Locus 7147

Sequence ID 2L_DroMel_CAF1
Location 20,018,584 – 20,018,683
Length 99
Max. P 0.991613
window11411 window11412

overview

Window 1

Location 20,018,584 – 20,018,683
Length 99
Sequences 4
Columns 99
Reading direction forward
Mean pairwise identity 91.07
Mean single sequence MFE -32.98
Consensus MFE -29.66
Energy contribution -30.97
Covariance contribution 1.31
Combinations/Pair 1.04
Mean z-score -1.58
Structure conservation index 0.90
SVM decision value 0.57
SVM RNA-class probability 0.786053
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20018584 99 + 22407834
GCCCAAAGCACAUCAAUUAUGCAGCUCCGGGCGAACACCAGCGGAGGUGUUUGAGGAAACCACCUGAUGAUGAUGAUGAGGUGGGAGGACGCGUCCGAA
((((..(((.(((.....)))..)))..)))).........((((.((((((.......((((((.((.......)).))))))..)))))).)))).. ( -35.00)
>DroSec_CAF1 196097 95 + 1
GCCCGAAGCACAUCAAUUAUGCAGCUCCGGGCGAACACCAGCGGAGGUGUUUGAGGAAACCACCUGAUGA---UGAUGAGGUGGGAGGAC-CGACCGAA
(((((.(((.(((.....)))..))).)))))(((((((......)))))))..((...((((((.((..---..)).)))))).....)-)....... ( -35.20)
>DroSim_CAF1 198687 95 + 1
GCCCGAAGCACAUCAAUUAUGCAGCUCCGGGCGAACACCAGCGGAGGUGUUUGAGGAAACCACCUGAUGA---UGAUGAGGUGGGAGGAC-CGACCGAA
(((((.(((.(((.....)))..))).)))))(((((((......)))))))..((...((((((.((..---..)).)))))).....)-)....... ( -35.20)
>DroYak_CAF1 194560 94 + 1
GCCCGAAGCACAUAAAUUAUGCAGCUCCUGGCGAACU-GAGGUGAGGUGUUCGAGGAAACCACCUGACGA---UGAUGAGGUGGGAGGAC-GCUCCGAA
(((.(.(((.((((...))))..))).).))).....-..((...(((((((.......((((((.(...---...).))))))..))))-)))))... ( -26.50)
>consensus
GCCCGAAGCACAUCAAUUAUGCAGCUCCGGGCGAACACCAGCGGAGGUGUUUGAGGAAACCACCUGAUGA___UGAUGAGGUGGGAGGAC_CGACCGAA
(((((.(((.(((.....)))..))).)))))(((((((......))))))).......((((((.((.......)).))))))..((......))... (-29.66 = -30.97 +   1.31)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 20,018,584 – 20,018,683
Length 99
Sequences 4
Columns 99
Reading direction reverse
Mean pairwise identity 91.07
Mean single sequence MFE -33.28
Consensus MFE -30.33
Energy contribution -30.95
Covariance contribution 0.62
Combinations/Pair 1.07
Mean z-score -2.56
Structure conservation index 0.91
SVM decision value 2.28
SVM RNA-class probability 0.991613
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20018584 99 - 22407834
UUCGGACGCGUCCUCCCACCUCAUCAUCAUCAUCAGGUGGUUUCCUCAAACACCUCCGCUGGUGUUCGCCCGGAGCUGCAUAAUUGAUGUGCUUUGGGC
...(((....)))..((((((.((.......)).))))))........((((((......)))))).(((((((((.((((.....))))))))))))) ( -35.10)
>DroSec_CAF1 196097 95 - 1
UUCGGUCG-GUCCUCCCACCUCAUCA---UCAUCAGGUGGUUUCCUCAAACACCUCCGCUGGUGUUCGCCCGGAGCUGCAUAAUUGAUGUGCUUCGGGC
.......(-(.....((((((.((..---..)).))))))...))...((((((......)))))).(((((((((.((((.....))))))))))))) ( -35.60)
>DroSim_CAF1 198687 95 - 1
UUCGGUCG-GUCCUCCCACCUCAUCA---UCAUCAGGUGGUUUCCUCAAACACCUCCGCUGGUGUUCGCCCGGAGCUGCAUAAUUGAUGUGCUUCGGGC
.......(-(.....((((((.((..---..)).))))))...))...((((((......)))))).(((((((((.((((.....))))))))))))) ( -35.60)
>DroYak_CAF1 194560 94 - 1
UUCGGAGC-GUCCUCCCACCUCAUCA---UCGUCAGGUGGUUUCCUCGAACACCUCACCUC-AGUUCGCCAGGAGCUGCAUAAUUUAUGUGCUUCGGGC
.(((((((-......((((((.((..---..)).)))))).((((((((((..........-.)))))..)))))..(((((...)))))))))))).. ( -26.80)
>consensus
UUCGGACG_GUCCUCCCACCUCAUCA___UCAUCAGGUGGUUUCCUCAAACACCUCCGCUGGUGUUCGCCCGGAGCUGCAUAAUUGAUGUGCUUCGGGC
...((......))..((((((.((.......)).))))))........((((((......)))))).(((((((((.((((.....))))))))))))) (-30.33 = -30.95 +   0.62)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:28:38 2006