AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i038_synecho_ctra_100.orf -o038_synecho_ctra_100.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	RCY32056	160	Synechocystis
#2	RCY16440	38	Synechocystis
#3	RCY42175	94	Synechocystis

Motif number 1

AAGTAGAAATATTTTTATTTTAATCATTCG	1	45	0	ATTTTTATTT	    0.949356	-116
AAATAAAAATATTTCTACTTTGCTTTAAAA	1	55	1	ATTTCTACTT	     0.98384	-106
ATGCTCTGACATTGCTACTTATTGCGGCTC	1	93	1	ATTGCTACTT	    0.989662	-68
ATTGATAGTGATTTCAATTTATAAATGAGA	1	133	1	ATTTCAATTT	    0.921674	-28
    TTAGGAATTCTCATTTATAAATTGAA	1	145	0	ATTCTCATTT	    0.901154	-16
AATTGATTAGATTGCCTCTTGAAGAAACCC	2	17	0	ATTGCCTCTT	    0.971853	-22
         AATTGTTTGTTGCGTGGCCAT	3	84	0	ATTGTTTGTT	    0.882661	-11
          **********

Masking position 1
Map Score:   6.05255

Number of sites scoring better than the average of aligned sites = 471
Number in coding regions = 393
Number in noncoding regions = 78
Number of orfs with sites within 600 bp upstream = 76
Fraction of orfs with sites within 600 bp upstream = 0.0122069


Motif number 2

ATTCGCTGAACTGCCATGGCCTACTTGGTTA	1	19	0	CTGCCTGGCC	    0.995795	-142
CATTCTTAACCTTGCTTGACCTTAGCTTTTT	3	11	0	CTTGCTGACC	    0.996325	-84
AACCCAAGCTGTTGCCTCGCCTAGAGCATAC	3	42	0	GTTGCTCGCC	    0.997429	-53
  AATTGTTTGTTGCGTGGCCATTGTCGACT	3	76	0	GTTGCTGGCC	    0.999039	-19
          ***** *****

Masking position 7
Map Score:   5.23707

Number of sites scoring better than the average of aligned sites = 36
Number in coding regions = 32
Number in noncoding regions = 4
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 3

  AATAATTTTAACCAAGTAGGCCATGGCA	1	9	1	TAACCAAGTA	    0.990121	-152
CTTGCTTTTAAAGCAAAGTAGAAATATTTT	1	60	0	AAGCAAAGTA	    0.926444	-101
CTTTGCTTTAAAAGCAAGTATATGCTCTGA	1	72	1	AAAGCAAGTA	     0.98195	-89
CCTCTTGAAGAAACCCATTAAA        	2	3	0	AAACCCATTA	    0.966735	-36
AGAGGCAATCTAATCAATTAA         	2	28	1	TAATCAATTA	    0.887541	-11
          **********

Masking position 7
Map Score:   2.45559

Number of sites scoring better than the average of aligned sites = 393
Number in coding regions = 338
Number in noncoding regions = 55
Number of orfs with sites within 600 bp upstream = 55
Fraction of orfs with sites within 600 bp upstream = 0.00883392


Motif number 4

TGGCCTACTTGGTTAAAATTATT       	1	4	0	GGTTAAAATT	    0.990638	-157
TTCAGCGAATGATTAAAATAAAAATATTTC	1	40	1	GATTAAAATA	    0.913484	-121
GGTCAAGCAAGGTTAAGAATGGTATGCTCT	3	21	1	GGTTAAGAAT	     0.98072	-74
CAACAGCTTGGGTTAATAGTCGACAATGGC	3	59	1	GGTTAATAGT	     0.98072	-36
          **********

Masking position 5
Map Score:   1.29482

Number of sites scoring better than the average of aligned sites = 247
Number in coding regions = 208
Number in noncoding regions = 39
Number of orfs with sites within 600 bp upstream = 46
Fraction of orfs with sites within 600 bp upstream = 0.00738837


Motif number 5

AGTAGGCCATGGCAGTTCAGCGAATGATTA	1	25	1	GGCAGTTCAG	    0.984133	-136
AAGTAGCAATGTCAGAGCATATACTTGCTT	1	83	0	GTCAGAGCAT	    0.992379	-78
CAATAAAGAAGTCAGAGCCGCAATAAGTAG	1	107	0	GTCAGAGCCG	    0.996661	-54
          **********

Masking position 4
Map Score:   0.311567

Number of sites scoring better than the average of aligned sites = 94
Number in coding regions = 87
Number in noncoding regions = 7
Number of orfs with sites within 600 bp upstream = 10
Fraction of orfs with sites within 600 bp upstream = 0.00160617


Motif number 6

          **********

No masking
Map Score:   -1.17788e-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:   -1.17788e-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:   -1.17788e-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