AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -imetR_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	TP0284	104	T. pallidum predicted coding region TP0284
#2	TP0329	117	serine hydroxymethyltransferase (glyA)

Motif number 1

ACTCAACCGAGTGAGAAAAAGAATCATCAC	1	29	0	GTGAGAAAAA	    0.994213	-76
GATACCCGTCGTGCGTAACAGGGGAACATA	2	14	0	GTGCGTAACA	    0.983834	-104
CATTCTTTGCGCTAGAAACAGAGCGAACAA	2	70	1	GCTAGAAACA	    0.967611	-48
GCTAGAAACAGAGCGAACAATATTCTGCCT	2	80	1	GAGCGAACAA	    0.988174	-38
CCTACCTGAGGAGAGAAAAAC         	2	107	1	GAGAGAAAAA	    0.994214	-11
          **********

Masking position 7
Map Score:   5.88729

Number of sites scoring better than the average of aligned sites = 133
Number in coding regions = 122
Number in noncoding regions = 11
Number of orfs with sites within 600 bp upstream = 11
Fraction of orfs with sites within 600 bp upstream = 0.00176678


Motif number 2

AAGAATCATCACATACTCAGCTCATGCAAT 	1	10	0	ACATACTCGC	    0.982522	-95
GAACCTTGCTCAAAACTTTTCTGAACTTTAA	1	78	0	CAAAACTTTC	    0.952902	-27
GCCGCATGCCCGATACCCGTCGTGCGTAACA	2	24	0	CGATACCCTC	    0.967805	-94
AAAGAATGGACAAAACGCCGCGCGCCGCATG	2	47	0	CAAAACGCGC	    0.987847	-71
GGCGTTTTGTCCATTCTTTGCGCTAGAAACA	2	59	1	CCATTCTTGC	    0.968022	-59
ACAGAGCGAACAATATTCTGCCTACCTGAGG	2	87	1	CAATATTCGC	    0.981145	-31
          ******** **

Masking position 3
Map Score:   2.36365

Number of sites scoring better than the average of aligned sites = 437
Number in coding regions = 418
Number in noncoding regions = 19
Number of orfs with sites within 600 bp upstream = 11
Fraction of orfs with sites within 600 bp upstream = 0.00176678


Motif number 3

       ATTGCATGAGCTGAGTATGTGATGA	1	4	1	GCATGGCGAG	    0.995009	-101
CATGCCCGATACCCGTCGTGCGTAACAGGGGA	2	19	0	ACCCGCGGCG	    0.994502	-99
CGGGTATCGGGCATGCGGCGCGCGGCGTTTTG	2	36	1	GCATGGGGCG	    0.998791	-82
TATTCTGCCTACCTGAGGAGAGAAAAAC    	2	100	1	ACCTGGGGAG	    0.998113	-18
          ***** ** ***

Masking position 5
Map Score:   2.114

Number of sites scoring better than the average of aligned sites = 172
Number in coding regions = 160
Number in noncoding regions = 12
Number of orfs with sites within 600 bp upstream = 12
Fraction of orfs with sites within 600 bp upstream = 0.0019274


Motif number 4

CTCGGTTGAGTGATCTTCGGGGCTGTGCTT	1	48	1	TGATCTTCGG	    0.981317	-57
TTTTGAGCAAGGTTCTCCTGC         	1	94	1	GGTTCTCCTG	    0.996057	-11
     TGGTATGTTCCCCTGTTACGCACGA	2	6	1	TGTTCCCCTG	    0.996057	-112
          **********

Masking position 4
Map Score:   0.74781

Number of sites scoring better than the average of aligned sites = 39
Number in coding regions = 35
Number in noncoding regions = 4
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 5

          **********

No masking
Map Score:   2.15595e-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:   2.15595e-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:   2.15595e-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