Locus 11305

Sequence ID dm3.chr3R
Location 20,225,092 – 20,225,197
Length 105
Max. P 0.995889
window15540 window15541 window15542 window15543

overview

Window 0

Location 20,225,092 – 20,225,190
Length 98
Sequences 4
Columns 98
Reading direction forward
Mean pairwise identity 80.60
Shannon entropy 0.31748
G+C content 0.57780
Mean single sequence MFE -30.60
Consensus MFE -20.98
Energy contribution -21.23
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -1.50
Structure conservation index 0.69
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.10
SVM RNA-class probability 0.543374
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 20225092 98 + 27905053
GCAGCAGCAGAAGAGAGGCAACAUUCAGACAUUUCUCCUGGCAACAAUGAGCAACACCCAGGCCGCUCGACAACCCUGGCAGUGGGCUCAGGGUUGCC
((....))....(((.(....).))).............((((((..(((((..((((((((............)))))..))).)))))..)))))) ( -30.80, z-score =  -0.26, R)
>droSim1.chr3R 20063208 81 + 27517382
-----------------GCAACAUUCAGACAUUUCUCGUGGCAACAAUGAGCAACACCCAGGCCGCUCGACAACCCUGGCAGUGAGCUCAGGGUUGCC
-----------------......................((((((..(((((..((((((((............)))))..))).)))))..)))))) ( -25.90, z-score =  -1.37, R)
>droSec1.super_0 20563658 81 + 21120651
-----------------GCAACAUUCAGACAUUUCUCGUGGCAACAAUGAGCAACACCCAGGCCGCUCGACAACCCUGGCAGUGAGCUCAGGGUUGCC
-----------------......................((((((..(((((..((((((((............)))))..))).)))))..)))))) ( -25.90, z-score =  -1.37, R)
>droEre2.scaffold_4820 2635281 96 - 10470090
--GCAGCAACAGAAGCUGCAACAUUCAGGCUCUUCGCCUGGCAACAAUGCGCAACACCCAUGCCGCUCGACAACCCUGGCAGCGUGCUCAGGGUUGUC
--(((((.......))))).....((((((.....)))))).......(((((.......)).)))..((((((((((((.....)).)))))))))) ( -39.80, z-score =  -3.01, R)
>consensus
_________________GCAACAUUCAGACAUUUCUCCUGGCAACAAUGAGCAACACCCAGGCCGCUCGACAACCCUGGCAGUGAGCUCAGGGUUGCC
......................................((....)).(((((............))))).((((((((((.....)).)))))))).. (-20.98 = -21.23 +   0.25)

alignment

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secondary structure

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dotplot

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Window 1

Location 20,225,092 – 20,225,190
Length 98
Sequences 4
Columns 98
Reading direction reverse
Mean pairwise identity 80.60
Shannon entropy 0.31748
G+C content 0.57780
Mean single sequence MFE -37.65
Consensus MFE -31.81
Energy contribution -30.88
Covariance contribution -0.94
Combinations/Pair 1.15
Mean z-score -2.32
Structure conservation index 0.84
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.32
SVM RNA-class probability 0.988354
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 20225092 98 - 27905053
GGCAACCCUGAGCCCACUGCCAGGGUUGUCGAGCGGCCUGGGUGUUGCUCAUUGUUGCCAGGAGAAAUGUCUGAAUGUUGCCUCUCUUCUGCUGCUGC
((((((((((.((.....))))))))))))(((((((......)))))))...((.((.((((((...(.(........).)..)))))))).))... ( -36.90, z-score =  -1.19, R)
>droSim1.chr3R 20063208 81 - 27517382
GGCAACCCUGAGCUCACUGCCAGGGUUGUCGAGCGGCCUGGGUGUUGCUCAUUGUUGCCACGAGAAAUGUCUGAAUGUUGC-----------------
((((((((((.((.....))))))))))))(((((((......)))))))......((.((((((....)))...))).))----------------- ( -31.60, z-score =  -1.87, R)
>droSec1.super_0 20563658 81 - 21120651
GGCAACCCUGAGCUCACUGCCAGGGUUGUCGAGCGGCCUGGGUGUUGCUCAUUGUUGCCACGAGAAAUGUCUGAAUGUUGC-----------------
((((((((((.((.....))))))))))))(((((((......)))))))......((.((((((....)))...))).))----------------- ( -31.60, z-score =  -1.87, R)
>droEre2.scaffold_4820 2635281 96 + 10470090
GACAACCCUGAGCACGCUGCCAGGGUUGUCGAGCGGCAUGGGUGUUGCGCAUUGUUGCCAGGCGAAGAGCCUGAAUGUUGCAGCUUCUGUUGCUGC--
((((((((((.((.....))))))))))))..((((((((((.((((((((....)))(((((.....)))))......))))).)))).))))))-- ( -50.50, z-score =  -4.35, R)
>consensus
GGCAACCCUGAGCUCACUGCCAGGGUUGUCGAGCGGCCUGGGUGUUGCUCAUUGUUGCCACGAGAAAUGUCUGAAUGUUGC_________________
((((((((((.((.....))))))))))))..(((((.((((..((.(((...........))).))..))))...)))))................. (-31.81 = -30.88 +  -0.94)

alignment

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secondary structure

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dotplot

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Window 2

Location 20,225,093 – 20,225,197
Length 104
Sequences 5
Columns 104
Reading direction forward
Mean pairwise identity 76.06
Shannon entropy 0.39962
G+C content 0.59618
Mean single sequence MFE -37.38
Consensus MFE -25.68
Energy contribution -26.28
Covariance contribution 0.60
Combinations/Pair 1.20
Mean z-score -2.52
Structure conservation index 0.69
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.57
SVM RNA-class probability 0.992912
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 20225093 104 + 27905053
CAGCAGCAGAAGAGAGGCAACAUUCAGACAUUUCUCCUGGCAACAAUGAGCAACACCCAGGCCGCUCGACAACCCUGGCAGUGGGCUCAGGGUUGCCGUUGUCG
..(((((....(((.(....).))).............((((((..(((((..((((((((............)))))..))).)))))..))))))))))).. ( -36.50, z-score =  -1.34, R)
>droSim1.chr3R 20063208 88 + 27517382
----------------GCAACAUUCAGACAUUUCUCGUGGCAACAAUGAGCAACACCCAGGCCGCUCGACAACCCUGGCAGUGAGCUCAGGGUUGCCGCUGUUG
----------------.(((((....((......))((((((((..(((((..((((((((............)))))..))).)))))..))))))))))))) ( -33.50, z-score =  -2.52, R)
>droSec1.super_0 20563658 88 + 21120651
----------------GCAACAUUCAGACAUUUCUCGUGGCAACAAUGAGCAACACCCAGGCCGCUCGACAACCCUGGCAGUGAGCUCAGGGUUGCCGCUGUCG
----------------..........((((......((((((((..(((((..((((((((............)))))..))).)))))..)))))))))))). ( -33.50, z-score =  -2.64, R)
>droYak2.chr3R 2552661 79 - 28832112
-------------------------ACGCAGCAGAAGCUGCAACAAUGAGCAGCGCCCAGGCCGCUCGGCAACCCUGGCAGCGAGCUCAGGGUUGUCGCUGUCG
-------------------------..(((((....)))))......((.((((((....)).....((((((((((((.....)).)))))))))))))))). ( -39.00, z-score =  -2.49, R)
>droEre2.scaffold_4820 2635282 102 - 10470090
CAGCAACAGAAGCU--GCAACAUUCAGGCUCUUCGCCUGGCAACAAUGCGCAACACCCAUGCCGCUCGACAACCCUGGCAGCGUGCUCAGGGUUGUCGCUGUCG
((((....((.((.--(((.....(((((.....)))))(((....)))..........))).))))((((((((((((.....)).))))))))))))))... ( -44.40, z-score =  -3.62, R)
>consensus
________________GCAACAUUCAGACAUUUCUCGUGGCAACAAUGAGCAACACCCAGGCCGCUCGACAACCCUGGCAGUGAGCUCAGGGUUGCCGCUGUCG
..........................((((......((((((((..(((((..((((((((............)))))..))).)))))..)))))))))))). (-25.68 = -26.28 +   0.60)

alignment

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secondary structure

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dotplot

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Window 3

Location 20,225,093 – 20,225,197
Length 104
Sequences 5
Columns 104
Reading direction reverse
Mean pairwise identity 76.06
Shannon entropy 0.39962
G+C content 0.59618
Mean single sequence MFE -40.68
Consensus MFE -33.88
Energy contribution -33.68
Covariance contribution -0.20
Combinations/Pair 1.16
Mean z-score -2.47
Structure conservation index 0.83
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.86
SVM RNA-class probability 0.995889
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 20225093 104 - 27905053
CGACAACGGCAACCCUGAGCCCACUGCCAGGGUUGUCGAGCGGCCUGGGUGUUGCUCAUUGUUGCCAGGAGAAAUGUCUGAAUGUUGCCUCUCUUCUGCUGCUG
((((((.((((((((((.((.....))))))))))))(((((((......))))))).)))))).(((((((...(.(........).)..)))))))...... ( -39.70, z-score =  -1.78, R)
>droSim1.chr3R 20063208 88 - 27517382
CAACAGCGGCAACCCUGAGCUCACUGCCAGGGUUGUCGAGCGGCCUGGGUGUUGCUCAUUGUUGCCACGAGAAAUGUCUGAAUGUUGC----------------
(((((((((((((((((.((.....))))))))))))(((((((......)))))))......))....(((....)))...))))).---------------- ( -36.00, z-score =  -2.19, R)
>droSec1.super_0 20563658 88 - 21120651
CGACAGCGGCAACCCUGAGCUCACUGCCAGGGUUGUCGAGCGGCCUGGGUGUUGCUCAUUGUUGCCACGAGAAAUGUCUGAAUGUUGC----------------
(((((((((((((((((.((.....))))))))))))(((((((......)))))))......))....(((....)))...))))).---------------- ( -35.70, z-score =  -2.00, R)
>droYak2.chr3R 2552661 79 + 28832112
CGACAGCGACAACCCUGAGCUCGCUGCCAGGGUUGCCGAGCGGCCUGGGCGCUGCUCAUUGUUGCAGCUUCUGCUGCGU-------------------------
.(((((.(.((((((((.((.....)))))))))).)(((((((......))))))).)))))(((((....)))))..------------------------- ( -40.70, z-score =  -2.52, R)
>droEre2.scaffold_4820 2635282 102 + 10470090
CGACAGCGACAACCCUGAGCACGCUGCCAGGGUUGUCGAGCGGCAUGGGUGUUGCGCAUUGUUGCCAGGCGAAGAGCCUGAAUGUUGC--AGCUUCUGUUGCUG
......(((((((((((.((.....)))))))))))))(((((((.(((.((((((((....)))(((((.....)))))......))--))))))))))))). ( -51.30, z-score =  -3.85, R)
>consensus
CGACAGCGGCAACCCUGAGCUCACUGCCAGGGUUGUCGAGCGGCCUGGGUGUUGCUCAUUGUUGCCACGAGAAAUGUCUGAAUGUUGC________________
((((((.((((((((((.((.....))))))))))))(((((((......))))))).))))))........................................ (-33.88 = -33.68 +  -0.20)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:40:26 2011