AlignACE 3.0 10/20/99
AlignACE2 -i TM/TM_operons024_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944252548
 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
CTTCTCAAAGTTAATAATATCAGATTTTTCAG	0	31	1
TTTATATGTCTCAATACTATCAATTCAAAAAA	1	87	0
AGAATATTGTTTATTTGTATCATATTGATAGA	1	226	1
CCCTATCTATTCAATGATACCACACACCGGAG	3	19	0
CCCTCCCACTTTTAGTTTATCATTAAATAGTG	5	17	1
CCTCCCTAAATTTTTTCTATCAATCAATTATA	7	17	1
TTTCTATCAATCAATTATATAAAATCTTGGGG	7	30	1
CCTCCCAGATTCAAGTATATCCTAAAAAAATA	7	74	0
CTCCTTAAACTCTATAGTATAATTTCAAACTG	8	22	0
TGAATATGATTTAATAGTATCAAAAGAAACCG	10	22	0
          *****  *****
MAP Score: 8.25946

Motif 3
TGTCTCAATACTATCAATTCAAAAAACCGC	1	83	0
GTATTGAGACATATAAAATCCTCCAGAAAT	1	102	1
TTAGTAATAAATATCTAATCCAACATGGGG	1	145	1
CTTGTTTTCCCTATCTATTCAATGATACCA	3	29	0
GTGAACATACCTCTCAAATCGCTTTTCTGG	4	162	1
AAGCCGTTGGATATTTAATGCTCGCTACCT	4	217	0
CTATCCTCCACTATTTAATGATAAACTAAA	5	27	0
TCAATCAATTATATAAAATCTTGGGGTATC	7	36	1
TCTTTTGATACTATTAAATCATATTCAGAT	10	27	1
          **********
MAP Score: 6.23248

Motif 4
GGAAATATCAGGAGGTGTAGAC        	0	2	0
TCCTTTTGGTAAATATGTTTGTTGACTCTT	1	271	0
TTTACCAAAAGGAGGTGTTTTT        	1	288	1
GAAAAAAGGGGAGGAGGTTTCTCCTCCCGA	2	19	0
AAAAATTTAGGGAGGTGTTTAC        	7	2	0
TATATCCTAAAAAAATATTTGAAATGATAC	7	61	0
CTTGAATCTGGGAGGTGTTTTCA       	7	91	1
TTTCAAACTGGGAGGTGTTGAC        	8	2	0
GTTTAAGGAGGGATATCTTTGGACAAAATT	8	44	1
CACAGGAAAAGGAGGTGCTGAGA       	9	18	1
          **********
MAP Score: 3.67316

Motif 5
ATATTTCCTTCTCAAAGTTAATAATATCAG	0	24	1
GATTAATTCTCTATCAATATGATACAAATA	1	237	0
  AGTGTCACCTCCTTGTTTTCCCTATCTA	3	42	0
CCTCTGATCGCCACCAGTTTCGCAAAGAAA	4	126	1
 AATTTATCCCTCCCACTTTTAGTTTATCA	5	9	1
GTAAACACCTCCCTAAATTTTTTCTATCAA	7	10	1
TGAAATGATACCCCAAGATTTTATATAATT	7	42	0
 TGAAAACACCTCCCAGATTCAAGTATATC	7	85	0
  GTCAACACCTCCCAGTTTGAAATTATAC	8	8	1
  CTCGATCCCTCCCGGTTTCTTTTGATAC	10	8	1
          **********
MAP Score: 1.80301