Locus 5278

Sequence ID dm3.chr2R
Location 19,128,438 – 19,128,549
Length 111
Max. P 0.987583
window7234 window7235

overview

Window 4

Location 19,128,438 – 19,128,549
Length 111
Sequences 3
Columns 111
Reading direction forward
Mean pairwise identity 77.07
Shannon entropy 0.29783
G+C content 0.58774
Mean single sequence MFE -36.50
Consensus MFE -32.96
Energy contribution -33.63
Covariance contribution 0.67
Combinations/Pair 1.12
Mean z-score -2.18
Structure conservation index 0.90
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.28
SVM RNA-class probability 0.987583
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 19128438 111 + 21146708
CUCCAUCGCAGGGCGGGGAACUUGAACCGAGAUCCCUAUUGGGGUCAACUUCCCGGGGGCUCCGACACACGCAUCGCAUGGUAUCUCUGUACGAAGCUCCCAUUUAACACA
..........((((((..........))).((((((....)))))).....)))(((((((.(((((.....(((....))).....))).)).))))))).......... ( -33.90, z-score =  -0.21, R)
>droSim1.chr2R 17710491 92 + 19596830
----------------CUCCUUCGCAGGGAGACCCUU-UUGGGGUCAACUUCCCGGGGGCUCCGACACACGCAUCGCAUGGUAUCUCUGUACGGAGCUCCCAUUUCCCG--
----------------..........(((((((((..-...)))))........(((((((((((((.....(((....))).....))).))))))))))...)))).-- ( -39.30, z-score =  -3.46, R)
>droSec1.super_9 2422093 92 + 3197100
----------------CUCCUUCGCAGGGAGACCCUU-UUGGGGUCAAAUUCCCGGGGGCUCCGACACACGCAUCGCAUGGUAUCUCUGUACGGAGCUCUCAUUUCCCG--
----------------..........(((((((((..-...)))))........(((((((((((((.....(((....))).....))).))))))))))...)))).-- ( -36.30, z-score =  -2.88, R)
>consensus
________________CUCCUUCGCAGGGAGACCCUU_UUGGGGUCAACUUCCCGGGGGCUCCGACACACGCAUCGCAUGGUAUCUCUGUACGGAGCUCCCAUUUCCCG__
..........................((((((((((....))))))........(((((((((((((.....(((....))).....))).))))))))))...))))... (-32.96 = -33.63 +   0.67)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 19,128,438 – 19,128,549
Length 111
Sequences 3
Columns 111
Reading direction reverse
Mean pairwise identity 77.07
Shannon entropy 0.29783
G+C content 0.58774
Mean single sequence MFE -34.18
Consensus MFE -27.91
Energy contribution -28.58
Covariance contribution 0.67
Combinations/Pair 1.07
Mean z-score -1.23
Structure conservation index 0.82
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.35
SVM RNA-class probability 0.655491
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 19128438 111 - 21146708
UGUGUUAAAUGGGAGCUUCGUACAGAGAUACCAUGCGAUGCGUGUGUCGGAGCCCCCGGGAAGUUGACCCCAAUAGGGAUCUCGGUUCAAGUUCCCCGCCCUGCGAUGGAG
.(((......(((.((((((.(((.......(((((...)))))))))))))).)))(((((.((((((((....))(....))).)))).))))))))((......)).. ( -35.41, z-score =  -0.38, R)
>droSim1.chr2R 17710491 92 - 19596830
--CGGGAAAUGGGAGCUCCGUACAGAGAUACCAUGCGAUGCGUGUGUCGGAGCCCCCGGGAAGUUGACCCCAA-AAGGGUCUCCCUGCGAAGGAG----------------
--.((((..((((.((((((.(((.......(((((...)))))))))))))).)))).......(((((...-..)))))))))..........---------------- ( -36.41, z-score =  -2.07, R)
>droSec1.super_9 2422093 92 - 3197100
--CGGGAAAUGAGAGCUCCGUACAGAGAUACCAUGCGAUGCGUGUGUCGGAGCCCCCGGGAAUUUGACCCCAA-AAGGGUCUCCCUGCGAAGGAG----------------
--.(((......(.((((((.(((.......(((((...))))))))))))))))))((((....(((((...-..)))))))))..........---------------- ( -30.71, z-score =  -1.23, R)
>consensus
__CGGGAAAUGGGAGCUCCGUACAGAGAUACCAUGCGAUGCGUGUGUCGGAGCCCCCGGGAAGUUGACCCCAA_AAGGGUCUCCCUGCGAAGGAG________________
...((((..((((.((((((.(((.......(((((...)))))))))))))).)))).......(((((......))))))))).......................... (-27.91 = -28.58 +   0.67)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:45:11 2011