AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i210_trans4_mthe_reg_300.orf -o210_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

Purged sequences:
RTH00858	16	M.thermo
RTH01019	18	M.thermo

Input sequences:
#1	RTH01790	170	M.thermo
#2	RTH00571	19	M.thermo
#3	RTH02039	22	M.thermo
#4	RTH00851	46	M.thermo
#5	RTH00189	109	M.thermo
#6	RTH01001	16	M.thermo
#7	RTH00961	18	M.thermo
#8	RTH01648	30	M.thermo

Motif number 1

      CCTCACCAGCGGAAAGTTTAAATAT	1	5	1	ACCAGCGGAA	    0.862657	-166
TCTGCGGTGGATCCGCTCACATTGTATGCTC	1	68	1	ATCCGCTCAA	    0.973241	-103
AAAACCACAGACCACATCGTATCAGAGCATA	1	92	0	ACCACATCGA	    0.697107	-79
CTGTGGTTTTACTTGCCCAGTCTGCATTGTG	1	113	1	ACTTGCCCAT	     0.68604	-58
  CTATTAATATCTGTCCGGATTTATTTATA	1	152	0	ATCTGTCCGA	    0.872131	-19
  TTAACTTTACCTCCTTACA          	2	1	0	ACCTCCTTAA	    0.961497	-19
ACTGATATGAATCTGTCCATATATA      	4	5	0	ATCTGTCCAA	    0.931095	-42
AATTTCAGGTATCCCCTTAAAAAGTTTTTTC	5	45	0	ATCCCCTTAA	    0.898322	-65
TGTATTCAGCATTTGCTGATAAACCCGAAAA	5	75	0	ATTTGCTGAA	    0.806835	-35
   TCAAGAAACCTCCTTGTATTCAGCATTT	5	92	0	ACCTCCTTGA	    0.926506	-18
         AACCAGCTGACAAGGA      	6	2	1	ACCAGCTGAA	    0.964147	-15
      TTTTATCTCTCCATAACC       	7	4	0	ATCTCTCCAA	    0.920845	-15
       TAAATCACCTCAGTAACTTTTAGT	8	17	0	ATCACCTCAT	    0.885243	-14
          ********* *

Masking position 1
Map Score:   8.80221

Number of sites scoring better than the average of aligned sites = 2401
Number in coding regions = 2179
Number in noncoding regions = 222
Number of orfs with sites within 600 bp upstream = 197
Fraction of orfs with sites within 600 bp upstream = 0.0316415


Motif number 2

TAGTACCTATTGCAATCTGCGGTGGATCCG	1	53	1	TGCAATCTGC	    0.901958	-118
TATCAGAGCATACAATGTGAGCGGATCCAC	1	74	0	TACAATGTGA	    0.917087	-97
TATGCTCTGATACGATGTGGTCTGTGGTTT	1	92	1	TACGATGTGG	    0.968925	-79
TTGCCCAGTCTGCATTGTGGAAATATTTAT	1	125	1	TGCATTGTGG	    0.960379	-46
          TGTAAGGAGGTAAAGTTAA 	2	1	1	TGTAAGGAGG	    0.968343	-19
      AAATAACCAGGAGGATATTCGG  	3	5	1	AACCAGGAGG	    0.910453	-18
AAATGCTGAATACAAGGAGGTTTCTTGA  	5	92	1	TACAAGGAGG	    0.988278	-18
      TCCTTGTCAGCTGGTT        	6	3	0	TGTCAGCTGG	     0.92115	-14
          **********

Masking position 9
Map Score:   5.43118

Number of sites scoring better than the average of aligned sites = 1274
Number in coding regions = 1216
Number in noncoding regions = 58
Number of orfs with sites within 600 bp upstream = 61
Fraction of orfs with sites within 600 bp upstream = 0.00979762


Motif number 3

TAAACTTTCCGCTGGTGAGG          	1	1	0	GCTGGTGAGG	    0.945361	-170
TCTGATACGATGTGGTCTGTGGTTTTACTT	1	97	1	TGTGGTCTGT	    0.905303	-74
ATTTCCACAATGCAGACTGGGCAAGTAAAA	1	119	0	TGCAGACTGG	    0.911057	-52
TATAAATAAATCCGGACAGATATTAATAG 	1	152	1	TCCGGACAGA	    0.972746	-19
      TATATATGGACAGATTCATATCAG	4	5	1	TATGGACAGA	    0.965307	-42
          GGAGGACTGGAAGGGGCATA	5	1	1	GGAGGACTGG	    0.970554	-109
AAGTTTTTTCGCTGGACTGGAAAATATGCC	5	25	0	GCTGGACTGG	    0.992471	-85
       GGTTATGGAGAGATAAAA     	7	4	1	TATGGAGAGA	    0.911959	-15
          **********

Masking position 5
Map Score:   5.89373

Number of sites scoring better than the average of aligned sites = 844
Number in coding regions = 788
Number in noncoding regions = 56
Number of orfs with sites within 600 bp upstream = 42
Fraction of orfs with sites within 600 bp upstream = 0.0067459


Motif number 4

ATCCATATTTAAACTTTCCGCTGGTGAGG   	1	8	0	AACTTTCGCT	    0.981156	-163
TAGGTACTAAAAATTGTATGGTATCCATATTT	1	30	0	AATTGTTGGT	    0.975544	-141
GGATCCGCTCACATTGTATGCTCTGATACGAT	1	76	1	AATTGTTGCT	    0.975541	-95
TGGAAGGGGCATATTTTCCAGTCCAGCGAAAA	5	18	1	AATTTTCAGT	    0.956576	-92
CCCCTTAAAAAGTTTTTTCGCTGGACTGGAAA	5	32	0	ATTTTTCGCT	    0.972321	-78
GGGATACCTGAAATTTTTCGGGTTTATCAGCA	5	61	1	AATTTTCGGG	    0.981156	-49
          * ***** ****

Masking position 7
Map Score:   2.54967

Number of sites scoring better than the average of aligned sites = 37
Number in coding regions = 29
Number in noncoding regions = 8
Number of orfs with sites within 600 bp upstream = 8
Fraction of orfs with sites within 600 bp upstream = 0.00128493


Motif number 5

          **********

No masking
Map Score:   8.26662e-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:   8.26662e-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:   8.26662e-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