Locus 4612

Sequence ID 3R_DroMel_CAF1
Location 12,127,672 – 12,127,821
Length 149
Max. P 0.999630
window7580 window7581 window7582

overview

Window 0

Location 12,127,672 – 12,127,792
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 95.22
Mean single sequence MFE -29.14
Consensus MFE -28.70
Energy contribution -28.12
Covariance contribution -0.58
Combinations/Pair 1.12
Mean z-score -1.73
Structure conservation index 0.98
SVM decision value 3.31
SVM RNA-class probability 0.998983
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12127672 120 + 27905053
AUAGCGUAUUGAAUAAUCCGAGUCAGGAUUAUAUCCAGCAGGCAACGUCGCAGCAUACGUUGCGUUAUCCUCCAUCCGCGUCGAUGUUGACGCCAACACCAACUACAAACACACCGACAC
...((.(.(((.(((((((......)))))))...))).).))...((((((((....)))))..............((((((....))))))......................))).. ( -28.90)
>DroVir_CAF1 40973 120 + 1
AUAGCGUAUUGAAUAAUCCGAGUCAGGAUUACAUACAACAGGCAACGUCGCAGCACACGUUGCGUUAUCCUCCAUCCGCGUCGAUGUUGACGCCAACACCAACUACAAAUACACCGACAC
...((.(.(((..((((((......))))))....))).).))...((((((((....)))))..............((((((....))))))......................))).. ( -27.80)
>DroPse_CAF1 38663 120 + 1
AUAGCGUAUUGAAUAAUCCGAGUCAGGAUUACAUCCAGCAGGCAACGUCGCAGCACACGCUGCGUUAUCCUCCAUCCGCGUCGAUGCUGACGCCCACACCAACUACAAACACACCGACAC
...((((......((((((......))))))....(((((..(.((((((((((....)))))).............)))).).)))))))))........................... ( -30.61)
>DroGri_CAF1 44275 120 + 1
AUAGCGUAUUGAAUAAUCCGAGUCAGGAUUACAUACAACAAGCAACGUCGCAGCACACGUUGCGUUAUCCUCCAUCCGCGUCGAUGUUGACGCCAACACCAACUACAAAUACACCGACAC
(((((((((....((((((......)))))).)))).....(((((((........)))))))))))).........((((((....))))))........................... ( -27.40)
>DroWil_CAF1 39734 120 + 1
AUAGCGUAUUGAAUAAUCCAAGUCAGGAUUAUAUACAGCAGGCGACGUCGCAGCAUACGUUGCGUUAUCCUCCAUCCGCGUCAAUGUUGACGCCAACACCAACUACAAAUACACCGACAC
...((((((...(((((((......))))))))))).)).(....)((((((((....)))))..............((((((....))))))......................))).. ( -29.50)
>DroPer_CAF1 37104 120 + 1
AUAGCGUAUUGAAUAAUCCGAGUCAGGAUUACAUCCAGCAGGCAACGUCGCAGCACACGCUGCGUUAUCCUCCAUCCGCGUCGAUGCUGACGCCCACACCAACUACAAACACACCGACAC
...((((......((((((......))))))....(((((..(.((((((((((....)))))).............)))).).)))))))))........................... ( -30.61)
>consensus
AUAGCGUAUUGAAUAAUCCGAGUCAGGAUUACAUACAGCAGGCAACGUCGCAGCACACGUUGCGUUAUCCUCCAUCCGCGUCGAUGUUGACGCCAACACCAACUACAAACACACCGACAC
...((.(.(((..((((((......))))))....))).).))...((((((((....)))))..............((((((....))))))......................))).. (-28.70 = -28.12 +  -0.58)

alignment

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secondary structure

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dotplot

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Window 1

Location 12,127,672 – 12,127,792
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 95.22
Mean single sequence MFE -40.17
Consensus MFE -36.83
Energy contribution -35.92
Covariance contribution -0.91
Combinations/Pair 1.19
Mean z-score -1.35
Structure conservation index 0.92
SVM decision value 0.98
SVM RNA-class probability 0.893483
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12127672 120 - 27905053
GUGUCGGUGUGUUUGUAGUUGGUGUUGGCGUCAACAUCGACGCGGAUGGAGGAUAACGCAACGUAUGCUGCGACGUUGCCUGCUGGAUAUAAUCCUGACUCGGAUUAUUCAAUACGCUAU
.....((((((((....((((((((((....))))))))))((((.....(.....)(((((((........)))))))))))..((.(((((((......))))))))))))))))).. ( -40.00)
>DroVir_CAF1 40973 120 - 1
GUGUCGGUGUAUUUGUAGUUGGUGUUGGCGUCAACAUCGACGCGGAUGGAGGAUAACGCAACGUGUGCUGCGACGUUGCCUGUUGUAUGUAAUCCUGACUCGGAUUAUUCAAUACGCUAU
.....((((((((.((((((.(.(((.(((((......)))))((((.....((((((((((((........)))))))..))))).....)))).))).).))))))..)))))))).. ( -41.20)
>DroPse_CAF1 38663 120 - 1
GUGUCGGUGUGUUUGUAGUUGGUGUGGGCGUCAGCAUCGACGCGGAUGGAGGAUAACGCAGCGUGUGCUGCGACGUUGCCUGCUGGAUGUAAUCCUGACUCGGAUUAUUCAAUACGCUAU
.....((((((((.((((((.(.((..(((((......)))))......(((((..((((((....))))))((((..((....)))))).))))).)).).))))))..)))))))).. ( -40.40)
>DroGri_CAF1 44275 120 - 1
GUGUCGGUGUAUUUGUAGUUGGUGUUGGCGUCAACAUCGACGCGGAUGGAGGAUAACGCAACGUGUGCUGCGACGUUGCUUGUUGUAUGUAAUCCUGACUCGGAUUAUUCAAUACGCUAU
.....((((((((.((((((.(.(((.(((((......)))))((((.....((((((((((((........)))))))..))))).....)))).))).).))))))..)))))))).. ( -41.20)
>DroWil_CAF1 39734 120 - 1
GUGUCGGUGUAUUUGUAGUUGGUGUUGGCGUCAACAUUGACGCGGAUGGAGGAUAACGCAACGUAUGCUGCGACGUCGCCUGCUGUAUAUAAUCCUGACUUGGAUUAUUCAAUACGCUAU
.....((((((((..((((.((((((.((((((....)))))).)))....(((..((((........))))..)))))).))))...(((((((......)))))))..)))))))).. ( -37.80)
>DroPer_CAF1 37104 120 - 1
GUGUCGGUGUGUUUGUAGUUGGUGUGGGCGUCAGCAUCGACGCGGAUGGAGGAUAACGCAGCGUGUGCUGCGACGUUGCCUGCUGGAUGUAAUCCUGACUCGGAUUAUUCAAUACGCUAU
.....((((((((.((((((.(.((..(((((......)))))......(((((..((((((....))))))((((..((....)))))).))))).)).).))))))..)))))))).. ( -40.40)
>consensus
GUGUCGGUGUAUUUGUAGUUGGUGUUGGCGUCAACAUCGACGCGGAUGGAGGAUAACGCAACGUGUGCUGCGACGUUGCCUGCUGGAUGUAAUCCUGACUCGGAUUAUUCAAUACGCUAU
.....((((((((....((((((((((....))))))))))((((.....(.....)(((((((........))))))))))).....(((((((......)))))))..)))))))).. (-36.83 = -35.92 +  -0.91)

alignment

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secondary structure

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dotplot

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Window 2

Location 12,127,712 – 12,127,821
Length 109
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 89.32
Mean single sequence MFE -23.80
Consensus MFE -23.65
Energy contribution -23.15
Covariance contribution -0.50
Combinations/Pair 1.17
Mean z-score -2.32
Structure conservation index 0.99
SVM decision value 3.81
SVM RNA-class probability 0.999630
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12127712 109 + 27905053
GGCAACGUCGCAGCAUACGUUGCGUUAUCCUCCAUCCGCGUCGAUGUUGACGCCAACACCAACUACAAACACACCGACACUUCCGUUGUAAUUUAU----AUAAAUAUAAA-GC------
.((((((.((((((....)))))).............((((((....))))))..............................))))))..(((((----(....))))))-..------ ( -23.00)
>DroPse_CAF1 38703 115 + 1
GGCAACGUCGCAGCACACGCUGCGUUAUCCUCCAUCCGCGUCGAUGCUGACGCCCACACCAACUACAAACACACCGACACUUCCGUUGUAAUUUAU----AUAAAUAUAAA-ACAAACAC
.((((((.((((((....)))))).............((((((....))))))..............................))))))..(((((----(....))))))-........ ( -25.60)
>DroGri_CAF1 44315 114 + 1
AGCAACGUCGCAGCACACGUUGCGUUAUCCUCCAUCCGCGUCGAUGUUGACGCCAACACCAACUACAAAUACACCGACACUUCCGUUGUAAUUUAUAUAUAUAAAUACAGAAAC------
.((((((.((((((....)))))).............((((((....))))))..............................)))))).((((((....))))))........------ ( -22.80)
>DroWil_CAF1 39774 109 + 1
GGCGACGUCGCAGCAUACGUUGCGUUAUCCUCCAUCCGCGUCAAUGUUGACGCCAACACCAACUACAAAUACACCGACACUUCCGUUGUAAUUUAU----AUAAAUAUAAA-AC------
.((((((.((((((....)))))).............((((((....))))))..............................))))))..(((((----(....))))))-..------ ( -23.40)
>DroAna_CAF1 29648 108 + 1
GGCAACGUCGCAGCACACGUUGCGUUAUCCUCCAUCCGCGUCGAUGCUGACGCCCACACCAACUACAAACACACCGACACUUCCGUUGUAAUUAA-----AAGAUUAAAAA-AA------
.((((((.((((((....)))))).............((((((....))))))..............................))))))......-----...........-..------ ( -22.40)
>DroPer_CAF1 37144 115 + 1
GGCAACGUCGCAGCACACGCUGCGUUAUCCUCCAUCCGCGUCGAUGCUGACGCCCACACCAACUACAAACACACCGACACUUCCGUUGUAAUUUAU----AUUAAUAUAAA-ACAAACAC
.((((((.((((((....)))))).............((((((....))))))..............................))))))..(((((----(....))))))-........ ( -25.60)
>consensus
GGCAACGUCGCAGCACACGUUGCGUUAUCCUCCAUCCGCGUCGAUGCUGACGCCAACACCAACUACAAACACACCGACACUUCCGUUGUAAUUUAU____AUAAAUAUAAA_AC______
.((((((.((((((....)))))).............((((((....))))))..............................))))))............................... (-23.65 = -23.15 +  -0.50)

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 11:34:38 2006