Locus 5446

Sequence ID dm3.chr2R
Location 20,364,860 – 20,364,943
Length 83
Max. P 0.836806
window7475 window7476

overview

Window 5

Location 20,364,860 – 20,364,943
Length 83
Sequences 6
Columns 84
Reading direction forward
Mean pairwise identity 65.12
Shannon entropy 0.66827
G+C content 0.60003
Mean single sequence MFE -25.67
Consensus MFE -10.86
Energy contribution -11.25
Covariance contribution 0.39
Combinations/Pair 1.44
Mean z-score -1.29
Structure conservation index 0.42
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.86
SVM RNA-class probability 0.836806
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 20364860 83 + 21146708
-GGCGCCUCGGUUUAAGCCACGCGAAUGUCCCUUCCUCAGUUCAGCUGCCCGACUUGGCCCGAGGAUCCGAAACCGGAUCCCAA
-((.(((((((....(((.((..(((......)))....))...)))..))))...)))))(.(((((((....)))))))).. ( -25.90, z-score =  -0.83, R)
>droAna3.scaffold_13266 15904346 72 + 19884421
GAAGUCUAUACUUUAAGUUAUGGCAGCAUGGCGGUGGCGGCUGUCACGCGAAAAUUGUCAACUCGCCUCAGG------------
(((((....))))).......(((.((.(((((((....))))))).))((......)).....))).....------------ ( -16.70, z-score =   0.52, R)
>droEre2.scaffold_4845 21726107 81 + 22589142
-GGUACUUCGAUUUAAGCCGCGAA-AUGUCCCUUCUCCAGUGCAGCCAUCCGACCUGCCC-GAGGAUCCGAAACCGGAUCCCCA
-((((..(((......((.(((..-.((.........)).))).))....)))..)))).-(.(((((((....))))))).). ( -21.80, z-score =  -1.68, R)
>droYak2.chr2R 20328113 83 + 21139217
-GGCACUUCGAUUUAAGCCACGGCCACGUCCCUUCUCCAGUGCAGCCAACCGAGCUGCCCCGAGGAUCCGAAACCGGAUCCCAA
-((((.((((......((....))(((............)))........)))).))))..(.(((((((....)))))))).. ( -24.60, z-score =  -1.77, R)
>droSec1.super_23 237580 83 + 989336
-GGCGCCUCGGCUUGAGCCACGCAAAUGUCCCUUCCUCGGUUCAGCUGCCCGACUUGGCCCGAGGAUCCGAAACCGGAUCCCAA
-((.(((..(((....)))..(((..((..((......))..))..))).......)))))(.(((((((....)))))))).. ( -32.20, z-score =  -2.09, R)
>droSim1.chr2R 18823704 83 + 19596830
-GGCGCCUCGGUUUGAGCCGCGCAAAUGUCCCUUCCUCGGUUCAGCUGCCCGACUUGGCCCGAGGAUCCGAAACCGGAUCCCAA
-((...(((((.(..((.((.(((..((..((......))..))..))).)).))..).)))))((((((....)))))))).. ( -32.80, z-score =  -1.89, R)
>consensus
_GGCGCCUCGGUUUAAGCCACGCAAAUGUCCCUUCCUCAGUUCAGCCGCCCGACUUGGCCCGAGGAUCCGAAACCGGAUCCCAA
.(((..........(((..(((....)))..)))..........)))................(((((((....)))))))... (-10.86 = -11.25 +   0.39)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 20,364,860 – 20,364,943
Length 83
Sequences 6
Columns 84
Reading direction reverse
Mean pairwise identity 65.12
Shannon entropy 0.66827
G+C content 0.60003
Mean single sequence MFE -28.90
Consensus MFE -14.03
Energy contribution -15.48
Covariance contribution 1.45
Combinations/Pair 1.41
Mean z-score -0.69
Structure conservation index 0.49
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.35
SVM RNA-class probability 0.655289
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 20364860 83 - 21146708
UUGGGAUCCGGUUUCGGAUCCUCGGGCCAAGUCGGGCAGCUGAACUGAGGAAGGGACAUUCGCGUGGCUUAAACCGAGGCGCC-
...(((((((....)))))))((((...((((((.((...((..((......))..))...)).))))))...))))......- ( -28.80, z-score =   0.19, R)
>droAna3.scaffold_13266 15904346 72 - 19884421
------------CCUGAGGCGAGUUGACAAUUUUCGCGUGACAGCCGCCACCGCCAUGCUGCCAUAACUUAAAGUAUAGACUUC
------------..(((((((((.........)))))(((.((((.((....))...)))).)))..))))((((....)))). ( -14.50, z-score =  -0.20, R)
>droEre2.scaffold_4845 21726107 81 - 22589142
UGGGGAUCCGGUUUCGGAUCCUC-GGGCAGGUCGGAUGGCUGCACUGGAGAAGGGACAU-UUCGCGGCUUAAAUCGAAGUACC-
.(((((((((....)))))))))-((.....((((..((((((.((.....)).((...-.))))))))....))))....))- ( -28.80, z-score =  -1.22, R)
>droYak2.chr2R 20328113 83 - 21139217
UUGGGAUCCGGUUUCGGAUCCUCGGGGCAGCUCGGUUGGCUGCACUGGAGAAGGGACGUGGCCGUGGCUUAAAUCGAAGUGCC-
..((((((((....))))))))...((((..(((((((((..(.((.....))((......)))..)))..))))))..))))- ( -32.00, z-score =  -0.85, R)
>droSec1.super_23 237580 83 - 989336
UUGGGAUCCGGUUUCGGAUCCUCGGGCCAAGUCGGGCAGCUGAACCGAGGAAGGGACAUUUGCGUGGCUCAAGCCGAGGCGCC-
..((((((((....))))))))..(((..(((((.((((.((..((......))..)).)))).)))))...((....)))))- ( -33.70, z-score =  -0.68, R)
>droSim1.chr2R 18823704 83 - 19596830
UUGGGAUCCGGUUUCGGAUCCUCGGGCCAAGUCGGGCAGCUGAACCGAGGAAGGGACAUUUGCGCGGCUCAAACCGAGGCGCC-
...(((((((....)))))))((((....(((((.((((.((..((......))..)).)))).)))))....))))......- ( -35.60, z-score =  -1.37, R)
>consensus
UUGGGAUCCGGUUUCGGAUCCUCGGGCCAAGUCGGGCAGCUGAACCGAGGAAGGGACAUUUGCGUGGCUUAAACCGAAGCGCC_
...(((((((....)))))))((((...((((((.(....((..((......))..))....).))))))...))))....... (-14.03 = -15.48 +   1.45)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:48:31 2011