AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i196_tpal_bbur_300.orf -o196_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

Input sequences:
#1	RTP01136	83	AE000520
#2	RTP01045	27	AE000520
#3	RTP00239	45	AE000520
#4	RTP00117	32	AE000520
#5	RBB00440	35	3615
#6	RBB00437	22	3615
#7	RBB00433	30	3615
#8	RBB00432	92	3615
#9	RBB00792	20	3615
#10	RBB00430	43	3615
#11	RBB00429	50	3615
#12	RBB00233	74	3615

Motif number 1

TCAAACCTCATTCTAAAATCTT          	6	1	0	TTCTAAAATT	    0.885972	-22
   AGGGTGTTTTTTATAAATTTATAACTTGT	8	8	1	TTTTTATATT	    0.981083	-85
ATATTAAATATTTTAACAAGTTATAAATTTAT	8	23	0	TTTTAACATT	    0.960914	-70
TTGTTAAAATATTTAATATATTTTTTGCTAAA	8	36	1	ATTTAATATT	    0.952157	-57
TTTATCAGCTATCTAATATATTGATTTTAGCA	8	61	0	ATCTAATATT	    0.907062	-32
TTAAATCTGTTTATAACAATTTGATTAATTTG	10	11	0	TTATAACATT	    0.885969	-33
          ATTTTATACCTTTAAATCTGTT	10	32	0	ATTTTATATT	    0.959589	-12
TTAATACACTTTATTATACTTTTTCATTATAA	11	19	0	TTATTATATT	      0.9497	-32
ACTCTCACTTTTTTTAATTCTTAAATTATATT	12	16	1	TTTTTAATTT	    0.705886	-59
TCTTAAATTATATTTATATATTATAATACAAT	12	34	1	TATTTATATT	    0.891501	-41
AAATTCCCTATGTTTATATATTGTATTATAAT	12	53	0	TGTTTATATT	    0.925674	-22
          ********  **

Masking position 6
Map Score:   10.4478

Number of sites scoring better than the average of aligned sites = 329
Number in coding regions = 99
Number in noncoding regions = 230
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 2

CTTTCTGGACACCCCATTAAACTTTTGTTTG	1	35	0	ACCCCATTAA	     0.74928	-49
     AACCTAACTCAATTTACACTACTAGA	5	20	0	AACTCAATTA	    0.959866	-16
      TCAAACCTCATTCTAAAATCTT   	6	8	0	ACCTCATTTA	    0.918379	-15
CTTTCTCCCCACCTTAATTTAT         	7	2	0	ACCTTAATTA	    0.830864	-29
ATAACTTGTTAAAATATTTAATATATTTTTT	8	31	1	AAAATATTAA	    0.764639	-62
TTTTTTGCTAAAATCAATATATTAGATAGCT	8	56	1	AAATCAATTA	    0.924088	-37
  TGTTTAAAAAAACATTGAAC         	9	2	0	AAAACATTAA	    0.898401	-19
         CAAATTAATCAAATTGTTATAA	10	2	1	AAATTAATAA	    0.764639	-42
AATTGTTATAAACAGATTTAAAGGTATAAAA	10	22	1	AACAGATTAA	    0.741962	-22
CAATCCCTTTAATACACTTTATTATACTTTT	11	28	0	AATACACTTA	     0.77367	-23
ATAATATATAAATATAATTTAAGAATTAAAA	12	27	0	AATATAATTA	    0.803144	-48
TATATATTATAATACAATATATAAACATAGG	12	48	1	AATACAATTA	    0.917417	-27
          ******** **

Masking position 6
Map Score:   6.36358

Number of sites scoring better than the average of aligned sites = 716
Number in coding regions = 222
Number in noncoding regions = 494
Number of orfs with sites within 600 bp upstream = 13
Fraction of orfs with sites within 600 bp upstream = 0.00208802


Motif number 3

    CATGAGGGGTGCCTTTTTTAACGGCA	1	7	1	GGGTGCCTTT	    0.989131	-77
AAGTTTAATGGGGTGTCCAGAAAGTTCGAG	1	42	1	GGGTGTCCAG	     0.97982	-42
GTATCTGGCTGAGTGTCTCG          	2	18	1	GAGTGTCTCG	    0.982559	-10
ATACAGACACGGCTGCCTCGGGG       	4	20	1	GGCTGCCTCG	    0.989022	-13
         AGGGTGTTTTTTATAAATTTA	8	2	1	GGGTGTTTTT	    0.941743	-91
          **********

Masking position 4
Map Score:   2.60623

Number of sites scoring better than the average of aligned sites = 203
Number in coding regions = 58
Number in noncoding regions = 145
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 4

GGACACCCCATTAAACTTTTGTTTGCCGTT	1	30	0	TTAAACTTTT	    0.964403	-54
CGCAAGTTCCTCGAACTTTCTGGACACCCC	1	51	0	TCGAACTTTC	    0.929622	-33
GAACTTGCGCTCAAGCTTTTCT        	1	72	1	TCAAGCTTTT	     0.97284	-12
AGCTGATAAATCACCCTTTT          	8	83	1	TCACCCTTTT	    0.974998	-10
ATACACTTTATTATACTTTTTCATTATAAT	11	18	0	TTATACTTTT	    0.914707	-33
   AAAATACTCTCACTTTTTTTAATTCTT	12	8	1	TCTCACTTTT	    0.963386	-67
          **********

Masking position 7
Map Score:   3.14773

Number of sites scoring better than the average of aligned sites = 201
Number in coding regions = 56
Number in noncoding regions = 145
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 5

          **********

No masking
Map Score:   -4.16788e-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:   -4.16788e-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:   -4.16788e-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