Locus 667

Sequence ID 2L_DroMel_CAF1
Location 1,966,242 – 1,966,374
Length 132
Max. P 0.966759
window1092 window1093 window1094

overview

Window 2

Location 1,966,242 – 1,966,335
Length 93
Sequences 5
Columns 93
Reading direction forward
Mean pairwise identity 92.15
Mean single sequence MFE -28.58
Consensus MFE -21.92
Energy contribution -23.72
Covariance contribution 1.80
Combinations/Pair 1.00
Mean z-score -1.99
Structure conservation index 0.77
SVM decision value 0.70
SVM RNA-class probability 0.828018
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1966242 93 + 22407834
CCGCCAUUUUGUUUCGCCGGGUUGCGCCUUCAAAUGUGCAACCAUCGCGGUUCCAGCGGCCCCAACCUAGACCCCAAGUGGGGUUUUAAAAAU
((((......(..((((..((((((((........))))))))...))))..)..)))).........(((((((....)))))))....... ( -32.30)
>DroSec_CAF1 8713 93 + 1
CCGCCAUUUUGUUUCGUCGGGUUGCGCCUUCAAAUGUGCAACCAUCGCGGUUCCAGCGGCCCCAACCUAGACCCCAAGUGGGGUUUUAAAAAU
((((......(..((((..((((((((........))))))))...))))..)..)))).........(((((((....)))))))....... ( -30.70)
>DroSim_CAF1 12859 93 + 1
CCGCCAUUUUGUUUCGUCGGGUUGCGCCUUCAAAUGUGCAACCAUCGCGGUUCCAGCGGCCCCAACCUAGACCCCAAGUGGGGUUUUAAAAAU
((((......(..((((..((((((((........))))))))...))))..)..)))).........(((((((....)))))))....... ( -30.70)
>DroEre_CAF1 17833 83 + 1
CCGCCAUUUUGUCAC----------GCCUUCAAAAGUGCAACCAUCGCGGUUCCAGCGGCCCCAACCUAGACCCCAAGUGGGGUUUUAAAAAU
((((..(((((....----------.....))))).((.((((.....)))).)))))).........(((((((....)))))))....... ( -20.20)
>DroYak_CAF1 15768 93 + 1
CCGCCAUUUUGUCUCGCCGCGUUGCGCCUUCAAAUGUGCAACCAUCGCGCUUCCAGCGGCCCCAACCUAGACCCCAAGUUGGGGUUUAAAAAU
..(((..........((...(((((((........)))))))....))((.....))))).......((((((((.....))))))))..... ( -29.00)
>consensus
CCGCCAUUUUGUUUCGCCGGGUUGCGCCUUCAAAUGUGCAACCAUCGCGGUUCCAGCGGCCCCAACCUAGACCCCAAGUGGGGUUUUAAAAAU
..(((..............((((((((........))))))))...((.......)))))........(((((((....)))))))....... (-21.92 = -23.72 +   1.80) 

alignment

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secondary structure

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Window 3

Location 1,966,281 – 1,966,374
Length 93
Sequences 5
Columns 93
Reading direction forward
Mean pairwise identity 97.85
Mean single sequence MFE -27.92
Consensus MFE -23.92
Energy contribution -24.52
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -2.14
Structure conservation index 0.86
SVM decision value 1.60
SVM RNA-class probability 0.966759
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1966281 93 + 22407834
AACCAUCGCGGUUCCAGCGGCCCCAACCUAGACCCCAAGUGGGGUUUUAAAAAUAAAUUCCCCAUUUGCGACUGGUAAUUUGCCGACUGUCUG
((((.....)))).(((((((......((((..(.(((((((((.((((....))))..))))))))).).))))......)))).))).... ( -28.30)
>DroSec_CAF1 8752 93 + 1
AACCAUCGCGGUUCCAGCGGCCCCAACCUAGACCCCAAGUGGGGUUUUAAAAAUAAAUUCCCCAUUUGCGACUGGUAAUUUGCCGACUGUCUG
((((.....)))).(((((((......((((..(.(((((((((.((((....))))..))))))))).).))))......)))).))).... ( -28.30)
>DroSim_CAF1 12898 93 + 1
AACCAUCGCGGUUCCAGCGGCCCCAACCUAGACCCCAAGUGGGGUUUUAAAAAUAAAUUCCCCAUUUGCGACUGGUAAUUUGCCGACUGUCUG
((((.....)))).(((((((......((((..(.(((((((((.((((....))))..))))))))).).))))......)))).))).... ( -28.30)
>DroEre_CAF1 17862 92 + 1
AACCAUCGCGGUUCCAGCGGCCCCAACCUAGACCCCAAGUGGGGUUUUAAAAAUAAAU-CCCCAUUUGCGACUGGUAAUUUGCCGACUGUCUG
((((.....)))).(((((((......((((..(.(((((((((.((((....)))).-))))))))).).))))......)))).))).... ( -29.30)
>DroYak_CAF1 15807 93 + 1
AACCAUCGCGCUUCCAGCGGCCCCAACCUAGACCCCAAGUUGGGGUUUAAAAAUAAAUUCCCCAUUUGCGAGUGGUAAUUUGCCGACUGUCUG
..............(((((((.......((((((((.....)))))))).....(((((..(((((....))))).))))))))).))).... ( -25.40)
>consensus
AACCAUCGCGGUUCCAGCGGCCCCAACCUAGACCCCAAGUGGGGUUUUAAAAAUAAAUUCCCCAUUUGCGACUGGUAAUUUGCCGACUGUCUG
((((.....)))).(((((((......((((....(((((((((..((.......))..)))))))))...))))......)))).))).... (-23.92 = -24.52 +   0.60) 

alignment

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secondary structure

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dotplot

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Window 4

Location 1,966,281 – 1,966,374
Length 93
Sequences 5
Columns 93
Reading direction reverse
Mean pairwise identity 97.85
Mean single sequence MFE -31.12
Consensus MFE -27.06
Energy contribution -27.66
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -1.72
Structure conservation index 0.87
SVM decision value 0.91
SVM RNA-class probability 0.880750
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1966281 93 - 22407834
CAGACAGUCGGCAAAUUACCAGUCGCAAAUGGGGAAUUUAUUUUUAAAACCCCACUUGGGGUCUAGGUUGGGGCCGCUGGAACCGCGAUGGUU
....(((.((((.....(((((((.(((.(((((..((((....)))).))))).))).)).)).)))....))))))).((((.....)))) ( -31.20)
>DroSec_CAF1 8752 93 - 1
CAGACAGUCGGCAAAUUACCAGUCGCAAAUGGGGAAUUUAUUUUUAAAACCCCACUUGGGGUCUAGGUUGGGGCCGCUGGAACCGCGAUGGUU
....(((.((((.....(((((((.(((.(((((..((((....)))).))))).))).)).)).)))....))))))).((((.....)))) ( -31.20)
>DroSim_CAF1 12898 93 - 1
CAGACAGUCGGCAAAUUACCAGUCGCAAAUGGGGAAUUUAUUUUUAAAACCCCACUUGGGGUCUAGGUUGGGGCCGCUGGAACCGCGAUGGUU
....(((.((((.....(((((((.(((.(((((..((((....)))).))))).))).)).)).)))....))))))).((((.....)))) ( -31.20)
>DroEre_CAF1 17862 92 - 1
CAGACAGUCGGCAAAUUACCAGUCGCAAAUGGGG-AUUUAUUUUUAAAACCCCACUUGGGGUCUAGGUUGGGGCCGCUGGAACCGCGAUGGUU
....(((.((((.....(((((((.(((.(((((-.((((....)))).))))).))).)).)).)))....))))))).((((.....)))) ( -33.30)
>DroYak_CAF1 15807 93 - 1
CAGACAGUCGGCAAAUUACCACUCGCAAAUGGGGAAUUUAUUUUUAAACCCCAACUUGGGGUCUAGGUUGGGGCCGCUGGAAGCGCGAUGGUU
.................((((.((((.....((...((((....))))(((((((((((...)))))))))))))((.....)))))))))). ( -28.70)
>consensus
CAGACAGUCGGCAAAUUACCAGUCGCAAAUGGGGAAUUUAUUUUUAAAACCCCACUUGGGGUCUAGGUUGGGGCCGCUGGAACCGCGAUGGUU
....(((.((((.....(((((((.(((.(((((..((((....)))).))))).))).)).)).)))....))))))).((((.....)))) (-27.06 = -27.66 +   0.60) 

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 09:42:26 2006