AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i150_ATP_synthase_1_mthe_reg_300.orf -o150_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	RTH00559	35	M.thermo
#2	RTH00866	17	M.thermo
#3	RTH00917	212	M.thermo
#4	RTH01204	103	M.thermo
#5	RTH02032	21	M.thermo

Motif number 1

     CCACCCCCAACATCCTTTTTCAGGAG	1	6	1	CCCACATCCT	    0.997613	-30
    AATTCACCCATCAACATCCATATGATT	3	7	1	CCCACAACAT	    0.987772	-206
CATATGATTGCCGATCACCCTTAAAGACTTA	3	29	1	CCGACACCCT	    0.989921	-184
CCGGGCAGATCCCACCATCACATCACAATTC	4	22	0	CCCACATCAC	    0.997613	-82
GTCGATCAGTTCCAGCATCACCGGGCAGATC	4	42	0	TCCACATCAC	    0.984768	-62
AACTGATCGACCGGAAATCCCGCAAGCGTAA	4	62	1	CCGGAATCCC	    0.951047	-42
          **** ******

Masking position 7
Map Score:   7.40393

Number of sites scoring better than the average of aligned sites = 275
Number in coding regions = 251
Number in noncoding regions = 24
Number of orfs with sites within 600 bp upstream = 18
Fraction of orfs with sites within 600 bp upstream = 0.0028911


Motif number 2

AAATATTGTCTTAATTCAAATTAAATTTCA	3	59	1	TTAATTCAAA	    0.974487	-154
ATTGAGTCATTTTATGAAATTTAATTTGAA	3	73	0	TTTATGAAAT	     0.78583	-140
CCTCCTGATGTTAATTGAGTCATTTTATGA	3	86	0	TTAATTGAGT	    0.938747	-127
AAAGGCTTGGTTAACTGAATGGGATTAGTT	3	122	1	TTAACTGAAT	    0.938745	-91
CTGAATGGGATTAGTTGAATATCATAAACT	3	136	1	TTAGTTGAAT	    0.938743	-77
CTTTTACTATTTTATTCAAAAGTTTATGAT	3	156	0	TTTATTCAAA	    0.942489	-57
      CCTATTAATGCAAAGGTCTATTTC	3	199	0	TTAATGCAAA	    0.962379	-14
          **********

Masking position 8
Map Score:   3.90665

Number of sites scoring better than the average of aligned sites = 74
Number in coding regions = 40
Number in noncoding regions = 34
Number of orfs with sites within 600 bp upstream = 37
Fraction of orfs with sites within 600 bp upstream = 0.00594282


Motif number 3

     TGGCTAACTCTCCTGAAAAAGGATG	1	21	0	AACTCTCCTG	    0.989603	-15
     CTGTTATCTCCCCTTTT        	2	3	0	ATCTCCCCTT	    0.989432	-15
AGCCTTTTGAATCCCTCCTGATGTTAATTG	3	99	0	ATCCCTCCTG	    0.992961	-114
TGATGGTGGGATCTGCCCGGTGATGCTGGA	4	33	1	ATCTGCCCGG	    0.987864	-71
          **********

Masking position 1
Map Score:   2.73392

Number of sites scoring better than the average of aligned sites = 179
Number in coding regions = 169
Number in noncoding regions = 10
Number of orfs with sites within 600 bp upstream = 10
Fraction of orfs with sites within 600 bp upstream = 0.00160617


Motif number 4

          **********

No masking
Map Score:   7.55607e-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

AAAAAGGATGTTGGGGGTGG          	1	1	0	TTGGGGGTGG	    0.921809	-35
CAACATCCTTTTTCAGGAGAGTTAGCCA  	1	18	1	TTTCAGGAGA	    0.956187	-18
ACTCAATTAACATCAGGAGGGATTCAAAAG	3	96	1	CATCAGGAGG	    0.921087	-117
TGCGTGGAATTGTGATGTGATGGTGGGATC	4	16	1	TGTGATGTGA	    0.785977	-88
TGGTGGGATCTGCCCGGTGATGCTGGAACT	4	36	1	TGCCCGGTGA	     0.96583	-68
GCTTGCGGGATTTCCGGTCGATCAGTTCCA	4	59	0	TTTCCGGTCG	    0.855296	-45
TAAAGTTAAACTGGAGGTGAAAAA      	4	90	1	CTGGAGGTGA	    0.969917	-14
    TTAGATCACCAGGTGAATGTA     	5	7	1	CACCAGGTGA	    0.965622	-15
          **********

Masking position 7
Map Score:   0.873735

Number of sites scoring better than the average of aligned sites = 2389
Number in coding regions = 2245
Number in noncoding regions = 144
Number of orfs with sites within 600 bp upstream = 132
Fraction of orfs with sites within 600 bp upstream = 0.0212014


Motif number 6

          **********

No masking
Map Score:   7.55607e-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:   7.55607e-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 8

          **********

No masking
Map Score:   7.55607e-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