AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_ctra.txt -z/home/amcguire/genomes/ctra.fna -igcvA_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	CT283	170	hypothetical protein
#2	lplA_1	264	Lipoate Protein Ligase

Motif number 1

TATTATCAAGTTTTCATGGACAAAGACCGA	1	51	0	TTTTCATGGA	     0.93922	-120
TCTCTTTCTCTCTTCGTAAAGGAATTCTGT	1	119	1	TCTTCGTAAA	    0.753882	-52
TTTTCCTTTTTTTTCTTAAAAGGA      	1	157	1	TTTTCTTAAA	    0.957566	-14
AGTTGCATCATTATCATAAATGTCGTATAT	2	47	0	TTATCATAAA	    0.791338	-218
ATGATGCAACTTTTCGTAAAGGGAAAGGAA	2	66	1	TTTTCGTAAA	    0.848406	-199
ATTAAAGCACTTTTTATAGCAGACTTTTTT	2	103	1	TTTTTATAGC	    0.765015	-162
TATAGCAGACTTTTTTTAAATTTTTAGAAG	2	117	1	TTTTTTTAAA	    0.939908	-148
TTTTTAGAAGCTTTTTTAGAGTCAGGCATT	2	137	1	CTTTTTTAGA	    0.839388	-128
GCATTATTTATTTTATTAGATCACTGTTCT	2	162	1	TTTTATTAGA	    0.890017	-103
ATGTAATATGTTTCCGTGAAATAAACGGGA	2	193	1	TTTCCGTGAA	    0.787518	-72
TCTCTGTCTGTTTATTTAGAATGGTTATAG	2	231	1	TTTATTTAGA	    0.729203	-34
          **********

Masking position 7
Map Score:   7.63107

Number of sites scoring better than the average of aligned sites = 606
Number in coding regions = 606
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

GAGGATCTGTACAGATCCTCCCTCCCTATTA	1	17	0	ACAGATCTCC	    0.989155	-154
GAGGATCTGTACAGATCCTCCCTTCGGTCTT	1	28	1	ACAGATCTCC	    0.989155	-143
AAAACTTGATAATAATCTTACGCAACAAGTA	1	67	1	AATAATTTAC	     0.85642	-104
AAAAAGGAAAACTACTTCTACAGAATTCCTT	1	137	0	ACTACTCTAC	    0.950804	-34
TATATGCTTGAAAAATATTCCACCTTGCCAT	2	21	0	AAAAATTTCC	    0.936059	-244
CATTTATGATAATGATGCAACTTTTCGTAAA	2	55	1	AATGATCAAC	    0.819842	-210
TGACTCTAAAAAAGCTTCTAAAAATTTAAAA	2	130	0	AAAGCTCTAA	    0.816509	-135
TATTTCACGGAAACATATTACATCAGAACAG	2	185	0	AAACATTTAC	    0.836664	-80
CAGACAGAGAACAACTTCTCCCGTTTATTTC	2	210	0	ACAACTCTCC	    0.979352	-55
          ****** ****

Masking position 6
Map Score:   6.17399

Number of sites scoring better than the average of aligned sites = 544
Number in coding regions = 544
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

   CTCTTCTAATAGGGAGGGAGGATCTGT	1	8	1	AATAGGGAGG	    0.979434	-163
GGACAAAGACCGAAGGGAGGATCTGTACAG	1	34	0	CGAAGGGAGG	     0.98389	-137
AATTCCTTTACGAAGAGAGAAAGAGATCCC	1	115	0	CGAAGAGAGA	    0.921705	-56
TTTTAAGAAAAAAAAGGAAAACTACTTCTA	1	148	0	AAAAAGGAAA	    0.851995	-23
CAACTTTTCGTAAAGGGAAAGGAATTGGGA	2	72	1	TAAAGGGAAA	    0.930983	-193
AAGGGAAAGGAATTGGGAGATTAAAGCACT	2	84	1	AATTGGGAGA	    0.945829	-181
TCCGTGAAATAAACGGGAGAAGTTGTTCTC	2	205	1	AAACGGGAGA	    0.983467	-60
          **********

Masking position 8
Map Score:   4.22588

Number of sites scoring better than the average of aligned sites = 290
Number in coding regions = 290
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

TCCTCCCTTCGGTCTTTGTCCATGAAAACT	1	43	1	GGTCTTTGTC	    0.982657	-128
ATTCTAGAGGGATCTCTTTCTCTCTTCGTA	1	107	1	GATCTCTTTC	    0.985368	-64
TATTTTATTAGATCACTGTTCTGATGTAAT	2	170	1	GATCACTGTT	    0.963882	-95
GGGAGAAGTTGTTCTCTGTCTGTTTATTTA	2	219	1	GTTCTCTGTC	     0.99346	-46
          **********

Masking position 7
Map Score:   2.02512

Number of sites scoring better than the average of aligned sites = 19
Number in coding regions = 19
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:   -5.09159e-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 6

          **********

No masking
Map Score:   -5.09159e-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:   -5.09159e-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