AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i244_regulatory1_synecho_reg_300.orf -o244_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	RCY15108	176	Synechocystis
#2	RCY52095	117	Synechocystis
#3	RCY47541	210	Synechocystis

Motif number 1

GGTAGGAATTTTAGCAGTGGGTGTACAATCGAAGGCAA	1	11	1	TACTGGGTCA	    0.943227	-166
TGAGACTAGGTTGCTCCAGGGAGGGAGAGAGTCATGTT	1	70	0	TGTAGGGGAA	     0.99087	-107
AGTCAGGCGATCGCCGTTGGGAATAATAAAGAAACTAT	2	66	0	TGCTGGGTAA	    0.990821	-52
TTAAGGAATGTTGCCAATGGGAAAGAGATAAAGACATT	3	36	1	TGCTGGGAAA	    0.983924	-175
AGCTACTGCATGGATGGTGGGCGGCTAATCTGTTCAAC	3	95	1	TGTTGGGGTA	    0.984006	-116
GCTAATCTGTTCAACTAAGGGACGGCCATGCCCTAGAA	3	118	1	TACAGGGGCA	    0.963563	-93
TGGAAAAATAGCGGTGTTGGGCTGAAAAGATGTCCATC	3	159	0	GGTTGGGGAA	    0.985133	-52
GCTGATTAACTAGTTATGGGGTGGAAAAATAGCGGTGT	3	180	0	TGTGGGGGAA	    0.989156	-31
          * * *  ****  * * *

Masking position 18
Map Score:   6.32939

Number of sites scoring better than the average of aligned sites = 631
Number in coding regions = 558
Number in noncoding regions = 73
Number of orfs with sites within 600 bp upstream = 81
Fraction of orfs with sites within 600 bp upstream = 0.01301


Motif number 2

TGTACAATCGAAGGCAAACTTTGTTTAAAG	1	32	1	AAGGCAAACT	    0.839173	-145
ACTTTGTTTAAAGTCCAACATAACATGACT	1	49	1	AAGTCCAACA	    0.972377	-128
CACAGAATAAATTTCAAACTTACTAATAGT	1	121	1	ATTTCAAACT	    0.864811	-56
TAAAGAAACTATTGCCATCAGTATTTTACG	2	48	0	ATTGCCATCA	    0.958408	-70
TTTCTTTATTATTCCCAACGGCGATCGCCT	2	70	1	ATTCCCAACG	    0.940477	-48
TCTCTTTCCCATTGGCAACATTCCTTAAGA	3	34	0	ATTGGCAACA	    0.901431	-177
ACGTAAACCCATTTCCAGCTACTGCATGGA	3	79	1	ATTTCCAGCT	    0.909064	-132
GGCTGAAAAGATGTCCATCAAATTCTAGGG	3	148	0	ATGTCCATCA	    0.960887	-63
GACATCTTTTCAGCCCAACACCGCTATTTT	3	163	1	CAGCCCAACA	    0.872099	-48
          **********

Masking position 7
Map Score:   4.71851

Number of sites scoring better than the average of aligned sites = 2470
Number in coding regions = 2309
Number in noncoding regions = 161
Number of orfs with sites within 600 bp upstream = 164
Fraction of orfs with sites within 600 bp upstream = 0.0263412


Motif number 3

TGACTCTCTCCCTCCCTGGAGCAACCTAGTCTCAGCCAGC	1	74	1	CCCCACAAGT	    0.997567	-103
CTAGTCTCAGCCAGCCATTACACACAGAATAAATTTCAAA	1	99	1	CCCCAAAAAT	    0.991584	-78
CCATTGGCAACATTCCTTAAGAAAGTAAAACAAGAGTATT	3	16	0	CACCAAAAAA	    0.907139	-195
AACAGATTAGCCGCCCACCATCCATGCAGTAGCTGGAAAT	3	89	0	CCCCACAAGT	    0.997605	-122
TAGGGCATGGCCGTCCCTTAGTTGAACAGATTAGCCGCCC	3	113	0	CCCCATGAGA	     0.95368	-98
CGCTATTTTTCCACCCCATAACTAGTTAATCAGCTCG   	3	184	1	CCCCACAAAT	    0.996247	-27
          **  **   * * *   ***

Masking position 10
Map Score:   2.30898

Number of sites scoring better than the average of aligned sites = 165
Number in coding regions = 144
Number in noncoding regions = 21
Number of orfs with sites within 600 bp upstream = 20
Fraction of orfs with sites within 600 bp upstream = 0.00321234


Motif number 4

ATGGCTGGCTGAGACTAGGTTGCTCCAGGGA	1	86	0	GAGATAGGTT	    0.986393	-91
AAATACTGATGGCAATAGTTTCTTTATTATT	2	52	1	GGCATAGTTT	    0.980302	-66
GCGATCGCCTGACTTTAGTTTCCCTCTAACC	2	90	1	GACTTAGTTT	    0.939078	-28
          GGGATCAGGTTAGAGGGAAAC	2	107	0	GGGACAGGTT	    0.986591	-11
AGCTGGAAATGGGTTTACGTTGCTCAATGTC	3	68	0	GGGTTACGTT	    0.970037	-143
          **** ******

Masking position 7
Map Score:   0.769377

Number of sites scoring better than the average of aligned sites = 241
Number in coding regions = 206
Number in noncoding regions = 35
Number of orfs with sites within 600 bp upstream = 43
Fraction of orfs with sites within 600 bp upstream = 0.00690652


Motif number 5

TACAATCGAAGGCAAACTTTGTTTAAAGTC	1	34	1	GGCAAACTTT	    0.958461	-143
CCTAGTCTCAGCCAGCCATTACACACAGAA	1	98	1	GCCAGCCATT	    0.982774	-79
TTGATCATCAGCAAGACTTTT         	1	166	1	GCAAGACTTT	     0.98409	-11
AACGGCGATCGCCTGACTTTAGTTTCCCTC	2	86	1	GCCTGACTTT	    0.989823	-32
          **********

Masking position 9
Map Score:   1.11599

Number of sites scoring better than the average of aligned sites = 212
Number in coding regions = 182
Number in noncoding regions = 30
Number of orfs with sites within 600 bp upstream = 37
Fraction of orfs with sites within 600 bp upstream = 0.00594282


Motif number 6

          **********

No masking
Map Score:   -3.24418e-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:   -3.24418e-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 8

          **********

No masking
Map Score:   -3.24418e-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