AlignACE 3.0 10/20/99
AlignACE2 -i TM/TM_fusions014_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944251364
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	TM0033	300	hypothetical protein
#1	TM0034	87	iron-sulfur cluster-binding protein
#2	TM0035	88	hypothetical protein
#3	TM0826	127	hypothetical protein
#4	TM0828	29	sugar kinase, pfkB family
#5	TM0839	54	rod shape-determining protein RodA
#6	TM0840	39	hypothetical protein
#7	TM0842	37	response regulator
#8	TM1263	49	phosphate ABC transporter, permease protein
#9	TM1264	224	phosphate ABC transporter, periplasmic phosphate-binding protein
#10	TM1695	98	conserved hypothetical protein

Motif 1
AGTTACAACTGATTTTATTCCCGATGCTCTT	0	108	1
GATATGTTGTAATTTTAACAAAAAATAACGG	0	235	0
CTCTTCTCGTGATTATACCCCCTTTGATGCA	0	277	0
TTTTCACTTAAATTCTACCACAA        	1	2	0
CTCCAGGATAGATTTTAACCCTGGAGACGTT	3	18	1
GGATCATTACAATTAAAACCCGGAGAATGTA	3	53	0
CCTCGTTTTTGATTCTAACCCCAAACCTTTA	3	97	0
CTTTATCACTAATTTTAACATCGA       	7	3	0
CTCTGGAACGAATTATAGCACAAAACGTTCT	9	22	1
TCCACATCAGGATTTTACCACTTCTTAGTTT	9	193	0
CTCCGGATAAGATTTTAGCAGAAGAAACACA	10	10	1
          ******* ***
MAP Score: 14.4791

Motif 2
GGGCTCTCTTGAGGTGTATGATTTTTCACT	1	25	0
CAAACCTTATGAGGAGGTCTTATTGTGAAA	2	31	1
ATCTATCCTGGAGGTGATTGG         	3	1	0
AATCAAAAACGAGGTGATGCCTC       	3	114	1
TTTTGACTTCGAGGTGATCGT         	4	18	1
GTGATAAAGGGAGGAGTTCGCA        	7	25	1
 CAGTTTTCTGAGGAAATTCGCCAGGGTTC	8	30	0
ATTCGTTCCAGAGGAGGTGCATACT     	9	5	0
TCCTGATGTGGAGGTGTCTCTT        	9	212	1
          **********
MAP Score: 9.47757

Motif 3
TGTGTGTAACAAAAAATCCATCGAAATCATA	0	175	1
CATACACCTCAAGAGAGCCCTGCTGGGCTCT	1	35	1
GAGAATTAAAAAGAGAGCCCAGCAGGGCTCT	1	48	0
  GGACCGCTAAAAGAACCAAACTGATCAAA	2	69	0
ATCGAAGCTGAACAGAACCCTGGCGAATTTC	8	16	1
AACGTTCTCAAAAAGAACGATTTTTCGTAGA	9	45	1
ATCGTTCTATAACAGAACGGAAAATAGAATT	9	75	0
TTCGTTCTGAAAGAGAACGATTTTGTGAGAC	9	107	0
          AAGAGACACCTCCACATCAGG	9	213	0
          ****** ****
MAP Score: 9.12684

Motif 4
TAGCACAAAACGTTCTCAAAAAGAACGATTTTTCG	9	37	1
GCCGACTCTTCGTTCTGAAAGAGAACGATTTTGTG	9	111	0
GTGAGACTATCGTTCTATAACAGAACGGAAAATAG	9	79	0
  GGTGGGACCATACCACACGAGAACAAACGAATA	5	8	1
TGCTATAATTCGTTCCAGAGGAGGTGCATACT   	9	7	0
         CCAATCACCTCCAGGATAGATTTTAA	3	1	1
ATAGAAGTGGCAAACCTTATGAGGAGGTCTTATTG	2	21	1
TAACGGCAACCGATCATTACATGGAGTCAATAACT	0	206	0
AAATCTAAGACTTTCAAGTAAAGAAGAGAGTTC  	6	8	0
GAGCTCAAGACATTCTCAAAGTGAGAAGAATGTGT	0	145	1
ATTCATTTTACATTATAAACCAGGAAACGGCAAAT	10	43	0
AGTGAAAAATCATACACCTCAAGAGAGCCCTGCTG	1	25	1
  GGAGGGATCGAAGCTGAACAGAACCCTGGCGAA	8	8	1
          *****   *  ****
MAP Score: 8.22788

Motif 5
TTATGATTTCGATGGATTTTTTGTTACACA	0	177	0
      TTGTGGTAGAATTTAAGTGAAAAA	1	4	1
TCACCTCCAGGATAGATTTTAACCCTGGAG	3	14	1
ACCTCCTCTGGAACGAATTATAGCACAAAA	9	17	1
TTCTCAAAAAGAACGATTTTTCGTAGAATT	9	49	1
TTCTGAAAGAGAACGATTTTGTGAGACTAT	9	104	0
          **********
MAP Score: 3.10496

Motif 6
ATATTAGAATTTGAACTATAATTCGAAATAATT	0	67	0
TGCCGTTATTTTTTGTTAAAATTACAACATATC	0	233	1
          TTGTGGTAGAATTTAAGTGAAAA	1	0	1
TGAGAACGTTTTGTGCTATAATTCGTTCCAGAG	9	22	0
AAAGAACGATTTTTCGTAGAATTCTATTTTCCG	9	56	1
          ****  ** ****
MAP Score: 2.29931

Motif 7
AAGGGGGTATAATCACGAGAAGAGGA       	0	284	1
    AAAGTGGTTTAATAGAAGTGGCAAACCTT	2	6	1
AAATAAGTTTTTTCACAATAAGACCTCCTCATA	2	38	0
GAACCAAACTGATCAAAATAAGTTTTTTCACAA	2	53	0
         GGACCGCTAAAAGAACCAAACTGA	2	74	0
        CCAATCACCTCCAGGATAGATTTTA	3	2	1
TAATTGTAATGATCCATACAAGTCCAATTAAAG	3	69	1
AGCACAAAACGTTCTCAAAAAGAACGATTTTTC	9	38	1
TGAGACTATCGTTCTATAACAGAACGGAAAATA	9	80	0
TCACAAAATCGTTCTCTTTCAGAACGAAGAGTC	9	110	1
AACCATGTGAAATCACACAAAGAAAACCTGGAA	9	162	1
          **** * * ****
MAP Score: 1.82793