Locus 12916

Sequence ID dm3.chrX
Location 3,233,065 – 3,233,197
Length 132
Max. P 0.997367
window17760 window17761 window17762

overview

Window 0

Location 3,233,065 – 3,233,161
Length 96
Sequences 4
Columns 96
Reading direction forward
Mean pairwise identity 66.84
Shannon entropy 0.55344
G+C content 0.73798
Mean single sequence MFE -47.73
Consensus MFE -29.04
Energy contribution -33.10
Covariance contribution 4.06
Combinations/Pair 1.21
Mean z-score -1.50
Structure conservation index 0.61
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.82
SVM RNA-class probability 0.969753
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 3233065 96 + 22422827
GGCGAGAGCACCACCACAGGCACAACCGGAACCACCGCUGCAUCCGCGCUAAGCGGAGCUGGUGGCGGUGGCGGUGGAGGCGGGGGAAUGGCACCC
.((....)).(((((...((.....))....(((((((..(.(((((.....)))))....)..))))))).))))).....(((........))) ( -46.00, z-score =  -1.74, R)
>droYak2.chrX 16623226 96 - 21770863
GGGGAGAGCACCACCACUGGCACCACCGGAACCACCGCCGCCUCCGCGCUAAGCGGGGCUGGUGGCGGUGGCGGUGCAGGCGGGGGUGUGGCACCU
(((....(((((.((.((.(((((.((...(((.((((((((.((((.....))))))).))))).))))).))))).)).)).)))))....))) ( -56.40, z-score =  -1.95, R)
>droEre2.scaffold_4690 644341 96 + 18748788
GGCGAGAGCACCACCACUGGCACCACCGGAACCACCGCCGCCUCCGCGCAAAGCGGGGCUGGCGGCGGUGGCGGUGCUGGAGGGGGAGUGGCACCU
((.(...((.((.((.(..(((((.((...(((.((((((((.((((.....))))))).))))).))))).)))))..).)).)).))..).)). ( -56.00, z-score =  -2.49, R)
>anoGam1.chr3R 22658757 78 + 53272125
---------ACGGAGGGCGGCACCAAGGACGCCACCCCGUCCUCCGCCCCGAGCAGUGCCGGUGGCAGCGCCACGGCCAAGAAUGGC---------
---------.(((.((((((.....((((((......)))))))))))).........)))(((((...))))).((((....))))--------- ( -32.50, z-score =   0.20, R)
>consensus
GGCGAGAGCACCACCACUGGCACCACCGGAACCACCGCCGCCUCCGCGCUAAGCGGGGCUGGUGGCGGUGGCGGUGCAGGCGGGGGAGUGGCACCU
..........((.((.((((((((.((...(((.((((((.((((((.....)))))).)))))).))))).)))))))).))))........... (-29.04 = -33.10 +   4.06)

alignment

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secondary structure

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dotplot

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Window 1

Location 3,233,065 – 3,233,161
Length 96
Sequences 4
Columns 96
Reading direction reverse
Mean pairwise identity 66.84
Shannon entropy 0.55344
G+C content 0.73798
Mean single sequence MFE -49.20
Consensus MFE -30.71
Energy contribution -34.02
Covariance contribution 3.31
Combinations/Pair 1.21
Mean z-score -2.24
Structure conservation index 0.62
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.09
SVM RNA-class probability 0.997367
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 3233065 96 - 22422827
GGGUGCCAUUCCCCCGCCUCCACCGCCACCGCCACCAGCUCCGCUUAGCGCGGAUGCAGCGGUGGUUCCGGUUGUGCCUGUGGUGGUGCUCUCGCC
(((..((((..(..(((..((...((((((((.....(((((((.....))))).)).))))))))...))..)))...)..))))..)))..... ( -43.60, z-score =  -1.62, R)
>droYak2.chrX 16623226 96 + 21770863
AGGUGCCACACCCCCGCCUGCACCGCCACCGCCACCAGCCCCGCUUAGCGCGGAGGCGGCGGUGGUUCCGGUGGUGCCAGUGGUGGUGCUCUCCCC
.((.(...((((.((((..((((((((((((((.((.(((((((.....)))).))))).))))))...))))))))..)))).))))..).)).. ( -56.00, z-score =  -3.26, R)
>droEre2.scaffold_4690 644341 96 - 18748788
AGGUGCCACUCCCCCUCCAGCACCGCCACCGCCGCCAGCCCCGCUUUGCGCGGAGGCGGCGGUGGUUCCGGUGGUGCCAGUGGUGGUGCUCUCGCC
.((((.(((..((.((...(((((((((((((((((.(((((((.....)))).))))))))))))...)))))))).)).))..)))....)))) ( -57.50, z-score =  -3.75, R)
>anoGam1.chr3R 22658757 78 - 53272125
---------GCCAUUCUUGGCCGUGGCGCUGCCACCGGCACUGCUCGGGGCGGAGGACGGGGUGGCGUCCUUGGUGCCGCCCUCCGU---------
---------((((....)))).(((((((((((.(((((...)).)))))).(((((((......))))))))))))))).......--------- ( -39.70, z-score =  -0.33, R)
>consensus
AGGUGCCACUCCCCCGCCUGCACCGCCACCGCCACCAGCCCCGCUUAGCGCGGAGGCGGCGGUGGUUCCGGUGGUGCCAGUGGUGGUGCUCUCGCC
.((((...((((.((((..((((((((...((((((.(((((((.....)))).)))...))))))...))))))))..)))).))))....)))) (-30.71 = -34.02 +   3.31)

alignment

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secondary structure

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dotplot

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Window 2

Location 3,233,084 – 3,233,197
Length 113
Sequences 8
Columns 113
Reading direction reverse
Mean pairwise identity 64.15
Shannon entropy 0.72083
G+C content 0.69881
Mean single sequence MFE -46.92
Consensus MFE -17.23
Energy contribution -18.31
Covariance contribution 1.08
Combinations/Pair 1.55
Mean z-score -1.22
Structure conservation index 0.37
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.54
SVM RNA-class probability 0.734326
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 3233084 113 - 22422827
ACCGUGUUGCGGUUGGUUUUGGCAGCCACCCGUUCUGGGUGCCAUUCCCCCGCCUCCACCGCCACCGCCACCAGCUCCGCUUAGCGCGGAUGCAGCGGUGGUUCCGGUUGUGC
((((((..((((..((...(((((.(((.......))).)))))..)).))))...))).((((((((.....(((((((.....))))).)).))))))))...)))..... ( -49.90, z-score =  -1.84, R)
>droSec1.super_10 2938671 113 - 3036183
ACCGUGUUGCGGUUGGUUUUGGCAGCCACCCGUUCUUGGUGCCACUCCCCCGCCUGCGCCGCCACCGCCCCCAGCCCCGCUUAGCGCGGAGGCGGCGGUGGUUCCGGUGGUGC
........((((..((...(((((.(((........))))))))..)).))))..((((((((((((((.((.(((((((.....)))).))))).))))))...)))))))) ( -57.30, z-score =  -1.86, R)
>droYak2.chrX 16623245 113 + 21770863
ACCGUGUUGCGGUUGGUUUUGGCAGCCACCCGUUCUAGGUGCCACACCCCCGCCUGCACCGCCACCGCCACCAGCCCCGCUUAGCGCGGAGGCGGCGGUGGUUCCGGUGGUGC
........((((..(((..(((((.((..........))))))).))).))))..((((((((((((((.((.(((((((.....)))).))))).))))))...)))))))) ( -57.70, z-score =  -2.05, R)
>droEre2.scaffold_4690 644360 113 - 18748788
ACCGUGUUGCGGUUGGUUUUGGCAGCCACCCGUUCUAGGUGCCACUCCCCCUCCAGCACCGCCACCGCCGCCAGCCCCGCUUUGCGCGGAGGCGGCGGUGGUUCCGGUGGUGC
(((.....((((.(((((.....))))).))))....)))...............(((((((((((((((((.(((((((.....)))).))))))))))))...)))))))) ( -60.20, z-score =  -3.13, R)
>droAna3.scaffold_12613 367086 98 + 519072
ACCGUGCUGGUGCUGGUUUUGGCUGCCACCCGUCUUAUUGCCGCCAGCCACGCCCCCGCCAGCAGCGCCGCCCGCC------AGCGCCGAGGUGGCAGUAGUGC---------
....((((((((..(((..((((((.(...((......))..).)))))).)))..))))))))((((..(..(((------(.(.....).)))).)..))))--------- ( -39.80, z-score =   0.19, R)
>dp4.chrXL_group1e 2776487 103 - 12523060
ACCUUGUUGCGCUUGAUUUUGCACGUCACCCGCUAUGGGAGCGACGCCACCUCCACCGCCGCCCCCACCCGACCCGCCACCCAUCGCCGCAGUGGCGGUGGUG----------
.....(((((((........))......(((.....))).)))))((((((.((((.((.((.......................)).)).)))).)))))).---------- ( -33.80, z-score =  -0.63, R)
>droPer1.super_18 1673607 104 - 1952607
ACCUUGUUGCGCUUGAUUUUGCACGUCACCCGCUAUGGGAGCGACGCCACCUCCACCGCCGCCCCCACCCGACCCGCCACCCAUCGCCGCAGUGGCGGUGGUGC---------
.....(((((((........))......(((.....))).)))))((((((.((((.((.((.......................)).)).)))).))))))..--------- ( -33.80, z-score =  -0.15, R)
>anoGam1.chr3R 22658776 97 - 53272125
---AUCUUGAAGC-GGUUCGGCUUCUCGCUCGGAUCCGCACUGCCAUUCUUGGCCGUGGCGCUGCCACCG---GCACUGCUCGGGGCGGAGGACGGGGUGGCGU---------
---........((-((((((((.....)).)))).))))((.((((....)))).)).((((..((.(((---.(.((((.....)))).)..)))))..))))--------- ( -42.90, z-score =  -0.26, R)
>consensus
ACCGUGUUGCGGUUGGUUUUGGCAGCCACCCGUUCUAGGUGCCACACCCCCGCCACCGCCGCCACCGCCCCCAGCCCCGCUUAGCGCGGAGGCGGCGGUGGUGC_________
........((((.((((.......)))).))))....((((.........))))...((((((.((((.......................)))).))))))........... (-17.23 = -18.31 +   1.08)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:11:17 2011