AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i308_tpal_bbur_300.orf -o308_tpal_bbur_300.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:
RBB00532	26	3615

Input sequences:
#1	RBB00533	52	3615
#2	RBB00883	74	3615
#3	RBB00339	77	3615
#4	RBB00328	18	3615
#5	RBB00301	35	3615

Motif number 1

TGAATATATAAAATTAAATTTTTGCTATAA	1	11	1	AAATTAAATT	     0.93621	-42
          ATAATATATATTATATAATA	2	1	1	ATAATATATA	    0.977912	-74
AATATAATGTATATTATATAATATATATTA	2	12	0	ATATTATATA	    0.973015	-63
TATATAATATACATTATATTTGAATTTATA	2	22	1	ACATTATATT	    0.916663	-53
AAAGGACATCAAAATTTATAAATTCAAATA	2	38	0	AAAATTTATA	    0.918703	-37
AGAAAATCTAAAAATAAAAAAATATCAATA	3	33	0	AAAATAAAAA	    0.901126	-45
TTTTCTTAAAAAAAGAAATAGAGGTAGGTT	3	57	1	AAAAGAAATA	    0.966017	-21
   AGCAAGTAAAAGATATTT         	4	8	1	AAAAGATATT	    0.946966	-11
TAAACCAAACATATTAAATAAGT       	5	4	0	ATATTAAATA	    0.967031	-32
          **********

Masking position 3
Map Score:   12.2664

Number of sites scoring better than the average of aligned sites = 311
Number in coding regions = 100
Number in noncoding regions = 211
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 2

GATTATAGCAAAAATTTAATTTTATATATTCA  	1	9	0	AAATTTTTTA	    0.901867	-44
AATTTTTGCTATAATCTTATTTTAAGAGAGAAAA	1	27	1	ATATTTTTTA	     0.98096	-26
TAATATACATTATATTTGAATTTATAAATTTTGA	2	26	1	TAATTATTTA	    0.868789	-49
TTTATAAATTTTGATGTCCTTTTGTTAAGGTTGT	2	46	1	TTATTTTTTG	    0.977707	-29
TGTCCTTTTGTTAAGGTTGTTTTAA         	2	60	1	TTAGTTTTTA	    0.987406	-15
ATATCAATAATGTATCAAGTTTTACTAATTA   	3	8	0	TGATATTTTA	    0.889084	-70
TGATACATTATTGATATTTTTTTATTTTTAGATT	3	25	1	TTATTTTTTA	     0.99465	-53
TTTTTTTATTTTTAGATTTTCTTAAAAAAAGAAA	3	41	1	TTAGTTCTTA	    0.943922	-37
 AAACCTACCTCTATTTCTTTTTTTAAGAAAATC	3	55	0	TCATTTTTTT	    0.901029	-23
          TTAATCTCCTTATAAACCAAACAT	5	22	0	TTATTTTATA	    0.963173	-14
          ** ** *  *****

Masking position 4
Map Score:   12.2803

Number of sites scoring better than the average of aligned sites = 365
Number in coding regions = 100
Number in noncoding regions = 265
Number of orfs with sites within 600 bp upstream = 11
Fraction of orfs with sites within 600 bp upstream = 0.00176678


Motif number 3

AAATTTAATTTTATATATTCA         	1	2	0	TTATATATTC	     0.91929	-51
TTTTCTCTCTTAAAATAAGATTATAGCAAA	1	31	0	TAAAATAAGA	    0.914632	-22
ATAATGTATATTATATAATATATATTAT  	2	9	0	TTATATAATA	    0.938564	-66
ACATCAAAATTTATAAATTCAAATATAATG	2	33	0	TTATAAATTC	    0.916296	-42
AATCTAAAAATAAAAAAATATCAATAATGT	3	29	0	TAAAAAAATA	    0.924873	-49
TTTCTTTTTTTAAGAAAATCTAAAAATAAA	3	45	0	TAAGAAAATC	     0.91957	-33
ACCAAACATATTAAATAAGT          	5	1	0	TTAAATAAGT	    0.848453	-35
          **********

Masking position 5
Map Score:   3.19304

Number of sites scoring better than the average of aligned sites = 450
Number in coding regions = 139
Number in noncoding regions = 311
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 4

          **********

No masking
Map Score:   2.72438e-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:   2.72438e-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:   2.72438e-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