AlignACE 3.0 10/20/99
AlignACE2 -i CT/CT_operons010_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944242225
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	oppA_1	176	Oligopeptide Binding Protein
#1	oppA_2	194	Oligopeptide binding protein permease
#2	CT196	223	hypothetical protein
#3	gcp_1	75	O-Sialoglycoprotein Endopeptidase
#4	oppB_1	158	Oligopeptide Permease
#5	oppC_1	31	Oligopeptide Permease
#6	vacB	292	Ribonuclease Family
#7	oppA_4	250	oligopeptide Binding Lipoprotein

Motif 1
CTTCTCCTCTCTTCTTTCTTAAGAGTAATTAA	6	82	1
TGCTATTTCATTTCTTTTGCAAAAACTCTCTA	2	171	1
AAAATGTTTCCCTCTTTTTTAAGTGTTCGCT 	3	54	1
AAAATTCAACTCTCTTTTAGAAAAAA      	7	4	0
GCTGCAAGAGCCCCTTTTTCAAGAGGCTCTTG	6	34	0
ATACGATCCTCTCCTTCCAAAATGTTTCCCTC	3	36	1
TCTATACCAGCTCCTTCCTAAATATTTTTTGA	7	65	1
GCTCTTGCAGCTTTTTTTTAAAAAATCCTTCT	6	55	1
TAGAAAAGATTCTCTCTTTAAAATGCGGAGAG	4	31	1
TCTAAAAATTTTACTTTTACAAAGTTGAAGCC	2	24	1
CAACTCTCTTTTTTTTTCTTAAAAGATTCTCT	7	36	1
ATACTGGGCATTTTTTTCATAAAGGGGGTGAT	1	12	0
GAAAAGCTTTTTCCTCTTACAAACAAGATGAT	7	118	0
ATGCTTTATTCATCTTCCTTAAGCAAGAGCCT	6	11	1
GGAAAAAGCTTTTCTTTTGCTATAATTCGCTA	7	136	1
TTTTGAAATATTTCTTTCAGTAAGTCGATCAT	7	91	1
GATGATGCAACATCTCTTAGAAATGGTGTTTA	6	163	0
CGGTACATTCTTACTTCTCAAACCCCCAAGGA	6	242	0
CCTTCCTAAATATTTTTTGAAATATTTCTTTC	7	77	1
       GAGTTTGTTTTAGAAATCCTTTATT	5	16	0
GTTAAGGTTTTTCTTTTTTTTATTGGTAACAG	1	66	1
          ********  **
MAP Score: 15.9737

Motif 2
CGCTGAAAAGAATGCTTTTCTCGTATTTTCAAAG	0	22	0
GTAAGAGGAAAAAGCTTTTCTTTTGCTATAATTC	7	130	1
AATAATTGTTAAGGTTTTTCTTTTTTTTATTGGT	1	59	1
CGTGCGTAGAAAAGATTCTCTCTTTAAAATGCGG	4	25	1
TTTTTTCTTAAAAGATTCTCTATACCAGCTCCTT	7	47	1
TTAGAAATAAAACGGTTTTTTTAATTAGTAAAAT	2	82	0
AAGAGAGGAGAAGGATTTTTTAAAAAAAAGCTGC	6	61	0
AAAAGCCAAAACTGTTTTTCTGTTACCAATAAAA	1	83	0
CTCCTTCCAAAATGTTTCCCTCTTTTTTAAGTGT	3	46	1
 TAATTTAATAAAGGATTTCTAAAACAAACTC  	5	9	1
GGCTTTTTGCTATGGTTTTTTGTACAATCCCCTG	1	110	1
GCTCCTTCCTAAATATTTTTTGAAATATTTCTTT	7	74	1
          ** * ******  *
MAP Score: 13.9229

Motif 3
CAAACAAAAACTTCTGATTCTACAGAAATACTCAAAA	0	142	1
      TTATCACCCCCTTTATGAAAAAAATGCCCAG	1	4	1
AAAGTTGAAGCCATTCTTTTGTCCCAAGTTTAGACTA	2	44	1
GAAATATCAACCGCTGGTTTAATAAAACCCAACTAGT	2	129	1
AATGCTATTTCATTTCTTTTGCAAAAACTCTCTACTT	2	169	1
ATGATACGATCCTCTCCTTCCAAAATGTTTCCCTCTT	3	33	1
GACAAGACCTCTCCGCATTTTAAAGAGAGAATCTTTT	4	34	0
AAGCTGCAAGAGCCCCTTTTTCAAGAGGCTCTTGCTT	6	31	0
GGGGCTCTTGCAGCTTTTTTTTAAAAAATCCTTCTCC	6	52	1
TCCTTCTCCTCTCTTCTTTCTTAAGAGTAATTAATCC	6	80	1
TGAAAATTCAACTCTCTTTTAGAAAAAA         	7	1	0
TTTCAACTCTCTTTTTTTTTCTTAAAAGATTCTCTAT	7	33	1
TTCTCTATACCAGCTCCTTCCTAAATATTTTTTGAAA	7	62	1
GTAAGTCGATCATCTTGTTTGTAAGAGGAAAAAGCTT	7	110	1
GAGGAAAAAGCTTTTCTTTTGCTATAATTCGCTAGTT	7	134	1
          *  *** ***   * **
MAP Score: 13.1979

Motif 4
TGGGGAAGTATTATACGTTTCTAGAATAGAACCGGCAACA	0	104	1
ACTGTTTTTCTGTTACCAATAAAAAAAAGAAAAACCTTAA	1	67	0
CTTCTAAAAATTTTACTTTTACAAAGTTGAAGCCATTCTT	2	22	1
GCCATTCTTTTGTCCCAAGTTTAGACTAGATTTTACTAAT	2	53	1
AAGATGTTTTTACTCCGTGCGTAGAAAAGATTCTCTCTTT	4	10	1
GAGTGATAATTTAACACTCTCTAGACAAGACCTCTCCGCA	4	54	0
 GATGCTTTATTCATCTTCCTTAAGCAAGAGCCTCTTGAA	6	9	1
TTAATTACTCTTAAGAAAGAAGAGAGGAGAAGGATTTTTT	6	74	0
GAAATGGTGTTTATGCCATAACAGTCAAGATACGTACTAT	6	136	0
         TTTTTTCTAAAAGAGAGTTGAATTTTCAACT	7	1	1
ATAGAGAATCTTTTAAGAAAAAAAAAGAGAGTTGAAAATT	7	30	0
AAGAAAAGCTTTTTCCTCTTACAAACAAGATGATCGACTT	7	112	0
TTTTGGTGCGTTTTCAACGAATAGAGGAGACAACGC    	7	224	1
          ** * *      ***  ***
MAP Score: 11.5409

Motif 5
TGAAAAGAATGCTTTTCTCGTATTTTCAAAG	0	22	0
AATTGTTAAGGTTTTTCTTTTTTTTATTGGT	1	62	1
CAAAGTTGAAGCCATTCTTTTGTCCCAAGTT	2	43	1
TAATGCTATTTCATTTCTTTTGCAAAAACTC	2	168	1
CTCATGATACGATCCTCTCCTTCCAAAATGT	3	30	1
CTTCCAAAATGTTTCCCTCTTTTTTAAGTGT	3	49	1
GCGTAGAAAAGATTCTCTCTTTAAAATGCGG	4	28	1
AAAAAATCCTTCTCCTCTCTTCTTTCTTAAG	6	74	1
TCAAAAACCGGCTGCCCTACTAACCCCAGAC	6	193	1
AGTTGAAAATTCAACTCTCTTTTAGAAAAAA	7	10	0
AGTTGAATTTTCAACTCTCTTTTTTTTTCTT	7	25	1
AAAGAAAAGCTTTTTCCTCTTACAAACAAGA	7	122	0
AGAGGAAAAAGCTTTTCTTTTGCTATAATTC	7	133	1
    GCGTTGTCTCCTCTATTCGTTGAAAAC	7	233	0
          *** *******
MAP Score: 8.695

Motif 6
TTTCTTTTGCAAAAACTCTCTACTTTAAATT	2	181	1
CGTGCGTAGAAAAGATTCTCTCTTTAAAATG	4	25	1
TTTTTTCTTAAAAGATTCTCTATACCAGCTC	7	47	1
AAAATACGAGAAAAGCATTCTTTTCAGCGAA	0	27	1
TTGGTAACAGAAAAACAGTTTTGGCTTTTTG	1	88	1
TACTAATTAAAAAAACCGTTTTATTTCTAAG	2	86	1
ATAGCAAAAGAAAAGCTTTTTCCTCTTACAA	7	128	0
TTCAAGATGCAAAAACATTCCTTGGGGGTTT	6	224	1
CACTCTTGGCAAAGGCCTTTTATGTTTTCAA	4	89	1
AGAAATACTCAAAAATATTTT          	0	165	1
GCCTCTTGAAAAAGGGGCTCTTGCAGCTTTT	6	39	1
CTTTTTTTTAAAAAATCCTTCTCCTCTCTTC	6	65	1
CTTTTCAGCGAAAAATACTGTGTATTTTTCT	0	46	1
          ****** ****
MAP Score: 6.74494

Motif 7
  AAATGAAACTCACTTTGAAAATACGAGAAAA	0	8	1
  TTATCACCCCCTTTATGAAAAAAATGCCCAG	1	8	1
ATTATTCAACCTCTCTATAGGATACTGGGCATT	1	32	0
TTTGCAAAAACTCTCTACTTTAAATTAATTTGG	2	186	1
TGATACGATCCTCTCCTTCCAAAATGTTTCCCT	3	34	1
CAAAATGTTTCCCTCTTTTTTAAGTGTTCGCT 	3	53	1
AGAAAAGATTCTCTCTTTAAAATGCGGAGAGGT	4	32	1
GTTAAATTATCACTCTTGGCAAAGGCCTTTTAT	4	79	1
TTAAGCAAGAGCCTCTTGAAAAAGGGGCTCTTG	6	29	1
TCCTTCTCCTCTCTTCTTTCTTAAGAGTAATTA	6	80	1
GAAAATTCAACTCTCTTTTAGAAAAAA      	7	4	0
GAATTTTCAACTCTCTTTTTTTTTCTTAAAAGA	7	29	1
          ********   **
MAP Score: 5.74926

Motif 8
AAATACGAGAAAAGCATTCTTTTCAGCGAAAA	0	28	1
AATAATTGTTAAGGTTTTTCTTTTTTTTATTG	1	59	1
AACCTTCTAAAAATTTTACTTTTACAAAGTTG	2	19	1
TACAAAGTTGAAGCCATTCTTTTGTCCCAAGT	2	41	1
ATTTCTTTTGCAAAAACTCTCTACTTTAAATT	2	180	1
CAATCTCATGATACGATCCTCTCCTTCCAAAA	3	26	1
TCTCCTTCCAAAATGTTTCCCTCTTTTTTAAG	3	45	1
CCGTGCGTAGAAAAGATTCTCTCTTTAAAATG	4	24	1
CTTTTTTTTAAAAAATCCTTCTCCTCTCTTCT	6	65	1
TCAAGATGCAAAAACATTCCTTGGGGGTTTGA	6	225	1
TTTTTTTCTTAAAAGATTCTCTATACCAGCTC	7	46	1
ATATTTTTTGAAATATTTCTTTCAGTAAGTCG	7	86	1
TAAGAGGAAAAAGCTTTTCTTTTGCTATAATT	7	131	1
          ***  *******
MAP Score: 3.13873

Motif 9
AGAAAAATACACAGTATTTTTCGCTGAAAAGAATGCTTT	0	38	0
TAACCTTCTAAAAATTTTACTTTTACAAAGTTGAAGCCA	2	18	1
CAAGTTTAGACTAGATTTTACTAATTAAAAAAACCGTTT	2	68	1
TTTAAAGTAGAGAGTTTTTGCAAAAGAAATGAAATAGCA	2	171	0
          AAAGGTTTTAAAGTCCAAATTAATTTAAA	2	204	0
CCGTGCGTAGAAAAGATTCTCTCTTTAAAATGCGGAGAG	4	24	1
 TAATTTAATAAAGGATTTCTAAAACAAACTC       	5	9	1
AGGGGCTCTTGCAGCTTTTTTTTAAAAAATCCTTCTCCT	6	51	1
CCTACTAACCCCAGACTTCAAGATGCAAAAACATTCCTT	6	208	1
GCTGGTATAGAGAATCTTTTAAGAAAAAAAAAGAGAGTT	7	37	0
          * **  ***    *  ***
MAP Score: 1.33194