AlignACE 3.0 10/20/99
AlignACE2 -i TP/TP_operons027_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944239883
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	TP0255	118	ribosomal protein L31 (rpmE)
#1	TP0256	44	CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase (pgsA)
#2	TP0267	300	conserved hypothetical protein
#3	TP0692	260	recA protein (recA)
#4	TP0754	41	conserved hypothetical protein
#5	TP0755	199	PTS system, nitrogen regulatory IIA component (ptsN-2)
#6	TP1018	171	conserved hypothetical protein

Motif 1
GGTTACATCCACCCTCTTCCAGAAGGCTCG	0	51	0
TTCTACAGCGCGCCGCGCCCTTAAAAAGGT	0	78	0
  CTGAATCGCTCCTTTCCCCATTCTACAG	0	100	0
TGTACCATTACGTCTTTCCCCTAGGTGAGT	1	24	1
CATATTATTCATCCTTCTCCTTCACCCTAC	2	91	1
CTTCTCCTTCACCCTACCCCTTTGCGTAAA	2	104	1
GAGAGGTCATACCCGTTCCCATCCCGAACA	2	158	1
AAGTCAAGCTCTCCTACGCCGATGATACTG	2	191	1
TGGCTACTACCTACTTTCCCGCGAAGGAGC	2	220	0
TAGCCAGGCTCCCCTTTGCCCATCACTCGC	2	244	1
ACACCCTCTCATCCTATCCCCATACCCCGA	3	28	0
GCGTCTCTTGCGCCTTGCGCGGGGTTTTTC	3	226	1
     TGCTTTCCCTCTGCCTGAACAATCC	4	26	0
AAACCAACCTCCCCTTTCTCTGTAACAAGA	5	67	0
ACGGAATCTTCCCCTTTTGCGCCCACTCAT	5	162	0
     GGTGCCCACTTTTCCTGACGGAATC	5	184	0
AGGGTATTATCGCCTTTTCCCTGCTGCGGT	6	12	1
ACACACCTCTAGCCTCTCGCAAGACAGTTT	6	120	1
          **********
MAP Score: 26.9633

Motif 2
GCAGTATCATCGGCGTAGGAGAGCTTGACTTCC	2	189	0
GCTGTAGAATGGGGAAAGGAGCGATTCAG    	0	99	1
    GTGATACACGCCAGGCGTGAGATTTCTAC	5	6	1
TGAAAAACCCCGCGCAAGGCGCAAGAGACGCGC	3	224	0
AGCGAGTGATGGGCAAAGGGGAGCCTGGCTACT	2	242	0
TGTCTTGCGAGAGGCTAGAGGTGTGTGCGAATT	6	113	0
AAGATTCCGTCAGGAAAAGTGGGCACC      	5	182	1
AAGGCTCGTACACGCCGGGTGTAACCGACACAC	0	26	0
 ACTCACCTAGGGGAAAGACGTAATGGTACACC	1	22	0
ACCTACTTTCCCGCGAAGGAGCAGTATCATCGG	2	209	0
AAGAAATTCTCACGATAGAAGAGGTTGCGCGGT	5	102	1
TTGACCGCAGCAGGGAAAAGGCGATAATACCCT	6	12	0
CAGGATTGTTCAGGCAGAGGGAAAGCA      	4	24	1
CCTTCTGGAAGAGGGTGGATGTAACCTTTTTAA	0	55	1
CGTAATGGTACACCACAGGTGTACTC       	1	3	0
TTTCGTAGATCGGGGTATGGGGATAGGATGAGA	3	19	1
CAAAGGGGTAGGGTGAAGGAGAAGGATGAATAA	2	95	0
GTGTATGAGTGGGCGCAAAAGGGGAAGATTCCG	5	158	1
TGCTACAAGTCCCGCCGGAAGGGCCTATAGCTC	3	108	1
CTTCCGTGTTCGGGATGGGAACGGGTATGACCT	2	161	0
TGTCTTGTTACAGAGAAAGGGGAGGTTGGTTTG	5	65	1
GTCAACATCTGACCCTAAACGGGAAAAAGAAAC	6	40	1
          ***** *** * *
MAP Score: 23.2111

Motif 3
GCGTGTACGAGCCTTCTGGAAGAGGGTGGATGTAA	0	44	1
GCGGCGCGCTGTAGAATGGGGAAAGGAGCGATTCA	0	92	1
CACTACAAGGTCGATAGGCTGGAGGTCTACGTACC	2	11	1
CAAAGGGGTAGGGTGAAGGAGAAGGATGAATAATA	2	93	0
TTTCGCCTGGTTGCCATGGTGGAGAGGTCATACCC	2	137	1
ACTTCCGTGTTCGGGATGGGAACGGGTATGACCTC	2	160	0
TTTGTCAAGCGAGTGATGGGCAAAGGGGAGCCTGG	2	247	0
TTCGTAGATCGGGGTATGGGGATAGGATGAGAGGG	3	20	1
ATAGCTCAGTTGGTTAGAGCAGCGGACTCATAATC	3	134	1
CATACTATTTGTGTGCAGGTGGTAGCGCGTCTCTT	3	200	1
GAGAGCAGGATTGTTCAGGCAGAGGGAAAGCA   	4	19	1
CAAGTGTGTCTTGTTACAGAGAAAGGGGAGGTTGG	5	59	1
GAAGAAATTCTCACGATAGAAGAGGTTGCGCGGTA	5	101	1
GTATGAGTGGGCGCAAAAGGGGAAGATTCCGTCAG	5	160	1
GATGTTGACCGCAGCAGGGAAAAGGCGATAATACC	6	14	0
GACCCTAAACGGGAAAAAGAAACGGGGACTCTCTG	6	50	1
AAACTGTCTTGCGAGAGGCTAGAGGTGTGTGCGAA	6	115	0
          * *  * ** *****
MAP Score: 17.2558

Motif 4
TTTCGTAGATCGGGGTATGGGGATAGGATGAG	3	19	1
ATGAAAAACCCCGCGCAAGGCGCAAGAGACGC	3	226	0
TTTTACGCAAAGGGGTAGGGTGAAGGAGAAGG	2	103	0
  ACTCACCTAGGGGAAAGACGTAATGGTACA	1	24	0
CGGGATGGGAACGGGTATGACCTCTCCACCAT	2	152	0
ACCTACTTTCCCGCGAAGGAGCAGTATCATCG	2	210	0
TAACCTTTTTAAGGGCGCGGCGCGCTGTAGAA	0	76	1
GACTCATAATCCGCGGGTCGCCGGTTCAAGTC	3	158	1
TGAAGAATTGACGCGTGTGTTGTTTCGTGCTA	3	81	1
ATATTTTGTCAAGCGAGTGATGGGCAAAGGGG	2	254	0
GTCTTGCGAGAGGCTAGAGGTGTGTGCGAATT	6	113	0
GGTAGGGTGAAGGAGAAGGATGAATAATATGG	2	90	0
TGTACAAACCCCGGGGAACACCCTCTCATCCT	3	43	0
TGACCGCAGCAGGGAAAAGGCGATAATACCCT	6	12	0
CAAGGTCGATAGGCTGGAGGTCTACGTACCGT	2	16	1
CTACAAGTCCCGCCGGAAGGGCCTATAGCTCA	3	110	1
TGATGGGCAAAGGGGAGCCTGGCTACTACCTA	2	237	0
GCAGTATCATCGGCGTAGGAGAGCTTGACTTC	2	190	0
GATACACGCCAGGCGTGAGATTTCTACGCAAC	5	12	1
CTCGTACACGCCGGGTGTAACCGACACACGTT	0	23	0
GTTACAGAGAAAGGGGAGGTTGGTTTGTCCGA	5	71	1
TGGGCGCAAAAGGGGAAGATTCCGTCAGGAAA	5	167	1
          ***** * ****
MAP Score: 12.728

Motif 5
TGTTTATTTCGTAGATCGGGGTATGGGGATAGGAT	3	13	1
    GTGATACACGCCAGGCGTGAGATTTCTACGC	5	6	1
ACACTACAAGGTCGATAGGCTGGAGGTCTACGTAC	2	10	1
TTGTGTGCAGGTGGTAGCGCGTCTCTTGCGCCTTG	3	208	1
CGGGGTTTTTCATGGGAGGCTTGTG          	3	245	1
CACGATAGAAGAGGTTGCGCGGTACCTGCGAATTT	5	112	1
GTACTAATAAGTCGTGAGGCTTGACCATATTATTC	2	66	1
ATGGGGATAGGATGAGAGGGTGTTCCCCGGGGTTT	3	35	1
CAAGGATCTTGTCGCAAGGTTGCTCAGAGAGTCCC	6	74	0
GACTTGAACCGGCGACCCGCGGATTATGAGTCCGC	3	155	0
CGTGTTCGGGATGGGAACGGGTATGACCTCTCCAC	2	155	0
AAGGCTCGTACACGCCGGGTGTAACCGACACACGT	0	24	0
TTTTTAAGGGCGCGGCGCGCTGTAGAATGGGGAAA	0	81	1
CGAATTTCTGAACGTACCGTGTATGAGTGGGCGCA	5	140	1
GCGTTTTGAAGAATTGACGCGTGTGTTGTTTCGTG	3	75	1
  GTAAGGAGACTGGAACGTGTGTCGGTTACACCC	0	8	1
TTTTACGCAAAGGGGTAGGGTGAAGGAGAAGGATG	2	100	0
TCTCTTGCGCCTTGCGCGGGGTTTTTCATGGGAGG	3	229	1
TCTTGCGAGAGGCTAGAGGTGTGTGCGAATTCTGT	6	109	0
GAGCTATAGGCCCTTCCGGCGGGACTTGTAGCACG	3	106	0
ACTTATTAGTACTGGTCGGCTTAATACCTTACGGT	2	43	0
GTTACAGAGAAAGGGGAGGTTGGTTTGTCCGAAGA	5	71	1
          *  *  ****** **
MAP Score: 12.5329

Motif 6
CGAGCCTTCTGGAAGAGGGTGGATGTAACCT	0	51	1
GCTGTAGAATGGGGAAAGGAGCGATTCAG  	0	99	1
CAAAGGGGTAGGGTGAAGGAGAAGGATGAAT	2	97	0
GCTCCTTCGCGGGAAAGTAGGTAGTAGCCAG	2	220	1
AGCGAGTGATGGGCAAAGGGGAGCCTGGCTA	2	244	0
TTCGTAGATCGGGGTATGGGGATAGGATGAG	3	20	1
TATGGGGATAGGATGAGAGGGTGTTCCCCGG	3	34	1
GGATTGTTCAGGCAGAGGGAAAGCA      	4	26	1
GTCTTGTTACAGAGAAAGGGGAGGTTGGTTT	5	66	1
TATGAGTGGGCGCAAAAGGGGAAGATTCCGT	5	161	1
GATTCCGTCAGGAAAAGTGGGCACC      	5	184	1
GACCGCAGCAGGGAAAAGGCGATAATACCCT	6	12	0
GACCCTAAACGGGAAAAAGAAACGGGGACTC	6	50	1
          *** *******
MAP Score: 12.0364

Motif 7
CTTTTTAAGGGCGCGGCGCGCTGTAGAATG	0	80	1
GAAATCTCACGCCTGGCGTGTATCAC    	5	6	0
CTTGCGCCTTGCGCGGGGTTTTTCATGGGA	3	232	1
AAGAATTGACGCGTGTGTTGTTTCGTGCTA	3	83	1
GACTCATAATCCGCGGGTCGCCGGTTCAAG	3	158	1
TGTCGGTTACACCCGGCGTGTACGAGCCTT	0	29	1
GCAGGTGGTAGCGCGTCTCTTGCGCCTTGC	3	214	1
GGAGACTGGAACGTGTGTCGGTTACACCCG	0	14	1
CTAATAAGTCGTGAGGCTTGACCATATTAT	2	69	1
CGTACCCCAAGTGTGTCTTGTTACAGAGAA	5	52	1
AGAGGGTGTTCCCCGGGGTTTGTACAGCGT	3	49	1
    GAGTACACCTGTGGTGTACCATTACG	1	6	1
GGTTTTTCATGGGAGGCTTGTG        	3	248	1
ATTTTGTCAAGCGAGTGATGGGCAAAGGGG	2	254	0
          **********
MAP Score: 11.1858

Motif 8
GAAGGCTCGTACACGCCGGGTGTAACCGACACACGT	0	24	0
      GAGTACACCTGTGGTGTACCATTACGTCTT	1	4	1
TACGGTACGTAGACCTCCAGCCTATCGACCTTGTAG	2	13	0
AGTACTAATAAGTCGTGAGGCTTGACCATATTATTC	2	65	1
CCCGGGGAACACCCTCTCATCCTATCCCCATACCCC	3	30	0
TGAAGAATTGACGCGTGTGTTGTTTCGTGCTACAAG	3	81	1
TGAGCTATAGGCCCTTCCGGCGGGACTTGTAGCACG	3	106	0
GCAGGTGGTAGCGCGTCTCTTGCGCCTTGCGCGGGG	3	214	1
TAGAAATCTCACGCCTGGCGTGTATCAC        	5	2	0
CACTTGGGGTACGCATCATGCGTTGCGTAGAAATCT	5	29	0
       GGTGCCCACTTTTCCTGACGGAATCTTCC	5	180	0
GAATTCGCACACACCTCTAGCCTCTCGCAAGACAGT	6	112	1
          ** * **  ****  *
MAP Score: 10.4192

Motif 9
CGGGAAAGTAGGTAGTAGCCAGGCTCCCCTTTGCCCATC	2	229	1
AACGTGTGTCGGTTACACCCGGCGTGTACGAGCCTTCTG	0	23	1
ATGGTGGAGAGGTCATACCCGTTCCCATCCCGAACACGG	2	152	1
CCCTTAAAAAGGTTACATCCACCCTCTTCCAGAAGGCTC	0	52	0
         TGCTTTCCCTCTGCCTGAACAATCCTGCTC	4	21	0
TTTGTGTGCAGGTGGTAGCGCGTCTCTTGCGCCTTGCGC	3	207	1
ATTTTTTAAGGGTGCGAAACTGTCTTGCGAGAGGCTAGA	6	127	0
GTACTGGTCGGCTTAATACCTTACGGTACGTAGACCTCC	2	31	0
GCGGGTCGCCGGTTCAAGTCCAGCTGGGCCCATACTATT	3	170	1
ACACACTTGGGGTACGCATCATGCGTTGCGTAGAAATCT	5	29	0
AACCAACTGAGCTATAGGCCCTTCCGGCGGGACTTGTAG	3	110	0
GAAATTCGCAGGTACCGCGCAACCTCTTCTATCGTGAGA	5	109	0
TCCCTGCTGCGGTCAACATCTGACCCTAAACGGGAAAAA	6	29	1
AGGATGAGAGGGTGTTCCCCGGGGTTTGTACAGCGTTTT	3	43	1
GCGTAGGAGAGCTTGACTTCCGTGTTCGGGATGGGAACG	2	171	0
        GTGATACACGCCAGGCGTGAGATTTCTACGC	5	2	1
CTTGTCGCAAGGTTGCTCAGAGAGTCCCCGTTTCTTTTT	6	63	0
          GGTGCCCACTTTTCCTGACGGAATCTTCC	5	180	0
CTACGCCGATGATACTGCTCCTTCGCGGGAAAGTAGGTA	2	204	1
          ***     ** * ***  *
MAP Score: 6.07171