AlignACE 3.0 10/20/99
AlignACE2 -i CT/CT_fusions003_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944241497
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	CT191	146	hypothetical protein
#1	CT192	26	hypothetical protein
#2	tgt	126	Queuine tRNA Ribosyl Transferase
#3	mgtE	300	Mg++ Transporter (CBS Domain)
#4	gyrB_2	300	DNA Gyrase Subunit B

Motif 1
AATACTTTGACTTTTTTAGTTCGCAACAAG	0	61	1
AGTATAAGAGCCTTCTTCCTGAGCCTTCTG	0	89	1
AAGAAAACCTTTGTCTTCGGACTCACCCA 	2	9	0
AAGACAAAGGTTTTCTTCGGGCTTTTTTCA	2	22	1
TTCTTCGGGCTTTTTTCACTATGTCTTTTC	2	34	1
TCACTATGTCTTTTCTCCCTCTCTCTTTAG	2	49	1
AATTTTATTATTTTTTTAGAATTCGCTTAG	2	90	1
TATTAAGAGACTTTTTTACGAAAACGACAA	3	125	0
TCTTTCACGCCCTTCTCCGTTCTTTATATA	3	228	0
TTCTATTTTGCTCTTTCACGCCCTTCTCCG	3	239	0
AACATCCAATTTTTCTTCGTTTCTATTTTG	3	259	0
  TTGGCTCATTCTCTTTGTTTCGTATTTT	4	8	1
ATTTTTGAGACTCTCTTCGTTCTCTGCATT	4	47	1
AACGGTTTTTCTATTTTCGTCTCCAGACTA	4	89	0
TTTTAGTCTTCTGTCTCACTAAGCAGTGTG	4	169	0
GGCGTAGTATTTCTTTTAGTCTTCTGTCTC	4	182	0
TAGCTGATTGTTTTCTCAGAAATTATAGAA	4	244	1
          **********
MAP Score: 12.1405

Motif 2
TTAGCGCTAATACTTTGACTTTTTTAGTTCGCAAC	0	53	1
AACGGCGCGATTATGAGATTCTTTTT         	1	10	1
CTTCGGGCTTTTTTCACTATGTCTTTTCTCCCTCT	2	36	1
ACTATGTCTTTTCTCCCTCTCTCTTTAGAATGATT	2	51	1
GATTCATGAATTTTATTATTTTTTTAGAATTCGCT	2	82	1
TGTATCTGTTTGTAAAGTATCTTTTTATAGTGAAG	3	60	1
ACAAAAAGTCTTCCGAGACTCTTAAACAAGAGTCC	3	94	0
AGACTATCTATTAAGAGACTTTTTTACGAAAACGA	3	128	0
AGGTATTAGATTTGGCGAGACTTTAGACCGAATGT	3	164	1
AATAGACGACTTTTAAGAGTCTTTATATAAAGAAC	3	205	1
CATCCAATTTTTCTTCGTTTCTATTTTGCTCTTTC	3	252	0
          TTGGCTCATTCTCTTTGTTTCGTAT	4	0	1
TCATTCTCTTTGTTTCGTATTTTTATACCAATATT	4	15	1
ATACCAATATTTTTGAGACTCTCTTCGTTCTCTGC	4	39	1
AACGCCTTTTTTAACGGTTTTTCTATTTTCGTCTC	4	96	0
AGCATAACTATTAGCTGATTGTTTTCTCAGAAATT	4	233	1
          **    ** ******
MAP Score: 10.6106

Motif 3
CGCAACAAGTATAAGAGCCTTCTTCCTGAGCCT	0	82	1
AGAGCCTTCTTCCTGAGCCTTCTGCGAAGGAAG	0	95	1
AACGGCGCGATTATGAGATTCTTTTT       	1	10	1
CGAGACTCTTAAACAAGAGTCCTTCACTATAAA	3	83	0
ACAAAAAGTCTTCCGAGACTCTTAAACAAGAGT	3	96	0
TTTAAGAGTCTCGGAAGACTTTTTGTCGTTTTC	3	103	1
AGACTATCTATTAAGAGACTTTTTTACGAAAAC	3	130	0
GTATTAGATTTGGCGAGACTTTAGACCGAATGT	3	166	1
CCGTTCTTTATATAAAGACTCTTAAAAGTCGTC	3	209	0
ATACCAATATTTTTGAGACTCTCTTCGTTCTCT	4	39	1
          *   *********
MAP Score: 9.0079

Motif 4
CGCTAATACTTTGACTTTTTTAGTTCGCAA	0	57	1
ACAAGTATAAGAGCCTTCTTCCTGAGCCTT	0	86	1
CCTTCTTCCTGAGCCTTCTGCGAAGGAAGG	0	99	1
GCGATTATGAGATTCTTTTT          	1	16	1
AAGAAAACCTTTGTCTTCGGACTCACCCA 	2	9	0
AAGACAAAGGTTTTCTTCGGGCTTTTTTCA	2	22	1
TGTAAGCTTCGTTTCTTCTG          	3	0	0
TGTTTGTAAAGTATCTTTTTATAGTGAAGG	3	66	1
GGAAGACTTTTTGTCGTTTTCGTAAAAAAG	3	115	1
TATCTATTAAGAGACTTTTTTACGAAAACG	3	129	0
CGACTTTTAAGAGTCTTTATATAAAGAACG	3	211	1
AACATCCAATTTTTCTTCGTTTCTATTTTG	3	259	0
GTATTTCTTTTAGTCTTCTGTCTCACTAAG	4	176	0
          **********
MAP Score: 7.66961

Motif 5
     TGGGTGAGTCCGAAGACAAAGGTTTT	2	5	1
TAGATTTGGCGAGACTTTAGACCGAATGTGT	3	170	1
ACTGCTTAGTGAGACAGAAGACTAAAAGAAA	4	172	1
ATAGTGAAAAAAGCCCGAAGAAAACCTTTGT	2	25	0
TTTCAATGCAGAGAACGAAGAGAGTCTCAAA	4	50	0
AAAAATTTTGTAGTCTGGAGACGAAAATAGA	4	79	1
TCTTTATATAAAGAACGGAGAAGGGCGTGAA	3	224	1
GTGAGCGGTGAGGACTTGAGATACTAAGATT	4	141	0
AAACGACAAAAAGTCTTCCGAGACTCTTAAA	3	103	0
CGACTTTTAAGAGTCTTTATATAAAGAACGG	3	211	1
CGCCAAATCTAATACCTCAGACTATCTATTA	3	150	0
          ******* ***
MAP Score: 7.53056

Motif 6
CTTTTCTCCCTCTCTCTTTAGAATGATTCATGAA	2	58	1
TGAATTTTATTATTTTTTTAGAATTCGCTTAGAT	2	88	1
CCTAAGTGTATCTGTTTGTAAAGTATCTTTTTAT	3	54	1
GTTTGTAAAGTATCTTTTTATAGTGAAGGACTCT	3	67	1
AGTGAAGGACTCTTGTTTAAGAGTCTCGGAAGAC	3	88	1
TACCTCAGACTATCTATTAAGAGACTTTTTTACG	3	135	0
CTTTTAAGAGTCTTTATATAAAGAACGGAGAAGG	3	214	1
GTCTCAAAAATATTGGTATAAAAATACGAAACAA	4	24	0
CGCCTTACATTATTTTTCTAAAGAGAGCATAACT	4	208	1
          *** * * ** ***
MAP Score: 7.32423

Motif 7
ACAAGTATAAGAGCCTTCTTCCTGAGCCTTCTGCGAAGG	0	86	1
TATGTCTTTTCTCCCTCTCTCTTTAGAATGATTCATGAA	2	53	1
CTGCCTAAGTGTATCTGTTTGTAAAGTATCTTTTTATAG	3	51	1
TATAGTGAAGGACTCTTGTTTAAGAGTCTCGGAAGACTT	3	85	1
TCGTAAAAAAGTCTCTTAATAGATAGTCTGAGGTATTAG	3	134	1
CGCCCTTCTCCGTTCTTTATATAAAGACTCTTAAAAGTC	3	212	0
    TTGGCTCATTCTCTTTGTTTCGTATTTTTATACCA	4	6	1
ATTTTTGAGACTCTCTTCGTTCTCTGCATTGAAAAAATT	4	47	1
TTTTAGTCTTCTGTCTCACTAAGCAGTGTGAGCGGTGAG	4	160	0
          *  ****  *    ** **
MAP Score: 5.6959

Motif 8
TAACTACCCATTTTAAGAATCCAAGGATTTAC	0	15	1
GATTCATGAATTTTATTATTTTTTTAGAATTC	2	82	1
AAGGACTCTTGTTTAAGAGTCTCGGAAGACTT	3	92	1
CTCGGAAGACTTTTTGTCGTTTTCGTAAAAAA	3	112	1
AATAGACGACTTTTAAGAGTCTTTATATAAAG	3	205	1
AACATCCAATTTTTCTTCGTTTCTATTTTGCT	3	257	0
CATTCTCTTTGTTTCGTATTTTTATACCAATA	4	16	1
TTATACCAATATTTTTGAGACTCTCTTCGTTC	4	37	1
CATTGAAAAAATTTTGTAGTCTGGAGACGAAA	4	73	1
TTTTTAACGGTTTTTCTATTTTCGTCTCCAGA	4	92	0
GTAGTATTTCTTTTAGTCTTCTGTCTCACTAA	4	177	0
          ****  ******
MAP Score: 4.61331

Motif 9
TTCTCCCTCTCTCTTTAGAATGATTCATGA	2	61	1
TGTAAAGTATCTTTTTATAGTGAAGGACTC	3	70	1
GTAAAAAAGTCTCTTAATAGATAGTCTGAG	3	136	1
TAATAGACGACTTTTAAGAGTCTTTATATA	3	204	1
CTTCTCCGTTCTTTATATAAAGACTCTTAA	3	217	0
          **********
MAP Score: 0.0611449