Locus 2368

Sequence ID dm3.chr2L
Location 18,386,447 – 18,386,506
Length 59
Max. P 0.951191
window3262 window3263

overview

Window 2

Location 18,386,447 – 18,386,506
Length 59
Sequences 5
Columns 61
Reading direction forward
Mean pairwise identity 86.76
Shannon entropy 0.21303
G+C content 0.64050
Mean single sequence MFE -23.60
Consensus MFE -17.76
Energy contribution -18.16
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -2.27
Structure conservation index 0.75
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.11
SVM RNA-class probability 0.893119
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr2L 18386447 59 + 23011544
CCGUUUAGGCCAUUUAGGCCGCCUUCGCCACU--CCCAAUAAAGGGGCGUGGCUCUUGGCC
.......((((.....))))(((...((((((--(((......)))).)))))....))). ( -27.10, z-score =  -2.81, R)
>droEre2.scaffold_4845 16706759 52 - 22589142
---------CCGUUUAGGCCGCCUUCGCCUGCGCCCCAACAAAGGGGCGUGGCUCUUGGCC
---------.......(((((.....(((.(((((((......))))))))))...))))) ( -26.20, z-score =  -2.33, R)
>droYak2.chr2R 4903479 50 + 21139217
---------CCGUUUAGGCCGCCUUUGCCACU--CCCAAUAAAGGGGCGUGGCUCUUGGCC
---------.......(((((.....((((((--(((......)))).)))))...))))) ( -21.80, z-score =  -2.09, R)
>droSec1.super_7 2013002 50 + 3727775
---------CCGUUUAGGCCGCCUUCGCCACU--CCCAAUAAAGGGGCGUGGCUCUUGGCC
---------.......(((((.....((((((--(((......)))).)))))...))))) ( -21.10, z-score =  -1.89, R)
>droSim1.chr2L 18074065 50 + 22036055
---------CCGUUUAGGCCGCCUUCGCCACU--CCCAAUAAUGGGGCGUGGCUCUUGGCC
---------.......(((((.....((((((--((((....))))).)))))...))))) ( -21.80, z-score =  -2.25, R)
>consensus
_________CCGUUUAGGCCGCCUUCGCCACU__CCCAAUAAAGGGGCGUGGCUCUUGGCC
................(((((.....(((((...(((......)))..)))))...))))) (-17.76 = -18.16 +   0.40)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 18,386,447 – 18,386,506
Length 59
Sequences 5
Columns 61
Reading direction reverse
Mean pairwise identity 86.76
Shannon entropy 0.21303
G+C content 0.64050
Mean single sequence MFE -24.22
Consensus MFE -19.88
Energy contribution -20.28
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -2.26
Structure conservation index 0.82
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.57
SVM RNA-class probability 0.951191
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr2L 18386447 59 - 23011544
GGCCAAGAGCCACGCCCCUUUAUUGGG--AGUGGCGAAGGCGGCCUAAAUGGCCUAAACGG
.(((....(((((..(((......)))--.)))))...)))((((.....))))....... ( -28.30, z-score =  -2.89, R)
>droEre2.scaffold_4845 16706759 52 + 22589142
GGCCAAGAGCCACGCCCCUUUGUUGGGGCGCAGGCGAAGGCGGCCUAAACGG---------
((((....(((.((((((......))))))..)))......)))).......--------- ( -25.70, z-score =  -1.77, R)
>droYak2.chr2R 4903479 50 - 21139217
GGCCAAGAGCCACGCCCCUUUAUUGGG--AGUGGCAAAGGCGGCCUAAACGG---------
((((....(((((..(((......)))--.)))))......)))).......--------- ( -21.30, z-score =  -1.79, R)
>droSec1.super_7 2013002 50 - 3727775
GGCCAAGAGCCACGCCCCUUUAUUGGG--AGUGGCGAAGGCGGCCUAAACGG---------
((((....(((((..(((......)))--.)))))......)))).......--------- ( -22.40, z-score =  -2.08, R)
>droSim1.chr2L 18074065 50 - 22036055
GGCCAAGAGCCACGCCCCAUUAUUGGG--AGUGGCGAAGGCGGCCUAAACGG---------
((((....(((((..((((....))))--.)))))......)))).......--------- ( -23.40, z-score =  -2.74, R)
>consensus
GGCCAAGAGCCACGCCCCUUUAUUGGG__AGUGGCGAAGGCGGCCUAAACGG_________
((((....(((((..(((......)))...)))))......))))................ (-19.88 = -20.28 +   0.40)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:49:57 2011