AlignACE 3.0 10/20/99
AlignACE2 -i AP/AP_operons013_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944249550
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	APE1416	300	165aa long hypothetical protein

Motif 1
   CATAATCTTCCTGGAGCTAAGCCTGCTGTCCTCCT	0	7	1
TCATAGCCTTCTACGGCTACGGCGATAGGAGGAGGATA	0	51	1
TAGGAGGAGGATAGCGCTACTGTACTTCGTCTGGACCC	0	76	1
TGTACTTCGTCTGGACCCACATAGCCGGGGCTCTAGCG	0	96	1
AGCCGGGGCTCTAGCGCTCCTCGGCGGCCTCTATTATG	0	118	1
CCTCCCTCCACTGTCGCGACGTCGAAGGTCCCCGTCTT	0	161	0
TAGTCTATTTCTCGAGCCCCGCGGACAGGAGTGTCTAC	0	204	1
ACAGGAGTGTCTACGCCGCCATAGCTGGGGTTAGCCTC	0	228	1
AGCTGGGGTTAGCCTCCTCCTAGGAATGCTTGTCAAGA	0	250	1
          ** * ** **   **  *
MAP Score: 9.31141

Motif 2
  CATAATCTTCCTGGAGCTAAGCCTGCTGTCCTCCTT	0	8	1
GCTGTCCTCCTTCCTCCTCATAGCCTTCTACGGCTACG	0	34	1
GTACTTCGTCTGGACCCACATAGCCGGGGCTCTAGCGC	0	97	1
GCCGGGGCTCTAGCGCTCCTCGGCGGCCTCTATTATGT	0	119	1
TGTTATCAAGACGGGGACCTTCGACGTCGCGACAGTGG	0	154	1
GATAGTCTATTTCTCGAGCCCCGCGGACAGGAGTGTCT	0	202	1
CCCCGCGGACAGGAGTGTCTACGCCGCCATAGCTGGGG	0	220	1
TACGCCGCCATAGCTGGGGTTAGCCTCCTCCTAGGAAT	0	239	1
CTTGTCAAGATGGCTGTATTCGGCGTGCACAT      	0	278	1
          * *  *  **  **** *
MAP Score: 8.68233

Motif 3
AATCTTCCTGGAGCTAAGCCTGCTGTCCTCCTT	0	13	1
CCTCCTTCCTCCTCATAGCCTTCTACGGCTACG	0	39	1
CTCCTCCTATCGCCGTAGCCGTAGAAGGCTATG	0	52	0
TAGCGCTACTGTACTTCGTCTGGACCCACATAG	0	87	1
TCGTCTGGACCCACATAGCCGGGGCTCTAGCGC	0	102	1
GGGCTCTAGCGCTCCTCGGCGGCCTCTATTATG	0	123	1
CGACGTCGAAGGTCCCCGTCTTGATAACATAAT	0	150	0
CCCTCCACTGTCGCGACGTCGAAGGTCCCCGTC	0	163	0
TCTATTTCTCGAGCCCCGCGGACAGGAGTGTCT	0	207	1
CGGACAGGAGTGTCTACGCCGCCATAGCTGGGG	0	225	1
CGCCATAGCTGGGGTTAGCCTCCTCCTAGGAAT	0	244	1
         ATGTGCACGCCGAATACAGCCATC	0	286	0
          ** * ****** *
MAP Score: 7.65575

Motif 4
CTTCCTGGAGCTAAGCCTGCTGTCCTCCTT	0	16	1
TCCTCATAGCCTTCTACGGCTACGGCGATA	0	48	1
GTACAGTAGCGCTATCCTCCTCCTATCGCC	0	71	0
TAGCGCTACTGTACTTCGTCTGGACCCACA	0	87	1
CTCTAGCGCTCCTCGGCGGCCTCTATTATG	0	126	1
AGACGGGGACCTTCGACGTCGCGACAGTGG	0	162	1
ACAGGAGTGTCTACGCCGCCATAGCTGGGG	0	228	1
CATAGCTGGGGTTAGCCTCCTCCTAGGAAT	0	247	1
          **********
MAP Score: 6.31571

Motif 5
        CATAATCTTCCTGGAGCTAAGC	0	2	1
TTCCTGGAGCTAAGCCTGCTGTCCTCCTTC	0	17	1
AAGCCTGCTGTCCTCCTTCCTCCTCATAGC	0	28	1
CTTCCTCCTCATAGCCTTCTACGGCTACGG	0	43	1
AGTAGCGCTATCCTCCTCCTATCGCCGTAG	0	67	0
AATAGACTATCCTGCCTCCCTCCACTGTCG	0	183	0
CAGGAGTGTCTACGCCGCCATAGCTGGGGT	0	229	1
ATAGCTGGGGTTAGCCTCCTCCTAGGAATG	0	248	1
CACGCCGAATACAGCCATCTTGACAAGCAT	0	275	0
          **********
MAP Score: 5.61835

Motif 6
GCTAAGCCTGCTGTCCTCCTTCCTCCTCAT	0	25	1
TACAGTAGCGCTATCCTCCTCCTATCGCCG	0	70	0
TCGGCGGCCTCTATTATGTTATCAAGACGG	0	138	1
GAGAAATAGACTATCCTGCCTCCCTCCACT	0	187	0
          **********
MAP Score: 2.06831