AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i232_tpal_bbur_100.orf -o232_tpal_bbur_100.ace -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/synecho.fna -g0.40 -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 =  	0.4
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RTP00486	40	AE000520
#2	RTP01007	118	AE000520
#3	RBB00664	114	3615

Motif number 1

ACGCAGGGTGCTGACCACCAAGGTAGATGAGT	1	12	0	CTGCCACAAG	    0.998404	-29
CCTGTATCACCTGGCCAACAAGCTCAATCTGC	2	32	1	CTGCCACAAG	    0.996489	-87
CAAGCTCAATCTGCGCAACAAGAATTGCCTCC	2	50	1	CTGGCACAAG	    0.996315	-69
TTGCCTCCACCTGCCCTGCCCGGTGCAAAGCC	2	74	1	CTGCCTCCCG	    0.971146	-45
AGCCCGCTCTCGGTCCATCGCCCACTC     	2	102	1	CGGCCACGCC	    0.987512	-17
          *** *** ****

Masking position 6
Map Score:   7.10131

Number of sites scoring better than the average of aligned sites = 122
Number in coding regions = 26
Number in noncoding regions = 96
Number of orfs with sites within 600 bp upstream = 1
Fraction of orfs with sites within 600 bp upstream = 0.000160617


Motif number 2

CTTGGTGGTCAGCACCCTGCGTATAGCTG 	1	22	1	AGCACCCTGC	    0.979002	-19
CTGGACCTGTATCACCTGGCCAACAAGCTC	2	27	1	ATCACCTGGC	    0.987671	-92
AAGAATTGCCTCCACCTGCCCTGCCCGGTG	2	69	1	TCCACCTGCC	    0.993626	-50
GAGCGGGCTTTGCACCGGGCAGGGCAGGTG	2	81	0	TGCACCGGGC	    0.997885	-38
CCGCTCTCGGTCCATCGCCCACTC      	2	105	1	TCCATCGCCC	    0.959957	-14
          **********

Masking position 4
Map Score:   3.79568

Number of sites scoring better than the average of aligned sites = 511
Number in coding regions = 163
Number in noncoding regions = 348
Number of orfs with sites within 600 bp upstream = 10
Fraction of orfs with sites within 600 bp upstream = 0.00160617


Motif number 3

TGCTGACCACCAAGGTAGATGAGTT     	1	6	0	CAAGGTAGAT	    0.990594	-35
ACCTGGCCAACAAGCTCAATCTGCGCAACA	2	40	1	CAAGCTCAAT	    0.994866	-79
GAGTTAATTTCAAGCTAAATTATATCAAAT	3	25	1	CAAGCTAAAT	    0.995682	-90
          **********

Masking position 3
Map Score:   2.51904

Number of sites scoring better than the average of aligned sites = 54
Number in coding regions = 14
Number in noncoding regions = 40
Number of orfs with sites within 600 bp upstream = 1
Fraction of orfs with sites within 600 bp upstream = 0.000160617


Motif number 4

AAAAAAAAAATTATTTGATATAATTTAGCT	3	37	0	TTATTTGATA	    0.989286	-78
TTTTTTTTTTTAAATTGATAATTATTTGGT	3	58	1	TAAATTGATA	    0.967391	-57
AAATTGATAATTATTTGGTATACTAATATT	3	69	1	TTATTTGGTA	     0.98728	-46
          **********

Masking position 3
Map Score:   1.29589

Number of sites scoring better than the average of aligned sites = 17
Number in coding regions = 5
Number in noncoding regions = 12
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:   -4.30999e-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:   -4.30999e-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:   -4.30999e-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