AlignACE 3.0 10/20/99
AlignACE2 -i CP/CP_operons019_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944238122
 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	CPn0622	300	CT503 hypothetical protein
#5	yciA	130	acyl-CoA Thioesterase
#6	dnaQ_2	24	DNA Polymerase III Epsilon Chain

Motif 1
GAGCCCAAGCTCTTGTCTTTCATAGACAAA	1	37	0
TAAGACCCGCGATCATCTCTATAAAATTAT	1	277	0
TCTAGGTTAGGATCATCTTTTAAAGACAAT	3	95	1
ACTTTGAACTTATTGTCTTTAAAAGATGAT	3	106	0
TATGGAAAAAGATCATCTTTAAAGAACACG	4	20	1
TCTCTGAACAGACTGTCTTTTCGTGCTCAG	4	67	1
CAAATAAGTTGCCTGTCTTTTTAAAAGTCA	4	206	1
TGAAATTTTTGATTATTTTTTAGAAATCGA	5	15	0
GAAAATCTATGATTTTCTTTCATAAGTTAC	5	45	0
GAAAATCATAGATTTTCTTTCAGTTGACCG	5	58	1
          **********
MAP Score: 11.2303

Motif 2
CTTTAATTTATCTGTTTTAAGACAAAAGAAATCTAGA	0	56	1
ACGACAGCAGTCTGTCGGTGGATGCAA          	1	0	0
GAGCTTGGGCTCTGTGGAACGAGCACACCCTAGAAGG	1	55	1
TACGGTTTAATCTGTACTTGGAAATCATTGTACTATA	1	167	1
TTATTACTTGTATGTAGTTGGATACAAATCGGGCTAC	1	236	1
TAGTGAATTCTCGGTTTCTAGAAAAAAATTTCCTGCT	3	43	0
GAAAAGACAGTCTGTTCAGAGAAGCCTTCAATTAAAA	4	52	0
AGTTTTTTAATCTGTAGAGTTATCCAAATAAGTTGCC	4	182	1
TGCGATAGTATCGGTCAACTGAAAGAAAATCTATGAT	5	62	0
          *****     ** * **
MAP Score: 8.62925

Motif 3
GGCGAACTATTTTTAAAAACATTTTCCACTG	0	23	0
TAATTTATCTGTTTTAAGACAAAAGAAATCT	0	59	1
TCGATGAGAGTTTCAAAAAAATATAAAATCC	0	246	1
TCGTTTTGTCTATGAAAGACAAGAGCTTGGG	1	33	1
AATTTCCTGCTATTTAAAACAGTCCTGTTTA	3	23	0
GAATTCTCGGTTTCTAGAAAAAAATTTCCTG	3	45	0
TAGGATCATCTTTTAAAGACAATAAGTTCAA	3	102	1
AAAGATCATCTTTAAAGAACACGCCTTTTAA	4	27	1
TAAGTGACTTTTAAAAAGACAGGCAACTTAT	4	209	0
 GCACTTCGATTTCTAAAAAATAATCAAAAA	5	9	1
TTCAGTAACTTATGAAAGAAAATCATAGATT	5	41	1
          *** *******
MAP Score: 8.34544

Motif 4
ATTTATCTGTTTTAAGACAAAAGAAATCTA	0	61	1
CTGCTCTCCTTGATAGAAAGAAGAGGTCCA	0	159	1
CGATGAGAGTTTCAAAAAAATATAAAATCC	0	247	1
TAAAATCCACCTAAAGAAAAAGCGATAGAG	0	269	1
GTTTTGTCTATGAAAGACAAGAGCTTGGGC	1	35	1
AATTCTCGGTTTCTAGAAAAAAATTTCCTG	3	45	0
GGATCATCTTTTAAAGACAATAAGTTCAAA	3	104	1
 TTTCTATCCTTATGGAAAAAGATCATCTT	4	9	1
AAGATCATCTTTAAAGAACACGCCTTTTAA	4	28	1
GCACTTCGATTTCTAAAAAATAATCAAAAA	5	10	1
CAGTAACTTATGAAAGAAAATCATAGATTT	5	43	1
ATCGGTCAACTGAAAGAAAATCTATGATTT	5	60	0
          **********
MAP Score: 7.89515

Motif 5
TTCATTTTATGATTTAAACTTCCTGTGGTGATCTAGAT	0	86	0
AAATGAAAATGATGGAGAGGTTCTAGTGCTCGTACTTT	0	117	1
CGAGATACTATATAGAAGTACACTATGGACCTCTTCTT	0	176	0
TTTTGTCTATGAAAGACAAGAGCTTGGGCTCTGTGGAA	1	36	1
GTCTGTGAATTACCCAAATCATCTAGGGGAGCTCTCTA	1	102	1
ACTATAATTTTATAGAGATGATCGCGGGTCTTACAC  	1	274	1
TCAGATGGTGGAATGGTAGACACTAGGGACTTAAAATC	4	93	1
CTCAGAACAAGACTCGAACTTGCACGGGCCTACGCCCA	4	134	0
CTTTTAAAAAGACAGGCAACTTATTTGGATAACTCTAC	4	195	0
TGACTCTACCGAAAGGATTTTTATAGGGTATTCTTGGT	5	99	0
          **  ** *    ** ***
MAP Score: 2.91596

Motif 6
TTCTCAGTGGAAAATGTTTTTAAAAATAGTTCGC	0	19	1
CTAGATCACCACAGGAAGTTTAAATCATAAAATG	0	88	1
CTTGATAGAAAGAAGAGGTCCATAGTGTACTTCT	0	167	1
GGCGTTATCGATGAGAGTTTCAAAAAAATATAAA	0	239	1
CTTTTTCTTTAGGTGGATTTTATATTTTTTTGAA	0	257	0
TCGGGCTACCACTATAATTTTATAGAGATGATCG	1	264	1
TCTTTTAAAGACAATAAGTTCAAAGTATTTCAGG	3	110	1
AATTCGTCATAAGTGACTTTTAAAAAGACAGGCA	4	215	0
ATGAATGATTAGGTTAATTTTAGAGGTACTCT  	4	278	1
GACTCTACCGAAAGGATTTTTATAGGGTATTCTT	5	102	0
          * * ** ***** *
MAP Score: 2.77334

Motif 7
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	5	91	1
          **** **  ****
MAP Score: 2.66195

Motif 8
GTTTAAATCATAAAATGAAAATGATGGAGAGGTTCTAGT	0	105	1
AAAATCCACCTAAAGAAAAAGCGATAGAGAAGGTTCGTA	0	270	1
GTTTTGTCTATGAAAGACAAGAGCTTGGGCTCTGTGGAA	1	35	1
GGGCTCTGTGGAACGAGCACACCCTAGAAGGGTATAAAG	1	61	1
AGTCTGTGAATTACCCAAATCATCTAGGGGAGCTCTCTA	1	101	1
GGTTTAATCTGTACTTGGAAATCATTGTACTATAATTTA	1	170	1
TACTTCATTATTACTTGTATGTAGTTGGATACAAATCGG	1	229	1
AATGATGCAGGCTCTAGGAACAACTTGGAGTATTTCCTA	2	30	1
CTCAGATGGTGGAATGGTAGACACTAGGGACTTAAAATC	4	92	1
TAGACACTAGGGACTTAAAATCCCTTGGGCGTAGGCCCG	4	109	1
TGACGAATTAGGACAAGAACTCAGTCGTATGCTATACGA	4	240	1
          * **  * *    ** ***
MAP Score: 0.181588