Locus 4745

Sequence ID 3R_DroMel_CAF1
Location 12,451,735 – 12,451,825
Length 90
Max. P 0.941222
window7788 window7789

overview

Window 8

Location 12,451,735 – 12,451,825
Length 90
Sequences 3
Columns 93
Reading direction forward
Mean pairwise identity 89.13
Mean single sequence MFE -26.60
Consensus MFE -24.90
Energy contribution -25.57
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -2.13
Structure conservation index 0.94
SVM decision value 1.32
SVM RNA-class probability 0.941222
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12451735 90 + 27905053
AAACAGCACACACAGCCACACUCACAAACGACGUACACUGCCAGCGCAUAAACAAGUGCUGUUGUGGUUGUUGUUGCUGCUGCUGCUC---GU
...(((((((.((((((((((((......)).)).......((((((........))))))..)))))))))).))))).........---.. ( -28.10)
>DroSim_CAF1 3603 93 + 1
AAACAGCACACACAGCCACACACACAAACGACGUACACUGCCAGCGCAUAAACAAGUGCUGUUGUGGUUGUUGUUGCUGCUGCUGCUCCUCCU
...(((((((.(((((((((............((.....))((((((........)))))).))))))))))).))))).............. ( -27.70)
>DroEre_CAF1 3906 85 + 1
GAACAGCACACACAUACACACA--CACUCGACGUACACUGCCAGCGCAUAAACAAGUGCUGUUGUGGUUGUUGUUGCUGCUG---CUC---GU
((.(((((((.(((.(((..((--((......((.....))((((((........)))))).))))..)))))))).)))))---.))---.. ( -24.00)
>consensus
AAACAGCACACACAGCCACACACACAAACGACGUACACUGCCAGCGCAUAAACAAGUGCUGUUGUGGUUGUUGUUGCUGCUGCUGCUC___GU
...(((((((.(((((((((............((.....))((((((........)))))).))))))))))).))))).............. (-24.90 = -25.57 +   0.67)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 12,451,735 – 12,451,825
Length 90
Sequences 3
Columns 93
Reading direction reverse
Mean pairwise identity 89.13
Mean single sequence MFE -30.77
Consensus MFE -25.17
Energy contribution -25.83
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -1.84
Structure conservation index 0.82
SVM decision value -0.01
SVM RNA-class probability 0.527502
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12451735 90 - 27905053
AC---GAGCAGCAGCAGCAACAACAACCACAACAGCACUUGUUUAUGCGCUGGCAGUGUACGUCGUUUGUGAGUGUGGCUGUGUGUGCUGUUU
..---(((((((((((((....(((..(((((((((.(........).))))...(....).....)))))..))).)))))...)))))))) ( -29.00)
>DroSim_CAF1 3603 93 - 1
AGGAGGAGCAGCAGCAGCAACAACAACCACAACAGCACUUGUUUAUGCGCUGGCAGUGUACGUCGUUUGUGUGUGUGGCUGUGUGUGCUGUUU
............(((((((...(((.(((((...((((.((....(((((.....)))))...))...)))).))))).)))...))))))). ( -29.50)
>DroEre_CAF1 3906 85 - 1
AC---GAG---CAGCAGCAACAACAACCACAACAGCACUUGUUUAUGCGCUGGCAGUGUACGUCGAGUG--UGUGUGUAUGUGUGUGCUGUUC
..---(((---(((((.((...(((..((((...(((((((....(((((.....)))))...))))))--).))))..))).)))))))))) ( -33.80)
>consensus
AC___GAGCAGCAGCAGCAACAACAACCACAACAGCACUUGUUUAUGCGCUGGCAGUGUACGUCGUUUGUGUGUGUGGCUGUGUGUGCUGUUU
............(((((((...(((.(((((...(((..((....(((((.....)))))...))..)))...))))).)))...))))))). (-25.17 = -25.83 +   0.67)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:37:54 2006