AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i210_trans4_mthe_reg_100.orf -o210_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	RTH00189	109	M.thermo
#2	RTH01001	16	M.thermo
#3	RTH01019	18	M.thermo
#4	RTH00961	18	M.thermo
#5	RTH01648	30	M.thermo

Motif number 1

AATATGCCCCTTCCAGTCCTCC          	1	1	0	TTCCAGTCCC	    0.996141	-109
GGGGCATATTTTCCAGTCCAGCGAAAAAACTT	1	23	1	TTCCAGTCGC	    0.994389	-87
CCCGAAAAATTTCAGGTATCCCCTTAAAAAGT	1	51	0	TTCAGGTTCC	    0.996799	-59
CCTGAAATTTTTCGGGTTTATCAGCAAATGCT	1	67	1	TTCGGGTTTC	    0.985046	-43
CCTCCTTGTATTCAGCATTTGCTGATAAACCC	1	80	0	TTCAGCATGC	    0.964991	-30
    TTTATTTTCCTCTTTACC          	3	1	0	TTCCTCTTCC	    0.989281	-18
          ******* * **

Masking position 2
Map Score:   6.33254

Number of sites scoring better than the average of aligned sites = 279
Number in coding regions = 255
Number in noncoding regions = 24
Number of orfs with sites within 600 bp upstream = 15
Fraction of orfs with sites within 600 bp upstream = 0.00240925


Motif number 2

CCTTAAAAAGTTTTTTCGCTGGACTGGAAAATA	1	29	0	TTTTCGCGGA	    0.978441	-81
GCGAAAAAACTTTTTAAGGGGATACCTGAAATT	1	43	1	TTTTAGGGAT	    0.995278	-67
ATTTTTCGGGTTTATCAGCAAATGCTGAATACA	1	73	1	TTTTAGCAAT	    0.982973	-37
        TCCTTGTCAGCTGGTT         	2	2	0	CTTTAGCGGT	    0.993347	-15
ATACTAAAAGTTACTGAGGTGATTTA       	5	15	1	TTATAGGGAT	    0.984633	-16
          *** * *** ***

Masking position 5
Map Score:   2.48377

Number of sites scoring better than the average of aligned sites = 100
Number in coding regions = 78
Number in noncoding regions = 22
Number of orfs with sites within 600 bp upstream = 16
Fraction of orfs with sites within 600 bp upstream = 0.00256987


Motif number 3

TATGCCCCTTCCAGTCCTCC          	1	1	0	CCAGTCCTCC	    0.992687	-109
GGCATATTTTCCAGTCCAGCGAAAAAACTT	1	25	1	CCAGTCCAGC	    0.989425	-85
          **********

Masking position 5
Map Score:   1.29248

Number of sites scoring better than the average of aligned sites = 24
Number in coding regions = 21
Number in noncoding regions = 3
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 4

CTGGACTGGAAAATATGCCCCTTCCAGTCC	1	14	0	AAATATGCCC	    0.976177	-96
GAAAAATTTCAGGTATCCCCTTAAAAAGTT	1	50	0	AGGTATCCCC	    0.986274	-60
CAGCATTTGCTGATAAACCCGAAAAATTTC	1	70	0	TGATAAACCC	     0.92863	-40
        TCAAGAAACCTCCTTGTATTCA	1	98	0	AAGAAACCTC	     0.95832	-12
         TAAATCACCTCAGTAACTTTT	5	20	0	AAATCACCTC	    0.969325	-11
          **********

Masking position 8
Map Score:   1.4486

Number of sites scoring better than the average of aligned sites = 617
Number in coding regions = 570
Number in noncoding regions = 47
Number of orfs with sites within 600 bp upstream = 45
Fraction of orfs with sites within 600 bp upstream = 0.00722775


Motif number 5

          **********

No masking
Map Score:   -3.30951e-14

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:   -3.30951e-14

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:   -3.30951e-14

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