Locus 3117

Sequence ID 3R_DroMel_CAF1
Location 8,206,098 – 8,206,298
Length 200
Max. P 0.942422
window5055 window5056 window5057

overview

Window 5

Location 8,206,098 – 8,206,218
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 92.92
Mean single sequence MFE -49.45
Consensus MFE -41.56
Energy contribution -42.88
Covariance contribution 1.31
Combinations/Pair 1.07
Mean z-score -2.44
Structure conservation index 0.84
SVM decision value 1.33
SVM RNA-class probability 0.942422
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8206098 120 - 27905053
AUGGUGAGGCAGUCGCCAGCCACAUACUCCUGGUCCUCCAGGAAGGUGUCCAGGUGGCCAAAGGCGCUGUCCACUUUCUGCAUGGCCUCUGGAUCGGCGGGAUGAUUAUUCCUUAUCUGU
..(((((((.(((((((.(((.(((..((((((....))))))..)))((((((.(((((...(((..(......)..))).)))))))))))..))).)).)))))...)))))))... ( -50.70)
>DroSim_CAF1 21773 120 - 1
AAGGUGAGGCAGUCGCCAGCCACAUACUCCUGGUCCUCCAGAAAGGUGUCCAGGUGGCCAAAGGCGCUGUCCACUUUCUGCAUGGCCUCUGGAUCGGCGGGCUGUUUGUUCCUUAUCUGU
.(((((((((((..(((.(((.(((....((((....))))....)))((((((.(((((...(((..(......)..))).)))))))))))..))).)))...)))..)))))))).. ( -46.00)
>DroEre_CAF1 18523 120 - 1
ACGGUGAGGCAGUCGCCAGCCACAUAUUCCUGGUCCUCCAGGAAGGUGUCCAGGUGCCCAAAGGCGGUGUCCACUUUCUGCAUGGCCACUGGAUCGGCCGGCUCUUUACUCCUUAUCUGU
..(((((((.(((.(((.(((.(((.(((((((....))))))).)))(((((..(((...(((.(((....))).)))....)))..)))))..))).))).....))))))))))... ( -49.60)
>DroYak_CAF1 27654 120 - 1
ACGGUGAGGCAGUCGCCAGCCACAUAUUCCUGGUCCUCCAGGAAGGUGUCCAGGUGCCCAAAGGCGGUGUCAACUUUCUGCAUGGCCUCUGGAUCAGCAGGCUGUUUGCUCCUUAUCUGU
..(((((((.(((...(((((.....(((((((....)))))))(.((((((((.(((...(((.(((....))).)))....))).)))))).)).).)))))...))))))))))... ( -51.50)
>consensus
ACGGUGAGGCAGUCGCCAGCCACAUACUCCUGGUCCUCCAGGAAGGUGUCCAGGUGCCCAAAGGCGCUGUCCACUUUCUGCAUGGCCUCUGGAUCGGCGGGCUGUUUACUCCUUAUCUGU
..(((((((.(((...(((((......((((((....)))))).(.((((((((.(((((...((((.(....)...)))).))))))))))).)).).)))))...))))))))))... (-41.56 = -42.88 +   1.31)

alignment

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secondary structure

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dotplot

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Window 6

Location 8,206,138 – 8,206,258
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 94.44
Mean single sequence MFE -49.57
Consensus MFE -40.30
Energy contribution -42.55
Covariance contribution 2.25
Combinations/Pair 1.00
Mean z-score -2.03
Structure conservation index 0.81
SVM decision value 0.39
SVM RNA-class probability 0.718370
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8206138 120 - 27905053
CUCAAAGGUGGAAACGGAGGCCAACAGGGCAAUGUCGGCAAUGGUGAGGCAGUCGCCAGCCACAUACUCCUGGUCCUCCAGGAAGGUGUCCAGGUGGCCAAAGGCGCUGUCCACUUUCUG
....((((((((..((..(((((...(((((((((.(((..((((((.....)))))))))))))..((((((....))))))...)))))...))))).....))...))))))))... ( -49.50)
>DroSim_CAF1 21813 120 - 1
CUCGAAGGUGGAAACGGAGGCCAAGAGCGCAAUGUCCGCCAAGGUGAGGCAGUCGCCAGCCACAUACUCCUGGUCCUCCAGAAAGGUGUCCAGGUGGCCAAAGGCGCUGUCCACUUUCUG
...(((((((((...((...))...(((((..((.(((((..(((..(((....))).)))((((....((((....))))....))))...))))).))...))))).))))))))).. ( -48.10)
>DroEre_CAF1 18563 120 - 1
CUCGAAGGUGGAAACGGAGGCCAACAGGGCAAUGUCAGCCACGGUGAGGCAGUCGCCAGCCACAUAUUCCUGGUCCUCCAGGAAGGUGUCCAGGUGCCCAAAGGCGGUGUCCACUUUCUG
...(((((((((.(((((.(((.....(((.......)))..(((..(((....))).))).....(((((((....)))))))))).)))...((((....)))))).))))))))).. ( -53.10)
>DroYak_CAF1 27694 120 - 1
CUCGAAGGUGGAAACGGAGGCCAACAGGGCAAUGUCAGCCACGGUGAGGCAGUCGCCAGCCACAUAUUCCUGGUCCUCCAGGAAGGUGUCCAGGUGCCCAAAGGCGGUGUCAACUUUCUG
...(((((((....).((.(((..(.(((((.((...(((..(((..(((....))).))).....(((((((....))))))))))...))..)))))...)..))).)).)))))).. ( -47.60)
>consensus
CUCGAAGGUGGAAACGGAGGCCAACAGGGCAAUGUCAGCCACGGUGAGGCAGUCGCCAGCCACAUACUCCUGGUCCUCCAGGAAGGUGUCCAGGUGCCCAAAGGCGCUGUCCACUUUCUG
...(((((((((...(((.(((.....(((.......)))..(((..(((....))).)))......((((((....)))))).))).))).((((((....)))))).))))))))).. (-40.30 = -42.55 +   2.25)

alignment

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secondary structure

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dotplot

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Window 7

Location 8,206,178 – 8,206,298
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 94.44
Mean single sequence MFE -47.10
Consensus MFE -41.31
Energy contribution -42.12
Covariance contribution 0.81
Combinations/Pair 1.03
Mean z-score -2.23
Structure conservation index 0.88
SVM decision value 1.22
SVM RNA-class probability 0.931746
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8206178 120 - 27905053
UGGCCACAUUUGGAUACUGGGCUAUAUCGAAGUCCACCACCUCAAAGGUGGAAACGGAGGCCAACAGGGCAAUGUCGGCAAUGGUGAGGCAGUCGCCAGCCACAUACUCCUGGUCCUCCA
...(((....)))....((((((.......))))))(((((.....)))))....(((((....(((((..((((.(((..((((((.....)))))))))))))..)))))..))))). ( -46.60)
>DroSim_CAF1 21853 120 - 1
GGGCCACAUUUGGAUACUGGGCUAUAUCGAAGUCCACCACCUCGAAGGUGGAAACGGAGGCCAAGAGCGCAAUGUCCGCCAAGGUGAGGCAGUCGCCAGCCACAUACUCCUGGUCCUCCA
((.(((....)))...))(((((.......))))).(((((.....)))))....((((((((.(((.((.......))...(((..(((....))).))).....))).))).))))). ( -42.50)
>DroEre_CAF1 18603 120 - 1
UGGCCACGUUUGGGUACUGGGCUAUAUCGAAGUCCACCACCUCGAAGGUGGAAACGGAGGCCAACAGGGCAAUGUCAGCCACGGUGAGGCAGUCGCCAGCCACAUAUUCCUGGUCCUCCA
...((((.(((((((..((((((.......))))))..))).)))).))))....((((((((....(((.......)))..(((..(((....))).))).........))).))))). ( -48.60)
>DroYak_CAF1 27734 120 - 1
UGGCCACGUUUGGGUACUGGGCUAUAUCGAAGUCCACUACCUCGAAGGUGGAAACGGAGGCCAACAGGGCAAUGUCAGCCACGGUGAGGCAGUCGCCAGCCACAUAUUCCUGGUCCUCCA
...((((.((((((((.((((((.......)))))).)))).)))).))))....((((((((....(((.......)))..(((..(((....))).))).........))).))))). ( -50.70)
>consensus
UGGCCACAUUUGGAUACUGGGCUAUAUCGAAGUCCACCACCUCGAAGGUGGAAACGGAGGCCAACAGGGCAAUGUCAGCCACGGUGAGGCAGUCGCCAGCCACAUACUCCUGGUCCUCCA
...((((.(((((((..((((((.......))))))..))).)))).))))....((((((((....(((.......)))..(((..(((....))).))).........))).))))). (-41.31 = -42.12 +   0.81)

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 10:53:31 2006