AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i250_fts_cell_wall_mthe_reg_300.orf -o250_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	RTH01854	151	M.thermo
#2	RTH01592	235	M.thermo

Motif number 1

TCTGTTTGAGTCAGAAATAACGGGATCCAT	1	21	1	TCAGAAATAA	    0.957898	-131
AACATATGAATCCTAATTAATATGGATCCC	1	42	0	TCCTAATTAA	     0.79149	-110
CCTATACCTGCCATAAATATATCCAAATAT	1	94	1	CCATAAATAT	    0.959069	-58
ATAAATATATCCAAATATAATTTGAGATCA	1	106	1	CCAAATATAA	    0.908374	-46
TAATTTGAGATCAGGTATATATAAGTAGGT	1	123	1	TCAGGTATAT	    0.725485	-29
GTCCACGTGGCCATGAATATCATGAATCTG	2	46	0	CCATGAATAT	    0.919709	-190
GCCACGTGGACCATCAATAATTTTATTTTG	2	65	1	CCATCAATAA	    0.932174	-171
TGGCTCACATTCAAAATTAAAAATCAATTT	2	130	0	TCAAAATTAA	     0.86944	-106
TTGTGATAAGACATATTTAAAAGCAACGGT	2	182	0	ACATATTTAA	    0.700621	-54
ATAACATATTTCATAGATAAGTGTGGGGGT	2	211	1	TCATAGATAA	    0.922315	-25
          **********

Masking position 8
Map Score:   5.79207

Number of sites scoring better than the average of aligned sites = 303
Number in coding regions = 219
Number in noncoding regions = 84
Number of orfs with sites within 600 bp upstream = 93
Fraction of orfs with sites within 600 bp upstream = 0.0149374


Motif number 2

GACTCAAACAGAAGGTGATGTT        	1	3	0	GAAGGTGATG	    0.969771	-149
GTATATATAAGTAGGTGGTGTTTTC     	1	137	1	GTAGGTGGTG	    0.959054	-15
TGAATATCATGAATCTGGGCGGGACCCCCC	2	33	0	GAATCTGGGC	     0.96367	-203
ATACCGGCTCAAGGTTGGGGCAAAATAAAA	2	85	0	AAGGTTGGGG	    0.937822	-151
TTTTAATTTTGAATGTGAGCCATGGCTCCA	2	138	1	GAATGTGAGC	    0.969286	-98
TTTCATAGATAAGTGTGGGGGTAGTAA   	2	219	1	AAGTGTGGGG	    0.980414	-17
          **********

Masking position 6
Map Score:   2.01969

Number of sites scoring better than the average of aligned sites = 889
Number in coding regions = 819
Number in noncoding regions = 70
Number of orfs with sites within 600 bp upstream = 51
Fraction of orfs with sites within 600 bp upstream = 0.00819146


Motif number 3

ATCCTAATTAATATGGATCCCGTTATTTCT	1	33	0	ATATGGATCC	      0.9931	-119
GGTAGTAAACATATGAATCCTAATTAATAT	1	49	0	ATATGAATCC	    0.973156	-103
TGAATGTGAGCCATGGCTCCATCGGTGCCA	2	147	1	CCATGGCTCC	    0.987126	-89
GCAACGGTTAATCTGGCACCGATGGAGCCA	2	160	0	ATCTGGCACC	    0.981038	-76
          **********

Masking position 4
Map Score:   1.61593

Number of sites scoring better than the average of aligned sites = 117
Number in coding regions = 106
Number in noncoding regions = 11
Number of orfs with sites within 600 bp upstream = 16
Fraction of orfs with sites within 600 bp upstream = 0.00256987


Motif number 4

ATGGCAGGTATAGGAAAAATTTTTATAAAG	1	78	0	TAGGAAAAAT	    0.976449	-74
CAAATTATATTTGGATATATTTATGGCAGG	1	100	0	TTGGATATAT	    0.877248	-52
CATGACATGTTATGAAAAAG          	2	1	0	TATGAAAAAG	    0.923518	-235
GTTATTGTGATAAGACATATTTAAAAGCAA	2	186	0	TAAGACATAT	    0.927413	-50
CACACTTATCTATGAAATATGTTATTGTGA	2	206	0	TATGAAATAT	    0.974625	-30
          **********

Masking position 5
Map Score:   0.586227

Number of sites scoring better than the average of aligned sites = 45
Number in coding regions = 29
Number in noncoding regions = 16
Number of orfs with sites within 600 bp upstream = 21
Fraction of orfs with sites within 600 bp upstream = 0.00337295


Motif number 5

          **********

No masking
Map Score:   -1.60993e-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:   -1.60993e-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:   -1.60993e-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