Locus 6887

Sequence ID dm3.chr3L
Location 10,508,927 – 10,509,006
Length 79
Max. P 0.996701
window9481 window9482

overview

Window 1

Location 10,508,927 – 10,509,006
Length 79
Sequences 5
Columns 87
Reading direction forward
Mean pairwise identity 79.69
Shannon entropy 0.35512
G+C content 0.31744
Mean single sequence MFE -15.92
Consensus MFE -11.80
Energy contribution -13.12
Covariance contribution 1.32
Combinations/Pair 1.18
Mean z-score -2.92
Structure conservation index 0.74
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.97
SVM RNA-class probability 0.996701
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr3L 10508927 79 + 24543557
--------UUCAUUUUCAAACUUUUAAAAUUGCUUAACAUUUCGAUAAAUUCUUAUCGAUAACAGAAUGUUAAGCAACAUAGCGCAU
--------.....................(((((((((((((((((((....)))))))......)))))))))))).......... ( -18.20, z-score =  -4.54, R)
>droEre2.scaffold_4784 10503144 87 + 25762168
UAUCAAGAUUCGUGUUCAAAAUUUCGAAAAUGCCUAACAUUCCGAUACAUUGCUAUCGAUAACACAGUGUUAGGCAACAGAGCACAU
...........((((((....((....)).(((((((((((.(((((......))))).......)))))))))))...)))))).. ( -21.30, z-score =  -3.35, R)
>droYak2.chr3L 10502227 79 + 24197627
--------UUUAUUUUCAAAUUUUCGAAACUGCCUAACAUUCCGAUACAUUCCUAUCGAUAACACACUGUUAAGCAACAGAGCACAU
--------.....((((........)))).(((.........(((((......)))))........(((((....))))).)))... (  -9.30, z-score =  -2.14, R)
>droSec1.super_0 2724491 85 + 21120651
--UUUUAAUCCAUUUUCAAACUUUUGAAAUAGCUUAACAUUUCGAUAAAUUCUUAUCGAUAACAGCGUGUUAAGCAACAGAGCGCAU
--...........((((((....))))))..(((((((((.(((((((....))))))).......)))))))))............ ( -17.80, z-score =  -3.12, R)
>droSim1.chr3L 9905461 85 + 22553184
--UUUUAAUACAUUUUCAAACUUUCGAAAUAACUUAACAUUUCGAUAGAUGCUUAUCGAUAACAGCAUGUUAAGCAACAGAGCGCAU
--..................((.(((((((........))))))).))((((.......((((.....)))).((......)))))) ( -13.00, z-score =  -1.46, R)
>consensus
__U____AUUCAUUUUCAAACUUUCGAAAUUGCUUAACAUUUCGAUAAAUUCUUAUCGAUAACAGAAUGUUAAGCAACAGAGCGCAU
...............................(((((((((((((((((....)))))))......))))))))))............ (-11.80 = -13.12 +   1.32)

alignment

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secondary structure

Postscript

dotplot

Postscript

Window 2

Location 10,508,927 – 10,509,006
Length 79
Sequences 5
Columns 87
Reading direction reverse
Mean pairwise identity 79.69
Shannon entropy 0.35512
G+C content 0.31744
Mean single sequence MFE -17.06
Consensus MFE -14.28
Energy contribution -13.28
Covariance contribution -1.00
Combinations/Pair 1.30
Mean z-score -1.31
Structure conservation index 0.84
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.99
SVM RNA-class probability 0.869263
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr3L 10508927 79 - 24543557
AUGCGCUAUGUUGCUUAACAUUCUGUUAUCGAUAAGAAUUUAUCGAAAUGUUAAGCAAUUUUAAAAGUUUGAAAAUGAA--------
.........(((((((((((((......(((((((....))))))))))))))))))))....................-------- ( -18.40, z-score =  -2.57, R)
>droEre2.scaffold_4784 10503144 87 - 25762168
AUGUGCUCUGUUGCCUAACACUGUGUUAUCGAUAGCAAUGUAUCGGAAUGUUAGGCAUUUUCGAAAUUUUGAACACGAAUCUUGAUA
.((((......(((((((((.....((.((((((......)))))))))))))))))..(((((....))))))))).......... ( -18.10, z-score =  -0.51, R)
>droYak2.chr3L 10502227 79 - 24197627
AUGUGCUCUGUUGCUUAACAGUGUGUUAUCGAUAGGAAUGUAUCGGAAUGUUAGGCAGUUUCGAAAAUUUGAAAAUAAA--------
..........((((((((((........((((((......))))))..))))))))))((((((....)))))).....-------- ( -15.40, z-score =  -0.99, R)
>droSec1.super_0 2724491 85 - 21120651
AUGCGCUCUGUUGCUUAACACGCUGUUAUCGAUAAGAAUUUAUCGAAAUGUUAAGCUAUUUCAAAAGUUUGAAAAUGGAUUAAAA--
......((((((((((((((........(((((((....)))))))..))))))))...(((((....)))))))))))......-- ( -16.00, z-score =  -0.92, R)
>droSim1.chr3L 9905461 85 - 22553184
AUGCGCUCUGUUGCUUAACAUGCUGUUAUCGAUAAGCAUCUAUCGAAAUGUUAAGUUAUUUCGAAAGUUUGAAAAUGUAUUAAAA--
(((((((.(((((..((((.....)))).))))))))..((.((((((((......)))))))).)).........)))).....-- ( -17.40, z-score =  -1.53, R)
>consensus
AUGCGCUCUGUUGCUUAACACUCUGUUAUCGAUAAGAAUGUAUCGAAAUGUUAAGCAAUUUCGAAAGUUUGAAAAUGAAU____A__
............((((((((........((((((......))))))..))))))))..((((((....))))))............. (-14.28 = -13.28 +  -1.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:16:25 2011