AlignACE 3.0 10/20/99
AlignACE2 -i HI/HI_fusions013_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944236688
 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
ATAACGATTGCTTTTCGTCATAAAGCCATTA	0	31	1
       AATTTATTCCTTATTCTTTAATAT	1	56	0
         TTTATTGATTATCGAAAACGCG	2	1	1
AATTTAGGCGTTTTTCATCATTTCAAATGAA	5	25	1
ATAATCATTCTTTTTCCTTATGTCCTATACT	5	89	0
ATGACCGCACTTTTTGTTGATTAACGAACAA	5	216	1
AGGGAAAATCCTTTTGTTCGTTAATCAACAA	5	229	0
CCTTAGTACTTTATTTATTATTCTTATTATC	5	273	1
GAATAATGGATTTTTGATTGTGAATTGATCT	6	53	0
AACATAGATACTTTTCGTCATATAAACAAAA	6	97	1
AAATATTCTTATTTTGTTTATATGACGAAAA	6	108	0
CAATGTGCGGTTATTTTTTATTGATTTTCCT	6	205	1
AGTGCGGTCGTTTTCTTTTATATTTTTGAGT	7	28	1
        ACTTTTCCCTTGTTAGAACTGTG	8	13	0
     AATTATTTTTCCTTATGCCTAAGGCT	9	38	0
TTAAGCCCCTTTATTTTTGATACTTTG    	10	6	0
GCCCCTTTTGTTGTTTTTTATTTTCTCTTTC	10	39	1
       ATCTTATCTATTGTGAACCTTCAA	11	3	1
ACCATTTTTCTTGTTCGTTATACTATCCAAA	12	35	0
TTTTAGGCGTATTTTCTTTATACTTTGTGCA	12	81	1
          ****** ****
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
CGTTATTTTATCCGCACTTATTAGAAAGGA	2	46	1
TGCTGATTATACCGAAATTTAGGCGTTTTT	5	10	1
GTCATTTTTCACCGCACTTTTTACCTGTTA	5	191	0
GTGAAAAATGACCGCACTTTTTGTTGATTA	5	209	1
TGTATTTTTAACCGCACTTTAGGTTTAAAC	6	174	1
ATAAAAAATAACCGCACATTGGGTTTAAAC	6	196	0
AAAGAAAACGACCGCACTTTGCGACCGTTT	7	16	0
          **********
MAP Score: 19.4736

Motif 4
AAAAGCAATCGTTATTTATATTTGAGAAATGA	0	14	0
TTAATCCCCAGTTGTTTTGATTGCTTGCCGAT	1	15	1
TTTTTCAACTCGCGTTTTCGATAATCAATAAA	2	10	0
TTCCTGTCTTGTTATTTTAGTTTGTTCCTGAC	4	54	1
AATATCAGAAGTTGTTTGTTTTAGCAAGTAAA	4	122	1
TAAGCCTAGGCTAGTTTTATTTAAATATGCAA	4	208	0
CCGAAATTTAGGCGTTTTTCATCATTTCAAAT	5	21	1
TACTCAAAAAGTCATTTTCATTTGAAATGATG	5	40	0
CTTTTTACCTGTTATTTGATTTTGCTAAATCA	5	173	0
ACAAAATATTCTTATTTTGTTTATATGACGAA	6	110	0
CCAATGTGCGGTTATTTTTTATTGATTTTCCT	6	204	1
GCAAAGTGCGGTCGTTTTCTTTTATATTTTTG	7	24	1
TGCCCCTTTTGTTGTTTTTTATTTTCTCTTTC	10	38	1
GCTTTTTAGGCGTATTTTCTTTATACTTTGTG	12	78	1
          ********  **
MAP Score: 14.8849

Motif 5
AAGGATTAATCCCCAGTTGTTTTGATTGCTTGCCGATA	1	10	1
GATTTCACGACTTCCTGTCTTGTTATTTTAGTTTGTTC	4	43	1
CCTCTCTAAGCCTAGGCTAGTTTTATTTAAATATGCAA	4	208	0
CATTCTTTTTCCTTATGTCCTATACTTTCTTTATGAAA	5	77	0
TATTATTCTGCCCACTCTTAGCTATTTGAGCAGCTATT	5	135	1
GAAAAATGACCGCACTTTTTGTTGATTAACGAACAAAA	5	211	1
GGATAGCATTCCCCTTAGTACTTTATTTATTATTCTTA	5	261	1
TAGGTTTAAACCCAATGTGCGGTTATTTTTTATTGATT	6	193	1
TTCCTCTTTTCGCGTTTTGCGATTTTTTCTAAAATATG	6	231	1
AGAAAACGACCGCACTTTGCGACCGTTTGGGATA    	7	6	0
AAAGTGCGGTCGTTTTCTTTTATATTTTTGAGTA    	7	26	1
AATTAAGCCCCTTTATTTTTGATACTTTG         	10	1	0
GGCTTAATTGCCCCTTTTGTTGTTTTTTATTTTCTCTT	10	30	1
CTCTAACCAACGTTATTGACTCTTTTTTGGATGAG   	11	45	1
CAAATGCCGTCGCTTTTTAGGCGTATTTTCTTTATACT	12	67	1
          ***  * *  * *  ***
MAP Score: 12.0217

Motif 6
       AAGGTACAATGCGTGCAATTTTT	3	3	1
CTATCTAATAGTAAAAATTGCACGCATTGT	3	15	0
TATACCGCCCGCAAAAATTGGGTTCCTAAA	4	92	0
GATATGGATCGCAAAATTTGAAGCAACCGT	4	178	1
TGCTCAAATAGCTAAGAGTGGGCAGAATAA	5	137	0
CAAATAACAGGTAAAAAGTGCGGTGAAAAA	5	187	1
AAAAAGTGCGGTGAAAAATGACCGCACTTT	5	199	1
AATTGATCTCGTAAAAAGAGGGCAAAGATC	6	32	0
TCCCCTCTCCGTAAAAATTGTGTATTTTTA	6	154	1
ATCGCAAAACGCGAAAAGAGGAAAATCAAT	6	224	0
TCATATTTTAGAAAAAATCGCAAAACGCGA	6	240	0
CCAAACGGTCGCAAAGTGCGGTCGTTTTCT	7	14	1
GAAAATACGCCTAAAAAGCGACGGCATTTG	12	67	0
          **********
MAP Score: 7.8711

Motif 7
TACAATGCGTGCAATTTTTACTATTAGATAGCGATT	3	14	1
GTTTTAGCAAGTAAATTTTCCTGAAAAATTTATTTT	4	139	1
CTAAGCCTAGGCTAGTTTTATTTAAATATGCAAACG	4	205	0
GCTTAGAGAGGCTGGAATTAATCTTTTATAAAA   	4	235	1
CCGAAATTTAGGCGTTTTTCATCATTTCAAATGAAA	5	21	1
AAAAATGACCGCACTTTTTGTTGATTAACGAACAAA	5	212	1
CCACAACATAGATACTTTTCGTCATATAAACAAAAT	6	93	1
AACCCAATGTGCGGTTATTTTTTATTGATTTTCCTC	6	201	1
TTCGCGTTTTGCGATTTTTTCTAAAATATGATAATT	6	239	1
CGCAAAGTGCGGTCGTTTTCTTTTATATTTTTGAGT	7	23	1
GGGCTTAATTGCCCCTTTTGTTGTTTTTTATTTTCT	10	29	1
CGCTTTTTAGGCGTATTTTCTTTATACTTTGTGCAT	12	77	1
          **   ****  * ***
MAP Score: 7.18805

Motif 8
GAAAAGCAATCGTTATTTATATTTGAGAAAT	0	16	0
CCATTATGATCTGTATTTTCGGATTTATTTA	0	56	1
ATTTATTTAACTCAATTATAGGAAAAATT  	0	78	1
CTTCCTGTCTTGTTATTTTAGTTTGTTCCTG	4	53	1
TGTTCCTGACTGCTATTTTAGGAACCCAATT	4	76	1
ATTTTAGGAACCCAATTTTTGCGGGCGGTAT	4	90	1
CTGATTATACCGAAATTTAGGCGTTTTTCAT	5	12	1
CATTTTTCACCGCACTTTTTACCTGTTATTT	5	188	0
GAAAAATGACCGCACTTTTTGTTGATTAACG	5	211	1
GATCTTTGCCCTCTTTTTACGAGATCAATTC	6	32	1
TATTTTTAACCGCACTTTAGGTTTAAACCCA	6	176	1
TTATTGATTTTCCTCTTTTCGCGTTTTGCGA	6	222	1
CGAAAAATTATCATATTTTAGAAAAAATCGC	6	249	0
AGAAAACGACCGCACTTTGCGACCGTTTGGG	7	13	0
TCGTTTTCTTTTATATTTTTGAGTA      	7	35	1
AATTAAGCCCCTTTATTTTTGATACTTTG  	10	8	0
GCTTAATTGCCCCTTTTGTTGTTTTTTATTT	10	31	1
ACGTTATTGACTCTTTTTTGGATGAG     	11	54	1
CAAATGCCGTCGCTTTTTAGGCGTATTTTCT	12	67	1
          ********* *
MAP Score: 5.00555

Motif 9
AGGATTAATCCCCAGTTGTTTTGATTGCTTGCC	1	11	1
ATTTTAGGAACCCAATTTTTGCGGGCGGTATAA	4	90	1
GATATGGATCGCAAAATTTGAAGCAACCGTTTG	4	178	1
AAAAATGACCGCACTTTTTGTTGATTAACGAAC	5	212	1
AGGATCTTTGCCCTCTTTTTACGAGATCAATTC	6	30	1
AACAAAATAAGAATATTTTGTTGTCTAGAATTT	6	121	1
GTTAAAAATACACAATTTTTACGGAGAGGGGAA	6	153	0
GCAATTAAGCCCCTTTATTTTTGATACTTTG  	10	8	0
GGGCTTAATTGCCCCTTTTGTTGTTTTTTATTT	10	29	1
CAACGTTATTGACTCTTTTTTGGATGAG     	11	52	1
          ***  ****** *
MAP Score: 2.51165