AlignACE 3.0 10/20/99
AlignACE2 -i AP/AP_operons024_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944249746
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	APE1716	55	104aa long hypothetical protein
#1	APES068	145	50aa long hypothetical 30S ribosomal protein S30
#2	APE2200	261	427aa long hypothetical L-asparaginase
#3	APE2202	153	642aa long hypothetical Glu-tRNA amidotransferase, subunit B

Motif 1
ATACCTATTACTGTCACAGGGGGATAAGCTAGA	0	15	1
GGGGGATAAGCTAGATTTGGGCGGAGATATCT 	0	33	1
TAGGCAGGGGCTAGCGCTGGGGAATAGCTTGCT	1	62	1
GAATAGCTTGCTAGGACGCGGTACAGTTTAAAT	1	83	1
TAGTCTAATCCTGTTTCAGGGCTATTTAAACTG	1	106	0
CAGGATTAGACTAGGATTGGGGAAGATCC    	1	126	1
AACAGTTTTGCTATGCCGGGGGGTCTCGAGACC	2	13	0
TGGGTAAATTCTAGCAGCGGACATGAATAGTTG	2	97	1
CTGGAGGTCTCTGGAGGTGGGTTTACCCTGGCT	2	157	1
TGGATATTGGCTAGAACCCGGGAGCTGGAGGTG	3	41	1
AACCCGGGAGCTGGAGGTGGTTAGGAAGATGTT	3	55	1
TAGACACCTCCTATATGGCGGTATAGCCTCAGT	3	127	0
          ****  * *****
MAP Score: 19.7948

Motif 2
CCTGTGACAGTAATAGGTATAGCCA         	0	1	0
GCAAGCTATTCCCCAGCGCTAGCCCCTGCCTATT	1	60	0
TTTAAACTGTACCGCGTCCTAGCAAGCTATTCCC	1	81	0
AATAGCCCTGAAACAGGATTAGACTAGGATTGGG	1	113	1
GTCTCGAGACCCCCCGGCATAGCAAAACTGTTTT	2	14	1
CGGCATAGCAAAACTGTTTTAGACAACAGCAGCT	2	28	1
AGGTCTCTGGAGGTGGGTTTACCCTGGCTGAAAC	2	161	1
TAGTAGTTAGACGAGGTTTCAGCCAGGGTAAACC	2	176	0
TATGGATACAAGGGTGTTGTAGCCAAGCTCCTCA	2	208	1
     TACATCGCCAGGTTTAGCACCGGCTTTAC	2	242	0
ACCTCCAGCTCCCGGGTTCTAGCCAATATCCAGG	3	39	0
CACCTCCTATATGGCGGTATAGCCTCAGTATGTG	3	122	0
          * *  *** *****
MAP Score: 13.0177

Motif 3
CACCTCCAGAGACCTCCAGTAGAGCCTAAAAGGGA	2	141	0
GGGTCTCGAGACCCCCCGGCATAGCAAAACTGTTT	2	12	1
GACACCTCCTATATGGCGGTATAGCCTCAGTATGT	3	123	0
GCAGGGGCTAGCGCTGGGGAATAGCTTGCTAGGAC	1	65	1
GGTTCTAGCCAATATCCAGGAGAGCTTCGCATAGG	3	24	0
TTCCAAAGAAATCTCGCTGGAGAGGTTAGCGAGAG	3	86	1
AGAGGAAGAGGATTTCCCTTATAGCTAGAAAGCTG	2	57	0
TTGTAGCCAAGCTCCTCAGTAAAGCCGGTGCTAAA	2	224	1
TATTTAAACTGTACCGCGTCCTAGCAAGCTATTCC	1	82	0
GCTAGAATTTACCCAGAAGAAGAGGAAGAGGATTT	2	77	0
CCCCTGTGACAGTAATAGGTATAGCCA        	0	2	0
          *  * ** * *****
MAP Score: 7.73167

Motif 4
AGCCAATATCCAGGAGAGCTTCGCATAGGCAGCC	3	19	0
TTGGCTAGAACCCGGGAGCTGGAGGTGGTTAGGA	3	47	1
AAACCCACCTCCAGAGACCTCCAGTAGAGCCTAA	2	147	0
    TGGGGTCTCGAGACCCCCCGGCATAGCAAA	2	6	1
TCCCTTATAGCTAGAAAGCTGCTGTTGTCTAAAA	2	44	0
ACCGGCTTTACTGAGGAGCTTGGCTACAACACCC	2	219	0
AGAAATCTCGCTGGAGAGGTTAGCGAGAGGCACA	3	92	1
        GACCAGCGAGGCTGCCTATGCGAAGC	3	2	1
GCAAGCTATTCCCCAGCGCTAGCCCCTGCCTATT	1	60	0
GTTTACCCTGGCTGAAACCTCGTCTAACTACTAT	2	177	1
          *  ******* * *
MAP Score: 6.30029

Motif 5
CCCAAATCTAGCTTATCCCCCTGTGACAGTAATA	0	20	0
CTATTCCCCAGCGCTAGCCCCTGCCTATTTCCAT	1	55	0
     TGGGGTCTCGAGACCCCCCGGCATAGCAA	2	5	1
CTAGCTATAAGGGAAATCCTCTTCCTCTTCTTCT	2	64	1
TTTCAGCCAGGGTAAACCCACCTCCAGAGACCTC	2	160	0
GTTTACCCTGGCTGAAACCTCGTCTAACTACTAT	2	177	1
GAGGAGCTTGGCTACAACACCCTTGTATCCATAG	2	207	0
TACATCGCCAGGTTTAGCACCGGCTTTACTGAGG	2	237	0
GGAGAGCTTCGCATAGGCAGCCTCGCTGGTC   	3	7	0
TGGAACATCTTCCTAACCACCTCCAGCTCCCGGG	3	57	0
TATGTGCCTCTCGCTAACCTCTCCAGCGAGATTT	3	94	0
CACATACTGAGGCTATACCGCCATATAGGAGGTG	3	122	1
          GGTTAGACACCTCCTATATGGCGG	3	139	0
          **  ** ***** *
MAP Score: 5.61887

Motif 6
ACTGTCACAGGGGGATAAGCTAGATTTGGGCGGAGATATCT   	0	24	1
ATTTAAAAATGGAAATAGGCAGGGGCTAGCGCTGGGGAATAGCT	1	47	1
GGCTAGCGCTGGGGAATAGCTTGCTAGGACGCGGTACAGTTTAA	1	70	1
GCCCTGAAACAGGATTAGACTAGGATTGGGGAAGATCC      	1	117	1
CTCTTCTTCTGGGTAAATTCTAGCAGCGGACATGAATAGTTGGC	2	88	1
CTCTGGAGGTGGGTTTACCCTGGCTGAAACCTCGTCTAACTACT	2	165	1
TAACTACTATGGATACAAGGGTGTTGTAGCCAAGCTCCTCAGTA	2	201	1
AAGCTCTCCTGGATATTGGCTAGAACCCGGGAGCTGGAGGTGGT	3	32	1
          *** * *  *  *     * *  *
MAP Score: 5.60586

Motif 7
         TGGCTATACCTATTACTGTCA	0	1	1
CGTCCTAGCAAGCTATTCCCCAGCGCTAGC	1	71	0
GCCGGGGGGTCTCGAGACCCCA        	2	2	0
CAGAGACCTCCAGTAGAGCCTAAAAGGGAT	2	140	0
GTTTCAGCCAGGGTAAACCCACCTCCAGAG	2	165	0
CCAAGCTCCTCAGTAAAGCCGGTGCTAAAC	2	230	1
AGCCAATATCCAGGAGAGCTTCGCATAGGC	3	23	0
CCTGGATATTGGCTAGAACCCGGGAGCTGG	3	39	1
AGAAATCTCGCTGGAGAGGTTAGCGAGAGG	3	92	1
TGGAGAGGTTAGCGAGAGGCACATACTGAG	3	103	1
TCCTATATGGCGGTATAGCCTCAGTATGTG	3	122	0
          **********
MAP Score: 3.14402