Locus 4877

Sequence ID dm3.chr2R
Location 16,123,918 – 16,124,054
Length 136
Max. P 0.976847
window6712 window6713 window6714 window6715

overview

Window 2

Location 16,123,918 – 16,124,015
Length 97
Sequences 6
Columns 97
Reading direction forward
Mean pairwise identity 92.85
Shannon entropy 0.14023
G+C content 0.61725
Mean single sequence MFE -42.10
Consensus MFE -39.79
Energy contribution -39.35
Covariance contribution -0.44
Combinations/Pair 1.21
Mean z-score -1.36
Structure conservation index 0.95
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.84
SVM RNA-class probability 0.832898
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr2R 16123918 97 + 21146708
UCUUGGUGGAGAGCAAACUGUUGCUGCUGAUUCUAGUGGUGCUGCCACUGGGCCUGAGCCACUGGGUGGCUGUGGUGGCGCUGGUGGCGGUGGCAGU
((((....))))....(((((..(((((....(((((((.....)))))))(((...(((((((.(....).)))))))...))))))))..))))) ( -43.10, z-score =  -1.50, R)
>droAna3.scaffold_13266 10665352 95 - 19884421
--UUUCGGAAGAGCAAACUGUUGCUGUUGCUCUUGGUGGGGCUGCCACUGGGCCUGAGCCACUGGCUGGUGGCGGUGGUGGUGUUGGCGGUGGCUGU
--.(((....)))...((.((..((((((((((....))))).((((((..(((...((((((....)))))))))))))))...)))))..)).)) ( -38.20, z-score =  -0.63, R)
>droEre2.scaffold_4845 10274274 97 + 22589142
UCUUGGUGGAGAGCAAACUGUUGCUGCUGAUUCUAGUGGUGCUGCCACUGGGCCUGAGCCACUGGGUGGCUGUGGUGGCGCUGGUGGCGGUGGCAGU
((((....))))....(((((..(((((....(((((((.....)))))))(((...(((((((.(....).)))))))...))))))))..))))) ( -43.10, z-score =  -1.50, R)
>droYak2.chr2R 8059458 97 - 21139217
UCUUGGUGGAGAGCAAACUGUUGCUGCUGAUUAUAGUGGUGCUGCCACUGGGCCUGAGCCACUGGGUGGCUGUGGUGGCGCUGGUGGCGGUGGCAGU
..(..((((..((((.(((((..(....)...)))))..)))).))))..)(((...(((((..(((.((....)).)).)..)))))...)))... ( -42.00, z-score =  -1.51, R)
>droSec1.super_1 13690168 97 + 14215200
UCUUGGUGGAGAGCAAACUGUUGCUGCUGAUUCUAGUGGUGCUGCCACUGGGCCUGAGCCACUGGGUGGCUGUGGUGGCGCUGGUGGCGGUGGCAGU
((((....))))....(((((..(((((....(((((((.....)))))))(((...(((((((.(....).)))))))...))))))))..))))) ( -43.10, z-score =  -1.50, R)
>droSim1.chr2R 14782288 97 + 19596830
UCUUGGUGGAGAGCAAACUGUUGCUGCUGAUUCUAGUGGUGCUGCCACUGGGCCUGAGCCACUGGGUGGCUGUGGUGGCGCUGGUGGCGGUGGCAGU
((((....))))....(((((..(((((....(((((((.....)))))))(((...(((((((.(....).)))))))...))))))))..))))) ( -43.10, z-score =  -1.50, R)
>consensus
UCUUGGUGGAGAGCAAACUGUUGCUGCUGAUUCUAGUGGUGCUGCCACUGGGCCUGAGCCACUGGGUGGCUGUGGUGGCGCUGGUGGCGGUGGCAGU
................(((((..(((((....(((((((.....)))))))(((...(((((((.(....).)))))))...))))))))..))))) (-39.79 = -39.35 +  -0.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 16,123,918 – 16,124,015
Length 97
Sequences 6
Columns 97
Reading direction reverse
Mean pairwise identity 92.85
Shannon entropy 0.14023
G+C content 0.61725
Mean single sequence MFE -27.57
Consensus MFE -22.90
Energy contribution -23.40
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -1.59
Structure conservation index 0.83
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.04
SVM RNA-class probability 0.515634
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr2R 16123918 97 - 21146708
ACUGCCACCGCCACCAGCGCCACCACAGCCACCCAGUGGCUCAGGCCCAGUGGCAGCACCACUAGAAUCAGCAGCAACAGUUUGCUCUCCACCAAGA
.(((((((.((.....))(((.....((((((...))))))..)))...))))))).............((.(((((....)))))))......... ( -27.80, z-score =  -1.39, R)
>droAna3.scaffold_13266 10665352 95 + 19884421
ACAGCCACCGCCAACACCACCACCGCCACCAGCCAGUGGCUCAGGCCCAGUGGCAGCCCCACCAAGAGCAACAGCAACAGUUUGCUCUUCCGAAA--
...(((((.(((....((((....((.....))..))))....)))...))))).........((((((((..((....))))))))))......-- ( -26.40, z-score =  -2.10, R)
>droEre2.scaffold_4845 10274274 97 - 22589142
ACUGCCACCGCCACCAGCGCCACCACAGCCACCCAGUGGCUCAGGCCCAGUGGCAGCACCACUAGAAUCAGCAGCAACAGUUUGCUCUCCACCAAGA
.(((((((.((.....))(((.....((((((...))))))..)))...))))))).............((.(((((....)))))))......... ( -27.80, z-score =  -1.39, R)
>droYak2.chr2R 8059458 97 + 21139217
ACUGCCACCGCCACCAGCGCCACCACAGCCACCCAGUGGCUCAGGCCCAGUGGCAGCACCACUAUAAUCAGCAGCAACAGUUUGCUCUCCACCAAGA
.(((((((.((.....))(((.....((((((...))))))..)))...))))))).............((.(((((....)))))))......... ( -27.80, z-score =  -1.87, R)
>droSec1.super_1 13690168 97 - 14215200
ACUGCCACCGCCACCAGCGCCACCACAGCCACCCAGUGGCUCAGGCCCAGUGGCAGCACCACUAGAAUCAGCAGCAACAGUUUGCUCUCCACCAAGA
.(((((((.((.....))(((.....((((((...))))))..)))...))))))).............((.(((((....)))))))......... ( -27.80, z-score =  -1.39, R)
>droSim1.chr2R 14782288 97 - 19596830
ACUGCCACCGCCACCAGCGCCACCACAGCCACCCAGUGGCUCAGGCCCAGUGGCAGCACCACUAGAAUCAGCAGCAACAGUUUGCUCUCCACCAAGA
.(((((((.((.....))(((.....((((((...))))))..)))...))))))).............((.(((((....)))))))......... ( -27.80, z-score =  -1.39, R)
>consensus
ACUGCCACCGCCACCAGCGCCACCACAGCCACCCAGUGGCUCAGGCCCAGUGGCAGCACCACUAGAAUCAGCAGCAACAGUUUGCUCUCCACCAAGA
.(((((((.(((....(.(((((............))))).).)))...)))))))................(((((....)))))........... (-22.90 = -23.40 +   0.50)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 16,123,941 – 16,124,054
Length 113
Sequences 5
Columns 113
Reading direction forward
Mean pairwise identity 99.29
Shannon entropy 0.01278
G+C content 0.60708
Mean single sequence MFE -48.28
Consensus MFE -46.44
Energy contribution -46.44
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.55
Structure conservation index 0.96
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.72
SVM RNA-class probability 0.795965
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 16123941 113 + 21146708
CUGCUGAUUCUAGUGGUGCUGCCACUGGGCCUGAGCCACUGGGUGGCUGUGGUGGCGCUGGUGGCGGUGGCAGUUUUUGUUUGGCGGGCGGCGGUGCCAAAUGAUGAUCAUGA
....((((((...(((..(((((.((..(((...(((((..(((.((....)).)).)..)))))...))).(((.......))).)).)))))..)))...))..))))... ( -46.80, z-score =  -0.95, R)
>droEre2.scaffold_4845 10274297 113 + 22589142
CUGCUGAUUCUAGUGGUGCUGCCACUGGGCCUGAGCCACUGGGUGGCUGUGGUGGCGCUGGUGGCGGUGGCAGUUUUUGUUUGGCGGGCGGCGGUGCCAAAUGAUGAUCAUGA
....((((((...(((..(((((.((..(((...(((((..(((.((....)).)).)..)))))...))).(((.......))).)).)))))..)))...))..))))... ( -46.80, z-score =  -0.95, R)
>droYak2.chr2R 8059481 113 - 21139217
CUGCUGAUUAUAGUGGUGCUGCCACUGGGCCUGAGCCACUGGGUGGCUGUGGUGGCGCUGGUGGCGGUGGCAGUUUUUGUUUGGCGGGUGGCGGUGCCAAAUGAUGAUCAUGA
....(((((((..(((..((((((((..(((...(((((..(((.((....)).)).)..)))))...))).(((.......))).))))))))..)))....)))))))... ( -54.20, z-score =  -3.94, R)
>droSec1.super_1 13690191 113 + 14215200
CUGCUGAUUCUAGUGGUGCUGCCACUGGGCCUGAGCCACUGGGUGGCUGUGGUGGCGCUGGUGGCGGUGGCAGUUUUUGUUUGGCGGGCGGCGGUGCCAAAUGAUGAUCAUGA
....((((((...(((..(((((.((..(((...(((((..(((.((....)).)).)..)))))...))).(((.......))).)).)))))..)))...))..))))... ( -46.80, z-score =  -0.95, R)
>droSim1.chr2R 14782311 113 + 19596830
CUGCUGAUUCUAGUGGUGCUGCCACUGGGCCUGAGCCACUGGGUGGCUGUGGUGGCGCUGGUGGCGGUGGCAGUUUUUGUUUGGCGGGCGGCGGUGCCAAAUGAUGAUCAUGA
....((((((...(((..(((((.((..(((...(((((..(((.((....)).)).)..)))))...))).(((.......))).)).)))))..)))...))..))))... ( -46.80, z-score =  -0.95, R)
>consensus
CUGCUGAUUCUAGUGGUGCUGCCACUGGGCCUGAGCCACUGGGUGGCUGUGGUGGCGCUGGUGGCGGUGGCAGUUUUUGUUUGGCGGGCGGCGGUGCCAAAUGAUGAUCAUGA
....(((((....(((..(((((.((..(((...(((((..(((.((....)).)).)..)))))...))).(((.......))).)).)))))..)))......)))))... (-46.44 = -46.44 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 16,123,941 – 16,124,054
Length 113
Sequences 5
Columns 113
Reading direction reverse
Mean pairwise identity 99.29
Shannon entropy 0.01278
G+C content 0.60708
Mean single sequence MFE -31.98
Consensus MFE -31.50
Energy contribution -31.50
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.28
Structure conservation index 0.98
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.96
SVM RNA-class probability 0.976847
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 16123941 113 - 21146708
UCAUGAUCAUCAUUUGGCACCGCCGCCCGCCAAACAAAAACUGCCACCGCCACCAGCGCCACCACAGCCACCCAGUGGCUCAGGCCCAGUGGCAGCACCACUAGAAUCAGCAG
...(((((....((((((..........))))))......(((((((.((.....))(((.....((((((...))))))..)))...)))))))........).)))).... ( -32.10, z-score =  -2.16, R)
>droEre2.scaffold_4845 10274297 113 - 22589142
UCAUGAUCAUCAUUUGGCACCGCCGCCCGCCAAACAAAAACUGCCACCGCCACCAGCGCCACCACAGCCACCCAGUGGCUCAGGCCCAGUGGCAGCACCACUAGAAUCAGCAG
...(((((....((((((..........))))))......(((((((.((.....))(((.....((((((...))))))..)))...)))))))........).)))).... ( -32.10, z-score =  -2.16, R)
>droYak2.chr2R 8059481 113 + 21139217
UCAUGAUCAUCAUUUGGCACCGCCACCCGCCAAACAAAAACUGCCACCGCCACCAGCGCCACCACAGCCACCCAGUGGCUCAGGCCCAGUGGCAGCACCACUAUAAUCAGCAG
...((((.....((((((..........))))))......(((((((.((.....))(((.....((((((...))))))..)))...)))))))..........)))).... ( -31.50, z-score =  -2.79, R)
>droSec1.super_1 13690191 113 - 14215200
UCAUGAUCAUCAUUUGGCACCGCCGCCCGCCAAACAAAAACUGCCACCGCCACCAGCGCCACCACAGCCACCCAGUGGCUCAGGCCCAGUGGCAGCACCACUAGAAUCAGCAG
...(((((....((((((..........))))))......(((((((.((.....))(((.....((((((...))))))..)))...)))))))........).)))).... ( -32.10, z-score =  -2.16, R)
>droSim1.chr2R 14782311 113 - 19596830
UCAUGAUCAUCAUUUGGCACCGCCGCCCGCCAAACAAAAACUGCCACCGCCACCAGCGCCACCACAGCCACCCAGUGGCUCAGGCCCAGUGGCAGCACCACUAGAAUCAGCAG
...(((((....((((((..........))))))......(((((((.((.....))(((.....((((((...))))))..)))...)))))))........).)))).... ( -32.10, z-score =  -2.16, R)
>consensus
UCAUGAUCAUCAUUUGGCACCGCCGCCCGCCAAACAAAAACUGCCACCGCCACCAGCGCCACCACAGCCACCCAGUGGCUCAGGCCCAGUGGCAGCACCACUAGAAUCAGCAG
...((((.....((((((..........))))))......(((((((.((.....))(((.....((((((...))))))..)))...)))))))..........)))).... (-31.50 = -31.50 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:37:52 2011