Locus 123

Sequence ID	3R_DroMel_CAF1
Location	681,231 – 681,370
Length	139
Max. P	0.980154

overview

Window 2

Location	681,231 – 681,351
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.08
Mean single sequence MFE	-29.08
Consensus MFE	-26.36
Energy contribution	-26.80
Covariance contribution	0.44
Combinations/Pair	1.03
Mean z-score	-1.72
Structure conservation index	0.91
SVM decision value	1.85
SVM RNA-class probability	0.980154
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 681231 120 + 27905053
AAUCUGUUCGGACAACAGUAUUUUCUUUUGCACACUCAUCGAAAGGUAAUUAAAAUGUUUCGAUUUGAUUUCGAGACGCCGCCAUAUUGUGUUCGAUUUUGGAACAAUCAUGUGGCAUUA
...(((((.....)))))...........((......(((....))).........(((((((.......))))))))).(((((((..(((((.......)))))...))))))).... ( -30.30)
>DroSec_CAF1 100636 120 + 1
AAUCUGUUCGGACAACAGUAUUUUCUUUUGCACACUCAUCGAAAGGUAAUUAAAAUGUUUCGAUUUGAUUUCGAGACGCCGCCAUAUUGUGUUCGAUUUGGGAACAAUCAUGUGGCAUUA
...(((((.....)))))...........((......(((....))).........(((((((.......))))))))).(((((((..(((((.......)))))...))))))).... ( -30.30)
>DroSim_CAF1 100895 120 + 1
AAUCUGUUCGGACAACAGUAUUUUCUUUUGCACACUCAUCGAAAGGUAAUUAAAAUGUUUCGAUUUGAUUUCGAGACGCCGCCAUAUUGUGUUCGAUUUUGGAACAAUCAUGUGGCAUUA
...(((((.....)))))...........((......(((....))).........(((((((.......))))))))).(((((((..(((((.......)))))...))))))).... ( -30.30)
>DroEre_CAF1 97941 120 + 1
AGUCCGUUCAGACAACAGUAUUUUCUUUUGCACACUCAUCGAAAGGUAAUUAAAAUGUUUCGAUUUGAUUUCGAGACGCCGCCAUAUUGUGUUCGAUUUUGGAACAAUCAUGUGGCAUUA
.(((((.(((((.....(((........))).......((((((.((.......)).)))))))))))...)).)))...(((((((..(((((.......)))))...))))))).... ( -30.20)
>DroYak_CAF1 110542 120 + 1
AAUCUGUUCGGACAACAGUAUUUUCUUUUGCACACUCAUCAUAAAGUGAUUAAAAUGUUUCGAUUUGAUUUUGAGACGCCGCCAUAUUGUUUUCAAUUUCGGAACAAUCAUGUGGCAUUA
...(((((.....)))))..............((((........))))........(((((((.......)))))))(((((...((((((((.......))))))))...))))).... ( -24.30)
>consensus
AAUCUGUUCGGACAACAGUAUUUUCUUUUGCACACUCAUCGAAAGGUAAUUAAAAUGUUUCGAUUUGAUUUCGAGACGCCGCCAUAUUGUGUUCGAUUUUGGAACAAUCAUGUGGCAUUA
...(((((.....)))))...........((......(((....))).........(((((((.......))))))))).(((((((..(((((.......)))))...))))))).... (-26.36 = -26.80 +   0.44)

alignment

secondary structure

dotplot

Window 3

Location	681,271 – 681,370
Length	99
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	84.89
Mean single sequence MFE	-31.32
Consensus MFE	-22.60
Energy contribution	-22.48
Covariance contribution	-0.12
Combinations/Pair	1.08
Mean z-score	-2.70
Structure conservation index	0.72
SVM decision value	1.64
SVM RNA-class probability	0.969592
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 681271 99 + 27905053
GAAAGGUAAUUAAAAUGUUUCGAUUUGAUUUCGAGACGCCGCCAUAUUGUGUUCGAUUUUGGAACAAUCAUGUGGCAUUAUAAUGA-----------------GUUGGUUG----CUGUA
....(((((((((...(((((((.......)))))))...(((((((..(((((.......)))))...)))))))..........-----------------.)))))))----))... ( -29.90)
>DroSec_CAF1 100676 99 + 1
GAAAGGUAAUUAAAAUGUUUCGAUUUGAUUUCGAGACGCCGCCAUAUUGUGUUCGAUUUGGGAACAAUCAUGUGGCAUUAUAAUGA-----------------GUUGCUUG----CUGUA
...((((((((.....(((((((.......)))))))...(((((((..(((((.......)))))...))))))).........)-----------------))))))).----..... ( -28.80)
>DroSim_CAF1 100935 99 + 1
GAAAGGUAAUUAAAAUGUUUCGAUUUGAUUUCGAGACGCCGCCAUAUUGUGUUCGAUUUUGGAACAAUCAUGUGGCAUUAUAAUGA-----------------GUUGCUUG----CUGUA
...((((((((.....(((((((.......)))))))...(((((((..(((((.......)))))...))))))).........)-----------------))))))).----..... ( -28.80)
>DroEre_CAF1 97981 116 + 1
GAAAGGUAAUUAAAAUGUUUCGAUUUGAUUUCGAGACGCCGCCAUAUUGUGUUCGAUUUUGGAACAAUCAUGUGGCAUUAUAAUGAUCUCGGGGACGCUGUGAGUUGGUUG----CUGUA
....(((((((((...(((((((.......)))))))((.(((((((..(((((.......)))))...)))))))..............(....)))......)))))))----))... ( -33.10)
>DroYak_CAF1 110582 120 + 1
AUAAAGUGAUUAAAAUGUUUCGAUUUGAUUUUGAGACGCCGCCAUAUUGUUUUCAAUUUCGGAACAAUCAUGUGGCAUUAUAAUGAUCUAAGGGCCGCUGUGAGUCGGUGGCUGGCUGUA
....((((((((....(((((((.......)))))))(((((...((((((((.......))))))))...))))).......)))))....((((((((.....)))))))).)))... ( -36.00)
>consensus
GAAAGGUAAUUAAAAUGUUUCGAUUUGAUUUCGAGACGCCGCCAUAUUGUGUUCGAUUUUGGAACAAUCAUGUGGCAUUAUAAUGA_________________GUUGGUUG____CUGUA
.....(((((......(((((((.......)))))))...(((((((..(((((.......)))))...))))))))))))....................................... (-22.60 = -22.48 +  -0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:33:49 2006