Locus 2394

Sequence ID 2R_DroMel_CAF1
Location 8,633,751 – 8,633,878
Length 127
Max. P 0.965549
window3960 window3961 window3962

overview

Window 0

Location 8,633,751 – 8,633,846
Length 95
Sequences 3
Columns 96
Reading direction forward
Mean pairwise identity 88.85
Mean single sequence MFE -25.47
Consensus MFE -22.17
Energy contribution -22.40
Covariance contribution 0.23
Combinations/Pair 1.09
Mean z-score -3.00
Structure conservation index 0.87
SVM decision value 1.58
SVM RNA-class probability 0.965549
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8633751 95 + 20766785
CCUCUCUCGCCAUGCUCCAUCCCACUCGCACUCUCUCCA-GAGAUACACAUAUAUCCCUUUCCACCAAAAUUUAAGUGGAUGCGGCGUGGAGAUGG
................((((((((((((((.((((....-))))................(((((..........)))))))))).)))).))))) ( -27.50)
>DroSec_CAF1 13911 96 + 1
CCCCUCUCGCCAUACUCCAUCCCACUCGCACUCUCUUCAGGACAUACACAUAUAUUCCCUUCCACCAAAAUUAAUGUGGAUGCGGAGUGGAGAUGG
................((((((((((((((.........(((.(((......))))))..(((((..........)))))))).)))))).))))) ( -25.90)
>DroSim_CAF1 17528 95 + 1
CCCCUCUCGGCAUGCUCUAUCCCACUUACACUCUCUCUA-GAGAUACACAUACAUCCCCUUCCACCAAAAUUAAAGUGGAUGCGGAGUGGAGAUGG
................(((((((((......((((....-))))..........(((.(.(((((..........))))).).))))))).))))) ( -23.00)
>consensus
CCCCUCUCGCCAUGCUCCAUCCCACUCGCACUCUCUCCA_GAGAUACACAUAUAUCCCCUUCCACCAAAAUUAAAGUGGAUGCGGAGUGGAGAUGG
................((((((((((((((.((((.....))))................(((((..........)))))))))).)))).))))) (-22.17 = -22.40 +   0.23)

alignment

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secondary structure

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dotplot

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Window 1

Location 8,633,751 – 8,633,846
Length 95
Sequences 3
Columns 96
Reading direction reverse
Mean pairwise identity 88.85
Mean single sequence MFE -33.16
Consensus MFE -25.22
Energy contribution -26.33
Covariance contribution 1.11
Combinations/Pair 1.04
Mean z-score -2.49
Structure conservation index 0.76
SVM decision value 0.45
SVM RNA-class probability 0.740712
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8633751 95 - 20766785
CCAUCUCCACGCCGCAUCCACUUAAAUUUUGGUGGAAAGGGAUAUAUGUGUAUCUC-UGGAGAGAGUGCGAGUGGGAUGGAGCAUGGCGAGAGAGG
(((((.((((..((((((((((........)))))).((((((((....)))))))-)........)))).)))))))))................ ( -35.30)
>DroSec_CAF1 13911 96 - 1
CCAUCUCCACUCCGCAUCCACAUUAAUUUUGGUGGAAGGGAAUAUAUGUGUAUGUCCUGAAGAGAGUGCGAGUGGGAUGGAGUAUGGCGAGAGGGG
(((((.(((((((((.(((((..........)))))(((..((((....))))..))).......))).))))))))))).......(....)... ( -32.40)
>DroSim_CAF1 17528 95 - 1
CCAUCUCCACUCCGCAUCCACUUUAAUUUUGGUGGAAGGGGAUGUAUGUGUAUCUC-UAGAGAGAGUGUAAGUGGGAUAGAGCAUGCCGAGAGGGG
((.((((...(((.(.((((((........)))))).).))).((((((.((((((-................))))))..)))))).)))).)). ( -31.79)
>consensus
CCAUCUCCACUCCGCAUCCACUUUAAUUUUGGUGGAAGGGGAUAUAUGUGUAUCUC_UGGAGAGAGUGCGAGUGGGAUGGAGCAUGGCGAGAGGGG
(((((((((..((((.((((((........))))))..(((((((....)))))))...............))))..))))).))))(....)... (-25.22 = -26.33 +   1.11)

alignment

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secondary structure

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dotplot

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Window 2

Location 8,633,780 – 8,633,878
Length 98
Sequences 3
Columns 99
Reading direction reverse
Mean pairwise identity 90.51
Mean single sequence MFE -25.38
Consensus MFE -19.86
Energy contribution -20.86
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -2.42
Structure conservation index 0.78
SVM decision value 0.35
SVM RNA-class probability 0.700781
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8633780 98 - 20766785
GCACUCUCACCCCCCCAACCGCAUCCCCACUUCCAUCUCCACGCCGCAUCCACUUAAAUUUUGGUGGAAAGGGAUAUAUGUGUAUCUC-UGGAGAGAGU
..((((((.((.....................................((((((........)))))).((((((((....)))))))-))).)))))) ( -25.30)
>DroSec_CAF1 13940 98 - 1
GCACUCUCACCC-UCCACCCGCAUCCCCACUUCCAUCUCCACUCCGCAUCCACAUUAAUUUUGGUGGAAGGGAAUAUAUGUGUAUGUCCUGAAGAGAGU
..((((((....-..((..(((((..((.((((((((.........................)))))))))).....)))))..)).......)))))) ( -22.93)
>DroSim_CAF1 17557 97 - 1
GCACUCUCACCC-UCCAACCGCAUCCCCACCUCCAUCUCCACUCCGCAUCCACUUUAAUUUUGGUGGAAGGGGAUGUAUGUGUAUCUC-UAGAGAGAGU
..((((((....-..((...((((((((...((((((.........................)))))).))))))))...))..((..-..)))))))) ( -27.91)
>consensus
GCACUCUCACCC_UCCAACCGCAUCCCCACUUCCAUCUCCACUCCGCAUCCACUUUAAUUUUGGUGGAAGGGGAUAUAUGUGUAUCUC_UGGAGAGAGU
..((((((...........(((((.(((.((((((((.........................)))))))))))....)))))...........)))))) (-19.86 = -20.86 +   1.00)

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 10:28:59 2006