AlignACE 3.0 10/20/99
AlignACE2 -i HI/HI_fusions014_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944236719
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	HI1080	300	amino acid ABC transporter, periplasmic-binding protein
#1	HI1180	126	arginine ABC transporter, ATP-binding protein (artP)
#2	HI1181	206	phosphoheptose isomerase (gmhA)

Motif 1
ATGCATAAAAATGTAATATTTTTTCATCTTATAAAGCATAGA	1	86	1
GTAATCACTTATATTAATTTTTTATAACTAAAATTCATAAAC	0	189	1
GGTTGATTTCAATCAAGTTTTTTAAATCCCAAAATTTCTTGG	1	15	1
CCAACTACTCAAACTTATTTTTTCGATCTAAATCGCAAAAAA	2	71	1
AAGTTTGAGTAGTTGGGGATTTTTCAAGATATGTTTATCTTA	2	45	0
CTAAATAAAAATTCATCTTTTTTCGATGAAATGATGATTTTT	2	108	0
GAGTAGATTGATTGCATTGTTTAGAAACGTATTTTTCTACAA	0	114	1
ATTAGACATTACAAGTTTATTTATAATCTTAAATTTCTATTA	0	29	1
GCCTTTCTTTAGAAAGGCATTTTTTTACTGAAATTTTATAAG	0	73	1
AACCATAAATAAATAATCTTTTTTTTTCATAAGTTTGGTTTT	0	228	1
GCGGTAGATTATTTTCTTATTTTGATAGTAATCACTTATATT	0	162	1
    TTAGATACGCTGCTTTTCTATTAGACATTACAAGTTTA	0	6	1
GTGTTTGTCTAAGCGTGATTATAAAAACCAAACTTATGAAAA	0	251	0
          *        ****  ***  **
MAP Score: 13.4612

Motif 2
TCTAAATCGCAAAAAATCATCATTTCATCG	2	97	1
CAAACTTATGAAAAAAAAAGATTATTTATT	0	235	0
TATCAAAATAAGAAAATAATCTACCGCACT	0	159	0
AATGTCTAATAGAAAAGCAGCGTATCTAA 	0	9	0
AAGTGCTATTAATAAAAAATCCCAAGAAAT	1	48	0
ATTTAGATCGAAAAAATAAGTTTGAGTAGT	2	74	0
GCCTTTCTAAAGAAAGGCATTAATAGAAAT	0	61	0
GCCTTTCTTTAGAAAGGCATTTTTTTACTG	0	73	1
TTATAAGATGAAAAAATATTACATTTTTAT	1	90	0
ATAAACCATAAATAAATAATCTTTTTTTTT	0	225	1
TCGCTAGCCTAAATAAAAATTCATCTTTTT	2	128	0
CATTTCATCGAAAAAAGATGAATTTTTATT	2	117	1
AATTTACGTAAGATAAACATATCTTGAAAA	2	37	1
TTTTTCATCTTATAAAGCATAGAGAAGAAA	1	105	1
TTTTGGGATTTAAAAAACTTGATTGAAATC	1	19	0
GAATTTTAGTTATAAAAAATTAATATAAGT	0	195	0
TTAAGATTATAAATAAACTTGTAATGTCTA	0	31	0
AGAAAGGCATTAATAGAAATTTAAGATTAT	0	51	0
          **********
MAP Score: 12.9398

Motif 3
TTAGATACGCTGCTTTTCTATTAGACATTACAAGTTTATTTA	0	10	1
CATTACAAGTTTATTTATAATCTTAAATTTCTATTAATGCCT	0	35	1
ATTAATGCCTTTCTTTAGAAAGGCATTTTTTTACTGAAATTT	0	67	1
ATTGATTGCATTGTTTAGAAACGTATTTTTCTACAAGAAAGT	0	120	1
TTAGTTATAAAAAATTAATATAAGTGATTACTATCAAAATAA	0	178	0
TATTTATTTATGGTTTATGAATTTTAGTTATAAAAAATTAAT	0	201	0
TCATAAACCATAAATAAATAATCTTTTTTTTTCATAAGTTTG	0	223	1
CCTTGTGTTGTGTTTGTCTAAGCGTGATTATAAAAACCAAAC	0	260	0
   AGTGCGGTTGATTTCAATCAAGTTTTTTAAATCCCAAAA	1	7	1
TTTCTTGGGATTTTTTATTAATAGCACTTGCATAATTATGCA	1	49	1
TGCATAATTATGCATAAAAATGTAATATTTTTTCATCTTATA	1	77	1
TAGTTGGGGATTTTTCAAGATATGTTTATCTTACGTAAATTC	2	36	0
TTCGCTAGCCTAAATAAAAATTCATCTTTTTTCGATGAAATG	2	117	0
          *  ** *  **      ** **
MAP Score: 9.30047

Motif 4
     TTAGATACGCTGCTTTTCTATTAGACA	0	5	1
TTTCTTTAGAAAGGCATTTTTTTACTGAAATT	0	76	1
GGCATTTTTTTACTGAAATTTTATAAGAGTAG	0	88	1
GAGTAGATTGATTGCATTGTTTAGAAACGTAT	0	114	1
ATTGTTTAGAAACGTATTTTTCTACAAGAAAG	0	129	1
AAAGTGCGGTAGATTATTTTCTTATTTTGATA	0	157	1
TAATCACTTATATTAATTTTTTATAACTAAAA	0	190	1
AACCATAAATAAATAATCTTTTTTTTTCATAA	0	228	1
GGTTGATTTCAATCAAGTTTTTTAAATCCCAA	1	15	1
CCAAAATTTCTTGGGATTTTTTATTAATAGCA	1	43	1
ATGCATAAAAATGTAATATTTTTTCATCTTAT	1	86	1
TTTGAGTAGTTGGGGATTTTTCAAGATATGTT	2	52	0
CAACTACTCAAACTTATTTTTTCGATCTAAAT	2	72	1
TTCGATGAAATGATGATTTTTTGCGATTTAGA	2	97	0
CCTAAATAAAAATTCATCTTTTTTCGATGAAA	2	119	0
          ** * *******
MAP Score: 4.91506

Motif 5
    TTAGATACGCTGCTTTTCTATTAGACATTAC	0	6	1
TATTAGACATTACAAGTTTATTTATAATCTTAAAT	0	28	1
TTTATTTATAATCTTAAATTTCTATTAATGCCTTT	0	44	1
TAAATTTCTATTAATGCCTTTCTTTAGAAAGGCAT	0	58	1
GCCTTTCTTTAGAAAGGCATTTTTTTACTGAAATT	0	73	1
AGGCATTTTTTTACTGAAATTTTATAAGAGTAGAT	0	87	1
TAAGAGTAGATTGATTGCATTGTTTAGAAACGTAT	0	111	1
GCATTGTTTAGAAACGTATTTTTCTACAAGAAAGT	0	127	1
AAAGTGCGGTAGATTATTTTCTTATTTTGATAGTA	0	157	1
GTAATCACTTATATTAATTTTTTATAACTAAAATT	0	189	1
TGAAAAAAAAAGATTATTTATTTATGGTTTATGAA	0	222	0
TTTTTTTCATAAGTTTGGTTTTTATAATCACGCTT	0	248	1
TTTCTTCCTTGTGTTGTGTTTGTCTAAGCGTGATT	0	273	0
ATCCCAAAATTTCTTGGGATTTTTTATTAATAGCA	1	40	1
AGATGAAAAAATATTACATTTTTATGCATAATTAT	1	80	0
GGGATTTTTCAAGATATGTTTATCTTACGTAAATT	2	37	0
TTAGATCGAAAAAATAAGTTTGAGTAGTTGGGGAT	2	67	0
TTTCGATGAAATGATGATTTTTTGCGATTTAGATC	2	95	0
TCATCGAAAAAAGATGAATTTTTATTTAGGCTAGC	2	121	1
GAATAAAATCGCGATGGCATTGTATAGCAGATGAA	2	164	0
          * ****  *** * *
MAP Score: 3.16934