Locus 3511

Sequence ID X_DroMel_CAF1
Location 9,425,109 – 9,425,256
Length 147
Max. P 0.842964
window5746 window5747

overview

Window 6

Location 9,425,109 – 9,425,220
Length 111
Sequences 4
Columns 116
Reading direction reverse
Mean pairwise identity 88.69
Mean single sequence MFE -26.23
Consensus MFE -20.44
Energy contribution -20.31
Covariance contribution -0.13
Combinations/Pair 1.12
Mean z-score -1.67
Structure conservation index 0.78
SVM decision value 0.35
SVM RNA-class probability 0.699648
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9425109 111 - 22224390
GAAACUGCGCACUAAAG----AGUUUGCAAAACGUAUUUUGUUGUUGUGUCGCUCACCAGCGAAUCCAAUAACUAUACUAUGCGAUCUGAGUUUGCGGUAUAA-AAUACAAAAAAA
...((((((.(((..((----(..(((((....((((...(((((((..(((((....)))))...))))))).))))..)))))))).))).))))))....-............ ( -29.60)
>DroSec_CAF1 6886 108 - 1
GAAACUGCGCAUCCAAG----AGUUUGCAAAACGUAUUUUGUUGUUGUGUCGCUCACCAGCGAAUCCAAUAACUAUACUAUGCGAUCUGAGUUUGCGGUAUAA-AAUACAA---AA
...((((((.(..((.(----(..(((((....((((...(((((((..(((((....)))))...))))))).))))..)))))))))..).))))))....-.......---.. ( -27.40)
>DroEre_CAF1 7079 112 - 1
CAAACUGCGUGGAAAAGACAAAGUGUGCAAUACGUAUUUUGUUGUUGUGUUGCUCGCUUGCGAAUCCAAUAACUAUACUAUGCGAUCUGAGUUUGCGGUAUAA-AAUACAA---AA
.........((((...(...(((((.((((((((...........)))))))).))))).)...)))).....((((((..((((.......)))))))))).-.......---.. ( -26.00)
>DroYak_CAF1 7359 108 - 1
GAAACUGCGCAGCAAAG----AGUUUGCAAAACGUAUU-UGUUGUUGUGUUGCUCGCUAACGAAUCCAAUAACUAUACUAUGCGAUCUGAGUUUGCGGCAUAAAAAUACAA---AA
....(((((.(((..((----(..(((((....((((.-.(((((((.(....(((....)))..)))))))).))))..))))))))..)))))))).............---.. ( -21.90)
>consensus
GAAACUGCGCAGCAAAG____AGUUUGCAAAACGUAUUUUGUUGUUGUGUCGCUCACCAGCGAAUCCAAUAACUAUACUAUGCGAUCUGAGUUUGCGGUAUAA_AAUACAA___AA
...((((((((..............)))....(((((...(((((((..((((......))))...)))))))......)))))..........)))))................. (-20.44 = -20.31 +  -0.13)

alignment

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secondary structure

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dotplot

Postscript

Window 7

Location 9,425,148 – 9,425,256
Length 108
Sequences 4
Columns 112
Reading direction reverse
Mean pairwise identity 87.42
Mean single sequence MFE -33.35
Consensus MFE -25.74
Energy contribution -25.43
Covariance contribution -0.31
Combinations/Pair 1.14
Mean z-score -1.96
Structure conservation index 0.77
SVM decision value 0.76
SVM RNA-class probability 0.842964
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9425148 108 - 22224390
ACGCAGUGCUGCACAACGCUGCUGCGAAAGUGUUGCGAAACUGCGCACUAAAG----AGUUUGCAAAACGUAUUUUGUUGUUGUGUCGCUCACCAGCGAAUCCAAUAACUAU
.((((((((........)).))))))...((.((((.(((((.(........)----))))))))).)).......(((((((..(((((....)))))...)))))))... ( -31.90)
>DroSec_CAF1 6922 108 - 1
AUGCAGUGCUGCACAACGUGGCGGCAAAAGUGUUGCGAAACUGCGCAUCCAAG----AGUUUGCAAAACGUAUUUUGUUGUUGUGUCGCUCACCAGCGAAUCCAAUAACUAU
..(((((((..(.....)..)).((((.....))))...)))))(((..(...----.)..)))............(((((((..(((((....)))))...)))))))... ( -31.80)
>DroEre_CAF1 7115 112 - 1
AUGCAGUGUUGCACAACGCUGCGGAGAAAGUGUUGCCAAACUGCGUGGAAAAGACAAAGUGUGCAAUACGUAUUUUGUUGUUGUGUUGCUCGCUUGCGAAUCCAAUAACUAU
(((((((.(((..(((((((........))))))).))))))))))(((...(...(((((.((((((((...........)))))))).))))).)...)))......... ( -36.40)
>DroYak_CAF1 7396 107 - 1
ACGCAGUGCUGCACAACGCUGCGGCGAAAGUGUUGCGAAACUGCGCAGCAAAG----AGUUUGCAAAACGUAUU-UGUUGUUGUGUUGCUCGCUAACGAAUCCAAUAACUAU
.(((((((........)))))))((....))(((((((....(((((((((..----.(..(((.....)))..-).)))))))))...)))).)))............... ( -33.30)
>consensus
ACGCAGUGCUGCACAACGCUGCGGCGAAAGUGUUGCGAAACUGCGCAGCAAAG____AGUUUGCAAAACGUAUUUUGUUGUUGUGUCGCUCACCAGCGAAUCCAAUAACUAU
.((((((....(.(((((((........))))))).)..)))))).............((((...)))).......(((((((..((((......))))...)))))))... (-25.74 = -25.43 +  -0.31)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:01:12 2006