Locus 2635

Sequence ID dm3.chr2L
Location 20,625,800 – 20,625,896
Length 96
Max. P 0.944871
window3617 window3618

overview

Window 7

Location 20,625,800 – 20,625,896
Length 96
Sequences 4
Columns 97
Reading direction forward
Mean pairwise identity 69.82
Shannon entropy 0.48850
G+C content 0.55019
Mean single sequence MFE -21.65
Consensus MFE -12.02
Energy contribution -12.90
Covariance contribution 0.88
Combinations/Pair 1.18
Mean z-score -1.43
Structure conservation index 0.56
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.73
SVM RNA-class probability 0.801071
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr2L 20625800 96 + 23011544
-CGCACACAUUGGUGCCUGUGAGGCACACUCAUGUGCAUUGUCCAUGCACAGAUGCGCCAGCCCACUCACACUCACACACACACGUGCAUACCACUC
-.((((....(((((..((((((((.((.((.(((((((.....))))))))))).))).......)))))..))).)).....))))......... ( -28.81, z-score =  -1.13, R)
>droSim1.chr2L 20188987 93 + 22036055
-CGCACACAUCGGUGCCUGUGACGCACACUCAUGUGCAUUGUCCAUGCACAGAUGCGCCCACCCUCUCUCACACACACACA---ACACACACCACUC
-.((...((((.((((.((.((((((((....)))))...))))).)))).)))).)).......................---............. ( -20.90, z-score =  -1.30, R)
>droSec1.super_18 505877 93 + 1342155
-CGCACACAUUGGUGCCUGUGACGCACACUCAUGUGCAUUGUCCAUGCACAGAUGCGCCCACCCUCUCUCACACACACACA---ACACACACUACUC
-........((((((..(((((((((...((.(((((((.....)))))))))))))...........)))))..))).))---)............ ( -20.70, z-score =  -1.12, R)
>droYak2.chr2R 6973813 75 + 21139217
CCACACAGAGUAGUGUCUUCAACGCACAC--ACAUGCAUUGUCCACACACUCUCACAC--GCUCGUGAACACAC-CACUC-----------------
.......((((.((((...(((.(((...--...))).)))...))))))))((((..--....))))......-.....----------------- ( -16.20, z-score =  -2.18, R)
>consensus
_CGCACACAUUGGUGCCUGUGACGCACACUCAUGUGCAUUGUCCAUGCACAGAUGCGCCCACCCUCUCACACACACACACA___ACACACACCACUC
.......((((.((((.((.(((((((......))))...))))).)))).)))).......................................... (-12.02 = -12.90 +   0.88)

alignment

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secondary structure

Postscript

dotplot

Postscript

Window 8

Location 20,625,800 – 20,625,896
Length 96
Sequences 4
Columns 97
Reading direction reverse
Mean pairwise identity 69.82
Shannon entropy 0.48850
G+C content 0.55019
Mean single sequence MFE -35.68
Consensus MFE -18.38
Energy contribution -17.38
Covariance contribution -1.00
Combinations/Pair 1.41
Mean z-score -2.03
Structure conservation index 0.51
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.50
SVM RNA-class probability 0.944871
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr2L 20625800 96 - 23011544
GAGUGGUAUGCACGUGUGUGUGUGAGUGUGAGUGGGCUGGCGCAUCUGUGCAUGGACAAUGCACAUGAGUGUGCCUCACAGGCACCAAUGUGUGCG-
.....(((((((...((((.(((((((.(....).)).(((((((((((((((.....))))))).)).))))))))))).))))...))))))).- ( -40.10, z-score =  -1.10, R)
>droSim1.chr2L 20188987 93 - 22036055
GAGUGGUGUGUGU---UGUGUGUGUGUGAGAGAGGGUGGGCGCAUCUGUGCAUGGACAAUGCACAUGAGUGUGCGUCACAGGCACCGAUGUGUGCG-
.....(((..(((---((.((((.(((((.......((.((((.(((((((((.....))))))).)))))).))))))).)))))))))..))).- ( -36.31, z-score =  -1.73, R)
>droSec1.super_18 505877 93 - 1342155
GAGUAGUGUGUGU---UGUGUGUGUGUGAGAGAGGGUGGGCGCAUCUGUGCAUGGACAAUGCACAUGAGUGUGCGUCACAGGCACCAAUGUGUGCG-
.....(((..(((---((.((((.(((((.......((.((((.(((((((((.....))))))).)))))).))))))).)))))))))..))).- ( -36.81, z-score =  -2.00, R)
>droYak2.chr2R 6973813 75 - 21139217
-----------------GAGUG-GUGUGUUCACGAGC--GUGUGAGAGUGUGUGGACAAUGCAUGU--GUGUGCGUUGAAGACACUACUCUGUGUGG
-----------------(((((-(((((((((((.((--........)).)))))))(((((((..--..)))))))....)))))))))....... ( -29.50, z-score =  -3.31, R)
>consensus
GAGUGGUGUGUGU___UGUGUGUGUGUGAGAGAGGGCGGGCGCAUCUGUGCAUGGACAAUGCACAUGAGUGUGCGUCACAGGCACCAAUGUGUGCG_
.......................................((((((.(((((((.....)))))))...)))))).......((((......)))).. (-18.38 = -17.38 +  -1.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:54:57 2011