Locus 8643

Sequence ID 3R_DroMel_CAF1
Location 23,112,644 – 23,112,804
Length 160
Max. P 0.939929
window13881 window13882 window13883

overview

Window 1

Location 23,112,644 – 23,112,764
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 89.50
Mean single sequence MFE -51.92
Consensus MFE -44.04
Energy contribution -44.12
Covariance contribution 0.08
Combinations/Pair 1.24
Mean z-score -1.81
Structure conservation index 0.85
SVM decision value 1.30
SVM RNA-class probability 0.939929
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23112644 120 + 27905053
CGCUUCCGCCGACUCAGUUGGCAUUUGUUGCGGCACAAAUGUGAUCAGGUCCGCCAACUGGCGGCCACCUGCUUUGUGCGGUCGCACGAAUUCCGCUGCGAUCUGCCGGCGGCGCUGCUG
.((..((((((((...)))((((...((((((((...........((((((((((....)))))..))))).(((((((....)))))))....)))))))).))))))))).))..... ( -52.40)
>DroSim_CAF1 18508 120 + 1
CGCUUCCGCCGACUCAGUUGGCAUUUGUUGCGGCACAAAUGUGAUCAGGUCCGCCAACUGGCGGCCACCUGCUUUGUGCGCUCGCACGAAUUCCGCUGCGAUCUGCCGGCGGCGCUGCUG
.((..((((((((...)))((((...((((((((...........((((((((((....)))))..))))).(((((((....)))))))....)))))))).))))))))).))..... ( -52.40)
>DroEre_CAF1 16161 120 + 1
CGGUUCCGCCGACUCAGUUGGCGCUUGUUGCGGCACAAAUGUGAUCAGGUCCGCCAGCUGGCGGCCACCUGUUUUGUGCGGUCGCACGAAUUCCGCUGCGAUCUGCCGGCGGCGCUGCUG
((((.((((((((...)))(((((.....)).(((((((......((((((((((....)))))..))))).)))))))(((((((((.....)).))))))).)))))))).))))... ( -56.00)
>DroYak_CAF1 16118 120 + 1
CGCUUCCGCCGACUCAGUUGGCGUUUGUUGCGGCACAAAUGUGAUCAAGUCCGCCAACUGGCGGCCACGUGCUUUGUGCGAUCGCACGAAUUCCGCUGCGAUCUACCGGCGGCGCUGCUG
.((...(((((((...)))))))...(((((.(((((((.(((.....(.(((((....))))))....))))))))))(((((((((.....)).))))))).....)))))))..... ( -49.10)
>DroAna_CAF1 15541 120 + 1
CGCUUCCGCCGUCUUAGCUGGCGGCUUUUGCGGCACAAGUGCGAGCAGGUUCGUCAACUAGCCGCCACCUGUUUUGUGCGCUCGCACGAGUUCCGUUGUGAUCUUCCAGCGGUACUGCUC
(((....((((((......))))))....)))((....((((((((.((((.(....).))))((((.......)).)))))))))).(((.((((((.(.....))))))).))))).. ( -49.70)
>consensus
CGCUUCCGCCGACUCAGUUGGCGUUUGUUGCGGCACAAAUGUGAUCAGGUCCGCCAACUGGCGGCCACCUGCUUUGUGCGCUCGCACGAAUUCCGCUGCGAUCUGCCGGCGGCGCUGCUG
.((...((((......(((((((...((((((((...........((((((((((....)))))..))))).(((((((....)))))))....)))))))).)))))))))))..)).. (-44.04 = -44.12 +   0.08)

alignment

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secondary structure

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dotplot

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Window 2

Location 23,112,644 – 23,112,764
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 89.50
Mean single sequence MFE -49.90
Consensus MFE -40.12
Energy contribution -41.48
Covariance contribution 1.36
Combinations/Pair 1.09
Mean z-score -1.76
Structure conservation index 0.80
SVM decision value 0.80
SVM RNA-class probability 0.853578
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23112644 120 - 27905053
CAGCAGCGCCGCCGGCAGAUCGCAGCGGAAUUCGUGCGACCGCACAAAGCAGGUGGCCGCCAGUUGGCGGACCUGAUCACAUUUGUGCCGCAACAAAUGCCAACUGAGUCGGCGGAAGCG
.....((.((((((((.(.(((((.((.....))))))).)(((((((.(((((..(((((....))))))))))......))))))).(((.....))).......))))))))..)). ( -52.60)
>DroSim_CAF1 18508 120 - 1
CAGCAGCGCCGCCGGCAGAUCGCAGCGGAAUUCGUGCGAGCGCACAAAGCAGGUGGCCGCCAGUUGGCGGACCUGAUCACAUUUGUGCCGCAACAAAUGCCAACUGAGUCGGCGGAAGCG
.....((.((((((((...(((((.((.....)))))))(((((((((.(((((..(((((....))))))))))......)))))).)))................))))))))..)). ( -54.30)
>DroEre_CAF1 16161 120 - 1
CAGCAGCGCCGCCGGCAGAUCGCAGCGGAAUUCGUGCGACCGCACAAAACAGGUGGCCGCCAGCUGGCGGACCUGAUCACAUUUGUGCCGCAACAAGCGCCAACUGAGUCGGCGGAACCG
........((((((((.(.(((((.((.....))))))).)(((((((.(((((..(((((....))))))))))......)))))))(((.....)))........))))))))..... ( -49.20)
>DroYak_CAF1 16118 120 - 1
CAGCAGCGCCGCCGGUAGAUCGCAGCGGAAUUCGUGCGAUCGCACAAAGCACGUGGCCGCCAGUUGGCGGACUUGAUCACAUUUGUGCCGCAACAAACGCCAACUGAGUCGGCGGAAGCG
.....((.((((((((.(((((((.((.....))))))))).(((.......))))))(((((((((((...(((..(((....)))...)))....))))))))).)).)))))..)). ( -51.10)
>DroAna_CAF1 15541 120 - 1
GAGCAGUACCGCUGGAAGAUCACAACGGAACUCGUGCGAGCGCACAAAACAGGUGGCGGCUAGUUGACGAACCUGCUCGCACUUGUGCCGCAAAAGCCGCCAGCUAAGACGGCGGAAGCG
..((....((((((...................((((....)))).....((.((((((((.(((....))).(((..(((....))).)))..)))))))).))....))))))..)). ( -42.30)
>consensus
CAGCAGCGCCGCCGGCAGAUCGCAGCGGAAUUCGUGCGACCGCACAAAGCAGGUGGCCGCCAGUUGGCGGACCUGAUCACAUUUGUGCCGCAACAAACGCCAACUGAGUCGGCGGAAGCG
..((....((((((((.(.(((((.((.....))))))).)(((((((.(((((..(((((....))))))))))......)))))))...................))))))))..)). (-40.12 = -41.48 +   1.36)

alignment

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secondary structure

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dotplot

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Window 3

Location 23,112,684 – 23,112,804
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 89.58
Mean single sequence MFE -52.60
Consensus MFE -44.34
Energy contribution -44.46
Covariance contribution 0.12
Combinations/Pair 1.24
Mean z-score -1.31
Structure conservation index 0.84
SVM decision value 0.01
SVM RNA-class probability 0.537171
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23112684 120 + 27905053
GUGAUCAGGUCCGCCAACUGGCGGCCACCUGCUUUGUGCGGUCGCACGAAUUCCGCUGCGAUCUGCCGGCGGCGCUGCUGGCCAGCGCCAAGUUGGCCGCGAAUCUGGAGGAGGAGAACU
((..((...(((.(((..(.(((((((...((((.(((((((((((((.....)).))))))).(((((((....)))))))..)))).))))))))))).)...))).))).))..)). ( -56.90)
>DroSim_CAF1 18548 120 + 1
GUGAUCAGGUCCGCCAACUGGCGGCCACCUGCUUUGUGCGCUCGCACGAAUUCCGCUGCGAUCUGCCGGCGGCGCUGCUGGCCAGCGCCAAGUUGGCCGCGAAUCUGGAGGAGGAGAACU
....((.((.(((((....))))))).(((.((..(..((((((((((.....)).)))))...(((((((((((((.....)))))))..)))))).)))....)..)).))).))... ( -53.60)
>DroEre_CAF1 16201 120 + 1
GUGAUCAGGUCCGCCAGCUGGCGGCCACCUGUUUUGUGCGGUCGCACGAAUUCCGCUGCGAUCUGCCGGCGGCGCUGCUGGCCAGCGCCAAGUUGGCCGCGAAUCUGGAGGAGGAGAACU
((..((...(((.((((.(.(((((((.((.....(((((((((((((.....)).))))))).(((((((....)))))))..))))..)).))))))).)..)))).))).))..)). ( -57.20)
>DroYak_CAF1 16158 120 + 1
GUGAUCAAGUCCGCCAACUGGCGGCCACGUGCUUUGUGCGAUCGCACGAAUUCCGCUGCGAUCUACCGGCGGCGCUGCUGGCCAGCGCCAAGUUGGCCGCGAAUCUGGAGGAGGAGAACU
((..((...(((.(((..(.((((((((..(((..(((.(((((((((.....)).)))))))))).)))(((((((.....)))))))..).))))))).)...))).))).))..)). ( -55.10)
>DroAna_CAF1 15581 120 + 1
GCGAGCAGGUUCGUCAACUAGCCGCCACCUGUUUUGUGCGCUCGCACGAGUUCCGUUGUGAUCUUCCAGCGGUACUGCUCUCCAGUGCUAAGUUAGCCGCUCAUCUGAGUGAUGAGAACU
((((((.((((.(....).))))((((.......)).))))))))..((((.((((((.(.....)))))))....))))....(.((((...))))).((((((.....)))))).... ( -40.20)
>consensus
GUGAUCAGGUCCGCCAACUGGCGGCCACCUGCUUUGUGCGCUCGCACGAAUUCCGCUGCGAUCUGCCGGCGGCGCUGCUGGCCAGCGCCAAGUUGGCCGCGAAUCUGGAGGAGGAGAACU
((..((...(((.(((..(.(((((((.(((((..(((.(((((((((.....)).)))))))))).)))(((((((.....))))))).)).))))))).)...))).))).))..)). (-44.34 = -44.46 +   0.12)

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 13:16:10 2006