AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i250_fts_cell_wall_mthe_reg_100.orf -o250_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	RTH01592	235	M.thermo

Motif number 1

ATCTGGGCGGGACCCCCCATCATGACATGTTA	1	19	0	GCCCCCCATA	    0.978058	-217
TGGGGGGTCCCGCCCAGATTCATGATATTCAT	1	32	1	CCCCAGATTA	    0.990646	-204
TGGTCCACGTGGCCATGAATATCATGAATCTG	1	46	0	GCCATGAATT	    0.801284	-190
TGGCCACGTGGACCATCAATAATTTTATTTTG	1	63	1	GCCATCAATA	     0.97341	-173
TTTTATTTTGCCCCAACCTTGAGCCGGTATTT	1	85	1	CCCAACCTTA	    0.974449	-151
ATGGAGCCATGGCTCACATTCAAAATTAAAAA	1	137	0	GCTCACATTA	    0.969043	-99
GGCTCCATCGGTGCCAGATTAACCGTTGCTTT	1	161	1	GGCCAGATTA	    0.966121	-75
    TTACTACCCCCACACTTATCTATGAAAT	1	218	0	CCCCACACTA	     0.98728	-18
          * ******** *

Masking position 10
Map Score:   5.08427

Number of sites scoring better than the average of aligned sites = 751
Number in coding regions = 701
Number in noncoding regions = 50
Number of orfs with sites within 600 bp upstream = 53
Fraction of orfs with sites within 600 bp upstream = 0.00851269


Motif number 2

AAGGTTGGGGCAAAATAAAATTATTGATGG	1	75	0	CAAAATAAAA	    0.987068	-161
GGCTCACATTCAAAATTAAAAATCAATTTC	1	129	0	CAAAATTAAA	    0.987005	-107
TGTGATAAGACATATTTAAAAGCAACGGTT	1	181	0	CATATTTAAA	      0.9448	-55
TATGTCTTATCACAATAACATATTTCATAG	1	197	1	CACAATAACA	    0.974118	-39
          **********

Masking position 6
Map Score:   2.56608

Number of sites scoring better than the average of aligned sites = 42
Number in coding regions = 24
Number in noncoding regions = 18
Number of orfs with sites within 600 bp upstream = 16
Fraction of orfs with sites within 600 bp upstream = 0.00256987


Motif number 3

TGATGGTCCACGTGGCCATGAATATCATGA	1	51	0	CGTGGCCATG	    0.772731	-185
GGCTCAAGGTTGGGGCAAAATAAAATTATT	1	80	0	TGGGGCAAAA	    0.951645	-156
CTGAAAATACCGGCTCAAGGTTGGGGCAAA	1	91	0	CGGCTCAAGG	    0.967047	-145
CTGGCACCGATGGAGCCATGGCTCACATTC	1	148	0	TGGAGCCATG	    0.984671	-88
ATGGCTCCATCGGTGCCAGATTAACCGTTG	1	159	1	CGGTGCCAGA	    0.986055	-77
          **********

Masking position 8
Map Score:   1.16391

Number of sites scoring better than the average of aligned sites = 647
Number in coding regions = 615
Number in noncoding regions = 32
Number of orfs with sites within 600 bp upstream = 22
Fraction of orfs with sites within 600 bp upstream = 0.00353357


Motif number 4

          CTTTTTCATAACATGTCATG	1	1	1	CTTTTTCATA	    0.934737	-235
CTTTTTCATAACATGTCATGATGGGGGGTC	1	11	1	ACATGTCATG	    0.970445	-225
TTGCTTTTAAATATGTCTTATCACAATAAC	1	186	1	ATATGTCTTA	    0.974206	-50
TCACAATAACATATTTCATAGATAAGTGTG	1	206	1	ATATTTCATA	     0.98405	-30
          **********

Masking position 6
Map Score:   0.231721

Number of sites scoring better than the average of aligned sites = 41
Number in coding regions = 33
Number in noncoding regions = 8
Number of orfs with sites within 600 bp upstream = 8
Fraction of orfs with sites within 600 bp upstream = 0.00128493


Motif number 5

          **********

No masking
Map Score:   3.64809e-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:   3.64809e-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:   3.64809e-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