Locus 4634

Sequence ID 3L_DroMel_CAF1
Location 13,171,947 – 13,172,052
Length 105
Max. P 0.991354
window7274 window7275

overview

Window 4

Location 13,171,947 – 13,172,052
Length 105
Sequences 5
Columns 117
Reading direction forward
Mean pairwise identity 92.29
Mean single sequence MFE -29.22
Consensus MFE -23.98
Energy contribution -23.62
Covariance contribution -0.36
Combinations/Pair 1.10
Mean z-score -1.38
Structure conservation index 0.82
SVM decision value 0.17
SVM RNA-class probability 0.616346
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13171947 105 + 23771897
AGUGCUUGUGUUUGGAAAGCAAAUAUUUUCUGACAAGUGGAAGUCAGAUGUCAUAUAUAUGCCAGGGGACUGGAAUCUGGUUUUGGAUCG------------GGAUCGGGGGAUUGC
..(((((.........)))))...(((..(((((...(.(((..(((((..(((....)))((((....)))).)))))..))).)....------------.).))))..)))... ( -27.70)
>DroSec_CAF1 23537 105 + 1
AGUGCUUGUGUUUGGAAAGCAAAUAUUUUCUGACAAGUGGAAGUCAGAUGUCAUAUAUAUGCCAGGGGACUGGAAUCUGGUUUCGGAUCG------------GGAUUGGGGGAUUGC
..(((((.........))))).......((((((........)))))).(((.........((((....))))..((..((..((...))------------..))..)).)))... ( -27.90)
>DroSim_CAF1 21699 105 + 1
AGUGCUUGUGUUUGGAAAGCAAAUAUUUUCUGACAAGUGGAAGUCAGAUGUCAUAUAUAUGCCAGGGGACUGGAAUCUGGUUUCGGAUCG------------GGAUCGGGGGAUUGC
..(((((.........))))).......((((((........)))))).(((.........((((....))))..((((((..((...))------------..)))))).)))... ( -29.40)
>DroEre_CAF1 26594 110 + 1
AGUGGUUGUGUUUGGAAAGCAAAUAUUUUCUGACAAGUGGAAGUCAGAUGUCAUAUAUAUGCCAGGGGAC-GGAAUCUGGUUUUGGAUCG------GGAUCUGGAUCGGGGGAUUGC
.(..((((((((((.....)))))))..((((((........)))))).............((..((..(-(((.(((((((...)))))------)).))))..))..)))))..) ( -27.70)
>DroYak_CAF1 22306 117 + 1
AGUGGUUGUAUUUGGAAAGCAAAUAUUUUCUGACAAGUGGAAGUCAGAUGUCAUAUAUAUGCCAGGGGACUGGAAUCUGGUUUUGGAUCGGCAACGGGAUAGGGAUCGGGGGAUUGC
.(..((((((((((.....)))))))..((((((........)))))).............((((....))))..(((((((((...(((....)))....))))))))).)))..) ( -33.40)
>consensus
AGUGCUUGUGUUUGGAAAGCAAAUAUUUUCUGACAAGUGGAAGUCAGAUGUCAUAUAUAUGCCAGGGGACUGGAAUCUGGUUUUGGAUCG____________GGAUCGGGGGAUUGC
.(((...(((((((.....)))))))..((((((........))))))...))).......((((....))))(((((....((.((((..............)))).))))))).. (-23.98 = -23.62 +  -0.36)

alignment

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secondary structure

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dotplot

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Window 5

Location 13,171,947 – 13,172,052
Length 105
Sequences 5
Columns 117
Reading direction reverse
Mean pairwise identity 92.29
Mean single sequence MFE -16.96
Consensus MFE -14.80
Energy contribution -14.80
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.97
Structure conservation index 0.87
SVM decision value 2.26
SVM RNA-class probability 0.991354
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13171947 105 - 23771897
GCAAUCCCCCGAUCC------------CGAUCCAAAACCAGAUUCCAGUCCCCUGGCAUAUAUAUGACAUCUGACUUCCACUUGUCAGAAAAUAUUUGCUUUCCAAACACAAGCACU
((........(((..------------.((((........))))...)))....((((...((((....((((((........))))))..)))).))))............))... ( -16.60)
>DroSec_CAF1 23537 105 - 1
GCAAUCCCCCAAUCC------------CGAUCCGAAACCAGAUUCCAGUCCCCUGGCAUAUAUAUGACAUCUGACUUCCACUUGUCAGAAAAUAUUUGCUUUCCAAACACAAGCACU
((.(((.........------------.)))..((((.(((((.((((....)))).............((((((........))))))....))))).)))).........))... ( -16.30)
>DroSim_CAF1 21699 105 - 1
GCAAUCCCCCGAUCC------------CGAUCCGAAACCAGAUUCCAGUCCCCUGGCAUAUAUAUGACAUCUGACUUCCACUUGUCAGAAAAUAUUUGCUUUCCAAACACAAGCACU
((........(((..------------..))).((((.(((((.((((....)))).............((((((........))))))....))))).)))).........))... ( -18.70)
>DroEre_CAF1 26594 110 - 1
GCAAUCCCCCGAUCCAGAUCC------CGAUCCAAAACCAGAUUCC-GUCCCCUGGCAUAUAUAUGACAUCUGACUUCCACUUGUCAGAAAAUAUUUGCUUUCCAAACACAACCACU
((((......((((.......------.)))).....((((.....-.....)))).............((((((........))))))......)))).................. ( -16.80)
>DroYak_CAF1 22306 117 - 1
GCAAUCCCCCGAUCCCUAUCCCGUUGCCGAUCCAAAACCAGAUUCCAGUCCCCUGGCAUAUAUAUGACAUCUGACUUCCACUUGUCAGAAAAUAUUUGCUUUCCAAAUACAACCACU
((((......((((..((......))..)))).........((.((((....)))).))..........((((((........))))))......)))).................. ( -16.40)
>consensus
GCAAUCCCCCGAUCC____________CGAUCCAAAACCAGAUUCCAGUCCCCUGGCAUAUAUAUGACAUCUGACUUCCACUUGUCAGAAAAUAUUUGCUUUCCAAACACAAGCACU
((((.................................((((...........)))).............((((((........))))))......)))).................. (-14.80 = -14.80 +  -0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:29:04 2006