Locus 7780

Sequence ID dm3.chr3L
Location 17,248,684 – 17,248,735
Length 51
Max. P 0.983816
window10702 window10703

overview

Window 2

Location 17,248,684 – 17,248,735
Length 51
Sequences 4
Columns 53
Reading direction forward
Mean pairwise identity 91.99
Shannon entropy 0.12602
G+C content 0.53912
Mean single sequence MFE -14.50
Consensus MFE -12.62
Energy contribution -12.62
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.06
Structure conservation index 0.87
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.15
SVM RNA-class probability 0.899796
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 17248684 51 + 24543557
--CGGAAGCUCUAUCCGAUUUUUCCGAGUGCAUCUGCAGUUGCCGCUGCACUC
--.(((((.((.....))..)))))(((((((.(.((....)).).))))))) ( -16.40, z-score =  -2.09, R)
>droYak2.chr3L 7373052 53 - 24197627
CACAAAACCUCUAUCCGCUUUUUCUGAGUGCAUCUGCAGUUGCCGCUGCACUC
.........................(((((((.(.((....)).).))))))) ( -12.40, z-score =  -2.10, R)
>droSec1.super_0 9299503 51 + 21120651
--CGAAAGCUCCAUCCGAUUUUUCCGAGUGCAUCUGCAGUUGCCGCUGCACUC
--.(((((.((.....)).))))).(((((((.(.((....)).).))))))) ( -14.60, z-score =  -2.02, R)
>droSim1.chr3L 16583795 51 + 22553184
--CGAAAGCUCCAUCCGAUUUUUCCGAGUGCAUCUGCAGUUGCCGCUGCACUC
--.(((((.((.....)).))))).(((((((.(.((....)).).))))))) ( -14.60, z-score =  -2.02, R)
>consensus
__CGAAAGCUCCAUCCGAUUUUUCCGAGUGCAUCUGCAGUUGCCGCUGCACUC
.........................(((((((.(.((....)).).))))))) (-12.62 = -12.62 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 17,248,684 – 17,248,735
Length 51
Sequences 4
Columns 53
Reading direction reverse
Mean pairwise identity 91.99
Shannon entropy 0.12602
G+C content 0.53912
Mean single sequence MFE -18.15
Consensus MFE -16.96
Energy contribution -16.65
Covariance contribution -0.31
Combinations/Pair 1.13
Mean z-score -2.42
Structure conservation index 0.93
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.15
SVM RNA-class probability 0.983816
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 17248684 51 - 24543557
GAGUGCAGCGGCAACUGCAGAUGCACUCGGAAAAAUCGGAUAGAGCUUCCG--
(((((((...((....))...)))))))((((...((.....))..)))).-- ( -20.10, z-score =  -3.17, R)
>droYak2.chr3L 7373052 53 + 24197627
GAGUGCAGCGGCAACUGCAGAUGCACUCAGAAAAAGCGGAUAGAGGUUUUGUG
(((((((...((....))...)))))))....(((((........)))))... ( -16.50, z-score =  -1.96, R)
>droSec1.super_0 9299503 51 - 21120651
GAGUGCAGCGGCAACUGCAGAUGCACUCGGAAAAAUCGGAUGGAGCUUUCG--
(((((((...((....))...))))))).((((..((.....))..)))).-- ( -18.00, z-score =  -2.28, R)
>droSim1.chr3L 16583795 51 - 22553184
GAGUGCAGCGGCAACUGCAGAUGCACUCGGAAAAAUCGGAUGGAGCUUUCG--
(((((((...((....))...))))))).((((..((.....))..)))).-- ( -18.00, z-score =  -2.28, R)
>consensus
GAGUGCAGCGGCAACUGCAGAUGCACUCGGAAAAAUCGGAUAGAGCUUUCG__
(((((((...((....))...)))))))((((...((.....))..))))... (-16.96 = -16.65 +  -0.31)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:33:16 2011