AlignACE 3.0 10/20/99
AlignACE2 -i AP/AP_operons020_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944249674
 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
GCGGGGTATCCAGCCTTGCCCCGGCCACGGG	0	11	1
TTCTCGCTAGTGCCCGTGGCCGGGGCAAGGC	0	23	0
TGGCTATCTATAGCCTTCCCCTAGCACTGGC	1	13	1
AGCCTTCCCCTAGCACTGGCATTACTTCCCG	1	24	1
CTCAGAATATCGGGGCTCGCCGGGCTCTACC	1	120	1
TAATAGTAGTTAGCATCCCCCCGGCTGTATC	1	151	1
AACAAGGGTATAGGATTGGCC          	1	204	1
       CAACGCCACCGGCCGGCGAGGCTA	2	3	1
CTGGATCGCATACCACTAGCCCGCAGGTTGA	2	68	1
          **** ******
MAP Score: 10.695

Motif 3
CTCGCTAGTGCCCGTGGCCGGGGCAAGGCTGGAT	0	18	0
CTATAGCCTTCCCCTAGCACTGGCATTACTTCCC	1	20	1
TATCGGGGCTCGCCGGGCTCTACCTAATAGTAGT	1	127	1
AGTTAGCATCCCCCCGGCTGTATCTCACTTCAAC	1	158	1
ACGTAACTAGAGCCAACAAGGGTATAGGATTGGC	1	190	1
ACCATAGCCTCGCCGGCCGGTGGCGTTG      	2	4	0
GCATACCACTAGCCCGCAGGTTGAGGAGGAGGAA	2	75	1
          **** *** **  *
MAP Score: 4.88783

Motif 4
GGGTATCCAGCCTTGCCCCGGCCACGGGCAC	0	14	1
GGCCTTTCTCGCTAGTGCCCGTGGCCGGGGC	0	28	0
GTAGAGCCCGGCGAGCCCCGATATTCTGAGT	1	119	0
ACTACTATTAGGTAGAGCCCGGCGAGCCCCG	1	130	0
ATAGTAGTTAGCATCCCCCCGGCTGTATCTC	1	153	1
      CAACGCCACCGGCCGGCGAGGCTAT	2	4	1
ACAAACCATCACAACCCCCGTATGTACCATA	2	32	0
GGATCGCATACCACTAGCCCGCAGGTTGAGG	2	70	1
          ** ********
MAP Score: 3.90398

Motif 5
  AGCGGGGTATCCAGCCTTGCCCCGGCCACGGGC	0	8	1
CTTTCTCGCTAGTGCCCGTGGCCGGGGCAAGGCTG	0	21	0
CTATCTATAGCCTTCCCCTAGCACTGGCATTACTT	1	16	1
CCGTTGTTTACGCCCTCTCAGGCGTTAACAGTATC	1	52	1
CAGGCGTTAACAGTATCCTGGCTGGTAAAGATCCT	1	70	1
TACTCAGAATATCGGGGCTCGCCGGGCTCTACCTA	1	118	1
TAGTAGTTAGCATCCCCCCGGCTGTATCTCACTTC	1	154	1
         CAACGCCACCGGCCGGCGAGGCTATG	2	1	1
TACTGGATCGCATACCACTAGCCCGCAGGTTGAGG	2	66	1
          *   * *** *****
MAP Score: 1.81374