Locus 7426

Sequence ID 3R_DroMel_CAF1
Location 19,768,843 – 19,768,939
Length 96
Max. P 0.947013
window12004 window12005

overview

Window 4

Location 19,768,843 – 19,768,939
Length 96
Sequences 5
Columns 117
Reading direction forward
Mean pairwise identity 80.15
Mean single sequence MFE -39.84
Consensus MFE -16.71
Energy contribution -17.55
Covariance contribution 0.84
Combinations/Pair 1.14
Mean z-score -2.06
Structure conservation index 0.42
SVM decision value 0.01
SVM RNA-class probability 0.539563
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19768843 96 + 27905053
GUAUAUAUAUGUCGGCUUUUUCGGAGCGCCGAGCUUUUUGCUCUCCGGCGAG--------AGCGGUG----CAAACUUUUCACC------GAAAAGC---UCUGUGGGUGGAGUGCC
.............(((...(((.(..(((.(((((((((((((((....)))--------)))((((----.((....))))))------)))))))---)).)))..).))).))) ( -35.10)
>DroSec_CAF1 8850 96 + 1
GUAUAUAUAUGUCGGCUUUUUCGGAGAGCCGAGCUUUUGGCUCUCUGGCGAG--------AGCGGUG----CAAACUUUUCACC------GAAAAGC---UCUGUGGGUGGAGUGCC
((((.....((((.((((((((((((((((((....)))))))))))).)))--------))).).)----)).....((((((------.(.....---....).)))))))))). ( -34.70)
>DroSim_CAF1 9180 96 + 1
GUAUAUAUAUGUCGGCUUUUUCGGAGAGCCGAGCUUUUGGCUCUCUGGCGAG--------AGCGAUG----CAAACUUUUCACC------GAAAAGC---UCUGUGGGUGGAGUGCC
..........((((.(((((((((((((((((....)))))))))))).)))--------))))))(----((..((.(((((.------((.....---)).))))).))..))). ( -34.80)
>DroEre_CAF1 8866 113 + 1
GCAUAUAUAUGUCGGCUUUUUCGGACCGCCGAGCUUUUGGCUCUCUCGCGAGUGCGCUGGAGAG----GAGUACACCUCUCACCGAGAGCGAAAAGCUCAUCUGCGGGUGGGGUGCC
((((....)))).(((..(..((..((((.((((((((.((((((..(((....)))..(((((----(......))))))...)))))).))))))))....)))).))..).))) ( -50.00)
>DroYak_CAF1 9030 108 + 1
GCAUAUAUAUGUCGGCUUUUUCGGAGCGCCGAGCUUUCGGCUCUCUCGCGAGU-CGCGAGAGCGGUGAGAGCACUCUUCUCUC----AGCU-AAAGC---UCUGCGGGUGGAGUGCC
((.........((((((((....))).)))))(((((((.(.((((((((...-)))))))).).)))))))(((((.(((.(----((..-.....---.))).))).))))))). ( -44.60)
>consensus
GUAUAUAUAUGUCGGCUUUUUCGGAGCGCCGAGCUUUUGGCUCUCUGGCGAG________AGCGGUG____CAAACUUUUCACC______GAAAAGC___UCUGUGGGUGGAGUGCC
.............(((....((((((.(((((....))))).)))))).............................(((((((......................))))))).))) (-16.71 = -17.55 +   0.84)

alignment

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secondary structure

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dotplot

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Window 5

Location 19,768,843 – 19,768,939
Length 96
Sequences 5
Columns 117
Reading direction reverse
Mean pairwise identity 80.15
Mean single sequence MFE -34.98
Consensus MFE -16.84
Energy contribution -17.24
Covariance contribution 0.40
Combinations/Pair 1.11
Mean z-score -2.60
Structure conservation index 0.48
SVM decision value 1.37
SVM RNA-class probability 0.947013
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19768843 96 - 27905053
GGCACUCCACCCACAGA---GCUUUUC------GGUGAAAAGUUUG----CACCGCU--------CUCGCCGGAGAGCAAAAAGCUCGGCGCUCCGAAAAAGCCGACAUAUAUAUAC
(((............((---((((((.------((((.........----))))(((--------(((....)))))).))))))))((....))......)))............. ( -30.70)
>DroSec_CAF1 8850 96 - 1
GGCACUCCACCCACAGA---GCUUUUC------GGUGAAAAGUUUG----CACCGCU--------CUCGCCAGAGAGCCAAAAGCUCGGCUCUCCGAAAAAGCCGACAUAUAUAUAC
(((............((---((((((.------((((.........----))))(((--------(((....)))))).))))))))((....))......)))............. ( -30.40)
>DroSim_CAF1 9180 96 - 1
GGCACUCCACCCACAGA---GCUUUUC------GGUGAAAAGUUUG----CAUCGCU--------CUCGCCAGAGAGCCAAAAGCUCGGCUCUCCGAAAAAGCCGACAUAUAUAUAC
(((.(((........))---).(((((------(((((..(((...----....)))--------.))))).(((((((........))))))).))))).)))............. ( -28.60)
>DroEre_CAF1 8866 113 - 1
GGCACCCCACCCGCAGAUGAGCUUUUCGCUCUCGGUGAGAGGUGUACUC----CUCUCCAGCGCACUCGCGAGAGAGCCAAAAGCUCGGCGGUCCGAAAAAGCCGACAUAUAUAUGC
(((.......((((....((((((((.((((((.(.((((((......)----))))))..(((....))).)))))).)))))))).)))).........)))............. ( -45.19)
>DroYak_CAF1 9030 108 - 1
GGCACUCCACCCGCAGA---GCUUU-AGCU----GAGAGAAGAGUGCUCUCACCGCUCUCGCG-ACUCGCGAGAGAGCCGAAAGCUCGGCGCUCCGAAAAAGCCGACAUAUAUAUGC
(((..((....(((.((---(((((-.(((----(((((.......)))))....((((((((-...)))))))))))..))))))).)))....))....)))............. ( -40.00)
>consensus
GGCACUCCACCCACAGA___GCUUUUC______GGUGAAAAGUUUG____CACCGCU________CUCGCCAGAGAGCCAAAAGCUCGGCGCUCCGAAAAAGCCGACAUAUAUAUAC
(((.................(((((((.........)))))))......................(((....))).)))....(.(((((...........)))))).......... (-16.84 = -17.24 +   0.40)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:45:41 2006