AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i133_Transmembrane_Transport_7_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	yjcH	88	orf, hypothetical protein
#2	BIME214	34	BIME
#3	acs	300	acetyl-CoA synthetase

Motif number 1

AACGCTCGGGTAACCCTTGCCGAAT       	1	4	0	TACCTTGCCG	    0.950414	-85
AAGGGTTACCCGAGCGTTAACCTTCTCCCATA	1	18	1	CAGCTTAACC	    0.939179	-71
         CCCACAATTGCCCGATGCGAGTC	2	2	1	CACATTGCCC	      0.9874	-33
          AAACCGTTACCGACTCGCATCG	2	23	0	AACCTTACCG	    0.950484	-12
CCCCTATGTGTAACAAATAACCACACTGTGAA	3	12	1	TACAATAACC	    0.896852	-289
TGCTGACCTTCAAAAATTACCCTGCCGTTTAT	3	163	1	CAAATTACCC	    0.940826	-138
AGTATTTGGGCGACAGATCACGCAAAAGTAGA	3	204	0	CACAATCACG	    0.903592	-97
CTAAACAAAACTGCCAATACCCCTACATTTAA	3	234	1	CGCCATACCC	    0.957377	-67
GCCAATACCCCTACATTTAACGCTTATGCCAC	3	246	1	CACATTAACG	     0.98317	-55
          * *** ******

Masking position 8
Map Score:   5.51719

Number of sites scoring better than the average of aligned sites = 1766
Number in coding regions = 1645
Number in noncoding regions = 121
Number of orfs with sites within 600 bp upstream = 119
Fraction of orfs with sites within 600 bp upstream = 0.0191134


Motif number 2

GTGGTATTTTACATGCACTTACAATTGATT	3	54	0	ACATGCACTT	    0.982352	-247
ATGCAGTTATGCATGCTGTTGAAAAAGAGG	3	105	0	GCATGCTGTT	    0.988608	-196
TCTTTGAGGAACATGCAGTTATGCATGCTG	3	117	0	ACATGCAGTT	    0.974597	-184
TCAAAAATTACCCTGCCGTTTATTTGCACA	3	172	1	CCCTGCCGTT	    0.985252	-129
          **********

Masking position 4
Map Score:   2.21941

Number of sites scoring better than the average of aligned sites = 137
Number in coding regions = 122
Number in noncoding regions = 15
Number of orfs with sites within 600 bp upstream = 18
Fraction of orfs with sites within 600 bp upstream = 0.0028911


Motif number 3

CATGTAAAATACCACTTTAGAGTTAGTCAG	3	69	1	ACCACTTTAG	     0.96658	-232
GTCAGTATCTTCCTCTTTTTCAACAGCATG	3	94	1	TCCTCTTTTT	    0.948438	-207
AAAGAATTAATCAACTTTTGTTGCTGACCT	3	142	1	TCAACTTTTG	    0.985439	-159
TTTGCACAATTCTACTTTTGCGTGATCTGT	3	194	1	TCTACTTTTG	    0.985443	-107
          **********

Masking position 6
Map Score:   0.970882

Number of sites scoring better than the average of aligned sites = 122
Number in coding regions = 103
Number in noncoding regions = 19
Number of orfs with sites within 600 bp upstream = 25
Fraction of orfs with sites within 600 bp upstream = 0.00401542


Motif number 4

GCTCGGGTAACCCTTGCCGAAT        	1	3	0	CCCTTGCCGA	    0.943168	-86
AATTCCCGCTCCCTTATGGGAGAAGGTTAA	1	34	0	CCCTTATGGG	    0.811703	-55
ATTAAAACAATCCCTACATTACCTCTGGAG	1	61	1	TCCCTACATT	    0.915861	-28
         GCCCCTATGTGTAACAAATAA	3	2	1	CCCCTATGTG	    0.957766	-299
TTCAAAAATTACCCTGCCGTTTATTTGCAC	3	171	1	ACCCTGCCGT	    0.943221	-130
ACTGCCAATACCCCTACATTTAACGCTTAT	3	243	1	CCCCTACATT	    0.969865	-58
GCTTTTGTTCTCCTTGTAGGATGTTAATAA	3	281	0	TCCTTGTAGG	    0.909102	-20
          **********

Masking position 5
Map Score:   1.51737

Number of sites scoring better than the average of aligned sites = 1495
Number in coding regions = 1305
Number in noncoding regions = 190
Number of orfs with sites within 600 bp upstream = 184
Fraction of orfs with sites within 600 bp upstream = 0.0295535


Motif number 5

          **********

No masking
Map Score:   -7.64954e-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:   -7.64954e-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:   -7.64954e-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