Locus 6108

Sequence ID	3R_DroMel_CAF1
Location	16,013,757 – 16,013,880
Length	123
Max. P	0.994523

overview

Window 8

Location	16,013,757 – 16,013,847
Length	90
Sequences	5
Columns	115
Reading direction	reverse
Mean pairwise identity	73.48
Mean single sequence MFE	-22.18
Consensus MFE	-15.12
Energy contribution	-14.84
Covariance contribution	-0.28
Combinations/Pair	1.35
Mean z-score	-2.22
Structure conservation index	0.68
SVM decision value	2.49
SVM RNA-class probability	0.994523
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16013757 90 - 27905053
UAGACUAUACUUGAUAGGUUAUGACAGCUAUACUUAGUUCGUCAUUAACUAAAUCAAGUGCUUAA-------------------------UAAGUGAUGUGUUUUCCUUACAACC
.......((((((((.((((((((((((((....))))).)))).)))))..)))))))).....-------------------------((((.((.......))))))..... ( -20.70)
>DroSec_CAF1 30224 90 - 1
UAGGCUAUACUUGAUAGGUUAUGACAGCUAUACUUAGUUCGUCAUUAACCAAAUCAAGUGCUAAA-------------------------UAAGUGAUUUGUUUUCUUCACAACC
..(((...(((((((.((((((((((((((....))))).)))).)))))..))))))))))...-------------------------...((((..........)))).... ( -25.10)
>DroSim_CAF1 13624 90 - 1
UAGGCUAUACUUGAUAGGUUAUGACAGCUAUACUUAGUUCGUCAUUAACCAAAUCAAGUGCUAAA-------------------------UAAGUGAUUUGUUUUCUUUGCAACC
..(((...(((((((.((((((((((((((....))))).)))).)))))..))))))))))...-------------------------........((((.......)))).. ( -22.50)
>DroEre_CAF1 13733 114 - 1
UAAGCUACAUCUGAUAGCUUAUGACAGCUGUACUAAGUUCGCCAUUAACCAAAUUAAGUGCUAAGUUCUAUUGUAGCCGCCGCUGUUUUGAAAGUGGUUUC-CUUAUUUGCAACC
...((((((...((.((((......))))(((((.((((.(........).)))).))))).....))...)))))).((((((........))))))...-............. ( -23.30)
>DroYak_CAF1 15088 96 - 1
UAAGCCACACUUGAUAGCUUAUGAUGGCUAUACUUAGUUCGUCAUUACCCAAAUUAAGUG-------------------CCGUUGUUUUGAAAGUGAUUUCCCUUAUUUAAAACC
..(((..((((((((.....((((((((((....))).))))))).......))))))))-------------------..)))((((((((((.(....).))..)))))))). ( -19.30)
>consensus
UAGGCUAUACUUGAUAGGUUAUGACAGCUAUACUUAGUUCGUCAUUAACCAAAUCAAGUGCUAAA_________________________UAAGUGAUUUGUUUUCUUUACAACC
.......((((((((.((((((((((((((....))))).)))).)))))..)))))))).................................((((..........)))).... (-15.12 = -14.84 +  -0.28)

alignment

secondary structure

dotplot

Window 9

Location	16,013,782 – 16,013,880
Length	98
Sequences	5
Columns	116
Reading direction	reverse
Mean pairwise identity	78.92
Mean single sequence MFE	-22.48
Consensus MFE	-17.54
Energy contribution	-17.22
Covariance contribution	-0.32
Combinations/Pair	1.28
Mean z-score	-2.04
Structure conservation index	0.78
SVM decision value	1.51
SVM RNA-class probability	0.960511
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16013782 98 - 27905053
---UUAGUUGAUAAUGUUUAUAAACAAAUUAGGUCGUAGACUAUACUUGAUAGGUUAUGACAGCUAUACUUAGUUCGUCAUUAACUAAAUCAAGUGCUUAA---------------
---.((((((((...((((......))))...)))...)))))((((((((.((((((((((((((....))))).)))).)))))..)))))))).....--------------- ( -22.80)
>DroSec_CAF1 30249 101 - 1
CAUUCAGUUGAUAAUGUUUAUAAACAAAUUAGGUCGUAGGCUAUACUUGAUAGGUUAUGACAGCUAUACUUAGUUCGUCAUUAACCAAAUCAAGUGCUAAA---------------
.........(((...((((......))))...)))...(((...(((((((.((((((((((((((....))))).)))).)))))..))))))))))...--------------- ( -23.90)
>DroSim_CAF1 13649 101 - 1
CAUUCAGUUGAUAAUGUUUAUAAACAAAUUAGGUCGUAGGCUAUACUUGAUAGGUUAUGACAGCUAUACUUAGUUCGUCAUUAACCAAAUCAAGUGCUAAA---------------
.........(((...((((......))))...)))...(((...(((((((.((((((((((((((....))))).)))).)))))..))))))))))...--------------- ( -23.90)
>DroEre_CAF1 13767 104 - 1
CA------------UGUUUAUAAACAAAUUAGGACGUAAGCUACAUCUGAUAGCUUAUGACAGCUGUACUAAGUUCGCCAUUAACCAAAUUAAGUGCUAAGUUCUAUUGUAGCCGC
..------------.........((((..(((((((((((((((....).)))))))).......(((((.((((.(........).)))).)))))...))))))))))...... ( -19.40)
>DroYak_CAF1 15123 97 - 1
CAUUCAGGUGAUAAUGUUUAUAAACAAAUUAGGACGUAAGCCACACUUGAUAGCUUAUGAUGGCUAUACUUAGUUCGUCAUUACCCAAAUUAAGUG-------------------C
...(((((((....((((....)))).....((.(....))).)))))))(((((......)))))(((((((((.(........).)))))))))-------------------. ( -22.40)
>consensus
CAUUCAGUUGAUAAUGUUUAUAAACAAAUUAGGUCGUAGGCUAUACUUGAUAGGUUAUGACAGCUAUACUUAGUUCGUCAUUAACCAAAUCAAGUGCUAAA_______________
...............((((((...(......)...))))))..((((((((.((((((((((((((....))))).)))).)))))..)))))))).................... (-17.54 = -17.22 +  -0.32)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:12:52 2006