AlignACE 3.0 10/20/99
AlignACE2 -i AP/AP_operons010_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944249416
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	APE0230	192	283aa long hypothetical nucleotide-binding protein
#1	APE0402	62	204aa long hypothetical membrane-associated ATPase gamma chain
#2	APE0404	32	466aa long hypothetical membrane-associated ATPase beta chain
#3	APE0673	121	686aa long hypothetical protein
#4	APE0675	143	117aa long hypothetical methionyl-tRNA synthetase
#5	APE1592	40	475aa long hypothetical cysteinyl-tRNA synthetase

Motif 1
GATGGGACAGCCAATAGGGGGGTTGGCATAAA	0	21	0
GATATATGGATGGGAAGCCGGGATGGGACAGC	0	42	0
TAATTTCTTGTCTACTCAGGAGGGTGGCAGAG	0	117	1
TGAGTACAAGGCTATCGCGGAGCGG       	0	177	1
CTTTATCCACTCTAGCGTGGGAGGTGTAAGGT	1	16	1
GTGCTTTGGCTGTAGACCCGAGGAAA      	1	46	1
          CCTTTACTGTGGCTCTCTAGAC	2	0	1
AGTTCCGCCGGTTACTCCGGAGACTTATTAAT	3	34	0
AAGAAATTCCCGTGGCGCGGAGTTCCGCCGGT	3	54	0
AATTACGCTTGCTCTCCCAGGGCTAATTGGGA	3	86	1
AGGGCTAATTGGGATTGCGGGGGACGG     	3	104	1
CTTGTCCGACCCTTTAGGGGGGTT        	4	2	0
AGCCTGGGGGTGTTGTGAGGAGTTCAGCCTTG	4	30	0
ACCCCCGGAAGGGAGCCTGGGGGTGTTGTGAG	4	43	0
GGGTGTTCAGTGTCGCCTGGGGTCGTCACCCC	4	71	1
CGCCTGGGGTCGTCACCCCGGGAATTAGATTC	4	84	1
GATTCTTTATCCTCCCGGAGGGATATTTCAGC	4	111	1
GTAGATGGGGTGGAGCCTGGGGC         	5	1	0
CTCCACCCCATCTACCCCGGGGTTTCAGGCGG	5	18	1
          ***  *******
MAP Score: 23.8208

Motif 2
TTTATGCCAACCCCCCTATTGGCTGTCCCATCCCGGCTTCCCATCC	0	21	1
CTCTGCCACCCTCCTGAGTAGACAAGAAATTACCCCTCCTACTATC	0	103	0
       CCGCTCCGCGATAGCCTTGTACTCACTCCTACTTACCCT	0	163	0
CTTACACCTCCCACGCTAGAGTGGATAAAGCATTTG          	1	0	0
       TTTCCTCGGGTCTACAGCCAAAGCACCTTACACCTCCCA	1	33	0
ATTAATAAGTCTCCGGAGTAACCGGCGGAACTCCGCGCCACGGGAA	3	34	1
GAACTCCGCGCCACGGGAATTTCTTAATTACGCTTGCTCTCCCAGG	3	61	1
      CCGTCCCCCGCAATCCCAATTAGCCCTGGGAGAGCAAGCG	3	91	0
        AACCCCCCTAAAGGGTCGGACAAGGCTGAACTCCTCAC	4	2	1
CAAGGCTGAACTCCTCACAACACCCCCAGGCTCCCTTCCGGGGGTG	4	30	1
GGGGTGACGACCCCAGGCGACACTGAACACCCCCGGAAGGGAGCCT	4	57	0
GGGGTCGTCACCCCGGGAATTAGATTCTTTATCCTCCCGGAGGGAT	4	89	1
         GCTTCACCACGCTGAAATATCCCTCCGGGAGGATAAA	4	116	0
         GCCCCAGGCTCCACCCCATCTACCCCGGGGTTTCAGG	5	1	1
          **** *      *       * ** *
MAP Score: 21.7051

Motif 3
ACACCCTTTTATGCCAACCCCCCTATTGGCTG	0	14	1
CCCCTATTGGCTGTCCCATCCCGGCTTCCCAT	0	33	1
GTAGACAAGAAATTACCCCTCCTACTATCTGA	0	100	0
CTTAGAAGCTCTGCCACCCTCCTGAGTAGACA	0	125	0
CCTACTTACCCTGAATCCCTTAGAAGCTCTGC	0	143	0
    CAAATGCTTTATCCACTCTAGCGTGGGA	1	6	1
GCCAAAGCACCTTACACCTCCCACGCTAGAGT	1	24	0
GGTGCTTTGGCTGTAGACCCGAGGAAA     	1	45	1
CTTAATTACGCTTGCTCTCCCAGGGCTAATTG	3	83	1
TCGGACAAGGCTGAACTCCTCACAACACCCCC	4	25	1
ACAACACCCCCAGGCTCCCTTCCGGGGGTGTT	4	46	1
CCAGGCGACACTGAACACCCCCGGAAGGGAGC	4	59	0
AATTCCCGGGGTGACGACCCCAGGCGACACTG	4	78	0
GAATTAGATTCTTTATCCTCCCGGAGGGATAT	4	105	1
CTTCACCACGCTGAAATATCCCTCCGGGAGGA	4	120	0
      GCCCCAGGCTCCACCCCATCTACCCC	5	4	1
      CCGCCTGAAACCCCGGGGTAGATGGG	5	24	0
          *** * ******
MAP Score: 20.0551

Motif 4
CCAGGCGACACTGAACACCCCCGGAAGGGAGCCT	4	57	0
CAGGCTCCACCCCATCTACCCCGGGGTTTCAGGC	5	14	1
CCCCTATTGGCTGTCCCATCCCGGCTTCCCATCC	0	33	1
GTCGCCTGGGGTCGTCACCCCGGGAATTAGATTC	4	82	1
GAATTAGATTCTTTATCCTCCCGGAGGGATATTT	4	105	1
CTGAACTCCTCACAACACCCCCAGGCTCCCTTCC	4	35	1
ACCGGCGGAACTCCGCGCCACGGGAATTTCTTAA	3	54	1
TCTTAATTACGCTTGCTCTCCCAGGGCTAATTGG	3	82	1
GGAGTGAGTACAAGGCTATCGCGGAGCGG     	0	173	1
     CCGTCCCCCGCAATCCCAATTAGCCCTGG	3	102	0
GGGGTAATTTCTTGTCTACTCAGGAGGGTGGCAG	0	113	1
GGTGCTTTGGCTGTAGACCCGAGGAAA       	1	45	1
CGGAGTTCCGCCGGTTACTCCGGAGACTTATTAA	3	35	0
GGCAGAGCTTCTAAGGGATTCAGGGTAAGTAGGA	0	142	1
          **   * *******
MAP Score: 18.5047

Motif 5
CCCCTATTGGCTGTCCCATCCCGGCTTCCCATCCA	0	33	1
AACCGGCGGAACTCCGCGCCACGGGAATTTCTTAA	3	53	1
CTTAATTACGCTTGCTCTCCCAGGGCTAATTGGGA	3	83	1
CTGAACTCCTCACAACACCCCCAGGCTCCCTTCCG	4	35	1
AACACCCCCAGGCTCCCTTCCGGGGGTGTTCAGTG	4	48	1
CGGGGGTGTTCAGTGTCGCCTGGGGTCGTCACCCC	4	68	1
TGTCGCCTGGGGTCGTCACCCCGGGAATTAGATTC	4	81	1
GAATTAGATTCTTTATCCTCCCGGAGGGATATTTC	4	105	1
GGGGTAGATGGGGTGGAGCCTGGGGC         	5	1	0
AGGCTCCACCCCATCTACCCCGGGGTTTCAGGCGG	5	15	1
          *   * * *******
MAP Score: 13.3546

Motif 6
ACAGCCAATAGGGGGGTTGGCATAAAAGGG	0	17	0
GATGGGAAGCCGGGATGGGACAGCCAATAG	0	36	0
ACTCAGATAGTAGGAGGGGTAATTTCTTGT	0	98	1
CTTGTCTACTCAGGAGGGTGGCAGAGCTTC	0	123	1
TTATCCACTCTAGCGTGGGAGGTGTAAGGT	1	18	1
AATTCCCGTGGCGCGGAGTTCCGCCGGTTA	3	52	0
ACGCTTGCTCTCCCAGGGCTAATTGGGATT	3	90	1
TCCGACCCTTTAGGGGGGTT          	4	0	0
AAGGGAGCCTGGGGGTGTTGTGAGGAGTTC	4	37	0
CAGGCTCCCTTCCGGGGGTGTTCAGTGTCG	4	56	1
GTGTTCAGTGTCGCCTGGGGTCGTCACCCC	4	73	1
GAATCTAATTCCCGGGGTGACGACCCCAGG	4	86	0
TTCTTTATCCTCCCGGAGGGATATTTCAGC	4	113	1
AGGGATATTTCAGCGTGGTGAAGC      	4	129	1
CCGGGGTAGATGGGGTGGAGCCTGGGGC  	5	8	0
ACCCCATCTACCCCGGGGTTTCAGGCGG  	5	22	1
          **********
MAP Score: 4.5148

Motif 7
ATTGGCTGTCCCATCCCGGCTTCCCATCCA	0	38	1
AACCGGCGGAACTCCGCGCCACGGGAATTT	3	53	1
ACTCCTCACAACACCCCCAGGCTCCCTTCC	4	39	1
CCCCAGGCTCCCTTCCGGGGGTGTTCAGTG	4	53	1
CCTGGGGTCGTCACCCCGGGAATTAGATTC	4	86	1
GATTCTTTATCCTCCCGGAGGGATATTTCA	4	111	1
GCCCCAGGCTCCACCCCATCTACCCCGGGG	5	10	1
          **********
MAP Score: 2.16531