AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -iarcA_tpal_opreg_300.orf -g0.528 -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 =  	0.528
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	TP0118	97	T. pallidum predicted coding region TP0118
#2	TP0120	129	amino acid ABC transporter, ATP-binding protein (abc)

Motif number 1

CATGCAAGGACAGACGTCCTGCCTAACTCTGG	1	18	0	CGAGTCCTGC	    0.994794	-80
AAGAGGGAGTGAGGTGCCCTGTACATACGCAG	1	54	1	GGGGCCCTGT	    0.971215	-44
GCATTGTAAACACTTCCCCTGCGTATGTACAG	1	72	0	CCTCCCCTGC	    0.985604	-26
ACCGTAGGATGCGCACTCGTGGTCC       	2	4	0	GGCCTCGTGG	    0.983227	-126
GCGTGTACAAGTCACGCCGTGCACCGCACCCG	2	46	1	GCAGCCGTGC	    0.987784	-84
ACGCCGTGCACCGCACCCGTGCTGCAGGATCG	2	59	1	CGCCCCGTGC	    0.997741	-71
ACACTACGGTATGCGATCCTGCAGCACGGGTG	2	72	0	AGCATCCTGC	    0.962256	-58
TACCTATTTGCAGAGACCCTGGTCCCC     	2	113	1	CGAACCCTGG	    0.989152	-17
          * ** *******

Masking position 10
Map Score:   8.5432

Number of sites scoring better than the average of aligned sites = 879
Number in coding regions = 804
Number in noncoding regions = 75
Number of orfs with sites within 600 bp upstream = 60
Fraction of orfs with sites within 600 bp upstream = 0.00963701


Motif number 2

CAGACGTCCTGCCTAACTCTGGCGGGGTA          	1	1	0	GCTCTGGGTA	    0.996923	-97
TAGGCAGGACGTCTGTCCTTGCATGGGTAAAGAGGGAGT	1	25	1	GCTCTCGGTA	    0.999124	-73
GCATTGTAAACACTTCCCCTGCGTATGTACAGGGCACCT	1	65	0	CCTCTCTGTA	    0.975815	-33
   GGACCACGAGTGCGCATCCTACGGTAAAAATGCATG	2	8	1	GGTGTCGGTA	    0.996192	-122
AAATAGGTACGTGTGTCAACACTACGGTATGCGATCCTG	2	83	0	GGTCCCGGTA	    0.998944	-47
  GGGGACCAGGGTCTCTGCAAATAGGTACGTGTGTCAA	2	103	0	GGTCCAGGTA	    0.994514	-27
          * **  *  * *   ****

Masking position 4
Map Score:   7.00812

Number of sites scoring better than the average of aligned sites = 23
Number in coding regions = 17
Number in noncoding regions = 6
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 3

GGTAAAGAGGGAGTGAGGTGCCCTGTACAT	1	50	1	GAGTGAGGTG	    0.979603	-48
GAAGTGTTTACAATGCGGTC          	1	88	1	CAATGCGGTC	    0.987068	-10
TTTTACCGTAGGATGCGCACTCGTGGTCC 	2	10	0	GGATGCGCAC	     0.98175	-120
CCTGCAGCACGGGTGCGGTGCACGGCGTGA	2	57	0	GGGTGCGGTG	     0.99694	-73
CAACACTACGGTATGCGATCCTGCAGCACG	2	76	0	GTATGCGATC	     0.97875	-54
          **********

Masking position 4
Map Score:   4.09519

Number of sites scoring better than the average of aligned sites = 354
Number in coding regions = 320
Number in noncoding regions = 34
Number of orfs with sites within 600 bp upstream = 31
Fraction of orfs with sites within 600 bp upstream = 0.00497912


Motif number 4

          TACCCCGCCAGAGTTAGGCA	1	1	1	TACCCCGCCA	    0.979045	-97
ACTCCCTCTTTACCCATGCAAGGACAGACG	1	34	0	TACCCATGCA	    0.994781	-64
TTGTAAACACTTCCCCTGCGTATGTACAGG	1	71	0	TTCCCCTGCG	    0.977473	-27
GGACCACGAGTGCGCATCCTACGGTAAAAA	2	11	1	TGCGCATCCT	     0.95254	-119
GTGACTTGTACACGCATGCATTTTTACCGT	2	31	0	CACGCATGCA	    0.990134	-99
CCGTGCACCGCACCCGTGCTGCAGGATCGC	2	62	1	CACCCGTGCT	    0.986245	-68
          **********

Masking position 5
Map Score:   5.74188

Number of sites scoring better than the average of aligned sites = 392
Number in coding regions = 355
Number in noncoding regions = 37
Number of orfs with sites within 600 bp upstream = 30
Fraction of orfs with sites within 600 bp upstream = 0.0048185


Motif number 5

          **********

No masking
Map Score:   -4.52315e-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:   -4.52315e-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:   -4.52315e-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