AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i035_Sugars_Metabolism_mthe_reg_100.orf -o035_mthe_100.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	RTH01371	145	M.thermo
#2	RTH00133	56	M.thermo
#3	RTH01743	127	M.thermo

Motif number 1

TATTATCAAGTTATTAAAGGGCCAGAT          	1	1	0	TTATAGGAGT	    0.980395	-145
ATCAGTATCGTCATATAAGATATAGATATTATCAAGT	1	27	0	TCATAGAAGT	    0.876975	-119
GATATATAAAATAATCAGAGGTGTGTTTCTGGGCTAT	1	61	1	ATAAAAGTGT	    0.903419	-85
       CTTTCCTCCATGAATCTGTTAAAATGATAT	1	126	0	TCCTAGATGT	     0.91913	-20
GGAGAAAAAAATCAGTAGGGGTGAGGTGGTGGAGGGG	2	12	0	ATCAAGGAGT	    0.979701	-45
ACATATATGTACATCAAAGGGAATGGTTAATAAACA 	3	10	0	ACATAGGTGT	    0.983695	-118
TGATGTACATATATGTACAGTAAAGTTTTAAATAGTT	3	31	1	ATATAAGAGT	    0.941531	-97
GCAGTAAGATATCTTTAAAGAACTATTTAAAACTTTA	3	51	0	ATCTAAGTAT	    0.742149	-77
AAAGATATCTTACTGCATGGAAATGATGATTTCATCA	3	72	1	TACTAGGTGT	    0.942837	-56
TGATGATTTCATCAGTAGGGACCAGTTCCAGCCATGA	3	95	1	ATCAAGGAGT	    0.980999	-33
          ****  * **   ** *

Masking position 7
Map Score:   7.16962

Number of sites scoring better than the average of aligned sites = 1158
Number in coding regions = 1067
Number in noncoding regions = 91
Number of orfs with sites within 600 bp upstream = 85
Fraction of orfs with sites within 600 bp upstream = 0.0136524


Motif number 2

TAATAACTTGATAATATCTATATCTTATATG	1	22	1	ATATATCTAT	    0.899147	-124
CTGATTATTTTATATATCAGTATCGTCATAT	1	48	0	TAATATCAGT	    0.979602	-98
GGGCTATATTTAAATATCTATGTTATCATAA	1	91	1	TAATATCTAT	    0.965223	-55
TTATCATAATACTATATCATTTTAACAGATT	1	113	1	ACATATCATT	    0.910273	-33
CTCCGGGAGAAAAAAATCAGTAGGGGTGAGG	2	23	0	AAAAATCAGT	    0.928342	-34
CCCTTTGATGTACATATATGTACAGTAAAGT	3	26	1	TAATATATGT	    0.890247	-102
TCCATGCAGTAAGATATCTTTAAAGAACTAT	3	62	0	AAATATCTTT	    0.973073	-66
          ** ********

Masking position 6
Map Score:   4.09012

Number of sites scoring better than the average of aligned sites = 137
Number in coding regions = 107
Number in noncoding regions = 30
Number of orfs with sites within 600 bp upstream = 47
Fraction of orfs with sites within 600 bp upstream = 0.00754899


Motif number 3

CATGAATCTGTTAAAATGATATAGTATTAT	1	118	0	TTAAAATGAT	    0.878598	-28
TGTACATCAAAGGGAATGGTTAATAAACA 	3	10	0	AGGGAATGGT	    0.976206	-118
TCTTACTGCATGGAAATGATGATTTCATCA	3	79	1	TGGAAATGAT	    0.991322	-49
ACCTCATGGCTGGAACTGGTCCCTACTGAT	3	105	0	TGGAACTGGT	    0.990445	-23
          **********

Masking position 5
Map Score:   0.70601

Number of sites scoring better than the average of aligned sites = 119
Number in coding regions = 102
Number in noncoding regions = 17
Number of orfs with sites within 600 bp upstream = 19
Fraction of orfs with sites within 600 bp upstream = 0.00305172


Motif number 4

          **********

No masking
Map Score:   1.3033e-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:   1.3033e-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:   1.3033e-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