AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i205_synecho_ctra_300.orf -o205_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	RCY38416	130	Synechocystis
#2	RCT00758	300	Chlamydia_trachomatis

Motif number 1

         TTACTAAAAATTTACTATATTTT	1	2	1	TAAAAAATTT	    0.960527	-129
CGGCAATCCATAGGAAAAAATATAGTAAATTT	1	18	0	TAAAAAAATA	    0.731058	-113
TAAAGGCTGCTCCACAGAATTTTCCCTTTCC 	1	110	1	TCCAGAATTT	    0.971873	-21
GCATCGCGTGTAAAAAAAATATTGTACGATGC	2	39	0	TAAAAAATAT	    0.899073	-262
AAGCACACATTCCCAAGAAAATTATAGTGCGT	2	104	0	TCAAGAAAAT	    0.932995	-197
TTCCTTTTTCTCTTAAGAATTTTGCTTCCCAA	2	152	1	TCAAGAATTT	    0.983876	-149
AGTCTTGTATTCCCCAAAAATTCAACACCGTT	2	184	1	TCCAAAAATT	    0.956473	-117
TATTGCGTGATCGAAAAAATTTTTTATTCGTA	2	267	0	TCAAAAATTT	     0.98419	-34
          **  ********

Masking position 6
Map Score:   7.81983

Number of sites scoring better than the average of aligned sites = 434
Number in coding regions = 325
Number in noncoding regions = 109
Number of orfs with sites within 600 bp upstream = 130
Fraction of orfs with sites within 600 bp upstream = 0.0208802


Motif number 2

TTGCCGACTTAAGTGCACTAATCAATGCAC	1	44	1	AAGTGCACTA	    0.573309	-87
ATCATCAAACTAGTGCATTGATTAGTGCAC	1	56	0	TAGTGCATTG	     0.82975	-75
AGCAGCCTTTAATTGTATGAGATTTATCGA	1	91	0	AATTGTATGA	    0.889715	-40
GTAAAAAAAATATTGTACGATGCTTATATT	2	32	0	TATTGTACGA	    0.921391	-269
AAGAAAATTATAGTGCGTTACCATGGCGGA	2	92	0	TAGTGCGTTA	     0.88732	-209
CTTTATCTAGTATTGCGTGATCGAAAAAAT	2	279	0	TATTGCGTGA	    0.973192	-22
          **********

Masking position 4
Map Score:   2.14024

Number of sites scoring better than the average of aligned sites = 135
Number in coding regions = 121
Number in noncoding regions = 14
Number of orfs with sites within 600 bp upstream = 16
Fraction of orfs with sites within 600 bp upstream = 0.00256987


Motif number 3

TATTTTTTCCTATGGATTGCCGACTTAAGT	1	28	1	TATGGATTGC	    0.975289	-103
CTAGTTTGATGATGGCTTTCGATAAATCTC	1	73	1	GATGGCTTTC	    0.979607	-58
CTTTCTCCCTGATGGATTCCTTTTTCTCTT	2	136	1	GATGGATTCC	    0.993616	-165
CTCGCGTTTCGAAGGTTTTCTGATACATAA	2	221	1	GAAGGTTTTC	    0.967875	-80
          **********

Masking position 7
Map Score:   2.04723

Number of sites scoring better than the average of aligned sites = 165
Number in coding regions = 152
Number in noncoding regions = 13
Number of orfs with sites within 600 bp upstream = 15
Fraction of orfs with sites within 600 bp upstream = 0.00240925


Motif number 4

TGCCCGCTCTTCGGCGATAAAGGATCCGCCAT	2	68	1	TCGCGAAAAG	    0.990842	-233
AAGGAATCCATCAGGGAGAAAGAAGCACACAT	2	126	0	TCGGGAAAAG	    0.995003	-175
GCAAAATTCTTAAGAGAAAAAGGAATCCATCA	2	145	0	TAGAGAAAAG	    0.991684	-156
TTATTCGTAGTAGGGGAACAGGCTCTTATGTA	2	244	0	TAGGGACAGG	     0.97398	-57
GATCACGCAATACTAGATAAAGCT        	2	287	1	TATAGAAAAG	    0.958072	-14
          ** **** ****

Masking position 7
Map Score:   2.03944

Number of sites scoring better than the average of aligned sites = 79
Number in coding regions = 66
Number in noncoding regions = 13
Number of orfs with sites within 600 bp upstream = 14
Fraction of orfs with sites within 600 bp upstream = 0.00224863


Motif number 5

TGTACGATGCTTATATTCACGAATAGTGGAT	2	18	0	TTATATTCCG	    0.975337	-283
ACAATATTTTTTTTACACGCGATGCCCGCTC	2	46	1	TTTTACACCG	    0.983915	-255
TCCCAAAGTCTTGTATTCCCCAAAAATTCAA	2	178	1	TTGTATTCCC	     0.97575	-123
TTCAACACCGTTGTACACTCGCGTTTCGAAG	2	204	1	TTGTACACCG	    0.994042	-97
          ******** **

Masking position 5
Map Score:   0.24852

Number of sites scoring better than the average of aligned sites = 17
Number in coding regions = 14
Number in noncoding regions = 3
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 6

          **********

No masking
Map Score:   9.48026e-14

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:   9.48026e-14

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:   9.48026e-14

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