AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -icynR_hpyl_opreg_300.orf -g0.389 -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 =  	0.389
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	HP0004	121	carbonic anhydrase (icfA)

Motif number 1

ATTTTACACTTTAAAGGGCTTTC        	1	3	0	TTAAAGGCTT	      0.9953	-119
TTCTTTTTGTTATAATGGCGTTATTTTACAC	1	25	0	TATAAGGCGT	    0.932949	-97
CTTATCATAGCTAAAATTCTTGCATTTCTTT	1	50	0	CTAAATTCTT	    0.969504	-72
TCGTTTGTTTTTAAAACGCTTATCATAGCTA	1	68	0	TTAAACGCTT	      0.9953	-54
CTCATTTTGATTAAAATTCGTTTGTTTTTAA	1	85	0	TTAAATTCGT	    0.989462	-37
TCTTTAACCCTTAAATCTCATTTTGATTAAA	1	101	0	TTAAACTCAT	    0.981576	-21
          ***** *****

Masking position 5
Map Score:   7.92489

Number of sites scoring better than the average of aligned sites = 629
Number in coding regions = 532
Number in noncoding regions = 97
Number of orfs with sites within 600 bp upstream = 76
Fraction of orfs with sites within 600 bp upstream = 0.0122069


Motif number 2

GAAAGCCCTTTAAAGTGTAAAATAACGCCA	1	11	1	TAAAGTGTAA	    0.953514	-111
GCCATTATAACAAAAAGAAATGCAAGAATT	1	37	1	CAAAAAGAAA	    0.992757	-85
ATAAGCGTTTTAAAAACAAACGAATTTTAA	1	76	1	TAAAAACAAA	    0.970631	-46
GAATTTTAATCAAAATGAGATTTAAGGGTT	1	97	1	CAAAATGAGA	     0.98771	-25
          **********

Masking position 4
Map Score:   2.1824

Number of sites scoring better than the average of aligned sites = 311
Number in coding regions = 257
Number in noncoding regions = 54
Number of orfs with sites within 600 bp upstream = 48
Fraction of orfs with sites within 600 bp upstream = 0.0077096


Motif number 3

          **********

No masking
Map Score:   -1.46782e-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 4

          **********

No masking
Map Score:   -1.46782e-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:   -1.46782e-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