AlignACE 3.0 10/20/99
AlignACE2 -i CP/CP_operons019_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944238103
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	ruvB	300	Holliday Junction Helicase
#1	CPn0408	300	CT102 hypothetical protein
#2	CPn0409	60	CT260 hypothetical protein
#3	ruvC	142	Crossover Junction Endonuclease
#4	yciA	130	acyl-CoA Thioesterase
#5	dnaQ_2	24	DNA Polymerase III Epsilon Chain

Motif 1
GGCGAACTATTTTTAAAAACATTTTCCACTG	0	23	0
TAATTTATCTGTTTTAAGACAAAAGAAATCT	0	59	1
CCCTGCTCTCCTTGATAGAAAGAAGAGGTCC	0	157	1
ATCGATGAGAGTTTCAAAAAAATATAAAATC	0	245	1
TCGTTTTGTCTATGAAAGACAAGAGCTTGGG	1	33	1
ACCACTATAATTTTATAGAGATGATCGCGGG	1	271	1
AATTTCCTGCTATTTAAAACAGTCCTGTTTA	3	23	0
CAGGAAATTTTTTTCTAGAAACCGAGAATTC	3	45	1
TAGGATCATCTTTTAAAGACAATAAGTTCAA	3	102	1
TTTTTGATTATTTTTTAGAAATCGAAGTGC 	4	9	0
TTCAGTAACTTATGAAAGAAAATCATAGATT	4	41	1
          **** ******
MAP Score: 7.6863

Motif 2
  ACTACCAACTTCTCAGTGGAAAATGTTTTT	0	8	1
TATCGCTTTTTCTTTAGGTGGATTTTATATTT	0	264	0
ACGACAGCAGTCTGTCGGTGGATGCAA     	1	5	0
TACGGTTTAATCTGTACTTGGAAATCATTGTA	1	167	1
TTATTACTTGTATGTAGTTGGATACAAATCGG	1	236	1
TCATAGATTTTCTTTCAGTTGACCGATACTAT	4	63	1
CTATAAAAATCCTTTCGGTAGAGTCAACA   	4	111	1
          *** ** *****
MAP Score: 5.58406

Motif 3
TAGTTCGCCATCTTTAATTTATCTGTTTTA	0	45	1
TCATTTTCATTTTATGATTTAAACTTCCTG	0	99	0
AAATTATAGTACAATGATTTCCAAGTACAG	1	178	0
AAATCATTGTACTATAATTTATATAGCATC	1	188	1
TCGGGCTACCACTATAATTTTATAGAGATG	1	264	1
TCTTTTAAAGACAATAAGTTCAAAGTATTT	3	110	1
TAAAAAATAATCAAAAATTTCAGTAACTTA	4	23	1
TGAAAGAAAATCTATGATTTTCTTTCATAA	4	50	0
          **********
MAP Score: 5.44596

Motif 4
TGTACTATGCCGAGTATAACCGATCGGCGTTAT	0	214	1
CTCTGTGGAACGAGCACACCCTAGAAGGGTATA	1	64	1
TATATTCCTGCAAGTACCGTCTAGAGAGCTCCC	1	128	0
CAATGATTTCCAAGTACAGATTAAACCGTAATC	1	164	0
GGAACAACTTGGAGTATTTCCTAA         	2	46	1
TTCTAGAAACCGAGAATTCACTACTTGAGAAGT	3	57	1
CTATCGCAACCAAGAATACCCTATAAAAATCCT	4	91	1
          **** **  ****
MAP Score: 4.65329

Motif 5
GAGCAGGGCCAAAGTACGAGCACTAGAACCTCTCCA	0	129	0
CCTTGATAGAAAGAAGAGGTCCATAGTGTACTTCTA	0	166	1
         GTACGAACCTTCTCTATCGCTTTTTCT	0	283	0
GGCTCTGTGGAACGAGCACACCCTAGAAGGGTATAA	1	62	1
CCAAATCATCTAGGGGAGCTCTCTAGACGGTACTTG	1	115	1
TTGGATACAAATCGGGCTACCACTATAATTTTATAG	1	253	1
TCAGCCAGCAATGATGCAGGCTCTAGGAACAACTTG	2	21	1
TTTTCTAGAAACCGAGAATTCACTACTTGAGAAGTG	3	55	1
TACTATCGCAACCAAGAATACCCTATAAAAATCCTT	4	89	1
          * ** **   * ****
MAP Score: 4.50539

Motif 6
CCTGCTCTCCTTGATAGAAAGAAGAGGTCC	0	158	1
TAGACGGTACTTGCAGGAATATACATGATT	1	138	1
CTGTTTTAAATAGCAGGAAATTTTTTTCTA	3	32	1
AGGAAATTTTTTTCTAGAAACCGAGAATTC	3	46	1
GTTCAAAGTATTTCAGGAATCGATT     	3	127	1
TCAGTAACTTATGAAAGAAAATCATAGATT	4	42	1
ATAGAGGAAGTAGAAGGAAATT        	5	12	1
          **********
MAP Score: 1.53018