Locus 444

Sequence ID 2L_DroMel_CAF1
Location 1,321,198 – 1,321,334
Length 136
Max. P 0.999551
window719 window720

overview

Window 9

Location 1,321,198 – 1,321,297
Length 99
Sequences 6
Columns 99
Reading direction forward
Mean pairwise identity 89.89
Mean single sequence MFE -28.53
Consensus MFE -25.83
Energy contribution -26.33
Covariance contribution 0.50
Combinations/Pair 1.11
Mean z-score -3.85
Structure conservation index 0.91
SVM decision value 3.71
SVM RNA-class probability 0.999551
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1321198 99 + 22407834
AAAACAAAGAACGUUAAACGUCUAUGCAUGCAAAAAUGCUAAAGAUUUUUUUAAUGAAGCCCGGCACACGCCUGGCACACAAAUCUCUCUGGGAUUUGA
...........(((((((.((((..((((......))))...))))...)))))))..(((.(((....))).)))...(((((((.....))))))). ( -28.50)
>DroSec_CAF1 78647 98 + 1
AAAACAAAGAACGUUAAACGUCUAUGCAUGCAAAAAUGCUAAAGAUUU-UUUAAUGAAGCCCGGCACACGCCUGGCACACAAAUCUCUCUGGGAUUUGA
...........(((((((.((((..((((......))))...))))..-)))))))..(((.(((....))).)))...(((((((.....))))))). ( -28.90)
>DroSim_CAF1 82129 99 + 1
AAAACAAAGAACGUUAAACGUCUAUGCAUGCAAAAAUGCUAAAGAUUUUUUUAAUGAAGCCCGGCACACGCCUGGCACACAAAUCUCUCUGGGAUUUGA
...........(((((((.((((..((((......))))...))))...)))))))..(((.(((....))).)))...(((((((.....))))))). ( -28.50)
>DroEre_CAF1 91842 98 + 1
AAAACAAAGAACGUUAAACAUCUAUGCAUGCAAGAAUGCUAGAGAUUU-UUUAAUGAAGCCAGGCACACGCCUGGCACACAAAUCUCCCUGGGAUUUGA
...........(((((((.((((..((((......))))...))))..-)))))))..(((((((....)))))))...(((((((.....))))))). ( -34.30)
>DroYak_CAF1 81838 99 + 1
AAAACAAAGAACGUUAAACAUCUAUGCAUGCAAAAAUGCCAAAGAUUUUUUUAAUGAAGCCCGGCACACGCCUGGCACACAAAUCUCUCUGGGAUUUGA
...........(((((((.((((..((((......))))...))))...)))))))..(((.(((....))).)))...(((((((.....))))))). ( -27.50)
>DroAna_CAF1 104906 89 + 1
AAG---AGG-------AGUGUCUAUGCAUGGAAAAAUGCAAAAGAUUUUUUUAAUGAAGCCCGGCACACGCCCCGUGGGCAAAUCUCUCUGGGAUUUGA
...---(((-------((.((((.(((((......)))))..)))).)))))......(((((((....)))....))))((((((.....)))))).. ( -23.50)
>consensus
AAAACAAAGAACGUUAAACGUCUAUGCAUGCAAAAAUGCUAAAGAUUUUUUUAAUGAAGCCCGGCACACGCCUGGCACACAAAUCUCUCUGGGAUUUGA
...........(((((((.((((..((((......))))...))))...)))))))..(((.(((....))).)))...(((((((.....))))))). (-25.83 = -26.33 +   0.50) 

alignment

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secondary structure

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dotplot

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Window 0

Location 1,321,226 – 1,321,334
Length 108
Sequences 6
Columns 119
Reading direction forward
Mean pairwise identity 83.15
Mean single sequence MFE -24.23
Consensus MFE -16.19
Energy contribution -17.67
Covariance contribution 1.47
Combinations/Pair 1.10
Mean z-score -1.91
Structure conservation index 0.67
SVM decision value 0.06
SVM RNA-class probability 0.565226
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1321226 108 + 22407834
U--------GCAAAAAUGCUAAAGAUUUUUUUAAUGAAGCCCGGCACACGCCUGGCACACAAAUCUCUCUGGGAUUUGACGAGCG---AAAAUUAAUACGAAAUCGAAAAAUCAUUUAC
.--------(((....)))....(((((((........(((.(((....))).)))...(((((((.....))))))).(((.((---..........))...))))))))))...... ( -25.60)
>DroSec_CAF1 78675 107 + 1
U--------GCAAAAAUGCUAAAGAUUU-UUUAAUGAAGCCCGGCACACGCCUGGCACACAAAUCUCUCUGGGAUUUGACGAGCG---AAAAUUAAUACGAAACCGAAAAAUCAUUUAC
.--------(((....)))....(((((-(((......(((.(((....))).)))...(((((((.....))))))).......---.................))))))))...... ( -25.60)
>DroEre_CAF1 91870 107 + 1
U--------GCAAGAAUGCUAGAGAUUU-UUUAAUGAAGCCAGGCACACGCCUGGCACACAAAUCUCCCUGGGAUUUGACGAGCG---AAAAUUAAUGCGAAAUCGAAAAAUCAUUUAC
.--------(((....)))....(((((-((..((...(((((((....)))))))...(((((((.....)))))))....(((---........)))...))..)))))))...... ( -31.00)
>DroWil_CAF1 112052 107 + 1
UUAGGGGGGAAAAAAAUUGGAAAUAUUUUUUUAAUGAAGU---------GACUG---CUAAAAUCUCACUGGGAUUUGACGCGCAGGCGAAAUUAAUAUGAAAUGGAAGAAUCAUUUAC
.(((.((..(.....((((((((....))))))))....)---------..)).---)))((((((.....))))))..(((....)))...........((((((.....)))))).. ( -16.20)
>DroYak_CAF1 81866 108 + 1
U--------GCAAAAAUGCCAAAGAUUUUUUUAAUGAAGCCCGGCACACGCCUGGCACACAAAUCUCUCUGGGAUUUGACGAGCG---AAAAUUAAUACGAAAUCGAAAAAUCAUUUAC
.--------(((....)))....(((((((........(((.(((....))).)))...(((((((.....))))))).(((.((---..........))...))))))))))...... ( -25.20)
>DroAna_CAF1 104924 108 + 1
U--------GGAAAAAUGCAAAAGAUUUUUUUAAUGAAGCCCGGCACACGCCCCGUGGGCAAAUCUCUCUGGGAUUUGACGAACG---AAAAUUAAUAUGAAAUCGAAAAAUCAUUUAC
.--------....(((((.....((((((.(((((...(((((((....)))....))))((((((.....))))))........---...)))))...)))))).......))))).. ( -21.80)
>consensus
U________GCAAAAAUGCUAAAGAUUUUUUUAAUGAAGCCCGGCACACGCCUGGCACACAAAUCUCUCUGGGAUUUGACGAGCG___AAAAUUAAUACGAAAUCGAAAAAUCAUUUAC
.............(((((.....((((((.(((((...(((.(((....))).)))...(((((((.....))))))).............)))))...)))))).......))))).. (-16.19 = -17.67 +   1.47) 

alignment

Postscript

secondary structure

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dotplot

Postscript


Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:36:22 2006