Locus 4664

Sequence ID	3L_DroMel_CAF1
Location	13,208,848 – 13,208,955
Length	107
Max. P	0.909635

overview

Window 9

Location	13,208,848 – 13,208,955
Length	107
Sequences	5
Columns	108
Reading direction	forward
Mean pairwise identity	81.42
Mean single sequence MFE	-25.33
Consensus MFE	-17.82
Energy contribution	-18.26
Covariance contribution	0.44
Combinations/Pair	1.06
Mean z-score	-2.12
Structure conservation index	0.70
SVM decision value	1.07
SVM RNA-class probability	0.909635
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13208848 107 + 23771897
AAUAGACA-GAAACUUUGGCUGAUUAUGUUGAAGCCAGGCGGUGGGCCACACGGCGUAUGCAUAAUCGUAUAAUUAAUUGCCAUAAAUGUUAAUUGCGCAUACGCCAC
........-.......((((.((((((((....(((..(.((....)).)..)))....))))))))(..((((((((..........))))))))..)....)))). ( -29.30)
>DroSec_CAF1 2444 87 + 1
AAUAGACA-GAAACUUCG--------------------GCGGUGUGCCACACGGCGUAUGCAUAAUCGUAUAAUUAAUUGCCAUAAAUGUUAAUUGCGCAUACGCCAC
........-........(--------------------((.....)))....(((((((((......(((........))).......((.....))))))))))).. ( -22.30)
>DroSim_CAF1 7421 87 + 1
AAUAGACA-GAAACUUCG--------------------GCGGUGUGCCACACGGCGUAUGCAUAAUCGUAUAAUUAAUUGCCAUAAAUGUUAAUUGCGCAUACGCCAC
........-........(--------------------((.....)))....(((((((((......(((........))).......((.....))))))))))).. ( -22.30)
>DroYak_CAF1 2139 94 + 1
AAUAGACA-GAAACUUUGGCUGAUUAUG-------------UUGUGCCACACGGCGUAUGCAUAAUCGUAUAAUUAAUUGCCAUAAAUGUUAAUUGCGCAUACGCCAC
........-.......((((.(((((((-------------(..((((....))))...))))))))(..((((((((..........))))))))..)....)))). ( -25.10)
>DroAna_CAF1 91951 95 + 1
AACAGACAUGGAACUCUAGCCCGACAUC-------------GGGGGCCACACGGCGUAUGCAUAAUCACAUAAUUAAUUGCCAUAAAUGUUAAUUGCGCAUACGCCGU
........(((....))).((((....)-------------)))......(((((((((((.((((.((((...............))))..)))).))))))))))) ( -27.66)
>consensus
AAUAGACA_GAAACUUUGGC_____AU___________GCGGUGUGCCACACGGCGUAUGCAUAAUCGUAUAAUUAAUUGCCAUAAAUGUUAAUUGCGCAUACGCCAC
.........................................(((.....)))(((((((((......(((........))).......((.....))))))))))).. (-17.82 = -18.26 +   0.44)

alignment

secondary structure

dotplot

Window 0

Location	13,208,848 – 13,208,955
Length	107
Sequences	5
Columns	108
Reading direction	reverse
Mean pairwise identity	81.42
Mean single sequence MFE	-25.78
Consensus MFE	-18.76
Energy contribution	-18.60
Covariance contribution	-0.16
Combinations/Pair	1.05
Mean z-score	-1.88
Structure conservation index	0.73
SVM decision value	0.71
SVM RNA-class probability	0.829974
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13208848 107 - 23771897
GUGGCGUAUGCGCAAUUAACAUUUAUGGCAAUUAAUUAUACGAUUAUGCAUACGCCGUGUGGCCCACCGCCUGGCUUCAACAUAAUCAGCCAAAGUUUC-UGUCUAUU
.(((((((((...((((..((....))..))))...)))))(((((((.....((((.((((....)))).)))).....))))))).)))).......-........ ( -28.50)
>DroSec_CAF1 2444 87 - 1
GUGGCGUAUGCGCAAUUAACAUUUAUGGCAAUUAAUUAUACGAUUAUGCAUACGCCGUGUGGCACACCGC--------------------CGAAGUUUC-UGUCUAUU
..(((((((((((.((........)).))...(((((....))))).)))))))))...((((.....))--------------------)).......-........ ( -22.70)
>DroSim_CAF1 7421 87 - 1
GUGGCGUAUGCGCAAUUAACAUUUAUGGCAAUUAAUUAUACGAUUAUGCAUACGCCGUGUGGCACACCGC--------------------CGAAGUUUC-UGUCUAUU
..(((((((((((.((........)).))...(((((....))))).)))))))))...((((.....))--------------------)).......-........ ( -22.70)
>DroYak_CAF1 2139 94 - 1
GUGGCGUAUGCGCAAUUAACAUUUAUGGCAAUUAAUUAUACGAUUAUGCAUACGCCGUGUGGCACAA-------------CAUAAUCAGCCAAAGUUUC-UGUCUAUU
..(((((((((((.((........)).))...(((((....))))).)))))))))...((((....-------------........)))).......-........ ( -22.30)
>DroAna_CAF1 91951 95 - 1
ACGGCGUAUGCGCAAUUAACAUUUAUGGCAAUUAAUUAUGUGAUUAUGCAUACGCCGUGUGGCCCCC-------------GAUGUCGGGCUAGAGUUCCAUGUCUGUU
((((((((((((.(((((.(((..((........)).)))))))).)))))))))))).((((((..-------------......))))))................ ( -32.70)
>consensus
GUGGCGUAUGCGCAAUUAACAUUUAUGGCAAUUAAUUAUACGAUUAUGCAUACGCCGUGUGGCACACCGC___________AU_____GCCAAAGUUUC_UGUCUAUU
.((((((((((((.((........)).))...(((((....))))).))))))))))................................................... (-18.76 = -18.60 +  -0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:30:05 2006