Locus 7172

Sequence ID dm3.chr3L
Location 12,707,647 – 12,707,746
Length 99
Max. P 0.824373
window9873 window9874

overview

Window 3

Location 12,707,647 – 12,707,746
Length 99
Sequences 9
Columns 118
Reading direction forward
Mean pairwise identity 73.36
Shannon entropy 0.51307
G+C content 0.46359
Mean single sequence MFE -29.33
Consensus MFE -16.89
Energy contribution -16.94
Covariance contribution 0.05
Combinations/Pair 1.18
Mean z-score -1.27
Structure conservation index 0.58
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.81
SVM RNA-class probability 0.824373
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 12707647 99 + 24543557
UGAGCUGUUGUCAGCGUGAUCGCGCCACAUGAACACGAUGGUUCUGUUGAUGUGGAUGAUCUUAAUC---AGUAUCCUCAUCCACUUCCACAUCCACAUCCA----------------
.((((((((((((((((....))))....)))...)))))))))(((.((.((((((((........---.......)))))))).)).)))..........---------------- ( -26.86, z-score =  -0.78, R)
>droSim1.chr3L 12091983 93 + 22553184
UGAGCUCUUGUCAGCGUGAUCGCGCCACAUGAACACGAUGGUUCUGUUGAUGUGGAUGAUCUUAAUC---AGUAUCCUCAUCCACAUCCACAUCCA----------------------
.(((((.((((((((((....))))....)))...))).)))))(((.(((((((((((........---.......))))))))))).)))....---------------------- ( -28.36, z-score =  -1.70, R)
>droSec1.super_0 4893041 93 + 21120651
UGAGCUGUUGUCAGCGUGAUCGCGCCACAUGAACACGAUGGUUCUGUUGAUGUGGAUGAUCUUAAUC---AGUAUCCUCAUCCACAACCACAUCCA----------------------
.((((((((((((((((....))))....)))...)))))))))(((.(.(((((((((........---.......))))))))).).)))....---------------------- ( -26.56, z-score =  -0.93, R)
>droYak2.chr3L 12778359 99 + 24197627
UGAGCUGUUGUCAGCGUGAUCGCGCCACAUGAACACGAUGGUUCUGUUGAUGUGGAUGAUCUUAAUC---AGUAUCCUCAUCCACAUCCACUUCCACAUCCA----------------
...((((....))))(((.(((.......))).)))((((.....((.(((((((((((........---.......))))))))))).)).....))))..---------------- ( -30.26, z-score =  -1.86, R)
>droEre2.scaffold_4784 12712817 99 + 25762168
UGAGCUGUUGUCAGCGUGAUCGCGCCACAUGAACACGAUGGUUCUGUUGAUGUGGAUGAUCUUAAUC---AGUAUCCUCAUCCACAUGCACAUCCACAUCCA----------------
.((((((((((((((((....))))....)))...)))))))))(((..((((((((((........---.......))))))))))..)))..........---------------- ( -27.16, z-score =  -0.21, R)
>droAna3.scaffold_13337 19976137 93 - 23293914
UGAGAUGUUGUCAGCGUGAUCGCGCCACAUGAACACGAUGAUUCUGUUGAUGUGGAUGAUCUUAAUC---AGUAUCACAGAAGGCCUC-UCUAUCCU---------------------
.((((.((..((...(((((.((.((((((.((((.((....)))))).)))))).((((....)))---)))))))).))..)).))-))......--------------------- ( -28.20, z-score =  -1.36, R)
>dp4.chrXR_group6 3501000 115 + 13314419
UGAAUUGUUGUCAGCGUGAUCGCGCCACAUGAACAUGAUGGUUCUGUUGAUGUGGAUGAUCUUAAUC---AGUAUCACAAAAGGCAUCGUCUACGAAGGACGUAGAGCGAGCCAGCCA
.............(((((((.((.((((((.((((.((....)))))).)))))).((((....)))---))))))))....(((.(((((((((.....)))))).)))))).)).. ( -39.20, z-score =  -2.24, R)
>droPer1.super_9 1796594 115 + 3637205
UGAAUUGUUGUCAGCGUGAUCGCGCCACAUGAACAUGAUGGUUCUGUUGAUGUGGAUGAUCUUAAUC---AGUAUCACAAAAGGCAUCGUCUACGAAGGACGUAGAGCGAGCCAGCCA
.............(((((((.((.((((((.((((.((....)))))).)))))).((((....)))---))))))))....(((.(((((((((.....)))))).)))))).)).. ( -39.20, z-score =  -2.24, R)
>droWil1.scaffold_181096 833222 90 + 12416693
-------------GUGUGAUCGCACCACAUGCUAGAAAUGGAUUUGUUGAUGUGAACGAUCUUAAUCCAUAAUACUGCGAGUCCAAUCAACGUUCAGACAUAG---------------
-------------((.(((.((((.....)))......(((((((((.(.(((....(((....)))....)))).)))))))))......).))).))....--------------- ( -18.20, z-score =  -0.09, R)
>consensus
UGAGCUGUUGUCAGCGUGAUCGCGCCACAUGAACACGAUGGUUCUGUUGAUGUGGAUGAUCUUAAUC___AGUAUCCUCAUCCACAUCCACAUCCACA__CA________________
.................(((((..((((((.((((.((....)))))).)))))).)))))......................................................... (-16.89 = -16.94 +   0.05)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 12,707,647 – 12,707,746
Length 99
Sequences 9
Columns 118
Reading direction reverse
Mean pairwise identity 73.36
Shannon entropy 0.51307
G+C content 0.46359
Mean single sequence MFE -30.38
Consensus MFE -13.87
Energy contribution -14.02
Covariance contribution 0.15
Combinations/Pair 1.12
Mean z-score -1.48
Structure conservation index 0.46
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.21
SVM RNA-class probability 0.596426
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 12707647 99 - 24543557
----------------UGGAUGUGGAUGUGGAAGUGGAUGAGGAUACU---GAUUAAGAUCAUCCACAUCAACAGAACCAUCGUGUUCAUGUGGCGCGAUCACGCUGACAACAGCUCA
----------------.((.(((.((((((((.(..(((.((....))---.))).....).)))))))).)))...))((((((((.....))))))))...((((....))))... ( -31.20, z-score =  -1.09, R)
>droSim1.chr3L 12091983 93 - 22553184
----------------------UGGAUGUGGAUGUGGAUGAGGAUACU---GAUUAAGAUCAUCCACAUCAACAGAACCAUCGUGUUCAUGUGGCGCGAUCACGCUGACAAGAGCUCA
----------------------(((.(((.(((((((((((.(((...---.)))....))))))))))).)))...)))..(.((((.(((((((......)))).))).)))).). ( -34.30, z-score =  -2.72, R)
>droSec1.super_0 4893041 93 - 21120651
----------------------UGGAUGUGGUUGUGGAUGAGGAUACU---GAUUAAGAUCAUCCACAUCAACAGAACCAUCGUGUUCAUGUGGCGCGAUCACGCUGACAACAGCUCA
----------------------.....(((((((((((((.(((...(---(((....))))))).)))).(((((((......)))).)))..)))))))))((((....))))... ( -29.90, z-score =  -1.27, R)
>droYak2.chr3L 12778359 99 - 24197627
----------------UGGAUGUGGAAGUGGAUGUGGAUGAGGAUACU---GAUUAAGAUCAUCCACAUCAACAGAACCAUCGUGUUCAUGUGGCGCGAUCACGCUGACAACAGCUCA
----------------.....((((..((((((((((((((.(((...---.)))....))))))))))).(((((((......)))).)))..)))..))))((((....))))... ( -33.70, z-score =  -1.86, R)
>droEre2.scaffold_4784 12712817 99 - 25762168
----------------UGGAUGUGGAUGUGCAUGUGGAUGAGGAUACU---GAUUAAGAUCAUCCACAUCAACAGAACCAUCGUGUUCAUGUGGCGCGAUCACGCUGACAACAGCUCA
----------------.....((((.(((((((((((((((.(((...---.)))....))))))))))..(((((((......)))).))).))))).))))((((....))))... ( -33.80, z-score =  -1.50, R)
>droAna3.scaffold_13337 19976137 93 + 23293914
---------------------AGGAUAGA-GAGGCCUUCUGUGAUACU---GAUUAAGAUCAUCCACAUCAACAGAAUCAUCGUGUUCAUGUGGCGCGAUCACGCUGACAACAUCUCA
---------------------......((-((.....((((((((..(---(((....)))).((((((.((((((....)).)))).))))))....))))))..)).....)))). ( -21.20, z-score =   0.45, R)
>dp4.chrXR_group6 3501000 115 - 13314419
UGGCUGGCUCGCUCUACGUCCUUCGUAGACGAUGCCUUUUGUGAUACU---GAUUAAGAUCAUCCACAUCAACAGAACCAUCAUGUUCAUGUGGCGCGAUCACGCUGACAACAAUUCA
.(((.((((((.((((((.....))))))))).)))....(((((..(---(((....)))).((((((.((((((....)).)))).))))))....))))))))............ ( -34.90, z-score =  -2.58, R)
>droPer1.super_9 1796594 115 - 3637205
UGGCUGGCUCGCUCUACGUCCUUCGUAGACGAUGCCUUUUGUGAUACU---GAUUAAGAUCAUCCACAUCAACAGAACCAUCAUGUUCAUGUGGCGCGAUCACGCUGACAACAAUUCA
.(((.((((((.((((((.....))))))))).)))....(((((..(---(((....)))).((((((.((((((....)).)))).))))))....))))))))............ ( -34.90, z-score =  -2.58, R)
>droWil1.scaffold_181096 833222 90 - 12416693
---------------CUAUGUCUGAACGUUGAUUGGACUCGCAGUAUUAUGGAUUAAGAUCGUUCACAUCAACAAAUCCAUUUCUAGCAUGUGGUGCGAUCACAC-------------
---------------............((.(((((.((.((((((...(((((((..(((.(....))))....))))))).....)).)))))).)))))))..------------- ( -19.50, z-score =  -0.15, R)
>consensus
________________UG__UGUGGAAGUGGAUGUGGAUGAGGAUACU___GAUUAAGAUCAUCCACAUCAACAGAACCAUCGUGUUCAUGUGGCGCGAUCACGCUGACAACAGCUCA
.........................................................((((..((((((.((((((....)).)))).))))))...))))................. (-13.87 = -14.02 +   0.15)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:21:50 2011