AlignACE 3.0 10/20/99
AlignACE2 -i TM/TM_operons024_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944252559
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	TM0167_TM0168	91	TM0167: phosphopentomutase, TM0168: leucyl-tRNA synthetase
#1	TM0402	300	ammonium transporter
#2	TM0404	47	deoxycytidylate deaminase, putative
#3	TM1085	60	methionyl-tRNA synthetase
#4	TM1095	300	adenylosuccinate lyase
#5	TM1358	50	conserved hypothetical protein
#6	TM1361	21	isoleucyl-tRNA synthetase
#7	TM1666	104	succinyl-diaminopimelate desuccinylase, putative
#8	TM1714	100	UDP-N-acetylenolpyruvoylglucosamine reductase
#9	TM1817	31	valyl-tRNA synthetase
#10	TM1819	55	chromate transport protein, putative

Motif 1
      GTCTACACCTCCTGATATTTCCTT	0	4	1
      AAAAACACCTCCTTTTGGTAAATA	1	286	0
GGAGGAGGTTTCTCCTCCCGAAAGGAAACC	2	10	0
     AAATCTCACCTCCGGTGTGTGGTAT	3	5	1
      AGTGTCACCTCCTTGTTTTCCCTA	3	46	0
AACCGTGAACATACCTCTCAAATCGCTTTT	4	158	1
      CTTTTTCCCTCCCAAACAGATCTC	4	286	0
     AATTTATCCCTCCCACTTTTAGTTT	5	5	1
 AAACTTTTCACACCTCCTGTG        	6	2	0
      GTAAACACCTCCCTAAATTTTTTC	7	4	1
     TGAAAACACCTCCCAGATTCAAGTA	7	89	0
      GTCAACACCTCCCAGTTTGAAATT	8	4	1
GTCCAAAGATATCCCTCCTTAAACTCTATA	8	38	0
     TCTCAGCACCTCCTTTTCCTGTGAT	9	16	0
      CTCGATCCCTCCCGGTTTCTTTTG	10	4	1
          **********
MAP Score: 41.4908

Motif 2
CCTGATATTTCCTTCTCAAAGTTAATAATA	0	20	1
CCTTCCAGCTCCTTTCCGAAAAATTCTATC	0	71	0
ACATATAAAATCCTCCAGAAATTTATTCCC	1	110	1
TCCAGAAATTTATTCCCGAAAATTAGTAAT	1	123	1
GGGGTTTGTGCCCTCTAAAAAAAAGAACCC	1	171	1
AGGAGGTTTCTCCTCCCGAAAGGAAACC  	2	8	0
CGTAATCTGTCCCTTTCAAATATTCGAACC	4	61	0
ACGGTTTTTTTCTTTGCGAAACTGGTGGCG	4	134	0
CCGTGAACATACCTCTCAAATCGCTTTTCT	4	160	1
TTCCACAACGCCATCGCAACGAGAAACCAG	4	188	0
    CTTTTTCCCTCCCAAACAGATCTCTC	4	284	0
    GTAAACACCTCCCTAAATTTTTTCTA	7	6	1
TCTTGGGGTATCATTTCAAATATTTTTTTA	7	54	1
   TGAAAACACCTCCCAGATTCAAGTATA	7	87	0
TTTTTGGATCTCTTCACAAAGCAGGCTGTG	8	72	1
    CTCGATCCCTCCCGGTTTCTTTTGAT	10	6	1
          **********
MAP Score: 12.0617

Motif 3
AGAAGGAAATATCAGGAGGTGTAGAC       	0	3	0
TATTATTAACTTTGAGAAGGAAATATCAGGAGG	0	17	0
ATGTTTCAGTTTGACTGGGAAGATTGTTAACAC	1	36	0
  GGTTTCCTTTCGGGAGGAGAAACCTCCTCCC	2	8	1
GGGAGGCCGAAAAAAGGGGAGGAGGTTTCTCCT	2	24	0
GTATCATTGAATAGATAGGGAAAACAAGGAGGT	3	31	1
GAACCCCTCGAGGACGAGGAGAAAGATCAGACT	4	33	0
GGTTCGAATATTTGAAAGGGACAGATTACGATC	4	61	1
GAGAGATCTGTTTGGGAGGGAAAAAG       	4	284	1
ATAAACTAAAAGTGGGAGGGATAAATT      	5	4	0
TTATCATTAAATAGTGGAGGATAGATT      	5	33	1
ACTATAGAGTTTAAGGAGGGATATCTTTGGACA	8	36	1
          ** * ****** *
MAP Score: 4.48534

Motif 4
CTCCTGATATTTCCTTCTCAAAGTTAATAATA	0	18	1
TCTCAAAGTTAATAATATCAGATTTTTCAGCC	0	33	1
CTTTCCGAAAAATTCTATCACAAATGGCTGAA	0	58	0
GAGTGTTAACAATCTTCCCAGTCAAACTGAAA	1	34	1
GTCAAACTGAAACATTCTCATAATTGACAGCG	1	54	1
TATATGTCTCAATACTATCAATTCAAAAAACC	1	85	0
AATATTGTTTATTTGTATCATATTGATAGAGA	1	228	1
GTCAACAAACATATTTACCAAAAGGAGGTGTT	1	275	1
AACCGTGAACATACCTCTCAAATCGCTTTTCT	4	158	1
      CTTTTTCCCTCCCAAACAGATCTCTC	4	284	0
     AATTTATCCCTCCCACTTTTAGTTTAT	5	5	1
          AAACTTTTCACACCTCCTGTG 	6	9	0
     TGAAAACACCTCCCAGATTCAAGTATA	7	87	0
          TAAAATATCACAGGAAAAGGAG	9	0	1
AATATGATTTAATAGTATCAAAAGAAACCGGG	10	20	0
          **** ***** *
MAP Score: 0.333715

Motif 5
TATCAGATTTTTCAGCCATTTGTGATAGAATTTTTCGGAAAGGA	0	48	1
AAAAAAGAACCCCATGGTGTTTGTTTTTTGTTTTTCAAGAATAT	1	189	1
TTTTCAAGAATATTGTTTATTTGTATCATATTGATAGAGAATTA	1	220	1
GCATTAAATATCCAACGGCTTCTTATCTTGTTTTTCCTGTTGTT	4	226	1
TATCTTGTTTTTCCTGTTGTTGCGCTCGTGTTCACGAGAGATCT	4	249	1
 AATTTATCCCTCCCACTTTTAGTTTATCATTAAATAGTGGAGG	5	9	1
TTTGAAATGATACCCCAAGATTTTATATAATTGATTGATAGAAA	7	30	0
CACCTCCCAGTTTGAAATTATACTATAGAGTTTAAGGAGGGATA	8	15	1
    TCTCAGCACCTCCTTTTCCTGTGATATTTTA         	9	1	0
CTCGATCCCTCCCGGTTTCTTTTGATACTATTAAATCATATTCA	10	10	1
          * *      **  * *   *** *
MAP Score: 0.190092