AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_aquae.txt -z/home/amcguire/genomes/aquae.fna -imetJ_aquae_opreg_300.orf -g0.435 -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 =  	0.435
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	metF	80	5,10-methylenetetrahydrofolate reductase
#2	metE	44	tetrahydropteroyltriglutamate methyltransferase

Motif number 1

AAAAAGTGTAAAAAACTTTCAAGGGAGGTGTG	1	13	0	AAAAATTTAA	     0.99157	-68
AAGGTGGACTAAGAATTTTTAAGAAATAAAAT	1	45	0	AAGAATTTAA	    0.998374	-36
      AAGGAAGTATTTTAAAGGTGGACTAA	1	65	0	AAGTATTTAA	    0.994944	-16
        AAAAGATATTTTAAAATAAGAAGT	2	3	1	AAGATTTTAA	    0.994861	-42
ATTTTAAAATAAGAAGTTCTAAAAGGAGGAGA	2	18	1	AAGAATTCAA	    0.996578	-27
          ***** *** **

Masking position 7
Map Score:   11.525

Number of sites scoring better than the average of aligned sites = 98
Number in coding regions = 89
Number in noncoding regions = 9
Number of orfs with sites within 600 bp upstream = 12
Fraction of orfs with sites within 600 bp upstream = 0.0019274


Motif number 2

     GGCACACCTCCCTTGAAAGTTTTTTA	1	6	1	ACCTCCCTTA	    0.990089	-75
GAAAGTTTTTTACACTTTTTATTTTATTTCT	1	25	1	TACACTTTTA	    0.977223	-56
AAATTCTTAGTCCACCTTTAAAATACTTCCT	1	59	1	TCCACCTTTA	     0.99799	-22
TTTTAGAACTTCTTATTTTAAAATATCTTTT	2	11	0	TCTTATTTTA	    0.922391	-34
   GGATTTCTCCTCCTTTTAGAACTTCTTA	2	27	0	TCCTCCTTTA	    0.998619	-18
          ********* *

Masking position 8
Map Score:   6.67262

Number of sites scoring better than the average of aligned sites = 550
Number in coding regions = 483
Number in noncoding regions = 67
Number of orfs with sites within 600 bp upstream = 78
Fraction of orfs with sites within 600 bp upstream = 0.0125281


Motif number 3

ATAAAATAAAAAGTGTAAAAAACTTTCAAGG	1	21	0	AAGTGTAAAA	    0.983766	-60
AGTATTTTAAAGGTGGACTAAGAATTTTTAA	1	55	0	AGGTGGATAA	    0.995287	-26
      AAGGAAGTATTTTAAAGGTGGACTA	1	66	0	AAGTATTTAA	     0.92071	-15
TTTTAAAATAAGAAGTTCTAAAAGGAGGAGA	2	19	1	AGAAGTTTAA	    0.948076	-26
AAGTTCTAAAAGGAGGAGAAATCC       	2	31	1	AGGAGGAAAA	    0.990372	-14
          ******* ***

Masking position 10
Map Score:   3.00303

Number of sites scoring better than the average of aligned sites = 743
Number in coding regions = 667
Number in noncoding regions = 76
Number of orfs with sites within 600 bp upstream = 87
Fraction of orfs with sites within 600 bp upstream = 0.0139737


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