Locus 13838

Sequence ID dm3.chrX
Location 9,488,534 – 9,488,642
Length 108
Max. P 0.782583
window19039 window19040

overview

Window 9

Location 9,488,534 – 9,488,642
Length 108
Sequences 4
Columns 110
Reading direction forward
Mean pairwise identity 80.06
Shannon entropy 0.31680
G+C content 0.51790
Mean single sequence MFE -31.80
Consensus MFE -20.71
Energy contribution -21.53
Covariance contribution 0.81
Combinations/Pair 1.05
Mean z-score -1.94
Structure conservation index 0.65
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.67
SVM RNA-class probability 0.782583
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 9488534 108 + 22422827
AACGAGCCCAAAUGCAAACCAAUUGAGCGCCUCUCUCGGCGGAACAAACCGCCAGAAACUGACU-UUGGCGAGCAUUACGGGUAUGC-UAUAGAUGUGGCUACUAUUACG
....((((((...(((.(((...((..((((..(((.(((((......))))))))........-..))))..)).....))).)))-......)).))))......... ( -31.90, z-score =  -2.13, R)
>droSim1.chrX_random 2730689 96 + 5698898
AACGAGCCCAAAUGCAAACCAAUUGAGCGCCUCUCUCGGCGGAACAAACCGCCAGAAACCGACU-CUGGCGGGCAUUACGGGUAUAC-UAUAGAUGUG------------
.....((((.(((((............((((......)))).......((((((((.......)-))))))))))))..))))....-..........------------ ( -33.20, z-score =  -3.16, R)
>droSec1.super_15 255281 96 + 1954846
AACGAGCCCAAAUGCAAACCAAUUGAGCGCCUCUCUCGGCGGAACAAACCGCCAGAAACCGAAU-CUGGCGGGCAGUACGGGUAUAC-UAUAGAUGUG------------
.....((((...(((............((((......)))).......((((((((.......)-))))))))))....))))....-..........------------ ( -31.70, z-score =  -2.34, R)
>droYak2.chrX 18081232 110 + 21770863
AACGAGCCCAAAUGCAAACCAAUUGAGUGAUUCUCUCGGCGGAACGAACCGCCAGAAACUGACUUCUGGAGGGUAGUACGUCUAUAGAUGCGGGUAGUACGGGUACUAGG
.....((((...(((...((......(((...((((((((((......)))))((((......)))).)))))...)))(((....)))..))...))).))))...... ( -30.40, z-score =  -0.15, R)
>consensus
AACGAGCCCAAAUGCAAACCAAUUGAGCGCCUCUCUCGGCGGAACAAACCGCCAGAAACCGACU_CUGGCGGGCAGUACGGGUAUAC_UAUAGAUGUG____________
.....((((.(((((...(((...(((.......)))(((((......))))).............)))...)))))..))))........................... (-20.71 = -21.53 +   0.81)

alignment

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secondary structure

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dotplot

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Window 0

Location 9,488,534 – 9,488,642
Length 108
Sequences 4
Columns 110
Reading direction reverse
Mean pairwise identity 80.06
Shannon entropy 0.31680
G+C content 0.51790
Mean single sequence MFE -31.35
Consensus MFE -24.30
Energy contribution -25.68
Covariance contribution 1.38
Combinations/Pair 1.07
Mean z-score -1.19
Structure conservation index 0.78
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.13
SVM RNA-class probability 0.559129
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 9488534 108 - 22422827
CGUAAUAGUAGCCACAUCUAUA-GCAUACCCGUAAUGCUCGCCAA-AGUCAGUUUCUGGCGGUUUGUUCCGCCGAGAGAGGCGCUCAAUUGGUUUGCAUUUGGGCUCGUU
.((.((((.........)))).-))...((((.(((((..(((((-(((...((((((((((......))))).)))))...)))...)))))..)))))))))...... ( -34.10, z-score =  -1.59, R)
>droSim1.chrX_random 2730689 96 - 5698898
------------CACAUCUAUA-GUAUACCCGUAAUGCCCGCCAG-AGUCGGUUUCUGGCGGUUUGUUCCGCCGAGAGAGGCGCUCAAUUGGUUUGCAUUUGGGCUCGUU
------------..........-.....((((.((((((((((((-((.....))))))))).(((...((((......))))..))).......)))))))))...... ( -33.70, z-score =  -1.88, R)
>droSec1.super_15 255281 96 - 1954846
------------CACAUCUAUA-GUAUACCCGUACUGCCCGCCAG-AUUCGGUUUCUGGCGGUUUGUUCCGCCGAGAGAGGCGCUCAAUUGGUUUGCAUUUGGGCUCGUU
------------........((-((((....)))))).(((((((-(.......))))))))........(((......)))((((((.((.....)).))))))..... ( -31.80, z-score =  -1.37, R)
>droYak2.chrX 18081232 110 - 21770863
CCUAGUACCCGUACUACCCGCAUCUAUAGACGUACUACCCUCCAGAAGUCAGUUUCUGGCGGUUCGUUCCGCCGAGAGAAUCACUCAAUUGGUUUGCAUUUGGGCUCGUU
..(((((....)))))((((((......((((....(((..(((((((....))))))).))).))))..((((((((.....)))..))))).)))....)))...... ( -25.80, z-score =   0.08, R)
>consensus
____________CACAUCUAUA_GUAUACCCGUAAUGCCCGCCAG_AGUCAGUUUCUGGCGGUUUGUUCCGCCGAGAGAGGCGCUCAAUUGGUUUGCAUUUGGGCUCGUU
............................((((.(((((..(((((.(((...((((((((((......))))).)))))...)))...)))))..)))))))))...... (-24.30 = -25.68 +   1.38)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:28:46 2011