AlignACE 3.0 10/20/99
AlignACE2 -i CT/CT_operons022_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944242803
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	CT039.1	87	hypothetical protein
#1	ruvB	41	Holliday Junction Helicase
#2	CT260	300	hypothetical protein
#3	ruvC	107	Crossover Junction Endonuclease
#4	cutE	63	Apolipoprotein N-Acetyltransferase
#5	yciA	135	Acyl-CoA Thioester Hydrolase
#6	CT538	300	hypothetical protein

Motif 1
TAGGAAAAGACTTTAGTTAGAAAAAAAAGAGATAAAAC	0	42	1
TAAAAGTTTGCTTTCTTTTTTAAAAAAATCTTTGCTAT	2	56	0
          TTTGGATTAGCGAATAAATAACTACTAT	1	0	1
TTTACACAAACTTTTTTTGAAAAAGAAACAGATTAACA	2	109	0
GTTAGGCCTGTTTTGCTTTTTGTAAAAATACTTTTGCA	6	152	1
TTAGTAACCCTTTCCTTTATTGTGTAAAATTTGCACAA	3	42	1
ACATAGAAGTTTTTCATTTGAATTCAAAGTCTTATTGA	6	30	1
CCCTTACTAGCTTACATTCAAGATGAGAGAAAAAGAAT	4	25	0
AGAAAGCAAACTTTTATCTGTATAAAAAGGTTGTTAAT	2	78	1
ACAGAAGTATTTTACTCTGCCGAAAAAACAACACTTAA	2	211	1
AATTTCTTGATTTTCTTCTATATCGAGACTACTATCCA	5	20	1
GTCTTGTCATTTTCTATATTTGTGCAAATTTTACACAA	3	61	0
GGCGGAAAGGCTTCCCTTTAGAAGGAGGCTGGTGATTA	6	223	1
AACTAAAGTCTTTTCCTAGAAATATAGATAACAAACAG	0	22	0
CACAAGCTCATTACGTTTTTCAATAAGACTTTGAATTC	6	49	0
          ***   **   **  ***
MAP Score: 9.69636

Motif 2
AGTTTTATCTCTTTTTTTTCTAACTAAAGTCTTTTCCTAGAAA	0	38	0
TAAAAGTTTGCTTTCTTTTTTAAAAAAATCTTTGCTATACCTC	2	51	0
AGAAAGCAAACTTTTATCTGTATAAAAAGGTTGTTAATCTGTT	2	78	1
GTTGTTAATCTGTTTCTTTTTCAAAAAAAGTTTGTGTAAAGAG	2	107	1
GTTAGTAACCCTTTCCTTTATTGTGTAAAATTTGCACAAATAT	3	41	1
TTCAATAAGACTTTGAATTCAAATGAAAAACTTCTATGTCGAG	6	26	0
GGCACAAGCTCATTACGTTTTTCAATAAGACTTTGAATTCAAA	6	46	0
GTTAGGCCTGTTTTGCTTTTTGTAAAAATACTTTTGCAAGGAA	6	152	1
          * **   ** *     **   **
MAP Score: 7.5178

Motif 3
ATATTTCTAGGAAAAGACTTTAGTTAGAAAA	0	35	1
AAAAAAAAGAGATAAAACTCTCAACACTACA	0	62	1
CGGAGGTATAGCAAAGATTTTTTTAAAAAAG	2	49	1
TTTTTATACAGATAAAAGTTTGCTTTCTTTT	2	75	0
TTTCTTTTTCAAAAAAAGTTTGTGTAAAGAG	2	119	1
GGGGGGGGAGAATAAAAATTTCTTCTTCCTA	2	167	0
        TAGTAAAGCCTTTTGGGAGATTC	3	2	1
TGTCGAGCAAGAAAATCATTTCT        	6	2	0
GAATTCAAATGAAAAACTTCTATGTCGAGCA	6	24	0
TACGTTTTTCAATAAGACTTTGAATTCAAAT	6	45	0
TGCTTTTTGTAAAAATACTTTTGCAAGGAAG	6	165	1
          ******* ***
MAP Score: 7.09525

Motif 4
TGTTTGTTATCTATATTTCTAGGAAAAGACTTTAGTTA	0	23	1
TAGGAAAAGACTTTAGTTAGAAAAAAAAGAGATAAAAC	0	42	1
TAAAAGTTTGCTTTCTTTTTTAAAAAAATCTTTGCTAT	2	56	0
AGAAAGCAAACTTTTATCTGTATAAAAAGGTTGTTAAT	2	78	1
GGTTGTTAATCTGTTTCTTTTTCAAAAAAAGTTTGTGT	2	106	1
AACAGAAGTATTTTACTCTGCCGAAAAAACAACACTTA	2	210	1
CTAGCTTACATTCAAGATGAGAGAAAAAGAATCCCCTT	4	19	0
CAATAAGACTTTGAATTCAAATGAAAAACTTCTATGTC	6	29	0
CGTAATGAGCTTGTGCCTAACGGAAAATCATGATAGCA	6	72	1
GTTAGGCCTGTTTTGCTTTTTGTAAAAATACTTTTGCA	6	152	1
TCTACCTACTCTCACTTCCTTGCAAAAGTATTTTTACA	6	172	0
          ** *  **     *****
MAP Score: 5.93689

Motif 5
TCTAACTAAAGTCTTTTCCTAGAAATATAGATA	0	30	0
AAAGTTTGCTTTCTTTTTTAAAAAAATCTTTGC	2	59	0
CAGATTAACAACCTTTTTATACAGATAAAAGTT	2	86	0
GTTAATCTGTTTCTTTTTCAAAAAAAGTTTGTG	2	110	1
TGTAAAGAGGGTCTATCTCCAAAAGATAGGAAG	2	141	1
   TAGTAAAGCCTTTTGGGAGATTCCTGATTT	3	7	1
CTCGCGTCTTGTCATTTTCTATATTTGTGCAAA	3	71	0
          GCCTTTCTTAACACTCGCGTCTT	3	94	0
AGAAATGATTTTCTTGCTCGACATAGAAGTTTT	6	10	1
TGAATTCAAAGTCTTATTGAAAAACGTAATGAG	6	48	1
AGGCCTGTTTTGCTTTTTGTAAAAATACTTTTG	6	155	1
          ********  * *
MAP Score: 5.7353

Motif 6
AAAGACTTTAGTTAGAAAAAAAAGAGATAAAACTC	0	47	1
GCAAACTTTTATCTGTATAAAAAGGTTGTTAATCT	2	83	1
TTCAAAAAAAGTTTGTGTAAAGAGGGTCTATCTCC	2	126	1
ATCTCCAAAAGATAGGAAGAAGAAATTTTTATTCT	2	155	1
GGAGGGGGGGGGGGGAGAATAAAAATTTCTTCTTC	2	170	0
CCTTTTAATAAGCCGTACTTAGAGGATTCGTACA 	2	276	1
ATGACAAGACGCGAGTGTTAAGAAAGGC       	3	89	1
CTTACATTCAAGATGAGAGAAAAAGAATCCCCTTA	4	18	0
TACAGAGATGACTGGGGAGTAGAGGTGGGCCTGTA	5	59	1
AACGTAATGAGCTTGTGCCTAACGGAAAATCATGA	6	70	1
GCAAGGAAGTGAGAGTAGGTAGAGAACAGGGATAT	6	187	1
GAGAACAGGGATATGGGCGGAAAGGCTTCCCTTTA	6	208	1
TTAGAAGGAGGCTGGTGATTAAAAGAAGAATCAGT	6	240	1
          *   ***  ******
MAP Score: 2.69432

Motif 7
      TTTGGATTAGCGAATAAATAACTACTA	1	4	1
  TTTCCATAGACGGTTGATAAATCAATCGCTT	2	8	1
GGGAGGGGGGGGGGGGAGAATAAAAATTTCTTC	2	173	0
TTACATTCAAGATGAGAGAAAAAGAATCCCCTT	4	19	0
TTACAGAGATGACTGGGGAGTAGAGGTGGGCCT	5	58	1
CTTTTGCAAGGAAGTGAGAGTAGGTAGAGAACA	6	182	1
TTTAGAAGGAGGCTGGTGATTAAAAGAAGAATC	6	239	1
          ** *** ** ***
MAP Score: 2.40399

Motif 8
TTTTTCTAACTAAAGTCTTTTCCTAGAAATATAGATAACAAACAG	0	22	0
TATTCGCAATAGTAGTTATTTATTCGCTAATCCAAA         	1	1	0
TCGGAGGTATAGCAAAGATTTTTTTAAAAAAGAAAGCAAACTTTT	2	48	1
TTAAAAAAGAAAGCAAACTTTTATCTGTATAAAAAGGTTGTTAAT	2	71	1
CCCATCAAACAGAAGTATTTTACTCTGCCGAAAAAACAACACTTA	2	203	1
ATTAAAAGGGAGGCAACTTTTGATACCCAACTATACTTAAGTGTT	2	240	0
TGATTTCGTTAGTAACCCTTTCCTTTATTGTGTAAAATTTGCACA	3	34	1
   TCCTCCAAGGAATTTCTTGATTTTCTTCTATATCGAGACTAC	5	7	1
          AGAAATGATTTTCTTGCTCGACATAGAAGTTTTTC	6	0	1
TGGGGAGGTTAGGCCTGTTTTGCTTTTTGTAAAAATACTTTTGCA	6	145	1
GATTAAAAGAAGAATCAGTTTGCCATTAAGCAACTGAAAAAAGTA	6	256	1
          ** *    *** **        * *
MAP Score: 0.395978