AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i174_Biotin_Biosynthesis_ecoli_reg_300.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	    0.769294	-297
GGAGGACGAGGTCGCACATTATAACGATTTCGTAGC	1	21	0	GCCTTTAACG	    0.933387	-280
GTGCGACCTCGTCCTCCCTGACGCAGTTTTTGCGCT	1	40	1	GCCTGCGCAG	    0.998266	-261
TTGCGCCAATGTCACCTTTTCCGCAGCGCAAAAACT	1	64	0	GCTTTCGCAG	    0.995638	-237
AAACAAAATATACCTTCGTTGCGCCAATGTCACCTT	1	82	0	TCCTTCGCCA	    0.929766	-219
TGTTAGACTTGACGGACATTGTGCAGCGATCTGCTG	1	133	0	GCCTTTGCAG	    0.995638	-168
CGGGACGCCGGTCTATTTTGCCCCAGAGTGTCAATG	1	167	0	GCTTGCCCAG	    0.968989	-134
ATAAATTCCAGCAGGCCGGGACGCCGGTCTATTTTG	1	183	0	GACGGCGCCG	    0.935408	-118
CAGCTGTCGGGGCATACGCTTTACAGACGGCGGTGA	1	230	1	GCCCTTACAG	    0.973383	-71
GTGTGATTGTGACAGGCGTTTCACCGCCGTCTGTAA	1	250	0	GCCTTCACCG	    0.996531	-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

  GCTGCCAATTGCTACGAAATCGTTATAA	1	9	1	TTGCTACGAA	    0.846436	-292
ACCTCGTCCTCCCTGACGCAGTTTTTGCGC	1	45	1	CCCTGACGCA	    0.957339	-256
GTCACCTTTTCCGCAGCGCAAAAACTGCGT	1	60	0	CCGCAGCGCA	    0.986338	-241
AAATATACCTTCGTTGCGCCAATGTCACCT	1	83	0	TCGTTGCGCC	    0.914986	-218
TGCTGCTATCCTCCGGCAAAAAACAAAATA	1	108	0	CTCCGGCAAA	    0.905577	-193
TAGCAGCAGATCGCTGCACAATGTCCGTCA	1	130	1	TCGCTGCACA	    0.969754	-171
CATTGACACTCTGGGGCAAAATAGACCGGC	1	167	1	CTGGGGCAAA	    0.882352	-134
TTCCAGCAGGCCGGGACGCCGGTCTATTTT	1	184	0	CCGGGACGCC	    0.982402	-117
CTGGAATTTATCGCTATGCATACAGCTGTC	1	208	1	TCGCTATGCA	    0.876056	-93
AAAGCGTATGCCCCGACAGCTGTATGCATA	1	222	0	CCCCGACAGC	    0.834501	-79
GCTTTACAGACGGCGGTGAAACGCCTGTCA	1	247	1	CGGCGGTGAA	    0.858286	-54
          **********

Masking position 7
Map Score:   6.41792

Number of sites scoring better than the average of aligned sites = 18755
Number in coding regions = 17884
Number in noncoding regions = 871
Number of orfs with sites within 600 bp upstream = 632
Fraction of orfs with sites within 600 bp upstream = 0.10151


Motif number 3

          **********

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 4

          **********

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 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