AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i016_Pentose_Phosphate_Shunt_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	xylB	71	xylulokinase
#2	xylA	300	D-xylose isomerase

Motif number 1

      CGGCTAACTGTGCAGTCCGTTGGC	1	5	1	TAACTGTGCA	    0.973091	-67
TCGCTACCGATAACCGGGCCAACGGACTGC	1	22	0	TAACCGGGCC	    0.983327	-50
ATCGGTAGCGATACCGGGCATTTTTTTAAG	1	41	1	ATACCGGGCA	    0.990951	-31
TTTAGCAACTAAACAGGGGAAAACAATTAC	2	16	1	AAACAGGGGA	    0.954981	-285
TGGAATGATGAAACTGGGTAATTCCTCGAA	2	142	0	AAACTGGGTA	    0.979164	-159
TGAAATAACATAATTGAGCAACTGAAAGGG	2	221	1	TAATTGAGCA	    0.907965	-80
TGATGTCGTAATATTGGGCACTCCCTTTCA	2	243	0	ATATTGGGCA	    0.973063	-58
          **********

Masking position 3
Map Score:   7.31118

Number of sites scoring better than the average of aligned sites = 1013
Number in coding regions = 895
Number in noncoding regions = 118
Number of orfs with sites within 600 bp upstream = 119
Fraction of orfs with sites within 600 bp upstream = 0.0191134


Motif number 2

  CGGCTAACTGTGCAGTCCGTTGGCCCGGTTA	1	9	1	TGTGCATGTT	    0.973552	-63
GTAGCGATACCGGGCATTTTTTTAAGGAACGAT	1	45	1	CGGGCATTTT	    0.933543	-27
TTACTTTTGTTGCGCAATTGTACTTATTGCATT	2	103	1	TGCGCATTAC	    0.919718	-198
ATGATGAAACTGGGTAATTCCTCGAAGAGAAAA	2	135	0	TGGGTATCTC	    0.979232	-166
AATTCACAAGTGTGCGCTCGCTCGCAAAATAAA	2	173	0	TGTGCGTCTC	     0.98543	-128
AGCGCACACTTGTGAATTATCTCAATAGCAGTG	2	188	1	TGTGAATCTC	    0.985809	-113
TCAATAGCAGTGTGAAATAACATAATTGAGCAA	2	209	1	TGTGAATCAT	     0.94129	-92
GTCGTAATATTGGGCACTCCCTTTCAGTTGCTC	2	236	0	TGGGCATCTT	    0.994844	-65
          ****** *  ***

Masking position 8
Map Score:   5.88148

Number of sites scoring better than the average of aligned sites = 585
Number in coding regions = 537
Number in noncoding regions = 48
Number of orfs with sites within 600 bp upstream = 48
Fraction of orfs with sites within 600 bp upstream = 0.0077096


Motif number 3

CCGGGCATTTTTTTAAGGAACGATCGAT     	1	54	1	TTTTAGACGA	    0.969748	-18
       CAATTTTTAGCAACTAAACAGGGGAA	2	4	1	TTTTTCACTA	    0.939798	-297
AATTACAGATTTTTATCTTTCGATTACGATTTT	2	40	1	TTTTATTCGA	    0.986198	-261
ACTTATTGCATTTTTCTCTTCGAGGAATTACCC	2	124	1	TTTTTCTCGA	    0.988539	-177
CATCATTCCATTTTATTTTGCGAGCGAGCGCAC	2	162	1	TTTTATTCGA	    0.986188	-139
AATTATGTTATTTCACACTGCTATTGAGATAAT	2	203	0	TTTCACTCTA	    0.952068	-98
          *****  ** ***

Masking position 3
Map Score:   2.88679

Number of sites scoring better than the average of aligned sites = 157
Number in coding regions = 115
Number in noncoding regions = 42
Number of orfs with sites within 600 bp upstream = 50
Fraction of orfs with sites within 600 bp upstream = 0.00803084


Motif number 4

ATGCCCGGTATCGCTACCGATAACCGGGCC	1	32	0	TCGCTACCGA	    0.912348	-40
   CAATTTTTAGCAACTAAACAGGGGAAA	2	8	1	TAGCAACTAA	    0.976776	-293
AAGTACAATTGCGCAACAAAAGTAAGATCT	2	98	0	GCGCAACAAA	    0.982779	-203
TAACATAATTGAGCAACTGAAAGGGAGTGC	2	226	1	GAGCAACTGA	     0.99016	-75
          **********

Masking position 6
Map Score:   0.968942

Number of sites scoring better than the average of aligned sites = 215
Number in coding regions = 200
Number in noncoding regions = 15
Number of orfs with sites within 600 bp upstream = 23
Fraction of orfs with sites within 600 bp upstream = 0.00369419


Motif number 5

GCATTTTTTTAAGGAACGATCGAT      	1	58	1	AAGGAACGAT	    0.981991	-14
AAAAATCGTAATCGAAAGATAAAAATCTGT	2	44	0	ATCGAAAGAT	    0.935481	-257
TTGCGCAACAAAAGTAAGATCTCGGTCATA	2	90	0	AAAGTAAGAT	    0.918497	-211
GCAAAATAAAATGGAATGATGAAACTGGGT	2	153	0	ATGGAATGAT	    0.976289	-148
          **********

Masking position 6
Map Score:   0.393837

Number of sites scoring better than the average of aligned sites = 68
Number in coding regions = 45
Number in noncoding regions = 23
Number of orfs with sites within 600 bp upstream = 23
Fraction of orfs with sites within 600 bp upstream = 0.00369419


Motif number 6

          **********

No masking
Map Score:   4.92707e-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:   4.92707e-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:   4.92707e-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