AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/alignace/lib/ORF_mtub.txt -z/skink1/amcguire/genomes/mtub.fna -ideoR_mtub_opreg_300.orf -g0.656 -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 =  	0.656
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	Rv0475	300	hypothetical protein Rv0475
#2	Rv0476	111	hypothetical protein Rv0476

Motif number 1

CATCTGGGTGAGGTCGACCGCAGGCTGATC	1	14	1	AGGTCGACCG	    0.705039	-287
GCGGCCGATCGGCTGGATCAGCCTGCGGTC	1	29	0	GGCTGGATCA	    0.882081	-272
CTGTTGGCCAGCGCGGCCGATCGGCTGGAT	1	41	0	GCGCGGCCGA	    0.930878	-260
GTCATCGACGGAGTCGCTGTTGGCCAGCGC	1	57	0	GAGTCGCTGT	    0.967458	-244
GACATGTAGTGACCGGATCAGCTGGGCCTG	1	100	1	GACCGGATCA	    0.924079	-201
GACATCTACGAACTCGACCGACAACCGACC	1	129	1	AACTCGACCG	    0.933856	-172
ACCGACAACCGACCCGACGATCAGAAGGTT	1	145	1	GACCCGACGA	    0.989636	-156
CATGGCACGCGACTTGCCGGGGAAACCTTC	1	168	0	GACTTGCCGG	    0.922241	-133
GACTAGTCAAGACCCGCGGATTGACATGGC	1	192	0	GACCCGCGGA	    0.933656	-109
CTCCCTGGAGGAGCCGACGCTTGCCCCAAC	1	222	1	GAGCCGACGC	    0.974436	-79
TACATCTTTGGTCTGGACGTTGGGGCAAGC	1	240	0	GTCTGGACGT	    0.773306	-61
GGGCGACTCGGAGTCGATGGTGATTCGGAG	2	16	0	GAGTCGATGG	    0.979823	-96
CATCGACTCCGAGTCGCCCACGGGGCGACT	2	27	1	GAGTCGCCCA	    0.993528	-85
CGTCGACTCCGAGTCGCCCCGTGGGCGACT	2	38	0	GAGTCGCCCC	    0.967725	-74
GGGCGACTCGGAGTCGACGTGTTGGATGCA	2	49	1	GAGTCGACGT	    0.947136	-63
GGTACCCACGAGGTGGCTCACGCATTCAGA	2	89	0	AGGTGGCTCA	    0.649513	-23
          **********

Masking position 6
Map Score:   23.5044

Number of sites scoring better than the average of aligned sites = 21934
Number in coding regions = 20362
Number in noncoding regions = 1572
Number of orfs with sites within 600 bp upstream = 958
Fraction of orfs with sites within 600 bp upstream = 0.153871


Motif number 2

CTGCACGTCATCGACGGAGTCGCTGTTGGCC	1	62	0	TCACGGAGTC	    0.981919	-239
ATGACGTGCAGCAAAGGAGACATGTAGTGAC	1	82	1	GCAAGGAGAC	    0.955698	-219
GTTGGGGCAAGCGTCGGCTCCTCCAGGGAGG	1	221	0	GCTCGGCTCC	    0.975422	-80
AGTCGATGGTGATTCGGAGCCCGA       	2	4	0	GATCGGAGCC	    0.957418	-108
CCCCGTGGGCGACTCGGAGTCGATGGTGATT	2	21	0	GATCGGAGTC	    0.518053	-91
CCCACGGGGCGACTCGGAGTCGACGTGTTGG	2	43	1	GATCGGAGTC	    0.518053	-69
          ** ********

Masking position 6
Map Score:   8.97414

Number of sites scoring better than the average of aligned sites = 1493
Number in coding regions = 1388
Number in noncoding regions = 105
Number of orfs with sites within 600 bp upstream = 98
Fraction of orfs with sites within 600 bp upstream = 0.0157404


Motif number 3

GGAGTCGCTGTTGGCCAGCGCGGCCGATCG	1	48	0	TTGGCCAGCG	    0.903648	-253
CGTAGATGTCAGGCCCAGCTGATCCGGTCA	1	109	0	AGGCCCAGCT	    0.815561	-192
GCGACTTGCCGGGGAAACCTTCTGATCGTC	1	160	0	GGGGAAACCT	    0.879212	-141
GCGGATTGACATGGCACGCGACTTGCCGGG	1	177	0	ATGGCACGCG	    0.978419	-124
TCTGGACGTTGGGGCAAGCGTCGGCTCCTC	1	229	0	GGGGCAAGCG	    0.995113	-72
GTCGCCCCGTGGGCGACTCGGAGTCGATGG	2	26	0	GGGCGACTCG	    0.968761	-86
GTCGCCCACGGGGCGACTCGGAGTCGACGT	2	39	1	GGGCGACTCG	    0.968761	-73
GACGTGTTGGATGCAAACCGCATAGTCTGA	2	64	1	ATGCAAACCG	    0.854718	-48
TACCCACGAGGTGGCTCACGCATTCAGACT	2	87	0	GTGGCTCACG	     0.90658	-25
GAGCCACCTCGTGGGTACCGTC        	2	100	1	GTGGGTACCG	    0.956272	-12
          **********

Masking position 9
Map Score:   7.75899

Number of sites scoring better than the average of aligned sites = 12267
Number in coding regions = 11333
Number in noncoding regions = 934
Number of orfs with sites within 600 bp upstream = 644
Fraction of orfs with sites within 600 bp upstream = 0.103437


Motif number 4

          **********

No masking
Map Score:   4.78496e-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 5

          **********

No masking
Map Score:   4.78496e-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:   4.78496e-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