Locus 11447

Sequence ID dm3.chr3R
Location 21,252,994 – 21,253,243
Length 249
Max. P 0.955508
window15733 window15734 window15735 window15736

overview

Window 3

Location 21,252,994 – 21,253,104
Length 110
Sequences 6
Columns 112
Reading direction forward
Mean pairwise identity 94.04
Shannon entropy 0.11165
G+C content 0.42292
Mean single sequence MFE -25.98
Consensus MFE -20.50
Energy contribution -21.03
Covariance contribution 0.53
Combinations/Pair 1.05
Mean z-score -2.45
Structure conservation index 0.79
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.02
SVM RNA-class probability 0.874483
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 21252994 110 + 27905053
AAUUGCUUUCCGCCUCG-UUUUUAUAACCCUUUCAACUCUGUAGAUUUAUGUUCCAUUUU-AGGUGGCGCCACCUGGCGUCGCCUACCUCUGGCAAUAAAAUAUAUAUACCA
...........(((...-....(((((..((..((....)).))..)))))........(-((((((((((....))))))))))).....))).................. ( -25.60, z-score =  -2.81, R)
>droAna3.scaffold_13340 14474430 112 - 23697760
AAUUGGUUUCCGCCUCGCUUUUUAUAACCCUUUCAACUUUGUGGAUUUAUGUUCCAUUUUUAGGUGGCGCCACCUGGCCUCGCAUUCCGCCGGCAAUAAAAUAUAUAUGCGA
....(((....)))((((....((((..............(((((.......)))))...((((((....))))))(((..((.....)).))).......))))...)))) ( -25.10, z-score =  -0.29, R)
>droEre2.scaffold_4820 3678439 110 - 10470090
AAUUACUUUCCGGCUCG-UUUUUAUAACCCUUUCAACUCUGUAGAUUUAUGUUCCACUUU-AGGUGGCGCCACCUGGCGUCGCCUACCUCUGGCAAUAAAAUAUAUAUACCA
...........((...(-((.....)))...........((((.((((.(((((((...(-((((((((((....)))))))))))....))).)))))))).))))..)). ( -26.30, z-score =  -2.79, R)
>droYak2.chr3R 3599838 110 - 28832112
AAUUACUUUCCGCCUCG-UUUUUAUAACCCUUUCAACUCCGUAGAUUUAUGUUCCACUUU-AGGUGGCGCCACCUGGCGUCGCCUACCUCUGGCAAUAAAAUAUAUAUAGCA
...........((...(-((.....)))............(((.((((.(((((((...(-((((((((((....)))))))))))....))).)))))))).)))...)). ( -25.80, z-score =  -2.70, R)
>droSec1.super_13 26869 110 + 2104621
AAUUGCUUUCCGCCUCG-UUUUUAUAACCCUUUCAACUCUGUAGAUUUAUGUUACAUUUU-AGGUGGCGCCACCUGGCGUCGCCUACCUCUGGCAAUAAAAUAUAUAUACCA
...........(((..(-(...(((((..((..((....)).))..)))))..))....(-((((((((((....))))))))))).....))).................. ( -27.20, z-score =  -3.23, R)
>droSim1.chr3R 21081429 110 + 27517382
AAUUGCUUUCCGCCUCG-UUUUUAUAACCCUUUCAACUCUGUAGAUUUAUGUUCCAUUUU-AGGUGGCGCCACCUGGCGUCGCCUACCUCCGGCAAUAAAAUAUAUAUACCA
...........(((...-....(((((..((..((....)).))..)))))........(-((((((((((....))))))))))).....))).................. ( -25.90, z-score =  -2.86, R)
>consensus
AAUUGCUUUCCGCCUCG_UUUUUAUAACCCUUUCAACUCUGUAGAUUUAUGUUCCAUUUU_AGGUGGCGCCACCUGGCGUCGCCUACCUCUGGCAAUAAAAUAUAUAUACCA
...........(((........(((((..((..((....)).))..)))))..........((((((((((....))))))))))......))).................. (-20.50 = -21.03 +   0.53)

alignment

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secondary structure

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dotplot

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Window 4

Location 21,253,033 – 21,253,130
Length 97
Sequences 6
Columns 102
Reading direction forward
Mean pairwise identity 89.49
Shannon entropy 0.19662
G+C content 0.41936
Mean single sequence MFE -28.25
Consensus MFE -23.47
Energy contribution -24.52
Covariance contribution 1.06
Combinations/Pair 1.04
Mean z-score -2.31
Structure conservation index 0.83
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.62
SVM RNA-class probability 0.955508
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 21253033 97 + 27905053
GUAGAUUUAUGUUCCAUUUU-AGGUGGCGCCACCUGGCGUCGCCUACCUCUGGCAAUAAAAUAUAUAUACCAAUGCUACUAUAUAUA----AAGGCGAACAA
.........(((((.....(-((((((((((....)))))))))))......((.......((((((((..........))))))))----...))))))). ( -28.00, z-score =  -2.65, R)
>droAna3.scaffold_13340 14474470 100 - 23697760
GUGGAUUUAUGUUCCAUUUUUAGGUGGCGCCACCUGGCCUCGCAUUCCGCCGGCAAUAAAAUAUAUAUGCGAUUGCACCCCGCCAUAUC--CCGGAGAACAA
.((((.......))))((((..(((((((((....))).((((((.....................)))))).........))))...)--)..)))).... ( -22.90, z-score =   0.95, R)
>droEre2.scaffold_4820 3678478 99 - 10470090
GUAGAUUUAUGUUCCACUUU-AGGUGGCGCCACCUGGCGUCGCCUACCUCUGGCAAUAAAAUAUAUAUACCAAUGCUUCUAUAUAUAUA--AAGGCGAACAA
.........(((((.....(-((((((((((....)))))))))))......((......(((((((((..........))))))))).--...))))))). ( -30.10, z-score =  -3.42, R)
>droYak2.chr3R 3599877 101 - 28832112
GUAGAUUUAUGUUCCACUUU-AGGUGGCGCCACCUGGCGUCGCCUACCUCUGGCAAUAAAAUAUAUAUAGCAAUGCUCCUAUAUAUAUAUAAAGGCGAACAA
.........(((((.....(-((((((((((....)))))))))))......((......((((((((((........))))))))))......))))))). ( -34.40, z-score =  -4.15, R)
>droSec1.super_13 26908 97 + 2104621
GUAGAUUUAUGUUACAUUUU-AGGUGGCGCCACCUGGCGUCGCCUACCUCUGGCAAUAAAAUAUAUAUACCAAUGCUACUAUAUAUA----AAGGCGAACAA
((...(((((((.......(-((((((((((....)))))))))))....(((((..................)))))....)))))----)).))...... ( -26.07, z-score =  -2.01, R)
>droSim1.chr3R 21081468 97 + 27517382
GUAGAUUUAUGUUCCAUUUU-AGGUGGCGCCACCUGGCGUCGCCUACCUCCGGCAAUAAAAUAUAUAUACCAAUGCUACUAUAUAUA----AAGGCGAACAA
.........(((((.....(-((((((((((....)))))))))))......((.......((((((((..........))))))))----...))))))). ( -28.00, z-score =  -2.60, R)
>consensus
GUAGAUUUAUGUUCCAUUUU_AGGUGGCGCCACCUGGCGUCGCCUACCUCUGGCAAUAAAAUAUAUAUACCAAUGCUACUAUAUAUA____AAGGCGAACAA
.........(((((.......((((((((((....)))))))))).......((.......((((((((..........)))))))).......))))))). (-23.47 = -24.52 +   1.06)

alignment

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secondary structure

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dotplot

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Window 5

Location 21,253,033 – 21,253,133
Length 100
Sequences 6
Columns 105
Reading direction forward
Mean pairwise identity 89.47
Shannon entropy 0.19719
G+C content 0.40859
Mean single sequence MFE -28.25
Consensus MFE -23.47
Energy contribution -24.52
Covariance contribution 1.06
Combinations/Pair 1.04
Mean z-score -2.23
Structure conservation index 0.83
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.50
SVM RNA-class probability 0.944192
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 21253033 100 + 27905053
GUAGAUUUAUGUUCCAUUUU-AGGUGGCGCCACCUGGCGUCGCCUACCUCUGGCAAUAAAAUAUAUAUACCAAUGCUACUAUAUAUA----AAGGCGAACAAUAA
.........(((((.....(-((((((((((....)))))))))))......((.......((((((((..........))))))))----...))))))).... ( -28.00, z-score =  -2.55, R)
>droAna3.scaffold_13340 14474470 103 - 23697760
GUGGAUUUAUGUUCCAUUUUUAGGUGGCGCCACCUGGCCUCGCAUUCCGCCGGCAAUAAAAUAUAUAUGCGAUUGCACCCCGCCAUAUC--CCGGAGAACAACAA
.((((.......))))((((..(((((((((....))).((((((.....................)))))).........))))...)--)..))))....... ( -22.90, z-score =   0.95, R)
>droEre2.scaffold_4820 3678478 102 - 10470090
GUAGAUUUAUGUUCCACUUU-AGGUGGCGCCACCUGGCGUCGCCUACCUCUGGCAAUAAAAUAUAUAUACCAAUGCUUCUAUAUAUAUA--AAGGCGAACAAUAA
.........(((((.....(-((((((((((....)))))))))))......((......(((((((((..........))))))))).--...))))))).... ( -30.10, z-score =  -3.29, R)
>droYak2.chr3R 3599877 104 - 28832112
GUAGAUUUAUGUUCCACUUU-AGGUGGCGCCACCUGGCGUCGCCUACCUCUGGCAAUAAAAUAUAUAUAGCAAUGCUCCUAUAUAUAUAUAAAGGCGAACAAUAA
.........(((((.....(-((((((((((....)))))))))))......((......((((((((((........))))))))))......))))))).... ( -34.40, z-score =  -4.04, R)
>droSec1.super_13 26908 100 + 2104621
GUAGAUUUAUGUUACAUUUU-AGGUGGCGCCACCUGGCGUCGCCUACCUCUGGCAAUAAAAUAUAUAUACCAAUGCUACUAUAUAUA----AAGGCGAACAAUAA
((...(((((((.......(-((((((((((....)))))))))))....(((((..................)))))....)))))----)).))......... ( -26.07, z-score =  -1.94, R)
>droSim1.chr3R 21081468 100 + 27517382
GUAGAUUUAUGUUCCAUUUU-AGGUGGCGCCACCUGGCGUCGCCUACCUCCGGCAAUAAAAUAUAUAUACCAAUGCUACUAUAUAUA----AAGGCGAACAAUAA
.........(((((.....(-((((((((((....)))))))))))......((.......((((((((..........))))))))----...))))))).... ( -28.00, z-score =  -2.52, R)
>consensus
GUAGAUUUAUGUUCCAUUUU_AGGUGGCGCCACCUGGCGUCGCCUACCUCUGGCAAUAAAAUAUAUAUACCAAUGCUACUAUAUAUA____AAGGCGAACAAUAA
.........(((((.......((((((((((....)))))))))).......((.......((((((((..........)))))))).......))))))).... (-23.47 = -24.52 +   1.06)

alignment

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secondary structure

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dotplot

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Window 6

Location 21,253,133 – 21,253,243
Length 110
Sequences 6
Columns 111
Reading direction forward
Mean pairwise identity 86.94
Shannon entropy 0.24880
G+C content 0.41187
Mean single sequence MFE -18.59
Consensus MFE -15.33
Energy contribution -15.38
Covariance contribution 0.06
Combinations/Pair 1.14
Mean z-score -1.50
Structure conservation index 0.82
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.51
SVM RNA-class probability 0.723550
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 21253133 110 + 27905053
AAACACAACUUCAUACACGACAUAAAUCAACCGGGCAGUUCAAGCAUGGCUGAAAUAUAACUCAGCCGAGAAGUUAAAUACAAACCGCCACCAGCUGACAGCAAAAAA-UG
......((((((......................((.......)).(((((((........))))))).))))))..................((.....))......-.. ( -18.60, z-score =  -1.43, R)
>droSim1.chr3R 21081568 110 + 27517382
AAACACAACUUCAUACACGACAUAAAUCAACCGGGCAGUUCAAGCAUGGCUGAAAUAUAACUCAGCCGAGAAGUUAAAUACAAACCGCCACCCACUGACAGCAAAAAA-UG
......((((((......................((.......)).(((((((........))))))).)))))).................................-.. ( -17.20, z-score =  -1.29, R)
>droSec1.super_13 27008 110 + 2104621
AAACACAACUUCAUACACGACAUAAAUCAACCGGGCAGUUCAAGCAUGGCUGAAAUAUAACUCAGCCGAGAAGUUAAAUACAAACCGCCACCCACUGACAG-AAAAAAAUG
......((((((......................((.......)).(((((((........))))))).))))))..........................-......... ( -17.20, z-score =  -1.56, R)
>droYak2.chr3R 3599981 111 - 28832112
AAACACAACUUCAUACACGACAUAAAUCAACCGGGCAGUUCAAGCAUGGCUGAAAUAUUACUCAGCCGAGAAGUUAAAUACAAUCUGCCACCCACUGACAACAAAAAAAUG
.................................(((((........(((((((........)))))))....((.....))...)))))...................... ( -18.20, z-score =  -1.89, R)
>droEre2.scaffold_4820 3678580 111 - 10470090
AAACACAACUUCAUACACGACAUAAAUCAAGCGGGCAGUUCAAGCAUGGCUGAAAUAUUACUCAGCCGAGAAGUUAAAUACAAACUGCCACCCACUGACAACAAAAAAAUG
..........................(((.(..(((((((......(((((((........)))))))....((.....)).)))))))..)...)))............. ( -20.80, z-score =  -2.56, R)
>droAna3.scaffold_13340 14474573 97 - 23697760
AAGCAAUAUUCCAUGCACGACAUAAAUCACCUGGGCAGUUCAAGCCGGGCUGAAUUAUUACUCGGCCGAGAAGUUAAAUAAAAGCCCGCAAAAAAUG--------------
.............(((.................(((.......)))(((((.....(((.(((....))).)))........)))))))).......-------------- ( -19.52, z-score =  -0.26, R)
>consensus
AAACACAACUUCAUACACGACAUAAAUCAACCGGGCAGUUCAAGCAUGGCUGAAAUAUAACUCAGCCGAGAAGUUAAAUACAAACCGCCACCCACUGACAGCAAAAAA_UG
......((((((......................((.......))..((((((........))))))..)))))).................................... (-15.33 = -15.38 +   0.06)

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 00:43:10 2011