AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i068_tpal_bbur_100.orf -o068_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	RTP00890	213	AE000520

Motif number 1

GAGTTTTCTGCCCTCTGCGCTCGTGTGTCG	1	37	1	CCCTCTGCGC	    0.988603	-177
CTGTTACCGGTGGACTGCGTGCTGCGCAGT	1	68	1	TGGACTGCGT	    0.988435	-146
TTGGAAAGCATCGACTGCGCAGCACGCAGT	1	81	0	TCGACTGCGC	    0.998661	-133
TATCTTGAAGCGGGCGGTGCCAGCGGCACA	1	138	1	CGGGCGGTGC	    0.992217	-76
TCAAAAGGTTTCGGCTGTGCCGCTGGCACC	1	153	0	TCGGCTGTGC	    0.998367	-61
TTTTGAGTTTTTGGCTGCGCTTGAAGCCTC	1	177	1	TTGGCTGCGC	    0.997811	-37
          **********

Masking position 5
Map Score:   12.7639

Number of sites scoring better than the average of aligned sites = 149
Number in coding regions = 43
Number in noncoding regions = 106
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 2

TCCCGTAGGATCTCACGCGCTTCTTCTG  	1	9	0	TCTCACGCGC	    0.991025	-205
GTAACAGGCGACACACGAGCGCAGAGGGCA	1	45	0	ACACACGAGC	    0.952782	-169
GCCTTTTCTTCCCCAAACGCTTTGGAAAGC	1	102	0	CCCCAAACGC	    0.987898	-112
CCGATCTTATCTTGAAGCGGGCGGTGCCAG	1	131	1	CTTGAAGCGG	    0.955972	-83
GCAGCCAAAAACTCAAAAGGTTTCGGCTGT	1	165	0	ACTCAAAAGG	    0.933273	-49
AGTTGGGAGGCTTCAAGCGCAGCCAAAAAC	1	183	0	CTTCAAGCGC	    0.994471	-31
          **********

Masking position 5
Map Score:   4.1303

Number of sites scoring better than the average of aligned sites = 512
Number in coding regions = 144
Number in noncoding regions = 368
Number of orfs with sites within 600 bp upstream = 19
Fraction of orfs with sites within 600 bp upstream = 0.00305172


Motif number 3

ACGAGCGCAGAGGGCAGAAAACTCCCGTAG	1	31	0	AGGGCAGAAA	    0.995404	-183
CAAAGCGTTTGGGGAAGAAAAGGCCGATCT	1	108	1	GGGGAAGAAA	    0.997497	-106
       GGAGGGGGAGAAGTTGGGAGGCT	1	201	0	GGGGGAGAAG	     0.99799	-13
          **********

Masking position 6
Map Score:   3.30808

Number of sites scoring better than the average of aligned sites = 280
Number in coding regions = 78
Number in noncoding regions = 202
Number of orfs with sites within 600 bp upstream = 13
Fraction of orfs with sites within 600 bp upstream = 0.00208802


Motif number 4

AGGATCTCACGCGCTTCTTCTG        	1	3	0	GCGCTTCTTC	    0.977074	-211
GAGATCCTACGGGAGTTTTCTGCCCTCTGC	1	25	1	GGGAGTTTTC	    0.987745	-189
AAGATAAGATCGGCCTTTTCTTCCCCAAAC	1	114	0	CGGCCTTTTC	    0.992045	-100
CCGCTGGCACCGCCCGCTTCAAGATAAGAT	1	134	0	CGCCCGCTTC	    0.988525	-80
GGGAGAAGTTGGGAGGCTTCAAGCGCAGCC	1	189	0	GGGAGGCTTC	     0.99492	-25
          **********

Masking position 8
Map Score:   4.19034

Number of sites scoring better than the average of aligned sites = 895
Number in coding regions = 272
Number in noncoding regions = 623
Number of orfs with sites within 600 bp upstream = 17
Fraction of orfs with sites within 600 bp upstream = 0.00273049


Motif number 5

GCGCGTGAGATCCTACGGGAGTTTTCTGCC	1	19	1	TCCTACGGGA	    0.883174	-195
CAGCACGCAGTCCACCGGTAACAGGCGACA	1	62	0	TCCACCGGTA	    0.986836	-152
AGCGGGCGGTGCCAGCGGCACAGCCGAAAC	1	146	1	GCCAGCGGCA	    0.983278	-68
          **********

Masking position 10
Map Score:   0.294646

Number of sites scoring better than the average of aligned sites = 225
Number in coding regions = 56
Number in noncoding regions = 169
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 6

          **********

No masking
Map Score:   -1.68098e-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:   -1.68098e-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 8

          **********

No masking
Map Score:   -1.68098e-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