AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00920_hpyl_reg_100.orf -o00920_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	HP0106	24	cystathionine gamma-synthase (metB)
#2	HP0107	38	cysteine synthetase (cysK)
#3	HP1210	300	serine acetyltransferase (cysE)

Motif number 1

GTTTTTCCTTTTTTATTGAATTT         	1	2	0	TTTTATGATT	    0.983726	-23
CAAAATTGAATTTTATTGTTTGTTATAGGAGA	2	16	1	TTTTATGTTG	    0.849072	-23
AATAAAACTATTTTAATGAAAAAATAAAAATG	3	40	0	TTTTATGAAA	    0.918114	-261
ATTAAAATAGTTTTATTCCAAATAAATGCCGA	3	55	1	TTTTATCAAA	    0.960314	-246
ACTAGTGAGTTTTTAAGCCTTTTTAAAGGATT	3	98	1	TTTTAGCTTT	     0.94068	-203
TTAAAGGATTGTTTAAGCGAATTTGAAAGGAT	3	120	1	GTTTAGCAAT	    0.927838	-181
ACGCTCTCTCTTTTAATCCTTTCAAATTCGCT	3	135	0	TTTTATCTTT	    0.976369	-166
AGAGAGAGCGTTTTACTCTATTAATTTTTTAC	3	156	1	TTTTATCATT	    0.990452	-145
TCTATTAATTTTTTACTCCATTTAAAGGAGTG	3	172	1	TTTTATCATT	    0.990451	-129
TTGCATCAAGTTTTATTGGAATGGGTGAGAAA	3	232	1	TTTTATGAAT	     0.98072	-69
ATCTGCTCATGTTGATTCAAATATATTCCAAC	3	266	1	GTTGATCAAT	    0.863183	-35
          ***** ** ***

Masking position 5
Map Score:   17.8224

Number of sites scoring better than the average of aligned sites = 585
Number in coding regions = 458
Number in noncoding regions = 127
Number of orfs with sites within 600 bp upstream = 112
Fraction of orfs with sites within 600 bp upstream = 0.0179891


Motif number 2

        AAATTCAATAAAAAAGGAAAAAC	1	3	1	ATTCAATAAA	    0.805307	-22
GTTAATAGTAATCTTTTTCAATCTGCATTTT	3	15	1	ATCTTTTCAA	     0.94038	-286
ATTTTTATTTTTTCATTAAAATAGTTTTATT	3	41	1	TTTCATTAAA	    0.719953	-260
CGCTTAAACAATCCTTTAAAAAGGCTTAAAA	3	108	0	ATCCTTTAAA	    0.985965	-193
CTCTCTTTTAATCCTTTCAAATTCGCTTAAA	3	131	0	ATCCTTTAAA	    0.985983	-170
TAATTTTTTACTCCATTTAAAGGAGTGTGAG	3	177	1	CTCCATTAAA	    0.971937	-124
ATTTTTTCTCACCCATTCCAATAAAACTTGA	3	237	0	ACCCATTCAA	    0.967087	-64
GTTGATTCAAATATATTCCAACCGGAGACTC	3	276	1	ATATATTCAA	    0.796512	-25
          ******* ***

Masking position 10
Map Score:   6.32603

Number of sites scoring better than the average of aligned sites = 718
Number in coding regions = 571
Number in noncoding regions = 147
Number of orfs with sites within 600 bp upstream = 115
Fraction of orfs with sites within 600 bp upstream = 0.0184709


Motif number 3

TCGCAAAATTGAATTTTATTGTTTGTTATA	2	13	1	GAATTTTATT	    0.886519	-26
TTTTCAATCTGCATTTTTATTTTTTCATTA	3	29	1	GCATTTTTAT	    0.958543	-272
CATTTATTCGGCATTTATTTGGAATAAAAC	3	64	0	GCATTTATTT	     0.98041	-237
AAAACTTGATGCAAATTTTTCTTGTCATTA	3	216	0	GCAAATTTTT	    0.965271	-85
ATCAACATGAGCAGATTTTTTCTCACCCAT	3	252	0	GCAGATTTTT	    0.976805	-49
TCTCCGGTTGGAATATATTTGAATCAACAT	3	274	0	GAATATATTT	    0.921403	-27
          **********

Masking position 6
Map Score:   5.1062

Number of sites scoring better than the average of aligned sites = 344
Number in coding regions = 316
Number in noncoding regions = 28
Number of orfs with sites within 600 bp upstream = 24
Fraction of orfs with sites within 600 bp upstream = 0.0038548


Motif number 4

          AAATTCAATAAAAAAGGAAA	1	1	1	AAATTCAATA	    0.853706	-24
          AATCGCAAAATTGAATTTTA	2	1	1	AATCGCAAAA	    0.805255	-38
AAAGGCTTAAAAACTCACTAGTCTATCATT	3	90	0	AAACTCACTA	    0.983422	-211
TAATAGAGTAAAACGCTCTCTCTTTTAATC	3	149	0	AAACGCTCTC	    0.976439	-152
CATTATACCTAAACTCACACTCCTTTAAAT	3	191	0	AAACTCACAC	    0.980389	-110
TTCCAACCGGAGACTCTATC          	3	291	1	AGACTCTATC	    0.920793	-10
          **********

Masking position 1
Map Score:   1.82939

Number of sites scoring better than the average of aligned sites = 783
Number in coding regions = 716
Number in noncoding regions = 67
Number of orfs with sites within 600 bp upstream = 51
Fraction of orfs with sites within 600 bp upstream = 0.00819146


Motif number 5

          **********

No masking
Map Score:   -3.31523e-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:   -3.31523e-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:   -3.31523e-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