Locus 14324

Sequence ID dm3.chrX
Location 12,639,994 – 12,640,134
Length 140
Max. P 0.998632
window19719 window19720

overview

Window 9

Location 12,639,994 – 12,640,134
Length 140
Sequences 3
Columns 140
Reading direction forward
Mean pairwise identity 81.38
Shannon entropy 0.25878
G+C content 0.42119
Mean single sequence MFE -43.39
Consensus MFE -33.15
Energy contribution -33.72
Covariance contribution 0.57
Combinations/Pair 1.22
Mean z-score -3.21
Structure conservation index 0.76
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.83
SVM RNA-class probability 0.995681
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 12639994 140 + 22422827
GAGCACUACAAGUAUAUUCGCAUAAAAAGCGGUGGCGGUUUAAGUAACAACCGCAUCAAAUGCGUUUGCGGUGUUUUACCACCGCAUUGUCUGUGUGUGGAACACAGACAAUACACAAAAAUAUGCGACGGAAUAGGACA
.................(((((((....(((((((..(((.....))).((((((...........))))))......)))))))(((((((((((.....))))))))))).........)))))))............ ( -47.90, z-score =  -3.78, R)
>droSec1.super_59 125241 135 + 165940
GAGCACUACAAAUAUACUCGCUUAAGAAGUGGUGGCUGGAUUACUCACA-CCGCAUAAUAUGCUCUUGCGGUGUUUUACCACCGUAAUGUCUGUGCGUAUUGCAU----AAUACACAAAAAUAUGCGGUGGAAAAAGACA
(((((............((......)).((((((...(.....)...))-))))......))))).....((.((((.((((((((.(((...((.(((((....----))))).))...))))))))))).)))).)). ( -39.20, z-score =  -2.22, R)
>droYak2.chrU 14197772 138 + 28119190
GAGCACUACAAAUAUACUUGCAUAAAAAGCGGUGGCUCUGUUACUAAUA-CCGCAUAAUAUGCGGUUGCGGUGUUUUACAACCGCUUUGUCUGUGUG-GGAACACAGACAAUACACAAAAAUAUGCGACGGAAUAAGACA
.................(((((((.((((((((........((((...(-((((((...)))))))...)))).......))))))))((((((((.-...))))))))............)))))))............ ( -43.06, z-score =  -3.64, R)
>consensus
GAGCACUACAAAUAUACUCGCAUAAAAAGCGGUGGCUGUAUUACUAACA_CCGCAUAAUAUGCGCUUGCGGUGUUUUACCACCGCAUUGUCUGUGUGUGGAACACAGACAAUACACAAAAAUAUGCGACGGAAUAAGACA
.................(((((((....(((((((..........((((.(((((...........)))))))))...)))))))..(((((((((.....)))))))))...........)))))))............ (-33.15 = -33.72 +   0.57)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 12,639,994 – 12,640,134
Length 140
Sequences 3
Columns 140
Reading direction reverse
Mean pairwise identity 81.38
Shannon entropy 0.25878
G+C content 0.42119
Mean single sequence MFE -44.17
Consensus MFE -30.72
Energy contribution -34.17
Covariance contribution 3.45
Combinations/Pair 1.07
Mean z-score -3.95
Structure conservation index 0.70
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.43
SVM RNA-class probability 0.998632
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 12639994 140 - 22422827
UGUCCUAUUCCGUCGCAUAUUUUUGUGUAUUGUCUGUGUUCCACACACAGACAAUGCGGUGGUAAAACACCGCAAACGCAUUUGAUGCGGUUGUUACUUAAACCGCCACCGCUUUUUAUGCGAAUAUACUUGUAGUGCUC
.(..((((....(((((((....((((((((((((((((.....)))))))))))((((((......))))))..)))))......((((((........))))))..........)))))))........))))..).. ( -51.60, z-score =  -5.48, R)
>droSec1.super_59 125241 135 - 165940
UGUCUUUUUCCACCGCAUAUUUUUGUGUAUU----AUGCAAUACGCACAGACAUUACGGUGGUAAAACACCGCAAGAGCAUAUUAUGCGG-UGUGAGUAAUCCAGCCACCACUUCUUAAGCGAGUAUAUUUGUAGUGCUC
..............((...(((.((((((((----....)))))))).)))......((((((...((((((((.((.....)).)))))-)))((....))..)))))).........))((((((.......)))))) ( -38.50, z-score =  -2.50, R)
>droYak2.chrU 14197772 138 - 28119190
UGUCUUAUUCCGUCGCAUAUUUUUGUGUAUUGUCUGUGUUCC-CACACAGACAAAGCGGUUGUAAAACACCGCAACCGCAUAUUAUGCGG-UAUUAGUAACAGAGCCACCGCUUUUUAUGCAAGUAUAUUUGUAGUGCUC
............(((((((..........((((((((((...-.)))))))))).((((((((........))))))))....)))))))-...........((((.((..(....((((....))))...)..)))))) ( -42.40, z-score =  -3.85, R)
>consensus
UGUCUUAUUCCGUCGCAUAUUUUUGUGUAUUGUCUGUGUUCCACACACAGACAAUGCGGUGGUAAAACACCGCAAACGCAUAUUAUGCGG_UGUUAGUAAAACAGCCACCGCUUUUUAUGCGAGUAUAUUUGUAGUGCUC
..............(((((.....(((((((((((((((.....)))))))))))))((((((..(((((((((...........))))).)))).........))))))))....)))))((((((.......)))))) (-30.72 = -34.17 +   3.45)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:38:03 2011