Locus 1624

Sequence ID 3L_DroMel_CAF1
Location 4,751,291 – 4,751,459
Length 168
Max. P 0.999416
window2509 window2510 window2511 window2512

overview

Window 9

Location 4,751,291 – 4,751,384
Length 93
Sequences 5
Columns 95
Reading direction forward
Mean pairwise identity 97.01
Mean single sequence MFE -34.40
Consensus MFE -31.04
Energy contribution -31.24
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -2.32
Structure conservation index 0.90
SVM decision value 3.01
SVM RNA-class probability 0.998126
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4751291 93 + 23771897
CCAUAAAAAGUGUCGCAGGCGGCAA--GGGGGCAGUUUUACGGCCCUUCUUCUGCUUGAGUUGCUGCUGCGGCUAUUUUAUUGUUGCGACAACAG
..........((((((((((((.((--((((((.(.....).)))).)))))))))).((((((....))))))...........)))))).... ( -34.40)
>DroSec_CAF1 11388 93 + 1
CCAUAAAAAGUGUCGCAGGCGGCAA--GGGGGCGGUUAUACGGCCCUUCUUCUGCUUGAGUUGCUGCUGCGGCUAUUUUAUUGUUGCGACAACAG
..........((((((((((((.((--((((((.(.....).)))).)))))))))).((((((....))))))...........)))))).... ( -36.20)
>DroSim_CAF1 12033 93 + 1
CCAUAAAAAGUGUCGCAGGCGGCAA--GGGGGCGGUUUUACGGCCCUUCUUCUGCUUGAGUUGCUGCUGCGGCUAUUUUAUUGUUGCGACAACAG
..........((((((((((((.((--((((((.(.....).)))).)))))))))).((((((....))))))...........)))))).... ( -36.20)
>DroEre_CAF1 3953 93 + 1
CCAUAAAAAGUGUCGCAGGCGGCAA--GGGGGAAGUUUUACGGCCCUUCUUCUACUUGAGUUGCUGCUGCGGCUAUUUUAUUGUUGCGACAACAG
..((((((...(((((((.((((((--(((((..(.....)..))))).(((.....))))))))))))))))..))))))(((((...))))). ( -29.70)
>DroYak_CAF1 10381 95 + 1
CCAUAAAAAGUGUCGCAGGCGGCAAAGGGGGGCAGUUUUACGGCCCUUCUUCUACUUGAGUUGCUGCUGCGGCUAUUUUAUUGUUGCGACAACAG
..((((((...(((((((.((((((((((((((.(.....).))))))))((.....)).)))))))))))))..))))))(((((...))))). ( -35.50)
>consensus
CCAUAAAAAGUGUCGCAGGCGGCAA__GGGGGCAGUUUUACGGCCCUUCUUCUGCUUGAGUUGCUGCUGCGGCUAUUUUAUUGUUGCGACAACAG
..((((((...(((((((.((((((..((((((.(.....).)))))).(((.....))))))))))))))))..))))))(((((...))))). (-31.04 = -31.24 +   0.20)

alignment

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secondary structure

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dotplot

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Window 0

Location 4,751,329 – 4,751,424
Length 95
Sequences 5
Columns 95
Reading direction forward
Mean pairwise identity 99.37
Mean single sequence MFE -28.34
Consensus MFE -27.38
Energy contribution -27.78
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -2.15
Structure conservation index 0.97
SVM decision value 2.63
SVM RNA-class probability 0.995889
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4751329 95 + 23771897
CGGCCCUUCUUCUGCUUGAGUUGCUGCUGCGGCUAUUUUAUUGUUGCGACAACAGCAACAUCACUAGUGUGUCCAGGCUUCGGCCAUUCCUCAAA
.((((........(((((.(((((((.((((((.........))))))....)))))))..(((....)))..)))))...)))).......... ( -29.50)
>DroSec_CAF1 11426 95 + 1
CGGCCCUUCUUCUGCUUGAGUUGCUGCUGCGGCUAUUUUAUUGUUGCGACAACAGCAACAUCACUAGUGUGUCCAGGCUUCGGCCAUUCCUCAAA
.((((........(((((.(((((((.((((((.........))))))....)))))))..(((....)))..)))))...)))).......... ( -29.50)
>DroSim_CAF1 12071 95 + 1
CGGCCCUUCUUCUGCUUGAGUUGCUGCUGCGGCUAUUUUAUUGUUGCGACAACAGCAACAUCACUAGUGUGUCCAGGCUUCGGCCAUUCCUCAAA
.((((........(((((.(((((((.((((((.........))))))....)))))))..(((....)))..)))))...)))).......... ( -29.50)
>DroEre_CAF1 3991 95 + 1
CGGCCCUUCUUCUACUUGAGUUGCUGCUGCGGCUAUUUUAUUGUUGCGACAACAGCAACAUCACUAGUGUGUCCAGGCUUCGGCCAUUCCUCAAA
.((.........((((((((((((((.((((((.........))))))....))))))).)))..))))......(((....)))...))..... ( -26.60)
>DroYak_CAF1 10421 95 + 1
CGGCCCUUCUUCUACUUGAGUUGCUGCUGCGGCUAUUUUAUUGUUGCGACAACAGCAACAUCACUAGUGUGUCCAGGCUUCGGCCAUUCCUCAAA
.((.........((((((((((((((.((((((.........))))))....))))))).)))..))))......(((....)))...))..... ( -26.60)
>consensus
CGGCCCUUCUUCUGCUUGAGUUGCUGCUGCGGCUAUUUUAUUGUUGCGACAACAGCAACAUCACUAGUGUGUCCAGGCUUCGGCCAUUCCUCAAA
.((((........(((((.(((((((.((((((.........))))))....)))))))..(((....)))..)))))...)))).......... (-27.38 = -27.78 +   0.40)

alignment

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secondary structure

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dotplot

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Window 1

Location 4,751,329 – 4,751,424
Length 95
Sequences 5
Columns 95
Reading direction reverse
Mean pairwise identity 99.37
Mean single sequence MFE -31.30
Consensus MFE -31.30
Energy contribution -31.30
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.53
Structure conservation index 1.00
SVM decision value 3.58
SVM RNA-class probability 0.999416
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4751329 95 - 23771897
UUUGAGGAAUGGCCGAAGCCUGGACACACUAGUGAUGUUGCUGUUGUCGCAACAAUAAAAUAGCCGCAGCAGCAACUCAAGCAGAAGAAGGGCCG
..........((((.....((((.....))))(((.(((((((((((.((............)).))))))))))))))...........)))). ( -31.30)
>DroSec_CAF1 11426 95 - 1
UUUGAGGAAUGGCCGAAGCCUGGACACACUAGUGAUGUUGCUGUUGUCGCAACAAUAAAAUAGCCGCAGCAGCAACUCAAGCAGAAGAAGGGCCG
..........((((.....((((.....))))(((.(((((((((((.((............)).))))))))))))))...........)))). ( -31.30)
>DroSim_CAF1 12071 95 - 1
UUUGAGGAAUGGCCGAAGCCUGGACACACUAGUGAUGUUGCUGUUGUCGCAACAAUAAAAUAGCCGCAGCAGCAACUCAAGCAGAAGAAGGGCCG
..........((((.....((((.....))))(((.(((((((((((.((............)).))))))))))))))...........)))). ( -31.30)
>DroEre_CAF1 3991 95 - 1
UUUGAGGAAUGGCCGAAGCCUGGACACACUAGUGAUGUUGCUGUUGUCGCAACAAUAAAAUAGCCGCAGCAGCAACUCAAGUAGAAGAAGGGCCG
..........((((.....((((.....))))(((.(((((((((((.((............)).))))))))))))))...........)))). ( -31.30)
>DroYak_CAF1 10421 95 - 1
UUUGAGGAAUGGCCGAAGCCUGGACACACUAGUGAUGUUGCUGUUGUCGCAACAAUAAAAUAGCCGCAGCAGCAACUCAAGUAGAAGAAGGGCCG
..........((((.....((((.....))))(((.(((((((((((.((............)).))))))))))))))...........)))). ( -31.30)
>consensus
UUUGAGGAAUGGCCGAAGCCUGGACACACUAGUGAUGUUGCUGUUGUCGCAACAAUAAAAUAGCCGCAGCAGCAACUCAAGCAGAAGAAGGGCCG
..........((((.....((((.....))))(((.(((((((((((.((............)).))))))))))))))...........)))). (-31.30 = -31.30 +   0.00)

alignment

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secondary structure

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dotplot

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Window 2

Location 4,751,347 – 4,751,459
Length 112
Sequences 5
Columns 112
Reading direction reverse
Mean pairwise identity 100.00
Mean single sequence MFE -29.52
Consensus MFE -29.52
Energy contribution -29.52
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.63
Structure conservation index 1.00
SVM decision value 1.23
SVM RNA-class probability 0.933103
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4751347 112 - 23771897
GACGUCAUGAAAAUCAGGAAACAGGAUAUAUUAAGUUUGAGGAAUGGCCGAAGCCUGGACACACUAGUGAUGUUGCUGUUGUCGCAACAAUAAAAUAGCCGCAGCAGCAACU
...(((((.....(((((.....((...((((..........)))).))....)))))........)))))(((((((((((.((............)).))))))))))). ( -29.52)
>DroSec_CAF1 11444 112 - 1
GACGUCAUGAAAAUCAGGAAACAGGAUAUAUUAAGUUUGAGGAAUGGCCGAAGCCUGGACACACUAGUGAUGUUGCUGUUGUCGCAACAAUAAAAUAGCCGCAGCAGCAACU
...(((((.....(((((.....((...((((..........)))).))....)))))........)))))(((((((((((.((............)).))))))))))). ( -29.52)
>DroSim_CAF1 12089 112 - 1
GACGUCAUGAAAAUCAGGAAACAGGAUAUAUUAAGUUUGAGGAAUGGCCGAAGCCUGGACACACUAGUGAUGUUGCUGUUGUCGCAACAAUAAAAUAGCCGCAGCAGCAACU
...(((((.....(((((.....((...((((..........)))).))....)))))........)))))(((((((((((.((............)).))))))))))). ( -29.52)
>DroEre_CAF1 4009 112 - 1
GACGUCAUGAAAAUCAGGAAACAGGAUAUAUUAAGUUUGAGGAAUGGCCGAAGCCUGGACACACUAGUGAUGUUGCUGUUGUCGCAACAAUAAAAUAGCCGCAGCAGCAACU
...(((((.....(((((.....((...((((..........)))).))....)))))........)))))(((((((((((.((............)).))))))))))). ( -29.52)
>DroYak_CAF1 10439 112 - 1
GACGUCAUGAAAAUCAGGAAACAGGAUAUAUUAAGUUUGAGGAAUGGCCGAAGCCUGGACACACUAGUGAUGUUGCUGUUGUCGCAACAAUAAAAUAGCCGCAGCAGCAACU
...(((((.....(((((.....((...((((..........)))).))....)))))........)))))(((((((((((.((............)).))))))))))). ( -29.52)
>consensus
GACGUCAUGAAAAUCAGGAAACAGGAUAUAUUAAGUUUGAGGAAUGGCCGAAGCCUGGACACACUAGUGAUGUUGCUGUUGUCGCAACAAUAAAAUAGCCGCAGCAGCAACU
...(((((.....(((((.....((...((((..........)))).))....)))))........)))))(((((((((((.((............)).))))))))))). (-29.52 = -29.52 +  -0.00)

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 Mon Dec 4 10:12:11 2006