Locus 4724

Sequence ID dm3.chr2R
Location 15,299,429 – 15,299,555
Length 126
Max. P 0.802603
window6483 window6484

overview

Window 3

Location 15,299,429 – 15,299,521
Length 92
Sequences 6
Columns 98
Reading direction reverse
Mean pairwise identity 74.52
Shannon entropy 0.47507
G+C content 0.34650
Mean single sequence MFE -19.62
Consensus MFE -9.54
Energy contribution -9.43
Covariance contribution -0.11
Combinations/Pair 1.27
Mean z-score -1.79
Structure conservation index 0.49
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.74
SVM RNA-class probability 0.802603
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 15299429 92 - 21146708
---AGUUGGUUCGGGUUGCAU---UUUUUUGGCUGAGCCAAGAAAUUGUUUUUCGAUUUAUCUUAGUCGUGUUGACAUUAUUUAUUUAUCUUUAGCAU
---.(((((.(((((..(((.---(((((((((...))))))))).)))..))))).........(((.....)))...............))))).. ( -21.60, z-score =  -2.67, R)
>droAna3.scaffold_13266 17920116 87 + 19884421
GGUUUCAGUUUUAAGUUUCAU-----UUUUGGCUGAGCCAAGAAAUUGUUAUUCGAUUUGUUAUCUCAGUCGCGACAUCGUU--UUGAUUGCCA----
(((.((((.............-----....(((((((..((.((((((.....)))))).))..)))))))(((....))).--))))..))).---- ( -22.20, z-score =  -2.69, R)
>droEre2.scaffold_4845 9497995 79 - 22589142
---AGUUGGUUCGGGUUGCAU-----UUUUGGCUGAGCCAAGAAAUUGUUUUUCGA-----------CGUGGUGACAUUAUUUAUUUAUCUGUAGGAC
---.......(((((..((((-----(((((((...))))))))..)))..)))))-----------.(((....))).................... ( -17.00, z-score =  -0.89, R)
>droYak2.chr2R 7262236 90 + 21139217
---ACUUGGCUCGAAUUGCAU-----UUUUGGCUGAGCCAAGAAAUUGUUUUUUGAUUUGUUAUCUUUGUCGUGACAUUAUGUAUUUAUCUUUAGAAC
---.(((((((((....((..-----.....))))))))))).....(((((..(((..((......(((....)))......))..)))...))))) ( -18.50, z-score =  -1.64, R)
>droSec1.super_1 12811981 94 - 14215200
---AGUUGGUUCGGGUUGCAUUUUUUUUUUGGCUGAGCCAAGAAAUUGUUUUUCGAUUUGUUAUCUUAGUCGUGUUGACA-UUAUUUAUCUUUAGCAU
---.(((((.(((((..(((....(((((((((...))))))))).)))..)))))..(((((.(........).)))))-..........))))).. ( -19.80, z-score =  -1.80, R)
>droSim1.chr2R 14011584 91 - 19596830
---AGUUGGUUCGGGUUGCAU----UUUUUGGCUGAGGCAAGAAAUUGUUGUUCGAUUUGUUAUCUUAGUGUUGACAUUAUUUAUUUAUCUCUAGCAU
---.(((((.(((..(.(((.----(((((.((....)).))))).))).)..)))..(((((.(.....).)))))..............))))).. ( -18.60, z-score =  -1.06, R)
>consensus
___AGUUGGUUCGGGUUGCAU_____UUUUGGCUGAGCCAAGAAAUUGUUUUUCGAUUUGUUAUCUUAGUCGUGACAUUAUUUAUUUAUCUUUAGCAU
..........(((((..(((......(((((((...)))))))...)))..))))).......................................... ( -9.54 =  -9.43 +  -0.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 15,299,458 – 15,299,555
Length 97
Sequences 6
Columns 107
Reading direction reverse
Mean pairwise identity 78.42
Shannon entropy 0.39463
G+C content 0.35991
Mean single sequence MFE -21.98
Consensus MFE -11.35
Energy contribution -11.11
Covariance contribution -0.24
Combinations/Pair 1.38
Mean z-score -1.81
Structure conservation index 0.52
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.20
SVM RNA-class probability 0.590660
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 15299458 97 - 21146708
UGUAGGAAU-CGAAUGAAGUAGUCGGU-UCGUUUUUAGUUGGUUCGGGUUGCAUU-----UUUUUGGCUGAGCCAAGAAAUUGUUUUUCGAUUUAUCUUAGUCG---
.....((((-(((.........)))))-))......((.(((.(((((..(((.(-----((((((((...))))))))).)))..))))).))).))......--- ( -24.40, z-score =  -2.25, R)
>droAna3.scaffold_13266 17920138 102 + 19884421
UGUAGAAAUGCGACUCA---AGUUUAUAGUAAUUUUUUUUGGUUUCAGUUUUAAGUUUCAUUUUUGGCUGAGCCAAGAAAUUGUUAUUCGAUUUGUUAUCUCAGU--
.(((....)))((..((---((((...((((((.((((((((((.(((((..((((...))))..)))))))))))))))..)))))).))))))...)).....-- ( -23.90, z-score =  -2.93, R)
>droEre2.scaffold_4845 9498022 83 - 22589142
UGUAGGAAU-UGAAUAA---AGUCGGU-UCGUUUUUAGUUGGUUCGGGUUGCA-------UUUUUGGCUGAGCCAAGAAAUUGUUUUUCGACGUG------------
.....((((-(((....---..)))))-)).............(((((..(((-------((((((((...))))))))..)))..)))))....------------ ( -19.40, z-score =  -1.34, R)
>droYak2.chr2R 7262264 93 + 21139217
UGUAGGAAU-UGAAUAA---AGUCGGU-UCGUUUUUACUUGGCUCGAAUUGCA-------UUUUUGGCUGAGCCAAGAAAUUGUUUUUUGAUUUGUUAUCUUUGU--
.((((((((-.((((..---.....))-)))))))))).(((((((((..(((-------((((((((...))))))))..)))..)))))...)))).......-- ( -19.80, z-score =  -1.11, R)
>droSec1.super_1 12812006 100 - 14215200
UGUAGGAAU-CGAAUGA---AGUCGGU-UCGUUUUUAGUUGGUUCGGGUUGCAUUUU--UUUUUUGGCUGAGCCAAGAAAUUGUUUUUCGAUUUGUUAUCUUAGUCG
.....((((-(((....---..)))))-)).............(((((..(((....--(((((((((...))))))))).)))..)))))................ ( -22.90, z-score =  -1.59, R)
>droSim1.chr2R 14011612 94 - 19596830
UGUAGGAAU-CGAAUGA---AGUCGGU-UCGUUUUUAGUUGGUUCGGGUUGCAU------UUUUUGGCUGAGGCAAGAAAUUGUUGUUCGAUUUGUUAUCUUAGU--
(((((((((-(((.(((---((.((..-.)).))))).)))))))...))))).------......((((((..((.((((((.....)))))).))..))))))-- ( -21.50, z-score =  -1.64, R)
>consensus
UGUAGGAAU_CGAAUGA___AGUCGGU_UCGUUUUUAGUUGGUUCGGGUUGCAU______UUUUUGGCUGAGCCAAGAAAUUGUUUUUCGAUUUGUUAUCUUAGU__
.....................(((((...((.((((..(((((((((.(................).))))))))))))).))....)))))............... (-11.35 = -11.11 +  -0.24)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:34:44 2011