AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i097_bsub_mtub_100.orf -o097_bsub_mtub_100.ace -a/home/amcguire/genomes/ORF_bsub.txt -z/home/amcguire/genomes/bsub.fna -g0.55 -x5 -e 
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 =  	0.55
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	pitB	233	pitB

Motif number 1

ACGGACAAGAGCCGGCCGGACCAAGGCCGG	1	13	1	GCCGGCCGGA	    0.510968	-221
TTGGCCGGCCGATGACCGGCCTTGGTCCGG	1	28	0	GATGACCGGC	    0.971249	-206
TTGCAGGCCTGTTGGCCGGCCGATGACCGG	1	39	0	GTTGGCCGGC	    0.584817	-195
TGCGCTCGAGACTTGCAGGCCTGTTGGCCG	1	51	0	ACTTGCAGGC	    0.829189	-183
AATCGGCTTTGACGACCGGCGGACCGAGCT	1	95	0	GACGACCGGC	    0.614168	-139
ACAGATGCGGGGAAATCGGCTTTGACGACC	1	108	0	GGAAATCGGC	    0.860184	-126
GCTGCATCGGACTGACCGGACAGATGCGGG	1	127	0	ACTGACCGGA	    0.959649	-107
GATGAATAACGGTGACCGACGCTGCATCGG	1	147	0	GGTGACCGAC	    0.920043	-87
GCTAGCAACGGGTAAACGCCGGATGAATAA	1	168	0	GGTAAACGCC	    0.842068	-66
TTTACCCGTTGCTAGCCGCCATGACGTAGC	1	182	1	GCTAGCCGCC	    0.874192	-52
GCGATCGAGCGTCAGCAGGCTACGTCATGG	1	200	0	GTCAGCAGGC	    0.746824	-34
GATCGCCAACACAAGCCGAC          	1	224	1	ACAAGCCGAC	    0.887124	-10
          **********

Masking position 8
Map Score:   21.9916

Number of sites scoring better than the average of aligned sites = 3596
Number in coding regions = 3358
Number in noncoding regions = 238
Number of orfs with sites within 600 bp upstream = 161
Fraction of orfs with sites within 600 bp upstream = 0.0258593


Motif number 2

GCCTTGGTCCGGCCGGCTCTTGTCCGTGC 	1	10	0	GGCCGGCTCT	    0.989183	-224
AAGTCTCGAGCGCAACATCTTCGTGGACAG	1	67	1	CGCAACATCT	    0.953515	-167
ACATCTTCGTGGACAGCTCGGTCCGCCGGT	1	81	1	GGACAGCTCG	    0.885739	-153
AAGCCGATTTCCCCGCATCTGTCCGGTCAG	1	116	1	CCCCGCATCT	    0.971926	-118
CGGTGACCGACGCTGCATCGGACTGACCGG	1	138	0	CGCTGCATCG	    0.704277	-96
AACGGGTAAACGCCGGATGAATAACGGTGA	1	162	0	CGCCGGATGA	    0.961944	-72
AGCGTCAGCAGGCTACGTCATGGCGGCTAG	1	193	0	GGCTACGTCA	    0.890474	-41
AGCCTGCTGACGCTCGATCGCCAACACAAG	1	209	1	CGCTCGATCG	    0.840303	-25
          **********

Masking position 8
Map Score:   5.92606

Number of sites scoring better than the average of aligned sites = 2228
Number in coding regions = 2074
Number in noncoding regions = 154
Number of orfs with sites within 600 bp upstream = 113
Fraction of orfs with sites within 600 bp upstream = 0.0181497


Motif number 3

CACGAAGATGTTGCGCTCGAGACTTGCAGG	1	62	0	TTGCGCTCGA	    0.978262	-172
AAATCGGCTTTGACGACCGGCGGACCGAGC	1	96	0	TGACGACCGG	    0.990906	-138
CGTAGCCTGCTGACGCTCGATCGCCAACAC	1	206	1	TGACGCTCGA	    0.996763	-28
          **********

Masking position 1
Map Score:   0.833848

Number of sites scoring better than the average of aligned sites = 42
Number in coding regions = 42
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 4

          **********

No masking
Map Score:   -3.30951e-14

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:   -3.30951e-14

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:   -3.30951e-14

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