Locus 4180

Sequence ID 2R_DroMel_CAF1
Location 13,752,104 – 13,752,239
Length 135
Max. P 0.815193
window6720 window6721

overview

Window 0

Location 13,752,104 – 13,752,210
Length 106
Sequences 6
Columns 118
Reading direction forward
Mean pairwise identity 80.54
Mean single sequence MFE -21.07
Consensus MFE -14.85
Energy contribution -14.60
Covariance contribution -0.25
Combinations/Pair 1.12
Mean z-score -1.56
Structure conservation index 0.70
SVM decision value 0.44
SVM RNA-class probability 0.738692
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13752104 106 + 20766785
---------CAGCGUUCGGCUAGUUUAAUAAAUAUAUCAAAUAACCUAAAGACGUGUUAGGGAACUUGUGACUUUAACACGUUCUCCACUUCUGGCCCGGCCACAAAACCC---AUUU
---------..(.((..((((((.........(((.....))).......((((((((((((.........))))))))))))........))))))..))).........---.... ( -21.80)
>DroVir_CAF1 62041 104 + 1
UUAAUA-AAAAUCGUUAUGCUAGUUUAAUAAAUAUAUCAAAUAACCUUAAGACGUGUUAGGGAACUUGUGACUUUAACACGUUCAGAACUU--------GCUACAAACUC-----UUU
......-......((...((.(((((......(((.....))).......((((((((((((.........))))))))))))..))))).--------)).))......-----... ( -17.20)
>DroPse_CAF1 50445 109 + 1
UGCAUGAAAAAUCGUUCAGCUAGUUUAAUAAAUAUAUCAAAUAACCUAAAGACGUGUUAGGGAACUUGUGACUUUAACACGUCCUC------AGAGUUUGCUACAAAACUC---AUUU
.((.((((......))))))..............................((((((((((((.........))))))))))))...------.((((((......))))))---.... ( -24.20)
>DroWil_CAF1 55049 110 + 1
UUAAUAAAAAAUCGUUAUGCUAGUUUAAUAAAUAUAUCAAAUAACCUAAAGACGUGUUAGGGAACUUGUGACUUUAACACGUUUCAAACUU--------GCUACAAAACUCUUCUUUU
.............((...((.(((((......(((.....)))......(((((((((((((.........))))))))))))).))))).--------)).)).............. ( -17.40)
>DroAna_CAF1 57750 109 + 1
UGCAUAAAAAAUUGUUCGGCUAGUUUAAUAAAUAUAUCAAAUAACCUAAAGACGUGUUAGGGAACUUGUGACUUUAACACGUUCA------CAGACUUGGCCGCAAAACUC---AUUU
...........(((..((((((((((......(((.....))).......((((((((((((.........))))))))))))..------.)))).))))))))).....---.... ( -21.60)
>DroPer_CAF1 50778 109 + 1
UGCAUGAAAAAUCGUUCAGCUAGUUUAAUAAAUAUAUCAAAUAACCUAAAGACGUGUUAGGGAACUUGUGACUUUAACACGUCCUC------AGAGUUUGCUACAAAACUC---AUUU
.((.((((......))))))..............................((((((((((((.........))))))))))))...------.((((((......))))))---.... ( -24.20)
>consensus
UGCAUAAAAAAUCGUUCAGCUAGUUUAAUAAAUAUAUCAAAUAACCUAAAGACGUGUUAGGGAACUUGUGACUUUAACACGUUCUC______AGA_UU_GCUACAAAACUC___AUUU
.............((..(((..((((.(((....))).))))........((((((((((((.........))))))))))))................))))).............. (-14.85 = -14.60 +  -0.25)

alignment

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secondary structure

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dotplot

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Window 1

Location 13,752,135 – 13,752,239
Length 104
Sequences 6
Columns 116
Reading direction forward
Mean pairwise identity 76.12
Mean single sequence MFE -20.84
Consensus MFE -13.35
Energy contribution -13.13
Covariance contribution -0.22
Combinations/Pair 1.08
Mean z-score -1.50
Structure conservation index 0.64
SVM decision value 0.66
SVM RNA-class probability 0.815193
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13752135 104 + 20766785
AUAACCUAAAGACGUGUUAGGGAACUUGUGACUUUAACACGUUCUCCACUUCUGGCCCGGCCACAAAACCC---AUUUUCGAAUAUCGUCUUACCUUUUCGGUUCGC---------
........((((((((((.((((((.(((.......))).)))).)).....((((...))))........---.......)))).))))))(((.....)))....--------- ( -21.40)
>DroVir_CAF1 62080 98 + 1
AUAACCUUAAGACGUGUUAGGGAACUUGUGACUUUAACACGUUCAGAACUU--------GCUACAAACUC-----UUUAAGCAUAUCAUUUUACAUUUGGGC-----AACCAGAAU
..........((((((((((((.........))))))))))))..((...(--------(((........-----....))))..))........(((((..-----..))))).. ( -22.30)
>DroPse_CAF1 50485 98 + 1
AUAACCUAAAGACGUGUUAGGGAACUUGUGACUUUAACACGUCCUC------AGAGUUUGCUACAAAACUC---AUUUUCGAAUAUCAUUUUACCUUUUCGGUCCAC---------
...(((....((((((((((((.........))))))))))))...------.((((((......))))))---..........................)))....--------- ( -23.30)
>DroWil_CAF1 55089 98 + 1
AUAACCUAAAGACGUGUUAGGGAACUUGUGACUUUAACACGUUUCAAACUU--------GCUACAAAACUCUUCUUUUUCGAAUAUCAUUUUACAUUUCGGGU-CGG---------
...(((...(((((((((((((.........))))))))))))).......--------....................((((.............)))))))-...--------- ( -16.42)
>DroAna_CAF1 57790 98 + 1
AUAACCUAAAGACGUGUUAGGGAACUUGUGACUUUAACACGUUCA------CAGACUUGGCCGCAAAACUC---AUUUUCGAAUAUCGUCUUACCUUUUCGGUUCGC---------
..((((.(((((((((((((((.........)))))))))))...------.((((.((..((.((((...---.))))))..))..))))...))))..))))...--------- ( -18.30)
>DroPer_CAF1 50818 98 + 1
AUAACCUAAAGACGUGUUAGGGAACUUGUGACUUUAACACGUCCUC------AGAGUUUGCUACAAAACUC---AUUUUCGAAUAUCAUUUUACCUUUUCGGUCCAC---------
...(((....((((((((((((.........))))))))))))...------.((((((......))))))---..........................)))....--------- ( -23.30)
>consensus
AUAACCUAAAGACGUGUUAGGGAACUUGUGACUUUAACACGUUCUC______AGA_UU_GCUACAAAACUC___AUUUUCGAAUAUCAUUUUACCUUUUCGGU_CGC_________
..........((((((((((((.........))))))))))))......................................................................... (-13.35 = -13.13 +  -0.22)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:13:40 2006