AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i149_Thioredoxin_synecho_reg_300.orf -o149_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	RCY51535	95	Synechocystis
#2	RCY29531	40	Synechocystis
#3	RCY10065	104	Synechocystis
#4	RCY35156	33	Synechocystis
#5	RCY03241	110	Synechocystis

Motif number 1

ATTTTCAGTGTAACGGATGGGAGTGTTGG  	1	9	0	TAACGGTGGG	    0.969108	-87
TAAGTATCACCATGGGTTGGGAATTTTTTTC	1	65	1	CATGGGTGGG	    0.993221	-31
TGGGAATTTTTTTCGCTAGAGACA       	1	82	1	TTTCGCAGAG	    0.936046	-14
GGATTAATATCTTTGCGAGGGAAAATACC  	2	22	1	CTTTGCAGGG	    0.985967	-19
CCAAACCTGTCTAGGCATGGGTATCAAGCGG	3	53	1	CTAGGCTGGG	    0.990909	-52
ATCAAGCGGCGATCGCCTGGGGCAATTTCGG	3	75	1	GATCGCTGGG	    0.987595	-30
AGAATAGAAACTTTGGATGAGCTAAAACCTA	5	23	1	CTTTGGTGAG	    0.971034	-88
          ****** ****

Masking position 5
Map Score:   6.27212

Number of sites scoring better than the average of aligned sites = 1473
Number in coding regions = 1318
Number in noncoding regions = 155
Number of orfs with sites within 600 bp upstream = 166
Fraction of orfs with sites within 600 bp upstream = 0.0266624


Motif number 2

AAATAAGCAGAGTATTAAGAATTATTAAAT	1	36	1	AGTATTAAGA	    0.959604	-60
CCCTCGCAAAGATATTAATCCAGTTCTAAC	2	13	0	GATATTAATC	    0.961459	-28
TCTAGGCATGGGTATCAAGCGGCGATCGCC	3	62	1	GGTATCAAGC	    0.987384	-43
TTCTATTCTTAGTATAAATCC         	5	2	0	AGTATAAATC	    0.955886	-109
TTAGTTAACCAATATTAAGCCGAGGAGAGG	5	87	1	AATATTAAGC	    0.982137	-24
          **********

Masking position 5
Map Score:   3.3168

Number of sites scoring better than the average of aligned sites = 73
Number in coding regions = 59
Number in noncoding regions = 14
Number of orfs with sites within 600 bp upstream = 17
Fraction of orfs with sites within 600 bp upstream = 0.00273049


Motif number 3

CTAGCGAAAAAAATTCCCAACCCATGGTGA	1	71	0	AAATTCCCAA	    0.963408	-25
       GGTATTTTCCCTCGCAAAGATAT	2	28	0	ATTTTCCCTC	    0.967708	-13
TTCAGCGACAATTTTCCCTAGTCCCATTAA	3	19	0	ATTTTCCCTA	     0.98519	-86
TCAACACCGAAATTGCCCCAGGCGATCGCC	3	82	0	AATTGCCCCA	    0.983702	-23
        AGCAATGCCCTATGCTCCTAGC	4	22	0	CAATGCCCTA	    0.970012	-12
          **********

Masking position 4
Map Score:   2.97385

Number of sites scoring better than the average of aligned sites = 613
Number in coding regions = 531
Number in noncoding regions = 82
Number of orfs with sites within 600 bp upstream = 100
Fraction of orfs with sites within 600 bp upstream = 0.0160617


Motif number 4

GCAAAGATATTAATCCAGTTCTAACAA   	2	8	0	TAATCCAGTT	    0.970613	-33
CAATTTTCCCTAGTCCCATTAAAGCATTCC	3	11	0	TAGTCCCATT	    0.965811	-94
TGCTCCTAGCTTGTCCAGCTT         	4	2	0	TTGTCCAGCT	    0.987188	-32
CCGTATTTATTTGTCCATTTAGTTCTGTCA	5	57	1	TTGTCCATTT	    0.979655	-54
          **********

Masking position 4
Map Score:   1.05404

Number of sites scoring better than the average of aligned sites = 149
Number in coding regions = 132
Number in noncoding regions = 17
Number of orfs with sites within 600 bp upstream = 20
Fraction of orfs with sites within 600 bp upstream = 0.00321234


Motif number 5

          **********

No masking
Map Score:   -7.43638e-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:   -7.43638e-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:   -7.43638e-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