Locus 10715

Sequence ID dm3.chr3R
Location 15,970,431 – 15,970,618
Length 187
Max. P 0.646711
window14727 window14728

overview

Window 7

Location 15,970,431 – 15,970,521
Length 90
Sequences 6
Columns 91
Reading direction forward
Mean pairwise identity 76.36
Shannon entropy 0.46309
G+C content 0.34900
Mean single sequence MFE -18.23
Consensus MFE -9.60
Energy contribution -10.35
Covariance contribution 0.75
Combinations/Pair 1.22
Mean z-score -1.48
Structure conservation index 0.53
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.33
SVM RNA-class probability 0.646711
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 15970431 90 + 27905053
UAGGAAUGUUUGCUCCUAGCAAACAAGAAUGAAUCGAUUACUUGUUUGC-CCGGCUUCAUUUGAAUAUGCAUGACAAAUAUUUGAUCUCUG
...(((((((((.((...((((((((((((......))).)))))))))-...(((((....)))...))..)))))))))))........ ( -19.60, z-score =  -1.67, R)
>droPer1.super_6 3110535 86 - 6141320
UAUGGAUUUAUAAUCUCUGCAAACAUAAAGAUAUAGGUAUAUAAUUUAUUCUUUCCUUUCAUGCAAAUAUAUG-CAUUGCCCCCACC----
...((((.....))))..((((....(((((.((((((.....))))))))))).......((((......))-)))))).......---- (  -9.20, z-score =   0.64, R)
>droEre2.scaffold_4770 12051243 91 - 17746568
UAGGAGUGUUUGCUCCAAGCAAACAAAAAUGAAUCGAUUACUUGUUUGCACCGGCUCCAUUCGAAUAUGCAAGACAAAUAUUUGAUCUCCG
..(((((((((((.....))))))).......(((((.((.(((((((((.(((......)))....))).)))))).)).))))))))). ( -24.10, z-score =  -3.03, R)
>droYak2.chr3R 4780012 91 + 28832112
UAGAAAUGUUUGCUCCAAGCAAACAACAAUGAAUCGAUUACUUGUUUGCCACGGCUUCAUUUGAAUAUGCAUGACAAAUAUUUGAUCUCUG
((((..(((((((.....)))))))..........(((((..((((((.((..(((((....)))...)).)).))))))..))))))))) ( -19.80, z-score =  -2.04, R)
>droSec1.super_27 41837 90 - 799419
UAGGAAUGUUUGCUUAUAUCAAACAAGAAUGAAUCGAUUACUUGUUUGC-CCGGCUUCAUUUGAAUAUGCAUGACAAAUAUUUGAUCUCUG
...(((((((((.((((..(((((((((((......))).)))))))).-...(((((....)))...)))))))))))))))........ ( -16.40, z-score =  -0.82, R)
>droSim1.chr3R 22013695 90 - 27517382
UAGGAAUGUUUGCUUAUAGCAAACAAGAAUGAAUCGAUUACUUGUUUGC-CCGGCUUCAUUUGAAUAUGCAUGACAAAUAUUUGAUCUCUG
...(((((((((.((((.((((((((((((......))).)))))))))-...(((((....)))...)))))))))))))))........ ( -20.30, z-score =  -1.98, R)
>consensus
UAGGAAUGUUUGCUCCUAGCAAACAAGAAUGAAUCGAUUACUUGUUUGC_CCGGCUUCAUUUGAAUAUGCAUGACAAAUAUUUGAUCUCUG
......(((((((.....))))))).......(((((.((.((((((((.....(.......).....))).))))).)).)))))..... ( -9.60 = -10.35 +   0.75)

alignment

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secondary structure

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dotplot

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Window 8

Location 15,970,521 – 15,970,618
Length 97
Sequences 6
Columns 97
Reading direction forward
Mean pairwise identity 74.48
Shannon entropy 0.50704
G+C content 0.43079
Mean single sequence MFE -16.68
Consensus MFE -10.39
Energy contribution -10.28
Covariance contribution -0.11
Combinations/Pair 1.14
Mean z-score -0.78
Structure conservation index 0.62
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.05
SVM RNA-class probability 0.520535
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 15970521 97 + 27905053
AAUCGCAGCUCAACUAAUCAGCUGUCAAAAUGAGAGCUGCUAAAAGCAACGAACAUGGGUAAAUGACUACACCAGCUACUCCUAUACAUCCGAACUA
..((((((((.........))))))......(((((((((.....))).......((((((......))).)))))).)))..........)).... ( -18.50, z-score =  -1.19, R)
>droAna3.scaffold_13340 2535053 97 + 23697760
AAUCGACGCUCAACUCAUCAGCUGUCAAAACAAGAGCUUCUGAUACGACAGGAAGCCCGCGAAAGGGGAGGAAUAUAACUAGCUUGCAACUAAACAG
....((((((.........))).)))....((((.((((((.........))))))((.(....).))..............))))........... ( -19.40, z-score =  -0.23, R)
>droEre2.scaffold_4770 12051334 77 - 17746568
AAUCGCAGCUCAACUAAUCAUCUGUCAAAAUGAGAGCUGCUAAA-GCACAGAACA-------------------GCCACUCCUACACAUCCGAACUA
..(((((((((......((((........)))))))))))....-((........-------------------))...............)).... ( -13.00, z-score =  -1.32, R)
>droYak2.chr3R 4780103 95 + 28832112
AAUCGCAGCUCAACUAAUCAUCUGUCAAAAUAAGAGCUGCUAAAAGCCA-GAACA-GGGGAAAUGACUACAGCAGCUACUCCUAUACAUCCAAACUA
....(((((((......................))))))).........-....(-((((...((.(....)))....))))).............. ( -16.15, z-score =  -0.46, R)
>droSec1.super_27 41927 92 - 799419
AAUCGCAGCUCAACUAAUCAGCUGUCAAAAUGAGAGCUGCUAAAAGCAACGAACAUGGGGAAAUGACUACACCUACA-----UAUACAUCCGAACUA
..(((..(((........(((((.((.....)).))))).....)))..)))...((((............))))..-----............... ( -15.92, z-score =  -0.94, R)
>droSim1.chr3R 22013785 97 - 27517382
AAUCGCAGCUCAACUAAUCAGCUGUCAAAAUGAGAGCUGCUAAAAGCAACGAACAUGGGGAAAUGACUACACCAGCUACUCCUAUACAUCCGAACUA
..(((..(((........(((((.((.....)).))))).....)))..)))..((((((...((.......)).....))))))............ ( -17.12, z-score =  -0.54, R)
>consensus
AAUCGCAGCUCAACUAAUCAGCUGUCAAAAUGAGAGCUGCUAAAAGCAACGAACAUGGGGAAAUGACUACACCAGCUACUCCUAUACAUCCGAACUA
....(((((((......................)))))))......................................................... (-10.39 = -10.28 +  -0.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:29:07 2011