AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i205_dna_mismatch_repair_ecoli_hinf_reg_300.orf -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.46 -x5 
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 =  	0.46
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	mutS	286	methyl-directed mismatch repair
#2	HI0701	108	conserved hypothetical protein
#3	HI0706	23	lipoprotein
#4	HI0707	132	DNA mismatch repair protein (mutS)

Motif number 1

CTGAAATGATTAACTCCGGTATCATGTGCG	1	197	1	TAACTCCGGT	    0.984108	-90
TCCCTGATATTAAATGGGGTGTGATGGTTT	1	252	0	TAAATGGGGT	    0.948264	-35
     GGGGTTATGTCCGGTTCCCTGATAT	1	272	0	TATGTCCGGT	    0.981749	-15
AACAAGAACAAAAGTGCGGTTATTTTAGTG	2	24	1	AAAGTGCGGT	    0.997606	-85
CTTCCTGTAAAAAGTGCGGTAAAAAATCTC	4	12	1	AAAGTGCGGT	    0.997606	-121
AAGCCAGATAAAAGTGCGGTAAAAATTTGT	4	43	0	AAAGTGCGGT	    0.997606	-90
          **********

Masking position 5
Map Score:   12.1554

Number of sites scoring better than the average of aligned sites = 55
Number in coding regions = 48
Number in noncoding regions = 7
Number of orfs with sites within 600 bp upstream = 6
Fraction of orfs with sites within 600 bp upstream = 0.000963701


Motif number 2

GTGCCCTTTAAGATTAAGATGTAATATAAAT	1	35	0	AGATAAGATG	    0.564995	-252
ATGCTGGTTCCGGGAAAGATGCTGTTTTGCA	1	140	0	CGGGAAGATG	    0.960424	-147
TTTCCCGGAACCAGCATCAAGAACTCGCCGT	1	154	1	CCAGATCAAG	    0.886715	-133
TAATCATTTCAGGGGAAGAAGCGAACGGCGA	1	178	0	AGGGAAGAAG	    0.953614	-109
ATGATTAACTCCGGTATCATGTGCGCCTTAT	1	202	1	CCGGATCATG	    0.884594	-85
  AATAAAATCCTTCAACAAGAACAAAAGTG	2	9	1	CCTTAACAAG	    0.868881	-100
CGGTTATTTTAGTGGATAAATCACGAAAAGT	2	40	1	AGTGATAAAT	    0.514945	-69
CAATTATTTTCGATAAAAAAGAGCCCTTAAC	2	87	1	CGATAAAAAG	    0.933359	-22
      TCTTCCTGTAAAAAGTGCGGTAAAA	4	5	1	CCTGAAAAAG	     0.96705	-128
GTAAAAAGTGCGGTAAAAAATCTCAACAAAT	4	18	1	CGGTAAAAAT	    0.856129	-115
GATAAAAGTGCGGTAAAAATTTGTTGAGATT	4	36	0	CGGTAAAATT	    0.713273	-97
GGGGAAAAAGCCAGATAAAAGTGCGGTAAAA	4	49	0	CCAGTAAAAG	    0.746302	-84
AGGTGCCGAAAGGGGAAAAAGCCAGATAAAA	4	60	0	AGGGAAAAAG	    0.970435	-73
CTGCTTTGAAACTGAATAAAGATAGGTTTTG	4	104	0	ACTGATAAAG	    0.815657	-29
          **** ******

Masking position 9
Map Score:   10.2835

Number of sites scoring better than the average of aligned sites = 4773
Number in coding regions = 4309
Number in noncoding regions = 464
Number of orfs with sites within 600 bp upstream = 449
Fraction of orfs with sites within 600 bp upstream = 0.0721169


Motif number 3

AACCGATACAATTTTGCGTACTTGCTTCAT	1	93	1	ATTTTGCGTA	    0.855758	-194
TGTTTTGCAGCTTTTGCGTGATGCTTATGA	1	119	0	CTTTTGCGTG	    0.870739	-168
AAAACAGCATCTTTCCCGGAACCAGCATCA	1	143	1	CTTTCCCGGA	    0.901733	-144
GGAGTTAATCATTTCAGGGGAAGAAGCGAA	1	184	0	ATTTCAGGGG	    0.966893	-103
GATGGTTTTTATTTTCGTTGTAATCACATA	1	230	0	ATTTTCGTTG	    0.930417	-57
ACCCCATTTAATATCAGGGAACCGGACATA	1	262	1	ATATCAGGGA	    0.720432	-25
AAGTGCGGTTATTTTAGTGGATAAATCACG	2	35	1	ATTTTAGTGG	    0.930765	-74
TTCTATGCGACTTTTCGTGATTTATCCACT	2	50	0	CTTTTCGTGA	    0.904947	-59
TCGCACAATTATTTTCGATAAAAAAGAGCC	2	82	1	ATTTTCGATA	    0.768437	-27
TGTGGCGGCTATTTTAGGTGCCGAAAGGGG	4	76	0	ATTTTAGGTG	    0.962577	-57
          **********

Masking position 4
Map Score:   5.05589

Number of sites scoring better than the average of aligned sites = 1354
Number in coding regions = 1166
Number in noncoding regions = 188
Number of orfs with sites within 600 bp upstream = 195
Fraction of orfs with sites within 600 bp upstream = 0.0313203


Motif number 4

CACCTCATTAAGATGTATTTATATTACATC	1	19	1	AGATGTATTT	    0.914638	-268
ACTCCAAAGAAGAAGGGTTAGCCAACCGAT	1	70	1	AGAAGGGTTA	    0.948905	-217
AAATGGGGTGTGATGGTTTTTATTTTCGTT	1	241	0	TGATGGTTTT	    0.957224	-46
TTGTTCTTGTTGAAGGATTTTATT      	2	5	0	TGAAGGATTT	     0.96496	-104
AACTGAATAAAGATAGGTTTTGTGGCGGCT	4	96	0	AGATAGGTTT	    0.943664	-37
          **********

Masking position 3
Map Score:   0.265243

Number of sites scoring better than the average of aligned sites = 422
Number in coding regions = 371
Number in noncoding regions = 51
Number of orfs with sites within 600 bp upstream = 56
Fraction of orfs with sites within 600 bp upstream = 0.00899454


Motif number 5

          **********

No masking
Map Score:   -8.36008e-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:   -8.36008e-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:   -8.36008e-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