Locus 10275

Sequence ID dm3.chr3R
Location 12,642,440 – 12,642,490
Length 50
Max. P 0.920409
window14125 window14126

overview

Window 5

Location 12,642,440 – 12,642,490
Length 50
Sequences 6
Columns 60
Reading direction forward
Mean pairwise identity 67.95
Shannon entropy 0.55175
G+C content 0.45533
Mean single sequence MFE -15.58
Consensus MFE -5.75
Energy contribution -5.56
Covariance contribution -0.19
Combinations/Pair 1.25
Mean z-score -1.72
Structure conservation index 0.37
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.13
SVM RNA-class probability 0.559406
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 12642440 50 + 27905053
UUGAAUCCUUUGUUAGGG-GUUCAUU--UCGGACGA-------UAAAUGAAGACAAAGGG
......((((((((....-.((((((--(.......-------.))))))))))))))). ( -11.90, z-score =  -1.61, R)
>droSim1.chr3R 18684252 50 - 27517382
UUGAAUCCUUUGUUAGGG-GUUCAUU--UCGGAGGA-------UAAAUGAAGACAAAGGG
......((((((((....-.((((((--(.......-------.))))))))))))))). ( -11.90, z-score =  -1.69, R)
>droSec1.super_12 611859 50 - 2123299
UUGAAUCCUUUGUUAGGG-GUUCAUU--UCGGAGGA-------UAAAUGAAGACAAAGGG
......((((((((....-.((((((--(.......-------.))))))))))))))). ( -11.90, z-score =  -1.69, R)
>droAna3.scaffold_13340 16445954 52 - 23697760
UCGGCUUCUUUGUUCGAGUACCCUUC--UUGGGGGAC------UAAGAGAAGACAAUGGU
..(.(((((((.....(((.((((..--..)))).))------).))))))).)...... ( -14.90, z-score =  -0.63, R)
>dp4.chr2 17629784 60 + 30794189
UCGGGUCCUUUGUUUGUGAUUUCCUCGGCUGUGGGAGGGAGGGGAACACAAAACAAAGGG
......((((((((((((.(..((((..((.....)).))))..).))).))))))))). ( -22.50, z-score =  -2.35, R)
>droPer1.super_0 11482997 56 + 11822988
UCGGGUCCUUUGUUUGCGAUUUCCUCGGCUGUGGGAG----GAGAACACAAAACAAAGGG
......((((((((((.(.(((((((........)))----)))).).).))))))))). ( -20.40, z-score =  -2.33, R)
>consensus
UCGAAUCCUUUGUUAGGG_GUUCAUC__UCGGAGGA_______UAAAAGAAGACAAAGGG
......((((((((.....................................)))))))). ( -5.75 =  -5.56 +  -0.19)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 12,642,440 – 12,642,490
Length 50
Sequences 6
Columns 60
Reading direction reverse
Mean pairwise identity 67.95
Shannon entropy 0.55175
G+C content 0.45533
Mean single sequence MFE -12.92
Consensus MFE -3.46
Energy contribution -3.80
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.90
Structure conservation index 0.27
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.28
SVM RNA-class probability 0.920409
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 12642440 50 - 27905053
CCCUUUGUCUUCAUUUA-------UCGUCCGA--AAUGAAC-CCCUAACAAAGGAUUCAA
.(((((((.(((((((.-------.......)--)))))).-.....)))))))...... ( -10.10, z-score =  -2.81, R)
>droSim1.chr3R 18684252 50 + 27517382
CCCUUUGUCUUCAUUUA-------UCCUCCGA--AAUGAAC-CCCUAACAAAGGAUUCAA
.(((((((.(((((((.-------.......)--)))))).-.....)))))))...... ( -10.10, z-score =  -3.38, R)
>droSec1.super_12 611859 50 + 2123299
CCCUUUGUCUUCAUUUA-------UCCUCCGA--AAUGAAC-CCCUAACAAAGGAUUCAA
.(((((((.(((((((.-------.......)--)))))).-.....)))))))...... ( -10.10, z-score =  -3.38, R)
>droAna3.scaffold_13340 16445954 52 + 23697760
ACCAUUGUCUUCUCUUA------GUCCCCCAA--GAAGGGUACUCGAACAAAGAAGCCGA
....(((.(((((...(------((.(((...--...))).))).......))))).))) (  -9.10, z-score =  -0.12, R)
>dp4.chr2 17629784 60 - 30794189
CCCUUUGUUUUGUGUUCCCCUCCCUCCCACAGCCGAGGAAAUCACAAACAAAGGACCCGA
.(((((((((.(((....((((............))))....))))))))))))...... ( -17.70, z-score =  -3.45, R)
>droPer1.super_0 11482997 56 - 11822988
CCCUUUGUUUUGUGUUCUC----CUCCCACAGCCGAGGAAAUCGCAAACAAAGGACCCGA
.(((((((((.(((...((----(((........)))))...))))))))))))...... ( -20.40, z-score =  -4.24, R)
>consensus
CCCUUUGUCUUCAUUUA_______UCCCCCAA__AAUGAAC_CCCUAACAAAGGAUCCAA
.(((((((.......................................)))))))...... ( -3.46 =  -3.80 +   0.33)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:20:47 2011