Locus 5066

Sequence ID X_DroMel_CAF1
Location 13,258,020 – 13,258,230
Length 210
Max. P 0.867341
window8233 window8234

overview

Window 3

Location 13,258,020 – 13,258,122
Length 102
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 89.56
Mean single sequence MFE -20.28
Consensus MFE -19.44
Energy contribution -19.40
Covariance contribution -0.04
Combinations/Pair 1.14
Mean z-score -1.14
Structure conservation index 0.96
SVM decision value -0.03
SVM RNA-class probability 0.518204
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13258020 102 - 22224390
UAACACAAGCGCAAGUAAAC------------------AGAGAAAAAUGAUGCUCAUUAACAUUAAAAUUUCGCUUCUUCCACUACAGUGGCCAUUGGAAUAAUGGUCGCCCCGACUCCA
........((....))....------------------.(((.....(((((........)))))......................((((((((((...)))))))))).....))).. ( -17.80)
>DroSec_CAF1 3697 102 - 1
UCACACAAGCGCAAGUAAAC------------------AGAGAAAAAUGAUGUUCAUUAACAUUAAAAUUUCACUUCUUCCACUACAGUGGCCAAUGGAAUAAUGGUCGCCCCGACUCCA
........((....))....------------------.(((.....(((((((....)))))))......................(((((((.........))))))).....))).. ( -16.90)
>DroSim_CAF1 3727 102 - 1
UAACACAAGCGCAAGUAAAC------------------AGAGAAAAAUGAUGUUCAUUAACAUUAAAAUUUCGCUUCUUCCACUACAGUGGCCAUUGGAAUAAUGGUCGCCCCGACUCCA
........((....))....------------------.(((.....(((((((....)))))))......................((((((((((...)))))))))).....))).. ( -19.80)
>DroEre_CAF1 5421 102 - 1
UAACACAAGCGCAAGUAAAC------------------AGAGAAAAAUGGUGUUCAUUAGCAUUAAAAUUUCGCUUCUUCCACUACAGUGGCCAUUGUAAUAAUGGCCGCCCCGACUCGA
........((....))....------------------.(((.....(((((......(((...........))).....)))))..((((((((((...)))))))))).....))).. ( -24.80)
>DroYak_CAF1 4161 120 - 1
UAACACAAGCGCAAGUAAACAGAAACGGACACACAAACAGAGAAAAAUGAUGUUCAUUAACAUUAAAAUGUCGCUUCUUCCACUACAGUGGCCAUUGUAAUAAUGGUCGCCCCGACUCCA
........((....)).........(((..........((.((....(((((((....))))))).....)).))............((((((((((...)))))))))).)))...... ( -22.10)
>consensus
UAACACAAGCGCAAGUAAAC__________________AGAGAAAAAUGAUGUUCAUUAACAUUAAAAUUUCGCUUCUUCCACUACAGUGGCCAUUGGAAUAAUGGUCGCCCCGACUCCA
........((....)).......................(((.....(((((((....)))))))......................((((((((((...)))))))))).....))).. (-19.44 = -19.40 +  -0.04)

alignment

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secondary structure

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dotplot

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Window 4

Location 13,258,122 – 13,258,230
Length 108
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 81.70
Mean single sequence MFE -23.15
Consensus MFE -11.60
Energy contribution -11.56
Covariance contribution -0.04
Combinations/Pair 1.05
Mean z-score -2.55
Structure conservation index 0.50
SVM decision value 0.85
SVM RNA-class probability 0.867341
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13258122 108 + 22224390
AGUGUCGCAAAUAAAUUCAUUAAAGUGACAUUUUUCAAUUUUAAUGAACAGUACUCGCCAAAAAA-----------AAAAAUGAAGCGCGGGAAAUGGACAUCCAAGA-AAUGAAUACAA
.(((((.........(((((((((((((......)).)))))))))))((...((((((......-----------.........).)))))...)))))))......-........... ( -19.16)
>DroSec_CAF1 3799 105 + 1
AGUGUCGCAAAUAAAUUCAUUAAAGUGACAUUUUUCUAUUUUAAUGAACAGCACUCACCGAAAAA-----------AAAAA---CGCGCGGGAAAUGGACAUCCAAGA-AAUGAAUACAA
.(((((((.......(((((((((((((......)).)))))))))))..((.............-----------.....---.))))).....(((....)))...-.....)))).. ( -16.81)
>DroSim_CAF1 3829 104 + 1
AGUGUCGCAAAUAAAUUCAUUAAAGUGACAUUUUUCAAUUUUAAUGAACAGCACUCGCCGAAAA------------AAAAA---CGCGCGGGAAAUGGACAUCCAAGA-AAUGAAUACAA
.(((((.........(((((((((((((......)).)))))))))))((...(((((((....------------.....---)).)))))...)))))))......-........... ( -21.70)
>DroEre_CAF1 5523 115 + 1
AGUGUCGCAAAUAAAUUCAUUAAAGUGGCAUUUUUCAAUUUUAAUGAACACCAUCC---GACGAGCG-AGCUGCCCAAAAAGCUCGCUCCCCAAAUGGACUUCCAAGA-AAUGAAUACAA
...((((........(((((((((((...........))))))))))).......)---)))(((((-((((........)))))))))......(((....)))...-........... ( -31.56)
>DroYak_CAF1 4281 116 + 1
AGUGUCGCAAAUAAAUUCAUUAAAGUGGCAUUUUUCAAUUUUAAUGAACAGCCCCCACCCAAAAGCGCAAAAGCGCAAAAA-CGCGG---GGAAAUGGACUUGCAAGAAAAUGAAUACAA
......((((.....(((((((((((...........)))))))))))((..((((.(......((((....)))).....-.).))---))...))...))))................ ( -26.50)
>consensus
AGUGUCGCAAAUAAAUUCAUUAAAGUGACAUUUUUCAAUUUUAAUGAACAGCACUCACCGAAAAA___________AAAAA___CGCGCGGGAAAUGGACAUCCAAGA_AAUGAAUACAA
.((((((........(((((((((((((......)).)))))))))))...............................................(((....)))......)).)))).. (-11.60 = -11.56 +  -0.04)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:39:14 2006