Locus 4277

Sequence ID X_DroMel_CAF1
Location 11,246,760 – 11,246,862
Length 102
Max. P 0.751126
window7030 window7031

overview

Window 0

Location 11,246,760 – 11,246,862
Length 102
Sequences 5
Columns 118
Reading direction forward
Mean pairwise identity 71.89
Mean single sequence MFE -25.92
Consensus MFE -15.18
Energy contribution -16.06
Covariance contribution 0.88
Combinations/Pair 1.31
Mean z-score -1.62
Structure conservation index 0.59
SVM decision value 0.48
SVM RNA-class probability 0.751126
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11246760 102 + 22224390
UGAUCUUCCAGGGAGA-UGAUCUCUGUUUUGUAGGGGU---UUCUGUUCG-------UCUUUUAAGUUAAUACUUUG-----GAUUCCCCUGGUUGUUCACAUUGCAUAGUGUGUACA
.......(((((((((-.((((((((.....)))))))---))))....(-------(((...((((....)))).)-----)))..)))))).(((.(((((......))))).))) ( -28.60)
>DroSec_CAF1 6236 102 + 1
UGAUCUUCCAGGGAAA-AGAUCUCUAUUUUGUAGGGGU---UUCUGUUCG-------UCUUUUAAGUUAAUACUUUG-----GAUCCCCCUGGUUGUUCACAUUGCAUAGUGUGUACA
.......((((((...-((((((((((...))))))))---))......(-------(((...((((....)))).)-----)))..)))))).(((.(((((......))))).))) ( -27.90)
>DroSim_CAF1 6720 102 + 1
UGAUCUUCCAGGGAAA-GGAUCUCUGUUUUGUAGGGGU---UUCUGUUCG-------UCUUUUAAGUUAAUACUUUG-----GAUCCCCCUGGUUGUUCACAUUGCAUAGUGUGUACA
.......((((((.(.-.((((((((.....)))))))---)..)....(-------(((...((((....)))).)-----)))..)))))).(((.(((((......))))).))) ( -27.40)
>DroYak_CAF1 6222 102 + 1
-------CCAGGGAGA-AAAUCUCUGUUUUUUGGGGGU---UUCUGUUUUAAGUUUAUCUUUUAAGUUCAUACUUUG-----GAUCCCCCUGGUUGUUCACAUUACAGAGCGUAUACG
-------(((((((((-((..(((........)))..)---))))...........((((...((((....)))).)-----)))..))))))..((((........))))....... ( -24.70)
>DroAna_CAF1 11255 94 + 1
------UCCAGGGAUACAG----------AGAAGGGAGUUAUUUCGUUAU-------CCUUUUGAGUUGAAGUUCUGUUAUUGA-GCCCUUGGUUCUGAGCAUUACAUACUGCGUACA
------.((((((...(((----------.(((((((............)-------))))))...)))..((((.......))-))))))))......(((........)))..... ( -21.00)
>consensus
UGAUCUUCCAGGGAAA_AGAUCUCUGUUUUGUAGGGGU___UUCUGUUCG_______UCUUUUAAGUUAAUACUUUG_____GAUCCCCCUGGUUGUUCACAUUGCAUAGUGUGUACA
.......((((((......(((((((.....))))))).........................((((....))))............)))))).(((.((((((....)))))).))) (-15.18 = -16.06 +   0.88)

alignment

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secondary structure

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dotplot

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Window 1

Location 11,246,760 – 11,246,862
Length 102
Sequences 5
Columns 118
Reading direction reverse
Mean pairwise identity 71.89
Mean single sequence MFE -18.70
Consensus MFE -11.52
Energy contribution -11.80
Covariance contribution 0.28
Combinations/Pair 1.30
Mean z-score -1.37
Structure conservation index 0.62
SVM decision value -0.03
SVM RNA-class probability 0.517621
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11246760 102 - 22224390
UGUACACACUAUGCAAUGUGAACAACCAGGGGAAUC-----CAAAGUAUUAACUUAAAAGA-------CGAACAGAA---ACCCCUACAAAACAGAGAUCA-UCUCCCUGGAAGAUCA
(((.((((........)))).)))...(((((....-----..((((....))))......-------(.....)..---.)))))..........((((.-(((....))).)))). ( -18.30)
>DroSec_CAF1 6236 102 - 1
UGUACACACUAUGCAAUGUGAACAACCAGGGGGAUC-----CAAAGUAUUAACUUAAAAGA-------CGAACAGAA---ACCCCUACAAAAUAGAGAUCU-UUUCCCUGGAAGAUCA
(((.((((........)))).)))...(((((..((-----..((((....))))....(.-------....).)).---.)))))..........(((((-((......))))))). ( -20.90)
>DroSim_CAF1 6720 102 - 1
UGUACACACUAUGCAAUGUGAACAACCAGGGGGAUC-----CAAAGUAUUAACUUAAAAGA-------CGAACAGAA---ACCCCUACAAAACAGAGAUCC-UUUCCCUGGAAGAUCA
(((.((((........)))).))).(((((((((((-----(.((((....))))......-------.....((..---....))........).)))))-...))))))....... ( -22.20)
>DroYak_CAF1 6222 102 - 1
CGUAUACGCUCUGUAAUGUGAACAACCAGGGGGAUC-----CAAAGUAUGAACUUAAAAGAUAAACUUAAAACAGAA---ACCCCCAAAAAACAGAGAUUU-UCUCCCUGG-------
........((((((..((....))....(((((...-----..((((....))))..(((.....))).........---.))))).....))))))....-.........------- ( -20.30)
>DroAna_CAF1 11255 94 - 1
UGUACGCAGUAUGUAAUGCUCAGAACCAAGGGC-UCAAUAACAGAACUUCAACUCAAAAGG-------AUAACGAAAUAACUCCCUUCU----------CUGUAUCCCUGGA------
.....(((........)))......(((.(((.-...(((.((((.(((........))).-------.....(((.........))))----------)))))))))))).------ ( -11.80)
>consensus
UGUACACACUAUGCAAUGUGAACAACCAGGGGGAUC_____CAAAGUAUUAACUUAAAAGA_______CGAACAGAA___ACCCCUACAAAACAGAGAUCU_UCUCCCUGGAAGAUCA
.((.((((........)))).))..(((((((((.........((((....))))...................(......)....................)))))))))....... (-11.52 = -11.80 +   0.28)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:21:00 2006