AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i255_tpal_bbur_100.orf -o255_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

Input sequences:
#1	RTP00279	205	AE000520
#2	RTP00278	115	AE000520
#3	RBB00234	23	3615
#4	RBB00232	158	3615
#5	RBB00107	107	3615

Motif number 1

AAAGGGCGTATTCCGCGCATGGATTCTGTAG	1	28	0	TTCCGCGCTG	    0.985077	-178
ATGTAGACGTTACCGCTTTTGGTTACCAGAA	1	57	0	TACCGCTTTG	    0.975241	-149
TGCTCTCGATGAGCGCTTGTGTGTTTTTGAT	1	119	0	GAGCGCTTTG	    0.990258	-87
AGCGCTCATCGAGAGCACCTGCAATTCCTGT	1	133	1	GAGAGCACTG	    0.957445	-73
TCGGAGTTTGGTGCGCGTGTGCTTATCAATA	1	163	0	GTGCGCGTTG	    0.996687	-43
ATGATTTCCGGACAGCGTGTGCTTATTGTGG	2	36	0	GACAGCGTTG	    0.986351	-80
AAAGATACCGTTGCGCGTGTGGTGCCGTATT	2	90	0	TTGCGCGTTG	    0.994755	-26
TTGATTCATTTTGAGCATTTGTAAGATGTAT	4	60	0	TTGAGCATTG	    0.961612	-99
          ******** **

Masking position 10
Map Score:   13.6817

Number of sites scoring better than the average of aligned sites = 33
Number in coding regions = 10
Number in noncoding regions = 23
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0


Motif number 2

ACAGAATCCATGCGCGGAATACGCCCTTTC	1	30	1	TGCGCGGAAT	    0.908918	-176
ACGTCTACATCATGCTGCACTGCATCGACA	1	78	1	CATGCTGCAC	    0.933479	-128
TTGATAAGCACACGCGCACCAAACTCCGAA	1	165	1	CACGCGCACC	    0.995133	-41
      GCTTTGCACTCAACTACTCATTTC	1	192	0	TGCACTCAAC	    0.863882	-14
        AGTGCGCGCAACGAGTTACCAT	2	3	1	TGCGCGCAAC	    0.993008	-113
AACGAGTTACCATGCGCCACAATAAGCACA	2	20	1	CATGCGCCAC	    0.983135	-96
ACAATAAGCACACGCTGTCCGGAAATCATC	2	38	1	CACGCTGTCC	    0.927205	-78
TACGGCACCACACGCGCAACGGTATCTTTC	2	92	1	CACGCGCAAC	    0.997358	-24
          **********

Masking position 5
Map Score:   8.13841

Number of sites scoring better than the average of aligned sites = 115
Number in coding regions = 30
Number in noncoding regions = 85
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 3

CGCGCAACGGTATCTTTCAAAC         	2	104	1	TATTTTCAAA	    0.979807	-12
   ATAACAATATGTATCAATATAACACTAT	4	8	1	TATTATCAAT	    0.859125	-151
GAAAAATATACATCTTACAAATGCTCAAAAT	4	53	1	CATTTACAAA	    0.898026	-106
TCTTTCTTGAAATTTAATAAAATTGATTCAT	4	82	0	AATTAATAAA	    0.644517	-77
TTAAAAAAAATATTTTACAAATTTTTTTCTT	4	109	0	TATTTACAAA	    0.968009	-50
TAAAGCATTTTATCTTTAAAAAAAATATTTT	4	124	0	TATTTTAAAA	    0.942534	-35
ATTAAACCTAAATTTTTAAAAGACCAATT  	5	9	0	AATTTTAAAA	     0.83826	-99
ATACTTTATATATGTTATAATTAAACCTAAA	5	28	0	TATTTATAAT	    0.902089	-80
ATTTTTTAAATATATTTTAATATTTATACTT	5	53	0	TATTTTTAAT	    0.932656	-55
TTATTTATTGTATTTTTTAAATATATTTTAA	5	64	0	TATTTTTAAA	    0.968281	-44
          *** *******

Masking position 5
Map Score:   10.1677

Number of sites scoring better than the average of aligned sites = 242
Number in coding regions = 63
Number in noncoding regions = 179
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 4

ATATTGATACATATTGTTAT          	4	1	0	ATATTGTTAT	    0.967677	-158
GCTTTCAGTAATAGTGTTATATTGATACAT	4	19	0	ATAGTGTTAT	    0.916833	-140
TGTAAGATGTATATTTTTCTTAAGCTTTCA	4	42	0	ATATTTTTCT	     0.97525	-117
TATTTTACAAATTTTTTTCTTTCTTGAAAT	4	100	0	ATTTTTTTCT	    0.906786	-59
AATTTGTAAAATATTTTTTTTAAAGATAAA	4	117	1	ATATTTTTTT	    0.935288	-42
TTTTTTAAATATATTTTAATATTTATACTT	5	53	0	ATATTTTAAT	    0.900037	-55
          **********

Masking position 5
Map Score:   3.8766

Number of sites scoring better than the average of aligned sites = 138
Number in coding regions = 46
Number in noncoding regions = 92
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:   1.16772e-12

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:   1.16772e-12

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:   1.16772e-12

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