AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i101_Iron_Transport_synecho_reg_100.orf -o101_synecho_100.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	RCY33239	167	Synechocystis
#2	RCY02899	51	Synechocystis
#3	RCY35187	264	Synechocystis

Motif number 1

CCCTGCCTTGTCCATGGCGATCGCTGTTTAT	1	13	0	TCCATGGCGT	    0.951707	-155
GGGAACTATTCCGGTTGCCCCCTTTTATTGA	1	41	1	CCGGTTGCCC	    0.932339	-127
AACCTAATTGCCCGACTCCGTTCTTTACTTT	1	95	0	CCCGACTCCT	    0.935019	-73
TACCTAAAGATCCGTGCCCTTTCTCCAATGC	1	132	1	TCCGTGCCCT	    0.947399	-36
CCAAAGACAACCCAAGGCCATTCCAGGCTAA	2	31	1	CCCAAGGCCT	    0.994232	-21
         CCCCATGACCTCATTTACTTGT	3	2	1	CCCATGACCC	    0.987814	-263
AGGAAGAATCCCCATGGCGACCAAGCATTTA	3	150	1	CCCATGGCGC	    0.992299	-115
GGCATTAAAACCCATTTCCCTGTCCCCCAGT	3	195	1	CCCATTTCCT	    0.973253	-70
TTTCCCTGTCCCCCAGTCCTCTACAATAATC	3	209	1	CCCCAGTCCC	    0.975176	-56
          ********* *

Masking position 8
Map Score:   9.63758

Number of sites scoring better than the average of aligned sites = 2610
Number in coding regions = 2370
Number in noncoding regions = 240
Number of orfs with sites within 600 bp upstream = 241
Fraction of orfs with sites within 600 bp upstream = 0.0387086


Motif number 2

ACAAGGCAGGGAACTATTCCGGTTGCCCCCT	1	33	1	GAACATTCCG	    0.966482	-135
GAACGGAGTCGGGCAATTAGGTTAATCCCTA	1	103	1	GGGCATTAGG	    0.990779	-65
GAAAGGGCACGGATCTTTAGGTAGGGATTAA	1	124	0	GGATTTTAGG	     0.96078	-44
CTTTGGAGTTGACCCGTTAGGTTTGA     	2	6	0	GACCGTTAGG	    0.968537	-46
TAATTGTTAAGAATAATTAGGAATAGTAAGA	3	89	0	GAATATTAGG	    0.980864	-176
ATTTAACAGAGGACTATTCGGCATTAAAACC	3	176	1	GGACATTCGG	    0.994968	-89
          **** ******

Masking position 7
Map Score:   3.61534

Number of sites scoring better than the average of aligned sites = 160
Number in coding regions = 137
Number in noncoding regions = 23
Number of orfs with sites within 600 bp upstream = 29
Fraction of orfs with sites within 600 bp upstream = 0.00465789


Motif number 3

GGCAATTAGGTTAATCCCTACCTAAAGATC	1	114	1	TTAATCCCTA	    0.982261	-54
TTCTTAACAATTAATAGCCACTACAGCAAT	3	107	1	TTAATAGCCA	    0.953803	-158
GGAAAAAGGAAGAATCCCCATGGCGACCAA	3	144	1	AGAATCCCCA	    0.944638	-121
CTATTCGGCATTAAAACCCATTTCCCTGTC	3	189	1	TTAAAACCCA	    0.931789	-76
GTCCTCTACAATAATCTCTAATCTTATTAG	3	224	1	ATAATCTCTA	    0.881932	-41
GTAGTTAATCTTAATAACTATG        	3	253	1	TTAATAACTA	    0.898612	-12
          **********

Masking position 4
Map Score:   1.70606

Number of sites scoring better than the average of aligned sites = 580
Number in coding regions = 508
Number in noncoding regions = 72
Number of orfs with sites within 600 bp upstream = 88
Fraction of orfs with sites within 600 bp upstream = 0.0141343


Motif number 4

          **********

No masking
Map Score:   -5.51791e-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:   -5.51791e-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:   -5.51791e-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