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_100.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	    0.958955	-46
CTAGCGCTGCGCTCGCCAACACGACGACAC	1	29	1	GCTCGCCAAC	    0.990108	-31
GCCAGTCACAGCGCGGCTCCTCGCGGTCGG	2	21	1	GCGCGGCTCC	    0.989529	-48
GTGATCGGCGGCCCGACCGCGAGGAGCCGC	2	33	0	GCCCGACCGC	    0.994579	-36
TCGGGCCGCCGATCACCTACTCTGCACAGA	2	47	1	GATCACCTAC	    0.795671	-22
        CTGCTTACCCCGATACCTTCGG	3	3	1	GCTTACCCCG	    0.946996	-93
CGGCTAGGATGCCCGCCCGCAAACGACGCC	3	31	0	GCCCGCCCGC	    0.995066	-65
TGCCGACCAAGGCCGGCTAGGATGCCCGCC	3	44	0	GGCCGGCTAG	    0.976564	-52
AGCCGGCCTTGGTCGGCACCGAAATCGGGG	3	56	1	GGTCGGCACC	    0.987641	-40
CGAAATCGGGGCTTGACCAGCGGTTGACCG	3	75	1	GCTTGACCAG	    0.972531	-21
CTTGACCAGCGGTTGACCGC          	3	86	1	GGTTGACCGC	    0.969735	-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

     CGAGGTCATTGCCCGAGCCTAGCGC	1	6	1	TCATTGCCCG	    0.980636	-54
CTCGCCAACACGACGACACGAAACCTTTGG	1	40	1	CGACGACACG	    0.949977	-20
GCGCTGTGACTGGCGGGACGAAAG      	2	5	0	TGGCGGGACG	    0.957718	-64
GTCCCGCCAGTCACAGCGCGGCTCCTCGCG	2	16	1	TCACAGCGCG	    0.919383	-53
AGTAGGTGATCGGCGGCCCGACCGCGAGGA	2	38	0	CGGCGGCCCG	    0.958482	-31
AAGGCCGGCTAGGATGCCCGCCCGCAAACG	3	36	0	AGGATGCCCG	    0.972262	-60
TCGGTGCCGACCAAGGCCGGCTAGGATGCC	3	48	0	CCAAGGCCGG	    0.977138	-48
CAACCGCTGGTCAAGCCCCGATTTCGGTGC	3	71	0	TCAAGCCCCG	    0.968465	-25
GCTTGACCAGCGGTTGACCGC         	3	85	1	CGGTTGACCG	     0.82789	-11
          **********

Masking position 10
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	2	1	GAGGCAGCCC	    0.994458	-58
CGTCGTGTTGGCGAGCGCAGCGCTAGGCTCGGG	1	22	0	GCGACGGCGC	    0.996117	-38
TTTCGTCCCGCCAGTCACAGCGCGGCTCCTCGC	2	12	1	CCAGCAGCGC	    0.987924	-57
TGCAGAGTAGGTGATCGGCGGCCCGACCGCGAG	2	40	0	GTGACGGGCC	    0.983917	-29
ATGCCCGCCCGCAAACGACGCCGAAGGTATCGG	3	20	0	GCAACGGCCG	    0.990863	-76
GATTTCGGTGCCGACCAAGGCCGGCTAGGATGC	3	49	0	CCGACAGCCG	    0.996006	-47
CGGTCAACCGCTGGTCAAGCCCCGATTTCGGTG	3	72	0	CTGGCACCCC	    0.978755	-24
          **** **  ****

Masking position 6
Map Score:   8.24875

Number of sites scoring better than the average of aligned sites = 13899
Number in coding regions = 13097
Number in noncoding regions = 802
Number of orfs with sites within 600 bp upstream = 545
Fraction of orfs with sites within 600 bp upstream = 0.0875361


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