Locus 13688

Sequence ID dm3.chrX
Location 8,401,025 – 8,401,124
Length 99
Max. P 0.984305
window18834 window18835

overview

Window 4

Location 8,401,025 – 8,401,124
Length 99
Sequences 5
Columns 110
Reading direction forward
Mean pairwise identity 77.95
Shannon entropy 0.38333
G+C content 0.50028
Mean single sequence MFE -34.82
Consensus MFE -20.82
Energy contribution -21.70
Covariance contribution 0.88
Combinations/Pair 1.28
Mean z-score -2.61
Structure conservation index 0.60
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.16
SVM RNA-class probability 0.984305
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 8401025 99 + 22422827
CGAUUGUGUUUUGGAUUGCCGGCGAAUUUUUGCGCCGGCGGCUGAUCCACUAAUCAAGUUGCAUUUAUAUGCCCCACCGAUCCGUCGGCUAUAUAAUUG-----------
.(((((((..(..(.(((((((((........))))))))))..)..))).)))).....((((....))))....((((....))))...........----------- ( -33.80, z-score =  -2.63, R)
>droSim1.chrX 6694536 99 + 17042790
CGAUUGUGUUUUGGAUUGCCGGCGAAUUUUUGCGCCGGCGGCUGAUCCACUAAUCAAGGUGCAUUUAUAUGCCCCACCGAUCCGCCGGCCAUAUAAUUG-----------
.(((((((..(..(.(((((((((........))))))))))..)..))).))))..((.((((....)))).)).(((......)))...........----------- ( -36.40, z-score =  -2.58, R)
>droSec1.super_35 250364 99 + 471130
CGAUUGUGUUUUGGAUUGCCGGCGAAUUUUUGCGCCGACGGCUGAUCCACUAAUCAAGGUGCAUUUAUAUGCCCCACCGAUCCGCCGGCCAUAUAAUUG-----------
((((((((...(((.....(((((........))))).((((.((((.(((......)))((((....))))......)))).)))).)))))))))))----------- ( -30.00, z-score =  -1.37, R)
>droYak2.chrX 8857617 89 - 21770863
CGAUUGUGUUUUGGAUUGCCGGCGG----------UGGCGGCUGAUCCACUAAUCAAGGUGCAUUUAUAUGCCCCACCGAUCCGGCGACUUUAUAAUUG-----------
((((((((....((.((((((((((----------(((.(((.(((.((((......)))).))).....)))))))))..))))))))).))))))))----------- ( -36.60, z-score =  -3.89, R)
>dp4.chrXL_group1e 3463629 108 + 12523060
CGAUUGUGUCGUUUGUCGUUUGUCGUCGUCUACGGCGGCAUCUGAUCCACUAAUCAAGGUGCAUUUAUAUGCCCAGCGGAUCCGAUGGCG--ACAAUUACAACCUGAUUG
.(.(((((....((((((((.(((((((....)))))))(((.(((((.((......((.((((....)))))))).))))).)))))))--)))).))))).)...... ( -37.30, z-score =  -2.60, R)
>consensus
CGAUUGUGUUUUGGAUUGCCGGCGAAUUUUUGCGCCGGCGGCUGAUCCACUAAUCAAGGUGCAUUUAUAUGCCCCACCGAUCCGCCGGCCAUAUAAUUG___________
((((((((.........(((((((........)))))))(((.((((.(((......)))((((....))))......)))).))).....))))))))........... (-20.82 = -21.70 +   0.88)

alignment

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secondary structure

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dotplot

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Window 5

Location 8,401,025 – 8,401,124
Length 99
Sequences 5
Columns 110
Reading direction reverse
Mean pairwise identity 77.95
Shannon entropy 0.38333
G+C content 0.50028
Mean single sequence MFE -31.34
Consensus MFE -17.70
Energy contribution -19.30
Covariance contribution 1.60
Combinations/Pair 1.20
Mean z-score -1.95
Structure conservation index 0.56
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.69
SVM RNA-class probability 0.788327
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 8401025 99 - 22422827
-----------CAAUUAUAUAGCCGACGGAUCGGUGGGGCAUAUAAAUGCAACUUGAUUAGUGGAUCAGCCGCCGGCGCAAAAAUUCGCCGGCAAUCCAAAACACAAUCG
-----------................((((.((((..((((....))))..).(((((....))))))))(((((((........))))))).))))............ ( -29.60, z-score =  -1.81, R)
>droSim1.chrX 6694536 99 - 17042790
-----------CAAUUAUAUGGCCGGCGGAUCGGUGGGGCAUAUAAAUGCACCUUGAUUAGUGGAUCAGCCGCCGGCGCAAAAAUUCGCCGGCAAUCCAAAACACAAUCG
-----------..........((((((((((((((((.((((....))))...((((((....))))))))))))........))))))))))................. ( -34.20, z-score =  -1.97, R)
>droSec1.super_35 250364 99 - 471130
-----------CAAUUAUAUGGCCGGCGGAUCGGUGGGGCAUAUAAAUGCACCUUGAUUAGUGGAUCAGCCGUCGGCGCAAAAAUUCGCCGGCAAUCCAAAACACAAUCG
-----------..........(((((((((((((((((((((....)))).)))(((((....)))))))))...........))))))))))................. ( -31.00, z-score =  -1.36, R)
>droYak2.chrX 8857617 89 + 21770863
-----------CAAUUAUAAAGUCGCCGGAUCGGUGGGGCAUAUAAAUGCACCUUGAUUAGUGGAUCAGCCGCCA----------CCGCCGGCAAUCCAAAACACAAUCG
-----------.............(((((..(((((((((((....)))).)).......((((.....))))))----------))))))))................. ( -28.00, z-score =  -2.13, R)
>dp4.chrXL_group1e 3463629 108 - 12523060
CAAUCAGGUUGUAAUUGU--CGCCAUCGGAUCCGCUGGGCAUAUAAAUGCACCUUGAUUAGUGGAUCAGAUGCCGCCGUAGACGACGACAAACGACAAACGACACAAUCG
.......(((((..((((--((.((((.((((((((((((((....)))).))......)))))))).)))).((.((....)).)).....)))))))))))....... ( -33.90, z-score =  -2.48, R)
>consensus
___________CAAUUAUAUAGCCGGCGGAUCGGUGGGGCAUAUAAAUGCACCUUGAUUAGUGGAUCAGCCGCCGGCGCAAAAAUUCGCCGGCAAUCCAAAACACAAUCG
.....................((((.(((((((((((.((((....))))...((((((....))))))))))))........))))).))))................. (-17.70 = -19.30 +   1.60)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:25:58 2011