AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i216_Ribosomal_Operon_3_mthe_reg_300.orf -o216_mthe_300.ace -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -g0.50 -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 =  	0.5
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RTH00518	35	M.thermo
#2	RTH01836	222	M.thermo
#3	RTH00222	184	M.thermo

Motif number 1

AGGTTTCTTCTCACATGGAGTTCACGGTGA	2	63	1	TCACATGGAG	    0.996135	-160
AATGTTCATGTCACCGTGAACTCCATGTGA	2	73	0	TCACCGTGAA	    0.890377	-150
CATGAACATTTCACATGGAGTTCACAGCGA	2	93	1	TCACATGGAG	    0.996135	-130
CACATGGAGTTCACAGCGATATGAACACCA	2	104	1	TCACAGCGAT	    0.935875	-119
CTGAGGTTCATCATATGGTGTTCATATCGC	2	119	0	TCATATGGTG	    0.929863	-104
CACCGGCATATCACATTCTGAGGTTCATCA	2	136	0	TCACATTCTG	     0.94097	-87
TATATATCTTTCACCGGCATATCACATTCT	2	147	0	TCACCGGCAT	    0.969942	-76
CATATAAAGGTCACAGGGTGGTGGGCGGCA	3	85	0	TCACAGGGTG	    0.994288	-100
      GGTTTCACCTGCAGTGATGGATAA	3	171	0	TCACCTGCAG	    0.990956	-14
          **********

Masking position 3
Map Score:   17.5347

Number of sites scoring better than the average of aligned sites = 642
Number in coding regions = 601
Number in noncoding regions = 41
Number of orfs with sites within 600 bp upstream = 39
Fraction of orfs with sites within 600 bp upstream = 0.00626405


Motif number 2

CCATTACCGGTAATATGATCTGATAGGTTT	2	39	1	TAATATGATC	     0.86617	-184
TTTCTTCTCACATGGAGTTCACGGTGACAT	2	66	1	CATGGAGTTC	     0.98647	-157
GAACATTTCACATGGAGTTCACAGCGATAT	2	96	1	CATGGAGTTC	     0.98647	-127
AGGTTCATCATATGGTGTTCATATCGCTGT	2	116	0	TATGGTGTTC	    0.988122	-107
CATATCTAGATAATGAATTCAATTTTCAAC	3	22	0	TAATGAATTC	    0.839361	-163
TGAGGACCTATATTAAGATCCTCAATCATA	3	48	0	TATTAAGATC	    0.916581	-137
CTTAATTATATAAGGTGATCCCAACAATAG	3	134	1	TAAGGTGATC	    0.980026	-51
          **********

Masking position 2
Map Score:   7.13728

Number of sites scoring better than the average of aligned sites = 515
Number in coding regions = 484
Number in noncoding regions = 31
Number of orfs with sites within 600 bp upstream = 29
Fraction of orfs with sites within 600 bp upstream = 0.00465789


Motif number 3

TCTTCTCACATGGAGTTCACGGTGACATGA	2	68	1	TGGAGTTCAC	     0.99427	-155
ACATTTCACATGGAGTTCACAGCGATATGA	2	98	1	TGGAGTTCAC	     0.99427	-125
GTTCATCATATGGTGTTCATATCGCTGTGA	2	114	0	TGGTGTTCAT	    0.982851	-109
TATCACATTCTGAGGTTCATCATATGGTGT	2	128	0	TGAGGTTCAT	    0.984158	-95
TTGTTGAAAATTGAATTCATTATCTAGATA	3	20	1	TTGAATTCAT	    0.824078	-165
TAGATATGATTGAGGATCTTAATATAGGTC	3	44	1	TGAGGATCTT	    0.848729	-141
TTAACTATTGTTGGGATCACCTTATATAAT	3	138	0	TTGGGATCAC	    0.970261	-47
          **********

Masking position 7
Map Score:   9.14328

Number of sites scoring better than the average of aligned sites = 502
Number in coding regions = 458
Number in noncoding regions = 44
Number of orfs with sites within 600 bp upstream = 32
Fraction of orfs with sites within 600 bp upstream = 0.00513974


Motif number 4

CTCACCTGTTCCCATTACCGGTAATATGAT	2	28	1	CCCATTACCG	    0.980817	-195
AGTATATATATCTTTCACCGGCATATCACA	2	151	0	TCTTTCACCG	    0.935049	-72
GGATCTGCCGCCCACCACCCTGTGACCTTT	3	80	1	CCCACCACCC	    0.994968	-105
GCACAGCCCATCCACCACTCTTAATTATAT	3	115	1	TCCACCACTC	    0.987849	-70
TTAATGATTATCCATCACTGCAGGTGAAAC	3	164	1	TCCATCACTG	    0.990967	-21
          **********

Masking position 7
Map Score:   3.99702

Number of sites scoring better than the average of aligned sites = 389
Number in coding regions = 354
Number in noncoding regions = 35
Number of orfs with sites within 600 bp upstream = 34
Fraction of orfs with sites within 600 bp upstream = 0.00546097


Motif number 5

TTCTTTTTTTGATTTGAAGGGGCCTCCAGC	1	14	1	GATTTGAAGG	    0.955057	-22
CCGGTAATATGATCTGATAGGTTTCTTCTC	2	45	1	GATCTGATAG	    0.962587	-178
CTCAGAATGTGATATGCCGGTGAAAGATAT	2	144	1	GATATGCCGG	    0.991019	-79
TCATTATCTAGATATGATTGAGGATCTTAA	3	36	1	GATATGATTG	    0.943289	-149
GTCCTCAAAGGATCTGCCGCCCACCACCCT	3	71	1	GATCTGCCGC	    0.979789	-114
          **********

Masking position 5
Map Score:   1.69122

Number of sites scoring better than the average of aligned sites = 229
Number in coding regions = 214
Number in noncoding regions = 15
Number of orfs with sites within 600 bp upstream = 18
Fraction of orfs with sites within 600 bp upstream = 0.0028911


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


Motif number 7

          **********

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 8

          **********

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