AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i300_mixed15_synecho_reg_100.orf -o300_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	RCY43837	121	Synechocystis
#2	RCY26609	38	Synechocystis
#3	RCY32578	235	Synechocystis

Motif number 1

TTCTGCCAATTGTGCAAGTTCCGCAAGCAAGTAGAGC	1	17	0	TGAAGTTAAG	    0.985494	-105
TTGCACAATTGGCAGAAGTTTAACTAACGGGCGAATT	1	37	1	GGAAGTTTAA	    0.942837	-85
TTTAACTAACGGGCGAATTTGTTAAAGGCACTACTGA	1	55	1	GGAATTTAAG	    0.976086	-67
AAGAGCGAACTGTCAAAGGTTCAGTAGTGCCTTTAAC	1	75	0	TGAAGGTTAG	    0.986109	-47
CCATTTTACAGGTAGGGGTGATGGAAGAAAC      	2	5	0	GGGGGTGAAG	    0.968231	-34
CACCCCTACCTGTAAAATGGGCTCTAG          	2	22	1	TGAATGGTAG	    0.947361	-17
AGAAGGCTGGGGAAAAGGGTAGCGAAGATGTCATAAT	3	62	0	GGAGGGTAAG	    0.992392	-174
TTAACCCATTGGGTGAAGGGAAGTTAGGTTGGAAAAC	3	152	0	GGAAGGGTAG	    0.996427	-84
TCACCCAATGGGTTAAAGTGTGAGAAGTCTGAAAAAA	3	173	1	GGAAGTGAAG	    0.996267	-63
          **   *****    ***

Masking position 16
Map Score:   10.4886

Number of sites scoring better than the average of aligned sites = 816
Number in coding regions = 728
Number in noncoding regions = 88
Number of orfs with sites within 600 bp upstream = 93
Fraction of orfs with sites within 600 bp upstream = 0.0149374


Motif number 2

AGTTAAACTTCTGCCAATTGTGCAAGTTCCGC	1	30	0	CTGCAATGTG	    0.987851	-92
AAAGAGCGAACTGTCAAAGGTTCAGTAGTGCC	1	81	0	CTGCAAGGTT	    0.988867	-41
TCTTTCAATGTTGGCAAAGGTTTT        	1	108	1	TTGCAAGGTT	    0.961629	-14
TCACCCCTACCTGTAAAATGGGCTCTAG    	2	21	1	CTGAAATGGG	    0.981134	-18
GCTACTACAGCAGAGAACTGGGGGTAAATCTT	3	12	1	CAGGAATGGG	    0.973693	-224
TTGAGAAGGCTGGGGAAAAGGGTAGCGAAGAT	3	70	0	TGGGAAAGGG	    0.859714	-166
TTCCCCAGCCTTCTCAATGGGGATTCATCATT	3	85	1	TTCCAAGGGG	    0.973542	-151
TTTGTCCAGACTGTGACTGGGGTTTTCCAACC	3	131	1	CTGGACGGGG	    0.984255	-105
AACTTCCCTTCACCCAATGGGTTAAAGTGTGA	3	164	1	CACCAAGGGT	    0.946182	-72
TGTGAGAAGTCTGAAAAAAGTTCCATAATTTA	3	191	1	CTGAAAAGTT	    0.868589	-45
          *** *** ****

Masking position 6
Map Score:   9.79235

Number of sites scoring better than the average of aligned sites = 2580
Number in coding regions = 2352
Number in noncoding regions = 228
Number of orfs with sites within 600 bp upstream = 240
Fraction of orfs with sites within 600 bp upstream = 0.038548


Motif number 3

AACAAAGATTACTAAAGATTTACCCCCAGT	3	28	0	ACTAAAGATT	    0.979399	-208
CATAATTTTTAACAAAGATTACTAAAGATT	3	38	0	AACAAAGATT	    0.953562	-198
GGAAAAGGGTAGCGAAGATGTCATAATTTT	3	59	0	AGCGAAGATG	    0.945956	-177
CATTCGGTGAACCAATGATGAATCCCCATT	3	100	0	ACCAATGATG	    0.980853	-136
CACAGTCTGGACAAAACATTCGGTGAACCA	3	116	0	ACAAAACATT	    0.860837	-120
GTGGATTGGGACTAACGATGGCTAAATTAT	3	215	0	ACTAACGATG	     0.97118	-21
          **********

Masking position 5
Map Score:   1.9282

Number of sites scoring better than the average of aligned sites = 507
Number in coding regions = 455
Number in noncoding regions = 52
Number of orfs with sites within 600 bp upstream = 61
Fraction of orfs with sites within 600 bp upstream = 0.00979762


Motif number 4

TTGCACAATTGGCAGAAGTTTAACTAACGG	1	37	1	GGCAGAAGTT	    0.867264	-85
TTAACTAACGGGCGAATTTGTTAAAGGCAC	1	56	1	GGCGAATTTG	    0.909385	-66
TTACAGGTAGGGGTGATGGAAGAAAC    	2	7	0	GGGTGATGGA	    0.955065	-32
GAGAAGGCTGGGGAAAAGGGTAGCGAAGAT	3	70	0	GGGAAAAGGG	     0.97687	-166
TTAACCCATTGGGTGAAGGGAAGTTAGGTT	3	159	0	GGGTGAAGGG	    0.992063	-77
TCACCCAATGGGTTAAAGTGTGAGAAGTCT	3	173	1	GGTTAAAGTG	    0.956615	-63
GACTAACGATGGCTAAATTATGGAACTTTT	3	206	0	GGCTAAATTA	    0.841208	-30
          GGTGGATTGGGACTAACGAT	3	226	0	GGTGGATTGG	    0.918073	-10
          **********

Masking position 6
Map Score:   5.01004

Number of sites scoring better than the average of aligned sites = 3516
Number in coding regions = 3132
Number in noncoding regions = 384
Number of orfs with sites within 600 bp upstream = 378
Fraction of orfs with sites within 600 bp upstream = 0.0607131


Motif number 5

          **********

No masking
Map Score:   8.19556e-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:   8.19556e-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:   8.19556e-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