AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -inagC_mthe_opreg_100.orf -g0.495 -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 =  	0.495
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	MTH171	141	glutamine-fructose-6-phosphate transaminase
#2	MTH1591	30	phosphonopyruvate decarboxylase
#3	MTH1592	21	conserved protein
#4	MTH1593	205	ribosomal protein S3a

Motif number 1

ATACTCAAATTCTTTAAAAGTGATAGT   	1	8	0	TCTTTAAAAG	     0.91499	-134
ACTGAATCGCAATATAACTCATAATAGAAT	1	77	0	AATATAACTC	    0.898942	-65
TTCGCAAGATTATATAACTGAATCGCAATA	1	93	0	TATATAACTG	    0.980214	-49
GATAAGGGAGTATTTAAATCTTGACATGGT	4	59	0	TATTTAAATC	    0.916343	-147
TATGGAATACTCTATAATAGGATAAGGGAG	4	79	0	TCTATAATAG	    0.824377	-127
ACTGGCGGTGTATGTAACTCTAAATCATGG	4	108	1	TATGTAACTC	    0.966765	-98
AAAAAATTCATATTTAACTGGTTAACCATG	4	133	0	TATTTAACTG	    0.983528	-73
ATCACCTTAATCTTTAACACCGTAAAAACA	4	183	0	TCTTTAACAC	     0.97531	-23
          **********

Masking position 6
Map Score:   8.23076

Number of sites scoring better than the average of aligned sites = 94
Number in coding regions = 71
Number in noncoding regions = 23
Number of orfs with sites within 600 bp upstream = 26
Fraction of orfs with sites within 600 bp upstream = 0.00417604


Motif number 2

GTTGATCAGGATTTCATACTCAAATTCTTT	1	23	0	ATTTCATACT	    0.897236	-119
ATCGCAATATAACTCATAATAGAATTTACA	1	72	0	AACTCATAAT	    0.792428	-70
TAATCTTGCGAAATCAGATTCATGCTTCTT	1	111	1	AAATCAGATT	    0.870763	-31
         TATTTCACCCTAAGAAGCATG	1	131	0	ATTTCACCCT	    0.956682	-11
      GATTAACCCACCTTCCTAGATTTA	2	17	0	AACCCACCTT	    0.960077	-14
ACAGCACCCCAAACCACCATGTCAAGATTT	4	44	1	AAACCACCAT	    0.906466	-162
ATTATAGAGTATTCCATACTGGCGGTGTAT	4	91	1	ATTCCATACT	    0.904386	-115
AAATTCAAAAAATTCATATTTAACTGGTTA	4	139	0	AATTCATATT	    0.928757	-67
ATTTATGTTAAATCCAGCTGTTTTTACGGT	4	165	1	AATCCAGCTG	    0.795725	-41
         TATATCACCTTAATCTTTAAC	4	195	0	ATATCACCTT	    0.933533	-11
          **********

Masking position 6
Map Score:   6.28601

Number of sites scoring better than the average of aligned sites = 633
Number in coding regions = 540
Number in noncoding regions = 93
Number of orfs with sites within 600 bp upstream = 86
Fraction of orfs with sites within 600 bp upstream = 0.013813


Motif number 3

TTGGAGAGTTGATCAGGATTTCATACTCAA	1	30	0	GATCAGGATT	    0.878931	-112
TCACCCTAAGAAGCATGAATCTGATTTCGC	1	118	0	AAGCATGAAT	    0.857405	-24
         AGATCATAAATCTAGGAAGGT	2	2	1	GATCATAAAT	    0.950961	-29
GGTGCTGTGTGGTCATGAATATGAACAGCC	4	22	0	GGTCATGAAT	    0.962135	-184
TTAACTGGTTAACCATGATTTAGAGTTACA	4	120	0	AACCATGATT	    0.577585	-86
          **********

Masking position 5
Map Score:   1.77938

Number of sites scoring better than the average of aligned sites = 145
Number in coding regions = 119
Number in noncoding regions = 26
Number of orfs with sites within 600 bp upstream = 24
Fraction of orfs with sites within 600 bp upstream = 0.0038548


Motif number 4

          **********

No masking
Map Score:   2.36911e-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:   2.36911e-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:   2.36911e-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