AlignACE 3.0 10/20/99
AlignACE2 -i AP/AP_fusions003_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944248541
 numcols =     	10
 undersample = 	1
 oversample = 	1

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

Motif 1
AGCTTATCAACCCCCTATCTTATCGTCAAAAAGG	0	13	1
AACTTCAAAACCCGCTCTTTCTTCCCTAATTTCT	0	63	1
AAGAGCCTTCCCCGATACCCGATCCGGAGATAAT	0	126	0
TAGATATTATCCTGCTAGCATGTCTAAAGAGCCT	0	152	0
CAAGTGTAAACCTCCGTGCTGGTCTTCAGGGAGA	0	202	1
  CCATTAGCCCCCCGCCTAGCTCCTAATTAAAA	0	266	0
    GTCTTACCCGATAACCCCTAAATCCTCCAC	1	6	1
AAGCCTTTTTCCCTCACGCCGGCAGACTAGGCGG	1	41	1
CAAACTTTTCCCCTCGCCCTCACCTTACCGGTAT	1	75	1
CGCGCATCCGCCTACATACCGGTAAGGTGAGGGC	1	90	0
CTATGATGGGCCTCCAATTCGCTATACTCCTGGG	2	69	1
CCAGAAGGCTCCCCAGGCCTGGCCAGCTGAAGGT	2	125	0
GCCTGGTGAGCCTTATCGTCGACATCATCTACGC	2	228	1
 TGGCAACCACCCCCTGACCTTTAGTACCTAACC	2	277	0
          *** **  *** **
MAP Score: 15.7117

Motif 2
AGCTTATCAACCCCCTATCTTATCGTCAAAAAGGTATTTTTCT	0	13	1
CCCGTCATTATCTCCGGATCGGGTATCGGGGAAGGCTCTTTAG	0	120	1
TAAAGAGCCTTCCCCGATACCCGATCCGGAGATAATGACGGGC	0	119	0
CAAGTGTAAACCTCCGTGCTGGTCTTCAGGGAGAGGCATATTT	0	202	1
CATTAGCCCCCCGCCTAGCTCCTAATTAAAACCTCTTAGATAT	0	254	0
CCTAAATCCTCCACAAAGCCTTTTTCCCTCACGCCGGCAGACT	1	26	1
AAGCCTTTTTCCCTCACGCCGGCAGACTAGGCGGCAAACTTTT	1	41	1
GAAAAGTTTGCCGCCTAGTCTGCCGGCGTGAGGGAAAAAGGCT	1	42	0
GGCAAACTTTTCCCCTCGCCCTCACCTTACCGGTATGTAGGCG	1	73	1
          TCCCCATTCTTTCGCGCATCCGCCTACATACCG	1	103	0
CTATGATGGGCCTCCAATTCGCTATACTCCTGGGAGGGGCGGT	2	69	1
TCAGTTAGAACCGCCCCTCCCAGGAGTATAGCGAATTGGAGGC	2	78	0
ACCAGAAGGCTCCCCAGGCCTGGCCAGCTGAAGGTAGCCTCAG	2	117	0
AATACTGTAACCCCCTGTATGGTGCTGTAGTCCCTATAGGATA	2	168	0
ACGATAAGGCTCACCAGGCCTACCATGAACGCGAAGAATACTG	2	204	0
          ** **  ***      *  *  *
MAP Score: 15.5251

Motif 3
ACCCCTAAATCCTCCACAAAGCCTTTTTCCCTCAC	1	23	1
GATATCCTCTCCACCAGAAGGCTCCCCAGGCCTGG	2	137	0
    TGGCAACCACCCCCTGACCTTTAGTACCTAA	2	279	0
  CCATTAGCCCCCCGCCTAGCTCCTAATTAAAAC	0	265	0
TTTCGCGCATCCGCCTACATACCGGTAAGGTGAGG	1	92	0
AAATATGCCTCTCCCTGAAGACCAGCACGGAGGTT	0	210	0
TCTAAAGAGCCTTCCCCGATACCCGATCCGGAGAT	0	129	0
ACTGAGGCTACCTTCAGCTGGCCAGGCCTGGGGAG	2	116	1
CTATGATGGGCCTCCAATTCGCTATACTCCTGGGA	2	69	1
AATACTGTAACCCCCTGTATGGTGCTGTAGTCCCT	2	176	0
AAACTTTTCCCCTCGCCCTCACCTTACCGGTATGT	1	76	1
TTTTTCCCTCACGCCGGCAGACTAGGCGGCAAACT	1	46	1
       GTCTTACCCGATAACCCCTAAATCCTCC	1	3	1
          ** ** * * *** *
MAP Score: 15.2972

Motif 4
ATCTCCGGATCGGGTATCGGGGAAGGCTCTTT	0	129	1
TGCTGGTCTTCAGGGAGAGGCATATTTACCAG	0	218	1
TAATTAGGAGCTAGGCGGGGGGCTAATGG   	0	269	1
CCTAGTCTGCCGGCGTGAGGGAAAAAGGCTTT	1	40	0
CCGGTAAGGTGAGGGCGAGGGGAAAAGTTTGC	1	74	0
CGCTATACTCCTGGGAGGGGCGGTTCTAACTG	2	88	1
CTTCAGCTGGCCAGGCCTGGGGAGCCTTCTGG	2	127	1
GGGGAGCCTTCTGGTGGAGAGGATATCCTATA	2	145	1
CGCGTTCATGGTAGGCCTGGTGAGCCTTATCG	2	214	1
TAGTCAACCCCAGGGTTAGGTACTAAAGGTCA	2	264	1
GTTAGGTACTAAAGGTCAGGGGGTGGTTGCCA	2	278	1
          * *** ******
MAP Score: 11.661

Motif 5
ATCTCCGGATCGGGTATCGGGGAAGGCTCTTT	0	129	1
TCCCTGAAGACCAGCACGGAGGTTTACACTTG	0	202	0
TGCTGGTCTTCAGGGAGAGGCATATTTACCAG	0	218	1
TAATTAGGAGCTAGGCGGGGGGCTAATGG   	0	269	1
GCCTAGTCTGCCGGCGTGAGGGAAAAAGGCTT	1	41	0
CGGTAAGGTGAGGGCGAGGGGAAAAGTTTGCC	1	73	0
CCTCACCTTACCGGTATGTAGGCGGATGCGCG	1	92	1
CGGATGCGCGAAAGAATGGGGA          	1	114	1
CGCTATACTCCTGGGAGGGGCGGTTCTAACTG	2	88	1
GAAGGCTCCCCAGGCCTGGCCAGCTGAAGGTA	2	124	0
GGGGAGCCTTCTGGTGGAGAGGATATCCTATA	2	145	1
TTAGGTACTAAAGGTCAGGGGGTGGTTGCCA 	2	279	1
          * **** *****
MAP Score: 6.94361

Motif 6
GTCTAAAGAGCCTTCCCCGATACCCGATCCGGA	0	132	0
TCCGTGCTGGTCTTCAGGGAGAGGCATATTTAC	0	214	1
  CCATTAGCCCCCCGCCTAGCTCCTAATTAAA	0	267	0
ACCCCTAAATCCTCCACAAAGCCTTTTTCCCTC	1	23	1
AAGCCTTTTTCCCTCACGCCGGCAGACTAGGCG	1	41	1
CAAACTTTTCCCCTCGCCCTCACCTTACCGGTA	1	75	1
GTTAGAACCGCCCCTCCCAGGAGTATAGCGAAT	2	85	0
ACTGAGGCTACCTTCAGCTGGCCAGGCCTGGGG	2	116	1
TCCACCAGAAGGCTCCCCAGGCCTGGCCAGCTG	2	130	0
CTATAGGATATCCTCTCCACCAGAAGGCTCCCC	2	145	0
TCGACGATAAGGCTCACCAGGCCTACCATGAAC	2	217	0
TAGTACCTAACCCTGGGGTTGACTATAGCGTAG	2	256	0
GGCAACCACCCCCTGACCTTTAGTACCTAACCC	2	276	0
          ***** **  ***
MAP Score: 5.14979

Motif 7
TTCTAACTATGCTTGCCCGTCATTATCTCCGGATCGGGTATCG	0	105	1
GTCTAAAGAGCCTTCCCCGATACCCGATCCGGAGATAATGACG	0	122	0
TAGCCCCCCGCCTAGCTCCTAATTAAAACCTCTTAGATATCCA	0	251	0
CCCGATAACCCCTAAATCCTCCACAAAGCCTTTTTCCCTCACG	1	16	1
AGGCGGCAAACTTTTCCCCTCGCCCTCACCTTACCGGTATGTA	1	69	1
CTCCCCAGGCCTGGCCAGCTGAAGGTAGCCTCAGTTAGAACCG	2	108	0
TATAGGATATCCTCTCCACCAGAAGGCTCCCCAGGCCTGGCCA	2	134	0
GAGAGGATATCCTATAGGGACTACAGCACCATACAGGGGGTTA	2	161	1
TCTTCGCGTTCATGGTAGGCCTGGTGAGCCTTATCGTCGACAT	2	210	1
TCGTCGACATCATCTACGCTATAGTCAACCCCAGGGTTAGGTA	2	243	1
          ***  * **       * **  *
MAP Score: 4.15544

Motif 8
GAGAAAAATACCTTTTTGACGATAAGATAGGGGGTTGATAAGC	0	14	0
TCTAACTATGCTTGCCCGTCATTATCTCCGGATCGGGTATCGG	0	106	1
TCGGGGAAGGCTCTTTAGACATGCTAGCAGGATAATATCTATT	0	145	1
ATATGCCTCTCCCTGAAGACCAGCACGGAGGTTTACACTTGAA	0	200	0
AGGCATATTTACCAGTTGGATATCTAAGAGGTTTTAATTAGGA	0	235	1
TACCCGATAACCCCTAAATCCTCCACAAAGCCTTTTTCCCTCA	1	14	1
AAGCCTTTTTCCCTCACGCCGGCAGACTAGGCGGCAAACTTTT	1	41	1
GCAAACTTTTCCCCTCGCCCTCACCTTACCGGTATGTAGGCGG	1	74	1
AACCGCCCCTCCCAGGAGTATAGCGAATTGGAGGCCCATCATA	2	70	0
ACTGAGGCTACCTTCAGCTGGCCAGGCCTGGGGAGCCTTCTGG	2	116	1
TCCTATAGGGACTACAGCACCATACAGGGGGTTACAGTATTCT	2	170	1
CCACCCCCTGACCTTTAGTACCTAACCCTGGGGTTGACTATAG	2	261	0
          *** *  * *   *     ** *
MAP Score: 3.39361

Motif 9
TTGCCCGTCATTATCTCCGGATCGGGTATCGGGGAA	0	117	1
GAGGTTTTAATTAGGAGCTAGGCGGGGGGCTAATGG	0	262	1
TGCCGCCTAGTCTGCCGGCGTGAGGGAAAAAGGCTT	1	41	0
TACATACCGGTAAGGTGAGGGCGAGGGGAAAAGTTT	1	76	0
CTAGGATAGCTGTGCACATGCTCAGGATAAGCCTCA	2	21	1
TCCAATTCGCTATACTCCTGGGAGGGGCGGTTCTAA	2	81	1
ACTGAGGCTACCTTCAGCTGGCCAGGCCTGGGGAGC	2	116	1
GCCTGGGGAGCCTTCTGGTGGAGAGGATATCCTATA	2	141	1
ACGCTATAGTCAACCCCAGGGTTAGGTACTAAAGGT	2	258	1
          * * * * ***  ***
MAP Score: 2.21355