AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i266_tpal_bbur_100.orf -o266_tpal_bbur_100.ace -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/synecho.fna -g0.40 -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 =  	0.4
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Purged sequences:
RTP00977	17	AE000520

Input sequences:
#1	RTP00660	78	AE000520
#2	RTP00663	29	AE000520
#3	RTP00665	147	AE000520

Motif number 1

CAAGGGGAAGGACACCGTTCTGCC         	1	2	0	GAACCGCTGC	    0.997394	-77
GTGGGGAACAGACGCCGCACTGCACCGTGATCC	1	50	1	GAGCCGCTGC	     0.99883	-29
TTCCCATGTGGATCCCGATCTGCCAAA      	2	13	1	GACCCGCTGC	     0.99884	-17
CTTGGAGACCCTACCCGTGATGCGGATAAAGCA	3	16	0	CTCCCGATGC	    0.958265	-132
GTACATCATCGAGCAGGGGCCGCGACACGTAGT	3	62	0	GACAGGCCGC	    0.994417	-86
GCCCCTGCTCGATGATGTACCGCAGAGTAGGAA	3	75	1	GAGATGCCGC	     0.98654	-73
ATGTACCGCAGAGTAGGAACTGCTGCAGTGACG	3	89	1	GATAGGCTGC	    0.975023	-59
TGGTATGGTGCAAGACGACACGCGCGTCACTGC	3	113	0	CAGACGACGC	    0.989631	-35
CGTCTTGCACCATACCATCACGCATCGGT    	3	129	1	CAACCAACGC	    0.890817	-19
          ** ****  ****

Masking position 13
Map Score:   16.8255

Number of sites scoring better than the average of aligned sites = 458
Number in coding regions = 122
Number in noncoding regions = 336
Number of orfs with sites within 600 bp upstream = 14
Fraction of orfs with sites within 600 bp upstream = 0.00224863


Motif number 2

CAAGGGGAAGGACACCGTTCTGCC      	1	5	0	GACACCGTTC	    0.976797	-74
GCGGCGTCTGTTCCCCACTCAATCGGTGCG	1	38	0	TTCCCCACTC	     0.95772	-41
GTGGGGAACAGACGCCGCACTGCACCGTGA	1	50	1	GACGCCGCAC	    0.979402	-29
ACTGCACCGTGATCCTGTTCC         	1	68	1	GATCCTGTTC	    0.980763	-11
TTCCCATGTGGATCCCGATCTGCCAAA   	2	13	1	GATCCCGATC	    0.921401	-17
CCATCTTGGAGACCCTACCCGTGATGCGGA	3	23	0	GACCCTACCC	    0.989063	-125
ACGTGTCGCGGCCCCTGCTCGATGATGTAC	3	65	1	GCCCCTGCTC	    0.996294	-83
CACTGCAGCAGTTCCTACTCTGCGGTACAT	3	89	0	GTTCCTACTC	    0.980344	-59
          **********

Masking position 5
Map Score:   12.9121

Number of sites scoring better than the average of aligned sites = 1015
Number in coding regions = 288
Number in noncoding regions = 727
Number of orfs with sites within 600 bp upstream = 19
Fraction of orfs with sites within 600 bp upstream = 0.00305172


Motif number 3

CAATCGGTGCGATCCAAGGGGAAGGACACCG	1	18	0	GTCCAAGGGG	    0.975487	-61
        CATTCCCATGTGGATCCCGATCT	2	3	1	TCCCATGTGG	     0.91145	-27
TTGGAGACCCTACCCGTGATGCGGATAAAGC	3	17	0	TCCCGTGATG	    0.983222	-131
ACGGGTAGGGTCTCCAAGATGGCTAATGAGC	3	31	1	TTCCAAGATG	    0.983862	-117
TCGAGCAGGGGCCGCGACACGTAGTGCTCAT	3	56	0	GCGCGACACG	    0.926725	-92
CGCGGCCCCTGCTCGATGATGTACCGCAGAG	3	71	1	GTCGATGATG	    0.962722	-77
GTGATGGTATGGTGCAAGACGACACGCGCGT	3	119	0	GTGCAAGACG	    0.987581	-29
       ACCGATGCGTGATGGTATGGTGCA	3	134	0	GTGCGTGATG	    0.989475	-14
          * *********

Masking position 11
Map Score:   6.65845

Number of sites scoring better than the average of aligned sites = 954
Number in coding regions = 302
Number in noncoding regions = 652
Number of orfs with sites within 600 bp upstream = 16
Fraction of orfs with sites within 600 bp upstream = 0.00256987


Motif number 4

          **********

No masking
Map Score:   -2.17836e-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:   -2.17836e-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:   -2.17836e-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