AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i301_mixed16_mgen_reg_100.orf -o301_mgen_100.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	RMG00037	202	Mycoplasma
#2	RMG04456	38	Mycoplasma
#3	RMG03425	36	Mycoplasma
#4	RMG04443	58	Mycoplasma

Motif number 1

TAAAAAGCATTAATTTTTAATTAATAAATG	1	44	0	TAATTTTTAA	    0.978242	-159
TAAAAATTAATGCTTTTTAAAGTTGAATCT	1	55	1	TGCTTTTTAA	    0.944611	-148
CATTTTTCAATACTTTTTTAGGCTTCCTAT	1	90	1	TACTTTTTTA	    0.985471	-113
TCTTAACTTTTACTTTTAGAAAAGCGTATT	1	134	0	TACTTTTAGA	    0.982534	-69
TTAAGAAAAGTACTTTTATTCAAACAAAAA	1	158	1	TACTTTTATT	    0.960198	-45
AACGTTTTTATAATTTTAGAGATAGTT   	1	186	1	TAATTTTAGA	    0.962212	-17
   GATAATATACTTATTTATCTAATATTC	2	8	1	TACTTATTTA	    0.938083	-31
ATTAAAAGTCTAATTTTTATTGTTAATT  	3	9	0	TAATTTTTAT	    0.941132	-28
ATAAAAATTAGACTTTTAATTATTAGCT  	3	19	1	GACTTTTAAT	    0.924475	-18
TTCGATTATTTAATTTTATAAGACTTTTAA	4	14	1	TAATTTTATA	    0.968462	-45
AATTTTATAAGACTTTTAAAATGTTTAATT	4	25	1	GACTTTTAAA	    0.971775	-34
TTAAAATGTTTAATTATTAATATATAGCT 	4	40	1	TAATTATTAA	    0.909598	-19
          **********

Masking position 5
Map Score:   22.7851

Number of sites scoring better than the average of aligned sites = 311
Number in coding regions = 262
Number in noncoding regions = 49
Number of orfs with sites within 600 bp upstream = 40
Fraction of orfs with sites within 600 bp upstream = 0.00642467


Motif number 2

AAAAACTCATTTTGAAAATAGATTAATTT     	1	6	0	TTGAAAAGTT	    0.946174	-197
TTAATAAATGTTGAAAAAACTCATTTTGAAAATA	1	20	0	TTAAAAATAT	    0.939555	-183
AGCATTAATTTTTAATTAATAAATGTTGAAAAAA	1	35	0	TTAATTAAAT	     0.89494	-168
AATTAATGCTTTTTAAAGTTGAATCTTAATTCAT	1	59	1	TTTAAAGGAT	    0.873939	-144
TAAAAAAGTATTGAAAAATGAATTAAGATTCAAC	1	76	0	TTAAAAAATT	    0.911594	-127
AGCGTATTAATTTAATTAAAGAATAGGAAGCCTA	1	108	0	TTAATTAGAT	    0.958933	-95
ACTTTTACTTTTAGAAAAGCGTATTAATTTAATT	1	125	0	TTGAAAAGAT	    0.980175	-78
ACGTTTTTGTTTGAATAAAAGTACTTTTCTTAAC	1	157	0	TTAATAAGAC	    0.888343	-46
ATCTCTAAAATTATAAAAACGTTTTTGTTTGAAT	1	175	0	TTTAAAAGTT	    0.886386	-28
  GGATTATGTTGGAATATTAGATAAATAAGTAT	2	17	0	TTGAATAAAT	    0.893583	-22
AAATTAGACTTTTAATTATTAGCT          	3	23	1	TTAATTAACT	    0.641462	-14
TCTTATAAAATTAAATAATCGAATTA        	4	3	0	TTAATAAGAT	    0.980561	-56
AATTAAACATTTTAAAAGTCTTATAAAATTAAAT	4	21	0	TTAAAAGTAT	    0.830823	-38
          ** *****  * **

Masking position 5
Map Score:   13.8576

Number of sites scoring better than the average of aligned sites = 675
Number in coding regions = 619
Number in noncoding regions = 56
Number of orfs with sites within 600 bp upstream = 36
Fraction of orfs with sites within 600 bp upstream = 0.0057822


Motif number 3

      AAATTAATCTATTTTCAAAATGAG	1	5	1	TAATCTATTT	     0.80225	-198
AATGTTGAAAAAACTCATTTTGAAAATAGA	1	18	0	AAACTCATTT	    0.592463	-185
AATTAAAAATTAATGCTTTTTAAAGTTGAA	1	52	1	TAATGCTTTT	    0.853446	-151
AGTTGAATCTTAATTCATTTTTCAATACTT	1	75	1	TAATTCATTT	    0.959108	-128
ATTCATTTTTCAATACTTTTTTAGGCTTCC	1	87	1	CAATACTTTT	    0.844417	-116
TTAATTAAATTAATACGCTTTTCTAAAAGT	1	123	1	TAATACGCTT	    0.969511	-80
TTATTCAAACAAAAACGTTTTTATAATTTT	1	173	1	AAAAACGTTT	    0.749759	-30
        GATAATATACTTATTTATCTAA	2	3	1	TAATATACTT	     0.84831	-36
          TAATTCGATTATTTAATTTT	4	1	1	TAATTCGATT	    0.880145	-58
ATAAGACTTTTAAAATGTTTAATTATTAAT	4	31	1	TAAAATGTTT	     0.84122	-28
          **********

Masking position 3
Map Score:   5.07792

Number of sites scoring better than the average of aligned sites = 406
Number in coding regions = 368
Number in noncoding regions = 38
Number of orfs with sites within 600 bp upstream = 25
Fraction of orfs with sites within 600 bp upstream = 0.00401542


Motif number 4

          **********

No masking
Map Score:   2.51122e-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:   2.51122e-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:   2.51122e-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