AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00220_tpal_reg_300.orf -o00220_tpal_300.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	    0.990034	-186
CTGTCAAGGGCACACGGCACAGAAACTGCC	1	49	0	CACACGGCAC	    0.997473	-165
CCCAACACCTCGCCCGGCTTATCCCCTATA	1	88	0	CGCCCGGCTT	     0.98228	-126
GGACCACACGCTCCCAACACCTCGCCCGGC	1	100	0	CTCCCAACAC	    0.969932	-114
CCTCTTTTACCGCACAGCACCGCGCAAGAG	1	140	0	CGCACAGCAC	    0.997436	-74
   GAATATTCACAGAGCATTTGGTTTTCC	2	8	1	CACAGAGCAT	    0.962402	-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

        GCGCGGCATGCTAGCACAGGCA	1	3	1	GCGGCATGCT	    0.895234	-211
GCGGCATGCTAGCACAGGCAAGATACTCAC	1	13	1	AGCACAGGCA	    0.974582	-201
AGATACTCACGGCAAGGGCAGTTTCTGTGC	1	33	1	GGCAAGGGCA	    0.986139	-181
CGGCGATTCTGTCAAGGGCACACGGCACAG	1	57	0	GTCAAGGGCA	    0.933044	-157
CAAGAAGTGGACCACACGCTCCCAACACCT	1	108	0	ACCACACGCT	    0.957445	-106
GACACGGAAAACCAAATGCTCTGTGAATAT	2	13	0	ACCAAATGCT	    0.938962	-38
TGTCGGATAGGGGGAGCGCAGC        	2	39	1	GGGGAGCGCA	    0.961822	-12
AAATCAGAGTAGGAAACGCT          	3	23	1	AGGAAACGCT	    0.965493	-10
          **********

Masking position 8
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

TCGCCCGGCTTATCCCCTATAACGGCGATT	1	79	0	TATCCCCTAT	    0.954643	-135
TGGTCCACTTCTTGCCCTCTTGCGCGGTGC	1	124	1	CTTGCCCTCT	    0.987125	-90
TCGAACGCGACGCCCCCTCTTTTACCGCAC	1	155	0	CGCCCCCTCT	    0.997205	-59
    GCTGCGCTCCCCCTATCCGACACGGA	2	35	0	CTCCCCCTAT	     0.99631	-16
     AGCGTTTCCTACTCTGATTTAAACA	3	18	0	TTCCTACTCT	    0.908369	-15
          **********

Masking position 8
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

CAAGATACTCACGGCAAGGGCAGTTTCTGT	1	31	1	ACGGCAAGGG	     0.95782	-183
TCAAGGGCACACGGCACAGAAACTGCCCTT	1	46	0	ACGGCACAGA	    0.980861	-168
TGTGCCCTTGACAGAATCGCCGTTATAGGG	1	65	1	ACAGAATCGC	    0.897336	-149
CCACACGCTCCCAACACCTCGCCCGGCTTA	1	97	0	CCAACACCTC	    0.927459	-117
CTTTTACCGCACAGCACCGCGCAAGAGGGC	1	137	0	ACAGCACCGC	     0.99641	-77
CTCCCCCTATCCGACACGGAAAACCAAATG	2	25	0	CCGACACGGA	    0.975121	-26
          **********

Masking position 6
Map Score:   1.73105

Number of sites scoring better than the average of aligned sites = 917
Number in coding regions = 842
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