Locus 6900

Sequence ID dm3.chr3L
Location 10,672,791 – 10,672,851
Length 60
Max. P 0.940617
window9500 window9501

overview

Window 0

Location 10,672,791 – 10,672,851
Length 60
Sequences 6
Columns 65
Reading direction forward
Mean pairwise identity 81.10
Shannon entropy 0.35505
G+C content 0.42990
Mean single sequence MFE -12.62
Consensus MFE -10.10
Energy contribution -10.13
Covariance contribution 0.03
Combinations/Pair 1.11
Mean z-score -1.70
Structure conservation index 0.80
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.44
SVM RNA-class probability 0.940617
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 10672791 60 + 24543557
CGAACAAAGCAUUAAAUGAUGCUUUGGCAUCG--ACUACCUUGCUUCUUCUUCG-UCGCUCAA--
(((((((((((((....)))))))))(((...--.......)))......))))-........-- ( -13.70, z-score =  -2.31, R)
>droSim1.chr3L 10064568 61 + 22553184
CGAACAAAGCAUUAAAUGAUGCUUUGGCAUCG-ACUUACCUUGCUUCUUCUUCG-CCGCUCAA--
(((((((((((((....)))))))))(((...-........)))......))))-........-- ( -13.40, z-score =  -2.05, R)
>droSec1.super_0 2893578 61 + 21120651
CGAACAAAGCAUUAAAUGAUGCUUUGGCAUCG-ACUUACCUUGCUUCUUCUUCG-CCGCUCAA--
(((((((((((((....)))))))))(((...-........)))......))))-........-- ( -13.40, z-score =  -2.05, R)
>droYak2.chr3L 10671498 61 + 24197627
CGAACAAAGCAUUAAAUGAUGCUUUGGCAUCG--ACUACCUUGCUUCUUCUUCU-CCGCUCAAU-
(((.(((((((((....)))))))))...)))--....................-.........- ( -12.40, z-score =  -2.36, R)
>droEre2.scaffold_4784 10671326 65 + 25762168
CGAACAAAGCAUUAAAUGAUGCUUUGGCAUCGCGACUACCUUGCUUCUUCUUCUGCUGCUCAAUU
.((....((((......(((((....)))))((((.....)))).........))))..)).... ( -13.40, z-score =  -1.47, R)
>dp4.chrXR_group6 9112635 52 + 13314419
CAAGCGUAGCAUUAAAUGAUGCUUUGGCAGCAACAUCAUCU--CUGCUUUUUAG-----------
...((..((((((....))))))...))((((.........--.))))......----------- (  -9.40, z-score =   0.03, R)
>consensus
CGAACAAAGCAUUAAAUGAUGCUUUGGCAUCG__ACUACCUUGCUUCUUCUUCG_CCGCUCAA__
....(((((((((....)))))))))....................................... (-10.10 = -10.13 +   0.03)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 10,672,791 – 10,672,851
Length 60
Sequences 6
Columns 65
Reading direction reverse
Mean pairwise identity 81.10
Shannon entropy 0.35505
G+C content 0.42990
Mean single sequence MFE -15.50
Consensus MFE -10.78
Energy contribution -11.20
Covariance contribution 0.42
Combinations/Pair 1.20
Mean z-score -1.60
Structure conservation index 0.70
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.71
SVM RNA-class probability 0.793422
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 10672791 60 - 24543557
--UUGAGCGA-CGAAGAAGAAGCAAGGUAGU--CGAUGCCAAAGCAUCAUUUAAUGCUUUGUUCG
--........-((((...((((((...(((.--.(((((....)))))..))).)))))).)))) ( -15.00, z-score =  -1.51, R)
>droSim1.chr3L 10064568 61 - 22553184
--UUGAGCGG-CGAAGAAGAAGCAAGGUAAGU-CGAUGCCAAAGCAUCAUUUAAUGCUUUGUUCG
--........-((((...((((((...(((((-.(((((....)))))))))).)))))).)))) ( -16.60, z-score =  -1.69, R)
>droSec1.super_0 2893578 61 - 21120651
--UUGAGCGG-CGAAGAAGAAGCAAGGUAAGU-CGAUGCCAAAGCAUCAUUUAAUGCUUUGUUCG
--........-((((...((((((...(((((-.(((((....)))))))))).)))))).)))) ( -16.60, z-score =  -1.69, R)
>droYak2.chr3L 10671498 61 - 24197627
-AUUGAGCGG-AGAAGAAGAAGCAAGGUAGU--CGAUGCCAAAGCAUCAUUUAAUGCUUUGUUCG
-...((((((-((.(((.((.((..((((..--...))))...)).)).)))....)))))))). ( -15.10, z-score =  -1.52, R)
>droEre2.scaffold_4784 10671326 65 - 25762168
AAUUGAGCAGCAGAAGAAGAAGCAAGGUAGUCGCGAUGCCAAAGCAUCAUUUAAUGCUUUGUUCG
....((((((((..(((.((.((..((((.......))))...)).)).)))..)))..))))). ( -15.20, z-score =  -0.87, R)
>dp4.chrXR_group6 9112635 52 - 13314419
-----------CUAAAAAGCAG--AGAUGAUGUUGCUGCCAAAGCAUCAUUUAAUGCUACGCUUG
-----------......((((.--((((((((((........))))))))))..))))....... ( -14.50, z-score =  -2.34, R)
>consensus
__UUGAGCGG_CGAAGAAGAAGCAAGGUAAU__CGAUGCCAAAGCAUCAUUUAAUGCUUUGUUCG
..................(.(((((((((.....(((((....)))))......)))))))))). (-10.78 = -11.20 +   0.42)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:16:41 2011