Locus 5796

Sequence ID dm3.chr3L
Location 1,348,196 – 1,348,325
Length 129
Max. P 0.989386
window7966 window7967 window7968

overview

Window 6

Location 1,348,196 – 1,348,307
Length 111
Sequences 5
Columns 111
Reading direction forward
Mean pairwise identity 95.03
Shannon entropy 0.08435
G+C content 0.40606
Mean single sequence MFE -33.88
Consensus MFE -30.52
Energy contribution -31.52
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -2.93
Structure conservation index 0.90
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.37
SVM RNA-class probability 0.989386
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 1348196 111 + 24543557
AAAGCGUGUCGUGCAAACCGUUUUAUGGUUAUUAUGUUUCUGCUUUACCUUGCAACGCUCGAAGGAAAUCGAGAAACAGUAACAAAAACAUUGCAUGCACGCAGAGCACAA
...(((((.(((((((...(((((...(((((..(((((((((........)))....((((......))))))))))))))).))))).))))))))))))......... ( -34.20, z-score =  -2.71, R)
>droSim1.chr3L 947181 111 + 22553184
AAAGCGUGUCGUGCAAACCGUUUUAUGGUUAUUAUGUUUCUGCUUUACCUUGCAACGCUCGAAGGAAAUCGAGAAACAGUAACAAAAACAUUGCAUGCACGCAGAGCACAA
...(((((.(((((((...(((((...(((((..(((((((((........)))....((((......))))))))))))))).))))).))))))))))))......... ( -34.20, z-score =  -2.71, R)
>droSec1.super_2 1390735 111 + 7591821
AAAGCGUGUCGUGCAAACCGUUUUAUGGUUAUUAUGUUUCUGCUUUACCUUGCAACGCUCGAAGGAAAUCGAGAAACAGUAACAAAAACAUUGCAUGCACGCAGAGCACAA
...(((((.(((((((...(((((...(((((..(((((((((........)))....((((......))))))))))))))).))))).))))))))))))......... ( -34.20, z-score =  -2.71, R)
>droEre2.scaffold_4784 1330976 108 + 25762168
AAAGCGUGUCGUGCAAACAGUUUUAU---UAUUAUGUUUCUGCUUUACCUUGCAACGCUCGAGGAAAAUCGAGAAACAGUAACAAAAACAUUGCAUGCACGCAGAGCAUAA
...(((((.(((((((...(((((..---.....((((((((.(((.(((((.......))))).))).).)))))))......))))).))))))))))))......... ( -32.02, z-score =  -2.93, R)
>droYak2.chr3L 1307229 108 + 24197627
AAAGCGUGUCGUGCAAUCGGUUUUAU---UAUUAUGUUUCUGCUUUACCUUGCAACGCUCGAGGAAAAUCAAGAAACAGUAACAAAAACGUUGCAUGCACGCAGAGCAUAA
...(((((.(((((((.((.((((.(---(((..(((((((..(((.(((((.......))))).)))...))))))))))).)))).))))))))))))))......... ( -34.80, z-score =  -3.57, R)
>consensus
AAAGCGUGUCGUGCAAACCGUUUUAUGGUUAUUAUGUUUCUGCUUUACCUUGCAACGCUCGAAGGAAAUCGAGAAACAGUAACAAAAACAUUGCAUGCACGCAGAGCACAA
...(((((.(((((((...(((((...(((((..(((((((((........)))....((((......))))))))))))))).))))).))))))))))))......... (-30.52 = -31.52 +   1.00)

alignment

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secondary structure

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dotplot

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Window 7

Location 1,348,196 – 1,348,307
Length 111
Sequences 5
Columns 111
Reading direction reverse
Mean pairwise identity 95.03
Shannon entropy 0.08435
G+C content 0.40606
Mean single sequence MFE -31.34
Consensus MFE -28.32
Energy contribution -28.16
Covariance contribution -0.16
Combinations/Pair 1.03
Mean z-score -2.05
Structure conservation index 0.90
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.19
SVM RNA-class probability 0.906916
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 1348196 111 - 24543557
UUGUGCUCUGCGUGCAUGCAAUGUUUUUGUUACUGUUUCUCGAUUUCCUUCGAGCGUUGCAAGGUAAAGCAGAAACAUAAUAACCAUAAAACGGUUUGCACGACACGCUUU
.........((((((.((((((((((((((((((((..(((((......)))))....))..))))..))))))))))...((((.......)))))))).).)))))... ( -32.30, z-score =  -2.01, R)
>droSim1.chr3L 947181 111 - 22553184
UUGUGCUCUGCGUGCAUGCAAUGUUUUUGUUACUGUUUCUCGAUUUCCUUCGAGCGUUGCAAGGUAAAGCAGAAACAUAAUAACCAUAAAACGGUUUGCACGACACGCUUU
.........((((((.((((((((((((((((((((..(((((......)))))....))..))))..))))))))))...((((.......)))))))).).)))))... ( -32.30, z-score =  -2.01, R)
>droSec1.super_2 1390735 111 - 7591821
UUGUGCUCUGCGUGCAUGCAAUGUUUUUGUUACUGUUUCUCGAUUUCCUUCGAGCGUUGCAAGGUAAAGCAGAAACAUAAUAACCAUAAAACGGUUUGCACGACACGCUUU
.........((((((.((((((((((((((((((((..(((((......)))))....))..))))..))))))))))...((((.......)))))))).).)))))... ( -32.30, z-score =  -2.01, R)
>droEre2.scaffold_4784 1330976 108 - 25762168
UUAUGCUCUGCGUGCAUGCAAUGUUUUUGUUACUGUUUCUCGAUUUUCCUCGAGCGUUGCAAGGUAAAGCAGAAACAUAAUA---AUAAAACUGUUUGCACGACACGCUUU
.........((((((.(((((.((((((((((.((((((((((......))))((.((((...)))).)).)))))))))))---..)))))...))))).).)))))... ( -30.00, z-score =  -2.08, R)
>droYak2.chr3L 1307229 108 - 24197627
UUAUGCUCUGCGUGCAUGCAACGUUUUUGUUACUGUUUCUUGAUUUUCCUCGAGCGUUGCAAGGUAAAGCAGAAACAUAAUA---AUAAAACCGAUUGCACGACACGCUUU
.........((((((.(((((((.((((((((.((((((((((......))))((.((((...)))).)).))))))...))---)))))).)).))))).).)))))... ( -29.80, z-score =  -2.12, R)
>consensus
UUGUGCUCUGCGUGCAUGCAAUGUUUUUGUUACUGUUUCUCGAUUUCCUUCGAGCGUUGCAAGGUAAAGCAGAAACAUAAUAACCAUAAAACGGUUUGCACGACACGCUUU
.........((((((.(((((.((((((((((.((((((((((......))))((.((((...)))).)).))))))))))).....)))))...))))).).)))))... (-28.32 = -28.16 +  -0.16)

alignment

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secondary structure

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dotplot

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Window 8

Location 1,348,214 – 1,348,325
Length 111
Sequences 5
Columns 111
Reading direction reverse
Mean pairwise identity 94.31
Shannon entropy 0.09534
G+C content 0.39525
Mean single sequence MFE -24.92
Consensus MFE -23.64
Energy contribution -23.08
Covariance contribution -0.56
Combinations/Pair 1.12
Mean z-score -1.23
Structure conservation index 0.95
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.44
SVM RNA-class probability 0.696332
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 1348214 111 - 24543557
CUUUAUCCAUCGUUGCAAUUGUGCUCUGCGUGCAUGCAAUGUUUUUGUUACUGUUUCUCGAUUUCCUUCGAGCGUUGCAAGGUAAAGCAGAAACAUAAUAACCAUAAAACG
..........(((((((..((..(.....)..)))))))))...((((((.((((((((((......))))((.((((...)))).)).)))))))))))).......... ( -25.50, z-score =  -1.30, R)
>droSim1.chr3L 947199 111 - 22553184
CUUUAUCCAUCGUUGCAAUUGUGCUCUGCGUGCAUGCAAUGUUUUUGUUACUGUUUCUCGAUUUCCUUCGAGCGUUGCAAGGUAAAGCAGAAACAUAAUAACCAUAAAACG
..........(((((((..((..(.....)..)))))))))...((((((.((((((((((......))))((.((((...)))).)).)))))))))))).......... ( -25.50, z-score =  -1.30, R)
>droSec1.super_2 1390753 111 - 7591821
CUUUAUCCAUCGUUGCAAUUGUGCUCUGCGUGCAUGCAAUGUUUUUGUUACUGUUUCUCGAUUUCCUUCGAGCGUUGCAAGGUAAAGCAGAAACAUAAUAACCAUAAAACG
..........(((((((..((..(.....)..)))))))))...((((((.((((((((((......))))((.((((...)))).)).)))))))))))).......... ( -25.50, z-score =  -1.30, R)
>droEre2.scaffold_4784 1330994 108 - 25762168
CUUCAUCCAUCGCUGCAAUUAUGCUCUGCGUGCAUGCAAUGUUUUUGUUACUGUUUCUCGAUUUUCCUCGAGCGUUGCAAGGUAAAGCAGAAACAUAAUA---AUAAAACU
...(((.((.(((.(((....)))...))))).)))..((((((((((((((((..(((((......)))))....))..))))..))))))))))....---........ ( -24.20, z-score =  -1.17, R)
>droYak2.chr3L 1307247 108 - 24197627
CUUCAUCCAUCGCUGCAAUUAUGCUCUGCGUGCAUGCAACGUUUUUGUUACUGUUUCUUGAUUUUCCUCGAGCGUUGCAAGGUAAAGCAGAAACAUAAUA---AUAAAACC
.................((((((.(((((.(((.((((((((((..(..(..(((....))).)..)..))))))))))..)))..)))))..)))))).---........ ( -23.90, z-score =  -1.08, R)
>consensus
CUUUAUCCAUCGUUGCAAUUGUGCUCUGCGUGCAUGCAAUGUUUUUGUUACUGUUUCUCGAUUUCCUUCGAGCGUUGCAAGGUAAAGCAGAAACAUAAUAACCAUAAAACG
.................((((((.(((((.(((.(((((((...............(((((......))))))))))))..)))..)))))..))))))............ (-23.64 = -23.08 +  -0.56)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:55:18 2011