AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_aquae.txt -z/home/amcguire/genomes/aquae.fna -imetJ_aquae_opreg_100.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

CACACCTCCCTTGAAAGTTTTTTACACTTTTT	1	13	1	TTAAATTTTT	    0.990927	-68
ATTTTATTTCTTAAAAATTCTTAGTCCACCTT	1	45	1	TTAAATTCTT	    0.998249	-36
TTAGTCCACCTTTAAAATACTTCCTT      	1	65	1	TTAAATACTT	    0.994514	-16
ACTTCTTATTTTAAAATATCTTTT        	2	3	0	TTAAAATCTT	    0.994438	-42
TCTCCTCCTTTTAGAACTTCTTATTTTAAAAT	2	18	0	TTGAATTCTT	    0.996287	-27
          ** *** *****

Masking position 6
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

TAAAAAACTTTCAAGGGAGGTGTGCC     	1	6	0	TAAGGGAGGT	    0.989177	-75
AGAAATAAAATAAAAAGTGTAAAAAACTTTC	1	25	0	TAAAAGTGTA	    0.975193	-56
AGGAAGTATTTTAAAGGTGGACTAAGAATTT	1	59	0	TAAAGGTGGA	    0.997812	-22
AAAAGATATTTTAAAATAAGAAGTTCTAAAA	2	11	1	TAAAATAAGA	    0.915784	-34
TAAGAAGTTCTAAAAGGAGGAGAAATCC   	2	27	1	TAAAGGAGGA	    0.998493	-18
          * *********

Masking position 4
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

CCTTGAAAGTTTTTTACACTTTTTATTTTAT	1	21	1	TTTTACACTT	    0.983024	-60
TTAAAAATTCTTAGTCCACCTTTAAAATACT	1	55	1	TTATCCACCT	    0.995069	-26
TAGTCCACCTTTAAAATACTTCCTT      	1	66	1	TTAAATACTT	     0.91733	-15
TCTCCTCCTTTTAGAACTTCTTATTTTAAAA	2	19	0	TTAAACTTCT	    0.945794	-26
       GGATTTCTCCTCCTTTTAGAACTT	2	31	0	TTTTCCTCCT	    0.989929	-14
          *** *******

Masking position 2
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