AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i216_Ribosomal_Operon_3_bbur_reg_100.orf -o216_borburg_100.ace -a/home/amcguire/genomes/ORF_borburg.txt -z/home/amcguire/genomes/borburg.fna -g0.28 -x5 -e 
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 =  	0.28
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Purged sequences:
RBB00067	53	3615

Input sequences:
#1	RBB00683	79	3615
#2	RBB00068	158	3615

Motif number 1

CAGTAATTGGTTTTTAATTTTAA        	1	3	0	TTTTTATTTT	    0.983362	-77
AATATTTTTATTTATTATAATATGAAATTGT	1	42	0	TTTATATAAT	    0.933968	-38
TTGACCTTTTTTTAAAATATTTTTATTTATT	1	57	0	TTTAAATATT	    0.977947	-23
         GTTTTTGATATTTTATGAATGT	2	2	1	TTTTTATATT	    0.993808	-157
CTAAAAAACATTTTACATCATAATATCACAT	2	29	0	TTTTAATCAT	    0.891718	-130
CAATACAATATTTTATCTATTCTTAAAAGAC	2	78	0	TTTTACTATT	    0.951896	-81
TGTATTGGTTTTTTTGATATGATATTTTATA	2	102	1	TTTTTATATG	     0.97414	-57
GATATGATATTTTATAATATTTTTTTTATTT	2	117	1	TTTATATATT	    0.987239	-42
TTATAATATTTTTTTTATTTTAAAAATAAAG	2	128	1	TTTTTATTTT	    0.983362	-31
          ***** *****

Masking position 8
Map Score:   17.2026

Number of sites scoring better than the average of aligned sites = 1224
Number in coding regions = 793
Number in noncoding regions = 431
Number of orfs with sites within 600 bp upstream = 90
Fraction of orfs with sites within 600 bp upstream = 0.0144555


Motif number 2

TTATCAGTAATTGGTTTTTAATTTTAA   	1	8	0	TTGGTTTTTA	     0.98204	-72
TTTTAAAATATTTTTATTTATTATAATATG	1	49	0	TTTTTATTTA	    0.907079	-31
        AATTGACCTTTTTTTAAAATAT	1	68	0	TTGACCTTTT	    0.856329	-12
      GTTTTTGATATTTTATGAATGTGA	2	5	1	TTGATATTTT	    0.959391	-154
ATGATGTAAAATGTTTTTTAGCCTTATAAA	2	39	1	ATGTTTTTTA	      0.9676	-120
AAAGGCATGTTTGTCTTTTAAGAATAGATA	2	66	1	TTGTCTTTTA	    0.965939	-93
AAATATTGTATTGGTTTTTTTGATATGATA	2	96	1	TTGGTTTTTT	    0.973923	-63
TTTTTTTGATATGATATTTTATAATATTTT	2	110	1	ATGATATTTT	    0.914526	-49
ATTTTATAATATTTTTTTTATTTTAAAAAT	2	125	1	ATTTTTTTTA	    0.893916	-34
ATACACCTCCTTTATTTTTAAAATAAAAAA	2	138	0	TTTATTTTTA	    0.949004	-21
          **********

Masking position 7
Map Score:   16.7565

Number of sites scoring better than the average of aligned sites = 1738
Number in coding regions = 1144
Number in noncoding regions = 594
Number of orfs with sites within 600 bp upstream = 100
Fraction of orfs with sites within 600 bp upstream = 0.0160617


Motif number 3

          **********

No masking
Map Score:   2.86649e-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 4

          **********

No masking
Map Score:   2.86649e-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:   2.86649e-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