Locus 7091

Sequence ID dm3.chr3L
Location 12,165,125 – 12,165,248
Length 123
Max. P 0.976603
window9767 window9768 window9769 window9770

overview

Window 7

Location 12,165,125 – 12,165,217
Length 92
Sequences 4
Columns 92
Reading direction forward
Mean pairwise identity 88.91
Shannon entropy 0.17647
G+C content 0.47247
Mean single sequence MFE -28.40
Consensus MFE -24.08
Energy contribution -24.32
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -2.33
Structure conservation index 0.85
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.68
SVM RNA-class probability 0.960080
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 12165125 92 + 24543557
CUUAAAGUGCUCAGUUCUGUUCUGUUCGUUGCAGUUUGGUUUUUAUCCUGCGGCAAUGGAAGCCGCGGGAUGAUUGCGCGGAUACAAUUAUC
.............(((((((.((((.....))))....((..((((((((((((.......))))))))))))..))))))).))....... ( -31.60, z-score =  -2.84, R)
>droYak2.chr3L 12213088 87 + 24197627
CUUAAAGUGCUCAGUUCUGUUCGUUGCUG-----UUUGGUUUUUAGCCUGCGGCAAUUGAAGCCGCGGGAUGAUUGCGCGGAUACAAUUAUC
......((((...((((((((((((((((-----(..(((.....))).))))))).)))....)))))))....))))............. ( -25.80, z-score =  -1.06, R)
>droSec1.super_0 4350206 82 + 21120651
CUUCAAGUGCUCAGUUCUGUUCUG----------UUUGGUUUUUAUCCUGCGGCAAUGGAAGCCGCGGGAUGAUUGCGCGGAUACAAUUAUC
.................(((((((----------(...((..((((((((((((.......))))))))))))..))))))).)))...... ( -28.90, z-score =  -2.96, R)
>droSim1.chr3L 11536445 82 + 22553184
CUUAAAGUGCUCAGUUCUGUUCUG----------UUUCGGUUUUAUCCUGCGGCAAUGGAAGCCGCGGGAUGAUUGCGCGGAUACAAUUAUC
......((((.(((.......)))----------........((((((((((((.......))))))))))))..))))............. ( -27.30, z-score =  -2.45, R)
>consensus
CUUAAAGUGCUCAGUUCUGUUCUG__________UUUGGUUUUUAUCCUGCGGCAAUGGAAGCCGCGGGAUGAUUGCGCGGAUACAAUUAUC
......((((.((....)).......................((((((((((((.......))))))))))))..))))............. (-24.08 = -24.32 +   0.25)

alignment

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secondary structure

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dotplot

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Window 8

Location 12,165,125 – 12,165,217
Length 92
Sequences 4
Columns 92
Reading direction reverse
Mean pairwise identity 88.91
Shannon entropy 0.17647
G+C content 0.47247
Mean single sequence MFE -18.85
Consensus MFE -16.67
Energy contribution -16.93
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -1.67
Structure conservation index 0.88
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.87
SVM RNA-class probability 0.839028
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 12165125 92 - 24543557
GAUAAUUGUAUCCGCGCAAUCAUCCCGCGGCUUCCAUUGCCGCAGGAUAAAAACCAAACUGCAACGAACAGAACAGAACUGAGCACUUUAAG
((((....)))).((.((.((((((.(((((.......))))).))))..........(((.......)))....))..)).))........ ( -20.40, z-score =  -1.99, R)
>droYak2.chr3L 12213088 87 - 24197627
GAUAAUUGUAUCCGCGCAAUCAUCCCGCGGCUUCAAUUGCCGCAGGCUAAAAACCAAA-----CAGCAACGAACAGAACUGAGCACUUUAAG
((((....)))).((((.........(((((.......))))).((.......))...-----..))......((....)).))........ ( -16.00, z-score =  -0.32, R)
>droSec1.super_0 4350206 82 - 21120651
GAUAAUUGUAUCCGCGCAAUCAUCCCGCGGCUUCCAUUGCCGCAGGAUAAAAACCAAA----------CAGAACAGAACUGAGCACUUGAAG
((((....))))...((....((((.(((((.......))))).))))..........----------(((.......))).))........ ( -19.50, z-score =  -2.20, R)
>droSim1.chr3L 11536445 82 - 22553184
GAUAAUUGUAUCCGCGCAAUCAUCCCGCGGCUUCCAUUGCCGCAGGAUAAAACCGAAA----------CAGAACAGAACUGAGCACUUUAAG
((((....))))...((....((((.(((((.......))))).))))..........----------(((.......))).))........ ( -19.50, z-score =  -2.18, R)
>consensus
GAUAAUUGUAUCCGCGCAAUCAUCCCGCGGCUUCCAUUGCCGCAGGAUAAAAACCAAA__________CAGAACAGAACUGAGCACUUUAAG
((((....))))...((....((((.(((((.......))))).)))).........................((....)).))........ (-16.67 = -16.93 +   0.25)

alignment

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secondary structure

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dotplot

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Window 9

Location 12,165,153 – 12,165,248
Length 95
Sequences 4
Columns 95
Reading direction forward
Mean pairwise identity 91.10
Shannon entropy 0.14200
G+C content 0.52197
Mean single sequence MFE -35.65
Consensus MFE -28.51
Energy contribution -29.32
Covariance contribution 0.81
Combinations/Pair 1.03
Mean z-score -2.89
Structure conservation index 0.80
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.95
SVM RNA-class probability 0.976603
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 12165153 95 + 24543557
UUGCAGUUUGGUUUUUAUCCUGCGGCAAUGGAAGCCGCGGGAUGAUUGCGCGGAUACAAUUAUCCAGCCACUCGGGUGAAAUGGGCGGGAAAACG
.....((((.....((((((((((((.......))))))))))))((.((((((((....))))).(((.....))).......))).)))))). ( -35.40, z-score =  -2.30, R)
>droYak2.chr3L 12213111 93 + 24197627
UUGCUGUUUGGUUUUUAGCCUGCGGCAAUUGAAGCCGCGGGAUGAUUGCGCGGAUACAAUUAUCCAGCCACUUGG-UGAAAUGG-CGGGAAAACG
(((.((((((((..(((.((((((((.......)))))))).)))..)).)))))))))...(((.((((.((..-..)).)))-).)))..... ( -33.40, z-score =  -2.16, R)
>droSec1.super_0 4350229 89 + 21120651
-----GUUUGGUUUUUAUCCUGCGGCAAUGGAAGCCGCGGGAUGAUUGCGCGGAUACAAUUAUCCAGGCACUUGGCUGAAAUGG-CGGGAAAGCG
-----.....((..((((((((((((.......))))))))))))..))(((((((....))))).....((((.(......).-))))...)). ( -35.80, z-score =  -3.20, R)
>droSim1.chr3L 11536468 89 + 22553184
-----GUUUCGGUUUUAUCCUGCGGCAAUGGAAGCCGCGGGAUGAUUGCGCGGAUACAAUUAUCCAGCCACUUGGCUGAAAUGG-CGGGAAAACG
-----((((.....((((((((((((.......))))))))))))((.((((((((....)))))((((....))))......)-)).)))))). ( -38.00, z-score =  -3.89, R)
>consensus
_____GUUUGGUUUUUAUCCUGCGGCAAUGGAAGCCGCGGGAUGAUUGCGCGGAUACAAUUAUCCAGCCACUUGGCUGAAAUGG_CGGGAAAACG
.....((((.....((((((((((((.......))))))))))))((.((((((((....)))))((((....))))......).)).)))))). (-28.51 = -29.32 +   0.81)

alignment

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secondary structure

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dotplot

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Window 0

Location 12,165,153 – 12,165,248
Length 95
Sequences 4
Columns 95
Reading direction reverse
Mean pairwise identity 91.10
Shannon entropy 0.14200
G+C content 0.52197
Mean single sequence MFE -27.90
Consensus MFE -22.64
Energy contribution -22.95
Covariance contribution 0.31
Combinations/Pair 1.04
Mean z-score -2.55
Structure conservation index 0.81
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.52
SVM RNA-class probability 0.946907
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 12165153 95 - 24543557
CGUUUUCCCGCCCAUUUCACCCGAGUGGCUGGAUAAUUGUAUCCGCGCAAUCAUCCCGCGGCUUCCAUUGCCGCAGGAUAAAAACCAAACUGCAA
.(((((..(((((((((.....))))))..(((((....)))))))).....((((.(((((.......))))).)))).))))).......... ( -28.20, z-score =  -2.17, R)
>droYak2.chr3L 12213111 93 - 24197627
CGUUUUCCCG-CCAUUUCA-CCAAGUGGCUGGAUAAUUGUAUCCGCGCAAUCAUCCCGCGGCUUCAAUUGCCGCAGGCUAAAAACCAAACAGCAA
.(((((.(((-((((((..-..))))))).((((.(((((......))))).)))).(((((.......))))).))...))))).......... ( -28.50, z-score =  -2.74, R)
>droSec1.super_0 4350229 89 - 21120651
CGCUUUCCCG-CCAUUUCAGCCAAGUGCCUGGAUAAUUGUAUCCGCGCAAUCAUCCCGCGGCUUCCAUUGCCGCAGGAUAAAAACCAAAC-----
.((......)-)............((((..(((((....)))))))))....((((.(((((.......))))).))))...........----- ( -25.20, z-score =  -2.30, R)
>droSim1.chr3L 11536468 89 - 22553184
CGUUUUCCCG-CCAUUUCAGCCAAGUGGCUGGAUAAUUGUAUCCGCGCAAUCAUCCCGCGGCUUCCAUUGCCGCAGGAUAAAACCGAAAC-----
.(((((..((-(......((((....))))(((((....)))))))).....((((.(((((.......))))).)))))))))......----- ( -29.70, z-score =  -2.98, R)
>consensus
CGUUUUCCCG_CCAUUUCAGCCAAGUGGCUGGAUAAUUGUAUCCGCGCAAUCAUCCCGCGGCUUCCAUUGCCGCAGGAUAAAAACCAAAC_____
.......(((.((((((.....)))))).)))...(((((......))))).((((.(((((.......))))).))))................ (-22.64 = -22.95 +   0.31)

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 Tue Apr 19 23:20:23 2011