AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i345_synecho_ctra_300.orf -o345_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	RCY06733	282	Synechocystis
#2	RCY09050	106	Synechocystis

Motif number 1

       TCATACAGACAAACTTATAGGAATATT	1	4	1	TCGCAAATTA	    0.991728	-279
GGAAAACGGCTTTAACGAAAGTTAATAAAAGAGT	1	74	0	TTAGAAATTA	    0.885567	-209
ACTACCAAAATCCAGATAAATTTTCTTCCGTTTT	1	135	0	TCGTAAATTT	     0.91179	-148
ATTTTGGTAGTACTGTTAAAGTTAATTTCACCAA	1	158	1	TCGTAAATTA	    0.970273	-125
TTAAAGTTAATTTCACCAAAATTAGTCAATGGGA	1	173	1	TTACAAATTA	    0.948293	-110
CACTCCAATATGTCGGGATAATTAGGTTCTTTTG	1	254	0	TTGGATATTA	    0.969604	-29
AACTTGATCCTCTAGCCATGTTTTTATTGATACT	2	13	0	TTGCATGTTT	    0.951701	-94
TTTGGTCTACTCCAGCCATGTTTAAGCAGAAATT	2	45	1	TCGCATGTTA	    0.987697	-62
    AAAAAATTTGGTCATGATTATTTTTATCTT	2	87	0	TTGCATGTTA	    0.984216	-20
          * * * **** ***

Masking position 8
Map Score:   8.57645

Number of sites scoring better than the average of aligned sites = 657
Number in coding regions = 529
Number in noncoding regions = 128
Number of orfs with sites within 600 bp upstream = 151
Fraction of orfs with sites within 600 bp upstream = 0.0242531


Motif number 2

TTTTCGTAAAACTAGGGTAATATTCCTATA	1	26	0	ACTAGGGTAA	    0.972661	-257
ATGGCGATCGCCTAAGGAAAACGGCTTTAA	1	93	0	CCTAAGGAAA	    0.991602	-190
CGCCATGGAGCAAAGGGAAAAACGGAAGAA	1	117	1	CAAAGGGAAA	    0.972661	-166
TTTTGACAGACCAAGGGAAAATGAGCACAG	1	229	0	CCAAGGGAAA	    0.994643	-54
AAATTAATTGCCTAAGATAAAAATAATCAT	2	74	1	CCTAAGATAA	    0.940441	-33
          **********

Masking position 4
Map Score:   5.65909

Number of sites scoring better than the average of aligned sites = 746
Number in coding regions = 633
Number in noncoding regions = 113
Number of orfs with sites within 600 bp upstream = 116
Fraction of orfs with sites within 600 bp upstream = 0.0186315


Motif number 3

TAGTTTTACGAAAAGGATCTCATTCCGTCA	1	42	1	AAAAGGATCT	    0.953366	-241
GAAAGTTAATAAAAGAGTCCTGACGGAATG	1	62	0	AAAAGAGTCC	    0.919852	-221
AAACGGAAGAAAATTTATCTGGATTTTGGT	1	136	1	AAATTTATCT	    0.793691	-147
AATTTCACCAAAATTAGTCAATGGGATAGC	1	181	1	AAATTAGTCA	    0.931594	-102
AGACCAAGGGAAAATGAGCACAGAATTGTC	1	222	0	AAAATGAGCA	    0.895531	-61
TTGGTCTGTCAAAAGAACCTAATTATCCCG	1	245	1	AAAAGAACCT	    0.773933	-38
GAGTAGACCAAACTTGATCCTCTAGCCATG	2	27	0	AACTTGATCC	     0.85225	-80
GCCTAAGATAAAAATAATCATGACCAAATT	2	83	1	AAAATAATCA	    0.953142	-24
      AAAAAATTTGGTCATGATTATTTT	2	93	0	AATTTGGTCA	    0.794755	-14
          **********

Masking position 2
Map Score:   2.46241

Number of sites scoring better than the average of aligned sites = 1044
Number in coding regions = 877
Number in noncoding regions = 167
Number of orfs with sites within 600 bp upstream = 173
Fraction of orfs with sites within 600 bp upstream = 0.0277867


Motif number 4

          TCATACAGACAAACTTATAG	1	1	1	TCATACAGAC	    0.947045	-282
GTTAATAAAAGAGTCCTGACGGAATGAGAT	1	58	0	GAGTCCTGAC	    0.917244	-225
GACTATGCTATCCCATTGACTAATTTTGGT	1	187	0	TCCCATTGAC	    0.922661	-96
CACAGAATTGTCGCACTGACTATGCTATCC	1	204	0	TCGCACTGAC	    0.960379	-79
CCAAACTTGATCCTCTAGCCATGTTTTTAT	2	20	0	TCCTCTAGCC	     0.94977	-87
AAGTTTGGTCTACTCCAGCCATGTTTAAGC	2	42	1	TACTCCAGCC	    0.964429	-65
AAGATAAAAATAATCATGACCAAATTTTTT	2	87	1	TAATCATGAC	     0.81693	-20
          **********

Masking position 8
Map Score:   0.869528

Number of sites scoring better than the average of aligned sites = 1490
Number in coding regions = 1316
Number in noncoding regions = 174
Number of orfs with sites within 600 bp upstream = 193
Fraction of orfs with sites within 600 bp upstream = 0.030999


Motif number 5

GTACTGTTAAAGTTAATTTCACCAAAATTA	1	167	1	AGTTAATTTC	    0.980141	-116
ATGTCGGGATAATTAGGTTCTTTTGACAGA	1	249	0	AATTAGGTTC	    0.976461	-34
TATCTTAGGCAATTAATTTCTGCTTAAACA	2	63	0	AATTAATTTC	    0.983255	-44
          **********

Masking position 5
Map Score:   0.0233885

Number of sites scoring better than the average of aligned sites = 87
Number in coding regions = 75
Number in noncoding regions = 12
Number of orfs with sites within 600 bp upstream = 16
Fraction of orfs with sites within 600 bp upstream = 0.00256987


Motif number 6

          **********

No masking
Map Score:   7.84029e-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:   7.84029e-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:   7.84029e-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