AlignACE 3.0 10/20/99
AlignACE2 -i MT/MT_fusions019_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944250527
 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
GCGAGGGCAAGGCTGGCGTGCCCGAGCAAGCC	1	101	0
AACGATGTCGGCGAGACATGCCAAGCTGAACC	1	134	1
CTCACCCTATGTGAGGCGGGTCGCAAATTACC	0	13	1
TGTCGCGGCCGCGAGACACGGCTTGCTCGGGC	1	82	1
TCATTCTTGCGTGCGGCATGCTGGAATTCCGA	2	14	1
TATACTAATTGTCTGTCGCGGCCGCGAGACAC	1	69	1
GGCTATGTGGGTCCGGTAGTGCCGCTAGGAGG	1	15	0
          *** **** ***
MAP Score: 10.1097

Motif 2
TAATTTGCGACCCGCCTCACATAGGGTGAGGTC   	0	7	0
          CAAGGCCTCCTAGCGGCACTACCGGA	1	0	1
AGCGGCACTACCGGACCCACATAGCCCCCAGGCGGT	1	21	1
GAGTATACTAATTGTCTGTCGCGGCCGCGAGACACG	1	66	1
GGCCGCGAGACACGGCTTGCTCGGGCACGCCAGCCT	1	88	1
CTCGGGCACGCCAGCCTTGCCCTCGCCAACGATGTC	1	107	1
  GGTTCAGCTTGGCATGTCTCGCCGACATCGTTGG	1	132	0
 ATCGGAATTCCAGCATGCCGCACGCAAGAATGAGC	2	12	0
          *  * **  * *****
MAP Score: 10.0999

Motif 3
GTAATTTGCGACCCGCCTCACATAGGGTGAGGTC     	0	5	0
GGGTCCGGTAGTGCCGCTAGGAGGCCTTG          	1	0	0
GGCACTACCGGACCCACATAGCCCCCAGGCGGTATTGGT	1	24	1
TATACTAATTGTCTGTCGCGGCCGCGAGACACGGCTTGC	1	69	1
GCAAGGCTGGCGTGCCCGAGCAAGCCGTGTCTCGCGGCC	1	88	0
ACATCGTTGGCGAGGGCAAGGCTGGCGTGCCCGAGCAAG	1	103	0
GCACGCCAGCCTTGCCCTCGCCAACGATGTCGGCGAGAC	1	112	1
AACGATGTCGGCGAGACATGCCAAGCTGAACC       	1	134	1
       GTGCTCATTCTTGCGTGCGGCATGCTGGAATT	2	3	1
          *   * *  *** ***  *
MAP Score: 3.29898

Motif 4
TAATTTGCGACCCGCCTCACATAGGGTGAGGTC   	0	7	0
          CAAGGCCTCCTAGCGGCACTACCGGA	1	0	1
ACCAATACCGCCTGGGGGCTATGTGGGTCCGGTAGT	1	27	0
CAAGCCGTGTCTCGCGGCCGCGACAGACAATTAGTA	1	71	0
GGCCGCGAGACACGGCTTGCTCGGGCACGCCAGCCT	1	88	1
CTCGGGCACGCCAGCCTTGCCCTCGCCAACGATGTC	1	107	1
GTCGGCGAGACATGCCAAGCTGAACC          	1	140	1
 GTGCTCATTCTTGCGTGCGGCATGCTGGAATTCCG	2	9	1
          * ****  **  * **
MAP Score: 2.52273

Motif 5
CCGGTAGTGCCGCTAGGAGGCCTTG          	1	0	0
GGGCTATGTGGGTCCGGTAGTGCCGCTAGGAGGCC	1	13	0
CCCACATAGCCCCCAGGCGGTATTGGTAAAGAGTA	1	36	1
CAAGCCGTGTCTCGCGGCCGCGACAGACAATTAGT	1	72	0
GCGGCCGCGAGACACGGCTTGCTCGGGCACGCCAG	1	86	1
GACACGGCTTGCTCGGGCACGCCAGCCTTGCCCTC	1	96	1
GGGCACGCCAGCCTTGCCCTCGCCAACGATGTCGG	1	110	1
AGCTTGGCATGTCTCGCCGACATCGTTGGCGAGGG	1	126	0
CAACGATGTCGGCGAGACATGCCAAGCTGAACC  	1	133	1
CTCATTCTTGCGTGCGGCATGCTGGAATTCCGAT 	2	13	1
          * *  *** **** *
MAP Score: 1.0703