AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i161_Porphyrin_Biosynthesis_2_mthe_reg_300.orf -o161_mthe_300.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	    0.976589	-138
CTCTCTAAACTTATATAGTTCCACCCCCTTA	1	20	0	TTATATATTC	    0.936566	-120
 TAGAACACCTTTAATAACTCTGTAGACATG	1	120	0	TTTAATACTC	    0.979858	-20
TAAGACTTGATTAAATCCCTCTAAGAAGGAC	2	42	0	TTAAATCCTC	    0.992649	-37
          TTTAATCCTTCACTGCCCTGT	3	1	1	TTTAATCTTC	    0.973931	-82
GAATTAGATGTTAAAAACCACCTTACAGGGC	3	25	0	TTAAAAACAC	    0.909906	-58
CACACACATTTTAAAACTTTCTGAATTAGAT	3	47	0	TTAAAACTTC	    0.973929	-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

TTATTATCATTATTTTTCTGTGGCACTCTC	1	46	0	TATTTTTCTG	     0.96476	-94
GGTCTGGTCATCCTTCTCTGGAAATATCCA	1	85	0	TCCTTCTCTG	    0.996817	-55
ATGATCAGTGTCCTTCTTAGAGGGATTTAA	2	33	1	TCCTTCTTAG	    0.948021	-46
     TTTAATCCTTCACTGCCCTGTAAGG	3	6	1	TCCTTCACTG	    0.995445	-77
     TAAAATATTTTACTGCACACACATT	3	68	0	TATTTTACTG	    0.950262	-15
          **********

Masking position 5
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

TATATAGTTCCACCCCCTTAAATAGGTCC 	1	10	0	CACCCCCTTA	    0.993571	-130
AAATATCCAGACCCGCCTTTATTATCATTA	1	64	0	ACCCGCCTTT	    0.969912	-76
       TAGAACACCTTTAATAACTCTGT	1	127	0	AACACCTTTA	    0.910028	-13
ACTTGATTAAATCCCTCTAAGAAGGACACT	2	39	0	ATCCCTCTAA	    0.914173	-40
 GAAGCCACCAACCGCCTAAGACTTGATTA	2	60	0	AACCGCCTAA	    0.993608	-19
AGATGTTAAAAACCACCTTACAGGGCAGTG	3	21	0	AACCACCTTA	    0.990686	-62
          **********

Masking position 8
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

AAACTTATATAGTTCCACCCCCTTAAATAG	1	15	0	AGTTCCACCC	    0.976418	-125
AAGTTTAGAGAGTGCCACAGAAAAATAATG	1	39	1	AGTGCCACAG	    0.987437	-101
GGGTCTGGATATTTCCAGAGAAGGATGACC	1	80	1	ATTTCCAGAG	    0.988398	-60
CCAGAGAAGGATGACCAGACCATCATCATG	1	94	1	ATGACCAGAC	     0.96153	-46
GACCATCATCATGTCTACAGAGTTATTAAA	1	111	1	ATGTCTACAG	    0.961774	-29
          **********

Masking position 7
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