AlignACE 3.0 10/20/99
AlignACE2 -i AP/AP_operons025_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944249767
 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
TGTCTGTTGAGCAGCTGCTGCCTCATAGCCAGGTTCTCCCTGC	0	27	0
ATGTCTGCAAGCCTCATGAGCTGGTGGAGATGTCTGTTGAGCA	0	57	0
ACCAGGTTATGGCCAGGCCGGACGTCTTCTACGGAGACCCTAC	0	126	1
CGGAGACCCTACCCAGGCTGTGGGAGGCCATGTGTTGGGCCAC	0	157	1
CCATGTGTTGGGCCACGCTCCCGGCGTCAGGGTGTACCTCAAG	0	184	1
GTGTACCTCAAGAAGAGCAGGGGGAACAAGAGGATAGCAAGGG	0	215	1
TAGACGCTCCACACTTGCCCGAGGGTGAGACGGTCTTCGCCAT	0	261	1
ATTAGGCTCTACAAATGCTGTAGACCTCTCAGGGTGTAGGCAG	2	12	0
TTGTTTAAACGGTTAAGCGGCTGGCTCATCTGTTCGGCTTCCC	2	67	1
AGCTATTAGAGGATTCTCCCCGGGATATTATGGCTGGCTAGTT	2	115	0
ATCCTCTAATAGCTGAGGCGCTGGTATTGGGCTGAGAGGCCCG	2	144	1
GGGCTGAGAGGCCCGCGCCGCAGGGGATGCAGGTTTGGGCGCC	2	172	1
          **    ** ** **       **
MAP Score: 15.8668

Motif 2
CCAGGTTCTCCCTGCCGGGGAACTCTGCTCTG          	0	0	0
GCAGGGAGAACCTGGCTATGAGGCAGCAGCTGCTCAACAGAC	0	27	1
GACATCTCCACCAGCTCATGAGGCTTGCAGACATTTTCAACG	0	66	1
CAGGTTATGGCCAGGCCGGACGTCTTCTACGGAGACCCTACC	0	128	1
GAGACCCTACCCAGGCTGTGGGAGGCCATGTGTTGGGCCACG	0	159	1
TGAGGTACACCCTGACGCCGGGAGCGTGGCCCAACACATGGC	0	183	0
ACGCTCCACACTTGCCCGAGGGTGAGACGGTCTTCGCCATAA	0	264	1
    GACTGCCTACACCCTGAGAGGTCTACAGCATTTGTAGA	2	6	1
AAATAACTAGCCAGCCATAATATCCCGGGGAGAATCCTCTAA	2	111	1
GGCGCTGGTATTGGGCTGAGAGGCCCGCGCCGCAGGGGATGC	2	160	1
AACATAGACCCTAGACTCGGCGCCCAAACCTGCATCCCCTGC	2	191	0
          ** ***   * * *     * *
MAP Score: 15.7943

Motif 3
GAGCAGAGTTCCCCGGCAGGGAGAACCTGGCTA	0	12	1
GGAGACCCTACCCAGGCTGTGGGAGGCCATGTG	0	158	1
TACACCCTGACGCCGGGAGCGTGGCCCAACACA	0	187	0
CCAGGTTATGGCCAGGCCGGACGTCTTCTACGG	0	127	1
GGCTGAGAGGCCCGCGCCGCAGGGGATGCAGGT	2	173	1
GCCATAATATCCCGGGGAGAATCCTCTAATAGC	2	124	1
CTCCACACTTGCCCGAGGGTGAGACGGTCTTCG	0	267	1
CTGTAGACCTCTCAGGGTGTAGGCAGTC     	2	5	0
CAGGTTTGGGCGCCGAGTCTAGGGTCTATGTTT	2	201	1
          ******* * * *
MAP Score: 14.3151

Motif 4
    CAGAGCAGAGTTCCCCGGCAGGGAGAAC	0	6	1
GTTCCCCGGCAGGGAGAACCTGGCTATGAGGC	0	19	1
CCTGGCTATGAGGCAGCAGCTGCTCAACAGAC	0	37	1
AACCAGGTTATGGCCAGGCCGGACGTCTTCTA	0	125	1
GACGTCTTCTACGGAGACCCTACCCAGGCTGT	0	146	1
ACCCAGGCTGTGGGAGGCCATGTGTTGGGCCA	0	167	1
TCCCGGCGTCAGGGTGTACCTCAAGAAGAGCA	0	202	1
CAAGAAGAGCAGGGGGAACAAGAGGATAGCAA	0	223	1
CACTTGCCCGAGGGTGAGACGGTCTTCGCCAT	0	272	1
GAGACGGTCTTCGCCATAACGGA         	0	287	1
  TAAAGCTTTCGCGAGAGCTGTTTAAATCAC	1	12	0
TGTTGTTTAAACGGTTAAGCGGCTGGCTCATC	2	65	1
GCTAGTTATTTCGGGAAGCCGAACAGATGAGC	2	90	0
GCGCTGGTATTGGGCTGAGAGGCCCGCGCCGC	2	161	1
CCCGCGCCGCAGGGGATGCAGGTTTGGGCGCC	2	183	1
          **** * *****
MAP Score: 10.0135

Motif 5
        CAGAGCAGAGTTCCCCGGCAGGGAGAACCTGG	0	2	1
GTTCCCCGGCAGGGAGAACCTGGCTATGAGGCAGCAGCTG	0	19	1
GATGTCTGTTGAGCAGCTGCTGCCTCATAGCCAGGTTCTC	0	32	0
TAACTAACCAGGTTATGGCCAGGCCGGACGTCTTCTACGG	0	120	1
CCCACAGCCTGGGTAGGGTCTCCGTAGAAGACGTCCGGCC	0	141	0
GACCCTACCCAGGCTGTGGGAGGCCATGTGTTGGGCCACG	0	161	1
GGGAGGCCATGTGTTGGGCCACGCTCCCGGCGTCAGGGTG	0	178	1
GGTGTACCTCAAGAAGAGCAGGGGGAACAAGAGGATAGCA	0	214	1
GGGGGAACAAGAGGATAGCAAGGGTAGTAGACGCTCCACA	0	234	1
GCCCGAGGGTGAGACGGTCTTCGCCATAACGGA       	0	277	1
TGTTTAAACGGTTAAGCGGCTGGCTCATCTGTTCGGCTTC	2	68	1
CTGGTATTGGGCTGAGAGGCCCGCGCCGCAGGGGATGCAG	2	164	1
GCCGCAGGGGATGCAGGTTTGGGCGCCGAGTCTAGGGTCT	2	188	1
          * * ** **  ***     *
MAP Score: 6.81498

Motif 6
GCAGAGTTCCCCGGCAGGGAGAACCTGGCTATGAGGCAGCAGCTGCT	0	14	1
ACCAGCTCATGAGGCTTGCAGACATTTTCAACGTAGCTGTGGTTATA	0	75	1
AGGTTATGGCCAGGCCGGACGTCTTCTACGGAGACCCTACCCAGGCT	0	129	1
AGACCCTACCCAGGCTGTGGGAGGCCATGTGTTGGGCCACGCTCCCG	0	160	1
AAACGGTTAAGCGGCTGGCTCATCTGTTCGGCTTCCCGAAATAACTA	2	73	1
TAATAGCTGAGGCGCTGGTATTGGGCTGAGAGGCCCGCGCCGCAGGG	2	150	1
AGAGGCCCGCGCCGCAGGGGATGCAGGTTTGGGCGCCGAGTCTAGGG	2	178	1
          * *** **            * *  **
MAP Score: 4.26578

Motif 7
        CAGAGCAGAGTTCCCCGGCAGGGAGAACCTG	0	2	1
TGAGCAGCTGCTGCCTCATAGCCAGGTTCTCCCTGCCGG	0	24	0
TTATAACTAACCAGGTTATGGCCAGGCCGGACGTCTTCT	0	117	1
CGGACGTCTTCTACGGAGACCCTACCCAGGCTGTGGGAG	0	144	1
GCCATGTGTTGGGCCACGCTCCCGGCGTCAGGGTGTACC	0	183	1
TCAGGGTGTACCTCAAGAAGAGCAGGGGGAACAAGAGGA	0	210	1
GTCTCACCCTCGGGCAAGTGTGGAGCGTCTACTACCCTT	0	253	0
ATGCTGTAGACCTCTCAGGGTGTAGGCAGTC        	2	2	0
CCTGAGAGGTCTACAGCATTTGTAGAGCCTAATAAGGCT	2	22	1
TCGGGAAGCCGAACAGATGAGCCAGCCGCTTAACCGTTT	2	73	0
CTGTTCGGCTTCCCGAAATAACTAGCCAGCCATAATATC	2	96	1
CGCGGGCCTCTCAGCCCAATACCAGCGCCTCAGCTATTA	2	150	0
AAACCTGCATCCCCTGCGGCGCGGGCCTCTCAGCCCAAT	2	169	0
ATGCAGGTTTGGGCGCCGAGTCTAGGGTCTATGTTTTA 	2	198	1
          *  *   *   ****** *
MAP Score: 3.95752

Motif 8
CAGGTTCTCCCTGCCGGGGAACTCTGCTCTG        	0	2	0
CCGGCAGGGAGAACCTGGCTATGAGGCAGCAGCTGCTCA	0	24	1
AAAATGTCTGCAAGCCTCATGAGCTGGTGGAGATGTCTG	0	64	0
TAGAAGACGTCCGGCCTGGCCATAACCTGGTTAGTTATA	0	118	0
TACGGAGACCCTACCCAGGCTGTGGGAGGCCATGTGTTG	0	155	1
GCCATGTGTTGGGCCACGCTCCCGGCGTCAGGGTGTACC	0	183	1
GCGTCAGGGTGTACCTCAAGAAGAGCAGGGGGAACAAGA	0	207	1
GTCTCACCCTCGGGCAAGTGTGGAGCGTCTACTACCCTT	0	253	0
        GACTGCCTACACCCTGAGAGGTCTACAGCAT	2	2	1
AGCATTTGTAGAGCCTAATAAGGCTGGACTGTTGTTTAA	2	36	1
AAACGGTTAAGCGGCTGGCTCATCTGTTCGGCTTCCCGA	2	73	1
AATAACTAGCCAGCCATAATATCCCGGGGAGAATCCTCT	2	112	1
ATTGGGCTGAGAGGCCCGCGCCGCAGGGGATGCAGGTTT	2	169	1
ATGCAGGTTTGGGCGCCGAGTCTAGGGTCTATGTTTTA 	2	198	1
          * ***  *    ** * **
MAP Score: 3.35017

Motif 9
     CAGAGCAGAGTTCCCCGGCAGGGAGAACC	0	5	1
GCAGCTGCTGCCTCATAGCCAGGTTCTCCCTGCC	0	26	0
TCTCCACCAGCTCATGAGGCTTGCAGACATTTTC	0	70	1
TAACTAACCAGGTTATGGCCAGGCCGGACGTCTT	0	120	1
CTTCTACGGAGACCCTACCCAGGCTGTGGGAGGC	0	151	1
GGGAGGCCATGTGTTGGGCCACGCTCCCGGCGTC	0	178	1
TTGCTATCCTCTTGTTCCCCCTGCTCTTCTTGAG	0	221	0
GTGTGGAGCGTCTACTACCCTTGCTATCCTCTTG	0	241	0
TGGCGAAGACCGTCTCACCCTCGGGCAAGTGTGG	0	269	0
AGACCTCTCAGGGTGTAGGCAGTC          	2	0	0
TGTTTAAACGGTTAAGCGGCTGGCTCATCTGTTC	2	68	1
ACTAGCCAGCCATAATATCCCGGGGAGAATCCTC	2	116	1
TCCTCTAATAGCTGAGGCGCTGGTATTGGGCTGA	2	145	1
CTGGTATTGGGCTGAGAGGCCCGCGCCGCAGGGG	2	164	1
GCGCCCAAACCTGCATCCCCTGCGGCGCGGGCCT	2	180	0
ACATAGACCCTAGACTCGGCGCCCAAACCTGCAT	2	198	0
          * *  ***** ***
MAP Score: 2.6652

Motif 10
         CAGAGCAGAGTTCCCCGGCAGGGAGAACCTG	0	1	1
CCCGGCAGGGAGAACCTGGCTATGAGGCAGCAGCTGCTCA	0	23	1
AAAATGTCTGCAAGCCTCATGAGCTGGTGGAGATGTCTGT	0	63	0
TAGAAGACGTCCGGCCTGGCCATAACCTGGTTAGTTATAA	0	117	0
ATGGCCTCCCACAGCCTGGGTAGGGTCTCCGTAGAAGACG	0	148	0
ACGCCGGGAGCGTGGCCCAACACATGGCCTCCCACAGCCT	0	171	0
TACCTCAAGAAGAGCAGGGGGAACAAGAGGATAGCAAGGG	0	218	1
GGGTAGTAGACGCTCCACACTTGCCCGAGGGTGAGACGGT	0	255	1
         GACTGCCTACACCCTGAGAGGTCTACAGCAT	2	1	1
TAAACGGTTAAGCGGCTGGCTCATCTGTTCGGCTTCCCGA	2	72	1
AAATAACTAGCCAGCCATAATATCCCGGGGAGAATCCTCT	2	111	1
GCCCAATACCAGCGCCTCAGCTATTAGAGGATTCTCCCCG	2	136	0
TATTGGGCTGAGAGGCCCGCGCCGCAGGGGATGCAGGTTT	2	168	1
  TAAAACATAGACCCTAGACTCGGCGCCCAAACCTGCAT	2	198	0
          ** ***  * *     * **
MAP Score: 2.61981

Motif 11
         CAGAGCAGAGTTCCCCGGCAGGGAGAACC	0	1	1
TTGAGCAGCTGCTGCCTCATAGCCAGGTTCTCCCTGCC	0	26	0
GACATCTCCACCAGCTCATGAGGCTTGCAGACATTTTC	0	66	1
GTTATAACTAACCAGGTTATGGCCAGGCCGGACGTCTT	0	116	1
ACGTCTTCTACGGAGACCCTACCCAGGCTGTGGGAGGC	0	147	1
GGGAGCGTGGCCCAACACATGGCCTCCCACAGCCTGGG	0	168	0
GTGTTGGGCCACGCTCCCGGCGTCAGGGTGTACCTCAA	0	188	1
TCAGGGTGTACCTCAAGAAGAGCAGGGGGAACAAGAGG	0	210	1
AGCAGGGGGAACAAGAGGATAGCAAGGGTAGTAGACGC	0	230	1
GGTAGTAGACGCTCCACACTTGCCCGAGGGTGAGACGG	0	256	1
TTCGGGAAGCCGAACAGATGAGCCAGCCGCTTAACCGT	2	75	0
TTCGGCTTCCCGAAATAACTAGCCAGCCATAATATCCC	2	99	1
CTCAGCTATTAGAGGATTCTCCCCGGGATATTATGGCT	2	123	0
GCCTCTCAGCCCAATACCAGCGCCTCAGCTATTAGAGG	2	146	0
ATTGGGCTGAGAGGCCCGCGCCGCAGGGGATGCAGGTT	2	169	1
TAAAACATAGACCCTAGACTCGGCGCCCAAACCTGCAT	2	198	0
          ** *     * *** ***
MAP Score: 2.37492