Locus 4390

Sequence ID 3L_DroMel_CAF1
Location 12,864,446 – 12,864,540
Length 94
Max. P 0.791427
window6802 window6803

overview

Window 2

Location 12,864,446 – 12,864,540
Length 94
Sequences 4
Columns 96
Reading direction forward
Mean pairwise identity 90.51
Mean single sequence MFE -16.07
Consensus MFE -14.52
Energy contribution -14.90
Covariance contribution 0.38
Combinations/Pair 1.10
Mean z-score -1.58
Structure conservation index 0.90
SVM decision value 0.59
SVM RNA-class probability 0.791427
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12864446 94 + 23771897
UCACACUGAAAUCUGGUCCUUUUCAACUGAUCCGUUUCAGAUCAGCUGGCCAGCGAUUUCAUCAU-CGACACUACACAGA-CCACUGCCAACACCC
.....(((....((((.((.......((((((.......))))))..))))))((((......))-))........))).-............... ( -16.60)
>DroSec_CAF1 102879 96 + 1
UCACACUGAAAUCUGGCCCUUUUUAACUGAUCCGUUUCAGAUCAGCUGACCAGCGAAUUCACCAUCCGACACUACACAGUUCCACUGCCAUCACAU
.............((((.......(((((...((((((((.....))))..))))...((.......)).......))))).....))))...... ( -12.50)
>DroEre_CAF1 108257 93 + 1
UCACACUGAAAUCUGGCUCUUU-UAACUGAUCCGUUUCAGAUCAGACGGCCAGCGAUUUCACCAU-CGACACUACACAGA-CCACUGCCAACACCC
.....(((....((((((.(((-...((((......))))...))).))))))((((......))-))........))).-............... ( -18.00)
>DroYak_CAF1 114249 93 + 1
UCACACUGAAAUCCGGCUCUUU-UAACUGAUCCGUUUCAGAUCAGAUGGCCAGCGAUUUCACCAU-CGACACCACACAGA-CCACUGCCAACACCC
......((((((((((((.(((-...((((......))))...))).)))).).)))))))....-..........(((.-...)))......... ( -17.20)
>consensus
UCACACUGAAAUCUGGCCCUUU_UAACUGAUCCGUUUCAGAUCAGAUGGCCAGCGAUUUCACCAU_CGACACUACACAGA_CCACUGCCAACACCC
......((((((((((((........((((((.......))))))..)))))..)))))))...............(((.....)))......... (-14.52 = -14.90 +   0.38)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 12,864,446 – 12,864,540
Length 94
Sequences 4
Columns 96
Reading direction reverse
Mean pairwise identity 90.51
Mean single sequence MFE -28.77
Consensus MFE -22.26
Energy contribution -23.08
Covariance contribution 0.81
Combinations/Pair 1.13
Mean z-score -1.85
Structure conservation index 0.77
SVM decision value 0.44
SVM RNA-class probability 0.736640
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12864446 94 - 23771897
GGGUGUUGGCAGUGG-UCUGUGUAGUGUCG-AUGAUGAAAUCGCUGGCCAGCUGAUCUGAAACGGAUCAGUUGAAAAGGACCAGAUUUCAGUGUGA
..(..((((.(.(((-(((..((...(.((-((......)))))..))(((((((((((...)))))))))))....))))))..).))))..).. ( -29.00)
>DroSec_CAF1 102879 96 - 1
AUGUGAUGGCAGUGGAACUGUGUAGUGUCGGAUGGUGAAUUCGCUGGUCAGCUGAUCUGAAACGGAUCAGUUAAAAAGGGCCAGAUUUCAGUGUGA
........(((.(((((...........(((((.....)))))((((((((((((((((...))))))))))......)))))).))))).))).. ( -28.60)
>DroEre_CAF1 108257 93 - 1
GGGUGUUGGCAGUGG-UCUGUGUAGUGUCG-AUGGUGAAAUCGCUGGCCGUCUGAUCUGAAACGGAUCAGUUA-AAAGAGCCAGAUUUCAGUGUGA
.((..(((((((...-.)))).)))..)).-(((.(((((((..(((((..((((((((...))))))))...-...).))))))))))).))).. ( -28.50)
>DroYak_CAF1 114249 93 - 1
GGGUGUUGGCAGUGG-UCUGUGUGGUGUCG-AUGGUGAAAUCGCUGGCCAUCUGAUCUGAAACGGAUCAGUUA-AAAGAGCCGGAUUUCAGUGUGA
(((..(((((.((((-((...(((((.(((-....))).))))).))))))((((((((...))))))))...-.....)))))..)))....... ( -29.00)
>consensus
GGGUGUUGGCAGUGG_UCUGUGUAGUGUCG_AUGGUGAAAUCGCUGGCCAGCUGAUCUGAAACGGAUCAGUUA_AAAGAGCCAGAUUUCAGUGUGA
.......((((.((........)).))))..(((.(((((((..(((((((((((((((...))))))))))......)))))))))))).))).. (-22.26 = -23.08 +   0.81)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:21:24 2006