AlignACE version 2.2  July 7, 1998
alignACE -aORF_aful.txt -zaful.fna -icytR_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	AF0913	144	A. fulgidus predicted coding region AF0913
#2	AF1342	126	thymidine phosphorylase (deoA-2)
#3	AF1753	39	lysophospholipase
#4	AF1755	115	conserved hypothetical protein

Motif number 1

AACCGAAAATTTAAAATTTTGCATATACCC	1	40	0	TTAAAATTTT	    0.976172	-105
TACGAGGGGTTAAAAACCTTTGACGTCATC	1	114	0	TAAAAACCTT	    0.934148	-31
GTCGTCAGCTTTAAAACCTTTTCAGGTGAG	2	22	1	TTAAAACCTT	    0.957908	-105
TGTTTATGTTTAAAAATTCTCACCTGAAAA	2	40	0	TAAAAATTCT	    0.975902	-87
CGAGAAAAAGTTAATATTCTTTCAGAGTTT	2	97	1	TTAATATTCT	    0.920933	-30
   TGAACTTCAAAAACTCTGAAAGAATAT	2	110	0	CAAAAACTCT	     0.91345	-17
AGAAAAAAGATTAAAATTTTTCGCAG    	3	7	0	TTAAAATTTT	    0.976172	-33
CTGATTTCCTTTGAAATTCTATCCAGCTCA	4	60	1	TTGAAATTCT	    0.945275	-56
          **********

Masking position 6
Map Score:   9.72417

Number of sites scoring better than the average of aligned sites = 207
Number in coding regions = 101
Number in noncoding regions = 106
Number of orfs with sites within 600 bp upstream = 121
Fraction of orfs with sites within 600 bp upstream = 0.0194346


Motif number 2

ACTTCTTAAAAAGGAGGTTAAGCGGGAAG   	1	8	0	AAGGAGTTAG	     0.99051	-137
TTGCATAGGCAATGCGGTTTAGCTTTGATGAC	1	88	1	AATGCGTTAG	    0.990516	-57
TTTAGCTTTGATGACGTCAAAGGTTTTTAACC	1	105	1	ATGACGCAAG	    0.885516	-40
CGCTATCGTGAAGAAGTTATAGATAATGTTGT	2	67	0	AAGAAGTAAG	    0.925341	-60
TTTCTGTCAGAATGAGCTTCAGAATTCCACCT	4	18	1	AATGAGTTAG	    0.988275	-98
TCCACCTGAAATTGCGTCTGATTTCCTTTGAA	4	43	1	ATTGCGCTAT	    0.875013	-73
  AAAGCCTTATTGAGTTTGAGAGGTAAACAC	4	96	0	ATTGAGTTAG	    0.985157	-20
          ****** ** **

Masking position 11
Map Score:   4.94484

Number of sites scoring better than the average of aligned sites = 572
Number in coding regions = 537
Number in noncoding regions = 35
Number of orfs with sites within 600 bp upstream = 34
Fraction of orfs with sites within 600 bp upstream = 0.00546097


Motif number 3

ATACCCACTTCTTAAAAAGGAGGTTAAGCG	1	16	0	CTTAAAAAGG	    0.934242	-129
AAAATTCTCACCTGAAAAGGTTTTAAAGCT	2	28	0	CCTGAAAAGG	    0.987397	-99
TTCTCGCTATCGTGAAGAAGTTATAGATAA	2	73	0	CGTGAAGAAG	    0.958179	-54
TTCACGATAGCGAGAAAAAGTTAATATTCT	2	87	1	CGAGAAAAAG	    0.957692	-40
CTGGTCTTGGCAGAAAAAAGATTAAAATTT	3	18	0	CAGAAAAAAG	    0.950802	-22
CTCATTCTGACAGAAAAATGAAA       	4	4	0	CAGAAAAATG	    0.930973	-112
CAGAATTCCACCTGAAATTGCGTCTGATTT	4	37	1	CCTGAAATTG	    0.915131	-79
          **********

Masking position 5
Map Score:   3.43355

Number of sites scoring better than the average of aligned sites = 788
Number in coding regions = 711
Number in noncoding regions = 77
Number of orfs with sites within 600 bp upstream = 45
Fraction of orfs with sites within 600 bp upstream = 0.00722775


Motif number 4

AGCAGGGAATGATGATGTAACCGAAAATTT	1	58	0	GATGATGTAA	    0.965785	-87
GTTTAGCTTTGATGACGTCAAAGGTTTTTA	1	104	1	GATGACGTCA	    0.995261	-41
AGGTTTTAAAGCTGACGACAATTTAACATC	2	11	0	GCTGACGACA	    0.990108	-116
          **********

Masking position 5
Map Score:   0.315522

Number of sites scoring better than the average of aligned sites = 44
Number in coding regions = 42
Number in noncoding regions = 2
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 5

CCCTGCTTTGCATAGGCAATGCGGTTTAGC	1	81	1	CATAGGCAAT	    0.989229	-64
CAAAGGAAATCAGACGCAATTTCAGGTGGA	4	43	0	CAGACGCAAT	    0.992707	-73
GATAGAATTTCAAAGGAAATCAGACGCAAT	4	53	0	CAAAGGAAAT	    0.976056	-63
GTTTACCTCTCAAACTCAATAAGGCTTT  	4	98	1	CAAACTCAAT	    0.976056	-18
          **********

Masking position 4
Map Score:   2.78576

Number of sites scoring better than the average of aligned sites = 46
Number in coding regions = 43
Number in noncoding regions = 3
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 6

          **********

No masking
Map Score:   -3.17312e-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:   -3.17312e-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:   -3.17312e-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