Locus 15603

Sequence ID dm3.chrX
Location 19,889,271 – 19,889,351
Length 80
Max. P 0.996881
window21516 window21517

overview

Window 6

Location 19,889,271 – 19,889,351
Length 80
Sequences 10
Columns 80
Reading direction forward
Mean pairwise identity 83.57
Shannon entropy 0.37517
G+C content 0.39277
Mean single sequence MFE -20.12
Consensus MFE -15.72
Energy contribution -15.95
Covariance contribution 0.23
Combinations/Pair 1.11
Mean z-score -2.43
Structure conservation index 0.78
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.58
SVM RNA-class probability 0.992952
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 19889271 80 + 22422827
CCGGAGUCAAAGUGUAGUGACAUUUAACGGAAAUGAAGAAAAUUUUUCUCAUUUCCUUUGAGUGAGGCGGUAGUGCCCAG
.....((((........))))((((((.((((((((.(((.....))))))))))).))))))(.((((....))))).. ( -21.30, z-score =  -2.07, R)
>droWil1.scaffold_180777 3941482 80 - 4753960
CCAAAGUCAAAGUGUAGUGACAUUUAACGGAAAUGAAGAAAAUUUUUCUCAUUUCCUUUGAAUGUUGGAUGAAUGGACAA
.....(((....(((..((((((((((.((((((((.(((.....))))))))))).)))))))))).)))....))).. ( -23.30, z-score =  -3.44, R)
>droPer1.super_13 1220295 68 + 2293547
CCAGAGUCAAAGUGUAGUGACAUUUAACGGAAAUGAAGAAAAUUUUUCUCAUUUCCUUUGAGUGAGCC------------
.....((((........))))((((((.((((((((.(((.....))))))))))).)))))).....------------ ( -17.30, z-score =  -2.70, R)
>dp4.chrXL_group1e 5193946 68 - 12523060
CCAGAGUCAAAGUGUAGUGACAUUUAACGGAAAUGAAGAAAAUUUUUCUCAUUUCCUUUGAGUGAGCC------------
.....((((........))))((((((.((((((((.(((.....))))))))))).)))))).....------------ ( -17.30, z-score =  -2.70, R)
>droAna3.scaffold_13417 5053369 77 - 6960332
CCAGAGUCAAAGUGUAGUGACAUUUAACGGAAAUGAAGAAAAUUUUUCUCAUUUCCUUUGAGUGA-GGCCG--UGCCCAG
...........(((..((..(((((((.((((((((.(((.....))))))))))).))))))).-.))..--))).... ( -20.30, z-score =  -2.67, R)
>droEre2.scaffold_4690 10040838 80 + 18748788
UCGGAGUCAAAGUGUAGUGACAUUUAACGGAAAUGAAGAAAAUUUUUCUCAUUUCCUUUGAGUGAGGCGGUAGUGCCCAA
.....((((........))))((((((.((((((((.(((.....))))))))))).))))))(.((((....))))).. ( -21.30, z-score =  -2.00, R)
>droYak2.chrX 10236127 80 - 21770863
CUGGAGUCAAAGUGUAGUGACAUUUAACGGAAAUGAAGAAAAUUUUUCUCAUUUCCUUUGAGUGAGGCGGUAGUGCCCAG
((((.(.((.......((..(((((((.((((((((.(((.....))))))))))).)))))))..)).....))))))) ( -23.10, z-score =  -2.65, R)
>droSec1.super_8 2120213 80 + 3762037
CCGGAGUCAAAGUGUAGUGACAUUUAACGGAAAUGAAGAAAAUUUUUCUCAUUUCCUUUAAGUGAGGCGGUAGUGCCCAG
.....((((........))))((((((.((((((((.(((.....))))))))))).))))))(.((((....))))).. ( -21.20, z-score =  -2.37, R)
>droSim1.chrX 15305192 80 + 17042790
CCGGAGUCAAAGUGUAGUGACAUUUAACGGAAAUGAAGAAAAUUUUUCUCAUUUCCUUUGAGUGAGGCGGUAGUGCCCAG
.....((((........))))((((((.((((((((.(((.....))))))))))).))))))(.((((....))))).. ( -21.30, z-score =  -2.07, R)
>droGri2.scaffold_14853 2842917 69 + 10151454
----------AGUGUAGCGACAUUUAAAGGAAAUUAACAAAUAUUUUCUCAUUUCCUUUC-GUGAGGCGUUCGCAUGCAG
----------..(((((((((....(((((((((................)))))))))(-....)..).)))).)))). ( -14.79, z-score =  -1.67, R)
>consensus
CCGGAGUCAAAGUGUAGUGACAUUUAACGGAAAUGAAGAAAAUUUUUCUCAUUUCCUUUGAGUGAGGCGGUAGUGCCCAG
....................(((((((.((((((((.(((.....))))))))))).)))))))................ (-15.72 = -15.95 +   0.23)

alignment

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secondary structure

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dotplot

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Window 7

Location 19,889,271 – 19,889,351
Length 80
Sequences 10
Columns 80
Reading direction reverse
Mean pairwise identity 83.57
Shannon entropy 0.37517
G+C content 0.39277
Mean single sequence MFE -17.70
Consensus MFE -12.62
Energy contribution -13.32
Covariance contribution 0.70
Combinations/Pair 1.00
Mean z-score -2.91
Structure conservation index 0.71
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.00
SVM RNA-class probability 0.996881
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 19889271 80 - 22422827
CUGGGCACUACCGCCUCACUCAAAGGAAAUGAGAAAAAUUUUCUUCAUUUCCGUUAAAUGUCACUACACUUUGACUCCGG
..((((......))))........(((((((((((.....))).))))))))(((((((((....))).))))))..... ( -19.80, z-score =  -3.36, R)
>droWil1.scaffold_180777 3941482 80 + 4753960
UUGUCCAUUCAUCCAACAUUCAAAGGAAAUGAGAAAAAUUUUCUUCAUUUCCGUUAAAUGUCACUACACUUUGACUUUGG
............((((........(((((((((((.....))).))))))))(((((((((....))).)))))).)))) ( -17.10, z-score =  -2.66, R)
>droPer1.super_13 1220295 68 - 2293547
------------GGCUCACUCAAAGGAAAUGAGAAAAAUUUUCUUCAUUUCCGUUAAAUGUCACUACACUUUGACUCUGG
------------............(((((((((((.....))).))))))))(((((((((....))).))))))..... ( -15.10, z-score =  -2.69, R)
>dp4.chrXL_group1e 5193946 68 + 12523060
------------GGCUCACUCAAAGGAAAUGAGAAAAAUUUUCUUCAUUUCCGUUAAAUGUCACUACACUUUGACUCUGG
------------............(((((((((((.....))).))))))))(((((((((....))).))))))..... ( -15.10, z-score =  -2.69, R)
>droAna3.scaffold_13417 5053369 77 + 6960332
CUGGGCA--CGGCC-UCACUCAAAGGAAAUGAGAAAAAUUUUCUUCAUUUCCGUUAAAUGUCACUACACUUUGACUCUGG
..((((.--..)))-)........(((((((((((.....))).))))))))(((((((((....))).))))))..... ( -18.00, z-score =  -2.33, R)
>droEre2.scaffold_4690 10040838 80 - 18748788
UUGGGCACUACCGCCUCACUCAAAGGAAAUGAGAAAAAUUUUCUUCAUUUCCGUUAAAUGUCACUACACUUUGACUCCGA
..((((......))))........(((((((((((.....))).))))))))(((((((((....))).))))))..... ( -19.80, z-score =  -3.35, R)
>droYak2.chrX 10236127 80 + 21770863
CUGGGCACUACCGCCUCACUCAAAGGAAAUGAGAAAAAUUUUCUUCAUUUCCGUUAAAUGUCACUACACUUUGACUCCAG
((((((......))).........(((((((((((.....))).))))))))(((((((((....))).))))))..))) ( -19.90, z-score =  -3.71, R)
>droSec1.super_8 2120213 80 - 3762037
CUGGGCACUACCGCCUCACUUAAAGGAAAUGAGAAAAAUUUUCUUCAUUUCCGUUAAAUGUCACUACACUUUGACUCCGG
..((((......))))........(((((((((((.....))).))))))))(((((((((....))).))))))..... ( -19.80, z-score =  -3.45, R)
>droSim1.chrX 15305192 80 - 17042790
CUGGGCACUACCGCCUCACUCAAAGGAAAUGAGAAAAAUUUUCUUCAUUUCCGUUAAAUGUCACUACACUUUGACUCCGG
..((((......))))........(((((((((((.....))).))))))))(((((((((....))).))))))..... ( -19.80, z-score =  -3.36, R)
>droGri2.scaffold_14853 2842917 69 - 10151454
CUGCAUGCGAACGCCUCAC-GAAAGGAAAUGAGAAAAUAUUUGUUAAUUUCCUUUAAAUGUCGCUACACU----------
......((((.((.....)-)(((((((((..(((....)))....))))))))).....))))......---------- ( -12.60, z-score =  -1.47, R)
>consensus
CUGGGCACUACCGCCUCACUCAAAGGAAAUGAGAAAAAUUUUCUUCAUUUCCGUUAAAUGUCACUACACUUUGACUCCGG
........................(((((((((((.....))).))))))))(((((((((....))).))))))..... (-12.62 = -13.32 +   0.70)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 02:02:35 2011