Locus 1395

Sequence ID dm3.chr2L
Location 10,814,418 – 10,814,470
Length 52
Max. P 0.799290
window1900 window1901

overview

Window 0

Location 10,814,418 – 10,814,470
Length 52
Sequences 8
Columns 52
Reading direction forward
Mean pairwise identity 91.30
Shannon entropy 0.15948
G+C content 0.35942
Mean single sequence MFE -10.86
Consensus MFE -8.52
Energy contribution -8.53
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.14
Structure conservation index 0.78
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.73
SVM RNA-class probability 0.799290
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr2L 10814418 52 + 23011544
CACACAUUUCACUGCACACACUUUUGUGCGAGCAUGAAUAUAAUUUCAUUUU
.......((((.(((.(.(((....))).).))))))).............. (  -9.20, z-score =  -2.38, R)
>droSim1.chr2L 10621200 52 + 22036055
CACGCAUUUCGCUGCACACACUUUUGUGCGAGCAUGAAUAUAAUUUCAUUUU
..........((((((((......))))).)))(((((......)))))... ( -12.50, z-score =  -2.45, R)
>droSec1.super_3 6232685 52 + 7220098
CACGCAUUUCGCUGCACACACUUUUGUGCGAGCAUGAAUAUAAUUUCAUUUU
..........((((((((......))))).)))(((((......)))))... ( -12.50, z-score =  -2.45, R)
>droYak2.chr2L 7221500 50 + 22324452
CACGCAUUUCACUGCACAC--UUUUGUGCGAGCAUGAAUAUAAUUUCAUUUU
............((((((.--...))))))...(((((......)))))... (  -8.30, z-score =  -1.18, R)
>droEre2.scaffold_4929 12025203 50 - 26641161
CACGCAUUUCACUGCACAC--UUUUGUGCGAGCAUGAAUAUAAUUUCAUUUU
............((((((.--...))))))...(((((......)))))... (  -8.30, z-score =  -1.18, R)
>droAna3.scaffold_12916 14665792 50 + 16180835
UAGGCAUUACGCUGCACAC--UUUUGUGCGAGCAUGAAUAUAAUUUCAUUUU
..........((((((((.--...))))).)))(((((......)))))... ( -12.30, z-score =  -2.27, R)
>dp4.chr4_group4 3018678 50 + 6586962
CACACAUUAUGUUGCACAC--UUUUGUGCGAGCAUGAAUAUAAUUUCAUUUC
......((((((((((((.--...))))).)))))))............... ( -11.90, z-score =  -2.58, R)
>droPer1.super_10 2033327 50 + 3432795
CACACAUUAUGUUGCACAC--UUUUGUGCGAGCAUGAAUAUAAUUUCAUUUC
......((((((((((((.--...))))).)))))))............... ( -11.90, z-score =  -2.58, R)
>consensus
CACGCAUUUCGCUGCACAC__UUUUGUGCGAGCAUGAAUAUAAUUUCAUUUU
............((((((......))))))...(((((......)))))... ( -8.52 =  -8.53 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 10,814,418 – 10,814,470
Length 52
Sequences 8
Columns 52
Reading direction reverse
Mean pairwise identity 91.30
Shannon entropy 0.15948
G+C content 0.35942
Mean single sequence MFE -11.26
Consensus MFE -9.88
Energy contribution -9.90
Covariance contribution 0.02
Combinations/Pair 1.08
Mean z-score -1.33
Structure conservation index 0.88
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.18
SVM RNA-class probability 0.580725
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr2L 10814418 52 - 23011544
AAAAUGAAAUUAUAUUCAUGCUCGCACAAAAGUGUGUGCAGUGAAAUGUGUG
..........(((((((((((.(((((....))))).))).)).)))))).. ( -13.60, z-score =  -2.51, R)
>droSim1.chr2L 10621200 52 - 22036055
AAAAUGAAAUUAUAUUCAUGCUCGCACAAAAGUGUGUGCAGCGAAAUGCGUG
...(((((......)))))(((((((((....)))))).))).......... ( -12.70, z-score =  -1.38, R)
>droSec1.super_3 6232685 52 - 7220098
AAAAUGAAAUUAUAUUCAUGCUCGCACAAAAGUGUGUGCAGCGAAAUGCGUG
...(((((......)))))(((((((((....)))))).))).......... ( -12.70, z-score =  -1.38, R)
>droYak2.chr2L 7221500 50 - 22324452
AAAAUGAAAUUAUAUUCAUGCUCGCACAAAA--GUGUGCAGUGAAAUGCGUG
...(((((......)))))(((.(((((...--.)))))))).......... (  -9.70, z-score =  -0.67, R)
>droEre2.scaffold_4929 12025203 50 + 26641161
AAAAUGAAAUUAUAUUCAUGCUCGCACAAAA--GUGUGCAGUGAAAUGCGUG
...(((((......)))))(((.(((((...--.)))))))).......... (  -9.70, z-score =  -0.67, R)
>droAna3.scaffold_12916 14665792 50 - 16180835
AAAAUGAAAUUAUAUUCAUGCUCGCACAAAA--GUGUGCAGCGUAAUGCCUA
...(((((......)))))(((.(((((...--.)))))))).......... ( -11.90, z-score =  -1.98, R)
>dp4.chr4_group4 3018678 50 - 6586962
GAAAUGAAAUUAUAUUCAUGCUCGCACAAAA--GUGUGCAACAUAAUGUGUG
((.(((((......)))))..))(((((...--.)))))............. (  -9.90, z-score =  -1.02, R)
>droPer1.super_10 2033327 50 - 3432795
GAAAUGAAAUUAUAUUCAUGCUCGCACAAAA--GUGUGCAACAUAAUGUGUG
((.(((((......)))))..))(((((...--.)))))............. (  -9.90, z-score =  -1.02, R)
>consensus
AAAAUGAAAUUAUAUUCAUGCUCGCACAAAA__GUGUGCAGCGAAAUGCGUG
...(((((......)))))(((.(((((......)))))))).......... ( -9.88 =  -9.90 +   0.02)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:31:05 2011