AlignACE version 2.2  July 7, 1998
alignACE -aORF_aful.txt -zaful.fna -imelR_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	AF0616	23	conserved hypothetical protein
#2	AF0617	106	LPS biosynthesis protein, putative

Motif number 1

     TAGCTAATATATCAAGCAAATTT  	1	6	1	AATATATCAA	    0.989838	-18
TTAATCTACAAGAACATCAAATTCGCTTAT	2	18	0	AGAACATCAA	    0.972755	-89
TTTCAGCAAAAAGATATTAATCTACAAGAA	2	34	0	AAGATATTAA	    0.988754	-73
TTTTTGCTGAAAAATATCAATATCCACCAC	2	52	1	AAAATATCAA	    0.992256	-55
CCTTTAATTTCAGATATTAAACTTTGTTGT	2	80	0	CAGATATTAA	    0.978993	-27
          **********

Masking position 6
Map Score:   8.31819

Number of sites scoring better than the average of aligned sites = 34
Number in coding regions = 22
Number in noncoding regions = 12
Number of orfs with sites within 600 bp upstream = 13
Fraction of orfs with sites within 600 bp upstream = 0.00208802


Motif number 2

          TAGCTAATATATCAAGCAAA	1	1	1	TAGCTAATAT	     0.98269	-23
CTAATATATCAAGCAAATTT          	1	14	1	AAGCAAATTT	     0.99387	-10
 GGAGGTCATAAGCGAATTTGATGTTCTTG	2	10	1	AAGCGAATTT	     0.99569	-97
          **********

Masking position 6
Map Score:   3.19096

Number of sites scoring better than the average of aligned sites = 22
Number in coding regions = 16
Number in noncoding regions = 6
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 3

        AAATTTGCTTGATATATTAGCTA   	1	8	0	ATTCGATATA	    0.894444	-16
GAATTTGATGTTCTTGTAGATTAATATCTTTTTG	2	24	1	TTTGGATTAA	    0.955334	-83
GATTAATATCTTTTTGCTGAAAAATATCAATATC	2	42	1	TTTGGAAAAA	    0.632129	-65
TTAAACTTTGTTGTGGTGGATATTGATATTTTTC	2	60	0	TTTGGATATT	    0.988958	-47
ATATCTGAAATTAAAGGGGAAAAT          	2	93	1	TTAGGAAAAT	    0.954892	-14
          ** * *  ******

Masking position 10
Map Score:   0.140387

Number of sites scoring better than the average of aligned sites = 202
Number in coding regions = 169
Number in noncoding regions = 33
Number of orfs with sites within 600 bp upstream = 33
Fraction of orfs with sites within 600 bp upstream = 0.00530035


Motif number 4

          **********

No masking
Map Score:   -7.57276e-14

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 5

          **********

No masking
Map Score:   -7.57276e-14

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:   -7.57276e-14

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