AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i252_chemotaxis1_tpal_reg_300.orf -o252_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	RTP00514	57	AE000520
#2	RTP00513	70	AE000520
#3	RTP00512	75	AE000520

Motif number 1

GCAACATCATCCAGCGTTCTTGGGGTATGCA	1	16	1	CCAGGTTCTT	    0.962172	-42
AGCTCGGACAGCGGAGGCCTTCTTGTC    	2	7	0	GCGGGGCCTT	    0.996872	-64
     CCATTGCGGTGGCCATCGCGTGGTTC	3	6	1	GCGGGGCCAT	    0.998691	-70
GGTGGCCATCGCGTGGTTCATTTGGAACAAG	3	18	1	GCGTGTTCAT	    0.989867	-58
  TCCCTCCAACGGCGTACATATTTTTTCCT	3	57	0	ACGGGTACAT	    0.981414	-19
          **** ******

Masking position 11
Map Score:   6.0461

Number of sites scoring better than the average of aligned sites = 103
Number in coding regions = 93
Number in noncoding regions = 10
Number of orfs with sites within 600 bp upstream = 13
Fraction of orfs with sites within 600 bp upstream = 0.00208802


Motif number 2

    CCTTCGCAACATCATCCAGCGTTCTTG	1	7	1	CAACATCATC	    0.903849	-51
GGTATGCATACTAAGCAATACGTCTCGTT  	1	39	1	CTAAGCAATC	    0.966095	-19
ACAAGAAGGCCTCCGCTGTCCGAGCTCTACC	2	12	1	CTCCGCTGTC	    0.992723	-59
GCTGTCCGAGCTCTACCGTGCTTCAGATGAG	2	26	1	CTCTACCGTC	    0.967261	-45
CTTTTCTTTTCTCAGTAGTTCG         	2	59	1	CTCAGTAGTC	    0.976314	-12
ACGCGATGGCCACCGCAATGG          	3	1	0	CACCGCAATG	    0.962392	-75
    TCCCTCCAACGGCGTACATATTTTTTC	3	59	0	CAACGGCGTC	    0.623668	-17
          ********* *

Masking position 9
Map Score:   3.54374

Number of sites scoring better than the average of aligned sites = 1065
Number in coding regions = 985
Number in noncoding regions = 80
Number of orfs with sites within 600 bp upstream = 62
Fraction of orfs with sites within 600 bp upstream = 0.00995824


Motif number 3

AGCTCGGACAGCGGAGGCCTTCTTGTC   	2	8	0	GCGGAGGCCT	    0.999188	-63
CCGTGCTTCAGATGAGCCCTTTTCTTTTCT	2	41	1	GATGAGCCCT	    0.989158	-30
     CCATTGCGGTGGCCATCGCGTGGTT	3	6	1	GCGGTGGCCA	    0.997507	-70
          **********

Masking position 6
Map Score:   2.83049

Number of sites scoring better than the average of aligned sites = 28
Number in coding regions = 22
Number in noncoding regions = 6
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 4

GGGGTATGCATACTAAGCAATACGTCTCGT	1	37	1	TACTAAGCAA	    0.990984	-21
     CGAACTACTGAGAAAAGAAAAGGGC	2	56	0	TACTGAGAAA	    0.990984	-15
AACAAGACGATTCTAGGAAAAAATATGTAC	3	43	1	TTCTAGGAAA	    0.984161	-33
          **********

Masking position 9
Map Score:   1.16946

Number of sites scoring better than the average of aligned sites = 6
Number in coding regions = 6
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

ACTAAGCAATACGTCTCGTT          	1	48	1	ACGTCTCGTT	    0.993451	-10
GCGGTGGCCATCGCGTGGTTCATTTGGAAC	3	16	1	TCGCGTGGTT	    0.991879	-60
TTTCCTAGAATCGTCTTGTTCCAAATGAAC	3	33	0	TCGTCTTGTT	     0.99449	-43
          **********

Masking position 6
Map Score:   0.951405

Number of sites scoring better than the average of aligned sites = 15
Number in coding regions = 13
Number in noncoding regions = 2
Number of orfs with sites within 600 bp upstream = 1
Fraction of orfs with sites within 600 bp upstream = 0.000160617


Motif number 6

          **********

No masking
Map Score:   2.227e-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:   2.227e-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:   2.227e-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