Locus 13816

Sequence ID	dm3.chrX
Location	9,348,928 – 9,349,028
Length	100
Max. P	0.879991

overview

Window 5

Location	9,348,928 – 9,349,028
Length	100
Sequences	4
Columns	108
Reading direction	forward
Mean pairwise identity	94.23
Shannon entropy	0.09014
G+C content	0.45343
Mean single sequence MFE	-22.20
Consensus MFE	-18.40
Energy contribution	-18.40
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.76
Structure conservation index	0.83
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.03
SVM RNA-class probability	0.509412
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chrX 9348928 100 + 22422827
UGCCAUAAAUCCGCCGACAUCCAUAAACCCGUCUUGCCAUUGUUACUCAAUCAAAUUUCCAUUAGGAAAGCCAGGCUAAUAGAGUUUCGUCUGUCUGGCG--------
...........((((((((..(..((((.(.....(((((((.....))))....(((((....)))))....))).....).)))).)..)))).))))-------- ( -22.00, z-score =  -1.97, R)
>droEre2.scaffold_4690 12982758 108 - 18748788
UGCCAUAAAUCCACGGACAUCCAUAAACCCGUCUUGCCAUUGUUACUCAAUCAAAUUUCCAUUAGGAAAGCCAGGCUAAUAGAGUUUCCUCUGUCUGGCGCUCGCUCU
.((.........((((............))))...((..................(((((....)))))(((((((....((((....)))))))))))))..))... ( -23.50, z-score =  -1.50, R)
>droYak2.chrX 17939349 100 + 21770863
UGCCAUAAAUCCGCCGACAUCCAUAAACCCGUCUUGCCAUUGUUACUCAAUCAAAUUUCCAUUAGGAAAGCCAGGCUAAUAGAGUUUCGCCUGUCUGGCG--------
...........((((((((.....((((.(.....(((((((.....))))....(((((....)))))....))).....).))))....)))).))))-------- ( -21.30, z-score =  -1.58, R)
>droSec1.super_15 117013 100 + 1954846
UGCCAUAAAUCCGCCGACAUCCAUAAACCCGUCUUGCCAUUGUUACUCAAUCAAAUUUCCAUUAGGAAAGCCAGGCUAAUAGAGUUUCGUCUGUCUGGCG--------
...........((((((((..(..((((.(.....(((((((.....))))....(((((....)))))....))).....).)))).)..)))).))))-------- ( -22.00, z-score =  -1.97, R)
>consensus
UGCCAUAAAUCCGCCGACAUCCAUAAACCCGUCUUGCCAUUGUUACUCAAUCAAAUUUCCAUUAGGAAAGCCAGGCUAAUAGAGUUUCGUCUGUCUGGCG________
.((((..........((((.....((((.(.....(((((((.....))))....(((((....)))))....))).....).))))....))))))))......... (-18.40 = -18.40 +   0.00)

alignment

secondary structure

dotplot

Window 6

Location	9,348,928 – 9,349,028
Length	100
Sequences	4
Columns	108
Reading direction	reverse
Mean pairwise identity	94.23
Shannon entropy	0.09014
G+C content	0.45343
Mean single sequence MFE	-29.33
Consensus MFE	-27.56
Energy contribution	-27.00
Covariance contribution	-0.56
Combinations/Pair	1.06
Mean z-score	-1.68
Structure conservation index	0.94
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.04
SVM RNA-class probability	0.879991
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chrX 9348928 100 - 22422827
--------CGCCAGACAGACGAAACUCUAUUAGCCUGGCUUUCCUAAUGGAAAUUUGAUUGAGUAACAAUGGCAAGACGGGUUUAUGGAUGUCGGCGGAUUUAUGGCA
--------((((.((((..((((((((.....(((....(((((....)))))....((((.....))))))).....)))))).))..))))))))........... ( -28.40, z-score =  -1.81, R)
>droEre2.scaffold_4690 12982758 108 + 18748788
AGAGCGAGCGCCAGACAGAGGAAACUCUAUUAGCCUGGCUUUCCUAAUGGAAAUUUGAUUGAGUAACAAUGGCAAGACGGGUUUAUGGAUGUCCGUGGAUUUAUGGCA
...((..(((((((.(((((....))))....).)))))(((((....)))))..................)).....((((((((((....))))))))))...)). ( -31.50, z-score =  -1.54, R)
>droYak2.chrX 17939349 100 - 21770863
--------CGCCAGACAGGCGAAACUCUAUUAGCCUGGCUUUCCUAAUGGAAAUUUGAUUGAGUAACAAUGGCAAGACGGGUUUAUGGAUGUCGGCGGAUUUAUGGCA
--------.((((....(.(((...(((((.((((((..(((((....)))))((((((((.....))))..)))).)))))).)))))..))).).......)))). ( -29.00, z-score =  -1.54, R)
>droSec1.super_15 117013 100 - 1954846
--------CGCCAGACAGACGAAACUCUAUUAGCCUGGCUUUCCUAAUGGAAAUUUGAUUGAGUAACAAUGGCAAGACGGGUUUAUGGAUGUCGGCGGAUUUAUGGCA
--------((((.((((..((((((((.....(((....(((((....)))))....((((.....))))))).....)))))).))..))))))))........... ( -28.40, z-score =  -1.81, R)
>consensus
________CGCCAGACAGACGAAACUCUAUUAGCCUGGCUUUCCUAAUGGAAAUUUGAUUGAGUAACAAUGGCAAGACGGGUUUAUGGAUGUCGGCGGAUUUAUGGCA
.........((((....(.(((...(((((.((((((..(((((....)))))((((((((.....))))..)))).)))))).)))))..))).).......)))). (-27.56 = -27.00 +  -0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:28:18 2011