AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i204_dna_repair1_hpyl_reg_100.orf -o204_hpyl_100.ace -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -g0.39 -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 =  	0.39
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RHP01384	159	AE000511
#2	RHP00791	66	AE000511

Motif number 1

GCGAACTGACAAGCCTTTTTGATGAAAGCC	1	95	1	AAGCCTTTTT	    0.980343	-65
     ACCTAATCCCTTTTAAAGTTTCTAA	1	145	0	ATCCCTTTTA	    0.988445	-15
AACGCTTTTTATCGCTTTATATTATAATCC	2	35	0	ATCGCTTTAT	    0.983256	-32
ACCCCTTAAGAACGCTTTTTATCGCTTTAT	2	45	0	AACGCTTTTT	    0.991771	-22
         AAACCCCTTAAGAACGCTTTT	2	56	0	AACCCCTTAA	    0.974707	-11
          **********

Masking position 7
Map Score:   5.55956

Number of sites scoring better than the average of aligned sites = 928
Number in coding regions = 775
Number in noncoding regions = 153
Number of orfs with sites within 600 bp upstream = 106
Fraction of orfs with sites within 600 bp upstream = 0.0170254


Motif number 2

GCAGTATTTCATTATAGAAGACACGAGCGAG	1	18	1	ATTATGAAGA	    0.828155	-142
GAGCGAGAAAATCAGCCAAGCGGAGTTTGAA	1	42	1	ATCAGCAAGC	    0.979596	-118
TGTTGCATTAAATTTTCAAACTCCGCTTGGC	1	56	0	AATTTCAAAC	     0.93549	-104
TTAATGCAACAATATTCAAGCGAACTGACAA	1	76	1	AATATCAAGC	    0.984556	-84
TATTCAAGCGAACTGACAAGCCTTTTTGATG	1	88	1	AACTGCAAGC	    0.967664	-72
ACAAGCCTTTTTGATGAAAGCCAGAGCTTGC	1	103	1	TTGATAAAGC	    0.827645	-57
CTAAAATTTCTTGTTGCAAGCTCTGGCTTTC	1	118	0	TTGTTCAAGC	    0.968766	-42
GCAACAAGAAATTTTAGAAACTTTAAAAGGG	1	132	1	ATTTTGAAAC	    0.907803	-28
          ***** *****

Masking position 8
Map Score:   4.5865

Number of sites scoring better than the average of aligned sites = 1868
Number in coding regions = 1721
Number in noncoding regions = 147
Number of orfs with sites within 600 bp upstream = 98
Fraction of orfs with sites within 600 bp upstream = 0.0157404


Motif number 3

GAAGACACGAGCGAGAAAATCAGCCAAGCG	1	34	1	GCGAGAAAAT	    0.990758	-126
AAAATTTAATGCAACAATATTCAAGCGAAC	1	71	1	GCAACAATAT	    0.967931	-89
AGAGCTTGCAACAAGAAATTTTAGAAACTT	1	125	1	ACAAGAAATT	    0.930534	-35
TATAATCCTAAAAACAAAATAGGGCGGTTA	2	13	0	AAAACAAAAT	    0.894128	-54
ATAATATAAAGCGATAAAAAGCGTTCTTAA	2	40	1	GCGATAAAAA	    0.922752	-27
          **********

Masking position 6
Map Score:   0.889267

Number of sites scoring better than the average of aligned sites = 680
Number in coding regions = 628
Number in noncoding regions = 52
Number of orfs with sites within 600 bp upstream = 47
Fraction of orfs with sites within 600 bp upstream = 0.00754899


Motif number 4

          **********

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 5

          **********

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 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