Locus 4507

Sequence ID X_DroMel_CAF1
Location 11,898,006 – 11,898,126
Length 120
Max. P 0.844835
window7411 window7412

overview

Window 1

Location 11,898,006 – 11,898,126
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 95.56
Mean single sequence MFE -37.73
Consensus MFE -33.94
Energy contribution -33.83
Covariance contribution -0.11
Combinations/Pair 1.07
Mean z-score -1.95
Structure conservation index 0.90
SVM decision value 0.32
SVM RNA-class probability 0.687390
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11898006 120 + 22224390
GUAGCUCCCCUGGAUCAUCUGUUCUGGGACCAAAUCCGCCAGCUGGCUCAGUUGUACCAUCGAUUCCUGUACUUCCUGGCGGAGCUGGCUCUUGGCCUUGGCAUCCUCGACCAAACAUUC
..((((((((..((........))..)).........(((((..((..(((..((.......))..)))..))..)))))))))))(((.....)))(((((......).))))...... ( -37.60)
>DroSec_CAF1 8809 120 + 1
GUAGCUCCCCUGGAUCAUCUGCUCCGGUACCAAAUCCGCCAGCUAGCCCAGUUGUACCAUCGAUUCCUGUACUUCCUGGCGGAUCUGGCUCUUGGCCUUGGCAUCCUCGACCGAACAUUC
((((.(((...)))....))))..((((.(((.(((((((((..((..(((..((.......))..)))..))..))))))))).)))......((....)).......))))....... ( -36.60)
>DroSim_CAF1 8111 120 + 1
GUAGAUCCCCUGGAUCAUCUGCUCCGGUACCAAAUCCGCCAGCUAGCUCAGUUGUACCAUCGAUUCCUGUACUUCCUGGCGGAUCUGGCUCUUGGCCUUGGCAUCCUCGACCGAACAUUC
...(((((...)))))........((((.(((.(((((((((..((..(((..((.......))..)))..))..))))))))).)))......((....)).......))))....... ( -39.00)
>consensus
GUAGCUCCCCUGGAUCAUCUGCUCCGGUACCAAAUCCGCCAGCUAGCUCAGUUGUACCAUCGAUUCCUGUACUUCCUGGCGGAUCUGGCUCUUGGCCUUGGCAUCCUCGACCGAACAUUC
...........(((((....(((..((..(((.(((((((((..((..(((..((.......))..)))..))..))))))))).)))..)).)))....).)))).............. (-33.94 = -33.83 +  -0.11)

alignment

Postscript

secondary structure

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dotplot

Postscript

Window 2

Location 11,898,006 – 11,898,126
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 95.56
Mean single sequence MFE -44.47
Consensus MFE -40.87
Energy contribution -41.09
Covariance contribution 0.23
Combinations/Pair 1.06
Mean z-score -2.15
Structure conservation index 0.92
SVM decision value 0.76
SVM RNA-class probability 0.844835
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11898006 120 - 22224390
GAAUGUUUGGUCGAGGAUGCCAAGGCCAAGAGCCAGCUCCGCCAGGAAGUACAGGAAUCGAUGGUACAACUGAGCCAGCUGGCGGAUUUGGUCCCAGAACAGAUGAUCCAGGGGAGCUAC
.....(((((((..((...))..)))))))....((((((.((.(((.((((...........))))..(((.(((....)))((((...)))).....)))....))).)))))))).. ( -37.90)
>DroSec_CAF1 8809 120 - 1
GAAUGUUCGGUCGAGGAUGCCAAGGCCAAGAGCCAGAUCCGCCAGGAAGUACAGGAAUCGAUGGUACAACUGGGCUAGCUGGCGGAUUUGGUACCGGAGCAGAUGAUCCAGGGGAGCUAC
....((((((((..((...))..))))....((((((((((((((..((..(((...............)))..))..)))))))))))))).(((((........))).)).))))... ( -47.16)
>DroSim_CAF1 8111 120 - 1
GAAUGUUCGGUCGAGGAUGCCAAGGCCAAGAGCCAGAUCCGCCAGGAAGUACAGGAAUCGAUGGUACAACUGAGCUAGCUGGCGGAUUUGGUACCGGAGCAGAUGAUCCAGGGGAUCUAC
...(((((((((..((...))..))))....((((((((((((((..(((.(((...............))).)))..))))))))))))))....)))))...(((((...)))))... ( -48.36)
>consensus
GAAUGUUCGGUCGAGGAUGCCAAGGCCAAGAGCCAGAUCCGCCAGGAAGUACAGGAAUCGAUGGUACAACUGAGCUAGCUGGCGGAUUUGGUACCGGAGCAGAUGAUCCAGGGGAGCUAC
...(((((((((..((...))..))))....((((((((((((((..(((.(((...............))).)))..))))))))))))))....))))).....(((...)))..... (-40.87 = -41.09 +   0.23)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:26:50 2006