Locus 9598

Sequence ID dm3.chr3R
Location 7,587,635 – 7,587,696
Length 61
Max. P 0.840822
window13173 window13174

overview

Window 3

Location 7,587,635 – 7,587,696
Length 61
Sequences 6
Columns 70
Reading direction forward
Mean pairwise identity 69.98
Shannon entropy 0.53252
G+C content 0.47150
Mean single sequence MFE -11.03
Consensus MFE -6.86
Energy contribution -6.87
Covariance contribution 0.00
Combinations/Pair 1.38
Mean z-score -0.92
Structure conservation index 0.62
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.59
SVM RNA-class probability 0.753136
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 7587635 61 + 27905053
-UCAAUUUCAAUUUCUCGGUCUCGGCUAGCUGGCACAGAUACUAGUGCCGUCUCUCUCACUU--------
-................((...((((..(((((........)))))))))...)).......-------- ( -10.40, z-score =  -0.64, R)
>droSim1.chr3R 13709727 61 - 27517382
-UCAAUUUCAAUUUCUCGGUCUCGGCUAGCUGGCACAGAUACUAGUGCCGUCUCUCUCACUU--------
-................((...((((..(((((........)))))))))...)).......-------- ( -10.40, z-score =  -0.64, R)
>droSec1.super_0 6742472 61 - 21120651
-UCAAUUUCAAUUUCUCGGUCUCGGCUAGCUGGCACAGAUACUAGUGCCGUCUCUCUCACUU--------
-................((...((((..(((((........)))))))))...)).......-------- ( -10.40, z-score =  -0.64, R)
>droYak2.chr3R 12001341 63 - 28832112
-------UCAAUUUCUCGGUCUCAGCUAGCUGGCACAGAUACUCGUGCCAUCUCCCUCUCUUCGCUUCAU
-------.........(((....((..((.((((((........)))))).))..))....)))...... ( -11.90, z-score =  -1.56, R)
>droEre2.scaffold_4770 3717480 63 - 17746568
-------UCAAUUUCUCGGUCUCUGCUGGCUGGCACAGAUACUCGUGCCGUCUCCCUCUCUGCGCUUCAU
-------..........((((......))))(((((........)))))..................... ( -11.80, z-score =   0.04, R)
>droGri2.scaffold_14853 8907310 56 + 10151454
UUAUUUAACAAUUUUUUGAUC-----UGAUUGGUAUAUCUUCCAGU-CGGGCUAUCUCGACU--------
................((..(-----(((((((........)))))-)))..))........-------- ( -11.30, z-score =  -2.07, R)
>consensus
_UCAAUUUCAAUUUCUCGGUCUCGGCUAGCUGGCACAGAUACUAGUGCCGUCUCUCUCACUU________
...........................((.((((((........)))))).))................. ( -6.86 =  -6.87 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 7,587,635 – 7,587,696
Length 61
Sequences 6
Columns 70
Reading direction reverse
Mean pairwise identity 69.98
Shannon entropy 0.53252
G+C content 0.47150
Mean single sequence MFE -12.60
Consensus MFE -7.17
Energy contribution -7.53
Covariance contribution 0.36
Combinations/Pair 1.12
Mean z-score -1.24
Structure conservation index 0.57
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.87
SVM RNA-class probability 0.840822
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 7587635 61 - 27905053
--------AAGUGAGAGAGACGGCACUAGUAUCUGUGCCAGCUAGCCGAGACCGAGAAAUUGAAAUUGA-
--------......(..((..(((((........)))))..))..)(((...(((....)))...))).- ( -13.00, z-score =  -1.43, R)
>droSim1.chr3R 13709727 61 + 27517382
--------AAGUGAGAGAGACGGCACUAGUAUCUGUGCCAGCUAGCCGAGACCGAGAAAUUGAAAUUGA-
--------......(..((..(((((........)))))..))..)(((...(((....)))...))).- ( -13.00, z-score =  -1.43, R)
>droSec1.super_0 6742472 61 + 21120651
--------AAGUGAGAGAGACGGCACUAGUAUCUGUGCCAGCUAGCCGAGACCGAGAAAUUGAAAUUGA-
--------......(..((..(((((........)))))..))..)(((...(((....)))...))).- ( -13.00, z-score =  -1.43, R)
>droYak2.chr3R 12001341 63 + 28832112
AUGAAGCGAAGAGAGGGAGAUGGCACGAGUAUCUGUGCCAGCUAGCUGAGACCGAGAAAUUGA-------
...........((..((...(((((((......))))))).))..)).....(((....))).------- ( -15.10, z-score =  -1.49, R)
>droEre2.scaffold_4770 3717480 63 + 17746568
AUGAAGCGCAGAGAGGGAGACGGCACGAGUAUCUGUGCCAGCCAGCAGAGACCGAGAAAUUGA-------
.....((((......(....)((((((......)))))).))..))......(((....))).------- ( -15.80, z-score =  -1.26, R)
>droGri2.scaffold_14853 8907310 56 - 10151454
--------AGUCGAGAUAGCCCG-ACUGGAAGAUAUACCAAUCA-----GAUCAAAAAAUUGUUAAAUAA
--------(((((........))-)))((........)).....-----..................... (  -5.70, z-score =  -0.40, R)
>consensus
________AAGUGAGAGAGACGGCACUAGUAUCUGUGCCAGCUAGCCGAGACCGAGAAAUUGAAAUUGA_
.....................(((((........))))).............(((....)))........ ( -7.17 =  -7.53 +   0.36)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:07:33 2011