AlignACE 3.0 10/20/99
AlignACE2 -i AP/AP_operons031_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944249837
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	APE0986	193	215aa long hypothetical protein
#1	APE1366	33	157aa long hypothetical 6,7-dimethyl-8-ribityllumazine synthase
#2	APES051	52	56aa long hypothetical protein
#3	APE1454	300	835aa long hypothetical cation-transporting ATPase
#4	APE2112	167	194aa long hypothetical protein
#5	APE2571	75	621aa long hypothetical heavy-metal transporting ATPase

Motif 1
TCTATATAACTGAGTCTAGGGCCTTGGGGAGTAATAT	0	36	0
GTTATATAGATGGATGGGAGGCTTCGGCCTTCTGGAT	0	63	1
TTCTGGATTGGGACGCGGTGTCCCGGGTAAGGTGTCG	0	92	1
TCCCGGGTAAGGTGTCGGCGGCTTGGAGGGCAGGTAT	0	112	1
CTAGTCTAGAGGGTTCCATCGCTAGGGCTGTCGATTC	0	153	1
ATTTGGATGTTCATGGCGGCGCGAGGAGCTGTATCTA	3	27	0
TCCAAATTAGTCTCTCCAGGGCTGAGGGCTGGCGATA	3	57	1
GGCTGAGGGCTGGCGATACTTCCTGGGTCTCACCACA	3	76	1
ACACGTCAGTAGAATCAGGAGCTGTGGAAGTAATACC	3	110	1
GAATGTAGTTTGCTGGAGTTTCCTAGGTATTACTTCC	3	135	0
TCTAGTCTAGTGTTTCTACTGCGGTTGTTAGAGGACC	3	170	1
      TTCTGGAAGAAGATGACGGGGAGCCGGTGGC	4	4	1
ACGGGGAGCCGGTGGCTGTGGCTCAGGAACAATCTTA	4	25	1
CAACTCTGGAGGCTTCGGGCGAGAGGAGGGGTATGAT	4	118	0
          **  ** *  ***  **
MAP Score: 13.7282

Motif 2
TATATAACTGAGTCTAGGGCCTTGGGGAGTAATATTT	0	34	0
GATGGATGGGAGGCTTCGGCCTTCTGGATTGGGACGC	0	71	1
CTTCTGGATTGGGACGCGGTGTCCCGGGTAAGGTGTC	0	91	1
GTCCCGGGTAAGGTGTCGGCGGCTTGGAGGGCAGGTA	0	111	1
TTAAATACGGGAGTTTTGGAGGTGAGGATGAA     	2	5	0
AGTCTCTCCAGGGCTGAGGGCTGGCGATACTTCCTGG	3	65	1
ACACGTCAGTAGAATCAGGAGCTGTGGAAGTAATACC	3	110	1
TTCTGGAAGAAGATGACGGGGAGCCGGTGGCTGTGGC	4	10	1
TCAACTCTGGAGGCTTCGGGCGAGAGGAGGGGTATGA	4	119	0
          *** *  ** *  * **
MAP Score: 13.404

Motif 3
TCTATATAACTGAGTCTAGGGCCTTGGGGAGTAATA	0	37	0
TAGATGGATGGGAGGCTTCGGCCTTCTGGATTGGGA	0	69	1
ACCTTACCCGGGACACCGCGTCCCAATCCAGAAGGC	0	89	0
TCCCGGGTAAGGTGTCGGCGGCTTGGAGGGCAGGTA	0	112	1
CGTTCCTCAGAGAATCGACAGCCCTAGCGATGGAAC	0	165	0
AGACCCAGGAAGTATCGCCAGCCCTCAGCCCTGGAG	3	70	0
ACACGTCAGTAGAATCAGGAGCTGTGGAAGTAATAC	3	110	1
GTAATACCTAGGAAACTCCAGCAAACTACATTCTAG	3	139	1
CAACCGCAGTAGAAACACTAGACTAGAATGTAGTTT	3	161	0
AAGATGACGGGGAGCCGGTGGCTGTGGCTCAGGAAC	4	19	1
GCCAGCTGATAGACACTGTGGTCTTCCTATCACTAG	4	74	1
GCTCAACTCTGGAGGCTTCGGGCGAGAGGAGGGGTA	4	122	0
          ***  *  *****  *
MAP Score: 10.2445

Motif 4
CTCCAGAGTTGAGCCCGTCAGCCTGTCTACACT       	4	144	1
CTGAGCCACAGCCACCGGCTCCCCGTCATCTTCTTCCAGA	4	11	0
CTAAATATTACTCCCCAAGGCCCTAGACTCAGTTATATAG	0	32	1
AGGCTTATACCTGCCCTCCAAGCCGCCGACACCTTACCCG	0	115	0
GAAGTATCGCCAGCCCTCAGCCCTGGAGAGACTAATTTGG	3	58	0
TACATCATACCCCTCCTCTCGCCCGAAGCCTCCAGAGTTG	4	115	1
AATCAAGTAACACCCCTTTATACTATCTCCTCAAATTAGT	3	263	0
CCTTACCCGGGACACCGCGTCCCAATCCAGAAGGCCGAAG	0	84	0
AAACTAGATACAGCTCCTCGCGCCGCCATGAACATCCAAA	3	23	1
AGAGAATCGACAGCCCTAGCGATGGAACCCTCTAGACTAG	0	153	0
          * ****     ** * *  *
MAP Score: 9.5372

Motif 5
CTAAATATTACTCCCCAAGGCCCTAGACTCA	0	32	1
TTACCCGGGACACCGCGTCCCAATCCAGAAG	0	91	0
TATACCTGCCCTCCAAGCCGCCGACACCTTA	0	119	0
TCCTCAGAGAATCGACAGCCCTAGCGATGGA	0	167	0
       TTCATCCTCACCTCCAAAACTCCC	2	3	1
CTAGATACAGCTCCTCGCGCCGCCATGAACA	3	26	1
CCAAATTAGTCTCTCCAGGGCTGAGGGCTGG	3	58	1
CCCAGGAAGTATCGCCAGCCCTCAGCCCTGG	3	72	0
TCCTGGGTCTCACCACACGTCAGTAGAATCA	3	96	1
TAGGTATTACTTCCACAGCTCCTGATTCTAC	3	118	0
CATCATACCCCTCCTCTCGCCCGAAGCCTCC	4	117	1
          **** ******
MAP Score: 9.41035

Motif 6
CGACACCTTACCCGGGACACCGCGTCCCAATCCAGAAGGC	0	89	0
CTTATACCTGCCCTCCAAGCCGCCGACACCTTACCCGGGA	0	112	0
        TTCATCCTCACCTCCAAAACTCCCGTATTTAA	2	2	1
   CTCTAAACCTTAAAAACTAGATACAGCTCCTCGCGCC	3	7	1
GGCGATACTTCCTGGGTCTCACCACACGTCAGTAGAATCA	3	87	1
GGAAGTAATACCTAGGAAACTCCAGCAAACTACATTCTAG	3	135	1
         ACCCGACAATCAAGTAACACCCCTTTATACT	3	279	0
GCCACCGGCTCCCCGTCATCTTCTTCCAGAA         	4	1	0
TAAGATTGTTCCTGAGCCACAGCCACCGGCTCCCCGTCAT	4	22	0
TAGCATTCTACATCATACCCCTCCTCTCGCCCGAAGCCTC	4	107	1
          ***   ** *  *  **  *
MAP Score: 7.15569

Motif 7
CTAAATATTACTCCCCAAGGCCCTAGACTCAGTTATAT	0	32	1
AAGGCCGAAGCCTCCCATCCATCTATATAACTGAGTCT	0	56	0
TTATACCTGCCCTCCAAGCCGCCGACACCTTACCCGGG	0	113	0
        TTCATCCTCACCTCCAAAACTCCCGTATTT	2	2	1
AGATACAGCTCCTCGCGCCGCCATGAACATCCAAATTA	3	28	1
GCTGGCGATACTTCCTGGGTCTCACCACACGTCAGTAG	3	84	1
CTAGGTATTACTTCCACAGCTCCTGATTCTACTGACGT	3	112	0
ACACTGTGGTCTTCCTATCACTAGCATTCTACATCATA	4	86	1
ACATCATACCCCTCCTCTCGCCCGAAGCCTCCAGAGTT	4	116	1
AGAGTTGAGCCCGTCAGCCTGTCTACACT         	4	148	1
          *****   *  **   **
MAP Score: 5.01674

Motif 8
TAAATATTACTCCCCAAGGCCCTAGACTCAGTTATATAG	0	33	1
CGCGTCCCAATCCAGAAGGCCGAAGCCTCCCATCCATCT	0	70	0
CTTATACCTGCCCTCCAAGCCGCCGACACCTTACCCGGG	0	113	0
TTCATCCTCACCTCCAAAACTCCCGTATTTAAACTATTT	2	10	1
TAGATACAGCTCCTCGCGCCGCCATGAACATCCAAATTA	3	27	1
GTATCGCCAGCCCTCAGCCCTGGAGAGACTAATTTGGAT	3	56	0
CCTGGGTCTCACCACACGTCAGTAGAATCAGGAGCTGTG	3	97	1
GGAAGTAATACCTAGGAAACTCCAGCAAACTACATTCTA	3	135	1
TGAGCCACAGCCACCGGCTCCCCGTCATCTTCTTCCAGA	4	11	0
GACACTGTGGTCTTCCTATCACTAGCATTCTACATCATA	4	85	1
TACATCATACCCCTCCTCTCGCCCGAAGCCTCCAGAGTT	4	115	1
          *** **   * *  * * *
MAP Score: 4.92815

Motif 9
ATATAACTGAGTCTAGGGCCTTGGGGAGTAATAT	0	36	0
TCGGCCTTCTGGATTGGGACGCGGTGTCCCGGGT	0	86	1
AGGGTTCCATCGCTAGGGCTGTCGATTCTCTGAG	0	162	1
AAATTAGTCTCTCCAGGGCTGAGGGCTGGCGATA	3	60	1
CGTCAGTAGAATCAGGAGCTGTGGAAGTAATACC	3	113	1
ATGACGGGGAGCCGGTGGCTGTGGCTCAGGAACA	4	22	1
AACAATCTTAGCACGTGGGTGAGCCAGCTGATAG	4	52	1
GGAGGCTTCGGGCGAGAGGAGGGGTATGATGTAG	4	114	0
CGCCCGAAGCCTCCAGAGTTGAGCCCGTCAGCCT	4	134	1
          * * **** ** **
MAP Score: 4.52688

Motif 10
CTGAGTCTAGGGCCTTGGGGAGTAATATTTAGGCG	0	29	0
TTATATAGATGGATGGGAGGCTTCGGCCTTCTGGA	0	64	1
GGGAGGCTTCGGCCTTCTGGATTGGGACGCGGTGT	0	78	1
TTCTGGATTGGGACGCGGTGTCCCGGGTAAGGTGT	0	92	1
TCCCGGGTAAGGTGTCGGCGGCTTGGAGGGCAGGT	0	112	1
TCGGCGGCTTGGAGGGCAGGTATAAGCCTAGTCTA	0	126	1
CGGGAGTTTTGGAGGTGAGGATGAA          	2	0	0
GTCTCTCCAGGGCTGAGGGCTGGCGATACTTCCTG	3	66	1
AGTAGAATCAGGAGCTGTGGAAGTAATACCTAGGA	3	117	1
TTCTGGAAGAAGATGACGGGGAGCCGGTGGCTGTG	4	10	1
GGGAGCCGGTGGCTGTGGCTCAGGAACAATCTTAG	4	28	1
GCTTCGGGCGAGAGGAGGGGTATGATGTAGAATGC	4	109	0
AGTGTAGACAGGCTGACGGGCTCAACTCTGGAGGC	4	142	0
          *** * ****  * *
MAP Score: 4.11323

Motif 11
AAATATTACTCCCCAAGGCCCTAGACTCAGTT	0	34	1
AATCCAGAAGGCCGAAGCCTCCCATCCATCTA	0	69	0
CCTTACCCGGGACACCGCGTCCCAATCCAGAA	0	92	0
TATACCTGCCCTCCAAGCCGCCGACACCTTAC	0	118	0
TCATCCTCACCTCCAAAACTCCCGTATTTAAA	2	11	1
CTAGATACAGCTCCTCGCGCCGCCATGAACAT	3	26	1
GTATCGCCAGCCCTCAGCCCTGGAGAGACTAA	3	63	0
CTGAGCCACAGCCACCGGCTCCCCGTCATCTT	4	19	0
CCTCCTCTCGCCCGAAGCCTCCAGAGTTGAGC	4	126	1
          *** ***** **
MAP Score: 3.04288

Motif 12
ATATTACTCCCCAAGGCCCTAGACTCAGTTATATAGATGGATGGGAG	0	36	1
ACCCGGGACACCGCGTCCCAATCCAGAAGGCCGAAGCCTCCCATCCA	0	73	0
ACGCGGTGTCCCGGGTAAGGTGTCGGCGGCTTGGAGGGCAGGTATAA	0	104	1
AATCGACAGCCCTAGCGATGGAACCCTCTAGACTAGGCTTATACCTG	0	142	0
CCTCCAAAACTCCCGTATTTAAACTATTTTCCGGAGGTTATA     	2	20	1
GCCATGAACATCCAAATTAGTCTCTCCAGGGCTGAGGGCTGGCGATA	3	47	1
TGGCGATACTTCCTGGGTCTCACCACACGTCAGTAGAATCAGGAGCT	3	86	1
TACATTCTAGTCTAGTGTTTCTACTGCGGTTGTTAGAGGACCTTGTT	3	165	1
CTACATCATACCCCTCCTCTCGCCCGAAGCCTCCAGAGTTGAGCCCG	4	114	1
          **  *    *   * *  *     ***
MAP Score: 2.97516

Motif 13
GACACCTTACCCGGGACACCGCGTCCCAATCCAGAAGGCC	0	88	0
CTTATACCTGCCCTCCAAGCCGCCGACACCTTACCCGGGA	0	112	0
        TTCATCCTCACCTCCAAAACTCCCGTATTTAA	2	2	1
GGCGATACTTCCTGGGTCTCACCACACGTCAGTAGAATCA	3	87	1
GGAAGTAATACCTAGGAAACTCCAGCAAACTACATTCTAG	3	135	1
TGAGCCACAGCCACCGGCTCCCCGTCATCTTCTTCCAGAA	4	10	0
TACATCATACCCCTCCTCTCGCCCGAAGCCTCCAGAGTTG	4	115	1
          **  *  * * **  **  *
MAP Score: 1.06473