AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i295_mixed10_hpyl_reg_300.orf -o295_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	RHP01336	120	AE000511
#2	RHP01340	80	AE000511

Motif number 1

TTTTTTAAAGAAAATTTTCAAAATGTG      	1	5	0	AAAATCAAAA	    0.963067	-116
TTGGCTTACAAAATCGTTTAAAAACTAACAATT	1	44	0	AAATTTAAAA	    0.983922	-77
TTGTAAGCCAAAAAAGGATACAATACCCTTAAG	1	66	1	AAAAATACAA	    0.982931	-55
GCCTTACTATAAAATAAATATAAAATCCTTAAG	1	93	0	AAAAATATAA	    0.985614	-28
TTAATAAAAGAAAAACCTTAAAAGGGAGCAAAA	2	15	0	AAAATTAAAA	    0.989917	-66
GCTATAATACAACTTTAATAAAAGAAAAACCTT	2	29	0	AACTATAAAA	    0.963066	-52
TTTATTTTTAAAAAGCTATAATACAACTTTAAT	2	43	0	AAAAATAATA	    0.965781	-38
AGCTTTTTAAAAATAAAATATAAGGATCGTTA 	2	59	1	AAATATATAA	    0.976879	-22
          ****   ******

Masking position 10
Map Score:   11.6546

Number of sites scoring better than the average of aligned sites = 712
Number in coding regions = 529
Number in noncoding regions = 183
Number of orfs with sites within 600 bp upstream = 160
Fraction of orfs with sites within 600 bp upstream = 0.0256987


Motif number 2

TTTTCTTTAAAAAAACCGCTAATTGTTAGT	1	24	1	AAAAACCGCT	    0.959181	-97
TTTTGGCTTACAAAATCGTTTAAAAACTAA	1	49	0	CAAAATCGTT	     0.98922	-72
AAAAAGGATACAATACCCTTAAGGATTTTA	1	76	1	CAATACCCTT	    0.984372	-45
AAAATAAATATAAAATCCTTAAGGGTATTG	1	86	0	TAAAATCCTT	    0.980023	-35
TTTAATAAAAGAAAAACCTTAAAAGGGAGC	2	19	0	GAAAAACCTT	    0.976351	-62
          **********

Masking position 5
Map Score:   3.8386

Number of sites scoring better than the average of aligned sites = 654
Number in coding regions = 574
Number in noncoding regions = 80
Number of orfs with sites within 600 bp upstream = 71
Fraction of orfs with sites within 600 bp upstream = 0.0114038


Motif number 3

CATTTTGAAAATTTTCTTTAAAAAAACCGCTA	1	13	1	ATTTTTTTAA	    0.951126	-108
AACCGCTAATTGTTAGTTTTTAAACGATTTTG	1	37	1	TGTTATTTTA	    0.926579	-84
AGGATTTTATATTTATTTTATAGTAAGGCAGT	1	97	1	ATTTATTTTA	    0.989223	-24
TTTTTCTTTTATTAAAGTTGTATTATAGCTTT	2	33	1	ATTAAGTTTA	    0.926001	-48
CGATCCTTATATTTTATTTTTAAAAAGCTATA	2	56	0	ATTTTTTTTA	    0.984692	-25
          ***** *** **

Masking position 8
Map Score:   1.07471

Number of sites scoring better than the average of aligned sites = 292
Number in coding regions = 213
Number in noncoding regions = 79
Number of orfs with sites within 600 bp upstream = 79
Fraction of orfs with sites within 600 bp upstream = 0.0126887


Motif number 4

          **********

No masking
Map Score:   1.65857e-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:   1.65857e-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:   1.65857e-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