Locus 5719

Sequence ID 3R_DroMel_CAF1
Location 14,939,438 – 14,939,578
Length 140
Max. P 0.702272
window9358 window9359

overview

Window 8

Location 14,939,438 – 14,939,558
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 90.83
Mean single sequence MFE -28.10
Consensus MFE -22.50
Energy contribution -24.25
Covariance contribution 1.75
Combinations/Pair 1.00
Mean z-score -1.70
Structure conservation index 0.80
SVM decision value 0.35
SVM RNA-class probability 0.702272
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14939438 120 - 27905053
GUCAUUUAACACACAUAUCUCUUAGUAAGUGGCCAGGCCAAUUAAGGCCGAUAAUUAAAGACACGGCUGCCAACACAGUUGCAACACUUCGAACACUUUGGCUGCCGUUUAGGCCAACUU
..........................((((((((.((((......)))).............(((((.(((((.....(((........))).....))))).)))))...)))).)))) ( -33.80)
>DroSec_CAF1 75077 120 - 1
GUCAUUUAACACACAUAUCUCUUAGUAAGUGGCCAGGCCAAUUAAGGCCGAUAAUUAAAGACACGGCUGCCAACACAGUUGCAACACUUCGAACACUUUGGCUGCCGUUUAGUCCAAAUU
(((.(((((..(((.(((......))).)))....((((......)))).....))))))))(((((.(((((.....(((........))).....))))).)))))............ ( -30.10)
>DroSim_CAF1 67938 120 - 1
GUCAUUUAACACACAUAUCUCAUAGUAAGUGGCCAGGCCAAUUAAGGCCGAUAAUUAAAGACACGGAUGCCAACACAGUUGCAACACUUCGAACACUUUGGCUGCCGUUUAGGCCAACUU
..........................((((((((.((((......)))).............((((..(((((.....(((........))).....)))))..))))...)))).)))) ( -29.40)
>DroYak_CAF1 72573 110 - 1
GUCAUUUAACACACAUCUUUCUUCAUAAGCGGCCAGGCCAA----------UAAUUAAAGACACGUCAGCCAACACACUUGCAACACUUCGAACACUUUGGCUGCCGUUUAGGCCAACUU
.........................((((((((..((((((----------...(..(((....((.((........)).))....)))..).....))))))))))))))......... ( -19.10)
>consensus
GUCAUUUAACACACAUAUCUCUUAGUAAGUGGCCAGGCCAAUUAAGGCCGAUAAUUAAAGACACGGCUGCCAACACAGUUGCAACACUUCGAACACUUUGGCUGCCGUUUAGGCCAACUU
..............................((((.((((......)))).............(((((.(((((.....(((........))).....))))).)))))...))))..... (-22.50 = -24.25 +   1.75)

alignment

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secondary structure

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dotplot

Postscript

Window 9

Location 14,939,478 – 14,939,578
Length 100
Sequences 4
Columns 107
Reading direction reverse
Mean pairwise identity 87.07
Mean single sequence MFE -24.77
Consensus MFE -16.51
Energy contribution -18.95
Covariance contribution 2.44
Combinations/Pair 1.07
Mean z-score -1.74
Structure conservation index 0.67
SVM decision value 0.11
SVM RNA-class probability 0.590357
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14939478 100 - 27905053
GGCA-------UUCGCAUAAUUUCUGCGUCAUUUAACACACAUAUCUCUUAGUAAGUGGCCAGGCCAAUUAAGGCCGAUAAUUAAAGACACGGCUGCCAACACAGUU
((((-------..((((.......)))(((.(((((..(((.(((......))).)))....((((......)))).....))))))))..)..))))......... ( -24.80)
>DroSec_CAF1 75117 107 - 1
GGCAUUCGGCAUUCGCAUAAUUUCUGCGUCAUUUAACACACAUAUCUCUUAGUAAGUGGCCAGGCCAAUUAAGGCCGAUAAUUAAAGACACGGCUGCCAACACAGUU
((((..((((...((((.......))))..........(((.(((......))).)))))).((((......))))...............)..))))......... ( -27.10)
>DroSim_CAF1 67978 107 - 1
GGCAUUCGGCAUUCGCAUAAUUUCUGCGUCAUUUAACACACAUAUCUCAUAGUAAGUGGCCAGGCCAAUUAAGGCCGAUAAUUAAAGACACGGAUGCCAACACAGUU
((((((((((...((((.......))))..........(((.(((......))).)))))).((((......))))...............)))))))......... ( -31.10)
>DroYak_CAF1 72613 97 - 1
GGCAUUUGGCAUUCGCAUAAUUUCUGCGUCAUUUAACACACAUCUUUCUUCAUAAGCGGCCAGGCCAA----------UAAUUAAAGACACGUCAGCCAACACACUU
(((...((((....(((.......)))(((.(((((.......(((.......))).(((...)))..----------...))))))))..)))))))......... ( -16.10)
>consensus
GGCAUUCGGCAUUCGCAUAAUUUCUGCGUCAUUUAACACACAUAUCUCUUAGUAAGUGGCCAGGCCAAUUAAGGCCGAUAAUUAAAGACACGGCUGCCAACACAGUU
((((.(((......(((.......)))(((.(((((..(((.(((......))).)))....((((......)))).....)))))))).))).))))......... (-16.51 = -18.95 +   2.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:02:46 2006