AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i183_synecho_ctra_300.orf -o183_synecho_ctra_300.ace -a/home/amcguire/genomes/ORF_synecho.txt -z/home/amcguire/genomes/synecho.fna -g0.46 -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 =  	0.46
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RCY18129	116	Synechocystis
#2	RCY22591	254	Synechocystis

Motif number 1

GAAAATGATAGACAGGAAGCGAGGTTGGCC	2	42	1	GACAGGAAGC	    0.985326	-213
AAGCGAGGTTGGCCGGAGTCGAACCGGCGG	2	58	1	GGCCGGAGTC	    0.985043	-197
GCCGGAGTCGAACCGGCGGCCCAGCGCTTA	2	69	1	AACCGGCGGC	    0.995294	-186
ATAAATCGTTGACCTGAGGTTGTAGCTCAG	2	120	0	GACCTGAGGT	    0.974362	-135
CAGGGAAATTGACCGGGGGCCGGTTTCACC	2	181	0	GACCGGGGGC	    0.991152	-74
          GACAGGCGGGTTGTAAATTA	2	245	0	GACAGGCGGG	     0.99254	-10
          **********

Masking position 6
Map Score:   9.16291

Number of sites scoring better than the average of aligned sites = 570
Number in coding regions = 529
Number in noncoding regions = 41
Number of orfs with sites within 600 bp upstream = 50
Fraction of orfs with sites within 600 bp upstream = 0.00803084


Motif number 2

TTGCAATTAAACGACAAAATCA        	1	3	0	ACGACAAAAT	    0.899667	-114
TTGTCGTTTAATTGCAAAATTTTGCTGGAT	1	16	1	ATTGCAAAAT	    0.966029	-101
GGCAACTCTTTTGGCCAAATCCAGCAAAAT	1	34	0	TTGGCCAAAT	    0.957042	-83
TGTCAATTTGAGGGGCAAATATGGCAAAAA	1	68	1	AGGGGCAAAT	     0.96544	-49
AGGGGCAAATATGGCAAAAATCTCCTTTTT	1	78	1	ATGGCAAAAA	    0.987714	-39
TTTAACTTAGATAGGAAAAAAGGAGATTTT	1	94	0	ATAGGAAAAA	    0.865034	-23
GTCGACAGCAAAGGGAAAATGATAGACAGG	2	28	1	AAGGGAAAAT	    0.970845	-227
TTTAGGGGATATGGCAGAATAAATCGTTGA	2	138	0	ATGGCAGAAT	    0.983143	-117
          **********

Masking position 8
Map Score:   7.3476

Number of sites scoring better than the average of aligned sites = 1583
Number in coding regions = 1364
Number in noncoding regions = 219
Number of orfs with sites within 600 bp upstream = 242
Fraction of orfs with sites within 600 bp upstream = 0.0388693


Motif number 3

AAAATTTTGCAATTAAACGACAAAATCA  	1	9	0	AATTAAACGA	    0.987505	-108
TTCCTATCTAAGTTAAACAG          	1	107	1	AGTTAAACAG	    0.956922	-10
 GGTTTAGGGAAGTAAACGTCGACAGCAAA	2	10	1	AAGTAAACGT	    0.970473	-245
CTACAACCTCAGGTCAACGATTTATTCTGC	2	125	1	AGGTCAACGA	    0.976423	-130
GCGGGTTGTAAATTAAACAAAGCTAAGCCA	2	230	0	AATTAAACAA	    0.972284	-25
          **********

Masking position 6
Map Score:   3.11859

Number of sites scoring better than the average of aligned sites = 122
Number in coding regions = 102
Number in noncoding regions = 20
Number of orfs with sites within 600 bp upstream = 20
Fraction of orfs with sites within 600 bp upstream = 0.00321234


Motif number 4

TCAAATTGACACAAAGGCAACTCTTTTGGC	1	49	0	ACAAAGGCAA	    0.943194	-68
         GGTTTAGGGAAGTAAACGTCG	2	2	1	GTTTAGGGAA	    0.976395	-253
AACGTCGACAGCAAAGGGAAAATGATAGAC	2	25	1	GCAAAGGGAA	    0.989475	-230
TCAGGGTATGATTTAGGGGATATGGCAGAA	2	149	0	ATTTAGGGGA	    0.862947	-106
CGGTTTCACCGCTCAGGGTATGATTTAGGG	2	161	0	GCTCAGGGTA	    0.969015	-94
ATTAAACAAAGCTAAGCCAATTAAGAATTG	2	219	0	GCTAAGCCAA	     0.95459	-36
          **********

Masking position 5
Map Score:   2.27213

Number of sites scoring better than the average of aligned sites = 1109
Number in coding regions = 953
Number in noncoding regions = 156
Number of orfs with sites within 600 bp upstream = 183
Fraction of orfs with sites within 600 bp upstream = 0.0293929


Motif number 5

AAATTTTGCTGGATTTGGCCAAAAGAGTTGC	1	32	1	GGATTGGCCA	     0.94871	-85
GAAAAAAGGAGATTTTTGCCATATTTGCCCC	1	79	0	GATTTTGCCA	     0.83302	-38
GACAGGAAGCGAGGTTGGCCGGAGTCGAACC	2	52	1	GAGTTGGCCG	    0.995367	-203
AGGTTGGCCGGAGTCGAACCGGCGGCCCAGC	2	63	1	GAGCGAACCG	     0.89598	-192
CGCCTCCTAAGCGCTGGGCCGCCGGTTCGAC	2	75	0	GCGTGGGCCG	    0.986915	-180
CCTGAGCGGTGAAACCGGCCCCCGGTCAATT	2	174	1	GAACCGGCCC	    0.959135	-81
CCCTACCAGGGAAATTGACCGGGGGCCGGTT	2	186	0	GAATTGACCG	    0.985836	-69
AGCCAATTAAGAATTGTACCCTACCAGGGAA	2	204	0	GAATGTACCC	    0.922961	-51
          *** *******

Masking position 9
Map Score:   4.51299

Number of sites scoring better than the average of aligned sites = 1713
Number in coding regions = 1583
Number in noncoding regions = 130
Number of orfs with sites within 600 bp upstream = 156
Fraction of orfs with sites within 600 bp upstream = 0.0250562


Motif number 6

          **********

No masking
Map Score:   -1.25466e-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:   -1.25466e-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:   -1.25466e-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