AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i314_mixed28_synecho_reg_300.orf -o314_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	RCY52315	300	Synechocystis
#2	RCY12179	25	Synechocystis
#3	RCY33601	300	Synechocystis

Motif number 1

TCAACAACCCAACGTCGAGGCAAAACCTCAAAACCCT	1	12	0	ATGGGCAACC	     0.99869	-289
TGCTTAAACGACGGTAGCGACCAAACCAAGCAAAGGT	1	53	0	ATGGACAACC	    0.995188	-248
TATGTTTGAAAAGTTCGAGGCAAAGCCTTCGGAGCAT	1	152	0	ATGGGCAACC	    0.998669	-149
AGCTCCCGTGAGAACTATGGCTAACCCTTGCCATTGC	1	215	1	ACAGGCAACC	    0.996034	-86
CGGTAGCGTAAAACCTGGGGCCCACCCATTAGCAATG	1	246	0	ACGGGCCACC	    0.996484	-55
GCTACCGTGGACAATAGTGACAATGCCAACACTTT  	1	276	1	ATGGACATCC	    0.977341	-25
AATAGCGTTAATTTCAATGGCTAATCCTGCAAGATTA	3	52	1	ACAGGCAACC	    0.996036	-249
          *   * * *** ** **

Masking position 1
Map Score:   14.8267

Number of sites scoring better than the average of aligned sites = 122
Number in coding regions = 109
Number in noncoding regions = 13
Number of orfs with sites within 600 bp upstream = 14
Fraction of orfs with sites within 600 bp upstream = 0.00224863


Motif number 2

AAGGGTTTTGAGGTTTTGCCTCGACGTTGGGTTG	1	11	1	AGGTTGCCCA	    0.997642	-290
TACCTTTGCTTGGTTTGGTCGCTACCGTCGTTTA	1	52	1	TGGTTGTCCA	    0.983693	-249
CATGCTCCGAAGGCTTTGCCTCGAACTTTTCAAA	1	151	1	AGGTTGCCCA	    0.997642	-150
AGCAATGGCAAGGGTTAGCCATAGTTCTCACGGG	1	219	0	AGGTTGCCTG	    0.993527	-82
CCATTGCTAATGGGTGGGCCCCAGGTTTTACGCT	1	245	1	TGGTGGCCCG	    0.995755	-56
   AAAGTGTTGGCATTGTCACTATTGTCCACGG	1	280	0	TGGATGTCCA	     0.95668	-21
TTAATCTTGCAGGATTAGCCATTGAAATTAACGC	3	56	0	AGGTTGCCTG	    0.993528	-245
CAGTCATAGAATGGAGTGCCCCAGGAGCTTTGTT	3	241	1	ATGAGGCCCG	    0.939522	-60
          *** ** *** * *

Masking position 8
Map Score:   13.5785

Number of sites scoring better than the average of aligned sites = 509
Number in coding regions = 463
Number in noncoding regions = 46
Number of orfs with sites within 600 bp upstream = 54
Fraction of orfs with sites within 600 bp upstream = 0.00867331


Motif number 3

TGTTGAACGTACCTTTGCTTGGTTTGGTCG	1	43	1	ACCTTTGCTT	     0.97928	-258
AATATTCATAATCCTTGCTTAAACGACGGT	1	75	0	ATCCTTGCTT	      0.9844	-226
GGCAACATAGAGCATTGTCTCACTGGTGGT	1	110	0	AGCATTGTCT	    0.928478	-191
ATGCTCCGAAGGCTTTGCCTCGAACTTTTC	1	152	1	GGCTTTGCCT	    0.974421	-149
ACTATGGCTAACCCTTGCCATTGCTAATGG	1	228	1	ACCCTTGCCA	    0.965212	-73
          AGCCTTCCTTGAATTTTATT	2	16	0	AGCCTTCCTT	    0.968661	-10
TCAAAAAGTTATCCTTGCCTTAAACGGCGA	3	164	1	ATCCTTGCCT	    0.990095	-137
GTGCCCCAGGAGCTTTGTTTTCCTAGCTGA	3	256	1	AGCTTTGTTT	    0.953878	-45
          **********

Masking position 5
Map Score:   10.1458

Number of sites scoring better than the average of aligned sites = 488
Number in coding regions = 405
Number in noncoding regions = 83
Number of orfs with sites within 600 bp upstream = 76
Fraction of orfs with sites within 600 bp upstream = 0.0122069


Motif number 4

TAGAGCATTGTCTCACTGGTGGTAGGTAAA	1	103	0	TCTCACTGGT	    0.859266	-198
ATATTCTTAAGTTCCTTTGGGCTTAAAAAA	1	186	1	GTTCCTTTGG	    0.737044	-115
TAGCCATAGTTCTCACGGGAGCTTTTTTAA	1	208	0	TCTCACGGGA	    0.880322	-93
CCTTGCCATTGCTAATGGGTGGGCCCCAGG	1	240	1	GCTAATGGGT	    0.933563	-61
CAGGTTTTACGCTACCGTGGACAATAGTGA	1	266	1	GCTACCGTGG	    0.919651	-35
TTCCTTGAATTTTATTGGGGT         	2	2	0	TTTATTGGGG	    0.770886	-24
ATAATCAATGTTTAACAGGGATGAAACGTC	3	92	0	TTTAACAGGG	    0.744722	-209
ATATTATCAATCTACTTGGTCATTAACCAT	3	124	1	TCTACTTGGT	     0.84554	-177
TAAACGGCGATCGCCTGGGGCCACTGACTT	3	184	1	TCGCCTGGGG	    0.954952	-117
GACTTGGCGGGTTCATAGGGGATGGAGCCA	3	209	1	GTTCATAGGG	    0.888419	-92
GGAAAACAAAGCTCCTGGGGCACTCCATTC	3	249	0	GCTCCTGGGG	    0.993423	-52
          **********

Masking position 9
Map Score:   6.29206

Number of sites scoring better than the average of aligned sites = 4521
Number in coding regions = 4104
Number in noncoding regions = 417
Number of orfs with sites within 600 bp upstream = 408
Fraction of orfs with sites within 600 bp upstream = 0.0655316


Motif number 5

          **********

No masking
Map Score:   2.86649e-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:   2.86649e-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:   2.86649e-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