AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i009_Nucleotide_Biosynthes_hinf_reg_100.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

TAACGTTAATGCCAATTTTAAGAACTTGGA	1	18	0	GCCAATTTTA	    0.994585	-83
TATAGTAACGGCAAATTTTAGGGGGATTT 	1	82	1	GCAAATTTTA	    0.980504	-19
ACAATCTTGAGCTATTTTTATAGGAAAAAT	2	45	1	GCTATTTTTA	    0.983864	-36
ATTTTTATAGGAAAAATTTAAGGTAAAACG	2	58	1	GAAAAATTTA	    0.891312	-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

CGTTATCACTAAATCAATGAAAAATCACTT	1	43	1	AAATCAATGA	    0.992399	-58
AATCAATGAAAAATCACTTAATATCAGGTA	1	54	1	AAATCACTTA	    0.990617	-47
TTGGTTGATAAAAGCACTGATTTATGAAAC	2	17	1	AAAGCACTGA	    0.996253	-64
          **********

Masking position 6
Map Score:   3.3789

Number of sites scoring better than the average of aligned sites = 17
Number in coding regions = 14
Number in noncoding regions = 3
Number of orfs with sites within 600 bp upstream = 1
Fraction of orfs with sites within 600 bp upstream = 0.000160617


Motif number 3

GTTAATGCCAATTTTAAGAACTTGGAAAGG	1	14	0	ATTTTAAGAA	    0.955072	-87
AAATCACTTAATATCAGGTATAGTAACGGC	1	64	1	ATATCAGGTA	    0.953154	-37
GTAACGGCAAATTTTAGGGGGATTT     	1	86	1	ATTTTAGGGG	     0.97738	-15
TTGAGCTATTTTTATAGGAAAAATTTAAGG	2	51	1	TTTATAGGAA	    0.913096	-30
TATAGGAAAAATTTAAGGTAAAACGATA  	2	63	1	ATTTAAGGTA	    0.978339	-18
          **********

Masking position 6
Map Score:   1.39467

Number of sites scoring better than the average of aligned sites = 396
Number in coding regions = 299
Number in noncoding regions = 97
Number of orfs with sites within 600 bp upstream = 105
Fraction of orfs with sites within 600 bp upstream = 0.0168648


Motif number 4

TTTTCATTGATTTAGTGATAACGTTAATGCC	1	35	0	TTTGTGATAA	    0.981966	-66
    TGTCCTTTGGTTGATAAAAGCACTGAT	2	7	1	TTGTTGATAA	    0.994519	-74
TAGCTCAAGATTGTTTCATAAATCAGTGCTT	2	28	0	TTGTTCATAA	    0.980189	-53
          *** *******

Masking position 8
Map Score:   0.391317

Number of sites scoring better than the average of aligned sites = 50
Number in coding regions = 43
Number in noncoding regions = 7
Number of orfs with sites within 600 bp upstream = 6
Fraction of orfs with sites within 600 bp upstream = 0.000963701


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


Motif number 7

          **********

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