Locus 4043

Sequence ID 3R_DroMel_CAF1
Location 11,035,614 – 11,035,774
Length 160
Max. P 0.773079
window6474 window6475

overview

Window 4

Location 11,035,614 – 11,035,734
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 81.67
Mean single sequence MFE -36.08
Consensus MFE -23.61
Energy contribution -23.03
Covariance contribution -0.58
Combinations/Pair 1.43
Mean z-score -2.13
Structure conservation index 0.65
SVM decision value 0.53
SVM RNA-class probability 0.773079
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11035614 120 + 27905053
GCUCAACUCCGCCGGCCAAAUCAUUGACAACAACAUACCCAAUCCACACCAGAAGGAGUACCUGAAGGUGUUUUUCCUGGUGCUACAGGUGUGCUACUACCUGGCCCUCGGGCAGGUAAA
(((....((((..(((((.....(((....)))((((((.......((((((.(((((((((....))))))))).)))))).....))))))........)))))..))))..)))... ( -35.10)
>DroVir_CAF1 8536 120 + 1
GCUUAAUUCAGCGGGCCAGAUAAUCGACAAUAACAUACCCAAUCCGCAUCAGAAGGAGUAUCUCAAGGUGUUUUUCCUGGUGCUGCAAGUGUGCUACUAUCUGGCACUGGGGCAGGUCAA
((((..(((((...((((((((.......................(((((((.(((((((((....))))))))).))))))).(((....)))...)))))))).)))))..))))... ( -35.50)
>DroPse_CAF1 9139 120 + 1
GCUGAACACCGCGGGACAAAUAAUCGACAAUAACAUACCUAAUCCGCACCAGAAGGAGUAUCUGAAAGUGUUCUUCCUUGUCCUGCAGGUCUGCUACUACCUGGCCCUGGGCCAGGUCAA
((.((...(.(((((((((......((((.....((((....(((.........))))))).......)))).....))))))))).).)).))....((((((((...))))))))... ( -35.70)
>DroGri_CAF1 11036 120 + 1
GCUCAAUUCAGCGGGUCAAAUUAUCGACAAUAAUAUACCCAAUCCGCAUCAGAAGGAGUAUCUCAAGGUGUUCUUUCUGGUGUUGCAAGUGUGCUACUAUUUGGCACUCGGCCAGGUGAA
((.((.....((((((...(((((.....)))))..)))).....(((((((((((((((((....))))))))))))))))).))...)).))...((((((((.....)))))))).. ( -38.50)
>DroWil_CAF1 20051 120 + 1
ACUCAAUUCGGCUGGACAGAUUAUUGAUAAUAAUAUACCCAAUCCACAUCAAAAGGAAUAUCUUAAGGUAUUCUUUUUGGUCCUACAAGUUUGCUAUUAUUUGGCCCUGGGCCAAGUGAA
.........((((((....(((((.....)))))....)))......(((((((((((((((....)))))))))))))))...........))).((((((((((...)))))))))). ( -32.80)
>DroAna_CAF1 8720 120 + 1
CCUCAAUUCCGCCGGCCAGAUAAUCGACAACAACAUCCCCAAUCCGCACCAAAAGGAGUACCUUAAGGUGUUCUUCUUGGUGCUUCAGGUGUGCUAUUACCUGGCUCUAGGUCAGGUUAA
..........((((((((((.........................(((((((.(((((((((....))))))))).))))))).(((((((......))))))).))).)))).)))... ( -38.90)
>consensus
GCUCAAUUCCGCGGGCCAAAUAAUCGACAAUAACAUACCCAAUCCGCACCAGAAGGAGUAUCUCAAGGUGUUCUUCCUGGUGCUGCAAGUGUGCUACUACCUGGCCCUGGGCCAGGUCAA
.................................(((((.......(((((((.(((((((((....))))))))).))))))).....))))).....(((((((.....)))))))... (-23.61 = -23.03 +  -0.58)

alignment

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secondary structure

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dotplot

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Window 5

Location 11,035,654 – 11,035,774
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 81.56
Mean single sequence MFE -35.12
Consensus MFE -24.10
Energy contribution -22.80
Covariance contribution -1.30
Combinations/Pair 1.45
Mean z-score -1.42
Structure conservation index 0.69
SVM decision value 0.07
SVM RNA-class probability 0.567696
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11035654 120 + 27905053
AAUCCACACCAGAAGGAGUACCUGAAGGUGUUUUUCCUGGUGCUACAGGUGUGCUACUACCUGGCCCUCGGGCAGGUAAAAACGGUGAAGCCUAGUCUCAAACAGCUGCAGAUGUCCAUA
......((((((.(((((((((....))))))))).))))))((.(((.(((((((.((((((.((....)))))))).....((.....)))))).....))).))).))......... ( -37.10)
>DroVir_CAF1 8576 120 + 1
AAUCCGCAUCAGAAGGAGUAUCUCAAGGUGUUUUUCCUGGUGCUGCAAGUGUGCUACUAUCUGGCACUGGGGCAGGUCAAGACGGUGAAGCCCAGUUUAAAGCAGCUGCAAAUGUCCAUA
.....(((((((.(((((((((....))))))))).)))))(((((....((((((.....))))))..((((...(((......))).))))........))))).))........... ( -35.60)
>DroPse_CAF1 9179 120 + 1
AAUCCGCACCAGAAGGAGUAUCUGAAAGUGUUCUUCCUUGUCCUGCAGGUCUGCUACUACCUGGCCCUGGGCCAGGUCAAGACCGUCAAGCCCAGCCUUAAGCAGCUCCAGAUGUCGAUA
.(((.(((...((((((.(((......)))))))))((.(..((((.(((((......((((((((...))))))))..)))))...(((......)))..))))..).)).))).))). ( -34.40)
>DroGri_CAF1 11076 120 + 1
AAUCCGCAUCAGAAGGAGUAUCUCAAGGUGUUCUUUCUGGUGUUGCAAGUGUGCUACUAUUUGGCACUCGGCCAGGUGAAGACGGUGAAGCCCAGCUUGAAACAGCUCCAGAUGUCCAUA
.....(((((((((((((((((....))))))))))))((.(((((((((((.((..((((((((.....)))))))).))))((.....))..)))))...)))).)).)))))..... ( -36.40)
>DroWil_CAF1 20091 120 + 1
AAUCCACAUCAAAAGGAAUAUCUUAAGGUAUUCUUUUUGGUCCUACAAGUUUGCUAUUAUUUGGCCCUGGGCCAAGUGAAGACAGUGAAGCCAAGCCUAAAGCAAUUACAAAUGUCCAUA
....((((((((((((((((((....))))))))))))))).......((((....((((((((((...)))))))))))))).))).......((.....))................. ( -31.70)
>DroAna_CAF1 8760 120 + 1
AAUCCGCACCAAAAGGAGUACCUUAAGGUGUUCUUCUUGGUGCUUCAGGUGUGCUAUUACCUGGCUCUAGGUCAGGUUAAAACAGUAAAACCCAGCCUUAAACAACUUCAAAUGUCCAUC
.....(((((((.(((((((((....))))))))).))))))).(((((((......)))))))....((((..((((..........))))..))))...................... ( -35.50)
>consensus
AAUCCGCACCAGAAGGAGUAUCUCAAGGUGUUCUUCCUGGUGCUGCAAGUGUGCUACUACCUGGCCCUGGGCCAGGUCAAGACGGUGAAGCCCAGCCUAAAACAGCUCCAAAUGUCCAUA
.....(((((((.(((((((((....))))))))).)))))))...((((..(((((((((((((.....)))))))......)))..)))...))))...................... (-24.10 = -22.80 +  -1.30)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:16:35 2006