AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i265_hypothetical10_hpyl_reg_100.orf -o265_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	RHP01418	228	AE000511

Motif number 1

TCGCTCTTTAATTTTAATCATTGACAAGGAG	1	25	0	ATTTTAATCT	    0.930697	-204
AAGAGCGATGTCCTTAATCGTCCAACTATTG	1	48	1	TCCTTAATCT	    0.983076	-181
AATCTTAAGATCTTTAAAGATTTTAAAAACT	1	86	0	TCTTTAAAGT	    0.942627	-143
GTGGGTTTTTTCTTAAATCTTAAGATCTTTA	1	101	0	TCTTAAATCT	    0.973745	-128
GAAAAAACCCACTTTAAAAATACCTAAAAAA	1	120	1	ACTTTAAAAT	    0.757306	-109
CTTTAAAAATACCTAAAAAATACAGAGCAAC	1	131	1	ACCTAAAAAT	    0.961109	-98
TAATGAAATTTTCTTAAAATTATACAATATG	1	190	0	TTCTTAAAAT	    0.916117	-39
AATTCCCCTTACTTAAATAATGAAATTTTCT	1	207	0	ACTTAAATAT	    0.967901	-22
          ********* *

Masking position 6
Map Score:   9.10647

Number of sites scoring better than the average of aligned sites = 690
Number in coding regions = 538
Number in noncoding regions = 152
Number of orfs with sites within 600 bp upstream = 149
Fraction of orfs with sites within 600 bp upstream = 0.0239319


Motif number 2

TCTTAACTACCAAACTCCTTGTCAATGATT	1	11	1	CAAACTCCTT	    0.952637	-218
CGATTAAGGACATCGCTCTTTAATTTTAAT	1	38	0	CATCGCTCTT	     0.98013	-191
ATTTAAGAAAAAACCCACTTTAAAAATACC	1	114	1	AAACCCACTT	    0.978696	-115
AAATACAGAGCAACGCCCTTAGATTATACT	1	148	1	CAACGCCCTT	     0.99643	-81
         TAATTCCCCTTACTTAAATAA	1	218	0	AATTCCCCTT	    0.969873	-11
          **********

Masking position 2
Map Score:   3.94562

Number of sites scoring better than the average of aligned sites = 580
Number in coding regions = 519
Number in noncoding regions = 61
Number of orfs with sites within 600 bp upstream = 51
Fraction of orfs with sites within 600 bp upstream = 0.00819146


Motif number 3

CTCCTTGTCAATGATTAAAATTAAAGAGCGAT	1	25	1	ATTTAAAATT	    0.909231	-204
ATCTTTAAAGATTTTAAAAACTAATACAGCAA	1	76	0	ATTAAAAACT	    0.957972	-153
TTTTTCTTAAATCTTAAGATCTTTAAAGATTT	1	94	0	ATTAAGATCT	    0.972424	-135
TAACTTAACTATAGTATAATCTAAGGGCGTTG	1	158	0	ATTATAATCT	    0.973906	-71
TAAGTTACATATTGTATAATTTTAAGAAAATT	1	183	1	ATTATAATTT	    0.966789	-46
CCTTACTTAAATAATGAAATTTTCTTAAAATT	1	200	0	ATTGAAATTT	    0.964976	-29
          **  ********

Masking position 5
Map Score:   4.17043

Number of sites scoring better than the average of aligned sites = 165
Number in coding regions = 117
Number in noncoding regions = 48
Number of orfs with sites within 600 bp upstream = 38
Fraction of orfs with sites within 600 bp upstream = 0.00610344


Motif number 4

TCAATGATTAAAATTAAAGAGCGATGTCCT	1	32	1	AAATTAAAGA	    0.925825	-197
AAGATTTAAGAAAAAACCCACTTTAAAAAT	1	111	1	AAAAAACCCA	    0.930182	-118
ACCCACTTTAAAAATACCTAAAAAATACAG	1	126	1	AAAATACCTA	    0.972108	-103
AAATACCTAAAAAATACAGAGCAACGCCCT	1	137	1	AAAATACAGA	     0.98488	-92
TACTATAGTTAAGTTACATATTGTATAATT	1	174	1	AAGTTACATA	    0.938935	-55
AATTTTCTTAAAATTATACAATATGTAACT	1	185	0	AAATTATACA	    0.925825	-44
          **********

Masking position 6
Map Score:   3.77667

Number of sites scoring better than the average of aligned sites = 164
Number in coding regions = 131
Number in noncoding regions = 33
Number of orfs with sites within 600 bp upstream = 28
Fraction of orfs with sites within 600 bp upstream = 0.00449727


Motif number 5

          **********

No masking
Map Score:   2.86649e-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:   2.86649e-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:   2.86649e-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