AlignACE 3.0 10/20/99
AlignACE2 -i CP/CP_operons033_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944238514
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	yqeV	100	Hypothetical Protein
#1	phnP	221	Metal Dependent Hydrolase
#2	CPn0480	32	CT383 hypothetical protein
#3	artJ	98	Arginine Periplasmic Binding Protein
#4	recA	300	RecA recombination protein
#5	CPn0912	85	CT768 hypothetical protein
#6	CPn0914	50	hypothetical protein
#7	ybeB	60	IojAP superfamily ortholog

Motif 1
TCTTTGTTAGTGAGAAAAAGAGTGATATTT	0	34	1
TGAGAAAATGTGAGAAATAACTGACGAACA	1	13	0
AAAAGATTCATGAGAAAATGTGAGAAATAA	1	23	0
TGTTTCCAGATGAGCAATTGGT        	1	209	1
TTAAATTTATTGAGAAATAACAAGCCATCT	4	79	1
GTATGCATAGAGAGCAAAACAATACAGAAT	4	148	1
CAACTAACTATGAGAAGAACTTCTCTATTT	4	216	1
CTGAGAATCGAGAGAAATAGAGAAGTTCTT	4	230	0
CTCGATTCTCAGAGAAACAGAACTATTCTC	4	248	1
GTGTGGGGCTTGACAAATAAAATTGTTAAA	5	52	0
          **********
MAP Score: 10.5791

Motif 2
TGTTAGTGAGAAAAAGAGTGATATTTTAAAA	0	38	1
TGCAGCGCAGTAAAAGATTCATGAGAAAATG	1	33	0
CTTAAAAATTTTCGAGAGGGATCTCGTGCAG	1	59	0
GATCCAAAGTTAAGAGACTGACTAATTATTT	1	167	1
TCAAAGAAGGAACAAGATTGC          	2	21	1
TTAAAACTTTTTCGAGTTTGATGTATTTATT	3	22	1
CTATCATGTGTTAAAGTTTACATAAAAAAAT	3	50	0
AAAAAGTAACTTCAAGATGGCTTGTTATTTC	4	92	0
CCATGGCAAATTCAAGTATGCATAGAGAGCA	4	133	1
ATAATTGACGTTAAAGATTGCTAGCAGCAGA	5	13	1
TTGTTAAAACTTAAAGTCTGCTGCTAGCAAT	5	29	0
ATCTTGGATAATCGAGTATCCTAAAGCTGGT	7	36	1
          ******* ***
MAP Score: 8.16889

Motif 3
TACCTCTAGAGACTTCAATAGATTTAGCGA	0	79	0
TTTGGATCTTAAAGTCAAGAAGTTGCTAGA	1	145	0
TTTAAGATCCAAAGTTAAGAGACTGACTAA	1	162	1
  AATTATTCAAAGTTAAAACTTTTTCGAG	3	8	1
TTTTTATGTAAACTTTAACACATGATAGAA	3	53	1
ATTTCTCAATAAATTTAAGAAAAGCACTAG	4	67	0
GGCAAAAAGTAACTTCAAGATGGCTTGTTA	4	96	0
CTGCCATGGCAAATTCAAGTATGCATAGAG	4	130	1
AGCAATCTTTAACGTCAATTATTTT     	5	5	0
GCTAGCAGCAGACTTTAAGTTTTAACAATT	5	32	1
          **********
MAP Score: 7.46308

Motif 4
TTTGTTAGTGAGAAAAAGAGTGATATTTTAAAA	0	36	1
AAGATTCATGAGAAAATGTGAGAAATAACTGAC	1	18	0
CGTGCAGCGCAGTAAAAGATTCATGAGAAAATG	1	33	0
TTGGGGTTCTAGCAACTTCTTGACTTTAAGATC	1	138	1
AAGTTTACATAAAAAAATAAATACATCAAACTC	3	35	0
TGTAAACTTTAACACATGATAGAATTTAGCGTA	3	59	1
CAATAAATTTAAGAAAAGCACTAGAATACAAGG	4	58	0
CAAGGCAAAAAGTAACTTCAAGATGGCTTGTTA	4	96	0
CATAGAGAGCAAAACAATACAGAATGATACACA	4	153	1
TAACTATGAGAAGAACTTCTCTATTTCTCTCGA	4	220	1
CGATTCTCAGAGAAACAGAACTATTCTCTGGGG	4	250	1
GGGCTTGACAAATAAAATTGTTAAAACTTAAAG	5	44	0
 TTCCATTTAAAAAAAAGCTCGACCTTATCTTG	7	9	1
          AAAACCAGCTTTAGGATACTCGA	7	47	0
          ** ******  **
MAP Score: 5.43718

Motif 5
     ATACCTCTAGAGACTTCAATAGATTTA	0	83	0
TCGTCAGTTATTTCTCACATTTTCTCATGAAT	1	16	1
TCTCACATTTTCTCATGAATCTTTTACTGCGC	1	28	1
ACGAGATCCCTCTCGAAAATTTTTAAGGATAG	1	63	1
TTTAGAATCCTCTATAGCTTTTTAAACCATAG	1	106	0
AAATTGGGGTTCTAGCAACTTCTTGACTTTAA	1	135	1
AATTAGTCAGTCTCTTAACTTTGGATCTTAAA	1	162	0
TACATCAAACTCGAAAAAGTTTTAACTTTGAA	3	15	0
GTCCTTGTATTCTAGTGCTTTTCTTAAATTTA	4	56	1
ATACACATCATCTAAAACCTTCCACCCCCAAA	4	179	1
CTTCTCTATTTCTCTCGATTCTCAGAGAAACA	4	235	1
GACTTTAAGTTTTAACAATTTTATTTGTCAAG	5	42	1
          **** *** ***
MAP Score: 5.31712

Motif 6
CTATTTTAAAATATCACTCTTTTTCTCACTAACAAAGA	0	34	0
TTCGTCAGTTATTTCTCACATTTTCTCATGAATCTTTT	1	15	1
AGACTGACTAATTATTTTTGTTTGCTTGTGTTTCCAGA	1	181	1
       GCAATCTTGTTCCTTCTTTGATACAAATTCA	2	11	0
AGGTCCTTGTATTCTAGTGCTTTTCTTAAATTTATTGA	4	54	1
AGCCATCTTGAAGTTACTTTTTGCCTTGACTGCCATGG	4	101	1
CTCTCTATGCATACTTGAATTTGCCATGGCAGTCAAGG	4	124	0
ACAATACAGAATGATACACATCATCTAAAACCTTCCAC	4	166	1
TATGAGAAGAACTTCTCTATTTCTCTCGATTCTCAGAG	4	224	1
TCCCCAGAGAATAGTTCTGTTTCTCTGAGAATCGAGAG	4	246	0
TTAAGTTTTAACAATTTTATTTGTCAAGCCCCACACCT	5	46	1
ATTTAAAAAAAAGCTCGACCTTATCTTGGATAATCGAG	7	14	1
          *   * **  ** *** *
MAP Score: 1.83964