Locus 9570

Sequence ID dm3.chr3R
Location 7,416,136 – 7,416,276
Length 140
Max. P 0.956484
window13133 window13134

overview

Window 3

Location 7,416,136 – 7,416,239
Length 103
Sequences 6
Columns 116
Reading direction reverse
Mean pairwise identity 92.11
Shannon entropy 0.14010
G+C content 0.30076
Mean single sequence MFE -22.87
Consensus MFE -20.32
Energy contribution -20.43
Covariance contribution 0.11
Combinations/Pair 1.07
Mean z-score -2.22
Structure conservation index 0.89
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.63
SVM RNA-class probability 0.956484
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 7416136 103 - 27905053
-------------ACAUUGUAUUACAUUACAUUAAAUAUGUAAUUUAAACGGUACGACAGCACUUUCUAAUGUGCACGUGCUAAUUAAGUGUAAAAAUACAAAAUUCAAGCGCGAA
-------------..(((((.(((.(((((((.....))))))).))))))))......((((........)))).((((((.......((((....)))).......)))))).. ( -24.04, z-score =  -2.54, R)
>droAna3.scaffold_13340 13861665 103 - 23697760
-------------ACAUUGUAUUACAUUACAUUAAAUAUGUAAUUUAAACAGUACGCCUGCACGUACUAAUGUGCACGUACUAAUUAAGUGUAAAAAUACAAAAUUCAAGCGCGAA
-------------...(((((((....(((((.....)))))((((((..((((((..(((((((....)))))))))))))..)))))).....))))))).............. ( -24.60, z-score =  -2.64, R)
>droEre2.scaffold_4770 3542573 102 + 17746568
-------------ACAUUGUAUUACAUUACAUUAAAUAUGUAAUUUAAACGGUACGCCCGCACUUUCUAAUGUGCACGUACUAAUUAAGUGU-AAAAUACAAAAUUCAAGCGCGAA
-------------...(((((((....(((((.....)))))((((((..((((((...((((........)))).))))))..))))))..-..))))))).............. ( -21.80, z-score =  -1.99, R)
>droYak2.chr3R 11824819 103 + 28832112
-------------ACAUUGUAUUACAUUACAUUAAAUAUGUAAUUUAAACGGUACGCCAGCACUUUCUAAUGUGCACGUACUAAUUAAGUGUAAAAAUACAAAAUUCAAGCGCGAA
-------------...(((((((....(((((.....)))))((((((..((((((...((((........)))).))))))..)))))).....))))))).............. ( -21.80, z-score =  -2.07, R)
>droSec1.super_0 6572133 103 + 21120651
-------------ACAUUGUAUUACAUUACAUUAAAUAUGUAAUUUAAACGGUACGACAGCACUUUCUAAUGUGCACGUGCUAAUUAAGUGUAAAAAUACAAAAUUCAAGCGCGAA
-------------..(((((.(((.(((((((.....))))))).))))))))......((((........)))).((((((.......((((....)))).......)))))).. ( -24.04, z-score =  -2.54, R)
>droSim1.chr3R_random 487469 115 - 1307089
ACAUACAUUACAUACAUUAUA-AACAUUACAUUAAAUAUGUAAUUUAAACGGUACGACAGCACUUUCUAAUGUGCACGUGCUAAUUAAGUGUAAAAAUACAAAAUUCAAGCGCGAA
..........(.(((....((-(..(((((((.....))))))))))....))).)...((((........)))).((((((.......((((....)))).......)))))).. ( -20.94, z-score =  -1.56, R)
>consensus
_____________ACAUUGUAUUACAUUACAUUAAAUAUGUAAUUUAAACGGUACGACAGCACUUUCUAAUGUGCACGUACUAAUUAAGUGUAAAAAUACAAAAUUCAAGCGCGAA
................(((((((....(((((.....)))))((((((..((((((...((((........)))).))))))..)))))).....))))))).............. (-20.32 = -20.43 +   0.11)

alignment

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secondary structure

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dotplot

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Window 4

Location 7,416,172 – 7,416,276
Length 104
Sequences 6
Columns 113
Reading direction reverse
Mean pairwise identity 86.11
Shannon entropy 0.23711
G+C content 0.30831
Mean single sequence MFE -16.30
Consensus MFE -13.17
Energy contribution -13.70
Covariance contribution 0.53
Combinations/Pair 1.05
Mean z-score -1.70
Structure conservation index 0.81
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.71
SVM RNA-class probability 0.795402
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 7416172 104 - 27905053
GAACACUCACGAAAACACAUACAU---------ACAUACAUUAUAAACAUUGUAUUACAUUACAUUAAAUAUGUAAUUUAAACGGUACGACAGCACUUUCUAAUGUGCACGUG
.......((((.............---------...............(((((.(((.(((((((.....))))))).))))))))......((((........)))).)))) ( -17.30, z-score =  -2.10, R)
>droAna3.scaffold_13340 13861701 96 - 23697760
GAACACACACAUAUAU-----------------ACAUACAUAAUAUACAUUGUAUUACAUUACAUUAAAUAUGUAAUUUAAACAGUACGCCUGCACGUACUAAUGUGCACGUA
................-----------------...............(((((.(((.(((((((.....))))))).))))))))..((.(((((((....))))))).)). ( -17.70, z-score =  -1.14, R)
>droEre2.scaffold_4770 3542608 96 + 17746568
GAACACUCACGAAAAC-----------------ACAUACAUUAUAAACAUUGUAUUACAUUACAUUAAAUAUGUAAUUUAAACGGUACGCCCGCACUUUCUAAUGUGCACGUA
........(((.....-----------------...............(((((.(((.(((((((.....))))))).))))))))......((((........)))).))). ( -15.70, z-score =  -1.62, R)
>droYak2.chr3R 11824855 96 + 28832112
GAACACUCACGAGAAC-----------------ACAUACAUUAUAAACAUUGUAUUACAUUACAUUAAAUAUGUAAUUUAAACGGUACGCCAGCACUUUCUAAUGUGCACGUA
........(((.....-----------------...............(((((.(((.(((((((.....))))))).))))))))......((((........)))).))). ( -15.60, z-score =  -1.42, R)
>droSec1.super_0 6572169 100 + 21120651
GAACACUCACGAAAAC----ACAU---------ACAUACAUUAUAAACAUUGUAUUACAUUACAUUAAAUAUGUAAUUUAAACGGUACGACAGCACUUUCUAAUGUGCACGUG
.......((((.....----....---------...............(((((.(((.(((((((.....))))))).))))))))......((((........)))).)))) ( -17.30, z-score =  -2.23, R)
>droSim1.chr3R_random 487505 112 - 1307089
GAACACUCACGAAAACACAUACAUACAUUAUAAACAUACAUUACAUACAUUAUA-AACAUUACAUUAAAUAUGUAAUUUAAACGGUACGACAGCACUUUCUAAUGUGCACGUG
.......((((................................(.(((....((-(..(((((((.....))))))))))....))).)...((((........)))).)))) ( -14.20, z-score =  -1.72, R)
>consensus
GAACACUCACGAAAAC_________________ACAUACAUUAUAAACAUUGUAUUACAUUACAUUAAAUAUGUAAUUUAAACGGUACGACAGCACUUUCUAAUGUGCACGUA
........(((.....................................(((((.(((.(((((((.....))))))).))))))))......((((........)))).))). (-13.17 = -13.70 +   0.53)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:07:00 2011