AlignACE version 2.2  July 7, 1998
alignACE -aORF_aful.txt -zaful.fna -imetR_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	AF0006	104	corrinoid methyltransferase protein (mtaC-1)
#2	AF0008	73	oxalate/formate antiporter (oxlT-1)
#3	AF1628	177	transposase, putative
#4	AF2113	44	A. fulgidus predicted coding region AF2113

Motif number 1

AGTCAGATAATTTTGTTATGAACTGATTCA	1	35	1	TTTTGTTATG	    0.892101	-70
AGAAGGCCTATTTTCTAATTTGGAGGTGTT	1	82	1	TTTTCTAATT	    0.969296	-23
        TTTTTTCTTATTTATGAACCAG	2	3	1	TTTTCTTATT	    0.980637	-71
TTGTGTAGTTTTGTCCTGTTGAAGGGGAAG	3	89	0	TTGTCCTGTT	    0.958855	-89
TGATTTAGGGTTGTGTAGTTTTGTCCTGTT	3	99	0	TTGTGTAGTT	    0.929918	-79
ATTTTGGTGGTTTTGTTTTTGATTTAGGGT	3	118	0	TTTTGTTTTT	     0.90441	-60
ATTGATTAATTTTTCGAATTTTGGTGGTTT	3	135	0	TTTTCGAATT	    0.920253	-43
AATTGAGTTATTTTCCTGTTAAAAAATTTT	4	23	0	TTTTCCTGTT	    0.976278	-22
          **********

Masking position 4
Map Score:   8.35643

Number of sites scoring better than the average of aligned sites = 242
Number in coding regions = 172
Number in noncoding regions = 70
Number of orfs with sites within 600 bp upstream = 69
Fraction of orfs with sites within 600 bp upstream = 0.0110826


Motif number 2

TGTTATGAATCAGTTCATAACAAAATTATC	1	40	0	CAGTTCATAA	    0.928383	-65
TGATTCATAACAGCTTTTATCTTTAGAAGG	1	58	1	CAGCTTTTAT	    0.898763	-47
     CTAAACACCTCCAAATTAGAAAATA	1	90	0	CACCTCCAAA	    0.944743	-15
ATTTATGAACCAGTTCATAACAGCCTTTAT	2	20	1	CAGTTCATAA	    0.928383	-54
CAGTTCATAACAGCCTTTATTTAGCACTCA	2	30	1	CAGCCTTTAT	    0.919548	-44
   CGCGAATCCCCTCTTAAGCAGAGATGA	2	57	0	CCCCTCTTAA	    0.938454	-17
GTTGAAGGAACACCCTATAACT        	3	3	0	CACCCTATAA	    0.954849	-175
GGTGTTCCTTCAACCCCTAACCCAATCTCC	3	19	1	CAACCCCTAA	    0.968667	-159
CAAAACTACACAACCCTAAATCAAAAACAA	3	106	1	CAACCCTAAA	    0.921778	-72
          **********

Masking position 9
Map Score:   7.67941

Number of sites scoring better than the average of aligned sites = 804
Number in coding regions = 711
Number in noncoding regions = 93
Number of orfs with sites within 600 bp upstream = 82
Fraction of orfs with sites within 600 bp upstream = 0.0131706


Motif number 3

TTTGATTAAAATAACTTGATTTGG       	1	4	0	ATAATTGATT	    0.897331	-101
CAAAAGTCAGATAATTTTGTTATGAACTGAT	1	31	1	ATAATTTGTT	    0.904606	-74
AAAAGCTGTTATGAATCAGTTCATAACAAAA	1	45	0	ATGATCAGTT	    0.991111	-60
TTTCTTATTTATGAACCAGTTCATAACAGCC	2	14	1	ATGACCAGTT	    0.976059	-60
CTGAAAAAGGATGATTCGGTTAGATTGATTA	3	157	0	ATGATCGGTT	     0.99176	-21
TAACAGGAAAATAACTCAATTAT        	4	32	1	ATAATCAATT	    0.959937	-13
          **** ******

Masking position 4
Map Score:   4.7093

Number of sites scoring better than the average of aligned sites = 57
Number in coding regions = 50
Number in noncoding regions = 7
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 4

          AGTTATAGGGTGTTCCTTCA	3	1	1	AGTTATAGGG	    0.903865	-177
TTGGGTTAGGGGTTGAAGGAACACCCTATA	3	14	0	GGTTGAAGGA	    0.991057	-164
TACAGAGGTAAATGGAAGGAGATTGGGTTA	3	36	0	AATGGAAGGA	    0.936791	-142
TGAAGGGGAAGGTGGAAGAGCTCGTTGTTC	3	70	0	GGTGGAAGAG	    0.981008	-108
AGTTTTGTCCTGTTGAAGGGGAAGGTGGAA	3	83	0	TGTTGAAGGG	    0.989194	-95
          **********

Masking position 7
Map Score:   1.91742

Number of sites scoring better than the average of aligned sites = 608
Number in coding regions = 571
Number in noncoding regions = 37
Number of orfs with sites within 600 bp upstream = 32
Fraction of orfs with sites within 600 bp upstream = 0.00513974


Motif number 5

          **********

No masking
Map Score:   -6.79689e-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:   -6.79689e-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:   -6.79689e-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