Locus 11922

Sequence ID dm3.chr3R
Location 24,542,626 – 24,542,751
Length 125
Max. P 0.973350
window16382 window16383

overview

Window 2

Location 24,542,626 – 24,542,751
Length 125
Sequences 6
Columns 132
Reading direction forward
Mean pairwise identity 81.91
Shannon entropy 0.34538
G+C content 0.48648
Mean single sequence MFE -38.62
Consensus MFE -17.57
Energy contribution -18.58
Covariance contribution 1.02
Combinations/Pair 1.23
Mean z-score -2.66
Structure conservation index 0.45
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.82
SVM RNA-class probability 0.827109
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 24542626 125 + 27905053
GAUGGCC---GUGCGACUUAACUGGUACUUAGGGCC-AACGCCUGCAAUUGCAUUAAUUGAACUCGAUGACAUUAAACUGCCGACUGGC---AGAUGUUCGAUUCCUAAGAUGACGGCCCAUUGUGGCCAUG
.((((((---((((.(......).))))...(((((-......(((....)))......(((.((((..((((....(((((....)))---)))))))))))))..........))))).....)))))). ( -40.90, z-score =  -3.08, R)
>droAna3.scaffold_13340 17348436 105 + 23697760
AAUAGCCGAAGUUCGGCUGAACUGGUACUUAAGCUC------------------GAAUUGAUCUCAAUGACAUUAAAUUGC-GACUAACCAGAGAUGUUCCGUCUCUUGGAUGACAAACAGUUG--------
..((((((.....))))))(((((............------------------...(((.((.((((........)))).-)).)))(((((((((...)))))).)))........))))).-------- ( -26.50, z-score =  -1.65, R)
>droEre2.scaffold_4820 6989536 125 - 10470090
GAUGGCC---GUGCGACUUAACUGGUACUUAGGGCC-AACGCCUGCAAUUGCAUAAAUUGAACUCGAUGACAUUAAACAGCCGACUGGC---AGGUGUUCGAGUGCUAAGAUGACGGCCCAUUGUAACGAUG
...((((---((.(((((.....))).(((((.(((-(((((((((..........((((....)))).........(((....)))))---))))))).).)).))))).))))))))(((((...))))) ( -38.60, z-score =  -1.94, R)
>droYak2.chr3R 6885212 128 - 28832112
GAUGGCCCC-GUGCGACUUAACUGGUACUUAGGGCCCAACGCCUGCAAUUGCAUAAAUUGAACUCGAUGACAUUAAACUGCCGACUGGC---AGAUGUUCGAGUCCUAAGAUGACGUCCCAUUGUGGCGAUG
...(((((.-((((.(......).))))...)))))...((((.((((((((((.....(.((((((..((((....(((((....)))---)))))))))))).)....))).))....)))))))))... ( -39.90, z-score =  -2.56, R)
>droSec1.super_4 3424266 125 + 6179234
GAUGGCC---GUGCGACUUAACUGGUACUUAGGGCC-AACGCCUGCAAUUGCAUAAAUUGAACUCGAUGACAUUAAACUGCCGACUGGC---AGAUGUUCGAGUCCUAAGAUGACGGCCCAUUGUGGCCAUG
.((((((---((((.(......).))))...(((((-..((.((.(((((.....))))).((((((..((((....(((((....)))---))))))))))))....)).))..))))).....)))))). ( -44.20, z-score =  -3.72, R)
>droSim1.chr3R 24240926 125 + 27517382
GAUGGCC---GUGUGACUUAACUGGUACUUAGGGCC-AACGCCUGCAAUUGCAUAAAUUGAACUCGAUGACAUUAAACUGCCGACUGGC---AGAUGUUCGAGUCCUAAGAUGACGGCCCAUUGUGGCCAUG
.((((((---(.(((.((.....)))))...(((((-..((.((.(((((.....))))).((((((..((((....(((((....)))---))))))))))))....)).))..)))))....))))))). ( -41.60, z-score =  -2.99, R)
>consensus
GAUGGCC___GUGCGACUUAACUGGUACUUAGGGCC_AACGCCUGCAAUUGCAUAAAUUGAACUCGAUGACAUUAAACUGCCGACUGGC___AGAUGUUCGAGUCCUAAGAUGACGGCCCAUUGUGGCCAUG
(((((..........(((.....))).((((((..........(((....)))........((((((..(((((.....(((....)))....)))))))))))))))))........)))))......... (-17.57 = -18.58 +   1.02)

alignment

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secondary structure

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dotplot

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Window 3

Location 24,542,626 – 24,542,751
Length 125
Sequences 6
Columns 132
Reading direction reverse
Mean pairwise identity 81.91
Shannon entropy 0.34538
G+C content 0.48648
Mean single sequence MFE -39.15
Consensus MFE -22.22
Energy contribution -22.85
Covariance contribution 0.63
Combinations/Pair 1.27
Mean z-score -2.75
Structure conservation index 0.57
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.89
SVM RNA-class probability 0.973350
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 24542626 125 - 27905053
CAUGGCCACAAUGGGCCGUCAUCUUAGGAAUCGAACAUCU---GCCAGUCGGCAGUUUAAUGUCAUCGAGUUCAAUUAAUGCAAUUGCAGGCGUU-GGCCCUAAGUACCAGUUAAGUCGCAC---GGCCAUC
.((((((.....((((((((......(((.((((((((((---(((....)))))....))))..)))).)))......(((....))))))...-)))))...((..(......)..))..---)))))). ( -39.50, z-score =  -2.35, R)
>droAna3.scaffold_13340 17348436 105 - 23697760
--------CAACUGUUUGUCAUCCAAGAGACGGAACAUCUCUGGUUAGUC-GCAAUUUAAUGUCAUUGAGAUCAAUUC------------------GAGCUUAAGUACCAGUUCAGCCGAACUUCGGCUAUU
--------.(((((((((((........))))))....(((..(((.(((-.((((........)))).))).)))..------------------))).........))))).(((((.....)))))... ( -23.70, z-score =  -0.80, R)
>droEre2.scaffold_4820 6989536 125 + 10470090
CAUCGUUACAAUGGGCCGUCAUCUUAGCACUCGAACACCU---GCCAGUCGGCUGUUUAAUGUCAUCGAGUUCAAUUUAUGCAAUUGCAGGCGUU-GGCCCUAAGUACCAGUUAAGUCGCAC---GGCCAUC
.............(((((((..(((((((((((((((...---(((....))).......)))..))))))...((((((((....)))(((...-.))).)))))....))))))..).))---))))... ( -35.90, z-score =  -1.69, R)
>droYak2.chr3R 6885212 128 + 28832112
CAUCGCCACAAUGGGACGUCAUCUUAGGACUCGAACAUCU---GCCAGUCGGCAGUUUAAUGUCAUCGAGUUCAAUUUAUGCAAUUGCAGGCGUUGGGCCCUAAGUACCAGUUAAGUCGCAC-GGGGCCAUC
((.((((....(((((.....)))))((((((((((((((---(((....)))))....))))..))))))))......(((....))))))).))((((((..((..(......)..))..-))))))... ( -45.10, z-score =  -3.50, R)
>droSec1.super_4 3424266 125 - 6179234
CAUGGCCACAAUGGGCCGUCAUCUUAGGACUCGAACAUCU---GCCAGUCGGCAGUUUAAUGUCAUCGAGUUCAAUUUAUGCAAUUGCAGGCGUU-GGCCCUAAGUACCAGUUAAGUCGCAC---GGCCAUC
.((((((.....((((((((......((((((((((((((---(((....)))))....))))..))))))))......(((....))))))...-)))))...((..(......)..))..---)))))). ( -45.50, z-score =  -3.94, R)
>droSim1.chr3R 24240926 125 - 27517382
CAUGGCCACAAUGGGCCGUCAUCUUAGGACUCGAACAUCU---GCCAGUCGGCAGUUUAAUGUCAUCGAGUUCAAUUUAUGCAAUUGCAGGCGUU-GGCCCUAAGUACCAGUUAAGUCACAC---GGCCAUC
.((((((.....((((((((......((((((((((((((---(((....)))))....))))..))))))))......(((....))))))...-)))))...((..(......)..))..---)))))). ( -45.20, z-score =  -4.23, R)
>consensus
CAUGGCCACAAUGGGCCGUCAUCUUAGGACUCGAACAUCU___GCCAGUCGGCAGUUUAAUGUCAUCGAGUUCAAUUUAUGCAAUUGCAGGCGUU_GGCCCUAAGUACCAGUUAAGUCGCAC___GGCCAUC
............(((((.........((((((((((((.....(((....)))......))))..))))))))......(((....))).......)))))..............(((.......))).... (-22.22 = -22.85 +   0.63)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:52:13 2011