Locus 6062

Sequence ID 3L_DroMel_CAF1
Location 16,142,113 – 16,142,271
Length 158
Max. P 0.995826
window9725 window9726 window9727

overview

Window 5

Location 16,142,113 – 16,142,233
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 97.33
Mean single sequence MFE -20.99
Consensus MFE -18.16
Energy contribution -18.32
Covariance contribution 0.16
Combinations/Pair 1.04
Mean z-score -1.44
Structure conservation index 0.87
SVM decision value 0.22
SVM RNA-class probability 0.641803
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16142113 120 + 23771897
ACGAGAAAAUAACCGAAGAAAAAGUCGAACAAAGCUUAAGAAAAGAACACUUGUAUGUACCUUCUCUGCAAAGGAUACACAAGUGUCUCAUUAAAAGAAAUAAAGGACAAGCCAAGCGCC
.............(((........)))......((((.......((((((((((.(((.((((.......))))))).)))))))).))...............((.....))))))... ( -21.10)
>DroSec_CAF1 4319 120 + 1
ACGAUAAAAUAACCGGAGAAUAAGUCGAACAAAGCUUAAGAAAAGAACACUUGUAUGUACCUUCUCUGCAAAGGAUACACAAGUGUCUCAUUAAAAGAAAUAAAGGACAAGCCAAGCGCC
.((((..................))))......((((.......((((((((((.(((.((((.......))))))).)))))))).))...............((.....))))))... ( -21.37)
>DroSim_CAF1 5089 120 + 1
ACGAGAAAAUAACCGGAGAAAAAGUCGAACAAAGCUUAAGAAAAGAACACUUGUAUGUACGUUCUCUGCAAAGGAUACACAAGUGUCUCAUUAAAAGAAAUAAAGGACAAGCCAAGCGCC
..............((((((...((((.((((..(((.....))).....)))).)).)).))))))((...((((((....))))))................((.....))..))... ( -17.70)
>DroEre_CAF1 3616 120 + 1
ACGAGAAAAUAACCUGAGAAAAAGUCGAACAAAGCUUAAGAAAAGGACACUUGUAUGUACCUUCUCUGCAAAGGAUACACAAGUGUCUCAUUAAAAGAAAUAAAGGACAAGCCAAGCGCC
.................................((((.......((((((((((.(((.((((.......))))))).))))))))))................((.....))))))... ( -23.20)
>DroYak_CAF1 4332 120 + 1
ACGAGAAAAUAACCUGAGAAAAAGUCGAACAAAGCAUAAGAAAAGGACACUUGUAUGUACCUUCUCUGCAAAGGAUACACAAGUGUCUCAUUAAAAGAAAUAAAGGACAAGCCAAGCGCC
.................................((.........((((((((((.(((.((((.......))))))).))))))))))................((.....))..))... ( -21.60)
>consensus
ACGAGAAAAUAACCGGAGAAAAAGUCGAACAAAGCUUAAGAAAAGAACACUUGUAUGUACCUUCUCUGCAAAGGAUACACAAGUGUCUCAUUAAAAGAAAUAAAGGACAAGCCAAGCGCC
.................................((((.......((((((((((.(((.((((.......))))))).)))))))).))...............((.....))))))... (-18.16 = -18.32 +   0.16)

alignment

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secondary structure

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Window 6

Location 16,142,113 – 16,142,233
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 97.33
Mean single sequence MFE -26.22
Consensus MFE -25.94
Energy contribution -26.10
Covariance contribution 0.16
Combinations/Pair 1.03
Mean z-score -1.78
Structure conservation index 0.99
SVM decision value 2.62
SVM RNA-class probability 0.995826
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16142113 120 - 23771897
GGCGCUUGGCUUGUCCUUUAUUUCUUUUAAUGAGACACUUGUGUAUCCUUUGCAGAGAAGGUACAUACAAGUGUUCUUUUCUUAAGCUUUGUUCGACUUUUUCUUCGGUUAUUUUCUCGU
.(.((..((((((....(((((......)))))(((((((((((..(((((.....)))))...))))))))))).......))))))..)).)((((........)))).......... ( -26.70)
>DroSec_CAF1 4319 120 - 1
GGCGCUUGGCUUGUCCUUUAUUUCUUUUAAUGAGACACUUGUGUAUCCUUUGCAGAGAAGGUACAUACAAGUGUUCUUUUCUUAAGCUUUGUUCGACUUAUUCUCCGGUUAUUUUAUCGU
.(.((..((((((....(((((......)))))(((((((((((..(((((.....)))))...))))))))))).......))))))..)).)...........((((......)))). ( -27.70)
>DroSim_CAF1 5089 120 - 1
GGCGCUUGGCUUGUCCUUUAUUUCUUUUAAUGAGACACUUGUGUAUCCUUUGCAGAGAACGUACAUACAAGUGUUCUUUUCUUAAGCUUUGUUCGACUUUUUCUCCGGUUAUUUUCUCGU
.(.((..((((((....(((((......)))))(((((((((((((.(((....)))...))))..))))))))).......))))))..)).)((((........)))).......... ( -20.40)
>DroEre_CAF1 3616 120 - 1
GGCGCUUGGCUUGUCCUUUAUUUCUUUUAAUGAGACACUUGUGUAUCCUUUGCAGAGAAGGUACAUACAAGUGUCCUUUUCUUAAGCUUUGUUCGACUUUUUCUCAGGUUAUUUUCUCGU
.(.((..((((((....(((((......)))))(((((((((((..(((((.....)))))...))))))))))).......))))))..)).)(((((......))))).......... ( -29.70)
>DroYak_CAF1 4332 120 - 1
GGCGCUUGGCUUGUCCUUUAUUUCUUUUAAUGAGACACUUGUGUAUCCUUUGCAGAGAAGGUACAUACAAGUGUCCUUUUCUUAUGCUUUGUUCGACUUUUUCUCAGGUUAUUUUCUCGU
.(.((..(((.......(((((......)))))(((((((((((..(((((.....)))))...)))))))))))..........)))..)).)(((((......))))).......... ( -26.60)
>consensus
GGCGCUUGGCUUGUCCUUUAUUUCUUUUAAUGAGACACUUGUGUAUCCUUUGCAGAGAAGGUACAUACAAGUGUUCUUUUCUUAAGCUUUGUUCGACUUUUUCUCCGGUUAUUUUCUCGU
.(.((..((((((....(((((......)))))(((((((((((..(((((.....)))))...))))))))))).......))))))..)).)((((........)))).......... (-25.94 = -26.10 +   0.16)

alignment

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secondary structure

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dotplot

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Window 7

Location 16,142,153 – 16,142,271
Length 118
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 96.90
Mean single sequence MFE -35.08
Consensus MFE -31.22
Energy contribution -31.18
Covariance contribution -0.04
Combinations/Pair 1.03
Mean z-score -1.96
Structure conservation index 0.89
SVM decision value 2.06
SVM RNA-class probability 0.986892
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16142153 118 - 23771897
GUCAGCCAGGGAUUCGAGU--CGACUUUAAGGACUUCGUCGGCGCUUGGCUUGUCCUUUAUUUCUUUUAAUGAGACACUUGUGUAUCCUUUGCAGAGAAGGUACAUACAAGUGUUCUUUU
...((((((((...(((((--(.........))).)))....).)))))))....................(((((((((((((..(((((.....)))))...))))))))).)))).. ( -33.50)
>DroSec_CAF1 4359 120 - 1
GUCUGCCAGGGAUUCGAGUCCCGACUUUAAGGACUUCGUCGGCGCUUGGCUUGUCCUUUAUUUCUUUUAAUGAGACACUUGUGUAUCCUUUGCAGAGAAGGUACAUACAAGUGUUCUUUU
.......((((((((((((.(((((............))))).))))))...)))))).............(((((((((((((..(((((.....)))))...))))))))).)))).. ( -36.70)
>DroSim_CAF1 5129 120 - 1
GUCUGCCAGGGAUUCGAGUCUCGACUUUAAGGACUUCGUCGGCGCUUGGCUUGUCCUUUAUUUCUUUUAAUGAGACACUUGUGUAUCCUUUGCAGAGAACGUACAUACAAGUGUUCUUUU
.(((((.((((((.(((((.((.......(((((...((((.....))))..)))))(((((......))))))).)))))...)))))).)))))(((((..........))))).... ( -32.40)
>DroEre_CAF1 3656 118 - 1
GAAUGCCAGGGAUUCGAGU--CGACUUUAAGGACUUCGUCGGCGCUUGGCUUGUCCUUUAUUUCUUUUAAUGAGACACUUGUGUAUCCUUUGCAGAGAAGGUACAUACAAGUGUCCUUUU
((..(((((((...(((((--(.........))).)))....).))))))...))..(((((......)))))(((((((((((..(((((.....)))))...)))))))))))..... ( -35.30)
>DroYak_CAF1 4372 118 - 1
GACUGCCAGGGAUUCGAGU--CGACUUUAAGGACUUCGUCGGCGCUUGGCUUGUCCUUUAUUUCUUUUAAUGAGACACUUGUGUAUCCUUUGCAGAGAAGGUACAUACAAGUGUCCUUUU
(((.(((((((...(((((--(.........))).)))....).))))))..)))..(((((......)))))(((((((((((..(((((.....)))))...)))))))))))..... ( -37.50)
>consensus
GUCUGCCAGGGAUUCGAGU__CGACUUUAAGGACUUCGUCGGCGCUUGGCUUGUCCUUUAUUUCUUUUAAUGAGACACUUGUGUAUCCUUUGCAGAGAAGGUACAUACAAGUGUUCUUUU
.......((((((((((((..((((............))))..))))))...))))))...............(((((((((((..(((((.....)))))...)))))))))))..... (-31.22 = -31.18 +  -0.04)

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 12:08:50 2006