AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i033_Pyruvate_Synthase_1_hpyl_reg_100.orf -o033_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	RHP00025	184	AE000511

Motif number 1

    GATTAAGGTAAATGGGGCGTTTTTTCTTTT	1	7	1	GTAAATGGCT	    0.980133	-178
TTTTGAATTGAGTAAAAAGTGTTTAGTATCTTCT	1	37	1	ATAAAATGTT	    0.978183	-148
TTTTTAATAAATTCTAAAATGCTTTAATAGTAGG	1	88	0	ATCTAATGCT	    0.963106	-97
TTTAGAATTTATTAAAAAAGGCTTGCTACAATTT	1	104	1	ATAAAAGGCT	    0.995866	-81
AGCCCTAGCAATCAAAATTTGCCTAAAATTGTAG	1	129	0	ACAAAATGCT	    0.983869	-56
TCTCCTTTGTGCTAAAAGCTGCATTTAAAGCCCT	1	157	0	GTAAAATGCT	     0.99587	-28
          * *****  *** *

Masking position 6
Map Score:   5.6821

Number of sites scoring better than the average of aligned sites = 330
Number in coding regions = 286
Number in noncoding regions = 44
Number of orfs with sites within 600 bp upstream = 47
Fraction of orfs with sites within 600 bp upstream = 0.00754899


Motif number 2

TTTTTACTCAATTCAAAAGAAAAAACGCCCCA	1	23	0	ATTAAAAGAA	    0.928654	-162
ATAGTAGGAACTTAAAATTAAAATGAGAAGAT	1	64	0	CTTAAATTAA	    0.885337	-121
TTCTAAAATGCTTTAATAGTAGGAACTTAAAA	1	79	0	CTTAATAGAG	    0.891485	-106
CAAAATTTGCCTAAAATTGTAGCAAGCCTTTT	1	119	0	CTAAATTGAG	    0.519787	-66
ATTGCTAGGGCTTTAAATGCAGCTTTTAGCAC	1	151	1	CTTAAATGAG	    0.967611	-34
          *** ***** **

Masking position 6
Map Score:   2.76495

Number of sites scoring better than the average of aligned sites = 208
Number in coding regions = 181
Number in noncoding regions = 27
Number of orfs with sites within 600 bp upstream = 25
Fraction of orfs with sites within 600 bp upstream = 0.00401542


Motif number 3

AAACACTTTTTACTCAATTCAAAAGAAAAA	1	31	0	TACTCAATTC	    0.990798	-154
AATGAGAAGATACTAAACACTTTTTACTCA	1	45	0	TACTAAACAC	    0.984679	-140
AAGCCTTTTTTAATAAATTCTAAAATGCTT	1	98	0	TAATAAATTC	    0.976809	-87
          **********

Masking position 6
Map Score:   0.733262

Number of sites scoring better than the average of aligned sites = 22
Number in coding regions = 19
Number in noncoding regions = 3
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 4

          **********

No masking
Map Score:   2.227e-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:   2.227e-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:   2.227e-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