Locus 10546

Sequence ID dm3.chr3R
Location 14,616,182 – 14,616,327
Length 145
Max. P 0.985634
window14500 window14501

overview

Window 0

Location 14,616,182 – 14,616,295
Length 113
Sequences 5
Columns 119
Reading direction forward
Mean pairwise identity 88.58
Shannon entropy 0.19210
G+C content 0.34615
Mean single sequence MFE -21.56
Consensus MFE -20.18
Energy contribution -20.18
Covariance contribution -0.00
Combinations/Pair 1.09
Mean z-score -1.49
Structure conservation index 0.94
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.16
SVM RNA-class probability 0.901948
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 14616182 113 + 27905053
UUUCAUUCAUGACUUCUGAUGUCGGAUGUCAACAGGAAUAUACAAAAUUAACAACGGCAACAAAAAAA------AAAAAAUGUCGAGUAUCGGCAUUAAAUUGCCAUCAACAAUGCUGU
....((((.((((.((((....)))).))))....))))..............(((((..........------....(((((((.....)))))))..((((.......))))))))) ( -23.30, z-score =  -2.06, R)
>droSim1.chr3R 20657735 119 - 27517382
UUUCAUUCAUGACUUCUGAUGUCGGAUGUCAACAGGAAUAUACAAAAUUAACAACGGCACCAAAAAAAAAAAAAAAAAUAUGUCGAGUAUCGGCAUUAAAUUGCCAUCAACAAUGCUGU
....((((.((((.((((....)))).))))....))))..............((((((..................((((.....)))).((((......))))........)))))) ( -22.10, z-score =  -1.62, R)
>droSec1.super_5 583103 109 - 5866729
UUUCAUUCAUGACUUCUGAUGUCGGAUGUCAACAGGAAUAUACAAAAUUAACAAUGGCAACAAA----------AAAAUAUGUCGAGUAUCGGCAUUAAAUUGCCAUCAACAAUGCUGU
....((((.((((.((((....)))).))))....))))..(((..(((....(((((((....----------.....((((((.....))))))....)))))))....)))..))) ( -23.72, z-score =  -1.87, R)
>droYak2.chr3R 3273774 105 + 28832112
UUUCAUUCAUGACUUCUGAUGUCGCAUGUCAACAGGAAUAUACAAAAUUAACAACAGCAACAAA-----------AAAC---UCGAGUAUCGGCAUUAAAUCGCCAUCAACAAUGCUGU
.............(((((.((.(....).)).)))))................((((((.....-----------..((---....))...(((........)))........)))))) ( -15.70, z-score =  -0.32, R)
>droEre2.scaffold_4770 10728017 104 - 17746568
UUUCAUUCAUGACUUCUGAUGUCGGAUGUCAACAGGAAUAUAUAUAAA-ACGAACAGCAGCAAA-----------AAAG---UCGAGUAUCGGCAUUAAAUUGCCAUCAACAAUGCUGU
....((((.((((.((((....)))).))))....)))).........-.......((((((..-----------....---..(.....)((((......))))........)))))) ( -23.00, z-score =  -1.60, R)
>consensus
UUUCAUUCAUGACUUCUGAUGUCGGAUGUCAACAGGAAUAUACAAAAUUAACAACGGCAACAAA__________AAAAUAUGUCGAGUAUCGGCAUUAAAUUGCCAUCAACAAUGCUGU
....((((.((((.((((....)))).))))....))))..............((((((.........................(.....)((((......))))........)))))) (-20.18 = -20.18 +  -0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 14,616,222 – 14,616,327
Length 105
Sequences 5
Columns 113
Reading direction forward
Mean pairwise identity 86.59
Shannon entropy 0.22212
G+C content 0.33619
Mean single sequence MFE -18.89
Consensus MFE -17.46
Energy contribution -17.66
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -2.25
Structure conservation index 0.92
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.21
SVM RNA-class probability 0.985634
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 14616222 105 + 27905053
--UACAAAAUUAACAACGGCAACAAAAAAAAAAAAA------UGUCGAGUAUCGGCAUUAAAUUGCCAUCAACAAUGCUGUCGUCUCGAUAAAGUAUUCAUGAAAUAUGCUCU
--...............((((...............------))))((((((.((((......)))).(((..((((((((((...))))..))))))..)))...)))))). ( -19.76, z-score =  -2.66, R)
>droSim1.chr3R 20657775 111 - 27517382
--UACAAAAUUAACAACGGCACCAAAAAAAAAAAAAAAAAUAUGUCGAGUAUCGGCAUUAAAUUGCCAUCAACAAUGCUGUCGUCUCGAUAAAGUAUUCAUGAAAUAUGCUCU
--...............((((.....................))))((((((.((((......)))).(((..((((((((((...))))..))))))..)))...)))))). ( -19.20, z-score =  -2.54, R)
>droSec1.super_5 583143 101 - 5866729
--UACAAAAUUAACAAUGGCAACAAAAAAAUA----------UGUCGAGUAUCGGCAUUAAAUUGCCAUCAACAAUGCUGUCGUCUCGAUAAAGUAUUCAUGAAAUAUGCUCU
--..............((....))........----------....((((((.((((......)))).(((..((((((((((...))))..))))))..)))...)))))). ( -20.30, z-score =  -2.46, R)
>droYak2.chr3R 3273814 97 + 28832112
--UACAAAAUUAACAACAGCAACAAAAAAC--------------UCGAGUAUCGGCAUUAAAUCGCCAUCAACAAUGCUGUCGUCUCGAUAAAGUAUUCAUGAAAUAUGCUCU
--............................--------------..((((((.(((........))).(((..((((((((((...))))..))))))..)))...)))))). ( -16.40, z-score =  -2.13, R)
>droEre2.scaffold_4770 10728057 96 - 17746568
UAUAUAAAACGAACAGCAGCAAAAAAG-----------------UCGAGUAUCGGCAUUAAAUUGCCAUCAACAAUGCUGUCGUCUCGAUCAAGUAUUCAUGAAAUAUGCUCU
.........(((((.((((((......-----------------..(.....)((((......))))........)))))).)).)))....(((((.........))))).. ( -18.80, z-score =  -1.49, R)
>consensus
__UACAAAAUUAACAACGGCAACAAAAAAA_A__________UGUCGAGUAUCGGCAUUAAAUUGCCAUCAACAAUGCUGUCGUCUCGAUAAAGUAUUCAUGAAAUAUGCUCU
..............................................((((((.((((......)))).(((..((((((((((...))))..))))))..)))...)))))). (-17.46 = -17.66 +   0.20)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:25:59 2011