AlignACE 3.0 10/20/99
AlignACE2 -i TM/TM_operons010_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944252011
 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	TM0110	107	transcriptional regulator, XylR-related
#5	TM0271	64	hypothetical protein
#6	TM0272	74	pyruvate,orthophosphate dikinase
#7	TM0273	41	fructose-bisphosphate aldolase
#8	TM0275	50	transcriptional regulator, GntR family
#9	TM0296	108	fructokinase
#10	TM0299	237	transcriptional regulator, LacI family
#11	TM0949	216	transcriptional regulator, LacI family
#12	TM0957	73	hypothetical protein
#13	TM0958	57	ribose ABC transporter, periplasmic ribose-binding protein
#14	TM0960	207	ribokinase
#15	TM1203	60	maltose ABC transporter, permease protein
#16	TM1204	300	maltose ABC transporter, periplasmic maltose-binding protein
#17	TM1222	55	oligopeptide ABC transporter, permease protein
#18	TM1223	131	oligopeptide ABC transporter, periplasmic oligopeptide-binding protein
#19	TM1856	206	transcriptional regulator, LacI family

Motif 1
CCGGCCTTTACATTGAAGGAGGT         	7	28	1
GTAATATCTACCCGCAAGGAGGTGAAGGTGGT	16	278	1
TATGATAACACAGGAAAGGAGGTAGCACG   	5	7	0
TTAAATATCACATATCAGGAGGG         	1	49	1
GGGTTTTAAAAAAAGAAGGAGGTAGGAGTC  	17	35	1
TGGTGAAGAAAAAAGAAGGAGGTTCTGAAC  	5	44	1
AATATTGAGATCCAAAAGGAGGAATCGAAG  	4	87	1
CCTTCAAGCCCCCATCAGGGGGCTTTTGTTTT	19	28	1
CATCCTCCTTTCTAAAAGGGGGCACCCGCTCA	12	47	0
CCCTTCCATACGTTCAGGGAGGGAAAACA   	15	41	1
TGGATACGAAAGGAAAAGGAGGGAGTCAGAAG	6	52	1
ACAAAGAAGAAAATCAGGGAGGCAGAGAAT  	0	81	1
ACCTCAAATTTCCTTAGGGAGGTGGGTTTT  	13	37	1
ATCTCATACTCTTTTAAGGGGGTGTTCTT   	18	112	1
TTAAGAGAAGAGTACAGGGAGGCAACAAC   	10	218	1
ACAAAACTTTTTTTTAAGGGGGTGTTTTT   	10	7	0
     ACAGCCAAAAAAGGAGAAAATAACAGA	4	5	1
CTGAGCTAATCTAGACAGGGGGACCCGCGACC	12	13	1
GCAAGAAAATCATTGAAGGAGTAGCAGCAATG	11	119	1
ATATGTAAGCGCTTACAGGAGGTGCAAACT  	19	186	1
GAACTGTTATTTTTCCGGGAGGGATCGTT   	9	7	0
CACCCCTGAAAAGAGGGGGAGGACTCCCCC  	3	8	0
AAGATACTCGACAGGAAGGAGAAATTAGC   	11	197	1
GATTATACTATAGACAAGGGGTGATCAAGA  	2	8	0
TTTCATCAAGACACAAGGGAGG          	14	195	1
          ** * *******
MAP Score: 28.9625

Motif 2
ACCATGAAGATTTTCTTTTTGAGAAAACCA	0	31	0
TAAAAAAAAGTTTTGTTTTTAGTAAAGCTT	10	23	1
ATCAGGGGGCTTTTGTTTTTTGTGAGTTTT	19	41	1
GATTTATGGTTTTTGTTTTTTTGAAATATG	1	18	1
GATCGAGATTCTTTGTTTTTCTCTCGTTGA	14	113	1
ACTCCTACCTCCTTCTTTTTTTAAAACCCC	17	34	0
TTCAGAACCTCCTTCTTTTTTCTTCACCAA	5	43	0
AAAAACAGTATTTTCTTCTTTTCAAAT   	13	7	0
GCCTCCCTGATTTTCTTCTTTGTCTACAAT	0	74	0
TCTCGTTGACTTTTCATTTTCCTTCGTGTT	14	134	1
AATCGTGCGGTTTTGATTTTATAATAAATT	6	20	1
AAGTTATCATATTTCTTTTTAATTTGAAAT	10	107	0
ATAGCTAAGTTTTTGTTTTGAATAGATAAA	11	25	1
CGGAAAACGATTTTCTATTTCATCTTCATT	9	72	0
TCTGTTATTTTCTCCTTTTTTGGCTGT   	4	7	0
AGATATCCGACCTTGATTTTAAATTATTTC	4	34	1
TTTGAAATAATCGTCTTTTTTGAGATTTTG	10	85	0
          **********
MAP Score: 21.3977

Motif 3
CATCCACCTCCATTTGAAAATGGTTTTCTCAAAAAG	0	11	1
TGGTTTTCTCAAAAAGAAAATCTTCATGGTATTATT	0	31	1
CATTAATTATATGCAGGAAATAATTTAAAATCAAGG	4	44	0
AATGAAGATGAAATAGAAAATCGTTTTCCGGCGGAG	9	72	1
TCATAAGATTACTATGAAAACATTTTCATTCAAAAT	10	55	1
TACGTTTTTCAGCAAGAAAATCATTGAAGGAGTAGC	11	108	1
   ATTTGAAAAGAAGAAAATACTGTTTTTACCTCA	13	7	1
GAAATTCTATATTATGAAAATTCTCGTTCATGGATA	14	26	1
TGTTACCATTCTTGTGAAAACGATTTCGAAAACGAT	14	160	1
TGTGAAAACGATTTCGAAAACGATTTCATCAAGACA	14	172	1
TTGTGTTGTGATTGTGAAAACTTTCT          	16	0	0
CTCTTCGTTCTCTTCGAAACTGTTTTTTATCTCTAC	16	78	0
TAAAAGTCGATTCCAGGAAATTATTTGGAAATAACG	16	179	1
TTTGGAAATAACGTTGAAAATCTCCTCGGGATGTCG	16	202	1
GTGTAAATGTACAGTGAAAATGTTTACATTCCAAAT	18	64	0
  GAGTTTTGATATGGAAAACCTTCAAGCCCCCATC	19	8	1
TAATTTCTCTTAATCGGAAATAGTTGAAGGTATTCG	19	105	1
ATCTTGATTTAACACGGAAATTTTTTGTATAAACGA	19	151	1
          *    ******  ***
MAP Score: 16.2799

Motif 4
AATAGAAAATCGTTTTCCGGCGGAGGTGTATTCTT 	9	83	1
TTGAGAAAACCATTTTCAAATGGAGGTGGATGT   	0	7	0
TTTCACTGTACATTTACACGTGGAGATAGCGATCTC	18	81	1
AAAAACAAAACTTTTTTTTAAGGGGGTGTTTTT   	10	7	0
ATTCCATCCTCCTTTCTAAAAGGGGGCACCCGCTCA	12	47	0
GATATGTAAGCGCTTACAGGAGGTGCAAACT     	19	185	1
AGTCCTCCCCCTCTTTTCAGGGGTGATCCG      	3	15	1
TCAACAGCAACACTCGTCAATGGTGGTACGCTCATA	11	61	0
AGGGGGCACCCGCTCATAGGTCGCGGGTCCCCCTGT	12	27	0
CGATCTCATACTCTTTTAAGGGGGTGTTCTT     	18	110	1
TTTTACCTCAAATTTCCTTAGGGAGGTGGGTTTT  	13	33	1
AATGATGACCCCGCCCCTCGGGGCGGGGTTTTAAAA	17	10	1
  ACCACCTTCACCTCCTTGCGGGTAGATATTACCA	16	276	0
TTCACGGTAACGTTTACGTATGGTAATATCTACCCG	16	256	1
   CATAAAACTTTTACGGGGCTGGGTCCCCAGCCC	15	7	1
AAAAAACAAAAGCCCCCTGATGGGGGCTTGAAGGTT	19	26	0
CAGAAATATTCGTTTTCTGGACGTAAAAGTCGATTC	16	156	1
  GCTAATTTCTCCTTCCTGTCGAGTATCTTCAATG	11	192	0
          * *** *  * ** **
MAP Score: 12.6657

Motif 5
TACCATGAAGATTTTCTTTTTGAGAAAACCATTTTC	0	26	0
AGATTTATGGTTTTTGTTTTTTTGAAATATGATTAA	1	17	1
TATTTCCTGCATATAATTAATGTGAACATAATATTG	4	58	1
ATTTTTCAATTATTCTGTATTTTGGAAGGATTGCAA	8	22	0
ATAATCGTCTTTTTTGAGATTTTGAATGAAAATGTT	10	73	0
GTTATCATATTTCTTTTTAATTTGAAATAATCGTCT	10	99	0
ATTAATAGCTAAGTTTTTGTTTTGAATAGATAAAAC	11	21	1
CAATGAAATTTTATCACTGATGAGAAGCCTTATTCT	11	161	0
TAAAAACAGTATTTTCTTCTTTTCAAAT        	13	2	0
GTTACCATGAAATTCTATATTATGAAAATTCTCGTT	14	18	1
AATCGATGATAAATGAATTTTTTGGATAATATCCAT	14	55	0
TTCCTTCGTGTTACCATTCTTGTGAAAACGATTTCG	14	152	1
AATTACTCTTGTGTTGTGATTGTGAAAACTTTCT  	16	8	0
CACAAGAGTAATTTTACTCTTCTGAATCAATAATGT	16	31	1
TCTGTGTTTCGTTTACATAATCTGGACTCTTTTGGT	16	124	0
AAACACAGAAATATTCGTTTTCTGGACGTAAAAGTC	16	151	1
ATCAGGGGGCTTTTGTTTTTTGTGAGTTTTGATTAA	19	41	1
          ** *   * ** ****
MAP Score: 8.89913

Motif 6
ATCAATTATAATAATACCATGAAGATTTTC	0	46	0
CATATAATTAATGTGAACATAATATTGAGA	4	67	1
ACCAAAACTTATGATAACACAGGAAAGGAG	5	18	0
GTTCAACACAATATTAACACACTTCGCCTT	9	35	1
TAAGATTACTATGAAAACATTTTCATTCAA	10	58	1
AAAAAGAAATATGATAACTTATCGTTCCAT	10	117	1
TAAATGTGATATGAAAAAATATGGAACGAT	10	137	0
          ATGAAATCATTATTAATAGC	11	0	1
ATAGAATTTCATGGTAACATGAGTAA    	14	6	0
TTTCACAAGAATGGTAACACGAAGGAAAAT	14	149	0
TTGCGGGTAGATATTACCATACGTAAACGT	16	265	0
TGGATTTGGAATGTAAACATTTTCACTGTA	18	61	1
          **********
MAP Score: 3.30448

Motif 7
TGGTTTTCTCAAAAAGAAAATCTTCATGGT	0	31	1
  ACAGCCAAAAAAGGAGAAAATAACAGAT	4	8	1
ATTGAGATCCAAAAGGAGGAATCGAAG   	4	90	1
GTTTTGGTGAAGAAAAAAGAAGGAGGTTCT	5	40	1
TCTTGGATACGAAAGGAAAAGGAGGGAGTC	6	49	1
ATACTCGACAGGAAGGAGAAATTAGC    	11	200	1
CCCCCTTTTAGAAAGGAGGATGGAAT    	12	57	1
      ATTTGAAAAGAAGAAAATACTGTT	13	4	1
CAACGAGAGAAAAACAAAGAATCTCGATCA	14	112	0
AGTTTCGAAGAGAACGAAGAGGGAAATTTA	16	93	1
TTATGTAAACGAAACACAGAAATATTCGTT	16	140	1
GGCGGGGTTTTAAAAAAAGAAGGAGGTAGG	17	31	1
          **********
MAP Score: 0.788732