AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i334_1_hpyl_reg_100.orf -o334_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	RHP01036	123	AE000511
#2	RHP01319	182	AE000511

Motif number 1

GAAGTTGAAAACGCCACAAAA          	1	1	0	ACCCACAAAA	    0.964298	-123
ACTTAAAAAGAAGCCCAATAATAAAAACCCA	1	46	0	AACCCAATAA	    0.892084	-78
AAAAAACGCAAAACTTAAAAAGAAGCCCAAT	1	58	0	AACTTAAAAA	    0.950815	-66
AAAATACAACAATCTAAAAAACGCAAAACTT	1	73	0	AACTAAAAAA	    0.981414	-51
   GCGAGACTACCTATAAAAAGATGTGAAT	1	106	0	TACTATAAAA	    0.950999	-18
GAGCGTTTTTAATCCTAAAAAGCTGTGTTAT	2	40	0	AACCTAAAAA	    0.974346	-143
AGGATTAAAAACGCTCAAAAATAGTCTCTTT	2	55	1	ACCTCAAAAA	    0.955137	-128
ATTTACCATAAAACCATAAAATTAAATAAAT	2	96	0	AACCATAAAA	    0.988264	-87
CCATTAAATTTACCAATAAAAGTGTAGGAAT	2	145	0	TACAATAAAA	    0.855048	-38
CAAACTCCTTTCTCCATTAAATTTACCAATA	2	158	0	TCCCATTAAA	    0.792535	-25
          ** ********

Masking position 10
Map Score:   11.6576

Number of sites scoring better than the average of aligned sites = 1926
Number in coding regions = 1628
Number in noncoding regions = 298
Number of orfs with sites within 600 bp upstream = 199
Fraction of orfs with sites within 600 bp upstream = 0.0319627


Motif number 2

CCATTACTGAGCTTAAAGAAGTTGAAAACGC	1	18	0	GTTAAAGAAG	    0.981694	-106
AAAAAGATGTGAATAAAAAATACAACAATCT	1	89	0	GATAAAAAAT	    0.949164	-35
ATAGCGGGTTGGATAACACAGCTTTTTAGGA	2	28	1	GATAACACAG	    0.952107	-155
AGCTTTTTAGGATTAAAAACGCTCAAAAATA	2	47	1	GTTAAAAACG	    0.959435	-136
AATAAATATGGTAGAAAAAAGAGACTATTTT	2	72	0	GAGAAAAAAG	    0.990105	-111
TAAATTTAATGGAGAAAGGAGTTTGGAAT  	2	164	1	GAGAAAGGAG	    0.973937	-19
          * *********

Masking position 6
Map Score:   2.67414

Number of sites scoring better than the average of aligned sites = 652
Number in coding regions = 607
Number in noncoding regions = 45
Number of orfs with sites within 600 bp upstream = 37
Fraction of orfs with sites within 600 bp upstream = 0.00594282


Motif number 3

AAAAATACAACAATCTAAAAAACGCAAAAC	1	75	0	CAATCTAAAA	    0.899137	-49
    GCGAGACTACCTATAAAAAGATGTGA	1	108	0	CTACCTATAA	    0.888097	-16
CAACCCGCTATAAACAAAAAGGTTTGTC  	2	9	0	TAAACAAAAA	    0.907172	-174
TGAGCGTTTTTAATCCTAAAAAGCTGTGTT	2	42	0	TAATCCTAAA	    0.828819	-141
TTTCAAAAATTTACCATAAAACCATAAAAT	2	105	0	TTACCATAAA	    0.956434	-78
TTATAACAATTTTTCAAAAATTTACCATAA	2	116	0	TTTTCAAAAA	    0.859079	-67
TCCATTAAATTTACCAATAAAAGTGTAGGA	2	147	0	TTACCAATAA	    0.955075	-36
          **********

Masking position 9
Map Score:   1.61017

Number of sites scoring better than the average of aligned sites = 929
Number in coding regions = 741
Number in noncoding regions = 188
Number of orfs with sites within 600 bp upstream = 164
Fraction of orfs with sites within 600 bp upstream = 0.0263412


Motif number 4

          **********

No masking
Map Score:   6.63809e-14

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:   6.63809e-14

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:   6.63809e-14

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