Locus 9872

Sequence ID dm3.chr3R
Location 9,539,576 – 9,539,764
Length 188
Max. P 0.906996
window13555 window13556 window13557

overview

Window 5

Location 9,539,576 – 9,539,698
Length 122
Sequences 6
Columns 124
Reading direction reverse
Mean pairwise identity 86.20
Shannon entropy 0.26348
G+C content 0.43758
Mean single sequence MFE -31.10
Consensus MFE -22.29
Energy contribution -23.18
Covariance contribution 0.89
Combinations/Pair 1.21
Mean z-score -1.70
Structure conservation index 0.72
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.24
SVM RNA-class probability 0.606452
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 9539576 122 - 27905053
GCAGGUCAGAGGUUAUGAUG-GUUUCGUACCUCU-UGUCAUUUACCUCAUUUGCACUUGAGAAUUUAUUUCGGCCUGCUCUGGGCUACGAAUGUCGUAUUUACUUAUUUACACUGACCUCUCCC
..(((((((((((.((((..-...))))))))).-.......(((..((((((.......(((.....)))(((((.....))))).))))))..)))...............))))))..... ( -31.60, z-score =  -2.07, R)
>droAna3.scaffold_13340 13203557 119 + 23697760
-----GCAGGCUUUGUGAAGCGUCUCCUACCUCCACGGCAUAUGCCUCAUUUGCACUUGAGUGUUUAUUUCGACCUGCGGGUCCCUACAAAUAAUGUGUUUAUUUAUUUACACUGUCCUUUUCU
-----(((((....(((.((.((.....)))).)))(((....)))...))))).....(((((..((...((((....)))).....((((((.....))))))))..))))).......... ( -22.20, z-score =   0.04, R)
>droEre2.scaffold_4770 5650757 122 + 17746568
GCAGGUCAGAGGUUAUGAUG-GUUUCGUACCUCU-UGUCAUUUACCUCAUUUGCACUUGAGAAUUUAUUUCGUCCUGCGGCGGGCUACGAAUGCUGUAUUUACUUAUUUACACUGACCUUUCCC
..(((((((((((.((((((-((.....)))...-.)))))..)))))....(((.(((.(((.....)))((((......))))..))).)))...................))))))..... ( -30.80, z-score =  -1.65, R)
>droYak2.chr3R 13847962 122 - 28832112
GCAGGUCAGAGGUUAUGAUG-GUUUCGUACCUCU-UGUCAUUUACCUCAUUUGCACUUGAGAAUUUAUUUCGGCCUGCGGUGUGCUACGAAUGCCGUAUUUACUUAUUUACACUGACCUUUCCC
(((((((((((((.((((..-...))))))))))-..........((((........))))..........)))))))((((((.((((.....))))..........)))))).......... ( -32.60, z-score =  -2.33, R)
>droSec1.super_0 8652638 122 + 21120651
GCAGGUCAGAGGUUAUGAUG-GCUUCGUACCUCU-UGUUAUUUACCUCAUUUGCACUUGAGAAUUUAUUUCGGCCUGCGGUGGGCUACGAAUGUCGUAUUUACUUGUUUACACUGACCUCUUCC
(((((((((((((.((((..-...))))))))))-..........((((........))))..........)))))))(((.((.((((.....))))......((....)))).)))...... ( -34.70, z-score =  -2.28, R)
>droSim1.chr3R 15620850 122 + 27517382
GCAGGUCAGAGGUUAUGAUG-GCUUCGUACCUCU-UGUCAUUUACCUCAUUUGCACUUGAGAAUUUAUUUCGGCCUGCGGUGGGCUACGAAUGUCGUAUUUACUUGUUUACACUGACCUCUUGA
(((((((((((((.((((..-...))))))))))-..........((((........))))..........)))))))(((.((.((((.....))))......((....)))).)))...... ( -34.70, z-score =  -1.93, R)
>consensus
GCAGGUCAGAGGUUAUGAUG_GUUUCGUACCUCU_UGUCAUUUACCUCAUUUGCACUUGAGAAUUUAUUUCGGCCUGCGGUGGGCUACGAAUGUCGUAUUUACUUAUUUACACUGACCUCUCCC
(((((((.(((((.((((......)))))))))............((((........))))..........))))))).......((((.....)))).......................... (-22.29 = -23.18 +   0.89)

alignment

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secondary structure

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dotplot

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Window 6

Location 9,539,698 – 9,539,764
Length 66
Sequences 3
Columns 67
Reading direction forward
Mean pairwise identity 75.68
Shannon entropy 0.31148
G+C content 0.59830
Mean single sequence MFE -7.77
Consensus MFE -6.71
Energy contribution -6.93
Covariance contribution 0.22
Combinations/Pair 1.09
Mean z-score -1.08
Structure conservation index 0.86
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.44
SVM RNA-class probability 0.697651
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr3R 9539698 66 + 27905053
CACCGAUCCCCCCUCCACCAAC-GAGCGACCCAUAAACGCCCACUUUGCCGAGCAUUUGACAGUCGA
............(((.......-)))((((...((((.((.(........).)).))))...)))). (  -6.50, z-score =  -0.53, R)
>droEre2.scaffold_4770 5650879 51 - 17746568
---------------CACCCCC-GACCGACCCGCAAACGCCCACUUUGUCGAGCAUUUGACAGUCGA
---------------.......-...((((...((((.((.(........).)).))))...)))). (  -9.30, z-score =  -1.69, R)
>droYak2.chr3R 13848084 52 + 28832112
---------------CACCCCCCGACCGACCCGAAAACGCCCACUUUGUCGAGCAUUUGACAGUCGA
---------------...........((((.((....)).......((((((....)))))))))). (  -7.50, z-score =  -1.01, R)
>consensus
_______________CACCCCC_GACCGACCCGAAAACGCCCACUUUGUCGAGCAUUUGACAGUCGA
..........................((((...((((.((.(........).)).))))...)))). ( -6.71 =  -6.93 +   0.22)

alignment

Postscript

secondary structure

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dotplot

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Window 7

Location 9,539,698 – 9,539,764
Length 66
Sequences 3
Columns 67
Reading direction reverse
Mean pairwise identity 75.68
Shannon entropy 0.31148
G+C content 0.59830
Mean single sequence MFE -18.23
Consensus MFE -14.70
Energy contribution -14.70
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.69
Structure conservation index 0.81
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.19
SVM RNA-class probability 0.906996
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr3R 9539698 66 - 27905053
UCGACUGUCAAAUGCUCGGCAAAGUGGGCGUUUAUGGGUCGCUC-GUUGGUGGAGGGGGGAUCGGUG
...((((((...(.(((.((....((((((.........)))))-)...)).))).)..)).)))). ( -18.90, z-score =  -0.84, R)
>droEre2.scaffold_4770 5650879 51 + 17746568
UCGACUGUCAAAUGCUCGACAAAGUGGGCGUUUGCGGGUCGGUC-GGGGGUG---------------
(((((((.((((((((((......)))))))))).....)))))-)).....--------------- ( -19.00, z-score =  -2.50, R)
>droYak2.chr3R 13848084 52 - 28832112
UCGACUGUCAAAUGCUCGACAAAGUGGGCGUUUUCGGGUCGGUCGGGGGGUG---------------
(((((((.((((((((((......)))))))))....).)))))))......--------------- ( -16.80, z-score =  -1.74, R)
>consensus
UCGACUGUCAAAUGCUCGACAAAGUGGGCGUUUACGGGUCGGUC_GGGGGUG_______________
.(((((...(((((((((......)))))))))...))))).......................... (-14.70 = -14.70 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:12:55 2011