AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00271_tpal_reg_300.orf -o00271_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	TP0757	40	polypeptide deformylase (def)
#2	TP0758	118	ribosomal protein S21 (rpsU)
#3	TP0794	53	S-adenosylmethionine synthetase (metK)
#4	TP0798	32	methionyl-tRNA synthetase (metG)

Motif number 1

ACCCAAGAGAAACTCATACCCGC        	1	3	0	ACTCATACCC	    0.979396	-38
CGCCTCTTCCCGCTCTTACCCAAGAGAAACT	1	20	0	CCTCTTACCC	    0.989981	-21
GCCTCCCCTGCACGCACACCCTACGTGTC  	2	9	0	CCGCACACCC	    0.993737	-110
CGAAAGCACTCCTGCCTCCCCTGCACGCACA	2	22	0	CTGCCTCCCC	    0.996146	-97
GTCTTTTGCGCTAGCCTACCCCTGGTAGGCT	2	75	1	CAGCCTACCC	    0.998971	-44
TGAAAAAAACACAGCCTACCAGGGGTAGGCT	2	87	0	AAGCCTACCA	    0.971705	-32
          CGACCCTCCCCTGAAAAAAAC	2	108	0	CACCCTCCCC	    0.994638	-11
          * *********

Masking position 5
Map Score:   13.2

Number of sites scoring better than the average of aligned sites = 288
Number in coding regions = 246
Number in noncoding regions = 42
Number of orfs with sites within 600 bp upstream = 35
Fraction of orfs with sites within 600 bp upstream = 0.00562159


Motif number 2

GCACTCCTGCCTCCCCTGCACGCACACCCTAC	2	16	0	CTCCCCTGCG	    0.994615	-103
CGCAAAAGACGTCCCCTGTCAATCGTTTCTTC	2	53	0	GTCCCCTGAA	    0.983572	-66
AAAACACAGCCTACCAGGGGTAGGCTAGCGCA	2	81	0	CTACCAGGTA	    0.854948	-38
     CGACCCTCCCCTGAAAAAAACACAGCC	2	102	0	CTCCCCTGAA	    0.995714	-17
    CCTTTACTCCTAGGTTCAGTGAGCTGCG	3	7	1	CTCCTAGGCA	    0.991101	-47
   CACTGTACTCCTCGATTCAAAATTACGCA	3	35	0	CTCCTCGACA	    0.981673	-19
  AGCGTTTCCTACTCTGATTTAAACAAGACT	4	13	0	CTACTCTGTT	     0.91115	-20
          ********  **

Masking position 2
Map Score:   7.07836

Number of sites scoring better than the average of aligned sites = 361
Number in coding regions = 318
Number in noncoding regions = 43
Number of orfs with sites within 600 bp upstream = 44
Fraction of orfs with sites within 600 bp upstream = 0.00706714


Motif number 3

CGCCTCTTCCCGCTCTTACCCAAGAGAAAC	1	21	0	CGCTCTTACC	    0.944418	-20
          CGCCTCTTCCCGCTCTTACC	1	31	0	CGCCTCTTCC	    0.996098	-10
CCCTGTCAATCGTTTCTTCCGAAAGCACTC	2	42	0	CGTTTCTTCC	    0.996093	-77
TGACAGGGGACGTCTTTTGCGCTAGCCTAC	2	64	1	CGTCTTTTGC	    0.976928	-55
TGGTAGGCTGTGTTTTTTTCAGGGGAGGGT	2	97	1	TGTTTTTTTC	    0.754215	-22
          CGACCCTCCCCTGAAAAAAA	2	109	0	CGACCCTCCC	    0.958381	-10
        AGCGTTTCCTACTCTGATTTAA	4	21	0	CGTTTCCTAC	    0.937634	-12
          **********

Masking position 2
Map Score:   5.67291

Number of sites scoring better than the average of aligned sites = 729
Number in coding regions = 668
Number in noncoding regions = 61
Number of orfs with sites within 600 bp upstream = 61
Fraction of orfs with sites within 600 bp upstream = 0.00979762


Motif number 4

        CGCCTCTTCCCGCTCTTACCCA	1	29	0	CCTCTTCCCG	    0.966071	-12
ACTCCTGCCTCCCCTGCACGCACACCCTAC	2	16	0	CCCCTGCACG	    0.998007	-103
CAAAAGACGTCCCCTGTCAATCGTTTCTTC	2	53	0	CCCCTGTCAA	    0.991518	-66
CGCTAGCCTACCCCTGGTAGGCTGTGTTTT	2	83	1	CCCCTGGTAG	    0.993047	-36
   CGACCCTCCCCTGAAAAAAACACAGCC	2	102	0	CCCCTGAAAA	     0.98694	-17
          **********

Masking position 5
Map Score:   5.65795

Number of sites scoring better than the average of aligned sites = 240
Number in coding regions = 216
Number in noncoding regions = 24
Number of orfs with sites within 600 bp upstream = 18
Fraction of orfs with sites within 600 bp upstream = 0.0028911


Motif number 5

CTTCCCGCTCTTACCCAAGAGAAACTCATA	1	16	0	TTACCCAAGA	    0.976174	-25
CGCAGCTCACTGAACCTAGGAGTAAAGG  	3	9	0	TGAACCTAGG	    0.989558	-45
TGCGTAATTTTGAATCGAGGAGTACAGTG 	3	35	1	TGAATCGAGG	    0.980952	-19
CTACTCTGATTTAAACAAGACTTC      	4	5	0	TTAAACAAGA	    0.962417	-28
          **********

Masking position 3
Map Score:   0.450656

Number of sites scoring better than the average of aligned sites = 22
Number in coding regions = 20
Number in noncoding regions = 2
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


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


Motif number 8

          **********

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