AlignACE version 2.2  July 7, 1998
alignACE -aORF_aful.txt -zaful.fna -itorR_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	AF1237	191	A. fulgidus predicted coding region AF1237

Motif number 1

ATTTTTCCGGTTTTAAATTTTGCTATCCTTT	1	25	1	TTTTAAATTT	    0.953327	-167
GCGGAAAGTTTTATCACTGTTAACTCCTGAG	1	65	1	TTATCACGTT	    0.996427	-127
AACTCCTGAGTTATCACTGTTAACAAAATGT	1	86	1	TTATCACGTT	    0.996427	-106
TGATGTGATTTTTTAAAGGTTTTGACAAATG	1	116	1	TTTTAAAGTT	    0.983726	-76
TCTACGATTTTTATCGCATTTGTCAAAACCT	1	132	0	TTATCGCTTT	    0.971795	-60
AATTTCCAATTTATAAAAGTTACTTCTACGA	1	156	0	TTATAAAGTT	    0.991212	-36
          ******* ***

Masking position 4
Map Score:   10.1118

Number of sites scoring better than the average of aligned sites = 80
Number in coding regions = 64
Number in noncoding regions = 16
Number of orfs with sites within 600 bp upstream = 18
Fraction of orfs with sites within 600 bp upstream = 0.0028911


Motif number 2

TAACTCAGGAGTTAACAGTGATAAAACTTT	1	69	0	GTTAACAGTG	    0.998405	-123
ATCACATTTTGTTAACAGTGATAACTCAGG	1	90	0	GTTAACAGTG	    0.998405	-102
          **********

Masking position 5
Map Score:   2.92344

Number of sites scoring better than the average of aligned sites = 2
Number in coding regions = 0
Number in noncoding regions = 2
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 3

GCAAAATTTAAAACCGGAAAAATAAAGGGGCAAGG	1	13	0	AAAGGAATAA	    0.997415	-179
CGCCTGTTACTAAAAGGATAGCAAAATTTAAAACC	1	33	0	TAAGGAAAAA	    0.983741	-159
AATGCGATAAAAATCGTAGAAGTAACTTTTATAAA	1	143	1	AAAGTAATAA	    0.989819	-49
TAACTTTTATAAATTGGAAATTTAATAGGTAAGGC	1	165	1	AAAGGAATAA	    0.997415	-27
          ***  *** *  ***

Masking position 8
Map Score:   2.20052

Number of sites scoring better than the average of aligned sites = 11
Number in coding regions = 7
Number in noncoding regions = 4
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 4

          **********

No masking
Map Score:   1.65857e-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:   1.65857e-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:   1.65857e-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