Locus 4787

Sequence ID	3R_DroMel_CAF1
Location	12,519,084 – 12,519,217
Length	133
Max. P	0.913652

overview

Window 5

Location	12,519,084 – 12,519,196
Length	112
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	86.89
Mean single sequence MFE	-20.79
Consensus MFE	-16.67
Energy contribution	-16.20
Covariance contribution	-0.47
Combinations/Pair	1.09
Mean z-score	-2.16
Structure conservation index	0.80
SVM decision value	0.30
SVM RNA-class probability	0.679900
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12519084 112 + 27905053
UCGAAAUAUUAUUAAGUCCCAAAGCUGCACUUCAAUUAAAAUGCAUUUUCGCAGUUUAUGGGCUUAAUCUCAUAAACAAUUUCUGCAUUGUUGCAAAUUCGCUCUCGUUCCU--------
.((((.....((((((.(((((((((((......................))))))).))))))))))...............((((....))))..))))...........-------- ( -22.95)
>DroPse_CAF1 6860 117 + 1
UCGAAAUAUUAUAAAGUCCCAAAGCUGCACUUCAAUUAAAAUGCAUUUUCGCAGUUUAUGAGCUUAAUCUCAUAAACAAUUUCUGUAUUGUUGCGUC---UCCCUCAACCCUCACCCCUC
.......................((.(((...((.......(((......)))(((((((((......)))))))))......))...))).))...---.................... ( -16.90)
>DroEre_CAF1 5716 112 + 1
UCGAAAUAUUAUUAAGUCCCAAAGCUGCACUUCAAUUAAAAUGCAUUUUCGCAGUUUAUGGGCUUAAUCUCAUAAACAAUUUCUGCAUUGUUGCAAAUUCGCUCUCCUUCCU--------
.((((.....((((((.(((((((((((......................))))))).))))))))))...............((((....))))..))))...........-------- ( -22.95)
>DroYak_CAF1 4957 112 + 1
UCGAAAUAUUAUUAAGUCCCAAAGCUGCACUUCAAUUAAAAUGCAUUUUCGCAGUUUAUGGGCUUAAUCUCAUAAACAAUUUCAGCAUUGUUGCAAAUUUGCUCUCCGCCCU--------
..........((((((.(((((((((((......................))))))).))))))))))......((((((......))))))(((....)))..........-------- ( -21.05)
>DroAna_CAF1 8877 110 + 1
UCGAAAUAUUAUUAAGUCCCAAAGCUGCACUUCAAUUAAAAUGCAUUUUCACAGUUUAUGAGCUUAAUCUCAUAAACAAUUUCUGCAUUGUGGCCGAGUGUUUCUUUUU--G--------
..((((((((.....(((.(((.((((((.((......)).))))........(((((((((......))))))))).......)).))).)))..)))))))).....--.-------- ( -24.00)
>DroPer_CAF1 10820 107 + 1
UCGAAAUAUUAUAAAGUCCCAAAGCUGCACUUCAAUUAAAAUGCAUUUUCGCAGUUUAUGAGCUUAAUCUCAUAAACAAUUUCUGUAUUGUUGCGUC---UCCCUCACCC----------
.......................((.(((...((.......(((......)))(((((((((......)))))))))......))...))).))...---..........---------- ( -16.90)
>consensus
UCGAAAUAUUAUUAAGUCCCAAAGCUGCACUUCAAUUAAAAUGCAUUUUCGCAGUUUAUGAGCUUAAUCUCAUAAACAAUUUCUGCAUUGUUGCAAAUU_GCUCUCAUCCCU________
...............((..(((.((((((.((......)).))))........(((((((((......))))))))).......)).)))..)).......................... (-16.67 = -16.20 +  -0.47)

alignment

secondary structure

dotplot

Window 6

Location	12,519,124 – 12,519,217
Length	93
Sequences	6
Columns	111
Reading direction	forward
Mean pairwise identity	77.96
Mean single sequence MFE	-19.85
Consensus MFE	-12.53
Energy contribution	-12.50
Covariance contribution	-0.03
Combinations/Pair	1.13
Mean z-score	-1.96
Structure conservation index	0.63
SVM decision value	1.09
SVM RNA-class probability	0.913652
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12519124 93 + 27905053
AUGCAUUUUCGCAGUUUAUGGGCUUAAUCUCAUAAACAAUUUCUGCAUUGUUGCAAAUUCGCUCUCGUUCCUCGA-CGUUUUGGC--------AUU---------GUUGAU
.(((......)))(((((((((......)))))))))......((((....)))).....(((..((((....))-))....)))--------...---------...... ( -19.70)
>DroSec_CAF1 8155 93 + 1
AUGCAUUUUCGCAGUUUAUGGGCUUAAUCUCAUAAACAAUUUCUGCAUUGUUGCAAAUUCGCUCUCCUUCCUAGA-CUUUUUGGC--------AUU---------GUUGAU
.(((......)))(((((((((......)))))))))....((.(((.(((((.(((.((.............))-.))).))))--------).)---------)).)). ( -17.32)
>DroSim_CAF1 7927 93 + 1
AUGCAUUUUCGCAGUUUAUGGGCUUAAUCUCAUAAACAAUUUCUGCAUUGUUGCAAAUUCGCUCUCCUUCCUCGA-CUUUUUGGC--------AUU---------GUUGAU
.(((......)))(((((((((......)))))))))....((.(((.(((((.(((.(((...........)))-.))).))))--------).)---------)).)). ( -18.20)
>DroYak_CAF1 4997 94 + 1
AUGCAUUUUCGCAGUUUAUGGGCUUAAUCUCAUAAACAAUUUCAGCAUUGUUGCAAAUUUGCUCUCCGCCCUCGGAUUUUUUGCC--------AUU---------GUUGAU
.(((......)))(((((((((......)))))))))....((((((.((..(((((.......((((....))))...))))))--------).)---------))))). ( -24.50)
>DroAna_CAF1 8917 88 + 1
AUGCAUUUUCACAGUUUAUGAGCUUAAUCUCAUAAACAAUUUCUGCAUUGUGGCCGAGUGUUUCUUUUU--GAAG-CAUAUUUGC--------------------GUUGAU
(((((........(((((((((......)))))))))....((.((......)).))(((((((.....--))))-)))...)))--------------------)).... ( -21.90)
>DroPer_CAF1 10860 105 + 1
AUGCAUUUUCGCAGUUUAUGAGCUUAAUCUCAUAAACAAUUUCUGUAUUGUUGCGUC---UCCCUCACCC--CCA-CUUAUUGGCUUUUUGCUACUUGAAUUCGCUCUGAU
..((.....(((((((((((((......)))))))))(((......)))..))))..---..........--...-.....((((.....)))).........))...... ( -17.50)
>consensus
AUGCAUUUUCGCAGUUUAUGGGCUUAAUCUCAUAAACAAUUUCUGCAUUGUUGCAAAUUCGCUCUCCUUCCUCGA_CUUUUUGGC________AUU_________GUUGAU
.(((......)))(((((((((......))))))))).......(((....)))......................................................... (-12.53 = -12.50 +  -0.03)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:38:56 2006