Locus 3078

Sequence ID dm3.chr2R
Location 2,059,187 – 2,059,265
Length 78
Max. P 0.807896
window4222 window4223

overview

Window 2

Location 2,059,187 – 2,059,265
Length 78
Sequences 14
Columns 80
Reading direction forward
Mean pairwise identity 84.96
Shannon entropy 0.37086
G+C content 0.53543
Mean single sequence MFE -26.30
Consensus MFE -19.88
Energy contribution -21.27
Covariance contribution 1.39
Combinations/Pair 1.78
Mean z-score -1.35
Structure conservation index 0.76
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.74
SVM RNA-class probability 0.803167
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 2059187 78 + 21146708
ACAUGGUCCUGUGGC--GCAAUGGAUAACGCGUCUGACUACGGAUCAGAAGAUUCCAGGUUCGACUCCUGGCAGGAUCGA
...((((((((((((--((..........))))).......(((((....)))))((((.......))))))))))))). ( -26.90, z-score =  -1.32, R)
>droSec1.super_26 701335 78 + 826190
ACAUGGUCCUGUGGC--GCAAUGGAUAACGCGUCUGACUACGGAUCAGAAGAUUCCAGGUUCGACUCCUGGCAGGAUCGA
...((((((((((((--((..........))))).......(((((....)))))((((.......))))))))))))). ( -26.90, z-score =  -1.32, R)
>droSim1.chr2R 953932 78 + 19596830
ACAUGGUCCUGUGGC--GCAAUGGAUAACGCGUCUGACUACGGAUCAGAAGAUUCCAGGUUCGACUCCUGGCAGGAUCGA
...((((((((((((--((..........))))).......(((((....)))))((((.......))))))))))))). ( -26.90, z-score =  -1.32, R)
>droYak2.chr2L 1906229 78 - 22324452
AUGUGGUCCUGUGGC--GCAAUGGAUAACGCGUCUGACUACGGAUCAGAAGAUUCCAGGUUCGACUCCUGGCAGGAUCGG
...((((((((((((--((..........))))).......(((((....)))))((((.......))))))))))))). ( -26.80, z-score =  -1.10, R)
>droEre2.scaffold_4929 6368344 78 - 26641161
AUGCGGUCCUGUGGC--GCAAUGGAUAACGCGUCUGACUACGGAUCAGAAGAUUCCAGGUUCGACUCCUGGCAGGAUCGA
...((((((((((((--((..........))))).......(((((....)))))((((.......))))))))))))). ( -28.60, z-score =  -1.55, R)
>dp4.chr3 17983685 78 + 19779522
AUGCGGUCCUGUGGC--GCAAUGGAUAACGCGUCUGACUACGGAUCAGAAGAUUCCAGGUUCGACUCCUGGCAGGAUCGA
...((((((((((((--((..........))))).......(((((....)))))((((.......))))))))))))). ( -28.60, z-score =  -1.55, R)
>droPer1.super_73 194627 78 - 267513
AUGCGGUCCUGUGGC--GCAAUGGAUAACGCGUCUGACUACGGAUCAGAAGAUUCCAGGUUCGACUCCUGGCAGGAUCGA
...((((((((((((--((..........))))).......(((((....)))))((((.......))))))))))))). ( -28.60, z-score =  -1.55, R)
>droAna3.scaffold_13266 1140944 75 - 19884421
---UGGUCCUGUGGC--GCAAUGGAUAACGCGUCUGACUACGGAUCAGAAGAUUCCAGGUUCGACUCCUGGCAGGAUCGA
---.(((((((((((--((..........))))).......(((((....)))))((((.......)))))))))))).. ( -26.60, z-score =  -1.40, R)
>droWil1.scaffold_180700 732170 78 - 6630534
ACACGGUCCUGUGGC--GCAAUGGAUAACGCGUCUGACUACGGAUCAGAAGAUUCCAGGUUCGACUCCUGGCAGGAUCGA
...((((((((((((--((..........))))).......(((((....)))))((((.......))))))))))))). ( -28.90, z-score =  -1.90, R)
>droVir3.scaffold_12875 4787536 78 + 20611582
AGGCGGUCCUGUGGC--GCAAUGGAUAACGCGUCUGACUACGGAUCAGAAGAUUCCAGGUUCGACUCCUGGCAGGAUCGA
...((((((((((((--((..........))))).......(((((....)))))((((.......))))))))))))). ( -28.60, z-score =  -1.32, R)
>droGri2.scaffold_15245 18126394 74 - 18325388
----GGUCCUGUGGC--GCAAUGGAUAACGCGUCUGACUACGGAUCAGAAGAUUCCAGGUUCGACUCCUGGCAGGAUCGC
----(((((((((((--((..........))))).......(((((....)))))((((.......)))))))))))).. ( -26.60, z-score =  -1.52, R)
>droMoj3.scaffold_6496 1583425 74 - 26866924
----GGUCCUGUGGC--GCAAUGGAUAACGCGUCUGACUACGGAUCAGAAGAUUCCAGGUUCGACUCCUGGCAGGAUCGA
----(((((((((((--((..........))))).......(((((....)))))((((.......)))))))))))).. ( -26.60, z-score =  -1.44, R)
>anoGam1.chr2R 5380044 77 - 62725911
AGAAGACUCCGUGGC--GCAACGG-UAGCGCGUCUGACUCCAGAUCAGAAGGUUGCGUGUUCAAAUCACGUCGGGGUCAA
....(((((((..((--((.....-..)))).((((((....).))))).....(((((.......)))))))))))).. ( -26.60, z-score =  -1.35, R)
>triCas2.chrUn_82 83276 69 + 117267
--ACAGUCUUAUUACUAGCGAUCCUUAAUGCGAAUGGUUAUCG--CAAAAUAUCA-GGAUUUGAGUUUUUUUGU------
--((((....(..(((...((((((...(((((.......)))--)).......)-)))))..)))..).))))------ ( -11.00, z-score =  -0.27, R)
>consensus
A_ACGGUCCUGUGGC__GCAAUGGAUAACGCGUCUGACUACGGAUCAGAAGAUUCCAGGUUCGACUCCUGGCAGGAUCGA
....(((((((.....................((((((....).))))).....(((((.......)))))))))))).. (-19.88 = -21.27 +   1.39)

alignment

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secondary structure

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dotplot

Postscript

Window 3

Location 2,059,187 – 2,059,265
Length 78
Sequences 14
Columns 80
Reading direction reverse
Mean pairwise identity 84.96
Shannon entropy 0.37086
G+C content 0.53543
Mean single sequence MFE -23.02
Consensus MFE -16.06
Energy contribution -16.19
Covariance contribution 0.12
Combinations/Pair 1.41
Mean z-score -1.55
Structure conservation index 0.70
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.75
SVM RNA-class probability 0.807896
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 2059187 78 - 21146708
UCGAUCCUGCCAGGAGUCGAACCUGGAAUCUUCUGAUCCGUAGUCAGACGCGUUAUCCAUUGC--GCCACAGGACCAUGU
..(.((((((((((.......))))).....((((((.....)))))).((((........))--))..))))).).... ( -23.80, z-score =  -1.40, R)
>droSec1.super_26 701335 78 - 826190
UCGAUCCUGCCAGGAGUCGAACCUGGAAUCUUCUGAUCCGUAGUCAGACGCGUUAUCCAUUGC--GCCACAGGACCAUGU
..(.((((((((((.......))))).....((((((.....)))))).((((........))--))..))))).).... ( -23.80, z-score =  -1.40, R)
>droSim1.chr2R 953932 78 - 19596830
UCGAUCCUGCCAGGAGUCGAACCUGGAAUCUUCUGAUCCGUAGUCAGACGCGUUAUCCAUUGC--GCCACAGGACCAUGU
..(.((((((((((.......))))).....((((((.....)))))).((((........))--))..))))).).... ( -23.80, z-score =  -1.40, R)
>droYak2.chr2L 1906229 78 + 22324452
CCGAUCCUGCCAGGAGUCGAACCUGGAAUCUUCUGAUCCGUAGUCAGACGCGUUAUCCAUUGC--GCCACAGGACCACAU
..(.((((((((((.......))))).....((((((.....)))))).((((........))--))..))))).).... ( -23.80, z-score =  -1.82, R)
>droEre2.scaffold_4929 6368344 78 + 26641161
UCGAUCCUGCCAGGAGUCGAACCUGGAAUCUUCUGAUCCGUAGUCAGACGCGUUAUCCAUUGC--GCCACAGGACCGCAU
.((.((((((((((.......))))).....((((((.....)))))).((((........))--))..))))).))... ( -24.70, z-score =  -1.64, R)
>dp4.chr3 17983685 78 - 19779522
UCGAUCCUGCCAGGAGUCGAACCUGGAAUCUUCUGAUCCGUAGUCAGACGCGUUAUCCAUUGC--GCCACAGGACCGCAU
.((.((((((((((.......))))).....((((((.....)))))).((((........))--))..))))).))... ( -24.70, z-score =  -1.64, R)
>droPer1.super_73 194627 78 + 267513
UCGAUCCUGCCAGGAGUCGAACCUGGAAUCUUCUGAUCCGUAGUCAGACGCGUUAUCCAUUGC--GCCACAGGACCGCAU
.((.((((((((((.......))))).....((((((.....)))))).((((........))--))..))))).))... ( -24.70, z-score =  -1.64, R)
>droAna3.scaffold_13266 1140944 75 + 19884421
UCGAUCCUGCCAGGAGUCGAACCUGGAAUCUUCUGAUCCGUAGUCAGACGCGUUAUCCAUUGC--GCCACAGGACCA---
..(.((((((((((.......))))).....((((((.....)))))).((((........))--))..))))).).--- ( -23.80, z-score =  -1.75, R)
>droWil1.scaffold_180700 732170 78 + 6630534
UCGAUCCUGCCAGGAGUCGAACCUGGAAUCUUCUGAUCCGUAGUCAGACGCGUUAUCCAUUGC--GCCACAGGACCGUGU
.((.((((((((((.......))))).....((((((.....)))))).((((........))--))..))))).))... ( -24.90, z-score =  -1.46, R)
>droVir3.scaffold_12875 4787536 78 - 20611582
UCGAUCCUGCCAGGAGUCGAACCUGGAAUCUUCUGAUCCGUAGUCAGACGCGUUAUCCAUUGC--GCCACAGGACCGCCU
.((.((((((((((.......))))).....((((((.....)))))).((((........))--))..))))).))... ( -24.70, z-score =  -1.57, R)
>droGri2.scaffold_15245 18126394 74 + 18325388
GCGAUCCUGCCAGGAGUCGAACCUGGAAUCUUCUGAUCCGUAGUCAGACGCGUUAUCCAUUGC--GCCACAGGACC----
....((((((((((.......))))).....((((((.....)))))).((((........))--))..)))))..---- ( -23.20, z-score =  -1.45, R)
>droMoj3.scaffold_6496 1583425 74 + 26866924
UCGAUCCUGCCAGGAGUCGAACCUGGAAUCUUCUGAUCCGUAGUCAGACGCGUUAUCCAUUGC--GCCACAGGACC----
....((((((((((.......))))).....((((((.....)))))).((((........))--))..)))))..---- ( -23.20, z-score =  -1.60, R)
>anoGam1.chr2R 5380044 77 + 62725911
UUGACCCCGACGUGAUUUGAACACGCAACCUUCUGAUCUGGAGUCAGACGCGCUA-CCGUUGC--GCCACGGAGUCUUCU
..(((.(((.((((.......))))......((((((.....)))))).((((..-.....))--))..))).))).... ( -22.20, z-score =  -1.29, R)
>triCas2.chrUn_82 83276 69 - 117267
------ACAAAAAAACUCAAAUCC-UGAUAUUUUG--CGAUAACCAUUCGCAUUAAGGAUCGCUAGUAAUAAGACUGU--
------........(((...((((-(.......((--(((.......)))))...)))))....)))...........-- ( -11.00, z-score =  -1.64, R)
>consensus
UCGAUCCUGCCAGGAGUCGAACCUGGAAUCUUCUGAUCCGUAGUCAGACGCGUUAUCCAUUGC__GCCACAGGACCGU_U
..(.((((((((((.......))))).....((((((.....)))))).....................))))).).... (-16.06 = -16.19 +   0.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:03:13 2011