Locus 13499

Sequence ID dm3.chrX
Location 6,943,116 – 6,943,209
Length 93
Max. P 0.847346
window18593 window18594

overview

Window 3

Location 6,943,116 – 6,943,209
Length 93
Sequences 6
Columns 95
Reading direction forward
Mean pairwise identity 65.22
Shannon entropy 0.65064
G+C content 0.59222
Mean single sequence MFE -30.80
Consensus MFE -10.72
Energy contribution -11.90
Covariance contribution 1.18
Combinations/Pair 1.27
Mean z-score -1.62
Structure conservation index 0.35
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.57
SVM RNA-class probability 0.747542
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 6943116 93 + 22422827
--GUCUCGAGGAUGUUGAGACAUAUCCUGGCCAGCGAGCAGCGAGCGACAGCAAAUGACAGGCCAUUAAAUGCCCGUUGCCUGCUCCGACCAGCC
--(((((((.....))))))).....((((...(.((((((...(((((.(((((((......))))...)))..))))))))))))..)))).. ( -31.60, z-score =  -1.91, R)
>droSim1.chrX_random 2203248 89 + 5698898
--GUCUCGAGGAUGUUGG---AUAUCCUGGCCAGCGAGCAGCAGGCGACAGCAAAUGACAGGCCAUUAAAUGCCCGUUGCCUGCGC-GACCAGCC
--(((.(.(((((((...---))))))).).......((.(((((((((.(((((((......))))...)))..)))))))))))-)))..... ( -31.80, z-score =  -1.18, R)
>droSec1.super_24 163260 89 + 912625
--GUCUCGAGGAUGUUGG---AUAUCCUGGCCAGCGAGCAGCAGGCGACAGCAAAUGACAGGCCAUUAAAUGCCCGUUGCCUGCUC-GACCAGCC
--......(((((((...---)))))))(((..(((((((...((((((.(((((((......))))...)))..)))))))))))-).)..))) ( -31.00, z-score =  -1.13, R)
>droEre2.scaffold_4690 15854480 85 + 18748788
--GUCCCGAGGACGCUGG---CUAUCCUGGCCAGCGAGCAGCAGGCGACGGCAACUGACAGGCCAUUAAAUGCCUGCCUCAUCCUCAAGU-----
--.....(((((.(((((---((.....)))))))(((..(((((((..(((.........)))......)))))))))).)))))....----- ( -37.30, z-score =  -2.94, R)
>droAna3.scaffold_13117 3507788 73 - 5790199
--GUCUCAAGCA----------UAUCCUGGCCAACUGCCAGCGGGC--UGGCA---GUAAGGCCAUUAAAUGCCUGCUGCCUGCGUGUCC-----
--.......(((----------(.(((((((.....))))).))((--.((((---(((.(((........)))))))))).))))))..----- ( -28.80, z-score =  -1.64, R)
>dp4.chrXL_group1e 5706711 76 - 12523060
CAGACGCGUCCAUGUGGU---GCAUGUAGAGAGGGUGCCAGCAGGCGCCAGCAAAUGACAGACCAUUAGACGGCUAGGC----------------
.((.(.((((...(((((---...(((...(..((((((....))))))..).....))).)))))..)))))))....---------------- ( -24.30, z-score =  -0.90, R)
>consensus
__GUCUCGAGGAUGUUGG___AUAUCCUGGCCAGCGAGCAGCAGGCGACAGCAAAUGACAGGCCAUUAAAUGCCCGUUGCCUGCUC_GAC_____
........(((((((......)))))))((((.((.....))..((....))........))))............................... (-10.72 = -11.90 +   1.18)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 6,943,116 – 6,943,209
Length 93
Sequences 6
Columns 95
Reading direction reverse
Mean pairwise identity 65.22
Shannon entropy 0.65064
G+C content 0.59222
Mean single sequence MFE -33.53
Consensus MFE -11.43
Energy contribution -12.60
Covariance contribution 1.17
Combinations/Pair 1.45
Mean z-score -1.84
Structure conservation index 0.34
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.90
SVM RNA-class probability 0.847346
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 6943116 93 - 22422827
GGCUGGUCGGAGCAGGCAACGGGCAUUUAAUGGCCUGUCAUUUGCUGUCGCUCGCUGCUCGCUGGCCAGGAUAUGUCUCAACAUCCUCGAGAC--
..((((((((((((((..((((((........))))))..))))))...((.....))...)))))))).....(((((.........)))))-- ( -34.10, z-score =  -1.06, R)
>droSim1.chrX_random 2203248 89 - 5698898
GGCUGGUC-GCGCAGGCAACGGGCAUUUAAUGGCCUGUCAUUUGCUGUCGCCUGCUGCUCGCUGGCCAGGAUAU---CCAACAUCCUCGAGAC--
(((..((.-((((((((.((((.((...(((((....))))))))))).)))))).))..))..)))(((((..---.....)))))......-- ( -35.50, z-score =  -1.68, R)
>droSec1.super_24 163260 89 - 912625
GGCUGGUC-GAGCAGGCAACGGGCAUUUAAUGGCCUGUCAUUUGCUGUCGCCUGCUGCUCGCUGGCCAGGAUAU---CCAACAUCCUCGAGAC--
(((..(.(-((((((.((((((((........)))))).....((....)).))))))))))..)))(((((..---.....)))))......-- ( -35.50, z-score =  -1.80, R)
>droEre2.scaffold_4690 15854480 85 - 18748788
-----ACUUGAGGAUGAGGCAGGCAUUUAAUGGCCUGUCAGUUGCCGUCGCCUGCUGCUCGCUGGCCAGGAUAG---CCAGCGUCCUCGGGAC--
-----.((((((((((((((((((.....(((((.........))))).))))))..)))((((((.......)---))))))))))))))..-- ( -41.40, z-score =  -2.90, R)
>droAna3.scaffold_13117 3507788 73 + 5790199
-----GGACACGCAGGCAGCAGGCAUUUAAUGGCCUUAC---UGCCA--GCCCGCUGGCAGUUGGCCAGGAUA----------UGCUUGAGAC--
-----..............(((((((....(((((..((---(((((--(....)))))))).)))))....)----------))))))....-- ( -35.00, z-score =  -3.73, R)
>dp4.chrXL_group1e 5706711 76 + 12523060
----------------GCCUAGCCGUCUAAUGGUCUGUCAUUUGCUGGCGCCUGCUGGCACCCUCUCUACAUGC---ACCACAUGGACGCGUCUG
----------------.....((((((((.((((((((....(((..((....))..)))........))).).---))))..)))))).))... ( -19.70, z-score =   0.12, R)
>consensus
_____GUC_GAGCAGGCAACAGGCAUUUAAUGGCCUGUCAUUUGCUGUCGCCUGCUGCUCGCUGGCCAGGAUAU___CCAACAUCCUCGAGAC__
...........(((....((((((........))))))....))).((((((.((.....)).))).(((((..........)))))...))).. (-11.43 = -12.60 +   1.17)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:22:37 2011