AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00220_tpal_reg_100.orf -o00220_tpal_100.ace -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -g0.53 -x5 -e 
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 =  	0.53
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	TP0350	213	glutamate-5-semialdehyde dehydrogenase (proA)
#2	TP0797	50	1-pyrroline-5-carboxylate reductase (proC)
#3	TP0798	32	methionyl-tRNA synthetase (metG)

Motif number 1

AGGCAAGATACTCACGGCAAGGGCAGTTTC	1	28	1	CTCACGGCAA	    0.990873	-186
CTGTCAAGGGCACACGGCACAGAAACTGCC	1	49	0	CACACGGCAC	    0.997687	-165
CCCAACACCTCGCCCGGCTTATCCCCTATA	1	88	0	CGCCCGGCTT	    0.983761	-126
GGACCACACGCTCCCAACACCTCGCCCGGC	1	100	0	CTCCCAACAC	    0.972426	-114
CCTCTTTTACCGCACAGCACCGCGCAAGAG	1	140	0	CGCACAGCAC	    0.997655	-74
   GAATATTCACAGAGCATTTGGTTTTCC	2	8	1	CACAGAGCAT	    0.965499	-43
          **********

Masking position 3
Map Score:   8.85397

Number of sites scoring better than the average of aligned sites = 403
Number in coding regions = 363
Number in noncoding regions = 40
Number of orfs with sites within 600 bp upstream = 33
Fraction of orfs with sites within 600 bp upstream = 0.00530035


Motif number 2

TGCCTGTGCTAGCATGCCGCGC        	1	3	0	AGCATGCCGC	    0.914499	-211
GTGAGTATCTTGCCTGTGCTAGCATGCCGC	1	13	0	TGCCTGTGCT	     0.97777	-201
GCACAGAAACTGCCCTTGCCGTGAGTATCT	1	33	0	TGCCCTTGCC	    0.988766	-181
CTGTGCCGTGTGCCCTTGACAGAATCGCCG	1	57	1	TGCCCTTGAC	    0.945802	-157
AGGTGTTGGGAGCGTGTGGTCCACTTCTTG	1	108	1	AGCGTGTGGT	    0.959256	-106
ATATTCACAGAGCATTTGGTTTTCCGTGTC	2	13	1	AGCATTTGGT	    0.949965	-38
        GCTGCGCTCCCCCTATCCGACA	2	39	0	TGCGCTCCCC	      0.9692	-12
          AGCGTTTCCTACTCTGATTT	3	23	0	AGCGTTTCCT	    0.971849	-10
          **********

Masking position 3
Map Score:   7.01705

Number of sites scoring better than the average of aligned sites = 1024
Number in coding regions = 961
Number in noncoding regions = 63
Number of orfs with sites within 600 bp upstream = 59
Fraction of orfs with sites within 600 bp upstream = 0.00947639


Motif number 3

AATCGCCGTTATAGGGGATAAGCCGGGCGA	1	79	1	ATAGGGGATA	    0.956145	-135
GCACCGCGCAAGAGGGCAAGAAGTGGACCA	1	124	0	AGAGGGCAAG	    0.987565	-90
GTGCGGTAAAAGAGGGGGCGTCGCGTTCGA	1	155	1	AGAGGGGGCG	    0.997302	-59
TCCGTGTCGGATAGGGGGAGCGCAGC    	2	35	1	ATAGGGGGAG	    0.996437	-16
TGTTTAAATCAGAGTAGGAAACGCT     	3	18	1	AGAGTAGGAA	    0.911261	-15
          **********

Masking position 3
Map Score:   3.97627

Number of sites scoring better than the average of aligned sites = 251
Number in coding regions = 213
Number in noncoding regions = 38
Number of orfs with sites within 600 bp upstream = 34
Fraction of orfs with sites within 600 bp upstream = 0.00546097


Motif number 4

ACAGAAACTGCCCTTGCCGTGAGTATCTTG	1	31	0	CCCTTGCCGT	    0.960021	-183
AAGGGCAGTTTCTGTGCCGTGTGCCCTTGA	1	46	1	TCTGTGCCGT	    0.981865	-168
CCCTATAACGGCGATTCTGTCAAGGGCACA	1	65	0	GCGATTCTGT	    0.902391	-149
TAAGCCGGGCGAGGTGTTGGGAGCGTGTGG	1	97	1	GAGGTGTTGG	    0.931148	-117
GCCCTCTTGCGCGGTGCTGTGCGGTAAAAG	1	137	1	GCGGTGCTGT	    0.996582	-77
CATTTGGTTTTCCGTGTCGGATAGGGGGAG	2	25	1	TCCGTGTCGG	     0.97642	-26
          **********

Masking position 5
Map Score:   1.73105

Number of sites scoring better than the average of aligned sites = 924
Number in coding regions = 849
Number in noncoding regions = 75
Number of orfs with sites within 600 bp upstream = 59
Fraction of orfs with sites within 600 bp upstream = 0.00947639


Motif number 5

          **********

No masking
Map Score:   -3.38628e-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:   -3.38628e-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:   -3.38628e-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