Locus 12466

Sequence ID	dm3.chrX
Location	395,738 – 395,834
Length	96
Max. P	0.991090

overview

Window 0

Location	395,738 – 395,828
Length	90
Sequences	6
Columns	109
Reading direction	forward
Mean pairwise identity	84.91
Shannon entropy	0.25902
G+C content	0.46502
Mean single sequence MFE	-25.92
Consensus MFE	-14.56
Energy contribution	-15.25
Covariance contribution	0.69
Combinations/Pair	1.05
Mean z-score	-2.32
Structure conservation index	0.56
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.20
SVM RNA-class probability	0.590704
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chrX 395738 90 + 22422827
---------UUCAGUUGACACCUGACUGCCAUGCUAAAUGGACAAUUCCGGUCAGAACUGACCUGCAUAUCAAUCAGCCCAUAACAG-AGUGAAAGAGAA---------
---------(((.((((....((((.((..((((.....(((....)))(((((....))))).))))..)).))))....)))).)-))..........--------- ( -20.50, z-score =  -1.28, R)
>droSim1.chrX 289643 90 + 17042790
---------CUCUGUUGACACCUGACUGCCAUGCUAAAUGGUCAAUUCCGGUCAGAACUGACCUGCAUAUCAAUCAGCCCAUAACAG-AGUGAAAGAGAA---------
---------((((((((....((((.((..((((.....((......))(((((....))))).))))..)).))))....))))))-))..........--------- ( -26.90, z-score =  -3.00, R)
>droSec1.super_10 251545 90 + 3036183
---------CUCUGUUGACACCUGACUGCCAUACUAAAUGGUCAAUUCCGGUCAGAACUGACCUGCAUAUCAAUCAGCCCAUAACAG-AGUGAAAGAGAA---------
---------((((((((....((((..(((((.....))))).......(((((....)))))..........))))....))))))-))..........--------- ( -23.50, z-score =  -2.25, R)
>droYak2.chrX 321954 90 + 21770863
---------CUCGGCUGACACCUGACUGCCAUGCUAAAUGGCCAAUUCCGGCCAGAACUGACCUGCAUAUCAAUCAGCCCAUAACAG-AGUGAAAGAGAA---------
---------(((((((((....(((.(((....(....(((((......))))).....)....)))..))).))))))(((.....-.)))...)))..--------- ( -23.80, z-score =  -1.84, R)
>droEre2.scaffold_4644 346780 90 + 2521924
---------CUCGGUUGACACCUGACUGCCAUGCUAAAUGGUCAAUUCCGGCCAGAACUGACCUGCAUAUCAAUCAGGCCAUAACAG-AGUGAAAGAGAA---------
---------(((.((((...(((((.((..((((.....(((((.(((......))).))))).))))..)).)))))...)))).)-))..........--------- ( -25.70, z-score =  -1.93, R)
>droAna3.scaffold_12929 809579 109 - 3277472
UUAAAGCAUUACAGGUGACACCUGACUGCCAUGCUAAAUGGCCAAUUCCGGUCAGGAGUGACCUGCAUGCCAAUCAGCCCAUGACGACAGUCCAUGAAAUUAAAGAGAA
.....((((..(((((.((.((((((((((((.....))))).......))))))).)).))))).)))).........((((((....)).))))............. ( -35.11, z-score =  -3.59, R)
>consensus
_________CUCAGUUGACACCUGACUGCCAUGCUAAAUGGUCAAUUCCGGUCAGAACUGACCUGCAUAUCAAUCAGCCCAUAACAG_AGUGAAAGAGAA_________
.............((((....((((.((..((((.....((......))(((((....))))).))))..)).))))....))))........................ (-14.56 = -15.25 +   0.69)

alignment

secondary structure

dotplot

Window 1

Location	395,738 – 395,828
Length	90
Sequences	6
Columns	109
Reading direction	reverse
Mean pairwise identity	84.91
Shannon entropy	0.25902
G+C content	0.46502
Mean single sequence MFE	-33.33
Consensus MFE	-26.19
Energy contribution	-26.25
Covariance contribution	0.06
Combinations/Pair	1.14
Mean z-score	-2.81
Structure conservation index	0.79
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	2.46
SVM RNA-class probability	0.991090
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chrX 395738 90 - 22422827
---------UUCUCUUUCACU-CUGUUAUGGGCUGAUUGAUAUGCAGGUCAGUUCUGACCGGAAUUGUCCAUUUAGCAUGGCAGUCAGGUGUCAACUGAA---------
---------......((((((-(......)))(((((((.(((((.(((((....)))))(((....))).....))))).)))))))........))))--------- ( -27.60, z-score =  -1.59, R)
>droSim1.chrX 289643 90 - 17042790
---------UUCUCUUUCACU-CUGUUAUGGGCUGAUUGAUAUGCAGGUCAGUUCUGACCGGAAUUGACCAUUUAGCAUGGCAGUCAGGUGUCAACAGAG---------
---------..........((-(((((...(.(((((((.(((((.((((((((((....)))))))))).....))))).))))))).)...)))))))--------- ( -36.10, z-score =  -4.18, R)
>droSec1.super_10 251545 90 - 3036183
---------UUCUCUUUCACU-CUGUUAUGGGCUGAUUGAUAUGCAGGUCAGUUCUGACCGGAAUUGACCAUUUAGUAUGGCAGUCAGGUGUCAACAGAG---------
---------..........((-(((((...(.(((((((.(((((.((((((((((....)))))))))).....))))).))))))).)...)))))))--------- ( -34.10, z-score =  -3.72, R)
>droYak2.chrX 321954 90 - 21770863
---------UUCUCUUUCACU-CUGUUAUGGGCUGAUUGAUAUGCAGGUCAGUUCUGGCCGGAAUUGGCCAUUUAGCAUGGCAGUCAGGUGUCAGCCGAG---------
---------..........((-(.(((...(.(((((((.(((((.((((((((((....)))))))))).....))))).))))))).)...))).)))--------- ( -30.90, z-score =  -1.64, R)
>droEre2.scaffold_4644 346780 90 - 2521924
---------UUCUCUUUCACU-CUGUUAUGGCCUGAUUGAUAUGCAGGUCAGUUCUGGCCGGAAUUGACCAUUUAGCAUGGCAGUCAGGUGUCAACCGAG---------
---------..........((-(.(((...(((((((((.(((((.((((((((((....)))))))))).....))))).)))))))))...))).)))--------- ( -36.30, z-score =  -4.15, R)
>droAna3.scaffold_12929 809579 109 + 3277472
UUCUCUUUAAUUUCAUGGACUGUCGUCAUGGGCUGAUUGGCAUGCAGGUCACUCCUGACCGGAAUUGGCCAUUUAGCAUGGCAGUCAGGUGUCACCUGUAAUGCUUUAA
...........((((((.((....))))))))......(((((((((((.((.((((((........(((((.....))))).)))))).)).)))))).))))).... ( -35.00, z-score =  -1.57, R)
>consensus
_________UUCUCUUUCACU_CUGUUAUGGGCUGAUUGAUAUGCAGGUCAGUUCUGACCGGAAUUGACCAUUUAGCAUGGCAGUCAGGUGUCAACAGAG_________
................................(((((((.(((((.((((((((((....)))))))))).....))))).)))))))..................... (-26.19 = -26.25 +   0.06)

alignment

secondary structure

dotplot

Window 2

Location	395,738 – 395,834
Length	96
Sequences	6
Columns	115
Reading direction	forward
Mean pairwise identity	86.45
Shannon entropy	0.23420
G+C content	0.44863
Mean single sequence MFE	-26.28
Consensus MFE	-14.88
Energy contribution	-15.63
Covariance contribution	0.75
Combinations/Pair	1.08
Mean z-score	-2.31
Structure conservation index	0.57
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.02
SVM RNA-class probability	0.505094
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chrX 395738 96 + 22422827
---------UUCAGUUGACACCUGACUGCCAUGCUAAAUGGACAAUUCCGGUCAGAACUGACCUGCAUAUCAAUCAGCCCAUAACAG----------AGUGAAAGAGAAACUUUU
---------....((((....((((.((..((((.....(((....)))(((((....))))).))))..)).))))....))))((----------(((.........))))). ( -21.50, z-score =  -1.46, R)
>droSim1.chrX 289643 96 + 17042790
---------CUCUGUUGACACCUGACUGCCAUGCUAAAUGGUCAAUUCCGGUCAGAACUGACCUGCAUAUCAAUCAGCCCAUAACAG----------AGUGAAAGAGAAACUUUU
---------((((((((....((((.((..((((.....((......))(((((....))))).))))..)).))))....))))))----------)).(((((.....))))) ( -27.30, z-score =  -3.03, R)
>droSec1.super_10 251545 96 + 3036183
---------CUCUGUUGACACCUGACUGCCAUACUAAAUGGUCAAUUCCGGUCAGAACUGACCUGCAUAUCAAUCAGCCCAUAACAG----------AGUGAAAGAGAAACUUUU
---------((((((((....((((..(((((.....))))).......(((((....)))))..........))))....))))))----------)).(((((.....))))) ( -23.90, z-score =  -2.27, R)
>droYak2.chrX 321954 96 + 21770863
---------CUCGGCUGACACCUGACUGCCAUGCUAAAUGGCCAAUUCCGGCCAGAACUGACCUGCAUAUCAAUCAGCCCAUAACAG----------AGUGAAAGAGAAACUUUC
---------(((((((((....(((.(((....(....(((((......))))).....)....)))..))).))))))(((.....----------.)))...)))........ ( -23.80, z-score =  -1.77, R)
>droEre2.scaffold_4644 346780 96 + 2521924
---------CUCGGUUGACACCUGACUGCCAUGCUAAAUGGUCAAUUCCGGCCAGAACUGACCUGCAUAUCAAUCAGGCCAUAACAG----------AGUGAAAGAGAAACUUUU
---------(((.((((...(((((.((..((((.....(((((.(((......))).))))).))))..)).)))))...)))).)----------)).(((((.....))))) ( -26.10, z-score =  -1.96, R)
>droAna3.scaffold_12929 809579 115 - 3277472
UUAAAGCAUUACAGGUGACACCUGACUGCCAUGCUAAAUGGCCAAUUCCGGUCAGGAGUGACCUGCAUGCCAAUCAGCCCAUGACGACAGUCCAUGAAAUUAAAGAGAAACUUUU
.....((((..(((((.((.((((((((((((.....))))).......))))))).)).))))).)))).........((((((....)).))))................... ( -35.11, z-score =  -3.36, R)
>consensus
_________CUCAGUUGACACCUGACUGCCAUGCUAAAUGGUCAAUUCCGGUCAGAACUGACCUGCAUAUCAAUCAGCCCAUAACAG__________AGUGAAAGAGAAACUUUU
.............((((....((((.((..((((.....((......))(((((....))))).))))..)).))))....))))...............(((((.....))))) (-14.88 = -15.63 +   0.75)

alignment

secondary structure

dotplot

Window 3

Location	395,738 – 395,834
Length	96
Sequences	6
Columns	115
Reading direction	reverse
Mean pairwise identity	86.45
Shannon entropy	0.23420
G+C content	0.44863
Mean single sequence MFE	-34.15
Consensus MFE	-26.19
Energy contribution	-26.25
Covariance contribution	0.06
Combinations/Pair	1.14
Mean z-score	-2.81
Structure conservation index	0.77
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	2.22
SVM RNA-class probability	0.985952
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chrX 395738 96 - 22422827
AAAAGUUUCUCUUUCACU----------CUGUUAUGGGCUGAUUGAUAUGCAGGUCAGUUCUGACCGGAAUUGUCCAUUUAGCAUGGCAGUCAGGUGUCAACUGAA---------
...((((.........((----------(......)))(((((((.(((((.(((((....)))))(((....))).....))))).))))))).....))))...--------- ( -28.00, z-score =  -1.52, R)
>droSim1.chrX 289643 96 - 17042790
AAAAGUUUCUCUUUCACU----------CUGUUAUGGGCUGAUUGAUAUGCAGGUCAGUUCUGACCGGAAUUGACCAUUUAGCAUGGCAGUCAGGUGUCAACAGAG---------
................((----------(((((...(.(((((((.(((((.((((((((((....)))))))))).....))))).))))))).)...)))))))--------- ( -36.10, z-score =  -3.94, R)
>droSec1.super_10 251545 96 - 3036183
AAAAGUUUCUCUUUCACU----------CUGUUAUGGGCUGAUUGAUAUGCAGGUCAGUUCUGACCGGAAUUGACCAUUUAGUAUGGCAGUCAGGUGUCAACAGAG---------
................((----------(((((...(.(((((((.(((((.((((((((((....)))))))))).....))))).))))))).)...)))))))--------- ( -34.10, z-score =  -3.54, R)
>droYak2.chrX 321954 96 - 21770863
GAAAGUUUCUCUUUCACU----------CUGUUAUGGGCUGAUUGAUAUGCAGGUCAGUUCUGGCCGGAAUUGGCCAUUUAGCAUGGCAGUCAGGUGUCAGCCGAG---------
(((((.....))))).((----------(.(((...(.(((((((.(((((.((((((((((....)))))))))).....))))).))))))).)...))).)))--------- ( -34.80, z-score =  -2.49, R)
>droEre2.scaffold_4644 346780 96 - 2521924
AAAAGUUUCUCUUUCACU----------CUGUUAUGGCCUGAUUGAUAUGCAGGUCAGUUCUGGCCGGAAUUGACCAUUUAGCAUGGCAGUCAGGUGUCAACCGAG---------
................((----------(.(((...(((((((((.(((((.((((((((((....)))))))))).....))))).)))))))))...))).)))--------- ( -36.30, z-score =  -3.89, R)
>droAna3.scaffold_12929 809579 115 + 3277472
AAAAGUUUCUCUUUAAUUUCAUGGACUGUCGUCAUGGGCUGAUUGGCAUGCAGGUCACUCCUGACCGGAAUUGGCCAUUUAGCAUGGCAGUCAGGUGUCACCUGUAAUGCUUUAA
.(((((.................(((((((((.....(((((.((((...(.(((((....))))).).....)))).))))))))))))))(((.....))).....))))).. ( -35.60, z-score =  -1.50, R)
>consensus
AAAAGUUUCUCUUUCACU__________CUGUUAUGGGCUGAUUGAUAUGCAGGUCAGUUCUGACCGGAAUUGACCAUUUAGCAUGGCAGUCAGGUGUCAACAGAG_________
......................................(((((((.(((((.((((((((((....)))))))))).....))))).)))))))..................... (-26.19 = -26.25 +   0.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:02:50 2011