Locus 34

Sequence ID dm3.chr2L
Location 249,542 – 249,639
Length 97
Max. P 0.975205
window54 window55

overview

Window 4

Location 249,542 – 249,639
Length 97
Sequences 5
Columns 97
Reading direction forward
Mean pairwise identity 80.31
Shannon entropy 0.34220
G+C content 0.35391
Mean single sequence MFE -20.29
Consensus MFE -13.22
Energy contribution -14.30
Covariance contribution 1.08
Combinations/Pair 1.19
Mean z-score -2.51
Structure conservation index 0.65
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.92
SVM RNA-class probability 0.975205
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 249542 97 + 23011544
AGACUAUCAAUAUAGAAAUAUUGAUGACAGCUACAGUGCAGCUUGGACCAAGAACACCAAAUUUGUUAUAAAAAGAAAAAGAUUGCACUCGAGUUGU
....(((((((((....)))))))))((((((..((((((((((........((((.......))))...........))).)))))))..)))))) ( -22.81, z-score =  -3.28, R)
>droEre2.scaffold_4929 296181 97 + 26641161
AGACUAUCAAUAUCGAAAUAUUGAUGCCAGCUACAGUGCAGCUUGGUCCAAGAAUACCAAAACAAGUAUAAAAAAAUAUUACAUAUACUCGAGUUUU
(((((((((((((....))))))))(((((((.......))).))))...............(.((((((.............)))))).)))))). ( -14.32, z-score =  -0.88, R)
>droYak2.chr2L 242882 90 + 22324452
AGACUAUCAAUAUCGAAAUAUUGAUGCCAGCUACAGUGCAGCUUGGUCCAACA-------AACCAACACGAAAAAAAGUUAAAUGUAGUCGAGUUUG
(((((((((((((....))))))))..(.((((((....((((((((......-------.))))...........))))...)))))).)))))). ( -16.00, z-score =  -0.88, R)
>droSec1.super_14 247086 97 + 2068291
AAACUAUCAAUAUCGAAAUAUUGAUGACAACUACAGUGCAGCUCGGACCGAGAACACCGAAUUAGGUAUAAAAAGAAAAAAAUCGCACUCGAGUUGU
....(((((((((....)))))))))((((((..(((((..((((...))))...(((......))).................)))))..)))))) ( -25.20, z-score =  -4.05, R)
>droSim1.chr2L 254824 97 + 22036055
AAACUAUCAAUAUCGAAAUAUUGAUGACAACUACAGUGCAGCUUGGACCGAGAACACCGAAUUAGGUAUAAAAAGAAAAAAAUCGCACUCGAGUUGU
....(((((((((....)))))))))((((((..(((((..((((...))))...(((......))).................)))))..)))))) ( -23.10, z-score =  -3.43, R)
>consensus
AGACUAUCAAUAUCGAAAUAUUGAUGACAGCUACAGUGCAGCUUGGACCAAGAACACCAAAUUAGGUAUAAAAAGAAAAAAAUUGCACUCGAGUUGU
....(((((((((....)))))))))((((((..(((((..((((...))))...(((......))).................)))))..)))))) (-13.22 = -14.30 +   1.08)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 249,542 – 249,639
Length 97
Sequences 5
Columns 97
Reading direction reverse
Mean pairwise identity 80.31
Shannon entropy 0.34220
G+C content 0.35391
Mean single sequence MFE -21.83
Consensus MFE -13.62
Energy contribution -12.22
Covariance contribution -1.40
Combinations/Pair 1.44
Mean z-score -2.17
Structure conservation index 0.62
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.14
SVM RNA-class probability 0.899031
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 249542 97 - 23011544
ACAACUCGAGUGCAAUCUUUUUCUUUUUAUAACAAAUUUGGUGUUCUUGGUCCAAGCUGCACUGUAGCUGUCAUCAAUAUUUCUAUAUUGAUAGUCU
(((.((..((((((..(((...((....(((.((....)).)))....))...))).))))))..)).))).((((((((....))))))))..... ( -16.00, z-score =  -0.48, R)
>droEre2.scaffold_4929 296181 97 - 26641161
AAAACUCGAGUAUAUGUAAUAUUUUUUUAUACUUGUUUUGGUAUUCUUGGACCAAGCUGCACUGUAGCUGGCAUCAAUAUUUCGAUAUUGAUAGUCU
......((((((((.............))))))))...((((........))))((((((...))))))(((((((((((....)))))))).))). ( -23.12, z-score =  -2.40, R)
>droYak2.chr2L 242882 90 - 22324452
CAAACUCGACUACAUUUAACUUUUUUUCGUGUUGGUU-------UGUUGGACCAAGCUGCACUGUAGCUGGCAUCAAUAUUUCGAUAUUGAUAGUCU
.......(((((((..............(((((((..-------((((((.(((.(((((...))))))))..))))))..))))))))).))))). ( -22.13, z-score =  -2.15, R)
>droSec1.super_14 247086 97 - 2068291
ACAACUCGAGUGCGAUUUUUUUCUUUUUAUACCUAAUUCGGUGUUCUCGGUCCGAGCUGCACUGUAGUUGUCAUCAAUAUUUCGAUAUUGAUAGUUU
((((((..((((((..............(((((......))))).((((...)))).))))))..)))))).((((((((....))))))))..... ( -24.50, z-score =  -2.87, R)
>droSim1.chr2L 254824 97 - 22036055
ACAACUCGAGUGCGAUUUUUUUCUUUUUAUACCUAAUUCGGUGUUCUCGGUCCAAGCUGCACUGUAGUUGUCAUCAAUAUUUCGAUAUUGAUAGUUU
((((((..((((((.(((....((....(((((......)))))....))...))).))))))..)))))).((((((((....))))))))..... ( -23.40, z-score =  -2.94, R)
>consensus
ACAACUCGAGUGCAAUUUUUUUCUUUUUAUACCUAAUUCGGUGUUCUUGGUCCAAGCUGCACUGUAGCUGUCAUCAAUAUUUCGAUAUUGAUAGUCU
.....(((((.(((....(((............))).....))).)))))....((((((...))))))...((((((((....))))))))..... (-13.62 = -12.22 +  -1.40)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:05:24 2011