AlignACE 3.0 10/20/99
AlignACE2 -i TM/TM_operons008_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944251926
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	TM0237	67	UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-diaminopimelate ligase
#1	TM0258	300	DNA topoisomerase
#2	TM0590	128	penicillin-binding protein 2
#3	TM0826	127	hypothetical protein
#4	TM0828	29	sugar kinase, pfkB family
#5	TM0839	54	rod shape-determining protein RodA
#6	TM0871	112	hypothetical protein
#7	TM0872	300	conserved hypothetical protein
#8	TM0887	55	methylated-DNA-protein-cysteine methyltransferase
#9	TM0916_TM0917	340	TM0916: conserved hypothetical protein, TM0917: phosphate permease, putative
#10	TM1279	37	hypothetical protein
#11	TM1574	69	pseudouridylate synthase I
#12	TM1575	271	hypothetical protein

Motif 1
ATTCGAGCTCTCCGTGGTGCGAAAGAATTA	1	103	0
ATGGGGTTCACCCGTGGTTCCAAAGACGAT	1	131	1
AGCTCGATTCATCGAGGTTATGGAAAGTTC	1	206	1
AAAATCTATCCTGGAGGTGATTGG      	3	4	0
TAGAATCAAAAACGAGGTGATGCCTC    	3	111	1
CACTTTTGACTTCGAGGTGATCGT      	4	15	1
ATATAATGAACCGGAGGTGAGAATTATGAG	7	51	0
TACGACCCCTCCTGTGGTGTGTTTTCTATT	9	10	1
CCAAATGTGGCCCGATGTGATAGAATTTAC	9	289	1
ATTTTAACAGCCGGAGTTGAAATAC     	11	5	0
TATAGCACGAATCGAGGTGAAAAG      	11	55	1
GAAACGGCTTCCTGTGGTGACGCTTGTTTA	12	107	1
          **********
MAP Score: 11.9122

Motif 2
        TTTTCTTACCTCCTGTCTGGAAA	0	2	1
         AGTAGAACCACCTCTGAAGGAA	0	55	0
ACATAATTCTTTCGCACCACGGAGAGCTCGA	1	100	1
TCTATCGTCTTTGGAACCACGGGTGAACCCC	1	133	0
        CAGTTCCTCCACCTCTTAAAAAG	1	287	0
TCTCTTCAGTGTTGCTCCCCGCTGTTGTCCT	2	11	1
       CGCTTCGATCCTCCCAGAATGAAC	2	114	0
       GAGGCATCACCTCGTTTTTGATTC	3	113	0
TACTTGTTCTTTCGCACCAACTTATTTTCAC	6	42	1
CTTAAGGCGGTTACCCCCACGAACAATAACA	6	90	0
TTTCTCATAATTCTCACCTCCGGTTCATTAT	7	48	1
TATCACGCCTTCTGATCCTCGTGTGGAAACA	7	277	0
GAGCATGAAAGTTGACCCCCCTATCCCCCTT	9	193	1
        GTTTTCCACCCCGAAACGATTAT	10	24	0
         CTTTTCACCTCGATTCGTGCTA	11	57	0
ACGGAGTACTTTACTTCCTCGGTGATGCGAC	12	40	1
          ** ********
MAP Score: 11.892

Motif 3
TAACCATAGCCGCCCCTATTGCTATATGCCCTTTCA 	1	9	0
GAACTATTAAAGCCTCTATCGTCTTTGGAACCACGGG	1	141	0
CAGTGTTGCTCCCCGCTGTTGTCCTTGTGGCTGTCGG	2	17	1
TTTTGCTTTCCGCCGCCACTGGCATCGTGTTCATTCT	2	86	1
        CTCCTCACTTTTGACTTCGAGGTGATCGT	4	2	1
     TACGACCCCTCCTGTGGTGTGTTTTCTATTGT	9	5	1
TGAAAGTTGACCCCCCTATCCCCCTTGAGATACACCC	9	198	1
CCTTGAGATACACCCCCCACGGCCTTGGCGGGCTCGA	9	220	1
CTCGGTGATGCGACTCCGACGTCATCTGAAATCGAGA	12	57	1
          * ** **  ** * * *
MAP Score: 10.187

Motif 4
AGTGTTAAAATTCCTTCAGAGGTGGTTCTACT    	0	45	1
CCAAGATAGCTCGATTCATCGAGGTTATGGAAAGTT	1	199	1
AAGTTCCGAATCGAATCAGGGTTGGACGGAGTACGA	1	230	1
         TTCTCTTCAGTGTTGCTCCCCGCTGTT	2	1	1
TGGCATCGTGTTCATTCTGGGAGGATCGAAGCG   	2	105	1
TTGCTGTGTTATTGTTCGTGGGGGTAACCGCCTTAA	6	84	1
ATATCCTTCATCTTTTCGTTCAGGTTTCTCATAATT	7	24	1
CATAGTATAATCGTTTCGGGGTGGAAAAC       	10	18	1
ACGGAGTACTTTACTTCCTCGGTGATGCGACTCCGA	12	40	1
GGAAGCCGTTTCCATTCCTCGATGATCTCGATTTCA	12	83	0
          **  *** * * ** *
MAP Score: 9.41688

Motif 5
     TTTTCTTACCTCCTGTCTGGAAAAGCTTTAAATAA	0	5	1
AAGTGTTAAAATTCCTTCAGAGGTGGTTCTACT       	0	44	1
TTCCTGTCGTACTCCGTCCAACCCTGATTCGATTCGGAAC	1	232	0
CATCCGAATTTCACCGACAAGACAGCCGACAGCCACAAGG	2	39	0
ACGGTTTTGCTTTCCGCCGCCACTGGCATCGTGTTCATTC	2	82	1
      CCAATCACCTCCAGGATAGATTTTAACCCTGGAG	3	4	1
CTCATAATTCTCACCTCCGGTTCATTATATTAGCACTTAA	7	51	1
TCAACCAAAAATCCCTTCAATTCGGCATTTTAAGAGGCCT	7	189	1
    TCTATCACGCCTTCTGATCCTCGTGTGGAAACATTA	7	274	0
  GGATTTCTACTCCTCCTTCTCGTTCAAGGCCCTGATAT	8	8	1
      TACGACCCCTCCTGTGGTGTGTTTTCTATTGTAT	9	4	1
GGCTCTTTCGAGCCCGCCAAGGCCGTGGGGGGTGTATCTC	9	224	0
TTGTATAAAAACCCCGCCAAATGTGGCCCGATGTGATAGA	9	273	1
      GAGTATCCCTCCTTAATATGATATTTGCTGTGTA	9	316	0
         CTCCCCATCATAGTATAATCGTTTCGGGGTG	10	1	1
CGGTGATGCGACTCCGACGTCATCTGAAATCGAGATCATC	12	59	1
ACCAGTCAGTACTCCTTCTTCAGAGAGAAGATCTCTCACA	12	163	0
          ** *****    * *    *
MAP Score: 8.832

Motif 6
TAACACTTTATTTAAAGCTTTTCCAGACAGGAGGTAAGAAA	0	11	0
AAATAAAGTGTTAAAATTCCTTCAGAGGTGGTTCTACT   	0	39	1
CACGGAGAGCTCGAATGGGGTTCACCCGTGGTTCCAAAGAC	1	117	1
CCTCCCAGAATGAACACGATGCCAGTGGCGGCGGAAAGCAA	2	88	0
GTCTCCAGGGTTAAAATCTATCCTGGAGGTGATTGG     	3	5	0
GAAGAATACGTTATAATGTTTCCACACGAGGATCAGAAGGC	7	261	1
AGTGATACAATAGAAAACACACCACAGGAGGGGTCGTA   	9	7	0
TTTTTTTGTATAAAAACCCCGCCAAATGTGGCCCGATGTGA	9	268	1
ATATTTGCTGTGTAAATTCTATCACATCGGGCCACATTTGG	9	289	0
CATCGAGGAATGGAAACGGCTTCCTGTGGTGACGCTTGTTT	12	95	1
TTTCCTTAGTTCGAATCTTGACAATGAGGGGTGTTCCCGAA	12	202	0
          *  ***     ***   * **
MAP Score: 8.55253

Motif 7
CCCCATTCGAGCTCTCCGTGGTGCGAAAGAATT	1	104	0
CTTCAGTGTTGCTCCCCGCTGTTGTCCTTGTGG	2	14	1
TGTCCTTGTGGCTGTCGGCTGTCTTGTCGGTGA	2	36	1
AAATTCGGATGCTGACGGTTTTGCTTTCCGCCG	2	68	1
GAATGAACACGATGCCAGTGGCGGCGGAAAGCA	2	89	0
GAATAGACTGGATCATAGTTGTTCTT       	5	38	1
TCACCATTGTGCTCGTTGCTGTGTTATTGTTCG	6	69	1
       TACGACCCCTCCTGTGGTGTGTTTTC	9	3	1
TCCTTAATATGATATTTGCTGTGTAAATTCTAT	9	308	0
AATGGAAACGGCTTCCTGTGGTGACGCTTGTTT	12	103	1
          ***  * ******
MAP Score: 5.1017

Motif 8
TTTCCAGACAGGAGGTAAGAAAA        	0	2	0
GCTCTCCGTGGTGCGAAAGAATTATGTGCTC	1	96	0
ACGACAGGAATTTGGGAAGAAGAATCTTTTT	1	262	1
GTTCATTCTGGGAGGATCGAAGCG       	2	114	1
ATTAAAGGTTTGGGGTTAGAATCAAAAACGA	3	95	1
AAATAAGTTGGTGCGAAAGAACAAGTACTCT	6	38	0
ATAATGAACCGGAGGTGAGAATTATGAGAAA	7	48	0
TTTTTGATTTTTACGGAAGAATACGTTATAA	7	246	1
AGGTACCCATTTAGGAAAGAAATTAGAATCT	9	129	1
CACGGCCTTGGCGGGCTCGAAAGAGCCCGCA	9	237	1
          ***** *****
MAP Score: 4.47888

Motif 9
TCCCCCTTGAGATACACCCCCCACGGCCTTGG	9	216	1
GACTGGTTCGGGAACACCCCTCATTGTCAAGA	12	196	1
TCTCTTCAGTGTTGCTCCCCGCTGTTGTCCTT	2	11	1
TGGAACCACGGGTGAACCCCATTCGAGCTCTC	1	121	0
 TCTTAAGGCGGTTACCCCCACGAACAATAAC	6	91	0
GAGCATGAAAGTTGACCCCCCTATCCCCCTTG	9	193	1
ATGAAGACTAGGAAAACCCAACAGAACTTCAT	9	82	1
TTTTTTTGTATAAAAACCCCGCCAAATGTGGC	9	268	1
         AGTAGAACCACCTCTGAAGGAAT	0	54	0
          * ******** *
MAP Score: 4.04207

Motif 10
GAGCTCTCCGTGGTGCGAAAGAATTATGTGCTC	1	96	0
GAAAATAAGTTGGTGCGAAAGAACAAGTACTCT	6	38	0
ATCTTACGTTTGATAAAACAAAATGTAAATGTT	7	91	1
AAATGTTTCTTGAAACAACAGAATGTCTCCTTT	7	117	1
TTTTTTTGATTTTTACGGAAGAATACGTTATAA	7	244	1
GGGTTCAAAGTGATACAATAGAAAACACACCAC	9	23	0
TTGAGACAGATGTATCATGAAAAGGGTTCAAAG	9	46	0
TCTCTTAACCTGTTACATTTAAAATGTACCATG	9	160	1
GGCGGGGTTTTTATACAAAAAAATGCGGGCTCT	9	258	0
AAATATGATCTGGTACAGTAAAAATATAGCACG	11	31	1
          ** ****  ****
MAP Score: 3.09708

Motif 11
GAACCACCTCTGAAGGAATTTTAACACTTT	0	43	0
AGAGAAATGGCGAAGAAATTGTCTATTCCA	1	45	1
CTCCGTGGTGCGAAAGAATTATGTGCTCTA	1	94	0
CGTCCAACCCTGATTCGATTCGGAACTTTC	1	228	0
TTTTAAGAGGTGGAGGAACTG         	1	289	1
GCTGTCTTGTCGGTGAAATTCGGATGCTGA	2	53	1
TAAGTTGGTGCGAAAGAACAAGTACTCTCG	6	36	0
AATGCCGAATTGAAGGGATTTTTGGTTGAT	7	188	0
TTGATTTTTACGGAAGAATACGTTATAATG	7	249	1
   CGCCTCCTGATAGAATTATATCAGGGC	8	38	0
GGGTTCAAAGTGATACAATAGAAAACACAC	9	26	0
TGGCCCGATGTGATAGAATTTACACAGCAA	9	296	1
TTTTCCACCCCGAAACGATTATACTATGAT	10	16	0
ACTTCCTCGGTGATGCGACTCCGACGTCAT	12	52	1
          **********
MAP Score: 0.95724