AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i137_tpal_bbur_300.orf -o137_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	RTP00721	95	AE000520
#2	RTP00722	90	AE000520
#3	RTP00723	31	AE000520

Motif number 1

     CAACGGCTTCGCGTTCACGACAGAATT	1	6	1	GTTCGGTTCA	    0.991019	-90
AGAAAGGCAAGCCCCGCGTCTAATTCTGTCGT	1	27	0	GCCCGGTCTA	    0.954024	-69
CCTTTCTTATGTTCCGTGCGCAGTTCCTGGTG	1	52	1	GTCCGGCGCA	    0.995932	-44
       CCCTTTTCGAGCCCACATGGAACCG	2	4	1	TTTCGGCCCA	    0.992663	-87
AATCGATATGGGTCCGGTTCCATGTGGGCTCG	2	18	0	GTCCGTTCCA	    0.995789	-73
GACACCTAGTGATTCGCTTGCAGTAATTTCAA	2	53	0	GTTCGTTGCA	    0.990267	-38
ACCGCCGCGGTTTTCGACACCTAGTGATTCGC	2	68	0	TTTCGCACCT	    0.891283	-23
GGGCGCACGAGTTTCGACACCACCT       	3	17	1	GTTCGCACCA	    0.995025	-15
          * **** *****

Masking position 6
Map Score:   12.1637

Number of sites scoring better than the average of aligned sites = 489
Number in coding regions = 142
Number in noncoding regions = 347
Number of orfs with sites within 600 bp upstream = 19
Fraction of orfs with sites within 600 bp upstream = 0.00305172


Motif number 2

ACGACAGAATTAGACGCGGGGCTTGCCTTT	1	27	1	TAGACGCGGG	     0.97781	-69
CGTGCGCAGTTCCTGGTGGGCTGGGCTATA	1	66	1	TCCTGGTGGG	    0.974881	-30
CCATGTGGGCTCGAAAAGGG          	2	1	0	TCGAAAAGGG	    0.978538	-90
TGGGTCCGGTTCCATGTGGGCTCGAAAAGG	2	12	0	TCCATGTGGG	    0.828224	-79
TTCAACGTAATCGATATGGGTCCGGTTCCA	2	28	0	TCGATATGGG	    0.984353	-63
          **********

Masking position 1
Map Score:   5.46114

Number of sites scoring better than the average of aligned sites = 316
Number in coding regions = 82
Number in noncoding regions = 234
Number of orfs with sites within 600 bp upstream = 9
Fraction of orfs with sites within 600 bp upstream = 0.00144555


Motif number 3

ACAGAATTAGACGCGGGGCTTGCCTTTCTT	1	30	1	ACGCGGGGCT	    0.986096	-66
GTGCGCAGTTCCTGGTGGGCTGGGCTATAC	1	67	1	CCTGGTGGGC	    0.991543	-29
GCTGGGCTATACGCAGCGGCA         	1	85	1	ACGCAGCGGC	     0.98432	-11
GGGTCCGGTTCCATGTGGGCTCGAAAAGGG	2	11	0	CCATGTGGGC	    0.978297	-80
GTGTCGAAAACCGCGGCGGTT         	2	80	1	CCGCGGCGGT	    0.995806	-11
TGGTGTCGAAACTCGTGCGCCCAAGTTC  	3	9	0	ACTCGTGCGC	    0.974116	-23
          **********

Masking position 2
Map Score:   5.71133

Number of sites scoring better than the average of aligned sites = 1312
Number in coding regions = 383
Number in noncoding regions = 929
Number of orfs with sites within 600 bp upstream = 26
Fraction of orfs with sites within 600 bp upstream = 0.00417604


Motif number 4

       CAACGGCTTCGCGTTCACGACAG	1	4	1	CGGCTTCGCG	    0.992985	-92
ATTAGACGCGGGGCTTGCCTTTCTTATGTT	1	35	1	GGGCTTGCCT	    0.985974	-61
AGTTCCTGGTGGGCTGGGCTATACGCAGCG	1	73	1	GGGCTGGGCT	     0.99731	-23
TCGACACCTAGTGATTCGCTTGCAGTAATT	2	57	0	GTGATTCGCT	    0.979993	-34
          **********

Masking position 5
Map Score:   3.60394

Number of sites scoring better than the average of aligned sites = 290
Number in coding regions = 80
Number in noncoding regions = 210
Number of orfs with sites within 600 bp upstream = 6
Fraction of orfs with sites within 600 bp upstream = 0.000963701


Motif number 5

          **********

No masking
Map Score:   -2.59896e-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:   -2.59896e-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 7

          **********

No masking
Map Score:   -2.59896e-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