AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i202_exonuclease_sbcc_synecho_reg_300.orf -o202_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	RCY44546	80	Synechocystis
#2	RCY49953	300	Synechocystis

Motif number 1

ACTAGAGGTCTTCCCTTTTTTTGTTGGAGA	1	52	1	TTCCCTTTTT	    0.918392	-29
GCAATGGGTGATCCCCGTTTTGATTAGTTA	2	68	0	ATCCCCGTTT	    0.923303	-233
GATCACCCATTGCTCTATGTCCACTGATTC	2	85	1	TGCTCTATGT	    0.943966	-216
TGTGCCCAGATTCCCTGTTTTTGACCCCGA	2	124	0	TTCCCTGTTT	    0.986439	-177
CCCTGGGTACAGCCGTGGGTGTAGGTTTAG	2	210	0	AGCCGTGGGT	    0.963774	-91
ATTGTGCTGTTGCCCTGGGTACAGCCGTGG	2	222	0	TGCCCTGGGT	    0.996295	-79
GCACAATAAAAGCGCTATGTTAGAATCAGC	2	245	1	AGCGCTATGT	    0.939628	-56
CACCTCAGCGTGCCCTGTGTATTGCTGATT	2	268	0	TGCCCTGTGT	    0.997904	-33
          **********

Masking position 10
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

TTCATCCTATGGTAATGGCCCGCTGGGGGA	1	16	0	GGTAATGGCC	    0.949564	-65
GAGGACTAGAGGTCTTCCCTTTTTTTGTTG	1	48	1	GGTCTTCCCT	    0.926983	-33
  GGTCATCAGGCGATCGCCAAAATATTTC	2	9	1	GGCGATCGCC	    0.499941	-292
TAGAGCAATGGGTGATCCCCGTTTTGATTA	2	72	0	GGTGATCCCC	    0.713841	-229
GTTGAGGTGAGGAAAACCCCACAGACGCAG	2	165	1	GGAAAACCCC	    0.892191	-136
CCCCACAGACGCAGTTCGCCATTCCACCGC	2	181	1	GCAGTTCGCC	    0.950497	-120
TACACCCACGGCTGTACCCAGGGCAACAGC	2	217	1	GCTGTACCCA	    0.862742	-84
CTTTTATTGTGCTGTTGCCCTGGGTACAGC	2	227	0	GCTGTTGCCC	    0.986595	-74
GGCACGCTGAGGTGATGGATTTAGATT   	2	284	1	GGTGATGGAT	    0.773473	-17
          **********

Masking position 1
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

ATCCTATGGTAATGGCCCGCTGGGGGACCTAA	1	11	0	AATGGCCCTG	    0.987856	-70
GGGGATCACCCATTGCTCTATGTCCACTGATT	2	82	1	CATTGCCATG	    0.592042	-219
TTAGCGGTGGAATGGCGAACTGCGTCTGTGGG	2	182	0	AATGGCACTG	     0.94952	-119
ACAGCACAATAAAAGCGCTATGTTAGAATCAG	2	242	1	AAAAGCCATG	    0.787514	-59
CAGCAATACACAGGGCACGCTGAGGTGATGGA	2	271	1	CAGGGCCCTG	    0.719833	-30
          ****** * ***

Masking position 2
Map Score:   2.98983

Number of sites scoring better than the average of aligned sites = 165
Number in coding regions = 149
Number in noncoding regions = 16
Number of orfs with sites within 600 bp upstream = 14
Fraction of orfs with sites within 600 bp upstream = 0.00224863


Motif number 4

GGTAATGGCCCGCTGGGGGACCTAA     	1	6	0	CGCTGGGGGA	    0.988171	-75
ATTCTGTTAACTGTCGGGGTCAAAAACAGG	2	111	1	CTGTCGGGGT	    0.980572	-190
AGGATTATGGCGGTTGAGGTGAGGAAAACC	2	153	1	CGGTTGAGGT	    0.964894	-148
CGAACTGCGTCTGTGGGGTTTTCCTCACCT	2	169	0	CTGTGGGGTT	    0.990708	-132
GTAGGTTTAGCGGTGGAATGGCGAACTGCG	2	190	0	CGGTGGAATG	    0.916939	-111
CTGGGTACAGCCGTGGGTGTAGGTTTAGCG	2	208	0	CCGTGGGTGT	    0.966254	-93
ACACAGGGCACGCTGAGGTGATGGATTTAG	2	278	1	CGCTGAGGTG	    0.934693	-23
          **********

Masking position 4
Map Score:   4.31683

Number of sites scoring better than the average of aligned sites = 3011
Number in coding regions = 2856
Number in noncoding regions = 155
Number of orfs with sites within 600 bp upstream = 174
Fraction of orfs with sites within 600 bp upstream = 0.0279473


Motif number 5

AAGACCTCTAGTCCTCCCTTCATCCTATGG	1	34	0	GTCCTCCCTT	    0.997512	-47
AGGACTAGAGGTCTTCCCTTTTTTTGTTGG	1	49	1	GTCTTCCCTT	    0.993242	-32
CACAGACGCAGTTCGCCATTCCACCGCTAA	2	184	1	GTTCGCCATT	    0.978386	-117
          **********

Masking position 2
Map Score:   0.921851

Number of sites scoring better than the average of aligned sites = 38
Number in coding regions = 26
Number in noncoding regions = 12
Number of orfs with sites within 600 bp upstream = 14
Fraction of orfs with sites within 600 bp upstream = 0.00224863


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


Motif number 8

          **********

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