AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i004_4_1_1_21_mthe_reg_300.orf -o004_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	RTH00928	141	M.thermo

Motif number 1

GTACACCTTCTGATACTCTGTAACTCTCTATT	1	13	1	TGATCTCTTA	    0.977764	-129
CTCTATTGGTAGAATCCCCTTATATACTGTTA	1	38	1	AGAACCCCTA	     0.96889	-104
CACCTCCCGCAGGGACCATTTACAGGTCTTCA	1	70	0	AGGGCCATTA	    0.992142	-72
TCCCTGCGGGAGGTGCCATCTATTAAATATGA	1	87	1	AGGTCCATTA	    0.996444	-55
AATCTATCGGAGGTCATATTTAATAGATGGCA	1	100	0	AGGTATATTA	    0.965002	-42
GACCTCCGATAGATTCTCTATATATAAAGTTA	1	117	1	AGATCTCTTA	    0.994421	-25
          **** **** **

Masking position 11
Map Score:   6.62703

Number of sites scoring better than the average of aligned sites = 275
Number in coding regions = 254
Number in noncoding regions = 21
Number of orfs with sites within 600 bp upstream = 27
Fraction of orfs with sites within 600 bp upstream = 0.00433665


Motif number 2

CAGTATATAAGGGGATTCTACCAATAGAGAGT	1	35	0	GGGGACTACC	    0.984759	-107
GGCACCTCCCGCAGGGACCATTTACAGGTCTT	1	72	0	GCAGGCCATT	    0.989348	-70
GGTCCCTGCGGGAGGTGCCATCTATTAAATAT	1	85	1	GGAGGCCATC	    0.928014	-57
AGAATCTATCGGAGGTCATATTTAATAGATGG	1	102	0	GGAGGATATT	    0.986986	-40
CTTTATATATAGAGAATCTATCGGAGGTCATA	1	114	0	AGAGACTATC	     0.98696	-28
          *****  *****

Masking position 10
Map Score:   3.26583

Number of sites scoring better than the average of aligned sites = 398
Number in coding regions = 376
Number in noncoding regions = 22
Number of orfs with sites within 600 bp upstream = 23
Fraction of orfs with sites within 600 bp upstream = 0.00369419


Motif number 3

GATACTCTGTAACTCTCTATTGGTAGAATC	1	24	1	AACTCTCTAT	    0.985564	-118
AGGTCTTCATAACAGTATATAAGGGGATTC	1	49	0	AACAGTATAT	    0.988341	-93
TGTTATGAAGACCTGTAAATGGTCCCTGCG	1	65	1	ACCTGTAAAT	    0.980254	-77
      CTTTAACTTTATATATAGAGAATC	1	128	0	AACTTTATAT	    0.987392	-14
          **********

Masking position 6
Map Score:   3.42248

Number of sites scoring better than the average of aligned sites = 35
Number in coding regions = 19
Number in noncoding regions = 16
Number of orfs with sites within 600 bp upstream = 18
Fraction of orfs with sites within 600 bp upstream = 0.0028911


Motif number 4

          **********

No masking
Map Score:   1.51646e-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:   1.51646e-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:   1.51646e-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