AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -ifur_mthe_opreg_100.orf -g0.495 -x5 
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 =  	0.495
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	MTH155	228	rubredoxin
#2	MTH1901	300	unknown

Motif number 1

CAAAAAAATAATATCTGCAGGACCCGGAGGT	1	26	0	ATATTGCAGG	    0.986468	-203
GATCTTCTTTTTATCAGCAGGTACCCTGCTC	1	91	1	TTATAGCAGG	    0.968788	-138
ATGGGCTGCCATAGGAGCAGGGTACCTGCTG	1	105	0	ATAGAGCAGG	      0.9755	-124
AAATTATCAGATGTATGCCGGGTCTCTCAAC	1	141	1	ATGTTGCCGG	    0.981263	-88
AGGGGATTCGTTGTTTTCAGGTACTGACTGT	2	39	1	TTGTTTCAGG	    0.936686	-262
ATAGTTTTGGATGAATGCGGCCAAGGAGCCG	2	129	0	ATGATGCGGC	    0.955766	-172
GTGAAGTTTTATATAATCGGCTTTCCATAAG	2	196	0	ATATATCGGC	    0.801607	-105
CCTTTTATAAATGAATGCAGAAATAGATAAC	2	236	1	ATGATGCAGA	    0.889889	-65
CTAGTTACTCTTGGGAGCGGGAGGCATTAA 	2	281	1	TTGGAGCGGG	    0.975741	-20
          **** ******

Masking position 2
Map Score:   6.18046

Number of sites scoring better than the average of aligned sites = 681
Number in coding regions = 632
Number in noncoding regions = 49
Number of orfs with sites within 600 bp upstream = 54
Fraction of orfs with sites within 600 bp upstream = 0.00867331


Motif number 2

TTTAAGGACCTCCGGGTCCTGCAGATATTA	1	19	1	TCCGGGTCCT	    0.995227	-210
TCAGCAGGTACCCTGCTCCTATGGCAGCCC	1	104	1	CCCTGCTCCT	    0.991614	-125
TCAGATGTATGCCGGGTCTCTCAACACTAT	1	147	1	GCCGGGTCTC	    0.973158	-82
AGTATATACTCGCGGCTCCTTGGCCGCATT	2	117	1	CGCGGCTCCT	    0.992557	-184
  TTAATGCCTCCCGCTCCCAAGAGTAACT	2	283	0	TCCCGCTCCC	    0.991889	-18
          **********

Masking position 7
Map Score:   3.86046

Number of sites scoring better than the average of aligned sites = 199
Number in coding regions = 183
Number in noncoding regions = 16
Number of orfs with sites within 600 bp upstream = 13
Fraction of orfs with sites within 600 bp upstream = 0.00208802


Motif number 3

CCCGGAGGTCCTTAAAAAAGAGTT      	1	5	0	CTTAAAAAAG	    0.900765	-224
CCAGATTAATCTCAAAAAAATAATATCTGC	1	39	0	CTCAAAAAAA	    0.964342	-190
TATGGCAGCCCATTAAACAAATTATCAGAT	1	123	1	CATTAAACAA	    0.832748	-106
GGTCTCTCAACACTATAAAGCTTTCGCAGT	1	161	1	CACTATAAAG	    0.907949	-68
ATTTAAAATTATCTATAAAATTCACTGCGA	1	184	0	ATCTATAAAA	    0.797023	-45
CAGTCAGTACCTGAAAACAACGAATCCCCT	2	39	0	CTGAAAACAA	    0.727253	-262
CTATCGCAATCACAATAACACCACCAAAAA	2	85	1	CACAATAACA	    0.724653	-216
ACAATAACACCACCAAAAAGAAGTATATAC	2	96	1	CACCAAAAAG	    0.855607	-205
TAAAACTTCACTTTAAAAAACCTTTTATAA	2	216	1	CTTTAAAAAA	    0.938956	-85
TTCTGCATTCATTTATAAAAGGTTTTTTAA	2	228	0	ATTTATAAAA	    0.659585	-73
          **********

Masking position 5
Map Score:   2.13261

Number of sites scoring better than the average of aligned sites = 462
Number in coding regions = 304
Number in noncoding regions = 158
Number of orfs with sites within 600 bp upstream = 114
Fraction of orfs with sites within 600 bp upstream = 0.0183103


Motif number 4

          **********

No masking
Map Score:   4.00336e-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:   4.00336e-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:   4.00336e-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