Locus 548

Sequence ID 3L_DroMel_CAF1
Location 1,577,868 – 1,577,988
Length 120
Max. P 0.881538
window841 window842

overview

Window 1

Location 1,577,868 – 1,577,988
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 95.50
Mean single sequence MFE -49.84
Consensus MFE -47.50
Energy contribution -46.50
Covariance contribution -1.00
Combinations/Pair 1.16
Mean z-score -1.28
Structure conservation index 0.95
SVM decision value 0.92
SVM RNA-class probability 0.881538
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1577868 120 + 23771897
GGACCAGCGCCUGCUUCAUAGACGCCUCAUCGCUGAGGGACGAGGAUGAGGUGUUGUCCUUCCCCAGCCUAGAUGGCCACGGCCAGGAGGAAGAAGUCGGGCAAGAGGCGACUGGCGACG
.(.(((((((((.((((...(((.((((...((((.((((..((((..(....)..)))))))))))).....((((....)))).)))).....)))..).)))))))).))))).... ( -52.40)
>DroSec_CAF1 22059 120 + 1
GGACCAGCGCCUGCUUCAUAGACGCCUCAUCGCUGAGGGACGAGGAUGAGGUGCUGUCCUUCCCCAGCCUAGAUGGCCACGGCCAGGAGGAAGAAGUCGGACAAGAGGCGACUGGCGACG
.(.(((((((((.(((....(((.((((...((((.((((..(((((........))))))))))))).....((((....)))).)))).....)))....)))))))).))))).... ( -51.40)
>DroSim_CAF1 22435 120 + 1
GGACCAGCGCCUGCUUCAUAGACGCCUCAUCGCUGAAGGACGAGGAUGAGGUGCUGUCCUUCCCCAGCCUAGAUGGCCACGGCCAGGAGGAAGAAGUCGGACAAGAGGCGACUGGCGACG
.(.(((((((((.(((...((.(((((((((.((........)))))))))))))((((..(..(..(((...((((....))))..)))..)..)..)))))))))))).))))).... ( -50.40)
>DroEre_CAF1 29221 120 + 1
GAACCAGCGCCUGCUUCAUAGACGCCUCAUCGCUGAGGGACGAGGACGAGGUGCUGUCCUUCCCCAGUCUAGAUGGUCACGGCCAGGAGGAAGAAGUCGGGCAAGAGGCGAUUGGCGACG
...(((((((((.((((...(((.((((...((((.((((..((((((......)))))))))))))).....((((....)))).)))).....)))..).)))))))).))))..... ( -47.00)
>DroYak_CAF1 23158 120 + 1
GAACCAGUGCCUGCUUCAUAGACGCCUCCUCGCUGAGGGACGAGGACGAGGUGCUGUCCUUCCCCAGUCUAGAUGGUCACGGUCAGGAGGAAGAAGUCGGGCAAGAGGCGACUGGCGACG
...(((((((((.((((...(((.((((((.((((.(((..(((((((......))))))).))).(.((....)).).)))).)))))).....)))..).))))))).)))))..... ( -48.00)
>consensus
GGACCAGCGCCUGCUUCAUAGACGCCUCAUCGCUGAGGGACGAGGAUGAGGUGCUGUCCUUCCCCAGCCUAGAUGGCCACGGCCAGGAGGAAGAAGUCGGGCAAGAGGCGACUGGCGACG
...(((((((((.(((....(((.((((...((((.((((..((((((......)))))))))))))).....((((....)))).)))).....)))....)))))))).))))..... (-47.50 = -46.50 +  -1.00) 

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 1,577,868 – 1,577,988
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 95.50
Mean single sequence MFE -47.02
Consensus MFE -40.44
Energy contribution -41.52
Covariance contribution 1.08
Combinations/Pair 1.03
Mean z-score -1.51
Structure conservation index 0.86
SVM decision value 0.71
SVM RNA-class probability 0.830383
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1577868 120 - 23771897
CGUCGCCAGUCGCCUCUUGCCCGACUUCUUCCUCCUGGCCGUGGCCAUCUAGGCUGGGGAAGGACAACACCUCAUCCUCGUCCCUCAGCGAUGAGGCGUCUAUGAAGCAGGCGCUGGUCC
....(((((.((((((((....((((((((((.((.((((.(((....)))))))))))))))).....(((((((((........)).))))))).)))....))).)))))))))).. ( -48.30)
>DroSec_CAF1 22059 120 - 1
CGUCGCCAGUCGCCUCUUGUCCGACUUCUUCCUCCUGGCCGUGGCCAUCUAGGCUGGGGAAGGACAGCACCUCAUCCUCGUCCCUCAGCGAUGAGGCGUCUAUGAAGCAGGCGCUGGUCC
....(((((.((((((((((((..((((..(((..((((....))))...)))..))))..)))).((.(((((((((........)).))))))).)).....))).)))))))))).. ( -52.00)
>DroSim_CAF1 22435 120 - 1
CGUCGCCAGUCGCCUCUUGUCCGACUUCUUCCUCCUGGCCGUGGCCAUCUAGGCUGGGGAAGGACAGCACCUCAUCCUCGUCCUUCAGCGAUGAGGCGUCUAUGAAGCAGGCGCUGGUCC
....(((((.((((((((((((..((((..(((..((((....))))...)))..))))..)))).((.(((((((((........)).))))))).)).....))).)))))))))).. ( -52.00)
>DroEre_CAF1 29221 120 - 1
CGUCGCCAAUCGCCUCUUGCCCGACUUCUUCCUCCUGGCCGUGACCAUCUAGACUGGGGAAGGACAGCACCUCGUCCUCGUCCCUCAGCGAUGAGGCGUCUAUGAAGCAGGCGCUGGUUC
....((((..(((((((((((.((........))..)))(((((((.((..(.((((((((((((........)))))..)))).))))...)).).))).)))))).))))).)))).. ( -37.70)
>DroYak_CAF1 23158 120 - 1
CGUCGCCAGUCGCCUCUUGCCCGACUUCUUCCUCCUGACCGUGACCAUCUAGACUGGGGAAGGACAGCACCUCGUCCUCGUCCCUCAGCGAGGAGGCGUCUAUGAAGCAGGCACUGGUUC
....((((((.(((((((....(((..(((((((((((.......((.......))(((((((((........)))))..)))))))).))))))).)))....))).)))))))))).. ( -45.10)
>consensus
CGUCGCCAGUCGCCUCUUGCCCGACUUCUUCCUCCUGGCCGUGGCCAUCUAGGCUGGGGAAGGACAGCACCUCAUCCUCGUCCCUCAGCGAUGAGGCGUCUAUGAAGCAGGCGCUGGUCC
....(((((.((((((((....((((((((((.((.((((...........))))))))))))).....(((((((((........)).))))))).)))....))).)))))))))).. (-40.44 = -41.52 +   1.08) 

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript


Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:45:06 2006