AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i316_mixed3_synecho_reg_300.orf -o316_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	RCY43260	300	Synechocystis

Motif number 1

CAATTTGGATAGTGGTGGGTGATCAACAGCA	1	26	0	AGGGTGGGTG	    0.997964	-275
GTTTCCAAAAAGCAGTGGGACAATTTGGATA	1	46	0	AGAGTGGGAC	    0.995497	-255
CTATGCGTGGATGAGTGGGACTGCCTGGGAC	1	227	1	ATAGTGGGAC	    0.989912	-74
AGGCAAATAGATTGGTGAGTCCCAGGCAGTC	1	245	0	ATGGTGAGTC	    0.983794	-56
CGATTGAATCAGAGGTCGGTGGTGAAAACTC	1	276	0	AGGGTCGGTG	    0.992866	-25
          ** ********

Masking position 6
Map Score:   6.30013

Number of sites scoring better than the average of aligned sites = 192
Number in coding regions = 180
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 2

        ACAAAAGATTTGATCTGCTGTT	1	3	1	AAAAGATTTG	    0.915183	-298
TACAAGGTGTAAAGAATTTGTTCCGTTTCC	1	71	0	AAAGAATTTG	    0.875882	-230
ACCTTGTAATGCAAGCTTTTACAGACCTTA	1	93	1	GCAAGCTTTT	    0.842624	-208
ACAGACCTTAATAAACTTTGTTTATCTCTC	1	113	1	ATAAACTTTG	    0.934364	-188
TATCTCTCTAATAAGATTTTCTGGGGCCTA	1	135	1	ATAAGATTTT	    0.915663	-166
AAAAAGGCGGACAAGATTTTCGCTATGGGC	1	194	0	ACAAGATTTT	    0.924362	-107
          **********

Masking position 7
Map Score:   3.88747

Number of sites scoring better than the average of aligned sites = 445
Number in coding regions = 357
Number in noncoding regions = 88
Number of orfs with sites within 600 bp upstream = 87
Fraction of orfs with sites within 600 bp upstream = 0.0139737


Motif number 3

AATTTGTTCCGTTTCCAAAAAGCAGTGGGA	1	57	0	GTTTCCAAAA	    0.966354	-244
TGTAATGCAAGCTTTTACAGACCTTAATAA	1	97	1	GCTTTTACAG	    0.944975	-204
TTCGCTATGGGCTTCCACAAACTACCACGT	1	176	0	GCTTCCACAA	    0.994469	-125
ATTTGCCTGAGTTTTCACCACCGACCTCTG	1	268	1	GTTTTCACCA	    0.977828	-33
          **********

Masking position 4
Map Score:   0.671408

Number of sites scoring better than the average of aligned sites = 304
Number in coding regions = 288
Number in noncoding regions = 16
Number of orfs with sites within 600 bp upstream = 20
Fraction of orfs with sites within 600 bp upstream = 0.00321234


Motif number 4

GTGGGACAATTTGGATAGTGGTGGGTGATCA	1	32	0	TTGGATGTGG	    0.976827	-269
AAACTACCACGTAAATTGGGGGTTAGGCCCC	1	157	0	GTAAATGGGG	    0.979249	-144
AATTTACGTGGTAGTTTGTGGAAGCCCATAG	1	171	1	GTAGTTGTGG	    0.952145	-130
GGACAAGATTTTCGCTATGGGCTTCCACAAA	1	185	0	TTCGCTTGGG	    0.881658	-116
TGTACTATGCGTGGATGAGTGGGACTGCCTG	1	223	1	GTGGATAGTG	    0.868557	-78
ACTCAGGCAAATAGATTGGTGAGTCCCAGGC	1	249	0	ATAGATGGTG	    0.900428	-52
TGAATCAGAGGTCGGTGGTGAAAACTCAGGC	1	272	0	GTCGGTGTGA	    0.838137	-29
CGACCTCTGATTCAATCGGGGT         	1	289	1	TTCAATGGGG	    0.972921	-12
          ****** ****

Masking position 6
Map Score:   1.4477

Number of sites scoring better than the average of aligned sites = 3763
Number in coding regions = 3390
Number in noncoding regions = 373
Number of orfs with sites within 600 bp upstream = 373
Fraction of orfs with sites within 600 bp upstream = 0.0599101


Motif number 5

          **********

No masking
Map Score:   7.91135e-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:   7.91135e-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:   7.91135e-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