AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i233_tpal_bbur_300.orf -o233_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	RTP00651	75	AE000520
#2	RTP00654	39	AE000520
#3	RTP00655	46	AE000520

Motif number 1

CCCGTAAAACTGTGCGGTGCGCGGT      	1	5	0	TGTCGGTGCG	    0.952072	-71
TACCGCATGTTCTCCCGTAAAACTGTGCGGT	1	18	0	TCTCCGTAAA	    0.898718	-58
ACAAATAATTTCTACCGCATGTTCTCCCGTA	1	30	0	TCTCCGCATG	    0.963607	-46
        CCTGTACGGTACGCACGCCCCCA	1	63	0	TGTCGGTACG	    0.609954	-13
TATTTTTTCCTCTCCGGCACAGGATTTGA  	2	21	1	TCTCGGCACA	    0.880361	-19
       ACATCTTCAATGAGTTTTTCGATG	3	4	1	TCTCAATGAG	    0.956742	-43
TTCAATGAGTTTTTCGATGAGCTTGTAGCCG	3	16	1	TTTCGATGAG	    0.956717	-31
          *** *******

Masking position 3
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

        ACCGCGCACCGCACAGTTTTAC	1	3	1	CGCGCACCGC	    0.998164	-73
CTGTACGGTACGCACGCCCCCATGACAAAT	1	55	0	CGCACGCCCC	     0.99766	-21
         AAGTAGGCCGCGGCTACAAGC	3	36	0	AGTAGGCCGC	    0.992787	-11
          **********

Masking position 7
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	    0.995128	-65
AGGAAAAAATAACCCGGTGCT         	2	2	0	AACCCGGTGC	    0.997203	-38
       TCAAATCCTGTGCCGGAGAGGAA	2	27	0	AATCCTGTGC	    0.998145	-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

    ACATCTTCAATGAGTTTTTCGATGAG	3	7	1	TCAATGAGTT	    0.993881	-40
AATGAGTTTTTCGATGAGCTTGTAGCCGCG	3	19	1	TCGATGAGCT	    0.997205	-28
          **********

Masking position 5
Map Score:   0.310387

Number of sites scoring better than the average of aligned sites = 1
Number in coding regions = 0
Number in noncoding regions = 1
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0


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