AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i061_tpal_bbur_100.orf -o061_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	RTP00963	233	AE000520

Motif number 1

     GTGTATGTACCTTGCACAACTGTTT	1	6	1	TGTACCTTGC	    0.939898	-228
CATTTCTGCGTGCGGCAGGCTTTTCTATCA	1	37	1	TGCGGCAGGC	    0.980234	-197
GGTACAGGCGTGTACCGCGTGATAGAAAAG	1	56	0	TGTACCGCGT	    0.968544	-178
GGTACACGCCTGTACCAGGCGTGTCACTAG	1	70	1	TGTACCAGGC	    0.992925	-164
AGTTCCAACGTGAAGCCCACTAGTGACACG	1	89	0	TGAAGCCCAC	    0.964821	-145
AGCGACGCGATGAAGCACGCCAATGGCAGC	1	119	0	TGAAGCACGC	    0.996257	-115
ATGGTAAAAATGAGCGACGCGATGAAGCAC	1	131	0	TGAGCGACGC	    0.985966	-103
TAGCAAGGACTGAGCCGCACATGCTCAAAA	1	196	1	TGAGCCGCAC	    0.987729	-38
          **********

Masking position 1
Map Score:   11.4246

Number of sites scoring better than the average of aligned sites = 533
Number in coding regions = 157
Number in noncoding regions = 376
Number of orfs with sites within 600 bp upstream = 15
Fraction of orfs with sites within 600 bp upstream = 0.00240925


Motif number 2

ATTTCTGCGTGCGGCAGGCTTTTCTATCACG	1	38	1	GCGGCAGGCT	    0.955332	-196
GTACAGGCGTGTACCGCGTGATAGAAAAGCC	1	54	0	GTACCGCGTA	    0.961981	-180
GTACACGCCTGTACCAGGCGTGTCACTAGTG	1	71	1	GTACCAGGCT	    0.967174	-163
GTTCCAACGTGAAGCCCACTAGTGACACGCC	1	87	0	GAAGCCCACA	    0.962816	-147
GCGACGCGATGAAGCACGCCAATGGCAGCAG	1	117	0	GAAGCACGCA	    0.992734	-117
TGGTAAAAATGAGCGACGCGATGAAGCACGC	1	129	0	GAGCGACGCA	    0.977201	-105
TTGCTAGGCAGTGTCCCGTTACCTAGATGCT	1	171	0	GTGTCCCGTA	    0.885811	-63
AGCAAGGACTGAGCCGCACATGCTCAAAAAA	1	197	1	GAGCCGCACT	    0.968479	-37
          ********* *

Masking position 1
Map Score:   3.89468

Number of sites scoring better than the average of aligned sites = 1172
Number in coding regions = 338
Number in noncoding regions = 834
Number of orfs with sites within 600 bp upstream = 23
Fraction of orfs with sites within 600 bp upstream = 0.00369419


Motif number 3

TGTATGTACCTTGCACAACTGTTTGCATTTC	1	12	1	TTGCACACTG	    0.994197	-222
GCACAACTGTTTGCATTTCTGCGTGCGGCAG	1	24	1	TTGCATTCTG	    0.963625	-210
GTGACACGCCTGGTACAGGCGTGTACCGCGT	1	66	0	TGGTACAGCG	    0.961224	-168
GTACCAGGCGTGTCACTAGTGGGCTTCACGT	1	81	1	TGTCACTGTG	    0.976571	-153
GGCTTCACGTTGGAACTGCTGCCATTGGCGT	1	102	1	TGGAACTCTG	    0.991386	-132
AGCCTCTTTTTTGAGCATGTGCGGCTCAGTC	1	203	0	TTGAGCAGTG	    0.965287	-31
          ******* ***

Masking position 1
Map Score:   3.62738

Number of sites scoring better than the average of aligned sites = 647
Number in coding regions = 207
Number in noncoding regions = 440
Number of orfs with sites within 600 bp upstream = 21
Fraction of orfs with sites within 600 bp upstream = 0.00337295


Motif number 4

TATGTACCTTGCACAACTGTTTGCATTTCT	1	14	1	GCACAACTGT	    0.857201	-220
ACAACTGTTTGCATTTCTGCGTGCGGCAGG	1	26	1	GCATTTCTGC	    0.735981	-208
CTTCACGTTGGAACTGCTGCCATTGGCGTG	1	104	1	GAACTGCTGC	    0.985365	-130
AATGAGCGACGCGATGAAGCACGCCAATGG	1	123	0	GCGATGAAGC	    0.911974	-111
CCATCAAACGGCACAGCATCTAGGTAACGG	1	157	1	GCACAGCATC	    0.962878	-77
CCTCTTTTTTGAGCATGTGCGGCTCAGTCC	1	202	0	GAGCATGTGC	    0.795045	-32
AAAAGAGGCTGAGAAGCAGC          	1	224	1	GAGAAGCAGC	    0.976892	-10
          **********

Masking position 1
Map Score:   2.64642

Number of sites scoring better than the average of aligned sites = 1714
Number in coding regions = 520
Number in noncoding regions = 1194
Number of orfs with sites within 600 bp upstream = 42
Fraction of orfs with sites within 600 bp upstream = 0.0067459


Motif number 5

TTTCTGCGTGCGGCAGGCTTTTCTATCACG	1	39	1	CGGCAGGCTT	    0.990322	-195
TACACGCCTGTACCAGGCGTGTCACTAGTG	1	72	1	TACCAGGCGT	     0.97748	-162
GGCGTGTCACTAGTGGGCTTCACGTTGGAA	1	87	1	TAGTGGGCTT	    0.986889	-147
CTGCTGCCATTGGCGTGCTTCATCGCGTCG	1	117	1	TGGCGTGCTT	    0.984427	-117
          **********

Masking position 10
Map Score:   1.49812

Number of sites scoring better than the average of aligned sites = 495
Number in coding regions = 146
Number in noncoding regions = 349
Number of orfs with sites within 600 bp upstream = 11
Fraction of orfs with sites within 600 bp upstream = 0.00176678


Motif number 6

          **********

No masking
Map Score:   -3.30951e-14

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:   -3.30951e-14

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 8

          **********

No masking
Map Score:   -3.30951e-14

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