AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00520_hpyl_reg_100.orf -o00520_hpyl_100.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	HP0360	216	UDP-glucose 4-epimerase
#2	HP0643	164	glutamyl-tRNA synthetase (gltX)

Motif number 1

GGTTAGAGCGCACCCCTGATAAGGGTGAGGT	1	65	0	CACCCTGATA	    0.954984	-152
CCTGAGCTATAAGCCCTTAAAAGCCAATAAA	1	97	1	AACCCTTAAA	     0.99296	-120
TTTTCTTAAAAAATCCTTAAATAATAAATGG	1	147	1	AATCCTTAAA	    0.940302	-70
ATAACATCTTAATCCCATTTATTATTTAAGG	1	161	0	AACCCATTTA	    0.961942	-56
        AAAACCCCTTTTAAAATGAAAAA	1	204	0	AACCCTTTTA	     0.99296	-13
          AAACGCTGTTAGCTTTTTGAT	2	1	1	AACGCTGTTA	    0.938839	-164
GCCAAGTGCTAATCTCTTAAATGATGCCTAT	2	58	1	AACTCTTAAA	    0.948174	-107
        AAAAACCCTTTATTTAAAAATAG	2	152	0	AACCCTTTAT	    0.961943	-13
          ** ********

Masking position 2
Map Score:   10.0401

Number of sites scoring better than the average of aligned sites = 1239
Number in coding regions = 1067
Number in noncoding regions = 172
Number of orfs with sites within 600 bp upstream = 126
Fraction of orfs with sites within 600 bp upstream = 0.0202377


Motif number 2

CCCCAAAGATTGTAAAAATGGTGGGCTTAG	1	18	1	TGTAAAAATG	    0.947091	-199
CCAATAAAGATGAAATTATAGATTAAATTT	1	120	1	TGAAATTATA	    0.898267	-97
TTAAATTTTCTTAAAAAATCCTTAAATAAT	1	142	1	TTAAAAAATC	    0.907732	-75
TAAAAAATCCTTAAATAATAAATGGGATTA	1	153	1	TTAAATAATA	    0.964105	-64
GGGATTAAGATGTTATAATAGTTGTTATTT	1	176	1	TGTTATAATA	     0.82006	-41
CCTTTTAAAATGAAAAAATAACAACTATTA	1	191	0	TGAAAAAATA	    0.977102	-26
TGCTAATCTCTTAAATGATGCCTATTCATG	2	64	1	TTAAATGATG	    0.847814	-101
AAACCCTTTATTTAAAAATAGTTTTTGATT	2	143	0	TTTAAAAATA	    0.943672	-22
          **********

Masking position 5
Map Score:   6.50522

Number of sites scoring better than the average of aligned sites = 705
Number in coding regions = 534
Number in noncoding regions = 171
Number of orfs with sites within 600 bp upstream = 144
Fraction of orfs with sites within 600 bp upstream = 0.0231288


Motif number 3

TAAGAAAATTTAATCTATAATTTCATCTTT	1	125	0	TAATCTATAA	    0.852415	-92
AGATTAAATTTTCTTAAAAAATCCTTAAAT	1	139	1	TTCTTAAAAA	    0.838712	-78
TTATGGTTGGTTATCAAAAAGCTAACAGCG	2	14	0	TTATCAAAAA	    0.960851	-151
AGTTCTGTTTTTATCAAACATGAATAGGCA	2	82	0	TTATCAAACA	    0.966331	-83
TCTTTAGGTATAATCAAAAACTATTTTTAA	2	132	1	TAATCAAAAA	     0.97653	-33
 AAAAACCCTTTATTTAAAAATAGTTTTTG	2	146	0	TTATTTAAAA	    0.892036	-19
          **********

Masking position 4
Map Score:   5.41072

Number of sites scoring better than the average of aligned sites = 508
Number in coding regions = 414
Number in noncoding regions = 94
Number of orfs with sites within 600 bp upstream = 77
Fraction of orfs with sites within 600 bp upstream = 0.0123675


Motif number 4

AAAATGGTGGGCTTAGGAGGAGTTGAACCTC	1	32	1	GCTTAGAGGA	    0.978434	-185
CCGACCTCACCCTTATCAGGGGTGCGCTCTA	1	62	1	CCTTATAGGG	    0.985315	-155
ATCTTTATTGGCTTTTAAGGGCTTATAGCTC	1	100	0	GCTTTTAGGG	    0.994042	-117
CTAACGCCAAGCTTTTTATGGTTGGTTATCA	2	28	0	GCTTTTATGG	    0.984574	-137
          ****** ****

Masking position 4
Map Score:   1.86044

Number of sites scoring better than the average of aligned sites = 124
Number in coding regions = 116
Number in noncoding regions = 8
Number of orfs with sites within 600 bp upstream = 8
Fraction of orfs with sites within 600 bp upstream = 0.00128493


Motif number 5

          **********

No masking
Map Score:   -6.79689e-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:   -6.79689e-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:   -6.79689e-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