AlignACE 3.0 10/20/99
AlignACE2 -i AP/AP_fusions003_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944248554
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	APE1582	288	363aa long hypothetical oligopeptide transport permease protein
#1	APE2257	173	515aa long hypothetical transport system binding protein
#2	APE2258	126	339aa long hypothetical peptide transport system permease protein
#3	APE2260	300	280aa long hypothetical peptide transport system permease protein

Motif 1
AGAAAAATACCTTTTTGACGATAAGATAGGGGGTTGATAAGCT	0	13	0
TATGCTTGCCCGTCATTATCTCCGGATCGGGTATCGGGGAAGG	0	112	1
AAATATGCCTCTCCCTGAAGACCAGCACGGAGGTTTACACTTG	0	202	0
ATATCTAAGAGGTTTTAATTAGGAGCTAGGCGGGGGGCTAATG	0	254	1
AATATCTCAACTACTATAGTTTAGGCTTGGAGAATAGGCCAAA	1	23	0
AAAGTAAATAGTGCATTATATAAGGCGGGGTTGATCATGAT  	1	142	1
AGTCTGCCGGCGTGAGGGAAAAAGGCTTTGTGGAGGATTTAGG	2	26	0
CGCCTACATACCGGTAAGGTGAGGGCGAGGGGAAAAGTTTGCC	2	73	0
CGGTATGTAGGCGGATGCGCGAAAGAATGGGGA          	2	103	1
GCCTCCAATTCGCTATACTCCTGGGAGGGGCGGTTCTAACTGA	3	78	1
CTGAGGCTACCTTCAGCTGGCCAGGCCTGGGGAGCCTTCTGGT	3	117	1
CAGTATTCTTCGCGTTCATGGTAGGCCTGGTGAGCCTTATCGT	3	204	1
CAACCCCAGGGTTAGGTACTAAAGGTCAGGGGGTGGTTGCCA 	3	268	1
          **          ****  ** **
MAP Score: 18.5831

Motif 2
ACCTTTTTGACGATAAGATAGGGGGTTGATAAGCT	0	13	0
ATTATCTCCGGATCGGGTATCGGGGAAGGCTCTTT	0	126	1
CCGTGCTGGTCTTCAGGGAGAGGCATATTTACCAG	0	215	1
TTTTAATTAGGAGCTAGGCGGGGGGCTAATGG   	0	266	1
AACTACTATAGTTTAGGCTTGGAGAATAGGCCAAA	1	23	0
GCCGCCTAGTCTGCCGGCGTGAGGGAAAAAGGCTT	2	41	0
TACCGGTAAGGTGAGGGCGAGGGGAAAAGTTTGCC	2	73	0
AGGCGGATGCGCGAAAGAATGGGGA          	2	111	1
ATTCGCTATACTCCTGGGAGGGGCGGTTCTAACTG	3	85	1
ACCTTCAGCTGGCCAGGCCTGGGGAGCCTTCTGGT	3	125	1
CCTGGGGAGCCTTCTGGTGGAGAGGATATCCTATA	3	142	1
AGGGACTACAGCACCATACAGGGGGTTACAGTATT	3	176	1
CTATAGTCAACCCCAGGGTTAGGTACTAAAGGTCA	3	261	1
GGGTTAGGTACTAAAGGTCAGGGGGTGGTTGCCA 	3	276	1
          *  * **  ******
MAP Score: 16.0833

Motif 3
CCTTTTTGACGATAAGATAGGGGGTTGATAAGCT	0	13	0
TTAGAAATTAGGGAAGAAAGAGCGGGTTTTGAAG	0	65	0
CCGATCCGGAGATAATGACGGGCAAGCATAGTTA	0	108	0
CCGTGCTGGTCTTCAGGGAGAGGCATATTTACCA	0	215	1
TTTTAATTAGGAGCTAGGCGGGGGGCTAATGG  	0	266	1
GTAAATAGTGCATTATATAAGGCGGGGTTGATCA	1	145	1
TCCCTCACGCCGGCAGACTAGGCGGCAAACTTTT	2	50	1
TACCGGTAAGGTGAGGGCGAGGGGAAAAGTTTGC	2	74	0
GGCGGATGCGCGAAAGAATGGGGA          	2	112	1
CTGTGCACATGCTCAGGATAAGCCTCATACCAAC	3	30	1
ATTCGCTATACTCCTGGGAGGGGCGGTTCTAACT	3	85	1
GGGAGGGGCGGTTCTAACTGAGGCTACCTTCAGC	3	100	1
AGGCTACCTTCAGCTGGCCAGGCCTGGGGAGCCT	3	120	1
CCTGGGGAGCCTTCTGGTGGAGAGGATATCCTAT	3	142	1
GGGACTACAGCACCATACAGGGGGTTACAGTATT	3	177	1
TATTCTTCGCGTTCATGGTAGGCCTGGTGAGCCT	3	207	1
GGGTTAGGTACTAAAGGTCAGGGGGTGGTTGCCA	3	276	1
          *  ****  *****
MAP Score: 11.5492

Motif 4
     AGCAGCTTATCAACCCCCTATCTTATCGTCA	0	5	1
TCTTCACAAACTTCAAAACCCGCTCTTTCTTCCCTA	0	55	1
ACTGGTAAATATGCCTCTCCCTGAAGACCAGCACGG	0	215	0
         CCATTAGCCCCCCGCCTAGCTCCTAAT	0	271	0
TCGTTTTTGGCCTATTCTCCAAGCCTAAACTATAGT	1	18	1
       ATCATGATCAACCCCGCCTTATATAATGC	1	154	0
   GTCTTACCCGATAACCCCTAAATCCTCCACAAA	2	7	1
TCCACAAAGCCTTTTTCCCTCACGCCGGCAGACTAG	2	35	1
AGGCGGCAAACTTTTCCCCTCGCCCTCACCTTACCG	2	69	1
GCACAGCTATCCTAGACTCCCTGAGC          	3	0	0
TCAGTTAGAACCGCCCCTCCCAGGAGTATAGCGAAT	3	85	0
TCTCCACCAGAAGGCTCCCCAGGCCTGGCCAGCTGA	3	129	0
GCGAAGAATACTGTAACCCCCTGTATGGTGCTGTAG	3	181	0
TGTCGACGATAAGGCTCACCAGGCCTACCATGAACG	3	216	0
       TGGCAACCACCCCCTGACCTTTAGTACCT	3	281	0
          * *   ***** * **
MAP Score: 11.1683

Motif 5
ATATTTCTAACTATGCTTGCCCGTCATTATC	0	101	1
AAAGAGCCTTCCCCGATACCCGATCCGGAGA	0	130	0
TTTTGGCCTATTCTCCAAGCCTAAACTATAG	1	22	1
TACCCGATAACCCCTAAATCCTCCACAAAGC	2	14	1
CCCTAAATCCTCCACAAAGCCTTTTTCCCTC	2	25	1
AAAGCCTTTTTCCCTCACGCCGGCAGACTAG	2	40	1
CGGCAAACTTTTCCCCTCGCCCTCACCTTAC	2	72	1
TCCCCTCGCCCTCACCTTACCGGTATGTAGG	2	83	1
TGAGGCTACCTTCAGCTGGCCAGGCCTGGGG	3	118	1
CACCAGAAGGCTCCCCAGGCCTGGCCAGCTG	3	130	0
GACGATAAGGCTCACCAGGCCTACCATGAAC	3	217	0
          ******* ***
MAP Score: 10.0844

Motif 6
CGTCATTATCTCCGGATCGGGTATCGGGGAAG	0	122	1
GGATCGGGTATCGGGGAAGGCTCTTTAGACAT	0	135	1
GTGCTGGTCTTCAGGGAGAGGCATATTTACCA	0	217	1
TAATTAGGAGCTAGGCGGGGGGCTAATGG   	0	269	1
GCCTAGTCTGCCGGCGTGAGGGAAAAAGGCTT	2	41	0
ACCGGTAAGGTGAGGGCGAGGGGAAAAGTTTG	2	75	0
GTGCACATGCTCAGGATAAGCCTCATACCAAC	3	32	1
TTCGCTATACTCCTGGGAGGGGCGGTTCTAAC	3	86	1
CTTCAGCTGGCCAGGCCTGGGGAGCCTTCTGG	3	127	1
TTCTTCGCGTTCATGGTAGGCCTGGTGAGCCT	3	209	1
ATAGTCAACCCCAGGGTTAGGTACTAAAGGTC	3	263	1
GTACTAAAGGTCAGGGGGTGGTTGCCA     	3	283	1
          ******  ****
MAP Score: 9.0934

Motif 7
 AGCAGCTTATCAACCCCCTATCTTATCGTCAAAAAGGTATT	0	9	1
CACAAACTTCAAAACCCGCTCTTTCTTCCCTAATTTCTAACT	0	59	1
TCTAACTATGCTTGCCCGTCATTATCTCCGGATCGGGTATCG	0	106	1
AGAATAGATATTATCCTGCTAGCATGTCTAAAGAGCCTTCCC	0	148	0
TCTTCAAGTGTAAACCTCCGTGCTGGTCTTCAGGGAGAGGCA	0	198	1
      CCATTAGCCCCCCGCCTAGCTCCTAATTAAAACCTC	0	262	0
CTAATCGTTTTTGGCCTATTCTCCAAGCCTAAACTATAGTAG	1	14	1
GTCTTACCCGATAACCCCTAAATCCTCCACAAAGCCTTTTTC	2	10	1
CTTTTTCCCTCACGCCGGCAGACTAGGCGGCAAACTTTTCCC	2	45	1
GGCGGCAAACTTTTCCCCTCGCCCTCACCTTACCGGTATGTA	2	70	1
AAGAATACTGTAACCCCCTGTATGGTGCTGTAGTCCCTATAG	3	172	0
          **  *****   *    *   *
MAP Score: 7.73454

Motif 8
   AGCAGCTTATCAACCCCCTATCTTATCGTCAA	0	7	1
      CCATTAGCCCCCCGCCTAGCTCCTAATTA	0	269	0
AGATATTTTGTAACGCAAGGCTAACGTTTTCACAA	1	59	1
   ATCATGATCAACCCCGCCTTATATAATGCACT	1	151	0
CAAAGCCTTTTTCCCTCACGCCGGCAGACTAGGCG	2	39	1
GCGGCAAACTTTTCCCCTCGCCCTCACCTTACCGG	2	71	1
TAGCCTCAGTTAGAACCGCCCCTCCCAGGAGTATA	3	91	0
CCACCAGAAGGCTCCCCAGGCCTGGCCAGCTGAAG	3	127	0
CGACGATAAGGCTCACCAGGCCTACCATGAACGCG	3	214	0
         TGGCAACCACCCCCTGACCTTTAGTA	3	284	0
          *  **** ****  *
MAP Score: 4.225

Motif 9
AGATATTATCCTGCTAGCATGTCTAAAGAGCC	0	153	0
CCCTGAAGACCAGCACGGAGGTTTACACTTGA	0	201	0
TTTTAATTAGGAGCTAGGCGGGGGGCTAATGG	0	266	1
AGCCTTTTTCCCTCACGCCGGCAGACTAGGCG	2	42	1
TCACGCCGGCAGACTAGGCGGCAAACTTTTCC	2	54	1
CCCTCGCCCTCACCTTACCGGTATGTAGGCGG	2	85	1
ATTCGCTATACTCCTGGGAGGGGCGGTTCTAA	3	85	1
AGGCTACCTTCAGCTGGCCAGGCCTGGGGAGC	3	120	1
CTCCACCAGAAGGCTCCCCAGGCCTGGCCAGC	3	132	0
GGGACTACAGCACCATACAGGGGGTTACAGTA	3	177	1
GTCGACGATAAGGCTCACCAGGCCTACCATGA	3	219	0
          * *** ******
MAP Score: 1.48145

Motif 10
GAGATAATGACGGGCAAGCATAGTTAGAAAT	0	103	0
GATCGGGTATCGGGGAAGGCTCTTTAGACAT	0	136	1
GATATTTTGTAACGCAAGGCTAACGTTTTCA	1	60	1
   GTCTTACCCGATAACCCCTAAATCCTCC	2	7	1
ACATACCGGTAAGGTGAGGGCGAGGGGAAAA	2	80	0
GCACATGCTCAGGATAAGCCTCATACCAACG	3	34	1
AACGATAACTATGATGGGCCTCCAATTCGCT	3	61	1
CGCTATACTCCTGGGAGGGGCGGTTCTAACT	3	88	1
CTACCTTCAGCTGGCCAGGCCTGGGGAGCCT	3	123	1
TATCCTCTCCACCAGAAGGCTCCCCAGGCCT	3	139	0
CTTCGCGTTCATGGTAGGCCTGGTGAGCCTT	3	211	1
GATGATGTCGACGATAAGGCTCACCAGGCCT	3	226	0
          * *********
MAP Score: 1.32563