AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00040_hpyl_reg_300.orf -o00040_hpyl_300.ace -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -0.39 -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 =  	0.38
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	HP0640	62	poly(A) polymerase (papS)
#2	HP0643	164	glutamyl-tRNA synthetase (gltX)
#3	HP1100	65	6-phosphogluconate dehydratase
#4	HP1386	70	D-ribulose-5-phosphate 3 epimerase (rpe)

Motif number 1

TTAGAATTTTTAAGGAATTTTG         	1	2	0	TAAGGATTTT	    0.956104	-61
ATAATAACACAAAGAAATTTTAAGAGTAAAA	1	39	1	AAAGAATTTT	    0.968375	-24
CTTTATTTAAAAATAGTTTTTGATTATACCT	2	137	0	AAATAGTTTT	    0.937831	-28
ATTTTTAAATAAAGGGTTTTT          	2	154	1	AAAGGGTTTT	    0.993777	-11
AAACACTCTAAAAGGGTTATTG         	3	2	0	AAAGGGTATT	    0.994733	-64
TAACCCTTTTAGAGTGTTTTTGAGTTATTAT	3	14	1	AGAGTGTTTT	    0.956139	-52
AATCTTAATTAAAGGGGTATTC         	3	54	1	AAAGGGTATT	    0.994875	-12
TCAAATCATAAAAGGGTTTTT          	4	1	0	AAAGGGTTTT	    0.993777	-70
          ****** ****

Masking position 3
Map Score:   17.8646

Number of sites scoring better than the average of aligned sites = 1415
Number in coding regions = 1216
Number in noncoding regions = 199
Number of orfs with sites within 600 bp upstream = 153
Fraction of orfs with sites within 600 bp upstream = 0.0245744


Motif number 2

TATTATATCTTTTTAGAATTTTTAAGGAAT	1	15	0	TTTTAGAATT	    0.893738	-48
ACAAAGAAATTTTAAGAGTAAAAAGC    	1	47	1	TTTAAGAGTA	    0.962802	-16
CGCTGTTAGCTTTTTGATAACCAACCATAA	2	14	1	TTTTTGATAA	    0.952115	-151
ATAGGCATCATTTAAGAGATTAGCACTTGG	2	59	0	TTTAAGAGAT	    0.938502	-106
TGCCTATTCATGTTTGATAAAAACAGAACT	2	82	1	TGTTTGATAA	    0.791028	-83
TTAAAAATAGTTTTTGATTATACCTAAAGA	2	132	0	TTTTTGATTA	    0.971493	-33
CAAAAACTATTTTTAAATAAAGGGTTTTT 	2	146	1	TTTTAAATAA	    0.651681	-19
 CAATAACCCTTTTAGAGTGTTTTTGAGTT	3	10	1	TTTTAGAGTG	    0.941354	-56
TTTTAGAGTGTTTTTGAGTTATTATTATAT	3	20	1	TTTTTGAGTT	    0.973642	-46
TACCCCTTTAATTAAGATTTAATATATAAT	3	43	0	ATTAAGATTT	    0.752201	-23
 AAAAACCCTTTTATGATTTGATTAAAGAT	4	10	1	TTTATGATTT	    0.952616	-61
          **********

Masking position 7
Map Score:   12.978

Number of sites scoring better than the average of aligned sites = 1589
Number in coding regions = 1309
Number in noncoding regions = 280
Number of orfs with sites within 600 bp upstream = 208
Fraction of orfs with sites within 600 bp upstream = 0.0334083


Motif number 3

TGTGTTATTATATCTTTTTAGAATTTTTAA	1	20	0	TATCTTTTTA	    0.962153	-43
 AAACGCTGTTAGCTTTTTGATAACCAACC	2	10	1	TAGCTTTTTG	    0.893186	-155
GGCTAACGCCAAGCTTTTTATGGTTGGTTA	2	31	0	AAGCTTTTTA	    0.970249	-134
TTGTGGTAGTTCTGTTTTTATCAAACATGA	2	89	0	TCTGTTTTTA	    0.898462	-76
ATAATCAAAAACTATTTTTAAATAAAGGGT	2	141	1	ACTATTTTTA	    0.809365	-24
      CAATAACCCTTTTAGAGTGTTTTT	3	5	1	AACCCTTTTA	    0.940972	-61
ACCCTTTTAGAGTGTTTTTGAGTTATTATT	3	16	1	AGTGTTTTTG	    0.817529	-50
       AAAAACCCTTTTATGATTTGATT	4	4	1	AACCCTTTTA	    0.940972	-67
CCCTATTTTCAATGTTTTCAAGTAAAATAT	4	44	0	AATGTTTTCA	     0.87437	-27
          **********

Masking position 6
Map Score:   6.19594

Number of sites scoring better than the average of aligned sites = 1461
Number in coding regions = 1162
Number in noncoding regions = 299
Number of orfs with sites within 600 bp upstream = 213
Fraction of orfs with sites within 600 bp upstream = 0.0342114


Motif number 4

          **********

No masking
Map Score:   -6.15168e-14

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 5

          **********

No masking
Map Score:   -6.15168e-14

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:   -6.15168e-14

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