AlignACE version 2.2  July 7, 1998
alignACE -aORF_aful.txt -zaful.fna -imalT_aful_opreg_300.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	AF0094	300	conserved hypothetical protein
#2	AF1608	59	spermidine/putrescine ABC transporter, ATP-binding protein (potA)

Motif number 1

AATTCGACTTTAAATGTCGAATAAATCAATAA	1	14	0	TAAATGTCGT	    0.875206	-287
TTTTGTAATTAAAAATTCGACTTTAAATGTCG	1	27	0	AAAAATTCGT	    0.990009	-274
TTTAGTTTAATAAATTTTGTTTTTGTAATTAA	1	47	0	TAAATTTTGT	    0.950257	-254
TTTATTAAACTAAAATTCGATGAGGACTTTCT	1	65	1	TAAAATTCGG	    0.928142	-236
GGACTTTCTGAACAATTCGGTTGGCTCCGAAC	1	88	1	AACAATTCGT	     0.96638	-213
GTTGGCTCCGAACAATTCGGAATTAATCGAAT	1	107	1	AACAATTCGA	    0.854531	-194
AAAATATATTAAAAATTCGATTAATTCCGAAT	1	121	0	AAAAATTCGT	    0.990007	-180
GCGTATTATAAAATTTTTGTTTTCGAAAATAT	1	146	0	AAATTTTTGT	    0.798628	-155
TTCAGTGAGCTAACATGCGTATTATAAAATTT	1	162	0	TAACATGCGT	    0.917904	-139
ACGAGTTTGTAAACGTTTGAATTATTCCCCCT	1	220	1	AAACGTTTGT	    0.903583	-81
TCGCAAACCCTAACATTTGGTTTAGGGGGAAT	1	243	0	TAACATTTGT	    0.966974	-58
ATCGGATATTTAACTTTTGTGAAGTGTCGCAA	1	269	0	TAACTTTTGA	    0.799039	-32
    TAGATAAAAAATTGGGCTGACACGAAAG	2	7	1	AAAAATTGGT	    0.935053	-53
TTTGTATAAAAAACTTTCGTGTCAGCCCAATT	2	20	0	AAACTTTCGT	    0.984731	-40
          *********  *

Masking position 2
Map Score:   21.2488

Number of sites scoring better than the average of aligned sites = 237
Number in coding regions = 175
Number in noncoding regions = 62
Number of orfs with sites within 600 bp upstream = 59
Fraction of orfs with sites within 600 bp upstream = 0.00947639


Motif number 2

TTGTAATTAAAAATTCGACTTTAAATGTCG	1	27	0	AAATTCGACT	    0.982317	-274
TAGTTTAATAAATTTTGTTTTTGTAATTAA	1	47	0	AATTTTGTTT	     0.80957	-254
TATTAAACTAAAATTCGATGAGGACTTTCT	1	67	1	AAATTCGATG	    0.963632	-234
ACTTTCTGAACAATTCGGTTGGCTCCGAAC	1	90	1	CAATTCGGTT	     0.97875	-211
AATATATTAAAAATTCGATTAATTCCGAAT	1	121	0	AAATTCGATT	    0.991098	-180
AAACGTTTACAAACTCGTTTTGGAAAGGCT	1	208	0	AAACTCGTTT	    0.933041	-93
CAAACCCTAACATTTGGTTTAGGGGGAATA	1	242	0	CATTTGGTTT	    0.892191	-59
  TAGATAAAAAATTGGGCTGACACGAAAG	2	9	1	AAATTGGGCT	    0.965889	-51
TTTTTTATACAAAATGGATTGATTGTGTTC	2	39	1	AAAATGGATT	    0.925878	-21
          **********

Masking position 5
Map Score:   10.5464

Number of sites scoring better than the average of aligned sites = 205
Number in coding regions = 160
Number in noncoding regions = 45
Number of orfs with sites within 600 bp upstream = 43
Fraction of orfs with sites within 600 bp upstream = 0.00690652


Motif number 3

CGACTTTAAATGTCGAATAAATCAATAATC	1	12	0	TGTCGAATAA	    0.903799	-289
GAATTTTTAATTACAAAAACAAAATTTATT	1	41	1	TTACAAAAAC	    0.919576	-260
TTTAATATATTTTCGAAAACAAAAATTTTA	1	140	1	TTTCGAAAAC	    0.993259	-161
ATTTCCAGCCTTTCCAAAACGAGTTTGTAA	1	202	1	TTTCCAAAAC	    0.982367	-99
TTTTGTGAAGTGTCGCAAACCCTAACATTT	1	257	0	TGTCGCAAAC	    0.986336	-44
          **********

Masking position 7
Map Score:   3.39192

Number of sites scoring better than the average of aligned sites = 313
Number in coding regions = 284
Number in noncoding regions = 29
Number of orfs with sites within 600 bp upstream = 24
Fraction of orfs with sites within 600 bp upstream = 0.0038548


Motif number 4

  CGATTATTGATTTATTCGACATTTAAAG	1	9	1	GATTTATTCG	    0.984243	-292
AGGACTTTCTGAACAATTCGGTTGGCTCCG	1	87	1	GAACAATTCG	    0.970348	-214
GATTAATTCCGAATTGTTCGGAGCCAACCG	1	105	0	GAATTGTTCG	    0.975799	-196
TTAAAAATTCGATTAATTCCGAATTGTTCG	1	115	0	GATTAATTCC	    0.984238	-186
ACTGAATTCAGACTATTTCCAGCCTTTCCA	1	188	1	GACTATTTCC	    0.941026	-113
GTAAACGTTTGAATTATTCCCCCTAAACCA	1	228	1	GAATTATTCC	    0.988569	-73
          **********

Masking position 7
Map Score:   7.69717

Number of sites scoring better than the average of aligned sites = 26
Number in coding regions = 17
Number in noncoding regions = 9
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 5

          **********

No masking
Map Score:   -4.23894e-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:   -4.23894e-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:   -4.23894e-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