AlignACE 3.0 10/20/99
AlignACE2 -i MT/MT_fusions023_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944250661
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	alaS	90	alaS
#1	Rv2556c	106	hypothetical protein Rv2556c
#2	aroA	54	aroA

Motif 1
TGTCCGACGGCCCAATTCGGCCCGC       	0	3	0
ATTATGAGAAGGCTGTCCGACGGCCCAATTCG	0	16	0
ACAGCCTTCTCATAATCCGGCGAATAGGCTGG	0	32	1
         TCTACGTTCTTCCTTGATCCGTG	0	77	0
   TCATTACCTTCCTCCGACGGGCCGGCCGG	1	7	1
TTGCCCATTGCCCCGGCCGGCCCGTCGGAGGA	1	19	0
CGGGGCAATGGGCAATCCGACGTCAATGGATT	1	36	1
GGTGGGGGCGCGCCAACCTGCCAATCCATTGA	1	58	0
GGTTGGCGCGCCCCCACCGTAGGCTGGGACGG	1	72	1
    ATCGGTATCCACCCGTCCCAGCCTACGG	1	88	0
CTGGTACCCACGACACCCGCCGACACGGCAGG	2	24	1
        CGCTTCATCCTGCCGTGTCGGCGG	2	40	0
          * ******* **
MAP Score: 22.0063

Motif 2
TATGAGAAGGCTGTCCGACGGCCCAATTCGGCCCGC      	0	4	0
TCTCATAATCCGGCGAATAGGCTGGTAATGGACTTAACCACG	0	39	1
TCATTACCTTCCTCCGACGGGCCGGCCGGGGCAATGGGCAAT	1	10	1
AATCCGACGTCAATGGATTGGCAGGTTGGCGCGCCCCCACCG	1	49	1
TTGGCGCGCCCCCACCGTAGGCTGGGACGGGTGGATACCGAT	1	74	1
CCACGACACCCGCCGACACGGCAGGATGAAGCG         	2	31	1
          *   *    *** **    ***
MAP Score: 14.849

Motif 3
       GCGGGCCGAATTGGGCCGTCGGACAG	0	3	1
CGAATTGGGCCGTCGGACAGCCTTCTCATAATC	0	16	1
TCTCATAATCCGGCGAATAGGCTGGTAATGGAC	0	39	1
TCATTACCTTCCTCCGACGGGCCGGCCGGGGCA	1	10	1
TCGGATTGCCCATTGCCCCGGCCGGCCCGTCGG	1	23	0
AATCCATTGACGTCGGATTGCCCATTGCCCCGG	1	35	0
AATCCGACGTCAATGGATTGGCAGGTTGGCGCG	1	49	1
CCGTCCCAGCCTACGGTGGGGGCGCGCCAACCT	1	71	0
ATCGGTATCCACCCGTCCCAGCCTACGGTGGGG	1	83	0
         GCTTCCTATGGTGCCTGGTACCCA	2	1	1
CCGTGTCGGCGGGTGTCGTGGGTACCAGGCACC	2	19	0
          ** ** ** ****
MAP Score: 4.31848

Motif 4
GGGCCGAATTGGGCCGTCGGACAGCCTTCTCAT	0	12	1
CCGGCCGGCCCGTCGGAGGAAGGTAATGA    	1	6	0
TCCTCCGACGGGCCGGCCGGGGCAATGGGCAAT	1	19	1
AATGGGCAATCCGACGTCAATGGATTGGCAGGT	1	42	1
TCAATGGATTGGCAGGTTGGCGCGCCCCCACCG	1	58	1
CCCGTCCCAGCCTACGGTGGGGGCGCGCCAACC	1	72	0
GTGCCTGGTACCCACGACACCCGCCGACACGGC	2	20	1
CCGCCGACACGGCAGGATGAAGCG         	2	40	1
          ** *** *** **
MAP Score: 2.53252