AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i107_TRK_operon_mtub_reg_300.orf -a/home/amcguire/alignace/lib/ORF_mtub.txt -z/skink1/amcguire/genomes/mtub.fna -g0.66 -x5 
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 =  	0.66
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	trkA	134	trkA

Motif number 1

CTCGGATAGGCCTACCCTTGGCTCTC    	1	7	0	CCTACCCTTG	    0.955704	-128
CAAGGGTAGGCCTATCCGAGCGTGGCGGTA	1	17	1	CCTATCCGAG	    0.996995	-118
GGTAGCGTTCCCTAGACGAGAATGTTCGCC	1	43	1	CCTAGACGAG	     0.99512	-92
ACCCGCGGTGGCCAGCCGATTTACGTCGGC	1	70	0	GCCAGCCGAT	     0.99196	-65
TACGCGATCGGCAACCCGCGGTGGCCAGCC	1	83	0	GCAACCCGCG	    0.992739	-52
TGTCCGGTGCGCCGTACGCGATCGGCAACC	1	97	0	GCCGTACGCG	    0.964161	-38
GCGCACCGGACACAGCCGAGAGGACCTCTA	1	115	1	CACAGCCGAG	    0.914485	-20
          **********

Masking position 7
Map Score:   11.2449

Number of sites scoring better than the average of aligned sites = 8086
Number in coding regions = 7470
Number in noncoding regions = 616
Number of orfs with sites within 600 bp upstream = 502
Fraction of orfs with sites within 600 bp upstream = 0.0806296


Motif number 2

TATCCGAGCGTGGCGGTAGCGTTCCCTAGA	1	29	1	TGGCGGTAGC	    0.992957	-106
TAGACGAGAATGTTCGCCGACGTAAATCGG	1	55	1	TGTTCGCCGA	    0.967468	-80
GTAAATCGGCTGGCCACCGCGGGTTGCCGA	1	76	1	TGGCCACCGC	    0.998195	-59
CACCGCGGGTTGCCGATCGCGTACGGCGCA	1	90	1	TGCCGATCGC	     0.99267	-45
CTCTCGGCTGTGTCCGGTGCGCCGTACGCG	1	107	0	TGTCCGGTGC	    0.990917	-28
          **********

Masking position 1
Map Score:   4.68093

Number of sites scoring better than the average of aligned sites = 11075
Number in coding regions = 10446
Number in noncoding regions = 629
Number of orfs with sites within 600 bp upstream = 470
Fraction of orfs with sites within 600 bp upstream = 0.0754899


Motif number 3

AGACGAGAATGTTCGCCGACGTAAATCGGC	1	56	1	GTTCGCCGAC	     0.97195	-79
GGCCACCGCGGGTTGCCGATCGCGTACGGC	1	87	1	GGTTGCCGAT	    0.992762	-48
GCTGTGTCCGGTGCGCCGTACGCGATCGGC	1	101	0	GTGCGCCGTA	     0.99523	-34
          **********

Masking position 5
Map Score:   1.67287

Number of sites scoring better than the average of aligned sites = 1395
Number in coding regions = 1325
Number in noncoding regions = 70
Number of orfs with sites within 600 bp upstream = 64
Fraction of orfs with sites within 600 bp upstream = 0.0102795


Motif number 4

          **********

No masking
Map Score:   1.09013e-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:   1.09013e-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:   1.09013e-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