Locus 3832

Sequence ID dm3.chr2R
Location 8,221,739 – 8,221,809
Length 70
Max. P 0.956252
window5252 window5253

overview

Window 2

Location 8,221,739 – 8,221,809
Length 70
Sequences 14
Columns 73
Reading direction forward
Mean pairwise identity 96.40
Shannon entropy 0.08936
G+C content 0.59658
Mean single sequence MFE -26.66
Consensus MFE -23.63
Energy contribution -24.01
Covariance contribution 0.38
Combinations/Pair 1.05
Mean z-score -2.39
Structure conservation index 0.89
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.63
SVM RNA-class probability 0.956252
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 8221739 70 + 21146708
GCCGUGACCAGGAUUCGAACCUGGGUUACCACGGCCACAACGUGGGGUCCUAACCACUAG---ACGAUCACGG
.(((((((((((.......)))))(((.(((((.......)))))(((....)))....)---))..)))))) ( -27.30, z-score =  -2.33, R)
>droSim1.chr2R 6690466 70 + 19596830
GCCGUGACCAGGAUUCGAACCUGGGUUACCACGGCCACAACGUGGGGUCCUAACCACUAG---ACGAUCACGG
.(((((((((((.......)))))(((.(((((.......)))))(((....)))....)---))..)))))) ( -27.30, z-score =  -2.33, R)
>droSec1.super_1 5767637 70 + 14215200
GCCGUGACCAGGAUUCGAACCUGGGUUACCACGGCCACAACGUGGGGUCCUAACCACUAG---ACGAUCACGG
.(((((((((((.......)))))(((.(((((.......)))))(((....)))....)---))..)))))) ( -27.30, z-score =  -2.33, R)
>droYak2.chr2R 12410438 70 - 21139217
GCCGUGACCAGGAUUCGAACCUGGGUUACCACGGCCACAACGUGGGGUCCUAACCACUAG---ACGAUCACGG
.(((((((((((.......)))))(((.(((((.......)))))(((....)))....)---))..)))))) ( -27.30, z-score =  -2.33, R)
>droEre2.scaffold_4845 5018593 70 - 22589142
GCCGUGACCAGGAUUCGAACCUGGGUUACCACGGCCACAACGUGGGGUCCUAACCACUAG---ACGAUCACGG
.(((((((((((.......)))))(((.(((((.......)))))(((....)))....)---))..)))))) ( -27.30, z-score =  -2.33, R)
>droAna3.scaffold_13266 5513618 70 + 19884421
GCCGUGACCAGGAUUCGAACCUGGGUUACCACGGCCACAACGUGGGGUCCUAACCACUAG---ACGAUCACGG
.(((((((((((.......)))))(((.(((((.......)))))(((....)))....)---))..)))))) ( -27.30, z-score =  -2.33, R)
>dp4.chr3 16979181 70 - 19779522
GCCGUGACCAGGAUUCGAACCUGGGUUACCACGGCCACAACGUGGGGUCCUAACCACUAG---ACGAUCACGG
.(((((((((((.......)))))(((.(((((.......)))))(((....)))....)---))..)))))) ( -27.30, z-score =  -2.33, R)
>droPer1.super_2 6045958 70 - 9036312
GCCGUGACCAGGAUUCGAACCUGGGUUACCACGGCCACAACGUGGGGUCCUAACCACUAG---ACGAUCACGG
.(((((((((((.......)))))(((.(((((.......)))))(((....)))....)---))..)))))) ( -27.30, z-score =  -2.33, R)
>droWil1.scaffold_180745 460670 70 + 2843958
GCCGUGACCAGGAUUCGAACCUGGGUUACCACGGCCACAACGUGGGGUCCUAACCACUAG---ACGAUCACGG
.(((((((((((.......)))))(((.(((((.......)))))(((....)))....)---))..)))))) ( -27.30, z-score =  -2.33, R)
>droVir3.scaffold_13324 2649809 70 + 2960039
GCCGUGACCAGGAUUCGAACCUGGGUUACCACGGCCACAACGUGGGGUCCUAACCACUAG---ACGAUCACGG
.(((((((((((.......)))))(((.(((((.......)))))(((....)))....)---))..)))))) ( -27.30, z-score =  -2.33, R)
>droMoj3.scaffold_6496 642387 70 - 26866924
GCCGUGACCAGGAUUCGAACCUGGGUUACCACGGCCACAACGUGGGGUCCUAACCACUAG---ACGAUCACGG
.(((((((((((.......)))))(((.(((((.......)))))(((....)))....)---))..)))))) ( -27.30, z-score =  -2.33, R)
>droGri2.scaffold_15112 4901074 70 + 5172618
GCCGUGACCAGGAUUCGAACCUGGGUUACCACGGCCACAACGUGGGGUCCUAACCACUAG---ACGAUCACGG
.(((((((((((.......)))))(((.(((((.......)))))(((....)))....)---))..)))))) ( -27.30, z-score =  -2.33, R)
>anoGam1.chr2L 19553485 70 - 48795086
GCCGUGACCAGGAUUCGAACCUGGGUUACUACGGCCACAACGUAGGGUCCUAACCACUAG---ACGAUCACGG
.(((((((((((.......)))))(((.(((((.......)))))(((....)))....)---))..)))))) ( -25.30, z-score =  -2.45, R)
>triCas2.ChLG7 1603140 62 + 17478683
GCCGUGACCAGGAUUCGAACCUGGUUUACUACGGCC-----------UCCUAACCACUAGCCGACGAUCACGG
.(((((((((((.......))))).......((((.-----------............))))....)))))) ( -20.32, z-score =  -3.06, R)
>consensus
GCCGUGACCAGGAUUCGAACCUGGGUUACCACGGCCACAACGUGGGGUCCUAACCACUAG___ACGAUCACGG
.(((((((((((.......)))))....(((((.......)))))(((....)))............)))))) (-23.63 = -24.01 +   0.38)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 8,221,739 – 8,221,809
Length 70
Sequences 14
Columns 73
Reading direction reverse
Mean pairwise identity 96.40
Shannon entropy 0.08936
G+C content 0.59658
Mean single sequence MFE -24.95
Consensus MFE -24.43
Energy contribution -24.54
Covariance contribution 0.11
Combinations/Pair 1.04
Mean z-score -1.13
Structure conservation index 0.98
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.60
SVM RNA-class probability 0.756562
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 8221739 70 - 21146708
CCGUGAUCGU---CUAGUGGUUAGGACCCCACGUUGUGGCCGUGGUAACCCAGGUUCGAAUCCUGGUCACGGC
((((((....---(((.((((((.(((.....))).)))))))))....(((((.......))))))))))). ( -25.10, z-score =  -1.00, R)
>droSim1.chr2R 6690466 70 - 19596830
CCGUGAUCGU---CUAGUGGUUAGGACCCCACGUUGUGGCCGUGGUAACCCAGGUUCGAAUCCUGGUCACGGC
((((((....---(((.((((((.(((.....))).)))))))))....(((((.......))))))))))). ( -25.10, z-score =  -1.00, R)
>droSec1.super_1 5767637 70 - 14215200
CCGUGAUCGU---CUAGUGGUUAGGACCCCACGUUGUGGCCGUGGUAACCCAGGUUCGAAUCCUGGUCACGGC
((((((....---(((.((((((.(((.....))).)))))))))....(((((.......))))))))))). ( -25.10, z-score =  -1.00, R)
>droYak2.chr2R 12410438 70 + 21139217
CCGUGAUCGU---CUAGUGGUUAGGACCCCACGUUGUGGCCGUGGUAACCCAGGUUCGAAUCCUGGUCACGGC
((((((....---(((.((((((.(((.....))).)))))))))....(((((.......))))))))))). ( -25.10, z-score =  -1.00, R)
>droEre2.scaffold_4845 5018593 70 + 22589142
CCGUGAUCGU---CUAGUGGUUAGGACCCCACGUUGUGGCCGUGGUAACCCAGGUUCGAAUCCUGGUCACGGC
((((((....---(((.((((((.(((.....))).)))))))))....(((((.......))))))))))). ( -25.10, z-score =  -1.00, R)
>droAna3.scaffold_13266 5513618 70 - 19884421
CCGUGAUCGU---CUAGUGGUUAGGACCCCACGUUGUGGCCGUGGUAACCCAGGUUCGAAUCCUGGUCACGGC
((((((....---(((.((((((.(((.....))).)))))))))....(((((.......))))))))))). ( -25.10, z-score =  -1.00, R)
>dp4.chr3 16979181 70 + 19779522
CCGUGAUCGU---CUAGUGGUUAGGACCCCACGUUGUGGCCGUGGUAACCCAGGUUCGAAUCCUGGUCACGGC
((((((....---(((.((((((.(((.....))).)))))))))....(((((.......))))))))))). ( -25.10, z-score =  -1.00, R)
>droPer1.super_2 6045958 70 + 9036312
CCGUGAUCGU---CUAGUGGUUAGGACCCCACGUUGUGGCCGUGGUAACCCAGGUUCGAAUCCUGGUCACGGC
((((((....---(((.((((((.(((.....))).)))))))))....(((((.......))))))))))). ( -25.10, z-score =  -1.00, R)
>droWil1.scaffold_180745 460670 70 - 2843958
CCGUGAUCGU---CUAGUGGUUAGGACCCCACGUUGUGGCCGUGGUAACCCAGGUUCGAAUCCUGGUCACGGC
((((((....---(((.((((((.(((.....))).)))))))))....(((((.......))))))))))). ( -25.10, z-score =  -1.00, R)
>droVir3.scaffold_13324 2649809 70 - 2960039
CCGUGAUCGU---CUAGUGGUUAGGACCCCACGUUGUGGCCGUGGUAACCCAGGUUCGAAUCCUGGUCACGGC
((((((....---(((.((((((.(((.....))).)))))))))....(((((.......))))))))))). ( -25.10, z-score =  -1.00, R)
>droMoj3.scaffold_6496 642387 70 + 26866924
CCGUGAUCGU---CUAGUGGUUAGGACCCCACGUUGUGGCCGUGGUAACCCAGGUUCGAAUCCUGGUCACGGC
((((((....---(((.((((((.(((.....))).)))))))))....(((((.......))))))))))). ( -25.10, z-score =  -1.00, R)
>droGri2.scaffold_15112 4901074 70 - 5172618
CCGUGAUCGU---CUAGUGGUUAGGACCCCACGUUGUGGCCGUGGUAACCCAGGUUCGAAUCCUGGUCACGGC
((((((....---(((.((((((.(((.....))).)))))))))....(((((.......))))))))))). ( -25.10, z-score =  -1.00, R)
>anoGam1.chr2L 19553485 70 + 48795086
CCGUGAUCGU---CUAGUGGUUAGGACCCUACGUUGUGGCCGUAGUAACCCAGGUUCGAAUCCUGGUCACGGC
((((((....---(((.((((((.(((.....))).)))))))))....(((((.......))))))))))). ( -25.40, z-score =  -1.78, R)
>triCas2.ChLG7 1603140 62 - 17478683
CCGUGAUCGUCGGCUAGUGGUUAGGA-----------GGCCGUAGUAAACCAGGUUCGAAUCCUGGUCACGGC
((((((......((((.(((((....-----------)))))))))...(((((.......))))))))))). ( -22.70, z-score =  -2.09, R)
>consensus
CCGUGAUCGU___CUAGUGGUUAGGACCCCACGUUGUGGCCGUGGUAACCCAGGUUCGAAUCCUGGUCACGGC
((((((.......(((.((((((.(((.....))).)))))))))....(((((.......))))))))))). (-24.43 = -24.54 +   0.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:17:38 2011