AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i184_thi_operon_mtub_reg_100.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	Rv0415	129	hypothetical protein Rv0415
#2	thiC	151	thiC

Motif number 1

     ATCGTGACGCTAGCGCGCTAGCGTG	1	6	1	GACGCTAGCG	    0.970179	-124
TACAGGGTTCCACGCTAGCGCGCTAGCGTC	1	16	0	CACGCTAGCG	    0.987784	-114
ACTCTCAGACCCCGCTCCCGGGACTCCCGT	1	49	0	CCCGCTCCCG	    0.655074	-81
ACGGTAAGGGCAGGCGCGCCCACTCTCAGA	1	70	0	CAGGCGCGCC	    0.923999	-60
GATCAGGTGTGACGGTAAGGGCAGGCGCGC	1	81	0	GACGGTAAGG	    0.816526	-49
CCGGCATGATCCGGATCAGGTGTGACGGTA	1	94	0	CCGGATCAGG	    0.718433	-36
CCGGATCATGCCGGCGAAGGGAGGTCAAGG	1	110	1	CCGGCGAAGG	    0.734514	-20
         CGCGGCATCGGGCCGTCCGTG	2	2	1	GCGGCATCGG	    0.923944	-150
CGCCGGTGTGCACGGACGGCCCGATGCCGC	2	12	0	CACGGACGGC	    0.688552	-140
CTAGCGCAGCGCGGCGCCGGTGTGCACGGA	2	26	0	GCGGCGCCGG	    0.501929	-126
TGGGTACCCCCACGCTAGCGCAGCGCGGCG	2	40	0	CACGCTAGCG	    0.987784	-112
GGCGTGCGCTCCCGCGTGGGTACCCCCACG	2	56	0	CCCGCGTGGG	    0.520852	-96
CTCAGCGCACTCGGCGTGCGCTCCCGCGTG	2	68	0	TCGGCGTGCG	    0.950323	-84
CGCTGAGAGGACGGCTCGGGGCCGTCGACC	2	91	1	ACGGCTCGGG	    0.775102	-61
CGGCTCGGGGCCGTCGACCGTACGAACCTG	2	102	1	CCGTCGACCG	    0.763324	-50
GCCGGCATTACCCGGTCAGGTTCGTACGGT	2	118	0	CCCGGTCAGG	     0.95237	-34
CCGGGTAATGCCGGCGTAGGGAGTTGCAA 	2	133	1	CCGGCGTAGG	    0.890599	-19
          **********

Masking position 4
Map Score:   37.6102

Number of sites scoring better than the average of aligned sites = 39926
Number in coding regions = 36877
Number in noncoding regions = 3049
Number of orfs with sites within 600 bp upstream = 1245
Fraction of orfs with sites within 600 bp upstream = 0.199968


Motif number 2

 ATCGTGACGCTAGCGCGCTAGCGTGGAACC	1	10	1	CTAGCGCCTA	    0.932927	-120
CCTGTAGACACGGGAGTCCCGGGAGCGGGGT	1	40	1	CGGGAGTCCG	    0.519328	-90
TAAGGGCAGGCGCGCCCACTCTCAGACCCCG	1	65	0	CGCGCCCCTC	    0.972444	-65
         CCTTGACCTCCCTTCGCCGGCA	1	118	0	CTTGACCCCC	      0.9553	-12
TCGGGCCGTCCGTGCACACCGGCGCCGCGCT	2	18	1	CGTGCACCCG	    0.992077	-134
TACCCCCACGCTAGCGCAGCGCGGCGCCGGT	2	35	0	CTAGCGCGCG	    0.976321	-117
TGCGCTCCCGCGTGGGTACCCCCACGCTAGC	2	51	0	CGTGGGTCCC	    0.984855	-101
GCGCACTCGGCGTGCGCTCCCGCGTGGGTAC	2	63	0	CGTGCGCCCC	    0.998892	-89
GAGCGCACGCCGAGTGCGCTGAGAGGACGGC	2	75	1	CGAGTGCCTG	    0.980012	-77
TTCGTACGGTCGACGGCCCCGAGCCGTCCTC	2	97	0	CGACGGCCCG	    0.626986	-55
          ******* ***

Masking position 1
Map Score:   14.5173

Number of sites scoring better than the average of aligned sites = 14062
Number in coding regions = 13073
Number in noncoding regions = 989
Number of orfs with sites within 600 bp upstream = 676
Fraction of orfs with sites within 600 bp upstream = 0.108577


Motif number 3

CTGTAGACACGGGAGTCCCGGGAGCGGGGT	1	41	1	GGGAGTCCCG	    0.930207	-89
GTCTGAGAGTGGGCGCGCCTGCCCTTACCG	1	69	1	GGGCGCGCCT	    0.517272	-61
ACCTGATCCGGATCATGCCGGCGAAGGGAG	1	103	1	GATCATGCCG	    0.883395	-27
     CGCGGCATCGGGCCGTCCGTGCACA	2	6	1	CATCGGGCCG	    0.895125	-146
AGCGCGGCGCCGGTGTGCACGGACGGCCCG	2	19	0	CGGTGTGCAC	    0.789977	-133
CACGCTAGCGCAGCGCGGCGCCGGTGTGCA	2	30	0	CAGCGCGGCG	    0.626711	-122
GCTCCCGCGTGGGTACCCCCACGCTAGCGC	2	49	0	GGGTACCCCC	    0.789609	-103
GTACCCACGCGGGAGCGCACGCCGAGTGCG	2	63	1	GGGAGCGCAC	    0.785095	-89
AGCGCACGCCGAGTGCGCTGAGAGGACGGC	2	76	1	GAGTGCGCTG	     0.80654	-76
AACCTGACCGGGTAATGCCGGCGTAGGGAG	2	126	1	GGTAATGCCG	    0.933052	-26
          **********

Masking position 8
Map Score:   9.96799

Number of sites scoring better than the average of aligned sites = 35085
Number in coding regions = 32475
Number in noncoding regions = 2610
Number of orfs with sites within 600 bp upstream = 1184
Fraction of orfs with sites within 600 bp upstream = 0.19017


Motif number 4

    CCTTGACCTCCCTTCGCCGGCATGAT	1	114	0	CCTCCCTTCG	    0.997388	-16
CACACCGGCGCCGCGCTGCGCTAGCGTGGG	2	32	1	CCGCGCTGCG	    0.996966	-120
CCCGAGCCGTCCTCTCAGCGCACTCGGCGT	2	81	0	CCTCTCAGCG	    0.993439	-71
     TTGCAACTCCCTACGCCGGCATTAC	2	137	0	ACTCCCTACG	     0.98973	-15
          **********

Masking position 6
Map Score:   4.88989

Number of sites scoring better than the average of aligned sites = 501
Number in coding regions = 449
Number in noncoding regions = 52
Number of orfs with sites within 600 bp upstream = 48
Fraction of orfs with sites within 600 bp upstream = 0.0077096


Motif number 5

          **********

No masking
Map Score:   -3.17312e-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:   -3.17312e-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:   -3.17312e-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