AlignACE 3.0 10/20/99
AlignACE2 -i MT/MT_fusions019_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944250532
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	Rv0269c	35	hypothetical protein Rv0269c
#1	ligB	156	ligB
#2	Rv3730c_ligC	37	Rv3730c: hypothetical protein Rv3730c, ligC: ligC

Motif 1
  GGTAATTTGCGACCCGCCTCACATAGGGTGAGGTC       	0	3	0
     CAAGGCCTCCTAGCGGCACTACCGGACCCACATAGCCCC	1	5	1
TTTACCAATACCGCCTGGGGGCTATGTGGGTCCGGTAGTGCCGC	1	22	0
TATACTAATTGTCTGTCGCGGCCGCGAGACACGGCTTGCTCGGG	1	69	1
TGTCGCGGCCGCGAGACACGGCTTGCTCGGGCACGCCAGCCTTG	1	82	1
ACACGGCTTGCTCGGGCACGCCAGCCTTGCCCTCGCCAACGATG	1	97	1
GCACGCCAGCCTTGCCCTCGCCAACGATGTCGGCGAGACATGCC	1	112	1
GTTCAGCTTGGCATGTCTCGCCGACATCGTTGGCGAGGGCAAGG	1	121	0
 GTGCTCATTCTTGCGTGCGGCATGCTGGAATTCCGAT      	2	9	1
          **  *   ****      *  * *
MAP Score: 17.3281

Motif 2
TAATTTGCGACCCGCCTCACATAGGGTGAGGTC   	0	7	0
          CAAGGCCTCCTAGCGGCACTACCGGA	1	0	1
AGCGGCACTACCGGACCCACATAGCCCCCAGGCGGT	1	21	1
TACTCTTTACCAATACCGCCTGGGGGCTATGTGGGT	1	35	0
ATACTAATTGTCTGTCGCGGCCGCGAGACACGGCTT	1	70	1
GGCCGCGAGACACGGCTTGCTCGGGCACGCCAGCCT	1	88	1
CTTGCTCGGGCACGCCAGCCTTGCCCTCGCCAACGA	1	103	1
GGCATGTCTCGCCGACATCGTTGGCGAGGGCAAGGC	1	120	0
      GTGCTCATTCTTGCGTGCGGCATGCTGGAA	2	4	1
          ** * * * *  ****
MAP Score: 9.58472

Motif 3
     GACCTCACCCTATGTGAGGCGGGTCGCAAATTAC	0	5	1
  CAAGGCCTCCTAGCGGCACTACCGGACCCACATAGCC	1	8	1
AAAGAGTATACTAATTGTCTGTCGCGGCCGCGAGACACG	1	63	1
CGTGCCCGAGCAAGCCGTGTCTCGCGGCCGCGACAGACA	1	78	0
TCGGGCACGCCAGCCTTGCCCTCGCCAACGATGTCGGCG	1	108	1
   GGTTCAGCTTGGCATGTCTCGCCGACATCGTTGGCG	1	130	0
       GTGCTCATTCTTGCGTGCGGCATGCTGGAATT	2	3	1
          *    * *  ** **** *
MAP Score: 8.00704

Motif 4
GTGGGTCCGGTAGTGCCGCTAGGAGGCCTTG       	1	3	0
GTATACTCTTTACCAATACCGCCTGGGGGCTATGTGGG	1	36	0
AGTATACTAATTGTCTGTCGCGGCCGCGAGACACGGCT	1	67	1
CGCGAGACACGGCTTGCTCGGGCACGCCAGCCTTGCCC	1	91	1
GGGCACGCCAGCCTTGCCCTCGCCAACGATGTCGGCGA	1	110	1
 GGTTCAGCTTGGCATGTCTCGCCGACATCGTTGGCGA	1	129	0
         GTGCTCATTCTTGCGTGCGGCATGCTGGA	2	1	1
          * **  * *  **  ***
MAP Score: 0.552394