AlignACE 3.0 10/20/99
AlignACE2 -i CT/CT_fusions003_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944241489
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	CT191	146	hypothetical protein
#1	gyrB_2	300	DNA Gyrase Subunit B

Motif 1
  TCAGTTAACTACCCATTTTAAGAATCCAAGGATTTACTA	0	8	1
GCGCTAATACTTTGACTTTTTTAGTTCGCAACAAGTATAAG	0	56	1
AGCCTTCTTCCTGAGCCTTCTGCGAAGGAAGGTGTGCTTGC	0	97	1
CGAAGAGAGTCTCAAAAATATTGGTATAAAAATACGAAACA	1	25	0
TTTTGAGACTCTCTTCGTTCTCTGCATTGAAAAAATTTTGT	1	49	1
TTTTTAACGGTTTTTCTATTTTCGTCTCCAGACTACAAAAT	1	83	0
TTCTGTCTCACTAAGCAGTGTGAGCGGTGAGGACTTGAGAT	1	150	0
GATTCGGGTTCTATAATTTCTGAGAAAACAATCAGCTAATA	1	241	0
          **   * ** *  *    ***
MAP Score: 5.49929

Motif 2
AAGTATAAGAGCCTTCTTCCTGAGCCTTCT	0	88	1
TTCTTCCTGAGCCTTCTGCGAAGGAAGGTG	0	101	1
        AACGCTCCTTCGATATGCGCAA	0	134	0
        TTGGCTCATTCTCTTTGTTTCG	1	2	1
GCGTTTCCACGGCTTAATCTTAGTATCTCA	1	126	1
TCAAACTTTTGCCTTATTCCACACACTCTT	1	280	1
          **********
MAP Score: 5.24803

Motif 3
ATACTTTGACTTTTTTAGTTCGCAACAAGTATA	0	62	1
 TTGGCTCATTCTCTTTGTTTCGTATTTTTATA	1	9	1
TTTTTGAGACTCTCTTCGTTCTCTGCATTGAAA	1	48	1
ATTGAAAAAATTTTGTAGTCTGGAGACGAAAAT	1	74	1
ACGGTTTTTCTATTTTCGTCTCCAGACTACAAA	1	85	0
GCGTAGTATTTCTTTTAGTCTTCTGTCTCACTA	1	178	0
          * **** **** *
MAP Score: 4.8742

Motif 4
TCGCAGAAGGCTCAGGAAGAAGGCTCTTATACT	0	89	0
CCTGAGCCTTCTGCGAAGGAAGGTGTGCTTGCG	0	106	1
GGTGTGCTTGCGCATATCGAAGGAGCGTT    	0	127	1
TTTTTCAATGCAGAGAACGAAGAGAGTCTCAAA	1	50	0
AATAGAAAAACCGTTAAAAAAGGCGTTTCCACG	1	104	1
ACACTGCTTAGTGAGACAGAAGACTAAAAGAAA	1	170	1
    AAGAGTGTGTGGAATAAGGCAAAAGTTTG	1	281	0
          * * ** ******
MAP Score: 3.57861

Motif 5
TAGTAAATCCTTGGATTCTTAAAATGGGTA	0	19	0
CGCTAATACTTTGACTTTTTTAGTTCGCAA	0	57	1
          TTGGCTCATTCTCTTTGTTT	1	0	1
ATACTACGCCTTACATTATTTTTCTAAAGA	1	202	1
AGCATAACTATTAGCTGATTGTTTTCTCAG	1	233	1
AATCAAACTTTTGCCTTATTCCACACACTC	1	278	1
          **********
MAP Score: 2.09696

Motif 6
ATACTTTGACTTTTTTAGTTCGCAACAAGTA	0	62	1
 TTGGCTCATTCTCTTTGTTTCGTATTTTTA	1	9	1
TTTTTGAGACTCTCTTCGTTCTCTGCATTGA	1	48	1
ATTGAAAAAATTTTGTAGTCTGGAGACGAAA	1	74	1
GCGTAGTATTTCTTTTAGTCTTCTGTCTCAC	1	180	0
          ****** ****
MAP Score: 1.7803