Locus 380

Sequence ID 3R_DroMel_CAF1
Location 1,451,857 – 1,452,010
Length 153
Max. P 0.993685
window632 window633

overview

Window 2

Location 1,451,857 – 1,451,970
Length 113
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 73.37
Mean single sequence MFE -19.45
Consensus MFE -13.24
Energy contribution -13.00
Covariance contribution -0.24
Combinations/Pair 1.21
Mean z-score -1.22
Structure conservation index 0.68
SVM decision value 0.09
SVM RNA-class probability 0.577496
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1451857 113 - 27905053
AGACAGCUAAAACAUAGGUAUCAGUGUUCCAACUCGCUGAUAUUACGAAAGCUACUUUAGAUAUGU-AGUUGUAUUUUAUCGCUACAAUUUU-CCC-----UAAUAAAGAUCAAAUUCCU
..((((((...(((((((((((((((........)))))))))).(....)..........)))))-))))))...................-...-----................... ( -20.30)
>DroSec_CAF1 24423 110 - 1
AGAAAGCUUAAACAUAGAUAUCAGUGUUCUAAGUCACUGAUAUUACGAAAGCUUUUUUAGAUAUC-----UGCCUAGCAUCACUACAAUUUAACCU-----UAAUAAAGAUCAAUUUCCU
(((((((((.......((((((((((........))))))))))....)))))))))..(((...-----(((...)))...............((-----(....))))))........ ( -18.60)
>DroSim_CAF1 22731 110 - 1
AGAAAGCUUAAACAUAGGUAUCAGUGUUCUAAGUCGCUGGUAUUACGAAAGCUUUUUUAGAUAUC-----UGCCUAGCAUCACUACAAUUUAACCU-----UAAUAAAGACCAAUUUCCU
...(((.(((((..((((((((((((........))))))))).......(((....(((....)-----))...)))....)))...))))).))-----).................. ( -16.50)
>DroEre_CAF1 26012 119 - 1
AUAAAGCUAAAACAUAGGUAUCAGUGUCAGAACUCGCUGAUAUUGUGAAAGCUAUUUUAGAUAUUGCUC-UUACAAUCAUUUGUACAUCAGUACCUUACAAUAAUAAAGGCCAGUUUCCU
....((((...(((...(((((((((........))))))))))))...))))......((.((((..(-((..........((((....))))............)))..)))).)).. ( -22.15)
>DroYak_CAF1 24445 108 - 1
ACAAAGCUAAAACAUAGAUAUCAGUGUUCAAAAUCGCUGAUACUGAAAAAGCUAUUUUA------GCUC-UUACAAUUAUUUGUAGCGUU-GACCUUA----AAUAAAGAUAAAUUUCAU
.(((.((((.....(((.((((((((........)))))))))))....(((((...))------))).-.............)))).))-)......----.................. ( -19.70)
>consensus
AGAAAGCUAAAACAUAGGUAUCAGUGUUCUAACUCGCUGAUAUUACGAAAGCUAUUUUAGAUAUC_____UGACUAUCAUCACUACAAUUUAACCU_____UAAUAAAGAUCAAUUUCCU
....((((........((((((((((........)))))))))).....))))................................................................... (-13.24 = -13.00 +  -0.24)

alignment

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secondary structure

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dotplot

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Window 3

Location 1,451,891 – 1,452,010
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 78.37
Mean single sequence MFE -27.10
Consensus MFE -16.86
Energy contribution -17.02
Covariance contribution 0.16
Combinations/Pair 1.29
Mean z-score -2.67
Structure conservation index 0.62
SVM decision value 2.42
SVM RNA-class probability 0.993685
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1451891 119 - 27905053
CAGCUAUGAUGACAUACUAAAUCUUUCGAAUGAUCUGGAAAGACAGCUAAAACAUAGGUAUCAGUGUUCCAACUCGCUGAUAUUACGAAAGCUACUUUAGAUAUGU-AGUUGUAUUUUAU
....((..((.((((((((((.((((((..((.(((....)))))...........((((((((((........)))))))))).))))))....))))).)))))-.))..))...... ( -29.80)
>DroSec_CAF1 24458 115 - 1
CAAUAAUGAUGACAUACUAGAUCUUUUGAAUGAUCUGGAAAGAAAGCUUAAACAUAGAUAUCAGUGUUCUAAGUCACUGAUAUUACGAAAGCUUUUUUAGAUAUC-----UGCCUAGCAU
.......((((.(...(((((((........))))))).((((((((((.......((((((((((........))))))))))....)))))))))).).))))-----.......... ( -30.70)
>DroSim_CAF1 22766 115 - 1
CAAUAAUGAUGACAUACUAGAUCUUUUGAAUGAUCUGGAAAGAAAGCUUAAACAUAGGUAUCAGUGUUCUAAGUCGCUGGUAUUACGAAAGCUUUUUUAGAUAUC-----UGCCUAGCAU
.......((((.(...(((((((........))))))).((((((((((.......((((((((((........))))))))))....)))))))))).).))))-----.......... ( -29.20)
>DroEre_CAF1 26052 119 - 1
AAAUAAUGAAGACAUAGCAAACCUUUUGAAUGAUUUGGAAAUAAAGCUAAAACAUAGGUAUCAGUGUCAGAACUCGCUGAUAUUGUGAAAGCUAUUUUAGAUAUUGCUC-UUACAAUCAU
.....((((...........((((.....(((.(((((........))))).)))))))(((((((........))))))).((((((.(((.............))).-)))))))))) ( -21.62)
>DroYak_CAF1 24480 113 - 1
AAACAAUGAUGACAUAUUAAAUCUAUUGAAUAAUUGGGAAACAAAGCUAAAACAUAGAUAUCAGUGUUCAAAAUCGCUGAUACUGAAAAAGCUAUUUUA------GCUC-UUACAAUUAU
...(((((((..........))).)))).((((((((....)..(((((((..((((.((((((((........))))))))((.....))))))))))------))).-...))))))) ( -24.20)
>consensus
CAAUAAUGAUGACAUACUAAAUCUUUUGAAUGAUCUGGAAAGAAAGCUAAAACAUAGGUAUCAGUGUUCUAACUCGCUGAUAUUACGAAAGCUAUUUUAGAUAUC_____UGACUAUCAU
................(((((((........)))))))......((((........((((((((((........)))))))))).....))))........................... (-16.86 = -17.02 +   0.16)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:41:52 2006