AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_ctra.txt -z/home/amcguire/genomes/ctra.fna -icpxR_ctra_opreg_100.orf -g0.413 -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 =  	0.413
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	htrA	138	DO Serine Protease

Motif number 1

ATCATCAGAGTAGTCCCCTTGATTTGCATC	1	27	1	TAGTCCCCTT	    0.984126	-112
GTCCCCTTGATTTGCATCATTAGATTTTGT	1	39	1	TTTGCATCAT	    0.968594	-100
AACAAGCAGATATGCAGCATACAAAATCTA	1	59	0	TATGCAGCAT	    0.993393	-80
TTTTTCATTTTATGCACCATAACAAGCAGA	1	79	0	TATGCACCAT	    0.997486	-60
TCTGGGCGTCTAGGCCCCTTTTTTTTTCAT	1	101	0	TAGGCCCCTT	    0.993446	-38
          **********

Masking position 1
Map Score:   8.75277

Number of sites scoring better than the average of aligned sites = 43
Number in coding regions = 43
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 2

TTTAGATTGGAGAATCATCAGAGTAGTCCCCT	1	14	1	AGAACATAGA	    0.986708	-125
CCCCTTGATTTGCATCATTAGATTTTGTATGC	1	41	1	TGCACATAGA	    0.998636	-98
CAAGCAGATATGCAGCATACAAAATCTAATGA	1	55	0	TGCACATCAA	    0.993797	-84
TTTCATTTTATGCACCATAACAAGCAGATATG	1	75	0	TGCACATACA	    0.997499	-64
          **** *** ***

Masking position 7
Map Score:   4.26123

Number of sites scoring better than the average of aligned sites = 16
Number in coding regions = 16
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 3

TGATGCAAATCAAGGGGACTACTCTGATGA	1	28	0	CAAGGGGACT	    0.998319	-111
AATGAAAAAAAAAGGGGCCTAGACGCCCAG	1	100	1	AAAGGGGCCT	    0.998311	-39
          **********

Masking position 3
Map Score:   1.16254

Number of sites scoring better than the average of aligned sites = 7
Number in coding regions = 7
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

TGATTCTCCAATCTAAAAAA          	1	1	0	ATCTAAAAAA	     0.96432	-138
AATGATGCAAATCAAGGGGACTACTCTGAT	1	30	0	ATCAAGGGGA	    0.982544	-109
GGTGCATAAAATGAAAAAAAAAGGGGCCTA	1	91	1	ATGAAAAAAA	    0.962275	-48
CAGATCGCTTATCAAGGAAAAG        	1	127	1	ATCAAGGAAA	    0.993923	-12
          **********

Masking position 5
Map Score:   1.96755

Number of sites scoring better than the average of aligned sites = 155
Number in coding regions = 155
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:   -9.70439e-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:   -9.70439e-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 7

          **********

No masking
Map Score:   -9.70439e-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