AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00030_aful_reg_300.orf -o00030_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	AF0941	52	A. fulgidus predicted coding region AF0941
#2	AF1419	24	ribose-phosphate pyrophosphokinase (prsA-2)
#3	AF1420	216	membrane protein
#4	AF1421	49	conserved hypothetical protein
#5	AF1422	35	aspartate racemase
#6	AF1423	112	conserved hypothetical protein

Motif number 1

AATGCATTATCGCAACGGATTTATAGCCCTTACCAATAACTCAAT	1	15	1	CGACATTACA	    0.979439	-38
ATAGACTATCCGGGAAGCTTTGAAGCTGAGTGACAGAGTATCGTG	3	44	0	CGAATTTACA	    0.997241	-173
GATTCGTTTTCTGCAATATCTCAATATCAAACTCATGAAAAACCT	3	155	1	CTAATCTACA	    0.981805	-62
TTGGTAGCACAGCAAACTTTTTAACATTCAAAGCAGAATTGCATT	4	15	1	AGAATTTACA	    0.979157	-35
ATCACCCAACCTAAAAAATTTTAACCTCAACTTCAAGCAAAATCC	6	12	0	CTAATTTACA	     0.99433	-101
AAAGGCCTGTCTTGAAGTATTTAGCGCATCACCCAACCTAAAAAA	6	39	0	CTAAATTACA	    0.987062	-74
GGCCTTTTAGCGGTAAATTTTTATCGGCCCAACCAGAACAACATC	6	77	1	CGAATTTACA	    0.997247	-36
          **  **  *** *          **

Masking position 13
Map Score:   6.72094

Number of sites scoring better than the average of aligned sites = 32
Number in coding regions = 21
Number in noncoding regions = 11
Number of orfs with sites within 600 bp upstream = 17
Fraction of orfs with sites within 600 bp upstream = 0.00273049


Motif number 2

AAATCCGTTGCGATAATGCATTTTTA        	1	3	0	CGATGCTTTT	    0.989364	-50
CAAAGCTTCCCGGATAGTCTATTTCACACTCCAT	3	67	1	CGAGTCATTT	    0.993613	-150
CACTCCATCAGGGCTATTCGTTTTGTCAAGTTAT	3	93	1	GGATTCTTTT	    0.983234	-124
TTCAAGACTTCGTGGATTCGTTTTCTGCAATATC	3	141	1	CGATTCTTTT	     0.99518	-76
TCTTGTTAGGCGATTAGTCTATTT          	5	22	1	CGAGTCATTT	    0.993613	-14
          **   **** ****

Masking position 6
Map Score:   3.86365

Number of sites scoring better than the average of aligned sites = 13
Number in coding regions = 9
Number in noncoding regions = 4
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 3

TGTCAAGTTATTCTGCTGGCAACGCTTCAA	3	116	1	TTCTGCTGGC	    0.976527	-101
ATGTTAAAAAGTTTGCTGTGCTACCAATAC	4	12	0	GTTTGCTGTG	    0.920937	-38
   AATGCAATTCTGCTTTGAATGTTAAAA	4	33	0	TTCTGCTTTG	    0.983718	-17
      TGGATTTTGCTTGAAGTTGAGGTT	6	5	1	TTTTGCTTGA	    0.956122	-108
GTTAAAATTTTTTAGGTTGGGTGATGCGCT	6	32	1	TTTAGGTTGG	    0.936161	-81
  TGATGTTGTTCTGGTTGGGCCGATAAAA	6	95	0	TTCTGGTTGG	    0.989414	-18
          **********

Masking position 7
Map Score:   3.66587

Number of sites scoring better than the average of aligned sites = 410
Number in coding regions = 365
Number in noncoding regions = 45
Number of orfs with sites within 600 bp upstream = 46
Fraction of orfs with sites within 600 bp upstream = 0.00738837


Motif number 4

AACGGATTTATAGCCCTTACCAATAACTCA	1	28	1	TAGCCCTTAC	    0.951177	-25
          AAGCCCTTCCTCTTTTTTTG	2	1	1	AAGCCCTTCC	    0.982891	-24
ACTATCCGGGAAGCTTTGAAGCTGAGTGAC	3	55	0	AAGCTTTGAA	    0.813151	-162
ACAAAACGAATAGCCCTGATGGAGTGTGAA	3	89	0	TAGCCCTGAT	    0.839207	-128
CGAAGTCTTGAAGCGTTGCCAGCAGAATAA	3	123	0	AAGCGTTGCC	    0.955046	-94
AGAGGCTAATAAGGTTTTTCATGAGTTTGA	3	181	0	AAGGTTTTTC	    0.851793	-36
       CCAAAGCTTTATCTTGTTAGGCG	5	4	1	AAGCTTTATC	    0.865396	-32
TTACCGCTAAAAGGCCTGTCTTGAAGTATT	6	63	0	AAGGCCTGTC	    0.974929	-50
          **********

Masking position 2
Map Score:   2.69744

Number of sites scoring better than the average of aligned sites = 1242
Number in coding regions = 1158
Number in noncoding regions = 84
Number of orfs with sites within 600 bp upstream = 71
Fraction of orfs with sites within 600 bp upstream = 0.0114038


Motif number 5

      GAATCAAAAAAAGAGGAAGGGCTT	2	11	0	CAAAAAAAGA	    0.956091	-14
TGAGATATTGCAGAAAACGAATCCACGAAG	3	148	0	CAGAAAACGA	    0.963971	-69
 ACGCAAATAAATAACAAGAGGCTAATAAG	3	198	0	AATAACAAGA	     0.94311	-19
AGACTAATCGCCTAACAAGATAAAGCTTTG	5	12	0	CCTAACAAGA	    0.974981	-24
TCGGCCCAACCAGAACAACATCA       	6	100	1	CAGAACAACA	    0.974363	-13
          **********

Masking position 5
Map Score:   1.12993

Number of sites scoring better than the average of aligned sites = 167
Number in coding regions = 147
Number in noncoding regions = 20
Number of orfs with sites within 600 bp upstream = 18
Fraction of orfs with sites within 600 bp upstream = 0.0028911


Motif number 6

          **********

No masking
Map Score:   -2.95996e-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:   -2.95996e-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:   -2.95996e-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