AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i179_folate_biosynthesis_synecho_reg_300.orf -o179_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	RCY45762	34	Synechocystis
#2	RCY12069	206	Synechocystis
#3	RCY48878	274	Synechocystis

Motif number 1

GCATCAACTGAATTTTGCCAACAATAATTG	1	13	1	AATTTTGCCA	    0.971879	-22
ATCAGCTCGGAATTTTCCCAAAACAGGTAA	2	138	1	AATTTTCCCA	    0.971879	-69
GTTTTTGGTTACCTTTGCCATCCCGTCGAG	3	94	0	ACCTTTGCCA	     0.99292	-181
GTAACCAAAAACCTTGCCCAAAAGTAGGAC	3	112	1	ACCTTGCCCA	    0.980872	-163
AAAAAATCTCCCCTGCCCCAAAATTACTGT	3	195	1	CCCTGCCCCA	    0.960889	-80
CCCCAAAATTACTGTCCCCATTCCCTTTGC	3	210	1	ACTGTCCCCA	    0.940485	-65
TGTCCCCATTCCCTTTGCTAACCTATGGCA	3	222	1	CCCTTTGCTA	    0.938839	-53
AGGCCTTCATCATTTTGCCATAGGTTAGCA	3	237	0	CATTTTGCCA	    0.971327	-38
          **********

Masking position 10
Map Score:   9.34086

Number of sites scoring better than the average of aligned sites = 1312
Number in coding regions = 1164
Number in noncoding regions = 148
Number of orfs with sites within 600 bp upstream = 163
Fraction of orfs with sites within 600 bp upstream = 0.0261805


Motif number 2

AATTATTGTTGGCAAAATTCAGTTGATGCAT 	1	10	0	GGAAAATCAG	    0.989768	-25
GAGAATTTAATGTAAAATTATGGAGTGTACAA	2	26	0	TGAAAATATG	    0.937054	-181
TACCTGTTTTGGGAAAATTCCGAGCTGATGCA	2	135	0	GGAAAATCCG	    0.993061	-72
TCCCAAAACAGGTAAAATCATTTACACTGAAA	2	153	1	GGAAAATATT	     0.96905	-54
        CAGGAATAATCCCTAAAAGTTAAA	2	193	0	GGATAATCCT	    0.894449	-14
ATGTGTCATAGGAGAAATAAAGTAATGAGGTG	3	62	1	GGGAAATAAG	     0.96101	-213
GCTAACCTATGGCAAAATGATGAAGGCCTAAC	3	238	1	GGAAAATATG	    0.991363	-37
          ** ***** ***

Masking position 6
Map Score:   7.33089

Number of sites scoring better than the average of aligned sites = 510
Number in coding regions = 415
Number in noncoding regions = 95
Number of orfs with sites within 600 bp upstream = 109
Fraction of orfs with sites within 600 bp upstream = 0.0175072


Motif number 3

AATTAACGATGAGAGAATTTAATGTAAAATTATG	2	36	0	GGAATTTATG	    0.984377	-171
CACATTCTCTGCGGTGGGTTAATGCTCTTTCTAC	3	33	0	GGGGGTTATG	    0.992369	-242
TCCTACTTTTGGGCAAGGTTTTTGGTTACCTTTG	3	107	0	GGAGGTTTTG	    0.988053	-168
AGATTTTTTGTCGCTGATTTTCTGCAATTTGATC	3	170	0	TGGATTTTTG	    0.939147	-105
TTTTGGGGCAGGGGAGATTTTTTGTCGCTGATTT	3	184	0	GGGATTTTTG	    0.990075	-91
        GGGAGGGAGTTTACTGTTAGGCCTTC	3	259	0	GGAGTTTATG	    0.990052	-16
          * *  ****** **

Masking position 9
Map Score:   5.04659

Number of sites scoring better than the average of aligned sites = 158
Number in coding regions = 133
Number in noncoding regions = 25
Number of orfs with sites within 600 bp upstream = 28
Fraction of orfs with sites within 600 bp upstream = 0.00449727


Motif number 4

ATGCATCAACTGAATTTTGCCAACAATAAT	1	11	1	TGAATTTTGC	    0.884269	-24
 TTAAACCTGTTCATTTTGTACACTCCATA	2	10	1	TTCATTTTGT	     0.95433	-197
TCTTAACTGCTTCCTTTGGTATATGAAAAT	2	91	0	TTCCTTTGGT	    0.885905	-116
AGATTTTCTTAACACTTTGCATCAGCTCGG	2	118	1	AACACTTTGC	     0.90849	-89
AGGTTTTTGGTTACCTTTGCCATCCCGTCG	3	96	0	TTACCTTTGC	    0.968227	-179
ACTGTCCCCATTCCCTTTGCTAACCTATGG	3	220	1	TTCCCTTTGC	    0.991127	-55
TTAGGCCTTCATCATTTTGCCATAGGTTAG	3	239	0	ATCATTTTGC	    0.970865	-36
          **********

Masking position 6
Map Score:   5.3008

Number of sites scoring better than the average of aligned sites = 981
Number in coding regions = 863
Number in noncoding regions = 118
Number of orfs with sites within 600 bp upstream = 143
Fraction of orfs with sites within 600 bp upstream = 0.0229682


Motif number 5

          **********

No masking
Map Score:   4.78496e-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:   4.78496e-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:   4.78496e-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