AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i316_mixed3_mthe_reg_100.orf -o316_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	RTH01836	222	M.thermo

Motif number 1

ACCTATCAGATCATATTACCGGTAATGGGAACAG	1	33	0	TCATTCGGTA	    0.992965	-190
CTGATAGGTTTCTTCTCACATGGAGTTCACGGTG	1	58	1	TCTTTCTGGA	    0.995651	-165
TGTGAAATGTTCATGTCACCGTGAACTCCATGTG	1	74	0	TCATTCGTGA	    0.996975	-149
GGTGACATGAACATTTCACATGGAGTTCACAGCG	1	88	1	ACATTCTGGA	     0.99094	-135
CATATGGTGTTCATATCGCTGTGAACTCCATGTG	1	104	0	TCATTCGTGA	    0.996975	-119
CCTCAGAATGTGATATGCCGGTGAAAGATATATA	1	143	1	TGATTCGTGA	    0.990192	-80
GGGAAGCTACTCTTTTAACTTGGATTACATTTAA	1	194	0	TCTTTCTGGA	    0.995651	-29
          **** *  * ****

Masking position 14
Map Score:   15.6831

Number of sites scoring better than the average of aligned sites = 157
Number in coding regions = 144
Number in noncoding regions = 13
Number of orfs with sites within 600 bp upstream = 10
Fraction of orfs with sites within 600 bp upstream = 0.00160617


Motif number 2

CCTATCAGATCATATTACCGGTAATGGGAACA	1	34	0	CATTTACGGT	    0.921613	-189
TGATAGGTTTCTTCTCACATGGAGTTCACGGT	1	59	1	CTTTCACTGG	    0.994579	-164
GTGAAATGTTCATGTCACCGTGAACTCCATGT	1	75	0	CATTCACGTG	    0.996754	-148
GTGACATGAACATTTCACATGGAGTTCACAGC	1	89	1	CATTCACTGG	    0.998007	-134
ATATGGTGTTCATATCGCTGTGAACTCCATGT	1	105	0	CATTCGCGTG	    0.987812	-118
CTTTCACCGGCATATCACATTCTGAGGTTCAT	1	138	0	CATTCACTTC	    0.992555	-85
ACTTGGATTACATTTAATCTTCAGTACATGAG	1	179	0	CATTAATTTC	    0.802439	-44
GGAAGCTACTCTTTTAACTTGGATTACATTTA	1	195	0	CTTTAACTGG	    0.980412	-28
          *** **** ***

Masking position 5
Map Score:   13.85

Number of sites scoring better than the average of aligned sites = 300
Number in coding regions = 281
Number in noncoding regions = 19
Number of orfs with sites within 600 bp upstream = 18
Fraction of orfs with sites within 600 bp upstream = 0.0028911


Motif number 3

AAGAAACCTATCAGATCATATTACCGGTAA	1	42	0	TCAGATCATA	    0.942888	-181
ATTCTGAGGTTCATCATATGGTGTTCATAT	1	122	0	TCATCATATG	    0.958005	-101
ATGATGAACCTCAGAATGTGATATGCCGGT	1	135	1	TCAGAATGTG	    0.984436	-88
CATTTAATCTTCAGTACATGAGTATATATA	1	171	0	TCAGTACATG	    0.989502	-52
          **********

Masking position 3
Map Score:   0.129167

Number of sites scoring better than the average of aligned sites = 160
Number in coding regions = 144
Number in noncoding regions = 16
Number of orfs with sites within 600 bp upstream = 20
Fraction of orfs with sites within 600 bp upstream = 0.00321234


Motif number 4

          **********

No masking
Map Score:   1.3033e-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:   1.3033e-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:   1.3033e-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