AlignACE 3.0 10/20/99
AlignACE2 -i AP/AP_operons025_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944249757
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	APE0121	300	246aa long hypothetical protein
#1	APE0122	32	184aa long hypothetical hit-like protein
#2	APE2109	226	447aa long hypothetical protein

Motif 1
GAGCAGAGTTCCCCGGCAGGGAGAACCTGGCTATGAGGCAGC	0	12	1
CTGCAAGCCTCATGAGCTGGTGGAGATGTCTGTTGAGCAGCT	0	54	0
CCAGGTTATGGCCAGGCCGGACGTCTTCTACGGAGACCCTAC	0	127	1
GGAGACCCTACCCAGGCTGTGGGAGGCCATGTGTTGGGCCAC	0	158	1
CATGTGTTGGGCCACGCTCCCGGCGTCAGGGTGTACCTCAAG	0	185	1
TGTACCTCAAGAAGAGCAGGGGGAACAAGAGGATAGCAAGGG	0	216	1
AGACGCTCCACACTTGCCCGAGGGTGAGACGGTCTTCGCCAT	0	262	1
TTAGGCTCTACAAATGCTGTAGACCTCTCAGGGTGTAGGCAG	2	12	0
TGTTTAAACGGTTAAGCGGCTGGCTCATCTGTTCGGCTTCCC	2	68	1
GCTATTAGAGGATTCTCCCCGGGATATTATGGCTGGCTAGTT	2	115	0
TCCTCTAATAGCTGAGGCGCTGGTATTGGGCTGAGAGGCCCG	2	145	1
GGCTGAGAGGCCCGCGCCGCAGGGGATGCAGGTTTGGGCGCC	2	173	1
          **   ** ** **       **
MAP Score: 15.3841

Motif 2
AGCAGAGTTCCCCGGCAGGGAGAACCTGGCTA	0	13	1
GCAGGGAGAACCTGGCTATGAGGCAGCAGCTG	0	27	1
GACATCTCCACCAGCTCATGAGGCTTGCAGAC	0	66	1
TTATAACTAACCAGGTTATGGCCAGGCCGGAC	0	117	1
GAGACCCTACCCAGGCTGTGGGAGGCCATGTG	0	159	1
CTGTGGGAGGCCATGTGTTGGGCCACGCTCCC	0	174	1
GGGCCACGCTCCCGGCGTCAGGGTGTACCTCA	0	193	1
TCCACACTTGCCCGAGGGTGAGACGGTCTTCG	0	268	1
TGTAGACCTCTCAGGGTGTAGGCAGTC     	2	5	0
GCCATAATATCCCGGGGAGAATCCTCTAATAG	2	124	1
TAGCTGAGGCGCTGGTATTGGGCTGAGAGGCC	2	153	1
ACCTGCATCCCCTGCGGCGCGGGCCTCTCAGC	2	174	0
CGCAGGGGATGCAGGTTTGGGCGCCGAGTCTA	2	190	1
          ******  ****
MAP Score: 11.3269

Motif 3
        CAGAGCAGAGTTCCCCGGCAGGGAGAACC	0	2	1
CCGGCAGGGAGAACCTGGCTATGAGGCAGCAGCTGCT	0	24	1
ACAGACATCTCCACCAGCTCATGAGGCTTGCAGACAT	0	63	1
TTATAACTAACCAGGTTATGGCCAGGCCGGACGTCTT	0	117	1
CGTCTTCTACGGAGACCCTACCCAGGCTGTGGGAGGC	0	148	1
TGTGGGAGGCCATGTGTTGGGCCACGCTCCCGGCGTC	0	175	1
TGCTCTTCTTGAGGTACACCCTGACGCCGGGAGCGTG	0	197	0
CCCTTGCTATCCTCTTGTTCCCCCTGCTCTTCTTGAG	0	221	0
AGTAGACGCTCCACACTTGCCCGAGGGTGAGACGGTC	0	259	1
TCGGGAAGCCGAACAGATGAGCCAGCCGCTTAACCGT	2	75	0
TCGGCTTCCCGAAATAACTAGCCAGCCATAATATCCC	2	100	1
CGGGGAGAATCCTCTAATAGCTGAGGCGCTGGTATTG	2	136	1
ATCCCCTGCGGCGCGGGCCTCTCAGCCCAATACCAGC	2	163	0
          ** *      *******
MAP Score: 10.5584

Motif 4
        CAGAGCAGAGTTCCCCGGCAGGGAGAACCTGGCTA	0	2	1
ACAGACATCTCCACCAGCTCATGAGGCTTGCAGACATTTTCAA	0	63	1
TTATAACTAACCAGGTTATGGCCAGGCCGGACGTCTTCTACGG	0	117	1
ACATGGCCTCCCACAGCCTGGGTAGGGTCTCCGTAGAAGACGT	0	147	0
TCTTCTTGAGGTACACCCTGACGCCGGGAGCGTGGCCCAACAC	0	188	0
GCAGGGGGAACAAGAGGATAGCAAGGGTAGTAGACGCTCCACA	0	231	1
GTAGTAGACGCTCCACACTTGCCCGAGGGTGAGACGGTCTTCG	0	257	1
TACAGCATTTGTAGAGCCTAATAAGGCTGGACTGTTGTTTAAA	2	33	1
ATATTATGGCTGGCTAGTTATTTCGGGAAGCCGAACAGATGAG	2	91	0
CGGGGAGAATCCTCTAATAGCTGAGGCGCTGGTATTGGGCTGA	2	136	1
CGCTGGTATTGGGCTGAGAGGCCCGCGCCGCAGGGGATGCAGG	2	162	1
ATGCAGGTTTGGGCGCCGAGTCTAGGGTCTATGTTTTA     	2	198	1
          *  *    *  * ****  *  *
MAP Score: 6.02293

Motif 5
GACCCTACCCAGGCTGTGGGAGGCCATGTGTTGGGCCACGCTCCC	0	161	1
GTTCCCCGGCAGGGAGAACCTGGCTATGAGGCAGCAGCTGCTCAA	0	19	1
GGCTCTACAAATGCTGTAGACCTCTCAGGGTGTAGGCAGTC    	2	6	0
GCCGCAGGGGATGCAGGTTTGGGCGCCGAGTCTAGGGTCTATGTT	2	188	1
CACTTGCCCGAGGGTGAGACGGTCTTCGCCATAACGGA       	0	272	1
TCCCGGCGTCAGGGTGTACCTCAAGAAGAGCAGGGGGAACAAGAG	0	202	1
CGCTGGTATTGGGCTGAGAGGCCCGCGCCGCAGGGGATGCAGGTT	2	162	1
GGTTATGGCCAGGCCGGACGTCTTCTACGGAGACCCTACCCAGGC	0	130	1
ATAACTAGCCAGCCATAATATCCCGGGGAGAATCCTCTAATAGCT	2	113	1
GAGGATAGCAAGGGTAGTAGACGCTCCACACTTGCCCGAGGGTGA	0	244	1
CCAGCTCATGAGGCTTGCAGACATTTTCAACGTAGCTGTGGTTAT	0	76	1
          **** *     * *   * *    *
MAP Score: 5.72265

Motif 6
AGCAGAGTTCCCCGGCAGGGAGAACCTGGCTATG	0	13	1
GCAGGGAGAACCTGGCTATGAGGCAGCAGCTGCT	0	27	1
GACATCTCCACCAGCTCATGAGGCTTGCAGACAT	0	66	1
CAGGTTATGGCCAGGCCGGACGTCTTCTACGGAG	0	128	1
GAGACCCTACCCAGGCTGTGGGAGGCCATGTGTT	0	159	1
ACGCTCCACACTTGCCCGAGGGTGAGACGGTCTT	0	264	1
CTGTTGTTTAAACGGTTAAGCGGCTGGCTCATCT	2	64	1
GGCGCTGGTATTGGGCTGAGAGGCCCGCGCCGCA	2	160	1
GGATGCAGGTTTGGGCGCCGAGTCTAGGGTCTAT	2	196	1
          ** *** * *** *
MAP Score: 5.53469

Motif 7
CAGAGCAGAGTTCCCCGGCAGGGAGAACCTGGCTATGAG	0	10	1
ACCAGCTCATGAGGCTTGCAGACATTTTCAACGTAGCTG	0	75	1
AACCAGGTTATGGCCAGGCCGGACGTCTTCTACGGAGAC	0	125	1
ACGGAGACCCTACCCAGGCTGTGGGAGGCCATGTGTTGG	0	156	1
GGTACACCCTGACGCCGGGAGCGTGGCCCAACACATGGC	0	183	0
CTCCACACTTGCCCGAGGGTGAGACGGTCTTCGCCATAA	0	267	1
AAACGGTTAAGCGGCTGGCTCATCTGTTCGGCTTCCCGA	2	73	1
CATCCCCTGCGGCGCGGGCCTCTCAGCCCAATACCAGCG	2	162	0
          * *** *** *      **
MAP Score: 4.33447

Motif 8
        CAGAGCAGAGTTCCCCGGCAGGGAGAACCTG	0	2	1
CCGGCAGGGAGAACCTGGCTATGAGGCAGCAGCTGCTCA	0	24	1
TTATAACTAACCAGGTTATGGCCAGGCCGGACGTCTTCT	0	117	1
CGTCTTCTACGGAGACCCTACCCAGGCTGTGGGAGGCCA	0	148	1
CCAGGCTGTGGGAGGCCATGTGTTGGGCCACGCTCCCGG	0	169	1
TCTTGAGGTACACCCTGACGCCGGGAGCGTGGCCCAACA	0	189	0
TCAGGGTGTACCTCAAGAAGAGCAGGGGGAACAAGAGGA	0	210	1
GTCTCACCCTCGGGCAAGTGTGGAGCGTCTACTACCCTT	0	253	0
ATGCTGTAGACCTCTCAGGGTGTAGGCAGTC        	2	2	0
TCGGGAAGCCGAACAGATGAGCCAGCCGCTTAACCGTTT	2	73	0
AGAGGATTCTCCCCGGGATATTATGGCTGGCTAGTTATT	2	112	0
CGGGGAGAATCCTCTAATAGCTGAGGCGCTGGTATTGGG	2	136	1
CGCTGGTATTGGGCTGAGAGGCCCGCGCCGCAGGGGATG	2	162	1
CCGCGCCGCAGGGGATGCAGGTTTGGGCGCCGAGTCTAG	2	184	1
          ** *     * ** *** *
MAP Score: 2.75208

Motif 9
       CAGAGCAGAGTTCCCCGGCAGGGAGAACCTGGCTA	0	3	1
CTGCTCAACAGACATCTCCACCAGCTCATGAGGCTTGCAGAC	0	56	1
TATAACTAACCAGGTTATGGCCAGGCCGGACGTCTTCTACGG	0	118	1
GTCTTCTACGGAGACCCTACCCAGGCTGTGGGAGGCCATGTG	0	149	1
GCCATGTGTTGGGCCACGCTCCCGGCGTCAGGGTGTACCTCA	0	183	1
AAGGGTAGTAGACGCTCCACACTTGCCCGAGGGTGAGACGGT	0	253	1
TTAAGCGGCTGGCTCATCTGTTCGGCTTCCCGAAATAACTAG	2	79	1
TAATAGCTGAGGCGCTGGTATTGGGCTGAGAGGCCCGCGCCG	2	150	1
TCGGCGCCCAAACCTGCATCCCCTGCGGCGCGGGCCTCTCAG	2	175	0
          *** *      * ***   * *
MAP Score: 2.14748

Motif 10
GAGTTCCCCGGCAGGGAGAACCTGGCTATGAGGCAGCAGCTGC	0	17	1
CTGCTCAACAGACATCTCCACCAGCTCATGAGGCTTGCAGACA	0	56	1
CCAGGTTATGGCCAGGCCGGACGTCTTCTACGGAGACCCTACC	0	127	1
CCATGTGTTGGGCCACGCTCCCGGCGTCAGGGTGTACCTCAAG	0	184	1
  TCCGTTATGGCGAAGACCGTCTCACCCTCGGGCAAGTGTGG	0	269	0
CATTTGTAGAGCCTAATAAGGCTGGACTGTTGTTTAAACGGTT	2	38	1
GCTGGTATTGGGCTGAGAGGCCCGCGCCGCAGGGGATGCAGGT	2	163	1
TGCAGGTTTGGGCGCCGAGTCTAGGGTCTATGTTTTA      	2	199	1
          ***       ** ** *    **
MAP Score: 2.13074

Motif 11
ACAGACATCTCCACCAGCTCATGAGGCTTGCAGACATTTTCAA	0	63	1
TTATAACTAACCAGGTTATGGCCAGGCCGGACGTCTTCTACGG	0	117	1
GGAGACCCTACCCAGGCTGTGGGAGGCCATGTGTTGGGCCACG	0	158	1
TCTTGTTCCCCCTGCTCTTCTTGAGGTACACCCTGACGCCGGG	0	203	0
AGTAGACGCTCCACACTTGCCCGAGGGTGAGACGGTCTTCGCC	0	259	1
     GACTGCCTACACCCTGAGAGGTCTACAGCATTTGTAGA	2	5	1
GGACTGTTGTTTAAACGGTTAAGCGGCTGGCTCATCTGTTCGG	2	61	1
CGGGGAGAATCCTCTAATAGCTGAGGCGCTGGTATTGGGCTGA	2	136	1
TGAGGCGCTGGTATTGGGCTGAGAGGCCCGCGCCGCAGGGGAT	2	157	1
          **       *  *****   * *
MAP Score: 1.49868

Motif 12
   CAGAGCAGAGTTCCCCGGCAGGGAGAACCTGGCTATGA	0	7	1
GAACCTGGCTATGAGGCAGCAGCTGCTCAACAGACATCTCC	0	34	1
TATAACTAACCAGGTTATGGCCAGGCCGGACGTCTTCTACG	0	118	1
GTCTTCTACGGAGACCCTACCCAGGCTGTGGGAGGCCATGT	0	149	1
GTGGGAGGCCATGTGTTGGGCCACGCTCCCGGCGTCAGGGT	0	176	1
CAGGGTGTACCTCAAGAAGAGCAGGGGGAACAAGAGGATAG	0	211	1
AAGGGTAGTAGACGCTCCACACTTGCCCGAGGGTGAGACGG	0	253	1
        GACTGCCTACACCCTGAGAGGTCTACAGCATTT	2	2	1
GTTGTTTAAACGGTTAAGCGGCTGGCTCATCTGTTCGGCTT	2	66	1
GGGGAGAATCCTCTAATAGCTGAGGCGCTGGTATTGGGCTG	2	137	1
CGCTGGTATTGGGCTGAGAGGCCCGCGCCGCAGGGGATGCA	2	162	1
CGCGCCGCAGGGGATGCAGGTTTGGGCGCCGAGTCTAGGGT	2	185	1
          * *     ** * *** *  *
MAP Score: 0.646815