AlignACE 3.0 10/20/99
AlignACE2 -i MT/MT_fusions030_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944250910
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	Rv1774	65	hypothetical protein Rv1774
#1	Rv3351c	81	hypothetical protein Rv3351c
#2	Rv3352c	142	hypothetical protein Rv3352c
#3	Rv3353c	30	hypothetical protein Rv3353c

Motif 1
GACCCCACGTGGTGCGGTCGGCCCCGGCCAGCCACGTCTG   	1	7	0
TGGCCGGGGCCGACCGCACCACGTGGGGTCTGGTTGACCCCGC	1	20	1
CACGTGGGGTCTGGTTGACCCCGCGGTCAGCTCATCCGGAGGC	1	39	1
      ATGACAATTGCCTCCGGATGAGCTGACCGCGGGGTCA	1	54	0
GCTCAAGATCGCTGTGCGCGGCGGCGGACATTCCTACATCGGC	2	23	1
GACATTCCTACATCGGCGCCTCGTCGGCCAATGGCGCCATGGT	2	49	1
CCTCGTCGGCCAATGGCGCCATGGTGCTCGATCTGCTGGGCCT	2	67	1
CTGTCGAAATGCACCCCGCCCGGTAGGCCCAGCAGATCGAGCA	2	91	0
GGGTGCATTTCGACAGCGCCACGAGAAACGTACG         	2	118	1
          *    ** ** **  *  *   *
MAP Score: 16.1295

Motif 2
CGGTCGGCCCCGGCCAGCCACGTCTG        	1	2	0
TGGCTGGCCGGGGCCGACCGCACCACGTGGGGTC	1	16	1
GCTGACCGCGGGGTCAACCAGACCCCACGTGGTG	1	36	0
GGTTGACCCCGCGGTCAGCTCATCCGGAGGCAAT	1	51	1
        CGGCGGCCAGCAAGCTCAAGATCGCT	2	2	1
GGAATGTCCGCCGCCGCGCACAGCGATCTTGAGC	2	23	0
TTCCTACATCGGCGCCTCGTCGGCCAATGGCGCC	2	53	1
TCGGCCAATGGCGCCATGGTGCTCGATCTGCTGG	2	72	1
CCCGCCCGGTAGGCCCAGCAGATCGAGCACCATG	2	86	0
CTGTCGAAATGCACCCCGCCCGGTAGGCCCAGCA	2	100	0
CATTTCGACAGCGCCACGAGAAACGTACG     	2	123	1
CAGGAACCTTGGTCCATGGTCGTCACAT      	3	12	1
          *****  ** ** *
MAP Score: 15.0597

Motif 3
     CAGACGTGGCTGGCCGGGGCCGACC	1	5	1
GTGGCTGGCCGGGGCCGACCGCACCACGTG	1	15	1
AGCTGACCGCGGGGTCAACCAGACCCCACG	1	41	0
TGCCTCCGGATGAGCTGACCGCGGGGTCAA	1	53	0
CTTGAGCTTGCTGGCCGCCG          	2	0	0
CAAGATCGCTGTGCGCGGCGGCGGACATTC	2	26	1
TGGCCGACGAGGCGCCGATGTAGGAATGTC	2	49	0
CATGGCGCCATTGGCCGACGAGGCGCCGAT	2	60	0
CGTCGGCCAATGGCGCCATGGTGCTCGATC	2	70	1
TGGCGCCATGGTGCTCGATCTGCTGGGCCT	2	80	1
CTCGATCTGCTGGGCCTACCGGGCGGGGTG	2	93	1
TGGGCCTACCGGGCGGGGTGCATTTCGACA	2	103	1
CGTTTCTCGTGGCGCTGTCGAAATGCACCC	2	118	0
CTCAGGAACCTTGGTCCATGGTCGTCACAT	3	10	1
          **********
MAP Score: 13.2982

Motif 4
GTGCGGTCGGCCCCGGCCAGCCACGTCTG  	1	8	0
CTGACCGCGGGGTCAACCAGACCCCACGTGG	1	38	0
CTGGTTGACCCCGCGGTCAGCTCATCCGGAG	1	49	1
          CGGCGGCCAGCAAGCTCAAGA	2	0	1
ATGTCCGCCGCCGCGCACAGCGATCTTGAGC	2	23	0
ATCGGCGCCTCGTCGGCCAATGGCGCCATGG	2	60	1
GCGCCATGGTGCTCGATCTGCTGGGCCTACC	2	82	1
          ** ********
MAP Score: 11.3832

Motif 5
         CAGACGTGGCTGGCCGGGGCCGACCGCACC	1	1	1
TGGCCGGGGCCGACCGCACCACGTGGGGTCTGGTTGACC	1	20	1
GATGAGCTGACCGCGGGGTCAACCAGACCCCACGTGGTG	1	36	0
GGAATGTCCGCCGCCGCGCACAGCGATCTTGAGCTTGCT	2	18	0
GACATTCCTACATCGGCGCCTCGTCGGCCAATGGCGCCA	2	49	1
CCTCGTCGGCCAATGGCGCCATGGTGCTCGATCTGCTGG	2	67	1
GGTGCTCGATCTGCTGGGCCTACCGGGCGGGGTGCATTT	2	89	1
GGGTGCATTTCGACAGCGCCACGAGAAACGTACG     	2	118	1
          *  * *****  *  *  *
MAP Score: 11.3496

Motif 6
GGGGCCGACCGCACCACGTGGGGTCTGGTTGACCCCG	1	25	1
CTCCGGATGAGCTGACCGCGGGGTCAACCAGACCCCA	1	43	0
GCTCAAGATCGCTGTGCGCGGCGGCGGACATTCCTAC	2	23	1
TGGCGCCATTGGCCGACGAGGCGCCGATGTAGGAATG	2	51	0
GATCTGCTGGGCCTACCGGGCGGGGTGCATTTCGACA	2	96	1
          **    ** **** * *
MAP Score: 10.5817

Motif 7
TGGTGCGGTCGGCCCCGGCCAGCCACGTCTG        	1	2	0
GGGCCGACCGCACCACGTGGGGTCTGGTTGACCCCGCGG	1	26	1
GTCTGGTTGACCCCGCGGTCAGCTCATCCGGAGGCAATT	1	47	1
GAATGTCCGCCGCCGCGCACAGCGATCTTGAGCTTGCTG	2	17	0
CCTACATCGGCGCCTCGTCGGCCAATGGCGCCATGGTGC	2	55	1
TGGCGCCATGGTGCTCGATCTGCTGGGCCTACCGGGCGG	2	80	1
TGGGCCTACCGGGCGGGGTGCATTTCGACAGCGCCACGA	2	103	1
          * ** **  * **   * *
MAP Score: 7.33579

Motif 8
        CAGACGTGGCTGGCCGGGGCCGACCGCACCACGTG	1	2	1
ACCGCACCACGTGGGGTCTGGTTGACCCCGCGGTCAGCTCATC	1	32	1
          CGGCGGCCAGCAAGCTCAAGATCGCTGTGCGCG	2	0	1
GCTCAAGATCGCTGTGCGCGGCGGCGGACATTCCTACATCGGC	2	23	1
ACCATGGCGCCATTGGCCGACGAGGCGCCGATGTAGGAATGTC	2	49	0
CACCCCGCCCGGTAGGCCCAGCAGATCGAGCACCATGGCGCCA	2	80	0
GTTTCTCGTGGCGCTGTCGAAATGCACCCCGCCCGGTAGGCCC	2	104	0
          *   ** * *   *  * **  *
MAP Score: 5.61993

Motif 9
  CAGACGTGGCTGGCCGGGGCCGACCGCACCACGTGGG	1	8	1
ACCGCACCACGTGGGGTCTGGTTGACCCCGCGGTCAGCT	1	32	1
GCAAGCTCAAGATCGCTGTGCGCGGCGGCGGACATTCCT	2	19	1
GATCGAGCACCATGGCGCCATTGGCCGACGAGGCGCCGA	2	61	0
GCGCCATGGTGCTCGATCTGCTGGGCCTACCGGGCGGGG	2	82	1
TGGGCCTACCGGGCGGGGTGCATTTCGACAGCGCCACGA	2	103	1
          * ***  * *   * ** *
MAP Score: 5.23274

Motif 10
AGACGTGGCTGGCCGGGGCCGACCGCACCACGTGGGGTC	1	11	1
TTGACCCCGCGGTCAGCTCATCCGGAGGCAATTGTCAT 	1	53	1
GCTCAAGATCGCTGTGCGCGGCGGCGGACATTCCTACAT	2	23	1
GACATTCCTACATCGGCGCCTCGTCGGCCAATGGCGCCA	2	49	1
GGTGCTCGATCTGCTGGGCCTACCGGGCGGGGTGCATTT	2	89	1
GGGTGCATTTCGACAGCGCCACGAGAAACGTACG     	2	118	1
          *  * * **  ** * * *
MAP Score: 4.84546

Motif 11
        CAGACGTGGCTGGCCGGGGCCGACCGCACCACG	1	2	1
AATTGCCTCCGGATGAGCTGACCGCGGGGTCAACCAGACCC	1	45	0
CAGCAAGCTCAAGATCGCTGTGCGCGGCGGCGGACATTCCT	2	17	1
GCGCGGCGGCGGACATTCCTACATCGGCGCCTCGTCGGCCA	2	38	1
TGGCGCCATGGTGCTCGATCTGCTGGGCCTACCGGGCGGGG	2	80	1
TCGATCTGCTGGGCCTACCGGGCGGGGTGCATTTCGACAGC	2	94	1
     CTCAGGAACCTTGGTCCATGGTCGTCACAT      	3	5	1
          *      *   ****** * *
MAP Score: 2.22917