AlignACE 3.0 10/20/99
AlignACE2 -i MT/MT_fusions033_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944251019
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	Rv1782	263	hypothetical protein Rv1782
#1	Rv1784	69	hypothetical protein Rv1784
#2	Rv3863	300	hypothetical protein Rv3863
#3	Rv3864	242	hypothetical protein Rv3864
#4	Rv3865	87	hypothetical protein Rv3865
#5	Rv3867	38	hypothetical protein Rv3867
#6	Rv3871	102	hypothetical protein Rv3871

Motif 1
GCATCGTCGCCGGCGCGGGCCGTTGGCGCCGCTCCTC	6	45	0
CCGAGCTCTAGTGCGCGCACCGCCGAGTACCAGGGCA	2	52	1
AAACTATTTCCATAGCGGGCCGTCGCGTCGCTAGATC	2	228	1
GCCTGTGGAACTGTCCGCTCCGCAGTCTACCTCGTTG	0	113	0
CGGCGTTTGACGGTGCGTTCCATCGTGCCGCGAACTT	3	88	1
TTTCCTTACGCTCGCCGTTCCGGTGCGCCATCATTAT	3	208	0
GAGCTCGGAGCTCGCCGAACCGGAGCCGCAGCACCGC	2	23	0
AGGTCTGTGCCATAGCGAGTCGAAGCCATAGCGAGTA	4	30	1
CCGGCTAGCCCACAGCGAGTCGAAGTCGATGTTGCCA	1	33	0
GGCGACGATGCAAAGCGCAGCGATGAGGAGGAGCGGC	6	18	1
GGCGACGATGCAAAGCGCAGCGATGAGGAGGAGCGGC	6	71	1
GCCGGAGAACGCGCGCGTTCCCCGGACCGTTGAACTT	3	55	0
TCCAGGTGTTCTGAGCAGACCGGAAGGTGATCTAGC 	0	237	1
GCACAGACCTGCTGGCGACTCGGTGTCCGA       	4	3	0
AGCTGTGTATCTGGCCTCGCCGGCGCGTATCCGACCC	2	104	1
GCGCAGGAATCTGAGCCTTCCGTCAGCACAGCACGGT	0	47	1
TCGCTGTGGGCTAGCCGGACCGACACC          	1	52	1
ACCGTTGAACTTGAGCGTTACGGCGTGCCTGTACTTG	3	30	0
AGTGGTGTTCGGTAGCCAACCGTGCTGTGCTGACGGA	0	65	0
AAATAGTTTCCTAGCCAAACCGAACTGCCGCTACAGT	2	200	0
AACACCACTACGTTGCAGGTCAACGAGGTAGACTGCG	0	93	1
CGGCGCGTATCCGACCCCTTCGGGCAGATCTTCCAGG	2	124	1
          * * ***  ***  * *
MAP Score: 51.4894

Motif 2
CAAAGCGCAGCGATGAGGAGGAGCGGCGCGC          	6	81	1
TTCCCCGGACCGTTGAACTTGAGCGTTACGGCGTGCCTGTA	3	34	0
TTGGATCTAGCGACGCGACGGCCCGCTATGGAAATAGTTTC	2	227	0
CCGAGTCCGCCTGTGGAACTGTCCGCTCCGCAGTCTACCTC	0	117	0
CGTCAAACGCCGGAGAACGCGCGCGTTCCCCGGACCGTTGA	3	59	0
CAAAGCGCAGCGATGAGGAGGAGCGGCGCCAACGGCCCGCG	6	28	1
 CTCTGCCTGCCTAGCGGTGCTGCGGCTCCGGTTCGGCGAG	2	9	1
CGGCGTTTGACGGTGCGTTCCATCGTGCCGCGAACTTGAAA	3	88	1
AGGATCTATGCCCTGGTACTCGGCGGTGCGCGCACTAGAGC	2	56	0
ACGACGAATCCTTGGGGGATCCGCGCAGTGGCAAATACCCA	0	188	1
CAGTCTACCTCGTTGACCTGCAACGTAGTGGTGTTCGGTAG	0	87	0
TCCTTACGCTCGCCGTTCCGGTGCGCCATCATTATCTGCAC	3	202	0
CTCCTCATCGCTGCGCTTTGCATCGTCGCCGGCGCGGG   	6	7	0
CTCCTCATCGCTGCGCTTTGCATCGTCGCCGGCGCGGGCCG	6	60	0
CACAGGCGGACTCGGTCATTCGCCGCTACCATGCCCAGTGA	0	143	1
CGTGCCTGTACTTGTGGGACGCTCGGAGCCGACC       	3	3	0
TGTTAATCAGCTGTGTATCTGGCCTCGCCGGCGCGTATCCG	2	96	1
      GTCGCCCATCTTGCGTCCGGCACCCGTGTGCGGGC	0	4	1
TGAAGTGAACTGTAGCGGCAGTTCGGTTTGGCTAGGAAACT	2	192	1
GACTTCGACTCGCTGTGGGCTAGCCGGACCGACACC     	1	43	1
          CCCCTCACATCTCCGCTACGACTTCAGAAAG	5	0	1
GAACACTTTTCCTGGAAGATCTGCCCGAAGGGGTCGGATAC	2	130	0
CTTCGACTCGCTATGGCACAGACCTGCTGGCGACTCGGTGT	4	14	0
CTGAGCCTTCCGTCAGCACAGCACGGTTGGCTACCGAACAC	0	57	1
          **  *     *  ***  ***
MAP Score: 46.3244

Motif 3
GTGTATCTGGCCTCGCCGGCGCGTATCCGACCCCTTC	2	108	1
GAAACTATTTCCATAGCGGGCCGTCGCGTCGCTAGAT	2	227	1
TGCTGCGGCTCCGGTTCGGCGAGCTCCGAGCTCTAGT	2	27	1
CGCCGCTCCTCCTCATCGCTGCGCTTTGCATCGTCGC	6	19	0
CGCCGCTCCTCCTCATCGCTGCGCTTTGCATCGTCGC	6	72	0
GTGCACCAACCCCCCTCCGAGCGCTGCTAAGCTCAAT	3	152	1
GCTCTAGTGCGCGCACCGCCGAGTACCAGGGCATAGA	2	56	1
CTTACGCTCGCCGTTCCGGTGCGCCATCATTATCTGC	3	204	0
GCGCTCGCCCGCACACGGGTGCCGGACGCAAGATGGG	0	14	0
CTCGCTGTGGGCTAGCCGGACCGACACC         	1	51	1
TGCATCGTCGCCGGCGCGGGCCGTTGGCGCCGCTCCT	6	46	0
         CCCGCGCCGGCGACGATGCAAAGCGCAG	6	1	1
GTGGAACTGTCCGCTCCGCAGTCTACCTCGTTGACCT	0	109	0
GCGTATCCGACCCCTTCGGGCAGATCTTCCAGGAAAA	2	128	1
TTGAACTTGAGCGTTACGGCGTGCCTGTACTTGTGGG	3	26	0
GTTCTCCGGCGTTTGACGGTGCGTTCCATCGTGCCGC	3	82	1
TGGGTATTTGCCACTGCGCGGATCCCCCAAGGATTCG	0	192	0
  CTCTGCCTGCCTAGCGGTGCTGCGGCTCCGGTTCG	2	8	1
GTACTTGTGGGACGCTCGGAGCCGACC          	3	0	0
CGAGTCGCCAGCAGGTCTGTGCCATAGCGAGTCGAAG	4	18	1
          ** *  *** ***   *
MAP Score: 38.7428

Motif 4
CGCCCGCACACGGGTGCCGGACGCAAGATGGGCGAC  	0	8	0
CGGCACCCGTGTGCGGGCGAGCGCAGGAATCTGAGCCT	0	27	1
TAGTGGTGTTCGGTAGCCAACCGTGCTGTGCTGACGGA	0	65	0
TCAACGAGGTAGACTGCGGAGCGGACAGTTCCACAGGC	0	112	1
CACGACGAATCCTTGGGGGATCCGCGCAGTGGCAAATA	0	187	1
TCCGGCTAGCCCACAGCGAGTCGAAGTCGATGTTGCCA	1	33	0
CTCGCTGTGGGCTAGCCGGACCGACACC          	1	51	1
CGGAGCTCGCCGAACCGGAGCCGCAGCACCGCTAGGCA	2	17	0
TCCGAGCTCTAGTGCGCGCACCGCCGAGTACCAGGGCA	2	51	1
GTCGGATACGCGCCGGCGAGGCCAGATACACAGCTGAT	2	101	0
CTCGCCGGCGCGTATCCGACCCCTTCGGGCAGATCTTC	2	119	1
GAAACTATTTCCATAGCGGGCCGTCGCGTCGCTAGATC	2	227	1
ACAAGTACAGGCACGCCGTAACGCTCAAGTTCAACGGT	3	29	1
CAAGTTCAACGGTCCGGGGAACGCGCGCGTTCTCCGGC	3	54	1
GGCGTTTTCAAGTTCGCGGCACGATGGAACGCACCGTC	3	96	0
AACTTGAAAACGCCAGCGTCACCAAAAAATTCGTGCAC	3	120	1
TAGCAGCGCTCGGAGGGGGGTTGGTGCACGAATTTTTT	3	143	0
GTGCAGATAATGATGGCGCACCGGAACGGCGAGCGTAA	3	202	1
        TCGGACACCGAGTCGCCAGCAGGTCTGTGC	4	2	1
CAGGTCTGTGCCATAGCGAGTCGAAGCCATAGCGAGTA	4	29	1
        CCCGCGCCGGCGACGATGCAAAGCGCAGCG	6	2	1
TGCATCGTCGCCGGCGCGGGCCGTTGGCGCCGCTCCTC	6	45	0
CGGCGACGATGCAAAGCGCAGCGATGAGGAGGAGCGGC	6	70	1
          **   *** * **  * *
MAP Score: 34.8698

Motif 5
CTTGCGTCCGGCACCCGTGTGCGGGCGAGCGCAGGAATC	0	19	1
GCAGGAATCTGAGCCTTCCGTCAGCACAGCACGGTTGGC	0	49	1
GTCAACGAGGTAGACTGCGGAGCGGACAGTTCCACAGGC	0	111	1
TCGGTCATTCGCCGCTACCATGCCCAGTGAAGACACGAC	0	154	1
GCCCAGTGAAGACACGACGAATCCTTGGGGGATCCGCGC	0	175	1
CCTGGCAACATCGACTTCGACTCGCTGTGGGCTAGCCGG	1	31	1
TAGCGGTGCTGCGGCTCCGGTTCGGCGAGCTCCGAGCTC	2	21	1
TCTAGTGCGCGCACCGCCGAGTACCAGGGCATAGATCCT	2	58	1
TTTCCATAGCGGGCCGTCGCGTCGCTAGATCCAAAATGT	2	234	1
CACAAGTACAGGCACGCCGTAACGCTCAAGTTCAACGGT	3	28	1
AAAAATTCGTGCACCAACCCCCCTCCGAGCGCTGCTAAG	3	144	1
AGATAATGATGGCGCACCGGAACGGCGAGCGTAAGGAAA	3	206	1
GCTGCGCTTTGCATCGTCGCCGGCGCGGG          	6	0	0
GATGCAAAGCGCAGCGATGAGGAGGAGCGGCGCCAACGG	6	24	1
AGGAGGAGCGGCGCCAACGGCCCGCGCCGGCGACGATGC	6	43	1
GCCCGCGCCGGCGACGATGCAAAGCGCAGCGATGAGGAG	6	62	1
          **  *  **   *** * *
MAP Score: 31.1759

Motif 6
TTGCGTCCGGCACCCGTGTGCGGGCGAGCGCAGGAA	0	20	1
GAATCTGAGCCTTCCGTCAGCACAGCACGGTTGGCT	0	53	1
AACACCACTACGTTGCAGGTCAACGAGGTAGACTGC	0	93	1
CAACGAGGTAGACTGCGGAGCGGACAGTTCCACAGG	0	113	1
ACGACGAATCCTTGGGGGATCCGCGCAGTGGCAAAT	0	188	1
      CTCTGCCTGCCTAGCGGTGCTGCGGCTCCG	2	4	1
GCGGTGCTGCGGCTCCGGTTCGGCGAGCTCCGAGCT	2	23	1
CCGAGCTCTAGTGCGCGCACCGCCGAGTACCAGGGC	2	52	1
AGCTGTGTATCTGGCCTCGCCGGCGCGTATCCGACC	2	104	1
CGGCGCGTATCCGACCCCTTCGGGCAGATCTTCCAG	2	124	1
AAACTATTTCCATAGCGGGCCGTCGCGTCGCTAGAT	2	228	1
       GGTCGGCTCCGAGCGTCCCACAAGTACAG	3	3	1
CAAGTACAGGCACGCCGTAACGCTCAAGTTCAACGG	3	30	1
AAGTTCAACGGTCCGGGGAACGCGCGCGTTCTCCGG	3	55	1
TGCACCAACCCCCCTCCGAGCGCTGCTAAGCTCAAT	3	153	1
ATAATGATGGCGCACCGGAACGGCGAGCGTAAGGAA	3	208	1
AGGTCTGTGCCATAGCGAGTCGAAGCCATAGCGAGT	4	30	1
          CCCGCGCCGGCGACGATGCAAAGCGC	6	0	1
GGCGACGATGCAAAGCGCAGCGATGAGGAGGAGCGG	6	18	1
CCGGCGCGGGCCGTTGGCGCCGCTCCTCCTCATCGC	6	37	0
GCGCCAACGGCCCGCGCCGGCGACGATGCAAAGCGC	6	53	1
GGCGACGATGCAAAGCGCAGCGATGAGGAGGAGCGG	6	71	1
          *   ***** **  **
MAP Score: 24.7162

Motif 7
TTCCTGCGCTCGCCCGCACACGGGTGCCGGACGCAAGATGGGCG	0	12	0
AGCCAACCGTGCTGTGCTGACGGAAGGCTCAGATTCCTGCGCTC	0	45	0
AGCACAGCACGGTTGGCTACCGAACACCACTACGTTGCAGGTCA	0	71	1
CAACGAGGTAGACTGCGGAGCGGACAGTTCCACAGGCGGACTCG	0	113	1
CGACGAATCCTTGGGGGATCCGCGCAGTGGCAAATACCCAGGTC	0	189	1
      GCTAGATCACCTTCCGGTCTGCTCAGAACACCTGGACA	0	235	0
TGGCAACATCGACTTCGACTCGCTGTGGGCTAGCCGGACCGACA	1	33	1
          GGTGTCGGTCCGGCTAGCCCACAGCGAGTCGAAG	1	45	0
      CTCTGCCTGCCTAGCGGTGCTGCGGCTCCGGTTCGGCG	2	4	1
GCGGTGCTGCGGCTCCGGTTCGGCGAGCTCCGAGCTCTAGTGCG	2	23	1
TGTGTATCTGGCCTCGCCGGCGCGTATCCGACCCCTTCGGGCAG	2	107	1
AGTGAACTGTAGCGGCAGTTCGGTTTGGCTAGGAAACTATTTCC	2	195	1
CTATTTCCATAGCGGGCCGTCGCGTCGCTAGATCCAAAATGTAG	2	231	1
CAAGTACAGGCACGCCGTAACGCTCAAGTTCAACGGTCCGGGGA	3	30	1
AAGTTCAACGGTCCGGGGAACGCGCGCGTTCTCCGGCGTTTGAC	3	55	1
CACGATGGAACGCACCGTCAAACGCCGGAGAACGCGCGCGTTCC	3	71	0
AGCTTAGCAGCGCTCGGAGGGGGGTTGGTGCACGAATTTTTTGG	3	141	0
TGCAGATAATGATGGCGCACCGGAACGGCGAGCGTAAGGAAACA	3	203	1
CTATGGCACAGACCTGCTGGCGACTCGGTGTCCGA         	4	1	0
CTTTCTACTCGCTATGGCTTCGACTCGCTATGGCACAGACCTGC	4	28	0
CCGCGCCGGCGACGATGCAAAGCGCAGCGATGAGGAGGAGCGGC	6	11	1
AAAGCGCAGCGATGAGGAGGAGCGGCGCCAACGGCCCGCGCCGG	6	29	1
GCTTTGCATCGTCGCCGGCGCGGGCCGTTGGCGCCGCTCCTCCT	6	43	0
GCCGCTCCTCCTCATCGCTGCGCTTTGCATCGTCGCCGGCGCGG	6	64	0
          * *  **   ***   **     *
MAP Score: 17.4985