AlignACE 3.0 10/20/99
AlignACE2 -i CT/CT_operons021_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944242780
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	flhA	181	Flagellar Secretion Protein
#1	fliA	107	Sigma-28/WhiG Family
#2	araD	83	Ribulose-P Epimerase
#3	rl13	222	L13 Ribosomal Protein
#4	rs9	25	S9 Ribosomal Protein
#5	proS	200	Prolyl tRNA Synthetase
#6	hrcA	68	HTH Transcriptional Repressor
#7	dnaK	25	HSP-70
#8	vacB	292	Ribonuclease Family
#9	CT398	255	hypothetical protein
#10	rpoD	148	RNA Polymerase Sigma-66
#11	CT616	300	hypothetical protein
#12	CT793	62	hypothetical protein

Motif 1
AAACATCAAGTTATTAAGAAATAAAGAATCTGA	5	70	1
GGAGAAGGATTTTTTAAAAAAAAGCTGCAAGAG	8	56	0
GCTTAAATTAATTTTAAGAAACAAACAAAAGAA	5	39	1
GTGACAGTTTATCTTAAGAAAAACAAGAAATCT	10	87	0
TCAAATAAAATTTTTAAACAATATCTACCCTTA	1	45	0
GAAAAAGATTTTCTTAAACAAAACGTGCTTTAC	9	64	1
CTAAAGAATTTAGAAAAGAAAAAATTTCAAAAA	3	118	0
TAGGGATTTTTAGATAAAAAAAAGCCTGTTGAT	10	55	0
AGACAATAAAATAGAAAGAAAAATAGGATAGAT	11	114	1
     GGAGATTTAAAAACAAAATTTGCAAAAA	5	5	1
CATGATTTACATAATAAAAAAAATAG       	3	3	0
ATATTCCAAAATTCAAAAAAACAATGATCAATC	11	229	1
CTGCTTTTTGTTTGGAAAAAATAATCATCAAAA	3	164	1
TCTACACTTCTTTCGAAAAAATATTTTAGGGAA	3	46	0
AAAAAGGGAGTTTTGAAAAAAGACGCGGACGAG	9	141	0
TTAAGAAACAAACAAAAGAAACATCAAGTTATT	5	52	1
TTTCTTTTACAAACTAAAAAATAAGGCTAAATC	1	76	0
TAAGGCTATTTTTGAAGGCAAAAAGAAAAGAGA	3	83	1
       GGATAAGTAGAAAAGACGGGAGGGGT	10	3	1
TCTTGTCTAGTATATAGGCAATATGCTAACTTC	0	144	0
GGATTAATTACTCTTAAGAAAGAAGAGAGGAGA	8	84	0
GACAAATTAAAACTAAGGAAAAATCGGCCTAGA	10	122	0
TTATTCATCTTCCTTAAGCAAGAGCCTCTTGAA	8	16	1
ATGCTCTTCCACACGAAACAATATAAAGCACTT	5	169	1
          **  ******* *
MAP Score: 20.1676

Motif 2
CTCCAGAAGGAAAAAGAAAAGATTAGTTAAG	0	14	1
TTTACAAACTAAAAAATAAGGCTAAATCAAA	1	73	0
TTTACATAATAAAAAAAATAG          	3	0	0
ATTTTTTCGAAAGAAGTGTAGAAGTGTAAGG	3	57	1
TTTTGAAGGCAAAAAGAAAAGAGATCTTTTT	3	92	1
  GGAGATTTAAAAACAAAATTTGCAAAAAC	5	8	1
ATTTTAAGAAACAAACAAAAGAAACATCAAG	5	49	1
TCAAGTTATTAAGAAATAAAGAATCTGAACT	5	75	1
AAAATCCAATAAGAACAAAAAAATCACAGAG	5	110	1
ACTCTTAAGAAAGAAGAGAGGAGAAGGATTT	8	77	0
TCTAGCATACATGAACAAAGGGATTAATTAC	8	106	0
ATTTTTCTGCAAGAAGTAAAGCACGTTTTGT	9	81	0
      GGATAAGTAGAAAAGACGGGAGGGG	10	4	1
GGATTTTTAGATAAAAAAAAGCCTGTTGATC	10	54	0
      GCTGACAAATTAAAACTAAGGAAAA	10	133	0
AGACCGACACAAAAACAGAAGTGTCGGCAGT	11	17	1
ATAAAATAGAAAGAAAAATAGGATAGATAAA	11	119	1
AATAGGATAGATAAAATAAAGGAGGGGGGAA	11	135	1
TTCCCCTACTACGAATAAAAAATTTTTTCGA	12	32	0
          ***** *****
MAP Score: 17.5558

Motif 3
AGGGATTTTTAGATAAAAAAAAGCCTGTTGAT	10	55	0
AAATCCAATAAGAACAAAAAAATCACAGAGAT	5	111	1
TGATATTCCAAAATTCAAAAAAACAATGATCA	11	227	1
CGCTATACTCCGATTTAAAAAAGTAGGAGCTA	0	110	1
TAGTATTGCGTGATCGAAAAAATTTTTTATTC	12	19	1
        GGAGATTTAAAAACAAAATTTGCA	5	2	1
CCAGACTTCAAGATGCAAAAACATTCCTTGGG	8	218	1
CAAGTTATTAAGAAATAAAGAATCTGAACTAG	5	76	1
AAAATAGGATAGATAAAATAAAGGAGGGGGGA	11	133	1
AGAAAAGAAAAAATTTCAAAAAGATCTCTTTT	3	108	0
ATTAATTTTAAGAAACAAACAAAAGAAACATC	5	45	1
  AGGACTCCAGAAGGAAAAAGAAAAGATTAG	0	8	1
ATGATTTACATAATAAAAAAAATAG       	3	3	0
AAAGACAATAAAATAGAAAGAAAAATAGGATA	11	112	1
ATTTCTTTTACAAACTAAAAAATAAGGCTAAA	1	78	0
AGGCTATTTTTGAAGGCAAAAAGAAAAGAGAT	3	85	1
AAATAAGGCTAAATCAAATAAAATTTTTAAAC	1	59	0
ATATCATAGTAGATTCTAAAACAGTTGATATT	11	202	1
          ****  ******
MAP Score: 11.164

Motif 4
AAAAGACGGGAGGGGTTTTTCTAGGCCTAA	10	20	1
CTCCCTTTTTAGGAAGTTTTTGAAGGCGTT	9	164	1
CTTCCTAAAAAGGGAGTTTTGAAAAAAGAC	9	150	0
CAAGAAATCTAGGGATTTTTAGATAAAAAA	10	67	0
TCTGATCAACAGGCTTTTTTTTATCTAAAA	10	51	1
AGAGAGGAGAAGGATTTTTTAAAAAAAAGC	8	64	0
ATCTTAGCATAGGAGTGTTTCTAGATCAAT	5	141	0
CAAACCCCCAAGGAATGTTTTTGCATCTTG	8	226	0
TGACCAGTGGAGACGGTTTTCTTATAATGA	6	39	1
TTAGTAGGGCAGCCGGTTTTTGATGATGCA	8	186	0
CCTATTTTAAAGGAAGTTTCAGTAGTTGCC	11	171	1
AGTTTGTAAAAGAAATTTTTTTT       	1	94	1
TAGAAGTGTAAGGCTATTTTTGAAGGCAAA	3	75	1
AAATTAATTTAAGCGTTTTTGCAAATTTTG	5	23	0
TATTCCTTACATGAATTTTTTGTCTGACCG	9	21	1
          **********
MAP Score: 10.7501

Motif 5
TCAAACCCCCAAGGAATGTTTTTGCATCTTGA	8	225	0
GCAAAAAGAAAAGAGATCTTTTTGAAATTTTT	3	100	1
TAGTTTGTAAAAGAAATTTTTTTT        	1	93	1
AAATTCATGTAAGGAATAATTTGAAGGAT   	9	7	0
ATATCAAGGTAAGGAAAGATTTCC        	9	241	1
ACTTCTTTCGAAAAAATATTTTAGGGAAGTTC	3	42	0
TGCGTGATCGAAAAAATTTTTTATTCGTAGTA	12	25	1
GAATTTAGAAAAGAAAAAATTTCAAAAAGATC	3	114	0
TGCAAGAAGTAAAGCACGTTTTGTTTAAGAAA	9	73	0
GAAGAGAGGAGAAGGATTTTTTAAAAAAAAGC	8	64	0
ACTTCCTAAAAAGGGAGTTTTGAAAAAAGACG	9	149	0
GGAGGGGGGAAAGAGACCTATTTTAAAGGAAG	11	155	1
GACCTATTTTAAAGGAAGTTTCAGTAGTTGCC	11	169	1
TACATGAACAAAGGGATTAATTACTCTTAAGA	8	98	0
ACTCCCTTTTTAGGAAGTTTTTGAAGGCGTTC	9	163	1
TTCTCCCATTGAAAAAGATTTTCTTAAACAAA	9	54	1
 GGAGATTTAAAAACAAAATTTGCAAAAACGC	5	9	1
GGCTAAATCAAATAAAATTTTTAAACAATATC	1	53	0
          ******  ****
MAP Score: 10.4514

Motif 6
CTTTTACAAACTAAAAAATAAGGCTAAATC	1	76	0
          AAAAAAAATTTCTTTTACAA	1	97	0
TTTACATAATAAAAAAAATAG         	3	1	0
ACACTTCTTTCGAAAAAATATTTTAGGGAA	3	46	0
GAAAAAATTTCAAAAAGATCTCTTTTCTTT	3	104	0
AAACAAACAAAAGAAACATCAAGTTATTAA	5	57	1
CCAATAAGAACAAAAAAATCACAGAGATTG	5	115	1
CTTCAAGATGCAAAAACATTCCTTGGGGGT	8	223	1
GTCGGTCAGACAAAAAATTCATGTAAGGAA	9	23	0
TTACTTCTTGCAGAAAAATCGGTAAACTTG	9	93	1
GGAACGCCTTCAAAAACTTCCTAAAAAGGG	9	166	0
ATTAAAACTAAGGAAAAATCGGCCTAGAAA	10	120	0
GAGACCGACACAAAAACAGAAGTGTCGGCA	11	16	1
GGTGAAAAGACAATAAAATAGAAAGAAAAA	11	107	1
ATAAAATAGAAAGAAAAATAGGATAGATAA	11	119	1
ATTGCGTGATCGAAAAAATTTTTTATTCGT	12	23	1
          **********
MAP Score: 8.06213

Motif 7
TTCGAATCCCTCTACTCCGATTCTTAACTA	0	37	0
CAGGCTGCGCTATACTCCGATTTAAAAAAG	0	103	1
TGCCGTTTCGTCTAGGCAGACTCGTCCGCG	9	121	1
GAGGGGTTTTTCTAGGCCTAAATCTGATCA	10	29	1
ACTGTCACTTTCTAGGCCGATTTTTCCTTA	10	112	1
          **********
MAP Score: 2.29709