Locus 69

Sequence ID	3L_DroMel_CAF1
Location	275,408 – 275,549
Length	141
Max. P	0.807138

overview

Window 7

Location	275,408 – 275,510
Length	102
Sequences	5
Columns	103
Reading direction	reverse
Mean pairwise identity	90.07
Mean single sequence MFE	-24.86
Consensus MFE	-19.31
Energy contribution	-19.35
Covariance contribution	0.04
Combinations/Pair	1.22
Mean z-score	-1.47
Structure conservation index	0.78
SVM decision value	0.04
SVM RNA-class probability	0.551253
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 275408 102 - 23771897
GCAUGCUUGCGCCUACAAGUAUGCAACCAAUUUGACAA-UUCCACUUGGUACUUUUACAAAUUGACAAGGGGAUUUUAGGGAUUUUUAUUGCAACAGUCAGGA
(((((((((......)))))))))......((((((((-((((.((((.................))))))))))...(.(((....))).)....)))))). ( -26.73)
>DroSec_CAF1 47818 102 - 1
GCAUGCUUGCGCCUACGAGUAUGCAACCAAUUUGACAA-UUCCACUUGGUACUUUUACAAAUUAACAAGGGGAUUUUAAGGAUUUUUAUUGCAACAGGCAGGA
(((((((((......)))))))))..((..(((((.((-((((.((((.................))))))))))))))).........(((.....))))). ( -25.83)
>DroSim_CAF1 43358 102 - 1
GCAUGCUUGCGCAUACAAGUAUGCAACCAAUUUGACAA-UUCCACUUGGUACUUUUACAAAUUAACAGGGGGAUUUUAGGGAUCUUUAUUGCAACAGGCAGGA
(((((((((......)))))))))..((..(((((.((-((((.((((.................))))))))))))))).........(((.....))))). ( -25.43)
>DroEre_CAF1 47554 103 - 1
GCAUGCUUGCGCCUACAAGUAUGCAACCAAUUUGACAUCUUCCACUUCCUACAUUUUCAAAUUAACCAGGGAAUUUUAGGGAUUUUCCUUGUAACUGGCAGGA
(((((((((......)))))))))..(((((((((.....................)))))))..((((.......(((((.....)))))...))))..)). ( -25.00)
>DroYak_CAF1 43910 103 - 1
GCAUGCUUGCGCCUACAAGUAUGCAACCAAUUUGACAACUUCCACUUCCUACACUUUCAAAUUGACCAGGGGAUUUCAGGGAUUUUUAUUGUAACUGGCAGGA
(((((((((......)))))))))................(((...((((......((.....))....))))..((((..((.......))..))))..))) ( -21.30)
>consensus
GCAUGCUUGCGCCUACAAGUAUGCAACCAAUUUGACAA_UUCCACUUGGUACUUUUACAAAUUAACAAGGGGAUUUUAGGGAUUUUUAUUGCAACAGGCAGGA
(((((((((......)))))))))..((..(((((....((((.((((.................))))))))..))))).........(((.....))))). (-19.31 = -19.35 +   0.04)

alignment

secondary structure

dotplot

Window 8

Location	275,448 – 275,549
Length	101
Sequences	5
Columns	103
Reading direction	reverse
Mean pairwise identity	91.19
Mean single sequence MFE	-20.80
Consensus MFE	-15.76
Energy contribution	-15.96
Covariance contribution	0.20
Combinations/Pair	1.19
Mean z-score	-1.98
Structure conservation index	0.76
SVM decision value	0.64
SVM RNA-class probability	0.807138
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 275448 101 - 23771897
UUGACUUCUUAUUACGCAAUGA-AGGGGUCAACUUUCUGCGCAUGCUUGCGCCUACAAGUAUGCAACCAAUUUGACAA-UUCCACUUGGUACUUUUACAAAUU
(((((((((((((....)))).-)))))))))........(((((((((......))))))))).(((((...((...-.))...)))))............. ( -25.20)
>DroSec_CAF1 47858 101 - 1
UUGCCUUCCUAUUACGCAAUGA-AGGAGUCAACUUACUGCGCAUGCUUGCGCCUACGAGUAUGCAACCAAUUUGACAA-UUCCACUUGGUACUUUUACAAAUU
.((((.((((.(((.....)))-))))(((((........(((((((((......))))))))).......)))))..-........))))............ ( -21.76)
>DroSim_CAF1 43398 101 - 1
UUGCCUUCCUAUUACGCAAUGA-AGGAGUCAACUUACUGCGCAUGCUUGCGCAUACAAGUAUGCAACCAAUUUGACAA-UUCCACUUGGUACUUUUACAAAUU
.((((.((((.(((.....)))-))))(((((........(((((((((......))))))))).......)))))..-........))))............ ( -22.06)
>DroEre_CAF1 47594 103 - 1
UUGCCUUCCUAUUACGCAAUAAAAAGAGCCAAUUUACUGCGCAUGCUUGCGCCUACAAGUAUGCAACCAAUUUGACAUCUUCCACUUCCUACAUUUUCAAAUU
...............(((.((((.........)))).)))(((((((((......)))))))))....(((((((.....................))))))) ( -16.70)
>DroYak_CAF1 43950 102 - 1
UUGCCUUCCUAUUACGCAACGA-AGGAGCCAAUUUACUGCGCAUGCUUGCGCCUACAAGUAUGCAACCAAUUUGACAACUUCCACUUCCUACACUUUCAAAUU
((((...........)))).((-(((.((.........))(((((((((......))))))))).............................)))))..... ( -18.30)
>consensus
UUGCCUUCCUAUUACGCAAUGA_AGGAGUCAACUUACUGCGCAUGCUUGCGCCUACAAGUAUGCAACCAAUUUGACAA_UUCCACUUGGUACUUUUACAAAUU
......((((.(((.....))).))))(((((........(((((((((......))))))))).......)))))........................... (-15.76 = -15.96 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:31:31 2006