AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i202_synecho_ctra_300.orf -o202_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	RCY44546	80	Synechocystis
#2	RCY49953	300	Synechocystis

Motif number 1

TCTCCAACAAAAAAAGGGAAGACCTCTAGT	1	52	0	AAAAAGGGAA	    0.918392	-29
TAACTAATCAAAACGGGGATCACCCATTGC	2	68	1	AAACGGGGAT	    0.923303	-233
GAATCAGTGGACATAGAGCAATGGGTGATC	2	85	0	ACATAGAGCA	    0.943966	-216
TCGGGGTCAAAAACAGGGAATCTGGGCACA	2	124	1	AAACAGGGAA	    0.986439	-177
CTAAACCTACACCCACGGCTGTACCCAGGG	2	210	1	ACCCACGGCT	    0.963774	-91
CCACGGCTGTACCCAGGGCAACAGCACAAT	2	222	1	ACCCAGGGCA	    0.996295	-79
GCTGATTCTAACATAGCGCTTTTATTGTGC	2	245	0	ACATAGCGCT	    0.939628	-56
AATCAGCAATACACAGGGCACGCTGAGGTG	2	268	1	ACACAGGGCA	    0.997904	-33
          **********

Masking position 1
Map Score:   11.1334

Number of sites scoring better than the average of aligned sites = 1203
Number in coding regions = 1117
Number in noncoding regions = 86
Number of orfs with sites within 600 bp upstream = 96
Fraction of orfs with sites within 600 bp upstream = 0.0154192


Motif number 2

TCCCCCAGCGGGCCATTACCATAGGATGAA	1	16	1	GGCCATTACC	     0.94936	-65
CAACAAAAAAAGGGAAGACCTCTAGTCCTC	1	48	0	AGGGAAGACC	    0.924682	-33
  GGTCATCAGGCGATCGCCAAAATATTTC	2	9	1	GGCGATCGCC	    0.499937	-292
TAATCAAAACGGGGATCACCCATTGCTCTA	2	72	1	GGGGATCACC	    0.718126	-229
CTGCGTCTGTGGGGTTTTCCTCACCTCAAC	2	165	0	GGGGTTTTCC	    0.889673	-136
GCGGTGGAATGGCGAACTGCGTCTGTGGGG	2	181	0	GGCGAACTGC	    0.950676	-120
GCTGTTGCCCTGGGTACAGCCGTGGGTGTA	2	217	0	TGGGTACAGC	    0.858486	-84
GCTGTACCCAGGGCAACAGCACAATAAAAG	2	227	1	GGGCAACAGC	    0.986182	-74
   AATCTAAATCCATCACCTCAGCGTGCC	2	284	0	ATCCATCACC	    0.767212	-17
          **********

Masking position 10
Map Score:   9.22373

Number of sites scoring better than the average of aligned sites = 8655
Number in coding regions = 7908
Number in noncoding regions = 747
Number of orfs with sites within 600 bp upstream = 495
Fraction of orfs with sites within 600 bp upstream = 0.0795053


Motif number 3

TTAGGTCCCCCAGCGGGCCATTACCATAGGA	1	11	1	CAGCGGCCAT	    0.997614	-70
       GGTCATCAGGCGATCGCCAAAATA	2	4	1	CATCAGCGAT	    0.950024	-297
AATCAGTGGACATAGAGCAATGGGTGATCCC	2	83	0	CATAGGCAAT	    0.967434	-218
CCCACAGACGCAGTTCGCCATTCCACCGCTA	2	182	1	CAGTTGCCAT	    0.952759	-119
CTGATTCTAACATAGCGCTTTTATTGTGCTG	2	243	0	CATAGGCTTT	    0.900291	-58
TCCATCACCTCAGCGTGCCCTGTGTATTGCT	2	272	0	CAGCGGCCCT	    0.994719	-29
          ***** *****

Masking position 2
Map Score:   3.40685

Number of sites scoring better than the average of aligned sites = 271
Number in coding regions = 256
Number in noncoding regions = 15
Number of orfs with sites within 600 bp upstream = 15
Fraction of orfs with sites within 600 bp upstream = 0.00240925


Motif number 4

AAGACCTCTAGTCCTCCCTTCATCCTATGG	1	34	0	GTCCTCCCTT	    0.947227	-47
AGGACTAGAGGTCTTCCCTTTTTTTGTTGG	1	49	1	GTCTTCCCTT	    0.975517	-32
AAATATTTTGGCGATCGCCTGATGACC   	2	8	0	GCGATCGCCT	    0.911461	-293
AGAGCAATGGGTGATCCCCGTTTTGATTAG	2	71	0	GTGATCCCCG	    0.989698	-230
CGCCATAATCCTGTGCCCAGATTCCCTGTT	2	135	0	CTGTGCCCAG	    0.902825	-166
TTTTATTGTGCTGTTGCCCTGGGTACAGCC	2	226	0	CTGTTGCCCT	    0.923339	-75
CATCACCTCAGCGTGCCCTGTGTATTGCTG	2	271	0	GCGTGCCCTG	    0.980978	-30
          **********

Masking position 8
Map Score:   2.43102

Number of sites scoring better than the average of aligned sites = 1310
Number in coding regions = 1211
Number in noncoding regions = 99
Number of orfs with sites within 600 bp upstream = 109
Fraction of orfs with sites within 600 bp upstream = 0.0175072


Motif number 5

          **********

No masking
Map Score:   -6.79689e-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:   -6.79689e-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:   -6.79689e-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