AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i270_hypothetical15_hpyl_reg_100.orf -o270_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	RHP01332	22	AE000511
#2	RHP01335	28	AE000511
#3	RHP01336	120	AE000511

Motif number 1

ATTCTCATGCTTTTAAAATCACTCT     	2	6	0	TTTTAAAATC	    0.991278	-23
TAAAGAAAATTTTCAAAATGTG        	3	3	0	TTTCAAAATG	    0.959918	-118
TGAAAATTTTCTTTAAAAAAACCGCTAATT	3	18	1	CTTTAAAAAA	    0.927073	-103
TTACAAAATCGTTTAAAAACTAACAATTAG	3	42	0	GTTTAAAAAC	    0.919717	-79
CTTTTTTGGCTTACAAAATCGTTTAAAAAC	3	52	0	TTACAAAATC	    0.984816	-69
TATAAAATAAATATAAAATCCTTAAGGGTA	3	89	0	ATATAAAATC	    0.974452	-32
GACTGCCTTACTATAAAATAAATATAAAAT	3	100	0	CTATAAAATA	    0.972297	-21
          **********

Masking position 5
Map Score:   10.2965

Number of sites scoring better than the average of aligned sites = 1207
Number in coding regions = 1016
Number in noncoding regions = 191
Number of orfs with sites within 600 bp upstream = 142
Fraction of orfs with sites within 600 bp upstream = 0.0228076


Motif number 2

         AATTCTTCTTTATGGCTATTC	1	12	0	ATTCTTCTTT	    0.990686	-11
ACATTTTGAAAATTTTCTTTAAAAAAACCG	3	12	1	AATTTTCTTT	    0.953329	-109
AAAACCGCTAATTGTTAGTTTTTAAACGAT	3	35	1	ATTGTTAGTT	    0.943805	-86
AGGGTATTGTATCCTTTTTTGGCTTACAAA	3	65	0	ATCCTTTTTT	    0.958143	-56
TAAGGATTTTATATTTATTTTATAGTAAGG	3	95	1	ATATTTATTT	    0.945261	-26
          **********

Masking position 5
Map Score:   2.14575

Number of sites scoring better than the average of aligned sites = 512
Number in coding regions = 439
Number in noncoding regions = 73
Number of orfs with sites within 600 bp upstream = 63
Fraction of orfs with sites within 600 bp upstream = 0.0101189


Motif number 3

 AATTCTTCTTTATGGCTATTCT        	1	3	0	TTAGGCTATT	     0.99157	-20
AAACTAACAATTAGCGGTTTTTTTAAAGAAA	3	25	0	TTACGGTTTT	      0.9953	-96
TGTTAGTTTTTAAACGATTTTGTAAGCCAAA	3	47	1	TAACGATTTT	    0.967473	-74
TATAAAATCCTTAAGGGTATTGTATCCTTTT	3	77	0	TTAGGGTATT	    0.995347	-44
          *** *******

Masking position 8
Map Score:   2.99483

Number of sites scoring better than the average of aligned sites = 127
Number in coding regions = 111
Number in noncoding regions = 16
Number of orfs with sites within 600 bp upstream = 14
Fraction of orfs with sites within 600 bp upstream = 0.00224863


Motif number 4

          **********

No masking
Map Score:   6.63809e-14

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:   6.63809e-14

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:   6.63809e-14

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