AlignACE 3.0 10/20/99
AlignACE2 -i EC_operons120_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	943442056
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	cof	87	orf, hypothetical protein
#1	ybhA	154	putative phosphatase
#2	b0822	145	orf, hypothetical protein
#3	b0844	26	orf, hypothetical protein
#4	b0845	83	putative DEOR-type transcriptional regulator

Motif 1
ATATACGGAAGTAATAGTGAATAGTTAAATA	0	28	0
ACGGTTAATGGTGATTGAGTATCACCTGATA	0	58	0
GTTGCTAAATGCAAAGGAGCATTC       	1	3	0
TCCGATAGTGGTATCGGTGTACCATTCGCGC	1	98	1
TCGAATGAAAGTAAGGATGAAATTGATGATG	2	52	0
AAATGAAACCGTAACAGTGTAATAACAATGT	2	105	0
TCCTCTCTCTGCAATTGTGTACAAATGTACA	4	16	1
          **** ******
MAP Score: 4.01116

Motif 2
    ATAAACCCGGAACAATATTATTTAACTATTCA	0	6	1
         TCTGTGACACGGTTAATGGTGATTGAG	0	70	0
TAGCAACTGACTGTAACAGCTAAAATTAGTCGCTTT	1	27	1
CGGGCTAAATCATTCACATCATCAATTTCATCCTTA	2	36	1
TTTGTGCTCTGCGTCACATTGTTATTACACTGTTAC	2	90	1
TGTTATTACACTGTTACGGTTTCATTTTCGAGCCAG	2	109	1
          * ** ***   * ***
MAP Score: 2.92866

Motif 3
         ATAAACCCGGAACAATATTATTTAACTATTCA	0	1	1
CGGTGTACCATTCGCGCAGACGAAAATTCTTAACCTTAATC	1	112	1
CCCGGCGGCGTCGTCGCCGGGCTAAATCATTCACATCATCA	2	19	1
AAATATAATTTGTGCTCTGCGTCACATTGTTATTACACTGT	2	82	1
          *   * * *    * *** **
MAP Score: 1.27801

Motif 4
GGTTAAGAATTTTCGTCTGCGCGAATGGTACA	1	115	0
          TCTCCTCGGCCCGGCGGCGTCG	2	0	1
CTCGGCCCGGCGGCGTCGTCGCCGGGCTAAAT	2	14	1
AAATATAATTTGTGCTCTGCGTCACATTGTTA	2	82	1
       AGGTGTGCTCCTGGCTCGAAAATGA	2	130	0
ACCTTGCTAATGTTGTCTTCCCTCTTCTTATT	4	49	1
          *** *** ****
MAP Score: 1.23639