Locus 1682

Sequence ID 3R_DroMel_CAF1
Location 4,825,005 – 4,825,116
Length 111
Max. P 0.922298
window2777 window2778

overview

Window 7

Location 4,825,005 – 4,825,116
Length 111
Sequences 4
Columns 115
Reading direction forward
Mean pairwise identity 82.52
Mean single sequence MFE -31.61
Consensus MFE -26.23
Energy contribution -26.86
Covariance contribution 0.63
Combinations/Pair 1.11
Mean z-score -2.00
Structure conservation index 0.83
SVM decision value 1.15
SVM RNA-class probability 0.922298
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4825005 111 + 27905053
UGAGCCGCAGAUGAUUGCGGCUAAGUGGGCAAGGCUGUGCAAUUUGUGUCUUUACA----GGUGUGUGCCAAAAAAAAUUACACCCUUAGCUAAGGCUUAAAUUGCUCAAUUUGG
..((((((((....)))))))).......((((..((.((((((((.(((((...(----((.(((((...........)))))))).....))))).)))))))).)).)))). ( -35.70)
>DroSec_CAF1 5879 115 + 1
UGAGCCGCAGAUGAUUGCGGCUAAGUGGGCAGGGCUGUGCAAUUUGUGUCUUUUCAGCUAGGUGUGUGCCAAAAAAAAUUACACCCUUAGCUAAGGCUUAAAUUGUUCAAUUUGG
..((((((((....)))))))).......((((..((.((((((((.(((((...(((((((.(((((...........))))).)))))))))))).)))))))).)).)))). ( -39.00)
>DroEre_CAF1 5956 104 + 1
UGAGCCGCAGAUGAUUGCGGUUAAGUGGGAAG--CU-UGCAAUUUGUAUCUUUUUA----GGUGUGUGCCAAAAAAAAUUACACCCUCAGCUAAGGCUAAAAUUGCUCAAU----
..((((((((....))))))))((((.....)--))-)(((((((...........----((((((.............))))))...(((....))).))))))).....---- ( -25.52)
>DroYak_CAF1 5930 91 + 1
UGAGCCGCAGAUGAUUGCGGU----------------UGCAAUUUGUAUCUUUUCA----GGUGUGUGCCAA----AAUUACACCCUUAGCUAGGGCUAAAAUUGCUCAAUUUGG
..((((((((....)))))))----------------)(((((((..........(----((.(((((....----...))))))))((((....)))))))))))......... ( -26.20)
>consensus
UGAGCCGCAGAUGAUUGCGGCUAAGUGGGCAG__CU_UGCAAUUUGUAUCUUUUCA____GGUGUGUGCCAAAAAAAAUUACACCCUUAGCUAAGGCUAAAAUUGCUCAAUUUGG
..((((((((....))))))))................((((((((.(((((........((((((.............)))))).......))))).))))))))......... (-26.23 = -26.86 +   0.63)

alignment

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secondary structure

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dotplot

Postscript

Window 8

Location 4,825,005 – 4,825,116
Length 111
Sequences 4
Columns 115
Reading direction reverse
Mean pairwise identity 82.52
Mean single sequence MFE -25.90
Consensus MFE -18.39
Energy contribution -19.20
Covariance contribution 0.81
Combinations/Pair 1.08
Mean z-score -2.14
Structure conservation index 0.71
SVM decision value 1.10
SVM RNA-class probability 0.915779
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4825005 111 - 27905053
CCAAAUUGAGCAAUUUAAGCCUUAGCUAAGGGUGUAAUUUUUUUUGGCACACACC----UGUAAAGACACAAAUUGCACAGCCUUGCCCACUUAGCCGCAAUCAUCUGCGGCUCA
......((.((((......((((....))))(((((((((.((((.(((......----))).))))...)))))))))....)))).))...(((((((......))))))).. ( -28.00)
>DroSec_CAF1 5879 115 - 1
CCAAAUUGAACAAUUUAAGCCUUAGCUAAGGGUGUAAUUUUUUUUGGCACACACCUAGCUGAAAAGACACAAAUUGCACAGCCCUGCCCACUUAGCCGCAAUCAUCUGCGGCUCA
.................(((....))).((((((((((((((((..((.........))..)))))).....)))))...)))))........(((((((......))))))).. ( -28.10)
>DroEre_CAF1 5956 104 - 1
----AUUGAGCAAUUUUAGCCUUAGCUGAGGGUGUAAUUUUUUUUGGCACACACC----UAAAAAGAUACAAAUUGCA-AG--CUUCCCACUUAACCGCAAUCAUCUGCGGCUCA
----..(((((....(((((....)))))((((((((((((((((((.......)----)))))))).....))))))-..--...))).......((((......))))))))) ( -24.70)
>DroYak_CAF1 5930 91 - 1
CCAAAUUGAGCAAUUUUAGCCCUAGCUAAGGGUGUAAUU----UUGGCACACACC----UGAAAAGAUACAAAUUGCA----------------ACCGCAAUCAUCUGCGGCUCA
.........(((((((..(((((.....)))))(((.((----((..((......----))..)))))))))))))).----------------.(((((......))))).... ( -22.80)
>consensus
CCAAAUUGAGCAAUUUAAGCCUUAGCUAAGGGUGUAAUUUUUUUUGGCACACACC____UGAAAAGACACAAAUUGCA_AG__CUGCCCACUUAACCGCAAUCAUCUGCGGCUCA
.........(((((((...((((....))))((((..........((......))...........)))))))))))................(((((((......))))))).. (-18.39 = -19.20 +   0.81)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:16:49 2006