Locus 9510

Sequence ID dm3.chr3R
Location 7,127,022 – 7,127,146
Length 124
Max. P 0.992809
window13043 window13044 window13045

overview

Window 3

Location 7,127,022 – 7,127,124
Length 102
Sequences 7
Columns 118
Reading direction reverse
Mean pairwise identity 72.93
Shannon entropy 0.45812
G+C content 0.51914
Mean single sequence MFE -27.81
Consensus MFE -13.95
Energy contribution -14.30
Covariance contribution 0.35
Combinations/Pair 1.12
Mean z-score -2.84
Structure conservation index 0.50
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.57
SVM RNA-class probability 0.992809
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 7127022 102 - 27905053
UCCACCUCCUGCUGAUUUCGAUGCU------------GCUCCUGAUGCACCUUUGAUAUGCAAUUUAUGCAUGUCAUCUGCG--CUGC--GUCUGCGUCCAUUGUCCUCCGGAUUUUC
......(((.(..(((...(((((.------------......((((((((..(((((((((.....)))))))))...).)--.)))--))).)))))....)))..).)))..... ( -27.40, z-score =  -2.83, R)
>droSec1.super_0 6292933 102 + 21120651
UCCACCUCCUGCUGAUUUCGAUGCU------------GCUCCUGAUGCACCUUUGAUAUGCAAUUUAUGCAUGUCAUCUGCG--CUGC--GUCUGCGUCCAUUGUCCUCCGGAUUUUC
......(((.(..(((...(((((.------------......((((((((..(((((((((.....)))))))))...).)--.)))--))).)))))....)))..).)))..... ( -27.40, z-score =  -2.83, R)
>droYak2.chr3R 11162844 114 - 28832112
UCCACCUCCUGCUGAUUUCGAUGCUGCUGCUGAUGCCGCUCCUGAUGCACCUUUGAUAUGCAAUUUAUGCAUGUCAUCUCCG--CUGC--GUCUGCGUCCAUUGUCCUCCGGAGUUUU
.....((((.(..(((...(((((.((.((....)).))....((((((.(..(((((((((.....))))))))).....)--.)))--))).)))))....)))..).)))).... ( -34.80, z-score =  -3.67, R)
>droAna3.scaffold_13340 12998660 93 + 23697760
-------------GCUGCUGAUGCU------------GCUCCUGAUGCACCUUUGAUAUGCAAUUUAUGCAUGUCAUCUGUGCCCUGCGAGUCUGCGUCCAUUGUCCUGUGAAAAGUG
-------------...((((((((.------------(((((....((((...(((((((((.....)))))))))...))))...).))))..)))))(((......)))...))). ( -29.00, z-score =  -3.59, R)
>dp4.chr2 1507967 83 + 30794189
--------CUGGUGCUGCCGCUGCU------------CCUCCCGAUGCACCUUUGAUAUGCAAUUUAUGCAUGUCAUCUGUGCGCUGC--GUCUGCGUCCAUUGU-------------
--------.((((((.(.(((.(((------------(.....)).((((...(((((((((.....)))))))))...)))))).))--).).))).)))....------------- ( -29.60, z-score =  -3.56, R)
>droPer1.super_6 1529435 83 + 6141320
--------CUGGUGCUGCCGCUGCU------------CCUCCCGAUGCACCUUUGAUAUGCAAUUUAUGCAUGUCAUCUGUGCGCUGC--GUCUGCGUCCAUUGU-------------
--------.((((((.(.(((.(((------------(.....)).((((...(((((((((.....)))))))))...)))))).))--).).))).)))....------------- ( -29.60, z-score =  -3.56, R)
>droVir3.scaffold_13047 15866635 80 + 19223366
-------------GCUGCCGCCGCU------------GCUCCUGAUGCACCUUUGAUAUGCAAUUUAUGCACGUCAUCUGCG--CUGC--GCUCAAAUCCAUUGUGUCC---------
-------------((.((.((.(((------------((.......)))....(((..((((.....))))..)))...)))--).))--)).................--------- ( -16.90, z-score =   0.13, R)
>consensus
________CUGCUGCUGCCGAUGCU____________GCUCCUGAUGCACCUUUGAUAUGCAAUUUAUGCAUGUCAUCUGCG__CUGC__GUCUGCGUCCAUUGUCCUC_G_A___U_
...........................................((((((....(((((((((.....)))))))))...((.....)).....))))))................... (-13.95 = -14.30 +   0.35)

alignment

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secondary structure

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dotplot

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Window 4

Location 7,127,056 – 7,127,146
Length 90
Sequences 5
Columns 90
Reading direction forward
Mean pairwise identity 73.79
Shannon entropy 0.44292
G+C content 0.52902
Mean single sequence MFE -20.37
Consensus MFE -12.24
Energy contribution -12.64
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -1.56
Structure conservation index 0.60
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.82
SVM RNA-class probability 0.826114
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 7127056 90 + 27905053
CAGAUGACAUGCAUAAAUUGCAUAUCAAAGGUGCAUCAGGAGCAGCAUCGAAAUCAGCAGGAGGUGGAGCGGGAGCAGGAGGUGGACCAG
....(((.(((((.....))))).)))..(((.((((........((((.............))))..((....))....)))).))).. ( -23.62, z-score =  -2.07, R)
>droSec1.super_0 6292967 90 - 21120651
CAGAUGACAUGCAUAAAUUGCAUAUCAAAGGUGCAUCAGGAGCAGCAUCGAAAUCAGCAGGAGGUGGAGCGGGAGCAGGAGGUGGAGCAG
....(((.(((((.....))))).)))..(.(.((((........((((.............))))..((....))....)))).).).. ( -19.12, z-score =  -0.67, R)
>droAna3.scaffold_13340 12998698 76 - 23697760
CAGAUGACAUGCAUAAAUUGCAUAUCAAAGGUGCAUCAGGAGCAGCAUCAGCAGCCAGAAUCAGCGGCCAGCGAGG--------------
....(((.(((((.....))))).)))..(((((..........))))).((.(((.........)))..))....-------------- ( -17.90, z-score =  -0.40, R)
>dp4.chr2 1507990 80 - 30794189
CAGAUGACAUGCAUAAAUUGCAUAUCAAAGGUGCAUCGGGAGGAGCAGCGGCAGCACCAGAGGAAGAGGAGGAGGCAUCG----------
..((((.((((((.....)))))......(((((.((....)).((....)).)))))...............).)))).---------- ( -20.60, z-score =  -2.35, R)
>droPer1.super_6 1529458 80 - 6141320
CAGAUGACAUGCAUAAAUUGCAUAUCAAAGGUGCAUCGGGAGGAGCAGCGGCAGCACCAGAGGAGGAGGAGGAGGCAUCG----------
..((((.((((((.....)))))......(((((.((....)).((....)).)))))...............).)))).---------- ( -20.60, z-score =  -2.31, R)
>consensus
CAGAUGACAUGCAUAAAUUGCAUAUCAAAGGUGCAUCAGGAGCAGCAUCGGCAGCACCAGAAGGUGGAGAGGGAGCAGCA__________
....(((.(((((.....))))).)))..(((((..(....)..)))))......................................... (-12.24 = -12.64 +   0.40)

alignment

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secondary structure

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dotplot

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Window 5

Location 7,127,056 – 7,127,146
Length 90
Sequences 5
Columns 90
Reading direction reverse
Mean pairwise identity 73.79
Shannon entropy 0.44292
G+C content 0.52902
Mean single sequence MFE -17.34
Consensus MFE -11.94
Energy contribution -11.94
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.97
Structure conservation index 0.69
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.06
SVM RNA-class probability 0.980887
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 7127056 90 - 27905053
CUGGUCCACCUCCUGCUCCCGCUCCACCUCCUGCUGAUUUCGAUGCUGCUCCUGAUGCACCUUUGAUAUGCAAUUUAUGCAUGUCAUCUG
..(((.((.(....((....((((....((.....))....)).)).))....).)).)))..(((((((((.....))))))))).... ( -15.80, z-score =  -1.14, R)
>droSec1.super_0 6292967 90 + 21120651
CUGCUCCACCUCCUGCUCCCGCUCCACCUCCUGCUGAUUUCGAUGCUGCUCCUGAUGCACCUUUGAUAUGCAAUUUAUGCAUGUCAUCUG
.(((..((......((((..((..........)).(....))).))......))..)))....(((((((((.....))))))))).... ( -14.50, z-score =  -1.47, R)
>droAna3.scaffold_13340 12998698 76 + 23697760
--------------CCUCGCUGGCCGCUGAUUCUGGCUGCUGAUGCUGCUCCUGAUGCACCUUUGAUAUGCAAUUUAUGCAUGUCAUCUG
--------------....((.(((.(((......))).)))...))(((.......)))....(((((((((.....))))))))).... ( -20.40, z-score =  -1.45, R)
>dp4.chr2 1507990 80 + 30794189
----------CGAUGCCUCCUCCUCUUCCUCUGGUGCUGCCGCUGCUCCUCCCGAUGCACCUUUGAUAUGCAAUUUAUGCAUGUCAUCUG
----------.(((..................(((((...((..........))..)))))...((((((((.....))))))))))).. ( -18.00, z-score =  -2.85, R)
>droPer1.super_6 1529458 80 + 6141320
----------CGAUGCCUCCUCCUCCUCCUCUGGUGCUGCCGCUGCUCCUCCCGAUGCACCUUUGAUAUGCAAUUUAUGCAUGUCAUCUG
----------.(((..................(((((...((..........))..)))))...((((((((.....))))))))))).. ( -18.00, z-score =  -2.93, R)
>consensus
__________CCAUGCUCCCUCCCCACCCCCUGCUGCUGCCGAUGCUGCUCCUGAUGCACCUUUGAUAUGCAAUUUAUGCAUGUCAUCUG
.........................................(.(((..........))).)..(((((((((.....))))))))).... (-11.94 = -11.94 +   0.00)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:05:49 2011