AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/alignace/lib/ORF_mtub.txt -z/skink1/amcguire/genomes/mtub.fna -iaraC_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	Rv3329	59	hypothetical protein Rv3329
#2	Rv3330	68	hypothetical protein Rv3330
#3	sugI	95	sugI

Motif number 1

CGAGCGCAGCGCTAGGCTCGGGCAATGACC	1	14	0	GCTAGGCTCG	    0.962147	-46
CTAGCGCTGCGCTCGCCAACACGACGACAC	1	29	1	GCTCGCCAAC	    0.990612	-31
GCCAGTCACAGCGCGGCTCCTCGCGGTCGG	2	21	1	GCGCGGCTCC	    0.990352	-48
GTGATCGGCGGCCCGACCGCGAGGAGCCGC	2	33	0	GCCCGACCGC	    0.995007	-36
TCGGGCCGCCGATCACCTACTCTGCACAGA	2	47	1	GATCACCTAC	     0.80903	-22
        CTGCTTACCCCGATACCTTCGG	3	3	1	GCTTACCCCG	    0.951069	-93
CGGCTAGGATGCCCGCCCGCAAACGACGCC	3	31	0	GCCCGCCCGC	    0.995072	-65
TGCCGACCAAGGCCGGCTAGGATGCCCGCC	3	44	0	GGCCGGCTAG	    0.978417	-52
AGCCGGCCTTGGTCGGCACCGAAATCGGGG	3	56	1	GGTCGGCACC	    0.988497	-40
CGAAATCGGGGCTTGACCAGCGGTTGACCG	3	75	1	GCTTGACCAG	    0.974695	-21
CTTGACCAGCGGTTGACCGC          	3	86	1	GGTTGACCGC	    0.972036	-10
          **********

Masking position 7
Map Score:   18.6217

Number of sites scoring better than the average of aligned sites = 26196
Number in coding regions = 24246
Number in noncoding regions = 1950
Number of orfs with sites within 600 bp upstream = 1075
Fraction of orfs with sites within 600 bp upstream = 0.172663


Motif number 2

GCGCTAGGCTCGGGCAATGACCTCG     	1	6	0	CGGGCAATGA	     0.98339	-54
CCAAAGGTTTCGTGTCGTCGTGTTGGCGAG	1	40	0	CGTGTCGTCG	    0.956708	-20
      CTTTCGTCCCGCCAGTCACAGCGC	2	5	1	CGTCCCGCCA	     0.96334	-64
CGCGAGGAGCCGCGCTGTGACTGGCGGGAC	2	16	0	CGCGCTGTGA	     0.93023	-53
TCCTCGCGGTCGGGCCGCCGATCACCTACT	2	38	1	CGGGCCGCCG	    0.952418	-31
CGTTTGCGGGCGGGCATCCTAGCCGGCCTT	3	36	1	CGGGCATCCT	    0.976149	-60
GGCATCCTAGCCGGCCTTGGTCGGCACCGA	3	48	1	CCGGCCTTGG	    0.980372	-48
GCACCGAAATCGGGGCTTGACCAGCGGTTG	3	71	1	CGGGGCTTGA	    0.972898	-25
         GCGGTCAACCGCTGGTCAAGC	3	85	0	CGGTCAACCG	    0.822248	-11
          **********

Masking position 1
Map Score:   9.81389

Number of sites scoring better than the average of aligned sites = 24423
Number in coding regions = 22546
Number in noncoding regions = 1877
Number of orfs with sites within 600 bp upstream = 1044
Fraction of orfs with sites within 600 bp upstream = 0.167684


Motif number 3

      CGAGGTCATTGCCCGAGCCTAGCG	1	5	1	GTCATTGCCC	    0.963805	-55
CGTCGTGTTGGCGAGCGCAGCGCTAGGCTC	1	25	0	GCGAGCGCAG	    0.981019	-35
GAGCCGCGCTGTGACTGGCGGGACGAAAG 	2	10	0	GTGACTGGCG	     0.97804	-59
CGGCCCGACCGCGAGGAGCCGCGCTGTGAC	2	25	0	GCGAGGAGCC	    0.889224	-44
TGCAGAGTAGGTGATCGGCGGCCCGACCGC	2	43	0	GTGATCGGCG	    0.993607	-26
         CGTCTGTGCAGAGTAGGTGAT	2	58	0	GTCTGTGCAG	    0.928225	-11
TTACCCCGATACCTTCGGCGTCGTTTGCGG	3	15	1	ACCTTCGGCG	    0.944951	-81
ATCCTAGCCGGCCTTGGTCGGCACCGAAAT	3	51	1	GCCTTGGTCG	     0.95288	-45
          **********

Masking position 7
Map Score:   3.7439

Number of sites scoring better than the average of aligned sites = 47968
Number in coding regions = 45143
Number in noncoding regions = 2825
Number of orfs with sites within 600 bp upstream = 1312
Fraction of orfs with sites within 600 bp upstream = 0.210729


Motif number 4

          **********

No masking
Map Score:   -1.82309e-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:   -1.82309e-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:   -1.82309e-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