AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i032_Pyruvate_Synthase_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	Rv2455c	231	hypothetical protein Rv2455c

Motif number 1

CTGGCGGTAGCGACGACACAGAACTGTGGTAT	1	14	0	CGACGCCAGA	    0.833223	-218
GTCGTCGCTACCGCCAGCCCTCGCTGACTTCG	1	29	1	CCGCCGCCTC	     0.98578	-203
GCCATATATGCGGCCGGTAACCGACCAAAAGG	1	61	0	CGGCCGAACC	    0.996326	-171
GCATCGGAGACCGCCTTACACCCGAAATGAAA	1	91	1	CCGCCTCACC	    0.998372	-141
ATAATCGCTACCGCCAGTGACACAAGCCGTGC	1	127	1	CCGCCGGACA	    0.984161	-105
AGCGACACCCCCGCGCCGCACGGCTTGTGTCA	1	144	0	CCGCGCCACG	    0.992975	-88
TACGCGTCGTCGGAGCGACACCCCCGCGCCGC	1	157	0	CGGAGGCACC	     0.99509	-75
GTCGCTCCGACGACGCGTAACCTGAAGCTGCA	1	170	1	CGACGGAACC	    0.972253	-62
GACAGGCACTCCGCGCTGCAGCTTCAGGTTAC	1	186	0	CCGCGTCAGC	    0.993617	-46
CATGTGTTATCGGACAGGCACTCCGCGCTGCA	1	198	0	CGGACGCACT	     0.96909	-34
      GTCTCCGCCTTCCATGTGTTATCGGA	1	216	0	CCGCCTCATG	    0.977132	-16
          ***** * ****

Masking position 1
Map Score:   19.7672

Number of sites scoring better than the average of aligned sites = 14761
Number in coding regions = 13629
Number in noncoding regions = 1132
Number of orfs with sites within 600 bp upstream = 729
Fraction of orfs with sites within 600 bp upstream = 0.11709


Motif number 2

TCGTCGCTACCGCCAGCCCTCGCTGACTTCG	1	30	1	CGCCACCCTC	    0.990333	-202
CATCGGAGACCGCCTTACACCCGAAATGAAA	1	92	1	CGCCTACACC	    0.994113	-140
GCGACACCCCCGCGCCGCACGGCTTGTGTCA	1	144	0	CGCGCGCACG	    0.776683	-88
GCGTCGTCGGAGCGACACCCCCGCGCCGCAC	1	155	0	AGCGAACCCC	    0.962099	-77
GCTCCGACGACGCGTAACCTGAAGCTGCAGC	1	173	1	CGCGTACCTG	    0.984026	-59
ACAGGCACTCCGCGCTGCAGCTTCAGGTTAC	1	186	0	CGCGCGCAGC	    0.989891	-46
     GTCTCCGCCTTCCATGTGTTATCGGA	1	216	0	CGCCTCCATG	    0.989288	-16
          ***** *****

Masking position 8
Map Score:   8.98745

Number of sites scoring better than the average of aligned sites = 6318
Number in coding regions = 5851
Number in noncoding regions = 467
Number of orfs with sites within 600 bp upstream = 381
Fraction of orfs with sites within 600 bp upstream = 0.061195


Motif number 3

GACACAGAACTGTGGTATTGG          	1	1	0	TTGGTATTGG	     0.98242	-231
ACCACAGTTCTGTGTCGTCGCTACCGCCAGC	1	16	1	TTGTCGTCGC	    0.973398	-216
CGCCTTTTGGTCGGTTACCGGCCGCATATAT	1	59	1	TGGTTACCGG	    0.976586	-173
CGGCCGCATATATGGCATCGGAGACCGCCTT	1	77	1	TTGGCATCGG	    0.997081	-155
CCGCACGGCTTGTGTCACTGGCGGTAGCGAT	1	130	0	TTGTCACTGG	    0.991409	-102
ACACAAGCCGTGCGGCGCGGGGGTGTCGCTC	1	146	1	TCGGCGCGGG	    0.966469	-86
CCGCCTTCCATGTGTTATCGGACAGGCACTC	1	207	0	TTGTTATCGG	    0.992751	-25
          * *********

Masking position 1
Map Score:   9.89707

Number of sites scoring better than the average of aligned sites = 2095
Number in coding regions = 1952
Number in noncoding regions = 143
Number of orfs with sites within 600 bp upstream = 121
Fraction of orfs with sites within 600 bp upstream = 0.0194346


Motif number 4

          CCAATACCACAGTTCTGTGT	1	1	1	CCAATACCAC	    0.981519	-231
GCTGGCGGTAGCGACGACACAGAACTGTGG	1	17	0	GCGACGACAC	    0.989283	-215
ATATATGCGGCCGGTAACCGACCAAAAGGC	1	60	0	CCGGTAACCG	    0.928769	-172
AAGGCGGTCTCCGATGCCATATATGCGGCC	1	78	0	CCGATGCCAT	    0.979233	-154
ATCGCTACCGCCAGTGACACAAGCCGTGCG	1	130	1	CCAGTGACAC	    0.979831	-102
CGTCGTCGGAGCGACACCCCCGCGCCGCAC	1	155	0	GCGACACCCC	    0.947753	-77
GGGTGTCGCTCCGACGACGCGTAACCTGAA	1	166	1	CCGACGACGC	    0.967764	-66
GAGTGCCTGTCCGATAACACATGGAAGGCG	1	207	1	CCGATAACAC	    0.995428	-25
          **********

Masking position 8
Map Score:   15.1564

Number of sites scoring better than the average of aligned sites = 8812
Number in coding regions = 8353
Number in noncoding regions = 459
Number of orfs with sites within 600 bp upstream = 386
Fraction of orfs with sites within 600 bp upstream = 0.0619981


Motif number 5

          **********

No masking
Map Score:   1.51646e-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:   1.51646e-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:   1.51646e-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