AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i297_mixed12_hpyl_reg_100.orf -o297_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	RHP00234	300	AE000511
#2	RHP00864	26	AE000511
#3	RHP00871	104	AE000511

Motif number 1

GTCCTGACGCTCTTACCTTAATTGAGAAAGCA	1	13	0	TCTTATTAAT	    0.825569	-288
TTTAATCAACTTTTTCATTAAAATGTCCTGAC	1	37	0	TTTTTTTAAA	    0.927092	-264
ATTCCTTCTTTCTTTACTATAACTTAGCATTT	1	67	0	TCTTTTATAA	    0.726814	-234
TAACATCGTTTTTTTTTTTTTTGGTATAATGC	1	130	0	TTTTTTTTTT	    0.936644	-171
GTTATTTGAACTTTATTTTTAACATTCTGTTT	1	158	1	CTTTATTTAA	    0.952591	-143
TAACATTCTGTTTTTCTTTTTTATAAAATGAA	1	177	1	TTTTTTTTTT	    0.936644	-124
ACTTAAAAAGTGTTTCATTTTATAAAAAAGAA	1	190	0	TGTTTTTTTA	    0.805704	-111
ATGAAACACTTTTTAAGTTTATTTATTTATTT	1	204	1	TTTTATTTAT	    0.969174	-97
TTAAGTTTATTTATTTATTTAATATTGGTGTT	1	216	1	TTATTTTTAA	    0.814768	-85
TTATAGCGATTCTTTCTTTTAAACACCAATAT	1	237	0	TCTTTTTTAA	    0.968845	-64
        GACTTTTCTTTTTTCATGGCTTGT	2	13	0	CTTTTTTTTT	    0.852531	-14
TTTTTGAAGGCTTGATTTTTAAAAGTTAGGCT	3	13	1	CTTGATTTAA	    0.833976	-92
AGGCTTAATCTTTTATGTTAAAATTCTGAGAT	3	40	1	TTTTATTAAA	    0.906545	-65
ATGTTAAAATTCTGAGATTTTATATATTTTAT	3	54	1	TCTGATTTTA	     0.78475	-51
ATTTTATATATTTTATATTTATCGTTAGGTTT	3	70	1	TTTTATTTAT	    0.969174	-35
TATCGTTAGGTTTTAGGTTTAAAGTT      	3	89	1	TTTTATTTAA	    0.978952	-16
          *****  *****

Masking position 8
Map Score:   20.9434

Number of sites scoring better than the average of aligned sites = 2337
Number in coding regions = 1715
Number in noncoding regions = 622
Number of orfs with sites within 600 bp upstream = 316
Fraction of orfs with sites within 600 bp upstream = 0.0507549


Motif number 2

          CTTGCTTTCTCAATTAAGGT	1	1	1	CTTGCTTTCT	    0.979979	-300
TTAAAATGTCCTGACGCTCTTACCTTAATT	1	22	0	CTGACGCTCT	    0.976493	-279
GTATTATATTCCTTCTTTCTTTACTATAAC	1	76	0	CCTTCTTTCT	    0.974087	-225
TATAATACGCCTTTCGCTCTTACCTTCGCC	1	98	1	CTTTCGCTCT	    0.989821	-203
TTTTAACATTCTGTTTTTCTTTTTTATAAA	1	174	1	CTGTTTTTCT	    0.945239	-127
          **********

Masking position 8
Map Score:   2.38382

Number of sites scoring better than the average of aligned sites = 122
Number in coding regions = 108
Number in noncoding regions = 14
Number of orfs with sites within 600 bp upstream = 9
Fraction of orfs with sites within 600 bp upstream = 0.00144555


Motif number 3

GAAAGGCGTATTATATTCCTTCTTTCTTTACTAT	1	79	0	TTAATTTTTT	    0.961039	-222
AAAGTTCAAATAACATCGTTTTTTTTTTTTTTGG	1	138	0	TAAATCTTTT	    0.960556	-163
ACTTTATTTTTAACATTCTGTTTTTCTTTTTTAT	1	167	1	TAAATTGTTT	     0.96162	-134
AAACACTTTTTAAGTTTATTTATTTATTTAATAT	1	207	1	TAATTTTTTT	    0.844866	-94
TTTATTTATTTAATATTGGTGTTTAAAAGAAAGA	1	225	1	TAAATTTGTT	    0.961572	-76
TTGTTTCAAATTATAGCGATTCTTTCTTTTAAAC	1	245	0	TTAAGCTTTT	    0.943757	-56
TTGAAACAATTTAAATCTATTGATGGGATAAAGG	1	270	1	TTAATCTTAT	    0.762317	-31
GCTTGATTTTTAAAAGTTAGGCTTAATCTTTTAT	3	22	1	TAAAGTGGTT	    0.944598	-83
TATTTTATATTTATCGTTAGGTTTTAGGTTTAAA	3	78	1	TTACGTGGTT	    0.786171	-27
          *** ***  ** **

Masking position 3
Map Score:   2.40078

Number of sites scoring better than the average of aligned sites = 680
Number in coding regions = 542
Number in noncoding regions = 138
Number of orfs with sites within 600 bp upstream = 126
Fraction of orfs with sites within 600 bp upstream = 0.0202377


Motif number 4

GACATTTTAATGAAAAAGTTGATTAAAATG	1	42	1	TGAAAAAGTT	    0.979523	-259
TTTTATAAAATGAAACACTTTTTAAGTTTA	1	195	1	TGAAACACTT	    0.955651	-106
CGCTATAATTTGAAACAATTTAAATCTATT	1	261	1	TGAAACAATT	      0.9735	-40
AGACAAGCCATGAAAAAAGAAAAGTC    	2	11	1	TGAAAAAAGA	    0.799887	-16
AGGCTTGATTTTTAAAAGTTAGGCTTAATC	3	20	1	TTTAAAAGTT	    0.798637	-85
TAATCTTTTATGTTAAAATTCTGAGATTTT	3	45	1	TGTTAAAATT	    0.854207	-60
          **********

Masking position 5
Map Score:   0.791309

Number of sites scoring better than the average of aligned sites = 541
Number in coding regions = 456
Number in noncoding regions = 85
Number of orfs with sites within 600 bp upstream = 64
Fraction of orfs with sites within 600 bp upstream = 0.0102795


Motif number 5

          **********

No masking
Map Score:   -7.57849e-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:   -7.57849e-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:   -7.57849e-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