AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i218_ecoli_mtub_300.orf -o218_ecoli_mtub_300.ace -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.58 -x5 -e 
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 =  	0.58
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	rpmB	216	50S ribosomal subunit protein L28
#2	radC	93	DNA repair protein
#3	rpmB2	112	rpmB2

Motif number 1

         CCCGCTATGCGCGATCCTTCGG	1	2	1	CGCTATGCGC	    0.993101	-215
TACGCTGACTCAGCGATGTGCTCAAGTCCCG	1	47	0	CGCGATGTGC	    0.994772	-170
GAACTCTCGATTGCCAGGCCCAAATGCCAAA	1	105	0	TGCCAGGCCC	    0.982475	-112
TCACATAGAACTGCGATGACCGGGCTGTAAA	1	134	1	CGCGATGACC	    0.990773	-83
CTGTAAAGCCTGACGAGGCGCCAATACCCCA	1	158	1	TACGAGGCGC	    0.966485	-59
GAGATTCACTTTGCGAGGCGCTTTCCAGGAT	2	13	1	TGCGAGGCGC	    0.996629	-81
TTTAACGAAACGGCTATGACAGGATGCGAGC	2	61	1	CGCTATGACA	    0.844763	-33
GTTTTCATTATTGCGACGTCGACGGTACAGT	3	31	1	TGCGACGTCG	    0.923313	-82
TTTTCGACAACAGCTAGGTGGCACTGTACCG	3	53	0	CGCTAGGTGG	    0.976377	-60
          * *********

Masking position 6
Map Score:   13.1599

Number of sites scoring better than the average of aligned sites = 1945
Number in coding regions = 1854
Number in noncoding regions = 91
Number of orfs with sites within 600 bp upstream = 100
Fraction of orfs with sites within 600 bp upstream = 0.0160617


Motif number 2

CAGACAAAGATCCCGAAGGATCGCGCATAGCGGG 	1	10	0	TCGGGATCCG	    0.987157	-207
TACTACGCCACCTTTGAGAATCTCGGGTTTGGCAT	1	78	1	CCTGAATCCG	    0.995265	-139
GCGCCAATACCCCATACGAAGCTCGAGCTAATTTG	1	175	1	CCTGAAGCCG	    0.998394	-42
        CTCCTTTGTGGTGCTCGCATCCTGTCA	2	77	0	CCTGGTGCCG	    0.995873	-17
AAAACTGTTATCGATAAGGAGGACG          	3	1	0	TCTGGAGGCG	    0.993038	-112
 GGGGCACCCTTCCTTCGAAGCTCGGCTTATTGAA	3	89	0	TTTGAAGCCG	    0.983924	-24
          **  *  ***** **

Masking position 8
Map Score:   6.18597

Number of sites scoring better than the average of aligned sites = 239
Number in coding regions = 224
Number in noncoding regions = 15
Number of orfs with sites within 600 bp upstream = 17
Fraction of orfs with sites within 600 bp upstream = 0.00273049


Motif number 3

TCCCGAAGGATCGCGCATAGCGGG       	1	4	0	TCCGCATAGC	    0.863433	-213
TCAGCGATGTGCTCAAGTCCCGAACAGACAA	1	38	0	GCCAAGTCCC	    0.978233	-179
CGATTGCCAGGCCCAAATGCCAAACCCGAGA	1	98	0	GCCAAATGCC	    0.985617	-119
CTATGTGAACTCTCGATTGCCAGGCCCAAAT	1	111	0	TCCGATTGCC	    0.957587	-106
GCCTGACGAGGCGCCAATACCCCATACGAAG	1	165	1	GCCCAATACC	    0.985617	-52
CCTTTGTGGTGCTCGCATCCTGTCATAGCCG	2	71	0	GCCGCATCCT	    0.986684	-23
       GGGGCACCCTTCCTTCGAAGCTCG	3	99	0	GCCCCTTCCT	     0.96462	-14
          ** ********

Masking position 8
Map Score:   3.49444

Number of sites scoring better than the average of aligned sites = 1328
Number in coding regions = 1233
Number in noncoding regions = 95
Number of orfs with sites within 600 bp upstream = 84
Fraction of orfs with sites within 600 bp upstream = 0.0134918


Motif number 4

CGCTTTCCAGGATTGAAAACTGGCCGTCGA	2	31	1	GATTGAAAAC	    0.975392	-63
 CGTCCTCCTTATCGATAACAGTTTTCATT	3	10	1	TATCGATAAC	    0.966996	-103
GACGTCGCAATAATGAAAACTGTTATCGAT	3	21	0	TAATGAAAAC	    0.964464	-92
ACCTAGCTGTTGTCGAAAATGATTTTCAAT	3	65	1	TGTCGAAAAT	    0.950674	-48
AAGCTCGGCTTATTGAAAATCATTTTCGAC	3	76	0	TATTGAAAAT	    0.975386	-37
          **********

Masking position 6
Map Score:   2.81112

Number of sites scoring better than the average of aligned sites = 311
Number in coding regions = 273
Number in noncoding regions = 38
Number of orfs with sites within 600 bp upstream = 46
Fraction of orfs with sites within 600 bp upstream = 0.00738837


Motif number 5

ACCTTTGAGAATCTCGGGTTTGGCATTTGG	1	87	1	ATCTCGGGTT	    0.907839	-130
GGGCCTGGCAATCGAGAGTTCACATAGAAC	1	115	1	ATCGAGAGTT	    0.922122	-102
CCCCATACGAAGCTCGAGCTAATTTGATTT	1	184	1	AGCTCGAGCT	    0.499923	-33
CTTCCTTCGAAGCTCGGCTTATTGAAAATC	3	85	0	AGCTCGGCTT	    0.960059	-28
          **********

Masking position 1
Map Score:   0.710255

Number of sites scoring better than the average of aligned sites = 121
Number in coding regions = 110
Number in noncoding regions = 11
Number of orfs with sites within 600 bp upstream = 6
Fraction of orfs with sites within 600 bp upstream = 0.000963701


Motif number 6

          **********

No masking
Map Score:   1.80068e-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:   1.80068e-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:   1.80068e-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