AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i068_Proline_Biosynthesis_tpal_reg_100.orf -o068_tpal_100.ace -a/home/amcguire/alignace/lib/ORF_tpal.txt -z/skink1/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	RTP00890	213	AE000520

Motif number 1

CGACACACGAGCGCAGAGGGCAGAAAACTC	1	37	0	GCGCAGAGGG	    0.988222	-177
ACTGCGCAGCACGCAGTCCACCGGTAACAG	1	68	0	ACGCAGTCCA	    0.988049	-146
ACTGCGTGCTGCGCAGTCGATGCTTTCCAA	1	81	1	GCGCAGTCGA	    0.998623	-133
TGTGCCGCTGGCACCGCCCGCTTCAAGATA	1	138	0	GCACCGCCCG	    0.991956	-76
GGTGCCAGCGGCACAGCCGAAACCTTTTGA	1	153	1	GCACAGCCGA	    0.998312	-61
GAGGCTTCAAGCGCAGCCAAAAACTCAAAA	1	177	0	GCGCAGCCAA	    0.997738	-37
          **********

Masking position 6
Map Score:   12.7639

Number of sites scoring better than the average of aligned sites = 296
Number in coding regions = 275
Number in noncoding regions = 21
Number of orfs with sites within 600 bp upstream = 17
Fraction of orfs with sites within 600 bp upstream = 0.00273049


Motif number 2

TCCCGTAGGATCTCACGCGCTTCTTCTG  	1	9	0	TCTCACGCGC	    0.991487	-205
GTAACAGGCGACACACGAGCGCAGAGGGCA	1	45	0	ACACACGAGC	    0.955168	-169
GCCTTTTCTTCCCCAAACGCTTTGGAAAGC	1	102	0	CCCCAAACGC	    0.988537	-112
CCGATCTTATCTTGAAGCGGGCGGTGCCAG	1	131	1	CTTGAAGCGG	    0.958223	-83
GCAGCCAAAAACTCAAAAGGTTTCGGCTGT	1	165	0	ACTCAAAAGG	    0.936507	-49
AGTTGGGAGGCTTCAAGCGCAGCCAAAAAC	1	183	0	CTTCAAGCGC	     0.99476	-31
          **********

Masking position 5
Map Score:   4.1303

Number of sites scoring better than the average of aligned sites = 1256
Number in coding regions = 1170
Number in noncoding regions = 86
Number of orfs with sites within 600 bp upstream = 64
Fraction of orfs with sites within 600 bp upstream = 0.0102795


Motif number 3

ACGAGCGCAGAGGGCAGAAAACTCCCGTAG	1	31	0	AGGGCAGAAA	    0.995404	-183
CAAAGCGTTTGGGGAAGAAAAGGCCGATCT	1	108	1	GGGGAAGAAA	    0.997497	-106
       GGAGGGGGAGAAGTTGGGAGGCT	1	201	0	GGGGGAGAAG	     0.99799	-13
          **********

Masking position 6
Map Score:   3.30808

Number of sites scoring better than the average of aligned sites = 44
Number in coding regions = 41
Number in noncoding regions = 3
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 4

        CAGAAGAAGCGCGTGAGATCCT	1	3	1	GAAGAAGCGC	    0.977074	-211
GCAGAGGGCAGAAAACTCCCGTAGGATCTC	1	25	0	GAAAACTCCC	    0.987745	-189
GTTTGGGGAAGAAAAGGCCGATCTTATCTT	1	114	1	GAAAAGGCCG	    0.992045	-100
ATCTTATCTTGAAGCGGGCGGTGCCAGCGG	1	134	1	GAAGCGGGCG	    0.988525	-80
GGCTGCGCTTGAAGCCTCCCAACTTCTCCC	1	189	1	GAAGCCTCCC	     0.99492	-25
          **********

Masking position 3
Map Score:   4.19034

Number of sites scoring better than the average of aligned sites = 225
Number in coding regions = 208
Number in noncoding regions = 17
Number of orfs with sites within 600 bp upstream = 12
Fraction of orfs with sites within 600 bp upstream = 0.0019274


Motif number 5

GCGCGTGAGATCCTACGGGAGTTTTCTGCC	1	19	1	TCCTACGGGA	    0.882793	-195
CAGCACGCAGTCCACCGGTAACAGGCGACA	1	62	0	TCCACCGGTA	    0.986821	-152
AGCGGGCGGTGCCAGCGGCACAGCCGAAAC	1	146	1	GCCAGCGGCA	    0.983236	-68
          **********

Masking position 10
Map Score:   0.294646

Number of sites scoring better than the average of aligned sites = 35
Number in coding regions = 31
Number in noncoding regions = 4
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 6

          **********

No masking
Map Score:   -1.68098e-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:   -1.68098e-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 8

          **********

No masking
Map Score:   -1.68098e-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