Locus 9845

Sequence ID dm3.chr3R
Location 9,379,277 – 9,379,391
Length 114
Max. P 0.923486
window13518 window13519

overview

Window 8

Location 9,379,277 – 9,379,391
Length 114
Sequences 8
Columns 114
Reading direction forward
Mean pairwise identity 86.98
Shannon entropy 0.27291
G+C content 0.50832
Mean single sequence MFE -33.43
Consensus MFE -22.16
Energy contribution -22.71
Covariance contribution 0.55
Combinations/Pair 1.13
Mean z-score -2.45
Structure conservation index 0.66
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.30
SVM RNA-class probability 0.923486
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 9379277 114 + 27905053
UCACCGUGUAGCUACCAGCAGCAGCUCAAAGCUCACGGCACACAGCACGCCACUAAUUGGACCCAGUGGUUCGCCAUCAUCAUCGUGAUCGCAUUUAAAUGUGCUGAUCAAUUU
...(((((.((((...(((....)))...)))))))))....((((((((((((..........))))))..((.(((((....))))).))........))))))........ ( -37.40, z-score =  -3.45, R)
>droGri2.scaffold_14906 10093802 92 - 14172833
---------------CAGAGCCACCUCCGCCCCCAUCGCA-ACGGCAUGCCACUAAUUGGACCCAGUGGUUCACCAUC------GUGAUCGCAUUUAAAUGUGCUGAUCAAUUU
---------------..(((((((.(((((.......)).-..((....)).......)))....)))))))......------.(((((((((......)))).))))).... ( -25.70, z-score =  -2.05, R)
>droAna3.scaffold_13340 1932074 114 + 23697760
UCGAAGUGCAACUACCAGCAGCAGCUCAAAGCUCACGGCACACAGCACGCCACUAAUUGGACCCAGCGGUUCGCCAUCAUCAUCGUGAUCGCAUUUAAAUGUGCUGAUCAAUUU
..((.((((..((...(((....)))...))......)))).(((((((.........(((((....)))))((.(((((....))))).)).......))))))).))..... ( -28.60, z-score =  -0.70, R)
>droEre2.scaffold_4770 5483158 114 - 17746568
UCACCGUGUAGCUACCAGCAGCAGCUCAAAGCUCACGGCACACAGCACGCCACUAAUUGGGCCCAGUGGUUCGCCAUCAUCAUCGUGAUCGCAUUUAAAUGUGCUGAUCAAUUU
...(((((.((((...(((....)))...)))))))))....((((((((((((..........))))))..((.(((((....))))).))........))))))........ ( -37.40, z-score =  -2.97, R)
>droYak2.chr3R 13686254 114 + 28832112
UCACCGUGUAGCUACCAGCAGCAGCUCAAAGCUCACGGCACACAGCACGCCACUAAUUGGACCCAGUGGUUCGCCAUCAUCAUCGUGAUCGCAUUUAAAUGUGCUGAUCAAUUU
...(((((.((((...(((....)))...)))))))))....((((((((((((..........))))))..((.(((((....))))).))........))))))........ ( -37.40, z-score =  -3.45, R)
>droSec1.super_0 8492685 114 - 21120651
UCACCGUGUAGCUACCAGCAGCAGCUCAAAGCUCACGGCACACAGCACGCCACUAAUUGGACCCAGUGGUUCGCCAUCAUCAUCGUGAUCGCAUUUAAAUGUGCUGAUCAAUUU
...(((((.((((...(((....)))...)))))))))....((((((((((((..........))))))..((.(((((....))))).))........))))))........ ( -37.40, z-score =  -3.45, R)
>droSim1.chr3R 15470773 114 - 27517382
UCACCGUGUAGCUACCAGCAGCAGCUCAAAGCUCACGGCACACAGCACGCCACUAAUUGGACCCAGUGGUUCGCCAUCAUCAUCGUGAUCGCAUUUAAAUGUGCUGAUCAAUUU
...(((((.((((...(((....)))...)))))))))....((((((((((((..........))))))..((.(((((....))))).))........))))))........ ( -37.40, z-score =  -3.45, R)
>droPer1.super_0 8251153 97 - 11822988
-------------ACCAGCAGCAGC----AGCUCCGGGCUCGCAGCACGCCACUAAUUGGACCCAGCGGUUCGCCAUCAUCAUCGUGAUCGCAUUUAAAUGUGCUGAUCAAUUU
-------------.((.(.(((...----.)))).)).....(((((((.........(((((....)))))((.(((((....))))).)).......)))))))........ ( -26.10, z-score =  -0.11, R)
>consensus
UCACCGUGUAGCUACCAGCAGCAGCUCAAAGCUCACGGCACACAGCACGCCACUAAUUGGACCCAGUGGUUCGCCAUCAUCAUCGUGAUCGCAUUUAAAUGUGCUGAUCAAUUU
.................((...(((.....)))....))...((((((..........(((((....)))))((.(((((....))))).))........))))))........ (-22.16 = -22.71 +   0.55)

alignment

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secondary structure

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dotplot

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Window 9

Location 9,379,277 – 9,379,391
Length 114
Sequences 8
Columns 114
Reading direction reverse
Mean pairwise identity 86.98
Shannon entropy 0.27291
G+C content 0.50832
Mean single sequence MFE -39.57
Consensus MFE -27.85
Energy contribution -29.76
Covariance contribution 1.91
Combinations/Pair 1.13
Mean z-score -1.99
Structure conservation index 0.70
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.73
SVM RNA-class probability 0.799353
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 9379277 114 - 27905053
AAAUUGAUCAGCACAUUUAAAUGCGAUCACGAUGAUGAUGGCGAACCACUGGGUCCAAUUAGUGGCGUGCUGUGUGCCGUGAGCUUUGAGCUGCUGCUGGUAGCUACACGGUGA
........((((((.......(((.((((......)))).)))..(((((((......))))))).))))))...((((((((((.(.(((....))).).)))).)))))).. ( -44.00, z-score =  -2.92, R)
>droGri2.scaffold_14906 10093802 92 + 14172833
AAAUUGAUCAGCACAUUUAAAUGCGAUCAC------GAUGGUGAACCACUGGGUCCAAUUAGUGGCAUGCCGU-UGCGAUGGGGGCGGAGGUGGCUCUG---------------
.........(((.(((((...(.(.(((.(------(((((((..(((((((......)))))))..))))))-)).))).).)....))))))))...--------------- ( -29.30, z-score =  -0.79, R)
>droAna3.scaffold_13340 1932074 114 - 23697760
AAAUUGAUCAGCACAUUUAAAUGCGAUCACGAUGAUGAUGGCGAACCGCUGGGUCCAAUUAGUGGCGUGCUGUGUGCCGUGAGCUUUGAGCUGCUGCUGGUAGUUGCACUUCGA
...((((.((((((.......(((.((((......)))).)))..(((((((......))))))).)))))).(((((....).....((((((.....)))))))))).)))) ( -35.40, z-score =  -0.16, R)
>droEre2.scaffold_4770 5483158 114 + 17746568
AAAUUGAUCAGCACAUUUAAAUGCGAUCACGAUGAUGAUGGCGAACCACUGGGCCCAAUUAGUGGCGUGCUGUGUGCCGUGAGCUUUGAGCUGCUGCUGGUAGCUACACGGUGA
........((((((.......(((.((((......)))).)))..(((((((......))))))).))))))...((((((((((.(.(((....))).).)))).)))))).. ( -44.00, z-score =  -2.86, R)
>droYak2.chr3R 13686254 114 - 28832112
AAAUUGAUCAGCACAUUUAAAUGCGAUCACGAUGAUGAUGGCGAACCACUGGGUCCAAUUAGUGGCGUGCUGUGUGCCGUGAGCUUUGAGCUGCUGCUGGUAGCUACACGGUGA
........((((((.......(((.((((......)))).)))..(((((((......))))))).))))))...((((((((((.(.(((....))).).)))).)))))).. ( -44.00, z-score =  -2.92, R)
>droSec1.super_0 8492685 114 + 21120651
AAAUUGAUCAGCACAUUUAAAUGCGAUCACGAUGAUGAUGGCGAACCACUGGGUCCAAUUAGUGGCGUGCUGUGUGCCGUGAGCUUUGAGCUGCUGCUGGUAGCUACACGGUGA
........((((((.......(((.((((......)))).)))..(((((((......))))))).))))))...((((((((((.(.(((....))).).)))).)))))).. ( -44.00, z-score =  -2.92, R)
>droSim1.chr3R 15470773 114 + 27517382
AAAUUGAUCAGCACAUUUAAAUGCGAUCACGAUGAUGAUGGCGAACCACUGGGUCCAAUUAGUGGCGUGCUGUGUGCCGUGAGCUUUGAGCUGCUGCUGGUAGCUACACGGUGA
........((((((.......(((.((((......)))).)))..(((((((......))))))).))))))...((((((((((.(.(((....))).).)))).)))))).. ( -44.00, z-score =  -2.92, R)
>droPer1.super_0 8251153 97 + 11822988
AAAUUGAUCAGCACAUUUAAAUGCGAUCACGAUGAUGAUGGCGAACCGCUGGGUCCAAUUAGUGGCGUGCUGCGAGCCCGGAGCU----GCUGCUGCUGGU-------------
........((((((.......(((.((((......)))).)))..(((((((......))))))).)))))).....(((((((.----...))).)))).------------- ( -31.90, z-score =  -0.40, R)
>consensus
AAAUUGAUCAGCACAUUUAAAUGCGAUCACGAUGAUGAUGGCGAACCACUGGGUCCAAUUAGUGGCGUGCUGUGUGCCGUGAGCUUUGAGCUGCUGCUGGUAGCUACACGGUGA
........((((((.......(((.((((......)))).)))..(((((((......))))))).))))))......(((((((.(.(((....))).).)))).)))..... (-27.85 = -29.76 +   1.91)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:12:22 2011