Locus 6539

Sequence ID	X_DroMel_CAF1
Location	16,368,051 – 16,368,163
Length	112
Max. P	0.981424

overview

Window 4

Location	16,368,051 – 16,368,163
Length	112
Sequences	4
Columns	115
Reading direction	forward
Mean pairwise identity	75.44
Mean single sequence MFE	-37.42
Consensus MFE	-19.19
Energy contribution	-25.38
Covariance contribution	6.19
Combinations/Pair	1.05
Mean z-score	-2.67
Structure conservation index	0.51
SVM decision value	1.89
SVM RNA-class probability	0.981424
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16368051 112 + 22224390
UGGCAAUUUCGGCUAGAUGGGCUAAAUGCCGCAAAUAGUUAAUUGUUUUCUUUGUGCCGUGCGAAACACUGGCGUGGCAUUUGGCCCAC---UCCCCAAUUAGCCGGAAGUGGUA
..((..((((((((((((((((((((((((((((((((....)))))).......((((((.....))).)))))))))))))))))).---))......)))))))))...)). ( -47.70)
>DroSec_CAF1 40556 112 + 1
UGGCAAUUGCGGCAAGAUGGGCUAAAUCCCGCAAAUAGUUAAUUGUUUUCUUUGUGCCGUGCACAACACUGGCGUGGCAUUUGGCCCAC---UCCCCAAUUAGCCGGAAGUGGUA
.((((((((.((..((.((((((((((.((((((((((....)))))).......((((((.....))).))))))).)))))))))))---).))))))).))).......... ( -39.80)
>DroEre_CAF1 26567 95 + 1
UGGCAAUUGUA-------------------GCAAAUAGUUAAUUGUUGUCUUUGUUUCGUG-GAAACACUGGCGUGGCAUGUGGCCCCCACCCCCCCAAUUAGCCGGAAGUGGUA
.((((((..((-------------------((.....))))...)))))).(..(((((((-....)))((((.(((...((((...))))....)))....))))))))..).. ( -28.70)
>DroYak_CAF1 25978 96 + 1
UGGCAAUUGCGGCUAGAUGGGCUAAAUGCCGCAAAUAGUUAAUUGUUUUCUUUGU----------------GUGCGCCACUUGGCCCCC---UCACCAAUUAGCCGGAAGUGCUA
(((((.((.((((((((.(((((((.((.((((.((((..((.....))..))))----------------.)))).)).)))))))..---))......)))))).)).))))) ( -33.50)
>consensus
UGGCAAUUGCGGCUAGAUGGGCUAAAUGCCGCAAAUAGUUAAUUGUUUUCUUUGUGCCGUG_GAAACACUGGCGUGGCAUUUGGCCCAC___UCCCCAAUUAGCCGGAAGUGGUA
.((((((((.((.....(((((((((((((((((((((....)))))).......((((((.....))).)))))))))))))))))).....)).))))).))).......... (-19.19 = -25.38 +   6.19)

alignment

secondary structure

dotplot

Window 5

Location	16,368,051 – 16,368,163
Length	112
Sequences	4
Columns	115
Reading direction	reverse
Mean pairwise identity	75.44
Mean single sequence MFE	-33.12
Consensus MFE	-16.21
Energy contribution	-20.90
Covariance contribution	4.69
Combinations/Pair	1.07
Mean z-score	-2.23
Structure conservation index	0.49
SVM decision value	0.48
SVM RNA-class probability	0.752527
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16368051 112 - 22224390
UACCACUUCCGGCUAAUUGGGGA---GUGGGCCAAAUGCCACGCCAGUGUUUCGCACGGCACAAAGAAAACAAUUAACUAUUUGCGGCAUUUAGCCCAUCUAGCCGAAAUUGCCA
..........(((...((((..(---((((((.(((((((..(((.(((.....))))))..........(((........))).))))))).))))).))..))))....))). ( -39.50)
>DroSec_CAF1 40556 112 - 1
UACCACUUCCGGCUAAUUGGGGA---GUGGGCCAAAUGCCACGCCAGUGUUGUGCACGGCACAAAGAAAACAAUUAACUAUUUGCGGGAUUUAGCCCAUCUUGCCGCAAUUGCCA
..........(((.(((((.((.---((((((.((((.((..(((.(((.....))))))..........(((........))).)).)))).))))))....)).)))))))). ( -38.70)
>DroEre_CAF1 26567 95 - 1
UACCACUUCCGGCUAAUUGGGGGGGUGGGGGCCACAUGCCACGCCAGUGUUUC-CACGAAACAAAGACAACAAUUAACUAUUUGC-------------------UACAAUUGCCA
..........(((.(((((..(.((((..(((.....))).))))..((((((-...)))))).....................)-------------------..)))))))). ( -24.20)
>DroYak_CAF1 25978 96 - 1
UAGCACUUCCGGCUAAUUGGUGA---GGGGGCCAAGUGGCGCAC----------------ACAAAGAAAACAAUUAACUAUUUGCGGCAUUUAGCCCAUCUAGCCGCAAUUGCCA
..(((.((.((((((......((---..((((.(((((.((((.----------------......................)))).))))).)))).)))))))).)).))).. ( -30.10)
>consensus
UACCACUUCCGGCUAAUUGGGGA___GGGGGCCAAAUGCCACGCCAGUGUUUC_CACGGCACAAAGAAAACAAUUAACUAUUUGCGGCAUUUAGCCCAUCUAGCCGCAAUUGCCA
..........(((.(((((.((....((((((.(((((((......(((.....))).............(((........))).))))))).))))))....)).)))))))). (-16.21 = -20.90 +   4.69)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:16:17 2006