AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i009_Nucleotide_Biosynthes_hinf_reg_300.orf -a/home/amcguire/alignace/lib/ORF_hinf.txt -z/skink1/amcguire/genomes/hinf.fna -g0.38 -x5 
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 =  	0.38
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	HI0899_HI0900	100	HI0899: dihydrofolate reductase (folA), HI0900: glutamate 5-kinase (gamma-glutamyl kinase) (proB)
#2	HI0901	80	conserved hypothetical protein

Motif number 1

TCCAAGTTCTTAAAATTGGCATTAACGTTA	1	18	1	TAAAATTGGC	    0.994712	-83
 AAATCCCCCTAAAATTTGCCGTTACTATA	1	82	0	TAAAATTTGC	    0.979969	-19
ATTTTTCCTATAAAAATAGCTCAAGATTGT	2	45	0	TAAAAATAGC	    0.984498	-36
CGTTTTACCTTAAATTTTTCCTATAAAAAT	2	58	0	TAAATTTTTC	    0.889859	-23
          **********

Masking position 4
Map Score:   5.35697

Number of sites scoring better than the average of aligned sites = 170
Number in coding regions = 140
Number in noncoding regions = 30
Number of orfs with sites within 600 bp upstream = 37
Fraction of orfs with sites within 600 bp upstream = 0.00594282


Motif number 2

AGTGATAACGTTAATGCCAATTTTAAGAACT	1	22	0	TAATGCCAAT	    0.945247	-79
TATCACTAAATCAATGAAAAATCACTTAATA	1	46	1	TAATGAAAAA	    0.987885	-55
TCAGGTATAGTAACGGCAAATTTTAGGGGGA	1	77	1	TACGGCAAAT	    0.964481	-24
AAAGCACTGATTTATGAAACAATCTTGAGCT	2	27	1	TTATGAAACA	      0.9369	-54
GAGCTATTTTTATAGGAAAAATTTAAGGTAA	2	53	1	TTAGGAAAAA	    0.985388	-28
TAGGAAAAATTTAAGGTAAAACGATA     	2	65	1	TAAGGTAAAA	    0.980673	-16
          * *********

Masking position 9
Map Score:   3.69346

Number of sites scoring better than the average of aligned sites = 681
Number in coding regions = 543
Number in noncoding regions = 138
Number of orfs with sites within 600 bp upstream = 129
Fraction of orfs with sites within 600 bp upstream = 0.0207196


Motif number 3

CATTAACGTTATCACTAAATCAATGAAAAA	1	37	1	ATCACTAAAT	    0.991353	-64
TCAATGAAAAATCACTTAATATCAGGTATA	1	56	1	ATCACTTAAT	    0.988039	-45
GGTTGATAAAAGCACTGATTTATGAAACAA	2	19	1	AGCACTGATT	    0.988283	-62
          **********

Masking position 4
Map Score:   1.98042

Number of sites scoring better than the average of aligned sites = 53
Number in coding regions = 43
Number in noncoding regions = 10
Number of orfs with sites within 600 bp upstream = 10
Fraction of orfs with sites within 600 bp upstream = 0.00160617


Motif number 4

          **********

No masking
Map Score:   -3.95472e-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:   -3.95472e-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:   -3.95472e-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