Locus 7575

Sequence ID dm3.chr3L
Location 15,647,981 – 15,648,168
Length 187
Max. P 0.856397
window10426 window10427 window10428

overview

Window 6

Location 15,647,981 – 15,648,098
Length 117
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 80.12
Shannon entropy 0.35363
G+C content 0.52924
Mean single sequence MFE -43.52
Consensus MFE -26.95
Energy contribution -27.75
Covariance contribution 0.80
Combinations/Pair 1.22
Mean z-score -1.97
Structure conservation index 0.62
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.87
SVM RNA-class probability 0.840702
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 15647981 117 + 24543557
CCUCCGGGAUUCCAACCUGAAGGUUUUGUCGAAC---AUUCGUCCGGUUUCUUGGUAGUCGUUGAAAAGCUUGGGAUUAUAGGACCGCCAGGAUUCCAUCCAGACGGGUGAGAGCUACUA
(((.((((.......)))).)))..........(---(((((((.((..((((((..((((((....)))(((......))))))..))))))......)).)))))))).......... ( -33.80, z-score =   0.42, R)
>droSim1.chr3L 14987350 117 + 22553184
CCGUCGGGAUUCCAACCUGACGGUUUUCUCGAGC---AUUCGUCUGGUUUCUUGGUAGUCGUUGAACCGCUUGGGAUUAUAGGACCGCCAGGAUUCCAUCCAGACGGGUGAGAGCUACUA
((((((((.......))))))))....(((...(---((((((((((..((((((..(((.((((.((.....)).))).).)))..))))))......))))))))))).)))...... ( -49.40, z-score =  -3.49, R)
>droSec1.super_0 7760214 117 + 21120651
CCGCCGGGAUUCCAACCUGACGGUUUUCUCGAGC---AUUCGUCUGGUUUCUUGGUAGUCGUUGAACCGCUUGGUAUUAUAGGACCGCCAGGAUUCCAUCCAGACGGGUGAGAGCUACUA
(((.((((.......)))).)))....(((...(---((((((((((..((((((..(((.(((((((....))).))).).)))..))))))......))))))))))).)))...... ( -44.30, z-score =  -2.40, R)
>droYak2.chr3L 18197604 117 + 24197627
CCGCCGGGAUUCCAGCCCGAAGGUUCUUGCGAACCACAUCCACAUGGUUUCUUGGUGG---UUGAGACUAUUGGGAUUAUAGGACCGCCAGGAUUCCAUCCUGGUGGGCGAGUUUCACCA
(((((((((..(((....((.(((((....)))))...))....)))..)))))))))---.(((((((.(((......)))..((((((((((...))))))))))...)))))))... ( -46.30, z-score =  -2.10, R)
>droEre2.scaffold_4784 17906041 114 + 25762168
CCGCCGGGAUUACAACCUGAAUUUGGCGAGCCAC---AUUCGUCUGGUUUCUUGGUAGUCCUUGGAGAGAUUGGGAUUAACGGACCGCCAGGAUUCCAACCAGAUGGGUGAGUGCGA---
.(((((((.(((.....))).))))))).(((.(---((((((((((((((((((..((((...((..........))...))))..))))))....))))))))))))).).))..--- ( -43.80, z-score =  -2.30, R)
>consensus
CCGCCGGGAUUCCAACCUGAAGGUUUUCUCGAAC___AUUCGUCUGGUUUCUUGGUAGUCGUUGAAACGCUUGGGAUUAUAGGACCGCCAGGAUUCCAUCCAGACGGGUGAGAGCUACUA
(((.((((.......)))).)))..............((((((((((..(((((((.(((......................))).)))))))......))))))))))........... (-26.95 = -27.75 +   0.80)

alignment

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secondary structure

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dotplot

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Window 7

Location 15,648,018 – 15,648,131
Length 113
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 69.10
Shannon entropy 0.52821
G+C content 0.52280
Mean single sequence MFE -35.92
Consensus MFE -19.89
Energy contribution -20.57
Covariance contribution 0.68
Combinations/Pair 1.14
Mean z-score -1.37
Structure conservation index 0.55
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.94
SVM RNA-class probability 0.856397
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 15648018 113 + 24543557
CGUCCGGUUUCUUGGUAGUCGUUGAAAAGCUUGGGAUUAUAGGACCGCCAGGAUUCCAUCCAGACGGGUGAGAGCUACUACAUCCGCAUGGUUUUCGGGUGGUUUUCUCUGGA-------
.....((..((((((..((((((....)))(((......))))))..))))))..)).((((((.....((((((((((....((....))......))))))))))))))))------- ( -37.60, z-score =  -0.88, R)
>droSim1.chr3L 14987387 88 + 22553184
CGUCUGGUUUCUUGGUAGUCGUUGAACCGCUUGGGAUUAUAGGACCGCCAGGAUUCCAUCCAGACGGGUGAGAGCUACUACAACCGCA--------------------------------
(((((((..((((((..(((.((((.((.....)).))).).)))..))))))......)))))))(((....)))............-------------------------------- ( -30.70, z-score =  -1.63, R)
>droSec1.super_0 7760251 88 + 21120651
CGUCUGGUUUCUUGGUAGUCGUUGAACCGCUUGGUAUUAUAGGACCGCCAGGAUUCCAUCCAGACGGGUGAGAGCUACUACAACCGCA--------------------------------
(((((((..((((((..(((.(((((((....))).))).).)))..))))))......)))))))(((....)))............-------------------------------- ( -30.60, z-score =  -1.93, R)
>droYak2.chr3L 18197644 111 + 24197627
CACAUGGUUUCUUGGUGGU---UGAGACUAUUGGGAUUAUAGGACCGCCAGGAUUCCAUCCUGGUGGGCGAGUUUCACCACAUCCACAUGGCUUUCGGGUGGUGGUCGUUGAGA------
.........(((..(((((---....)))))..)))........((((((((((...))))))))))((((.(.(((((....((....))......))))).).)))).....------ ( -38.60, z-score =  -0.78, R)
>droEre2.scaffold_4784 17906078 117 + 25762168
CGUCUGGUUUCUUGGUAGUCCUUGGAGAGAUUGGGAUUAACGGACCGCCAGGAUUCCAACCAGAUGGGUGAG---UGCGACAUCCGCAUGGUUUUUCGGUGGUUGUCGAAGCUGUUGUCA
(((((((((((((((..((((...((..........))...))))..))))))....)))))))))(((...---..(((((.((((.(((....))))))).)))))..)))....... ( -42.10, z-score =  -1.60, R)
>consensus
CGUCUGGUUUCUUGGUAGUCGUUGAAACGCUUGGGAUUAUAGGACCGCCAGGAUUCCAUCCAGACGGGUGAGAGCUACUACAUCCGCAUGG_UUU__GGUGGU__UC___G_________
.((((((..(((((((.(((......................))).)))))))......))))))(((((..........)))))................................... (-19.89 = -20.57 +   0.68)

alignment

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secondary structure

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dotplot

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Window 8

Location 15,648,058 – 15,648,168
Length 110
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 60.97
Shannon entropy 0.54668
G+C content 0.55180
Mean single sequence MFE -39.90
Consensus MFE -20.98
Energy contribution -20.99
Covariance contribution 0.01
Combinations/Pair 1.35
Mean z-score -1.10
Structure conservation index 0.53
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.42
SVM RNA-class probability 0.686536
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 15648058 110 + 24543557
AGGACCGCCAGGAUUCCAUCCAGACGGGUGAGAGCUACUACAUCCGCAUGGUUUUCGGGUGGUUUUCU------CUG-GAGGAGGAGUGCUAUUUGGUGGUUCGGUGUUCUUAGUGC---
.((((((((((.(((((.(((...((((.((((((((((....((....))......)))))))))))------)))-..)))))))).)....)))))))))..............--- ( -41.40, z-score =  -1.90, R)
>droYak2.chr3L 18197681 104 + 24197627
AGGACCGCCAGGAUUCCAUCCUGGUGGGCGAGUUUCACCACAUCCACAUGGCUUUCGGGUGGUGGUCG------UUGAGACGAUAGGGAUUAUAGGACCGCCUGGAUUCC----------
....((((((((((...))))))))))....((((((..((..((((...(((....))).))))..)------)))))))....((((((.((((....))))))))))---------- ( -38.40, z-score =  -0.74, R)
>droEre2.scaffold_4784 17906118 116 + 25762168
CGGACCGCCAGGAUUCCAACCAGAUGGGUGAG---UGCGACAUCCGCAUGGUUUUUCGGUGGUUGUCGAAGCUGUUGUCACUGGAGGAGGUCUAUG-UGGCUUAGUCCUUCGAGUAGUGC
..(((((((..((..((.(((.....)))..(---((((.....)))))))..))..))))))).(((((((((..(((((((((.....)))).)-)))).)))..))))))....... ( -39.90, z-score =  -0.65, R)
>consensus
AGGACCGCCAGGAUUCCAUCCAGAUGGGUGAG___UACCACAUCCGCAUGGUUUUCGGGUGGUUGUCG______UUG_GACGAGAGGAGCUAUAUG_UGGCUUGGUCUUC__AGU_____
..(((((((.(((..((((...(.((((((..........)))))))))))..))).))))))).....................(((((................)))))......... (-20.98 = -20.99 +   0.01)

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 23:29:29 2011