Locus 1746

Sequence ID dm3.chr2L
Location 13,484,543 – 13,484,679
Length 136
Max. P 0.998624
window2397 window2398 window2399 window2400

overview

Window 7

Location 13,484,543 – 13,484,648
Length 105
Sequences 7
Columns 114
Reading direction forward
Mean pairwise identity 85.67
Shannon entropy 0.27165
G+C content 0.58522
Mean single sequence MFE -28.16
Consensus MFE -21.19
Energy contribution -21.68
Covariance contribution 0.49
Combinations/Pair 1.10
Mean z-score -2.69
Structure conservation index 0.75
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.19
SVM RNA-class probability 0.984995
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 13484543 105 + 23011544
CUGGCGAUCAACGCAGCCCAUCCUCAGCCCGCCACUCAACUGCGCCAGCCCUUCGACUUC--------GAGGCUGACGCAGUUUUUCAAA-CGCCACAGCUACAGAAAAACCCC
.(((((......((.((.........))..)).....(((((((.(((((..(((....)--------))))))).))))))).......-))))).................. ( -30.60, z-score =  -3.19, R)
>droSim1.chr2L 13266422 105 + 22036055
CUGGCGAUCAACGCAGCCCAUCCUCAGCCCGCCACUCAACUGCGCCAGCCCUUCGACUUC--------GAGGCUGACGCAGUUUUUCAAA-CGCCACAGCUACAGAAAAACCCC
.(((((......((.((.........))..)).....(((((((.(((((..(((....)--------))))))).))))))).......-))))).................. ( -30.60, z-score =  -3.19, R)
>droSec1.super_16 1629816 104 + 1878335
CUGGCGAUCAACGCAGCCCAUCCUCAGCCCGCCACUCAACUGCGCCAGCCCUUCGACUUC--------GAGGCUGACGCAGUUUUUCAAA-CGCCACAGCUACAGAAAAACCC-
.(((((......((.((.........))..)).....(((((((.(((((..(((....)--------))))))).))))))).......-))))).................- ( -30.60, z-score =  -3.11, R)
>droYak2.chr2L 9912689 105 + 22324452
CUGGCGAUCAACGCAGCCCAUCCUCAGCCCGCCACUCAACUGCGCCAGCCCUUCGACUCC--------GAGGCUGACGCAGUUUUUCAAA-CGCCACAGCUACAGAAAAACCCC
.(((((......((.((.........))..)).....(((((((.(((((..(((....)--------))))))).))))))).......-))))).................. ( -30.00, z-score =  -3.05, R)
>droEre2.scaffold_4929 14676358 105 - 26641161
CUGGCGAUCAACGCAGCCCAUCCUCAGCCCGCCACUCAACUGCGCCAGCCCUUCGAUUCC--------GAGGCUGACGCAGUUUUUCAAA-CGCCACAGCUACAGAAAAACCCC
.(((((......((.((.........))..)).....(((((((.(((((..(((....)--------))))))).))))))).......-))))).................. ( -30.00, z-score =  -3.12, R)
>droAna3.scaffold_12943 2188770 95 + 5039921
CUGGCGAUCAACGCAGCCCAUCCUCAGCCCGCCACUCAACUGCGCCAG----UCACUUCC--------G--GCUGACGCAGUUUUCCAAC-AACCA-GGCUACAGAAAGAA---
((((((.....)))((((........(....).....(((((((.(((----((......--------)--)))).))))))).......-.....-)))).)))......--- ( -25.90, z-score =  -1.67, R)
>droWil1.scaffold_180708 7317033 109 - 12563649
CUGUCGAUCAACGCAGCCCAUCCUCAGCCCGCCACUCAACUGCGCCAGUGCCCCUCUCUCUCUACUCAGUCACUGACGCAGUUUCUCAACCAAUCACAGCAGCAAACAA-----
((((.(((....((.((.........))..)).....(((((((.(((((.(................).))))).))))))).........)))))))..........----- ( -19.39, z-score =  -1.48, R)
>consensus
CUGGCGAUCAACGCAGCCCAUCCUCAGCCCGCCACUCAACUGCGCCAGCCCUUCGACUUC________GAGGCUGACGCAGUUUUUCAAA_CGCCACAGCUACAGAAAAACCCC
.(((((......((.((.........))..)).....(((((((.(((((....................))))).)))))))........))))).................. (-21.19 = -21.68 +   0.49)

alignment

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secondary structure

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dotplot

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Window 8

Location 13,484,543 – 13,484,648
Length 105
Sequences 7
Columns 114
Reading direction reverse
Mean pairwise identity 85.67
Shannon entropy 0.27165
G+C content 0.58522
Mean single sequence MFE -42.57
Consensus MFE -34.91
Energy contribution -34.80
Covariance contribution -0.11
Combinations/Pair 1.12
Mean z-score -2.24
Structure conservation index 0.82
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.88
SVM RNA-class probability 0.972789
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 13484543 105 - 23011544
GGGGUUUUUCUGUAGCUGUGGCG-UUUGAAAAACUGCGUCAGCCUC--------GAAGUCGAAGGGCUGGCGCAGUUGAGUGGCGGGCUGAGGAUGGGCUGCGUUGAUCGCCAG
..((((.......)))).(((((-.(..(..(((((((((((((((--------(....)))..))))))))))))).....((((.((......)).)))).)..).))))). ( -44.80, z-score =  -2.50, R)
>droSim1.chr2L 13266422 105 - 22036055
GGGGUUUUUCUGUAGCUGUGGCG-UUUGAAAAACUGCGUCAGCCUC--------GAAGUCGAAGGGCUGGCGCAGUUGAGUGGCGGGCUGAGGAUGGGCUGCGUUGAUCGCCAG
..((((.......)))).(((((-.(..(..(((((((((((((((--------(....)))..))))))))))))).....((((.((......)).)))).)..).))))). ( -44.80, z-score =  -2.50, R)
>droSec1.super_16 1629816 104 - 1878335
-GGGUUUUUCUGUAGCUGUGGCG-UUUGAAAAACUGCGUCAGCCUC--------GAAGUCGAAGGGCUGGCGCAGUUGAGUGGCGGGCUGAGGAUGGGCUGCGUUGAUCGCCAG
-.((((.......)))).(((((-.(..(..(((((((((((((((--------(....)))..))))))))))))).....((((.((......)).)))).)..).))))). ( -44.80, z-score =  -2.60, R)
>droYak2.chr2L 9912689 105 - 22324452
GGGGUUUUUCUGUAGCUGUGGCG-UUUGAAAAACUGCGUCAGCCUC--------GGAGUCGAAGGGCUGGCGCAGUUGAGUGGCGGGCUGAGGAUGGGCUGCGUUGAUCGCCAG
..((((.......)))).(((((-.(..(..(((((((((((((((--------(....)))..))))))))))))).....((((.((......)).)))).)..).))))). ( -43.90, z-score =  -2.07, R)
>droEre2.scaffold_4929 14676358 105 + 26641161
GGGGUUUUUCUGUAGCUGUGGCG-UUUGAAAAACUGCGUCAGCCUC--------GGAAUCGAAGGGCUGGCGCAGUUGAGUGGCGGGCUGAGGAUGGGCUGCGUUGAUCGCCAG
..((((.......)))).(((((-.(..(..(((((((((((((((--------(....)))..))))))))))))).....((((.((......)).)))).)..).))))). ( -43.90, z-score =  -2.32, R)
>droAna3.scaffold_12943 2188770 95 - 5039921
---UUCUUUCUGUAGCC-UGGUU-GUUGGAAAACUGCGUCAGC--C--------GGAAGUGA----CUGGCGCAGUUGAGUGGCGGGCUGAGGAUGGGCUGCGUUGAUCGCCAG
---.(((.(((.(((((-((.(.-.((....((((((((((((--(--------....).).----))))))))))).))..)))))))).))).)))..(((.....)))... ( -38.90, z-score =  -2.03, R)
>droWil1.scaffold_180708 7317033 109 + 12563649
-----UUGUUUGCUGCUGUGAUUGGUUGAGAAACUGCGUCAGUGACUGAGUAGAGAGAGAGGGGCACUGGCGCAGUUGAGUGGCGGGCUGAGGAUGGGCUGCGUUGAUCGACAG
-----..........(((((((..(......(((((((((((((.((.............))..))))))))))))).....((((.((......)).)))).)..))).)))) ( -36.92, z-score =  -1.67, R)
>consensus
GGGGUUUUUCUGUAGCUGUGGCG_UUUGAAAAACUGCGUCAGCCUC________GAAGUCGAAGGGCUGGCGCAGUUGAGUGGCGGGCUGAGGAUGGGCUGCGUUGAUCGCCAG
..................((((.........((((((((((((((..................)))))))))))))).....((((.((......)).)))).......)))). (-34.91 = -34.80 +  -0.11)

alignment

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secondary structure

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dotplot

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Window 9

Location 13,484,582 – 13,484,679
Length 97
Sequences 5
Columns 97
Reading direction forward
Mean pairwise identity 98.56
Shannon entropy 0.02489
G+C content 0.52685
Mean single sequence MFE -22.26
Consensus MFE -22.26
Energy contribution -22.26
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -4.00
Structure conservation index 1.00
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.42
SVM RNA-class probability 0.998624
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr2L 13484582 97 + 23011544
CUGCGCCAGCCCUUCGACUUCGAGGCUGACGCAGUUUUUCAAACGCCACAGCUACAGAAAAACCCCCCAAAAAACCAACCACCACAAGAACUACAGC
.((((.(((((..(((....)))))))).))))(((((((....((....))....))))))).................................. ( -22.50, z-score =  -4.07, R)
>droSim1.chr2L 13266461 97 + 22036055
CUGCGCCAGCCCUUCGACUUCGAGGCUGACGCAGUUUUUCAAACGCCACAGCUACAGAAAAACCCCCCAAAAAACCAACCACCACAAGAACUACAGC
.((((.(((((..(((....)))))))).))))(((((((....((....))....))))))).................................. ( -22.50, z-score =  -4.07, R)
>droSec1.super_16 1629855 96 + 1878335
CUGCGCCAGCCCUUCGACUUCGAGGCUGACGCAGUUUUUCAAACGCCACAGCUACAGAAAAACCCCC-AAAAAACCAACCACCACAAGAACUACAGC
.((((.(((((..(((....)))))))).))))(((((((....((....))....)))))))....-............................. ( -22.50, z-score =  -3.80, R)
>droYak2.chr2L 9912728 97 + 22324452
CUGCGCCAGCCCUUCGACUCCGAGGCUGACGCAGUUUUUCAAACGCCACAGCUACAGAAAAACCCCCCAAAAAACCAACCACCACAAGAACUACAGC
.((((.(((((..(((....)))))))).))))(((((((....((....))....))))))).................................. ( -21.90, z-score =  -3.97, R)
>droEre2.scaffold_4929 14676397 97 - 26641161
CUGCGCCAGCCCUUCGAUUCCGAGGCUGACGCAGUUUUUCAAACGCCACAGCUACAGAAAAACCCCCCAAAAAACCAACCACCACAAGAACUACAGC
.((((.(((((..(((....)))))))).))))(((((((....((....))....))))))).................................. ( -21.90, z-score =  -4.09, R)
>consensus
CUGCGCCAGCCCUUCGACUUCGAGGCUGACGCAGUUUUUCAAACGCCACAGCUACAGAAAAACCCCCCAAAAAACCAACCACCACAAGAACUACAGC
.((((.(((((..(((....)))))))).))))(((((((....((....))....))))))).................................. (-22.26 = -22.26 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 0

Location 13,484,582 – 13,484,679
Length 97
Sequences 5
Columns 97
Reading direction reverse
Mean pairwise identity 98.56
Shannon entropy 0.02489
G+C content 0.52685
Mean single sequence MFE -31.26
Consensus MFE -31.24
Energy contribution -31.24
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.37
Structure conservation index 1.00
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.98
SVM RNA-class probability 0.866260
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr2L 13484582 97 - 23011544
GCUGUAGUUCUUGUGGUGGUUGGUUUUUUGGGGGGUUUUUCUGUAGCUGUGGCGUUUGAAAAACUGCGUCAGCCUCGAAGUCGAAGGGCUGGCGCAG
((..(((...)))..))................((((((((....((....))....))))))))((((((((((((....)))..))))))))).. ( -31.60, z-score =  -1.49, R)
>droSim1.chr2L 13266461 97 - 22036055
GCUGUAGUUCUUGUGGUGGUUGGUUUUUUGGGGGGUUUUUCUGUAGCUGUGGCGUUUGAAAAACUGCGUCAGCCUCGAAGUCGAAGGGCUGGCGCAG
((..(((...)))..))................((((((((....((....))....))))))))((((((((((((....)))..))))))))).. ( -31.60, z-score =  -1.49, R)
>droSec1.super_16 1629855 96 - 1878335
GCUGUAGUUCUUGUGGUGGUUGGUUUUUU-GGGGGUUUUUCUGUAGCUGUGGCGUUUGAAAAACUGCGUCAGCCUCGAAGUCGAAGGGCUGGCGCAG
((..((((((....))............(-(.(((....))).))))))..))..........((((((((((((((....)))..))))))))))) ( -31.70, z-score =  -1.61, R)
>droYak2.chr2L 9912728 97 - 22324452
GCUGUAGUUCUUGUGGUGGUUGGUUUUUUGGGGGGUUUUUCUGUAGCUGUGGCGUUUGAAAAACUGCGUCAGCCUCGGAGUCGAAGGGCUGGCGCAG
((..(((...)))..))................((((((((....((....))....))))))))((((((((((((....)))..))))))))).. ( -30.70, z-score =  -1.04, R)
>droEre2.scaffold_4929 14676397 97 + 26641161
GCUGUAGUUCUUGUGGUGGUUGGUUUUUUGGGGGGUUUUUCUGUAGCUGUGGCGUUUGAAAAACUGCGUCAGCCUCGGAAUCGAAGGGCUGGCGCAG
((..(((...)))..))................((((((((....((....))....))))))))((((((((((((....)))..))))))))).. ( -30.70, z-score =  -1.23, R)
>consensus
GCUGUAGUUCUUGUGGUGGUUGGUUUUUUGGGGGGUUUUUCUGUAGCUGUGGCGUUUGAAAAACUGCGUCAGCCUCGAAGUCGAAGGGCUGGCGCAG
((..(((...)))..))................((((((((....((....))....))))))))((((((((((((....)))..))))))))).. (-31.24 = -31.24 +   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 Tue Apr 19 21:38:01 2011