AlignACE 3.0 10/20/99
AlignACE2 -i HI/HI_fusions012_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944236632
 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
AAATATTTGCTTGATAAAACAACGCGATATTCCG	1	25	1
GCATAAGACATTGATAATCAACATTTTTCTTAAA	1	84	0
AGTTTTGTTGGTGAAAACTCAATGCAGCAATTGG	1	117	0
CAAATTCGCCTTGCTAATTAATCGTTTTCTATGG	1	198	0
CTTGAGTATATTGAAAATCCAAGGATAAATTATA	2	54	1
TTGCATACTCTTGAAAAGAAACTCACAAAAAATT	2	122	0
CTGATTTACATTGATAAAACTTGGGGGCGTATTG	2	160	0
TCTGTGTTAGGTGAAAATGAAGTGATTTTGGATA	3	41	1
GAAGAAACGGATGAAAAGCCATTTGAATCAGGTA	3	86	1
GGCTACCAAATTGAGAAGAAAGTTTGTAGAACGG	3	140	0
AGCCTTATATTTGAAAGAAAATGGTTTTTCAAAT	3	232	1
ACACGCACATTTGAAAAACCATTTTCTTTCAAAT	3	240	0
TGAATGTTTTTTGCAAATACACGCACATTTGAAA	3	258	0
          *******  **  *
MAP Score: 14.0536

Motif 2
        TGTTTTTTCCTTAATTTTTACGAAA	0	2	1
CGGACAATTGTATCTTATTTATTGGTTTTCGTA	0	28	0
AAACTTATCCTTTTTTACGCAAATTCTTAGGCG	1	146	1
TAATTAATCGTTTTCTATGGATAATAGAGCCTC	1	185	0
      TTTTTTTCCTTTTGAAAATCGCTGCAA	1	283	0
         CTCTTTTCCCTATACGGTGGATTT	2	1	1
GGGTGACGTATATCTTCCTAAAAGTGCGGTCAA	2	91	1
TTTTTGTGAGTTTCTTTTCAAGAGTATGCAAGC	2	125	1
    AATTATTCTCTTTCTGATTTACATTGATA	2	178	0
TTCTACAAACTTTCTTCTCAATTTGGTAGCCTT	3	143	1
GAAAAACCATTTTCTTTCAAATATAAGGCTTGT	3	229	0
TTAATGAATGTTTTTTGCAAATACACGCACATT	3	263	0
          ****** *  ***
MAP Score: 6.61962

Motif 3
CAAAAATTTTAAAAGTTGGCTTATTGATTAA	0	76	0
TTTGCGCCTAAGAATTTGCGTAAAAAAGGAT	1	152	0
ATTAGCAAGGCGAATTTGCGTTCATAGAGTG	1	214	1
TATATCTTCCTAAAAGTGCGGTCAATTTTTT	2	99	1
TTACATTGATAAAACTTGGGGGCGTATTGTA	2	158	0
CACCTAACACAGAAATTGCCTCGACTTCCAC	3	23	0
TGATCAAAGTAAAAGTTACGTGTTGTATTGT	3	175	1
AATGGTTTTTCAAATGTGCGTGTATTTGCAA	3	251	1
          **** ******
MAP Score: 4.35612

Motif 4
ATATTCCGCACGCGTTGCAAACGGCTGATTTAT	1	51	1
TGATTTGCAGCGATTTTCAAAAGGAAAAAAA  	1	279	1
GTCATGTGTACCTGATTCAAATGGCTTTTCATC	3	95	0
GTACACATGACGTCATTCAAATGCCGTTCTACA	3	117	1
GAAAGAAAATGGTTTTTCAAATGTGCGTGTATT	3	244	1
          **  ******* *
MAP Score: 3.04193

Motif 5
GAAAACCAATAAATAAGATACAATTGTCCGCTATTGTATAG	0	31	1
ATTTGCTTGATAAAACAACGCGATATTCCGCACGCGTTGCA	1	29	1
TTTCACCAACAAAACTTATCCTTTTTTACGCAAATTCTTAG	1	135	1
AAAACGATTAATTAGCAAGGCGAATTTGCGTTCATAGAGTG	1	204	1
CGGTGGATTTAGTCGAGATTCTAGTTTACGCTTGAGTATAT	2	24	1
ATTTTTTGTGAGTTTCTTTTCAAGAGTATGCAAGCTACAAT	2	123	1
TCTTTTCAAGAGTATGCAAGCTACAATACGCCCCCAAGTTT	2	137	1
TTTGAAAGAAAATGGTTTTTCAAATGTGCGTGTATTTGCAA	3	241	1
          * *    *  * * * * ***
MAP Score: 2.15622

Motif 6
GTGCGGAATATCGCGTTGTTTTATCAAGCAA	1	31	0
GATATTCCGCACGCGTTGCAAACGGCTGATT	1	50	1
GAACGCAAATTCGCCTTGCTAATTAATCGTT	1	206	0
CATTTGAATGACGTCATGTGTACCTGATTCA	3	109	0
AGTAAAAGTTACGTGTTGTATTGTGAACGTG	3	182	1
TGTATTGTGAACGTGGTGTGATGAGTAAATT	3	198	1
          ********* *
MAP Score: 0.422865

Motif 7
        TGTTTTTTCCTTAATTTTTACGAAA	0	2	1
     AACGTTATTAAGCATAAATATTTGCTTG	1	5	1
CGCGTTGTTTTATCAAGCAAATATTTATGCTTA	1	18	0
GGCTGATTTATTTTAAGAAAAATGTTGATTATC	1	73	1
ATTATCAATGTCTTATGCCAATTGCTGCATTGA	1	100	1
ACTTATCCTTTTTTACGCAAATTCTTAGGCGCA	1	148	1
GTGACGTTCATATTACGTTTATAGTGCCTTTAT	1	242	1
TTGACCGCACTTTTAGGAAGATATACGTCACCC	2	91	0
GCAATTTCTGTGTTAGGTGAAAATGAAGTGATT	3	35	1
TTAATGAATGTTTTTTGCAAATACACGCACATT	3	263	0
          * *** ** ****
MAP Score: 0.120641