Locus 3934

Sequence ID dm3.chr2R
Location 9,178,943 – 9,178,999
Length 56
Max. P 0.873424
window5388 window5389

overview

Window 8

Location 9,178,943 – 9,178,999
Length 56
Sequences 5
Columns 56
Reading direction forward
Mean pairwise identity 94.16
Shannon entropy 0.10313
G+C content 0.59780
Mean single sequence MFE -22.16
Consensus MFE -18.42
Energy contribution -18.62
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -1.82
Structure conservation index 0.83
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.22
SVM RNA-class probability 0.601222
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 9178943 56 + 21146708
AAGCUUCCGCCAGCUGGUUCUGUGGCUCUGUGGUGACGUGAACUGUCACCGGCAGA
..(((...(((....))).....)))((((((((((((....).)))))).))))) ( -19.80, z-score =  -0.83, R)
>droSim1.chr2R 7637391 54 + 19596830
AAGCUUCCGCCAGCUGGUU--GUGGCUCUGUGGUGACGUGAACUGUCACCGGCAGA
..(((.(.(((....))).--).)))((((((((((((....).)))))).))))) ( -21.60, z-score =  -1.66, R)
>droSec1.super_1 6701666 54 + 14215200
AAGCUUCCGCCAGCUGGUU--GUGGCUCUGUGGUGACGUGAACUGUCACCGGCAGA
..(((.(.(((....))).--).)))((((((((((((....).)))))).))))) ( -21.60, z-score =  -1.66, R)
>droYak2.chr2R 13358223 54 - 21139217
AAGCUUCCGCCAGCUGGUG--GUGGCUCUGUGGUGACGUGAACUGUCACCGGCAGC
.((((.(((((....))))--).))))(((((((((((....).)))))).)))). ( -26.50, z-score =  -2.88, R)
>droEre2.scaffold_4845 5953565 53 - 22589142
AAGCU-CCACCAGCUGGAU--GUGGCUCUGUGGUGACGUGAACUGUCACCGCCAGA
..((.-.((((....)).)--)..))((((((((((((....).))))))).)))) ( -21.30, z-score =  -2.06, R)
>consensus
AAGCUUCCGCCAGCUGGUU__GUGGCUCUGUGGUGACGUGAACUGUCACCGGCAGA
.((((...(((....))).....))))(((((((((((.....)))))))).))). (-18.42 = -18.62 +   0.20)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 9,178,943 – 9,178,999
Length 56
Sequences 5
Columns 56
Reading direction reverse
Mean pairwise identity 94.16
Shannon entropy 0.10313
G+C content 0.59780
Mean single sequence MFE -20.88
Consensus MFE -17.00
Energy contribution -17.44
Covariance contribution 0.44
Combinations/Pair 1.07
Mean z-score -2.38
Structure conservation index 0.81
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.01
SVM RNA-class probability 0.873424
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 9178943 56 - 21146708
UCUGCCGGUGACAGUUCACGUCACCACAGAGCCACAGAACCAGCUGGCGGAAGCUU
((((((((((((.......))))))....(((..........)))))))))..... ( -20.40, z-score =  -2.22, R)
>droSim1.chr2R 7637391 54 - 19596830
UCUGCCGGUGACAGUUCACGUCACCACAGAGCCAC--AACCAGCUGGCGGAAGCUU
((((((((((((.......))))))....(((...--.....)))))))))..... ( -21.30, z-score =  -2.82, R)
>droSec1.super_1 6701666 54 - 14215200
UCUGCCGGUGACAGUUCACGUCACCACAGAGCCAC--AACCAGCUGGCGGAAGCUU
((((((((((((.......))))))....(((...--.....)))))))))..... ( -21.30, z-score =  -2.82, R)
>droYak2.chr2R 13358223 54 + 21139217
GCUGCCGGUGACAGUUCACGUCACCACAGAGCCAC--CACCAGCUGGCGGAAGCUU
(((.((((((((.......)))))).....((((.--(....).)))))).))).. ( -21.60, z-score =  -2.41, R)
>droEre2.scaffold_4845 5953565 53 + 22589142
UCUGGCGGUGACAGUUCACGUCACCACAGAGCCAC--AUCCAGCUGGUGG-AGCUU
((((..((((((.......)))))).))))((..(--(((.....)))).-.)).. ( -19.80, z-score =  -1.64, R)
>consensus
UCUGCCGGUGACAGUUCACGUCACCACAGAGCCAC__AACCAGCUGGCGGAAGCUU
((((((((((((.......))))))....(((..........)))))))))..... (-17.00 = -17.44 +   0.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:19:33 2011