AlignACE 3.0 10/20/99
AlignACE2 -i TM/TM_fusions014_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944251380
 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
TAGAAGTGGCAAACCTTATGAGGAGGTCTTA	2	22	1
GATAGATTTTAACCCTGGAGACGTTTTATTA	3	24	1
ATTACAATTAAAACCCGGAGAATGTAATAAA	3	48	0
TTAGAATCAAAAACGAGGTGATGCCTC    	3	110	1
AGCTGAACAGAACCCTGGCGAATTTCCTCAG	8	21	1
ATTTCTTAACAAACCATGTGAAATCACACAA	9	151	1
CACACAAAGAAAACCTGGAAACTAAGAAGTG	9	175	1
TTTACATTATAAACCAGGAAACGGCAAATTC	10	41	0
          ******** **
MAP Score: 12.9437

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
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 4
TGCCGTTATTTTTTGTTAAAATTACAACATATC	0	233	1
TATACCCCCTTTGATGCAGAATTCACTTCGATA	0	262	0
          TTGTGGTAGAATTTAAGTGAAAA	1	0	1
GAATCCCTCCTTTTTTGAGAATTAAAAAGAGAG	1	62	0
ACCCCAAACCTTTAATTGGACTTGTATGGATCA	3	78	0
AACTCTCTTCTTTACTTGAAAGTCTTAGATTTG	6	11	1
      CAGTTTTCTGAGGAAATTCGCCAGGGT	8	32	0
AAAATCGTTCTTTTTGAGAACGTTTTGTGCTAT	9	36	0
AAAGAACGATTTTTCGTAGAATTCTATTTTCCG	9	56	1
AAGAGAACGATTTTGTGAGACTATCGTTCTATA	9	95	0
TTTCACATGGTTTGTTAAGAAATGTTAAGCCGA	9	141	0
CCGGATAAGATTTTAGCAGAAGAAACACAGAAT	10	12	1
          ***  * ******
MAP Score: 6.30592

Motif 5
TTCTTCTCACTTTGAGAATGTCTTGAGCTC	0	145	0
TCCCTCCTTTTTTGAGAATTAAAAAGAGAG	1	62	0
TGGCAAACCTTATGAGGAGGTCTTATTGTG	2	28	1
AATCGTTCTTTTTGAGAACGTTTTGTGCTA	9	37	0
TATCGTTCTATAACAGAACGGAAAATAGAA	9	77	0
AATCGTTCTCTTTCAGAACGAAGAGTCGGC	9	116	1
GAACCGCAAGTTTCAGGAGGGATGGCTG  	10	80	1
          **********
MAP Score: 5.07997

Motif 6
CCGGATAAGATTTTAGCAGAAGAAACACAGA	10	12	1
TCAAAATAAGTTTTTTCACAATAAGACCTCC	2	43	0
TTCACTTAAATTCTACCACAA          	1	0	0
CTGGAACGAATTATAGCACAAAACGTTCTCA	9	24	1
GACTATCGTTCTATAACAGAACGGAAAATAG	9	79	0
GAACTCCTCCCTTTATCACTAATTTTAACAT	7	13	0
CAAAATCGTTCTCTTTCAGAACGAAGAGTCG	9	113	1
TATGTTGTAATTTTAACAAAAAATAACGGCA	0	233	0
GAATCCCTCCTTTTTTGAGAATTAAAAAGAG	1	64	0
AAAAATCGTTCTTTTTGAGAACGTTTTGTGC	9	39	0
ATAAAATCAGTTGTAACTCAAAGAAAATATT	0	95	0
CACATCAGGATTTTACCACTTCTTAGTTTCC	9	191	0
GAAAATAGAATTCTACGAAAAATCGTTCTTT	9	56	0
          ***** *****
MAP Score: 4.73794

Motif 7
TCAGTTGTAACTCAAAGAAAATATTAGAATTT	0	88	0
TAAGTTTTTTCACAATAAGACCTCCTCATAAG	2	36	0
      GGACCGCTAAAAGAACCAAACTGATC	2	72	0
AACCCGGAGAATGTAATAAAACGTCTCCAGGG	3	36	0
ACAAAACGTTCTCAAAAAGAACGATTTTTCGT	9	41	1
ATAACAGAACGGAAAATAGAATTCTACGAAAA	9	66	0
GACTATCGTTCTATAACAGAACGGAAAATAGA	9	78	0
ACTCTTCGTTCTGAAAGAGAACGATTTTGTGA	9	110	0
TGTGAAATCACACAAAGAAAACCTGGAAACTA	9	167	1
          * **** *****
MAP Score: 3.30328

Motif 8
CATACACCTCAAGAGAGCCCTGCTGGGCTCTC	1	35	1
GAGAATTAAAAAGAGAGCCCAGCAGGGCTCTC	1	47	0
ATCGAAGCTGAACAGAACCCTGGCGAATTTCC	8	16	1
AAATCACACAAAGAAAACCTGGAAACTAAGAA	9	171	1
          ****** *** *
MAP Score: 2.64461

Motif 9
TTGTAACTCAAAGAAAATATTAGAATTTGA	0	86	0
GAATGTGTGTAACAAAAAATCCATCGAAAT	0	172	1
AACAAAAAATAACGGCAACCGATCATTACA	0	220	0
TTGTAATTTTAACAAAAAATAACGGCAACC	0	230	0
CATACACCTCAAGAGAGCCCTGCTGGGCTC	1	35	1
GAGAATTAAAAAGAGAGCCCAGCAGGGCTC	1	49	0
CATACCACACGAGAACAAACGAATAGACTG	5	18	1
          AAGAACAACTATGATCCAGT	5	44	0
ATCGAAGCTGAACAGAACCCTGGCGAATTT	8	16	1
TCTATAACAGAACGGAAAATAGAATTCTAC	9	71	0
AACATTTCTTAACAAACCATGTGAAATCAC	9	148	1
AAATCACACAAAGAAAACCTGGAAACTAAG	9	171	1
          AAGAGACACCTCCACATCAG	9	214	0
TAAACCAGGAAACGGCAAATTCTGTGTTTC	10	33	0
          **********
MAP Score: 2.04597

Motif 10
AAAAAGTACAAACACGAGTAATACTCATTTTT	0	12	1
ATGAGTGAATAACAGGAATTATTTCGAATTAT	0	51	1
TGGAAAGAGCATCGGGAATAAAATCAGTTGTA	0	111	0
ACCGATCATTACATGGAGTCAATAACTTATGA	0	201	0
AAATTACAACATATCGAAGTGAATTCTGCATC	0	251	1
AGGGGGTATAATCACGAGAAGAGGA       	0	285	1
TAATTCTCAAAAAAGGAGGGATTCAC      	1	71	1
GGCAAACCTTATGAGGAGGTCTTATTGTGAAA	2	29	1
TTAAAATCTATCCTGGAGGTGATTGG      	3	4	0
TAGATTTTAACCCTGGAGACGTTTTATTACAT	3	26	1
GTTAGAATCAAAAACGAGGTGATGCCTC    	3	109	1
    ACGATCACCTCGAAGTCAAAAGTGAGGA	4	11	0
CACACGAGAACAAACGAATAGACTGGATCATA	5	23	1
AATTAGTGATAAAGGGAGGAGTTCGCA     	7	20	1
GTTCTCTTTCAGAACGAAGAGTCGGCTTAACA	9	120	1
TAAAATCCTGATGTGGAGGTGTCTCTT     	9	207	1
AACCGCAAGTTTCAGGAGGGATGGCTG     	10	81	1
          * ******* **
MAP Score: 1.80711

Motif 11
ACTATAATTCGAAATAATTCCTGTTATTCACTC	0	53	0
AGTTACAACTGATTTTATTCCCGATGCTCTTTC	0	108	1
ACAACATATCGAAGTGAATTCTGCATCAAAGGG	0	256	1
TCCTCTTCTCGTGATTATACCCCCTTTGATGCA	0	277	0
CTCCAGGATAGATTTTAACCCTGGAGACGTTTT	3	18	1
AATCAAAAACGAGGTGATGCCTC          	3	114	1
GATCGAAGCTGAACAGAACCCTGGCGAATTTCC	8	15	1
          **  **** ****
MAP Score: 0.0694623