AlignACE 3.0 10/20/99
AlignACE2 -i HI/HI_fusions010_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944236583
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	HI0837	53	response regulator (cpxR)
#1	HI0839	116	conserved hypothetical protein
#2	HI0884	191	aerobic respiration control protein ARCA (arcA)
#3	HI1379	300	phosphate regulon transcriptional regulatory protein (phoB)
#4	HI1708	62	transcriptional regulatory protein (ygiX)
#5	HI1709	114	conserved hypothetical protein
#6	HI1710	254	H. influenzae predicted coding region HI1710
#7	HI1711	59	PTS system, glucose-specific IIA component (crr)
#8	HI1712	79	phosphoenolpyruvate-protein phosphotransferase (ptsI)
#9	HI1713	158	phosphocarrier protein HPr (ptsH)
#10	HI1714	70	conserved hypothetical protein

Motif 1
TTCTCTTATTAAAAAGTAAAAGTTTGGTGA	3	226	1
TTTAGATCACAAAAAGGAAAATCAGGTAAA	2	79	1
TAACTAACTTAAAAAGGAAACGTT      	5	100	1
TTTCAGCAAGAAAAAAGAAATTATTTAGGT	1	61	0
AGTCTTTTCAAAAAAGTATAGTCCTCTTAA	5	13	1
AGGTAACTATAATAAATAAAAAATCCGCAC	6	39	0
TTAACAAAGTAATAAATAAACAATAGCCAT	8	41	0
GATTGTGAATAATAAATAAACTATTTAGCT	9	17	1
TTTTGCTTTGAAAAAGGATACTAGGGCAAT	9	93	1
CATACGCCAAAATAAGTATAAGGATGGAAA	2	171	1
 AATGTTAAAAATAAAAAAAATTTGGCTTA	1	9	1
TGTTTTTGGTAAAATGAAAAAAATTTTTGC	10	27	0
ACCACACTACAATAAGAATAATTGGTAAAA	0	23	1
TCAATAATTAAAAATATAAAACCAGAAAAT	9	121	0
TAGTGTGGTGAAAATAAAAAGA        	0	2	0
TGTGTATTAAAACAAATAAATCTTAATAAA	5	46	0
          **********
MAP Score: 22.0509

Motif 2
GGTTATAATTTGCGGCAAATTTTTCAAAG     	1	97	1
AATAAAAAAGTGCGGTGATTTTTTACCTGATTTT	2	96	0
GCTCCGACTATACGGCATTTATGTATTTGGGTGA	3	94	1
CGCGGTAAAATGGGGTAGTTATTTTGAGTTCTCT	3	198	1
TTTCTGAAAATGCGAGCATTAGCTCGCTGTTTTT	4	13	1
GTTTATAAAGTGCGGTCAATTTTTT         	4	47	1
TCCGCACAAAGGCGGACTTTTTTTACCGTAAACA	6	12	0
TCCGCCTTTGTGCGGATTTTTTATTTATTATAGT	6	30	1
AAGCACAAAGTGCGAGTATTTTATTAGTA     	6	235	1
AAAAGGATACTAGGGCAATTTTCTGGTTTTATAT	9	104	1
AGGTATCCTATGCAAAAATTTTTTTCATTTTACC	10	16	1
     AAAAGTGCGGTCGTTTTTTCCCTTGTTTT	10	51	0
          *****   **** *
MAP Score: 21.8148

Motif 3
TGCAAAAATTTTTTTCATTTTACCAAAAACAA	10	26	1
TTTGTGCGGATTTTTTATTTATTATAGTTACC	6	36	1
AAGCCAAATTTTTTTTATTTTTAACATT    	1	6	0
        TCTTTTTATTTTCACCACACTACA	0	2	1
TTTATGGCTATTGTTTATTTATTACTTTGTTA	8	38	1
   ACAAAATTATTTGATTTTACGTTAAAATA	7	7	1
CTTTTTAAGTTAGTTAATTTCAAGCTCCATTG	5	84	0
TATTAAGATTTATTTGTTTTAATACACACATC	5	48	1
ATAAGCTAAATAGTTTATTTATTATTCACAAT	9	18	0
TAAAATGGGGTAGTTATTTTGAGTTCTCTTAT	3	203	1
TTCAAGATGGTTGCTATTTTAACGTAAAATCA	7	21	0
ACCTAAATAATTTCTTTTTTCTTGCTGAAAAA	1	61	1
ATCACCGCACTTTTTTATTGTTACAATAATGT	2	111	1
TGGTTTTATATTTTTAATTATTGATTAGTCGA	9	127	1
ATTTATTACTTTGTTAATTGTTTCGGAAGGTA	8	54	1
ATAAACTATTTAGCTTATTTTTATGATTTAAT	9	32	1
TAGCTCGCTGTTTTTGTTTATAAAGTGCGGTC	4	32	1
AAAGTGCGAGTATTTTATTAGTA         	6	241	1
CTAGGGCAATTTTCTGGTTTTATATTTTTAAT	9	113	1
          ***** **** *
MAP Score: 18.2895

Motif 4
         TCTTTTTATTTTCACCACACTACA	0	1	1
AGCCAAATTTTTTTTATTTTTAACATT      	1	4	0
TAAATCATAGTTTTAGGTATTCAAATTTCTTTG	2	50	0
ATCACCGCACTTTTTTATTGTTACAATAATGTT	2	111	1
CTCACCAAACTTTTACTTTTTAATAAGAGAACT	3	224	0
TAGCTCGCTGTTTTTGTTTATAAAGTGCGGTCA	4	32	1
TTATTAAGATTTATTTGTTTTAATACACACATC	5	47	1
        AACGTTTCCTTTTTAAGTTAGTTAA	5	99	0
TTGTGCGGATTTTTTATTTATTATAGTTACCTA	6	37	1
ATACTCGCACTTTGTGCTTTTAAATGATGTGTT	6	221	0
    ACAAAATTATTTGATTTTACGTTAAAATA	7	6	1
TTATGGCTATTGTTTATTTATTACTTTGTTAAT	8	39	1
TTTAGCTTATTTTTATGATTTAATTCAGGCTTT	9	40	1
TAATTCAGGCTTTTTAGTGTTTATTCTTGATTA	9	60	1
AATTTTCTGGTTTTATATTTTTAATTATTGATT	9	120	1
ATGCAAAAATTTTTTTCATTTTACCAAAAACAA	10	25	1
          *****  **** *
MAP Score: 14.6822

Motif 5
AAATAATTTCTTTTTTCTTGCTGAAAAAGTGCGGTTATAATTTGC	1	65	1
CCTAAAACTATGATTTAGATCACAAAAAGGAAAATCAGGTAAAAA	2	66	1
TGTGCAACATTATTGTAACAATAAAAAAGTGCGGTGATTTTTTAC	2	104	0
TACAGAAGATTATATTCGCGGTAAAATGGGGTAGTTATTTTGAGT	3	182	1
ACTCCTTCATTTGATTTATGGCATAAAAGTGAAGTGAGAAATAAT	3	262	0
ATTAGCTCGCTGTTTTTGTTTATAAAGTGCGGTCAATTTTTT   	4	30	1
          TAAAGTCTTTTCAAAAAAGTATAGTCCTCTTAATC	5	0	1
CACATTCATATTGAATATTTTGCAAAGCGAAATCTTTTGCTGACG	6	172	0
CAAAATTATTTGATTTTACGTTAAAATAGCAACCATCTTGAATGG	7	11	1
       TTCTTACTTAGCCATAAAATTGTGAAATTTTATGGCTA	8	3	1
TTATTCTTGATTATTTTGCTTTGAAAAAGGATACTAGGGCAATTT	9	80	1
AAAATTTTTTTCATTTTACCAAAAACAAGGGAAAAAACGACCGCA	10	30	1
          *   **  *    ***  * *   *
MAP Score: 8.16596