AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i230_clp_protease_ecoli_hinf_reg_300.orf -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.46 -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 =  	0.46
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	yljA	300	orf, hypothetical protein
#2	clpA	30	ATP-binding component of serine protease

Motif number 1

TGAACAGCCCCCTCTCTGACCCCGGTTTATTCCATC	1	23	0	CCTCCGACGT	     0.94898	-278
CTGTTCAAAACCTCGCCAACTCTAGAAATACAATTT	1	52	1	CCTCCAACGA	    0.996976	-249
GCTTGACGGCTCGCCCTAATTCTCTAAATTGTATTT	1	77	0	TCGCCAACTA	    0.923396	-224
CCCCTTGTCCCCTGTCAAATGCTTGACGGCTCGCCC	1	97	0	CCTGCAACGA	    0.997609	-204
CTGTCACATTCCTGTCAATAGCGTTAACTGCTTCAA	1	151	0	CCTGCATCTA	     0.99413	-150
AGCTTATTTGCCTGACCAATCTACTCCACATGATAG	1	220	0	CCTGCAATTC	    0.944363	-81
GGCAGAACGCCCTGCCGCTGACAAGAGCTTATTTGC	1	245	0	CCTGCCTCGA	    0.992004	-56
GGCAGGGCGTTCTGCCGATAACCGTAACCGAAGATG	1	265	1	TCTGCATCTA	    0.971016	-36
     AGGCACCTCCCCCAATTTTTATGCCTGCAT 	2	10	0	CCTCCCATTA	    0.966904	-21
          **** * **  *  **

Masking position 6
Map Score:   10.5644

Number of sites scoring better than the average of aligned sites = 611
Number in coding regions = 550
Number in noncoding regions = 61
Number of orfs with sites within 600 bp upstream = 65
Fraction of orfs with sites within 600 bp upstream = 0.0104401


Motif number 2

GTCAAATGCTTGACGGCTCGCCCTAATTCTC	1	89	0	TGACGGTCGC	    0.969853	-212
GTCAAGCATTTGACAGGGGACAAGGGGCAGG	1	106	1	TGACAGGGAC	    0.955959	-195
TTAACGCTATTGACAGGAATGTGACAGATGT	1	160	1	TGACAGAATG	    0.932275	-141
GACAGGAATGTGACAGATGTCGCTGATGCCA	1	171	1	TGACAGTGTC	    0.995861	-130
CAACGATAGATGATAGTTATCTATCATGTGG	1	200	1	TGATAGTATC	    0.974125	-101
TCATCTTCGGTTACGGTTATCGGCAGAACGC	1	271	0	TTACGGTATC	    0.962026	-30
          TGTCAGTTATCATCTTCGGTT	1	290	0	TGTCAGTATC	    0.983675	-11
          ****** ****

Masking position 1
Map Score:   5.5705

Number of sites scoring better than the average of aligned sites = 654
Number in coding regions = 580
Number in noncoding regions = 74
Number of orfs with sites within 600 bp upstream = 78
Fraction of orfs with sites within 600 bp upstream = 0.0125281


Motif number 3

TGGCATCAGCGACATCTGTCACATTCCTGT	1	172	0	GACATCTGTC	    0.701545	-129
CCACATGATAGATAACTATCATCTATCGTT	1	201	0	GATAACTATC	    0.804015	-100
GCGTTCTGCCGATAACCGTAACCGAAGATG	1	271	1	GATAACCGTA	    0.975357	-30
AACCGAAGATGATAACTGACA         	1	290	1	GATAACTGAC	    0.978912	-11
          **********

Masking position 4
Map Score:   2.01439

Number of sites scoring better than the average of aligned sites = 225
Number in coding regions = 206
Number in noncoding regions = 19
Number of orfs with sites within 600 bp upstream = 20
Fraction of orfs with sites within 600 bp upstream = 0.00321234


Motif number 4

ATACAAGTAAGATGGAATAAACCGGGGTCA	1	13	1	GATGGAATAA	    0.910519	-288
GGGACAAGGGGCAGGTATGAATCAAAAATT	1	122	1	GCAGGTATGA	    0.977452	-179
ATCATCTATCGTTGGCATCAGCGACATCTG	1	184	0	GTTGGCATCA	    0.971404	-117
ACGCCCTGCCGCTGACAAGAGCTTATTTGC	1	245	0	GCTGACAAGA	    0.935282	-56
        ATGCAGGCATAAAAATTGGGGG	2	3	1	GCAGGCATAA	    0.990961	-28
          **********

Masking position 7
Map Score:   1.11815

Number of sites scoring better than the average of aligned sites = 1511
Number in coding regions = 1385
Number in noncoding regions = 126
Number of orfs with sites within 600 bp upstream = 126
Fraction of orfs with sites within 600 bp upstream = 0.0202377


Motif number 5

GCCCCCTCTCTGACCCCGGTTTATTCCATC	1	23	0	TGACCCCGGT	    0.994334	-278
GGTTTTGAACAGCCCCCTCTCTGACCCCGG	1	34	0	AGCCCCCTCT	    0.989554	-267
ACCTGCCCCTTGTCCCCTGTCAAATGCTTG	1	108	0	TGTCCCCTGT	    0.994142	-193
CTTATTTGCCTGACCAATCTACTCCACATG	1	224	0	TGACCAATCT	     0.94984	-77
          **********

Masking position 10
Map Score:   1.50798

Number of sites scoring better than the average of aligned sites = 66
Number in coding regions = 53
Number in noncoding regions = 13
Number of orfs with sites within 600 bp upstream = 14
Fraction of orfs with sites within 600 bp upstream = 0.00224863


Motif number 6

          **********

No masking
Map Score:   4.64285e-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:   4.64285e-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:   4.64285e-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