AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_ctra.txt -z/home/amcguire/genomes/ctra.fna -icpxR6_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

         TGAGTAATCAAAGTTGATTGAAG	1	2	1	GAGAATAAAG	    0.974503	-68
GAAGTAAAAAGAATAATAAAAGATAAGGAGGA	1	30	1	GAAAATAAAG	    0.992014	-40
AGATAAGGAGGAAAAATTAAAGGGTTATTT  	1	50	1	GAAAATAAAG	    0.992014	-20
TTAGATTGGAGAATCATCAGAGTAGTCCCCTT	2	15	1	GAACATAGAG	     0.99532	-124
CCCTTGATTTGCATCATTAGATTTTGTATGCT	2	42	1	GCACATAGAT	    0.980085	-97
AAGCAGATATGCAGCATACAAAATCTAATGAT	2	54	0	GCACATCAAA	     0.96989	-85
TTCATTTTATGCACCATAACAAGCAGATATGC	2	74	0	GCACATACAA	    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

TATCTTTTATTATTCTTTTTACTTCAATCA	1	25	0	TATTCTTTTT	    0.915894	-45
CTTTAATTTTTCCTCCTTATCTTTTATTAT	1	42	0	TCCTCCTTAT	    0.950668	-28
ATCAGAGTAGTCCCCTTGATTTGCATCATT	2	30	1	TCCCCTTGAT	    0.990107	-109
ATGCTGCATATCTGCTTGTTATGGTGCATA	2	69	1	TCTGCTTGTT	    0.975761	-70
GCCCCTTTTTTTTTCATTTTATGCACCATA	2	88	0	TTTTCATTTT	    0.825704	-51
GGGCGTCTAGGCCCCTTTTTTTTTCATTTT	2	98	0	GCCCCTTTTT	    0.970764	-41
        CTTTTCCTTGATAAGCGATCTG	2	127	0	TTTCCTTGAT	    0.965521	-12
          **********

Masking position 7
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

AAAGTTGATTGAAGTAAAAAGAATAATAAA	1	20	1	GAAGTAAAAA	    0.925617	-50
TAAAAGATAAGGAGGAAAAATTAAAGGGTT	1	46	1	GGAGGAAAAA	     0.96614	-24
AAAATCTAATGATGCAAATCAAGGGGACTA	2	37	0	GATGCAAATC	    0.978986	-102
GATTTTGTATGCTGCATATCTGCTTGTTAT	2	61	1	GCTGCATATC	    0.968703	-78
TGCTTGTTATGGTGCATAAAATGAAAAAAA	2	81	1	GGTGCATAAA	    0.987093	-58
          **********

Masking position 6
Map Score:   1.5864

Number of sites scoring better than the average of aligned sites = 213
Number in coding regions = 212
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 4

AATCATCAGAGTAGTCCCCTTGATTTGCAT	2	26	1	GTAGTCCCCT	    0.997378	-113
ATCTGGGCGTCTAGGCCCCTTTTTTTTTCA	2	102	0	CTAGGCCCCT	    0.996603	-37
          **********

Masking position 3
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