AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_ctra.txt -z/home/amcguire/genomes/ctra.fna -icpxR9_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

GATGCAAATCAAGGGGACTACTCTGATGAT	1	27	0	AAGGGGACTA	    0.985767	-112
ACAAAATCTAATGATGCAAATCAAGGGGAC	1	39	0	ATGATGCAAA	    0.971887	-100
TAGATTTTGTATGCTGCATATCTGCTTGTT	1	59	1	ATGCTGCATA	    0.994102	-80
TCTGCTTGTTATGGTGCATAAAATGAAAAA	1	79	1	ATGGTGCATA	    0.997748	-60
ATGAAAAAAAAAGGGGCCTAGACGCCCAGA	1	101	1	AAGGGGCCTA	     0.99335	-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

TTTTAGATTGGAGAATCATCAGAGTAGTCCC	1	13	1	GAGAATCACA	    0.973965	-126
TAGTCCCCTTGATTTGCATCATTAGATTTTG	1	37	1	GATTTGCACA	    0.996069	-102
ATAACAAGCAGATATGCAGCATACAAAATCT	1	60	0	GATATGCACA	     0.99844	-79
TTTTTTTCATTTTATGCACCATAACAAGCAG	1	80	0	TTTATGCACA	    0.984559	-59
          ******** **

Masking position 8
Map Score:   3.54543

Number of sites scoring better than the average of aligned sites = 51
Number in coding regions = 50
Number in noncoding regions = 1
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0


Motif number 3

ATGCAAATCAAGGGGACTACTCTGATGATTCT	1	24	0	AGGGGCTACC	    0.998868	-115
TGAAAAAAAAAGGGGCCTAGACGCCCAGATCG	1	102	1	AGGGGCTAGC	    0.999385	-37
TTCCTTGATAAGCGATCTGGGCGTCTAGGCCC	1	114	0	AGCGACTGGC	    0.996301	-25
          ***** **** *

Masking position 1
Map Score:   1.2221

Number of sites scoring better than the average of aligned sites = 5
Number in coding regions = 5
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

          TTTTTTAGATTGGAGAATCA	1	1	1	TTTTTTAGAT	    0.965982	-138
ATCAGAGTAGTCCCCTTGATTTGCATCATT	1	30	1	TCCCCTTGAT	    0.983374	-109
TAGGCCCCTTTTTTTTTCATTTTATGCACC	1	91	0	TTTTTTTCAT	    0.964034	-48
        CTTTTCCTTGATAAGCGATCTG	1	127	0	TTTCCTTGAT	    0.994216	-12
          **********

Masking position 6
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