AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i345_weak6_mtub_reg_300.orf -a/home/amcguire/alignace/lib/ORF_mtub.txt -z/skink1/amcguire/genomes/mtub.fna -g0.66 -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 =  	0.66
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	Rv0266c	176	hypothetical protein Rv0266c

Motif number 1

CGCTGATGTCGCCCGCTTGTCGACAGGAGA	1	19	0	GCCCGCTTGT	    0.990026	-158
GCCGTCATTACCGCTGATGTCGCCCGCTTG	1	30	0	CCGCTGATGT	    0.935374	-147
CGCTAAAGAGACCCTGTTACCGGCCCGGAT	1	64	1	ACCCTGTTAC	    0.970727	-113
CCTGTTACCGGCCCGGATGCGCGCTGTTAC	1	76	1	GCCCGGATGC	    0.999053	-101
GCCCGGATGCGCGCTGTTACAGCGGAGATA	1	86	1	GCGCTGTTAC	    0.989065	-91
GGTGGCTTCGGCCCGTCTGCCGTTGTGAGG	1	122	1	GCCCGTCTGC	    0.996259	-55
GTGAGGACGGGACCGGCTGCGAGCGTGAAG	1	146	1	GACCGGCTGC	    0.995616	-31
          **********

Masking position 8
Map Score:   12.1056

Number of sites scoring better than the average of aligned sites = 6832
Number in coding regions = 6287
Number in noncoding regions = 545
Number of orfs with sites within 600 bp upstream = 426
Fraction of orfs with sites within 600 bp upstream = 0.0684227


Motif number 2

CCTGTCGACAAGCGGGCGACATCAGCGGTA	1	22	1	AGCGGGCGAC	    0.979636	-155
AGCGGTAATGACGGCTCGACGCTAAAGAGA	1	45	1	ACGGCTCGAC	    0.990138	-132
GACCCTGTTACCGGCCCGGATGCGCGCTGT	1	73	1	CCGGCCCGGA	     0.98616	-104
CTCCGCTGTAACAGCGCGCATCCGGGCCGG	1	83	0	ACAGCGCGCA	     0.94147	-94
ACAACGGCAGACGGGCCGAAGCCACCTAAA	1	118	0	ACGGGCCGAA	    0.994576	-59
GTTGTGAGGACGGGACCGGCTGCGAGCGTG	1	143	1	CGGGACCGGC	    0.981515	-34
GCGAGCGTGAAGGGGGAGTCCGG       	1	164	1	AGGGGGAGTC	    0.940175	-13
          **********

Masking position 4
Map Score:   6.63514

Number of sites scoring better than the average of aligned sites = 13472
Number in coding regions = 12330
Number in noncoding regions = 1142
Number of orfs with sites within 600 bp upstream = 748
Fraction of orfs with sites within 600 bp upstream = 0.120141


Motif number 3

GCTTGTCGACAGGAGACCTAACCG      	1	5	0	AGGAGACCTA	    0.992419	-172
GTCGACAAGCGGGCGACATCAGCGGTAATG	1	25	1	GGGCGACATC	    0.962126	-152
CTCGACGCTAAAGAGACCCTGTTACCGGCC	1	59	1	AAGAGACCCT	     0.97602	-118
TGTTACAGCGGAGATACCTTTAGGTGGCTT	1	100	1	GAGATACCTT	    0.896805	-77
AGACGGGCCGAAGCCACCTAAAGGTATCTC	1	110	0	AAGCCACCTA	    0.980045	-67
          **********

Masking position 6
Map Score:   2.20724

Number of sites scoring better than the average of aligned sites = 728
Number in coding regions = 673
Number in noncoding regions = 55
Number of orfs with sites within 600 bp upstream = 57
Fraction of orfs with sites within 600 bp upstream = 0.00915516


Motif number 4

TCGAGCCGTCATTACCGCTGATGTCGCCCG	1	34	0	ATTACCGCTG	    0.989059	-143
GTAATGACGGCTCGACGCTAAAGAGACCCT	1	49	1	CTCGACGCTA	    0.973267	-128
ACCGGCCCGGATGCGCGCTGTTACAGCGGA	1	82	1	ATGCGCGCTG	    0.967891	-95
ACCTAAAGGTATCTCCGCTGTAACAGCGCG	1	95	0	ATCTCCGCTG	    0.992899	-82
CGGACTCCCCCTTCACGCTCGCAGCCGGTC	1	156	0	CTTCACGCTC	    0.984616	-21
          **********

Masking position 2
Map Score:   2.8682

Number of sites scoring better than the average of aligned sites = 1466
Number in coding regions = 1358
Number in noncoding regions = 108
Number of orfs with sites within 600 bp upstream = 118
Fraction of orfs with sites within 600 bp upstream = 0.0189528


Motif number 5

          **********

No masking
Map Score:   4.57179e-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:   4.57179e-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:   4.57179e-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