AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_ctra.txt -z/home/amcguire/genomes/ctra.fna -icpxR_ctra_opreg_300.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	sucC	69	Succinyl-CoA Synthetase, Beta
#2	htrA	138	DO Serine Protease

Motif number 1

CTTCAATCAACTTTGATTACTCA         	1	2	0	CTTTATTCTC	    0.974503	-68
TCCTCCTTATCTTTTATTATTCTTTTTACTTC	1	30	0	CTTTATTTTC	    0.992014	-40
  AAATAACCCTTTAATTTTTCCTCCTTATCT	1	50	0	CTTTATTTTC	    0.992014	-20
AAGGGGACTACTCTGATGATTCTCCAATCTAA	2	15	0	CTCTATGTTC	     0.99532	-124
AGCATACAAAATCTAATGATGCAAATCAAGGG	2	42	0	ATCTATGTGC	    0.980085	-97
ATCATTAGATTTTGTATGCTGCATATCTGCTT	2	54	1	TTTGATGTGC	     0.96989	-85
GCATATCTGCTTGTTATGGTGCATAAAATGAA	2	74	1	TTGTATGTGC	    0.979236	-65
          **** *** ***

Masking position 6
Map Score:   9.11361

Number of sites scoring better than the average of aligned sites = 94
Number in coding regions = 94
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

TGATTGAAGTAAAAAGAATAATAAAAGATA	1	25	1	AAAAAGAATA	     0.91067	-45
ATAATAAAAGATAAGGAGGAAAAATTAAAG	1	42	1	ATAAGGAGGA	     0.94748	-28
AATGATGCAAATCAAGGGGACTACTCTGAT	2	30	0	ATCAAGGGGA	    0.989439	-109
TATGCACCATAACAAGCAGATATGCAGCAT	2	69	0	AACAAGCAGA	     0.97415	-70
TATGGTGCATAAAATGAAAAAAAAAGGGGC	2	88	1	AAAATGAAAA	    0.816004	-51
AAAATGAAAAAAAAAGGGGCCTAGACGCCC	2	98	1	AAAAAGGGGC	    0.968832	-41
CAGATCGCTTATCAAGGAAAAG        	2	127	1	ATCAAGGAAA	    0.963255	-12
          **********

Masking position 4
Map Score:   4.50967

Number of sites scoring better than the average of aligned sites = 617
Number in coding regions = 615
Number in noncoding regions = 2
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 3

CAAAGTTGATTGAAGTAAAAAGAATAATAA	1	19	1	TGAAGTAAAA	    0.915165	-51
CAAAATCTAATGATGCAAATCAAGGGGACT	2	38	0	TGATGCAAAT	    0.987506	-101
AGATTTTGTATGCTGCATATCTGCTTGTTA	2	60	1	TGCTGCATAT	    0.985797	-79
CTGCTTGTTATGGTGCATAAAATGAAAAAA	2	80	1	TGGTGCATAA	    0.946275	-59
          **********

Masking position 7
Map Score:   2.48857

Number of sites scoring better than the average of aligned sites = 51
Number in coding regions = 51
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

ATGCAAATCAAGGGGACTACTCTGATGATT	2	26	0	AGGGGACTAC	    0.997589	-113
TGAAAAAAAAAGGGGCCTAGACGCCCAGAT	2	102	1	AGGGGCCTAG	    0.996581	-37
          **********

Masking position 8
Map Score:   0.355481

Number of sites scoring better than the average of aligned sites = 2
Number in coding regions = 2
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:   -2.59896e-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:   -2.59896e-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:   -2.59896e-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