AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i270_hypothetical15_hpyl_reg_300.orf -o270_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	RHP01332	22	AE000511
#2	RHP01335	28	AE000511
#3	RHP01336	120	AE000511
#4	RHP01340	80	AE000511

Motif number 1

          AGAATAGCCATAAAGAAGAATT 	1	1	1	AAATACCTAA	    0.990931	-22
ATTTTCTTTAAAAAAACCGCTAATTGTTAGTTT	3	23	1	AAAAACGTAA	     0.99672	-98
TTTTTGGCTTACAAAATCGTTTAAAAACTAACA	3	47	0	AAAAACGTTA	    0.986837	-74
TAAAATAAATATAAAATCCTTAAGGGTATTGTA	3	84	0	AAAAACCTAA	    0.997629	-37
CTTTAATAAAAGAAAAACCTTAAAAGGGAGCAA	4	17	0	AAAAACCTAA	     0.99774	-64
ATTTTATTTTTAAAAAGCTATAATACAACTTTA	4	45	0	TAAAACTTAA	    0.964429	-36
          * **** ** ***

Masking position 6
Map Score:   11.7696

Number of sites scoring better than the average of aligned sites = 177
Number in coding regions = 149
Number in noncoding regions = 28
Number of orfs with sites within 600 bp upstream = 24
Fraction of orfs with sites within 600 bp upstream = 0.0038548


Motif number 2

      AGAATAGCCATAAAGAAGAATT   	1	5	1	TGCCATAAAG	    0.774882	-18
GCCATTCTCATGCTTTTAAAATCACTCT   	2	8	0	TCTTTTAAAA	    0.966413	-21
CAATTAGCGGTTTTTTTAAAGAAAATTTTCA	3	18	0	TTTTTTAAAG	    0.982127	-103
CGCTAATTGTTAGTTTTTAAACGATTTTGTA	3	40	1	TGTTTTTAAA	    0.897231	-81
GGGTATTGTATCCTTTTTTGGCTTACAAAAT	3	63	0	TCTTTTTTGG	    0.876194	-58
AAGGATACAATACCCTTAAGGATTTTATATT	3	79	1	TCCCTTAAGG	    0.931771	-42
GATTTTATATTTATTTTATAGTAAGGCAGTC	3	99	1	TATTTTATAG	    0.898635	-22
GCTTTTTTGCTCCCTTTTAAGGTTTTTCTTT	4	11	1	TCCTTTTAAG	    0.966661	-70
AAGGTTTTTCTTTTATTAAAGTTGTATTATA	4	29	1	TTTATTAAAG	     0.93268	-52
TTTATTAAAGTTGTATTATAGCTTTTTAAAA	4	40	1	TGTATTATAG	    0.917405	-41
CCTTATATTTTATTTTTAAAAAGCTATAATA	4	53	0	TTTTTTAAAA	    0.932587	-28
          * *********

Masking position 7
Map Score:   10.7073

Number of sites scoring better than the average of aligned sites = 2580
Number in coding regions = 2176
Number in noncoding regions = 404
Number of orfs with sites within 600 bp upstream = 283
Fraction of orfs with sites within 600 bp upstream = 0.0454545


Motif number 3

GAATAGCCATAAAGAAGAATT          	1	12	1	AAAGAAAATT	    0.987944	-11
CGGTTTTTTTAAAGAAAATTTTCAAAATGTG	3	11	0	AAAGAAATTT	    0.974266	-110
ATCGTTTAAAAACTAACAATTAGCGGTTTTT	3	34	0	AACTAAAATT	    0.950546	-87
CCTTACTATAAAATAAATATAAAATCCTTAA	3	94	0	AAATAATATA	    0.799386	-27
AACTTTAATAAAAGAAAAACCTTAAAAGGGA	4	21	0	AAAGAAAACC	    0.944316	-60
AGCTTTTTAAAAATAAAATATAAGGATCGTT	4	59	1	AAATAAATAT	    0.893448	-22
          ****** ****

Masking position 6
Map Score:   1.70298

Number of sites scoring better than the average of aligned sites = 627
Number in coding regions = 539
Number in noncoding regions = 88
Number of orfs with sites within 600 bp upstream = 78
Fraction of orfs with sites within 600 bp upstream = 0.0125281


Motif number 4

          **********

No masking
Map Score:   4.07441e-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:   4.07441e-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:   4.07441e-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