AlignACE 3.0 10/20/99
AlignACE2 -i TM/TM_operons012_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944252123
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	TM0110	107	transcriptional regulator, XylR-related
#1	TM0276	300	L-arabinose isomerase
#2	TM0280	188	hypothetical protein
#3	TM0281	21	alpha-L-arabinofuranosidase
#4	TM0282	28	aldose 1-epimerase
#5	TM0433	246	pectate lyase
#6	TM0434	89	alpha-glucosidase, putative
#7	TM0436	55	alcohol dehydrogenase, zinc-containing
#8	TM0952	300	glycerol kinase
#9	TM1069_TM1070	107	TM1069: transcriptional regulator, DeoR family, TM1070: hypothetical protein
#10	TM1429	209	glycerol uptake facilitator protein
#11	TM1430	31	glycerol kinase
#12	TM1432	80	conserved hypothetical protein
#13	TM1437	300	dimethyladenosine transferase
#14	TM1667	104	xylose isomerase

Motif 1
ATTGAGATCCAAAAGGAGGAATCGAAG   	0	90	1
CTATTTTTAGGCAGGGGGGATTTGTATGAA	1	113	0
ATGTTATACTAAAAGGATGAAACCATGAGA	1	266	1
GAAACCATGAGAAAGGAGGTCGGAGA    	1	284	1
TAAATGTATGAAAAGGAGGAATATCGTTT 	2	169	1
       GAGATGAGGAGGGAAAAGAGT  	3	3	1
AAAAACTGTTGCCAGGAGGAGAAAGAA   	4	11	1
AAAATCTTATGTTAGGAGGGGAGAGTT   	5	7	0
AGATATCTCAGTAGGGAGGG          	5	236	1
GTTAACATTTGGAGGGGGGAGACCCCCTCT	6	27	1
TTCAAATACAAAGAGGGGGTCTCCCCCCTC	6	38	0
ACCCGGAATTTAGAGGAGGTGCACAC    	6	73	1
  GAATAAGTGCAAGGGTGATTGATATGTT	8	8	1
TTAGAGTGGTTCAAGGAGGGAAATTAGA  	8	282	1
TTTTCGAAAGGAAAGGAGGTGTTGAT    	9	91	1
ACGGATACACACTGGGGGGTCTCTTTTTCT	10	137	0
TATGGATACTGCTGGGGGGTTAAATATTTA	10	168	1
ATATTTACATACAAGGAGGATTGGGAAA  	10	191	1
ATCTTATCGCAAAAGGAGGGGTCTTC    	11	15	1
CTCTTTTTGTTTAAGGAGGTGCAAACG   	12	63	1
TATACTTGAATCTGGGAGGTGTTTTCA   	14	7	0
TAGAAAAAATTTAGGGAGGTGTTTAC    	14	88	1
          **********
MAP Score: 27.7795

Motif 2
TCACCTCGTTGATCTTCTCGGTTAAAATCT	1	54	0
TCTTTCTCATCATCACCTCGTTGATCTTCT	1	66	0
TCTTCATACAAATCCCCCCTGCCTAAAAAT	1	111	1
GGAGGGGGGAGACCCCCTCTTTGTATTTGA	6	37	1
     GTGTGCACCTCCTCTAAATTCCGGG	6	74	0
GTTTACCGTTAAACCCCTGGATGAAGAAGC	8	35	1
AGGAATTCTGCAACCGCTCCACCGAGACCT	8	128	0
CAGTTTTTGCAATCCCCTCTGGCGCAAGGC	8	250	0
TTCCCTCCTTGAACCACTCTAAGACAGTTT	8	274	0
      TATTCATCACCTCTGGGTACGAAT	9	4	1
        ATCAACACCTCCTTTCCTTTCG	9	95	0
        GAAGACCCCTCCTTTTGCGATA	11	19	0
TCATTCTTTCGATCATCTCGTGGAGATGCC	13	45	0
CAACAGTTCCGATCCACTCGTGGAAAGGGT	13	97	1
GAACCTCTACGATCAACTCGTTTCTGGAAG	13	250	1
       TGAAAACACCTCCCAGATTCAAG	14	3	1
        GTAAACACCTCCCTAAATTTTT	14	92	0
          **********
MAP Score: 12.9871

Motif 3
CCGCGTTGTCTGGAGAACAGAGAACGGAGATTT	1	27	1
ACCATGAGAAAGGAGGTCGGAGA          	1	287	1
    GAGATGAGGAGGGAAAAGAGT        	3	6	1
AACTGTTGCCAGGAGGAGAAAGAA         	4	14	1
ATCTTATGTTAGGAGGGGAGAGTT         	5	1	0
CGTTAACATTTGGAGGGGGGAGACCCCCTCTTT	6	26	1
TCAGAGCTGCTCGAGAAACAGGAAGAATAGTAA	8	70	1
ATAGCATTTTTGGAGGTCTCGGTGGAGCGGTTG	8	115	1
ATAATTCACATCGAGGCATAACAAAAAAGTAAA	10	90	1
TTTACATACAAGGAGGATTGGGAAA        	10	194	1
      TTCTTGAAGGAGAGAGAAAAGAGAGAG	12	4	1
          ******   ****
MAP Score: 11.9971

Motif 4
TTATATGCAGGAAATAATTTAAAATCAAGGTCGGATA	0	37	0
CTAAAAGGATGAAACCATGAGAAAGGAGGTCGGAGA 	1	274	1
GATAGTTTGTGAAAAAATGAGAAACCATAAGAAAAGA	2	13	1
GACTTGAATCGAAAAGATGTGGTAACATCACTGACGT	5	183	1
TCACTGACGTGAAAATTTGAAACATCAGATATCTCAG	5	210	1
AGGAAGAATAGTAACCGTTGAGGAACATAGCATTTTT	8	89	1
TAGGAGTAGGTAAATTTTGAGAAAGGAATTCTGCAAC	8	144	0
TATTTGTGATAAAATTTTTCGAAAGGAAAGGAGGTGT	9	76	1
CGAGATGATCGAAAGAATGATAGATCTTTCGAAAAAG	13	55	1
TAGATCTTTCGAAAAAGTACTACAACAGTTCCGATCC	13	75	1
TCCACTCGTGGAAAGGGTTTTGAATCAGATGCTGAGA	13	109	1
TCAATTATATAAAATCTTGGGGTATCATTTCAAATAT	14	47	0
          ****   **  * * **
MAP Score: 9.32491

Motif 5
TTCTCATCATCACCTCGTTGATCTTCTCGGTTAAAATCT	1	54	0
GATGAAGAAGCAGTTTTCAGAGCTGCTCGAGAAACAGGA	8	54	1
 AACGTGGCTCAACGGAACGAACGACTGGATCTACAGGC	13	9	1
AAAGATCTATCATTCTTTCGATCATCTCGTGGAGATGCC	13	45	0
AAAGTACTACAACAGTTCCGATCCACTCGTGGAAAGGGT	13	88	1
AACTATTTCTCGCACAATCGAGCGACTGGGCTTTCATCA	13	147	1
GAGGTTTCTGAACCTCTACGATCAACTCGTTTCTGGAAG	13	241	1
          **      *** *  ****
MAP Score: 8.60182

Motif 6
CCTTGATTTTAAATTATTTCCTGCATATAAT	0	44	1
TTAATAGATACAAATATTTCCGTTTAAAAGC	2	50	0
TTTGTTAAATCAAGTATATTTCTGGACAAAT	2	96	0
          AAACGATATTCCTCCTTTTCA	2	177	0
TGATTAGAAACAATTATATCCAATTATTGTG	5	128	1
GAATTATGGTAAACTATATCTGAAACATCAA	7	20	1
TCGGGTATCCCAAGGATTTTCATAGGAGTAG	8	172	0
TCACAAAAGTCAACGATATTTGTGATAAAAT	9	60	1
CTCTAAACCCCAATTATTTACTTTTTTGTTA	10	108	0
CTCCCAGATTCAAGTATATCCTAAAAAAATA	14	19	1
GGTATCATTTCAAATATTTTTTTAGGATATA	14	33	0
          *** *******
MAP Score: 8.57601

Motif 7
AGTCAATTAGTTAACATAAATCTCCGCAGA	1	202	1
TCCTTTTAGTATAACATAAAAGTACGTACC	1	253	0
GTTTCTCATTTTTTCACAAACTATCCTT  	2	8	0
TATACTTGATTTAACAAAAATGGACAATGT	2	109	1
TACATTATTCTTTACGCAAATTCTACATTG	2	133	0
ATACATAAAGTTATCATAAATTAATCACAA	9	36	1
TATCATAAATTAATCACAAAAGTCAACGAT	9	47	1
TCGAAAAATTTTATCACAAATATCGTTGAC	9	68	0
CTATATTGACATAAAACAAAAGGTTTGTTA	10	61	1
TCGATGTGAATTATAACAAACCTTTTGTTT	10	74	0
ACATCGAGGCATAACAAAAAAGTAAATAAT	10	97	1
  TGCTAATCTTATCGCAAAAGGAGGGGTC	11	8	1
TGCACCTCCTTAAACAAAAAGAGCCATACC	12	56	0
          **********
MAP Score: 7.61748

Motif 8
CGTTGTCTGGAGAACAGAGAACGGAGATTTTAACCG	1	30	1
TAAAAATAGTGGATAACGGTACGTACCGATGGTAGT	1	134	1
TTTTAGTATAACATAAAAGTACGTACCATTATACGT	1	244	0
ATTTGCGTAAAGAATAATGTACGTACCTAAATGTAT	2	142	1
ATGAGTATCCGGTTACAGGAACGCAGGATGAAGTTT	8	202	1
    AACGTGGCTCAACGGAACGAACGACTGGATCT	13	6	1
TTCAATACGCGGAAAACAGAACGAAGCTTCACATAA	13	204	1
ACTCGTTTCTGGAAGAATAGACGAAGAGATGCTAAG	13	265	1
          ***  *  * *** **
MAP Score: 6.07967

Motif 9
CTTGATTTTAAATTATTTCCTGCATATAATTAAT	0	45	1
GATGGTAGTATATCATATCTGTCAACAAAGAATT	1	161	1
TTCATCCTTTTAGTATAACATAAAAGTACGTACC	1	253	0
GTATCTATTAAGGTATAACATGCAATATTTGTCC	2	70	1
AATTATGGTAAACTATATCTGAAACATCAAACAT	7	21	1
GTTTAACGGTAAACATATCAATCACCCTTGCACT	8	15	0
CCTTTCGAAAAATTTTATCACAAATATCGTTGAC	9	68	0
ATTCACATCGAGGCATAACAAAAAAGTAAATAAT	10	93	1
      TGCTAATCTTATCGCAAAAGGAGGGGTC	11	4	1
GAAAAGAGAGAGCCATATCCCACAAGAGTGGGGT	12	25	1
ATGCTGAGAGAACTATTTCTCGCACAATCGAGCG	13	137	1
TCCCAGATTCAAGTATATCCTAAAAAAATATTTG	14	20	1
CACCTCCCTAAATTTTTTCTATCAATCAATTATA	14	75	0
          ** ******   **
MAP Score: 5.16667

Motif 10
GATCTTCTCGGTTAAAATCTCCGTTCTCTGTTCT	1	40	0
AAGATCAACAGTAAAAATCTCTTCATACAAATCC	1	92	1
AAATCTCTTCATACAAATCCCCCCTGCCTAAAAA	1	106	1
CAATTAGTTAACATAAATCTCCGCAGAAACGGAC	1	205	1
CTTAATAGATACAAATATTTCCGTTTAAAAGCTC	2	48	0
TACAAAGAGGGGGTCTCCCCCCTCCAAATGTTAA	6	28	0
          GTGTGCACCTCCTCTAAATTCCGG	6	75	0
CAACCGCTCCACCGAGACCTCCAAAAATGCTATG	8	114	0
          ATCAACACCTCCTTTCCTTTCGAA	9	93	0
    CAGAAAATAACAACTTCCACATAAGATGAA	10	6	1
GTTTAGAGAAAAAGAGACCCCCCAGTGTGTATCC	10	131	1
          GAAGACCCCTCCTTTTGCGATAAG	11	17	0
GACTGGATCTACAGGCATCTCCACGAGATGATCG	13	32	1
CATCTGATTCAAAACCCTTTCCACGAGTGGATCG	13	106	0
         TGAAAACACCTCCCAGATTCAAGTA	14	1	1
          GTAAACACCTCCCTAAATTTTTTC	14	90	0
          * * * ****** *
MAP Score: 0.583551