Locus 2284

Sequence ID 2L_DroMel_CAF1
Location 6,177,714 – 6,177,857
Length 143
Max. P 0.868736
window3668 window3669

overview

Window 8

Location 6,177,714 – 6,177,826
Length 112
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 83.23
Mean single sequence MFE -41.12
Consensus MFE -29.88
Energy contribution -34.32
Covariance contribution 4.44
Combinations/Pair 1.12
Mean z-score -1.79
Structure conservation index 0.73
SVM decision value 0.39
SVM RNA-class probability 0.716676
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6177714 112 + 22407834
--------CCGCUGAUUUCUUUGACUGCCGGGCAGGCGAACAAGCCGUUUGACAGACAGCGCAUGCCCAACGGCUUUGGCCGGAAUGGGUAUGAGUUAUGGUUGGAAGUUGGCAAUGCUU
--------..((..((((((....(((.(((((.(((......)))))))).)))..(((.((((((((.((((....))))...)))))))).)))......))))))..))....... ( -46.00)
>DroSec_CAF1 14096 104 + 1
--------CCGCUGAUUUGUUUGACUGCCGGGCAGGCGAACAAGCCGUUUGACAGACAGCGCAUGCCCAACGGCUUCGGCCGGAAUGGGUAUGAGUUAUGGUUGGAAGUUGG--------
--------((((((.((((((.((((((...)))(((......)))))).)))))))))).((((((((.((((....))))...))))))))..........)).......-------- ( -44.00)
>DroSim_CAF1 23572 104 + 1
--------CCGCUGAUUUGUUUGAUGGCCGGGCAGGCGAACAAGCCGUUUGAUAGACAGCGCAUGCCCAACGGCUUCGGCCGGAAUGGGUAUGAGUUAUGGUUGGAAGUUGG--------
--------((((((.((((((.((((((..(.........)..)))))).)))))))))).((((((((.((((....))))...))))))))..........)).......-------- ( -42.70)
>DroEre_CAF1 13814 101 + 1
--------CCGCUGAUUUGUUUAACUGCC--------UAACAUGCCGCUUGACAGACAGCGCAUGCCCAACGGCUUCGG--GUACUGGGUAUGAGUUAUGGUUGGAAGUUGGCAAUGCC-
--------..((..((((.(......(((--------((((....((((........))))((((((((..(.(....)--.)..)))))))).)))).))).).))))..))......- ( -30.70)
>DroYak_CAF1 24704 119 + 1
CGGCUCCUCCGCUGAUUUGUUUAACUGCCGGGCAGGCAAACAAGCUGCUUGACAGACAGCGCAUGCCCAACUGCUUCGGCUGCACUGGGUAUGAGUUAUGGCUGGAAGUUGGCAAUGCC-
.(((......((..((((......(((.(((((((.(......)))))))).))).((((.((((((((...((....)).....)))))))).......)))).))))..))...)))- ( -42.20)
>consensus
________CCGCUGAUUUGUUUGACUGCCGGGCAGGCGAACAAGCCGUUUGACAGACAGCGCAUGCCCAACGGCUUCGGCCGGAAUGGGUAUGAGUUAUGGUUGGAAGUUGGCAAUGC__
..........((..((((......(((.(((((.(((......)))))))).)))..(((.((((((((.((((....))))...)))))))).)))........))))..))....... (-29.88 = -34.32 +   4.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 6,177,746 – 6,177,857
Length 111
Sequences 5
Columns 115
Reading direction forward
Mean pairwise identity 83.36
Mean single sequence MFE -41.34
Consensus MFE -27.52
Energy contribution -30.78
Covariance contribution 3.26
Combinations/Pair 1.26
Mean z-score -2.25
Structure conservation index 0.67
SVM decision value 0.86
SVM RNA-class probability 0.868736
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6177746 111 + 22407834
CAAGCCGUUUGACAGACAGCGCAUGCCCAACGGCUUUGGCCGGAAUGGGUAUGAGUUAUGGUUGGAAGUUGGCAAUGCUUCUGCUGUCUGCUGUUUGUUUGUACACUCGG----A
(((((.....(.((((((((.((((((((.((((....))))...))))))))..........((((((.......))))))))))))))).....))))).........----. ( -43.00)
>DroSec_CAF1 14128 100 + 1
CAAGCCGUUUGACAGACAGCGCAUGCCCAACGGCUUCGGCCGGAAUGGGUAUGAGUUAUGGUUGGAAGUUGG-----------CUGUCUGCUGUUGGUUUGCACACUCGG----A
(((((((...(.((((((((.((((((((.((((....))))...))))))))..(((....)))......)-----------))))))))...))))))).........----. ( -43.20)
>DroSim_CAF1 23604 100 + 1
CAAGCCGUUUGAUAGACAGCGCAUGCCCAACGGCUUCGGCCGGAAUGGGUAUGAGUUAUGGUUGGAAGUUGG-----------CUGUCUGCUGUUUGUUUGCACACUCGG----A
....(((...((((((((((.((((((((.((((....))))...))))))))....(((((..(...)..)-----------))))..))))))))))........)))----. ( -40.00)
>DroEre_CAF1 13838 106 + 1
CAUGCCGCUUGACAGACAGCGCAUGCCCAACGGCUUCGG--GUACUGGGUAUGAGUUAUGGUUGGAAGUUGGCAAUGCC---GCUGUCUGCCGGUUGUCUGCGCACUCCG----A
......((..(.((((((((.((((((((..(.(....)--.)..)))))))).....((((.(..(((.(((...)))---)))..).)))))))))))))))......----. ( -37.40)
>DroYak_CAF1 24744 112 + 1
CAAGCUGCUUGACAGACAGCGCAUGCCCAACUGCUUCGGCUGCACUGGGUAUGAGUUAUGGCUGGAAGUUGGCAAUGCC---ACUGUUGGCCGUUUGUUUGCACACUUUGCCAUU
...(.(((..((((((((((.((((((((...((....)).....)))))))).)))..(((..(.(((.(((...)))---))).)..)))))))))).))))........... ( -43.10)
>consensus
CAAGCCGUUUGACAGACAGCGCAUGCCCAACGGCUUCGGCCGGAAUGGGUAUGAGUUAUGGUUGGAAGUUGGCAAUGC_____CUGUCUGCUGUUUGUUUGCACACUCGG____A
......((..((((((((((.((((((((.((((....))))...)))))))).)))..(((.((.(((.(((...)))...))).)).)))))))))).))............. (-27.52 = -30.78 +   3.26)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:24:03 2006