Locus 1757

Sequence ID	dm3.chr2L
Location	13,548,801 – 13,548,860
Length	59
Max. P	0.960146

overview

Window 6

Location	13,548,801 – 13,548,860
Length	59
Sequences	6
Columns	62
Reading direction	forward
Mean pairwise identity	86.40
Shannon entropy	0.26050
G+C content	0.52814
Mean single sequence MFE	-22.83
Consensus MFE	-18.76
Energy contribution	-18.96
Covariance contribution	0.20
Combinations/Pair	1.09
Mean z-score	-2.15
Structure conservation index	0.82
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.68
SVM RNA-class probability	0.960146
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 13548801 59 + 23011544
AAACAAGUUCUGGGCGCACAGUGGGGCAAGCUUAGAACU---GUAGUGACCACUGUGCGGCA
............(.((((((((((..((.((........---))..)).)))))))))).). ( -23.20, z-score =  -2.07, R)
>dp4.Unknown_group_668 8459 53 - 12025
AAACAAGUUCUAGCC-UACAGUGGGGCACA-UUAGGGUU-------UGCCCACUGUGCAGCA
............((.-(((((((((.((.(-(....)).-------)))))))))))..)). ( -17.00, z-score =  -0.73, R)
>droEre2.scaffold_4929 14738399 62 - 26641161
AAACAAGUUCUGGGCGCACAGUGGUGCAAGCUUAGAAGUCUAGUGGUGACCACUGUGCGGCA
............(.(((((((((((.((.(((.((....)))))..))))))))))))).). ( -27.40, z-score =  -3.13, R)
>droYak2.chr2L 9973012 62 + 22324452
AAACAAGUUCUGGGCGCACAGUGGGGCAAGUUUAGAAGUUUAGUAGUGACCACUGUGCGGCA
............(.((((((((((..((...((((....))))...)).)))))))))).). ( -23.00, z-score =  -2.84, R)
>droSec1.super_16 1688671 59 + 1878335
AAACAAGUUCUGGGCGCACAGUGGGGCAAGCUUAGAACU---GUAGUGACCACUGUGCGGCA
............(.((((((((((..((.((........---))..)).)))))))))).). ( -23.20, z-score =  -2.07, R)
>droSim1.chr2L 13321949 59 + 22036055
AAACAAGUUCUGGGCGCACAGUGGGGCAAGCUUAGAACU---GUAGUGACCACUGUGCGGCA
............(.((((((((((..((.((........---))..)).)))))))))).). ( -23.20, z-score =  -2.07, R)
>consensus
AAACAAGUUCUGGGCGCACAGUGGGGCAAGCUUAGAACU___GUAGUGACCACUGUGCGGCA
............(.((((((((((.........................)))))))))).). (-18.76 = -18.96 +   0.20)

alignment

secondary structure

dotplot

Window 7

Location	13,548,801 – 13,548,860
Length	59
Sequences	6
Columns	62
Reading direction	reverse
Mean pairwise identity	86.40
Shannon entropy	0.26050
G+C content	0.52814
Mean single sequence MFE	-17.98
Consensus MFE	-15.02
Energy contribution	-15.21
Covariance contribution	0.19
Combinations/Pair	1.10
Mean z-score	-1.94
Structure conservation index	0.83
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.41
SVM RNA-class probability	0.936641
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 13548801 59 - 23011544
UGCCGCACAGUGGUCACUAC---AGUUCUAAGCUUGCCCCACUGUGCGCCCAGAACUUGUUU
...((((((((((.((....---(((.....)))))..)))))))))).............. ( -17.50, z-score =  -1.61, R)
>dp4.Unknown_group_668 8459 53 + 12025
UGCUGCACAGUGGGCA-------AACCCUAA-UGUGCCCCACUGUA-GGCUAGAACUUGUUU
.(((..((((((((..-------.((.....-.))..)))))))).-)))............ ( -17.60, z-score =  -1.45, R)
>droEre2.scaffold_4929 14738399 62 + 26641161
UGCCGCACAGUGGUCACCACUAGACUUCUAAGCUUGCACCACUGUGCGCCCAGAACUUGUUU
...(((((((((((((....(((....)))....)).))))))))))).............. ( -21.70, z-score =  -2.99, R)
>droYak2.chr2L 9973012 62 - 22324452
UGCCGCACAGUGGUCACUACUAAACUUCUAAACUUGCCCCACUGUGCGCCCAGAACUUGUUU
...((((((((((.........................)))))))))).............. ( -16.11, z-score =  -2.38, R)
>droSec1.super_16 1688671 59 - 1878335
UGCCGCACAGUGGUCACUAC---AGUUCUAAGCUUGCCCCACUGUGCGCCCAGAACUUGUUU
...((((((((((.((....---(((.....)))))..)))))))))).............. ( -17.50, z-score =  -1.61, R)
>droSim1.chr2L 13321949 59 - 22036055
UGCCGCACAGUGGUCACUAC---AGUUCUAAGCUUGCCCCACUGUGCGCCCAGAACUUGUUU
...((((((((((.((....---(((.....)))))..)))))))))).............. ( -17.50, z-score =  -1.61, R)
>consensus
UGCCGCACAGUGGUCACUAC___AGUUCUAAGCUUGCCCCACUGUGCGCCCAGAACUUGUUU
...((((((((((.........................)))))))))).............. (-15.02 = -15.21 +   0.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:38:15 2011