AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i107_TRK_operon_mthe_reg_300.orf -o107_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	RTH00419	300	M.thermo
#2	RTH00556	142	M.thermo

Motif number 1

GGATGAAGGTCCGCTGTTAAGCTATTTTCT	1	61	1	CCGCTGTTAA	    0.995783	-240
TTAAAAGCAGCTGGTGTTATTATGGAAGAA	1	87	0	CTGGTGTTAT	    0.967609	-214
ATAACACCAGCTGCTTTTAAACCCTCATTT	1	97	1	CTGCTTTTAA	    0.959667	-204
TGTCTGTATGCTGCTGTTTATGGGGGAATA	1	130	0	CTGCTGTTTA	    0.983041	-171
TTTAGAGCGGCCGCTGGAATATGCTGTATT	1	188	0	CCGCTGGAAT	    0.901444	-113
ATTCCAGCGGCCGCTCTAAAAACCTATATT	1	198	1	CCGCTCTAAA	    0.977693	-103
CCATAACCTGCCGCTCTAAAAATTTATATT	1	261	1	CCGCTCTAAA	    0.977693	-40
GTGGTGTTTACTTGTGTTAAACCTCATCAT	2	77	0	CTTGTGTTAA	    0.902605	-66
ATCAATGTAAGTGGTGTTTACTTGTGTTAA	2	87	0	GTGGTGTTTA	    0.812752	-56
          **********

Masking position 5
Map Score:   11.6346

Number of sites scoring better than the average of aligned sites = 317
Number in coding regions = 280
Number in noncoding regions = 37
Number of orfs with sites within 600 bp upstream = 27
Fraction of orfs with sites within 600 bp upstream = 0.00433665


Motif number 2

CTTAACAGCGGACCTTCATCCTACCGCTGA	1	52	0	GACCTTCATC	    0.941834	-249
GCTGCTTTTAAACCCTCATTTAGATATTCC	1	106	1	AACCCTCATT	    0.992301	-195
CCGCTCTAAAAACCTATATTGCAATATCCT	1	208	1	AACCTATATT	    0.898995	-93
GAGTTACTGAAACCCTTATTATAAGTGGAA	2	36	1	AACCCTTATT	    0.990718	-107
ATAAGTGGAAAAACCTTATTAATGATGAGG	2	56	1	AAACCTTATT	    0.966809	-87
TACTTGTGTTAAACCTCATCATTAATAAGG	2	69	0	AAACCTCATC	    0.977002	-74
AAATCAATGTAACCGGTATCAATGTAAGTG	2	104	0	AACCGGTATC	    0.930516	-39
          **********

Masking position 8
Map Score:   7.60914

Number of sites scoring better than the average of aligned sites = 286
Number in coding regions = 253
Number in noncoding regions = 33
Number of orfs with sites within 600 bp upstream = 29
Fraction of orfs with sites within 600 bp upstream = 0.00465789


Motif number 3

AGAAAATAGCTTAACAGCGGACCTTCATCCT	1	60	0	TTAACAGGGA	    0.909502	-241
GCTGGTGTTATTATGGAAGAAAATAGCTTAA	1	77	0	TTATGGAGAA	    0.956817	-224
ATGCTGCTGTTTATGGGGGAATATCTAAATG	1	122	0	TTATGGGGAA	     0.99305	-179
GAGCGGCAGGTTATGGGTGGATAGTAGTTGA	1	246	0	TTATGGGGGA	    0.997645	-55
AGATCATTTTTTATGGGTTGAGCA       	2	4	0	TTATGGGTGA	    0.984882	-139
GAAACCCTTATTATAAGTGGAAAAACCTTAT	2	44	1	TTATAAGGGA	    0.964904	-99
          ******* ***

Masking position 3
Map Score:   6.88296

Number of sites scoring better than the average of aligned sites = 133
Number in coding regions = 110
Number in noncoding regions = 23
Number of orfs with sites within 600 bp upstream = 26
Fraction of orfs with sites within 600 bp upstream = 0.00417604


Motif number 4

ACCTGAACCAAAAAATAAATTTCGATGAGT	1	22	0	AAAAATAAAT	    0.906452	-279
CGGCCGCTCTAAAAACCTATATTGCAATAT	1	205	1	AAAAACCTAT	    0.975852	-96
CTGCCGCTCTAAAAATTTATATTGCAATGT	1	268	1	AAAAATTTAT	    0.892181	-33
TATAAGTGGAAAAACCTTATTAATGATGAG	2	55	1	AAAACCTTAT	    0.922215	-88
AGATTCAGGGAAAAATCAATGTAACCGGTA	2	116	0	AAAAATCAAT	    0.963375	-27
          **********

Masking position 4
Map Score:   2.58539

Number of sites scoring better than the average of aligned sites = 54
Number in coding regions = 25
Number in noncoding regions = 29
Number of orfs with sites within 600 bp upstream = 35
Fraction of orfs with sites within 600 bp upstream = 0.00562159


Motif number 5

TTTATTTTTTGGTTCAGGTTCAGCGGTAGG	1	33	1	GGTTCAGGTT	    0.939197	-268
TTCAGGTTCAGCGGTAGGATGAAGGTCCGC	1	45	1	GCGGTAGGAT	    0.973854	-256
GGGTTTAAAAGCAGCTGGTGTTATTATGGA	1	91	0	GCAGCTGGTG	    0.956817	-210
CTGTCTGTATGCTGCTGTTTATGGGGGAAT	1	131	0	GCTGCTGTTT	    0.942958	-170
TAGTTGAGTAGCGTCAGGATATTGCAATAT	1	223	0	GCGTCAGGAT	    0.987857	-78
AATTTTTAGAGCGGCAGGTTATGGGTGGAT	1	255	0	GCGGCAGGTT	    0.997779	-46
          **********

Masking position 7
Map Score:   5.68113

Number of sites scoring better than the average of aligned sites = 350
Number in coding regions = 329
Number in noncoding regions = 21
Number of orfs with sites within 600 bp upstream = 22
Fraction of orfs with sites within 600 bp upstream = 0.00353357


Motif number 6

          **********

No masking
Map Score:   -1.88842e-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:   -1.88842e-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 8

          **********

No masking
Map Score:   -1.88842e-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