AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i155_Hydrogenase_2_pyro_reg_100.orf -o155_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	RPH01185	211	Pyrococcus_OT3

Motif number 1

ATATTTAAGCCCCGCACCTTGACCTTTTATTT	1	21	0	CCCGACTTGA	    0.998403	-191
ATCATCAAAGCTTGGTCTTTGAAAAAAAGAGT	1	67	1	CTTGTCTTGA	      0.9915	-145
CGTTTTTAAACCCGAAAATTGAAAACCAAAGG	1	105	0	CCCGAATTGA	    0.989764	-107
GCTTTTTTATCCTGGACTTTAACTCGTTATCG	1	136	1	CCTGACTTAA	     0.99609	-76
GATGCTCATCCCTGATCCTCGATAACGAGTTA	1	155	0	CCTGTCTCGA	    0.996386	-57
CATGGTTAATCCTGTTCATTAATGGAGGTGAT	1	186	1	CCTGTCTTAA	     0.99609	-26
          **** ** ****

Masking position 9
Map Score:   13.2265

Number of sites scoring better than the average of aligned sites = 65
Number in coding regions = 57
Number in noncoding regions = 8
Number of orfs with sites within 600 bp upstream = 9
Fraction of orfs with sites within 600 bp upstream = 0.00144555


Motif number 2

ATGATAAATATATTTAAGCCCCGCACCTTGAC	1	30	0	TTTTAACCCC	    0.994703	-182
ATATTTATCATATATAATCATCAAAGCTTGGT	1	51	1	TTATAACATC	    0.910172	-161
TAAAAAAGCGTTTTTAAACCCGAAAATTGAAA	1	113	0	TTTTAACCCG	    0.996357	-99
TTAAAAACGCTTTTTTATCCTGGACTTTAACT	1	128	1	TTTTTACCTG	    0.987183	-84
ATGAGCATCATGGTTAATCCTGTTCATTAATG	1	178	1	TGTTAACCTG	    0.991315	-34
          * ***** ****

Masking position 7
Map Score:   4.17981

Number of sites scoring better than the average of aligned sites = 87
Number in coding regions = 72
Number in noncoding regions = 15
Number of orfs with sites within 600 bp upstream = 17
Fraction of orfs with sites within 600 bp upstream = 0.00273049


Motif number 3

CCCGCACCTTGACCTTTTATTTGGTGAAAA	1	13	0	GACCTTTTAT	    0.963495	-199
TTCAAAGACCAAGCTTTGATGATTATATAT	1	60	0	AAGCTTTGAT	    0.984432	-152
AAGGTTGAGAACTCTTTTTTTCAAAGACCA	1	79	0	ACTCTTTTTT	    0.958655	-133
AAGAGTTCTCAACCTTTGGTTTTCAATTTT	1	93	1	AACCTTTGGT	    0.981049	-119
GGGTTTAAAAACGCTTTTTTATCCTGGACT	1	124	1	ACGCTTTTTT	    0.984433	-88
          **********

Masking position 5
Map Score:   3.37089

Number of sites scoring better than the average of aligned sites = 169
Number in coding regions = 139
Number in noncoding regions = 30
Number of orfs with sites within 600 bp upstream = 35
Fraction of orfs with sites within 600 bp upstream = 0.00562159


Motif number 4

          **********

No masking
Map Score:   -1.60993e-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:   -1.60993e-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:   -1.60993e-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