Locus 3362

Sequence ID X_DroMel_CAF1
Location 8,978,887 – 8,979,071
Length 184
Max. P 0.988048
window5502 window5503 window5504 window5505 window5506 window5507

overview

Window 2

Location 8,978,887 – 8,979,001
Length 114
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 90.03
Mean single sequence MFE -28.91
Consensus MFE -23.58
Energy contribution -24.07
Covariance contribution 0.50
Combinations/Pair 1.04
Mean z-score -2.84
Structure conservation index 0.82
SVM decision value 1.77
SVM RNA-class probability 0.976293
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8978887 114 + 22224390
UCUACAGCGAUCCUCCGACUUU------AUAUCAGCCAUAUAUUAUUUUUCGCUGUGUACACAGCGAAUGCCCUAUCGGUUAUAUGGCCCCUCAACUGGGCAUACAACUGUCCAUCAAAC
........(((...........------......((((((((......((((((((....)))))))).(((.....))))))))))).........(((((......)))))))).... ( -29.40)
>DroSec_CAF1 7453 114 + 1
UCUACAUGGAUCCUCCGACUUU------AUGUCAGUCAUAUACUAUUUUUCGCUGUGUACACAGCGAAUGCCCUAUCGGUUAUAUGGCCGCUCAACUGGGCAUACAACUGUCCAUCAAAC
.....((((((.....(((...------..))).((((((((......((((((((....)))))))).(((.....))))))))))).((((....))))........))))))..... ( -33.00)
>DroSim_CAF1 2110 114 + 1
UCUACAUCGAUCCUCCGACUUU------AUGUCAGUCAUAUAUUAUUUUUCGCUGUGUACACAGCGAAUGCCCUAUCGGUUAUAUGGCCGCUCAACUGGGCAUACAACUGUCCAUCAAAC
................(((...------..))).((((((((......((((((((....)))))))).(((.....)))))))))))........((((((......))))))...... ( -29.50)
>DroEre_CAF1 889 119 + 1
UCUACAUCGAUCCCCAAGCUGUAUAUGUAUAUCAGCCACAUAAU-UUUUUCGCUGUGUACAAAGCGAAUUCCCUAUCGGUUAUAUUGCCGCUCAACUGGGCAUACAACUGUCCAUCAAAC
........(((.....((.(((((.((((((.((((........-......))))))))))..((((((..((....))..)).)))).((((....))))))))).))....))).... ( -23.74)
>consensus
UCUACAUCGAUCCUCCGACUUU______AUAUCAGCCAUAUAUUAUUUUUCGCUGUGUACACAGCGAAUGCCCUAUCGGUUAUAUGGCCGCUCAACUGGGCAUACAACUGUCCAUCAAAC
........(((.......................((((((((......((((((((....))))))))...((....)).)))))))).........(((((......)))))))).... (-23.58 = -24.07 +   0.50)

alignment

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secondary structure

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Window 3

Location 8,978,887 – 8,979,001
Length 114
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 90.03
Mean single sequence MFE -32.83
Consensus MFE -27.28
Energy contribution -27.34
Covariance contribution 0.06
Combinations/Pair 1.09
Mean z-score -1.72
Structure conservation index 0.83
SVM decision value 0.56
SVM RNA-class probability 0.780254
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8978887 114 - 22224390
GUUUGAUGGACAGUUGUAUGCCCAGUUGAGGGGCCAUAUAACCGAUAGGGCAUUCGCUGUGUACACAGCGAAAAAUAAUAUAUGGCUGAUAU------AAAGUCGGAGGAUCGCUGUAGA
.........(((((.((...((.........(((((((((.((....))...((((((((....))))))))......)))))))))(((..------...)))))...)).)))))... ( -34.60)
>DroSec_CAF1 7453 114 - 1
GUUUGAUGGACAGUUGUAUGCCCAGUUGAGCGGCCAUAUAACCGAUAGGGCAUUCGCUGUGUACACAGCGAAAAAUAGUAUAUGACUGACAU------AAAGUCGGAGGAUCCAUGUAGA
.....(((((.(((..(((((((.......(((........)))...)))).((((((((....)))))))).......)))..)))(((..------...)))......)))))..... ( -34.10)
>DroSim_CAF1 2110 114 - 1
GUUUGAUGGACAGUUGUAUGCCCAGUUGAGCGGCCAUAUAACCGAUAGGGCAUUCGCUGUGUACACAGCGAAAAAUAAUAUAUGACUGACAU------AAAGUCGGAGGAUCGAUGUAGA
.....(((..((((..(((((((.......(((........)))...)))).((((((((....)))))))).......)))..)))).)))------...((((......))))..... ( -33.60)
>DroEre_CAF1 889 119 - 1
GUUUGAUGGACAGUUGUAUGCCCAGUUGAGCGGCAAUAUAACCGAUAGGGAAUUCGCUUUGUACACAGCGAAAAA-AUUAUGUGGCUGAUAUACAUAUACAGCUUGGGGAUCGAUGUAGA
.........(((.(((.((.((((((((..((((.((((((((....))...((((((........))))))...-.)))))).))))(((....))).)))).)))).))))))))... ( -29.00)
>consensus
GUUUGAUGGACAGUUGUAUGCCCAGUUGAGCGGCCAUAUAACCGAUAGGGCAUUCGCUGUGUACACAGCGAAAAAUAAUAUAUGACUGACAU______AAAGUCGGAGGAUCGAUGUAGA
..........((((..(((((((.((((..............)))).)))).((((((((....)))))))).......)))..))))................................ (-27.28 = -27.34 +   0.06)

alignment

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secondary structure

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dotplot

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Window 4

Location 8,978,921 – 8,979,041
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 90.52
Mean single sequence MFE -33.92
Consensus MFE -28.95
Energy contribution -29.32
Covariance contribution 0.37
Combinations/Pair 1.07
Mean z-score -2.22
Structure conservation index 0.85
SVM decision value 1.42
SVM RNA-class probability 0.952016
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8978921 120 + 22224390
UAUUAUUUUUCGCUGUGUACACAGCGAAUGCCCUAUCGGUUAUAUGGCCCCUCAACUGGGCAUACAACUGUCCAUCAAACGAAUUGGGUUCGAAACGGAUCCGAUACGAUCCGAUCCGAU
........((((((((....))))))))......(((((.....((..(((.....((((((......))))))((....))...)))..))...((((((......))))))..))))) ( -37.30)
>DroSec_CAF1 7487 112 + 1
UACUAUUUUUCGCUGUGUACACAGCGAAUGCCCUAUCGGUUAUAUGGCCGCUCAACUGGGCAUACAACUGUCCAUCAAACGGACUGGGUUCGAAACGGAUCCGAUACGAUCC--------
........((((((((....)))))))).((((....((((.((((.(((......))).)))).))))((((.......)))).)))).......(((((......)))))-------- ( -36.70)
>DroSim_CAF1 2144 112 + 1
UAUUAUUUUUCGCUGUGUACACAGCGAAUGCCCUAUCGGUUAUAUGGCCGCUCAACUGGGCAUACAACUGUCCAUCAAACGGACUGGGUUCGAAACGGAUCCGAUACGAUCC--------
........((((((((....)))))))).((((....((((.((((.(((......))).)))).))))((((.......)))).)))).......(((((......)))))-------- ( -36.70)
>DroEre_CAF1 929 109 + 1
UAAU-UUUUUCGCUGUGUACAAAGCGAAUUCCCUAUCGGUUAUAUUGCCGCUCAACUGGGCAUACAACUGUCCAUCAAACGAACUGGGAUCGAAACGUUUCCGAUACGAU----------
....-...((((((........)))))).((((..(((((......))).......((((((......))))))......))...))))......(((.......)))..---------- ( -25.00)
>consensus
UAUUAUUUUUCGCUGUGUACACAGCGAAUGCCCUAUCGGUUAUAUGGCCGCUCAACUGGGCAUACAACUGUCCAUCAAACGAACUGGGUUCGAAACGGAUCCGAUACGAUCC________
........((((((((....)))))))).((((..(((((......))).......((((((......))))))......))...)))).......(((((......)))))........ (-28.95 = -29.32 +   0.37)

alignment

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secondary structure

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Window 5

Location 8,978,921 – 8,979,041
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 90.52
Mean single sequence MFE -39.38
Consensus MFE -33.62
Energy contribution -33.88
Covariance contribution 0.25
Combinations/Pair 1.03
Mean z-score -2.89
Structure conservation index 0.85
SVM decision value 2.10
SVM RNA-class probability 0.988048
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8978921 120 - 22224390
AUCGGAUCGGAUCGUAUCGGAUCCGUUUCGAACCCAAUUCGUUUGAUGGACAGUUGUAUGCCCAGUUGAGGGGCCAUAUAACCGAUAGGGCAUUCGCUGUGUACACAGCGAAAAAUAAUA
.(((((.((((((......)))))).))))).(((...(((((.....))).(((((((((((.......))).)))))))).))..)))..((((((((....))))))))........ ( -44.90)
>DroSec_CAF1 7487 112 - 1
--------GGAUCGUAUCGGAUCCGUUUCGAACCCAGUCCGUUUGAUGGACAGUUGUAUGCCCAGUUGAGCGGCCAUAUAACCGAUAGGGCAUUCGCUGUGUACACAGCGAAAAAUAGUA
--------(((((......)))))........(((.((((((...)))))).((((((((.((........)).)))))))).....)))..((((((((....))))))))........ ( -39.80)
>DroSim_CAF1 2144 112 - 1
--------GGAUCGUAUCGGAUCCGUUUCGAACCCAGUCCGUUUGAUGGACAGUUGUAUGCCCAGUUGAGCGGCCAUAUAACCGAUAGGGCAUUCGCUGUGUACACAGCGAAAAAUAAUA
--------(((((......)))))........(((.((((((...)))))).((((((((.((........)).)))))))).....)))..((((((((....))))))))........ ( -39.80)
>DroEre_CAF1 929 109 - 1
----------AUCGUAUCGGAAACGUUUCGAUCCCAGUUCGUUUGAUGGACAGUUGUAUGCCCAGUUGAGCGGCAAUAUAACCGAUAGGGAAUUCGCUUUGUACACAGCGAAAAA-AUUA
----------.(((...((....))...)))((((.((((((...)))))).(((((((((((......).))).))))))).....)))).((((((........))))))...-.... ( -33.00)
>consensus
________GGAUCGUAUCGGAUCCGUUUCGAACCCAGUCCGUUUGAUGGACAGUUGUAUGCCCAGUUGAGCGGCCAUAUAACCGAUAGGGCAUUCGCUGUGUACACAGCGAAAAAUAAUA
...........(((...((....))...))).(((.((((((...)))))).(((((((((((......).))).))))))).....)))..((((((((....))))))))........ (-33.62 = -33.88 +   0.25)

alignment

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secondary structure

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dotplot

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Window 6

Location 8,978,961 – 8,979,071
Length 110
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 83.18
Mean single sequence MFE -34.30
Consensus MFE -22.36
Energy contribution -22.30
Covariance contribution -0.06
Combinations/Pair 1.12
Mean z-score -2.25
Structure conservation index 0.65
SVM decision value 0.92
SVM RNA-class probability 0.882822
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8978961 110 + 22224390
UAUAUGGCCCCUCAACUGGGCAUACAACUGUCCAUCAAACGAAUUGGGUUCGAAACGGAUCCGAUACGAUCCGAUCCGAUCCGAUCCGAGGUCUUAUCUCGGGUUCCCGG----------
...((((..((((...((((((......))))))......(.((((((((.((..((((((......)))))).)).)))))))).)))))..))))..(((....))).---------- ( -35.40)
>DroSec_CAF1 7527 100 + 1
UAUAUGGCCGCUCAACUGGGCAUACAACUGUCCAUCAAACGGACUGGGUUCGAAACGGAUCCGAUACGAUCC----------GAUCCGAGGUCUUAUCUCGGGUUCCCUG----------
..((((.(((......))).)))).....((((.......)))).(((..(....((((((......)))))----------)..(((((((...))))))))..)))..---------- ( -33.50)
>DroSim_CAF1 2184 100 + 1
UAUAUGGCCGCUCAACUGGGCAUACAACUGUCCAUCAAACGGACUGGGUUCGAAACGGAUCCGAUACGAUCC----------GAUCCGAGGUCUUAUCUCGGGUUCCCUG----------
..((((.(((......))).)))).....((((.......)))).(((..(....((((((......)))))----------)..(((((((...))))))))..)))..---------- ( -33.50)
>DroEre_CAF1 968 105 + 1
UAUAUUGCCGCUCAACUGGGCAUACAACUGUCCAUCAAACGAACUGGGAUCGAAACGUUUCCGAUACGAU---------------CCCAGUUCUUAUCUCGGGUUCUCAGUUCUGAGUUC
.........((((...((((((......))))))......((((((((((((...((....))...))))---------------)))))))).......)))).((((....))))... ( -34.80)
>consensus
UAUAUGGCCGCUCAACUGGGCAUACAACUGUCCAUCAAACGAACUGGGUUCGAAACGGAUCCGAUACGAUCC__________GAUCCGAGGUCUUAUCUCGGGUUCCCUG__________
................((((((......))))))......((((((((((((...))))))))......................(((((((...))))))))))).............. (-22.36 = -22.30 +  -0.06)

alignment

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secondary structure

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dotplot

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Window 7

Location 8,978,961 – 8,979,071
Length 110
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 83.18
Mean single sequence MFE -37.38
Consensus MFE -23.95
Energy contribution -24.45
Covariance contribution 0.50
Combinations/Pair 1.04
Mean z-score -2.34
Structure conservation index 0.64
SVM decision value 0.98
SVM RNA-class probability 0.893922
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8978961 110 - 22224390
----------CCGGGAACCCGAGAUAAGACCUCGGAUCGGAUCGGAUCGGAUCGUAUCGGAUCCGUUUCGAACCCAAUUCGUUUGAUGGACAGUUGUAUGCCCAGUUGAGGGGCCAUAUA
----------..(((...(((((.......))))).(((((.((((((.(((...))).)))))).))))).))).....(((.....)))...(((((((((.......))).)))))) ( -39.10)
>DroSec_CAF1 7527 100 - 1
----------CAGGGAACCCGAGAUAAGACCUCGGAUC----------GGAUCGUAUCGGAUCCGUUUCGAACCCAGUCCGUUUGAUGGACAGUUGUAUGCCCAGUUGAGCGGCCAUAUA
----------..(((...(((((.......)))))..(----------(((((......)))))).......))).(.(((((..((((.((......)).))).)..))))).)..... ( -34.50)
>DroSim_CAF1 2184 100 - 1
----------CAGGGAACCCGAGAUAAGACCUCGGAUC----------GGAUCGUAUCGGAUCCGUUUCGAACCCAGUCCGUUUGAUGGACAGUUGUAUGCCCAGUUGAGCGGCCAUAUA
----------..(((...(((((.......)))))..(----------(((((......)))))).......))).(.(((((..((((.((......)).))).)..))))).)..... ( -34.50)
>DroEre_CAF1 968 105 - 1
GAACUCAGAACUGAGAACCCGAGAUAAGAACUGGG---------------AUCGUAUCGGAAACGUUUCGAUCCCAGUUCGUUUGAUGGACAGUUGUAUGCCCAGUUGAGCGGCAAUAUA
...((((....))))...((.......((((((((---------------((((...((....))...))))))))))))(((..((((.((......)).))).)..)))))....... ( -41.40)
>consensus
__________CAGGGAACCCGAGAUAAGACCUCGGAUC__________GGAUCGUAUCGGAUCCGUUUCGAACCCAGUCCGUUUGAUGGACAGUUGUAUGCCCAGUUGAGCGGCCAUAUA
............(((...(((((.......)))))................(((...((....))...))).)))...(((((..((((.((......)).))).)..)))))....... (-23.95 = -24.45 +   0.50)

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 10:57:30 2006