Locus 4993

Sequence ID dm3.chr2R
Location 16,998,675 – 16,998,772
Length 97
Max. P 0.871561
window6857 window6858

overview

Window 7

Location 16,998,675 – 16,998,772
Length 97
Sequences 6
Columns 98
Reading direction forward
Mean pairwise identity 90.34
Shannon entropy 0.18407
G+C content 0.49987
Mean single sequence MFE -32.85
Consensus MFE -25.76
Energy contribution -27.52
Covariance contribution 1.75
Combinations/Pair 1.11
Mean z-score -2.20
Structure conservation index 0.78
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.00
SVM RNA-class probability 0.871561
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 16998675 97 + 21146708
AAGGAUGCGCAAUCCAGGACUCUGGCUGGCAGAUGAAAGUGAAACUUUUCAUACUCAAGGCAGCGGGCGCCGCUAAGUAGGCUACAAUUUUGCGCUC-
......((((((....((.(.((.((((.(...(((..(((((....)))))..))).).)))).)).)))(((.....))).......))))))..- ( -28.60, z-score =  -0.11, R)
>droAna3.scaffold_13266 12922715 95 - 19884421
AAGGAUGCGUAAUC-AGGACUAUGGUAGUCAGAUGAAAGGGAAACUUUUCCCAUUCA-GACAGCGUGCGCAGUUAAGUAGGCUACACUUUU-UGCCAA
...(((.....)))-.......((((((((...((((.(((((....))))).))))-)))(((.(((........))).)))........-))))). ( -25.20, z-score =  -1.09, R)
>droEre2.scaffold_4845 11142911 96 + 22589142
AAGGAUGCGCAAUC-AGGACUCCGUCCUGCAGAUGAAAGGGAAACUUUUCAUACUCAAGGCAGCGGGCGCCGCUAAGUAGGCUACAAUUUUGCGCUC-
......((((((..-.((..((((((((..((((((((((....)))))))).))..)))..)))))..))(((.....))).......))))))..- ( -34.50, z-score =  -2.33, R)
>droYak2.chr2R 8943104 96 - 21139217
AAGGAUGCGCAAUC-AGGACUCUGGCUUGCAGAUGAAAGGGAAACUUUUCCUACUCAAGGCAGCGGACGCCACUAAGUAGGCUACAAUUUUGCGCUC-
......((((((..-.(..(.(((.((((.((..((((((....))))))...)))))).))).)..)(((........))).......))))))..- ( -34.20, z-score =  -2.91, R)
>droSec1.super_9 328099 96 + 3197100
AAGGAUGCGCAAUC-AGGACUCUGGCUUGCAGAUGAAAGGGAAACUUUUCAUACUCAAGGCAGCGGGCGCCGCUAAGUAGGCUACAAUUUUGCGCUC-
......((((((..-.(..(.(((.((((.((((((((((....)))))))).)))))).))).)..)(((........))).......))))))..- ( -37.30, z-score =  -3.39, R)
>droSim1.chr2R 15655737 96 + 19596830
AAGGAUGCGCAAUC-AGGACUCUGGCUUGCAGAUGAAAGGGAAACUUUUCAUACUCAAGGCAGCGGGCGCCGCUAAGUAGGCUACAAUUUUGCGCUC-
......((((((..-.(..(.(((.((((.((((((((((....)))))))).)))))).))).)..)(((........))).......))))))..- ( -37.30, z-score =  -3.39, R)
>consensus
AAGGAUGCGCAAUC_AGGACUCUGGCUUGCAGAUGAAAGGGAAACUUUUCAUACUCAAGGCAGCGGGCGCCGCUAAGUAGGCUACAAUUUUGCGCUC_
......((((((....(..(.(((.((((.((((((((((....)))))))).)))))).))).)..)(((........))).......))))))... (-25.76 = -27.52 +   1.75)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 16,998,675 – 16,998,772
Length 97
Sequences 6
Columns 98
Reading direction reverse
Mean pairwise identity 90.34
Shannon entropy 0.18407
G+C content 0.49987
Mean single sequence MFE -29.15
Consensus MFE -20.14
Energy contribution -20.28
Covariance contribution 0.14
Combinations/Pair 1.16
Mean z-score -2.06
Structure conservation index 0.69
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.02
SVM RNA-class probability 0.506321
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 16998675 97 - 21146708
-GAGCGCAAAAUUGUAGCCUACUUAGCGGCGCCCGCUGCCUUGAGUAUGAAAAGUUUCACUUUCAUCUGCCAGCCAGAGUCCUGGAUUGCGCAUCCUU
-..((((((....((((..(((((((((((....)))))..))))))(((((........))))).))))...((((....)))).))))))...... ( -30.20, z-score =  -1.62, R)
>droAna3.scaffold_13266 12922715 95 + 19884421
UUGGCA-AAAAGUGUAGCCUACUUAACUGCGCACGCUGUC-UGAAUGGGAAAAGUUUCCCUUUCAUCUGACUACCAUAGUCCU-GAUUACGCAUCCUU
...((.-....((((((.........))))))..(..(((-((((.(((((....))))).))))...(((((...)))))..-)))..)))...... ( -21.70, z-score =  -1.25, R)
>droEre2.scaffold_4845 11142911 96 - 22589142
-GAGCGCAAAAUUGUAGCCUACUUAGCGGCGCCCGCUGCCUUGAGUAUGAAAAGUUUCCCUUUCAUCUGCAGGACGGAGUCCU-GAUUGCGCAUCCUU
-..((((((....((((..(((((((((((....)))))..))))))(((((........))))).))))(((((...)))))-..))))))...... ( -31.20, z-score =  -1.81, R)
>droYak2.chr2R 8943104 96 + 21139217
-GAGCGCAAAAUUGUAGCCUACUUAGUGGCGUCCGCUGCCUUGAGUAGGAAAAGUUUCCCUUUCAUCUGCAAGCCAGAGUCCU-GAUUGCGCAUCCUU
-..((((((..(((((((((((((((.((((.....))))))))))))).((((.....))))...))))))..(((....))-).))))))...... ( -32.20, z-score =  -2.95, R)
>droSec1.super_9 328099 96 - 3197100
-GAGCGCAAAAUUGUAGCCUACUUAGCGGCGCCCGCUGCCUUGAGUAUGAAAAGUUUCCCUUUCAUCUGCAAGCCAGAGUCCU-GAUUGCGCAUCCUU
-..((((((..((((((..(((((((((((....)))))..))))))(((((........))))).))))))..(((....))-).))))))...... ( -29.80, z-score =  -2.37, R)
>droSim1.chr2R 15655737 96 - 19596830
-GAGCGCAAAAUUGUAGCCUACUUAGCGGCGCCCGCUGCCUUGAGUAUGAAAAGUUUCCCUUUCAUCUGCAAGCCAGAGUCCU-GAUUGCGCAUCCUU
-..((((((..((((((..(((((((((((....)))))..))))))(((((........))))).))))))..(((....))-).))))))...... ( -29.80, z-score =  -2.37, R)
>consensus
_GAGCGCAAAAUUGUAGCCUACUUAGCGGCGCCCGCUGCCUUGAGUAUGAAAAGUUUCCCUUUCAUCUGCAAGCCAGAGUCCU_GAUUGCGCAUCCUU
...((((((..........(((((((((((....)))))..)))))).((((........)))).((((.....))))........))))))...... (-20.14 = -20.28 +   0.14)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:39:51 2011