AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i174_Biotin_Biosynthesis_synecho_reg_300.orf -o174_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	RCY43755	46	Synechocystis
#2	RCY14039	107	Synechocystis
#3	RCY51943	111	Synechocystis

Motif number 1

TCAAAAGTTCACCCAACATTCTACTAGGGG     	1	6	0	ACCCACTCAT	     0.99719	-41
ACGGGTTAAAATCCATCTACCCAATTGATCAAGTT	2	20	0	ATCCACCCAT	     0.98438	-88
ATGGATTTTAACCCGTAGGCTCATTGGTCAGCTCA	2	39	1	ACCCGACTAT	    0.930721	-69
     GAATTACCCACCCCCCAATACAACAAAATA	2	88	0	ACCCACCCAA	    0.995184	-20
CGATATACTGACCCCGCGTCCCCATTCCCA     	3	6	0	ACCCCCCCCT	    0.995074	-106
AGTCAACAAAACCCGATATTCTACTAAAAGACTAA	3	51	1	ACCCGTTCAT	    0.968779	-61
AAAAGACTAAACACATCGTTTTCCAACGCTAGAGC	3	76	1	ACACACTTCA	    0.795488	-36
    TGGCCCACCCAGCTCTAGCGTTGGAAAACGA	3	91	0	ACCCACTACT	    0.981387	-21
          ***** *  ** * *

Masking position 1
Map Score:   7.0462

Number of sites scoring better than the average of aligned sites = 838
Number in coding regions = 756
Number in noncoding regions = 82
Number of orfs with sites within 600 bp upstream = 99
Fraction of orfs with sites within 600 bp upstream = 0.0159011


Motif number 2

       CCCCTAGTAGAATGTTGGGTGAACTTTTG	1	4	1	CTGTAGTTGG	    0.993155	-43
CTTAACTTGATCAATTGGGTAGATGGATTTTAACCC	2	17	1	TCATTGTGGG	    0.980589	-91
TGGATTTTAACCCGTAGGCTCATTGGTCAGCTCAAG	2	40	1	CCGTAGTAGG	    0.984092	-68
CTAATCGTATTTTGTTGTATTGGGGGGTGGGTAATT	2	81	1	TTGTTGTGGG	     0.99747	-27
AATATCGGGTTTTGTTGACTAGGCGATCGCCGATAT	3	35	0	TTGTTGTGGA	    0.983876	-77
GTTTAGTCTTTTAGTAGAATATCGGGTTTTGTTGAC	3	52	0	TTGTAGTTGG	    0.994297	-60
          ** ****  * *  **

Masking position 10
Map Score:   4.83946

Number of sites scoring better than the average of aligned sites = 311
Number in coding regions = 278
Number in noncoding regions = 33
Number of orfs with sites within 600 bp upstream = 36
Fraction of orfs with sites within 600 bp upstream = 0.0057822


Motif number 3

     GCTGTGCTTAACTTGATCAATTGGG	2	6	1	GCTTAACTTG	    0.974981	-102
GATTAGTAAAGCTTGAGCTGACCAATGAGC	2	57	0	GCTTGAGCTG	    0.998129	-51
GTTTTCCAACGCTAGAGCTGGGTGGGCCA 	3	93	1	GCTAGAGCTG	    0.996706	-19
          **********

Masking position 6
Map Score:   2.23043

Number of sites scoring better than the average of aligned sites = 51
Number in coding regions = 45
Number in noncoding regions = 6
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 4

          **********

No masking
Map Score:   2.79544e-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 5

          **********

No masking
Map Score:   2.79544e-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:   2.79544e-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