Locus 9742

Sequence ID dm3.chr3R
Location 8,646,476 – 8,646,596
Length 120
Max. P 0.652527
window13359 window13360 window13361 window13362

overview

Window 9

Location 8,646,476 – 8,646,594
Length 118
Sequences 5
Columns 119
Reading direction forward
Mean pairwise identity 88.01
Shannon entropy 0.21747
G+C content 0.31700
Mean single sequence MFE -25.72
Consensus MFE -16.82
Energy contribution -19.40
Covariance contribution 2.58
Combinations/Pair 1.03
Mean z-score -2.11
Structure conservation index 0.65
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.09
SVM RNA-class probability 0.540076
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 8646476 118 + 27905053
UAAACAGUGGUGUGCACUUAUUUUUGAUAAUUUACACAUUUUUAUUAUCUGGAAACUAAUAAAUAAGUGUCUGAACG-UGUAAUCGAUAAGAGCACAUUUUUCACCCAGUGCACUUUAU
.....((((((((((.((((((....(((.((((.((((((...((((..(....)..))))..)))))).))))..-)))....)))))).))))))....(((...))))))).... ( -24.60, z-score =  -1.64, R)
>droSim1.chr3R 14746590 118 - 27517382
UAAAGAGUUGUGUGCACUUAUUUCUGAUAAUUUACACAUGUUUAUUAUCUGGAAACUAAUAAAUAUGUGUCUGAACC-UAUAAUCGAUAAGAACACAUUUUUCACCCAGUGCACUUUAU
....(((..(((((..((((((....(((.(((((((((((((((((...(....)))))))))))))))..)))..-)))....))))))..)))))..)))................ ( -27.00, z-score =  -3.18, R)
>droSec1.super_0 7777874 119 - 21120651
UAAAGAGUAGUGUGCACUUAUUUCUGAUAAUUUACACAUGUUUAUUAUCUGGAAACUAAUAAAUAUGUGUCUGAACCGUGUAAUCGAUAAGAACACAUUUUUCACCCAGUGCACUUUAU
......((((.(((((((...............((((((((((((((...(....))))))))))))))).((((..((((..((.....))..))))..))))...))))))).)))) ( -30.70, z-score =  -3.63, R)
>droYak2.chr3R 12939213 118 + 28832112
UGUAUAGAAGGGAGAACUCAUUUGUGAUAACUUACACAUAUUUAUUAUCUGUGAACCAAUAAAUAUGUGUCUGAACC-UGAAAUCGAUAAGAACACAUUUUUCACCCAGUGCACUGUAU
(((((....(((.(((......((((....(..(((((((((((((....(....).)))))))))))))..)....-.....((.....)).))))...))).))).)))))...... ( -22.60, z-score =  -0.66, R)
>droEre2.scaffold_4770 4743575 117 - 17746568
UUUACAGGAGUGUGCACUUGUUUGUGAUAAUUUACACAUGUUUAUUAUCAGUAAACUAAUAAAUAAGCCUCUGAACC-UGUAAUCGAUAAGAACCCAUUUU-CACCCAGUGCACUUUGU
......((((((..(.(((((((((((((((..((....))..))))))((....)).)))))))))....((((..-((...((.....))...))..))-))....)..)))))).. ( -23.70, z-score =  -1.46, R)
>consensus
UAAACAGUAGUGUGCACUUAUUUCUGAUAAUUUACACAUGUUUAUUAUCUGGAAACUAAUAAAUAUGUGUCUGAACC_UGUAAUCGAUAAGAACACAUUUUUCACCCAGUGCACUUUAU
...........(((((((...............((((((((((((((...(....))))))))))))))).((((...(((..((.....))..)))...))))...)))))))..... (-16.82 = -19.40 +   2.58)

alignment

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secondary structure

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dotplot

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Window 0

Location 8,646,476 – 8,646,594
Length 118
Sequences 5
Columns 119
Reading direction reverse
Mean pairwise identity 88.01
Shannon entropy 0.21747
G+C content 0.31700
Mean single sequence MFE -26.49
Consensus MFE -19.82
Energy contribution -20.94
Covariance contribution 1.12
Combinations/Pair 1.10
Mean z-score -1.83
Structure conservation index 0.75
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.34
SVM RNA-class probability 0.652527
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 8646476 118 - 27905053
AUAAAGUGCACUGGGUGAAAAAUGUGCUCUUAUCGAUUACA-CGUUCAGACACUUAUUUAUUAGUUUCCAGAUAAUAAAAAUGUGUAAAUUAUCAAAAAUAAGUGCACACCACUGUUUA
.....(((((((...((((...((((.((.....)).))))-..)))).((((...(((((((.........)))))))...))))...............)))))))........... ( -23.20, z-score =  -1.26, R)
>droSim1.chr3R 14746590 118 + 27517382
AUAAAGUGCACUGGGUGAAAAAUGUGUUCUUAUCGAUUAUA-GGUUCAGACACAUAUUUAUUAGUUUCCAGAUAAUAAACAUGUGUAAAUUAUCAGAAAUAAGUGCACACAACUCUUUA
.....(((((((.((((((..(((((((...(((.......-)))...))))))).)))))).(((((..((((((..((....))..)))))).))))).)))))))........... ( -27.60, z-score =  -2.63, R)
>droSec1.super_0 7777874 119 + 21120651
AUAAAGUGCACUGGGUGAAAAAUGUGUUCUUAUCGAUUACACGGUUCAGACACAUAUUUAUUAGUUUCCAGAUAAUAAACAUGUGUAAAUUAUCAGAAAUAAGUGCACACUACUCUUUA
.....(((((((.((((((..(((((((...((((......))))...))))))).)))))).(((((..((((((..((....))..)))))).))))).)))))))........... ( -29.40, z-score =  -2.90, R)
>droYak2.chr3R 12939213 118 - 28832112
AUACAGUGCACUGGGUGAAAAAUGUGUUCUUAUCGAUUUCA-GGUUCAGACACAUAUUUAUUGGUUCACAGAUAAUAAAUAUGUGUAAGUUAUCACAAAUGAGUUCUCCCUUCUAUACA
.....(((....(((.(((...((((..(((...((.....-...))..((((((((((((((.........)))))))))))))))))....))))......))).))).....))). ( -25.00, z-score =  -0.83, R)
>droEre2.scaffold_4770 4743575 117 + 17746568
ACAAAGUGCACUGGGUG-AAAAUGGGUUCUUAUCGAUUACA-GGUUCAGAGGCUUAUUUAUUAGUUUACUGAUAAUAAACAUGUGUAAAUUAUCACAAACAAGUGCACACUCCUGUAAA
.....((((((((.(((-((((((((((((.(((.......-)))..))).))))))))..((((((((...............))))))))))))...).)))))))........... ( -27.26, z-score =  -1.52, R)
>consensus
AUAAAGUGCACUGGGUGAAAAAUGUGUUCUUAUCGAUUACA_GGUUCAGACACAUAUUUAUUAGUUUCCAGAUAAUAAACAUGUGUAAAUUAUCACAAAUAAGUGCACACUACUCUUUA
.....(((((((...((((...((((.((.....)).))))...)))).((((((.(((((((.........))))))).))))))...............)))))))........... (-19.82 = -20.94 +   1.12)

alignment

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secondary structure

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dotplot

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Window 1

Location 8,646,478 – 8,646,596
Length 118
Sequences 5
Columns 119
Reading direction forward
Mean pairwise identity 88.60
Shannon entropy 0.20595
G+C content 0.32378
Mean single sequence MFE -25.98
Consensus MFE -16.82
Energy contribution -19.40
Covariance contribution 2.58
Combinations/Pair 1.03
Mean z-score -2.16
Structure conservation index 0.65
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.09
SVM RNA-class probability 0.538432
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 8646478 118 + 27905053
AACAGUGGUGUGCACUUAUUUUUGAUAAUUUACACAUUUUUAUUAUCUGGAAACUAAUAAAUAAGUGUCUGAACG-UGUAAUCGAUAAGAGCACAUUUUUCACCCAGUGCACUUUAUAG
...((((((((((.((((((....(((.((((.((((((...((((..(....)..))))..)))))).))))..-)))....)))))).))))))....(((...)))))))...... ( -24.60, z-score =  -1.55, R)
>droSim1.chr3R 14746592 118 - 27517382
AAGAGUUGUGUGCACUUAUUUCUGAUAAUUUACACAUGUUUAUUAUCUGGAAACUAAUAAAUAUGUGUCUGAACC-UAUAAUCGAUAAGAACACAUUUUUCACCCAGUGCACUUUAUAG
..(((..(((((..((((((....(((.(((((((((((((((((...(....)))))))))))))))..)))..-)))....))))))..)))))..))).................. ( -27.00, z-score =  -2.93, R)
>droSec1.super_0 7777876 119 - 21120651
AAGAGUAGUGUGCACUUAUUUCUGAUAAUUUACACAUGUUUAUUAUCUGGAAACUAAUAAAUAUGUGUCUGAACCGUGUAAUCGAUAAGAACACAUUUUUCACCCAGUGCACUUUAUAG
....((((.(((((((...............((((((((((((((...(....))))))))))))))).((((..((((..((.....))..))))..))))...))))))).)))).. ( -31.40, z-score =  -3.70, R)
>droYak2.chr3R 12939215 118 + 28832112
UAUAGAAGGGAGAACUCAUUUGUGAUAACUUACACAUAUUUAUUAUCUGUGAACCAAUAAAUAUGUGUCUGAACC-UGAAAUCGAUAAGAACACAUUUUUCACCCAGUGCACUGUAUAG
.......(((.(((......((((....(..(((((((((((((....(....).)))))))))))))..)....-.....((.....)).))))...))).))).............. ( -21.50, z-score =  -0.68, R)
>droEre2.scaffold_4770 4743577 117 - 17746568
UACAGGAGUGUGCACUUGUUUGUGAUAAUUUACACAUGUUUAUUAUCAGUAAACUAAUAAAUAAGCCUCUGAACC-UGUAAUCGAUAAGAACCCAUUUU-CACCCAGUGCACUUUGUAG
(((((.((((..(.(((((((((((((((..((....))..))))))((....)).)))))))))....((((..-((...((.....))...))..))-))....)..))))))))). ( -25.40, z-score =  -1.95, R)
>consensus
AACAGUAGUGUGCACUUAUUUCUGAUAAUUUACACAUGUUUAUUAUCUGGAAACUAAUAAAUAUGUGUCUGAACC_UGUAAUCGAUAAGAACACAUUUUUCACCCAGUGCACUUUAUAG
.........(((((((...............((((((((((((((...(....))))))))))))))).((((...(((..((.....))..)))...))))...)))))))....... (-16.82 = -19.40 +   2.58)

alignment

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secondary structure

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dotplot

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Window 2

Location 8,646,478 – 8,646,596
Length 118
Sequences 5
Columns 119
Reading direction reverse
Mean pairwise identity 88.60
Shannon entropy 0.20595
G+C content 0.32378
Mean single sequence MFE -26.29
Consensus MFE -19.82
Energy contribution -20.94
Covariance contribution 1.12
Combinations/Pair 1.10
Mean z-score -1.75
Structure conservation index 0.75
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.10
SVM RNA-class probability 0.541968
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 8646478 118 - 27905053
CUAUAAAGUGCACUGGGUGAAAAAUGUGCUCUUAUCGAUUACA-CGUUCAGACACUUAUUUAUUAGUUUCCAGAUAAUAAAAAUGUGUAAAUUAUCAAAAAUAAGUGCACACCACUGUU
.......(((((((...((((...((((.((.....)).))))-..)))).((((...(((((((.........)))))))...))))...............)))))))......... ( -23.20, z-score =  -1.36, R)
>droSim1.chr3R 14746592 118 + 27517382
CUAUAAAGUGCACUGGGUGAAAAAUGUGUUCUUAUCGAUUAUA-GGUUCAGACACAUAUUUAUUAGUUUCCAGAUAAUAAACAUGUGUAAAUUAUCAGAAAUAAGUGCACACAACUCUU
.......(((((((.((((((..(((((((...(((.......-)))...))))))).)))))).(((((..((((((..((....))..)))))).))))).)))))))......... ( -27.60, z-score =  -2.54, R)
>droSec1.super_0 7777876 119 + 21120651
CUAUAAAGUGCACUGGGUGAAAAAUGUGUUCUUAUCGAUUACACGGUUCAGACACAUAUUUAUUAGUUUCCAGAUAAUAAACAUGUGUAAAUUAUCAGAAAUAAGUGCACACUACUCUU
.......(((((((.((((((..(((((((...((((......))))...))))))).)))))).(((((..((((((..((....))..)))))).))))).)))))))......... ( -29.40, z-score =  -2.93, R)
>droYak2.chr3R 12939215 118 - 28832112
CUAUACAGUGCACUGGGUGAAAAAUGUGUUCUUAUCGAUUUCA-GGUUCAGACACAUAUUUAUUGGUUCACAGAUAAUAAAUAUGUGUAAGUUAUCACAAAUGAGUUCUCCCUUCUAUA
..............(((.(((...((((..(((...((.....-...))..((((((((((((((.........)))))))))))))))))....))))......))).)))....... ( -24.00, z-score =  -0.58, R)
>droEre2.scaffold_4770 4743577 117 + 17746568
CUACAAAGUGCACUGGGUG-AAAAUGGGUUCUUAUCGAUUACA-GGUUCAGAGGCUUAUUUAUUAGUUUACUGAUAAUAAACAUGUGUAAAUUAUCACAAACAAGUGCACACUCCUGUA
.......((((((((.(((-((((((((((((.(((.......-)))..))).))))))))..((((((((...............))))))))))))...).)))))))......... ( -27.26, z-score =  -1.35, R)
>consensus
CUAUAAAGUGCACUGGGUGAAAAAUGUGUUCUUAUCGAUUACA_GGUUCAGACACAUAUUUAUUAGUUUCCAGAUAAUAAACAUGUGUAAAUUAUCACAAAUAAGUGCACACUACUCUU
.......(((((((...((((...((((.((.....)).))))...)))).((((((.(((((((.........))))))).))))))...............)))))))......... (-19.82 = -20.94 +   1.12)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:10:12 2011