AlignACE 3.0 10/20/99
AlignACE2 -i MT/MT_fusions030_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944250905
 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
GTGCGGTCGGCCCCGGCCAGCCACGTCTG       	1	3	0
CCGGGGCCGACCGCACCACGTGGGGTCTGGTTGACC	1	23	1
CTGGTTGACCCCGCGGTCAGCTCATCCGGAGGCAAT	1	49	1
          CGGCGGCCAGCAAGCTCAAGATCGCT	2	0	1
ATGTCCGCCGCCGCGCACAGCGATCTTGAGCTTGCT	2	18	0
CTGTGCGCGGCGGCGGACATTCCTACATCGGCGCCT	2	34	1
ATTCCTACATCGGCGCCTCGTCGGCCAATGGCGCCA	2	52	1
CGTCGGCCAATGGCGCCATGGTGCTCGATCTGCTGG	2	70	1
CCGGTAGGCCCAGCAGATCGAGCACCATGGCGCCAT	2	79	0
TCGAAATGCACCCCGCCCGGTAGGCCCAGCAGATCG	2	95	0
TGCATTTCGACAGCGCCACGAGAAACGTACG     	2	121	1
          ******** *     *
MAP Score: 25.2895

Motif 2
  AGCAAAACTCCTGGTCCGTATTTCGAATCATTGTG	0	40	0
GTGCGGTCGGCCCCGGCCAGCCACGTCTG        	1	2	0
ACGTGGCTGGCCGGGGCCGACCGCACCACGTGGGGTC	1	13	1
ACCGCACCACGTGGGGTCTGGTTGACCCCGCGGTCAG	1	32	1
CTGGTTGACCCCGCGGTCAGCTCATCCGGAGGCAATT	1	49	1
          CGGCGGCCAGCAAGCTCAAGATCGCTG	2	0	1
TAGGAATGTCCGCCGCCGCGCACAGCGATCTTGAGCT	2	22	0
ACCATGGCGCCATTGGCCGACGAGGCGCCGATGTAGG	2	55	0
ACCCCGCCCGGTAGGCCCAGCAGATCGAGCACCATGG	2	85	0
          * * **** **    **
MAP Score: 11.8727

Motif 3
CCCACGTGGTGCGGTCGGCCCCGGCCAGCCACGTCTG  	1	8	0
TGGCCGGGGCCGACCGCACCACGTGGGGTCTGGTTGACC	1	20	1
CGTGGGGTCTGGTTGACCCCGCGGTCAGCTCATCCGGAG	1	41	1
         CGGCGGCCAGCAAGCTCAAGATCGCTGTGC	2	1	1
GCTCAAGATCGCTGTGCGCGGCGGCGGACATTCCTACAT	2	23	1
GACATTCCTACATCGGCGCCTCGTCGGCCAATGGCGCCA	2	49	1
CGCCCGGTAGGCCCAGCAGATCGAGCACCATGGCGCCAT	2	79	0
TGGCGCTGTCGAAATGCACCCCGCCCGGTAGGCCCAGCA	2	100	0
GGGTGCATTTCGACAGCGCCACGAGAAACGTACG     	2	118	1
          *    ** ** **  ** *
MAP Score: 11.7304

Motif 4
      CAGACGTGGCTGGCCGGGGCCGACCGCACC	1	4	1
CGGGGCCGACCGCACCACGTGGGGTCTGGTTGACCC	1	24	1
AGCTCAAGATCGCTGTGCGCGGCGGCGGACATTCCT	2	22	1
ATGGCGCCATTGGCCGACGAGGCGCCGATGTAGGAA	2	53	0
CCCAGCAGATCGAGCACCATGGCGCCATTGGCCGAC	2	71	0
ATCTGCTGGGCCTACCGGGCGGGGTGCATTTCGACA	2	97	1
          **  *  ** **** *
MAP Score: 10.3213

Motif 5
  AACTGCAATATAGTGAACCGAAATACGGATCACAATGATTC	0	8	1
AAATACGGATCACAATGATTCGAAATACGGACCAGGAGTTTTG	0	30	1
        CAGACGTGGCTGGCCGGGGCCGACCGCACCACGTG	1	2	1
TGACCGCGGGGTCAACCAGACCCCACGTGGTGCGGTCGGCCCC	1	25	0
TCTGGTTGACCCCGCGGTCAGCTCATCCGGAGGCAATTGTCAT	1	48	1
GGCCAGCAAGCTCAAGATCGCTGTGCGCGGCGGCGGACATTCC	2	14	1
TGTGCGCGGCGGCGGACATTCCTACATCGGCGCCTCGTCGGCC	2	35	1
GCAGATCGAGCACCATGGCGCCATTGGCCGACGAGGCGCCGAT	2	60	0
CCATGGTGCTCGATCTGCTGGGCCTACCGGGCGGGGTGCATTT	2	85	1
GGTGCATTTCGACAGCGCCACGAGAAACGTACG          	2	119	1
          * *   *   **     *** **
MAP Score: 8.78022

Motif 6
GCAATATAGTGAACCGAAATACGGATCACAATGATTC	0	14	1
GGATCACAATGATTCGAAATACGGACCAGGAGTTTTG	0	36	1
       CAGACGTGGCTGGCCGGGGCCGACCGCACC	1	3	1
TCAACCAGACCCCACGTGGTGCGGTCGGCCCCGGCCA	1	20	0
ATTGCCTCCGGATGAGCTGACCGCGGGGTCAACCAGA	1	48	0
GCTCAAGATCGCTGTGCGCGGCGGCGGACATTCCTAC	2	23	1
GCGCCATTGGCCGACGAGGCGCCGATGTAGGAATGTC	2	49	0
CCTCGTCGGCCAATGGCGCCATGGTGCTCGATCTGCT	2	67	1
TGCTCGATCTGCTGGGCCTACCGGGCGGGGTGCATTT	2	91	1
TTTCGACAGCGCCACGAGAAACGTACG          	2	125	1
   CTCAGGAACCTTGGTCCATGGTCGTCACAT    	3	7	1
          **  **    **** **
MAP Score: 8.31856

Motif 7
GGTCGGCCCCGGCCAGCCACGTCTG        	1	2	0
GGCTGGCCGGGGCCGACCGCACCACGTGGGGTC	1	17	1
CACCACGTGGGGTCTGGTTGACCCCGCGGTCAG	1	36	1
TTGACCCCGCGGTCAGCTCATCCGGAGGCAATT	1	53	1
TCAAGATCGCTGTGCGCGGCGGCGGACATTCCT	2	25	1
GCGGCGGACATTCCTACATCGGCGCCTCGTCGG	2	43	1
GCGCCTCGTCGGCCAATGGCGCCATGGTGCTCG	2	64	1
CATGGTGCTCGATCTGCTGGGCCTACCGGGCGG	2	86	1
GCGGGGTGCATTTCGACAGCGCCACGAGAAACG	2	115	1
          **** **  ****
MAP Score: 7.40422

Motif 8
CTGCAATATAGTGAACCGAAATACGGATCACAATGATTC	0	12	1
ACGGATCACAATGATTCGAAATACGGACCAGGAGTTTTG	0	34	1
GCTGGCCGGGGCCGACCGCACCACGTGGGGTCTGGTTGA	1	18	1
GTCCGCCGCCGCGCACAGCGATCTTGAGCTTGCTGGCCG	2	13	0
CGCGGCGGCGGACATTCCTACATCGGCGCCTCGTCGGCC	2	39	1
CGCCTCGTCGGCCAATGGCGCCATGGTGCTCGATCTGCT	2	65	1
ATGGCGCCATGGTGCTCGATCTGCTGGGCCTACCGGGCG	2	79	1
CATTTCGACAGCGCCACGAGAAACGTACG          	2	123	1
          * *   **  *  *** **
MAP Score: 1.36077

Motif 9
  CAGACGTGGCTGGCCGGGGCCGACCGCACCACGTGG	1	8	1
GGGGCCGACCGCACCACGTGGGGTCTGGTTGACCCCGC	1	25	1
CTGACCGCGGGGTCAACCAGACCCCACGTGGTGCGGTC	1	31	0
AATGTCCGCCGCCGCGCACAGCGATCTTGAGCTTGCTG	2	17	0
TGGCGCCATTGGCCGACGAGGCGCCGATGTAGGAATGT	2	50	0
AGCAGATCGAGCACCATGGCGCCATTGGCCGACGAGGC	2	66	0
TGCTCGATCTGCTGGGCCTACCGGGCGGGGTGCATTTC	2	91	1
          ** ** **  ***    *
MAP Score: 0.0362312