Locus 11130

Sequence ID dm3.chr3R
Location 18,841,788 – 18,841,926
Length 138
Max. P 0.995690
window15295 window15296 window15297 window15298

overview

Window 5

Location 18,841,788 – 18,841,899
Length 111
Sequences 5
Columns 111
Reading direction forward
Mean pairwise identity 94.26
Shannon entropy 0.10340
G+C content 0.55716
Mean single sequence MFE -45.70
Consensus MFE -40.92
Energy contribution -40.80
Covariance contribution -0.12
Combinations/Pair 1.11
Mean z-score -2.33
Structure conservation index 0.90
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.69
SVM RNA-class probability 0.961541
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 18841788 111 + 27905053
UCCGCGUCCAGUCCAGCUAGUGCAAUGCAGAAAUUGAUUUGCUGCUGCUCCUGCUGAUGCUGCCACUUCUGAUGGCGGUGCAGUAUUGUGGGUGCGGAUUAGUAGGAAUGA
(((((..(((...((((..(.(((..(((((......)))))...))).)..))))..((((((((....).))))))).........)))..)))))............. ( -39.80, z-score =  -0.96, R)
>droSim1.chr3R 18655820 109 + 27517382
UCCGCGUCCAGU--AGCGAGUGCGAUGCAGAAAUUGAUUUGCUGCUGCUCCUGCUGUUGCUGCCACUUCUGAUGGCGGUGCAGCAUUGUGGGUGCGGAUUAGUCGGAAUGG
(((((..(((((--(((((((.((((......))))))))))))))((...((((((.((((((((....).)))))))))))))..))))..)))))............. ( -47.40, z-score =  -2.71, R)
>droSec1.super_0 19205362 109 + 21120651
UCCGCGUCCAGU--AGCGAGUGCGAUGCAGAAAUUGAUUUGCUGCUGCUCCUGCUGUUGCUGCCACUUCUGAUGGCGGUGCAGCAUUGUGGGUGCGGAUUAGUCGGAAUGG
(((((..(((((--(((((((.((((......))))))))))))))((...((((((.((((((((....).)))))))))))))..))))..)))))............. ( -47.40, z-score =  -2.71, R)
>droYak2.chr3R 19703152 109 + 28832112
UCCGCGUCCAGU--GGCGAGUGCGAUGCAGAAAUUGAUUUGCCGCUGCUCCUGCUGUUGCUGCCACUUCUGAUGGCGGUGCAGCAUUGUGGGUGCGGAUUAGUCGGAAUGG
(((((..(((((--(((((((.((((......))))))))))))))((...((((((.((((((((....).)))))))))))))..))))..)))))............. ( -49.00, z-score =  -2.83, R)
>droEre2.scaffold_4820 1242387 106 - 10470090
UCCACGUCCAGU--AGCGAGUGCGAUGCAGAAAUUGAUUUGC---UGCCCCUGCUGUUGCUGCCACUUCUGAUGGCGGUGCAGCAUUGUGGGCGCGGAUUAGUCGGAAUGG
(((.((((((((--(((((((.((((......))))))))))---)))...((((((.((((((((....).)))))))))))))...)))))).)))............. ( -44.90, z-score =  -2.42, R)
>consensus
UCCGCGUCCAGU__AGCGAGUGCGAUGCAGAAAUUGAUUUGCUGCUGCUCCUGCUGUUGCUGCCACUUCUGAUGGCGGUGCAGCAUUGUGGGUGCGGAUUAGUCGGAAUGG
((((((((((((..(((((((.((((......)))))))))))...))...(((((.(((((((((....).)))))))))))))...))))))))))............. (-40.92 = -40.80 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 6

Location 18,841,788 – 18,841,899
Length 111
Sequences 5
Columns 111
Reading direction reverse
Mean pairwise identity 94.26
Shannon entropy 0.10340
G+C content 0.55716
Mean single sequence MFE -34.70
Consensus MFE -30.52
Energy contribution -31.04
Covariance contribution 0.52
Combinations/Pair 1.07
Mean z-score -1.82
Structure conservation index 0.88
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.72
SVM RNA-class probability 0.798933
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 18841788 111 - 27905053
UCAUUCCUACUAAUCCGCACCCACAAUACUGCACCGCCAUCAGAAGUGGCAGCAUCAGCAGGAGCAGCAGCAAAUCAAUUUCUGCAUUGCACUAGCUGGACUGGACGCGGA
.............(((((..(((......(((...(((((.....))))).)))(((((.((.(((((((.(((....)))))))..))).)).)))))..)))..))))) ( -34.10, z-score =  -1.81, R)
>droSim1.chr3R 18655820 109 - 27517382
CCAUUCCGACUAAUCCGCACCCACAAUGCUGCACCGCCAUCAGAAGUGGCAGCAACAGCAGGAGCAGCAGCAAAUCAAUUUCUGCAUCGCACUCGCU--ACUGGACGCGGA
.............(((((..(((...((((((.(((((((.....))))).((....)).)).))))))(((..........)))...((....)).--..)))..))))) ( -34.80, z-score =  -2.07, R)
>droSec1.super_0 19205362 109 - 21120651
CCAUUCCGACUAAUCCGCACCCACAAUGCUGCACCGCCAUCAGAAGUGGCAGCAACAGCAGGAGCAGCAGCAAAUCAAUUUCUGCAUCGCACUCGCU--ACUGGACGCGGA
.............(((((..(((...((((((.(((((((.....))))).((....)).)).))))))(((..........)))...((....)).--..)))..))))) ( -34.80, z-score =  -2.07, R)
>droYak2.chr3R 19703152 109 - 28832112
CCAUUCCGACUAAUCCGCACCCACAAUGCUGCACCGCCAUCAGAAGUGGCAGCAACAGCAGGAGCAGCGGCAAAUCAAUUUCUGCAUCGCACUCGCC--ACUGGACGCGGA
.............(((((..(((....(((((.(((((((.....))))).((....)).)).)))))(((.......................)))--..)))..))))) ( -34.80, z-score =  -1.63, R)
>droEre2.scaffold_4820 1242387 106 + 10470090
CCAUUCCGACUAAUCCGCGCCCACAAUGCUGCACCGCCAUCAGAAGUGGCAGCAACAGCAGGGGCA---GCAAAUCAAUUUCUGCAUCGCACUCGCU--ACUGGACGUGGA
.............((((((.(((...((((((.(((((((.....))))).((....)).)).)))---)))................((....)).--..))).)))))) ( -35.00, z-score =  -1.53, R)
>consensus
CCAUUCCGACUAAUCCGCACCCACAAUGCUGCACCGCCAUCAGAAGUGGCAGCAACAGCAGGAGCAGCAGCAAAUCAAUUUCUGCAUCGCACUCGCU__ACUGGACGCGGA
.............(((((..(((...((((((.(((((((.....))))).((....)).)).))))))(((..........)))...((....)).....)))..))))) (-30.52 = -31.04 +   0.52)

alignment

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secondary structure

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dotplot

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Window 7

Location 18,841,826 – 18,841,926
Length 100
Sequences 6
Columns 104
Reading direction forward
Mean pairwise identity 75.00
Shannon entropy 0.47571
G+C content 0.56199
Mean single sequence MFE -38.40
Consensus MFE -33.29
Energy contribution -33.55
Covariance contribution 0.26
Combinations/Pair 1.41
Mean z-score -1.56
Structure conservation index 0.87
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.12
SVM RNA-class probability 0.982994
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 18841826 100 + 27905053
---UUGCUGCUGCUCC-UGCUGAUGCUGCCACUUCUGAUGGCGGUGCAGUAUUGUGGGUGCGGAUUAGUAGGAAUGACCGGAAUAAACGGCCGUAUCCCGUGGU
---.(((((((((.((-..(.((((((((.(((.(.....).))))))))))))..)).))))..)))))((((((.(((.......))).))).)))...... ( -35.90, z-score =  -1.17, R)
>droSim1.chr3R 18655856 100 + 27517382
---UUGCUGCUGCUCC-UGCUGUUGCUGCCACUUCUGAUGGCGGUGCAGCAUUGUGGGUGCGGAUUAGUCGGAAUGGCCGGAAUAAGCGGCCGUAUCCCGUGGU
---(..(..((((.((-..(...((((((.(((.(.....).)))))))))..)..)).)))).......((((((((((.......))))))).))).)..). ( -40.90, z-score =  -1.09, R)
>droSec1.super_0 19205398 100 + 21120651
---UUGCUGCUGCUCC-UGCUGUUGCUGCCACUUCUGAUGGCGGUGCAGCAUUGUGGGUGCGGAUUAGUCGGAAUGGCCGGAAUAAGCGGCCGUAUCCCGUGGU
---(..(..((((.((-..(...((((((.(((.(.....).)))))))))..)..)).)))).......((((((((((.......))))))).))).)..). ( -40.90, z-score =  -1.09, R)
>droYak2.chr3R 19703188 100 + 28832112
---UUGCCGCUGCUCC-UGCUGUUGCUGCCACUUCUGAUGGCGGUGCAGCAUUGUGGGUGCGGAUUAGUCGGAAUGGCCGGAAUAAACGGCCGUAUCCCGUGGU
---..((((((((.((-..(...((((((.(((.(.....).)))))))))..)..)).)))........((((((((((.......))))))).))).))))) ( -44.30, z-score =  -2.30, R)
>droEre2.scaffold_4820 1242423 97 - 10470090
------UUGCUGCCCC-UGCUGUUGCUGCCACUUCUGAUGGCGGUGCAGCAUUGUGGGCGCGGAUUAGUCGGAAUGGCCGGAAUAAACGGCCAUAUCCCGUGGU
------((((.(((((-((((((.((((((((....).)))))))))))))..).)))))))).......((((((((((.......))))))).)))...... ( -44.10, z-score =  -2.44, R)
>droVir3.scaffold_12822 4027219 84 - 4096053
UUUCUGAUGAUGCUUUGUGAUGCUGCUGCUGCCGUCGUCAACAGUGCAGUAGC-CAGGCUUCGACAAACUUUAAUUACAGACAAC-------------------
..((((.((((..(((((((.((((((((((((..........).))))))))-..))).)).))))).....))))))))....------------------- ( -24.30, z-score =  -1.29, R)
>consensus
___UUGCUGCUGCUCC_UGCUGUUGCUGCCACUUCUGAUGGCGGUGCAGCAUUGUGGGUGCGGAUUAGUCGGAAUGGCCGGAAUAAACGGCCGUAUCCCGUGGU
......((((.((((..((((((.((((((((....).)))))))))))))....)))))))).......((((((((((.......))))))).)))...... (-33.29 = -33.55 +   0.26)

alignment

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secondary structure

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dotplot

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Window 8

Location 18,841,826 – 18,841,926
Length 100
Sequences 6
Columns 104
Reading direction reverse
Mean pairwise identity 75.00
Shannon entropy 0.47571
G+C content 0.56199
Mean single sequence MFE -32.95
Consensus MFE -24.78
Energy contribution -26.57
Covariance contribution 1.78
Combinations/Pair 1.23
Mean z-score -2.21
Structure conservation index 0.75
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.83
SVM RNA-class probability 0.995690
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 18841826 100 - 27905053
ACCACGGGAUACGGCCGUUUAUUCCGGUCAUUCCUACUAAUCCGCACCCACAAUACUGCACCGCCAUCAGAAGUGGCAGCAUCAGCA-GGAGCAGCAGCAA---
.....((((...(((((.......)))))..))))....................((((.(((((((.....))))).((....)).-)).))))......--- ( -27.50, z-score =  -1.41, R)
>droSim1.chr3R 18655856 100 - 27517382
ACCACGGGAUACGGCCGCUUAUUCCGGCCAUUCCGACUAAUCCGCACCCACAAUGCUGCACCGCCAUCAGAAGUGGCAGCAACAGCA-GGAGCAGCAGCAA---
....((((((..(((((.......)))))))))))..................((((((.(((((((.....))))).((....)).-)).))))))....--- ( -37.00, z-score =  -3.30, R)
>droSec1.super_0 19205398 100 - 21120651
ACCACGGGAUACGGCCGCUUAUUCCGGCCAUUCCGACUAAUCCGCACCCACAAUGCUGCACCGCCAUCAGAAGUGGCAGCAACAGCA-GGAGCAGCAGCAA---
....((((((..(((((.......)))))))))))..................((((((.(((((((.....))))).((....)).-)).))))))....--- ( -37.00, z-score =  -3.30, R)
>droYak2.chr3R 19703188 100 - 28832112
ACCACGGGAUACGGCCGUUUAUUCCGGCCAUUCCGACUAAUCCGCACCCACAAUGCUGCACCGCCAUCAGAAGUGGCAGCAACAGCA-GGAGCAGCGGCAA---
.((.((((((..(((((.......)))))))))))...................(((((.(((((((.....))))).((....)).-)).)))))))...--- ( -37.90, z-score =  -3.14, R)
>droEre2.scaffold_4820 1242423 97 + 10470090
ACCACGGGAUAUGGCCGUUUAUUCCGGCCAUUCCGACUAAUCCGCGCCCACAAUGCUGCACCGCCAUCAGAAGUGGCAGCAACAGCA-GGGGCAGCAA------
....(((((..((((((.......)))))))))))........((((((....(((((..(.(((((.....))))).)...)))))-.)))).))..------ ( -39.90, z-score =  -3.12, R)
>droVir3.scaffold_12822 4027219 84 + 4096053
-------------------GUUGUCUGUAAUUAAAGUUUGUCGAAGCCUG-GCUACUGCACUGUUGACGACGGCAGCAGCAGCAUCACAAAGCAUCAUCAGAAA
-------------------....((((.........(((((.((.((...-(((.((((..((....))...)))).))).)).))))))).......)))).. ( -18.39, z-score =   1.05, R)
>consensus
ACCACGGGAUACGGCCGUUUAUUCCGGCCAUUCCGACUAAUCCGCACCCACAAUGCUGCACCGCCAUCAGAAGUGGCAGCAACAGCA_GGAGCAGCAGCAA___
....((((((..(((((.......)))))))))))..................((((((.(((((((.....))))).((....))..)).))))))....... (-24.78 = -26.57 +   1.78)

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 00:37:01 2011