Locus 3066

Sequence ID	3L_DroMel_CAF1
Location	8,855,270 – 8,855,369
Length	99
Max. P	0.825598

overview

Window 3

Location	8,855,270 – 8,855,369
Length	99
Sequences	5
Columns	99
Reading direction	forward
Mean pairwise identity	85.73
Mean single sequence MFE	-23.00
Consensus MFE	-17.74
Energy contribution	-18.14
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-1.68
Structure conservation index	0.77
SVM decision value	0.29
SVM RNA-class probability	0.672009
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8855270 99 + 23771897
CAAAGUCUUGCCAGAUCAAAUAACUACCAUGCCUCAUGCCCCUUUGGCCAAUUGAUGCAUAUGCUCUGAAGCAUUUCAAUAUGUCAGAGCGGAACUAAG
....((((....))))..........((((((.(((.(((.....)))....))).))))..((((((..((((......))))))))))))....... ( -23.30)
>DroSec_CAF1 115245 90 + 1
CAA---------AGAUAAAAUAACUCCCAUGCCCCAUGCCCCUUUGGCCAAUUGAUGCAUAUGCUCUGAAGCAUUUCAAUAUGUCAGAGCGGAGCUAAG
...---------...........((((.((((..((.(((.....)))....))..))))..((((((..((((......))))))))))))))..... ( -23.50)
>DroSim_CAF1 111663 90 + 1
CAA---------AGAUCAAAUAACUCCCAUGCCCCAUGCCCCUUUGGCCAAUUGAUGCAUAUGCUCUGAAGCAUUUCAAUAUGUCAGAGCGGAGCUAAG
...---------...........((((.((((..((.(((.....)))....))..))))..((((((..((((......))))))))))))))..... ( -23.50)
>DroEre_CAF1 119473 92 + 1
CAAAGUCUCGCCAGAUCAAAUGACUCCCAU-------GCCCCUUCGGCCAAUUGAUGCAUAUGCUCUGAAGCAUUUCAAUAUGUCAGAGCGGAGCCAAG
....(.(((((...((((((((.....)))-------(((.....)))...)))))))...(((((((..((((......)))))))))))))).)... ( -21.60)
>DroYak_CAF1 118401 92 + 1
CCAACUCUUGUUAGAUCAAAUGACUGCCAU-------GCCCCUUUGGCCAAUUGAUGCAUAUGCUCUGAAGCAUUUCAAUAUGUCAGAGCGGAGCUAAG
....(((((((...(((((.((...((((.-------.......)))))).))))))))...((((((..((((......))))))))))))))..... ( -23.10)
>consensus
CAAA_UCU_G__AGAUCAAAUAACUCCCAUGCC_CAUGCCCCUUUGGCCAAUUGAUGCAUAUGCUCUGAAGCAUUUCAAUAUGUCAGAGCGGAGCUAAG
.....................................(((((((((((..(((((.....(((((....))))).)))))..))))))).)).)).... (-17.74 = -18.14 +   0.40)

alignment

secondary structure

dotplot

Window 4

Location	8,855,270 – 8,855,369
Length	99
Sequences	5
Columns	99
Reading direction	reverse
Mean pairwise identity	85.73
Mean single sequence MFE	-28.48
Consensus MFE	-21.94
Energy contribution	-22.94
Covariance contribution	1.00
Combinations/Pair	1.08
Mean z-score	-1.91
Structure conservation index	0.77
SVM decision value	0.70
SVM RNA-class probability	0.825598
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8855270 99 - 23771897
CUUAGUUCCGCUCUGACAUAUUGAAAUGCUUCAGAGCAUAUGCAUCAAUUGGCCAAAGGGGCAUGAGGCAUGGUAGUUAUUUGAUCUGGCAAGACUUUG
...((((..(((..((((.((((..((((((((((((....)).)).....(((.....))).))))))))..))))....)).)).)))..))))... ( -25.20)
>DroSec_CAF1 115245 90 - 1
CUUAGCUCCGCUCUGACAUAUUGAAAUGCUUCAGAGCAUAUGCAUCAAUUGGCCAAAGGGGCAUGGGGCAUGGGAGUUAUUUUAUCU---------UUG
..(((((((((((((((((......)))..))))))).(((((..((....(((.....))).))..))))))))))))........---------... ( -31.60)
>DroSim_CAF1 111663 90 - 1
CUUAGCUCCGCUCUGACAUAUUGAAAUGCUUCAGAGCAUAUGCAUCAAUUGGCCAAAGGGGCAUGGGGCAUGGGAGUUAUUUGAUCU---------UUG
..(((((((((((((((((......)))..))))))).(((((..((....(((.....))).))..))))))))))))........---------... ( -31.60)
>DroEre_CAF1 119473 92 - 1
CUUGGCUCCGCUCUGACAUAUUGAAAUGCUUCAGAGCAUAUGCAUCAAUUGGCCGAAGGGGC-------AUGGGAGUCAUUUGAUCUGGCGAGACUUUG
..(((((((((((((((((......)))..))))))).(((((.((....))((....))))-------)))))))))).................... ( -29.40)
>DroYak_CAF1 118401 92 - 1
CUUAGCUCCGCUCUGACAUAUUGAAAUGCUUCAGAGCAUAUGCAUCAAUUGGCCAAAGGGGC-------AUGGCAGUCAUUUGAUCUAACAAGAGUUGG
..((((((.((((((((((......)))..)))))))......(((((.((((((.......-------.))))...)).))))).......)))))). ( -24.60)
>consensus
CUUAGCUCCGCUCUGACAUAUUGAAAUGCUUCAGAGCAUAUGCAUCAAUUGGCCAAAGGGGCAUG_GGCAUGGGAGUUAUUUGAUCU__C_AGA_UUUG
..(((((((((((((((((......)))..))))))).(((((........(((.....))).....)))))))))))).................... (-21.94 = -22.94 +   1.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:48:43 2006