AlignACE 3.0 10/20/99
AlignACE2 -i TM/TM_operons018_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944252334
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	TM0143	93	response regulator
#1	TM0309	300	oligopeptide ABC transporter, periplasmic oligopeptide-binding protein
#2	TM0310	43	beta-D-galactosidase
#3	TM0311	92	hypothetical protein
#4	TM0312	50	conserved hypothetical protein
#5	TM0972	221	conserved hypothetical protein, GGDEF domain
#6	TM1006	128	oxidoreductase, aldo/keto reductase family
#7	TM1009	300	oxidoreductase, aldo/keto reductase family
#8	TM1162	207	conserved hypothetical protein
#9	TM1182_TM1183	73	TM1182: chromosome segregation SMC protein, putative, TM1183: oxidoreductase, aldo/keto reductase family
#10	TM1596	49	purine nucleoside phosphorylase
#11	TM1743	84	oxidoreductase, aldo/keto reductase family
#12	TM1788	215	conserved hypothetical protein, GGDEF domain
#13	TM1790	100	hypothetical protein
#14	TM1791	300	conserved hypothetical protein
#15	TM1832	23	transposase
#16	TM1833	82	methyl-accepting chemotaxis-related protein
#17	TM1834	134	alpha-glucosidase
#18	TM1836	300	maltose ABC transporter, permease protein

Motif 1
CGGGGTTTTTTGGAGGTGAACATGG     	2	28	1
AGCTTCGTATAGGGGGTGTG          	3	82	1
TTTAGCAGAAAGGAGATGAAAGAAATC   	6	7	0
TTAGAGCGAAAGGAGGGGGAAGT       	6	115	1
CCCAGAAAGAAGGGGTTGAAAGTCTCAGAA	7	30	0
ATCCATCTATAGGAGGTGTTAAC       	7	287	1
AAGCGGTCCGAGGAGGTGTGAAA       	8	3	0
ATGCTTTTTCGGGAGGTGATTTCTAAGTGG	8	58	0
AATCTAAAATGGGAGGTGGTAAC       	8	194	1
GATAACTGCAAGGAGGTGAAAAT       	9	3	0
TCTAACGTGTGGGAGGGGATCGGT      	9	59	1
CTACTATAAAGTGAGGTGTTG         	10	1	0
AATAGTTACGTGGAGGTGATCACAAGTT  	10	31	1
CAAATCGTGTGGGAGGTGACAGG       	11	3	0
AGACTAATTCAGGAGGTGGTTGGA      	11	70	1
TGTATTCAAGGGGGGATGGAT         	13	89	1
GATTACCTCAGGGATGTGAAGGGTCTTGGA	14	48	1
GGAAAAAACAAGGTGGTGGATCACCTTGGA	14	132	1
 TATAATTGAATGGGGTGATAGGT      	15	9	1
ACGAAATACAGGGAGGTGTTTTT       	17	121	1
TGTGTCCAACAGGAGTTGTGGTTCCAGCCA	18	120	0
GGTGCGTTTGAAGAGGTGAGTGA       	18	287	1
          **********
MAP Score: 34.2843

Motif 2
TATATTATCAGAGAAAAAAACGAGTTGAAC	0	39	0
AAAAAGCCTTCAGAAAAGAAACTCGACGTT	1	98	0
AATTTCTTTAGAGGAAAAAATAAAAACATT	1	267	1
GAAAAATCACGTGAAAGAAG          	4	40	1
ATATTTTTGGGAGGAAGACTTTGGTGTCGT	5	84	1
TAATTCTGGAGTGAAAAAAGCAGGTACATG	5	160	1
AAAATTTTAGCAGAAAGGAGATGAAAGAAA	6	12	0
ATGTTTTAGAGCGAAAGGAGGGGGAAGT  	6	110	1
AAATATTGCCCAGAAAGAAGGGGTTGAAAG	7	38	0
GAAGCAATACCAGAAAGAAGGACAGCTCCC	7	118	0
AGTATAAAAGCCGAAAGGAGTATGGCGTAC	7	193	0
AAGAAAATCGGAGAAAGAATCAGTATAAAA	7	214	0
CTTTTTTACGGAGGAAGACTGGTGCTTTCC	8	30	1
TAACATCACACCGGAAGAAACACCAGTACA	8	104	1
AACACCAGTACAGAAAGAAAAATTTTTCAA	8	122	1
ACGTTAATTTCCGAAAAGAGTATAATCTAA	8	171	1
TGAGGAAGTTGAGAAAGACAAAAGAGATGA	14	20	1
CTTTCTTTTTCAGAAAGAGAATTGTTCCCA	14	103	0
    AAGGATCTGAAAGGGGCCTGAAAGGC	16	6	1
GCGTTCGAAGGAGGAAGAGGACAGGACTTC	18	182	1
TTCCTCCAACGAGGAAGAATATGATGATGG	18	231	0
          **********
MAP Score: 22.136

Motif 3
         ACCCCCTTTGATGAATGTTTT	1	289	0
GGGCGGAAATCCGCCCTTGAACATACTCCT	3	23	0
          TCCCCCTTGAGATTCCTTAC	5	0	1
GCTAAAATTTTACCCTTTGATGGAAAATCA	6	31	1
GGTTCTCCATCCTCTTCTGAGACTTTCAAC	7	16	1
   TTTCACACCTCCTCGGACCGCTTTTTT	8	7	1
ACTTAGAAATCACCTCCCGAAAAAGCATCT	8	60	1
    TCCAACCACCTCCTGAATTAGTCTAG	11	68	0
  AGGTGATTTTCCCTCTGATATCACACCA	12	8	1
TCACGGCTATCACCCTTTGAGATTCAACTT	12	94	0
GGCTCACTGATATCTTTTGAATTTCAAGAC	13	18	0
TAAGAAAAAGCCCCGCTTGATGCGGGGCTC	13	43	0
    ATCCATCCCCCCTTGAATACAAATTT	13	84	0
GCACAGATCGCTGCTCTTGAGTGTGCAAAA	14	249	1
AACCTCTCCGCATCTTTTGAGCCATTTTGC	14	273	0
CCCCCACTATCTTCTTTGGATTTTCCAACA	16	57	0
   CACGTTTCCGCTTCTGATGACCACTGT	18	7	1
CTGTCCTCTTCCTCCTTCGAACGCGAGTTT	18	176	0
TCATATTCTTCCTCGTTGGAGGAATCAGCT	18	237	1
          **********
MAP Score: 18.6857

Motif 4
TATTCGAACTCTGCGTGAAAACAGTTTCATG	1	28	0
GAACATACTCCTGTTGGCAAAACTC      	3	4	0
CGTTTAATTCTGGAGTGAAAAAAGCAGGTAC	5	156	1
ATTTTACCCTTTGATGGAAAATCAGGCAAAT	6	37	1
TTCTTCACGGTAGCGGGAAAAGTTGGTACGA	7	239	1
AAGGAATGTGTTCGTTGAAAAATTTTTCTTT	8	135	0
GGTGTGATATCAGAGGGAAAATCACCT    	12	6	0
CCTGGAAAGCGACAGTGAAAATGAGAAACTA	12	191	1
CGTCGAAAGACTGATGGAAAACGAGTTTTTG	14	197	1
CGCTGCTCTTGAGTGTGCAAAATGGCTCAAA	14	257	1
ATAATATAATGTGTTGGAAAATCCAAAGAAG	16	46	1
AAAGAAGATAGTGGGGGAAAAG         	16	70	1
AGCGTTTGAATTCATGGAAAAAACGTTCGGA	17	65	1
          *** *******
MAP Score: 9.49577

Motif 5
GAACTCTGCGTGAAAACAGTTTCATGATAA	1	24	0
CGATTTCAGATGAGAAAATTGACGGTAAAA	1	142	1
        AATGAAAACATTTTCAGACTAT	4	2	1
AATTCTGGAGTGAAAAAAGCAGGTACATGC	5	161	1
CCTCTCACCATGATATAATTTCCTGTGATT	5	194	1
ATCTCCTTTCTGCTAAAATTTTACCCTTTG	6	20	1
ATGTGTTCGTTGAAAAATTTTTCTTTCTGT	8	131	0
CATTGTGGAGTGATAAAATTGATAACTGCA	9	23	0
CACTCCACAATGATAAAATCTAACGTGTGG	9	41	1
TAACCTGAGGTGTTAAAATTCAATCAAATC	11	27	0
AAGAATACTGTGATAAAATTCAGACAATAA	12	63	1
TCTGAATTATTGAAAAAAGTGCTTTATTCT	12	135	1
CAAACGCTTCTTAAAAAATTAAAAGGCTGG	17	43	0
          **********
MAP Score: 7.36628

Motif 6
GTCATCGGTTCAACTCGTTTTTTTCTCTGATAATATAT	0	32	1
AGTTTCTTTTCTGAAGGCTTTTTCAAATTAGGAAATAC	1	105	1
TAATTCCAGAAAATCGGATTTTTTCGTGTTTGGTTCTC	1	197	1
CCCCGGCGATCGCCGGGGTTTTTTGGAGGTGAACATGG	2	15	1
CACGTAGATACTACTCGCTTTTTCGAAGTGTTCCTGCG	7	81	0
CGCCATACTCCTTTCGGCTTTTATACTGATTCTTTCTC	7	196	1
CACACCTCCTCGGACCGCTTTTTTACGGAGGAAGACTG	8	13	1
CCCCGCATCAAGCGGGGCTTTTTCTTATACATTTTATG	13	46	1
GGTGATCCACCACCTTGTTTTTTCCTTTCTTTTTCAGA	14	119	0
TATATACTTTCCGAACGTTTTTTCCATGAATTCAAACG	17	67	0
          *    ** ******   *
MAP Score: 6.19582

Motif 7
GTCATCGGTTCAACTCGTTTTTTTCTCTGATAA	0	32	1
TATCGATTTTTACCGTCAATTTTCTCATCTGAA	1	146	0
CCCCGGCGATCGCCGGGGTTTTTTGGAGGTGAA	2	15	1
AAGGGCGGATTTCCGCCCTTTTTTGTTCTGGTG	3	35	1
AATTTTACGACACCGCGATTTGAGAAACATCTA	5	122	1
GGACCGCATGTACCTGCTTTTTTCACTCCAGAA	5	163	0
CACGTAGATACTACTCGCTTTTTCGAAGTGTTC	7	86	0
TGGATCCATGCTCCTGAAATTCTCGTACCAACT	7	259	0
     GTTAACACCTCCTATAGATGGATCCATG	7	282	0
     GTTACCACCTCCCATTTTAGATTATACT	8	189	0
       CAACACCTCACTTTATAGTAGAATAG	10	3	1
AACTTGTGATCACCTCCACGTAACTATTCTACT	10	26	0
TGAATTTTAACACCTCAGGTTATAATAATAATA	11	35	1
 TCCAACCACCTCCTGAATTAGTCTAGTATTAT	11	62	0
GGTGATCCACCACCTTGTTTTTTCCTTTCTTTT	14	124	0
AGGAGAACCTCTCCGCATCTTTTGAGCCATTTT	14	275	0
     AAAAACACCTCCCTGTATTTCGTATCCA	17	116	0
          *******  ** *
MAP Score: 5.7757

Motif 8
TAGAAATCACCTCCCGAAAAAGCATCTGCGTAGA	8	63	1
TGGATCCATGCTCCTGAAATTCTCGTACCAACTT	7	258	0
TTGAAAAAGCCTTCAGAAAAGAAACTCGACGTTA	1	97	0
TCAATTTTCTCATCTGAAATCGTATTTCCTAATT	1	130	0
 TCCAACCACCTCCTGAATTAGTCTAGTATTATT	11	61	0
CAAAGTCTTCCTCCCAAAAATATAAATCTGAATT	5	73	0
GCTTTTTTCACTCCAGAATTAAACGGTAGATGTT	5	147	0
TCGAATAATTCCTCTGAAACCGGATACCAGGGAA	1	52	1
TTCCTTTCTTTTTCAGAAAGAGAATTGTTCCCAT	14	102	0
CCATGTTCACCTCCAAAAAACCCCGGCGATCGCC	2	19	0
TGGAAAAAACGTTCGGAAAGTATATAGTTGTAAC	17	79	1
TCTAACATCACACCGGAAGAAACACCAGTACAGA	8	102	1
CGCAGGAACACTTCGAAAAAGCGAGTAGTATCTA	7	81	1
CCACAGTGGTCATCAGAAGCGGAAACGTG     	18	5	0
ATTATACTCTTTTCGGAAATTAACGTTGAAGAAG	8	163	0
TGGTTTTGTTCTCCTGGAAAGCGACAGTGAAAAT	12	179	1
       AAGGATCTGAAAGGGGCCTGAAAGGCC	16	3	1
CAAATTCTAACACCAGAACAAAAAAGGGCGGAAA	3	44	0
CACAGTATTCTTTCAAAAATGACCAAATAATTTT	12	41	0
ACCAGTCTTCCTCCGTAAAAAAGCGGTCCGAGGA	8	19	0
          **** ****  * *
MAP Score: 3.28958