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

Motif number 1

 AGGCAAGGTTCGGTCCACCCCGTGCCGCCC	1	10	1	TCGGCCACCC	    0.998605	-92
TGTACTGTGGTTGGGGCGGCACGGGGTGGAC	1	23	0	TTGGGCGGCA	    0.903405	-79
AGTACAAATATTCGCCGACCCTGCTTGTTCG	1	48	1	TTCGCGACCC	    0.984975	-54
CCGACCCTGCTTGTTCGCCCCGGGCGATGCG	1	62	1	TTGTCGCCCC	    0.943682	-40
CGCACCACCGTCGCATCGCCCGGGGCGAACA	1	73	0	TCGCTCGCCC	    0.993354	-29
   ACCATCATCGCACCACCGTCGCATCGCC	1	84	0	TCGCCCACCG	    0.973696	-18
GAGAAGGCTGTCCGACGGCCCAATTCGGCCC	2	13	0	TCCGCGGCCC	    0.997468	-78
ATTACCTTCCTCCGACGGGCCGGCCGGGGCA	3	13	1	TCCGCGGGCC	    0.995067	-94
GGATTGCCCATTGCCCCGGCCGGCCCGTCGG	3	24	0	TTGCCCGGCC	     0.99499	-83
TCCATTGACGTCGGATTGCCCATTGCCCCGG	3	36	0	TCGGTTGCCC	    0.974113	-71
GATTGGCAGGTTGGCGCGCCCCCACCGTAGG	3	65	1	TTGGGCGCCC	    0.995706	-42
CGGTATCCACCCGTCCCAGCCTACGGTGGGG	3	84	0	CCGTCCAGCC	    0.925283	-23
          **** ******

Masking position 10
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	    0.928749	-93
TTGTACTGTGGTTGGGGCGGCACGGGGTGG	1	25	0	GTTGGGGCGG	    0.968737	-77
ACCCTGCTTGTTCGCCCCGGGCGATGCGAC	1	65	1	TTCGCCCCGG	     0.99338	-37
TCGCACCACCGTCGCATCGCCCGGGGCGAA	1	75	0	GTCGCATCGC	    0.989853	-27
    ACCATCATCGCACCACCGTCGCATCG	1	86	0	ATCGCACCAC	     0.94579	-16
GACGGCCCAATTCGGCCCGC          	2	1	0	TTCGGCCCGC	    0.997664	-90
GAATTGGGCCGTCGGACAGCCTTCTCATAA	2	18	1	GTCGGACAGC	    0.985883	-73
ACCTTCCTCCGACGGGCCGGCCGGGGCAAT	3	16	1	GACGGGCCGG	    0.981193	-91
CGGATTGCCCATTGCCCCGGCCGGCCCGTC	3	26	0	ATTGCCCCGG	    0.962885	-81
ATCCATTGACGTCGGATTGCCCATTGCCCC	3	38	0	GTCGGATTGC	    0.936005	-69
GGATTGGCAGGTTGGCGCGCCCCCACCGTA	3	64	1	GTTGGCGCGC	    0.990054	-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

 AGGCAAGGTTCGGTCCACCCCGTGCCGCCC	1	10	1	TCGGTCACCC	    0.895643	-92
CCACCCCGTGCCGCCCCAACCACAGTACAAA	1	25	1	CCGCCCAACC	       0.987	-77
ATTCGCCGACCCTGCTTGTTCGCCCCGGGCG	1	57	1	CCTGCTGTTC	    0.826531	-45
CTTGTTCGCCCCGGGCGATGCGACGGTGGTG	1	71	1	CCGGGCATGC	     0.95852	-31
GGCTGTCCGACGGCCCAATTCGGCCCGC   	2	8	0	CGGCCCATTC	    0.953013	-83
GGGCCGTCGGACAGCCTTCTCATAATCCGGC	2	23	1	ACAGCCTCTC	    0.864432	-68
AAGTCCATTACCAGCCTATTCGCCGGATTAT	2	44	0	CCAGCCATTC	    0.992806	-47
GCCCATTGCCCCGGCCGGCCCGTCGGAGGAA	3	19	0	CCGGCCGCCC	    0.998021	-88
GGCGCGCCAACCTGCCAATCCATTGACGTCG	3	54	0	CCTGCCATCC	    0.994743	-53
  ATCGGTATCCACCCGTCCCAGCCTACGGT	3	88	0	CCACCCTCCC	    0.982665	-19
          ****** ****

Masking position 11
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