Locus 2484

Sequence ID dm3.chr2L
Location 19,396,622 – 19,396,736
Length 114
Max. P 0.580076
window3411 window3412

overview

Window 1

Location 19,396,622 – 19,396,736
Length 114
Sequences 6
Columns 121
Reading direction forward
Mean pairwise identity 68.33
Shannon entropy 0.59984
G+C content 0.38378
Mean single sequence MFE -25.16
Consensus MFE -8.73
Energy contribution -8.43
Covariance contribution -0.30
Combinations/Pair 1.36
Mean z-score -1.64
Structure conservation index 0.35
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.18
SVM RNA-class probability 0.578827
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 19396622 114 + 23011544
AAUGUUCGGGUCUGGUAGCAUAUUUCAUUUCCACACAAAAUAAAAGC------AUAUGGCCGAUCCGGUAUCAACCUCCAGCUAAUUAUAACAAUUAGCGGUAAUUAUACCGGCAA-CACG
.......(((((.(((..(((((........................------)))))))))))))(((((......((.(((((((.....))))))))).....)))))(....-)... ( -24.36, z-score =  -1.43, R)
>droAna3.scaffold_12916 11153481 105 - 16180835
-------------AAUACCCUCAUUUGAUCGCUCCGAUAGGAAUUACAACA--AAUUCGCCGGAUCGGUGACAAUUAUCGACUAAUUAUGAAUAUUAGCAAUAAUUAUAGCAGUGAGUAC-
-------------......((((((..((((.((((....(((((......--)))))..)))).))))...((((((.(.(((((.......)))))).)))))).....))))))...- ( -19.70, z-score =  -0.83, R)
>droEre2.scaffold_4845 17691143 115 - 22589142
----AAAGUGGGCAAUAGCAUGUUUUAUUUGCAUUCAAAAUAAAAGCGAGC-CAAGCUGACCAUUCGGUAUCAACCUCCAGCUAAUUAUAACAAUUAGCAAUAAUUACUCCGGCAA-CGCG
----...((((((....((...((((((((.......))))))))))..))-)..(((((((....)))...........(((((((.....)))))))...........))))..-))). ( -25.50, z-score =  -1.68, R)
>droYak2.chr2R 5894786 116 + 21139217
----AAGGGGGUGGAAAGCAAGUUUCAUUUGUAUUUAAAAUAGAAGCUACUGCAAAUGGACGAUUCGGUAUCAACCUCCAGCUAAUUAUAACAAUUAGCAAUAAUUAUUCCCGCAA-CGCG
----..(((((((((..(((((((((((((.......)))).))))))..)))....((..(((.....)))..))))).(((((((.....))))))).......))))))....-.... ( -28.60, z-score =  -2.26, R)
>droSec1.super_7 3012891 114 + 3727775
AAUGUUGCCUUUUGAUAGCAUAUUUCAUUUGCACUCAAAAUAAAAGC------AUGUGGUCGAUUCGGUAUCAACCUCCAGCUAAUUAUAACAAUUAGCAGUAAUUAUACCGGCAA-CGCC
...((((((..(((((.((((.(((.((((.......)))).)))..------)))).)))))...(((((.........(((((((.....))))))).......))))))))))-)... ( -27.29, z-score =  -2.65, R)
>droSim1.chr2L 19078305 113 + 22036055
AAUGUUGCGGUUUGGUAGCAUAUUUCGUUUGCACUCAAAAUAAAAGC------GUAUGGUCGAAUCGGUAUCAACCUCCAGCUAAUUAUAACAAUUAGCAGUAAUUA-ACCGGCAA-CGCG
.(((((((......)))))))........................((------((...((((....(((....)))....(((((((.....)))))))........-..)))).)-))). ( -25.50, z-score =  -0.97, R)
>consensus
____UUGGGGUUUGAUAGCAUAUUUCAUUUGCACUCAAAAUAAAAGC______AAAUGGACGAUUCGGUAUCAACCUCCAGCUAAUUAUAACAAUUAGCAAUAAUUAUACCGGCAA_CGCG
............................((((..................................(((....)))....(((((((.....))))))).............))))..... ( -8.73 =  -8.43 +  -0.30)

alignment

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secondary structure

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dotplot

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Window 2

Location 19,396,622 – 19,396,736
Length 114
Sequences 6
Columns 121
Reading direction reverse
Mean pairwise identity 68.33
Shannon entropy 0.59984
G+C content 0.38378
Mean single sequence MFE -28.41
Consensus MFE -9.73
Energy contribution -10.35
Covariance contribution 0.62
Combinations/Pair 1.46
Mean z-score -1.70
Structure conservation index 0.34
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.18
SVM RNA-class probability 0.580076
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 19396622 114 - 23011544
CGUG-UUGCCGGUAUAAUUACCGCUAAUUGUUAUAAUUAGCUGGAGGUUGAUACCGGAUCGGCCAUAU------GCUUUUAUUUUGUGUGGAAAUGAAAUAUGCUACCAGACCCGAACAUU
.(((-(..((((((((((..((((((((((...)))))))).))..))).))))))).((((......------((...(((((..(......)..))))).))........)))))))). ( -31.34, z-score =  -1.91, R)
>droAna3.scaffold_12916 11153481 105 + 16180835
-GUACUCACUGCUAUAAUUAUUGCUAAUAUUCAUAAUUAGUCGAUAAUUGUCACCGAUCCGGCGAAUU--UGUUGUAAUUCCUAUCGGAGCGAUCAAAUGAGGGUAUU-------------
-((((((..(((((((((((((((((((.......))))).))))))))))..(((((..((.(((((--......)))))))))))))))).((....)))))))).------------- ( -27.00, z-score =  -2.28, R)
>droEre2.scaffold_4845 17691143 115 + 22589142
CGCG-UUGCCGGAGUAAUUAUUGCUAAUUGUUAUAAUUAGCUGGAGGUUGAUACCGAAUGGUCAGCUUG-GCUCGCUUUUAUUUUGAAUGCAAAUAAAACAUGCUAUUGCCCACUUU----
.(((-..(((............((((((((...))))))))...((((((((........)))))))))-)).)))((((((((.......))))))))...((....)).......---- ( -24.70, z-score =   0.45, R)
>droYak2.chr2R 5894786 116 - 21139217
CGCG-UUGCGGGAAUAAUUAUUGCUAAUUGUUAUAAUUAGCUGGAGGUUGAUACCGAAUCGUCCAUUUGCAGUAGCUUCUAUUUUAAAUACAAAUGAAACUUGCUUUCCACCCCCUU----
....-....(((..........((((((((...))))))))((((((.((((.....)))).))....(((..((.(((.((((.......))))))).)))))..))))..)))..---- ( -20.90, z-score =   0.27, R)
>droSec1.super_7 3012891 114 - 3727775
GGCG-UUGCCGGUAUAAUUACUGCUAAUUGUUAUAAUUAGCUGGAGGUUGAUACCGAAUCGACCACAU------GCUUUUAUUUUGAGUGCAAAUGAAAUAUGCUAUCAAAAGGCAACAUU
...(-((((((((((.....(.((((((((...)))))))).)..(((((((.....)))))))..))------)))....((((((..(((.........)))..))))))))))))... ( -33.50, z-score =  -3.20, R)
>droSim1.chr2L 19078305 113 - 22036055
CGCG-UUGCCGGU-UAAUUACUGCUAAUUGUUAUAAUUAGCUGGAGGUUGAUACCGAUUCGACCAUAC------GCUUUUAUUUUGAGUGCAAACGAAAUAUGCUACCAAACCGCAACAUU
...(-((((.(((-(.......((((((((...))))))))(((.((((((.......))))))....------((...(((((((........))))))).))..))))))))))))... ( -33.00, z-score =  -3.53, R)
>consensus
CGCG_UUGCCGGUAUAAUUACUGCUAAUUGUUAUAAUUAGCUGGAGGUUGAUACCGAAUCGACCAUAU______GCUUUUAUUUUGAGUGCAAAUGAAAUAUGCUAUCAAACCCCAA____
.........((((((((((.(((((((((.....))))))).)).)))).))))))..................((...(((((((........))))))).))................. ( -9.73 = -10.35 +   0.62)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:52:01 2011