AlignACE 3.0 10/20/99
AlignACE2 -i CY/CY_sum_all106_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944235562
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	transposase	300	transposase
#1	transposase	164	transposase
#2	transposase	114	transposase
#3	transposase	79	transposase
#4	transposase	73	transposase
#5	hypothetical	300	hypothetical protein

Motif 1
TTTGAAAAGTAGGGTGAAGAATGGAAAATGGTGAAAAGA	0	250	1
AGAATGGAAAATGGTGAAAAGAATAAAATTTTCACCATA	0	267	1
     TAATTATGGTGAAAATTTTATTCTTTTCACCATT	0	276	0
TTTGAAAAGTAGGGTGAAGAATGGAAAATGGTGAAAAGA	1	114	1
AGAATGGAAAATGGTGAAAAGAATAAAATTTTCACCATA	1	131	1
     TAATTATGGTGAAAATTTTATTCTTTTCACCATT	1	140	0
TTTGAAAAGTAGGGTGAAGAATGGAAAATGGTGAAAAGA	2	64	1
AGAATGGAAAATGGTGAAAAGAATAAAATTTTCACCATA	2	81	1
     TAATTATGGTGAAAATTTTATTCTTTTCACCATT	2	90	0
TTTGAAAAGTAGGGTGAAGAATGGAAAATGGTGAAAAGA	3	29	1
AGAATGGAAAATGGTGAAAAGAATAAAATTTTCACCATA	3	46	1
     TAATTATGGTGAAAATTTTATTCTTTTCACCATT	3	55	0
          * ****** *    *   *
MAP Score: 62.4477

Motif 2
AAGGTTTCACTCGATAATTCCCCCAATTTCCGATCTAG	0	181	1
TTCACCATTTTCCATTCTTCACCCTACTTTTCAAACAC	0	247	0
GTGAAAATTTTATTCTTTTCACCATTTTCCATTCTTCA	0	264	0
GTGAAAAGAATAAAATTTTCACCATAATTA        	0	280	1
TTCACCATTTTCCATTCTTCACCCTACTTTTCAAACAC	1	111	0
GTGAAAATTTTATTCTTTTCACCATTTTCCATTCTTCA	1	128	0
GTGAAAAGAATAAAATTTTCACCATAATTA        	1	144	1
TTCACCATTTTCCATTCTTCACCCTACTTTTCAAACAC	2	61	0
GTGAAAATTTTATTCTTTTCACCATTTTCCATTCTTCA	2	78	0
GTGAAAAGAATAAAATTTTCACCATAATTA        	2	94	1
TTCACCATTTTCCATTCTTCACCCTACTTTTCAAACAC	3	26	0
GTGAAAATTTTATTCTTTTCACCATTTTCCATTCTTCA	3	43	0
GTGAAAAGAATAAAATTTTCACCATAATTA        	3	59	1
          *    * ****** *  *
MAP Score: 60.0862

Motif 3
AAATAGGCTGATTATTATTCCAAAGCTAATGAAAAAT	0	122	1
GTTTCACTCGATAATTCCCCCAATTTCCGATCTAGTC	0	184	1
ACCATTTTCCATTCTTCACCCTACTTTTCAAACACGC	0	245	0
TGAAAATTTTATTCTTTTCACCATTTTCCATTCTTCA	0	264	0
TGAAAAGAATAAAATTTTCACCATAATTA        	0	281	1
AGTCTGACACATACTTTCGACAACGTTAAACAATAAA	1	42	1
ACCATTTTCCATTCTTCACCCTACTTTTCAAACACGC	1	109	0
TGAAAATTTTATTCTTTTCACCATTTTCCATTCTTCA	1	128	0
TGAAAAGAATAAAATTTTCACCATAATTA        	1	145	1
ACCATTTTCCATTCTTCACCCTACTTTTCAAACACGC	2	59	0
TGAAAATTTTATTCTTTTCACCATTTTCCATTCTTCA	2	78	0
TGAAAAGAATAAAATTTTCACCATAATTA        	2	95	1
ACCATTTTCCATTCTTCACCCTACTTTTCAAACACGC	3	24	0
TGAAAATTTTATTCTTTTCACCATTTTCCATTCTTCA	3	43	0
TGAAAAGAATAAAATTTTCACCATAATTA        	3	60	1
CGCCCAGACTAAACTTGGCACAATATCTTTTCGAGCC	5	258	1
          ** ***  *** *   *
MAP Score: 48.8946

Motif 4
AAAGTAGGGTGAAGAATGGAAAATGGTGAA	0	255	1
AAAGTAGGGTGAAGAATGGAAAATGGTGAA	1	119	1
AAAGTAGGGTGAAGAATGGAAAATGGTGAA	2	69	1
AAAGTAGGGTGAAGAATGGAAAATGGTGAA	3	34	1
ATGGCGGAAAGAAGAATGGATCGAGGAACA	5	216	0
          **********
MAP Score: 19.8637

Motif 5
AATGCCTCCTTTTTGCATGGCATAGTAACGATCAGCGT	0	25	1
AAAAGTAGGGTGAAGAATGGAAAATGGTGAAAAGAATA	0	254	1
GAATGGAAAATGGTGAAAAGAATAAAATTTTCACCATA	0	268	1
AAAAGTAGGGTGAAGAATGGAAAATGGTGAAAAGAATA	1	118	1
GAATGGAAAATGGTGAAAAGAATAAAATTTTCACCATA	1	132	1
AAAAGTAGGGTGAAGAATGGAAAATGGTGAAAAGAATA	2	68	1
GAATGGAAAATGGTGAAAAGAATAAAATTTTCACCATA	2	82	1
AAAAGTAGGGTGAAGAATGGAAAATGGTGAAAAGAATA	3	33	1
GAATGGAAAATGGTGAAAAGAATAAAATTTTCACCATA	3	47	1
GGCGATTACCTGATTGATGGCTTAGGTTGTTAGCTTGT	5	143	1
          *** * * ** * *   *
MAP Score: 18.9658

Motif 6
          TTCCCCGGACGCCACAATGCCTC	0	0	1
GCGTTGATCAATCCCTTTATGTTGCTGAATCCC	0	59	1
CACTCGATAATTCCCCCAATTTCCGATCTAGTC	0	188	1
TTTTCCATTCTTCACCCTACTTTTCAAACACGC	0	245	0
TTTTATTCTTTTCACCATTTTCCATTCTTCACC	0	262	0
TTTTCCATTCTTCACCCTACTTTTCAAACACGC	1	109	0
TTTTATTCTTTTCACCATTTTCCATTCTTCACC	1	126	0
TTTTCCATTCTTCACCCTACTTTTCAAACACGC	2	59	0
TTTTATTCTTTTCACCATTTTCCATTCTTCACC	2	76	0
TTTTCCATTCTTCACCCTACTTTTCAAACACGC	3	24	0
TTTTATTCTTTTCACCATTTTCCATTCTTCACC	3	41	0
TGATAAGTTTTGCCCATACCTTCTCCTCATAAC	4	13	1
GGGCCTTGGTTGCCTAAGACTTTCCGCTTGTTC	5	188	1
TATCTTTTCGAGCCCATGGCTTCTCCACG    	5	281	1
          ******   ****
MAP Score: 18.5479

Motif 7
CTAAGAGCGTGTTTGAAAAGTAGGGTGAAGAATGG	0	239	1
TTAAGAGCGTGTTTGAAAAGTAGGGTGAAGAATGG	1	103	1
CTTAGAGCGTGTTTGAAAAGTAGGGTGAAGAATGG	2	53	1
TTTAGAGCGTGTTTGAAAAGTAGGGTGAAGAATGG	3	18	1
TAGGTTGTTAGCTTGTAGAATTGGGGCCTTGGTTG	5	165	1
          * *** * * * ***
MAP Score: 14.6048

Motif 8
GAGCGTGTTTGAAAAGTAGGGTGAAGAATGGAAAATGGT	0	243	1
GGTGAAGAATGGAAAATGGTGAAAAGAATAAAATTTTCA	0	262	1
GTGAAAAGAATAAAATTTTCACCATAATTA         	0	280	1
GAGCGTGTTTGAAAAGTAGGGTGAAGAATGGAAAATGGT	1	107	1
GGTGAAGAATGGAAAATGGTGAAAAGAATAAAATTTTCA	1	126	1
AAAGTAGGGTGAAGAATGGAAAATGGTGAAAAGAATAAA	2	69	1
GTGAAAAGAATAAAATTTTCACCATAATTA         	2	94	1
GAGCGTGTTTGAAAAGTAGGGTGAAGAATGGAAAATGGT	3	22	1
GGTGAAGAATGGAAAATGGTGAAAAGAATAAAATTTTCA	3	41	1
          * *** * *    * ** *
MAP Score: 7.48403