Locus 4671

Sequence ID	X_DroMel_CAF1
Location	12,191,563 – 12,191,727
Length	164
Max. P	0.889054

overview

Window 3

Location	12,191,563 – 12,191,664
Length	101
Sequences	4
Columns	110
Reading direction	forward
Mean pairwise identity	85.15
Mean single sequence MFE	-34.88
Consensus MFE	-23.42
Energy contribution	-23.68
Covariance contribution	0.25
Combinations/Pair	1.14
Mean z-score	-2.37
Structure conservation index	0.67
SVM decision value	0.95
SVM RNA-class probability	0.889054
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12191563 101 + 22224390
GGUUACAGUCUGGGCUUGUUGCACAUGGCGUAUACGCCAU-----GUCCGGCGAGGAUGCAAAG----UCAGUGGCCCAAGAUUGAAGCAGAUUGAAGGACGCAAACAAA
.(((.((((((((((((((((.((((((((....))))))-----)).)))))).(((.....)----))....)))).)))))).)))..................... ( -37.20)
>DroSec_CAF1 17979 101 + 1
GGUUACAGUCUGGGCUUGUUGCACAUGGCGUAUACGCCAU-----GUCCGGCGUGGAUGCAAAG----UCAGUGGCCCAAGAUUGAAGCAGAUUGAAGGACGCAAACAAA
.(((.(((((((((((.((((.((((((((....))))))-----)).))))...(((.....)----))...))))).)))))).)))..................... ( -36.50)
>DroSim_CAF1 19181 101 + 1
GGUUACAGUCUGGGCUUGUUGCACAUGGCGUAUACGCCAU-----GUCCGGCGUGGAUGCAAAG----UCAGUGGCCCAAGAUUGAAGCAGAUUGAAGGACGCAAACAAA
.(((.(((((((((((.((((.((((((((....))))))-----)).))))...(((.....)----))...))))).)))))).)))..................... ( -36.50)
>DroYak_CAF1 2420 96 + 1
AG--------------UGUUGCACAUGGCGUAUACGCUAUUCGCAGUCCGGCGAGGAUGCAAAGUCAGGUGGUGGCCCAAGAUUGAAGCAGAUUGAAGGACGCAAACGAG
.(--------------(.((((..((((((....)))))).....((((..(((...(((....((((.(((....)))...)))).)))..)))..))))))))))... ( -29.30)
>consensus
GGUUACAGUCUGGGCUUGUUGCACAUGGCGUAUACGCCAU_____GUCCGGCGAGGAUGCAAAG____UCAGUGGCCCAAGAUUGAAGCAGAUUGAAGGACGCAAACAAA
...............(((((((..((((((....)))))).....((((..(((...(((........(((((........))))).)))..)))..)))))).))))). (-23.42 = -23.68 +   0.25)

alignment

secondary structure

dotplot

Window 4

Location	12,191,634 – 12,191,727
Length	93
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	80.40
Mean single sequence MFE	-22.21
Consensus MFE	-14.83
Energy contribution	-15.19
Covariance contribution	0.36
Combinations/Pair	1.05
Mean z-score	-1.77
Structure conservation index	0.67
SVM decision value	0.39
SVM RNA-class probability	0.715633
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12191634 93 - 22224390
CAAGGCGAGUGUAUUCAUUGCAUUCAUUUCUGACGUACGCUCACGUA----------UAUAUUCCUUUCUC-------GAUUUGUUUGCGUCCUUCAAUCU----------GCUUCAAUC
..(((((((((((.....)))))))......((((((.((...((..----------.............)-------)....)).)))))).........----------))))..... ( -17.66)
>DroSec_CAF1 18050 93 - 1
CAAGGCGAGUGUAUUCAUUGCAUUCAUUUCUGACGUACGCUCACGCA----------UAUAUUCCUUUCUC-------GAUUUGUUUGCGUCCUUCAAUCU----------GCUUCAAUC
..(((((((((((((((.............))).))))))))(((((----------.(((.((.......-------))..))).)))))..........----------))))..... ( -18.82)
>DroSim_CAF1 19252 93 - 1
CAAGGCGAGUGUAUUCAUUGCAUUCAUUUCUGGCGUACGCUCACGUA----------UAUAUUCCUUUCUC-------GAUUUGUUUGCGUCCUUCAAUCU----------GCUUCAAUC
..(((((((((((.....)))))))......((((((.((...((..----------.............)-------)....)).)))))).........----------))))..... ( -17.06)
>DroEre_CAF1 17665 93 - 1
CG-GGCGAGUGUAUUCAUUGCAUUCAUUUCUGACGUAC------------------GUGAAUUCCUUCCC--------GACUUGUUUGCGUCCUUCAAUCUGCCUCCAGCUGCUUCAAUC
.(-((((((((((.....))))))).....(((.(.((------------------(..(((........--------.....)))..))).).)))....))))............... ( -20.82)
>DroYak_CAF1 2486 110 - 1
CGAGGCGAGUGUAUUCAUUGCAUUCAUUUCUGGCGUACGCUCACGUACGUACAUACGAGUAUUCCUUGCUCGCAUAAGGACUCGUUUGCGUCCUUCAAUCU----------GCUUCAAUC
.((((((((((((.....))))))).......(((((((....))))))).....((((((.....))))))...((((((........))))))......----------))))).... ( -36.70)
>consensus
CAAGGCGAGUGUAUUCAUUGCAUUCAUUUCUGACGUACGCUCACGUA__________UAUAUUCCUUUCUC_______GAUUUGUUUGCGUCCUUCAAUCU__________GCUUCAAUC
..(((((((((((.....)))))))......((((((.((...........................................)).))))))...................))))..... (-14.83 = -15.19 +   0.36)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:30:36 2006