Locus 7311

Sequence ID dm3.chr3L
Location 13,792,997 – 13,793,065
Length 68
Max. P 0.997915
window10062 window10063

overview

Window 2

Location 13,792,997 – 13,793,065
Length 68
Sequences 7
Columns 72
Reading direction forward
Mean pairwise identity 75.40
Shannon entropy 0.44939
G+C content 0.53070
Mean single sequence MFE -18.20
Consensus MFE -17.79
Energy contribution -17.29
Covariance contribution -0.51
Combinations/Pair 1.21
Mean z-score -4.92
Structure conservation index 0.98
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.10
SVM RNA-class probability 0.997431
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 13792997 68 + 24543557
GAAUGGCUGCGUCGUCUGUUUUAUAAUUUUCACAGACGUCGCCCCCAUCACAAGCCCCCCUCCCCACC----
((.(((..(((.(((((((............))))))).)))..)))))...................---- ( -18.90, z-score =  -5.42, R)
>droEre2.scaffold_4784 13799886 70 + 25762168
GAAUGGCUGCGUCGUCUGUUUUAUAAUUUUCACAGACGUCGCCCCCAUCACAAGUCCCCCCACUUUCCCC--
((.(((..(((.(((((((............))))))).)))..))))).....................-- ( -18.90, z-score =  -5.62, R)
>droYak2.chr3L 13893283 72 + 24197627
GAAUGGCUGCGUCGUCUGUUUUAUAAUUUUCACAGACGUCGCCCCCAUCACAAGUCCACCCCCCUCCCCCCA
((.(((..(((.(((((((............))))))).)))..)))))....................... ( -18.90, z-score =  -5.75, R)
>droSim1.chr3L 13179058 62 + 22553184
GAAUGGCUGCGUCGUCUGUUUUAUAAUUUUCACAGACGUCGCCCCCAUCACAAGACCCCCCC----------
((.(((..(((.(((((((............))))))).)))..))))).............---------- ( -18.90, z-score =  -5.15, R)
>droSec1.super_0 5954675 63 + 21120651
GAAUGGCUGCGUCGUCUGUUUUAUAAUUUUCACAGACGUCGCCCCCACCACAAGACCCCCCCU---------
...(((..(((.(((((((............))))))).)))..)))................--------- ( -17.80, z-score =  -4.74, R)
>dp4.chrXR_group8 2643976 62 - 9212921
CAGUGACUGCGUCGUCUGUUU---AAUUUUCACAGACAUCGCCUUCGCUUUCUCCCACACGCACA-------
.(((((..(((..((((((..---.......))))))..)))..)))))................------- ( -17.00, z-score =  -3.87, R)
>droPer1.super_36 714704 62 + 818889
CAGUGACUGCGUCGUCUGUUU---AAUUUUCACAGACAUCGCCUUCGCUUUCUCCCACACGCACA-------
.(((((..(((..((((((..---.......))))))..)))..)))))................------- ( -17.00, z-score =  -3.87, R)
>consensus
GAAUGGCUGCGUCGUCUGUUUUAUAAUUUUCACAGACGUCGCCCCCAUCACAAGCCCCCCCCCC________
..((((..(((.(((((((............))))))).)))..))))........................ (-17.79 = -17.29 +  -0.51)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 13,792,997 – 13,793,065
Length 68
Sequences 7
Columns 72
Reading direction reverse
Mean pairwise identity 75.40
Shannon entropy 0.44939
G+C content 0.53070
Mean single sequence MFE -21.01
Consensus MFE -20.55
Energy contribution -19.57
Covariance contribution -0.98
Combinations/Pair 1.33
Mean z-score -2.97
Structure conservation index 0.98
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.21
SVM RNA-class probability 0.997915
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 13792997 68 - 24543557
----GGUGGGGAGGGGGGCUUGUGAUGGGGGCGACGUCUGUGAAAAUUAUAAAACAGACGACGCAGCCAUUC
----.(..((........))..)(((((..(((.(((((((............))))))).)))..))))). ( -21.70, z-score =  -3.05, R)
>droEre2.scaffold_4784 13799886 70 - 25762168
--GGGGAAAGUGGGGGGACUUGUGAUGGGGGCGACGUCUGUGAAAAUUAUAAAACAGACGACGCAGCCAUUC
--.......(..((....))..)(((((..(((.(((((((............))))))).)))..))))). ( -25.60, z-score =  -4.95, R)
>droYak2.chr3L 13893283 72 - 24197627
UGGGGGGAGGGGGGUGGACUUGUGAUGGGGGCGACGUCUGUGAAAAUUAUAAAACAGACGACGCAGCCAUUC
.......(.(((......))).)(((((..(((.(((((((............))))))).)))..))))). ( -21.30, z-score =  -2.87, R)
>droSim1.chr3L 13179058 62 - 22553184
----------GGGGGGGUCUUGUGAUGGGGGCGACGUCUGUGAAAAUUAUAAAACAGACGACGCAGCCAUUC
----------.............(((((..(((.(((((((............))))))).)))..))))). ( -20.70, z-score =  -3.02, R)
>droSec1.super_0 5954675 63 - 21120651
---------AGGGGGGGUCUUGUGGUGGGGGCGACGUCUGUGAAAAUUAUAAAACAGACGACGCAGCCAUUC
---------............(((((....(((.(((((((............))))))).))).))))).. ( -20.40, z-score =  -2.63, R)
>dp4.chrXR_group8 2643976 62 + 9212921
-------UGUGCGUGUGGGAGAAAGCGAAGGCGAUGUCUGUGAAAAUU---AAACAGACGACGCAGUCACUG
-------.(((..((((.......((....))..(((((((.......---..))))))).))))..))).. ( -18.70, z-score =  -2.14, R)
>droPer1.super_36 714704 62 - 818889
-------UGUGCGUGUGGGAGAAAGCGAAGGCGAUGUCUGUGAAAAUU---AAACAGACGACGCAGUCACUG
-------.(((..((((.......((....))..(((((((.......---..))))))).))))..))).. ( -18.70, z-score =  -2.14, R)
>consensus
________GGGGGGGGGGCUUGUGAUGGGGGCGACGUCUGUGAAAAUUAUAAAACAGACGACGCAGCCAUUC
.......................(((((..(((.(((((((............))))))).)))..))))). (-20.55 = -19.57 +  -0.98)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:24:28 2011