AlignACE 3.0 10/20/99
AlignACE2 -i AP/AP_operons020_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944249668
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	APE1895	58	537aa long hypothetical protein
#1	APE2206	215	213aa long hypothetical protein
#2	APE2207	115	310aa long hypothetical protein

Motif 1
GGGGTATCCAGCCTTGCCCCGGCCACGGGCACT	0	13	1
TTGCCCCGGCCACGGGCACTAGCGAGAAAGGCC	0	26	1
GCTATCTATAGCCTTCCCCTAGCACTGGCATTA	1	15	1
ATCGGGGCTCGCCGGGCTCTACCTAATAGTAGT	1	128	1
ATAGTAGTTAGCATCCCCCCGGCTGTATCTCAC	1	153	1
        GGCCAATCCTATACCCTTGTTGGCT	1	200	0
          CAACGCCACCGGCCGGCGAGGCT	2	0	1
CCCGTATGTACCATAGCCTCGCCGGCCGGTGGC	2	14	0
ATACTGGATCGCATACCACTAGCCCGCAGGTTG	2	65	1
          ***  ** *****
MAP Score: 17.0846

Motif 2
       AGCGGGGTATCCAGCCTTGCCCCGGC	0	3	1
GCTATCTATAGCCTTCCCCTAGCACTGGCATTA	1	15	1
CCCTAGCACTGGCATTACTTCCCGTTGTTTACG	1	31	1
CGTTGTTTACGCCCTCTCAGGCGTTAACAGTAT	1	53	1
TCAGGCGTTAACAGTATCCTGGCTGGTAAAGAT	1	69	1
CAGAATATCGGGGCTCGCCGGGCTCTACCTAAT	1	122	1
AATAGTAGTTAGCATCCCCCCGGCTGTATCTCA	1	152	1
AACGTAACTAGAGCCAACAAGGGTATAGGATTG	1	189	1
         CAACGCCACCGGCCGGCGAGGCTA	2	1	1
CCCCGTATGTACCATAGCCTCGCCGGCCGGTGG	2	15	0
GTATCGACAAACCATCACAACCCCCGTATGTAC	2	36	0
CTTTTCCTCCTCCTCAACCTGCGGGCTAGTGGT	2	79	0
         TGCCTCCCCTTCTCTTTTCCTCCT	2	101	0
          *** ** ** ***
MAP Score: 6.86313

Motif 3
GTGCCCGTGGCCGGGGCAAGGCTGGATACCCC	0	13	0
          CCTGTAGAAGGCCTTTCTCGCT	0	46	0
AATGCCAGTGCTAGGGGAAGGCTATAGATAGC	1	15	0
CGTTAACAGTATCCTGGCTGGTAAAGATCCTA	1	74	1
TACTCAGAATATCGGGGCTCGCCGGGCTCTAC	1	118	1
TGAGATACAGCCGGGGGGATGCTAACTACTAT	1	153	0
CATAGCCTCGCCGGCCGGTGGCGTTG      	2	4	0
TGGTTTGTCGATACTGGATCGCATACCACTAG	2	55	1
GGATCGCATACCACTAGCCCGCAGGTTGAGGA	2	70	1
          ** ***** ***
MAP Score: 5.73893

Motif 4
TGCCCGTGGCCGGGGCAAGGCTGGATACCCCG	0	12	0
CAGCCTTGCCCCGGCCACGGGCACTAGCGAGA	0	21	1
ACGGGCACTAGCGAGAAAGGCCTTCTACAGG 	0	37	1
ATGCCAGTGCTAGGGGAAGGCTATAGATAGCC	1	14	0
TTAGGTAGAGCCCGGCGAGCCCCGATATTCTG	1	122	0
GAGATACAGCCGGGGGGATGCTAACTACTATT	1	152	0
CATAGCCTCGCCGGCCGGTGGCGTTG      	2	4	0
CCTCAACCTGCGGGCTAGTGGTATGCGATCCA	2	69	0
          ***** * ****
MAP Score: 4.73903

Motif 5
CGTGGCCGGGGCAAGGCTGGATACCCCGCT	0	10	0
CCAGCCTTGCCCCGGCCACGGGCACTAGCG	0	20	1
CCTGTAGAAGGCCTTTCTCGCTAGTGCCCG	0	38	0
GCTATCTATAGCCTTCCCCTAGCACTGGCA	1	15	1
CTTCCCCTAGCACTGGCATTACTTCCCGTT	1	27	1
GTTGTTTACGCCCTCTCAGGCGTTAACAGT	1	54	1
GTTAACAGTATCCTGGCTGGTAAAGATCCT	1	75	1
ACTCAGAATATCGGGGCTCGCCGGGCTCTA	1	119	1
GTTAGCATCCCCCCGGCTGTATCTCACTTC	1	159	1
CAATCCTATACCCTTGTTGGCTCTAGTTAC	1	192	0
    CAACGCCACCGGCCGGCGAGGCTATG	2	6	1
ACCATCACAACCCCCGTATGTACCATAGCC	2	29	0
GATCGCATACCACTAGCCCGCAGGTTGAGG	2	71	1
     TGCCTCCCCTTCTCTTTTCCTCCTC	2	100	0
          **********
MAP Score: 1.52115