Locus 5067

Sequence ID dm3.chr2R
Location 17,483,984 – 17,484,050
Length 66
Max. P 0.989421
window6955 window6956

overview

Window 5

Location 17,483,984 – 17,484,050
Length 66
Sequences 3
Columns 67
Reading direction forward
Mean pairwise identity 65.96
Shannon entropy 0.44478
G+C content 0.72203
Mean single sequence MFE -20.07
Consensus MFE -11.26
Energy contribution -12.60
Covariance contribution 1.34
Combinations/Pair 1.13
Mean z-score -2.55
Structure conservation index 0.56
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.37
SVM RNA-class probability 0.989421
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr2R 17483984 66 + 21146708
AGGCGGCAGCCAGGACAGUCGCCUGUCCCGCUGCCAC-GCCUCCCUCCCCCCUAACCCCCCCUCGAU
((((((((((..((((((....)))))).))))))..-))))......................... ( -25.20, z-score =  -4.18, R)
>droYak2.chr2R 9449149 55 - 21139217
AGGCGGCAGCGAGGACAGCCGCCACGCCCCCCGACACCGACCCCUUAUCCCCUGA------------
.((((((..........))))))................................------------ ( -12.70, z-score =  -0.17, R)
>droSec1.super_9 810997 52 + 3197100
AGGCGGCAGCCAGGACAGUCUCUUGUCCCGCUGCCAC-GCCCCCCGAACCCCU--------------
.(((((((((..((((((....)))))).))))))..-)))............-------------- ( -22.30, z-score =  -3.31, R)
>consensus
AGGCGGCAGCCAGGACAGUCGCCUGUCCCGCUGCCAC_GCCCCCCUAACCCCU_A____________
.((((((((.(.((((((....)))))).))))))...))).......................... (-11.26 = -12.60 +   1.34)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 17,483,984 – 17,484,050
Length 66
Sequences 3
Columns 67
Reading direction reverse
Mean pairwise identity 65.96
Shannon entropy 0.44478
G+C content 0.72203
Mean single sequence MFE -25.17
Consensus MFE -19.86
Energy contribution -20.87
Covariance contribution 1.00
Combinations/Pair 1.13
Mean z-score -0.96
Structure conservation index 0.79
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.77
SVM RNA-class probability 0.811480
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr2R 17483984 66 - 21146708
AUCGAGGGGGGGUUAGGGGGGAGGGAGGC-GUGGCAGCGGGACAGGCGACUGUCCUGGCUGCCGCCU
.........................((((-..(((((((((((((....))))))).)))))))))) ( -30.30, z-score =  -2.17, R)
>droYak2.chr2R 9449149 55 + 21139217
------------UCAGGGGAUAAGGGGUCGGUGUCGGGGGGCGUGGCGGCUGUCCUCGCUGCCGCCU
------------..........(((((.(((((..(((.(((......))).))).))))))).))) ( -20.20, z-score =   0.83, R)
>droSec1.super_9 810997 52 - 3197100
--------------AGGGGUUCGGGGGGC-GUGGCAGCGGGACAAGAGACUGUCCUGGCUGCCGCCU
--------------...........((((-..((((((((((((......)))))).)))))))))) ( -25.00, z-score =  -1.55, R)
>consensus
____________U_AGGGGAUAGGGGGGC_GUGGCAGCGGGACAGGCGACUGUCCUGGCUGCCGCCU
..............................(((((((((((((((....)))))))).))))))).. (-19.86 = -20.87 +   1.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:41:14 2011