AlignACE 3.0 10/20/99
AlignACE2 -i CY/CY_fusions020_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944246768
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	gcp	159	sialoglycoprotease
#1	hypothetical	53	hypothetical protein
#2	rfbB	77	dTDP-glucose 4-6-dehydratase
#3	putA	300	delta-1-pyrroline-5-carboxylate dehydrogenase
#4	hypothetical	300	hypothetical protein
#5	hypothetical	44	hypothetical protein
#6	envD	244	acriflavin resistance protein
#7	gabD	100	succinate-semialdehyde dehydrogenase (NADP+)
#8	fmt	213	methionyl-tRNA formyltransferase

Motif 1
ATCCCCGGATCACGGTAACAGGTTGCGAATCTTGCT	0	62	0
GTTACCGTGATCCGGGGATCGTTAGCCGATAATAGG	0	79	1
AAAAAAACATCCCGGAATTTCTCCGCATTTACCTAC	4	86	0
TAAGGGTTTTCCCGCTTTTCAGTGCCCTGTGAGTTC	4	149	1
TGTGAGTTCTCCCGGGTTTAACTACCTAGCTGAATT	4	176	1
CCTGGACCAACCTGGATACCAACACCTTGGCA    	5	22	1
AAAAAGTGGCTCTGGATTTCCCCCGCCGGTGGGTCT	6	26	1
TTAAAGAAACTCTGGGGATTGGCTCCATTCCCCAGA	6	76	1
ATCTTTGCACTCTGGACATTCCCGCCCCCGGCGATC	6	133	1
ATTCCGTGAGTCCGGTTTACCTTTCCGCCGTCCCCC	6	212	1
CAACTTAAACTCTGGAATTTTCCAGCTTGAGGGGGA	7	63	1
CTTTAACTACCATGGTCTTAATTACCCTTAACAATG	8	153	0
          *****  **   * **
MAP Score: 13.605

Motif 2
ACCTTATTTTCTCAGGGGTAAACAAAGTGAATTGCAC	2	48	1
CCCGGAATTTCTCCGCATTTACCTACGTGTTTCACCA	4	75	0
GGTAGTTAAACCCGGGAGAACTCACAGGGCACTGAAA	4	165	0
TAAAAAGTGGCTCTGGATTTCCCCCGCCGGTGGGTCT	6	25	1
TTTAAATTTGCCCTGCCCTAGACCCACCGGCGGGGGA	6	44	0
TTTAAAGAAACTCTGGGGATTGGCTCCATTCCCCAGA	6	75	1
GATCTTTGCACTCTGGACATTCCCGCCCCCGGCGATC	6	132	1
ACATTCCCGCCCCCGGCGATCGCCATGGGTAGGGGAA	6	148	1
GCAACTTAAACTCTGGAATTTTCCAGCTTGAGGGGGA	7	62	1
GAAACGGCATCTCTGCATTAATCCTTCTAGTGAATTA	8	103	0
          *** **  **  **  *
MAP Score: 12.2992

Motif 3
GCTTATTTATTTAGCCGCCTTTTTAGTCTTT	0	34	0
CGACGGTTTATTAGCCCAGTCTTTCCTATTA	0	108	0
TTTCAATCAATTTGCCCCACTAATTTTTCAG	1	28	0
 CCAAAAATTTTTGCCACACCCAAAAATTGA	3	9	1
AGAGACTAATTTTGCCATTTCATTAGGATGA	3	200	1
TTGGTAAGGTATTCCCAACCCTTCATTGTAC	3	256	0
TTTTTTTCACTTGCCCCCATTCATCGGAATA	4	115	1
ATGTAAGGGTTTTCCCGCTTTTCAGTGCCCT	4	146	1
TGGCTCTGGATTTCCCCCGCCGGTGGGTCTA	6	32	1
TTTCTTTAAATTTGCCCTGCCCTAGACCCAC	6	54	0
CACTCTGGACATTCCCGCCCCCGGCGATCGC	6	140	1
GGGAAAAAAGCTTCCCCTACCCATGGCGATC	6	165	0
GGGAAGCTTTTTTCCCCTGTTGCCGTCAATG	6	180	1
CCGGTTTACCTTTCCGCCGTCCCCCAGGTTT	6	223	1
          ******** **
MAP Score: 12.2964

Motif 4
CAACCTGTTACCGTGATCCGGGGATCGTTAGCC	0	73	1
AGCCGATAATAGGAAAGACTGGGCTAATAAACC	0	102	1
CCTTACCAAACAGATCGCCCAGAAGATAAGCC 	3	278	1
  AATTGGTTGAGTCTGCCAAGGTTTATTGATA	4	8	1
GGTAAATGCGGAGAAATTCCGGGATGTTTTTTT	4	89	1
AGTGCCCTGTGAGTTCTCCCGGGTTTAACTACC	4	169	1
GTTGGTATCCAGGTTGGTCCAGGTTCCAGCAAT	5	12	0
TCAGGGTAAAAAGTGGCTCTGGATTTCCCCCGC	6	19	1
TTTCCCCCGCCGGTGGGTCTAGGGCAGGGCAAA	6	42	1
GGCAAATTTAAAGAAACTCTGGGGATTGGCTCC	6	69	1
CCCATCTTAAAGGTTTTTCTGGGGAATGGAGCC	6	96	0
CGCCGGGGGCGGGAATGTCCAGAGTGCAAAGAT	6	133	0
CCTACCCATGGCGATCGCCGGGGGCGGGAATGT	6	148	0
TCAATGGATTCCGTGAGTCCGGTTTACCTTTCC	6	205	1
TACCTTTCCGCCGTCCCCCAGGTTT        	6	229	1
AATATCTAGAAAGTCTGCCCAGTTCATTACACC	8	188	0
          ****  *** ***
MAP Score: 11.1362

Motif 5
AAAAATTAGTGGGGCAAATTGATTGAAAAA	1	31	1
ATTTTCTCAGGGGTAAACAAAGTGAATTGC	2	53	1
CCGATGAATGGGGGCAAGTGAAAAAAACAT	4	112	0
GCGCTGATCAGGGTAAAAAGTGGCTCTGGA	6	12	1
GTCTAGGGCAGGGCAAATTTAAAGAAACTC	6	58	1
GCGATCGCCGGGGGCGGGAATGTCCAGAGT	6	141	0
GCCATGGGTAGGGGAAGCTTTTTTCCCCTG	6	169	1
 CAAGATTGGGGGCCAGCAACCTAGACTAG	7	9	1
CAATGGCTTTGGGGCAACTTAAACTCTGGA	7	49	1
CCAGCTTGAGGGGGAGGCATTAACCC    	7	84	1
TCCTCAAAAAGGGTAGATTTAGTCCGATGA	8	19	1
AGTACAATTCGGGCCGATAGTTAAGCAAAT	8	71	0
GTAATGAACTGGGCAGACTTTCTAGATATT	8	191	1
          **********
MAP Score: 5.77362

Motif 6
GCAACCTGTTACCGTGATCCGGGGATCGTTAGCCGA	0	72	1
GAAAAGCTGAAAAATTAGTGGGGCAAATTGATTGAA	1	22	1
ACCGTACCTTATTTTCTCAGGGGTAAACAAAGTGAA	2	43	1
TTTTTCGGCAATTTTCATTATGGAAATTTAGCTGTT	3	158	1
TATCTTCTGGGCGATCTGTTTGGTAAGGTATTCCCA	3	270	0
AATACTTTGAAGTTTTTTTTGGGTATGATGGTGAAA	4	47	1
GCTTGAAGCTAGAGTCTTTCGGCAAGCCTTCGTTGT	4	213	1
        GGGCGCTGATCAGGGTAAAAAGTGGCTC	6	2	1
TTCCCCCGCCGGTGGGTCTAGGGCAGGGCAAATTTA	6	43	1
CCCATCTTAAAGGTTTTTCTGGGGAATGGAGCCAAT	6	93	0
CCCGGCGATCGCCATGGGTAGGGGAAGCTTTTTTCC	6	159	1
GGAATCCATTGACGGCAACAGGGGAAAAAAGCTTCC	6	181	0
AAGTGAAGCCAATGGCTTTGGGGCAACTTAAACTCT	7	40	1
ACAATTCTTTACATTGTTAAGGGTAATTAAGACCAT	8	142	1
AGTTAAAGGTGTAATGAACTGGGCAGACTTTCTAGA	8	181	1
          *   *** * *** **
MAP Score: 4.65561

Motif 7
AGAATCGTTTCCTTGGTTAAACAAAAGACT	0	11	1
AATAGGAAAGACTGGGCTAATAAACCGTCG	0	109	1
      CTTGACTTTACTGAAAAGCTGAAA	1	4	1
TAGTGGGGCAAATTGATTGAAAAAAT    	1	37	1
AGTGCAATTCACTTTGTTTACCCCTGAGAA	2	56	0
AACCGACAATCCTTTGTTGACTAAGCTCAA	3	36	0
TTGTCGGTTGATTTGGCTGAAAATTAGTTA	3	57	1
          AATTGGTTGAGTCTGCCAAG	4	0	1
TATCAATAAACCTTGGCAGACTCAACCAAT	4	11	0
CTACGACTGTACTTGGTTGTAATTTGCTTA	8	50	1
ACTTGGTTGTAATTTGCTTAACTATCGGCC	8	60	1
GGTGTAATGAACTGGGCAGACTTTCTAGAT	8	188	1
          **********
MAP Score: 3.6967

Motif 8
         TCGGCTGTGTTCCTTCATACCAGTTAACTGG	2	1	1
CCAGTTAACTGGCAACCGTACCTTATTTTCTCAGGGGTAA	2	29	1
AAAATTGCCGAAAAAGTGAGCTTTTATACCTTAAATAAGA	3	133	0
CCTTCGTTGTGCTAACCGCTGCTTGAATCCTAAATAATTT	4	239	1
GGCGGGGGAAATCCAGAGCCACTTTTTACCCTGATCAGCG	6	13	0
AAATTTAAAGAAACTCTGGGGATTGGCTCCATTCCCCAGA	6	72	1
TGGGATCTTTGCACTCTGGACATTCCCGCCCCCGGCGATC	6	129	1
GATCGCCATGGGTAGGGGAAGCTTTTTTCCCCTGTTGCCG	6	165	1
GATTCCGTGAGTCCGGTTTACCTTTCCGCCGTCCCCCAGG	6	211	1
GTATATCCTCAAAAAGGGTAGATTTAGTCCGATGAACTAC	8	14	1
          *  * * *  ****    **
MAP Score: 3.16647

Motif 9
CGTCGTCTTTTGGATCAAACTCAAACTAGCA	0	134	1
GAAAAATTAGTGGGGCAAATTGATTGAAAAA	1	30	1
AATGAAGGGTTGGGAATACCTTACCAAACAG	3	260	1
TGCTGGAACCTGGACCAACCTGGATACCAAC	5	14	1
CCAATGGCTTTGGGGCAACTTAAACTCTGGA	7	48	1
TGTAATGAACTGGGCAGACTTTCTAGATATT	8	190	1
          **** ******
MAP Score: 1.46235

Motif 10
CGGCTGTGTTCCTTCATACCAGTTAACTGG	2	11	1
GCCAAATCAACCGACAATCCTTTGTTGACT	3	44	0
TTATTGATAACCGTGAATACTTTGAAGTTT	4	32	1
ACGTGTTTCACCATCATACCCAAAAAAAAC	4	58	0
GCACTGAAAAGCGGGAAAACCCTTACATTA	4	144	0
GTAGTTAAACCCGGGAGAACTCACAGGGCA	4	171	0
GCTAACCGCTGCTTGAATCCTAAATAATTT	4	249	1
CCTGGACCAACCTGGATACCAACACCTTGG	5	22	1
TCAATGGATTCCGTGAGTCCGGTTTACCTT	6	205	1
          **********
MAP Score: 1.14968

Motif 11
GAATCGTTTCCTTGGTTAAACAAAAGACTA	0	12	1
CTTATTTTCTCAGGGGTAAACAAAGTGAAT	2	50	1
GTGAGTTCTCCCGGGTTTAACTACCTAGCT	4	177	1
       ATTCGGGACAAAAAGACTCGAAA	4	287	0
GGGCGCTGATCAGGGTAAAAAGTGGCTCTG	6	10	1
GACCCACCGGCGGGGGAAATCCAGAGCCAC	6	31	0
GGGTCTAGGGCAGGGCAAATTTAAAGAAAC	6	56	1
AAAGGTTTTTCTGGGGAATGGAGCCAATCC	6	91	0
TTGACGGCAACAGGGGAAAAAAGCTTCCCC	6	179	0
          **********
MAP Score: 0.219482