AlignACE 3.0 10/20/99
AlignACE2 -i TM/TM_operons010_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944252040
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	TM0065	101	transcriptional regulator, IclR family
#1	TM0066	62	2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase
#2	TM0101	50	hypothetical protein
#3	TM0103	35	sugar ABC transporter, ATP-binding protein
#4	TM0107	76	conserved hypothetical protein
#5	TM0110	107	transcriptional regulator, XylR-related
#6	TM0271	64	hypothetical protein
#7	TM0272	74	pyruvate,orthophosphate dikinase
#8	TM0273	41	fructose-bisphosphate aldolase
#9	TM0275	50	transcriptional regulator, GntR family
#10	TM0296	108	fructokinase
#11	TM0299	237	transcriptional regulator, LacI family
#12	TM0949	216	transcriptional regulator, LacI family
#13	TM0950	38	hypothetical protein
#14	TM0952	300	glycerol kinase
#15	TM0957	73	hypothetical protein
#16	TM0958	57	ribose ABC transporter, periplasmic ribose-binding protein
#17	TM0960	207	ribokinase
#18	TM1203	60	maltose ABC transporter, permease protein
#19	TM1204	300	maltose ABC transporter, periplasmic maltose-binding protein
#20	TM1222	55	oligopeptide ABC transporter, permease protein
#21	TM1223	131	oligopeptide ABC transporter, periplasmic oligopeptide-binding protein
#22	TM1225	52	conserved hypothetical protein
#23	TM1227	158	endo-1,4-beta-mannosidase
#24	TM1234	42	sugar ABC transporter, permease protein
#25	TM1235	22	conserved hypothetical protein
#26	TM1856	206	transcriptional regulator, LacI family
#27	TM1864	71	hypothetical protein

Motif 1
GACAAAGAAGAAAATCAGGGAGGCAGAGAAT  	0	80	1
ATTAAATATCACATATCAGGAGGG         	1	48	1
TCACCCCTGAAAAGAGGGGGAGGACTCCCCC  	3	8	0
CACGTTGAAAATGTGGAGGGAGGATTCG     	4	5	0
TAATATTGAGATCCAAAAGGAGGAATCGAAG  	5	86	1
TTATGATAACACAGGAAAGGAGGTAGCACG   	6	7	0
TTGGTGAAGAAAAAAGAAGGAGGTTCTGAAC  	6	43	1
TTGGATACGAAAGGAAAAGGAGGGAGTCAGAAG	7	51	1
CCCGGCCTTTACATTGAAGGAGGT         	8	27	1
TGAACTGTTATTTTTCCGGGAGGGATCGTT   	10	7	0
AACAAAACTTTTTTTTAAGGGGGTGTTTTT   	11	7	0
ATTAAGAGAAGAGTACAGGGAGGCAACAAC   	11	217	1
TGTCTTAGAGTGGTTCAAGGAGGGAAATTAGA 	14	278	1
ACTGAGCTAATCTAGACAGGGGGACCCGCGACC	15	12	1
GGTGCCCCCTTTTAGAAAGGAGGATGGAAT   	15	53	1
TACCTCAAATTTCCTTAGGGAGGTGGGTTTT  	16	36	1
ATTTCATCAAGACACAAGGGAGG          	17	194	1
CCCCTTCCATACGTTCAGGGAGGGAAAACA   	18	40	1
GGTAATATCTACCCGCAAGGAGGTGAAGGTGGT	19	277	1
GGGGTTTTAAAAAAAGAAGGAGGTAGGAGTC  	20	34	1
GATCTCATACTCTTTTAAGGGGGTGTTCTT   	21	111	1
GTGGGGCTCTAAATCTAAGGAGGGAAGCATGG 	22	30	1
AAAGTTTACTAATTAACGGGAGGTATCGGT   	23	138	1
          ** *  *******
MAP Score: 36.3824

Motif 2
AGACAAAGAAGAAAATCAGGGAGGCAGAGAAT 	0	79	1
GGATCACCCCTGAAAAGAGGGGGAGGACTCCCC	3	11	0
CTACCACGTTGAAAATGTGGAGGGAGGATTCG 	4	9	0
TGATAACACAGGAAAGGAGGTAGCACG      	6	4	0
TTTGGTGAAGAAAAAAGAAGGAGGTTCTGAAC 	6	42	1
GATACGAAAGGAAAAGGAGGGAGTCAGAAG   	7	54	1
AGAGCTGCTCGAGAAACAGGAAGAATAGTAACC	14	72	1
TCCGGTTACAGGAACGCAGGATGAAGTTTTAAA	14	209	1
GCCCCCTTTTAGAAAGGAGGATGGAAT      	15	56	1
CAGTTTCGAAGAGAACGAAGAGGGAAATTTAGA	19	92	1
GTTTTAAAAAAAGAAGGAGGTAGGAGTC     	20	37	1
GTGCACCCCCGGAAAAGGGGTGGGGATCCCCAC	24	18	0
       GGTGAGAAAGTGGTTGTTTTTC    	25	3	1
          ***** ****  *
MAP Score: 18.0373

Motif 3
CACCTCCATTTGAAAATGGTTTTCTCAAAAAG	0	15	1
AGATTTTGAATGAAAATGTTTTCATAGTAATC	11	61	0
CCTACTCCTATGAAAATCCTTGGGATACCCGA	14	171	1
ACCATTCTTGTGAAAACGATTTCGAAAACGAT	17	164	1
AAGATGAAATAGAAAATCGTTTTCCGGCGGAG	10	76	1
AAAACGATTTCGAAAACGATTTCATCAAGACA	17	176	1
TGATTTAACACGGAAATTTTTTGTATAAACGA	26	155	1
TTTTTCAGCAAGAAAATCATTGAAGGAGTAGC	12	112	1
AGTCGATTCCAGGAAATTATTTGGAAATAACG	19	183	1
AATTATATGCAGGAAATAATTTAAAATCAAGG	5	44	0
TTCTATATTATGAAAATTCTCGTTCATGGATA	17	30	1
AGATTCTAATCGGAAATAATTGCTCACTTTCA	23	16	1
TTCTCTTAATCGGAAATAGTTGAAGGTATTCG	26	109	1
GTTGTGATTGTGAAAACTTTCT          	19	0	0
AAATGTACAGTGAAAATGTTTACATTCCAAAT	21	64	0
CGAGCAGCTCTGAAAACTGCTTCTTCATCCAG	14	51	0
GAAATAACGTTGAAAATCTCCTCGGGATGTCG	19	206	1
TTTCTCAAAAAGAAAATCTTCATGGTATTATT	0	35	1
          *******  ***
MAP Score: 17.1806

Motif 4
ACCATGAAGATTTTCTTTTTGAGAAAACCA	0	31	0
GCCTCCCTGATTTTCTTCTTTGTCTACAAT	0	74	0
GATTTATGGTTTTTGTTTTTTTGAAATATG	1	18	1
AGATATCCGACCTTGATTTTAAATTATTTC	5	34	1
TTCAGAACCTCCTTCTTTTTTCTTCACCAA	6	43	0
AATCGTGCGGTTTTGATTTTATAATAAATT	7	20	1
CGGAAAACGATTTTCTATTTCATCTTCATT	10	72	0
TAAAAAAAAGTTTTGTTTTTAGTAAAGCTT	11	23	1
TTTGAAATAATCGTCTTTTTTGAGATTTTG	11	85	0
AAGTTATCATATTTCTTTTTAATTTGAAAT	11	107	0
ATAGCTAAGTTTTTGTTTTGAATAGATAAA	12	25	1
AAAAACAGTATTTTCTTCTTTTCAAAT   	16	7	0
GATCGAGATTCTTTGTTTTTCTCTCGTTGA	17	113	1
TCTCGTTGACTTTTCATTTTCCTTCGTGTT	17	134	1
ACTCCTACCTCCTTCTTTTTTTAAAACCCC	20	34	0
GTCCTATTTTTCGTGATTTTCGAGTTTTAT	23	51	0
ATCAGGGGGCTTTTGTTTTTTGTGAGTTTT	26	41	1
          **********
MAP Score: 16.7332

Motif 5
TGATTGTAGACAAAGAAGAAAATCAGGGAG	0	72	1
CACCCCTGAAAAGAGGGGGAGGACTCCCCC	3	10	0
  ACAGCCAAAAAAGGAGAAAATAACAGAT	5	8	1
ATTGAGATCCAAAAGGAGGAATCGAAG   	5	90	1
GATAACACAGGAAAGGAGGTAGCACG    	6	6	0
TGGTGAAGAAAAAAGAAGGAGGTTCTGAAC	6	44	1
ATACGAAAGGAAAAGGAGGGAGTCAGAAG 	7	55	1
TGAAGTGATTAAGAGAAGAGTACAGGGAGG	11	210	1
ATGGGAGGTTAAAAGAATAAGGCTTCTCAT	12	148	1
ATACTCGACAGGAAGGAGAAATTAGC    	12	200	1
AGCTAATCTAGACAGGGGGACCCGCGACCT	15	16	1
CCTCCTTTCTAAAAGGGGGCACCCGCTCAT	15	46	0
CCCCCTTTTAGAAAGGAGGATGGAAT    	15	57	1
     ATTTGAAAAGAAGAAAATACTGTTT	16	5	1
TTATTGATTCAGAAGAGTAAAATTACTCTT	19	34	0
TCGAAGAGAACGAAGAGGGAAATTTAGACC	19	97	1
GGGTTTTAAAAAAAGAAGGAGGTAGGAGTC	20	35	1
          **********
MAP Score: 10.2616

Motif 6
CCACCTCCATTTGAAAATGGTTTTCTCAAAAAGAAAATCTTC	0	14	1
CTTCATGGTATTATTATAATTGATTGTAGACAAAGAAGAAAA	0	52	1
CTTTCCTGTGTTATCATAAGTTTTGGTGAAGAAAAAAGAAGG	6	21	1
CATAGTAATCTTATGAGTAAGCTTTACTAAAAACAAAACTTT	11	29	0
ATAATCGTCTTTTTTGAGATTTTGAATGAAAATGTTTTCATA	11	67	0
AATAGCTAAGTTTTTGTTTTGAATAGATAAAACAGGGTATGA	12	24	1
ACTCTTTATATTTACGTTTTTCAGCAAGAAAATCATTGAAGG	12	96	1
AAAATTCTCGTTCATGGATATTATCCAAAAAATTCATTTATC	17	42	1
TTAATAAGAATTATTGGGTTTTATGATCGAGATTCTTTGTTT	17	89	1
ACTAATTAGGTTGACATTATTGATTCAGAAGAGTAAAATTAC	19	38	0
CCCGAGGAGATTTTCAACGTTATTTCCAAATAATTTCCTGGA	19	190	0
   AGAAAAGTTGTTGCAAATAATCAGAAATAAATCTTGATA	21	7	1
        GATTTTAGATTCTAATCGGAAATAATTGCTCACT	23	2	1
TTTTTCGTGATTTTCGAGTTTTATTTGTGAAAGTGAGCAATT	23	33	0
ACTTTACTTATTTATCAGGGTCATCGAGAAAAAATGTACCAT	23	101	0
GGGCTTTTGTTTTTTGTGAGTTTTGATTAAAATTGAGATTTT	26	47	1
AAAATTGAGATTTTGCGTCATAATCCTGAATAATTTCTCTTA	26	75	1
     AAGATTTTTCGGCTGTGATAAAATAAATTCAGCCTCA	27	5	1
          ** * *    * **    ** *
MAP Score: 9.52166

Motif 7
TGAAAATGGTTTTCTCAAAAAGAAAATCTTCATGGT	0	25	1
TTATAATTGATTGTAGACAAAGAAGAAAATCAGGGA	0	65	1
TTTAATCATATTTCAAAAAAACAAAAACCATAAATC	1	18	0
ATCATAAGTTTTGGTGAAGAAAAAAGAAGGAGGTTC	6	33	1
ATGAGTAAGCTTTACTAAAAACAAAACTTTTTTTTA	11	23	0
AAGACGATTATTTCAAATTAAAAAGAAATATGATAA	11	98	1
TATTATAACGTTTCCCACGAACTAAGCAAACGTTTG	11	169	0
TAAGTTTTTGTTTTGAATAGATAAAACAGGGTATGA	12	30	1
TATATTTACGTTTTTCAGCAAGAAAATCATTGAAGG	12	102	1
         ATTTGAAAAGAAGAAAATACTGTTTTT	16	1	1
CGGGGCGGGGTTTTAAAAAAAGAAGGAGGTAGGAGT	20	28	1
CCTTCAACTATTTCCGATTAAGAGAAATTATTCAGG	26	99	0
          ***   *  ** ****
MAP Score: 8.45419

Motif 8
ACAGATATCCGACCTTGATTTTAAATTATTTCCTG	5	32	1
TTAATCGTGCGGTTTTGATTTTATAATAAATTCTT	7	18	1
ACCTCCGCCGGAAAACGATTTTCTATTTCATCTTC	10	75	0
GATTTTGAATGAAAATGTTTTCATAGTAATCTTAT	11	57	0
TCTCAAAAAAGACGATTATTTCAAATTAAAAAGAA	11	90	1
CCTGGATGAAGAAGCAGTTTTCAGAGCTGCTCGAG	14	50	1
AGGAACGCAGGATGAAGTTTTAAAACACTACGGCC	14	218	1
AATCGTTTTCGAAATCGTTTTCACAAGAATGGTAA	17	162	0
AAACGATTTCGAAAACGATTTCATCAAGACACAAG	17	177	1
CGCCCCTCGGGGCGGGGTTTTAAAAAAAGAAGGAG	20	21	1
TACACGTGGAGATAGCGATCTCATACTCTTTTAAG	21	95	1
GCTTGAAATAGATCTTGATTTAACACGGAAATTTT	26	140	1
          **    ******* *
MAP Score: 8.30865

Motif 9
TTATGGTTTTTGTTTTTTTGAAATATGATTAAAT	1	21	1
AGATATCCGACCTTGATTTTAAATTATTTCCTGC	5	34	1
TGGATCTCAATATTATGTTCACATTAATTATATG	5	67	0
AGTGTGTTAATATTGTGTTGAACTGTTATTTTTC	10	24	0
TATGAAAACATTTTCATTCAAAATCTCAAAAAAG	11	67	1
TCATATTTCTTTTTAATTTGAAATAATCGTCTTT	11	97	0
GTTCCATATTTTTTCATATCACATTTACGCAAAC	11	140	1
AATAGCTAAGTTTTTGTTTTGAATAGATAAAACA	12	24	1
TGAGAAGCCTTATTCTTTTAACCTCCCATTGCTG	12	143	0
AACAGTATTTTCTTCTTTTCAAAT          	16	0	0
   TTACTCATGTTACCATGAAATTCTATATTAT	17	7	1
TATCTCTACTAATTAGGTTGACATTATTGATTCA	19	53	0
AATCTGGACTCTTTTGGTCTAAATTTCCCTCTTC	19	108	0
AATATTTCTGTGTTTCGTTTACATAATCTGGACT	19	132	0
AGATTTTCAACGTTATTTCCAAATAATTTCCTGG	19	191	0
CCTACCTCCTTCTTTTTTTAAAACCCCGCCCCGA	20	27	0
TAGTTGAAGGTATTCGCTTGAAATAGATCTTGAT	26	125	1
TTGAAATAGATCTTGATTTAACACGGAAATTTTT	26	142	1
          * **  *** ****
MAP Score: 6.81838

Motif 10
TTTTGAATGAAAATGTTTTCATAGTAATCTTATGAG	11	54	0
TTATCGTTCCATATTTTTTCATATCACATTTACGCA	11	135	1
CTCATCAGTGATAAAATTTCATTGAAGATACTCGAC	12	173	1
CGGGTATCCCAAGGATTTTCATAGGAGTAGGTAAAT	14	166	0
TTTTCATAATATAGAATTTCATGGTAACATGAGTAA	17	10	0
CGTTATTTCCAAATAATTTCCTGGAATCGACTTTTA	19	179	0
TTTGGAATGTAAACATTTTCACTGTACATTTACACG	21	65	1
CGTTTATACAAAAAATTTCCGTGTTAAATCAAGATC	26	150	0
          * *   ****** * *
MAP Score: 0.0676674