AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i179_folate_biosynthesis_synecho_reg_100.orf -o179_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	RCY45762	34	Synechocystis
#2	RCY12069	206	Synechocystis
#3	RCY48878	274	Synechocystis

Motif number 1

CAATTATTGTTGGCAAAATTCAGTTGATGC	1	13	0	TGGCAAAATT	      0.9731	-22
TTACCTGTTTTGGGAAAATTCCGAGCTGAT	2	138	0	TGGGAAAATT	      0.9731	-69
CTCGACGGGATGGCAAAGGTAACCAAAAAC	3	94	1	TGGCAAAGGT	    0.993234	-181
GTCCTACTTTTGGGCAAGGTTTTTGGTTAC	3	112	0	TGGGCAAGGT	     0.98171	-163
ACAGTAATTTTGGGGCAGGGGAGATTTTTT	3	195	0	TGGGGCAGGG	    0.962569	-80
GCAAAGGGAATGGGGACAGTAATTTTGGGG	3	210	0	TGGGGACAGT	    0.942989	-65
TGCCATAGGTTAGCAAAGGGAATGGGGACA	3	222	0	TAGCAAAGGG	    0.941408	-53
TGCTAACCTATGGCAAAATGATGAAGGCCT	3	237	1	TGGCAAAATG	    0.972571	-38
          **********

Masking position 1
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

 ATGCATCAACTGAATTTTGCCAACAATAATT	1	10	1	CTGATTTTCC	    0.989893	-25
TTGTACACTCCATAATTTTACATTAAATTCTC	2	26	1	CATATTTTCA	    0.937785	-181
TGCATCAGCTCGGAATTTTCCCAAAACAGGTA	2	135	1	CGGATTTTCC	    0.993139	-72
TTTCAGTGTAAATGATTTTACCTGTTTTGGGA	2	153	0	AATATTTTCC	    0.969421	-54
TTTAACTTTTAGGGATTATTCCTG        	2	193	1	AGGATTATCC	    0.895619	-14
CACCTCATTACTTTATTTCTCCTATGACACAT	3	62	0	CTTATTTCCC	    0.961474	-213
GTTAGGCCTTCATCATTTTGCCATAGGTTAGC	3	238	0	CATATTTTCC	    0.991469	-37
          *** ***** **

Masking position 5
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

CATAATTTTACATTAAATTCTCTCATCGTTAATT	2	36	1	CATAAATTCC	    0.986365	-171
GTAGAAAGAGCATTAACCCACCGCAGAGAATGTG	3	33	1	CATAACCCCC	    0.993362	-242
CAAAGGTAACCAAAAACCTTGCCCAAAAGTAGGA	3	107	1	CAAAACCTCC	    0.989602	-168
GATCAAATTGCAGAAAATCAGCGACAAAAAATCT	3	170	1	CAAAAATCCA	    0.946691	-105
AAATCAGCGACAAAAAATCTCCCCTGCCCCAAAA	3	184	1	CAAAAATCCC	    0.991363	-91
GAAGGCCTAACAGTAAACTCCCTCCC        	3	259	1	CATAAACTCC	    0.991337	-16
          ** ******  * *

Masking position 6
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