AlignACE 3.0 10/20/99
AlignACE2 -i HI/HI_fusions012_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944236651
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	HI0176	107	sfhB protein (sfhB)
#1	HI0412	300	conserved hypothetical protein
#2	HI0616	197	ATP-dependent helicase (hepA)
#3	HI1436	300	conserved hypothetical protein

Motif 1
CGGAATATCGCGTTGTTTTATCAAGCAAATATTT	1	25	0
TTTAAGAAAAATGTTGATTATCAATGTCTTATGC	1	84	1
CCAATTGCTGCATTGAGTTTTCACCAACAAAACT	1	117	1
CCATAGAAAACGATTAATTAGCAAGGCGAATTTG	1	198	1
TATAATTTATCCTTGGATTTTCAATATACTCAAG	2	54	0
AATTTTTTGTGAGTTTCTTTTCAAGAGTATGCAA	2	122	1
CAATACGCCCCCAAGTTTTATCAATGTAAATCAG	2	160	1
TATCCAAAATCACTTCATTTTCACCTAACACAGA	3	41	0
TACCTGATTCAAATGGCTTTTCATCCGTTTCTTC	3	86	0
ATTTGAAAAACCATTTTCTTTCAAATATAAGGCT	3	232	0
ATTTGAAAGAAAATGGTTTTTCAAATGTGCGTGT	3	240	1
TTTCAAATGTGCGTGTATTTGCAAAAAACATTCA	3	258	1
          *  **  *******
MAP Score: 13.2626

Motif 2
TAATTTTTACGAAAACCAATAAATAAGATACAAT	0	21	1
CTATTGTATAGAACATTAATCAATAAGCCAACTT	0	61	1
TTGCTTGATAAAACAACGCGATATTCCGCACGCG	1	31	1
TTTATTTTAAGAAAAATGTTGATTATCAATGTCT	1	79	1
CTTAGGCGCAAAAAGAGGCTCTATTATCCATAGA	1	171	1
ATTATCCATAGAAAACGATTAATTAGCAAGGCGA	1	193	1
AACGTAATATGAACGTCACTCTATGAACGCAAAT	1	227	0
TTTTCCTTTTGAAAATCGCTGCAAATCATATCAT	1	273	0
ATGTAAATCAGAAAGAGAATAATT          	2	183	1
TGTGTTAGGTGAAAATGAAGTGATTTTGGATATT	3	43	1
GAAACGGATGAAAAGCCATTTGAATCAGGTACAC	3	89	1
AAAGTTTGTAGAACGGCATTTGAATGACGTCATG	3	122	0
TGATCAAAGTAAAAGTTACGTGTTGTATTGTGAA	3	175	1
GTTGTATTGTGAACGTGGTGTGATGAGTAAATTA	3	196	1
CCTTATATTTGAAAGAAAATGGTTTTTCAAATGT	3	234	1
GTGTATTTGCAAAAAACATTCATTAATTAGGATA	3	270	1
          ***** ** *  **
MAP Score: 5.40195

Motif 3
      TTTTTTTCCTTTTGAAAATCGCTGCAAA	1	282	0
AGCATAAATATTTGCTTGATAAAACAACGCGATA	1	20	1
AAACGGCTGATTTATTTTAAGAAAAATGTTGATT	1	69	1
TCAAATGTGCGTGTATTTGCAAAAAACATTCATT	3	260	1
AAAGGATAAGTTTTGTTGGTGAAAACTCAATGCA	1	125	0
TGAAAAACCATTTTCTTTCAAATATAAGGCTTGT	3	229	0
TAATTTATCCTTGGATTTTCAATATACTCAAGCG	2	52	0
ATCTTATTTATTGGTTTTCGTAAAAATTAAGGAA	0	16	0
TCTTTCTGATTTACATTGATAAAACTTGGGGGCG	2	165	0
TTTTTTGTGAGTTTCTTTTCAAGAGTATGCAAGC	2	124	1
TACGTTTATAGTGCCTTTATGATATGATTTGCAG	1	255	1
ACACGTAACTTTTACTTTGATCAAGGCTACCAAA	3	164	0
          ***  ***  ****
MAP Score: 4.64152

Motif 4
ATTGAAAATCCAAGGATAAATTATATTGGG	2	63	1
AATCGTTTTCTATGGATAATAGAGCCTCTT	1	183	0
  AACGTTATTAAGCATAAATATTTGCTTG	1	8	1
TTCTGATTTACATTGATAAAACTTGGGGGC	2	166	0
TCGTAAAAATTAAGGAAAAAACA       	0	3	0
TGTGCGTGTATTTGCAAAAAACATTCATTA	3	265	1
CGCCTAAGAATTTGCGTAAAAAAGGATAAG	1	149	0
TGGCATAAGACATTGATAATCAACATTTTT	1	90	0
CATTCATTAATTAGGATATAAAAT      	3	286	1
TCAATATACTCAAGCGTAAACTAGAATCTC	2	38	0
CGCTTGAGTATATTGAAAATCCAAGGATAA	2	52	1
ATGAAGTGATTTTGGATATTCGTAGCCCAG	3	57	1
TATTTATTGGTTTTCGTAAAAATTAAGGAA	0	16	0
 TTTTTTTCCTTTTGAAAATCGCTGCAAAT	1	281	0
GTTGTTTTATCAAGCAAATATTTATGCTTA	1	18	0
AAACCATTTTCTTTCAAATATAAGGCTTGT	3	229	0
          **********
MAP Score: 4.50051

Motif 5
AGATACAATTGTCCGCTATTGTATAGAACATTAATCAATA	0	46	1
GCGGAATATCGCGTTGTTTTATCAAGCAAATATTTATGCT	1	20	0
GTTGCAAACGGCTGATTTATTTTAAGAAAAATGTTGATTA	1	64	1
GCAAAAAGAGGCTCTATTATCCATAGAAAACGATTAATTA	1	178	1
ATTGTAGCTTGCATACTCTTGAAAAGAAACTCACAAAAAA	2	124	0
TCTCAATTTGGTAGCCTTGATCAAAGTAAAAGTTACGTGT	3	158	1
TAAATTACAAGCCTTATATTTGAAAGAAAATGGTTTTTCA	3	223	1
          **    *  *   *** ***
MAP Score: 4.43745

Motif 6
ATCTTATTTATTGGTTTTCGTAAAAATTAAGGAAAAAACA	0	10	0
TTTGCGTTCATAGAGTGACGTTCATATTACGTTTATAGTG	1	228	1
AAGCGTAAACTAGAATCTCGACTAAATCCACCGTATAGGG	2	17	0
TAGTTTACGCTTGAGTATATTGAAAATCCAAGGATAAATT	2	45	1
TAAATTATATTGGGGTGACGTATATCTTCCTAAAAGTGCG	2	79	1
GAGGCAATTTCTGTGTTAGGTGAAAATGAAGTGATTTTGG	3	32	1
GAAAAGCCATTTGAATCAGGTACACATGACGTCATTCAAA	3	98	1
TTTGGTAGCCTTGATCAAAGTAAAAGTTACGTGTTGTATT	3	164	1
ATTGTGAACGTGGTGTGATGAGTAAATTACAAGCCTTATA	3	201	1
          * *  * * **  *  * **
MAP Score: 3.98121

Motif 7
     TGTTTTTTCCTTAATTTTTACGAAAAC	0	5	1
ATTTTAAAAGTTGGCTTATTGATTAATGTTCT	0	70	0
AGCAAATATTTATGCTTAATAACGTT      	1	4	0
AGCATAAATATTTGCTTGATAAAACAACGCGA	1	20	1
CAACAAAACTTATCCTTTTTTACGCAAATTCT	1	141	1
TACGTTTATAGTGCCTTTATGATATGATTTGC	1	255	1
      TTTTTTTCCTTTTGAAAATCGCTGCA	1	284	0
CTCAATTTGGTAGCCTTGATCAAAGTAAAAGT	3	159	1
    ATTTTATATCCTAATTAATGAATGTTTT	3	282	0
          ******* ** *
MAP Score: 3.89258

Motif 8
GTTTTTTCCTTAATTTTTACGAAAACCAATAAATA	0	11	1
AAACGGCTGATTTATTTTAAGAAAAATGTTGATTA	1	69	1
CAAAACTTATCCTTTTTTACGCAAATTCTTAGGCG	1	144	1
AAAGAGGCTCTATTATCCATAGAAAACGATTAATT	1	182	1
CGCCCCCAAGTTTTATCAATGTAAATCAGAAAGAG	2	165	1
ATTTGGTAGCCTTGATCAAAGTAAAAGTTACGTGT	3	163	1
TTACAAGCCTTATATTTGAAAGAAAATGGTTTTTC	3	227	1
CAAATGTGCGTGTATTTGCAAAAAACATTCATTAA	3	261	1
          * * *** * * ***
MAP Score: 0.0935821