Locus 12031

Sequence ID	dm3.chr3R
Location	25,246,617 – 25,246,719
Length	102
Max. P	0.976016

overview

Window 8

Location	25,246,617 – 25,246,719
Length	102
Sequences	5
Columns	114
Reading direction	forward
Mean pairwise identity	84.49
Shannon entropy	0.26231
G+C content	0.48471
Mean single sequence MFE	-33.86
Consensus MFE	-21.60
Energy contribution	-22.12
Covariance contribution	0.52
Combinations/Pair	1.20
Mean z-score	-2.95
Structure conservation index	0.64
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.94
SVM RNA-class probability	0.976016
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 25246617 102 + 27905053
CUCCAUUUAAAUAGAAAAGAAAGCACAGGCACGCGUAUAAAGCCAUCUGUGCAUCGAUGAGCAUGUGUGUGUG------------CGAAGGGUGUUCCCCCGGUUUAAGUCGAG
(((.((((((((..........(((((.((((((.......)).....((((........)))))))).))))------------)...(((......))).)))))))).))) ( -30.90, z-score =  -2.51, R)
>droSec1.super_4 4105695 101 + 6179234
CUCCAUUUAAAUAGAAAAGAAAGCACAGGCACGCGUAUAAAGCCAUCUGUGCAUCGAUGGGCAUGUGUGUGUG------------CGAAGGGGGUUCCCCGG-UUUAAGUCGAG
(((.((((((((..........(((((.(((((.((......(((((........))))))).))))).))))------------)...((((...)))).)-))))))).))) ( -34.40, z-score =  -2.73, R)
>droYak2.chr3R 7592699 113 - 28832112
CUCCAUUUAAAUAGAAAAGAAAGCACAGGCGCGCGUAUAAAGCCAUCUGUGCAUCGAUGAGCAUGUGUGUGUGUGUAUGUGUGUGCGAAGGGGGUUCCCCCG-UUUAAGUCGAG
(((.((((((((......(...(((((.(((((((((((..((((((........)))).))...))))))))))).)))))...)...((((....)))))-))))))).))) ( -40.60, z-score =  -4.12, R)
>droEre2.scaffold_4820 7702825 105 - 10470090
CUCCAUUUAAAUAGAAAAGAAAGCACAGGCACGCGUAUAAAGCCAUCUGUGCAUCGAUGAGCAUGUGUGUGUGUGUA--------CGAAGGGGUUUCCCCCG-UUUAAGUCGAG
(((.((((((((..........(((((.((((((((.....((((((........)))).)))))))))).))))).--------....((((....)))))-))))))).))) ( -37.00, z-score =  -4.55, R)
>droAna3.scaffold_12911 4935340 95 + 5364042
CUCCAUUUAAAUAGAAAAGAAAACACUGGCGGGCGCAUAAAGCCAUCUGUGCAUCAGUGUGUGGGUGGGUGUG----------------CGGGGUUCC---GUGUUAAGUCAAG
..................((.(((((.((....((((((...(((((((..((....))..))))))).))))----------------)).....))---)))))...))... ( -26.40, z-score =  -0.83, R)
>consensus
CUCCAUUUAAAUAGAAAAGAAAGCACAGGCACGCGUAUAAAGCCAUCUGUGCAUCGAUGAGCAUGUGUGUGUG____________CGAAGGGGGUUCCCCCG_UUUAAGUCGAG
(((.(((((((...........(((((.(((.((.(((...(((....).))....))).)).))).))))).................((((....))))..))))))).))) (-21.60 = -22.12 +   0.52)

alignment

secondary structure

dotplot

Window 9

Location	25,246,617 – 25,246,719
Length	102
Sequences	5
Columns	114
Reading direction	reverse
Mean pairwise identity	84.49
Shannon entropy	0.26231
G+C content	0.48471
Mean single sequence MFE	-23.71
Consensus MFE	-16.40
Energy contribution	-17.04
Covariance contribution	0.64
Combinations/Pair	1.13
Mean z-score	-1.79
Structure conservation index	0.69
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.17
SVM RNA-class probability	0.577743
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 25246617 102 - 27905053
CUCGACUUAAACCGGGGGAACACCCUUCG------------CACACACACAUGCUCAUCGAUGCACAGAUGGCUUUAUACGCGUGCCUGUGCUUUCUUUUCUAUUUAAAUGGAG
(((.(.(((((..((((.....))))..(------------((((..(((.....((((........))))((.......)))))..)))))...........))))).).))) ( -24.50, z-score =  -1.72, R)
>droSec1.super_4 4105695 101 - 6179234
CUCGACUUAAA-CCGGGGAACCCCCUUCG------------CACACACACAUGCCCAUCGAUGCACAGAUGGCUUUAUACGCGUGCCUGUGCUUUCUUUUCUAUUUAAAUGGAG
(((.(.(((((-..((((...))))...(------------((((....((((((((((........)))))........)))))..)))))...........))))).).))) ( -25.90, z-score =  -2.23, R)
>droYak2.chr3R 7592699 113 + 28832112
CUCGACUUAAA-CGGGGGAACCCCCUUCGCACACACAUACACACACACACAUGCUCAUCGAUGCACAGAUGGCUUUAUACGCGCGCCUGUGCUUUCUUUUCUAUUUAAAUGGAG
.((((......-.((((....))))...(((....................)))...)))).((((((.((((.......)).)).)))))).......(((((....))))). ( -25.25, z-score =  -2.12, R)
>droEre2.scaffold_4820 7702825 105 + 10470090
CUCGACUUAAA-CGGGGGAAACCCCUUCG--------UACACACACACACAUGCUCAUCGAUGCACAGAUGGCUUUAUACGCGUGCCUGUGCUUUCUUUUCUAUUUAAAUGGAG
(((.(.(((((-.((((....))))...(--------((((..(((.(....((.((((........)))))).......).)))..)))))...........))))).).))) ( -28.80, z-score =  -3.17, R)
>droAna3.scaffold_12911 4935340 95 - 5364042
CUUGACUUAACAC---GGAACCCCG----------------CACACCCACCCACACACUGAUGCACAGAUGGCUUUAUGCGCCCGCCAGUGUUUUCUUUUCUAUUUAAAUGGAG
...((...(((((---((.....((----------------((.......(((....(((.....))).))).....))))....)).))))).))...(((((....))))). ( -14.10, z-score =   0.32, R)
>consensus
CUCGACUUAAA_CGGGGGAACCCCCUUCG____________CACACACACAUGCUCAUCGAUGCACAGAUGGCUUUAUACGCGUGCCUGUGCUUUCUUUUCUAUUUAAAUGGAG
(((.(.((((...((((....))))..................................((.((((((..(((.......)).)..))))))..))........)))).).))) (-16.40 = -17.04 +   0.64)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:54:22 2011