AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i164_NIF1_hpyl_reg_100.orf -o164_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	RHP01169	173	AE000511
#2	RHP01170	21	AE000511

Motif number 1

GAACACCCCCCTATCAAAAACCAACAACAG	1	26	0	CTATCAAAAA	    0.933322	-148
GTGTTCGCATTTCTCAAAATGTTTTCAAAA	1	50	1	TTCTCAAAAT	    0.975771	-124
TCTCAAAATGTTTTCAAAAATTCATCTTAT	1	61	1	TTTTCAAAAA	    0.936913	-113
TTTCTTAATTTTAACTTAAAATAAGATGAA	1	81	0	TTAACTTAAA	    0.889412	-93
ATACAAGATATTTTCTTAATTTTAACTTAA	1	92	0	TTTTCTTAAT	    0.940388	-82
ATCTTGTATTTAATCATAATTTAGACTTAG	1	113	1	TAATCATAAT	    0.876281	-61
ATAGATTTTCTTATCTAAGTCTAAATTATG	1	127	0	TTATCTAAGT	    0.925832	-47
CCTCAAAAATTTTACATAGATTTTCTTATC	1	142	0	TTTACATAGA	    0.849729	-32
GTTAATATTCTCCTCAAAAATTTTACATAG	1	153	0	TCCTCAAAAA	     0.92892	-21
          **********

Masking position 8
Map Score:   8.6418

Number of sites scoring better than the average of aligned sites = 2067
Number in coding regions = 1774
Number in noncoding regions = 293
Number of orfs with sites within 600 bp upstream = 219
Fraction of orfs with sites within 600 bp upstream = 0.0351751


Motif number 2

TGTTTTCAAAAATTCATCTTATTTTAAGTT	1	69	1	AATTCATCTT	    0.865804	-105
TATTTTCTTAATTTTAACTTAAAATAAGAT	1	84	0	ATTTTAACTT	    0.957455	-90
TAAATACAAGATATTTTCTTAATTTTAACT	1	95	0	ATATTTTCTT	    0.924358	-79
AATATCTTGTATTTAATCATAATTTAGACT	1	110	1	ATTTAATCAT	    0.940924	-64
TTTAATCATAATTTAGACTTAGATAAGAAA	1	121	1	ATTTAGACTT	    0.882388	-53
TTTTACATAGATTTTCTTATCTAAGTCTAA	1	133	0	ATTTTCTTAT	    0.816874	-41
TCTCCTCAAAAATTTTACATAGATTTTCTT	1	145	0	AATTTTACAT	    0.841229	-29
     GGTTAATATTCTCCTCAAAAATTTT	1	159	0	ATATTCTCCT	    0.895829	-15
          **********

Masking position 1
Map Score:   2.92593

Number of sites scoring better than the average of aligned sites = 1596
Number in coding regions = 1373
Number in noncoding regions = 223
Number of orfs with sites within 600 bp upstream = 195
Fraction of orfs with sites within 600 bp upstream = 0.0313203


Motif number 3

     GCGACTTGGTAGCGGCTGTTGTTGG	1	6	1	TTGGTAGCGG	    0.996931	-168
TTGTTGGTTTTTGATAGGGGGGTGTTCGCA	1	29	1	TTGATAGGGG	    0.996622	-145
          **********

Masking position 5
Map Score:   0.111329

Number of sites scoring better than the average of aligned sites = 12
Number in coding regions = 11
Number in noncoding regions = 1
Number of orfs with sites within 600 bp upstream = 1
Fraction of orfs with sites within 600 bp upstream = 0.000160617


Motif number 4

          **********

No masking
Map Score:   2.37484e-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:   2.37484e-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:   2.37484e-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