AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i307_mixed21_hpyl_reg_300.orf -o307_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	RHP01463	37	AE000511
#2	RHP01464	263	AE000511

Motif number 1

TTAATCCCATTAAATTAAAAATAGTGTC     	1	20	1	TAATTAAAAA	    0.798973	-18
TTTTAAGTTTAAATTTAAAAATAAAGGATACTT	2	12	0	AAATTAAAAA	     0.79746	-252
TTTTAAATTTAAACTTAAAATTATAGCATAAGT	2	25	1	AAATTAAAAA	    0.968037	-239
TAAGTCATAATAAATTAAAACCACTCTAAAGTT	2	53	1	TAATTAAAAA	    0.989973	-211
AAACCACTCTAAAGTTAAATAAAATTTGACTTT	2	70	1	AAATTAAATA	    0.930892	-194
AAAATTTGACTTTGTTAAAAAAATTATGATAGC	2	90	1	TTTTTAAAAA	    0.934061	-174
AAGCTAAAGCATTCTTAAAAAATTAGTGTAACC	2	181	0	ATTTTAAAAT	    0.798689	-83
TTGTTGCAATTAAGATAAAAATACAAAAAGCTA	2	208	0	TAAATAAAAA	    0.945595	-56
GAAATCTCTTTTTGTTAAAAGGAAATTTA    	2	245	1	TTTTTAAAAA	    0.969173	-19
          *** ******  *

Masking position 7
Map Score:   15.3015

Number of sites scoring better than the average of aligned sites = 314
Number in coding regions = 201
Number in noncoding regions = 113
Number of orfs with sites within 600 bp upstream = 103
Fraction of orfs with sites within 600 bp upstream = 0.0165435


Motif number 2

CATAGCAAAGAATTACGAAATTCAACACTTGTGGCAT	2	122	1	AATACATCAA	    0.991901	-142
AGATGCTAATAAGTGGCCCATGCCACAAGTGTTGAAT	2	141	0	AATGGATCAA	    0.989102	-123
ATTCTTAAAAAATTAGTGTAACCAAAAGATGCTAATA	2	167	0	AATAGAACAA	    0.991713	-97
ATTAAGATAAAAATACAAAAAGCTAAAGCATTCTTAA	2	196	0	AATACAACAA	    0.994334	-68
TTTTTATCTTAATTGCAACAAACTAGAAATCTCTTTT	2	220	1	AATGCAACAA	    0.994744	-44
          ** ***   ** * * *

Masking position 10
Map Score:   3.38408

Number of sites scoring better than the average of aligned sites = 33
Number in coding regions = 28
Number in noncoding regions = 5
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 3

         CAAGTATCCTTTATTTTTAAAT	2	2	1	AAGTTCCTTT	    0.991929	-262
TATTTAACTTTAGAGTGGTTTTAATTTATTA	2	60	0	TAGATGGTTT	    0.898762	-204
GGCCACTTATTAGCATCTTTTGGTTACACTA	2	160	1	TAGCTCTTTT	    0.945009	-104
CTAATTTTTTAAGAATGCTTTAGCTTTTTGT	2	188	1	AAGATGCTTT	    0.978063	-76
AACAAACTAGAAATCTCTTTTTGTTAAAAGG	2	236	1	AAATTCTTTT	    0.910037	-28
         TAAATTTCCTTTTAACAAAAAG	2	252	0	AAATTCCTTT	    0.976054	-12
          **** ******

Masking position 6
Map Score:   3.02619

Number of sites scoring better than the average of aligned sites = 254
Number in coding regions = 205
Number in noncoding regions = 49
Number of orfs with sites within 600 bp upstream = 45
Fraction of orfs with sites within 600 bp upstream = 0.00722775


Motif number 4

CACTATTTTTAATTTAATGGGATTAATTAGGG	1	14	0	AATTAATGGA	    0.948946	-24
GTTTAAATTTAAAAATAAAGGATACTTG    	2	7	0	AAAATAAAGA	    0.820176	-257
GAGTGGTTTTAATTTATTATGACTTATGCTAT	2	47	0	AATTATTAGA	    0.965049	-217
TCTAAAGTTAAATAAAATTTGACTTTGTTAAA	2	77	1	AATAAATTGA	    0.916192	-187
GACTTTGTTAAAAAAATTATGATAGCATAGCA	2	97	1	AAAAATTAGA	    0.971445	-167
ATAGCATAGCAAAGAATTACGAAATTCAACAC	2	118	1	AAAAATTAGA	    0.971455	-146
TGGTTACACTAATTTTTTAAGAATGCTTTAGC	2	180	1	AATTTTTAGA	    0.909994	-84
ATTTCCTTTTAACAAAAAGAGATTTCTAGTTT	2	239	0	AACAAAAGGA	    0.831014	-25
          *** ***** **

Masking position 2
Map Score:   4.24423

Number of sites scoring better than the average of aligned sites = 292
Number in coding regions = 225
Number in noncoding regions = 67
Number of orfs with sites within 600 bp upstream = 62
Fraction of orfs with sites within 600 bp upstream = 0.00995824


Motif number 5

          **********

No masking
Map Score:   -4.80737e-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:   -4.80737e-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:   -4.80737e-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