Locus 1853

Sequence ID X_DroMel_CAF1
Location 5,119,131 – 5,119,234
Length 103
Max. P 0.993719
window3012 window3013

overview

Window 2

Location 5,119,131 – 5,119,234
Length 103
Sequences 3
Columns 106
Reading direction forward
Mean pairwise identity 65.18
Mean single sequence MFE -28.31
Consensus MFE -15.59
Energy contribution -15.93
Covariance contribution 0.34
Combinations/Pair 1.17
Mean z-score -1.93
Structure conservation index 0.55
SVM decision value 2.42
SVM RNA-class probability 0.993719
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5119131 103 + 22224390
AAAGGGGCGAACGGGCGAAAG--GGGCGUGGCGCGUCAGAAAUUAAUGGAGCGUAAUUUAUGAAAAUUAUACAAUUGCC-AGCAUGGUCACGCCCACAUUGCACAC
......((((.....(....)--(((((((((((..((........))..))(((((((((((...))))).)))))).-......)))))))))...)))).... ( -31.80)
>DroWil_CAF1 33938 99 + 1
--AUGGGUCAACUGGUG---U--GGGCGGGGUCCUUACGAAAUUAAUGGUUCGUAAUUUAUGAAAAUUAUACAAUUGCUCUGGACAACCAUGCCCACCAAACGCCG
--...(((......(.(---(--((((((((((((((((((........))))))).....((.((((....))))..)).))))..)).))))))))....))). ( -27.00)
>DroAna_CAF1 39747 85 + 1
------------AGGCGGUAGGGGGGCGUG--------GAAAUUAAUGGAGCGUAAUUUAUGAAAAUUAUACAAUUGCC-AGACUGGCCACGCCCACAAUGCACAA
------------.....(((..((((((((--------(.......(((.(..((((((....))))))..).....))-)......)))))))).)..))).... ( -26.12)
>consensus
__A_GGG__AACAGGCG__AG__GGGCGUGG__C_U__GAAAUUAAUGGAGCGUAAUUUAUGAAAAUUAUACAAUUGCC_AGAAUGGCCACGCCCACAAUGCACAA
..............(((......(((((((((......(............)(((((((((((...))))).))))))........)))))))))....))).... (-15.59 = -15.93 +   0.34)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 5,119,131 – 5,119,234
Length 103
Sequences 3
Columns 106
Reading direction reverse
Mean pairwise identity 65.18
Mean single sequence MFE -24.21
Consensus MFE -12.74
Energy contribution -12.63
Covariance contribution -0.11
Combinations/Pair 1.17
Mean z-score -1.48
Structure conservation index 0.53
SVM decision value 0.24
SVM RNA-class probability 0.649542
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5119131 103 - 22224390
GUGUGCAAUGUGGGCGUGACCAUGCU-GGCAAUUGUAUAAUUUUCAUAAAUUACGCUCCAUUAAUUUCUGACGCGCCACGCCC--CUUUCGCCCGUUCGCCCCUUU
..(((.(((..(((((.......(((-(((.......((((((....)))))).((..((........))..)))))).))..--....)))))))))))...... ( -21.72)
>DroWil_CAF1 33938 99 - 1
CGGCGUUUGGUGGGCAUGGUUGUCCAGAGCAAUUGUAUAAUUUUCAUAAAUUACGAACCAUUAAUUUCGUAAGGACCCCGCCC--A---CACCAGUUGACCCAU--
((((.....((((((..((..((((.(((.((((....))))))).....(((((((........))))))))))).))))))--)---)....))))......-- ( -27.80)
>DroAna_CAF1 39747 85 - 1
UUGUGCAUUGUGGGCGUGGCCAGUCU-GGCAAUUGUAUAAUUUUCAUAAAUUACGCUCCAUUAAUUUC--------CACGCCCCCCUACCGCCU------------
..(((......((((((((((.....-)))....(..((((((....))))))..)............--------)))))))......)))..------------ ( -23.10)
>consensus
CUGUGCAUUGUGGGCGUGGCCAUCCU_GGCAAUUGUAUAAUUUUCAUAAAUUACGCUCCAUUAAUUUC__A_G__CCACGCCC__CU__CGCCAGUU__CCC_U__
....((.....((((((((((......))).......((((((....)))))).......................))))))).......)).............. (-12.74 = -12.63 +  -0.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:20:16 2006