AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i039_Mannose_Metabolism_hpyl_reg_100.orf -o039_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	RHP00999	126	AE000511
#2	RHP01003	62	AE000511
#3	RHP01004	69	AE000511
#4	RHP00655	101	AE000511

Motif number 1

TCCCATAATAACAAAAAAAATTCTCATTAA	1	23	0	ACAAAAAAAA	    0.962677	-104
TACTGGTGCAACCAAAAAACACAAGTCCCA	1	48	0	ACCAAAAAAC	    0.980265	-79
AAGGTGCATGAGATGAAAAAAAGCCCTTGC	1	77	1	AGATGAAAAA	    0.956063	-50
TCAAACAAGGCCCTAAAAATTACGAAGAAA	2	29	1	CCCTAAAAAT	    0.893277	-34
CTAAAAATTACGAAGAAAACCTGATTTTCC	2	41	1	CGAAGAAAAC	    0.955897	-22
GCTATAATAACCCTAAAAAACAAAAGAGAG	3	34	1	CCCTAAAAAA	    0.971369	-36
AGAGAGCCTGACAAGAAAACGC        	3	58	1	ACAAGAAAAC	    0.970192	-12
GCTAATCGTTAGCTGAAAAAATAAAAATTA	4	23	0	AGCTGAAAAA	    0.977144	-79
GCTAACGATTAGCAAAAACATGGTTTAATT	4	40	1	AGCAAAAACA	    0.905291	-62
          **********

Masking position 6
Map Score:   10.9684

Number of sites scoring better than the average of aligned sites = 1016
Number in coding regions = 904
Number in noncoding regions = 112
Number of orfs with sites within 600 bp upstream = 76
Fraction of orfs with sites within 600 bp upstream = 0.0122069


Motif number 2

AATAACAAAAAAAATTCTCATTAAATTCCTA	1	16	0	AAAATCTCAT	    0.937066	-111
ACCAAAAAACACAAGTCCCATAATAACAAAA	1	37	0	ACAATCCCAT	    0.985055	-90
ATGAGATGAAAAAAAGCCCTTGCACATTGTT	1	84	1	AAAAGCCCTT	    0.991987	-43
CCCCTTTCAAACAAGGCCCTAAAAATTACGA	2	23	1	ACAAGCCCTA	    0.991381	-40
      CTCAAAAATCCCCAATTAAAAACGC	3	5	1	AAAACCCCAA	    0.972402	-65
TCCCCAATTAAAAACGCTATAATAACCCTAA	3	19	1	AAAAGCTATA	     0.87638	-51
CTAGCAAATGACAAAGCCAATTAAACCATGT	4	57	0	ACAAGCCAAT	    0.981555	-45
          **** ******

Masking position 4
Map Score:   7.80721

Number of sites scoring better than the average of aligned sites = 1064
Number in coding regions = 955
Number in noncoding regions = 109
Number of orfs with sites within 600 bp upstream = 85
Fraction of orfs with sites within 600 bp upstream = 0.0136524


Motif number 3

 GCGAGATTTAACCTGTTTTCATAACAATGTG	1	106	0	AACCTGTTTA	    0.994805	-21
TTACGAAGAAAACCTGATTTTCCCC       	2	48	1	AACCTGTTTC	    0.988539	-15
TGAAAAAATAAAAATTATTTTAACATTTC   	4	8	0	AAAATTTTTA	    0.904579	-94
GATTAGCAAAAACATGGTTTAATTGGCTTTGT	4	46	1	AACATGTTTA	    0.988369	-56
 CAGACTCTCAAACTCCTTTAATTACTAGCAA	4	81	0	AAACTCTTTA	    0.969419	-21
          ****** *** *

Masking position 5
Map Score:   2.58613

Number of sites scoring better than the average of aligned sites = 141
Number in coding regions = 114
Number in noncoding regions = 27
Number of orfs with sites within 600 bp upstream = 29
Fraction of orfs with sites within 600 bp upstream = 0.00465789


Motif number 4

AATTTTTTTTGTTATTATGGGACTTGTGTT	1	31	1	GTTATTATGG	    0.986002	-96
CTTGCACATTGTTATGAAAACAGGTTAAAT	1	102	1	GTTATGAAAA	    0.889711	-25
GTTTTTTAGGGTTATTATAGCGTTTTTAAT	3	25	0	GTTATTATAG	    0.984889	-45
GCTCTCTTTTGTTTTTTAGGGTTATTATAG	3	35	0	GTTTTTTAGG	    0.903111	-35
TCATTTGCTAGTAATTAAAGGAGTTTGAGA	4	77	1	GTAATTAAAG	    0.965969	-25
          **********

Masking position 5
Map Score:   1.66562

Number of sites scoring better than the average of aligned sites = 254
Number in coding regions = 219
Number in noncoding regions = 35
Number of orfs with sites within 600 bp upstream = 29
Fraction of orfs with sites within 600 bp upstream = 0.00465789


Motif number 5

AAAAAAAATTCTCATTAAATTCCTATTTAT	1	11	0	CTCATTAAAT	    0.877306	-116
TTTTTTTCATCTCATGCACCTTACTGGTGC	1	69	0	CTCATGCACC	    0.954706	-58
TGAAAAAAAGCCCTTGCACATTGTTATGAA	1	90	1	CCCTTGCACA	    0.968721	-37
CTCGCATCACCCCTTTCAAACAAGGCCCTA	2	14	1	CCCTTTCAAA	     0.97829	-49
TCAAAAATCCCCAATTAAAAACGCTATAAT	3	12	1	CCAATTAAAA	    0.947553	-58
AATGACAAAGCCAATTAAACCATGTTTTTG	4	52	0	CCAATTAAAC	    0.951228	-50
          **********

Masking position 5
Map Score:   1.30211

Number of sites scoring better than the average of aligned sites = 784
Number in coding regions = 702
Number in noncoding regions = 82
Number of orfs with sites within 600 bp upstream = 74
Fraction of orfs with sites within 600 bp upstream = 0.0118856


Motif number 6

          **********

No masking
Map Score:   -3.59945e-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:   -3.59945e-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 8

          **********

No masking
Map Score:   -3.59945e-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