Locus 4152

Sequence ID dm3.chr2R
Location 10,854,991 – 10,855,041
Length 50
Max. P 0.968655
window5694 window5695

overview

Window 4

Location 10,854,991 – 10,855,041
Length 50
Sequences 7
Columns 61
Reading direction forward
Mean pairwise identity 64.73
Shannon entropy 0.58804
G+C content 0.44829
Mean single sequence MFE -13.23
Consensus MFE -9.95
Energy contribution -9.10
Covariance contribution -0.85
Combinations/Pair 1.42
Mean z-score -1.01
Structure conservation index 0.75
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.80
SVM RNA-class probability 0.968655
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 10854991 50 + 21146708
UUUAAGGUAUAGGGUAGCAGUACAGCUCCCUCGAUGCUCCUUAUUGCAUU-----------
..........((((.(((......))))))).(((((........)))))----------- ( -12.80, z-score =  -1.17, R)
>droPer1.super_2 755926 61 - 9036312
UUAAGGGUAAAGGCUUAUUGCAGGGUAUCCUCAGUGCAGGACCUCGCCUUGUUAAUGCAUU
............((.....(((((((.((((......))))....)))))))....))... ( -13.80, z-score =   0.41, R)
>dp4.chr3 13341505 61 + 19779522
UUAAGGGUAAAGGCUUAUUGCAGGGUAUCCUCAGUGCAGGACCUCGCCUUGUUAAUGCAUU
............((.....(((((((.((((......))))....)))))))....))... ( -13.80, z-score =   0.41, R)
>droEre2.scaffold_4845 7590469 50 - 22589142
GUUCAUUUGUAGGGUAGCAGUACAGCUCCCUCGAUGCUCCUUAUUGCAUU-----------
........(.((((.(((......))))))))(((((........)))))----------- ( -13.30, z-score =  -1.95, R)
>droYak2.chr2R 10785174 50 + 21139217
GUUUAUUUGCAGGGUAGCAGUACAGCUCCCUCGAUGCUCCUUAUUGCAUU-----------
........(.((((.(((......))))))))(((((........)))))----------- ( -13.30, z-score =  -1.63, R)
>droSec1.super_1 8367570 50 + 14215200
UUUUAUGUAUAGGGUAGCAGUACAGCUCCCUCGAUGCUCCUUAUUGCAUU-----------
..........((((.(((......))))))).(((((........)))))----------- ( -12.80, z-score =  -1.71, R)
>droSim1.chr2R 9615367 50 + 19596830
GUUUAUGUAUAGGGUAGCAGUACAGCUCCCUCGAUGCUCCUUAUUGCAUU-----------
..........((((.(((......))))))).(((((........)))))----------- ( -12.80, z-score =  -1.47, R)
>consensus
UUUAAUGUAUAGGGUAGCAGUACAGCUCCCUCGAUGCUCCUUAUUGCAUU___________
..........((((.(((......))))))).(((((........)))))........... ( -9.95 =  -9.10 +  -0.85)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 10,854,991 – 10,855,041
Length 50
Sequences 7
Columns 61
Reading direction reverse
Mean pairwise identity 64.73
Shannon entropy 0.58804
G+C content 0.44829
Mean single sequence MFE -12.13
Consensus MFE -7.56
Energy contribution -7.31
Covariance contribution -0.24
Combinations/Pair 1.22
Mean z-score -1.22
Structure conservation index 0.62
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.67
SVM RNA-class probability 0.959925
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 10854991 50 - 21146708
-----------AAUGCAAUAAGGAGCAUCGAGGGAGCUGUACUGCUACCCUAUACCUUAAA
-----------.......(((((.......(((((((......))).))))...))))).. ( -13.50, z-score =  -1.81, R)
>droPer1.super_2 755926 61 + 9036312
AAUGCAUUAACAAGGCGAGGUCCUGCACUGAGGAUACCCUGCAAUAAGCCUUUACCCUUAA
...........((((.(((((..((((....((....))))))....)))))...)))).. ( -10.90, z-score =   0.21, R)
>dp4.chr3 13341505 61 - 19779522
AAUGCAUUAACAAGGCGAGGUCCUGCACUGAGGAUACCCUGCAAUAAGCCUUUACCCUUAA
...........((((.(((((..((((....((....))))))....)))))...)))).. ( -10.90, z-score =   0.21, R)
>droEre2.scaffold_4845 7590469 50 + 22589142
-----------AAUGCAAUAAGGAGCAUCGAGGGAGCUGUACUGCUACCCUACAAAUGAAC
-----------.((((........))))..(((((((......))).)))).......... ( -12.40, z-score =  -1.97, R)
>droYak2.chr2R 10785174 50 - 21139217
-----------AAUGCAAUAAGGAGCAUCGAGGGAGCUGUACUGCUACCCUGCAAAUAAAC
-----------.((((........))))..(((((((......))).)))).......... ( -12.40, z-score =  -1.53, R)
>droSec1.super_1 8367570 50 - 14215200
-----------AAUGCAAUAAGGAGCAUCGAGGGAGCUGUACUGCUACCCUAUACAUAAAA
-----------.((((........))))..(((((((......))).)))).......... ( -12.40, z-score =  -1.75, R)
>droSim1.chr2R 9615367 50 - 19596830
-----------AAUGCAAUAAGGAGCAUCGAGGGAGCUGUACUGCUACCCUAUACAUAAAC
-----------.((((........))))..(((((((......))).)))).......... ( -12.40, z-score =  -1.93, R)
>consensus
___________AAUGCAAUAAGGAGCAUCGAGGGAGCUGUACUGCUACCCUAUACAUAAAA
..............((........))....(((((((......))).)))).......... ( -7.56 =  -7.31 +  -0.24)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:23:46 2011