Locus 4620

Sequence ID dm3.chr2R
Location 14,626,980 – 14,627,079
Length 99
Max. P 0.996980
window6337 window6338

overview

Window 7

Location 14,626,980 – 14,627,079
Length 99
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 75.81
Shannon entropy 0.32067
G+C content 0.51582
Mean single sequence MFE -17.72
Consensus MFE -13.51
Energy contribution -13.29
Covariance contribution -0.22
Combinations/Pair 1.06
Mean z-score -3.08
Structure conservation index 0.76
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.02
SVM RNA-class probability 0.996980
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 14626980 99 + 21146708
CACCGCCUAAAAACCAUCAGAAAGCCCUAAAAACCACCUUUCACCAUCCCAGGCCGAAAAACCCCAG---------------------CCAUCUUCGAUGCGAUGCCAUCAGGCAGUGUG
(((.((((......((((.(((((.............)))))..((((...(((.(........).)---------------------))......)))).)))).....)))).))).. ( -19.22, z-score =  -2.55, R)
>droSec1.super_1 12135715 90 + 14215200
CACCGCCUAAAAACCACCAGAAAGCCCUAAAAACCACCUUUCACCAUCCCAU---------CCACAG---------------------CCAUCUUCGAAGCGAUGCCAUCAGGCAGUGUG
(((.((((...........(((((.............)))))..........---------.....(---------------------.((((........)))).)...)))).))).. ( -14.22, z-score =  -2.34, R)
>droYak2.chr2R 6566976 120 - 21139217
CACCGCCUAAAAACCACCAGAAAGCCCUAAAAACCACCUUUCACCACCCGAAAACCAAAAACCCAAAACCCAUAACCCAAAACAUCGCCCGUCUUCGAUGCGAUGCCAUCAGGCAGUGUG
(((.((((...........(((((.............)))))........................................((((((.((....))..)))))).....)))).))).. ( -19.72, z-score =  -4.35, R)
>consensus
CACCGCCUAAAAACCACCAGAAAGCCCUAAAAACCACCUUUCACCAUCCCAA__C_AAAAACCCCAG_____________________CCAUCUUCGAUGCGAUGCCAUCAGGCAGUGUG
(((.((((...........(((((.............)))))...............................................((((........)))).....)))).))).. (-13.51 = -13.29 +  -0.22)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 14,626,980 – 14,627,079
Length 99
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 75.81
Shannon entropy 0.32067
G+C content 0.51582
Mean single sequence MFE -32.90
Consensus MFE -21.85
Energy contribution -21.74
Covariance contribution -0.11
Combinations/Pair 1.08
Mean z-score -2.15
Structure conservation index 0.66
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.17
SVM RNA-class probability 0.903832
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 14626980 99 - 21146708
CACACUGCCUGAUGGCAUCGCAUCGAAGAUGG---------------------CUGGGGUUUUUCGGCCUGGGAUGGUGAAAGGUGGUUUUUAGGGCUUUCUGAUGGUUUUUAGGCGGUG
..((((((((((.(.((((.(((((.....((---------------------(((((....))))))).....)))))..(((.((((.....)))).))))))).)..)))))))))) ( -34.70, z-score =  -2.28, R)
>droSec1.super_1 12135715 90 - 14215200
CACACUGCCUGAUGGCAUCGCUUCGAAGAUGG---------------------CUGUGG---------AUGGGAUGGUGAAAGGUGGUUUUUAGGGCUUUCUGGUGGUUUUUAGGCGGUG
..((((((((((.(.(((((((..((((((.(---------------------((....---------((......))....))).))))))..))).....)))).)..)))))))))) ( -28.40, z-score =  -1.75, R)
>droYak2.chr2R 6566976 120 + 21139217
CACACUGCCUGAUGGCAUCGCAUCGAAGACGGGCGAUGUUUUGGGUUAUGGGUUUUGGGUUUUUGGUUUUCGGGUGGUGAAAGGUGGUUUUUAGGGCUUUCUGGUGGUUUUUAGGCGGUG
..((((((((((.((((((((.(((....)))))))))))(..((....((((((((((...(((.((((((.....)))))).)))..))))))))))))..)......)))))))))) ( -35.60, z-score =  -2.42, R)
>consensus
CACACUGCCUGAUGGCAUCGCAUCGAAGAUGG_____________________CUGGGGUUUUU_G__AUGGGAUGGUGAAAGGUGGUUUUUAGGGCUUUCUGGUGGUUUUUAGGCGGUG
..((((((((((.(.((((.((((................................................)))).....(((.((((.....)))).))))))).)..)))))))))) (-21.85 = -21.74 +  -0.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:32:44 2011