Locus 11309

Sequence ID dm3.chr3R
Location 20,257,730 – 20,257,856
Length 126
Max. P 0.998668
window15549 window15550 window15551 window15552

overview

Window 9

Location 20,257,730 – 20,257,820
Length 90
Sequences 6
Columns 104
Reading direction forward
Mean pairwise identity 77.76
Shannon entropy 0.39338
G+C content 0.33294
Mean single sequence MFE -18.83
Consensus MFE -9.15
Energy contribution -9.99
Covariance contribution 0.84
Combinations/Pair 1.33
Mean z-score -2.31
Structure conservation index 0.49
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.94
SVM RNA-class probability 0.858195
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 20257730 90 + 27905053
CAUUUGAAACUUGGACAACAGAUGUCCGCUAUAAAAUUAUUCCUAUUUCUUUGGCUAUGUAUAU-----UCUAUACAUAGCCAGAAAUGUAUAUA---------
............(((((.....)))))................(((((((..(((((((((((.-----..))))))))))))))))))......--------- ( -24.70, z-score =  -4.55, R)
>droAna3.scaffold_13088 297639 92 + 569066
CAUUUGAAACUUGGACAACAGAUGUCUGCU-UAAAAUUAUUCCUUCACCCCACAUACCCCACA-----------ACAUAGUGAAGACUUUAUGUACGGAAAUAA
..((((......(((((.....)))))...-...........((((((...............-----------.....))))))..........))))..... (  -9.55, z-score =   0.82, R)
>droEre2.scaffold_4820 2667960 84 - 10470090
CAUUUGAAAGUUGGACAACAGAUGUCCGCUGUAAAAUUAUUCCUAUUUCUU-GGCCACGAAUGU----------ACAUAGCCAGAAAUGUAUAUA---------
.((((...(((.(((((.....))))))))...))))......(((((((.-(((.........----------.....))))))))))......--------- ( -16.24, z-score =  -1.03, R)
>droYak2.chr3R 2585911 92 - 28832112
CAUUUGAAAGUUGGACAACAGAUGUCCGCUACAAAAUGAUUCCUAUUUCUU-GGCUACGAAUAUAU--ACAUAAACAUGCCCAGAAACGUAUAUA---------
(((((...(((.(((((.....))))))))...))))).......(((((.-(((...........--..........))).)))))........--------- ( -17.60, z-score =  -1.94, R)
>droSec1.super_0 20594718 89 + 21120651
CAUUUGAAACUUGGACAACAGAUGUCCGCUAUAAAAUUAUUCCUAUUUCUU-GGCUACGUAUAU-----UGUAUACAUAGCCAGAAAUGUAUAUA---------
............(((((.....)))))................(((((((.-(((((.(((((.-----..))))).))))))))))))......--------- ( -22.00, z-score =  -3.39, R)
>droSim1.chr3R 20095877 94 + 27517382
CAUUUGAAACUUGGACAACAGAUGUCCGCUAUAAAAUUAUUCCUAUUUCUU-GGCUACGUAUAUAUCUAUCUAUACAUAGCCAGAAAUGUAUAUA---------
............(((((.....)))))................(((((((.-(((((.(((((........))))).))))))))))))......--------- ( -22.90, z-score =  -3.78, R)
>consensus
CAUUUGAAACUUGGACAACAGAUGUCCGCUAUAAAAUUAUUCCUAUUUCUU_GGCUACGUAUAU_____U_UAUACAUAGCCAGAAAUGUAUAUA_________
............(((((.....)))))................(((((((..(((((.(................).))))))))))))............... ( -9.15 =  -9.99 +   0.84)

alignment

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secondary structure

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dotplot

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Window 0

Location 20,257,730 – 20,257,820
Length 90
Sequences 6
Columns 104
Reading direction reverse
Mean pairwise identity 77.76
Shannon entropy 0.39338
G+C content 0.33294
Mean single sequence MFE -23.97
Consensus MFE -14.58
Energy contribution -14.76
Covariance contribution 0.17
Combinations/Pair 1.44
Mean z-score -3.35
Structure conservation index 0.61
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.35
SVM RNA-class probability 0.998414
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 20257730 90 - 27905053
---------UAUAUACAUUUCUGGCUAUGUAUAGA-----AUAUACAUAGCCAAAGAAAUAGGAAUAAUUUUAUAGCGGACAUCUGUUGUCCAAGUUUCAAAUG
---------......(((((.((((((((((((..-----.))))))))))))..(((((..(((....))).....(((((.....)))))..)))))))))) ( -25.50, z-score =  -4.45, R)
>droAna3.scaffold_13088 297639 92 - 569066
UUAUUUCCGUACAUAAAGUCUUCACUAUGU-----------UGUGGGGUAUGUGGGGUGAAGGAAUAAUUUUA-AGCAGACAUCUGUUGUCCAAGUUUCAAAUG
...((.((.((((((....((((((.....-----------.)))))))))))).)).)).(((((.......-(((((....)))))......)))))..... ( -20.92, z-score =  -1.17, R)
>droEre2.scaffold_4820 2667960 84 + 10470090
---------UAUAUACAUUUCUGGCUAUGU----------ACAUUCGUGGCC-AAGAAAUAGGAAUAAUUUUACAGCGGACAUCUGUUGUCCAACUUUCAAAUG
---------.......(((((((((((((.----------.....)))))))-.))))))..(((.......(((((((....)))))))......)))..... ( -23.32, z-score =  -3.79, R)
>droYak2.chr3R 2585911 92 + 28832112
---------UAUAUACGUUUCUGGGCAUGUUUAUGU--AUAUAUUCGUAGCC-AAGAAAUAGGAAUCAUUUUGUAGCGGACAUCUGUUGUCCAACUUUCAAAUG
---------.......((((((.((((((..(((..--..)))..))).)))-.))))))......(((((...((.(((((.....)))))..))...))))) ( -19.60, z-score =  -1.31, R)
>droSec1.super_0 20594718 89 - 21120651
---------UAUAUACAUUUCUGGCUAUGUAUACA-----AUAUACGUAGCC-AAGAAAUAGGAAUAAUUUUAUAGCGGACAUCUGUUGUCCAAGUUUCAAAUG
---------.......(((((((((((((((((..-----.)))))))))))-.)))))).(((((......(((((((....)))))))....)))))..... ( -26.40, z-score =  -4.77, R)
>droSim1.chr3R 20095877 94 - 27517382
---------UAUAUACAUUUCUGGCUAUGUAUAGAUAGAUAUAUACGUAGCC-AAGAAAUAGGAAUAAUUUUAUAGCGGACAUCUGUUGUCCAAGUUUCAAAUG
---------.......(((((((((((((((((........)))))))))))-.)))))).(((((......(((((((....)))))))....)))))..... ( -28.10, z-score =  -4.61, R)
>consensus
_________UAUAUACAUUUCUGGCUAUGUAUA_A_____AUAUACGUAGCC_AAGAAAUAGGAAUAAUUUUAUAGCGGACAUCUGUUGUCCAAGUUUCAAAUG
................(((((((((((((................)))))))..)))))).(((((......(((((((....)))))))....)))))..... (-14.58 = -14.76 +   0.17)

alignment

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secondary structure

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dotplot

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Window 1

Location 20,257,755 – 20,257,856
Length 101
Sequences 6
Columns 112
Reading direction forward
Mean pairwise identity 72.66
Shannon entropy 0.49943
G+C content 0.30105
Mean single sequence MFE -24.06
Consensus MFE -10.03
Energy contribution -11.87
Covariance contribution 1.84
Combinations/Pair 1.36
Mean z-score -3.18
Structure conservation index 0.42
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.85
SVM RNA-class probability 0.995797
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 20257755 101 + 27905053
CCGCUAUAAAAUUAUUCCUAUUUCUUUGGCUAUGUAUAU-----UCUAUACAUAGCCAGAAAUGUAUAUA---AAUGAUAUACAAUAAAUAAAGGUU---UUCGUGGUGUGA
.(((((..(((.....(((.....((((((((((((((.-----..))))))))))))))..(((((((.---....)))))))........))).)---))..)))))... ( -29.90, z-score =  -5.13, R)
>droAna3.scaffold_13088 297664 99 + 569066
CUGCU-UAAAAUUAUUCCUUCACCCCACAUACCCCACA-----------ACAUAGUGAAGACUUUAUGUACGGAAAUAAGAAUCUUAUAUACAAAUAUAUAUUUAGGAGGA-
.....-.........((((((.((..((((((..(((.-----------.....)))..)....)))))..))............((((((....))))))....))))))- ( -13.20, z-score =  -0.38, R)
>droEre2.scaffold_4820 2667985 94 - 10470090
CCGCUGUAAAAUUAUUCCUAUUUCUU-GGCCACGAAUGU----------ACAUAGCCAGAAAUGUAUAUA---AAUGAUAUACGAUAAAUAAAGGUU---UUUGUGGUGGA-
((((..(((((.....(((((((((.-(((.........----------.....)))))))))((((((.---....)))))).........))).)---))))..)))).- ( -23.74, z-score =  -2.69, R)
>droYak2.chr3R 2585936 105 - 28832112
CCGCUACAAAAUGAUUCCUAUUUCUU-GGCUACGAAUAUA--UACAUAAACAUGCCCAGAAACGUAUAUA---AAUGAUAUACAAUAAAUAAAGGUUAGAUUCGUAAUGGA-
(((.(((.........(((.(((((.-(((..........--...........))).))))).((((((.---....)))))).........)))........))).))).- ( -16.93, z-score =  -1.02, R)
>droSec1.super_0 20594743 99 + 21120651
CCGCUAUAAAAUUAUUCCUAUUUCUU-GGCUACGUAUAU-----UGUAUACAUAGCCAGAAAUGUAUAUA---AAUUAUAUACAAUAAAUAAAGGUU---UUCGUGGUGGA-
((((((..(((.....(((((((((.-(((((.(((((.-----..))))).)))))))))))(((((((---...))))))).........))).)---))..)))))).- ( -29.90, z-score =  -4.88, R)
>droSim1.chr3R 20095902 104 + 27517382
CCGCUAUAAAAUUAUUCCUAUUUCUU-GGCUACGUAUAUAUCUAUCUAUACAUAGCCAGAAAUGUAUAUA---AAUGAUAUACAAUAAAUAAAGGUU---UUCGUGGUGGA-
((((((..(((.....(((((((((.-(((((.(((((........))))).)))))))))))((((((.---....)))))).........))).)---))..)))))).- ( -30.70, z-score =  -5.00, R)
>consensus
CCGCUAUAAAAUUAUUCCUAUUUCUU_GGCUACGUAUAU_____U_UAUACAUAGCCAGAAAUGUAUAUA___AAUGAUAUACAAUAAAUAAAGGUU___UUCGUGGUGGA_
(((((((.........(((((((((..(((((.(................).)))))))))))((((((........)))))).........)))........))))))).. (-10.03 = -11.87 +   1.84)

alignment

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secondary structure

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dotplot

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Window 2

Location 20,257,755 – 20,257,856
Length 101
Sequences 6
Columns 112
Reading direction reverse
Mean pairwise identity 72.66
Shannon entropy 0.49943
G+C content 0.30105
Mean single sequence MFE -23.45
Consensus MFE -10.96
Energy contribution -12.02
Covariance contribution 1.06
Combinations/Pair 1.36
Mean z-score -3.34
Structure conservation index 0.47
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.44
SVM RNA-class probability 0.998668
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 20257755 101 - 27905053
UCACACCACGAA---AACCUUUAUUUAUUGUAUAUCAUU---UAUAUACAUUUCUGGCUAUGUAUAGA-----AUAUACAUAGCCAAAGAAAUAGGAAUAAUUUUAUAGCGG
........((..---.....((((((...((((((....---.))))))(((((((((((((((((..-----.)))))))))))..))))))..))))))........)). ( -24.06, z-score =  -4.55, R)
>droAna3.scaffold_13088 297664 99 - 569066
-UCCUCCUAAAUAUAUAUUUGUAUAUAAGAUUCUUAUUUCCGUACAUAAAGUCUUCACUAUGU-----------UGUGGGGUAUGUGGGGUGAAGGAAUAAUUUUA-AGCAG
-..........((((((....))))))..((((((.((.((.((((((....((((((.....-----------.)))))))))))).)).)))))))).......-..... ( -19.60, z-score =  -0.46, R)
>droEre2.scaffold_4820 2667985 94 + 10470090
-UCCACCACAAA---AACCUUUAUUUAUCGUAUAUCAUU---UAUAUACAUUUCUGGCUAUGU----------ACAUUCGUGGCC-AAGAAAUAGGAAUAAUUUUACAGCGG
-(((........---..............((((((....---.))))))(((((((((((((.----------.....)))))))-.)))))).)))............... ( -21.60, z-score =  -3.78, R)
>droYak2.chr3R 2585936 105 + 28832112
-UCCAUUACGAAUCUAACCUUUAUUUAUUGUAUAUCAUU---UAUAUACGUUUCUGGGCAUGUUUAUGUA--UAUAUUCGUAGCC-AAGAAAUAGGAAUCAUUUUGUAGCGG
-.((.(((((((.....(((.........((((((....---.))))))((((((.((((((..(((...--.)))..))).)))-.)))))))))......))))))).)) ( -22.50, z-score =  -2.08, R)
>droSec1.super_0 20594743 99 - 21120651
-UCCACCACGAA---AACCUUUAUUUAUUGUAUAUAAUU---UAUAUACAUUUCUGGCUAUGUAUACA-----AUAUACGUAGCC-AAGAAAUAGGAAUAAUUUUAUAGCGG
-.......((..---.....((((((...(((((((...---)))))))(((((((((((((((((..-----.)))))))))))-.))))))..))))))........)). ( -25.96, z-score =  -4.75, R)
>droSim1.chr3R 20095902 104 - 27517382
-UCCACCACGAA---AACCUUUAUUUAUUGUAUAUCAUU---UAUAUACAUUUCUGGCUAUGUAUAGAUAGAUAUAUACGUAGCC-AAGAAAUAGGAAUAAUUUUAUAGCGG
-.......((..---.....((((((...((((((....---.))))))(((((((((((((((((........)))))))))))-.))))))..))))))........)). ( -26.96, z-score =  -4.42, R)
>consensus
_UCCACCACGAA___AACCUUUAUUUAUUGUAUAUCAUU___UAUAUACAUUUCUGGCUAUGUAUA_A_____AUAUACGUAGCC_AAGAAAUAGGAAUAAUUUUAUAGCGG
.(((.........................((((((........))))))(((((((((((((................)))))))..)))))).)))............... (-10.96 = -12.02 +   1.06)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:40:33 2011