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

Motif number 1

TTATTGATTTATTCGACATTTAAAGTCGAATT	1	14	1	ACGACATTTA	    0.897034	-287
CGACATTTAAAGTCGAATTTTTAATTACAAAA	1	27	1	ACGAATTTTT	    0.991941	-274
TTAATTACAAAAACAAAATTTATTAAACTAAA	1	47	1	ACAAAATTTA	    0.959563	-254
AGAAAGTCCTCATCGAATTTTAGTTTAATAAA	1	65	0	CCGAATTTTA	    0.941332	-236
GTTCGGAGCCAACCGAATTGTTCAGAAAGTCC	1	88	0	ACGAATTGTT	    0.972749	-213
ATTCGATTAATTCCGAATTGTTCGGAGCCAAC	1	107	0	TCGAATTGTT	    0.879478	-194
ATTCGGAATTAATCGAATTTTTAATATATTTT	1	121	1	ACGAATTTTT	    0.991939	-180
ATATTTTCGAAAACAAAAATTTTATAATACGC	1	146	1	ACAAAAATTT	    0.831263	-155
AAATTTTATAATACGCATGTTAGCTCACTGAA	1	162	1	ACGCATGTTA	    0.932828	-139
AGGGGGAATAATTCAAACGTTTACAAACTCGT	1	220	0	ACAAACGTTT	    0.920885	-81
ATTCCCCCTAAACCAAATGTTAGGGTTTGCGA	1	243	1	ACAAATGTTA	    0.972701	-58
TTGCGACACTTCACAAAAGTTAAATATCCGAT	1	269	1	TCAAAAGTTA	    0.831626	-32
CTTTCGTGTCAGCCCAATTTTTTATCTA    	2	7	0	ACCAATTTTT	    0.947047	-53
AATTGGGCTGACACGAAAGTTTTTTATACAAA	2	20	1	ACGAAAGTTT	    0.987669	-40
          *  *********

Masking position 11
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

CGACATTTAAAGTCGAATTTTTAATTACAA	1	27	1	AGTCGAATTT	    0.983485	-274
TTAATTACAAAAACAAAATTTATTAAACTA	1	47	1	AAACAAAATT	    0.819988	-254
AGAAAGTCCTCATCGAATTTTAGTTTAATA	1	67	0	CATCGAATTT	    0.965981	-234
GTTCGGAGCCAACCGAATTGTTCAGAAAGT	1	90	0	AACCGAATTG	    0.980149	-211
ATTCGGAATTAATCGAATTTTTAATATATT	1	121	1	AATCGAATTT	    0.991666	-180
AGCCTTTCCAAAACGAGTTTGTAAACGTTT	1	208	1	AAACGAGTTT	    0.933895	-93
TATTCCCCCTAAACCAAATGTTAGGGTTTG	1	242	1	AAACCAAATG	    0.898682	-59
CTTTCGTGTCAGCCCAATTTTTTATCTA  	2	9	0	AGCCCAATTT	    0.968109	-51
GAACACAATCAATCCATTTTGTATAAAAAA	2	39	0	AATCCATTTT	    0.930491	-21
          **********

Masking position 6
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

GATTATTGATTTATTCGACATTTAAAGTCG	1	12	1	TTATTCGACA	    0.903799	-289
AATAAATTTTGTTTTTGTAATTAAAAATTC	1	41	0	GTTTTTGTAA	    0.919576	-260
TAAAATTTTTGTTTTCGAAAATATATTAAA	1	140	0	GTTTTCGAAA	    0.993259	-161
TTACAAACTCGTTTTGGAAAGGCTGGAAAT	1	202	0	GTTTTGGAAA	    0.982367	-99
AAATGTTAGGGTTTGCGACACTTCACAAAA	1	257	1	GTTTGCGACA	    0.986336	-44
          **********

Masking position 4
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	    0.984884	-292
AGGACTTTCTGAACAATTCGGTTGGCTCCG	1	87	1	GAACAATTCG	    0.971538	-214
GATTAATTCCGAATTGTTCGGAGCCAACCG	1	105	0	GAATTGTTCG	    0.976775	-196
TTAAAAATTCGATTAATTCCGAATTGTTCG	1	115	0	GATTAATTCC	    0.984879	-186
ACTGAATTCAGACTATTTCCAGCCTTTCCA	1	188	1	GACTATTTCC	    0.943324	-113
GTAAACGTTTGAATTATTCCCCCTAAACCA	1	228	1	GAATTATTCC	    0.989004	-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