AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i068_Proline_Biosynthesis_tpal_reg_300.orf -o068_tpal_300.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

GAGTTTTCTGCCCTCTGCGCTCGTGTGTCG	1	37	1	CCCTCTGCGC	    0.987691	-177
CTGTTACCGGTGGACTGCGTGCTGCGCAGT	1	68	1	TGGACTGCGT	     0.98751	-146
TTGGAAAGCATCGACTGCGCAGCACGCAGT	1	81	0	TCGACTGCGC	    0.998568	-133
TATCTTGAAGCGGGCGGTGCCAGCGGCACA	1	138	1	CGGGCGGTGC	    0.991591	-76
TCAAAAGGTTTCGGCTGTGCCGCTGGCACC	1	153	0	TCGGCTGTGC	    0.998236	-61
TTTTGAGTTTTTGGCTGCGCTTGAAGCCTC	1	177	1	TTGGCTGCGC	    0.997635	-37
          **********

Masking position 5
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	    0.991753	-205
GTAACAGGCGACACACGAGCGCAGAGGGCA	1	45	0	ACACACGAGC	    0.956548	-169
GCCTTTTCTTCCCCAAACGCTTTGGAAAGC	1	102	0	CCCCAAACGC	    0.988905	-112
CCGATCTTATCTTGAAGCGGGCGGTGCCAG	1	131	1	CTTGAAGCGG	    0.959526	-83
GCAGCCAAAAACTCAAAAGGTTTCGGCTGT	1	165	0	ACTCAAAAGG	    0.938379	-49
AGTTGGGAGGCTTCAAGCGCAGCCAAAAAC	1	183	0	CTTCAAGCGC	    0.994927	-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

CTACGGGAGTTTTCTGCCCTCTGCGCTCGT	1	31	1	TTTCTGCCCT	    0.994479	-183
AGATCGGCCTTTTCTTCCCCAAACGCTTTG	1	108	0	TTTCTTCCCC	    0.996992	-106
AGCCTCCCAACTTCTCCCCCTCC       	1	201	1	CTTCTCCCCC	    0.997584	-13
          **********

Masking position 5
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	    0.977043	-211
GCAGAGGGCAGAAAACTCCCGTAGGATCTC	1	25	0	GAAAACTCCC	    0.987728	-189
GTTTGGGGAAGAAAAGGCCGATCTTATCTT	1	114	1	GAAAAGGCCG	    0.992034	-100
ATCTTATCTTGAAGCGGGCGGTGCCAGCGG	1	134	1	GAAGCGGGCG	    0.988509	-80
GGCTGCGCTTGAAGCCTCCCAACTTCTCCC	1	189	1	GAAGCCTCCC	    0.994912	-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

GGCAGAAAACTCCCGTAGGATCTCACGCGC	1	19	0	TCCCGTAGGA	    0.883174	-195
TGTCGCCTGTTACCGGTGGACTGCGTGCTG	1	62	1	TACCGGTGGA	    0.986836	-152
GTTTCGGCTGTGCCGCTGGCACCGCCCGCT	1	146	0	TGCCGCTGGC	    0.983278	-68
          **********

Masking position 1
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