AlignACE 3.0 10/20/99
AlignACE2 -i HI/HI_fusions014_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944236709
 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)

Motif 1
AATCTTTTTTTTTCATAAGTTTGGTTTTTATAATCACGCTTAG	0	242	1
AATCCCAAAATTTCTTGGGATTTTTTATTAATAGCACTTGCAT	1	39	1
TACAAGTTTATTTATAATCTTAAATTTCTATTAATGCCTTTCT	0	38	1
GATTGCATTGTTTAGAAACGTATTTTTCTACAAGAAAGTGCGG	0	123	1
AGAAAGGCATTTTTTTACTGAAATTTTATAAGAGTAGATTGAT	0	83	1
          TTAGATACGCTGCTTTTCTATTAGACATTACAA	0	0	1
         TTTTCTTCTCTATGCTTTATAAGATGAAAAAATA	1	102	0
AGTGCGGTAGATTATTTTCTTATTTTGATAGTAATCACTTATA	0	159	1
TTTATGAATTTTAGTTATAAAAAATTAATATAAGTGATTACTA	0	187	0
AATTTTGGGATTTAAAAAACTTGATTGAAATCAACCGCACT  	1	8	0
    TTTTTCTTCCTTGTGTTGTGTTTGTCTAAGCGTGATTAT	0	271	0
          ***  *    *   **  **  *
MAP Score: 15.6025

Motif 2
ACTTATATTAATTTTTTATAACTAAAATTCA	0	195	1
TTTCTTCTCTATGCTTTATAAGATGAAAAAA	1	104	0
ACATTACAAGTTTATTTATAATCTTAAATTT	0	34	1
GATTGATTGCATTGTTTAGAAACGTATTTTT	0	119	1
ATTTCTTGGGATTTTTTATTAATAGCACTTG	1	48	1
TTATTTATTTATGGTTTATGAATTTTAGTTA	0	213	0
TATTAATGCCTTTCTTTAGAAAGGCATTTTT	0	66	1
TTTTTTACTGAAATTTTATAAGAGTAGATTG	0	93	1
ATAAATAATCTTTTTTTTTCATAAGTTTGGT	0	236	1
GATTTCAATCAAGTTTTTTAAATCCCAAAAT	1	19	1
TAAAAATGTAATATTTTTTCATCTTATAAAG	1	91	1
AAAAAAAAAGATTATTTATTTATGGTTTATG	0	224	0
TTTCATAAGTTTGGTTTTTATAATCACGCTT	0	252	1
          *** *******
MAP Score: 12.5469

Motif 3
ATTACAAGTTTATTTATAATCTTAAATTTCTATTAATGCCTT	0	36	1
TTAATGCCTTTCTTTAGAAAGGCATTTTTTTACTGAAATTTT	0	68	1
TTTTACTGAAATTTTATAAGAGTAGATTGATTGCATTGTTTA	0	95	1
TTGATTGCATTGTTTAGAAACGTATTTTTCTACAAGAAAGTG	0	121	1
CTTATATTAATTTTTTATAACTAAAATTCATAAACCATAAAT	0	196	1
ATAAATAATCTTTTTTTTTCATAAGTTTGGTTTTTATAATCA	0	236	1
TCAATCAAGTTTTTTAAATCCCAAAATTTCTTGGGATTTTTT	1	23	1
TTCTTGGGATTTTTTATTAATAGCACTTGCATAATTATGCAT	1	50	1
          * ***   *    *  **  **
MAP Score: 6.68954

Motif 4
GATACGCTGCTTTTCTATTAGACATTACAAGTTTAT	0	13	1
TTAGAAAGGCATTTTTTTACTGAAATTTTATAAGAG	0	81	1
AGAAACGTATTTTTCTACAAGAAAGTGCGGTAGATT	0	136	1
CGGTAGATTATTTTCTTATTTTGATAGTAATCACTT	0	163	1
ACTTATATTAATTTTTTATAACTAAAATTCATAAAC	0	195	1
AAAAAAAAGATTATTTATTTATGGTTTATGAATTTT	0	218	0
ATAAATAATCTTTTTTTTTCATAAGTTTGGTTTTTA	0	236	1
ATAAGTTTGGTTTTTATAATCACGCTTAGACAAACA	0	256	1
TTCAATCAAGTTTTTTAAATCCCAAAATTTCTTGGG	1	22	1
ATTTCTTGGGATTTTTTATTAATAGCACTTGCATAA	1	48	1
AAAATATTACATTTTTATGCATAATTATGCAAGTGC	1	72	0
AAAATGTAATATTTTTTCATCTTATAAAGCATAGAG	1	93	1
          TTTTCTTCTCTATGCTTTATAAGATG	1	110	0
          ******* *    * *
MAP Score: 4.37293