AlignACE 3.0 10/20/99
AlignACE2 -i CP/CP_operons033_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944238505
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	yqeV	100	Hypothetical Protein
#1	recA	300	RecA recombination protein
#2	CPn0912	85	CT768 hypothetical protein
#3	CPn0914	50	hypothetical protein
#4	ybeB	60	IojAP superfamily ortholog

Motif 1
CTTTGTTAGTGAGAAAAAGAGTGATATTTTA	0	35	1
TAAATTTATTGAGAAATAACAAGCCATCTTG	1	80	1
TATGCATAGAGAGCAAAACAATACAGAATGA	1	149	1
TGAGAATCGAGAGAAATAGAGAAGTTCTTCT	1	228	0
TCGATTCTCAGAGAAACAGAACTATTCTCTG	1	249	1
TGTGGGGCTTGACAAATAAAATTGTTAAAAC	2	50	0
          ****** ****
MAP Score: 6.26755

Motif 2
TGAAACTAAGGTCCTTGTATTCTAGTGCTTT	1	46	1
TTGTATTCTAGTGCTTTTCTTAAATTTATTG	1	60	1
GAGAGAAATAGAGAAGTTCTTCTCATAGTTA	1	220	0
      GTAAATGCTCCTCTTGGTTTCCATA	1	285	0
TCTGTTCCCTGTGATGATCTTTATGAAGTTG	3	27	1
AGATAAGGTCGAGCTTTTTTTTAAATGGAA 	4	9	0
AAAAAAGCTCGACCTTATCTTGGATAATCGA	4	20	1
GAGTATCCTAAAGCTGGTTTT          	4	49	1
          ****** ****
MAP Score: 4.06221

Motif 3
   GTAGTTTTCTTCTAGGACATCGAATCT	0	7	1
CGATGAGTGGCTATTTTAAAATATCACTCT	0	52	0
TTTAGATATACTATCTGAAACTAAGGTCCT	1	31	1
ATTCTAGTGCTTTTCTTAAATTTATTGAGA	1	64	1
AAATAACAAGCCATCTTGAAGTTACTTTTT	1	93	1
ATGATACACATCATCTAAAACCTTCCACCC	1	176	1
        TTCCATTTAAAAAAAAGCTCGA	4	2	1
AAGCTCGACCTTATCTTGGATAATCGAGTA	4	24	1
          **********
MAP Score: 1.92555

Motif 4
GAGAAATAACAAGCCATCTTGAAGTTACTTTTTGCCTT	1	90	1
       GTAAATGCTCCTCTTGGTTTCCATATTCCCC	1	279	0
GAAATAGAGAAGTTCTTCTCATAGTTAGTTGAGAGATT	1	209	0
         AAAACCAGCTTTAGGATACTCGATTATCC	4	41	0
ATATTTTAAAATAGCCACTCATCGCTAAATCTATTGAA	0	58	1
         TAACTCGTCTACTCTCTTCTGTTCCCTGT	3	1	1
AGAATGATACACATCATCTAAAACCTTCCACCCCCAAA	1	173	1
TTCTTCTAGGACATCGAATCTTTGTTAGTGAGAAAAAG	0	16	1
TTAAAACTTAAAGTCTGCTGCTAGCAATCTTTAACGTC	2	19	0
          *   *  **  * *****
MAP Score: 1.5084