AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i174_Biotin_Biosynthesis_ecoli_reg_100.orf -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.5 -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 =  	0.5
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	accB	300	acetylCoA carboxylase, BCCP subunit; carrier of biotin

Motif number 1

       GCTGCCAATTGCTACGAAATCGTTATAAT	1	4	1	GCTCTCGAAA	    0.745295	-297
GGAGGACGAGGTCGCACATTATAACGATTTCGTAGC	1	21	0	GCCTTTAACG	    0.924788	-280
GTGCGACCTCGTCCTCCCTGACGCAGTTTTTGCGCT	1	40	1	GCCTGCGCAG	    0.998025	-261
TTGCGCCAATGTCACCTTTTCCGCAGCGCAAAAACT	1	64	0	GCTTTCGCAG	    0.995033	-237
AAACAAAATATACCTTCGTTGCGCCAATGTCACCTT	1	82	0	TCCTTCGCCA	     0.92074	-219
TGTTAGACTTGACGGACATTGTGCAGCGATCTGCTG	1	133	0	GCCTTTGCAG	    0.995033	-168
CGGGACGCCGGTCTATTTTGCCCCAGAGTGTCAATG	1	167	0	GCTTGCCCAG	    0.964812	-134
ATAAATTCCAGCAGGCCGGGACGCCGGTCTATTTTG	1	183	0	GACGGCGCCG	     0.92705	-118
CAGCTGTCGGGGCATACGCTTTACAGACGGCGGTGA	1	230	1	GCCCTTACAG	     0.96978	-71
GTGTGATTGTGACAGGCGTTTCACCGCCGTCTGTAA	1	250	0	GCCTTCACCG	    0.996049	-51
          * *   * ** *****

Masking position 3
Map Score:   10.4015

Number of sites scoring better than the average of aligned sites = 4498
Number in coding regions = 4292
Number in noncoding regions = 206
Number of orfs with sites within 600 bp upstream = 190
Fraction of orfs with sites within 600 bp upstream = 0.0305172


Motif number 2

AGCGCAAAAACTGCGTCAGGGAGGACGAGG	1	46	0	CTGCGTCAGG	    0.968048	-255
GACGCAGTTTTTGCGCTGCGGAAAAGGTGA	1	59	1	TTGCGCTGCG	    0.975226	-242
AAGGTGACATTGGCGCAACGAAGGTATATT	1	82	1	TGGCGCAACG	     0.98735	-219
TTGACGGACATTGTGCAGCGATCTGCTGCT	1	131	0	TTGTGCAGCG	    0.987501	-170
CAAAATAGACCGGCGTCCCGGCCTGCTGGA	1	183	1	CGGCGTCCCG	     0.95053	-118
CGACAGCTGTATGCATAGCGATAAATTCCA	1	209	0	ATGCATAGCG	    0.858632	-92
TCACCGCCGTCTGTAAAGCGTATGCCCCGA	1	236	0	CTGTAAAGCG	    0.941373	-65
TTACAGACGGCGGTGAAACGCCTGTCACAA	1	250	1	CGGTGAAACG	    0.961477	-51
TTTAGTGTGATTGTGACAGGCGTTTCACCG	1	260	0	TTGTGACAGG	    0.906737	-41
          **********

Masking position 3
Map Score:   8.09511

Number of sites scoring better than the average of aligned sites = 7658
Number in coding regions = 7284
Number in noncoding regions = 374
Number of orfs with sites within 600 bp upstream = 339
Fraction of orfs with sites within 600 bp upstream = 0.0544491


Motif number 3

CAATGTCACCTTTTCCGCAGCGCAAAAACT	1	64	0	TTTTCCGCAG	    0.991432	-237
AAAAGGTGACATTGGCGCAACGAAGGTATA	1	80	1	ATTGGCGCAA	    0.954734	-221
TATTTTGTTTTTTGCCGGAGGATAGCAGCA	1	108	1	TTTGCCGGAG	    0.992819	-193
TTGCCGGAGGATAGCAGCAGATCGCTGCAC	1	119	1	ATAGCAGCAG	    0.980526	-182
GCCGGTCTATTTTGCCCCAGAGTGTCAATG	1	167	0	TTTGCCCCAG	    0.992787	-134
ATAGCGATAAATTCCAGCAGGCCGGGACGC	1	195	0	ATTCCAGCAG	    0.983039	-106
          **********

Masking position 2
Map Score:   7.53108

Number of sites scoring better than the average of aligned sites = 1876
Number in coding regions = 1762
Number in noncoding regions = 114
Number of orfs with sites within 600 bp upstream = 116
Fraction of orfs with sites within 600 bp upstream = 0.0186315


Motif number 4

ATTATAACGATTTCGTAGCAATTGGCAGC 	1	10	0	TTTCGTAGCA	    0.980686	-291
ATGTCACCTTTTCCGCAGCGCAAAAACTGC	1	62	0	TTCCGCAGCG	    0.981725	-239
CAAAATATACCTTCGTTGCGCCAATGTCAC	1	85	0	CTTCGTTGCG	    0.969833	-216
TTTGCCGGAGGATAGCAGCAGATCGCTGCA	1	118	1	GATAGCAGCA	    0.959441	-183
GATAGCAGCAGATCGCTGCACAATGTCCGT	1	128	1	GATCGCTGCA	     0.98852	-173
          **********

Masking position 5
Map Score:   2.10758

Number of sites scoring better than the average of aligned sites = 1180
Number in coding regions = 1109
Number in noncoding regions = 71
Number of orfs with sites within 600 bp upstream = 73
Fraction of orfs with sites within 600 bp upstream = 0.011725


Motif number 5

          **********

No masking
Map Score:   7.91135e-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:   7.91135e-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:   7.91135e-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