AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i243_regulatory_hpyl_reg_100.orf -o243_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	RHP00155	93	AE000511
#2	RHP00156	41	AE000511
#3	RHP00158	91	AE000511
#4	RHP00160	119	AE000511

Motif number 1

TCGCTTGATTAAAATGAAGCTCTT       	1	4	0	AAAATAAGCT	    0.900386	-90
TGATTGTGTCAAAATACGGCAAAAAACTTTG	1	61	1	AAAATCGGCA	    0.995153	-33
 ATTTGTGTTAAAATACCGAATGCGCCAACG	3	10	1	AAAATCCGAA	    0.892899	-82
CTTACTAGCCAAAAACTAGCAAGCGTTTTAG	3	41	0	AAAAATAGCA	    0.870053	-51
TAAAAGATTTAAAACACCGCTTACTAGCCAA	3	60	0	AAAACCCGCT	    0.991352	-32
CATAAGGCTAAAAGCACGGCTAAAGCGTGGC	4	19	1	AAAGCCGGCT	    0.992873	-101
AAGCACGGCTAAAGCGTGGCTAAAGCGTGGC	4	30	1	AAAGCTGGCT	    0.978568	-90
AAGCGTGGCTAAAGCGTGGCTGGAGCGTGGG	4	41	1	AAAGCTGGCT	    0.978568	-79
TAACAAAAAAAAAAAAACGCAAACCCCCACG	4	66	0	AAAAAACGCA	    0.913255	-54
TTTTTTTGTTAAAATGCGTCAGAAAATTCGG	4	86	1	AAAATCGTCA	    0.941784	-34
AATGCGTCAGAAAATTCGGCATGAGGGCAAA	4	98	1	AAAATCGGCA	    0.995153	-22
          ***** *****

Masking position 3
Map Score:   19.9614

Number of sites scoring better than the average of aligned sites = 804
Number in coding regions = 743
Number in noncoding regions = 61
Number of orfs with sites within 600 bp upstream = 35
Fraction of orfs with sites within 600 bp upstream = 0.00562159


Motif number 2

TTCATTTTAATCAAGCGATAAGTTTTTAAAG	1	17	1	TCAAGCGTAA	    0.954966	-77
GATAAGTTTTTAAAGCGCTTTTTAACCTTGA	1	33	1	TAAAGCGTTT	    0.906773	-61
TATCAAAGTTTTTTGCCGTATTTTGACACAA	1	64	0	TTTTGCCTAT	    0.887861	-30
AACCCATTCAGCATGCGTTTAACACAGATTT	2	17	1	GCATGCGTTA	    0.965337	-25
TAGCGTTGGCGCATTCGGTATTTTAACACAA	3	13	0	GCATTCGTAT	    0.915199	-79
CCAAAAACTAGCAAGCGTTTTAGCGTTGGCG	3	33	0	GCAAGCGTTT	    0.990123	-59
TTTTTGGCTAGTAAGCGGTGTTTTAAATCTT	3	57	1	GTAAGCGTGT	    0.958313	-35
TAGCCGTGCTTTTAGCCTTATGGCTAACTT 	4	10	0	TTTAGCCTAT	     0.88724	-110
GAGCGTGGGGGTTTGCGTTTTTTTTTTTTTG	4	63	1	GTTTGCGTTT	    0.958519	-57
  TTTTGCCCTCATGCCGAATTTTCTGACGC	4	101	0	TCATGCCAAT	    0.828601	-19
          ******* ***

Masking position 6
Map Score:   8.87253

Number of sites scoring better than the average of aligned sites = 2083
Number in coding regions = 1897
Number in noncoding regions = 186
Number of orfs with sites within 600 bp upstream = 111
Fraction of orfs with sites within 600 bp upstream = 0.0178285


Motif number 3

TTGCCGTATTTTGACACAATCAAGGTTAAA	1	53	0	TTGACACAAT	    0.974496	-41
CAGCATGCGTTTAACACAGATTTGATA   	2	25	1	TTAACACAGA	    0.989747	-17
ATTCGGTATTTTAACACAAAT         	3	2	0	TTAACACAAA	    0.993946	-90
CTGACGCATTTTAACAAAAAAAAAAAAACG	4	78	0	TTAACAAAAA	    0.976415	-42
          **********

Masking position 6
Map Score:   4.69174

Number of sites scoring better than the average of aligned sites = 26
Number in coding regions = 19
Number in noncoding regions = 7
Number of orfs with sites within 600 bp upstream = 6
Fraction of orfs with sites within 600 bp upstream = 0.000963701


Motif number 4

TTTGACACAATCAAGGTTAAAAAGCGCTTT	1	44	0	TCAAGGTTAA	    0.849922	-50
GCTTGCTAGTTTTTGGCTAGTAAGCGGTGT	3	48	1	TTTTGGCTAG	    0.930613	-44
GCTTTTAGCCTTATGGCTAACTT       	4	4	0	TTATGGCTAA	    0.976022	-116
AAGGCTAAAAGCACGGCTAAAGCGTGGCTA	4	22	1	GCACGGCTAA	    0.988462	-98
CACGGCTAAAGCGTGGCTAAAGCGTGGCTG	4	33	1	GCGTGGCTAA	    0.995154	-87
CGTGGCTAAAGCGTGGCTGGAGCGTGGGGG	4	44	1	GCGTGGCTGG	    0.984189	-76
          **********

Masking position 8
Map Score:   4.79514

Number of sites scoring better than the average of aligned sites = 342
Number in coding regions = 325
Number in noncoding regions = 17
Number of orfs with sites within 600 bp upstream = 11
Fraction of orfs with sites within 600 bp upstream = 0.00176678


Motif number 5

          **********

No masking
Map Score:   -5.58897e-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:   -5.58897e-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:   -5.58897e-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