Locus 2770

Sequence ID 2L_DroMel_CAF1
Location 7,831,145 – 7,831,283
Length 138
Max. P 0.896520
window4401 window4402

overview

Window 1

Location 7,831,145 – 7,831,243
Length 98
Sequences 3
Columns 98
Reading direction forward
Mean pairwise identity 93.88
Mean single sequence MFE -17.16
Consensus MFE -16.43
Energy contribution -16.87
Covariance contribution 0.45
Combinations/Pair 1.04
Mean z-score -1.59
Structure conservation index 0.96
SVM decision value 0.29
SVM RNA-class probability 0.668681
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 7831145 98 + 22407834
AAGACCCGAUUAAAACUAAGCUGAACAAAAAUUGUCUGCUCAAAAGCAUGCAAAUAUAUUCUAGAUAAAUUUUUUAUUGAUCUUAAUAGGAAAUUUUA
...............................((((.((((....)))).)))).............(((((((((((((....))))))))))))).. ( -12.50)
>DroSec_CAF1 3108 98 + 1
AAGACUCUAUUAAAACUAAGCUGGUCAAAAAUUGUGUGCUCAAAAGCAUGCAAAUAUAUUCCAGAUAUAUUUUUUAUUGAUGUUAAUAGGAAAUUUUA
.....((((((((.......((((.......(((((((((....))))))))).......))))...((((.......))))))))))))........ ( -18.84)
>DroSim_CAF1 3250 98 + 1
AAAACUCGAUUAAAACUAAGCUGGUCAAAAAUUGUGUGCUCAAAAGCAUGCAAAUAUAUUCCAGAUAUAUUUUUUAUUGAUGUUAAUAGGAAAUUUUA
..((((((((.((((.((..((((.......(((((((((....))))))))).......))))...)).)))).))))).))).............. ( -20.14)
>consensus
AAGACUCGAUUAAAACUAAGCUGGUCAAAAAUUGUGUGCUCAAAAGCAUGCAAAUAUAUUCCAGAUAUAUUUUUUAUUGAUGUUAAUAGGAAAUUUUA
....................((((.......(((((((((....))))))))).......))))....(((((((((((....))))))))))).... (-16.43 = -16.87 +   0.45)

alignment

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secondary structure

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dotplot

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Window 2

Location 7,831,163 – 7,831,283
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 83.14
Mean single sequence MFE -27.12
Consensus MFE -16.26
Energy contribution -19.08
Covariance contribution 2.82
Combinations/Pair 1.19
Mean z-score -2.57
Structure conservation index 0.60
SVM decision value 0.99
SVM RNA-class probability 0.896520
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 7831163 120 + 22407834
AGCUGAACAAAAAUUGUCUGCUCAAAAGCAUGCAAAUAUAUUCUAGAUAAAUUUUUUAUUGAUCUUAAUAGGAAAUUUUAUCGGGGCAUGCACUUGAUGAAAAUCAAUAAUCAGUAAUCG
.(((((.....................((((((............((((((((((((((((....)))))))))).))))))...))))))..(((((....)))))...)))))..... ( -26.96)
>DroSec_CAF1 3126 120 + 1
AGCUGGUCAAAAAUUGUGUGCUCAAAAGCAUGCAAAUAUAUUCCAGAUAUAUUUUUUAUUGAUGUUAAUAGGAAAUUUUAUCGGGGCUUCCACUUGAUAAAAAUCAAUAAUCAGUAAUCG
..((((.......(((((((((....))))))))).......))))...((((..((((((((............((((((((((.......))))))))))))))))))..)))).... ( -28.64)
>DroSim_CAF1 3268 120 + 1
AGCUGGUCAAAAAUUGUGUGCUCAAAAGCAUGCAAAUAUAUUCCAGAUAUAUUUUUUAUUGAUGUUAAUAGGAAAUUUUAUCGGGGCUUGCACUUGAUGAAAAUCAAUAAUCAGUAAUCG
.((.((((.....(((((((((....))))))))).......((.((((.(((((((((((....)))))))))))..)))))))))).))..(((((....)))))............. ( -30.50)
>DroEre_CAF1 3308 118 + 1
UACUGAAACAAAA--GUGUGCUGAAAAUCGUGAAAAUAUAUUCAAGAUAUAUUUUUUAUUACUCCUAAUAGGAAAUUUUAUCUGGGCAUGCACUCGAUGAAAAUCAAUAAUCAGUAAUCG
((((((.......--(((((((........((((......))))(((((.(((((((((((....)))))))))))..))))).)))))))....(((....))).....)))))).... ( -28.30)
>DroYak_CAF1 3264 105 + 1
---------------UUGUGCUCUACAUCAUGCAAAUGUUUUCUAGAUAUAUUUUUUAACGAUUUUAAUAGGAAAUUUUAUCUGGGCAUGCACUUGGUGGAAAUCAAUAAUGAGUAAUCG
---------------...(((((.......((((..(((...(((((((.((((((((..........))))))))..)))))))))))))).(((((....)))))....))))).... ( -21.20)
>consensus
AGCUGAACAAAAAUUGUGUGCUCAAAAGCAUGCAAAUAUAUUCCAGAUAUAUUUUUUAUUGAUCUUAAUAGGAAAUUUUAUCGGGGCAUGCACUUGAUGAAAAUCAAUAAUCAGUAAUCG
.(((((.......(((((((((....)))))))))..........(((...((((((((((....))))))))))((((((((((.......))))))))))))).....)))))..... (-16.26 = -19.08 +   2.82)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:35:47 2006