUCUUUUAACUUCGAACUCCUGGA
....((((((((..((...))..)))))))).((((.-.................)))).......... ( -14.67, z-score =  -1.44, R)
>droSec1.super_4 5905687 68 - 6179234
GACAACUGCCAGACGGGAACCAACUGGCAGUCCGAAA-CUCUUAACUCUUUUAACUUCGAACUCCUGGA
....((((((((..((...))..)))))))).((((.-.................)))).......... ( -14.67, z-score =  -1.44, R)
>droYak2.chrX 2494153 68 + 21770863
GACAACUGCCAGACGGGAACCAACUGGCAGUCCGAAA-CUCUUAACUCUUUUAACUUCGAACUCCCGGA
....((((((((..((...))..))))))))......-.................((((......)))) ( -15.10, z-score =  -1.39, R)
>droEre2.scaffold_4690 15458300 69 + 18748788
GACAACUGCCAGACGGGAACCAACUGGCAGUCCGAAAACUCUUAACUCUUUUAACUUCGAACUCCCGGG
....((((((((..((...))..))))))))(((...............................))). ( -15.08, z-score =  -1.20, R)
>consensus
GACAACUGCCAGACGGGAACCAACUGGCAGUCCGAAA_CUCUUAACUCUUUUAACUUCGAACUCCCGGA
....((((((((..((...))..)))))))).((((...................)))).......... (-14.61 = -14.61 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 6,531,112 – 6,531,180
Length 68
Sequences 5
Columns 69
Reading direction reverse
Mean pairwise identity 97.95
Shannon entropy 0.03500
G+C content 0.49557
Mean single sequence MFE -21.90
Consensus MFE -19.91
Energy contribution -20.31
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -2.71
Structure conservation index 0.91
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.95
SVM RNA-class probability 0.976449
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 6531112 68 - 22422827
UCCGGGAGUUCGAAGUUAAAAGAGUUAAGAG-UUUCGGACUGCCAGUUGGUUCCCGUCUGGCAGUUGUC
((((..(.((..((.((....)).))..)).-)..))))(((((((.(((...))).)))))))..... ( -23.60, z-score =  -3.17, R)
>droSim1.chrX 5133414 68 - 17042790
UCCAGGAGUUCGAAGUUAAAAGAGUUAAGAG-UUUCGGACUGCCAGUUGGUUCCCGUCUGGCAGUUGUC
....(((..((.................)).-.))).(((((((((.(((...))).)))))))))... ( -19.43, z-score =  -2.12, R)
>droSec1.super_4 5905687 68 + 6179234
UCCAGGAGUUCGAAGUUAAAAGAGUUAAGAG-UUUCGGACUGCCAGUUGGUUCCCGUCUGGCAGUUGUC
....(((..((.................)).-.))).(((((((((.(((...))).)))))))))... ( -19.43, z-score =  -2.12, R)
>droYak2.chrX 2494153 68 - 21770863
UCCGGGAGUUCGAAGUUAAAAGAGUUAAGAG-UUUCGGACUGCCAGUUGGUUCCCGUCUGGCAGUUGUC
((((..(.((..((.((....)).))..)).-)..))))(((((((.(((...))).)))))))..... ( -23.60, z-score =  -3.17, R)
>droEre2.scaffold_4690 15458300 69 - 18748788
CCCGGGAGUUCGAAGUUAAAAGAGUUAAGAGUUUUCGGACUGCCAGUUGGUUCCCGUCUGGCAGUUGUC
.(((..(..((.................))..)..)))((((((((.(((...))).)))))))).... ( -23.43, z-score =  -2.95, R)
>consensus
UCCGGGAGUUCGAAGUUAAAAGAGUUAAGAG_UUUCGGACUGCCAGUUGGUUCCCGUCUGGCAGUUGUC
.((((((.(((.................))).))))))((((((((.(((...))).)))))))).... (-19.91 = -20.31 +   0.40)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:21:22 2011