Locus 754

Sequence ID dm3.chr2L
Location 5,296,744 – 5,296,876
Length 132
Max. P 0.998817
window1008 window1009 window1010

overview

Window 8

Location 5,296,744 – 5,296,839
Length 95
Sequences 4
Columns 95
Reading direction forward
Mean pairwise identity 73.90
Shannon entropy 0.41925
G+C content 0.32935
Mean single sequence MFE -20.68
Consensus MFE -13.73
Energy contribution -15.72
Covariance contribution 2.00
Combinations/Pair 1.15
Mean z-score -1.95
Structure conservation index 0.66
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.68
SVM RNA-class probability 0.960716
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 5296744 95 + 23011544
UUUCAAAGAAUGUGUGCUAUUACGAAACAUAGAUCAGCUUAGAUUGUACUAGAUGCAUAGAAGACUGGUCUUCUGUGUAAUUAAGAACAACACUG
...........((((.(((.(((((.....((.....))....))))).))).(((((((((((....)))))))))))..........)))).. ( -21.40, z-score =  -1.20, R)
>droSim1.chr2L_random 334773 92 + 909653
UUUAAAAGAAUGUAUGCUAUUAAGAAACAUAGAUCAGCUUAGAUUGUACUUGAUGCACAGAAGACUGGUCUUCUGUGUAAUUAACAACACUG---
..........(((......(((((.......((((......))))...)))))(((((((((((....)))))))))))....)))......--- ( -19.60, z-score =  -1.33, R)
>droSec1.super_5 3375771 95 + 5866729
UUUAAAAGAAUGUAUGCUAUUAAGAAACAUAGAUCAGUUUAGAUUGUACUUGAUGCACAGAAGACUCGUCUUCUGUGUAAUUAAGAACAACCCUG
((((((...((.((((...........)))).))...))))))((((.((((((((((((((((....)))))))))).)))))).))))..... ( -26.00, z-score =  -4.04, R)
>droYak2.chr2L 8423655 85 - 22324452
--AAUCAUAUUAAGAACGAGUAAGAAACAUAUGC-----UAGAUUAUCCUAAGUGCAUAUAAGACUGCUCUUUUCUGUGAUUAUGAUCCACA---
--.((((((...((((.(((((......((((((-----(((......)))...)))))).....)))))..)))).....)))))).....--- ( -15.70, z-score =  -1.23, R)
>consensus
UUUAAAAGAAUGUAUGCUAUUAAGAAACAUAGAUCAGCUUAGAUUGUACUAGAUGCACAGAAGACUGGUCUUCUGUGUAAUUAAGAACAACA___
...........................................((((.((((((((((((((((....)))))))))).)))))).))))..... (-13.73 = -15.72 +   2.00)

alignment

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secondary structure

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dotplot

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Window 9

Location 5,296,784 – 5,296,876
Length 92
Sequences 3
Columns 94
Reading direction forward
Mean pairwise identity 80.29
Shannon entropy 0.26818
G+C content 0.34543
Mean single sequence MFE -27.50
Consensus MFE -19.37
Energy contribution -21.15
Covariance contribution 1.78
Combinations/Pair 1.04
Mean z-score -3.98
Structure conservation index 0.70
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.50
SVM RNA-class probability 0.998817
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 5296784 92 + 23011544
AGAUUGUACUAGAUGCAUAGAAGACUGGUCUUCUGUGUAAUUAAGAACAACACUGCAAUAUCAUCUUAAG--UCAUUCUUAAGAACUAUAGAAU
...((((.((.(((((((((((((....)))))))))).))).)).)))).............(((((((--.....))))))).......... ( -23.40, z-score =  -2.48, R)
>droSim1.chr2L_random 334813 83 + 909653
AGAUUGUACUUGAUGCACAGAAGACUGGUCUUCUGUGUAAUUAA---CAACACUGCAUUAUCUUGUUAAAGUUAAUACUGUAGAAC--------
....(((..(((((((((((((((....)))))))))).)))))---..)))((((((((.(((....))).)))...)))))...-------- ( -22.70, z-score =  -2.62, R)
>droSec1.super_5 3375811 86 + 5866729
AGAUUGUACUUGAUGCACAGAAGACUCGUCUUCUGUGUAAUUAAGAACAACCCUGCAGUAUCUUCUUCAAGUUGAUACUGUAGAAC--------
...((((.((((((((((((((((....)))))))))).)))))).))))..((((((((((..(.....)..))))))))))...-------- ( -36.40, z-score =  -6.85, R)
>consensus
AGAUUGUACUUGAUGCACAGAAGACUGGUCUUCUGUGUAAUUAAGAACAACACUGCAAUAUCUUCUUAAAGUUAAUACUGUAGAAC________
...((((.((((((((((((((((....)))))))))).)))))).))))..(((((.(((.............))).)))))........... (-19.37 = -21.15 +   1.78)

alignment

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secondary structure

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dotplot

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Window 0

Location 5,296,784 – 5,296,876
Length 92
Sequences 3
Columns 94
Reading direction reverse
Mean pairwise identity 80.29
Shannon entropy 0.26818
G+C content 0.34543
Mean single sequence MFE -23.27
Consensus MFE -13.12
Energy contribution -15.57
Covariance contribution 2.45
Combinations/Pair 1.08
Mean z-score -2.70
Structure conservation index 0.56
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.04
SVM RNA-class probability 0.878782
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 5296784 92 - 23011544
AUUCUAUAGUUCUUAAGAAUGA--CUUAAGAUGAUAUUGCAGUGUUGUUCUUAAUUACACAGAAGACCAGUCUUCUAUGCAUCUAGUACAAUCU
....(((...(((((((.....--)))))))..))).((((((((.((.....)).))))((((((....)))))).))))............. ( -18.90, z-score =  -0.97, R)
>droSim1.chr2L_random 334813 83 - 909653
--------GUUCUACAGUAUUAACUUUAACAAGAUAAUGCAGUGUUG---UUAAUUACACAGAAGACCAGUCUUCUGUGCAUCAAGUACAAUCU
--------........(((((....(((((((.((......)).)))---))))...(((((((((....))))))))).....)))))..... ( -21.90, z-score =  -3.19, R)
>droSec1.super_5 3375811 86 - 5866729
--------GUUCUACAGUAUCAACUUGAAGAAGAUACUGCAGGGUUGUUCUUAAUUACACAGAAGACGAGUCUUCUGUGCAUCAAGUACAAUCU
--------...((.(((((((..(.....)..))))))).))((((((.(((.....(((((((((....)))))))))....))).)))))). ( -29.00, z-score =  -3.94, R)
>consensus
________GUUCUACAGUAUCAACUUUAAGAAGAUAAUGCAGUGUUGUUCUUAAUUACACAGAAGACCAGUCUUCUGUGCAUCAAGUACAAUCU
...........((.(((((((...........))))))).)).(((((.(((.....(((((((((....)))))))))....))).))))).. (-13.12 = -15.57 +   2.45)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:18:44 2011