AlignACE 3.0 10/20/99
AlignACE2 -i CT/CT_profile008_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944243599
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	CT386	280	predicted metal dependent hydrolase
#1	CT460	300	SWIB (YM74) complex protein
#2	CT472	300	hypothetical protein
#3	fliI	73	Flagellum-specific ATP Synthase
#4	fliF	272	Flagellar M-Ring Protein
#5	pgm	296	Phosphoglycerate Mutase
#6	ftsK	300	Cell Division Protein FtsK

Motif 1
ATGTGATGTAGGTAAAGAAGATCTAGGGCTT	0	119	1
CTAGGGCTTCGAACAGGAAAATACCTTCAGC	0	141	1
ATAGCTCTTTGAAAAAGAAGAGTTTAAAGTT	1	19	0
GGAAATAACTGGCAAGGAAAATAGCTCTTTG	1	39	0
GCCAAGTCTTCAGCAAGAAGAGAGGTAAAAG	1	178	0
TAAAAGAGTTGCGAAGGAAGAGCCCTAAACT	1	246	1
ATGACTCCTAGTTAAAGAAGATGATAAGAAA	1	277	0
CCACTTCCGCAAAAAAGAAGACATGAAGAAT	2	49	1
TCCTATCTATTTTAAAGAAAAAATTGGAGGA	2	136	1
TCTATATCGTTGAAAGGAAGAGTGTCTCATA	2	266	0
TTGTCTTCTGTAACAAAAAGAGGCTATTAAA	4	66	0
TTCTTCTTGTGAACAAGAAGAAAATTAGCAT	4	146	0
AGAAAAGGATGAAAAAGAAGGCTTCTTCTTG	4	168	0
CTAAGTATCCTACAAAGAAAAGGATGAAAAA	4	183	0
ATAATCCGCAAACAAGGAAGATGAAGCCTTT	5	248	1
TTTAGGAAACTATAAAGAAGGGCGAACGACG	6	120	0
TAGCTTGTTATAACAGGAAAAATAAAAGAAT	6	163	0
          ** ********
MAP Score: 17.319

Motif 2
TCCTGTTCGAAGCCCTAGATCTTCTTTACCT	0	128	0
GCTTGATATTAATCCTAAACTGCAAGTAGGA	0	177	1
AAAAGCTGAAAATCCTCCATCCTACTTGCAG	0	196	0
AACAACAAACAAACCTCGGCCGGTAGTACCA	0	232	0
AAAACGATTTATTCCTCGGACTATTACGCAA	1	139	0
GCGAAGGAAGAGCCCTAAACTTTTCTTATCA	1	256	1
GCGTATACCAATTCCGCCACTTCCGCAAAAA	2	33	1
TTCTCTGATAAATCCTCCAATTTTTTCTTTA	2	148	0
AAACCAAGGAATCCCCCAACCACGTACATGG	3	51	1
CCCTTGCTCTATTCCTCAACCTATACGTAGA	4	223	1
TTGCAAAGATAATCCGCAAACAAGGAAGATG	5	240	1
CCATGGTGAAACTCCCCAACTAGCAGAGCGT	6	27	0
TCGGAACCACAATCCGACGCTCTAACCAACT	6	70	0
ACGGGGTTCGAACCCGCGACCTTCGGAACCA	6	92	0
          * *********
MAP Score: 7.66214

Motif 3
AGGATGGAGGATTTTCAGCTTTTGGATATGGTA	0	204	1
ATCCAACTTTAAACTCTTCTTTTTCAAAGAGCT	1	15	1
TTTCAAAGAGCTATTTTCCTTGCCAGTTATTTC	1	36	1
AAATCGTTTTCTAATTCGCTTTTACCTCTCTTC	1	160	1
TTCGCTTTTACCTCTCTTCTTGCTGAAGACTTG	1	174	1
CTAAACTTTTCTTATCATCTTCTTTAACTAGGA	1	270	1
GCTGATTCTTCATGTCTTCTTTTTTGCGGAAGT	2	51	0
AAGTAAAAAACCTCTCAGCTTACAAATTCCTAT	2	109	1
TCTGCAAAAGCCTATCCCCTTATTGTAAGAAAC	2	226	1
TTAAAAGAGCCCTTTTGTCTTCTGTAACAAAAA	4	78	0
TTGAGAGTCCCTTTTGAGCTTCTCGGTCATCCC	4	111	1
ATCCCGGATGCTAATTTTCTTCTTGTTCACAAG	4	139	1
         GCCAGTCCTCTTGTCTTTCGACTG	5	1	1
          *** ** **** *
MAP Score: 7.19729

Motif 4
CGTTCTTTAAACTCTCTTTTTAAAAATTTT	0	45	0
CCAACTTTAAACTCTTCTTTTTCAAAGAGC	1	17	1
GTAACATGATCTTCTCTTAGGGATCAATTT	1	108	1
TCGTTTTCTAATTCGCTTTTACCTCTCTTC	1	163	1
TTCGCTTTTACCTCTCTTCTTGCTGAAGAC	1	174	1
TTCCTTCGCAACTCTTTTATGCCTTAACTA	1	235	0
GCAAAAGCCTATCCCCTTATTGTAAGAAAC	2	229	1
TGTTTTTAATAGCCTCTTTTTGTTACAGAA	4	62	1
CAATTAAAAGAGCCCTTTTGTCTTCTGTAA	4	84	0
TTTAATTGAGAGTCCCTTTTGAGCTTCTCG	4	106	1
AAAAAGAAGGCTTCTTCTTGTGAACAAGAA	4	158	0
TTTCTTAGATAGTCGCTTATTAGTGAACTT	5	46	0
AACACCGGGAACTCTCTTAGATTCAAGGGT	5	91	1
TTCATTTGTGAGCCTCTTTGAGAGGAGAAC	5	176	0
GAGTTCCCCCCCTCCCTTATAAGGTAAAAA	5	206	1
GACTACTTCGATTCTTTTATTTTTCCTGTT	6	153	1
    AGTTCCTCTCTCTTATCTAACTGATA	6	284	0
          **********
MAP Score: 2.76326

Motif 5
AGGTAAAAAATCTTTGCAAAGATAATCCGCAA	5	227	1
GAAGAAGTTCTCCTCTCAAAGAGGCTCACAAA	5	170	1
AAAAATAAATCCTTTACAAAGCTCGCATTAAG	0	85	0
TTAAACTCTTCTTTTTCAAAGAGCTATTTTCC	1	23	1
TGAAGTAAGTTCTTACAAAAGCTCTACGTATA	4	244	0
GAGACACTCTTCCTTTCAACGATATAGATGTA	2	269	1
ATAGGAAAAATTTTTAAAAAGAGAGTTTAAAG	0	39	1
CAAACAAAGTCTCTGCAAAAGCCTATCCCCTT	2	215	1
GTACGAGAGATCCTAAAAAACCAAGGAATCCC	3	34	1
          ****  ******
MAP Score: 0.576842

Motif 6
CTGCTTAATGCGAGCTTTGTAAAGGATTTATTTTT	0	82	1
AAGAAGATCTAGGGCTTCGAACAGGAAAATACCTT	0	133	1
CAAGGAAAATAGCTCTTTGAAAAAGAAGAGTTTAA	1	23	0
TACTCAAACAAAGTCTCTGCAAAAGCCTATCCCCT	2	211	1
TTCTTACAAAAGCTCTACGTATAGGTTGAGGAATA	4	232	0
CATCATATCAAGATTTCAGTAGAGAGTCCAGAAGA	5	140	1
ATAAGGTAAAAAATCTTTGCAAAGATAATCCGCAA	5	224	1
          ** ***  * * ***
MAP Score: 0.393091