AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_ctra.txt -z/home/amcguire/genomes/ctra.fna -icpxR6_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	    0.985528	-112
ACAAAATCTAATGATGCAAATCAAGGGGAC	1	39	0	ATGATGCAAA	    0.971407	-100
TAGATTTTGTATGCTGCATATCTGCTTGTT	1	59	1	ATGCTGCATA	    0.993999	-80
TCTGCTTGTTATGGTGCATAAAATGAAAAA	1	79	1	ATGGTGCATA	     0.99771	-60
ATGAAAAAAAAAGGGGCCTAGACGCCCAGA	1	101	1	AAGGGGCCTA	     0.99337	-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

GGGACTACTCTGATGATTCTCCAATCTAAAA	1	13	0	TGTGATTCTC	    0.970336	-126
CAAAATCTAATGATGCAAATCAAGGGGACTA	1	37	0	TGTGCAAATC	    0.995506	-102
AGATTTTGTATGCTGCATATCTGCTTGTTAT	1	60	1	TGTGCATATC	    0.998217	-79
CTGCTTGTTATGGTGCATAAAATGAAAAAAA	1	80	1	TGTGCATAAA	    0.982381	-59
          ** ********

Masking position 4
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	    0.998877	-115
TGAAAAAAAAAGGGGCCTAGACGCCCAGATCG	1	102	1	AGGGGCTAGC	     0.99939	-37
TTCCTTGATAAGCGATCTGGGCGTCTAGGCCC	1	114	0	AGCGACTGGC	     0.99633	-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

TGATTCTCCAATCTAAAAAA          	1	1	0	ATCTAAAAAA	    0.927229	-138
AATGATGCAAATCAAGGGGACTACTCTGAT	1	30	0	ATCAAGGGGA	    0.974415	-109
GCAGATATGCAGCATACAAAATCTAATGAT	1	54	0	AGCATACAAA	    0.898783	-85
TATGCACCATAACAAGCAGATATGCAGCAT	1	69	0	AACAAGCAGA	     0.96938	-70
GGTGCATAAAATGAAAAAAAAAGGGGCCTA	1	91	1	ATGAAAAAAA	    0.922141	-48
CAGATCGCTTATCAAGGAAAAG        	1	127	1	ATCAAGGAAA	    0.992103	-12
          **********

Masking position 1
Map Score:   2.73741

Number of sites scoring better than the average of aligned sites = 646
Number in coding regions = 646
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