AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -iarcA_tpal_opreg_100.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

CCAGAGTTAGGCAGGACGTCTGTCCTTGCATG	1	18	1	GCAGGACCTG	    0.994632	-80
GTCTGTCCTTGCATGGGTAAAGAGGGAGTGAG	1	35	1	GCATGGGAAG	    0.919652	-63
CTGCGTATGTACAGGGCACCTCACTCCCTCTT	1	54	0	ACAGGGCCTC	    0.978269	-44
CTGTACATACGCAGGGGAAGTGTTTACAATGC	1	72	1	GCAGGGGGTG	    0.996209	-26
       GGACCACGAGTGCGCATCCTACGGT	2	4	1	CCACGAGCGC	    0.964172	-126
CGGGTGCGGTGCACGGCGTGACTTGTACACGC	2	46	0	GCACGGCGAC	    0.983059	-84
CGATCCTGCAGCACGGGTGCGGTGCACGGCGT	2	59	0	GCACGGGCGG	    0.997324	-71
CACCCGTGCTGCAGGATCGCATACCGTAGTGT	2	72	1	GCAGGATCAT	    0.907105	-58
     GGGGACCAGGGTCTCTGCAAATAGGTA	2	113	0	CCAGGGTCTG	    0.988822	-17
          *******  ***

Masking position 3
Map Score:   10.282

Number of sites scoring better than the average of aligned sites = 975
Number in coding regions = 888
Number in noncoding regions = 87
Number of orfs with sites within 600 bp upstream = 67
Fraction of orfs with sites within 600 bp upstream = 0.0107613


Motif number 2

TATGTACAGGGCACCTCACTCCCTCTTTACCC	1	49	0	GCACTCACCC	    0.996861	-49
TTTACCGTAGGATGCGCACTCGTGGTCC    	2	7	0	GATCGCACCG	    0.986093	-123
TCCTACGGTAAAAATGCATGCGTGTACAAGTC	2	27	1	AAATGCATCG	    0.905343	-103
GCATGCGTGTACAAGTCACGCCGTGCACCGCA	2	42	1	ACAGTCACCC	    0.969674	-88
GTCACGCCGTGCACCGCACCCGTGCTGCAGGA	2	56	1	GCACGCACCG	    0.998974	-74
CCGTGCTGCAGGATCGCATACCGTAGTGTTGA	2	75	1	GGACGCATCC	    0.956359	-55
          *** ***** **

Masking position 8
Map Score:   5.33472

Number of sites scoring better than the average of aligned sites = 657
Number in coding regions = 605
Number in noncoding regions = 52
Number of orfs with sites within 600 bp upstream = 49
Fraction of orfs with sites within 600 bp upstream = 0.00787022


Motif number 3

GTTAGGCAGGACGTCTGTCCTTGCATGGGT	1	23	1	ACGTCTGTCC	     0.99138	-75
GCACCTCACTCCCTCTTTACCCATGCAAGG	1	41	0	CCCTCTTTAC	    0.855147	-57
CACTTCCCCTGCGTATGTACAGGGCACCTC	1	64	0	GCGTATGTAC	    0.964769	-34
TACGCAGGGGAAGTGTTTACAATGCGGTC 	1	79	1	AAGTGTTTAC	    0.930833	-19
     GGACCACGAGTGCGCATCCTACGGT	2	6	1	ACGAGTGCGC	    0.923197	-124
GTAAAAATGCATGCGTGTACAAGTCACGCC	2	34	1	ATGCGTGTAC	    0.913738	-96
GCAAATAGGTACGTGTGTCAACACTACGGT	2	94	0	ACGTGTGTCA	    0.960896	-36
TGACACACGTACCTATTTGCAGAGACCCTG	2	104	1	ACCTATTTGC	    0.911366	-26
          **********

Masking position 6
Map Score:   2.57622

Number of sites scoring better than the average of aligned sites = 1330
Number in coding regions = 1232
Number in noncoding regions = 98
Number of orfs with sites within 600 bp upstream = 85
Fraction of orfs with sites within 600 bp upstream = 0.0136524


Motif number 4

         GACCGCATTGTAAACACTTCC	1	87	0	ACCGCATTGT	    0.982777	-11
ATGCATTTTTACCGTAGGATGCGCACTCGT	2	16	0	ACCGTAGGAT	     0.96273	-114
CCGCACCCGTGCTGCAGGATCGCATACCGT	2	69	1	GCTGCAGGAT	     0.97624	-61
AGGATCGCATACCGTAGTGTTGACACACGT	2	84	1	ACCGTAGTGT	    0.953599	-46
          **********

Masking position 6
Map Score:   3.17142

Number of sites scoring better than the average of aligned sites = 88
Number in coding regions = 78
Number in noncoding regions = 10
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


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