AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i067_2_1_1_13_hinf_reg_300.orf -a/home/amcguire/alignace/lib/ORF_hinf.txt -z/skink1/amcguire/genomes/hinf.fna -g0.38 -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 =  	0.38
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	HI1702	192	5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferase (metE)
#2	HI1704	107	conserved hypothetical protein

Motif number 1

TCAATTCAGCTAACTTATTTCCTTAAAA  	1	9	0	TAACTTATTT	    0.988539	-184
GCTTGATTATGAATTTATTTAATGTAAATC	1	67	1	GAATTTATTT	    0.962636	-126
TTTATTATGCAAACTTATTATTTTCAGGAT	1	94	0	AAACTTATTA	    0.933223	-99
TGCTTGATCTTCATTTATTATGCAAACTTA	1	107	0	TCATTTATTA	    0.921094	-86
CAATTTAAAGTAATTTTTTTAATCATTTAG	1	165	0	TAATTTTTTT	    0.937126	-28
TCGCATATGATAACTTATTTTCGCTGAATT	2	34	0	TAACTTATTT	    0.988539	-74
          **********

Masking position 5
Map Score:   7.56045

Number of sites scoring better than the average of aligned sites = 96
Number in coding regions = 71
Number in noncoding regions = 25
Number of orfs with sites within 600 bp upstream = 24
Fraction of orfs with sites within 600 bp upstream = 0.0038548


Motif number 2

AGCTAACTTATTTCCTTAAAA          	1	1	0	TTTCTTAAAA	    0.872953	-192
ATCTATCAAATAACGATGAATCAATTCAGCT	1	28	0	TAACATGAAT	    0.881174	-165
AAAGAATGCTTGATTATGAATTTATTTAATG	1	60	1	TGATATGAAT	    0.822274	-133
TTTTCAGGATTTACATTAAATAAATTCATAA	1	73	0	TTACTTAAAT	    0.981146	-120
ATTAAAAAAATTACTTTAAATTGGAGTTATT	1	172	1	TTACTTAAAT	    0.982763	-21
      TTGTTGTCCTTAAATTTCTGTTTAA	2	5	1	TGTCTTAAAT	    0.974627	-103
GATAACTTATTTTCGCTGAATTAAACAGAAA	2	25	0	TTTCCTGAAT	    0.977966	-83
ATTTCGTTTGTTTTTCTAAATCTAAAACGGA	2	84	0	TTTTCTAAAT	    0.915408	-24
          **** ******

Masking position 9
Map Score:   7.10869

Number of sites scoring better than the average of aligned sites = 473
Number in coding regions = 383
Number in noncoding regions = 90
Number of orfs with sites within 600 bp upstream = 77
Fraction of orfs with sites within 600 bp upstream = 0.0123675


Motif number 3

AAGGAAATAAGTTAGCTGAATTGATTCATCG	1	15	1	GTAGCTGAAT	    0.956804	-178
ATAGATAAAAGAATGCTTGATTATGAATTTA	1	53	1	GATGCTTGAT	      0.9914	-140
AAAATAATAAGTTTGCATAATAAATGAAGAT	1	100	1	GTTGCATAAT	    0.949103	-93
TACCAATATAGAATGCTTGATCTTCATTTAT	1	119	0	GATGCTTGAT	      0.9914	-74
ACGTTTAGCCGTCTAAATGATTAAAAAAATT	1	153	1	GTTAAATGAT	    0.707494	-40
GGTCGCATATGATAACTTATTTTCGCTGAAT	2	35	0	GAAACTTATT	    0.811513	-73
TAAAACGGAGGAAAACTGGATAAAATCGGTC	2	62	0	GAAACTGGAT	    0.966492	-46
          ** ********

Masking position 11
Map Score:   4.30196

Number of sites scoring better than the average of aligned sites = 345
Number in coding regions = 310
Number in noncoding regions = 35
Number of orfs with sites within 600 bp upstream = 24
Fraction of orfs with sites within 600 bp upstream = 0.0038548


Motif number 4

ATAGATAAAAGAATGCTTGATTATGAATTT	1	53	1	GAATGCTTGA	     0.99601	-140
TACCAATATAGAATGCTTGATCTTCATTTA	1	120	0	GAATGCTTGA	     0.99601	-73
TAAAACGGAGGAAAACTGGATAAAATCGGT	2	63	0	GAAAACTGGA	    0.980133	-45
          **********

Masking position 3
Map Score:   2.92382

Number of sites scoring better than the average of aligned sites = 12
Number in coding regions = 10
Number in noncoding regions = 2
Number of orfs with sites within 600 bp upstream = 1
Fraction of orfs with sites within 600 bp upstream = 0.000160617


Motif number 5

          **********

No masking
Map Score:   -3.38628e-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:   -3.38628e-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:   -3.38628e-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