Locus 9997

Sequence ID dm3.chr3R
Location 10,425,579 – 10,425,670
Length 91
Max. P 0.935519
window13738 window13739

overview

Window 8

Location 10,425,579 – 10,425,670
Length 91
Sequences 7
Columns 102
Reading direction forward
Mean pairwise identity 58.97
Shannon entropy 0.77259
G+C content 0.55780
Mean single sequence MFE -31.32
Consensus MFE -9.94
Energy contribution -12.17
Covariance contribution 2.23
Combinations/Pair 1.53
Mean z-score -1.77
Structure conservation index 0.32
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.40
SVM RNA-class probability 0.935519
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 10425579 91 + 27905053
CCCUUUUUUUGAGGUGGGG---GGAUGGGAAAUGCC-UGUGCUUCAUUUUCCAU-------GACGCGGCACGCAGCGUGAAAAUGCUGCACCCCAUCCGCGG
((((((....)))).))(.---(((((((...((((-.(((..((((.....))-------))))))))).(((((((....)))))))..))))))).).. ( -40.50, z-score =  -3.02, R)
>droSim1.chr3R 16478479 87 - 27517382
-CCCUUUUUUGGGGUGGG----AGU--GGAAAUGCC-UAUGCUUCAUUUUCCAU-------GACGCGGCACGCAGCGUGAAAAUGCUGCACCCCAUCCGCGG
-..........(((((((----.((--.....((((-...((.((((.....))-------)).)))))).(((((((....)))))))))))))))).... ( -35.60, z-score =  -2.53, R)
>droSec1.super_0 9509048 89 - 21120651
CCCUUUUUUUGGGAUGGGG---AGU--GGAAAUGCC-UGUGCUUCAUUUUCCAU-------GACGCGGCACGCAGCGUGAAAAUGCUGCACCCCAUCCGCGG
...........((((((((---...--.....((((-.(((..((((.....))-------))))))))).(((((((....))))))).)))))))).... ( -39.00, z-score =  -3.36, R)
>droYak2.chr3R 12823503 76 - 28832112
---CCCUUUUGGGGGA---------------AUGCU-UGUGCUUCAUUUUCCAU-------GACGCGGCACGCAGCGUGAAAAUGCUGCACCCCAUCCGCGG
---(((...(((((..---------------.....-.(((((((((.....))-------))...)))))(((((((....))))))).)))))...).)) ( -30.50, z-score =  -2.47, R)
>droEre2.scaffold_4770 9959312 88 + 17746568
---CCCUUUUGGGGCAGG----------GGCAUGCC-CGUGCCUCGUUUUCCAUUUGCCAUGACGCGGCACGCAGCGUGAAAAUGCUGCACCCCAUCCGCGG
---(((...(((((...(----------((....))-)(((((.((((.............)))).)))))(((((((....))))))).)))))...).)) ( -39.82, z-score =  -2.18, R)
>droAna3.scaffold_13340 566125 70 + 23697760
---CCCGGCCGGAUUCCU----------GGGCUGCC-UCCGCUCCGUUUUCCGU-------GAAGCGGCACGCAGCGUGGAAAUGCUUUGA-----------
---.(((.((((....))----------))(((((.-.((((((((.....)).-------).)))))...))))).)))...........----------- ( -23.70, z-score =   0.43, R)
>droWil1.scaffold_181089 3282766 100 + 12369635
UCUUUUUUAUGAACUUAACUCCAAUCGGGAGGUACUAUAAAAUUUAUGCCUCGA--AAUCUGAAACUUCCCAUUCCUCCAAUACAUUCGGCCAUAUAUUUAG
.......((((..(......((....))((((((..(......)..))))))..--................................)..))))....... ( -10.10, z-score =   0.70, R)
>consensus
_C_CUUUUUUGGGGUGGG_________GGAAAUGCC_UGUGCUUCAUUUUCCAU_______GACGCGGCACGCAGCGUGAAAAUGCUGCACCCCAUCCGCGG
...(((....)))..................................................(((((...(((((((....))))))).......))))). ( -9.94 = -12.17 +   2.23)

alignment

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secondary structure

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dotplot

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Window 9

Location 10,425,579 – 10,425,670
Length 91
Sequences 7
Columns 102
Reading direction reverse
Mean pairwise identity 58.97
Shannon entropy 0.77259
G+C content 0.55780
Mean single sequence MFE -29.77
Consensus MFE -11.32
Energy contribution -11.82
Covariance contribution 0.50
Combinations/Pair 1.71
Mean z-score -1.19
Structure conservation index 0.38
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.95
SVM RNA-class probability 0.859140
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 10425579 91 - 27905053
CCGCGGAUGGGGUGCAGCAUUUUCACGCUGCGUGCCGCGUC-------AUGGAAAAUGAAGCACA-GGCAUUUCCCAUCC---CCCCACCUCAAAAAAAGGG
....((((((((.(((((........)))))(((((((.((-------((.....)))).))...-))))).))))))))---.(((............))) ( -34.70, z-score =  -2.19, R)
>droSim1.chr3R 16478479 87 + 27517382
CCGCGGAUGGGGUGCAGCAUUUUCACGCUGCGUGCCGCGUC-------AUGGAAAAUGAAGCAUA-GGCAUUUCC--ACU----CCCACCCCAAAAAAGGG-
((.....(((((((((((........)))))(((((((.((-------((.....)))).))...-)))))....--...----...)))))).....)).- ( -31.80, z-score =  -1.68, R)
>droSec1.super_0 9509048 89 + 21120651
CCGCGGAUGGGGUGCAGCAUUUUCACGCUGCGUGCCGCGUC-------AUGGAAAAUGAAGCACA-GGCAUUUCC--ACU---CCCCAUCCCAAAAAAAGGG
..(.((((((((.(((((........)))))(((((((.((-------((.....)))).))...-)))))....--...---))))))))).......... ( -35.60, z-score =  -2.78, R)
>droYak2.chr3R 12823503 76 + 28832112
CCGCGGAUGGGGUGCAGCAUUUUCACGCUGCGUGCCGCGUC-------AUGGAAAAUGAAGCACA-AGCAU---------------UCCCCCAAAAGGG---
((.....(((((.(((((........)))))((((....((-------((.....)))).)))).-.....---------------..)))))...)).--- ( -26.80, z-score =  -0.93, R)
>droEre2.scaffold_4770 9959312 88 - 17746568
CCGCGGAUGGGGUGCAGCAUUUUCACGCUGCGUGCCGCGUCAUGGCAAAUGGAAAACGAGGCACG-GGCAUGCC----------CCUGCCCCAAAAGGG---
((.....(((((((((((........)))))(((((.((((((.....)))....))).)))))(-((....))----------)..))))))...)).--- ( -37.30, z-score =  -0.79, R)
>droAna3.scaffold_13340 566125 70 - 23697760
-----------UCAAAGCAUUUCCACGCUGCGUGCCGCUUC-------ACGGAAAACGGAGCGGA-GGCAGCCC----------AGGAAUCCGGCCGGG---
-----------.....((..((((..(((((.(.(((((((-------.........))))))))-.)))))..----------.))))....))....--- ( -26.50, z-score =  -0.88, R)
>droWil1.scaffold_181089 3282766 100 - 12369635
CUAAAUAUAUGGCCGAAUGUAUUGGAGGAAUGGGAAGUUUCAGAUU--UCGAGGCAUAAAUUUUAUAGUACCUCCCGAUUGGAGUUAAGUUCAUAAAAAAGA
.......((((..(..((((.((((((...((((....))))..))--)))).))))..............((((.....))))....)..))))....... ( -15.70, z-score =   0.93, R)
>consensus
CCGCGGAUGGGGUGCAGCAUUUUCACGCUGCGUGCCGCGUC_______AUGGAAAAUGAAGCACA_GGCAUUUCC_________CCCACCCCAAAAAAG_G_
.......(((((.(((((........)))))((((..(((...............)))..))))........................)))))......... (-11.32 = -11.82 +   0.50)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:15:25 2011