AlignACE 3.0 10/20/99
AlignACE2 -i CT/CT_operons004_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944241830
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	araD	83	Ribulose-P Epimerase
#1	murE	300	UDP-N-acetylmuramoylalanylglutamyl DAP Ligase
#2	yabC	277	PBP2B Family methyltransferase
#3	pbpB	300	PBP2-transglycolase/transpeptidase
#4	secA_2	258	Protein Translocase
#5	rodA	91	Rod Shape Protein
#6	zntA	23	Metal Transport P-type ATPase
#7	CT728	36	hypothetical protein
#8	serS	41	Seryl tRNA Synthetase
#9	efp_2	219	Elongation Factor P
#10	murF	300	UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diaminoligase
#11	mraY	145	Muramoyl-Pentapeptide Transferase

Motif 1
TTGTTTTGATAGAAATCGTTTTTATTACTACAAA	3	225	1
ATTACTACAAAGAAAGTGTTTTTAAACGGGCTCC	3	248	1
GTAAAAGATCAGAATTTCTTTTTAGAATAGAAAT	11	10	1
AGGAAAGAAAAGAGAATCTTTTTAGGAGATGGCG	10	198	1
TCTCGGTTTCAGAGCGATTTTTTTCGCAAAAA  	3	8	0
TATAATGGTTAGAGAATCTTTTTTTCTAAAAACA	9	23	1
GCTCCATATAAGAGTTACTTTTTTTGTGAAAGAG	1	134	1
AGAAAATCTAAGAATTTGTTTTGATAGAAATCGT	3	210	1
AAACTATTTGAGAAAGCTTTTTGAAGCCCTTGTG	1	255	1
AAAAAGCTTCAGGAAAAATTTTTTCTTCATCCTG	10	90	0
TTTAGCTACAAGGGAATTTTTTGAAAGCTGTACT	2	190	1
TATGGAGCAAAGAAATGTTTTGTTTGTGAGATGT	1	108	0
AAAAGAAAAGAGGAGATTTTTGTAAGAAAATCTA	3	186	1
CAACCTCTAAAGAAACGCTTTTCACTCATATAAA	10	122	0
CAAAGACAAGAGAACTCGTCTTTTTACTCTTTCA	1	160	0
AGTCGCTGTAAGATGCTCTTTTTAACTTGCCTTT	11	56	1
TAATGGATATAGAATAATTTTTAAGACTGCTAGT	10	162	1
AAAATCTCAAAGAAATAGATTTTAGAAGATGCAC	10	237	0
TTGTTGAGAATGAGAGGGTTTTGAGTTAATTACA	3	69	1
CTATACAACAAGGATGGTTCTTTTCTATTTCTTT	4	184	0
TCATAAAAATTGAACTGTTTTGTAATTAACTCAA	3	89	0
GTGCATTTTCTGGGATCTTTTTTTTGTAAGCAGG	10	60	1
GAGAACGTAAAGCAAAGGTTTTTAAGGTATTAGA	2	80	1
          ****    ******
MAP Score: 28.4699

Motif 2
ATGAAATTGCTCTTTTCTTTATTATTAGTT	1	74	0
ACAAAACATTTCTTTGCTCCATATAAGAGT	1	119	1
AGAACTCGTCTTTTTACTCTTTCACAAAAA	1	154	0
AGTTCTCTTGTCTTTGCTCTTTCTCTGACA	1	178	1
ACCTTAAAAACCTTTGCTTTACGTTCTCCC	2	78	0
GCCAACATGGCTTTTGCTCTCGGTTTCAGA	3	29	0
AAAAATCTCCTCTTTTCTTTTAGCCAAACC	3	177	0
         CCTTTTTCTCTCTTGTAAGTA	4	1	1
GCTCGAGTGCTTTTTGTTTTCTTTTTCTCT	4	61	1
TTTTTGTTTTCTTTTTCTCTAGGAAAGTCT	4	71	1
TGCACGGATTTCTTTTCTCTCGAGTAGCCT	4	115	1
CAAGGATGGTTCTTTTCTATTTCTTTTTGA	4	180	0
GGTTAGAGAATCTTTTTTTCTAAAAACATA	9	29	1
TAACCCGTTATCTTTTCTCCATCTATGTTA	9	191	0
TTTTCTGGGATCTTTTTTTTGTAAGCAGGA	10	65	1
TCAGGAAAAATTTTTTCTTCATCCTGCTTA	10	86	0
AAAAAGATTCTCTTTTCTTTCCTCTACTAG	10	191	0
          **********
MAP Score: 27.7648

Motif 3
AGCCTGGCATAAGGAAAGCGGGAGAGGAAA	1	46	1
ACTAATAATAAAGAAAAGAGCAATTTCATA	1	75	1
AGAAAGAGCAAAGACAAGAGAACTCGTCTT	1	172	0
GTCATCTGTCAGAGAAAGAGCAAAGACAAG	1	184	0
TAATCGGGGGAGGGAAAAAGTCAAGTATGG	2	43	1
  TTTTTGCGAAAAAAATCGCTCTGAAACC	3	8	1
TCTGAAACCGAGAGCAAAAGCCATGTTGGC	3	29	1
GTTTGGCTAAAAGAAAAGAGGAGATTTTTG	3	178	1
ATTTGTTTTGATAGAAATCGTTTTTATTAC	3	223	1
TTATTACTACAAAGAAAGTGTTTTTAAACG	3	246	1
TACTTACAAGAGAGAAAAAGG         	4	1	0
AGACTTTCCTAGAGAAAAAGAAAACAAAAA	4	71	0
TAATTATCAAAAAGAAATAGAAAAGAACCA	4	174	1
CTATGTTTTTAGAAAAAAAGATTCTCTAAC	9	30	0
TGTTCTCGTGAGGGTAATAGTTGGGCTACT	9	78	1
TGCAAGAAAGAGGGAAAGCGTTTGTTTCGC	9	127	1
TAGTAGAGGAAAGAAAAGAGAATCTTTTTA	10	192	1
AAAAAATCTCAAAGAAATAGATTTTAGAAG	10	243	0
TCTTTTTAGAATAGAAATAGTTAACTTTCA	11	26	1
          **********
MAP Score: 25.5503

Motif 4
AAAGAAATGTTTTGTTTGTGAGATGTAATTATG	1	101	0
AAACAAAACATTTCTTTGCTCCATATAAGAGTT	1	117	1
TAAGAGTTACTTTTTTTGTGAAAGAGTAAAAAG	1	142	1
GTCTTTGCTCTTTCTCTGACAGATGACGTAGTT	1	187	1
TTCAGAGCGATTTTTTTCGCAAAAA        	3	2	0
AATCTCCTCTTTTCTTTTAGCCAAACCCCCATC	3	171	0
ATTCTTAGATTTTCTTACAAAAATCTCCTCTTT	3	192	0
TTAAAAACACTTTCTTTGTAGTAATAAAAACGA	3	240	0
      CCTTTTTCTCTCTTGTAAGTAAGCCCA	4	4	1
TTTTGTTTTCTTTTTCTCTAGGAAAGTCTAGAA	4	72	1
ACGGATTTCTTTTCTCTCGAGTAGCCTTTCCCT	4	118	1
TCGAGTAGCCTTTCCCTGAGAGAGTTTGTGCGT	4	134	1
TTCTTTTCTATTTCTTTTTGATAATTATCTTTT	4	168	0
TTAGAGAATCTTTTTTTCTAAAAACATAGTATG	9	31	1
AAGAAACGCTTTTCACTCATATAAAAAAGCTTC	10	114	0
AAGATTCTCTTTTCTTTCCTCTACTAGCAGTCT	10	185	0
CTAAAATCTATTTCTTTGAGATTTTTTAGTTGT	10	246	1
AAGATCAGAATTTCTTTTTAGAATAGAAATAGT	11	14	1
          ********  * *
MAP Score: 16.8562

Motif 5
TTTCCTCTCCCGCTTTCCTTATGCCAGGCTG	1	45	0
TATGAAATTGCTCTTTTCTTTATTATTAGTT	1	74	0
TCACAAACAAAACATTTCTTTGCTCCATATA	1	113	1
GCTCCATATAAGAGTTACTTTTTTTGTGAAA	1	134	1
TACCTTAAAAACCTTTGCTTTACGTTCTCCC	2	78	0
TGTATTGAAGAGCTGTGCTTTTAACTAAACA	2	136	1
ATTTTTTGAAAGCTGTACTTTCGCAGCTAAG	2	205	1
ACATCTTGCCAACATGGCTTTTGCTCTCGGT	3	35	0
CAAAAATCTCCTCTTTTCTTTTAGCCAAACC	3	177	0
ACAAATTCTTAGATTTTCTTACAAAAATCTC	3	198	0
AGAAAATCTAAGAATTTGTTTTGATAGAAAT	3	210	1
CCGTTTAAAAACACTTTCTTTGTAGTAATAA	3	246	0
AAAGAGGGAAAGCGTTTGTTTCGCGACATTC	9	133	1
ATTTTCTGGGATCTTTTTTTTGTAAGCAGGA	10	64	1
ATGAGTGAAAAGCGTTTCTTTAGAGGTTGAA	10	127	1
TAAAAAGATTCTCTTTTCTTTCCTCTACTAG	10	191	0
GTAAAAGATCAGAATTTCTTTTTAGAATAGA	11	10	1
TTTAAGATAGAGAATTTCTTATAGGAGCTTC	11	102	1
          *** *******
MAP Score: 10.4185

Motif 6
CACAAGGGCTTCAAAAAGCTTTCTCAAATAG	1	258	0
TGTAATTAACTCAAAACCCTCTCATTCTCAA	3	72	0
TACCAACAACTAAAAAATCTCAAAGAAATAG	10	253	0
AGATTTTCTTACAAAAATCTCCTCTTTTCTT	3	188	0
TTCACTCATATAAAAAAGCTTCAGGAAAAAT	10	105	0
TATTCCAAACACAAAAATCTTAGGTTTTGGA	3	133	0
AGTACAGCTTTCAAAAAATTCCCTTGTAGCT	2	193	0
AATCTTGTGGTCAAAAATTTTAACCCTCTAC	0	30	0
ATCTAATACCTTAAAAACCTTTGCTTTACGT	2	84	0
GGAGCCCGTTTAAAAACACTTTCTTTGTAGT	3	251	0
GAGTGCATCTTCTAAAATCTATTTCTTTGAG	10	235	1
GAAAAAGAAAACAAAAAGCACTCGAGCAATA	4	57	0
AATCTTTTTTTCTAAAAACATAGTATGAAGA	9	37	1
          ******* ***
MAP Score: 8.7756

Motif 7
ATGTAATTATGAAATTGCTCTTTTCTTTATTATT	1	78	0
ATGGAGCAAAGAAATGTTTTGTTTGTGAGATGTA	1	107	0
CTCTTTCACAAAAAAAGTAACTCTTATATGGAGC	1	134	0
TGAAAGAGTAAAAAGACGAGTTCTCTTGTCTTTG	1	160	1
TAATACCTTAAAAACCTTTGCTTTACGTTCTCCC	2	78	0
GGAATTTTTTGAAAGCTGTACTTTCGCAGCTAAG	2	202	1
AGTTAATTACAAAACAGTTCAATTTTTATGAGTT	3	92	1
GTTAATTTCCAAAACCTAAGATTTTTGTGTTTGG	3	126	1
TGGCTAAAAGAAAAGAGGAGATTTTTGTAAGAAA	3	181	1
TTTTTGTAAGAAAATCTAAGAATTTGTTTTGATA	3	202	1
TTGTAGTAATAAAAACGATTTCTATCAAAACAAA	3	224	0
AGCCCGTTTAAAAACACTTTCTTTGTAGTAATAA	3	246	0
CGAGAGAAAAGAAATCCGTGCATTCAGGCACATT	4	103	0
TGTTTTTAGAAAAAAAGATTCTCTAACCATTATA	9	23	0
TATGAAGATGGAACAAGTTGTTCTCGTGAGGGTA	9	60	1
TCTTGCAAAAGAAAACTATACTTTTAAGTAGCCC	9	100	0
AAGAAAGAGGGAAAGCGTTTGTTTCGCGACATTC	9	130	1
AAGCTTCAGGAAAAATTTTTTCTTCATCCTGCTT	10	87	0
TATATGAGTGAAAAGCGTTTCTTTAGAGGTTGAA	10	124	1
TAGAGGAAAGAAAAGAGAATCTTTTTAGGAGATG	10	195	1
TGCATCTTCTAAAATCTATTTCTTTGAGATTTTT	10	238	1
TTTTAGAATAGAAATAGTTAACTTTCAAGTCGCT	11	29	1
CTTGCCTTTTGAAAGCTTAAGTTTAAGATAGAGA	11	81	1
          **** ** *  ***
MAP Score: 8.02845

Motif 8
CCCTCTACGATAAGAAGGAGAGTGTACA          	0	0	0
GTGCAGCCTGGCATAAGGAAAGCGGGAGAGGAAACTAA	1	42	1
TTGTGAGATGTAATTATGAAATTGCTCTTTTCTTTATT	1	81	0
AGAGTTACTTTTTTTGTGAAAGAGTAAAAAGACGAGTT	1	144	1
CTACGTCATCTGTCAGAGAAAGAGCAAAGACAAGAGAA	1	180	0
CTCCCCCGATTATGATTGAGATTGTGAGCCTCTCAAGG	2	17	0
AAAATCGCTCTGAAACCGAGAGCAAAAGCCATGTTGGC	3	21	1
TGTTGATTGTTGAGAATGAGAGGGTTTTGAGTTAATTA	3	63	1
AAGAATTTGTTTTGATAGAAATCGTTTTTATTACTACA	3	219	1
TCGAGTAGCCTTTCCCTGAGAGAGTTTGTGCGTAAAAA	4	134	1
AAGATAATTATCAAAAAGAAATAGAAAAGAACCATCCT	4	170	1
TATAGGCGCCTTTAAATAAGAGGGTAGGTTCGTTTCAA	4	213	1
        CCTTATAGTGAGATAGAAAGCTAGAGGAGC	7	2	1
TACTCAACCTGAAAAATCAGATAGCGAGAGAGATGCAA	8	11	1
ATAGTTTTCTTTTGCAAGAAAGAGGGAAAGCGTTTGTT	9	115	1
AAAGAGAATCTTTTTAGGAGATGGCGGGGGAGTGCATC	10	206	1
AACTAAAAAATCTCAAAGAAATAGATTTTAGAAGATGC	10	239	0
          * * *  ***** *   *
MAP Score: 6.80674