AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00630_mgen_reg_100.orf -o00630_mgen_100.ace -a/home/amcguire/genomes/ORF_mgen.txt -z/home/amcguire/genomes/mgen.fna -g0.32 -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 =  	0.32
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	MG013	239	methylenetetrahydrofolate dehydrogenase/methylenetetrahydrofolate cyclohydrolase (folD)

Motif number 1

 AAAATTAGCTGTTTTGATTATAAAAACTGTTA	1	10	1	TGTTGATTAA	    0.976885	-230
TTATAAAAACTGTTAAAATTCGAGGGGTATTTT	1	28	1	TGTTAATTCA	    0.976868	-212
AGGGGTATTTTGGTTAAATTAAAATTGTTATAA	1	50	1	TGGTAATTAA	    0.993422	-190
ATAGCTCAGTTGGTTAGAGCACACCCCTGATAA	1	120	1	TGGTGAGCAA	    0.986262	-120
GTGAGGTCGATGGTTCAAGTCCATTTACTTCCA	1	155	1	TGGTAAGTCA	    0.994829	-85
TCCCCATTATTGGTGGAAGTAAATGGACTTGAA	1	168	0	TGGTAAGTAA	    0.995806	-72
          ****  ***** *

Masking position 8
Map Score:   8.31055

Number of sites scoring better than the average of aligned sites = 27
Number in coding regions = 22
Number in noncoding regions = 5
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 2

TTTATAATCAAAACAGCTAATTTT       	1	4	0	AACAGCTAAT	    0.939581	-236
GGTGTGCTCTAACCAACTGAGCTATACTTCC	1	114	0	AACAACTGAG	    0.990015	-126
TGGTTAGAGCACACCCCTGATAAGGGTGAGG	1	130	1	ACCCCCTGAT	    0.990161	-110
TGGGGATGTAGCTCAACTGATAGAGCACCTG	1	195	1	GCCAACTGAT	    0.987981	-45
TCAACTGATAGAGCACCTGATTTGCACTCAG	1	207	1	GACACCTGAT	    0.995544	-33
    ACCCTCAACCTCCTGAGTGCAAATCAG	1	223	0	AACTCCTGAG	    0.985486	-17
          ** ********

Masking position 8
Map Score:   6.74831

Number of sites scoring better than the average of aligned sites = 76
Number in coding regions = 61
Number in noncoding regions = 15
Number of orfs with sites within 600 bp upstream = 6
Fraction of orfs with sites within 600 bp upstream = 0.000963701


Motif number 3

AAAATTCGAGGGGTATTTTGGTTAAATTAAAA	1	42	1	GGGTATTGGT	    0.986397	-198
ATAATCCTAAGGGTATTTAACTAATTATTATA	1	78	0	GGGTATTACT	    0.936447	-162
TAAATACCCTTAGGATTATGCTTGGAAGTATA	1	91	1	TAGGATTGCT	    0.956385	-149
ACCCTTATCAGGGGTGTGCTCTAACCAACTGA	1	125	0	GGGGTGTTCT	    0.938149	-115
TGATAAGGGTGAGGTCGATGGTTCAAGTCCAT	1	147	1	GAGGTCGGGT	    0.977601	-93
CACCAATAATGGGGATGTAGCTCAACTGATAG	1	186	1	GGGGATGGCT	    0.997631	-54
TTGCACTCAGGAGGTTGAGGGT          	1	228	1	GAGGTTGGGT	    0.991692	-12
          *******  ***

Masking position 12
Map Score:   4.62788

Number of sites scoring better than the average of aligned sites = 119
Number in coding regions = 90
Number in noncoding regions = 29
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 4

TTAAAATTCGAGGGGTATTTTGGTTAAATT	1	40	1	AGGGGTATTT	    0.992205	-200
GCATAATCCTAAGGGTATTTAACTAATTAT	1	82	0	AAGGGTATTT	    0.960615	-158
AAATACCCTTAGGATTATGCTTGGAAGTAT	1	92	1	AGGATTATGC	    0.942279	-148
CACCCTTATCAGGGGTGTGCTCTAACCAAC	1	128	0	AGGGGTGTGC	    0.991319	-112
ACCCCTGATAAGGGTGAGGTCGATGGTTCA	1	142	1	AGGGTGAGGT	    0.974737	-98
TCCACCAATAATGGGGATGTAGCTCAACTG	1	184	1	ATGGGGATGT	    0.983564	-56
          **********

Masking position 1
Map Score:   6.01839

Number of sites scoring better than the average of aligned sites = 45
Number in coding regions = 35
Number in noncoding regions = 10
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 5

TTTAATTTAACCAAAATACCCCTCGAATTTT	1	42	0	CCAAAATCCC	    0.983149	-198
ATAATAATTAGTTAAATACCCTTAGGATTAT	1	79	1	GTTAAATCCC	    0.981673	-161
AACCAACTGAGCTATACTTCCAAGCATAATC	1	104	0	GCTATACTCC	    0.981486	-136
TATCAGTTGAGCTACATCCCCATTATTGGTG	1	186	0	GCTACATCCC	     0.99394	-54
        ACCCTCAACCTCCTGAGTGCAAA	1	227	0	CCTCAACTCC	    0.976435	-13
          ******* ***

Masking position 6
Map Score:   1.72997

Number of sites scoring better than the average of aligned sites = 35
Number in coding regions = 21
Number in noncoding regions = 14
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 6

          **********

No masking
Map Score:   -2.7468e-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 7

          **********

No masking
Map Score:   -2.7468e-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 8

          **********

No masking
Map Score:   -2.7468e-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