AlignACE 3.0 10/20/99
AlignACE2 -i AG/AG_operons014_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944242801
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	AF1127	213	LSU ribosomal protein L18E (rpl18E)
#1	AF1131	75	DNA-directed RNA polymerase, subunit K (rpoK)
#2	AF1132	108	enolase (eno)
#3	AF2285	104	SSU ribosomal protein S13P (rps13P)
#4	AF2289	216	mevalonate kinase (mvk)
#5	AF2310	46	conserved hypothetical protein

Motif 1
AACTCGGGTCACGGCGTCCCGAACGCCGCAGGATCACCAGG	1	10	0
ATAATAGCCTCCATCCTCCCAGCCTCCGCTGCGGGGTCGGA	4	94	1
CCGAAGTTCTACACCGTCTACACCTCCGACCCCGCAGCGGA	4	118	0
TTCCGGCTCAACGACCTCGTAATCCCTCAGCTCCTCCATAA	4	57	1
TTCACACTCAACCGTCTCGTTTCCCCTGCTGTCGAAAACGA	2	47	0
AAGATAGAGGACATACTCTCGTTCACACGAGGGAGCACTAC	4	10	0
TTACAGGCTTGCTTCCTCTTAGACGGTGATGTT        	3	81	1
TTTGGATTTGACTTCCTCCTCTGCCAGCTTCCTTATCTTGC	0	127	0
CGCCTTCGCAACAACCTCCCCAGCAACGACTTCACACTCAA	2	77	0
TCAAATCCAAACCTCGTTACTCTCATCGATGTACTGCTGAG	0	157	1
GACGCCGTGACCCGAGTTCAAATCTCGGCGGCCCCATCTGC	1	33	1
TTGATAATTGAGGACGTTCACTACAGAGTCGTTTTCGACAG	2	19	1
          **  ****     * * *  *
MAP Score: 15.0162

Motif 2
TTTAATGTTCCTTCCGCGGAAGGCTAAAAACGATTTCGAT	0	15	0
AATTAACATGCGGCAAAGATTTAAATTACGTAATGTAACG	0	55	1
ATCAACTACACCTCAGCGTAGTTTTGACCGTTACATTACG	0	83	0
ATAAGGAAGCTGGCAGAGGAGGAAGTCAAATCCAAACCTC	0	132	1
CTCAGCAGTACATCGATGAGAGTAACGAGGTTTGGATTTG	0	158	0
CATCGATGTACTGCTGAGCGAGTCAGCAAAAAATGAGGCG	0	180	1
CCTGGTGATCCTGCGGCGTTCGGGACGCCGTGACCCGAGT	1	10	1
GCAGATGGGGCCGCCGAGATTTGAACTCGGGTCACGGCGT	1	34	0
AGGACGTTCACTACAGAGTCGTTTTCGACAGCAGGGGAAA	2	29	1
GAAGTCGTTGCTGGGGAGGTTGTTGCGAAGGCG       	2	85	1
GAGCCGGAACCGGCAAAGATAGAGGACATACTCTCGTTCA	4	26	0
TCCGACCCCGCAGCGGAGGCTGGGAGGATGGAGGCTATTA	4	95	0
GCCTCCGCTGCGGGGTCGGAGGTGTAGACGGTGTAGAACT	4	115	1
AAACGATCTTCATGAGAGAATGTTTGCACAAAATTCTTTA	4	164	1
          * ** ***   **    * *
MAP Score: 12.4051

Motif 3
CCCAGCCTCCGCTGCGGGGTCGGAGGTGTAGACGGT	4	111	1
 CCTGGTGATCCTGCGGCGTTCGGGACGCCGTGACC	1	9	1
CGCAGCGGAGGCTGGGAGGATGGAGGCTATTATGGA	4	91	0
AAGGAAGCTGGCAGAGGAGGAAGTCAAATCCAAACC	0	134	1
TGAAGTCGTTGCTGGGGAGGTTGTTGCGAAGGCG  	2	84	1
TCAAAACTACGCTGAGGTGTAGTTGATATGAGCAAG	0	96	1
ACCCCTTAAAGCAGATGGGGCCGCCGAGATTTGAAC	1	48	0
TCATCGATGTACTGCTGAGCGAGTCAGCAAAAAATG	0	179	1
GGGAAACGAGACGGTTGAGTGTGAAGTCGTTGCTGG	2	63	1
 GTAGTGCTCCCTCGTGTGAACGAGAGTATGTCCTC	4	9	1
TGAGCCGGAACCGGCAAAGATAGAGGACATACTCTC	4	31	0
GGAGGTGTAGACGGTGTAGAACTTCGGGTGAAAAAC	4	132	1
GACGTTCACTACAGAGTCGTTTTCGACAGCAGGGGA	2	31	1
TTGGAATAATCCTCAATTGAAGGGGGGCACATAACC	3	34	1
          **** ** *   * **
MAP Score: 11.9774

Motif 4
AAGGAAGCTGGCAGAGGAGGAAGTCAAATC	0	134	1
CTCCGACCCCGCAGCGGAGGCTGGGAGGAT	4	106	0
TGAAGTCGTTGCTGGGGAGGTTGTTGCGAA	2	84	1
TCGATGTACTGCTGAGCGAGTCAGCAAAAA	0	182	1
ACCCCTTAAAGCAGATGGGGCCGCCGAGAT	1	54	0
CATCACCGTCTAAGAGGAAGCAAGCCTGTA	3	82	0
TTATGGAGGAGCTGAGGGATTACGAGGTCG	4	68	0
TAATGTTCCTTCCGCGGAAGGCTAAAAACG	0	23	0
GTTTTCGACAGCAGGGGAAACGAGACGGTT	2	49	1
ATCCTCAATTGAAGGGGGGCACATAACCTT	3	42	1
CTCTCGTTCACACGAGGGAGCACTAC    	4	6	0
GTGTAGTTGATATGAGCAAGATAAGGAAGC	0	112	1
TCAAAACTACGCTGAGGTGTAGTTGATATG	0	96	1
          **********
MAP Score: 10.3321

Motif 5
CGTTTTTAGCCTTCCGCGGAAGGAACATTAAAAAT	0	23	1
CAAAACTACGCTGAGGTGTAGTTGATATGAGCAAG	0	97	1
AGGAAGCTGGCAGAGGAGGAAGTCAAATCCAAACC	0	135	1
CATCGATGTACTGCTGAGCGAGTCAGCAAAAAATG	0	180	1
CCTGGTGATCCTGCGGCGTTCGGGACGCCGTGACC	1	10	1
CCCCTTAAAGCAGATGGGGCCGCCGAGATTTGAAC	1	48	0
TCGTTTTCGACAGCAGGGGAAACGAGACGGTTGAG	2	47	1
TGTGAAGTCGTTGCTGGGGAGGTTGTTGCGAAGGC	2	82	1
ACCTCCGACCCCGCAGCGGAGGCTGGGAGGATGGA	4	103	0
          **** * **  ** *
MAP Score: 4.10504

Motif 6
ATCGTTTTTAGCCTTCCGCGGAAGGAACATT	0	21	1
TTTAAATCTTTGCCGCATGTTAATTTTTAAT	0	49	0
CTCTGCCAGCTTCCTTATCTTGCTCATATCA	0	119	0
TGGATTTGACTTCCTCCTCTGCCAGCTTCCT	0	135	0
  CCTGGTGATCCTGCGGCGTTCGGGACGCC	1	8	1
AAATCTCGGCGGCCCCATCTGCTTTAAGGGG	1	52	1
ACCGTCTCGTTTCCCCTGCTGTCGAAAACGA	2	47	0
CTTACAGGCTTGCTTCCTCTTAGACGGTGAT	3	80	1
      GTAGTGCTCCCTCGTGTGAACGAGA	4	4	1
CGAGAGTATGTCCTCTATCTTTGCCGGTTCC	4	30	1
CCTCTATCTTTGCCGGTTCCGGCTCAACGAC	4	41	1
GACCTCGTAATCCCTCAGCTCCTCCATAATA	4	69	1
CTCCATAATAGCCTCCATCCTCCCAGCCTCC	4	90	1
CCATCCTCCCAGCCTCCGCTGCGGGGTCGGA	4	104	1
          ****** ****
MAP Score: 3.24668

Motif 7
CGTTTTTAGCCTTCCGCGGAAGGAACATTAAA	0	23	1
TTGCTGACTCGCTCAGCAGTACATCGATGAGA	0	177	0
CGAGTTCAAATCTCGGCGGCCCCATCTGCTTT	1	45	1
CCTCGTAATCCCTCAGCTCCTCCATAATAGCC	4	71	1
ATCCTCCCAGCCTCCGCTGCGGGGTCGGAGGT	4	106	1
ACCGTCTACACCTCCGACCCCGCAGCGGAGGC	4	115	0
          ******* ** *
MAP Score: 0.133404

Motif 8
AACTACACCTCAGCGTAGTTTTGACCGTTACATTAC	0	84	0
CCTGGTGATCCTGCGGCGTTCGGGACGCCGTGACCC	1	10	1
ACGTTCACTACAGAGTCGTTTTCGACAGCAGGGGAA	2	32	1
AGCAGGGGAAACGAGACGGTTGAGTGTGAAGTCGTT	2	58	1
GAAGTCGTTGCTGGGGAGGTTGTTGCGAAGGCG   	2	85	1
CTTGCTTCCTCTTAGACGGTGATGTT          	3	88	1
TGTCCTCTATCTTTGCCGGTTCCGGCTCAACGACCT	4	38	1
GACCCCGCAGCGGAGGCTGGGAGGATGGAGGCTATT	4	96	0
TCCGCTGCGGGGTCGGAGGTGTAGACGGTGTAGAAC	4	118	1
          * * * *****  * *
MAP Score: 0.0172474