AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i282_hypothetical7_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	Rv0038	101	hypothetical protein Rv0038
#2	alaS	90	alaS
#3	Rv2556c	106	hypothetical protein Rv2556c

Motif number 1

GGGCGGCACGGGGTGGACCGAACCTTGCCT 	1	10	0	GGGTGGCCGA	    0.998605	-92
GTCCACCCCGTGCCGCCCCAACCACAGTACA	1	23	1	TGCCGCCCAA	    0.903405	-79
CGAACAAGCAGGGTCGGCGAATATTTGTACT	1	48	0	GGGTCGCGAA	    0.984975	-54
CGCATCGCCCGGGGCGAACAAGCAGGGTCGG	1	62	0	GGGGCGACAA	    0.943682	-40
TGTTCGCCCCGGGCGATGCGACGGTGGTGCG	1	73	1	GGGCGAGCGA	    0.993354	-29
GGCGATGCGACGGTGGTGCGATGATGGT   	1	84	1	CGGTGGGCGA	    0.973696	-18
GGGCCGAATTGGGCCGTCGGACAGCCTTCTC	2	13	1	GGGCCGCGGA	    0.997468	-78
TGCCCCGGCCGGCCCGTCGGAGGAAGGTAAT	3	13	0	GGCCCGCGGA	    0.995067	-94
CCGACGGGCCGGCCGGGGCAATGGGCAATCC	3	24	1	GGCCGGGCAA	     0.99499	-83
CCGGGGCAATGGGCAATCCGACGTCAATGGA	3	36	1	GGGCAACCGA	    0.974113	-71
CCTACGGTGGGGGCGCGCCAACCTGCCAATC	3	65	0	GGGCGCCCAA	    0.995706	-42
CCCCACCGTAGGCTGGGACGGGTGGATACCG	3	84	1	GGCTGGACGG	    0.925283	-23
          ****** ****

Masking position 2
Map Score:   25.3122

Number of sites scoring better than the average of aligned sites = 10036
Number in coding regions = 9229
Number in noncoding regions = 807
Number of orfs with sites within 600 bp upstream = 523
Fraction of orfs with sites within 600 bp upstream = 0.0840026


Motif number 2

  AGGCAAGGTTCGGTCCACCCCGTGCCGC	1	9	1	TTCGGTCCAC	    0.909849	-93
TTGTACTGTGGTTGGGGCGGCACGGGGTGG	1	25	0	GTTGGGGCGG	    0.959975	-77
ACCCTGCTTGTTCGCCCCGGGCGATGCGAC	1	65	1	TTCGCCCCGG	    0.991464	-37
TCGCACCACCGTCGCATCGCCCGGGGCGAA	1	75	0	GTCGCATCGC	    0.986929	-27
    ACCATCATCGCACCACCGTCGCATCG	1	86	0	ATCGCACCAC	    0.931067	-16
GACGGCCCAATTCGGCCCGC          	2	1	0	TTCGGCCCGC	    0.997024	-90
GAATTGGGCCGTCGGACAGCCTTCTCATAA	2	18	1	GTCGGACAGC	    0.982261	-73
ACCTTCCTCCGACGGGCCGGCCGGGGCAAT	3	16	1	GACGGGCCGG	    0.975837	-91
CGGATTGCCCATTGCCCCGGCCGGCCCGTC	3	26	0	ATTGCCCCGG	    0.952563	-81
ATCCATTGACGTCGGATTGCCCATTGCCCC	3	38	0	GTCGGATTGC	    0.918834	-69
GGATTGGCAGGTTGGCGCGCCCCCACCGTA	3	64	1	GTTGGCGCGC	    0.987296	-43
          **********

Masking position 4
Map Score:   20.1624

Number of sites scoring better than the average of aligned sites = 14164
Number in coding regions = 12991
Number in noncoding regions = 1173
Number of orfs with sites within 600 bp upstream = 782
Fraction of orfs with sites within 600 bp upstream = 0.125602


Motif number 3

GGGCGGCACGGGGTGGACCGAACCTTGCCT 	1	10	0	GGGTGACCGA	    0.899945	-92
TTTGTACTGTGGTTGGGGCGGCACGGGGTGG	1	25	0	GGTTGGGCGG	    0.987588	-77
CGCCCGGGGCGAACAAGCAGGGTCGGCGAAT	1	57	0	GAACAGCAGG	    0.833152	-45
CACCACCGTCGCATCGCCCGGGGCGAACAAG	1	71	0	GCATGCCCGG	    0.960345	-31
   GCGGGCCGAATTGGGCCGTCGGACAGCC	2	8	1	GAATGGGCCG	    0.955069	-83
GCCGGATTATGAGAAGGCTGTCCGACGGCCC	2	23	0	GAGAGGCTGT	    0.869834	-68
ATAATCCGGCGAATAGGCTGGTAATGGACTT	2	44	1	GAATGGCTGG	    0.993133	-47
TTCCTCCGACGGGCCGGCCGGGGCAATGGGC	3	19	1	GGGCGGCCGG	    0.998111	-88
CGACGTCAATGGATTGGCAGGTTGGCGCGCC	3	54	1	GGATGGCAGG	    0.994983	-53
ACCGTAGGCTGGGACGGGTGGATACCGAT  	3	88	1	GGGAGGGTGG	    0.983446	-19
          **** ******

Masking position 1
Map Score:   13.8087

Number of sites scoring better than the average of aligned sites = 12304
Number in coding regions = 11495
Number in noncoding regions = 809
Number of orfs with sites within 600 bp upstream = 594
Fraction of orfs with sites within 600 bp upstream = 0.0954064


Motif number 4

          **********

No masking
Map Score:   5.70866e-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:   5.70866e-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:   5.70866e-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