AlignACE 3.0 10/20/99
AlignACE2 -i HI/HI_fusions009_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944236537
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	HI1123	80	oligopeptide ABC transporter, permease protein (oppB)
#1	HI1124	295	oligopeptide ABC transporter, periplasmic-binding protein (oppA)
#2	HI1187	89	dipeptide ABC transporter, permease protein (dppB)
#3	HI1188	300	DNA helicase II (uvrD)
#4	HI1638	69	peptide ABC transporter, periplasmic-binding protein (sapA)

Motif 1
GTATTTTTTGACCGCACTTTTCGCCCATTTTGGTTGGAG	0	46	1
ATCTAGGATGTATTGATTTTTCCTATTGTAAATATTTTC	1	90	0
GCCTCTCATATCATCACTTTTAGCAATTTTTTTAGCGAT	1	134	1
AACTCACAAAACTCAATTTTTCTTCAAATAATTTCCTGA	1	184	1
TTAGCTCAAAAATTCATTTTTGTAAAGATTTGTCAGGAA	1	216	0
TCTTTACAAAAATGAATTTTTGAGCTAATAAATAGAAGA	1	227	1
GCTAATAAATAGAAGACTTTTTATAAAAATATCGCCTAA	1	250	1
ATTCAAGAGTATTATATTTTTTACCGATTAATTTCTTTG	2	11	1
AATGCAAGGTTTCTCATTTTTCCAAAAATACCCATGATG	3	48	0
ACTATTTATAAACAAACTTTTAATTCGTTTACCTCTCAT	3	93	0
TATGCTTTGAAAGCTATTTTTATACTATTTATAAACAAA	3	116	0
AAAGTAGGGTAGAACATTTTAAGAATAATATTAAGCGGG	3	190	0
AAAATGTTCTACCCTACTTTTGATATACTCACAAATCTT	3	209	1
          AAACTATCTTTAATCTGTTTAAATTTACA	3	281	0
 TCAATATCCTAGCCATTTTTACTAATATGCCTTACAAT	4	9	1
          *    ******   * * *
MAP Score: 16.4468

Motif 2
CTCGTATTTAAGTGCGGTTAAAAATCGTCGT	0	17	1
ATGGGCGAAAAGTGCGGTCAAAAAATACGAC	0	43	0
TTCTTTGAAGAGTGCGGTGAATTTTTACCGC	2	43	1
AGATAATAAAAGTGCGGTAAAAATTCACCGC	2	56	0
          ******** **
MAP Score: 12.4661

Motif 3
TTTAAGTGCGGTTAAAAATCGTCGTATTTTT	0	23	1
TGAGTTGTGTCTAATAAATCGCTAAAAAAAT	1	159	0
TTAGACACAACTCACAAAACTCAATTTTTCT	1	176	1
AAATAATTTCCTGACAAATCTTTACAAAAAT	1	209	1
AATTTTTGAGCTAATAAATAGAAGACTTTTT	1	241	1
AGGCGATATTTTTATAAAAAGTCTTCTATTT	1	256	0
AAATTAATCGGTAAAAAATATAATACTCTTG	2	14	0
TAAAAGTTTGTTTATAAATAGTATAAAAATA	3	110	1
TTTTGATATACTCACAAATCTTATTGTTTCA	3	226	1
          ** ********
MAP Score: 6.01829

Motif 4
AAAAGTGCGGTCAAAAAATACGACGATTTTTAACCGCACTT	0	26	0
GCCTCTCATATCATCACTTTTAGCAATTTTTTTAGCGATTT	1	134	1
TATTAGACACAACTCACAAAACTCAATTTTTCTTCAAATAA	1	174	1
TCCTGACAAATCTTTACAAAAATGAATTTTTGAGCTAATAA	1	217	1
GCGATATTTTTATAAAAAGTCTTCTATTTATTAGCTCAAAA	1	244	0
TTGAGCCTCCTTGTCATTAGGCGATATTTTTATAAAAAGTC	1	264	0
         AATTCAAGAGTATTATATTTTTTACCGATTAA	2	1	1
TTAATTTCTTTGAAGAGTGCGGTGAATTTTTACCGCACTTT	2	38	1
CTATGCTATTATTGTCATCATGGGTATTTTTGGAAAAATGA	3	33	1
CCCATCTATCTTGTGAAACAATAAGATTTGTGAGTATATCA	3	229	0
          *    * *     * ******
MAP Score: 2.40117

Motif 5
CTCCTTGAATGGACTTGTTTAAATCTAATCAG	1	16	1
CATTAAAAGGGTAATTTATGTAGGAAAATATT	1	67	1
TTTTCCTATTGTAAATATTTTCCTACATAAAT	1	80	0
ATCACTTTTAGCAATTTTTTTAGCGATTTATT	1	146	1
GATTTGTCAGGAAATTATTTGAAGAAAAATTG	1	197	0
GTCATTAGGCGATATTTTTATAAAAAGTCTTC	1	261	0
TCAAGAGTATTATATTTTTTACCGATTAATTT	2	13	1
AATTTTTACCGCACTTTTATTATCTACGAGTG	2	62	1
ACATTCCTATGCTATTATTGTCATCATGGGTA	3	27	1
TGTCATCATGGGTATTTTTGGAAAAATGAGAA	3	45	1
TGCTTTGAAAGCTATTTTTATACTATTTATAA	3	121	0
          * ******* **
MAP Score: 0.0110027