AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i313_mixed27_synecho_reg_100.orf -o313_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	RCY33113	109	Synechocystis
#2	RCY42122	216	Synechocystis

Motif number 1

CCCCATCGAACTAAATTTGATCACCCTTTCAA    	1	7	0	CAATTTCCCC	    0.997469	-103
AGGACGGGGACGCAGTCCTACCCCCCATCGAACTAA	1	29	0	CCATCCCCCC	    0.991993	-81
GATACTAAAGCCATTTTTAATCTAGCCAAATAAATA	1	69	1	CATTTTCAGC	    0.894316	-41
AATCTCAAATCACTGTCTACTCACCCTAGGATGAGG	2	14	1	CCTTCTCCCC	     0.99545	-203
TCACTGGGGACGATTTTCCCTCATCCTAGGGTGAGT	2	32	0	CATTTCCTCC	    0.966614	-185
TTAACATTAGCCAATTTTTGCCTCCCTCGATTAAGA	2	84	1	CAATTTCCCC	    0.997469	-133
AGATTAGGAACTATATTTTGGCCCCTGCCACTTTTT	2	117	1	CATTTTCCCT	     0.98903	-100
  AGTAAATCCTCATTTTCAAAGCCTGAAGCAGCCA	2	193	0	CCATTTACCT	     0.90799	-24
          * ** ***   * ***

Masking position 6
Map Score:   9.10167

Number of sites scoring better than the average of aligned sites = 733
Number in coding regions = 640
Number in noncoding regions = 93
Number of orfs with sites within 600 bp upstream = 108
Fraction of orfs with sites within 600 bp upstream = 0.0173466


Motif number 2

CTAAATTTGATCACCCTTTCAA          	1	1	0	TCCCCTTCAA	    0.941815	-109
ACGCAGTCCTACCCCCCATCGAACTAAATTTG	1	24	0	ACCCCCTCGA	    0.988431	-86
GGTAGGACTGCGTCCCCGTCCTGTAGGATACT	1	43	1	CGCCCCTCCT	    0.987455	-67
GAGGGAAAATCGTCCCCAGTGACCAAACGCTG	2	46	1	CGCCCCGTGA	    0.990211	-171
GACCAAACGCTGACCCCTTTAACATTAGCCAA	2	66	1	TGCCCCTTAA	    0.987755	-151
AGCCAATTTTTGCCTCCCTCGATTAAGATTAG	2	92	1	TGCTCCTCGA	     0.98856	-125
AACTATATTTTGGCCCCTGCCACTTTTTTATG	2	125	1	TGCCCCGCCA	    0.989238	-92
          ** **** ****

Masking position 6
Map Score:   7.62367

Number of sites scoring better than the average of aligned sites = 1187
Number in coding regions = 1092
Number in noncoding regions = 95
Number of orfs with sites within 600 bp upstream = 102
Fraction of orfs with sites within 600 bp upstream = 0.0163829


Motif number 3

TTTTAATCTAGCCAAATAAATATTCACACC	1	83	1	GCCAAATAAA	    0.980166	-27
AATCGAGGGAGGCAAAAATTGGCTAATGTT	2	86	0	GGCAAAAATT	    0.952632	-131
AGTGGCAGGGGCCAAAATATAGTTCCTAAT	2	119	0	GCCAAAATAT	    0.986075	-98
GACTCCCATTGCCATAAAAAAGTGGCAGGG	2	139	0	GCCATAAAAA	    0.980166	-78
GCCTGAAGCAGCCAAAAAATCTAGCTTCGA	2	177	0	GCCAAAAAAT	    0.995726	-40
          **********

Masking position 6
Map Score:   6.82003

Number of sites scoring better than the average of aligned sites = 314
Number in coding regions = 272
Number in noncoding regions = 42
Number of orfs with sites within 600 bp upstream = 49
Fraction of orfs with sites within 600 bp upstream = 0.00787022


Motif number 4

          **********

No masking
Map Score:   6.91659e-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 5

          **********

No masking
Map Score:   6.91659e-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:   6.91659e-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