AlignACE version 2.2  July 7, 1998
alignACE -aORF_aful.txt -zaful.fna -iphoB_aful_opreg_100.orf -g0.49 -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 =  	0.49
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	AF0433	122	conserved hypothetical protein
#2	AF0477	140	AAA superfamily ATPase
#3	AF0521	39	protease synthase and sporulation regulator Pai1, putative
#4	AF1356	96	phosphate ABC transporter, periplasmic phosphate-binding protein (phoX)
#5	AF1608	59	spermidine/putrescine ABC transporter, ATP-binding protein (potA)

Motif number 1

AATTTTTCTTCTCATAAATTTACTGTTCTTTG	1	20	1	CTATAATTTA	    0.922243	-103
ACACCAAAAACCAAAATTTTAATCTTCAGTCT	1	64	1	CCAAATTTAA	    0.947884	-59
CAAGCTGATTCAGAAAACTTTATCAAATCCGA	2	25	0	CAAAAATTTA	    0.981743	-116
TCTGAATCAGCTTGTAACTTTAAACCTAAAAC	2	43	1	CTGTAATTTA	    0.852906	-98
TAACTTTAAACCTAAAACTTAACCAAAAACGA	2	57	1	CCAAAATTAA	    0.972304	-84
GGCAGAACTCCCAAAAAATTTAAATCACGATT	2	94	1	CCAAAATTTA	    0.991033	-47
AGGGAAAACGCATAAATATTTAGATTTTCACG	4	18	0	CAAAATTTTA	    0.965551	-79
TTCGTGTCAGCCCAATTTTTTATCTA      	5	5	0	CCAATTTTTA	    0.901779	-55
ATTGGGCTGACACGAAAGTTTTTTATACAAAA	5	21	1	CAGAAATTTT	    0.805626	-39
          ** **** ****

Masking position 9
Map Score:   9.16786

Number of sites scoring better than the average of aligned sites = 189
Number in coding regions = 94
Number in noncoding regions = 95
Number of orfs with sites within 600 bp upstream = 120
Fraction of orfs with sites within 600 bp upstream = 0.019274


Motif number 2

TTACCAAAGGTTACAAAGAACAGTAAATTTA	1	34	0	TTACAAGAAC	    0.826871	-89
ACCTTTGGTAACACCAAAAACCAAAATTTTA	1	54	1	ACACCAAAAC	    0.981748	-69
TTGTGTGGTGTTACTAACAACTGTGCTAATG	1	98	0	TTACTACAAC	    0.776736	-25
GTTAGTAACACCACACAAAAAG         	1	111	1	CCACAAAAAA	    0.861822	-12
       GATTTTCCTAAAAATCGGATTTGA	2	4	1	TTTCCAAAAA	    0.940873	-137
TTACAAGCTGATTCAGAAAACTTTATCAAAT	2	29	0	ATTCAAAAAC	    0.924724	-112
TTGTAACTTTAAACCTAAAACTTAACCAAAA	2	54	1	AAACCAAAAC	    0.959796	-87
ACCTAAAACTTAACCAAAAACGAAGTCAGGC	2	66	1	TAACCAAAAC	    0.959796	-75
GTCAGGCAGAACTCCCAAAAAATTTAAATCA	2	90	1	ACTCCAAAAA	    0.940044	-51
  CTGGGACACTTCCTACAAATCACCGAATC	2	122	0	CTTCCACAAA	    0.866331	-19
          ***** *****

Masking position 7
Map Score:   6.64505

Number of sites scoring better than the average of aligned sites = 735
Number in coding regions = 632
Number in noncoding regions = 103
Number of orfs with sites within 600 bp upstream = 102
Fraction of orfs with sites within 600 bp upstream = 0.0163829


Motif number 3

TAGTTAGTAAATGTTGTATATACCATCCCT	4	51	0	ATGTTGTATA	    0.992519	-46
TACTAACTATATGATGTATATTTTAATGCG	4	72	1	ATGATGTATA	    0.986883	-25
CAATCAATCCATTTTGTATAAAAAACTTTC	5	34	0	ATTTTGTATA	    0.979855	-26
          **********

Masking position 8
Map Score:   2.10308

Number of sites scoring better than the average of aligned sites = 7
Number in coding regions = 2
Number in noncoding regions = 5
Number of orfs with sites within 600 bp upstream = 6
Fraction of orfs with sites within 600 bp upstream = 0.000963701


Motif number 4

AAGGTTACAAAGAACAGTAAATTTATGAGA	1	29	0	AGAACAGTAA	     0.92066	-94
GTCTGCCATTAGCACAGTTGTTAGTAACAC	1	92	1	AGCACAGTTG	    0.985577	-31
AGCTCTTAAAAGCCCAGTATATAAGCCTGA	3	17	1	AGCCCAGTAT	    0.992066	-23
CTTTCGTGTCAGCCCAATTTTTTATCTA  	5	9	0	AGCCCAATTT	     0.96937	-51
          **********

Masking position 6
Map Score:   0.503865

Number of sites scoring better than the average of aligned sites = 48
Number in coding regions = 37
Number in noncoding regions = 11
Number of orfs with sites within 600 bp upstream = 11
Fraction of orfs with sites within 600 bp upstream = 0.00176678


Motif number 5

          **********

No masking
Map Score:   -5.51791e-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:   -5.51791e-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:   -5.51791e-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