AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i303_tpal_bbur_100.orf -o303_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	RTP00417	194	AE000520
#2	RTP00592	140	AE000520

Motif number 1

TTTCACTGATGGTCGAGTTCCGCT         	1	2	0	GGCGTTCCGC	    0.998451	-193
TTAGATGCCAACACGGATACCTCTCCAAAGGAG	1	51	1	ACCGTACCTC	    0.973181	-144
CCGCCGATCGGGAAGCAATCCGCACACATGATC	1	97	1	GGAGATCCGC	    0.945599	-98
CCTGCCCCACACGCTCCTTCCACGTGCGGTAAA	1	147	1	ACCTTTCCAC	    0.975837	-48
AAGAGCTCGAGCCCTTTTACCGCACGTGGAAGG	1	162	0	GCCTTACCGC	    0.993642	-33
GTACCCATTGTGCCTGTTTCCGCCGTTTTCTTA	2	29	0	TGCTTTCCGC	    0.987447	-112
TCACCGTCTTACCCGCCTTCCGGACAACCATGC	2	70	0	ACCGTTCCGG	    0.990445	-71
          ** **  ******

Masking position 10
Map Score:   6.7473

Number of sites scoring better than the average of aligned sites = 350
Number in coding regions = 111
Number in noncoding regions = 239
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 2

       AGCGGAACTCGACCATCAGTGAA	1	4	1	GGAACTCGAC	    0.954043	-191
AGATAGATCTGCAACCCGCCGATCGGGAAG	1	82	1	GCAACCCGCC	    0.994202	-113
TGTGCGGATTGCTTCCCGATCGGCGGGTTG	1	93	0	GCTTCCCGAT	    0.908317	-102
TTTTCTTAAAGCTACCCATCACATCT    	2	7	0	GCTACCCATC	     0.98833	-134
TGCGGGCTTGCGTACCCATTGTGCCTGTTT	2	43	0	CGTACCCATT	    0.906973	-98
TACTCACCGTCTTACCCGCCTTCCGGACAA	2	76	0	CTTACCCGCC	    0.976668	-65
TAAGTACTAAGGTACTCACCGTCTTACCCG	2	88	0	GGTACTCACC	    0.980918	-53
          **********

Masking position 5
Map Score:   6.42937

Number of sites scoring better than the average of aligned sites = 1002
Number in coding regions = 284
Number in noncoding regions = 718
Number of orfs with sites within 600 bp upstream = 34
Fraction of orfs with sites within 600 bp upstream = 0.00546097


Motif number 3

TTGGCATCTAAAACGAGATATGATTATTTT	1	32	0	AAACGAGATA	    0.981535	-163
ATACCTCTCCAAAGGAGATAGATCTGCAAC	1	67	1	AAAGGAGATA	    0.981555	-128
CACGTGCGGTAAAAGGGCTCGAGCTCTTTT	1	167	1	AAAAGGGCTC	    0.988871	-28
  GAAAACGAAAAAGAGCTCGAGCCCTTTT	1	177	0	AAAAGAGCTC	    0.993441	-18
          **********

Masking position 3
Map Score:   2.683

Number of sites scoring better than the average of aligned sites = 79
Number in coding regions = 28
Number in noncoding regions = 51
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 4

CGTTTTAGATGCCAACACGGATACCTCTCC	1	47	1	GCCAACACGG	     0.99035	-148
GAAGCAATCCGCACACATGATCATACTTTT	1	108	1	GCACACATGA	    0.968995	-87
CAATCACCTGCCCCACACGCTCCTTCCACG	1	141	1	CCCCACACGC	    0.987066	-54
AGCCCTTTTACCGCACGTGGAAGGAGCGTG	1	156	0	CCGCACGTGG	    0.696976	-39
GGGTACGCAAGCCCGCATGGTTGTCCGGAA	2	56	1	GCCCGCATGG	    0.969012	-85
          **********

Masking position 6
Map Score:   3.39574

Number of sites scoring better than the average of aligned sites = 404
Number in coding regions = 123
Number in noncoding regions = 281
Number of orfs with sites within 600 bp upstream = 9
Fraction of orfs with sites within 600 bp upstream = 0.00144555


Motif number 5

          **********

No masking
Map Score:   2.43208e-15

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:   2.43208e-15

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:   2.43208e-15

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