AlignACE 3.0 10/20/99
AlignACE2 -i TM/TM_fusions009_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944251256
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	TM0278	300	sugar ABC transporter, permease protein
#1	TM1222	55	oligopeptide ABC transporter, permease protein
#2	TM1223	131	oligopeptide ABC transporter, periplasmic oligopeptide-binding protein
#3	TM1225	52	conserved hypothetical protein
#4	TM1227	158	endo-1,4-beta-mannosidase
#5	TM1234	42	sugar ABC transporter, permease protein
#6	TM1235	22	conserved hypothetical protein
#7	TM1374	47	phosphoglycerate mutase
#8	TM1375	166	spermidine/putrescine ABC transporter, periplasmic spermidine/putrescine-binding protein

Motif 1
TTTTTTAAAACCCCGCCCCGAGGGGCGGGG	1	18	0
  AATGATGACCCCGCCCCTCGGGGCGGGG	1	8	1
GGGTGGGGATCCCCACCCCGGGTA      	5	4	0
GGGTGGGGATCCCCACCCCTTTTCCGGGGG	5	16	1
    ATTTTCCCCCACCCTCTTGGGTGGGG	3	6	1
ATCCGAGAGTTCCCGCCCTCGAGGTAACGT	0	87	1
TGGGTTCGAATCCCACCGCCGCCTCCAGAG	8	97	1
AGAGGGGGCGCTCTGCCCCCTTTTGCC   	0	283	1
TTTTGCAGACCCCCGCCTTTGACCGCTTGG	8	57	0
GATCAGCGGCCCTCACCTCGGGATCCTGGA	0	60	0
AGCGCCCCCTCTTCACCTCCTTATTTTCCA	0	265	0
TCTGGAGAACTCCCGCTCTCCATGGAAACG	0	200	1
       GACTCCTACCTCCTTCTTTTTTT	1	42	0
GACCGCTTGGCTACGCCGCCATCCACATAG	8	37	0
AGATTTAGAGCCCCACCCAAGAGGGTGGGG	3	16	0
TGAGATTCGCCGTCGCTCCTGCCAGAATCT	0	24	1
          **********
MAP Score: 30.886

Motif 2
AATCTCAACACTCCAGGATCCCGAGGTGAGGG	0	49	1
GTCTTGGTTCCTCTGGAATCCTTGGCCTGTGG	0	130	0
GGAACCAAGACTCGAAGACATCACCGTTGAGA	0	151	1
TTGAGACCTTCTCCAAGATCCTCTCTGGAGAA	0	177	1
AAGATCCTCTCTGGAGAACTCCCGCTCTCCAT	0	191	1
CATGGAAACGCTGAACGATCTCGCAAAGAAAT	0	220	1
CTCCTTCTTTTTTTAAAACCCCGCCCCGAGGG	1	24	0
AGAAATAAATCTTGATAATCCCGGGAGACTGG	2	32	1
ACAAATAAAACTCGAAAATCACGAAAAATAGG	4	47	1
TACATTTTTTCTCGATGACCCTGATAAATAAG	4	105	1
AGGCGGGGGTCTGCAAAATCCCTATTCGTGGG	8	69	1
          *** * ******
MAP Score: 11.2785

Motif 3
TCTCAACACTCCAGGATCCCGAGGTGAGGGCCGC	0	51	1
AGGTGAGGGCCGCTGATCCGAGAGTTCCCGCCCT	0	72	1
TCCGAGAGTTCCCGCCCTCGAGGTAACGTACGTT	0	88	1
ACGTACGTTTCTCAGACCCACAGGCCAAGGATTC	0	113	1
CTGGAGAACTCCCGCTCTCCATGGAAACGCTGAA	0	201	1
  AATGATGACCCCGCCCCTCGGGGCGGGGTTTT	1	8	1
ACATTCCAAATCCAGTCTCCCGGGATTATCAAGA	2	41	0
AGCGATCTCATACTCTTTTAAGGGGGTGTTCTT 	2	108	1
    ATTTTCCCCCACCCTCTTGGGTGGGGCTCT	3	6	1
GGGGTGGGGATCCCCACCCCGGGTA         	5	1	0
GGGATCCCCACCCCTTTTCCGGGGGTGCACC   	5	21	1
AATATAATACCACATATGCAAGGGTGT       	8	3	0
GTCTGCAAAATCCCTATTCGTGGGTTCGAATCCC	8	77	1
CGAATCCCACCGCCGCCTCCAGAGAGCCAGGCTA	8	103	1
          ***   **** ***
MAP Score: 9.7398

Motif 4
ATCTCAACACTCCAGGATCCCGAGGTGAGGGCCGCTGATCC	0	50	1
AACGTACGTTTCTCAGACCCACAGGCCAAGGATTCCAGAGG	0	112	1
         AATGATGACCCCGCCCCTCGGGGCGGGGTTTT	1	1	1
GAAATAAATCTTGATAATCCCGGGAGACTGGATTTGGAATG	2	33	1
GAGATAGCGATCTCATACTCTTTTAAGGGGGTGTTCTT   	2	103	1
      ATTTTCCCCCACCCTCTTGGGTGGGGCTCTAAATC	3	4	1
CAAATAAAACTCGAAAATCACGAAAAATAGGACTTGACTTT	4	48	1
ACATTTTTTCTCGATGACCCTGATAAATAAGTAAAGTTTAC	4	106	1
CGGGGTGGGGATCCCCACCCCTTTTCCGGGGGTGCACC   	5	14	1
AATAGGGATTTTGCAGACCCCCGCCTTTGACCGCTTGGCTA	8	54	0
          ** *  ****        ***
MAP Score: 6.53202

Motif 5
CCTGAGATTCGCCGTCGCTCCTGCCAGAATCTC	0	22	1
CTGCCAGAATCTCAACACTCCAGGATCCCGAGG	0	42	1
GGATCAGCGGCCCTCACCTCGGGATCCTGGAGT	0	58	0
ATCCGAGAGTTCCCGCCCTCGAGGTAACGTACG	0	87	1
TAACGTACGTTTCTCAGACCCACAGGCCAAGGA	0	111	1
GTCTTGGTTCCTCTGGAATCCTTGGCCTGTGGG	0	129	0
TTGAGACCTTCTCCAAGATCCTCTCTGGAGAAC	0	177	1
TCTGGAGAACTCCCGCTCTCCATGGAAACGCTG	0	200	1
GAGCGCCCCCTCTTCACCTCCTTATTTTCCAAG	0	263	0
GAAGAGGGGGCGCTCTGCCCCCTTTTGCC    	0	281	1
    AATGATGACCCCGCCCCTCGGGGCGGGGT	1	6	1
TCCTTCTTTTTTTAAAACCCCGCCCCGAGGGGC	1	22	0
        GACTCCTACCTCCTTCTTTTTTTAA	1	40	0
       ATTTTCCCCCACCCTCTTGGGTGGGG	3	3	1
CCTCCTTAGATTTAGAGCCCCACCCAAGAGGGT	3	20	0
       CCATGCTTCCCTCCTTAGATTTAGAG	3	36	0
TACATTTTTTCTCGATGACCCTGATAAATAAGT	4	105	1
GGGGTGGGGATCCCCACCCCGGGTA        	5	2	0
          GGTGCACCCCCGGAAAAGGGGTG	5	29	0
CGCTTGGCTACGCCGCCATCCACATAGAATATA	8	31	0
ATAGGGATTTTGCAGACCCCCGCCTTTGACCGC	8	61	0
TCGAATCCCACCGCCGCCTCCAGAGAGCCAGGC	8	102	1
          ***  ****** *
MAP Score: 6.3932

Motif 6
CTGGAGTGTTGAGATTCTGGCAGGAGCGACGG	0	33	0
TCGGATCAGCGGCCCTCACCTCGGGATCCTGG	0	61	0
CTCGAGGGCGGGAACTCTCGGATCAGCGGCCC	0	78	0
GGTTCCTCTGGAATCCTTGGCCTGTGGGTCTG	0	125	0
CATCACCGTTGAGACCTTCTCCAAGATCCTCT	0	169	1
ATCCTCTCTGGAGAACTCCCGCTCTCCATGGA	0	194	1
AGGGGGCAGAGCGCCCCCTCTTCACCTCCTTA	0	272	0
       AATGATGACCCCGCCCCTCGGGGCG	1	3	1
TCTTTTTTTAAAACCCCGCCCCGAGGGGCGGG	1	19	0
          GACTCCTACCTCCTTCTTTTTT	1	43	0
        AAGAACACCCCCTTAAAAGAGTAT	2	117	0
CTTAGATTTAGAGCCCCACCCAAGAGGGTGGG	3	17	0
      CCATGCTTCCCTCCTTAGATTTAGAG	3	36	0
       ACCGATACCTCCCGTTAATTAGTAA	4	143	0
AAGGGGTGGGGATCCCCACCCCGGGTA     	5	5	0
         GGTGCACCCCCGGAAAAGGGGTG	5	29	0
GGATTTTGCAGACCCCCGCCTTTGACCGCTTG	8	58	0
TCGTGGGTTCGAATCCCACCGCCGCCTCCAGA	8	94	1
          ** **** ****
MAP Score: 3.58356

Motif 7
GATCAGCGGCCCTCACCTCGGGATCCTGGAGTGTTGAG	0	52	0
TCCGAGAGTTCCCGCCCTCGAGGTAACGTACGTTTCTC	0	88	1
GTACGTTTCTCAGACCCACAGGCCAAGGATTCCAGAGG	0	115	1
TGGAGAACTCCCGCTCTCCATGGAAACGCTGAACGATC	0	202	1
TTTTTTAAAACCCCGCCCCGAGGGGCGGGGTCATCATT	1	10	0
     ATTTTCCCCCACCCTCTTGGGTGGGGCTCTAAA	3	5	1
GGGTGGGGATCCCCACCCCTTTTCCGGGGGTGCACC  	5	16	1
AGGGATTTTGCAGACCCCCGCCTTTGACCGCTTGGCTA	8	54	0
CGAATCCCACCGCCGCCTCCAGAGAGCCAGGCTACACG	8	103	1
          **** ****  *     *
MAP Score: 3.5532