AlignACE 3.0 10/20/99
AlignACE2 -i MJ/MJ_operons037_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944241474
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	MJ0101	93	signal recognition particle, subunit SRP54
#1	MJ0102	300	Phenylacrylic acid decarboxylase
#2	MJ0210	86	succinyl-CoA synthetase, beta subunit
#3	MJ0291	137	signal recognition particle, receptor
#4	MJ0547	165	cell division inhibitor minD
#5	MJ0548	111	conserved hypothetical protein
#6	MJ1246	300	succinyl-CoA synthetase, alpha subunit (sucD)
#7	MJ1642	300	conserved hypothetical protein

Motif 1
TGTTTTCAGAAATTTTAGAATTATACT          	0	0	0
GAAAACAATAAAATTTTTAATTGAAGAAATATAATAT	0	30	1
TAATTGAAGAAATATAATATTTTATTAAGTGTTGTAT	0	47	1
TTAGGTTGTTATATTTATTTTTTTAGATTTATGGATT	1	211	1
AAAAACTGTTAAGTTAAGATTTAAAAAATAAATACTA	1	261	0
          AAATTCACCATTAAAAACTGTTAAGTT	1	283	0
        TAAACCTATAAATTTATCACCAAATTTTT	2	2	1
GCAAAATTTTAAAATTATCATATAAAAAATTTGGTGA	2	26	0
GATAATTTTAAAATTTTGCATTAAAAAGAAATTTATC	2	44	1
CATTAAAAAGAAATTTATCATTTAAGGTGATAGG   	2	62	1
TATTGTTCGTAATTTTATTATATTAAAATTACTTTAA	3	58	1
CCGATATATAAATATTAAATTTGAATAAAGCATTGTT	3	93	0
ACTTAACTATAACTTTAGTGTTGTAAATAGGTAATAT	4	126	1
GTAAATAGGTAATATAAAGATTTTAGA          	4	148	1
CAAACTAACAAATATTACTATTTAATAACTAATATAT	5	29	1
TATTATTATTATCGTTAATCTTATATATTAGTTATTA	5	51	0
ATAAATCAGAAAGATTTAAGTTATTTAAAAAATGGTG	6	13	1
GAACTTTCACAATTTATATATTTATAAGGCACTTTGA	6	218	0
GGGATATATAAATTTTACGGTTTAATAC         	6	282	1
CGGCGAGACAAACATTAGTTTTATATACTTGAAATTA	7	111	1
          **  ***   ** ** *
MAP Score: 22.4726

Motif 2
         TCTCTCACCCCTTAGACTAATAATATT	5	94	0
CTGCCGTGGTCCAGCGCCCTATAGGCAACTGGAGTC	6	88	1
TATTGGAATGACGATACCCTTTAGGCATCAAAGTGC	6	191	1
GTTTGTCTCGCCGCCTCCCTATCTTCGAGCGTAGCA	7	88	0
ACCAACCTGCCCTGTGACCTATCGGCGACGATAAGT	7	191	1
CACGGAACACCCTGCTACTTATCGTCGCCGATAGGT	7	207	0
CGTGTTGGAACCTCCACCCTTTAGGTGGAGAGAAGA	7	239	1
          **  * **** * * *
MAP Score: 4.62618

Motif 3
       AGTATAATTCTAAAATTTCTGAAAACA	0	3	1
AAAATTTCTGAAAACAATAAAATTTTTAATTGAA	0	21	1
TTTTAATTGAAGAAATATAATATTTTATTAAGTG	0	44	1
TCGGGCTACAAAATCTGAAAGATTTTGTTTAACT	1	123	1
AACCTAAAATAAAATAATAAAATGGTGCCGAGGG	1	184	0
CATAAATCTAAAAAAATAAATATAACAACCTAAA	1	210	0
AAGATTTAAAAAATAAATACTATTTAAAAATAGT	1	249	0
         TAAACCTATAAATTTATCACCAAAT	2	1	1
TTTTTATATGATAATTTTAAAATTTTGCATTAAA	2	35	1
AAGTAATTTTAATATAATAAAATTACGAACAATA	3	58	0
GCCGATATATAAATATTAAATTTGAATAAAGCAT	3	97	0
TTAGTGTTGTAAATAGGTAATATAAAGATTTTAG	4	140	1
TATTAGTTATTAAATAGTAATATTTGTTAGTTTG	5	29	0
ATTTAATAACTAATATATAAGATTAACGATAATA	5	48	1
AAGATTAACGATAATAATAATACTAACTAATATT	5	66	1
CTCACCCCTTAGACTAATAATATTAGTTAGTATT	5	84	0
     AAAATAAATCAGAAAGATTTAAGTTATTT	6	5	1
CTTCACAGGAATAAATCTACTATTGGAATGACGA	6	171	1
AGTGCCTTATAAATATATAAATTGTGAAAGTTCT	6	222	1
     GTATTAAACCGTAAAATTTATATATCCCC	6	281	0
          ***  * *** ***
MAP Score: 4.47382

Motif 4
GGCATTGCCGAGCGTAGCGAGGCAATGCATCC	1	15	1
ATAGCTGGAAAGCGTAGCTTTCCATTTCATCA	1	52	0
TTTATATATCGGCATAGGAGGGATTACAA   	3	118	1
AAAAAATGGTGGGGGTGCTGGGATTTGAACCC	6	39	1
GCGGGGGTGTGGTGTAGCCAGGTCTATCATCG	6	126	0
CCTATCTTCGAGCGTAGCAAGGAGAGTTAATG	7	75	0
GCTACGCTCGAAGATAGGGAGGCGGCGAGACA	7	89	1
TGCTTTATTGAGGGTAGCTCTGACTCTGCCCG	7	154	1
GATAGGTCACAGGGCAGGTTGGTGTCATCGGG	7	182	0
          ********  **
MAP Score: 4.35474

Motif 5
       TAAGAGGCATTGCCGAGCGTAGC	1	3	1
CGAGCGTAGCGAGGCAATGCATCCTATTTT	1	23	1
GCAAACAGAACAGAGATTACATATAAATAT	3	31	1
ATCGGCATAGGAGGGATTACAA        	3	125	1
AACCCAGGTCCAGGGATTTCTCCTGCCGTG	6	66	1
AATGAAATTCGAAGGATTTCATCTGAATCC	7	49	0
          **********
MAP Score: 2.32591