AlignACE 3.0 10/20/99
AlignACE2 -i CP/CP_fusions004_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944236917
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	CPn0276	263	CT191 hypothetical protein
#1	gyrB_2	300	DNA Gyrase Subunit B

Motif 1
TAAGAATTCCTCTTCGTCTTATTGACTTTT	0	77	1
GTCTTTTCTCTGTTTTTCTTTATGATCAGT	0	170	0
AACTTATGGATCTTAGTCTTGGGAATGTAT	1	165	0
TTGTCCTATCCGCTCTTCTTAAAAATTCAA	1	267	1
AGATCCATAAGTTTCGTCTTAGTACGAAAC	1	182	1
ATATGCGCTGTGTTATTCTTCAGGTAGGAT	0	243	1
AGACCTTTATGTCTCGTCTTTTCTCTGTTT	0	185	0
TTGAGCTTGTCCCTTTTCTTGGCGCAAAAT	1	219	1
TCCCGTGTTTTGTTCTTCCTTGATTAGGAA	1	17	1
TACCCGAACCTCTTTTTCCTAATCAAGGAA	1	32	0
GTCTTATTGACTTTTTTCGTTTCTGTGGAT	0	92	1
          **********
MAP Score: 10.1731

Motif 2
CTCGTCTTTTCTCTGTTTTTCTTTATGATC	0	173	0
TTTGATAAATCTGTGTTTTTGTGATATGCG	0	220	1
ATGTAACGACATGTGTGTTTACTGCTCTCT	0	11	1
 TTGCAGTTCCCGTGTTTTGTTCTTCCTTG	1	9	1
TTTCTTTATGATCAGTTTTTAAATAAAGTT	0	156	0
TTCGGGTAAGATGCGTTTTGAGCTCCTCGG	1	54	1
GTGATATGCGCTGTGTTATTCTTCAGGTAG	0	240	1
TTGATTGCTTATCTATTTTGCGCCAAGAAA	1	233	0
TCTTACCCGAACCTCTTTTTCCTAATCAAG	1	35	0
TATGATAAAAATCCCTTTTAGGGGCTGTAA	0	49	0
          **********
MAP Score: 6.37758

Motif 3
GTCTTATTGACTTTTTTCGTTTCTGTGGATAT	0	92	1
CGTCTTTTCTCTGTTTTTCTTTATGATCAGTT	0	169	0
TTTGATAAATCTGTGTTTTTGTGATATGCGCT	0	220	1
GTGATATGCGCTGTGTTATTCTTCAGGTAGGA	0	240	1
TGCAGTTCCCGTGTTTTGTTCTTCCTTGATTA	1	11	1
CAGTTTAAAGCTGAGTTCATGTAATAGCGATA	1	136	1
          GTGTGATATTTTGTTGAATTTT	1	288	0
          *******  ***
MAP Score: 5.05249

Motif 4
TTATTTAAAAACTGATCATAAAGAAAAACA	0	160	1
CAGAGAAAAGACGAGACATAAAGGTCTCTC	0	188	1
GGAGCTCAAAACGCATCTTACCCGAACCTC	1	50	0
TATTACATGAACTCAGCTTTAAACTGCATA	1	132	0
TCATGTAATAGCGATACATTCCCAAGACTA	1	152	1
TCGTACTAAGACGAAACTTATGGATCTTAG	1	179	0
TCGTCTTAGTACGAAACTTATATGTTGAGC	1	195	1
AAAGGGACAAGCTCAACATATAAGTTTCGT	1	205	0
CCTTTTCTTGGCGCAAAATAGATAAGCAAT	1	230	1
TGTCCTATCCGCTCTTCTTAAAAATTCAAC	1	268	1
          **********
MAP Score: 4.76524

Motif 5
ATGTTAAGAGAGCAGTAAACACACATGTCGTTA	0	14	0
ACATCTTTACAGCCCCTAAAAGGGATTTTTATC	0	43	1
AGAATAACACAGCGCATATCACAAAAACACAGA	0	229	0
TAATCAAGGAAGAACAAAACACGGGAACTGCAA	1	10	0
CTCCCCGAGGAGCTCAAAACGCATCTTACCCGA	1	55	0
AAAAGGGACAAGCTCAACATATAAGTTTCGTAC	1	203	0
CCCTTTTCTTGGCGCAAAATAGATAAGCAATCA	1	229	1
TTTTAAGAAGAGCGGATAGGACAATCTTTTGAT	1	258	0
          *** * *** ***
MAP Score: 0.152998