Locus 6710

Sequence ID dm3.chr3L
Location 9,112,586 – 9,112,680
Length 94
Max. P 0.873603
window9236 window9237

overview

Window 6

Location 9,112,586 – 9,112,680
Length 94
Sequences 3
Columns 95
Reading direction forward
Mean pairwise identity 75.75
Shannon entropy 0.31634
G+C content 0.44638
Mean single sequence MFE -26.03
Consensus MFE -18.49
Energy contribution -19.27
Covariance contribution 0.78
Combinations/Pair 1.05
Mean z-score -1.91
Structure conservation index 0.71
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.01
SVM RNA-class probability 0.873603
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 9112586 94 + 24543557
AACUGAUUGUGUGUGUGUGUAGAUUGUAUGUGUAUGUGUGUAUAAAUAGUUGGGG-CAUGAAGACGCUGCUAACUAUUUCUGUAGACGCAGCUGA
...........(((((.(((((((((((..(......)..)))))((((((((((-(........))).)))))))).)))))).)))))..... ( -22.30, z-score =  -0.24, R)
>droSim1.chr3L_random 428740 76 + 1049610
-----------------AACUUAUUGUGUGUGUGUCUGU--AUACAUAGUUGGGGGCGUGAAGACGCUGCCAACUAUUUCUGUAGACGCAGCUGA
-----------------.............(((((((((--(.(.((((((((.(((((....))))).)))))))).).))))))))))..... ( -29.70, z-score =  -3.58, R)
>droSec1.super_0 1375333 78 + 21120651
-----------------CACUGAUUGUGUGUGUGUGUGUGUAUACAUAGUUGGGGGCGUGAAGAAGCUGCCAACUAUUUCUGUAGACGCAGCUGA
-----------------(((.....)))......(((((.((((.((((((((.(((........))).))))))))...)))).)))))..... ( -26.10, z-score =  -1.90, R)
>consensus
_________________AACUGAUUGUGUGUGUGUGUGUGUAUACAUAGUUGGGGGCGUGAAGACGCUGCCAACUAUUUCUGUAGACGCAGCUGA
..................................(((((.((((.((((((((.(((........))).))))))))...)))).)))))..... (-18.49 = -19.27 +   0.78)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 9,112,586 – 9,112,680
Length 94
Sequences 3
Columns 95
Reading direction reverse
Mean pairwise identity 75.75
Shannon entropy 0.31634
G+C content 0.44638
Mean single sequence MFE -15.53
Consensus MFE -9.60
Energy contribution -9.60
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -2.12
Structure conservation index 0.62
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.81
SVM RNA-class probability 0.822951
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 9112586 94 - 24543557
UCAGCUGCGUCUACAGAAAUAGUUAGCAGCGUCUUCAUG-CCCCAACUAUUUAUACACACAUACACAUACAAUCUACACACACACACAAUCAGUU
...(((((..(((......)))...))))).........-....................................................... ( -10.50, z-score =  -1.05, R)
>droSim1.chr3L_random 428740 76 - 1049610
UCAGCUGCGUCUACAGAAAUAGUUGGCAGCGUCUUCACGCCCCCAACUAUGUAU--ACAGACACACACACAAUAAGUU-----------------
...(.((.((((......((((((((..((((....))))..))))))))....--..)))).)))............----------------- ( -21.00, z-score =  -3.64, R)
>droSec1.super_0 1375333 78 - 21120651
UCAGCUGCGUCUACAGAAAUAGUUGGCAGCUUCUUCACGCCCCCAACUAUGUAUACACACACACACACACAAUCAGUG-----------------
...(.((.((.((((....(((((((..((........))..))))))))))).)).))).......(((.....)))----------------- ( -15.10, z-score =  -1.66, R)
>consensus
UCAGCUGCGUCUACAGAAAUAGUUGGCAGCGUCUUCACGCCCCCAACUAUGUAUACACACACACACACACAAUCAGUA_________________
...(((((..(((......)))...)))))................................................................. ( -9.60 =  -9.60 +  -0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:13:00 2011