Locus 7283

Sequence ID 2L_DroMel_CAF1
Location 20,407,007 – 20,407,294
Length 287
Max. P 0.926242
window11650 window11651 window11652

overview

Window 0

Location 20,407,007 – 20,407,115
Length 108
Sequences 6
Columns 118
Reading direction forward
Mean pairwise identity 68.91
Mean single sequence MFE -21.30
Consensus MFE -12.78
Energy contribution -12.33
Covariance contribution -0.44
Combinations/Pair 1.25
Mean z-score -1.61
Structure conservation index 0.60
SVM decision value 1.17
SVM RNA-class probability 0.926242
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20407007 108 + 22407834
ACAUUCGUUCACAAUACAUUCGUUGUUCAUAUGAAA----AUGGA--UUGGAGUCAAAGUGGCACACUUAA----UCCAUUUUUAUUUGUGUCUCAAAUGCUCCAAUAUCAAAUGCAA
...(((((..(((((......)))))....))))).----.((((--(((((((....(.((((((..(((----.......)))..)))))).)....)))))))).)))....... ( -24.30)
>DroSec_CAF1 1663 99 + 1
ACAUUCGUUCACAU---------CGCUCAUAUGGAA----AUGGA--UUGGAGUCAAAGUGGCACACUUAA----ACACUUUUUAUUUGUGUCUCAAAUGCUCCAAUAUCAAAUGCAA
....(((((..(((---------.......)))..)----))))(--(((((((....(.((((((..(((----(.....))))..)))))).)....))))))))........... ( -22.30)
>DroSim_CAF1 2658 99 + 1
ACAUUCGUUCACAA---------UGCUCAUAUGGAA----AUGGA--UUGGAGUCAAAGUGGCACACUUAA----UCAGUUUUUAUUUGUGUCUCAAAUGCUCCAAUAUCAAAUGCAA
..............---------(((((((......----))))(--(((((((....(.((((((..(((----.......)))..)))))).)....)))))))).......))). ( -21.60)
>DroEre_CAF1 1621 102 + 1
ACUUUCGUGUACAUUA------UUGCAUAUAUCGU--------CA--UUGGAGUCAAAGUGGCAUUCUUCAAAAAUAAUAUUUGAUCUGUGUCUCAAAUGCUCCAACAUAAACUAGAA
...((((((((.....------.))))).......--------..--(((((((....(.(((((...(((((.......)))))...))))).)....))))))).........))) ( -19.70)
>DroYak_CAF1 1668 101 + 1
ACUUUCGUCUACAUUA------UUGCAUAUAUCGU--------CA--UUGGAGUCAAAGUGGCAUUCUUCAAAAAUAAUAUUCGAUCUGUGUCUCAAAAGCUCCAACAUAAAC-AGAU
......((((.((...------.))..........--------..--(((((((....(.(((((...((.............))...))))).)....))))))).......-)))) ( -13.62)
>DroAna_CAF1 1638 109 + 1
GUGUUUGAAUACAUUA------U---CCUUAAGGUAUAUCCUGUAUCCUGGAGUCAAAGUGGCAUUUAUGGGAACUCUUAUCCGAUUUGUGUCUCAAAUACUCCAAAACAAACUAGUG
..(((((.(((((.((------(---((....)).)))...)))))..((((((....(.(((((..((.(((.......))).))..))))).)....))))))...)))))..... ( -26.30)
>consensus
ACAUUCGUUCACAUUA______UUGCUCAUAUGGAA____AUGGA__UUGGAGUCAAAGUGGCACACUUAA____UCAUAUUUGAUUUGUGUCUCAAAUGCUCCAAUAUAAAAUACAA
...............................................(((((((....(.(((((...(((...........)))...))))).)....)))))))............ (-12.78 = -12.33 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 1

Location 20,407,115 – 20,407,225
Length 110
Sequences 6
Columns 115
Reading direction forward
Mean pairwise identity 68.36
Mean single sequence MFE -21.04
Consensus MFE -14.70
Energy contribution -13.98
Covariance contribution -0.72
Combinations/Pair 1.21
Mean z-score -0.76
Structure conservation index 0.70
SVM decision value 0.05
SVM RNA-class probability 0.560879
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20407115 110 + 22407834
AGGCGAACGGCAUCCUGAAUAAUUAUGCAUAUUAUAACAGAUGACUUGUGUUCGCCUACAAUAGCUCCUGA-----UAGCUUUACAUUCCUUUAUAAGACUCCCGUCUUCGGAGA
((((((((((((((.((.(((((.......)))))..)))))).))...)))))))).....((((.....-----.)))).....((((.....(((((....))))).)))). ( -24.60)
>DroSec_CAF1 1762 110 + 1
AGACGAACGGCAUCCUGAAUAAUUAUGCAUAUUAUAACAGAUGACUUGUGUUCGUCUACAAUAGCUCCUGA-----UAGCUUUACACUCCUUCAUAGAACUCCAGUCCCCGGAGA
((((((((((((((.((.(((((.......)))))..)))))).))...)))))))).....((((.....-----.))))..................((((.......)))). ( -21.90)
>DroSim_CAF1 2757 110 + 1
AGACGAACGGCAUCCUGAAUAAUUAUGCAUAUUAUAACAGAUGACUUGUGUUCGUCUACAAUACCUUCUGA-----UAGCUUUACACUCCUUCUUAGAACUCCAGUCCCCGGAGA
((((((((((((((.((.(((((.......)))))..)))))).))...))))))))........((((((-----.................))))))((((.......)))). ( -20.93)
>DroEre_CAF1 1723 98 + 1
GGUCGAACGGCAUCCUGUAUAAUCCU-CAUAUUAUAGCAGAUGACUUAAGUUGGACUACAAUAGUAUUAAAUGAUUCAGGUCACUAAUUC----------------CCUGGGAGA
((((.(((((((((.((((((((...-...))))).))))))).))...))).)))).................((((((..........----------------))))))... ( -18.30)
>DroYak_CAF1 1769 98 + 1
AGUCGAACGGCAUCCUGGAUAAUCCU-CAUAUUAUAGCAGAUGACUUGUGUUCGACUACAAUAUUAUUAAAUGAUAUAGCUCAAUAAUUC----------------CUCGGGAGA
((((((((((((((.((.(((((...-...)))))..)))))).))...))))))))...(((((((...)))))))..........(((----------------(...)))). ( -18.60)
>DroAna_CAF1 1747 91 + 1
AGACGGACGGCAUCCUGAAUAAUGUAUCCUAUUAUAUCAGAUGACUUGUGUUCGUCUACAUU---------------------CUACCCCUUUUAAGAUCUC---UUUGUGGAGA
((((((((((((((.(((((((((.....)))))).))))))).))...)))))))).....---------------------...............((((---(....))))) ( -21.90)
>consensus
AGACGAACGGCAUCCUGAAUAAUUAUGCAUAUUAUAACAGAUGACUUGUGUUCGUCUACAAUAGCUUCUGA_____UAGCUUUACACUCCUU__UAGAACUC___UCCCCGGAGA
((((((((((((((....(((((.......)))))....)))).))...)))))))).......................................................... (-14.70 = -13.98 +  -0.72)

alignment

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secondary structure

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dotplot

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Window 2

Location 20,407,188 – 20,407,294
Length 106
Sequences 6
Columns 115
Reading direction forward
Mean pairwise identity 68.95
Mean single sequence MFE -21.27
Consensus MFE -15.22
Energy contribution -15.05
Covariance contribution -0.17
Combinations/Pair 1.11
Mean z-score -1.16
Structure conservation index 0.72
SVM decision value 1.05
SVM RNA-class probability 0.906735
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20407188 106 + 22407834
GCUUUACAUUCCUUUAUAAGACUCCCGUCUUCGGAGACAAAGUUUACAUGCUAAGGA---UAAG--AUCUUUUUCGUGUCUACAAUGCUCCAAGAGCAAAUGU----UCGUUUAA
(((((............(((((....))))).((((.((..((..(((((..(((((---(...--))))))..)))))..))..)))))).)))))......----........ ( -25.20)
>DroSec_CAF1 1835 106 + 1
GCUUUACACUCCUUCAUAGAACUCCAGUCCCCGGAGACAAAGUUUACAUGCUAAGGA---UAAG--AUCUUUUUCGUGUCUACAAUGCUCCAAGAGCAAAUGA----UCGUUUAA
(((((......((....)).............((((.((..((..(((((..(((((---(...--))))))..)))))..))..)))))).)))))......----........ ( -20.70)
>DroSim_CAF1 2830 106 + 1
GCUUUACACUCCUUCUUAGAACUCCAGUCCCCGGAGACAAAGUUUACAUGCUAAGGA---UAAG--AUCUUUUUCGUGUCUACAAUGCUCCAAGAGCAAAUGU----UCGUUCAA
..................((((..........((((.((..((..(((((..(((((---(...--))))))..)))))..))..))))))..((((....))----)))))).. ( -24.90)
>DroEre_CAF1 1800 95 + 1
GGUCACUAAUUC----------------CCUGGGAGACAAAGUUUACAUGUAAAAGAUUAUGUGGCUUCUUUUUCGUGUCUACAAUGCUCCAAAAUAAACUGU----UCGUUUAA
............----------------....((((.((..((..(((((.((((((..........)))))).)))))..))..))))))....(((((...----..))))). ( -19.30)
>DroYak_CAF1 1846 92 + 1
GCUCAAUAAUUC----------------CUCGGGAGACAAAGUUUACAUGUUAAGGA---UGUGGCUUCUUUUUCGUGUCUACAAUGCUCCAACAUAAACUGU----UCGUUUAA
............----------------....((((.((..((..(((((..(((((---.......)))))..)))))..))..))))))....(((((...----..))))). ( -19.50)
>DroAna_CAF1 1809 105 + 1
-----CUACCCCUUUUAAGAUCUC---UUUGUGGAGACAAAGUUUACAUGUUGAAGUCCUUACA--AUCUUCCUCGUGUCUACAACGCUCCUAGAACAGCCCCCAACUCGAACGG
-----.....((.((..((.((((---(....)))))....((..(((((..((((........--..))))..)))))..))...(((........)))......))..)).)) ( -18.00)
>consensus
GCUUUACACUCCUU__UAGAACUC___UCCCCGGAGACAAAGUUUACAUGCUAAGGA___UAAG__AUCUUUUUCGUGUCUACAAUGCUCCAAGAGCAAAUGU____UCGUUUAA
................................((((.((..((..(((((..(((((..........)))))..)))))..))..))))))........................ (-15.22 = -15.05 +  -0.17)

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 12:32:14 2006