AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00473_synecho_reg_100.orf -o00473_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	slr1874	86	ddlA; D-alanine--D-alanine ligase (D-alanylalanine synthetase).
#2	slr1875	119	exoD; exopolysaccharide synthesis protein ExoD.
#3	slr0827	294	alr; probable alanine racemase. [EC:5.1.1.1] [SP:ALR_SYNY3]

Motif number 1

CCGATAATCTCCGCTGAAACGCTAAATTTT	1	40	0	CCGCTGAAAC	    0.964596	-47
ATAGGCTTAGCCAGTAAAACCCGCAAGAGT	2	25	1	CCAGTAAAAC	    0.981685	-95
CTTTAGTAAACCGGGTAAACTCTTGCGGGT	2	43	0	CCGGGTAAAC	     0.98195	-77
TGATTTTTTGCCCAAAAAACATATTCCTTT	3	36	0	CCCAAAAAAC	    0.975694	-259
CAGGCGATCGCCCGAAAAACAAATTACCAT	3	145	0	CCCGAAAAAC	    0.995249	-150
TAATTGCTGACCGGAAAAACTGCCCAGTTG	3	248	0	CCGGAAAAAC	    0.996734	-47
          **********

Masking position 7
Map Score:   8.51038

Number of sites scoring better than the average of aligned sites = 233
Number in coding regions = 207
Number in noncoding regions = 26
Number of orfs with sites within 600 bp upstream = 27
Fraction of orfs with sites within 600 bp upstream = 0.00433665


Motif number 2

     ATGGATAGGGAATAAAGCCTTGGGAGTGAA	1	6	1	TGGAAAACCT	    0.965143	-81
TACTAAAGGTTTGGACAACAACTCTTTTGAAGCAA	2	65	1	TGGCAAATCT	    0.995377	-55
GAAGCAAGACTAGACAAAAAACTCTCAGATTAAGG	2	93	1	TGAAAAATCT	    0.920893	-27
TTCCTTTGTATTGGGTACTAATTCTCCCCTTA   	3	8	0	TGGTAAATCT	    0.976323	-287
AATATGTTTTTTGGGCAAAAAATCAGCCAATGCCG	3	41	1	TGGCAAATCA	    0.992604	-254
GGAAAATTTGTATGTCAATAAATAAAACAAAACGA	3	80	1	TTGCAAATAA	    0.854191	-215
CGATCGCCTGTGGGTAAAGAATTAATTTACAGAGC	3	165	1	TGGAAAATAA	    0.962095	-130
GGCAGTTTTTCCGGTCAGCAATTATGGTTGCAAGG	3	254	1	CGGCAAATAT	     0.95718	-41
          * ** **  ** ***

Masking position 7
Map Score:   6.31209

Number of sites scoring better than the average of aligned sites = 588
Number in coding regions = 519
Number in noncoding regions = 69
Number of orfs with sites within 600 bp upstream = 80
Fraction of orfs with sites within 600 bp upstream = 0.0128493


Motif number 3

CTAAATTTTTCACTCCCAAGGCTTTATTCC	1	19	0	CACTCCCAAG	    0.989823	-68
TCCGATGGATCACCAGCAAGCAC       	1	74	1	CACCAGCAAG	    0.974275	-13
TAGCCAGTAAAACCCGCAAGAGTTTACCCG	2	32	1	AACCCGCAAG	    0.992877	-88
CCCAGTTGCCAAGCCCCCAGAATTTCGCTC	3	226	0	AAGCCCCCAG	    0.984185	-69
TGACCGGAAAAACTGCCCAGTTGCCAAGCC	3	241	0	AACTGCCCAG	    0.973182	-54
          **********

Masking position 2
Map Score:   3.13981

Number of sites scoring better than the average of aligned sites = 404
Number in coding regions = 372
Number in noncoding regions = 32
Number of orfs with sites within 600 bp upstream = 35
Fraction of orfs with sites within 600 bp upstream = 0.00562159


Motif number 4

AATCACCGATAATCTCCGCTGAAACGCTAA	1	45	0	AATCTCCGCT	    0.993696	-42
GATCCATCGGAATCACCGATAATCTCCGCT	1	55	0	AATCACCGAT	    0.975806	-32
TAGACAAAAAACTCTCAGATTAAGGAT   	2	103	1	ACTCTCAGAT	    0.955672	-17
TTGGGTACTAATTCTCCCCTTA        	3	3	0	ATTCTCCCCT	    0.970886	-292
          **********

Masking position 3
Map Score:   0.50664

Number of sites scoring better than the average of aligned sites = 124
Number in coding regions = 111
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

          **********

No masking
Map Score:   -8.78641e-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:   -8.78641e-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:   -8.78641e-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