AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i300_mixed15_mtub_reg_100.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	dxs	143	dxs
#2	idsA	22	idsA

Motif number 1

GACAATGAGTCGCCGACCAGGCTTCCCGGC	1	31	1	CGCCGACCAG	    0.999093	-113
GTGGCCGGCGCGCCGGGAAGCCTGGTCGGC	1	42	0	CGCCGGGAAG	    0.992751	-102
CTTCCCGGCGCGCCGGCCACCGACGCTATC	1	52	1	CGCCGGCCAC	    0.997987	-92
CGATCAAAAGGGCCGAACCACTTTGATAGC	1	76	0	GGCCGAACCA	     0.98037	-68
AGCATGCGGCCGCCGATCAAAAGGGCCGAA	1	89	0	CGCCGATCAA	    0.996188	-55
CCCCCCCATTGGCCCAGCATGCGGCCGCCG	1	104	0	GGCCCAGCAT	    0.979765	-40
          **********

Masking position 4
Map Score:   10.3388

Number of sites scoring better than the average of aligned sites = 8370
Number in coding regions = 7902
Number in noncoding regions = 468
Number of orfs with sites within 600 bp upstream = 416
Fraction of orfs with sites within 600 bp upstream = 0.0668166


Motif number 2

         ATCGAACTCCGGAGTTGGATGA	1	2	1	TCGAACCCGG	    0.985734	-142
AGCCTGGTCGGCGACTCATTGTCATCCAACT	1	23	0	GCGACTATTG	    0.920188	-121
CCGGCGCGCCGGGAAGCCTGGTCGGCGACTC	1	37	0	GGGAAGCTGG	    0.985423	-107
TTTGATAGCGTCGGTGGCCGGCGCGCCGGGA	1	54	0	TCGGTGCCGG	     0.77082	-90
CTTTTGATCGGCGGCCGCATGCTGGGCCAAT	1	96	1	GCGGCCCATG	    0.977884	-48
GGCCGCATGCTGGGCCAATGGGGGGGTTGCT	1	108	1	TGGGCCATGG	    0.944011	-36
GGGGGTTGCTGCGTACACTAGCGAA      	1	129	1	GCGTACCTAG	    0.974052	-15
        GAGCGAATGCTAGATTCACGCA 	2	3	1	GCGAATCTAG	    0.976604	-20
          ****** ****

Masking position 3
Map Score:   5.73942

Number of sites scoring better than the average of aligned sites = 16744
Number in coding regions = 15513
Number in noncoding regions = 1231
Number of orfs with sites within 600 bp upstream = 803
Fraction of orfs with sites within 600 bp upstream = 0.128975


Motif number 3

CACCGACGCTATCAAAGTGGTTCGGCCCTT	1	69	1	ATCAAAGTGG	    0.993053	-75
GCGGCCGCCGATCAAAAGGGCCGAACCACT	1	84	0	ATCAAAAGGG	    0.992991	-60
CGCATGCTGGGCCAATGGGGGGGTTGCTGC	1	111	1	GCCAATGGGG	    0.981926	-33
          **********

Masking position 5
Map Score:   1.32967

Number of sites scoring better than the average of aligned sites = 57
Number in coding regions = 49
Number in noncoding regions = 8
Number of orfs with sites within 600 bp upstream = 9
Fraction of orfs with sites within 600 bp upstream = 0.00144555


Motif number 4

          **********

No masking
Map Score:   -2.03625e-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:   -2.03625e-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:   -2.03625e-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