AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00910_tpal_reg_100.orf -o00910_tpal_100.ace -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -g0.53 -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 =  	0.53
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	TP0556	104	asparagine synthetase (asnA)
#2	TP0736	233	hydrogenase, gamma chain (hydG)

Motif number 1

          ACCACCTCCCTGCTGTCAGA	1	1	1	ACCACCTCCC	    0.990604	-104
ATTGCACTACACCGCCACCCTATTAAATAA	1	41	1	ACCGCCACCC	    0.995429	-64
      AGTTAACGCCAACCTTTTACCTTG	1	91	0	AACGCCAACC	     0.98243	-14
         GTAAACCTCCCCGACACGTAT	2	2	1	TAAACCTCCC	    0.961279	-232
ATTCAAGCAAAACGCCATCGGCGCCGAGAA	2	49	0	AACGCCATCG	    0.958988	-185
GACTGCACGCAAAACCTGCCAGGAAACAAT	2	82	1	AAAACCTGCC	    0.961973	-152
TTGTCAAAGAAAAGCCTTTCTTCAGCTCTG	2	154	0	AAAGCCTTTC	    0.908648	-80
CGCTGTACTATCATCCATCCCTCCGAGAGT	2	193	1	TCATCCATCC	    0.859642	-41
          **********

Masking position 5
Map Score:   8.8528

Number of sites scoring better than the average of aligned sites = 438
Number in coding regions = 387
Number in noncoding regions = 51
Number of orfs with sites within 600 bp upstream = 48
Fraction of orfs with sites within 600 bp upstream = 0.0077096


Motif number 2

AGTGCAATACTCAAGTAATCTGACAGCAGGGA	1	17	0	TCAAGAACTG	    0.988398	-88
CGCCACCCTATTAAATAATGCGTGCACAGTTT	1	53	1	TTAAAAAGCG	    0.776124	-52
TTTTACCTTGTTGAGTAAACTGTGCACGCATT	1	69	0	TTGAGAACTG	     0.98142	-36
CAGTCCTCATTCAAGCAAAACGCCATCGGCGC	2	55	0	TCAAGAAACG	    0.928154	-179
GTCGCACAAGGCAACTAACGCGCCGACCGCTG	2	123	0	GCAACAAGCG	    0.963247	-111
GTTGCCTTGTGCGACAGAGCTGAAGAAAGGCT	2	140	1	GCGACGACTG	    0.963894	-94
AGGCTTTTCTTTGACAAATCTGCATTCGCTGT	2	167	1	TTGACAACTG	    0.985792	-67
CATGCCTCCTTCGACCAAACTCTCGGAGGGAT	2	209	0	TCGACAACTC	     0.96708	-25
          ***** ** ***

Masking position 8
Map Score:   3.69204

Number of sites scoring better than the average of aligned sites = 174
Number in coding regions = 157
Number in noncoding regions = 17
Number of orfs with sites within 600 bp upstream = 16
Fraction of orfs with sites within 600 bp upstream = 0.00256987


Motif number 3

CAGATATACGTGTCGGGGAGGTTTAC    	2	7	0	TGTCGGGGAG	    0.993433	-227
ATCGGACCCTTCTCGGCGCCGATGGCGTTT	2	40	1	TCTCGGCGCC	    0.996481	-194
GAAAAGCAGCGGTCGGCGCGTTAGTTGCCT	2	117	1	GGTCGGCGCG	    0.997756	-117
TCGACCAAACTCTCGGAGGGATGGATGATA	2	201	0	TCTCGGAGGG	    0.993434	-33
          **********

Masking position 3
Map Score:   3.01604

Number of sites scoring better than the average of aligned sites = 50
Number in coding regions = 45
Number in noncoding regions = 5
Number of orfs with sites within 600 bp upstream = 8
Fraction of orfs with sites within 600 bp upstream = 0.00128493


Motif number 4

      ACCACCTCCCTGCTGTCAGATTAC	1	5	1	CCTCCCTGCT	    0.954515	-100
GTTTTGCGTGCAGTCCTCATTCAAGCAAAA	2	67	0	CAGTCCTCAT	    0.971106	-167
CCGACCGCTGCTTTTCTCATCATTGTTTCC	2	103	0	CTTTTCTCAT	    0.908459	-131
AAAGAAAAGCCTTTCTTCAGCTCTGTCGCA	2	149	0	CTTTCTTCAG	    0.891624	-85
TACTATCATCCATCCCTCCGAGAGTTTGGT	2	198	1	CATCCCTCCG	    0.992329	-36
       AGCCATGCCTCCTTCGACCAAAC	2	221	0	CATGCCTCCT	    0.988343	-13
          **********

Masking position 7
Map Score:   1.99642

Number of sites scoring better than the average of aligned sites = 333
Number in coding regions = 283
Number in noncoding regions = 50
Number of orfs with sites within 600 bp upstream = 45
Fraction of orfs with sites within 600 bp upstream = 0.00722775


Motif number 5

          **********

No masking
Map Score:   -4.09683e-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:   -4.09683e-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:   -4.09683e-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