Locus 2608

Sequence ID dm3.chr2L
Location 20,486,980 – 20,487,050
Length 70
Max. P 0.877264
window3582 window3583

overview

Window 2

Location 20,486,980 – 20,487,050
Length 70
Sequences 11
Columns 70
Reading direction forward
Mean pairwise identity 99.22
Shannon entropy 0.01884
G+C content 0.37192
Mean single sequence MFE -12.01
Consensus MFE -11.85
Energy contribution -11.95
Covariance contribution 0.09
Combinations/Pair 1.00
Mean z-score -1.10
Structure conservation index 0.99
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.40
SVM RNA-class probability 0.679686
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 20486980 70 + 23011544
CCCAGUCACAUAUAAACACACUUCAGUGCGCUUAAAAAUUGCUUUAUUGCAGUUGGACUAUAAAAACGCA
...((((.....(((.(.(((....))).).)))..((((((......)))))).))))........... ( -12.30, z-score =  -1.16, R)
>droSim1.chr2L 20050434 69 + 22036055
CCCAGUCACAUAUAAACACACUUCAGUGCGCUUAAAAAUUGCUUUAUUGCAGUUGGACUAUAAAAACGC-
...((((.....(((.(.(((....))).).)))..((((((......)))))).))))..........- ( -12.30, z-score =  -1.21, R)
>droSec1.super_18 365217 70 + 1342155
CCCAGUCACAUAUAAACACACUUCAGUGCGCUUAAAAAUUGCUUUAUUGCAGUUGGACUAUAAAAACGCA
...((((.....(((.(.(((....))).).)))..((((((......)))))).))))........... ( -12.30, z-score =  -1.16, R)
>droYak2.chr2R 6842276 70 + 21139217
CCCAGUCACAUAUAAACACACUUCAGUGCGCUUAAAAAUUGCUUUAUUGCAGUUGGACUAUAAAAACGCA
...((((.....(((.(.(((....))).).)))..((((((......)))))).))))........... ( -12.30, z-score =  -1.16, R)
>droEre2.scaffold_4845 18634328 70 - 22589142
CCCAGUCACAUAUAAACACACUUCAGUGCGCUUAAAAAUUGCUUUAUUGCAGUUGGACUAUAAAAACGCA
...((((.....(((.(.(((....))).).)))..((((((......)))))).))))........... ( -12.30, z-score =  -1.16, R)
>droAna3.scaffold_12916 6985354 70 + 16180835
CCCAGUCACAUAUAAACACACUUCAGUGCGCUUAAAAAUUGCUUUAUUGCAGUUGGACUAUAAAAACGCA
...((((.....(((.(.(((....))).).)))..((((((......)))))).))))........... ( -12.30, z-score =  -1.16, R)
>dp4.chr4_group3 3846040 70 - 11692001
CCCAGUCACAUAUAAACACACUUCAGUGCGCUUAAAAAUUGCUUUAUUGCAGUUGGACUAUAAAAACGCA
...((((.....(((.(.(((....))).).)))..((((((......)))))).))))........... ( -12.30, z-score =  -1.16, R)
>droPer1.super_1 990231 70 - 10282868
CCCAGUCACAUAUAAACACACUUCAGUGCGCUUAAAAAUUGCUUUAUUGCAGUUGGACUAUAAAAUCGCA
...((((.....(((.(.(((....))).).)))..((((((......)))))).))))........... ( -12.30, z-score =  -1.24, R)
>droVir3.scaffold_12963 6592263 70 - 20206255
CCCAGUCACAUAUAAACACACUUCACUGCGCUUAAAAAUUGCUUUAUUGCAGUUGGACUAUAAAAACGCA
...((((.((..............((((((..((((......)))).))))))))))))........... (  -9.13, z-score =  -0.35, R)
>droMoj3.scaffold_6500 24554713 70 + 32352404
CCCAGUCACAUAUAAACACACUUCAGUGCGCUUAAAAAUUGCUUUAUUGCAGUUGGACUAUAAAAACGCA
...((((.....(((.(.(((....))).).)))..((((((......)))))).))))........... ( -12.30, z-score =  -1.16, R)
>droGri2.scaffold_15126 6249956 70 + 8399593
CCCAGUCACAUAUAAACACACUUCAGUGCGCUUAAAAAUUGCUUUAUUGCAGUUGGACUAUAAAAACGCA
...((((.....(((.(.(((....))).).)))..((((((......)))))).))))........... ( -12.30, z-score =  -1.16, R)
>consensus
CCCAGUCACAUAUAAACACACUUCAGUGCGCUUAAAAAUUGCUUUAUUGCAGUUGGACUAUAAAAACGCA
...((((.....(((.(.(((....))).).)))..((((((......)))))).))))........... (-11.85 = -11.95 +   0.09)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 20,486,980 – 20,487,050
Length 70
Sequences 11
Columns 70
Reading direction reverse
Mean pairwise identity 99.22
Shannon entropy 0.01884
G+C content 0.37192
Mean single sequence MFE -17.48
Consensus MFE -17.35
Energy contribution -17.45
Covariance contribution 0.09
Combinations/Pair 1.00
Mean z-score -1.50
Structure conservation index 0.99
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.03
SVM RNA-class probability 0.877264
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 20486980 70 - 23011544
UGCGUUUUUAUAGUCCAACUGCAAUAAAGCAAUUUUUAAGCGCACUGAAGUGUGUUUAUAUGUGACUGGG
..........(((((((..(((......))).....(((((((((....)))))))))..)).))))).. ( -17.80, z-score =  -1.59, R)
>droSim1.chr2L 20050434 69 - 22036055
-GCGUUUUUAUAGUCCAACUGCAAUAAAGCAAUUUUUAAGCGCACUGAAGUGUGUUUAUAUGUGACUGGG
-.........(((((((..(((......))).....(((((((((....)))))))))..)).))))).. ( -17.80, z-score =  -1.74, R)
>droSec1.super_18 365217 70 - 1342155
UGCGUUUUUAUAGUCCAACUGCAAUAAAGCAAUUUUUAAGCGCACUGAAGUGUGUUUAUAUGUGACUGGG
..........(((((((..(((......))).....(((((((((....)))))))))..)).))))).. ( -17.80, z-score =  -1.59, R)
>droYak2.chr2R 6842276 70 - 21139217
UGCGUUUUUAUAGUCCAACUGCAAUAAAGCAAUUUUUAAGCGCACUGAAGUGUGUUUAUAUGUGACUGGG
..........(((((((..(((......))).....(((((((((....)))))))))..)).))))).. ( -17.80, z-score =  -1.59, R)
>droEre2.scaffold_4845 18634328 70 + 22589142
UGCGUUUUUAUAGUCCAACUGCAAUAAAGCAAUUUUUAAGCGCACUGAAGUGUGUUUAUAUGUGACUGGG
..........(((((((..(((......))).....(((((((((....)))))))))..)).))))).. ( -17.80, z-score =  -1.59, R)
>droAna3.scaffold_12916 6985354 70 - 16180835
UGCGUUUUUAUAGUCCAACUGCAAUAAAGCAAUUUUUAAGCGCACUGAAGUGUGUUUAUAUGUGACUGGG
..........(((((((..(((......))).....(((((((((....)))))))))..)).))))).. ( -17.80, z-score =  -1.59, R)
>dp4.chr4_group3 3846040 70 + 11692001
UGCGUUUUUAUAGUCCAACUGCAAUAAAGCAAUUUUUAAGCGCACUGAAGUGUGUUUAUAUGUGACUGGG
..........(((((((..(((......))).....(((((((((....)))))))))..)).))))).. ( -17.80, z-score =  -1.59, R)
>droPer1.super_1 990231 70 + 10282868
UGCGAUUUUAUAGUCCAACUGCAAUAAAGCAAUUUUUAAGCGCACUGAAGUGUGUUUAUAUGUGACUGGG
..........(((((((..(((......))).....(((((((((....)))))))))..)).))))).. ( -17.80, z-score =  -1.77, R)
>droVir3.scaffold_12963 6592263 70 + 20206255
UGCGUUUUUAUAGUCCAACUGCAAUAAAGCAAUUUUUAAGCGCAGUGAAGUGUGUUUAUAUGUGACUGGG
..........(((((((..(((......))).....((((((((......))))))))..)).))))).. ( -14.30, z-score =  -0.22, R)
>droMoj3.scaffold_6500 24554713 70 - 32352404
UGCGUUUUUAUAGUCCAACUGCAAUAAAGCAAUUUUUAAGCGCACUGAAGUGUGUUUAUAUGUGACUGGG
..........(((((((..(((......))).....(((((((((....)))))))))..)).))))).. ( -17.80, z-score =  -1.59, R)
>droGri2.scaffold_15126 6249956 70 - 8399593
UGCGUUUUUAUAGUCCAACUGCAAUAAAGCAAUUUUUAAGCGCACUGAAGUGUGUUUAUAUGUGACUGGG
..........(((((((..(((......))).....(((((((((....)))))))))..)).))))).. ( -17.80, z-score =  -1.59, R)
>consensus
UGCGUUUUUAUAGUCCAACUGCAAUAAAGCAAUUUUUAAGCGCACUGAAGUGUGUUUAUAUGUGACUGGG
..........(((((((..(((......))).....(((((((((....)))))))))..)).))))).. (-17.35 = -17.45 +   0.09)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:54:28 2011