AlignACE 3.0 10/20/99
AlignACE2 -i CT/CT_profile001_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944243198
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	rs1	244	S1 Ribosomal Protein
#1	zwf	300	Glucose-6-P Dehyrogenase
#2	acpP	300	Acyl Carrier Protein
#3	rl7	31	L7/L12 Ribosomal Protein
#4	rl10	21	L10 Ribosomal Protein
#5	rl1	22	L1 Ribosomal Protein
#6	rl11	105	L11 Ribosomal Protein
#7	proS	200	Prolyl tRNA Synthetase
#8	hrcA	68	HTH Transcriptional Repressor
#9	dnaK	25	HSP-70
#10	pcnB_1	214	PolyA Polymerase
#11	CT645	100	hypothetical protein
#12	clpP_2	166	CLP Protease
#13	rsbV_2	153	Sigma Regulatory Factor

Motif 1
CTTAAATTAATTTTAAGAAACAAACAAAAGAAAC	7	40	1
CCCTTGAAAATTTTTAGAAACATATAGGTGATTT	10	74	1
TTCCCCCTCGTTTTGAGAGGAATACTAAGGTAGA	6	69	1
GAGAGAAATCTTTTTAGGCACATATTCGTTTTTT	1	20	1
GACTTTGTAGTTTTTAGGAGAACATCATTAA   	0	223	1
ATCTTGCCTTTTTTAAGGTGAATATTTACACTAC	0	182	1
AGAGCGCTCATTTTAAAAAATAAAAACATCTTTT	11	40	1
AAGAATTGCTTTTTTAAATAGAAAAAAAGTGAGA	13	44	1
TTCTTTATCTTTTTAAAATGAAGAGCGCTCATTT	11	19	1
AGTGTTAATTTTTTAAGAGAGAGCCCACAATACC	1	55	0
        TGTTTTATGAGAGAGAAATCTTTTTA	1	2	1
AAAAACATCTTTTTCAAGAAAAACATTAATTATA	11	61	1
ATCCTTGAGATTTTCAAGGATATCGGAGGGGG  	0	8	0
   TTCTAAGTTTAAAGAGGAAAA          	4	7	1
AACATCAAGTTATTAAGAAATAAAGAATCTGAAC	7	71	1
TAGTGAAACTTTTTTTAATAAAGAGATGCATCTT	0	127	1
AAAAATTACGTTTACAAGGGCAAAATCACCTATA	10	96	0
AGGCGCTTCATTTTGAAATGAAAGTAAGGATCAT	2	273	1
          **** *** * * *
MAP Score: 23.6328

Motif 2
TGCATCTCTTTATTAAAAAAAGTTTCACTAGTTTCTGTGTAATTTT	0	111	0
TTATTACTTGTAGTGCAAGGGAAATCTTGCCTTTTTTAAGGTGAAT	0	159	1
TTAAGGTGAATATTTACACTACTCTTTTTGACTTTGTAGTTTTTAG	0	194	1
GAGAGAGAAATCTTTTTAGGCACATATTCGTTTTTTTGGTATTGTG	1	18	1
ACAAACAAAGTTTTCGGATAGACGTCCTTCCTTTGTTAAATTGTAT	1	216	0
TTTATGCTTCTCGCCCTAAGCCCTTCTGAGTTTTTGATTTAGAAGG	2	13	1
TTGGTTACTCTAGTTTTATTTAAAGCTAGATTTTTTTTGCTATAGA	2	164	1
TTCTCTATGTTCTTATAATTTAACTTTTTCGTTTTTCCCCCTCGTT	6	35	1
TTTGTTTGTTTCTTAAAATTAATTTAAGCGTTTTTGCAAATTTTGT	7	22	0
ATTCTTTATTTCTTAATAACTTGATGTTTCTTTTGTTTGTTTCTTA	7	53	0
CATAGGAGTGTTTCTAGATCAATCTCTGTGATTTTTTTGTTCTTAT	7	118	0
CCCTTGAAAATTTTTAGAAACATATAGGTGATTTTGCCCTTGTAAA	10	74	1
TTAATGTTTTTCTTGAAAAAGATGTTTTTATTTTTTAAAATGAGCG	11	44	0
TGCGTAGGTGTATTTTGAATTAGATGGGGTCTTTCTTTTCTAGGGT	12	71	1
ACCTTTTATCTTCCAATAAGGGTTTCTCACTTTTTTTCTATTTAAA	13	56	0
          * **   *      *      *****
MAP Score: 11.5579

Motif 3
TTTTTTAATAAAGAGATGCATCTTATTACTTGTA	0	137	1
CAAAGTCAAAAAGAGTAGTGTAAATATTCACCTT	0	196	0
TAGTTTTTAGGAGAACATCATTAA          	0	230	1
TGTTTTATGAGAGAGAAATCTTTTTAGGCACATA	1	10	1
AATTTTTTAAGAGAGAGCCCACAATACCAAAAAA	1	49	0
AGGGCTTAGGGCGAGAAGCATAAACCG       	2	3	0
TATAGACTCTGCGAGAAACCCAATGGCCCATTTT	2	204	1
   TTAGTTAAAGAGCTGCATAATT         	5	7	1
AGAAACAAACAAAAGAAACATCAAGTTATTAAGA	7	55	1
     AAGGAGAGAGAGTCATAAAGCTGTTGATG	10	5	1
AGCTTTCCTGGAGAGAACTCTAAAAGCCTTCTTG	10	144	1
TAAAAAGATAAAGAAAAACGCTAA          	11	0	0
CATCTTTTTCAAGAAAAACATTAATTATAAACAG	11	66	1
CGCTTGACCCAAGAGACACTTAAACATAGAATTC	12	27	1
GACCCTAGAAAAGAAAGACCCCATCTAATTCAAA	12	84	0
TTCTAGGGTCAAGAGTAGCCATAACGTAAGCACA	12	108	1
AGAATCTAAAAAGAATTGCTTTTTTAAATAGAAA	13	34	1
GAAAAAAAGTGAGAAACCCTTATTGGAAGATAAA	13	64	1
TTCTTCCGTCAAGAATTTCATCATTAGATTACAA	13	108	1
          ******  * * **
MAP Score: 11.0166

Motif 4
GAAAAAGATGTTTTTATTTTTTAAAATGAGCGCTC	11	41	0
TAAACGTAATTTTTTCTATTATAGGAAGAGCTTTC	10	116	1
TTAGATGGGGTCTTTCTTTTCTAGGGTCAAGAGTA	12	90	1
TAGTATAGAGTGTTAATTTTTTAAGAGAGAGCCCA	1	62	0
ATATAGGTGATTTTGCCCTTGTAAACGTAATTTTT	10	95	1
          TGTTAACATTCTAAAAAATAAGGGT	3	0	1
TTAGCGTTTTTCTTTATCTTTTTAAAATGAAGAGC	11	10	1
TTTAGGCACATATTCGTTTTTTTGGTATTGTGGGC	1	32	1
TCTGTGATTTTTTTGTTCTTATTGGATTTTAACTA	7	105	0
GCAAGGGAAATCTTGCCTTTTTTAAGGTGAATATT	0	173	1
TTATAATTAATGTTTTTCTTGAAAAAGATGTTTTT	11	61	0
TTTCTCACTTTTTTTCTATTTAAAAAAGCAATTCT	13	45	0
AAAGCTAGATTTTTTTTGCTATAGACTCTGCGAGA	2	185	1
ATGTTTCTTTTGTTTGTTTCTTAAAATTAATTTAA	7	41	0
ACACTACTCTTTTTGACTTTGTAGTTTTTAGGAGA	0	209	1
TAGTTCAGATTCTTTATTTCTTAATAACTTGATGT	7	72	0
          * **  * ** ****
MAP Score: 10.6146

Motif 5
GTTCTCTCCAGGAAAGCTCTTCCTATAATAG	10	131	0
TTTGATCGCAGGAAAACGCTTGACCCAAGAG	12	11	1
ACAAAATTTGCAAAAACGCTTAAATTAATTT	7	22	1
GCTCAGTATGCTAAAACCCTTACGCATAGAA	2	107	1
GAAAAAAAGTGAGAAACCCTTATTGGAAGAT	13	64	1
CTTGACCTCTAGGAAGCTCTTTCCTGCTTTA	1	186	1
TGCTTAAGATGGAAGGCGCTTCATTTTGAAA	2	260	1
ACGAAACAATATAAAGCACTTCCTTCCCT  	7	181	1
GGAGAGAACTCTAAAAGCCTTCTTGCTCAAG	10	153	1
ATCAAAAACTCAGAAGGGCTTAGGGCGAGAA	2	20	0
ACATCCCCATGGAAAGGACTGTCAATCCTTG	0	35	0
        TTAAAAAACTCTGTTTATAATTA	11	87	0
CGCTTGACCCAAGAGACACTTAAACATAGAA	12	27	1
GTTGCGAGCGCTAAAATTCTTGACCAGTGGA	8	19	1
AAAAGATAAAGAAAAACGCTAA         	11	1	0
TAATCTAATGATGAAATTCTTGACGGAAGAA	13	108	0
          ******* ***
MAP Score: 6.23656

Motif 6
CTTTTTTTAATAAAGAGATGCATCTTATTACTT	0	135	1
  TGTTTTATGAGAGAGAAATCTTTTTAGGCAC	1	8	1
AATTTTTTAAGAGAGAGCCCACAATACCAAAAA	1	50	0
TATAAAGCAGGAAAGAGCTTCCTAGAGGTCAAG	1	186	0
TAGAATGTGCGAAAGAGTAGACTTGTAGGGATT	2	133	1
     TTAGTTAAAGAGCTGCATAATT      	5	5	1
TGTTTCGTGTGGAAGAGCATCTTAGCATAGGAG	7	156	0
    AGGGAAGGAAGTGCTTTATATTGTTTCGT	7	181	0
       AAGGAGAGAGAGTCATAAAGCTGTTG	10	3	1
TTCTATTATAGGAAGAGCTTTCCTGGAGAGAAC	10	129	1
AGAGCTTTCCTGGAGAGAACTCTAAAAGCCTTC	10	142	1
CTTTTTAAAATGAAGAGCGCTCATTTTAAAAAA	11	27	1
TTTTCTAGGGTCAAGAGTAGCCATAACGTAAGC	12	106	1
GAAGATAAAAGGTAGAGACTTCTTCCGTCAAGA	13	89	1
          ********   **
MAP Score: 5.6806

Motif 7
CTAGTGAAACTTTTTTTAATAAAGAGATGCATCT	0	126	1
AATCTTGCCTTTTTTAAGGTGAATATTTACACTA	0	181	1
TACACTACTCTTTTTGACTTTGTAGTTTTTAGGA	0	208	1
CACATATTCGTTTTTTTGGTATTGTGGGCTCTCT	1	38	1
TCGTGGTTATTTTTGGTGCTACAGGAGACTTGAC	1	158	1
CCCTTCTGAGTTTTTGATTTAGAAGGCATTTCGT	2	33	1
AAAGCTAGATTTTTTTTGCTATAGACTCTGCGAG	2	185	1
TTTTTGCAAATTTTGTTTTTAAATCTCC      	7	4	0
AAGGCACGTCTTTTTGATCATCAACAGCTTTATG	10	23	0
TAAACGTAATTTTTTCTATTATAGGAAGAGCTTT	10	116	1
TCCTCCAGACTTTTTAACTTTCAATGTCATATA 	10	191	1
TTTCTTTATCTTTTTAAAATGAAGAGCGCTCATT	11	18	1
GAAAAAGATGTTTTTATTTTTTAAAATGAGCGCT	11	42	0
ATAATTAATGTTTTTCTTGAAAAAGATGTTTTTA	11	60	0
AAAGAATTGCTTTTTTAAATAGAAAAAAAGTGAG	13	43	1
          ***** *  ** **
MAP Score: 5.34682