AlignACE 3.0 10/20/99
AlignACE2 -i MT/MT_fusions023_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944250657
 numcols =     	10
 undersample = 	1
 oversample = 	1

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

Motif 1
TTCTCATAATCCGGCGAATAGGCTGGTAATGGACTT	0	38	1
TTACCTTCCTCCGACGGGCCGGCCGGGGCAATGGGC	1	13	1
CCCACGACACCCGCCGACACGGCAGGATGAAGCG  	2	30	1
CGCGCCCCCACCGTAGGCTGGGACGGGTGGATACCG	1	78	1
CCGAATTGGGCCGTCGGACAGCCTTCTCATAATCCG	0	15	1
CAATCCGACGTCAATGGATTGGCAGGTTGGCGCGCC	1	48	1
          *** **    *** **
MAP Score: 16.1218

Motif 2
CGAATTGGGCCGTCGGACAGCCTTCTCATAATC	0	16	1
TCTCATAATCCGGCGAATAGGCTGGTAATGGAC	0	39	1
TCCTCCGACGGGCCGGCCGGGGCAATGGGCAAT	1	19	1
AATCCATTGACGTCGGATTGCCCATTGCCCCGG	1	35	0
TGGATTGGCAGGTTGGCGCGCCCCCACCGTAGG	1	62	1
CCCCACCGTAGGCTGGGACGGGTGGATACCGAT	1	83	1
CCTGCCGTGTCGGCGGGTGTCGTGGGTACCAGG	2	23	0
          ** ****  ****
MAP Score: 11.3895

Motif 3
         GCGGGCCGAATTGGGCCGTCGGAC	0	1	1
CCGAATTGGGCCGTCGGACAGCCTTCTCATAAT	0	15	1
ACCAGCCTATTCGCCGGATTATGAGAAGGCTGT	0	32	0
TCCGGCGAATAGGCTGGTAATGGACTTAACCAC	0	47	1
CCCGGCCGGCCCGTCGGAGGAAGGTAATGA   	1	7	0
GACGGGCCGGCCGGGGCAATGGGCAATCCGACG	1	25	1
AATGGGCAATCCGACGTCAATGGATTGGCAGGT	1	42	1
GTCAATGGATTGGCAGGTTGGCGCGCCCCCACC	1	57	1
CCCGTCCCAGCCTACGGTGGGGGCGCGCCAACC	1	72	0
TAGGCTGGGACGGGTGGATACCGAT        	1	91	1
GCCGTGTCGGCGGGTGTCGTGGGTACCAGGCAC	2	20	0
CCCGCCGACACGGCAGGATGAAGCG        	2	39	1
          *** **** * **
MAP Score: 8.94105

Motif 4
CCGAATTGGGCCGTCGGACAGCCTTCTCATAATCCGGCGAATAGGC	0	15	1
TTCTCATAATCCGGCGAATAGGCTGGTAATGGACTTAACCACGGAT	0	38	1
TCATTACCTTCCTCCGACGGGCCGGCCGGGGCAATGGGCAATCCGA	1	10	1
AATGGGCAATCCGACGTCAATGGATTGGCAGGTTGGCGCGCCCCCA	1	42	1
GGTTGGCGCGCCCCCACCGTAGGCTGGGACGGGTGGATACCGAT  	1	72	1
GTGCCTGGTACCCACGACACCCGCCGACACGGCAGGATGAAGCG  	2	20	1
          **  ** *   **       **   *
MAP Score: 6.69404

Motif 5
ATTATGAGAAGGCTGTCCGACGGCCCAATTCGGCCC	0	12	0
TCCATTACCAGCCTATTCGCCGGATTATGAGAAGGC	0	35	0
GCTGGTAATGGACTTAACCACGGATCAAGGAAGAAC	0	59	1
ACTTAACCACGGATCAAGGAAGAACGTAGA      	0	70	1
CATTGCCCCGGCCGGCCCGTCGGAGGAAGGTAATGA	1	10	0
ACCTGCCAATCCATTGACGTCGGATTGCCCATTGCC	1	39	0
GGTTGGCGCGCCCCCACCGTAGGCTGGGACGGGTGG	1	72	1
TCGTGGGTACCAGGCACCATAGGAAGC         	2	1	0
CCTATGGTGCCTGGTACCCACGACACCCGCCGACAC	2	14	1
CTGGTACCCACGACACCCGCCGACACGGCAGGATGA	2	24	1
          **    *** **** *
MAP Score: 6.53251

Motif 6
CCGAATTGGGCCGTCGGACAGCCTTCTCATAAT	0	15	1
TACCTTCCTCCGACGGGCCGGCCGGGGCAATGG	1	14	1
CAATCCATTGACGTCGGATTGCCCATTGCCCCG	1	36	0
TCCCAGCCTACGGTGGGGGCGCGCCAACCTGCC	1	68	0
CCCCCACCGTAGGCTGGGACGGGTGGATACCGA	1	82	1
CCCACGACACCCGCCGACACGGCAGGATGAAGC	2	30	1
          *******   ***
MAP Score: 6.19158

Motif 7
TGTCCGACGGCCCAATTCGGCCCGC          	0	0	0
TCGGACAGCCTTCTCATAATCCGGCGAATAGGCTG	0	28	1
    TCATTACCTTCCTCCGACGGGCCGGCCGGGG	1	6	1
CGGATTGCCCATTGCCCCGGCCGGCCCGTCGGAGG	1	20	0
   ATCGGTATCCACCCGTCCCAGCCTACGGTGGG	1	84	0
       GCTTCCTATGGTGCCTGGTACCCACGAC	2	3	1
GTGCCTGGTACCCACGACACCCGCCGACACGGCAG	2	20	1
          *** *  * *** **
MAP Score: 2.10027

Motif 8
TGTCCGACGGCCCAATTCGGCCCGC          	0	0	0
   TCATTACCTTCCTCCGACGGGCCGGCCGGGGC	1	7	1
CGTCGGATTGCCCATTGCCCCGGCCGGCCCGTCGG	1	23	0
TACGGTGGGGGCGCGCCAACCTGCCAATCCATTGA	1	58	0
TGGCGCGCCCCCACCGTAGGCTGGGACGGGTGGAT	1	75	1
      GCTTCCTATGGTGCCTGGTACCCACGACA	2	4	1
GTGCCTGGTACCCACGACACCCGCCGACACGGCAG	2	20	1
          ** *   **** ***
MAP Score: 0.757736