AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -itrpR_mthe_opreg_300.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

    TATTATACAGACAAGATTTAAATAGTA	1	7	1	ACAACAAGAT	    0.960566	-72
GACAAGATTTAAATAGTACCTCCGTGTATAT	1	20	1	AAAAGTACCT	    0.951025	-59
CTCTGTATCCACAAAGTACATATACACGGAG	1	39	0	ACAAGTACAT	     0.97722	-40
TCCTGTACATGCATATCACCTCTGTATCCAC	1	58	0	GCAATCACCT	    0.993528	-21
GCAACCATGAACACATCAGCAA         	2	2	0	ACAATCAGCA	    0.990024	-36
   ACTCCCAGCAAACCAGCAACCATGAACA	2	20	0	GCAACCAGCA	    0.992204	-18
          *** *******

Masking position 5
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	    0.990941	-46
        TCCTGTACATGCATATCACCTC	1	67	0	CTGTACATGC	    0.995356	-12
  TTGCTGATGTGTTCATGGTTGCTGGTTT	2	9	1	GTGTTCATGG	    0.996138	-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

TTTAAATAGTACCTCCGTGTATATGTACTT	1	27	1	ACCTCCGTGT	    0.972449	-52
CATGCATATCACCTCTGTATCCACAAAGTA	1	52	0	ACCTCTGTAT	    0.995034	-27
    TCCTGTACATGCATATCACCTCTGTA	1	63	0	ACATGCATAT	    0.585819	-16
          **********

Masking position 1
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