Locus 963

Sequence ID	2L_DroMel_CAF1
Location	2,779,516 – 2,779,662
Length	146
Max. P	0.978560

overview

Window 3

Location	2,779,516 – 2,779,632
Length	116
Sequences	5
Columns	116
Reading direction	reverse
Mean pairwise identity	89.33
Mean single sequence MFE	-21.60
Consensus MFE	-19.64
Energy contribution	-19.40
Covariance contribution	-0.24
Combinations/Pair	1.06
Mean z-score	-1.49
Structure conservation index	0.91
SVM decision value	0.86
SVM RNA-class probability	0.868564
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2779516 116 - 22407834
UAUACAUACAUACUACAUAGGUAUCAACAUAACCGAGCGAUAUGCAUACAUAUAUAUACACCAGGACAUAAGGUCCACGAGUACAUUUCCCAGGAGCUAUCCAUCCUUCGGUUCAG
.........(((((.....)))))......(((((((.(((......................((((.....))))................(((....)))))).)))))))... ( -20.10)
>DroSec_CAF1 2893 116 - 1
UAUACAUACAUACUACACAGGUAUCCACAUAACCGAGCGAUGUGCAUACAUACAUAUACACCAGGACAUAAGGUCCACGAGUACUUUUCCCAGGAGCUAUCCAUCCUUCGGUUCAG
.........(((((.....)))))......(((((((.((((((((((......)))......((((.....))))....))))........(((....)))))).)))))))... ( -21.90)
>DroSim_CAF1 2856 116 - 1
UAUACAUACAUACUACAUAGGUAUCCACAUAACCGAGCGAUAUGCAUACAUACAUAUACACCUGGACAUAAGGUCCACGAGUACUUUUCCCAGGAGCUAUCCAUCCUUCGGUUCAG
.........(((((.....)))))......(((((((.(((...............(((.(.(((((.....))))).).))).........(((....)))))).)))))))... ( -22.60)
>DroEre_CAF1 2765 109 - 1
UAUACAUAAAU---ACAUAAGUAUCCACAUAACCGAGCGAUAUGCAUAC----AUAUACACCAGGACAUAAGGUCCACAAUUACUUUUCACAGGAGCUAUCCAUCCCUCGGUUCAG
.........((---((....))))......(((((((.(((........----..........((((.....))))................(((....)))))).)))))))... ( -21.10)
>DroYak_CAF1 1475 103 - 1
UAUACAUA---------CAAGUAUCCACUUAACCGAGCGAUAUGCAUAC----AUAUACACCAGGACAUAAGGUCCACAAGUACUUUUCCCAGGAGCUAUCCAUCCCUCGGUUCAG
.((((...---------...))))...((.(((((((.(((........----..........((((.....))))................(((....)))))).))))))).)) ( -22.30)
>consensus
UAUACAUACAUACUACAUAGGUAUCCACAUAACCGAGCGAUAUGCAUACAUA_AUAUACACCAGGACAUAAGGUCCACGAGUACUUUUCCCAGGAGCUAUCCAUCCUUCGGUUCAG
..............................(((((((.(((......................((((.....))))................(((....)))))).)))))))... (-19.64 = -19.40 +  -0.24)

alignment

secondary structure

dotplot

Window 4

Location	2,779,556 – 2,779,662
Length	106
Sequences	5
Columns	106
Reading direction	forward
Mean pairwise identity	90.22
Mean single sequence MFE	-31.50
Consensus MFE	-24.32
Energy contribution	-24.96
Covariance contribution	0.64
Combinations/Pair	1.03
Mean z-score	-2.65
Structure conservation index	0.77
SVM decision value	1.82
SVM RNA-class probability	0.978560
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2779556 106 + 22407834
GGACCUUAUGUCCUGGUGUAUAUAUAUGUAUGCAUAUCGCUCGGUUAUGUUGAUACCUAUGUAGUAUGUAUGUAUAUGCCGUAUGCUGUGUUCAUACUAUGCGGUG
((((.....)))).((((((((((((((((((((((....((((.....))))....)))))).))))))))))))))))....(((((((.......))))))). ( -30.80)
>DroSec_CAF1 2933 106 + 1
GGACCUUAUGUCCUGGUGUAUAUGUAUGUAUGCACAUCGCUCGGUUAUGUGGAUACCUGUGUAGUAUGUAUGUAUAUGCCGUAUGCUGUGUUCAUACUAUGCGGUG
((((.....))))..((((((((....))))))))(((((..(((...((((((((..(((((((((((....))))))..))))).)))))))))))..))))). ( -33.90)
>DroSim_CAF1 2896 106 + 1
GGACCUUAUGUCCAGGUGUAUAUGUAUGUAUGCAUAUCGCUCGGUUAUGUGGAUACCUAUGUAGUAUGUAUGUAUAUGCCGUAUGCUGUGUUCAUACUAUGCCGUG
((((.....)))).((((.(((((((....)))))))))))((((..(((((((((.((((..((((((....))))))..))))..)))))))))....)))).. ( -32.70)
>DroEre_CAF1 2805 99 + 1
GGACCUUAUGUCCUGGUGUAUAU----GUAUGCAUAUCGCUCGGUUAUGUGGAUACUUAUGU---AUUUAUGUAUAUGCCGUAUGCUGUGUUCAUACUAUGCGGUG
((((.....)))).(.((((((.----(((((.((((.((.(((((((((((((((....))---)))))))))...))))...)).)))).))))))))))).). ( -32.70)
>DroYak_CAF1 1515 93 + 1
GGACCUUAUGUCCUGGUGUAUAU----GUAUGCAUAUCGCUCGGUUAAGUGGAUACUUG---------UAUGUAUAUGCCGUAUGCUGUGUUCAUACUAUGCGGUG
((((.....)))).(.((((((.----(((((.((((.((.((((...(((.(((....---------))).)))..))))...)).)))).))))))))))).). ( -27.40)
>consensus
GGACCUUAUGUCCUGGUGUAUAU_UAUGUAUGCAUAUCGCUCGGUUAUGUGGAUACCUAUGUAGUAUGUAUGUAUAUGCCGUAUGCUGUGUUCAUACUAUGCGGUG
((((.....))))....(((((.....(((((.((((.((.((((.(((((.((((...........)))).)))))))))...)).)))).)))))))))).... (-24.32 = -24.96 +   0.64)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:49:44 2006