Locus 11091

Sequence ID dm3.chr3R
Location 18,655,684 – 18,655,825
Length 141
Max. P 0.711036
window15234 window15235

overview

Window 4

Location 18,655,684 – 18,655,796
Length 112
Sequences 10
Columns 120
Reading direction forward
Mean pairwise identity 78.58
Shannon entropy 0.43612
G+C content 0.41318
Mean single sequence MFE -21.33
Consensus MFE -15.51
Energy contribution -15.35
Covariance contribution -0.16
Combinations/Pair 1.05
Mean z-score -0.91
Structure conservation index 0.73
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.30
SVM RNA-class probability 0.634873
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 18655684 112 + 27905053
--------CGCGCUUUUCCUUAAGCACCACGCCCCCACAGCCGCCCACUUUUUAUUGUUAUUGUUUGUAAUUGAAAUGGUGCAAACGUACAAGCGAUAAAAUGUAAAACCAAACGCAAGU
--------.((((((......)))).....((.......)).)).....((((((..((((((((((((.(((........)))...))))))))))))...))))))....((....)) ( -21.90, z-score =  -0.50, R)
>droPer1.super_145 16134 102 - 90410
----------UGCCCCCCCCCUA--GCCACCCCC---UGGCCACCCACUUUUUACUGUUAUUGUUUGUAAUUGAAAUGGUGCAAACGUACAAGCGAUAAAAUGUAAAACCAAAUGCA---
----------.((..........--((((.....---))))........((((((..((((((((((((.(((........)))...))))))))))))...))))))......)).--- ( -22.20, z-score =  -2.51, R)
>droSim1.chr3R 18469229 110 + 27517382
--------CGCGCUUUUCCUUAAGCACCACGCCC--ACAGCCGCCCACUUUUUAUUGUUAUUGUUUGUAAUUGAAAUGGUGCAAACGUACAAGCGAUAAAAUGUAAAAUCAAACGCAAGU
--------.((((((......)))).....((..--...)).)).....((((((..((((((((((((.(((........)))...))))))))))))...))))))....((....)) ( -22.30, z-score =  -0.43, R)
>droSec1.super_0 19017222 110 + 21120651
--------CGCGCUUUACCUUAAGCACCACGCCC--ACAGCCGCCCACUUUUUAUUGUUAUUGUUUGUAAUUGAAAUGGUGCAAACGUACAAGCGAUAAAAUGUAAAACCAAACGCAAGU
--------.((((((......)))).....((..--...)).)).....((((((..((((((((((((.(((........)))...))))))))))))...))))))....((....)) ( -22.20, z-score =  -0.34, R)
>droYak2.chr3R 19509860 110 + 28832112
--------CGCGCUUUUUCUUAAGCACCACGCCC--ACUGCCGCCCACUUUUUAUUGUUAUUGUUUGUAAUUGAAAUGGUGCAAACGUACAAGCGAUAAAAUGUAAAACCAAACGCAAGU
--------.((((((......)))).....((..--...)).)).....((((((..((((((((((((.(((........)))...))))))))))))...))))))....((....)) ( -22.00, z-score =  -0.16, R)
>droEre2.scaffold_4820 1058885 110 - 10470090
--------CGCGAUUUUCCUUAAGCACCACGCCC--ACUGCCGCCCACUUUUUAUUGUUAUUGUUUGUAAUUGAAAUGGUGCAAACGUACAAGCGAUAAAAUGUAAAACCAAACGCAAGU
--------.(((...........((.....))..--.............((((((..((((((((((((.(((........)))...))))))))))))...)))))).....))).... ( -20.10, z-score =   0.06, R)
>droAna3.scaffold_13340 11038094 110 - 23697760
--------CGCGCUUU-CUUCAACUGCCACGCCCA-CUUGGCGCCCGGUUUUUAUUGUUAUUGUUUGUAAUUGAAAUGGUGCAAACGUACAAGCGAUAAAAUGUAAAAUCAAACUCGAUU
--------........-..(((((((...((((..-...))))..)))))(((((..((((((((((((.(((........)))...))))))))))))...))))).........)).. ( -23.00, z-score =  -0.04, R)
>droMoj3.scaffold_6540 1177169 98 - 34148556
-------------CCGUUUGC-GUCCCAGAGCUCU--UCAUCGUCCACAUUUUACUGUUAUUGUUUGUAAUUGAAAUGGUGCAAACGUACAAGCGAUAAAAUGUAAAACCGAAC------
-------------..((..((-(....((....))--....)))..)).((((((..((((((((((((.(((........)))...))))))))))))...))))))......------ ( -19.50, z-score =  -0.87, R)
>droVir3.scaffold_12822 3885887 97 - 4096053
-------------UCGUGCUC-GUCCCGUAG-UCU--CCUUCGUACACAUUUUAUUGUUAUUGUUUGUAAUUGAAAUGGUGCAAACGUACAAGCGAUAAAAUGUAAAACCAAAC------
-------------..((((..-.........-...--.....))))(((((((((((((..((((((((..........))))))))....)))))))))))))..........------ ( -19.81, z-score =  -1.56, R)
>droGri2.scaffold_15074 3459576 112 + 7742996
CGUGUCCGUCCUGUAGUCCCCUGCCUCCUCCUCCU--CCUUCGUCCACAUUUUAUUGUUAUUGUUUGUAAUUGAAAUGGUGCAAACGUACAAGCGAUAAAAUGUAAAACCAAAC------
.(((..((....((((....))))...........--....))..))).((((((..((((((((((((.(((........)))...))))))))))))...))))))......------ ( -20.31, z-score =  -2.71, R)
>consensus
________CGCGCUUUUCCUCAAGCACCACGCCC__ACAGCCGCCCACUUUUUAUUGUUAUUGUUUGUAAUUGAAAUGGUGCAAACGUACAAGCGAUAAAAUGUAAAACCAAACGCAAGU
.................................................((((((..((((((((((((.(((........)))...))))))))))))...))))))............ (-15.51 = -15.35 +  -0.16)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 18,655,716 – 18,655,825
Length 109
Sequences 7
Columns 109
Reading direction forward
Mean pairwise identity 87.40
Shannon entropy 0.26192
G+C content 0.39884
Mean single sequence MFE -26.20
Consensus MFE -18.73
Energy contribution -20.21
Covariance contribution 1.49
Combinations/Pair 1.04
Mean z-score -1.87
Structure conservation index 0.71
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.48
SVM RNA-class probability 0.711036
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 18655716 109 + 27905053
CCGCCCACUUUUUAUUGUUAUUGUUUGUAAUUGAAAUGGUGCAAACGUACAAGCGAUAAAAUGUAAAACCAAACGCAAGUCUCGACUCCGGAUUUUCUCUGGGGAUGUG
.....(((.((((((..((((((((((((.(((........)))...))))))))))))...))))))....((....)).....(((((((.....)))))))..))) ( -26.60, z-score =  -1.50, R)
>droPer1.super_145 16159 91 - 90410
CCACCCACUUUUUACUGUUAUUGUUUGUAAUUGAAAUGGUGCAAACGUACAAGCGAUAAAAUGUAAAACCAAAUGCAGGACUCUCCCUGUG------------------
.........((((((..((((((((((((.(((........)))...))))))))))))...))))))......(((((......))))).------------------ ( -23.00, z-score =  -3.23, R)
>droSim1.chr3R 18469259 109 + 27517382
CCGCCCACUUUUUAUUGUUAUUGUUUGUAAUUGAAAUGGUGCAAACGUACAAGCGAUAAAAUGUAAAAUCAAACGCAAGUCUCGACUCCGGAUUUUCUCUGGGGAUGUG
.....(((.((((((..((((((((((((.(((........)))...))))))))))))...))))))....((....)).....(((((((.....)))))))..))) ( -26.70, z-score =  -1.68, R)
>droSec1.super_0 19017252 109 + 21120651
CCGCCCACUUUUUAUUGUUAUUGUUUGUAAUUGAAAUGGUGCAAACGUACAAGCGAUAAAAUGUAAAACCAAACGCAAGUCUCGACUCCGGAUUUUCUCUGGGGAUGUG
.....(((.((((((..((((((((((((.(((........)))...))))))))))))...))))))....((....)).....(((((((.....)))))))..))) ( -26.60, z-score =  -1.50, R)
>droYak2.chr3R 19509890 109 + 28832112
CCGCCCACUUUUUAUUGUUAUUGUUUGUAAUUGAAAUGGUGCAAACGUACAAGCGAUAAAAUGUAAAACCAAACGCAAGUCUCGACUCCGGAUUUUCUCUGGGGAUGUG
.....(((.((((((..((((((((((((.(((........)))...))))))))))))...))))))....((....)).....(((((((.....)))))))..))) ( -26.60, z-score =  -1.50, R)
>droEre2.scaffold_4820 1058915 109 - 10470090
CCGCCCACUUUUUAUUGUUAUUGUUUGUAAUUGAAAUGGUGCAAACGUACAAGCGAUAAAAUGUAAAACCAAACGCAAGUCUCGACUCCGGAUUUUCUCUGGGGAUGUG
.....(((.((((((..((((((((((((.(((........)))...))))))))))))...))))))....((....)).....(((((((.....)))))))..))) ( -26.60, z-score =  -1.50, R)
>droAna3.scaffold_13340 11038124 103 - 23697760
GCGCCCGGUUUUUAUUGUUAUUGUUUGUAAUUGAAAUGGUGCAAACGUACAAGCGAUAAAAUGUAAAAUCAAACUCGAUUCUCGACUC------UUCCAAGGGAGCGAC
((.(((((((((.....((((((((((((.(((........)))...)))))))))))).....))))))....(((.....)))...------......))).))... ( -27.30, z-score =  -2.18, R)
>consensus
CCGCCCACUUUUUAUUGUUAUUGUUUGUAAUUGAAAUGGUGCAAACGUACAAGCGAUAAAAUGUAAAACCAAACGCAAGUCUCGACUCCGGAUUUUCUCUGGGGAUGUG
.........((((((..((((((((((((.(((........)))...))))))))))))...)))))).................(((((((.....)))))))..... (-18.73 = -20.21 +   1.49)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:36:11 2011