AlignACE version 2.2  July 7, 1998
alignACE -aORF_aful.txt -zaful.fna -icpxR6_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	AF1351	238	ISA1083-2, ISORF2
#2	AF1354	68	membrane protein, putative

Motif number 1

TGTTGACTTATTTTAAGGTTTTCAAATTGT	1	24	1	TTTTAAGGTT	    0.803412	-215
ATTCGTAGGGTTTAAATGTTATGGATTTTT	1	58	1	TTTAAATGTT	     0.97676	-181
AATATCTACGATTAATTGTCGCAAAAAATC	1	81	0	ATTAATTGTC	     0.95358	-158
TAATATTTTATTAAAATGTTGCATTTAACT	1	111	0	TTAAAATGTT	    0.971521	-128
ATGTGTCCTTTTAAAATTTTCACAAAAGCC	1	159	1	TTAAAATTTT	    0.870418	-80
CAGAAGGGGAATTTATTGTCCTGAGCAAAA	1	188	1	ATTTATTGTC	    0.866526	-51
TATCTATAGTATAAATAGTTTTGCTCAGGA	1	206	0	ATAAATAGTT	    0.925709	-33
          TTTAATTTTTGTTACCATCA	2	1	1	TTTAATTTTT	    0.910648	-68
ACATGGGGGTATAAATAGTTAAGCATAAAA	2	43	0	ATAAATAGTT	    0.925709	-26
          **********

Masking position 5
Map Score:   8.9618

Number of sites scoring better than the average of aligned sites = 260
Number in coding regions = 137
Number in noncoding regions = 123
Number of orfs with sites within 600 bp upstream = 158
Fraction of orfs with sites within 600 bp upstream = 0.0253774


Motif number 2

 AATAGTTCATTTTTGTTGACTTATTTTAAG	1	10	1	TTTTTGTTAC	    0.977545	-229
TGTTATGGATTTTTTGCGACAATTAATCGTA	1	74	1	TTTTTGCGCA	     0.97251	-165
TAATCGTAGATATTAGTTAAATGCAACATTT	1	97	1	TATTAGTTAA	    0.764696	-142
ACTCAAGCTTTATATGTGTCCTTTTAAAATT	1	146	1	TATATGTGCC	    0.923165	-93
CCCCTTCTGGCTTTTGTGAAAATTTTAAAAG	1	166	0	CTTTTGTGAA	    0.930532	-73
     TTTAATTTTTGTTACCATCATAAACT	2	6	1	TTTTTGTTCC	    0.981333	-63
ACTGCTATCTTTTATGCTTAACTATTTATAC	2	34	1	TTTATGCTAA	      0.9134	-35
          ******** **

Masking position 3
Map Score:   2.46075

Number of sites scoring better than the average of aligned sites = 234
Number in coding regions = 184
Number in noncoding regions = 50
Number of orfs with sites within 600 bp upstream = 50
Fraction of orfs with sites within 600 bp upstream = 0.00803084


Motif number 3

          **********

No masking
Map Score:   3.29282e-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 4

          **********

No masking
Map Score:   3.29282e-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 5

          **********

No masking
Map Score:   3.29282e-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