Locus 9901

Sequence ID dm3.chr3R
Location 9,709,560 – 9,709,691
Length 131
Max. P 0.992300
window13604 window13605

overview

Window 4

Location 9,709,560 – 9,709,653
Length 93
Sequences 6
Columns 115
Reading direction reverse
Mean pairwise identity 79.69
Shannon entropy 0.35643
G+C content 0.45141
Mean single sequence MFE -29.38
Consensus MFE -22.13
Energy contribution -23.05
Covariance contribution 0.92
Combinations/Pair 1.07
Mean z-score -2.55
Structure conservation index 0.75
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.53
SVM RNA-class probability 0.992300
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 9709560 93 - 27905053
--------UUAGAUCCACAGAUCUGCACA-------------UUUUCCGAUCU-UGAGAUCGUGAGAGGCGCAAGGCGCAAAACAACAGUUGCAAUCCGCAACGGAAUGCAAAUU
--------.((((((....))))))....-------------((((((((((.-...))))).)))))((((...))))..........(((((.((((...)))).)))))... ( -28.90, z-score =  -2.89, R)
>droSim1.chr3R 15799647 93 + 27517382
--------UAAGAUCCACAGAUCUGCACA-------------UUUUCCGAUCU-UGAGAUCGUGAGAGGCGCAAGGCGCAAAACAACAGUUGCAAUCCGCAACGGAAUGCAAAUU
--------..(((((....)))))((...-------------.(((((((((.-...))))).))))(.(....).)))..........(((((.((((...)))).)))))... ( -28.40, z-score =  -2.80, R)
>droSec1.super_0 8820890 93 + 21120651
--------UAAGAUCCACAGAUCUGCACA-------------UUUUCCGAUCU-UGAGAUCGUGAGAGGCGCAAGGCGCAAAACAACAGUUGCAAUCCGCAACGGAAUGCAAAUU
--------..(((((....)))))((...-------------.(((((((((.-...))))).))))(.(....).)))..........(((((.((((...)))).)))))... ( -28.40, z-score =  -2.80, R)
>droYak2.chr3R 14023815 114 - 28832112
AAAGAUACCCAGAUCCACAGAUCUGCACAUUUUGGUUUUCCAUUUUCCGAUCC-UCAAAUCGUGAGAGGCGCAAGGCGCAAAACAACAGUUGCAAUCCGCAACGGAAUGCAAAUU
.(((((...((((((....))))))...))))).((.((((.(((((((((..-....)))).)))))((((...)))).........(((((.....))))))))).))..... ( -30.60, z-score =  -2.37, R)
>droEre2.scaffold_4770 5824563 108 + 17746568
AGAGAUCCCCAGAUCCACAGAUCUGCACA------UUUUCCAUUUUCCGAUCC-UCAGAUCGUGAGAGGCGCAAGGCGCAAAACAACAGUUGCAAUCCGCAACGGAAUGCAAAUU
.((((....((((((....))))))....------.))))..((((((((((.-...))))).)))))((((...))))..........(((((.((((...)))).)))))... ( -31.50, z-score =  -3.05, R)
>droAna3.scaffold_13340 1064824 107 + 23697760
-----GCAGUUUUUUUGUAGAUUUUUUUGCUUUAAGUUU---UUUGCAGAUUUGGCAGAUCGUGAGAGGCACAAGGCGCAAAACAACAGUUGCAAUCCGCAACGGAAUGCAAAUU
-----...(((.(((((((((....)))(((((..((((---((..(.((((.....)))))..))))))..))))))))))).)))..(((((.((((...)))).)))))... ( -28.50, z-score =  -1.36, R)
>consensus
________UAAGAUCCACAGAUCUGCACA_____________UUUUCCGAUCU_UCAGAUCGUGAGAGGCGCAAGGCGCAAAACAACAGUUGCAAUCCGCAACGGAAUGCAAAUU
..........(((((....)))))..................((((((((((.....))))).)))))((((...))))..........(((((.((((...)))).)))))... (-22.13 = -23.05 +   0.92)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 9,709,600 – 9,709,691
Length 91
Sequences 6
Columns 113
Reading direction reverse
Mean pairwise identity 73.43
Shannon entropy 0.47723
G+C content 0.48000
Mean single sequence MFE -26.03
Consensus MFE -13.23
Energy contribution -13.51
Covariance contribution 0.28
Combinations/Pair 1.30
Mean z-score -1.68
Structure conservation index 0.51
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.71
SVM RNA-class probability 0.794854
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 9709600 91 - 27905053
CAACUGCAAACCGUUCCAAAUUGCCAAGCUGCAGACUCUUAG--------AUCCACAGAUCUGCA-------------CAUUUUCCGAUCUUG-AGAUCGUGAGAGGCGCAAG
......................(((..(.((((((.(((...--------......)))))))))-------------)..(((((((((...-.))))).)))))))..... ( -22.30, z-score =  -1.15, R)
>droSim1.chr3R 15799687 91 + 27517382
CAACAGCCAACCGUUCCAAAUUGCCAAGCUGCAGCCUCUAAG--------AUCCACAGAUCUGCA-------------CAUUUUCCGAUCUUG-AGAUCGUGAGAGGCGCAAG
.....((..............(((......)))((((((..(--------(((((.(((((....-------------........)))))))-.))))...))))))))... ( -24.90, z-score =  -2.21, R)
>droSec1.super_0 8820930 91 + 21120651
CAACAGCCAACCGUUCCAAAUUGCCAAGCUGCAGACUCUAAG--------AUCCACAGAUCUGCA-------------CAUUUUCCGAUCUUG-AGAUCGUGAGAGGCGCAAG
.....(((...................(.((((((.(((...--------......)))))))))-------------)..(((((((((...-.))))).)))))))..... ( -22.70, z-score =  -1.60, R)
>droYak2.chr3R 14023855 112 - 28832112
CCGCAGCAAACCGUUCCAAAUUGCCAAGCUGCGGACUCAAAGAUACCCAGAUCCACAGAUCUGCACAUUUUGGUUUUCCAUUUUCCGAUCCUC-AAAUCGUGAGAGGCGCAAG
(((((((....((........))....))))))).(((.........((((((....))))))(((....(((....)))......(((....-..)))))).)))....... ( -27.10, z-score =  -1.55, R)
>droEre2.scaffold_4770 5824603 103 + 17746568
---CGGCAAGCGGUUCCAAAUUGCCAAGCUGCGGACUCAGAGAUCCCCAGAUCCACAGAUCUGCACA------UUUUCCAUUUUCCGAUCCUC-AGAUCGUGAGAGGCGCAAG
---.(((((..(....)...)))))....((((..(((.((((....((((((....))))))....------.)))).....(((((((...-.))))).))))).)))).. ( -30.40, z-score =  -1.56, R)
>droAna3.scaffold_13340 1064864 105 + 23697760
UAACUGAAAACUGUUCCAAAUUACCGAGCUGCAGAUCUGCAGUUU-----UUUUGUAGAUUUUUUUGCUU---UAAGUUUUUUGCAGAUUUGGCAGAUCGUGAGAGGCACAAG
...........(((.((...((((.((.((((((((((((((.((-----(...(((((....)))))..---.)))....)))))))))).)))).))))))..)).))).. ( -28.80, z-score =  -2.04, R)
>consensus
CAACAGCAAACCGUUCCAAAUUGCCAAGCUGCAGACUCUAAG________AUCCACAGAUCUGCA_____________CAUUUUCCGAUCUUG_AGAUCGUGAGAGGCGCAAG
.....................((((.....(((((.((...................))))))).................(((((((((.....))))).)))))))).... (-13.23 = -13.51 +   0.28)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:13:33 2011