Locus 5434

Sequence ID dm3.chr2R
Location 20,273,725 – 20,273,775
Length 50
Max. P 0.981846
window7456 window7457

overview

Window 6

Location 20,273,725 – 20,273,775
Length 50
Sequences 10
Columns 51
Reading direction forward
Mean pairwise identity 95.35
Shannon entropy 0.10180
G+C content 0.40325
Mean single sequence MFE -11.09
Consensus MFE -10.53
Energy contribution -10.31
Covariance contribution -0.22
Combinations/Pair 1.23
Mean z-score -2.32
Structure conservation index 0.95
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.09
SVM RNA-class probability 0.981846
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 20273725 50 + 21146708
CGGCUUCCUCUGACACUUUUCAAAA-CUAUUGAUGUUGUCAUUGGCCAUAU
.((((.....(((((....((((..-...))))...)))))..)))).... ( -11.90, z-score =  -2.78, R)
>droSim1.chr2R 18724921 50 + 19596830
CGGCUUCCUCUGACACUUUUCAAAA-CUAUUGAUGUUGUCAUUGGCCAUAU
.((((.....(((((....((((..-...))))...)))))..)))).... ( -11.90, z-score =  -2.78, R)
>droSec1.super_23 144177 50 + 989336
CGGCUUCCUCUGACACUUUUCAAAA-CUAUUGAUGUUGUCAUUGGCCAUAU
.((((.....(((((....((((..-...))))...)))))..)))).... ( -11.90, z-score =  -2.78, R)
>droEre2.scaffold_4845 21631974 50 + 22589142
CGGCUUCCUCUGACACUUUUCAAAA-CUAUUGAUGUUGUCAUUGGCCAUAU
.((((.....(((((....((((..-...))))...)))))..)))).... ( -11.90, z-score =  -2.78, R)
>droYak2.chr2R 20234747 50 + 21139217
CGGCUUCCUCUGACACUUUUCAAAA-CUAUUGAUGUUGUCAUUGGCCAUAU
.((((.....(((((....((((..-...))))...)))))..)))).... ( -11.90, z-score =  -2.78, R)
>droAna3.scaffold_13266 5737169 50 - 19884421
CGGCUUCCUCUGACACUUUUCAAAA-CUAUUGAUGUUGUCAUUGGCCAUAU
.((((.....(((((....((((..-...))))...)))))..)))).... ( -11.90, z-score =  -2.78, R)
>dp4.chr3 1378201 50 - 19779522
CGGCUUCCUCUGACACUUUUCAAAA-CUAUUGAUGUUGUCAUUGGGUCUAU
.(((..((..(((((....((((..-...))))...)))))..)))))... ( -10.60, z-score =  -1.98, R)
>droVir3.scaffold_12875 7389301 50 + 20611582
CGGCUUCCUCUGACAGUUUUCAAAA-CUAUUGAUGUUGUCAUUGGCUAUAU
.((((.....((((((...((((..-...))))..))))))..)))).... ( -10.20, z-score =  -1.69, R)
>droMoj3.scaffold_6496 26185151 50 + 26866924
CGGCCUCCUCUGACACUUUGCGAAA-CUAUUGAUGUUGUCAUUGGCUACAG
.((((.....(((((.....(((..-...)))....)))))..)))).... (  -9.30, z-score =  -0.82, R)
>droGri2.scaffold_15245 938631 51 + 18325388
CGGCUUCCUCUGACACUUUUCAAAAACUAUUGAUGUUGUCAUUGGCUAUAU
.((((.....(((((....((((......))))...)))))..)))).... (  -9.40, z-score =  -2.06, R)
>consensus
CGGCUUCCUCUGACACUUUUCAAAA_CUAUUGAUGUUGUCAUUGGCCAUAU
.((((.....(((((....((((......))))...)))))..)))).... (-10.53 = -10.31 +  -0.22)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 20,273,725 – 20,273,775
Length 50
Sequences 10
Columns 51
Reading direction reverse
Mean pairwise identity 95.35
Shannon entropy 0.10180
G+C content 0.40325
Mean single sequence MFE -10.82
Consensus MFE -9.84
Energy contribution -10.04
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -2.15
Structure conservation index 0.91
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.52
SVM RNA-class probability 0.946084
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 20273725 50 - 21146708
AUAUGGCCAAUGACAACAUCAAUAG-UUUUGAAAAGUGUCAGAGGAAGCCG
....(((...(((((...((((...-..))))....)))))......))). ( -11.60, z-score =  -2.32, R)
>droSim1.chr2R 18724921 50 - 19596830
AUAUGGCCAAUGACAACAUCAAUAG-UUUUGAAAAGUGUCAGAGGAAGCCG
....(((...(((((...((((...-..))))....)))))......))). ( -11.60, z-score =  -2.32, R)
>droSec1.super_23 144177 50 - 989336
AUAUGGCCAAUGACAACAUCAAUAG-UUUUGAAAAGUGUCAGAGGAAGCCG
....(((...(((((...((((...-..))))....)))))......))). ( -11.60, z-score =  -2.32, R)
>droEre2.scaffold_4845 21631974 50 - 22589142
AUAUGGCCAAUGACAACAUCAAUAG-UUUUGAAAAGUGUCAGAGGAAGCCG
....(((...(((((...((((...-..))))....)))))......))). ( -11.60, z-score =  -2.32, R)
>droYak2.chr2R 20234747 50 - 21139217
AUAUGGCCAAUGACAACAUCAAUAG-UUUUGAAAAGUGUCAGAGGAAGCCG
....(((...(((((...((((...-..))))....)))))......))). ( -11.60, z-score =  -2.32, R)
>droAna3.scaffold_13266 5737169 50 + 19884421
AUAUGGCCAAUGACAACAUCAAUAG-UUUUGAAAAGUGUCAGAGGAAGCCG
....(((...(((((...((((...-..))))....)))))......))). ( -11.60, z-score =  -2.32, R)
>dp4.chr3 1378201 50 + 19779522
AUAGACCCAAUGACAACAUCAAUAG-UUUUGAAAAGUGUCAGAGGAAGCCG
......((..(((((...((((...-..))))....)))))..))...... ( -10.60, z-score =  -2.87, R)
>droVir3.scaffold_12875 7389301 50 - 20611582
AUAUAGCCAAUGACAACAUCAAUAG-UUUUGAAAACUGUCAGAGGAAGCCG
......((..(((((...((((...-..))))....)))))..))...... (  -9.40, z-score =  -2.04, R)
>droMoj3.scaffold_6496 26185151 50 - 26866924
CUGUAGCCAAUGACAACAUCAAUAG-UUUCGCAAAGUGUCAGAGGAGGCCG
..((..((..(((((..........-..........)))))..))..)).. (  -7.95, z-score =   0.02, R)
>droGri2.scaffold_15245 938631 51 - 18325388
AUAUAGCCAAUGACAACAUCAAUAGUUUUUGAAAAGUGUCAGAGGAAGCCG
......((..(((((...((((......))))....)))))..))...... ( -10.70, z-score =  -2.73, R)
>consensus
AUAUGGCCAAUGACAACAUCAAUAG_UUUUGAAAAGUGUCAGAGGAAGCCG
......((..(((((...((((......))))....)))))..))...... ( -9.84 = -10.04 +   0.20)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:48:15 2011