AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i183_thiamin_biosynthesis_synecho_reg_300.orf -o183_synecho_300.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	RCY18129	116	Synechocystis
#2	RCY22591	254	Synechocystis

Motif number 1

GAAAATGATAGACAGGAAGCGAGGTTGGCC	2	42	1	GACAGGAAGC	    0.985909	-213
AAGCGAGGTTGGCCGGAGTCGAACCGGCGG	2	58	1	GGCCGGAGTC	    0.985524	-197
GCCGGAGTCGAACCGGCGGCCCAGCGCTTA	2	69	1	AACCGGCGGC	    0.995478	-186
ATAAATCGTTGACCTGAGGTTGTAGCTCAG	2	120	0	GACCTGAGGT	    0.975365	-135
CAGGGAAATTGACCGGGGGCCGGTTTCACC	2	181	0	GACCGGGGGC	    0.990894	-74
          GACAGGCGGGTTGTAAATTA	2	245	0	GACAGGCGGG	    0.992838	-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	    0.878644	-114
TTGTCGTTTAATTGCAAAATTTTGCTGGAT	1	16	1	ATTGCAAAAT	    0.958289	-101
GGCAACTCTTTTGGCCAAATCCAGCAAAAT	1	34	0	TTGGCCAAAT	    0.947343	-83
TGTCAATTTGAGGGGCAAATATGGCAAAAA	1	68	1	AGGGGCAAAT	    0.957555	-49
AGGGGCAAATATGGCAAAAATCTCCTTTTT	1	78	1	ATGGCAAAAA	    0.984829	-39
TTTAACTTAGATAGGAAAAAAGGAGATTTT	1	94	0	ATAGGAAAAA	    0.838062	-23
GTCGACAGCAAAGGGAAAATGATAGACAGG	2	28	1	AAGGGAAAAT	    0.964142	-227
TTTAGGGGATATGGCAGAATAAATCGTTGA	2	138	0	ATGGCAGAAT	    0.979207	-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

  TGATTTTGTCGTTTAATTGCAAAATTTT	1	9	1	TCGTTTAATT	    0.985145	-108
          CTGTTTAACTTAGATAGGAA	1	107	0	CTGTTTAACT	     0.94908	-10
TTTGCTGTCGACGTTTACTTCCCTAAACC 	2	10	0	ACGTTTACTT	    0.965271	-245
GCAGAATAAATCGTTGACCTGAGGTTGTAG	2	125	0	TCGTTGACCT	    0.972042	-130
TGGCTTAGCTTTGTTTAATTTACAACCCGC	2	230	1	TTGTTTAATT	    0.967142	-25
          **********

Masking position 5
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

GCCAAAAGAGTTGCCTTTGTGTCAATTTGA	1	49	1	TTGCCTTTGT	    0.947334	-68
CGACGTTTACTTCCCTAAACC         	2	2	0	TTCCCTAAAC	    0.978171	-253
GTCTATCATTTTCCCTTTGCTGTCGACGTT	2	25	0	TTCCCTTTGC	    0.990277	-230
TTCTGCCATATCCCCTAAATCATACCCTGA	2	149	1	TCCCCTAAAT	    0.872142	-106
CCCTAAATCATACCCTGAGCGGTGAAACCG	2	161	1	TACCCTGAGC	     0.97133	-94
CAATTCTTAATTGGCTTAGCTTTGTTTAAT	2	219	1	TTGGCTTAGC	    0.957936	-36
          **********

Masking position 6
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	    0.947283	-85
GAAAAAAGGAGATTTTTGCCATATTTGCCCC	1	79	0	GATTTTGCCA	    0.828949	-38
GACAGGAAGCGAGGTTGGCCGGAGTCGAACC	2	52	1	GAGTTGGCCG	    0.995231	-203
AGGTTGGCCGGAGTCGAACCGGCGGCCCAGC	2	63	1	GAGCGAACCG	    0.893406	-192
CGCCTCCTAAGCGCTGGGCCGCCGGTTCGAC	2	75	0	GCGTGGGCCG	    0.986577	-180
CCTGAGCGGTGAAACCGGCCCCCGGTCAATT	2	174	1	GAACCGGCCC	    0.958009	-81
CCCTACCAGGGAAATTGACCGGGGGCCGGTT	2	186	0	GAATTGACCG	    0.985426	-69
AGCCAATTAAGAATTGTACCCTACCAGGGAA	2	204	0	GAATGTACCC	    0.920876	-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