AlignACE 3.0 10/20/99
AlignACE2 -i HI/HI_fusions013_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944236665
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	HI0056	97	conserved hypothetical transmembrane protein
#1	HI0058	70	3-deoxy-D-manno-octulosonate cytidylyltransferase (kdsB)
#2	HI0059	72	conserved hypothetical protein
#3	HI0060	40	ABC transporter, ATP-binding protein (msbA)
#4	HI0061	258	recombination protein (rec2)
#5	HI0107	300	conserved hypothetical protein
#6	HI0301	300	hemolysin, putative
#7	HI0452	50	conserved hypothetical protein
#8	HI0453	26	conserved hypothetical protein
#9	HI0454	54	conserved hypothetical protein
#10	HI0457	69	conserved hypothetical protein
#11	HI0458	70	stationary phase survival protein SurA, putative
#12	HI0459	131	pyrimidine operon regulatory protein (pyrR)

Motif 1
TAATGGCTTTATGACGAAAAGCAATCGTTAT	0	31	0
ATATTAAAGAATAAGGAATAAATT       	1	56	1
CGCGTTTTCGATAATCAATAAA         	2	1	0
TTCATTTGAAATGATGAAAAACGCCTAAATT	5	25	0
AGTATAGGACATAAGGAAAAAGAATGATTAT	5	89	1
TTGTTCGTTAATCAACAAAAAGTGCGGTCAT	5	216	0
TTGTTGATTAACGAACAAAAGGATTTTCCCT	5	229	1
GATAATAAGAATAATAAATAAAGTACTAAGG	5	273	0
AGATCAATTCACAATCAAAAATCCATTATTC	6	53	1
TTTTGTTTATATGACGAAAAGTATCTATGTT	6	97	0
TTTTCGTCATATAAACAAAATAAGAATATTT	6	108	1
AGGAAAATCAATAAAAAATAACCGCACATTG	6	205	0
ACTCAAAAATATAAAAGAAAACGACCGCACT	7	28	0
CACAGTTCTAACAAGGGAAAAGT        	8	13	1
AGCCTTAGGCATAAGGAAAAATAATT     	9	38	1
    CAAAGTATCAAAAATAAAGGGGCTTAA	10	6	1
GAAAGAGAAAATAAAAAACAACAAAAGGGGC	10	39	0
TTGAAGGTTCACAATAGATAAGAT       	11	3	0
TTTGGATAGTATAACGAACAAGAAAAATGGT	12	35	1
TGCACAAAGTATAAAGAAAATACGCCTAAAA	12	81	0
          **** ******
MAP Score: 20.1539

Motif 2
ATCATTTCTCAAATATAAATAACGATTGCTTT	0	13	1
ATAAAGCTGAAATATTAAAGAATAAGGAATAA	1	45	1
AGTCAGGAACAAACTAAAATAACAAGACAGGA	4	55	0
TATAGGACATAAGGAAAAAGAATGATTATTTA	5	91	1
TTTGTTCGTTAATCAACAAAAAGTGCGGTCAT	5	216	0
TTTGTTGATTAACGAACAAAAGGATTTTCCCT	5	228	1
AGATAATAAGAATAATAAATAAAGTACTAAGG	5	273	0
GAGGAAAATCAATAAAAAATAACCGCACATTG	6	205	0
  TACTCAAAAATATAAAAGAAAACGACCGCA	7	30	0
CCTTAGGCATAAGGAAAAATAATT        	9	40	1
        CAAAGTATCAAAAATAAAGGGGCT	10	2	1
AGAAAATAAAAAACAACAAAAGGGGCAATTAA	10	33	0
AGCTATAAGAAAGAGAAAATAAAAAACAACAA	10	46	0
ATCTATTGTGAACCTTCAATAGAATTGTTACT	11	15	1
TCATCCAAAAAAGAGTCAATAACGTTGGTTAG	11	47	0
TGGATAGTATAACGAACAAGAAAAATGGTGCA	12	37	1
TCAATGCACAAAGTATAAAGAAAATACGCCTA	12	84	0
          **  ********
MAP Score: 19.8713

Motif 3
ACAATGCGTGCAATTTTTACTATTAGATAGC	3	15	1
TTTAGGAACCCAATTTTTGCGGGCGGTATAA	4	92	1
TTTTAGCAAGTAAATTTTCCTGAAAAATTTA	4	140	1
CCTGAAAAATTTATTTTTACGATATGGATCG	4	158	1
ACGGTTGCTTCAAATTTTGCGATCCATATCG	4	177	0
TAAATAATCATTCTTTTTCCTTATGTCCTAT	5	92	0
TTTTTCACCGCACTTTTTACCTGTTATTTGA	5	186	0
AAAATGACCGCACTTTTTGTTGATTAACGAA	5	213	1
GATCTTTGCCCTCTTTTTACGAGATCAATTC	6	32	1
TAAAAATACACAATTTTTACGGAGAGGGGAA	6	153	0
ATTGATTTTCCTCTTTTCGCGTTTTGCGATT	6	224	1
TCGCGTTTTGCGATTTTTTCTAAAATATGAT	6	240	1
TAAAATATGATAATTTTTCGCCGTCAATAAG	6	260	1
        AATTATTTTTCCTTATGCCTAAG	9	41	0
TTGTTGTTTTTTATTTTCTCTTTCTTATAGC	10	46	1
ACGTTATTGACTCTTTTTTGGATGAG     	11	54	1
CAAATGCCGTCGCTTTTTAGGCGTATTTTCT	12	67	1
          ******** **
MAP Score: 17.3005

Motif 4
CTCGCGTTATTTTATCCGCACTTATTAGAAAGG	2	42	1
TGCGGTCATTTTTCACCGCACTTTTTACCTGTT	5	192	0
ATTGTGTATTTTTAACCGCACTTTAGGTTTAAA	6	170	1
TGCGGTGAAAAATGACCGCACTTTTTGTTGATT	5	205	1
TTTTTTATTGATTTTCCTCTTTTCGCGTTTTGC	6	218	1
GATAAGGATCTTTGCCCTCTTTTTACGAGATCA	6	26	1
AAAGGGGCTTAATTGCCCCTTTTGTTGTTTTTT	10	25	1
CAGGTATTATTCTGCCCACTCTTAGCTATTTGA	5	131	1
GTTGTCTAGAATTTTCCCCTCTCCGTAAAAATT	6	140	1
TATAAAAGAAAACGACCGCACTTTGCGACCGTT	7	17	0
ATCAATAAAAAATAACCGCACATTGGGTTTAAA	6	197	0
AAGCGACGGCATTTGCACCATTTTTCTTGTTCG	12	49	0
AATTTAGGCGTTTTTCATCATTTCAAATGAAAA	5	25	1
TAACCAACGTTATTGACTCTTTTTTGGATGAG 	11	48	1
TTTCGGATTTATTTAACTCAATTATAGGAAAAA	0	72	1
          ***  ** *****
MAP Score: 14.9867

Motif 5
TCGTCATAAAGCCATTATGATCTGTATTTTCGGATTTAT	0	45	1
TTAATCCCCAGTTGTTTTGATTGCTTGCCGATAAAGCTG	1	15	1
TACAATGCGTGCAATTTTTACTATTAGATAGCGATT   	3	14	1
TTCCTGTCTTGTTATTTTAGTTTGTTCCTGACTGCTATT	4	54	1
GTTTTAGCAAGTAAATTTTCCTGAAAAATTTATTTTTAC	4	139	1
CTAAGCCTAGGCTAGTTTTATTTAAATATGCAAACGGTT	4	202	0
         TGCTGATTATACCGAAATTTAGGCGTTTTT	5	1	1
ATTTTTCACCGCACTTTTTACCTGTTATTTGATTTTGCT	5	179	0
AAAAATGACCGCACTTTTTGTTGATTAACGAACAAAAGG	5	212	1
GATGTGATAAGGATCTTTGCCCTCTTTTTACGAGATCAA	6	21	1
TGTGAATAATGGATTTTTGATTGTGAATTGATCTCGTAA	6	48	0
ATTTTTAACCGCACTTTAGGTTTAAACCCAATGTGCGGT	6	177	1
AACCCAATGTGCGGTTATTTTTTATTGATTTTCCTCTTT	6	201	1
TTCGCGTTTTGCGATTTTTTCTAAAATATGATAATTTTT	6	239	1
GCAAAGTGCGGTCGTTTTCTTTTATATTTTTGAGTA   	7	24	1
GGGCAATTAAGCCCCTTTATTTTTGATACTTTG      	10	4	0
GGGCTTAATTGCCCCTTTTGTTGTTTTTTATTTTCTCTT	10	29	1
CGCTTTTTAGGCGTATTTTCTTTATACTTTGTGCATTGA	12	77	1
          **   ***  ***  *  *
MAP Score: 11.6814

Motif 6
AAAAACTCGCGTTATTTTATCCGCACTTAT	2	37	1
TTCCTGTCTTGTTATTTTAGTTTGTTCCTG	4	54	1
GTTCCTGACTGCTATTTTAGGAACCCAATT	4	77	1
AATATCAGAAGTTGTTTGTTTTAGCAAGTA	4	122	1
CCCACTCTTAGCTATTTGAGCAGCTATTTG	5	145	1
TATTTGAGCAGCTATTTGATTTAGCAAAAT	5	157	1
CTTTTTACCTGTTATTTGATTTTGCTAAAT	5	175	0
CCAATGTGCGGTTATTTTTTATTGATTTTC	6	204	1
TTCGCGTTTTGCGATTTTTTCTAAAATATG	6	239	1
TGCCCCTTTTGTTGTTTTTTATTTTCTCTT	10	38	1
          **********
MAP Score: 11.5275

Motif 7
ATCATTTCTCAAATATAAATAACGATTGCTTTTCGTCA	0	13	1
ATTGAGTTAAATAAATCCGAAAATACAGATCATAATGG	0	56	0
CTTTATCGGCAAGCAATCAAAACAACTGGGGATTAATC	1	13	0
GATAAAGCTGAAATATTAAAGAATAAGGAATAAATT  	1	44	1
   AATCGCTATCTAATAGTAAAAATTGCACGCATTGT	3	15	0
GAACAAACTAAAATAACAAGACAGGAAGTCGTGAAATC	4	43	0
TTTCATTTGAAATGATGAAAAACGCCTAAATTTCGGTA	5	19	0
TTTGTTCGTTAATCAACAAAAAGTGCGGTCATTTTTCA	5	210	0
AAACAGATAATAAGAATAATAAATAAAGTACTAAGGGG	5	271	0
AATCAATAAAAAATAACCGCACATTGGGTTTAAACCTA	6	193	0
CATATTTTAGAAAAAATCGCAAAACGCGAAAAGAGGAA	6	231	0
 TACTCAAAAATATAAAAGAAAACGACCGCACTTTGCG	7	23	0
         CAAAGTATCAAAAATAAAGGGGCTTAATT	10	1	1
AAGAGAAAATAAAAAACAACAAAAGGGGCAATTAAGCC	10	30	0
   CTCATCCAAAAAAGAGTCAATAACGTTGGTTAGAG	11	45	0
TGGATAGTATAACGAACAAGAAAAATGGTGCAAATGCC	12	37	1
TCAATGCACAAAGTATAAAGAAAATACGCCTAAAAAGC	12	78	0
          **  ** ** ***    *
MAP Score: 4.34313

Motif 8
TCGTTATTTATATTTGAGAAATGATTGA   	0	7	0
CCTGTCTTGTTATTTTAGTTTGTTCCTGACT	4	56	1
TCCTGACTGCTATTTTAGGAACCCAATTTTT	4	79	1
AGAAGTTGTTTGTTTTAGCAAGTAAATTTTC	4	128	1
AAAATTATCATATTTTAGAAAAAATCGCAAA	6	246	0
TAAGCCCCTTTATTTTTGATACTTTG     	10	5	0
          ******** **
MAP Score: 1.10992