AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -itrpR_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	MTH1655	78	anthranilate synthase component I
#2	MTH1660	37	tryptophan synthase, subunit alpha 

Motif number 1

TACTATTTAAATCTTGTCTGTATAATA    	1	7	0	ATCTTGTTGT	     0.96703	-72
ATATACACGGAGGTACTATTTAAATCTTGTC	1	20	0	AGGTACTTTT	     0.95877	-59
CTCCGTGTATATGTACTTTGTGGATACAGAG	1	39	1	ATGTACTTGT	    0.980997	-40
GTGGATACAGAGGTGATATGCATGTACAGGA	1	58	1	AGGTGATTGC	    0.994619	-21
         TTGCTGATGTGTTCATGGTTGC	2	2	1	TGCTGATTGT	    0.991701	-36
TGTTCATGGTTGCTGGTTTGCTGGGAGT   	2	20	1	TGCTGGTTGC	    0.993517	-18
          ******* ***

Masking position 7
Map Score:   5.00684

Number of sites scoring better than the average of aligned sites = 529
Number in coding regions = 482
Number in noncoding regions = 47
Number of orfs with sites within 600 bp upstream = 41
Fraction of orfs with sites within 600 bp upstream = 0.00658529


Motif number 2

TAGTACCTCCGTGTATATGTACTTTGTGGA	1	33	1	GTGTATATGT	    0.992008	-46
        TCCTGTACATGCATATCACCTC	1	67	0	CTGTACATGC	    0.995769	-12
  TTGCTGATGTGTTCATGGTTGCTGGTTT	2	9	1	GTGTTCATGG	    0.996625	-29
          **********

Masking position 7
Map Score:   2.4096

Number of sites scoring better than the average of aligned sites = 45
Number in coding regions = 39
Number in noncoding regions = 6
Number of orfs with sites within 600 bp upstream = 8
Fraction of orfs with sites within 600 bp upstream = 0.00128493


Motif number 3

AAGTACATATACACGGAGGTACTATTTAAA	1	27	0	ACACGGAGGT	    0.969229	-52
TACTTTGTGGATACAGAGGTGATATGCATG	1	52	1	ATACAGAGGT	     0.99559	-27
TACAGAGGTGATATGCATGTACAGGA    	1	63	1	ATATGCATGT	    0.577406	-16
          **********

Masking position 7
Map Score:   1.79965

Number of sites scoring better than the average of aligned sites = 55
Number in coding regions = 48
Number in noncoding regions = 7
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


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