AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00562_ctra_reg_300.orf -o00562_ctra_300.ace -a/home/amcguire/genomes/ORF_ctra.txt -z/home/amcguire/genomes/ctra.fna -g0.41 -x5 -e 
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 =  	0.41
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	valS	126	Valyl tRNA Synthetase
#2	atpK	41	ATP Synthase Subunit K
#3	CT309	166	hypothetical protein
#4	atpE	108	ATP Synthase Subunit E

Motif number 1

GGTTGATGTGCGTTTTTTTGAAAAAAATAG	2	19	1	CGTTTTTTTG	    0.995335	-23
GCAAACTCGGAGTTTTTTTGTATGCGTTGA	3	81	1	AGTTTTTTTG	    0.976125	-86
TGATTTTAAACGTTGTTATGATCTAACCTT	4	24	1	CGTTGTTATG	    0.985914	-85
CATAATTGATCGTTTTTTTAAGATAAACGT	4	69	1	CGTTTTTTTA	    0.981719	-40
TTAAGATAAACGTTGTTTTTCTTGGTATCA	4	86	1	CGTTGTTTTT	    0.983042	-23
          **********

Masking position 6
Map Score:   7.77573

Number of sites scoring better than the average of aligned sites = 39
Number in coding regions = 39
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

ATCATAATCAAGCTCTAAAGGCAATATGTTCT	1	26	1	AGCTCTAGGC	    0.996288	-101
TCGTACTTATAGCTCAATCGGTTAATTAGAGA	1	72	1	AGCTCACGGT	    0.919826	-55
TAACCAACATAGCCCCTTAAGCCAAAGATCCT	3	11	0	AGCCCCAAGC	    0.987757	-156
TGACGATGGAAGCTCCGCAAACTCGGAGTTTT	3	65	1	AGCTCCAAAC	     0.98306	-102
CTCTCTAGACAGCTCTCCAGAGATAGTTCTTC	3	116	0	AGCTCTAGAG	     0.97463	-51
TCAACTAAGAAACTCTCTAGACAGCTCTCCAG	3	128	0	AACTCTAGAC	    0.946092	-39
TGATCCGGTTAGCCCCTAAGGTTAGATCATAA	4	39	0	AGCCCCAGGT	    0.990026	-70
          ******  ****

Masking position 1
Map Score:   6.06995

Number of sites scoring better than the average of aligned sites = 126
Number in coding regions = 126
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

        GGCACCTCTTGCTTGATCATAAT	1	3	1	CACCTCTGCT	    0.991595	-124
CCGTTAAAGTCACCTCGTACTTATAGCTCAA	1	58	1	CACCTCTACT	    0.996196	-69
ACTATTCTCGCATCTCTAATTAACCGATTGA	1	85	0	CATCTCAATT	    0.921229	-42
CAAAAAAACGCACATCAACCTTCTGGAT   	2	8	0	CACATCACCT	    0.971474	-34
ACGATGGAAGCTCCGCAAACTCGGAGTTTTT	3	67	1	CTCCGCAACT	    0.977818	-100
TCCGCTCTTACACCTTCAACTAAGAAACTCT	3	144	0	CACCTTAACT	    0.986945	-23
          ****** ****

Masking position 11
Map Score:   4.55583

Number of sites scoring better than the average of aligned sites = 95
Number in coding regions = 95
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

        GGCACCTCTTGCTTGATCATAA	1	3	1	CACCTCTTGC	    0.916708	-124
GCAATATGTTCTCCGTTAAAGTCACCTCGT	1	46	1	CTCCGTTAAA	     0.83138	-81
CCGTTAAAGTCACCTCGTACTTATAGCTCA	1	58	1	CACCTCGTAC	    0.950731	-69
ACTATTCTCGCATCTCTAATTAACCGATTG	1	86	0	CATCTCTAAT	    0.767056	-41
GCGGAGCTTCCATCGTCAACGAATTTTCCC	3	53	0	CATCGTCAAC	    0.934362	-114
ACGATGGAAGCTCCGCAAACTCGGAGTTTT	3	67	1	CTCCGCAAAC	     0.93732	-100
CTTCTTTTCTCAACGCATACAAAAAAACTC	3	90	0	CAACGCATAC	    0.954603	-77
TCCGCTCTTACACCTTCAACTAAGAAACTC	3	145	0	CACCTTCAAC	    0.957024	-22
TAGATCATAACAACGTTTAAAATCAAATAC	4	19	0	CAACGTTTAA	    0.873947	-90
CCAAGAAAAACAACGTTTATCTTAAAAAAA	4	81	0	CAACGTTTAT	    0.873947	-28
          **********

Masking position 4
Map Score:   5.21909

Number of sites scoring better than the average of aligned sites = 300
Number in coding regions = 300
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

   AGGATCTTTGGCTTAAGGGGCTATGTT	3	8	1	TTGGCTTAAG	    0.954924	-159
AGGGGCTATGTTGGTTAAATCGTTATTGGG	3	26	1	TTGGTTAAAT	    0.941276	-141
TAAATCGTTATTGGGAAAATTCGTTGACGA	3	41	1	TTGGGAAAAT	    0.972623	-126
TTTGTATGCGTTGAGAAAAGAAGAACTATC	3	97	1	TTGAGAAAAG	     0.93879	-70
GTTGTTTTTCTTGGTATCAGAT        	4	97	1	TTGGTATCAG	    0.940729	-12
          **********

Masking position 2
Map Score:   0.0904302

Number of sites scoring better than the average of aligned sites = 182
Number in coding regions = 182
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:   -5.51791e-13

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:   -5.51791e-13

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 8

          **********

No masking
Map Score:   -5.51791e-13

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