AlignACE 3.0 10/20/99
AlignACE2 -i TM/TM_fusions007_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944251161
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	TM0300	237	oligopeptide ABC transporter, periplasmic oligopeptide-binding protein, putative
#1	TM0301	64	oligopeptide ABC transporter, permease protein
#2	TM0411	161	transcriptional regulator, XylR-related
#3	TM0413	46	creatinine amidohydrolase, putative
#4	TM0417	93	conserved hypothetical protein
#5	TM0418	59	sugar ABC transporter, periplasmic sugar-binding protein, putative
#6	TM0419	38	sugar ABC transporter, permease protein
#7	TM0593	38	amino acid ABC transporter, periplasmic amino acid-binding protein
#8	TM0594	54	conserved hypothetical protein
#9	TM0595	94	sugar ABC transporter, periplasmic sugar-binding protein, putative
#10	TM1153	25	oligopeptide ABC transporter, permease protein
#11	TM1155	82	glucose-6-phosphate 1-dehydrogenase
#12	TM1196	21	oligopeptide ABC transporter, ATP-binding protein
#13	TM1198	69	oligopeptide ABC transporter, permease protein
#14	TM1199	154	oligopeptide ABC transporter, periplasmic oligopeptide-binding protein
#15	TM1403	135	antibiotic ABC transporter, ATP-binding protein, putative

Motif 1
CTTTGTGTTAAAATTCCTTAAAAGGGGGG          	11	0	0
ATTCAAGGGGAAAACATCGAGAAGGGAGGGATTCCT   	9	68	1
GAAGTGATTAAGAGAAGAGTACAGGGAGGCAACAAC   	0	7	0
ACTAAAAACAAAACTTTTTTTTAAGGGGGTGTTTTT   	0	211	1
GTCATTCCTGAAAAATCCAGAGAAGGAGGTAGAAACT  	4	66	1
GGTAAATGGCAGATTCCTCCTGAAGGAGGACAC      	3	23	1
ATCACCTCACAAAAGCGAAGTGAGGGGGAACCCCC    	6	6	0
TCATTTACTATGACACCAGTAGAGGGGGGATTTTC    	14	129	1
GATTGTGAAGAAACTCAAGGAAAGAGAGGTCTGAGT   	9	7	0
TAATGTGATAAAATAAATAAAAATGGGGGGTGAGATT  	5	32	1
ATTTCGTGGTAAAAATCCAGAAAGGCAGGTGAGATC   	11	56	1
GGAGTTTTAAACAAAAGAAAAGCGGGAGGAACAGCCTCC	8	13	0
AACTATAAGAAAAATTAGAAAAAAAGAGGAAACAAAAGT	2	73	0
TTTGTTCTTTTCAAGTTAAGGGAGGGGGAACCCCTCCCC	13	23	0
CTGGGATTATAAAATAATATGCATGGATGTGTCAATCAG	15	59	0
          ***         *******
MAP Score: 26.8436

Motif 2
       GTTGTTGCCTCCCTGTACTCTTC	0	3	1
CTATTATAACGTTTCCCACGAACTAAGCAA	0	51	1
          CATTCCCCCGCCCCAGACGG	1	0	1
GGAAACAAAAGTTTCCTCGGGTTAAAGGAG	2	55	0
GGAAACTTTTGTTTCCTCTTTTTTTCTAAT	2	69	1
GTAAATGGCAGATTCCTCCTGAAGGAGGAC	3	24	1
          GTGTCCTCCTTCAGGAGGAA	3	36	0
       GGGGGTTCCCCCTCACTTCGCTT	6	3	1
 GCGGGAGGCTGTTCCTCCCGCTTTTCTTT	8	9	1
CCTTCTCGATGTTTTCCCCTTGAATTATAC	9	63	0
TTCGGGGAGGGGTTCCCCCTCCCTTAACTT	13	20	1
  GTTCGATCTTTTCCTCCTTTGTTCTTTT	13	51	0
          GTTTTCCCCTCCAAATTAAT	15	0	1
          **********
MAP Score: 20.443

Motif 3
   GTTGTTGCCTCCCTGTACTCTTCTCTTAATCA	0	7	1
AAATAATCGTCTTTTTTGAGATTTTGAATGAAAAT	0	146	1
ACGGGGCGGGCTCTTCTTTGAGATTAGACATAAGG	1	26	1
TTTGTTTCCTCTTTTTTTCTAATTTTTCTTATAGT	2	76	1
      TTTTCCATTCCTTTCGTTTGTTATCGTTA	2	142	0
TTTCTACCTCCTTCTCTGGATTTTTCAGGAATGAC	4	66	0
TCTCACCCCCCATTTTTATTTATTTTATCACATTA	5	32	0
  GGGGGTTCCCCCTCACTTCGCTTTTGTGAGGTG	6	8	1
     ATTATCACCTCCGATTTATTATAACACAAT	7	18	0
CTGTTCCTCCCGCTTTTCTTTTGTTTAAAACTCCT	8	18	1
ACTCAGACCTCTCTTTCCTTGAGTTTCTTCACAAT	9	10	1
AGGAATCCCTCCCTTCTCGATGTTTTCCCCTTGAA	9	69	0
       CCCCCCTTTTAAGGAATTTTAACACAAA	11	3	1
ATCTCACCTGCCTTTCTGGATTTTTACCACGAAAT	11	56	0
GGAGGGGGAACCCCTCCCCGAAAGTTCCATGA   	13	7	0
GGAGGGGTTCCCCCTCCCTTAACTTGAAAAGAACA	13	25	1
CGATCTTTTCCTCCTTTGTTCTTTTCAAGTTAAGG	13	41	0
          CTTTTTCTGACAATTACAGGTGATT	14	0	1
TGTGGTTAATCTTTTCTTTTTCTTTTTTTCAACCT	14	58	1
TTTTTTTCAACCTTTTCTTATTCTTGATTTTACGT	14	80	1
  GAAAATCCCCCCTCTACTGGTGTCATAGTAAAT	14	131	0
     GTTTTCCCCTCCAAATTAATAGATCCTTTT	15	5	1
ATTAATAGATCCTTTTCTCTGTCTTCAAGTTCAAA	15	24	1
          *******  *   **
MAP Score: 20.075

Motif 4
CCTATGCGGTATAATTCAAGGGGAAAACATCGAG	9	55	1
ATATTATTTTATAATCCCAGAGGATATATCTATC	15	78	1
TTGATTGTGAAGAAACTCAAGGAAAGAGAGGTCT	9	14	0
CCTTAACTTGAAAAGAACAAAGGAGGAAAAGATC	13	41	1
GTAAAAATCCAGAAAGGCAGGTGAGATC      	11	64	1
 CTTTTTCTGACAATTACAGGTGATTATCTGGAA	14	9	1
AAGAAAAATTAGAAAAAAAGAGGAAACAAAAGTT	2	72	0
GTCATTCCTGAAAAATCCAGAGAAGGAGGTAGAA	4	66	1
GTTAACGATAACAAACGAAAGGAATGGAAAA   	2	140	1
TCTTTTCAAGTTAAGGGAGGGGGAACCCCTCCCC	13	23	0
TAAACAAAAGAAAAGCGGGAGGAACAGCCTCCCG	8	11	0
TGTGTTATAATAAATCGGAGGTGATAAT      	7	20	1
CTCACAAAAGCGAAGTGAGGGGGAACCCCC    	6	6	0
AAAATAAATAAAAATGGGGGGTGAGATT      	5	41	1
TTAAGGAATTTTAACACAAAGGAAATTAGTTATT	11	18	1
AAAGGTTGAAAAAAAGAAAAAGAAAAGATTAACC	14	61	0
CAAGGGGAAAACATCGAGAAGGGAGGGATTCCT 	9	71	1
CTCCTTATGTCTAATCTCAAAGAAGAGCCCGCCC	1	29	0
AAGGATCTATTAATTTGGAGGGGAAAAC      	15	4	0
ATATTCTCCTTTAACCCGAGGAAACTTTTGTTTC	2	50	1
ACGATTATTTCAAATTAAAAAGAAATATGATAAC	0	122	0
ATTTTCATTCAAAATCTCAAAAAAGACGATTATT	0	147	0
AAAGAAAAGATTAACCACAAATAAATCTTTCTAT	14	43	0
ACGTTCACGTAAAATCAAGAATAAGAAAAGGTTG	14	87	0
          * **   *******
MAP Score: 19.8702

Motif 5
TTTCAAGTTAAGGGAGGGGGAACCCCTCCCCG	13	22	0
     CAATAACGGAGGTGTTATTGC      	12	5	1
TTTTGACTCTATGGAGGTGTCAGAG       	15	120	1
ACAAAAGCGAAGTGAGGGGGAACCCCC     	6	5	0
AAATCCAGAGAAGGAGGTAGAAACT       	4	78	1
ATCTATTAATTTGGAGGGGAAAAC        	15	2	0
CGCCCCGTCTGGGGCGGGGGAATG        	1	2	0
TTATAATAAATCGGAGGTGATAAT        	7	24	1
AATAAATAAAAATGGGGGGTGAGATT      	5	43	1
ACTTTTTTTTAAGGGGGTGTTTTT        	0	223	1
TATGACACCAGTAGAGGGGGGATTTTC     	14	137	1
AACATCGAGAAGGGAGGGATTCCT        	9	80	1
AAATCCAGAAAGGCAGGTGAGATC        	11	68	1
AATAATATGCATGGATGTGTCAATCAGTTTGA	15	54	0
GATTAGACATAAGGAGTGAGAAAAATT     	1	47	1
AGAAGAGTACAGGGAGGCAACAAC        	0	2	0
CCCGCCCCAGACGGGGCGGGCTCTTCTTTGAG	1	16	1
AAACAAAAGAAAAGCGGGAGGAACAGCCTCCC	8	12	0
          * ******** *
MAP Score: 18.6059

Motif 6
   GTTGTTGCCTCCCTGTACTCTTCTCTTAATCA	0	7	1
TGATAACTTATCGTTCCATATTTTTTCATATCACA	0	94	0
      TTTTCCATTCCTTTCGTTTGTTATCGTTA	2	142	0
      AATCTCACCCCCCATTTTTATTTATTTTA	5	40	0
  GGGGGTTCCCCCTCACTTCGCTTTTGTGAGGTG	6	8	1
  GCGGGAGGCTGTTCCTCCCGCTTTTCTTTTGTT	8	8	1
CTCAGACCTCTCTTTCCTTGAGTTTCTTCACAATC	9	11	1
GGAGGGGTTCCCCCTCCCTTAACTTGAAAAGAACA	13	25	1
TTCGATCTTTTCCTCCTTTGTTCTTTTCAAGTTAA	13	43	0
TTGTGGTTAATCTTTTCTTTTTCTTTTTTTCAACC	14	57	1
TTTTTTTCAACCTTTTCTTATTCTTGATTTTACGT	14	80	1
ATTAATAGATCCTTTTCTCTGTCTTCAAGTTCAAA	15	24	1
          ** **** *   ***
MAP Score: 9.91125

Motif 7
ATTATAACGTTTCCCACGAACTAAGCAAAC	0	53	1
        CATTCCCCCGCCCCAGACGGGG	1	2	1
     AATTTTTCTCACTCCTTATGTCTAA	1	49	0
CATAAAAATATTCTCCTTTAACCCGAGGAA	2	43	1
     GGGGGTTCCCCCTCACTTCGCTTTT	6	5	1
GGGAGGCTGTTCCTCCCGCTTTTCTTTTGT	8	12	1
  ACTCAGACCTCTCTTTCCTTGAGTTTCT	9	8	1
    AGGAATCCCTCCCTTCTCGATGTTTT	9	78	0
         CCCCCCTTTTAAGGAATTTTA	11	1	1
AATTAGTTATTCCTCATTTCGTGGTAAAAA	11	41	1
CGGGGAGGGGTTCCCCCTCCCTTAACTTGA	13	22	1
     GAAAATCCCCCCTCTACTGGTGTCA	14	139	0
        GTTTTCCCCTCCAAATTAATAG	15	2	1
          **********
MAP Score: 6.92369

Motif 8
TAACTTATCGTTCCATATTTTTTCATATCACA	0	94	0
AGTTATCATATTTCTTTTTAATTTGAAATAAT	0	121	1
AAATAATCGTCTTTTTTGAGATTTTGAATGAA	0	146	1
ATGAAAATGTTTTCATAGTAATCTTATGAGTA	0	173	1
GGGGCGGGCTCTTCTTTGAGATTAGACATAAG	1	28	1
GAAACAAAAGTTTCCTCGGGTTAAAGGAGAAT	2	52	0
AAACTTTTGTTTCCTCTTTTTTTCTAATTTTT	2	71	1
TTTTCTAATTTTTCTTATAGTTGACAAATTGA	2	90	1
TTCCATTCCTTTCGTTTGTTATCGTTAACTAA	2	137	0
TTTCTACCTCCTTCTCTGGATTTTTCAGGAAT	4	69	0
CACCCCCCATTTTTATTTATTTTATCACATTA	5	32	0
TCCTCCCGCTTTTCTTTTGTTTAAAACTCCTT	8	22	1
CAGACCTCTCTTTCCTTGAGTTTCTTCACAAT	9	13	1
CTCGATGTTTTCCCCTTGAATTATACCGCATA	9	57	0
AATAACTAATTTCCTTTGTGTTAAAATTCCTT	11	20	0
GGGGTTCCCCCTCCCTTAACTTGAAAAGAACA	13	28	1
TGGTTAATCTTTTCTTTTTCTTTTTTTCAACC	14	60	1
TTTTCAACCTTTTCTTATTCTTGATTTTACGT	14	83	1
AATAGATCCTTTTCTCTGTCTTCAAGTTCAAA	15	27	1
CGATAGATATATCCTCTGGGATTATAAAATAA	15	81	0
          ********  **
MAP Score: 6.05268

Motif 9
AGAGCCCGCCCCGTCTGGGGCGGGGGAATG      	1	4	0
TTGAGATTAGACATAAGGAGTGAGAAAAATT     	1	43	1
TAAAATAAATAAAAATGGGGGGTGAGATT       	5	40	1
ATCACCTCACAAAAGCGAAGTGAGGGGGAACCCCC 	6	9	0
AGTTTTAAACAAAAGAAAAGCGGGAGGAACAGCCTC	8	14	0
AAGGGGAAAACATCGAGAAGGGAGGGATTCCT    	9	72	1
   TCATGGAACTTTCGGGGAGGGGTTCCCCCTCCC	13	7	1
TGTTCTTTTCAAGTTAAGGGAGGGGGAACCCCTCCC	13	24	0
ACTTGAAAAGAACAAAGGAGGAAAAGATCGAAC   	13	46	1
ATTTACTATGACACCAGTAGAGGGGGGATTTTC   	14	131	1
          **    **** * ***
MAP Score: 4.62042