AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i142_Cytochrome_Oxidase_hpyl_reg_300.orf -o142_hpyl_300.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	RHP01099	300	AE000511

Motif number 1

TTTTCATGGGCATGATTATAG         	1	2	0	CATGATTATA	    0.957798	-299
TAATCATGCCCATGAAAATACAAAAATAAA	1	14	1	CATGAAAATA	    0.709211	-287
CATGAAAATACAAAAATAAAGCCAAGCGTT	1	24	1	CAAAAATAAA	    0.963617	-277
CGGTGCGCCTAAAAAATACAACAGCGTTGC	1	69	1	AAAAAATACA	    0.846396	-232
AAAGGTTAAACATGATTAAACAAACCCTCA	1	122	0	CATGATTAAA	    0.977514	-179
ATCTTTGGCTAAAGGTTAAACATGATTAAA	1	132	0	AAAGGTTAAA	    0.944354	-169
TGAGTTATTACAATGTTACAGAAAAAGATT	1	200	1	CAATGTTACA	    0.772354	-101
TGTTACAGAAAAAGATTAAAAATTAAGCTT	1	213	1	AAAGATTAAA	    0.964408	-88
GCTTTTTGAAAAAGAATAAAATTTTATAAT	1	239	1	AAAGAATAAA	    0.957986	-62
CAAAGATAAACATAATTATAAAATTTTATT	1	253	0	CATAATTATA	     0.90054	-48
GTAAATTCAACAAAGATAAACATAATTATA	1	263	0	CAAAGATAAA	    0.943144	-38
          **********

Masking position 8
Map Score:   14.5023

Number of sites scoring better than the average of aligned sites = 901
Number in coding regions = 769
Number in noncoding regions = 132
Number of orfs with sites within 600 bp upstream = 101
Fraction of orfs with sites within 600 bp upstream = 0.0162223


Motif number 2

CCGGTGCGCCTAAAAAATACAACAGCGTTG	1	68	1	TAAAAAATAC	    0.776347	-233
AGCGTTGCGATAAAAAAAGGGGCAAGAATG	1	91	1	TAAAAAAAGG	    0.968929	-210
GCAATTTGGCTTAAAAATGCCATTCAAATG	1	166	1	TTAAAAATGC	    0.943081	-135
AAAAATGCCATTCAAATGGGATTGAGTTAT	1	178	1	TTCAAATGGG	    0.942643	-123
TTTATTCTTTTTCAAAAAGCTTAATTTTTA	1	229	0	TTCAAAAAGC	     0.98458	-72
TTGTAGTAAATTCAACAAAGATAAACATAA	1	268	0	TTCAACAAAG	    0.875613	-33
TTGAATTTACTACAAATAGGAGTATTGC  	1	283	1	TACAAATAGG	    0.965539	-18
          **********

Masking position 5
Map Score:   4.48876

Number of sites scoring better than the average of aligned sites = 1612
Number in coding regions = 1366
Number in noncoding regions = 246
Number of orfs with sites within 600 bp upstream = 166
Fraction of orfs with sites within 600 bp upstream = 0.0266624


Motif number 3

TTGTATTTTCATGGGCATGATTATAG    	1	7	0	ATGGGCATGA	     0.98446	-294
TACAACAGCGTTGCGATAAAAAAAGGGGCA	1	85	1	TTGCGATAAA	    0.853314	-216
CGATAAAAAAAGGGGCAAGAATGATGAGGG	1	98	1	AGGGGCAAGA	    0.958621	-203
TGCTACTATCTTTGGCTAAAGGTTAAACAT	1	139	0	TTTGGCTAAA	    0.905494	-162
ATAGTAGCAATTTGGCTTAAAAATGCCATT	1	160	1	TTTGGCTTAA	    0.953646	-141
TGCCATTCAAATGGGATTGAGTTATTACAA	1	183	1	ATGGGATTGA	    0.975578	-118
          **********

Masking position 10
Map Score:   2.48931

Number of sites scoring better than the average of aligned sites = 982
Number in coding regions = 932
Number in noncoding regions = 50
Number of orfs with sites within 600 bp upstream = 30
Fraction of orfs with sites within 600 bp upstream = 0.0048185


Motif number 4

          **********

No masking
Map Score:   7.91135e-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:   7.91135e-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:   7.91135e-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