AlignACE 3.0 10/20/99
AlignACE2 -i HI/HI_fusions008_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944236471
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	HI0408	171	ABC transporter, ATP-binding protein (yebM)
#1	HI0501	167	high affinity ribose transport protein (rbsD)
#2	HI1019	300	thiamin ABC transporter, periplasmic-binding protein (tbpA)
#3	HI1157	71	ATP-binding protein protein (cydD)
#4	HI1158	73	thioredoxin reductase (trxB)
#5	HI1159	284	conserved hypothetical protein
#6	HI1300	300	ABC transporter, ATP-binding protein

Motif 1
GATAAAAGGAAAATCAGCCATGTTTTATCCTTGTGA	5	74	0
ATGCTAACAGAAATGTTCCAAATTTTTGAATCTGAT	6	46	1
          AAAATCGCCGTGTTTTCAACAATGGT	0	155	0
AACGTTTCTAAAATCTTCCGCACTTTGCTAAAATCA	5	25	1
CACTTTGCTAAAATCAGCCATTATTTTTTTCACAAG	5	45	1
TGATTATAGAAAAAGTTCCCCTCTTTAAAAGAGTTA	3	34	0
TAGTGCCAAAAAATCCGCCGATTCTTTATGCGTTGG	5	189	0
ATATAATCGCAAATAATCCGCTTCTTCCTTTCTTCA	6	132	0
AATTCAGTGAAAATTAACCGCACTATTCTATACGGT	6	260	0
        CTAAAAGCTCCTTTTTGTTATCGAAACG	1	149	0
TTCCAAGAATAAATTGTCCTTGATATTGTTCTGCAA	5	235	0
          AAAGAATCCTTGTTTGTAGTTAAGTA	4	57	0
AGAATTCTATAAAAATGCGTTATTTTCCCCAACCAT	0	124	1
ATTTTGTGATCAATATCCCAAATTTGAAATTTCTTA	1	71	1
GGTTTGCATAAAAAATCCCATCAATTCGATGGGATT	6	227	0
ATCTTCTAACCAATTCCCCTCTTTTAACTCTTTTAA	3	10	1
          ****   **   ****
MAP Score: 17.3616

Motif 2
GGAAAAAGCATTATTCAAACGCTTAAATATTCGACATAAGA	0	71	1
TGCCAACGGCTTTTTAAAAAGAAATAAACTTTCTACATTTT	2	104	0
          TAATAGAAATGGTAAAACGTTTCTAAAATCT	5	0	1
GCAGCAATAATGACGAAAAGGAGATAAGGTTATATTCCTAG	2	242	0
CAGAGAATGCTAACAGAAATGTTCCAAATTTTTGAATCTGA	6	40	1
ATCACAAAATTTCTAGATAGGATAAAAAATTCTCCGACCAA	1	40	0
GAATAATGCTTTTTCCATAGGAATGAATTTTCTTTATAATC	0	46	0
AATAACGCATTTTTATAGAATTCTCAAGATTTTCTCTCTTA	0	107	0
CTCTTTTAACTCTTTTAAAGAGGGGAACTTTTTCTATAATC	3	28	1
GTAGTCTGAATGCTGAAAACTTTTTTATTTTAGGG      	0	4	0
GCTTTCTAGTGTATTAAAATTTACTAAGATTGCCAACGGCT	2	134	0
AATGGCTGATTTTAGCAAAGTGCGGAAGATTTTAGAAACGT	5	26	0
       ATTTTGTATAGATTTCTTTAATTTACAATGAGTT	2	3	1
CCCCAACCATTGTTGAAAACACGGCGATTTT          	0	150	1
          *  *  *** *    **  **
MAP Score: 9.89892

Motif 3
AATAAAAAAGTTTTCAGCATTCAGACTACAGATTATAAA	0	16	1
ATTTTCTCTCTTATGTCGAATATTTAAGCGTTTGAATAA	0	81	0
AATAACGCATTTTTATAGAATTCTCAAGATTTTCTCTCT	0	109	0
AATCGCCGTGTTTTCAACAATGGTTGGGGAAAATAACGC	0	140	0
TTACAATGAGTTATCTTCATTTTTATAGACTAGTGCACT	2	32	1
AGTTTATTTCTTTTTAAAAAGCCGTTGGCAATCTTAGTA	2	115	1
CCTTATCTCCTTTTCGTCATTATTGCTGCCTTTTAATCA	2	254	1
TATTGCTGCCTTTTAATCATAAATAAGGATGTAATA   	2	274	1
        TGTTTTGGTCGTGATTATAGAAAAAGTTCCC	3	50	0
AGCCATTATTTTTTTCACAAGGATAAAACATGGCTGATT	5	60	1
TTCAGTAAGATTTTGTTCGTTGATCTCAACGATAAAAGG	5	101	0
GACAAGTGGTTTTTCCTAAGGATTGTTGCAGTATTTCAG	5	135	0
GAAAAACCACTTGTCATCAATTTTTACGCGCCAACGCAT	5	159	1
ATCGGCGGATTTTTTGGCACTACTTGAGCAAGTTGCAGA	5	203	1
AAGAAGCGGATTATTTGCGATTATATTGCAGGTATGTCG	6	142	1
          ****   ** *  *   **
MAP Score: 8.1103

Motif 4
AGATTATAAAGAAAATTCATTCCTATGGAAA	0	45	1
CATTCCTATGGAAAAAGCATTATTCAAACGC	0	62	1
AGAATTCTATAAAAATGCGTTATTTTCCCCA	0	124	1
AACAAAAATAGAAAAACAACTAAGAAATTTC	1	96	0
TTTCGATAACAAAAAGGAGCTTTTAG     	1	151	1
ATTTCTTTTTAAAAAGCCGTTGGCAATCTTA	2	120	1
CAATAATGACGAAAAGGAGATAAGGTTATAT	2	248	0
CGCACTTTGCTAAAATCAGCCATTATTTTTT	5	43	1
ACGATAAAAGGAAAATCAGCCATGTTTTATC	5	81	0
CAATCCTTAGGAAAAACCACTTGTCATCAAT	5	149	1
AGTAGTGCCAAAAAATCCGCCGATTCTTTAT	5	196	0
TTTATTCTTGGAAAAGTAAATTGTGAAAAAG	5	258	1
AGTAAATTGTGAAAAAGAGCGA         	5	272	1
TATAATCGCAAATAATCCGCTTCTTCCTTTC	6	136	0
AAAATTCAGTGAAAATTAACCGCACTATTCT	6	267	0
          ***** *****
MAP Score: 7.72724

Motif 5
TCGTCATTATTGCTGCCTTTTAATCATAAAT	2	267	1
AACATGGCTGATTTTCCTTTTATCGTTGAGA	5	86	1
AATAATCCGCTTCTTCCTTTCTTCAGGGGCA	6	126	0
     CTAAAAGCTCCTTTTTGTTATCGAAA	1	151	0
ACAATGAGTTATCTTCATTTTTATAGACTAG	2	34	1
GAAATAAACTTTCTACATTTTCTGAAAAAAT	2	94	0
ATATAACCTTATCTCCTTTTCGTCATTATTG	2	248	1
CTTTTTCACAATTTACTTTTCCAAGAATAAA	5	258	0
TAATGCAATAAGTTGCATTTTACTGATTATA	4	20	0
TTTAGAAACGTTTTACCATTTCTATTA    	5	6	0
TTCTTAGTTGTTTTTCTATTTTTGTTATCTA	1	101	1
GTAGAAAGTTTATTTCTTTTTAAAAAGCCGT	2	109	1
ATAGGAATGAATTTTCTTTATAATCTGTAGT	0	40	0
          **** ******
MAP Score: 7.43096

Motif 6
TAAAATAAAAAAGTTTTCAGCATTCAGACTACAG	0	13	1
CGTTTGAATAATGCTTTTTCCATAGGAATGAATT	0	58	0
TCTTATGTCGAATATTTAAGCGTTTGAATAATGC	0	78	0
AAAATAACGCATTTTTATAGAATTCTCAAGATTT	0	116	0
GTTTTCAACAATGGTTGGGGAAAATAACGCATTT	0	136	0
TGGTCGGAGAATTTTTTATCCTATCTAGAAATTT	1	41	1
AGTTATCTTCATTTTTATAGACTAGTGCACTTGC	2	40	1
CAGCCCCTTTATTTTTTCAGAAAATGTAGAAAGT	2	84	1
GTTCACGGGTATGATCTCAGCGTATTGCACCCCG	2	180	0
CCTTTTCGTCATTATTGCTGCCTTTTAATCATAA	2	262	1
 TATTACATCCTTATTTATGATTAAAAGGCAGCA	2	277	0
AAAATAATGGCTGATTTTAGCAAAGTGCGGAAGA	5	38	0
AAATCCGCCGATTCTTTATGCGTTGGCGCGTAAA	5	181	0
GAATCGGCGGATTTTTTGGCACTACTTGAGCAAG	5	201	1
TTCTGTTAGCATTCTCTGCCCTTTATATTCGATT	6	24	0
GAAGAAGCGGATTATTTGCGATTATATTGCAGGT	6	141	1
AATTGATGGGATTTTTTATGCAAACCGTATAGAA	6	237	1
AGTGCGGTTAATTTTCACTGAATTTTTATGGGGC	6	272	1
          *** ***  ** **
MAP Score: 7.32904

Motif 7
AGAAAATTCATTCCTATGGAAAAAGCATTATTCAAACGCTTA	0	54	1
TCAACAATGGTTGGGGAAAATAACGCATTTTTATAGAATTCT	0	124	0
TCTAGAAATTTTGTGATCAATATCCCAAATTTGAAATTTCTT	1	64	1
ATCGAAACGTTTCGATAACAAAAAGGAGCTTTTAG       	1	142	1
TACATCCTTATTTATGATTAAAAGGCAGCAATAATGACGAAA	2	265	0
CAAAAAGTTTATAATCAGTAAAATGCAACTTATTGCATTATA	4	11	1
ATATTATTACTTAACTACAAACAAGGATTCTTT         	4	50	1
TCTTCCGCACTTTGCTAAAATCAGCCATTATTTTTTTCACAA	5	38	1
CATTATTTTTTTCACAAGGATAAAACATGGCTGATTTTCCTT	5	63	1
TACTGCAACAATCCTTAGGAAAAACCACTTGTCATCAATTTT	5	141	1
AAGCGGATTATTTGCGATTATATTGCAGGTATGTCGGATGCA	6	145	1
TCTATACGGTTTGCATAAAAAATCCCATCAATTCGATGGGAT	6	228	0
          **    *  * ** ***    *
MAP Score: 6.66593

Motif 8
      CCCTAAAATAAAAAAGTTTTCAGCAT	0	4	1
AAAATTTCTAGATAGGATAAAAAATTCTCCGA	1	44	0
ATAGATAACAAAAATAGAAAAACAACTAAGAA	1	101	0
ATTTTTTCAGAAAATGTAGAAAGTTTATTTCT	2	94	1
CGGCTTTTTAAAAAGAAATAAACTTTCTACAT	2	107	0
ATTTATGATTAAAAGGCAGCAATAATGACGAA	2	266	0
TCCCCTCTTTAAAAGAGTTAAAAGAGGGGAAT	3	22	0
GTTAAGTAATAATATAATGCAATAAGTTGCAT	4	33	0
     TAATAGAAATGGTAAAACGTTTCTAAA	5	5	1
AAATCTTACTGAAATACTGCAACAATCCTTAG	5	127	1
AATGCTAACAGAAATGTTCCAAATTTTTGAAT	6	45	1
TTATTACCTCGAAATACTGCAAATCGTTGGCG	6	91	1
TGCCCCTGAAGAAAGGAAGAAGCGGATTATTT	6	126	1
          ****** * ***
MAP Score: 6.40195

Motif 9
GTCGAATATTTAAGCGTTTGAATAATGCTTTTTCCATA	0	68	0
AGTTATCTTCATTTTTATAGACTAGTGCACTTGCTAAT	2	40	1
GTTCACGGGTATGATCTCAGCGTATTGCACCCCGACTA	2	176	0
TTATAATCAGTAAAATGCAACTTATTGCATTATATTAT	4	19	1
AACGAACAAAATCTTACTGAAATACTGCAACAATCCTT	5	119	1
ATTGTTCTGCAACTTGCTCAAGTAGTGCCAAAAAATCC	5	209	0
CAGAGCGTTTATTACCTCGAAATACTGCAAATCGTTGG	6	83	1
GAAATACTGCAAATCGTTGGCGTAATGCCCCTGAAGAA	6	101	1
TTTTTATGCAAACCGTATAGAATAGTGCGGTTAATTTT	6	249	1
          **     * ** ** ***
MAP Score: 6.17169

Motif 10
AATAATGCTTTTTCCATAGGAATGAATTTTCTT	0	53	0
CCAAATTTACATTCAATCGGAATCGGAGAATAA	1	11	0
TGTTGCAGTATTTCAGTAAGATTTTGTTCGTTG	5	118	0
ACAAGTGGTTTTTCCTAAGGATTGTTGCAGTAT	5	140	0
GTGTATTAAAATTTACTAAGATTGCCAACGGCT	2	134	0
TATCGAAACGTTTCGATAAGACAAATATAGATA	1	126	0
CCATTATTTTTTTCACAAGGATAAAACATGGCT	5	62	1
TTGAATGTAAATTTGGTCGGAGAATTTTTTATC	1	28	1
AATCCCATCAATTCGATGGGATTCTCTCTTAAA	6	217	0
CAGCCCCTTTATTTTTTCAGAAAATGTAGAAAG	2	84	1
GCCAACGGCTTTTTAAAAAGAAATAAACTTTCT	2	111	0
GATTTCTTTAATTTACAATGAGTTATCTTCATT	2	20	1
AAAATAACGCATTTTTATAGAATTCTCAAGATT	0	117	0
AGTTATCTTCATTTTTATAGACTAGTGCACTTG	2	40	1
AGTGCGGTTAATTTTCACTGAATTTTTATGGGG	6	272	1
         ATTTTGTATAGATTTCTTTAATTT	2	1	1
CACAATTTACTTTTCCAAGAATAAATTGTCCTT	5	250	0
          ****  ***** *
MAP Score: 4.98993

Motif 11
ATTTGTCTTATCGAAACGTTTCGATAACAAA	1	133	1
TAGTCGGGGTGCAATACGCTGAGATCATACC	2	176	1
          GCAAAAAGTTTATAATCAGTA	4	0	1
ATAATATAATGCAATAAGTTGCATTTTACTG	4	26	0
AATAGAAATGGTAAAACGTTTCTAAAATCTT	5	11	1
CCCTTTATATTCGATTCGTTGAGTATCTAC 	6	9	0
TCGAAATACTGCAAATCGTTGGCGTAATGCC	6	99	1
AAAAATCCCATCAATTCGATGGGATTCTCTC	6	222	0
GATTTTTTATGCAAACCGTATAGAATAGTGC	6	246	1
          ***** *****
MAP Score: 4.21637