AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00580_synecho_reg_300.orf -o00580_synecho_300.ace -a/home/amcguire/genomes/ORF_synecho.txt -z/home/amcguire/genomes/synecho.fna -g0.48 -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 =  	0.48
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	sll1236	300	hypothetical protein. [EC:3.1.4.46]

Motif number 1

ATACTATTTTTCCCCCGTTAATTGGCAATTA	1	13	0	TCCCCGTTAA	    0.993744	-288
CTTTTACCTGTCCCTAGTAAAAGGAGCAAAA	1	150	0	TCCCTGTAAA	    0.995339	-151
AGCGATACTCTCCCCAGGAGATTTCCCAGGG	1	179	1	TCCCCGGAGA	    0.688455	-122
GTGGTCCAACTCCCTGGGAAATCTCCTGGGG	1	190	0	TCCCTGGAAA	     0.99464	-111
GATTCGCCCAACCCCCGTCAAATTCATCGGA	1	277	1	ACCCCGTCAA	    0.988511	-24
          ***** *****

Masking position 11
Map Score:   7.68123

Number of sites scoring better than the average of aligned sites = 309
Number in coding regions = 271
Number in noncoding regions = 38
Number of orfs with sites within 600 bp upstream = 46
Fraction of orfs with sites within 600 bp upstream = 0.00738837


Motif number 2

GGTTTTTGGGATTAATGTTAATTAATGTTA	1	105	1	ATTAATGTTA	    0.993908	-196
ATTAATGTTAATTAATGTTAATGGTTATTA	1	115	1	ATTAATGTTA	    0.993908	-186
GTTAATGGTTATTAATGATTTTTGCTCCTT	1	131	1	ATTAATGATT	    0.937267	-170
TCAAGGTTAAAATAATGTTAAGGCTTGCTG	1	249	0	AATAATGTTA	      0.9802	-52
GGTTGGGCGAATCAAGGTTAAAATAATGTT	1	260	0	ATCAAGGTTA	    0.970693	-41
          **********

Masking position 5
Map Score:   7.62871

Number of sites scoring better than the average of aligned sites = 43
Number in coding regions = 36
Number in noncoding regions = 7
Number of orfs with sites within 600 bp upstream = 8
Fraction of orfs with sites within 600 bp upstream = 0.00128493


Motif number 3

ATACTATTTTTCCCCCGTTAATTGGCAATT	1	14	0	TCCCCCGTTA	    0.990351	-287
CTTTTACCTGTCCCTAGTAAAAGGAGCAAA	1	151	0	TCCCTAGTAA	    0.977251	-150
AGCGATACTCTCCCCAGGAGATTTCCCAGG	1	179	1	TCCCCAGGAG	    0.971156	-122
GTGGTCCAACTCCCTGGGAAATCTCCTGGG	1	191	0	TCCCTGGGAA	    0.697398	-110
GATTCGCCCAACCCCCGTCAAATTCATCGG	1	277	1	ACCCCCGTCA	    0.981564	-24
          **********

Masking position 4
Map Score:   4.68672

Number of sites scoring better than the average of aligned sites = 601
Number in coding regions = 539
Number in noncoding regions = 62
Number of orfs with sites within 600 bp upstream = 74
Fraction of orfs with sites within 600 bp upstream = 0.0118856


Motif number 4

ACAAGATAAATACGGGATTTTGACAAGCTAA	1	50	0	TACGGATTTT	    0.975942	-251
TCTGTATCGGTGCAGGTTTTTGGGATTAATG	1	91	1	TGCGGTTTTT	    0.993732	-210
TAATTAATGTTAATGGTTATTAATGATTTTT	1	123	1	TAAGGTTATT	    0.962685	-178
TGTTAAGGCTTGCTGATTATTAACTCAAACT	1	233	0	TGCGATTATT	    0.975554	-68
          *** *******

Masking position 8
Map Score:   0.463025

Number of sites scoring better than the average of aligned sites = 206
Number in coding regions = 187
Number in noncoding regions = 19
Number of orfs with sites within 600 bp upstream = 23
Fraction of orfs with sites within 600 bp upstream = 0.00369419


Motif number 5

AATAGTATCAGCTATTAGCTTGTCAAAATC	1	36	1	GCTATTAGCT	    0.991486	-265
GGTTATTAATGATTTTTGCTCCTTTTACTA	1	137	1	GATTTTTGCT	    0.977114	-164
GGAGAGTATCGCTTTTACCTGTCCCTAGTA	1	162	0	GCTTTTACCT	    0.991117	-139
          **********

Masking position 5
Map Score:   0.371102

Number of sites scoring better than the average of aligned sites = 66
Number in coding regions = 52
Number in noncoding regions = 14
Number of orfs with sites within 600 bp upstream = 13
Fraction of orfs with sites within 600 bp upstream = 0.00208802


Motif number 6

          **********

No masking
Map Score:   7.91135e-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:   7.91135e-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:   7.91135e-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