Locus 3068

Sequence ID 3R_DroMel_CAF1
Location 8,103,009 – 8,103,148
Length 139
Max. P 0.888869
window4980 window4981 window4982

overview

Window 0

Location 8,103,009 – 8,103,108
Length 99
Sequences 5
Columns 109
Reading direction reverse
Mean pairwise identity 89.67
Mean single sequence MFE -21.07
Consensus MFE -16.50
Energy contribution -16.58
Covariance contribution 0.08
Combinations/Pair 1.08
Mean z-score -1.73
Structure conservation index 0.78
SVM decision value 0.56
SVM RNA-class probability 0.782803
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8103009 99 - 27905053
CUGAAAUUGUAUUCUGUUGCUCGGAGUCGCGUACACAAAUGUGAAAUUCGCCAGCCACAAAAA----------ACGAAAUUCAACAGCAACAAAAACUUUUGUUGUUAC
.((((.((((.((.(((.(((.((..((((((......))))))......))))).))).)).----------))))..))))..(((((((((....))))))))).. ( -23.40)
>DroSec_CAF1 54710 104 - 1
CUGAAAUUGUAUUCUGUUGCUCGGAGUCGCGUACACAAAUGUGAAAUUCGCCAGCCAAAAAAAA-----AACAACGAAAUUCAACAGCAACUAAAACUUUUGUUGUUAC
...............((((..((((.((((((......))))))..)))).)))).........-----((((((((((..................)))))))))).. ( -16.47)
>DroSim_CAF1 26801 109 - 1
CUGAAAUUGUAUUCUGUUGCUCGGAGUCGCGUACACAAAUGUGAAAUUCGCCAGCCACAAAAAAAAAACAACAACGAAAUUCAACGGCAACAAAAACUUUUGUUGUUAC
..............(((.(((.((..((((((......))))))......))))).)))..........((((((((((......(....)......)))))))))).. ( -21.30)
>DroEre_CAF1 29741 107 - 1
CUGAAAUUGUAUUCCGUUGCUCGGAGUCGCGUACACAAAUGUGAAAUUCGCCAGCCACAAAAAAAAG--AAAAAACAAAUUCAACAGCAACAAAAACCUUUGUUGUUAG
.((((.((((((((((.....)))))).(((..(((....))).....)))................--.....)))).))))..(((((((((....))))))))).. ( -23.00)
>DroYak_CAF1 23274 99 - 1
CUGAAAUUGUAUUCUGUUGCCCGGAGUCGCGUACACAAAUGUGAAAUUCGCCAGCCACAAAA----------AACCAAAUUCAACAGCAAGAAACACUUUUGUUGUUAA
..(((.(((..((.(((.((.((((.((((((......))))))..))))...)).))).))----------...))).)))((((((((((.....)))))))))).. ( -21.20)
>consensus
CUGAAAUUGUAUUCUGUUGCUCGGAGUCGCGUACACAAAUGUGAAAUUCGCCAGCCACAAAAAA_____AA_AACGAAAUUCAACAGCAACAAAAACUUUUGUUGUUAC
.((((...(.((((((.....)))))))(((..(((....))).....)))............................))))..(((((((((....))))))))).. (-16.50 = -16.58 +   0.08)

alignment

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secondary structure

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dotplot

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Window 1

Location 8,103,038 – 8,103,148
Length 110
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.26
Mean single sequence MFE -25.87
Consensus MFE -21.90
Energy contribution -21.94
Covariance contribution 0.04
Combinations/Pair 1.04
Mean z-score -1.38
Structure conservation index 0.85
SVM decision value 0.38
SVM RNA-class probability 0.710984
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8103038 110 + 27905053
AUUUCGU----------UUUUUGUGGCUGGCGAAUUUCACAUUUGUGUACGCGACUCCGAGCAACAGAAUACAAUUUCAGCAUUUUCCAGCCACGACCAGCUCCACUUUCACAAUGAAUC
.....((----------(..((((((((((.((((.......((((((.(((........))....).)))))).......)))).))))))))))..)))................... ( -24.84)
>DroSec_CAF1 54739 115 + 1
AUUUCGUUGUU-----UUUUUUUUGGCUGGCGAAUUUCACAUUUGUGUACGCGACUCCGAGCAACAGAAUACAAUUUCAGCAUUUUCCAGCCACGACCAGCUCCACUUUCACAAUGAAUC
..((((((((.-----.......(((((((.((((.......((((((.(((........))....).)))))).......)))).))))))).((..((.....)).)))))))))).. ( -23.24)
>DroSim_CAF1 26830 120 + 1
AUUUCGUUGUUGUUUUUUUUUUGUGGCUGGCGAAUUUCACAUUUGUGUACGCGACUCCGAGCAACAGAAUACAAUUUCAGCAUUUUCCAGCCACGACCAGCUCCACUUUCACAAUGAAUC
..((((((((.((.......((((((((((.((((.......((((((.(((........))....).)))))).......)))).))))))))))........))....)))))))).. ( -28.40)
>DroEre_CAF1 29770 117 + 1
AUUUGUUUUUU--CUUUUUUUUGUGGCUGGCGAAUUUCACAUUUGUGUACGCGACUCCGAGCAACGGAAUACAAUUUCAGCAUUUUCCAGCCACGGCC-GCUCCACUUUCACAAUGAAUC
..((((.....--.........((((((((.((((.......((((((.......((((.....)))))))))).......)))).))))))))((..-...))......))))...... ( -25.45)
>DroYak_CAF1 23303 110 + 1
AUUUGGUU----------UUUUGUGGCUGGCGAAUUUCACAUUUGUGUACGCGACUCCGGGCAACAGAAUACAAUUUCAGCAUUUUCCAGCCACGACCAGCUCCACUUUCACAAUGAAUC
..((((((----------....((((((((.((((..(((....)))...((.......(....).(((......))).)))))).)))))))))))))).................... ( -27.40)
>consensus
AUUUCGUU_UU_____UUUUUUGUGGCUGGCGAAUUUCACAUUUGUGUACGCGACUCCGAGCAACAGAAUACAAUUUCAGCAUUUUCCAGCCACGACCAGCUCCACUUUCACAAUGAAUC
....................((((((((((.((((.......((((((.(((........))....).)))))).......)))).))))))))))........................ (-21.90 = -21.94 +   0.04)

alignment

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secondary structure

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dotplot

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Window 2

Location 8,103,038 – 8,103,148
Length 110
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.26
Mean single sequence MFE -29.52
Consensus MFE -28.26
Energy contribution -28.30
Covariance contribution 0.04
Combinations/Pair 1.04
Mean z-score -1.29
Structure conservation index 0.96
SVM decision value 0.95
SVM RNA-class probability 0.888869
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8103038 110 - 27905053
GAUUCAUUGUGAAAGUGGAGCUGGUCGUGGCUGGAAAAUGCUGAAAUUGUAUUCUGUUGCUCGGAGUCGCGUACACAAAUGUGAAAUUCGCCAGCCACAAAAA----------ACGAAAU
..((((((.....)))))).......((((((((..(((............(((((.....)))))((((((......)))))).)))..)))))))).....----------....... ( -28.90)
>DroSec_CAF1 54739 115 - 1
GAUUCAUUGUGAAAGUGGAGCUGGUCGUGGCUGGAAAAUGCUGAAAUUGUAUUCUGUUGCUCGGAGUCGCGUACACAAAUGUGAAAUUCGCCAGCCAAAAAAAA-----AACAACGAAAU
..(((.((((.......(.(((((((((((((....(((((.......)))))(((.....))))))))))..(((....)))......)))))))........-----.)))).))).. ( -26.99)
>DroSim_CAF1 26830 120 - 1
GAUUCAUUGUGAAAGUGGAGCUGGUCGUGGCUGGAAAAUGCUGAAAUUGUAUUCUGUUGCUCGGAGUCGCGUACACAAAUGUGAAAUUCGCCAGCCACAAAAAAAAAACAACAACGAAAU
..(((.((((((.((.....))..))((((((((..(((............(((((.....)))))((((((......)))))).)))..))))))))............)))).))).. ( -30.40)
>DroEre_CAF1 29770 117 - 1
GAUUCAUUGUGAAAGUGGAGC-GGCCGUGGCUGGAAAAUGCUGAAAUUGUAUUCCGUUGCUCGGAGUCGCGUACACAAAUGUGAAAUUCGCCAGCCACAAAAAAAAG--AAAAAACAAAU
..((((((.....))))))..-....((((((((..(((............(((((.....)))))((((((......)))))).)))..)))))))).........--........... ( -31.10)
>DroYak_CAF1 23303 110 - 1
GAUUCAUUGUGAAAGUGGAGCUGGUCGUGGCUGGAAAAUGCUGAAAUUGUAUUCUGUUGCCCGGAGUCGCGUACACAAAUGUGAAAUUCGCCAGCCACAAAA----------AACCAAAU
..((((((.....))))))..((((.((((((((..(((((.......)))))........((((.((((((......))))))..))))))))))))....----------.))))... ( -30.20)
>consensus
GAUUCAUUGUGAAAGUGGAGCUGGUCGUGGCUGGAAAAUGCUGAAAUUGUAUUCUGUUGCUCGGAGUCGCGUACACAAAUGUGAAAUUCGCCAGCCACAAAAAA_____AA_AACGAAAU
..((((((.....)))))).......((((((((..(((............(((((.....)))))((((((......)))))).)))..))))))))...................... (-28.26 = -28.30 +   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 10:52:19 2006