AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i306_mixed20_synecho_reg_100.orf -o306_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	RCY48542	119	Synechocystis
#2	RCY39948	129	Synechocystis
#3	RCY09678	84	Synechocystis

Motif number 1

 GGAAAATGCCTAGGGAAAATGGGAAGATT	1	10	1	CTAGGGAAAA	    0.917627	-110
AGATTAATCCCTGGGAGCAAGACACGGTTC	1	80	0	CTGGGAGCAA	     0.99155	-40
TTTATTTTCATTGGGGAGAGATTAATCCCT	1	98	0	TTGGGGAGAG	    0.977242	-22
TGGCCATGGACCGGGGGCAAGCCGTCACTG	2	77	0	CCGGGGGCAA	    0.997046	-53
TGGGGGGAAGCAGAGGACAATGGCCATGGA	2	97	0	CAGAGGACAA	    0.934812	-33
AAACTTAGGGCTGGGGGGAAGCAGAGGACA	2	108	0	CTGGGGGGAA	    0.997932	-22
TTACTGTTACTTGGGGGCAGTTTATTTTTC	3	55	1	TTGGGGGCAG	    0.993113	-30
          **********

Masking position 9
Map Score:   11.6111

Number of sites scoring better than the average of aligned sites = 2393
Number in coding regions = 2105
Number in noncoding regions = 288
Number of orfs with sites within 600 bp upstream = 295
Fraction of orfs with sites within 600 bp upstream = 0.0473819


Motif number 2

    GGAAAATGCCTAGGGAAAATGGGAAG	1	7	1	TGCCTAGGGA	    0.660553	-113
GAGAGATTAATCCCTGGGAGCAAGACACGG	1	83	0	TCCCTGGGAG	    0.935907	-37
 ACTTTATTTTCATTGGGGAGAGATTAATC	1	101	0	TCATTGGGGA	     0.95249	-19
CAATGGCCATGGACCGGGGGCAAGCCGTCA	2	80	0	GGACCGGGGG	    0.988891	-50
 AAAAACTTAGGGCTGGGGGGAAGCAGAGG	2	111	0	GGGCTGGGGG	    0.995318	-19
TTCTTACTGTTACTTGGGGGCAGTTTATTT	3	52	1	TACTTGGGGG	    0.982805	-33
          **********

Masking position 7
Map Score:   5.30318

Number of sites scoring better than the average of aligned sites = 3016
Number in coding regions = 2712
Number in noncoding regions = 304
Number of orfs with sites within 600 bp upstream = 320
Fraction of orfs with sites within 600 bp upstream = 0.0513974


Motif number 3

         GGAAAATGCCTAGGGAAAATGG	1	2	1	GAAATGCCTA	     0.97854	-118
ATAGTCGAGAAAATCTTCCCATTTTCCCTAG	1	20	0	AAACTTCCCA	    0.925332	-100
CCAGGGATTAATCTCTCCCCAATGAAAATAA	1	96	1	ATCCTCCCCA	     0.90425	-24
        ACAAATCTGGCTAAATTTATGCC	2	3	1	AAACTGGCTA	    0.966787	-127
ATCTGGCTAAATTTATGCCCAACCTCGGAAA	2	15	1	ATTATGCCCA	     0.87966	-115
ACTGCCTATTGAAGATGGCTCGACTTCGGTT	2	50	0	GAAATGGCTC	    0.919737	-80
GGGGCAAGCCGTCACTGCCTATTGAAGATGG	2	63	0	GTCCTGCCTA	    0.978752	-67
GGAAGCAGAGGACAATGGCCATGGACCGGGG	2	91	0	GACATGGCCA	    0.978381	-39
CTAAGAAAAATAAACTGCCCCCAAGTAACAG	3	58	0	TAACTGCCCC	    0.942811	-27
          *** *******

Masking position 6
Map Score:   6.66843

Number of sites scoring better than the average of aligned sites = 3398
Number in coding regions = 3123
Number in noncoding regions = 275
Number of orfs with sites within 600 bp upstream = 273
Fraction of orfs with sites within 600 bp upstream = 0.0438484


Motif number 4

ATTTTCTCGACTATTGTAGTCAGTGGTGCC	1	37	1	CTATTGTAGT	    0.906059	-83
AGACACGGTTCGGATGTAAATCTTGGCACC	1	61	0	CGGATGTAAA	    0.879026	-59
TAATCTCTCCCCAATGAAAATAAAGT    	1	104	1	CCAATGAAAA	    0.889955	-16
GGCTCGACTTCGGTTTAAGTTTCCGAGGTT	2	35	0	CGGTTTAAGT	    0.865079	-95
CCGTCACTGCCTATTGAAGATGGCTCGACT	2	56	0	CTATTGAAGA	    0.980756	-74
TTCAACATTACCGTTGAAGA          	3	1	0	CCGTTGAAGA	    0.991276	-84
TTCAACGGTAATGTTGAACAAAGACGGTAG	3	13	1	ATGTTGAACA	    0.794982	-72
          **********

Masking position 8
Map Score:   1.45911

Number of sites scoring better than the average of aligned sites = 1593
Number in coding regions = 1444
Number in noncoding regions = 149
Number of orfs with sites within 600 bp upstream = 143
Fraction of orfs with sites within 600 bp upstream = 0.0229682


Motif number 5

          **********

No masking
Map Score:   -4.38104e-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:   -4.38104e-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:   -4.38104e-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