AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i142_Cytochrome_Oxidase_hpyl_reg_100.orf -o142_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	RHP01099	300	AE000511

Motif number 1

         CTATAATCATGCCCATGAAAA	1	2	1	TATAATCATG	    0.958078	-299
TTTATTTTTGTATTTTCATGGGCATGATTA	1	14	0	TATTTTCATG	    0.710658	-287
AACGCTTGGCTTTATTTTTGTATTTTCATG	1	24	0	TTTATTTTTG	    0.963863	-277
GCAACGCTGTTGTATTTTTTAGGCGCACCG	1	69	0	TGTATTTTTT	    0.847307	-232
TGAGGGTTTGTTTAATCATGTTTAACCTTT	1	122	1	TTTAATCATG	    0.977668	-179
TTTAATCATGTTTAACCTTTAGCCAAAGAT	1	132	1	TTTAACCTTT	    0.944722	-169
AATCTTTTTCTGTAACATTGTAATAACTCA	1	200	0	TGTAACATTG	    0.773588	-101
AAGCTTAATTTTTAATCTTTTTCTGTAACA	1	213	0	TTTAATCTTT	    0.964648	-88
ATTATAAAATTTTATTCTTTTTCAAAAAGC	1	239	0	TTTATTCTTT	    0.958268	-62
AATAAAATTTTATAATTATGTTTATCTTTG	1	253	1	TATAATTATG	    0.901084	-48
TATAATTATGTTTATCTTTGTTGAATTTAC	1	263	1	TTTATCTTTG	     0.94352	-38
          **********

Masking position 3
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

CAACGCTGTTGTATTTTTTAGGCGCACCGG	1	68	0	GTATTTTTTA	    0.790631	-233
CATTCTTGCCCCTTTTTTTATCGCAACGCT	1	91	0	CCTTTTTTTA	    0.971367	-210
CATTTGAATGGCATTTTTAAGCCAAATTGC	1	166	0	GCATTTTTAA	    0.947437	-135
ATAACTCAATCCCATTTGAATGGCATTTTT	1	178	0	CCCATTTGAA	    0.947031	-123
TAAAAATTAAGCTTTTTGAAAAAGAATAAA	1	229	1	GCTTTTTGAA	    0.985807	-72
TTATGTTTATCTTTGTTGAATTTACTACAA	1	268	1	CTTTGTTGAA	      0.8845	-33
  GCAATACTCCTATTTGTAGTAAATTCAA	1	283	0	CCTATTTGTA	    0.968234	-18
          **********

Masking position 10
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	    0.996705	-294
CGATAAAAAAAGGGGCAAGAATGATGAGGG	1	98	1	AGGGGCAAGA	    0.993114	-203
TGCCATTCAAATGGGATTGAGTTATTACAA	1	183	1	ATGGGATTGA	    0.984356	-118
          **********

Masking position 1
Map Score:   1.63698

Number of sites scoring better than the average of aligned sites = 66
Number in coding regions = 62
Number in noncoding regions = 4
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 4

GTATTTTCATGGGCATGATTATAG      	1	5	0	GGGCATGATT	    0.994581	-296
ACCTAACGCTTGGCTTTATTTTTGTATTTT	1	28	0	TGGCTTTATT	    0.906235	-273
ATAAAAAAAGGGGCAAGAATGATGAGGGTT	1	100	1	GGGCAAGAAT	    0.956697	-201
AGAATGATGAGGGTTTGTTTAATCATGTTT	1	115	1	GGGTTTGTTT	    0.952687	-186
CCATTCAAATGGGATTGAGTTATTACAATG	1	185	1	GGGATTGAGT	    0.974912	-116
          **********

Masking position 10
Map Score:   1.83917

Number of sites scoring better than the average of aligned sites = 699
Number in coding regions = 648
Number in noncoding regions = 51
Number of orfs with sites within 600 bp upstream = 43
Fraction of orfs with sites within 600 bp upstream = 0.00690652


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


Motif number 7

          **********

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