Locus 12015

Sequence ID dm3.chr3R
Location 25,158,958 – 25,159,073
Length 115
Max. P 0.974585
window16515 window16516 window16517

overview

Window 5

Location 25,158,958 – 25,159,059
Length 101
Sequences 5
Columns 113
Reading direction reverse
Mean pairwise identity 70.93
Shannon entropy 0.51172
G+C content 0.41419
Mean single sequence MFE -27.30
Consensus MFE -16.92
Energy contribution -16.88
Covariance contribution -0.04
Combinations/Pair 1.06
Mean z-score -1.73
Structure conservation index 0.62
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.91
SVM RNA-class probability 0.974585
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 25158958 101 - 27905053
AGGUUAGGGCUAUCUAGAUUUAGCCAUGAACCGGCUAGUCAUGGUGAAAACAUUAUCGAUGCGAUAAGAAAACCUAGGGAUUCCUGAUCUUAAAAACAUCA------------
(((((((((...(((((.(((.(((((((.(......)))))))).)))...((((((...))))))......)))))...)))))))))...........------------ ( -26.50, z-score =  -1.79, R)
>droEre2.scaffold_4820 7606027 113 + 10470090
AGGUUGGGGCUAUCUGGAUUUAGCCAUGAACUGGCUAGUCAUGGUGCAAACAUUAUUGAUACCAUGGGAAAAUGUAGGGCUCGAAAAAUGGUUUCCUCACCUUCAAAACAUCA
((((.((((..(((.....(((((((.....)))))))(((((((((((......))).))))))))......................)))..))))))))........... ( -29.00, z-score =  -0.30, R)
>droYak2.chr3R 7502531 112 + 28832112
AGGUGAGGGCUAUCUAGAUUUAGCCAUGAACUGGCUAGUCAUGGUGAAAACAUUAUUGAUACCAUAAGAAAAUGCGGAA-UCGACAAAUGGAUUCCUGACCUAAAAAACAUCA
((((.((((..(((((....((((((.....))))))(((((((((....)))))).(((.((............)).)-)))))...))))))))).))))........... ( -28.90, z-score =  -2.33, R)
>droSec1.super_4 4019553 101 - 6179234
AGGUUGGGGCUAUCUAGAUUUAGCCAUGAACCGGCUAGUCAUGGUGGAAACAUUAUCGAUGCGAUAAGAAAACGUAGCGAUUCCUGACCUUAAAAACAUCA------------
((((..(((.......((((.((((.......)))))))).(((((....)))))(((.((((.........)))).))).)))..))))...........------------ ( -28.80, z-score =  -2.15, R)
>droSim1.chrU 1044333 84 + 15797150
AGGUUAGGGCUAUCUAGAUUUAGCCGUGAACCGGCUAGUCAUGGUGGAAACAUUAUCGAUGCGAUAAGAAAACGUAGGGAUAGA-----------------------------
.........((((((.((((.(((((.....)))))))))((((((....))))))...((((.........)))).)))))).----------------------------- ( -23.30, z-score =  -2.05, R)
>consensus
AGGUUAGGGCUAUCUAGAUUUAGCCAUGAACCGGCUAGUCAUGGUGAAAACAUUAUCGAUGCGAUAAGAAAACGUAGGGAUCGAUAAACGGAAAAACAACA____________
.((((..(((((........)))))...)))).....(((((((((....)))))).)))..................................................... (-16.92 = -16.88 +  -0.04)

alignment

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secondary structure

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dotplot

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Window 6

Location 25,158,978 – 25,159,073
Length 95
Sequences 5
Columns 107
Reading direction forward
Mean pairwise identity 81.77
Shannon entropy 0.31333
G+C content 0.44851
Mean single sequence MFE -24.69
Consensus MFE -18.50
Energy contribution -17.70
Covariance contribution -0.80
Combinations/Pair 1.22
Mean z-score -1.84
Structure conservation index 0.75
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.11
SVM RNA-class probability 0.892796
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 25158978 95 + 27905053
------------AUCCCUAGGUUUUCUUAUCGCAUCGAUAAUGUUUUCACCAUGACUAGCCGGUUCAUGGCUAAAUCUAGAUAGCCCUAACCUAGGGCAUAUGGCUC
------------..(((((((((...(((((((((.....))))............((((((.....))))))......)))))....))))))))).......... ( -25.70, z-score =  -1.71, R)
>droEre2.scaffold_4820 7606047 107 - 10470090
AACCAUUUUUCGAGCCCUACAUUUUCCCAUGGUAUCAAUAAUGUUUGCACCAUGACUAGCCAGUUCAUGGCUAAAUCCAGAUAGCCCCAACCUAGGGCAUACGGCUC
...........(((((...........((((((..(((......))).))))))..((((((.....))))))..........((((.......))))....))))) ( -30.60, z-score =  -3.39, R)
>droYak2.chr3R 7502551 106 - 28832112
-AUCCAUUUGUCGAUUCCGCAUUUUCUUAUGGUAUCAAUAAUGUUUUCACCAUGACUAGCCAGUUCAUGGCUAAAUCUAGAUAGCCCUCACCUAGGGCAUAUGACUC
-........(((((((..........(((((((...............))))))).((((((.....))))))))))......(((((.....)))))....))).. ( -25.06, z-score =  -2.06, R)
>droSec1.super_4 4019573 95 + 6179234
------------AUCGCUACGUUUUCUUAUCGCAUCGAUAAUGUUUCCACCAUGACUAGCCGGUUCAUGGCUAAAUCUAGAUAGCCCCAACCUAGGGCAUACGGCUC
------------...(((.........((((((((.....))))............((((((.....))))))......))))((((.......))))....))).. ( -19.90, z-score =  -0.18, R)
>droSim1.chrU 1044336 95 - 15797150
------------AUCCCUACGUUUUCUUAUCGCAUCGAUAAUGUUUCCACCAUGACUAGCCGGUUCACGGCUAAAUCUAGAUAGCCCUAACCUAGGGCAUACAGCUC
------------...................(((((......(((........)))((((((.....))))))......))).((((((...)))))).....)).. ( -22.20, z-score =  -1.87, R)
>consensus
____________AUCCCUACGUUUUCUUAUCGCAUCGAUAAUGUUUCCACCAUGACUAGCCGGUUCAUGGCUAAAUCUAGAUAGCCCUAACCUAGGGCAUACGGCUC
...............................(((((......(((........)))((((((.....))))))......))).((((.......)))).....)).. (-18.50 = -17.70 +  -0.80)

alignment

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secondary structure

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dotplot

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Window 7

Location 25,158,978 – 25,159,073
Length 95
Sequences 5
Columns 107
Reading direction reverse
Mean pairwise identity 81.77
Shannon entropy 0.31333
G+C content 0.44851
Mean single sequence MFE -30.44
Consensus MFE -22.28
Energy contribution -21.68
Covariance contribution -0.60
Combinations/Pair 1.17
Mean z-score -2.01
Structure conservation index 0.73
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.29
SVM RNA-class probability 0.921674
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 25158978 95 - 27905053
GAGCCAUAUGCCCUAGGUUAGGGCUAUCUAGAUUUAGCCAUGAACCGGCUAGUCAUGGUGAAAACAUUAUCGAUGCGAUAAGAAAACCUAGGGAU------------
..........(((((((((...(((((...((((.((((.......))))))))))))).......((((((...))))))...)))))))))..------------ ( -28.60, z-score =  -2.15, R)
>droEre2.scaffold_4820 7606047 107 + 10470090
GAGCCGUAUGCCCUAGGUUGGGGCUAUCUGGAUUUAGCCAUGAACUGGCUAGUCAUGGUGCAAACAUUAUUGAUACCAUGGGAAAAUGUAGGGCUCGAAAAAUGGUU
(((((.((((((((.....)))))..(((....(((((((.....))))))).((((((((((......))).))))))))))....))).)))))........... ( -39.30, z-score =  -3.18, R)
>droYak2.chr3R 7502551 106 + 28832112
GAGUCAUAUGCCCUAGGUGAGGGCUAUCUAGAUUUAGCCAUGAACUGGCUAGUCAUGGUGAAAACAUUAUUGAUACCAUAAGAAAAUGCGGAAUCGACAAAUGGAU-
..(((....(((((.....)))))..(((.((((.(((((.....)))))))))((((((..((.....))..)))))).)))............)))........- ( -26.50, z-score =  -1.34, R)
>droSec1.super_4 4019573 95 - 6179234
GAGCCGUAUGCCCUAGGUUGGGGCUAUCUAGAUUUAGCCAUGAACCGGCUAGUCAUGGUGGAAACAUUAUCGAUGCGAUAAGAAAACGUAGCGAU------------
..(((((..(((((.....)))))((((......(((((.......)))))(((((((((....)))))).)))..)))).....)))..))...------------ ( -28.00, z-score =  -1.33, R)
>droSim1.chrU 1044336 95 + 15797150
GAGCUGUAUGCCCUAGGUUAGGGCUAUCUAGAUUUAGCCGUGAACCGGCUAGUCAUGGUGGAAACAUUAUCGAUGCGAUAAGAAAACGUAGGGAU------------
...((.(((((((((...))))))((((......((((((.....))))))(((((((((....)))))).)))..)))).......))).))..------------ ( -29.80, z-score =  -2.05, R)
>consensus
GAGCCGUAUGCCCUAGGUUAGGGCUAUCUAGAUUUAGCCAUGAACCGGCUAGUCAUGGUGAAAACAUUAUCGAUGCGAUAAGAAAACGUAGGGAU____________
...((....(((((.....)))))..(((.....(((((.......)))))(((((((((....)))))).)))......))).......))............... (-22.28 = -21.68 +  -0.60)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:54:05 2011