Locus 3890

Sequence ID 3L_DroMel_CAF1
Location 11,259,424 – 11,259,514
Length 90
Max. P 0.824029
window6057 window6058

overview

Window 7

Location 11,259,424 – 11,259,514
Length 90
Sequences 4
Columns 95
Reading direction forward
Mean pairwise identity 86.71
Mean single sequence MFE -17.77
Consensus MFE -12.84
Energy contribution -12.71
Covariance contribution -0.13
Combinations/Pair 1.08
Mean z-score -2.03
Structure conservation index 0.72
SVM decision value 0.69
SVM RNA-class probability 0.824029
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11259424 90 + 23771897
AAGCAUACAA--ACUAUGUAUAUAUAUACCUAUAUAUAUAGGAUUAUAUGCCAUAUAGAUUAACAAUUGUAAUCGCUGUUGUUGUAGCUG---CU
..(((((...--.(((((((((((......))))))))))).....)))))....(((..(((((((.((....)).)))))))...)))---.. ( -21.10)
>DroSec_CAF1 60215 78 + 1
AAGCAUACAA--ACUAUGUAUAU------------AUAUGGGAUUAUAUGCCAUAUAGAUUAACAAUUGUAAUCGCUGUUGUUGUAGCUG---CU
.(((.(((((--.....((...(------------((((((.((...)).)))))))(((((.(....)))))))).....)))))))).---.. ( -16.70)
>DroSim_CAF1 61888 78 + 1
AAGCAUACCA--ACUAUGUAUAU------------AUAUGGGAUUAUAUGCCAUAUAGAUUAACAAUUGUAAUCGCUGUUGUUGUAGCUG---CU
.((((((.((--((...((...(------------((((((.((...)).)))))))(((((.(....)))))))).)))).))).))).---.. ( -16.80)
>DroYak_CAF1 63811 83 + 1
AAGCAUACAAAAACUAUAUUUGU------------AUAUGGGAUUAUAUGCCAAAUAGAUUAACAAUUGUAAUCGCUGUUGUUGUAGCUGCUGCU
.(((.(((((.(((..(((((((------------(((((....)))))).))))))(((((.(....))))))...))).))))))))...... ( -16.50)
>consensus
AAGCAUACAA__ACUAUGUAUAU____________AUAUGGGAUUAUAUGCCAUAUAGAUUAACAAUUGUAAUCGCUGUUGUUGUAGCUG___CU
..(((((.((...((((((................))))))..)).)))))....(((..(((((((.((....)).)))))))...)))..... (-12.84 = -12.71 +  -0.13)

alignment

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secondary structure

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dotplot

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Window 8

Location 11,259,424 – 11,259,514
Length 90
Sequences 4
Columns 95
Reading direction reverse
Mean pairwise identity 86.71
Mean single sequence MFE -15.62
Consensus MFE -9.59
Energy contribution -9.90
Covariance contribution 0.31
Combinations/Pair 1.05
Mean z-score -2.09
Structure conservation index 0.61
SVM decision value 0.03
SVM RNA-class probability 0.546252
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11259424 90 - 23771897
AG---CAGCUACAACAACAGCGAUUACAAUUGUUAAUCUAUAUGGCAUAUAAUCCUAUAUAUAUAGGUAUAUAUAUACAUAGU--UUGUAUGCUU
..---..(((........)))((((((....).))))).....(((((((((..((((.((((((......)))))).)))).--))))))))). ( -19.10)
>DroSec_CAF1 60215 78 - 1
AG---CAGCUACAACAACAGCGAUUACAAUUGUUAAUCUAUAUGGCAUAUAAUCCCAUAU------------AUAUACAUAGU--UUGUAUGCUU
((---(((((........)))...(((((.(((.....(((((((.........))))))------------)...)))....--))))))))). ( -13.60)
>DroSim_CAF1 61888 78 - 1
AG---CAGCUACAACAACAGCGAUUACAAUUGUUAAUCUAUAUGGCAUAUAAUCCCAUAU------------AUAUACAUAGU--UGGUAUGCUU
((---((....((((...((((((....))))))....(((((((.........))))))------------)........))--))...)))). ( -15.30)
>DroYak_CAF1 63811 83 - 1
AGCAGCAGCUACAACAACAGCGAUUACAAUUGUUAAUCUAUUUGGCAUAUAAUCCCAUAU------------ACAAAUAUAGUUUUUGUAUGCUU
......((((((((.(((((((((....))))))....((((((..((((......))))------------.))))))..))).))))).))). ( -14.50)
>consensus
AG___CAGCUACAACAACAGCGAUUACAAUUGUUAAUCUAUAUGGCAUAUAAUCCCAUAU____________AUAUACAUAGU__UUGUAUGCUU
......((((((((..((((((((....)))))).....((((((.........)))))).....................))..))))).))). ( -9.59 =  -9.90 +   0.31)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:09:18 2006