Locus 8439

Sequence ID dm3.chr3L
Location 22,751,922 – 22,751,991
Length 69
Max. P 0.791449
window11596 window11597

overview

Window 6

Location 22,751,922 – 22,751,991
Length 69
Sequences 5
Columns 70
Reading direction forward
Mean pairwise identity 67.16
Shannon entropy 0.55757
G+C content 0.42462
Mean single sequence MFE -14.14
Consensus MFE -5.09
Energy contribution -5.29
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -1.82
Structure conservation index 0.36
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.28
SVM RNA-class probability 0.626059
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 22751922 69 + 24543557
UCCCAGUUCA-GGUGCUUAACCCCUGACCAUUUUAGGACACAUAUAUUGGUCAAGAACAAAGUCGGCUCG
.....((((.-(((.....)))..((((((...((.......))...)))))).))))............ ( -14.00, z-score =  -0.65, R)
>droSim1.chr3L 22040030 57 + 22553184
UCCCAAUUCA-GGAGCUUAACC--UGACCA----------CAUAUAAUGGUCAAUAACAAAGUCAGCUCG
..........-.(((((.....--((((((----------.......))))))...........))))). ( -10.59, z-score =  -2.17, R)
>droSec1.super_11 2672551 59 + 2888827
UCCCAAUUCA-GGGGCUUAACCCCUGACCA----------CAUAUAAUGGUCAAUAACAAUGUCGGCUCG
..((.....(-((((.....)))))(((((----------.......)))))............)).... ( -15.30, z-score =  -2.09, R)
>droYak2.chr3L 23243090 65 + 24197627
UACUAAUUAAUGGGGCUUAACCUCUGACCAUUUUAGAACAAUCAUAACGGUCAAUAGUGUAGUUG-----
(((((......((((.....))))(((((.((...((....))..)).))))).)))))......----- ( -11.30, z-score =  -0.65, R)
>droEre2.scaffold_4784 22403994 61 + 25762168
CUCCAAUUCA-GGAGCUUAACCCUUGACCAUUUUAGGACAAUCAUAAUGGUCAACAGGGAAA--------
((((......-)))).....((((((((((((....(.....)..))))))))..))))...-------- ( -19.50, z-score =  -3.52, R)
>consensus
UCCCAAUUCA_GGAGCUUAACCCCUGACCAUUUUAG_ACACAUAUAAUGGUCAAUAACAAAGUCGGCUCG
........................((((((.................))))))................. ( -5.09 =  -5.29 +   0.20)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 22,751,922 – 22,751,991
Length 69
Sequences 5
Columns 70
Reading direction reverse
Mean pairwise identity 67.16
Shannon entropy 0.55757
G+C content 0.42462
Mean single sequence MFE -17.03
Consensus MFE -6.61
Energy contribution -6.53
Covariance contribution -0.08
Combinations/Pair 1.33
Mean z-score -1.86
Structure conservation index 0.39
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.70
SVM RNA-class probability 0.791449
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 22751922 69 - 24543557
CGAGCCGACUUUGUUCUUGACCAAUAUAUGUGUCCUAAAAUGGUCAGGGGUUAAGCACC-UGAACUGGGA
......(.(((.(..((((((((.................))))))))..).)))).((-(.....))). ( -16.13, z-score =  -0.08, R)
>droSim1.chr3L 22040030 57 - 22553184
CGAGCUGACUUUGUUAUUGACCAUUAUAUG----------UGGUCA--GGUUAAGCUCC-UGAAUUGGGA
.(((((((((.......(((((((.....)----------))))))--)))).))))).-.......... ( -17.01, z-score =  -2.50, R)
>droSec1.super_11 2672551 59 - 2888827
CGAGCCGACAUUGUUAUUGACCAUUAUAUG----------UGGUCAGGGGUUAAGCCCC-UGAAUUGGGA
....((((..........((((((.....)----------)))))(((((.....))))-)...)))).. ( -20.60, z-score =  -2.52, R)
>droYak2.chr3L 23243090 65 - 24197627
-----CAACUACACUAUUGACCGUUAUGAUUGUUCUAAAAUGGUCAGAGGUUAAGCCCCAUUAAUUAGUA
-----.......(((((((((((((..((....))...))))))))).((.....))........)))). ( -13.20, z-score =  -1.54, R)
>droEre2.scaffold_4784 22403994 61 - 25762168
--------UUUCCCUGUUGACCAUUAUGAUUGUCCUAAAAUGGUCAAGGGUUAAGCUCC-UGAAUUGGAG
--------...((((..((((((((.((.......)).)))))))))))).....((((-......)))) ( -18.20, z-score =  -2.66, R)
>consensus
CGAGCCGACUUUGUUAUUGACCAUUAUAUGUGU_CUAAAAUGGUCAGGGGUUAAGCCCC_UGAAUUGGGA
........(((..((.(((((((.................))))))).))..)))............... ( -6.61 =  -6.53 +  -0.08)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:45:42 2011