AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00272_ctra_reg_300.orf -o00272_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	CT389	181	hypothetical protein
#2	aspC	89	Aspartate Aminotransferase
#3	greA	113	Transcription Elongation Factor G
#4	tyrB	187	Aromatic AA Aminotransferase
#5	cysS	254	Cysteinyl tRNA Synthetase

Motif number 1

GCATACTCATTCTGGATTTCATTGCCTCCT	1	49	1	TCTGGATTTC	    0.909779	-133
CTCCTAAAAATCTTGTTTTTTCTCTACTTC	1	125	1	TCTTGTTTTT	    0.978828	-57
GAGAGTCTCATCTTTATATTACCGTCCACC	2	49	1	TCTTTATATT	    0.767166	-41
AAAATCTCGATCTTTTATTTAATAATAAAA	3	15	1	TCTTTTATTT	     0.86266	-99
ATAAAATTTTTCTTGTTTTTTGTGATGTAA	3	39	1	TCTTGTTTTT	    0.978828	-75
GTAATATTGCTCTTTTTTGTTATTCGGCGT	3	65	1	TCTTTTTTGT	    0.903002	-49
CTGCTTACTGTCTTTTTTTCCAGTAAGATG	4	143	0	TCTTTTTTTC	    0.981671	-45
TTCGATGGTGTCGTTATTTCTAACGAACAA	5	28	0	TCGTTATTTC	    0.841037	-227
AGAGGGGTTCTCTGGGTTTTCGATGGTGTC	5	46	0	TCTGGGTTTT	    0.909482	-209
TCGTGTATATTCTTTTTTTCATTAAAAGCA	5	101	1	TCTTTTTTTC	    0.981671	-154
AAGAGTAGAATCTTTGTTTGCTTTTAATGA	5	119	0	TCTTTGTTTG	     0.89598	-136
          **********

Masking position 1
Map Score:   11.4928

Number of sites scoring better than the average of aligned sites = 232
Number in coding regions = 232
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

ACAATTAACTAACCAACAAGCATACTCATT	1	30	1	AACCAACAAG	    0.966554	-152
GGAAGTAGAGAAAAAACAAGATTTTTAGGA	1	126	0	AAAAAACAAG	    0.969699	-56
ATTACATCACAAAAAACAAGAAAAATTTTA	3	40	0	AAAAAACAAG	    0.969699	-74
TACGCCGAATAACAAAAAAGAGCAATATTA	3	66	0	AACAAAAAAG	      0.9561	-48
TATATTTCCGGACTAAAAAGGGGAGCCATC	3	94	1	GACTAAAAAG	    0.788559	-20
ACACGATTTAGGACAACAAGCTGTCATCTT	4	119	1	GGACAACAAG	    0.941841	-69
TCATCTTACTGGAAAAAAAGACAGTAAGCA	4	142	1	GGAAAAAAAG	    0.924268	-46
CGTTATTTCTAACGAACAAGTAAGGAGTAG	5	17	0	AACGAACAAG	     0.94013	-238
TTGCTTTTAATGAAAAAAAGAATATACACG	5	102	0	TGAAAAAAAG	    0.754406	-153
TTTCATTAAAAGCAAACAAAGATTCTACTC	5	117	1	AGCAAACAAA	     0.82849	-138
          **********

Masking position 5
Map Score:   10.3841

Number of sites scoring better than the average of aligned sites = 215
Number in coding regions = 214
Number in noncoding regions = 1
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 3

CACTCGAGCGCTCTTCTCCTAAAAATCTTGTT	1	110	1	CTCTCTCCTA	    0.995401	-72
CTTGTTTTTTCTCTACTTCCGAGTTATAACGC	1	136	1	CTCTCTTCCA	     0.97639	-46
     GATGGCTCCCCTTTTTAGTCCGGAAAT	3	97	0	CTCCCTTTTA	    0.890629	-17
CTCTATAGCGCACTGCTGCTTACTGTCTTTTT	4	156	0	CACTCTGCTA	    0.911526	-32
      GAATTCCTACTCCTTACTTGTTCGTT	5	5	1	TCCTCTCCTA	    0.960213	-250
ACCCAGAGAACCCCTCTCCCAAAGCAGCTTTT	5	59	1	CCCCCTCCCA	    0.966979	-196
CAAACAAAGATTCTACTCTTGAAAACGACATA	5	129	1	TTCTCTCTTA	     0.89353	-126
AACGACATAGCTATGCTTCTGATTTTGGAATA	5	152	1	CTATCTTCTA	    0.904283	-103
GATAAGCAACCTTTTCTCCTTAGTCTATAGAA	5	233	0	CTTTCTCCTA	    0.960269	-22
          **** ***** *

Masking position 7
Map Score:   6.80238

Number of sites scoring better than the average of aligned sites = 285
Number in coding regions = 285
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

TTTAGGAGAAGAGCGCTCGAGTGTCGGCTT	1	103	0	GAGCGCTCGA	    0.986242	-79
 CTTTTCTCAGTGCTCTCTAAAAATTACGC	2	10	1	GTGCTCTCTA	    0.989077	-80
AATGCCATTGTTGCGCTCTACCAACTGAGC	4	53	1	TTGCGCTCTA	    0.978484	-135
GTAAGCAGCAGTGCGCTATAGAGAGGTTTT	4	165	1	GTGCGCTATA	    0.989077	-23
          **********

Masking position 7
Map Score:   2.76786

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 5

          **********

No masking
Map Score:   1.38088e-12

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:   1.38088e-12

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:   1.38088e-12

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