Locus 12908

Sequence ID dm3.chrX
Location 3,165,085 – 3,165,188
Length 103
Max. P 0.990543
window17747 window17748 window17749 window17750

overview

Window 7

Location 3,165,085 – 3,165,187
Length 102
Sequences 5
Columns 102
Reading direction forward
Mean pairwise identity 95.63
Shannon entropy 0.07566
G+C content 0.39051
Mean single sequence MFE -27.72
Consensus MFE -27.14
Energy contribution -27.34
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -2.30
Structure conservation index 0.98
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.22
SVM RNA-class probability 0.985983
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 3165085 102 + 22422827
UGACGGUAUUUUUAUAUAAGAUGAACAAGAGAUGCUUCUGCAAUUUUUGUCAACAGGUUGUCUUCUGACAGCCGCCAGCAUAUUUGGCUUACAUAAAACCUU
....(((...(((((.((((.(((.((((((.(((....))).))))))))).).(((((((....)))))))(((((.....)))))))).)))))))).. ( -29.20, z-score =  -3.35, R)
>droSim1.chrX 2253691 100 + 17042790
UGGCGGUAUUUAUAUAUAAGAUGAACAAGA--UGCUCCUGCAAUUUUUGUCAACAGGUUGUCUUCUGACAGCCGCCAGCAUAUUUGGCUUACAUAAAACCUU
....(((.(((((......(.(((.(((((--(((....)))..)))))))).).(((((((....)))))))(((((.....)))))....)))))))).. ( -27.40, z-score =  -2.39, R)
>droSec1.super_10 2872644 100 + 3036183
UGGCGGUAUUUAUAUAUAAGAUGAACAAGA--UGCUCCUGCAAUUUUUGUCAACAGGUUGUCUUCUGACAGCCGCCAGCAUAUUUGGCUUACAUAAAACCUU
....(((.(((((......(.(((.(((((--(((....)))..)))))))).).(((((((....)))))))(((((.....)))))....)))))))).. ( -27.40, z-score =  -2.39, R)
>droYak2.chrX 16552424 100 - 21770863
UGGCGGUGUUUAUAUAUAAAAUGAACAAGA--UGCUUCUGCAGUUUUUGUCAACAGGUUGUCUUCUGACAGCCGCCAGCAUAUUUGGCUUACAUAAAACCUU
.((((.(((((((.......)))))))...--))))......((((((((.....(((((((....)))))))(((((.....)))))..))).)))))... ( -27.40, z-score =  -1.99, R)
>droEre2.scaffold_4690 573806 100 + 18748788
UGGCGGUAUUUAUAUAUGGGAUGAACAAGA--UGCUUCUGCAGUUUUUGUCAACAGGUUGUCUUCUGACAGCCGCCAGCAUAUUUGGCUUACAUAAAACCUU
....(((.(((((........(((.(((((--(((....)))..))))))))...(((((((....)))))))(((((.....)))))....)))))))).. ( -27.20, z-score =  -1.41, R)
>consensus
UGGCGGUAUUUAUAUAUAAGAUGAACAAGA__UGCUUCUGCAAUUUUUGUCAACAGGUUGUCUUCUGACAGCCGCCAGCAUAUUUGGCUUACAUAAAACCUU
....(((.(((((........(((.(((((..(((....)))..))))))))...(((((((....)))))))(((((.....)))))....)))))))).. (-27.14 = -27.34 +   0.20)

alignment

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secondary structure

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dotplot

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Window 8

Location 3,165,085 – 3,165,187
Length 102
Sequences 5
Columns 102
Reading direction reverse
Mean pairwise identity 95.63
Shannon entropy 0.07566
G+C content 0.39051
Mean single sequence MFE -23.86
Consensus MFE -23.62
Energy contribution -23.82
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -1.23
Structure conservation index 0.99
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.83
SVM RNA-class probability 0.828747
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 3165085 102 - 22422827
AAGGUUUUAUGUAAGCCAAAUAUGCUGGCGGCUGUCAGAAGACAACCUGUUGACAAAAAUUGCAGAAGCAUCUCUUGUUCAUCUUAUAUAAAAAUACCGUCA
..((((((((((((((((.......))))((.((((....)))).))....(((((....(((....)))....)))))....)))))))))...))).... ( -23.70, z-score =  -1.56, R)
>droSim1.chrX 2253691 100 - 17042790
AAGGUUUUAUGUAAGCCAAAUAUGCUGGCGGCUGUCAGAAGACAACCUGUUGACAAAAAUUGCAGGAGCA--UCUUGUUCAUCUUAUAUAUAAAUACCGCCA
..(((((((((((.((((.......)))).((((((....)))..(((((...........)))))))).--..............)))))))).))).... ( -24.90, z-score =  -1.32, R)
>droSec1.super_10 2872644 100 - 3036183
AAGGUUUUAUGUAAGCCAAAUAUGCUGGCGGCUGUCAGAAGACAACCUGUUGACAAAAAUUGCAGGAGCA--UCUUGUUCAUCUUAUAUAUAAAUACCGCCA
..(((((((((((.((((.......)))).((((((....)))..(((((...........)))))))).--..............)))))))).))).... ( -24.90, z-score =  -1.32, R)
>droYak2.chrX 16552424 100 + 21770863
AAGGUUUUAUGUAAGCCAAAUAUGCUGGCGGCUGUCAGAAGACAACCUGUUGACAAAAACUGCAGAAGCA--UCUUGUUCAUUUUAUAUAUAAACACCGCCA
..(((((((((((.((((.......))))((.((((....)))).))....(((((....(((....)))--..))))).......)))))))).))).... ( -22.90, z-score =  -0.94, R)
>droEre2.scaffold_4690 573806 100 - 18748788
AAGGUUUUAUGUAAGCCAAAUAUGCUGGCGGCUGUCAGAAGACAACCUGUUGACAAAAACUGCAGAAGCA--UCUUGUUCAUCCCAUAUAUAAAUACCGCCA
..(((((((((((.((((.......))))((.((((....)))).))....(((((....(((....)))--..))))).......)))))))).))).... ( -22.90, z-score =  -1.03, R)
>consensus
AAGGUUUUAUGUAAGCCAAAUAUGCUGGCGGCUGUCAGAAGACAACCUGUUGACAAAAAUUGCAGAAGCA__UCUUGUUCAUCUUAUAUAUAAAUACCGCCA
..(((((((((((.((((.......))))((.((((....)))).))....(((((....(((....)))....))))).......)))))))).))).... (-23.62 = -23.82 +   0.20)

alignment

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secondary structure

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dotplot

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Window 9

Location 3,165,086 – 3,165,188
Length 102
Sequences 5
Columns 102
Reading direction forward
Mean pairwise identity 95.63
Shannon entropy 0.07566
G+C content 0.39051
Mean single sequence MFE -27.68
Consensus MFE -27.14
Energy contribution -27.34
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -2.48
Structure conservation index 0.98
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.43
SVM RNA-class probability 0.990543
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 3165086 102 + 22422827
GACGGUAUUUUUAUAUAAGAUGAACAAGAGAUGCUUCUGCAAUUUUUGUCAACAGGUUGUCUUCUGACAGCCGCCAGCAUAUUUGGCUUACAUAAAACCUUU
...(((...(((((.((((.(((.((((((.(((....))).))))))))).).(((((((....)))))))(((((.....)))))))).))))))))... ( -29.20, z-score =  -3.54, R)
>droSim1.chrX 2253692 100 + 17042790
GGCGGUAUUUAUAUAUAAGAUGAACAAGA--UGCUCCUGCAAUUUUUGUCAACAGGUUGUCUUCUGACAGCCGCCAGCAUAUUUGGCUUACAUAAAACCUUU
...(((.(((((......(.(((.(((((--(((....)))..)))))))).).(((((((....)))))))(((((.....)))))....))))))))... ( -27.40, z-score =  -2.58, R)
>droSec1.super_10 2872645 100 + 3036183
GGCGGUAUUUAUAUAUAAGAUGAACAAGA--UGCUCCUGCAAUUUUUGUCAACAGGUUGUCUUCUGACAGCCGCCAGCAUAUUUGGCUUACAUAAAACCUUU
...(((.(((((......(.(((.(((((--(((....)))..)))))))).).(((((((....)))))))(((((.....)))))....))))))))... ( -27.40, z-score =  -2.58, R)
>droYak2.chrX 16552425 100 - 21770863
GGCGGUGUUUAUAUAUAAAAUGAACAAGA--UGCUUCUGCAGUUUUUGUCAACAGGUUGUCUUCUGACAGCCGCCAGCAUAUUUGGCUUACAUAAAACCUUU
((((.(((((((.......)))))))...--))))......((((((((.....(((((((....)))))))(((((.....)))))..))).))))).... ( -27.20, z-score =  -2.11, R)
>droEre2.scaffold_4690 573807 100 + 18748788
GGCGGUAUUUAUAUAUGGGAUGAACAAGA--UGCUUCUGCAGUUUUUGUCAACAGGUUGUCUUCUGACAGCCGCCAGCAUAUUUGGCUUACAUAAAACCUUU
...(((.(((((........(((.(((((--(((....)))..))))))))...(((((((....)))))))(((((.....)))))....))))))))... ( -27.20, z-score =  -1.61, R)
>consensus
GGCGGUAUUUAUAUAUAAGAUGAACAAGA__UGCUUCUGCAAUUUUUGUCAACAGGUUGUCUUCUGACAGCCGCCAGCAUAUUUGGCUUACAUAAAACCUUU
...(((.(((((........(((.(((((..(((....)))..))))))))...(((((((....)))))))(((((.....)))))....))))))))... (-27.14 = -27.34 +   0.20)

alignment

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secondary structure

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dotplot

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Window 0

Location 3,165,086 – 3,165,188
Length 102
Sequences 5
Columns 102
Reading direction reverse
Mean pairwise identity 95.63
Shannon entropy 0.07566
G+C content 0.39051
Mean single sequence MFE -23.86
Consensus MFE -23.62
Energy contribution -23.82
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -1.47
Structure conservation index 0.99
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.20
SVM RNA-class probability 0.908428
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 3165086 102 - 22422827
AAAGGUUUUAUGUAAGCCAAAUAUGCUGGCGGCUGUCAGAAGACAACCUGUUGACAAAAAUUGCAGAAGCAUCUCUUGUUCAUCUUAUAUAAAAAUACCGUC
...((((((((((((((((.......))))((.((((....)))).))....(((((....(((....)))....)))))....)))))))))...)))... ( -23.70, z-score =  -1.77, R)
>droSim1.chrX 2253692 100 - 17042790
AAAGGUUUUAUGUAAGCCAAAUAUGCUGGCGGCUGUCAGAAGACAACCUGUUGACAAAAAUUGCAGGAGCA--UCUUGUUCAUCUUAUAUAUAAAUACCGCC
...(((((((((((.((((.......)))).((((((....)))..(((((...........)))))))).--..............)))))))).)))... ( -24.90, z-score =  -1.56, R)
>droSec1.super_10 2872645 100 - 3036183
AAAGGUUUUAUGUAAGCCAAAUAUGCUGGCGGCUGUCAGAAGACAACCUGUUGACAAAAAUUGCAGGAGCA--UCUUGUUCAUCUUAUAUAUAAAUACCGCC
...(((((((((((.((((.......)))).((((((....)))..(((((...........)))))))).--..............)))))))).)))... ( -24.90, z-score =  -1.56, R)
>droYak2.chrX 16552425 100 + 21770863
AAAGGUUUUAUGUAAGCCAAAUAUGCUGGCGGCUGUCAGAAGACAACCUGUUGACAAAAACUGCAGAAGCA--UCUUGUUCAUUUUAUAUAUAAACACCGCC
...(((((((((((.((((.......))))((.((((....)))).))....(((((....(((....)))--..))))).......)))))))).)))... ( -22.90, z-score =  -1.15, R)
>droEre2.scaffold_4690 573807 100 - 18748788
AAAGGUUUUAUGUAAGCCAAAUAUGCUGGCGGCUGUCAGAAGACAACCUGUUGACAAAAACUGCAGAAGCA--UCUUGUUCAUCCCAUAUAUAAAUACCGCC
...(((((((((((.((((.......))))((.((((....)))).))....(((((....(((....)))--..))))).......)))))))).)))... ( -22.90, z-score =  -1.29, R)
>consensus
AAAGGUUUUAUGUAAGCCAAAUAUGCUGGCGGCUGUCAGAAGACAACCUGUUGACAAAAAUUGCAGAAGCA__UCUUGUUCAUCUUAUAUAUAAAUACCGCC
...(((((((((((.((((.......))))((.((((....)))).))....(((((....(((....)))....))))).......)))))))).)))... (-23.62 = -23.82 +   0.20)

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 01:11:07 2011