AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i119_Spermidine_putrescine_Transport_mgen_reg_100.orf -o119_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	RMG01155	197	Mycoplasma
#2	RMG02204	52	Mycoplasma

Motif number 1

TTTTTACTATTAAAAAATAAACAGATTTAA	1	30	0	TAAAAAATAA	    0.984665	-168
TTTTTAATAGTAAAAACACAATTTAACCTT	1	44	1	TAAAAACACA	    0.890562	-154
CCAATTTTGTTAAATAGAAACAAGGTTAAA	1	65	0	TAAATAGAAA	    0.913284	-133
AATTTTGCTGTAAAAAATTAAGATATTTTT	1	111	1	TAAAAAATTA	     0.97714	-87
TAATTTTTGATAAAAAATATCTTAATTTTT	1	123	0	TAAAAAATAT	    0.910198	-75
ATATTTTTTATCAAAAATTAGCATAAAAAA	1	133	1	TCAAAAATTA	    0.943952	-65
AAAATTAGCATAAAAAATTGTTATACTAAT	1	146	1	TAAAAAATTG	    0.949691	-52
TACTTAATTTTCAATAAAAAACGTTAATTA	1	172	0	TCAATAAAAA	     0.89214	-26
        TTTAAATACTTAATTTTCAATA	1	186	0	TAAATACTTA	    0.798767	-12
AGATGCACATTAAGAaAAAATACTGACTTC	2	13	1	TAAGAaAAAA	    0.910623	-40
       TAATAAAAAGAAGGGGAGCAGAA	2	40	0	TAAAAAGAAG	    0.919172	-13
          **********

Masking position 6
Map Score:   14.4571

Number of sites scoring better than the average of aligned sites = 803
Number in coding regions = 673
Number in noncoding regions = 130
Number of orfs with sites within 600 bp upstream = 74
Fraction of orfs with sites within 600 bp upstream = 0.0118856


Motif number 2

       CTTAGCATATTTTAATCAATTAAATC	1	4	1	AGCATATTAT	    0.966532	-194
TTAAAAAATAAACAGATTTAATTGATTAAAATA	1	18	0	AACAGATTAT	    0.987101	-180
GTTAAATAGAAACAAGGTTAAATTGTGTTTTTA	1	54	0	AACAAGTTAT	    0.975142	-144
GTTTCTATTTAACAAAATTGGTTTGAAAAAGGC	1	74	1	AACAAATTGT	    0.614802	-124
AATTTTTTACAGCAAAATTGATAGCCTTTTTCA	1	97	0	AGCAAATTAA	    0.956054	-101
TAATTAGTATAACAATTTTTTATGCTAATTTTT	1	145	0	AACAATTTTT	    0.836219	-53
AATTTTCAATAAAAAACGTTAATTAGTATAACA	1	164	0	AAAAAAGTAT	    0.888301	-34
AAAGAAGGGGAGCAGAAGTCAGTATTTTtTCTT	2	24	0	AGCAGAGTAT	    0.979517	-29
          ****** ** * *

Masking position 4
Map Score:   5.5399

Number of sites scoring better than the average of aligned sites = 267
Number in coding regions = 242
Number in noncoding regions = 25
Number of orfs with sites within 600 bp upstream = 23
Fraction of orfs with sites within 600 bp upstream = 0.00369419


Motif number 3

ATTGATTAAAATATGCTAAG          	1	1	0	ATATGCTAAG	    0.963225	-197
TAAATTGTGTTTTTACTATTAAAAAATAAA	1	39	0	TTTTACTATT	    0.922767	-159
TAACAATTTTTTATGCTAATTTTTGATAAA	1	139	0	TTATGCTAAT	    0.990961	-59
TAAAAAATTGTTATACTAATTAACGTTTTT	1	156	1	TTATACTAAT	    0.987036	-42
          **********

Masking position 4
Map Score:   2.50894

Number of sites scoring better than the average of aligned sites = 25
Number in coding regions = 22
Number in noncoding regions = 3
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:   -3.95472e-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:   -3.95472e-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:   -3.95472e-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