Locus 4200

Sequence ID dm3.chr2R
Location 11,218,249 – 11,218,386
Length 137
Max. P 0.972725
window5758 window5759

overview

Window 8

Location 11,218,249 – 11,218,386
Length 137
Sequences 6
Columns 139
Reading direction forward
Mean pairwise identity 71.10
Shannon entropy 0.56357
G+C content 0.55640
Mean single sequence MFE -50.02
Consensus MFE -30.52
Energy contribution -31.53
Covariance contribution 1.01
Combinations/Pair 1.46
Mean z-score -1.48
Structure conservation index 0.61
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.87
SVM RNA-class probability 0.972725
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 11218249 137 + 21146708
CCCGCCGUCGCUCAGCUUUUUUGAGUCAUGAUGGCGACCGGGCGUUCUCUGCUCUUUCGAGUGCCUU--GGUAUGUGUGCUUGUGUGUGUGCGCAGAGAGCGCAGAGCCGGGUGUUUAUUGGAGAUUGCGAUUGCGGCU
.((((.(((((....((((..((((.(((..((((......(((((((((((........((((...--.))))(((..(......)..))))))))))))))...)))).)))))))..))))...))))).)))).. ( -56.70, z-score =  -1.99, R)
>droSec1.super_1 8710900 136 + 14215200
CCCGUCGUCGCUCAGCUUUUUUGAGUCAUGAUGGCGACCGGGCGUUCUCUGCUCUUUCGAGUGCCU---GGUGUGUGUGCUUGUGUGUGUGCGCAGAGAGCGCAGAGCCGGGUGUUUAUUGGAGAUUGCGAUUGCGGCU
.((((.(((((....((((..((((.(((..((((.(((((((((((...........))))))))---))).(.(((((((.((((....))))..))))))).))))).)))))))..))))...))))).)))).. ( -55.40, z-score =  -1.72, R)
>droEre2.scaffold_4845 7942525 136 - 22589142
---GCCGGCGCUCAGCUUUUUUGAGUCAUGAUGGCUACCGAACGUUCUCUGCUCUUUCGAGUGCCUGUGUGUGUGUGCGCUUGUGUGUGUGCGCAGAGAGCGCAGAGCCGGGUGUUUAUUGGAGAUUGCGAUUGUGGCU
---((((.(((....((((..((((.(((..(((((......((((((((((((....))))........(((((..(((....)))..)))))))))))))...))))).)))))))..))))...)))....)))). ( -49.10, z-score =  -0.27, R)
>droAna3.scaffold_13266 7635357 122 + 19884421
UCUACCUUUGC-CACCGUUCUUG--UCAUGAUGGCGGCCGAGCGCUCUCUGCUCUUUUGAGUUU--------------GCCUGUGUGUGUGCGCAGAGAGCGCAGAGCCGGGUGUUUAUUGGAGAUUCCGAUUGUGGCU
.........((-(((((..(..(--((.....)))((((..(((((((((((((....))....--------------(((.......).))))))))))))).).))))..))...(((((.....))))).))))). ( -45.80, z-score =  -1.59, R)
>droSim1.chr2R 9955029 136 + 19596830
CCCGCCGUCGCUCAGCUUUUUUGAGUCAUGAUGGCGACCGGGCGUUCUCUGCUCUUUCGAGUGCCU---GGUGUGUGUGCUUGUGUGUGUGCGCAGAGAGCGCAGAGCCGGGUGUUUAUUGGAGAUUGCGAUUGCGGCU
.((((.(((((....((((..((((.(((..((((.(((((((((((...........))))))))---))).(.(((((((.((((....))))..))))))).))))).)))))))..))))...))))).)))).. ( -56.90, z-score =  -1.87, R)
>anoGam1.chr2R 16557442 107 + 62725911
CCCGCGAUGGAAGAAAUCGCUUCCAUUGCAAUUGCAACCGGA-GCCAUCAUUAUCAUCGAAUGCCAU--UCCAUGUGUGUGUGUGUGCGUGGGAGUAGUGUGUAGGGCUG-----------------------------
(((((((((((((......)))))))))).(((((..(((..-((((((((...(((.((((...))--)).)))...))).))).)).)))..))))).....)))...----------------------------- ( -36.20, z-score =  -1.43, R)
>consensus
CCCGCCGUCGCUCAGCUUUUUUGAGUCAUGAUGGCGACCGGGCGUUCUCUGCUCUUUCGAGUGCCU___GGUGUGUGUGCUUGUGUGUGUGCGCAGAGAGCGCAGAGCCGGGUGUUUAUUGGAGAUUGCGAUUGCGGCU
..(((((((((((((.....))))))...))))))).(((((((((((((((.(...((((((((.........).))))))).......).)))))))))))....))))............................ (-30.52 = -31.53 +   1.01)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 11,218,249 – 11,218,386
Length 137
Sequences 6
Columns 139
Reading direction reverse
Mean pairwise identity 71.10
Shannon entropy 0.56357
G+C content 0.55640
Mean single sequence MFE -37.43
Consensus MFE -20.20
Energy contribution -21.50
Covariance contribution 1.30
Combinations/Pair 1.35
Mean z-score -1.71
Structure conservation index 0.54
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.85
SVM RNA-class probability 0.971142
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 11218249 137 - 21146708
AGCCGCAAUCGCAAUCUCCAAUAAACACCCGGCUCUGCGCUCUCUGCGCACACACACAAGCACACAUACC--AAGGCACUCGAAAGAGCAGAGAACGCCCGGUCGCCAUCAUGACUCAAAAAAGCUGAGCGACGGCGGG
..((((..((((.................(((((..(((.(((((((((..........)).........--.......((....))))))))).)))..)))))...(((.(.((......))))))))))..)))). ( -41.60, z-score =  -2.10, R)
>droSec1.super_1 8710900 136 - 14215200
AGCCGCAAUCGCAAUCUCCAAUAAACACCCGGCUCUGCGCUCUCUGCGCACACACACAAGCACACACACC---AGGCACUCGAAAGAGCAGAGAACGCCCGGUCGCCAUCAUGACUCAAAAAAGCUGAGCGACGACGGG
..(((...((((.................(((((..(((.(((((((............((.(.......---.)))..((....))))))))).)))..)))))...(((.(.((......))))))))))...))). ( -36.60, z-score =  -1.15, R)
>droEre2.scaffold_4845 7942525 136 + 22589142
AGCCACAAUCGCAAUCUCCAAUAAACACCCGGCUCUGCGCUCUCUGCGCACACACACAAGCGCACACACACACAGGCACUCGAAAGAGCAGAGAACGUUCGGUAGCCAUCAUGACUCAAAAAAGCUGAGCGCCGGC---
.(((..........................(((((((((.(((((((((.(........).))................((....))))))))).)))..)).)))).....(.((((.......)))))...)))--- ( -34.20, z-score =  -0.64, R)
>droAna3.scaffold_13266 7635357 122 - 19884421
AGCCACAAUCGGAAUCUCCAAUAAACACCCGGCUCUGCGCUCUCUGCGCACACACACAGGC--------------AAACUCAAAAGAGCAGAGAGCGCUCGGCCGCCAUCAUGA--CAAGAACGGUG-GCAAAGGUAGA
.(((((..((((.....))..........(((((..(((((((((((((.(.......)))--------------....((....)))))))))))))..))))).........--...))...)))-))......... ( -45.50, z-score =  -3.98, R)
>droSim1.chr2R 9955029 136 - 19596830
AGCCGCAAUCGCAAUCUCCAAUAAACACCCGGCUCUGCGCUCUCUGCGCACACACACAAGCACACACACC---AGGCACUCGAAAGAGCAGAGAACGCCCGGUCGCCAUCAUGACUCAAAAAAGCUGAGCGACGGCGGG
..((((..((((.................(((((..(((.(((((((............((.(.......---.)))..((....))))))))).)))..)))))...(((.(.((......))))))))))..)))). ( -41.90, z-score =  -2.10, R)
>anoGam1.chr2R 16557442 107 - 62725911
-----------------------------CAGCCCUACACACUACUCCCACGCACACACACACACAUGGA--AUGGCAUUCGAUGAUAAUGAUGGC-UCCGGUUGCAAUUGCAAUGGAAGCGAUUUCUUCCAUCGCGGG
-----------------------------.................(((..((.((..((......))..--.))))...(((((.....(((.((-(.(.(((((....))))).).))).))).....))))).))) ( -24.80, z-score =  -0.27, R)
>consensus
AGCCGCAAUCGCAAUCUCCAAUAAACACCCGGCUCUGCGCUCUCUGCGCACACACACAAGCACACACACC___AGGCACUCGAAAGAGCAGAGAACGCCCGGUCGCCAUCAUGACUCAAAAAAGCUGAGCGACGGCGGG
.(((.........................(((((..(((.(((((((((..........))..................((....))))))))).)))..))))).........((((.......))))....)))... (-20.20 = -21.50 +   1.30)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:24:40 2011