AlignACE 3.0 10/20/99
AlignACE2 -i CY/CY_fusions016_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944246661
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	transposase	300	transposase
#1	transposase	125	transposase
#2	ycf22	162	hypothetical protein
#3	ABC	22	ABC transporter
#4	hypothetical	231	hypothetical protein
#5	transposase	300	transposase
#6	transposase	300	transposase

Motif 1
AGCCAGTAGCAATTGGTAGAATCCAATCTCC	0	23	1
CCCAAGCAAAAAGTGGGGGAAGAAAACGGAA	0	54	1
CGGAAAACTAATCTGAGGGAAGTGCTTAATG	0	80	1
ATTCTTCGCCATTTGGGAAAATCATGGGGCA	0	153	0
  TGATAATTAAATGGGAAATTTTCCAGCTT	1	8	1
AAGTAGGCATAATTGGGAAAAATGGTGAAGA	1	85	1
TACGACGCTAAGATGGGGGAACCCATTGGCC	2	14	1
CTAGAACCATATCTGGGGGAATTTTCCCTTC	4	198	0
AAAGTTGCTATGCTGGGGAAAGAGAAGGATC	5	32	0
AAGTCGGCATAATTGGGAAAAATGGTGAAGA	5	143	1
ACCGTAATGATACTGAGAGAATTTTACAGCA	5	187	1
AGCCAGTAGCAATTGGTAGAATCCAATCTCC	5	232	1
CCCAAGCAAAAAGTGGGGGAAGAAAACGGAA	5	263	1
CGGAAAACTAATCCGAGGGAA          	5	289	1
AAGTCGGCATAATTGGGAAAAATGGTGAAGA	6	143	1
ACCGTAATGATACTGAGAGAATTTTACAGCA	6	187	1
AGCCAGTAGCAATTGGTAGAATCCAATCTCC	6	232	1
CCCAAGCAAAAAGTGGGGGAAGAAAACGGAA	6	263	1
CGGAAAACTAATCCGAGGGAA          	6	289	1
          ** ********
MAP Score: 44.3839

Motif 2
GTGATAGCCAGTAGCAATTGGTAGAATCCAATCTC	0	18	1
TCTCCCCCAAGCAAAAAGTGGGGGAAGAAAACGGA	0	49	1
CTCTGAGCATGTAAAAAATGGCATTAAGCACTTCC	0	97	0
TTCCCAAATGGCGAAGAATGGTTATTTCCGACAGT	0	165	1
ACGGTACCTGGAAAAAATTGAATCACATCCTCAGA	0	209	1
AGTCCTGATAGAAAAAGCTGGAAAATTTCCCATTT	1	18	0
AGGCATAATTGGGAAAAATGGTGAAGAATATAGAA	1	89	1
ACTCAGAAAAGCAAAAAGTGTTTTATTTGAGCATC	4	136	1
CGGCATAATTGGGAAAAATGGTGAAGAATATAGAA	5	147	1
GTGATAGCCAGTAGCAATTGGTAGAATCCAATCTC	5	227	1
TCTCCCCCAAGCAAAAAGTGGGGGAAGAAAACGGA	5	258	1
CGGCATAATTGGGAAAAATGGTGAAGAATATAGAA	6	147	1
GTGATAGCCAGTAGCAATTGGTAGAATCCAATCTC	6	227	1
TCTCCCCCAAGCAAAAAGTGGGGGAAGAAAACGGA	6	258	1
          * ***** ***   *
MAP Score: 33.5309

Motif 3
TAGAATCCAATCTCCCCCAAGCAAAAAGTG	0	39	1
TTCCGTTTTCTTCCCCCACTTTTTGCTTGG	0	55	0
CTTGACGACTTCTGCCCCATGATTTTCCCA	0	141	1
TGCCCCATGATTTTCCCAAATGGCGAAGAA	0	153	1
TCTTCACCATTTTTCCCAATTATGCCTACT	1	86	0
AATTCTATATTCTTCACCATTTTTCCCAAT	1	96	0
GAATATAGAATTTTCACCATA         	1	114	1
GGGCCAATGGGTTCCCCCATCTTAGCGTCG	2	16	0
TTTTTGAACGTTTCCTCCCGCAAGGAACTC	2	90	1
TCTTCACCATTTTTCCCAATTATGCCGACT	5	144	0
AATTCTATATTCTTCACCATTTTTCCCAAT	5	154	0
TAGAATCCAATCTCCCCCAAGCAAAAAGTG	5	248	1
TTCCGTTTTCTTCCCCCACTTTTTGCTTGG	5	264	0
AGATGGTGCTTCTCCTCCCTGTCGCATATA	6	99	1
TCTTCACCATTTTTCCCAATTATGCCGACT	6	144	0
AATTCTATATTCTTCACCATTTTTCCCAAT	6	154	0
TAGAATCCAATCTCCCCCAAGCAAAAAGTG	6	248	1
TTCCGTTTTCTTCCCCCACTTTTTGCTTGG	6	264	0
          **********
MAP Score: 31.4342

Motif 4
AATTGGTAGAATCCAATCTCCCCCAAGCAAAAAGT	0	33	1
GAAGTGCTTAATGCCATTTTTTACATGCTCAGAGC	0	98	1
TGTCGGAAATAACCATTCTTCGCCATTTGGGAAAA	0	163	0
TGAGGATGTGATTCAATTTTTTCCAGGTACCGTCT	0	207	0
TATGGTGAAAATTCTATATTCTTCACCATTTTTCC	1	100	0
TACTAAAATAATTCGTTCTTTTCCATGCCTAATTC	4	63	0
TACGGTGAAAATTCTATATTCTTCACCATTTTTCC	5	158	0
AATTGGTAGAATCCAATCTCCCCCAAGCAAAAAGT	5	242	1
TACGGTGAAAATTCTATATTCTTCACCATTTTTCC	6	158	0
AATTGGTAGAATCCAATCTCCCCCAAGCAAAAAGT	6	242	1
          ** * ** ***  **
MAP Score: 23.5029

Motif 5
          CGACATCAGTGATAGCCAGTAGCA	0	0	1
TGGTTATTTCCGACAGTGGTAGGAAGACGGTACC	0	183	1
TTTGAAAAGTAGGCATAATTGGGAAAAATGGTGA	1	79	1
CTTTATTTTTCGGCCCTATTGAGACATTGCGT  	2	140	1
AACTTGACCATGTCAAAAGGGAGAGGCGATCGCC	5	89	0
TTTGAAAAGTCGGCATAATTGGGAAAAATGGTGA	5	137	1
TTTACAGCAGCGACATCAGTGATAGCCAGTAGCA	5	209	1
CTCTTATATGCGACAGGGAGGAGAAGCACCATCT	6	99	0
TTTGAAAAGTCGGCATAATTGGGAAAAATGGTGA	6	137	1
TTTACAGCAGCGACATCAGTGATAGCCAGTAGCA	6	209	1
          ** **  * *****
MAP Score: 16.4399

Motif 6
GTGATAGCCAGTAGCAATTGGTAGAATCCAATC	0	18	1
TTGAAAAGTAGGCATAATTGGGAAAAATGGTGA	1	80	1
TTTATTTTTCGGCCCTATTGAGACATTGCGT  	2	141	1
CGGTCCCCCAGGTGGAATTAGGCATGGAAAAGA	4	49	1
TTGAAAAGTCGGCATAATTGGGAAAAATGGTGA	5	138	1
GTGATAGCCAGTAGCAATTGGTAGAATCCAATC	5	227	1
CAAATGCCTCGGATGGATTAGGATCGCCAACAT	6	62	1
TTGAAAAGTCGGCATAATTGGGAAAAATGGTGA	6	138	1
GTGATAGCCAGTAGCAATTGGTAGAATCCAATC	6	227	1
          **   ********
MAP Score: 12.9367

Motif 7
AAGCACTTCCCTCAGATTAGTTTTCCGTTTTCT	0	74	0
TTTTTACATGCTCAGAGCGGGTTGTGCTTGACG	0	115	1
      TTCCCTCGGATTAGTTTTCCGTTTTCT	6	283	0
      TTCCCTCGGATTAGTTTTCCGTTTTCT	5	283	0
TTTTGCTTGGGGGAGATTGGATTCTACCAATTG	0	32	0
TTTTGCTTGGGGGAGATTGGATTCTACCAATTG	6	241	0
TTTTGCTTGGGGGAGATTGGATTCTACCAATTG	5	241	0
GGAAAATTCCCCCAGATATGGTTCTAGATCACT	4	202	1
CGTAATGATACTGAGAGAATTTTACAGCAGCGA	5	189	1
CGTAATGATACTGAGAGAATTTTACAGCAGCGA	6	189	1
AGTCAAATGCCTCGGATGGATTAGGATCGCCAA	6	59	1
ATCACATCCTCAGAAAGAAGATTCGACTTAAGG	0	230	1
TCAAGTTGCCCTAAGAGCGTGTTTGAAAAGTCG	5	116	1
          * ***** ** **
MAP Score: 10.2178

Motif 8
TGGATTCTACCAATTGCTACTGGCTATCAC	0	18	0
CATTCTTCGCCATTTGGGAAAATCATGGGG	0	155	0
   TGATAATTAAATGGGAAATTTTCCAGC	1	7	1
AAAGTAGGCATAATTGGGAAAAATGGTGAA	1	84	1
CGCAATGTCTCAATAGGGCCGAAAAATAAA	2	141	0
TTGACCATGTCAAAAGGGAGAGGCGATCGC	5	90	0
AAAGTCGGCATAATTGGGAAAAATGGTGAA	5	142	1
TGGATTCTACCAATTGCTACTGGCTATCAC	5	227	0
AACACGCTCTTATATGCGACAGGGAGGAGA	6	109	0
AAAGTCGGCATAATTGGGAAAAATGGTGAA	6	142	1
TGGATTCTACCAATTGCTACTGGCTATCAC	6	227	0
          **********
MAP Score: 7.79543

Motif 9
TCCCCCACTTTTTGCTTGGGGGAGATTGGAT	0	43	0
CATTAAGCACTTCCCTCAGATTAGTTTTCCG	0	80	0
TGATTCAATTTTTTCCAGGTACCGTCTTCCT	0	203	0
GGCCAATGGGTTCCCCCATCTTAGCGTCGTA	2	14	0
TTTTGAACGTTTCCTCCCGCAAGGAACTCCT	2	91	1
AATAAAGCGATTCGCCTAGGGGGCAAGGAGT	2	116	0
AAAAAGTCCCTTCCCTGGGCTTT        	4	2	0
CATTATAGCGGTCCCCCAGGTGGAATTAGGC	4	41	1
CACTTTTTGCTTTTCTGAGTTAAATTTAGCC	4	125	0
GAAGGGAAAATTCCCCCAGATATGGTTCTAG	4	198	1
CTAATCATTGCCCTCACAGGATCCTTCTCTT	5	13	1
GATCCTTCTCTTTCCCCAGCATAGCAACTTT	5	32	1
TGCTGTAAAATTCTCTCAGTATCATTACGGT	5	187	0
TCCCCCACTTTTTGCTTGGGGGAGATTGGAT	5	252	0
          TTCCCTCGGATTAGTTTTCCG	5	289	0
GAATATAGAATTTTCACCGTAATGATACTGA	6	172	1
TGCTGTAAAATTCTCTCAGTATCATTACGGT	6	187	0
TCCCCCACTTTTTGCTTGGGGGAGATTGGAT	6	252	0
          TTCCCTCGGATTAGTTTTCCG	6	289	0
          ********* *
MAP Score: 1.88684