Locus 10335

Sequence ID dm3.chr3R
Location 13,139,892 – 13,139,953
Length 61
Max. P 0.905890
window14210 window14211

overview

Window 0

Location 13,139,892 – 13,139,953
Length 61
Sequences 5
Columns 61
Reading direction forward
Mean pairwise identity 67.87
Shannon entropy 0.58470
G+C content 0.37296
Mean single sequence MFE -10.10
Consensus MFE -4.90
Energy contribution -5.10
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -0.94
Structure conservation index 0.49
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.10
SVM RNA-class probability 0.544959
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 13139892 61 + 27905053
CAUUGGAGUUCAUAAGCUCUUUGAGUUGAACAAGGGAUGGAUUACAUUUAUAUAUACAGUU
.((((..(((((...((((...)))))))))...(((((.....))))).......)))). ( -10.20, z-score =  -0.93, R)
>droEre2.scaffold_4770 9258005 52 - 17746568
GAUUAAGGUUCAGAAGCUCUUCCAGUUGAGCAUGGGAUAUACUUCCAUUGUU---------
...............((((........))))((((((.....))))))....--------- ( -10.10, z-score =  -0.21, R)
>droYak2.chr3R 17230543 51 + 28832112
----------CAGAAGCUCUUUCAGUUGAGCAAGGGAUAUAACACUCAUAUAUCCACAGUC
----------.....((((........))))...(((((((.......)))))))...... ( -12.80, z-score =  -3.07, R)
>droSec1.super_12 1116168 61 - 2123299
CAUUGGAGUUCAUAAGCUCUUUCGGUUGAGCAAGGGUUGGAUUACAUAUAUUUAUACAGUC
...((.((((((...((((((.(......).)))))))))))).))............... (  -8.80, z-score =  -0.24, R)
>droSim1.chr3R 19184880 61 - 27517382
CAUUGGAGUUCAUAAGCUCUUUCGGUUGAGCAAGAAUUGGAUUACAUAUAUUUAUACAGUC
...((.((((((...((((........))))......)))))).))............... (  -8.60, z-score =  -0.24, R)
>consensus
CAUUGGAGUUCAUAAGCUCUUUCAGUUGAGCAAGGGAUGGAUUACAUAUAUUUAUACAGUC
...............((((........)))).............................. ( -4.90 =  -5.10 +   0.20)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 13,139,892 – 13,139,953
Length 61
Sequences 5
Columns 61
Reading direction reverse
Mean pairwise identity 67.87
Shannon entropy 0.58470
G+C content 0.37296
Mean single sequence MFE -6.64
Consensus MFE -4.68
Energy contribution -4.52
Covariance contribution -0.16
Combinations/Pair 1.25
Mean z-score -0.76
Structure conservation index 0.70
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.18
SVM RNA-class probability 0.905890
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 13139892 61 - 27905053
AACUGUAUAUAUAAAUGUAAUCCAUCCCUUGUUCAACUCAAAGAGCUUAUGAACUCCAAUG
.....(((((....)))))...........(((((.(((...)))....)))))....... (  -3.80, z-score =  -0.10, R)
>droEre2.scaffold_4770 9258005 52 + 17746568
---------AACAAUGGAAGUAUAUCCCAUGCUCAACUGGAAGAGCUUCUGAACCUUAAUC
---------....((((.........))))((((........))))............... (  -7.10, z-score =   0.00, R)
>droYak2.chr3R 17230543 51 - 28832112
GACUGUGGAUAUAUGAGUGUUAUAUCCCUUGCUCAACUGAAAGAGCUUCUG----------
......(((((((.......)))))))...((((........)))).....---------- ( -11.50, z-score =  -1.96, R)
>droSec1.super_12 1116168 61 + 2123299
GACUGUAUAAAUAUAUGUAAUCCAACCCUUGCUCAACCGAAAGAGCUUAUGAACUCCAAUG
..............................((((........))))............... (  -5.00, z-score =  -0.97, R)
>droSim1.chr3R 19184880 61 + 27517382
GACUGUAUAAAUAUAUGUAAUCCAAUUCUUGCUCAACCGAAAGAGCUUAUGAACUCCAAUG
.........................(((..((((........))))....)))........ (  -5.80, z-score =  -0.78, R)
>consensus
GACUGUAUAAAUAUAUGUAAUCCAUCCCUUGCUCAACUGAAAGAGCUUAUGAACUCCAAUG
..............................((((........))))............... ( -4.68 =  -4.52 +  -0.16)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:21:59 2011