Locus 11503

Sequence ID dm3.chr3R
Location 21,647,274 – 21,647,350
Length 76
Max. P 0.895392
window15806 window15807

overview

Window 6

Location 21,647,274 – 21,647,350
Length 76
Sequences 9
Columns 77
Reading direction forward
Mean pairwise identity 66.25
Shannon entropy 0.72768
G+C content 0.49745
Mean single sequence MFE -22.72
Consensus MFE -6.29
Energy contribution -6.72
Covariance contribution 0.44
Combinations/Pair 1.40
Mean z-score -2.04
Structure conservation index 0.28
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.12
SVM RNA-class probability 0.895392
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 21647274 76 + 27905053
UGGCGGAAUGCCAAACGAUGCCGAAAGGUCGCAGAAAUGGCAGCCAUCUAAUGGCAUCGAGACAUUUAAAAA-CAUU
((((.....))))..((((((((..((((.((..........)).))))..)))))))).............-.... ( -21.80, z-score =  -2.10, R)
>droSim1.chr3R 21477052 76 + 27517382
UGGCGGAAUGCCAAAGGAUGCCGAAAGGUCGCAGGAAUGGCAGCCACCUAAUGGCAUCGAGCCAUUUAAAAA-CAUC
((((((....))....(((((((..((((.((..........)).))))..)))))))..))))........-.... ( -24.70, z-score =  -2.01, R)
>droSec1.super_13 436097 75 + 2104621
UGGCGGAAUGCCAAAGGAUGCCGAA-GGUCGCAGGAAUGGCAGCCAUCUAAUGGCAUCGAGCCAUUUAAAAA-CAUC
((((...((((((..(((((.(...-.((((......)))).).)))))..))))))...))))........-.... ( -22.80, z-score =  -1.42, R)
>droYak2.chr3R 4006069 76 - 28832112
UGGCGGAAUGCCAAAGGAUGCCGAAAGCUGGCAGGAAUGGCAGCCAUCUAAUGGCAUCGAGCCAUUUAAAAA-CAUC
((((...((((((..(((((......((((.((....)).)))))))))..))))))...))))........-.... ( -27.10, z-score =  -2.66, R)
>droEre2.scaffold_4820 4077034 76 - 10470090
UGGCGGAAUGCCAAAGGAUGCCGAAAGGUUGCAGGAAUGGCAGCCAUCUAAUGGCGUCGAGCCAUUUAAAAA-CAUC
((((...((((((..(((((.(....)(((((.......))))))))))..))))))...))))........-.... ( -26.00, z-score =  -2.43, R)
>droAna3.scaffold_13340 12204959 60 - 23697760
-----------------UGGCCACCAGCCACUUGGAAUGCCACCAGUCUUGUGGCAUCGCGCCAUUUAAAAAACAUC
-----------------(((((.((((....)))).(((((((.......))))))).).))))............. ( -17.00, z-score =  -1.71, R)
>dp4.chr2 7353952 62 - 30794189
UGGCGGAAUGCCAC----UGCCAU----CCGCAGGAUGAG-----AUCUAAUGGCAUCGAGCCAUUUAAAAA-CAU-
((((...((((((.----..((((----((...))))).)-----......))))))...))))........-...- ( -18.50, z-score =  -1.74, R)
>droPer1.super_3 1164273 63 - 7375914
UGGCGGAAUGCCAU----UGCCAU----CCGCAGGAUGAG-----AUCUAAUGGCAUCGAGCCAUUUAAAAA-CAUC
((((...(((((((----((((((----((...))))).)-----...)))))))))...))))........-.... ( -21.30, z-score =  -2.61, R)
>droWil1.scaffold_181130 2265362 75 - 16660200
GGGCCACAAGACAGACGGGAACUUGAUGUGACACAGACAC--ACAACCUGGUGUUGUCUUUUUGGCCAAGAAGUGGC
.(((((.(((((((.((((...(((.((((.......)))--))))))))...)))))))..))))).......... ( -25.30, z-score =  -1.71, R)
>consensus
UGGCGGAAUGCCAAAGGAUGCCGAAAGGUCGCAGGAAUGGCAGCCAUCUAAUGGCAUCGAGCCAUUUAAAAA_CAUC
((((.....))))....................................((((((.....))))))........... ( -6.29 =  -6.72 +   0.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 21,647,274 – 21,647,350
Length 76
Sequences 9
Columns 77
Reading direction reverse
Mean pairwise identity 66.25
Shannon entropy 0.72768
G+C content 0.49745
Mean single sequence MFE -21.71
Consensus MFE -6.67
Energy contribution -7.02
Covariance contribution 0.36
Combinations/Pair 1.33
Mean z-score -1.57
Structure conservation index 0.31
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.55
SVM RNA-class probability 0.740541
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 21647274 76 - 27905053
AAUG-UUUUUAAAUGUCUCGAUGCCAUUAGAUGGCUGCCAUUUCUGCGACCUUUCGGCAUCGUUUGGCAUUCCGCCA
....-......((((((.(((((((...((.(.((..........)).).))...)))))))...))))))...... ( -20.30, z-score =  -1.49, R)
>droSim1.chr3R 21477052 76 - 27517382
GAUG-UUUUUAAAUGGCUCGAUGCCAUUAGGUGGCUGCCAUUCCUGCGACCUUUCGGCAUCCUUUGGCAUUCCGCCA
....-......((((((.....)))))).(((((.(((((....(((((....)).))).....)))))..))))). ( -25.50, z-score =  -2.11, R)
>droSec1.super_13 436097 75 - 2104621
GAUG-UUUUUAAAUGGCUCGAUGCCAUUAGAUGGCUGCCAUUCCUGCGACC-UUCGGCAUCCUUUGGCAUUCCGCCA
((((-((....((((((.....)))))).((.((.(((.......))).))-.))))))))...((((.....)))) ( -21.90, z-score =  -1.36, R)
>droYak2.chr3R 4006069 76 + 28832112
GAUG-UUUUUAAAUGGCUCGAUGCCAUUAGAUGGCUGCCAUUCCUGCCAGCUUUCGGCAUCCUUUGGCAUUCCGCCA
((((-((....((((((.....)))))).((.(((((.((....)).))))).))))))))...((((.....)))) ( -25.50, z-score =  -2.21, R)
>droEre2.scaffold_4820 4077034 76 + 10470090
GAUG-UUUUUAAAUGGCUCGACGCCAUUAGAUGGCUGCCAUUCCUGCAACCUUUCGGCAUCCUUUGGCAUUCCGCCA
((((-((....((((((.....)))))).((.((.(((.......))).))..))))))))...((((.....)))) ( -21.10, z-score =  -1.48, R)
>droAna3.scaffold_13340 12204959 60 + 23697760
GAUGUUUUUUAAAUGGCGCGAUGCCACAAGACUGGUGGCAUUCCAAGUGGCUGGUGGCCA-----------------
.............(((...((((((((.......)))))))))))..((((.....))))----------------- ( -18.00, z-score =  -0.30, R)
>dp4.chr2 7353952 62 + 30794189
-AUG-UUUUUAAAUGGCUCGAUGCCAUUAGAU-----CUCAUCCUGCGG----AUGGCA----GUGGCAUUCCGCCA
-...-........((((..(((((((((.(..-----.((((((...))----))))))----))))))))..)))) ( -21.10, z-score =  -1.97, R)
>droPer1.super_3 1164273 63 + 7375914
GAUG-UUUUUAAAUGGCUCGAUGCCAUUAGAU-----CUCAUCCUGCGG----AUGGCA----AUGGCAUUCCGCCA
((((-...((.((((((.....)))))).)).-----..))))..((((----(..((.----...))..))))).. ( -21.60, z-score =  -2.10, R)
>droWil1.scaffold_181130 2265362 75 + 16660200
GCCACUUCUUGGCCAAAAAGACAACACCAGGUUGU--GUGUCUGUGUCACAUCAAGUUCCCGUCUGUCUUGUGGCCC
..........(((((..((((((((...((.((((--(((.......)))).))).))...)).)))))).))))). ( -20.40, z-score =  -1.10, R)
>consensus
GAUG_UUUUUAAAUGGCUCGAUGCCAUUAGAUGGCUGCCAUUCCUGCGACCUUUCGGCAUCCUUUGGCAUUCCGCCA
.......(((((.((((.....)))))))))..................................(((.....))). ( -6.67 =  -7.02 +   0.36)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:44:10 2011