Locus 10235

Sequence ID 3R_DroMel_CAF1
Location 27,428,007 – 27,428,135
Length 128
Max. P 0.935817
window16310 window16311

overview

Window 0

Location 27,428,007 – 27,428,109
Length 102
Sequences 6
Columns 116
Reading direction reverse
Mean pairwise identity 77.43
Mean single sequence MFE -26.73
Consensus MFE -15.10
Energy contribution -14.30
Covariance contribution -0.80
Combinations/Pair 1.20
Mean z-score -1.60
Structure conservation index 0.56
SVM decision value 0.08
SVM RNA-class probability 0.573588
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27428007 102 - 27905053
-----GCCAAGGACUGCGAGAACGAAAGGACGA-AUUCCGCUCCCUUCCACUUCUCCUCCUUGC-----G-AUUUCAUCUG-GGCCUAGUUUUCUUUUUGCACUUU-CCCGACACU
-----((.(((((..(.(((((.(((.(((((.-....)).))).)))...)))))))))))))-----.-........((-((...(((...........)))..-))))..... ( -21.20)
>DroPse_CAF1 3320 106 - 1
AG---AGAGAGGACUGCGAGAACGAAAGCGAGACAUCCUGCUCAUUUCCACUUCUCCUCCUCCUCAUACGCAUAUUGUGUGUGGCCUAGUUUUCUUU-UGCAA------CGGCACU
.(---(((((((((((((((((.((((..(((.(.....)))).))))...)))))........(((((((.....)))))))))..))))))))))-)((..------..))... ( -29.80)
>DroEre_CAF1 3280 102 - 1
-----GCCAAGGACUGCGAGAACGAAAGGACGA-AUUCCGCUCCUUUCCACUUCUCCUCCUUGC-----G-AUUUUAUCUG-GGCCUAGUUUUCUUUUUGCACUUU-CCCGACACU
-----((.(((((..(.(((((.(((((((((.-....)).)))))))...)))))))))))))-----.-........((-((...(((...........)))..-))))..... ( -25.30)
>DroYak_CAF1 5938 102 - 1
-----GCCAAGGACUGCGAGAACGAAAGGACGA-AUACCGCUCCUUUCCACUUCUCCUCCUUGC-----G-AUUUUCUCUG-GGCCUAGUUUUCUUUUUGCACUUU-CCCGACACU
-----((.(((((..(.(((((.(((((((((.-....)).)))))))...)))))))))))))-----.-........((-((...(((...........)))..-))))..... ( -25.30)
>DroAna_CAF1 2891 104 - 1
UGGAAGUCAAGGACUGCGAGAACGAAAGGACGA-GCCCCUCUCCUUUCCACUUCUCCUCCUUGCCC---G-AUU-----CA-GGCCUAGUUUUCUUU-UGCAAUCUCCUCGACACU
.....(((.((((.((((((((.(((((((.((-(...))))))))))...)))))...((.(((.---.-...-----..-)))..))........-.)))...)))).)))... ( -29.00)
>DroPer_CAF1 3334 106 - 1
AG---AGAGAGGACUGCGAGAACGAAAGCGAGACAUCCUGCUCAUUUCCACUUCUCCUCCUCCUCAUACGCAUAUUGUGUGUGGCCUAGUUUUCUUU-UGCAA------CGGCACU
.(---(((((((((((((((((.((((..(((.(.....)))).))))...)))))........(((((((.....)))))))))..))))))))))-)((..------..))... ( -29.80)
>consensus
_____GCCAAGGACUGCGAGAACGAAAGGACGA_AUCCCGCUCCUUUCCACUUCUCCUCCUUGC_____G_AUUUUAUCUG_GGCCUAGUUUUCUUU_UGCAAUUU_CCCGACACU
.....((.(((((..(.(((((.(((((((.(........))))))))...)))))))))))))...................((..((....))....))............... (-15.10 = -14.30 +  -0.80)

alignment

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secondary structure

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dotplot

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Window 1

Location 27,428,045 – 27,428,135
Length 90
Sequences 6
Columns 103
Reading direction reverse
Mean pairwise identity 78.94
Mean single sequence MFE -23.60
Consensus MFE -15.00
Energy contribution -14.20
Covariance contribution -0.80
Combinations/Pair 1.24
Mean z-score -2.24
Structure conservation index 0.64
SVM decision value 1.25
SVM RNA-class probability 0.935817
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27428045 90 - 27905053
GCUGAAAAUAAAAG-CAAACAAAAUUU-----GCCAAGGACUGCGAGAACGAAAGGACGA-AUUCCGCUCCCUUCCACUUCUCCUCCUUGC-----G-AUUUC
(((.........))-).........((-----((.(((((..(.(((((.(((.(((((.-....)).))).)))...)))))))))))))-----)-).... ( -20.80)
>DroPse_CAF1 3353 100 - 1
GCUGAAAAUAAAAGUCAAACAAGCGAGAG---AGAGAGGACUGCGAGAACGAAAGCGAGACAUCCUGCUCAUUUCCACUUCUCCUCCUCCUCAUACGCAUAUU
......................(((...(---((.(((((..(.(((((.((((..(((.(.....)))).))))...))))))))))))))...)))..... ( -23.60)
>DroEre_CAF1 3318 90 - 1
GCUGAAAAUAAAAG-CAAACAAAAUUU-----GCCAAGGACUGCGAGAACGAAAGGACGA-AUUCCGCUCCUUUCCACUUCUCCUCCUUGC-----G-AUUUU
(((.........))-).....(((.((-----((.(((((..(.(((((.(((((((((.-....)).)))))))...)))))))))))))-----)-).))) ( -25.00)
>DroYak_CAF1 5976 90 - 1
GCUGAAAAUAAAAG-CAAACAAAAUUU-----GCCAAGGACUGCGAGAACGAAAGGACGA-AUACCGCUCCUUUCCACUUCUCCUCCUUGC-----G-AUUUU
(((.........))-).....(((.((-----((.(((((..(.(((((.(((((((((.-....)).)))))))...)))))))))))))-----)-).))) ( -25.00)
>DroAna_CAF1 2926 95 - 1
GCUGAAAAUAGAAU-CAAACAAUCUUUUGGAAGUCAAGGACUGCGAGAACGAAAGGACGA-GCCCCUCUCCUUUCCACUUCUCCUCCUUGCCC---G-AUU--
..............-...........((((..(.((((((..(.(((((.(((((((.((-(...))))))))))...)))))))))))))))---)-)..-- ( -23.60)
>DroPer_CAF1 3367 100 - 1
GCUGAAAAUAAAAGUCAAACAAGCGAGAG---AGAGAGGACUGCGAGAACGAAAGCGAGACAUCCUGCUCAUUUCCACUUCUCCUCCUCCUCAUACGCAUAUU
......................(((...(---((.(((((..(.(((((.((((..(((.(.....)))).))))...))))))))))))))...)))..... ( -23.60)
>consensus
GCUGAAAAUAAAAG_CAAACAAAAUUU_____GCCAAGGACUGCGAGAACGAAAGGACGA_AUCCCGCUCCUUUCCACUUCUCCUCCUUGC_____G_AUUUU
................................((.(((((..(.(((((.(((((((.(........))))))))...)))))))))))))............ (-15.00 = -14.20 +  -0.80)

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 13:52:15 2006