Locus 5440

Sequence ID dm3.chr2R
Location 20,296,855 – 20,296,954
Length 99
Max. P 0.897856
window7466 window7467

overview

Window 6

Location 20,296,855 – 20,296,954
Length 99
Sequences 4
Columns 99
Reading direction forward
Mean pairwise identity 73.77
Shannon entropy 0.42823
G+C content 0.48314
Mean single sequence MFE -29.95
Consensus MFE -20.61
Energy contribution -21.05
Covariance contribution 0.44
Combinations/Pair 1.21
Mean z-score -1.51
Structure conservation index 0.69
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.14
SVM RNA-class probability 0.897856
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 20296855 99 + 21146708
UAAUUCCAUAUGAACUGGUGCUUAUAUGCUAAUGGUUAAGUCAAGGUAACUCACCUCGUUGUUGGCCAGCUUGGGGGCCAGUGGAUCGGUGACCUUGGC
............(((((..((......))...)))))..(((((((....(((((...(..((((((........))))))..)...)))))))))))) ( -32.20, z-score =  -1.24, R)
>droSim1.chr2R 18750168 94 + 19596830
UAAUUGGAUUUGAAUUGGUGCUUAUA-----AUGGUUAAGUCAGGGGAACUCACCUCGUUGUUGGCCAGUUUGGGGGCCAGUGGAUCGGUGACCUUGGC
......((((...((((((.((((..-----.(((((((....((((......))))....)))))))...)))).)))))).))))(....)...... ( -28.30, z-score =  -0.88, R)
>droSec1.super_23 167089 99 + 989336
UAAUUGCAUUUGAAUUGGUGCUUAUAUGCUAAUGGUUAAGUCAGGGGAACUCACCUCGUUGUUGGCCAGCUUGGGGGCCAGUGGAUCGGUGACCUUGGC
.....(((((......)))))..................(((((((....(((((...(..((((((........))))))..)...)))))))))))) ( -31.60, z-score =  -0.90, R)
>droAna3.scaffold_13266 15834312 82 + 19884421
-----------GGGGCAAUAGUUACAGG---AUUCUUAAGGCAAG---ACUUACCUCAUUAUUGGCCAAUCGUGGAGCCAAAGGAUCCGUGACUUUUGC
-----------...((((.((((((.((---((((((..(((...---.....((........))(((....))).))).)))))))))))))).)))) ( -27.70, z-score =  -3.00, R)
>consensus
UAAUUGCAUUUGAAUUGGUGCUUAUAUG___AUGGUUAAGUCAAGGGAACUCACCUCGUUGUUGGCCAGCUUGGGGGCCAGUGGAUCGGUGACCUUGGC
.......................................(((((((....(((((...(..((((((........))))))..)...)))))))))))) (-20.61 = -21.05 +   0.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 20,296,855 – 20,296,954
Length 99
Sequences 4
Columns 99
Reading direction reverse
Mean pairwise identity 73.77
Shannon entropy 0.42823
G+C content 0.48314
Mean single sequence MFE -21.66
Consensus MFE -12.59
Energy contribution -12.96
Covariance contribution 0.37
Combinations/Pair 1.17
Mean z-score -1.36
Structure conservation index 0.58
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.12
SVM RNA-class probability 0.551419
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 20296855 99 - 21146708
GCCAAGGUCACCGAUCCACUGGCCCCCAAGCUGGCCAACAACGAGGUGAGUUACCUUGACUUAACCAUUAGCAUAUAAGCACCAGUUCAUAUGGAAUUA
..((((((((((.......(((((........))))).......)))))....))))).............(((((.(((....))).)))))...... ( -24.94, z-score =  -1.33, R)
>droSim1.chr2R 18750168 94 - 19596830
GCCAAGGUCACCGAUCCACUGGCCCCCAAACUGGCCAACAACGAGGUGAGUUCCCCUGACUUAACCAU-----UAUAAGCACCAAUUCAAAUCCAAUUA
.....(((((((.......(((((........))))).......))))).......((.((((.....-----..))))))))................ ( -17.54, z-score =  -0.85, R)
>droSec1.super_23 167089 99 - 989336
GCCAAGGUCACCGAUCCACUGGCCCCCAAGCUGGCCAACAACGAGGUGAGUUCCCCUGACUUAACCAUUAGCAUAUAAGCACCAAUUCAAAUGCAAUUA
((((.(((((((.......(((((........))))).......)))))....)).))............((......))............))..... ( -19.14, z-score =  -0.08, R)
>droAna3.scaffold_13266 15834312 82 - 19884421
GCAAAAGUCACGGAUCCUUUGGCUCCACGAUUGGCCAAUAAUGAGGUAAGU---CUUGCCUUAAGAAU---CCUGUAACUAUUGCCCC-----------
((((.(((.((((((.((((((((........))))))...(((((((...---..))))))))).))---)).)).))).))))...----------- ( -25.00, z-score =  -3.19, R)
>consensus
GCCAAGGUCACCGAUCCACUGGCCCCCAAACUGGCCAACAACGAGGUGAGUUCCCCUGACUUAACCAU___CAUAUAAGCACCAAUUCAAAUGCAAUUA
....((.(((((.......(((((........))))).......))))).))............................................... (-12.59 = -12.96 +   0.37)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:48:24 2011