Locus 1753

Sequence ID 2R_DroMel_CAF1
Location 6,586,201 – 6,586,345
Length 144
Max. P 0.998288
window2921 window2922 window2923

overview

Window 1

Location 6,586,201 – 6,586,305
Length 104
Sequences 3
Columns 104
Reading direction forward
Mean pairwise identity 85.71
Mean single sequence MFE -21.30
Consensus MFE -21.30
Energy contribution -21.30
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -3.30
Structure conservation index 1.00
SVM decision value 3.06
SVM RNA-class probability 0.998288
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6586201 104 + 20766785
CCACUUCACUCCGCAUCGCCAUCCACAUCCCCUUUCGCAUUCCCAUUUCCAUCCGCUUGUGCUGCUUUUGCAGAGCUUUUGUUCUACCCUUCUGGCCAAGUGGA
...................................................((((((((.(((((....))(((((....)))))........))))))))))) ( -21.30)
>DroSec_CAF1 138877 86 + 1
CCACUUCACUCCGCAUCCCC------------------AUUCCCAUUCCCAUCCGCUUGUGCUGCUCUUGCAGAGCUUUUGUUCUACCCUUCUGGCCAAGUGGA
....................------------------.............((((((((.(((((....))(((((....)))))........))))))))))) ( -21.30)
>DroSim_CAF1 125178 86 + 1
CCACUUCACUCCGCAUCCCC------------------AUUCCCAUUCCCAUCCGCUUGUGCUGCUCUUGCAGAGCUUUUGUUCUACCCUUCUGGCCAAGUGGA
....................------------------.............((((((((.(((((....))(((((....)))))........))))))))))) ( -21.30)
>consensus
CCACUUCACUCCGCAUCCCC__________________AUUCCCAUUCCCAUCCGCUUGUGCUGCUCUUGCAGAGCUUUUGUUCUACCCUUCUGGCCAAGUGGA
...................................................((((((((.(((((....))(((((....)))))........))))))))))) (-21.30 = -21.30 +   0.00)

alignment

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secondary structure

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dotplot

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Window 2

Location 6,586,201 – 6,586,305
Length 104
Sequences 3
Columns 104
Reading direction reverse
Mean pairwise identity 85.71
Mean single sequence MFE -23.13
Consensus MFE -20.60
Energy contribution -20.60
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.35
Structure conservation index 0.89
SVM decision value 0.15
SVM RNA-class probability 0.608435
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6586201 104 - 20766785
UCCACUUGGCCAGAAGGGUAGAACAAAAGCUCUGCAAAAGCAGCACAAGCGGAUGGAAAUGGGAAUGCGAAAGGGGAUGUGGAUGGCGAUGCGGAGUGAAGUGG
.((((((.(((.....))).........((((((((...((..((((.....((....)).....(.(....).)..))))....))..)))))))).)))))) ( -27.60)
>DroSec_CAF1 138877 86 - 1
UCCACUUGGCCAGAAGGGUAGAACAAAAGCUCUGCAAGAGCAGCACAAGCGGAUGGGAAUGGGAAU------------------GGGGAUGCGGAGUGAAGUGG
.((((((.(((.....))).........((((((((....((...((..(......)..))....)------------------)....)))))))).)))))) ( -20.90)
>DroSim_CAF1 125178 86 - 1
UCCACUUGGCCAGAAGGGUAGAACAAAAGCUCUGCAAGAGCAGCACAAGCGGAUGGGAAUGGGAAU------------------GGGGAUGCGGAGUGAAGUGG
.((((((.(((.....))).........((((((((....((...((..(......)..))....)------------------)....)))))))).)))))) ( -20.90)
>consensus
UCCACUUGGCCAGAAGGGUAGAACAAAAGCUCUGCAAGAGCAGCACAAGCGGAUGGGAAUGGGAAU__________________GGGGAUGCGGAGUGAAGUGG
.((((((.(((.....))).........((((((((......((....))..((....)).............................)))))))).)))))) (-20.60 = -20.60 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 3

Location 6,586,239 – 6,586,345
Length 106
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 83.03
Mean single sequence MFE -27.46
Consensus MFE -15.78
Energy contribution -17.26
Covariance contribution 1.48
Combinations/Pair 1.04
Mean z-score -2.80
Structure conservation index 0.57
SVM decision value 1.19
SVM RNA-class probability 0.928802
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6586239 106 + 20766785
AUUCCCAUUUCCAUCCGCU---------UGUGCUGCUUUUGCAGAGCU-----UUUGUUCUACCCUUCUGGCCAAGUGGAUGUUAUAACUUGGUAAUUCGAUUUGCACAAAGUAUUUUCC
...........((((((((---------((.(((((....))(((((.-----...)))))........))))))))))))).....((((.((((......))))...))))....... ( -30.20)
>DroSec_CAF1 138897 106 + 1
AUUCCCAUUCCCAUCCGCU---------UGUGCUGCUCUUGCAGAGCU-----UUUGUUCUACCCUUCUGGCCAAGUGGAUGUUAUAACUUGGUAAUUCGAUUUGCACAAAGUAUUUUCC
...........((((((((---------((.(((((....))(((((.-----...)))))........))))))))))))).....((((.((((......))))...))))....... ( -30.20)
>DroSim_CAF1 125198 106 + 1
AUUCCCAUUCCCAUCCGCU---------UGUGCUGCUCUUGCAGAGCU-----UUUGUUCUACCCUUCUGGCCAAGUGGAUGUUAUAACUUGGUAAUUCGAUUUGCACAAAGUAUUUUCC
...........((((((((---------((.(((((....))(((((.-----...)))))........))))))))))))).....((((.((((......))))...))))....... ( -30.20)
>DroEre_CAF1 138616 90 + 1
----------------GCU---------CGUGCUGCUUUGGCAGUGCU-----UUUGUUCUACCCUUCUGGCCAAGUGGAUGUUAUAACUUGGUAAUUCGAUUUGCACAAAGUAUUUUCC
----------------...---------.(..((((....))))..)(-----(((((.(..........(((((((..........)))))))..........).))))))........ ( -21.85)
>DroAna_CAF1 140962 118 + 1
--UACCGCUUCCUUCUGCUCUUCUUUUUUCUCCUUCUGCAGCAGGGCUUUGGCUUUGUUCUACCCUUCUGGCCAAGUGGAUGUUAUAACUUGGUAAUUUGAUUUGCACAAAGUAUUUUCC
--....((..(((.((((...................)))).)))))....(((((((.(..........(((((((..........)))))))..........).)))))))....... ( -24.86)
>consensus
AUUCCCAUUCCCAUCCGCU_________UGUGCUGCUCUUGCAGAGCU_____UUUGUUCUACCCUUCUGGCCAAGUGGAUGUUAUAACUUGGUAAUUCGAUUUGCACAAAGUAUUUUCC
...........((((((((..........(..((((....))))..)................((....))...)))))))).....((((.((((......))))...))))....... (-15.78 = -17.26 +   1.48)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:12:23 2006