AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i303_mixed18_hpyl_reg_300.orf -o303_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	RHP01209	157	AE000511
#2	RHP01210	111	AE000511
#3	RHP01211	72	AE000511
#4	RHP01212	53	AE000511

Motif number 1

TAAATTCTTTCAATATTATTTTAGTGAAAATAT	1	26	1	CAATTTTTTA	    0.964024	-132
GATTCATTAGCAATACTTTTAAGCAGAATATCT	1	61	1	CAATCTTTAG	    0.931693	-97
GTGTTTGAAACAAGCTTATAATAAAAATGAAAT	1	103	0	CAAGTTTAAA	    0.950558	-55
GCCATTATCAAAATTTTGTATTATAATTTG   	1	138	1	AAATTTTATA	    0.927757	-20
GCTTTGATCAAAATGGTTTTTGGCTAAATAAAG	2	39	0	AAATGTTTTG	    0.782421	-73
CCATTTTGATCAAAGCTCTAAAATCAAGAGCAT	2	56	1	CAAACTTAAA	    0.897098	-56
AAGAGCATAGAAAATTTATTAGAAGATTTAAAA	2	81	1	AAAATTTTAA	    0.880363	-31
         AAAAGCCTTTTTAAATCTTCTAAT	2	98	0	AAAGCTTTTA	    0.961871	-14
TTTAACCCTCAAAGGTTTTTAAAACGC      	3	5	0	AAAGTTTTAA	    0.956097	-68
TTGAGGGTTAAAATAGTGTAAAATAGTAAAGAT	3	26	1	AAATGTTAAA	    0.893909	-47
GTAAAATAGTAAAGATTTTAAAACTCAAAAAGG	3	43	1	AAAGTTTAAA	    0.932956	-30
       TATCAATCCTTTTTGAGTTTTAAAAT	3	57	0	CAATCTTTTA	    0.973869	-16
         TCAATCCTTTTTCAAAAATAACCA	4	40	0	CAATCTTTTA	    0.973869	-14
          **** ** *** *

Masking position 3
Map Score:   17.2966

Number of sites scoring better than the average of aligned sites = 1245
Number in coding regions = 1044
Number in noncoding regions = 201
Number of orfs with sites within 600 bp upstream = 166
Fraction of orfs with sites within 600 bp upstream = 0.0266624


Motif number 2

TGGCTGGTGTTTGAAACAAGCTTATAATAAA	1	111	0	TTAAACAAGC	    0.937039	-47
ATACAAAATTTTGATAATGGCTGGTGTTTGA	1	128	0	TTATAATGGC	     0.95838	-30
GGTTTTTGGCTAAATAAAGGCCATCTCATTC	2	27	0	TAATAAAGGC	    0.958385	-85
AAAAACCATTTTGATCAAAGCTCTAAAATCA	2	51	1	TTATCAAAGC	    0.886454	-61
TATTAGAAGATTTAAAAAGGCTTTT      	2	97	1	TTAAAAAGGC	    0.996422	-15
CCTCAAAGGTTTTTAAAACGC          	3	1	0	TTTAAAACGC	    0.894068	-72
GATTTTAAAACTCAAAAAGGATTGATA    	3	56	1	CTAAAAAGGA	    0.964036	-17
TTTTGTTATCCTAAAAAAGACAAGAAATGGT	4	13	1	CTAAAAAGAC	    0.930292	-41
ATGGTTATTTTTGAAAAAGGATTGA      	4	39	1	TTAAAAAGGA	    0.982091	-15
          ** ********

Masking position 4
Map Score:   8.96307

Number of sites scoring better than the average of aligned sites = 1753
Number in coding regions = 1528
Number in noncoding regions = 225
Number of orfs with sites within 600 bp upstream = 153
Fraction of orfs with sites within 600 bp upstream = 0.0245744


Motif number 3

GTCTAGCCCTTTGATTAAATTCTTTCAATAT	1	11	1	TTATTAAATT	    0.702042	-147
ATCATATATTTTCACTAAAATAATATTGAAA	1	33	0	TTACTAAAAT	    0.943578	-125
TTTAAGCAGAATATCTAAAATTTAAATTTCA	1	78	1	ATTCTAAAAT	    0.947045	-80
AAACAAGCTTATAATAAAAATGAAATTTAAA	1	98	0	ATATAAAAAT	     0.83304	-60
AACACCAGCCATTATCAAAATTTTGTATTAT	1	131	1	ATATCAAAAT	    0.845755	-27
ATCAAAATTTTGTATTATAATTTG       	1	144	1	TGATTATAAT	     0.72984	-14
TTTTAGAGCTTTGATCAAAATGGTTTTTGGC	2	48	0	TTATCAAAAT	    0.897165	-64
TTTTGATCAAAGCTCTAAAATCAAGAGCATA	2	59	1	AGTCTAAAAT	    0.957274	-53
ATTTATTAGAAGATTTAAAAAGGCTTTT   	2	94	1	AGTTTAAAAA	    0.757308	-18
AAAACCTTTGAGGGTTAAAATAGTGTAAAAT	3	19	1	AGGTTAAAAT	    0.908853	-54
ATCCTTTTTGAGTTTTAAAATCTTTACTATT	3	47	0	AGTTTAAAAT	    0.837813	-26
  TCAATCCTTTTTCAAAAATAACCATTTCT	4	35	0	TTTCAAAAAT	     0.74916	-19
          ** ********

Masking position 7
Map Score:   12.1066

Number of sites scoring better than the average of aligned sites = 1255
Number in coding regions = 1047
Number in noncoding regions = 208
Number of orfs with sites within 600 bp upstream = 187
Fraction of orfs with sites within 600 bp upstream = 0.0300353


Motif number 4

          **********

No masking
Map Score:   4.64285e-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:   4.64285e-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:   4.64285e-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