Locus 8129

Sequence ID dm3.chr3L
Location 20,484,761 – 20,484,818
Length 57
Max. P 0.912846
window11184 window11185

overview

Window 4

Location 20,484,761 – 20,484,818
Length 57
Sequences 6
Columns 60
Reading direction forward
Mean pairwise identity 70.27
Shannon entropy 0.58165
G+C content 0.44664
Mean single sequence MFE -13.85
Consensus MFE -6.79
Energy contribution -7.54
Covariance contribution 0.75
Combinations/Pair 1.25
Mean z-score -1.40
Structure conservation index 0.49
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.01
SVM RNA-class probability 0.873591
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 20484761 57 + 24543557
AGAUAGAGAUAGUUGUCUAC--CGACCCUAUCGCUAUCUCACCCCAGGUGAUUAAGUGG-
.(((((.(((((..(((...--.))).))))).)))))(((((...)))))........- ( -18.00, z-score =  -3.00, R)
>dp4.chrXR_group8 7892956 52 + 9212921
------AGCUCUAUAUCUAUAUAUAUA-UAUCAUUCCUUUAUCUUUUCUGAUAAAGUGG-
------.....................-........(((((((......)))))))...- (  -6.20, z-score =  -1.09, R)
>droAna3.scaffold_13337 10843533 60 + 23293914
CGACAGAGAUAGCUGUCUGCGGUUGGGCUAACGCUAUCUCAUUCGGUGUGAUUAAGUACG
(((..((((((((.((..((......))..))))))))))..)))............... ( -18.30, z-score =  -1.58, R)
>droYak2.chr3L 4123117 57 - 24197627
AGAUAGAGAUAGCUGUCUAC--GUCCCCUAUCGCUAUCUCACCCCAGGCGAUCAAGUGG-
((((((......))))))..--...((((((((((...........))))))..)).))- ( -11.80, z-score =  -0.14, R)
>droSec1.super_11 375528 57 + 2888827
AGAUAGAGAUAGCUGUCUAC--CUACCCUAUCGCUAUCUCACCACAGGUGAUUAAGUGG-
.(((((.(((((..((....--..)).))))).)))))(((((...)))))........- ( -14.40, z-score =  -1.24, R)
>droSim1.chr3L 19834366 57 + 22553184
AGAUAGAGAUAGCUGUCUAC--CUACCCUAUCGCUAUCUCACCCCAGGUGAUUAAGUGG-
.(((((.(((((..((....--..)).))))).)))))(((((...)))))........- ( -14.40, z-score =  -1.36, R)
>consensus
AGAUAGAGAUAGCUGUCUAC__CUACCCUAUCGCUAUCUCACCCCAGGUGAUUAAGUGG_
.....((((((((...................)))))))).................... ( -6.79 =  -7.54 +   0.75)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 20,484,761 – 20,484,818
Length 57
Sequences 6
Columns 60
Reading direction reverse
Mean pairwise identity 70.27
Shannon entropy 0.58165
G+C content 0.44664
Mean single sequence MFE -15.70
Consensus MFE -6.79
Energy contribution -8.54
Covariance contribution 1.75
Combinations/Pair 1.14
Mean z-score -1.80
Structure conservation index 0.43
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.23
SVM RNA-class probability 0.912846
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 20484761 57 - 24543557
-CCACUUAAUCACCUGGGGUGAGAUAGCGAUAGGGUCG--GUAGACAACUAUCUCUAUCU
-........(((((...)))))(((((.(((((.(((.--...)))..))))).))))). ( -19.60, z-score =  -2.55, R)
>dp4.chrXR_group8 7892956 52 - 9212921
-CCACUUUAUCAGAAAAGAUAAAGGAAUGAUA-UAUAUAUAUAGAUAUAGAGCU------
-...(((((((......)))))))....(...-(((((......)))))...).------ (  -7.30, z-score =  -1.76, R)
>droAna3.scaffold_13337 10843533 60 - 23293914
CGUACUUAAUCACACCGAAUGAGAUAGCGUUAGCCCAACCGCAGACAGCUAUCUCUGUCG
...............(((..(((((((((((.((......)).))).))))))))..))) ( -18.00, z-score =  -3.90, R)
>droYak2.chr3L 4123117 57 + 24197627
-CCACUUGAUCGCCUGGGGUGAGAUAGCGAUAGGGGAC--GUAGACAGCUAUCUCUAUCU
-...............((((((((((((..(((....)--.))....)))))))).)))) ( -15.90, z-score =  -0.31, R)
>droSec1.super_11 375528 57 - 2888827
-CCACUUAAUCACCUGUGGUGAGAUAGCGAUAGGGUAG--GUAGACAGCUAUCUCUAUCU
-........(((((...)))))(((((.(((((.((..--....))..))))).))))). ( -16.70, z-score =  -1.23, R)
>droSim1.chr3L 19834366 57 - 22553184
-CCACUUAAUCACCUGGGGUGAGAUAGCGAUAGGGUAG--GUAGACAGCUAUCUCUAUCU
-........(((((...)))))(((((.(((((.((..--....))..))))).))))). ( -16.70, z-score =  -1.04, R)
>consensus
_CCACUUAAUCACCUGGGGUGAGAUAGCGAUAGGGUAG__GUAGACAGCUAUCUCUAUCU
.........((((.....))))(((((.(((((...............))))).))))). ( -6.79 =  -8.54 +   1.75)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:39:59 2011