AlignACE 3.0 10/20/99
AlignACE2 -i CP/CP_fusions005_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944236941
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	CPn0408	300	CT102 hypothetical protein
#1	CPn0409	60	CT260 hypothetical protein
#2	dnaQ_2	24	DNA Polymerase III Epsilon Chain
#3	uhpC	243	Hexosphosphate Transport
#4	mutS	300	DNA Mismatch Repair

Motif 1
TTGCAGGAATATACATGATTACGGTTTAATCT	0	148	1
TAAAACTATACTTCATTATTACTTGTATGTAG	0	221	1
TTCCTAGAGCCTGCATCATTGCTGGCTGATAA	1	18	0
CACTCTACTAATGCATCTTTACTCTCGCAACC	3	119	1
GGAGTTAAGAATGCTGCATTACGAGCCGGTCC	4	95	0
TAATTGATTACTGCTTTATTACCGTGGCTTTT	4	219	0
ATGTATTGAGCTAATTGATTACTGCTTTATTA	4	230	0
          ** *** *****
MAP Score: 5.75863

Motif 2
CTAGAAGGGTATAAAGGAGTCTGTGAATTACC	0	84	1
CATACAAGTAATAATGAAGTATAGTTTTAGTC	0	218	0
TCAGCCAGCAATGATGCAGGCTCTAGGAACAA	1	21	1
GGTTGCGAGAGTAAAGATGCATTAGTAGAGTG	3	119	0
CCTTGATATGGTAAAGTAGGCTTTTCTTCGCA	3	179	1
GGACCGGCTCGTAATGCAGCATTCTTAACTCC	4	95	1
AGCCACGGTAATAAAGCAGTAATCAATTAGCT	4	222	1
          ****** ** **
MAP Score: 4.58278

Motif 3
CAGACTCCTTTATACCCTTCTAGGGTGTGCT	0	76	0
GGGAGCTCTCTAGACGGTACTTGCAGGAATA	0	128	1
AAGTACAGATTAAACCGTAATCATGTATATT	0	155	0
GATTACGGTTTAATCTGTACTTGGAAATCAT	0	164	1
AGCATCGACTAAAACTATACTTCATTATTAC	0	212	1
GAAATACTAAAACAGCGTATTTTTACTGCTC	3	60	0
AACCAAGAAAAACACTCTACTAATGCATCTT	3	107	1
AAATGCGAAGAAAAGCCTACTTTACCATATC	3	183	0
GGCTCGTTCGAAAACTCTACTTTCTTGTATA	4	170	1
          ** ********
MAP Score: 2.82358

Motif 4
GTACAGATTAAACCGTAATCATGTATATTCCT	0	152	0
   GTGTAAGACCCGCGATCATCTCTATAAAA	0	281	0
ATCTAGTATTATCAGCCAGCAATGATGCAGGC	1	10	1
TAGTCAAAGCAACCGTTAGCAAAAGCCACGGT	4	199	1
ACGGTAATAAAGCAGTAATCAATTAGCTCAAT	4	226	1
          * **** *****
MAP Score: 2.26256

Motif 5
GTACTTGGAAATCATTGTACTATAATTTATATAGCATCGA	0	180	1
TAATTTATATAGCATCGACTAAAACTATACTTCATTATTA	0	202	1
ATTATCAGCCAGCAATGATGCAGGCTCTAGGAACAACTTG	1	17	1
ATTTGAAAGTCTCATCGTGACATAATTAACTTTGGGAGGC	3	17	0
AATTAAAAATAACCAAGAAAAACACTCTACTAATGCATCT	3	97	1
AGGATGAAAAAACAAGGAGGGAATCGTTTCAGGTTGCGAG	3	142	0
CGCATTTCATCTCAGTGAAAAAGATTTTACACATGGAAAT	3	207	1
TTTACAGCATCCCAGGGAAGGATTTACTACCGAGAATTGC	4	15	1
ACGAGCCGGTCCCCTTGAGAAAAGATAAACAGGATGGGAT	4	67	0
          * **  **   *   * ***
MAP Score: 1.88443

Motif 6
GGGAGCTCTCTAGACGGTACTTGCAGGAATAT	0	128	1
GATTACGGTTTAATCTGTACTTGGAAATCATT	0	164	1
AGTATAGTTTTAGTCGATGCTATATAAATTAT	0	201	0
AGCATCGACTAAAACTATACTTCATTATTACT	0	212	1
AACCAAGAAAAACACTCTACTAATGCATCTTT	3	107	1
TATGGTAAAGTAGGCTTTTCTTCGCATTTCAT	3	185	1
CATCCCAGGGAAGGATTTACTACCGAGAATTG	4	22	1
GGCTCGTTCGAAAACTCTACTTTCTTGTATAG	4	170	1
          *** ** *****
MAP Score: 1.85526

Motif 7
TAGATTTACAACTGAGGCTGTCTCTCAGGAA	4	132	1
CTGCTTTATTACCGTGGCTTTTGCTAACGGT	4	210	0
TGATATGGTAAAGTAGGCTTTTCTTCGCATT	3	182	1
GCTTTTGCTAACGGTTGCTTTGACTATACAA	4	194	0
TTGCGAGAGTAAAGATGCATTAGTAGAGTGT	3	118	0
GAAGGGTATAAAGGAGTCTGTGAATTACCCA	0	87	1
GGGAGTTAAGAATGCTGCATTACGAGCCGGT	4	97	0
GGAGCAGTAAAAATACGCTGTTTTAGTATTT	3	59	1
ATCAGCCAGCAATGATGCAGGCTCTAGGAAC	1	20	1
          ** ********
MAP Score: 1.59904