AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i105_Manganese_Transport_synecho_reg_300.orf -o105_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	RCY20071	98	Synechocystis
#2	RCY34291	164	Synechocystis

Motif number 1

    AAACAACTTTGTGTTTTGACACGTTGAGTT	1	7	1	CTGGTTTTAC	    0.970109	-92
TGTTTTGACACGTTGAGTTTTTCTGTAATCAACT	1	22	1	CTGGTTTTCT	    0.988331	-77
TGGACTTAATCTTGACGATTTACCACTACCTAAA	1	55	1	CTAGATTTCC	    0.981414	-44
CTGGTAAGCTCGTGGGCTTTTTCTGA        	2	3	0	CTGCTTTTCT	    0.992796	-162
AGTTAAAATTTCTTAACTTTTACCAACTGGTAAG	2	29	0	TTACTTTTCC	    0.938987	-136
TCTCATTTTTCATTATCTTCTCATAATTGCAGTG	2	72	0	CTACTTCTAT	    0.968869	-93
AATGGTCTTTCATGATCATCTCATTTTTCATTAT	2	90	0	CTACATCTAT	    0.950981	-75
ATCACTATGGCAACATCATTTGCTTCCCGGGGAG	2	124	1	CAACATTTCT	    0.940144	-41
          * * * ***** **

Masking position 9
Map Score:   6.45847

Number of sites scoring better than the average of aligned sites = 895
Number in coding regions = 781
Number in noncoding regions = 114
Number of orfs with sites within 600 bp upstream = 132
Fraction of orfs with sites within 600 bp upstream = 0.0212014


Motif number 2

TCTTGACGATTTACCACTACCTAAAATCTG	1	64	1	TTACCACTAC	    0.980499	-35
AGTTAAGAAATTTTAACTCCCCGTTTTCAC	2	45	1	TTTTAACTCC	    0.947312	-120
TAACTCCCCGTTTTCACTGCAATTATGAGA	2	58	1	TTTTCACTGC	    0.989455	-107
ATCATCTCATTTTTCATTATCTTCTCATAA	2	80	0	TTTTCATTAT	    0.931526	-85
TGAAAGACCATTATCACTATGGCAACATCA	2	112	1	TTATCACTAT	    0.980213	-53
          **********

Masking position 6
Map Score:   3.33548

Number of sites scoring better than the average of aligned sites = 261
Number in coding regions = 223
Number in noncoding regions = 38
Number of orfs with sites within 600 bp upstream = 45
Fraction of orfs with sites within 600 bp upstream = 0.00722775


Motif number 3

TACAGAAAAACTCAACGTGTCAAAACACAA	1	19	0	CTCAACGTGT	    0.987574	-80
TTTTTCTGTAATCAACTGGACTTAATCTTG	1	39	1	ATCAACTGGA	    0.904002	-60
AAAATCTGAACCCCTCTTTTGCC       	1	86	1	CCCCTCTTTT	    0.887279	-13
CTTAACTTTTACCAACTGGTAAGCTCGTGG	2	22	0	ACCAACTGGT	    0.911317	-143
GTTAAAATTTCTTAACTTTTACCAACTGGT	2	32	0	CTTAACTTTT	    0.805222	-133
GAAATTTTAACTCCCCGTTTTCACTGCAAT	2	51	1	CTCCCCGTTT	    0.974704	-114
GCCAGCAGTCCTCCCCGGGAAGCAAATGAT	2	138	0	CTCCCCGGGA	    0.976626	-27
          **********

Masking position 6
Map Score:   2.36952

Number of sites scoring better than the average of aligned sites = 2443
Number in coding regions = 2224
Number in noncoding regions = 219
Number of orfs with sites within 600 bp upstream = 239
Fraction of orfs with sites within 600 bp upstream = 0.0383874


Motif number 4

          **********

No masking
Map Score:   -1.75204e-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:   -1.75204e-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:   -1.75204e-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