AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00130_tpal_reg_100.orf -o00130_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	TP0489	300	conserved hypothetical protein
#2	TP0492	23	DNA primase (dnaG)
#3	TP0683	92	octaprenyl-diphosphate synthase

Motif number 1

CGAACCCTAGACCTCGAGATTACA         	1	2	0	ACTCGGATTC	    0.951756	-299
CAACAGATTTACAGTCTGCTCCCTTTGACCACT	1	73	0	ACGTCGCTCC	    0.990016	-228
CGAATCCTTGACTCCCCACTTTCGTCTTCCGTT	1	124	1	ACCCCACTTC	    0.963476	-177
CACGAAAAGAACATCCTGCACTCAAGAAAGTGA	1	233	0	ACTCCGCACC	    0.995584	-68
ATCCTTCCGCACCGCGCGCACGCGCACGAAAAG	1	257	0	ACGCGGCACC	    0.997348	-44
ACCTTCCTACACGCCCCCCATGCTATGTGTTAC	3	11	1	ACCCCCCATC	      0.9535	-82
TATGTGTTACACTGACAGCTCCCACACATCGTG	3	34	1	ACGACGCTCC	    0.990016	-59
CAGCTCCCACACATCGTGCTCGCACAAAAGGCA	3	49	1	ACTCGGCTCC	    0.997126	-44
GTACCGTTATACGGCGTGTTTGCCTTTTGTGCG	3	69	0	ACGCGGTTTC	    0.976044	-24
          ** *** **** *

Masking position 1
Map Score:   14.1114

Number of sites scoring better than the average of aligned sites = 427
Number in coding regions = 391
Number in noncoding regions = 36
Number of orfs with sites within 600 bp upstream = 27
Fraction of orfs with sites within 600 bp upstream = 0.00433665


Motif number 2

ACTCGGGAAACTCCCCAAACGAACAAGCCAACTT	1	42	0	CCCCAAGAAC	    0.981721	-259
TGCTCCCTTTGACCACTCGGGAAACTCCCCAAAC	1	56	0	GCCCCGGAAA	    0.982336	-245
AAGTCAGACACTACCCAAAAGCAAACGGAAGACG	1	146	0	CACCAAGCAA	    0.978093	-155
CTAGCAAAAACGCCTGGAACGAAACGCCAGGGAA	1	184	0	CCCGAAGAAA	    0.967499	-117
AAAGAACATCCTGCACTCAAGAAAGTGACAAGAG	1	227	0	CGCCCAGAAA	     0.99696	-74
CGCACCGCGCGCACGCGCACGAAAAGAACATCCT	1	249	0	GACCCAGAAA	    0.984893	-52
  GTCCCCTCCTCCGCCACTGAAATCCTTCCGCA	1	279	0	CCCCACGAAA	    0.981722	-22
CCTTCCTACACGCCCCCCATGCTATGTGTTACAC	3	12	1	CCCCCAGCTA	    0.981808	-81
GTTACACTGACAGCTCCCACACATCGTGCTCGCA	3	39	1	CGCCCAACAT	    0.865311	-54
CCCACACATCGTGCTCGCACAAAAGGCAAACACG	3	54	1	GGCCCAAAAA	    0.962107	-39
          * ** * ** ****

Masking position 4
Map Score:   11.0035

Number of sites scoring better than the average of aligned sites = 536
Number in coding regions = 489
Number in noncoding regions = 47
Number of orfs with sites within 600 bp upstream = 37
Fraction of orfs with sites within 600 bp upstream = 0.00594282


Motif number 3

GAATCCCTAAGTTGGCTTGTTCGTTTGGGG	1	34	1	GTTGGCTTGT	    0.977443	-267
CTGTAAATCTGTTGGCGTTGTCTTCCAAGG	1	92	1	GTTGGCGTTG	     0.98298	-209
TTCGTCTTCCGTTTGCTTTTGGGTAGTGTC	1	144	1	GTTTGCTTTT	    0.967663	-157
TAGTGTCTGACTTGTCTTTCCCTGGCGTTT	1	167	1	CTTGTCTTTC	    0.921769	-134
CTTGTCTTTCCCTGGCGTTTCGTTCCAGGC	1	177	1	CCTGGCGTTT	    0.988949	-124
GCGTTTCGTTCCAGGCGTTTTTGCTAGCTG	1	191	1	CCAGGCGTTT	    0.941205	-110
GCAGGATGTTCTTTTCGTGCGCGTGCGCGC	1	247	1	CTTTTCGTGC	    0.843422	-54
TATACGGCGTGTTTGCCTTTTGTGCGAGCA	3	65	0	GTTTGCCTTT	    0.946097	-28
          **********

Masking position 8
Map Score:   6.00394

Number of sites scoring better than the average of aligned sites = 298
Number in coding regions = 273
Number in noncoding regions = 25
Number of orfs with sites within 600 bp upstream = 26
Fraction of orfs with sites within 600 bp upstream = 0.00417604


Motif number 4

CCAACTTAGGGATTCGAACCCTAGACCTCG	1	19	0	GATTCGAACC	    0.573295	-282
GGGAGTCAAGGATTCGAACCTTGGAAGACA	1	110	0	GATTCGAACC	    0.573295	-191
TTTCCCTGGCGTTTCGTTCCAGGCGTTTTT	1	183	1	GTTTCGTTCC	    0.961387	-118
          **********

Masking position 4
Map Score:   3.19636

Number of sites scoring better than the average of aligned sites = 14
Number in coding regions = 4
Number in noncoding regions = 10
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 5

          **********

No masking
Map Score:   -3.17312e-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:   -3.17312e-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:   -3.17312e-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