AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i233_tpal_bbur_100.orf -o233_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	RTP00651	75	AE000520
#2	RTP00654	39	AE000520
#3	RTP00655	46	AE000520

Motif number 1

      ACCGCGCACCGCACAGTTTTACGGG	1	5	1	CGCACCGACA	     0.95559	-71
ACCGCACAGTTTTACGGGAGAACATGCGGTA	1	18	1	TTTACGGAGA	    0.903271	-58
TACGGGAGAACATGCGGTAGAAATTATTTGT	1	30	1	CATGCGGAGA	    0.963102	-46
TGGGGGCGTGCGTACCGTACAGG        	1	63	1	CGTACCGACA	    0.618304	-13
  TCAAATCCTGTGCCGGAGAGGAAAAAATA	2	21	0	TGTGCCGAGA	    0.887493	-19
CATCGAAAAACTCATTGAAGATGT       	3	4	0	CTCATTGAGA	    0.952577	-43
CGGCTACAAGCTCATCGAAAAACTCATTGAA	3	16	0	CTCATCGAAA	    0.952554	-31
          ******* ***

Masking position 9
Map Score:   8.86601

Number of sites scoring better than the average of aligned sites = 624
Number in coding regions = 191
Number in noncoding regions = 433
Number of orfs with sites within 600 bp upstream = 17
Fraction of orfs with sites within 600 bp upstream = 0.00273049


Motif number 2

GTAAAACTGTGCGGTGCGCGGT        	1	3	0	GCGGTGCGCG	    0.998164	-73
ATTTGTCATGGGGGCGTGCGTACCGTACAG	1	55	1	GGGGCGTGCG	     0.99766	-21
GCTTGTAGCCGCGGCCTACTT         	3	36	1	GCGGCCTACT	    0.992787	-11
          **********

Masking position 4
Map Score:   1.65079

Number of sites scoring better than the average of aligned sites = 26
Number in coding regions = 6
Number in noncoding regions = 20
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0


Motif number 3

GTTCTCCCGTAAAACTGTGCGGTGCGCGGT	1	11	0	AAAACTGTGC	    0.994898	-65
AGGAAAAAATAACCCGGTGCT         	2	2	0	AACCCGGTGC	    0.997197	-38
       TCAAATCCTGTGCCGGAGAGGAA	2	27	0	AATCCTGTGC	    0.998063	-13
          **********

Masking position 2
Map Score:   4.66098

Number of sites scoring better than the average of aligned sites = 65
Number in coding regions = 18
Number in noncoding regions = 47
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0


Motif number 4

TTCTCCCGTAAAACTGTGCGGTGCGCGGT 	1	10	0	AAACTGTGCG	    0.984026	-66
CATGCGGTAGAAATTATTTGTCATGGGGGC	1	40	1	AAATTATTTG	    0.912154	-36
GCTCATCGAAAAACTCATTGAAGATGT   	3	8	0	AAACTCATTG	    0.991701	-39
CCGCGGCTACAAGCTCATCGAAAAACTCAT	3	20	0	AAGCTCATCG	    0.991254	-27
          **********

Masking position 5
Map Score:   1.1108

Number of sites scoring better than the average of aligned sites = 316
Number in coding regions = 101
Number in noncoding regions = 215
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 5

          **********

No masking
Map Score:   7.34864e-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:   7.34864e-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:   7.34864e-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