AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i218_Ribosomal_Operon_5_mtub_reg_300.orf -a/home/amcguire/alignace/lib/ORF_mtub.txt -z/skink1/amcguire/genomes/mtub.fna -g0.66 -x5 
Parameter values:
 expect =  	5
 ncols =   	10
 npass =   	1000
 maxnpass =	100
 nruns =   	1000
 maxnruns =	100
 repeat =  	15
 maxreps = 	3
 nread =   	500
 ncycles = 	1
 fragment =	1
 psfact =  	0.1
 gcback =  	0.66
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	rpmB2	112	rpmB2

Motif number 1

  CGTCCTCCTTATCGATAACAGTTTTCAT	1	9	1	TTATCGATAA	    0.499962	-104
TCGATAACAGTTTTCATTATTGCGACGTCG	1	22	1	TTTTCATTAT	    0.964512	-91
TTGAAAATCATTTTCGACAACAGCTAGGTG	1	64	0	TTTTCGACAA	    0.580043	-49
TCGAAAATGATTTTCAATAAGCCGAGCTTC	1	77	1	TTTTCAATAA	    0.750041	-36
          **********

Masking position 4
Map Score:   5.93426

Number of sites scoring better than the average of aligned sites = 21
Number in coding regions = 14
Number in noncoding regions = 7
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 2

AATAATGAAAACTGTTATCGATAAGGAGGA	1	13	0	ACTGTTATCG	    0.995672	-100
GTGGCACTGTACCGTCGACGTCGCAATAAT	1	37	0	ACCGTCGACG	    0.996038	-76
GTGCCACCTAGCTGTTGTCGAAAATGATTT	1	60	1	GCTGTTGTCG	    0.998108	-53
          **********

Masking position 5
Map Score:   2.91168

Number of sites scoring better than the average of aligned sites = 663
Number in coding regions = 632
Number in noncoding regions = 31
Number of orfs with sites within 600 bp upstream = 28
Fraction of orfs with sites within 600 bp upstream = 0.00449727


Motif number 3

CGACGTCGACGGTACAGTGCCACCTAGCTG	1	44	1	GGTACAGTGC	    0.996472	-69
GAGCTTCGAAGGAAGGGTGCCCC       	1	100	1	GGAAGGGTGC	    0.989789	-13
          **********

Masking position 4
Map Score:   0.20652

Number of sites scoring better than the average of aligned sites = 28
Number in coding regions = 23
Number in noncoding regions = 5
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 4

          **********

No masking
Map Score:   1.3033e-13

Number of sites scoring better than the average of aligned sites = 0
Number in coding regions = 0
Number in noncoding regions = 0
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0


Motif number 5

          **********

No masking
Map Score:   1.3033e-13

Number of sites scoring better than the average of aligned sites = 0
Number in coding regions = 0
Number in noncoding regions = 0
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0


Motif number 6

          **********

No masking
Map Score:   1.3033e-13

Number of sites scoring better than the average of aligned sites = 0
Number in coding regions = 0
Number in noncoding regions = 0
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0