AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -inarP_hpyl_opreg_300.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

AACGCTTGGCTTTATTTTTGTATTTTCATG	1	25	0	TTTATTTTTG	    0.960978	-276
GCAACGCTGTTGTATTTTTTAGGCGCACCG	1	70	0	TGTATTTTTT	      0.9217	-231
AGCTTAATTTTTAATCTTTTTCTGTAACAT	1	213	0	TTAATCTTTT	     0.98775	-88
AGATTAAAAATTAAGCTTTTTGAAAAAGAT	1	226	1	TTAAGCTTTT	    0.949567	-75
ATTATAAAATTTTATCTTTTTCAAAAAGCT	1	239	0	TTTATCTTTT	    0.993537	-62
TATAATTATGTTTATCTTTGTTGAATTTAC	1	263	1	TTTATCTTTG	    0.986866	-38
TTTCTAACGATTTATTTTTTATTAATCGTT	2	18	1	TTTATTTTTT	    0.980538	-38
TTATTTTTTATTAATCGTTTTATTTTAGCA	2	29	1	TTAATCGTTT	    0.949598	-27
 GTAATAACCTTTATCTTTTAATAGATTTG	3	58	0	TTTATCTTTT	    0.993537	-19
          **********

Masking position 4
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

CCTATAATCATGCCCATGAAAATACAAAAATA	1	11	1	TGCCCTAAAA	    0.995773	-290
ACCCATCCGGTGCGCCTAAAAAATACAACAGC	1	63	1	TGCGCTAAAA	    0.997793	-238
ACAACAGCGTTGCGATAAAAAAAGGGGCAAGA	1	87	1	TGCGAAAAAA	    0.974158	-214
TAGTAGCAATTTGGCTTAAAAATGCCATTCAA	1	162	1	TTGGCTAAAA	    0.941313	-139
GGCTTAAAAATGCCATTCAAATGGGATTGAGT	1	174	1	TGCCATAAAT	    0.951699	-127
     TAAAATGCGCATAAAAAAGCGATTATT	3	6	1	TGCGCTAAAA	    0.997793	-71
          ***** * ****

Masking position 9
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

GCCCATGAAAATACAAAAATAAAGCCAAGC	1	22	1	ATACAAAAAT	    0.788163	-279
TTAAGCCAAATTGCTACTATCTTTGGCTAA	1	151	0	TTGCTACTAT	    0.921235	-150
TGGGATTGAGTTATTACAATGTTACAGAAA	1	195	1	TTATTACAAT	    0.926239	-106
TTTGTTGAATTTACTACAAATAGGAGTATT	1	279	1	TTACTACAAA	    0.972986	-22
AATAAAACGATTAATAAAAAATAAATCGTT	2	23	0	TTAATAAAAA	    0.732747	-33
    TGGTGCATGCTAAAATAAAACGATTA	2	40	0	ATGCTAAAAT	    0.922785	-16
ACTAGGTATCTTACTACAATAATCGCTTTT	3	25	0	TTACTACAAT	     0.98807	-52
          **********

Masking position 6
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	    0.982148	-298
TAATCATGCCCATGAAAATACAAAAATAAA	1	15	1	CATGAAAATA	    0.917864	-286
CATGAAAATACAAAAATAAAGCCAAGCGTT	1	25	1	CAAAAATAAA	    0.798786	-276
AAAGGTTAAACATGATTAAACAAACCCTCA	1	123	0	CATGATTAAA	    0.987111	-178
TGTTACAGAAAAAGATTAAAAATTAAGCTT	1	214	1	AAAGATTAAA	    0.812699	-87
CAAAGATAAACATAATTATAAAATTTTATC	1	253	0	CATAATTATA	    0.922628	-48
     TGGTGCATGCTAAAATAAAACGATT	2	41	0	CATGCTAAAA	     0.91145	-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

   CCTATAATCATGCCCATGAAAATACAA	1	8	1	TCATGCCCAT	    0.996442	-293
CCCTCATCATTCTTGCCCCTTTTTTTATCG	1	99	0	TCTTGCCCCT	    0.984854	-202
TTGTAATAACTCAATCCCATTTGAATGGCA	1	184	0	TCAATCCCAT	    0.965399	-117
AATCGCTTTTTTATGCGCATTTTA      	3	5	0	TTATGCGCAT	    0.963359	-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