AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i068_tpal_bbur_300.orf -o068_tpal_bbur_300.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

CGACACACGAGCGCAGAGGGCAGAAAACTC	1	37	0	GCGCAGAGGG	    0.987015	-177
ACTGCGCAGCACGCAGTCCACCGGTAACAG	1	68	0	ACGCAGTCCA	    0.986824	-146
ACTGCGTGCTGCGCAGTCGATGCTTTCCAA	1	81	1	GCGCAGTCGA	    0.998499	-133
TGTGCCGCTGGCACCGCCCGCTTCAAGATA	1	138	0	GCACCGCCCG	    0.991128	-76
GGTGCCAGCGGCACAGCCGAAACCTTTTGA	1	153	1	GCACAGCCGA	    0.998138	-61
GAGGCTTCAAGCGCAGCCAAAAACTCAAAA	1	177	0	GCGCAGCCAA	    0.997504	-37
          **********

Masking position 6
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

  CAGAAGAAGCGCGTGAGATCCTACGGGA	1	9	1	GCGCGTGAGA	     0.99111	-205
TGCCCTCTGCGCTCGTGTGTCGCCTGTTAC	1	45	1	GCTCGTGTGT	    0.953223	-169
GCTTTCCAAAGCGTTTGGGGAAGAAAAGGC	1	102	1	GCGTTTGGGG	    0.988017	-112
CTGGCACCGCCCGCTTCAAGATAAGATCGG	1	131	0	CCGCTTCAAG	    0.956389	-83
ACAGCCGAAACCTTTTGAGTTTTTGGCTGC	1	165	1	CCTTTTGAGT	    0.933872	-49
GTTTTTGGCTGCGCTTGAAGCCTCCCAACT	1	183	1	GCGCTTGAAG	    0.994525	-31
          **********

Masking position 6
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	    0.995203	-183
CAAAGCGTTTGGGGAAGAAAAGGCCGATCT	1	108	1	GGGGAAGAAA	    0.997388	-106
       GGAGGGGGAGAAGTTGGGAGGCT	1	201	0	GGGGGAGAAG	    0.997902	-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	    0.975997	-211
GAGATCCTACGGGAGTTTTCTGCCCTCTGC	1	25	1	GGGAGTTTTC	    0.987163	-189
AAGATAAGATCGGCCTTTTCTTCCCCAAAC	1	114	0	CGGCCTTTTC	    0.991666	-100
CCGCTGGCACCGCCCGCTTCAAGATAAGAT	1	134	0	CGCCCGCTTC	     0.98798	-80
GGGAGAAGTTGGGAGGCTTCAAGCGCAGCC	1	189	0	GGGAGGCTTC	    0.994677	-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

GGCAGAAAACTCCCGTAGGATCTCACGCGC	1	19	0	TCCCGTAGGA	    0.879327	-195
TGTCGCCTGTTACCGGTGGACTGCGTGCTG	1	62	1	TACCGGTGGA	    0.986672	-152
GTTTCGGCTGTGCCGCTGGCACCGCCCGCT	1	146	0	TGCCGCTGGC	    0.982845	-68
          **********

Masking position 1
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