Locus 535

Sequence ID	3R_DroMel_CAF1
Location	1,966,648 – 1,966,743
Length	95
Max. P	0.803830

overview

Window 1

Location	1,966,648 – 1,966,743
Length	95
Sequences	6
Columns	105
Reading direction	forward
Mean pairwise identity	80.26
Mean single sequence MFE	-21.70
Consensus MFE	-14.77
Energy contribution	-14.93
Covariance contribution	0.17
Combinations/Pair	1.00
Mean z-score	-1.77
Structure conservation index	0.68
SVM decision value	0.63
SVM RNA-class probability	0.803830
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1966648 95 + 27905053
ACA----AUCGGAUGGACAGACAAUGUGCAAAAAAUAAUGAAUAUUGCAUUCAAAUUUUACAAGUGCCACUUAGGCACGCGCACCCCC---ACCCUC---UCCCG
...----...(((.((........(((((.........(((((.....)))))..........(((((.....)))))))))).....---...)).---))).. ( -20.89)
>DroVir_CAF1 148468 96 + 1
AGC----UUUUGGCCGACAGACAAUGUGCAAAGAAUAAUGAAUAUUACAUUCAAAUUGUACGAGUGCCACUUAGGCACGCGC---ACACACACACAGAC-UCCC-
...----.((((.....))))...(((((.........(((((.....)))))........(.(((((.....))))).)))---)))...........-....- ( -19.30)
>DroPse_CAF1 106621 92 + 1
ACGGGCAGACGGACCGACAGACAAUGUGCAAAAAAUAAUGAAUAUUACAUUCAAAUUUUACGAGUGCCACUUAGGCACGCGC---CCC---GCU-------CCCC
..(((.((.(((..(....).....((((.........(((((.....)))))..........(((((.....)))))))))---.))---)))-------))). ( -24.60)
>DroYak_CAF1 129797 95 + 1
ACA----UUCGGACGGACAGACAAUGUGCAAAAAAUAAUGAAUAUUGCAUUCAAAUUUUACGAGUGCCACUUAGGCACGCGC---CCC---ACCCUCUCCCCCCU
...----...((..(((.((.....((((.........(((((.....)))))..........(((((.....)))))))))---...---...)).)))..)). ( -21.20)
>DroAna_CAF1 106725 95 + 1
ACGG-CGAACGUACAGACAGACAAUGUGCAAAAAAUAAUGAAUAUUACAUUCAAAUUUUACGAGUGCCACUUAGGCACGCCC---CCG---CAUUUC---GCCCG
..((-((((.(((((.........))))).........(((((.....)))))..........(((((.....)))))((..---..)---)..)))---))).. ( -24.10)
>DroPer_CAF1 107750 92 + 1
ACGGACAGACGGACCGACAGACAAUGUGCAAAAAAUAAUGAAUAUUACAUUCAAAUUUUACGAGUGCCACUUAGGCACGCGC---CCC---GCU-------CCCC
..((..((.(((..(....).....((((.........(((((.....)))))..........(((((.....)))))))))---.))---)))-------..)) ( -20.10)
>consensus
ACG____AACGGACCGACAGACAAUGUGCAAAAAAUAAUGAAUAUUACAUUCAAAUUUUACGAGUGCCACUUAGGCACGCGC___CCC___ACUCUC____CCCC
.........................((((.........(((((.....)))))..........(((((.....)))))))))....................... (-14.77 = -14.93 +   0.17)

alignment

secondary structure

dotplot

Window 2

Location	1,966,648 – 1,966,743
Length	95
Sequences	6
Columns	105
Reading direction	reverse
Mean pairwise identity	80.26
Mean single sequence MFE	-31.14
Consensus MFE	-14.84
Energy contribution	-15.48
Covariance contribution	0.64
Combinations/Pair	1.09
Mean z-score	-2.24
Structure conservation index	0.48
SVM decision value	-0.04
SVM RNA-class probability	0.514976
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1966648 95 - 27905053
CGGGA---GAGGGU---GGGGGUGCGCGUGCCUAAGUGGCACUUGUAAAAUUUGAAUGCAAUAUUCAUUAUUUUUUGCACAUUGUCUGUCCAUCCGAU----UGU
...((---..((((---(((.(.((..(((((.....))))).(((((((..((((((...)))))).....)))))))....)).).)))))))..)----).. ( -28.50)
>DroVir_CAF1 148468 96 - 1
-GGGA-GUCUGUGUGUGUGU---GCGCGUGCCUAAGUGGCACUCGUACAAUUUGAAUGUAAUAUUCAUUAUUCUUUGCACAUUGUCUGUCGGCCAAAA----GCU
-((.(-(.(.((((((.(((---(((.(((((.....))))).))))))...((((((...)))))).........)))))).).)).))(((.....----))) ( -31.80)
>DroPse_CAF1 106621 92 - 1
GGGG-------AGC---GGG---GCGCGUGCCUAAGUGGCACUCGUAAAAUUUGAAUGUAAUAUUCAUUAUUUUUUGCACAUUGUCUGUCGGUCCGUCUGCCCGU
(((.-------(((---(((---.((((((((.....)))))..((((((..((((((...)))))).....)))))).........).)).)))).)).))).. ( -33.00)
>DroYak_CAF1 129797 95 - 1
AGGGGGGAGAGGGU---GGG---GCGCGUGCCUAAGUGGCACUCGUAAAAUUUGAAUGCAAUAUUCAUUAUUUUUUGCACAUUGUCUGUCCGUCCGAA----UGU
.(((.(((.(((((---(..---(((.(((((.....))))).)))..........(((((.............))))))))..))).))).)))...----... ( -30.32)
>DroAna_CAF1 106725 95 - 1
CGGGC---GAAAUG---CGG---GGGCGUGCCUAAGUGGCACUCGUAAAAUUUGAAUGUAAUAUUCAUUAUUUUUUGCACAUUGUCUGUCUGUACGUUCG-CCGU
..(((---(((.((---(((---(((((((((.....)))))..((((((..((((((...)))))).....)))))).....))))..)))))..))))-)).. ( -32.60)
>DroPer_CAF1 107750 92 - 1
GGGG-------AGC---GGG---GCGCGUGCCUAAGUGGCACUCGUAAAAUUUGAAUGUAAUAUUCAUUAUUUUUUGCACAUUGUCUGUCGGUCCGUCUGUCCGU
(((.-------(((---(((---.((((((((.....)))))..((((((..((((((...)))))).....)))))).........).)).)))).)).))).. ( -30.60)
>consensus
CGGG____GAGAGU___GGG___GCGCGUGCCUAAGUGGCACUCGUAAAAUUUGAAUGUAAUAUUCAUUAUUUUUUGCACAUUGUCUGUCGGUCCGAA____CGU
.................(((...(((.(((((.....))))).)((((((..((((((...)))))).....)))))).........))...))).......... (-14.84 = -15.48 +   0.64)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:45:26 2006