AlignACE 3.0 10/20/99
AlignACE2 -i CT/CT_operons031_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944243083
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	ribC_CT406	392	ribC: Riboflavin Synthase, CT406: hypothetical protein
#1	CT409	101	Amino acid permease
#2	pcnB_1	214	PolyA Polymerase
#3	gltX	271	Glutamyl-tRNA Synthetase
#4	euo	300	CHLPS Euo Protein
#5	clpP_2	166	CLP Protease
#6	tig	300	Trigger Factor-peptidyl prolyl isomerase

Motif 1
CAGAAATGAAAGAAAGAGGTAGCTTGGGGG	0	66	1
GTCTTGTGTTGAAAAGAACCTCTTCTTAGA	0	210	1
ACCTCTTCTTAGAAAGGTTTTCTCTACGGG	0	227	1
GATCAGATCCGGAGAGGGCTTTTTCGTGTA	0	308	1
GATCCTTGAAAGAAAGAATTTTTTG     	1	5	0
TTTGTTTGGTAGAGAGATCCTTGAAAGAAA	1	20	0
      AAGGAGAGAGAGTCATAAAGCTGT	2	4	1
TTTCTATTATAGGAAGAGCTTTCCTGGAGA	2	128	1
GAGCTTTCCTGGAGAGAACTCTAAAAGCCT	2	143	1
          AGATAGAGCCTTCTCTGTAA	3	0	1
GGGCACAGCAGGGGAGAGCTTGGGCCTCCT	3	30	1
TTTTTTGTTGAAAAAGAGCTCCGAAAAACT	3	83	1
AAACGATACCAGAGAGATTCATTCTTGGCG	3	136	0
AGAATAGAGTGGAAAGGGCTTGTCCGACTT	4	159	1
TAAGTGGACGAGGGAGGACTAAACAGTCGT	4	280	1
ACCCTAGAAAAGAAAGACCCCATCTAATTC	5	87	0
TAGAGGAAGAAGAGAGGGTCAAAATTTTCA	6	20	0
          **********
MAP Score: 15.3158

Motif 2
CTCTTCTTCCTCTATTTTTCCCCTTTTTAAA	6	36	1
CCCTATATTATCTCTTTTTTCCTTTTTGTTT	1	43	0
AATGTTACCTTCTCTTTTTAAGGATTTTGCA	4	94	1
GTCCAATTTTTCTTTTTTTACCACCTCTTCA	6	77	1
TTAGATGGGGTCTTTCTTTTCTAGGGTCAAG	5	90	1
CCAAGCTACCTCTTTCTTTCATTTCTGAAGG	0	62	0
  CAAAAAATTCTTTCTTTCAAGGATCTCTC	1	8	1
AAAAATAAATGCTATTTTTGAAACAAAGTTT	4	27	0
GTTTTTCGGAGCTCTTTTTCAACAAAAAAAA	3	81	0
AATGATGAATTCTATGTTTAAGTGTCTCTTG	5	36	0
AGGAAACTTTTCTATCTTTATGAAATGAACA	3	232	0
TTTTCGTGTATCTAGTTTTTCAAGATTGCTA	0	328	1
ATTTTGACCCTCTCTTCTTCCTCTATTTTTC	6	25	1
GATGAGAGGATTTATTTTTAAGTGGACGAGG	4	262	1
AAAAATAGCATTTATTTTTAACAAACCGCTT	4	39	1
CCGGAGGGGGGCTTTTTTTTTGTTGAAAAAG	3	68	1
TATCTAGAATGCTCTTCTTCTCGCGGGTGTA	6	182	1
          ********* *
MAP Score: 15.2255

Motif 3
CCTTTTTGTTTGGTAGAGAGATCCTTGAAA	1	24	0
TCGCTACACTAGGAAGAGAGAATAGAGTGG	4	141	1
TTCTTTTCTAGGGTCAAGAGTAGCCATAAC	5	103	1
TTTTTTGAGAAGGTGAAGAGGTGGTAAAAA	6	91	0
TGTAGCTCAGTGGTAGAGCGCCACGTTGCC	6	209	1
GAAAAATAGAGGAAGAAGAGAGGGTCAAAA	6	26	0
TATTTTTAAGTGGACGAGGGAGGACTAAAC	4	274	1
TTTTTTTTGTTGAAAAAGAGCTCCGAAAAA	3	81	1
AGTGTCTCTTGGGTCAAGCGTTTTCCTGCG	5	17	0
TACACCCGCGAGAAGAAGAGCATTCTAGAT	6	183	0
AAAGAGAAGCGGGTGATGAGGCTTGAACTC	6	253	0
CCAAACAAAAAGGAAAAAAGAGATAATATA	1	41	1
GCCAACGTGAAGGTCGTGAGTTCAAGCCTC	6	236	1
        AAGGAGAGAGAGTCATAAAGCT	2	2	1
GAGAGATCCTTGAAAGAAAGAATTTTTTG 	1	9	0
CCTTCAGAAATGAAAGAAAGAGGTAGCTTG	0	62	1
AAAAAAACTTTGGAAAAAGGTTTTTTGAGA	6	111	0
          **********
MAP Score: 9.60551

Motif 4
CAAGCTACCTCTTTCTTTCATTTCTGAAGGG	0	61	0
TTTGTGGTGATTTTTTTTCAAAAGTCGCCTA	0	123	1
ATACCACGGTTTTTATTTTAATGGATAAAAT	0	174	1
 CAAAAAATTCTTTCTTTCAAGGATCTCTCT	1	9	1
TTCAAGGAATTTTAGTTTTAATCATATATTT	1	79	1
TCCAGACTTTTTAACTTTCAATGTCATATA 	2	194	1
TTTTTCGGAGCTCTTTTTCAACAAAAAAAAA	3	80	0
CTTTACAAAACTTTGTTTCAAAAATAGCATT	4	20	1
AAAAATAGCATTTATTTTTAACAAACCGCTT	4	39	1
GATGAGAGGATTTATTTTTAAGTGGACGAGG	4	262	1
TTTTCCAAAGTTTTTTTGTAAAACCTACAAG	6	124	1
          **** ******
MAP Score: 8.5087

Motif 5
CCTCTTTCTTTCATTTCTGAAGGGCCTATCGTAG	0	51	0
TTTGTGGTGATTTTTTTTCAAAAGTCGCCTAATA	0	123	1
ATACCACGGTTTTTATTTTAATGGATAAAATCCT	0	174	1
GAAAAGAACCTCTTCTTAGAAAGGTTTTCTCTAC	0	220	1
TAGAAAGGTTTTCTCTACGGGCGGTCTCGGAGTA	0	236	1
   CAAAAAATTCTTTCTTTCAAGGATCTCTCTA	1	7	1
ATCTCTTTTTTCCTTTTTGTTTGGTAGAGAGATC	1	31	0
AAACGTAATTTTTTCTATTATAGGAAGAGCTTTC	2	117	1
  AGATAGAGCCTTCTCTGTAAGGGCACAGCAGG	3	8	1
GGAGGGGGGCTTTTTTTTTGTTGAAAAAGAGCTC	3	70	1
GATAGAAAAGTTTCCTTTCCTGGGTTAGTAGCGA	3	247	1
AAATGTTACCTTCTCTTTTTAAGGATTTTGCAAT	4	93	1
TTCCACTCTATTCTCTCTTCCTAGTGTAGCGAGC	4	139	0
TAAAAATAAATCCTCTCATCTTGGCCTGTCTTGT	4	248	0
ATGAGAGGATTTATTTTTAAGTGGACGAGGGAGG	4	263	1
TAGATGGGGTCTTTCTTTTCTAGGGTCAAGAGTA	5	91	1
CCTCTATTTTTCCCCTTTTTAAAGCTGTTTGCAG	6	44	1
TCTAGAATGCTCTTCTTCTCGCGGGTGTAGCTCA	6	184	1
CATCACCCGCTTCTCTTTCCCGGATAACTTACCA	6	265	1
          ********    **
MAP Score: 7.42026

Motif 6
GAAAGGTTTTCTCTACGGGCGGTCTCGGAGTATAA	0	238	1
CGAAAAAGCCCTCTCCGGATCTGATCAAGGCAAAC	0	299	0
AAAATTCTTTCTTTCAAGGATCTCTCTACCAAACA	1	13	1
TTTTAGAGTTCTCTCCAGGAAAGCTCTTCCTATAA	2	134	0
AAAAAAGCCCCCCTCCGGAATTCCGGAGGAGGCCC	3	51	0
AATGAACACCCCGTCCCGGGTTCCTGTCCTATGAA	3	205	0
GAAAAGTTTCCTTTCCTGGGTTAGTAGCGA     	3	251	1
ACTGTTTAGTCCTCCCTCGTCCACTTAAAAATAAA	4	272	0
TTGCGAAAAACTCCCCAGATTATCTAGAATGCTCT	6	162	1
ACCCGCTTCTCTTTCCCGGATAACTTACCAATGGG	6	269	1
          ****** **    **
MAP Score: 6.73452

Motif 7
TATTTGAATTTTAGGAGGAATCTCCC        	0	2	0
AGGCGACTTTTGAAAAAAAATCACCACAAATCAC	0	119	0
GTGTCTTGTGTTGAAAAGAACCTCTTCTTAGAAA	0	208	1
TATTTTTTGATTATAAGTAACCGCTGTTTGCCTT	0	274	1
TCTTCCTATAATAGAAAAAATTACGTTTACAAGG	2	111	0
AAGCGGTTTGTTAAAAATAAATGCTATTTTTGAA	4	36	0
TTGGCCTGTCTTGTGAATAATGGCTCTGTGACCT	4	228	0
CCTCGTCCACTTAAAAATAAATCCTCTCATCTTG	4	259	0
ACCAAATGATTTGAGAGGAAGCACACAT      	5	148	1
CTTGTAGGTTTTACAAAAAAACTTTGGAAAAAGG	6	121	0
AAGCAAAGGATTGCGAAAAACTCCCCAGATTATC	6	152	1
          *** *** ** * *
MAP Score: 4.88278

Motif 8
TAGATCCCCCAAGCTACCTCTTTCTTTCATT	0	70	0
TTGTGTTGAAAAGAACCTCTTCTTAGAAAGG	0	213	1
GCCCGTAGAGAAAACCTTTCTAAGAAGAGGT	0	227	0
ATACACGAAAAAGCCCTCTCCGGATCTGATC	0	308	0
CCTTGAAAGAAAGAATTTTTTG         	1	1	0
CTTTCTTTCAAGGATCTCTCTACCAAACAAA	1	19	1
CTCTCCAGGAAAGCTCTTCCTATAATAGAAA	2	128	0
AGAGAACTCTAAAAGCCTTCTTGCTCAAGGA	2	155	1
GCTCAAGGACAAAATCCTCCAGACTTTTTAA	2	177	1
       AGATAGAGCCTTCTCTGTAAGGGC	3	3	1
GAGGAGGCCCAAGCTCTCCCCTGCTGTGCCC	3	30	0
AACAAAAAAAAAGCCCCCCTCCGGAATTCCG	3	61	0
GAGTTTTTCGGAGCTCTTTTTCAACAAAAAA	3	83	0
TTTCCCAACAAAAAACTTATTAATCAAGCGG	4	64	0
CTAGTGTAGCGAGCGCTTACTGAAAAATTGC	4	122	0
TAAGTCGGACAAGCCCTTTCCACTCTATTCT	4	159	0
CTAGAAAAGAAAGACCCCATCTAATTCAAAA	5	83	0
CACCTTCTCAAAAAACCTTTTTCCAAAGTTT	6	106	1
AAGGATTGCGAAAAACTCCCCAGATTATCTA	6	157	1
CCGCGAGAAGAAGAGCATTCTAGATAATCTG	6	177	0
          **** ******
MAP Score: 0.825924