Locus 1174

Sequence ID	3L_DroMel_CAF1
Location	3,365,193 – 3,365,363
Length	170
Max. P	0.687792

overview

Window 8

Location	3,365,193 – 3,365,313
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	97.83
Mean single sequence MFE	-27.97
Consensus MFE	-26.44
Energy contribution	-26.24
Covariance contribution	-0.20
Combinations/Pair	1.07
Mean z-score	-1.22
Structure conservation index	0.95
SVM decision value	0.23
SVM RNA-class probability	0.642699
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3365193 120 - 23771897
GGCCAUCGGUUAAACCUCUAAAGUGCCAUAGAUUAUUAUAACACACGCGCUAUGCGACUGUGCUGCGGUUAGCCGCAAAACUCAAAACCGAAACAGACACUCCAAGCCAAAGGCCCCACA
((((.((((((.....((((........)))).........((((..(((...)))..)))).(((((....)))))........))))))....(......)........))))..... ( -28.30)
>DroSec_CAF1 32488 120 - 1
GGCCAUCGGUUAAACCUCUAAAGUGCCAUAGAUUAUUAUAACACACGCGCUAUGCGACUGUGCUGCGGUUAGUCGCAAAACUCAAAACCGAAACAGACACUCCAAGCCAAAGGCCCCACA
((((.((((((..........(((((....................))))).((((((((.((....))))))))))........))))))....(......)........))))..... ( -28.95)
>DroSim_CAF1 30167 120 - 1
GGCCAUCGGUUAAACCUCUAAAGUGCCAUAGAUUAUUAUAACACACGCGCUAUGCGACUGUGCUGCGGUUAGCCGCAAAACUCAAAACCGAAACAGACACUCCAAGCCAAAGGCCCCACA
((((.((((((.....((((........)))).........((((..(((...)))..)))).(((((....)))))........))))))....(......)........))))..... ( -28.30)
>DroEre_CAF1 31188 119 - 1
GACCAUCGGUUAAACCUCUAAAGUGCCAUAGAUUAUUAUAACACACGCGCUUUGCGACUGUGCUGCGGUUAGCCGCAA-ACUCAAAGCCGAAACAGACACUCCGAGCCAAAGGCCCCACA
.....((((.......(((...(((..((((....))))..))).((.((((((.....((..(((((....))))).-)).))))))))....)))....))))(((...)))...... ( -26.00)
>DroYak_CAF1 31029 120 - 1
GGCCAUCGGUUAAACCUCUAAAGUGCCAUAGAUUAUUAUAACACACGCGCUAUGCGACUGUGCUGCGGUUAGCCGCAAAACUCAAAGCCGAAACAGACACUCCAAGCCAAAGGCCCCACA
((((.((((((.....((((........)))).........((((..(((...)))..)))).(((((....)))))........))))))....(......)........))))..... ( -28.30)
>consensus
GGCCAUCGGUUAAACCUCUAAAGUGCCAUAGAUUAUUAUAACACACGCGCUAUGCGACUGUGCUGCGGUUAGCCGCAAAACUCAAAACCGAAACAGACACUCCAAGCCAAAGGCCCCACA
((((.((((((.....((((........)))).........((((..(((...)))..)))).(((((....)))))........))))))....(......)........))))..... (-26.44 = -26.24 +  -0.20)

alignment

secondary structure

dotplot

Window 9

Location	3,365,273 – 3,365,363
Length	90
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	69.59
Mean single sequence MFE	-16.90
Consensus MFE	-11.94
Energy contribution	-11.45
Covariance contribution	-0.49
Combinations/Pair	1.16
Mean z-score	-1.05
Structure conservation index	0.71
SVM decision value	0.32
SVM RNA-class probability	0.687792
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3365273 90 - 23771897
AUCUCUAUCUCUAU------------CUUCAUCUGUAUGUGCAGAUG------------------UAUCUGUAUCUAUCCGGCCAUCGGUUAAACCUCUAAAGUGCCAUAGAUUAUUAUA
..............------------...(((((((....)))))))------------------.......((((((..((((.(..(........)..).).)))))))))....... ( -14.50)
>DroEre_CAF1 31267 91 - 1
AUCUGUA------------------UCUCCAUCUGUAUCUACAGAUAUAUCUCUG-------CUGUAUCUGUAUC----CGACCAUCGGUUAAACCUCUAAAGUGCCAUAGAUUAUUAUA
.......------------------.....((((((...((((((((((......-------.)))))))))).(----((.....)))..................))))))....... ( -16.20)
>DroYak_CAF1 31109 120 - 1
AACUGUAUCUGUAUCUCUAUCUGUAUCUCUAUCUGUAUCUGUAGAUAUAUCUGUAGAUAUAUCUGUAUCUGUAUCUAUGCGGCCAUCGGUUAAACCUCUAAAGUGCCAUAGAUUAUUAUA
.((.((((..((((.(((((..((((.(((((........))))).))))..))))).))))..))))..))(((((((..((....((.....))......))..)))))))....... ( -20.00)
>consensus
AUCUGUAUCU_UAU___________UCUCCAUCUGUAUCUGCAGAUAUAUCU_U________CUGUAUCUGUAUCUAU_CGGCCAUCGGUUAAACCUCUAAAGUGCCAUAGAUUAUUAUA
..............................((((((...((((((((((..............))))))))))..............(((..............)))))))))....... (-11.94 = -11.45 +  -0.49)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:01:13 2006