AlignACE 3.0 10/20/99
AlignACE2 -i TM/TM_operons011_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944252076
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	TM0129	60	carboxypeptidase G2, putative
#1	TM0140	40	indole-3-glycerol phosphate synthase
#2	TM0143	93	response regulator
#3	TM0335	26	dihydroorotase
#4	TM0337	278	conserved hypothetical protein
#5	TM0539	45	tryptophan synthase, beta subunit
#6	TM0558	211	carbamoyl-phosphate synthetase, small subunit
#7	TM0711	51	hypothetical protein
#8	TM0713	44	hypothetical protein
#9	TM0717	290	propionyl-CoA carboxylase, gamma subunit
#10	TM1095	300	adenylosuccinate lyase
#11	TM1632	62	conserved hypothetical protein
#12	TM1642	35	aspartate carbamoyltransferase, catalytic and regulatory chains
#13	TM1820	55	GMP synthase

Motif 1
        TTTCTGTTCCTCCACAGTGTTGTAC	11	47	0
CAGATAAGCACCGCTGTCTCCACCGAACGAAA 	8	9	0
GTCTGATCTTTCTCCTCGTCCTCGAGGGGTTCG	10	34	1
TCTGGTGCTGTCCTTCTTTCCTCTGATCGCCAC	10	107	1
AGGGTGATACTGTGTTTCTTCCCACAACACGTG	4	250	1
TCTGTTTTCCTGTGTTTTTCCACCAAAAATCTC	4	126	0
        TTTCTCCTCCTCCAGCCGGTTTTTT	9	275	0
ATGATCACCATCTTTCTGTTCGGAATAGTGACA	9	19	1
ACTGCTATCACCTCTTCGTTCTCTTCTGAATAC	9	150	0
TCGGTTCAACTCGTTTTTTTCTCTGATAATATA	2	36	1
         CTCGATCCCTCCCGGTTTCTTTTG	13	41	0
TTTCTTATTCTGTATTTGTTCTCCATTGTTTTG	9	64	1
AAGTGCCGTACCCCTGCGTCCCCATTTTTTAAC	4	178	1
  GTTCTCGCCGTCTATCTCCAGAATATCTTTC	1	19	0
GGACCTCCCGTCTTTTTCTTTACTTTGAATTAA	6	146	0
 GTTGCACCTCCTTCCCTTTCTCAGAGATTATA	6	189	0
    TCGTTGTGTCTCCTTCCGGAGGGATTCAA	11	6	1
CGTTTTTCTCTGCTTTTTTTCACAGAAACTATT	9	225	0
CCACCAAAAATCTCTATGACCACATCCAGCGGT	4	107	0
TTGTTATTCTTCTTTCTGTTTTCCTGTGTTTTT	4	140	0
AGTTCTAACATCTTCTTCACCTCCTTTCAGATA	4	71	0
GAATACCTGGTCTTCTTTTCTTCAACAACAGCG	9	123	0
       ATTCCCCCTCCTTCAGTGATATAATC	5	29	0
CCTGTTGTTGCGCTCGTGTTCACGAGAGATCTG	10	261	1
CTCCAGAATATCTTTCTTTTTGGCT        	1	2	0
CCTCCTCCAGCCGGTTTTTTTCCACGCTTCGTA	9	262	0
     AACATCCCTCCTCACCGGGGTTTTCTTA	0	5	1
     CAATCTCCACCCTATCCCTGAGTTTTCA	2	75	0
          *** * ***** *
MAP Score: 23.2692

Motif 2
ATATATTATTATGAAAACTCAGGGATAGGGTG	2	64	1
CGAGGACGAGGAGAAAGATCAGACTCACATGA	10	26	0
ACTATTCTTTAAGAAAACCCCGGTGAGGAGGG	0	15	0
TATATTATCAGAGAAAAAAACGAGTTGAACCG	2	37	0
TCGATTACCTGCGAAAGCACCGCTGAGATAAC	9	181	0
GCGCAACAACAGGAAAAACAAGATAAGAAGCC	10	242	0
GAGATTTTTGGTGGAAAAACACAGGAAAACAG	4	126	1
CGCCATCGCAACGAGAAACCAGAAAAGCGATT	10	178	0
ATTCAAAGTAAAGAAAAAGACGGGAGGTCCTT	6	149	1
TAGTTTCTGTGAAAAAAAGCAGAGAAAAACGA	9	227	1
TTCTCGGGAAAAGAGAAACCCGCTGTTGTTGA	9	103	1
          GAGAAAAGACCCTGTTTCATGT	10	0	1
TACGAAGCGTGGAAAAAAACCGGCTGGAGGAG	9	262	1
CGTGTTGTGGGAAGAAACACAGTATCACCCTA	4	249	0
TATAATCTCTGAGAAAGGGAAGGAGGTGCAAC	6	189	1
CTTTGAATTAAAGGAAAGTCACAGGACTTTAA	6	125	0
AGTTTCGCAAAGAAAAAAACCGTGAACATACC	10	141	1
AGGTATTCAGAAGAGAACGAAGAGGTGATAGC	9	148	1
GTACAACACTGTGGAGGAACAGAAA       	11	47	1
CGCTGTTGTTGAAGAAAAGAAGACCAGGTATT	9	123	1
CGATCAGAGGAAAGAAGGACAGCACCAGAAAC	10	104	0
AAGAAGAATAACAAAAAGTAAGTGCCGTACCC	4	159	1
TGGTTAAAAAATGGGGACGCAGGGGTACGGCA	4	181	0
          * ****** ***
MAP Score: 21.4251

Motif 3
      GTTGCACCTCCTTCCCTTTCTCAGA	6	196	0
       TTTCTCCTCCTCCAGCCGGTTTTT	9	276	0
      ATTCCCCCTCCTTCAGTGATATAAT	5	30	0
    TCGTTGTGTCTCCTTCCGGAGGGATTC	11	6	1
      AACATCCCTCCTCACCGGGGTTTTC	0	4	1
        CTTTTTCCCTCCCAAACAGATCT	10	287	0
ATGGCTTAAACATCACCTTCCAAACCAATCA	6	25	0
ATTTAATGCTCGCTACCTTCCACAACGCCAT	10	204	0
    TCACGATACCCCCTTCAGACAAAAAAA	12	18	0
        CTCGATCCCTCCCGGTTTCTTTT	13	42	0
GGTGATACTGTGTTTCTTCCCACAACACGTG	4	252	1
TCTGGTGCTGTCCTTCTTTCCTCTGATCGCC	10	107	1
AGATGGTGATCATTACCTCACC         	9	1	0
       TTTCTGTTCCTCCACAGTGTTGTA	11	48	0
      AGCTCTTCACCTCAAGAGAGATTAT	5	4	1
ACATCTTCTTCACCTCCTTTCAGATATCATC	4	66	0
         CTCCCTCTTCAACCTTAAAACA	7	39	0
GATCGTAATCTGTCCCTTTCAAATATTCGAA	10	63	0
ACCTGGTCTTCTTTTCTTCAACAACAGCGGG	9	121	0
        TTTTATCCCTCCAACTACATTAT	0	47	0
ACCTCCCGTCTTTTTCTTTACTTTGAATTAA	6	146	0
AGTCCTGTGACTTTCCTTTAATTCAAAGTAA	6	129	1
          * *********
MAP Score: 19.4291

Motif 4
GTATAATGTAGTTGGAGGGATAAAA          	0	45	1
AGGAAAGGAATTCGGAGGGAAAAGT          	3	11	1
TACATTTACAGGCGAAGGATGATGATATCTGAAAG	4	46	1
GATGATGATATCTGAAAGGAGGTGAAGAAGATGTT	4	63	1
CTTTGATTGGTTTGGAAGGTGATGTTTAAGCCATT	6	22	1
GTATAATCTCTGAGAAAGGGAAGGAGGTGCAAC  	6	188	1
AAAAAAACCGGCTGGAGGAGGAGAAA         	9	274	1
TTCTCCTCGTCCTCGAGGGGTTCGAATATTTGAAA	10	43	1
GGTTCGAATATTTGAAAGGGACAGATTACGATCGA	10	61	1
GCGATGGCGTTGTGGAAGGTAGCGAGCATTAAATA	10	201	1
GCGCTCGTGTTCACGAGAGATCTGTTTGGGAGGGA	10	270	1
AGAGATCTGTTTGGGAGGGAAAAAG          	10	285	1
TGTGTCTCCTTCCGGAGGGATTCAATATGTATTGT	11	14	1
TGTACAACACTGTGGAGGAACAGAAA         	11	46	1
TCAAAAGAAACCGGGAGGGATCGAG          	13	40	1
          ** ******    **
MAP Score: 7.4343

Motif 5
CTCCAGAATATCTTTCTTTTTGGCT      	1	4	0
TCGGTTCAACTCGTTTTTTTCTCTGATAATA	2	36	1
GTTATTCTTCTTTCTGTTTTCCTGTGTTTTT	4	140	0
GGCACTTACTTTTTGTTATTCTTCTTTCTGT	4	154	0
GAAACGAGGCTTTTTTTGTTTTAAAATACAT	4	219	1
CTCCCGTCTTTTTCTTTACTTTGAATTAAAG	6	144	0
ATGATCACCATCTTTCTGTTCGGAATAGTGA	9	19	1
GTGACAGTGTTCTTTGTATTTCTTATTCTGT	9	46	1
ACAGCGGGTTTCTCTTTTCCCGAGAAAAACT	9	98	0
ATACCTGGTCTTCTTTTCTTCAACAACAGCG	9	123	0
TATCACCTCTTCGTTCTCTTCTGAATACCTG	9	147	0
CGTATCCTCGTTTTTCTCTGCTTTTTTTCAC	9	235	0
CCAGCCGGTTTTTTTCCACGCTTCGTATCCT	9	258	0
GTGAGTCTGATCTTTCTCCTCGTCCTCGAGG	10	30	1
TCTGGTGCTGTCCTTCTTTCCTCTGATCGCC	10	107	1
GTTCACGGTTTTTTTCTTTGCGAAACTGGTG	10	137	0
ACCTCTCAAATCGCTTTTCTGGTTTCTCGTT	10	170	1
CGGCTTCTTATCTTGTTTTTCCTGTTGTTGC	10	241	1
  GTGCGATATTTTTTTGTCTGAAGGGGGTA	12	8	1
          ******* ***
MAP Score: 2.58845

Motif 6
TCGGTTCAACTCGTTTTTTTCTCTGATAATA	2	36	1
TTCTGTTTTCCTGTGTTTTTCCACCAAAAAT	4	129	0
GGTGATACTGTGTTTCTTCCCACAACACGTG	4	252	1
AAAGGACCTCCCGTCTTTTTCTTTACTTTGA	6	151	0
GTGGAGACAGCGGTGCTTATCTGGGAGTCAT	8	19	1
ATGATCACCATCTTTCTGTTCGGAATAGTGA	9	19	1
TTTCTTATTCTGTATTTGTTCTCCATTGTTT	9	64	1
TCCATTGTTTTGAAGTTTTTCTCGGGAAAAG	9	85	1
CTTCGTATCCTCGTTTTTCTCTGCTTTTTTT	9	238	0
CTCCTCCAGCCGGTTTTTTTCCACGCTTCGT	9	263	0
GTGAGTCTGATCTTTCTCCTCGTCCTCGAGG	10	30	1
GAGTTGTTTCTGGTGCTGTCCTTCTTTCCTC	10	99	1
GGTATGTTCACGGTTTTTTTCTTTGCGAAAC	10	142	0
AAATCGCTTTTCTGGTTTCTCGTTGCGATGG	10	177	1
CGGCTTCTTATCTTGTTTTTCCTGTTGTTGC	10	241	1
          **** ******
MAP Score: 2.07034