AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i270_hypothetical15_synecho_reg_300.orf -o270_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	RCY52916	300	Synechocystis
#2	RCY27405	123	Synechocystis

Motif number 1

ACTTTTGTAGGCTTTCGCCGACATTT    	1	7	0	GCTTTCGCCG	    0.956559	-294
GTTTCATTTTCCTATCCCTGTCGTGACAAT	1	54	0	CCTATCCCTG	     0.97845	-247
AGTTGCCGCTCCTTTCCTCCCTGAACCGAT	1	140	1	CCTTTCCTCC	    0.912106	-161
AGTTGATGCCGTTTACCGTGGTCTGGGTTC	1	199	1	GTTTACCGTG	    0.914547	-102
CGGGGTGATTGCGAACCCAGACCACGGTAA	1	211	0	GCGAACCCAG	    0.921435	-90
ACCCCTTTCACTTTACCCAGGAAATACGGA	1	272	1	CTTTACCCAG	    0.965948	-29
         AGTTTACCGTCCGTATTTCCT	1	290	0	GTTTACCGTC	    0.878706	-11
AACCCCGACGGTTATCCCACTCAGGCAATT	2	36	0	GTTATCCCAC	    0.942014	-88
GCTTAACCGAACTAACCCCGACGGTTATCC	2	49	0	ACTAACCCCG	    0.947283	-75
CGGTTAAGCACCTTTCCCCCAATCCACCGT	2	70	1	CCTTTCCCCC	    0.989354	-54
          **********

Masking position 6
Map Score:   8.41941

Number of sites scoring better than the average of aligned sites = 3873
Number in coding regions = 3427
Number in noncoding regions = 446
Number of orfs with sites within 600 bp upstream = 438
Fraction of orfs with sites within 600 bp upstream = 0.0703501


Motif number 2

TCGGCGAAAGCCTACAAAAGTTAGGAACATTTTGG	1	16	1	CCTACAAGGG	    0.970215	-285
GTGGCGAGGAGCTACTAAGGTCAGGCCCTTTCTTT	1	103	0	GCTACAGGGG	    0.998568	-198
AAATATTCTTGCTAGATTGGCAGGTTCATCGGTTC	1	162	0	GCTAGTGGGT	    0.962312	-139
GTTGATGCCGTTTACCGTGGTCTGGGTTCGCAATC	1	200	1	TTTACTGGGG	    0.965557	-101
AACTAGTGTTGCTACCAAAGCCGGGGTGATTGCGA	1	227	0	GCTACAAGGG	    0.995455	-74
TTGACTAGATCCTACGGTGGATTGGGGGAAAGGTG	2	78	0	CCTACTGGGG	    0.996749	-46
          *****  ***   **

Masking position 4
Map Score:   5.86162

Number of sites scoring better than the average of aligned sites = 264
Number in coding regions = 236
Number in noncoding regions = 28
Number of orfs with sites within 600 bp upstream = 32
Fraction of orfs with sites within 600 bp upstream = 0.00513974


Motif number 3

CAATTTACCAAAATGTTCCTAACTTTTGTAGGC	1	25	0	AAAGTCCAAC	      0.9817	-276
ACCGAAAAAGAAAGGGCCTGACCTTAGTAGCTC	1	97	1	AAAGGCTACC	    0.991795	-204
AGACCACGGTAAACGGCATCAACTGCAAATATT	1	190	0	AAAGGATAAC	    0.991673	-111
TGAAAGGGGTCAATGGGATGAACTAGTGTTGCT	1	249	0	CAAGGATAAC	    0.981702	-52
GGATTGGGGGAAAGGTGCTTAACCGAACTAACC	2	62	0	AAAGTCTAAC	    0.991673	-62
          *** ** ** ***

Masking position 3
Map Score:   2.45265

Number of sites scoring better than the average of aligned sites = 62
Number in coding regions = 53
Number in noncoding regions = 9
Number of orfs with sites within 600 bp upstream = 10
Fraction of orfs with sites within 600 bp upstream = 0.00160617


Motif number 4

TTAGGAACATTTTGGTAAATTGTCACGACA	1	36	1	TTTGGTAAAT	    0.880385	-265
GAAAATGAAACTCGGTCATTATTGACCGAA	1	73	1	CTCGGTCATT	    0.962063	-228
CCCTTTCTTTTTCGGTCAATAATGACCGAG	1	83	0	TTCGGTCAAT	    0.988915	-218
GAACCCAGACCACGGTAAACGGCATCAACT	1	199	0	CACGGTAAAC	     0.93042	-102
TCCGTATTTCCTGGGTAAAGTGAAAGGGGT	1	272	0	CTGGGTAAAG	    0.934816	-29
GGTTATCCCACTCAGGCAATTCTTAACATC	2	27	0	CTCAGGCAAT	    0.829801	-97
TCGGGGTTAGTTCGGTTAAGCACCTTTCCC	2	58	1	TTCGGTTAAG	    0.970435	-66
AGGCCTCGATTTCCGTTAAC          	2	114	1	TTCCGTTAAC	     0.86323	-10
          **********

Masking position 8
Map Score:   2.96761

Number of sites scoring better than the average of aligned sites = 1009
Number in coding regions = 871
Number in noncoding regions = 138
Number of orfs with sites within 600 bp upstream = 154
Fraction of orfs with sites within 600 bp upstream = 0.024735


Motif number 5

GGAGCTACTAAGGTCAGGCCCTTTCTTTTT	1	101	0	AGGTCAGGCC	    0.991704	-200
GAATATTTGCAGTTGATGCCGTTTACCGTG	1	189	1	AGTTGATGCC	    0.992473	-112
TAGCAACACTAGTTCATCCCATTGACCCCT	1	248	1	AGTTCATCCC	    0.980075	-53
 GTTAACGGAAATCGAGGCCTGTTGACTAG	2	105	0	AATCGAGGCC	    0.967859	-19
          **********

Masking position 6
Map Score:   0.99119

Number of sites scoring better than the average of aligned sites = 143
Number in coding regions = 128
Number in noncoding regions = 15
Number of orfs with sites within 600 bp upstream = 16
Fraction of orfs with sites within 600 bp upstream = 0.00256987


Motif number 6

          **********

No masking
Map Score:   -5.51791e-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:   -5.51791e-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:   -5.51791e-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