Locus 4470

Sequence ID 3L_DroMel_CAF1
Location 12,962,143 – 12,962,295
Length 152
Max. P 0.998579
window6968 window6969

overview

Window 8

Location 12,962,143 – 12,962,255
Length 112
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 89.65
Mean single sequence MFE -24.14
Consensus MFE -21.86
Energy contribution -21.62
Covariance contribution -0.24
Combinations/Pair 1.16
Mean z-score -2.29
Structure conservation index 0.91
SVM decision value 3.15
SVM RNA-class probability 0.998579
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12962143 112 + 23771897
U--------UUACAAUUACAAUUAUGUUUUGCCAAAUGGCAUCAAAGUGCAGAGUUCUGCAUAUAAAAAGCUGCUUAAUAUAACUAAGAUUAAAAUCGGAAACUCGUCCAAGUAGCAUCC
.--------...............((...((((....)))).))..((((((....)))))).......(((((((...........(((....)))(((......)))))))))).... ( -26.30)
>DroSec_CAF1 79394 120 + 1
UUCGUUCAUUGACAAUUACAAUUAUGUUUUGCUAAAUGGCAUCAAAGUGCAGAGUUCUGCAUACAAAAAGCUGCUUAAUAUAACUAAGAUUAAAAUCGGAAACUCGUCCAAGUAGCAUCC
........(((.............((...((((....)))).))..((((((....)))))).)))...(((((((...........(((....)))(((......)))))))))).... ( -24.40)
>DroSim_CAF1 84116 112 + 1
U--------UUACAAUUACAAUUAUGUUUUGCUAAAUGGCAUCAAAGUGCAGAGUUCUGCAUACAAAAAGCUGCUUAAUAUAACUAAGAUUAAAAUCGGAAACUUGUCCAAGUGGCAUCC
.--------...............((...((((....)))).))..((((((....)))))).......((..(((...........(((....)))(((......))))))..)).... ( -22.60)
>DroEre_CAF1 85417 110 + 1
A--------UUACAAUCACAAUUUUGU--UGCUAAAGGGCAUCAUAGUGCAGAGUCCUGCACACAAAAAGCUGCUUAAUACAACUAAGAUUAAAAUCAGAAACUCGUCCAAGUAGCUUCC
.--------............((((((--((((....)))).....((((((....))))))))))))((((((((...((......(((....))).(.....)))..))))))))... ( -23.90)
>DroYak_CAF1 83335 110 + 1
U--------UUACAAUUACAAUUAUGU--UGCUAAAAGGCAUCGUAGUGCAGAGUUCUGCAUACAAAAAGCUGCUUAAUACAACUAAGAUUAAAAUCAGAAACUCGUCCAAGUAGCUUCC
.--------.............((((.--((((....)))).))))((((((....)))))).....(((((((((...((......(((....))).(.....)))..))))))))).. ( -23.50)
>consensus
U________UUACAAUUACAAUUAUGUUUUGCUAAAUGGCAUCAAAGUGCAGAGUUCUGCAUACAAAAAGCUGCUUAAUAUAACUAAGAUUAAAAUCGGAAACUCGUCCAAGUAGCAUCC
........................((...((((....)))).))..((((((....)))))).......(((((((...........(((....)))(((......)))))))))).... (-21.86 = -21.62 +  -0.24)

alignment

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secondary structure

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dotplot

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Window 9

Location 12,962,175 – 12,962,295
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 95.83
Mean single sequence MFE -27.80
Consensus MFE -24.80
Energy contribution -25.17
Covariance contribution 0.38
Combinations/Pair 1.06
Mean z-score -2.36
Structure conservation index 0.89
SVM decision value 1.23
SVM RNA-class probability 0.933094
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12962175 120 + 23771897
AUCAAAGUGCAGAGUUCUGCAUAUAAAAAGCUGCUUAAUAUAACUAAGAUUAAAAUCGGAAACUCGUCCAAGUAGCAUCCAAAUGAGCUGAAAAUAGCAGAGAAAGUUCUGUUUCGUGCA
.(((..((((((....)))))).......(((((((...........(((....)))(((......)))))))))).......)))((((((....((((((....)))))))))).)). ( -29.80)
>DroSec_CAF1 79434 120 + 1
AUCAAAGUGCAGAGUUCUGCAUACAAAAAGCUGCUUAAUAUAACUAAGAUUAAAAUCGGAAACUCGUCCAAGUAGCAUCCAAAUGAGCUGAAAAUAGCAGAGAAAGUUCUGUUUCGUACA
.(((..((((((....)))))).......(((((((...........(((....)))(((......)))))))))).......))).........(((((((....)))))))....... ( -26.50)
>DroSim_CAF1 84148 120 + 1
AUCAAAGUGCAGAGUUCUGCAUACAAAAAGCUGCUUAAUAUAACUAAGAUUAAAAUCGGAAACUUGUCCAAGUGGCAUCCAAAUGAGCUGAAAAUAGCAGAGAAAGUUCUGUUUCGUGCA
.(((..((((((....)))))).......((..(((...........(((....)))(((......))))))..)).......)))((((((....((((((....)))))))))).)). ( -28.60)
>DroYak_CAF1 83365 120 + 1
AUCGUAGUGCAGAGUUCUGCAUACAAAAAGCUGCUUAAUACAACUAAGAUUAAAAUCAGAAACUCGUCCAAGUAGCUUCCAAAUGAGCUGAAAAUAGCACAGAAAGUUCUGUUUCGUGCA
.((((.((((((....)))))).....(((((((((...((......(((....))).(.....)))..)))))))))....))))..........((((.((((......)))))))). ( -26.30)
>consensus
AUCAAAGUGCAGAGUUCUGCAUACAAAAAGCUGCUUAAUAUAACUAAGAUUAAAAUCGGAAACUCGUCCAAGUAGCAUCCAAAUGAGCUGAAAAUAGCAGAGAAAGUUCUGUUUCGUGCA
.(((..((((((....)))))).......(((((((...........(((....)))(((......)))))))))).......)))((((((....((((((....)))))))))).)). (-24.80 = -25.17 +   0.38)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:24:04 2006