AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i211_transcription_translation_hpyl_reg_300.orf -o211_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

Purged sequences:
RHP01464	263	AE000511

Input sequences:
#1	RHP01465	263	AE000511

Motif number 1

GAAATCTCTTTTTGTTAAAAGGAAATTTA    	1	7	0	TTTTTAAAAA	    0.977819	-257
TTGTTGCAATTAAGATAAAAATACAAAAAGCTA	1	44	1	TAAATAAAAA	    0.961254	-220
AAGCTAAAGCATTCTTAAAAAATTAGTGTAACC	1	71	1	ATTTTAAAAT	    0.898521	-193
AAAATTTGACTTTGTTAAAAAAATTATGATAGC	1	162	0	TTTTTAAAAA	    0.923925	-102
CACTCTAAAGTTAAATAAAATTTGACTTTGTTA	1	178	0	TTAATAAAAT	    0.904097	-86
TAAGTCATAATAAATTAAAACCACTCTAAAGTT	1	199	0	TAATTAAAAA	    0.985903	-65
TTTTAAATTTAAACTTAAAATTATAGCATAAGT	1	227	0	AAATTAAAAA	    0.944789	-37
TTTTAAGTTTAAATTTAAAAATAAAGGATACTT	1	240	1	AAATTAAAAA	    0.710353	-24
          *** ******  *

Masking position 7
Map Score:   10.4491

Number of sites scoring better than the average of aligned sites = 413
Number in coding regions = 273
Number in noncoding regions = 140
Number of orfs with sites within 600 bp upstream = 122
Fraction of orfs with sites within 600 bp upstream = 0.0195952


Motif number 2

TTTCCTTTTAACAAAAAGAGATTTCTAGTTTG	1	15	1	ACAAAGAGAT	    0.886004	-249
TCTTAATTGCAACAAACTAGAAATCTCTTTTT	1	27	0	AAAAATAGAA	    0.950018	-237
AGATAAAAATACAAAAAGCTAAAGCATTCTTA	1	56	1	ACAAAGCTAA	    0.969083	-208
AATTAGTGTAACCAAAAGATGCTAATAAGTGG	1	91	1	ACAAAGATGC	    0.947935	-173
GCAAAGAATTACGAAATTCAACACTTGTGGCA	1	127	0	ACAAATCAAC	    0.948259	-137
GACTTTGTTAAAAAAATTATGATAGCATAGCA	1	156	0	AAAAATATGA	    0.918062	-108
TAATTTTTTTAACAAAGTCAAATTTTATTTAA	1	169	1	AAAAATCAAA	     0.93558	-95
CATAAGTCATAATAAATTAAAACCACTCTAAA	1	202	0	AAAAATAAAA	    0.946257	-62
TAAATTTAAAAATAAAGGATACTTG       	1	249	1	AAAAAGATAC	    0.966591	-15
          ** *** *****

Masking position 6
Map Score:   7.94686

Number of sites scoring better than the average of aligned sites = 699
Number in coding regions = 577
Number in noncoding regions = 122
Number of orfs with sites within 600 bp upstream = 108
Fraction of orfs with sites within 600 bp upstream = 0.0173466


Motif number 3

 TAAATTTCCTTTTAACAAAAAGAGATTTC	1	10	1	TTTTAACAAA	    0.949769	-254
ATTTTTATCTTAATTGCAACAAACTAGAAA	1	36	0	TAATTGCAAC	    0.890621	-228
ATGGGCCACTTATTAGCATCTTTTGGTTAC	1	98	0	TATTAGCATC	    0.970586	-166
AAAAAAATTATGATAGCATAGCAAAGAATT	1	149	0	TGATAGCATA	    0.970983	-115
ATCATAATTTTTTTAACAAAGTCAAATTTT	1	165	1	TTTTAACAAA	    0.949769	-99
AAACTTAAAATTATAGCATAAGTCATAATA	1	220	0	TTATAGCATA	    0.982765	-44
          **********

Masking position 4
Map Score:   4.73416

Number of sites scoring better than the average of aligned sites = 184
Number in coding regions = 127
Number in noncoding regions = 57
Number of orfs with sites within 600 bp upstream = 68
Fraction of orfs with sites within 600 bp upstream = 0.0109219


Motif number 4

          **********

No masking
Map Score:   -2.81785e-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:   -2.81785e-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:   -2.81785e-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