Locus 5311

Sequence ID dm3.chr2R
Location 19,384,300 – 19,384,538
Length 238
Max. P 0.869000
window7280 window7281

overview

Window 0

Location 19,384,300 – 19,384,425
Length 125
Sequences 6
Columns 140
Reading direction forward
Mean pairwise identity 70.04
Shannon entropy 0.56259
G+C content 0.50410
Mean single sequence MFE -41.03
Consensus MFE -16.52
Energy contribution -18.58
Covariance contribution 2.06
Combinations/Pair 1.29
Mean z-score -1.58
Structure conservation index 0.40
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.29
SVM RNA-class probability 0.628705
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 19384300 125 + 21146708
CUCCGACUGUAUCUCGCACGGAUACAUC------GGUUAAAUCCGCUCUUGUGGGCACCAGUAAGUAUGGACCUG--------CUGGCAUGUAGGAAUCACCGUUGAG-GACCCUCAGCUCAAAGGCAAUGUCAGUAAAU
..((((.(((((((.....)))))))))------)).....((((..(((((((...))).))))..))))..((--------(((((((((.((.....))((((((-....))))))......)).)))))))))... ( -40.90, z-score =  -1.79, R)
>droSim1.chr2R 17972895 125 + 19596830
CUCCGACUGUAUCUCGCACGGAUACAUC------GGUUAAAUCCGCUCUUGAGGCCACCAGUAAGUGUGGACCUG--------CUGGCAUGUAGGAAUCACCGUUGAG-GACCCUCAGCUCAAAGGCAAUGUCAGUAAAU
..((((.(((((((.....)))))))))------)).....(((((.((((..(....)..)))).)))))..((--------(((((((((.((.....))((((((-....))))))......)).)))))))))... ( -42.60, z-score =  -2.20, R)
>droSec1.super_9 2673181 125 + 3197100
CUCCGACUGUAUCUCGCACGGAUACAUC------GGUUAAAUCCGCUCUUGAGGCCACCAGUAAGUGUGGACCUG--------CUGGCAUGUAGGAAUCACCGUUGAG-GACCCUCAGCUCAAAGGCAAUGUCAGUAAAU
..((((.(((((((.....)))))))))------)).....(((((.((((..(....)..)))).)))))..((--------(((((((((.((.....))((((((-....))))))......)).)))))))))... ( -42.60, z-score =  -2.20, R)
>droYak2.chr2R 19352276 125 + 21139217
CUCCGGCAGUAUCUCGUACGGAUACAUC------GGUUAAAUCCGCUCUUGAGGCGACCAUCAAGUGUGGACCUG--------CUGGCAUGUGGGAAACACCGUCGAG-GGCCCUCAGCUCAAAGGAUAUGCCAGUAAAU
..((((..((((((.....)))))).))------)).....(((((.(((((((...)).))))).)))))..((--------(((((((((((......))((.(((-....))).)).......)))))))))))... ( -45.30, z-score =  -1.99, R)
>droEre2.scaffold_4845 20750216 139 + 22589142
CGCCGACAGCAUCUUGCACGGAUACAUCCGCUCCGAUUAAAUCCGCUCUUGAGGCCACCAUUAAGUGUGGACCUGUGGAGCUGCUGGCAUGUGGGAAGCAGCACUGAG-GGUCCUCAGCUCAAAGGAUAUGCCAGUAAAU
..(((...((.....)).)))........((((((......(((((.(((((((...)).))))).)))))....))))))(((((((((((.(....)....(((((-....)))))........)))))))))))... ( -47.60, z-score =  -0.68, R)
>droAna3.scaffold_13266 8023142 114 + 19884421
-------------------------UUCAGGAAACGAAGCACCUCCUCCUUGAGCAUCAAUUAAAUUUAUAAUCAUUGCUGAGAUUAAAUG-GAGAGCUGCAUUCGAGUGCCCCUGAGCUCAAAGGUUGUUUCAGCCAAU
-------------------------((((((...(((((((.(((.(((((.((((...((((......))))...)))).)).......)-))))).))).))))......))))))......(((((...)))))... ( -27.21, z-score =  -0.59, R)
>consensus
CUCCGACUGUAUCUCGCACGGAUACAUC______GGUUAAAUCCGCUCUUGAGGCCACCAGUAAGUGUGGACCUG________CUGGCAUGUAGGAAUCACCGUUGAG_GACCCUCAGCUCAAAGGCAAUGUCAGUAAAU
........((((((.....))))))................(((((.(((((........))))).)))))............(((((((...((.....))((((((.....)))))).........)))))))..... (-16.52 = -18.58 +   2.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 19,384,425 – 19,384,538
Length 113
Sequences 5
Columns 116
Reading direction forward
Mean pairwise identity 92.99
Shannon entropy 0.12061
G+C content 0.49297
Mean single sequence MFE -38.72
Consensus MFE -31.30
Energy contribution -31.66
Covariance contribution 0.36
Combinations/Pair 1.09
Mean z-score -2.30
Structure conservation index 0.81
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.99
SVM RNA-class probability 0.869000
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 19384425 113 + 21146708
GAGAGUUUAACAGCAGGGAUGAAGAGGCAAGUAGAGUGCCAAUUACUGCUUCACUUACCUUUGAGAGUCCCAGCCAGUUGGCCCCGGAUAUAAGUCCAGC---AGUGACUCACUGA
..(((((..((.((.(((((..(((((.((((..((((........))))..)))).)))))....))))).(((....)))...((((....)))).))---.)))))))..... ( -35.80, z-score =  -2.02, R)
>droSim1.chr2R 17973020 113 + 19596830
GAGAGUUUAACAGCAGGGAUGAAGAGGCAAGUAGAGUGCCAAUUACUGCUUCACUUACCUUUGAGAGUCCCAGCCAGUUGGCCCCGGAUUUAAGUCCUGC---AGUGACUCACUGA
..(((((..((.((((((....(((((.((((..((((........))))..)))).)))))..((((((..(((....)))...))))))...))))))---.)))))))..... ( -36.40, z-score =  -1.83, R)
>droSec1.super_9 2673306 113 + 3197100
GAGAGUUUAACAGCAGGGAUGAAGAGGCAAGUAGAGUGCCAAUUACUGCUUCACUUACCUUUGAGAGUCCCAGCCAGUUGGCCCCGGAUUUAAGUCCUGC---AGUGACUCACUGA
..(((((..((.((((((....(((((.((((..((((........))))..)))).)))))..((((((..(((....)))...))))))...))))))---.)))))))..... ( -36.40, z-score =  -1.83, R)
>droYak2.chr2R 19352401 116 + 21139217
GAGAGUUUAACUGCAGGGAUGAAGAGGAAAGUAGAGUGCCAAUUACUGCUUCACUUACCUUUGAGUGUCCCUGCCAGUUGGCUCCGGAUUUAAGUCCUCCUGGAGUGACUCGCUGA
..(((((((((((((((((((.(((((.((((..((((........))))..)))).)))))...)))))))).))))))(((((((((....))))....))))))))))..... ( -45.60, z-score =  -3.67, R)
>droEre2.scaffold_4845 20750355 113 + 22589142
GAGAGUUUAACUGCGGGGAAGAAGAGGAAAGUGGAGUGCCAAUUACUGUUUCACUUACCUUUGAGAGUUCCUGCCAGUUGGCCCAGGAUUUAAGUCCUGC---AGUGACUCGCUGA
..(((((..(((((((((....(((((.(((((((..(........)..))))))).)))))......(((((((....)))..))))......))))))---))))))))..... ( -39.40, z-score =  -2.15, R)
>consensus
GAGAGUUUAACAGCAGGGAUGAAGAGGCAAGUAGAGUGCCAAUUACUGCUUCACUUACCUUUGAGAGUCCCAGCCAGUUGGCCCCGGAUUUAAGUCCUGC___AGUGACUCACUGA
..(((((.....((((((....(((((.((((.(((.((........))))))))).)))))..((((((..(((....)))...))))))...))))))......)))))..... (-31.30 = -31.66 +   0.36)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:45:49 2011