Locus 9865

Sequence ID dm3.chr3R
Location 9,499,097 – 9,499,177
Length 80
Max. P 0.952559
window13546 window13547

overview

Window 6

Location 9,499,097 – 9,499,177
Length 80
Sequences 9
Columns 88
Reading direction forward
Mean pairwise identity 76.11
Shannon entropy 0.47934
G+C content 0.42428
Mean single sequence MFE -24.17
Consensus MFE -8.18
Energy contribution -8.68
Covariance contribution 0.50
Combinations/Pair 1.39
Mean z-score -2.92
Structure conservation index 0.34
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.49
SVM RNA-class probability 0.943577
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 9499097 80 + 27905053
AAACAUGCAA----AUGAAUUUUUCAUUUGCAUGUGUCCUUCGC----CCAAUGAGCGUAAGGACUUGUGGACACACUGGCACAACUG
..((((((((----((((.....))))))))))))(((((((((----.......))).))))))(((((..(.....).)))))... ( -30.00, z-score =  -4.55, R)
>droSim1.chr3R 15580916 80 - 27517382
AAACAUGCAA----AUGAAUUUUUCAUUUGCAUGUGUCCUUCGC----CCAAUGAGCGUAAGGACUUGUGGACACACUGGCACAACUG
..((((((((----((((.....))))))))))))(((((((((----.......))).))))))(((((..(.....).)))))... ( -30.00, z-score =  -4.55, R)
>droSec1.super_0 8612709 80 - 21120651
AAACAUGCAA----AUGAAUUUUUCAUUUGCAUGUGUCCUUCGC----CCAAUGAGCGUAAGGACUUGUGGACACACUGGCACAACUG
..((((((((----((((.....))))))))))))(((((((((----.......))).))))))(((((..(.....).)))))... ( -30.00, z-score =  -4.55, R)
>droYak2.chr3R 13807447 80 + 28832112
AAACAUGCAA----AUGAAUUUUUCAUUUGCAUGUGUCCUUCGC----CCAAUGAGCGUAAGGACUUGUGGACACACUGGCACAACUG
..((((((((----((((.....))))))))))))(((((((((----.......))).))))))(((((..(.....).)))))... ( -30.00, z-score =  -4.55, R)
>droEre2.scaffold_4770 5610176 80 - 17746568
AAACAUGCAA----AUGAAUUUUUCAUUUGCAUGUGUCCUUCGC----CCAAUGAGCGUAAGGAUUUGUGGACAUACUGGCACAACGG
..((((((((----((((.....))))))))))))(((((((((----.......))).))))))(((((..(.....).)))))... ( -27.90, z-score =  -3.61, R)
>droAna3.scaffold_13340 2046363 67 + 23697760
AAACAUGGAA----AUGAAAAAUUCAUUUGCAUGUGUCCUUCGG----C-----------AGGAUUUGUGGACACACUGGAAAAAC--
..(((((.((----((((.....)))))).)))))(((((....----.-----------)))))..(((....))).........-- ( -16.90, z-score =  -2.00, R)
>dp4.chr2 16940291 82 + 30794189
AAACGUGCAA----AUUAAAAAUUCAUUUGCAUGCGUCCUUCGCUUCGCAAAUAAGCGCCUGGAUUUGAGAACACACUGGC--AACUG
...(((((((----((.........))))))))).((((..(((((.......)))))...)))).............(..--..).. ( -16.70, z-score =  -0.28, R)
>droPer1.super_0 8373476 82 - 11822988
AAACGUGCAA----AUUAAAAAUUCAUUUGCAUGCGUCCUUCGCUUCGCAAAUAAGCGCCUGGAUUUGCGAACACACUGGC--AACUG
...(((((((----((.........))))))))).(((......(((((((((.((...))..)))))))))......)))--..... ( -19.10, z-score =  -0.90, R)
>droVir3.scaffold_13047 9272525 77 + 19223366
AAAUUGGCUACAACAUGAAUUAUUUAGUUGUAUGCGCGUUUUUC-----AGAUAAGCGCCAAGAUUCUUGG-CACCCAAACUG-----
...((((.((((((.(((.....)))))))))(((((((((...-----....))))))((((...)))))-)).))))....----- ( -16.90, z-score =  -1.29, R)
>consensus
AAACAUGCAA____AUGAAUUUUUCAUUUGCAUGUGUCCUUCGC____CCAAUGAGCGUAAGGAUUUGUGGACACACUGGCACAACUG
...(((((((....((((.....))))))))))).((((..(((...........)))...))))....................... ( -8.18 =  -8.68 +   0.50)

alignment

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secondary structure

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dotplot

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Window 7

Location 9,499,097 – 9,499,177
Length 80
Sequences 9
Columns 88
Reading direction reverse
Mean pairwise identity 76.11
Shannon entropy 0.47934
G+C content 0.42428
Mean single sequence MFE -26.36
Consensus MFE -7.83
Energy contribution -7.93
Covariance contribution 0.10
Combinations/Pair 1.30
Mean z-score -3.21
Structure conservation index 0.30
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.58
SVM RNA-class probability 0.952559
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 9499097 80 - 27905053
CAGUUGUGCCAGUGUGUCCACAAGUCCUUACGCUCAUUGG----GCGAAGGACACAUGCAAAUGAAAAAUUCAU----UUGCAUGUUU
...(((((.(.....)..)))))((((((.((((.....)----)))))))))((((((((((((.....))))----)))))))).. ( -32.50, z-score =  -4.77, R)
>droSim1.chr3R 15580916 80 + 27517382
CAGUUGUGCCAGUGUGUCCACAAGUCCUUACGCUCAUUGG----GCGAAGGACACAUGCAAAUGAAAAAUUCAU----UUGCAUGUUU
...(((((.(.....)..)))))((((((.((((.....)----)))))))))((((((((((((.....))))----)))))))).. ( -32.50, z-score =  -4.77, R)
>droSec1.super_0 8612709 80 + 21120651
CAGUUGUGCCAGUGUGUCCACAAGUCCUUACGCUCAUUGG----GCGAAGGACACAUGCAAAUGAAAAAUUCAU----UUGCAUGUUU
...(((((.(.....)..)))))((((((.((((.....)----)))))))))((((((((((((.....))))----)))))))).. ( -32.50, z-score =  -4.77, R)
>droYak2.chr3R 13807447 80 - 28832112
CAGUUGUGCCAGUGUGUCCACAAGUCCUUACGCUCAUUGG----GCGAAGGACACAUGCAAAUGAAAAAUUCAU----UUGCAUGUUU
...(((((.(.....)..)))))((((((.((((.....)----)))))))))((((((((((((.....))))----)))))))).. ( -32.50, z-score =  -4.77, R)
>droEre2.scaffold_4770 5610176 80 + 17746568
CCGUUGUGCCAGUAUGUCCACAAAUCCUUACGCUCAUUGG----GCGAAGGACACAUGCAAAUGAAAAAUUCAU----UUGCAUGUUU
...(((((.(.....)..))))).(((((.((((.....)----)))))))).((((((((((((.....))))----)))))))).. ( -28.70, z-score =  -4.20, R)
>droAna3.scaffold_13340 2046363 67 - 23697760
--GUUUUUCCAGUGUGUCCACAAAUCCU-----------G----CCGAAGGACACAUGCAAAUGAAUUUUUCAU----UUCCAUGUUU
--((((((((((..(........)..))-----------)----..)))))))(((((.((((((.....))))----)).))))).. ( -15.70, z-score =  -2.40, R)
>dp4.chr2 16940291 82 - 30794189
CAGUU--GCCAGUGUGUUCUCAAAUCCAGGCGCUUAUUUGCGAAGCGAAGGACGCAUGCAAAUGAAUUUUUAAU----UUGCACGUUU
.....--....(((((((((....((....(((......)))....)))))))))))((((((.........))----))))...... ( -19.10, z-score =   0.08, R)
>droPer1.super_0 8373476 82 + 11822988
CAGUU--GCCAGUGUGUUCGCAAAUCCAGGCGCUUAUUUGCGAAGCGAAGGACGCAUGCAAAUGAAUUUUUAAU----UUGCACGUUU
.....--....((((((((((........))((((.......))))...))))))))((((((.........))----))))...... ( -19.60, z-score =   0.35, R)
>droVir3.scaffold_13047 9272525 77 - 19223366
-----CAGUUUGGGUG-CCAAGAAUCUUGGCGCUUAUCU-----GAAAAACGCGCAUACAACUAAAUAAUUCAUGUUGUAGCCAAUUU
-----(((..((((((-(((((...))))))))))).))-----)......(.((.((((((............)))))))))..... ( -24.10, z-score =  -3.69, R)
>consensus
CAGUUGUGCCAGUGUGUCCACAAAUCCUUACGCUCAUUGG____GCGAAGGACACAUGCAAAUGAAAAAUUCAU____UUGCAUGUUU
.......((..((((((((..............................))))))))))............................. ( -7.83 =  -7.93 +   0.10)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:12:46 2011