Locus 10009

Sequence ID dm3.chr3R
Location 10,516,356 – 10,516,429
Length 73
Max. P 0.814217
window13756 window13757

overview

Window 6

Location 10,516,356 – 10,516,429
Length 73
Sequences 5
Columns 73
Reading direction forward
Mean pairwise identity 90.96
Shannon entropy 0.15858
G+C content 0.41370
Mean single sequence MFE -21.16
Consensus MFE -17.24
Energy contribution -16.44
Covariance contribution -0.80
Combinations/Pair 1.32
Mean z-score -2.03
Structure conservation index 0.81
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.78
SVM RNA-class probability 0.814217
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 10516356 73 + 27905053
UCUAAUAGUUGCUGCAUCGCUCUUUGAGGUUUACUUUGAGCGAUUAGCAUAGUGGCCACAUAAUGUGACAUCA
.........(((((.(((((((...(((.....))).))))))))))))..(((..(((.....))).))).. ( -21.70, z-score =  -2.09, R)
>droSim1.chr3R 16570596 73 - 27517382
UCUAAUAGUUGCUGCAACGCUUUUUGAGGUUUACCUUAAGCGAUUAGCAUAGUGGCCACAUAAUGUGACAUCA
.........(((((...((((...(((((....)))))))))..)))))..(((..(((.....))).))).. ( -16.90, z-score =  -0.82, R)
>droSec1.super_0 9703822 73 - 21120651
UCUAAUAGUUGCUGCAACGCUUUUUGAGGUUUACCUUAAGCGAUUAGCAUAGUGGUCACAUAAUGUGACACCA
.........(((((...((((...(((((....)))))))))..))))).....(((((.....))))).... ( -20.40, z-score =  -2.24, R)
>droYak2.chr3R 12915666 73 - 28832112
UCUAAUAGUGGCUGCAUCGCUUUUUGAGGUUUACCUCAGGCGAUUAGCAUAGUCGCCACAUAAUGUGACAUCA
..........((((.((((((...(((((....)))))))))))))))...(((((........))))).... ( -24.70, z-score =  -3.34, R)
>droEre2.scaffold_4770 10050844 73 + 17746568
UCUAAUAGUGGCUGCAUUGCUUGUUGAGGUUUACCUCAAGCGAUUAGCACUGUGGCAACAUAAUGUGACAUCA
......((((.(((.((((((...(((((....))))))))))))))))))((.(((......))).)).... ( -22.10, z-score =  -1.65, R)
>consensus
UCUAAUAGUUGCUGCAUCGCUUUUUGAGGUUUACCUUAAGCGAUUAGCAUAGUGGCCACAUAAUGUGACAUCA
..........((((.(((((((...((((....)))))))))))))))...((.((........)).)).... (-17.24 = -16.44 +  -0.80)

alignment

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secondary structure

Postscript

dotplot

Postscript

Window 7

Location 10,516,356 – 10,516,429
Length 73
Sequences 5
Columns 73
Reading direction reverse
Mean pairwise identity 90.96
Shannon entropy 0.15858
G+C content 0.41370
Mean single sequence MFE -18.77
Consensus MFE -14.82
Energy contribution -15.54
Covariance contribution 0.72
Combinations/Pair 1.11
Mean z-score -1.82
Structure conservation index 0.79
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.22
SVM RNA-class probability 0.599878
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 10516356 73 - 27905053
UGAUGUCACAUUAUGUGGCCACUAUGCUAAUCGCUCAAAGUAAACCUCAAAGAGCGAUGCAGCAACUAUUAGA
....(((((.....))))).....((((.(((((((...............)))))))..))))......... ( -19.76, z-score =  -2.43, R)
>droSim1.chr3R 16570596 73 + 27517382
UGAUGUCACAUUAUGUGGCCACUAUGCUAAUCGCUUAAGGUAAACCUCAAAAAGCGUUGCAGCAACUAUUAGA
....(((((.....))))).....((((...(((((.(((....)))....)))))....))))......... ( -16.60, z-score =  -1.07, R)
>droSec1.super_0 9703822 73 + 21120651
UGGUGUCACAUUAUGUGACCACUAUGCUAAUCGCUUAAGGUAAACCUCAAAAAGCGUUGCAGCAACUAUUAGA
(((((((((.....)))).)))))((((...(((((.(((....)))....)))))....))))......... ( -20.10, z-score =  -2.51, R)
>droYak2.chr3R 12915666 73 + 28832112
UGAUGUCACAUUAUGUGGCGACUAUGCUAAUCGCCUGAGGUAAACCUCAAAAAGCGAUGCAGCCACUAUUAGA
...((((((.....)))))).....(((.(((((.(((((....)))))....)))))..))).......... ( -22.20, z-score =  -2.93, R)
>droEre2.scaffold_4770 10050844 73 - 17746568
UGAUGUCACAUUAUGUUGCCACAGUGCUAAUCGCUUGAGGUAAACCUCAACAAGCAAUGCAGCCACUAUUAGA
..............(((((.....((((....(.((((((....))))))).))))..))))).......... ( -15.20, z-score =  -0.18, R)
>consensus
UGAUGUCACAUUAUGUGGCCACUAUGCUAAUCGCUUAAGGUAAACCUCAAAAAGCGAUGCAGCAACUAUUAGA
....(((((.....)))))......(((.(((((((.(((....)))....)))))))..))).......... (-14.82 = -15.54 +   0.72)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:15:39 2011