Locus 1508

Sequence ID dm3.chr2L
Location 11,683,917 – 11,683,979
Length 62
Max. P 0.914955
window2060 window2061

overview

Window 0

Location 11,683,917 – 11,683,979
Length 62
Sequences 5
Columns 62
Reading direction forward
Mean pairwise identity 94.19
Shannon entropy 0.10118
G+C content 0.44839
Mean single sequence MFE -19.06
Consensus MFE -15.38
Energy contribution -16.22
Covariance contribution 0.84
Combinations/Pair 1.06
Mean z-score -2.53
Structure conservation index 0.81
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.24
SVM RNA-class probability 0.914955
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 11683917 62 + 23011544
UGGCCAAGUGUCAAGGGUUGGGCAAAUGUCCCACUCUCGAUUUCUUGCCUUUAUUAUUUAUG
.(((.(((.(((.(((((.((((....)))).))))).)))..))))))............. ( -20.20, z-score =  -3.21, R)
>droSim1.chr2L 11493447 62 + 22036055
UGGCCAAGUGUCAAGGGUUGGGCAAAUGUCCCACUCUCGAUUUCUUGCCUUUAUUAUUUAUG
.(((.(((.(((.(((((.((((....)))).))))).)))..))))))............. ( -20.20, z-score =  -3.21, R)
>droSec1.super_3 7075965 62 + 7220098
UGGCCAAGUGUCAAGGGUUGGGCAAAUGUCCCACUCUCGAUUUCUUGUCUUUAUUAUUUAUG
.((.((((.(((.(((((.((((....)))).))))).)))..)))).))............ ( -17.60, z-score =  -2.73, R)
>droYak2.chr2L 8107203 62 + 22324452
UGGCCAAGUGUCAAGGGUUGGGCCAAUGUCCCACUCUCGAUUUCUAGCCUUUAUUAUUUAUG
.(((.....(((.(((((.((((....)))).))))).))).....)))............. ( -17.40, z-score =  -1.88, R)
>droEre2.scaffold_4929 12915026 62 - 26641161
UGGCCAAGUGUCGCGGGUUGGGCCAAAGGGCCACUCUCGAUUUCUAGCCUUUAUUAUUUAUG
.(((.....((((.((((..((((....)))))))).)))).....)))............. ( -19.90, z-score =  -1.61, R)
>consensus
UGGCCAAGUGUCAAGGGUUGGGCAAAUGUCCCACUCUCGAUUUCUUGCCUUUAUUAUUUAUG
.(((.(((.(((.(((((.((((....)))).))))).)))..))))))............. (-15.38 = -16.22 +   0.84)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 11,683,917 – 11,683,979
Length 62
Sequences 5
Columns 62
Reading direction reverse
Mean pairwise identity 94.19
Shannon entropy 0.10118
G+C content 0.44839
Mean single sequence MFE -16.60
Consensus MFE -12.08
Energy contribution -12.52
Covariance contribution 0.44
Combinations/Pair 1.08
Mean z-score -2.41
Structure conservation index 0.73
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.37
SVM RNA-class probability 0.662072
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 11683917 62 - 23011544
CAUAAAUAAUAAAGGCAAGAAAUCGAGAGUGGGACAUUUGCCCAACCCUUGACACUUGGCCA
.............((((((...(((((.(((((.(....)))).)).)))))..))).))). ( -16.70, z-score =  -2.56, R)
>droSim1.chr2L 11493447 62 - 22036055
CAUAAAUAAUAAAGGCAAGAAAUCGAGAGUGGGACAUUUGCCCAACCCUUGACACUUGGCCA
.............((((((...(((((.(((((.(....)))).)).)))))..))).))). ( -16.70, z-score =  -2.56, R)
>droSec1.super_3 7075965 62 - 7220098
CAUAAAUAAUAAAGACAAGAAAUCGAGAGUGGGACAUUUGCCCAACCCUUGACACUUGGCCA
...............((((...(((((.(((((.(....)))).)).)))))..)))).... ( -13.70, z-score =  -2.31, R)
>droYak2.chr2L 8107203 62 - 22324452
CAUAAAUAAUAAAGGCUAGAAAUCGAGAGUGGGACAUUGGCCCAACCCUUGACACUUGGCCA
.............((((((...(((((.(((((.......))).)).)))))...)))))). ( -18.30, z-score =  -2.66, R)
>droEre2.scaffold_4929 12915026 62 + 26641161
CAUAAAUAAUAAAGGCUAGAAAUCGAGAGUGGCCCUUUGGCCCAACCCGCGACACUUGGCCA
.............((((((...(((.(.((((((....))))..)).).)))...)))))). ( -17.60, z-score =  -1.94, R)
>consensus
CAUAAAUAAUAAAGGCAAGAAAUCGAGAGUGGGACAUUUGCCCAACCCUUGACACUUGGCCA
.............(((......(((((.(((((.......))).)).)))))......))). (-12.08 = -12.52 +   0.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:33:19 2011