Locus 4181

Sequence ID 3L_DroMel_CAF1
Location 12,206,164 – 12,206,304
Length 140
Max. P 0.647616
window6485 window6486

overview

Window 5

Location 12,206,164 – 12,206,278
Length 114
Sequences 5
Columns 119
Reading direction forward
Mean pairwise identity 94.38
Mean single sequence MFE -30.06
Consensus MFE -26.14
Energy contribution -27.14
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -1.27
Structure conservation index 0.87
SVM decision value 0.24
SVM RNA-class probability 0.647616
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12206164 114 + 23771897
GAAAAUUUCCCCAAGGUGGCGUGUUUAAAACACUGCGUGACCAUUUUGGGUGGCAUGGUGUUAAGUUGGGUCACAGUAAUGCCAAUUGAACUAUUUAAGUAUGACAAAUUUACA-----
(.((((((.(((((((((((((((..........))))).))))))))))((((((.(((...........)))....)))))).....................)))))).).----- ( -26.80)
>DroSec_CAF1 20490 119 + 1
GAAAAUUUCCCCAAGGUGGCGUGUUUAAAACGCUGCGUGACCAUUUUGGUUGGCAUGGUGUUAAGUUGGGUCACAGUAAUGCCAAUUUAACUAUUUAAGUAUGUCAAAUUUACAUAUAU
..........((((((((((((((..........))))).)))))))))((((((((.(((((((((((....((....))))))))))))......).))))))))............ ( -29.30)
>DroSim_CAF1 20880 119 + 1
GAAAAUUUCCCCAAGGUGGCGUGUUUAAAACGCUGCGUGACCAUUUUGGUUGGCAUGGUGUUAAGUUGGGUCACAGUAAUGCCAAUUUAACUAUUUAAGUAUGUCAAAUUUACAUAUAU
..........((((((((((((((..........))))).)))))))))((((((((.(((((((((((....((....))))))))))))......).))))))))............ ( -29.30)
>DroEre_CAF1 21037 114 + 1
GAAAAUUUCCCCAAGGUGGCGUGUUUAAAACGCUGCGUGACCAUUUUGGGCGGCAUGGUGUUAAGUUGGGUCACAGUAAUGCCAAUUUAACUAUUUAAGUAUGUCACAUUUGCG-----
...........((((((((((((((((((..(((((.(((.....))).))))).....((((((((((....((....))))))))))))..)))))))))))))).))))..----- ( -33.20)
>DroYak_CAF1 20837 114 + 1
GAAAAUUUCCCCAAGGUGGCGUGUUUAAAACGCUGCGUGACCAUUUUGGGUGGCAUGGUGUUAAGUUGGGUCACAGUAAUGCCAAUUUAACUAUUUAAGUAUGUCAAAUUUGCA-----
.........(((((((((((((((..........))))).))))))))))(((((((.(((((((((((....((....))))))))))))......).)))))))........----- ( -31.70)
>consensus
GAAAAUUUCCCCAAGGUGGCGUGUUUAAAACGCUGCGUGACCAUUUUGGGUGGCAUGGUGUUAAGUUGGGUCACAGUAAUGCCAAUUUAACUAUUUAAGUAUGUCAAAUUUACA_____
(.((((((.(((((((((((((((..........))))).)))))))))).((((((.(((((((((((............))))))))))......).)))))))))))).)...... (-26.14 = -27.14 +   1.00)

alignment

Postscript

secondary structure

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dotplot

Postscript

Window 6

Location 12,206,203 – 12,206,304
Length 101
Sequences 4
Columns 112
Reading direction forward
Mean pairwise identity 84.99
Mean single sequence MFE -25.10
Consensus MFE -17.07
Energy contribution -17.51
Covariance contribution 0.44
Combinations/Pair 1.12
Mean z-score -1.56
Structure conservation index 0.68
SVM decision value 0.06
SVM RNA-class probability 0.561810
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12206203 101 + 23771897
ACCAUUUUGGGUGGCAUGGUGUUAAGUUGGGUCACAGUAAUGCCAAUUGAACUAUUUAAGUAUGACAAAUUUACA-----------AGCAUAUUGUUUCGGUUGCUACCGAA
.........((((((.((((((((...((.....)).))))))))....((((.....((((((.(.........-----------.))))))).....))))))))))... ( -22.60)
>DroSec_CAF1 20529 110 + 1
ACCAUUUUGGUUGGCAUGGUGUUAAGUUGGGUCACAGUAAUGCCAAUUUAACUAUUUAAGUAUGUCAAAUUUACAUAUAUUUUACAUGCAUAUUC--AAGGUUGUUACCGAA
((.(((((((...(((((..((((((((((....((....)))))))))))).......((((((.......))))))......)))))....))--))))).))....... ( -25.00)
>DroEre_CAF1 21076 99 + 1
ACCAUUUUGGGCGGCAUGGUGUUAAGUUGGGUCACAGUAAUGCCAAUUUAACUAUUUAAGUAUGUCACAUUUGCG-----------UACACAUUC--AAGGUUGCCACAGUA
......(((((((((.....((((((((((....((....)))))))))))).......((((((.......)))-----------)))......--...)))))).))).. ( -25.80)
>DroYak_CAF1 20876 99 + 1
ACCAUUUUGGGUGGCAUGGUGUUAAGUUGGGUCACAGUAAUGCCAAUUUAACUAUUUAAGUAUGUCAAAUUUGCA-----------UACAUACUC--AAGGUUGCUACCGAA
.........(((((((....((((((((((....((....)))))))))))).......((((((.......)))-----------)))......--.....)))))))... ( -27.00)
>consensus
ACCAUUUUGGGUGGCAUGGUGUUAAGUUGGGUCACAGUAAUGCCAAUUUAACUAUUUAAGUAUGUCAAAUUUACA___________UACAUAUUC__AAGGUUGCUACCGAA
.........((((((.((((((((...((.....)).))))))))....((((.....((((((........................)))))).....))))))))))... (-17.07 = -17.51 +   0.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:16:15 2006