AlignACE version 2.2  July 7, 1998
alignACE -aORF_aful.txt -zaful.fna -ifis_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	AF0421	25	A. fulgidus predicted coding region AF0421
#2	AF0422	138	uroporphyrin-III C-methyltransferase (cysG-1)
#3	AF1485	87	queuine tRNA-ribosyltransferase (tgtB)
#4	AF1664	147	ribonucleotide reductase (nrd)

Motif number 1

TGACCTGAGGTTAAGAAAAAACAG       	1	12	1	TTAAGAAAAA	    0.933138	-14
GCTTAAACCAGAAAGCGCAAATTTCGAAATT	2	62	0	GAAAGCCAAA	    0.928073	-77
ATATTTTTAGGTAAGCTTAAACCAGAAAGCG	2	76	0	GTAAGCTAAA	    0.944094	-63
GGGAGTTGTGGGAAGGTTAAAAAACTTCTCG	2	114	0	GGAAGGTAAA	    0.982688	-25
TGTTGCTATTTGAAAATAAAAGATTTTGTGA	3	18	1	TGAAAAAAAA	    0.846167	-70
TGAGGTCACCGAAAGGGAATAATCTTTTAAG	3	46	1	GAAAGGAATA	    0.893637	-42
TAAATTGACAGAAAACTTAAAAGATTATTCC	3	61	0	GAAAACTAAA	    0.772149	-27
TTGAGATGCTGTAAGAAAAATTTTTCTATTC	4	57	1	GTAAGAAAAT	    0.833661	-91
AAGGAAAAATTGAATAGAAAAATTTTTCTTA	4	68	0	TGAATAAAAA	    0.757244	-80
GAGCATCTATTGAAGGAAAAATTGAATAGAA	4	80	0	TGAAGGAAAA	    0.978708	-68
GCTCTCGAAGGGCAGGCAAAATTGTTTTATC	4	107	1	GGCAGGAAAA	    0.960731	-41
TGGTAGATAAGAAAGATAAAACAATTTTGCC	4	121	0	GAAAGAAAAA	    0.982561	-27
          ****** ****

Masking position 4
Map Score:   12.134

Number of sites scoring better than the average of aligned sites = 1155
Number in coding regions = 1002
Number in noncoding regions = 153
Number of orfs with sites within 600 bp upstream = 143
Fraction of orfs with sites within 600 bp upstream = 0.0229682


Motif number 2

TTAGGCAATATATAAGAATTTCGAAATTTGCG	2	46	1	TATAAATTTC	    0.952604	-93
GTGGGAAGGTTAAAAAACTTCTCGATTGCAGA	2	106	0	TAAAAATTCT	    0.969323	-33
TATTTGAAAATAAAAGATTTTGTGAGGTCACC	3	24	1	TAAAAATTTG	    0.963792	-64
ACAGAAAACTTAAAAGATTATTCCCTTTCGGT	3	53	0	TAAAAATATT	    0.949768	-35
TGACATTAACTTTAATACTTTTCAAGAAGACA	4	18	0	TTTAAATTTT	    0.919479	-130
AAAAATTGAATAGAAAAATTTTTCTTACAGCA	4	63	0	TAGAAATTTT	    0.978834	-85
ATAAGAAAGATAAAACAATTTTGCCTGCCCTT	4	114	0	TAAAAATTTT	     0.98991	-34
          ***** * ****

Masking position 7
Map Score:   6.20873

Number of sites scoring better than the average of aligned sites = 104
Number in coding regions = 39
Number in noncoding regions = 65
Number of orfs with sites within 600 bp upstream = 82
Fraction of orfs with sites within 600 bp upstream = 0.0131706


Motif number 3

         TTGACCTGAGGTTAAGAAAAAA	1	2	1	TGACTGAGGT	    0.977625	-24
GGACTTGCAATTACAGGAGGTGAACGA    	2	7	0	TTACGGAGGT	    0.987716	-132
CGATTGCAGATATTTTTAGGTAAGCTTAAAC	2	85	0	TATTTTAGGT	    0.863666	-54
AAATAAAAGATTTTGTGAGGTCACCGAAAGG	3	31	1	TTTTTGAGGT	    0.984046	-57
AATGTCAAGTTTTCTTGAGATGCTGTAAGAA	4	43	1	TTTCTGAGAT	    0.970391	-105
       CAGTTATGGTAGATAAGAAAGATA	4	134	0	TTATGTAGAT	    0.853772	-14
          **** ******

Masking position 8
Map Score:   2.28142

Number of sites scoring better than the average of aligned sites = 300
Number in coding regions = 255
Number in noncoding regions = 45
Number of orfs with sites within 600 bp upstream = 51
Fraction of orfs with sites within 600 bp upstream = 0.00819146


Motif number 4

CCTAAAAAGAGGGGGACTTGCAATTACAGG	2	21	0	GGGGGACTTG	     0.99841	-118
        AAGGGGGAGTTGTGGGAAGGTT	2	127	0	GGGGGAGTTG	    0.998417	-12
          **********

Masking position 6
Map Score:   0.852606

Number of sites scoring better than the average of aligned sites = 15
Number in coding regions = 12
Number in noncoding regions = 3
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 5

          **********

No masking
Map Score:   2.36911e-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:   2.36911e-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:   2.36911e-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