AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00280_mjan_reg_100.orf -o00280_mjan_100.ace -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -g0.31 -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 =  	0.31
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	MJ1008	100	branched-chain amino acid aminotransferase (ilvE)
#2	MJ1530	178	ribosomal protein S18 alanine acetyltransferase

Motif number 1

GAATAGACTCTATTTTTATTTTTTGCAAAT	1	17	1	TATTTTTATT	    0.967475	-84
GACAATTTTATATATTAAATATTCATTTTA	1	48	1	TATATTAAAT	    0.959724	-53
ATATTCATTTTATTTTTATTTTGACAATTT	1	66	1	TATTTTTATT	    0.967475	-35
 AAGACCACCTTTGTTAAATTGTCAAAATA	1	82	0	TTTGTTAAAT	    0.863795	-19
TGGTCCTTAGTATTTCAAAATGTTTTAAAA	2	46	1	TATTTCAAAA	    0.861159	-133
TTTTATAGAGTCTTTTAAAACATTTTGAAA	2	58	0	TCTTTTAAAA	    0.943226	-121
TATTTTAAATTCTTTTTATAGAGTCTTTTA	2	71	0	TCTTTTTATA	    0.852963	-108
ATTTTAGTATTATTTTAAATTCTTTTTATA	2	81	0	TATTTTAAAT	     0.98835	-98
TATTAAATTCTATTTTAATTTTAGTATTAT	2	98	0	TATTTTAATT	    0.980192	-81
TGTTGTGTAATTTATTAAATTCTATTTTAA	2	110	0	TTTATTAAAT	    0.882857	-69
AGCCTTTGAATAATTTTAATCAATGAATGT	2	137	0	TAATTTTAAT	    0.865507	-42
          **********

Masking position 8
Map Score:   17.2805

Number of sites scoring better than the average of aligned sites = 2247
Number in coding regions = 1714
Number in noncoding regions = 533
Number of orfs with sites within 600 bp upstream = 384
Fraction of orfs with sites within 600 bp upstream = 0.0616768


Motif number 2

ATAGACTCTATTTTTATTTTTTGCAAATAGA	1	19	1	TTTTATTTTT	    0.965026	-82
AATATATAAAATTGTCTATTTGCAAAAAATA	1	33	0	ATTTCTATTT	    0.728035	-68
AATAGACAATTTTATATATTAAATATTCATT	1	44	1	TTTTATATTA	     0.91823	-57
TTAAATATTCATTTTATTTTTATTTTGACAA	1	62	1	ATTTATTTTT	    0.957258	-39
TTATTGGTCCTTAGTATTTCAAAATGTTTTA	2	42	1	TTATATTTCA	    0.851942	-137
TTCTTTTTATAGAGTCTTTTAAAACATTTTG	2	61	0	AGATCTTTTA	    0.872717	-118
TTTAATTTTAGTATTATTTTAAATTCTTTTT	2	84	0	GTATATTTTA	    0.909822	-95
AATTTATTAAATTCTATTTTAATTTTAGTAT	2	101	0	ATTTATTTTA	    0.970405	-78
CAATGAATGTTGTGTAATTTATTAAATTCTA	2	116	0	TGTTAATTTA	    0.888829	-63
GTAAAGCCTTTGAATAATTTTAATCAATGAA	2	140	0	TGATAATTTT	    0.786981	-39
          *** *******

Masking position 5
Map Score:   6.66967

Number of sites scoring better than the average of aligned sites = 2946
Number in coding regions = 2071
Number in noncoding regions = 875
Number of orfs with sites within 600 bp upstream = 592
Fraction of orfs with sites within 600 bp upstream = 0.0950851


Motif number 3

       AAGACCACCTTTGTTAAATTGTC	1	88	0	ACCACCTTTG	    0.971971	-13
 TGAATTTTGAACGCTTTCATAAAGGGGGT	2	10	1	AACGCTTTCA	    0.902202	-169
ACCAATAAACACCCCCTTTATGAAAGCGTT	2	20	0	ACCCCCTTTA	    0.960841	-159
AGAGTCTTTTAAAACATTTTGAAATACTAA	2	52	0	AAAACATTTT	    0.834154	-127
GACTCTATAAAAAGAATTTAAAATAATACT	2	76	1	AAAGAATTTA	    0.788072	-103
AATAAATTACACAACATTCATTGATTAAAA	2	124	1	ACAACATTCA	    0.936802	-55
AACCTTTAGTAAAGCCTTTGAATAATTTTA	2	149	0	AAAGCCTTTG	    0.973926	-30
          **********

Masking position 1
Map Score:   1.12145

Number of sites scoring better than the average of aligned sites = 929
Number in coding regions = 823
Number in noncoding regions = 106
Number of orfs with sites within 600 bp upstream = 98
Fraction of orfs with sites within 600 bp upstream = 0.0157404


Motif number 4

          **********

No masking
Map Score:   -5.44113e-14

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 5

          **********

No masking
Map Score:   -5.44113e-14

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:   -5.44113e-14

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