Locus 10195

Sequence ID dm3.chr3R
Location 12,057,719 – 12,057,877
Length 158
Max. P 0.998490
window14019 window14020 window14021 window14022

overview

Window 9

Location 12,057,719 – 12,057,809
Length 90
Sequences 3
Columns 90
Reading direction forward
Mean pairwise identity 87.31
Shannon entropy 0.17346
G+C content 0.43241
Mean single sequence MFE -25.70
Consensus MFE -22.43
Energy contribution -22.10
Covariance contribution -0.33
Combinations/Pair 1.12
Mean z-score -3.49
Structure conservation index 0.87
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.11
SVM RNA-class probability 0.997466
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 12057719 90 + 27905053
GUCUCUUUUCUCGACUUCGUCAAACUCGUUUGAACUGCGCAAGUUAGGUUAUGGCUCGGGGAUUUCCCCUAGAAUAUAACUAAUUUGUGU
(((.........)))....(((((....)))))...(((((((((((.(((((.((.((((....)))).))..)))))))))))))))) ( -26.50, z-score =  -3.20, R)
>droSim1.chr3R 18108921 88 - 27517382
--GUCUUCUCUCGACUUCGUCAAACUCGUUAGCAUCGCGCAAGUUAAGUUAUUGCUGAGGGACUUCCCCUCAAAUAUAACUAAUUUGUGU
--(((.......))).....................((((((((((.(((((...((((((.....))))))...))))))))))))))) ( -24.90, z-score =  -4.10, R)
>droSec1.super_219 16512 88 - 23606
--GUCUUCUCUCGACUUCGUCAAGCUCGUUUGAACCGCGCAAGUUAAGUUAUUGCUGGGGGACUUCCCCUCAAACAUAACUAAUUUGUGU
--(((.......)))....(((((....)))))...((((((((((.(((((...((((((.....))))))...))))))))))))))) ( -25.70, z-score =  -3.16, R)
>consensus
__GUCUUCUCUCGACUUCGUCAAACUCGUUUGAACCGCGCAAGUUAAGUUAUUGCUGGGGGACUUCCCCUCAAAUAUAACUAAUUUGUGU
............(((...)))...............(((((((((.((((((...((((((.....))))))...))))))))))))))) (-22.43 = -22.10 +  -0.33)

alignment

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secondary structure

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dotplot

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Window 0

Location 12,057,756 – 12,057,846
Length 90
Sequences 3
Columns 90
Reading direction forward
Mean pairwise identity 81.25
Shannon entropy 0.24488
G+C content 0.35029
Mean single sequence MFE -21.47
Consensus MFE -19.86
Energy contribution -19.53
Covariance contribution -0.33
Combinations/Pair 1.15
Mean z-score -3.41
Structure conservation index 0.93
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.38
SVM RNA-class probability 0.998490
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 12057756 90 + 27905053
CGCAAGUUAGGUUAUGGCUCGGGGAUUUCCCCUAGAAUAUAACUAAUUUGUGUAUAAAUAAAUGUUGCACCUUACCAAAACUAACUGACU
.(..((((((((((((.((.((((....)))).))..))))))......(((((...........)))))..........))))))..). ( -22.20, z-score =  -2.26, R)
>droSim1.chr3R 18108956 76 - 27517382
CGCAAGUUAAGUUAUUGCUGAGGGACUUCCCCUCAAAUAUAACUAAUUUGUGUAUAAAUAAAUAUUGCACCUUACU--------------
(((((((((.(((((...((((((.....))))))...))))))))))))))........................-------------- ( -21.90, z-score =  -4.78, R)
>droSec1.super_219 16547 76 - 23606
CGCAAGUUAAGUUAUUGCUGGGGGACUUCCCCUCAAACAUAACUAAUUUGUGUAUAAAUAAAUAUUGCACCUUACU--------------
(((((((((.(((((...((((((.....))))))...))))))))))))))........................-------------- ( -20.30, z-score =  -3.20, R)
>consensus
CGCAAGUUAAGUUAUUGCUGGGGGACUUCCCCUCAAAUAUAACUAAUUUGUGUAUAAAUAAAUAUUGCACCUUACU______________
((((((((.((((((...((((((.....))))))...))))))))))))))...................................... (-19.86 = -19.53 +  -0.33)

alignment

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secondary structure

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dotplot

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Window 1

Location 12,057,756 – 12,057,846
Length 90
Sequences 3
Columns 90
Reading direction reverse
Mean pairwise identity 81.25
Shannon entropy 0.24488
G+C content 0.35029
Mean single sequence MFE -20.75
Consensus MFE -16.19
Energy contribution -15.86
Covariance contribution -0.33
Combinations/Pair 1.10
Mean z-score -2.84
Structure conservation index 0.78
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.37
SVM RNA-class probability 0.989515
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 12057756 90 - 27905053
AGUCAGUUAGUUUUGGUAAGGUGCAACAUUUAUUUAUACACAAAUUAGUUAUAUUCUAGGGGAAAUCCCCGAGCCAUAACCUAACUUGCG
.((.((((((((.((((...(((...............))).................((((....))))..)))).)).)))))).)). ( -21.36, z-score =  -2.07, R)
>droSim1.chr3R 18108956 76 + 27517382
--------------AGUAAGGUGCAAUAUUUAUUUAUACACAAAUUAGUUAUAUUUGAGGGGAAGUCCCUCAGCAAUAACUUAACUUGCG
--------------.((((((((..(((......))).))).....((((((..(((((((.....)))))))..))))))...))))). ( -20.50, z-score =  -3.62, R)
>droSec1.super_219 16547 76 + 23606
--------------AGUAAGGUGCAAUAUUUAUUUAUACACAAAUUAGUUAUGUUUGAGGGGAAGUCCCCCAGCAAUAACUUAACUUGCG
--------------.((((((((..(((......))).))).....((((((..(((.((((....)))))))..))))))...))))). ( -20.40, z-score =  -2.82, R)
>consensus
______________AGUAAGGUGCAAUAUUUAUUUAUACACAAAUUAGUUAUAUUUGAGGGGAAGUCCCCCAGCAAUAACUUAACUUGCG
...............((((((((...............)))......(((((..(((.((((....)))))))..)))))....))))). (-16.19 = -15.86 +  -0.33)

alignment

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secondary structure

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dotplot

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Window 2

Location 12,057,774 – 12,057,877
Length 103
Sequences 3
Columns 103
Reading direction forward
Mean pairwise identity 80.14
Shannon entropy 0.25855
G+C content 0.32321
Mean single sequence MFE -15.20
Consensus MFE -10.81
Energy contribution -10.70
Covariance contribution -0.11
Combinations/Pair 1.18
Mean z-score -1.67
Structure conservation index 0.71
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.06
SVM RNA-class probability 0.522368
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr3R 12057774 103 + 27905053
UCGGGGAUUUCCCCUAGAAUAUAACUAAUUUGUGUAUAAAUAAAUGUUGCACCUUACCAAAACUAACUGACUGCCAUAAACACCCAUAUUCGUUUUAUAAUAC
..((((....))))..((((((.........(((((...........))))).....((........))................))))))............ ( -14.00, z-score =  -0.48, R)
>droSim1.chr3R 18108974 86 - 27517382
UGAGGGACUUCCCCUCAAAUAUAACUAAUUUGUGUAUAAAUAAAUAUUGCACCUUAC--------------UGCCAUAAAUACACAUCUUCGUUUUAUAU---
((((((.....)))))).(((.(((.((..(((((((.......(((.(((......--------------))).))).)))))))..)).))).)))..--- ( -18.20, z-score =  -3.84, R)
>droSec1.super_219 16565 86 - 23606
UGGGGGACUUCCCCUCAAACAUAACUAAUUUGUGUAUAAAUAAAUAUUGCACCUUAC--------------UGCCAUAAAUACCCAUCAUCGUUUUAUAU---
((((((.....)))))).((((((.....)))))).........(((.(((......--------------))).)))......................--- ( -13.40, z-score =  -0.70, R)
>consensus
UGGGGGACUUCCCCUCAAAUAUAACUAAUUUGUGUAUAAAUAAAUAUUGCACCUUAC______________UGCCAUAAAUACCCAUCUUCGUUUUAUAU___
((((((.....))))))..............(((((...........)))))................................................... (-10.81 = -10.70 +  -0.11)

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 00:19:19 2011