AlignACE 3.0 10/20/99
AlignACE2 -i AP/AP_operons021_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944249686
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	APE0011	300	212aa long hypothetical protein
#1	APE2502	300	327aa long hypothetical protein
#2	APE2503	121	243aa long hypothetical 3-oxoacyl-[acyl-carrier protein] reductase

Motif 1
TTTGTCCAATTTTGAGGCTAGGGTTTTACC	0	21	0
AGATTCCGGAGGAGAGGCTGGATCCTAGGT	0	239	1
TAGAGAGGTTGTTGAAGCGGGTGTTGACGC	0	276	1
TGAAGCGGGTGTTGACGCTATA        	0	288	1
CGTGGTTTACGTAGAAGCTAATATAGTCCA	1	10	0
GAGATACTATGTTGAGGCGGCCTCCACAGG	1	71	1
ACTCAGCAGGGTTGAGGCTCTCCAGGCTAT	1	158	1
TCACGCCGAGGGAGAGGCTCACGCCTATAG	1	184	0
       ACCGTAGAAGCTCCCCGCTATTA	2	3	1
ACATGAAGAGGTACAAGCTAGTCTTGGTGG	2	73	1
          **********
MAP Score: 20.8282

Motif 2
CCAATTTTGAGGCTAGGGTTTTACCAGTTTATGAT	0	11	0
AGTGAAGTACTGCTAGGGGGTTTCCGATATTGATT	0	101	1
AGATTCCGGAGGAGAGGCTGGATCCTAGGTTGTTG	0	239	1
GAGATACTATGTTGAGGCGGCCTCCACAGGCACAG	1	71	1
CTAAACCTATGACGAGCCCTGTGCCTGTGGAGGCC	1	89	0
CATGATAATGGGCGGCGCATATGCCGGCCTAACAC	1	125	1
CCTATAGCCTGGAGAGCCTCAACCCTGCTGAGTGT	1	156	0
TCACGCCGAGGGAGAGGCTCACGCCTATAGCCTGG	1	179	0
GCGTGATACTGGCGGGGCTACTGGCGTCCCTGCTA	1	208	1
       ACCGTAGAAGCTCCCCGCTATTATCCTG	2	3	1
          ********     **
MAP Score: 14.9781

Motif 3
 AATCATAAACTGGTAAAACCCTAGCCTCAAAATTGG	0	9	1
AGCCTCTCCTCCGGAATCTCTCCAGGCCCATGCTCGA	0	221	0
AGAGATTCCGGAGGAGAGGCTGGATCCTAGGTTGTTG	0	237	1
      TATAGCGTCAACACCCGCTTCAACAACCTCT	0	279	0
TCGAGATACTATGTTGAGGCGGCCTCCACAGGCACAG	1	69	1
GCGGCCTCCACAGGCACAGGGCTCGTCATAGGTTTAG	1	87	1
GGCGCATATGCCGGCCTAACACTCAGCAGGGTTGAGG	1	138	1
CGCCTATAGCCTGGAGAGCCTCAACCCTGCTGAGTGT	1	156	0
TATCACGCCGAGGGAGAGGCTCACGCCTATAGCCTGG	1	179	0
CGTGATACTGGCGGGGCTACTGGCGTCCCTGCTACTT	1	209	1
ACCCCCCGTGATGGCACTACTGAAAGCTAGGTTCTGG	1	248	1
GTCCTCTTGCCAGGGGCCACCAGAACCTAGCTTTCAG	1	267	0
         ACCGTAGAAGCTCCCCGCTATTATCCTG	2	1	1
          * ** *  ** * * **
MAP Score: 10.71

Motif 4
ATGAATTACGTTCTCGCCACTATACTATAGTGAAGTACTGCT	0	73	1
CGATATTGATTTCCTCACAGGACGTTGGTAAGCGAGTAAGAC	0	125	1
TCGAGCATGGGCCTGGAGAGATTCCGGAGGAGAGGCTGGATC	0	221	1
CTAGGTTGTTGATTAGAGAGGTTGTTGAAGCGGGTGTTGACG	0	263	1
ACCACGCCCGTGAAGCCTACCTTCGAGGAGAGCATTCGAGAT	1	34	1
GAGGAGAGCATTCGAGATACTATGTTGAGGCGGCCTCCACAG	1	58	1
CCGCCCATTATCATGGCTAAACCTATGACGAGCCCTGTGCCT	1	98	0
CGGCGCATATGCCGGCCTAACACTCAGCAGGGTTGAGGCTCT	1	137	1
GCAGGGTTGAGGCTCTCCAGGCTATAGGCGTGAGCCTCTCCC	1	163	1
GACGCCAGTAGCCCCGCCAGTATCACGCCGAGGGAGAGGCTC	1	194	0
ATGGCACTACTGAAAGCTAGGTTCTGGTGGCCCCTGGCAAGA	1	258	1
AAAATAACTTTAATACCCAGGATAATAGCGGGGAGCTTCTAC	2	13	0
TTTTCCCAGCTGCTTCCAACTTACATGAAGAGGTACAAGCTA	2	51	1
          * *  ** **  *   *  * *
MAP Score: 10.6568

Motif 5
AGGCTATAGGCGTGAGCCTCTCCCTCGGCGTGA	1	181	1
GCAGGGACGCCAGTAGCCCCGCCAGTATCACGC	1	208	0
ACTCAGCAGGGTTGAGGCTCTCCAGGCTATAGG	1	158	1
TCCGGAATCTCTCCAGGCCCATGCTCGATCCCA	0	216	0
TTAGCTTCTACGTAAACCACGCCCGTGAAGCCT	1	19	1
GTCCCTGCTACTTATACCCCCCGTGATGGCACT	1	233	1
       ACCGTAGAAGCTCCCCGCTATTATCC	2	3	1
ACAACCTAGGATCCAGCCTCTCCTCCGGAATCT	0	239	0
CCAAGACTAGCTTGTACCTCTTCATGTAAGTTG	2	67	0
AAGCTAGGTTCTGGTGGCCCCTGGCAAGAGGAC	1	271	1
AAACCACGCCCGTGAAGCCTACCTTCGAGGAGA	1	32	1
AAATCAATATCGGAAACCCCCTAGCAGTACTTC	0	104	0
ACACCCGCTTCAACAACCTCTCTAATCAACAAC	0	267	0
CCTCCACAGGCACAGGGCTCGTCATAGGTTTAG	1	91	1
GTTAGGCCGGCATATGCGCCGCCCATTATCATG	1	125	0
          **  ****** **
MAP Score: 9.85019

Motif 6
GGTTGAGGCTCTCCAGGCTATAGGCGTGAGCCTCT	1	167	1
CCTGGAGAGATTCCGGAGGAGAGGCTGGATCCTAG	0	232	1
GCCTAACACTCAGCAGGGTTGAGGCTCTCCAGGCT	1	151	1
GTTCTGGTGGCCCCTGGCAAGAGGACGCAAGA   	1	278	1
GCCAGTATCACGCCGAGGGAGAGGCTCACGCCTAT	1	186	0
TCGAGAATACTTCCAGATGGTAGGTCTGTTATATT	0	169	1
TGCCAGGGGCCACCAGAACCTAGCTTTCAGTAGTG	1	262	0
CATGCTCGATCCCATGATCAAAGGCGAATATAACA	0	195	0
GAGGCGGCCTCCACAGGCACAGGGCTCGTCATAGG	1	84	1
TCCGGAATCTCTCCAGGCCCATGCTCGATCCCATG	0	214	0
TCGAATGCTCTCCTCGAAGGTAGGCTTCACGGGCG	1	38	0
ATTGATTTCCTCACAGGACGTTGGTAAGCGAGTAA	0	129	1
CAAGACCGATCCACCAAGACTAGCTTGTACCTCTT	2	78	0
          * ** **   *****
MAP Score: 9.66162

Motif 7
TCGAGCATGGGCCTGGAGAGATTCCGGAGGAGAGG	0	221	1
CAACAACCTAGGATCCAGCCTCTCCTCCGGAATCT	0	239	0
CGTAAACCACGCCCGTGAAGCCTACCTTCGAGGAG	1	29	1
CGAGCCCTGTGCCTGTGGAGGCCGCCTCAACATAG	1	77	0
GTGTTAGGCCGGCATATGCGCCGCCCATTATCATG	1	125	0
ACACTCAGCAGGGTTGAGGCTCTCCAGGCTATAGG	1	156	1
CCAGGCTATAGGCGTGAGCCTCTCCCTCGGCGTGA	1	179	1
TAGCAGGGACGCCAGTAGCCCCGCCAGTATCACGC	1	208	0
CTGAAAGCTAGGTTCTGGTGGCCCCTGGCAAGAGG	1	267	1
TTGGTGGATCGGTCTTGGAGACAACTTATGCTCTA	2	96	1
          *** * ** * * **
MAP Score: 8.7212

Motif 8
TGTCCAATTTTGAGGCTAGGGTTTTACCAGTTTATGAT	0	11	0
GGAATCTCTCCAGGCCCATGCTCGATCCCATGATCAAA	0	208	0
GGAGAGATTCCGGAGGAGAGGCTGGATCCTAGGTTGTT	0	235	1
ATTCGAGATACTATGTTGAGGCGGCCTCCACAGGCACA	1	67	1
GCGGCCTCCACAGGCACAGGGCTCGTCATAGGTTTAGC	1	87	1
GAGTGTTAGGCCGGCATATGCGCCGCCCATTATCATGG	1	124	0
TAACACTCAGCAGGGTTGAGGCTCTCCAGGCTATAGGC	1	154	1
AGTATCACGCCGAGGGAGAGGCTCACGCCTATAGCCTG	1	180	0
GTGATACTGGCGGGGCTACTGGCGTCCCTGCTACTTAT	1	210	1
CTACTGAAAGCTAGGTTCTGGTGGCCCCTGGCAAGAGG	1	264	1
          * ***    *** *  **
MAP Score: 2.07019

Motif 9
ATCATGGGATCGAGCATGGGCCTGGAGAGATTCCGG	0	212	1
GGAGAGATTCCGGAGGAGAGGCTGGATCCTAGGTTG	0	235	1
ATTCGAGATACTATGTTGAGGCGGCCTCCACAGGCA	1	67	1
TGATAATGGGCGGCGCATATGCCGGCCTAACACTCA	1	127	1
CTCAGCAGGGTTGAGGCTCTCCAGGCTATAGGCGTG	1	159	1
AGTATCACGCCGAGGGAGAGGCTCACGCCTATAGCC	1	182	0
GGCGTGATACTGGCGGGGCTACTGGCGTCCCTGCTA	1	207	1
AAAGCTAGGTTCTGGTGGCCCCTGGCAAGAGGACGC	1	270	1
        ACCGTAGAAGCTCCCCGCTATTATCCTG	2	2	1
          **  *  ** ** ***
MAP Score: 1.67263

Motif 10
ATTCGCCTTTGATCATGGGATCGAGCATGGGCCTGGAG	0	201	1
GGCCTGGAGAGATTCCGGAGGAGAGGCTGGATCCTAGG	0	230	1
CTGGATCCTAGGTTGTTGATTAGAGAGGTTGTTGAAGC	0	256	1
CCGTGAAGCCTACCTTCGAGGAGAGCATTCGAGATACT	1	41	1
CGGCCTAACACTCAGCAGGGTTGAGGCTCTCCAGGCTA	1	149	1
AGGCTCTCCAGGCTATAGGCGTGAGCCTCTCCCTCGGC	1	172	1
GCGTGAGCCTCTCCCTCGGCGTGATACTGGCGGGGCTA	1	190	1
AGGTTCTGGTGGCCCCTGGCAAGAGGACGCAAGA    	1	276	1
TAATACCCAGGATAATAGCGGGGAGCTTCTACGGT   	2	7	0
          * ** * *  * ***  *
MAP Score: 0.621978