Locus 10187

Sequence ID dm3.chr3R
Location 12,015,325 – 12,015,444
Length 119
Max. P 0.983068
window14004 window14005 window14006 window14007

overview

Window 4

Location 12,015,325 – 12,015,442
Length 117
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 50.99
Shannon entropy 0.69134
G+C content 0.48947
Mean single sequence MFE -24.99
Consensus MFE -14.23
Energy contribution -14.90
Covariance contribution 0.67
Combinations/Pair 1.27
Mean z-score -1.17
Structure conservation index 0.57
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.12
SVM RNA-class probability 0.983068
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 12015325 117 + 27905053
CUAAUGGCUAUACACACUGGCGUGUGCCAC-AUUGUCAUCUCUCUCUAACACACUAUUUAUGACCACUCG--AUCGGACCUCACUCAGCUGCAGAGGCUGUUCGUGCCUCUGCCGCAGCG
......(((.......((((((.(((....-...(((((....................)))))))).))--.))))..........((.((((((((.......)))))))).))))). ( -31.16, z-score =  -1.06, R)
>droAna3.scaffold_12966 14940 103 + 443544
----------------CAAGUUGAGCCUCC-AUCGUCAUCUCUUUCCAUCUCACAACUUUCGGUAACUCUUCAACGGACCUCUCUCACCAGCAGAGACUGCUACCGUCUCUGCUGCUAUG
----------------...((((((.....-((((.........................)))).....)))))).............((((((((((.......))))))))))..... ( -22.61, z-score =  -2.25, R)
>droVir3.scaffold_13324 1398567 113 + 2960039
----CAAUUAAUCACUCAAAAUUGUGCAACUAUUGUUCGCCGUUGCUGUU-CUUCAGUCAAAGCUGUACG--AUCAGACCUCACUCAGCAGCGGAGUCUCUCUUUGUCUCUGUUACUAUG
----(((......((((......(((.(((....))))))((((((((..-....(((.....(((....--..))).....)))))))))))))))......))).............. ( -21.20, z-score =  -0.19, R)
>consensus
________UA__CAC_CAAGAUUGUGCAAC_AUUGUCAUCUCUUUCUAUC_CACAACUUAAGGCAACUCG__AUCGGACCUCACUCAGCAGCAGAGACUGUUACUGUCUCUGCUGCUAUG
.......................................................................................(((((((((((.......))))))))))).... (-14.23 = -14.90 +   0.67)

alignment

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secondary structure

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dotplot

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Window 5

Location 12,015,325 – 12,015,442
Length 117
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 50.99
Shannon entropy 0.69134
G+C content 0.48947
Mean single sequence MFE -32.00
Consensus MFE -13.84
Energy contribution -14.31
Covariance contribution 0.46
Combinations/Pair 1.48
Mean z-score -1.19
Structure conservation index 0.43
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.95
SVM RNA-class probability 0.859061
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 12015325 117 - 27905053
CGCUGCGGCAGAGGCACGAACAGCCUCUGCAGCUGAGUGAGGUCCGAU--CGAGUGGUCAUAAAUAGUGUGUUAGAGAGAGAUGACAAU-GUGGCACACGCCAGUGUGUAUAGCCAUUAG
((((((.((((((((.......)))))))).))..)))).........--..((((((((((....((((((((.(..(......)..)-.)))))))).....))))....)))))).. ( -38.60, z-score =  -1.21, R)
>droAna3.scaffold_12966 14940 103 - 443544
CAUAGCAGCAGAGACGGUAGCAGUCUCUGCUGGUGAGAGAGGUCCGUUGAAGAGUUACCGAAAGUUGUGAGAUGGAAAGAGAUGACGAU-GGAGGCUCAACUUG----------------
..((.((((((((((.......)))))))))).)).(((...(((((((.....(((((....)..))))..(....).......))))-)))..)))......---------------- ( -32.20, z-score =  -2.30, R)
>droVir3.scaffold_13324 1398567 113 - 2960039
CAUAGUAACAGAGACAAAGAGAGACUCCGCUGCUGAGUGAGGUCUGAU--CGUACAGCUUUGACUGAAG-AACAGCAACGGCGAACAAUAGUUGCACAAUUUUGAGUGAUUAAUUG----
........(((((.....((.((((..((((....))))..))))..)--)......)))))(((.(((-(...(((((...........)))))....)))).))).........---- ( -25.20, z-score =  -0.04, R)
>consensus
CAUAGCAGCAGAGACAAAAACAGACUCUGCUGCUGAGUGAGGUCCGAU__CGAGUAGCCAUAAAUAGUG_GAUAGAAAGAGAUGACAAU_GUAGCACAAACUUG_GUG__UA________
..(((((((((((((.......))))))))))))).......((((((......((....))........))))))............................................ (-13.84 = -14.31 +   0.46)

alignment

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secondary structure

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dotplot

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Window 6

Location 12,015,329 – 12,015,444
Length 115
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 53.41
Shannon entropy 0.65517
G+C content 0.49191
Mean single sequence MFE -24.35
Consensus MFE -14.46
Energy contribution -15.13
Covariance contribution 0.67
Combinations/Pair 1.20
Mean z-score -0.70
Structure conservation index 0.59
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.08
SVM RNA-class probability 0.887753
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 12015329 115 + 27905053
UGGCUAUACACACUGGCGUGUGCCAC-AUUGUCAUCUCUCUCUAACACACUAUUUAUGACCACUCG--AUCGGACCUCACUCAGCUGCAGAGGCUGUUCGUGCCUCUGCCGCAGCGCU--
..(((.......((((((.(((....-...(((((....................)))))))).))--.))))..........((.((((((((.......)))))))).)))))...-- ( -31.16, z-score =  -0.52, R)
>droAna3.scaffold_12966 14944 103 + 443544
-----------------UUGAGCCUCCAUCGUCAUCUCUUUCCAUCUCACAACUUUCGGUAACUCUUCAACGGACCUCUCUCACCAGCAGAGACUGCUACCGUCUCUGCUGCUAUGCUUU
-----------------..((((...............................((((............))))..........((((((((((.......))))))))))....)))). ( -21.00, z-score =  -1.91, R)
>droVir3.scaffold_13324 1398571 111 + 2960039
----UAAUCACUCAAAAUUGUGCAACUAUUGUUCGCCGUUGCUG-UUCUUCAGUCAAAGCUGUACG--AUCAGACCUCACUCAGCAGCGGAGUCUCUCUUUGUCUCUGUUACUAUGCU--
----.....((((......(((.(((....))))))((((((((-......(((.....(((....--..))).....))))))))))))))).........................-- ( -20.90, z-score =   0.34, R)
>consensus
____UA__CAC_C____UUGUGCCAC_AUUGUCAUCUCUUUCUA_CUCACAACUUAAGGCAACUCG__AUCGGACCUCACUCAGCAGCAGAGACUGUUACUGUCUCUGCUGCUAUGCU__
.....................((.................................................((......)).(((((((((((.......)))))))))))...))... (-14.46 = -15.13 +   0.67)

alignment

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secondary structure

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dotplot

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Window 7

Location 12,015,329 – 12,015,444
Length 115
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 53.41
Shannon entropy 0.65517
G+C content 0.49191
Mean single sequence MFE -32.17
Consensus MFE -16.08
Energy contribution -16.54
Covariance contribution 0.46
Combinations/Pair 1.43
Mean z-score -1.15
Structure conservation index 0.50
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.26
SVM RNA-class probability 0.918195
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 12015329 115 - 27905053
--AGCGCUGCGGCAGAGGCACGAACAGCCUCUGCAGCUGAGUGAGGUCCGAU--CGAGUGGUCAUAAAUAGUGUGUUAGAGAGAGAUGACAAU-GUGGCACACGCCAGUGUGUAUAGCCA
--.(((((((.((((((((.......)))))))).)).......(((..(((--(....)))).......((((((((.(..(......)..)-.))))))))))))))))......... ( -39.10, z-score =  -0.98, R)
>droAna3.scaffold_12966 14944 103 - 443544
AAAGCAUAGCAGCAGAGACGGUAGCAGUCUCUGCUGGUGAGAGAGGUCCGUUGAAGAGUUACCGAAAGUUGUGAGAUGGAAAGAGAUGACGAUGGAGGCUCAA-----------------
......((.((((((((((.......)))))))))).)).(((...(((((((.....(((((....)..))))..(....).......)))))))..)))..----------------- ( -32.20, z-score =  -2.74, R)
>droVir3.scaffold_13324 1398571 111 - 2960039
--AGCAUAGUAACAGAGACAAAGAGAGACUCCGCUGCUGAGUGAGGUCUGAU--CGUACAGCUUUGACUGAAGAA-CAGCAACGGCGAACAAUAGUUGCACAAUUUUGAGUGAUUA----
--..........(((((.....((.((((..((((....))))..))))..)--)......)))))(((.((((.-..(((((...........)))))....)))).))).....---- ( -25.20, z-score =   0.27, R)
>consensus
__AGCAUAGCAGCAGAGACAAAAACAGACUCUGCUGCUGAGUGAGGUCCGAU__CGAGUAGCCAUAAAUAGUGAG_UAGAAAGAGAUGACAAU_GUGGCACAA____G_GUG__UA____
...((.(((((((((((((.......))))))))))))).......((((((......((....))........)))))).................))..................... (-16.08 = -16.54 +   0.46)

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 00:19:08 2011