AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i232_formulase_mgen_reg_300.orf -o232_mgen_300.ace -a/home/amcguire/alignace/lib/ORF_mgen.txt -z/skink1/amcguire/genomes/mgen.fna -g0.32 -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 =  	0.32
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RMG01880	63	Mycoplasma
#2	RMG02914	110	Mycoplasma

Motif number 1

          TTAGGTTATTAATTAGTTTTAGAG	1	1	1	TTAGTTTTAT	    0.989083	-63
TTAGAGTATATTATTATCTTGATTATATTGTAAC	1	29	1	TTATATTTAT	    0.982794	-35
AACAACTTTTTTACGATAATGATTTTGAAATTTG	2	11	1	TTAGATATAT	    0.995216	-100
TATTTTATTGTTACGATGATTAATTTTGTCTGGC	2	60	0	TTAGATATAT	    0.995216	-51
AAATAGTACCTTCTGATGTTAAGTCTTTTTGT  	2	89	1	TTCGATTTAT	    0.992608	-22
          *** *** ** * *

Masking position 7
Map Score:   6.23394

Number of sites scoring better than the average of aligned sites = 28
Number in coding regions = 27
Number in noncoding regions = 1
Number of orfs with sites within 600 bp upstream = 1
Fraction of orfs with sites within 600 bp upstream = 0.000160617


Motif number 2

   TTAGGTTATTAATTAGTTTTAGAGTAT	1	8	1	ATTAATTAGT	    0.919707	-56
AATCAAGATAATAATATACTCTAAAACTAA	1	23	0	ATAATATACT	    0.739221	-41
TATTATCTTGATTATATTGTAACTAGAACC	1	40	1	ATTATATTGT	    0.899172	-24
CATTATCGTAAAAAAGTTGTT         	2	2	0	AAAAAGTTGT	    0.884915	-109
ATAATGATTTTGAAATTTGTGCTGTTGTAA	2	26	1	TGAAATTTGT	     0.87718	-85
GTTACGATGATTAATTTTGTCTGGCTGAGT	2	55	0	TTAATTTTGT	    0.945783	-56
CATCGTAACAATAAAATAGTACCTTCTGAT	2	76	1	ATAAAATAGT	    0.946503	-35
          **********

Masking position 4
Map Score:   4.98746

Number of sites scoring better than the average of aligned sites = 315
Number in coding regions = 274
Number in noncoding regions = 41
Number of orfs with sites within 600 bp upstream = 24
Fraction of orfs with sites within 600 bp upstream = 0.0038548


Motif number 3

ATATGGTTCTAGTTACAATATAATCAAGAT	1	44	0	AGTTACAATA	    0.988254	-20
TGTCTGGCTGAGTTACAACAGCACAAATTT	2	38	0	AGTTACAACA	    0.988415	-73
AATTAATCATCGTAACAATAAAATAGTACC	2	69	1	CGTAACAATA	    0.992517	-42
 ACAAAAAGACTTAACATCAGAAGGTACTA	2	92	0	CTTAACATCA	    0.953459	-19
          **********

Masking position 5
Map Score:   4.26926

Number of sites scoring better than the average of aligned sites = 23
Number in coding regions = 19
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 4

          **********

No masking
Map Score:   4.35863e-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:   4.35863e-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:   4.35863e-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