Locus 4604

Sequence ID	X_DroMel_CAF1
Location	12,063,123 – 12,063,256
Length	133
Max. P	0.984143

overview

Window 7

Location	12,063,123 – 12,063,221
Length	98
Sequences	5
Columns	105
Reading direction	reverse
Mean pairwise identity	92.66
Mean single sequence MFE	-22.02
Consensus MFE	-19.20
Energy contribution	-20.40
Covariance contribution	1.20
Combinations/Pair	1.00
Mean z-score	-1.86
Structure conservation index	0.87
SVM decision value	1.96
SVM RNA-class probability	0.984143
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12063123 98 - 22224390
GCCAGCG----GCCGGCAAAACACUCUUAAUAC---CGCUUAGCAAAUGUUAAUUGUUUUUCCCCUGGUAAGAACGAUUGCAUUUGCCUAAUCUGUAUCUGUUAA
(((....----...)))............((((---.(.(((((((((((.((((((((((((...)).))))))))))))))))).)))).).))))....... ( -24.50)
>DroSec_CAF1 94597 98 - 1
GCCAGCG----GCUGGCAAAACACUCUUAAUAC---CGCUUAGCAAAUGUUAAUUGUUUUUCCCCUGGUAACAACGAUUGCAUUUGCCUAAUCUGUAUCUGUUAC
(((((..----.)))))............((((---.(.(((((((((((.(((((((.((((...)).)).)))))))))))))).)))).).))))....... ( -23.80)
>DroSim_CAF1 71640 98 - 1
GCCAGCG----GCUGGCAAAACACUCUUAAUAC---CGCUUAGCAAAUGUUAAUUGUUUUUCCCCUGGUAACAACGAUUGCAUUUGCCUAAUCUGUAUCUGUUAC
(((((..----.)))))............((((---.(.(((((((((((.(((((((.((((...)).)).)))))))))))))).)))).).))))....... ( -23.80)
>DroEre_CAF1 92236 98 - 1
GCCAGCG----ACUGGCAAAACUCUCCUAAUAC---CGCUUAGCAAAUGUUAAUUGUUUUUCCCCUGAUAACAACGAUUGCAUUUGCGUAAUCUGUAUCUGUUAC
(((((..----.))))).........(..((((---.(.(((((((((((.(((((((..((....))....))))))))))))))).))).).))))..).... ( -22.60)
>DroYak_CAF1 94506 105 - 1
UCCAGCGGCCAACUGGCAAAACACUCUUAAUACCACCACUUAGCAAAUGUUAAUUGUUUUUCCCCUGGUAACAACGAUUGCAUUUCCCUAAUCUGUAUCUGUUAC
.((((.((((....)))...................((.(((((....))))).)).......)))))((((((((((((........))))).))...))))). ( -15.40)
>consensus
GCCAGCG____GCUGGCAAAACACUCUUAAUAC___CGCUUAGCAAAUGUUAAUUGUUUUUCCCCUGGUAACAACGAUUGCAUUUGCCUAAUCUGUAUCUGUUAC
((((((.....)))))).........................((((((((.(((((((.((.(....).)).))))))))))))))).................. (-19.20 = -20.40 +   1.20)

alignment

secondary structure

dotplot

Window 8

Location	12,063,148 – 12,063,256
Length	108
Sequences	5
Columns	115
Reading direction	reverse
Mean pairwise identity	92.69
Mean single sequence MFE	-17.21
Consensus MFE	-13.94
Energy contribution	-15.34
Covariance contribution	1.40
Combinations/Pair	1.00
Mean z-score	-1.36
Structure conservation index	0.81
SVM decision value	0.00
SVM RNA-class probability	0.535582
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12063148 108 - 22224390
AAAAAUUCCAACAAUUUCCCUAAUUUCCCACAUUUGCCAGCG----GCCGGCAAAACACUCUUAAUAC---CGCUUAGCAAAUGUUAAUUGUUUUUCCCCUGGUAAGAACGAUUG
.............................((((((((.((((----(....................)---))))..))))))))(((((((((((((...)).))))))))))) ( -21.85)
>DroSec_CAF1 94622 108 - 1
AAAAAUUCCAACAUUUUCCCUAAUUUCCCACAUUUGCCAGCG----GCUGGCAAAACACUCUUAAUAC---CGCUUAGCAAAUGUUAAUUGUUUUUCCCCUGGUAACAACGAUUG
.............................((((((((.((((----(....................)---))))..))))))))((((((((.((((...)).)).)))))))) ( -18.25)
>DroSim_CAF1 71665 108 - 1
AAAAAUUGCAACAUUUUCCCUAAUUUCCCACAUUUGCCAGCG----GCUGGCAAAACACUCUUAAUAC---CGCUUAGCAAAUGUUAAUUGUUUUUCCCCUGGUAACAACGAUUG
.............................((((((((.((((----(....................)---))))..))))))))((((((((.((((...)).)).)))))))) ( -18.25)
>DroEre_CAF1 92261 108 - 1
AAAAAUUCAAACAUUUUCCCUAAUUUCCCACAUUUGCCAGCG----ACUGGCAAAACUCUCCUAAUAC---CGCUUAGCAAAUGUUAAUUGUUUUUCCCCUGAUAACAACGAUUG
.........(((((((................((((((((..----.))))))))......((((...---...)))).)))))))(((((((..((....))....))))))). ( -15.60)
>DroYak_CAF1 94531 115 - 1
AAAAAUUCUAACAUUUCCCCUAAUUUCCCACAUUUUCCAGCGGCCAACUGGCAAAACACUCUUAAUACCACCACUUAGCAAAUGUUAAUUGUUUUUCCCCUGGUAACAACGAUUG
....................................((((.((((....)))...................((.(((((....))))).)).......)))))............ ( -12.10)
>consensus
AAAAAUUCCAACAUUUUCCCUAAUUUCCCACAUUUGCCAGCG____GCUGGCAAAACACUCUUAAUAC___CGCUUAGCAAAUGUUAAUUGUUUUUCCCCUGGUAACAACGAUUG
.........(((((((................(((((((((.....))))))))).................((...)))))))))(((((((.((.(....).)).))))))). (-13.94 = -15.34 +   1.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:29:11 2006