AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i155_Hydrogenase_2_pyro_reg_300.orf -o155_pyro_300.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	    0.998419	-191
ATCATCAAAGCTTGGTCTTTGAAAAAAAGAGT	1	67	1	CTTGTCTTGA	    0.991584	-145
CGTTTTTAAACCCGAAAATTGAAAACCAAAGG	1	105	0	CCCGAATTGA	    0.989866	-107
GCTTTTTTATCCTGGACTTTAACTCGTTATCG	1	136	1	CCTGACTTAA	    0.996129	-76
GATGCTCATCCCTGATCCTCGATAACGAGTTA	1	155	0	CCTGTCTCGA	    0.996422	-57
CATGGTTAATCCTGTTCATTAATGGAGGTGAT	1	186	1	CCTGTCTTAA	    0.996129	-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

GTCAAGGTGCGGGGCTTAAATATATTTATCAT	1	30	1	GGGGTTAAAA	    0.995369	-182
ACCAAGCTTTGATGATTATATATGATAAATAT	1	51	0	GATGTTATAA	    0.920618	-161
TTTCAATTTTCGGGTTTAAAAACGCTTTTTTA	1	113	1	CGGGTTAAAA	    0.996816	-99
AGTTAAAGTCCAGGATAAAAAAGCGTTTTTAA	1	128	0	CAGGTAAAAA	    0.988783	-84
CATTAATGAACAGGATTAACCATGATGCTCAT	1	178	0	CAGGTTAACA	    0.992403	-34
          **** ***** *

Masking position 6
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	     0.96162	-199
TTCAAAGACCAAGCTTTGATGATTATATAT	1	60	0	AAGCTTTGAT	    0.983614	-152
AAGGTTGAGAACTCTTTTTTTCAAAGACCA	1	79	0	ACTCTTTTTT	    0.956543	-133
AAGAGTTCTCAACCTTTGGTTTTCAATTTT	1	93	1	AACCTTTGGT	    0.980107	-119
GGGTTTAAAAACGCTTTTTTATCCTGGACT	1	124	1	ACGCTTTTTT	    0.983615	-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