AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i288_moxr_hypothetical_synecho_reg_300.orf -o288_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	RCY23271	201	Synechocystis
#2	RCY11277	49	Synechocystis
#3	RCY18066	196	Synechocystis

Motif number 1

GCTTTTCCAAAGATTTTCTCGGACTAGGTT	1	24	0	AGATTTTCTC	    0.940666	-178
AATGGTACGACGCTTTTCCAAAGATTTTCT	1	35	0	CGCTTTTCCA	    0.976755	-167
GAATTCCGATAGATTTTTCAATGGTACGAC	1	54	0	AGATTTTTCA	    0.953422	-148
TTTGCAAAGGAGAATTTTCACAAAACTTCT	1	85	1	AGAATTTTCA	    0.785796	-117
GTTGAAAGTGAATTTTTCCCTGGGCAGTCA	1	123	1	AATTTTTCCC	    0.945663	-79
GAGTAAAGAAAGTTTTACCCACAAAGTTTC	3	14	1	AGTTTTACCC	    0.965344	-183
TTTTGGCAATCAATTTACCAGAAACTTTGT	3	34	0	CAATTTACCA	    0.809304	-163
GATTGCCAAAAGCTTTTCCCTGCTTTTTAT	3	53	1	AGCTTTTCCC	    0.991575	-144
          **********

Masking position 5
Map Score:   7.08876

Number of sites scoring better than the average of aligned sites = 2104
Number in coding regions = 1828
Number in noncoding regions = 276
Number of orfs with sites within 600 bp upstream = 292
Fraction of orfs with sites within 600 bp upstream = 0.0469001


Motif number 2

CTAGGTTAAAGACCAAGTTT          	1	1	0	GACCAAGTTT	    0.892473	-201
GATTTTCTCGGACTAGGTTAAAGACCAAGT	1	13	0	GACTAGGTTA	    0.953113	-189
AAAACTTCTTGACCGGGGTTGAAAGTGAAT	1	106	1	GACCGGGGTT	    0.976195	-96
TAGACTGACTGCCCAGGGAAAAATTCACTT	1	128	0	GCCCAGGGAA	     0.97882	-74
TGGGCAGTCAGTCTAGGGTGTGATAGAGAG	1	143	1	GTCTAGGGTG	    0.976995	-59
TCTAGTTCTCGACCAGTGGAGCAGATATT 	2	10	0	GACCAGTGGA	    0.944688	-40
CACCCGATGTGCCCAAGGTGACTGTGTATT	3	112	0	GCCCAAGGTG	    0.985038	-85
TAGCGCCGCAGGCTAGGGGGATTTGGATAA	3	167	0	GGCTAGGGGG	    0.976938	-30
          **********

Masking position 3
Map Score:   6.27765

Number of sites scoring better than the average of aligned sites = 2963
Number in coding regions = 2717
Number in noncoding regions = 246
Number of orfs with sites within 600 bp upstream = 259
Fraction of orfs with sites within 600 bp upstream = 0.0415997


Motif number 3

ACGACGCTTTTCCAAAGATTTTCTCGGACTA	1	28	0	TCCAAAGTTT	    0.915076	-174
GGAGAATTTTCACAAAACTTCTTGACCGGGG	1	93	1	CACAAAATTC	    0.940893	-109
CTAGACTGTCCCCAATCATTCCAAC      	2	35	1	CCCAATCTTC	    0.981693	-15
AAGTTTTACCCACAAAGTTTCTGGTAAATTG	3	23	1	CACAAAGTTC	    0.990374	-174
AAATTGATTGCCAAAAGCTTTTCCCTGCTTT	3	48	1	CCAAAAGTTT	    0.915076	-149
ATTTGCGAATCCCATTGGTTCACCATTGATG	3	84	0	CCCATTGTTC	    0.979819	-113
TAGCCTGCGGCGCTATGCTTCCCCT      	3	182	1	CGCTATGTTC	    0.932384	-15
          ******* ***

Masking position 9
Map Score:   3.36893

Number of sites scoring better than the average of aligned sites = 953
Number in coding regions = 861
Number in noncoding regions = 92
Number of orfs with sites within 600 bp upstream = 102
Fraction of orfs with sites within 600 bp upstream = 0.0163829


Motif number 4

CCTTTGCAAAGGAATTCCGATAGATTTTTC	1	65	0	GGAATTCCGA	    0.985351	-137
GTGAACCAATGGGATTCGCAAATACACAGT	3	92	1	GGGATTCGCA	    0.994565	-105
GCAGGCTAGGGGGATTTGGATAACAAATTA	3	160	0	GGGATTTGGA	    0.991978	-37
          **********

Masking position 4
Map Score:   0.0372895

Number of sites scoring better than the average of aligned sites = 58
Number in coding regions = 52
Number in noncoding regions = 6
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 5

          **********

No masking
Map Score:   -3.81261e-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:   -3.81261e-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:   -3.81261e-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