AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i115_tpal_bbur_100.orf -o115_tpal_bbur_100.ace -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/synecho.fna -g0.40 -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 =  	0.4
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RBB00590	153	3615

Motif number 1

    AATTCTAGTTTAATTGGTATAAATTGTA	1	7	1	AGTTTTTGGT	    0.957996	-147
ATCTTTTGTTAATACAATTTATACCAATTAAA	1	19	0	AATACTTTAT	    0.918443	-135
GATCCTTTAAAGGATCTTTTGTTAATACAATT	1	32	0	AGGATTTTGT	    0.995244	-122
GATCCTTTAAAGGATCTTTTGTTTTTTTATTT	1	48	1	AGGATTTTGT	    0.995244	-106
TAATAATTTTAGTATAATTTATAATGATGTGT	1	96	1	AGTATTTTAT	    0.993785	-58
ATAAGCCTGCATTATGCTTTATAACACATCAT	1	119	0	ATTATTTTAT	    0.968206	-35
          *****  *****

Masking position 8
Map Score:   6.87461

Number of sites scoring better than the average of aligned sites = 116
Number in coding regions = 39
Number in noncoding regions = 77
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 2

        AATTCTAGTTTAATTGGTATAA	1	3	1	TTCTAGTTTA	    0.972469	-151
AAGGATCTTTTGTTAATACAATTTATACCA	1	25	0	TGTTAATACA	    0.945462	-129
TCTTTTGTTTTTTTATTTCAGATCGGCAAA	1	62	1	TTTTATTTCA	    0.970735	-92
AATTTAATAATTTTAGTATAATTTATAATG	1	92	1	TTTTAGTATA	    0.983564	-62
          **********

Masking position 5
Map Score:   1.02829

Number of sites scoring better than the average of aligned sites = 127
Number in coding regions = 43
Number in noncoding regions = 84
Number of orfs with sites within 600 bp upstream = 1
Fraction of orfs with sites within 600 bp upstream = 0.000160617


Motif number 3

          **********

No masking
Map Score:   -8.99385e-14

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:   -8.99385e-14

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:   -8.99385e-14

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