Locus 1684

Sequence ID	3R_DroMel_CAF1
Location	4,827,016 – 4,827,123
Length	107
Max. P	0.846415

overview

Window 0

Location	4,827,016 – 4,827,123
Length	107
Sequences	5
Columns	115
Reading direction	forward
Mean pairwise identity	80.27
Mean single sequence MFE	-20.42
Consensus MFE	-15.54
Energy contribution	-16.06
Covariance contribution	0.52
Combinations/Pair	1.12
Mean z-score	-1.79
Structure conservation index	0.76
SVM decision value	0.77
SVM RNA-class probability	0.846415
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4827016 107 + 27905053
A-----AUUCACAAUCUGUUGCAAUAU---GGCUUAAUGUUCAAGGCAUUGCAAAUAAGUAAUUAACGCGGUUCUUGCAUCGUGUAUCUCUUAUUUGCAAUUGUUUUUAUUUUUU
.-----............(((.(((((---......))))))))(((((((((((((((..((..(((((((......)))))))))..))))))))))).)))).......... ( -23.20)
>DroSec_CAF1 7944 112 + 1
AAUUGAAUUCACAAUUUGUUGCAAUAU---GGCUUAAUCUUCCAGGCAUUGCAAAUAUAUAAUUAACGCGUUUCUUACAUCGCGUAUCUCUUAUUUGCAAUUGUUUUUAUUUUUU
...((((..((........(((....(---((.........))).)))(((((((((........(((((..........)))))......))))))))).))..))))...... ( -18.64)
>DroSim_CAF1 7996 107 + 1
A-----AUUCACAAUUUGUUGCAAUAU---GGCUUAAUCUUCCAGGCAUUGCAAAUAUAUAAUUAACGCGGUUCUUGCAUCGCGUAUCUCUUAUUUGCAAUUGUUUUUAUUUUUU
.-----....((((.....(((....(---((.........))).)))(((((((((........(((((((......)))))))......)))))))))))))........... ( -20.94)
>DroEre_CAF1 7917 98 + 1
------------AAUUUUUUGCAAUUUGUUUGCUUAAUGUUCAAGGCAUUACGAAUAAAUAAUCAACGCGGUUCUUGCAAAGCCUAUCUCUUAUUUGCAAUUGUUU-----UCUU
------------......((((((((((((((..((((((.....))))))))))))))).........((((.......))))...........)))))......-----.... ( -15.90)
>DroYak_CAF1 7966 100 + 1
A-----AAU--GAAUUUUUUGCAAUGU---AGCUUUAUAUUUAGGGCAUUGCAAAUAAAUAAUCAACGCGGUUCUUGCAUCGCGUAUCUUCUAUUUGCAAUUGUCU-----UCUU
.-----..(--((((.....((.....---.)).....)))))((((((((((((((........(((((((......)))))))......))))))))).)))))-----.... ( -23.44)
>consensus
A_____AUUCACAAUUUGUUGCAAUAU___GGCUUAAUCUUCAAGGCAUUGCAAAUAAAUAAUUAACGCGGUUCUUGCAUCGCGUAUCUCUUAUUUGCAAUUGUUUUUAUUUUUU
....................(((((......((((........))))..((((((((........(((((((......)))))))......)))))))))))))........... (-15.54 = -16.06 +   0.52)

alignment

secondary structure

dotplot

Window 1

Location	4,827,016 – 4,827,123
Length	107
Sequences	5
Columns	115
Reading direction	reverse
Mean pairwise identity	80.27
Mean single sequence MFE	-18.18
Consensus MFE	-13.72
Energy contribution	-14.36
Covariance contribution	0.64
Combinations/Pair	1.17
Mean z-score	-1.57
Structure conservation index	0.75
SVM decision value	0.31
SVM RNA-class probability	0.683607
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4827016 107 - 27905053
AAAAAAUAAAAACAAUUGCAAAUAAGAGAUACACGAUGCAAGAACCGCGUUAAUUACUUAUUUGCAAUGCCUUGAACAUUAAGCC---AUAUUGCAACAGAUUGUGAAU-----U
...........(((((((((((((((.(((....(((((.......))))).))).))))))))).(((.(((((...))))).)---)).........))))))....-----. ( -20.50)
>DroSec_CAF1 7944 112 - 1
AAAAAAUAAAAACAAUUGCAAAUAAGAGAUACGCGAUGUAAGAAACGCGUUAAUUAUAUAUUUGCAAUGCCUGGAAGAUUAAGCC---AUAUUGCAACAAAUUGUGAAUUCAAUU
...........(((((((((((((.((...(((((.(......).)))))...))...)))))))..(((.(((.........))---)....)))...)))))).......... ( -18.30)
>DroSim_CAF1 7996 107 - 1
AAAAAAUAAAAACAAUUGCAAAUAAGAGAUACGCGAUGCAAGAACCGCGUUAAUUAUAUAUUUGCAAUGCCUGGAAGAUUAAGCC---AUAUUGCAACAAAUUGUGAAU-----U
...........(((((((((((((.((...(((((..........)))))...))...)))))))..(((.(((.........))---)....)))...))))))....-----. ( -18.40)
>DroEre_CAF1 7917 98 - 1
AAGA-----AAACAAUUGCAAAUAAGAGAUAGGCUUUGCAAGAACCGCGUUGAUUAUUUAUUCGUAAUGCCUUGAACAUUAAGCAAACAAAUUGCAAAAAAUU------------
....-----......((((((.....((((((.(..(((.......)))..).))))))........(((.((((...)))))))......))))))......------------ ( -12.10)
>DroYak_CAF1 7966 100 - 1
AAGA-----AGACAAUUGCAAAUAGAAGAUACGCGAUGCAAGAACCGCGUUGAUUAUUUAUUUGCAAUGCCCUAAAUAUAAAGCU---ACAUUGCAAAAAAUUC--AUU-----U
..((-----(....((((((((((((.((((((((..........)))))..))).))))))))))))..............((.---.....))......)))--...-----. ( -21.60)
>consensus
AAAAAAUAAAAACAAUUGCAAAUAAGAGAUACGCGAUGCAAGAACCGCGUUAAUUAUUUAUUUGCAAUGCCUUGAACAUUAAGCC___AUAUUGCAACAAAUUGUGAAU_____U
..............((((((((((((.((((((((.(......).)))))..))).))))))))))))..............((.........)).................... (-13.72 = -14.36 +   0.64)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:16:52 2006