AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -ityrR_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	TP0342	120	cytidylate kinase (cmk)
#2	TP0708	65	T. pallidum predicted coding region TP0708

Motif number 1

ATGTTGGCGAAACCGCAACCGAACT     	1	6	0	AACCGCAACC	    0.993889	-115
CCACAGCCGGCACCACCACCATGTTGGCGA	1	26	0	CACCACCACC	    0.994914	-95
TATCCACCAGATCCACAGCCGGCACCACCA	1	38	0	ATCCACAGCC	    0.989114	-83
CAGCCTGTCTCACTTCACCCTATATCCACC	1	60	0	CACTTCACCC	    0.974201	-61
ATCACCATCCATTCGCAGCCTGTCTCACTT	1	75	0	ATTCGCAGCC	    0.961674	-46
CCGCTCTTTGCATCACCATCCATTCGCAGC	1	86	0	CATCACCATC	    0.924275	-35
    GCACCCCTCCGCACTCCGCTCTTTGC	1	105	0	CTCCGCACTC	     0.99111	-16
    AGCTCACACTACACGCTTGGAAACAG	2	7	1	CACTACACGC	    0.966086	-59
          **********

Masking position 6
Map Score:   11.8276

Number of sites scoring better than the average of aligned sites = 1489
Number in coding regions = 1317
Number in noncoding regions = 172
Number of orfs with sites within 600 bp upstream = 132
Fraction of orfs with sites within 600 bp upstream = 0.0212014


Motif number 2

     AGTTCGGTTGCGGTTTCGCCAACAT	1	6	1	GGTTGCGGTT	    0.952406	-115
ACATGGTGGTGGTGCCGGCTGTGGATCTGG	1	32	1	GGTGCCGGCT	     0.98956	-89
TGCCGGCTGTGGATCTGGTGGATATAGGGT	1	44	1	GGATCTGGTG	    0.988921	-77
CCATCCATTCGCAGCCTGTCTCACTTCACC	1	71	0	GCAGCCTGTC	    0.974571	-50
GTTTCGTCAAGGACCTGTTTCCAAGCGTGT	2	21	0	GGACCTGTTT	    0.955747	-45
GAGCTAGTCTGCAGCTGGTTTTTTGTTTCG	2	45	0	GCAGCTGGTT	    0.995975	-21
          GGAGCTAGTCTGCAGCTGGT	2	56	0	GGAGCTAGTC	    0.986877	-10
          **********

Masking position 1
Map Score:   8.03699

Number of sites scoring better than the average of aligned sites = 537
Number in coding regions = 491
Number in noncoding regions = 46
Number of orfs with sites within 600 bp upstream = 34
Fraction of orfs with sites within 600 bp upstream = 0.00546097


Motif number 3

TTCGGTTGCGGTTTCGCCAACATGGTGGTG	1	13	1	GTTTCGCCAA	    0.996583	-108
CTGGTTTTTTGTTTCGTCAAGGACCTGTTT	2	31	0	GTTTCGTCAA	    0.995676	-35
          **********

Masking position 4
Map Score:   1.66286

Number of sites scoring better than the average of aligned sites = 2
Number in coding regions = 1
Number in noncoding regions = 1
Number of orfs with sites within 600 bp upstream = 1
Fraction of orfs with sites within 600 bp upstream = 0.000160617


Motif number 4

GTGGATCTGGTGGATATAGGGTGAAGTGAG	1	52	1	TGGATATAGG	    0.991163	-69
ATAGGGTGAAGTGAGACAGGCTGCGAATGG	1	67	1	GTGAGACAGG	    0.992915	-54
ACTACACGCTTGGAAACAGGTCCTTGACGA	2	18	1	TGGAAACAGG	    0.996751	-48
          **********

Masking position 6
Map Score:   1.49251

Number of sites scoring better than the average of aligned sites = 20
Number in coding regions = 17
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 5

          **********

No masking
Map Score:   4.57179e-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:   4.57179e-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:   4.57179e-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