AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i298_mixed13_synecho_reg_100.orf -o298_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	RCY20391	256	Synechocystis
#2	RCY49700	117	Synechocystis

Motif number 1

       GGGTAAGGGGAGACTAAATGGGC	1	4	1	TAAGGGGAGA	    0.925653	-253
AGGGGAGACTAAATGGGCTAATCTTTAAGA	1	16	1	AAATGGGCTA	    0.918348	-241
AACGAAGCGCTCCGGGGAAAAGATCCGTTA	1	75	0	TCCGGGGAAA	    0.973578	-182
ATAGCAATATAGCTGGGCAATACTGGGTGG	1	167	0	AGCTGGGCAA	    0.964734	-90
ACAAGCAAAAACAGGGGCTAGATAGCAATA	1	188	0	ACAGGGGCTA	    0.990249	-69
GTTAATTCCTTCGGGGGTTACTCATAATTA	1	216	1	TCGGGGGTTA	    0.958963	-41
CACAAGTTTCTGGTGGGGAAGGATTTAAAC	2	43	0	TGGTGGGGAA	    0.918409	-75
GGCAATGGGGTGAGGGGCGACAGCGGTGGC	2	73	0	TGAGGGGCGA	    0.990369	-45
AAAGTCAACTACGGGGGCAATGGGGTGAGG	2	88	0	ACGGGGGCAA	    0.993777	-30
          **********

Masking position 10
Map Score:   11.5266

Number of sites scoring better than the average of aligned sites = 2674
Number in coding regions = 2368
Number in noncoding regions = 306
Number of orfs with sites within 600 bp upstream = 299
Fraction of orfs with sites within 600 bp upstream = 0.0480244


Motif number 2

AGATCCGTTACCCTAGGAATTTACATCCGT	1	55	0	CCCTAGGAAT	    0.974947	-202
ACGGATCTTTTCCCCGGAGCGCTTCGTTCC	1	77	1	TCCCCGGAGC	    0.987948	-180
CTCAAATACTCCCTAGGAACGAAGCGCTCC	1	92	0	CCCTAGGAAC	     0.98872	-165
TTATGAGTAACCCCCGAAGGAATTAACAAG	1	213	0	CCCCCGAAGG	    0.893617	-44
AATCCTTCCCCACCAGAAACTTGTGGCCAC	2	48	1	CACCAGAAAC	    0.946869	-70
CACCCCATTGCCCCCGTAGTTGACTTTTTC	2	91	1	CCCCCGTAGT	    0.985653	-27
          **********

Masking position 8
Map Score:   6.07906

Number of sites scoring better than the average of aligned sites = 1296
Number in coding regions = 1184
Number in noncoding regions = 112
Number of orfs with sites within 600 bp upstream = 132
Fraction of orfs with sites within 600 bp upstream = 0.0212014


Motif number 3

          GGGTAAGGGGAGACTAAATG	1	1	1	GGGTAAGGGG	    0.998113	-256
TAAATTCCTAGGGTAACGGATCTTTTCCCC	1	62	1	GGGTAACGGA	    0.992223	-195
GAAGCGCTCCGGGGAAAAGATCCGTTACCC	1	72	0	GGGGAAAAGA	    0.946828	-185
AGTTTCTGGTGGGGAAGGATTTAAACAACC	2	39	0	GGGGAAGGAT	    0.975682	-79
GGGGGCAATGGGGTGAGGGGCGACAGCGGT	2	76	0	GGGTGAGGGG	    0.995822	-42
          **********

Masking position 6
Map Score:   5.41328

Number of sites scoring better than the average of aligned sites = 942
Number in coding regions = 825
Number in noncoding regions = 117
Number of orfs with sites within 600 bp upstream = 118
Fraction of orfs with sites within 600 bp upstream = 0.0189528


Motif number 4

TTTGAGGATTTTAAGGTTGTGCTTACTAAA	1	116	1	TTAAGGTTGT	    0.988664	-141
TAGCCCCTGTTTTTGCTTGTTAATTCCTTC	1	198	1	TTTTGCTTGT	    0.979564	-59
TTTGGGCTGGTTATGGTTGTTTAAATCCTT	2	25	1	TTATGGTTGT	    0.993606	-93
          **********

Masking position 7
Map Score:   1.37364

Number of sites scoring better than the average of aligned sites = 27
Number in coding regions = 19
Number in noncoding regions = 8
Number of orfs with sites within 600 bp upstream = 9
Fraction of orfs with sites within 600 bp upstream = 0.00144555


Motif number 5

CCGTGTAAACTTTTCTTAAAGATTAGCCCA	1	29	0	TTTTCTTAAA	    0.909755	-228
TTGGCTCGACTTTTTAGTAAGCACAACCTT	1	128	0	TTTTTAGTAA	    0.955712	-129
TTATTCACTTTTGTTATTAAGTAA      	1	243	1	TTGTTATTAA	     0.90466	-14
        TTTTTTCATTAATCTTTGGGCT	2	3	1	TTTTCATTAA	    0.979259	-115
GTAGTTGACTTTTTCTGTACCT        	2	106	1	TTTTCTGTAC	    0.941888	-12
          **********

Masking position 4
Map Score:   0.674024

Number of sites scoring better than the average of aligned sites = 374
Number in coding regions = 279
Number in noncoding regions = 95
Number of orfs with sites within 600 bp upstream = 99
Fraction of orfs with sites within 600 bp upstream = 0.0159011


Motif number 6

          **********

No masking
Map Score:   2.44017e-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:   2.44017e-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:   2.44017e-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