AlignACE 3.0 10/20/99
AlignACE2 -i CY/CY_fusions022_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944246858
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	hypothetical	163	hypothetical protein
#1	hypothetical	107	hypothetical protein
#2	hypothetical	228	hypothetical protein
#3	hypothetical	73	hypothetical protein
#4	hypothetical	191	hypothetical protein
#5	ycf37	227	ycf37 gene product
#6	hypothetical	124	hypothetical protein

Motif 1
TATCAACACTGGCGGGGTTTGGCCCCGGATTTTTGGCGAT	0	41	0
AATTATTCTAGGCCATGGTTTACCCATCCCCGGGGATTAT	0	78	0
GAATAATTGTCAGTAAGTGTCGCCCCCGTAATCCGTCAAC	0	110	1
AATCCGTCAACAGTGACCGTCACCCCATTTTAGG      	0	139	1
GGTTAAATAGGGTAGGGCCCAACACCTTGGTGGT      	1	4	0
TAAGCTGGGAGACTGTAACGTTCCCCCACGACGGCTCAAA	1	67	1
TCTGGACCGGGGTTAAAACTGACCCCAATAATTGTGCTGG	2	69	0
TCCAGAAAATCGGCGATAATCTCCCCTGGGTCGGTTTTTG	2	103	1
TGGGTTGATCCATTAGCTTTAACCCCATTGTCTCCACTGA	4	66	1
CTCCACTGACGGTAATAGTTTTCCCCACTGCGATTAATTG	4	97	1
GTTTTGTTTGGAGGAGGGACTGCCCCACCGTCAGCCCGCC	4	136	1
GGAGGCTCGTCACAATACATTTCACCGTAGGCTGCTTCTC	5	11	1
CAACATCTTTGGCGATCGCTAACCCCAGAAGCCCATTGTA	5	128	0
CGGGCGACAAAATAGGCAACGGCCCCGACGGCCAACATCT	5	160	0
TTTTGTCGCCCGTTAATTCTTTCACCGAAGTATTAAGTTC	5	188	1
          *** *    *  ****   *
MAP Score: 16.3474

Motif 2
TAAATTACAACCGGCGATCGCCAAAAATCCGGGGCCAAACCC	0	25	1
CGCCAAAAATCCGGGGCCAAACCCCGCCAGTGTTGATAATCC	0	43	1
TTACCCATCCCCGGGGATTATCAACACTGGCGGGGTTTGGCC	0	57	0
AGCACAATTATTGGGGTCAGTTTTAACCCCGGTCCAGAAAAT	2	71	1
ATTTTCTGGACCGGGGTTAAAACTGACCCCAATAATTGTGCT	2	71	0
GTCCAGAAAATCGGCGATAATCTCCCCTGGGTCGGTTTTTGA	2	102	1
GATAATCTCCCCTGGGTCGGTTTTTGACTGGGGAAAGAAGAG	2	117	1
CGGTTTTTGACTGGGGAAAGAAGAGAAACACGGCCTGTGCTA	2	134	1
AGAAACACGGCCTGTGCTAGTATCTAAGGCATGAATTTTCGT	2	157	1
TAACGTTTCTTCGGCGATCGAGAGGGATAGAGAAGCAGCCTA	5	38	0
CAATGGGCTTCTGGGGTTAGCGATCGCCAAAGATGTTGGCCG	5	130	1
GCCAACATCTTTGGCGATCGCTAACCCCAGAAGCCCATTGTA	5	128	0
AAAGAATTAACGGGCGACAAAATAGGCAACGGCCCCGACGGC	5	168	0
ACTTAATACTTCGGTGAAAGAATTAACGGGCGACAAAATAGG	5	184	0
          ******   *      *  * *
MAP Score: 15.7008

Motif 3
GCCCCGGATTTTTGGCGATCGCCGGTTGTAA	0	29	0
ACTGGCGGGGTTTGGCCCCGGATTTTTGGCG	0	43	0
TGTCAGTAAGTGTCGCCCCCGTAATCCGTCA	0	117	1
TATCGCCGATTTTCTGGACCGGGGTTAAAAC	2	90	0
ACAGTCAGTATTTTGCGGCTGGCTAG     	2	212	1
GGGCGGTGCTTTTGTGGGTTGATCCATTAGC	4	52	1
TTAACCCCATTGTCTCCACTGACGGTAATAG	4	84	1
CGGTAATAGTTTTCCCCACTGCGATTAATTG	4	106	1
AATGCAAAACTATGGCGGCGGGCTGACGGTG	4	161	0
TTAACGTTTCTTCGGCGATCGAGAGGGATAG	5	50	0
GGCCAACATCTTTGGCGATCGCTAACCCCAG	5	140	0
CGCCAAAGATGTTGGCCGTCGGGGCCGTTGC	5	154	1
CGTTGCCTATTTTGTCGCCCGTTAATTCTTT	5	179	1
          ******* ***
MAP Score: 12.5878

Motif 4
GGGCCAAACCCCGCCAGTGTTGATAATCCCCGGGGATGGGT	0	56	1
ACAATTATTCTAGGCCATGGTTTACCCATCCCCGGGGATTA	0	79	0
CCTAGAATAATTGTCAGTAAGTGTCGCCCCCGTAATCCGTC	0	106	1
CCCCCGTAATCCGTCAACAGTGACCGTCACCCCATTTTAGG	0	132	1
TTTGGGTAAGCTGGGAGACTGTAACGTTCCCCCACGACGGC	1	61	1
CTAGCACAGGCCGTGTTTCTCTTCTTTCCCCAGTCAAAAAC	2	136	0
ATTGTCTCCACTGACGGTAATAGTTTTCCCCACTGCGATTA	4	92	1
GGCGGGCTGACGGTGGGGCAGTCCCTCCTCCAAACAAAACA	4	135	0
CGTCAGCCCGCCGCCATAGTTTTGCATTTCCACTGCC    	4	164	1
ATACATTTCACCGTAGGCTGCTTCTCTATCCCTCTCGATCG	5	25	1
AGCATTTTCCTAGTGAGATGGAAGCGTAACCACGTACAATG	5	94	1
GCCAAAGATGTTGGCCGTCGGGGCCGTTGCCTATTTTGTCG	5	155	1
GCCTATTTTGTCGCCCGTTAATTCTTTCACCGAAGTATTAA	5	183	1
CAATACTTTTTAGCCTGATCTTGCCTATACCCA        	6	101	1
          * * * *    *  * ** **
MAP Score: 11.8872

Motif 5
GGATTATCAACACTGGCGGGGTTTGGCCCCGGATTTT	0	48	0
ATGGTTTACCCATCCCCGGGGATTATCAACACTGGCG	0	67	0
GACAATTATTCTAGGCCATGGTTTACCCATCCCCGGG	0	84	0
GGGAACGTTACAGTCTCCCAGCTTACCCAAAGCAAAA	1	55	0
ATAATCTCCCCTGGGTCGGTTTTTGACTGGGGAAAGA	2	118	1
TAGATACTAGCACAGGCCGTGTTTCTCTTCTTTCCCC	2	146	0
GTGCTAGTATCTAAGGCATGAATTTTCGTGAAGTTAA	2	170	1
CCCACAAAAGCACCGCCCCATCTTACCTGAATATCGG	4	33	0
ACCGTCAGCCCGCCGCCATAGTTTTGCATTTCCACTG	4	162	1
GCCGTCGGGGCCGTTGCCTATTTTGTCGCCCGTTAAT	5	168	1
AATCCATTTTCTCTTCCTTTGTTTACCGGCTATGTAT	6	60	1
TGCAATACTTTTTAGCCTGATCTTGCCTATACCCA  	6	99	1
          *   *** * ****  *
MAP Score: 11.6636

Motif 6
TCTAAATTACAACCGGCGATCGCCAAAAATCCGG	0	23	1
GTTTACCCATCCCCGGGGATTATCAACACTGGCG	0	67	0
TAAGTGTCGCCCCCGTAATCCGTCAACAGTGACC	0	123	1
CTGTAACGTTCCCCCACGACGGCTCAAAACATTG	1	79	1
TCGATCAAATCACCAAAATCAGTTCCAGCACAAT	2	45	1
GCGATAATCTCCCCTGGGTCGGTTTTTGACTGGG	2	115	1
GGAGGGACTGCCCCACCGTCAGCCCGCCGCCATA	4	148	1
CAATACATTTCACCGTAGGCTGCTTCTCTATCCC	5	23	1
GCTTCTCTATCCCTCTCGATCGCCGAAGAAACGT	5	44	1
TAGGCAACGGCCCCGACGGCCAACATCTTTGGCG	5	154	0
          ****  ** * ***
MAP Score: 8.20406

Motif 7
TAGATACTAGCACAGGCCGTGTTTCTCTTCTTTCCCCAGTC	2	142	0
GGATTATCAACACTGGCGGGGTTTGGCCCCGGATTTTTGGC	0	44	0
TAGGAAAATGCTCTGGCCTAGGTTGTTAACGTTTCTTCGGC	5	65	0
TCTTTGATATCTTTGGCACAGTTCCCAATCCATTTTCTCTT	6	34	1
CGATAATCTCCCCTGGGTCGGTTTTTGACTGGGGAAAGAAG	2	116	1
GTTGATAATCCCCGGGGATGGGTAAACCATGGCCTAGAATA	0	74	1
TTAGGTTTTGCTTTGGGTAAGCTGGGAGACTGTAACGTTCC	1	50	1
AGATGTTGGCCGTCGGGGCCGTTGCCTATTTTGTCGCCCGT	5	160	1
ACCGTCAGCCCGCCGCCATAGTTTTGCATTTCCACTGCC  	4	162	1
AATCCATTTTCTCTTCCTTTGTTTACCGGCTATGTATGTTG	6	60	1
CAGCACAATTATTGGGGTCAGTTTTAACCCCGGTCCAGAAA	2	70	1
CCTGAATATCGGCTTGCTCCGATAATGCCCCTGAG      	4	4	0
          * * ***   ***      **
MAP Score: 7.72073

Motif 8
TGGCCCCGGATTTTTGGCGATCGCCGGTTGTAATTTAGA	0	23	0
AACCCCGCCAGTGTTGATAATCCCCGGGGATGGGTAAAC	0	62	1
AGAATAATTGTCAGTAAGTGTCGCCCCCGTAATCCGTCA	0	109	1
  CCTAAAATGGGGTGACGGTCACTGTTGACGGATTACG	0	136	0
AAGCTGGGAGACTGTAACGTTCCCCCACGACGGCTCAAA	1	68	1
CCAGAAAATCGGCGATAATCTCCCCTGGGTCGGTTTTTG	2	104	1
TCCACTGACGGTAATAGTTTTCCCCACTGCGATTAATTG	4	98	1
GCAGTGGAAATGCAAAACTATGGCGGCGGGCTGACGGTG	4	161	0
GAGGCTCGTCACAATACATTTCACCGTAGGCTGCTTCTC	5	12	1
TGCTTCTCTATCCCTCTCGATCGCCGAAGAAACGTTAAC	5	43	1
ATCTCACTAGGAAAATGCTCTGGCCTAGGTTGTTAACGT	5	74	0
TGGGCTTCTGGGGTTAGCGATCGCCAAAGATGTTGGCCG	5	133	1
TTTGTCGCCCGTTAATTCTTTCACCGAAGTATTAAGTTC	5	189	1
          *   *  ** *****   *
MAP Score: 4.59924

Motif 9
CCCGGATTTTTGGCGATCGCCGGTTGTAATTTA	0	25	0
GATCGCCAAAAATCCGGGGCCAAACCCCGCCAG	0	40	1
GGGGATGGGTAAACCATGGCCTAGAATAATTGT	0	87	1
ACTGTAACGTTCCCCCACGACGGCTCAAAACAT	1	78	1
GGGTCAGTTTTAACCCCGGTCCAGAAAATCGGC	2	84	1
GGCGATAATCTCCCCTGGGTCGGTTTTTGACTG	2	114	1
AGGAGGGACTGCCCCACCGTCAGCCCGCCGCCA	4	147	1
TCTCTATCCCTCTCGATCGCCGAAGAAACGTTA	5	47	1
GAAACGTTAACAACCTAGGCCAGAGCATTTTCC	5	71	1
CTTCTGGGGTTAGCGATCGCCAAAGATGTTGGC	5	137	1
TAGGCAACGGCCCCGACGGCCAACATCTTTGGC	5	155	0
GTGAAAGAATTAACGGGCGACAAAATAGGCAAC	5	180	0
AGTATTGCAACATACATAGCCGGTAAACAAAGG	6	75	0
          ** **  ******
MAP Score: 2.53717

Motif 10
AAATTACAACCGGCGATCGCCAAAAATCCGGGGCCAAACCCC	0	26	1
TACCCATCCCCGGGGATTATCAACACTGGCGGGGTTTGGCCC	0	56	0
TGACGGATTACGGGGGCGACACTTACTGACAATTATTCTAGG	0	106	0
 CCTAAAATGGGGTGACGGTCACTGTTGACGGATTACGGGGG	0	132	0
GTTAAATAGGGTAGGGCCCAACACCTTGGTGGT         	1	1	0
TTTGGGTAAGCTGGGAGACTGTAACGTTCCCCCACGACGGCT	1	61	1
CGTTCCCCCACGACGGCTCAAAACATTGATCG          	1	85	1
TCCAGAAAATCGGCGATAATCTCCCCTGGGTCGGTTTTTGAC	2	103	1
        CTCAGGGGCATTATCGGAGCAAGCCGATATTCAG	4	2	1
AGGTAAGATGGGGCGGTGCTTTTGTGGGTTGATCCATTAGCT	4	42	1
GTTTTCCCCACTGCGATTAATTGTTTTGTTTGGAGGAGGGAC	4	114	1
AAAACTATGGCGGCGGGCTGACGGTGGGGCAGTCCCTCCTCC	4	145	0
GAGAAGCAGCCTACGGTGAAATGTATTGTGACGAGCCTCCA 	5	9	0
GTTAACGTTTCTTCGGCGATCGAGAGGGATAGAGAAGCAGCC	5	40	0
GCAACGGCCCCGACGGCCAACATCTTTGGCGATCGCTAACCC	5	143	0
          *******         **   *
MAP Score: 0.841675