AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i161_Porphyrin_Biosynthesis_2_mthe_reg_100.orf -o161_mthe_100.ace -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -g0.50 -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 =  	0.5
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RTH00498	139	M.thermo
#2	RTH01395	78	M.thermo
#3	RTH01946	82	M.thermo

Motif number 1

TTCCACCCCCTTAAATAGGTCC         	1	2	0	TTAAATAGTC	    0.978373	-138
CTCTCTAAACTTATATAGTTCCACCCCCTTA	1	20	0	TTATATATTC	    0.941215	-120
 TAGAACACCTTTAATAACTCTGTAGACATG	1	120	0	TTTAATACTC	    0.981397	-20
TAAGACTTGATTAAATCCCTCTAAGAAGGAC	2	42	0	TTAAATCCTC	    0.993218	-37
          TTTAATCCTTCACTGCCCTGT	3	1	1	TTTAATCTTC	    0.975912	-82
GAATTAGATGTTAAAAACCACCTTACAGGGC	3	25	0	TTAAAAACAC	    0.916334	-58
CACACACATTTTAAAACTTTCTGAATTAGAT	3	47	0	TTAAAACTTC	     0.97591	-36
          ******* ***

Masking position 5
Map Score:   8.76194

Number of sites scoring better than the average of aligned sites = 78
Number in coding regions = 50
Number in noncoding regions = 28
Number of orfs with sites within 600 bp upstream = 29
Fraction of orfs with sites within 600 bp upstream = 0.00465789


Motif number 2

GAGAGTGCCACAGAAAAATAATGATAATAA	1	46	1	CAGAAAAATA	    0.963271	-94
TGGATATTTCCAGAGAAGGATGACCAGACC	1	85	1	CAGAGAAGGA	    0.996678	-55
TTAAATCCCTCTAAGAAGGACACTGATCAT	2	33	0	CTAAGAAGGA	    0.945864	-46
CCTTACAGGGCAGTGAAGGATTAAA     	3	6	0	CAGTGAAGGA	    0.995246	-77
AATGTGTGTGCAGTAAAATATTTTA     	3	68	1	CAGTAAAATA	    0.948193	-15
          **********

Masking position 6
Map Score:   5.40849

Number of sites scoring better than the average of aligned sites = 389
Number in coding regions = 368
Number in noncoding regions = 21
Number of orfs with sites within 600 bp upstream = 22
Fraction of orfs with sites within 600 bp upstream = 0.00353357


Motif number 3

 GGACCTATTTAAGGGGGTGGAACTATATA	1	10	1	TAAGGGGGTG	     0.99301	-130
TAATGATAATAAAGGCGGGTCTGGATATTT	1	64	1	AAAGGCGGGT	    0.967359	-76
ACAGAGTTATTAAAGGTGTTCTA       	1	127	1	TAAAGGTGTT	    0.902899	-13
AGTGTCCTTCTTAGAGGGATTTAATCAAGT	2	39	1	TTAGAGGGAT	    0.907339	-40
TAATCAAGTCTTAGGCGGTTGGTGGCTTC 	2	60	1	TTAGGCGGTT	    0.993052	-19
CACTGCCCTGTAAGGTGGTTTTTAACATCT	3	21	1	TAAGGTGGTT	    0.989877	-62
          **********

Masking position 3
Map Score:   5.06595

Number of sites scoring better than the average of aligned sites = 411
Number in coding regions = 360
Number in noncoding regions = 51
Number of orfs with sites within 600 bp upstream = 50
Fraction of orfs with sites within 600 bp upstream = 0.00803084


Motif number 4

CTATTTAAGGGGGTGGAACTATATAAGTTT	1	15	1	GGGTGGAACT	    0.974314	-125
CATTATTTTTCTGTGGCACTCTCTAAACTT	1	39	0	CTGTGGCACT	    0.986301	-101
GGTCATCCTTCTCTGGAAATATCCAGACCC	1	80	0	CTCTGGAAAT	    0.987348	-60
CATGATGATGGTCTGGTCATCCTTCTCTGG	1	94	0	GTCTGGTCAT	     0.95815	-46
TTTAATAACTCTGTAGACATGATGATGGTC	1	111	0	CTGTAGACAT	    0.958541	-29
          **********

Masking position 4
Map Score:   1.15246

Number of sites scoring better than the average of aligned sites = 310
Number in coding regions = 282
Number in noncoding regions = 28
Number of orfs with sites within 600 bp upstream = 28
Fraction of orfs with sites within 600 bp upstream = 0.00449727


Motif number 5

          **********

No masking
Map Score:   8.97716e-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:   8.97716e-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 7

          **********

No masking
Map Score:   8.97716e-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