Locus 4580

Sequence ID 3R_DroMel_CAF1
Location 12,077,607 – 12,077,824
Length 217
Max. P 0.989199
window7516 window7517 window7518 window7519

overview

Window 6

Location 12,077,607 – 12,077,719
Length 112
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 95.19
Mean single sequence MFE -31.27
Consensus MFE -27.96
Energy contribution -27.48
Covariance contribution -0.48
Combinations/Pair 1.04
Mean z-score -1.85
Structure conservation index 0.89
SVM decision value 2.15
SVM RNA-class probability 0.989199
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12077607 112 + 27905053
GC---UAACUUCGCUGCCGGCGUCGCUGCUUAUAAAUCUUCGACAUGAAGC--GCAACAAAAAGCCGCAAAAAA---AGAAGGCAGAAACAGCAAGCGGCGCGCAUUGAAAAUUGCUCUA
((---....((((.(((..(((((((((((......(((((........((--((........).)))......---.))))).......))).))))))))))).))))....)).... ( -30.68)
>DroSec_CAF1 14356 116 + 1
GCCGCCAACUUCGCUGCCGGCGUCGCUGCUUAUAAAUCUUCGACAUGAAGC--GCAACAAAAAGCCGCAAAAAA--AAGAAGGCAGAAACAGCAAGCGGCGCGCAUUGAAAAUUGCUCUA
...((....((((.(((..(((((((((((......(((((........((--((........).)))......--..))))).......))).))))))))))).))))....)).... ( -30.71)
>DroSim_CAF1 14551 115 + 1
GC---CAACUUCGCUGCCGGCGUCGCUGCUUAUAAAUCUUCGACAUGAAGC--GCAACAAAAAGCCGCAAAAAAAGAAGAAGGCAGAAACAGCAAGCGGCGCGCAUUGAAAAUUGCUCUA
..---......((((((..((((..((((((.....(((((........((--((........).))).......)))))))))))..)).))..)))))).(((.(....).))).... ( -32.06)
>DroEre_CAF1 16295 115 + 1
GC---CAACUUCGCUGCCGACGUCGCUGCUUAUAAAUCUUCGACAUGAAGCGCGCAACAAAAAGCCGCAAAAAA--AGGAAGGCAGAAACAGCAAGCGGCGUGCAUUGAAAAUUGCUCUA
((---....((((.(((..(((((((((((......(((((........(((.((........)))))......--..))))).......))).))))))))))).))))....)).... ( -30.91)
>DroYak_CAF1 16563 115 + 1
GC---CAACUUCGCUGCCGACGUCGCUGCUUAUAAAUCUUCGACAUGAAGCGCGCAACAAAAAGCCGCAAAAAA--AAGAAGGCAGAAACAGCAAGCGGCGUGCAUUGAAAAUUGCUCUA
((---....((((.(((..(((((((((((......(((((........(((.((........)))))......--..))))).......))).))))))))))).))))....)).... ( -32.01)
>consensus
GC___CAACUUCGCUGCCGGCGUCGCUGCUUAUAAAUCUUCGACAUGAAGC__GCAACAAAAAGCCGCAAAAAA__AAGAAGGCAGAAACAGCAAGCGGCGCGCAUUGAAAAUUGCUCUA
.........((((.(((..(((((((((((.......((((.....)))).............(((...............)))......))).))))))))))).)))).......... (-27.96 = -27.48 +  -0.48)

alignment

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secondary structure

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dotplot

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Window 7

Location 12,077,679 – 12,077,799
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 100.00
Mean single sequence MFE -45.00
Consensus MFE -44.40
Energy contribution -44.40
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.37
Structure conservation index 0.99
SVM decision value 0.01
SVM RNA-class probability 0.536886
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12077679 120 + 27905053
AGGCAGAAACAGCAAGCGGCGCGCAUUGAAAAUUGCUCUAAUUCGCCAAAAACAGCUGAUUUGGUCGACGACGCCGCCGUCGCGGUGGCUUCCUGUCUCCGUCGCGACCGCUGCCUCCGC
((((((...((((....((((.(((.(....).))).......)))).......))))....(((((.(((((((((((...))))))).....(....)))))))))).)))))).... ( -45.00)
>DroSec_CAF1 14432 120 + 1
AGGCAGAAACAGCAAGCGGCGCGCAUUGAAAAUUGCUCUAAUUCGCCAAAAACAGCUGAUUUGGUCGACGACGCCGCCGUCGCGGUGGCUUCCUGUCUCCGUCGCGACCGCUGCCUCCGC
((((((...((((....((((.(((.(....).))).......)))).......))))....(((((.(((((((((((...))))))).....(....)))))))))).)))))).... ( -45.00)
>DroSim_CAF1 14626 120 + 1
AGGCAGAAACAGCAAGCGGCGCGCAUUGAAAAUUGCUCUAAUUCGCCAAAAACAGCUGAUUUGGUCGACGACGCCGCCGUCGCGGUGGCUUCCUGUCUCCGUCGCGACCGCUGCCUCCGC
((((((...((((....((((.(((.(....).))).......)))).......))))....(((((.(((((((((((...))))))).....(....)))))))))).)))))).... ( -45.00)
>consensus
AGGCAGAAACAGCAAGCGGCGCGCAUUGAAAAUUGCUCUAAUUCGCCAAAAACAGCUGAUUUGGUCGACGACGCCGCCGUCGCGGUGGCUUCCUGUCUCCGUCGCGACCGCUGCCUCCGC
((((((...((((....((((.(((........))).......)))).......))))....(((((.(((((((((((...))))))).....(....)))))))))).)))))).... (-44.40 = -44.40 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 8

Location 12,077,679 – 12,077,799
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 100.00
Mean single sequence MFE -54.80
Consensus MFE -54.80
Energy contribution -54.80
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.71
Structure conservation index 1.00
SVM decision value 1.87
SVM RNA-class probability 0.980645
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12077679 120 - 27905053
GCGGAGGCAGCGGUCGCGACGGAGACAGGAAGCCACCGCGACGGCGGCGUCGUCGACCAAAUCAGCUGUUUUUGGCGAAUUAGAGCAAUUUUCAAUGCGCGCCGCUUGCUGUUUCUGCCU
((((((((((((((((((..(....).((...))..))))))((((((((..(((.(((((.........))))))))......(((........))))))))))))))))))))))).. ( -54.80)
>DroSec_CAF1 14432 120 - 1
GCGGAGGCAGCGGUCGCGACGGAGACAGGAAGCCACCGCGACGGCGGCGUCGUCGACCAAAUCAGCUGUUUUUGGCGAAUUAGAGCAAUUUUCAAUGCGCGCCGCUUGCUGUUUCUGCCU
((((((((((((((((((..(....).((...))..))))))((((((((..(((.(((((.........))))))))......(((........))))))))))))))))))))))).. ( -54.80)
>DroSim_CAF1 14626 120 - 1
GCGGAGGCAGCGGUCGCGACGGAGACAGGAAGCCACCGCGACGGCGGCGUCGUCGACCAAAUCAGCUGUUUUUGGCGAAUUAGAGCAAUUUUCAAUGCGCGCCGCUUGCUGUUUCUGCCU
((((((((((((((((((..(....).((...))..))))))((((((((..(((.(((((.........))))))))......(((........))))))))))))))))))))))).. ( -54.80)
>consensus
GCGGAGGCAGCGGUCGCGACGGAGACAGGAAGCCACCGCGACGGCGGCGUCGUCGACCAAAUCAGCUGUUUUUGGCGAAUUAGAGCAAUUUUCAAUGCGCGCCGCUUGCUGUUUCUGCCU
((((((((((((((((((..(....).((...))..))))))((((((((..(((.(((((.........))))))))......(((........))))))))))))))))))))))).. (-54.80 = -54.80 +   0.00)

alignment

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secondary structure

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dotplot

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Window 9

Location 12,077,719 – 12,077,824
Length 105
Sequences 3
Columns 105
Reading direction reverse
Mean pairwise identity 100.00
Mean single sequence MFE -45.00
Consensus MFE -45.00
Energy contribution -45.00
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.53
Structure conservation index 1.00
SVM decision value 0.32
SVM RNA-class probability 0.689059
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12077719 105 - 27905053
GUGGGGACGUCGAUUGGCAGCAGAGGCGGAGGCAGCGGUCGCGACGGAGACAGGAAGCCACCGCGACGGCGGCGUCGUCGACCAAAUCAGCUGUUUUUGGCGAAU
.......((((((..((((((.(..((....))..)((((((((((....).....(((.(((...))).))))))).)))))......)))))).))))))... ( -45.00)
>DroSec_CAF1 14472 105 - 1
GUGGGGACGUCGAUUGGCAGCAGAGGCGGAGGCAGCGGUCGCGACGGAGACAGGAAGCCACCGCGACGGCGGCGUCGUCGACCAAAUCAGCUGUUUUUGGCGAAU
.......((((((..((((((.(..((....))..)((((((((((....).....(((.(((...))).))))))).)))))......)))))).))))))... ( -45.00)
>DroSim_CAF1 14666 105 - 1
GUGGGGACGUCGAUUGGCAGCAGAGGCGGAGGCAGCGGUCGCGACGGAGACAGGAAGCCACCGCGACGGCGGCGUCGUCGACCAAAUCAGCUGUUUUUGGCGAAU
.......((((((..((((((.(..((....))..)((((((((((....).....(((.(((...))).))))))).)))))......)))))).))))))... ( -45.00)
>consensus
GUGGGGACGUCGAUUGGCAGCAGAGGCGGAGGCAGCGGUCGCGACGGAGACAGGAAGCCACCGCGACGGCGGCGUCGUCGACCAAAUCAGCUGUUUUUGGCGAAU
.......((((((..((((((.(..((....))..)((((((((((....).....(((.(((...))).))))))).)))))......)))))).))))))... (-45.00 = -45.00 +   0.00)

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 11:33:32 2006