Locus 6494

Sequence ID	dm3.chr3L
Location	7,084,197 – 7,084,292
Length	95
Max. P	0.992793

overview

Window 3

Location	7,084,197 – 7,084,292
Length	95
Sequences	6
Columns	95
Reading direction	forward
Mean pairwise identity	75.72
Shannon entropy	0.47374
G+C content	0.55985
Mean single sequence MFE	-29.87
Consensus MFE	-19.24
Energy contribution	-21.03
Covariance contribution	1.80
Combinations/Pair	1.33
Mean z-score	-1.39
Structure conservation index	0.64
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.05
SVM RNA-class probability	0.881846
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 7084197 95 + 24543557
AGACAUGCCCAAAUUAGGGCUAAAACACUGCGCCCAAACGACCUUCGGCUGGACUGGAUGGGACCAGUCUGAAACGGACUGGACGAGUGGCCGCC
......((((......)))).........(((.(((..((.(((((((.....))))).))..((((((((...)))))))).))..))).))). ( -34.10, z-score =  -2.39, R)
>droWil1.scaffold_180698 1940462 83 - 11422946
AAACACACACACACACAAGCAAAAAUGGUAUGCCUGAAUGACCUU-----------GAUAUCAC-GUUUGGGGUUGGACUUGUCGUGCAGUCACU
...........(((((((((......((....)).....(((((.-----------.(......-..)..))))).).))))).)))........ ( -16.30, z-score =   1.00, R)
>droEre2.scaffold_4784 21497761 95 - 25762168
AGACAUGCCCAAUCUAGGGCUAAAGCACUGCGCCCGACCGACCUUCGGCUGGACUGGAUGGGACCAGUCUGAAACGAACUGGACGAGUGGCCGCC
......((((......)))).........(((.(((..((.((((((..((((((((......))))))))...))))..)).))..))).))). ( -32.60, z-score =  -1.18, R)
>droYak2.chr3L 7677732 85 + 24197627
AGACAUGCCCAAACUAGGGCUAAAACAG----------CGACCUUCGGCUGGACUGGAUGGGACCAGUCUGAAACGGACUGGAGAAGUGGCCGCC
......((((......)))).......(----------((.(((((((.....))))).))..((((((((...)))))))).........))). ( -27.60, z-score =  -1.15, R)
>droSec1.super_2 7010497 95 + 7591821
AGACAUGCCCAAAUUAGGGCUAAAACACUGCGCCCAAACGACCUUCGGCUGGACUGGAUGGGACCAGUCUGAAGCGGACUGGACGAGUGGUUGCC
......((((......)))).........(((.(((..((.((.((.((((((((((......)))))))..))).))..)).))..))).))). ( -34.50, z-score =  -2.24, R)
>droSim1.chr3L 6590175 95 + 22553184
AGACAUGCCCAAAUUAGGGCUAAAACACUGCGCCCAAACGACCUUCGGCUGGACUGGAUGGGACCAGUCUGAAACGGACUGGACGAGUGGCCGCC
......((((......)))).........(((.(((..((.(((((((.....))))).))..((((((((...)))))))).))..))).))). ( -34.10, z-score =  -2.39, R)
>consensus
AGACAUGCCCAAACUAGGGCUAAAACACUGCGCCCAAACGACCUUCGGCUGGACUGGAUGGGACCAGUCUGAAACGGACUGGACGAGUGGCCGCC
......((((......)))).........(((.(((..((.(((((((.....))))).))..((((((((...)))))))).))..))).))). (-19.24 = -21.03 +   1.80)

alignment

secondary structure

dotplot

Window 4

Location	7,084,197 – 7,084,292
Length	95
Sequences	6
Columns	95
Reading direction	reverse
Mean pairwise identity	75.72
Shannon entropy	0.47374
G+C content	0.55985
Mean single sequence MFE	-32.70
Consensus MFE	-20.60
Energy contribution	-22.65
Covariance contribution	2.05
Combinations/Pair	1.36
Mean z-score	-2.29
Structure conservation index	0.63
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	2.57
SVM RNA-class probability	0.992793
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 7084197 95 - 24543557
GGCGGCCACUCGUCCAGUCCGUUUCAGACUGGUCCCAUCCAGUCCAGCCGAAGGUCGUUUGGGCGCAGUGUUUUAGCCCUAAUUUGGGCAUGUCU
.(((.(((..((.((..((.(((...((((((......)))))).))).)).)).))..))).))).........((((......))))...... ( -36.60, z-score =  -2.97, R)
>droWil1.scaffold_180698 1940462 83 + 11422946
AGUGACUGCACGACAAGUCCAACCCCAAAC-GUGAUAUC-----------AAGGUCAUUCAGGCAUACCAUUUUUGCUUGUGUGUGUGUGUGUUU
(((((((.((((.................)-))).....-----------..)))))))((.(((((((((........))).)))))).))... ( -17.93, z-score =   0.60, R)
>droEre2.scaffold_4784 21497761 95 + 25762168
GGCGGCCACUCGUCCAGUUCGUUUCAGACUGGUCCCAUCCAGUCCAGCCGAAGGUCGGUCGGGCGCAGUGCUUUAGCCCUAGAUUGGGCAUGUCU
((((((.((((((((...........((((((......))))))..((((.....)))).))))).))))))...((((......))))..))). ( -38.30, z-score =  -2.24, R)
>droYak2.chr3L 7677732 85 - 24197627
GGCGGCCACUUCUCCAGUCCGUUUCAGACUGGUCCCAUCCAGUCCAGCCGAAGGUCG----------CUGUUUUAGCCCUAGUUUGGGCAUGUCU
(((((((.((.....))((.(((...((((((......)))))).))).)).)))))----------))......((((......))))...... ( -29.30, z-score =  -2.39, R)
>droSec1.super_2 7010497 95 - 7591821
GGCAACCACUCGUCCAGUCCGCUUCAGACUGGUCCCAUCCAGUCCAGCCGAAGGUCGUUUGGGCGCAGUGUUUUAGCCCUAAUUUGGGCAUGUCU
((((..(((((((((((.(((((...((((((......)))))).)))....))....))))))).)))).....((((......)))).)))). ( -37.50, z-score =  -3.75, R)
>droSim1.chr3L 6590175 95 - 22553184
GGCGGCCACUCGUCCAGUCCGUUUCAGACUGGUCCCAUCCAGUCCAGCCGAAGGUCGUUUGGGCGCAGUGUUUUAGCCCUAAUUUGGGCAUGUCU
.(((.(((..((.((..((.(((...((((((......)))))).))).)).)).))..))).))).........((((......))))...... ( -36.60, z-score =  -2.97, R)
>consensus
GGCGGCCACUCGUCCAGUCCGUUUCAGACUGGUCCCAUCCAGUCCAGCCGAAGGUCGUUUGGGCGCAGUGUUUUAGCCCUAAUUUGGGCAUGUCU
.(((.(((..((.((..((.(((...((((((......)))))).))).)).)).))..))).))).........((((......))))...... (-20.60 = -22.65 +   2.05)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:08:53 2011