AlignACE 3.0 10/20/99
AlignACE2 -i TM/TM_operons014_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944252189
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	TM0132	300	flagellin, putative
#1	TM0379	300	NADH oxidase
#2	TM0381	300	dihydrolipoamide dehydrogenase
#3	TM0398	300	conserved hypothetical protein
#4	TM0755	111	conserved hypothetical protein
#5	TM0863	82	ribosomal protein L9
#6	TM0868	29	glutaredoxin-related protein
#7	TM0943	183	glutamine synthetase
#8	TM1058	99	glutamate synthase-related protein
#9	TM1429	209	glycerol uptake facilitator protein
#10	TM1430	31	glycerol kinase
#11	TM1432	80	conserved hypothetical protein
#12	TM1632	62	conserved hypothetical protein

Motif 1
ATCACCCCTCCCTTCGGGAGGGGTTTTCTCAGG	2	266	1
ATGCTTTTCTCCTTCAGGAGGTGAATGCC    	3	281	1
GAAAAATTTCTCTTTTGGAGGGGAAAAC     	1	282	1
TTTTTTATGTTCAAGAGGAGGTGTTGTT     	7	165	1
GGGAGGGGTTTTCTCAGGAGGGGACGAAC    	2	281	1
TAATCTTATCGCAAAAGGAGGGGTCTTC     	10	13	1
TAAGGAAAAATTTTCAGGAGGTGATTTGTT   	5	62	1
GAATCCCTAATTTAATGGAGGTGTCTCTGT   	4	91	1
   ATAAATTCCATTTGGGGGGGAACGGTAGTG	8	7	1
GGCTCTTTTTGTTTAAGGAGGTGCAAACG    	11	61	1
     AAAGGCCGTTGGGAGGTCGTCTAACGGT	3	5	1
TTGGTAGAATTATATCGGAGGTGAAAAA     	6	11	1
CGTTGTGTCTCCTTCCGGAGGGATTCAATATGT	12	11	1
CTCGGTAAACCTCTTCGGAGATGGGCATATCTA	1	87	0
TATAATCTTGAAAAGAGGAGGTGTGAAGT    	5	6	0
CCCTCCCAGCCAGAAAGGGGATGCAATGCATCC	3	81	1
          ** *  *******
MAP Score: 30.5437

Motif 2
TAAGGCAAAGCGCTGTGGGGTCAAAGTGATAA	0	125	0
TCACAGCTTTCACAGTGAAGGCACCTTCTACA	1	31	0
ATTTCAACTGCAAAGGTAGAGAAATTACGGTG	1	211	0
AAAAATTTCTCTTTTGGAGGGGAAAAC     	1	283	1
CATGCGGGACCGCTGTGAGAGCAGGAGCAACA	2	122	1
CACTCATGTACGGTTTGAAGGCATACGAAATC	2	209	1
AAACCCCTCCCGAAGGGAGGGGTGATGTTATT	2	260	0
    AAAGGCCGTTGGGAGGTCGTCTAACGGT	3	6	1
GGTCGTCTAACGGTAGGACGGCGGACTCTGGA	3	24	1
ACTCTGGATCCGCTGGTGGAGGTTCGAGTCCT	3	48	1
TCCCCTTTCTGGCTGGGAGGGGAGGACTCGAA	3	70	0
   ATAAATTCCATTTGGGGGGGAACGGTAGT	8	7	1
AACGGATACACACTGGGGGGTCTCTTTTTCTC	9	136	0
AATCTTATCGCAAAAGGAGGGGTCTTC     	10	14	1
          *  *********
MAP Score: 6.63536

Motif 3
TTTATTTATGTATCCACATTCACTGCATAGC	0	66	1
ACAAAATAGATATGCCCATCTCCGAAGAGGT	1	81	1
CACCGTAATTTCTCTACCTTTGCAGTTGAAA	1	211	1
         GTTTTCCCCTCCAAAAGAGAAA	1	288	0
GAAAATAACATCACCCCTCCCTTCGGGAGGG	2	257	1
        GTTCGTCCCCTCCTGAGAAAACC	2	287	0
AGGTTCGAGTCCTCCCCTCCCAGCCAGAAAG	3	67	1
GGATGCATTGCATCCCCTTTCTGGCTGGGAG	3	83	0
GGATGCAATGCATCCCCTTTTTCTTTATCCA	3	99	1
        GGCATTCACCTCCTGAAGGAGAA	3	287	0
         TTTTTCACCTCCGATATAATTC	6	17	0
TTCCCACTACCGTTCCCCCCCAAATGGAATT	8	13	0
          TTTCCCAATCCTCCTTGTATG	9	198	0
        CGTTTGCACCTCCTTAAACAAAA	11	67	0
    TCGTTGTGTCTCCTTCCGGAGGGATTC	12	6	1
          * *********
MAP Score: 4.54027

Motif 4
TGTTGAGATCTTTCACCACGATCTTTCCAG	0	159	1
GAAGAGGTGGTTTCCCTTCGTAAACGACTC	1	117	0
GACACCGTAATTTCTCTACCTTTGCAGTTG	1	209	1
TTTTTCACGATCTTCCATTCACAATTCTAC	1	258	0
TCGTGAAAAATTTCTCTTTTGGAGGGGAAA	1	278	1
        GTTTTCCCCTCCAAAAGAGAAA	1	288	0
GTGTCGAGGATTTCTTCTTCTGTTGCTCCT	2	144	0
       GTTCGTCCCCTCCTGAGAAAACC	2	287	0
AGGTTCGAGTCCTCCCCTCCCAGCCAGAAA	3	67	1
GCATCCCCTTTTTCTTTATCCACAGACCAA	3	108	1
CCATATGTGTTCTCTCAATCAAAGGACTGT	3	221	0
TATTCATGCTTTTCTCCTTCAGGAGGTGAA	3	276	1
CCTGAAAATTTTTCCTTATCTATTCTATCA	5	50	0
        TTTTTCACCTCCGATATAATTC	6	17	0
AGAGGGGTTTTTTCTTTTTGCATCTTTATG	7	43	0
GGTCTCTTTTTCTCTAAACCCCAATTATTT	9	120	0
          TTTCCCAATCCTCCTTGTAT	9	199	0
CTCTCTTTTCTCTCTCCTTCAAGAA     	11	5	0
GGGATATGGCTCTCTCTTTTCTCTCTCCTT	11	16	0
    TCGTTGTGTCTCCTTCCGGAGGGATT	12	6	1
          TTTCTGTTCCTCCACAGTGT	12	52	0
          **********
MAP Score: 4.13874

Motif 5
TAGATATGCCCATCTCCGAAGAGGTTTACCGAGTCGTTTACG	1	87	1
GAAGGGAAACCACCTCTTCAGTCGATGAGAGATCTCATGAGA	1	128	1
CCTGAGAAAACCCCTCCCGAAGGGAGGGGTGATGTTATTTTC	2	257	0
GGAGGACTCGAACCTCCACCAGCGGATCCAGAGTCCGCCGTC	3	40	0
TGCATTGCATCCCCTTTCTGGCTGGGAGGGGAGGACTCGAAC	3	69	0
AAAGAAAAAACCCCTCTGTCCCCGGGGACAGAAAAGGTTGTT	7	56	1
TGGCCCAAACAACTTCATTTCATGTCTTGGGATATTGATTAT	7	113	1
GGTAGTGGGAAACCTCAGAAGGCCAAATGCGAACGAAGCGAC	8	33	1
    CGTTTGCACCTCCTTAAACAAAAAGAGCCATACCCCAC	11	52	0
          ******       *    * **
MAP Score: 4.05413

Motif 6
TTCATTATGGAAAGGGGGGATTTAGG      	0	284	1
ATGCCCATCTCCGAAGAGGTTTACCGAGTCGT	1	92	1
TCATCGACTGAAGAGGTGGTTTCCCTTCGTAA	1	124	0
GCAGGAGCAACAGAAGAAGAAATCCTCGACAC	2	142	1
CCCCTCCCGAAGGGAGGGGTGATGTTATTTTC	2	257	0
CCCCTCCCTTCGGGAGGGGTTTTCTCAGGAGG	2	270	1
GGGGTTTTCTCAGGAGGGGACGAAC       	2	285	1
CCTCCCAGCCAGAAAGGGGATGCAATGCATCC	3	82	1
GATAAAGAAAAAGGGGATGCATTGCATCCCCT	3	96	0
TTTTCTCCTTCAGGAGGTGAATGCC       	3	285	1
TAATCTTGAAAAGAGGAGGTGTGAAGT     	5	5	0
GAAAAATTTTCAGGAGGTGATTTGTT      	5	66	1
CCGGGGACAGAAAAGGTTGTTGTTTTTGATTT	7	77	1
TTTTTATGTTCAAGAGGAGGTGTTGTT     	7	166	1
TTCAACCGCTCAAGGGATGTTGTCCCT     	8	82	1
ACGGATACACACTGGGGGGTCTCTTTTTCTCT	9	135	0
ATATTTACATACAAGGAGGATTGGGAAA    	9	191	1
AATCTTATCGCAAAAGGAGGGGTCTTC     	10	14	1
CCATATCCCACAAGAGTGGGGTATGGCTCTTT	11	37	1
CTTTTTGTTTAAGGAGGTGCAAACG       	11	65	1
          *********  *
MAP Score: 3.911

Motif 7
TCACTTTGACCCCACAGCGCTTTGCCTTAAATGTTG	0	128	1
CACGATCTTTCCAGTTTGGCTTTCGCTGACAAGATC	0	175	1
CCCCCCTTTCCATAATGAATTTTATCAGAACGTGCA	0	267	0
TTATTAGACACCGTAATTTCTCTACCTTTGCAGTTG	1	203	1
GATATGAGTTCCTTCGTTTTTGTGTCGAGTGCTTTC	2	40	0
ATACAGACTGCCACTTTGATTGTGTCGAGGATTTCT	2	159	0
TGCAATGCATCCCCTTTTTCTTTATCCACAGACCAA	3	102	1
AACATTTATACCATATGTGTTCTCTCAATCAAAGGA	3	225	0
ATTAGGGATTCCAAAGTGATTATAGCAGAAAATGTA	4	66	0
GAAAATTTTTCCTTATCTATTCTATCATGCTTGATT	5	41	0
TTTTTCACCTCCGATATAATTCTACCAAA       	6	3	0
TCAAAAACAACAACCTTTTCTGTCCCCGGGGACAGA	7	70	0
TCGCATTTGGCCTTCTGAGGTTTCCCACTACCGTTC	8	29	0
TTATAACAAACCTTTTGTTTTATGTCAATATAGTTA	9	58	0
CCAATTATTTACTTTTTTGTTATGCCTCGATGTGAA	9	94	0
GGATATGGCTCTCTCTTTTCTCTCTCCTTCAAGAA 	11	9	0
          **   **  ** ****
MAP Score: 3.83584

Motif 8
TAGATATGCCCATCTCCGAAGAGGTTTACCGAGTCGTTTACGAAGG	1	87	1
CAGGCTTCTTCTCATGAGATCTCTCATCGACTGAAGAGGTGGTTTC	1	133	0
TCGTTTTTGTGTCGAGTGCTTTCGGGCTTTCAGCCGCGTGAACGTA	2	17	0
TGTATCGTCTGGCATGCGGGACCGCTGTGAGAGCAGGAGCAACAGA	2	110	1
CCGTACATGAGTGCTGGGCCACCGCCCATACAGACTGCCACTTTGA	2	176	0
CATCACCCCTCCCTTCGGGAGGGGTTTTCTCAGGAGGGGACGAAC 	2	265	1
     AAAGGCCGTTGGGAGGTCGTCTAACGGTAGGACGGCGGACT	3	5	1
GTAGGACGGCGGACTCTGGATCCGCTGGTGGAGGTTCGAGTCCTCC	3	36	1
AAACAACAACCTTTTCTGTCCCCGGGGACAGAGGGGTTTTTTCTTT	7	56	0
AAGAGACCCCCCAGTGTGTATCCGTTTATGGATACTGCTGGGGGGT	9	142	1
          *   ** *    **      ***  *
MAP Score: 0.21175