AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i214_ecoli_bsub_100.orf -o214_ecoli_bsub_100.ace -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.47 -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 =  	0.47
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	rplM	218	50S ribosomal subunit protein L13
#2	rplM	162	ribosomal protein L13

Motif number 1

CTGTCACAAATCACAAAAAGGGGTCGATCT	1	14	1	TCACAAAAAG	    0.973292	-205
CTATGCCAGCACACAAAAAGTTTTGGGAAA	1	95	0	ACACAAAAAG	    0.991729	-124
GTTGAGGTTCACACGACAAAGTCCGGCAAA	1	143	0	ACACGACAAA	    0.965789	-76
 TAAAAGCTTACCCAATAAATAGTTACACG	1	200	0	ACCCAATAAA	    0.955009	-19
TATTTCAACCCCACGATAAGCCCCGGAACT	2	73	1	CCACGATAAG	    0.984654	-90
CTATTTCACAACACAATAAGTTCCGGGGCT	2	91	0	ACACAATAAG	    0.994213	-72
          **********

Masking position 6
Map Score:   8.06532

Number of sites scoring better than the average of aligned sites = 75
Number in coding regions = 54
Number in noncoding regions = 21
Number of orfs with sites within 600 bp upstream = 30
Fraction of orfs with sites within 600 bp upstream = 0.0048185


Motif number 2

GGTCAAAGATCGACCCCTTTTTGTGATTTG	1	20	0	CGACCCCTTT	    0.983061	-199
GGTCGATCTTTGACCCCGACTTCTCTATAA	1	35	1	TGACCCCGAC	    0.962857	-184
TATAATCCTGCGACCCCACGTTACAAGAAA	1	60	1	CGACCCCACG	    0.995922	-159
TCCGGCAAACCTACCCCTTCGAATAGCCTA	1	122	0	CTACCCCTTC	    0.990324	-97
GTATGTATTTCAACCCCACGATAAGCCCCG	2	68	1	CAACCCCACG	    0.984258	-95
      TGAATTTCCCCTCCTAAATGATCT	2	149	0	TTTCCCCTCC	    0.950558	-14
          **********

Masking position 5
Map Score:   5.28008

Number of sites scoring better than the average of aligned sites = 271
Number in coding regions = 240
Number in noncoding regions = 31
Number of orfs with sites within 600 bp upstream = 33
Fraction of orfs with sites within 600 bp upstream = 0.00530035


Motif number 3

    AACCTGTCACAAATCACAAAAAGGGG	1	7	1	TCACAAATCA	    0.977922	-212
AAAGTTTTTTTCCCAAAACTTTTTGTGTGC	1	87	1	TCCCAAAACT	    0.944284	-132
GAATAGCCTATGCCAGCACACAAAAAGTTT	1	102	0	TGCCAGCACA	    0.976641	-117
TTGTTGAGGTTCACACGACAAAGTCCGGCA	1	145	0	TCACACGACA	    0.965982	-74
ACGTTCTATTTCACAACACAATAAGTTCCG	2	96	0	TCACAACACA	     0.98894	-67
TTATTGAAAATGACAGATCATTTAGGAGGG	2	135	1	TGACAGATCA	    0.959783	-28
          **********

Masking position 5
Map Score:   4.28713

Number of sites scoring better than the average of aligned sites = 165
Number in coding regions = 135
Number in noncoding regions = 30
Number of orfs with sites within 600 bp upstream = 36
Fraction of orfs with sites within 600 bp upstream = 0.0057822


Motif number 4

GTTTTGGGAAAAAAACTTTCTTGTAACGTG	1	76	0	AAAAACTTTC	    0.970869	-143
GCCAGCACACAAAAAGTTTTGGGAAAAAAA	1	91	0	AAAAAGTTTT	    0.852943	-128
CTTACCCAATAAATAGTTACACGTTGGTGA	1	193	0	AAATAGTTAC	    0.971451	-26
         TAAAAGCTTACCCAATAAATA	1	208	0	AAAAGCTTAC	    0.952991	-11
CGTGGGGTTGAAATACATACCATATGTTAT	2	58	0	AAATACATAC	    0.893564	-105
TTCACAACACAATAAGTTCCGGGGCTTATC	2	87	0	AATAAGTTCC	    0.901884	-76
          **********

Masking position 8
Map Score:   1.96278

Number of sites scoring better than the average of aligned sites = 225
Number in coding regions = 177
Number in noncoding regions = 48
Number of orfs with sites within 600 bp upstream = 59
Fraction of orfs with sites within 600 bp upstream = 0.00947639


Motif number 5

          **********

No masking
Map Score:   -6.79689e-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:   -6.79689e-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:   -6.79689e-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