AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i230_synecho_ctra_100.orf -o230_synecho_ctra_100.ace -a/home/amcguire/genomes/ORF_synecho.txt -z/home/amcguire/genomes/synecho.fna -g0.46 -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 =  	0.46
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RCY49953	300	Synechocystis
#2	RCT00274	264	Chlamydia_trachomatis

Motif number 1

GCAATGGGTGATCCCCGTTTTGATTAGTTA	1	68	0	ATCCCCGTTT	    0.836398	-233
GATCACCCATTGCTCTATGTCCACTGATTC	1	85	1	TGCTCTATGT	    0.947563	-216
TGTGCCCAGATTCCCTGTTTTTGACCCCGA	1	124	0	TTCCCTGTTT	    0.968635	-177
CCCTGGGTACAGCCGTGGGTGTAGGTTTAG	1	210	0	AGCCGTGGGT	    0.938579	-91
ATTGTGCTGTTGCCCTGGGTACAGCCGTGG	1	222	0	TGCCCTGGGT	    0.993904	-79
GCACAATAAAAGCGCTATGTTAGAATCAGC	1	245	1	AGCGCTATGT	    0.904469	-56
CACCTCAGCGTGCCCTGTGTATTGCTGATT	1	268	0	TGCCCTGTGT	    0.996558	-33
GGAGAAGTTGTTCTCTGTCTGTTTATTTAG	2	36	0	TTCTCTGTCT	    0.876251	-229
          **********

Masking position 10
Map Score:   7.21067

Number of sites scoring better than the average of aligned sites = 1119
Number in coding regions = 1037
Number in noncoding regions = 82
Number of orfs with sites within 600 bp upstream = 91
Fraction of orfs with sites within 600 bp upstream = 0.0146161


Motif number 2

AACTAATCAAAACGGGGATCACCCATTGCT	1	69	1	AACGGGGATC	    0.975987	-232
TTTTGACCCCGACAGTTAACAGAATCAGTG	1	106	0	GACAGTTAAC	    0.938917	-195
CGGGGTCAAAAACAGGGAATCTGGGCACAG	1	125	1	AACAGGGAAT	    0.969774	-176
ATCAGCAATACACAGGGCACGCTGAGGTGA	1	269	1	CACAGGGCAC	    0.978013	-32
TAAATAAACAGACAGAGAACAACTTCTCCC	2	37	1	GACAGAGAAC	    0.982563	-228
ATTACATCAGAACAGTGATCTAATAAAATA	2	86	1	AACAGTGATC	    0.980132	-179
          **********

Masking position 2
Map Score:   3.16692

Number of sites scoring better than the average of aligned sites = 347
Number in coding regions = 302
Number in noncoding regions = 45
Number of orfs with sites within 600 bp upstream = 50
Fraction of orfs with sites within 600 bp upstream = 0.00803084


Motif number 3

   GGTCATCAGGCGATCGCCAAAATATTTCT	1	8	1	AGGGATCCCA	     0.55516	-293
ATAGAGCAATGGGTGATCCCCGTTTTGATTAG	1	71	0	GGGGATCCCG	    0.672026	-230
GGTCAAAAACAGGGAATCTGGGCACAGGATTA	1	128	1	AGGAATCGGG	      0.9555	-173
GGTTGAGGTGAGGAAAACCCCACAGACGCAGT	1	164	1	AGGAAACCCA	    0.977893	-137
AGCGGTGGAATGGCGAACTGCGTCTGTGGGGT	1	180	0	TGGGAACGCG	    0.970725	-121
GGCTGTACCCAGGGCAACAGCACAATAAAAGC	1	226	1	AGGCAACGCA	    0.980252	-75
          *** **** ***

Masking position 6
Map Score:   2.27411

Number of sites scoring better than the average of aligned sites = 2752
Number in coding regions = 2507
Number in noncoding regions = 245
Number of orfs with sites within 600 bp upstream = 271
Fraction of orfs with sites within 600 bp upstream = 0.0435271


Motif number 4

TATTTCTGATAATTTCACTAAGTTTGACTGA	1	33	1	AATTCACTAA	    0.950057	-268
GTTTGACTGAAATTTAACTAATCAAAACGGG	1	54	1	AATTAACTAA	    0.965833	-247
 TATTCAATAAATATCTATAACCATTCTAAA	2	10	1	AATTCTATAA	    0.854426	-255
ATCTATAACCATTCTAAATAAACAGACAGAG	2	23	1	ATTTAAATAA	    0.912005	-242
GTGATCTAATAAAATAAATAATGCCTGACTC	2	100	1	AAATAAATAA	    0.897144	-165
ATAATGCCTGACTCTAAAAAAGCTTCTAAAA	2	117	1	ACTTAAAAAA	    0.869841	-148
AGCTTCTAAAAATTTAAAAAAAGTCTGCTAT	2	137	1	AATTAAAAAA	    0.948106	-128
          *** *******

Masking position 10
Map Score:   2.33486

Number of sites scoring better than the average of aligned sites = 138
Number in coding regions = 86
Number in noncoding regions = 52
Number of orfs with sites within 600 bp upstream = 60
Fraction of orfs with sites within 600 bp upstream = 0.00963701


Motif number 5

GTCAAACTTAGTGAAATTATCAGAAATATTT	1	30	0	GTGAATTATC	    0.900354	-271
ATATGTTTCCGTGAAATAAACGGGAGAAGTT	2	57	0	GTGAATAAAC	    0.951191	-208
GATCACTGTTCTGATGTAATATGTTTCCGTG	2	75	0	CTGATTAATA	    0.957977	-190
CATCAGAACAGTGATCTAATAAAATAAATAA	2	90	1	GTGATTAATA	    0.977586	-175
TAAAAAAAGTCTGCTATAAAAAGTGCTTTAA	2	151	1	CTGCTTAAAA	    0.910147	-114
GCTATAAAAAGTGCTTTAATCTCCCAATTCC	2	163	1	GTGCTTAATC	    0.982716	-102
          ***** *****

Masking position 7
Map Score:   1.80584

Number of sites scoring better than the average of aligned sites = 102
Number in coding regions = 78
Number in noncoding regions = 24
Number of orfs with sites within 600 bp upstream = 24
Fraction of orfs with sites within 600 bp upstream = 0.0038548


Motif number 6

          **********

No masking
Map Score:   -1.17707e-12

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:   -1.17707e-12

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:   -1.17707e-12

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