AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i202_exonuclease_sbcc_synecho_reg_100.orf -o202_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	RCY44546	80	Synechocystis
#2	RCY49953	300	Synechocystis

Motif number 1

ACTAGAGGTCTTCCCTTTTTTTGTTGGAGA	1	52	1	TTCCCTTTTT	    0.922516	-29
GCAATGGGTGATCCCCGTTTTGATTAGTTA	2	68	0	ATCCCCGTTT	    0.927194	-233
GATCACCCATTGCTCTATGTCCACTGATTC	2	85	1	TGCTCTATGT	    0.946872	-216
TGTGCCCAGATTCCCTGTTTTTGACCCCGA	2	124	0	TTCCCTGTTT	    0.987173	-177
CCCTGGGTACAGCCGTGGGTGTAGGTTTAG	2	210	0	AGCCGTGGGT	    0.965522	-91
ATTGTGCTGTTGCCCTGGGTACAGCCGTGG	2	222	0	TGCCCTGGGT	    0.996496	-79
GCACAATAAAAGCGCTATGTTAGAATCAGC	2	245	1	AGCGCTATGT	    0.942746	-56
CACCTCAGCGTGCCCTGTGTATTGCTGATT	2	268	0	TGCCCTGTGT	    0.998018	-33
          **********

Masking position 10
Map Score:   11.1334

Number of sites scoring better than the average of aligned sites = 1203
Number in coding regions = 1117
Number in noncoding regions = 86
Number of orfs with sites within 600 bp upstream = 96
Fraction of orfs with sites within 600 bp upstream = 0.0154192


Motif number 2

TCCCCCAGCGGGCCATTACCATAGGATGAA	1	16	1	GGCCATTACC	    0.949323	-65
CAACAAAAAAAGGGAAGACCTCTAGTCCTC	1	48	0	AGGGAAGACC	    0.924314	-33
  GGTCATCAGGCGATCGCCAAAATATTTC	2	9	1	GGCGATCGCC	    0.499936	-292
TAATCAAAACGGGGATCACCCATTGCTCTA	2	72	1	GGGGATCACC	      0.7188	-229
CTGCGTCTGTGGGGTTTTCCTCACCTCAAC	2	165	0	GGGGTTTTCC	    0.889268	-136
GCGGTGGAATGGCGAACTGCGTCTGTGGGG	2	181	0	GGCGAACTGC	    0.950699	-120
GCTGTTGCCCTGGGTACAGCCGTGGGTGTA	2	217	0	TGGGTACAGC	    0.857808	-84
GCTGTACCCAGGGCAACAGCACAATAAAAG	2	227	1	GGGCAACAGC	    0.986115	-74
   AATCTAAATCCATCACCTCAGCGTGCC	2	284	0	ATCCATCACC	    0.766218	-17
          **********

Masking position 10
Map Score:   9.22373

Number of sites scoring better than the average of aligned sites = 8655
Number in coding regions = 7908
Number in noncoding regions = 747
Number of orfs with sites within 600 bp upstream = 495
Fraction of orfs with sites within 600 bp upstream = 0.0795053


Motif number 3

TCCTATGGTAATGGCCCGCTGGGGGACCTAA	1	11	0	ATGGCCGCTG	    0.997891	-70
TATTTTGGCGATCGCCTGATGACC       	2	4	0	ATCGCTGATG	    0.955581	-297
GGGATCACCCATTGCTCTATGTCCACTGATT	2	83	1	ATTGCCTATG	    0.971114	-218
TAGCGGTGGAATGGCGAACTGCGTCTGTGGG	2	182	0	ATGGCAACTG	    0.958025	-119
CAGCACAATAAAAGCGCTATGTTAGAATCAG	2	243	1	AAAGCCTATG	    0.910859	-58
AGCAATACACAGGGCACGCTGAGGTGATGGA	2	272	1	AGGGCCGCTG	    0.995331	-29
          ***** *****

Masking position 10
Map Score:   3.40685

Number of sites scoring better than the average of aligned sites = 271
Number in coding regions = 256
Number in noncoding regions = 15
Number of orfs with sites within 600 bp upstream = 15
Fraction of orfs with sites within 600 bp upstream = 0.00240925


Motif number 4

AAGACCTCTAGTCCTCCCTTCATCCTATGG	1	34	0	GTCCTCCCTT	    0.953583	-47
AGGACTAGAGGTCTTCCCTTTTTTTGTTGG	1	49	1	GTCTTCCCTT	    0.978543	-32
AAATATTTTGGCGATCGCCTGATGACC   	2	8	0	GCGATCGCCT	    0.921769	-293
AGAGCAATGGGTGATCCCCGTTTTGATTAG	2	71	0	GTGATCCCCG	    0.990987	-230
CGCCATAATCCTGTGCCCAGATTCCCTGTT	2	135	0	CTGTGCCCAG	    0.907759	-166
TTTTATTGTGCTGTTGCCCTGGGTACAGCC	2	226	0	CTGTTGCCCT	    0.932367	-75
CATCACCTCAGCGTGCCCTGTGTATTGCTG	2	271	0	GCGTGCCCTG	    0.983334	-30
          **********

Masking position 8
Map Score:   2.43102

Number of sites scoring better than the average of aligned sites = 1310
Number in coding regions = 1211
Number in noncoding regions = 99
Number of orfs with sites within 600 bp upstream = 109
Fraction of orfs with sites within 600 bp upstream = 0.0175072


Motif number 5

          **********

No masking
Map Score:   -6.79689e-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:   -6.79689e-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:   -6.79689e-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