Locus 4830

Sequence ID	2L_DroMel_CAF1
Location	13,755,464 – 13,755,559
Length	95
Max. P	0.983688

overview

Window 3

Location	13,755,464 – 13,755,559
Length	95
Sequences	5
Columns	97
Reading direction	forward
Mean pairwise identity	77.16
Mean single sequence MFE	-22.42
Consensus MFE	-6.92
Energy contribution	-6.28
Covariance contribution	-0.64
Combinations/Pair	1.30
Mean z-score	-2.15
Structure conservation index	0.31
SVM decision value	1.02
SVM RNA-class probability	0.900810
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13755464 95 + 22407834
UCAUAAAAUUGCAAUUGACUUUGAGCCUGGCAUAUAUAC--GAGUACAGUAAUAGUACUCGUACAUAUUCGCCUUGCCUUUUGGCUUCGCAAAAUGU
........((((................(((((((.(((--((((((.......))))))))).))))..)))..(((....)))...))))..... ( -26.80)
>DroSec_CAF1 19090 78 + 1
UCAUAAAAUUGCAAUUGACUUCGAGCCCGGCAUA--UAC--GAG-----------UACUCGU----GUGCUCCUUGCCUUUUGGCUUCGCAAAAUGU
........((((....(....)(((((.((((..--...--(((-----------(((....----))))))..))))....))))).))))..... ( -21.00)
>DroSim_CAF1 21201 78 + 1
UCAUAAAAUUGCAAUUGACUUCGAGCCCGGCAUA--UAC--GAG-----------UACUCGU----GUGCUCCUUGCCUUUUGGCUUCGCAAAAUGU
........((((....(....)(((((.((((..--...--(((-----------(((....----))))))..))))....))))).))))..... ( -21.00)
>DroEre_CAF1 20979 89 + 1
UCAUAAAAUUGCAAUUGACUUUGAGCCCGGAAUA--UGCAGUAUUCCGGCCAAAG--CCCGC----CGACUCCUUGCCUUUUGGCUUCGUAAAAUGU
........((((......(((((.(((.((((((--(...)))))))))))))))--...((----(((...........)))))...))))..... ( -22.80)
>DroYak_CAF1 22218 89 + 1
UCAUAAAAUUGCAAUUGACUUUGAGCCCGGAAUA--CACAGUUUUCCGGCCAAAG--CCCGC----CAACUCCUUGCCUUUUGGCUUCGUAAAAUGU
........((((......(((((.(((.((((.(--(...)).))))))))))))--...((----(((...........)))))...))))..... ( -20.50)
>consensus
UCAUAAAAUUGCAAUUGACUUUGAGCCCGGCAUA__UAC__GAGU_C_G__A_AGUACUCGU____CUACUCCUUGCCUUUUGGCUUCGCAAAAUGU
........((((........(((....))).............................................(((....)))...))))..... ( -6.92 =  -6.28 +  -0.64)

alignment

secondary structure

dotplot

Window 4

Location	13,755,464 – 13,755,559
Length	95
Sequences	5
Columns	97
Reading direction	reverse
Mean pairwise identity	77.16
Mean single sequence MFE	-25.76
Consensus MFE	-10.34
Energy contribution	-10.74
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-2.53
Structure conservation index	0.40
SVM decision value	1.95
SVM RNA-class probability	0.983688
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13755464 95 - 22407834
ACAUUUUGCGAAGCCAAAAGGCAAGGCGAAUAUGUACGAGUACUAUUACUGUACUC--GUAUAUAUGCCAGGCUCAAAGUCAAUUGCAAUUUUAUGA
.(((.((((((.(((....)))..(((..((((((((((((((.......))))))--))))))))))).(((.....)))..))))))....))). ( -36.10)
>DroSec_CAF1 19090 78 - 1
ACAUUUUGCGAAGCCAAAAGGCAAGGAGCAC----ACGAGUA-----------CUC--GUA--UAUGCCGGGCUCGAAGUCAAUUGCAAUUUUAUGA
.(((.((((((.(((....)))...((((..----.((.(((-----------...--...--..))))).))))........))))))....))). ( -20.10)
>DroSim_CAF1 21201 78 - 1
ACAUUUUGCGAAGCCAAAAGGCAAGGAGCAC----ACGAGUA-----------CUC--GUA--UAUGCCGGGCUCGAAGUCAAUUGCAAUUUUAUGA
.(((.((((((.(((....)))...((((..----.((.(((-----------...--...--..))))).))))........))))))....))). ( -20.10)
>DroEre_CAF1 20979 89 - 1
ACAUUUUACGAAGCCAAAAGGCAAGGAGUCG----GCGGG--CUUUGGCCGGAAUACUGCA--UAUUCCGGGCUCAAAGUCAAUUGCAAUUUUAUGA
........(((..((.........))..)))----((.((--((((((((((((((.....--)))))).))).)))))))....)).......... ( -26.70)
>DroYak_CAF1 22218 89 - 1
ACAUUUUACGAAGCCAAAAGGCAAGGAGUUG----GCGGG--CUUUGGCCGGAAAACUGUG--UAUUCCGGGCUCAAAGUCAAUUGCAAUUUUAUGA
............(((....)))..(((((((----...((--((((((((((((.((...)--).)))).))).))))))).....))))))).... ( -25.80)
>consensus
ACAUUUUGCGAAGCCAAAAGGCAAGGAGCAC____ACGAGUACU_U__C_G_ACUC__GUA__UAUGCCGGGCUCAAAGUCAAUUGCAAUUUUAUGA
.(((.((((((.(((....)))................................................(((.....)))..))))))....))). (-10.34 = -10.74 +   0.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:28:39 2006