Locus 4446

Sequence ID	3R_DroMel_CAF1
Location	11,752,431 – 11,752,552
Length	121
Max. P	0.999729

overview

Window 9

Location	11,752,431 – 11,752,528
Length	97
Sequences	5
Columns	99
Reading direction	forward
Mean pairwise identity	83.92
Mean single sequence MFE	-13.44
Consensus MFE	-9.26
Energy contribution	-9.70
Covariance contribution	0.44
Combinations/Pair	1.06
Mean z-score	-1.60
Structure conservation index	0.69
SVM decision value	-0.04
SVM RNA-class probability	0.511400
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11752431 97 + 27905053
GCUGGCAAGAAAUAUUUCCUAUAAUUUAAGCUCAUACUAUUAUAUAUUUAUUCUUGU--UUUUUUUUUCUUUGUAAAACUUGUCAGCGCCACCCACUUU
(((((((((..........((((((.............))))))..(((((......--.............))))).)))))))))............ ( -14.03)
>DroSec_CAF1 85180 88 + 1
GCUGCCAAGAAAUAUUUACUAUAAUUUAAGCUCAUACUCGUAUAUAUUUAUUCUUG-----------UUUUUGUAAAACUUGUCAGUGCCACCCACUUU
((((.((((((((((.(((....................))).)))))).......-----------(((....))).)))).))))............ (  -8.15)
>DroSim_CAF1 86878 99 + 1
GCUGCCAAGAAAUAUUUACUAUAAUUUAAGCUCAUACUCGUAUAUAUUUAUUCUUGUAUUUUUCUUUUUUUUGUAAAACUUGUCAGCGCCACCCACUUU
((((.((((.....(((((...((...(((...((((..(.(((....))).)..))))....)))..))..))))).)))).))))............ ( -12.10)
>DroEre_CAF1 85534 87 + 1
GCUGGCAAGAAAUAUUUCCUAUAAUUUUAGCUCAU------AUAUAUUUAUUCUUGU--UUCUC----UUUUGUAAAACUUGUCAGCGCCACCCACUUU
(((((((((..((((...(((......)))...))------))...(((((....(.--....)----....))))).)))))))))............ ( -15.20)
>DroYak_CAF1 89254 83 + 1
GCUGGCAAGAAGUAUUUCAUAUAAUUUUAGCGCAU------AUAUUGUUAUUCUUGU--U--------UUUUGUAAAACUUGUCAGCGCCACCCACUUU
(((((((((...(((.....((((...(((((...------....)))))...))))--.--------....)))...)))))))))............ ( -17.70)
>consensus
GCUGGCAAGAAAUAUUUCCUAUAAUUUAAGCUCAUACU__UAUAUAUUUAUUCUUGU__UU_U____UUUUUGUAAAACUUGUCAGCGCCACCCACUUU
(((((((((...(((.....))).......................(((((.....................))))).)))))))))............ ( -9.26 =  -9.70 +   0.44)

alignment

secondary structure

dotplot

Window 0

Location	11,752,452 – 11,752,552
Length	100
Sequences	5
Columns	102
Reading direction	reverse
Mean pairwise identity	83.91
Mean single sequence MFE	-25.58
Consensus MFE	-23.02
Energy contribution	-24.10
Covariance contribution	1.08
Combinations/Pair	1.05
Mean z-score	-3.85
Structure conservation index	0.90
SVM decision value	3.96
SVM RNA-class probability	0.999729
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11752452 100 - 27905053
GUGGAACUAGCCGGCGCUGCCUAGAAAGUGGGUGGCGCUGACAAGUUUUACAAAGAAAAAAAAA--ACAAGAAUAAAUAUAUAAUAGUAUGAGCUUAAAUUA
((((((((.(.((((((..((((.....))))..)))))).).)))))))).............--..(((.....((((......))))...)))...... ( -29.10)
>DroSec_CAF1 85201 91 - 1
GUGGAACAAGCCGGCGCUGCCUAGAAAGUGGGUGGCACUGACAAGUUUUACAAAAA-----------CAAGAAUAAAUAUAUACGAGUAUGAGCUUAAAUUA
(((((((..(.(((.((..((((.....))))..)).))).)..))))))).....-----------.................((((....))))...... ( -22.10)
>DroSim_CAF1 86899 102 - 1
GCGGAACAAGCUGGCGCUGCCUAGAAAGUGGGUGGCGCUGACAAGUUUUACAAAAAAAAGAAAAAUACAAGAAUAAAUAUAUACGAGUAUGAGCUUAAAUUA
(..((((..(..(((((..((((.....))))..)))))..)..))))..)......(((....((((..(.(((....))).)..))))...)))...... ( -24.70)
>DroEre_CAF1 85555 89 - 1
GUGGAACUAGU-GGCGCUGCCUAGAAAGUGGGUGGCGCUGACAAGUUUUACAAAA----GAGAA--ACAAGAAUAAAUAUAU------AUGAGCUAAAAUUA
((((((((.((-(((((..((((.....))))..))))).)).))))))))....----.....--................------.............. ( -26.90)
>DroYak_CAF1 89275 86 - 1
GUGGAAAUAGCCGGCGCUGCCUAGAAAGUGGGUGGCGCUGACAAGUUUUACAAAA--------A--ACAAGAAUAACAAUAU------AUGCGCUAAAAUUA
.......((((((((((..((((.....))))..))))))....(((((....))--------)--))..............------....))))...... ( -25.10)
>consensus
GUGGAACUAGCCGGCGCUGCCUAGAAAGUGGGUGGCGCUGACAAGUUUUACAAAAA____A_AA__ACAAGAAUAAAUAUAUA__AGUAUGAGCUUAAAUUA
((((((((.(.((((((..((((.....))))..)))))).).))))))))................................................... (-23.02 = -24.10 +   1.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:29:30 2006