AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_pyro.txt -z/home/amcguire/genomes/pyro.fna -intrC_pyro_opreg_300.orf -g0.419 -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 =  	0.419
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	PH0359	300	443aa long hypothetical glutamine synthetase
#2	PH1815	24	284aa long hypothetical cobalt transport ATP-binding protein

Motif number 1

ATTAGAGAAATTATCATTAACAGGGTTCCA	1	27	0	TTATCATTAA	    0.897953	-274
AAGTGCTCCCTGACTATTAGAGAAATTATC	1	42	0	TGACTATTAG	     0.90871	-259
TCATGAACATTGAACATTAGACGAAGAAAT	1	216	0	TGAACATTAG	    0.981038	-85
TAATGTTCAATGTTCATGAGTAAAGACTTA	1	227	1	TGTTCATGAG	    0.980242	-74
TTTGGTATATTGTTCACTAAAAGCGGATGA	1	259	1	TGTTCACTAA	    0.967317	-42
TAAAAGCGGATGATCATTAGATAACTATTC	1	276	1	TGATCATTAG	    0.995258	-25
ATTAGATAACTATTCACTAG          	1	291	1	TATTCACTAG	    0.943772	-10
          **********

Masking position 6
Map Score:   7.47599

Number of sites scoring better than the average of aligned sites = 115
Number in coding regions = 98
Number in noncoding regions = 17
Number of orfs with sites within 600 bp upstream = 14
Fraction of orfs with sites within 600 bp upstream = 0.00224863


Motif number 2

        TATTCGCCTTCCTTTATGGAAC	1	3	1	TTCGCCTTCC	    0.989267	-298
TTTATATAGCCTTGACTCTCGGAAGTGCTC	1	64	0	CTTGACTCTC	    0.983494	-237
ACTAAGTTTACTTGCCTTCCTAACCCTCTT	1	93	1	CTTGCCTTCC	    0.995794	-208
        TACTCCCCTCTCCTTGGGAGCA	2	13	0	CTCCCCTCTC	    0.992733	-12
          **********

Masking position 7
Map Score:   2.40269

Number of sites scoring better than the average of aligned sites = 138
Number in coding regions = 132
Number in noncoding regions = 6
Number of orfs with sites within 600 bp upstream = 8
Fraction of orfs with sites within 600 bp upstream = 0.00128493


Motif number 3

TCCTTTATGGAACCCTGTTAATGATAATTT	1	20	1	AACCCTGTTA	    0.982221	-281
TTGCCTTCCTAACCCTCTTACTTGCTGGGG	1	104	1	AACCCTCTTA	    0.993306	-197
AAAGCACAATAACCCCCAAATTTTAACTGA	1	158	1	AACCCCCAAA	     0.98015	-143
AGAAATCTTCTACCCACTAATATACTGTCA	1	192	0	TACCCACTAA	    0.970857	-109
          **********

Masking position 2
Map Score:   2.33936

Number of sites scoring better than the average of aligned sites = 116
Number in coding regions = 107
Number in noncoding regions = 9
Number of orfs with sites within 600 bp upstream = 12
Fraction of orfs with sites within 600 bp upstream = 0.0019274


Motif number 4

          **********

No masking
Map Score:   3.36387e-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:   3.36387e-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:   3.36387e-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