AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i196_mixed_replication_rec__bbur_reg_100.orf -o196_borburg_100.ace -a/home/amcguire/genomes/ORF_borburg.txt -z/home/amcguire/genomes/borburg.fna -g0.28 -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 =  	0.28
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RBB00440	35	3615
#2	RBB00437	22	3615
#3	RBB00433	30	3615
#4	RBB00432	92	3615
#5	RBB00792	20	3615
#6	RBB00430	43	3615
#7	RBB00429	50	3615
#8	RBB00233	74	3615

Motif number 1

TCAAACCTCATTCTAAAATCTT          	2	1	0	TTCTAAAATT	    0.927065	-22
   AGGGTGTTTTTTATAAATTTATAACTTGT	4	8	1	TTTTTATATT	    0.985835	-85
ATATTAAATATTTTAACAAGTTATAAATTTAT	4	23	0	TTTTAACATT	    0.975735	-70
TTGTTAAAATATTTAATATATTTTTTGCTAAA	4	36	1	ATTTAATATT	    0.969887	-57
TTTATCAGCTATCTAATATATTGATTTTAGCA	4	61	0	ATCTAATATT	     0.94076	-32
TTAAATCTGTTTATAACAATTTGATTAATTTG	6	11	0	TTATAACATT	    0.927061	-33
          ATTTTATACCTTTAAATCTGTT	6	32	0	ATTTTATATT	    0.974799	-12
TTAATACACTTTATTATACTTTTTCATTATAA	7	19	0	TTATTATATT	    0.968619	-32
ACTCTCACTTTTTTTAATTCTTAAATTATATT	8	16	1	TTTTTAATTT	     0.79701	-59
TCTTAAATTATATTTATATATTATAATACAAT	8	34	1	TATTTATATT	    0.928441	-41
AAATTCCCTATGTTTATATATTGTATTATAAT	8	53	0	TGTTTATATT	    0.953149	-22
          ********  **

Masking position 6
Map Score:   15.1401

Number of sites scoring better than the average of aligned sites = 1796
Number in coding regions = 1169
Number in noncoding regions = 627
Number of orfs with sites within 600 bp upstream = 141
Fraction of orfs with sites within 600 bp upstream = 0.022647


Motif number 2

     AACCTAACTCAATTTACACTACTAGA	1	20	0	AACTCAATTA	    0.981849	-16
      TCAAACCTCATTCTAAAATCTT   	2	8	0	ACCTCATTTA	    0.934127	-15
CTTTCTCCCCACCTTAATTTAT         	3	2	0	ACCTTAATTA	    0.898579	-29
ATAACTTGTTAAAATATTTAATATATTTTTT	4	31	1	AAAATATTAA	    0.874451	-62
TTTTTTGCTAAAATCAATATATTAGATAGCT	4	56	1	AAATCAATTA	    0.971513	-37
  TGTTTAAAAAAACATTGAAC         	5	2	0	AAAACATTAA	    0.942267	-19
         CAAATTAATCAAATTGTTATAA	6	2	1	AAATTAATAA	    0.895628	-42
AATTGTTATAAACAGATTTAAAGGTATAAAA	6	22	1	AACAGATTAA	    0.832686	-22
CAATCCCTTTAATACACTTTATTATACTTTT	7	28	0	AATACACTTA	    0.905446	-23
ATAATATATAAATATAATTTAAGAATTAAAA	8	27	0	AATATAATTA	    0.929652	-48
TATATATTATAATACAATATATAAACATAGG	8	48	1	AATACAATTA	    0.968857	-27
          ******** **

Masking position 6
Map Score:   10.9489

Number of sites scoring better than the average of aligned sites = 879
Number in coding regions = 543
Number in noncoding regions = 336
Number of orfs with sites within 600 bp upstream = 98
Fraction of orfs with sites within 600 bp upstream = 0.0157404


Motif number 3

AACCTAACTCAATTTACACTACTAGAAAAA	1	16	0	AATTTACACT	    0.918166	-20
AAATTTATAAAAAACACCCT          	4	1	0	AAAACACCCT	     0.99303	-92
GATAGCTGATAAATCACCCTTTT       	4	80	1	AAATCACCCT	    0.990047	-13
CAATCCCTTTAATACACTTTATTATACTTT	7	29	0	AATACACTTT	    0.924178	-22
          AAAATACTCTCACTTTTTTT	8	1	1	AAAATACTCT	    0.974624	-74
          **********

Masking position 6
Map Score:   4.36521

Number of sites scoring better than the average of aligned sites = 81
Number in coding regions = 51
Number in noncoding regions = 30
Number of orfs with sites within 600 bp upstream = 14
Fraction of orfs with sites within 600 bp upstream = 0.00224863


Motif number 4

          **********

No masking
Map Score:   2.227e-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:   2.227e-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:   2.227e-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