AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i266_hypothetical11_tpal_reg_100.orf -o266_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

Purged sequences:
RTP00977	17	AE000520

Input sequences:
#1	RTP00660	78	AE000520
#2	RTP00663	29	AE000520
#3	RTP00665	147	AE000520

Motif number 1

         GGCAGAACGGTGTCCTTCCCCTTG	1	2	1	GCAGACGGTC	    0.998662	-77
GGATCACGGTGCAGTGCGGCGTCTGTTCCCCAC	1	50	0	GCAGGCGGTC	    0.996349	-29
      TTTGGCAGATCGGGATCCACATGGGAA	2	13	0	GCAGTCGGTC	    0.997855	-17
TGCTTTATCCGCATCACGGGTAGGGTCTCCAAG	3	16	1	GCATACGGAG	    0.973774	-132
AGCAGGGGCCGCGACACGTAGTGCTCATTAGCC	3	51	0	GCGAACGTTG	    0.983893	-97
TTCCTACTCTGCGGTACATCATCGAGCAGGGGC	3	75	0	GCGGACATTC	    0.982019	-73
CGTCACTGCAGCAGTTCCTACTCTGCGGTACAT	3	89	0	GCAGTCCTTC	     0.97511	-59
GCAGTGACGCGCGTGTCGTCTTGCACCATACCA	3	113	1	GCGTTCGTTG	    0.989713	-35
    ACCGATGCGTGATGGTATGGTGCAAGACG	3	129	0	GCGTATGGTG	    0.967456	-19
          **** ****  **

Masking position 2
Map Score:   16.58

Number of sites scoring better than the average of aligned sites = 397
Number in coding regions = 361
Number in noncoding regions = 36
Number of orfs with sites within 600 bp upstream = 33
Fraction of orfs with sites within 600 bp upstream = 0.00530035


Motif number 2

CAAGGGGAAGGACACCGTTCTGCC      	1	5	0	GACACCGTTC	    0.978428	-74
GCGGCGTCTGTTCCCCACTCAATCGGTGCG	1	38	0	TTCCCCACTC	    0.960655	-41
GTGGGGAACAGACGCCGCACTGCACCGTGA	1	50	1	GACGCCGCAC	    0.980858	-29
ACTGCACCGTGATCCTGTTCC         	1	68	1	GATCCTGTTC	    0.981106	-11
TTCCCATGTGGATCCCGATCTGCCAAA   	2	13	1	GATCCCGATC	    0.917962	-17
CCATCTTGGAGACCCTACCCGTGATGCGGA	3	23	0	GACCCTACCC	    0.989845	-125
ACGTGTCGCGGCCCCTGCTCGATGATGTAC	3	65	1	GCCCCTGCTC	    0.996549	-83
CACTGCAGCAGTTCCTACTCTGCGGTACAT	3	89	0	GTTCCTACTC	    0.981731	-59
          **********

Masking position 5
Map Score:   12.9121

Number of sites scoring better than the average of aligned sites = 460
Number in coding regions = 413
Number in noncoding regions = 47
Number of orfs with sites within 600 bp upstream = 34
Fraction of orfs with sites within 600 bp upstream = 0.00546097


Motif number 3

ATCGGTGCGATCCAAGGGGAAGGACACCGT	1	17	0	TCCAAGGGGA	    0.876293	-62
GACGCCGCACTGCACCGTGATCCTGTTCC 	1	60	1	TGCACCGTGA	    0.961103	-19
       CATTCCCATGTGGATCCCGATCT	2	4	1	TCCCATGTGG	    0.890411	-26
GGGTAGGGTCTCCAAGATGGCTAATGAGCA	3	33	1	TCCAAGATGG	    0.989915	-115
TCGCGGCCCCTGCTCGATGATGTACCGCAG	3	70	1	TGCTCGATGA	    0.959448	-78
GATGGTATGGTGCAAGACGACACGCGCGTC	3	118	0	TGCAAGACGA	    0.975195	-30
     ACCGATGCGTGATGGTATGGTGCAA	3	133	0	TGCGTGATGG	    0.946865	-15
          **********

Masking position 1
Map Score:   4.0657

Number of sites scoring better than the average of aligned sites = 473
Number in coding regions = 434
Number in noncoding regions = 39
Number of orfs with sites within 600 bp upstream = 35
Fraction of orfs with sites within 600 bp upstream = 0.00562159


Motif number 4

          **********

No masking
Map Score:   -2.17836e-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 5

          **********

No masking
Map Score:   -2.17836e-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:   -2.17836e-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