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

Motif number 1

     AGTTCGGTTGCGGTTTCGCCAACAT	1	6	1	GGTTGCGGTT	    0.993378	-115
TCGCCAACATGGTGGTGGTGCCGGCTGTGG	1	26	1	GGTGGTGGTG	    0.994486	-95
TGGTGGTGCCGGCTGTGGATCTGGTGGATA	1	38	1	GGCTGTGGAT	    0.988204	-83
GGTGGATATAGGGTGAAGTGAGACAGGCTG	1	60	1	GGGTGAAGTG	    0.972079	-61
AAGTGAGACAGGCTGCGAATGGATGGTGAT	1	75	1	GGCTGCGAAT	    0.958566	-46
GCTGCGAATGGATGGTGATGCAAAGAGCGG	1	86	1	GATGGTGATG	    0.918388	-35
GCAAAGAGCGGAGTGCGGAGGGGTGC    	1	105	1	GAGTGCGGAG	    0.990365	-16
CTGTTTCCAAGCGTGTAGTGTGAGCT    	2	7	0	GCGTGTAGTG	    0.963321	-59
          **********

Masking position 5
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

ATGTTGGCGAAACCGCAACCGAACT     	1	6	0	AACCGCAACC	    0.949742	-115
CCAGATCCACAGCCGGCACCACCACCATGT	1	32	0	AGCCGGCACC	    0.988951	-89
ACCCTATATCCACCAGATCCACAGCCGGCA	1	44	0	CACCAGATCC	    0.988276	-77
GGTGAAGTGAGACAGGCTGCGAATGGATGG	1	71	1	GACAGGCTGC	    0.973112	-50
ACACGCTTGGAAACAGGTCCTTGACGAAAC	2	21	1	AAACAGGTCC	    0.953261	-45
CGAAACAAAAAACCAGCTGCAGACTAGCTC	2	45	1	AACCAGCTGC	    0.995739	-21
ACCAGCTGCAGACTAGCTCC          	2	56	1	GACTAGCTCC	    0.986115	-10
          **********

Masking position 10
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

CACCACCATGTTGGCGAAACCGCAACCGAA	1	13	0	TTGGCGAAAC	    0.996602	-108
AAACAGGTCCTTGACGAAACAAAAAACCAG	2	31	1	TTGACGAAAC	    0.995804	-35
          **********

Masking position 7
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	    0.990965	-69
ATAGGGTGAAGTGAGACAGGCTGCGAATGG	1	67	1	GTGAGACAGG	    0.992754	-54
ACTACACGCTTGGAAACAGGTCCTTGACGA	2	18	1	TGGAAACAGG	    0.996677	-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