AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_mpneu.txt -z/home/amcguire/genomes/mpneu.fna -igalR_mpneu_opreg_100.orf -g0.400 -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 =  	0.4
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	1674278	300	MG116 homolog, from M. genitalium

Motif number 1

ATTGCCGTGGCCTGCAGTGGGGTAGCGGGTC	1	82	1	CCTCAGTGGG	    0.895604	-219
ATTGGAAAACCAAGCAGTTGGTAGCTTGTTT	1	120	1	CAACAGTTGG	    0.706074	-181
TGAAACAAAACTACCAGCTGGCTCTAGAAAC	1	186	1	CTACAGCTGG	    0.941211	-115
ATTTTTTGCACAAAAAGCTGGCGCAATTCGT	1	215	0	CAAAAGCTGG	    0.968181	-86
AAAAATCTTGCAAACAGTTGAACACATTTTA	1	240	1	CAACAGTTGA	    0.967475	-61
          *** *******

Masking position 6
Map Score:   5.96734

Number of sites scoring better than the average of aligned sites = 54
Number in coding regions = 50
Number in noncoding regions = 4
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 2

TTTCACGAACACAATAACGCGATACAGCAC	1	17	0	ACAATAACGC	    0.970552	-284
TAGGTTTAATGCAAAAACTCAATGTTGATA	1	53	1	GCAAAAACTC	    0.961994	-248
GATGCATTGGAAAACCAAGCAGTTGGTAGC	1	115	1	AAAACCAAGC	    0.961071	-186
AATCACACAGAAAAACAAGCTACCAACTGC	1	133	0	AAAAACAAGC	    0.958106	-168
CTTGTTGGCAACAATCACACAGAAAAACAA	1	145	0	ACAATCACAC	    0.946431	-156
TTATGACTTTGAAACAAAACTACCAGCTGG	1	177	1	GAAACAAAAC	    0.916368	-124
AGCTTTTTGTGCAAAAAATCTTGCAAACAG	1	227	1	GCAAAAAATC	    0.954464	-74
          **********

Masking position 4
Map Score:   4.92967

Number of sites scoring better than the average of aligned sites = 292
Number in coding regions = 250
Number in noncoding regions = 42
Number of orfs with sites within 600 bp upstream = 34
Fraction of orfs with sites within 600 bp upstream = 0.00546097


Motif number 3

AGTTTTTGCATTAAACCTAACGCCATTTCA	1	42	0	TTAAACCTAA	    0.982466	-259
ACCTAAGAAATTTCACTTAAAATGTGTTCA	1	258	0	TTTCACTTAA	    0.951735	-43
TTAAACCTTATTTAACCTAAGAAATTTCAC	1	272	0	TTTAACCTAA	    0.992102	-29
 CTTGTTCTCTTAAACCTTATTTAACCTAA	1	282	0	TTAAACCTTA	    0.981411	-19
          **********

Masking position 5
Map Score:   4.35827

Number of sites scoring better than the average of aligned sites = 38
Number in coding regions = 29
Number in noncoding regions = 9
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 4

CACGGTGCTGTATCGCGTTATTGTGTTCGT	1	13	1	TATCGCGTTA	    0.822551	-288
GTGTTCGTGAAATGGCGTTAGGTTTAATGC	1	35	1	AATGGCGTTA	    0.980274	-266
AAAACTACCAGCTGGCTCTAGAAACGAATT	1	192	1	GCTGGCTCTA	    0.988369	-109
TGCACAAAAAGCTGGCGCAATTCGTTTCTA	1	210	0	GCTGGCGCAA	     0.99257	-91
          **********

Masking position 3
Map Score:   0.33875

Number of sites scoring better than the average of aligned sites = 48
Number in coding regions = 39
Number in noncoding regions = 9
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 5

          **********

No masking
Map Score:   7.91135e-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:   7.91135e-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:   7.91135e-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