AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00561_pyro_reg_100.orf -o00561_pyro_100.ace -a/home/amcguire/genomes/ORF_pyro.txt -z/home/amcguire/genomes/pyro.fna -g0.42 -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 =  	0.42
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	PH1884	27	231aa long hypothetical triosephosphate isomerase
#2	PH1886	206	272aa long hypothetical L-isoaspartyl protein carboxyl methyltransferase

Motif number 1

ACACGATAGAGTGGCCGGGGTGGTGTAGCC	2	71	1	GTGGCCGGGG	    0.999481	-136
CCGGGGTGGTGTAGCCTGGTTAGCACAGGG	2	85	1	GTAGCCTGGT	    0.976304	-122
GGGATCCACAGTCCCCTGTGCTAACCAGGC	2	98	0	GTCCCCTGTG	    0.976702	-109
ATTTGAACCCGGGCCAGGGGATCCACAGTC	2	115	0	GGGCCAGGGG	    0.996355	-92
GTCTGTTTCTGGGGCCGGGGCCGGGATTTG	2	140	0	GGGGCCGGGG	    0.999519	-67
          **********

Masking position 5
Map Score:   9.39321

Number of sites scoring better than the average of aligned sites = 82
Number in coding regions = 69
Number in noncoding regions = 13
Number of orfs with sites within 600 bp upstream = 14
Fraction of orfs with sites within 600 bp upstream = 0.00224863


Motif number 2

AGTTTTCGCCAAAATCGAGAGAAGAAGGAG	2	20	0	AAAATCGAGA	    0.991715	-187
CCAGGAGCACACGATAGAGTGGCCGGGGTG	2	63	1	ACGATAGAGT	    0.963948	-144
GACTTTTCTGAAAATAAAGATTTAACAAAG	2	167	1	AAAATAAAGA	     0.95116	-40
GCTTCTTCAAGCAATCGAGAC         	2	196	1	GCAATCGAGA	    0.990874	-11
          **********

Masking position 5
Map Score:   1.09525

Number of sites scoring better than the average of aligned sites = 139
Number in coding regions = 128
Number in noncoding regions = 11
Number of orfs with sites within 600 bp upstream = 14
Fraction of orfs with sites within 600 bp upstream = 0.00224863


Motif number 3

ATCGTGTGCTCCTGGATTAGATTTATAAAGT	2	47	0	CCGGATTAGA	    0.986537	-160
GGGATTTGAACCCGGGCCAGGGGATCCACAG	2	117	0	CCGGGCCAGG	    0.604344	-90
GGGGCCGGGGCCGGGATTTGAACCCGGGCCA	2	129	0	CCGGATTTGA	    0.989838	-78
GGCCCCGGCCCCAGAAACAGACTTTTCTGAA	2	148	1	CCGAAACAGA	    0.960493	-59
          ** ********

Masking position 4
Map Score:   0.949159

Number of sites scoring better than the average of aligned sites = 77
Number in coding regions = 73
Number in noncoding regions = 4
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 4

          **********

No masking
Map Score:   7.34864e-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:   7.34864e-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 6

          **********

No masking
Map Score:   7.34864e-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