Locus 9526

Sequence ID dm3.chr3R
Location 7,193,113 – 7,193,264
Length 151
Max. P 0.992486
window13065 window13066

overview

Window 5

Location 7,193,113 – 7,193,229
Length 116
Sequences 6
Columns 117
Reading direction reverse
Mean pairwise identity 88.70
Shannon entropy 0.22016
G+C content 0.52156
Mean single sequence MFE -37.82
Consensus MFE -30.29
Energy contribution -31.93
Covariance contribution 1.64
Combinations/Pair 1.10
Mean z-score -3.01
Structure conservation index 0.80
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.54
SVM RNA-class probability 0.992486
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 7193113 116 - 27905053
CGGAUAUGGACACGAGCACGGCGAGAUAC-AGAUACGGAUACGUAUACUAGUAUUCCGACCAGGCACGCAAUGGAAAUGGCCAGAAAAUGGCCAUAUGUGGCCAAGUCGGCUCCCAU
.....((((....((((.(((((..((((-(((((((....))))).)).))))..).....(((.((((......(((((((.....))))))).)))))))..)))))))))))) ( -42.90, z-score =  -3.80, R)
>droSim1.chr3R 13356199 116 + 27517382
CGGAUAUAGACACGAGCACGGCGAGAUAC-AGAUACGGAUACGAACACUAGUAUUCCGACCAGGCACGCAAUGGAAAUGGCCAGAAAAUGGCCAUAUGUGGCCAAGUCGGCUCCCAC
.............((((.((((.......-.....(((((((........))).))))....(((.((((......(((((((.....))))))).)))))))..)))))))).... ( -38.10, z-score =  -3.45, R)
>droSec1.super_0 6358776 116 + 21120651
CGGAUAUAGACACGAGCACGGCGAGAUAC-AUAUACGGAUACGUACACUAGUAUUCCGACCAGGCACGCAAUGGAAAUGGCCAGAAAAUGGCCAUAUGUGGCCAAGUCGGCUCCCGC
(((..........((((.((((.......-.....(((((((........))).))))....(((.((((......(((((((.....))))))).)))))))..))))))))))). ( -38.20, z-score =  -2.56, R)
>droYak2.chr3R 11235072 114 - 28832112
CGGAUAUAGACACGAGCACGACGAGAUAC-AGAUACGGAUACG--UACUAGUAUUCCGACCAGGCACGCAAUGGAAAUGGCCAGAAAAUGGCCAUAUGUGGCCAAGUCGGCUCCCAC
.............((((.(((((..((((-((.((((....))--)))).))))..).....(((.((((......(((((((.....))))))).)))))))..)))))))).... ( -40.70, z-score =  -4.41, R)
>droEre2.scaffold_4770 3326035 115 + 17746568
CGGAUAUAGACACGAGCACGGCGAGAUACGAGCUACGGAUACG--UACUAGUGUUCCGACCAGGCACGCAAUGGAAAUGGCCAGAAAAUGGCCAUAUGUGGCCAAGUCGGCUCCCAC
.............((((.(((((..((((.((.((((....))--)))).))))..).....(((.((((......(((((((.....))))))).)))))))..)))))))).... ( -40.70, z-score =  -2.77, R)
>droAna3.scaffold_13340 13064855 101 + 23697760
UAUAUAUAGACUAGAAUAC----AGAUAC-AGAUACGGAUACGGAUA--------CGGGCCAGGCACGCAAUGG---CAGCCAGAAAAUGGCCAUAUGUGGCCAAGUCGGCUCCCAC
...................----......-.....((....))....--------.(((((.(((..((....)---).))).((...((((((....))))))..))))))).... ( -26.30, z-score =  -1.09, R)
>consensus
CGGAUAUAGACACGAGCACGGCGAGAUAC_AGAUACGGAUACG_AUACUAGUAUUCCGACCAGGCACGCAAUGGAAAUGGCCAGAAAAUGGCCAUAUGUGGCCAAGUCGGCUCCCAC
.............((((.((((.............(((((((........))).))))....(((.((((......(((((((.....))))))).)))))))..)))))))).... (-30.29 = -31.93 +   1.64)

alignment

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secondary structure

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dotplot

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Window 6

Location 7,193,152 – 7,193,264
Length 112
Sequences 6
Columns 118
Reading direction reverse
Mean pairwise identity 80.28
Shannon entropy 0.37038
G+C content 0.49442
Mean single sequence MFE -26.90
Consensus MFE -17.01
Energy contribution -19.10
Covariance contribution 2.09
Combinations/Pair 1.10
Mean z-score -1.91
Structure conservation index 0.63
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.98
SVM RNA-class probability 0.867721
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 7193152 112 - 27905053
GCACACACUG-----CCGUACAUUGCAGCCUAGGAUACUACGGAUAUGGACACGAGCACGGCGAGAUAC-AGAUACGGAUACGUAUACUAGUAUUCCGACCAGGCACGCAAUGGAAAU
(((.....))-----)....((((((..(((((....))).))............((..((((..((((-(((((((....))))).)).))))..)).))..))..))))))..... ( -31.20, z-score =  -2.65, R)
>droSim1.chr3R 13356238 112 + 27517382
GCACACACUG-----CCGUACAUUGCAGCCUGGGAUACUACGGAUAUAGACACGAGCACGGCGAGAUAC-AGAUACGGAUACGAACACUAGUAUUCCGACCAGGCACGCAAUGGAAAU
(((.....))-----)....((((((.((((((....(....)..........................-.....(((((((........))).)))).))))))..))))))..... ( -28.90, z-score =  -2.55, R)
>droSec1.super_0 6358815 112 + 21120651
GCACAUACUG-----UCGUACAUUGCAGCCUGGGAUACUACGGAUAUAGACACGAGCACGGCGAGAUAC-AUAUACGGAUACGUACACUAGUAUUCCGACCAGGCACGCAAUGGAAAU
..........-----.....((((((.((((((....(....)...............(((...(((((-...((((....)))).....)))))))).))))))..))))))..... ( -29.10, z-score =  -1.84, R)
>droYak2.chr3R 11235111 115 - 28832112
GCACACACUGCCGUACCGUACAUUGCAGCUAGGGAUACUACGGAUAUAGACACGAGCACGACGAGAUAC-AGAUACGGAUACGUA--CUAGUAUUCCGACCAGGCACGCAAUGGAAAU
(((.....))).........((((((.(((.((....(....)..................((..((((-((.((((....))))--)).))))..)).)).)))..))))))..... ( -26.40, z-score =  -1.24, R)
>droEre2.scaffold_4770 3326074 111 + 17746568
GCACACACUG-----CCGUACAUUGCAGCCUGGGAUACUACGGAUAUAGACACGAGCACGGCGAGAUACGAGCUACGGAUACGUA--CUAGUGUUCCGACCAGGCACGCAAUGGAAAU
(((.....))-----)....((((((.((((((....(....)..........((((((....((.((((..(....)...))))--)).))))))...))))))..))))))..... ( -34.80, z-score =  -2.60, R)
>droAna3.scaffold_13340 13064893 87 + 23697760
-----------------GCACA-GGCACACAAACAUAUAGCAUAUAUAUAGACUAGAAUAC--AGAUAC-AGAUACGGAUACGGA--------UACGGGCCAGGCACGCAAUGGCA--
-----------------((...-.((........(((((.....)))))............--......-......((...((..--------..))..))......))....)).-- ( -11.00, z-score =  -0.60, R)
>consensus
GCACACACUG_____CCGUACAUUGCAGCCUGGGAUACUACGGAUAUAGACACGAGCACGGCGAGAUAC_AGAUACGGAUACGUA__CUAGUAUUCCGACCAGGCACGCAAUGGAAAU
....................((((((.((((((....(....)................................(((((((........)))).))).))))))..))))))..... (-17.01 = -19.10 +   2.09)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:06:06 2011