Locus 4499

Sequence ID dm3.chr2R
Location 13,500,080 – 13,500,171
Length 91
Max. P 0.976535
window6152 window6153

overview

Window 2

Location 13,500,080 – 13,500,171
Length 91
Sequences 6
Columns 93
Reading direction forward
Mean pairwise identity 79.01
Shannon entropy 0.39544
G+C content 0.49145
Mean single sequence MFE -22.04
Consensus MFE -10.57
Energy contribution -11.93
Covariance contribution 1.36
Combinations/Pair 1.07
Mean z-score -2.89
Structure conservation index 0.48
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.95
SVM RNA-class probability 0.976535
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 13500080 91 + 21146708
UUGGAGGCGAUAUCCAG--CGACUCACUAAUUAUUCAGUCGCUGGCCAAAAUCCAACAUUCAAACUUCCAAAUUGCCGCCAGUUUCGCCUCGA
...(((((((...((((--(((((............))))))))).........................(((((....)))))))))))).. ( -27.30, z-score =  -3.96, R)
>droSim1.chr2R 12237579 83 + 19596830
UUGGAGGCGAUAUCCAG--CGACUCACUAAUUAUCCAGUCGCUGGCCAAAAUCCAACAUCCAA--------AUUGCCGCCAGUUUCGCCUCGA
...(((((((...((((--(((((............))))))))).................(--------((((....)))))))))))).. ( -27.30, z-score =  -3.94, R)
>droSec1.super_1 10999180 90 + 14215200
UUGGAGGCGAUAUCCAG--CGACUCACUAAUUAUCCAGUCGCUGGCCAAAAUCCAACAUCCAA-CAUCCAAAUUGCCGCCAGUUUCGCCUCGA
...(((((((...((((--(((((............)))))))))..................-......(((((....)))))))))))).. ( -27.30, z-score =  -3.96, R)
>droYak2.chr2R 5453563 92 - 21139217
UUGAAGGCGGUAUCCAGUGCGACUCACUAAUUAUCCAAUCGCAGGCCAAAAUCGAAAAUCCAA-AAACCAAAUUGCCGCCAGUUUCGCCUCCA
.....(((((((.....(((((................)))))((..................-...))....)))))))............. ( -16.39, z-score =  -0.35, R)
>droEre2.scaffold_4845 7728655 90 + 22589142
UUGGAGGCGAUAUCCAG--CGACUCACUAAUUAUCCAGUCGCAGGCCAAAAUCCAAAAUCCGA-AAUCCAAAUUGCCGCCAGUUUCGCCUCCA
.(((((((((......(--(((((............)))))).(((...(((...........-.......)))...)))....))))))))) ( -26.67, z-score =  -4.07, R)
>dp4.chr3 9066970 72 - 19779522
----UUCCGAUAUUCAA--CGACUCACUAAUUAUCCAGUGCCCGUCCCCAGUCGCAUACCA---------------UGCCAGUUUCGCCCCAA
----...(((.(((...--.((((((((........)))).........))))((((...)---------------))).))).)))...... (  -7.30, z-score =  -1.04, R)
>consensus
UUGGAGGCGAUAUCCAG__CGACUCACUAAUUAUCCAGUCGCUGGCCAAAAUCCAACAUCCAA__AUCCAAAUUGCCGCCAGUUUCGCCUCGA
...(((((((.........(((((............)))))..(((...............................)))....))))))).. (-10.57 = -11.93 +   1.36)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 13,500,080 – 13,500,171
Length 91
Sequences 6
Columns 93
Reading direction reverse
Mean pairwise identity 79.01
Shannon entropy 0.39544
G+C content 0.49145
Mean single sequence MFE -30.55
Consensus MFE -15.29
Energy contribution -17.82
Covariance contribution 2.53
Combinations/Pair 1.17
Mean z-score -2.75
Structure conservation index 0.50
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.86
SVM RNA-class probability 0.971886
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 13500080 91 - 21146708
UCGAGGCGAAACUGGCGGCAAUUUGGAAGUUUGAAUGUUGGAUUUUGGCCAGCGACUGAAUAAUUAGUGAGUCG--CUGGAUAUCGCCUCCAA
..(((((((..(..(((.(((.........)))..)))..).......(((((((((.(........).)))))--))))...)))))))... ( -33.70, z-score =  -3.32, R)
>droSim1.chr2R 12237579 83 - 19596830
UCGAGGCGAAACUGGCGGCAAU--------UUGGAUGUUGGAUUUUGGCCAGCGACUGGAUAAUUAGUGAGUCG--CUGGAUAUCGCCUCCAA
..(((((((..(..(((.(...--------...).)))..).......(((((((((.(........).)))))--))))...)))))))... ( -33.40, z-score =  -3.40, R)
>droSec1.super_1 10999180 90 - 14215200
UCGAGGCGAAACUGGCGGCAAUUUGGAUG-UUGGAUGUUGGAUUUUGGCCAGCGACUGGAUAAUUAGUGAGUCG--CUGGAUAUCGCCUCCAA
..(((((((..(..(((.((((......)-)))..)))..).......(((((((((.(........).)))))--))))...)))))))... ( -36.70, z-score =  -3.83, R)
>droYak2.chr2R 5453563 92 + 21139217
UGGAGGCGAAACUGGCGGCAAUUUGGUUU-UUGGAUUUUCGAUUUUGGCCUGCGAUUGGAUAAUUAGUGAGUCGCACUGGAUACCGCCUUCAA
((((((((...(..(.(((...((((...-........)))).....)))(((((((.(........).))))))))..)....)))))))). ( -26.40, z-score =  -0.96, R)
>droEre2.scaffold_4845 7728655 90 - 22589142
UGGAGGCGAAACUGGCGGCAAUUUGGAUU-UCGGAUUUUGGAUUUUGGCCUGCGACUGGAUAAUUAGUGAGUCG--CUGGAUAUCGCCUCCAA
(((((((((....(((.(.((((..((..-......))..)))).).))).((((((.(........).)))))--)......))))))))). ( -36.70, z-score =  -4.10, R)
>dp4.chr3 9066970 72 + 19779522
UUGGGGCGAAACUGGCA---------------UGGUAUGCGACUGGGGACGGGCACUGGAUAAUUAGUGAGUCG--UUGAAUAUCGGAA----
.....((.......)).---------------(((((((((((((....)...((((((....)))))))))))--)...))))))...---- ( -16.40, z-score =  -0.87, R)
>consensus
UCGAGGCGAAACUGGCGGCAAUUUGGAU__UUGGAUGUUGGAUUUUGGCCAGCGACUGGAUAAUUAGUGAGUCG__CUGGAUAUCGCCUCCAA
..(((((((..(((((.(.((((..(...........)..)))).).)))))(((((.(........).))))).........)))))))... (-15.29 = -17.82 +   2.53)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:30:11 2011