AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i068_Proline_Biosynthesis_synecho_reg_100.orf -o068_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	RCY53629	161	Synechocystis
#2	RCY42873	96	Synechocystis
#3	RCY48238	125	Synechocystis

Motif number 1

TCCACCGGTTGGCGGTTTGGGTTTGAATTT	1	28	0	GGCGGTTTGG	    0.986595	-134
ACCGCCAACCGGTGGAATTGAACCGCACTT	1	42	1	GGTGGAATTG	    0.977264	-120
GTCTATTGTTGGTGGCTGTGTTGGGGATTT	1	84	1	GGTGGCTGTG	    0.962341	-78
TGGCTGTGTTGGGGATTTTGTTCTCCAGCT	1	96	1	GGGGATTTTG	    0.964653	-66
ACGCAATTTAGGAGGCATGGT         	1	151	1	GGAGGCATGG	    0.991326	-11
TGGTTTTAAGGTGGGCTTGGCCCACTTTTT	2	38	1	GTGGGCTTGG	     0.96885	-59
TATTTTGGGAGGAAAAATTGCCATAAAAAA	2	64	0	GGAAAAATTG	    0.735028	-33
GCTTGAACCTGGGGGAATGGCT        	3	3	0	GGGGGAATGG	    0.992044	-123
TTTCGGACAGGGCAACTTTGGGGGGCAAAC	3	70	0	GGCAACTTTG	    0.916095	-56
          **********

Masking position 1
Map Score:   11.9483

Number of sites scoring better than the average of aligned sites = 3935
Number in coding regions = 3625
Number in noncoding regions = 310
Number of orfs with sites within 600 bp upstream = 290
Fraction of orfs with sites within 600 bp upstream = 0.0465789


Motif number 2

TTGGCGGTTTGGGTTTGAATTTCTGTCCATG	1	19	0	GGGTTTGATT	    0.913098	-143
GCCAACCGGTGGAATTGAACCGCACTTCTTT	1	45	1	GGAATTGACC	      0.9114	-117
      TCGAGGGCTAGCCGCCACACAATAT	2	5	1	GGGCTAGCGC	    0.991983	-92
GTTTTAAGGTGGGCTTGGCCCACTTTTTTTA	2	40	1	GGGCTTGCCC	     0.80435	-57
AAAATATTTACGGCTTGAACCTGGGGGAATG	3	14	0	CGGCTTGACC	    0.992333	-112
CTGCGCTTTGCTGTTTGCCCCCCAAAGTTGC	3	58	1	CTGTTTGCCC	    0.957818	-68
          GGGTTAGACGTTGACGATGCA	3	115	0	GGGTTAGCGT	    0.962117	-11
          ******* ***

Masking position 5
Map Score:   5.7957

Number of sites scoring better than the average of aligned sites = 1453
Number in coding regions = 1318
Number in noncoding regions = 135
Number of orfs with sites within 600 bp upstream = 151
Fraction of orfs with sites within 600 bp upstream = 0.0242531


Motif number 3

AGACCCAGGTATAAAGAAGTGCGGTTCAAT	1	58	0	ATAAAGAAGT	    0.958228	-104
AAAAGTTTAGTTAAAGAAATAGCTGGAGAA	1	116	0	TTAAAGAAAT	    0.971012	-46
AAATTGCGTATTAAAAAAGTTTAGTTAAAG	1	130	0	TTAAAAAAGT	    0.985899	-32
AAAATTGCCATAAAAAAAGTGGGCCAAGCC	2	51	0	TAAAAAAAGT	    0.955057	-46
GGGAAAGTATTTAAAAATATTTACGGCTTG	3	28	0	TTAAAAATAT	    0.904133	-98
          **********

Masking position 5
Map Score:   4.23307

Number of sites scoring better than the average of aligned sites = 102
Number in coding regions = 83
Number in noncoding regions = 19
Number of orfs with sites within 600 bp upstream = 24
Fraction of orfs with sites within 600 bp upstream = 0.0038548


Motif number 4

          **********

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 5

          **********

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 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