Locus 138

Sequence ID	dm3.chr2L
Location	919,841 – 919,904
Length	63
Max. P	0.831325

overview

Window 6

Location	919,841 – 919,904
Length	63
Sequences	6
Columns	63
Reading direction	forward
Mean pairwise identity	72.35
Shannon entropy	0.53413
G+C content	0.55643
Mean single sequence MFE	-18.12
Consensus MFE	-11.02
Energy contribution	-11.00
Covariance contribution	-0.02
Combinations/Pair	1.38
Mean z-score	-0.94
Structure conservation index	0.61
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.58
SVM RNA-class probability	0.749206
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 919841 63 + 23011544
CGGGGCCACGACUCGCGCCAGAUAUAUUGCGGAAAAUGUACGCGAAUUGGCAGUAGAGUUGGC
....((((..(((((((((((.....(((((.........))))).))))).)).)))))))) ( -18.90, z-score =  -1.08, R)
>droEre2.scaffold_4929 982375 63 + 26641161
CGGGGCCAGGAGUCCCGCCAGAUAUAUUGCGGCAAAUUUACGCGAAUUGGCAGAAGACUUGGC
....((((((..((..(((((.....(((((.........))))).))))).))...)))))) ( -18.80, z-score =  -0.94, R)
>droYak2.chr2L 907027 63 + 22324452
CAGGGCCAUGAGUUCCGCCAGAUACAUUGCGGCAAAUUUACGCGAAUUGGCAGAGGACUUGGC
....((((..(((((((((((.....(((((.........))))).))))).).))))))))) ( -18.70, z-score =  -1.44, R)
>droSec1.super_14 891298 62 + 2068291
CGGGGACACGACUCCCGCCAGAUAUAUUGCGG-AAAUUUACGCGAAUUGGCAGAAGAGUUGCC
.(....).((((((..(((((.....(((((.-.......))))).)))))....)))))).. ( -18.40, z-score =  -2.02, R)
>droSim1.chr2L 909487 62 + 22036055
CGGGGCCACGACUCCCGCCAGAUAUAUUGCGG-AAAUUUACGCGAAUUGGCAGAAGAGUUCGC
.((((.......))))(((((.....(((((.-.......))))).)))))............ ( -15.70, z-score =  -0.24, R)
>droVir3.scaffold_13047 12264714 56 + 19223366
-------UUCACCUUGGGCACACGCUGUGCUGAACGUGCACGUGCGGUUGCGCUAGUUUCGGG
-------....(((((((((..((((((((.......))))).)))..))).))))....)). ( -18.20, z-score =   0.06, R)
>consensus
CGGGGCCACGACUCCCGCCAGAUAUAUUGCGG_AAAUUUACGCGAAUUGGCAGAAGAGUUGGC
........((((((..(((((.....(((((.........))))).)))))....)))))).. (-11.02 = -11.00 +  -0.02)

alignment

secondary structure

dotplot

Window 7

Location	919,841 – 919,904
Length	63
Sequences	6
Columns	63
Reading direction	reverse
Mean pairwise identity	72.35
Shannon entropy	0.53413
G+C content	0.55643
Mean single sequence MFE	-17.15
Consensus MFE	-9.31
Energy contribution	-11.53
Covariance contribution	2.22
Combinations/Pair	1.28
Mean z-score	-1.33
Structure conservation index	0.54
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.84
SVM RNA-class probability	0.831325
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 919841 63 - 23011544
GCCAACUCUACUGCCAAUUCGCGUACAUUUUCCGCAAUAUAUCUGGCGCGAGUCGUGGCCCCG
((((((((...((((((((.(((.........)))))).....))))).))))..)))).... ( -15.00, z-score =  -1.07, R)
>droEre2.scaffold_4929 982375 63 - 26641161
GCCAAGUCUUCUGCCAAUUCGCGUAAAUUUGCCGCAAUAUAUCUGGCGGGACUCCUGGCCCCG
((((.(..(((((((((((((.(((....))))).))).....))))))))..).)))).... ( -18.50, z-score =  -1.64, R)
>droYak2.chr2L 907027 63 - 22324452
GCCAAGUCCUCUGCCAAUUCGCGUAAAUUUGCCGCAAUGUAUCUGGCGGAACUCAUGGCCCUG
((((.(...((((((((((((.(((....))))).))).....)))))))...).)))).... ( -16.90, z-score =  -1.45, R)
>droSec1.super_14 891298 62 - 2068291
GGCAACUCUUCUGCCAAUUCGCGUAAAUUU-CCGCAAUAUAUCUGGCGGGAGUCGUGUCCCCG
((((...((((((((((((.(((.......-.)))))).....)))))))))...)))).... ( -19.70, z-score =  -2.89, R)
>droSim1.chr2L 909487 62 - 22036055
GCGAACUCUUCUGCCAAUUCGCGUAAAUUU-CCGCAAUAUAUCUGGCGGGAGUCGUGGCCCCG
((.(...((((((((((((.(((.......-.)))))).....)))))))))...).)).... ( -18.00, z-score =  -1.26, R)
>droVir3.scaffold_13047 12264714 56 - 19223366
CCCGAAACUAGCGCAACCGCACGUGCACGUUCAGCACAGCGUGUGCCCAAGGUGAA-------
.((.......(((....)))..(..((((((......))))))..)....))....------- ( -14.80, z-score =   0.31, R)
>consensus
GCCAACUCUUCUGCCAAUUCGCGUAAAUUU_CCGCAAUAUAUCUGGCGGGAGUCGUGGCCCCG
((((...(((((((((((..(((.........)))...))...)))))))))...)))).... ( -9.31 = -11.53 +   2.22)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:07:23 2011