AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00562_synecho_reg_100.orf -o00562_synecho_100.ace -a/home/amcguire/alignace/lib/ORF_synecho.txt -z/skink1/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	sll0776	77	probable serine/threonine-protein kinase sll0776. [EC:2.7.1.-]
#2	sll0775	222	merR; hypothetical protein.

Motif number 1

TTTTTTACAGTTCAATTGATTGAATTAAAGTTGAATTTA	1	12	1	TTGTTATAAA	    0.958956	-66
AATCAAAAAATTGAAATACTTAAATTCAACTTTAATTCA	1	32	0	TTATTATCAA	    0.968449	-46
AGTATTTCAATTTTTTGATTTTAGATAAACAAACAAC  	1	51	1	TTATTGTAAA	    0.948545	-27
TGCTATCCCATTGACTAATTTTGGTGAAATTAACTTTAA	2	17	1	TTATTGGAAA	    0.817874	-206
TTTATCTGGATTTTGGTAGTACTGTTAAAGTTAATTTCA	2	41	0	TTATAGTAAA	    0.977021	-182
TCAGGACTCTTTTATTAACTTTCGTTAAAGCCGTTTTCC	2	121	0	TTATTGTAAA	    0.848234	-102
TATAGGAATATTACCCTAGTTTTACGAAAAGGATCTCAT	2	164	0	TTATTAGAAA	    0.971737	-59
          **     * **  * ****

Masking position 18
Map Score:   7.16387

Number of sites scoring better than the average of aligned sites = 85
Number in coding regions = 63
Number in noncoding regions = 22
Number of orfs with sites within 600 bp upstream = 25
Fraction of orfs with sites within 600 bp upstream = 0.00401542


Motif number 2

AATTCAACTTTAATTCAATCAATTGAACTGTAAAAAA	1	12	0	TATCAACAAA	     0.92595	-66
GTTGTTTGTTTATCTAAAATCAAAAAATTGAAATACT	1	51	0	TACAAATAAA	    0.991851	-27
AAAGTTAATTTCACCAAAATTAGTCAATGGGATAGCA	2	17	0	TCCAAATAAA	     0.99015	-206
TTAACAGTACTACCAAAATCCAGATAAATTTTCTTCC	2	52	1	TACAAACAAA	    0.990215	-171
AAAACGGCTTTAACGAAAGTTAATAAAAGAGTCCTGA	2	123	1	TACAAATAAA	    0.991809	-100
GAGATCCTTTTCGTAAAACTAGGGTAATATTCCTATA	2	166	1	TCTAAATGAA	    0.925533	-57
          ** * *** * *   **

Masking position 8
Map Score:   2.14812

Number of sites scoring better than the average of aligned sites = 89
Number in coding regions = 70
Number in noncoding regions = 19
Number of orfs with sites within 600 bp upstream = 22
Fraction of orfs with sites within 600 bp upstream = 0.00353357


Motif number 3

 TGACTATGCTATCCCATTGACTAATTTTG	2	10	1	TATCCCATTG	     0.98569	-213
TTCTTCCGTTTTTCCCTTTGCTCCATGGCG	2	82	1	TTTCCCTTTG	    0.995353	-141
GTTAAAGCCGTTTTCCTTAGGCGATCGCCA	2	107	0	TTTTCCTTAG	    0.978037	-116
          **********

Masking position 3
Map Score:   0.915385

Number of sites scoring better than the average of aligned sites = 120
Number in coding regions = 101
Number in noncoding regions = 19
Number of orfs with sites within 600 bp upstream = 25
Fraction of orfs with sites within 600 bp upstream = 0.00401542


Motif number 4

TTCACCAAAATTAGTCAATGGGATAGCATAGT	2	13	0	TTATCAAGGG	    0.980307	-210
GCGATCGCCATGGAGCAAAGGGAAAAACGGAA	2	85	0	TGGGCAAGGG	      0.9888	-138
GGCGATCGCCTAAGGAAAACGGCTTTAACGAA	2	108	1	TAAGAAACGG	    0.898266	-115
TTAACGAAAGTTAATAAAAGAGTCCTGACGGA	2	132	1	TTATAAAGAG	    0.938754	-91
AAAAGAGTCCTGACGGAATGAGATCCTTTTCG	2	147	1	TGAGGAAGAG	     0.98107	-76
TACCCTAGTTTTACGAAAAGGATCTCATTCCG	2	160	0	TTAGAAAGGA	    0.947237	-63
TTTGTCTGTATGAGGCAACGATACGGCT    	2	205	1	TGAGCAAGAT	     0.95554	-18
          *** **** ***

Masking position 7
Map Score:   2.39378

Number of sites scoring better than the average of aligned sites = 1023
Number in coding regions = 886
Number in noncoding regions = 137
Number of orfs with sites within 600 bp upstream = 146
Fraction of orfs with sites within 600 bp upstream = 0.02345


Motif number 5

          **********

No masking
Map Score:   -3.38628e-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 6

          **********

No masking
Map Score:   -3.38628e-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:   -3.38628e-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