Locus 4908

Sequence ID 2L_DroMel_CAF1
Location 14,045,818 – 14,045,943
Length 125
Max. P 0.999955
window7785 window7786 window7787 window7788

overview

Window 5

Location 14,045,818 – 14,045,917
Length 99
Sequences 5
Columns 99
Reading direction forward
Mean pairwise identity 96.16
Mean single sequence MFE -22.62
Consensus MFE -20.44
Energy contribution -20.20
Covariance contribution -0.24
Combinations/Pair 1.05
Mean z-score -1.73
Structure conservation index 0.90
SVM decision value 1.81
SVM RNA-class probability 0.978210
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14045818 99 + 22407834
CGUUUAUACAACAGUUAUACUUUGCACACCCAGUACAACUGGGAUACCCAGCACUGCCACACUCGCUCAAAAGAAGAACGUCGUGCCGUAUCUGUAUCU
.....((((..(((((.((((..........)))).)))))((((((...((((.((.....((........)).....)).)))).)))))))))).. ( -20.00)
>DroSec_CAF1 134733 99 + 1
CUGUUAUCCAACAGUUAUACUUUGCACACCCAGUAUAACUGGGAUAACCAGCACAGCCACACUCGCUCAAAAGAAGAACGUCGUGCCGUAUCUGUAUCU
..(((((((..((((((((((..........)))))))))))))))))..((((.((.....((........)).....)).))))............. ( -24.00)
>DroSim_CAF1 137947 99 + 1
CUGUUAUCCAACAGUUAUACUUUGCACACCCAGUACAACUGGGAUAACCAGCACAGCCACACUCGCUCAAAAGAAGAACGUCGUGCCGUAUCUGUAUCU
(((((....)))))..((((..(((...(((((.....))))).......((((.((.....((........)).....)).)))).)))...)))).. ( -20.90)
>DroEre_CAF1 136761 99 + 1
CUGUUAUCCAACAGUUACACUUUGCACACCCAGUACAACUGGGAUAACCGGCACAGCCACACUCGCUCAAAAGAAGAACGUCGUGCCGUAUCUGUAUCU
..........((((.(((..........(((((.....)))))......(((((.((.....((........)).....)).)))))))).)))).... ( -25.70)
>DroYak_CAF1 144257 99 + 1
CUGUUAUCCAACAGUUACACUUUGCACACCCAGUACAACUGGGAUAACCAGCACAGCCACAGUCGCUCAAAAGAAGAACGUCGUGCCGUAUCUGUAUCU
..........((((.(((..........(((((.....))))).......((((.((.....((........)).....)).)))).))).)))).... ( -22.50)
>consensus
CUGUUAUCCAACAGUUAUACUUUGCACACCCAGUACAACUGGGAUAACCAGCACAGCCACACUCGCUCAAAAGAAGAACGUCGUGCCGUAUCUGUAUCU
..........((((.(((..........(((((.....))))).......((((.((.....((........)).....)).)))).))).)))).... (-20.44 = -20.20 +  -0.24)

alignment

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secondary structure

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dotplot

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Window 6

Location 14,045,818 – 14,045,917
Length 99
Sequences 5
Columns 99
Reading direction reverse
Mean pairwise identity 96.16
Mean single sequence MFE -37.22
Consensus MFE -34.64
Energy contribution -35.24
Covariance contribution 0.60
Combinations/Pair 1.06
Mean z-score -3.51
Structure conservation index 0.93
SVM decision value 4.84
SVM RNA-class probability 0.999955
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14045818 99 - 22407834
AGAUACAGAUACGGCACGACGUUCUUCUUUUGAGCGAGUGUGGCAGUGCUGGGUAUCCCAGUUGUACUGGGUGUGCAAAGUAUAACUGUUGUAUAAACG
..((((((...(.((((..(((((.......))))).)))).)(((((((..(((((((((.....))))).))))..)))...))))))))))..... ( -32.60)
>DroSec_CAF1 134733 99 - 1
AGAUACAGAUACGGCACGACGUUCUUCUUUUGAGCGAGUGUGGCUGUGCUGGUUAUCCCAGUUAUACUGGGUGUGCAAAGUAUAACUGUUGGAUAACAG
.....(((.(((((((((.(((((.......)))))..))).)))))))))(((((((((((((((((..(....)..))))))))))..))))))).. ( -40.30)
>DroSim_CAF1 137947 99 - 1
AGAUACAGAUACGGCACGACGUUCUUCUUUUGAGCGAGUGUGGCUGUGCUGGUUAUCCCAGUUGUACUGGGUGUGCAAAGUAUAACUGUUGGAUAACAG
.....(((.(((((((((.(((((.......)))))..))).)))))))))(((((((((((((((((..(....)..))))))))))..))))))).. ( -40.30)
>DroEre_CAF1 136761 99 - 1
AGAUACAGAUACGGCACGACGUUCUUCUUUUGAGCGAGUGUGGCUGUGCCGGUUAUCCCAGUUGUACUGGGUGUGCAAAGUGUAACUGUUGGAUAACAG
...........((((((..(((((.......)))))((.....))))))))(((((((((((((((((..(....)..))))))))))..))))))).. ( -36.20)
>DroYak_CAF1 144257 99 - 1
AGAUACAGAUACGGCACGACGUUCUUCUUUUGAGCGACUGUGGCUGUGCUGGUUAUCCCAGUUGUACUGGGUGUGCAAAGUGUAACUGUUGGAUAACAG
.....(((.(((((((((.(((((.......)))))..))).)))))))))(((((((((((((((((..(....)..))))))))))..))))))).. ( -36.70)
>consensus
AGAUACAGAUACGGCACGACGUUCUUCUUUUGAGCGAGUGUGGCUGUGCUGGUUAUCCCAGUUGUACUGGGUGUGCAAAGUAUAACUGUUGGAUAACAG
.....(((.(((((((((.(((((.......)))))..))).)))))))))(((((((((((((((((..(....)..))))))))))..))))))).. (-34.64 = -35.24 +   0.60)

alignment

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secondary structure

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dotplot

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Window 7

Location 14,045,846 – 14,045,943
Length 97
Sequences 4
Columns 97
Reading direction forward
Mean pairwise identity 94.85
Mean single sequence MFE -30.65
Consensus MFE -27.62
Energy contribution -27.88
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -3.74
Structure conservation index 0.90
SVM decision value 1.88
SVM RNA-class probability 0.981198
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14045846 97 + 22407834
CCCAGUACAACUGGGAUACCCAGCACUGCCACACUCGCUCAAAAGAAGAACGUCGUGCCGUAUCUGUAUCUUUAUCUGUGCGAUACAGAUACAGAUA
(((((.....))))).......((((.((.....((........)).....)).))))..(((((((((((.((((.....)))).))))))))))) ( -30.80)
>DroSec_CAF1 134761 97 + 1
CCCAGUAUAACUGGGAUAACCAGCACAGCCACACUCGCUCAAAAGAAGAACGUCGUGCCGUAUCUGUAUCUUUAUCUGUGCGAUACAGAUACAGAUA
(((((.....))))).......((((.((.....((........)).....)).))))..(((((((((((.((((.....)))).))))))))))) ( -30.80)
>DroSim_CAF1 137975 97 + 1
CCCAGUACAACUGGGAUAACCAGCACAGCCACACUCGCUCAAAAGAAGAACGUCGUGCCGUAUCUGUAUCUUUAUCUGUGCGAUACAGAUACAGAUA
(((((.....))))).......((((.((.....((........)).....)).))))..(((((((((((.((((.....)))).))))))))))) ( -30.80)
>DroEre_CAF1 136789 91 + 1
CCCAGUACAACUGGGAUAACCGGCACAGCCACACUCGCUCAAAAGAAGAACGUCGUGCCGUAUCUGUAUCUUUAUCUGUGCGAUACAGAUA------
(((((.....))))).....((((((.((.....((........)).....)).))))))((((((((((...........))))))))))------ ( -30.20)
>consensus
CCCAGUACAACUGGGAUAACCAGCACAGCCACACUCGCUCAAAAGAAGAACGUCGUGCCGUAUCUGUAUCUUUAUCUGUGCGAUACAGAUACAGAUA
(((((.....))))).......((((.((.....((........)).....)).)))).(((((((((((...........)))))))))))..... (-27.62 = -27.88 +   0.25)

alignment

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secondary structure

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dotplot

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Window 8

Location 14,045,846 – 14,045,943
Length 97
Sequences 4
Columns 97
Reading direction reverse
Mean pairwise identity 94.85
Mean single sequence MFE -39.15
Consensus MFE -35.31
Energy contribution -36.88
Covariance contribution 1.56
Combinations/Pair 1.03
Mean z-score -4.47
Structure conservation index 0.90
SVM decision value 1.42
SVM RNA-class probability 0.951925
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14045846 97 - 22407834
UAUCUGUAUCUGUAUCGCACAGAUAAAGAUACAGAUACGGCACGACGUUCUUCUUUUGAGCGAGUGUGGCAGUGCUGGGUAUCCCAGUUGUACUGGG
(((((((((((.((((.....)))).)))))))))))(.((((..(((((.......))))).)))).)((((((((((...))))))...)))).. ( -40.60)
>DroSec_CAF1 134761 97 - 1
UAUCUGUAUCUGUAUCGCACAGAUAAAGAUACAGAUACGGCACGACGUUCUUCUUUUGAGCGAGUGUGGCUGUGCUGGUUAUCCCAGUUAUACUGGG
(((((((((((.((((.....)))).)))))))))))((((((..(((((.......)))))((.....)))))))).....(((((.....))))) ( -40.00)
>DroSim_CAF1 137975 97 - 1
UAUCUGUAUCUGUAUCGCACAGAUAAAGAUACAGAUACGGCACGACGUUCUUCUUUUGAGCGAGUGUGGCUGUGCUGGUUAUCCCAGUUGUACUGGG
(((((((((((.((((.....)))).)))))))))))((((((..(((((.......)))))((.....)))))))).....(((((.....))))) ( -40.00)
>DroEre_CAF1 136789 91 - 1
------UAUCUGUAUCGCACAGAUAAAGAUACAGAUACGGCACGACGUUCUUCUUUUGAGCGAGUGUGGCUGUGCCGGUUAUCCCAGUUGUACUGGG
------((((((((((...........))))))))))((((((..(((((.......)))))((.....)))))))).....(((((.....))))) ( -36.00)
>consensus
UAUCUGUAUCUGUAUCGCACAGAUAAAGAUACAGAUACGGCACGACGUUCUUCUUUUGAGCGAGUGUGGCUGUGCUGGUUAUCCCAGUUGUACUGGG
(((((((((((.((((.....)))).)))))))))))((((((..(((((.......)))))((.....)))))))).....(((((.....))))) (-35.31 = -36.88 +   1.56)

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 11:30:46 2006