AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -inarP_hpyl_opreg_100.orf -g0.389 -x5 
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 =  	0.389
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	HP0144	300	cytochrome c oxidase, heme b and copper-binding subunit, membrane-bound (fixN)
#2	HP0376	55	ferrochelatase (hemH)
#3	HP0377	76	thiol:disulfide interchange protein (dsbC), putative

Motif number 1

CATGAAAATACAAAAATAAAGCCAAGCGTT	1	25	1	CAAAAATAAA	    0.964784	-276
CGGTGCGCCTAAAAAATACAACAGCGTTGC	1	70	1	AAAAAATACA	    0.929054	-231
ATGTTACAGAAAAAGATTAAAAATTAAGCT	1	213	1	AAAAGATTAA	    0.988974	-88
ATCTTTTTCAAAAAGCTTAATTTTTAATCT	1	226	0	AAAAGCTTAA	    0.954426	-75
AGCTTTTTGAAAAAGATAAAATTTTATAAT	1	239	1	AAAAGATAAA	    0.994186	-62
GTAAATTCAACAAAGATAAACATAATTATA	1	263	0	CAAAGATAAA	    0.988178	-38
AACGATTAATAAAAAATAAATCGTTAGAAA	2	18	0	AAAAAATAAA	    0.982471	-38
TGCTAAAATAAAACGATTAATAAAAAATAA	2	29	0	AAACGATTAA	    0.954462	-27
CAAATCTATTAAAAGATAAAGGTTATTAC 	3	58	1	AAAAGATAAA	    0.994186	-19
          **********

Masking position 7
Map Score:   20.964

Number of sites scoring better than the average of aligned sites = 218
Number in coding regions = 178
Number in noncoding regions = 40
Number of orfs with sites within 600 bp upstream = 42
Fraction of orfs with sites within 600 bp upstream = 0.0067459


Motif number 2

TATTTTTGTATTTTCATGGGCATGATTATAGG	1	11	0	TTTTAGGGCA	    0.995137	-290
GCTGTTGTATTTTTTAGGCGCACCGGATGGGT	1	63	0	TTTTAGCGCA	    0.997459	-238
TCTTGCCCCTTTTTTTATCGCAACGCTGTTGT	1	87	0	TTTTTTCGCA	    0.970345	-214
TTGAATGGCATTTTTAAGCCAAATTGCTACTA	1	162	0	TTTTAGCCAA	    0.932987	-139
ACTCAATCCCATTTGAATGGCATTTTTAAGCC	1	174	0	ATTTATGGCA	    0.944759	-127
AATAATCGCTTTTTTATGCGCATTTTA     	3	6	0	TTTTAGCGCA	    0.997458	-71
          **** * *****

Masking position 4
Map Score:   7.37576

Number of sites scoring better than the average of aligned sites = 374
Number in coding regions = 353
Number in noncoding regions = 21
Number of orfs with sites within 600 bp upstream = 17
Fraction of orfs with sites within 600 bp upstream = 0.00273049


Motif number 3

GCTTGGCTTTATTTTTGTATTTTCATGGGC	1	22	0	ATTTTTGTAT	    0.794292	-279
TTAGCCAAAGATAGTAGCAATTTGGCTTAA	1	151	1	ATAGTAGCAA	    0.923802	-150
TTTCTGTAACATTGTAATAACTCAATCCCA	1	195	0	ATTGTAATAA	    0.928509	-106
AATACTCCTATTTGTAGTAAATTCAACAAA	1	279	0	TTTGTAGTAA	    0.973892	-22
AACGATTTATTTTTTATTAATCGTTTTATT	2	23	1	TTTTTATTAA	    0.739809	-33
TAATCGTTTTATTTTAGCATGCACCA    	2	40	1	ATTTTAGCAT	    0.925341	-16
AAAAGCGATTATTGTAGTAAGATACCTAGT	3	25	1	ATTGTAGTAA	    0.988477	-52
          **********

Masking position 9
Map Score:   4.25068

Number of sites scoring better than the average of aligned sites = 219
Number in coding regions = 147
Number in noncoding regions = 72
Number of orfs with sites within 600 bp upstream = 75
Fraction of orfs with sites within 600 bp upstream = 0.0120463


Motif number 4

TTTTCATGGGCATGATTATAGG        	1	3	0	CATGATTATA	    0.982871	-298
TAATCATGCCCATGAAAATACAAAAATAAA	1	15	1	CATGAAAATA	    0.921486	-286
CATGAAAATACAAAAATAAAGCCAAGCGTT	1	25	1	CAAAAATAAA	    0.806552	-276
AAAGGTTAAACATGATTAAACAAACCCTCA	1	123	0	CATGATTAAA	    0.987715	-178
TGTTACAGAAAAAGATTAAAAATTAAGCTT	1	214	1	AAAGATTAAA	    0.820049	-87
CAAAGATAAACATAATTATAAAATTTTATC	1	253	0	CATAATTATA	    0.924302	-48
     TGGTGCATGCTAAAATAAAACGATT	2	41	0	CATGCTAAAA	    0.915329	-15
          **********

Masking position 8
Map Score:   6.22642

Number of sites scoring better than the average of aligned sites = 421
Number in coding regions = 380
Number in noncoding regions = 41
Number of orfs with sites within 600 bp upstream = 36
Fraction of orfs with sites within 600 bp upstream = 0.0057822


Motif number 5

TTGTATTTTCATGGGCATGATTATAGG   	1	8	0	ATGGGCATGA	    0.996683	-293
CGATAAAAAAAGGGGCAAGAATGATGAGGG	1	99	1	AGGGGCAAGA	    0.985872	-202
TGCCATTCAAATGGGATTGAGTTATTACAA	1	184	1	ATGGGATTGA	    0.967681	-117
      TAAAATGCGCATAAAAAAGCGATT	3	5	1	ATGCGCATAA	    0.965771	-72
          **********

Masking position 1
Map Score:   1.78498

Number of sites scoring better than the average of aligned sites = 219
Number in coding regions = 210
Number in noncoding regions = 9
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 6

          **********

No masking
Map Score:   7.76924e-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:   7.76924e-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 8

          **********

No masking
Map Score:   7.76924e-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