AlignACE 3.0 10/20/99
AlignACE2 -i CT/CT_operons022_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944242823
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	CT039.1	87	hypothetical protein
#1	ruvB	41	Holliday Junction Helicase
#2	CT260	300	hypothetical protein
#3	ruvC	107	Crossover Junction Endonuclease
#4	CT503	286	hypothetical protein
#5	gapA	43	Glyceraldehyde-3-P Dehydrogenase
#6	rs11	21	S11 Ribosomal Protein
#7	rs13	55	S13 Ribosomal Protein
#8	secY	22	Translocase
#9	rl18	21	L18 Ribosomal Protein
#10	rl6	27	L6 Ribosomal Protein
#11	rl16	32	L16 Ribosomal Protein
#12	rl2	23	L2 Ribosomal Protein
#13	rl3	300	L3 Ribosomal Protein
#14	cutE	63	Apolipoprotein N-Acetyltransferase
#15	yciA	135	Acyl-CoA Thioester Hydrolase
#16	CT538	300	hypothetical protein

Motif 1
      TAAAGGGGCTCCCTTACTAGCTTA	14	49	0
TTTTACTAGTGGAGCTTCCTTGGAAGAAAA	13	21	0
TCTAGGGGTAGGGGCATCCTGAATCGACTA	16	112	0
TAACTTCTAAGGGGATTCTTTTTCTCTCAT	14	11	1
     ACGAAGGGCCTCCCTTAAAGTAATA	7	40	0
AAGCCTTTTGGGAGATTCCTGATTTCGTTA	3	15	1
TTTTTGGTGTGGGATTTCTTAGCGTCAAGA	13	84	1
TATTTAACTCGGGGTATCTTTTTG      	4	272	1
CAAAGAAAACGCGGCTCCTTAAAGCAAACA	13	168	0
  TCCTCCAAGGAATTTCTTGATTTTCTTC	15	8	1
CGTGCGTGCTAGAACTTCTTGTAAAGCTGT	4	67	1
ATGGGCGGAAAGGCTTCCCTTTAGAAGGAG	16	220	1
          **********
MAP Score: 11.2637

Motif 2
GAGAGTTTTATCTCTTTTTTTTCTAACTAA	0	54	0
AAAAGTTTGCTTTCTTTTTTAAAAAAATCT	2	63	0
TGTTAATCTGTTTCTTTTTCAAAAAAAGTT	2	109	1
AGAATAAAAATTTCTTCTTCCTATCTTTTG	2	160	0
  GAAGTTCATTGCTTTTTTTTAGAACTTT	4	8	1
GAGACAATAATACCTTTTTGATTTATAGAT	4	233	1
TAACTCGGGGTATCTTTTTG          	4	276	1
TATTCTTCTCTTCCTTCTTTA         	12	1	0
TTTTTCAGGCTTTGTTTTTGCGATTTTTGG	13	61	1
GGAGCCGCGTTTTCTTTGTCGTGGAAATCG	13	180	1
TTCTAAGGGGATTCTTTTTCTCTCATCTTG	14	15	1
ATTTCTTGATTTTCTTCTATATCGAGACTA	15	21	1
TAGGCCTGTTTTGCTTTTTGTAAAAATACT	16	154	1
TGGCAAACTGATTCTTCTTTTAATCACCAG	16	251	0
  ACTTATCCTTACTTTTTTCAGTTGCTTA	16	282	0
          **********
MAP Score: 10.3157

Motif 3
          TTTGGATTAGCGAATAAATAACTACTAT	1	0	1
AGGAGCCGCGTTTTCTTTGTCGTGGAAATCGCTCTTGC	13	179	1
GTTAGGCCTGTTTTGCTTTTTGTAAAAATACTTTTGCA	16	152	1
TTAGTAACCCTTTCCTTTATTGTGTAAAATTTGCACAA	3	42	1
TAAAAGTTTGCTTTCTTTTTTAAAAAAATCTTTGCTAT	2	56	0
AGTTTTATCTCTTTTTTTTCTAACTAAAGTCTTTTCCT	0	43	0
TTTACACAAACTTTTTTTGAAAAAGAAACAGATTAACA	2	109	0
CCCTTACTAGCTTACATTCAAGATGAGAGAAAAAGAAT	14	25	0
ACATAGAAGTTTTTCATTTGAATTCAAAGTCTTATTGA	16	30	1
ACAGAAGTATTTTACTCTGCCGAAAAAACAACACTTAA	2	211	1
GATTAACAACCTTTTTATACAGATAAAAGTTTGCTTTC	2	79	0
GTCTTGTCATTTTCTATATTTGTGCAAATTTTACACAA	3	61	0
GGATTGTATGTTAAAGTTCTAAAAAAAAGCAATGAACT	4	12	0
          ***   **   **  ***
MAP Score: 7.08562

Motif 4
ACACAAACTTTTTTTGAAAAAGAAACAGATT	2	113	0
CCTGTTTTGCTTTTTGTAAAAATACTTTTGC	16	158	1
TACTCTCACTTCCTTGCAAAAGTATTTTTAC	16	173	0
TTATCTATATTTCTAGGAAAAGACTTTAGTT	0	29	1
GTGCTAGAACTTCTTGTAAAGCTGTGGCGAG	4	72	1
GTAGTCAGTGTTTTCGAAAAATTAGCATCA 	5	9	0
CATTCCACCATCTGAGCAAAAACGACGAGGA	4	115	0
TTTGCTTTCTTTTTTAAAAAAATCTTTGCTA	2	57	0
ATTCAAAGTCTTATTGAAAAACGTAATGAGC	16	51	1
TCAAAAAAAGTTTGTGTAAAGAGGGTCTATC	2	127	1
TATGTTAAAGTTCTAAAAAAAAGCAATGAAC	4	13	0
CTAATTACACTTTTAGCAAACGGCCATGCCC	13	225	0
TAGTGGAGCTTCCTTGGAAGAAAACTTATAA	13	14	0
CAAACTTTTATCTGTATAAAAAGGTTGTTAA	2	84	1
   CTAGAACTTTTAGGTAAAGTTT      	8	7	1
ATTTTCTATATTTGTGCAAATTTTACACAAT	3	60	0
          ****** ****
MAP Score: 6.77955

Motif 5
CTTTTTGTAAAAATACTTTTGCAAGGAAGTGAGAGTAGG	16	167	1
AGCGTCAAGAAAAATCTCTTGTGTGGATGTCGCAGGTCA	13	104	1
ATTTGAATTCAAAGTCTTATTGAAAAACGTAATGAGCTT	16	45	1
ATATGGGCGGAAAGGCTTCCCTTTAGAAGGAGGCTGGTG	16	218	1
CGGCAGAGTAAAATACTTCTGTTTGATGGGAGGGGGGGG	2	194	0
GTGCTCAGAACAAGACTCGAACTTGCACGGGCCAAAGCC	4	174	0
          AAATTCTCTCGACTGTTTGTTATCTATAT	0	0	1
GCCGAAAAAACAACACTTAAGTATAGTTGGGTATCAAAA	2	229	1
GAGGTATAGCAAAGATTTTTTTAAAAAAGAAAGCAAACT	2	51	1
CTTTTTCAAAAAAAGTTTGTGTAAAGAGGGTCTATCTCC	2	122	1
      TAGTAAAGCCTTTTGGGAGATTCCTGATTTCGT	3	4	1
AAAAGAGATAAAACTCTCAACACTACAGCAT        	0	66	1
ATTTCTAGGAAAAGACTTTAGTTAGAAAAAAAAGAGATA	0	37	1
   AAAATAACAATTTTTGACCTAAGATGCTTATATTAC	7	7	1
AAAAGAAAGCAAACTTTTATCTGTATAAAAAGGTTGTTA	2	75	1
          ***  ***     ** * *
MAP Score: 5.44963

Motif 6
          TTTCCATAGACGGTTGATAAATCAATC	2	0	1
AATACTTCTGTTTGATGGGAGGGGGGGGGGGGAGAAT	2	185	0
TCCATTGTAGCTTTTCCAGTCGTGCGTGCTAGAACTT	4	47	1
GCTAGAACTTCTTGTAAAGCTGTGGCGAGGACTCTTT	4	74	1
CCTCGTCGTTTTTGCTCAGATGGTGGAATGGTAGACA	4	116	1
 TGCAGATAGGTTATAAGGGTGTGTGAATTATT    	11	9	1
AGAAAAATCTCTTGTGTGGATGTCGCAGGTCATATAC	13	111	1
GTGGAAATCGCTCTTGCAGGATGGAGGGCATGGCCGT	13	200	1
TCTGTGAAGCGTTGTCAAGTTGTGTGATAAGGTAATT	13	269	1
GGCTATTAGACTCATATAGAAGGGTGAT         	15	117	1
CCTCCCCATGCTCTAGGGGTAGGGGCATCCTGAATCG	16	116	0
TAAAAATACTTTTGCAAGGAAGTGAGAGTAGGTAGAG	16	174	1
AAAGGCTTCCCTTTAGAAGGAGGCTGGTGATTAAAAG	16	228	1
          ***    **  *** **
MAP Score: 4.25794

Motif 7
TAAGATTCTCGGAGGTATAGCAAAGATTTTTTTAA	2	40	1
ATGGGAGGGGGGGGGGGGAGAATAAAAATTTCTTC	2	173	0
GTGTTGTTTTTTCGGCAGAGTAAAATACTTCTGTT	2	210	0
      TAAAGAAGGAAGAGAAGAATAAC      	12	4	1
TTACAGAGATGACTGGGGAGTAGAGGTGGGCCTGT	15	58	1
TACCCCTAGAGCATGGGGAGGTTAGGCCTGTTTTG	16	132	1
GGAAGTGAGAGTAGGTAGAGAACAGGGATATGGGC	16	191	1
          *  ** **** * **
MAP Score: 4.07958

Motif 8
     TTTCCATAGACGGTTGATAAATCAATCGCT	2	5	1
TTTGATGGGAGGGGGGGGGGGGAGAATAAAAATTT	2	177	0
 CAAATTAAAAGATTAGGACGGTAACGA       	10	9	1
         TAAAGAAGGAAGAGAAGAATAAC   	12	1	1
ATTAGGCACCGGGGGCGGTCTGTGAAGCGTTGTCA	13	251	1
TATCCATTACAGAGATGACTGGGGAGTAGAGGTGG	15	52	1
CTGGGGAGTAGAGGTGGGCCTGTAACTCTGAGACT	15	70	1
CAAGGAAGTGAGAGTAGGTAGAGAACAGGGATATG	16	188	1
TAGAGAACAGGGATATGGGCGGAAAGGCTTCCCTT	16	206	1
CTTCCCTTTAGAAGGAGGCTGGTGATTAAAAGAAG	16	233	1
          ****  **  ** **
MAP Score: 3.67736

Motif 9
TTGATGGGAGGGGGGGGGGGGAGAATAAAAATT	2	178	0
AAACAAAGGCGGCGAATGGGCAATGGTATATGA	13	140	0
AATCGCTCTTGCAGGATGGAGGGCATGGCCGTT	13	205	1
AGTGTAATTAGGCACCGGGGGCGGTCTGTGAAG	13	245	1
CCATTACAGAGATGACTGGGGAGTAGAGGTGGG	15	55	1
CCATGCTCTAGGGGTAGGGGCATCCTGAATCGA	16	115	0
CCCTACCCCTAGAGCATGGGGAGGTTAGGCCTG	16	129	1
GTAGAGAACAGGGATATGGGCGGAAAGGCTTCC	16	205	1
CCCTTTAGAAGGAGGCTGGTGATTAAAAGAAGA	16	236	1
          ** *  *******
MAP Score: 2.95059

Motif 10
         TAGTAAAGCCTTTTGGGAGATTC	3	1	1
AATCCCTTGGGCTTTGGCCCGTGCAAGTTCGA	4	165	1
TATTACTTTAAGGGAGGCCCTTCGT       	7	40	1
TTAGGCACCGGGGGCGGTCTGTGAAGCGTTGT	13	252	1
TAAGCTAGTAAGGGAGCCCCTTTA        	14	49	1
TCTACTCCCCAGTCATCTCTGTAATGGATAGT	15	50	0
TGGGGAGTAGAGGTGGGCCTGTAACTCTGAGA	15	71	1
TAGTCGATTCAGGATGCCCCTACCCCTAGAGC	16	112	1
AGCATGGGGAGGTTAGGCCTGTTTTGCTTTTT	16	141	1
CTCCTTCTAAAGGGAAGCCTTTCCGCCCATAT	16	218	0
          ***  *******
MAP Score: 2.88214

Motif 11
TATTTCTAGGAAAAGACTTTAGTTAGAAAA	0	36	1
TCTTTTTTAAAAAAATCTTTGCTATACCTC	2	51	0
ATCTGTATAAAAAGGTTGTTAATCTGTTTC	2	93	1
GGGGGAGAATAAAAATTTCTTCTTCCTATC	2	165	0
CCCATCAAACAGAAGTATTTTACTCTGCCG	2	203	1
GGAATCTCCCAAAAGGCTTTACTA      	3	4	0
ATCTTAGGTCAAAAATTGTTATTTT     	7	5	0
ACAAAGCCTGAAAAATCGTTCTAGGTTTTA	13	46	0
TAGCGTCAAGAAAAATCTCTTGTGTGGATG	13	103	1
TGCTCGACATAGAAGTTTTTCATTTGAATT	16	24	1
ACTTCCTTGCAAAAGTATTTTTACAAAAAG	16	167	0
          **********
MAP Score: 1.50152