AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00630_aful_reg_300.orf -o00630_aful_300.ace -a/home/amcguire/genomes/ORF_aful.txt -z/home/amcguire/genomes/aful.fna -g0.49 -x5 -e 
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 = 	1

Input sequences:
#1	AF1342	126	thymidine phosphorylase (deoA-2)
#2	AF1588	51	conserved hypothetical protein
#3	AF1590	300	A. fulgidus predicted coding region AF1590
#4	AF1638	31	ribulose bisphosphate carboxylase, large subunit (rbcL-2)

Motif number 1

TTTAAAAATTCTCACCTGAAAAGGTTTTAA	1	32	0	CTCACCTGAA	    0.943568	-95
CACTTCTTTGCTCCCGAGAACTCACAAAAA	3	54	1	CTCCCGAGAA	       0.984	-247
CTCCCGAGAACTCACAAAAAAGACGGTTTC	3	64	1	CTCACAAAAA	    0.968011	-237
GAGTAAAAATCTCCCTAAAATCGCATGGGT	3	94	1	CTCCCTAAAA	    0.991008	-207
CAATAAAGGTCTCACCAAATTCCGCAATAA	3	144	0	CTCACCAAAT	    0.981239	-157
TAATTTTATCCTCCCTAAGTTTTCCCGCTC	3	215	1	CTCCCTAAGT	    0.936518	-86
CCGCTCGCTTCCCCCCAAAACTAGGGTAGA	3	239	1	CCCCCCAAAA	    0.987081	-62
          **********

Masking position 5
Map Score:   8.10784

Number of sites scoring better than the average of aligned sites = 247
Number in coding regions = 222
Number in noncoding regions = 25
Number of orfs with sites within 600 bp upstream = 23
Fraction of orfs with sites within 600 bp upstream = 0.00369419


Motif number 2

AATTCTCACCTGAAAAGGTTTTAAAGCTGA	1	26	0	TGAAAAGGTT	    0.975213	-101
AAGAAGTTATAGATAATGTTGTTTATGTTT	1	59	0	AGATAATGTT	    0.935155	-68
CTCGCTATCGTGAAGAAGTTATAGATAATG	1	71	0	TGAAGAAGTT	    0.967965	-56
CACGATAGCGAGAAAAAGTTAATATTCTTT	1	89	1	AGAAAAAGTT	    0.985505	-38
TCGGGAGCAAAGAAGTGGTTGCTTGAAGCC	3	41	0	AGAAGTGGTT	    0.937553	-260
CTAAGGAGGTAAATAAAGTT          	4	1	0	AAATAAAGTT	    0.849232	-31
          **********

Masking position 3
Map Score:   3.68389

Number of sites scoring better than the average of aligned sites = 285
Number in coding regions = 260
Number in noncoding regions = 25
Number of orfs with sites within 600 bp upstream = 28
Fraction of orfs with sites within 600 bp upstream = 0.00449727


Motif number 3

AATTGTCGTCAGCTTTAAAACCTTTTCAGGTGAGA	1	18	1	AGTTAACTTT	     0.96178	-109
AATGTTGTTTATGTTTAAAAATTCTCACCTGAAAA	1	40	0	ATTTAATTCT	    0.848336	-87
TAGCGAGAAAAAGTTAATATTCTTTCAGAGTTTTT	1	94	1	AATTAACTTT	    0.985662	-33
        TGAACTTCAAAAACTCTGAAAGAATAT	1	110	0	AATTAACTCT	    0.988097	-17
TTGTGTCAGCAAATATAAAGATTTTGATTTAATGT	2	17	0	AATAAATTTT	    0.890087	-35
AAGCCTCTACAAATTGATTGGCTTTATTTCTCGCC	3	11	0	AATTATCTTT	    0.933386	-290
GGGAGGATAAAATTAAAGAAACTCTTTGTAAGCCA	3	195	0	AATAAACTCT	    0.973073	-106
          ** ** * *  ****

Masking position 7
Map Score:   2.86832

Number of sites scoring better than the average of aligned sites = 108
Number in coding regions = 75
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

TTAACTTTTTCTCGCTATCGTGAAGAAGTT	1	81	0	CTCGCTATCG	    0.992338	-46
GAGATTTTTACTCGAAACCGTCTTTTTTGT	3	77	0	CTCGAAACCG	     0.97502	-224
AGTTTTCCCGCTCGCTTCCCCCCAAAACTA	3	232	1	CTCGCTTCCC	    0.983854	-69
GAGTGATGGTCCCTCTACCCTAGTTTTGGG	3	252	0	CCCTCTACCC	    0.975658	-49
TTAATCTTGACTCTCAATAGTAGAAAAGAG	3	279	0	CTCTCAATAG	    0.884756	-22
          **********

Masking position 3
Map Score:   0.739044

Number of sites scoring better than the average of aligned sites = 524
Number in coding regions = 507
Number in noncoding regions = 17
Number of orfs with sites within 600 bp upstream = 9
Fraction of orfs with sites within 600 bp upstream = 0.00144555


Motif number 5

AGGTTTTAAAGCTGACGACAATTTAACATC	1	11	0	GCTGACGACA	    0.974133	-116
CTTCAAAAACTCTGAAAGAATATTAACTTT	1	103	0	TCTGAAAGAA	    0.884004	-24
CTTTATATTTGCTGACACAACCCCAAATTT	2	32	1	GCTGACACAA	    0.977238	-20
AAGGGAAGCAGCTGAACCCATGCGATTTTA	3	109	0	GCTGAACCCA	    0.981026	-192
CCGCAATAATGCTGAAGGGAAGCAGCTGAA	3	123	0	GCTGAAGGGA	    0.981026	-178
          **********

Masking position 5
Map Score:   0.412685

Number of sites scoring better than the average of aligned sites = 440
Number in coding regions = 406
Number in noncoding regions = 34
Number of orfs with sites within 600 bp upstream = 33
Fraction of orfs with sites within 600 bp upstream = 0.00530035


Motif number 6

          **********

No masking
Map Score:   -8.78641e-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:   -8.78641e-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 8

          **********

No masking
Map Score:   -8.78641e-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